include module.mk
# process what the module.mks defined
-OBJ := $(patsubst %.cxx,%.o, $(filter %.cxx,$(SRC)))
+OBJ := $(patsubst %.cpp,%.o, $(filter %.cpp,$(SRC)))
DEPS := $(OBJ:.o=.d)
targets: $(TARGETLIBS) $(TARGETBINS)
$(CXX) -MM -MF $3 -MP -MT $2 $(CFLAGS) $(CXXFLAGS) $1
endef
-%.d: %.cxx
+%.d: %.cpp
$(call make-depend,$<,$@,$(subst .o,.d,$@))
# makedepend -o.d $(dirname $^) $(CFLAGS) $(CXXFILAGS) $^ -f- > $@
-%.o: %.cxx
+%.o: %.cpp
$(CXX) -c -o $@ $(CXXFLAGS) $^
include $(DEPS)
--- /dev/null
+#include "alg/color.hpp"
+#include <math.h>
+
+Color::Color()
+{
+ set(0.0, 0.0, 0.0, 0.0);
+}
+
+Color::Color(const Color &c)
+{
+ set(c.colors[RedChannel],
+ c.colors[GreenChannel],
+ c.colors[BlueChannel],
+ c.colors[AlphaChannel]);
+}
+
+Color::Color(float red, float green, float blue, float alpha)
+{
+ set(red, green, blue, alpha);
+}
+
+void Color::set(float r, float g, float b, float a)
+{
+ colors[RedChannel] = r;
+ colors[GreenChannel] = g;
+ colors[BlueChannel] = b;
+ colors[AlphaChannel] = a;
+}
+
+const float *const Color::get() const
+{
+ return colors;
+}
+
+void Color::setR(float r)
+{
+ colors[RedChannel] = r;
+}
+
+float Color::r() const
+{
+ return colors[RedChannel];
+}
+
+void Color::setG(float g)
+{
+ colors[GreenChannel] = g;
+}
+
+float Color::g() const
+{
+ return colors[GreenChannel];
+}
+
+void Color::setB(float b)
+{
+ colors[BlueChannel] = b;
+}
+
+float Color::b() const
+{
+ return colors[BlueChannel];
+}
+
+void Color::setA(float a)
+{
+ colors[AlphaChannel] = a;
+}
+
+float Color::a() const
+{
+ return colors[AlphaChannel];
+}
+
+static bool close(float l, float r, float t=1e-6)
+{
+ float difference = fabsf(l-r);
+ l = fabsf(l);
+ r = fabsf(r);
+
+ return (difference <= (t*l) or difference <= (t*r));
+}
+bool operator==(const Color &x, const Color &y)
+{
+ return (close(x.colors[Color::RedChannel] ,y.colors[Color::RedChannel]) and
+ close(x.colors[Color::GreenChannel],y.colors[Color::GreenChannel]) and
+ close(x.colors[Color::BlueChannel] ,y.colors[Color::BlueChannel]) and
+ close(x.colors[Color::AlphaChannel],y.colors[Color::AlphaChannel]));
+}
+
+std::ostream &operator<<(std::ostream &out, const Color &c)
+{
+ out << "Color(" << c.r() << ", "
+ << c.g() << ", "
+ << c.b() << ", "
+ << c.a() << ")";
+}
+++ /dev/null
-#include "alg/color.h"
-#include <math.h>
-
-Color::Color()
-{
- set(0.0, 0.0, 0.0, 0.0);
-}
-
-Color::Color(const Color &c)
-{
- set(c.colors[RedChannel],
- c.colors[GreenChannel],
- c.colors[BlueChannel],
- c.colors[AlphaChannel]);
-}
-
-Color::Color(float red, float green, float blue, float alpha)
-{
- set(red, green, blue, alpha);
-}
-
-void Color::set(float r, float g, float b, float a)
-{
- colors[RedChannel] = r;
- colors[GreenChannel] = g;
- colors[BlueChannel] = b;
- colors[AlphaChannel] = a;
-}
-
-const float *const Color::get() const
-{
- return colors;
-}
-
-void Color::setR(float r)
-{
- colors[RedChannel] = r;
-}
-
-float Color::r() const
-{
- return colors[RedChannel];
-}
-
-void Color::setG(float g)
-{
- colors[GreenChannel] = g;
-}
-
-float Color::g() const
-{
- return colors[GreenChannel];
-}
-
-void Color::setB(float b)
-{
- colors[BlueChannel] = b;
-}
-
-float Color::b() const
-{
- return colors[BlueChannel];
-}
-
-void Color::setA(float a)
-{
- colors[AlphaChannel] = a;
-}
-
-float Color::a() const
-{
- return colors[AlphaChannel];
-}
-
-static bool close(float l, float r, float t=1e-6)
-{
- float difference = fabsf(l-r);
- l = fabsf(l);
- r = fabsf(r);
-
- return (difference <= (t*l) or difference <= (t*r));
-}
-bool operator==(const Color &x, const Color &y)
-{
- return (close(x.colors[Color::RedChannel] ,y.colors[Color::RedChannel]) and
- close(x.colors[Color::GreenChannel],y.colors[Color::GreenChannel]) and
- close(x.colors[Color::BlueChannel] ,y.colors[Color::BlueChannel]) and
- close(x.colors[Color::AlphaChannel],y.colors[Color::AlphaChannel]));
-}
-
-std::ostream &operator<<(std::ostream &out, const Color &c)
-{
- out << "Color(" << c.r() << ", "
- << c.g() << ", "
- << c.b() << ", "
- << c.a() << ")";
-}
+++ /dev/null
-#ifndef _GLCOLOR_H_
-#define _GLCOLOR_H_
-
-#include <ostream>
-
-//! convienece class for handling opengl colors
-class Color
-{
-public:
- Color();
- Color(const Color &);
- //! initialize with red, green, blue, alpha
- Color(float r, float g, float b, float a=0.0);
-
- //! set all channels simultaneously
- void set(float r, float g, float b, float a=0.0);
- //! return an array of 4 colors (stored by class)
- const float* const get() const;
- void setR(float);
- float r() const;
- void setG(float);
- float g() const;
- void setB(float);
- float b() const;
- void setA(float);
- float a() const;
-
- enum color_channels { RedChannel, GreenChannel, BlueChannel, AlphaChannel };
- friend bool operator==(const Color&, const Color&);
- friend std::ostream& operator<<(std::ostream&, const Color&);
-
-protected:
- float colors[4];
-};
-
-#endif
-
--- /dev/null
+#ifndef _GLCOLOR_H_
+#define _GLCOLOR_H_
+
+#include <ostream>
+
+//! convienece class for handling opengl colors
+class Color
+{
+public:
+ Color();
+ Color(const Color &);
+ //! initialize with red, green, blue, alpha
+ Color(float r, float g, float b, float a=0.0);
+
+ //! set all channels simultaneously
+ void set(float r, float g, float b, float a=0.0);
+ //! return an array of 4 colors (stored by class)
+ const float* const get() const;
+ void setR(float);
+ float r() const;
+ void setG(float);
+ float g() const;
+ void setB(float);
+ float b() const;
+ void setA(float);
+ float a() const;
+
+ enum color_channels { RedChannel, GreenChannel, BlueChannel, AlphaChannel };
+ friend bool operator==(const Color&, const Color&);
+ friend std::ostream& operator<<(std::ostream&, const Color&);
+
+protected:
+ float colors[4];
+};
+
+#endif
+
--- /dev/null
+#include "alg/conserved_path.hpp"
+#include <stdexcept>
+
+using namespace std;
+
+/////////////////////
+
+ConservedPath::ConservedPath()
+ : score(0.0),
+ track_indexes()
+{
+}
+
+ConservedPath::ConservedPath(const ConservedPath::ConservedPath& other)
+ : score(other.score),
+ track_indexes(other.track_indexes)
+{
+}
+
+ConservedPath::ConservedPath(double s, ConservedPath::path_type path)
+ : score(s),
+ track_indexes(path)
+{
+}
+
+void ConservedPath::clear()
+{
+ score = 0.0;
+ track_indexes.clear();
+}
+
+ConservedPath::path_element&
+ConservedPath::operator[](ConservedPath::size_type index)
+{
+ return track_indexes[index];
+}
+
+bool operator==(const ConservedPath::ConservedPath& a,
+ const ConservedPath::ConservedPath& b)
+{
+ // this isn't good as score is now a double
+ return ( (a.score == b.score)
+ and (a.track_indexes.size() == b.track_indexes.size())
+ and (a.track_indexes == b.track_indexes));
+}
+
+bool operator!=(const ConservedPath::ConservedPath& a,
+ const ConservedPath::ConservedPath& b)
+{
+ return not (a == b);
+}
+
+std::ostream& operator<<(std::ostream& out, const ConservedPath& path)
+{
+ out << "<path score=" << path.score
+ << " len=" << path.track_indexes.size();
+ if (path.track_indexes.size() > 0)
+ {
+ // print the first element
+ ConservedPath::const_iterator itor = path.begin();
+ out << ">" << *itor;
+ // print the remaining elements
+ for (;
+ itor != path.end();
+ ++itor)
+ {
+ out << ", " << *itor;
+ }
+ out << "</path>";
+ }
+ else
+ {
+ // if we had no elements just close the block
+ out << "/>";
+ }
+ return out;
+}
+
+void ConservedPath::push_back(const ConservedPath::path_element& element)
+{
+ track_indexes.push_back(element);
+}
+
+void ConservedPath::pop_back()
+{
+ track_indexes.pop_back();
+}
+
+ConservedPath::size_type ConservedPath::size() const
+{
+ return track_indexes.size();
+}
+
+ConservedPath::iterator ConservedPath::begin()
+{
+ return track_indexes.begin();
+}
+
+ConservedPath::const_iterator ConservedPath::begin() const
+{
+ return track_indexes.begin();
+}
+
+ConservedPath::iterator ConservedPath::end()
+{
+ return track_indexes.end();
+}
+
+ConservedPath::const_iterator ConservedPath::end() const
+{
+ return track_indexes.end();
+}
+
+bool ConservedPath::nextTo(const ConservedPath& next) const
+{
+ if (size() != next.size() ) {
+ throw runtime_error("paths must be the same length");
+ }
+ ConservedPath::const_iterator this_itor = begin();
+ ConservedPath::const_iterator next_itor = next.begin();
+ for (; this_itor != end(); ++this_itor, ++next_itor)
+ {
+ if ( (*this_itor + 1) != *next_itor )
+ return false;
+ }
+ return true;
+}
+
+/////////////////////
+ExtendedConservedPath::ExtendedConservedPath()
+ : ConservedPath(),
+ window_size(0)
+{
+}
+
+ExtendedConservedPath::ExtendedConservedPath(const ExtendedConservedPath& other)
+ : ConservedPath(other),
+ window_size(other.window_size)
+{
+}
+
+ExtendedConservedPath::ExtendedConservedPath(int win_size, ConservedPath other)
+ : ConservedPath(other),
+ window_size(win_size)
+{
+}
+
+ExtendedConservedPath::ExtendedConservedPath(int win_size,
+ double s,
+ ConservedPath::path_type p)
+ : ConservedPath(s, p),
+ window_size(win_size)
+{
+}
+
+ExtendedConservedPath& ExtendedConservedPath::extend(int growth)
+{
+ window_size += growth;
+
+ // What does this actually do? Tristan's code was doing this operation
+ // but I don't understand how it properly adjusts reverse compliment
+ // windows?
+ for(ConservedPath::iterator path_i = begin();
+ path_i != end();
+ ++path_i)
+ {
+ if (*path_i < 0)
+ *path_i += growth;
+ }
+ return *this;
+}
+
+
+++ /dev/null
-#include "alg/conserved_path.h"
-#include <stdexcept>
-
-using namespace std;
-
-/////////////////////
-
-ConservedPath::ConservedPath()
- : score(0.0),
- track_indexes()
-{
-}
-
-ConservedPath::ConservedPath(const ConservedPath::ConservedPath& other)
- : score(other.score),
- track_indexes(other.track_indexes)
-{
-}
-
-ConservedPath::ConservedPath(double s, ConservedPath::path_type path)
- : score(s),
- track_indexes(path)
-{
-}
-
-void ConservedPath::clear()
-{
- score = 0.0;
- track_indexes.clear();
-}
-
-ConservedPath::path_element&
-ConservedPath::operator[](ConservedPath::size_type index)
-{
- return track_indexes[index];
-}
-
-bool operator==(const ConservedPath::ConservedPath& a,
- const ConservedPath::ConservedPath& b)
-{
- // this isn't good as score is now a double
- return ( (a.score == b.score)
- and (a.track_indexes.size() == b.track_indexes.size())
- and (a.track_indexes == b.track_indexes));
-}
-
-bool operator!=(const ConservedPath::ConservedPath& a,
- const ConservedPath::ConservedPath& b)
-{
- return not (a == b);
-}
-
-std::ostream& operator<<(std::ostream& out, const ConservedPath& path)
-{
- out << "<path score=" << path.score
- << " len=" << path.track_indexes.size();
- if (path.track_indexes.size() > 0)
- {
- // print the first element
- ConservedPath::const_iterator itor = path.begin();
- out << ">" << *itor;
- // print the remaining elements
- for (;
- itor != path.end();
- ++itor)
- {
- out << ", " << *itor;
- }
- out << "</path>";
- }
- else
- {
- // if we had no elements just close the block
- out << "/>";
- }
- return out;
-}
-
-void ConservedPath::push_back(const ConservedPath::path_element& element)
-{
- track_indexes.push_back(element);
-}
-
-void ConservedPath::pop_back()
-{
- track_indexes.pop_back();
-}
-
-ConservedPath::size_type ConservedPath::size() const
-{
- return track_indexes.size();
-}
-
-ConservedPath::iterator ConservedPath::begin()
-{
- return track_indexes.begin();
-}
-
-ConservedPath::const_iterator ConservedPath::begin() const
-{
- return track_indexes.begin();
-}
-
-ConservedPath::iterator ConservedPath::end()
-{
- return track_indexes.end();
-}
-
-ConservedPath::const_iterator ConservedPath::end() const
-{
- return track_indexes.end();
-}
-
-bool ConservedPath::nextTo(const ConservedPath& next) const
-{
- if (size() != next.size() ) {
- throw runtime_error("paths must be the same length");
- }
- ConservedPath::const_iterator this_itor = begin();
- ConservedPath::const_iterator next_itor = next.begin();
- for (; this_itor != end(); ++this_itor, ++next_itor)
- {
- if ( (*this_itor + 1) != *next_itor )
- return false;
- }
- return true;
-}
-
-/////////////////////
-ExtendedConservedPath::ExtendedConservedPath()
- : ConservedPath(),
- window_size(0)
-{
-}
-
-ExtendedConservedPath::ExtendedConservedPath(const ExtendedConservedPath& other)
- : ConservedPath(other),
- window_size(other.window_size)
-{
-}
-
-ExtendedConservedPath::ExtendedConservedPath(int win_size, ConservedPath other)
- : ConservedPath(other),
- window_size(win_size)
-{
-}
-
-ExtendedConservedPath::ExtendedConservedPath(int win_size,
- double s,
- ConservedPath::path_type p)
- : ConservedPath(s, p),
- window_size(win_size)
-{
-}
-
-ExtendedConservedPath& ExtendedConservedPath::extend(int growth)
-{
- window_size += growth;
-
- // What does this actually do? Tristan's code was doing this operation
- // but I don't understand how it properly adjusts reverse compliment
- // windows?
- for(ConservedPath::iterator path_i = begin();
- path_i != end();
- ++path_i)
- {
- if (*path_i < 0)
- *path_i += growth;
- }
- return *this;
-}
-
-
+++ /dev/null
-#ifndef _CONSERVED_PATH_H
-#define _CONSERVED_PATH_H
-#include <vector>
-#include <ostream>
-
-struct ConservedPath
-{
- typedef int path_element;
- typedef std::vector<path_element> path_type;
- typedef path_type::iterator iterator;
- typedef path_type::const_iterator const_iterator;
- typedef path_type::size_type size_type;
-
- ConservedPath();
- ConservedPath(const ConservedPath& );
- ConservedPath(double score, path_type path);
-
- //! reset our path to be empty (including setting threshold to 0)
- void clear();
- path_element& operator[](size_type index);
- void push_back(const path_element& );
- void pop_back();
-
- size_type size() const;
- iterator begin();
- const_iterator begin() const;
- iterator end();
- const_iterator end() const;
-
- friend bool operator==(const ConservedPath& a, const ConservedPath &b);
- friend bool operator!=(const ConservedPath& a, const ConservedPath &b);
- friend std::ostream& operator<<(std::ostream&, const ConservedPath&);
-
- //! return true if all elements of the path are "next to" our current path.
- /*! Next to is defined as being window index + 1
- * that definition may not properly track reverse compliment
- */
- bool nextTo(const ConservedPath& next) const;
-
- //! either number of conserved bases or average entropy
- double score;
- //! offsets into each of our sequences representing the start of our window
- std::vector<path_element> track_indexes;
-};
-
-struct ExtendedConservedPath : public ConservedPath
-{
- ExtendedConservedPath();
- ExtendedConservedPath(const ExtendedConservedPath& other);
- ExtendedConservedPath(int win_size, ConservedPath conserved_path);
- ExtendedConservedPath(int win_size, double score, std::vector<int> path);
-
- //! extend our current path
- /*! (aka increment our window size by growth)
- */
- ExtendedConservedPath& extend(int growth=1);
-
- //! size of extended window
- int window_size;
-};
-#endif
--- /dev/null
+#ifndef _CONSERVED_PATH_H
+#define _CONSERVED_PATH_H
+#include <vector>
+#include <ostream>
+
+struct ConservedPath
+{
+ typedef int path_element;
+ typedef std::vector<path_element> path_type;
+ typedef path_type::iterator iterator;
+ typedef path_type::const_iterator const_iterator;
+ typedef path_type::size_type size_type;
+
+ ConservedPath();
+ ConservedPath(const ConservedPath& );
+ ConservedPath(double score, path_type path);
+
+ //! reset our path to be empty (including setting threshold to 0)
+ void clear();
+ path_element& operator[](size_type index);
+ void push_back(const path_element& );
+ void pop_back();
+
+ size_type size() const;
+ iterator begin();
+ const_iterator begin() const;
+ iterator end();
+ const_iterator end() const;
+
+ friend bool operator==(const ConservedPath& a, const ConservedPath &b);
+ friend bool operator!=(const ConservedPath& a, const ConservedPath &b);
+ friend std::ostream& operator<<(std::ostream&, const ConservedPath&);
+
+ //! return true if all elements of the path are "next to" our current path.
+ /*! Next to is defined as being window index + 1
+ * that definition may not properly track reverse compliment
+ */
+ bool nextTo(const ConservedPath& next) const;
+
+ //! either number of conserved bases or average entropy
+ double score;
+ //! offsets into each of our sequences representing the start of our window
+ std::vector<path_element> track_indexes;
+};
+
+struct ExtendedConservedPath : public ConservedPath
+{
+ ExtendedConservedPath();
+ ExtendedConservedPath(const ExtendedConservedPath& other);
+ ExtendedConservedPath(int win_size, ConservedPath conserved_path);
+ ExtendedConservedPath(int win_size, double score, std::vector<int> path);
+
+ //! extend our current path
+ /*! (aka increment our window size by growth)
+ */
+ ExtendedConservedPath& extend(int growth=1);
+
+ //! size of extended window
+ int window_size;
+};
+#endif
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+// ----------------------------------------
+// ---------- flp.cc -----------
+// ----------------------------------------
+
+#include "alg/flp.hpp"
+
+#include <fstream>
+#include <iostream>
+#include <string>
+#include <stdexcept>
+#include <cassert>
+
+using namespace std;
+
+bool operator==(const FLPs::match& a, const FLPs::match& b)
+{
+ return (a.index == b.index && a.score == b.score);
+}
+
+ostream &operator<<(ostream& out, const FLPs::match& m)
+{
+ out << "(" << m.score << ", " << m.index << ")";
+ return out;
+}
+
+FLPs::FLPs() :
+ window_size(0),
+ hard_threshold(0),
+ all_matches(0)
+{
+}
+
+void
+FLPs::setup(int win_size, int hard_thres)
+{
+ window_size = win_size;
+ hard_threshold = hard_thres;
+}
+
+void FLPs::alloc_matches(string::size_type len1)
+{
+ if (all_matches != 0) {
+ // if we're being called again its likely because
+ // seqcomp is being called to do the reverse compliment
+ // so we shouldn't reallocate ourselves.
+ return;
+ }
+ all_matches = new std::vector<list<FLPs::match> >;
+
+ list<FLPs::match> empty_match_list;
+ std::vector<list<FLPs::match> >::size_type window_count;
+ if (len1 > 0) {
+ // we actually know how much to preallocate
+ window_count = len1 - window_size+1;
+ } else {
+ // we have no idea, so don't allocate anything
+ window_count = 0;
+ }
+
+ for (std::vector<list<FLPs::match> >::size_type i=0; i < window_count; ++i) {
+ all_matches->push_back(empty_match_list);
+ }
+ assert (all_matches->size() == window_count);
+}
+
+
+int
+FLPs::size() const
+{
+ if (all_matches != 0) {
+ return all_matches->size();
+ } else {
+ return 0;
+ }
+}
+
+
+/*
+bool
+FLPs::match_less(match *match1, match *match2)
+{
+ if (match1->score < match2->score)
+ return true;
+ else if ( (match1->score == match2->score) &&
+ (match1->index < match2->index) )
+ return true;
+ else
+ return false;
+}
+
+void
+FLPs::sort()
+{
+ int i;
+
+ for(i = 0; i < seq1_win_num; i++)
+ if (!all_matches[i].empty())
+ all_matches[i].sort(&FLPs::match_less);
+}
+*/
+
+list<FLPs::match>
+FLPs::matches(int index) const
+{
+ if (all_matches == 0)
+ throw runtime_error("please call FLPs.seqcomp first");
+
+ list<FLPs::match>::iterator list_i, list_end;
+
+ index = abs(index);
+ list_i = (*all_matches)[index].begin();
+ list_end = (*all_matches)[index].end();
+ list<FLPs::match> these_matches(list_i, list_end);
+ return these_matches;
+}
+
+list<int>
+FLPs::match_locations(int index) const
+{
+ if (all_matches == 0)
+ throw runtime_error("please call FLPs.seqcomp first");
+
+ list<int> these_matches;
+ list<FLPs::match>::iterator list_i, list_end;
+
+ index = abs(index);
+ list_i = (*all_matches)[index].begin();
+ list_end = (*all_matches)[index].end();
+ while (list_i != list_end)
+ {
+ these_matches.push_back(list_i->index);
+ ++list_i;
+ }
+ return these_matches;
+}
+
+list<int>
+FLPs::thres_matches(int index, int thres) const
+{
+ if (all_matches == 0)
+ throw runtime_error("please call FLPs.seqcomp first");
+
+ list<int> thres_matches;
+ list<FLPs::match>::iterator list_i, list_end;
+
+ index = abs(index);
+ list_i = (*all_matches)[index].begin();
+ list_end = (*all_matches)[index].end();
+ thres_matches.clear();
+
+ while (list_i != list_end)
+ {
+ if (list_i->score >= thres)
+ thres_matches.push_back(list_i->index);
+ ++list_i;
+ }
+ return thres_matches;
+}
+
+void
+FLPs::save(string save_file_path)
+{
+ if (all_matches == 0)
+ throw runtime_error("please call FLPs.seqcomp first");
+
+ fstream save_file;
+ save_file.open(save_file_path.c_str(), ios::out);
+
+ save_file << "<Seqcomp win=" << window_size
+ << " thres=" << hard_threshold << endl;
+
+ for(vector<list<FLPs::match> >::const_iterator win_citor = all_matches->begin();
+ win_citor != all_matches->end();
+ ++win_citor)
+ {
+ if (!win_citor->empty())
+ {
+ for( list<FLPs::match>::const_iterator match_itor = win_citor->begin();
+ match_itor != win_citor->end();
+ ++match_itor)
+ {
+ save_file << match_itor->index << "," << match_itor->score << " ";
+ }
+ }
+ save_file << endl;
+ }
+
+ save_file << "</Seqcomp>\n";
+
+ save_file.close();
+}
+
+void
+FLPs::load(string file_path)
+{
+ fstream data_file;
+ string file_data, file_data_line, pair_data, index_data, score_data;
+ match a_match;
+ string::size_type split_index, comma_index;
+ bool tag_open = false;
+ list<FLPs::match> a_match_list;
+ // initialize our all_matches pointer
+ alloc_matches();
+
+
+ data_file.open(file_path.c_str(), ios::in);
+
+ getline(data_file,file_data_line);
+ // parse seqcomp open tag and parameters
+ // eg <Seqcomp type=mussa win=30 thres=21>
+ // if parse successful...
+ tag_open = true;
+
+ while ((!data_file.eof()) && tag_open)
+ {
+ // intialize list to empty
+ a_match_list.clear();
+
+ getline(data_file,file_data_line);
+ if (file_data_line == "</Seqcomp>")
+ {
+ tag_open = false;
+ }
+ // parse line of matches
+ else if (file_data_line == "")
+ {
+ //cout << "empty line\n";
+ all_matches->push_back(a_match_list);
+ }
+ else
+ {
+ split_index = file_data_line.find(" ");
+
+ while (split_index != string::npos)
+ {
+ pair_data = file_data_line.substr(0,split_index);
+ file_data_line = file_data_line.substr(split_index+1);
+ //cout << "pair_data = " << pair_data << "...";
+ // parse out the 2 pieces of data, index and score of pair match
+ comma_index = pair_data.find(",");
+ index_data = pair_data.substr(0, comma_index);
+ a_match.index = atoi(index_data.c_str() );
+ score_data = pair_data.substr(comma_index+1);
+ a_match.score = atoi(score_data.c_str() );
+ //cout << a_match.index << "," << a_match.score << " ";
+
+ a_match_list.push_back(a_match);
+
+ split_index = file_data_line.find(" ");
+ }
+ all_matches->push_back(a_match_list);
+ //cout << all_matches->size() << "\n";
+ }
+ }
+ //cout << "windows in flp = " << all_matches->size() << endl;
+ data_file.close();
+}
+
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-// ----------------------------------------
-// ---------- flp.cc -----------
-// ----------------------------------------
-
-#include "flp.hh"
-
-#include <fstream>
-#include <iostream>
-#include <string>
-#include <stdexcept>
-#include <cassert>
-
-using namespace std;
-
-bool operator==(const FLPs::match& a, const FLPs::match& b)
-{
- return (a.index == b.index && a.score == b.score);
-}
-
-ostream &operator<<(ostream& out, const FLPs::match& m)
-{
- out << "(" << m.score << ", " << m.index << ")";
- return out;
-}
-
-FLPs::FLPs() :
- window_size(0),
- hard_threshold(0),
- all_matches(0)
-{
-}
-
-void
-FLPs::setup(int win_size, int hard_thres)
-{
- window_size = win_size;
- hard_threshold = hard_thres;
-}
-
-void FLPs::alloc_matches(string::size_type len1)
-{
- if (all_matches != 0) {
- // if we're being called again its likely because
- // seqcomp is being called to do the reverse compliment
- // so we shouldn't reallocate ourselves.
- return;
- }
- all_matches = new std::vector<list<FLPs::match> >;
-
- list<FLPs::match> empty_match_list;
- std::vector<list<FLPs::match> >::size_type window_count;
- if (len1 > 0) {
- // we actually know how much to preallocate
- window_count = len1 - window_size+1;
- } else {
- // we have no idea, so don't allocate anything
- window_count = 0;
- }
-
- for (std::vector<list<FLPs::match> >::size_type i=0; i < window_count; ++i) {
- all_matches->push_back(empty_match_list);
- }
- assert (all_matches->size() == window_count);
-}
-
-
-int
-FLPs::size() const
-{
- if (all_matches != 0) {
- return all_matches->size();
- } else {
- return 0;
- }
-}
-
-
-/*
-bool
-FLPs::match_less(match *match1, match *match2)
-{
- if (match1->score < match2->score)
- return true;
- else if ( (match1->score == match2->score) &&
- (match1->index < match2->index) )
- return true;
- else
- return false;
-}
-
-void
-FLPs::sort()
-{
- int i;
-
- for(i = 0; i < seq1_win_num; i++)
- if (!all_matches[i].empty())
- all_matches[i].sort(&FLPs::match_less);
-}
-*/
-
-list<FLPs::match>
-FLPs::matches(int index) const
-{
- if (all_matches == 0)
- throw runtime_error("please call FLPs.seqcomp first");
-
- list<FLPs::match>::iterator list_i, list_end;
-
- index = abs(index);
- list_i = (*all_matches)[index].begin();
- list_end = (*all_matches)[index].end();
- list<FLPs::match> these_matches(list_i, list_end);
- return these_matches;
-}
-
-list<int>
-FLPs::match_locations(int index) const
-{
- if (all_matches == 0)
- throw runtime_error("please call FLPs.seqcomp first");
-
- list<int> these_matches;
- list<FLPs::match>::iterator list_i, list_end;
-
- index = abs(index);
- list_i = (*all_matches)[index].begin();
- list_end = (*all_matches)[index].end();
- while (list_i != list_end)
- {
- these_matches.push_back(list_i->index);
- ++list_i;
- }
- return these_matches;
-}
-
-list<int>
-FLPs::thres_matches(int index, int thres) const
-{
- if (all_matches == 0)
- throw runtime_error("please call FLPs.seqcomp first");
-
- list<int> thres_matches;
- list<FLPs::match>::iterator list_i, list_end;
-
- index = abs(index);
- list_i = (*all_matches)[index].begin();
- list_end = (*all_matches)[index].end();
- thres_matches.clear();
-
- while (list_i != list_end)
- {
- if (list_i->score >= thres)
- thres_matches.push_back(list_i->index);
- ++list_i;
- }
- return thres_matches;
-}
-
-void
-FLPs::save(string save_file_path)
-{
- if (all_matches == 0)
- throw runtime_error("please call FLPs.seqcomp first");
-
- fstream save_file;
- save_file.open(save_file_path.c_str(), ios::out);
-
- save_file << "<Seqcomp win=" << window_size
- << " thres=" << hard_threshold << endl;
-
- for(vector<list<FLPs::match> >::const_iterator win_citor = all_matches->begin();
- win_citor != all_matches->end();
- ++win_citor)
- {
- if (!win_citor->empty())
- {
- for( list<FLPs::match>::const_iterator match_itor = win_citor->begin();
- match_itor != win_citor->end();
- ++match_itor)
- {
- save_file << match_itor->index << "," << match_itor->score << " ";
- }
- }
- save_file << endl;
- }
-
- save_file << "</Seqcomp>\n";
-
- save_file.close();
-}
-
-void
-FLPs::load(string file_path)
-{
- fstream data_file;
- string file_data, file_data_line, pair_data, index_data, score_data;
- match a_match;
- string::size_type split_index, comma_index;
- bool tag_open = false;
- list<FLPs::match> a_match_list;
- // initialize our all_matches pointer
- alloc_matches();
-
-
- data_file.open(file_path.c_str(), ios::in);
-
- getline(data_file,file_data_line);
- // parse seqcomp open tag and parameters
- // eg <Seqcomp type=mussa win=30 thres=21>
- // if parse successful...
- tag_open = true;
-
- while ((!data_file.eof()) && tag_open)
- {
- // intialize list to empty
- a_match_list.clear();
-
- getline(data_file,file_data_line);
- if (file_data_line == "</Seqcomp>")
- {
- tag_open = false;
- }
- // parse line of matches
- else if (file_data_line == "")
- {
- //cout << "empty line\n";
- all_matches->push_back(a_match_list);
- }
- else
- {
- split_index = file_data_line.find(" ");
-
- while (split_index != string::npos)
- {
- pair_data = file_data_line.substr(0,split_index);
- file_data_line = file_data_line.substr(split_index+1);
- //cout << "pair_data = " << pair_data << "...";
- // parse out the 2 pieces of data, index and score of pair match
- comma_index = pair_data.find(",");
- index_data = pair_data.substr(0, comma_index);
- a_match.index = atoi(index_data.c_str() );
- score_data = pair_data.substr(comma_index+1);
- a_match.score = atoi(score_data.c_str() );
- //cout << a_match.index << "," << a_match.score << " ";
-
- a_match_list.push_back(a_match);
-
- split_index = file_data_line.find(" ");
- }
- all_matches->push_back(a_match_list);
- //cout << all_matches->size() << "\n";
- }
- }
- //cout << "windows in flp = " << all_matches->size() << endl;
- data_file.close();
-}
-
+++ /dev/null
-#ifndef _MUSSA_FLP_H_
-#define _MUSSA_FLP_H_
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-// ----------------------------------------
-// ---------- flp.hh -----------
-// ----------------------------------------
-
-#include <list>
-#include <string>
-#include <vector>
-#include <iostream>
-
-//! FLP = Fixed Length Pairs (Data)
-/*!
- * vector of linked lists of the match type struct
- */
-class FLPs
-{
- public:
- FLPs();
- //! Setup a FLP and reserve space for the match lists
- /*!
- * Initialize the all_matches structure with a list of matches
- * for enough windows for the size of sequence 1
- */
-
- struct match
- {
- int index;
- int score;
-
- friend bool operator==(const match&, const match& );
- friend std::ostream &operator<<(std::ostream&, const match&);
- };
-
- void setup(int win_size, int hard_thres);
- //! compare two sequences and store the list of results in all_matches
- void seqcomp(std::string seq1, std::string seq2, bool is_RC);
- //bool FLPs::match_less(match *match1, match *match2);
- //void FLPs::sort();
- //! Return all the matches for a particular window?
- std::list<match> matches(int index) const;
- //! Return all the match indexes for a particular window?
- std::list<int> match_locations(int index) const;
- //! Return all the match indexes for a particular window above a threshold
- std::list<int> thres_matches(int index, int thres) const;
- //! Return the number of windows stored in this FLPs
- /*! (this is should be the same as seq1_len-window_size+1
- */
- int size() const;
- //! Save all the FLPs to save_file_path
- void save(std::string save_file_path);
- //! Load a vector of a lists of FLPs
- void load(std::string file_path);
- private:
- //! the number of base pairs in the sliding window
- int window_size;
- //! the minimum tnumber of base pairs need for this window to be saved.
- int hard_threshold;
-
- //! add a match from location seq1_i to seq2_i with a threshold of a_score
- /*! i2_offset is used to shift the window start when doing a reverse
- * compliment. (This is called by seqcomp() )
- */
- inline void add(int seq1_i, int seq2_i, int a_score, int i2_offset);
- //! this list of matches between the two sequences
- /*! All of the matches are stored here, it appears each window position
- * in sequence 1 gets an entry in the vector, the list contains matches
- * between sequence 1 and sequence 2
- */
- std::vector<std::list<match> > *all_matches;
- //! reserve space for the appropriate number of windows.
- /*! this is mostly so seqcomp can use operator[]
- */
- void alloc_matches(std::string::size_type len1=0);
-
-
-};
-#endif
--- /dev/null
+#ifndef _MUSSA_FLP_H_
+#define _MUSSA_FLP_H_
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+// ----------------------------------------
+// ---------- flp.hh -----------
+// ----------------------------------------
+
+#include <list>
+#include <string>
+#include <vector>
+#include <iostream>
+
+//! FLP = Fixed Length Pairs (Data)
+/*!
+ * vector of linked lists of the match type struct
+ */
+class FLPs
+{
+ public:
+ FLPs();
+ //! Setup a FLP and reserve space for the match lists
+ /*!
+ * Initialize the all_matches structure with a list of matches
+ * for enough windows for the size of sequence 1
+ */
+
+ struct match
+ {
+ int index;
+ int score;
+
+ friend bool operator==(const match&, const match& );
+ friend std::ostream &operator<<(std::ostream&, const match&);
+ };
+
+ void setup(int win_size, int hard_thres);
+ //! compare two sequences and store the list of results in all_matches
+ void seqcomp(std::string seq1, std::string seq2, bool is_RC);
+ //bool FLPs::match_less(match *match1, match *match2);
+ //void FLPs::sort();
+ //! Return all the matches for a particular window?
+ std::list<match> matches(int index) const;
+ //! Return all the match indexes for a particular window?
+ std::list<int> match_locations(int index) const;
+ //! Return all the match indexes for a particular window above a threshold
+ std::list<int> thres_matches(int index, int thres) const;
+ //! Return the number of windows stored in this FLPs
+ /*! (this is should be the same as seq1_len-window_size+1
+ */
+ int size() const;
+ //! Save all the FLPs to save_file_path
+ void save(std::string save_file_path);
+ //! Load a vector of a lists of FLPs
+ void load(std::string file_path);
+ private:
+ //! the number of base pairs in the sliding window
+ int window_size;
+ //! the minimum tnumber of base pairs need for this window to be saved.
+ int hard_threshold;
+
+ //! add a match from location seq1_i to seq2_i with a threshold of a_score
+ /*! i2_offset is used to shift the window start when doing a reverse
+ * compliment. (This is called by seqcomp() )
+ */
+ inline void add(int seq1_i, int seq2_i, int a_score, int i2_offset);
+ //! this list of matches between the two sequences
+ /*! All of the matches are stored here, it appears each window position
+ * in sequence 1 gets an entry in the vector, the list contains matches
+ * between sequence 1 and sequence 2
+ */
+ std::vector<std::list<match> > *all_matches;
+ //! reserve space for the appropriate number of windows.
+ /*! this is mostly so seqcomp can use operator[]
+ */
+ void alloc_matches(std::string::size_type len1=0);
+
+
+};
+#endif
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+// ----------------------------------------
+// ---------- flp_seqcomp.cc -----------
+// ----------------------------------------
+
+#include "alg/flp.hpp"
+#include <cassert>
+using namespace std;
+
+// Note one recording RC matches. This version of 'seqcomp' records RC matches
+// as index of the window start in its nonRC form. However, past versions of
+// the analysis recorded it as the index of the rear of the window, as the
+// following legacy comment indicates. FR still uses this method
+
+// Titus thinks the start of an RC window should be its "rear" in the
+// normal version of the sequence. He's wrong, of course, and in the
+// future my followers will annihilate his in the Final Battle, but for
+// now I'll let him have his way.
+
+// note seq2_i is actually the index of the leaving bp, so need to +1
+
+inline void
+FLPs::add(int seq1_i, int seq2_i, int a_score, int i2_offset)
+{
+ match a_match;
+
+
+ if (a_score >= hard_threshold)
+ {
+ a_match.index = seq2_i + i2_offset;
+ a_match.score = a_score;
+
+ (*all_matches)[seq1_i].push_back(a_match);
+ }
+}
+
+
+void
+FLPs::seqcomp(string sseq1, string sseq2, bool is_RC)
+{
+ int start_i, seq1_i, seq2_i, win_i; // loop variables
+ int matches; // number of matches in to a window
+ int i2_offset;
+ char * seq1, * seq2;
+ int seq1_win_num = sseq1.size() - window_size + 1;
+ int seq2_win_num = sseq2.size() - window_size + 1;
+ alloc_matches(sseq1.size());
+ assert(seq1_win_num == size());
+
+ seq1 = (char *) sseq1.c_str();
+ seq2 = (char *) sseq2.c_str();
+
+
+ if (is_RC)
+ i2_offset = window_size - sseq2.size();
+ else
+ i2_offset = 0;
+
+
+ // this does the "upper diagonals" of the search
+
+ // loop thru the start positions for sequence 1
+ for(start_i = 0; start_i < size(); start_i++)
+ {
+ matches = 0;
+ // compare initial window
+ for(win_i = 0; win_i < window_size; win_i++)
+ if ((seq1[start_i+win_i] == seq2[win_i]) &&
+ (seq1[start_i+win_i] != 'N')) // N's match nothing **
+ matches++;
+
+ //seq2_i is always 0 for initial win
+ seq2_i = 0;
+
+ // call inlined function that adds match if it is above threshold
+ add(start_i, seq2_i, matches, i2_offset);
+
+ // run through rest of seq1 and seq2 with current seq1 offset (ie start_i)
+ // compare the bps leaving and entering the window and modify matches count
+ seq1_i = start_i;
+ while( (seq1_i < seq1_win_num-1) && (seq2_i < seq2_win_num-1) )
+ {
+ // copmpare the bp leaving the window
+ if ((seq1[seq1_i] == seq2[seq2_i]) && (seq1[seq1_i] != 'N')) {
+ // N's match nothing
+ matches = matches -1;
+ }
+
+ // compare the bp entering the window
+ if ((seq1[seq1_i+window_size] == seq2[seq2_i+window_size]) &&
+ (seq1[seq1_i+window_size] != 'N')) { // N's match nothing
+ matches = matches + 1;
+ }
+ add(seq1_i + 1, seq2_i + 1, matches, i2_offset);
+
+ seq1_i = seq1_i + 1; // increment seq1_i to next window
+ seq2_i = seq2_i + 1; // increment seq2_i to next window
+ } // end of loop thru the current offset sequence
+ } // end of loop thru the start positions of seq1 sequence
+
+
+ // this does the "lower diagonals" of the search
+
+ // loop thru the start positions for sequence 1
+ for(start_i = 1; start_i < seq2_win_num; start_i++)
+ {
+ matches = 0;
+
+ // compare initial window
+ for(win_i = 0; win_i < window_size; win_i++)
+ if ((seq2[start_i+win_i] == seq1[win_i]) &&
+ (seq2[start_i+win_i] != 'N')) // N's match nothing
+ matches++;
+
+ //seq2_i is always start_i for initial window
+ seq2_i = start_i;
+
+ add(0, seq2_i, matches, i2_offset);
+
+ // run through rest of seq1 and seq2 with current seq1 offset (ie start_i)
+ // compare the bps leaving and entering the window and modify matches count
+ seq1_i = 0;
+ while( (seq1_i < seq1_win_num-1) && (seq2_i < seq2_win_num-1) )
+ {
+ // copmpare the bp leaving the window
+ if ((seq1[seq1_i] == seq2[seq2_i]) &&
+ (seq1[seq1_i] != 'N')) // N's match nothing
+ matches = matches - 1;
+
+ // compare the bp entering the window
+ if ((seq1[seq1_i+window_size] == seq2[seq2_i+window_size]) &&
+ (seq1[seq1_i+window_size] != 'N')) // N's match nothing
+ matches = matches + 1;
+
+ add(seq1_i + 1, seq2_i + 1, matches, i2_offset);
+
+ seq1_i = seq1_i + 1; // increment seq1_i to next window
+ seq2_i = seq2_i + 1; // increment seq2_i to next window
+ } // end of loop thru the current offset sequence
+ } // end of loop thru the start positions of seq2 sequence
+}
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-// ----------------------------------------
-// ---------- flp_seqcomp.cc -----------
-// ----------------------------------------
-
-#include "alg/flp.hh"
-#include <cassert>
-using namespace std;
-
-// Note one recording RC matches. This version of 'seqcomp' records RC matches
-// as index of the window start in its nonRC form. However, past versions of
-// the analysis recorded it as the index of the rear of the window, as the
-// following legacy comment indicates. FR still uses this method
-
-// Titus thinks the start of an RC window should be its "rear" in the
-// normal version of the sequence. He's wrong, of course, and in the
-// future my followers will annihilate his in the Final Battle, but for
-// now I'll let him have his way.
-
-// note seq2_i is actually the index of the leaving bp, so need to +1
-
-inline void
-FLPs::add(int seq1_i, int seq2_i, int a_score, int i2_offset)
-{
- match a_match;
-
-
- if (a_score >= hard_threshold)
- {
- a_match.index = seq2_i + i2_offset;
- a_match.score = a_score;
-
- (*all_matches)[seq1_i].push_back(a_match);
- }
-}
-
-
-void
-FLPs::seqcomp(string sseq1, string sseq2, bool is_RC)
-{
- int start_i, seq1_i, seq2_i, win_i; // loop variables
- int matches; // number of matches in to a window
- int i2_offset;
- char * seq1, * seq2;
- int seq1_win_num = sseq1.size() - window_size + 1;
- int seq2_win_num = sseq2.size() - window_size + 1;
- alloc_matches(sseq1.size());
- assert(seq1_win_num == size());
-
- seq1 = (char *) sseq1.c_str();
- seq2 = (char *) sseq2.c_str();
-
-
- if (is_RC)
- i2_offset = window_size - sseq2.size();
- else
- i2_offset = 0;
-
-
- // this does the "upper diagonals" of the search
-
- // loop thru the start positions for sequence 1
- for(start_i = 0; start_i < size(); start_i++)
- {
- matches = 0;
- // compare initial window
- for(win_i = 0; win_i < window_size; win_i++)
- if ((seq1[start_i+win_i] == seq2[win_i]) &&
- (seq1[start_i+win_i] != 'N')) // N's match nothing **
- matches++;
-
- //seq2_i is always 0 for initial win
- seq2_i = 0;
-
- // call inlined function that adds match if it is above threshold
- add(start_i, seq2_i, matches, i2_offset);
-
- // run through rest of seq1 and seq2 with current seq1 offset (ie start_i)
- // compare the bps leaving and entering the window and modify matches count
- seq1_i = start_i;
- while( (seq1_i < seq1_win_num-1) && (seq2_i < seq2_win_num-1) )
- {
- // copmpare the bp leaving the window
- if ((seq1[seq1_i] == seq2[seq2_i]) && (seq1[seq1_i] != 'N')) {
- // N's match nothing
- matches = matches -1;
- }
-
- // compare the bp entering the window
- if ((seq1[seq1_i+window_size] == seq2[seq2_i+window_size]) &&
- (seq1[seq1_i+window_size] != 'N')) { // N's match nothing
- matches = matches + 1;
- }
- add(seq1_i + 1, seq2_i + 1, matches, i2_offset);
-
- seq1_i = seq1_i + 1; // increment seq1_i to next window
- seq2_i = seq2_i + 1; // increment seq2_i to next window
- } // end of loop thru the current offset sequence
- } // end of loop thru the start positions of seq1 sequence
-
-
- // this does the "lower diagonals" of the search
-
- // loop thru the start positions for sequence 1
- for(start_i = 1; start_i < seq2_win_num; start_i++)
- {
- matches = 0;
-
- // compare initial window
- for(win_i = 0; win_i < window_size; win_i++)
- if ((seq2[start_i+win_i] == seq1[win_i]) &&
- (seq2[start_i+win_i] != 'N')) // N's match nothing
- matches++;
-
- //seq2_i is always start_i for initial window
- seq2_i = start_i;
-
- add(0, seq2_i, matches, i2_offset);
-
- // run through rest of seq1 and seq2 with current seq1 offset (ie start_i)
- // compare the bps leaving and entering the window and modify matches count
- seq1_i = 0;
- while( (seq1_i < seq1_win_num-1) && (seq2_i < seq2_win_num-1) )
- {
- // copmpare the bp leaving the window
- if ((seq1[seq1_i] == seq2[seq2_i]) &&
- (seq1[seq1_i] != 'N')) // N's match nothing
- matches = matches - 1;
-
- // compare the bp entering the window
- if ((seq1[seq1_i+window_size] == seq2[seq2_i+window_size]) &&
- (seq1[seq1_i+window_size] != 'N')) // N's match nothing
- matches = matches + 1;
-
- add(seq1_i + 1, seq2_i + 1, matches, i2_offset);
-
- seq1_i = seq1_i + 1; // increment seq1_i to next window
- seq2_i = seq2_i + 1; // increment seq2_i to next window
- } // end of loop thru the current offset sequence
- } // end of loop thru the start positions of seq2 sequence
-}
--- /dev/null
+#include "alg/glsequence.hpp"
+
+#include <iostream>
+#include <cassert>
+#include <math.h>
+#include <stdexcept>
+using namespace std;
+
+GlSequence::GlSequence(const Sequence &s)
+ : seq(s),
+ seq_x(0.0),
+ seq_y(0.0),
+ seq_z(1.0),
+ seq_height(12.0),
+ drawColor(0.0, 0.0, 0.0),
+ char_pix_per_world_unit(5.0)
+{
+}
+
+GlSequence::GlSequence(const GlSequence &s)
+ : seq(s.seq),
+ seq_x(s.seq_x),
+ seq_y(s.seq_y),
+ seq_z(s.seq_z),
+ seq_height(s.seq_height),
+ drawColor(s.drawColor),
+ char_pix_per_world_unit(s.char_pix_per_world_unit)
+{
+}
+
+GlSequence &GlSequence::operator=(const GlSequence & s)
+{
+ if (this != &s) {
+ const_cast<Sequence &>(seq) = s.seq;
+ seq_x = s.seq_x;
+ seq_y = s.seq_y;
+ seq_z = s.seq_z;
+ seq_height = s.seq_height;
+ drawColor = s.drawColor;
+ assert(char_pix_per_world_unit == s.char_pix_per_world_unit);
+ }
+ return *this;
+}
+
+const Sequence& GlSequence::sequence() const
+{
+ return seq;
+}
+
+void GlSequence::setX(GLfloat value)
+{
+ seq_x = value;
+}
+
+GLfloat GlSequence::x() const
+{
+ return seq_x;
+}
+
+void GlSequence::setY(GLfloat value)
+{
+ seq_y = value;
+}
+
+GLfloat GlSequence::y() const
+{
+ return seq_y;
+}
+
+GLfloat GlSequence::length() const
+{
+ return seq.size();
+}
+
+Sequence::size_type GlSequence::leftbase(GLfloat left) const
+{
+ assert (seq_x == 0);
+ left = ceil(left);
+ if (left < seq_x)
+ return 0;
+ else
+ return (Sequence::size_type)left;
+}
+
+Sequence::size_type GlSequence::rightbase(GLfloat right) const
+{
+ assert (seq_x == 0);
+ right = floor(right);
+ if (right > seq.size())
+ return seq.size();
+ else
+ return (Sequence::size_type)right;
+}
+
+Sequence::const_iterator GlSequence::sequence_begin() const
+{
+ return seq.begin();
+}
+
+Sequence::const_iterator GlSequence::sequence_end() const
+{
+ return seq.end();
+}
+
+Sequence::const_iterator
+GlSequence::sequence_begin(GLfloat left, GLfloat right) const
+{
+ // the following code will be wrong when sequences can be slid around
+ // so make sure we break.
+ assert (seq_x == 0);
+
+ if ( leftbase(left) > seq.size() or left > right )
+ return seq.end();
+ else
+ return seq.begin() + leftbase(left);
+}
+
+Sequence::const_iterator
+GlSequence::sequence_end(GLfloat left, GLfloat right) const
+{
+ // the following code will be wrong when sequences can be slid around
+ // so make sure we break.
+ assert (seq_x == 0);
+
+ if ( rightbase(right) > seq.size() or left > right )
+ return seq.end();
+ else
+ return seq.begin() + rightbase(right);
+}
+
+
+//! set default track draw color
+void GlSequence::setColor(Color &c)
+{
+ drawColor = c;
+}
+
+//! get default track draw color
+Color GlSequence::color()
+{
+ return drawColor;
+}
+
+
+int GlSequence::get_viewport_pixel_width()
+{
+ int viewport[4];
+ glGetIntegerv(GL_VIEWPORT, viewport);
+ return viewport[3]; // grab the viewport width
+}
+
+bool GlSequence::is_sequence_renderable(GLfloat left,
+ GLfloat right,
+ int viewport_width) const
+{
+ // if called with default argument, go get the viewable width
+ if (viewport_width == -1) {
+ viewport_width = get_viewport_pixel_width();
+ }
+ GLfloat world_width = right - left;
+ GLfloat pixels_needed = (char_pix_per_world_unit * world_width);
+
+ // if the number of pixels taken up by rendering the characters
+ // that'd show up in the current ortho width is less than the window
+ // width we can actually draw something
+ return pixels_needed < viewport_width;
+}
+
+
+void GlSequence::draw(GLfloat left, GLfloat right) const
+{
+ if ( not is_sequence_renderable(left, right) ) {
+ draw_track(left, right);
+ } else {
+ draw_sequence(left, right);
+ }
+ draw_annotations(left, right);
+}
+
+void GlSequence::draw_box(GLfloat left, GLfloat right,
+ GLfloat height, GLfloat z) const
+{
+ GLfloat offset = height/2.0;
+ GLfloat top = seq_y + offset;
+ GLfloat bottom = seq_y - offset;
+
+ glBegin(GL_QUADS);
+ glVertex3f(left, top, z);
+ glVertex3f(left, bottom, z);
+ glVertex3f(right, bottom, z);
+ glVertex3f(right, top, z);
+ glEnd();
+}
+void GlSequence::draw_track(GLfloat left, GLfloat right) const
+{
+ glColor3fv(drawColor.get());
+ // draw main sequence track
+ draw_box(seq_x, seq_x+seq.size(), seq_height, 0.0);
+}
+
+void GlSequence::draw_annotations(GLfloat left, GLfloat right) const
+{
+ // draw annotations
+ glLineWidth(seq_height);
+ GLfloat annotation_z = seq_z + 1.0;
+ std::list<annot> annots = seq.annotations();
+ for (std::list<annot>::const_iterator annot_itor = annots.begin();
+ annot_itor != annots.end();
+ ++annot_itor, ++annotation_z)
+ {
+ glColor3f(0.0, 0.5, 0.0);
+ draw_box(seq_x+annot_itor->start, seq_x+annot_itor->end,
+ seq_height, annotation_z);
+ }
+}
+
+const int PT = 1;
+const int STROKE = 2;
+const int END =3;
+
+typedef struct charpoint {
+ GLfloat x, y;
+ int type;
+} CP;
+
+CP Adata[] = {
+ {0, -5, PT}, {2.5, 5, PT}, {5, -5, STROKE},
+ {0.75, -2, PT}, {4.25, -2, END}
+};
+
+CP Tdata[] = {
+ {2.5, -5, PT}, {2.5,5, STROKE}, {0, 5, PT}, {5, 5, END}
+};
+
+CP Gdata[] = {
+ {5, 3, PT}, {3, 5, PT}, {2, 5, PT}, {0, 3, PT}, {0, -3, PT},
+ {2, -5, PT}, {3, -5, PT}, {5, -3, STROKE},
+ {2.5, -1, PT}, {5, -1,PT}, {5, -5, END}
+};
+
+CP Cdata[] = {
+ {4.9, 3, PT}, {3, 5, PT}, {2, 5, PT}, {0, 3, PT}, {0, -3, PT},
+ {2, -5, PT}, {3, -5, PT}, {5, -3, END}
+};
+
+CP Xdata[] = {{ 0, 5, PT}, {5, -5,STROKE},{0,-5,PT},{5, 5, END}};
+CP Ndata[] = {{ 0, -5, PT}, {0, 5, PT}, {5, -5, PT}, {5, 5, END}};
+
+static void drawLetter(CP *l, GLfloat z)
+{
+ glBegin(GL_LINE_STRIP);
+ while(1) {
+ switch (l->type) {
+ case PT:
+ glVertex3f(l->x, l->y, z);
+ break;
+ case STROKE:
+ glVertex3f(l->x, l->y, z);
+ glEnd();
+ glBegin(GL_LINE_STRIP);
+ break;
+ case END:
+ glVertex3f(l->x, l->y, z);
+ glEnd();
+ return;
+ break;
+ default:
+ throw runtime_error("data structure failure");
+ }
+ l++;
+ }
+}
+
+void GlSequence::draw_sequence(GLfloat left, GLfloat right) const
+{
+ // FIXME: basically this needs to be greater than the number of annotations
+ const GLfloat z = 30;
+ glLineWidth(0.3);
+ glColor3fv(drawColor.get());
+
+ Sequence::const_iterator seq_itor = sequence_begin(left, right);
+ Sequence::const_iterator seq_end = sequence_end(left, right);
+ Sequence::size_type basepair = 0;
+
+ assert(seq_end - seq_itor >= 0);
+ while(seq_itor != seq_end)
+ {
+ assert ( basepair < seq.size() );
+ glPushMatrix();
+ glTranslatef( leftbase(left) + basepair, seq_y, 1.0 );
+ glScalef(0.1, 1.0, 1.0);
+ switch (*seq_itor) {
+ case 'A': case 'a':
+ drawLetter(Adata, z);
+ break;
+ case 'T': case 't':
+ drawLetter(Tdata, z);
+ break;
+ case 'G': case 'g':
+ drawLetter(Gdata, z);
+ break;
+ case 'C': case 'c':
+ drawLetter(Cdata, z);
+ break;
+ case 'N': case 'n':
+ drawLetter(Ndata, z);
+ break;
+ default:
+ drawLetter(Xdata, z);
+ break;
+ }
+ glPopMatrix();
+ ++seq_itor;
+ ++basepair;
+ }
+}
+
+bool operator==(const GlSequence &left, const GlSequence &right)
+{
+ return ( (left.seq_x == right.seq_x) and
+ (left.seq_y == right.seq_y) and
+ (left.seq_z == right.seq_z) and
+ (left.seq_height == right.seq_height) and
+ (left.drawColor == right.drawColor));
+}
+
+++ /dev/null
-#include "alg/glsequence.h"
-
-#include <iostream>
-#include <cassert>
-#include <math.h>
-#include <stdexcept>
-using namespace std;
-
-GlSequence::GlSequence(const Sequence &s)
- : seq(s),
- seq_x(0.0),
- seq_y(0.0),
- seq_z(1.0),
- seq_height(12.0),
- drawColor(0.0, 0.0, 0.0),
- char_pix_per_world_unit(5.0)
-{
-}
-
-GlSequence::GlSequence(const GlSequence &s)
- : seq(s.seq),
- seq_x(s.seq_x),
- seq_y(s.seq_y),
- seq_z(s.seq_z),
- seq_height(s.seq_height),
- drawColor(s.drawColor),
- char_pix_per_world_unit(s.char_pix_per_world_unit)
-{
-}
-
-GlSequence &GlSequence::operator=(const GlSequence & s)
-{
- if (this != &s) {
- const_cast<Sequence &>(seq) = s.seq;
- seq_x = s.seq_x;
- seq_y = s.seq_y;
- seq_z = s.seq_z;
- seq_height = s.seq_height;
- drawColor = s.drawColor;
- assert(char_pix_per_world_unit == s.char_pix_per_world_unit);
- }
- return *this;
-}
-
-const Sequence& GlSequence::sequence() const
-{
- return seq;
-}
-
-void GlSequence::setX(GLfloat value)
-{
- seq_x = value;
-}
-
-GLfloat GlSequence::x() const
-{
- return seq_x;
-}
-
-void GlSequence::setY(GLfloat value)
-{
- seq_y = value;
-}
-
-GLfloat GlSequence::y() const
-{
- return seq_y;
-}
-
-GLfloat GlSequence::length() const
-{
- return seq.size();
-}
-
-Sequence::size_type GlSequence::leftbase(GLfloat left) const
-{
- assert (seq_x == 0);
- left = ceil(left);
- if (left < seq_x)
- return 0;
- else
- return (Sequence::size_type)left;
-}
-
-Sequence::size_type GlSequence::rightbase(GLfloat right) const
-{
- assert (seq_x == 0);
- right = floor(right);
- if (right > seq.size())
- return seq.size();
- else
- return (Sequence::size_type)right;
-}
-
-Sequence::const_iterator GlSequence::sequence_begin() const
-{
- return seq.begin();
-}
-
-Sequence::const_iterator GlSequence::sequence_end() const
-{
- return seq.end();
-}
-
-Sequence::const_iterator
-GlSequence::sequence_begin(GLfloat left, GLfloat right) const
-{
- // the following code will be wrong when sequences can be slid around
- // so make sure we break.
- assert (seq_x == 0);
-
- if ( leftbase(left) > seq.size() or left > right )
- return seq.end();
- else
- return seq.begin() + leftbase(left);
-}
-
-Sequence::const_iterator
-GlSequence::sequence_end(GLfloat left, GLfloat right) const
-{
- // the following code will be wrong when sequences can be slid around
- // so make sure we break.
- assert (seq_x == 0);
-
- if ( rightbase(right) > seq.size() or left > right )
- return seq.end();
- else
- return seq.begin() + rightbase(right);
-}
-
-
-//! set default track draw color
-void GlSequence::setColor(Color &c)
-{
- drawColor = c;
-}
-
-//! get default track draw color
-Color GlSequence::color()
-{
- return drawColor;
-}
-
-
-int GlSequence::get_viewport_pixel_width()
-{
- int viewport[4];
- glGetIntegerv(GL_VIEWPORT, viewport);
- return viewport[3]; // grab the viewport width
-}
-
-bool GlSequence::is_sequence_renderable(GLfloat left,
- GLfloat right,
- int viewport_width) const
-{
- // if called with default argument, go get the viewable width
- if (viewport_width == -1) {
- viewport_width = get_viewport_pixel_width();
- }
- GLfloat world_width = right - left;
- GLfloat pixels_needed = (char_pix_per_world_unit * world_width);
-
- // if the number of pixels taken up by rendering the characters
- // that'd show up in the current ortho width is less than the window
- // width we can actually draw something
- return pixels_needed < viewport_width;
-}
-
-
-void GlSequence::draw(GLfloat left, GLfloat right) const
-{
- if ( not is_sequence_renderable(left, right) ) {
- draw_track(left, right);
- } else {
- draw_sequence(left, right);
- }
- draw_annotations(left, right);
-}
-
-void GlSequence::draw_box(GLfloat left, GLfloat right,
- GLfloat height, GLfloat z) const
-{
- GLfloat offset = height/2.0;
- GLfloat top = seq_y + offset;
- GLfloat bottom = seq_y - offset;
-
- glBegin(GL_QUADS);
- glVertex3f(left, top, z);
- glVertex3f(left, bottom, z);
- glVertex3f(right, bottom, z);
- glVertex3f(right, top, z);
- glEnd();
-}
-void GlSequence::draw_track(GLfloat left, GLfloat right) const
-{
- glColor3fv(drawColor.get());
- // draw main sequence track
- draw_box(seq_x, seq_x+seq.size(), seq_height, 0.0);
-}
-
-void GlSequence::draw_annotations(GLfloat left, GLfloat right) const
-{
- // draw annotations
- glLineWidth(seq_height);
- GLfloat annotation_z = seq_z + 1.0;
- std::list<annot> annots = seq.annotations();
- for (std::list<annot>::const_iterator annot_itor = annots.begin();
- annot_itor != annots.end();
- ++annot_itor, ++annotation_z)
- {
- glColor3f(0.0, 0.5, 0.0);
- draw_box(seq_x+annot_itor->start, seq_x+annot_itor->end,
- seq_height, annotation_z);
- }
-}
-
-const int PT = 1;
-const int STROKE = 2;
-const int END =3;
-
-typedef struct charpoint {
- GLfloat x, y;
- int type;
-} CP;
-
-CP Adata[] = {
- {0, -5, PT}, {2.5, 5, PT}, {5, -5, STROKE},
- {0.75, -2, PT}, {4.25, -2, END}
-};
-
-CP Tdata[] = {
- {2.5, -5, PT}, {2.5,5, STROKE}, {0, 5, PT}, {5, 5, END}
-};
-
-CP Gdata[] = {
- {5, 3, PT}, {3, 5, PT}, {2, 5, PT}, {0, 3, PT}, {0, -3, PT},
- {2, -5, PT}, {3, -5, PT}, {5, -3, STROKE},
- {2.5, -1, PT}, {5, -1,PT}, {5, -5, END}
-};
-
-CP Cdata[] = {
- {4.9, 3, PT}, {3, 5, PT}, {2, 5, PT}, {0, 3, PT}, {0, -3, PT},
- {2, -5, PT}, {3, -5, PT}, {5, -3, END}
-};
-
-CP Xdata[] = {{ 0, 5, PT}, {5, -5,STROKE},{0,-5,PT},{5, 5, END}};
-CP Ndata[] = {{ 0, -5, PT}, {0, 5, PT}, {5, -5, PT}, {5, 5, END}};
-
-static void drawLetter(CP *l, GLfloat z)
-{
- glBegin(GL_LINE_STRIP);
- while(1) {
- switch (l->type) {
- case PT:
- glVertex3f(l->x, l->y, z);
- break;
- case STROKE:
- glVertex3f(l->x, l->y, z);
- glEnd();
- glBegin(GL_LINE_STRIP);
- break;
- case END:
- glVertex3f(l->x, l->y, z);
- glEnd();
- return;
- break;
- default:
- throw runtime_error("data structure failure");
- }
- l++;
- }
-}
-
-void GlSequence::draw_sequence(GLfloat left, GLfloat right) const
-{
- // FIXME: basically this needs to be greater than the number of annotations
- const GLfloat z = 30;
- glLineWidth(0.3);
- glColor3fv(drawColor.get());
-
- Sequence::const_iterator seq_itor = sequence_begin(left, right);
- Sequence::const_iterator seq_end = sequence_end(left, right);
- Sequence::size_type basepair = 0;
-
- assert(seq_end - seq_itor >= 0);
- while(seq_itor != seq_end)
- {
- assert ( basepair < seq.size() );
- glPushMatrix();
- glTranslatef( leftbase(left) + basepair, seq_y, 1.0 );
- glScalef(0.1, 1.0, 1.0);
- switch (*seq_itor) {
- case 'A': case 'a':
- drawLetter(Adata, z);
- break;
- case 'T': case 't':
- drawLetter(Tdata, z);
- break;
- case 'G': case 'g':
- drawLetter(Gdata, z);
- break;
- case 'C': case 'c':
- drawLetter(Cdata, z);
- break;
- case 'N': case 'n':
- drawLetter(Ndata, z);
- break;
- default:
- drawLetter(Xdata, z);
- break;
- }
- glPopMatrix();
- ++seq_itor;
- ++basepair;
- }
-}
-
-bool operator==(const GlSequence &left, const GlSequence &right)
-{
- return ( (left.seq_x == right.seq_x) and
- (left.seq_y == right.seq_y) and
- (left.seq_z == right.seq_z) and
- (left.seq_height == right.seq_height) and
- (left.drawColor == right.drawColor));
-}
-
+++ /dev/null
-#ifndef _GL_SEQUENCE_H_
-#define _GL_SEQUENCE_H_
-
-#include "alg/sequence.hh"
-#include "alg/color.h"
-#include <GL/gl.h>
-//! Manage rendering a mussa sequence track
-/*! The idea is this will keep track of the location of where the sequence
- * is being rendered, and handle displaying annotations on that track
- */
-class GlSequence
-{
-public:
- GlSequence(const Sequence & s);
- GlSequence(const GlSequence & s);
- GlSequence &operator=(const GlSequence &s);
-
- //! draw a track
- /*! left and right are the edges of the current viewport
- */
- void draw(GLfloat left, GLfloat right) const;
-
- const Sequence& sequence() const;
- //! set our starting x (horizontal) coordinate
- void setX(GLfloat);
- //! get our starting x (horizontal) coordinate
- GLfloat x() const;
- //! set our current y (vertical) position
- void setY(GLfloat);
- //! get our current y (vertical) position
- GLfloat y() const;
- //! how long is our sequence track? (computed from the sequence)
- GLfloat length() const;
-
- //! return the left (lowest) base index that is fully visible
- Sequence::size_type GlSequence::leftbase(GLfloat left) const;
- //! return one past rightmost (highest ) base index that is fully visible
- /*! done mostly so all the iterator logic continues to work correctly.
- */
- Sequence::size_type GlSequence::rightbase(GLfloat right) const;
-
- //! return iterator to the start of the stored sequence
- Sequence::const_iterator sequence_begin() const;
- //! return iterator to the end of the stored sequence
- Sequence::const_iterator sequence_end() const;
- //! provide an iterator to the sequence starting at world coordinate left
- Sequence::const_iterator sequence_begin(GLfloat left, GLfloat right) const;
- //! provide an iterator to the sequence ending at world coordinate right
- Sequence::const_iterator sequence_end(GLfloat left, GLfloat right) const;
-
- //! set track color
- void setColor(Color &);
- Color color();
-
- //! are we close enough that it would make sense to view the base pairs?
- /*! though we don't actually check to see if there's sequence in our
- * view, just that there's enough pixels to render something if
- * there were.
- * \param[in] left the left edge of the viewable region in world coordinates
- * \param[in] right the right edge of the viewable region in world
- * coordinates
- * \param[in] pixel_width allow setting the current viewport pixel width
- */
- bool is_sequence_renderable(GLfloat left,
- GLfloat right,
- int pixel_width=-1) const;
-
- friend bool operator==(const GlSequence &left, const GlSequence &right);
-
-protected:
- const Sequence& seq;
- GLfloat seq_x;
- GLfloat seq_y;
- GLfloat seq_z;
- GLfloat seq_height;
- Color drawColor;
- const GLfloat char_pix_per_world_unit;
-
- //! Return the pixel width of the opengl viewport.
- static int get_viewport_pixel_width();
- //! draw a from left to right +/- height/2
- void draw_box(GLfloat left, GLfloat right, GLfloat height, GLfloat z) const;
- //! draw sequence as a bar
- void draw_track(GLfloat, GLfloat) const;
- void draw_annotations(GLfloat, GLfloat) const;
- //! render a sequence as ATGC
- /*! left and right are the current edges of the viewable world
- */
- void draw_sequence(GLfloat, GLfloat) const;
-};
-#endif
--- /dev/null
+#ifndef _GL_SEQUENCE_H_
+#define _GL_SEQUENCE_H_
+
+#include "alg/sequence.hpp"
+#include "alg/color.hpp"
+#include <GL/gl.h>
+//! Manage rendering a mussa sequence track
+/*! The idea is this will keep track of the location of where the sequence
+ * is being rendered, and handle displaying annotations on that track
+ */
+class GlSequence
+{
+public:
+ GlSequence(const Sequence & s);
+ GlSequence(const GlSequence & s);
+ GlSequence &operator=(const GlSequence &s);
+
+ //! draw a track
+ /*! left and right are the edges of the current viewport
+ */
+ void draw(GLfloat left, GLfloat right) const;
+
+ const Sequence& sequence() const;
+ //! set our starting x (horizontal) coordinate
+ void setX(GLfloat);
+ //! get our starting x (horizontal) coordinate
+ GLfloat x() const;
+ //! set our current y (vertical) position
+ void setY(GLfloat);
+ //! get our current y (vertical) position
+ GLfloat y() const;
+ //! how long is our sequence track? (computed from the sequence)
+ GLfloat length() const;
+
+ //! return the left (lowest) base index that is fully visible
+ Sequence::size_type GlSequence::leftbase(GLfloat left) const;
+ //! return one past rightmost (highest ) base index that is fully visible
+ /*! done mostly so all the iterator logic continues to work correctly.
+ */
+ Sequence::size_type GlSequence::rightbase(GLfloat right) const;
+
+ //! return iterator to the start of the stored sequence
+ Sequence::const_iterator sequence_begin() const;
+ //! return iterator to the end of the stored sequence
+ Sequence::const_iterator sequence_end() const;
+ //! provide an iterator to the sequence starting at world coordinate left
+ Sequence::const_iterator sequence_begin(GLfloat left, GLfloat right) const;
+ //! provide an iterator to the sequence ending at world coordinate right
+ Sequence::const_iterator sequence_end(GLfloat left, GLfloat right) const;
+
+ //! set track color
+ void setColor(Color &);
+ Color color();
+
+ //! are we close enough that it would make sense to view the base pairs?
+ /*! though we don't actually check to see if there's sequence in our
+ * view, just that there's enough pixels to render something if
+ * there were.
+ * \param[in] left the left edge of the viewable region in world coordinates
+ * \param[in] right the right edge of the viewable region in world
+ * coordinates
+ * \param[in] pixel_width allow setting the current viewport pixel width
+ */
+ bool is_sequence_renderable(GLfloat left,
+ GLfloat right,
+ int pixel_width=-1) const;
+
+ friend bool operator==(const GlSequence &left, const GlSequence &right);
+
+protected:
+ const Sequence& seq;
+ GLfloat seq_x;
+ GLfloat seq_y;
+ GLfloat seq_z;
+ GLfloat seq_height;
+ Color drawColor;
+ const GLfloat char_pix_per_world_unit;
+
+ //! Return the pixel width of the opengl viewport.
+ static int get_viewport_pixel_width();
+ //! draw a from left to right +/- height/2
+ void draw_box(GLfloat left, GLfloat right, GLfloat height, GLfloat z) const;
+ //! draw sequence as a bar
+ void draw_track(GLfloat, GLfloat) const;
+ void draw_annotations(GLfloat, GLfloat) const;
+ //! render a sequence as ATGC
+ /*! left and right are the current edges of the viewable world
+ */
+ void draw_sequence(GLfloat, GLfloat) const;
+};
+#endif
CURDIR := $(BASEDIR)alg/
-SOURCES.cxx := color.cxx \
- conserved_path.cxx \
- flp.cxx \
- flp_seqcomp.cxx \
- mussa_class.cxx \
- nway_paths.cxx \
- nway_entropy.cxx \
- nway_other.cxx \
- sequence.cxx
- # mussa_nway_refine.cxx (broken)
+SOURCES.cpp := color.cpp \
+ conserved_path.cpp \
+ flp.cpp \
+ flp_seqcomp.cpp \
+ mussa.cpp \
+ nway_paths.cpp \
+ nway_entropy.cpp \
+ nway_other.cpp \
+ sequence.cpp
+ # mussa_nway_refine.cpp (broken)
-MUSSA_ALG_SRC := $(addprefix $(CURDIR), $(SOURCES.cxx))
-MUSSA_ALG_OBJ := $(MUSSA_ALG_SRC:.cxx=$(OBJEXT))
+MUSSA_ALG_SRC := $(addprefix $(CURDIR), $(SOURCES.cpp))
+MUSSA_ALG_OBJ := $(MUSSA_ALG_SRC:.cpp=$(OBJEXT))
-GLSOURCES.cxx := glsequence.cxx
-MUSSA_ALG_GL_SRC := $(addprefix $(CURDIR), $(GLSOURCES.cxx))
-MUSSA_ALG_GL_OBJ := $(MUSSA_ALG_GL_SRC:.cxx=$(OBJEXT))
+GLSOURCES.cpp := glsequence.cpp
+MUSSA_ALG_GL_SRC := $(addprefix $(CURDIR), $(GLSOURCES.cpp))
+MUSSA_ALG_GL_OBJ := $(MUSSA_ALG_GL_SRC:.cpp=$(OBJEXT))
SRC += $(MUSSA_ALG_SRC) $(MUSSA_ALG_GL_SRC)
CXXFLAGS +=
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+// ----------------------------------------
+// ---------- mussa_class.cc -----------
+// ----------------------------------------
+
+#include <fstream>
+#include <iostream>
+#include <sstream>
+
+#include "mussa_exceptions.hpp"
+#include "alg/mussa.hpp"
+#include "alg/flp.hpp"
+
+using namespace std;
+
+Mussa::Mussa()
+{
+ clear();
+}
+
+// set all parameters to null state
+void
+Mussa::clear()
+{
+ analysis_name = "";
+ ana_mode = TransitiveNway;
+ window = 0;
+ threshold = 0;
+ soft_thres = 0;
+ win_append = false;
+ thres_append = false;
+ seq_files.clear();
+ fasta_indices.clear();
+ annot_files.clear();
+ sub_seq_starts.clear();
+ sub_seq_ends.clear();
+}
+
+// these 5 simple methods manually set the parameters for doing an analysis
+// used so that the gui can take input from user and setup the analysis
+// note - still need a set_append(bool, bool) method...
