/* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.gui; import java.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.bin.Cache; import jalview.commands.*; import jalview.datamodel.*; import jalview.io.*; import jalview.jbgui.*; import jalview.schemes.*; import jalview.ws.*; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; /** * 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 with specific width and height. * * @param al * @param width * @param height */ public AlignFrame(AlignmentI al, int width, int height) { this(al, null, width, height); } /** * Creates a new AlignFrame object with specific width, height and * sequenceSetId * * @param al * @param width * @param height * @param sequenceSetId */ public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId) { this(al, null, width, height, sequenceSetId); } /** * Creates a new AlignFrame object with specific width, height and * sequenceSetId * * @param al * @param width * @param height * @param sequenceSetId * @param viewId */ public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId, String viewId) { this(al, null, width, height, sequenceSetId, viewId); } /** * new alignment window with hidden columns * * @param al * AlignmentI * @param hiddenColumns * ColumnSelection or null * @param width * Width of alignment frame * @param height * height of frame. */ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height) { this(al, hiddenColumns, width, height, null); } /** * Create alignment frame for al with hiddenColumns, a specific width and * height, and specific sequenceId * * @param al * @param hiddenColumns * @param width * @param height * @param sequenceSetId * (may be null) */ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height, String sequenceSetId) { this(al, hiddenColumns, width, height, sequenceSetId, null); } /** * Create alignment frame for al with hiddenColumns, a specific width and * height, and specific sequenceId * * @param al * @param hiddenColumns * @param width * @param height * @param sequenceSetId * (may be null) * @param viewId * (may be null) */ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height, String sequenceSetId, String viewId) { setSize(width, height); viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); 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(); } /** * initalise the alignframe from the underlying viewport data and the * configurations */ 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(); toggleHiddenRegions(toggleSeqs, toggleCols); 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; Desktop.instance.addJalviewPropertyChangeListener("services", thisListener = new java.beans.PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { // // System.out.println("Discoverer property change."); // if (evt.getPropertyName().equals("services")) { SwingUtilities.invokeLater(new Runnable() { public void run() { System.err .println("Rebuild WS Menu for service change"); BuildWebServiceMenu(); } }); } } }); addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { System.out.println("deregistering discoverer listener"); Desktop.instance.removeJalviewPropertyChangeListener("services", thisListener); closeMenuItem_actionPerformed(true); }; }); // Finally, build the menu once to get current service state new Thread(new Runnable() { public void run() { BuildWebServiceMenu(); } }).start(); } public void setGUINucleotide(boolean nucleotide) { showTranslation.setVisible(nucleotide); conservationMenuItem.setEnabled(!nucleotide); modifyConservation.setEnabled(!nucleotide); showGroupConservation.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); showNonconservedMenuItem.setSelected(av.showUnconserved); showGroupConsensus.setSelected(av.showGroupConsensus); showGroupConservation.setSelected(av.showGroupConservation); showConsensusHistogram.setSelected(av.showConsensusHistogram); showSequenceLogo.setSelected(av.showSequenceLogo); setColourSelected(ColourSchemeProperty.getColourName(av .getGlobalColourScheme())); showSeqFeatures.setSelected(av.showSequenceFeatures); hiddenMarkers.setState(av.showHiddenMarkers); applyToAllGroups.setState(av.colourAppliesToAllGroups); showNpFeatsMenuitem.setSelected(av.isShowNpFeats()); showDbRefsMenuitem.setSelected(av.isShowDbRefs()); setShowProductsEnabled(); updateEditMenuBar(); } Hashtable progressBars, progressBarHandlers; /* * (non-Javadoc) * * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ public void setProgressBar(String message, long id) { if (progressBars == null) { progressBars = new Hashtable(); progressBarHandlers = new Hashtable(); } JPanel progressPanel; Long lId = new Long(id); GridLayout layout = (GridLayout) statusPanel.getLayout(); if (progressBars.get(lId) != null) { progressPanel = (JPanel) progressBars.get(new Long(id)); statusPanel.remove(progressPanel); progressBars.remove(lId); progressPanel = null; if (message != null) { statusBar.setText(message); } if (progressBarHandlers.contains(lId)) { progressBarHandlers.remove(lId); } layout.setRows(layout.getRows() - 1); } else { progressPanel = new JPanel(new BorderLayout(10, 5)); JProgressBar progressBar = new JProgressBar(); progressBar.setIndeterminate(true); progressPanel.add(new JLabel(message), BorderLayout.WEST); progressPanel.add(progressBar, BorderLayout.CENTER); layout.setRows(layout.getRows() + 1); statusPanel.add(progressPanel); progressBars.put(lId, progressPanel); } // update GUI setMenusForViewport(); validate(); } public void registerHandler(final long id, final IProgressIndicatorHandler handler) { if (progressBarHandlers == null || !progressBars.contains(new Long(id))) { throw new Error( "call setProgressBar before registering the progress bar's handler."); } progressBarHandlers.put(new Long(id), handler); final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); if (handler.canCancel()) { JButton cancel = new JButton("Cancel"); final IProgressIndicator us = this; cancel.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); us.setProgressBar( "Cancelled " + ((JLabel) progressPanel.getComponent(0)) .getText(), id); } }); progressPanel.add(cancel, BorderLayout.EAST); } } /** * * @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) { // TODO: work out how to recover feature settings for correct view(s) when // file is reloaded. if (currentFileFormat.equals("Jalview")) { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); for (int i = 0; i < frames.length; i++) { if (frames[i] instanceof AlignFrame && frames[i] != this && ((AlignFrame) frames[i]).fileName.equals(fileName)) { try { frames[i].setSelected(true); Desktop.instance.closeAssociatedWindows(); } catch (java.beans.PropertyVetoException ex) { } } } Desktop.instance.closeAssociatedWindows(); FileLoader loader = new FileLoader(); String protocol = fileName.startsWith("http:") ? "URL" : "File"; loader.LoadFile(viewport, fileName, protocol, currentFileFormat); } else { Rectangle bounds = this.getBounds(); FileLoader loader = new FileLoader(); String protocol = fileName.startsWith("http:") ? "URL" : "File"; AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat); newframe.setBounds(bounds); if (featureSettings != null && featureSettings.isShowing()) { final Rectangle fspos = featureSettings.frame.getBounds(); // TODO: need a 'show feature settings' function that takes bounds - // need to refactor Desktop.addFrame newframe.featureSettings_actionPerformed(null); final FeatureSettings nfs = newframe.featureSettings; SwingUtilities.invokeLater(new Runnable() { public void run() { nfs.frame.setBounds(fspos); } }); this.featureSettings.close(); this.featureSettings = null; } this.closeMenuItem_actionPerformed(true); } } } public void addFromText_actionPerformed(ActionEvent e) { Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport); } public void addFromURL_actionPerformed(ActionEvent e) { Desktop.instance.inputURLMenuItem_actionPerformed(viewport); } public void save_actionPerformed(ActionEvent e) { if (fileName == null || (currentFileFormat == null || !jalview.io.FormatAdapter .isValidIOFormat(currentFileFormat, true)) || fileName.startsWith("http")) { saveAs_actionPerformed(null); } else { saveAlignment(fileName, currentFileFormat); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void saveAs_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS, jalview.io.AppletFormatAdapter.WRITABLE_FNAMES, currentFileFormat, false); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Save Alignment to file"); chooser.setToolTipText("Save"); int value = chooser.showSaveDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { currentFileFormat = chooser.getSelectedFormat(); if (currentFileFormat == null) { JOptionPane.showInternalMessageDialog(Desktop.desktop, "You must select a file format before saving!", "File format not specified", JOptionPane.WARNING_MESSAGE); value = chooser.showSaveDialog(this); return; } fileName = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat); jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName); if (currentFileFormat.indexOf(" ") > -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)) { warningMessage("Cannot save file " + fileName + " using format " + format, "Alignment output format not supported"); saveAs_actionPerformed(null); // JBPNote need to have a raise_gui flag here 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; } private void warningMessage(String warning, String title) { if (new jalview.util.Platform().isHeadless()) { System.err.println("Warning: " + title + "\nWarning: " + warning); } else { JOptionPane.showInternalMessageDialog(this, warning, title, JOptionPane.WARNING_MESSAGE); } return; } /** * 