1 #include "alg/glseqbrowser.hpp"
2 #include "mussa_exceptions.hpp"
10 GlSeqBrowser::GlSeqBrowser()
12 cur_ortho(400.0, 0.0, 600.0, 0.0),
13 viewport_size(600, 400),
14 viewport_center((cur_ortho.right-cur_ortho.left)/2+cur_ortho.left),
21 GlSeqBrowser::GlSeqBrowser(const GlSeqBrowser& gt)
22 : border_width(gt.border_width),
23 cur_ortho(gt.cur_ortho),
24 viewport_size(gt.viewport_size),
25 viewport_center(gt.viewport_center),
26 zoom_level(gt.zoom_level),
27 color_mapper(gt.color_mapper),
28 track_container(gt.track_container)
32 void GlSeqBrowser::initializeGL()
34 glEnable(GL_DEPTH_TEST);
35 glClearColor(1.0, 1.0, 1.0, 0.0);
36 glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
37 glShadeModel(GL_FLAT);
40 void GlSeqBrowser::resizeGL(int width, int height)
42 viewport_size.x = width;
43 viewport_size.y = height;
44 glViewport(0, 0, (GLsizei)width, (GLsizei)height);
45 update_viewport(viewport_center, zoom_level);
48 void GlSeqBrowser::paintGL() const
50 glClear(GL_COLOR_BUFFER_BIT|GL_DEPTH_BUFFER_BIT);
53 glMatrixMode(GL_PROJECTION);
55 glOrtho(cur_ortho.left, cur_ortho.right,
56 cur_ortho.bottom, cur_ortho.top,
65 void GlSeqBrowser::processSelection(GLuint hits, GLuint buffer[], GLuint bufsize, const rect<float>& r)
69 GLuint consumed_names = 0;
74 GLuint path_index = 0;
75 GLuint pair_key_0 = 0;
76 GLuint pair_key_1 = 0;
79 selected_paths.clear();
80 selected_tracks.clear();
82 ptr = (GLuint *) buffer;
85 for (GLuint i=0; i < hits; ++i)
87 if ((i + 5) > bufsize) {
88 std::clog << "*** selection overflow***" << std::endl;
92 z1 = ((float)*ptr++)/0x7fffffff;
93 z2 = ((float)*ptr++)/0x7fffffff;
94 objtype = *ptr++; ++consumed_names;
97 path_index = *ptr++; ++consumed_names;
98 pair_key_0 = *ptr++; ++consumed_names;
99 pair_key_1 = *ptr++; ++consumed_names;
100 if (path_index < path_segments.size()) {
101 segment_key k(pair_key_0, pair_key_1);
102 pair_segment_map::iterator psm_i;
103 psm_i = path_segments[path_index].find(k);
104 if (psm_i != path_segments[path_index].end()) {
105 Segment &seg = psm_i->second;
106 selected_paths.insert(seg.path_ids.begin(), seg.path_ids.end());
108 // else something else is wrong
110 // something wasn't right
111 clog << "invalid path_index " << path_index
112 << " should have been [0,"<<path_segments.size()
118 objid = *ptr++; ++consumed_names;
120 int left = track_container[objid]->leftbase(r.left);
121 int right = track_container[objid]->rightbase(r.right);
122 // the static_cast should be ok, since basepairs line up on
124 //TrackRegion track(objid, left, right);
125 track.set(objid, left, right);
126 selected_tracks.push_back(track);
127 //clog << "selected track " << objid
128 // << "(" << left << ", " << right << ")" << endl;
132 cout << "unknown type " << objtype << " ";
133 for(; consumed_names < names; ++consumed_names) {
134 cout << consumed_names << "," << *ptr++ << " ";
143 void GlSeqBrowser::selectRegion(int top, int left, int bottom, int right)
145 GLfloat x_scale = cur_ortho.width()/((float)viewport_size.x);
146 GLfloat y_scale = cur_ortho.height()/((float)viewport_size.y);
147 GLfloat x_left = cur_ortho.left + (left*x_scale);
148 GLfloat x_right = cur_ortho.left + (right * x_scale);
151 // woah, someone gave us a rectangle with the origin in the lower left
156 // swap the orientation of canvas coordinates
157 GLfloat y_top = cur_ortho.top-(bottom*y_scale);
158 GLfloat y_bottom = cur_ortho.top - top * y_scale;
159 selectedRegion = rect<float>(y_top, x_left, y_bottom, x_right);
161 // hopefully this will make a buffer big enough to receive
162 // everything being selected
163 //const size_t pathz_count = mussaAnalysis->paths().refined_pathz.size();
164 //const GLuint select_buf_size = 1 + 5 * (pathz_count + sequences.size());
