X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=alg%2Fglseqbrowser.cpp;h=107099bd824105df653a994699472f3a122cf2fb;hb=55f0a3e9612b3e1df2c588682d7f605203eab421;hp=e82cfe1f48fab2cd13fb3f82dba47e6d62bef5f9;hpb=48ddb0a496be84b7f6c7d3dc3205bd0ffd11ab26;p=mussa.git diff --git a/alg/glseqbrowser.cpp b/alg/glseqbrowser.cpp index e82cfe1..107099b 100644 --- a/alg/glseqbrowser.cpp +++ b/alg/glseqbrowser.cpp @@ -1,6 +1,7 @@ #include "alg/glseqbrowser.hpp" #include "mussa_exceptions.hpp" +#include #include #include #include @@ -25,7 +26,8 @@ GlSeqBrowser::GlSeqBrowser(const GlSeqBrowser& gt) viewport_center(gt.viewport_center), zoom_level(gt.zoom_level), color_mapper(gt.color_mapper), - track_container(gt.track_container) + track_container(gt.track_container), + path_segments(gt.path_segments) { } @@ -223,6 +225,15 @@ float GlSeqBrowser::right() const } } +float GlSeqBrowser::get_pixel_width() const +{ + GLint viewport[4]; + glGetIntegerv(GL_VIEWPORT, viewport); + GLint vp_width = viewport[3]; // grab the viewport width + + return round((cur_ortho.right-cur_ortho.left)/vp_width); +} + void GlSeqBrowser::setViewportCenter(float x) { update_viewport(x, zoom_level); @@ -254,6 +265,16 @@ float GlSeqBrowser::viewportWidth() const return cur_ortho.right - cur_ortho.left; } +int GlSeqBrowser::viewportPixelHeight() const +{ + return viewport_size.y; +} + +int GlSeqBrowser::viewportPixelWidth() const +{ + return viewport_size.x; +} + double GlSeqBrowser::zoomOut() { @@ -287,14 +308,14 @@ double GlSeqBrowser::zoom() const return zoom_level; } -void GlSeqBrowser::setColorMapper(boost::shared_ptr cm) +void GlSeqBrowser::setColorMapper(AnnotationColorsRef cm) { color_mapper = cm; } -const AnnotationColors& GlSeqBrowser::colorMapper() +const AnnotationColorsRef GlSeqBrowser::colorMapper() { - return *color_mapper; + return color_mapper; } void GlSeqBrowser::clear() @@ -315,34 +336,36 @@ void GlSeqBrowser::clear_selection() void GlSeqBrowser::push_sequence(const Sequence& s) { - boost::shared_ptr seq_copy(new Sequence(s)); - GlSequence gs(seq_copy, color_mapper); + GlSequenceRef gs(new GlSequence(s, color_mapper)); push_sequence(gs); } - -void GlSeqBrowser::push_sequence(boost::shared_ptr s) +void GlSeqBrowser::push_sequence(SequenceRef s) { - boost::shared_ptr gs(new GlSequence(s, color_mapper)); + GlSequenceRef gs(new GlSequence(*s, color_mapper)); push_sequence(gs); } void GlSeqBrowser::push_sequence(GlSequence gs) { - boost::shared_ptr new_gs(new GlSequence(gs)); + GlSequenceRef new_gs(new GlSequence(gs)); push_sequence(new_gs); } -void GlSeqBrowser::push_sequence(boost::shared_ptr gs) +void GlSeqBrowser::push_sequence(GlSequenceRef gs) { + GlSequenceRef new_gs(new GlSequence(gs)); + // mark where the sequence is + new_gs->add_annotations_for_defined_sequence(draw_track); + clear_links(); - track_container.push_back(gs); + track_container.push_back(new_gs); update_layout(); if (track_container.size() > 1) path_segments.push_back(pair_segment_map()); } -const std::vector >& GlSeqBrowser::sequences() const +const std::vector& GlSeqBrowser::sequences() const { return track_container; } @@ -440,11 +463,10 @@ list GlSeqBrowser::selectedTracks() const //! copy sequence from selected track using formating function template -void GlSeqBrowser::copySelectedTracks(std::list& result, - Item (*formatter)(boost::shared_ptr s, - int left, - int right)) +size_t GlSeqBrowser::copySelectedTracks(std::list& result, + Item (*formatter)(const Sequence& s, int left, int right)) { + size_t base_pairs_copied = 0; result.clear(); for(selected_track_iterator track_i = selected_tracks.begin(); @@ -458,30 +480,30 @@ void GlSeqBrowser::copySelectedTracks(std::list& result, << endl; } else { // we should be safe - boost::shared_ptr seq = track_container[track_index]->sequence(); + Sequence seq(*track_container[track_index]); result.push_back(formatter(seq, track_i->left, track_i->right)); + base_pairs_copied += max(track_i->right-track_i->left, 0); } } + return base_pairs_copied; } //! copy sequence from selected tracks as FASTA sequences -void GlSeqBrowser::copySelectedTracksAsFasta(std::string& copy_buffer) +size_t GlSeqBrowser::copySelectedTracksAsFasta(std::string& copy_buffer) { std::list result; struct AsFasta { - static string formatter(boost::shared_ptr seq, - int left, - int right) + static string formatter(const Sequence& seq, int left, int right) { stringstream s; - s << ">" << seq->get_fasta_header() + s << ">" << seq.get_fasta_header() << "|" << "subregion=" << left << "-" << right+1 << std::endl - << seq->subseq(left, right-left+1) << std::endl; + << seq.subseq(left, right-left+1) << std::endl; return