+void
+Mussa::set_name(string a_name)
+{
+ analysis_name = a_name;
+}
+
+string Mussa::get_name()
+{
+ return analysis_name;
+}
+
+int
+Mussa::size() const
+{
+ if (the_seqs.size() > 0)
+ return the_seqs.size();
+ else if (seq_files.size() > 0)
+ return seq_files.size();
+ else
+ return 0;
+}
+
+void
+Mussa::set_window(int a_window)
+{
+ window = a_window;
+}
+
+int Mussa::get_window() const
+{
+ return window;
+}
+
+void
+Mussa::set_threshold(int a_threshold)
+{
+ threshold = a_threshold;
+ //soft_thres = a_threshold;
+}
+
+int Mussa::get_threshold() const
+{
+ return threshold;
+}
+
+void
+Mussa::set_soft_thres(int sft_thres)
+{
+ soft_thres = sft_thres;
+}
+
+void
+Mussa::set_analysis_mode(enum analysis_modes new_ana_mode)
+{
+ ana_mode = new_ana_mode;
+}
+
+enum Mussa::analysis_modes Mussa::get_analysis_mode() const
+{
+ return ana_mode;
+}
+
+string Mussa::get_analysis_mode_name() const
+{
+ switch (ana_mode)
+ {
+ case TransitiveNway:
+ return string("Transitive");
+ break;
+ case RadialNway:
+ return string("Radial");
+ break;
+ case EntropyNway:
+ return string("Entropy");
+ break;
+ case RecursiveNway:
+ return string("[deprecated] Recursive");
+ break;
+ default:
+ throw runtime_error("invalid analysis mode type");
+ break;
+ }
+}
+
+const NwayPaths& Mussa::paths() const
+{
+ return the_paths;
+}
+
+// takes a string and sets it as the next seq
+void
+Mussa::add_a_seq(string a_seq)
+{
+ Sequence aSeq;
+
+ aSeq.set_seq(a_seq);
+ the_seqs.push_back(aSeq);
+}
+
+
+// sets info for just 1 seq at a time
+void
+Mussa::set_seq_info(string seq_file, string annot_file, int fa_i, int a_start, int the_end)
+{
+ seq_files.push_back(seq_file);
+ fasta_indices.push_back(fa_i);
+ annot_files.push_back(annot_file);
+ sub_seq_starts.push_back(a_start);
+ sub_seq_ends.push_back(the_end);
+}
+
+const vector<Sequence>&
+Mussa::sequences() const
+{
+ return the_seqs;
+}
+
+void
+Mussa::load_mupa_file(string para_file_path)
+{
+ ifstream para_file;
+ string file_data_line;
+ string param, value, annot_file;
+ int split_index, fasta_index;
+ int sub_seq_start, sub_seq_end;
+ bool seq_params, did_seq;
+ string err_msg;
+ bool parsing_path;
+ string::size_type new_index, dir_index;
+
+ // initialize values
+ clear();
+
+ para_file.open(para_file_path.c_str(), ios::in);
+
+ // if file was opened, read the parameter values
+ if (para_file)
+ {
+ // need to find the path to the .mupa file
+ parsing_path = true;
+ dir_index = 0;
+ while (parsing_path)
+ {
+ new_index = (para_file_path.substr(dir_index)).find("/");
+ if (new_index != string::npos)
+ dir_index += new_index + 1;
+ else
+ parsing_path = false;
+ }
+
+ file_path_base = para_file_path.substr(0,dir_index);
+
+ // setup loop by getting file's first line
+ getline(para_file,file_data_line);
+ split_index = file_data_line.find(" ");
+ param = file_data_line.substr(0,split_index);
+ value = file_data_line.substr(split_index+1);
+
+ while (!para_file.eof())
+ {
+ did_seq = false;
+ if (param == "ANA_NAME")
+ analysis_name = value;
+ else if (param == "APPEND_WIN")
+ win_append = true;
+ else if (param == "APPEND_THRES")
+ thres_append = true;
+ else if (param == "SEQUENCE_NUM")
+ ; // ignore sequence_num now
+ else if (param == "WINDOW")
+ window = atoi(value.c_str());
+ else if (param == "THRESHOLD")
+ threshold = atoi(value.c_str());
+ else if (param == "SEQUENCE")
+ {
+ seq_files.push_back(file_path_base + value);
+ //cout << "seq_file_name " << seq_files.back() << endl;
+ fasta_index = 1;
+ annot_file = "";
+ sub_seq_start = 0;
+ sub_seq_end = 0;
+ seq_params = true;
+
+ while ((!para_file.eof()) && seq_params)
+ {
+ getline(para_file,file_data_line);
+ split_index = file_data_line.find(" ");
+ param = file_data_line.substr(0,split_index);
+ value = file_data_line.substr(split_index+1);
+
+ if (param == "FASTA_INDEX")
+ fasta_index = atoi(value.c_str());
+ else if (param == "ANNOTATION")
+ annot_file = file_path_base + value;
+ else if (param == "SEQ_START")
+ sub_seq_start = atoi(value.c_str());
+ else if (param == "SEQ_END")
+ {
+ sub_seq_end = atoi(value.c_str());
+ }
+ //ignore empty lines or that start with '#'
+ else if ((param == "") || (param == "#")) {}
+ else seq_params = false;
+ }
+
+ fasta_indices.push_back(fasta_index);
+ annot_files.push_back(annot_file);
+ sub_seq_starts.push_back(sub_seq_start);
+ sub_seq_ends.push_back(sub_seq_end);
+ did_seq = true;
+ }
+ //ignore empty lines or that start with '#'
+ else if ((param == "") || (param == "#")) {}
+ else
+ {
+ clog << "Illegal/misplaced mussa parameter in file\n";
+ clog << param << "\n";
+ }
+
+ if (!did_seq)
+ {
+ getline(para_file,file_data_line);
+ split_index = file_data_line.find(" ");
+ param = file_data_line.substr(0,split_index);
+ value = file_data_line.substr(split_index+1);
+ did_seq = false;
+ }
+ }
+
+ para_file.close();
+
+ soft_thres = threshold;
+ //cout << "nway mupa: analysis_name = " << analysis_name
+ // << " window = " << window
+ // << " threshold = " << threshold << endl;
+ }
+ // no file was loaded, signal error
+ else
+ {
+ throw mussa_load_error("Config File: " + para_file_path + " not found");
+ }
+}
+
+
+void
+Mussa::analyze(int w, int t, enum Mussa::analysis_modes the_ana_mode, double new_ent_thres)
+{
+ time_t t1, t2, begin, end;
+ double seqloadtime, seqcomptime, nwaytime, savetime, totaltime;
+
+ begin = time(NULL);
+
+ ana_mode = the_ana_mode;
+ ent_thres = new_ent_thres;
+ if (w > 0)
+ window = w;
+ if (t > 0)
+ {
+ threshold = t;
+ soft_thres = t;
+ }
+
+ t1 = time(NULL);
+ load_sequence_data();
+
+ if (the_seqs.size() < 2) {
+ throw mussa_analysis_error("you need to have at least 2 sequences to "
+ "do an analysis.");
+ }
+ //cout << "nway ana: seq_num = " << the_seqs.size() << endl;
+
+ t2 = time(NULL);
+ seqloadtime = difftime(t2, t1);
+
+ t1 = time(NULL);
+ seqcomp();
+ t2 = time(NULL);
+ seqcomptime = difftime(t2, t1);
+
+
+ t1 = time(NULL);
+ the_paths.setup(window, threshold);
+ nway();
+ t2 = time(NULL);
+ nwaytime = difftime(t2, t1);
+
+ t1 = time(NULL);
+ save();
+ t2 = time(NULL);
+ savetime = difftime(t2, t1);
+
+ end = time(NULL);
+ totaltime = difftime(end, begin);
+
+
+ //cout << "seqload\tseqcomp\tnway\tsave\ttotal\n";
+ //cout << seqloadtime << "\t";
+ //cout << seqcomptime << "\t";
+ //cout << nwaytime << "\t";
+ //cout << savetime << "\t";
+ //cout << totaltime << "\n";
+}
+
+
+void
+Mussa::load_sequence_data()
+{
+ list<string>::iterator seq_files_i, annot_files_i;
+ list<int>::iterator fasta_indices_i, seq_starts_i, seq_ends_i;
+ Sequence aSeq;
+ string err_msg;
+
+
+ seq_files_i = seq_files.begin();
+ fasta_indices_i = fasta_indices.begin();
+ annot_files_i = annot_files.begin();
+ seq_starts_i = sub_seq_starts.begin();
+ seq_ends_i = sub_seq_ends.begin();
+
+ while ( (seq_files_i != seq_files.end()) && (err_msg == "") )
+ /* it should be guarenteed that each of the following exist
+ should I bother checking, and how to deal with if not true...
+ &&
+ (fasta_indices_i != fasta_indices.end()) &&
+ (annot_files_i != annot_files.end()) &&
+ (seq_starts_i != sub_seq_starts.end()) &&
+ (seq_ends_i != sub_seq_ends.end()) )
+ */
+ {
+ aSeq.load_fasta(*seq_files_i, *fasta_indices_i,*seq_starts_i, *seq_ends_i);
+ if (annot_files_i->size() > 0)
+ aSeq.load_annot(*annot_files_i, *seq_starts_i, *seq_ends_i);
+
+ the_seqs.push_back(aSeq);
+ //cout << aSeq.get_header() << endl;
+ //cout << aSeq.get_seq() << endl;
+ aSeq.clear();
+ ++seq_files_i; // advance all the iterators
+ ++fasta_indices_i;
+ ++annot_files_i;
+ ++seq_starts_i;
+ ++seq_ends_i;
+ }
+}
+
+
+void
+Mussa::seqcomp()
+{
+ vector<int> seq_lens;
+ vector<FLPs> empty_FLP_vector;
+ FLPs dummy_comp;
+ string save_file_string;
+
+ empty_FLP_vector.clear();
+ for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
+ {
+ all_comps.push_back(empty_FLP_vector);
+ for(vector<Sequence>::size_type i2 = 0; i2 < the_seqs.size(); i2++)
+ all_comps[i].push_back(dummy_comp);
+ }
+ for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
+ seq_lens.push_back(the_seqs[i].size());
+
+ for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
+ for(vector<Sequence>::size_type i2 = i+1; i2 < the_seqs.size(); i2++)
+ {
+ //cout << "seqcomping: " << i << " v. " << i2 << endl;
+ all_comps[i][i2].setup(window, threshold);
+ all_comps[i][i2].seqcomp(the_seqs[i].get_seq(), the_seqs[i2].get_seq(), false);
+ all_comps[i][i2].seqcomp(the_seqs[i].get_seq(),the_seqs[i2].rev_comp(),true);
+ }
+}
+
+void
+Mussa::nway()
+{
+ vector<string> some_Seqs;
+
+ the_paths.set_soft_thres(soft_thres);
+
+ if (ana_mode == TransitiveNway) {
+ the_paths.trans_path_search(all_comps);
+ }
+ else if (ana_mode == RadialNway) {
+ the_paths.radiate_path_search(all_comps);
+ }
+ else if (ana_mode == EntropyNway)
+ {
+ //unlike other methods, entropy needs to look at the sequence at this stage
+ some_Seqs.clear();
+ for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
+ {
+ some_Seqs.push_back(the_seqs[i].get_seq());
+ }
+
+ the_paths.setup_ent(ent_thres, some_Seqs); // ent analysis extra setup
+ the_paths.entropy_path_search(all_comps);
+ }
+
+ // old recursive transitive analysis function
+ else if (ana_mode == RecursiveNway)
+ the_paths.find_paths_r(all_comps);
+
+ the_paths.simple_refine();
+}
+
+void
+Mussa::save()
+{
+ string save_name, save_path, create_dir_cmd, flp_filepath;
+ fstream save_file;
+ ostringstream append_info;
+ int dir_create_status;
+
+
+ // not sure why, but gotta close file each time since can't pass file streams
+
+ save_name = analysis_name;
+
+ // gotta do bit with adding win & thres if to be appended
+ if (win_append)
+ {
+ append_info.str("");
+ append_info << "_w" << window;
+ save_name += append_info.str();
+ }
+
+ if (thres_append)
+ {
+ append_info.str("");
+ append_info << "_t" << threshold;
+ save_name += append_info.str();
+ }
+
+//#include <stdlib.h>
+ // ******* use appropriate for os ------- 1 of 4
+ // the additions for osX make it more sane where it saves the analysis
+ // will come up with a cleaner sol'n later...
+ create_dir_cmd = "mkdir " + save_name; //linux
+ //create_dir_cmd = "mkdir " + file_path_base + save_name; //osX
+
+ dir_create_status = system( (const char*) create_dir_cmd.c_str());
+ //cout << "action: " << dir_create_status << endl;
+
+ // save sequence and annots to a special mussa file
+
+ // ******** use appropriate for OS ---------- 2 of 4
+ save_path = save_name + "/" + save_name + ".museq"; //linux
+ //save_path = file_path_base + save_name + "/" + save_name + ".museq"; //osX
+
+ save_file.open(save_path.c_str(), ios::out);
+ save_file << "<Mussa_Sequence>" << endl;
+ //save_file.close();
+
+ for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
+ {
+ the_seqs[i].save(save_file);
+ }
+
+ //save_file.open(save_path.c_str(), ios::app);
+ save_file << "</Mussa_Sequence>" << endl;
+ save_file.close();
+
+ // save nway paths to its mussa save file
+
+ // ******** use appropriate for OS -------- 3 of 4
+ save_path = save_name + "/" + save_name + ".muway"; //linux
+ //save_path = file_path_base + save_name + "/" + save_name + ".muway"; //os X
+ the_paths.save(save_path);
+
+ for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
+ for(vector<Sequence>::size_type i2 = i+1; i2 < the_seqs.size(); i2++)
+ {
+ append_info.str("");
+ append_info << "_sp_" << i << "v" << i2;
+ // ******** use appropriate for OS --------- 4 of 4
+ //linux
+ save_path = save_name + "/" + save_name + append_info.str() + ".flp";
+ //osX
+ //save_path = file_path_base + save_name + "/" + save_name + append_info.str() + ".flp";
+ all_comps[i][i2].save(save_path);
+ }
+}
+
+void
+Mussa::save_muway(string save_path)
+{
+ the_paths.save(save_path);
+}
+
+void
+Mussa::load(string ana_file)
+{
+ int i, i2;
+ string::size_type start_index, end_index;
+ string file_path_base, a_file_path, ana_path;
+ bool parsing_path;
+ Sequence tmp_seq;
+ string err_msg;
+ ostringstream append_info;
+ vector<FLPs> empty_FLP_vector;
+ FLPs dummy_comp;
+
+ //cout << "ana_file name " << ana_file << endl;
+ ana_path = ana_file;
+ parsing_path = true;
+ end_index = ana_path.size()-1;
+ if (ana_path[end_index] == '/') {
+ --end_index;
+ }
+ start_index = ana_path.rfind('/', end_index);
+ if (start_index == string::npos) {
+ // no / to be found
+ start_index = 0;
+ } else {
+ // skip the / we found
+ ++start_index;
+ }
+ analysis_name = ana_path.substr(start_index, end_index-start_index+1);
+ //cout << " ana_name " << analysis_name << endl;
+ file_path_base = ana_path.substr(0, start_index) + analysis_name
+ + "/" + analysis_name;
+ a_file_path = file_path_base + ".muway";
+ //cout << " loading museq: " << a_file_path << endl;
+ the_paths.load(a_file_path);
+
+ int seq_num = the_paths.sequence_count();
+
+ a_file_path = file_path_base + ".museq";
+
+ // this is a bit of a hack due to C++ not acting like it should with files
+ for (i = 1; i <= seq_num; i++)
+ {
+ tmp_seq.clear();
+ //cout << "mussa_class: loading museq frag... " << a_file_path << endl;
+ tmp_seq.load_museq(a_file_path, i);
+ the_seqs.push_back(tmp_seq);
+ }
+
+ empty_FLP_vector.clear();
+ for(i = 0; i < seq_num; i++)
+ {
+ all_comps.push_back(empty_FLP_vector);
+ for(i2 = 0; i2 < seq_num; i2++)
+ all_comps[i].push_back(dummy_comp);
+ }
+
+ for(i = 0; i < seq_num; i++)
+ {
+ for(i2 = i+1; i2 < seq_num; i2++)
+ {
+ append_info.str("");
+ append_info << "_sp_" << i << "v" << i2;
+ //cout << append_info.str() << endl;
+ a_file_path = file_path_base + append_info.str() + ".flp";
+ all_comps[i][i2].load(a_file_path);
+ //cout << "real size = " << all_comps[i][i2].size() << endl;
+ }
+ }
+}
+
+
+void
+Mussa::save_old()
+{
+ fstream save_file;
+
+ save_file.open(analysis_name.c_str(), ios::out);
+
+ for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
+ save_file << the_seqs[i].get_seq() << endl;
+
+ save_file << window << endl;
+ save_file.close();
+ //note more complex eventually since analysis_name may need to have
+ //window size, threshold and other stuff to modify it...
+ the_paths.save_old(analysis_name);
+}
+
+
+void
+Mussa::load_old(char * load_file_path, int s_num)
+{
+ fstream save_file;
+ string file_data_line;
+ int i, space_split_i, comma_split_i;
+ vector<int> loaded_path;
+ string node_pair, node;
+ Sequence a_seq;
+
+ int seq_num = s_num;
+ the_paths.setup(0, 0);
+ save_file.open(load_file_path, ios::in);
+
+ // currently loads old mussa format
+
+ // get sequences
+ for(i = 0; i < seq_num; i++)
+ {
+ getline(save_file, file_data_line);
+ a_seq.set_seq(file_data_line);
+ the_seqs.push_back(a_seq);
+ }
+
+ // get window size
+ getline(save_file, file_data_line);
+ window = atoi(file_data_line.c_str());
+ // get paths
+
+ while (!save_file.eof())
+ {
+ loaded_path.clear();
+ getline(save_file, file_data_line);
+ if (file_data_line != "")
+ for(i = 0; i < seq_num; i++)
+ {
+ space_split_i = file_data_line.find(" ");
+ node_pair = file_data_line.substr(0,space_split_i);
+ //cout << "np= " << node_pair;
+ comma_split_i = node_pair.find(",");
+ node = node_pair.substr(comma_split_i+1);
+ //cout << "n= " << node << " ";
+ loaded_path.push_back(atoi (node.c_str()));
+ file_data_line = file_data_line.substr(space_split_i+1);
+ }
+ //cout << endl;
+ // FIXME: do we have any information about what the threshold should be?
+ the_paths.add_path(0, loaded_path);
+ }
+ save_file.close();
+
+ //the_paths.save("tmp.save");
+}
--- /dev/null
+#ifndef _MUSSA_CLASS_H_
+#define _MUSSA_CLASS_H_
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+// ----------------------------------------
+// ---------- mussa_class.hh -----------
+// ----------------------------------------
+
+#include <list>
+#include <string>
+#include <vector>
+
+#include "alg/nway_paths.hpp"
+#include "alg/sequence.hpp"
+
+std::string int_to_str(int an_int);
+
+class Mussa
+{
+ friend class ConnWindow;
+ public:
+ enum analysis_modes { TransitiveNway, RadialNway, EntropyNway,
+ RecursiveNway };
+
+ Mussa();
+
+ void save();
+ void save_muway(std::string save_path);
+ //! load a saved analysis directory
+ void load(std::string ana_path);
+
+ //! clear parameters and initialize data lists
+ void clear();
+
+ // set parameters from a file - 'mupa' ~ mussa parameters
+ void load_mupa_file(std::string para_file_path);
+
+ // set parameters individually (eg from user input into gui classes)
+ //! set analysis name
+ void set_name(std::string a_name);
+ //! return name for this analysis
+ std::string get_name();
+
+ //! return number of sequences in this analyzis
+ /*! this returns either the_seqs.size() or seq_files.size()
+ * depending on which has data loaded in
+ * (silly delayed loading of sequence data)
+ */
+ int size() const;
+ //! set number of bases for this window size
+ void set_window(int a_window);
+ //! get number of bases for the sliding window
+ int get_window() const;
+ //! set number of bases that must match for a window to be saved
+ void set_threshold(int a_threshold);
+ //! get number of bases that must match for a window to be saved
+ int get_threshold() const;
+ void set_soft_thres(int sft_thres);
+
+ void set_analysis_mode(enum analysis_modes new_ana_mode);
+ enum analysis_modes get_analysis_mode() const;
+ //! return a string name for an analysis mode
+ std::string get_analysis_mode_name() const;
+
+ //! return the refined paths found by the nway analysis.
+ const NwayPaths& paths() const;
+
+ //! run seqcomp and the nway filtering algorithm.
+ /*!analyze will run seqcomp and then the nway algorithm
+ * on whatever sequences have been loaded into this mussa instance.
+ * w & t are for command line override functionality, set to 0 to ignore
+ * \throws mussa_analysis_error
+ */
+ void analyze(int w=0, int t=0,
+ enum analysis_modes ana_mode=TransitiveNway,
+ double ent_thres=0.0);
+ /*! Run the nway filtering algorithm,
+ * this might be used when changing the soft threshhold?
+ */
+ void nway();
+
+ //! appends a string sequence to the list of the_seqs
+ void add_a_seq(std::string a_seq);
+ // sets info to load a seq and annotations from a fasta file
+ void set_seq_info(std::string seq_file, std::string annot_file,
+ int fa_i, int a_start, int the_end);
+ //! allow examining the sequences we have loaded
+ const std::vector<Sequence>& sequences() const;
+
+ // deprecated - support bridge for python version of mussa
+ // these save & load from the old file format
+ void save_old();
+ void load_old(char * load_file_path, int s_num);
+
+ private:
+ // Private variables
+ // parameters needed for a mussa analysis
+ std::string analysis_name;
+ std::string file_path_base;
+ int window, threshold, soft_thres;
+ enum analysis_modes ana_mode;
+ double ent_thres;
+ std::list<std::string> seq_files, annot_files;
+ std::list<int> fasta_indices, sub_seq_starts, sub_seq_ends;
+ bool win_override, thres_override;
+ bool win_append, thres_append;
+
+ //! sequence data
+ std::vector<Sequence> the_seqs;
+ //! the seqcomp data
+ std::vector<std::vector<FLPs> > all_comps;
+ //! N-way data, ie the mussa results
+ NwayPaths the_paths;
+
+ // Private methods
+ //! loads sequence and annotations from fasta and annotation file
+ void load_sequence_data();
+ void seqcomp();
+
+};
+#endif
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-// ----------------------------------------
-// ---------- mussa_class.cc -----------
-// ----------------------------------------
-
-#include "mussa_exceptions.hh"
-#include "mussa_class.hh"
-#include "flp.hh"
-#include <fstream>
-#include <iostream>
-#include <sstream>
-
-using namespace std;
-
-Mussa::Mussa()
-{
- clear();
-}
-
-// set all parameters to null state
-void
-Mussa::clear()
-{
- analysis_name = "";
- ana_mode = TransitiveNway;
- window = 0;
- threshold = 0;
- soft_thres = 0;
- win_append = false;
- thres_append = false;
- seq_files.clear();
- fasta_indices.clear();
- annot_files.clear();
- sub_seq_starts.clear();
- sub_seq_ends.clear();
-}
-
-// these 5 simple methods manually set the parameters for doing an analysis
-// used so that the gui can take input from user and setup the analysis
-// note - still need a set_append(bool, bool) method...
-void
-Mussa::set_name(string a_name)
-{
- analysis_name = a_name;
-}
-
-string Mussa::get_name()
-{
- return analysis_name;
-}
-
-int
-Mussa::size() const
-{
- if (the_seqs.size() > 0)
- return the_seqs.size();
- else if (seq_files.size() > 0)
- return seq_files.size();
- else
- return 0;
-}
-
-void
-Mussa::set_window(int a_window)
-{
- window = a_window;
-}
-
-int Mussa::get_window() const
-{
- return window;
-}
-
-void
-Mussa::set_threshold(int a_threshold)
-{
- threshold = a_threshold;
- //soft_thres = a_threshold;
-}
-
-int Mussa::get_threshold() const
-{
- return threshold;
-}
-
-void
-Mussa::set_soft_thres(int sft_thres)
-{
- soft_thres = sft_thres;
-}
-
-void
-Mussa::set_analysis_mode(enum analysis_modes new_ana_mode)
-{
- ana_mode = new_ana_mode;
-}
-
-enum Mussa::analysis_modes Mussa::get_analysis_mode() const
-{
- return ana_mode;
-}
-
-string Mussa::get_analysis_mode_name() const
-{
- switch (ana_mode)
- {
- case TransitiveNway:
- return string("Transitive");
- break;
- case RadialNway:
- return string("Radial");
- break;
- case EntropyNway:
- return string("Entropy");
- break;
- case RecursiveNway:
- return string("[deprecated] Recursive");
- break;
- default:
- throw runtime_error("invalid analysis mode type");
- break;
- }
-}
-
-const NwayPaths& Mussa::paths() const
-{
- return the_paths;
-}
-
-// takes a string and sets it as the next seq
-void
-Mussa::add_a_seq(string a_seq)
-{
- Sequence aSeq;
-
- aSeq.set_seq(a_seq);
- the_seqs.push_back(aSeq);
-}
-
-
-// sets info for just 1 seq at a time
-void
-Mussa::set_seq_info(string seq_file, string annot_file, int fa_i, int a_start, int the_end)
-{
- seq_files.push_back(seq_file);
- fasta_indices.push_back(fa_i);
- annot_files.push_back(annot_file);
- sub_seq_starts.push_back(a_start);
- sub_seq_ends.push_back(the_end);
-}
-
-const vector<Sequence>&
-Mussa::sequences() const
-{
- return the_seqs;
-}
-
-void
-Mussa::load_mupa_file(string para_file_path)
-{
- ifstream para_file;
- string file_data_line;
- string param, value, annot_file;
- int split_index, fasta_index;
- int sub_seq_start, sub_seq_end;
- bool seq_params, did_seq;
- string err_msg;
- bool parsing_path;
- string::size_type new_index, dir_index;
-
- // initialize values
- clear();
-
- para_file.open(para_file_path.c_str(), ios::in);
-
- // if file was opened, read the parameter values
- if (para_file)
- {
- // need to find the path to the .mupa file
- parsing_path = true;
- dir_index = 0;
- while (parsing_path)
- {
- new_index = (para_file_path.substr(dir_index)).find("/");
- if (new_index != string::npos)
- dir_index += new_index + 1;
- else
- parsing_path = false;
- }
-
- file_path_base = para_file_path.substr(0,dir_index);
-
- // setup loop by getting file's first line
- getline(para_file,file_data_line);
- split_index = file_data_line.find(" ");
- param = file_data_line.substr(0,split_index);
- value = file_data_line.substr(split_index+1);
-
- while (!para_file.eof())
- {
- did_seq = false;
- if (param == "ANA_NAME")
- analysis_name = value;
- else if (param == "APPEND_WIN")
- win_append = true;
- else if (param == "APPEND_THRES")
- thres_append = true;
- else if (param == "SEQUENCE_NUM")
- ; // ignore sequence_num now
- else if (param == "WINDOW")
- window = atoi(value.c_str());
- else if (param == "THRESHOLD")
- threshold = atoi(value.c_str());
- else if (param == "SEQUENCE")
- {
- seq_files.push_back(file_path_base + value);
- //cout << "seq_file_name " << seq_files.back() << endl;
- fasta_index = 1;
- annot_file = "";
- sub_seq_start = 0;
- sub_seq_end = 0;
- seq_params = true;
-
- while ((!para_file.eof()) && seq_params)
- {
- getline(para_file,file_data_line);
- split_index = file_data_line.find(" ");
- param = file_data_line.substr(0,split_index);
- value = file_data_line.substr(split_index+1);
-
- if (param == "FASTA_INDEX")
- fasta_index = atoi(value.c_str());
- else if (param == "ANNOTATION")
- annot_file = file_path_base + value;
- else if (param == "SEQ_START")
- sub_seq_start = atoi(value.c_str());
- else if (param == "SEQ_END")
- {
- sub_seq_end = atoi(value.c_str());
- }
- //ignore empty lines or that start with '#'
- else if ((param == "") || (param == "#")) {}
- else seq_params = false;
- }
-
- fasta_indices.push_back(fasta_index);
- annot_files.push_back(annot_file);
- sub_seq_starts.push_back(sub_seq_start);
- sub_seq_ends.push_back(sub_seq_end);
- did_seq = true;
- }
- //ignore empty lines or that start with '#'
- else if ((param == "") || (param == "#")) {}
- else
- {
- clog << "Illegal/misplaced mussa parameter in file\n";
- clog << param << "\n";
- }
-
- if (!did_seq)
- {
- getline(para_file,file_data_line);
- split_index = file_data_line.find(" ");
- param = file_data_line.substr(0,split_index);
- value = file_data_line.substr(split_index+1);
- did_seq = false;
- }
- }
-
- para_file.close();
-
- soft_thres = threshold;
- //cout << "nway mupa: analysis_name = " << analysis_name
- // << " window = " << window
- // << " threshold = " << threshold << endl;
- }
- // no file was loaded, signal error
- else
- {
- throw mussa_load_error("Config File: " + para_file_path + " not found");
- }
-}
-
-
-void
-Mussa::analyze(int w, int t, enum Mussa::analysis_modes the_ana_mode, double new_ent_thres)
-{
- time_t t1, t2, begin, end;
- double seqloadtime, seqcomptime, nwaytime, savetime, totaltime;
-
- begin = time(NULL);
-
- ana_mode = the_ana_mode;
- ent_thres = new_ent_thres;
- if (w > 0)
- window = w;
- if (t > 0)
- {
- threshold = t;
- soft_thres = t;
- }
-
- t1 = time(NULL);
- load_sequence_data();
-
- if (the_seqs.size() < 2) {
- throw mussa_analysis_error("you need to have at least 2 sequences to "
- "do an analysis.");
- }
- //cout << "nway ana: seq_num = " << the_seqs.size() << endl;
-
- t2 = time(NULL);
- seqloadtime = difftime(t2, t1);
-
- t1 = time(NULL);
- seqcomp();
- t2 = time(NULL);
- seqcomptime = difftime(t2, t1);
-
-
- t1 = time(NULL);
- the_paths.setup(window, threshold);
- nway();
- t2 = time(NULL);
- nwaytime = difftime(t2, t1);
-
- t1 = time(NULL);
- save();
- t2 = time(NULL);
- savetime = difftime(t2, t1);
-
- end = time(NULL);
- totaltime = difftime(end, begin);
-
-
- //cout << "seqload\tseqcomp\tnway\tsave\ttotal\n";
- //cout << seqloadtime << "\t";
- //cout << seqcomptime << "\t";
- //cout << nwaytime << "\t";
- //cout << savetime << "\t";
- //cout << totaltime << "\n";
-}
-
-
-void
-Mussa::load_sequence_data()
-{
- list<string>::iterator seq_files_i, annot_files_i;
- list<int>::iterator fasta_indices_i, seq_starts_i, seq_ends_i;
- Sequence aSeq;
- string err_msg;
-
-
- seq_files_i = seq_files.begin();
- fasta_indices_i = fasta_indices.begin();
- annot_files_i = annot_files.begin();
- seq_starts_i = sub_seq_starts.begin();
- seq_ends_i = sub_seq_ends.begin();
-
- while ( (seq_files_i != seq_files.end()) && (err_msg == "") )
- /* it should be guarenteed that each of the following exist
- should I bother checking, and how to deal with if not true...
- &&
- (fasta_indices_i != fasta_indices.end()) &&
- (annot_files_i != annot_files.end()) &&
- (seq_starts_i != sub_seq_starts.end()) &&
- (seq_ends_i != sub_seq_ends.end()) )
- */
- {
- aSeq.load_fasta(*seq_files_i, *fasta_indices_i,*seq_starts_i, *seq_ends_i);
- if (annot_files_i->size() > 0)
- aSeq.load_annot(*annot_files_i, *seq_starts_i, *seq_ends_i);
-
- the_seqs.push_back(aSeq);
- //cout << aSeq.get_header() << endl;
- //cout << aSeq.get_seq() << endl;
- aSeq.clear();
- ++seq_files_i; // advance all the iterators
- ++fasta_indices_i;
- ++annot_files_i;
- ++seq_starts_i;
- ++seq_ends_i;
- }
-}
-
-
-void
-Mussa::seqcomp()
-{
- vector<int> seq_lens;
- vector<FLPs> empty_FLP_vector;
- FLPs dummy_comp;
- string save_file_string;
-
- empty_FLP_vector.clear();
- for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
- {
- all_comps.push_back(empty_FLP_vector);
- for(vector<Sequence>::size_type i2 = 0; i2 < the_seqs.size(); i2++)
- all_comps[i].push_back(dummy_comp);
- }
- for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
- seq_lens.push_back(the_seqs[i].size());
-
- for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
- for(vector<Sequence>::size_type i2 = i+1; i2 < the_seqs.size(); i2++)
- {
- //cout << "seqcomping: " << i << " v. " << i2 << endl;
- all_comps[i][i2].setup(window, threshold);
- all_comps[i][i2].seqcomp(the_seqs[i].get_seq(), the_seqs[i2].get_seq(), false);
- all_comps[i][i2].seqcomp(the_seqs[i].get_seq(),the_seqs[i2].rev_comp(),true);
- }
-}
-
-void
-Mussa::nway()
-{
- vector<string> some_Seqs;
-
- the_paths.set_soft_thres(soft_thres);
-
- if (ana_mode == TransitiveNway) {
- the_paths.trans_path_search(all_comps);
- }
- else if (ana_mode == RadialNway) {
- the_paths.radiate_path_search(all_comps);
- }
- else if (ana_mode == EntropyNway)
- {
- //unlike other methods, entropy needs to look at the sequence at this stage
- some_Seqs.clear();
- for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
- {
- some_Seqs.push_back(the_seqs[i].get_seq());
- }
-
- the_paths.setup_ent(ent_thres, some_Seqs); // ent analysis extra setup
- the_paths.entropy_path_search(all_comps);
- }
-
- // old recursive transitive analysis function
- else if (ana_mode == RecursiveNway)
- the_paths.find_paths_r(all_comps);
-
- the_paths.simple_refine();
-}
-
-void
-Mussa::save()
-{
- string save_name, save_path, create_dir_cmd, flp_filepath;
- fstream save_file;
- ostringstream append_info;
- int dir_create_status;
-
-
- // not sure why, but gotta close file each time since can't pass file streams
-
- save_name = analysis_name;
-
- // gotta do bit with adding win & thres if to be appended
- if (win_append)
- {
- append_info.str("");
- append_info << "_w" << window;
- save_name += append_info.str();
- }
-
- if (thres_append)
- {
- append_info.str("");
- append_info << "_t" << threshold;
- save_name += append_info.str();
- }
-
-//#include <stdlib.h>
- // ******* use appropriate for os ------- 1 of 4
- // the additions for osX make it more sane where it saves the analysis
- // will come up with a cleaner sol'n later...
- create_dir_cmd = "mkdir " + save_name; //linux
- //create_dir_cmd = "mkdir " + file_path_base + save_name; //osX
-
- dir_create_status = system( (const char*) create_dir_cmd.c_str());
- //cout << "action: " << dir_create_status << endl;
-
- // save sequence and annots to a special mussa file
-
- // ******** use appropriate for OS ---------- 2 of 4
- save_path = save_name + "/" + save_name + ".museq"; //linux
- //save_path = file_path_base + save_name + "/" + save_name + ".museq"; //osX
-
- save_file.open(save_path.c_str(), ios::out);
- save_file << "<Mussa_Sequence>" << endl;
- //save_file.close();
-
- for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
- {
- the_seqs[i].save(save_file);
- }
-
- //save_file.open(save_path.c_str(), ios::app);
- save_file << "</Mussa_Sequence>" << endl;
- save_file.close();
-
- // save nway paths to its mussa save file
-
- // ******** use appropriate for OS -------- 3 of 4
- save_path = save_name + "/" + save_name + ".muway"; //linux
- //save_path = file_path_base + save_name + "/" + save_name + ".muway"; //os X
- the_paths.save(save_path);
-
- for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
- for(vector<Sequence>::size_type i2 = i+1; i2 < the_seqs.size(); i2++)
- {
- append_info.str("");
- append_info << "_sp_" << i << "v" << i2;
- // ******** use appropriate for OS --------- 4 of 4
- //linux
- save_path = save_name + "/" + save_name + append_info.str() + ".flp";
- //osX
- //save_path = file_path_base + save_name + "/" + save_name + append_info.str() + ".flp";
- all_comps[i][i2].save(save_path);
- }
-}
-
-void
-Mussa::save_muway(string save_path)
-{
- the_paths.save(save_path);
-}
-
-void
-Mussa::load(string ana_file)
-{
- int i, i2;
- string::size_type start_index, end_index;
- string file_path_base, a_file_path, ana_path;
- bool parsing_path;
- Sequence tmp_seq;
- string err_msg;
- ostringstream append_info;
- vector<FLPs> empty_FLP_vector;
- FLPs dummy_comp;
-
- //cout << "ana_file name " << ana_file << endl;
- ana_path = ana_file;
- parsing_path = true;
- end_index = ana_path.size()-1;
- if (ana_path[end_index] == '/') {
- --end_index;
- }
- start_index = ana_path.rfind('/', end_index);
- if (start_index == string::npos) {
- // no / to be found
- start_index = 0;
- } else {
- // skip the / we found
- ++start_index;
- }
- analysis_name = ana_path.substr(start_index, end_index-start_index+1);
- //cout << " ana_name " << analysis_name << endl;
- file_path_base = ana_path.substr(0, start_index) + analysis_name
- + "/" + analysis_name;
- a_file_path = file_path_base + ".muway";
- //cout << " loading museq: " << a_file_path << endl;
- the_paths.load(a_file_path);
-
- int seq_num = the_paths.sequence_count();
-
- a_file_path = file_path_base + ".museq";
-
- // this is a bit of a hack due to C++ not acting like it should with files
- for (i = 1; i <= seq_num; i++)
- {
- tmp_seq.clear();
- //cout << "mussa_class: loading museq frag... " << a_file_path << endl;
- tmp_seq.load_museq(a_file_path, i);
- the_seqs.push_back(tmp_seq);
- }
-
- empty_FLP_vector.clear();
- for(i = 0; i < seq_num; i++)
- {
- all_comps.push_back(empty_FLP_vector);
- for(i2 = 0; i2 < seq_num; i2++)
- all_comps[i].push_back(dummy_comp);
- }
-
- for(i = 0; i < seq_num; i++)
- {
- for(i2 = i+1; i2 < seq_num; i2++)
- {
- append_info.str("");
- append_info << "_sp_" << i << "v" << i2;
- //cout << append_info.str() << endl;
- a_file_path = file_path_base + append_info.str() + ".flp";
- all_comps[i][i2].load(a_file_path);
- //cout << "real size = " << all_comps[i][i2].size() << endl;
- }
- }
-}
-
-
-void
-Mussa::save_old()
-{
- fstream save_file;
-
- save_file.open(analysis_name.c_str(), ios::out);
-
- for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
- save_file << the_seqs[i].get_seq() << endl;
-
- save_file << window << endl;
- save_file.close();
- //note more complex eventually since analysis_name may need to have
- //window size, threshold and other stuff to modify it...
- the_paths.save_old(analysis_name);
-}
-
-
-void
-Mussa::load_old(char * load_file_path, int s_num)
-{
- fstream save_file;
- string file_data_line;
- int i, space_split_i, comma_split_i;
- vector<int> loaded_path;
- string node_pair, node;
- Sequence a_seq;
-
- int seq_num = s_num;
- the_paths.setup(0, 0);
- save_file.open(load_file_path, ios::in);
-
- // currently loads old mussa format
-
- // get sequences
- for(i = 0; i < seq_num; i++)
- {
- getline(save_file, file_data_line);
- a_seq.set_seq(file_data_line);
- the_seqs.push_back(a_seq);
- }
-
- // get window size
- getline(save_file, file_data_line);
- window = atoi(file_data_line.c_str());
- // get paths
-
- while (!save_file.eof())
- {
- loaded_path.clear();
- getline(save_file, file_data_line);
- if (file_data_line != "")
- for(i = 0; i < seq_num; i++)
- {
- space_split_i = file_data_line.find(" ");
- node_pair = file_data_line.substr(0,space_split_i);
- //cout << "np= " << node_pair;
- comma_split_i = node_pair.find(",");
- node = node_pair.substr(comma_split_i+1);
- //cout << "n= " << node << " ";
- loaded_path.push_back(atoi (node.c_str()));
- file_data_line = file_data_line.substr(space_split_i+1);
- }
- //cout << endl;
- // FIXME: do we have any information about what the threshold should be?
- the_paths.add_path(0, loaded_path);
- }
- save_file.close();
-
- //the_paths.save("tmp.save");
-}
+++ /dev/null
-#ifndef _MUSSA_CLASS_H_
-#define _MUSSA_CLASS_H_
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-// ----------------------------------------
-// ---------- mussa_class.hh -----------
-// ----------------------------------------
-
-#include <list>
-#include <string>
-#include <vector>
-
-#include "nway_paths.hh"
-#include "sequence.hh"
-
-std::string int_to_str(int an_int);
-
-class Mussa
-{
- friend class ConnWindow;
- public:
- enum analysis_modes { TransitiveNway, RadialNway, EntropyNway,
- RecursiveNway };
-
- Mussa();
-
- void save();
- void save_muway(std::string save_path);
- //! load a saved analysis directory
- void load(std::string ana_path);
-
- //! clear parameters and initialize data lists
- void clear();
-
- // set parameters from a file - 'mupa' ~ mussa parameters
- void load_mupa_file(std::string para_file_path);
-
- // set parameters individually (eg from user input into gui classes)
- //! set analysis name
- void set_name(std::string a_name);
- //! return name for this analysis
- std::string get_name();
-
- //! return number of sequences in this analyzis
- /*! this returns either the_seqs.size() or seq_files.size()
- * depending on which has data loaded in
- * (silly delayed loading of sequence data)
- */
- int size() const;
- //! set number of bases for this window size
- void set_window(int a_window);
- //! get number of bases for the sliding window
- int get_window() const;
- //! set number of bases that must match for a window to be saved
- void set_threshold(int a_threshold);
- //! get number of bases that must match for a window to be saved
- int get_threshold() const;
- void set_soft_thres(int sft_thres);
-
- void set_analysis_mode(enum analysis_modes new_ana_mode);
- enum analysis_modes get_analysis_mode() const;
- //! return a string name for an analysis mode
- std::string get_analysis_mode_name() const;
-
- //! return the refined paths found by the nway analysis.
- const NwayPaths& paths() const;
-
- //! run seqcomp and the nway filtering algorithm.
- /*!analyze will run seqcomp and then the nway algorithm
- * on whatever sequences have been loaded into this mussa instance.
- * w & t are for command line override functionality, set to 0 to ignore
- * \throws mussa_analysis_error
- */
- void analyze(int w=0, int t=0,
- enum analysis_modes ana_mode=TransitiveNway,
- double ent_thres=0.0);
- /*! Run the nway filtering algorithm,
- * this might be used when changing the soft threshhold?
- */
- void nway();
-
- //! appends a string sequence to the list of the_seqs
- void add_a_seq(std::string a_seq);
- // sets info to load a seq and annotations from a fasta file
- void set_seq_info(std::string seq_file, std::string annot_file,
- int fa_i, int a_start, int the_end);
- //! allow examining the sequences we have loaded
- const std::vector<Sequence>& sequences() const;
-
- // deprecated - support bridge for python version of mussa
- // these save & load from the old file format
- void save_old();
- void load_old(char * load_file_path, int s_num);
-
- private:
- // Private variables
- // parameters needed for a mussa analysis
- std::string analysis_name;
- std::string file_path_base;
- int window, threshold, soft_thres;
- enum analysis_modes ana_mode;
- double ent_thres;
- std::list<std::string> seq_files, annot_files;
- std::list<int> fasta_indices, sub_seq_starts, sub_seq_ends;
- bool win_override, thres_override;
- bool win_append, thres_append;
-
- //! sequence data
- std::vector<Sequence> the_seqs;
- //! the seqcomp data
- std::vector<std::vector<FLPs> > all_comps;
- //! N-way data, ie the mussa results
- NwayPaths the_paths;
-
- // Private methods
- //! loads sequence and annotations from fasta and annotation file
- void load_sequence_data();
- void seqcomp();
-
-};
-#endif
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+
+#include "alg/nway_paths.hpp"
+#include <math.h>
+#include <iostream>
+using namespace std;
+
+// vars that will be availble to entropy function when in its nway class
+//vector<char *> c_sequences;
+//int window = 5, seq_num;
+
+
+void
+NwayPaths::setup_ent(double new_entropy_thres, vector<string> some_seqs)
+{
+ ent_thres = new_entropy_thres;
+
+ c_sequences.clear();
+ for (vector<string>::size_type i = 0; i < some_seqs.size(); i++)
+ c_sequences.push_back((char *)some_seqs[i].c_str());
+}
+
+
+double
+NwayPaths::path_entropy(vector<int> path)
+{
+ int bp_occurences[5];
+ double bp_prob, frac_ent, avg_entropy;
+ vector<double> entropies;
+ int i, i2;
+ int window = win_size;
+
+ for(i = 0; i < window; i++) // loop thru all bp positions
+ {
+ for(i2 = 0; i2 < 5; i2++) // clear old occurences
+ bp_occurences[i2] = 0;
+
+ //loop thru all sequences at pos i
+ for(vector<int>::size_type seq_i = 0; seq_i != path.size(); seq_i++)
+ {
+ if (path[seq_i] > -1)
+ {
+ switch (c_sequences[seq_i][i+path[seq_i]])
+ {
+ case 'A':
+ ++bp_occurences[0];
+ break;
+ case 'T':
+ ++bp_occurences[1];
+ break;
+ case 'G':
+ ++bp_occurences[2];
+ break;
+ case 'C':
+ ++bp_occurences[3];
+ break;
+ case 'N':
+ ++bp_occurences[4];
+ break;
+ default:
+ cout << "error, nonAGCTN on seq: " << seq_i << " at index: ";
+ cout << i+path[seq_i] << endl;
+ }
+ }
+ else
+ {
+ switch (c_sequences[seq_i][-1 * (i + path[seq_i] - window + 1) ])
+ {
+ case 'A':
+ ++bp_occurences[1];
+ break;
+ case 'T':
+ ++bp_occurences[0];
+ break;
+ case 'G':
+ ++bp_occurences[3];
+ break;
+ case 'C':
+ ++bp_occurences[2];
+ break;
+ case 'N':
+ ++bp_occurences[4];
+ break;
+ default:
+ cout << "error, nonAGCTN on seq: " << seq_i << " at index: ";
+ cout << (i + path[seq_i] - window + 1) << endl;
+ }
+ }
+ }
+
+ entropies.push_back(0.000);
+ for(i2 = 0; i2 < 5; i2++) //calculate entropies
+ {
+ bp_prob = (double) bp_occurences[i2] / (double) path.size();
+ //cout << bp_prob << "::";
+ if (bp_prob == 0.0000)
+ frac_ent = 0.0000;
+ else
+ frac_ent = bp_prob * ( log10(bp_prob) / log10(2.0) );
+ //cout << frac_ent << " ";
+ entropies[i] += frac_ent;
+ }
+ //cout << endl;
+ }
+
+ avg_entropy = 0;
+ for(i = 0; i < window; i++)
+ {
+ avg_entropy += entropies[i];
+ //cout << entropies[i] << endl;
+ }
+
+ avg_entropy = -1.00 * (avg_entropy / (double) window);
+ //cout << "average entropy: " << avg_entropy << endl;
+ return avg_entropy;
+}
+
+void
+NwayPaths::entropy_path_search(vector<vector<FLPs> > all_comparisons)
+{
+ vector<int> path;
+ double avg_entropy;
+ int win_i, sp_depth, window_num;
+ unsigned int sp_i;
+ bool some_matches, still_paths, not_advanced;
+ list<int> new_nodes, trans_check_nodes;
+ vector<list<int> > all_matches;
+ vector<list<int>::iterator> sp_nodes, sp_nodes_end;
+ list<int>::iterator debug_i;
+
+
+ pathz.clear();
+ window_num = all_comparisons[0][1].size();
+ cout << window_num << endl; // just a sanity check
+
+ sp_nodes.reserve(all_comparisons.size());
+ sp_nodes_end.reserve(all_comparisons.size());
+
+ // loop thru all windows in first species
+ for (win_i = 0; win_i < window_num; win_i++)
+ {
+ // first we see if the first seq has matches to all other seqs at this win
+ some_matches = true;
+ sp_i = 1;
+ all_matches.clear();
+ while ( (sp_i < all_comparisons.size()) && (some_matches) )
+ {
+ new_nodes.clear();
+ new_nodes = all_comparisons[0][sp_i].match_locations(win_i);
+ if (new_nodes.empty())
+ some_matches = false;
+
+ all_matches.push_back(new_nodes);
+ sp_i++;
+ }
+ //cout << "fee\n";
+
+ // if 1st seq does match to all others, make all possible paths
+ // out of all these matches
+ if (some_matches)
+ {
+ sp_nodes.clear();
+ sp_nodes_end.clear();
+ // set each species list of matches to beginning
+ for (sp_i = 0; sp_i < all_comparisons.size()-1; sp_i++)
+ {
+ sp_nodes.push_back(all_matches[sp_i].begin());
+ sp_nodes_end.push_back(all_matches[sp_i].end());
+ }
+
+ still_paths = true;
+ //cout << "fie\n";
+ while (still_paths)
+ {
+ // add path that each species iterator is pointing to
+ path.clear();
+ path.push_back(win_i);
+
+ //cout << win_i;
+ for (sp_i = 0; sp_i < all_comparisons.size()-1; sp_i++)
+ {
+ //cout << ", " << *(sp_nodes[sp_i]);
+ path.push_back(*(sp_nodes[sp_i]));
+ }
+ //cout << endl;
+
+ // check entropy <---------------------------------------------------
+ avg_entropy = path_entropy(path);
+ if (avg_entropy <= ent_thres)
+ pathz.push_back(ConservedPath(avg_entropy, path));
+
+ // now advance the right iterator
+ not_advanced = true;
+ sp_depth = all_comparisons.size()- 2; // this roves up & down species list
+ while ( (not_advanced) && (sp_depth != -1) )
+ {
+ //cout << "foe\n";
+ //cout << sp_depth << ".." << *(sp_nodes[sp_depth]) << endl;
+ (sp_nodes[sp_depth])++; // advance iter at current depth
+ //cout << sp_depth << ".." << *(sp_nodes[sp_depth]) << endl;
+
+ // if we reached the end of the list, reset iter & go up one depth
+ if (sp_nodes[sp_depth] == sp_nodes_end[sp_depth])
+ {
+ //cout << "fum\n";
+ sp_nodes[sp_depth] = all_matches[sp_depth].begin();
+ sp_depth--;
+ //cout << "depth = " << sp_depth << endl;
+ }
+ else
+ not_advanced = false;
+ }
+
+ if (sp_depth == -1) // jumped up to first species, all paths searched
+ still_paths = false;
+ else // otherwise just reset to max depth and continue
+ sp_depth = all_comparisons.size() - 2;
+ }
+ }
+ }
+}
+
+
+//initial coding testing
+/*
+int main(int argc, char **argv)
+{
+ vector<string> sequences;
+ vector<int> i_starts;
+ double avg_entropy;
+ int seq_i;
+
+ sequences.clear();
+ sequences.push_back("AAAAA");
+ sequences.push_back("AAAAT");
+ sequences.push_back("AATTG");
+ sequences.push_back("ATTGC");
+
+ seq_num = 4;
+
+ c_sequences.clear();
+ i_starts.clear();
+ for(seq_i = 0; seq_i < seq_num; seq_i++) //loop thru all sequences at pos i
+ {
+ c_sequences.push_back((char *)sequences[seq_i].c_str());
+ i_starts.push_back(0);
+ }
+
+ avg_entropy = Window_Entropy(i_starts);
+
+ cout << "average entropy: " << avg_entropy << endl;
+}
+*/
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-
-#include "nway_paths.hh"
-#include <math.h>
-#include <iostream>
-using namespace std;
-
-// vars that will be availble to entropy function when in its nway class
-//vector<char *> c_sequences;
-//int window = 5, seq_num;
-
-
-void
-NwayPaths::setup_ent(double new_entropy_thres, vector<string> some_seqs)
-{
- ent_thres = new_entropy_thres;
-
- c_sequences.clear();
- for (vector<string>::size_type i = 0; i < some_seqs.size(); i++)
- c_sequences.push_back((char *)some_seqs[i].c_str());
-}
-
-
-double
-NwayPaths::path_entropy(vector<int> path)
-{
- int bp_occurences[5];
- double bp_prob, frac_ent, avg_entropy;
- vector<double> entropies;
- int i, i2;
- int window = win_size;
-
- for(i = 0; i < window; i++) // loop thru all bp positions
- {
- for(i2 = 0; i2 < 5; i2++) // clear old occurences
- bp_occurences[i2] = 0;
-
- //loop thru all sequences at pos i
- for(vector<int>::size_type seq_i = 0; seq_i != path.size(); seq_i++)
- {
- if (path[seq_i] > -1)
- {
- switch (c_sequences[seq_i][i+path[seq_i]])
- {
- case 'A':
- ++bp_occurences[0];
- break;
- case 'T':
- ++bp_occurences[1];
- break;
- case 'G':
- ++bp_occurences[2];
- break;
- case 'C':
- ++bp_occurences[3];
- break;
- case 'N':
- ++bp_occurences[4];
- break;
- default:
- cout << "error, nonAGCTN on seq: " << seq_i << " at index: ";
- cout << i+path[seq_i] << endl;
- }
- }
- else
- {
- switch (c_sequences[seq_i][-1 * (i + path[seq_i] - window + 1) ])
- {
- case 'A':
- ++bp_occurences[1];
- break;
- case 'T':
- ++bp_occurences[0];
- break;
- case 'G':
- ++bp_occurences[3];
- break;
- case 'C':
- ++bp_occurences[2];
- break;
- case 'N':
- ++bp_occurences[4];
- break;
- default:
- cout << "error, nonAGCTN on seq: " << seq_i << " at index: ";
- cout << (i + path[seq_i] - window + 1) << endl;
- }
- }
- }
-
- entropies.push_back(0.000);
- for(i2 = 0; i2 < 5; i2++) //calculate entropies
- {
- bp_prob = (double) bp_occurences[i2] / (double) path.size();
- //cout << bp_prob << "::";
- if (bp_prob == 0.0000)
- frac_ent = 0.0000;
- else
- frac_ent = bp_prob * ( log10(bp_prob) / log10(2.0) );
- //cout << frac_ent << " ";
- entropies[i] += frac_ent;
- }
- //cout << endl;
- }
-
- avg_entropy = 0;
- for(i = 0; i < window; i++)
- {
- avg_entropy += entropies[i];
- //cout << entropies[i] << endl;
- }
-
- avg_entropy = -1.00 * (avg_entropy / (double) window);
- //cout << "average entropy: " << avg_entropy << endl;
- return avg_entropy;
-}
-
-void
-NwayPaths::entropy_path_search(vector<vector<FLPs> > all_comparisons)
-{
- vector<int> path;
- double avg_entropy;
- int win_i, sp_depth, window_num;
- unsigned int sp_i;
- bool some_matches, still_paths, not_advanced;
- list<int> new_nodes, trans_check_nodes;
- vector<list<int> > all_matches;
- vector<list<int>::iterator> sp_nodes, sp_nodes_end;
- list<int>::iterator debug_i;
-
-
- pathz.clear();
- window_num = all_comparisons[0][1].size();
- cout << window_num << endl; // just a sanity check
-
- sp_nodes.reserve(all_comparisons.size());
- sp_nodes_end.reserve(all_comparisons.size());
-
- // loop thru all windows in first species
- for (win_i = 0; win_i < window_num; win_i++)
- {
- // first we see if the first seq has matches to all other seqs at this win
- some_matches = true;
- sp_i = 1;
- all_matches.clear();
- while ( (sp_i < all_comparisons.size()) && (some_matches) )
- {
- new_nodes.clear();
- new_nodes = all_comparisons[0][sp_i].match_locations(win_i);
- if (new_nodes.empty())
- some_matches = false;
-
- all_matches.push_back(new_nodes);
- sp_i++;
- }
- //cout << "fee\n";
-
- // if 1st seq does match to all others, make all possible paths
- // out of all these matches
- if (some_matches)
- {
- sp_nodes.clear();
- sp_nodes_end.clear();
- // set each species list of matches to beginning
- for (sp_i = 0; sp_i < all_comparisons.size()-1; sp_i++)
- {
- sp_nodes.push_back(all_matches[sp_i].begin());
- sp_nodes_end.push_back(all_matches[sp_i].end());
- }
-
- still_paths = true;
- //cout << "fie\n";
- while (still_paths)
- {
- // add path that each species iterator is pointing to
- path.clear();
- path.push_back(win_i);
-
- //cout << win_i;
- for (sp_i = 0; sp_i < all_comparisons.size()-1; sp_i++)
- {
- //cout << ", " << *(sp_nodes[sp_i]);
- path.push_back(*(sp_nodes[sp_i]));
- }
- //cout << endl;
-
- // check entropy <---------------------------------------------------
- avg_entropy = path_entropy(path);
- if (avg_entropy <= ent_thres)
- pathz.push_back(ConservedPath(avg_entropy, path));
-
- // now advance the right iterator
- not_advanced = true;
- sp_depth = all_comparisons.size()- 2; // this roves up & down species list
- while ( (not_advanced) && (sp_depth != -1) )
- {
- //cout << "foe\n";
- //cout << sp_depth << ".." << *(sp_nodes[sp_depth]) << endl;
- (sp_nodes[sp_depth])++; // advance iter at current depth
- //cout << sp_depth << ".." << *(sp_nodes[sp_depth]) << endl;
-
- // if we reached the end of the list, reset iter & go up one depth
- if (sp_nodes[sp_depth] == sp_nodes_end[sp_depth])
- {
- //cout << "fum\n";
- sp_nodes[sp_depth] = all_matches[sp_depth].begin();
- sp_depth--;
- //cout << "depth = " << sp_depth << endl;
- }
- else
- not_advanced = false;
- }
-
- if (sp_depth == -1) // jumped up to first species, all paths searched
- still_paths = false;
- else // otherwise just reset to max depth and continue
- sp_depth = all_comparisons.size() - 2;
- }
- }
- }
-}
-
-
-//initial coding testing
-/*
-int main(int argc, char **argv)
-{
- vector<string> sequences;
- vector<int> i_starts;
- double avg_entropy;
- int seq_i;
-
- sequences.clear();
- sequences.push_back("AAAAA");
- sequences.push_back("AAAAT");
- sequences.push_back("AATTG");
- sequences.push_back("ATTGC");
-
- seq_num = 4;
-
- c_sequences.clear();
- i_starts.clear();
- for(seq_i = 0; seq_i < seq_num; seq_i++) //loop thru all sequences at pos i
- {
- c_sequences.push_back((char *)sequences[seq_i].c_str());
- i_starts.push_back(0);
- }
-
- avg_entropy = Window_Entropy(i_starts);
-
- cout << "average entropy: " << avg_entropy << endl;
-}
-*/
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+#include "nway_paths.hpp"
+#include <iostream>
+
+using namespace std;
+
+//! dump the matches for a particular window
+void dump_matches_win(int win_i, vector<list<int> > all_matches)
+{
+ cout << "<win_debug win=" << win_i << ">" << endl;
+ for (vector<list<int> >::const_iterator sp_i = all_matches.begin();
+ sp_i != all_matches.end();
+ ++sp_i)
+ {
+ for(list<int>::const_iterator debug_i = sp_i->begin();
+ debug_i != sp_i->end();
+ ++debug_i)
+ {
+ cout << *debug_i << " ";
+ }
+ cout << endl;
+ }
+ cout << "</win_debug>"<< endl;
+}
+
+/*! (re-)initialize all_matches with the list of matches between
+ * species (sequence) 0 and all the other sequences
+ * \return true if there were matches against all the species, false otherwise
+ */
+bool
+make_all_seq_win_matches(const vector<vector<FLPs> >& all_comparisons,
+ vector<list<int> >& all_matches,
+ int window_index, int soft_threshold)
+{
+ list<int> new_nodes;
+ bool some_matches=true;
+ all_matches.clear();
+ for(vector<FLPs>::size_type sp_i=1;
+ (sp_i < all_comparisons.size()) && (some_matches); sp_i++ )
+ {
+ new_nodes.clear();
+ // --thres
+ //new_nodes = all_comparisons[0][sp_i].matches(win_i);
+ new_nodes = all_comparisons[0][sp_i].thres_matches(window_index,
+ soft_threshold);
+ if (new_nodes.empty())
+ some_matches = false;
+ else
+ all_matches.push_back(new_nodes);
+ }
+ // we only record matches from seq 0 to another seq, so we should have seq-1
+ // matches if there were enough matches.
+ // if there weren't enough we should have even fewer matches
+ // (this complicated boolean hides all the logic in one assert call,
+ // hopefully allowing the assert to be optimized away)
+ assert(( some_matches && (all_matches.size() == (all_comparisons.size()-1)))
+ ||(!some_matches && (all_matches.size() < (all_comparisons.size()-1))));
+ return some_matches;
+}
+
+/*! reset all the speces begin and end iterators to the start and end
+ * of the match pairs stored in all_matches
+ */
+void reset_species_iterators(vector<list<int> >& all_matches,
+ vector<list<int>::iterator>& sp_itor_begin,
+ vector<list<int>::iterator>& sp_itor_end)
+{
+ sp_itor_begin.clear();
+ sp_itor_end.clear();
+ // set each species list of matches to beginning
+ for (list<int>::size_type sp_i = 0; sp_i < all_matches.size(); sp_i++)
+ {
+ sp_itor_begin.push_back(all_matches[sp_i].begin());
+ sp_itor_end.push_back(all_matches[sp_i].end());
+ }
+}
+
+/*! Set the path vector to be the list of window positions from
+ * the current locations of our species beginning iterators
+ */
+void set_path_to_cur_sp_itor_track(
+ vector<int>& path,
+ int base_window_index,
+ const vector<list<int>::iterator>& sp_itor_begin)
+{
+ // add path that each species iterator is pointing to
+ path.clear();
+ path.push_back(base_window_index);
+
+ for (vector<int>::size_type sp_i = 0; sp_i < sp_itor_begin.size(); sp_i++)
+ {
+ path.push_back(*(sp_itor_begin[sp_i]));
+ }
+}
+
+/*! advance the species iterator track
+ * if we were able to advance the track return true
+ * if we weren't able to advance, we've looked at every track so return false
+ */
+bool advance_sp_itor_track(vector<list<int>::iterator>& sp_itor_begin,
+ const vector<list<int>::iterator>& sp_itor_end,
+ vector<list<int> >& all_matches)
+{
+ bool not_advanced = true;
+ int sp_depth = all_matches.size() - 1; // this roves up & down species list
+ while ( (not_advanced) && (sp_depth != -1) )
+ {
+ //cout << sp_depth << ".." << *(sp_itor_begin[sp_depth]) << endl;
+ (sp_itor_begin[sp_depth])++; // advance iter at current depth
+ //cout << sp_depth << ".." << *(sp_itor_begin[sp_depth]) << endl;
+
+ // if we reached the end of the list, reset iter & go up one depth
+ if (sp_itor_begin[sp_depth] == sp_itor_end[sp_depth])
+ {
+ sp_itor_begin[sp_depth] = all_matches[sp_depth].begin();
+ sp_depth--;
+ //cout << "depth = " << sp_depth << endl;
+ }
+ else
+ not_advanced = false;
+ }
+ if (sp_depth == -1) // jumped up to first species, all paths searched
+ return false;
+ else
+ return true;
+}
+
+void
+NwayPaths::radiate_path_search(vector<vector<FLPs> > all_comparisons)
+{
+ vector<int> path;
+ int win_i, window_num;
+ bool still_paths;
+ vector<list<int> > all_matches;
+ vector<list<int>::iterator> sp_itor_begin(all_comparisons.size());
+ vector<list<int>::iterator> sp_itor_end(all_comparisons.size());
+
+ pathz.clear();
+ window_num = all_comparisons[0][1].size();
+
+ // loop thru all windows in first species
+ for (win_i = 0; win_i < window_num; win_i++)
+ {
+ // if 1st seq does have match to all the others, then make all possible
+ // paths out of all these matches (in all_matches)
+ if(make_all_seq_win_matches(all_comparisons, all_matches, win_i, soft_thres))
+ {
+ //debug dump_matches_win(win_i, all_matches);
+ reset_species_iterators(all_matches, sp_itor_begin, sp_itor_end);
+
+ still_paths = true;
+ while (still_paths)
+ {
+ // add path that each species iterator is pointing to
+ set_path_to_cur_sp_itor_track(path, win_i, sp_itor_begin);
+
+ pathz.push_back(ConservedPath(soft_thres, path));
+
+ // now advance the right iterator
+ still_paths = advance_sp_itor_track(sp_itor_begin,
+ sp_itor_end,
+ all_matches);
+ }
+ }
+ }
+}
+
+bool is_transitive_path(const vector<int>& path,
+ const vector<vector<FLPs> >& all_comparisons,
+ const int soft_threshold)
+{
+ int cur_node;
+ list<int> trans_check_nodes;
+
+ for (vector<int>::size_type sp_depth=1; sp_depth != path.size()-1; ++sp_depth)
+ {
+ cur_node = path[sp_depth];
+ for(vector<int>::size_type i = sp_depth+1; i != path.size()-1; i++)
+ {
+ // --thres
+ //trans_check_nodes = all_comparisons[sp_depth][i].matches(cur_node);
+ trans_check_nodes =
+ all_comparisons[sp_depth][i].thres_matches(cur_node, soft_threshold);
+
+ if ( (trans_check_nodes.end() == find(trans_check_nodes.begin(),
+ trans_check_nodes.end(),
+ path[i]) )
+ &&(trans_check_nodes.end() == find(trans_check_nodes.begin(),
+ trans_check_nodes.end(),
+ path[i] * -1) ) )
+ return false;
+ }
+ }
+ return true;
+}
+
+void
+NwayPaths::trans_path_search(vector<vector<FLPs> > all_comparisons)
+{
+ if (all_comparisons.size() == 0 or all_comparisons[0].size() == 0)
+ return;
+ vector<int> path;
+ int win_i, window_num;
+ bool still_paths;
+ list<int> trans_check_nodes;
+ vector<list<int> > all_matches;
+ vector<list<int>::iterator> sp_itor_begin(all_comparisons.size());
+ vector<list<int>::iterator> sp_itor_end(all_comparisons.size());
+
+
+ //cout << "trans: softhres = " << soft_thres;
+ //cout << ", window = " << win_size << ", ";
+
+ pathz.clear();
+ window_num = all_comparisons[0][1].size();
+ //cout << "window number = " << window_num << endl; // just a sanity check
+ //cout << "trans: comparison size= " << all_comparisons.size() << endl;
+ // loop thru all windows in first species
+ for (win_i = 0; win_i != window_num; win_i++)
+ {
+ // if 1st seq has a match to all the others for this window,
+ // then make all possible paths out of all these matches (in all_matches)
+ if(make_all_seq_win_matches(all_comparisons, all_matches, win_i, soft_thres))
+ {
+ //debug? //dump_matches_win(win_i, all_matches);
+ reset_species_iterators(all_matches, sp_itor_begin, sp_itor_end);
+ still_paths = true;
+ while (still_paths)
+ {
+ // initialize a path to however far each species iterator has been
+ // advanced.
+ set_path_to_cur_sp_itor_track(path, win_i, sp_itor_begin);
+
+ // if the path is transitive, save the path
+ if (is_transitive_path(path, all_comparisons, soft_thres))
+ pathz.push_back(ConservedPath(soft_thres, path));
+
+ // now advance the right iterator
+ still_paths = advance_sp_itor_track(sp_itor_begin,
+ sp_itor_end,
+ all_matches);
+ }
+ }
+ }
+ //clog << "all_cmp=" << all_comparisons.size();
+ //if (pathz.begin() != pathz.end())
+ // clog << " path_size=" << pathz.begin()->size();
+ //else
+ // clog << " path empty";
+ //clog << endl;
+ assert ( (pathz.begin() == pathz.end())
+ || (pathz.begin()->size() == 0)
+ || (all_comparisons.size() == pathz.begin()->size()));
+}
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-#include "nway_paths.hh"
-#include <iostream>
-
-using namespace std;
-
-//! dump the matches for a particular window
-void dump_matches_win(int win_i, vector<list<int> > all_matches)
-{
- cout << "<win_debug win=" << win_i << ">" << endl;
- for (vector<list<int> >::const_iterator sp_i = all_matches.begin();
- sp_i != all_matches.end();
- ++sp_i)
- {
- for(list<int>::const_iterator debug_i = sp_i->begin();
- debug_i != sp_i->end();
- ++debug_i)
- {
- cout << *debug_i << " ";
- }
- cout << endl;
- }
- cout << "</win_debug>"<< endl;
-}
-
-/*! (re-)initialize all_matches with the list of matches between
- * species (sequence) 0 and all the other sequences
- * \return true if there were matches against all the species, false otherwise
- */
-bool
-make_all_seq_win_matches(const vector<vector<FLPs> >& all_comparisons,
- vector<list<int> >& all_matches,
- int window_index, int soft_threshold)
-{
- list<int> new_nodes;
- bool some_matches=true;
- all_matches.clear();
- for(vector<FLPs>::size_type sp_i=1;
- (sp_i < all_comparisons.size()) && (some_matches); sp_i++ )
- {
- new_nodes.clear();
- // --thres
- //new_nodes = all_comparisons[0][sp_i].matches(win_i);
- new_nodes = all_comparisons[0][sp_i].thres_matches(window_index,
- soft_threshold);
- if (new_nodes.empty())
- some_matches = false;
- else
- all_matches.push_back(new_nodes);
- }
- // we only record matches from seq 0 to another seq, so we should have seq-1
- // matches if there were enough matches.
- // if there weren't enough we should have even fewer matches
- // (this complicated boolean hides all the logic in one assert call,
- // hopefully allowing the assert to be optimized away)
- assert(( some_matches && (all_matches.size() == (all_comparisons.size()-1)))
- ||(!some_matches && (all_matches.size() < (all_comparisons.size()-1))));
- return some_matches;
-}
-
-/*! reset all the speces begin and end iterators to the start and end
- * of the match pairs stored in all_matches
- */
-void reset_species_iterators(vector<list<int> >& all_matches,
- vector<list<int>::iterator>& sp_itor_begin,
- vector<list<int>::iterator>& sp_itor_end)
-{
- sp_itor_begin.clear();
- sp_itor_end.clear();
- // set each species list of matches to beginning
- for (list<int>::size_type sp_i = 0; sp_i < all_matches.size(); sp_i++)
- {
- sp_itor_begin.push_back(all_matches[sp_i].begin());
- sp_itor_end.push_back(all_matches[sp_i].end());
- }
-}
-
-/*! Set the path vector to be the list of window positions from
- * the current locations of our species beginning iterators
- */
-void set_path_to_cur_sp_itor_track(
- vector<int>& path,
- int base_window_index,
- const vector<list<int>::iterator>& sp_itor_begin)
-{
- // add path that each species iterator is pointing to
- path.clear();
- path.push_back(base_window_index);
-
- for (vector<int>::size_type sp_i = 0; sp_i < sp_itor_begin.size(); sp_i++)
- {
- path.push_back(*(sp_itor_begin[sp_i]));
- }
-}
-
-/*! advance the species iterator track
- * if we were able to advance the track return true
- * if we weren't able to advance, we've looked at every track so return false
- */
-bool advance_sp_itor_track(vector<list<int>::iterator>& sp_itor_begin,
- const vector<list<int>::iterator>& sp_itor_end,
- vector<list<int> >& all_matches)
-{
- bool not_advanced = true;
- int sp_depth = all_matches.size() - 1; // this roves up & down species list
- while ( (not_advanced) && (sp_depth != -1) )
- {
- //cout << sp_depth << ".." << *(sp_itor_begin[sp_depth]) << endl;
- (sp_itor_begin[sp_depth])++; // advance iter at current depth
- //cout << sp_depth << ".." << *(sp_itor_begin[sp_depth]) << endl;
-
- // if we reached the end of the list, reset iter & go up one depth
- if (sp_itor_begin[sp_depth] == sp_itor_end[sp_depth])
- {
- sp_itor_begin[sp_depth] = all_matches[sp_depth].begin();
- sp_depth--;
- //cout << "depth = " << sp_depth << endl;
- }
- else
- not_advanced = false;
- }
- if (sp_depth == -1) // jumped up to first species, all paths searched
- return false;
- else
- return true;
-}
-
-void
-NwayPaths::radiate_path_search(vector<vector<FLPs> > all_comparisons)
-{
- vector<int> path;
- int win_i, window_num;
- bool still_paths;
- vector<list<int> > all_matches;
- vector<list<int>::iterator> sp_itor_begin(all_comparisons.size());
- vector<list<int>::iterator> sp_itor_end(all_comparisons.size());
-
- pathz.clear();
- window_num = all_comparisons[0][1].size();
-
- // loop thru all windows in first species
- for (win_i = 0; win_i < window_num; win_i++)
- {
- // if 1st seq does have match to all the others, then make all possible
- // paths out of all these matches (in all_matches)
- if(make_all_seq_win_matches(all_comparisons, all_matches, win_i, soft_thres))
- {
- //debug dump_matches_win(win_i, all_matches);
- reset_species_iterators(all_matches, sp_itor_begin, sp_itor_end);
-
- still_paths = true;
- while (still_paths)
- {
- // add path that each species iterator is pointing to
- set_path_to_cur_sp_itor_track(path, win_i, sp_itor_begin);
-
- pathz.push_back(ConservedPath(soft_thres, path));
-
- // now advance the right iterator
- still_paths = advance_sp_itor_track(sp_itor_begin,
- sp_itor_end,
- all_matches);
- }
- }
- }
-}
-
-bool is_transitive_path(const vector<int>& path,
- const vector<vector<FLPs> >& all_comparisons,
- const int soft_threshold)
-{
- int cur_node;
- list<int> trans_check_nodes;
-
- for (vector<int>::size_type sp_depth=1; sp_depth != path.size()-1; ++sp_depth)
- {
- cur_node = path[sp_depth];
- for(vector<int>::size_type i = sp_depth+1; i != path.size()-1; i++)
- {
- // --thres
- //trans_check_nodes = all_comparisons[sp_depth][i].matches(cur_node);
- trans_check_nodes =
- all_comparisons[sp_depth][i].thres_matches(cur_node, soft_threshold);
-
- if ( (trans_check_nodes.end() == find(trans_check_nodes.begin(),
- trans_check_nodes.end(),
- path[i]) )
- &&(trans_check_nodes.end() == find(trans_check_nodes.begin(),
- trans_check_nodes.end(),
- path[i] * -1) ) )
- return false;
- }
- }
- return true;
-}
-
-void
-NwayPaths::trans_path_search(vector<vector<FLPs> > all_comparisons)
-{
- if (all_comparisons.size() == 0 or all_comparisons[0].size() == 0)
- return;
- vector<int> path;
- int win_i, window_num;
- bool still_paths;
- list<int> trans_check_nodes;
- vector<list<int> > all_matches;
- vector<list<int>::iterator> sp_itor_begin(all_comparisons.size());
- vector<list<int>::iterator> sp_itor_end(all_comparisons.size());
-
-
- //cout << "trans: softhres = " << soft_thres;
- //cout << ", window = " << win_size << ", ";
-
- pathz.clear();
- window_num = all_comparisons[0][1].size();
- //cout << "window number = " << window_num << endl; // just a sanity check
- //cout << "trans: comparison size= " << all_comparisons.size() << endl;
- // loop thru all windows in first species
- for (win_i = 0; win_i != window_num; win_i++)
- {
- // if 1st seq has a match to all the others for this window,
- // then make all possible paths out of all these matches (in all_matches)
- if(make_all_seq_win_matches(all_comparisons, all_matches, win_i, soft_thres))
- {
- //debug? //dump_matches_win(win_i, all_matches);
- reset_species_iterators(all_matches, sp_itor_begin, sp_itor_end);
- still_paths = true;
- while (still_paths)
- {
- // initialize a path to however far each species iterator has been
- // advanced.
- set_path_to_cur_sp_itor_track(path, win_i, sp_itor_begin);
-
- // if the path is transitive, save the path
- if (is_transitive_path(path, all_comparisons, soft_thres))
- pathz.push_back(ConservedPath(soft_thres, path));
-
- // now advance the right iterator
- still_paths = advance_sp_itor_track(sp_itor_begin,
- sp_itor_end,
- all_matches);
- }
- }
- }
- //clog << "all_cmp=" << all_comparisons.size();
- //if (pathz.begin() != pathz.end())
- // clog << " path_size=" << pathz.begin()->size();
- //else
- // clog << " path empty";
- //clog << endl;
- assert ( (pathz.begin() == pathz.end())
- || (pathz.begin()->size() == 0)
- || (all_comparisons.size() == pathz.begin()->size()));
-}
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+// ----------------------------------------
+// ---------- mussa_nway.cc -----------
+// ----------------------------------------
+
+#include "alg/nway_paths.hpp"
+#include "alg/conserved_path.hpp"
+#include "mussa_exceptions.hpp"
+
+#include <fstream>
+#include <iostream>
+#include <stdexcept>
+
+using namespace std;
+
+NwayPaths::NwayPaths()
+{
+}
+
+void
+NwayPaths::setup(int w, int t)
+{
+ threshold = t;
+ soft_thres = threshold;
+ win_size = w;
+ pathz.clear();
+
+ //cout << "nway: thres = " << threshold
+ // << ", soft threo = " << soft_thres << endl;
+}
+
+void
+NwayPaths::set_soft_thres(int sft_thres)
+{
+ soft_thres = sft_thres;
+}
+
+
+// dumbly goes thru and combines path windows exactly adjacent (ie + 1 index)
+// doesn't deal with interleaved adjacency
+void
+NwayPaths::simple_refine()
+{
+ // ext_path remembers the first window set in an extending path
+ ExtendedConservedPath ext_path, new_path;
+ list<ConservedPath>::iterator cur_path, next_path;
+ list<ConservedPath>::iterator pathz_i;
+ int win_ext_len = 0;
+ bool extending, end = false;
+
+ refined_pathz.clear();
+
+ //cout << "path number is: " << pathz.size() << endl;
+ pathz_i = pathz.begin();
+
+ // only try to extend when pathz isn't empty.
+ if (pathz_i != pathz.end())
+ {
+ ext_path = ExtendedConservedPath( win_size, *pathz_i);
+
+ while(pathz_i != pathz.end())
+ {
+ // keep track of current path and advance to next path
+ cur_path = pathz_i;
+ ++pathz_i;
+ if (pathz_i == pathz.end())
+ end = true;
+ else
+ next_path = pathz_i;
+
+ if (not end)
+ {
+ // if node for each seq is equal to the next node+1 then for all
+ // sequences then we are extending
+ extending = cur_path->nextTo(*next_path);
+ }
+ else
+ extending = false;
+
+ if (extending)
+ {
+ win_ext_len++;
+ }
+ else
+ {
+ // add the extend window length as first element and add as refined
+ // now that we have the path to extend save it
+ new_path = ext_path;
+ new_path.extend(win_ext_len);
+ refined_pathz.push_back(new_path);
+ // reset stuff
+ win_ext_len = 0;
+ ext_path = ExtendedConservedPath( win_size, *next_path);
+ }
+ }
+ }
+ //cout << "r_path number is: " << refined_pathz.size() << endl;
+}
+
+
+void
+NwayPaths::add_path(int threshold, vector<int>& loaded_path)
+{
+ pathz.push_back(ConservedPath(threshold, loaded_path));
+}
+
+void
+NwayPaths::add_path(ConservedPath loaded_path)
+{
+ pathz.push_back(loaded_path);
+}
+
+
+void
+NwayPaths::save(string save_file_path)
+{
+ fstream save_file;
+ list<ExtendedConservedPath >::iterator path_i, paths_end;
+
+ save_file.open(save_file_path.c_str(), ios::out);
+
+ save_file << "<Mussa type=flp seq_count=" << sequence_count();
+ save_file << " win=" << win_size;
+ // add a function para new_thres defaults to -1 to later deal with
+ // reanalysis with higher thres - if statement whether to record base thres
+ // or new thres (ie if -1, then base)
+ save_file << " thres=" << threshold << " >\n";
+
+ path_i = refined_pathz.begin();
+ paths_end = refined_pathz.end();
+ //path_i = pathz.begin();
+ //paths_end = pathz.end();
+ while (path_i != paths_end)
+ {
+ ExtendedConservedPath& a_path = *path_i;
+ //cout << a_path.size() << endl;
+ //first entry is the window length of the windows in the path
+ save_file << a_path.window_size << ":";
+ for(size_t i = 0; i != sequence_count(); ++i)
+ {
+ save_file << a_path[i];
+ if (i != sequence_count())
+ save_file << ",";
+ }
+ save_file << endl;
+ ++path_i;
+ }
+
+ save_file << "</Mussa>\n";
+ save_file.close();
+}
+
+
+size_t
+NwayPaths::sequence_count()
+{
+ if (refined_pathz.begin() == refined_pathz.end() )
+ return 0;
+ else
+ return refined_pathz.begin()->size();
+}
+
+
+void
+NwayPaths::load(string load_file_path)
+{
+ fstream load_file;
+ string file_data_line, header_data, data, path_node, path_width;
+ int space_split_i, equal_split_i, comma_split_i, colon_split_i;
+ vector<int> loaded_path;
+
+ load_file.open(load_file_path.c_str(), ios::in);
+
+ if (!load_file)
+ {
+ throw mussa_load_error("Sequence File: " + load_file_path + " not found");
+ }
+ else
+ {
+ // get header data
+ // grab mussa tag - discard for now...maybe check in future...
