/* * 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 Softwarechang * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.gui; import java.beans.*; import java.io.*; import java.util.*; import java.awt.*; import java.awt.datatransfer.*; import java.awt.dnd.*; import java.awt.event.*; import java.awt.print.*; import javax.swing.*; import javax.swing.event.MenuEvent; import jalview.analysis.*; import jalview.commands.*; import jalview.datamodel.*; import jalview.io.*; import jalview.jbgui.*; import jalview.schemes.*; import jalview.ws.*; /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ public class AlignFrame extends GAlignFrame implements DropTargetListener, IProgressIndicator { /** DOCUMENT ME!! */ public static final int DEFAULT_WIDTH = 700; /** DOCUMENT ME!! */ public static final int DEFAULT_HEIGHT = 500; public AlignmentPanel alignPanel; AlignViewport viewport; Vector alignPanels = new Vector(); /** * Last format used to load or save alignments in this window */ String currentFileFormat = null; /** * Current filename for this alignment */ String fileName = null; /** * Creates a new AlignFrame object. * * @param al DOCUMENT ME! */ public AlignFrame(AlignmentI al, int width, int height) { this(al, null, width, height); } /** * new alignment window with hidden columns * @param al AlignmentI * @param hiddenColumns ColumnSelection or null */ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height) { this.setSize(width, height); viewport = new AlignViewport(al, hiddenColumns); alignPanel = new AlignmentPanel(this, viewport); if(al.getDataset()==null) { al.setDataset(null); } addAlignmentPanel(alignPanel, true); init(); } /** * Make a new AlignFrame from exisiting alignmentPanels * @param ap AlignmentPanel * @param av AlignViewport */ public AlignFrame(AlignmentPanel ap) { viewport = ap.av; alignPanel = ap; addAlignmentPanel(ap, false); init(); } void init() { if (viewport.conservation == null) { BLOSUM62Colour.setEnabled(false); conservationMenuItem.setEnabled(false); modifyConservation.setEnabled(false); // PIDColour.setEnabled(false); // abovePIDThreshold.setEnabled(false); // modifyPID.setEnabled(false); } String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort"); if (sortby.equals("Id")) { sortIDMenuItem_actionPerformed(null); } else if (sortby.equals("Pairwise Identity")) { sortPairwiseMenuItem_actionPerformed(null); } if (Desktop.desktop != null) { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); addServiceListeners(); setGUINucleotide(viewport.alignment.isNucleotide()); } setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); if (viewport.wrapAlignment) { wrapMenuItem_actionPerformed(null); } if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW",false)) { this.overviewMenuItem_actionPerformed(null); } addKeyListener(); } /** * Change the filename and format for the alignment, and * enable the 'reload' button functionality. * @param file valid filename * @param format format of file */ public void setFileName(String file, String format) { fileName = file; currentFileFormat = format; reload.setEnabled(true); } void addKeyListener() { addKeyListener(new KeyAdapter() { public void keyPressed(KeyEvent evt) { if (viewport.cursorMode && ( (evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9) ) && Character.isDigit(evt.getKeyChar())) alignPanel.seqPanel.numberPressed(evt.getKeyChar()); switch (evt.getKeyCode()) { case 27: // escape key deselectAllSequenceMenuItem_actionPerformed(null); break; case KeyEvent.VK_DOWN: if (evt.isAltDown() || !viewport.cursorMode) moveSelectedSequences(false); if (viewport.cursorMode) alignPanel.seqPanel.moveCursor(0, 1); break; case KeyEvent.VK_UP: if (evt.isAltDown() || !viewport.cursorMode) moveSelectedSequences(true); if (viewport.cursorMode) alignPanel.seqPanel.moveCursor(0, -1); break; case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); else alignPanel.seqPanel.moveCursor( -1, 0); break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); else alignPanel.seqPanel.moveCursor(1, 0); break; case KeyEvent.VK_SPACE: if (viewport.cursorMode) { alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() || evt.isShiftDown() || evt.isAltDown()); } break; case KeyEvent.VK_DELETE: case KeyEvent.VK_BACK_SPACE: if (!viewport.cursorMode) { cut_actionPerformed(null); } else { alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown() || evt.isAltDown()); } break; case KeyEvent.VK_S: if (viewport.cursorMode) { alignPanel.seqPanel.setCursorRow(); } break; case KeyEvent.VK_C: if (viewport.cursorMode && !evt.isControlDown()) { alignPanel.seqPanel.setCursorColumn(); } break; case KeyEvent.VK_P: if (viewport.cursorMode) { alignPanel.seqPanel.setCursorPosition(); } break; case KeyEvent.VK_ENTER: case KeyEvent.VK_COMMA: if (viewport.cursorMode) { alignPanel.seqPanel.setCursorRowAndColumn(); } break; case KeyEvent.VK_Q: if (viewport.cursorMode) { alignPanel.seqPanel.setSelectionAreaAtCursor(true); } break; case KeyEvent.VK_M: if (viewport.cursorMode) { alignPanel.seqPanel.setSelectionAreaAtCursor(false); } break; case KeyEvent.VK_F2: viewport.cursorMode = !viewport.cursorMode; statusBar.setText("Keyboard editing mode is " + (viewport.cursorMode ? "on" : "off")); if (viewport.cursorMode) { alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; } alignPanel.seqPanel.seqCanvas.repaint(); break; case KeyEvent.VK_F1: try { ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help"); javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); javax.help.HelpBroker hb = hs.createHelpBroker(); hb.setCurrentID("home"); hb.setDisplayed(true); } catch (Exception ex) { ex.printStackTrace(); } break ; case KeyEvent.VK_H: { boolean toggleSeqs = !evt.isControlDown(); boolean toggleCols = !evt.isShiftDown(); boolean hide = false; SequenceGroup sg = viewport.getSelectionGroup(); if (toggleSeqs) { if (sg != null && sg.getSize() != viewport.alignment.getHeight()) { hideSelSequences_actionPerformed(null); hide = true; } else if (! (toggleCols && viewport.colSel.getSelected().size() > 0)) { showAllSeqs_actionPerformed(null); } } if (toggleCols) { if (viewport.colSel.getSelected().size() > 0) { hideSelColumns_actionPerformed(null); if (!toggleSeqs) { viewport.selectionGroup = sg; } } else if (!hide) { showAllColumns_actionPerformed(null); } } break; } case KeyEvent.VK_PAGE_UP: if (viewport.wrapAlignment) { alignPanel.scrollUp(true); } else { alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - viewport.endSeq + viewport.startSeq); } break; case KeyEvent.VK_PAGE_DOWN: if (viewport.wrapAlignment) { alignPanel.scrollUp(false); } else { alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + viewport.endSeq - viewport.startSeq); } break; } } public void keyReleased(KeyEvent evt) { switch(evt.getKeyCode()) { case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); break; } } }); } public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel) { ap.alignFrame = this; alignPanels.addElement(ap); PaintRefresher.Register(ap, ap.av.getSequenceSetId()); int aSize = alignPanels.size(); tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null); if (aSize == 1 && ap.av.viewName==null) { this.getContentPane().add(ap, BorderLayout.CENTER); } else { if (aSize == 2) { setInitialTabVisible(); } expandViews.setEnabled(true); gatherViews.setEnabled(true); tabbedPane.addTab(ap.av.viewName, ap); ap.setVisible(false); } if(newPanel) { if (ap.av.padGaps) { ap.av.alignment.padGaps(); } ap.av.updateConservation(ap); ap.av.updateConsensus(ap); } } public void setInitialTabVisible() { expandViews.setEnabled(true); gatherViews.setEnabled(true); tabbedPane.setVisible(true); AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement(); tabbedPane.addTab(first.av.viewName,first); this.getContentPane().add(tabbedPane, BorderLayout.CENTER); } public AlignViewport getViewport() { return viewport; } /* Set up intrinsic listeners for dynamically generated GUI bits. */ private void addServiceListeners() { final java.beans.PropertyChangeListener thisListener; // Do this once to get current state BuildWebServiceMenu(); Desktop.discoverer.addPropertyChangeListener( thisListener = new java.beans.PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { // System.out.println("Discoverer property change."); if (evt.getPropertyName().equals("services")) { // System.out.println("Rebuilding web service menu"); BuildWebServiceMenu(); } } }); addInternalFrameListener(new javax.swing.event. InternalFrameAdapter() { public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { // System.out.println("deregistering discoverer listener"); Desktop.discoverer.removePropertyChangeListener(thisListener); closeMenuItem_actionPerformed(true); } ; }); } public void setGUINucleotide(boolean nucleotide) { showTranslation.setVisible( nucleotide ); conservationMenuItem.setEnabled( !nucleotide ); modifyConservation.setEnabled( !nucleotide ); //Remember AlignFrame always starts as protein if(!nucleotide) { calculateMenu.remove(calculateMenu.getItemCount()-2); } } /** * set up menus for the currently viewport. * This may be called after any operation that affects the data in the current view (selection changed, etc) to update the menus to reflect the new state. */ public void setMenusForViewport() { setMenusFromViewport(viewport); } /** * Need to call this method when tabs are selected for multiple views, * or when loading from Jalview2XML.java * @param av AlignViewport */ void setMenusFromViewport(AlignViewport av) { padGapsMenuitem.setSelected(av.padGaps); colourTextMenuItem.setSelected(av.showColourText); abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); conservationMenuItem.setSelected(av.getConservationSelected()); seqLimits.setSelected(av.getShowJVSuffix()); idRightAlign.setSelected(av.rightAlignIds); centreColumnLabelsMenuItem.setState(av.centreColumnLabels); renderGapsMenuItem.setSelected(av.renderGaps); wrapMenuItem.setSelected(av.wrapAlignment); scaleAbove.setVisible(av.wrapAlignment); scaleLeft.setVisible(av.wrapAlignment); scaleRight.setVisible(av.wrapAlignment); annotationPanelMenuItem.setState(av.showAnnotation); viewBoxesMenuItem.setSelected(av.showBoxes); viewTextMenuItem.setSelected(av.showText); setColourSelected(ColourSchemeProperty. getColourName(av.getGlobalColourScheme())); showSeqFeatures.setSelected(av.showSequenceFeatures); hiddenMarkers.setState(av.showHiddenMarkers); applyToAllGroups.setState(av.colourAppliesToAllGroups); setShowProductsEnabled(); updateEditMenuBar(); } Hashtable progressBars; /* (non-Javadoc) * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ public void setProgressBar(String message, long id) { if(progressBars == null) { progressBars = new Hashtable(); } JPanel progressPanel; GridLayout layout = (GridLayout) statusPanel.getLayout(); if(progressBars.get( new Long(id) )!=null) { progressPanel = (JPanel)progressBars.get( new Long(id) ); statusPanel.remove(progressPanel); progressBars.remove( progressPanel ); progressPanel = null; if(message!=null) { statusBar.setText(message); } 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(new Long(id), progressPanel); } // update GUI setMenusForViewport(); validate(); } /** * * @return true if any progress bars are still active */ public boolean operationInProgress() { if (progressBars!=null && progressBars.size()>0) { return true; } return false; } /* Added so Castor Mapping file can obtain Jalview Version */ public String getVersion() { return jalview.bin.Cache.getProperty("VERSION"); } public FeatureRenderer getFeatureRenderer() { return alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); } public void fetchSequence_actionPerformed(ActionEvent e) { new SequenceFetcher(this); } public void addFromFile_actionPerformed(ActionEvent e) { Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); } public void reload_actionPerformed(ActionEvent e) { if(fileName!=null) { if(currentFileFormat.equals("Jalview")) { JInternalFrame [] frames = Desktop.desktop.getAllFrames(); for(int i=0; i-1) { currentFileFormat = currentFileFormat.substring(0, currentFileFormat.indexOf(" ")); } saveAlignment(fileName, currentFileFormat); } } public boolean saveAlignment(String file, String format) { boolean success = true; if (format.equalsIgnoreCase("Jalview")) { String shortName = title; if (shortName.indexOf(java.io.File.separatorChar) > -1) { shortName = shortName.substring(shortName.lastIndexOf( java.io.File.separatorChar) + 1); } success = new Jalview2XML().SaveAlignment(this, file, shortName); statusBar.setText("Successfully saved to file: " +fileName+" in " +format +" format."); } else { if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) { // JBPNote need to have a raise_gui flag here JOptionPane.showInternalMessageDialog( this, "Cannot save file " + fileName + " using format "+format, "Alignment output format not supported", JOptionPane.WARNING_MESSAGE); saveAs_actionPerformed(null); return false; } String[] omitHidden = null; if (viewport.hasHiddenColumns) { int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, "The Alignment contains hidden columns." + "\nDo you want to save only the visible alignment?", "Save / Omit Hidden Columns", JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); if (reply == JOptionPane.YES_OPTION) { omitHidden = viewport.getViewAsString(false); } } FormatAdapter f = new FormatAdapter(); String output = f.formatSequences( format, (Alignment) viewport.alignment, // class cast exceptions will occur in the distant future omitHidden, f.getCacheSuffixDefault(format), viewport.colSel); if (output == null) { success = false; } else { try { java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter(file)); out.print(output); out.close(); this.setTitle(file); statusBar.setText("Successfully saved to file: " + fileName + " in " + format + " format."); } catch (Exception ex) { success = false; ex.printStackTrace(); } } } if (!success) { JOptionPane.showInternalMessageDialog( this, "Couldn't save file: " + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE); } return success; } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void