/**
* use the identity matrix for calculating similarity between sequences.
*/
- private boolean useidentity=false;
+ private boolean nucleotide=false;
/**
* Creates a new PCAPanel object.
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();
try
{
calcSettings.setEnabled(false);
- pca = new PCA(seqstrings.getSequenceStrings(' '), useidentity);
+ pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide);
pca.run();
// Now find the component coordinates
rc.repaint();
addKeyListener(rc);
+ nuclSetting.setSelected(nucleotide);
+ protSetting.setSelected(!nucleotide);
} catch (OutOfMemoryError er)
{
@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)
{
- useidentity=false;
+ nucleotide=false;
Thread worker = new Thread(this);
worker.start();
}
protected JMenu associateViewsMenu = new JMenu();
protected JMenu calcSettings=new JMenu();
- JMenuItem nuclSetting=new JMenuItem();
- JMenuItem protSetting=new JMenuItem();
+ protected JCheckBoxMenuItem nuclSetting=new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem protSetting=new JCheckBoxMenuItem();
public GPCAPanel()
{
try