+ getline(load_file,file_data_line);
+ space_split_i = file_data_line.find(" ");
+ file_data_line = file_data_line.substr(space_split_i+1);
+ // grab type tag - need in future to distinguish between flp and vlp paths
+ space_split_i = file_data_line.find(" ");
+ file_data_line = file_data_line.substr(space_split_i+1);
+ // get species/seq number
+ space_split_i = file_data_line.find(" ");
+ header_data = file_data_line.substr(0,space_split_i);
+ equal_split_i = header_data.find("=");
+ data = file_data_line.substr(equal_split_i+1);
+ unsigned int species_num = atoi (data.c_str());
+ file_data_line = file_data_line.substr(space_split_i+1);
+ // get window size
+ space_split_i = file_data_line.find(" ");
+ header_data = file_data_line.substr(0,space_split_i);
+ equal_split_i = header_data.find("=");
+ data = file_data_line.substr(equal_split_i+1);
+ win_size = atoi (data.c_str());
+ file_data_line = file_data_line.substr(space_split_i+1);
+ // get window size
+ space_split_i = file_data_line.find(" ");
+ header_data = file_data_line.substr(0,space_split_i);
+ equal_split_i = header_data.find("=");
+ data = file_data_line.substr(equal_split_i+1);
+ threshold = atoi (data.c_str());
+ file_data_line = file_data_line.substr(space_split_i+1);
+
+ //cout << "seq_num=" << species_num << " win=" << win_size;
+ //cout << " thres=" << threshold << endl;
+
+ // clear out the current data
+ refined_pathz.clear();
+
+ int temp;
+
+ getline(load_file,file_data_line);
+ while ( (!load_file.eof()) && (file_data_line != "</Mussa>") )
+ {
+ if (file_data_line != "")
+ {
+ loaded_path.clear();
+ colon_split_i = file_data_line.find(":");
+ // whats our window size?
+ path_width = file_data_line.substr(0,colon_split_i);
+ file_data_line = file_data_line.substr(colon_split_i+1);
+ for(size_t i = 0; i < species_num; i++)
+ {
+ comma_split_i = file_data_line.find(",");
+ path_node = file_data_line.substr(0, comma_split_i);
+ temp = atoi (path_node.c_str());
+ loaded_path.push_back(temp);
+ file_data_line = file_data_line.substr(comma_split_i+1);
+ }
+ assert (loaded_path.size() == species_num );
+ refined_pathz.push_back(ExtendedConservedPath(atoi(path_width.c_str()),
+ threshold,
+ loaded_path));
+ }
+ getline(load_file,file_data_line);
+ }
+ load_file.close();
+ }
+}
+
+
+void
+NwayPaths::path_search(vector<vector<FLPs> > all_comparisons, ConservedPath path, int depth)
+{
+ list<int> new_nodes, trans_check_nodes;
+ list<int>::iterator new_nodes_i, new_nodes_end;
+ int i;
+ bool trans_check_good;
+
+ new_nodes = all_comparisons[depth - 1][depth].match_locations(path[depth-1]);
+ new_nodes_i = new_nodes.begin();
+ new_nodes_end = new_nodes.end();
+ while(new_nodes_i != new_nodes_end)
+ {
+ //cout << " * species " << depth << " node: " << *new_nodes_i << endl;
+ // check transitivity with previous nodes in path
+ trans_check_good = true;
+ for(i = 0; i < depth - 1; i++)
+ {
+ trans_check_nodes = all_comparisons[i][depth].match_locations(path[i]);
+ if ( (trans_check_nodes.end() == find(trans_check_nodes.begin(),
+ trans_check_nodes.end(),
+ *new_nodes_i) ) &&
+ (trans_check_nodes.end() == find(trans_check_nodes.begin(),
+ trans_check_nodes.end(),
+ *new_nodes_i * -1) ) )
+ trans_check_good = false;
+ }
+
+ if (trans_check_good)
+ {
+ // this makes sure path nodes are recorded with RC status relative to
+ // the base species
+ if ( path[depth-1] >= 0)
+ path.push_back(*new_nodes_i);
+ else
+ path.push_back(*new_nodes_i * -1);
+
+ if (depth < all_comparisons.size() - 1)
+ path_search(all_comparisons, path, depth + 1);
+ else
+ pathz.push_back(path);
+ path.pop_back();
+ }
+ ++new_nodes_i;
+ }
+}
+/* use this if I ever get the friggin seqcomp match lists to sort...
+ if (binary_search(trans_check_nodes.begin(), trans_check_nodes.end(),
+ *new_nodes_i))
+*/
+
+void
+NwayPaths::find_paths_r(vector<vector<FLPs> > all_comparisons)
+{
+ ConservedPath path;
+ int win_i, window_num;
+ list<int> new_nodes;
+ list<int>::iterator new_nodes_i, new_nodes_end;
+
+ pathz.clear();
+ window_num = all_comparisons[0][1].size();
+ // loop thru all windows in first species
+ for (win_i = 0; win_i < window_num; win_i++)
+ {
+ path.clear();
+ path.push_back(win_i);
+ new_nodes = all_comparisons[0][1].match_locations(path[0]);
+ new_nodes_i = new_nodes.begin();
+ new_nodes_end = new_nodes.end();
+ //if (new_nodes_i != new_nodes_end)
+ //cout << "* species 0 node: " << win_i << endl;
+ path.push_back(0);
+ while(new_nodes_i != new_nodes_end)
+ {
+ //cout << " * species 1 node: " << *new_nodes_i << endl;
+ path[1] = *new_nodes_i;
+ path_search(all_comparisons, path, 2);
+ ++new_nodes_i;
+ }
+ }
+}
+
+
+void
+NwayPaths::save_old(string save_file_path)
+{
+ fstream save_file;
+ list<ConservedPath >::iterator path_i, paths_end;
+ int i;
+
+ save_file.open(save_file_path.c_str(), ios::app);
+
+ path_i = pathz.begin();
+ paths_end = pathz.end();
+ while(path_i != paths_end)
+ {
+ ConservedPath& a_path = *path_i;
+ //cout << a_path.size() << endl;
+ for(i = 0; i < path_i->size(); ++i)
+ save_file << i << "," << a_path[i] << " ";
+ save_file << endl;
+ ++path_i;
+ }
+ save_file.close();
+}
+
+
+/*
+void
+NwayPaths::find_paths(vector<vector<FLPs> > all_comparisons)
+{
+ int win_i, sp_i;
+ vector<list<list<int> > > path_src_tree;
+ list<int> new_nodes;
+ list<int>::iterator node_i, node_end;
+ <list<list<int> > >::iterator branch_i, branch_end;
+
+ pathz.clear();
+ path_src_tree.reserve(all_comparisons.size()- 1);
+
+
+ // loop thru all windows in first species
+ for (win_i = 0; win_i < window_num; win_i++)
+ {
+ // clear the path search tree
+ for(i = 0; i < all_comparisons.size(); i++)
+ path_src_tree[i].clear();
+
+ // top level kept empty even tho implicity has one entry of the first
+ // species at this window - why bother, adds a little speed
+
+ // get connection list for first species, creating a list of nodes
+ // of second species connected to the first species at this window
+ new_nodes = all_comparisons[0][1];
+ path_src_tree[1].push_back(new_nodes);
+
+ // loop thru rest of species for this window to see if any paths of matches
+ // go across all species
+ // if path search tree becomes empty, break out of loop, no reason to search further
+ sp_i = 1;
+ while ((sp_i < all_comparisons.size()) && (path tree not empty))
+ {
+ branch_i = path_src_tree[1].begin();
+ branch_end = path_src_tree[1].end();
+ while (branch_i != branch_end)
+ {
+ node_i = branch_i->begin();
+ node_end = branch_i->end();
+ }
+
+
+ // loop over all current nodes
+ // get connection list for each node
+ // loop over each previous node in list
+ // get those nodes connection list
+ // intersect previous node connections with current
+
+ ++sp_i;
+ }
+
+ // insert any of the paths found into the master list of paths
+
+ // add no paths if tmp_pathz is empty...
+ }
+}
+
+void NwayPaths::refine()
+{
+}
+*/
+
+
+void NwayPaths::print(list<vector<int> >& dump_path)
+{
+ list<vector<int> >::iterator pathz_i;
+ vector<int>::iterator path_i;
+
+ cout << "printing list of lists\n";
+ for (pathz_i = dump_path.begin(); pathz_i != dump_path.end(); ++pathz_i)
+ {
+ for (path_i = pathz_i->begin(); path_i != pathz_i->end(); ++path_i)
+ cout << *path_i << " ";
+ cout << endl;
+ }
+}
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-// ----------------------------------------
-// ---------- mussa_nway.cc -----------
-// ----------------------------------------
-
-#include "alg/nway_paths.hh"
-#include "alg/conserved_path.h"
-#include "mussa_exceptions.hh"
-
-#include <fstream>
-#include <iostream>
-#include <stdexcept>
-
-using namespace std;
-
-NwayPaths::NwayPaths()
-{
-}
-
-void
-NwayPaths::setup(int w, int t)
-{
- threshold = t;
- soft_thres = threshold;
- win_size = w;
- pathz.clear();
-
- //cout << "nway: thres = " << threshold
- // << ", soft threo = " << soft_thres << endl;
-}
-
-void
-NwayPaths::set_soft_thres(int sft_thres)
-{
- soft_thres = sft_thres;
-}
-
-
-// dumbly goes thru and combines path windows exactly adjacent (ie + 1 index)
-// doesn't deal with interleaved adjacency
-void
-NwayPaths::simple_refine()
-{
- // ext_path remembers the first window set in an extending path
- ExtendedConservedPath ext_path, new_path;
- list<ConservedPath>::iterator cur_path, next_path;
- list<ConservedPath>::iterator pathz_i;
- int win_ext_len = 0;
- bool extending, end = false;
-
- refined_pathz.clear();
-
- //cout << "path number is: " << pathz.size() << endl;
- pathz_i = pathz.begin();
-
- // only try to extend when pathz isn't empty.
- if (pathz_i != pathz.end())
- {
- ext_path = ExtendedConservedPath( win_size, *pathz_i);
-
- while(pathz_i != pathz.end())
- {
- // keep track of current path and advance to next path
- cur_path = pathz_i;
- ++pathz_i;
- if (pathz_i == pathz.end())
- end = true;
- else
- next_path = pathz_i;
-
- if (not end)
- {
- // if node for each seq is equal to the next node+1 then for all
- // sequences then we are extending
- extending = cur_path->nextTo(*next_path);
- }
- else
- extending = false;
-
- if (extending)
- {
- win_ext_len++;
- }
- else
- {
- // add the extend window length as first element and add as refined
- // now that we have the path to extend save it
- new_path = ext_path;
- new_path.extend(win_ext_len);
- refined_pathz.push_back(new_path);
- // reset stuff
- win_ext_len = 0;
- ext_path = ExtendedConservedPath( win_size, *next_path);
- }
- }
- }
- //cout << "r_path number is: " << refined_pathz.size() << endl;
-}
-
-
-void
-NwayPaths::add_path(int threshold, vector<int>& loaded_path)
-{
- pathz.push_back(ConservedPath(threshold, loaded_path));
-}
-
-void
-NwayPaths::add_path(ConservedPath loaded_path)
-{
- pathz.push_back(loaded_path);
-}
-
-
-void
-NwayPaths::save(string save_file_path)
-{
- fstream save_file;
- list<ExtendedConservedPath >::iterator path_i, paths_end;
-
- save_file.open(save_file_path.c_str(), ios::out);
-
- save_file << "<Mussa type=flp seq_count=" << sequence_count();
- save_file << " win=" << win_size;
- // add a function para new_thres defaults to -1 to later deal with
- // reanalysis with higher thres - if statement whether to record base thres
- // or new thres (ie if -1, then base)
- save_file << " thres=" << threshold << " >\n";
-
- path_i = refined_pathz.begin();
- paths_end = refined_pathz.end();
- //path_i = pathz.begin();
- //paths_end = pathz.end();
- while (path_i != paths_end)
- {
- ExtendedConservedPath& a_path = *path_i;
- //cout << a_path.size() << endl;
- //first entry is the window length of the windows in the path
- save_file << a_path.window_size << ":";
- for(size_t i = 0; i != sequence_count(); ++i)
- {
- save_file << a_path[i];
- if (i != sequence_count())
- save_file << ",";
- }
- save_file << endl;
- ++path_i;
- }
-
- save_file << "</Mussa>\n";
- save_file.close();
-}
-
-
-size_t
-NwayPaths::sequence_count()
-{
- if (refined_pathz.begin() == refined_pathz.end() )
- return 0;
- else
- return refined_pathz.begin()->size();
-}
-
-
-void
-NwayPaths::load(string load_file_path)
-{
- fstream load_file;
- string file_data_line, header_data, data, path_node, path_width;
- int space_split_i, equal_split_i, comma_split_i, colon_split_i;
- vector<int> loaded_path;
-
- load_file.open(load_file_path.c_str(), ios::in);
-
- if (!load_file)
- {
- throw mussa_load_error("Sequence File: " + load_file_path + " not found");
- }
- else
- {
- // get header data
- // grab mussa tag - discard for now...maybe check in future...
- getline(load_file,file_data_line);
- space_split_i = file_data_line.find(" ");
- file_data_line = file_data_line.substr(space_split_i+1);
- // grab type tag - need in future to distinguish between flp and vlp paths
- space_split_i = file_data_line.find(" ");
- file_data_line = file_data_line.substr(space_split_i+1);
- // get species/seq number
- space_split_i = file_data_line.find(" ");
- header_data = file_data_line.substr(0,space_split_i);
- equal_split_i = header_data.find("=");
- data = file_data_line.substr(equal_split_i+1);
- unsigned int species_num = atoi (data.c_str());
- file_data_line = file_data_line.substr(space_split_i+1);
- // get window size
- space_split_i = file_data_line.find(" ");
- header_data = file_data_line.substr(0,space_split_i);
- equal_split_i = header_data.find("=");
- data = file_data_line.substr(equal_split_i+1);
- win_size = atoi (data.c_str());
- file_data_line = file_data_line.substr(space_split_i+1);
- // get window size
- space_split_i = file_data_line.find(" ");
- header_data = file_data_line.substr(0,space_split_i);
- equal_split_i = header_data.find("=");
- data = file_data_line.substr(equal_split_i+1);
- threshold = atoi (data.c_str());
- file_data_line = file_data_line.substr(space_split_i+1);
-
- //cout << "seq_num=" << species_num << " win=" << win_size;
- //cout << " thres=" << threshold << endl;
-
- // clear out the current data
- refined_pathz.clear();
-
- int temp;
-
- getline(load_file,file_data_line);
- while ( (!load_file.eof()) && (file_data_line != "</Mussa>") )
- {
- if (file_data_line != "")
- {
- loaded_path.clear();
- colon_split_i = file_data_line.find(":");
- // whats our window size?
- path_width = file_data_line.substr(0,colon_split_i);
- file_data_line = file_data_line.substr(colon_split_i+1);
- for(size_t i = 0; i < species_num; i++)
- {
- comma_split_i = file_data_line.find(",");
- path_node = file_data_line.substr(0, comma_split_i);
- temp = atoi (path_node.c_str());
- loaded_path.push_back(temp);
- file_data_line = file_data_line.substr(comma_split_i+1);
- }
- assert (loaded_path.size() == species_num );
- refined_pathz.push_back(ExtendedConservedPath(atoi(path_width.c_str()),
- threshold,
- loaded_path));
- }
- getline(load_file,file_data_line);
- }
- load_file.close();
- }
-}
-
-
-void
-NwayPaths::path_search(vector<vector<FLPs> > all_comparisons, ConservedPath path, int depth)
-{
- list<int> new_nodes, trans_check_nodes;
- list<int>::iterator new_nodes_i, new_nodes_end;
- int i;
- bool trans_check_good;
-
- new_nodes = all_comparisons[depth - 1][depth].match_locations(path[depth-1]);
- new_nodes_i = new_nodes.begin();
- new_nodes_end = new_nodes.end();
- while(new_nodes_i != new_nodes_end)
- {
- //cout << " * species " << depth << " node: " << *new_nodes_i << endl;
- // check transitivity with previous nodes in path
- trans_check_good = true;
- for(i = 0; i < depth - 1; i++)
- {
- trans_check_nodes = all_comparisons[i][depth].match_locations(path[i]);
- if ( (trans_check_nodes.end() == find(trans_check_nodes.begin(),
- trans_check_nodes.end(),
- *new_nodes_i) ) &&
- (trans_check_nodes.end() == find(trans_check_nodes.begin(),
- trans_check_nodes.end(),
- *new_nodes_i * -1) ) )
- trans_check_good = false;
- }
-
- if (trans_check_good)
- {
- // this makes sure path nodes are recorded with RC status relative to
- // the base species
- if ( path[depth-1] >= 0)
- path.push_back(*new_nodes_i);
- else
- path.push_back(*new_nodes_i * -1);
-
- if (depth < all_comparisons.size() - 1)
- path_search(all_comparisons, path, depth + 1);
- else
- pathz.push_back(path);
- path.pop_back();
- }
- ++new_nodes_i;
- }
-}
-/* use this if I ever get the friggin seqcomp match lists to sort...
- if (binary_search(trans_check_nodes.begin(), trans_check_nodes.end(),
- *new_nodes_i))
-*/
-
-void
-NwayPaths::find_paths_r(vector<vector<FLPs> > all_comparisons)
-{
- ConservedPath path;
- int win_i, window_num;
- list<int> new_nodes;
- list<int>::iterator new_nodes_i, new_nodes_end;
-
- pathz.clear();
- window_num = all_comparisons[0][1].size();
- // loop thru all windows in first species
- for (win_i = 0; win_i < window_num; win_i++)
- {
- path.clear();
- path.push_back(win_i);
- new_nodes = all_comparisons[0][1].match_locations(path[0]);
- new_nodes_i = new_nodes.begin();
- new_nodes_end = new_nodes.end();
- //if (new_nodes_i != new_nodes_end)
- //cout << "* species 0 node: " << win_i << endl;
- path.push_back(0);
- while(new_nodes_i != new_nodes_end)
- {
- //cout << " * species 1 node: " << *new_nodes_i << endl;
- path[1] = *new_nodes_i;
- path_search(all_comparisons, path, 2);
- ++new_nodes_i;
- }
- }
-}
-
-
-void
-NwayPaths::save_old(string save_file_path)
-{
- fstream save_file;
- list<ConservedPath >::iterator path_i, paths_end;
- int i;
-
- save_file.open(save_file_path.c_str(), ios::app);
-
- path_i = pathz.begin();
- paths_end = pathz.end();
- while(path_i != paths_end)
- {
- ConservedPath& a_path = *path_i;
- //cout << a_path.size() << endl;
- for(i = 0; i < path_i->size(); ++i)
- save_file << i << "," << a_path[i] << " ";
- save_file << endl;
- ++path_i;
- }
- save_file.close();
-}
-
-
-/*
-void
-NwayPaths::find_paths(vector<vector<FLPs> > all_comparisons)
-{
- int win_i, sp_i;
- vector<list<list<int> > > path_src_tree;
- list<int> new_nodes;
- list<int>::iterator node_i, node_end;
- <list<list<int> > >::iterator branch_i, branch_end;
-
- pathz.clear();
- path_src_tree.reserve(all_comparisons.size()- 1);
-
-
- // loop thru all windows in first species
- for (win_i = 0; win_i < window_num; win_i++)
- {
- // clear the path search tree
- for(i = 0; i < all_comparisons.size(); i++)
- path_src_tree[i].clear();
-
- // top level kept empty even tho implicity has one entry of the first
- // species at this window - why bother, adds a little speed
-
- // get connection list for first species, creating a list of nodes
- // of second species connected to the first species at this window
- new_nodes = all_comparisons[0][1];
- path_src_tree[1].push_back(new_nodes);
-
- // loop thru rest of species for this window to see if any paths of matches
- // go across all species
- // if path search tree becomes empty, break out of loop, no reason to search further
- sp_i = 1;
- while ((sp_i < all_comparisons.size()) && (path tree not empty))
- {
- branch_i = path_src_tree[1].begin();
- branch_end = path_src_tree[1].end();
- while (branch_i != branch_end)
- {
- node_i = branch_i->begin();
- node_end = branch_i->end();
- }
-
-
- // loop over all current nodes
- // get connection list for each node
- // loop over each previous node in list
- // get those nodes connection list
- // intersect previous node connections with current
-
- ++sp_i;
- }
-
- // insert any of the paths found into the master list of paths
-
- // add no paths if tmp_pathz is empty...
- }
-}
-
-void NwayPaths::refine()
-{
-}
-*/
-
-
-void NwayPaths::print(list<vector<int> >& dump_path)
-{
- list<vector<int> >::iterator pathz_i;
- vector<int>::iterator path_i;
-
- cout << "printing list of lists\n";
- for (pathz_i = dump_path.begin(); pathz_i != dump_path.end(); ++pathz_i)
- {
- for (path_i = pathz_i->begin(); path_i != pathz_i->end(); ++path_i)
- cout << *path_i << " ";
- cout << endl;
- }
-}
+++ /dev/null
-#ifndef _MUSSA_NWAY_H_
-#define _MUSSA_NWAY_H_
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-// ----------------------------------------
-// ---------- mussa_nway.hh -----------
-// ----------------------------------------
-
-#include <list>
-#include <string>
-#include <vector>
-
-#include "alg/flp.hh"
-#include "alg/conserved_path.h"
-
-class NwayPaths
-{
- friend class ConnView;
- friend class SeqView;
- protected:
- int threshold;
- int win_size;
- int soft_thres;
-
- double ent_thres;
- std::vector<char *> c_sequences; //used by entropy_path_search
-
- public:
- NwayPaths();
- //! setup an nway comparison, initialize # of species, window size,
- //! threshold
- void setup(int w, int t);
- void setup_ent(double new_entropy_thres, std::vector<std::string> some_Seqs);
- void set_soft_thres(int soft_thres);
-
- void radiate_path_search(std::vector<std::vector<FLPs> > all_comparisons);
- void trans_path_search(std::vector<std::vector<FLPs> > all_comparisons);
- void entropy_path_search(std::vector<std::vector<FLPs> > all_comparisons);
- double path_entropy(std::vector<int> path);
-
- // old recursive transitive nway ... has issues checking all links?
- void find_paths_r(std::vector<std::vector<FLPs> > all_comparisons);
- void path_search(std::vector<std::vector<FLPs> > all_comparisons, ConservedPath path, int depth);
-
- void simple_refine();
- void save(std::string save_file_path);
- //! load a muway file, \throws mussa_load_error
- void load(std::string load_file_path);
- void add_path(int threshold, std::vector<int>& loaded_path);
- void add_path(ConservedPath loaded_path);
- //! how many sequences are in our comparison
- size_t sequence_count();
-
- void find_paths(std::vector<std::vector<FLPs> > all_comparisons);
- void refine();
-
- void save_old(std::string save_file_path);
- void print(std::list<std::vector<int> >&);
-
- std::list<ConservedPath>::iterator pbegin() { return pathz.begin() ; }
- std::list<ConservedPath>::iterator pend() { return pathz.end() ; }
- std::list<ExtendedConservedPath>::iterator rpbegin() { return refined_pathz.begin() ; }
- std::list<ExtendedConservedPath>::iterator rpend() { return refined_pathz.end() ; }
- // these probably shouldn't be public, but lets start
- // simple
- std::list<ConservedPath> pathz;
- std::list<ExtendedConservedPath > refined_pathz;
-};
-#endif
--- /dev/null
+#ifndef _MUSSA_NWAY_H_
+#define _MUSSA_NWAY_H_
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+// ----------------------------------------
+// ---------- mussa_nway.hh -----------
+// ----------------------------------------
+
+#include <list>
+#include <string>
+#include <vector>
+
+#include "alg/flp.hpp"
+#include "alg/conserved_path.hpp"
+
+class NwayPaths
+{
+ friend class ConnView;
+ friend class SeqView;
+ protected:
+ int threshold;
+ int win_size;
+ int soft_thres;
+
+ double ent_thres;
+ std::vector<char *> c_sequences; //used by entropy_path_search
+
+ public:
+ NwayPaths();
+ //! setup an nway comparison, initialize # of species, window size,
+ //! threshold
+ void setup(int w, int t);
+ void setup_ent(double new_entropy_thres, std::vector<std::string> some_Seqs);
+ void set_soft_thres(int soft_thres);
+
+ void radiate_path_search(std::vector<std::vector<FLPs> > all_comparisons);
+ void trans_path_search(std::vector<std::vector<FLPs> > all_comparisons);
+ void entropy_path_search(std::vector<std::vector<FLPs> > all_comparisons);
+ double path_entropy(std::vector<int> path);
+
+ // old recursive transitive nway ... has issues checking all links?
+ void find_paths_r(std::vector<std::vector<FLPs> > all_comparisons);
+ void path_search(std::vector<std::vector<FLPs> > all_comparisons, ConservedPath path, int depth);
+
+ void simple_refine();
+ void save(std::string save_file_path);
+ //! load a muway file, \throws mussa_load_error
+ void load(std::string load_file_path);
+ void add_path(int threshold, std::vector<int>& loaded_path);
+ void add_path(ConservedPath loaded_path);
+ //! how many sequences are in our comparison
+ size_t sequence_count();
+
+ void find_paths(std::vector<std::vector<FLPs> > all_comparisons);
+ void refine();
+
+ void save_old(std::string save_file_path);
+ void print(std::list<std::vector<int> >&);
+
+ std::list<ConservedPath>::iterator pbegin() { return pathz.begin() ; }
+ std::list<ConservedPath>::iterator pend() { return pathz.end() ; }
+ std::list<ExtendedConservedPath>::iterator rpbegin() { return refined_pathz.begin() ; }
+ std::list<ExtendedConservedPath>::iterator rpend() { return refined_pathz.end() ; }
+ // these probably shouldn't be public, but lets start
+ // simple
+ std::list<ConservedPath> pathz;
+ std::list<ExtendedConservedPath > refined_pathz;
+};
+#endif
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+PathList
+ExtendPathWindows(PathList raw_list)
+{
+ // to keep track of everything, this function acts like a finite state
+ // automata: 3 bitfields: reset, extending, scanning - ie 8 states
+ int reset = 0, extending = 0, scanning = 0;
+
+ int species_num = raw_list.SpeciesNum();
+ int win_num = raw_list.WinNum();
+
+ int *cur_path, *next_path;
+
+ cur_path = new int[species_num];
+ next_path = new int[species_num];
+
+ raw_list.ResetIndex();
+
+ while (no more windows avaible)
+ {
+ //cur_indices[0] + ref_ext == next_indices[0] + 1:
+
+ // state 000 - start/nominal search
+ //
+ if !reset && !extending && !scanning
+ {
+ if cur_path[0] == next_path[0]
+ {
+ scanning = 1; // go to state 001
+ raw_list.IncreIndex();
+ }
+ else if cur_path[0] + 1 == next_path[0]
+ {
+ extending = 1; // go to state 010
+ win_ext = 1;
+ raw_list.SetDirty();
+ raw_list.IncreIndex();
+ }
+ else
+ reset = 1; // go to state 100
+ }
+
+ // state 001 - scanning for ext window thru possible interleaving
+ //
+ else if !reset && !extending && scanning
+ {
+ if cur_path[0] == next_path[0]
+ raw_list.IncreIndex();
+ else if cur_path[0] + 1 == next_path[0]
+ {
+ extending = 1; // go to state 011
+ win_ext = 1;
+ raw_list.SetDirty();
+ raw_list.IncreIndex();
+ }
+ else
+ reset = 1; // go to state 101
+ }
+
+ // state 010 - extending window with no interleaving
+ //
+ else if !reset && extending && !scanning
+ {
+ if (cur_path[0] + win_ext) == next_path[0]
+ {
+ extending = 1; // go to state 011
+ raw_list.IncreIndex();
+ }
+ else if (cur_path[0] + win_ext + 1) == next_path[0]
+ {
+ win_ext++;
+ raw_list.SetDirty();
+ raw_list.IncreIndex();
+ }
+ else
+ reset = 1; // go to state 110
+ }
+
+ // state 011 - extending window with interleaving
+ //
+ else if !reset && extending && scanning
+ {
+ if (cur_path[0] + win_ext) == next_path[0]
+ raw_list.IncreIndex();
+ else if (cur_path[0] + win_ext + 1) == next_path[0]
+ {
+ win_ext++;
+ raw_list.SetDirty();
+ raw_list.IncreIndex();
+ }
+ else
+ reset = 1; // go to state 111
+ }
+
+
+ // reset condition states, return to 000 after taking appropiate action
+
+ // state 100 - no extended window, no scanning happened
+ // save basic window to extended window list
+ if reset && !extending && !scanning
+ {
+ // return to start/nominal search state
+ reset = 0;
+ }
+
+ // state 101 - no extended window, scanned for interleaving
+ // save basic window to extended window list, return to first clean
+ else if reset && !extending && scanning
+ {
+ // return to start/nominal search state
+ reset = 0;
+ scanning = 0;
+ }
+
+ // state 110 - extended window, no interleaving
+ // calc extended window, save to extended window list
+ else if reset && extending && !scanning
+ {
+ // return to start/nominal search state
+ reset = 0;
+ extending = 0;
+ }
+
+ // state 111 - extended window, interleaved
+ // calc extended window, save to ext win list, return to first clean
+ else if reset && extending && scanning
+ {
+ // return to start/nominal search state
+ reset = 0;
+ extending = 0;
+ scanning = 0;
+ }
+
+ return ext_win;
+}
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-PathList
-ExtendPathWindows(PathList raw_list)
-{
- // to keep track of everything, this function acts like a finite state
- // automata: 3 bitfields: reset, extending, scanning - ie 8 states
- int reset = 0, extending = 0, scanning = 0;
-
- int species_num = raw_list.SpeciesNum();
- int win_num = raw_list.WinNum();
-
- int *cur_path, *next_path;
-
- cur_path = new int[species_num];
- next_path = new int[species_num];
-
- raw_list.ResetIndex();
-
- while (no more windows avaible)
- {
- //cur_indices[0] + ref_ext == next_indices[0] + 1:
-
- // state 000 - start/nominal search
- //
- if !reset && !extending && !scanning
- {
- if cur_path[0] == next_path[0]
- {
- scanning = 1; // go to state 001
- raw_list.IncreIndex();
- }
- else if cur_path[0] + 1 == next_path[0]
- {
- extending = 1; // go to state 010
- win_ext = 1;
- raw_list.SetDirty();
- raw_list.IncreIndex();
- }
- else
- reset = 1; // go to state 100
- }
-
- // state 001 - scanning for ext window thru possible interleaving
- //
- else if !reset && !extending && scanning
- {
- if cur_path[0] == next_path[0]
- raw_list.IncreIndex();
- else if cur_path[0] + 1 == next_path[0]
- {
- extending = 1; // go to state 011
- win_ext = 1;
- raw_list.SetDirty();
- raw_list.IncreIndex();
- }
- else
- reset = 1; // go to state 101
- }
-
- // state 010 - extending window with no interleaving
- //
- else if !reset && extending && !scanning
- {
- if (cur_path[0] + win_ext) == next_path[0]
- {
- extending = 1; // go to state 011
- raw_list.IncreIndex();
- }
- else if (cur_path[0] + win_ext + 1) == next_path[0]
- {
- win_ext++;
- raw_list.SetDirty();
- raw_list.IncreIndex();
- }
- else
- reset = 1; // go to state 110
- }
-
- // state 011 - extending window with interleaving
- //
- else if !reset && extending && scanning
- {
- if (cur_path[0] + win_ext) == next_path[0]
- raw_list.IncreIndex();
- else if (cur_path[0] + win_ext + 1) == next_path[0]
- {
- win_ext++;
- raw_list.SetDirty();
- raw_list.IncreIndex();
- }
- else
- reset = 1; // go to state 111
- }
-
-
- // reset condition states, return to 000 after taking appropiate action
-
- // state 100 - no extended window, no scanning happened
- // save basic window to extended window list
- if reset && !extending && !scanning
- {
- // return to start/nominal search state
- reset = 0;
- }
-
- // state 101 - no extended window, scanned for interleaving
- // save basic window to extended window list, return to first clean
- else if reset && !extending && scanning
- {
- // return to start/nominal search state
- reset = 0;
- scanning = 0;
- }
-
- // state 110 - extended window, no interleaving
- // calc extended window, save to extended window list
- else if reset && extending && !scanning
- {
- // return to start/nominal search state
- reset = 0;
- extending = 0;
- }
-
- // state 111 - extended window, interleaved
- // calc extended window, save to ext win list, return to first clean
- else if reset && extending && scanning
- {
- // return to start/nominal search state
- reset = 0;
- extending = 0;
- scanning = 0;
- }
-
- return ext_win;
-}
--- /dev/null
+#include <boost/program_options.hpp>
+namespace po = boost::program_options;
+
+#include <string>
+#include <iostream>
+
+#include "alg/mussa.hpp"
+#include "alg/parse_options.hpp"
+
+Mussa *initialize_mussa(int argc, char **argv)
+{
+ po::options_description options("Mussa options");
+ po::positional_options_description pos_options;
+ pos_options.add("run-analysis", -1);
+
+ options.add_options()
+ ("help", "help message")
+ ("run-analysis,p", po::value<std::string>(),
+ "run an analysis defined by the mussa parameter file")
+ ("view-analysis", po::value<std::string>(),
+ "load a previously run analysis")
+ ;
+
+ po::variables_map vm;
+ po::store(po::command_line_parser(argc, argv).options(options).positional(pos_options).run(), vm);
+ po::notify(vm);
+
+ if (vm.count("help")) {
+ std::cout << options << std::endl;
+ return 0;
+ }
+
+ Mussa *m = new Mussa();
+ // currently we can only have one analysis loaded, so
+ // running trumps viewing.
+ if (vm.count("run-analysis")) {
+ m->load_mupa_file( vm["run-analysis"].as< std::string >() );
+ std::cout << "I apologize for blocking the gui while running the analysis"
+ << std::endl;
+ m->analyze();
+ }
+ else if (vm.count("view-analysis")) {
+ m->load( vm["view-analysis"].as< std::string >() );
+ }
+ return m;
+}
+
+++ /dev/null
-#include <boost/program_options.hpp>
-namespace po = boost::program_options;
-
-#include <string>
-#include <iostream>
-
-#include "alg/mussa_class.hh"
-#include "alg/parse_options.h"
-
-Mussa *initialize_mussa(int argc, char **argv)
-{
- po::options_description options("Mussa options");
- po::positional_options_description pos_options;
- pos_options.add("run-analysis", -1);
-
- options.add_options()
- ("help", "help message")
- ("run-analysis,p", po::value<std::string>(),
- "run an analysis defined by the mussa parameter file")
- ("view-analysis", po::value<std::string>(),
- "load a previously run analysis")
- ;
-
- po::variables_map vm;
- po::store(po::command_line_parser(argc, argv).options(options).positional(pos_options).run(), vm);
- po::notify(vm);
-
- if (vm.count("help")) {
- std::cout << options << std::endl;
- return 0;
- }
-
- Mussa *m = new Mussa();
- // currently we can only have one analysis loaded, so
- // running trumps viewing.
- if (vm.count("run-analysis")) {
- m->load_mupa_file( vm["run-analysis"].as< std::string >() );
- std::cout << "I apologize for blocking the gui while running the analysis"
- << std::endl;
- m->analyze();
- }
- else if (vm.count("view-analysis")) {
- m->load( vm["view-analysis"].as< std::string >() );
- }
- return m;
-}
-
+++ /dev/null
-#ifndef _PARSE_OPTIONS_H_
-#define _PARSE_OPTIONS_H_
-
-class Mussa;
-
-//! initialize a mussa analysis from command line arguments
-Mussa *initialize_mussa(int argc, char** argv);
-#endif
-
--- /dev/null
+#ifndef _PARSE_OPTIONS_H_
+#define _PARSE_OPTIONS_H_
+
+class Mussa;
+
+//! initialize a mussa analysis from command line arguments
+Mussa *initialize_mussa(int argc, char** argv);
+#endif
+
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+// ----------------------------------------
+// ---------- sequence.cc -----------
+// ----------------------------------------
+
+#include "alg/sequence.hpp"
+#include "mussa_exceptions.hpp"
+
+#include <string>
+#include <iostream>
+
+using namespace std;
+
+Sequence::Sequence()
+{
+}
+
+Sequence::Sequence(string seq)
+{
+ set_filtered_sequence(seq);
+}
+
+Sequence &Sequence::operator=(const Sequence& s)
+{
+ if (this != &s) {
+ sequence = s.sequence;
+ header = s.header;
+ species = s.species;
+ annots = s.annots;
+ }
+ return *this;
+}
+
+Sequence &Sequence::operator=(const std::string& s)
+{
+ set_filtered_sequence(s);
+ return *this;
+}
+
+//! load a fasta file into a sequence
+/*!
+ * \param file_path the location of the fasta file in the filesystem
+ * \param seq_num which sequence in the file to load
+ * \param start_index starting position in the fasta sequence, 0 for beginning
+ * \param end_index ending position in the fasta sequence, 0 for end
+ * \return error message, empty string if no error. (gag!)
+ */
+void
+Sequence::load_fasta(string file_path, int seq_num,
+ int start_index, int end_index)
+{
+ fstream data_file;
+ string file_data_line;
+ int header_counter = 0;
+ bool read_seq = true;
+ string rev_comp;
+ string sequence_raw;
+ string seq_tmp; // holds sequence during basic filtering
+
+ data_file.open(file_path.c_str(), ios::in);
+
+ if (!data_file)
+ {
+ throw mussa_load_error("Sequence File: " + file_path + " not found");
+ }
+ // if file opened okay, read it
+ else
+ {
+ // search for the header of the fasta sequence we want
+ while ( (!data_file.eof()) && (header_counter < seq_num) )
+ {
+ getline(data_file,file_data_line);
+ if (file_data_line.substr(0,1) == ">")
+ header_counter++;
+ }
+
+ header = file_data_line.substr(1);
+
+ sequence_raw = "";
+
+ while ( !data_file.eof() && read_seq )
+ {
+ getline(data_file,file_data_line);
+ if (file_data_line.substr(0,1) == ">")
+ read_seq = false;
+ else sequence_raw += file_data_line;
+ }
+
+ data_file.close();
+
+ // Lastly, if subselection of the sequence was specified we keep cut out
+ // and only keep that part
+ // end_index = 0 means no end was specified, so cut to the end
+ if (end_index == 0)
+ end_index = sequence_raw.size();
+
+ // sequence filtering for upcasing agctn and convert non AGCTN to N
+ set_filtered_sequence(sequence_raw, start_index, end_index-start_index);
+ }
+}
+
+void Sequence::set_filtered_sequence(const string &old_seq,
+ string::size_type start,
+ string::size_type count)
+{
+ char conversionTable[257];
+
+ if ( count == 0)
+ count = old_seq.size() - start;
+ sequence.clear();
+ sequence.reserve(count);
+
+ // Make a conversion table
+
+ // everything we don't specify below will become 'N'
+ for(int table_i=0; table_i < 256; table_i++)
+ {
+ conversionTable[table_i] = 'N';
+ }
+ // add end of string character for printing out table for testing purposes
+ conversionTable[256] = '\0';
+
+ // we want these to map to themselves - ie not to change
+ conversionTable[(int)'A'] = 'A';
+ conversionTable[(int)'T'] = 'T';
+ conversionTable[(int)'G'] = 'G';
+ conversionTable[(int)'C'] = 'C';
+ // this is to upcase
+ conversionTable[(int)'a'] = 'A';
+ conversionTable[(int)'t'] = 'T';
+ conversionTable[(int)'g'] = 'G';
+ conversionTable[(int)'c'] = 'C';
+
+ // finally, the actual conversion loop
+ for(string::size_type seq_index = 0; seq_index < count; seq_index++)
+ {
+ sequence += conversionTable[ (int)old_seq[seq_index+start]];
+ }
+}
+
+ // this doesn't work properly under gcc 3.x ... it can't recognize toupper
+ //transform(sequence.begin(), sequence.end(), sequence.begin(), toupper);
+
+
+void
+Sequence::load_annot(string file_path, int start_index, int end_index)
+{
+ fstream data_file;
+ string file_data_line;
+ annot an_annot;
+ string::size_type space_split_i;
+ string annot_value;
+ list<annot>::iterator list_i;
+ string err_msg;
+
+
+ annots.clear();
+ data_file.open(file_path.c_str(), ios::in);
+
+ if (!data_file)
+ {
+ throw mussa_load_error("Sequence File: " + file_path + " not found");
+ }
+ // if file opened okay, read it
+ else
+ {
+ getline(data_file,file_data_line);
+ species = file_data_line;
+
+ // end_index = 0 means no end was specified, so cut to the end
+ if (end_index == 0)
+ end_index = sequence.length();
+
+ //cout << "START: " << start_index << " END: " << end_index << endl;
+
+ while ( !data_file.eof() )
+ {
+ getline(data_file,file_data_line);
+ if (file_data_line != "")
+ {
+ // need to get 4 values...almost same code 4 times...
+ // get annot start index
+ space_split_i = file_data_line.find(" ");
+ annot_value = file_data_line.substr(0,space_split_i);
+ an_annot.start = atoi (annot_value.c_str());
+ file_data_line = file_data_line.substr(space_split_i+1);
+ // get annot end index
+ space_split_i = file_data_line.find(" ");
+ annot_value = file_data_line.substr(0,space_split_i);
+ an_annot.end = atoi (annot_value.c_str());
+ file_data_line = file_data_line.substr(space_split_i+1);
+
+ //cout << "seq, annots: " << an_annot.start << ", " << an_annot.end
+ // << endl;
+
+ // get annot name
+ space_split_i = file_data_line.find(" ");
+ if (space_split_i == string::npos) // no entries for name & type
+ {
+ cout << "seq, annots - no name or type\n";
+ an_annot.name = "";
+ an_annot.type = "";
+ }
+ else
+ {
+ annot_value = file_data_line.substr(0,space_split_i);
+ an_annot.name = annot_value;
+ file_data_line = file_data_line.substr(space_split_i+1);
+ // get annot type
+ space_split_i = file_data_line.find(" ");
+ if (space_split_i == string::npos) // no entry for type
+ an_annot.type = "";
+ else
+ {
+ annot_value = file_data_line.substr(0,space_split_i);
+ an_annot.type = annot_value;
+ }
+ }
+
+
+ // add annot to list if it falls within the range of sequence specified
+ if ((start_index <= an_annot.start) && (end_index >= an_annot.end))
+ {
+ an_annot.start -= start_index;
+ an_annot.end -= start_index;
+ annots.push_back(an_annot);
+ }
+ else
+ cout << "FAILED!!!!!!\n";
+ }
+ }
+
+ data_file.close();
+ /*
+ // debugging check
+ for(list_i = annots.begin(); list_i != annots.end(); ++list_i)
+ {
+ cout << (*list_i).start << "," << (*list_i).end << "\t";
+ cout << (*list_i).name << "\t" << (*list_i).type << endl;
+ }
+ */
+ }
+}
+
+bool Sequence::empty() const
+{
+ return (size() == 0);
+}
+
+const std::list<annot> Sequence::annotations() const
+{
+ return annots;
+}
+
+string::size_type Sequence::length() const
+{
+ return size();
+}
+
+string::size_type Sequence::size() const
+{
+ return sequence.size();
+}
+
+Sequence::iterator Sequence::begin()
+{
+ return sequence.begin();
+}
+
+Sequence::const_iterator Sequence::begin() const
+{
+ return sequence.begin();
+}
+
+Sequence::iterator Sequence::end()
+{
+ return sequence.end();
+}
+
+Sequence::const_iterator Sequence::end() const
+{
+ return sequence.end();
+}
+
+
+const string&
+Sequence::get_seq() const
+{
+ return sequence;
+}
+
+
+string
+Sequence::subseq(int start, int end) const
+{
+ return sequence.substr(start, end);
+}
+
+
+const char *
+Sequence::c_seq() const
+{
+ return sequence.c_str();
+}
+
+string
+Sequence::rev_comp() const
+{
+ string rev_comp;
+ char conversionTable[257];
+ int seq_i, table_i, len;
+
+ len = sequence.length();
+ rev_comp.reserve(len);
+ // make a conversion table
+ // init all parts of conversion table to '~' character
+ // '~' I doubt will ever appear in a sequence file (jeez, I hope)
+ // and may the fleas of 1000 camels infest the genitals of any biologist (and
+ // seven generations of their progeny) who decides to make it mean
+ // something special!!!
+ // PS - double the curse for any smartass non-biologist who tries it as well
+ for(table_i=0; table_i < 256; table_i++)
+ {
+ conversionTable[table_i] = '~';
+ }
+ // add end of string character for printing out table for testing purposes
+ conversionTable[256] = '\0';
+
+ // add in the characters for the bases we want to convert
+ conversionTable[(int)'A'] = 'T';
+ conversionTable[(int)'T'] = 'A';
+ conversionTable[(int)'G'] = 'C';
+ conversionTable[(int)'C'] = 'G';
+ conversionTable[(int)'N'] = 'N';
+
+ // finally, the actual conversion loop
+ for(seq_i = len - 1; seq_i >= 0; seq_i--)
+ {
+ table_i = (int) sequence[seq_i];
+ rev_comp += conversionTable[table_i];
+ }
+
+ return rev_comp;
+}
+
+
+const string&
+Sequence::get_header() const
+{
+ return header;
+}
+/*
+//FIXME: i don't think this code is callable
+string
+Sequence::sp_name() const
+{
+ return species;
+}
+*/
+
+void
+Sequence::set_seq(const string& a_seq)
+{
+ set_filtered_sequence(a_seq);
+}
+
+
+/*
+string
+Sequence::species()
+{
+ return species;
+}
+*/
+
+void
+Sequence::clear()
+{
+ sequence = "";
+ header = "";
+ species = "";
+ annots.clear();
+}
+
+void
+Sequence::save(fstream &save_file)
+ //string save_file_path)
+{
+ //fstream save_file;
+ list<annot>::iterator annots_i;
+
+ // not sure why, or if i'm doing something wrong, but can't seem to pass
+ // file pointers down to this method from the mussa control class
+ // so each call to save a sequence appends to the file started by mussa_class
+ //save_file.open(save_file_path.c_str(), ios::app);
+
+ save_file << "<Sequence>" << endl;
+ save_file << sequence << endl;
+ save_file << "</Sequence>" << endl;
+
+ save_file << "<Annotations>" << endl;
+ save_file << species << endl;
+ for (annots_i = annots.begin(); annots_i != annots.end(); ++annots_i)
+ {
+ save_file << annots_i->start << " " << annots_i->end << " " ;
+ save_file << annots_i->name << " " << annots_i->type << endl;
+ }
+ save_file << "</Annotations>" << endl;
+ //save_file.close();
+}
+
+void
+Sequence::load_museq(string load_file_path, int seq_num)
+{
+ fstream load_file;
+ string file_data_line;
+ int seq_counter;
+ annot an_annot;
+ string::size_type space_split_i;
+ string annot_value;
+
+ annots.clear();
+ load_file.open(load_file_path.c_str(), ios::in);
+
+ seq_counter = 0;
+ // search for the seq_num-th sequence
+ while ( (!load_file.eof()) && (seq_counter < seq_num) )
+ {
+ getline(load_file,file_data_line);
+ if (file_data_line == "<Sequence>")
+ seq_counter++;
+ }
+ getline(load_file, file_data_line);
+ sequence = file_data_line;
+ getline(load_file, file_data_line);
+ getline(load_file, file_data_line);
+ if (file_data_line == "<Annotations>")
+ {
+ getline(load_file, file_data_line);
+ species = file_data_line;
+ while ( (!load_file.eof()) && (file_data_line != "</Annotations>") )
+ {
+ getline(load_file,file_data_line);
+ if ((file_data_line != "") && (file_data_line != "</Annotations>"))
+ {
+ // need to get 4 values...almost same code 4 times...
+ // get annot start index
+ space_split_i = file_data_line.find(" ");
+ annot_value = file_data_line.substr(0,space_split_i);
+ an_annot.start = atoi (annot_value.c_str());
+ file_data_line = file_data_line.substr(space_split_i+1);
+ // get annot end index
+ space_split_i = file_data_line.find(" ");
+ annot_value = file_data_line.substr(0,space_split_i);
+ an_annot.end = atoi (annot_value.c_str());
+
+ if (space_split_i == string::npos) // no entry for type or name
+ {
+ cout << "seq, annots - no type or name\n";
+ an_annot.type = "";
+ an_annot.name = "";
+ }
+ else // else get annot type
+ {
+ file_data_line = file_data_line.substr(space_split_i+1);
+ space_split_i = file_data_line.find(" ");
+ annot_value = file_data_line.substr(0,space_split_i);
+ an_annot.type = annot_value;
+ if (space_split_i == string::npos) // no entry for name
+ {
+ cout << "seq, annots - no name\n";
+ an_annot.name = "";
+ }
+ else // get annot name
+ {
+ file_data_line = file_data_line.substr(space_split_i+1);
+ space_split_i = file_data_line.find(" ");
+ annot_value = file_data_line.substr(0,space_split_i);
+ an_annot.type = annot_value;
+ }
+ }
+ annots.push_back(an_annot); // don't forget to actually add the annot
+ }
+ //cout << "seq, annots: " << an_annot.start << ", " << an_annot.end
+ // << "-->" << an_annot.type << "::" << an_annot.name << endl;
+ }
+ }
+ load_file.close();
+}
+
+
+string
+Sequence::rc_motif(string a_motif)
+{
+ string rev_comp;
+ char conversionTable[257];
+ int seq_i, table_i, len;
+
+ len = a_motif.length();
+ rev_comp.reserve(len);
+
+ for(table_i=0; table_i < 256; table_i++)
+ {
+ conversionTable[table_i] = '~';
+ }
+ // add end of string character for printing out table for testing purposes
+ conversionTable[256] = '\0';
+
+ // add in the characters for the bases we want to convert (IUPAC)
+ conversionTable[(int)'A'] = 'T';
+ conversionTable[(int)'T'] = 'A';
+ conversionTable[(int)'G'] = 'C';
+ conversionTable[(int)'C'] = 'G';
+ conversionTable[(int)'N'] = 'N';
+ conversionTable[(int)'M'] = 'K';
+ conversionTable[(int)'R'] = 'Y';
+ conversionTable[(int)'W'] = 'W';
+ conversionTable[(int)'S'] = 'S';
+ conversionTable[(int)'Y'] = 'R';
+ conversionTable[(int)'K'] = 'M';
+ conversionTable[(int)'V'] = 'B';
+ conversionTable[(int)'H'] = 'D';
+ conversionTable[(int)'D'] = 'H';
+ conversionTable[(int)'B'] = 'V';
+
+ // finally, the actual conversion loop
+ for(seq_i = len - 1; seq_i >= 0; seq_i--)
+ {
+ //cout << "** i = " << seq_i << " bp = " <<
+ table_i = (int) a_motif[seq_i];
+ rev_comp += conversionTable[table_i];
+ }
+
+ //cout << "seq: " << a_motif << endl;
+ //cout << "rc: " << rev_comp << endl;
+
+ return rev_comp;
+}
+
+string
+Sequence::motif_validate(string a_motif)
+{
+ string valid_motif;
+ int seq_i, len;
+
+ len = a_motif.length();
+ valid_motif.reserve(len);
+
+ // this just upcases IUPAC symbols. Eventually should return an error if non IUPAC is present.
+ // current nonIUPAC symbols are omitted, which is not reported atm
+ for(seq_i = 0; seq_i < len; seq_i++)
+ {
+ if ((a_motif[seq_i] == 'a') || (a_motif[seq_i] == 'A'))
+ valid_motif += 'A';
+ else if ((a_motif[seq_i] == 't') || (a_motif[seq_i] == 'T'))
+ valid_motif += 'T';
+ else if ((a_motif[seq_i] == 'g') || (a_motif[seq_i] == 'G'))
+ valid_motif += 'G';
+ else if ((a_motif[seq_i] == 'c') || (a_motif[seq_i] == 'C'))
+ valid_motif += 'C';
+ else if ((a_motif[seq_i] == 'n') || (a_motif[seq_i] == 'N'))
+ valid_motif += 'N';
+ else if ((a_motif[seq_i] == 'm') || (a_motif[seq_i] == 'M'))
+ valid_motif += 'M';
+ else if ((a_motif[seq_i] == 'r') || (a_motif[seq_i] == 'R'))
+ valid_motif += 'R';
+ else if ((a_motif[seq_i] == 'w') || (a_motif[seq_i] == 'W'))
+ valid_motif += 'W';
+ else if ((a_motif[seq_i] == 's') || (a_motif[seq_i] == 'S'))
+ valid_motif += 'S';
+ else if ((a_motif[seq_i] == 'y') || (a_motif[seq_i] == 'Y'))
+ valid_motif += 'Y';
+ else if ((a_motif[seq_i] == 'k') || (a_motif[seq_i] == 'K'))
+ valid_motif += 'G';
+ else if ((a_motif[seq_i] == 'v') || (a_motif[seq_i] == 'V'))
+ valid_motif += 'V';
+ else if ((a_motif[seq_i] == 'h') || (a_motif[seq_i] == 'H'))
+ valid_motif += 'H';
+ else if ((a_motif[seq_i] == 'd') || (a_motif[seq_i] == 'D'))
+ valid_motif += 'D';
+ else if ((a_motif[seq_i] == 'b') || (a_motif[seq_i] == 'B'))
+ valid_motif += 'B';
+ }
+
+ //cout << "valid_motif is: " << valid_motif << endl;
+
+ return valid_motif;
+}
+
+
+vector<int>
+Sequence::find_motif(string a_motif)
+{
+ vector<int> motif_match_starts;
+ string a_motif_rc;
+
+
+ motif_match_starts.clear();
+
+ //cout << "motif is: " << a_motif << endl;
+ a_motif = motif_validate(a_motif);
+ //cout << "motif is: " << a_motif << endl;
+
+
+ if (a_motif != "")
+ {
+ //cout << "Sequence: none blank motif\n";
+ motif_scan(a_motif, &motif_match_starts);
+
+ a_motif_rc = rc_motif(a_motif);
+ // make sure not to do search again if it is a palindrome
+ if (a_motif_rc != a_motif)
+ motif_scan(a_motif_rc, &motif_match_starts);
+ }
+ return motif_match_starts;
+}
+
+void
+Sequence::motif_scan(string a_motif, vector<int> * motif_match_starts)
+{
+ char * seq_c;
+ string::size_type seq_i;
+ int motif_i, motif_len;
+
+ // faster to loop thru the sequence as a old c string (ie char array)
+ seq_c = (char*)sequence.c_str();
+ //cout << "Sequence: motif, seq len = " << sequence.length() << endl;
+ motif_len = a_motif.length();
+
+ //cout << "motif_length: " << motif_len << endl;
+ //cout << "RAAARRRRR\n";
+
+ motif_i = 0;
+
+ //cout << "motif: " << a_motif << endl;
+
+ //cout << "Sequence: motif, length= " << length << endl;
+ seq_i = 0;
+ while (seq_i < sequence.length())
+ {
+ //cout << seq_c[seq_i];
+ //cout << seq_c[seq_i] << "?" << a_motif[motif_i] << ":" << motif_i << " ";
+ // this is pretty much a straight translation of Nora's python code
+ // to match iupac letter codes
+ if (a_motif[motif_i] =='N')
+ motif_i++;
+ else if (a_motif[motif_i] == seq_c[seq_i])
+ motif_i++;
+ else if ((a_motif[motif_i] =='M') &&
+ ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='C')))
+ motif_i++;
+ else if ((a_motif[motif_i] =='R') &&
+ ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='G')))
+ motif_i++;
+ else if ((a_motif[motif_i] =='W') &&
+ ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='T')))
+ motif_i++;
+ else if ((a_motif[motif_i] =='S') &&
+ ((seq_c[seq_i]=='C') || (seq_c[seq_i]=='G')))
+ motif_i++;
+ else if ((a_motif[motif_i] =='Y') &&
+ ((seq_c[seq_i]=='C') || (seq_c[seq_i]=='T')))
+ motif_i++;
+ else if ((a_motif[motif_i] =='K') &&
+ ((seq_c[seq_i]=='G') || (seq_c[seq_i]=='T')))
+ motif_i++;
+ else if ((a_motif[motif_i] =='V') &&
+ ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='C') ||
+ (seq_c[seq_i]=='G')))
+ motif_i++;
+ else if ((a_motif[seq_i] =='H') &&
+ ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='C') ||
+ (seq_c[seq_i]=='T')))
+ motif_i++;
+ else if ((a_motif[motif_i] =='D') &&
+ ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='G') ||
+ (seq_c[seq_i]=='T')))
+ motif_i++;
+ else if ((a_motif[motif_i] =='B') &&
+ ((seq_c[seq_i]=='C') || (seq_c[seq_i]=='G') ||
+ (seq_c[seq_i]=='T')))
+ motif_i++;
+
+ else
+ {
+ seq_i -= motif_i;
+ motif_i = 0;
+ }
+
+ // end Nora stuff, now we see if a match is found this pass
+ if (motif_i == motif_len)
+ {
+ //cout << "!!";
+ motif_match_starts->push_back(seq_i - motif_len + 1);
+ motif_i = 0;
+ }
+
+ seq_i++;
+ }
+ cout << endl;
+}
+
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-// ----------------------------------------
-// ---------- sequence.cc -----------
-// ----------------------------------------
-
-#include "sequence.hh"
-#include "mussa_exceptions.hh"
-
-#include <string>
-#include <iostream>
-
-using namespace std;
-
-Sequence::Sequence()
-{
-}
-
-Sequence::Sequence(string seq)
-{
- set_filtered_sequence(seq);
-}
-
-Sequence &Sequence::operator=(const Sequence& s)
-{
- if (this != &s) {
- sequence = s.sequence;
- header = s.header;
- species = s.species;
- annots = s.annots;
- }
- return *this;
-}
-
-Sequence &Sequence::operator=(const std::string& s)
-{
- set_filtered_sequence(s);
- return *this;
-}
-
-//! load a fasta file into a sequence
-/*!
- * \param file_path the location of the fasta file in the filesystem
- * \param seq_num which sequence in the file to load
- * \param start_index starting position in the fasta sequence, 0 for beginning
- * \param end_index ending position in the fasta sequence, 0 for end
- * \return error message, empty string if no error. (gag!)
- */
-void
-Sequence::load_fasta(string file_path, int seq_num,
- int start_index, int end_index)
-{
- fstream data_file;
- string file_data_line;
- int header_counter = 0;
- bool read_seq = true;
- string rev_comp;
- string sequence_raw;
- string seq_tmp; // holds sequence during basic filtering
-
- data_file.open(file_path.c_str(), ios::in);
-
- if (!data_file)
- {
- throw mussa_load_error("Sequence File: " + file_path + " not found");
- }
- // if file opened okay, read it
- else
- {
- // search for the header of the fasta sequence we want
- while ( (!data_file.eof()) && (header_counter < seq_num) )
- {
- getline(data_file,file_data_line);
- if (file_data_line.substr(0,1) == ">")
- header_counter++;
- }
-
- header = file_data_line.substr(1);
-
- sequence_raw = "";
-
- while ( !data_file.eof() && read_seq )
- {
- getline(data_file,file_data_line);
- if (file_data_line.substr(0,1) == ">")
- read_seq = false;
- else sequence_raw += file_data_line;
- }
-
- data_file.close();
-
- // Lastly, if subselection of the sequence was specified we keep cut out
- // and only keep that part
- // end_index = 0 means no end was specified, so cut to the end
- if (end_index == 0)
- end_index = sequence_raw.size();
-
- // sequence filtering for upcasing agctn and convert non AGCTN to N
- set_filtered_sequence(sequence_raw, start_index, end_index-start_index);
- }
-}
-
-void Sequence::set_filtered_sequence(const string &old_seq,
- string::size_type start,
- string::size_type count)
-{
- char conversionTable[257];
-
- if ( count == 0)
- count = old_seq.size() - start;
- sequence.clear();
- sequence.reserve(count);
-
- // Make a conversion table
-
- // everything we don't specify below will become 'N'
- for(int table_i=0; table_i < 256; table_i++)
- {
- conversionTable[table_i] = 'N';
- }
- // add end of string character for printing out table for testing purposes
- conversionTable[256] = '\0';
-
- // we want these to map to themselves - ie not to change
- conversionTable[(int)'A'] = 'A';
- conversionTable[(int)'T'] = 'T';
- conversionTable[(int)'G'] = 'G';
- conversionTable[(int)'C'] = 'C';
- // this is to upcase
- conversionTable[(int)'a'] = 'A';
- conversionTable[(int)'t'] = 'T';
- conversionTable[(int)'g'] = 'G';
- conversionTable[(int)'c'] = 'C';
-
- // finally, the actual conversion loop
- for(string::size_type seq_index = 0; seq_index < count; seq_index++)
- {
- sequence += conversionTable[ (int)old_seq[seq_index+start]];
- }
-}
-
- // this doesn't work properly under gcc 3.x ... it can't recognize toupper
- //transform(sequence.begin(), sequence.end(), sequence.begin(), toupper);
-
-
-void
-Sequence::load_annot(string file_path, int start_index, int end_index)
-{
- fstream data_file;
- string file_data_line;
- annot an_annot;
- string::size_type space_split_i;
- string annot_value;
- list<annot>::iterator list_i;
- string err_msg;
-
-
- annots.clear();
- data_file.open(file_path.c_str(), ios::in);
-
- if (!data_file)
- {
- throw mussa_load_error("Sequence File: " + file_path + " not found");
- }
- // if file opened okay, read it
- else
- {
- getline(data_file,file_data_line);
- species = file_data_line;
-
- // end_index = 0 means no end was specified, so cut to the end
- if (end_index == 0)
- end_index = sequence.length();
-
- //cout << "START: " << start_index << " END: " << end_index << endl;
-
- while ( !data_file.eof() )
- {
- getline(data_file,file_data_line);
- if (file_data_line != "")
- {
- // need to get 4 values...almost same code 4 times...
- // get annot start index
- space_split_i = file_data_line.find(" ");
- annot_value = file_data_line.substr(0,space_split_i);
- an_annot.start = atoi (annot_value.c_str());
- file_data_line = file_data_line.substr(space_split_i+1);
- // get annot end index
- space_split_i = file_data_line.find(" ");
- annot_value = file_data_line.substr(0,space_split_i);
- an_annot.end = atoi (annot_value.c_str());
- file_data_line = file_data_line.substr(space_split_i+1);
-
- //cout << "seq, annots: " << an_annot.start << ", " << an_annot.end
- // << endl;
-
- // get annot name
- space_split_i = file_data_line.find(" ");
- if (space_split_i == string::npos) // no entries for name & type
- {
- cout << "seq, annots - no name or type\n";
- an_annot.name = "";
- an_annot.type = "";
- }
- else
- {
- annot_value = file_data_line.substr(0,space_split_i);
- an_annot.name = annot_value;
- file_data_line = file_data_line.substr(space_split_i+1);
- // get annot type
- space_split_i = file_data_line.find(" ");
- if (space_split_i == string::npos) // no entry for type
- an_annot.type = "";
- else
- {
- annot_value = file_data_line.substr(0,space_split_i);
- an_annot.type = annot_value;
- }
- }
-
-
- // add annot to list if it falls within the range of sequence specified
- if ((start_index <= an_annot.start) && (end_index >= an_annot.end))
- {
- an_annot.start -= start_index;
- an_annot.end -= start_index;
- annots.push_back(an_annot);
- }
- else
- cout << "FAILED!!!!!!\n";
- }
- }
-
- data_file.close();
- /*
- // debugging check
- for(list_i = annots.begin(); list_i != annots.end(); ++list_i)
- {
- cout << (*list_i).start << "," << (*list_i).end << "\t";
- cout << (*list_i).name << "\t" << (*list_i).type << endl;
- }
- */
- }
-}
-
-bool Sequence::empty() const
-{
- return (size() == 0);
-}
-
-const std::list<annot> Sequence::annotations() const
-{
- return annots;
-}
-
-string::size_type Sequence::length() const
-{
- return size();
-}
-
-string::size_type Sequence::size() const
-{
- return sequence.size();
-}
-
-Sequence::iterator Sequence::begin()
-{
- return sequence.begin();
-}
-
-Sequence::const_iterator Sequence::begin() const
-{
- return sequence.begin();
-}
-
-Sequence::iterator Sequence::end()
-{
- return sequence.end();
-}
-
-Sequence::const_iterator Sequence::end() const
-{
- return sequence.end();
-}
-
-
-const string&
-Sequence::get_seq() const
-{
- return sequence;
-}
-
-
-string
-Sequence::subseq(int start, int end) const
-{
- return sequence.substr(start, end);
-}
-
-
-const char *
-Sequence::c_seq() const
-{
- return sequence.c_str();
-}
-
-string
-Sequence::rev_comp() const
-{
- string rev_comp;
- char conversionTable[257];
- int seq_i, table_i, len;
-
- len = sequence.length();
- rev_comp.reserve(len);
- // make a conversion table
- // init all parts of conversion table to '~' character
- // '~' I doubt will ever appear in a sequence file (jeez, I hope)
- // and may the fleas of 1000 camels infest the genitals of any biologist (and
- // seven generations of their progeny) who decides to make it mean
- // something special!!!
- // PS - double the curse for any smartass non-biologist who tries it as well
- for(table_i=0; table_i < 256; table_i++)
- {
- conversionTable[table_i] = '~';
- }
- // add end of string character for printing out table for testing purposes
- conversionTable[256] = '\0';
-
- // add in the characters for the bases we want to convert
- conversionTable[(int)'A'] = 'T';
- conversionTable[(int)'T'] = 'A';
- conversionTable[(int)'G'] = 'C';
- conversionTable[(int)'C'] = 'G';
- conversionTable[(int)'N'] = 'N';
-
- // finally, the actual conversion loop
- for(seq_i = len - 1; seq_i >= 0; seq_i--)
- {
- table_i = (int) sequence[seq_i];
- rev_comp += conversionTable[table_i];
- }
-
- return rev_comp;
-}
-
-
-const string&
-Sequence::get_header() const
-{
- return header;
-}
-/*
-//FIXME: i don't think this code is callable
-string
-Sequence::sp_name() const
-{
- return species;
-}
-*/
-
-void
-Sequence::set_seq(const string& a_seq)
-{
- set_filtered_sequence(a_seq);
-}
-
-
-/*
-string
-Sequence::species()
-{
- return species;
-}
-*/
-
-void
-Sequence::clear()
-{
- sequence = "";
- header = "";
- species = "";
- annots.clear();
-}
-
-void
-Sequence::save(fstream &save_file)
- //string save_file_path)
-{
- //fstream save_file;
- list<annot>::iterator annots_i;
-
- // not sure why, or if i'm doing something wrong, but can't seem to pass
- // file pointers down to this method from the mussa control class
- // so each call to save a sequence appends to the file started by mussa_class
- //save_file.open(save_file_path.c_str(), ios::app);
-
- save_file << "<Sequence>" << endl;
- save_file << sequence << endl;
- save_file << "</Sequence>" << endl;
-
- save_file << "<Annotations>" << endl;
- save_file << species << endl;
- for (annots_i = annots.begin(); annots_i != annots.end(); ++annots_i)
- {
- save_file << annots_i->start << " " << annots_i->end << " " ;
- save_file << annots_i->name << " " << annots_i->type << endl;
- }
- save_file << "</Annotations>" << endl;
- //save_file.close();
-}
-
-void
-Sequence::load_museq(string load_file_path, int seq_num)
-{
- fstream load_file;
- string file_data_line;
- int seq_counter;
- annot an_annot;
- string::size_type space_split_i;
- string annot_value;
-
- annots.clear();
- load_file.open(load_file_path.c_str(), ios::in);
-
- seq_counter = 0;
- // search for the seq_num-th sequence
- while ( (!load_file.eof()) && (seq_counter < seq_num) )
- {
- getline(load_file,file_data_line);
- if (file_data_line == "<Sequence>")
- seq_counter++;
- }
- getline(load_file, file_data_line);
- sequence = file_data_line;
- getline(load_file, file_data_line);
- getline(load_file, file_data_line);
- if (file_data_line == "<Annotations>")
- {
- getline(load_file, file_data_line);
- species = file_data_line;
- while ( (!load_file.eof()) && (file_data_line != "</Annotations>") )
- {
- getline(load_file,file_data_line);
- if ((file_data_line != "") && (file_data_line != "</Annotations>"))
- {
- // need to get 4 values...almost same code 4 times...
- // get annot start index
- space_split_i = file_data_line.find(" ");
- annot_value = file_data_line.substr(0,space_split_i);
- an_annot.start = atoi (annot_value.c_str());
- file_data_line = file_data_line.substr(space_split_i+1);
- // get annot end index
- space_split_i = file_data_line.find(" ");
- annot_value = file_data_line.substr(0,space_split_i);
- an_annot.end = atoi (annot_value.c_str());
-
- if (space_split_i == string::npos) // no entry for type or name
- {
- cout << "seq, annots - no type or name\n";
- an_annot.type = "";
- an_annot.name = "";
- }
- else // else get annot type
- {
- file_data_line = file_data_line.substr(space_split_i+1);
- space_split_i = file_data_line.find(" ");
- annot_value = file_data_line.substr(0,space_split_i);
- an_annot.type = annot_value;
- if (space_split_i == string::npos) // no entry for name
- {
- cout << "seq, annots - no name\n";
- an_annot.name = "";
- }
- else // get annot name
- {
- file_data_line = file_data_line.substr(space_split_i+1);
- space_split_i = file_data_line.find(" ");
- annot_value = file_data_line.substr(0,space_split_i);
- an_annot.type = annot_value;
- }
- }
- annots.push_back(an_annot); // don't forget to actually add the annot
- }
- //cout << "seq, annots: " << an_annot.start << ", " << an_annot.end
- // << "-->" << an_annot.type << "::" << an_annot.name << endl;
- }
- }
- load_file.close();
-}
-
-
-string
-Sequence::rc_motif(string a_motif)
-{
- string rev_comp;
- char conversionTable[257];
- int seq_i, table_i, len;
-
- len = a_motif.length();
- rev_comp.reserve(len);
-
- for(table_i=0; table_i < 256; table_i++)
- {
- conversionTable[table_i] = '~';
- }
- // add end of string character for printing out table for testing purposes
- conversionTable[256] = '\0';
-
- // add in the characters for the bases we want to convert (IUPAC)
- conversionTable[(int)'A'] = 'T';
- conversionTable[(int)'T'] = 'A';
- conversionTable[(int)'G'] = 'C';
- conversionTable[(int)'C'] = 'G';
- conversionTable[(int)'N'] = 'N';
- conversionTable[(int)'M'] = 'K';
- conversionTable[(int)'R'] = 'Y';
- conversionTable[(int)'W'] = 'W';
- conversionTable[(int)'S'] = 'S';
- conversionTable[(int)'Y'] = 'R';
- conversionTable[(int)'K'] = 'M';
- conversionTable[(int)'V'] = 'B';
- conversionTable[(int)'H'] = 'D';
- conversionTable[(int)'D'] = 'H';
- conversionTable[(int)'B'] = 'V';
-
- // finally, the actual conversion loop
- for(seq_i = len - 1; seq_i >= 0; seq_i--)
- {
- //cout << "** i = " << seq_i << " bp = " <<
- table_i = (int) a_motif[seq_i];
- rev_comp += conversionTable[table_i];
- }
-
- //cout << "seq: " << a_motif << endl;
- //cout << "rc: " << rev_comp << endl;
-
- return rev_comp;
-}
-
-string
-Sequence::motif_validate(string a_motif)
-{
- string valid_motif;
- int seq_i, len;
-
- len = a_motif.length();
- valid_motif.reserve(len);
-
- // this just upcases IUPAC symbols. Eventually should return an error if non IUPAC is present.
- // current nonIUPAC symbols are omitted, which is not reported atm
- for(seq_i = 0; seq_i < len; seq_i++)
- {
- if ((a_motif[seq_i] == 'a') || (a_motif[seq_i] == 'A'))
- valid_motif += 'A';
- else if ((a_motif[seq_i] == 't') || (a_motif[seq_i] == 'T'))
- valid_motif += 'T';
- else if ((a_motif[seq_i] == 'g') || (a_motif[seq_i] == 'G'))
- valid_motif += 'G';
- else if ((a_motif[seq_i] == 'c') || (a_motif[seq_i] == 'C'))
- valid_motif += 'C';
- else if ((a_motif[seq_i] == 'n') || (a_motif[seq_i] == 'N'))
- valid_motif += 'N';
- else if ((a_motif[seq_i] == 'm') || (a_motif[seq_i] == 'M'))
- valid_motif += 'M';
- else if ((a_motif[seq_i] == 'r') || (a_motif[seq_i] == 'R'))
- valid_motif += 'R';
- else if ((a_motif[seq_i] == 'w') || (a_motif[seq_i] == 'W'))
- valid_motif += 'W';
- else if ((a_motif[seq_i] == 's') || (a_motif[seq_i] == 'S'))
- valid_motif += 'S';
- else if ((a_motif[seq_i] == 'y') || (a_motif[seq_i] == 'Y'))
- valid_motif += 'Y';
- else if ((a_motif[seq_i] == 'k') || (a_motif[seq_i] == 'K'))
- valid_motif += 'G';
- else if ((a_motif[seq_i] == 'v') || (a_motif[seq_i] == 'V'))
- valid_motif += 'V';
- else if ((a_motif[seq_i] == 'h') || (a_motif[seq_i] == 'H'))
- valid_motif += 'H';
- else if ((a_motif[seq_i] == 'd') || (a_motif[seq_i] == 'D'))
- valid_motif += 'D';
- else if ((a_motif[seq_i] == 'b') || (a_motif[seq_i] == 'B'))
- valid_motif += 'B';
- }
-
- //cout << "valid_motif is: " << valid_motif << endl;
-
- return valid_motif;
-}
-
-
-vector<int>
-Sequence::find_motif(string a_motif)
-{
- vector<int> motif_match_starts;
- string a_motif_rc;
-
-
- motif_match_starts.clear();
-
- //cout << "motif is: " << a_motif << endl;
- a_motif = motif_validate(a_motif);
- //cout << "motif is: " << a_motif << endl;
-
-
- if (a_motif != "")
- {
- //cout << "Sequence: none blank motif\n";
- motif_scan(a_motif, &motif_match_starts);
-
- a_motif_rc = rc_motif(a_motif);
- // make sure not to do search again if it is a palindrome
- if (a_motif_rc != a_motif)
- motif_scan(a_motif_rc, &motif_match_starts);
- }
- return motif_match_starts;
-}
-
-void
-Sequence::motif_scan(string a_motif, vector<int> * motif_match_starts)
-{
- char * seq_c;
- string::size_type seq_i;
- int motif_i, motif_len;
-
- // faster to loop thru the sequence as a old c string (ie char array)
- seq_c = (char*)sequence.c_str();
- //cout << "Sequence: motif, seq len = " << sequence.length() << endl;
- motif_len = a_motif.length();
-
- //cout << "motif_length: " << motif_len << endl;
- //cout << "RAAARRRRR\n";
-
- motif_i = 0;
-
- //cout << "motif: " << a_motif << endl;
-
- //cout << "Sequence: motif, length= " << length << endl;
- seq_i = 0;
- while (seq_i < sequence.length())
- {
- //cout << seq_c[seq_i];
- //cout << seq_c[seq_i] << "?" << a_motif[motif_i] << ":" << motif_i << " ";
- // this is pretty much a straight translation of Nora's python code
- // to match iupac letter codes
- if (a_motif[motif_i] =='N')
- motif_i++;
- else if (a_motif[motif_i] == seq_c[seq_i])
- motif_i++;
- else if ((a_motif[motif_i] =='M') &&
- ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='C')))
- motif_i++;
- else if ((a_motif[motif_i] =='R') &&
- ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='G')))
- motif_i++;
- else if ((a_motif[motif_i] =='W') &&
- ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='T')))
- motif_i++;
- else if ((a_motif[motif_i] =='S') &&
- ((seq_c[seq_i]=='C') || (seq_c[seq_i]=='G')))
- motif_i++;
- else if ((a_motif[motif_i] =='Y') &&
- ((seq_c[seq_i]=='C') || (seq_c[seq_i]=='T')))
- motif_i++;
- else if ((a_motif[motif_i] =='K') &&
- ((seq_c[seq_i]=='G') || (seq_c[seq_i]=='T')))
- motif_i++;
- else if ((a_motif[motif_i] =='V') &&
- ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='C') ||
- (seq_c[seq_i]=='G')))
- motif_i++;
- else if ((a_motif[seq_i] =='H') &&
- ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='C') ||
- (seq_c[seq_i]=='T')))
- motif_i++;
- else if ((a_motif[motif_i] =='D') &&
- ((seq_c[seq_i]=='A') || (seq_c[seq_i]=='G') ||
- (seq_c[seq_i]=='T')))
- motif_i++;
- else if ((a_motif[motif_i] =='B') &&
- ((seq_c[seq_i]=='C') || (seq_c[seq_i]=='G') ||
- (seq_c[seq_i]=='T')))
- motif_i++;
-
- else
- {
- seq_i -= motif_i;
- motif_i = 0;
- }
-
- // end Nora stuff, now we see if a match is found this pass
- if (motif_i == motif_len)
- {
- //cout << "!!";
- motif_match_starts->push_back(seq_i - motif_len + 1);
- motif_i = 0;
- }
-
- seq_i++;
- }
- cout << endl;
-}
-
+++ /dev/null
-#ifndef _MUSSA_SEQUENCE_H_
-#define _MUSSA_SEQUENCE_H_
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-// ----------------------------------------
-// ---------- sequence.hh -----------
-// ----------------------------------------
-
-
-#include <fstream>
-#include <list>
-#include <string>
-#include <vector>
-
-// Sequence data class
-
-//! Attach annotation information to a sequence track
-struct annot
-{
- int start, end;
- std::string name, type;
-};
-
-//! sequence track for mussa.
