X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=alg%2Fglseqbrowser.cpp;h=107099bd824105df653a994699472f3a122cf2fb;hb=55f0a3e9612b3e1df2c588682d7f605203eab421;hp=e9d55b985571fa2785fca31c10ee480bc8cefbd6;hpb=7d4fbcb6060a60a8ea25ca1303fcaaaf8574f24a;p=mussa.git

diff --git a/alg/glseqbrowser.cpp b/alg/glseqbrowser.cpp
index e9d55b9..107099b 100644
--- a/alg/glseqbrowser.cpp
+++ b/alg/glseqbrowser.cpp
@@ -308,14 +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()
@@ -336,32 +336,36 @@ void GlSeqBrowser::clear_selection()
 
 void GlSeqBrowser::push_sequence(const Sequence& s)
 {
-  GlSequence gs(s, 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;
 }