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rename ExtendedConservedPath for the old fltk code
author
Diane Trout
<diane@caltech.edu>
Tue, 23 May 2006 05:44:08 +0000
(
05:44
+0000)
committer
Diane Trout
<diane@caltech.edu>
Tue, 23 May 2006 05:44:08 +0000
(
05:44
+0000)
gui/ConnView.cpp
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|
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|
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gui/ConnView.hpp
patch
|
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gui/SeqView.cpp
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gui/SeqView.hpp
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gui/SeqWindow.cpp
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gui/SeqWindow.hpp
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diff --git
a/gui/ConnView.cpp
b/gui/ConnView.cpp
index b6ba9468a1d5263cb31deb4095433d460c633b53..4c089edf1314365ce5f20e7167cd71824f0e887f 100644
(file)
--- a/
gui/ConnView.cpp
+++ b/
gui/ConnView.cpp
@@
-125,8
+125,8
@@
ConnView::setup(string name, int sq_num, int win_len,
void
ConnView::scale_paths()
{
void
ConnView::scale_paths()
{
-
Extended
ConservedPath a_path;
- list<
Extended
ConservedPath >::iterator pathz_i;
+ ConservedPath a_path;
+ list<ConservedPath >::iterator pathz_i;
int i2;
int i2;
@@
-246,7
+246,7
@@
ConnView::draw()
void
ConnView::draw_paths()
{
void
ConnView::draw_paths()
{
- list<
Extended
ConservedPath >::iterator i;
+ list<ConservedPath >::iterator i;
int i2, i3, y_loc, x_loc, x_start, x_end;
list<bool>::iterator highlight_i;
int window_size;
int i2, i3, y_loc, x_loc, x_start, x_end;
list<bool>::iterator highlight_i;
int window_size;
@@
-257,7
+257,7
@@
ConnView::draw_paths()
highlight.clear();
for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i)
{
highlight.clear();
for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i)
{
-
Extended
ConservedPath& a_path = *i;
+ ConservedPath& 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]);
// determine if path falls within the selected region and mark it for
// highlighted color
path_start = abs(a_path[ref_seq_num]);
@@
-276,7
+276,7
@@
ConnView::draw_paths()
highlight_i = highlight.begin();
for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i)
{
highlight_i = highlight.begin();
for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i)
{
-
Extended
ConservedPath& a_path = *i;
+ ConservedPath& a_path = *i;
y_loc = y()+y_pad;
window_size = a_path.window_size;
y_loc = y()+y_pad;
window_size = a_path.window_size;
@@
-311,7
+311,7
@@
ConnView::draw_paths()
highlight_i = highlight.begin();
for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i)
{
highlight_i = highlight.begin();
for(i = scaled_pathz.begin(); i != scaled_pathz.end(); ++i)
{
-
Extended
ConservedPath& a_path = *i;
+ ConservedPath& a_path = *i;
y_loc = y()+y_pad;
// get window size to determine line width
y_loc = y()+y_pad;
// get window size to determine line width
@@
-606,8
+606,8
@@
ConnView::check_new_motifs()
void
ConnView::spawnSeq()
{
void
ConnView::spawnSeq()
{
- list<
Extended
ConservedPath > selected_paths;
- list<
Extended
ConservedPath >::iterator pathz_i;
+ list<ConservedPath > selected_paths;
+ list<ConservedPath >::iterator pathz_i;
int i2, i3, y_loc, x_loc, x_start, x_end;
list<bool>::iterator highlight_i;
int y_max;
