X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=885c3bf8a2026a9c05418479999d03e5103bf171;hb=5c45059a31d5f2ed14a8898d700ead9b3431bccf;hp=1a9f466f84081fbfc0a329ba632dc28a1ec74a67;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java old mode 100755 new mode 100644 index 1a9f466..885c3bf --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,33 +1,59 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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 file is part of Jalview. * - * 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 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 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.api.analysis.ViewBasedAnalysisI; +import jalview.bin.Cache; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.SeqCigar; +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.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! @@ -35,50 +61,108 @@ import jalview.jbgui.*; * @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; + AlignmentViewport av; - AlignmentView seqstrings; + PCAModel pcaModel; - SequenceI[] seqs; + int top = 0; /** - * Creates a new PCAPanel object. + * Creates a new PCAPanel object using default score model and parameters * - * @param av - * DOCUMENT ME! - * @param s - * DOCUMENT ME! + * @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()), + SimilarityParams.SeqSpace); + } - boolean sameLength = true; + /** + * Constructor given sequence data, a similarity (or distance) score model, + * and score calculation parameters + * + * @param alignPanel + * @param scoreModel + * @param params + */ + public PCAPanel(AlignmentPanel alignPanel, ScoreModelI scoreModel, + 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) + 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.alignment.getSequencesArray(); + seqs = av.getAlignment().getSequencesArray(); } else { - seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); + seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); + } + + // TODO can we allow PCA on unaligned data given choice of + // similarity measure parameters? + if (!checkAligned(seqstrings)) + { + JvOptionPane.showMessageDialog(Desktop.desktop, + MessageManager.getString("label.pca_sequences_not_aligned"), + MessageManager.getString("label.sequences_not_aligned"), + JvOptionPane.WARNING_MESSAGE); + + return; } + + pcaModel = 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(); + } + + /** + * Answers true if all sequences have the same aligned length, else false + * + * @param seqstrings + * @return + */ + protected boolean checkAligned(AlignmentView seqstrings) + { SeqCigar sq[] = seqstrings.getSequences(); int length = sq[0].getWidth(); - - for (int i = 0; i < seqs.length; i++) + boolean sameLength = true; + for (int i = 0; i < sq.length; i++) { if (sq[i].getWidth() != length) { @@ -86,35 +170,72 @@ public class PCAPanel extends GPCAPanel implements Runnable break; } } + return sameLength; + } - 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); + /** + * Ensure references to potentially very large objects (the PCA matrices) are + * nulled when the frame is closed + */ + protected void close_actionPerformed() + { + pcaModel = null; + } - return; + /** + * 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 = configureScoreModel(sm); + pcaModel.setScoreModel(sm2); + Thread worker = new Thread(PCAPanel.this); + worker.start(); + } + } + }); + scoreModelMenu.add(jm); + } } - - Desktop - .addInternalFrame(this, "Principal component analysis", 400, - 400); - - PaintRefresher.Register(this, av.getSequenceSetId()); - - rc = new RotatableCanvas(ap); - this.getContentPane().add(rc, BorderLayout.CENTER); - Thread worker = new Thread(this); - worker.start(); } + @Override public void bgcolour_actionPerformed(ActionEvent e) { - Color col = JColorChooser.showDialog(this, "Select Background Colour", + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_background_colour"), rc.bgColour); if (col != null) @@ -127,58 +248,86 @@ public class PCAPanel extends GPCAPanel implements Runnable /** * 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()); + jvVersionSetting.setSelected(pcaModel.isJvCalcMode()); + 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); + } + } - 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()) { - new OOMWarning("calculating PCA", er); - + pcaModel.setNucleotide(false); + pcaModel.setScoreModel(ScoreModels.getInstance() + .getDefaultModel(true)); + Thread worker = new Thread(this); + worker.start(); } + } + @Override + protected void jvVersionSetting_actionPerfomed(ActionEvent arg0) + { + pcaModel.setJvCalcMode(jvVersionSetting.isSelected()); + Thread worker = new Thread(this); + worker.start(); } /** @@ -194,14 +343,7 @@ public class PCAPanel extends GPCAPanel implements Runnable 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(); @@ -212,8 +354,9 @@ public class PCAPanel extends GPCAPanel implements Runnable * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void xCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); @@ -223,8 +366,9 @@ public class PCAPanel extends GPCAPanel implements Runnable * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void yCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); @@ -234,37 +378,49 @@ public class PCAPanel extends GPCAPanel implements Runnable * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * 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) + if (pcaModel.getSeqtrings() == null) { jalview.bin.Cache.log .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); @@ -286,14 +442,15 @@ public class PCAPanel extends GPCAPanel implements Runnable { } ; - Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc); + 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 + AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]); + AlignmentI dataset = (av != null && av.getAlignment() != null) ? av .getAlignment().getDataset() : null; if (dataset != null) { @@ -314,16 +471,17 @@ public class PCAPanel extends GPCAPanel implements Runnable // 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"); - * } + * "\n"); } * * Desktop.addInternalFrame(cap, "Original Data", 400, 400); */ @@ -331,6 +489,7 @@ public class PCAPanel extends GPCAPanel implements Runnable class PCAPrinter extends Thread implements Printable { + @Override public void run() { PrinterJob printJob = PrinterJob.getPrinterJob(); @@ -350,6 +509,7 @@ public class PCAPanel extends GPCAPanel implements Runnable } } + @Override public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -377,41 +537,51 @@ public class PCAPanel extends GPCAPanel implements Runnable * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * 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! + * 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.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.PNG, - "Make PNG image from PCA", width, height, null, null); + 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()); + 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) @@ -426,6 +596,7 @@ public class PCAPanel extends GPCAPanel implements Runnable } } + @Override public void viewMenu_menuSelected() { buildAssociatedViewMenu(); @@ -461,6 +632,7 @@ public class PCAPanel extends GPCAPanel implements Runnable buttonGroup.add(item); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { rc.applyToAllViews = false; @@ -480,6 +652,7 @@ public class PCAPanel extends GPCAPanel implements Runnable itemf.setSelected(rc.applyToAllViews); itemf.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { rc.applyToAllViews = itemf.isSelected(); @@ -489,4 +662,186 @@ public class PCAPanel extends GPCAPanel implements Runnable } + /* + * (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); + } + + /** + * If the score model is one that requires to get state data from the current + * view, allow it to do so + * + * @param sm + * @return + */ + protected ScoreModelI configureScoreModel(ScoreModelI sm) + { + if (sm instanceof ViewBasedAnalysisI) + { + try + { + sm = sm.getClass().newInstance(); + ((ViewBasedAnalysisI) sm).configureFromAlignmentView(ap); + } catch (Exception q) + { + Cache.log.error("Couldn't create a scoremodel instance for " + + sm.getName()); + } + } + return sm; + } }