/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.util.*;
-
import java.awt.*;
import java.awt.event.*;
import java.awt.print.*;
+
import javax.swing.*;
-import jalview.analysis.*;
import jalview.datamodel.*;
import jalview.jbgui.*;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
+import jalview.viewmodel.PCAModel;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class PCAPanel
- extends GPCAPanel implements Runnable
+public class PCAPanel extends GPCAPanel implements Runnable,
+ IProgressIndicator
{
- PCA pca;
- int top;
+
RotatableCanvas rc;
+
AlignmentPanel ap;
+
AlignViewport av;
- AlignmentView seqstrings;
- SequenceI[] seqs;
+
+ PCAModel pcaModel;
+
+ int top = 0;
/**
* Creates a new PCAPanel object.
- *
- * @param av DOCUMENT ME!
- * @param s DOCUMENT ME!
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param s
+ * DOCUMENT ME!
*/
public PCAPanel(AlignmentPanel ap)
{
this.ap = ap;
boolean sameLength = true;
-
- seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
- if (av.getSelectionGroup() == null)
+ 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.alignment.getSequencesArray();
+ seqs = av.getAlignment().getSequencesArray();
}
else
{
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
}
SeqCigar sq[] = seqstrings.getSequences();
int length = sq[0].getWidth();
if (!sameLength)
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- "The sequences must be aligned before calculating PCA.\n" +
- "Try using the Pad function in the edit menu,\n" +
- "or one of the multiple sequence alignment web services.",
- "Sequences not aligned",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ "The sequences must be aligned before calculating PCA.\n"
+ + "Try using the Pad function in the edit menu,\n"
+ + "or one of the multiple sequence alignment web services.",
+ "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
return;
}
-
- Desktop.addInternalFrame(this, "Principal component analysis",
- 400, 400);
-
+ pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
PaintRefresher.Register(this, av.getSequenceSetId());
rc = new RotatableCanvas(ap);
Thread worker = new Thread(this);
worker.start();
}
-
+ @Override
+ protected void scoreMatrix_menuSelected()
+ {
+ scoreMatrixMenu.removeAll();
+ for (final String sm:ResidueProperties.scoreMatrices.keySet())
+ {
+ if (ResidueProperties.getScoreMatrix(sm) != 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())
+ {
+ final PCAPanel us = this;
+ jm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (!pcaModel.getScore_matrix().equals((String) sm))
+ {
+ pcaModel.setScore_matrix((String) sm);
+ Thread worker = new Thread(us);
+ worker.start();
+ }
+ }
+ });
+ scoreMatrixMenu.add(jm);
+ }
+ }
+ }
+ }
public void bgcolour_actionPerformed(ActionEvent e)
{
Color col = JColorChooser.showDialog(this, "Select Background Colour",
- rc.bgColour);
+ rc.bgColour);
if (col != null)
{
*/
public void run()
{
+ long progId = System.currentTimeMillis();
+ IProgressIndicator progress = this;
+ String message = "Recalculating PCA";
+ if (getParent() == null)
+ {
+ progress = ap.alignFrame;
+ message = "Calculating PCA";
+ }
+ progress.setProgressBar(message, progId);
try
{
- pca = new PCA(seqstrings.getSequenceStrings(' '));
- pca.run();
-
- // Now find the component coordinates
- int ii = 0;
-
- while ( (ii < seqs.length) && (seqs[ii] != null))
- {
- ii++;
- }
-
- double[][] comps = new double[ii][ii];
-
- for (int i = 0; i < ii; i++)
- {
- if (pca.getEigenvalue(i) > 1e-4)
- {
- comps[i] = pca.component(i);
- }
- }
-
- //////////////////
+ calcSettings.setEnabled(false);
+ pcaModel.run();
+ // ////////////////
xCombobox.setSelectedIndex(0);
yCombobox.setSelectedIndex(1);
zCombobox.setSelectedIndex(2);
- top = pca.getM().rows - 1;
+ pcaModel.updateRc(rc);
+ // rc.invalidate();
+ nuclSetting.setSelected(pcaModel.isNucleotide());
+ protSetting.setSelected(!pcaModel.isNucleotide());
+ jvVersionSetting.setSelected(pcaModel.isJvCalcMode());
+ top = pcaModel.getTop();
- Vector points = new Vector();
- float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
+ } catch (OutOfMemoryError er)
+ {
+ new OOMWarning("calculating PCA", er);
+ return;
+ } finally
+ {
+ progress.setProgressBar("", progId);
+ }
+ calcSettings.setEnabled(true);
+ repaint();
+ if (getParent() == null)
+ {
+ addKeyListener(rc);
+ Desktop.addInternalFrame(this, MessageManager.getString("label.principal_component_analysis"), 475,
+ 450);
+ }
+ }
- for (int i = 0; i < pca.getM().rows; i++)
- {
- SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
