/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
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);
+ }
}
}
}