X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=254f5faef06f3aef64975256d0cfad4c3eb3f1ce;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=0941c7dcc18a92c011c965d65d40cc09e2e28ad2;hpb=c9cb2ef932ff18d9f0b7318df8b622e7d665f9ef;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java old mode 100755 new mode 100644 index 0941c7d..254f5fa --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,32 +1,35 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * 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 . + * 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! @@ -34,27 +37,19 @@ import jalview.jbgui.*; * @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; + PCAModel pcaModel; - SequenceI[] seqs; - - /** - * use the identity matrix for calculating similarity between sequences. - */ - private boolean nucleotide=false; + int top = 0; /** * Creates a new PCAPanel object. @@ -70,16 +65,18 @@ public class PCAPanel extends GPCAPanel implements Runnable this.ap = ap; boolean sameLength = true; - - seqstrings = av.getAlignmentView(av.getSelectionGroup() != null); - nucleotide=av.getAlignment().isNucleotide(); - if (av.getSelectionGroup() == null) - { - seqs = av.alignment.getSequencesArray(); + 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.getAlignment().getSequencesArray(); } else { - seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); + seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); } SeqCigar sq[] = seqstrings.getSequences(); int length = sq[0].getWidth(); @@ -105,7 +102,7 @@ public class PCAPanel extends GPCAPanel implements Runnable return; } - + pcaModel = new PCAModel(seqstrings, seqs, nucleotide); PaintRefresher.Register(this, av.getSequenceSetId()); rc = new RotatableCanvas(ap); @@ -113,7 +110,43 @@ public class PCAPanel extends GPCAPanel implements Runnable 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", @@ -131,78 +164,83 @@ public class PCAPanel extends GPCAPanel implements Runnable */ 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 { calcSettings.setEnabled(false); - pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide); - 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); - } - } - + pcaModel.run(); // //////////////// xCombobox.setSelectedIndex(0); yCombobox.setSelectedIndex(1); zCombobox.setSelectedIndex(2); - top = pca.getM().rows - 1; - - Vector points = new Vector(); - float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100); - - for (int i = 0; i < pca.getM().rows; i++) - { - SequencePoint sp = new SequencePoint(seqs[i], scores[i]); - points.addElement(sp); - } - - rc.setPoints(points, pca.getM().rows); + pcaModel.updateRc(rc); // rc.invalidate(); - nuclSetting.setSelected(nucleotide); - protSetting.setSelected(!nucleotide); + nuclSetting.setSelected(pcaModel.isNucleotide()); + protSetting.setSelected(!pcaModel.isNucleotide()); + jvVersionSetting.setSelected(pcaModel.isJvCalcMode()); + top = pcaModel.getTop(); } catch (OutOfMemoryError er) { new OOMWarning("calculating PCA", er); return; + } finally + { + progress.setProgressBar("", progId); } calcSettings.setEnabled(true); repaint(); - if (getParent()==null) + if (getParent() == null) { addKeyListener(rc); - Desktop.addInternalFrame(this, "Principal component analysis", 400, 400); + Desktop.addInternalFrame(this, MessageManager.getString("label.principal_component_analysis"), 475, + 450); } } + @Override protected void nuclSetting_actionPerfomed(ActionEvent arg0) { - nucleotide=true; - Thread worker = new Thread(this); - worker.start(); + if (!pcaModel.isNucleotide()) + { + pcaModel.setNucleotide(true); + pcaModel.setScore_matrix("DNA"); + Thread worker = new Thread(this); + worker.start(); + } + } + @Override protected void protSetting_actionPerfomed(ActionEvent arg0) { - nucleotide=false; + + if (pcaModel.isNucleotide()) + { + 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(); } + /** * DOCUMENT ME! */ @@ -216,14 +254,7 @@ public class PCAPanel extends GPCAPanel implements Runnable 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(); @@ -268,8 +299,8 @@ public class PCAPanel extends GPCAPanel implements Runnable CutAndPasteTransfer cap = new CutAndPasteTransfer(); try { - cap.setText(pca.getDetails()); - Desktop.addInternalFrame(cap, "PCA details", 500, 500); + cap.setText(pcaModel.getDetails()); + Desktop.addInternalFrame(cap, MessageManager.getString("label.pca_details"), 500, 500); } catch (OutOfMemoryError oom) { new OOMWarning("opening PCA details", oom); @@ -292,7 +323,7 @@ public class PCAPanel extends GPCAPanel implements Runnable { // 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) + if (pcaModel.getSeqtrings() == null) { jalview.bin.Cache.log .