- points.addElement(sp);
- }
+ @Override
+ protected void nuclSetting_actionPerfomed(ActionEvent arg0)
+ {
+ if (!pcaModel.isNucleotide())
+ {
+ pcaModel.setNucleotide(true);
+ pcaModel.setScore_matrix("DNA");
+ Thread worker = new Thread(this);
+ worker.start();
+ }
- rc.setPoints(points, pca.getM().rows);
- rc.repaint();
+ }
- addKeyListener(rc);
+ @Override
+ protected void protSetting_actionPerfomed(ActionEvent arg0)
+ {
- }
- catch (OutOfMemoryError er)
+ if (pcaModel.isNucleotide())
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of memory calculating PCA!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- JOptionPane.WARNING_MESSAGE);
- System.out.println("PCAPanel: " + er);
- System.gc();
-
+ pcaModel.setNucleotide(false);
+ pcaModel.setScore_matrix("BLOSUM62");
+ 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();
}
/**
int dim1 = top - xCombobox.getSelectedIndex();
int dim2 = top - yCombobox.getSelectedIndex();
int dim3 = top - zCombobox.getSelectedIndex();
-
- float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
-
- for (int i = 0; i < pca.getM().rows; i++)
- {
- ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];
- }
-
+ pcaModel.updateRcView(dim1, dim2, dim3);
rc.img = null;
rc.rotmat.setIdentity();
rc.initAxes();
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void xCombobox_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void yCombobox_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void zCombobox_actionPerformed(ActionEvent e)
{
public void outputValues_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
- Desktop.addInternalFrame(cap, "PCA details", 500,
- 500);
-
- cap.setText(pca.getDetails());
+ try
+ {
+ cap.setText(pcaModel.getDetails());
+ Desktop.addInternalFrame(cap, MessageManager.getString("label.pca_details"), 500, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("opening PCA details", oom);
+ cap.dispose();
+ }
}
public void showLabels_actionPerformed(ActionEvent e)
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 (seqstrings == null)
+ // 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 warrant a new window to be created
- // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+ // decide if av alignment is sufficiently different to original data to
+ // warrant a new window to be created
+ // create new alignmnt window with hidden regions (unhiding hidden regions
+ // yields unaligned seqs)
// or create a selection box around columns in alignment view
// test Alignment(SeqCigar[])
char gc = '-';
- try {
+ try
+ {
// we try to get the associated view's gap character
// but this may fail if the view was closed...
- gc = av.
- getGapCharacter();
- } catch (Exception ex) {};
- Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc);
+ gc = av.getGapCharacter();
+ } catch (Exception ex)
+ {
+ }
+ ;
+ Object[] alAndColsel = pcaModel.getSeqtrings()
+ .getAlignmentAndColumnSelection(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;
+ Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+ Alignment 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,
+ (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
- //>>>This is a fix for the moment, until a better solution is found!!<<<
+ // >>>This is a fix for the moment, until a better solution is
+ // found!!<<<
// af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
- // af.addSortByOrderMenuItem(ServiceName + " Ordering",
- // msaorder);
+ // af.addSortByOrderMenuItem(ServiceName + " Ordering",
+ // msaorder);
- Desktop.addInternalFrame(af, "Original Data for " + this.title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, MessageManager.formatMessage("label.original_data_for_params", new String[]{this.title}),
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
}
- /* CutAndPasteTransfer cap = new CutAndPasteTransfer();
- for (int i = 0; i < seqs.length; i++)
- {
- cap.appendText(new jalview.util.Format("%-" + 15 + "s").form(
- seqs[i].getName()));
- cap.appendText(" " + seqstrings[i] + "\n");
-
- }
-
- Desktop.addInternalFrame(cap, "Original Data",
- 400, 400);
+ /*
+ * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
+ * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
+ * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
+ * "\n"); }
+ *
+ * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
*/
}
- class PCAPrinter
- extends Thread implements Printable
+ class PCAPrinter extends Thread implements Printable
{
public void run()
{
try
{
printJob.print();
- }
- catch (Exception PrintException)
+ } catch (Exception PrintException)
{
