X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=5ff0881e45edc7a2bf00b587ee0bb34b7aa7508b;hb=refs%2Fheads%2Ffeatures%2FJAL-1767pcaInProject;hp=f861a7c1cba3229922092a33d05568e313fc7148;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index f861a7c..5ff0881 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -21,15 +21,17 @@ 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.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; 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; @@ -46,7 +48,6 @@ 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; @@ -54,16 +55,14 @@ 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; @@ -73,26 +72,11 @@ public class PCAPanel extends GPCAPanel PCAModel pcaModel; - private static final int MIN_WIDTH = 470; - - private static final int MIN_HEIGHT = 250; - int top = 0; - /** - * 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); - } + private IProgressIndicator progressBar; + + private boolean working; /** * Constructor given sequence data, a similarity (or distance) score model @@ -142,8 +126,11 @@ public class PCAPanel extends GPCAPanel rc = new RotatableCanvas(alignPanel); this.getContentPane().add(rc, BorderLayout.CENTER); - Thread worker = new Thread(this); - worker.start(); + + addKeyListener(rc); + validate(); + + this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); } /** @@ -155,58 +142,8 @@ public class PCAPanel extends GPCAPanel 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()) - { - 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); - } - } - } - - @Override - public void bgcolour_actionPerformed(ActionEvent e) + protected void bgcolour_actionPerformed() { Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_background_colour"), @@ -220,11 +157,12 @@ public class PCAPanel extends GPCAPanel } /** - * 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"); @@ -236,70 +174,43 @@ public class PCAPanel extends GPCAPanel progress.setProgressBar(message, progId); try { - calcSettings.setEnabled(false); - pcaModel.run(); - // //////////////// + pcaModel.calculate(); + xCombobox.setSelectedIndex(0); yCombobox.setSelectedIndex(1); zCombobox.setSelectedIndex(2); pcaModel.updateRc(rc); // rc.invalidate(); - nuclSetting.setSelected(pcaModel.isNucleotide()); - protSetting.setSelected(!pcaModel.isNucleotide()); top = pcaModel.getTop(); } catch (OutOfMemoryError er) { new OOMWarning("calculating PCA", er); + working = false; 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); - this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); - } - } - - @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(); + Desktop.addInternalFrame(this, + MessageManager.formatMessage("label.calc_title", "PCA", + pcaModel.getScoreModelName()), + 475, 450); } + working = false; } /** - * 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) { @@ -310,50 +221,35 @@ public class PCAPanel extends GPCAPanel 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()); + rc.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 @@ -369,32 +265,35 @@ public class PCAPanel extends GPCAPanel } @Override - public void showLabels_actionPerformed(ActionEvent e) + protected void showLabels_actionPerformed() { rc.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 (pcaModel.getInputData() == null) { - jalview.bin.Cache.log.info( + 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 + // 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[]) @@ -407,8 +306,8 @@ public class PCAPanel extends GPCAPanel } catch (Exception ex) { } - ; - Object[] alAndColsel = pcaModel.getSeqtrings() + + Object[] alAndColsel = pcaModel.getInputData() .getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) @@ -459,7 +358,16 @@ public class PCAPanel extends GPCAPanel 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); @@ -481,9 +389,9 @@ public class PCAPanel extends GPCAPanel { pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); - rc.drawBackground(pg, rc.bgColour); + rc.drawBackground(pg); rc.drawScene(pg); - if (rc.drawAxes == true) + if (rc.drawAxes) { rc.drawAxes(pg); } @@ -500,61 +408,53 @@ public class PCAPanel extends GPCAPanel } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Handler for 'Save as EPS' option */ @Override - public void eps_actionPerformed(ActionEvent e) + protected void eps_actionPerformed() { - makePCAImage(jalview.util.ImageMaker.TYPE.EPS); + makePCAImage(ImageMaker.TYPE.EPS); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Handler for 'Save as PNG' option */ @Override - public void png_actionPerformed(ActionEvent e) + protected void png_actionPerformed() { - makePCAImage(jalview.util.ImageMaker.TYPE.PNG); + makePCAImage(ImageMaker.TYPE.PNG); } - void makePCAImage(jalview.util.ImageMaker.TYPE type) + void makePCAImage(ImageMaker.TYPE type) { int width = rc.getWidth(); int height = rc.getHeight(); - jalview.util.ImageMaker im; - - 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.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); - + ImageMaker im; + + switch (type) + { + case PNG: + im = new ImageMaker(this, ImageMaker.TYPE.PNG, + "Make PNG image from PCA", width, height, null, null, null, 0, + false); + break; + case EPS: + im = new ImageMaker(this, ImageMaker.TYPE.EPS, + "Make EPS file from PCA", width, height, null, + this.getTitle(), null, 0, false); + break; + default: + im = new ImageMaker(this, 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.drawBackground(im.getGraphics()); rc.drawScene(im.getGraphics()); - if (rc.drawAxes == true) + if (rc.drawAxes) { rc.drawAxes(im.getGraphics()); } @@ -563,11 +463,15 @@ public class PCAPanel extends GPCAPanel } @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 @@ -590,12 +494,12 @@ 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.viewName, ap.av == rc.av); + final AlignmentPanel panel = aps[i]; + item = new JRadioButtonMenuItem(panel.av.viewName, panel.av == rc.av); buttonGroup.add(item); item.addActionListener(new ActionListener() { @@ -603,9 +507,10 @@ public class PCAPanel extends GPCAPanel public void actionPerformed(ActionEvent evt) { rc.applyToAllViews = false; - rc.av = ap.av; - rc.ap = ap; - PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId()); + rc.av = panel.av; + rc.ap = panel; + PaintRefresher.Register(PCAPanel.this, + panel.av.getSequenceSetId()); } }); @@ -638,7 +543,7 @@ public class PCAPanel extends GPCAPanel * ) */ @Override - protected void outputPoints_actionPerformed(ActionEvent e) + protected void outputPoints_actionPerformed() { CutAndPasteTransfer cap = new CutAndPasteTransfer(); try @@ -664,7 +569,7 @@ public class PCAPanel extends GPCAPanel * .ActionEvent) */ @Override - protected void outputProjPoints_actionPerformed(ActionEvent e) + protected void outputProjPoints_actionPerformed() { CutAndPasteTransfer cap = new CutAndPasteTransfer(); try @@ -779,7 +684,7 @@ 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 @@ -788,4 +693,52 @@ public class PCAPanel extends GPCAPanel top = t; zCombobox.setSelectedIndex(2); } + + /** + * Answers true if PCA calculation is in progress, else false + * + * @return + */ + public boolean isWorking() + { + 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) + { + pcaModel.setInputData(data); + originalSeqData.setVisible(data != null); + } }