X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=084311fa6b8942e46247dd52abeb2d55249ad660;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=ea4f44e2f7bc3ab40aee3dd63439053f70fbba44;hpb=f3bc67915e61855d87866b4a614fe7a953813408;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index ea4f44e..084311f 100755 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,413 +1,571 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 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.analysis.*; - -import jalview.datamodel.*; - -import jalview.jbgui.*; - -import java.awt.*; -import java.awt.event.*; - -import java.util.*; -import javax.swing.*; -import java.awt.print.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class PCAPanel extends GPCAPanel implements Runnable -{ - PCA pca; - int top; - RotatableCanvas rc; - AlignViewport av; - AlignmentView seqstrings; - SequenceI [] seqs; - - /** - * Creates a new PCAPanel object. - * - * @param av DOCUMENT ME! - * @param s DOCUMENT ME! - */ - public PCAPanel(AlignViewport av) - { - this.av = av; - - boolean sameLength = true; - - 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(); - - for (int i = 0; i < seqs.length; i++) - { - if (sq[i].getWidth() != length) - { - sameLength = false; - break; - } - } - - 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); - - return; - } - - - Desktop.addInternalFrame(this, "Principal component analysis", - 400, 400); - - - rc = new RotatableCanvas(av); - this.getContentPane().add(rc, BorderLayout.CENTER); - Thread worker = new Thread(this); - worker.start(); - } - - public void bgcolour_actionPerformed(ActionEvent e) - { - Color col = JColorChooser.showDialog(this, "Select Background Colour", - rc.bgColour); - - if(col!=null) - rc.bgColour = col; - rc.repaint(); - } - - - - - /** - * DOCUMENT ME! - */ - public void run() - { - 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); - } - } - - ////////////////// - 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); - } - - rc.setPoints(points, pca.getM().rows); - rc.repaint(); - } - 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(); - - } - - } - - /** - * DOCUMENT ME! - */ - 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()); - } - - /** - * 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(); - Desktop.addInternalFrame(cap, "PCA details", 500, - 500); - - cap.setText(pca.getDetails()); - } - - 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 (seqstrings==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[]) - Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av. - getGapCharacter()); - - - if (alAndColsel != null && alAndColsel[0]!=null) - { - // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); - - Alignment al = new Alignment((SequenceI[]) alAndColsel[0]); - Alignment dataset = av.getAlignment().getDataset(); - 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, "Original Data for " + 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.EPS); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void png_actionPerformed(ActionEvent e) - { - makePCAImage(jalview.util.ImageMaker.PNG); - } - - void makePCAImage(int type) - { - int width = rc.getWidth(); - int height = rc.getHeight(); - - jalview.util.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 - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.EPS, - "Make EPS 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(); - } - } - } +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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 . + */ +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.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class PCAPanel extends GPCAPanel implements Runnable +{ + + PCA pca; + + int top; + + RotatableCanvas rc; + + AlignmentPanel ap; + + AlignViewport av; + + AlignmentView seqstrings; + + SequenceI[] seqs; + + /** + * Creates a new PCAPanel object. + * + * @param av + * DOCUMENT ME! + * @param s + * DOCUMENT ME! + */ + public PCAPanel(AlignmentPanel ap) + { + this.av = ap.av; + this.ap = ap; + + boolean sameLength = true; + + 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(); + + for (int i = 0; i < seqs.length; i++) + { + if (sq[i].getWidth() != length) + { + sameLength = false; + break; + } + } + + 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); + + return; + } + + 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(); + } + + public void bgcolour_actionPerformed(ActionEvent e) + { + Color col = JColorChooser.showDialog(this, "Select Background Colour", + rc.bgColour); + + if (col != null) + { + rc.bgColour = col; + } + rc.repaint(); + } + + /** + * DOCUMENT ME! + */ + public void run() + { + 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); + } + } + + // //////////////// + 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); + } + + rc.setPoints(points, pca.getM().rows); + rc.repaint(); + + addKeyListener(rc); + + } catch (OutOfMemoryError er) + { + new OOMWarning("calculating PCA", er); + + } + + } + + /** + * DOCUMENT ME! + */ + 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()); + } + + /** + * 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(pca.getDetails()); + Desktop.addInternalFrame(cap, "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 (seqstrings == 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 = seqstrings.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, "Original Data for " + 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.EPS); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void png_actionPerformed(ActionEvent e) + { + makePCAImage(jalview.util.ImageMaker.PNG); + } + + void makePCAImage(int type) + { + int width = rc.getWidth(); + int height = rc.getHeight(); + + jalview.util.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 + { + im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, + "Make EPS 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(getPointsasCsv(false)); + Desktop.addInternalFrame(cap, "Points for "+getTitle(), 500, 500); + } catch (OutOfMemoryError oom) + { + new OOMWarning("exporting PCA points",oom); + cap.dispose(); + } + } + + private String getPointsasCsv(boolean transformed) + { + StringBuffer csv = new StringBuffer(); + csv.append("\"Sequence\""); + if (transformed) { + csv.append(","); + csv.append(xCombobox.getSelectedIndex()); + csv.append(","); + csv.append(yCombobox.getSelectedIndex()); + csv.append(","); + csv.append(zCombobox.getSelectedIndex()); + } else { + for (int d=1,dmax=pca.component(1).length;d<=dmax;d++) + { + csv.append(","+d); + } + } + csv.append("\n"); + for (int s=0;s=0;d--) + { + csv.append(","); + csv.append(fl[d]); + } + } else { + // output current x,y,z coords for points + fl = rc.getPointPosition(s); + for (int d=0; d