s.str(); } }; - copySelectedTracks(result, AsFasta::formatter); + size_t base_pairs_copied = copySelectedTracks(result, AsFasta::formatter); // I wish there was some way to use for_each and bind here for (list::iterator result_i = result.begin(); result_i != result.end(); @@ -489,52 +511,53 @@ void GlSeqBrowser::copySelectedTracksAsFasta(std::string& copy_buffer) { copy_buffer.append(*result_i); } + return base_pairs_copied; } //! copy sequence from selected tracks as new sequences -void GlSeqBrowser::copySelectedTracksAsSequences(std::list& result) +size_t GlSeqBrowser::copySelectedTracksAsSequences(std::list& result) { struct AsSequence { - static Sequence formatter(boost::shared_ptr seq, + static Sequence formatter(const Sequence& seq, int left, int right) { - return seq->subseq(left, right-left+1); + return seq.subseq(left, right-left+1); } }; - copySelectedTracks(result, AsSequence::formatter); + return copySelectedTracks(result, AsSequence::formatter); } -void GlSeqBrowser::copySelectedTracksAsSeqLocation( +size_t GlSeqBrowser::copySelectedTracksAsSeqLocation( std::list& result) { struct AsSeqLocation { - static SequenceLocation formatter(boost::shared_ptr seq, + static SequenceLocation formatter(const Sequence& seq, int left, int right) { return SequenceLocation(seq, left, right); } }; - copySelectedTracks(result, AsSeqLocation::formatter); + return copySelectedTracks(result, AsSeqLocation::formatter); } //! copy sequence from selected tracks as plain sequences -void GlSeqBrowser::copySelectedTracksAsString(std::string& copy_buffer) +size_t GlSeqBrowser::copySelectedTracksAsString(std::string& copy_buffer) { std::list result; struct AsString { - static string formatter(boost::shared_ptr seq, + static string formatter(const Sequence& seq, int left, int right) { stringstream s; - s << seq->subseq(left, right-left+1) << std::endl; + s << seq.subseq(left, right-left+1); return s.str(); } }; - copySelectedTracks(result, AsString::formatter); + size_t base_pairs_copied = copySelectedTracks(result, AsString::formatter); // I wish there was some way to use for_each and bind here for (list::iterator result_i = result.begin(); result_i != result.end(); @@ -542,7 +565,7 @@ void GlSeqBrowser::copySelectedTracksAsString(std::string& copy_buffer) { copy_buffer.append(*result_i); } - + return base_pairs_copied; } void GlSeqBrowser::centerOnPath(const vector& paths) @@ -650,6 +673,8 @@ void GlSeqBrowser::draw_segments() const glEnable(GL_BLEND); glDepthMask(GL_FALSE); const float zdepth = -1.0; + const float min_segment_width = max((float)(1.0), get_pixel_width()); + // each vector contains path_segment_maps of all the connections // between this track and the next path_segment_map_vector::const_iterator psmv_i; @@ -677,12 +702,14 @@ void GlSeqBrowser::draw_segments() const back_inserter(selected)); if (not s.reversed) { + // forward if (selected_paths.size() == 0 or selected.size() > 0) { glColor4f(1.0, 0.0, 0.0, 1.0); } else { glColor4f(1.0, 0.7, 0.7, 0.4); } } else { + // reverse if (selected_paths.size() == 0 or selected.size() > 0) { glColor4f(0.0, 0.0, 1.0, 1.0); } else { @@ -695,24 +722,30 @@ void GlSeqBrowser::draw_segments() const + track_container[path_index]->x(); float seq_end_x = s.end.x + track_container[path_index+1]->x(); - // add in length - float seq_start_x_length = s.start.x + if (s.length <= min_segment_width) { + // use lines for elements of length <=1 or < 1 pixel. + // and try to center the line + const float offset = s.length * 0.5; + glBegin(GL_LINES); + glVertex3f(seq_start_x+offset, s.start.y, -1); + glVertex3f(seq_end_x +offset, s.end.y, -1); + glEnd(); + } else { + // otherwise use quads + // compute length + float seq_start_x_length = s.start.x + + s.length + + track_container[path_index]->x(); + float seq_end_x_length = s.end.x + s.length - + track_container[path_index]->x(); - float seq_end_x_length = s.end.x - + s.length - + track_container[path_index+1]->x(); - //glBegin(GL_LINES); - // glVertex3f(seq_start_x, s.start.y, -1); - // glVertex3f(seq_end_x , s.end.y, -1); - //glEnd(); - - glBegin(GL_QUADS); - glVertex3f(seq_start_x, s.start.y, zdepth); - glVertex3f(seq_end_x, s.end.y, zdepth); - glVertex3f(seq_end_x_length, s.end.y, zdepth); - glVertex3f(seq_start_x_length, s.start.y, zdepth); - glEnd(); + + track_container[path_index+1]->x(); + glBegin(GL_QUADS); + glVertex3f(seq_start_x, s.start.y, zdepth); + glVertex3f(seq_end_x, s.end.y, zdepth); + glVertex3f(seq_end_x_length, s.end.y, zdepth); + glVertex3f(seq_start_x_length, s.start.y, zdepth); + glEnd(); + } // clear the names glPopName(); glPopName(); glPopName(); }