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Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4
[jalview.git]
/
src
/
jalview
/
gui
/
TreeCanvas.java
diff --git
a/src/jalview/gui/TreeCanvas.java
b/src/jalview/gui/TreeCanvas.java
index
efa23bd
..
55ce44a
100755
(executable)
--- a/
src/jalview/gui/TreeCanvas.java
+++ b/
src/jalview/gui/TreeCanvas.java
@@
-1148,14
+1148,22
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
if (aa != null)
{
ContactMatrixI cm = av.getContactMatrix(aa);
if (aa != null)
{
ContactMatrixI cm = av.getContactMatrix(aa);
+ // generally, we assume cm has 1:1 mapping to annotation row - probably wrong
+ // but.. if
if (cm instanceof MappableContactMatrixI)
{
if (cm instanceof MappableContactMatrixI)
{
+ int[] pos;
+ // use the mappable's mapping - always the case for PAE Matrices so good
+ // for 2.11.3
MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
- int pos[]=mcm.getMappedPositionsFor(rseq, colm+1);
- if (pos!=null)
+ pos = mcm.getMappedPositionsFor(rseq, colm + 1);
+ // finally, look up the position of the column
+ if (pos != null)
{
{
- offp=rseq.findIndex(pos[0]);
+ offp = rseq.findIndex(pos[0]);
}
}
+ } else {
+ offp = colm;
}
}
if (offp<=0)
}
}
if (offp<=0)
@@
-1262,6
+1270,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
}
}
}
}
}
+ PaintRefresher.Refresh(tp, av.getSequenceSetId());
}
public void createSeqGroupFor(AlignmentPanel[] aps, Vector<BinaryNode> l,
}
public void createSeqGroupFor(AlignmentPanel[] aps, Vector<BinaryNode> l,