-class Sequence
-{
- friend class ConnView;
- friend class SeqView;
- private:
- std::string sequence;
- std::string header;
- std::string species;
-
- std::list<annot> annots;
-
- void motif_scan(std::string a_motif, std::vector<int> * motif_match_starts);
- std::string rc_motif(std::string a_motif);
- std::string motif_validate(std::string a_motif);
- public:
- typedef std::string::iterator iterator;
- typedef std::string::const_iterator const_iterator;
- typedef std::string::size_type size_type;
-
- Sequence();
- Sequence(std::string seq);
- //! assignment to constant sequences
- Sequence &operator=(const Sequence&);
- Sequence &operator=(const std::string &);
-
- //! set sequence to a (sub)string containing nothing but AGCTN
- void set_filtered_sequence(const std::string& seq,
- std::string::size_type start=0,
- std::string::size_type count=0);
-
- //! load sequence AGCT from fasta file
- /*! \throws mussa_load_error
- */
- void load_fasta(const std::string file_path, int seq_num=1,
- int start_index=0, int end_index=0);
- //! load sequence annotations
- /*! \throws mussa_load_error
- */
- void load_annot(const std::string file_path, int start_index, int end_index);
- const std::list<annot> annotations() const;
-
- // simple access functions
- void set_seq(const std::string& a_seq);
- const std::string& get_seq() const;
- const char *c_seq() const;
- std::string subseq(int start, int end) const;
- std::string rev_comp() const;
-
- // string-like functions
- iterator begin();
- const_iterator begin() const;
- iterator end();
- const_iterator end() const;
- bool empty() const;
- //! alias for size, (included as this is much like a string)
- std::string::size_type length() const;
- //! the number of base pairs in this sequence
- std::string::size_type size() const;
- void clear();
-
- const std::string& get_header() const;
- std::vector<int> find_motif(std::string a_motif);
- void save(std::fstream &save_file);
- void load_museq(std::string load_file_path, int seq_num);
-};
-#endif
--- /dev/null
+#ifndef _MUSSA_SEQUENCE_H_
+#define _MUSSA_SEQUENCE_H_
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+// ----------------------------------------
+// ---------- sequence.hh -----------
+// ----------------------------------------
+
+
+#include <fstream>
+#include <list>
+#include <string>
+#include <vector>
+
+// Sequence data class
+
+//! Attach annotation information to a sequence track
+struct annot
+{
+ int start, end;
+ std::string name, type;
+};
+
+//! sequence track for mussa.
+class Sequence
+{
+ friend class ConnView;
+ friend class SeqView;
+ private:
+ std::string sequence;
+ std::string header;
+ std::string species;
+
+ std::list<annot> annots;
+
+ void motif_scan(std::string a_motif, std::vector<int> * motif_match_starts);
+ std::string rc_motif(std::string a_motif);
+ std::string motif_validate(std::string a_motif);
+ public:
+ typedef std::string::iterator iterator;
+ typedef std::string::const_iterator const_iterator;
+ typedef std::string::size_type size_type;
+
+ Sequence();
+ Sequence(std::string seq);
+ //! assignment to constant sequences
+ Sequence &operator=(const Sequence&);
+ Sequence &operator=(const std::string &);
+
+ //! set sequence to a (sub)string containing nothing but AGCTN
+ void set_filtered_sequence(const std::string& seq,
+ std::string::size_type start=0,
+ std::string::size_type count=0);
+
+ //! load sequence AGCT from fasta file
+ /*! \throws mussa_load_error
+ */
+ void load_fasta(const std::string file_path, int seq_num=1,
+ int start_index=0, int end_index=0);
+ //! load sequence annotations
+ /*! \throws mussa_load_error
+ */
+ void load_annot(const std::string file_path, int start_index, int end_index);
+ const std::list<annot> annotations() const;
+
+ // simple access functions
+ void set_seq(const std::string& a_seq);
+ const std::string& get_seq() const;
+ const char *c_seq() const;
+ std::string subseq(int start, int end) const;
+ std::string rev_comp() const;
+
+ // string-like functions
+ iterator begin();
+ const_iterator begin() const;
+ iterator end();
+ const_iterator end() const;
+ bool empty() const;
+ //! alias for size, (included as this is much like a string)
+ std::string::size_type length() const;
+ //! the number of base pairs in this sequence
+ std::string::size_type size() const;
+ void clear();
+
+ const std::string& get_header() const;
+ std::vector<int> find_motif(std::string a_motif);
+ void save(std::fstream &save_file);
+ void load_museq(std::string load_file_path, int seq_num);
+};
+#endif
CURDIR := $(BASEDIR)alg/test/
-SOURCES.cxx := test_conserved_path.cxx \
- test_flp.cxx \
- test_glsequence.cxx \
- test_color.cxx \
- test_main.cxx \
- test_mussa.cxx \
- test_nway.cxx \
- test_sequence.cxx
+SOURCES.cpp := test_conserved_path.cpp \
+ test_flp.cpp \
+ test_glsequence.cpp \
+ test_color.cpp \
+ test_main.cpp \
+ test_mussa.cpp \
+ test_nway.cpp \
+ test_sequence.cpp
-TESTSRC := $(addprefix $(CURDIR), $(SOURCES.cxx))
-TESTOBJ := $(TESTSRC:.cxx=$(OBJEXT))
+TESTSRC := $(addprefix $(CURDIR), $(SOURCES.cpp))
+TESTOBJ := $(TESTSRC:.cpp=$(OBJEXT))
SRC += $(TESTSRC)
CXXFLAGS +=
--- /dev/null
+#include <boost/test/auto_unit_test.hpp>
+#include <boost/test/floating_point_comparison.hpp>
+#include <string>
+
+#include "alg/color.hpp"
+
+using namespace std;
+
+BOOST_AUTO_TEST_CASE ( color )
+{
+ const float tolerance = 1e-6;
+ const float zero = 0.0;
+ const float dotone = 0.1;
+ const float dottwo = 0.2;
+ const float dotthree = 0.3;
+ const float dotfour = 0.4;
+ Color c1;
+ BOOST_CHECK_CLOSE (c1.r(), zero, tolerance );
+ BOOST_CHECK_CLOSE (c1.g(), zero, tolerance );
+ BOOST_CHECK_CLOSE (c1.b(), zero, tolerance );
+ BOOST_CHECK_CLOSE (c1.a(), zero, tolerance );
+
+ Color c2(dotone, dottwo, dotthree, dotfour);
+ BOOST_CHECK_CLOSE (c2.r(), dotone, tolerance );
+ BOOST_CHECK_CLOSE (c2.g(), dottwo, tolerance );
+ BOOST_CHECK_CLOSE (c2.b(), dotthree, tolerance );
+ BOOST_CHECK_CLOSE (c2.a(), dotfour, tolerance );
+
+ Color c3(c2);
+ BOOST_CHECK_CLOSE (c3.r(), dotone, tolerance );
+ BOOST_CHECK_CLOSE (c3.g(), dottwo, tolerance );
+ BOOST_CHECK_CLOSE (c3.b(), dotthree, tolerance );
+ BOOST_CHECK_CLOSE (c3.a(), dotfour, tolerance );
+ BOOST_CHECK_EQUAL ( c2, c3 );
+
+ const float *colors = c3.get();
+ BOOST_CHECK_CLOSE (colors[Color::RedChannel ], dotone, tolerance );
+ BOOST_CHECK_CLOSE (colors[Color::GreenChannel ], dottwo, tolerance );
+ BOOST_CHECK_CLOSE (colors[Color::BlueChannel ], dotthree, tolerance );
+ BOOST_CHECK_CLOSE (colors[Color::AlphaChannel ], dotfour, tolerance );
+}
+
+
+++ /dev/null
-#include <boost/test/auto_unit_test.hpp>
-#include <boost/test/floating_point_comparison.hpp>
-#include <string>
-
-#include "alg/color.h"
-
-using namespace std;
-
-BOOST_AUTO_TEST_CASE ( color )
-{
- const float tolerance = 1e-6;
- const float zero = 0.0;
- const float dotone = 0.1;
- const float dottwo = 0.2;
- const float dotthree = 0.3;
- const float dotfour = 0.4;
- Color c1;
- BOOST_CHECK_CLOSE (c1.r(), zero, tolerance );
- BOOST_CHECK_CLOSE (c1.g(), zero, tolerance );
- BOOST_CHECK_CLOSE (c1.b(), zero, tolerance );
- BOOST_CHECK_CLOSE (c1.a(), zero, tolerance );
-
- Color c2(dotone, dottwo, dotthree, dotfour);
- BOOST_CHECK_CLOSE (c2.r(), dotone, tolerance );
- BOOST_CHECK_CLOSE (c2.g(), dottwo, tolerance );
- BOOST_CHECK_CLOSE (c2.b(), dotthree, tolerance );
- BOOST_CHECK_CLOSE (c2.a(), dotfour, tolerance );
-
- Color c3(c2);
- BOOST_CHECK_CLOSE (c3.r(), dotone, tolerance );
- BOOST_CHECK_CLOSE (c3.g(), dottwo, tolerance );
- BOOST_CHECK_CLOSE (c3.b(), dotthree, tolerance );
- BOOST_CHECK_CLOSE (c3.a(), dotfour, tolerance );
- BOOST_CHECK_EQUAL ( c2, c3 );
-
- const float *colors = c3.get();
- BOOST_CHECK_CLOSE (colors[Color::RedChannel ], dotone, tolerance );
- BOOST_CHECK_CLOSE (colors[Color::GreenChannel ], dottwo, tolerance );
- BOOST_CHECK_CLOSE (colors[Color::BlueChannel ], dotthree, tolerance );
- BOOST_CHECK_CLOSE (colors[Color::AlphaChannel ], dotfour, tolerance );
-}
-
-
--- /dev/null
+#include <boost/test/auto_unit_test.hpp>
+#include <boost/assign/std/vector.hpp>
+using namespace boost::assign;
+
+#include <vector>
+using namespace std;
+
+#include "alg/conserved_path.hpp"
+
+//! write tests for our conserved path types (just to make sure they
+//! don't change on us.
+BOOST_AUTO_TEST_CASE ( conserved_path_simple )
+{
+ vector<int> path;
+ path += 3,4,5,1; // magic from boost assign
+
+ ConservedPath cp1;
+ BOOST_CHECK_EQUAL( cp1.size(), 0 ); //empty
+ BOOST_CHECK( cp1.begin() == cp1.end() );
+
+ cp1.score = 18;
+ cp1.track_indexes = path;
+ BOOST_CHECK_EQUAL( cp1.size(), path.size() );
+
+ ConservedPath cp2(18, path);
+ BOOST_CHECK_EQUAL (cp1, cp2);
+ BOOST_CHECK_EQUAL( cp2.size(), path.size() );
+
+ ConservedPath::iterator cp2_itor;
+ vector<int>::iterator path_itor;
+ for (cp2_itor = cp2.begin(), path_itor = path.begin();
+ cp2_itor != cp2.end() && path_itor != path.end();
+ ++cp2_itor, ++path_itor)
+ {
+ BOOST_CHECK_EQUAL( *cp2_itor, *path_itor );
+ }
+
+ ConservedPath cp3( cp2 );
+ BOOST_CHECK_EQUAL( cp3.size(), cp2.size() );
+ ConservedPath::iterator cp3_itor;
+ for (cp2_itor = cp2.begin(), cp3_itor = cp3.begin();
+ cp2_itor != cp2.end() && cp3_itor != cp3.end();
+ ++cp2_itor, ++cp3_itor)
+ {
+ BOOST_CHECK_EQUAL( *cp2_itor, *cp3_itor );
+ }
+}
+
+//! do vector like operations work?
+BOOST_AUTO_TEST_CASE ( conserved_path_vector )
+{
+ ConservedPath cp;
+ cp.score = 21.0;
+
+ BOOST_CHECK_EQUAL( cp.size(), 0 );
+ cp.push_back( 3 );
+ BOOST_CHECK_EQUAL( cp.size(), 1);
+ BOOST_CHECK_EQUAL( cp[0], 3 );
+ cp.push_back( 4 );
+ BOOST_CHECK_EQUAL( cp.size(), 2);
+ BOOST_CHECK_EQUAL( cp[1], 4 );
+ cp.pop_back();
+ BOOST_CHECK_EQUAL( cp.size(), 1 );
+}
+
+BOOST_AUTO_TEST_CASE ( extended_conserved_path_simple )
+{
+ vector<int> path;
+ path += 3,4,5,1; // magic from boost assign
+
+ ExtendedConservedPath ecp1;
+ ecp1.window_size = 30;
+ ecp1.score = 18;
+ ecp1.track_indexes = path;
+ BOOST_CHECK_EQUAL ( ecp1.size(), path.size() );
+
+ ExtendedConservedPath ecp2(30, 18.0, path);
+ BOOST_CHECK_EQUAL ( ecp1, ecp2 );
+ BOOST_CHECK_EQUAL ( ecp2.size(), path.size() );
+
+ ExtendedConservedPath ecp_ne(35, 20.0, path);
+ BOOST_CHECK(ecp2 != ecp_ne);
+
+ ConservedPath cp1;
+ cp1.score = 18;
+ cp1.track_indexes = path;
+
+ ExtendedConservedPath ecp3(30, cp1);
+ BOOST_CHECK_EQUAL( ecp2, ecp3 );
+ BOOST_CHECK_EQUAL( ecp3.size(), path.size() );
+}
+
+//! Can we grow succesfully?
+BOOST_AUTO_TEST_CASE ( extended_conserved_path_growth )
+{
+ vector<int> path_base;
+ path_base += 3,4,5,1; // magic from boost assign
+ vector<int> path_next;
+ path_next += 4,5,6,2;
+ vector<int> path_next_reversed;
+ path_next_reversed += 4,5,6,-2;
+ vector<int> path_not_next;
+ path_not_next += 4,5,6,5;
+ const int window_size = 4;
+
+ ExtendedConservedPath ecp_base(window_size, 20, path_base);
+ ConservedPath cp_next(25, path_next);
+ ConservedPath cp_next_reversed(25, path_next_reversed);
+ ConservedPath cp_not_next(22, path_not_next);
+
+ BOOST_CHECK(ecp_base.nextTo(cp_next));
+ BOOST_CHECK(!ecp_base.nextTo(cp_not_next));
+ // FIXME: should something like this actually extend?
+ BOOST_CHECK(!ecp_base.nextTo(cp_next_reversed));
+
+ const int growth = 2;
+ ecp_base.extend(growth);
+ BOOST_CHECK_EQUAL( ecp_base.window_size, window_size + growth );
+}
+++ /dev/null
-#include <boost/test/auto_unit_test.hpp>
-#include <boost/assign/std/vector.hpp>
-using namespace boost::assign;
-
-#include <vector>
-using namespace std;
-
-#include "alg/conserved_path.h"
-
-//! write tests for our conserved path types (just to make sure they
-//! don't change on us.
-BOOST_AUTO_TEST_CASE ( conserved_path_simple )
-{
- vector<int> path;
- path += 3,4,5,1; // magic from boost assign
-
- ConservedPath cp1;
- BOOST_CHECK_EQUAL( cp1.size(), 0 ); //empty
- BOOST_CHECK( cp1.begin() == cp1.end() );
-
- cp1.score = 18;
- cp1.track_indexes = path;
- BOOST_CHECK_EQUAL( cp1.size(), path.size() );
-
- ConservedPath cp2(18, path);
- BOOST_CHECK_EQUAL (cp1, cp2);
- BOOST_CHECK_EQUAL( cp2.size(), path.size() );
-
- ConservedPath::iterator cp2_itor;
- vector<int>::iterator path_itor;
- for (cp2_itor = cp2.begin(), path_itor = path.begin();
- cp2_itor != cp2.end() && path_itor != path.end();
- ++cp2_itor, ++path_itor)
- {
- BOOST_CHECK_EQUAL( *cp2_itor, *path_itor );
- }
-
- ConservedPath cp3( cp2 );
- BOOST_CHECK_EQUAL( cp3.size(), cp2.size() );
- ConservedPath::iterator cp3_itor;
- for (cp2_itor = cp2.begin(), cp3_itor = cp3.begin();
- cp2_itor != cp2.end() && cp3_itor != cp3.end();
- ++cp2_itor, ++cp3_itor)
- {
- BOOST_CHECK_EQUAL( *cp2_itor, *cp3_itor );
- }
-}
-
-//! do vector like operations work?
-BOOST_AUTO_TEST_CASE ( conserved_path_vector )
-{
- ConservedPath cp;
- cp.score = 21.0;
-
- BOOST_CHECK_EQUAL( cp.size(), 0 );
- cp.push_back( 3 );
- BOOST_CHECK_EQUAL( cp.size(), 1);
- BOOST_CHECK_EQUAL( cp[0], 3 );
- cp.push_back( 4 );
- BOOST_CHECK_EQUAL( cp.size(), 2);
- BOOST_CHECK_EQUAL( cp[1], 4 );
- cp.pop_back();
- BOOST_CHECK_EQUAL( cp.size(), 1 );
-}
-
-BOOST_AUTO_TEST_CASE ( extended_conserved_path_simple )
-{
- vector<int> path;
- path += 3,4,5,1; // magic from boost assign
-
- ExtendedConservedPath ecp1;
- ecp1.window_size = 30;
- ecp1.score = 18;
- ecp1.track_indexes = path;
- BOOST_CHECK_EQUAL ( ecp1.size(), path.size() );
-
- ExtendedConservedPath ecp2(30, 18.0, path);
- BOOST_CHECK_EQUAL ( ecp1, ecp2 );
- BOOST_CHECK_EQUAL ( ecp2.size(), path.size() );
-
- ExtendedConservedPath ecp_ne(35, 20.0, path);
- BOOST_CHECK(ecp2 != ecp_ne);
-
- ConservedPath cp1;
- cp1.score = 18;
- cp1.track_indexes = path;
-
- ExtendedConservedPath ecp3(30, cp1);
- BOOST_CHECK_EQUAL( ecp2, ecp3 );
- BOOST_CHECK_EQUAL( ecp3.size(), path.size() );
-}
-
-//! Can we grow succesfully?
-BOOST_AUTO_TEST_CASE ( extended_conserved_path_growth )
-{
- vector<int> path_base;
- path_base += 3,4,5,1; // magic from boost assign
- vector<int> path_next;
- path_next += 4,5,6,2;
- vector<int> path_next_reversed;
- path_next_reversed += 4,5,6,-2;
- vector<int> path_not_next;
- path_not_next += 4,5,6,5;
- const int window_size = 4;
-
- ExtendedConservedPath ecp_base(window_size, 20, path_base);
- ConservedPath cp_next(25, path_next);
- ConservedPath cp_next_reversed(25, path_next_reversed);
- ConservedPath cp_not_next(22, path_not_next);
-
- BOOST_CHECK(ecp_base.nextTo(cp_next));
- BOOST_CHECK(!ecp_base.nextTo(cp_not_next));
- // FIXME: should something like this actually extend?
- BOOST_CHECK(!ecp_base.nextTo(cp_next_reversed));
-
- const int growth = 2;
- ecp_base.extend(growth);
- BOOST_CHECK_EQUAL( ecp_base.window_size, window_size + growth );
-}
--- /dev/null
+#include <iostream>
+#include <list>
+
+#include <boost/test/auto_unit_test.hpp>
+#include <boost/filesystem/operations.hpp>
+#include <boost/filesystem/path.hpp>
+
+#include "alg/flp.hpp"
+#include "alg/sequence.hpp"
+#include <iostream>
+#include <list>
+
+BOOST_AUTO_TEST_CASE( flp_simple )
+{
+ FLPs f;
+ f.setup(5, 4);
+ f.seqcomp("AAGGTAAGGT", "AAGGTAAGGT", false);
+
+ // are the match_locations correct?
+ for (int i=0; i != f.size(); i++)
+ {
+ std::list<int> window_locations = f.match_locations(i);
+ std::list<FLPs::match> window_matches = f.matches(i);
+ std::list<int>::iterator loc_i = window_locations.begin();
+ std::list<FLPs::match>::iterator match_i = window_matches.begin();
+ for (; loc_i != window_locations.end(); ++loc_i, ++match_i)
+ {
+ // I'm missing pythons easy lists and in operator here.
+ if (i == 0) BOOST_CHECK( *loc_i == 0 || *loc_i == 5);
+ else if (i == 1) BOOST_CHECK( *loc_i == 1 || *loc_i == 6);
+ else if (i == 2) BOOST_CHECK( *loc_i == 2 );
+ else if (i == 3) BOOST_CHECK( *loc_i == 3 );
+ else if (i == 4) BOOST_CHECK( *loc_i == 4 );
+ else if (i == 6) BOOST_CHECK( *loc_i == 5 || *loc_i == 0);
+ BOOST_CHECK_EQUAL( *loc_i, match_i->index );
+ }
+ }
+}
+
+BOOST_AUTO_TEST_CASE( flp_save )
+{
+ std::string seq("AAGGCCTTAAGGCCTT");
+ int win_size = 4;
+ FLPs f1;
+ FLPs f2;
+ f1.setup(win_size,3);
+ f1.seqcomp(seq, seq, false);
+ std::string fname("flp_save_this_is_a_horrible_filename_because_"
+ "im_too_lazy_to_write_a_portable_mktmp.flp");
+
+ f1.save(fname);
+ f2.load(fname);
+ boost::filesystem::remove( boost::filesystem::path(fname) );
+
+ BOOST_CHECK_EQUAL( f1.size(), seq.size()-win_size+1);
+ BOOST_CHECK_EQUAL( f2.size(), seq.size()-win_size+1);
+ BOOST_CHECK_EQUAL( f1.size(), f2.size() );
+ for (int win=0; win < f1.size(); ++win)
+ {
+ std::list<FLPs::match> f1_matches = f1.matches(win);
+ std::list<FLPs::match> f2_matches = f2.matches(win);
+ std::list<FLPs::match>::const_iterator f1_match_i = f1_matches.begin();
+ std::list<FLPs::match>::const_iterator f2_match_i = f2_matches.begin();
+ for( ;
+ f1_match_i != f1_matches.end() && f2_match_i != f2_matches.end();
+ ++f1_match_i, ++f2_match_i)
+ {
+ BOOST_CHECK_EQUAL( *f1_match_i, *f2_match_i);
+ }
+ }
+}
+
+/*! Apparently when we run multiple seqcomps we want to
+ * save all the FLPs generated
+ */
+BOOST_AUTO_TEST_CASE( flp_reverse_compliment )
+{
+ FLPs f1;
+ Sequence s1("AAAATTTT");
+ Sequence s2("AACAGGGG");
+ f1.setup(4,3);
+ f1.seqcomp(s1.get_seq(), s2.get_seq(), false);
+ f1.seqcomp(s1.get_seq(), s2.rev_comp(), true);
+
+ FLPs f2;
+ f2.setup(4,3);
+ f2.seqcomp(s1.get_seq(), s2.rev_comp(), true);
+ f2.seqcomp(s1.get_seq(), s2.get_seq(), false);
+
+ // The order of doing the reverse compliment search shouldn't matter
+ // when we're using exactly the same sequence
+ BOOST_CHECK_EQUAL( f1.size(), f2.size() );
+ for (int i = 0; i < f1.size(); ++i )
+ {
+ BOOST_CHECK_EQUAL( f1.matches(i).size(), f2.matches(i).size() );
+ // FIXME: should we test the individual lists?
+ }
+}
+++ /dev/null
-#include <iostream>
-#include <list>
-
-#include <boost/test/auto_unit_test.hpp>
-#include <boost/filesystem/operations.hpp>
-#include <boost/filesystem/path.hpp>
-
-#include "alg/flp.hh"
-#include "alg/sequence.hh"
-#include <iostream>
-#include <list>
-
-BOOST_AUTO_TEST_CASE( flp_simple )
-{
- FLPs f;
- f.setup(5, 4);
- f.seqcomp("AAGGTAAGGT", "AAGGTAAGGT", false);
-
- // are the match_locations correct?
- for (int i=0; i != f.size(); i++)
- {
- std::list<int> window_locations = f.match_locations(i);
- std::list<FLPs::match> window_matches = f.matches(i);
- std::list<int>::iterator loc_i = window_locations.begin();
- std::list<FLPs::match>::iterator match_i = window_matches.begin();
- for (; loc_i != window_locations.end(); ++loc_i, ++match_i)
- {
- // I'm missing pythons easy lists and in operator here.
- if (i == 0) BOOST_CHECK( *loc_i == 0 || *loc_i == 5);
- else if (i == 1) BOOST_CHECK( *loc_i == 1 || *loc_i == 6);
- else if (i == 2) BOOST_CHECK( *loc_i == 2 );
- else if (i == 3) BOOST_CHECK( *loc_i == 3 );
- else if (i == 4) BOOST_CHECK( *loc_i == 4 );
- else if (i == 6) BOOST_CHECK( *loc_i == 5 || *loc_i == 0);
- BOOST_CHECK_EQUAL( *loc_i, match_i->index );
- }
- }
-}
-
-BOOST_AUTO_TEST_CASE( flp_save )
-{
- std::string seq("AAGGCCTTAAGGCCTT");
- int win_size = 4;
- FLPs f1;
- FLPs f2;
- f1.setup(win_size,3);
- f1.seqcomp(seq, seq, false);
- std::string fname("flp_save_this_is_a_horrible_filename_because_"
- "im_too_lazy_to_write_a_portable_mktmp.flp");
-
- f1.save(fname);
- f2.load(fname);
- boost::filesystem::remove( boost::filesystem::path(fname) );
-
- BOOST_CHECK_EQUAL( f1.size(), seq.size()-win_size+1);
- BOOST_CHECK_EQUAL( f2.size(), seq.size()-win_size+1);
- BOOST_CHECK_EQUAL( f1.size(), f2.size() );
- for (int win=0; win < f1.size(); ++win)
- {
- std::list<FLPs::match> f1_matches = f1.matches(win);
- std::list<FLPs::match> f2_matches = f2.matches(win);
- std::list<FLPs::match>::const_iterator f1_match_i = f1_matches.begin();
- std::list<FLPs::match>::const_iterator f2_match_i = f2_matches.begin();
- for( ;
- f1_match_i != f1_matches.end() && f2_match_i != f2_matches.end();
- ++f1_match_i, ++f2_match_i)
- {
- BOOST_CHECK_EQUAL( *f1_match_i, *f2_match_i);
- }
- }
-}
-
-/*! Apparently when we run multiple seqcomps we want to
- * save all the FLPs generated
- */
-BOOST_AUTO_TEST_CASE( flp_reverse_compliment )
-{
- FLPs f1;
- Sequence s1("AAAATTTT");
- Sequence s2("AACAGGGG");
- f1.setup(4,3);
- f1.seqcomp(s1.get_seq(), s2.get_seq(), false);
- f1.seqcomp(s1.get_seq(), s2.rev_comp(), true);
-
- FLPs f2;
- f2.setup(4,3);
- f2.seqcomp(s1.get_seq(), s2.rev_comp(), true);
- f2.seqcomp(s1.get_seq(), s2.get_seq(), false);
-
- // The order of doing the reverse compliment search shouldn't matter
- // when we're using exactly the same sequence
- BOOST_CHECK_EQUAL( f1.size(), f2.size() );
- for (int i = 0; i < f1.size(); ++i )
- {
- BOOST_CHECK_EQUAL( f1.matches(i).size(), f2.matches(i).size() );
- // FIXME: should we test the individual lists?
- }
-}
--- /dev/null
+#include <boost/test/auto_unit_test.hpp>
+
+#include <string>
+
+#include "alg/glsequence.hpp"
+#include "alg/sequence.hpp"
+
+using namespace std;
+
+BOOST_AUTO_TEST_CASE ( glsequence_operator_equal )
+{
+ // I don't trust my operator = hack so lets make sure it works.
+ string s0("AAGGCCTT");
+ string s1("TTGGCCAA");
+ Sequence seq0(s0);
+ Sequence seq1(s1);
+
+ GlSequence glseq0(seq0);
+ BOOST_CHECK (glseq0.sequence().get_seq() == s0);
+ GlSequence glseq1(seq1);
+ GlSequence glseq_copy0(glseq0);
+
+ BOOST_CHECK(glseq_copy0.sequence().get_seq() == glseq0.sequence().get_seq());
+ BOOST_CHECK( &(glseq_copy0.sequence()) == &(glseq0.sequence()));
+
+ glseq0 = glseq1;
+
+ BOOST_CHECK( glseq0.sequence().get_seq() == s1 );
+}
+
+BOOST_AUTO_TEST_CASE( glsequence_color )
+{
+ Color black(0.0, 0.0, 0.0, 0.0);
+ Color c(0.1, 0.2, 0.3, 0.4);
+ Sequence seq("AAGGCCTT");
+ GlSequence s(seq);
+
+ BOOST_CHECK_EQUAL(s.color(), black );
+ s.setColor( c );
+ BOOST_CHECK_EQUAL( s.color(), c );
+}
+
+BOOST_AUTO_TEST_CASE( glsequence_renderable )
+{
+ Sequence seq("AAGGCCTT");
+ GlSequence s(seq);
+
+ // way more base pairs than viewport pixel width
+ BOOST_CHECK_EQUAL(s.is_sequence_renderable( 0, 1000, 500), false );
+ // way fewer basepairs than viewport pixel width
+ BOOST_CHECK_EQUAL(s.is_sequence_renderable( 0, 10, 500), true);
+}
+
+BOOST_AUTO_TEST_CASE( glsequence_sequence )
+{
+ string seq_string("AAGGCCTTNNAAGGCCTTNNAAGGCCTTNN");
+ string::size_type seqlen = seq_string.size();
+ Sequence seq(seq_string);
+ GlSequence glseq(seq);
+
+ BOOST_CHECK( glseq.sequence_begin(0, 50) == seq.begin() );
+ // always make sure we return seq.end() regardless of how much extra
+ // is asked for
+ BOOST_CHECK( glseq.sequence_end(0, seqlen+10) == seq.end() );
+ // do we get the right end pointer?
+ BOOST_CHECK( glseq.sequence_end(0, 5) == seq.begin()+5 );
+
+ // when we request far too much sequence what do we get?
+ BOOST_CHECK( glseq.sequence_begin(seqlen+10, seqlen+20) == seq.end() );
+ BOOST_CHECK( glseq.sequence_end(seqlen+10, seqlen+20) == seq.end() );
+
+ // we cant ask for reversed sequences with sequence_begin/end
+ BOOST_CHECK( glseq.sequence_begin(10, 5) == seq.end() );
+ BOOST_CHECK( glseq.sequence_end(10, 5) == seq.end() );
+
+ Sequence::const_iterator seq_itor;
+
+ // if we as for an empty segment? start and end should equal
+ seq_itor = glseq.sequence_begin(10, 10);
+ BOOST_CHECK( seq_itor == glseq.sequence_end(10, 10) );
+
+ // reuse seq_itor downhere
+ string::const_iterator str_itor;
+ for(str_itor = seq.begin(),
+ seq_itor = glseq.sequence_begin();
+ str_itor != seq.end() and
+ seq_itor != glseq.sequence_end();
+ ++str_itor, ++seq_itor)
+ {
+ BOOST_CHECK_EQUAL( *str_itor, *seq_itor );
+ }
+}
+
+// make sure the computation of the leftmost and rightmost base is correct
+BOOST_AUTO_TEST_CASE( glsequence_leftright_base )
+{
+ std::string seq_string = "AAGGCCTT";
+ Sequence seq(seq_string);
+ GlSequence glseq(seq);
+
+ BOOST_CHECK_EQUAL( glseq.leftbase( -50.0 ), 0 );
+ BOOST_CHECK_EQUAL( glseq.leftbase( 0.5 ), 1 );
+ BOOST_CHECK_EQUAL( glseq.rightbase( 1000.0 ), seq_string.size() );
+ BOOST_CHECK_EQUAL( glseq.rightbase( seq_string.size()-0.5),
+ seq_string.size()-1);
+}
+++ /dev/null
-#include <boost/test/auto_unit_test.hpp>
-
-#include <string>
-
-#include "alg/glsequence.h"
-#include "alg/sequence.hh"
-
-using namespace std;
-
-BOOST_AUTO_TEST_CASE ( glsequence_operator_equal )
-{
- // I don't trust my operator = hack so lets make sure it works.
- string s0("AAGGCCTT");
- string s1("TTGGCCAA");
- Sequence seq0(s0);
- Sequence seq1(s1);
-
- GlSequence glseq0(seq0);
- BOOST_CHECK (glseq0.sequence().get_seq() == s0);
- GlSequence glseq1(seq1);
- GlSequence glseq_copy0(glseq0);
-
- BOOST_CHECK(glseq_copy0.sequence().get_seq() == glseq0.sequence().get_seq());
- BOOST_CHECK( &(glseq_copy0.sequence()) == &(glseq0.sequence()));
-
- glseq0 = glseq1;
-
- BOOST_CHECK( glseq0.sequence().get_seq() == s1 );
-}
-
-BOOST_AUTO_TEST_CASE( glsequence_color )
-{
- Color black(0.0, 0.0, 0.0, 0.0);
- Color c(0.1, 0.2, 0.3, 0.4);
- Sequence seq("AAGGCCTT");
- GlSequence s(seq);
-
- BOOST_CHECK_EQUAL(s.color(), black );
- s.setColor( c );
- BOOST_CHECK_EQUAL( s.color(), c );
-}
-
-BOOST_AUTO_TEST_CASE( glsequence_renderable )
-{
- Sequence seq("AAGGCCTT");
- GlSequence s(seq);
-
- // way more base pairs than viewport pixel width
- BOOST_CHECK_EQUAL(s.is_sequence_renderable( 0, 1000, 500), false );
- // way fewer basepairs than viewport pixel width
- BOOST_CHECK_EQUAL(s.is_sequence_renderable( 0, 10, 500), true);
-}
-
-BOOST_AUTO_TEST_CASE( glsequence_sequence )
-{
- string seq_string("AAGGCCTTNNAAGGCCTTNNAAGGCCTTNN");
- string::size_type seqlen = seq_string.size();
- Sequence seq(seq_string);
- GlSequence glseq(seq);
-
- BOOST_CHECK( glseq.sequence_begin(0, 50) == seq.begin() );
- // always make sure we return seq.end() regardless of how much extra
- // is asked for
- BOOST_CHECK( glseq.sequence_end(0, seqlen+10) == seq.end() );
- // do we get the right end pointer?
- BOOST_CHECK( glseq.sequence_end(0, 5) == seq.begin()+5 );
-
- // when we request far too much sequence what do we get?
- BOOST_CHECK( glseq.sequence_begin(seqlen+10, seqlen+20) == seq.end() );
- BOOST_CHECK( glseq.sequence_end(seqlen+10, seqlen+20) == seq.end() );
-
- // we cant ask for reversed sequences with sequence_begin/end
- BOOST_CHECK( glseq.sequence_begin(10, 5) == seq.end() );
- BOOST_CHECK( glseq.sequence_end(10, 5) == seq.end() );
-
- Sequence::const_iterator seq_itor;
-
- // if we as for an empty segment? start and end should equal
- seq_itor = glseq.sequence_begin(10, 10);
- BOOST_CHECK( seq_itor == glseq.sequence_end(10, 10) );
-
- // reuse seq_itor downhere
- string::const_iterator str_itor;
- for(str_itor = seq.begin(),
- seq_itor = glseq.sequence_begin();
- str_itor != seq.end() and
- seq_itor != glseq.sequence_end();
- ++str_itor, ++seq_itor)
- {
- BOOST_CHECK_EQUAL( *str_itor, *seq_itor );
- }
-}
-
-// make sure the computation of the leftmost and rightmost base is correct
-BOOST_AUTO_TEST_CASE( glsequence_leftright_base )
-{
- std::string seq_string = "AAGGCCTT";
- Sequence seq(seq_string);
- GlSequence glseq(seq);
-
- BOOST_CHECK_EQUAL( glseq.leftbase( -50.0 ), 0 );
- BOOST_CHECK_EQUAL( glseq.leftbase( 0.5 ), 1 );
- BOOST_CHECK_EQUAL( glseq.rightbase( 1000.0 ), seq_string.size() );
- BOOST_CHECK_EQUAL( glseq.rightbase( seq_string.size()-0.5),
- seq_string.size()-1);
-}
--- /dev/null
+#define BOOST_AUTO_TEST_MAIN
+#include <boost/test/auto_unit_test.hpp>
+
+++ /dev/null
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
-
--- /dev/null
+#include <boost/test/auto_unit_test.hpp>
+
+#include <string>
+
+#include "alg/mussa.hpp"
+
+//! can we initialize a mussa object?
+BOOST_AUTO_TEST_CASE( mussa_simple )
+{
+ Mussa m;
+ BOOST_CHECK_EQUAL(m.get_name(), "" );
+ BOOST_CHECK_EQUAL(m.get_window(), 0);
+ BOOST_CHECK_EQUAL(m.get_threshold(), 0);
+ BOOST_CHECK_EQUAL(m.get_analysis_mode(), Mussa::TransitiveNway);
+ m.set_name( "hello" );
+ BOOST_CHECK_EQUAL(m.get_name(), "hello" );
+ m.set_window(30);
+ BOOST_CHECK_EQUAL(m.get_window(), 30);
+ m.set_threshold(21);
+ BOOST_CHECK_EQUAL(m.get_threshold(), 21);
+ m.set_analysis_mode(Mussa::RadialNway);
+ BOOST_CHECK_EQUAL(m.get_analysis_mode(), Mussa::RadialNway);
+
+ m.clear();
+ BOOST_CHECK_EQUAL(m.get_name(), "" );
+ BOOST_CHECK_EQUAL(m.get_window(), 0);
+ BOOST_CHECK_EQUAL(m.get_threshold(), 0);
+ BOOST_CHECK_EQUAL(m.get_analysis_mode(), Mussa::TransitiveNway);
+}
+
+BOOST_AUTO_TEST_CASE( mussa_analysis_name )
+{
+ Mussa m;
+ m.set_analysis_mode( Mussa::TransitiveNway );
+ BOOST_CHECK_EQUAL( m.get_analysis_mode_name(), "Transitive" );
+ m.set_analysis_mode( Mussa::RadialNway );
+ BOOST_CHECK_EQUAL( m.get_analysis_mode_name(), "Radial" );
+ m.set_analysis_mode( Mussa::EntropyNway );
+ BOOST_CHECK_EQUAL( m.get_analysis_mode_name(), "Entropy" );
+ m.set_analysis_mode( Mussa::RecursiveNway);
+ BOOST_CHECK_EQUAL( m.get_analysis_mode_name(), "[deprecated] Recursive" );
+}
+
+BOOST_AUTO_TEST_CASE( mussa_sequences )
+{
+ std::string s0("AAAANNNN");
+ std::string s1("GGGGNNNN");
+ std::string s2("TTTTNNNN");
+
+ Mussa analysis;
+ analysis.add_a_seq(s0);
+ analysis.add_a_seq(s1);
+ analysis.add_a_seq(s2);
+
+ BOOST_CHECK_EQUAL( analysis.sequences().size(), 3 );
+ BOOST_CHECK_EQUAL( analysis.sequences()[0].get_seq(), s0);
+ BOOST_CHECK_EQUAL( analysis.sequences()[1].get_seq(), s1);
+ BOOST_CHECK_EQUAL( analysis.sequences()[2].get_seq(), s2);
+}
+
+// for some reason we can call nway once safely but it
+// somehow changed things and caused a segfault
+// fixed by adding a return statement in trans_path_search
+BOOST_AUTO_TEST_CASE ( empty_mussa_set_threshold )
+{
+ Mussa m;
+ m.set_soft_thres(15);
+ m.nway();
+
+ m.set_soft_thres(25);
+ m.nway();
+}
+
+#include <unistd.h>
+BOOST_AUTO_TEST_CASE( mussa_load_mupa )
+{
+ Mussa m1;
+ chdir( "examples" );
+ m1.load_mupa_file( "mck3test.mupa" );
+ m1.analyze(0, 0);
+ BOOST_CHECK_EQUAL( m1.get_name(), std::string("mck3test") );
+ BOOST_CHECK( m1.size() > 0 );
+
+ Mussa m2;
+ std::string saved_analysis_path("mck3test_w30_t20");
+ m2.load( saved_analysis_path );
+ chdir( ".." );
+
+ BOOST_CHECK_EQUAL( m2.get_name(), saved_analysis_path );
+ BOOST_CHECK_EQUAL( m1.size(), m2.size() );
+
+}
+
+BOOST_AUTO_TEST_CASE( mussa_load_full_path )
+{
+ Mussa m1;
+ chdir( "examples" );
+ const int bufsize = 1024;
+ char path_buf[bufsize];
+ getcwd(path_buf, bufsize);
+ std::string path(path_buf);
+ chdir( ".." );
+ path += "/mck3test.mupa";
+ m1.load_mupa_file( path );
+ m1.analyze(0, 0);
+
+ BOOST_CHECK( m1.size() > 0);
+}
+++ /dev/null
-#include <boost/test/auto_unit_test.hpp>
-
-#include <string>
-
-#include "alg/mussa_class.hh"
-
-//! can we initialize a mussa object?
-BOOST_AUTO_TEST_CASE( mussa_simple )
-{
- Mussa m;
- BOOST_CHECK_EQUAL(m.get_name(), "" );
- BOOST_CHECK_EQUAL(m.get_window(), 0);
- BOOST_CHECK_EQUAL(m.get_threshold(), 0);
- BOOST_CHECK_EQUAL(m.get_analysis_mode(), Mussa::TransitiveNway);
- m.set_name( "hello" );
- BOOST_CHECK_EQUAL(m.get_name(), "hello" );
- m.set_window(30);
- BOOST_CHECK_EQUAL(m.get_window(), 30);
- m.set_threshold(21);
- BOOST_CHECK_EQUAL(m.get_threshold(), 21);
- m.set_analysis_mode(Mussa::RadialNway);
- BOOST_CHECK_EQUAL(m.get_analysis_mode(), Mussa::RadialNway);
-
- m.clear();
- BOOST_CHECK_EQUAL(m.get_name(), "" );
- BOOST_CHECK_EQUAL(m.get_window(), 0);
- BOOST_CHECK_EQUAL(m.get_threshold(), 0);
- BOOST_CHECK_EQUAL(m.get_analysis_mode(), Mussa::TransitiveNway);
-}
-
-BOOST_AUTO_TEST_CASE( mussa_analysis_name )
-{
- Mussa m;
- m.set_analysis_mode( Mussa::TransitiveNway );
- BOOST_CHECK_EQUAL( m.get_analysis_mode_name(), "Transitive" );
- m.set_analysis_mode( Mussa::RadialNway );
- BOOST_CHECK_EQUAL( m.get_analysis_mode_name(), "Radial" );
- m.set_analysis_mode( Mussa::EntropyNway );
- BOOST_CHECK_EQUAL( m.get_analysis_mode_name(), "Entropy" );
- m.set_analysis_mode( Mussa::RecursiveNway);
- BOOST_CHECK_EQUAL( m.get_analysis_mode_name(), "[deprecated] Recursive" );
-}
-
-BOOST_AUTO_TEST_CASE( mussa_sequences )
-{
- std::string s0("AAAANNNN");
- std::string s1("GGGGNNNN");
- std::string s2("TTTTNNNN");
-
- Mussa analysis;
- analysis.add_a_seq(s0);
- analysis.add_a_seq(s1);
- analysis.add_a_seq(s2);
-
- BOOST_CHECK_EQUAL( analysis.sequences().size(), 3 );
- BOOST_CHECK_EQUAL( analysis.sequences()[0].get_seq(), s0);
- BOOST_CHECK_EQUAL( analysis.sequences()[1].get_seq(), s1);
- BOOST_CHECK_EQUAL( analysis.sequences()[2].get_seq(), s2);
-}
-
-// for some reason we can call nway once safely but it
-// somehow changed things and caused a segfault
-// fixed by adding a return statement in trans_path_search
-BOOST_AUTO_TEST_CASE ( empty_mussa_set_threshold )
-{
- Mussa m;
- m.set_soft_thres(15);
- m.nway();
-
- m.set_soft_thres(25);
- m.nway();
-}
-
-#include <unistd.h>
-BOOST_AUTO_TEST_CASE( mussa_load_mupa )
-{
- Mussa m1;
- chdir( "examples" );
- m1.load_mupa_file( "mck3test.mupa" );
- m1.analyze(0, 0);
- BOOST_CHECK_EQUAL( m1.get_name(), std::string("mck3test") );
- BOOST_CHECK( m1.size() > 0 );
-
- Mussa m2;
- std::string saved_analysis_path("mck3test_w30_t20");
- m2.load( saved_analysis_path );
- chdir( ".." );
-
- BOOST_CHECK_EQUAL( m2.get_name(), saved_analysis_path );
- BOOST_CHECK_EQUAL( m1.size(), m2.size() );
-
-}
-
-BOOST_AUTO_TEST_CASE( mussa_load_full_path )
-{
- Mussa m1;
- chdir( "examples" );
- const int bufsize = 1024;
- char path_buf[bufsize];
- getcwd(path_buf, bufsize);
- std::string path(path_buf);
- chdir( ".." );
- path += "/mck3test.mupa";
- m1.load_mupa_file( path );
- m1.analyze(0, 0);
-
- BOOST_CHECK( m1.size() > 0);
-}
--- /dev/null
+#include <boost/test/auto_unit_test.hpp>
+
+#include <string>
+#include <iostream>
+
+#include "alg/mussa.hpp"
+#include "alg/nway_paths.hpp"
+#include "alg/sequence.hpp"
+
+using namespace std;
+
+//! there should be no matches
+BOOST_AUTO_TEST_CASE( nway_null )
+{
+ string s0("AAAANNNN");
+ string s1("GGGGNNNN");
+ string s2("TTTTNNNN");
+
+ Mussa analysis;
+ analysis.add_a_seq(s0);
+ analysis.add_a_seq(s1);
+ analysis.add_a_seq(s2);
+ analysis.analyze(4,3);
+ NwayPaths npath = analysis.paths();
+ // there should be no paths for these sequences
+ for (std::list<ConservedPath >::iterator pathz_i = npath.pathz.begin();
+ pathz_i != npath.pathz.end();
+ ++pathz_i)
+ {
+ BOOST_CHECK_EQUAL( pathz_i->size(), 0);
+ }
+}
+
+BOOST_AUTO_TEST_CASE( nway_test )
+{
+ string s0("ATATGCGC");
+ string s1("GGGGGGGC");
+ Sequence seq1(s1);
+
+ Mussa analysis;
+ analysis.add_a_seq(s0);
+ analysis.add_a_seq(s1);
+ analysis.analyze(4,3);
+ NwayPaths npath = analysis.paths();
+ for (std::list<ConservedPath >::iterator pathz_i = npath.pathz.begin();
+ pathz_i != npath.pathz.end();
+ ++pathz_i)
+ {
+ for( ConservedPath::iterator path_i = pathz_i->begin();
+ path_i != pathz_i->end();
+ ++path_i)
+ {
+ BOOST_CHECK( *path_i == 4 || *path_i == -4);
+ }
+ }
+}
+
+
+++ /dev/null
-#include <boost/test/auto_unit_test.hpp>
-
-#include <string>
-#include <iostream>
-
-#include "alg/mussa_class.hh"
-#include "alg/nway_paths.hh"
-#include "alg/sequence.hh"
-
-using namespace std;
-
-//! there should be no matches
-BOOST_AUTO_TEST_CASE( nway_null )
-{
- string s0("AAAANNNN");
- string s1("GGGGNNNN");
- string s2("TTTTNNNN");
-
- Mussa analysis;
- analysis.add_a_seq(s0);
- analysis.add_a_seq(s1);
- analysis.add_a_seq(s2);
- analysis.analyze(4,3);
- NwayPaths npath = analysis.paths();
- // there should be no paths for these sequences
- for (std::list<ConservedPath >::iterator pathz_i = npath.pathz.begin();
- pathz_i != npath.pathz.end();
- ++pathz_i)
- {
- BOOST_CHECK_EQUAL( pathz_i->size(), 0);
- }
-}
-
-BOOST_AUTO_TEST_CASE( nway_test )
-{
- string s0("ATATGCGC");
- string s1("GGGGGGGC");
- Sequence seq1(s1);
-
- Mussa analysis;
- analysis.add_a_seq(s0);
- analysis.add_a_seq(s1);
- analysis.analyze(4,3);
- NwayPaths npath = analysis.paths();
- for (std::list<ConservedPath >::iterator pathz_i = npath.pathz.begin();
- pathz_i != npath.pathz.end();
- ++pathz_i)
- {
- for( ConservedPath::iterator path_i = pathz_i->begin();
- path_i != pathz_i->end();
- ++path_i)
- {
- BOOST_CHECK( *path_i == 4 || *path_i == -4);
- }
- }
-}
-
-
--- /dev/null
+#include <boost/test/auto_unit_test.hpp>
+
+#include "alg/sequence.hpp"
+#include "mussa_exceptions.hpp"
+
+//! when we try to load a missing file, do we get an error?
+BOOST_AUTO_TEST_CASE( sequence_load_exception )
+{
+ Sequence s;
+ // there should be errors when we try to load something that doesn't exist
+ BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
+ BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
+}
+
+//! Do simple operations work correctly?
+BOOST_AUTO_TEST_CASE( sequence_filter )
+{
+ Sequence s1("AATTGGCC");
+ BOOST_CHECK_EQUAL(s1.get_seq(), "AATTGGCC");
+
+ Sequence s2("aattggcc");
+ BOOST_CHECK_EQUAL(s2.get_seq(), "AATTGGCC");
+ BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
+ BOOST_CHECK_EQUAL(s2.size(), s2.get_seq().size());
+ BOOST_CHECK_EQUAL(s2.c_seq(), s2.get_seq().c_str());
+
+ Sequence s3("asdfg");
+ BOOST_CHECK_EQUAL(s3.get_seq(), "ANNNG");
+ BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
+
+ s3.set_filtered_sequence("AAGGCCTT", 0, 2);
+ BOOST_CHECK_EQUAL(s3.get_seq(), "AA");
+ s3.set_filtered_sequence("AAGGCCTT", 2, 2);
+ BOOST_CHECK_EQUAL( s3.get_seq(), "GG");
+ s3.set_filtered_sequence("AAGGCCTT", 4);
+ BOOST_CHECK_EQUAL( s3.get_seq(), "CCTT");
+
+ s3.clear();
+ BOOST_CHECK_EQUAL(s3.get_seq(), "");
+
+ s3.set_seq("AAGGFF");
+ BOOST_CHECK_EQUAL(s3.get_seq(), "AAGGNN");
+}
+
+//! Can we load data from a file
+BOOST_AUTO_TEST_CASE( sequence_load )
+{
+ Sequence s;
+ s.load_fasta("examples/seq/human_mck_pro.fa");
+ BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
+ BOOST_CHECK_EQUAL(s.get_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
+ "muscle creatine kinase gene (CKMM), "
+ "5' flank");
+}
+
+BOOST_AUTO_TEST_CASE ( sequence_empty )
+{
+ Sequence s;
+ BOOST_CHECK_EQUAL( s.empty(), true );
+ s = "AAAGGG";
+ BOOST_CHECK_EQUAL( s.empty(), false );
+}
+
+BOOST_AUTO_TEST_CASE ( sequence_iterators )
+{
+ std::string seq_string = "AAGGCCTTNNTATA";
+ Sequence s(seq_string);
+ const Sequence cs(s);
+ std::string::size_type count = 0;
+
+ std::string::iterator str_itor;
+ Sequence::iterator s_itor;
+ Sequence::const_iterator cs_itor;
+
+ for( str_itor = seq_string.begin(),
+ s_itor = s.begin(),
+ cs_itor = cs.begin();
+ str_itor != seq_string.end() and
+ s_itor != s.end() and
+ cs_itor != cs.end();
+ ++str_itor, ++s_itor, ++cs_itor, ++count)
+ {
+ BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
+ BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
+ BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
+ }
+ BOOST_CHECK_EQUAL( seq_string.size(), count );
+ BOOST_CHECK_EQUAL( s.size(), count );
+ BOOST_CHECK_EQUAL( cs.size(), count );
+}
+++ /dev/null
-#include <boost/test/auto_unit_test.hpp>
-
-#include "alg/sequence.hh"
-#include "mussa_exceptions.hh"
-
-//! when we try to load a missing file, do we get an error?
-BOOST_AUTO_TEST_CASE( sequence_load_exception )
-{
- Sequence s;
- // there should be errors when we try to load something that doesn't exist
- BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
- BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
-}
-
-//! Do simple operations work correctly?
-BOOST_AUTO_TEST_CASE( sequence_filter )
-{
- Sequence s1("AATTGGCC");
- BOOST_CHECK_EQUAL(s1.get_seq(), "AATTGGCC");
-
- Sequence s2("aattggcc");
- BOOST_CHECK_EQUAL(s2.get_seq(), "AATTGGCC");
- BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
- BOOST_CHECK_EQUAL(s2.size(), s2.get_seq().size());
- BOOST_CHECK_EQUAL(s2.c_seq(), s2.get_seq().c_str());
-
- Sequence s3("asdfg");
- BOOST_CHECK_EQUAL(s3.get_seq(), "ANNNG");
- BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
-
- s3.set_filtered_sequence("AAGGCCTT", 0, 2);
- BOOST_CHECK_EQUAL(s3.get_seq(), "AA");
- s3.set_filtered_sequence("AAGGCCTT", 2, 2);
- BOOST_CHECK_EQUAL( s3.get_seq(), "GG");
- s3.set_filtered_sequence("AAGGCCTT", 4);
- BOOST_CHECK_EQUAL( s3.get_seq(), "CCTT");
-
- s3.clear();
- BOOST_CHECK_EQUAL(s3.get_seq(), "");
-
- s3.set_seq("AAGGFF");
- BOOST_CHECK_EQUAL(s3.get_seq(), "AAGGNN");
-}
-
-//! Can we load data from a file
-BOOST_AUTO_TEST_CASE( sequence_load )
-{
- Sequence s;
- s.load_fasta("examples/seq/human_mck_pro.fa");
- BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
- BOOST_CHECK_EQUAL(s.get_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
- "muscle creatine kinase gene (CKMM), "
- "5' flank");
-}
-
-BOOST_AUTO_TEST_CASE ( sequence_empty )
-{
- Sequence s;
- BOOST_CHECK_EQUAL( s.empty(), true );
- s = "AAAGGG";
- BOOST_CHECK_EQUAL( s.empty(), false );
-}
-
-BOOST_AUTO_TEST_CASE ( sequence_iterators )
-{
- std::string seq_string = "AAGGCCTTNNTATA";
- Sequence s(seq_string);
- const Sequence cs(s);
- std::string::size_type count = 0;
-
- std::string::iterator str_itor;
- Sequence::iterator s_itor;
- Sequence::const_iterator cs_itor;
-
- for( str_itor = seq_string.begin(),
- s_itor = s.begin(),
- cs_itor = cs.begin();
- str_itor != seq_string.end() and
- s_itor != s.end() and
- cs_itor != cs.end();
- ++str_itor, ++s_itor, ++cs_itor, ++count)
- {
- BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
- BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
- BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
- }
- BOOST_CHECK_EQUAL( seq_string.size(), count );
- BOOST_CHECK_EQUAL( s.size(), count );
- BOOST_CHECK_EQUAL( cs.size(), count );
-}
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+#include "gui/AnnotWindow.hpp"
+#include <iostream>
+#include <FL/fl_show_colormap.H>
+
+using namespace std;
+
+annot_color
+new_blank_annot()
+{
+ annot_color *a_annot;
+
+ a_annot = new annot_color;
+ a_annot->type = "";
+ a_annot->color = (Fl_Color) 5;
+ //cout << "type: " << a_annot->type << endl;
+
+ return *a_annot;
+}
+
+
+void
+cb_annot_color(Fl_Button* o, void* v)
+{
+ annot_instance * blah = (annot_instance *) v;
+ AnnotWindow* T= blah->mw_ptr;
+ T->cb_annot_color_i(o,blah->index);
+}
+
+AnnotWindow::AnnotWindow(int w, int h, const char* title,
+ vector<annot_color> * some_annots):Fl_Window(w,h,title)
+{
+ int i, annot_num;
+
+ the_annots = some_annots;
+ annot_count = 0;
+
+ annot_color_buttons.clear();
+
+ begin();
+ annot_input_pack = new Fl_Pack(0, 0, w, h);
+ annot_input_pack->spacing(4);
+
+ // button to add new annot inputs
+ add_annot = new Fl_Button(0,0,100,24,"Add Annot Slot");
+ add_annot->callback((Fl_Callback*)add_annot_cb, this);
+ annot_input_pack->add(add_annot);
+ // test button to make sure annot data is being stored
+ test = new Fl_Button(0,0,100,24,"show annots");
+ test->callback((Fl_Callback*)print_cb, this);
+ annot_input_pack->add(test);
+
+ // creat an initial set of annot input widgets and attach to annot vector
+ annot_num = some_annots->size();
+ for (i = 0; i < annot_num; i++)
+ {
+ add_annot_input(i);
+ annot_count++;
+ }
+
+ add(annot_input_pack);
+
+ end();
+ resizable(this);
+ show();
+}
+
+ //tmp_input->user_data((void*) i);
+
+AnnotWindow::~AnnotWindow(){}
+
+void
+AnnotWindow::add_annot_input(int index)
+{
+ Fl_Output * new_input;
+ Fl_Button *new_color_button;
+ annot_instance * something;
+ Fl_Pack * annot_hor_pack;
+
+
+ something = new annot_instance;
+ something->mw_ptr = this;
+ something->index = index;
+
+ annot_hor_pack = new Fl_Pack(0, 0, w(), 24);
+ annot_hor_pack->type(Fl_Pack::HORIZONTAL);
+ annot_hor_pack->spacing(4);
+
+ // setup the color display/selection button
+ new_color_button = new Fl_Button(0, 0, 24, 24, "");
+ new_color_button->color((*the_annots)[index].color);
+ new_color_button->box(FL_FLAT_BOX);
+ new_color_button->callback((Fl_Callback*)cb_annot_color, (void*) something);
+ annot_color_buttons.push_back(new_color_button);
+ annot_hor_pack->add(new_color_button);
+
+
+ // setup the annot inputs
+ new_input = new Fl_Output(0, 0, 200, 24, "");
+ new_input->value( ((*the_annots)[index].type).c_str() );
+ //new_input->callback((Fl_Callback*)cb_annot_in, (void*) something);
+ annot_ins.push_back(new_input);
+ annot_hor_pack->add(new_input);
+
+ annot_input_pack->add(annot_hor_pack);
+}
+/*
+ cout << "fee\n";
+ cout << "fie\n";
+ cout << "foe\n";
+ cout << "fum\n";
+*/
+
+void
+AnnotWindow::cb_annot_in_i(Fl_Input* o, int i)
+{
+ (*the_annots)[i].type = o->value();
+}
+
+void
+AnnotWindow::cb_annot_color_i(Fl_Button* o, int i)
+{
+ //Fl_Color new_color;
+
+ (*the_annots)[i].color = fl_show_colormap((*the_annots)[i].color);
+ //annot_color_buttons[i]->
+ o->color((*the_annots)[i].color);
+ redraw();
+}
+
+void AnnotWindow::add_annot_cb(Fl_Button* o, void* v)
+{
+ AnnotWindow* T=(AnnotWindow*)v;
+ T->add_annot_cb_real(o,v);
+}
+
+
+void AnnotWindow::add_annot_cb_real(Fl_Button* , void*)
+{
+ annot_color blank_annot;
+
+ //blank_annot.name = "";
+ //blank_annot.seq = "";
+ blank_annot = new_blank_annot();
+ (*the_annots).push_back(blank_annot);
+ add_annot_input(annot_count++);
+ redraw();
+}
+
+
+void AnnotWindow::print_cb(Fl_Button* o, void* v)
+{
+ AnnotWindow* T=(AnnotWindow*)v;
+ T->print_cb_real(o,v);
+}
+
+
+void AnnotWindow::print_cb_real(Fl_Button* , void*)
+{
+ int i;
+
+ for (i = 0; i < annot_count; i++)
+ cout << (*the_annots)[i].type << endl;
+}
+
+/*
+void
+cb_annot_in(Fl_Input* o, void* v)
+{
+ annot_instance * blah = (annot_instance *) v;
+ AnnotWindow* T= blah->mw_ptr;
+ T->cb_annot_in_i(o,blah->index);
+}
+
+
+*/
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-#include "AnnotWindow.hh"
-#include <iostream>
-#include <FL/fl_show_colormap.H>
-
-using namespace std;
-
-annot_color
-new_blank_annot()
-{
- annot_color *a_annot;
-
- a_annot = new annot_color;
- a_annot->type = "";
- a_annot->color = (Fl_Color) 5;
- //cout << "type: " << a_annot->type << endl;
-
- return *a_annot;
-}
-
-
-void
-cb_annot_color(Fl_Button* o, void* v)
-{
- annot_instance * blah = (annot_instance *) v;
- AnnotWindow* T= blah->mw_ptr;
- T->cb_annot_color_i(o,blah->index);
-}
-
-AnnotWindow::AnnotWindow(int w, int h, const char* title,
- vector<annot_color> * some_annots):Fl_Window(w,h,title)
-{
- int i, annot_num;
-
- the_annots = some_annots;
- annot_count = 0;
-
- annot_color_buttons.clear();
-
- begin();
- annot_input_pack = new Fl_Pack(0, 0, w, h);
- annot_input_pack->spacing(4);
-
- // button to add new annot inputs
- add_annot = new Fl_Button(0,0,100,24,"Add Annot Slot");
- add_annot->callback((Fl_Callback*)add_annot_cb, this);
- annot_input_pack->add(add_annot);
- // test button to make sure annot data is being stored
- test = new Fl_Button(0,0,100,24,"show annots");
- test->callback((Fl_Callback*)print_cb, this);
- annot_input_pack->add(test);
-
- // creat an initial set of annot input widgets and attach to annot vector
- annot_num = some_annots->size();
- for (i = 0; i < annot_num; i++)
- {
- add_annot_input(i);
- annot_count++;
- }
-
- add(annot_input_pack);
-
- end();
- resizable(this);
- show();
-}
-
- //tmp_input->user_data((void*) i);
-
-AnnotWindow::~AnnotWindow(){}
-
-void
-AnnotWindow::add_annot_input(int index)
-{
- Fl_Output * new_input;
- Fl_Button *new_color_button;
- annot_instance * something;
- Fl_Pack * annot_hor_pack;
-
-
- something = new annot_instance;
- something->mw_ptr = this;
- something->index = index;
-
- annot_hor_pack = new Fl_Pack(0, 0, w(), 24);
- annot_hor_pack->type(Fl_Pack::HORIZONTAL);
- annot_hor_pack->spacing(4);
-
- // setup the color display/selection button
- new_color_button = new Fl_Button(0, 0, 24, 24, "");
- new_color_button->color((*the_annots)[index].color);
- new_color_button->box(FL_FLAT_BOX);
- new_color_button->callback((Fl_Callback*)cb_annot_color, (void*) something);
- annot_color_buttons.push_back(new_color_button);
- annot_hor_pack->add(new_color_button);
-
-
- // setup the annot inputs
- new_input = new Fl_Output(0, 0, 200, 24, "");
- new_input->value( ((*the_annots)[index].type).c_str() );
- //new_input->callback((Fl_Callback*)cb_annot_in, (void*) something);
- annot_ins.push_back(new_input);
- annot_hor_pack->add(new_input);
-
- annot_input_pack->add(annot_hor_pack);
-}
-/*
- cout << "fee\n";
- cout << "fie\n";
- cout << "foe\n";
- cout << "fum\n";
-*/
-
-void
-AnnotWindow::cb_annot_in_i(Fl_Input* o, int i)
-{
- (*the_annots)[i].type = o->value();
-}
-
-void
-AnnotWindow::cb_annot_color_i(Fl_Button* o, int i)
-{
- //Fl_Color new_color;
-
- (*the_annots)[i].color = fl_show_colormap((*the_annots)[i].color);
- //annot_color_buttons[i]->
- o->color((*the_annots)[i].color);
- redraw();
-}
-
-void AnnotWindow::add_annot_cb(Fl_Button* o, void* v)
-{
- AnnotWindow* T=(AnnotWindow*)v;
- T->add_annot_cb_real(o,v);
-}
-
-
-void AnnotWindow::add_annot_cb_real(Fl_Button* , void*)
-{
- annot_color blank_annot;
-
- //blank_annot.name = "";
- //blank_annot.seq = "";
- blank_annot = new_blank_annot();
- (*the_annots).push_back(blank_annot);
- add_annot_input(annot_count++);
- redraw();
-}
-
-
-void AnnotWindow::print_cb(Fl_Button* o, void* v)
-{
- AnnotWindow* T=(AnnotWindow*)v;
- T->print_cb_real(o,v);
-}
-
-
-void AnnotWindow::print_cb_real(Fl_Button* , void*)
-{
- int i;
-
- for (i = 0; i < annot_count; i++)
- cout << (*the_annots)[i].type << endl;
-}
-
-/*
-void
-cb_annot_in(Fl_Input* o, void* v)
-{
- annot_instance * blah = (annot_instance *) v;
- AnnotWindow* T= blah->mw_ptr;
- T->cb_annot_in_i(o,blah->index);
-}
-
-
-*/
+++ /dev/null
-#ifndef _MUSSA_GUI_ANNOT_WINDOW_H_
-#define _MUSSA_GUI_ANNOT_WINDOW_H_
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-#include <list>
-#include <string>
-#include <vector>
-
-#include <FL/Fl_Window.H>
-#include <FL/Fl_Button.H>
-
-#include <FL/Fl_Input.H>
-#include <FL/Fl_Output.H>
-#include <FL/Fl_Pack.H>
-
-#include "MotifWindow.hh"
-
-struct annot_color
-{
- std::string type;
- Fl_Color color;
-};
-
-//typedef annot_ptr *annot;
-
-
-class AnnotWindow : public Fl_Window
-{
- public:
- AnnotWindow(int w, int h, const char* title,
- std::vector<annot_color> * some_annots);
- ~AnnotWindow();
- Fl_Pack * annot_input_pack;
- std::list<Fl_Output*> annot_ins;
- std::vector<Fl_Button*> annot_color_buttons;
- std::list<Fl_Input*> name_ins;
- Fl_Button* test;
- Fl_Button* add_annot;
-
- void cb_annot_in_i(Fl_Input*, int i);
- void cb_annot_color_i(Fl_Button* o, int i);
-
- private:
- std::vector<annot_color> * the_annots;
- int annot_count;
-
- void add_annot_input(int index);
-
- static void add_annot_cb(Fl_Button*, void*);
- inline void add_annot_cb_real(Fl_Button*, void*);
-
- static void print_cb(Fl_Button*, void*);
- inline void print_cb_real(Fl_Button*, void*);
-};
-
-// crazy whacked shite Titus taught me to do to get an index value associated
-// with each instance of an input associated with the callback...
-struct annot_instance
-{
- AnnotWindow * mw_ptr;
- int index;
-};
-
-annot_color new_blank_annot();
-#endif
--- /dev/null
+#ifndef _MUSSA_GUI_ANNOT_WINDOW_H_
+#define _MUSSA_GUI_ANNOT_WINDOW_H_
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+#include <list>
+#include <string>
+#include <vector>
+
+#include <FL/Fl_Window.H>
+#include <FL/Fl_Button.H>
+
+#include <FL/Fl_Input.H>
+#include <FL/Fl_Output.H>
+#include <FL/Fl_Pack.H>
+
+#include "gui/MotifWindow.hpp"
+
+struct annot_color
+{
+ std::string type;
+ Fl_Color color;
+};
+
+//typedef annot_ptr *annot;
+
+
+class AnnotWindow : public Fl_Window
+{
+ public:
+ AnnotWindow(int w, int h, const char* title,
+ std::vector<annot_color> * some_annots);
+ ~AnnotWindow();
+ Fl_Pack * annot_input_pack;
+ std::list<Fl_Output*> annot_ins;
+ std::vector<Fl_Button*> annot_color_buttons;
+ std::list<Fl_Input*> name_ins;
+ Fl_Button* test;
+ Fl_Button* add_annot;
+
+ void cb_annot_in_i(Fl_Input*, int i);
+ void cb_annot_color_i(Fl_Button* o, int i);
+
+ private:
+ std::vector<annot_color> * the_annots;
+ int annot_count;
+
+ void add_annot_input(int index);
+
+ static void add_annot_cb(Fl_Button*, void*);
+ inline void add_annot_cb_real(Fl_Button*, void*);
+
+ static void print_cb(Fl_Button*, void*);
+ inline void print_cb_real(Fl_Button*, void*);
+};
+
+// crazy whacked shite Titus taught me to do to get an index value associated
+// with each instance of an input associated with the callback...
+struct annot_instance
+{
+ AnnotWindow * mw_ptr;
+ int index;
+};
+
+annot_color new_blank_annot();
+#endif
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+#include "gui/ConnView.hpp"
+
+#include <iomanip>
+#include <math.h>
+
+#include <FL/Fl.H>
+#include <FL/fl_draw.H>
+
+using namespace std;
+
+void
+ConnView::setup(string name, int sq_num, int win_len,
+ vector<Sequence> *some_seqs,
+ NwayPaths *some_paths)
+{
+ int i, i2, seq_length;
+ Sequence a_seq;
+ motif blank_motif;
+ annot_color new_annot;
+
+
+ analysis_name = name;
+ seq_num = sq_num;
+ window = win_len;
+ S = some_seqs;
+ P = some_paths;
+
+ cout << "num of paths = " << some_paths->refined_pathz.size() << endl;
+
+ cout << "x()=" << x() << " y()=" << y() << " w()=" << w() << " h()=" << h();
+ cout << endl;
+
+ max_seq_len = 0;
+ for(i = 0; i < seq_num; ++i)
+ {
+ a_seq = (*S)[i];
+ cout << a_seq.size() << endl;
+ seq_length = a_seq.size();
+ seq_lens.push_back(seq_length);
+ if (seq_length > max_seq_len)
+ max_seq_len = seq_length;
+ if (seq_length < 1000)
+ seq_scales.push_back(1);
+ else if (seq_length < 1000000)
+ seq_scales.push_back(2);
+ else
+ seq_scales.push_back(3);
+ }
+
+ name_pad = 80;
+ y_pad = 20;
+
+ x_scale_factor = (float) max_seq_len / (w() - name_pad);
+ cout << "scale factor is " << x_scale_factor << endl;
+ y_seq_incre = (h()-(y_pad*2)) / (seq_num - 1);
+
+
+ drag_start = -1000;
+ drag_end = -1000;
+ ref_seq_num = 0;
+
+ dragging = false;
+ selected = false;
+
+ highlight.clear();
+ show_bars = false;
+ show_lines = false;
+ bar_interval = max_seq_len / 20;
+ line_interval = max_seq_len / 20;
+ ref_seq_num = 0;
+
+
+ some_motifs.clear();
+ for(i = 0; i < 5; ++i)
+ {
+ blank_motif = new_blank_motif();
+ some_motifs.push_back(blank_motif);
+ }
+
+ // find all unique annotation type ids
+ some_annots.clear();
+ vector<annot_color>::iterator annot_type_i;
+ list<annot>::iterator annot_i;
+
+ // loop thru all sequences
+ for(i2 = 0; i2 < seq_num; i2++)
+ {
+ cout << "ConnView: annotation loop\n";
+ // loop thru all annotation entries in this sequence
+ for(annot_i = (*S)[i2].annots.begin(); annot_i != (*S)[i2].annots.end(); ++annot_i)
+ {
+ cout << annot_i->start << ", " << annot_i->end << " : ";
+ cout << annot_i->name << " " << annot_i->type << endl;
+ // loop thru annotation types
+ annot_type_i = some_annots.begin();
+ bool type_unfound = true;
+ while ((annot_type_i != some_annots.end()) && type_unfound)
+ {
+ if (annot_i->type == annot_type_i->type)
+ type_unfound = false; // stop search if found
+ ++annot_type_i;
+ }
+ //if unfound, then add to list
+ if (type_unfound)
+ {
+ new_annot = new_blank_annot();
+ new_annot.type = annot_i->type;
+ some_annots.push_back(new_annot);
+ }
+ }
+ }
+}
+
+
+void
+ConnView::scale_paths()
+{
+ ExtendedConservedPath a_path;
+ list<ExtendedConservedPath >::iterator pathz_i;
+ int i2;
+
+
+ scaled_pathz.clear();
+
+ for(pathz_i = P->refined_pathz.begin(); pathz_i != P->refined_pathz.end(); ++pathz_i)
+ {
+ a_path = *pathz_i;
+ a_path.window_size = (int)(a_path.window_size / x_scale_factor);
+ for(i2 = 0; i2 != a_path.size(); i2++)
+ {
+ a_path[i2] = (int) (a_path[i2] / x_scale_factor);
+ }
+ scaled_pathz.push_back(a_path);
+ }
+}
+
+void
+ConnView::toggle_bars()
+{
+ show_bars = !show_bars;
+ redraw();
+}
+
+void
+ConnView::set_bar_interval(int new_bar_len)
+{
+ bar_interval = new_bar_len;
+ cout << "bar interval = " << bar_interval << endl;
+ redraw();
+}
+
+void
+ConnView::toggle_lines()
+{
+ show_lines = !show_lines;
+ redraw();
+}
+
+void
+ConnView::set_line_interval(int new_line_len)
+{
+ line_interval = new_line_len;
+ cout << "line interval = " << line_interval << endl;
+ redraw();
+}
+
+
+void
+ConnView::draw()
+{
+ // this is temporary - check if new motifs have been added
+ check_new_motifs();
+
+ // clear drawing area and set background to white
+ fl_color(FL_WHITE);
+ fl_rectf(x(), y(), w(), h());
+
+ // draw the scale indicators if they are on
+ // put into own method soon...
