X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=alg%2Fglseqbrowser.cpp;h=107099bd824105df653a994699472f3a122cf2fb;hb=55f0a3e9612b3e1df2c588682d7f605203eab421;hp=3342042755d16ca411a5ea5bce39e4657342c57a;hpb=4db52f646d31d4f078e145c0b23eb6fab6693d43;p=mussa.git

diff --git a/alg/glseqbrowser.cpp b/alg/glseqbrowser.cpp
index 3342042..107099b 100644
--- a/alg/glseqbrowser.cpp
+++ b/alg/glseqbrowser.cpp
@@ -26,7 +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)
 {
 }
 
@@ -264,6 +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()
 {
 
@@ -297,14 +308,14 @@ double GlSeqBrowser::zoom() const
   return zoom_level;
 }
 
-void GlSeqBrowser::setColorMapper(boost::shared_ptr<AnnotationColors> 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()
@@ -325,34 +336,36 @@ void GlSeqBrowser::clear_selection()
 
 void GlSeqBrowser::push_sequence(const Sequence& s)
 {
-  boost::shared_ptr<Sequence> 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<Sequence> s)
+void GlSeqBrowser::push_sequence(SequenceRef s)
 {
-  boost::shared_ptr<GlSequence> 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<GlSequence> new_gs(new GlSequence(gs));
+  GlSequenceRef new_gs(new GlSequence(gs));
   push_sequence(new_gs);
 }
 
-void GlSeqBrowser::push_sequence(boost::shared_ptr<GlSequence> 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<boost::shared_ptr<GlSequence> >& GlSeqBrowser::sequences() const
+const std::vector<GlSequenceRef >& GlSeqBrowser::sequences() const
 {
   return track_container;
 }
@@ -450,11 +463,10 @@ list<TrackRegion> GlSeqBrowser::selectedTracks() const
 
 //! copy sequence from selected track using formating function
 template<class Item>
-void GlSeqBrowser::copySelectedTracks(std::list<Item>& result, 
-             Item (*formatter)(boost::shared_ptr<Sequence> s, 
-                               int left, 
-                               int right))
+size_t GlSeqBrowser::copySelectedTracks(std::list<Item>& 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();
@@ -468,30 +480,30 @@ void GlSeqBrowser::copySelectedTracks(std::list<Item>& result,
            << endl;
     } else {
       // we should be safe
-      boost::shared_ptr<Sequence> 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<std::string> result;
   struct AsFasta {
-    static string formatter(boost::shared_ptr<Sequence> 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<string>::iterator result_i = result.begin();
        result_i != result.end();
@@ -499,52 +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<Sequence>& result)
+size_t GlSeqBrowser::copySelectedTracksAsSequences(std::list<Sequence>& result)
 {
   struct AsSequence {
-    static Sequence formatter(boost::shared_ptr<Sequence> 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<SequenceLocation>& result)
 {
   struct AsSeqLocation {
-    static SequenceLocation formatter(boost::shared_ptr<Sequence> 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<string> result;
   struct AsString {
-    static string formatter(boost::shared_ptr<Sequence> 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<string>::iterator result_i = result.begin();
        result_i != result.end();
@@ -552,7 +565,7 @@ void GlSeqBrowser::copySelectedTracksAsString(std::string& copy_buffer)
   {
     copy_buffer.append(*result_i);
   }
-
+  return base_pairs_copied;
 }
 
 void GlSeqBrowser::centerOnPath(const vector<int>& paths)
@@ -689,12 +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 {