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); try { cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), viewport.alignment, omitHidden, viewport.colSel)); Desktop.addInternalFrame(cap, "Alignment output - " + e.getActionCommand(), 600, 500); } catch (OutOfMemoryError oom) { new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom); cap.dispose(); } } /** * 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); } } /** * Close the current view or all views in the alignment frame. If the frame * only contains one view then the alignment will be removed from memory. * * @param closeAllTabs */ public void closeMenuItem_actionPerformed(boolean closeAllTabs) { if (alignPanels != null && alignPanels.size() < 2) { closeAllTabs = true; } try { if (alignPanels != null) { if (closeAllTabs) { if (this.isClosed()) { // really close all the windows - otherwise wait till // setClosed(true) is called for (int i = 0; i < alignPanels.size(); i++) { AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i); ap.closePanel(); } } } else { closeView(alignPanel); } } if (closeAllTabs) { this.setClosed(true); } } catch (Exception ex) { ex.printStackTrace(); } } /** * close alignPanel2 and shuffle tabs appropriately. * * @param alignPanel2 */ public void closeView(AlignmentPanel alignPanel2) { int index = tabbedPane.getSelectedIndex(); int closedindex = tabbedPane.indexOfComponent(alignPanel2); alignPanels.removeElement(alignPanel2); // Unnecessary // if (viewport == alignPanel2.av) // { // viewport = null; // } alignPanel2.closePanel(); alignPanel2 = null; tabbedPane.removeTabAt(closedindex); tabbedPane.validate(); if (index > closedindex || index == tabbedPane.getTabCount()) { // modify currently selected tab index if necessary. index--; } this.tabSelectionChanged(index); } /** * 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 != null && viewport.colSel.getHiddenColumns() != null && viewport.colSel .getHiddenColumns().size() > 0); } } /** * * @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 != null && viewport.colSel.getHiddenColumns() != null && viewport.colSel .getHiddenColumns().size() > 0); 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 != null && viewport.colSel.getHiddenColumns() != null && viewport.colSel .getHiddenColumns().size() > 0); 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) { new OOMWarning("copying region", er); return; } Vector hiddenColumns = null; if (viewport.hasHiddenColumns) { hiddenColumns = new Vector(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport .getSelectionGroup().getEndRes(); for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() .size(); i++) { int[] region = (int[]) viewport.getColumnSelection() .getHiddenColumns().elementAt(i); if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) { 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) { new OOMWarning("Out of memory pasting sequences!!", er); 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 < newseq.length; i++) { sequences[i] = new Sequence(newseq[i]); } alignment = new Alignment(sequences); externalPaste = false; } else { // parse the clipboard as an alignment. alignment = new FormatAdapter().readFile(str, "Paste", format); sequences = alignment.getSequencesArray(); } int alwidth = 0; if (newAlignment) { if (Desktop.jalviewClipboard != null) { // dataset is inherited alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]); } else { // new dataset is constructed alignment.setDataset(null); } alwidth = alignment.getWidth() + 1; } else { AlignmentI pastedal = alignment; // preserve pasted alignment object // Add pasted sequences and dataset into existing alignment. alignment = viewport.getAlignment(); alwidth = alignment.getWidth() + 1; // decide if we need to import sequences from an existing dataset boolean importDs = Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[1] != alignment.getDataset(); // importDs==true instructs us to copy over new dataset sequences from // an existing alignment Vector newDs = (importDs) ? new Vector() : null; // used to create // minimum dataset set for (int i = 0; i < sequences.length; i++) { if (importDs) { newDs.addElement(null); } SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple // paste if (importDs && ds != null) { if (!newDs.contains(ds)) { newDs.setElementAt(ds, i); ds = new Sequence(ds); // update with new dataset sequence sequences[i].setDatasetSequence(ds); } else { ds = sequences[newDs.indexOf(ds)].getDatasetSequence(); } } else { // copy and derive new dataset sequence sequences[i] = sequences[i].deriveSequence(); alignment.getDataset().addSequence( sequences[i].getDatasetSequence()); // TODO: avoid creation of duplicate dataset sequences with a // 'contains' method using SequenceI.equals()/SequenceI.contains() } alignment.addSequence(sequences[i]); // merges dataset } if (newDs != null) { newDs.clear(); // tidy up } if (pastedal.getAlignmentAnnotation() != null) { // Add any annotation attached to alignment. AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation(); for (int i = 0; i < alann.length; i++) { annotationAdded = true; if (alann[i].sequenceRef == null && !alann[i].autoCalculated) { AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]); newann.padAnnotation(alwidth); alignment.addAnnotation(newann); } } } } if (!newAlignment) { // ///// // ADD HISTORY ITEM // addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment)); } // Add any annotations attached to sequences for (int i = 0; i < sequences.length; i++) { if (sequences[i].getAnnotation() != null) { for (int a = 0; a < sequences[i].getAnnotation().length; a++) { annotationAdded = true; sequences[i].getAnnotation()[a].adjustForAlignment(); sequences[i].getAnnotation()[a].padAnnotation(alwidth); alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation // was // duplicated // earlier alignment .setAnnotationIndex(sequences[i].getAnnotation()[a], a); } } } if (!newAlignment) { // propagate alignment changed. viewport.setEndSeq(alignment.getHeight()); if (annotationAdded) { // Duplicate sequence annotation in all views. AlignmentI[] alview = this.getViewAlignments(); for (int i = 0; i < sequences.length; i++) { AlignmentAnnotation sann[] = sequences[i].getAnnotation(); if (sann == null) continue; for (int avnum = 0; avnum < alview.length; avnum++) { if (alview[avnum] != alignment) { // duplicate in a view other than the one with input focus int avwidth = alview[avnum].getWidth() + 1; // this relies on sann being preserved after we // modify the sequence's annotation array for each duplication for (int a = 0; a < sann.length; a++) { AlignmentAnnotation newann = new AlignmentAnnotation( sann[a]); sequences[i].addAlignmentAnnotation(newann); newann.padAnnotation(avwidth); alview[avnum].addAnnotation(newann); // annotation was // duplicated earlier alview[avnum].setAnnotationIndex(newann, a); } } } } buildSortByAnnotationScoresMenu(); } viewport.firePropertyChange("alignment", null, alignment.getSequences()); } else { AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT); String newtitle = new String("Copied sequences"); if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { Vector hc = (Vector) Desktop.jalviewClipboard[2]; for (int i = 0; i < hc.size(); i++) { int[] region = (int[]) hc.elementAt(i); af.viewport.hideColumns(region[0], region[1]); } } // >>>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 < seqs.size(); i++) { cut[i] = (SequenceI) seqs.elementAt(i); } /* * //ADD HISTORY ITEM */ addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, viewport.alignment)); viewport.setSelectionGroup(null); viewport.sendSelection(); viewport.alignment.deleteGroup(sg); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); if (viewport.getAlignment().getHeight() < 1) { try { this.setClosed(true); } catch (Exception ex) { } } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void deleteGroups_actionPerformed(ActionEvent e) { viewport.alignment.deleteAllGroups(); viewport.sequenceColours = null; viewport.setSelectionGroup(null); PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = new SequenceGroup(); for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); } sg.setEndRes(viewport.alignment.getWidth() - 1); viewport.setSelectionGroup(sg); viewport.sendSelection(); alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { if (viewport.cursorMode) { alignPanel.seqPanel.keyboardNo1 = null; alignPanel.seqPanel.keyboardNo2 = null; } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); alignPanel.idPanel.idCanvas.searchResults = null; alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void invertSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = viewport.getSelectionGroup(); if (sg == null) { selectAllSequenceMenuItem_actionPerformed(null); return; } for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); } alignPanel.paintAlignment(true); viewport.sendSelection(); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } public void invertColSel_actionPerformed(ActionEvent e) { viewport.invertColumnSelection(); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void remove2LeftMenuItem_actionPerformed(ActionEvent e) { trimAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void remove2RightMenuItem_actionPerformed(ActionEvent e) { trimAlignment(false); } void trimAlignment(boolean trimLeft) { ColumnSelection colSel = viewport.getColumnSelection(); int column; if (colSel.size() > 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()); } // else { // if (justifySeqs>0) { // alignment.justify(justifySeqs!