+ int i, div_num, x_loc;
+ float div_len_scaled;
+
+ if (show_bars)
+ {
+ div_num = max_seq_len / bar_interval;
+ div_len_scaled = ((float) bar_interval) / x_scale_factor;
+ fl_color(230,230,230);
+ for(i = 0; i <= div_num; i+=2)
+ {
+ x_loc = (int)(i * div_len_scaled+x());
+ fl_rectf(x_loc, y(), (int) div_len_scaled, h());
+ }
+ }
+
+ if (show_lines)
+ {
+ div_num = max_seq_len / line_interval;
+ div_len_scaled = ((float) line_interval) / x_scale_factor;
+ fl_color(0,0,0);
+ fl_line_style(FL_SOLID, 1, NULL);
+ for(i = 0; i <= div_num; i++)
+ {
+ x_loc = (int)(i * div_len_scaled+x());
+ fl_line(x_loc, y(), x_loc, h()+y());
+ }
+ }
+
+
+ // divide up the space with some light blue lines
+ fl_color(150,200,255);
+ fl_line_style(FL_SOLID, 2, NULL);
+ fl_rect(x(), y(), w(), h());
+ fl_line(w()+x()-name_pad, y(), w()+x()-name_pad, h()+y());
+
+ draw_paths();
+
+ // white out any overdraw from path area into name/info area
+ fl_color(FL_WHITE);
+ fl_rectf(w()+x()-name_pad, y(), w()+x(), h());
+
+ draw_sequence_stuff();
+
+ // draw selection box
+ /*
+ if (selected)
+ {
+ fl_color(FL_BLACK);
+ fl_line_style(FL_SOLID, 1, NULL);
+ fl_rect(drag_start,(ref_seq_num*y_seq_incre)+y(),drag_end-drag_start,
+ 16);
+ }
+ */
+}
+
+
+void
+ConnView::draw_paths()
+{
+ list<ExtendedConservedPath >::iterator i;
+ int i2, i3, y_loc, x_loc, x_start, x_end;
+ list<bool>::iterator highlight_i;
+ int window_size;
+ bool rc_color;
+ int path_start, path_end;
+
+ // determine which paths to highlight
+ highlight.clear();
+ for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i)
+ {
+ ExtendedConservedPath& a_path = *i;
+ // determine if path falls within the selected region and mark it for
+ // highlighted color
+ path_start = abs(a_path[ref_seq_num]);
+ path_end = path_start + a_path[0];
+ if ( ( (path_start >= drag_start-x()) && (path_end <= drag_end-x()) ) ||
+ ( (path_start < drag_start-x()) && (path_end > drag_end-x()) ) ||
+ ( (path_start < drag_start-x()) && (path_end > drag_start-x()) ) ||
+ ( (path_start < drag_end-x()) && (path_end > drag_end-x()) ) )
+ highlight.push_back(true);
+ else
+ highlight.push_back(false);
+ }
+
+ fl_line_style(FL_SOLID, 1, NULL);
+ // draw non-highlight paths (ie not in the selection box)
+ highlight_i = highlight.begin();
+ for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i)
+ {
+ ExtendedConservedPath& a_path = *i;
+ y_loc = y()+y_pad;
+
+ window_size = a_path.window_size;
+ // make sure width is at least 1 - might be zero to my slack rounding
+ if (window_size == 0)
+ window_size = 1;
+
+ if (!(*highlight_i))
+ for(i2 = 0; i2 < a_path.size()-1; i2++)
+ {
+ // RC case handling
+ // ugh, an xor...only want blue if one of the nodes is rc
+ if ( ((a_path[i2] < 0) || (a_path[i2+1] < 0)) &&
+ !((a_path[i2] < 0) && (a_path[i2+1] < 0)) )
+ fl_color(200,200,255);
+ else
+ fl_color(255,200,200);
+
+ fl_line_style(FL_SOLID, 1, NULL);
+ fl_polygon((int)abs(a_path[i2])+x(), y_loc + 3,
+ (int)abs(a_path[i2])+window_size+x(), y_loc + 3,
+ (int)abs(a_path[i2+1])+window_size+x(), y_loc + y_seq_incre - 3,
+ (int)abs(a_path[i2+1])+x(), y_loc + y_seq_incre - 3);
+
+ y_loc += y_seq_incre;
+ }
+ ++highlight_i;
+ }
+
+ // draw highlighted paths (ie in or partially in selection)
+ // drawing these separately and after other paths so they are on top
+ highlight_i = highlight.begin();
+ for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i)
+ {
+ ExtendedConservedPath& a_path = *i;
+ y_loc = y()+y_pad;
+
+ // get window size to determine line width
+ window_size = a_path.window_size;
+ // make sure width is at least 1 - might be zero to my slack rounding
+ if (window_size == 0)
+ window_size = 1;
+
+ if (*highlight_i)
+ for(i2 = 0; i2 != a_path.size()-1 ; i2++)
+ {
+ // RC case handling
+ // ugh, an xor...only want blue if one of the nodes is rc
+ if ( ((a_path[i2] < 0) || (a_path[i2+1] < 0)) &&
+ !((a_path[i2] < 0) && (a_path[i2+1] < 0)) )
+ fl_color(FL_BLUE);
+ else
+ fl_color(FL_RED);
+
+ fl_polygon((int)abs(a_path[i2])+x(), y_loc + 3,
+ (int)abs(a_path[i2])+window_size+x(), y_loc + 3,
+ (int)abs(a_path[i2+1])+window_size+x(), y_loc + y_seq_incre - 3,
+ (int)abs(a_path[i2+1])+x(), y_loc + y_seq_incre - 3);
+
+ y_loc += y_seq_incre;
+ }
+ ++highlight_i;
+ }
+}
+
+/*
+ list<vector<int> >::iterator i;
+ int window_size;
+ bool rc_color;
+ int path_start, path_end;
+ Sequence a_seq;
+ vector<int> a_path;
+*/
+
+void
+ConnView::draw_sequence_stuff()
+{
+ int i2, i3, y_loc, y_offset, x_loc, x_start, x_end, mv_offset;
+ list<annot>::iterator annot_i;
+ string species_name, seq_length;
+ stringstream raw_length;
+
+
+ // draw sequence representation lines
+ fl_font(FL_COURIER, 14);
+ //fl_color(FL_BLACK);
+ fl_color(100,100,100);
+ // normally size 7, adjust for various screenshotage
+ fl_line_style(FL_SOLID, 11, NULL);
+ y_loc = y()+y_pad;
+ y_offset = 5;
+ for(i2 = 0; i2 < seq_num; i2++)
+ {
+ if (i2 == seq_num - 1)
+ y_offset = -10;
+ x_loc = (int)(seq_lens[i2] / x_scale_factor) + x();
+ //report_float("seq scaled len", x_loc);
+ fl_line(x(),y_loc,x_loc,y_loc);
+
+ species_name = (*S)[i2].species;
+ fl_draw(species_name.c_str(), x()+w()-name_pad+5, y_loc+y_offset);
+
+ // funkiness to figure out which genomic scale to report size in
+ if (seq_scales[i2] == 1)
+ raw_length << setprecision(3) << seq_lens[i2] << " bp";
+ else if (seq_scales[i2] == 2)
+ raw_length << setprecision(3) << seq_lens[i2] / 1000.0 << " Kb";
+ else if (seq_scales[i2] == 3)
+ raw_length << setprecision(3) << seq_lens[i2] /1000000.0<< " Mb";
+ seq_length = raw_length.str();
+ fl_draw(seq_length.c_str(), x()+w()-name_pad+5, y_loc+y_offset+15);
+ raw_length.str("");
+
+ y_loc += y_seq_incre;
+ }
+
+ //fl_line(x(),y()+y_pad/2,w()-name_pad,y()+y_pad/2);
+ //fl_line(x(),y()+h()-y_pad/2,w()-name_pad,y()+h()-y_pad/2);
+
+ // draw annotations
+ vector<annot_color>::iterator annot_type_i;
+
+ fl_color(FL_GREEN);
+ fl_line_style(FL_SOLID, 3, NULL);
+ y_loc = y()+y_pad;
+ for(i2 = 0; i2 < seq_num; i2++)
+ {
+ // loop thru all annotation entries
+ for(annot_i = (*S)[i2].annots.begin(); annot_i != (*S)[i2].annots.end(); ++annot_i)
+ {
+ fl_line_style(FL_SOLID, 7, NULL);
+ mv_offset = 0;
+
+ // loop thru annotation types to determine color
+ annot_type_i = some_annots.begin();
+ bool type_unfound = true;
+ while ((annot_type_i != some_annots.end()) && type_unfound)
+ {
+ if (annot_i->type == annot_type_i->type)
+ {
+ fl_color(annot_type_i->color);
+ type_unfound = false;
+ }
+ else
+ fl_color(FL_GREEN);
+ ++annot_type_i;
+ }
+
+ // calculate scaled start and end, and draw
+ x_start = (int)(annot_i->start / x_scale_factor) + x();
+ x_end = (int)(annot_i->end / x_scale_factor) + x();
+ fl_line(x_start,y_loc+mv_offset,x_end,y_loc+mv_offset);
+ }
+ y_loc += y_seq_incre;
+ }
+
+
+ // draw motifs found
+ vector<motif>::iterator motif_i;
+ vector<int> some_motif_locs;
+ vector<int>::iterator i_locs;
+ int scale_len, motif_len;
+
+ fl_color(255,0,255);
+ fl_line_style(FL_SOLID, 9, NULL);
+ motif_i = some_motifs.begin();
+ while (motif_i != some_motifs.end())
+ {
+ fl_color(motif_i->color);
+ motif_len = motif_i->seq.length();
+ scale_len = (int) (motif_len / x_scale_factor);
+ if (scale_len == 0)
+ scale_len = 1;
+ y_loc = y()+y_pad;
+ if (!motif_i->locations.empty())
+ for(i2 = 0; i2 < seq_num; i2++)
+ {
+ some_motif_locs = (*motif_i).locations[i2];
+
+ i_locs = some_motif_locs.begin();
+ while (i_locs != some_motif_locs.end())
+ {
+ x_start = (int)(*i_locs / x_scale_factor) + x();
+ fl_line(x_start,y_loc,x_start+scale_len,y_loc);
+ ++i_locs;
+ }
+ y_loc += y_seq_incre;
+ }
+ ++motif_i;
+ }
+}
+
+
+void
+ConnView::resize(int new_x, int new_y, int new_w, int new_h)
+{
+
+ x(new_x);
+ y(new_y);
+ w(new_w);
+ h(new_h);
+
+ x_scale_factor = (float) max_seq_len / (w() - name_pad);
+ cout << "scale factor is " << x_scale_factor << endl;
+ y_seq_incre = (h()-(2*y_pad)) / (seq_num - 1);
+
+ scale_paths();
+}
+
+
+void
+ConnView::reporter(string var, int value)
+{
+ cout << var << " : " << value << endl;
+}
+
+
+void
+ConnView::report_float(string var, float value)
+{
+ cout << var << " : " << value << endl;
+}
+
+int
+ConnView::handle(int e)
+{
+ int return_value;
+ float y_calc_tmp;
+
+ // this empty string needs to be put on cout, otherwise the -O optimize
+ // compile option seems to throw this function away with the following:
+ // gcc version 3.2.2 20030222 (Red Hat Linux 3.2.2-5)
+ cout << "";
+
+ // why do I need a -O for this module? Well, originally I just used the
+ // same compile flags for all modules. I changed that. However, on debian
+ // systems I need the -O otherwise the behavior I observe on redhat machines
+ // with above compiler happens if I don't have that empty cout. WTF
+
+ switch(e)
+ {
+ case FL_PUSH:
+ if (Fl::event_button3())
+ {
+ spawnSeq();
+ return_value = 1;
+ }
+ else if (Fl::event_button2())
+ {
+ find_motifs();
+ return_value = 1;
+ }
+ break;
+ case FL_DRAG:
+ if (!dragging)
+ {
+ drag_start = Fl::event_x();
+ y_drag_start = (float) Fl::event_y();
+ ref_seq_num = (int) (round ( (y_drag_start/y_seq_incre) ) );
+ dragging = true;
+ selected = false;
+ return_value = 1;
+ }
+ fl_line_style(FL_SOLID, 1, NULL);
+ fl_overlay_rect(drag_start, (ref_seq_num*y_seq_incre)+y(),
+ Fl::event_x()-drag_start, 16);
+
+ break;
+ case FL_RELEASE:
+ if (dragging)
+ {
+ drag_end = Fl::event_x();
+ dragging = false;
+ selected = true;
+ redraw();
+ return_value = 1;
+ }
+ break;
+ default:
+ return_value = Fl_Widget::handle(e);
+ }
+
+ return return_value;
+}
+
+
+
+void
+ConnView::check_new_motifs()
+{
+ vector<motif>::iterator i;
+ int i2;
+ vector<int> some_motif_locs;
+ vector<int>::iterator i_locs;
+
+ i = some_motifs.begin();
+ while (i != some_motifs.end())
+ {
+ if (i->dirty)
+ {
+ cout << i->seq << " is new\n";
+ i->locations.clear();
+ //i_locs = i->locations;
+ for(i2 = 0; i2 < seq_num; i2++)
+ {
+ some_motif_locs = (*S)[i2].find_motif(i->seq);
+ (*i).locations.push_back(some_motif_locs);
+
+
+ i_locs = some_motif_locs.begin();
+ while (i_locs != some_motif_locs.end())
+ {
+ cout << *i_locs << " ";
+ ++i_locs;
+ }
+ cout << endl;
+
+ }
+
+ i->dirty = false;
+ }
+ ++i;
+ }
+}
+
+
+void
+ConnView::spawnSeq()
+{
+ list<ExtendedConservedPath > selected_paths;
+ list<ExtendedConservedPath >::iterator pathz_i;
+ int i2, i3, y_loc, x_loc, x_start, x_end;
+ list<bool>::iterator highlight_i;
+ int y_max;
+ string window_name;
+
+ if (selected)
+ {
+ // make new list of connections that are highlighted
+ selected_paths.clear();
+ highlight_i = highlight.begin();
+ for(pathz_i = P->refined_pathz.begin();
+ pathz_i != P->refined_pathz.end(); ++pathz_i)
+ {
+ if (*highlight_i)
+ {
+ ExtendedConservedPath& a_path = *pathz_i;
+ selected_paths.push_back(a_path);
+ }
+ ++highlight_i;
+ }
+
+ // give 50 pixels of height per sequence
+ y_max = seq_num * 50;
+ window_name = "Mussa Sequence: " + analysis_name;
+
+ a_seq_win = new SeqWindow(800, y_max, (const char*) window_name.c_str(),
+ seq_num, S, selected_paths, seq_lens,
+ &some_motifs);
+ }
+}
+
+
+void
+ConnView::find_motifs()
+{
+ motif_find_window = new MotifWindow(300, 300, "Motifs", &some_motifs);
+}
+
+void
+ConnView::annot_win()
+{
+ annot_color_window = new AnnotWindow(300, 300, "Annotations", &some_annots);
+}
+
+// @!@! special hacked in color coding for the myf5/6 region annots
+
+/*
+ if (annot_i->type == "mvista")
+ {
+ fl_color(255,230,0);
+ fl_line_style(FL_SOLID, 8, NULL);
+ mv_offset = -4;
+ }
+ else if (annot_i->type == "reg")
+ {
+ fl_line_style(FL_SOLID, 10, NULL);
+ mv_offset = -8;
+
+ if (annot_i->name == "CNS")
+ fl_color(255,150,0);
+ else if (annot_i->name == "ELA")
+ fl_color(0,200,120);
+ else if (annot_i->name == "ES")
+ fl_color(0,200,200);
+ else if (annot_i->name == "NA")
+ fl_color(120,120,120);
+ else if (annot_i->name == "EA")
+ {
+ fl_line_style(FL_SOLID, 7, NULL);
+ mv_offset = -13;
+ fl_color(0,200,120);
+ }
+ else if (annot_i->name == "VS")
+ {
+ fl_line_style(FL_SOLID, 7, NULL);
+ mv_offset = -6;
+ fl_color(255,255,0);
+ }
+ else if (annot_i->name == "SP")
+ {
+ fl_line_style(FL_SOLID, 7, NULL);
+ mv_offset = -13;
+ fl_color(255,230,150);
+ }
+ else if (annot_i->name == "L")
+ {
+ fl_line_style(FL_SOLID, 7, NULL);
+ mv_offset = -6;
+ fl_color(0,0,100);
+ }
+ else if (annot_i->name == "TCM")
+ fl_color(0,130,230);
+ }
+*/
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-#include "ConnView.hh"
-
-#include <iomanip>
-#include <math.h>
-
-#include <FL/Fl.H>
-#include <FL/fl_draw.H>
-
-using namespace std;
-
-void
-ConnView::setup(string name, int sq_num, int win_len,
- vector<Sequence> *some_seqs,
- NwayPaths *some_paths)
-{
- int i, i2, seq_length;
- Sequence a_seq;
- motif blank_motif;
- annot_color new_annot;
-
-
- analysis_name = name;
- seq_num = sq_num;
- window = win_len;
- S = some_seqs;
- P = some_paths;
-
- cout << "num of paths = " << some_paths->refined_pathz.size() << endl;
-
- cout << "x()=" << x() << " y()=" << y() << " w()=" << w() << " h()=" << h();
- cout << endl;
-
- max_seq_len = 0;
- for(i = 0; i < seq_num; ++i)
- {
- a_seq = (*S)[i];
- cout << a_seq.size() << endl;
- seq_length = a_seq.size();
- seq_lens.push_back(seq_length);
- if (seq_length > max_seq_len)
- max_seq_len = seq_length;
- if (seq_length < 1000)
- seq_scales.push_back(1);
- else if (seq_length < 1000000)
- seq_scales.push_back(2);
- else
- seq_scales.push_back(3);
- }
-
- name_pad = 80;
- y_pad = 20;
-
- x_scale_factor = (float) max_seq_len / (w() - name_pad);
- cout << "scale factor is " << x_scale_factor << endl;
- y_seq_incre = (h()-(y_pad*2)) / (seq_num - 1);
-
-
- drag_start = -1000;
- drag_end = -1000;
- ref_seq_num = 0;
-
- dragging = false;
- selected = false;
-
- highlight.clear();
- show_bars = false;
- show_lines = false;
- bar_interval = max_seq_len / 20;
- line_interval = max_seq_len / 20;
- ref_seq_num = 0;
-
-
- some_motifs.clear();
- for(i = 0; i < 5; ++i)
- {
- blank_motif = new_blank_motif();
- some_motifs.push_back(blank_motif);
- }
-
- // find all unique annotation type ids
- some_annots.clear();
- vector<annot_color>::iterator annot_type_i;
- list<annot>::iterator annot_i;
-
- // loop thru all sequences
- for(i2 = 0; i2 < seq_num; i2++)
- {
- cout << "ConnView: annotation loop\n";
- // loop thru all annotation entries in this sequence
- for(annot_i = (*S)[i2].annots.begin(); annot_i != (*S)[i2].annots.end(); ++annot_i)
- {
- cout << annot_i->start << ", " << annot_i->end << " : ";
- cout << annot_i->name << " " << annot_i->type << endl;
- // loop thru annotation types
- annot_type_i = some_annots.begin();
- bool type_unfound = true;
- while ((annot_type_i != some_annots.end()) && type_unfound)
- {
- if (annot_i->type == annot_type_i->type)
- type_unfound = false; // stop search if found
- ++annot_type_i;
- }
- //if unfound, then add to list
- if (type_unfound)
- {
- new_annot = new_blank_annot();
- new_annot.type = annot_i->type;
- some_annots.push_back(new_annot);
- }
- }
- }
-}
-
-
-void
-ConnView::scale_paths()
-{
- ExtendedConservedPath a_path;
- list<ExtendedConservedPath >::iterator pathz_i;
- int i2;
-
-
- scaled_pathz.clear();
-
- for(pathz_i = P->refined_pathz.begin(); pathz_i != P->refined_pathz.end(); ++pathz_i)
- {
- a_path = *pathz_i;
- a_path.window_size = (int)(a_path.window_size / x_scale_factor);
- for(i2 = 0; i2 != a_path.size(); i2++)
- {
- a_path[i2] = (int) (a_path[i2] / x_scale_factor);
- }
- scaled_pathz.push_back(a_path);
- }
-}
-
-void
-ConnView::toggle_bars()
-{
- show_bars = !show_bars;
- redraw();
-}
-
-void
-ConnView::set_bar_interval(int new_bar_len)
-{
- bar_interval = new_bar_len;
- cout << "bar interval = " << bar_interval << endl;
- redraw();
-}
-
-void
-ConnView::toggle_lines()
-{
- show_lines = !show_lines;
- redraw();
-}
-
-void
-ConnView::set_line_interval(int new_line_len)
-{
- line_interval = new_line_len;
- cout << "line interval = " << line_interval << endl;
- redraw();
-}
-
-
-void
-ConnView::draw()
-{
- // this is temporary - check if new motifs have been added
- check_new_motifs();
-
- // clear drawing area and set background to white
- fl_color(FL_WHITE);
- fl_rectf(x(), y(), w(), h());
-
- // draw the scale indicators if they are on
- // put into own method soon...
- int i, div_num, x_loc;
- float div_len_scaled;
-
- if (show_bars)
- {
- div_num = max_seq_len / bar_interval;
- div_len_scaled = ((float) bar_interval) / x_scale_factor;
- fl_color(230,230,230);
- for(i = 0; i <= div_num; i+=2)
- {
- x_loc = (int)(i * div_len_scaled+x());
- fl_rectf(x_loc, y(), (int) div_len_scaled, h());
- }
- }
-
- if (show_lines)
- {
- div_num = max_seq_len / line_interval;
- div_len_scaled = ((float) line_interval) / x_scale_factor;
- fl_color(0,0,0);
- fl_line_style(FL_SOLID, 1, NULL);
- for(i = 0; i <= div_num; i++)
- {
- x_loc = (int)(i * div_len_scaled+x());
- fl_line(x_loc, y(), x_loc, h()+y());
- }
- }
-
-
- // divide up the space with some light blue lines
- fl_color(150,200,255);
- fl_line_style(FL_SOLID, 2, NULL);
- fl_rect(x(), y(), w(), h());
- fl_line(w()+x()-name_pad, y(), w()+x()-name_pad, h()+y());
-
- draw_paths();
-
- // white out any overdraw from path area into name/info area
- fl_color(FL_WHITE);
- fl_rectf(w()+x()-name_pad, y(), w()+x(), h());
-
- draw_sequence_stuff();
-
- // draw selection box
- /*
- if (selected)
- {
- fl_color(FL_BLACK);
- fl_line_style(FL_SOLID, 1, NULL);
- fl_rect(drag_start,(ref_seq_num*y_seq_incre)+y(),drag_end-drag_start,
- 16);
- }
- */
-}
-
-
-void
-ConnView::draw_paths()
-{
- list<ExtendedConservedPath >::iterator i;
- int i2, i3, y_loc, x_loc, x_start, x_end;
- list<bool>::iterator highlight_i;
- int window_size;
- bool rc_color;
- int path_start, path_end;
-
- // determine which paths to highlight
- highlight.clear();
- for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i)
- {
- ExtendedConservedPath& a_path = *i;
- // determine if path falls within the selected region and mark it for
- // highlighted color
- path_start = abs(a_path[ref_seq_num]);
- path_end = path_start + a_path[0];
- if ( ( (path_start >= drag_start-x()) && (path_end <= drag_end-x()) ) ||
- ( (path_start < drag_start-x()) && (path_end > drag_end-x()) ) ||
- ( (path_start < drag_start-x()) && (path_end > drag_start-x()) ) ||
- ( (path_start < drag_end-x()) && (path_end > drag_end-x()) ) )
- highlight.push_back(true);
- else
- highlight.push_back(false);
- }
-
- fl_line_style(FL_SOLID, 1, NULL);
- // draw non-highlight paths (ie not in the selection box)
- highlight_i = highlight.begin();
- for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i)
- {
- ExtendedConservedPath& a_path = *i;
- y_loc = y()+y_pad;
-
- window_size = a_path.window_size;
- // make sure width is at least 1 - might be zero to my slack rounding
- if (window_size == 0)
- window_size = 1;
-
- if (!(*highlight_i))
- for(i2 = 0; i2 < a_path.size()-1; i2++)
- {
- // RC case handling
- // ugh, an xor...only want blue if one of the nodes is rc
- if ( ((a_path[i2] < 0) || (a_path[i2+1] < 0)) &&
- !((a_path[i2] < 0) && (a_path[i2+1] < 0)) )
- fl_color(200,200,255);
- else
- fl_color(255,200,200);
-
- fl_line_style(FL_SOLID, 1, NULL);
- fl_polygon((int)abs(a_path[i2])+x(), y_loc + 3,
- (int)abs(a_path[i2])+window_size+x(), y_loc + 3,
- (int)abs(a_path[i2+1])+window_size+x(), y_loc + y_seq_incre - 3,
- (int)abs(a_path[i2+1])+x(), y_loc + y_seq_incre - 3);
-
- y_loc += y_seq_incre;
- }
- ++highlight_i;
- }
-
- // draw highlighted paths (ie in or partially in selection)
- // drawing these separately and after other paths so they are on top
- highlight_i = highlight.begin();
- for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i)
- {
- ExtendedConservedPath& a_path = *i;
- y_loc = y()+y_pad;
-
- // get window size to determine line width
- window_size = a_path.window_size;
- // make sure width is at least 1 - might be zero to my slack rounding
- if (window_size == 0)
- window_size = 1;
-
- if (*highlight_i)
- for(i2 = 0; i2 != a_path.size()-1 ; i2++)
- {
- // RC case handling
- // ugh, an xor...only want blue if one of the nodes is rc
- if ( ((a_path[i2] < 0) || (a_path[i2+1] < 0)) &&
- !((a_path[i2] < 0) && (a_path[i2+1] < 0)) )
- fl_color(FL_BLUE);
- else
- fl_color(FL_RED);
-
- fl_polygon((int)abs(a_path[i2])+x(), y_loc + 3,
- (int)abs(a_path[i2])+window_size+x(), y_loc + 3,
- (int)abs(a_path[i2+1])+window_size+x(), y_loc + y_seq_incre - 3,
- (int)abs(a_path[i2+1])+x(), y_loc + y_seq_incre - 3);
-
- y_loc += y_seq_incre;
- }
- ++highlight_i;
- }
-}
-
-/*
- list<vector<int> >::iterator i;
- int window_size;
- bool rc_color;
- int path_start, path_end;
- Sequence a_seq;
- vector<int> a_path;
-*/
-
-void
-ConnView::draw_sequence_stuff()
-{
- int i2, i3, y_loc, y_offset, x_loc, x_start, x_end, mv_offset;
- list<annot>::iterator annot_i;
- string species_name, seq_length;
- stringstream raw_length;
-
-
- // draw sequence representation lines
- fl_font(FL_COURIER, 14);
- //fl_color(FL_BLACK);
- fl_color(100,100,100);
- // normally size 7, adjust for various screenshotage
- fl_line_style(FL_SOLID, 11, NULL);
- y_loc = y()+y_pad;
- y_offset = 5;
- for(i2 = 0; i2 < seq_num; i2++)
- {
- if (i2 == seq_num - 1)
- y_offset = -10;
- x_loc = (int)(seq_lens[i2] / x_scale_factor) + x();
- //report_float("seq scaled len", x_loc);
- fl_line(x(),y_loc,x_loc,y_loc);
-
- species_name = (*S)[i2].species;
- fl_draw(species_name.c_str(), x()+w()-name_pad+5, y_loc+y_offset);
-
- // funkiness to figure out which genomic scale to report size in
- if (seq_scales[i2] == 1)
- raw_length << setprecision(3) << seq_lens[i2] << " bp";
- else if (seq_scales[i2] == 2)
- raw_length << setprecision(3) << seq_lens[i2] / 1000.0 << " Kb";
- else if (seq_scales[i2] == 3)
- raw_length << setprecision(3) << seq_lens[i2] /1000000.0<< " Mb";
- seq_length = raw_length.str();
- fl_draw(seq_length.c_str(), x()+w()-name_pad+5, y_loc+y_offset+15);
- raw_length.str("");
-
- y_loc += y_seq_incre;
- }
-
- //fl_line(x(),y()+y_pad/2,w()-name_pad,y()+y_pad/2);
- //fl_line(x(),y()+h()-y_pad/2,w()-name_pad,y()+h()-y_pad/2);
-
- // draw annotations
- vector<annot_color>::iterator annot_type_i;
-
- fl_color(FL_GREEN);
- fl_line_style(FL_SOLID, 3, NULL);
- y_loc = y()+y_pad;
- for(i2 = 0; i2 < seq_num; i2++)
- {
- // loop thru all annotation entries
- for(annot_i = (*S)[i2].annots.begin(); annot_i != (*S)[i2].annots.end(); ++annot_i)
- {
- fl_line_style(FL_SOLID, 7, NULL);
- mv_offset = 0;
-
- // loop thru annotation types to determine color
- annot_type_i = some_annots.begin();
- bool type_unfound = true;
- while ((annot_type_i != some_annots.end()) && type_unfound)
- {
- if (annot_i->type == annot_type_i->type)
- {
- fl_color(annot_type_i->color);
- type_unfound = false;
- }
- else
- fl_color(FL_GREEN);
- ++annot_type_i;
- }
-
- // calculate scaled start and end, and draw
- x_start = (int)(annot_i->start / x_scale_factor) + x();
- x_end = (int)(annot_i->end / x_scale_factor) + x();
- fl_line(x_start,y_loc+mv_offset,x_end,y_loc+mv_offset);
- }
- y_loc += y_seq_incre;
- }
-
-
- // draw motifs found
- vector<motif>::iterator motif_i;
- vector<int> some_motif_locs;
- vector<int>::iterator i_locs;
- int scale_len, motif_len;
-
- fl_color(255,0,255);
- fl_line_style(FL_SOLID, 9, NULL);
- motif_i = some_motifs.begin();
- while (motif_i != some_motifs.end())
- {
- fl_color(motif_i->color);
- motif_len = motif_i->seq.length();
- scale_len = (int) (motif_len / x_scale_factor);
- if (scale_len == 0)
- scale_len = 1;
- y_loc = y()+y_pad;
- if (!motif_i->locations.empty())
- for(i2 = 0; i2 < seq_num; i2++)
- {
- some_motif_locs = (*motif_i).locations[i2];
-
- i_locs = some_motif_locs.begin();
- while (i_locs != some_motif_locs.end())
- {
- x_start = (int)(*i_locs / x_scale_factor) + x();
- fl_line(x_start,y_loc,x_start+scale_len,y_loc);
- ++i_locs;
- }
- y_loc += y_seq_incre;
- }
- ++motif_i;
- }
-}
-
-
-void
-ConnView::resize(int new_x, int new_y, int new_w, int new_h)
-{
-
- x(new_x);
- y(new_y);
- w(new_w);
- h(new_h);
-
- x_scale_factor = (float) max_seq_len / (w() - name_pad);
- cout << "scale factor is " << x_scale_factor << endl;
- y_seq_incre = (h()-(2*y_pad)) / (seq_num - 1);
-
- scale_paths();
-}
-
-
-void
-ConnView::reporter(string var, int value)
-{
- cout << var << " : " << value << endl;
-}
-
-
-void
-ConnView::report_float(string var, float value)
-{
- cout << var << " : " << value << endl;
-}
-
-int
-ConnView::handle(int e)
-{
- int return_value;
- float y_calc_tmp;
-
- // this empty string needs to be put on cout, otherwise the -O optimize
- // compile option seems to throw this function away with the following:
- // gcc version 3.2.2 20030222 (Red Hat Linux 3.2.2-5)
- cout << "";
-
- // why do I need a -O for this module? Well, originally I just used the
- // same compile flags for all modules. I changed that. However, on debian
- // systems I need the -O otherwise the behavior I observe on redhat machines
- // with above compiler happens if I don't have that empty cout. WTF
-
- switch(e)
- {
- case FL_PUSH:
- if (Fl::event_button3())
- {
- spawnSeq();
- return_value = 1;
- }
- else if (Fl::event_button2())
- {
- find_motifs();
- return_value = 1;
- }
- break;
- case FL_DRAG:
- if (!dragging)
- {
- drag_start = Fl::event_x();
- y_drag_start = (float) Fl::event_y();
- ref_seq_num = (int) (round ( (y_drag_start/y_seq_incre) ) );
- dragging = true;
- selected = false;
- return_value = 1;
- }
- fl_line_style(FL_SOLID, 1, NULL);
- fl_overlay_rect(drag_start, (ref_seq_num*y_seq_incre)+y(),
- Fl::event_x()-drag_start, 16);
-
- break;
- case FL_RELEASE:
- if (dragging)
- {
- drag_end = Fl::event_x();
- dragging = false;
- selected = true;
- redraw();
- return_value = 1;
- }
- break;
- default:
- return_value = Fl_Widget::handle(e);
- }
-
- return return_value;
-}
-
-
-
-void
-ConnView::check_new_motifs()
-{
- vector<motif>::iterator i;
- int i2;
- vector<int> some_motif_locs;
- vector<int>::iterator i_locs;
-
- i = some_motifs.begin();
- while (i != some_motifs.end())
- {
- if (i->dirty)
- {
- cout << i->seq << " is new\n";
- i->locations.clear();
- //i_locs = i->locations;
- for(i2 = 0; i2 < seq_num; i2++)
- {
- some_motif_locs = (*S)[i2].find_motif(i->seq);
- (*i).locations.push_back(some_motif_locs);
-
-
- i_locs = some_motif_locs.begin();
- while (i_locs != some_motif_locs.end())
- {
- cout << *i_locs << " ";
- ++i_locs;
- }
- cout << endl;
-
- }
-
- i->dirty = false;
- }
- ++i;
- }
-}
-
-
-void
-ConnView::spawnSeq()
-{
- list<ExtendedConservedPath > selected_paths;
- list<ExtendedConservedPath >::iterator pathz_i;
- int i2, i3, y_loc, x_loc, x_start, x_end;
- list<bool>::iterator highlight_i;
- int y_max;
- string window_name;
-
- if (selected)
- {
- // make new list of connections that are highlighted
- selected_paths.clear();
- highlight_i = highlight.begin();
- for(pathz_i = P->refined_pathz.begin();
- pathz_i != P->refined_pathz.end(); ++pathz_i)
- {
- if (*highlight_i)
- {
- ExtendedConservedPath& a_path = *pathz_i;
- selected_paths.push_back(a_path);
- }
- ++highlight_i;
- }
-
- // give 50 pixels of height per sequence
- y_max = seq_num * 50;
- window_name = "Mussa Sequence: " + analysis_name;
-
- a_seq_win = new SeqWindow(800, y_max, (const char*) window_name.c_str(),
- seq_num, S, selected_paths, seq_lens,
- &some_motifs);
- }
-}
-
-
-void
-ConnView::find_motifs()
-{
- motif_find_window = new MotifWindow(300, 300, "Motifs", &some_motifs);
-}
-
-void
-ConnView::annot_win()
-{
- annot_color_window = new AnnotWindow(300, 300, "Annotations", &some_annots);
-}
-
-// @!@! special hacked in color coding for the myf5/6 region annots
-
-/*
- if (annot_i->type == "mvista")
- {
- fl_color(255,230,0);
- fl_line_style(FL_SOLID, 8, NULL);
- mv_offset = -4;
- }
- else if (annot_i->type == "reg")
- {
- fl_line_style(FL_SOLID, 10, NULL);
- mv_offset = -8;
-
- if (annot_i->name == "CNS")
- fl_color(255,150,0);
- else if (annot_i->name == "ELA")
- fl_color(0,200,120);
- else if (annot_i->name == "ES")
- fl_color(0,200,200);
- else if (annot_i->name == "NA")
- fl_color(120,120,120);
- else if (annot_i->name == "EA")
- {
- fl_line_style(FL_SOLID, 7, NULL);
- mv_offset = -13;
- fl_color(0,200,120);
- }
- else if (annot_i->name == "VS")
- {
- fl_line_style(FL_SOLID, 7, NULL);
- mv_offset = -6;
- fl_color(255,255,0);
- }
- else if (annot_i->name == "SP")
- {
- fl_line_style(FL_SOLID, 7, NULL);
- mv_offset = -13;
- fl_color(255,230,150);
- }
- else if (annot_i->name == "L")
- {
- fl_line_style(FL_SOLID, 7, NULL);
- mv_offset = -6;
- fl_color(0,0,100);
- }
- else if (annot_i->name == "TCM")
- fl_color(0,130,230);
- }
-*/
+++ /dev/null
-#ifndef _MUSSA_GUI_CONN_VIEW_H_
-#define _MUSSA_GUI_CONN_VIEW_H_
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-#include <list>
-#include <sstream>
-#include <string>
-#include <vector>
-
-#include "alg/sequence.hh"
-#include "alg/nway_paths.hh"
-#include "SeqView.hh"
-#include "SeqWindow.hh"
-#include "MotifWindow.hh"
-#include "AnnotWindow.hh" // aparently for annot_color
-
-#include <FL/Fl_Box.H>
-
-class NwayPaths;
-class ConnView : public Fl_Box
-{
- public:
- ConnView(int x_top,int y_top,int x_bot,int y_bot) :
- Fl_Box(x_top,y_top,x_bot,y_bot)
- {}
-
- void setup(std::string name, int sq_num, int win_len,
- std::vector<Sequence> *, NwayPaths *);
- void scale_paths();
-
- void spawnSeq();
- void find_motifs();
- void annot_win();
-
- void toggle_bars();
- void set_bar_interval(int new_bar_len);
- void toggle_lines();
- void set_line_interval(int new_line_len);
-
-
- private:
- std::string analysis_name;
- int seq_num, window, threshold;
- bool win_append, thres_append;
-
- //this data is passed as pointers to the instantiated classes
- std::vector<Sequence> *S;
- //! Store the nway paths our analysis did, we mostly need the refined paths
- NwayPaths *P;
-
- int name_pad, y_pad;
- float x_scale_factor;
- int y_seq_incre;
- int drag_start, drag_end;
- float y_drag_start;
- int ref_seq_num, max_seq_len;
- bool dragging, selected;
- std::list<bool> highlight;
-
- //path data scaled for current view size
- std::list<ExtendedConservedPath > scaled_pathz;
- std::vector<int> seq_lens;
- std::vector<int> seq_scales;
- int bar_interval, line_interval;
- bool show_bars, show_lines;
-
- //keeps track of all the motifs the user has inputed
- std::vector<motif> some_motifs;
- MotifWindow *motif_find_window;
-
- //keeps track of the colors assigned to each motif type
- std::vector<annot_color> some_annots;
- AnnotWindow *annot_color_window;
-
- SeqWindow *a_seq_win;
-
- void draw();
- void draw_paths();
- void draw_sequence_stuff();
-
- void resize(int x, int y, int w, int h);
- int handle(int e);
- void check_new_motifs();
-
- //for drawing function debugging
- void reporter(std::string var, int value);
- void report_float(std::string var, float value);
-};
-#endif
--- /dev/null
+#ifndef _MUSSA_GUI_CONN_VIEW_H_
+#define _MUSSA_GUI_CONN_VIEW_H_
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+#include <list>
+#include <sstream>
+#include <string>
+#include <vector>
+
+#include "alg/sequence.hpp"
+#include "alg/nway_paths.hpp"
+#include "gui/SeqView.hpp"
+#include "gui/SeqWindow.hpp"
+#include "gui/MotifWindow.hpp"
+#include "gui/AnnotWindow.hpp" // aparently for annot_color
+
+#include <FL/Fl_Box.H>
+
+class NwayPaths;
+class ConnView : public Fl_Box
+{
+ public:
+ ConnView(int x_top,int y_top,int x_bot,int y_bot) :
+ Fl_Box(x_top,y_top,x_bot,y_bot)
+ {}
+
+ void setup(std::string name, int sq_num, int win_len,
+ std::vector<Sequence> *, NwayPaths *);
+ void scale_paths();
+
+ void spawnSeq();
+ void find_motifs();
+ void annot_win();
+
+ void toggle_bars();
+ void set_bar_interval(int new_bar_len);
+ void toggle_lines();
+ void set_line_interval(int new_line_len);
+
+
+ private:
+ std::string analysis_name;
+ int seq_num, window, threshold;
+ bool win_append, thres_append;
+
+ //this data is passed as pointers to the instantiated classes
+ std::vector<Sequence> *S;
+ //! Store the nway paths our analysis did, we mostly need the refined paths
+ NwayPaths *P;
+
+ int name_pad, y_pad;
+ float x_scale_factor;
+ int y_seq_incre;
+ int drag_start, drag_end;
+ float y_drag_start;
+ int ref_seq_num, max_seq_len;
+ bool dragging, selected;
+ std::list<bool> highlight;
+
+ //path data scaled for current view size
+ std::list<ExtendedConservedPath > scaled_pathz;
+ std::vector<int> seq_lens;
+ std::vector<int> seq_scales;
+ int bar_interval, line_interval;
+ bool show_bars, show_lines;
+
+ //keeps track of all the motifs the user has inputed
+ std::vector<motif> some_motifs;
+ MotifWindow *motif_find_window;
+
+ //keeps track of the colors assigned to each motif type
+ std::vector<annot_color> some_annots;
+ AnnotWindow *annot_color_window;
+
+ SeqWindow *a_seq_win;
+
+ void draw();
+ void draw_paths();
+ void draw_sequence_stuff();
+
+ void resize(int x, int y, int w, int h);
+ int handle(int e);
+ void check_new_motifs();
+
+ //for drawing function debugging
+ void reporter(std::string var, int value);
+ void report_float(std::string var, float value);
+};
+#endif
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+#include "gui/ConnWindow.hpp"
+#include "mussa_exceptions.hpp"
+
+#include <iostream>
+using namespace std;
+
+void
+load_ana_cb(Fl_Button* o, void* v)
+{
+ ConnWindow* T=(ConnWindow*)v;
+ T->real_load_ana_cb();
+}
+
+
+void
+ConnWindow::real_load_ana_cb()
+{
+ char *picked_file;
+ string a_file_path;
+ string err_msg;
+
+ cout << "Load! Load! Load, ye yellow-bellied seadogs!\n";
+ //picked_file = fl_file_chooser("Find an Analysis", "", "", 1);
+ picked_file = fl_dir_chooser("Find an Analysis", "", 1);
+ if (picked_file != NULL)
+ {
+ a_file_path = picked_file;
+ cout << "doo wah diddy diddy dum diddy doo\n";
+ cout << a_file_path << endl;
+
+ // load the analysis
+ an_analysis = new Mussa();
+ try {
+ an_analysis->load(a_file_path);
+ } catch (mussa_load_error e) {
+ fl_alert(e.what());
+ return;
+ }
+ //.substr(0,a_file_path.find(".mu")));
+
+ // relabel window with the analysis name
+ window_name = "Mussa: " + an_analysis->get_name();
+ label((const char*)window_name.c_str());
+ // show the user the analysis
+ conn_box->setup(an_analysis->get_name(), an_analysis->size(),
+ an_analysis->get_window(), &(an_analysis->the_seqs),
+ &(an_analysis->the_paths));
+ conn_box->scale_paths();
+ }
+}
+
+
+void
+do_ana_cb(Fl_Button* o, void* v)
+{
+ ConnWindow* T=(ConnWindow*)v;
+ T->real_do_ana_cb();
+}
+
+
+void
+ConnWindow::real_do_ana_cb()
+{
+ char *picked_file;
+ string a_file_path;
+ string err_msg;
+
+ picked_file = fl_file_chooser("Analysis Config File", "", "", 1);
+ if (picked_file != NULL)
+ {
+ a_file_path = picked_file;
+
+ an_analysis = new Mussa();
+ try {
+ an_analysis->load_mupa_file(a_file_path);
+ } catch (mussa_load_error e) {
+ fl_alert(e.what());
+ return;
+ }
+
+ try {
+ an_analysis->analyze(0, 0, Mussa::TransitiveNway, 0.0);
+ // relabel window with the analysis name
+ window_name = "Mussa: " + an_analysis->get_name();
+ label((const char*)window_name.c_str());
+ // show the user the analysis
+ conn_box->setup(an_analysis->get_name(), an_analysis->size(),
+ an_analysis->get_window(), &(an_analysis->the_seqs),
+ &(an_analysis->the_paths));
+ conn_box->scale_paths();
+ } catch (mussa_analysis_error e) {
+ fl_alert(e.what());
+ }
+ }
+ conn_box->redraw();
+}
+
+
+void
+setup_ana_cb(Fl_Button* o, void* v)
+{
+ ConnWindow* T=(ConnWindow*)v;
+ T->real_setup_ana_cb();
+}
+
+void
+ConnWindow::real_setup_ana_cb()
+{
+ an_analysis = new Mussa();
+ setup_win = new SetupWindow(650,700,"Analysis Setup", an_analysis);
+
+ while(setup_win->visible())
+ Fl::wait(.1);
+ cout << "Like a warm summer day\n";
+
+ if (setup_win->done())
+ {
+ // relabel window with the analysis name
+ window_name = "Mussa: " + an_analysis->get_name();
+ label((const char*)window_name.c_str());
+ // is it this easy? what if setup window encounters an error...??
+ conn_box->setup(an_analysis->get_name(), an_analysis->size(),
+ an_analysis->get_window(), &(an_analysis->the_seqs),
+ &(an_analysis->the_paths));
+
+ conn_box->scale_paths();
+ }
+}
+
+
+void
+subana_cb(Fl_Button* o, void* v)
+{
+ ConnWindow* T=(ConnWindow*)v;
+ T->real_subana_cb();
+}
+
+void
+ConnWindow::real_subana_cb()
+{
+ string subana_name;
+
+ if (an_analysis == 0 || an_analysis->the_seqs.size() == 0) {
+ fl_message("please load an analysis before creating a subanalysis");
+ return;
+ }
+
+ sub_analysis = new Mussa();
+ subana_win = new SubAnalysisWindow(500,400,"Sub Analysis Setup", sub_analysis,
+ an_analysis->the_seqs);
+
+ while(subana_win->visible())
+ Fl::wait(.1);
+ cout << "Like a warm summer day\n";
+
+ if (subana_win->done())
+ {
+ subana_name = "SubMussa: " + sub_analysis->get_name();
+ sub_conn_win = new ConnWindow(w(), h(), (const char*) subana_name.c_str());
+ cout << "Like a warm day in may\n";
+ sub_conn_win->add_ana(sub_analysis);
+ //Fl::visual(FL_DOUBLE|FL_INDEX);
+ //sub_conn_box->show();
+ }
+}
+
+
+void
+seq_show_cb(Fl_Button* o, void* v)
+{
+ ConnWindow* T=(ConnWindow*)v;
+ T->real_seq_show_cb();
+}
+
+void
+ConnWindow::real_seq_show_cb()
+{
+ show_seq_win = new SeqTextWindow(500,400,"Seq Show", an_analysis->the_seqs);
+}
+
+void
+seq_win_spawn_cb(Fl_Button* o, void* v)
+{
+ ConnWindow* T=(ConnWindow*)v;
+ T->real_seq_win_spawn_cb();
+}
+
+void
+ConnWindow::real_seq_win_spawn_cb()
+{
+ conn_box->spawnSeq();
+}
+
+void
+motif_find_cb(Fl_Button* o, void* v)
+{
+ ConnWindow* T=(ConnWindow*)v;
+ T->real_motif_find_cb();
+}
+
+void
+ConnWindow::real_motif_find_cb()
+{
+ conn_box->find_motifs();
+}
+
+void
+annot_win_cb(Fl_Button* o, void* v)
+{
+ ConnWindow* T=(ConnWindow*)v;
+ T->real_annot_win_cb();
+}
+
+void
+ConnWindow::real_annot_win_cb()
+{
+ conn_box->annot_win();
+}
+
+
+// all the crap needed for dealing with the scale bars
+void
+toggle_scale_bars_cb(Fl_Button* o, void* v)
+{
+ ConnWindow* T=(ConnWindow*)v;
+ T->real_toggle_bars_cb();
+}
+
+void
+ConnWindow::real_toggle_bars_cb()
+{
+ conn_box->toggle_bars();
+}
+
+void
+set_bar_len_cb(Fl_Input* o, void* v)
+{
+ ConnWindow* T=(ConnWindow*)v;
+ cout << "WAAAAAAAAA\n";
+ T->real_set_bar_len_cb(o);
+}
+
+void
+ConnWindow::real_set_bar_len_cb(Fl_Input* o)
+{
+ int new_bar_len;
+
+ new_bar_len = atoi(o->value());
+ cout << "new bar len = " << new_bar_len << endl;
+ conn_box->set_bar_interval(new_bar_len);
+}
+
+
+// all the crap needed for dealing with the scale lines
+void
+toggle_scale_lines_cb(Fl_Button* o, void* v)
+{
+ ConnWindow* T=(ConnWindow*)v;
+ T->real_toggle_lines_cb();
+}
+
+void
+ConnWindow::real_toggle_lines_cb()
+{
+ conn_box->toggle_lines();
+}
+
+void
+set_line_len_cb(Fl_Input* o, void* v)
+{
+ ConnWindow* T=(ConnWindow*)v;
+ cout << "WAAAAAAAAA\n";
+ T->real_set_line_len_cb(o);
+}
+
+void
+ConnWindow::real_set_line_len_cb(Fl_Input* o)
+{
+ int new_line_len;
+
+ new_line_len = atoi(o->value());
+ cout << "new line len = " << new_line_len << endl;
+ conn_box->set_line_interval(new_line_len);
+}
+
+
+// setting new soft threshold
+
+void
+set_soft_thres_cb(Fl_Input* o, void* v)
+{
+ ConnWindow* T=(ConnWindow*)v;
+ cout << "WAAAAAAAAA\n";
+ T->real_set_soft_thres_cb(o);
+}
+
+void
+ConnWindow::real_set_soft_thres_cb(Fl_Input* o)
+{
+ int new_soft_thres;
+
+ new_soft_thres = atoi(o->value());
+ cout << "new soft thres = " << new_soft_thres << endl;
+
+ an_analysis->set_soft_thres(new_soft_thres);
+ an_analysis->set_analysis_mode(Mussa::TransitiveNway);
+ an_analysis->nway();
+ conn_box->scale_paths();
+ conn_box->redraw();
+
+ // hacked in stuff to save muway files at different thresholds
+ string save_path;
+ ostringstream append_info;
+
+ save_path = an_analysis->get_name() + "/"
+ + an_analysis->get_name().substr(0,an_analysis->get_name().find("_t"));
+ append_info.str("");
+ append_info << "_t" << new_soft_thres << ".muway";
+ //<< "_w" << an_analysis->window
+ save_path += append_info.str();
+ cout << "saving as: " << save_path << endl;
+ an_analysis->save_muway(save_path);
+}
+
+
+
+
+ConnWindow::ConnWindow(int w, int h, const char* title):
+ Fl_Double_Window(w,h,title)
+{
+ int button_len = 120;
+ Fl_Color a_color = fl_rgb_color(150, 200, 255);
+
+ padding = 5;
+
+ begin();
+ //fl_color(150,200,255);
+ color(FL_WHITE);
+ resizable(this);
+
+
+ // create file menu button
+ file_menu = new Fl_Menu_Button(padding, 2, button_len, 30, "Analysis");
+ file_menu->color(FL_WHITE,a_color);
+ file_menu->box(FL_BORDER_BOX);
+ file_menu->clear();
+
+ // add menu items
+ file_menu->add("Do Analysis", 0, (Fl_Callback *) do_ana_cb, this);
+ file_menu->add("Load Analysis", 0, (Fl_Callback *) load_ana_cb, this);
+ file_menu->add("Setup Analysis", 0, (Fl_Callback *) setup_ana_cb, this);
+ file_menu->add("Sub Analysis", 0, (Fl_Callback *) subana_cb, this);
+
+
+ view_menu = new Fl_Menu_Button(padding+button_len,2, button_len, 30, "View");
+ view_menu->color(FL_WHITE,a_color);
+ view_menu->box(FL_BORDER_BOX);
+ view_menu->clear();
+ view_menu->add("Sequence Zoom", 0, (Fl_Callback*) seq_win_spawn_cb, this);
+ view_menu->add("Motif Finder", 0, (Fl_Callback*) motif_find_cb, this);
+ view_menu->add("Annotations", 0, (Fl_Callback*) annot_win_cb, this);
+ view_menu->add("Copy Seq", 0, (Fl_Callback*) seq_show_cb, this);
+ view_menu->add("Toggle Bars", 0, (Fl_Callback*) toggle_scale_bars_cb, this,
+ FL_MENU_TOGGLE|FL_MENU_VALUE);
+ view_menu->add("Toggle Lines", 0, (Fl_Callback*) toggle_scale_lines_cb, this,
+ FL_MENU_TOGGLE|FL_MENU_VALUE);
+
+ bar_input = new Fl_Input(padding+3*button_len, 2, button_len, 30, "Bar Length (bp)");
+ bar_input->value("");
+ bar_input->when(FL_WHEN_ENTER_KEY);
+ bar_input->callback((Fl_Callback*)set_bar_len_cb, this);
+
+ line_input = new Fl_Input(padding+5*button_len, 2, button_len, 30, "Line Interval (bp)");
+ line_input->value("");
+ line_input->when(FL_WHEN_ENTER_KEY);
+ line_input->callback((Fl_Callback*)set_line_len_cb, this);
+
+
+ thres_input = new Fl_Input(padding+7*button_len, 2, button_len, 30, "Threshold");
+ thres_input->value("");
+ thres_input->when(FL_WHEN_ENTER_KEY);
+ thres_input->callback((Fl_Callback*)set_soft_thres_cb, this);
+
+
+ // create the connections box
+ conn_box = new ConnView(padding, padding + 30, w-2*padding, h-2*padding-30);
+ //conn_box = new ConnView(padding, padding, w-2*padding, h-2*padding);
+
+ end();
+ show();
+}
+
+
+ConnWindow::~ConnWindow()
+{}
+
+
+void
+ConnWindow::add_ana(Mussa *the_ana)
+{
+ an_analysis = the_ana;
+
+ // relabel window with the analysis name
+ window_name = "Mussa: " + an_analysis->get_name();
+ label((const char*)window_name.c_str());
+
+ conn_box->setup(an_analysis->get_name(), an_analysis->size(),
+ an_analysis->get_window(), &(an_analysis->the_seqs),
+ &(an_analysis->the_paths));
+ conn_box->scale_paths();
+}
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-#include "ConnWindow.hh"
-#include "mussa_exceptions.hh"
-
-#include <iostream>
-using namespace std;
-
-void
-load_ana_cb(Fl_Button* o, void* v)
-{
- ConnWindow* T=(ConnWindow*)v;
- T->real_load_ana_cb();
-}
-
-
-void
-ConnWindow::real_load_ana_cb()
-{
- char *picked_file;
- string a_file_path;
- string err_msg;
-
- cout << "Load! Load! Load, ye yellow-bellied seadogs!\n";
- //picked_file = fl_file_chooser("Find an Analysis", "", "", 1);
- picked_file = fl_dir_chooser("Find an Analysis", "", 1);
- if (picked_file != NULL)
- {
- a_file_path = picked_file;
- cout << "doo wah diddy diddy dum diddy doo\n";
- cout << a_file_path << endl;
-
- // load the analysis
- an_analysis = new Mussa();
- try {
- an_analysis->load(a_file_path);
- } catch (mussa_load_error e) {
- fl_alert(e.what());
- return;
- }
- //.substr(0,a_file_path.find(".mu")));
-
- // relabel window with the analysis name
- window_name = "Mussa: " + an_analysis->get_name();
- label((const char*)window_name.c_str());
- // show the user the analysis
- conn_box->setup(an_analysis->get_name(), an_analysis->size(),
- an_analysis->get_window(), &(an_analysis->the_seqs),
- &(an_analysis->the_paths));
- conn_box->scale_paths();
- }
-}
-
-
-void
-do_ana_cb(Fl_Button* o, void* v)
-{
- ConnWindow* T=(ConnWindow*)v;
- T->real_do_ana_cb();
-}
-
-
-void
-ConnWindow::real_do_ana_cb()
-{
- char *picked_file;
- string a_file_path;
- string err_msg;
-
- picked_file = fl_file_chooser("Analysis Config File", "", "", 1);
- if (picked_file != NULL)
- {
- a_file_path = picked_file;
-
- an_analysis = new Mussa();
- try {
- an_analysis->load_mupa_file(a_file_path);
- } catch (mussa_load_error e) {
- fl_alert(e.what());
- return;
- }
-
- try {
- an_analysis->analyze(0, 0, Mussa::TransitiveNway, 0.0);
- // relabel window with the analysis name
- window_name = "Mussa: " + an_analysis->get_name();
- label((const char*)window_name.c_str());
- // show the user the analysis
- conn_box->setup(an_analysis->get_name(), an_analysis->size(),
- an_analysis->get_window(), &(an_analysis->the_seqs),
- &(an_analysis->the_paths));
- conn_box->scale_paths();
- } catch (mussa_analysis_error e) {
- fl_alert(e.what());
- }
- }
- conn_box->redraw();
-}
-
-
-void
-setup_ana_cb(Fl_Button* o, void* v)
-{
- ConnWindow* T=(ConnWindow*)v;
- T->real_setup_ana_cb();
-}
-
-void
-ConnWindow::real_setup_ana_cb()
-{
- an_analysis = new Mussa();
- setup_win = new SetupWindow(650,700,"Analysis Setup", an_analysis);
-
- while(setup_win->visible())
- Fl::wait(.1);
- cout << "Like a warm summer day\n";
-
- if (setup_win->done())
- {
- // relabel window with the analysis name
- window_name = "Mussa: " + an_analysis->get_name();
- label((const char*)window_name.c_str());
- // is it this easy? what if setup window encounters an error...??
- conn_box->setup(an_analysis->get_name(), an_analysis->size(),
- an_analysis->get_window(), &(an_analysis->the_seqs),
- &(an_analysis->the_paths));
-
- conn_box->scale_paths();
- }
-}
-
-
-void
-subana_cb(Fl_Button* o, void* v)
-{
- ConnWindow* T=(ConnWindow*)v;
- T->real_subana_cb();
-}
-
-void
-ConnWindow::real_subana_cb()
-{
- string subana_name;
-
- if (an_analysis == 0 || an_analysis->the_seqs.size() == 0) {
- fl_message("please load an analysis before creating a subanalysis");
- return;
- }
-
- sub_analysis = new Mussa();
- subana_win = new SubAnalysisWindow(500,400,"Sub Analysis Setup", sub_analysis,
- an_analysis->the_seqs);
-
- while(subana_win->visible())
- Fl::wait(.1);
- cout << "Like a warm summer day\n";
-
- if (subana_win->done())
- {
- subana_name = "SubMussa: " + sub_analysis->get_name();
- sub_conn_win = new ConnWindow(w(), h(), (const char*) subana_name.c_str());
- cout << "Like a warm day in may\n";
- sub_conn_win->add_ana(sub_analysis);
- //Fl::visual(FL_DOUBLE|FL_INDEX);
- //sub_conn_box->show();
- }
-}
-
-
-void
-seq_show_cb(Fl_Button* o, void* v)
-{
- ConnWindow* T=(ConnWindow*)v;
- T->real_seq_show_cb();
-}
-
-void
-ConnWindow::real_seq_show_cb()
-{
- show_seq_win = new SeqTextWindow(500,400,"Seq Show", an_analysis->the_seqs);
-}
-
-void
-seq_win_spawn_cb(Fl_Button* o, void* v)
-{
- ConnWindow* T=(ConnWindow*)v;
- T->real_seq_win_spawn_cb();
-}
-
-void
-ConnWindow::real_seq_win_spawn_cb()
-{
- conn_box->spawnSeq();
-}
-
-void
-motif_find_cb(Fl_Button* o, void* v)
-{
- ConnWindow* T=(ConnWindow*)v;
- T->real_motif_find_cb();
-}
-
-void
-ConnWindow::real_motif_find_cb()
-{
- conn_box->find_motifs();
-}
-
-void
-annot_win_cb(Fl_Button* o, void* v)
-{
- ConnWindow* T=(ConnWindow*)v;
- T->real_annot_win_cb();
-}
-
-void
-ConnWindow::real_annot_win_cb()
-{
- conn_box->annot_win();
-}
-
-
-// all the crap needed for dealing with the scale bars
-void
-toggle_scale_bars_cb(Fl_Button* o, void* v)
-{
- ConnWindow* T=(ConnWindow*)v;
- T->real_toggle_bars_cb();
-}
-
-void
-ConnWindow::real_toggle_bars_cb()
-{
- conn_box->toggle_bars();
-}
-
-void
-set_bar_len_cb(Fl_Input* o, void* v)
-{
- ConnWindow* T=(ConnWindow*)v;
- cout << "WAAAAAAAAA\n";
- T->real_set_bar_len_cb(o);
-}
-
-void
-ConnWindow::real_set_bar_len_cb(Fl_Input* o)
-{
- int new_bar_len;
-
- new_bar_len = atoi(o->value());
- cout << "new bar len = " << new_bar_len << endl;
- conn_box->set_bar_interval(new_bar_len);
-}
-
-
-// all the crap needed for dealing with the scale lines
-void
-toggle_scale_lines_cb(Fl_Button* o, void* v)
-{
- ConnWindow* T=(ConnWindow*)v;
- T->real_toggle_lines_cb();
-}
-
-void
-ConnWindow::real_toggle_lines_cb()
-{
- conn_box->toggle_lines();
-}
-
-void
-set_line_len_cb(Fl_Input* o, void* v)
-{
- ConnWindow* T=(ConnWindow*)v;
- cout << "WAAAAAAAAA\n";
- T->real_set_line_len_cb(o);
-}
-
-void
-ConnWindow::real_set_line_len_cb(Fl_Input* o)
-{
- int new_line_len;
-
- new_line_len = atoi(o->value());
- cout << "new line len = " << new_line_len << endl;
- conn_box->set_line_interval(new_line_len);
-}
-
-
-// setting new soft threshold
-
-void
-set_soft_thres_cb(Fl_Input* o, void* v)
-{
- ConnWindow* T=(ConnWindow*)v;
- cout << "WAAAAAAAAA\n";
- T->real_set_soft_thres_cb(o);
-}
-
-void
-ConnWindow::real_set_soft_thres_cb(Fl_Input* o)
-{
- int new_soft_thres;
-
- new_soft_thres = atoi(o->value());
- cout << "new soft thres = " << new_soft_thres << endl;
-
- an_analysis->set_soft_thres(new_soft_thres);
- an_analysis->set_analysis_mode(Mussa::TransitiveNway);
- an_analysis->nway();
- conn_box->scale_paths();
- conn_box->redraw();
-
- // hacked in stuff to save muway files at different thresholds
- string save_path;
- ostringstream append_info;
-
- save_path = an_analysis->get_name() + "/"
- + an_analysis->get_name().substr(0,an_analysis->get_name().find("_t"));
- append_info.str("");
- append_info << "_t" << new_soft_thres << ".muway";
- //<< "_w" << an_analysis->window
- save_path += append_info.str();
- cout << "saving as: " << save_path << endl;
- an_analysis->save_muway(save_path);
-}
-
-
-
-
-ConnWindow::ConnWindow(int w, int h, const char* title):
- Fl_Double_Window(w,h,title)
-{
- int button_len = 120;
- Fl_Color a_color = fl_rgb_color(150, 200, 255);
-
- padding = 5;
-
- begin();
- //fl_color(150,200,255);
- color(FL_WHITE);
- resizable(this);
-
-
- // create file menu button
- file_menu = new Fl_Menu_Button(padding, 2, button_len, 30, "Analysis");
- file_menu->color(FL_WHITE,a_color);
- file_menu->box(FL_BORDER_BOX);
- file_menu->clear();
-
- // add menu items
- file_menu->add("Do Analysis", 0, (Fl_Callback *) do_ana_cb, this);
- file_menu->add("Load Analysis", 0, (Fl_Callback *) load_ana_cb, this);
- file_menu->add("Setup Analysis", 0, (Fl_Callback *) setup_ana_cb, this);
- file_menu->add("Sub Analysis", 0, (Fl_Callback *) subana_cb, this);
-
-
- view_menu = new Fl_Menu_Button(padding+button_len,2, button_len, 30, "View");
- view_menu->color(FL_WHITE,a_color);
- view_menu->box(FL_BORDER_BOX);
- view_menu->clear();
- view_menu->add("Sequence Zoom", 0, (Fl_Callback*) seq_win_spawn_cb, this);
- view_menu->add("Motif Finder", 0, (Fl_Callback*) motif_find_cb, this);
- view_menu->add("Annotations", 0, (Fl_Callback*) annot_win_cb, this);
- view_menu->add("Copy Seq", 0, (Fl_Callback*) seq_show_cb, this);
- view_menu->add("Toggle Bars", 0, (Fl_Callback*) toggle_scale_bars_cb, this,
- FL_MENU_TOGGLE|FL_MENU_VALUE);
- view_menu->add("Toggle Lines", 0, (Fl_Callback*) toggle_scale_lines_cb, this,
- FL_MENU_TOGGLE|FL_MENU_VALUE);
-
- bar_input = new Fl_Input(padding+3*button_len, 2, button_len, 30, "Bar Length (bp)");
- bar_input->value("");
- bar_input->when(FL_WHEN_ENTER_KEY);
- bar_input->callback((Fl_Callback*)set_bar_len_cb, this);
-
- line_input = new Fl_Input(padding+5*button_len, 2, button_len, 30, "Line Interval (bp)");
- line_input->value("");
- line_input->when(FL_WHEN_ENTER_KEY);
- line_input->callback((Fl_Callback*)set_line_len_cb, this);
-
-
- thres_input = new Fl_Input(padding+7*button_len, 2, button_len, 30, "Threshold");
- thres_input->value("");
- thres_input->when(FL_WHEN_ENTER_KEY);
- thres_input->callback((Fl_Callback*)set_soft_thres_cb, this);
-
-
- // create the connections box
- conn_box = new ConnView(padding, padding + 30, w-2*padding, h-2*padding-30);
- //conn_box = new ConnView(padding, padding, w-2*padding, h-2*padding);
-
- end();
- show();
-}
-
-
-ConnWindow::~ConnWindow()
-{}
-
-
-void
-ConnWindow::add_ana(Mussa *the_ana)
-{
- an_analysis = the_ana;
-
- // relabel window with the analysis name
- window_name = "Mussa: " + an_analysis->get_name();
- label((const char*)window_name.c_str());
-
- conn_box->setup(an_analysis->get_name(), an_analysis->size(),
- an_analysis->get_window(), &(an_analysis->the_seqs),
- &(an_analysis->the_paths));
- conn_box->scale_paths();
-}
+++ /dev/null
-#ifndef _MUSSA_GUI_CONN_WINDOW_H_
-#define _MUSSA_GUI_CONN_WINDOW_H_
-
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-#include <string>
-
-#include <FL/Fl_Double_Window.H>
-#include <FL/Fl_Menu_Bar.H>
-#include <FL/Fl_Menu_Item.H>
-
-#include "ConnView.hh"
-#include "SetupWindow.hh"
-#include "SubAnalysisWindow.hh"
-#include "SeqTextWindow.hh"
-
-//! Window for showing the lines connecting the various sequences together
-class ConnWindow : public Fl_Double_Window
-{
- private:
- Mussa *an_analysis, *sub_analysis;
- ConnWindow *sub_conn_win;
-
- Fl_Menu_Button *file_menu;
- Fl_Menu_Button *view_menu;
- Fl_Menu_Bar *menu_bar;
- Fl_Input *bar_input;
- Fl_Input *line_input;
- Fl_Input *thres_input;
- ConnView *conn_box;
- SetupWindow *setup_win;
- SubAnalysisWindow *subana_win;
- SeqTextWindow *show_seq_win;
- int padding, name_pad;
- std::string window_name;
-
- public:
- ConnWindow(int w, int h, const char* title);
- ~ConnWindow();
- void add_ana(Mussa *the_ana);
-
- void real_load_ana_cb();
- void real_do_ana_cb();
- void real_setup_ana_cb();
- void real_subana_cb();
- void real_resthres();
- void real_seq_show_cb();
-
- void real_seq_win_spawn_cb();
- void real_motif_find_cb();
- void real_annot_win_cb();
-
- void real_toggle_bars_cb();
- void real_set_bar_len_cb(Fl_Input* o);
- void real_toggle_lines_cb();
- void real_set_line_len_cb(Fl_Input* o);
- void real_set_soft_thres_cb(Fl_Input* o);
-};
-
-#endif
--- /dev/null
+#ifndef _MUSSA_GUI_CONN_WINDOW_H_
+#define _MUSSA_GUI_CONN_WINDOW_H_
+
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+#include <string>
+
+#include <FL/Fl_Double_Window.H>
+#include <FL/Fl_Menu_Bar.H>
+#include <FL/Fl_Menu_Item.H>
+
+#include "gui/ConnView.hpp"
+#include "gui/SetupWindow.hpp"
+#include "gui/SubAnalysisWindow.hpp"
+#include "gui/SeqTextWindow.hpp"
+
+//! Window for showing the lines connecting the various sequences together
+class ConnWindow : public Fl_Double_Window
+{
+ private:
+ Mussa *an_analysis, *sub_analysis;
+ ConnWindow *sub_conn_win;
+
+ Fl_Menu_Button *file_menu;
+ Fl_Menu_Button *view_menu;
+ Fl_Menu_Bar *menu_bar;
+ Fl_Input *bar_input;
+ Fl_Input *line_input;
+ Fl_Input *thres_input;
+ ConnView *conn_box;
+ SetupWindow *setup_win;
+ SubAnalysisWindow *subana_win;
+ SeqTextWindow *show_seq_win;
+ int padding, name_pad;
+ std::string window_name;
+
+ public:
+ ConnWindow(int w, int h, const char* title);
+ ~ConnWindow();
+ void add_ana(Mussa *the_ana);
+
+ void real_load_ana_cb();
+ void real_do_ana_cb();
+ void real_setup_ana_cb();
+ void real_subana_cb();
+ void real_resthres();
+ void real_seq_show_cb();
+
+ void real_seq_win_spawn_cb();
+ void real_motif_find_cb();
+ void real_annot_win_cb();
+
+ void real_toggle_bars_cb();
+ void real_set_bar_len_cb(Fl_Input* o);
+ void real_toggle_lines_cb();
+ void real_set_line_len_cb(Fl_Input* o);
+ void real_set_soft_thres_cb(Fl_Input* o);
+};
+
+#endif
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+#include "gui/MotifWindow.hpp"
+
+#include <iostream>
+
+#include <FL/fl_show_colormap.H>
+
+using namespace std;
+
+motif
+new_blank_motif()
+{
+ motif *a_motif;
+
+ a_motif = new motif;
+ a_motif->name = "";
+ a_motif->seq = "";
+ a_motif->color = (Fl_Color) 5;
+ a_motif->locations.clear();
+ a_motif->dirty = false;
+
+ cout << "name: " << a_motif->name << " seq: " << a_motif->seq << endl;
+
+ return *a_motif;
+}
+
+
+void
+cb_motif_in(Fl_Input* o, void* v)
+{
+ motif_instance * blah = (motif_instance *) v;
+ MotifWindow* T= blah->mw_ptr;
+ T->cb_motif_in_i(o,blah->index);
+}
+
+
+void
+cb_motif_color(Fl_Button* o, void* v)
+{
+ motif_instance * blah = (motif_instance *) v;
+ MotifWindow* T= blah->mw_ptr;
+ T->cb_motif_color_i(o,blah->index);
+}
+
+
+MotifWindow::MotifWindow(int w, int h, const char* title,
+ vector<motif> * some_motifs):Fl_Window(w,h,title)
+{
+ int i;
+
+ the_motifs = some_motifs;
+ motif_count = 0;
+
+ motif_color_buttons.clear();
+
+ begin();
+ motif_input_pack = new Fl_Pack(0, 0, w, h);
+ motif_input_pack->spacing(4);
+
+ // button to add new motif inputs
+ add_motif = new Fl_Button(0,0,100,24,"Add Motif Slot");
+ add_motif->callback((Fl_Callback*)add_motif_cb, this);
+ motif_input_pack->add(add_motif);
+ // test button to make sure motif data is being stored
+ test = new Fl_Button(0,0,100,24,"show motifs");
+ test->callback((Fl_Callback*)print_cb, this);
+ motif_input_pack->add(test);
+ // creat an initial set of motif input widgets and attach to motif vector
+ for (i = 0; i < 5; i++)
+ {
+ add_motif_input(i);
+ motif_count++;
+ }
+
+
+
+
+ add(motif_input_pack);
+
+ end();
+ resizable(this);
+ show();
+}
+
+ //tmp_input->user_data((void*) i);
+
+MotifWindow::~MotifWindow(){}
+
+void
+MotifWindow::add_motif_input(int index)
+{
+ Fl_Input * new_input;
+ Fl_Button *new_color_button;
+ motif_instance * something;
+ Fl_Pack * motif_hor_pack;
+
+
+ something = new motif_instance;
+ something->mw_ptr = this;
+ something->index = index;
+
+ motif_hor_pack = new Fl_Pack(0, 0, w(), 24);
+ motif_hor_pack->type(Fl_Pack::HORIZONTAL);
+ motif_hor_pack->spacing(4);
+
+ // setup the color display/selection button
+ new_color_button = new Fl_Button(0, 0, 24, 24, "");
+ new_color_button->color((*the_motifs)[index].color);
+ new_color_button->box(FL_FLAT_BOX);
+ new_color_button->callback((Fl_Callback*)cb_motif_color, (void*) something);
+ motif_color_buttons.push_back(new_color_button);
+ motif_hor_pack->add(new_color_button);
+
+
+ // setup the motif inputs
+ new_input = new Fl_Input(0, 0, 200, 24, "");
+ new_input->value( ((*the_motifs)[index].seq).c_str() );
+ new_input->callback((Fl_Callback*)cb_motif_in, (void*) something);
+ motif_ins.push_back(new_input);
+ motif_hor_pack->add(new_input);
+
+ motif_input_pack->add(motif_hor_pack);
+}
+/*
+ cout << "fee\n";
+ cout << "fie\n";
+ cout << "foe\n";
+ cout << "fum\n";
+*/
+
+void
+MotifWindow::cb_motif_in_i(Fl_Input* o, int i)
+{
+ (*the_motifs)[i].seq = o->value();
+ (*the_motifs)[i].dirty = true;
+}
+
+void
+MotifWindow::cb_motif_color_i(Fl_Button* o, int i)
+{
+ //Fl_Color new_color;
+
+ (*the_motifs)[i].color = fl_show_colormap((*the_motifs)[i].color);
+ //motif_color_buttons[i]->
+ o->color((*the_motifs)[i].color);
+ redraw();
+}
+
+void MotifWindow::add_motif_cb(Fl_Button* o, void* v)
+{
+ MotifWindow* T=(MotifWindow*)v;
+ T->add_motif_cb_real(o,v);
+}
+
+
+void MotifWindow::add_motif_cb_real(Fl_Button* , void*)
+{
+ motif blank_motif;
+
+ //blank_motif.name = "";
+ //blank_motif.seq = "";
+ blank_motif = new_blank_motif();
+ (*the_motifs).push_back(blank_motif);
+ add_motif_input(motif_count++);
+ redraw();
+}
+
+
+void MotifWindow::print_cb(Fl_Button* o, void* v)
+{
+ MotifWindow* T=(MotifWindow*)v;
+ T->print_cb_real(o,v);
+}
+
+
+void MotifWindow::print_cb_real(Fl_Button* , void*)
+{
+ int i;
+
+ for (i = 0; i < motif_count; i++)
+ cout << (*the_motifs)[i].seq << endl;
+}
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-#include "MotifWindow.hh"
-
-#include <iostream>
-
-#include <FL/fl_show_colormap.H>
-
-using namespace std;
-
-motif
-new_blank_motif()
-{
- motif *a_motif;
-
- a_motif = new motif;
- a_motif->name = "";
- a_motif->seq = "";
- a_motif->color = (Fl_Color) 5;
- a_motif->locations.clear();
- a_motif->dirty = false;
-
- cout << "name: " << a_motif->name << " seq: " << a_motif->seq << endl;
-
- return *a_motif;
-}
-
-
-void
-cb_motif_in(Fl_Input* o, void* v)
-{
- motif_instance * blah = (motif_instance *) v;
- MotifWindow* T= blah->mw_ptr;
- T->cb_motif_in_i(o,blah->index);
-}
-
-
-void
-cb_motif_color(Fl_Button* o, void* v)
-{
- motif_instance * blah = (motif_instance *) v;
- MotifWindow* T= blah->mw_ptr;
- T->cb_motif_color_i(o,blah->index);
-}
-
-
-MotifWindow::MotifWindow(int w, int h, const char* title,
- vector<motif> * some_motifs):Fl_Window(w,h,title)
-{
- int i;
-
- the_motifs = some_motifs;
- motif_count = 0;
-
- motif_color_buttons.clear();
-
- begin();
- motif_input_pack = new Fl_Pack(0, 0, w, h);
- motif_input_pack->spacing(4);
-
- // button to add new motif inputs
- add_motif = new Fl_Button(0,0,100,24,"Add Motif Slot");
- add_motif->callback((Fl_Callback*)add_motif_cb, this);
- motif_input_pack->add(add_motif);
- // test button to make sure motif data is being stored
- test = new Fl_Button(0,0,100,24,"show motifs");
- test->callback((Fl_Callback*)print_cb, this);
- motif_input_pack->add(test);
- // creat an initial set of motif input widgets and attach to motif vector
- for (i = 0; i < 5; i++)
- {
- add_motif_input(i);
- motif_count++;
- }
-
-
-
-
- add(motif_input_pack);
-
- end();
- resizable(this);
- show();
-}
-
- //tmp_input->user_data((void*) i);
-
-MotifWindow::~MotifWindow(){}
-
-void
-MotifWindow::add_motif_input(int index)
-{
- Fl_Input * new_input;
- Fl_Button *new_color_button;
- motif_instance * something;
- Fl_Pack * motif_hor_pack;
-
-
- something = new motif_instance;
- something->mw_ptr = this;
- something->index = index;
-
- motif_hor_pack = new Fl_Pack(0, 0, w(), 24);
- motif_hor_pack->type(Fl_Pack::HORIZONTAL);
- motif_hor_pack->spacing(4);
-
- // setup the color display/selection button
- new_color_button = new Fl_Button(0, 0, 24, 24, "");
- new_color_button->color((*the_motifs)[index].color);
- new_color_button->box(FL_FLAT_BOX);
- new_color_button->callback((Fl_Callback*)cb_motif_color, (void*) something);
- motif_color_buttons.push_back(new_color_button);
- motif_hor_pack->add(new_color_button);
-
-
- // setup the motif inputs
- new_input = new Fl_Input(0, 0, 200, 24, "");
- new_input->value( ((*the_motifs)[index].seq).c_str() );
- new_input->callback((Fl_Callback*)cb_motif_in, (void*) something);
- motif_ins.push_back(new_input);
- motif_hor_pack->add(new_input);
-
- motif_input_pack->add(motif_hor_pack);
-}
-/*
- cout << "fee\n";
- cout << "fie\n";
- cout << "foe\n";
- cout << "fum\n";
-*/
-
-void
-MotifWindow::cb_motif_in_i(Fl_Input* o, int i)
-{
- (*the_motifs)[i].seq = o->value();
- (*the_motifs)[i].dirty = true;
-}
-
-void
-MotifWindow::cb_motif_color_i(Fl_Button* o, int i)
-{
- //Fl_Color new_color;
-
- (*the_motifs)[i].color = fl_show_colormap((*the_motifs)[i].color);
- //motif_color_buttons[i]->
- o->color((*the_motifs)[i].color);
- redraw();
-}
-
-void MotifWindow::add_motif_cb(Fl_Button* o, void* v)
-{
- MotifWindow* T=(MotifWindow*)v;
- T->add_motif_cb_real(o,v);
-}
-
-
-void MotifWindow::add_motif_cb_real(Fl_Button* , void*)
-{
- motif blank_motif;
-
- //blank_motif.name = "";
- //blank_motif.seq = "";
- blank_motif = new_blank_motif();
- (*the_motifs).push_back(blank_motif);
- add_motif_input(motif_count++);
- redraw();
-}
-
-
-void MotifWindow::print_cb(Fl_Button* o, void* v)
-{
- MotifWindow* T=(MotifWindow*)v;
- T->print_cb_real(o,v);
-}
-
-
-void MotifWindow::print_cb_real(Fl_Button* , void*)
-{
- int i;
-
- for (i = 0; i < motif_count; i++)
- cout << (*the_motifs)[i].seq << endl;
-}
+++ /dev/null
-#ifndef _MUSSA_GUI_MOTIF_WINDOW_H_
-#define _MUSSA_GUI_MOTIF_WINDOW_H_
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-#include <list>
-#include <string>
-#include <vector>
-
-#include <FL/Fl_Window.H>
-#include <FL/Fl_Button.H>
-
-#include <FL/Fl_Input.H>
-#include <FL/Fl_Pack.H>
-
-#include "alg/mussa_class.hh"
-
-struct motif
-{
- std::string name, seq;
- Fl_Color color;
- std::vector<std::vector<int> > locations;
- bool dirty;
-};
-
-//typedef motif_ptr *motif;
-
-
-class MotifWindow : public Fl_Window
-{
- public:
- MotifWindow(int w, int h, const char* title, std::vector<motif> * some_motifs);
- ~MotifWindow();
- Fl_Pack * motif_input_pack;
- std::list<Fl_Input*> motif_ins;
- std::vector<Fl_Button*> motif_color_buttons;
- std::list<Fl_Input*> name_ins;
- Fl_Button* test;
- Fl_Button* add_motif;
-
- void cb_motif_in_i(Fl_Input*, int i);
- void cb_motif_color_i(Fl_Button* o, int i);
-
- private:
- std::vector<motif> * the_motifs;
- int motif_count;
-
- void add_motif_input(int index);
-
- static void add_motif_cb(Fl_Button*, void*);
- inline void add_motif_cb_real(Fl_Button*, void*);
-
- static void print_cb(Fl_Button*, void*);
- inline void print_cb_real(Fl_Button*, void*);
-};
-
-// crazy whacked shite Titus taught me to do to get an index value associated
-// with each instance of an input associated with the callback...
-struct motif_instance
-{
- MotifWindow * mw_ptr;
- int index;
-};
-
-motif new_blank_motif();
-#endif
--- /dev/null
+#ifndef _MUSSA_GUI_MOTIF_WINDOW_H_
+#define _MUSSA_GUI_MOTIF_WINDOW_H_
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+#include <list>
+#include <string>
+#include <vector>
+
+#include <FL/Fl_Window.H>
+#include <FL/Fl_Button.H>
+
+#include <FL/Fl_Input.H>
+#include <FL/Fl_Pack.H>
+
+#include "alg/mussa.hpp"
+
+struct motif
+{
+ std::string name, seq;
+ Fl_Color color;
+ std::vector<std::vector<int> > locations;
+ bool dirty;
+};
+
+//typedef motif_ptr *motif;
+
+
+class MotifWindow : public Fl_Window
+{
+ public:
+ MotifWindow(int w, int h, const char* title, std::vector<motif> * some_motifs);
+ ~MotifWindow();
+ Fl_Pack * motif_input_pack;
+ std::list<Fl_Input*> motif_ins;
+ std::vector<Fl_Button*> motif_color_buttons;
+ std::list<Fl_Input*> name_ins;
+ Fl_Button* test;
+ Fl_Button* add_motif;
+
+ void cb_motif_in_i(Fl_Input*, int i);
+ void cb_motif_color_i(Fl_Button* o, int i);
+
+ private:
+ std::vector<motif> * the_motifs;
+ int motif_count;
+
+ void add_motif_input(int index);
+
+ static void add_motif_cb(Fl_Button*, void*);
+ inline void add_motif_cb_real(Fl_Button*, void*);
+
+ static void print_cb(Fl_Button*, void*);
+ inline void print_cb_real(Fl_Button*, void*);
+};
+
+// crazy whacked shite Titus taught me to do to get an index value associated
+// with each instance of an input associated with the callback...