PrintException.printStackTrace();
}
}
public int print(Graphics pg, PageFormat pf, int pi)
- throws PrinterException
+ throws PrinterException
{
- pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+ pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
rc.drawBackground(pg, rc.bgColour);
rc.drawScene(pg);
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void eps_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void png_actionPerformed(ActionEvent e)
{
if (type == jalview.util.ImageMaker.PNG)
{
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.PNG,
- "Make PNG image from PCA",
- width, height,
- null, null);
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
+ "Make PNG image from PCA", width, height, null, null);
}
else
{
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.EPS,
- "Make EPS file from PCA",
- width, height,
- null, this.getTitle());
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+ "Make EPS file from PCA", width, height, null,
+ this.getTitle());
}
if (im.getGraphics() != null)
}
}
+
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);
}
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
+ * )
+ */
+ protected void outputPoints_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ try
+ {
+ 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);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("exporting PCA points", oom);
+ cap.dispose();
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ protected void outputProjPoints_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ try
+ {
+ cap.setText(pcaModel.getPointsasCsv(true,
+ xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
+ zCombobox.getSelectedIndex()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage("label.transformed_points_for_params", new String[]{this.getTitle()}),
+ 500, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("exporting transformed PCA points", oom);
+ cap.dispose();
+ }
+ }
+
+ // methods for implementing IProgressIndicator
+ // need to refactor to a reusable stub class
+ Hashtable progressBars, progressBarHandlers;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+ */
+ @Override
+ public void setProgressBar(String message, long id)
+ {
+ if (progressBars == null)
+ {
+ progressBars = new Hashtable();
+ progressBarHandlers = new Hashtable();
+ }
+
+ JPanel progressPanel;
+ Long lId = new Long(id);
+ GridLayout layout = (GridLayout) statusPanel.getLayout();
+ if (progressBars.get(lId) != null)
+ {
+ progressPanel = (JPanel) progressBars.get(new Long(id));
+ statusPanel.remove(progressPanel);
+ progressBars.remove(lId);
+ progressPanel = null;
+ if (message != null)
+ {
+ statusBar.setText(message);
+ }
+ if (progressBarHandlers.contains(lId))
+ {
+ progressBarHandlers.remove(lId);
+ }
+ layout.setRows(layout.getRows() - 1);
+ }
+ else
+ {
+ progressPanel = new JPanel(new BorderLayout(10, 5));
+
+ JProgressBar progressBar = new JProgressBar();
+ progressBar.setIndeterminate(true);
+
+ progressPanel.add(new JLabel(message), BorderLayout.WEST);
+ progressPanel.add(progressBar, BorderLayout.CENTER);
+
+ layout.setRows(layout.getRows() + 1);
+ statusPanel.add(progressPanel);
+
+ progressBars.put(lId, progressPanel);
+ }
+ // update GUI
+ // setMenusForViewport();
+ validate();
+ }
+
+ @Override
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
+ {
+ if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+ {
+ throw new Error(
+ "call setProgressBar before registering the progress bar's handler.");
+ }
+ progressBarHandlers.put(new Long(id), handler);
+ final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+ if (handler.canCancel())
+ {
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+ final IProgressIndicator us = this;
+ cancel.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ handler.cancelActivity(id);
+ us.setProgressBar(
+ "Cancelled "
+ + ((JLabel) progressPanel.getComponent(0))
+ .getText(), id);
+ }
+ });
+ progressPanel.add(cancel, BorderLayout.EAST);
+ }
+ }
+
+ /**
+ *
+ * @return true if any progress bars are still active
+ */
+ @Override
+ public boolean operationInProgress()
+ {
+ if (progressBars != null && progressBars.size() > 0)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ @Override
+ protected void resetButton_actionPerformed(ActionEvent e)
+ {
+ int t = top;
+ top = 0; // ugly - prevents dimensionChanged events from being processed
+ xCombobox.setSelectedIndex(0);
+ yCombobox.setSelectedIndex(1);
+ top = t;
+ zCombobox.setSelectedIndex(2);
+ }
}
git://source.jalview.org / jalview.git / blobdiff