=RIGHT_JUSTIFY); } } // } /** * 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 < comps.size(); i++) { if (comps.elementAt(i) instanceof AlignmentPanel) { AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i); if (!existingNames.contains(ap.av.viewName)) { existingNames.addElement(ap.av.viewName); } } } while (existingNames.contains(newViewName)) { newViewName = "View " + (++index); } newap.av.viewName = newViewName; addAlignmentPanel(newap, true); if (alignPanels.size() == 2) { viewport.gatherViewsHere = true; } tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); } public void expandViews_actionPerformed(ActionEvent e) { Desktop.instance.explodeViews(this); } public void gatherViews_actionPerformed(ActionEvent e) { Desktop.instance.gatherViews(this); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void font_actionPerformed(ActionEvent e) { new FontChooser(alignPanel); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void seqLimit_actionPerformed(ActionEvent e) { viewport.setShowJVSuffix(seqLimits.isSelected()); alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel .calculateIdWidth()); alignPanel.paintAlignment(true); } public void idRightAlign_actionPerformed(ActionEvent e) { viewport.rightAlignIds = idRightAlign.isSelected(); alignPanel.paintAlignment(true); } public void centreColumnLabels_actionPerformed(ActionEvent e) { viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState(); alignPanel.paintAlignment(true); } /* * (non-Javadoc) * * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() */ protected void followHighlight_actionPerformed() { if (viewport.followHighlight = this.followHighlightMenuItem.getState()) { alignPanel.scrollToPosition( alignPanel.seqPanel.seqCanvas.searchResults, false); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void colourTextMenuItem_actionPerformed(ActionEvent e) { viewport.setColourText(colourTextMenuItem.isSelected()); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void wrapMenuItem_actionPerformed(ActionEvent e) { scaleAbove.setVisible(wrapMenuItem.isSelected()); scaleLeft.setVisible(wrapMenuItem.isSelected()); scaleRight.setVisible(wrapMenuItem.isSelected()); viewport.setWrapAlignment(wrapMenuItem.isSelected()); alignPanel.setWrapAlignment(wrapMenuItem.isSelected()); } public void showAllSeqs_actionPerformed(ActionEvent e) { viewport.showAllHiddenSeqs(); } public void showAllColumns_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); repaint(); } public void hideSelSequences_actionPerformed(ActionEvent e) { viewport.hideAllSelectedSeqs(); alignPanel.paintAlignment(true); } /** * called by key handler and the hide all/show all menu items * * @param toggleSeqs * @param toggleCols */ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) { boolean hide = false; SequenceGroup sg = viewport.getSelectionGroup(); if (!toggleSeqs && !toggleCols) { // Hide everything by the current selection - this is a hack - we do the // invert and then hide // first check that there will be visible columns after the invert. if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel .getSelected().size() > 0) || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg .getEndRes())) { // now invert the sequence set, if required - empty selection implies // that no hiding is required. if (sg != null) { invertSequenceMenuItem_actionPerformed(null); sg = viewport.getSelectionGroup(); toggleSeqs = true; } viewport.expandColSelection(sg, true); // finally invert the column selection and get the new sequence // selection. invertColSel_actionPerformed(null); toggleCols = true; } } 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); } } } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. * event.ActionEvent) */ public void hideAllButSelection_actionPerformed(ActionEvent e) { toggleHiddenRegions(false, false); } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event * .ActionEvent) */ public void hideAllSelection_actionPerformed(ActionEvent e) { SequenceGroup sg = viewport.getSelectionGroup(); viewport.expandColSelection(sg, false); viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. * ActionEvent) */ public void showAllhidden_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); viewport.showAllHiddenSeqs(); alignPanel.paintAlignment(true); } public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); } public void hiddenMarkers_actionPerformed(ActionEvent e) { viewport.setShowHiddenMarkers(hiddenMarkers.isSelected()); repaint(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void scaleAbove_actionPerformed(ActionEvent e) { viewport.setScaleAboveWrapped(scaleAbove.isSelected()); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void viewTextMenuItem_actionPerformed(ActionEvent e) { viewport.setShowText(viewTextMenuItem.isSelected()); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { viewport.setRenderGaps(renderGapsMenuItem.isSelected()); alignPanel.paintAlignment(true); } public