outputText_actionPerformed(ActionEvent e) { String [] omitHidden = null; if(viewport.hasHiddenColumns) { int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, "The Alignment contains hidden columns." +"\nDo you want to output only the visible alignment?", "Save / Omit Hidden Columns", JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); if(reply==JOptionPane.YES_OPTION) { omitHidden = viewport.getViewAsString(false); } } CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); Desktop.addInternalFrame(cap, "Alignment output - " + e.getActionCommand(), 600, 500); cap.setText(new FormatAdapter().formatSequences( e.getActionCommand(), viewport.alignment, omitHidden, viewport.colSel)); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void htmlMenuItem_actionPerformed(ActionEvent e) { new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); } public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void createPNG(File f) { alignPanel.makePNG(f); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void createEPS(File f) { alignPanel.makeEPS(f); } public void pageSetup_actionPerformed(ActionEvent e) { PrinterJob printJob = PrinterJob.getPrinterJob(); PrintThread.pf = printJob.pageDialog(printJob.defaultPage()); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void printMenuItem_actionPerformed(ActionEvent e) { //Putting in a thread avoids Swing painting problems PrintThread thread = new PrintThread(alignPanel); thread.start(); } public void exportFeatures_actionPerformed(ActionEvent e) { new AnnotationExporter().exportFeatures(alignPanel); } public void exportAnnotations_actionPerformed(ActionEvent e) { new AnnotationExporter().exportAnnotations( alignPanel, viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null, viewport.alignment.getGroups(), ((Alignment)viewport.alignment).alignmentProperties ); } public void associatedData_actionPerformed(ActionEvent e) { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. getProperty( "LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Load Jalview Annotations or Features File"); chooser.setToolTipText("Load Jalview Annotations / Features file"); int value = chooser.showOpenDialog(null); if (value == JalviewFileChooser.APPROVE_OPTION) { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); loadJalviewDataFile(choice); } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void closeMenuItem_actionPerformed(boolean closeAllTabs) { if(alignPanels!=null && alignPanels.size()<2) { closeAllTabs = true; } try { if(alignPanels!=null) { if (closeAllTabs) { for (int i = 0; i < alignPanels.size(); i++) { AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i); jalview.structure.StructureSelectionManager.getStructureSelectionManager() .removeStructureViewerListener(ap.seqPanel, null); PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas); PaintRefresher.RemoveComponent(ap.idPanel.idCanvas); PaintRefresher.RemoveComponent(ap); ap.av.alignment = null; } } else { int index = tabbedPane.getSelectedIndex(); alignPanels.removeElement(alignPanel); PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); PaintRefresher.RemoveComponent(alignPanel); viewport.alignment = null; alignPanel = null; viewport = null; tabbedPane.removeTabAt(index); tabbedPane.validate(); if(index==tabbedPane.getTabCount()) { index --; } this.tabSelectionChanged(index); } } if (closeAllTabs) { this.setClosed(true); } } catch (Exception ex) { ex.printStackTrace(); } } /** * DOCUMENT ME! */ void updateEditMenuBar() { if (viewport.historyList.size() > 0) { undoMenuItem.setEnabled(true); CommandI command = (CommandI) viewport.historyList.peek(); undoMenuItem.setText("Undo " + command.getDescription()); } else { undoMenuItem.setEnabled(false); undoMenuItem.setText("Undo"); } if (viewport.redoList.size() > 0) { redoMenuItem.setEnabled(true); CommandI command = (CommandI) viewport.redoList.peek(); redoMenuItem.setText("Redo " + command.getDescription()); } else { redoMenuItem.setEnabled(false); redoMenuItem.setText("Redo"); } } public void addHistoryItem(CommandI command) { if(command.getSize()>0) { viewport.historyList.push(command); viewport.redoList.clear(); updateEditMenuBar(); viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; } } /** * * @return alignment objects for all views */ AlignmentI[] getViewAlignments() { if (alignPanels!=null) { Enumeration e = alignPanels.elements(); AlignmentI[] als = new AlignmentI[alignPanels.size()]; for (int i=0; e.hasMoreElements(); i++) { als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment(); } return als; } if (viewport!=null) { return new AlignmentI[] { viewport.alignment }; } return null; } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void undoMenuItem_actionPerformed(ActionEvent e) { if (viewport.historyList.empty()) return; CommandI command = (CommandI)viewport.historyList.pop(); viewport.redoList.push(command); command.undoCommand(getViewAlignments()); AlignViewport originalSource = getOriginatingSource(command); updateEditMenuBar(); if(originalSource!=null) { originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences()); } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void redoMenuItem_actionPerformed(ActionEvent e) { if(viewport.redoList.size()<1) { return; } CommandI command = (CommandI) viewport.redoList.pop(); viewport.historyList.push(command); command.doCommand(getViewAlignments()); AlignViewport originalSource = getOriginatingSource(command); updateEditMenuBar(); if(originalSource!=null) { originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences()); } } AlignViewport getOriginatingSource(CommandI command) { AlignViewport originalSource = null; //For sequence removal and addition, we need to fire //the property change event FROM the viewport where the //original alignment was altered AlignmentI al=null; if (command instanceof EditCommand) { EditCommand editCommand = (EditCommand) command; al = editCommand.getAlignment(); Vector comps = (Vector) PaintRefresher.components .get(viewport.getSequenceSetId()); for (int i = 0; i < comps.size(); i++) { if (comps.elementAt(i) instanceof AlignmentPanel) { if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment) { originalSource = ( (AlignmentPanel) comps.elementAt(i)).av; break; } } } } if (originalSource == null) { //The original view is closed, we must validate //the current view against the closed view first if (al != null) { PaintRefresher.validateSequences(al, viewport.alignment); } originalSource = viewport; } return originalSource; } /** * DOCUMENT ME! * * @param up DOCUMENT ME! */ public void moveSelectedSequences(boolean up) { SequenceGroup sg = viewport.getSelectionGroup(); if (sg == null) { return; } if (up) { for (int i = 1; i < viewport.alignment.getHeight(); i++) { SequenceI seq = viewport.alignment.getSequenceAt(i); if (!sg.getSequences(null).