X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=25f83637bc69d5f6381cf0c1e6a5e4eef39a399c;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=c1e935a0e848985c77100cc08aaf2f5c5398a3d0;hpb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index c1e935a..25f8363 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -21,15 +21,20 @@ package jalview.gui; import jalview.analysis.scoremodels.ScoreModels; -import jalview.analysis.scoremodels.SimilarityParams; +import jalview.api.AlignViewportI; import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.SimilarityParamsI; +import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; +import jalview.gui.ImageExporter.ImageWriterI; +import jalview.gui.JalviewColourChooser.ColourChooserListener; import jalview.jbgui.GPCAPanel; +import jalview.math.RotatableMatrix.Axis; +import jalview.util.ImageMaker; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.PCAModel; @@ -46,57 +51,36 @@ 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! - * - * @author $author$ - * @version $Revision$ + * The panel holding the Principal Component Analysis 3-D visualisation */ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator { + private static final int MIN_WIDTH = 470; - private IProgressIndicator progressBar; + private static final int MIN_HEIGHT = 250; - RotatableCanvas rc; + private RotatableCanvas rc; AlignmentPanel ap; AlignmentViewport av; - PCAModel pcaModel; - - private static final int MIN_WIDTH = 470; + private PCAModel pcaModel; - private static final int MIN_HEIGHT = 250; + private int top = 0; - int top = 0; + private IProgressIndicator progressBar; private boolean working; /** - * Creates a new PCAPanel object using default score model and parameters - * - * @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 * @@ -138,14 +122,15 @@ public class PCAPanel extends GPCAPanel ScoreModelI scoreModel = ScoreModels.getInstance() .getScoreModel(modelName, ap); - pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel, - params); + setPcaModel(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(); + setRotatableCanvas(new RotatableCanvas(alignPanel)); + this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER); + + addKeyListener(getRotatableCanvas()); + validate(); } /** @@ -154,79 +139,39 @@ public class PCAPanel extends GPCAPanel */ 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 scoreModel_menuSelected() - { - scoreModelMenu.removeAll(); - for (final ScoreModelI sm : ScoreModels.getInstance().getModels()) + setPcaModel(null); + if (this.rc != null) { - 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 = ScoreModels.getInstance() - .getScoreModel(name, ap); - pcaModel.setScoreModel(sm2); - Thread worker = new Thread(PCAPanel.this); - worker.start(); - } - } - }); - scoreModelMenu.add(jm); - } + this.rc.sequencePoints = null; + this.rc.setAxisEndPoints(null); + this.rc = null; } } @Override - public void bgcolour_actionPerformed(ActionEvent e) + protected void bgcolour_actionPerformed() { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_background_colour"), - rc.bgColour); - - if (col != null) + String ttl = MessageManager.getString("label.select_background_colour"); + ColourChooserListener listener = new ColourChooserListener() { - rc.bgColour = col; - } - rc.repaint(); + @Override + public void colourSelected(Color c) + { + rc.setBgColour(c); + rc.repaint(); + } + }; + JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(), + listener); } /** - * DOCUMENT ME! + * Calculates the PCA and displays the results */ @Override public void run() { + working = true; long progId = System.currentTimeMillis(); IProgressIndicator progress = this; String message = MessageManager.getString("label.pca_recalculating"); @@ -236,21 +181,17 @@ public class PCAPanel extends GPCAPanel message = MessageManager.getString("label.pca_calculating"); } progress.setProgressBar(message, progId); - working = true; try { - calcSettings.setEnabled(false); - pcaModel.run(); - // //////////////// + getPcaModel().calculate(); + xCombobox.setSelectedIndex(0); yCombobox.setSelectedIndex(1); zCombobox.setSelectedIndex(2); - pcaModel.updateRc(rc); + getPcaModel().updateRc(getRotatableCanvas()); // rc.invalidate(); - nuclSetting.setSelected(pcaModel.isNucleotide()); - protSetting.setSelected(!pcaModel.isNucleotide()); - top = pcaModel.getTop(); + setTop(getPcaModel().getTop()); } catch (OutOfMemoryError er) { @@ -261,109 +202,69 @@ public class PCAPanel extends GPCAPanel { progress.setProgressBar("", progId); } - calcSettings.setEnabled(true); + repaint(); if (getParent() == null) { - addKeyListener(rc); - Desktop.addInternalFrame(this, MessageManager - .getString("label.principal_component_analysis"), 475, 450); + Desktop.addInternalFrame(this, + MessageManager.formatMessage("label.calc_title", "PCA", + getPcaModel().getScoreModelName()), + 475, 450); this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); } working = false; } - @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(); - } - - } - - @Override - protected void protSetting_actionPerfomed(ActionEvent arg0) - { - - if (pcaModel.isNucleotide()) - { - pcaModel.setNucleotide(false); - pcaModel.setScoreModel( - ScoreModels.getInstance().getDefaultModel(true)); - Thread worker = new Thread(this); - worker.start(); - } - } - /** - * DOCUMENT ME! + * Updates the PCA display after a change of component to use for x, y or z + * axis */ - void doDimensionChange() + @Override + protected void doDimensionChange() { - if (top == 0) + if (getTop() == 0) { return; } - int dim1 = top - xCombobox.getSelectedIndex(); - int dim2 = top - yCombobox.getSelectedIndex(); - int dim3 = top - zCombobox.getSelectedIndex(); - pcaModel.updateRcView(dim1, dim2, dim3); - rc.img = null; - rc.rotmat.setIdentity(); - rc.initAxes(); - rc.paint(rc.getGraphics()); + int dim1 = getTop() - xCombobox.getSelectedIndex(); + int dim2 = getTop() - yCombobox.getSelectedIndex(); + int dim3 = getTop() - zCombobox.getSelectedIndex(); + getPcaModel().updateRcView(dim1, dim2, dim3); + getRotatableCanvas().resetView(); } /** - * DOCUMENT ME! + * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for + * the given axis (X/Y/Z) * - * @param e - * DOCUMENT ME! + * @param index + * @param axis */ - @Override - protected void xCombobox_actionPerformed(ActionEvent e) + public void setSelectedDimensionIndex(int index, Axis axis) { - doDimensionChange(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - protected void yCombobox_actionPerformed(ActionEvent e) - { - doDimensionChange(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - protected void zCombobox_actionPerformed(ActionEvent e) - { - doDimensionChange(); + switch (axis) + { + case X: + xCombobox.setSelectedIndex(index); + break; + case Y: + yCombobox.setSelectedIndex(index); + break; + case Z: + zCombobox.setSelectedIndex(index); + break; + default: + } } @Override - public void outputValues_actionPerformed(ActionEvent e) + protected void outputValues_actionPerformed() { CutAndPasteTransfer cap = new CutAndPasteTransfer(); try { - cap.setText(pcaModel.getDetails()); + cap.setText(getPcaModel().getDetails()); Desktop.addInternalFrame(cap, MessageManager.getString("label.pca_details"), 500, 500); } catch (OutOfMemoryError oom) @@ -374,32 +275,35 @@ public class PCAPanel extends GPCAPanel } @Override - public void showLabels_actionPerformed(ActionEvent e) + protected void showLabels_actionPerformed() { - rc.showLabels(showLabels.getState()); + getRotatableCanvas().showLabels(showLabels.getState()); } @Override - public void print_actionPerformed(ActionEvent e) + protected void print_actionPerformed() { PCAPrinter printer = new PCAPrinter(); printer.start(); } + /** + * If available, shows the data which formed the inputs for the PCA as a new + * alignment + */ @Override - public void originalSeqData_actionPerformed(ActionEvent e) + public void originalSeqData_actionPerformed() { - // 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) + // JAL-2647 disabled after load from project (until save to project done) + if (getPcaModel().getInputData() == null) { - jalview.bin.Cache.log.info( + Cache.