*/
package jalview.gui;
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.ScoreModelI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GPCAPanel;
-import jalview.schemes.ResidueProperties;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.PCAModel;
protected void scoreMatrix_menuSelected()
{
scoreMatrixMenu.removeAll();
- for (final String sm : ResidueProperties.scoreMatrices.keySet())
+ for (ScoreModelI sm : ScoreModels.getInstance().getModels())
{
- if (ResidueProperties.getScoreMatrix(sm) != null)
+ if (sm instanceof ScoreMatrix)
{
+ final String name = sm.getName();
// 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())
+ name));
+ jm.setSelected(pcaModel.getScore_matrix().equals(name));
+ if ((!pcaModel.isNucleotide() && !sm.isDNA())
+ || (pcaModel.isNucleotide() && sm.isDNA()))
{
- final PCAPanel us = this;
jm.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- if (!pcaModel.getScore_matrix().equals(sm))
+ if (!pcaModel.getScore_matrix().equals(name))
{
- pcaModel.setScore_matrix(sm);
- Thread worker = new Thread(us);
+ pcaModel.setScore_matrix(name);
+ Thread worker = new Thread(PCAPanel.this);
worker.start();
}
}