+struct motif_instance
+{
+ MotifWindow * mw_ptr;
+ int index;
+};
+
+motif new_blank_motif();
+#endif
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+#include "gui/SeqTextWindow.hpp"
+
+#include <iostream>
+using namespace std;
+void
+get_seq_cb(Fl_Button* o, void* v)
+{
+ SeqTextWindow* T=(SeqTextWindow*)v;
+ T->real_get_seq_cb();
+}
+
+void
+SeqTextWindow::real_get_seq_cb()
+{
+ string sub_seq_formatted;
+ int seq_len, i, line_len;
+
+
+ cout << "length = " << seq_end-seq_start << endl;
+
+ // make sure inputed values within valid ranges
+ if ((seq_end > seq_start) && (seq_id > -1) && (seq_id < the_seqs.size()) )
+ {
+ sub_sequence = the_seqs[seq_id].subseq(seq_start, seq_end-seq_start);
+
+ sub_seq_formatted = "";
+ seq_len = sub_sequence.size();
+ line_len = 40;
+ for (i = 0; i < seq_len; i += line_len)
+ {
+ sub_seq_formatted.append(sub_sequence.substr(i,line_len));
+ sub_seq_formatted.append("\n");
+ }
+
+ seq_display->value((const char *)sub_seq_formatted.c_str());
+ }
+}
+
+
+// *** input seq index id
+
+void
+set_seq_id_cb(Fl_Input* o, void* v)
+{
+ SeqTextWindow* T=(SeqTextWindow*)v;
+ T->real_set_seq_id_cb(o);
+}
+
+void
+SeqTextWindow::real_set_seq_id_cb(Fl_Input* o)
+{
+ seq_id = atoi(o->value()) - 1; // -1 since arrays start at 0
+}
+
+
+// *** input seq start index
+
+void
+set_seq_start_cb(Fl_Input* o, void* v)
+{
+ SeqTextWindow* T=(SeqTextWindow*)v;
+ T->real_set_seq_start_cb(o);
+}
+
+void
+SeqTextWindow::real_set_seq_start_cb(Fl_Input* o)
+{
+ seq_start = atoi(o->value());
+}
+
+// *** input seq end index
+
+void
+set_seq_end_cb(Fl_Input* o, void* v)
+{
+ SeqTextWindow* T=(SeqTextWindow*)v;
+ T->real_set_seq_end_cb(o);
+}
+
+void
+SeqTextWindow::real_set_seq_end_cb(Fl_Input* o)
+{
+ seq_end = atoi(o->value());
+}
+
+
+SeqTextWindow::SeqTextWindow(int w, int h, const char* title,
+ vector<Sequence> some_Seqs):Fl_Window(w,h,title)
+{
+ string a_name;
+ color(FL_WHITE);
+ the_seqs = some_Seqs;
+
+
+ seq_id = -1;
+ seq_start = 1000000;
+ seq_end = -1000000;
+
+ begin();
+
+ seq_id_input = new Fl_Input(80,10,30,30, "Seq num: ");
+ seq_id_input->value("");
+ seq_id_input->callback((Fl_Callback*)set_seq_id_cb, this);
+
+ seq_start_input = new Fl_Input(160,10,100,30, " start: ");
+ seq_start_input->value("");
+ seq_start_input->callback((Fl_Callback*)set_seq_start_cb, this);
+
+ seq_end_input = new Fl_Input(310,10,100,30, "end: ");
+ seq_end_input->value("");
+ seq_end_input->callback((Fl_Callback*)set_seq_end_cb, this);
+
+ seq_display = new Fl_Multiline_Output(10, 50, w-20, h-60, "");
+ seq_display->value("");
+
+ //seq_display2 = new Fl_Text_Display(10,100, w-20, h-110,"");
+
+ // button to get the sequence
+ get_seq_but = new Fl_Button(w-80,10,80,30,"Get Seq");
+ get_seq_but->callback((Fl_Callback*)get_seq_cb, this);
+
+
+ end();
+ //resizable(this);
+ show();
+}
+
+
+SeqTextWindow::~SeqTextWindow(){}
+
+/*
+ cout << "fee\n";
+ cout << "fie\n";
+ cout << "foe\n";
+ cout << "fum\n";
+*/
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-#include "gui/SeqTextWindow.hh"
-
-#include <iostream>
-using namespace std;
-void
-get_seq_cb(Fl_Button* o, void* v)
-{
- SeqTextWindow* T=(SeqTextWindow*)v;
- T->real_get_seq_cb();
-}
-
-void
-SeqTextWindow::real_get_seq_cb()
-{
- string sub_seq_formatted;
- int seq_len, i, line_len;
-
-
- cout << "length = " << seq_end-seq_start << endl;
-
- // make sure inputed values within valid ranges
- if ((seq_end > seq_start) && (seq_id > -1) && (seq_id < the_seqs.size()) )
- {
- sub_sequence = the_seqs[seq_id].subseq(seq_start, seq_end-seq_start);
-
- sub_seq_formatted = "";
- seq_len = sub_sequence.size();
- line_len = 40;
- for (i = 0; i < seq_len; i += line_len)
- {
- sub_seq_formatted.append(sub_sequence.substr(i,line_len));
- sub_seq_formatted.append("\n");
- }
-
- seq_display->value((const char *)sub_seq_formatted.c_str());
- }
-}
-
-
-// *** input seq index id
-
-void
-set_seq_id_cb(Fl_Input* o, void* v)
-{
- SeqTextWindow* T=(SeqTextWindow*)v;
- T->real_set_seq_id_cb(o);
-}
-
-void
-SeqTextWindow::real_set_seq_id_cb(Fl_Input* o)
-{
- seq_id = atoi(o->value()) - 1; // -1 since arrays start at 0
-}
-
-
-// *** input seq start index
-
-void
-set_seq_start_cb(Fl_Input* o, void* v)
-{
- SeqTextWindow* T=(SeqTextWindow*)v;
- T->real_set_seq_start_cb(o);
-}
-
-void
-SeqTextWindow::real_set_seq_start_cb(Fl_Input* o)
-{
- seq_start = atoi(o->value());
-}
-
-// *** input seq end index
-
-void
-set_seq_end_cb(Fl_Input* o, void* v)
-{
- SeqTextWindow* T=(SeqTextWindow*)v;
- T->real_set_seq_end_cb(o);
-}
-
-void
-SeqTextWindow::real_set_seq_end_cb(Fl_Input* o)
-{
- seq_end = atoi(o->value());
-}
-
-
-SeqTextWindow::SeqTextWindow(int w, int h, const char* title,
- vector<Sequence> some_Seqs):Fl_Window(w,h,title)
-{
- string a_name;
- color(FL_WHITE);
- the_seqs = some_Seqs;
-
-
- seq_id = -1;
- seq_start = 1000000;
- seq_end = -1000000;
-
- begin();
-
- seq_id_input = new Fl_Input(80,10,30,30, "Seq num: ");
- seq_id_input->value("");
- seq_id_input->callback((Fl_Callback*)set_seq_id_cb, this);
-
- seq_start_input = new Fl_Input(160,10,100,30, " start: ");
- seq_start_input->value("");
- seq_start_input->callback((Fl_Callback*)set_seq_start_cb, this);
-
- seq_end_input = new Fl_Input(310,10,100,30, "end: ");
- seq_end_input->value("");
- seq_end_input->callback((Fl_Callback*)set_seq_end_cb, this);
-
- seq_display = new Fl_Multiline_Output(10, 50, w-20, h-60, "");
- seq_display->value("");
-
- //seq_display2 = new Fl_Text_Display(10,100, w-20, h-110,"");
-
- // button to get the sequence
- get_seq_but = new Fl_Button(w-80,10,80,30,"Get Seq");
- get_seq_but->callback((Fl_Callback*)get_seq_cb, this);
-
-
- end();
- //resizable(this);
- show();
-}
-
-
-SeqTextWindow::~SeqTextWindow(){}
-
-/*
- cout << "fee\n";
- cout << "fie\n";
- cout << "foe\n";
- cout << "fum\n";
-*/
+++ /dev/null
-#ifndef _MUSSA_GUI_SEQ_TEXT_H_
-#define _MUSSA_GUI_SEQ_TEXT_H_
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-#include <string>
-#include <vector>
-
-#include <FL/Fl_Button.H>
-#include <FL/Fl_Input.H>
-#include <FL/Fl_Text_Buffer.H>
-#include <FL/Fl_Text_Display.H>
-#include <FL/Fl_Multiline_Output.H>
-#include <FL/Fl_Window.H>
-
-#include "alg/sequence.hh"
-
-class SeqTextWindow : public Fl_Window
-{
- public:
- SeqTextWindow(int w, int h, const char* title, std::vector<Sequence> some_Seqs);
- ~SeqTextWindow();
-
- Fl_Button* get_seq_but;
- Fl_Multiline_Output* seq_display;
- Fl_Text_Buffer* seq_buffer;
- Fl_Text_Display* seq_display2;
- Fl_Input *seq_id_input;
- Fl_Input *seq_start_input;
- Fl_Input *seq_end_input;
-
- // callback receiver functions
-
- void real_get_seq_cb();
- void real_set_seq_id_cb(Fl_Input* o);
- void real_set_seq_start_cb(Fl_Input* o);
- void real_set_seq_end_cb(Fl_Input* o);
-
- private:
- // sequence data
- std::vector<Sequence> the_seqs;
- std::string sub_sequence;
- int seq_id, seq_start, seq_end;
-};
-#endif
--- /dev/null
+#ifndef _MUSSA_GUI_SEQ_TEXT_H_
+#define _MUSSA_GUI_SEQ_TEXT_H_
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+#include <string>
+#include <vector>
+
+#include <FL/Fl_Button.H>
+#include <FL/Fl_Input.H>
+#include <FL/Fl_Text_Buffer.H>
+#include <FL/Fl_Text_Display.H>
+#include <FL/Fl_Multiline_Output.H>
+#include <FL/Fl_Window.H>
+
+#include "alg/sequence.hpp"
+
+class SeqTextWindow : public Fl_Window
+{
+ public:
+ SeqTextWindow(int w, int h, const char* title, std::vector<Sequence> some_Seqs);
+ ~SeqTextWindow();
+
+ Fl_Button* get_seq_but;
+ Fl_Multiline_Output* seq_display;
+ Fl_Text_Buffer* seq_buffer;
+ Fl_Text_Display* seq_display2;
+ Fl_Input *seq_id_input;
+ Fl_Input *seq_start_input;
+ Fl_Input *seq_end_input;
+
+ // callback receiver functions
+
+ void real_get_seq_cb();
+ void real_set_seq_id_cb(Fl_Input* o);
+ void real_set_seq_start_cb(Fl_Input* o);
+ void real_set_seq_end_cb(Fl_Input* o);
+
+ private:
+ // sequence data
+ std::vector<Sequence> the_seqs;
+ std::string sub_sequence;
+ int seq_id, seq_start, seq_end;
+};
+#endif
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+#include "gui/SeqView.hpp"
+#include <iostream>
+#include <sstream>
+
+#include <FL/Fl.H>
+#include <FL/fl_draw.H>
+
+using namespace std;
+
+void
+SeqView::setup(string name, int sq_num,
+ vector<Sequence> *some_seqs,
+ list<ExtendedConservedPath > some_paths, vector<int> some_lens,
+ vector<motif> *some_motifs)
+{
+ int seq_i;
+ list<ExtendedConservedPath >::iterator pathz_i;
+
+ analysis_name = name;
+ seq_num = sq_num;
+ S = some_seqs;
+ P = some_paths;
+ seq_lens = some_lens;
+ the_motifs = some_motifs;
+
+ y_seq_incre = (y_max-10-10) / (seq_num - 1);
+
+ fl_font(FL_COURIER, 14);
+ cout << "font width: " << fl_width('A') << endl;
+
+ index_pad = 6 * (int) fl_width('A') + 5;
+
+ align_offsets(0);
+
+ raw_sequence.clear();
+ for(seq_i = 0; seq_i < seq_num; ++seq_i)
+ raw_sequence.push_back( (*S)[seq_i].get_seq() );
+
+ for(pathz_i = P.begin(); pathz_i != P.end(); ++pathz_i)
+ {
+ show_aligns.push_back(true);
+ }
+
+ dragging = false;
+ scroll_offset = 0;
+ //scroll_pos = 0;
+ drag_change = 0;
+
+ cout << "waaaaa!\n";
+ cout << x() << " " << y() << " " << w() << " " << h() << endl;
+}
+
+void
+SeqView::resize(int new_x, int new_y, int new_w, int new_h)
+{
+ x(new_x);
+ y(new_y);
+ w(new_w);
+ h(new_h);
+
+ // hmmm, why do I use these values on the the widgets inherent ones?
+ // I think there was a reason...once?
+ x_max = new_w;
+ y_max = new_h;
+ x_min = new_x;
+ y_min = new_y;
+
+ // things that need to be recalculated
+ y_seq_incre = (y_max-10-10) / (seq_num - 1);
+}
+
+
+void
+SeqView::draw()
+{
+ double ch_width;
+
+
+ // clear drawing area and set background to white
+ fl_color(FL_WHITE);
+ fl_rectf(x(), y(), w(), h());
+
+ fl_font(FL_COURIER, 14);
+ //blatantly stolen from FR2
+ ch_width = fl_width('A'); // monospaced: all characters are same width
+
+
+ if (show_bars)
+ {
+ int grey_box_num, grey_box_len;
+ int i;
+ // draw in some light grey boxes every 10bp to delineate for user
+ //fl_color(200,235,235);
+ fl_color(180,180,180);
+ grey_box_num = (((x_max - index_pad) / (int) ch_width) / 10) + 1;
+ grey_box_len = 10 * (int) ch_width;
+ for(i = 0; i < grey_box_num; i++)
+ if ((i % 2) != 0)
+ fl_rectf(x()+index_pad-1 + (i * grey_box_len), y(), grey_box_len, h());
+ }
+
+ if (show_motifs)
+ draw_motifs(ch_width);
+
+ draw_sequence(ch_width);
+
+ draw_match_lines(ch_width);
+
+ draw_indices(ch_width);
+
+
+ // draw some bounding boxes to visually separate things
+ fl_color(150,200,255);
+ fl_line_style(FL_SOLID, 2, NULL);
+ fl_rect(x(), y(), w(), h());
+ fl_rect(x()+index_pad-1, y(), w()-2*(index_pad-1), h());
+}
+
+void
+SeqView::draw_motifs(double ch_width)
+{
+ vector<motif>::iterator motif_i;
+ vector<int> some_motif_locs;
+ vector<int>::iterator i_locs;
+ int scale_len, motif_len, i2;
+ int y_loc, x_start;
+
+ //fl_color(255,0,255);
+ fl_line_style(FL_SOLID, 10, NULL);
+ motif_i = the_motifs->begin();
+ while (motif_i != the_motifs->end())
+ {
+ fl_color(motif_i->color);
+ motif_len = motif_i->seq.length();
+ scale_len = (int) (motif_len * ch_width);
+ y_loc = y_min + 10;
+ if (!motif_i->locations.empty())
+ for(i2 = 0; i2 < seq_num; i2++)
+ {
+ some_motif_locs = (*motif_i).locations[i2];
+
+ i_locs = some_motif_locs.begin();
+ while (i_locs != some_motif_locs.end())
+ {
+ x_start = (int) ((*i_locs +scroll_offset - seq_align_offsets[i2])
+ * ch_width) + index_pad + x();
+
+ //cout << *i_locs << ":" << x_start << " ";
+ // don't draw highlights outside of box range, they can wraparound past some boundry
+ if ((x_start > 0) && (x_start < w()))
+ fl_line(x_start,y_loc,x_start+scale_len,y_loc);
+ ++i_locs;
+ }
+ //cout << endl;
+ y_loc += y_seq_incre;
+ }
+ ++motif_i;
+ }
+}
+
+void
+SeqView::draw_sequence(double ch_width)
+{
+ int i, seq_i, y_loc;
+ Sequence a_seq;
+ string sub_seq;
+ int seq_len, sub_seq_start, sub_seq_len;
+
+
+
+ fl_color(FL_BLACK);
+ y_loc = y_min + 10 + 5;
+
+ for(seq_i = 0; seq_i < seq_num; seq_i++)
+ {
+ seq_len = raw_sequence[seq_i].length();
+ sub_seq_start = seq_align_offsets[seq_i] - scroll_offset;
+ sub_seq_len = (x_max - index_pad) / (int) ch_width;
+ //cout << x_max << " index_pad: " << index_pad << " y - ip: " << (x_max - index_pad) << endl;
+
+ // gotta check thru boundary conditions to make sure we're producing the
+ // right string for the current position (otherwise gonna crash due to
+ // illegal indexing into substr
+ if (sub_seq_start < 0)
+ {
+ sub_seq_len = sub_seq_len - sub_seq_start;
+ if (sub_seq_len < 0)
+ sub_seq_len = 0;
+ sub_seq_start = 0;
+ }
+ else if (sub_seq_start >= seq_len)
+ {
+ sub_seq_start = seq_len;
+ sub_seq_len = 0;
+ }
+ else if ((sub_seq_start + sub_seq_len) >= seq_len)
+ sub_seq_len = seq_len - sub_seq_start;
+
+ sub_seq = raw_sequence[seq_i].substr(sub_seq_start, sub_seq_len);
+ fl_draw(sub_seq.c_str(), index_pad, y_loc);
+ y_loc += y_seq_incre;
+ }
+}
+
+
+void
+SeqView::draw_match_lines(double ch_width)
+{
+ int i, y_loc;
+ list<ExtendedConservedPath >::iterator pathz_i;
+ int i2, i3;
+ int x_start, y_start, x_end, y_end;
+ int window_length, win_i;
+ int rc_1 = 0;
+ int rc_2 = 0;
+ int offset1, offset2;
+ float center1, center2;
+ bool rc_color;
+ vector<bool> rc_list;
+ bool full_match;
+ vector<bool> matched;
+ int align_counter;
+
+
+ align_counter = 0;
+ for(pathz_i = P.begin(); pathz_i != P.end(); ++pathz_i)
+ {
+ if (show_aligns[align_counter])
+ {
+ ExtendedConservedPath& a_path = *pathz_i;
+ window_length = a_path.window_size;
+
+ // determine which parts of the path are RC relative to first species
+ rc_list.clear();
+ for(i2 = 0; i2 < a_path.size()-1; i2++)
+ {
+ if (a_path[i2] < 0)
+ rc_list.push_back(true);
+ else
+ rc_list.push_back(false);
+ }
+
+ // loop over each bp in the conserved region for all sequences
+ for(win_i = 0; win_i < window_length; win_i++)
+ {
+ // determine which exact base pairs match between the sequences
+ full_match = true;
+ for(i2 = 0; i2 < a_path.size()-1; i2++)
+ {
+ // assume not rc as most likely, adjust below
+ rc_1 = 0;
+ rc_2 = 0;
+ // no matter the case, any RC node needs adjustments
+ if (a_path[i2] < 0)
+ rc_1 = window_length-1;
+ if (a_path[i2+1] < 0)
+ rc_2 = window_length-1;
+
+ x_start = (abs(a_path[i2]-rc_1+win_i));
+ x_end = (abs(a_path[i2+1]-rc_2+win_i));
+
+ // RC case handling
+ // ugh, and xor...only want rc coloring if just one of the nodes is rc
+ // if both nodes are rc, then they are 'normal' relative to each other
+ if ( ( rc_list[i2] || rc_list[i2+1] ) &&
+ !(rc_list[i2] && rc_list[i2+1] ) )
+ { //the hideous rc matching logic - not complex, but annoying
+ if ( !( ( (raw_sequence[i2][x_start] == 'A') &&
+ (raw_sequence[i2+1][x_end] == 'T') ) ||
+ ( (raw_sequence[i2][x_start] == 'T') &&
+ (raw_sequence[i2+1][x_end] == 'A') ) ||
+ ( (raw_sequence[i2][x_start] == 'G') &&
+ (raw_sequence[i2+1][x_end] == 'C') ) ||
+ ( (raw_sequence[i2][x_start] == 'C') &&
+ (raw_sequence[i2+1][x_end] == 'G') ) ) )
+ full_match = false;
+ }
+ else
+ {
+ if (!( (raw_sequence[i2][x_start] == raw_sequence[i2+1][x_end]) &&
+ (raw_sequence[i2][x_start] != 'N') &&
+ (raw_sequence[i2+1][x_end] != 'N') ) )
+ full_match = false;
+ }
+ }
+
+ // draw for matches stretching across all sequences
+ if (full_match)
+ {
+ fl_line_style(FL_SOLID, 1, NULL);
+
+ // now can draw the line for each bp in this window that matches
+ // grrr, need to ask if anyone cares if I switch the seq
+ // top-bot order...
+ i3 = 0;
+ y_loc = y_min + 5;
+ for(i2 = 0; i2 < a_path.size()-1; i2++)
+ {
+ // assume not rc as most likely, adjust below
+ rc_1 = 0;
+ rc_2 = 0;
+ // this makes the lines start in the middle of the drawn char/bp
+ center1 = 0.5;
+ center2 = 0.5;
+ // no matter the case, any RC node needs adjustments
+ if (a_path[i2] < 0)
+ {
+ rc_1 = window_length;
+ center1 = -center1;
+ }
+ if (a_path[i2] < 0)
+ {
+ rc_2 = window_length;
+ center2 = -center2;
+ }
+
+ // set offset based on current alignment for which bp to show
+ offset1 = seq_align_offsets[i2];
+ offset2 = seq_align_offsets[i2+1];
+
+ if ( ( rc_list[i2] || rc_list[i2+1] ) &&
+ !(rc_list[i2] && rc_list[i2+1] ) )
+ fl_color(FL_BLUE);
+ else
+ fl_color(FL_RED);
+
+ // maybe shouldn't recalc these, but store values from first loop
+ x_start = (abs((int) (a_path[i2]-rc_1+win_i)));
+ x_end = (abs((int) (a_path[i2+1]-rc_2+win_i)));
+
+ fl_line( (int)((x_start+center1-offset1+scroll_offset)*ch_width)
+ + index_pad, y_loc + 10,
+ (int)((x_end+center2-offset2+scroll_offset)*ch_width)
+ + index_pad, y_loc+y_seq_incre );
+ y_loc += y_seq_incre;
+ }
+ }
+ }
+ }
+ align_counter++;
+ }
+}
+
+void
+SeqView::draw_indices(double ch_width)
+{
+ int seq_i;
+ Sequence a_seq;
+ int y_loc;
+ ostringstream an_index;
+ int shown_seq_len;
+
+
+ // clear out space on sides to draw in index values
+ // I block out the sides rather than adding offsets to the drawing of seq
+ // and conservation lines since the lines need to draw off the 'edge'
+ fl_color(FL_WHITE);
+ fl_rectf(0, y_min, index_pad, h()+y_min);
+ fl_rectf(w()-index_pad, y_min, index_pad, h()+y_min);
+
+ // now can draw in the indices of the start and end of the shown sequence
+ fl_color(FL_BLACK);
+ y_loc = y_min + 10 + 5;
+ for(seq_i = 0; seq_i < seq_num; seq_i++)
+ {
+ an_index.str("");
+ an_index << (seq_align_offsets[seq_i]-scroll_offset);
+ fl_draw((an_index.str()).c_str(), 2, y_loc);
+
+ shown_seq_len = (w() - 2 * index_pad) / (int) ch_width;
+ an_index.str("");
+ an_index << (seq_align_offsets[seq_i]-scroll_offset+shown_seq_len);
+ fl_draw((an_index.str()).c_str(), w()-index_pad+2, y_loc);
+ y_loc += y_seq_incre;
+ }
+}
+
+
+void
+SeqView::toggle_align(int align_num)
+{
+ //cout << align_num << endl;
+ //cout << show_aligns[align_num] << endl;
+ show_aligns[align_num] = !show_aligns[align_num];
+ //cout << show_aligns[align_num] << endl;
+}
+
+
+void
+SeqView::align_offsets(int align_num)
+{
+ list<ExtendedConservedPath >::iterator pathz_i;
+ int i;
+ int window_length;
+
+ cout << "alignment: " << align_num << endl;
+
+ if (P.begin() == P.end())
+ cout << "crud....\n";
+ else
+ {
+ pathz_i = P.begin();
+
+ while(pathz_i != P.end())
+ ++pathz_i;
+
+ // find the path specified
+ i = 0;
+ pathz_i = P.begin();
+ while( (i < align_num) && (pathz_i != P.end()) )
+ {
+ ++i;
+ ++pathz_i;
+ }
+
+ // now set the alignment offsets - basically where the path starts
+ seq_align_offsets.clear();
+ for(i = 0; i < seq_num ; i++)
+ {
+ //cout << (*pathz_i)[i+1] << endl;
+ seq_align_offsets.push_back( abs((*pathz_i)[i+1]) );
+ // for testing purposes: to see everything in the short test sequences
+ //seq_align_offsets.push_back(0);
+ }
+ // reset any dragging done, otherwise might be hard to find selected align
+ scroll_offset = 0;
+ }
+}
+
+
+
+int
+SeqView::handle(int e)
+{
+ int return_value;
+
+ // this empty string needs to be put on cout, otherwise the -O optimize
+ // compile option seems to throw this function away with the following:
+ // gcc version 3.2.2 20030222 (Red Hat Linux 3.2.2-5)
+ cout << "";
+
+ switch(e)
+ {
+ case FL_PUSH:
+ if (Fl::event_button3())
+ {
+ cout << "menu menu menu!\n";
+ return_value = 1;
+ }
+ break;
+ case FL_DRAG:
+ if (!dragging)
+ {
+ drag_change = Fl::event_x();
+ dragging = true;
+ return_value = 1;
+ }
+ drag_change = Fl::event_x() - drag_change;
+ scroll_offset += drag_change;
+ drag_change = Fl::event_x();
+ redraw();
+ break;
+ case FL_RELEASE:
+ if (dragging)
+ {
+ //scroll_offset += Fl::event_x() - drag_start;
+ //scroll_dist = Fl::event_x() - drag_start;
+ //scroll_offset += scroll_dist;
+ //scroll_offset += scroll_pos;
+ dragging = false;
+ redraw();
+ return_value = 1;
+ }
+ break;
+ default:
+ return_value = Fl_Widget::handle(e);
+ }
+
+ return return_value;
+}
+
+void
+SeqView::toggle_bars()
+{
+ show_bars = !show_bars;
+ redraw();
+}
+
+
+void
+SeqView::toggle_motifs()
+{
+ show_motifs = !show_motifs;
+ redraw();
+}
+
+
+void
+SeqView::reporter(string id, int value)
+{
+ cout << id << " : " << value << endl;
+}
+
+
+/*
+ cout << "fee\n";
+ cout << "fie\n";
+ cout << "foe\n";
+ cout << "fum\n";
+*/
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-#include "SeqView.hh"
-#include <iostream>
-#include <sstream>
-
-#include <FL/Fl.H>
-#include <FL/fl_draw.H>
-
-using namespace std;
-
-void
-SeqView::setup(string name, int sq_num,
- vector<Sequence> *some_seqs,
- list<ExtendedConservedPath > some_paths, vector<int> some_lens,
- vector<motif> *some_motifs)
-{
- int seq_i;
- list<ExtendedConservedPath >::iterator pathz_i;
-
- analysis_name = name;
- seq_num = sq_num;
- S = some_seqs;
- P = some_paths;
- seq_lens = some_lens;
- the_motifs = some_motifs;
-
- y_seq_incre = (y_max-10-10) / (seq_num - 1);
-
- fl_font(FL_COURIER, 14);
- cout << "font width: " << fl_width('A') << endl;
-
- index_pad = 6 * (int) fl_width('A') + 5;
-
- align_offsets(0);
-
- raw_sequence.clear();
- for(seq_i = 0; seq_i < seq_num; ++seq_i)
- raw_sequence.push_back( (*S)[seq_i].get_seq() );
-
- for(pathz_i = P.begin(); pathz_i != P.end(); ++pathz_i)
- {
- show_aligns.push_back(true);
- }
-
- dragging = false;
- scroll_offset = 0;
- //scroll_pos = 0;
- drag_change = 0;
-
- cout << "waaaaa!\n";
- cout << x() << " " << y() << " " << w() << " " << h() << endl;
-}
-
-void
-SeqView::resize(int new_x, int new_y, int new_w, int new_h)
-{
- x(new_x);
- y(new_y);
- w(new_w);
- h(new_h);
-
- // hmmm, why do I use these values on the the widgets inherent ones?
- // I think there was a reason...once?
- x_max = new_w;
- y_max = new_h;
- x_min = new_x;
- y_min = new_y;
-
- // things that need to be recalculated
- y_seq_incre = (y_max-10-10) / (seq_num - 1);
-}
-
-
-void
-SeqView::draw()
-{
- double ch_width;
-
-
- // clear drawing area and set background to white
- fl_color(FL_WHITE);
- fl_rectf(x(), y(), w(), h());
-
- fl_font(FL_COURIER, 14);
- //blatantly stolen from FR2
- ch_width = fl_width('A'); // monospaced: all characters are same width
-
-
- if (show_bars)
- {
- int grey_box_num, grey_box_len;
- int i;
- // draw in some light grey boxes every 10bp to delineate for user
- //fl_color(200,235,235);
- fl_color(180,180,180);
- grey_box_num = (((x_max - index_pad) / (int) ch_width) / 10) + 1;
- grey_box_len = 10 * (int) ch_width;
- for(i = 0; i < grey_box_num; i++)
- if ((i % 2) != 0)
- fl_rectf(x()+index_pad-1 + (i * grey_box_len), y(), grey_box_len, h());
- }
-
- if (show_motifs)
- draw_motifs(ch_width);
-
- draw_sequence(ch_width);
-
- draw_match_lines(ch_width);
-
- draw_indices(ch_width);
-
-
- // draw some bounding boxes to visually separate things
- fl_color(150,200,255);
- fl_line_style(FL_SOLID, 2, NULL);
- fl_rect(x(), y(), w(), h());
- fl_rect(x()+index_pad-1, y(), w()-2*(index_pad-1), h());
-}
-
-void
-SeqView::draw_motifs(double ch_width)
-{
- vector<motif>::iterator motif_i;
- vector<int> some_motif_locs;
- vector<int>::iterator i_locs;
- int scale_len, motif_len, i2;
- int y_loc, x_start;
-
- //fl_color(255,0,255);
- fl_line_style(FL_SOLID, 10, NULL);
- motif_i = the_motifs->begin();
- while (motif_i != the_motifs->end())
- {
- fl_color(motif_i->color);
- motif_len = motif_i->seq.length();
- scale_len = (int) (motif_len * ch_width);
- y_loc = y_min + 10;
- if (!motif_i->locations.empty())
- for(i2 = 0; i2 < seq_num; i2++)
- {
- some_motif_locs = (*motif_i).locations[i2];
-
- i_locs = some_motif_locs.begin();
- while (i_locs != some_motif_locs.end())
- {
- x_start = (int) ((*i_locs +scroll_offset - seq_align_offsets[i2])
- * ch_width) + index_pad + x();
-
- //cout << *i_locs << ":" << x_start << " ";
- // don't draw highlights outside of box range, they can wraparound past some boundry
- if ((x_start > 0) && (x_start < w()))
- fl_line(x_start,y_loc,x_start+scale_len,y_loc);
- ++i_locs;
- }
- //cout << endl;
- y_loc += y_seq_incre;
- }
- ++motif_i;
- }
-}
-
-void
-SeqView::draw_sequence(double ch_width)
-{
- int i, seq_i, y_loc;
- Sequence a_seq;
- string sub_seq;
- int seq_len, sub_seq_start, sub_seq_len;
-
-
-
- fl_color(FL_BLACK);
- y_loc = y_min + 10 + 5;
-
- for(seq_i = 0; seq_i < seq_num; seq_i++)
- {
- seq_len = raw_sequence[seq_i].length();
- sub_seq_start = seq_align_offsets[seq_i] - scroll_offset;
- sub_seq_len = (x_max - index_pad) / (int) ch_width;
- //cout << x_max << " index_pad: " << index_pad << " y - ip: " << (x_max - index_pad) << endl;
-
- // gotta check thru boundary conditions to make sure we're producing the
- // right string for the current position (otherwise gonna crash due to
- // illegal indexing into substr
- if (sub_seq_start < 0)
- {
- sub_seq_len = sub_seq_len - sub_seq_start;
- if (sub_seq_len < 0)
- sub_seq_len = 0;
- sub_seq_start = 0;
- }
- else if (sub_seq_start >= seq_len)
- {
- sub_seq_start = seq_len;
- sub_seq_len = 0;
- }
- else if ((sub_seq_start + sub_seq_len) >= seq_len)
- sub_seq_len = seq_len - sub_seq_start;
-
- sub_seq = raw_sequence[seq_i].substr(sub_seq_start, sub_seq_len);
- fl_draw(sub_seq.c_str(), index_pad, y_loc);
- y_loc += y_seq_incre;
- }
-}
-
-
-void
-SeqView::draw_match_lines(double ch_width)
-{
- int i, y_loc;
- list<ExtendedConservedPath >::iterator pathz_i;
- int i2, i3;
- int x_start, y_start, x_end, y_end;
- int window_length, win_i;
- int rc_1 = 0;
- int rc_2 = 0;
- int offset1, offset2;
- float center1, center2;
- bool rc_color;
- vector<bool> rc_list;
- bool full_match;
- vector<bool> matched;
- int align_counter;
-
-
- align_counter = 0;
- for(pathz_i = P.begin(); pathz_i != P.end(); ++pathz_i)
- {
- if (show_aligns[align_counter])
- {
- ExtendedConservedPath& a_path = *pathz_i;
- window_length = a_path.window_size;
-
- // determine which parts of the path are RC relative to first species
- rc_list.clear();
- for(i2 = 0; i2 < a_path.size()-1; i2++)
- {
- if (a_path[i2] < 0)
- rc_list.push_back(true);
- else
- rc_list.push_back(false);
- }
-
- // loop over each bp in the conserved region for all sequences
- for(win_i = 0; win_i < window_length; win_i++)
- {
- // determine which exact base pairs match between the sequences
- full_match = true;
- for(i2 = 0; i2 < a_path.size()-1; i2++)
- {
- // assume not rc as most likely, adjust below
- rc_1 = 0;
- rc_2 = 0;
- // no matter the case, any RC node needs adjustments
- if (a_path[i2] < 0)
- rc_1 = window_length-1;
- if (a_path[i2+1] < 0)
- rc_2 = window_length-1;
-
- x_start = (abs(a_path[i2]-rc_1+win_i));
- x_end = (abs(a_path[i2+1]-rc_2+win_i));
-
- // RC case handling
- // ugh, and xor...only want rc coloring if just one of the nodes is rc
- // if both nodes are rc, then they are 'normal' relative to each other
- if ( ( rc_list[i2] || rc_list[i2+1] ) &&
- !(rc_list[i2] && rc_list[i2+1] ) )
- { //the hideous rc matching logic - not complex, but annoying
- if ( !( ( (raw_sequence[i2][x_start] == 'A') &&
- (raw_sequence[i2+1][x_end] == 'T') ) ||
- ( (raw_sequence[i2][x_start] == 'T') &&
- (raw_sequence[i2+1][x_end] == 'A') ) ||
- ( (raw_sequence[i2][x_start] == 'G') &&
- (raw_sequence[i2+1][x_end] == 'C') ) ||
- ( (raw_sequence[i2][x_start] == 'C') &&
- (raw_sequence[i2+1][x_end] == 'G') ) ) )
- full_match = false;
- }
- else
- {
- if (!( (raw_sequence[i2][x_start] == raw_sequence[i2+1][x_end]) &&
- (raw_sequence[i2][x_start] != 'N') &&
- (raw_sequence[i2+1][x_end] != 'N') ) )
- full_match = false;
- }
- }
-
- // draw for matches stretching across all sequences
- if (full_match)
- {
- fl_line_style(FL_SOLID, 1, NULL);
-
- // now can draw the line for each bp in this window that matches
- // grrr, need to ask if anyone cares if I switch the seq
- // top-bot order...
- i3 = 0;
- y_loc = y_min + 5;
- for(i2 = 0; i2 < a_path.size()-1; i2++)
- {
- // assume not rc as most likely, adjust below
- rc_1 = 0;
- rc_2 = 0;
- // this makes the lines start in the middle of the drawn char/bp
- center1 = 0.5;
- center2 = 0.5;
- // no matter the case, any RC node needs adjustments
- if (a_path[i2] < 0)
- {
- rc_1 = window_length;
- center1 = -center1;
- }
- if (a_path[i2] < 0)
- {
- rc_2 = window_length;
- center2 = -center2;
- }
-
- // set offset based on current alignment for which bp to show
- offset1 = seq_align_offsets[i2];
- offset2 = seq_align_offsets[i2+1];
-
- if ( ( rc_list[i2] || rc_list[i2+1] ) &&
- !(rc_list[i2] && rc_list[i2+1] ) )
- fl_color(FL_BLUE);
- else
- fl_color(FL_RED);
-
- // maybe shouldn't recalc these, but store values from first loop
- x_start = (abs((int) (a_path[i2]-rc_1+win_i)));
- x_end = (abs((int) (a_path[i2+1]-rc_2+win_i)));
-
- fl_line( (int)((x_start+center1-offset1+scroll_offset)*ch_width)
- + index_pad, y_loc + 10,
- (int)((x_end+center2-offset2+scroll_offset)*ch_width)
- + index_pad, y_loc+y_seq_incre );
- y_loc += y_seq_incre;
- }
- }
- }
- }
- align_counter++;
- }
-}
-
-void
-SeqView::draw_indices(double ch_width)
-{
- int seq_i;
- Sequence a_seq;
- int y_loc;
- ostringstream an_index;
- int shown_seq_len;
-
-
- // clear out space on sides to draw in index values
- // I block out the sides rather than adding offsets to the drawing of seq
- // and conservation lines since the lines need to draw off the 'edge'
- fl_color(FL_WHITE);
- fl_rectf(0, y_min, index_pad, h()+y_min);
- fl_rectf(w()-index_pad, y_min, index_pad, h()+y_min);
-
- // now can draw in the indices of the start and end of the shown sequence
- fl_color(FL_BLACK);
- y_loc = y_min + 10 + 5;
- for(seq_i = 0; seq_i < seq_num; seq_i++)
- {
- an_index.str("");
- an_index << (seq_align_offsets[seq_i]-scroll_offset);
- fl_draw((an_index.str()).c_str(), 2, y_loc);
-
- shown_seq_len = (w() - 2 * index_pad) / (int) ch_width;
- an_index.str("");
- an_index << (seq_align_offsets[seq_i]-scroll_offset+shown_seq_len);
- fl_draw((an_index.str()).c_str(), w()-index_pad+2, y_loc);
- y_loc += y_seq_incre;
- }
-}
-
-
-void
-SeqView::toggle_align(int align_num)
-{
- //cout << align_num << endl;
- //cout << show_aligns[align_num] << endl;
- show_aligns[align_num] = !show_aligns[align_num];
- //cout << show_aligns[align_num] << endl;
-}
-
-
-void
-SeqView::align_offsets(int align_num)
-{
- list<ExtendedConservedPath >::iterator pathz_i;
- int i;
- int window_length;
-
- cout << "alignment: " << align_num << endl;
-
- if (P.begin() == P.end())
- cout << "crud....\n";
- else
- {
- pathz_i = P.begin();
-
- while(pathz_i != P.end())
- ++pathz_i;
-
- // find the path specified
- i = 0;
- pathz_i = P.begin();
- while( (i < align_num) && (pathz_i != P.end()) )
- {
- ++i;
- ++pathz_i;
- }
-
- // now set the alignment offsets - basically where the path starts
- seq_align_offsets.clear();
- for(i = 0; i < seq_num ; i++)
- {
- //cout << (*pathz_i)[i+1] << endl;
- seq_align_offsets.push_back( abs((*pathz_i)[i+1]) );
- // for testing purposes: to see everything in the short test sequences
- //seq_align_offsets.push_back(0);
- }
- // reset any dragging done, otherwise might be hard to find selected align
- scroll_offset = 0;
- }
-}
-
-
-
-int
-SeqView::handle(int e)
-{
- int return_value;
-
- // this empty string needs to be put on cout, otherwise the -O optimize
- // compile option seems to throw this function away with the following:
- // gcc version 3.2.2 20030222 (Red Hat Linux 3.2.2-5)
- cout << "";
-
- switch(e)
- {
- case FL_PUSH:
- if (Fl::event_button3())
- {
- cout << "menu menu menu!\n";
- return_value = 1;
- }
- break;
- case FL_DRAG:
- if (!dragging)
- {
- drag_change = Fl::event_x();
- dragging = true;
- return_value = 1;
- }
- drag_change = Fl::event_x() - drag_change;
- scroll_offset += drag_change;
- drag_change = Fl::event_x();
- redraw();
- break;
- case FL_RELEASE:
- if (dragging)
- {
- //scroll_offset += Fl::event_x() - drag_start;
- //scroll_dist = Fl::event_x() - drag_start;
- //scroll_offset += scroll_dist;
- //scroll_offset += scroll_pos;
- dragging = false;
- redraw();
- return_value = 1;
- }
- break;
- default:
- return_value = Fl_Widget::handle(e);
- }
-
- return return_value;
-}
-
-void
-SeqView::toggle_bars()
-{
- show_bars = !show_bars;
- redraw();
-}
-
-
-void
-SeqView::toggle_motifs()
-{
- show_motifs = !show_motifs;
- redraw();
-}
-
-
-void
-SeqView::reporter(string id, int value)
-{
- cout << id << " : " << value << endl;
-}
-
-
-/*
- cout << "fee\n";
- cout << "fie\n";
- cout << "foe\n";
- cout << "fum\n";
-*/
+++ /dev/null
-#ifndef _MUSSA_GUI_SEQ_VIEW_H_
-#define _MUSSA_GUI_SEQ_VIEW_H_
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-#include <list>
-#include <string>
-#include <vector>
-
-#include <FL/Fl_Box.H>
-
-#include "MotifWindow.hh"
-#include "SetupWindow.hh"
-
-class SeqView : public Fl_Box
-{
- public:
- SeqView(int x_top,int y_top,int x_bot,int y_bot) :
- Fl_Box(x_top,y_top,x_bot,y_bot)
- {
- x_max = x_bot;
- y_max = y_bot;
- x_min = x_top;
- y_min = y_top;
- show_bars = true;
- show_motifs = true;
- }
-
- void setup(std::string name, int sq_num, std::vector<Sequence> *some_seqs,
- std::list<ExtendedConservedPath > some_paths,
- std::vector<int> some_lens, std::vector<motif> *some_motifs);
- void align_offsets(int align_num);
- void toggle_align(int align_num);
- void toggle_bars();
- void toggle_motifs();
-
- private:
- std::string analysis_name;
- int seq_num;
- int base_window_len;
-
- //this data is passed as pointers to the instantiated classes
- std::vector<Sequence> *S;
- //list of paths in selection box
- std::list<ExtendedConservedPath > P;
- std::vector<int> seq_lens;
- //pointer to passed motif data
- std::vector<motif> *the_motifs;
-
- int x_max, y_max, x_min, y_min;
- int y_seq_incre;
- int index_pad;
- std::vector<int> seq_align_offsets;
- std::vector<std::string> raw_sequence;
- bool dragging;
- int drag_change, scroll_offset;
- bool show_bars, show_motifs;
- std::vector<bool> show_aligns;
-
- void resize(int new_x, int new_y, int new_w, int new_h);
- void draw();
- void draw_motifs(double ch_width);
- void draw_sequence(double ch_width);
- void draw_match_lines(double ch_width);
- void draw_indices(double ch_width);
- int handle(int e);
- void reporter(std::string id, int value);
-};
-#endif
--- /dev/null
+#ifndef _MUSSA_GUI_SEQ_VIEW_H_
+#define _MUSSA_GUI_SEQ_VIEW_H_
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+#include <list>
+#include <string>
+#include <vector>
+
+#include <FL/Fl_Box.H>
+
+#include "gui/MotifWindow.hpp"
+#include "gui/SetupWindow.hpp"
+
+class SeqView : public Fl_Box
+{
+ public:
+ SeqView(int x_top,int y_top,int x_bot,int y_bot) :
+ Fl_Box(x_top,y_top,x_bot,y_bot)
+ {
+ x_max = x_bot;
+ y_max = y_bot;
+ x_min = x_top;
+ y_min = y_top;
+ show_bars = true;
+ show_motifs = true;
+ }
+
+ void setup(std::string name, int sq_num, std::vector<Sequence> *some_seqs,
+ std::list<ExtendedConservedPath > some_paths,
+ std::vector<int> some_lens, std::vector<motif> *some_motifs);
+ void align_offsets(int align_num);
+ void toggle_align(int align_num);
+ void toggle_bars();
+ void toggle_motifs();
+
+ private:
+ std::string analysis_name;
+ int seq_num;
+ int base_window_len;
+
+ //this data is passed as pointers to the instantiated classes
+ std::vector<Sequence> *S;
+ //list of paths in selection box
+ std::list<ExtendedConservedPath > P;
+ std::vector<int> seq_lens;
+ //pointer to passed motif data
+ std::vector<motif> *the_motifs;
+
+ int x_max, y_max, x_min, y_min;
+ int y_seq_incre;
+ int index_pad;
+ std::vector<int> seq_align_offsets;
+ std::vector<std::string> raw_sequence;
+ bool dragging;
+ int drag_change, scroll_offset;
+ bool show_bars, show_motifs;
+ std::vector<bool> show_aligns;
+
+ void resize(int new_x, int new_y, int new_w, int new_h);
+ void draw();
+ void draw_motifs(double ch_width);
+ void draw_sequence(double ch_width);
+ void draw_match_lines(double ch_width);
+ void draw_indices(double ch_width);
+ int handle(int e);
+ void reporter(std::string id, int value);
+};
+#endif
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+#include "gui/SeqWindow.hpp"
+
+#include <sstream>
+
+#include <FL/Fl.H>
+
+using namespace std;
+
+void
+set_align_cb(Fl_Widget* widg, void* the_data)
+{
+ menu_align_data_bundle * blah = (menu_align_data_bundle *) the_data;
+ SeqWindow* T= blah->swm_ptr;
+ T->real_set_align_cb(blah->which_align);
+}
+
+
+void
+SeqWindow::real_set_align_cb(int which_align)
+{
+ seq_box->align_offsets(which_align);
+ seq_box->redraw();
+}
+
+
+void
+show_align_cb(Fl_Widget* widg, void* the_data)
+{
+ menu_align_data_bundle * blah = (menu_align_data_bundle *) the_data;
+ SeqWindow* T= blah->swm_ptr;
+ T->real_show_align_cb(blah->which_align);
+}
+
+
+void
+SeqWindow::real_show_align_cb(int which_align)
+{
+ vector<int> a_path;
+ int window_length;
+
+
+ cout << "fumish\n";
+ seq_box->toggle_align(which_align);
+ seq_box->redraw();
+}
+
+
+void
+toggle_bars_cb(Fl_Button* o, void* v)
+{
+ SeqWindow* T=(SeqWindow*)v;
+ T->real_toggle_bars_cb();
+}
+
+
+void
+SeqWindow::real_toggle_bars_cb()
+{
+ seq_box->toggle_bars();
+}
+
+
+void
+toggle_motifs_cb(Fl_Button* o, void* v)
+{
+ SeqWindow* T=(SeqWindow*)v;
+ T->real_toggle_motifs_cb();
+}
+
+
+void
+SeqWindow::real_toggle_motifs_cb()
+{
+ seq_box->toggle_motifs();
+}
+
+
+// main code, window creation
+
+SeqWindow::SeqWindow(int w, int h, const char* title, int sq_num,
+ vector<Sequence> *some_seqs,
+ list<ExtendedConservedPath > some_paths,
+ vector<int> some_lens,
+ vector<motif> *some_motifs):
+ Fl_Double_Window(w,h,title)
+{
+ menu_align_data_bundle * some_menu_data;
+ int window_length, align_number;
+ int i;
+ ostringstream align_id_ostr;
+ string align_id_string;
+ list<ExtendedConservedPath >::iterator align_iter;
+
+ // most of this stuff is here just to pass to SeqView object
+ // some is needed to setup the window menus
+ seq_num = sq_num;
+ S = some_seqs;
+ P = some_paths;
+ seq_lens = some_lens;
+ the_motifs = some_motifs;
+
+
+ begin();
+ color(FL_WHITE);
+ resizable(this);
+
+ // make the menu that allows alignment selection
+ choose_align_menu = new Fl_Menu_Button(5, 2, 180, 30, "Choose Alignment");
+ choose_align_menu->color(FL_WHITE,FL_BLUE);
+ choose_align_menu->box(FL_BORDER_BOX);
+ choose_align_menu->clear();
+
+ // make the menu that allows alignment selection
+ show_align_menu = new Fl_Menu_Button(190, 2, 180, 30, "Show Alignment");
+ show_align_menu->color(FL_WHITE,FL_BLUE);
+ show_align_menu->box(FL_BORDER_BOX);
+ show_align_menu->clear();
+
+
+ // adds menu items for each path
+ align_iter = P.begin();
+ align_number = 0;
+ while(align_iter != P.end())
+ {
+ some_menu_data = new menu_align_data_bundle;
+ some_menu_data->swm_ptr = this;
+ some_menu_data->which_align = align_number;
+ align_id_ostr << (*align_iter)[0] << ": ";
+ for(i = 1; i <= seq_num; i++)
+ align_id_ostr << (*align_iter)[i] << ", ";
+ align_id_string = align_id_ostr.str();
+ choose_align_menu->add((const char*)align_id_string.c_str(), 0,
+ (Fl_Callback *) set_align_cb,
+ (void*) some_menu_data);
+ show_align_menu->add((const char*)align_id_string.c_str(), 0,
+ (Fl_Callback *) show_align_cb,
+ (void*) some_menu_data, FL_MENU_TOGGLE|FL_MENU_VALUE);
+
+ align_id_ostr.str("");
+ ++align_number;
+ ++align_iter;
+ }
+
+ /*
+ show_align_menu->add("f&ee");
+ show_align_menu->add("f&ie");
+ show_align_menu->add("f&oe");
+ show_align_menu->add("f&um");
+ */
+
+ Fl_Button *test_but = new Fl_Button(375, 2, 150, 30, "Toggle Motifs");
+ test_but->color(FL_WHITE,FL_BLUE);
+ test_but->box(FL_BORDER_BOX);
+ test_but->callback((Fl_Callback*) toggle_motifs_cb, this);
+
+ toggle_bars = new Fl_Button(530, 2, 150, 30, "Toggle 10bp bars");
+ toggle_bars->color(FL_WHITE,FL_BLUE);
+ toggle_bars->box(FL_BORDER_BOX);
+ toggle_bars->callback((Fl_Callback*) toggle_bars_cb, this);
+
+
+ // make the view of the sequence
+ seq_box = new SeqView(0, 34, w, h-34);
+ seq_box->setup(analysis_name, seq_num, S, P, seq_lens, the_motifs);
+ //real_set_align_cb(2);
+
+ end();
+ Fl::visual(FL_DOUBLE|FL_INDEX);
+ show();
+}
+
+
+
+/*
+ some_menu_data = new menu_align_data_bundle;
+ some_menu_data->swm_ptr = this;
+ some_menu_data->which_align = 2;
+ choose_align_menu->add("f&ie", FL_ALT+'i', (Fl_Callback *) set_align_cb,
+ (void*) some_menu_data);
+
+ some_menu_data = new menu_align_data_bundle;
+ some_menu_data->swm_ptr = this;
+ some_menu_data->which_align = 3;
+ choose_align_menu->add("f&oe", FL_ALT+'o', (Fl_Callback *) set_align_cb,
+ (void*) some_menu_data);
+
+ some_menu_data = new menu_align_data_bundle;
+ some_menu_data->swm_ptr = this;
+ some_menu_data->which_align = 4;
+ choose_align_menu->add("f&um", FL_ALT+'u', (Fl_Callback *) set_align_cb,
+ (void*) some_menu_data);
+*/
+
+
+
+
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-#include "SeqWindow.hh"
-
-#include <sstream>
-
-#include <FL/Fl.H>
-
-using namespace std;
-
-void
-set_align_cb(Fl_Widget* widg, void* the_data)
-{
- menu_align_data_bundle * blah = (menu_align_data_bundle *) the_data;
- SeqWindow* T= blah->swm_ptr;
- T->real_set_align_cb(blah->which_align);
-}
-
-
-void
-SeqWindow::real_set_align_cb(int which_align)
-{
- seq_box->align_offsets(which_align);
- seq_box->redraw();
-}
-
-
-void
-show_align_cb(Fl_Widget* widg, void* the_data)
-{
- menu_align_data_bundle * blah = (menu_align_data_bundle *) the_data;
- SeqWindow* T= blah->swm_ptr;
- T->real_show_align_cb(blah->which_align);
-}
-
-
-void
-SeqWindow::real_show_align_cb(int which_align)
-{
- vector<int> a_path;
- int window_length;
-
-
- cout << "fumish\n";
- seq_box->toggle_align(which_align);
- seq_box->redraw();
-}
-
-
-void
-toggle_bars_cb(Fl_Button* o, void* v)
-{
- SeqWindow* T=(SeqWindow*)v;
- T->real_toggle_bars_cb();
-}
-
-
-void
-SeqWindow::real_toggle_bars_cb()
-{
- seq_box->toggle_bars();
-}
-
-
-void
-toggle_motifs_cb(Fl_Button* o, void* v)
-{
- SeqWindow* T=(SeqWindow*)v;
- T->real_toggle_motifs_cb();
-}
-
-
-void
-SeqWindow::real_toggle_motifs_cb()
-{
- seq_box->toggle_motifs();
-}
-
-
-// main code, window creation
-
-SeqWindow::SeqWindow(int w, int h, const char* title, int sq_num,
- vector<Sequence> *some_seqs,
- list<ExtendedConservedPath > some_paths,
- vector<int> some_lens,
- vector<motif> *some_motifs):
- Fl_Double_Window(w,h,title)
-{
- menu_align_data_bundle * some_menu_data;
- int window_length, align_number;
- int i;
- ostringstream align_id_ostr;
- string align_id_string;
- list<ExtendedConservedPath >::iterator align_iter;
-
- // most of this stuff is here just to pass to SeqView object
- // some is needed to setup the window menus
- seq_num = sq_num;
- S = some_seqs;
- P = some_paths;
- seq_lens = some_lens;
- the_motifs = some_motifs;
-
-
- begin();
- color(FL_WHITE);
- resizable(this);
-
- // make the menu that allows alignment selection
- choose_align_menu = new Fl_Menu_Button(5, 2, 180, 30, "Choose Alignment");
- choose_align_menu->color(FL_WHITE,FL_BLUE);
- choose_align_menu->box(FL_BORDER_BOX);
- choose_align_menu->clear();
-
- // make the menu that allows alignment selection
- show_align_menu = new Fl_Menu_Button(190, 2, 180, 30, "Show Alignment");
- show_align_menu->color(FL_WHITE,FL_BLUE);
- show_align_menu->box(FL_BORDER_BOX);
- show_align_menu->clear();
-
-
- // adds menu items for each path
- align_iter = P.begin();
- align_number = 0;
- while(align_iter != P.end())
- {
- some_menu_data = new menu_align_data_bundle;
- some_menu_data->swm_ptr = this;
- some_menu_data->which_align = align_number;
- align_id_ostr << (*align_iter)[0] << ": ";
- for(i = 1; i <= seq_num; i++)
- align_id_ostr << (*align_iter)[i] << ", ";
- align_id_string = align_id_ostr.str();
- choose_align_menu->add((const char*)align_id_string.c_str(), 0,
- (Fl_Callback *) set_align_cb,
- (void*) some_menu_data);
- show_align_menu->add((const char*)align_id_string.c_str(), 0,
- (Fl_Callback *) show_align_cb,
- (void*) some_menu_data, FL_MENU_TOGGLE|FL_MENU_VALUE);
-
- align_id_ostr.str("");
- ++align_number;
- ++align_iter;
- }
-
- /*
- show_align_menu->add("f&ee");
- show_align_menu->add("f&ie");
- show_align_menu->add("f&oe");
- show_align_menu->add("f&um");
- */
-
- Fl_Button *test_but = new Fl_Button(375, 2, 150, 30, "Toggle Motifs");
- test_but->color(FL_WHITE,FL_BLUE);
- test_but->box(FL_BORDER_BOX);
- test_but->callback((Fl_Callback*) toggle_motifs_cb, this);
-
- toggle_bars = new Fl_Button(530, 2, 150, 30, "Toggle 10bp bars");
- toggle_bars->color(FL_WHITE,FL_BLUE);
- toggle_bars->box(FL_BORDER_BOX);
- toggle_bars->callback((Fl_Callback*) toggle_bars_cb, this);
-
-
- // make the view of the sequence
- seq_box = new SeqView(0, 34, w, h-34);
- seq_box->setup(analysis_name, seq_num, S, P, seq_lens, the_motifs);
- //real_set_align_cb(2);
-
- end();
- Fl::visual(FL_DOUBLE|FL_INDEX);
- show();
-}
-
-
-
-/*
- some_menu_data = new menu_align_data_bundle;
- some_menu_data->swm_ptr = this;
- some_menu_data->which_align = 2;
- choose_align_menu->add("f&ie", FL_ALT+'i', (Fl_Callback *) set_align_cb,
- (void*) some_menu_data);
-
- some_menu_data = new menu_align_data_bundle;
- some_menu_data->swm_ptr = this;
- some_menu_data->which_align = 3;
- choose_align_menu->add("f&oe", FL_ALT+'o', (Fl_Callback *) set_align_cb,
- (void*) some_menu_data);
-
- some_menu_data = new menu_align_data_bundle;
- some_menu_data->swm_ptr = this;
- some_menu_data->which_align = 4;
- choose_align_menu->add("f&um", FL_ALT+'u', (Fl_Callback *) set_align_cb,
- (void*) some_menu_data);
-*/
-
-
-
-
+++ /dev/null
-#ifndef _MUSSA_GUI_SEQ_H_
-#define _MUSSA_GUI_SEQ_H_
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-#include <iostream>
-#include <list>
-#include <string>
-#include <vector>
-
-#include "SeqView.hh"
-
-#include <FL/Fl_Menu_Bar.H>
-#include <FL/Fl_Menu_Item.H>
-#include <FL/Fl_Menu_Button.H>
-#include <FL/Fl_Double_Window.H>
-
-class SeqWindow : public Fl_Double_Window
-{
- private:
- std::string analysis_name;
- int base_window_len;
-
- //this data is passed as pointers to the instantiated classes
- std::vector<Sequence> *S;
- // list of paths in selection box
- std::list<ExtendedConservedPath > P;
- std::vector<int> seq_lens;
- //pointer to passed motif data
- std::vector<motif> *the_motifs;
-
- int x_max, y_max;
- Fl_Menu_Button *choose_align_menu;
- Fl_Menu_Button *show_align_menu;
- Fl_Button *toggle_bars;
- SeqView *seq_box;
-
- public:
- int seq_num;
-
- SeqWindow(int w, int h, const char* title, int sq_num,
- std::vector<Sequence> *some_seqs,
- std::list<ExtendedConservedPath > some_paths,
- std::vector<int> some_lens,
- std::vector<motif> *some_motifs);
- virtual ~SeqWindow(){ std::cout << "dying\n"; }
-
- void make_choose_menu();
- void make_show_menu();
- void real_set_align_cb(int which_align);
- void real_show_align_cb(int which_align);
- void real_toggle_bars_cb();
- void real_toggle_motifs_cb();
-};
-
-
-struct menu_align_data_bundle
-{
- SeqWindow * swm_ptr;
- int which_align;
-};
-#endif
--- /dev/null
+#ifndef _MUSSA_GUI_SEQ_H_
+#define _MUSSA_GUI_SEQ_H_
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+#include <iostream>
+#include <list>
+#include <string>
+#include <vector>
+
+#include "gui/SeqView.hpp"
+
+#include <FL/Fl_Menu_Bar.H>
+#include <FL/Fl_Menu_Item.H>
+#include <FL/Fl_Menu_Button.H>
+#include <FL/Fl_Double_Window.H>
+
+class SeqWindow : public Fl_Double_Window
+{
+ private:
+ std::string analysis_name;
+ int base_window_len;
+
+ //this data is passed as pointers to the instantiated classes
+ std::vector<Sequence> *S;
+ // list of paths in selection box
+ std::list<ExtendedConservedPath > P;
+ std::vector<int> seq_lens;
+ //pointer to passed motif data
+ std::vector<motif> *the_motifs;
+
+ int x_max, y_max;
+ Fl_Menu_Button *choose_align_menu;
+ Fl_Menu_Button *show_align_menu;
+ Fl_Button *toggle_bars;
+ SeqView *seq_box;
+
+ public:
+ int seq_num;
+
+ SeqWindow(int w, int h, const char* title, int sq_num,
+ std::vector<Sequence> *some_seqs,
+ std::list<ExtendedConservedPath > some_paths,
+ std::vector<int> some_lens,
+ std::vector<motif> *some_motifs);
+ virtual ~SeqWindow(){ std::cout << "dying\n"; }
+
+ void make_choose_menu();
+ void make_show_menu();
+ void real_set_align_cb(int which_align);
+ void real_show_align_cb(int which_align);
+ void real_toggle_bars_cb();
+ void real_toggle_motifs_cb();
+};
+
+
+struct menu_align_data_bundle
+{
+ SeqWindow * swm_ptr;
+ int which_align;
+};
+#endif
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+#include "gui/SetupWindow.hpp"
+#include "alg/mussa.hpp"
+#include "mussa_exceptions.hpp"
+#include <iostream>
+#include <FL/Fl_File_Chooser.H>
+
+using namespace std;
+
+bool
+SetupWindow::done()
+{
+ return all_done;
+}
+
+
+void
+do_analysis_cb(Fl_Button* o, void* v)
+{
+ SetupWindow* T=(SetupWindow*)v;
+ T->real_do_analysis();
+}
+
+
+// passes the parameters to the mussa class object and orders it to run
+void
+SetupWindow::real_do_analysis()
+{
+ int i;
+ string err_msg;
+
+ // <-- need a check here to make sure all vars have a valid value
+
+ an_analysis->clear();
+ an_analysis->set_name(analysis_name);
+ an_analysis->set_window(window);
+ an_analysis->set_threshold(threshold);
+
+ for(i=0; i < seq_num; i++)
+ an_analysis->set_seq_info(seq_files[i], annot_files[i], fasta_indices[i],
+ sub_seq_starts[i], sub_seq_ends[i]);
+
+ try {
+ an_analysis->analyze();
+ } catch (mussa_analysis_error e) {
+ fl_alert(e.what());
+ }
+
+ all_done = true;
+
+ hide();
+}
+
+
+void
+choose_seq_file_cb(Fl_Button* o, void* v)
+{
+ seq_data_instance * blah = (seq_data_instance *) v;
+ SetupWindow* T= blah->sw_ptr;
+ T->real_choose_seq_file_cb(blah->index);
+}
+
+
+void
+SetupWindow::real_choose_seq_file_cb(int i)
+{
+ char *picked_file;
+ string a_file_path;
+
+ picked_file = fl_file_chooser("Find an Analysis", "", "", 1);
+ a_file_path = picked_file;
+ seq_files[i] = a_file_path;
+ seq_inputs[i]->value((const char *)picked_file);
+}
+
+
+void
+seq_file_in_cb(Fl_Input* o, void* v)
+{
+ seq_data_instance * blah = (seq_data_instance *) v;
+ SetupWindow* T= blah->sw_ptr;
+ T->real_seq_file_in_cb(o,blah->index);
+}
+
+
+void
+SetupWindow::real_seq_file_in_cb(Fl_Input* o, int i)
+{
+ seq_files[i] = o->value();
+ // leaving this as a reminder that bools will need to be set to determine
+ // if all needed fields have been filled with some value before an analysis
+ // is attempted
+ //(*the_motifs)[i].dirty = true;
+}
+
+//char *picked_file;
+//picked_file = fl_file_chooser("Find an Analysis", "", "", 1);
+
+// *** Annot file selection
+
+void
+choose_annot_file_cb(Fl_Button* o, void* v)
+{
+ seq_data_instance * blah = (seq_data_instance *) v;
+ SetupWindow* T= blah->sw_ptr;
+ T->real_choose_annot_file_cb(blah->index);
+}
+
+
+void
+SetupWindow::real_choose_annot_file_cb(int i)
+{
+ char *picked_file;
+ string a_file_path;
+
+ picked_file = fl_file_chooser("Find an Analysis", "", "", 1);
+ a_file_path = picked_file;
+ annot_files[i] = a_file_path;
+ annot_inputs[i]->value((const char *)picked_file);
+}
+
+void
+annot_file_in_cb(Fl_Input* o, void* v)
+{
+ seq_data_instance * blah = (seq_data_instance *) v;
+ SetupWindow* T= blah->sw_ptr;
+ T->real_annot_file_in_cb(o,blah->index);
+}
+
+void
+SetupWindow::real_annot_file_in_cb(Fl_Input* o, int i)
+{
+ annot_files[i] = o->value();
+}
+
+
+// *** fasta index selection
+
+void
+fa_index_in_cb(Fl_Input* o, void* v)
+{
+ seq_data_instance * blah = (seq_data_instance *) v;
+ SetupWindow* T= blah->sw_ptr;
+ T->real_fa_index_in_cb(o,blah->index);
+}
+
+void
+SetupWindow::real_fa_index_in_cb(Fl_Input* o, int i)
+{
+ fasta_indices[i] = atoi(o->value());
+}
+
+// *** subsequence start select
+
+void
+sub_start_in_cb(Fl_Input* o, void* v)
+{
+ seq_data_instance * blah = (seq_data_instance *) v;
+ SetupWindow* T= blah->sw_ptr;
+ T->real_sub_start_in_cb(o,blah->index);
+}
+
+void
+SetupWindow::real_sub_start_in_cb(Fl_Input* o, int i)
+{
+ sub_seq_starts[i] = atoi(o->value());
+}
+
+// *** subsequence end select
+
+void
+sub_end_in_cb(Fl_Input* o, void* v)
+{
+ seq_data_instance * blah = (seq_data_instance *) v;
+ SetupWindow* T= blah->sw_ptr;
+ T->real_sub_end_in_cb(o,blah->index);
+}
+
+void
+SetupWindow::real_sub_end_in_cb(Fl_Input* o, int i)
+{
+ sub_seq_ends[i] = atoi(o->value());
+
+}
+
+// *** input analysis name
+
+void
+set_ana_name_cb(Fl_Input* o, void* v)
+{
+ SetupWindow* T=(SetupWindow*)v;
+ T->real_set_ana_name_cb(o);
+}
+
+void
+SetupWindow::real_set_ana_name_cb(Fl_Input* o)
+{
+ analysis_name = o->value();
+}
+
+// *** input window size
+
+void
+set_win_size_cb(Fl_Input* o, void* v)
+{
+ SetupWindow* T=(SetupWindow*)v;
+ T->real_set_win_size_cb(o);
+}
+
+void
+SetupWindow::real_set_win_size_cb(Fl_Input* o)
+{
+ window = atoi(o->value());
+}
+
+// *** input threshold
+
+void
+set_threshold_cb(Fl_Input* o, void* v)
+{
+ SetupWindow* T=(SetupWindow*)v;
+ T->real_set_threshold_cb(o);
+}
+
+void
+SetupWindow::real_set_threshold_cb(Fl_Input* o)
+{
+ threshold = atoi(o->value());
+}
+
+void
+set_seq_num_cb(Fl_Input* o, void* v)
+{
+ SetupWindow* T=(SetupWindow*)v;
+ T->real_set_seq_num_cb(o);
+}
+
+// *** input number of sequences, add appropriate inputs for each sequence
+
+void
+SetupWindow::real_set_seq_num_cb(Fl_Input* o)
+{
+ int i;
+
+ seq_num = atoi(o->value());
+ seq_inputs.clear();
+ annot_inputs.clear();
+
+ seq_scroll = new Fl_Scroll(5,80,w()-10,h()-115);
+ seq_scroll->color(FL_WHITE);
+
+ for (i = 0; i < seq_num; i++)
+ {
+ seq_files.push_back("");
+ annot_files.push_back("");
+ fasta_indices.push_back(1);
+ sub_seq_starts.push_back(0);
+ sub_seq_ends.push_back(0);
+ add_seq_input(i);
+ }
+ seq_scroll->box(FL_DOWN_FRAME);
+ add(seq_scroll);
+ redraw();
+}
+
+
+SetupWindow::SetupWindow(int w, int h, const char* title, Mussa *the_analysis):Fl_Window(w,h,title)
+{
+ color(FL_WHITE);
+
+ an_analysis = the_analysis;
+ all_done = false;
+
+ begin();
+
+ name_input = new Fl_Input(110, 10, w-120, 30, "Analysis Name ");
+ name_input->value("");
+ //name_input->when(FL_WHEN_ENTER_KEY);
+ name_input->box(FL_BORDER_BOX);
+ name_input->callback((Fl_Callback*)set_ana_name_cb, this);
+
+ // add in radio buttons for win_append and thres_append eventually
+ win_append = true;
+ thres_append = true;
+
+ win_input = new Fl_Input(65,45,100,30, "Window ");
+ win_input->value("");
+ win_input->callback((Fl_Callback*)set_win_size_cb, this);
+
+ thres_input = new Fl_Input(250,45,100,30, "Threshold ");
+ thres_input->value("");
+ thres_input->callback((Fl_Callback*)set_threshold_cb, this);
+
+ seq_num_input = new Fl_Input(480,45,100, 30, "Number of Seqs");
+ seq_num_input->value("");
+ seq_num_input->callback((Fl_Callback*)set_seq_num_cb, this);
+
+ // button to launch the analysis
+ test = new Fl_Button(w-100,h-30,100,30,"Do Analysis");
+ test->callback((Fl_Callback*)do_analysis_cb, this);
+
+ // test button to make sure setup data is being stored
+ test = new Fl_Button(w-200,h-30,100,30,"show setup");
+ test->callback((Fl_Callback*)print_cb, this);
+
+ // generic input, keeping around as template for future additions
+ //_input = new Fl_Input(0, , 30, "");
+ //_input->value("");
+ //_input->when(FL_WHEN_ENTER_KEY);
+ //_input->callback((Fl_Callback*)set__cb, this);
+
+ end();
+ //resizable(this);
+ show();
+}
+
+
+SetupWindow::~SetupWindow(){}
+
+
+void
+SetupWindow::add_seq_input(int i)
+{
+ Fl_Input *fasta_input, *start_input, *end_input;
+ Fl_Button *seq_browse, *annot_browse;
+
+
+ // this remembers what seq index each input is associated with
+ seq_data_instance * something;
+ something = new seq_data_instance;
+ something->sw_ptr = this;
+ something->index = i;
+
+
+ // setup sequence file input for text input or file browsing
+ seq_inputs.push_back(new Fl_Input(55, 85+(i*105), w()-165, 30, "seq "));
+ seq_inputs[i]->value("");
+ seq_inputs[i]->callback((Fl_Callback*)seq_file_in_cb, (void*) something);
+
+ seq_browse = new Fl_Button(w()-105, 85+(i*105), 80, 30, "Browse");
+ seq_browse->callback((Fl_Callback*)choose_seq_file_cb, (void*) something);
+
+ // setup annotation file input for text input or file browsing
+ annot_inputs.push_back(new Fl_Input(55, 120+(i*105), w()-165, 30, "annot "));
+ annot_inputs[i]->value("");
+ annot_inputs[i]->callback((Fl_Callback*)annot_file_in_cb,(void*)something);
+
+ annot_browse = new Fl_Button(w()-105, 120+(i*105), 80, 30, "Browse");
+ annot_browse->callback((Fl_Callback*)choose_annot_file_cb, (void*)something);
+
+ // index of fasta seq wanted if more than 1 seq in file
+ fasta_input = new Fl_Input(90, 155+(i*105), 50, 30, "fasta index");
+ fasta_input->value("");
+ fasta_input->callback((Fl_Callback*)fa_index_in_cb, (void*) something);
+
+ // subsequence select, index of first bp wanted
+ start_input = new Fl_Input(225, 155+(i*105), 50, 30, "start index");
+ start_input->value("");
+ start_input->callback((Fl_Callback*)sub_start_in_cb, (void*) something);
+
+ // subsequence select, index of last bp wanted
+ end_input = new Fl_Input(355, 155+(i*105), 50, 30, "end index");
+ end_input->value("");
+ end_input->callback((Fl_Callback*)sub_end_in_cb, (void*) something);
+
+ seq_scroll->add(seq_inputs[i]);
+ seq_scroll->add(seq_browse);
+ seq_scroll->add(annot_inputs[i]);
+ seq_scroll->add(annot_browse);
+ seq_scroll->add(fasta_input);
+ seq_scroll->add(start_input);
+ seq_scroll->add(end_input);
+}
+
+/*
+ cout << "fee\n";
+ cout << "fie\n";
+ cout << "foe\n";
+ cout << "fum\n";
+*/
+
+void SetupWindow::print_cb(Fl_Button* o, void* v)
+{
+ SetupWindow* T=(SetupWindow*)v;
+ T->print_cb_real(o,v);
+}
+
+
+void SetupWindow::print_cb_real(Fl_Button* , void*)
+{
+ cout << "analysis_name: " << analysis_name << endl;
+ cout << "win: " << window << endl;
+ cout << "thres: " << threshold << endl;
+ cout << "seq_num: " << seq_num << endl;
+ //cout << "win_add: " << win_append << end;
+ //cout << "thres_add: " << thres_append << endl;
+
+ int i;
+
+
+
+ for (i = 0; i < seq_num; i++)
+ {
+ cout << seq_files[i] << endl;
+ cout << annot_files[i] << endl;
+ cout << "fasta: " << fasta_indices[i];
+ cout << " start: " << sub_seq_starts[i];
+ cout << " end: " << sub_seq_ends[i] << endl;
+ cout << "blargle!\n";
+ }
+ cout << "end of inputs\n" << endl;
+}
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-#include "SetupWindow.hh"
-#include "alg/mussa_class.hh"
-#include "mussa_exceptions.hh"
-#include <iostream>
-#include <FL/Fl_File_Chooser.H>
-
-using namespace std;
-
-bool
-SetupWindow::done()
-{
- return all_done;
-}
-
-
-void
-do_analysis_cb(Fl_Button* o, void* v)
-{
- SetupWindow* T=(SetupWindow*)v;
- T->real_do_analysis();
-}
-
-
-// passes the parameters to the mussa class object and orders it to run
-void
-SetupWindow::real_do_analysis()
-{
- int i;
- string err_msg;
-
- // <-- need a check here to make sure all vars have a valid value
-
- an_analysis->clear();
- an_analysis->set_name(analysis_name);
- an_analysis->set_window(window);
- an_analysis->set_threshold(threshold);
-
- for(i=0; i < seq_num; i++)
- an_analysis->set_seq_info(seq_files[i], annot_files[i], fasta_indices[i],
- sub_seq_starts[i], sub_seq_ends[i]);
-
- try {
- an_analysis->analyze();
- } catch (mussa_analysis_error e) {
- fl_alert(e.what());
- }
-
- all_done = true;
-
- hide();
-}
-
-
-void
-choose_seq_file_cb(Fl_Button* o, void* v)
-{
- seq_data_instance * blah = (seq_data_instance *) v;
- SetupWindow* T= blah->sw_ptr;
- T->real_choose_seq_file_cb(blah->index);
-}
-
-
-void
-SetupWindow::real_choose_seq_file_cb(int i)
-{
- char *picked_file;
- string a_file_path;
-
- picked_file = fl_file_chooser("Find an Analysis", "", "", 1);
- a_file_path = picked_file;
- seq_files[i] = a_file_path;
- seq_inputs[i]->value((const char *)picked_file);
-}
-
-
-void
-seq_file_in_cb(Fl_Input* o, void* v)
-{
- seq_data_instance * blah = (seq_data_instance *) v;
- SetupWindow* T= blah->sw_ptr;
- T->real_seq_file_in_cb(o,blah->index);
-}
-
-
-void
-SetupWindow::real_seq_file_in_cb(Fl_Input* o, int i)
-{
- seq_files[i] = o->value();
- // leaving this as a reminder that bools will need to be set to determine
- // if all needed fields have been filled with some value before an analysis
- // is attempted
- //(*the_motifs)[i].dirty = true;
-}
-
-//char *picked_file;
-//picked_file = fl_file_chooser("Find an Analysis", "", "", 1);
-
-// *** Annot file selection
-
-void
-choose_annot_file_cb(Fl_Button* o, void* v)
-{
- seq_data_instance * blah = (seq_data_instance *) v;
- SetupWindow* T= blah->sw_ptr;
- T->real_choose_annot_file_cb(blah->index);
-}
-
-
-void
-SetupWindow::real_choose_annot_file_cb(int i)
-{
- char *picked_file;
- string a_file_path;
-
- picked_file = fl_file_chooser("Find an Analysis", "", "", 1);
- a_file_path = picked_file;
- annot_files[i] = a_file_path;
- annot_inputs[i]->value((const char *)picked_file);
-}
-
-void
-annot_file_in_cb(Fl_Input* o, void* v)
-{
- seq_data_instance * blah = (seq_data_instance *) v;
- SetupWindow* T= blah->sw_ptr;
- T->real_annot_file_in_cb(o,blah->index);
-}
-
-void
-SetupWindow::real_annot_file_in_cb(Fl_Input* o, int i)
-{
- annot_files[i] = o->value();
-}
-
-
-// *** fasta index selection
-
-void
-fa_index_in_cb(Fl_Input* o, void* v)
-{
- seq_data_instance * blah = (seq_data_instance *) v;
- SetupWindow* T= blah->sw_ptr;
- T->real_fa_index_in_cb(o,blah->index);
-}
-
-void
-SetupWindow::real_fa_index_in_cb(Fl_Input* o, int i)
-{
- fasta_indices[i] = atoi(o->value());
-}
-
-// *** subsequence start select
-
-void
-sub_start_in_cb(Fl_Input* o, void* v)
-{
- seq_data_instance * blah = (seq_data_instance *) v;
- SetupWindow* T= blah->sw_ptr;
- T->real_sub_start_in_cb(o,blah->index);
-}
-
-void
-SetupWindow::real_sub_start_in_cb(Fl_Input* o, int i)
-{
- sub_seq_starts[i] = atoi(o->value());
-}
-
-// *** subsequence end select
-
-void
-sub_end_in_cb(Fl_Input* o, void* v)
-{
- seq_data_instance * blah = (seq_data_instance *) v;
- SetupWindow* T= blah->sw_ptr;
- T->real_sub_end_in_cb(o,blah->index);
-}
-
-void
-SetupWindow::real_sub_end_in_cb(Fl_Input* o, int i)
-{
- sub_seq_ends[i] = atoi(o->value());
-
-}
-
-// *** input analysis name
-
-void
-set_ana_name_cb(Fl_Input* o, void* v)
-{
- SetupWindow* T=(SetupWindow*)v;
- T->real_set_ana_name_cb(o);
-}
-
-void
-SetupWindow::real_set_ana_name_cb(Fl_Input* o)
-{
- analysis_name = o->value();
-}
-
-// *** input window size
-
-void
-set_win_size_cb(Fl_Input* o, void* v)
-{
- SetupWindow* T=(SetupWindow*)v;
- T->real_set_win_size_cb(o);
-}
-
-void
-SetupWindow::real_set_win_size_cb(Fl_Input* o)
-{
- window = atoi(o->value());
-}
-
-// *** input threshold
-
-void
-set_threshold_cb(Fl_Input* o, void* v)
-{
- SetupWindow* T=(SetupWindow*)v;
- T->real_set_threshold_cb(o);
-}
-
-void
-SetupWindow::real_set_threshold_cb(Fl_Input* o)
-{
- threshold = atoi(o->value());
-}
-
-void
-set_seq_num_cb(Fl_Input* o, void* v)
-{
- SetupWindow* T=(SetupWindow*)v;
- T->real_set_seq_num_cb(o);
-}
-
-// *** input number of sequences, add appropriate inputs for each sequence
-
-void
-SetupWindow::real_set_seq_num_cb(Fl_Input* o)
-{
- int i;
-
- seq_num = atoi(o->value());
- seq_inputs.clear();
- annot_inputs.clear();
-
- seq_scroll = new Fl_Scroll(5,80,w()-10,h()-115);
- seq_scroll->color(FL_WHITE);
-
- for (i = 0; i < seq_num; i++)
- {
- seq_files.push_back("");
- annot_files.push_back("");
- fasta_indices.push_back(1);
- sub_seq_starts.push_back(0);
- sub_seq_ends.push_back(0);
- add_seq_input(i);
- }
- seq_scroll->box(FL_DOWN_FRAME);
- add(seq_scroll);
- redraw();
-}
-
-
-SetupWindow::SetupWindow(int w, int h, const char* title, Mussa *the_analysis):Fl_Window(w,h,title)
-{
- color(FL_WHITE);
-
- an_analysis = the_analysis;
- all_done = false;
-
- begin();
-
- name_input = new Fl_Input(110, 10, w-120, 30, "Analysis Name ");
- name_input->value("");
- //name_input->when(FL_WHEN_ENTER_KEY);
- name_input->box(FL_BORDER_BOX);
- name_input->callback((Fl_Callback*)set_ana_name_cb, this);
-
- // add in radio buttons for win_append and thres_append eventually
- win_append = true;
- thres_append = true;
-
- win_input = new Fl_Input(65,45,100,30, "Window ");
- win_input->value("");
- win_input->callback((Fl_Callback*)set_win_size_cb, this);
-
- thres_input = new Fl_Input(250,45,100,30, "Threshold ");
- thres_input->value("");
- thres_input->callback((Fl_Callback*)set_threshold_cb, this);
-
- seq_num_input = new Fl_Input(480,45,100, 30, "Number of Seqs");
- seq_num_input->value("");
- seq_num_input->callback((Fl_Callback*)set_seq_num_cb, this);
-
- // button to launch the analysis
- test = new Fl_Button(w-100,h-30,100,30,"Do Analysis");
- test->callback((Fl_Callback*)do_analysis_cb, this);
-
- // test button to make sure setup data is being stored
- test = new Fl_Button(w-200,h-30,100,30,"show setup");
- test->callback((Fl_Callback*)print_cb, this);
-
- // generic input, keeping around as template for future additions
- //_input = new Fl_Input(0, , 30, "");
- //_input->value("");
- //_input->when(FL_WHEN_ENTER_KEY);
- //_input->callback((Fl_Callback*)set__cb, this);
-
- end();
- //resizable(this);
- show();
-}
-
-
-SetupWindow::~SetupWindow(){}
-
-
-void
-SetupWindow::add_seq_input(int i)
-{
- Fl_Input *fasta_input, *start_input, *end_input;
- Fl_Button *seq_browse, *annot_browse;
-
-
- // this remembers what seq index each input is associated with
- seq_data_instance * something;
- something = new seq_data_instance;
- something->sw_ptr = this;
- something->index = i;
-
-
- // setup sequence file input for text input or file browsing
- seq_inputs.push_back(new Fl_Input(55, 85+(i*105), w()-165, 30, "seq "));
- seq_inputs[i]->value("");
- seq_inputs[i]->callback((Fl_Callback*)seq_file_in_cb, (void*) something);
-
- seq_browse = new Fl_Button(w()-105, 85+(i*105), 80, 30, "Browse");
- seq_browse->callback((Fl_Callback*)choose_seq_file_cb, (void*) something);
-
- // setup annotation file input for text input or file browsing
- annot_inputs.push_back(new Fl_Input(55, 120+(i*105), w()-165, 30, "annot "));
- annot_inputs[i]->value("");
- annot_inputs[i]->callback((Fl_Callback*)annot_file_in_cb,(void*)something);
-
- annot_browse = new Fl_Button(w()-105, 120+(i*105), 80, 30, "Browse");
- annot_browse->callback((Fl_Callback*)choose_annot_file_cb, (void*)something);
-
- // index of fasta seq wanted if more than 1 seq in file
- fasta_input = new Fl_Input(90, 155+(i*105), 50, 30, "fasta index");
- fasta_input->value("");
- fasta_input->callback((Fl_Callback*)fa_index_in_cb, (void*) something);
-
- // subsequence select, index of first bp wanted
- start_input = new Fl_Input(225, 155+(i*105), 50, 30, "start index");
- start_input->value("");
- start_input->callback((Fl_Callback*)sub_start_in_cb, (void*) something);
-
- // subsequence select, index of last bp wanted
- end_input = new Fl_Input(355, 155+(i*105), 50, 30, "end index");
- end_input->value("");
- end_input->callback((Fl_Callback*)sub_end_in_cb, (void*) something);
-
- seq_scroll->add(seq_inputs[i]);
- seq_scroll->add(seq_browse);
- seq_scroll->add(annot_inputs[i]);
- seq_scroll->add(annot_browse);
- seq_scroll->add(fasta_input);
- seq_scroll->add(start_input);
- seq_scroll->add(end_input);
-}
-
-/*
- cout << "fee\n";
- cout << "fie\n";
- cout << "foe\n";
- cout << "fum\n";
-*/
-
-void SetupWindow::print_cb(Fl_Button* o, void* v)
-{
- SetupWindow* T=(SetupWindow*)v;
- T->print_cb_real(o,v);
-}
-
-
-void SetupWindow::print_cb_real(Fl_Button* , void*)
-{
- cout << "analysis_name: " << analysis_name << endl;
- cout << "win: " << window << endl;
- cout << "thres: " << threshold << endl;
- cout << "seq_num: " << seq_num << endl;
- //cout << "win_add: " << win_append << end;
- //cout << "thres_add: " << thres_append << endl;
-
- int i;
-
-
-
- for (i = 0; i < seq_num; i++)
- {
- cout << seq_files[i] << endl;
- cout << annot_files[i] << endl;
- cout << "fasta: " << fasta_indices[i];
- cout << " start: " << sub_seq_starts[i];
- cout << " end: " << sub_seq_ends[i] << endl;
- cout << "blargle!\n";
- }
- cout << "end of inputs\n" << endl;
-}
+++ /dev/null
-#ifndef _MUSSA_GUI_LOAD_WINDOW_H_
-#define _MUSSA_GUI_LOAD_WINDOW_H_
-
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-#include <string>
-#include <vector>
-
-#include <FL/Fl_Button.H>
-#include <FL/Fl_Input.H>
-#include <FL/Fl_Scroll.H>
-#include <FL/Fl_Window.H>
-
-class Mussa;
-#include "SetupWindow.hh"
-
-class SetupWindow : public Fl_Window
-{
- public:
- SetupWindow(int w, int h, const char* title, Mussa *an_analysis);
- ~SetupWindow();
-
- bool done();
-
- //did I put these in public for a reason?
