package jalview.gui;
import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
import jalview.api.analysis.ViewBasedAnalysisI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GPCAPanel;
import jalview.util.MessageManager;
int top = 0;
/**
- * Creates a new PCAPanel object.
+ * Creates a new PCAPanel object using default score model and parameters
*
- * @param av
- * DOCUMENT ME!
- * @param s
- * DOCUMENT ME!
+ * @param alignPanel
+ */
+ public PCAPanel(AlignmentPanel alignPanel)
+ {
+ this(alignPanel, ScoreModels.getInstance().getDefaultModel(
+ !alignPanel.av.getAlignment().isNucleotide()),
+ SimilarityParams.SeqSpace);
+ }
+
+ /**
+ * Constructor given sequence data, a similarity (or distance) score model,
+ * and score calculation parameters
+ *
+ * @param alignPanel
+ * @param scoreModel
+ * @param params
*/
- public PCAPanel(AlignmentPanel ap)
+ public PCAPanel(AlignmentPanel alignPanel, ScoreModelI scoreModel,
+ SimilarityParamsI params)
{
super();
- this.av = ap.av;
- this.ap = ap;
+ this.av = alignPanel.av;
+ this.ap = alignPanel;
+ boolean nucleotide = av.getAlignment().isNucleotide();
progressBar = new ProgressBar(statusPanel, statusBar);
- boolean sameLength = true;
+ addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent e)
+ {
+ close_actionPerformed();
+ }
+ });
+
boolean selected = av.getSelectionGroup() != null
&& av.getSelectionGroup().getSize() > 0;
AlignmentView seqstrings = av.getAlignmentView(selected);
- boolean nucleotide = av.getAlignment().isNucleotide();
SequenceI[] seqs;
if (!selected)
{
{
seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
}
- SeqCigar sq[] = seqstrings.getSequences();
- int length = sq[0].getWidth();
-
- for (int i = 0; i < seqs.length; i++)
- {
- if (sq[i].getWidth() != length)
- {
- sameLength = false;
- break;
- }
- }
-
- if (!sameLength)
- {
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.getString("label.pca_sequences_not_aligned"),
- MessageManager.getString("label.sequences_not_aligned"),
- JvOptionPane.WARNING_MESSAGE);
-
- return;
- }
- addInternalFrameListener(new InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(InternalFrameEvent e)
- {
- close_actionPerformed();
- }
- });
-
- pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
+ pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
+ params);
PaintRefresher.Register(this, av.getSequenceSetId());
- rc = new RotatableCanvas(ap);
+ rc = new RotatableCanvas(alignPanel);
this.getContentPane().add(rc, BorderLayout.CENTER);
Thread worker = new Thread(this);
worker.start();
for (final ScoreModelI sm : ScoreModels.getInstance().getModels())
{
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_",
- name));
+ JCheckBoxMenuItem jm = new JCheckBoxMenuItem(name);
+
+ /*
+ * if the score model doesn't provide a description, try to look one
+ * up in the text bundle, falling back on its name
+ */
+ String tooltip = sm.getDescription();
+ if (tooltip == null)
+ {
+ tooltip = MessageManager.getStringOrReturn("label.score_model_",
+ name);
+ }
+ jm.setToolTipText(tooltip);
jm.setSelected(pcaModel.getScoreModelName().equals(name));
if ((pcaModel.isNucleotide() && sm.isDNA())
|| (!pcaModel.isNucleotide() && sm.isProtein()))
// rc.invalidate();
nuclSetting.setSelected(pcaModel.isNucleotide());
protSetting.setSelected(!pcaModel.isNucleotide());
- jvVersionSetting.setSelected(pcaModel.isJvCalcMode());
top = pcaModel.getTop();
} catch (OutOfMemoryError er)
}
}
- @Override
- protected void jvVersionSetting_actionPerfomed(ActionEvent arg0)
- {
- pcaModel.setJvCalcMode(jvVersionSetting.isSelected());
- Thread worker = new Thread(this);
- worker.start();
- }
-
/**
* DOCUMENT ME!
*/