X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=57a14a0cc38e01ca3047bb47bc318c475c981458;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=8f3ff73b400231b7781748f7eaebed0de5aa92bd;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java old mode 100755 new mode 100644 index 8f3ff73..57a14a0 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,141 +1,739 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ - -package jalview.gui; - -import jalview.datamodel.*; -import jalview.analysis.PCA; -import jalview.jbgui.*; -import java.awt.*; -import java.awt.event.*; -import java.util.*; - - -public class PCAPanel extends GPCAPanel implements Runnable -{ - PCA pca; - int top; - RotatableCanvas rc; - AlignViewport av; - - public void run() - { - // do stuff - } - - public PCAPanel(AlignViewport av, SequenceI[] s) { - - this.av = av; - if(av.getSelectionGroup()!=null && av.getSelectionGroup().getSize()>3) - { - s = new Sequence[av.getSelectionGroup().getSize()]; - for(int i=0; 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(s[i],scores[i]); - points.addElement(sp); - } - - rc = new RotatableCanvas(av,points,pca.getM().rows); - - //rc.printPoints(); - - add(rc, BorderLayout.CENTER); - } - - - void doDimensionChange() - { - if(top==0) - return; - - int dim1 = top - xCombobox.getSelectedIndex(); - int dim2 = top - yCombobox.getSelectedIndex(); - int dim3 = top - zCombobox.getSelectedIndex(); - - float[][] scores = pca.getComponents(dim1,dim2,dim3,100); - for (int i=0; i < pca.getM().rows; i++) { - ((SequencePoint)rc.points.elementAt(i)).coord = scores[i]; - } - - rc.img = null; - rc.rotmat.setIdentity(); - rc.initAxes(); - rc.paint(rc.getGraphics()); - } - - protected void xCombobox_actionPerformed(ActionEvent e) - { - doDimensionChange(); - } - - protected void yCombobox_actionPerformed(ActionEvent e) - { - doDimensionChange(); - } - - protected void zCombobox_actionPerformed(ActionEvent e) - { - doDimensionChange(); - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +import jalview.datamodel.Alignment; +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 +{ + + private IProgressIndicator progressBar; + + RotatableCanvas rc; + + AlignmentPanel ap; + + AlignmentViewport av; + + PCAModel pcaModel; + + int top = 0; + + /** + * Creates a new PCAPanel object. + * + * @param av + * DOCUMENT ME! + * @param s + * DOCUMENT ME! + */ + public PCAPanel(AlignmentPanel ap) + { + this.av = ap.av; + this.ap = ap; + + progressBar = new ProgressBar(statusPanel, statusBar); + + 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 (!selected) + { + seqs = av.getAlignment().getSequencesArray(); + } + else + { + seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment()); + } + SeqCigar sq[] = seqstrings.getSequences(); + int length = sq[0].getWidth(); + + for (int i = 0; i < seqs.length; i++) + { + if (sq[i].getWidth() != length) + { + sameLength = false; + break; + } + } + + if (!sameLength) + { + 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); + } + } + } + } + + public void bgcolour_actionPerformed(ActionEvent e) + { + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_backgroud_colour"), + rc.bgColour); + + if (col != null) + { + rc.bgColour = col; + } + rc.repaint(); + } + + /** + * DOCUMENT ME! + */ + 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 + { + calcSettings.setEnabled(false); + pcaModel.run(); + // //////////////// + xCombobox.setSelectedIndex(0); + yCombobox.setSelectedIndex(1); + zCombobox.setSelectedIndex(2); + + pcaModel.updateRc(rc); + // rc.invalidate(); + nuclSetting.setSelected(pcaModel.isNucleotide()); + protSetting.setSelected(!pcaModel.isNucleotide()); + jvVersionSetting.setSelected(pcaModel.isJvCalcMode()); + top = pcaModel.getTop(); + + } 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); + } + } + + @Override + protected void nuclSetting_actionPerfomed(ActionEvent arg0) + { + if (!pcaModel.isNucleotide()) + { + pcaModel.setNucleotide(true); + 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! + */ + void doDimensionChange() + { + if (top == 0) + { + return; + } + + int dim1 = top - xCombobox.getSelectedIndex(); + int dim2 = top - yCombobox.getSelectedIndex(); + int dim3 = top - zCombobox.getSelectedIndex(); + pcaModel.updateRcView(dim1, dim2, dim3); + rc.img = null; + rc.rotmat.setIdentity(); + rc.initAxes(); + rc.paint(rc.getGraphics()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void xCombobox_actionPerformed(ActionEvent e) + { + doDimensionChange(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void yCombobox_actionPerformed(ActionEvent e) + { + doDimensionChange(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void zCombobox_actionPerformed(ActionEvent e) + { + doDimensionChange(); + } + + public void