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); @@ -314,7 +345,8 @@ public class PCAPanel extends GPCAPanel implements Runnable { } ; - Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc); + Object[] alAndColsel = pcaModel.getSeqtrings() + .getAlignmentAndColumnSelection(gc); if (alAndColsel != null && alAndColsel[0] != null) { @@ -342,7 +374,7 @@ public class PCAPanel extends GPCAPanel implements Runnable // af.addSortByOrderMenuItem(ServiceName + " Ordering", // msaorder); - Desktop.addInternalFrame(af, "Original Data for " + this.title, + Desktop.addInternalFrame(af, MessageManager.formatMessage("label.original_data_for_params", new String[]{this.title}), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } } @@ -453,6 +485,7 @@ public class PCAPanel extends GPCAPanel implements Runnable } } + public void viewMenu_menuSelected() { buildAssociatedViewMenu(); @@ -528,8 +561,10 @@ public class PCAPanel extends GPCAPanel implements Runnable CutAndPasteTransfer cap = new CutAndPasteTransfer(); try { - cap.setText(getPointsasCsv(false)); - Desktop.addInternalFrame(cap, "Points for " + getTitle(), 500, 500); + 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); @@ -537,76 +572,141 @@ public class PCAPanel extends GPCAPanel implements Runnable } } - private String getPointsasCsv(boolean transformed) + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event + * .ActionEvent) + */ + protected void outputProjPoints_actionPerformed(ActionEvent e) { - StringBuffer csv = new StringBuffer(); - csv.append("\"Sequence\""); - if (transformed) + 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) { - csv.append(","); - csv.append(xCombobox.getSelectedIndex()); - csv.append(","); - csv.append(yCombobox.getSelectedIndex()); - csv.append(","); - csv.append(zCombobox.getSelectedIndex()); + new OOMWarning("exporting transformed PCA points", oom); + cap.dispose(); } - else + } + + // 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) { - for (int d = 1, dmax = pca.component(1).length; d <= dmax; d++) - { - csv.append("," + d); - } + progressBars = new Hashtable(); + progressBarHandlers = new Hashtable(); } - csv.append("\n"); - for (int s = 0; s < seqs.length; s++) + + JPanel progressPanel; + Long lId = new Long(id); + GridLayout layout = (GridLayout) statusPanel.getLayout(); + if (progressBars.get(lId) != null) { - csv.append("\"" + seqs[s].getName() + "\""); - double fl[]; - if (!transformed) + progressPanel = (JPanel) progressBars.get(new Long(id)); + statusPanel.remove(progressPanel); + progressBars.remove(lId); + progressPanel = null; + if (message != null) { - // output pca in correct order - fl = pca.component(s); - for (int d = fl.length - 1; d >= 0; d--) - { - csv.append(","); - csv.append(fl[d]); - } + statusBar.setText(message); } - else + 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() { - // output current x,y,z coords for points - fl = rc.getPointPosition(s); - for (int d = 0; d < fl.length; d++) + + @Override + public void actionPerformed(ActionEvent e) { - csv.append(","); - csv.append(fl[d]); + handler.cancelActivity(id); + us.setProgressBar( + "Cancelled " + + ((JLabel) progressPanel.getComponent(0)) + .getText(), id); } - } - csv.append("\n"); + }); + progressPanel.add(cancel, BorderLayout.EAST); } - return csv.toString(); } - /* - * (non-Javadoc) + /** * - * @see - * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event - * .ActionEvent) + * @return true if any progress bars are still active */ - protected void outputProjPoints_actionPerformed(ActionEvent e) + @Override + public boolean operationInProgress() { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - try + if (progressBars != null && progressBars.size() > 0) { - cap.setText(getPointsasCsv(true)); - Desktop.addInternalFrame(cap, "Transformed points for " + getTitle(), - 500, 500); - } catch (OutOfMemoryError oom) - { - new OOMWarning("exporting transformed PCA points", oom); - cap.dispose(); + 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); + } }