X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=da1dffe3380aff4f6a4485a8c5a87c781b2f7f50;hb=ac5f0c912a1c7819530456bab13942ad3734460b;hp=64253b41ec5850047d9ba8a70e0a8c636e660708;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java old mode 100755 new mode 100644 index 64253b4..da1dffe --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,363 +1,744 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.gui; - -import jalview.analysis.*; - -import jalview.datamodel.*; - -import jalview.jbgui.*; - -import java.awt.*; -import java.awt.event.*; - -import java.util.*; -import javax.swing.*; -import java.awt.print.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class PCAPanel extends GPCAPanel implements Runnable -{ - PCA pca; - int top; - RotatableCanvas rc; - AlignViewport av; - SequenceI [] seqs; - - /** - * Creates a new PCAPanel object. - * - * @param av DOCUMENT ME! - * @param s DOCUMENT ME! - */ - public PCAPanel(AlignViewport av) - { - this.av = av; - - boolean sameLength = true; - - if ((av.getSelectionGroup() != null) && - (av.getSelectionGroup().getSize(false) > 3)) - { - seqs = new Sequence[av.getSelectionGroup().getSize(false)]; - int length = av.getSelectionGroup().getSequenceAt(0).getLength(); - for (int i = 0; i < av.getSelectionGroup().getSize(false); i++) - { - seqs[i] = av.getSelectionGroup().getSequenceAt(i); - if(seqs[i].getLength()!=length) - { - sameLength = false; - break; - } - } - } - else - { - seqs = new Sequence[av.getAlignment().getHeight()]; - int length = av.alignment.getSequenceAt(0).getLength(); - - for (int i = 0; i < av.getAlignment().getHeight(); i++) - { - seqs[i] = av.getAlignment().getSequenceAt(i); - if(seqs[i].getLength()!=length) - { - sameLength = false; - break; - } - - } - } - - 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); - - return; - } - - - Desktop.addInternalFrame(this, "Principal component analysis", - 400, 400); - - - rc = new RotatableCanvas(av); - this.getContentPane().add(rc, BorderLayout.CENTER); - Thread worker = new Thread(this); - worker.start(); - } - - public void bgcolour_actionPerformed(ActionEvent e) - { - Color col = JColorChooser.showDialog(this, "Select Background Colour", - rc.bgColour); - - if(col!=null) - rc.bgColour = col; - rc.repaint(); - } - - - - - /** - * DOCUMENT ME! - */ - public void run() - { - try{ - pca = new PCA(seqs); - 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); - } - } - - ////////////////// - 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); - rc.repaint(); - seqs = null; - } - catch(OutOfMemoryError er) - { JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory calculating PCA!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - JOptionPane.WARNING_MESSAGE); - System.out.println("PCAPanel: "+er); - System.gc(); - - } - - } - - /** - * DOCUMENT ME! - */ - void doDimensionChange() - { - if (top == 0) - { - return; - } - - 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]; - } - - rc.img = null; - rc.rotmat.setIdentity(); - rc.initAxes(); - rc.paint(rc.getGraphics()); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void xCombobox_actionPerformed(ActionEvent e) - { - doDimensionChange(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void yCombobox_actionPerformed(ActionEvent e) - { - doDimensionChange(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void zCombobox_actionPerformed(ActionEvent e) - { - doDimensionChange(); - } - - - public void outputValues_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - Desktop.addInternalFrame(cap, "PCA details", 500, - 500); - - cap.setText(pca.getDetails()); - } - - public void showLabels_actionPerformed(ActionEvent e) - { - rc.showLabels(showLabels.getState()); - } - - public void print_actionPerformed(ActionEvent e) - { - PCAPrinter printer = new PCAPrinter(); - printer.start(); - } - - - class PCAPrinter extends Thread implements Printable - { - public void run() - { - PrinterJob printJob = PrinterJob.getPrinterJob(); - PageFormat pf = printJob.pageDialog(printJob.defaultPage()); - - printJob.setPrintable(this, pf); - - if (printJob.printDialog()) - { - try - { - printJob.print(); - } - catch (Exception PrintException) - { - PrintException.printStackTrace(); - } - } - } - - public int print(Graphics pg, PageFormat pf, int pi) - throws PrinterException - { - pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY()); - - rc.drawBackground(pg, rc.bgColour); - rc.drawScene(pg); - if (rc.drawAxes == true) - { - rc.drawAxes(pg); - } - - if (pi == 0) - return Printable.PAGE_EXISTS; - else - return Printable.NO_SUCH_PAGE; - } - } - - - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void eps_actionPerformed(ActionEvent e) - { - makePCAImage(jalview.util.ImageMaker.EPS); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void png_actionPerformed(ActionEvent e) - { - makePCAImage(jalview.util.ImageMaker.PNG); - } - - void makePCAImage(int type) - { - int width = rc.getWidth(); - int height = rc.getHeight(); - - jalview.util.ImageMaker im; - - if(type == jalview.util.ImageMaker.PNG) - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.PNG, - "Make PNG image from PCA", - width, height, - null, null); - else - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.EPS, - "Make EPS file from PCA", - width, height, - null, this.getTitle()); - - if(im.getGraphics()!