- Fl_Button* test;
- Fl_Input *name_input;
- Fl_Input *win_input;
- Fl_Input *thres_input;
- Fl_Input *seq_num_input;
- Fl_Scroll *seq_scroll;
- // need to keep track of these so a browsed file search can set the input
- // fields to teh selected file
- std::vector<Fl_Input*> seq_inputs, annot_inputs;
-
-
- // callback receiver functions
-
- void real_do_analysis();
-
- void real_set_ana_name_cb(Fl_Input* o);
- void real_set_win_size_cb(Fl_Input* o);
- void real_set_threshold_cb(Fl_Input* o);
- void real_set_seq_num_cb(Fl_Input* o);
-
- void real_seq_file_in_cb(Fl_Input* o, int i);
- void real_choose_seq_file_cb(int i);
- void real_annot_file_in_cb(Fl_Input* o, int i);
- void real_choose_annot_file_cb(int i);
-
- void real_fa_index_in_cb(Fl_Input* o, int i);
- void real_sub_start_in_cb(Fl_Input* o, int i);
- void real_sub_end_in_cb(Fl_Input* o, int i);
-
- private:
- Mussa *an_analysis;
- std::string analysis_name;
- int window, threshold, seq_num;
- std::vector<std::string> seq_files, annot_files;
- std::vector<int> fasta_indices, sub_seq_starts, sub_seq_ends;
- bool win_append, thres_append;
-
- bool all_done;
- static void print_cb(Fl_Button*, void*);
- inline void print_cb_real(Fl_Button*, void*);
-
- void add_seq_input(int index);
-};
-
-// crazy whacked shite Titus taught me to do to get an index value associated
-// with each instance of an input associated with the callback...
-
-struct seq_data_instance
-{
- SetupWindow * sw_ptr;
- int index;
-};
-
-#endif
--- /dev/null
+#ifndef _MUSSA_GUI_LOAD_WINDOW_H_
+#define _MUSSA_GUI_LOAD_WINDOW_H_
+
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+#include <string>
+#include <vector>
+
+#include <FL/Fl_Button.H>
+#include <FL/Fl_Input.H>
+#include <FL/Fl_Scroll.H>
+#include <FL/Fl_Window.H>
+
+class Mussa;
+#include "gui/SetupWindow.hpp"
+
+class SetupWindow : public Fl_Window
+{
+ public:
+ SetupWindow(int w, int h, const char* title, Mussa *an_analysis);
+ ~SetupWindow();
+
+ bool done();
+
+ //did I put these in public for a reason?
+ Fl_Button* test;
+ Fl_Input *name_input;
+ Fl_Input *win_input;
+ Fl_Input *thres_input;
+ Fl_Input *seq_num_input;
+ Fl_Scroll *seq_scroll;
+ // need to keep track of these so a browsed file search can set the input
+ // fields to teh selected file
+ std::vector<Fl_Input*> seq_inputs, annot_inputs;
+
+
+ // callback receiver functions
+
+ void real_do_analysis();
+
+ void real_set_ana_name_cb(Fl_Input* o);
+ void real_set_win_size_cb(Fl_Input* o);
+ void real_set_threshold_cb(Fl_Input* o);
+ void real_set_seq_num_cb(Fl_Input* o);
+
+ void real_seq_file_in_cb(Fl_Input* o, int i);
+ void real_choose_seq_file_cb(int i);
+ void real_annot_file_in_cb(Fl_Input* o, int i);
+ void real_choose_annot_file_cb(int i);
+
+ void real_fa_index_in_cb(Fl_Input* o, int i);
+ void real_sub_start_in_cb(Fl_Input* o, int i);
+ void real_sub_end_in_cb(Fl_Input* o, int i);
+
+ private:
+ Mussa *an_analysis;
+ std::string analysis_name;
+ int window, threshold, seq_num;
+ std::vector<std::string> seq_files, annot_files;
+ std::vector<int> fasta_indices, sub_seq_starts, sub_seq_ends;
+ bool win_append, thres_append;
+
+ bool all_done;
+ static void print_cb(Fl_Button*, void*);
+ inline void print_cb_real(Fl_Button*, void*);
+
+ void add_seq_input(int index);
+};
+
+// crazy whacked shite Titus taught me to do to get an index value associated
+// with each instance of an input associated with the callback...
+
+struct seq_data_instance
+{
+ SetupWindow * sw_ptr;
+ int index;
+};
+
+#endif
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+#include "gui/SubAnalysisWindow.hpp"
+#include "alg/mussa.hpp"
+#include "mussa_exceptions.hpp"
+
+#include <iostream>
+using namespace std;
+
+void
+do_subana_cb(Fl_Button* o, void* v)
+{
+ SubAnalysisWindow* T=(SubAnalysisWindow*)v;
+ T->real_do_subana();
+}
+
+
+// passes the parameters to the mussa class object and orders it to run
+void
+SubAnalysisWindow::real_do_subana()
+{
+ int i;
+ string a_sequence, err_msg;
+
+ // <-- need a check here to make sure all vars have a valid value
+
+ an_analysis->clear();
+ an_analysis->set_name(analysis_name);
+ an_analysis->set_window(window);
+ an_analysis->set_threshold(threshold);
+
+ for(i=0; i < seq_num; i++)
+ {
+ a_sequence = the_seqs[i].get_seq();
+ cout << a_sequence.length() << endl;
+ a_sequence = a_sequence.substr(sub_seq_starts[i],
+ sub_seq_ends[i] - sub_seq_starts[i] );
+ cout << a_sequence.length() << endl;
+ an_analysis->add_a_seq(a_sequence);
+ }
+
+ try {
+ an_analysis->analyze();
+ } catch( mussa_analysis_error e) {
+ fl_alert( e.what() );
+ }
+
+ all_done = true;
+
+ hide();
+}
+
+
+
+// *** subsequence start select
+
+void
+sub_start_in_cb1(Fl_Input* o, void* v)
+{
+ sub_seq_data_instance * blah = (sub_seq_data_instance *) v;
+ SubAnalysisWindow* T= blah->sw_ptr;
+ T->real_sub_start_in_cb(o,blah->index);
+}
+
+void
+SubAnalysisWindow::real_sub_start_in_cb(Fl_Input* o, int i)
+{
+ sub_seq_starts[i] = atoi(o->value());
+}
+
+// *** subsequence end select
+
+void
+sub_end_in_cb1(Fl_Input* o, void* v)
+{
+ sub_seq_data_instance * blah = (sub_seq_data_instance *) v;
+ SubAnalysisWindow* T= blah->sw_ptr;
+ T->real_sub_end_in_cb(o,blah->index);
+}
+
+void
+SubAnalysisWindow::real_sub_end_in_cb(Fl_Input* o, int i)
+{
+ sub_seq_ends[i] = atoi(o->value());
+
+}
+
+// *** input analysis name
+
+void
+set_ana_name_cb1(Fl_Input* o, void* v)
+{
+ SubAnalysisWindow* T=(SubAnalysisWindow*)v;
+ T->real_set_ana_name_cb(o);
+}
+
+void
+SubAnalysisWindow::real_set_ana_name_cb(Fl_Input* o)
+{
+ analysis_name = o->value();
+}
+
+// *** input window size
+
+void
+set_win_size_cb1(Fl_Input* o, void* v)
+{
+ SubAnalysisWindow* T=(SubAnalysisWindow*)v;
+ T->real_set_win_size_cb(o);
+}
+
+void
+SubAnalysisWindow::real_set_win_size_cb(Fl_Input* o)
+{
+ window = atoi(o->value());
+}
+
+// *** input threshold
+
+void
+set_threshold_cb1(Fl_Input* o, void* v)
+{
+ SubAnalysisWindow* T=(SubAnalysisWindow*)v;
+ T->real_set_threshold_cb(o);
+}
+
+void
+SubAnalysisWindow::real_set_threshold_cb(Fl_Input* o)
+{
+ threshold = atoi(o->value());
+}
+
+
+bool
+SubAnalysisWindow::done()
+{
+ return all_done;
+}
+
+
+SubAnalysisWindow::SubAnalysisWindow(int w, int h, const char* title,Mussa *the_analysis,
+ vector<Sequence> some_Seqs):Fl_Window(w,h,title)
+{
+ string a_name;
+
+ color(FL_WHITE);
+
+ an_analysis = the_analysis;
+ the_seqs = some_Seqs;
+ all_done = false;
+
+ // initialize parameters
+ analysis_name = "";
+ window = -1;
+ threshold = -1;
+
+ begin();
+
+ name_input = new Fl_Input(135, 10, w-140, 30, "SubAnalysis Name ");
+ name_input->value("");
+ //name_input->when(FL_WHEN_ENTER_KEY);
+ name_input->box(FL_BORDER_BOX);
+ name_input->callback((Fl_Callback*)set_ana_name_cb1, this);
+
+ // add in radio buttons for win_append and thres_append eventually
+ win_append = true;
+ thres_append = true;
+
+ win_input = new Fl_Input(135,45,100,30, "Window: ");
+ win_input->value("");
+ win_input->callback((Fl_Callback*)set_win_size_cb1, this);
+
+ thres_input = new Fl_Input(320,45,100,30, "Threshold: ");
+ thres_input->value("");
+ thres_input->callback((Fl_Callback*)set_threshold_cb1, this);
+
+ // button to launch the analysis
+ test = new Fl_Button(w-100,h-30,100,30,"Do Analysis");
+ test->callback((Fl_Callback*)do_subana_cb, this);
+
+ // test button to make sure setup data is being stored
+ test = new Fl_Button(w-200,h-30,100,30,"show setup");
+ test->callback((Fl_Callback*)print_cb, this);
+
+ // add all the inputs for the sub sequence starts & ends
+ int i;
+
+ seq_num = the_seqs.size();
+
+ seq_scroll = new Fl_Scroll(5,80,w-10,h-115);
+ seq_scroll->color(FL_WHITE);
+
+ for (i = 0; i < seq_num; i++)
+ {
+ sub_seq_starts.push_back(0);
+ sub_seq_ends.push_back(0);
+ //a_name = the_seqs[i].sp_name();
+ //cout << a_name << endl;
+ add_seq_input(i, a_name);
+ }
+ seq_scroll->box(FL_DOWN_FRAME);
+ //add(seq_scroll);
+ //redraw();
+
+ end();
+ //resizable(this);
+ show();
+}
+
+
+SubAnalysisWindow::~SubAnalysisWindow(){}
+
+
+void
+SubAnalysisWindow::add_seq_input(int i, string a_name)
+{
+ Fl_Input *start_input, *end_input;
+
+
+ // this remembers what seq index each input is associated with
+ sub_seq_data_instance * something;
+ something = new sub_seq_data_instance;
+ something->sw_ptr = this;
+ something->index = i;
+
+
+ // subsequence select, index of first bp wanted
+ start_input = new Fl_Input(150, 85+(i*35), 70, 30, "start index: ");
+ start_input->value("");
+ start_input->callback((Fl_Callback*)sub_start_in_cb1, (void*) something);
+
+ // subsequence select, index of last bp wanted
+ end_input = new Fl_Input(300, 85+(i*35), 70, 30, "end index: ");
+ end_input->value("");
+ end_input->callback((Fl_Callback*)sub_end_in_cb1, (void*) something);
+
+ seq_scroll->add(start_input);
+ seq_scroll->add(end_input);
+}
+
+/*
+ cout << "fee\n";
+ cout << "fie\n";
+ cout << "foe\n";
+ cout << "fum\n";
+*/
+
+void SubAnalysisWindow::print_cb(Fl_Button* o, void* v)
+{
+ SubAnalysisWindow* T=(SubAnalysisWindow*)v;
+ T->print_cb_real(o,v);
+}
+
+
+void SubAnalysisWindow::print_cb_real(Fl_Button* , void*)
+{
+ cout << "analysis_name: " << analysis_name << endl;
+ cout << "win: " << window << endl;
+ cout << "thres: " << threshold << endl;
+ cout << "seq_num: " << seq_num << endl;
+ //cout << "win_add: " << win_append << end;
+ //cout << "thres_add: " << thres_append << endl;
+
+ int i;
+
+
+
+ for (i = 0; i < seq_num; i++)
+ {
+ cout << " start: " << sub_seq_starts[i];
+ cout << " end: " << sub_seq_ends[i] << endl;
+ cout << "blargle!\n";
+ }
+ cout << "end of inputs\n" << endl;
+}
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-#include "SubAnalysisWindow.hh"
-#include "alg/mussa_class.hh"
-#include "mussa_exceptions.hh"
-
-#include <iostream>
-using namespace std;
-
-void
-do_subana_cb(Fl_Button* o, void* v)
-{
- SubAnalysisWindow* T=(SubAnalysisWindow*)v;
- T->real_do_subana();
-}
-
-
-// passes the parameters to the mussa class object and orders it to run
-void
-SubAnalysisWindow::real_do_subana()
-{
- int i;
- string a_sequence, err_msg;
-
- // <-- need a check here to make sure all vars have a valid value
-
- an_analysis->clear();
- an_analysis->set_name(analysis_name);
- an_analysis->set_window(window);
- an_analysis->set_threshold(threshold);
-
- for(i=0; i < seq_num; i++)
- {
- a_sequence = the_seqs[i].get_seq();
- cout << a_sequence.length() << endl;
- a_sequence = a_sequence.substr(sub_seq_starts[i],
- sub_seq_ends[i] - sub_seq_starts[i] );
- cout << a_sequence.length() << endl;
- an_analysis->add_a_seq(a_sequence);
- }
-
- try {
- an_analysis->analyze();
- } catch( mussa_analysis_error e) {
- fl_alert( e.what() );
- }
-
- all_done = true;
-
- hide();
-}
-
-
-
-// *** subsequence start select
-
-void
-sub_start_in_cb1(Fl_Input* o, void* v)
-{
- sub_seq_data_instance * blah = (sub_seq_data_instance *) v;
- SubAnalysisWindow* T= blah->sw_ptr;
- T->real_sub_start_in_cb(o,blah->index);
-}
-
-void
-SubAnalysisWindow::real_sub_start_in_cb(Fl_Input* o, int i)
-{
- sub_seq_starts[i] = atoi(o->value());
-}
-
-// *** subsequence end select
-
-void
-sub_end_in_cb1(Fl_Input* o, void* v)
-{
- sub_seq_data_instance * blah = (sub_seq_data_instance *) v;
- SubAnalysisWindow* T= blah->sw_ptr;
- T->real_sub_end_in_cb(o,blah->index);
-}
-
-void
-SubAnalysisWindow::real_sub_end_in_cb(Fl_Input* o, int i)
-{
- sub_seq_ends[i] = atoi(o->value());
-
-}
-
-// *** input analysis name
-
-void
-set_ana_name_cb1(Fl_Input* o, void* v)
-{
- SubAnalysisWindow* T=(SubAnalysisWindow*)v;
- T->real_set_ana_name_cb(o);
-}
-
-void
-SubAnalysisWindow::real_set_ana_name_cb(Fl_Input* o)
-{
- analysis_name = o->value();
-}
-
-// *** input window size
-
-void
-set_win_size_cb1(Fl_Input* o, void* v)
-{
- SubAnalysisWindow* T=(SubAnalysisWindow*)v;
- T->real_set_win_size_cb(o);
-}
-
-void
-SubAnalysisWindow::real_set_win_size_cb(Fl_Input* o)
-{
- window = atoi(o->value());
-}
-
-// *** input threshold
-
-void
-set_threshold_cb1(Fl_Input* o, void* v)
-{
- SubAnalysisWindow* T=(SubAnalysisWindow*)v;
- T->real_set_threshold_cb(o);
-}
-
-void
-SubAnalysisWindow::real_set_threshold_cb(Fl_Input* o)
-{
- threshold = atoi(o->value());
-}
-
-
-bool
-SubAnalysisWindow::done()
-{
- return all_done;
-}
-
-
-SubAnalysisWindow::SubAnalysisWindow(int w, int h, const char* title,Mussa *the_analysis,
- vector<Sequence> some_Seqs):Fl_Window(w,h,title)
-{
- string a_name;
-
- color(FL_WHITE);
-
- an_analysis = the_analysis;
- the_seqs = some_Seqs;
- all_done = false;
-
- // initialize parameters
- analysis_name = "";
- window = -1;
- threshold = -1;
-
- begin();
-
- name_input = new Fl_Input(135, 10, w-140, 30, "SubAnalysis Name ");
- name_input->value("");
- //name_input->when(FL_WHEN_ENTER_KEY);
- name_input->box(FL_BORDER_BOX);
- name_input->callback((Fl_Callback*)set_ana_name_cb1, this);
-
- // add in radio buttons for win_append and thres_append eventually
- win_append = true;
- thres_append = true;
-
- win_input = new Fl_Input(135,45,100,30, "Window: ");
- win_input->value("");
- win_input->callback((Fl_Callback*)set_win_size_cb1, this);
-
- thres_input = new Fl_Input(320,45,100,30, "Threshold: ");
- thres_input->value("");
- thres_input->callback((Fl_Callback*)set_threshold_cb1, this);
-
- // button to launch the analysis
- test = new Fl_Button(w-100,h-30,100,30,"Do Analysis");
- test->callback((Fl_Callback*)do_subana_cb, this);
-
- // test button to make sure setup data is being stored
- test = new Fl_Button(w-200,h-30,100,30,"show setup");
- test->callback((Fl_Callback*)print_cb, this);
-
- // add all the inputs for the sub sequence starts & ends
- int i;
-
- seq_num = the_seqs.size();
-
- seq_scroll = new Fl_Scroll(5,80,w-10,h-115);
- seq_scroll->color(FL_WHITE);
-
- for (i = 0; i < seq_num; i++)
- {
- sub_seq_starts.push_back(0);
- sub_seq_ends.push_back(0);
- //a_name = the_seqs[i].sp_name();
- //cout << a_name << endl;
- add_seq_input(i, a_name);
- }
- seq_scroll->box(FL_DOWN_FRAME);
- //add(seq_scroll);
- //redraw();
-
- end();
- //resizable(this);
- show();
-}
-
-
-SubAnalysisWindow::~SubAnalysisWindow(){}
-
-
-void
-SubAnalysisWindow::add_seq_input(int i, string a_name)
-{
- Fl_Input *start_input, *end_input;
-
-
- // this remembers what seq index each input is associated with
- sub_seq_data_instance * something;
- something = new sub_seq_data_instance;
- something->sw_ptr = this;
- something->index = i;
-
-
- // subsequence select, index of first bp wanted
- start_input = new Fl_Input(150, 85+(i*35), 70, 30, "start index: ");
- start_input->value("");
- start_input->callback((Fl_Callback*)sub_start_in_cb1, (void*) something);
-
- // subsequence select, index of last bp wanted
- end_input = new Fl_Input(300, 85+(i*35), 70, 30, "end index: ");
- end_input->value("");
- end_input->callback((Fl_Callback*)sub_end_in_cb1, (void*) something);
-
- seq_scroll->add(start_input);
- seq_scroll->add(end_input);
-}
-
-/*
- cout << "fee\n";
- cout << "fie\n";
- cout << "foe\n";
- cout << "fum\n";
-*/
-
-void SubAnalysisWindow::print_cb(Fl_Button* o, void* v)
-{
- SubAnalysisWindow* T=(SubAnalysisWindow*)v;
- T->print_cb_real(o,v);
-}
-
-
-void SubAnalysisWindow::print_cb_real(Fl_Button* , void*)
-{
- cout << "analysis_name: " << analysis_name << endl;
- cout << "win: " << window << endl;
- cout << "thres: " << threshold << endl;
- cout << "seq_num: " << seq_num << endl;
- //cout << "win_add: " << win_append << end;
- //cout << "thres_add: " << thres_append << endl;
-
- int i;
-
-
-
- for (i = 0; i < seq_num; i++)
- {
- cout << " start: " << sub_seq_starts[i];
- cout << " end: " << sub_seq_ends[i] << endl;
- cout << "blargle!\n";
- }
- cout << "end of inputs\n" << endl;
-}
+++ /dev/null
-#ifndef _MUSSA_GUI_SUBANA_H_
-#define _MUSSA_GUI_SUBANA_H_
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-#include <string>
-#include <vector>
-
-#include <FL/Fl_Button.H>
-#include <FL/Fl_Window.H>
-#include <FL/Fl_Input.H>
-#include <FL/Fl_File_Chooser.H>
-#include <FL/Fl_Scroll.H>
-
-#include "alg/mussa_class.hh"
-#include "SeqTextWindow.hh"
-
-class SubAnalysisWindow : public Fl_Window
-{
- public:
- SubAnalysisWindow(int w, int h, const char* title, Mussa *an_analysis,
- std::vector<Sequence> some_Seqs);
- ~SubAnalysisWindow();
- bool done();
-
-
- Fl_Button* test;
-
- Fl_Input *name_input;
- Fl_Input *win_input;
- Fl_Input *thres_input;
- Fl_Input *seq_num_input;
- Fl_Scroll *seq_scroll;
- // need to keep track of these so a browsed file search can set the input
- // fields to the selected file
- std::vector<Fl_Input*> seq_inputs, annot_inputs;
-
-
- // callback receiver functions
-
- void real_do_subana();
-
- void real_set_ana_name_cb(Fl_Input* o);
- void real_set_win_size_cb(Fl_Input* o);
- void real_set_threshold_cb(Fl_Input* o);
-
- void real_sub_start_in_cb(Fl_Input* o, int i);
- void real_sub_end_in_cb(Fl_Input* o, int i);
-
- private:
- // sequence data
- std::vector<Sequence> the_seqs;
- Mussa *an_analysis;
- std::string analysis_name;
- int window, threshold, seq_num;
- std::vector<int> sub_seq_starts, sub_seq_ends;
- bool win_append, thres_append;
- bool all_done;
-
- static void print_cb(Fl_Button*, void*);
- inline void print_cb_real(Fl_Button*, void*);
-
- void add_seq_input(int index, std::string a_name);
-};
-
-// crazy whacked shite Titus taught me to do to get an index value associated
-// with each instance of an input associated with the callback...
-
-
-struct sub_seq_data_instance
-{
- SubAnalysisWindow * sw_ptr;
- int index;
-};
-#endif
--- /dev/null
+#ifndef _MUSSA_GUI_SUBANA_H_
+#define _MUSSA_GUI_SUBANA_H_
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+#include <string>
+#include <vector>
+
+#include <FL/Fl_Button.H>
+#include <FL/Fl_Window.H>
+#include <FL/Fl_Input.H>
+#include <FL/Fl_File_Chooser.H>
+#include <FL/Fl_Scroll.H>
+
+#include "alg/mussa.hpp"
+#include "gui/SeqTextWindow.hpp"
+
+class SubAnalysisWindow : public Fl_Window
+{
+ public:
+ SubAnalysisWindow(int w, int h, const char* title, Mussa *an_analysis,
+ std::vector<Sequence> some_Seqs);
+ ~SubAnalysisWindow();
+ bool done();
+
+
+ Fl_Button* test;
+
+ Fl_Input *name_input;
+ Fl_Input *win_input;
+ Fl_Input *thres_input;
+ Fl_Input *seq_num_input;
+ Fl_Scroll *seq_scroll;
+ // need to keep track of these so a browsed file search can set the input
+ // fields to the selected file
+ std::vector<Fl_Input*> seq_inputs, annot_inputs;
+
+
+ // callback receiver functions
+
+ void real_do_subana();
+
+ void real_set_ana_name_cb(Fl_Input* o);
+ void real_set_win_size_cb(Fl_Input* o);
+ void real_set_threshold_cb(Fl_Input* o);
+
+ void real_sub_start_in_cb(Fl_Input* o, int i);
+ void real_sub_end_in_cb(Fl_Input* o, int i);
+
+ private:
+ // sequence data
+ std::vector<Sequence> the_seqs;
+ Mussa *an_analysis;
+ std::string analysis_name;
+ int window, threshold, seq_num;
+ std::vector<int> sub_seq_starts, sub_seq_ends;
+ bool win_append, thres_append;
+ bool all_done;
+
+ static void print_cb(Fl_Button*, void*);
+ inline void print_cb_real(Fl_Button*, void*);
+
+ void add_seq_input(int index, std::string a_name);
+};
+
+// crazy whacked shite Titus taught me to do to get an index value associated
+// with each instance of an input associated with the callback...
+
+
+struct sub_seq_data_instance
+{
+ SubAnalysisWindow * sw_ptr;
+ int index;
+};
+#endif
CURDIR := $(BASEDIR)gui/
-SOURCES.cxx := AnnotWindow.cxx \
- ConnView.cxx \
- ConnWindow.cxx \
- MotifWindow.cxx \
- SeqTextWindow.cxx \
- SeqView.cxx \
- SeqWindow.cxx \
- SetupWindow.cxx \
- SubAnalysisWindow.cxx
+SOURCES.cpp := AnnotWindow.cpp \
+ ConnView.cpp \
+ ConnWindow.cpp \
+ MotifWindow.cpp \
+ SeqTextWindow.cpp \
+ SeqView.cpp \
+ SeqWindow.cpp \
+ SetupWindow.cpp \
+ SubAnalysisWindow.cpp
-MUSSA_FLTK_SRC := $(addprefix $(CURDIR), $(SOURCES.cxx))
-MUSSA_FLTK_OBJ := $(MUSSA_FLTK_SRC:.cxx=$(OBJEXT))
+MUSSA_FLTK_SRC := $(addprefix $(CURDIR), $(SOURCES.cpp))
+MUSSA_FLTK_OBJ := $(MUSSA_FLTK_SRC:.cpp=$(OBJEXT))
SRC += $(MUSSA_FLTK_SRC)
CXXFLAGS +=
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+#include "gui/ConnWindow.hpp"
+#include "alg/mussa.hpp"
+#include "mussa_exceptions.hpp"
+#include <iostream>
+using namespace std;
+
+char
+parse_args(int argc, char **argv, string *a_file_path, int *window,
+ int *threshold, enum Mussa::analysis_modes *ana_mode, float *ent_thres);
+
+
+int main(int argc, char **argv)
+{
+ Mussa an_analysis;
+ string a_file_path;
+ char * picked_file;
+ int window, threshold;
+ float ent_thres;
+ char run_mode;
+ enum Mussa::analysis_modes ana_mode;
+ int x_max=1000;
+ int y_max=500;
+ string err_msg;
+
+
+ err_msg = "";
+
+ // yeah, its horrible to be passing these by reference, but I just don't see
+ // any other way without making parse_args part of MussaClass, which just
+ // seems wrong (args are after all, an io type thing, and the gui only mode
+ // will have it own way as well...
+ run_mode = parse_args(argc, argv, &a_file_path, &window, &threshold,
+ &ana_mode, &ent_thres);
+
+ cout << "mussa: run mode = " << run_mode;
+ cout << "\tfile_path = "<< a_file_path << endl;
+ cout << "mussa: ent_thres = " << ent_thres << endl;
+
+ // if no error from parse args (run_mode = 'e', ie error), run in proper mode
+ if (run_mode != 'e')
+ {
+ if ((run_mode == 'f') || (run_mode == 'n'))
+ {
+ an_analysis.load_mupa_file(a_file_path);
+ an_analysis.analyze(window, threshold, ana_mode, ent_thres);
+ //an_overlord.do_analysis();
+ }
+
+ if (run_mode == 'v')
+ an_analysis.load(a_file_path);
+ //an_overlord.get_analysis();
+
+ // no longer needed, but still semi-useful reality check...
+ if (run_mode == 'g')
+ {
+ cout << "GTV - All Gui, All the Time\n";
+ }
+
+ if (err_msg == "")
+ {
+ if ((run_mode == 'f') || (run_mode == 'v') || (run_mode == 'g'))
+ {
+ //an_overlord.spawnConnView(1000,500);
+ ConnWindow *a_conn_win = new ConnWindow(x_max, y_max, "Mussa");
+
+ // we have an analysis already if in these 2 modes
+ if ((run_mode == 'f') || (run_mode == 'v'))
+ a_conn_win->add_ana(&an_analysis);
+
+ Fl::run();
+ }
+ }
+ else
+ cout << err_msg << endl;
+ }
+}
+
+
+// minimal arg reading function, not very robust to errors
+char
+parse_args(int argc, char **argv, string *a_file_path, int *window,
+ int *threshold, enum Mussa::analysis_modes *ana_mode, float *ent_thres)
+{
+ int i, else_i;
+ string an_arg;
+ char run_mode;
+
+ // initialize these to 0 as flag if they are not changed
+ *window = 0;
+ *threshold = 0;
+ *ent_thres = 0.0;
+ run_mode = 'e'; //error default if no run mode set implicitly or explicitly
+ *ana_mode = Mussa::TransitiveNway; // default to transitivie analyses mode
+
+ // no args means gui only mode
+ if (argc == 1)
+ run_mode = 'g';
+ else
+ {
+ else_i = 0;
+ i = 1;
+ while (i < argc)
+ {
+ an_arg = * ++argv;
+ i++;
+
+ // see what alternate mode the user wants to run in
+ if (an_arg == "-m")
+ {
+ an_arg = * ++argv;
+ i++;
+ if ( (an_arg == "v") || (an_arg == "n") ) //only 2 valid modes so far
+ run_mode = an_arg[0];
+ else
+ {
+ cout << "Error: \'" << an_arg;
+ cout << "\' is not a valid analysis mode for -a argument" << endl;
+ throw cmdline_error("not valid -a argument");
+ }
+ *a_file_path = * ++argv;
+ i++;
+ }
+ // alternate analyses modes
+ else if (an_arg == "-a")
+ {
+ an_arg = * ++argv;
+ i++;
+ // t = transitive, r = radial, e = entropy
+ if (an_arg == "t") *ana_mode = Mussa::TransitiveNway;
+ else if (an_arg == "r") *ana_mode = Mussa::RadialNway;
+ else if (an_arg == "e") *ana_mode = Mussa::EntropyNway;
+ else
+ {
+ cout << "Error: \'" << an_arg;
+ cout << "\' is not a valid run mode for -m argument" << endl;
+ throw cmdline_error("bad argument -m");
+ }
+ }
+ else if (an_arg == "-w") // alternate window size arg
+ {
+ *window = atoi(* ++argv);
+ i++;
+ }
+ else if (an_arg == "-t") // alternate threshold arg
+ {
+ *threshold = atoi(* ++argv);
+ i++;
+ }
+ else if (an_arg == "-et") // alternate entropy threshold arg
+ {
+ *ent_thres = atof(* ++argv);
+ i++;
+ }
+ else
+ {
+ if (else_i == 0)
+ {
+ *a_file_path = an_arg;
+ run_mode = 'f';
+ else_i++;
+ }
+ else
+ {
+ //cout << "Error, unknown arg: \'" << an_arg << "\'" << endl;
+ cout << "Error, too many filenames: \'" << an_arg << "\'" << endl;
+ run_mode == 'e';
+ }
+ }
+ }
+ }
+ return run_mode;
+}
+
+
+/*
+ cout << "fee\n";
+ cout << "fie\n";
+ cout << "foe\n";
+ cout << "fum\n";
+*/
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-#include "gui/ConnWindow.hh"
-#include "alg/mussa_class.hh"
-#include "mussa_exceptions.hh"
-#include <iostream>
-using namespace std;
-
-char
-parse_args(int argc, char **argv, string *a_file_path, int *window,
- int *threshold, enum Mussa::analysis_modes *ana_mode, float *ent_thres);
-
-
-int main(int argc, char **argv)
-{
- Mussa an_analysis;
- string a_file_path;
- char * picked_file;
- int window, threshold;
- float ent_thres;
- char run_mode;
- enum Mussa::analysis_modes ana_mode;
- int x_max=1000;
- int y_max=500;
- string err_msg;
-
-
- err_msg = "";
-
- // yeah, its horrible to be passing these by reference, but I just don't see
- // any other way without making parse_args part of MussaClass, which just
- // seems wrong (args are after all, an io type thing, and the gui only mode
- // will have it own way as well...
- run_mode = parse_args(argc, argv, &a_file_path, &window, &threshold,
- &ana_mode, &ent_thres);
-
- cout << "mussa: run mode = " << run_mode;
- cout << "\tfile_path = "<< a_file_path << endl;
- cout << "mussa: ent_thres = " << ent_thres << endl;
-
- // if no error from parse args (run_mode = 'e', ie error), run in proper mode
- if (run_mode != 'e')
- {
- if ((run_mode == 'f') || (run_mode == 'n'))
- {
- an_analysis.load_mupa_file(a_file_path);
- an_analysis.analyze(window, threshold, ana_mode, ent_thres);
- //an_overlord.do_analysis();
- }
-
- if (run_mode == 'v')
- an_analysis.load(a_file_path);
- //an_overlord.get_analysis();
-
- // no longer needed, but still semi-useful reality check...
- if (run_mode == 'g')
- {
- cout << "GTV - All Gui, All the Time\n";
- }
-
- if (err_msg == "")
- {
- if ((run_mode == 'f') || (run_mode == 'v') || (run_mode == 'g'))
- {
- //an_overlord.spawnConnView(1000,500);
- ConnWindow *a_conn_win = new ConnWindow(x_max, y_max, "Mussa");
-
- // we have an analysis already if in these 2 modes
- if ((run_mode == 'f') || (run_mode == 'v'))
- a_conn_win->add_ana(&an_analysis);
-
- Fl::run();
- }
- }
- else
- cout << err_msg << endl;
- }
-}
-
-
-// minimal arg reading function, not very robust to errors
-char
-parse_args(int argc, char **argv, string *a_file_path, int *window,
- int *threshold, enum Mussa::analysis_modes *ana_mode, float *ent_thres)
-{
- int i, else_i;
- string an_arg;
- char run_mode;
-
- // initialize these to 0 as flag if they are not changed
- *window = 0;
- *threshold = 0;
- *ent_thres = 0.0;
- run_mode = 'e'; //error default if no run mode set implicitly or explicitly
- *ana_mode = Mussa::TransitiveNway; // default to transitivie analyses mode
-
- // no args means gui only mode
- if (argc == 1)
- run_mode = 'g';
- else
- {
- else_i = 0;
- i = 1;
- while (i < argc)
- {
- an_arg = * ++argv;
- i++;
-
- // see what alternate mode the user wants to run in
- if (an_arg == "-m")
- {
- an_arg = * ++argv;
- i++;
- if ( (an_arg == "v") || (an_arg == "n") ) //only 2 valid modes so far
- run_mode = an_arg[0];
- else
- {
- cout << "Error: \'" << an_arg;
- cout << "\' is not a valid analysis mode for -a argument" << endl;
- throw cmdline_error("not valid -a argument");
- }
- *a_file_path = * ++argv;
- i++;
- }
- // alternate analyses modes
- else if (an_arg == "-a")
- {
- an_arg = * ++argv;
- i++;
- // t = transitive, r = radial, e = entropy
- if (an_arg == "t") *ana_mode = Mussa::TransitiveNway;
- else if (an_arg == "r") *ana_mode = Mussa::RadialNway;
- else if (an_arg == "e") *ana_mode = Mussa::EntropyNway;
- else
- {
- cout << "Error: \'" << an_arg;
- cout << "\' is not a valid run mode for -m argument" << endl;
- throw cmdline_error("bad argument -m");
- }
- }
- else if (an_arg == "-w") // alternate window size arg
- {
- *window = atoi(* ++argv);
- i++;
- }
- else if (an_arg == "-t") // alternate threshold arg
- {
- *threshold = atoi(* ++argv);
- i++;
- }
- else if (an_arg == "-et") // alternate entropy threshold arg
- {
- *ent_thres = atof(* ++argv);
- i++;
- }
- else
- {
- if (else_i == 0)
- {
- *a_file_path = an_arg;
- run_mode = 'f';
- else_i++;
- }
- else
- {
- //cout << "Error, unknown arg: \'" << an_arg << "\'" << endl;
- cout << "Error, too many filenames: \'" << an_arg << "\'" << endl;
- run_mode == 'e';
- }
- }
- }
- }
- return run_mode;
-}
-
-
-/*
- cout << "fee\n";
- cout << "fie\n";
- cout << "foe\n";
- cout << "fum\n";
-*/
+++ /dev/null
-#ifndef _MUSSA_EXCEPTIONS_H_
-#define _MUSSA_EXCEPTIONS_H_
-#include <stdexcept>
-
-//! Error processing commandline arguments
-class cmdline_error : public std::runtime_error
-{
-public:
- explicit cmdline_error(const std::string& msg): std::runtime_error(msg) {};
-};
-
-//! Error loading information
-class mussa_load_error : public std::runtime_error
-{
-public:
- explicit mussa_load_error(const std::string& msg) :
- std::runtime_error(msg) {};
-};
-
-//! failure running analysis
-class mussa_analysis_error : public std::runtime_error
-{
-public:
- explicit mussa_analysis_error(const std::string& msg) :
- std::runtime_error(msg) {};
-};
-#endif
--- /dev/null
+#ifndef _MUSSA_EXCEPTIONS_H_
+#define _MUSSA_EXCEPTIONS_H_
+#include <stdexcept>
+
+//! Error processing commandline arguments
+class cmdline_error : public std::runtime_error
+{
+public:
+ explicit cmdline_error(const std::string& msg): std::runtime_error(msg) {};
+};
+
+//! Error loading information
+class mussa_load_error : public std::runtime_error
+{
+public:
+ explicit mussa_load_error(const std::string& msg) :
+ std::runtime_error(msg) {};
+};
+
+//! failure running analysis
+class mussa_analysis_error : public std::runtime_error
+{
+public:
+ explicit mussa_analysis_error(const std::string& msg) :
+ std::runtime_error(msg) {};
+};
+#endif
--- /dev/null
+#include <QApplication>
+
+#include "qui/PathWindow.hpp"
+#include "alg/parse_options.hpp"
+
+int main(int argc, char **argv)
+{
+ QApplication app(argc, argv);
+ Mussa *analysis = initialize_mussa(argc, argv);
+
+ if (analysis == 0) {
+ return 1;
+ }
+
+ PathWindow win(analysis);
+ win.show();
+ app.exec();
+ return 0;
+}
+++ /dev/null
-#include <QApplication>
-
-#include "qui/PathWindow.h"
-#include "alg/parse_options.h"
-
-int main(int argc, char **argv)
-{
- QApplication app(argc, argv);
- Mussa *analysis = initialize_mussa(argc, argv);
-
- if (analysis == 0) {
- return 1;
- }
-
- PathWindow win(analysis);
- win.show();
- app.exec();
- return 0;
-}
INCLUDEPATH += . alg qui
# Input
-HEADERS += mussa_exceptions.hh \
- qui/PathWidget.h \
- qui/PathWindow.h \
- qui/PathScene.h \
- qui/ThresholdWidget.h \
- qui/ImageScaler.h \
- qui/ImageSaveDialog.h \
- alg/color.h \
- alg/conserved_path.h \
- alg/flp.hh \
- alg/glsequence.h \
- alg/mussa_class.hh \
- alg/nway_paths.hh \
- alg/parse_options.h \
- alg/sequence.hh
-SOURCES += mussagl.cxx \
- qui/PathWidget.cxx \
- qui/PathWindow.cxx \
- qui/PathScene.cxx \
- qui/ThresholdWidget.cxx \
- qui/ImageScaler.cxx \
- qui/ImageSaveDialog.cxx \
- alg/color.cxx \
- alg/conserved_path.cxx \
- alg/flp.cxx \
- alg/flp_seqcomp.cxx \
- alg/glsequence.cxx \
- alg/mussa_class.cxx \
- alg/nway_entropy.cxx \
- alg/nway_other.cxx \
- alg/nway_paths.cxx \
- alg/parse_options.cxx \
-# alg/nway_refine.cxx \
- alg/sequence.cxx
-# test/test_flp.cxx \
-# test/test_main.cxx \
-# test/test_mussa.cxx \
-# test/test_nway.cxx \
-# test/test_sequence.cxx
+HEADERS += mussa_exceptions.hpp \
+ qui/PathWidget.hpp \
+ qui/PathWindow.hpp \
+ qui/PathScene.hpp \
+ qui/ThresholdWidget.hpp \
+ qui/ImageScaler.hpp \
+ qui/ImageSaveDialog.hpp \
+ alg/color.hpp \
+ alg/conserved_path.hpp \
+ alg/flp.hpp \
+ alg/glsequence.hpp \
+ alg/mussa.hpp \
+ alg/nway_paths.hpp \
+ alg/parse_options.hpp \
+ alg/sequence.hpp
+SOURCES += mussagl.cpp \
+ qui/PathWidget.cpp \
+ qui/PathWindow.cpp \
+ qui/PathScene.cpp \
+ qui/ThresholdWidget.cpp \
+ qui/ImageScaler.cpp \
+ qui/ImageSaveDialog.cpp \
+ alg/color.cpp \
+ alg/conserved_path.cpp \
+ alg/flp.cpp \
+ alg/flp_seqcomp.cpp \
+ alg/glsequence.cpp \
+ alg/mussa.cpp \
+ alg/nway_entropy.cpp \
+ alg/nway_other.cpp \
+ alg/nway_paths.cpp \
+ alg/parse_options.cpp \
+# alg/nway_refine.cpp \
+ alg/sequence.cpp
+# test/test_flp.cpp \
+# test/test_main.cpp \
+# test/test_mussa.cpp \
+# test/test_nway.cpp \
+# test/test_sequence.cpp
LIBS += -lm
QT += opengl
--- /dev/null
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
+#include <boost/python.hpp>
+#include <vector>
+using namespace boost::python;
+
+#include "alg/conserved_path.hpp"
+
+void export_conserved_path()
+{
+
+ class_<std::vector<int> >("intvec")
+ .def(vector_indexing_suite<std::vector<int> >())
+ ;
+
+ class_<ConservedPath>("ConservedPath")
+ .def_readwrite("score", &ConservedPath::score)
+ .def_readwrite("track_indexes", &ConservedPath::track_indexes)
+ //.add_property("track_indexes", //iterator<std::vector<int> >())
+ // range(&ConservedPath::track_indexes.begin(),
+ // &ConservedPath::track_indexes.end()))
+ ;
+
+ class_<ExtendedConservedPath, bases<ConservedPath> >("ExtendedConservedPath")
+ .def_readwrite("window_size", &ExtendedConservedPath::window_size)
+ ;
+}
+++ /dev/null
-#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-#include <boost/python.hpp>
-#include <vector>
-using namespace boost::python;
-
-#include "alg/conserved_path.h"
-
-void export_conserved_path()
-{
-
- class_<std::vector<int> >("intvec")
- .def(vector_indexing_suite<std::vector<int> >())
- ;
-
- class_<ConservedPath>("ConservedPath")
- .def_readwrite("score", &ConservedPath::score)
- .def_readwrite("track_indexes", &ConservedPath::track_indexes)
- //.add_property("track_indexes", //iterator<std::vector<int> >())
- // range(&ConservedPath::track_indexes.begin(),
- // &ConservedPath::track_indexes.end()))
- ;
-
- class_<ExtendedConservedPath, bases<ConservedPath> >("ExtendedConservedPath")
- .def_readwrite("window_size", &ExtendedConservedPath::window_size)
- ;
-}
--- /dev/null
+#include <boost/python.hpp>
+using namespace boost::python;
+
+#include "alg/glsequence.hpp"
+#include "alg/sequence.hpp"
+
+void export_glsequence()
+{
+ class_<GlSequence>("GlSequence", init<Sequence &>())
+ .def(init<GlSequence &>())
+ .def("draw", &GlSequence::draw)
+ .def("sequence", &GlSequence::sequence,
+ return_internal_reference<>())
+ .add_property("x", &GlSequence::x, &GlSequence::setX)
+ .add_property("y", &GlSequence::y, &GlSequence::setY)
+ .add_property("length", &GlSequence::length)
+ ;
+}
+++ /dev/null
-#include <boost/python.hpp>
-using namespace boost::python;
-
-#include "alg/glsequence.h"
-#include "alg/sequence.hh"
-
-void export_glsequence()
-{
- class_<GlSequence>("GlSequence", init<Sequence &>())
- .def(init<GlSequence &>())
- .def("draw", &GlSequence::draw)
- .def("sequence", &GlSequence::sequence,
- return_internal_reference<>())
- .add_property("x", &GlSequence::x, &GlSequence::setX)
- .add_property("y", &GlSequence::y, &GlSequence::setY)
- .add_property("length", &GlSequence::length)
- ;
-}
--- /dev/null
+#include <boost/python.hpp>
+using namespace boost::python;
+
+void export_conserved_path();
+void export_glsequence();
+void export_mussa();
+void export_nway_paths();
+void export_sequence();
+
+BOOST_PYTHON_MODULE(mussa)
+{
+ export_conserved_path();
+ export_glsequence();
+ export_mussa();
+ export_nway_paths();
+ export_sequence();
+}
+++ /dev/null
-#include <boost/python.hpp>
-using namespace boost::python;
-
-void export_conserved_path();
-void export_glsequence();
-void export_mussa();
-void export_nway_paths();
-void export_sequence();
-
-BOOST_PYTHON_MODULE(mussa)
-{
- export_conserved_path();
- export_glsequence();
- export_mussa();
- export_nway_paths();
- export_sequence();
-}
CURDIR := $(BASEDIR)py/
-SOURCES.cxx := module.cxx \
- conserved_path.cxx \
- glsequence.cxx \
- mussa.cxx \
- nway_paths.cxx \
- sequence.cxx
+SOURCES.cpp := module.cpp \
+ conserved_path.cpp \
+ glsequence.cpp \
+ mussa.cpp \
+ nway_paths.cpp \
+ sequence.cpp
-MUSSA_PY_SRC := $(addprefix $(CURDIR), $(SOURCES.cxx))
-MUSSA_PY_OBJ := $(MUSSA_PY_SRC:.cxx=$(OBJEXT))
+MUSSA_PY_SRC := $(addprefix $(CURDIR), $(SOURCES.cpp))
+MUSSA_PY_OBJ := $(MUSSA_PY_SRC:.cpp=$(OBJEXT))
SRC += $(MUSSA_PY_SRC)
CXXFLAGS +=
--- /dev/null
+#include <boost/python.hpp>
+
+using namespace boost::python;
+
+#include "alg/mussa.hpp"
+
+void export_mussa()
+{
+ //BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(mussa_analyze_overloads,
+ // &Mussa::analyze, 0, 4);
+
+ class_<Mussa>("Mussa")
+ .def("save", &Mussa::save)
+ .def("load", &Mussa::load, "Load previous run analysis")
+ .def("load_mupa", &Mussa::load_mupa_file, "Load mussa parameter file")
+ .def("clear", &Mussa::clear, "Clear the current analysis")
+ .add_property("name", &Mussa::get_name, &Mussa::set_name)
+ .def("size", &Mussa::size, "Number of sequences to be used "
+ "in this analysis")
+ .add_property("window", &Mussa::get_window, &Mussa::set_window,
+ "the number of base pairs in the sliding window")
+ .add_property("threshold", &Mussa::get_threshold, &Mussa::set_threshold,
+ "how many base pairs must match between two windows")
+ .def("softThreshold", &Mussa::set_soft_thres)
+ .add_property("analysisMode", &Mussa::get_analysis_mode,
+ &Mussa::set_analysis_mode)
+ .add_property("analysisModeName", &Mussa::get_analysis_mode_name)
+ .def("analyze", &Mussa::analyze)
+ .def("paths", &Mussa::paths, return_internal_reference<>())
+ //.def("sequences", &Mussa::sequences)
+ .def("addSequence", &Mussa::add_a_seq) ;
+
+ enum_<Mussa::analysis_modes>("analysis_modes")
+ .value("TransitiveNway", Mussa::TransitiveNway )
+ .value("RadialNway", Mussa::RadialNway )
+ .value("EntropyNway", Mussa::EntropyNway )
+ .value("RecursiveNway", Mussa::RecursiveNway )
+ ;
+}
+++ /dev/null
-#include <boost/python.hpp>
-
-using namespace boost::python;
-
-#include "alg/mussa_class.hh"
-
-void export_mussa()
-{
- //BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(mussa_analyze_overloads,
- // &Mussa::analyze, 0, 4);
-
- class_<Mussa>("Mussa")
- .def("save", &Mussa::save)
- .def("load", &Mussa::load, "Load previous run analysis")
- .def("load_mupa", &Mussa::load_mupa_file, "Load mussa parameter file")
- .def("clear", &Mussa::clear, "Clear the current analysis")
- .add_property("name", &Mussa::get_name, &Mussa::set_name)
- .def("size", &Mussa::size, "Number of sequences to be used "
- "in this analysis")
- .add_property("window", &Mussa::get_window, &Mussa::set_window,
- "the number of base pairs in the sliding window")
- .add_property("threshold", &Mussa::get_threshold, &Mussa::set_threshold,
- "how many base pairs must match between two windows")
- .def("softThreshold", &Mussa::set_soft_thres)
- .add_property("analysisMode", &Mussa::get_analysis_mode,
- &Mussa::set_analysis_mode)
- .add_property("analysisModeName", &Mussa::get_analysis_mode_name)
- .def("analyze", &Mussa::analyze)
- .def("paths", &Mussa::paths, return_internal_reference<>())
- //.def("sequences", &Mussa::sequences)
- .def("addSequence", &Mussa::add_a_seq) ;
-
- enum_<Mussa::analysis_modes>("analysis_modes")
- .value("TransitiveNway", Mussa::TransitiveNway )
- .value("RadialNway", Mussa::RadialNway )
- .value("EntropyNway", Mussa::EntropyNway )
- .value("RecursiveNway", Mussa::RecursiveNway )
- ;
-}
--- /dev/null
+#include <boost/python.hpp>
+using namespace boost::python;
+
+#include "alg/nway_paths.hpp"
+
+void export_nway_paths()
+{
+ class_<NwayPaths>("NwayPaths")
+ .add_property("pathz", range(&NwayPaths::pbegin,
+ &NwayPaths::pend))
+ .add_property("refinedPathz", range(&NwayPaths::rpbegin,
+ &NwayPaths::rpend))
+ ;
+}
+
+++ /dev/null
-#include <boost/python.hpp>
-using namespace boost::python;
-
-#include "alg/nway_paths.hh"
-
-void export_nway_paths()
-{
- class_<NwayPaths>("NwayPaths")
- .add_property("pathz", range(&NwayPaths::pbegin,
- &NwayPaths::pend))
- .add_property("refinedPathz", range(&NwayPaths::rpbegin,
- &NwayPaths::rpend))
- ;
-}
-
--- /dev/null
+#include <boost/python.hpp>
+using namespace boost::python;
+
+#include <string>
+#include "alg/glsequence.hpp"
+
+void export_sequence()
+{
+ class_<Sequence>("Sequence")
+ .def(init<std::string>())
+ //.add_property("seq", &Sequence::get_seq, &Sequence::set_seq)
+ .def("size", &Sequence::size)
+ .def("__len__", &Sequence::size)
+ //.add_property("header", &Sequence::get_header)
+ ;
+}
+++ /dev/null
-#include <boost/python.hpp>
-using namespace boost::python;
-
-#include <string>
-#include "alg/glsequence.h"
-
-void export_sequence()
-{
- class_<Sequence>("Sequence")
- .def(init<std::string>())
- //.add_property("seq", &Sequence::get_seq, &Sequence::set_seq)
- .def("size", &Sequence::size)
- .def("__len__", &Sequence::size)
- //.add_property("header", &Sequence::get_header)
- ;
-}
--- /dev/null
+#include <QDialog>
+#include <QFileDialog>
+#include <QGridLayout>
+#include <QLabel>
+#include <QPixmap>
+#include <QPushButton>
+//#include <QVBoxLayout>
+#include <QGLWidget>
+
+#include "ImageSaveDialog.hpp"
+#include "ImageScaler.hpp"
+
+#include <iostream>
+
+ImageSaveDialog::ImageSaveDialog(QGLWidget *newglwidget, QWidget *parent)
+ : QDialog(parent)
+{
+ setWindowTitle(tr("Save Mussa Image"));
+
+ // Init
+ glwidget = newglwidget;
+ //pixmap = 0;
+ imageScaler = new ImageScaler();
+
+ if (glwidget)
+ {
+ QSize tmpSize;
+ tmpSize = glwidget->size();
+ imageScaler->setWidth(tmpSize.width());
+ imageScaler->setHeight(tmpSize.height());
+ }
+
+ // File Path Label
+ filePathLabel = new QLabel();
+ filePathLabel->setFrameStyle(QFrame::Panel | QFrame::Sunken);
+ filePathLabel->setMinimumWidth(30);
+
+ // Browse Button
+ browseButton = new QPushButton(tr("Browse..."));
+ connect(browseButton, SIGNAL(clicked()),
+ this, SLOT(promptFileDialog()));
+
+ // Save Button
+ saveButton = new QPushButton(tr("Save"));
+ saveButton->setDefault(true);
+ connect(saveButton, SIGNAL(clicked()),
+ this, SLOT(accept()));
+
+ // Cancel Button
+ cancelButton = new QPushButton(tr("Cancel"));
+ connect(cancelButton, SIGNAL(clicked()),
+ this, SLOT(reject()));
+
+ // Layout
+ QGridLayout *layout = new QGridLayout;
+ layout->addWidget(imageScaler, 0, 0, 1, 0, Qt::AlignCenter);
+ layout->addWidget(filePathLabel, 1, 0);
+ layout->addWidget(browseButton, 1, 1);
+ layout->addWidget(saveButton, 2, 0);
+ layout->addWidget(cancelButton, 2, 1);
+ setLayout(layout);
+}
+
+
+void ImageSaveDialog::accept()
+{
+ std::cout << "Accepted!\n";
+ savePixmap();
+ done(1);
+}
+
+void ImageSaveDialog::reject()
+{
+ std::cout << "Rejected!\n";
+ done(0);
+}
+
+void ImageSaveDialog::setSize(int width, int height)
+{
+ imageScaler->setWidth(width);
+ imageScaler->setHeight(height);
+}
+
+//int ImageSaveDialog::exec()
+//{
+// if (glwidget)
+// {
+// QSize tmpSize;
+// tmpSize = glwidget->size();
+// imageScaler->setWidth(tmpSize.width());
+// imageScaler->setHeight(tmpSize.height());
+// }
+// return QDialog::exec();
+//}
+
+
+void ImageSaveDialog::promptFileDialog()
+{
+ QString filePath;
+ filePath = QFileDialog::getSaveFileName(this,
+ "Choose a filename to save image",
+ ".",
+ "Images (*.png *.jpg)");
+ if (filePath.isEmpty())
+ return;
+
+ filePathLabel->setText(filePath);
+}
+
+QSize ImageSaveDialog::getOpenGlPixmapSize()
+{
+ int width = imageScaler->getWidth();
+ int height = imageScaler->getHeight();
+
+ if (height > 0 && width > 0)
+ {
+ return QSize(width, height);
+ }
+
+ return QSize();
+}
+
+QPixmap ImageSaveDialog::renderOpenGlPixmap()
+{
+ if (!glwidget)
+ return QPixmap();
+
+
+ QSize size = getOpenGlPixmapSize();
+ if (size.isValid())
+ {
+ QPixmap pixmap = glwidget->renderPixmap(size.width(), size.height());
+ return pixmap;
+ }
+ return QPixmap();
+}
+
+void ImageSaveDialog::savePixmap()
+{
+ QString filePath;
+ filePath = filePathLabel->text();
+
+ if (filePath.isEmpty())
+ //FIXME: Include prompt telling user of failure
+ return;
+
+ QPixmap pixmap;
+ pixmap = renderOpenGlPixmap();
+
+ //Save pixelmap to file!
+ if (filePath.endsWith(".png"))
+ pixmap.save(filePath, "PNG");
+ else if (filePath.endsWith(".jpg"))
+ pixmap.save(filePath, "JPG");
+ else
+ //FIXME: Include prompt telling user of failure
+ return;
+ return;
+}
+++ /dev/null
-#include <QDialog>
-#include <QFileDialog>
-#include <QGridLayout>
-#include <QLabel>
-#include <QPixmap>
-#include <QPushButton>
-//#include <QVBoxLayout>
-#include <QGLWidget>
-
-#include "ImageSaveDialog.h"
-#include "ImageScaler.h"
-
-#include <iostream>
-
-ImageSaveDialog::ImageSaveDialog(QGLWidget *newglwidget, QWidget *parent)
- : QDialog(parent)
-{
- setWindowTitle(tr("Save Mussa Image"));
-
- // Init
- glwidget = newglwidget;
- //pixmap = 0;
- imageScaler = new ImageScaler();
-
- if (glwidget)
- {
- QSize tmpSize;
- tmpSize = glwidget->size();
- imageScaler->setWidth(tmpSize.width());
- imageScaler->setHeight(tmpSize.height());
- }
-
- // File Path Label
- filePathLabel = new QLabel();
- filePathLabel->setFrameStyle(QFrame::Panel | QFrame::Sunken);
- filePathLabel->setMinimumWidth(30);
-
- // Browse Button
- browseButton = new QPushButton(tr("Browse..."));
- connect(browseButton, SIGNAL(clicked()),
- this, SLOT(promptFileDialog()));
-
- // Save Button
- saveButton = new QPushButton(tr("Save"));
- saveButton->setDefault(true);
- connect(saveButton, SIGNAL(clicked()),
- this, SLOT(accept()));
-
- // Cancel Button
- cancelButton = new QPushButton(tr("Cancel"));
- connect(cancelButton, SIGNAL(clicked()),
- this, SLOT(reject()));
-
- // Layout
- QGridLayout *layout = new QGridLayout;
- layout->addWidget(imageScaler, 0, 0, 1, 0, Qt::AlignCenter);
- layout->addWidget(filePathLabel, 1, 0);
- layout->addWidget(browseButton, 1, 1);
- layout->addWidget(saveButton, 2, 0);
- layout->addWidget(cancelButton, 2, 1);
- setLayout(layout);
-}
-
-
-void ImageSaveDialog::accept()
-{
- std::cout << "Accepted!\n";
- savePixmap();
- done(1);
-}
-
-void ImageSaveDialog::reject()
-{
- std::cout << "Rejected!\n";
- done(0);
-}
-
-void ImageSaveDialog::setSize(int width, int height)
-{
- imageScaler->setWidth(width);
- imageScaler->setHeight(height);
-}
-
-//int ImageSaveDialog::exec()
-//{
-// if (glwidget)
-// {
-// QSize tmpSize;
-// tmpSize = glwidget->size();
-// imageScaler->setWidth(tmpSize.width());
-// imageScaler->setHeight(tmpSize.height());
-// }
-// return QDialog::exec();
-//}
-
-
-void ImageSaveDialog::promptFileDialog()
-{
- QString filePath;
- filePath = QFileDialog::getSaveFileName(this,
- "Choose a filename to save image",
- ".",
- "Images (*.png *.jpg)");
- if (filePath.isEmpty())
- return;
-
- filePathLabel->setText(filePath);
-}
-
-QSize ImageSaveDialog::getOpenGlPixmapSize()
-{
- int width = imageScaler->getWidth();
- int height = imageScaler->getHeight();
-
- if (height > 0 && width > 0)
- {
- return QSize(width, height);
- }
-
- return QSize();
-}
-
-QPixmap ImageSaveDialog::renderOpenGlPixmap()
-{
- if (!glwidget)
- return QPixmap();
-
-
- QSize size = getOpenGlPixmapSize();
- if (size.isValid())
- {
- QPixmap pixmap = glwidget->renderPixmap(size.width(), size.height());
- return pixmap;
- }
- return QPixmap();
-}
-
-void ImageSaveDialog::savePixmap()
-{
- QString filePath;
- filePath = filePathLabel->text();
-
- if (filePath.isEmpty())
- //FIXME: Include prompt telling user of failure
- return;
-
- QPixmap pixmap;
- pixmap = renderOpenGlPixmap();
-
- //Save pixelmap to file!
- if (filePath.endsWith(".png"))
- pixmap.save(filePath, "PNG");
- else if (filePath.endsWith(".jpg"))
- pixmap.save(filePath, "JPG");
- else
- //FIXME: Include prompt telling user of failure
- return;
- return;
-}
+++ /dev/null
-#ifndef _IMAGESAVEDIALOG_H_
-#define _IMAGESAVEDIALOG_H_
-
-#include <QDialog>
-
-class ImageScaler;
-class QLabel;
-class QPixmap;
-class QPushButton;
-class QGLWidget;
-
-class ImageSaveDialog : public QDialog
-{
- Q_OBJECT
-
-public:
- ImageSaveDialog(QGLWidget *qlwidget = 0, QWidget *parent = 0);
-
-public slots:
- void accept();
- void reject();
- // int exec();
- void promptFileDialog();
- void setSize(int width, int height);
-
-signals:
-
-private:
- void savePixmap();
- QSize getOpenGlPixmapSize();
- QPixmap renderOpenGlPixmap();
-
- ImageScaler *imageScaler;
- //QPixmap *pixmap;
- QLabel *filePathLabel;
- QPushButton *browseButton;
- QPushButton *saveButton;
- QPushButton *cancelButton;
- QGLWidget *glwidget;
-
-};
-
-#endif
--- /dev/null
+#ifndef _IMAGESAVEDIALOG_H_
+#define _IMAGESAVEDIALOG_H_
+
+#include <QDialog>
+
+class ImageScaler;
+class QLabel;
+class QPixmap;
+class QPushButton;
+class QGLWidget;
+
+class ImageSaveDialog : public QDialog
+{
+ Q_OBJECT
+
+public:
+ ImageSaveDialog(QGLWidget *qlwidget = 0, QWidget *parent = 0);
+
+public slots:
+ void accept();
+ void reject();
+ // int exec();
+ void promptFileDialog();
+ void setSize(int width, int height);
+
+signals:
+
+private:
+ void savePixmap();
+ QSize getOpenGlPixmapSize();
+ QPixmap renderOpenGlPixmap();
+
+ ImageScaler *imageScaler;
+ //QPixmap *pixmap;
+ QLabel *filePathLabel;
+ QPushButton *browseButton;
+ QPushButton *saveButton;
+ QPushButton *cancelButton;
+ QGLWidget *glwidget;
+
+};
+
+#endif
--- /dev/null
+#include <QAction>
+#include <QCheckBox>
+#include <QLabel>
+#include <QSpinBox>
+#include <QGridLayout>
+
+//#include <iostream>
+#include <cmath>
+
+#include "ImageScaler.hpp"
+
+ImageScaler::ImageScaler(QWidget *parent)
+ : QWidget(parent)
+{
+ lockAspectRatio = false;
+ aspectRatio = 1.0;
+ minWidth = 1;
+ minHeight = 1;
+ curWidth = 1;
+ curHeight = 1;
+
+ //lockAspectAction = new QAction(
+ //lockAspectAction->setCheckable(true);
+
+ lockButton = new QCheckBox();
+ lockButton->setIcon(QIcon(tr("icons/lock.png")));
+ lockButton->setToolTip(tr("Lock aspect ratio"));
+ lockButton->setWhatsThis(tr("Lock aspect ratio"));
+ connect(lockButton, SIGNAL(stateChanged(int)),
+ this, SLOT(setLockAspectRatio(int)));
+
+
+
+ widthBox = new QSpinBox();
+ widthBox->setMinimum(minWidth);
+ setMaxWidth(4048);
+ connect(this, SIGNAL(widthChanged(int)),
+ widthBox, SLOT(setValue(int)));
+ connect(widthBox, SIGNAL(valueChanged(int)),
+ this, SLOT(setWidth(int)));
+
+ widthLabel = new QLabel(tr("Width:"));
+ //widthLabel.setBuddy(widthBox);
+
+ heightBox = new QSpinBox();
+ heightBox->setMinimum(1);
+ setMaxHeight(4048);
+ connect(this, SIGNAL(heightChanged(int)),
+ heightBox, SLOT(setValue(int)));
+ connect(heightBox, SIGNAL(valueChanged(int)),
+ this, SLOT(setHeight(int)));
+
+ heightLabel = new QLabel(tr("Height:"));
+ //heightLabel.setBuddy(heightBox);
+
+ QGridLayout *layout = new QGridLayout;
+ layout->addWidget(widthLabel, 0, 0);
+ layout->addWidget(widthBox, 0, 1);
+ layout->addWidget(heightLabel, 1, 0);
+ layout->addWidget(heightBox, 1, 1);
+ layout->addWidget(lockButton, 0, 2, 1, 2, Qt::AlignCenter);
+ setLayout(layout);
+
+ setWidth(curWidth);
+ setHeight(curHeight);
+}
+
+
+int ImageScaler::getMaxWidth() const
+{
+ return maxWidth;
+}
+
+int ImageScaler::getMaxHeight() const
+{
+ return maxHeight;
+}
+
+int ImageScaler::getWidth() const
+{
+ return widthBox->value();
+}
+
+int ImageScaler::getHeight() const
+{
+ return heightBox->value();
+}
+
+
+void ImageScaler::setMaxWidth(int newValue)
+{
+ maxWidth = newValue;
+ widthBox->setMaximum(maxWidth);
+ emit maxWidthChanged(maxWidth);
+}
+
+void ImageScaler::setMaxHeight(int newValue)
+{
+ maxHeight = newValue;
+ heightBox->setMaximum(maxHeight);
+ emit maxHeightChanged(maxHeight);
+}
+
+void ImageScaler::setLockAspectRatio(int state)
+{
+ if (state == Qt::Checked)
+ {
+ setLockAspectRatio(true);
+ }
+ else if (state == Qt::Unchecked)
+ {
+ setLockAspectRatio(false);
+ }
+}
+
+void ImageScaler::setLockAspectRatio(bool state)
+{
+ if (state == true)
+ {
+ lockAspectRatio = true;
+ aspectRatio = (float) curHeight / (float) curWidth;
+ }
+ else if (state == false)
+ {
+ lockAspectRatio = false;
+ }
+}
+
+void ImageScaler::setWidth(int newValue)
+{
+
+ if (curWidth == newValue)
+ {
+ return;
+ }
+
+ // Make sure newValue is within legal range.
+ if (newValue < minWidth || newValue > maxWidth)
+ {
+ return;
+ }
+
+ if (!lockAspectRatio)
+ {
+ curWidth = newValue;
+ emit widthChanged(newValue);
+ return;
+ }
+ else if (lockAspectRatio)
+ {
+
+ if (curHeight <= 0)
+ {
+ curWidth = newValue;
+ emit widthChanged(newValue);
+ return;
+ }
+
+ int newHeight = (int) rint((double) aspectRatio * (double) newValue);
+
+ if (newValue != curWidth)
+ {
+ curWidth = newValue;
+ emit widthChanged(newValue);
+ }
+ curHeight = newHeight;
+ emit heightChanged(newHeight);
+ }
+}
+
+void ImageScaler::setHeight(int newValue)
+{
+
+ if (curHeight == newValue)
+ {
+ return;
+ }
+
+ // Make sure newValue is within legal range.
+ if (newValue < minHeight || newValue > maxHeight)
+ {
+ return;
+ }
+
+ // Just change current height if not in locked
+ // aspect ratio mode.
+ if (!lockAspectRatio)
+ {
+ curHeight = newValue;
+ emit heightChanged(newValue);
+ return;
+ }
+ // Handle locked aspect ratio mode.
+ else if (lockAspectRatio)
+ {
+ if (curWidth <= 0)
+ {
+ curHeight = newValue;
+ emit heightChanged(newValue);
+ return;
+ }
+
+ int newWidth = (int) rint( (1.0 /(double) aspectRatio) * (double) newValue);
+
+ if (newValue != curHeight)
+ {
+ curHeight = newValue;
+ emit heightChanged(newValue);
+ }
+ curWidth = newWidth;
+ emit widthChanged(newWidth);
+ }
+}
+++ /dev/null
-#include <QAction>
-#include <QCheckBox>
-#include <QLabel>
-#include <QSpinBox>
-#include <QGridLayout>
-
-//#include <iostream>
-#include <cmath>
-
-#include "ImageScaler.h"
-
-ImageScaler::ImageScaler(QWidget *parent)
- : QWidget(parent)
-{
- lockAspectRatio = false;
- aspectRatio = 1.0;
- minWidth = 1;
- minHeight = 1;
- curWidth = 1;
- curHeight = 1;
-
- //lockAspectAction = new QAction(
- //lockAspectAction->setCheckable(true);
-
- lockButton = new QCheckBox();
- lockButton->setIcon(QIcon(tr("icons/lock.png")));
- lockButton->setToolTip(tr("Lock aspect ratio"));
- lockButton->setWhatsThis(tr("Lock aspect ratio"));
- connect(lockButton, SIGNAL(stateChanged(int)),
- this, SLOT(setLockAspectRatio(int)));
-
-
-
- widthBox = new QSpinBox();
- widthBox->setMinimum(minWidth);
- setMaxWidth(4048);
- connect(this, SIGNAL(widthChanged(int)),
- widthBox, SLOT(setValue(int)));
- connect(widthBox, SIGNAL(valueChanged(int)),
- this, SLOT(setWidth(int)));
-
- widthLabel = new QLabel(tr("Width:"));
- //widthLabel.setBuddy(widthBox);
-
- heightBox = new QSpinBox();
- heightBox->setMinimum(1);
- setMaxHeight(4048);
- connect(this, SIGNAL(heightChanged(int)),
- heightBox, SLOT(setValue(int)));
- connect(heightBox, SIGNAL(valueChanged(int)),
- this, SLOT(setHeight(int)));
-
- heightLabel = new QLabel(tr("Height:"));
- //heightLabel.setBuddy(heightBox);
-
- QGridLayout *layout = new QGridLayout;
- layout->addWidget(widthLabel, 0, 0);
- layout->addWidget(widthBox, 0, 1);
- layout->addWidget(heightLabel, 1, 0);
- layout->addWidget(heightBox, 1, 1);
- layout->addWidget(lockButton, 0, 2, 1, 2, Qt::AlignCenter);
- setLayout(layout);
-
- setWidth(curWidth);
- setHeight(curHeight);
-}
-
-
-int ImageScaler::getMaxWidth() const
-{
- return maxWidth;
-}
-
-int ImageScaler::getMaxHeight() const
-{
- return maxHeight;
-}
-
-int ImageScaler::getWidth() const
-{
- return widthBox->value();
-}
-
-int ImageScaler::getHeight() const
-{
- return heightBox->value();
-}
-
-
-void ImageScaler::setMaxWidth(int newValue)
-{
- maxWidth = newValue;
- widthBox->setMaximum(maxWidth);
- emit maxWidthChanged(maxWidth);
-}
-
-void ImageScaler::setMaxHeight(int newValue)
-{
- maxHeight = newValue;
- heightBox->setMaximum(maxHeight);
- emit maxHeightChanged(maxHeight);
-}
-
-void ImageScaler::setLockAspectRatio(int state)
-{
- if (state == Qt::Checked)
- {
- setLockAspectRatio(true);
- }
- else if (state == Qt::Unchecked)
- {
- setLockAspectRatio(false);
- }
-}
-
-void ImageScaler::setLockAspectRatio(bool state)
-{
- if (state == true)
- {
- lockAspectRatio = true;
- aspectRatio = (float) curHeight / (float) curWidth;
- }
- else if (state == false)
- {
- lockAspectRatio = false;
- }
-}
-
-void ImageScaler::setWidth(int newValue)
-{
-
- if (curWidth == newValue)
- {
- return;
- }
-
- // Make sure newValue is within legal range.
