X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=885c3bf8a2026a9c05418479999d03e5103bf171;hb=5c45059a31d5f2ed14a8898d700ead9b3431bccf;hp=3d38a873ec2245c1fa88e5ed392c8d6a8433afe5;hpb=fbd03b3f123f3462c5fe685c988e5c4ae601558c;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java old mode 100755 new mode 100644 index 3d38a87..885c3bf --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,32 +1,59 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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. - * + * 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 . + * 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.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; +import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.PCAModel; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Graphics; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.print.PageFormat; +import java.awt.print.Printable; +import java.awt.print.PrinterException; +import java.awt.print.PrinterJob; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JColorChooser; +import javax.swing.JMenuItem; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; /** * DOCUMENT ME! @@ -34,51 +61,108 @@ 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; + private IProgressIndicator progressBar; RotatableCanvas rc; AlignmentPanel ap; - AlignViewport av; + AlignmentViewport av; - AlignmentView seqstrings; + PCAModel pcaModel; - SequenceI[] seqs; + 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); + } - boolean sameLength = true; + /** + * 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); + + addInternalFrameListener(new InternalFrameAdapter() + { + @Override + public void internalFrameClosed(InternalFrameEvent e) + { + close_actionPerformed(); + } + }); - seqstrings = av.getAlignmentView(av.getSelectionGroup() != null); - if (av.getSelectionGroup() == null) + boolean selected = av.getSelectionGroup() != null + && av.getSelectionGroup().getSize() > 0; + AlignmentView seqstrings = av.getAlignmentView(selected); + 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()); } + + // 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"), + MessageManager.getString("label.sequences_not_aligned"), + JvOptionPane.WARNING_MESSAGE); + + return; + } + + pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel, + params); + PaintRefresher.Register(this, av.getSequenceSetId()); + + rc = new RotatableCanvas(alignPanel); + this.getContentPane().add(rc, BorderLayout.CENTER); + Thread worker = new Thread(this); + worker.start(); + } + + /** + * Answers true if all sequences have the same aligned length, else false + * + * @param seqstrings + * @return + */ + protected boolean checkAligned(AlignmentView seqstrings) + { SeqCigar sq[] = seqstrings.getSequences(); int length = sq[0].getWidth(); - - for (int i = 0; i < seqs.length; i++) + boolean sameLength = true; + for (int i = 0; i < sq.length; i++) { if (sq[i].getWidth() != length) { @@ -86,35 +170,72 @@ public class PCAPanel extends GPCAPanel implements Runnable break; } } + return sameLength; + } - 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); + /** + * Ensure references to potentially very large objects (the PCA matrices) are + * nulled when the frame is closed + */ + protected void close_actionPerformed() + { + pcaModel = null; + } - return; + /** + * 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() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (!pcaModel.getScoreModelName().equals(name)) + { + ScoreModelI sm2 = configureScoreModel(sm); + pcaModel.setScoreModel(sm2); + Thread worker = new Thread(PCAPanel.this); + worker.start(); + } + } + }); + scoreModelMenu.add(jm); + } } - - Desktop - .addInternalFrame(this, "Principal component analysis", 400, - 400); - - PaintRefresher.Register(this, av.getSequenceSetId()); - - rc = new RotatableCanvas(ap); - this.getContentPane().add(rc, BorderLayout.CENTER); - Thread worker = new Thread(this); - worker.start(); } + @Override public void bgcolour_actionPerformed(ActionEvent e) { - Color col = JColorChooser.showDialog(this, "Select Background Colour", + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_background_colour"), rc.bgColour); if (col != null) @@ -127,58 +248,86 @@ public class PCAPanel extends GPCAPanel implements Runnable /** * DOCUMENT ME! */ + @Override public void run() { + long progId = System.currentTimeMillis(); + IProgressIndicator progress = this; + String message = MessageManager.getString("label.pca_recalculating"); + if (getParent() == null) + { + progress = ap.alignFrame; + message = MessageManager.getString("label.pca_calculating"); + } + 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.setScoreModel(ScoreModels.getInstance().getDefaultModel( + false)); + 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()) { - new OOMWarning("calculating PCA", er); - + pcaModel.setNucleotide(false); + 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(); } /** @@ -194,14 +343,7 @@ 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(); @@ -214,6 +356,7 @@ public class PCAPanel extends GPCAPanel implements Runnable * @param e * DOCUMENT ME! */ + @Override protected void xCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); @@ -225,6 +368,7 @@ public class PCAPanel extends GPCAPanel implements Runnable * @param e * DOCUMENT ME! */ + @Override protected void yCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); @@ -236,40 +380,47 @@ public class PCAPanel extends GPCAPanel implements Runnable * @param e * DOCUMENT ME! */ + @Override protected void zCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); } + @Override public void outputValues_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); - try { - cap.setText(pca.getDetails()); - Desktop.addInternalFrame(cap, "PCA details", 500, 500); + try + { + cap.setText(pcaModel.getDetails()); + Desktop.addInternalFrame(cap, + MessageManager.getString("label.pca_details"), 500, 500); } catch (OutOfMemoryError oom) { - new OOMWarning("opening PCA details",oom); + new OOMWarning("opening PCA details", oom); cap.dispose(); } } + @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 (seqstrings == null) + if (pcaModel.getSeqtrings() == null) { jalview.bin.Cache.log .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); @@ -291,14 +442,15 @@ public class PCAPanel extends GPCAPanel implements Runnable { } ; - Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc); + 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 + AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); + AlignmentI dataset = (av != null && av.getAlignment() != null) ? av .getAlignment().getDataset() : null; if (dataset != null) { @@ -319,8 +471,10 @@ public class PCAPanel extends GPCAPanel implements Runnable // 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); } } /* @@ -335,6 +489,7 @@ public class PCAPanel extends GPCAPanel implements Runnable class PCAPrinter extends Thread implements Printable { + @Override public void run() { PrinterJob printJob = PrinterJob.getPrinterJob(); @@ -354,6 +509,7 @@ public class PCAPanel extends GPCAPanel implements Runnable } } + @Override public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -383,9 +539,10 @@ public class PCAPanel extends GPCAPanel implements Runnable * @param e * DOCUMENT ME! */ + @Override public void eps_actionPerformed(ActionEvent e) { - makePCAImage(jalview.util.ImageMaker.EPS); + makePCAImage(jalview.util.ImageMaker.TYPE.EPS); } /** @@ -394,28 +551,37 @@ public class PCAPanel extends GPCAPanel implements Runnable * @param e * DOCUMENT ME! */ + @Override public void png_actionPerformed(ActionEvent e) { - makePCAImage(jalview.util.ImageMaker.PNG); + makePCAImage(jalview.util.ImageMaker.TYPE.PNG); } - void makePCAImage(int type) + void makePCAImage(jalview.util.ImageMaker.TYPE type) { int width = rc.getWidth(); int height = rc.getHeight(); jalview.util.ImageMaker im; - if (type == jalview.util.ImageMaker.PNG) + if (type == 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, null, 0, false); + } + else if (type == jalview.util.ImageMaker.TYPE.EPS) { - 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.TYPE.EPS, "Make EPS file from PCA", + width, height, null, this.getTitle(), null, 0, false); } 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.TYPE.SVG, "Make SVG file from PCA", + width, height, null, this.getTitle(), null, 0, false); + } if (im.getGraphics() != null) @@ -430,6 +596,7 @@ public class PCAPanel extends GPCAPanel implements Runnable } } + @Override public void viewMenu_menuSelected() { buildAssociatedViewMenu(); @@ -465,6 +632,7 @@ public class PCAPanel extends GPCAPanel implements Runnable buttonGroup.add(item); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { rc.applyToAllViews = false; @@ -484,6 +652,7 @@ public class PCAPanel extends GPCAPanel implements Runnable itemf.setSelected(rc.applyToAllViews); itemf.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { rc.applyToAllViews = itemf.isSelected(); @@ -492,80 +661,187 @@ public class PCAPanel extends GPCAPanel implements Runnable associateViewsMenu.add(itemf); } - /* (non-Javadoc) - * @see jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent) + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent + * ) */ + @Override protected void outputPoints_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); - try { - cap.setText(getPointsasCsv(false)); - Desktop.addInternalFrame(cap, "Points for "+getTitle(), 500, 500); + 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); + new OOMWarning("exporting PCA points", oom); cap.dispose(); } } - private String getPointsasCsv(boolean transformed) - { - StringBuffer csv = new StringBuffer(); - csv.append("\"Sequence\""); - if (transformed) { - csv.append(","); - csv.append(xCombobox.getSelectedIndex()); - csv.append(","); - csv.append(yCombobox.getSelectedIndex()); - csv.append(","); - csv.append(zCombobox.getSelectedIndex()); - } else { - for (int d=1,dmax=pca.component(1).length;d<=dmax;d++) - { - csv.append(","+d); - } - } - csv.append("\n"); - for (int s=0;s=0;d--) - { - csv.append(","); - csv.append(fl[d]); - } - } else { - // output current x,y,z coords for points - fl = rc.getPointPosition(s); - for (int d=0; d