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i - 1); if (sg.getSequences(null).contains(temp)) { continue; } viewport.alignment.getSequences().setElementAt(temp, i); viewport.alignment.getSequences().setElementAt(seq, i - 1); } } else { for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) { SequenceI seq = viewport.alignment.getSequenceAt(i); if (!sg.getSequences(null).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i + 1); if (sg.getSequences(null).contains(temp)) { continue; } viewport.alignment.getSequences().setElementAt(temp, i); viewport.alignment.getSequences().setElementAt(seq, i + 1); } } alignPanel.paintAlignment(true); } synchronized void slideSequences(boolean right, int size) { Vector sg = new Vector(); if(viewport.cursorMode) { sg.addElement(viewport.alignment.getSequenceAt( alignPanel.seqPanel.seqCanvas.cursorY)); } else if(viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight()) { sg = viewport.getSelectionGroup().getSequences( viewport.hiddenRepSequences); } if(sg.size()<1) { return; } Vector invertGroup = new Vector(); for (int i = 0; i < viewport.alignment.getHeight(); i++) { if(!sg.contains(viewport.alignment.getSequenceAt(i))) invertGroup.add(viewport.alignment.getSequenceAt(i)); } SequenceI[] seqs1 = new SequenceI[sg.size()]; for (int i = 0; i < sg.size(); i++) seqs1[i] = (SequenceI) sg.elementAt(i); SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; for (int i = 0; i < invertGroup.size(); i++) seqs2[i] = (SequenceI) invertGroup.elementAt(i); SlideSequencesCommand ssc; if (right) ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, viewport.getGapCharacter() ); else ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, viewport.getGapCharacter() ); int groupAdjustment = 0; if (ssc.getGapsInsertedBegin() && right) { if (viewport.cursorMode) alignPanel.seqPanel.moveCursor(size, 0); else groupAdjustment = size; } else if (!ssc.getGapsInsertedBegin() && !right) { if (viewport.cursorMode) alignPanel.seqPanel.moveCursor( -size, 0); else groupAdjustment = -size; } if (groupAdjustment != 0) { viewport.getSelectionGroup().setStartRes( viewport.getSelectionGroup().getStartRes() + groupAdjustment); viewport.getSelectionGroup().setEndRes( viewport.getSelectionGroup().getEndRes() + groupAdjustment); } boolean appendHistoryItem = false; if(viewport.historyList!=null && viewport.historyList.size()>0 && viewport.historyList.peek() instanceof SlideSequencesCommand) { appendHistoryItem = ssc.appendSlideCommand( (SlideSequencesCommand)viewport.historyList.peek()) ; } if(!appendHistoryItem) addHistoryItem(ssc); repaint(); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void copy_actionPerformed(ActionEvent e) { System.gc(); if (viewport.getSelectionGroup() == null) { return; } // TODO: preserve the ordering of displayed alignment annotation in any internal paste (particularly sequence associated annotation) SequenceI [] seqs = viewport.getSelectionAsNewSequence(); String[] omitHidden = null; if (viewport.hasHiddenColumns) { omitHidden = viewport.getViewAsString(true); } String output = new FormatAdapter().formatSequences( "Fasta", seqs, omitHidden); StringSelection ss = new StringSelection(output); try { jalview.gui.Desktop.internalCopy = true; //Its really worth setting the clipboard contents //to empty before setting the large StringSelection!! Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(""), null); Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(ss, Desktop.instance); } catch (OutOfMemoryError er) { er.printStackTrace(); javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, "Out of memory copying region!!" + "\nSee help files for increasing Java Virtual Machine memory." , "Out of memory", javax.swing.JOptionPane.WARNING_MESSAGE); } }); return; } Vector hiddenColumns = null; if(viewport.hasHiddenColumns) { hiddenColumns =new Vector(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size(); i++) { int[] region = (int[]) viewport.getColumnSelection().getHiddenColumns().elementAt(i); hiddenColumns.addElement(new int[] {region[0] - hiddenOffset, region[1]-hiddenOffset}); } } Desktop.jalviewClipboard = new Object[] { seqs, viewport.alignment.getDataset(), hiddenColumns}; statusBar.setText("Copied "+seqs.length+" sequences to clipboard."); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void pasteNew_actionPerformed(ActionEvent e) { paste(true); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void pasteThis_actionPerformed(ActionEvent e) { paste(false); } /** * Paste contents of Jalview clipboard * * @param newAlignment true to paste to a new alignment, otherwise add to this. */ void paste(boolean newAlignment) { boolean externalPaste=true; try { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); Transferable contents = c.getContents(this); if (contents == null) { return; } String str, format; try { str = (String) contents.getTransferData(DataFlavor.stringFlavor); if (str.length() < 1) { return; } format = new IdentifyFile().Identify(str, "Paste"); } catch (OutOfMemoryError er) { er.printStackTrace(); javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, "Out of memory pasting sequences!!" + "\nSee help files for increasing Java Virtual Machine memory." , "Out of memory", javax.swing.JOptionPane.WARNING_MESSAGE); } }); return; } SequenceI[] sequences; boolean annotationAdded = false; AlignmentI alignment = null; if(Desktop.jalviewClipboard!=null) { // The clipboard was filled from within Jalview, we must use the sequences // And dataset from the copied alignment SequenceI[] newseq = (SequenceI[])Desktop.jalviewClipboard[0]; // be doubly sure that we create *new* sequence objects. sequences = new SequenceI[newseq.length]; for (int i=0;i>>This is a fix for the moment, until a better solution is found!!<<< af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings( alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the title a concatenation of operations. if (!externalPaste) { if (title.startsWith("Copied sequences")) { newtitle = title; } else { newtitle = newtitle.concat("- from " + title); } } else { newtitle = new String("Pasted sequences"); } Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); } } catch (Exception ex) { ex.printStackTrace(); System.out.println("Exception whilst pasting: "+ex); // could be anything being pasted in here } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void cut_actionPerformed(ActionEvent e) { copy_actionPerformed(null); delete_actionPerformed(null); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void delete_actionPerformed(ActionEvent evt) { SequenceGroup sg = viewport.getSelectionGroup(); if (sg == null) { return; } Vector seqs = new Vector(); SequenceI seq; for (int i = 0; i < sg.getSize(); i++) { seq = sg.getSequenceAt(i); seqs.addElement(seq); } // If the cut affects all sequences, remove highlighted columns if (sg.getSize() == viewport.alignment.getHeight()) { viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); } SequenceI [] cut = new SequenceI[seqs.size()]; for(int i=0; i 0) { if(trimLeft) { column = colSel.getMin(); } else { column = colSel.getMax(); } SequenceI [] seqs; if(viewport.getSelectionGroup()!