- if (newValue < minWidth || newValue > maxWidth)
- {
- return;
- }
-
- if (!lockAspectRatio)
- {
- curWidth = newValue;
- emit widthChanged(newValue);
- return;
- }
- else if (lockAspectRatio)
- {
-
- if (curHeight <= 0)
- {
- curWidth = newValue;
- emit widthChanged(newValue);
- return;
- }
-
- int newHeight = (int) rint((double) aspectRatio * (double) newValue);
-
- if (newValue != curWidth)
- {
- curWidth = newValue;
- emit widthChanged(newValue);
- }
- curHeight = newHeight;
- emit heightChanged(newHeight);
- }
-}
-
-void ImageScaler::setHeight(int newValue)
-{
-
- if (curHeight == newValue)
- {
- return;
- }
-
- // Make sure newValue is within legal range.
- if (newValue < minHeight || newValue > maxHeight)
- {
- return;
- }
-
- // Just change current height if not in locked
- // aspect ratio mode.
- if (!lockAspectRatio)
- {
- curHeight = newValue;
- emit heightChanged(newValue);
- return;
- }
- // Handle locked aspect ratio mode.
- else if (lockAspectRatio)
- {
- if (curWidth <= 0)
- {
- curHeight = newValue;
- emit heightChanged(newValue);
- return;
- }
-
- int newWidth = (int) rint( (1.0 /(double) aspectRatio) * (double) newValue);
-
- if (newValue != curHeight)
- {
- curHeight = newValue;
- emit heightChanged(newValue);
- }
- curWidth = newWidth;
- emit widthChanged(newWidth);
- }
-}
+++ /dev/null
-#ifndef _IMAGESCALER_H_
-#define _IMAGESCALER_H_
-
-#include <QWidget>
-
-class QSpinBox;
-class QLabel;
-class QAction;
-class QCheckBox;
-
-class ImageScaler : public QWidget
-{
- Q_OBJECT
-
-public:
- ImageScaler(QWidget *parent = 0);
-
- int getMaxHeight() const;
- int getMaxWidth() const;
- int getWidth() const;
- int getHeight() const;
-
-public slots:
- void setMaxWidth(int newValue);
- void setMaxHeight(int newValue);
-
- //! Locks apsect ratio with true/false.
- void setLockAspectRatio(bool state);
- //! Locks aspect ratio with parameter Qt::Checked or Qt::Unchecked.
- void setLockAspectRatio(int state);
-
-
- void setWidth(int newValue);
- void setHeight(int newValue);
-
-signals:
- void maxWidthChanged(int newWidth);
- void maxHeightChanged(int newHeight);
- void widthChanged(int newWidth);
- void heightChanged(int newHeight);
-
-private:
- QSpinBox *widthBox;
- QSpinBox *heightBox;
- QLabel *widthLabel;
- QLabel *heightLabel;
- QAction *lockAspectAction;
- QCheckBox *lockButton;
-
- bool lockAspectRatio;
- float aspectRatio;
- int maxWidth;
- int minWidth;
- int curWidth;
- int maxHeight;
- int minHeight;
- int curHeight;
-
-};
-
-#endif
--- /dev/null
+#ifndef _IMAGESCALER_H_
+#define _IMAGESCALER_H_
+
+#include <QWidget>
+
+class QSpinBox;
+class QLabel;
+class QAction;
+class QCheckBox;
+
+class ImageScaler : public QWidget
+{
+ Q_OBJECT
+
+public:
+ ImageScaler(QWidget *parent = 0);
+
+ int getMaxHeight() const;
+ int getMaxWidth() const;
+ int getWidth() const;
+ int getHeight() const;
+
+public slots:
+ void setMaxWidth(int newValue);
+ void setMaxHeight(int newValue);
+
+ //! Locks apsect ratio with true/false.
+ void setLockAspectRatio(bool state);
+ //! Locks aspect ratio with parameter Qt::Checked or Qt::Unchecked.
+ void setLockAspectRatio(int state);
+
+
+ void setWidth(int newValue);
+ void setHeight(int newValue);
+
+signals:
+ void maxWidthChanged(int newWidth);
+ void maxHeightChanged(int newHeight);
+ void widthChanged(int newWidth);
+ void heightChanged(int newHeight);
+
+private:
+ QSpinBox *widthBox;
+ QSpinBox *heightBox;
+ QLabel *widthLabel;
+ QLabel *heightLabel;
+ QAction *lockAspectAction;
+ QCheckBox *lockButton;
+
+ bool lockAspectRatio;
+ float aspectRatio;
+ int maxWidth;
+ int minWidth;
+ int curWidth;
+ int maxHeight;
+ int minHeight;
+ int curHeight;
+
+};
+
+#endif
--- /dev/null
+#include <QDir>
+#include <QFileDialog>
+#include <QMessageBox>
+#include <QMouseEvent>
+#include <QRubberBand>
+#include <QRect>
+#include <QString>
+#include <iostream>
+#include <set>
+
+#include <GL/gl.h>
+#include <math.h>
+
+#include "qui/PathScene.hpp"
+#include "alg/glsequence.hpp"
+#include "mussa_exceptions.hpp"
+
+using namespace std;
+
+PathScene::PathScene(Mussa* analysis, QWidget *parent) :
+ QGLWidget(parent),
+ viewport_height(0),
+ viewport_width(0),
+ clipZ(30.0),
+ zoom(2),
+ maxOrtho2d(-50.0, -50, 3000000.0, 300.0),
+ curOrtho2d(maxOrtho2d),
+ viewport_center(((curOrtho2d.right()-curOrtho2d.left())/2)+curOrtho2d.left()),
+ selectedMode(false),
+ rubberBand(0),
+ drawingBand(false)
+{
+ if (analysis == 0)
+ {
+ mussaAnalysis = new Mussa;
+ }
+ else
+ {
+ mussaAnalysis = analysis;
+ }
+ updateScene();
+}
+
+QSize PathScene::sizeHint() const
+{
+ return QSize(400, 400);
+}
+
+float PathScene::left()
+{
+ return maxOrtho2d.left();
+}
+
+float PathScene::right()
+{
+ return maxOrtho2d.right();
+}
+
+float PathScene::viewportLeft()
+{
+ return curOrtho2d.left();
+}
+
+float PathScene::viewportRight()
+{
+ return curOrtho2d.right();
+}
+
+float PathScene::viewportCenter()
+{
+ return viewport_center;
+}
+
+void PathScene::updateViewport(float center, int new_zoom)
+{
+ float max_width = maxOrtho2d.width();
+ if (new_zoom < 1) new_zoom = 1;
+ float new_max_width = max_width / new_zoom;
+ //curOrtho2d.setLeft(max(center-new_max_width, maxOrtho2d.left()));
+ //curOrtho2d.setRight(min(center+new_max_width, maxOrtho2d.right()));
+ curOrtho2d.setLeft(center-new_max_width);
+ curOrtho2d.setRight(center+new_max_width);
+ emit viewportChanged();
+}
+
+void PathScene::setViewportX(float x)
+{
+ //hopefully this calculates a sufficiently reasonable == for a float
+ if (x != viewport_center )
+ {
+ updateViewport(x, zoom);
+ viewport_center = x;
+ update();
+ }
+}
+
+void PathScene::setZoom(int new_zoom)
+{
+ if (zoom != new_zoom) {
+ // try to figure out where we should be now?
+ updateViewport(viewport_center, new_zoom);
+ zoom = new_zoom;
+ update();
+ }
+}
+
+void PathScene::setClipPlane(int newZ)
+{
+ if (clipZ != (double) newZ){
+ clipZ = (double) newZ;
+ update();
+ }
+}
+
+void PathScene::loadMupa()
+{
+ QString caption("Load a mussa parameter file");
+ QString filter("Mussa Parameters (*.mupa)");
+ QString mupa_path = QFileDialog::getOpenFileName(this,
+ caption,
+ QDir::currentPath(),
+ filter);
+ // user hit cancel?
+ if (mupa_path.isNull())
+ return;
+ // try to load safely
+ try {
+ Mussa *m = new Mussa;
+ m->load_mupa_file(mupa_path.toStdString());
+ m->analyze(0, 0, Mussa::TransitiveNway, 0.0);
+ // only switch mussas if we loaded without error
+ delete mussaAnalysis;
+ mussaAnalysis = m;
+ updateScene();
+ } catch (mussa_load_error e) {
+ QString msg("Unable to load ");
+ msg += mupa_path;
+ msg += "\n";
+ msg += e.what();
+ QMessageBox::warning(this, "Load Parameter", msg);
+ }
+ assert (mussaAnalysis != 0);
+}
+
+void PathScene::loadSavedAnalysis()
+{
+ QString caption("Load a previously run analysis");
+ QString muway_dir = QFileDialog::getExistingDirectory(this,
+ caption,
+ QDir::currentPath());
+ // user hit cancel?
+ if (muway_dir.isNull())
+ return;
+ // try to safely load
+ try {
+ Mussa *m = new Mussa;
+ m->load(muway_dir.toStdString());
+ // only switch mussas if we loaded without error
+ delete mussaAnalysis;
+ mussaAnalysis = m;
+ updateScene();
+ } catch (mussa_load_error e) {
+ QString msg("Unable to load ");
+ msg += muway_dir;
+ msg += "\n";
+ msg += e.what();
+ QMessageBox::warning(this, "Load Parameter", msg);
+ }
+ assert (mussaAnalysis != 0);
+}
+
+void PathScene::setSoftThreshold(int threshold)
+{
+ if (mussaAnalysis->get_threshold() != threshold) {
+ mussaAnalysis->set_soft_thres(threshold);
+ mussaAnalysis->nway();
+ update();
+ }
+}
+
+////////////////////
+// Rendering code
+void PathScene::initializeGL()
+{
+ glEnable(GL_DEPTH_TEST);
+ glClearColor(1.0, 1.0, 1.0, 0.0);
+ glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
+ glShadeModel(GL_FLAT);
+}
+
+void PathScene::resizeGL(int width, int height)
+{
+ viewport_width = width;
+ viewport_height = height;
+ assert (geometry().width() == width);
+ assert (geometry().height() == height);
+ glViewport(0, 0, (GLsizei)width, (GLsizei)height);
+ glMatrixMode(GL_PROJECTION);
+ glLoadIdentity();
+ // I'm abusing this as Qt and OpenGL disagree about the direction of the
+ // y axis
+ glOrtho(curOrtho2d.left(), curOrtho2d.right(),
+ curOrtho2d.top(), curOrtho2d.bottom(),
+ -50.0, clipZ);
+}
+
+void PathScene::paintGL()
+{
+ glClear(GL_COLOR_BUFFER_BIT|GL_DEPTH_BUFFER_BIT);
+
+ glPushMatrix();
+ glMatrixMode(GL_PROJECTION);
+ glLoadIdentity();
+ glOrtho(curOrtho2d.left(), curOrtho2d.right(),
+ curOrtho2d.top(), curOrtho2d.bottom(),
+ -50.0, clipZ);
+ glMatrixMode(GL_MODELVIEW);
+ mussaesque();
+ glEnable(GL_BLEND);
+ glDepthMask(GL_FALSE);
+ if (selectedMode && !drawingBand) {
+ glColor4f(0.6, 0.6, 0.6, 0.9);
+ glRectf(previousBand.x(), previousBand.y(),
+ previousBand.right(), previousBand.bottom());
+ }
+ glDepthMask(GL_TRUE);
+ glDisable(GL_BLEND);
+ glPopMatrix();
+ glFlush();
+}
+
+void PathScene::updateScene()
+{
+ // Delete old glsequences
+ // FIXME: does this actually free the memory from the new'ed GlSequences?
+ tracks.clear();
+
+ // save a reference to our GlSequences
+ GlSequence *gl_seq;
+ float y = mussaAnalysis->sequences().size() * 100 ;
+ float max_base_pairs = 0;
+ typedef vector<Sequence>::const_iterator seqs_itor_t;
+ for(seqs_itor_t seq_itor = mussaAnalysis->sequences().begin();
+ seq_itor != mussaAnalysis->sequences().end();
+ ++seq_itor)
+ {
+ y = y - 100;
+ gl_seq = new GlSequence(*seq_itor);
+ gl_seq->setX(0);
+ gl_seq->setY(y);
+ if (gl_seq->length() > max_base_pairs ) max_base_pairs = gl_seq->length();
+ tracks.push_back( *gl_seq );
+ }
+ maxOrtho2d.setWidth(max_base_pairs + 100.0);
+ maxOrtho2d.setHeight((mussaAnalysis->sequences().size()) * 100 );
+ curOrtho2d = maxOrtho2d;
+ viewport_center = (curOrtho2d.right()-curOrtho2d.left())/2+curOrtho2d.left();
+}
+
+void PathScene::processSelection(GLuint hits, GLuint buffer[], GLuint bufsize)
+{
+ const size_t pathz_count = mussaAnalysis->paths().refined_pathz.size();
+ GLuint *ptr;
+ GLuint names;
+ float z1;
+ float z2;
+ GLuint objtype;
+ GLuint objid;
+
+ selectedPaths.clear();
+ selectedPaths.reserve(pathz_count);
+ selectedPaths.insert(selectedPaths.begin(), pathz_count, false);
+ selectedTrack = 0x7fffffff;
+
+ std::cout << "hits = " << hits << " " << pathz_count << std::endl;
+ ptr = (GLuint *) buffer;
+ if (hits > 0)
+ selectedMode = true;
+ for (GLuint i=0; i < hits; ++i)
+ {
+ if ((i + 5) > bufsize) {
+ std::clog << "*** selection overflow***" << std::endl;
+ } else {
+ names = *ptr++;
+ z1 = ((float)*ptr++)/0x7fffffff;
+ z2 = ((float)*ptr++)/0x7fffffff;
+ objtype = *ptr++;
+ objid = *ptr++;
+ if (names != 2) {
+ std::clog << "wrong number of glNames, selection is having trouble ";
+ std::clog << " got " << names << std::endl;
+ std::clog << " names: " ;
+ for (GLuint j = 0 ; j < names-2; ++j) {
+ std::clog << *ptr++ << " ";
+ }
+ std::clog << endl;
+ return;
+ }
+ switch (objtype) {
+ case MussaPaths:
+ selectedPaths[objid] = true;
+ break;
+ case MussaTracks:
+ if (objid < selectedTrack) {
+ selectedTrack = objid;
+ }
+ break;
+ }
+ }
+ }
+}
+
+void PathScene::mousePressEvent( QMouseEvent *e)
+{
+ drawingBand = true;
+ std::cout << "x=" << e->x() << " y=" << e->y() << std::endl;
+
+ selectedMode = false;
+ bandOrigin = e->pos();
+ if (!rubberBand)
+ rubberBand = new QRubberBand(QRubberBand::Rectangle, this);
+
+ rubberBand->setGeometry(QRect(bandOrigin, QSize()));
+ rubberBand->show();
+}
+
+void PathScene::mouseMoveEvent( QMouseEvent *e)
+{
+ if (drawingBand)
+ rubberBand->setGeometry(QRect(bandOrigin, e->pos()).normalized());
+}
+
+void dumpRect(const QRect &r)
+{
+ std::cout << "x=" << r.x() << " y=" << r.y()
+ << " w=" << r.width() << " h=" << r.height() << std::endl;
+}
+
+void PathScene::mouseReleaseEvent( QMouseEvent *e)
+{
+ drawingBand = false;
+ rubberBand->hide();
+ QRect r = QRect(bandOrigin, e->pos()).normalized();
+ bandOrigin = r.topLeft();
+ std::cout << "band ";
+ dumpRect(r);
+
+ std::cout << "window ";
+ dumpRect(geometry());
+
+ GLfloat x_scale = curOrtho2d.width()/((float)geometry().width());
+ GLfloat y_scale = curOrtho2d.height()/((float)geometry().height());
+ GLfloat x_left = curOrtho2d.left() + (r.x()*x_scale);
+ GLfloat x_right = x_left + r.width() * x_scale;
+ // using QRectF with Y axis swapped
+ GLfloat y_top = curOrtho2d.bottom()-(r.y()*y_scale);
+ GLfloat y_bottom = y_top - r.height() * y_scale;
+ previousBand.setCoords(x_left, y_top, x_right, y_bottom);
+ std::cout << x_left << " " << x_right << " " << y_top << " " << y_bottom
+ << std::endl;
+
+ // hopefully this will make a buffer big enough to receive
+ // everything being selected
+ const size_t pathz_count = mussaAnalysis->paths().refined_pathz.size();
+ const GLuint select_buf_size = 1 + 5 * (pathz_count + tracks.size()) ;
+ GLuint selectBuf[select_buf_size];
+ glSelectBuffer(select_buf_size, selectBuf);
+ GLint hits;
+
+ (void)glRenderMode(GL_SELECT);
+ glPushMatrix();
+ glMatrixMode(GL_PROJECTION);
+ glLoadIdentity();
+ glOrtho(x_left, x_right, y_top, y_bottom, -50.0, 50.0);
+ glMatrixMode(GL_MODELVIEW);
+ glLoadIdentity();
+
+ mussaesque();
+ glFlush();
+
+ glPopMatrix();
+ hits = glRenderMode(GL_RENDER);
+ processSelection(hits, selectBuf, select_buf_size);
+
+ resizeGL(geometry().width(), geometry().height());
+}
+
+
+//////
+// openGl rendering code
+
+void PathScene::draw_tracks() const
+{
+ glPushMatrix();
+ glPushName(0);
+ for (vector<GlSequence>::size_type i = 0; i != tracks.size(); ++i )
+ {
+ glLoadName(i);
+ tracks[i].draw(curOrtho2d.left(), curOrtho2d.right());
+ }
+ glPopName();
+ glPopMatrix();
+}
+
+void PathScene::draw_lines() const
+{
+ GLfloat x;
+ GLfloat y;
+ GLuint pathid=0;
+ GLint objid=0;
+ bool reversed = false;
+ bool prevReversed = false;
+ const NwayPaths& nway = mussaAnalysis->paths();
+
+ glPushName(pathid);
+ glLineWidth(2);
+ vector<GlSequence>::const_iterator track_itor;
+
+ typedef list<ExtendedConservedPath> conserved_paths;
+ typedef conserved_paths::const_iterator const_conserved_paths_itor;
+ for(const_conserved_paths_itor path_itor = nway.refined_pathz.begin();
+ path_itor != nway.refined_pathz.end();
+ ++path_itor, ++objid)
+ {
+ track_itor = tracks.begin();
+ // since we were drawing to the start of a window, and opengl lines
+ // are centered around the two connecting points our lines were slightly
+ // offset. the idea of window_offset is to adjust them to the
+ // right for forward compliment or left for reverse compliment
+ // FIXME: figure out how to unit test these computations
+ GLfloat window_offset = (path_itor->window_size)/2.0;
+
+ glBegin(GL_LINE_STRIP);
+ for (vector<int>::const_iterator sp_itor = path_itor->begin();
+ sp_itor != path_itor->end();
+ ++sp_itor, ++track_itor)
+ {
+ x = *sp_itor;
+ y = track_itor->y();
+ // at some point when we modify the pathz data structure to keep
+ // track of the score we can put grab the depth here.
+ //
+ // are we reverse complimented?
+ if ( x>=0) {
+ reversed = false;
+ } else {
+ reversed = true;
+ x = -x; // make positive
+ }
+ if (!reversed)
+ x += window_offset; // move right for forward compliment
+ else
+ x -= window_offset; // move left for reverse compliment
+ // the following boolean implements logical xor
+ if ( (reversed || prevReversed) && (!reversed || !prevReversed)) {
+ // we have a different orientation
+ if (not selectedMode or selectedPaths[objid] == true) {
+ // if we have nothing selected, or we're the highlight, be bright
+ glColor3f(0.0, 0.0, 1.0);
+ } else {
+ // else be dim
+ glColor3f(0.7, 0.7, 1.0);
+ }
+ } else {
+ // both current and previous path have the same orientation
+ if (not selectedMode or selectedPaths[objid] == true) {
+ glColor3f(1.0, 0.0, 0.0);
+ } else {
+ glColor3f(1.0, 0.7, 0.7);
+ }
+ }
+ prevReversed = reversed;
+ glVertex3f(x, y, -1.0);
+ }
+ glEnd();
+ glLoadName(++pathid);
+ }
+ glPopName();
+}
+
+GLuint PathScene::make_line_list()
+{
+ GLuint line_list = glGenLists(1);
+ glNewList(line_list, GL_COMPILE);
+
+ draw_lines();
+
+ glEndList();
+ return line_list;
+
+}
+
+void PathScene::mussaesque()
+{
+ //static GLuint theLines = make_line_list();
+
+ glInitNames();
+ glPushName(MussaPaths);
+ //glCallList(theLines);
+ draw_lines();
+ glLoadName(MussaTracks);
+ draw_tracks();
+ glPopName();
+}
+
+++ /dev/null
-#include "PathScene.h"
-
-#include <QDir>
-#include <QFileDialog>
-#include <QMessageBox>
-#include <QMouseEvent>
-#include <QRubberBand>
-#include <QRect>
-#include <QString>
-#include <iostream>
-#include <set>
-
-#include <GL/gl.h>
-#include <math.h>
-
-#include "alg/glsequence.h"
-#include "mussa_exceptions.hh"
-
-using namespace std;
-
-PathScene::PathScene(Mussa* analysis, QWidget *parent) :
- QGLWidget(parent),
- viewport_height(0),
- viewport_width(0),
- clipZ(30.0),
- zoom(2),
- maxOrtho2d(-50.0, -50, 3000000.0, 300.0),
- curOrtho2d(maxOrtho2d),
- viewport_center(((curOrtho2d.right()-curOrtho2d.left())/2)+curOrtho2d.left()),
- selectedMode(false),
- rubberBand(0),
- drawingBand(false)
-{
- if (analysis == 0)
- {
- mussaAnalysis = new Mussa;
- }
- else
- {
- mussaAnalysis = analysis;
- }
- updateScene();
-}
-
-QSize PathScene::sizeHint() const
-{
- return QSize(400, 400);
-}
-
-float PathScene::left()
-{
- return maxOrtho2d.left();
-}
-
-float PathScene::right()
-{
- return maxOrtho2d.right();
-}
-
-float PathScene::viewportLeft()
-{
- return curOrtho2d.left();
-}
-
-float PathScene::viewportRight()
-{
- return curOrtho2d.right();
-}
-
-float PathScene::viewportCenter()
-{
- return viewport_center;
-}
-
-void PathScene::updateViewport(float center, int new_zoom)
-{
- float max_width = maxOrtho2d.width();
- if (new_zoom < 1) new_zoom = 1;
- float new_max_width = max_width / new_zoom;
- //curOrtho2d.setLeft(max(center-new_max_width, maxOrtho2d.left()));
- //curOrtho2d.setRight(min(center+new_max_width, maxOrtho2d.right()));
- curOrtho2d.setLeft(center-new_max_width);
- curOrtho2d.setRight(center+new_max_width);
- emit viewportChanged();
-}
-
-void PathScene::setViewportX(float x)
-{
- //hopefully this calculates a sufficiently reasonable == for a float
- if (x != viewport_center )
- {
- updateViewport(x, zoom);
- viewport_center = x;
- update();
- }
-}
-
-void PathScene::setZoom(int new_zoom)
-{
- if (zoom != new_zoom) {
- // try to figure out where we should be now?
- updateViewport(viewport_center, new_zoom);
- zoom = new_zoom;
- update();
- }
-}
-
-void PathScene::setClipPlane(int newZ)
-{
- if (clipZ != (double) newZ){
- clipZ = (double) newZ;
- update();
- }
-}
-
-void PathScene::loadMupa()
-{
- QString caption("Load a mussa parameter file");
- QString filter("Mussa Parameters (*.mupa)");
- QString mupa_path = QFileDialog::getOpenFileName(this,
- caption,
- QDir::currentPath(),
- filter);
- // user hit cancel?
- if (mupa_path.isNull())
- return;
- // try to load safely
- try {
- Mussa *m = new Mussa;
- m->load_mupa_file(mupa_path.toStdString());
- m->analyze(0, 0, Mussa::TransitiveNway, 0.0);
- // only switch mussas if we loaded without error
- delete mussaAnalysis;
- mussaAnalysis = m;
- updateScene();
- } catch (mussa_load_error e) {
- QString msg("Unable to load ");
- msg += mupa_path;
- msg += "\n";
- msg += e.what();
- QMessageBox::warning(this, "Load Parameter", msg);
- }
- assert (mussaAnalysis != 0);
-}
-
-void PathScene::loadSavedAnalysis()
-{
- QString caption("Load a previously run analysis");
- QString muway_dir = QFileDialog::getExistingDirectory(this,
- caption,
- QDir::currentPath());
- // user hit cancel?
- if (muway_dir.isNull())
- return;
- // try to safely load
- try {
- Mussa *m = new Mussa;
- m->load(muway_dir.toStdString());
- // only switch mussas if we loaded without error
- delete mussaAnalysis;
- mussaAnalysis = m;
- updateScene();
- } catch (mussa_load_error e) {
- QString msg("Unable to load ");
- msg += muway_dir;
- msg += "\n";
- msg += e.what();
- QMessageBox::warning(this, "Load Parameter", msg);
- }
- assert (mussaAnalysis != 0);
-}
-
-void PathScene::setSoftThreshold(int threshold)
-{
- if (mussaAnalysis->get_threshold() != threshold) {
- mussaAnalysis->set_soft_thres(threshold);
- mussaAnalysis->nway();
- update();
- }
-}
-
-////////////////////
-// Rendering code
-void PathScene::initializeGL()
-{
- glEnable(GL_DEPTH_TEST);
- glClearColor(1.0, 1.0, 1.0, 0.0);
- glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
- glShadeModel(GL_FLAT);
-}
-
-void PathScene::resizeGL(int width, int height)
-{
- viewport_width = width;
- viewport_height = height;
- assert (geometry().width() == width);
- assert (geometry().height() == height);
- glViewport(0, 0, (GLsizei)width, (GLsizei)height);
- glMatrixMode(GL_PROJECTION);
- glLoadIdentity();
- // I'm abusing this as Qt and OpenGL disagree about the direction of the
- // y axis
- glOrtho(curOrtho2d.left(), curOrtho2d.right(),
- curOrtho2d.top(), curOrtho2d.bottom(),
- -50.0, clipZ);
-}
-
-void PathScene::paintGL()
-{
- glClear(GL_COLOR_BUFFER_BIT|GL_DEPTH_BUFFER_BIT);
-
- glPushMatrix();
- glMatrixMode(GL_PROJECTION);
- glLoadIdentity();
- glOrtho(curOrtho2d.left(), curOrtho2d.right(),
- curOrtho2d.top(), curOrtho2d.bottom(),
- -50.0, clipZ);
- glMatrixMode(GL_MODELVIEW);
- mussaesque();
- glEnable(GL_BLEND);
- glDepthMask(GL_FALSE);
- if (selectedMode && !drawingBand) {
- glColor4f(0.6, 0.6, 0.6, 0.9);
- glRectf(previousBand.x(), previousBand.y(),
- previousBand.right(), previousBand.bottom());
- }
- glDepthMask(GL_TRUE);
- glDisable(GL_BLEND);
- glPopMatrix();
- glFlush();
-}
-
-void PathScene::updateScene()
-{
- // Delete old glsequences
- // FIXME: does this actually free the memory from the new'ed GlSequences?
- tracks.clear();
-
- // save a reference to our GlSequences
- GlSequence *gl_seq;
- float y = mussaAnalysis->sequences().size() * 100 ;
- float max_base_pairs = 0;
- typedef vector<Sequence>::const_iterator seqs_itor_t;
- for(seqs_itor_t seq_itor = mussaAnalysis->sequences().begin();
- seq_itor != mussaAnalysis->sequences().end();
- ++seq_itor)
- {
- y = y - 100;
- gl_seq = new GlSequence(*seq_itor);
- gl_seq->setX(0);
- gl_seq->setY(y);
- if (gl_seq->length() > max_base_pairs ) max_base_pairs = gl_seq->length();
- tracks.push_back( *gl_seq );
- }
- maxOrtho2d.setWidth(max_base_pairs + 100.0);
- maxOrtho2d.setHeight((mussaAnalysis->sequences().size()) * 100 );
- curOrtho2d = maxOrtho2d;
- viewport_center = (curOrtho2d.right()-curOrtho2d.left())/2+curOrtho2d.left();
-}
-
-void PathScene::processSelection(GLuint hits, GLuint buffer[], GLuint bufsize)
-{
- const size_t pathz_count = mussaAnalysis->paths().refined_pathz.size();
- GLuint *ptr;
- GLuint names;
- float z1;
- float z2;
- GLuint objtype;
- GLuint objid;
-
- selectedPaths.clear();
- selectedPaths.reserve(pathz_count);
- selectedPaths.insert(selectedPaths.begin(), pathz_count, false);
- selectedTrack = 0x7fffffff;
-
- std::cout << "hits = " << hits << " " << pathz_count << std::endl;
- ptr = (GLuint *) buffer;
- if (hits > 0)
- selectedMode = true;
- for (GLuint i=0; i < hits; ++i)
- {
- if ((i + 5) > bufsize) {
- std::clog << "*** selection overflow***" << std::endl;
- } else {
- names = *ptr++;
- z1 = ((float)*ptr++)/0x7fffffff;
- z2 = ((float)*ptr++)/0x7fffffff;
- objtype = *ptr++;
- objid = *ptr++;
- if (names != 2) {
- std::clog << "wrong number of glNames, selection is having trouble ";
- std::clog << " got " << names << std::endl;
- std::clog << " names: " ;
- for (GLuint j = 0 ; j < names-2; ++j) {
- std::clog << *ptr++ << " ";
- }
- std::clog << endl;
- return;
- }
- switch (objtype) {
- case MussaPaths:
- selectedPaths[objid] = true;
- break;
- case MussaTracks:
- if (objid < selectedTrack) {
- selectedTrack = objid;
- }
- break;
- }
- }
- }
-}
-
-void PathScene::mousePressEvent( QMouseEvent *e)
-{
- drawingBand = true;
- std::cout << "x=" << e->x() << " y=" << e->y() << std::endl;
-
- selectedMode = false;
- bandOrigin = e->pos();
- if (!rubberBand)
- rubberBand = new QRubberBand(QRubberBand::Rectangle, this);
-
- rubberBand->setGeometry(QRect(bandOrigin, QSize()));
- rubberBand->show();
-}
-
-void PathScene::mouseMoveEvent( QMouseEvent *e)
-{
- if (drawingBand)
- rubberBand->setGeometry(QRect(bandOrigin, e->pos()).normalized());
-}
-
-void dumpRect(const QRect &r)
-{
- std::cout << "x=" << r.x() << " y=" << r.y()
- << " w=" << r.width() << " h=" << r.height() << std::endl;
-}
-
-void PathScene::mouseReleaseEvent( QMouseEvent *e)
-{
- drawingBand = false;
- rubberBand->hide();
- QRect r = QRect(bandOrigin, e->pos()).normalized();
- bandOrigin = r.topLeft();
- std::cout << "band ";
- dumpRect(r);
-
- std::cout << "window ";
- dumpRect(geometry());
-
- GLfloat x_scale = curOrtho2d.width()/((float)geometry().width());
- GLfloat y_scale = curOrtho2d.height()/((float)geometry().height());
- GLfloat x_left = curOrtho2d.left() + (r.x()*x_scale);
- GLfloat x_right = x_left + r.width() * x_scale;
- // using QRectF with Y axis swapped
- GLfloat y_top = curOrtho2d.bottom()-(r.y()*y_scale);
- GLfloat y_bottom = y_top - r.height() * y_scale;
- previousBand.setCoords(x_left, y_top, x_right, y_bottom);
- std::cout << x_left << " " << x_right << " " << y_top << " " << y_bottom
- << std::endl;
-
- // hopefully this will make a buffer big enough to receive
- // everything being selected
- const size_t pathz_count = mussaAnalysis->paths().refined_pathz.size();
- const GLuint select_buf_size = 1 + 5 * (pathz_count + tracks.size()) ;
- GLuint selectBuf[select_buf_size];
- glSelectBuffer(select_buf_size, selectBuf);
- GLint hits;
-
- (void)glRenderMode(GL_SELECT);
- glPushMatrix();
- glMatrixMode(GL_PROJECTION);
- glLoadIdentity();
- glOrtho(x_left, x_right, y_top, y_bottom, -50.0, 50.0);
- glMatrixMode(GL_MODELVIEW);
- glLoadIdentity();
-
- mussaesque();
- glFlush();
-
- glPopMatrix();
- hits = glRenderMode(GL_RENDER);
- processSelection(hits, selectBuf, select_buf_size);
-
- resizeGL(geometry().width(), geometry().height());
-}
-
-
-//////
-// openGl rendering code
-
-void PathScene::draw_tracks() const
-{
- glPushMatrix();
- glPushName(0);
- for (vector<GlSequence>::size_type i = 0; i != tracks.size(); ++i )
- {
- glLoadName(i);
- tracks[i].draw(curOrtho2d.left(), curOrtho2d.right());
- }
- glPopName();
- glPopMatrix();
-}
-
-void PathScene::draw_lines() const
-{
- GLfloat x;
- GLfloat y;
- GLuint pathid=0;
- GLint objid=0;
- bool reversed = false;
- bool prevReversed = false;
- const NwayPaths& nway = mussaAnalysis->paths();
-
- glPushName(pathid);
- glLineWidth(2);
- vector<GlSequence>::const_iterator track_itor;
-
- typedef list<ExtendedConservedPath> conserved_paths;
- typedef conserved_paths::const_iterator const_conserved_paths_itor;
- for(const_conserved_paths_itor path_itor = nway.refined_pathz.begin();
- path_itor != nway.refined_pathz.end();
- ++path_itor, ++objid)
- {
- track_itor = tracks.begin();
- // since we were drawing to the start of a window, and opengl lines
- // are centered around the two connecting points our lines were slightly
- // offset. the idea of window_offset is to adjust them to the
- // right for forward compliment or left for reverse compliment
- // FIXME: figure out how to unit test these computations
- GLfloat window_offset = (path_itor->window_size)/2.0;
-
- glBegin(GL_LINE_STRIP);
- for (vector<int>::const_iterator sp_itor = path_itor->begin();
- sp_itor != path_itor->end();
- ++sp_itor, ++track_itor)
- {
- x = *sp_itor;
- y = track_itor->y();
- // at some point when we modify the pathz data structure to keep
- // track of the score we can put grab the depth here.
- //
- // are we reverse complimented?
- if ( x>=0) {
- reversed = false;
- } else {
- reversed = true;
- x = -x; // make positive
- }
- if (!reversed)
- x += window_offset; // move right for forward compliment
- else
- x -= window_offset; // move left for reverse compliment
- // the following boolean implements logical xor
- if ( (reversed || prevReversed) && (!reversed || !prevReversed)) {
- // we have a different orientation
- if (not selectedMode or selectedPaths[objid] == true) {
- // if we have nothing selected, or we're the highlight, be bright
- glColor3f(0.0, 0.0, 1.0);
- } else {
- // else be dim
- glColor3f(0.7, 0.7, 1.0);
- }
- } else {
- // both current and previous path have the same orientation
- if (not selectedMode or selectedPaths[objid] == true) {
- glColor3f(1.0, 0.0, 0.0);
- } else {
- glColor3f(1.0, 0.7, 0.7);
- }
- }
- prevReversed = reversed;
- glVertex3f(x, y, -1.0);
- }
- glEnd();
- glLoadName(++pathid);
- }
- glPopName();
-}
-
-GLuint PathScene::make_line_list()
-{
- GLuint line_list = glGenLists(1);
- glNewList(line_list, GL_COMPILE);
-
- draw_lines();
-
- glEndList();
- return line_list;
-
-}
-
-void PathScene::mussaesque()
-{
- //static GLuint theLines = make_line_list();
-
- glInitNames();
- glPushName(MussaPaths);
- //glCallList(theLines);
- draw_lines();
- glLoadName(MussaTracks);
- draw_tracks();
- glPopName();
-}
-
+++ /dev/null
-#ifndef _PATHSCENE_H_
-#define _PATHSCENE_H_
-
-#include <QGLWidget>
-#include <QRectF>
-#include <QPoint>
-#include <vector>
-
-#include "alg/mussa_class.hh"
-#include "alg/glsequence.h"
-#include "GL/gl.h"
-
-class QMouseEvent;
-class QRubberBand;
-
-/*! \brief Render mussa sequences and paths
- */
-class PathScene: public QGLWidget
-{
- Q_OBJECT
-
-public:
- PathScene(Mussa *analysis=0, QWidget *parent=0);
-
- QSize sizeHint() const;
-
- Mussa* mussaAnalysis;
- std::vector<GlSequence> tracks;
-
- float left();
- float right();
- float viewportLeft();
- float viewportRight();
- float viewportCenter();
-
-public slots:
- void setClipPlane(int z);
- //! set the center of the current viewport
- void setViewportX(float x);
- //! set our magnification level
- void setZoom(int);
- //! load a mussa parameter file (which specifies an analysis to run)
- void loadMupa( );
- //! load a previously run analysis
- void loadSavedAnalysis();
- //! set the soft threshold used by the Nway_Path algorithm
- void setSoftThreshold(int thres);
- //! indicate that we should update our scene
- void updateScene();
-
-signals:
- //! emitted when our analysis has changed
- void analysisUpdated();
- void viewportChanged();
-
-protected:
- int viewport_height;
- int viewport_width;
- double clipZ;
- int zoom;
- QRectF maxOrtho2d;
- QRectF curOrtho2d;
- //! where the "center" of the viewport is
- float viewport_center;
- //! true if we have a selection
- bool selectedMode;
- //! indicate which paths are selected
- std::vector<bool> selectedPaths;
- //! which track is selected (it only makes sense to have one track selected).
- unsigned int selectedTrack;
-
- void initializeGL();
- void resizeGL(int width, int height);
- void paintGL();
- // recompute our current viewport dimensions, used by setViewportX & setZoom
- void updateViewport(float left, int new_zoom);
-
- void mussaesque();
- //! draw all of our sequence tracks
- void draw_tracks() const;
- void draw_lines() const;
- GLuint make_line_list();
- //! convert opengl selections into the list of paths we should highlight
- void processSelection(GLuint hits, GLuint buffer[], GLuint bufsize);
- //! Provide a logical name for a type discriminator for our glName stack
- enum FeatureType { MussaTracks, MussaPaths };
-
- //! \defgroup Selection
- QRubberBand *rubberBand;
- QPoint bandOrigin;
- QRectF previousBand;
- bool drawingBand;
- void mousePressEvent(QMouseEvent *);
- void mouseMoveEvent(QMouseEvent *);
- void mouseReleaseEvent(QMouseEvent *);
-
-};
-#endif
--- /dev/null
+#ifndef _PATHSCENE_H_
+#define _PATHSCENE_H_
+
+#include <QGLWidget>
+#include <QRectF>
+#include <QPoint>
+#include <vector>
+#include <GL/gl.h>
+
+#include "alg/mussa.hpp"
+#include "alg/glsequence.hpp"
+
+class QMouseEvent;
+class QRubberBand;
+
+/*! \brief Render mussa sequences and paths
+ */
+class PathScene: public QGLWidget
+{
+ Q_OBJECT
+
+public:
+ PathScene(Mussa *analysis=0, QWidget *parent=0);
+
+ QSize sizeHint() const;
+
+ Mussa* mussaAnalysis;
+ std::vector<GlSequence> tracks;
+
+ float left();
+ float right();
+ float viewportLeft();
+ float viewportRight();
+ float viewportCenter();
+
+public slots:
+ void setClipPlane(int z);
+ //! set the center of the current viewport
+ void setViewportX(float x);
+ //! set our magnification level
+ void setZoom(int);
+ //! load a mussa parameter file (which specifies an analysis to run)
+ void loadMupa( );
+ //! load a previously run analysis
+ void loadSavedAnalysis();
+ //! set the soft threshold used by the Nway_Path algorithm
+ void setSoftThreshold(int thres);
+ //! indicate that we should update our scene
+ void updateScene();
+
+signals:
+ //! emitted when our analysis has changed
+ void analysisUpdated();
+ void viewportChanged();
+
+protected:
+ int viewport_height;
+ int viewport_width;
+ double clipZ;
+ int zoom;
+ QRectF maxOrtho2d;
+ QRectF curOrtho2d;
+ //! where the "center" of the viewport is
+ float viewport_center;
+ //! true if we have a selection
+ bool selectedMode;
+ //! indicate which paths are selected
+ std::vector<bool> selectedPaths;
+ //! which track is selected (it only makes sense to have one track selected).
+ unsigned int selectedTrack;
+
+ void initializeGL();
+ void resizeGL(int width, int height);
+ void paintGL();
+ // recompute our current viewport dimensions, used by setViewportX & setZoom
+ void updateViewport(float left, int new_zoom);
+
+ void mussaesque();
+ //! draw all of our sequence tracks
+ void draw_tracks() const;
+ void draw_lines() const;
+ GLuint make_line_list();
+ //! convert opengl selections into the list of paths we should highlight
+ void processSelection(GLuint hits, GLuint buffer[], GLuint bufsize);
+ //! Provide a logical name for a type discriminator for our glName stack
+ enum FeatureType { MussaTracks, MussaPaths };
+
+ //! \defgroup Selection
+ QRubberBand *rubberBand;
+ QPoint bandOrigin;
+ QRectF previousBand;
+ bool drawingBand;
+ void mousePressEvent(QMouseEvent *);
+ void mouseMoveEvent(QMouseEvent *);
+ void mouseReleaseEvent(QMouseEvent *);
+
+};
+#endif
--- /dev/null
+#include <iostream>
+
+#include <QVBoxLayout>
+#include <QWidget>
+
+#include "qui/PathScene.hpp"
+#include "qui/PathWidget.hpp"
+
+#include <math.h>
+using namespace std;
+
+// whats the maximum reasonable range for a scrollbar
+const float max_scrollbar_range = 100000;
+
+PathWidget::PathWidget(PathScene *scene, QWidget *parent) :
+ QWidget(parent),
+ scene(scene),
+ viewportBar(Qt::Horizontal)
+{
+ QVBoxLayout *layout = new QVBoxLayout;
+
+ layout->addWidget(scene);
+ layout->addWidget(&viewportBar);
+
+ connect(&viewportBar, SIGNAL(valueChanged(int)), this, SLOT(setViewportX(int)));
+ connect(scene, SIGNAL(viewportChanged()), this, SLOT(updateScrollBar()));
+ setLayout(layout);
+
+ // sets range & scale
+ updateScrollBar();
+}
+
+void PathWidget::updateScrollBar()
+{
+ float max_right = scene->right();
+ float max_left = scene->left();
+ float max_range = max_right - max_left;
+ float cur_left = scene->viewportLeft();
+ float cur_right = scene->viewportRight();
+ float cur_center = ((cur_right-cur_left)/2)+cur_left;
+ // set range to min
+ thumb = (int)cur_center;
+ viewportBar.setRange((int)max_left, (int)max_right);
+ viewportBar.setValue(thumb);
+}
+
+void PathWidget::setViewportX(int x)
+{
+ if (x != thumb) {
+ thumb = x;
+ scene->setViewportX(thumb);
+ }
+}
+++ /dev/null
-#include <iostream>
-
-#include <QVBoxLayout>
-#include <QWidget>
-
-#include "qui/PathScene.h"
-#include "qui/PathWidget.h"
-
-#include <math.h>
-using namespace std;
-
-// whats the maximum reasonable range for a scrollbar
-const float max_scrollbar_range = 100000;
-
-PathWidget::PathWidget(PathScene *scene, QWidget *parent) :
- QWidget(parent),
- scene(scene),
- viewportBar(Qt::Horizontal)
-{
- QVBoxLayout *layout = new QVBoxLayout;
-
- layout->addWidget(scene);
- layout->addWidget(&viewportBar);
-
- connect(&viewportBar, SIGNAL(valueChanged(int)), this, SLOT(setViewportX(int)));
- connect(scene, SIGNAL(viewportChanged()), this, SLOT(updateScrollBar()));
- setLayout(layout);
-
- // sets range & scale
- updateScrollBar();
-}
-
-void PathWidget::updateScrollBar()
-{
- float max_right = scene->right();
- float max_left = scene->left();
- float max_range = max_right - max_left;
- float cur_left = scene->viewportLeft();
- float cur_right = scene->viewportRight();
- float cur_center = ((cur_right-cur_left)/2)+cur_left;
- // set range to min
- thumb = (int)cur_center;
- viewportBar.setRange((int)max_left, (int)max_right);
- viewportBar.setValue(thumb);
-}
-
-void PathWidget::setViewportX(int x)
-{
- if (x != thumb) {
- thumb = x;
- scene->setViewportX(thumb);
- }
-}
+++ /dev/null
-#ifndef _PATH_WIDGET_H_
-#define _PATH_WIDGET_H_
-
-#include <QScrollBar>
-#include <QWidget>
-class PathScene;
-
-class PathWidget : public QWidget
-{
- Q_OBJECT
-
-public:
- PathWidget(PathScene *, QWidget *parent=0);
-
-public slots:
- //! update the scrollbar with current viewport information
- void updateScrollBar();
- //! update scene with the properly scalled scrollbar offset
- void setViewportX(int x);
-
-private:
- PathScene *scene;
- QScrollBar viewportBar;
- int thumb;
-
- float range;
- float scale;
-
-
-};
-
-#endif
--- /dev/null
+#ifndef _PATH_WIDGET_H_
+#define _PATH_WIDGET_H_
+
+#include <QScrollBar>
+#include <QWidget>
+class PathScene;
+
+class PathWidget : public QWidget
+{
+ Q_OBJECT
+
+public:
+ PathWidget(PathScene *, QWidget *parent=0);
+
+public slots:
+ //! update the scrollbar with current viewport information
+ void updateScrollBar();
+ //! update scene with the properly scalled scrollbar offset
+ void setViewportX(int x);
+
+private:
+ PathScene *scene;
+ QScrollBar viewportBar;
+ int thumb;
+
+ float range;
+ float scale;
+
+
+};
+
+#endif
--- /dev/null
+#include <QAction>
+#include <QDir>
+#include <QFileDialog>
+#include <QHBoxLayout>
+#include <QIcon>
+#include <QMenuBar>
+#include <QMessageBox>
+#include <QScrollBar>
+#include <QSpinBox>
+#include <QStatusBar>
+#include <QString>
+#include <QToolBar>
+#include <QWhatsThis>
+
+#include "qui/PathScene.hpp"
+#include "qui/PathWidget.hpp"
+#include "qui/PathWindow.hpp"
+#include "qui/ThresholdWidget.hpp"
+#include "qui/ImageSaveDialog.hpp"
+
+#include <iostream>
+
+PathWindow::PathWindow(Mussa *analysis, QWidget *) :
+ closeAction(0) // initialize one of the pointers to null as a saftey flag
+{
+ scene = new PathScene(analysis, this);
+
+ setupActions();
+ setupMainMenu();
+
+ //This next setWhatsThis function prevents
+ // a segfault when using WhatsThis feature with
+ // opengl widget.
+ scene->setWhatsThis(tr("Mussa in OpenGL!"));
+ // make a widget so we can have a scroll bar
+ PathWidget *path_widget = new PathWidget(scene, this);
+ setCentralWidget(path_widget);
+
+ mussaViewTB = new QToolBar("Path Views");
+ mussaViewTB->addAction(toggleMotifsAction);
+
+ QSpinBox *zoom = new QSpinBox();
+ zoom->setWhatsThis("zoom magnification factor");
+ zoom->setRange(2,1000);
+ mussaViewTB->addWidget(zoom);
+ connect(zoom, SIGNAL(valueChanged(int)), scene, SLOT(setZoom(int)));
+
+ ThresholdWidget *threshold = new ThresholdWidget;
+ threshold->setRange(19, 30);
+ threshold->setThreshold(19);
+ scene->setClipPlane(20);
+ // FIXME: for when we get the paths drawn at the appropriate depth
+ //connect(threshold, SIGNAL(thresholdChanged(int)),
+ // scene, SLOT(setClipPlane(int)));
+ connect(threshold, SIGNAL(thresholdChanged(int)),
+ scene, SLOT(setSoftThreshold(int)));
+ mussaViewTB->addWidget(threshold);
+
+ //Image Save Dialog
+ imageSaveDialog = new ImageSaveDialog(scene, this);
+
+ addToolBar(mussaViewTB);
+
+ statusBar()->showMessage("Welcome to mussa", 2000);
+}
+
+void PathWindow::setupActions()
+{
+ // we really don't want to run this more than once.
+ assert (closeAction == 0);
+
+ // the ever popular about box
+ aboutAction = new QAction(tr("&About"), this);
+ connect(aboutAction, SIGNAL(triggered()), this, SLOT(about()));
+ aboutAction->setIcon(QIcon("icons/info.png"));
+
+ // add exit
+ closeAction = new QAction(tr("&Close"), this);
+ closeAction->setStatusTip(tr("Close this window"));
+ connect(closeAction, SIGNAL(triggered()), this, SLOT(close()));
+ closeAction->setIcon(QIcon("icons/exit.png"));
+
+ createNewAnalysisAction = new QAction(tr("Define Analysis"), this);
+ connect(createNewAnalysisAction, SIGNAL(triggered()),
+ this, SLOT(createNewAnalysis()));
+ createNewAnalysisAction->setIcon(QIcon("icons/filenew.png"));
+
+ createSubAnalysisAction = new QAction(tr("Define SubAnalysis"), this);
+ connect(createSubAnalysisAction, SIGNAL(triggered()),
+ this, SLOT(createSubAnalysis()));
+
+ loadMotifListAction = new QAction(tr("Load Motif List"), this);
+ connect(loadMotifListAction, SIGNAL(triggered()),
+ this, SLOT(loadMotifList()));
+
+ loadMupaAction = new QAction(tr("Load Mussa Parameters"), this);
+ connect(loadMupaAction, SIGNAL(triggered()),
+ scene, SLOT(loadMupa()));
+
+ loadSavedAnalysisAction = new QAction(tr("Load &Analysis"), this);
+ connect(loadSavedAnalysisAction, SIGNAL(triggered()),
+ scene, SLOT(loadSavedAnalysis()));
+ loadSavedAnalysisAction->setIcon(QIcon("icons/fileopen.png"));
+
+ saveMotifListAction = new QAction(tr("Save Motifs"), this);
+ connect(saveMotifListAction, SIGNAL(triggered()),
+ this, SLOT(saveMotifList()));
+ saveMotifListAction->setIcon(QIcon("icons/filesave.png"));
+
+ showMussaViewToolbarAction = new QAction(tr("Show Toolbar"), this);
+ connect(showMussaViewToolbarAction, SIGNAL(triggered()),
+ this, SLOT(showMussaToolbar()));
+ showMussaViewToolbarAction->setCheckable(true);
+ showMussaViewToolbarAction->setChecked(true);
+
+ toggleMotifsAction = new QAction(tr("Toggle Motifs"), this);
+ connect(toggleMotifsAction, SIGNAL(triggered()),
+ this, SLOT(toggleMotifs()));
+ toggleMotifsAction->setCheckable(true);
+ toggleMotifsAction->setIcon(QIcon("icons/motif_icon.png"));
+ toggleMotifsAction->setWhatsThis(tr("Toggle motif annotations on/off\n\n"
+ "You can load motif annotations via "
+ "'File->Load Motif List' menu option."));
+
+ whatsThisAction = QWhatsThis::createAction(this);
+ whatsThisAction->setIcon(QIcon("icons/help.png"));
+
+ //Save pixel map action
+ saveOpenGlPixmapAction = new QAction(tr("Save to image..."), this);
+ connect(saveOpenGlPixmapAction, (SIGNAL(triggered())),
+ this, SLOT(promptSaveOpenGlPixmap()));
+ saveOpenGlPixmapAction->setIcon(QIcon("icons/image2.png"));
+}
+
+void PathWindow::setupMainMenu()
+{
+ // we need to run setupActions first
+ assert (closeAction != 0);
+
+ QMenu *newMenu;
+ newMenu = menuBar()->addMenu(tr("&File"));
+ newMenu->addAction(createNewAnalysisAction);
+ newMenu->addAction(loadMupaAction);
+ newMenu->addAction(loadSavedAnalysisAction);
+ newMenu->addAction(createSubAnalysisAction);
+ newMenu->addSeparator();
+ newMenu->addAction(loadMotifListAction);
+ newMenu->addAction(saveMotifListAction);
+ newMenu->addSeparator();
+ newMenu->addAction(saveOpenGlPixmapAction);
+ newMenu->addSeparator();
+ newMenu->addAction(closeAction);
+
+ newMenu = menuBar()->addMenu(tr("&View"));
+ newMenu->addAction(showMussaViewToolbarAction);
+
+ newMenu = menuBar()->addMenu(tr("&Help"));
+ newMenu->addAction(whatsThisAction);
+ newMenu->addSeparator();
+ newMenu->addAction(aboutAction);
+}
+
+void PathWindow::about()
+{
+ QMessageBox::about(this, tr("About mussa"),
+ tr("Welcome to Multiple Species Sequence Analysis\n"
+ "(c) 2005-2006 California Institute of Technology\n"
+ "Tristan De Buysscher, Diane Trout\n"));
+}
+
+void PathWindow::createNewAnalysis()
+{
+ NotImplementedBox();
+}
+
+void PathWindow::createSubAnalysis()
+{
+ NotImplementedBox();
+}
+
+void PathWindow::loadMotifList()
+{
+ NotImplementedBox();
+}
+
+void PathWindow::saveMotifList()
+{
+ NotImplementedBox();
+}
+
+void PathWindow::showMussaToolbar()
+{
+ std::clog << "isVis?" << mussaViewTB->isVisible() <<std::endl;
+ if (mussaViewTB->isVisible())
+ mussaViewTB->hide();
+ else
+ mussaViewTB->show();
+ std::clog << "isVis?" << mussaViewTB->isVisible() <<std::endl;
+}
+
+void PathWindow::toggleMotifs()
+{
+ NotImplementedBox();
+}
+
+void PathWindow::NotImplementedBox()
+{
+ QMessageBox::warning(this, QObject::tr("mussa"), QObject::tr("Not implemented yet"));
+}
+
+void PathWindow::promptSaveOpenGlPixmap()
+{
+ QSize size;
+ size = scene->size();
+ imageSaveDialog->setSize(size.width(), size.height());
+ int result = imageSaveDialog->exec();
+ std::cout << "Result: " << result << "\n";
+}
+
+++ /dev/null
-#include <QAction>
-#include <QDir>
-#include <QFileDialog>
-#include <QHBoxLayout>
-#include <QIcon>
-#include <QMenuBar>
-#include <QMessageBox>
-#include <QScrollBar>
-#include <QSpinBox>
-#include <QStatusBar>
-#include <QString>
-#include <QToolBar>
-#include <QWhatsThis>
-
-#include "qui/PathScene.h"
-#include "qui/PathWidget.h"
-#include "qui/PathWindow.h"
-#include "qui/ThresholdWidget.h"
-#include "qui/ImageSaveDialog.h"
-
-#include <iostream>
-
-PathWindow::PathWindow(Mussa *analysis, QWidget *) :
- closeAction(0) // initialize one of the pointers to null as a saftey flag
-{
- scene = new PathScene(analysis, this);
-
- setupActions();
- setupMainMenu();
-
- //This next setWhatsThis function prevents
- // a segfault when using WhatsThis feature with
- // opengl widget.
- scene->setWhatsThis(tr("Mussa in OpenGL!"));
- // make a widget so we can have a scroll bar
- PathWidget *path_widget = new PathWidget(scene, this);
- setCentralWidget(path_widget);
-
- mussaViewTB = new QToolBar("Path Views");
- mussaViewTB->addAction(toggleMotifsAction);
-
- QSpinBox *zoom = new QSpinBox();
- zoom->setWhatsThis("zoom magnification factor");
- zoom->setRange(2,1000);
- mussaViewTB->addWidget(zoom);
- connect(zoom, SIGNAL(valueChanged(int)), scene, SLOT(setZoom(int)));
-
- ThresholdWidget *threshold = new ThresholdWidget;
- threshold->setRange(19, 30);
- threshold->setThreshold(19);
- scene->setClipPlane(20);
- // FIXME: for when we get the paths drawn at the appropriate depth
- //connect(threshold, SIGNAL(thresholdChanged(int)),
- // scene, SLOT(setClipPlane(int)));
- connect(threshold, SIGNAL(thresholdChanged(int)),
- scene, SLOT(setSoftThreshold(int)));
- mussaViewTB->addWidget(threshold);
-
- //Image Save Dialog
- imageSaveDialog = new ImageSaveDialog(scene, this);
-
- addToolBar(mussaViewTB);
-
- statusBar()->showMessage("Welcome to mussa", 2000);
-}
-
-void PathWindow::setupActions()
-{
- // we really don't want to run this more than once.
- assert (closeAction == 0);
-
- // the ever popular about box
- aboutAction = new QAction(tr("&About"), this);
- connect(aboutAction, SIGNAL(triggered()), this, SLOT(about()));
- aboutAction->setIcon(QIcon("icons/info.png"));
-
- // add exit
- closeAction = new QAction(tr("&Close"), this);
- closeAction->setStatusTip(tr("Close this window"));
- connect(closeAction, SIGNAL(triggered()), this, SLOT(close()));
- closeAction->setIcon(QIcon("icons/exit.png"));
-
- createNewAnalysisAction = new QAction(tr("Define Analysis"), this);
- connect(createNewAnalysisAction, SIGNAL(triggered()),
- this, SLOT(createNewAnalysis()));
- createNewAnalysisAction->setIcon(QIcon("icons/filenew.png"));
-
- createSubAnalysisAction = new QAction(tr("Define SubAnalysis"), this);
- connect(createSubAnalysisAction, SIGNAL(triggered()),
- this, SLOT(createSubAnalysis()));
-
- loadMotifListAction = new QAction(tr("Load Motif List"), this);
- connect(loadMotifListAction, SIGNAL(triggered()),
- this, SLOT(loadMotifList()));
-
- loadMupaAction = new QAction(tr("Load Mussa Parameters"), this);
- connect(loadMupaAction, SIGNAL(triggered()),
- scene, SLOT(loadMupa()));
-
- loadSavedAnalysisAction = new QAction(tr("Load &Analysis"), this);
- connect(loadSavedAnalysisAction, SIGNAL(triggered()),
- scene, SLOT(loadSavedAnalysis()));
- loadSavedAnalysisAction->setIcon(QIcon("icons/fileopen.png"));
-
- saveMotifListAction = new QAction(tr("Save Motifs"), this);
- connect(saveMotifListAction, SIGNAL(triggered()),
- this, SLOT(saveMotifList()));
- saveMotifListAction->setIcon(QIcon("icons/filesave.png"));
-
- showMussaViewToolbarAction = new QAction(tr("Show Toolbar"), this);
- connect(showMussaViewToolbarAction, SIGNAL(triggered()),
- this, SLOT(showMussaToolbar()));
- showMussaViewToolbarAction->setCheckable(true);
- showMussaViewToolbarAction->setChecked(true);
-
- toggleMotifsAction = new QAction(tr("Toggle Motifs"), this);
- connect(toggleMotifsAction, SIGNAL(triggered()),
- this, SLOT(toggleMotifs()));
- toggleMotifsAction->setCheckable(true);
- toggleMotifsAction->setIcon(QIcon("icons/motif_icon.png"));
- toggleMotifsAction->setWhatsThis(tr("Toggle motif annotations on/off\n\n"
- "You can load motif annotations via "
- "'File->Load Motif List' menu option."));
-
- whatsThisAction = QWhatsThis::createAction(this);
- whatsThisAction->setIcon(QIcon("icons/help.png"));
-
- //Save pixel map action
- saveOpenGlPixmapAction = new QAction(tr("Save to image..."), this);
- connect(saveOpenGlPixmapAction, (SIGNAL(triggered())),
- this, SLOT(promptSaveOpenGlPixmap()));
- saveOpenGlPixmapAction->setIcon(QIcon("icons/image2.png"));
-}
-
-void PathWindow::setupMainMenu()
-{
- // we need to run setupActions first
- assert (closeAction != 0);
-
- QMenu *newMenu;
- newMenu = menuBar()->addMenu(tr("&File"));
- newMenu->addAction(createNewAnalysisAction);
- newMenu->addAction(loadMupaAction);
- newMenu->addAction(loadSavedAnalysisAction);
- newMenu->addAction(createSubAnalysisAction);
- newMenu->addSeparator();
- newMenu->addAction(loadMotifListAction);
- newMenu->addAction(saveMotifListAction);
- newMenu->addSeparator();
- newMenu->addAction(saveOpenGlPixmapAction);
- newMenu->addSeparator();
- newMenu->addAction(closeAction);
-
- newMenu = menuBar()->addMenu(tr("&View"));
- newMenu->addAction(showMussaViewToolbarAction);
-
- newMenu = menuBar()->addMenu(tr("&Help"));
- newMenu->addAction(whatsThisAction);
- newMenu->addSeparator();
- newMenu->addAction(aboutAction);
-}
-
-void PathWindow::about()
-{
- QMessageBox::about(this, tr("About mussa"),
- tr("Welcome to Multiple Species Sequence Analysis\n"
- "(c) 2005-2006 California Institute of Technology\n"
- "Tristan De Buysscher, Diane Trout\n"));
-}
-
-void PathWindow::createNewAnalysis()
-{
- NotImplementedBox();
-}
-
-void PathWindow::createSubAnalysis()
-{
- NotImplementedBox();
-}
-
-void PathWindow::loadMotifList()
-{
- NotImplementedBox();
-}
-
-void PathWindow::saveMotifList()
-{
- NotImplementedBox();
-}
-
-void PathWindow::showMussaToolbar()
-{
- std::clog << "isVis?" << mussaViewTB->isVisible() <<std::endl;
- if (mussaViewTB->isVisible())
- mussaViewTB->hide();
- else
- mussaViewTB->show();
- std::clog << "isVis?" << mussaViewTB->isVisible() <<std::endl;
-}
-
-void PathWindow::toggleMotifs()
-{
- NotImplementedBox();
-}
-
-void PathWindow::NotImplementedBox()
-{
- QMessageBox::warning(this, QObject::tr("mussa"), QObject::tr("Not implemented yet"));
-}
-
-void PathWindow::promptSaveOpenGlPixmap()
-{
- QSize size;
- size = scene->size();
- imageSaveDialog->setSize(size.width(), size.height());
- int result = imageSaveDialog->exec();
- std::cout << "Result: " << result << "\n";
-}
-
+++ /dev/null
-#ifndef _PATHWINDOW_H_
-#define _PATHWINDOW_H_
-
-#include <QMainWindow>
-#include <QPixmap>
-class QAction;
-class PathScene;
-class ImageSaveDialog;
-class Mussa;
-
-class PathWindow : public QMainWindow
-{
- Q_OBJECT
-
-public:
- PathWindow(Mussa* analysis=0, QWidget *parent=0);
-
-public slots:
- //! display an about box, contemplating the politics of the author list
- void about();
-
- //! \defgroup AnalysisFunctions Components related to running analyses
- //\@{
- //! open a window to collect the information needed to create a new analysis
- void createNewAnalysis();
- //! launch a sub analysis
- void createSubAnalysis();
- //\@}
-
- //! \defgroup MotifHandling Handling of motif lists
- //\@{
- void loadMotifList();
- void saveMotifList();
- void toggleMotifs();
- //\@}
-
- void showMussaToolbar();
-
- void promptSaveOpenGlPixmap();
-
-protected:
- // display our wonderful mussa output
- PathScene *scene;
- QToolBar *mussaViewTB;
- ImageSaveDialog *imageSaveDialog;
-
- QAction *aboutAction;
- QAction *closeAction;
- QAction *createNewAnalysisAction;
- QAction *createSubAnalysisAction;
- QAction *loadMotifListAction;
- QAction *loadMupaAction;
- QAction *loadSavedAnalysisAction;
- QAction *saveMotifListAction;
- QAction *showMussaViewToolbarAction;
- QAction *toggleMotifsAction;
- QAction *whatsThisAction;
- QAction *saveOpenGlPixmapAction;
-
- //! initialze the actions
- void setupActions();
- //! initialize this windows menu object
- void setupMainMenu();
- //! stub function to fill in QActions
- void NotImplementedBox();
-};
-
-#endif
--- /dev/null
+#ifndef _PATHWINDOW_H_
+#define _PATHWINDOW_H_
+
+#include <QMainWindow>
+#include <QPixmap>
+class QAction;
+class PathScene;
+class ImageSaveDialog;
+class Mussa;
+
+class PathWindow : public QMainWindow
+{
+ Q_OBJECT
+
+public:
+ PathWindow(Mussa* analysis=0, QWidget *parent=0);
+
+public slots:
+ //! display an about box, contemplating the politics of the author list
+ void about();
+
+ //! \defgroup AnalysisFunctions Components related to running analyses
+ //\@{
+ //! open a window to collect the information needed to create a new analysis
+ void createNewAnalysis();
+ //! launch a sub analysis
+ void createSubAnalysis();
+ //\@}
+
+ //! \defgroup MotifHandling Handling of motif lists
+ //\@{
+ void loadMotifList();
+ void saveMotifList();
+ void toggleMotifs();
+ //\@}
+
+ void showMussaToolbar();
+
+ void promptSaveOpenGlPixmap();
+
+protected:
+ // display our wonderful mussa output
+ PathScene *scene;
+ QToolBar *mussaViewTB;
+ ImageSaveDialog *imageSaveDialog;
+
+ QAction *aboutAction;
+ QAction *closeAction;
+ QAction *createNewAnalysisAction;
+ QAction *createSubAnalysisAction;
+ QAction *loadMotifListAction;
+ QAction *loadMupaAction;
+ QAction *loadSavedAnalysisAction;
+ QAction *saveMotifListAction;
+ QAction *showMussaViewToolbarAction;
+ QAction *toggleMotifsAction;
+ QAction *whatsThisAction;
+ QAction *saveOpenGlPixmapAction;
+
+ //! initialze the actions
+ void setupActions();
+ //! initialize this windows menu object
+ void setupMainMenu();
+ //! stub function to fill in QActions
+ void NotImplementedBox();
+};
+
+#endif
--- /dev/null
+#include <QHBoxLayout>
+#include <QLCDNumber>
+#include <QSlider>
+
+#include "qui/ThresholdWidget.hpp"
+
+// This is completely and totally derived from the Qt example
+// LCDRange.cpp
+ThresholdWidget::ThresholdWidget(QWidget *parent, int min, int max)
+ : QWidget(parent)
+{
+ QLCDNumber *lcd = new QLCDNumber(threshold_max_display_digits);
+ lcd->setSegmentStyle(QLCDNumber::Flat);
+
+ slider = new QSlider(Qt::Horizontal);
+ slider->setRange(min, max);
+
+ connect(slider, SIGNAL(valueChanged(int)), lcd, SLOT(display(int)));
+ connect(slider, SIGNAL(valueChanged(int)),
+ this, SIGNAL(thresholdChanged(int)));
+
+ slider->setValue(min);
+ lcd->display(min);
+
+ QHBoxLayout *layout = new QHBoxLayout;
+ layout->addWidget(slider);
+ layout->addWidget(lcd);
+ setLayout(layout);
+}
+/*
+void ThresholdWidget::setMinimumThreshold(int min)
+{
+ slider->setMinimum(min);
+}
+
+int ThresholdWidget::getMinimumThreshold()
+{
+ return slider->minimum();
+}
+
+void ThresholdWidget::setMaximumThreshold(int max)
+{
+ slider->setMaximum(max);
+}
+
+int ThresholdWidget::getMaximumThreshold()
+{
+ return slider->maximum();
+}
+*/
+void ThresholdWidget::setRange(int min, int max)
+{
+ slider->setRange(min, max);
+}
+
+float ThresholdWidget::percent() const
+{
+ return ((float)threshold())/((float)slider->maximum());
+}
+
+void ThresholdWidget::setThreshold(int threshold)
+{
+ if (slider->value() != threshold)
+ {
+ slider->setValue(threshold);
+ emit thresholdChanged(threshold);
+ }
+}
+
+int ThresholdWidget::threshold() const
+{
+ return slider->value();
+}
+
+
+++ /dev/null
-#include "qui/ThresholdWidget.h"
-
-#include <QHBoxLayout>
-#include <QLCDNumber>
-#include <QSlider>
-
-// This is completely and totally derived from the Qt example
-// LCDRange.cpp
-ThresholdWidget::ThresholdWidget(QWidget *parent, int min, int max)
- : QWidget(parent)
-{
- QLCDNumber *lcd = new QLCDNumber(threshold_max_display_digits);
- lcd->setSegmentStyle(QLCDNumber::Flat);
-
- slider = new QSlider(Qt::Horizontal);
- slider->setRange(min, max);
-
- connect(slider, SIGNAL(valueChanged(int)), lcd, SLOT(display(int)));
- connect(slider, SIGNAL(valueChanged(int)),
- this, SIGNAL(thresholdChanged(int)));
-
- slider->setValue(min);
- lcd->display(min);
-
- QHBoxLayout *layout = new QHBoxLayout;
- layout->addWidget(slider);
- layout->addWidget(lcd);
- setLayout(layout);
-}
-/*
-void ThresholdWidget::setMinimumThreshold(int min)
-{
- slider->setMinimum(min);
-}
-
-int ThresholdWidget::getMinimumThreshold()
-{
- return slider->minimum();
-}
-
-void ThresholdWidget::setMaximumThreshold(int max)
-{
- slider->setMaximum(max);
-}
-
-int ThresholdWidget::getMaximumThreshold()
-{
- return slider->maximum();
-}
-*/
-void ThresholdWidget::setRange(int min, int max)
-{
- slider->setRange(min, max);
-}
-
-float ThresholdWidget::percent() const
-{
- return ((float)threshold())/((float)slider->maximum());
-}
-
-void ThresholdWidget::setThreshold(int threshold)
-{
- if (slider->value() != threshold)
- {
- slider->setValue(threshold);
- emit thresholdChanged(threshold);
- }
-}
-
-int ThresholdWidget::threshold() const
-{
- return slider->value();
-}
-
-
+++ /dev/null
-#ifndef _THRESHOLD_WIDGET_H_
-#define _THRESHOLD_WIDGET_H_
-
-#include <QWidget>
-
-class QSlider;
-
-class ThresholdWidget : public QWidget
-{
- Q_OBJECT
-
-public:
- ThresholdWidget(QWidget *parent = 0, int min=21, int max=30);
-
- //! return what percent of our maximum threshold we are.
- float percent() const;
- //! return our current threshold
- int threshold() const;
-
-public slots:
- void setThreshold(int threshold);
- void setRange(int min, int max);
-
-signals:
- void thresholdChanged(int new_threshold);
-
-protected:
- QSlider *slider;
-
-};
-const int threshold_max_display_digits = 2;
-
-#endif
--- /dev/null
+#ifndef _THRESHOLD_WIDGET_H_
+#define _THRESHOLD_WIDGET_H_
+
+#include <QWidget>
+
+class QSlider;
+
+class ThresholdWidget : public QWidget
+{
+ Q_OBJECT
+
+public:
+ ThresholdWidget(QWidget *parent = 0, int min=21, int max=30);
+
+ //! return what percent of our maximum threshold we are.
+ float percent() const;
+ //! return our current threshold
+ int threshold() const;
+
+public slots:
+ void setThreshold(int threshold);
+ void setRange(int min, int max);
+
+signals:
+ void thresholdChanged(int new_threshold);
+
+protected:
+ QSlider *slider;
+
+};
+const int threshold_max_display_digits = 2;
+
+#endif
--- /dev/null
+// This file is part of the Mussa source distribution.
+// http://mussa.caltech.edu/
+// Contact author: Tristan De Buysscher, tristan@caltech.edu
+
+// This program and all associated source code files are Copyright (C) 2005
+// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
+// under the GNU Public License; please see the included LICENSE.txt
+// file for more information, or contact Tristan directly.
+
+
+#include "flp.hh"
+#include "sequence.hh"
+#include <time.h>
+#include <iomanip>
+
+using namespace std;
+
+int main(int argc, char **argv)
+{
+ Sequence seqA, seqB;
+ FLPs analysis;
+ string seqA_file, seqB_file, output_file;
+ string ana_type;
+ int window, threshold;
+ int seqA_len, seqB_len;
+
+ time_t t1, t2, begin, end;
+ double setuptime, comp1time, comp2time, sorttime, savetime, totaltime;
+
+ begin = time(NULL);
+
+ cout << "fee fie foe fum" << endl;
+
+ ana_type = * ++argv;
+ seqA_file = * ++argv;
+ seqB_file = * ++argv;
+ window = atoi(* ++argv);
+ threshold = atoi(* ++argv);
+ output_file = * ++argv;
+
+ t1 = time(NULL);
+
+ seqA.load_fasta(seqA_file, 1, 0, 0);
+ seqA_len = seqA.len();
+ //cout << setw(60) << seqA.hdr() << "\n";
+
+ seqB.load_fasta(seqB_file, 1, 0, 0);
+ seqB_len = seqB.len();
+ //cout << seqB.hdr() << "\n";
+
+
+ cout << "Length: Seq A = " << seqA_len;
+ cout << "; Seq B = " << seqB_len << "\n";
+
+ analysis.setup(ana_type, window, threshold, seqA_len, seqB_len);
+
+ t2 = time(NULL);
+ setuptime = difftime(t2, t1);
+
+ t1 = time(NULL);
+ analysis.seqcomp(seqA.seq(), seqB.seq(), false);
+ t2 = time(NULL);
+ comp1time = difftime(t2, t1);
+
+ t1 = time(NULL);
+ analysis.seqcomp(seqA.seq(), seqB.rev_comp(), true);
+ t2 = time(NULL);
+ comp2time = difftime(t2, t1);
+ /*
+ t1 = time(NULL);
+ analysis.sort();
+ t2 = time(NULL);
+ sorttime = difftime(t2, t1);
+ */
+ t1 = time(NULL);
+ analysis.save(output_file);
+ t2 = time(NULL);
+ savetime = difftime(t2, t1);
+
+ end = time(NULL);
+ totaltime = difftime(end, begin);
+
+ cout << "setup\tcomp\trc_comp\tsave\ttotal\n";
+ cout << setuptime << "\t";
+ cout << comp1time << "\t";
+ cout << comp2time << "\t";
+ //cout << sorttime << "\t";
+ cout << savetime << "\t";
+ cout << totaltime << "\n";
+}
+
+/*
+ cout << "fee\n";
+ cout << "fie\n";
+ cout << "foe ";
+ cout << "fum\n";
+*/
+++ /dev/null
-// This file is part of the Mussa source distribution.
-// http://mussa.caltech.edu/
-// Contact author: Tristan De Buysscher, tristan@caltech.edu
-
-// This program and all associated source code files are Copyright (C) 2005
-// the California Institute of Technology, Pasadena, CA, 91125 USA. It is
-// under the GNU Public License; please see the included LICENSE.txt
-// file for more information, or contact Tristan directly.
-
-
-#include "flp.hh"
-#include "sequence.hh"
-#include <time.h>
-#include <iomanip>
-
-using namespace std;
-
-int main(int argc, char **argv)
-{
- Sequence seqA, seqB;
- FLPs analysis;
- string seqA_file, seqB_file, output_file;
- string ana_type;
- int window, threshold;
- int seqA_len, seqB_len;
-
- time_t t1, t2, begin, end;
- double setuptime, comp1time, comp2time, sorttime, savetime, totaltime;
-
- begin = time(NULL);
-
- cout << "fee fie foe fum" << endl;
-
- ana_type = * ++argv;
- seqA_file = * ++argv;
- seqB_file = * ++argv;
- window = atoi(* ++argv);
- threshold = atoi(* ++argv);
- output_file = * ++argv;
-
- t1 = time(NULL);
-
- seqA.load_fasta(seqA_file, 1, 0, 0);
- seqA_len = seqA.len();
- //cout << setw(60) << seqA.hdr() << "\n";
-
- seqB.load_fasta(seqB_file, 1, 0, 0);
- seqB_len = seqB.len();
- //cout << seqB.hdr() << "\n";
-
-
- cout << "Length: Seq A = " << seqA_len;
- cout << "; Seq B = " << seqB_len << "\n";
-
- analysis.setup(ana_type, window, threshold, seqA_len, seqB_len);
-
- t2 = time(NULL);
- setuptime = difftime(t2, t1);
-
- t1 = time(NULL);
- analysis.seqcomp(seqA.seq(), seqB.seq(), false);
- t2 = time(NULL);
- comp1time = difftime(t2, t1);
-
- t1 = time(NULL);
- analysis.seqcomp(seqA.seq(), seqB.rev_comp(), true);
- t2 = time(NULL);
- comp2time = difftime(t2, t1);
- /*
- t1 = time(NULL);
- analysis.sort();
- t2 = time(NULL);
- sorttime = difftime(t2, t1);
- */
- t1 = time(NULL);
- analysis.save(output_file);
- t2 = time(NULL);
- savetime = difftime(t2, t1);
-
- end = time(NULL);
- totaltime = difftime(end, begin);
-
- cout << "setup\tcomp\trc_comp\tsave\ttotal\n";
- cout << setuptime << "\t";
- cout << comp1time << "\t";
- cout << comp2time << "\t";
- //cout << sorttime << "\t";
- cout << savetime << "\t";
- cout << totaltime << "\n";
-}
-
-/*
- cout << "fee\n";
- cout << "fie\n";
- cout << "foe ";
- cout << "fum\n";
-*/
projects / mussa.git / commitdiff