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JAL-4134 efficiency improvement
author
James Procter
<j.procter@dundee.ac.uk>
Mon, 22 May 2023 15:05:17 +0000
(16:05 +0100)
committer
James Procter
<j.procter@dundee.ac.uk>
Mon, 22 May 2023 15:05:17 +0000
(16:05 +0100)
src/jalview/gui/TreeCanvas.java
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diff --git
a/src/jalview/gui/TreeCanvas.java
b/src/jalview/gui/TreeCanvas.java
index
f6b842d
..
bb028bf
100755
(executable)
--- a/
src/jalview/gui/TreeCanvas.java
+++ b/
src/jalview/gui/TreeCanvas.java
@@
-1160,6
+1160,16
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
return;
}
return;
}
+ // TODO - sort indices for faster lookup
+ ColumnSelection cs = av.getColumnSelection();
+ HiddenColumns hc = av.getAlignment().getHiddenColumns();
+ ContactMatrixI cm = av.getContactMatrix(tp.assocAnnotation);
+ MappableContactMatrixI mcm = null;
+ int offp;
+ if (cm instanceof MappableContactMatrixI)
+ {
+ mcm = (MappableContactMatrixI) cm;
+ }
for (BinaryNode bn : l)
{
int colm = -1;
for (BinaryNode bn : l)
{
int colm = -1;
@@
-1171,15
+1181,8
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
{
continue;
}
{
continue;
}
- // TODO - sort indices for faster lookup
- ColumnSelection cs = av.getColumnSelection();
- HiddenColumns hc = av.getAlignment().getHiddenColumns();
- ContactMatrixI cm = av.getContactMatrix(tp.assocAnnotation);
- MappableContactMatrixI mcm = null;
- int offp;
- if (cm instanceof MappableContactMatrixI)
+ if (mcm!=null)
{
{
- mcm = (MappableContactMatrixI) cm;
int[] seqpos = mcm.getMappedPositionsFor(
tp.assocAnnotation.sequenceRef, colm);
if (seqpos == null)
int[] seqpos = mcm.getMappedPositionsFor(
tp.assocAnnotation.sequenceRef, colm);
if (seqpos == null)