=null) { seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. hiddenRepSequences); } else { seqs = viewport.alignment.getSequencesArray(); } TrimRegionCommand trimRegion; if(trimLeft) { trimRegion = new TrimRegionCommand("Remove Left", TrimRegionCommand.TRIM_LEFT, seqs, column, viewport.alignment, viewport.colSel, viewport.selectionGroup); viewport.setStartRes(0); } else { trimRegion = new TrimRegionCommand("Remove Right", TrimRegionCommand.TRIM_RIGHT, seqs, column, viewport.alignment, viewport.colSel, viewport.selectionGroup); } statusBar.setText("Removed "+trimRegion.getSize()+" columns."); addHistoryItem(trimRegion); Vector groups = viewport.alignment.getGroups(); for (int i = 0; i < groups.size(); i++) { SequenceGroup sg = (SequenceGroup) groups.get(i); if ( (trimLeft && !sg.adjustForRemoveLeft(column)) || (!trimLeft && !sg.adjustForRemoveRight(column))) { viewport.alignment.deleteGroup(sg); } } viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { int start = 0, end = viewport.alignment.getWidth()-1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. hiddenRepSequences); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else { seqs = viewport.alignment.getSequencesArray(); } RemoveGapColCommand removeGapCols = new RemoveGapColCommand("Remove Gapped Columns", seqs, start, end, viewport.alignment); addHistoryItem(removeGapCols); statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns."); //This is to maintain viewport position on first residue //of first sequence SequenceI seq = viewport.alignment.getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); viewport.setStartRes(seq.findIndex(startRes)-1); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { int start = 0, end = viewport.alignment.getWidth()-1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. hiddenRepSequences); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else { seqs = viewport.alignment.getSequencesArray(); } //This is to maintain viewport position on first residue //of first sequence SequenceI seq = viewport.alignment.getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, viewport.alignment)); viewport.setStartRes(seq.findIndex(startRes)-1); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void padGapsMenuitem_actionPerformed(ActionEvent e) { viewport.padGaps = padGapsMenuitem.isSelected(); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void findMenuItem_actionPerformed(ActionEvent e) { new Finder(); } public void newView_actionPerformed(ActionEvent e) { AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel, true); newap.av.gatherViewsHere = false; if (viewport.viewName == null) { viewport.viewName = "Original"; } newap.av.historyList = viewport.historyList; newap.av.redoList = viewport.redoList; int index = Desktop.getViewCount(viewport.getSequenceSetId()); String newViewName = "View " +index; Vector comps = (Vector) PaintRefresher.components.get(viewport. getSequenceSetId()); Vector existingNames = new Vector(); for(int i=0; i"); float avg = 0; int min=Integer.MAX_VALUE, max=0; for(int i=0; imax) max = size; if(sizeSequences: "+ viewport.alignment.getHeight()); contents.append("
Minimum Sequence Length: "+min); contents.append("
Maximum Sequence Length: "+max); contents.append("
Average Length: "+(int)avg); if (((Alignment)viewport.alignment).getProperties() != null) { Hashtable props = ((Alignment)viewport.alignment).getProperties(); Enumeration en = props.keys(); contents.append("

"); while(en.hasMoreElements()) { String key = en.nextElement().toString(); StringBuffer val = new StringBuffer(); String vals = props.get(key).toString(); int pos=0, npos; do { npos = vals.indexOf("\n",pos); if (npos==-1) { val.append(vals.substring(pos)); } else { val.append(vals.substring(pos, npos)); val.append("
"); } pos = npos+1; } while (npos!=-1); contents.append(""); } contents.append("
"+key+""+val+"
"); } editPane.setText(contents.toString()+""); JInternalFrame frame = new JInternalFrame(); frame.getContentPane().add(new JScrollPane(editPane)); Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void overviewMenuItem_actionPerformed(ActionEvent e) { if (alignPanel.overviewPanel != null) { return; } JInternalFrame frame = new JInternalFrame(); OverviewPanel overview = new OverviewPanel(alignPanel); frame.setContentPane(overview); Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame.getWidth(), frame.getHeight()); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { alignPanel.setOverviewPanel(null); } ; }); alignPanel.setOverviewPanel(overview); } public void textColour_actionPerformed(ActionEvent e) { new TextColourChooser().chooseColour(alignPanel, null); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void noColourmenuItem_actionPerformed(ActionEvent e) { changeColour(null); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void clustalColour_actionPerformed(ActionEvent e) { changeColour(new ClustalxColourScheme( viewport.alignment.getSequences(), viewport.alignment.getWidth())); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void zappoColour_actionPerformed(ActionEvent e) { changeColour(new ZappoColourScheme()); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void taylorColour_actionPerformed(ActionEvent e) { changeColour(new TaylorColourScheme()); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void hydrophobicityColour_actionPerformed(ActionEvent e) { changeColour(new HydrophobicColourScheme()); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void helixColour_actionPerformed(ActionEvent e) { changeColour(new HelixColourScheme()); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void strandColour_actionPerformed(ActionEvent e) { changeColour(new StrandColourScheme()); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void turnColour_actionPerformed(ActionEvent e) { changeColour(new TurnColourScheme()); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void buriedColour_actionPerformed(ActionEvent e) { changeColour(new BuriedColourScheme()); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void nucleotideColour_actionPerformed(ActionEvent e) { changeColour(new NucleotideColourScheme()); } public void annotationColour_actionPerformed(ActionEvent e) { new AnnotationColourChooser(viewport, alignPanel); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void applyToAllGroups_actionPerformed(ActionEvent e) { viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); } /** * DOCUMENT ME! * * @param cs DOCUMENT ME! */ public void changeColour(ColourSchemeI cs) { int threshold = 0; if(cs!