int i2, i3, y_loc, x_loc, x_start, x_end;
list<bool>::iterator highlight_i;
int y_max;
diff --git
a/gui/ConnView.hpp
b/gui/ConnView.hpp
index 6d52a5fe6f4970806bd26bc40b86cae1bb6af6fd..ed0066ae5f9f8f039918ab148cf5340cb86abff3 100644
(file)
--- a/
gui/ConnView.hpp
+++ b/
gui/ConnView.hpp
@@
-65,7
+65,7
@@
class ConnView : public Fl_Box
std::list<bool> highlight;
//path data scaled for current view size
std::list<bool> highlight;
//path data scaled for current view size
- std::list<
Extended
ConservedPath > scaled_pathz;
+ std::list<ConservedPath > scaled_pathz;
std::vector<int> seq_lens;
std::vector<int> seq_scales;
int bar_interval, line_interval;
std::vector<int> seq_lens;
std::vector<int> seq_scales;
int bar_interval, line_interval;
diff --git
a/gui/SeqView.cpp
b/gui/SeqView.cpp
index 419d21e2d887ae70b9709a14a8c2bf56c81de1d2..66a6714d27687eab603d9b2bdff1500e5b3ca7fd 100644
(file)
--- a/
gui/SeqView.cpp
+++ b/
gui/SeqView.cpp
@@
-20,7
+20,7
@@
using namespace std;
void
SeqView::setup(string name, int sq_num,
vector<Sequence> *some_seqs,
void
SeqView::setup(string name, int sq_num,
vector<Sequence> *some_seqs,
- list<
Extended
ConservedPath > some_paths, vector<int> some_lens,
+ list<ConservedPath > some_paths, vector<int> some_lens,
vector<fltk_motif> *some_motifs)
{
int seq_i;
vector<fltk_motif> *some_motifs)
{
int seq_i;
@@
-45,7
+45,7
@@
SeqView::setup(string name, int sq_num,
for(seq_i = 0; seq_i < seq_num; ++seq_i)
raw_sequence.push_back( (*S)[seq_i].get_seq() );
for(seq_i = 0; seq_i < seq_num; ++seq_i)
raw_sequence.push_back( (*S)[seq_i].get_seq() );
- for(list<
Extended
ConservedPath >::iterator pathz_i = P.begin();
+ for(list<ConservedPath >::iterator pathz_i = P.begin();
pathz_i != P.end();
++pathz_i)
{
pathz_i != P.end();
++pathz_i)
{
@@
-233,13
+233,13
@@
SeqView::draw_match_lines(double ch_width)
align_counter = 0;
align_counter = 0;
- for(list<
Extended
ConservedPath >::iterator pathz_i = P.begin();
+ for(list<ConservedPath >::iterator pathz_i = P.begin();
pathz_i != P.end();
++pathz_i)
{
if (show_aligns[align_counter])
{
pathz_i != P.end();
++pathz_i)
{
if (show_aligns[align_counter])
{
-
Extended
ConservedPath& a_path = *pathz_i;
+ ConservedPath& a_path = *pathz_i;
window_length = a_path.window_size;
// determine which parts of the path are RC relative to first species
rc_list = a_path.reverseComplimented();
window_length = a_path.window_size;
// determine which parts of the path are RC relative to first species
rc_list = a_path.reverseComplimented();
@@
-393,7
+393,7
@@
SeqView::toggle_align(int align_num)
void
SeqView::align_offsets(int align_num)
{
void
SeqView::align_offsets(int align_num)
{
- list<
Extended
ConservedPath >::iterator pathz_i;
+ list<ConservedPath >::iterator pathz_i;
int i;
int window_length;
int i;
int window_length;
diff --git
a/gui/SeqView.hpp
b/gui/SeqView.hpp
index aab023fbeb5594d7a9365f7798fce7aa31999d89..354acd90641d5c9766b3135ecb21300c879bff8c 100644
(file)
--- a/
gui/SeqView.hpp
+++ b/
gui/SeqView.hpp
@@
-33,7
+33,7
@@
class SeqView : public Fl_Box
}
void setup(std::string name, int sq_num, std::vector<Sequence> *some_seqs,
}
void setup(std::string name, int sq_num, std::vector<Sequence> *some_seqs,
- std::list<
Extended
ConservedPath > some_paths,
+ std::list<ConservedPath > some_paths,
std::vector<int> some_lens, std::vector<fltk_motif> *some_motifs);
