#include <boost/filesystem/fstream.hpp>
namespace fs = boost::filesystem;
-#include <boost/spirit/core.hpp>
-#include <boost/spirit/actor/push_back_actor.hpp>
-#include <boost/spirit/iterator/file_iterator.hpp>
-#include <boost/spirit/utility/chset.hpp>
-namespace spirit = boost::spirit;
-
#include <iostream>
#include <sstream>
#include "mussa_exceptions.hpp"
-#include "alg/mussa.hpp"
#include "alg/flp.hpp"
+#include "alg/mussa.hpp"
+#include "alg/motif_parser.hpp"
using namespace std;
: color_mapper(new AnnotationColors)
{
clear();
- connect(&the_paths, SIGNAL(progress(const std::string&, int, int)),
- this, SIGNAL(progress(const std::string&, int, int)));
+ connect(&the_paths, SIGNAL(progress(const QString&, int, int)),
+ this, SIGNAL(progress(const QString&, int, int)));
}
Mussa::Mussa(const Mussa& m)
analysis_path(m.analysis_path),
dirty(m.dirty)
{
- connect(&the_paths, SIGNAL(progress(const std::string&, int, int)),
- this, SIGNAL(progress(const std::string&, int, int)));
+ connect(&the_paths, SIGNAL(progress(const QString&, int, int)),
+ this, SIGNAL(progress(const QString&, int, int)));
+}
+
+MussaRef Mussa::init()
+{
+ boost::shared_ptr<Mussa> m(new Mussa());
+ return m;
}
boost::filesystem::path Mussa::get_analysis_path() const
the_seqs.clear();
the_paths.clear();
analysis_path = fs::path();
- dirty = false;
+ set_dirty(false);
+}
+
+void Mussa::set_dirty(bool new_state)
+{
+ if (dirty != new_state) {
+ dirty = new_state;
+ emit isModified(dirty);
+ }
}
bool Mussa::is_dirty() const
Mussa::set_name(string a_name)
{
analysis_name = a_name;
- dirty = true;
+ set_dirty(true);
}
string Mussa::get_name() const
Mussa::set_window(int a_window)
{
window = a_window;
- dirty = true;
+ set_dirty(true);
}
int Mussa::get_window() const
Mussa::set_threshold(int a_threshold)
{
threshold = a_threshold;
- dirty = true;
+ set_dirty(true);
if (a_threshold > soft_thres) {
soft_thres = a_threshold;
}
Mussa::set_analysis_mode(enum analysis_modes new_ana_mode)
{
ana_mode = new_ana_mode;
- dirty = true;
+ set_dirty(true);
}
enum Mussa::analysis_modes Mussa::get_analysis_mode() const
{
boost::shared_ptr<Sequence> seq_copy(new Sequence(a_seq));
the_seqs.push_back(seq_copy);
- dirty = true;
+ set_dirty(true);
}
void Mussa::append_sequence(boost::shared_ptr<Sequence> a_seq)
{
the_seqs.push_back(a_seq);
- dirty = true;
+ set_dirty(true);
}
-const vector<boost::shared_ptr<Sequence> >&
+const vector<SequenceRef>&
Mussa::sequences() const
{
return the_seqs;
aseq->set_species(*name);
}
the_seqs.push_back(aseq);
- dirty = true;
+ set_dirty(true);
}
void
// << " threshold = " << threshold << endl;
}
// no file was loaded, signal error
- dirty = true;
+ set_dirty(true);
}
void
Mussa::save(fs::path save_path)
{
- fs::path flp_filepath;
fs::fstream save_file;
ostringstream append_info;
int dir_create_status;
if (not fs::exists(save_path)) {
fs::create_directory(save_path);
}
+
+ std::string basename = save_path.leaf();
+ fs::path museq(basename + ".museq", fs::native);
+
// save sequence and annots to a special mussa file
- save_file.open(save_path / (save_path.leaf()+".museq"), ios::out);
+ save_file.open(save_path / museq, ios::out);
save_file << "<Mussa_Sequence>" << endl;
for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
// if we have any motifs, save them.
