X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=51d247d4ce659230218ca4280504b9e5f6db05f2;hb=853624fb32058cccc544ae7d13af6ad4b0800b6c;hp=eb7806f136cbb00a5bad662c0dc0998a0c128eec;hpb=55c883270e9f64da9562a24f09dfe5f2f079e59a;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java old mode 100755 new mode 100644 index eb7806f..51d247d --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,51 +1,75 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * 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. - * + * 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 . + * 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 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.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.schemes.ResidueProperties; +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.JOptionPane; +import javax.swing.JRadioButtonMenuItem; + /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ -public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator +public class PCAPanel extends GPCAPanel implements Runnable, + IProgressIndicator { + private IProgressIndicator progressBar; RotatableCanvas rc; AlignmentPanel ap; - AlignViewport av; + AlignmentViewport av; + PCAModel pcaModel; - int top=0; + + int top = 0; /** * Creates a new PCAPanel object. @@ -60,12 +84,15 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator this.av = ap.av; this.ap = ap; - boolean sameLength = true; + progressBar = new ProgressBar(statusPanel, statusBar); - AlignmentView seqstrings = av.getAlignmentView(av.getSelectionGroup() != null); - boolean nucleotide=av.getAlignment().isNucleotide(); + boolean sameLength = true; + boolean selected = av.getSelectionGroup() != null + && av.getSelectionGroup().getSize() > 0; + AlignmentView seqstrings = av.getAlignmentView(selected); + boolean nucleotide = av.getAlignment().isNucleotide(); SequenceI[] seqs; - if (av.getSelectionGroup() == null) + if (!selected) { seqs = av.getAlignment().getSequencesArray(); } @@ -87,28 +114,65 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator 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); + JOptionPane.showMessageDialog(Desktop.desktop, + MessageManager.getString("label.pca_sequences_not_aligned"), + MessageManager.getString("label.sequences_not_aligned"), + JOptionPane.WARNING_MESSAGE); return; } pcaModel = new PCAModel(seqstrings, seqs, nucleotide); PaintRefresher.Register(this, av.getSequenceSetId()); - + rc = new RotatableCanvas(ap); this.getContentPane().add(rc, BorderLayout.CENTER); Thread worker = new Thread(this); worker.start(); } + @Override + protected void scoreMatrix_menuSelected() + { + scoreMatrixMenu.removeAll(); + for (final String sm : ResidueProperties.scoreMatrices.keySet()) + { + if (ResidueProperties.getScoreMatrix(sm) != null) + { + // create an entry for this score matrix for use in PCA + JCheckBoxMenuItem jm = new JCheckBoxMenuItem(); + jm.setText(MessageManager.getStringOrReturn("label.score_model_", + sm)); + jm.setSelected(pcaModel.getScore_matrix().equals(sm)); + if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices + .get(sm).isProtein()) + || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices + .get(sm).isDNA()) + { + final PCAPanel us = this; + jm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (!pcaModel.getScore_matrix().equals(sm)) + { + pcaModel.setScore_matrix(sm); + Thread worker = new Thread(us); + worker.start(); + } + } + }); + scoreMatrixMenu.add(jm); + } + } + } + } + + @Override public void bgcolour_actionPerformed(ActionEvent e) { - Color col = JColorChooser.showDialog(this, "Select Background Colour", + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_backgroud_colour"), rc.bgColour); if (col != null) @@ -121,14 +185,16 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator /** * DOCUMENT ME! */ + @Override public void run() { - long progId=System.currentTimeMillis(); - IProgressIndicator progress=this; - String message="Recalculating PCA"; - if (getParent()==null) { - progress=ap.alignFrame; - message = "Calculating PCA"; + 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 @@ -139,51 +205,66 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator xCombobox.setSelectedIndex(0); yCombobox.setSelectedIndex(1); zCombobox.setSelectedIndex(2); - + pcaModel.updateRc(rc); // rc.invalidate(); nuclSetting.setSelected(pcaModel.isNucleotide()); protSetting.setSelected(!pcaModel.isNucleotide()); - top=pcaModel.getTop(); + jvVersionSetting.setSelected(pcaModel.isJvCalcMode()); + top = pcaModel.getTop(); } catch (OutOfMemoryError er) { new OOMWarning("calculating PCA", er); return; - } - finally { + } finally + { progress.setProgressBar("", progId); } calcSettings.setEnabled(true); repaint(); - if (getParent()==null) + if (getParent() == null) { addKeyListener(rc); - Desktop.addInternalFrame(this, "Principal component analysis", 475, 450); + Desktop.addInternalFrame(this, MessageManager + .getString("label.principal_component_analysis"), 475, 450); } } + @Override protected void nuclSetting_actionPerfomed(ActionEvent arg0) { if (!pcaModel.isNucleotide()) { pcaModel.setNucleotide(true); - Thread worker = new Thread(this); - worker.start(); + pcaModel.setScore_matrix("DNA"); + Thread worker = new Thread(this); + worker.start(); } - + } + @Override protected void protSetting_actionPerfomed(ActionEvent arg0) { - + if (pcaModel.isNucleotide()) { pcaModel.setNucleotide(false); + pcaModel.setScore_matrix("BLOSUM62"); + 