X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=da1dffe3380aff4f6a4485a8c5a87c781b2f7f50;hb=ac5f0c912a1c7819530456bab13942ad3734460b;hp=15c3d590d105bf0fa853cbafde74d205c6cbcc2d;hpb=2c99f6f286b5a4bb09b79131f620eb44d70ee3fe;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java old mode 100755 new mode 100644 index 15c3d59..da1dffe --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,112 +1,153 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 + * 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. - * - * 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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.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; /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ + * The panel holding the Principal Component Analysis 3-D visualisation */ -public class PCAPanel - extends GPCAPanel implements Runnable +public class PCAPanel extends GPCAPanel + implements Runnable, IProgressIndicator { - PCA pca; - int top; + private static final int MIN_WIDTH = 470; + + private static final int MIN_HEIGHT = 250; + RotatableCanvas rc; + AlignmentPanel ap; - AlignViewport av; - AlignmentView seqstrings; - SequenceI[] seqs; + + AlignmentViewport av; + + PCAModel pcaModel; + + int top = 0; + + private IProgressIndicator progressBar; + + private boolean working; /** - * Creates a new PCAPanel object. - * - * @param av DOCUMENT ME! - * @param s DOCUMENT ME! + * 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(); - boolean sameLength = true; + progressBar = new ProgressBar(statusPanel, statusBar); - seqstrings = av.getAlignmentView(av.getSelectionGroup() != null); - if (av.getSelectionGroup() == null) + addInternalFrameListener(new InternalFrameAdapter() { - seqs = av.alignment.getSequencesArray(); - } - else - { - seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); - } - SeqCigar sq[] = seqstrings.getSequences(); - int length = sq[0].getWidth(); - - for (int i = 0; i < seqs.length; i++) - { - if (sq[i].getWidth() != length) + @Override + public void internalFrameClosed(InternalFrameEvent e) { - sameLength = false; - break; + close_actionPerformed(); } - } + }); - if (!sameLength) + boolean selected = av.getSelectionGroup() != null + && av.getSelectionGroup().getSize() > 0; + AlignmentView seqstrings = av.getAlignmentView(selected); + SequenceI[] seqs; + if (!selected) { - 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; + seqs = av.getAlignment().getSequencesArray(); + } + else + { + seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); } - Desktop.addInternalFrame(this, "Principal component analysis", - 400, 400); - + 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(); + + 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; } - public void bgcolour_actionPerformed(ActionEvent e) + @Override + protected void bgcolour_actionPerformed() { - Color col = JColorChooser.showDialog(this, "Select Background Colour", - rc.bgColour); + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_background_colour"), + rc.bgColour); if (col != null) { @@ -116,74 +157,60 @@ public class PCAPanel } /** - * 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"); + 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++; - } + pcaModel.calculate(); - 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); - } + pcaModel.updateRc(rc); + // rc.invalidate(); + top = pcaModel.getTop(); - rc.setPoints(points, pca.getM().rows); - rc.repaint(); - - addKeyListener(rc); - - } - catch (OutOfMemoryError er) + } 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(); - + 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; } /** - * 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) { @@ -193,97 +220,104 @@ public class PCAPanel 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(); + pcaModel.updateRcView(dim1, dim2, dim3); + rc.resetView(); } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for + * the given axis (X/Y/Z) + * + * @param index + * @param axis */ - protected void yCombobox_actionPerformed(ActionEvent e) + public void setSelectedDimensionIndex(int index, Axis axis) { - doDimensionChange(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - 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: + } } - public void outputValues_actionPerformed(ActionEvent e) + @Override + protected void outputValues_actionPerformed() { CutAndPasteTransfer cap = new CutAndPasteTransfer(); - Desktop.addInternalFrame(cap, "PCA details", 500, - 500); - - cap.setText(pca.getDetails()); + 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(); + } } - public void showLabels_actionPerformed(ActionEvent e) + @Override + protected void showLabels_actionPerformed() { rc.showLabels(showLabels.getState()); } - public void print_actionPerformed(ActionEvent e) + @Override + protected void print_actionPerformed() { PCAPrinter printer = new PCAPrinter(); printer.start(); } - public void originalSeqData_actionPerformed(ActionEvent e) + /** + * If available, shows the data which formed the inputs for the PCA as a new + * alignment + */ + @Override + 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 (seqstrings == null) + // JAL-2647 disabled after load from project (until save to project done) + if (pcaModel.getInputData() == null) { - jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); + 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 yields unaligned seqs) + // 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 { + 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 = seqstrings.getAlignmentAndColumnSelection(gc); + gc = av.getGapCharacter(); + } catch (Exception ex) + { + } + + Object[] alAndColsel = pcaModel.getInputData() + .getAlignmentAndHiddenColumns(gc); if (alAndColsel != null && alAndColsel[0] != null) { // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); - Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]); - Alignment dataset = av.getAlignment().getDataset(); + AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); + AlignmentI dataset = (av != null && av.getAlignment() != null) + ? av.getAlignment().getDataset() + : null; if (dataset != null) { al.setDataset(dataset); @@ -292,43 +326,48 @@ public class PCAPanel 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!!<<< + // >>>This is a fix for the moment, until a better solution is + // found!!<<< // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer()); - // af.addSortByOrderMenuItem(ServiceName + " Ordering", - // msaorder); + // 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); } } - /* 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); + /* + * 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 + 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); @@ -337,22 +376,22 @@ public class PCAPanel try { printJob.print(); - } - catch (Exception PrintException) + } catch (Exception PrintException) { PrintException.printStackTrace(); } } } + @Override public int print(Graphics pg, PageFormat pf, int pi) - throws PrinterException + throws PrinterException { - pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY()); + 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); } @@ -369,54 +408,53 @@ public class PCAPanel } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Handler for 'Save as EPS' option */ - public void eps_actionPerformed(ActionEvent e) + @Override + protected void eps_actionPerformed() { - makePCAImage(jalview.util.ImageMaker.EPS); + makePCAImage(ImageMaker.TYPE.EPS); } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Handler for 'Save as PNG' option */ - public void png_actionPerformed(ActionEvent e) + @Override + protected void png_actionPerformed() { - makePCAImage(jalview.util.ImageMaker.PNG); + makePCAImage(ImageMaker.TYPE.PNG); } - void makePCAImage(int type) + void makePCAImage(ImageMaker.TYPE type) { int width = rc.getWidth(); int height = rc.getHeight(); - jalview.util.ImageMaker im; + 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 + switch (type) { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.EPS, - "Make EPS file from PCA", - width, height, - null, this.getTitle()); + 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()); } @@ -424,15 +462,20 @@ public class PCAPanel } } - public void viewMenu_menuSelected() + @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()); + AlignmentPanel[] aps = PaintRefresher + .getAssociatedPanels(av.getSequenceSetId()); if (aps.length == 1 && rc.av == aps[0].av) { associateViewsMenu.setVisible(false); @@ -441,7 +484,8 @@ public class PCAPanel associateViewsMenu.setVisible(true); - if ( (viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) + if ((viewMenu + .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) { viewMenu.insertSeparator(viewMenu.getItemCount() - 1); } @@ -450,34 +494,38 @@ public class PCAPanel 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); + 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 = 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()); } }); 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(); @@ -487,4 +535,210 @@ public class PCAPanel } + /* + * (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); + } }