165 const GLuint select_buf_size = 500000;
166 GLuint selectBuf[select_buf_size];
167 glSelectBuffer(select_buf_size, selectBuf);
170 (void)glRenderMode(GL_SELECT);
172 glMatrixMode(GL_PROJECTION);
174 glOrtho(x_left, x_right, y_top, y_bottom, -50.0, 50.0);
175 glMatrixMode(GL_MODELVIEW);
182 hits = glRenderMode(GL_RENDER);
183 processSelection(hits, selectBuf, select_buf_size, selectedRegion);
186 float GlSeqBrowser::border() const
191 float GlSeqBrowser::left() const
194 if (track_container.size() == 0)
196 return cur_ortho.left;
198 vector<boost::shared_ptr<GlSequence> >::const_iterator track_i = track_container.begin();
199 left = (*track_i)->x();
200 for( ; track_i != track_container.end(); ++track_i)
202 if ((*track_i)->x() < left) {
203 left = (*track_i)->x();
206 return left-border_width;
210 float GlSeqBrowser::right() const
213 if (track_container.size() == 0) {
214 return cur_ortho.right;
216 vector<boost::shared_ptr<GlSequence> >::const_iterator track_i = track_container.begin();
217 right = (*track_i)->right();
218 for( ; track_i != track_container.end(); ++track_i) {
219 if ((*track_i)->right() > right)
220 right = (*track_i)->right();
222 return right+border_width;
226 void GlSeqBrowser::setViewportCenter(float x)
228 update_viewport(x, zoom_level);
232 float GlSeqBrowser::viewportLeft() const
234 return cur_ortho.left;
237 float GlSeqBrowser::viewportCenter() const
239 return viewport_center;
242 float GlSeqBrowser::viewportRight() const
244 return cur_ortho.right;
247 float GlSeqBrowser::viewportHeight() const
249 return cur_ortho.top - cur_ortho.bottom;
252 float GlSeqBrowser::viewportWidth() const
254 return cur_ortho.right - cur_ortho.left;
257 double GlSeqBrowser::zoomOut()
260 if (right() - left() > 0) {
261 cur_ortho.left = left();
262 cur_ortho.right = right();
263 zoom_level = (right() - left()) / (double)viewport_size.x;
266 // made up number representing 50 bp / pixel
271 double GlSeqBrowser::zoomToSequence()
273 // (experimentally determined zoom level)
274 const double friendly_zoom = 0.10;
275 setZoom(friendly_zoom);
276 return friendly_zoom;
279 void GlSeqBrowser::setZoom(double new_zoom)
281 update_viewport(viewport_center, new_zoom);
282 zoom_level = new_zoom;
285 double GlSeqBrowser::zoom() const
290 void GlSeqBrowser::setColorMapper(boost::shared_ptr<AnnotationColors> cm)
295 const AnnotationColors& GlSeqBrowser::colorMapper()
297 return *color_mapper;
300 void GlSeqBrowser::clear()
304 path_segments.clear();
305 track_container.clear();
308 void GlSeqBrowser::clear_selection()
310 selectedMode = false;
311 selectedRegion.clear();
312 selected_paths.clear();
313 selected_tracks.clear();
316 void GlSeqBrowser::push_sequence(const Sequence& s)
318 boost::shared_ptr<Sequence> seq_copy(new Sequence(s));
319 GlSequence gs(seq_copy, color_mapper);
324 void GlSeqBrowser::push_sequence(boost::shared_ptr<Sequence> s)
326 boost::shared_ptr<GlSequence> gs(new GlSequence(s, color_mapper));
330 void GlSeqBrowser::push_sequence(GlSequence gs)
332 boost::shared_ptr<GlSequence> new_gs(new GlSequence(gs));
333 push_sequence(new_gs);
336 void GlSeqBrowser::push_sequence(boost::shared_ptr<GlSequence> gs)
339 track_container.push_back(gs);
341 if (track_container.size() > 1)
342 path_segments.push_back(pair_segment_map());
345 const std::vector<boost::shared_ptr<GlSequence> >& GlSeqBrowser::sequences() const
347 return track_container;
350 void GlSeqBrowser::clear_links()
352 path_segments.clear();
353 for (int i = track_container.size()-1; i > 0; --i)
355 path_segments.push_back(pair_segment_map());
361 GlSeqBrowser::link(const vector<int>& path, const vector<bool>& rc, int length)
363 if (path.size() < 2) {
364 // should i throw an error instead?