=null) { if (viewport.getAbovePIDThreshold()) { threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); viewport.setGlobalColourScheme(cs); } else { cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); } if (viewport.getConservationSelected()) { Alignment al = (Alignment) viewport.alignment; Conservation c = new Conservation("All", ResidueProperties.propHash, 3, al.getSequences(), 0, al.getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); cs.setConservation(c); cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs, "Background")); } else { cs.setConservation(null); } cs.setConsensus(viewport.hconsensus); } viewport.setGlobalColourScheme(cs); if (viewport.getColourAppliesToAllGroups()) { Vector groups = viewport.alignment.getGroups(); for (int i = 0; i < groups.size(); i++) { SequenceGroup sg = (SequenceGroup) groups.elementAt(i); if (cs == null) { sg.cs = null; continue; } if (cs instanceof ClustalxColourScheme) { sg.cs = new ClustalxColourScheme( sg.getSequences(viewport.hiddenRepSequences), sg.getWidth()); } else if (cs instanceof UserColourScheme) { sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours()); } else { try { sg.cs = (ColourSchemeI) cs.getClass().newInstance(); } catch (Exception ex) { } } if (viewport.getAbovePIDThreshold() || cs instanceof PIDColourScheme || cs instanceof Blosum62ColourScheme) { sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); sg.cs.setConsensus(AAFrequency.calculate( sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(), sg.getEndRes()+1)); } else { sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); } if (viewport.getConservationSelected()) { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, sg.getSequences(viewport. hiddenRepSequences), sg.getStartRes(), sg.getEndRes()+1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); sg.cs.setConservation(c); } else { sg.cs.setConservation(null); } } } if (alignPanel.getOverviewPanel() != null) { alignPanel.getOverviewPanel().updateOverviewImage(); } alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void modifyPID_actionPerformed(ActionEvent e) { if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null) { SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background"); SliderPanel.showPIDSlider(); } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void modifyConservation_actionPerformed(ActionEvent e) { if (viewport.getConservationSelected() && viewport.globalColourScheme!=null) { SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme, "Background"); SliderPanel.showConservationSlider(); } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void conservationMenuItem_actionPerformed(ActionEvent e) { viewport.setConservationSelected(conservationMenuItem.isSelected()); viewport.setAbovePIDThreshold(false); abovePIDThreshold.setSelected(false); changeColour(viewport.getGlobalColourScheme()); modifyConservation_actionPerformed(null); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void abovePIDThreshold_actionPerformed(ActionEvent e) { viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); conservationMenuItem.setSelected(false); viewport.setConservationSelected(false); changeColour(viewport.getGlobalColourScheme()); modifyPID_actionPerformed(null); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void userDefinedColour_actionPerformed(ActionEvent e) { if (e.getActionCommand().equals("User Defined...")) { new UserDefinedColours(alignPanel, null); } else { UserColourScheme udc = (UserColourScheme) UserDefinedColours. getUserColourSchemes().get(e.getActionCommand()); changeColour(udc); } } public void updateUserColourMenu() { Component[] menuItems = colourMenu.getMenuComponents(); int i, iSize = menuItems.length; for (i = 0; i < iSize; i++) { if (menuItems[i].getName() != null && menuItems[i].getName().equals("USER_DEFINED")) { colourMenu.remove(menuItems[i]); iSize--; } } if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) { java.util.Enumeration userColours = jalview.gui.UserDefinedColours. getUserColourSchemes().keys(); while (userColours.hasMoreElements()) { final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( userColours. nextElement().toString()); radioItem.setName("USER_DEFINED"); radioItem.addMouseListener(new MouseAdapter() { public void mousePressed(MouseEvent evt) { if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) { radioItem.removeActionListener(radioItem.getActionListeners()[0]); int option = JOptionPane.showInternalConfirmDialog(jalview.gui. Desktop.desktop, "Remove from default list?", "Remove user defined colour", JOptionPane.YES_NO_OPTION); if(option == JOptionPane.YES_OPTION) { jalview.gui.UserDefinedColours.removeColourFromDefaults( radioItem.getText()); colourMenu.remove(radioItem); } else { radioItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); } }); } } } }); radioItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); } }); colourMenu.insert(radioItem, 15); colours.add(radioItem); } } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void PIDColour_actionPerformed(ActionEvent e) { changeColour(new PIDColourScheme()); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void BLOSUM62Colour_actionPerformed(ActionEvent e) { changeColour(new Blosum62ColourScheme()); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0), null); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment)); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void sortIDMenuItem_actionPerformed(ActionEvent e) { SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment)); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void sortGroupMenuItem_actionPerformed(ActionEvent e) { SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByGroup(viewport.getAlignment()); addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment)); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { new RedundancyPanel(alignPanel, this); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { if ( (viewport.getSelectionGroup() == null) || (viewport.getSelectionGroup().getSize() < 2)) { JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE); } else { JInternalFrame frame = new JInternalFrame(); frame.setContentPane(new PairwiseAlignPanel(viewport)); Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500); } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void PCAMenuItem_actionPerformed(ActionEvent e) { if ( ( (viewport.getSelectionGroup() != null) && (viewport.getSelectionGroup().getSize() < 4) && (viewport.getSelectionGroup().getSize() > 0)) || (viewport.getAlignment().getHeight() < 4)) { JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n" + "at least 4 input sequences.", "Sequence selection insufficient", JOptionPane.WARNING_MESSAGE); return; } new PCAPanel(alignPanel); } public void autoCalculate_actionPerformed(ActionEvent e) { viewport.autoCalculateConsensus = autoCalculate.isSelected(); if(viewport.autoCalculateConsensus) { viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("AV", "PID", "Average distance tree using PID"); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); } /** * DOCUMENT ME! * * @param type DOCUMENT ME! * @param pwType DOCUMENT ME! * @param title DOCUMENT ME! */ void NewTreePanel(String type, String pwType, String title) { TreePanel tp; if (viewport.getSelectionGroup() != null) { if (viewport.getSelectionGroup().getSize() < 3) { JOptionPane.showMessageDialog(Desktop.desktop, "You need to have more than two sequences selected to build a tree!", "Not enough sequences", JOptionPane.WARNING_MESSAGE); return; } int s = 0; SequenceGroup sg = viewport.getSelectionGroup(); /* Decide if the selection is a column region */ while (s < sg.getSize()) { if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg.getEndRes()) { JOptionPane.showMessageDialog(Desktop.desktop, "The selected region to create a tree may\nonly contain residues or gaps.