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Mark real sequence instead of Ns
[mussa.git]
/
alg
/
glseqbrowser.cpp
diff --git
a/alg/glseqbrowser.cpp
b/alg/glseqbrowser.cpp
index e9d55b985571fa2785fca31c10ee480bc8cefbd6..107099bd824105df653a994699472f3a122cf2fb 100644
(file)
--- a/
alg/glseqbrowser.cpp
+++ b/
alg/glseqbrowser.cpp
@@
-308,14
+308,14
@@
double GlSeqBrowser::zoom() const
return zoom_level;
}
return zoom_level;
}
-void GlSeqBrowser::setColorMapper(
boost::shared_ptr<AnnotationColors>
cm)
+void GlSeqBrowser::setColorMapper(
AnnotationColorsRef
cm)
{
color_mapper = cm;
}
{
color_mapper = cm;
}
-const AnnotationColors
&
GlSeqBrowser::colorMapper()
+const AnnotationColors
Ref
GlSeqBrowser::colorMapper()
{
{
- return
*
color_mapper;
+ return color_mapper;
}
void GlSeqBrowser::clear()
}
void GlSeqBrowser::clear()
@@
-336,32
+336,36
@@
void GlSeqBrowser::clear_selection()
void GlSeqBrowser::push_sequence(const Sequence& s)
{
void GlSeqBrowser::push_sequence(const Sequence& s)
{
- GlSequence
gs(s, color_mapper
);
+ GlSequence
Ref gs(new GlSequence(s, color_mapper)
);
push_sequence(gs);
}
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)
{
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);
}
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();
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());
}
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;
}
{
return track_container;
}