X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=7ceceee81c4ae38fdf4b01cad4ad5fbf9f1bec4f;hb=e34a4c5332c2d4d92651e0adc99ab7c5d262d13b;hp=14aa5888295c2075e86d43bfd0930eac65163f77;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 14aa588..7ceceee 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,6 +1,6 @@ /* - * 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. * @@ -20,19 +20,23 @@ */ 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; @@ -45,8 +49,9 @@ import javax.swing.ButtonGroup; 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! @@ -54,8 +59,8 @@ import javax.swing.JRadioButtonMenuItem; * @author $author$ * @version $Revision$ */ -public class PCAPanel extends GPCAPanel implements Runnable, - IProgressIndicator +public class PCAPanel extends GPCAPanel + implements Runnable, IProgressIndicator { private IProgressIndicator progressBar; @@ -68,28 +73,59 @@ public class PCAPanel extends GPCAPanel implements Runnable, 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) { @@ -99,78 +135,83 @@ public class PCAPanel extends GPCAPanel implements Runnable, { 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) @@ -183,6 +224,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, /** * DOCUMENT ME! */ + @Override public void run() { long progId = System.currentTimeMillis(); @@ -194,6 +236,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, message = MessageManager.getString("label.pca_calculating"); } progress.setProgressBar(message, progId); + working = true; try { calcSettings.setEnabled(false); @@ -207,12 +250,12 @@ public class PCAPanel extends GPCAPanel implements Runnable, // 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 { @@ -225,7 +268,9 @@ public class PCAPanel extends GPCAPanel implements Runnable, addKeyListener(rc); Desktop.addInternalFrame(this, MessageManager .getString("label.principal_component_analysis"), 475, 450); + this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); } + working = false; } @Override @@ -234,7 +279,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, if (!pcaModel.isNucleotide()) { pcaModel.setNucleotide(true); - pcaModel.setScore_matrix("DNA"); + pcaModel.setScoreModel( + ScoreModels.getInstance().getDefaultModel(false)); Thread worker = new Thread(this); worker.start(); } @@ -248,20 +294,13 @@ public class PCAPanel extends GPCAPanel implements Runnable, 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! */ @@ -288,6 +327,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, * @param e * DOCUMENT ME! */ + @Override protected void xCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); @@ -299,6 +339,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, * @param e * DOCUMENT ME! */ + @Override protected void yCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); @@ -310,11 +351,13 @@ 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(); @@ -330,25 +373,28 @@ public class PCAPanel extends GPCAPanel implements Runnable, } } + @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 @@ -368,15 +414,16 @@ public class PCAPanel extends GPCAPanel implements Runnable, } ; 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); @@ -385,9 +432,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, 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!!<<< @@ -397,8 +443,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, // 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); } } @@ -414,10 +460,20 @@ public class PCAPanel extends GPCAPanel implements Runnable, 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); @@ -433,6 +489,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, } } + @Override public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -462,6 +519,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, * @param e * DOCUMENT ME! */ + @Override public void eps_actionPerformed(ActionEvent e) { makePCAImage(jalview.util.ImageMaker.TYPE.EPS); @@ -473,6 +531,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, * @param e * DOCUMENT ME! */ + @Override public void png_actionPerformed(ActionEvent e) { makePCAImage(jalview.util.ImageMaker.TYPE.PNG); @@ -489,19 +548,19 @@ public class PCAPanel extends GPCAPanel implements Runnable, { 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); } @@ -517,6 +576,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, } } + @Override public void viewMenu_menuSelected() { buildAssociatedViewMenu(); @@ -524,8 +584,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, 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); @@ -534,7 +594,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, associateViewsMenu.setVisible(true); - if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) + if ((viewMenu + .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) { viewMenu.insertSeparator(viewMenu.getItemCount() - 1); } @@ -552,6 +613,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, buttonGroup.add(item); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { rc.applyToAllViews = false; @@ -564,13 +626,15 @@ public class PCAPanel extends GPCAPanel implements Runnable, 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(); @@ -587,6 +651,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent * ) */ + @Override protected void outputPoints_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); @@ -595,9 +660,9 @@ public class PCAPanel extends GPCAPanel implements Runnable, 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); @@ -612,6 +677,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event * .ActionEvent) */ + @Override protected void outputProjPoints_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); @@ -621,8 +687,8 @@ public class PCAPanel extends GPCAPanel implements Runnable, 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); @@ -736,4 +802,14 @@ public class PCAPanel extends GPCAPanel implements Runnable, top = t; zCombobox.setSelectedIndex(2); } + + /** + * Answers true if PCA calculation is in progress, else false + * + * @return + */ + public boolean isWorking() + { + return working; + } }