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:
e122bcd
)
JAL-4134 - store colours in annotation row, so colour by annotation can be used to...
author
James Procter
<j.procter@dundee.ac.uk>
Fri, 24 Mar 2023 13:29:40 +0000
(13:29 +0000)
committer
James Procter
<j.procter@dundee.ac.uk>
Fri, 24 Mar 2023 13:29:50 +0000
(13:29 +0000)
src/jalview/gui/TreeCanvas.java
patch
|
blob
|
history
diff --git
a/src/jalview/gui/TreeCanvas.java
b/src/jalview/gui/TreeCanvas.java
index
29826f0
..
8de161f
100755
(executable)
--- a/
src/jalview/gui/TreeCanvas.java
+++ b/
src/jalview/gui/TreeCanvas.java
@@
-54,6
+54,7
@@
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactMatrixI;
@@
-1028,6
+1029,21
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
cm.setColorForGroup(gp, colors.get(gp));
}
}
cm.setColorForGroup(gp, colors.get(gp));
}
}
+ // stash colors in linked annotation row.
+ // doesn't work yet. TESTS!
+ int sstart=aa.sequenceRef!=null ? aa.sequenceRef.getStart()-1 : 0;
+ for (BitSet gp : colors.keySet())
+ {
+ Color gpcol = colors.get(gp);
+ for (int p = gp.nextSetBit(0); p >= 0; p = gp.nextSetBit(p + 1))
+ {
+ Annotation ae = aa.getAnnotationForPosition(p+sstart);
+ if (ae != null)
+ {
+ ae.colour = gpcol.brighter().darker();
+ }
+ }
+ }
}
}
}
}