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JAL-1013 - rename nucleotide and ensure current calculation score model reflected...
[jalview.git]
/
src
/
jalview
/
gui
/
PCAPanel.java
diff --git
a/src/jalview/gui/PCAPanel.java
b/src/jalview/gui/PCAPanel.java
index
eec9b6d
..
e3959ea
100755
(executable)
--- a/
src/jalview/gui/PCAPanel.java
+++ b/
src/jalview/gui/PCAPanel.java
@@
-54,7
+54,7
@@
public class PCAPanel extends GPCAPanel implements Runnable
/**
* use the identity matrix for calculating similarity between sequences.
*/
/**
* use the identity matrix for calculating similarity between sequences.
*/
- private boolean useidentity=false;
+ private boolean nucleotide=false;
/**
* Creates a new PCAPanel object.
/**
* Creates a new PCAPanel object.
@@
-72,7
+72,7
@@
public class PCAPanel extends GPCAPanel implements Runnable
boolean sameLength = true;
seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
boolean sameLength = true;
seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
- useidentity=av.getAlignment().isNucleotide();
+ nucleotide=av.getAlignment().isNucleotide();
if (av.getSelectionGroup() == null)
{
seqs = av.alignment.getSequencesArray();
if (av.getSelectionGroup() == null)
{
seqs = av.alignment.getSequencesArray();
@@
-136,7
+136,7
@@
public class PCAPanel extends GPCAPanel implements Runnable
try
{
calcSettings.setEnabled(false);
try
{
calcSettings.setEnabled(false);
- pca = new PCA(seqstrings.getSequenceStrings(' '), useidentity);
+ pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide);
pca.run();
// Now find the component coordinates
pca.run();
// Now find the component coordinates
@@
-177,6
+177,8
@@
public class PCAPanel extends GPCAPanel implements Runnable
rc.repaint();
addKeyListener(rc);
rc.repaint();
addKeyListener(rc);
+ nuclSetting.setSelected(nucleotide);
+ protSetting.setSelected(!nucleotide);
} catch (OutOfMemoryError er)
{
} catch (OutOfMemoryError er)
{
@@
-188,14
+190,14
@@
public class PCAPanel extends GPCAPanel implements Runnable
@Override
protected void nuclSetting_actionPerfomed(ActionEvent arg0)
{
@Override
protected void nuclSetting_actionPerfomed(ActionEvent arg0)
{
- useidentity=true;
+ nucleotide=true;
Thread worker = new Thread(this);
worker.start();
}
@Override
protected void protSetting_actionPerfomed(ActionEvent arg0)
{
Thread worker = new Thread(this);
worker.start();
}
@Override
protected void protSetting_actionPerfomed(ActionEvent arg0)
{
- useidentity=false;
+ nucleotide=false;
Thread worker = new Thread(this);
worker.start();
}
Thread worker = new Thread(this);
worker.start();
}