X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=1a9f466f84081fbfc0a329ba632dc28a1ec74a67;hb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;hp=06f1b25d48fbbf92aa7cf8d27fdb3816bb4590b7;hpb=feda4a6c19b530b08c3dca57abb86cd70412e984;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 06f1b25..1a9f466 100755 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,17 +1,17 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * + * 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 + * * 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 @@ -31,26 +31,33 @@ import jalview.jbgui.*; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class PCAPanel - extends GPCAPanel implements Runnable +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! + * + * @param av + * DOCUMENT ME! + * @param s + * DOCUMENT ME! */ public PCAPanel(AlignmentPanel ap) { @@ -82,18 +89,20 @@ public class PCAPanel 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, + "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); + Desktop + .addInternalFrame(this, "Principal component analysis", 400, + 400); PaintRefresher.Register(this, av.getSequenceSetId()); @@ -106,7 +115,7 @@ public class PCAPanel public void bgcolour_actionPerformed(ActionEvent e) { Color col = JColorChooser.showDialog(this, "Select Background Colour", - rc.bgColour); + rc.bgColour); if (col != null) { @@ -128,7 +137,7 @@ public class PCAPanel // Now find the component coordinates int ii = 0; - while ( (ii < seqs.length) && (seqs[ii] != null)) + while ((ii < seqs.length) && (seqs[ii] != null)) { ii++; } @@ -143,7 +152,7 @@ public class PCAPanel } } - ////////////////// + // //////////////// xCombobox.setSelectedIndex(0); yCombobox.setSelectedIndex(1); zCombobox.setSelectedIndex(2); @@ -164,17 +173,9 @@ public class PCAPanel addKeyListener(rc); - } - catch (OutOfMemoryError er) + } 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(); + new OOMWarning("calculating PCA", er); } @@ -198,7 +199,7 @@ public class PCAPanel for (int i = 0; i < pca.getM().rows; i++) { - ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i]; + ((SequencePoint) rc.points.elementAt(i)).coord = scores[i]; } rc.img = null; @@ -209,8 +210,9 @@ public class PCAPanel /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void xCombobox_actionPerformed(ActionEvent e) { @@ -219,8 +221,9 @@ public class PCAPanel /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void yCombobox_actionPerformed(ActionEvent e) { @@ -229,8 +232,9 @@ public class PCAPanel /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void zCombobox_actionPerformed(ActionEvent e) { @@ -240,8 +244,7 @@ public class PCAPanel public void outputValues_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); - Desktop.addInternalFrame(cap, "PCA details", 500, - 500); + Desktop.addInternalFrame(cap, "PCA details", 500, 500); cap.setText(pca.getDetails()); } @@ -259,31 +262,39 @@ public class PCAPanel 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 + // 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."); + 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) {}; + 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; + Alignment al = new Alignment((SequenceI[]) alAndColsel[0]); + Alignment dataset = (av != null && av.getAlignment() != null) ? av + .getAlignment().getDataset() : null; if (dataset != null) { al.setDataset(dataset); @@ -292,38 +303,33 @@ 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); + 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 { public void run() { @@ -337,8 +343,7 @@ public class PCAPanel try { printJob.print(); - } - catch (Exception PrintException) + } catch (Exception PrintException) { PrintException.printStackTrace(); } @@ -346,9 +351,9 @@ public class PCAPanel } 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); @@ -370,8 +375,9 @@ public class PCAPanel /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void eps_actionPerformed(ActionEvent e) { @@ -380,8 +386,9 @@ public class PCAPanel /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void png_actionPerformed(ActionEvent e) { @@ -397,19 +404,14 @@ public class PCAPanel 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); + 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()); + im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, + "Make EPS file from PCA", width, height, null, this + .getTitle()); } if (im.getGraphics() != null) @@ -431,8 +433,8 @@ 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 +443,7 @@ 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); }