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(); - } } + /** * DOCUMENT ME! */ @@ -210,6 +291,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator * @param e * DOCUMENT ME! */ + @Override protected void xCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); @@ -221,6 +303,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator * @param e * DOCUMENT ME! */ + @Override protected void yCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); @@ -232,18 +315,21 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator * @param e * DOCUMENT ME! */ + @Override protected void zCombobox_actionPerformed(ActionEvent e) { doDimensionChange(); } + @Override public void outputValues_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); try { cap.setText(pcaModel.getDetails()); - Desktop.addInternalFrame(cap, "PCA details", 500, 500); + Desktop.addInternalFrame(cap, + MessageManager.getString("label.pca_details"), 500, 500); } catch (OutOfMemoryError oom) { new OOMWarning("opening PCA details", oom); @@ -251,17 +337,20 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator } } + @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 @@ -288,14 +377,15 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator { } ; - Object[] alAndColsel = pcaModel.getSeqtrings().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) { @@ -316,8 +406,10 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator // 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); } } /* @@ -332,6 +424,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator class PCAPrinter extends Thread implements Printable { + @Override public void run() { PrinterJob printJob = PrinterJob.getPrinterJob(); @@ -351,6 +444,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator } } + @Override public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -380,9 +474,10 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator * @param e * DOCUMENT ME! */ + @Override public void eps_actionPerformed(ActionEvent e) { - makePCAImage(jalview.util.ImageMaker.EPS); + makePCAImage(jalview.util.ImageMaker.TYPE.EPS); } /** @@ -391,28 +486,37 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator * @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); + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA", + width, height, null, null, null, 0, false); + } + else if (type == jalview.util.ImageMaker.TYPE.EPS) + { + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA", + width, height, null, this.getTitle(), null, 0, false); } else { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.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) @@ -427,6 +531,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator } } + @Override public void viewMenu_menuSelected() { buildAssociatedViewMenu(); @@ -462,6 +567,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator buttonGroup.add(item); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { rc.applyToAllViews = false; @@ -481,6 +587,7 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator itemf.setSelected(rc.applyToAllViews); itemf.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { rc.applyToAllViews = itemf.isSelected(); @@ -497,13 +604,18 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator * 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, "Points for " + getTitle(), 500, 500); + 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); @@ -511,8 +623,6 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator } } - - /* * (non-Javadoc) * @@ -520,14 +630,18 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator * 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, "Transformed points for " + getTitle(), - 500, 500); + 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); @@ -535,116 +649,110 @@ public class PCAPanel extends GPCAPanel implements Runnable, IProgressIndicator } } - // methods for implementing IProgressIndicator - // need to refactor to a reusable stub class - Hashtable progressBars, progressBarHandlers; - /* * (non-Javadoc) - * + * * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ @Override public void setProgressBar(String message, long 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(); + 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) { - if (progressBarHandlers == null || !progressBars.contains(new Long(id))) - { - throw new Error( - "call setProgressBar before registering the progress bar's handler."); - } - progressBarHandlers.put(new Long(id), handler); - final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); - if (handler.canCancel()) - { - JButton cancel = new JButton("Cancel"); - final IProgressIndicator us = this; - cancel.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - handler.cancelActivity(id); - us.setProgressBar( - "Cancelled " - + ((JLabel) progressPanel.getComponent(0)) - .getText(), id); - } - }); - progressPanel.add(cancel, BorderLayout.EAST); - } + 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() { - if (progressBars != null && progressBars.size() > 0) - { - return true; - } - return false; + return progressBar.operationInProgress(); } + @Override protected void resetButton_actionPerformed(ActionEvent e) { - int t=top; - top=0; // ugly - prevents dimensionChanged events from being processed + int t = top; + top = 0; // ugly - prevents dimensionChanged events from being processed xCombobox.setSelectedIndex(0); yCombobox.setSelectedIndex(1); - top=t; + top = t; zCombobox.setSelectedIndex(2); } }