=null) - { - rc.drawBackground(im.getGraphics(), Color.black); - rc.drawScene(im.getGraphics()); - if (rc.drawAxes == true) - { - rc.drawAxes(im.getGraphics()); - } - im.writeImage(); - } - } - } +/* + * 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. + * + * 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 jalview.analysis.scoremodels.ScoreModels; +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; + +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; +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.JColorChooser; +import javax.swing.JMenuItem; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; + +/** + * 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 static final int MIN_HEIGHT = 250; + + RotatableCanvas rc; + + AlignmentPanel ap; + + AlignmentViewport av; + + PCAModel pcaModel; + + int top = 0; + + private IProgressIndicator progressBar; + + private boolean working; + + /** + * Constructor given sequence data, a similarity (or distance) score model + * name, and score calculation parameters + * + * @param alignPanel + * @param modelName + * @param params + */ + public PCAPanel(AlignmentPanel alignPanel, String modelName, + 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(); + } + }); + + boolean selected = av.getSelectionGroup() != null + && av.getSelectionGroup().getSize() > 0; + AlignmentView seqstrings = av.getAlignmentView(selected); + SequenceI[] seqs; + if (!selected) + { + seqs = av.getAlignment().getSequencesArray(); + } + else + { + seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); + } + + ScoreModelI scoreModel = ScoreModels.getInstance() + .getScoreModel(modelName, ap); + pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel, + params); + PaintRefresher.Register(this, av.getSequenceSetId()); + + rc = new RotatableCanvas(alignPanel); + this.getContentPane().add(rc, BorderLayout.CENTER); + + addKeyListener(rc); + validate(); + + this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); + } + + /** + * Ensure references to potentially very large objects (the PCA matrices) are + * nulled when the frame is closed + */ + protected void close_actionPerformed() + { + pcaModel = null; + } + + @Override + protected void bgcolour_actionPerformed() + { + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_background_colour"), + rc.bgColour); + + if (col != null) + { + rc.bgColour = col; + } + rc.repaint(); + } + + /** + * 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"); + if (getParent() == null) + { + progress = ap.alignFrame; + message = MessageManager.getString("label.pca_calculating"); + } + progress.setProgressBar(message, progId); + try + { + pcaModel.calculate(); + + xCombobox.setSelectedIndex(0); + yCombobox.setSelectedIndex(1); + zCombobox.setSelectedIndex(2); + + pcaModel.updateRc(rc); + // rc.invalidate(); + top = pcaModel.getTop(); + + } catch (OutOfMemoryError er) + { + new OOMWarning("calculating PCA", er); + working = false; + return; + } finally + { + progress.setProgressBar("", progId); + } + + repaint(); + if (getParent() == null) + { + Desktop.addInternalFrame(this, + MessageManager.formatMessage("label.calc_title", "PCA", + pcaModel.getScoreModelName()), + 475, 450); + } + working = false; + } + + /** + * Updates the PCA display after a change of component to use for x, y or z + * axis + */ + @Override + protected void doDimensionChange() + { + if (top == 0) + { + return; + } + + int dim1 = top - xCombobox.getSelectedIndex(); + int dim2 = top - yCombobox.getSelectedIndex(); + int dim3 = top - zCombobox.getSelectedIndex(); + pcaModel.updateRcView(dim1, dim2, dim3); + rc.resetView(); + } + + /** + * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for + * the given axis (X/Y/Z) + * + * @param index + * @param axis + */ + public void setSelectedDimensionIndex(int index, Axis axis) + { + switch (axis) + { + case X: + xCombobox.setSelectedIndex(index); + break; + case Y: + yCombobox.setSelectedIndex(index); + break; + case Z: + zCombobox.setSelectedIndex(index); + break; + default: + } + } + + @Override + protected void outputValues_actionPerformed() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + try + { + cap.setText(pcaModel.getDetails()); + Desktop.addInternalFrame(cap, + MessageManager.getString("label.pca_details"), 500, 500); + } catch (OutOfMemoryError oom) + { + new OOMWarning("opening PCA details", oom); + cap.dispose(); + } + } + + @Override + protected void showLabels_actionPerformed() + { + rc.showLabels(showLabels.getState()); + } + + @Override + 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() + { + // JAL-2647 disabled after load from project (until save to project done) + if (pcaModel.getInputData() == null) + { + 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 alignment window with hidden regions (unhiding hidden regions + // yields unaligned seqs) + // or create a selection box around columns in alignment view + // test Alignment(SeqCigar[]) + char gc = '-'; + try + { + // we try to get the associated view's gap character + // but this may fail if the view was closed... + gc = av.getGapCharacter(); + } catch (Exception ex) + { + } + + Object[] alAndColsel = pcaModel.getInputData() + .getAlignmentAndHiddenColumns(gc); + + if (alAndColsel != null && alAndColsel[0] != null) + { + // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); + + AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); + AlignmentI dataset = (av != null && av.getAlignment() != null) + ? av.getAlignment().getDataset() + : null; + if (dataset != null) + { + al.setDataset(dataset); + } + + if (true) + { + // make a new frame! + 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!!