git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
53de002
)
JAL-1923 add groups to codon-complement and notify annotation update for all linked...
author
Jim Procter
<jprocter@issues.jalview.org>
Thu, 15 Oct 2015 12:59:22 +0000
(13:59 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Thu, 15 Oct 2015 12:59:22 +0000
(13:59 +0100)
src/jalview/gui/TreeCanvas.java
patch
|
blob
|
history
diff --git
a/src/jalview/gui/TreeCanvas.java
b/src/jalview/gui/TreeCanvas.java
index
68573ef
..
aa79451
100755
(executable)
--- a/
src/jalview/gui/TreeCanvas.java
+++ b/
src/jalview/gui/TreeCanvas.java
@@
-891,12
+891,13
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
aps[a].av.setSelectionGroup(null);
aps[a].av.getAlignment().deleteAllGroups();
aps[a].av.clearSequenceColours();
aps[a].av.setSelectionGroup(null);
aps[a].av.getAlignment().deleteAllGroups();
aps[a].av.clearSequenceColours();
- }
- if (av.getCodingComplement() != null)
- {
- av.getCodingComplement().setSelectionGroup(null);
- av.getCodingComplement().getAlignment().deleteAllGroups();
- av.getCodingComplement().clearSequenceColours();
+ if (aps[a].av.getCodingComplement() != null)
+ {
+ aps[a].av.getCodingComplement().setSelectionGroup(null);
+ aps[a].av.getCodingComplement().getAlignment()
+ .deleteAllGroups();
+ aps[a].av.getCodingComplement().clearSequenceColours();
+ }
}
colourGroups();
}
}
colourGroups();
}
@@
-977,41
+978,45
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
aps[a].av.getAlignment().addGroup(new SequenceGroup(sg));
}
aps[a].av.getAlignment().addGroup(new SequenceGroup(sg));
- }
-
- // TODO can we push all of the below into AlignViewportI?
- final AlignViewportI codingComplement = av.getCodingComplement();
- if (codingComplement != null)
- {
- SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
- codingComplement);
- if (mappedGroup.getSequences().size() > 0)
+ // TODO can we push all of the below into AlignViewportI?
+ final AlignViewportI codingComplement = aps[a].av
+ .getCodingComplement();
+ if (codingComplement != null)
{
{
- codingComplement.getAlignment().addGroup(mappedGroup);
- for (SequenceI seq : mappedGroup.getSequences())
+ if (codingComplement != null)
{
{
- codingComplement.setSequenceColour(seq, col.brighter());
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
+ av, codingComplement);
+ if (mappedGroup.getSequences().size() > 0)
+ {
+ codingComplement.getAlignment().addGroup(mappedGroup);
+ for (SequenceI seq : mappedGroup.getSequences())
+ {
+ codingComplement.setSequenceColour(seq, col.brighter());
+ }
+ }
}
}
}
}
}
}
}
}
- // notify the panel to redo any group specific stuff.
+ // notify the panel(s) to redo any group specific stuff.
for (int a = 0; a < aps.length; a++)
{
aps[a].updateAnnotation();
// TODO: JAL-868 - need to ensure view colour change message is broadcast
// to any Jmols listening in
for (int a = 0; a < aps.length; a++)
{
aps[a].updateAnnotation();
// TODO: JAL-868 - need to ensure view colour change message is broadcast
// to any Jmols listening in
- }
+ final AlignViewportI codingComplement = aps[a].av
+ .getCodingComplement();
+ if (codingComplement != null)
+ {
+ ((AlignViewport) codingComplement).getAlignPanel()
+ .updateAnnotation();
+
+ }
- if (av.getCodingComplement() != null)
- {
- ((AlignViewport) av.getCodingComplement()).getAlignPanel()
- .updateAnnotation();
- /*
- * idPanel. repaint ()
- */
}
}
+
}
/**
}
/**