\n" + "Try using the Pad function in the edit menu,\n" + "or one of the multiple sequence alignment web services.", "Sequences in selection are not aligned", JOptionPane.WARNING_MESSAGE); return; } } title = title + " on region"; tp = new TreePanel(alignPanel, type, pwType); } else { //are the sequences aligned? if (!viewport.alignment.isAligned()) { JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.\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; } if(viewport.alignment.getHeight()<2) { return; } tp = new TreePanel(alignPanel, type, pwType); } title += " from "; if(viewport.viewName!=null) { title+= viewport.viewName+" of "; } title += this.title; Desktop.addInternalFrame(tp, title, 600, 500); } /** * DOCUMENT ME! * * @param title DOCUMENT ME! * @param order DOCUMENT ME! */ public void addSortByOrderMenuItem(String title, final AlignmentOrder order) { final JMenuItem item = new JMenuItem("by " + title); sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); // TODO: JBPNote - have to map order entries to curent SequenceI pointers AlignmentSorter.sortBy(viewport.getAlignment(), order); addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.alignment)); alignPanel.paintAlignment(true); } }); } /** * Add a new sort by annotation score menu item * @param sort the menu to add the option to * @param scoreLabel the label used to retrieve scores for each sequence on the alignment */ public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel) { final JMenuItem item = new JMenuItem(scoreLabel); sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());//,viewport.getSelectionGroup()); addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment)); alignPanel.paintAlignment(true); } }); } /** * last hash for alignment's annotation array - used to minimise cost of rebuild. */ protected int _annotationScoreVectorHash; /** * search the alignment and rebuild the sort by annotation score submenu * the last alignment annotation vector hash is stored to minimize * cost of rebuilding in subsequence calls. * */ public void buildSortByAnnotationScoresMenu() { if(viewport.alignment.getAlignmentAnnotation()==null) { return; } if (viewport.alignment.getAlignmentAnnotation().hashCode()!=_annotationScoreVectorHash) { sortByAnnotScore.removeAll(); // almost certainly a quicker way to do this - but we keep it simple Hashtable scoreSorts=new Hashtable(); AlignmentAnnotation aann[]; Enumeration sq = viewport.alignment.getSequences().elements(); while (sq.hasMoreElements()) { aann = ((SequenceI) sq.nextElement()).getAnnotation(); for (int i=0;aann!=null && i0); scoreSorts.clear(); _annotationScoreVectorHash = viewport.alignment.getAlignmentAnnotation().hashCode(); } } /** * Maintain the Order by->Displayed Tree menu. * Creates a new menu item for a TreePanel with an appropriate * jalview.analysis.AlignmentSorter call. Listeners are added * to remove the menu item when the treePanel is closed, and adjust * the tree leaf to sequence mapping when the alignment is modified. * @param treePanel Displayed tree window. * @param title SortBy menu item title. */ public void buildTreeMenu() { sortByTreeMenu.removeAll(); Vector comps = (Vector) PaintRefresher.components.get(viewport. getSequenceSetId()); Vector treePanels = new Vector(); int i, iSize = comps.size(); for(i=0; i 1)) { // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface! /*SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new SequenceI[sz = seqs.getSize(false)]; for (int i = 0; i < sz; i++) { msa[i] = (SequenceI) seqs.getSequenceAt(i); } */ msa = viewport.getAlignmentView(true); } else { /*Vector seqs = viewport.getAlignment().getSequences(); if (seqs.size() > 1) { msa = new SequenceI[seqs.size()]; for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI) seqs.elementAt(i); } }*/ msa = viewport.getAlignmentView(false); } return msa; } /** * Decides what is submitted to a secondary structure prediction service: * the first sequence in the alignment, or in the current selection, * or, if the alignment is 'aligned' (ie padded with gaps), then the * currently selected region or the whole alignment. * (where the first sequence in the set is the one that the prediction * will be for). */ public AlignmentView gatherSeqOrMsaForSecStrPrediction() { AlignmentView seqs = null; if ( (viewport.getSelectionGroup() != null) && (viewport.getSelectionGroup().getSize() > 0)) { seqs = viewport.getAlignmentView(true); } else { seqs = viewport.getAlignmentView(false); } // limit sequences - JBPNote in future - could spawn multiple prediction jobs // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment. if (!viewport.alignment.isAligned()) { seqs.setSequences(new SeqCigar[] {seqs.getSequences()[0]}); } return seqs; } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. getProperty( "LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Select a newick-like tree file"); chooser.setToolTipText("Load a tree file"); int value = chooser.showOpenDialog(null); if (value == JalviewFileChooser.APPROVE_OPTION) { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); jalview.io.NewickFile fin = null; try { fin = new jalview.io.NewickFile(choice, "File"); viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); } catch (Exception ex) { JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), "Problem reading tree file", JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } if (fin!=null && fin.hasWarningMessage()) { JOptionPane.showMessageDialog(Desktop.desktop, fin.getWarningMessage(), "Possible problem with tree file", JOptionPane.WARNING_MESSAGE); } } } public TreePanel ShowNewickTree(NewickFile nf, String title) { return ShowNewickTree(nf,title,600,500,4,5); } public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input) { return ShowNewickTree(nf,title, input, 600,500,4,5); } public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h, int x, int y) { return ShowNewickTree(nf, title, null, w, h, x, y); } /** * Add a treeviewer for the tree extracted from a newick file object to the current alignment view * * @param nf the tree * @param title tree viewer title * @param input Associated alignment input data (or null) * @param w width * @param h height * @param x position * @param y position * @return TreePanel handle */ public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w, int h, int x, int y) { TreePanel tp = null; try { nf.parse(); if (nf.getTree() != null) { tp = new TreePanel(alignPanel, "FromFile", title, nf, input); tp.setSize(w,h); if(x>0 && y>0) { tp.setLocation(x,y); } Desktop.addInternalFrame(tp, title, w, h); } } catch (Exception ex) { ex.printStackTrace(); } return tp; } /** * Generates menu items and listener event actions for web service