*/
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.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GPCAPanel;
-import jalview.schemes.ResidueProperties;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.PCAModel;
import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
import javax.swing.JRadioButtonMenuItem;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
/**
* DOCUMENT ME!
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 ap)
+ public PCAPanel(AlignmentPanel alignPanel)
{
- this.av = ap.av;
- this.ap = ap;
+ 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 alignPanel, ScoreModelI scoreModel,
+ SimilarityParamsI params)
+ {
+ super();
+ 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)
+ // TODO can we allow PCA on unaligned data given choice of
+ // similarity measure parameters?
+ if (!checkAligned(seqstrings))
{
JvOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.getString("label.pca_sequences_not_aligned"),
return;
}
- 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();
}
- @Override
- protected void scoreMatrix_menuSelected()
+ /**
+ * Answers true if all sequences have the same aligned length, else false
+ *
+ * @param seqstrings
+ * @return
+ */
+ protected boolean checkAligned(AlignmentView seqstrings)
{
- scoreMatrixMenu.removeAll();
- for (final String sm : ResidueProperties.scoreMatrices.keySet())
+ SeqCigar sq[] = seqstrings.getSequences();
+ int length = sq[0].getWidth();
+ boolean sameLength = true;
+ for (int i = 0; i < sq.length; i++)
{
- if (ResidueProperties.getScoreMatrix(sm) != null)
+ if (sq[i].getWidth() != length)
{
- // 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())
+ sameLength = false;
+ break;
+ }
+ }
+ return sameLength;
+ }
+
+ /**
+ * Ensure references to potentially very large objects (the PCA matrices) are
+ * nulled when the frame is closed
+ */
+ protected void close_actionPerformed()
+ {
+ pcaModel = null;
+ }
+
+ /**
+ * Repopulate the options and actions under the score model menu when it is
+ * selected. Options will depend on whether 'nucleotide' or 'peptide'
+ * modelling is selected (and also possibly on whether any additional score
+ * models have been added).
+ */
+ @Override
+ protected void scoreModel_menuSelected()
+ {
+ scoreModelMenu.removeAll();
+ for (final ScoreModelI sm : ScoreModels.getInstance().getModels())
+ {
+ final String name = sm.getName();
+ 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()))
+ {
+ jm.addActionListener(new ActionListener()
{
- final PCAPanel us = this;
- jm.addActionListener(new ActionListener()
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- @Override
- public void actionPerformed(ActionEvent e)
+ if (!pcaModel.getScoreModelName().equals(name))
{
- if (!pcaModel.getScore_matrix().equals(sm))
- {
- pcaModel.setScore_matrix(sm);
- Thread worker = new Thread(us);
- worker.start();
- }
+ ScoreModelI sm2 = configureScoreModel(sm);
+ pcaModel.setScoreModel(sm2);
+ Thread worker = new Thread(PCAPanel.this);
+ worker.start();
}
- });
- scoreMatrixMenu.add(jm);
- }
+ }
+ });
+ scoreModelMenu.add(jm);
}
}
}
if (!pcaModel.isNucleotide())
{
pcaModel.setNucleotide(true);
- pcaModel.setScore_matrix("DNA");
+ pcaModel.setScoreModel(ScoreModels.getInstance().getDefaultModel(
+ false));
Thread worker = new Thread(this);
worker.start();
}
if (pcaModel.isNucleotide())
{
pcaModel.setNucleotide(false);
- pcaModel.setScore_matrix("BLOSUM62");
+ pcaModel.setScoreModel(ScoreModels.getInstance()
+ .getDefaultModel(true));
Thread worker = new Thread(this);
worker.start();
}
top = t;
zCombobox.setSelectedIndex(2);
}
+
+ /**
+ * If the score model is one that requires to get state data from the current
+ * view, allow it to do so
+ *
+ * @param sm
+ * @return
+ */
+ protected ScoreModelI configureScoreModel(ScoreModelI sm)
+ {
+ if (sm instanceof ViewBasedAnalysisI)
+ {
+ try
+ {
+ sm = sm.getClass().newInstance();
+ ((ViewBasedAnalysisI) sm).configureFromAlignmentView(ap);
+ } catch (Exception q)
+ {
+ Cache.log.error("Couldn't create a scoremodel instance for "
+ + sm.getName());
+ }
+ }
+ return sm;
+ }
}
git://source.jalview.org / jalview.git / blobdiff