/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
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.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SeqCigar;
+import jalview.datamodel.HiddenColumns;
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 java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JRadioButtonMenuItem;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class PCAPanel extends GPCAPanel implements Runnable,
- IProgressIndicator
+public class PCAPanel extends GPCAPanel
+ implements Runnable, IProgressIndicator
{
private IProgressIndicator progressBar;
PCAModel pcaModel;
+ private static final int MIN_WIDTH = 470;
+
+ private static final int MIN_HEIGHT = 250;
+
int top = 0;
+ private boolean working;
+
/**
- * 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())
+ .getName(),
+ SimilarityParams.SeqSpace);
+ }
+
+ /**
+ * Constructor given sequence data, a similarity (or distance) score model
+ * name, and score calculation parameters
+ *
+ * @param alignPanel
+ * @param modelName
+ * @param params
*/
- public PCAPanel(AlignmentPanel ap)
+ public PCAPanel(AlignmentPanel alignPanel, String modelName,
+ SimilarityParamsI params)
{
- this.av = ap.av;
- this.ap = ap;
+ 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)
- {
- JOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.getString("label.pca_sequences_not_aligned"),
- MessageManager.getString("label.sequences_not_aligned"),
- JOptionPane.WARNING_MESSAGE);
-
- return;
- }
- pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getScoreModel(modelName, ap);
+ 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();
}
+ /**
+ * 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 scoreMatrix_menuSelected()
+ protected void scoreModel_menuSelected()
{
- scoreMatrixMenu.removeAll();
- for (final String sm : ResidueProperties.scoreMatrices.keySet())
- {
- if (ResidueProperties.getScoreMatrix(sm) != null)
+ 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)
{
- // 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())
+ 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 = ScoreModels.getInstance()
+ .getScoreModel(name, ap);
+ pcaModel.setScoreModel(sm2);
+ Thread worker = new Thread(PCAPanel.this);
+ worker.start();
}
- });
- scoreMatrixMenu.add(jm);
- }
+ }
+ });
+ scoreModelMenu.add(jm);
}
}
}
+ @Override
public void bgcolour_actionPerformed(ActionEvent e)
{
Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_backgroud_colour"),
+ MessageManager.getString("label.select_background_colour"),
rc.bgColour);
if (col != null)
/**
* DOCUMENT ME!
*/
+ @Override
public void run()
{
long progId = System.currentTimeMillis();
message = MessageManager.getString("label.pca_calculating");
}
progress.setProgressBar(message, progId);
+ working = true;
try
{
calcSettings.setEnabled(false);
// rc.invalidate();
nuclSetting.setSelected(pcaModel.isNucleotide());
protSetting.setSelected(!pcaModel.isNucleotide());
- jvVersionSetting.setSelected(pcaModel.isJvCalcMode());
top = pcaModel.getTop();
} catch (OutOfMemoryError er)
{
new OOMWarning("calculating PCA", er);
+ working = false;
return;
} finally
{
addKeyListener(rc);
Desktop.addInternalFrame(this, MessageManager
.getString("label.principal_component_analysis"), 475, 450);
+ this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
+ working = false;
}
@Override
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();
}
}
- @Override
- protected void jvVersionSetting_actionPerfomed(ActionEvent arg0)
- {
- pcaModel.setJvCalcMode(jvVersionSetting.isSelected());
- Thread worker = new Thread(this);
- worker.start();
- }
-
/**
* DOCUMENT ME!