<<< + // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer()); + + // af.addSortByOrderMenuItem(ServiceName + " Ordering", + // msaorder); + + Desktop.addInternalFrame(af, MessageManager.formatMessage( + "label.original_data_for_params", new String[] + { this.title }), AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + } + } + /* + * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i < + * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 + + * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] + + * "\n"); } + * + * Desktop.addInternalFrame(cap, "Original Data", 400, 400); + */ + } + + class PCAPrinter extends Thread implements Printable + { + @Override + public void run() + { + PrinterJob printJob = PrinterJob.getPrinterJob(); + PageFormat defaultPage = printJob.defaultPage(); + PageFormat pf = printJob.pageDialog(defaultPage); + + if (defaultPage == pf) + { + /* + * user cancelled + */ + return; + } + + printJob.setPrintable(this, pf); + + if (printJob.printDialog()) + { + try + { + printJob.print(); + } catch (Exception PrintException) + { + PrintException.printStackTrace(); + } + } + } + + @Override + public int print(Graphics pg, PageFormat pf, int pi) + throws PrinterException + { + pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); + + rc.drawBackground(pg); + rc.drawScene(pg); + if (rc.drawAxes) + { + rc.drawAxes(pg); + } + + if (pi == 0) + { + return Printable.PAGE_EXISTS; + } + else + { + return Printable.NO_SUCH_PAGE; + } + } + } + + /** + * Handler for 'Save as EPS' option + */ + @Override + protected void eps_actionPerformed() + { + makePCAImage(ImageMaker.TYPE.EPS); + } + + /** + * Handler for 'Save as PNG' option + */ + @Override + protected void png_actionPerformed() + { + makePCAImage(ImageMaker.TYPE.PNG); + } + + void makePCAImage(ImageMaker.TYPE type) + { + int width = rc.getWidth(); + int height = rc.getHeight(); + + 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()); + rc.drawScene(im.getGraphics()); + if (rc.drawAxes) + { + rc.drawAxes(im.getGraphics()); + } + im.writeImage(); + } + } + + @Override + 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) + { + associateViewsMenu.setVisible(false); + return; + } + + associateViewsMenu.setVisible(true); + + if ((viewMenu + .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) + { + viewMenu.insertSeparator(viewMenu.getItemCount() - 1); + } + + associateViewsMenu.removeAll(); + + JRadioButtonMenuItem item; + ButtonGroup buttonGroup = new ButtonGroup(); + 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); + buttonGroup.add(item); + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent evt) + { + rc.applyToAllViews = false; + rc.av = panel.av; + rc.ap = panel; + PaintRefresher.Register(PCAPanel.this, + panel.av.getSequenceSetId()); + } + }); + + associateViewsMenu.add(item); + } + + 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(); + } + }); + associateViewsMenu.add(itemf); + + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent + * ) + */ + @Override + protected void outputPoints_actionPerformed() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + 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); + cap.dispose(); + } + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event + * .ActionEvent) + */ + @Override + protected void outputProjPoints_actionPerformed() + { + 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) + { + new OOMWarning("exporting transformed PCA points", oom); + cap.dispose(); + } + } + + /* + * (non-Javadoc) + * + * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) + */ + @Override + public void setProgressBar(String message, long id) + { + progressBar.setProgressBar(message, id); + // if (progressBars == null) + // { + // progressBars = new Hashtable(); + // progressBarHandlers = new Hashtable(); + // } + // + // JPanel progressPanel; + // Long lId = new Long(id); + // GridLayout layout = (GridLayout) statusPanel.getLayout(); + // if (progressBars.get(lId) != null) + // { + // progressPanel = (JPanel) progressBars.get(new Long(id)); + // statusPanel.remove(progressPanel); + // progressBars.remove(lId); + // progressPanel = null; + // if (message != null) + // { + // statusBar.setText(message); + // } + // 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) + { + progressBar.registerHandler(id, handler); + // if (progressBarHandlers == null || !progressBars.contains(new Long(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)); + // if (handler.canCancel()) + // { + // JButton cancel = new JButton( + // MessageManager.getString("action.cancel")); + // final IProgressIndicator us = this; + // cancel.addActionListener(new ActionListener() + // { + // + // @Override + // public void actionPerformed(ActionEvent e) + // { + // handler.cancelActivity(id); + // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", + // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id); + // } + // }); + // progressPanel.add(cancel, BorderLayout.EAST); + // } + } + + /** + * + * @return true if any progress bars are still active + */ + @Override + public boolean operationInProgress() + { + return progressBar.operationInProgress(); + } + + @Override + protected void resetButton_actionPerformed() + { + int t = top; + top = 0; // ugly - prevents dimensionChanged events from being processed + xCombobox.setSelectedIndex(0); + yCombobox.setSelectedIndex(1); + 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); + } +}