X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=e9ba1e7ef6c6f2c5ace0f55232174698cb14b163;hb=e67e5f3a5b922e8a7729a0e9e9b174f46b11456c;hp=06f1b25d48fbbf92aa7cf8d27fdb3816bb4590b7;hpb=feda4a6c19b530b08c3dca57abb86cd70412e984;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java old mode 100755 new mode 100644 index 06f1b25..e9ba1e7 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,112 +1,213 @@ /* - * 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.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.SequenceI; +import jalview.jbgui.GPCAPanel; +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.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 $Revision$ */ -public class PCAPanel - extends GPCAPanel implements Runnable +public class PCAPanel extends GPCAPanel implements Runnable, + IProgressIndicator { - PCA pca; - int top; + + private IProgressIndicator progressBar; + RotatableCanvas rc; + AlignmentPanel ap; - AlignViewport av; - AlignmentView seqstrings; - SequenceI[] seqs; + + AlignmentViewport av; + + PCAModel pcaModel; + + private static final int MIN_WIDTH = 470; + + private static final int MIN_HEIGHT = 250; + + int top = 0; /** - * Creates a new PCAPanel object. - * - * @param av DOCUMENT ME! - * @param s DOCUMENT ME! + * Creates a new PCAPanel object using default score model and parameters + * + * @param alignPanel */ - public PCAPanel(AlignmentPanel ap) + public PCAPanel(AlignmentPanel alignPanel) { - this.av = ap.av; - this.ap = ap; + this(alignPanel, ScoreModels.getInstance() + .getDefaultModel(!alignPanel.av.getAlignment().isNucleotide()) + .getName(), SimilarityParams.SeqSpace); + } - boolean sameLength = true; + /** + * 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(); - seqstrings = av.getAlignmentView(av.getSelectionGroup() != null); - if (av.getSelectionGroup() == null) - { - seqs = av.alignment.getSequencesArray(); - } - else - { - seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); - } - SeqCigar sq[] = seqstrings.getSequences(); - int length = sq[0].getWidth(); + progressBar = new ProgressBar(statusPanel, statusBar); - for (int i = 0; i < seqs.length; i++) + addInternalFrameListener(new InternalFrameAdapter() { - 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(); } + /** + * 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 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) { - 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) { @@ -118,66 +219,78 @@ public class PCAPanel /** * DOCUMENT ME! */ + @Override public void run() { + 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++; - } - - double[][] comps = new double[ii][ii]; - - for (int i = 0; i < ii; i++) - { - if (pca.getEigenvalue(i) > 1e-4) - { - comps[i] = pca.component(i); - } - } - - ////////////////// + calcSettings.setEnabled(false); + pcaModel.run(); + // //////////////// xCombobox.setSelectedIndex(0); yCombobox.setSelectedIndex(1); zCombobox.setSelectedIndex(2); - top = pca.getM().rows - 1; + pcaModel.updateRc(rc); + // rc.invalidate(); + nuclSetting.setSelected(pcaModel.isNucleotide()); + protSetting.setSelected(!pcaModel.isNucleotide()); + top = pcaModel.getTop(); - Vector points = new Vector(); - float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100); + } catch (OutOfMemoryError er) + { + new OOMWarning("calculating PCA", er); + 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)); + } + } - for (int i = 0; i < pca.getM().rows; i++) - { - SequencePoint sp = new SequencePoint(seqs[i], scores[i]); - points.addElement(sp); - } + @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(); + } - rc.setPoints(points, pca.getM().rows); - rc.repaint(); + } - addKeyListener(rc); + @Override + protected void protSetting_actionPerfomed(ActionEvent arg0) + { - } - catch (OutOfMemoryError er) + if (pcaModel.isNucleotide()) { - 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(); - + pcaModel.setNucleotide(false); + pcaModel.setScoreModel(ScoreModels.getInstance() + .getDefaultModel(true)); + Thread worker = new Thread(this); + worker.start(); } - } /** @@ -193,14 +306,7 @@ 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]; - } - + pcaModel.updateRcView(dim1, dim2, dim3); rc.img = null; rc.rotmat.setIdentity(); rc.initAxes(); @@ -209,9 +315,11 @@ public class PCAPanel /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void xCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); @@ -219,9 +327,11 @@ public class PCAPanel /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void yCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); @@ -229,61 +339,82 @@ public class PCAPanel /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override protected void zCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); } + @Override public void outputValues_actionPerformed(ActionEvent e) { 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(); + } } + @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 (seqstrings == null) + // 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 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 alignmnt 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.getSeqtrings() + .getAlignmentAndColumnSelection(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); @@ -292,39 +423,36 @@ 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, + (ColumnSelection) 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(); @@ -337,18 +465,18 @@ 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.drawScene(pg); @@ -370,46 +498,53 @@ public class PCAPanel /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void eps_actionPerformed(ActionEvent e) { - makePCAImage(jalview.util.ImageMaker.EPS); + makePCAImage(jalview.util.ImageMaker.TYPE.EPS); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ + @Override public void png_actionPerformed(ActionEvent e) { - makePCAImage(jalview.util.ImageMaker.PNG); + makePCAImage(jalview.util.ImageMaker.TYPE.PNG); } - void makePCAImage(int type) + void makePCAImage(jalview.util.ImageMaker.TYPE type) { int width = rc.getWidth(); int height = rc.getHeight(); jalview.util.ImageMaker im; - if (type == jalview.util.ImageMaker.PNG) + if (type == jalview.util.ImageMaker.TYPE.PNG) { im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.PNG, - "Make PNG image from PCA", - width, height, - null, null); + 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.EPS, - "Make EPS file from PCA", - width, height, - null, this.getTitle()); + jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", + width, height, null, this.getTitle(), null, 0, false); + } if (im.getGraphics() != null) @@ -424,6 +559,7 @@ public class PCAPanel } } + @Override public void viewMenu_menuSelected() { buildAssociatedViewMenu(); @@ -431,8 +567,8 @@ public class PCAPanel 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 +577,7 @@ 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); } @@ -459,6 +595,7 @@ public class PCAPanel buttonGroup.add(item); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { rc.applyToAllViews = false; @@ -478,6 +615,7 @@ public class PCAPanel itemf.setSelected(rc.applyToAllViews); itemf.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { rc.applyToAllViews = itemf.isSelected(); @@ -487,4 +625,162 @@ public class PCAPanel } + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent + * ) + */ + @Override + protected void outputPoints_actionPerformed(ActionEvent e) + { + 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(ActionEvent e) + { + 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(ActionEvent e) + { + int t = top; + top = 0; // ugly - prevents dimensionChanged events from being processed + xCombobox.setSelectedIndex(0); + yCombobox.setSelectedIndex(1); + top = t; + zCombobox.setSelectedIndex(2); + } }