void align_offsets(int align_num);
void toggle_align(int align_num);
std::vector<int> some_lens, std::vector<fltk_motif> *some_motifs);
void align_offsets(int align_num);
void toggle_align(int align_num);
@@
-48,7
+48,7
@@
class SeqView : public Fl_Box
//this data is passed as pointers to the instantiated classes
std::vector<Sequence> *S;
//list of paths in selection box
//this data is passed as pointers to the instantiated classes
std::vector<Sequence> *S;
//list of paths in selection box
- std::list<
Extended
ConservedPath > P;
+ std::list<ConservedPath > P;
std::vector<int> seq_lens;
//pointer to passed fltk_motif data
std::vector<fltk_motif> *the_motifs;
std::vector<int> seq_lens;
//pointer to passed fltk_motif data
std::vector<fltk_motif> *the_motifs;
diff --git
a/gui/SeqWindow.cpp
b/gui/SeqWindow.cpp
index 8578f4974e1d2c0fa11e01807bc5cd77342e5a46..5a3351cdddb5f42b8a4d86c868e78bc852a2e194 100644
(file)
--- a/
gui/SeqWindow.cpp
+++ b/
gui/SeqWindow.cpp
@@
-88,7
+88,7
@@
SeqWindow::real_toggle_motifs_cb()
SeqWindow::SeqWindow(int w, int h, const char* title, int sq_num,
vector<Sequence> *some_seqs,
SeqWindow::SeqWindow(int w, int h, const char* title, int sq_num,
vector<Sequence> *some_seqs,
- list<
Extended
ConservedPath > some_paths,
+ list<ConservedPath > some_paths,
vector<int> some_lens,
vector<fltk_motif> *some_motifs):
Fl_Double_Window(w,h,title)
vector<int> some_lens,
vector<fltk_motif> *some_motifs):
Fl_Double_Window(w,h,title)
@@
-98,7
+98,7
@@
SeqWindow::SeqWindow(int w, int h, const char* title, int sq_num,
int i;
ostringstream align_id_ostr;
string align_id_string;
int i;
ostringstream align_id_ostr;
string align_id_string;
- list<
Extended
ConservedPath >::iterator align_iter;
+ list<ConservedPath >::iterator align_iter;
// most of this stuff is here just to pass to SeqView object
// some is needed to setup the window menus
// most of this stuff is here just to pass to SeqView object
// some is needed to setup the window menus
diff --git
a/gui/SeqWindow.hpp
b/gui/SeqWindow.hpp
index c6b8cc829002036d4eb7bee483eaaad9a30d474c..920d49671499e4bbb324ada0fb005e1d61226143 100644
(file)
--- a/
gui/SeqWindow.hpp
+++ b/
gui/SeqWindow.hpp
@@
-30,7
+30,7
@@
class SeqWindow : public Fl_Double_Window
//this data is passed as pointers to the instantiated classes
std::vector<Sequence> *S;
// list of paths in selection box
//this data is passed as pointers to the instantiated classes
std::vector<Sequence> *S;
// list of paths in selection box
- std::list<
Extended
ConservedPath > P;
+ std::list<ConservedPath > P;
std::vector<int> seq_lens;
//pointer to passed fltk_motif data
std::vector<fltk_motif> *the_motifs;
std::vector<int> seq_lens;
//pointer to passed fltk_motif data
std::vector<fltk_motif> *the_motifs;
@@
-46,7
+46,7
@@
class SeqWindow : public Fl_Double_Window
SeqWindow(int w, int h, const char* title, int sq_num,
std::vector<Sequence> *some_seqs,
SeqWindow(int w, int h, const char* title, int sq_num,
std::vector<Sequence> *some_seqs,
- std::list<
Extended
ConservedPath > some_paths,
+ std::list<ConservedPath > some_paths,
std::vector<int> some_lens,
std::vector<fltk_motif> *some_motifs);
virtual ~SeqWindow(){ std::cout << "dying\n"; }
std::vector<int> some_lens,
std::vector<fltk_motif> *some_motifs);
virtual ~SeqWindow(){ std::cout << "dying\n"; }