outputValues_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + 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) + { + rc.showLabels(showLabels.getState()); + } + + public void print_actionPerformed(ActionEvent e) + { + PCAPrinter printer = new PCAPrinter(); + printer.start(); + } + + 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 (pcaModel.getSeqtrings() == null) + { + 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) + // or create a selection box around columns in alignment view + // test Alignment(SeqCigar[]) + char gc = '-'; + try + { + // we try to get the associated view's gap character + // but this may fail if the view was closed... + gc = av.getGapCharacter(); + } catch (Exception ex) + { + } + ; + Object[] alAndColsel = pcaModel.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; + if (dataset != null) + { + al.setDataset(dataset); + } + + if (true) + { + // make a new frame! + 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!!<<< + // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer()); + + // af.addSortByOrderMenuItem(ServiceName + " Ordering", + // msaorder); + + Desktop.addInternalFrame(af, MessageManager.formatMessage( + "label.original_data_for_params", + new String[] { this.title }), AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + } + } + /* + * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i < + * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 + + * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] + + * "\n"); } + * + * Desktop.addInternalFrame(cap, "Original Data", 400, 400); + */ + } + + class PCAPrinter extends Thread implements Printable + { + public void run() + { + PrinterJob printJob = PrinterJob.getPrinterJob(); + PageFormat pf = printJob.pageDialog(printJob.defaultPage()); + + printJob.setPrintable(this, pf); + + if (printJob.printDialog()) + { + try + { + printJob.print(); + } catch (Exception PrintException) + { + PrintException.printStackTrace(); + } + } + } + + public int print(Graphics pg, PageFormat pf, int pi) + throws PrinterException + { + pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); + + rc.drawBackground(pg, rc.bgColour); + rc.drawScene(pg); + if (rc.drawAxes == true) + { + rc.drawAxes(pg); + } + + if (pi == 0) + { + return Printable.PAGE_EXISTS; + } + else + { + return Printable.NO_SUCH_PAGE; + } + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void eps_actionPerformed(ActionEvent e) + { + makePCAImage(jalview.util.ImageMaker.TYPE.EPS); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void png_actionPerformed(ActionEvent e) + { + makePCAImage(jalview.util.ImageMaker.TYPE.PNG); + } + + void makePCAImage(jalview.util.ImageMaker.TYPE type) + { + int width = rc.getWidth(); + int height = rc.getHeight(); + + jalview.util.ImageMaker im; + + 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); + } + 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()); + } + else + { + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", + width, height, null, this.getTitle()); + + } + + if (im.getGraphics() != null) + { + rc.drawBackground(im.getGraphics(), Color.black); + rc.drawScene(im.getGraphics()); + if (rc.drawAxes == true) + { + rc.drawAxes(im.getGraphics()); + } + im.writeImage(); + } + } + + public void viewMenu_menuSelected() + { + buildAssociatedViewMenu(); + } + + void buildAssociatedViewMenu() + { + AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av + .getSequenceSetId()); + if (aps.length == 1 && rc.av == aps[0].av) + { + associateViewsMenu.setVisible(false); + return; + } + + associateViewsMenu.setVisible(true); + + if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem)) + { + viewMenu.insertSeparator(viewMenu.getItemCount() - 1); + } + + associateViewsMenu.removeAll(); + + JRadioButtonMenuItem item; + ButtonGroup buttonGroup = new ButtonGroup(); + int i, iSize = aps.length; + final PCAPanel thisPCAPanel = this; + for (i = 0; i < iSize; i++) + { + final AlignmentPanel ap = aps[i]; + item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av); + buttonGroup.add(item); + item.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + rc.applyToAllViews = false; + rc.av = ap.av; + rc.ap = ap; + PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId()); + } + }); + + associateViewsMenu.add(item); + } + + final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views"); + + buttonGroup.add(itemf); + + itemf.setSelected(rc.applyToAllViews); + itemf.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + rc.applyToAllViews = itemf.isSelected(); + } + }); + associateViewsMenu.add(itemf); + + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent + * ) + */ + 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) + */ + 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); + } +}