From 2c99f6f286b5a4bb09b79131f620eb44d70ee3fe Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 13 Aug 2008 13:31:06 +0000 Subject: [PATCH] ensure input data can be recovered for tree and PCA even if alignment view was closed --- src/jalview/appletgui/PCAPanel.java | 10 +- src/jalview/appletgui/TreePanel.java | 10 +- src/jalview/gui/PCAPanel.java | 974 +++++++++++++++++----------------- src/jalview/gui/TreePanel.java | 10 +- 4 files changed, 514 insertions(+), 490 deletions(-) diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java index a5268bf..ee54478 100755 --- a/src/jalview/appletgui/PCAPanel.java +++ b/src/jalview/appletgui/PCAPanel.java @@ -219,8 +219,14 @@ public class PCAPanel // 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()); + 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) { diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java index 5ddea1d..6ab01aa 100755 --- a/src/jalview/appletgui/TreePanel.java +++ b/src/jalview/appletgui/TreePanel.java @@ -120,8 +120,14 @@ public class TreePanel // test Alignment(SeqCigar[]) if (tree.seqData != null) { - Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av. - getGapCharacter()); + 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 = tree.seqData.getAlignmentAndColumnSelection(gc); if (alAndColsel != null && alAndColsel[0] != null) { diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 772e67e..15c3d59 100755 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,484 +1,490 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 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) - { - 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(); - } - } - - 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); - - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 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 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) + { + 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[]) + 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.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(); + } + } + + 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); + + } + +} diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 72bdbf1..762ad58 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -410,8 +410,14 @@ public class TreePanel // 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 = tree.seqData.getAlignmentAndColumnSelection(av. - getGapCharacter()); + 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 = tree.seqData.getAlignmentAndColumnSelection(gc); if (alAndColsel != null && alAndColsel[0] != null) { -- 1.7.10.2