*/
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void xCombobox_actionPerformed(ActionEvent e)
{
doDimensionChange();
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void yCombobox_actionPerformed(ActionEvent e)
{
doDimensionChange();
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void zCombobox_actionPerformed(ActionEvent e)
{
doDimensionChange();
}
+ @Override
public void outputValues_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
}
}
+ @Override
public void showLabels_actionPerformed(ActionEvent e)
{
rc.showLabels(showLabels.getState());
}
+ @Override
public void print_actionPerformed(ActionEvent e)
{
PCAPrinter printer = new PCAPrinter();
printer.start();
}
+ @Override
public void originalSeqData_actionPerformed(ActionEvent e)
{
// this was cut'n'pasted from the equivalent TreePanel method - we should
// make this an abstract function of all jalview analysis windows
if (pcaModel.getSeqtrings() == null)
{
- jalview.bin.Cache.log
- .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+ jalview.bin.Cache.log.info(
+ "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
// decide if av alignment is sufficiently different to original data to
}
;
Object[] alAndColsel = pcaModel.getSeqtrings()
- .getAlignmentAndColumnSelection(gc);
+ .getAlignmentAndHiddenColumns(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
- Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
- Alignment dataset = (av != null && av.getAlignment() != null) ? av
- .getAlignment().getDataset() : null;
+ AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
+ AlignmentI dataset = (av != null && av.getAlignment() != null)
+ ? av.getAlignment().getDataset()
+ : null;
if (dataset != null)
{
al.setDataset(dataset);
if (true)
{
// make a new frame!
- AlignFrame af = new AlignFrame(al,
- (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
// msaorder);
Desktop.addInternalFrame(af, MessageManager.formatMessage(
- "label.original_data_for_params",
- new String[] { this.title }), AlignFrame.DEFAULT_WIDTH,
+ "label.original_data_for_params", new String[]
+ { this.title }), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
}
class PCAPrinter extends Thread implements Printable
{
+ @Override
public void run()
{
PrinterJob printJob = PrinterJob.getPrinterJob();
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+ PageFormat defaultPage = printJob.defaultPage();
+ PageFormat pf = printJob.pageDialog(defaultPage);
+
+ if (defaultPage == pf)
+ {
+ /*
+ * user cancelled
+ */
+ return;
+ }
printJob.setPrintable(this, pf);
}
}
+ @Override
public int print(Graphics pg, PageFormat pf, int pi)
throws PrinterException
{
* @param e
* DOCUMENT ME!
*/
+ @Override
public void eps_actionPerformed(ActionEvent e)
{
makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
* @param e
* DOCUMENT ME!
*/
+ @Override
public void png_actionPerformed(ActionEvent e)
{
makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
{
im = new jalview.util.ImageMaker(this,
jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
- width, height, null, null);
+ width, height, null, null, null, 0, false);
}
else if (type == jalview.util.ImageMaker.TYPE.EPS)
{
im = new jalview.util.ImageMaker(this,
jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
- width, height, null, this.getTitle());
+ width, height, null, this.getTitle(), null, 0, false);
}
else
{
im = new jalview.util.ImageMaker(this,
jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
- width, height, null, this.getTitle());
+ width, height, null, this.getTitle(), null, 0, false);
}
}
}
+ @Override
public void viewMenu_menuSelected()
{
buildAssociatedViewMenu();
void buildAssociatedViewMenu()
{
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
- .getSequenceSetId());
+ AlignmentPanel[] aps = PaintRefresher
+ .getAssociatedPanels(av.getSequenceSetId());
if (aps.length == 1 && rc.av == aps[0].av)
{
associateViewsMenu.setVisible(false);
associateViewsMenu.setVisible(true);
- if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+ if ((viewMenu
+ .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
{
viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
}
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
rc.applyToAllViews = false;
associateViewsMenu.add(item);
}
- final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+ final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
+ "All Views");
buttonGroup.add(itemf);
itemf.setSelected(rc.applyToAllViews);
itemf.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
rc.applyToAllViews = itemf.isSelected();
* jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
* )
*/
+ @Override
protected void outputPoints_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setText(pcaModel.getPointsasCsv(false,
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.points_for_params", new String[] { this.getTitle() }),
- 500, 500);
+ Desktop.addInternalFrame(cap, MessageManager
+ .formatMessage("label.points_for_params", new String[]
+ { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting PCA points", oom);
* jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
* .ActionEvent)
*/
+ @Override
protected void outputProjPoints_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.transformed_points_for_params",
- new String[] { this.getTitle() }), 500, 500);
+ "label.transformed_points_for_params", new String[]
+ { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting transformed PCA points", oom);
top = t;
zCombobox.setSelectedIndex(2);
}
+
+ /**
+ * Answers true if PCA calculation is in progress, else false
+ *
+ * @return
+ */
+ public boolean isWorking()
+ {
+ return working;
+ }
}
git://source.jalview.org / jalview.git / blobdiff