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 + // create new alignment window with hidden regions (unhiding hidden regions // yields unaligned seqs) // or create a selection box around columns in alignment view // test Alignment(SeqCigar[]) @@ -412,8 +316,8 @@ public class PCAPanel extends GPCAPanel } catch (Exception ex) { } - ; - Object[] alAndColsel = pcaModel.getSeqtrings() + + Object[] alAndColsel = getPcaModel().getInputData() .getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) @@ -495,11 +399,11 @@ public class PCAPanel extends GPCAPanel { pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); - rc.drawBackground(pg, rc.bgColour); - rc.drawScene(pg); - if (rc.drawAxes == true) + getRotatableCanvas().drawBackground(pg); + getRotatableCanvas().drawScene(pg); + if (getRotatableCanvas().drawAxes) { - rc.drawAxes(pg); + getRotatableCanvas().drawAxes(pg); } if (pi == 0) @@ -513,80 +417,44 @@ public class PCAPanel extends GPCAPanel } } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void eps_actionPerformed(ActionEvent e) - { - makePCAImage(jalview.util.ImageMaker.TYPE.EPS); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void png_actionPerformed(ActionEvent e) - { - makePCAImage(jalview.util.ImageMaker.TYPE.PNG); - } - - void makePCAImage(jalview.util.ImageMaker.TYPE type) + public void makePCAImage(ImageMaker.TYPE type) { - int width = rc.getWidth(); - int height = rc.getHeight(); - - jalview.util.ImageMaker im; - - if (type == jalview.util.ImageMaker.TYPE.PNG) + int width = getRotatableCanvas().getWidth(); + int height = getRotatableCanvas().getHeight(); + ImageWriterI writer = new ImageWriterI() { - 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.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.TYPE.SVG, "Make SVG file from PCA", - width, height, null, this.getTitle(), null, 0, false); - - } - - if (im.getGraphics() != null) - { - rc.drawBackground(im.getGraphics(), Color.black); - rc.drawScene(im.getGraphics()); - if (rc.drawAxes == true) + @Override + public void exportImage(Graphics g) throws Exception { - rc.drawAxes(im.getGraphics()); + RotatableCanvas canvas = getRotatableCanvas(); + canvas.drawBackground(g); + canvas.drawScene(g); + if (canvas.drawAxes) + { + canvas.drawAxes(g); + } } - im.writeImage(); - } + }; + String pca = MessageManager.getString("label.pca"); + ImageExporter exporter = new ImageExporter(writer, null, type, pca); + exporter.doExport(null, this, width, height, pca); } @Override - public void viewMenu_menuSelected() + protected void viewMenu_menuSelected() { buildAssociatedViewMenu(); } + /** + * Builds the menu showing the choice of possible views (for the associated + * sequence data) to which the PCA may be linked + */ void buildAssociatedViewMenu() { AlignmentPanel[] aps = PaintRefresher .getAssociatedPanels(av.getSequenceSetId()); - if (aps.length == 1 && rc.av == aps[0].av) + if (aps.length == 1 && getRotatableCanvas().av == aps[0].av) { associateViewsMenu.setVisible(false); return; @@ -604,22 +472,20 @@ public class PCAPanel extends GPCAPanel JRadioButtonMenuItem item; ButtonGroup buttonGroup = new ButtonGroup(); - int i, iSize = aps.length; - final PCAPanel thisPCAPanel = this; - for (i = 0; i < iSize; i++) + int iSize = aps.length; + + for (int i = 0; i < iSize; i++) { - final AlignmentPanel ap = aps[i]; - item = new JRadioButtonMenuItem(ap.av.getViewName(), ap.av == rc.av); + final AlignmentPanel panel = aps[i]; + item = new JRadioButtonMenuItem(panel.av.getViewName(), + panel.av == getRotatableCanvas().av); buttonGroup.add(item); item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { - rc.applyToAllViews = false; - rc.av = ap.av; - rc.ap = ap; - PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId()); + selectAssociatedView(panel); } }); @@ -631,13 +497,13 @@ public class PCAPanel extends GPCAPanel buttonGroup.add(itemf); - itemf.setSelected(rc.applyToAllViews); + itemf.setSelected(getRotatableCanvas().isApplyToAllViews()); itemf.