if (motif_sequences.size()) {
- save_motifs(save_path/(save_path.leaf()+".mtl"));
+ fs::path mtl(basename + ".mtl", fs::native);
+ save_motifs(save_path / mtl);
}
// save nway paths to its mussa save file
- the_paths.save(save_path / (save_path.leaf()+ ".muway"));
+ fs::path muway(basename + ".muway", fs::native);
+ the_paths.save(save_path / muway);
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;
- all_comps[i][i2].save(save_path/(save_path.leaf()+append_info.str()+".flp"));
+ fs::path flp(basename+append_info.str()+".flp", fs::native);
+ all_comps[i][i2].save(save_path / flp);
}
}
- dirty = false;
+ set_dirty(false);
analysis_path = save_path;
}
analysis_path = ana_file;
analysis_name = ana_path.leaf();
- file_path_base = ana_path.branch_path() / analysis_name;
- a_file_path = file_path_base / (analysis_name + ".muway");
+ fs::path muway(analysis_name+".muway", fs::native);
+ a_file_path = analysis_path / muway;
the_paths.load(a_file_path);
// perhaps this could be more elegent, but at least this'll let
// us know what our threshold and window sizes were when we load a muway
int seq_num = the_paths.sequence_count();
- a_file_path = file_path_base / (analysis_name + ".museq");
+ fs::path museq(analysis_name + ".museq", fs::native);
+ a_file_path = analysis_path / 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++)
the_seqs.push_back(tmp_seq);
}
- fs::path motif_file = file_path_base / (analysis_name + ".mtl");
+ fs::path mtl(analysis_name + ".mtl", fs::native);
+ fs::path motif_file = analysis_path / mtl;
if (fs::exists(motif_file)) {
load_motifs(motif_file);
}
append_info.str("");
append_info << analysis_name << "_sp_" << i << "v" << i2 << ".flp";
//clog << append_info.str() << endl;
- a_file_path = file_path_base / append_info.str();
- //clog << "path " << a_file_path.string() << endl;
+ fs::path flp(append_info.str(), fs::native);
+ a_file_path = analysis_path / flp;
all_comps[i][i2].load(a_file_path);
- //clog << "real size = " << all_comps[i][i2].size() << endl;
}
}
}
-
void
Mussa::save_old()
{
{
motif_sequences.insert(motif);
color_mapper->appendInstanceColor("motif", motif.get_sequence(), color);
- dirty = true;
+ set_dirty(true);
}
void Mussa::set_motifs(const vector<Sequence>& motifs,
update_sequences_motifs();
}
-// Helper functor to append created motifs to our Mussa analysis
-struct push_back_motif {
- Mussa::motif_set& motifs;
- boost::shared_ptr<AnnotationColors> color_mapper;
- std::string& seq_string;
- std::string& name;
- float& red;
- float& green;
- float& blue;
- float& alpha;
- int& parsed;
-
- push_back_motif(Mussa::motif_set& motifs_,
- boost::shared_ptr<AnnotationColors> color_mapper_,
- std::string& seq_,
- std::string& name_,
- float &red_, float &green_, float &blue_, float &alpha_,
- int &parsed_)
- : motifs(motifs_),
- color_mapper(color_mapper_),
- seq_string(seq_),
- name(name_),
- red(red_),
- green(green_),
- blue(blue_),
- alpha(alpha_),
- parsed(parsed_)
- {
- }
-
- void operator()(std::string::const_iterator,
- std::string::const_iterator) const
- {
- Sequence seq(seq_string, Sequence::nucleic_alphabet);
- // shouldn't we have a better field than "fasta header" and speices?
- seq.set_fasta_header(name);
- // we need to clear the name in case the next motif doesn't have one.
- name.clear();
- // be nice if glsequence was a subclass of sequence so we could
- // just attach colors directly to the motif.
- Color c(red, green, blue, alpha);
- color_mapper->appendInstanceColor("motif", seq.c_str(), c);
- alpha = 1.0;
- motifs.insert(seq);
- ++parsed;
- };
-};
-
void Mussa::load_motifs(fs::path filename)
{
fs::ifstream f;
f.open(filename, ifstream::in);
load_motifs(f);
}
-
-// I mostly split the ifstream out so I can use a stringstream to test it.
+
void Mussa::load_motifs(std::istream &in)
{
std::string data;
- const char *alphabet = Alphabet::nucleic_alphabet.c_str();
- string seq;
- string name;
- float red = 1.0;
- float green = 0.0;
- float blue = 0.0;
- float alpha = 1.0;
- int parsed = 1;
+ const char *alphabet = Alphabet::dna_cstr;
+ motif_parser::ParsedMotifs parsed_motifs(motif_sequences, color_mapper);
// slurp our data into a string
std::streamsize bytes_read = 1;
bytes_read = in.readsome(buf, bufsiz);
data.append(buf, buf+bytes_read);
}
- // parse our string
- bool ok = spirit::parse(data.begin(), data.end(),
- *(
- (
- (
- (+spirit::chset<>(alphabet))[spirit::assign_a(seq)] >>
- +spirit::space_p
- ) >>
- !(
- (
- // names can either be letter followed by non-space characters
- (spirit::alpha_p >> *spirit::graph_p)[spirit::assign_a(name)]
- |
- // or a quoted string
- (
- spirit::ch_p('"') >>
- (+(~spirit::ch_p('"')))[spirit::assign_a(name)] >>
- spirit::ch_p('"')
- )
- ) >> +spirit::space_p
- ) >>
- spirit::real_p[spirit::assign_a(red)] >> +spirit::space_p >>
- spirit::real_p[spirit::assign_a(green)] >> +spirit::space_p >>
- spirit::real_p[spirit::assign_a(blue)] >> +spirit::space_p >>
- !(spirit::real_p[spirit::assign_a(alpha)] >> +spirit::space_p)
- )[push_back_motif(motif_sequences, color_mapper, seq, name, red, green, blue, alpha, parsed)]
- )).full;
- if (not ok) {
- stringstream msg;
- msg << "Error parsing motif #" << parsed;
- // erase our potentially broken motif list
- motif_sequences.clear();
- throw motif_load_error(msg.str());
- }
+ parsed_motifs.parse(data);
update_sequences_motifs();
}
projects / mussa.git / blobdiff