367 if (path.size() != track_container.size() ) {
369 msg << "Path size [" << path.size() << "] and track size ["
370 << track_container.size() << "] don't match" << endl;
371 throw mussa_error(msg.str());
373 if (path.size() != rc.size()) {
374 throw runtime_error("path and reverse compliment must be the same length");
376 vector<int>::const_iterator path_i = path.begin();
377 vector<bool>::const_iterator rc_i = rc.begin();
379 int prev_x = *path_i; ++path_i;
380 bool prev_rc = *rc_i; ++rc_i;
381 while (path_i != path.end() and rc_i != rc.end())
383 segment_key p(prev_x, *path_i);
384 pair_segment_map::iterator found_segment = path_segments[track_i].find(p);
385 if (found_segment == path_segments[track_i].end()) {
387 float y1 = track_container[track_i]->y();
388 y1 -= track_container[track_i]->height()/2;
389 float y2 = track_container[track_i+1]->y();
390 y2 += track_container[track_i+1]->height()/2;
392 bool rcFlag = (prev_rc or *rc_i) and !(prev_rc and *rc_i);
393 Segment s(prev_x, y1, *path_i, y2, rcFlag, length);
394 s.path_ids.insert(pathid);
395 path_segments[track_i][p] = s;
398 found_segment->second.path_ids.insert(pathid);
399 // make each segment the size of the largest of any link between these
401 if (found_segment->second.length < length) {
402 found_segment->second.length = length;
411 // pathid is reset by push_sequence
415 void GlSeqBrowser::setSelectedPaths(std::vector<int> paths)
417 selected_paths.clear();
418 for(std::vector<int>::iterator itor = paths.begin();
422 selected_paths.insert(*itor);
426 const set<int>& GlSeqBrowser::selectedPaths() const
428 return selected_paths;
431 void GlSeqBrowser::appendSelectedTrack(GLuint track, int start, int stop)
433 selected_tracks.push_back(TrackRegion(track, start, stop));
436 list<TrackRegion> GlSeqBrowser::selectedTracks() const
438 return selected_tracks;
441 //! copy sequence from selected track using formating function
443 void GlSeqBrowser::copySelectedTracks(std::list<Item>& result,
444 Item (*formatter)(boost::shared_ptr<Sequence> s,
450 for(selected_track_iterator track_i = selected_tracks.begin();
451 track_i != selected_tracks.end();
454 int track_index = track_i->track_id;
455 if (track_index >= track_container.size()) {
456 // should this be an exception instead?
457 clog << "track " << track_index << " > " << track_container.size()
461 boost::shared_ptr<Sequence> seq = track_container[track_index]->sequence();
462 result.push_back(formatter(seq, track_i->left, track_i->right));
467 //! copy sequence from selected tracks as FASTA sequences
468 void GlSeqBrowser::copySelectedTracksAsFasta(std::string& copy_buffer)
470 std::list<std::string> result;
472 static string formatter(boost::shared_ptr<Sequence> seq,
477 s << ">" << seq->get_fasta_header()
478 << "|" << "subregion=" << left << "-" << right+1
480 << seq->subseq(left, right-left+1) << std::endl;
484 copySelectedTracks(result, AsFasta::formatter);
485 // I wish there was some way to use for_each and bind here
486 for (list<string>::iterator result_i = result.begin();
487 result_i != result.end();
490 copy_buffer.append(*result_i);
494 //! copy sequence from selected tracks as new sequences
495 void GlSeqBrowser::copySelectedTracksAsSequences(std::list<Sequence>& result)
498 static Sequence formatter(boost::shared_ptr<Sequence> seq,
502 return seq->subseq(left, right-left+1);
505 copySelectedTracks(result, AsSequence::formatter);
508 void GlSeqBrowser::copySelectedTracksAsSeqLocation(
509 std::list<SequenceLocation>& result)
511 struct AsSeqLocation {
512 static SequenceLocation formatter(boost::shared_ptr<Sequence> seq,
516 return SequenceLocation(seq, left, right);
519 copySelectedTracks(result, AsSeqLocation::formatter);
522 //! copy sequence from selected tracks as plain sequences
523 void GlSeqBrowser::copySelectedTracksAsString(std::string& copy_buffer)
525 std::list<string> result;
527 static string formatter(boost::shared_ptr<Sequence> seq,
532 s << seq->subseq(left, right-left+1) << std::endl;
537 copySelectedTracks(result, AsString::formatter);
538 // I wish there was some way to use for_each and bind here
539 for (list<string>::iterator result_i = result.begin();
540 result_i != result.end();
543 copy_buffer.append(*result_i);
548 void GlSeqBrowser::centerOnPath(const vector<int>& paths)
550 if (paths.size() != track_container.size()) {
551 throw mussa_error("Path length didn't match the number of sequences");