clients * */ public void BuildWebServiceMenu() { // TODO: add support for context dependent disabling of services based on alignment and current selection // TODO: add additional serviceHandle parameter to specify abstract handler class independently of AbstractName // TODO: add in rediscovery GUI function to restart discoverer // TODO: group services by location as well as function and/or introduce object broker mechanism. if ( (Discoverer.services != null) && (Discoverer.services.size() > 0)) { // TODO: refactor to allow list of AbstractName/Handler bindings to be stored or retrieved from elsewhere Vector msaws = (Vector) Discoverer.services.get("MsaWS"); Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred"); Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch"); // TODO: move GUI generation code onto service implementation - so a client instance attaches itself to the GUI with method call like jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance, alignframe) Vector wsmenu = new Vector(); final IProgressIndicator af = this; if (msaws != null) { // Add any Multiple Sequence Alignment Services final JMenu msawsmenu = new JMenu("Alignment"); for (int i = 0, j = msaws.size(); i < j; i++) { final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws. get(i); jalview.ws.WSClient impl = jalview.ws.Discoverer.getServiceClient(sh); impl.attachWSMenuEntry(msawsmenu, this); } wsmenu.add(msawsmenu); } if (secstrpr != null) { // Add any secondary structure prediction services final JMenu secstrmenu = new JMenu("Secondary Structure Prediction"); for (int i = 0, j = secstrpr.size(); i < j; i++) { final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr.get(i); jalview.ws.WSClient impl = jalview.ws.Discoverer.getServiceClient(sh); impl.attachWSMenuEntry(secstrmenu, this); } wsmenu.add(secstrmenu); } if (seqsrch!=null) { // Add any sequence search services final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); for (int i = 0, j = seqsrch.size(); i < j; i++) { final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch.elementAt(i); jalview.ws.WSClient impl = jalview.ws.Discoverer.getServiceClient(sh); impl.attachWSMenuEntry(seqsrchmenu, this); } // finally, add the whole shebang onto the webservices menu wsmenu.add(seqsrchmenu); } resetWebServiceMenu(); for (int i = 0, j = wsmenu.size(); i < j; i++) { webService.add( (JMenu) wsmenu.get(i)); } } else { resetWebServiceMenu(); this.webService.add(this.webServiceNoServices); } } /** * empty the web service menu and add any ad-hoc functions * not dynamically discovered. * */ private void resetWebServiceMenu() { webService.removeAll(); // Temporary hack - DBRef Fetcher always top level ws entry. JMenuItem rfetch = new JMenuItem("Fetch DB References"); rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences"); webService.add(rfetch); rfetch.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { public void run() { new jalview.ws.DBRefFetcher( alignPanel.av.getSequenceSelection(), alignPanel.alignFrame).fetchDBRefs(false); } }).start(); } }); } /* public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export to Vamsas file"); chooser.setToolTipText("Export"); int value = chooser.showSaveDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport); //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this); } }*/ /** * prototype of an automatically enabled/disabled analysis function * */ protected void setShowProductsEnabled() { SequenceI [] selection = viewport.getSequenceSelection(); if (canShowProducts(selection, viewport.getSelectionGroup()!=null, viewport.getAlignment().getDataset())) { showProducts.setEnabled(true); } else { showProducts.setEnabled(false); } } /** * search selection for sequence xRef products and build the * show products menu. * @param selection * @param dataset * @return true if showProducts menu should be enabled. */ public boolean canShowProducts(SequenceI[] selection, boolean isRegionSelection, Alignment dataset) { boolean showp=false; try { showProducts.removeAll(); final boolean dna = viewport.getAlignment().isNucleotide(); final Alignment ds = dataset; String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection, dataset); //Object[] prods = CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(), selection, dataset, true); final SequenceI[] sel = selection; for (int t=0; ptypes!=null && t -1 || file.indexOf("file:") > -1) { protocol = "URL"; } boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport. alignment, file, protocol); if (!isAnnotation) { // try to see if its a JNet 'concise' style annotation file *before* we try to parse it as a features file String format = new IdentifyFile().Identify(file, protocol); if(format.equalsIgnoreCase("JnetFile")) { jalview.io.JPredFile predictions = new jalview.io.JPredFile( file, protocol); new JnetAnnotationMaker().add_annotation(predictions, viewport.getAlignment(), 0, false); isAnnotation=true; } else { // try to parse it as a features file boolean isGroupsFile = parseFeaturesFile(file,protocol); // if it wasn't a features file then we just treat it as a general alignment file to load into the current view. if (!isGroupsFile) { new FileLoader().LoadFile(viewport, file, protocol, format); } else { alignPanel.paintAlignment(true); } } } if (isAnnotation) { alignPanel.adjustAnnotationHeight(); viewport.updateSequenceIdColours(); buildSortByAnnotationScoresMenu(); alignPanel.paintAlignment(true); } } catch (Exception ex) { ex.printStackTrace(); } } public void tabSelectionChanged(int index) { if (index > -1) { alignPanel = (AlignmentPanel) alignPanels.elementAt(index); viewport = alignPanel.av; setMenusFromViewport(viewport); } } public void tabbedPane_mousePressed(MouseEvent e) { if(SwingUtilities.isRightMouseButton(e)) { String reply = JOptionPane.showInternalInputDialog(this, "Enter View Name", "Edit View Name", JOptionPane.QUESTION_MESSAGE); if (reply != null) { viewport.viewName = reply; tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply); } } } public AlignViewport getCurrentView() { return viewport; } /** * Open the dialog for regex description parsing. */ protected void extractScores_actionPerformed(ActionEvent e) { ParseProperties pp = new jalview.analysis.ParseProperties(viewport.alignment); // TODO: verify regex and introduce GUI dialog for version 2.5 //if (pp.getScoresFromDescription("col", "score column ", "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)", true)>0) if (pp.getScoresFromDescription("description column", "score in description column ", "\\W*([-+eE0-9.]+)", true)>0) { buildSortByAnnotationScoresMenu(); } } } class PrintThread extends Thread { AlignmentPanel ap; public PrintThread(AlignmentPanel ap) { this.ap = ap; } static PageFormat pf; public void run() { PrinterJob printJob = PrinterJob.getPrinterJob(); if (pf != null) { printJob.setPrintable(ap, pf); } else { printJob.setPrintable(ap); } if (printJob.printDialog()) { try { printJob.print(); } catch (Exception PrintException) { PrintException.printStackTrace(); } } } }