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JAL-1473 exclude score models not compatible with PCA algorithm
author
Jim Procter
<jprocter@dundee.ac.uk>
Tue, 3 Jun 2014 13:29:45 +0000
(14:29 +0100)
committer
Jim Procter
<jprocter@dundee.ac.uk>
Tue, 3 Jun 2014 13:29:45 +0000
(14:29 +0100)
src/jalview/gui/PCAPanel.java
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diff --git
a/src/jalview/gui/PCAPanel.java
b/src/jalview/gui/PCAPanel.java
index
d1216b9
..
133c0ce
100644
(file)
--- a/
src/jalview/gui/PCAPanel.java
+++ b/
src/jalview/gui/PCAPanel.java
@@
-116,26
+116,34
@@
public class PCAPanel extends GPCAPanel implements Runnable,
scoreMatrixMenu.removeAll();
for (final String sm:ResidueProperties.scoreMatrices.keySet())
{
scoreMatrixMenu.removeAll();
for (final String sm:ResidueProperties.scoreMatrices.keySet())
{
- JCheckBoxMenuItem jm=new JCheckBoxMenuItem();
- jm.setText(MessageManager.getStringOrReturn("label.score_model", sm));
- jm.setSelected(pcaModel.getScore_matrix().equals(sm));
- if (pcaModel.isNucleotide()==ResidueProperties.scoreMatrices.get(sm).isDNA())
+ if (ResidueProperties.getScoreMatrix(sm) != null)
{
{
- final PCAPanel us = this;
- jm.addActionListener(new ActionListener()
+ // create an entry for this score matrix for use in PCA
+ JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
+ jm.setText(MessageManager
+ .getStringOrReturn("label.score_model", sm));
+ jm.setSelected(pcaModel.getScore_matrix().equals(sm));
+ if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
+ .get(sm).isProtein())
+ || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices
+ .get(sm).isDNA())
{
{
- @Override
- public void actionPerformed(ActionEvent e)
+ final PCAPanel us = this;
+ jm.addActionListener(new ActionListener()
{
{
- if (!pcaModel.getScore_matrix().equals((String) sm))
+ @Override
+ public void actionPerformed(ActionEvent e)
{
{
- pcaModel.setScore_matrix((String) sm);
- Thread worker = new Thread(us);
- worker.start();
+ if (!pcaModel.getScore_matrix().equals((String) sm))
+ {
+ pcaModel.setScore_matrix((String) sm);
+ Thread worker = new Thread(us);
+ worker.start();
+ }
}
}
- }
- });
- scoreMatrixMenu.add(jm);
+ });
+ scoreMatrixMenu.add(jm);
+ }
}
}
}
}
}
}