554 for(size_t track_i = 0; track_i != track_container.size(); ++track_i)
556 // -15 = shift more to the left
557 track_container[track_i]->setX((viewport_center-15) - paths[track_i]);
561 void GlSeqBrowser::update_viewport(float center, double new_zoom)
563 // limit how close we can get
564 if (new_zoom < 0.01) {
567 double new_width = (new_zoom * (float)viewport_size.x);
568 cur_ortho.left = center-new_width/2.0;
569 cur_ortho.right = center+new_width/2.0;
572 void GlSeqBrowser::update_layout()
574 typedef std::vector<boost::shared_ptr<GlSequence> >::iterator glseq_itor_type;
575 float available_height = (float)cur_ortho.top - 2 * (float)border_width;
576 float max_base_pairs = 0;
577 size_t track_count = track_container.size();
579 if (track_count > 1) {
580 // we have several sequences
581 float track_spacing = available_height / (track_count-1);
582 float y = available_height + (float)border_width;
583 for(glseq_itor_type seq_i = track_container.begin();
584 seq_i != track_container.end();
585 ++seq_i, y-=track_spacing)
589 if ((*seq_i)->size() > max_base_pairs)
590 max_base_pairs = (*seq_i)->size();
592 } else if (track_count == 1) {
593 // center the single track
594 glseq_itor_type seq_i = track_container.begin();
596 (*seq_i)->setY(viewport_size.x /2);
597 max_base_pairs = (*seq_i)->size();
599 // nothing to do as we're empty
602 cur_ortho.right = max_base_pairs + border_width;
603 cur_ortho.left = -border_width;
604 cur_ortho.top = viewport_size.x;
605 cur_ortho.bottom = 0;
606 viewport_center = (cur_ortho.width()/2) + cur_ortho.left;
610 void GlSeqBrowser::draw() const
612 glMatrixMode(GL_MODELVIEW);
614 glPushName(MussaSegment);
616 glLoadName(MussaTrack);
619 // a selection shouldn't have a glName associated with it
623 void GlSeqBrowser::draw_selection() const
625 // draw selection box
627 glDepthMask(GL_FALSE);
629 glColor4f(0.6, 0.6, 0.6, 0.9);
630 glRectf(selectedRegion.left, selectedRegion.top,
631 selectedRegion.right, selectedRegion.bottom);
633 glDepthMask(GL_TRUE);
637 void GlSeqBrowser::draw_tracks() const
639 for(size_t track_i = 0; track_i != track_container.size(); ++track_i)
642 track_container[track_i]->draw(cur_ortho.left, cur_ortho.right);
647 void GlSeqBrowser::draw_segments() const
651 glDepthMask(GL_FALSE);
652 const float zdepth = -1.0;
653 // each vector contains path_segment_maps of all the connections
654 // between this track and the next
655 path_segment_map_vector::const_iterator psmv_i;
656 for(psmv_i = path_segments.begin();
657 psmv_i != path_segments.end();
660 path_segment_map_vector::difference_type path_index;
661 path_index = psmv_i - path_segments.begin();
662 // these maps contain the pair index (used so we dont keep drawing the
663 // same segment) and the actual segment structure.
664 pair_segment_map::const_iterator psm_i;
665 for(psm_i = psmv_i->begin();
666 psm_i != psmv_i->end();
669 // grab the index into our segment map
670 const segment_key& key = psm_i->first;
671 // the second element of our map pair is a segment
672 const Segment &s = psm_i->second;
673 // need to do something so we can detect our selection
674 vector<int> selected;
675 set_intersection(selected_paths.begin(), selected_paths.end(),
676 s.path_ids.begin(), s.path_ids.end(),
677 back_inserter(selected));
679 if (not s.reversed) {
680 if (selected_paths.size() == 0 or selected.size() > 0) {
681 glColor4f(1.0, 0.0, 0.0, 1.0);
683 glColor4f(1.0, 0.7, 0.7, 0.4);
686 if (selected_paths.size() == 0 or selected.size() > 0) {
687 glColor4f(0.0, 0.0, 1.0, 1.0);
689 glColor4f(0.7, 0.7, 1.0, 0.4);
692 // save the multipart name for our segment
693 glPushName(path_index); glPushName(key.first); glPushName(key.second);
694 float seq_start_x = s.start.x
695 + track_container[path_index]->x();
696 float seq_end_x = s.end.x
697 + track_container[path_index+1]->x();
699 float seq_start_x_length = s.start.x
701 + track_container[path_index]->x();
702 float seq_end_x_length = s.end.x
704 + track_container[path_index+1]->x();
706 // glVertex3f(seq_start_x, s.start.y, -1);
707 // glVertex3f(seq_end_x , s.end.y, -1);
711 glVertex3f(seq_start_x, s.start.y, zdepth);
712 glVertex3f(seq_end_x, s.end.y, zdepth);
713 glVertex3f(seq_end_x_length, s.end.y, zdepth);
714 glVertex3f(seq_start_x_length, s.start.y, zdepth);
717 glPopName(); glPopName(); glPopName();
720 glDepthMask(GL_TRUE);