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JAL-2344 now flagging formats as 'identifiable' instead of 'dynamic'
[jalview.git]
/
src
/
jalview
/
gui
/
PCAPanel.java
diff --git
a/src/jalview/gui/PCAPanel.java
b/src/jalview/gui/PCAPanel.java
index
47add28
..
4f5a018
100644
(file)
--- a/
src/jalview/gui/PCAPanel.java
+++ b/
src/jalview/gui/PCAPanel.java
@@
-21,6
+21,7
@@
package jalview.gui;
import jalview.datamodel.Alignment;
package jalview.gui;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SeqCigar;
@@
-113,10
+114,10
@@
public class PCAPanel extends GPCAPanel implements Runnable,
if (!sameLength)
{
if (!sameLength)
{
- JOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.getString("label.pca_sequences_not_aligned"),
MessageManager.getString("label.sequences_not_aligned"),
MessageManager.getString("label.pca_sequences_not_aligned"),
MessageManager.getString("label.sequences_not_aligned"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
return;
}
@@
-139,8
+140,8
@@
public class PCAPanel extends GPCAPanel implements Runnable,
{
// create an entry for this score matrix for use in PCA
JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
{
// create an entry for this score matrix for use in PCA
JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
- jm.setText(MessageManager
- .getStringOrReturn("label.score_model", sm));
+ 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())
jm.setSelected(pcaModel.getScore_matrix().equals(sm));
if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
.get(sm).isProtein())
@@
-383,8
+384,8
@@
public class PCAPanel extends GPCAPanel implements Runnable,
{
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
{
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
- Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
- Alignment dataset = (av != null && av.getAlignment() != null) ? av
+ AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
+ AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
.getAlignment().getDataset() : null;
if (dataset != null)
{
.getAlignment().getDataset() : null;
if (dataset != null)
{