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { - rc.applyToAllViews = itemf.isSelected(); + getRotatableCanvas().setApplyToAllViews(itemf.isSelected()); } }); associateViewsMenu.add(itemf); @@ -652,12 +518,12 @@ public class PCAPanel extends GPCAPanel * ) */ @Override - protected void outputPoints_actionPerformed(ActionEvent e) + protected void outputPoints_actionPerformed() { CutAndPasteTransfer cap = new CutAndPasteTransfer(); try { - cap.setText(pcaModel.getPointsasCsv(false, + cap.setText(getPcaModel().getPointsasCsv(false, xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), zCombobox.getSelectedIndex())); Desktop.addInternalFrame(cap, MessageManager @@ -678,12 +544,12 @@ public class PCAPanel extends GPCAPanel * .ActionEvent) */ @Override - protected void outputProjPoints_actionPerformed(ActionEvent e) + protected void outputProjPoints_actionPerformed() { CutAndPasteTransfer cap = new CutAndPasteTransfer(); try { - cap.setText(pcaModel.getPointsasCsv(true, + cap.setText(getPcaModel().getPointsasCsv(true, xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(), zCombobox.getSelectedIndex())); Desktop.addInternalFrame(cap, MessageManager.formatMessage( @@ -712,11 +578,11 @@ public class PCAPanel extends GPCAPanel // } // // JPanel progressPanel; - // Long lId = new Long(id); + // Long lId = Long.valueOf(id); // GridLayout layout = (GridLayout) statusPanel.getLayout(); // if (progressBars.get(lId) != null) // { - // progressPanel = (JPanel) progressBars.get(new Long(id)); + // progressPanel = (JPanel) progressBars.get(Long.valueOf(id)); // statusPanel.remove(progressPanel); // progressBars.remove(lId); // progressPanel = null; @@ -755,13 +621,13 @@ public class PCAPanel extends GPCAPanel final IProgressIndicatorHandler handler) { progressBar.registerHandler(id, handler); - // if (progressBarHandlers == null || !progressBars.contains(new Long(id))) + // if (progressBarHandlers == null || !progressBars.contains(Long.valueOf(id))) // { // throw new // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler")); // } - // progressBarHandlers.put(new Long(id), handler); - // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); + // progressBarHandlers.put(Long.valueOf(id), handler); + // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id)); // if (handler.canCancel()) // { // JButton cancel = new JButton( @@ -793,13 +659,13 @@ public class PCAPanel extends GPCAPanel } @Override - protected void resetButton_actionPerformed(ActionEvent e) + protected void resetButton_actionPerformed() { - int t = top; - top = 0; // ugly - prevents dimensionChanged events from being processed + int t = getTop(); + setTop(0); // ugly - prevents dimensionChanged events from being processed xCombobox.setSelectedIndex(0); yCombobox.setSelectedIndex(1); - top = t; + setTop(t); zCombobox.setSelectedIndex(2); } @@ -812,4 +678,94 @@ public class PCAPanel extends GPCAPanel { return working; } + + /** + * Answers the selected checkbox item index for PCA dimension for the X, Y or + * Z axis of the display + * + * @param axis + * @return + */ + public int getSelectedDimensionIndex(Axis axis) + { + switch (axis) + { + case X: + return xCombobox.getSelectedIndex(); + case Y: + return yCombobox.getSelectedIndex(); + default: + return zCombobox.getSelectedIndex(); + } + } + + public void setShowLabels(boolean show) + { + showLabels.setSelected(show); + } + + /** + * Sets the input data used to calculate the PCA. This is provided for + * 'restore from project', which does not currently support this (AL-2647), so + * sets the value to null, and hides the menu option for "Input Data...". J + * + * @param data + */ + public void setInputData(AlignmentView data) + { + getPcaModel().setInputData(data); + originalSeqData.setVisible(data != null); + } + + public AlignViewportI getAlignViewport() + { + return av; + } + + public PCAModel getPcaModel() + { + return pcaModel; + } + + public void setPcaModel(PCAModel pcaModel) + { + this.pcaModel = pcaModel; + } + + public RotatableCanvas getRotatableCanvas() + { + return rc; + } + + public void setRotatableCanvas(RotatableCanvas rc) + { + this.rc = rc; + } + + public int getTop() + { + return top; + } + + public void setTop(int top) + { + this.top = top; + } + + /** + * set the associated view for this PCA. + * + * @param panel + */ + public void selectAssociatedView(AlignmentPanel panel) + { + getRotatableCanvas().setApplyToAllViews(false); + + ap = panel; + av = panel.av; + + getRotatableCanvas().av = panel.av; + getRotatableCanvas().ap = panel; + PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId()); + } }