FeatureSettings featureSettings; public void featureSettings_actionPerformed(ActionEvent e) { if (featureSettings != null) { featureSettings.close(); featureSettings = null; } if (!showSeqFeatures.isSelected()) { // make sure features are actually displayed showSeqFeatures.setSelected(true); showSeqFeatures_actionPerformed(null); } featureSettings = new FeatureSettings(this); } /** * Set or clear 'Show Sequence Features' * * @param evt * DOCUMENT ME! */ public void showSeqFeatures_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); alignPanel.paintAlignment(true); if (alignPanel.getOverviewPanel() != null) { alignPanel.getOverviewPanel().updateOverviewImage(); } } /** * Set or clear 'Show Sequence Features' * * @param evt * DOCUMENT ME! */ public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight .isSelected()); if (viewport.getShowSequenceFeaturesHeight()) { // ensure we're actually displaying features viewport.setShowSequenceFeatures(true); showSeqFeatures.setSelected(true); } alignPanel.paintAlignment(true); if (alignPanel.getOverviewPanel() != null) { alignPanel.getOverviewPanel().updateOverviewImage(); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { viewport.setShowAnnotation(annotationPanelMenuItem.isSelected()); alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected()); } public void alignmentProperties() { JEditorPane editPane = new JEditorPane("text/html", ""); editPane.setEditable(false); StringBuffer contents = new StringBuffer(""); float avg = 0; int min = Integer.MAX_VALUE, max = 0; for (int i = 0; i < viewport.alignment.getHeight(); i++) { int size = viewport.alignment.getSequenceAt(i).getEnd() - viewport.alignment.getSequenceAt(i).getStart(); avg += size; if (size > max) max = size; if (size < min) min = size; } avg = avg / (float) viewport.alignment.getHeight(); contents.append("
Sequences: " + 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 sortLengthMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByLength(viewport.getAlignment()); addHistoryItem(new OrderCommand("Length 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 visible sequences aligned? if (!viewport.alignment.isAligned(false)) { 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 && i < aann.length; i++) { if (aann[i].hasScore() && aann[i].sequenceRef != null) { scoreSorts.put(aann[i].label, aann[i].label); } } } Enumeration labels = scoreSorts.keys(); while (labels.hasMoreElements()) { addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels.nextElement()); } sortByAnnotScore.setVisible(scoreSorts.size() > 0); 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 < iSize; i++) { if (comps.elementAt(i) instanceof TreePanel) { treePanels.add(comps.elementAt(i)); } } iSize = treePanels.size(); if (iSize < 1) { sortByTreeMenu.setVisible(false); return; } sortByTreeMenu.setVisible(true); for (i = 0; i < treePanels.size(); i++) { TreePanel tp = (TreePanel) treePanels.elementAt(i); final JMenuItem item = new JMenuItem(tp.getTitle()); final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree(); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment() .getSequencesArray(); AlignmentSorter.sortByTree(viewport.getAlignment(), tree); addHistoryItem(new OrderCommand("Tree Sort", oldOrder, viewport.alignment)); alignPanel.paintAlignment(true); } }); sortByTreeMenu.add(item); } } /** * Work out whether the whole set of sequences or just the selected set will * be submitted for multiple alignment. * */ public jalview.datamodel.AlignmentView gatherSequencesForAlignment() { // Now, check we have enough sequences AlignmentView msa = null; if ((viewport.getSelectionGroup() != null) && (viewport.getSelectionGroup().getSize() > 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(false)) { seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] }); // TODO: if seqs.getSequences().length>1 then should really have warned // user! } 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; } private boolean buildingMenu = false; /** * Generates menu items and listener event actions for web service clients * */ public void BuildWebServiceMenu() { while (buildingMenu) { try { System.err.println("Waiting for building menu to finish."); Thread.sleep(10); } catch (Exception e) { } ; } final AlignFrame me = this; buildingMenu = true; new Thread(new Runnable() { public void run() { try { System.err.println("Building ws menu again " + Thread.currentThread()); // 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. final Vector wsmenu = new Vector(); final IProgressIndicator af = me; if (Cache.getDefault("SHOW_JWS1_SERVICES", true) && 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) 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.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer .getServiceClient(sh); impl.attachWSMenuEntry(msawsmenu, me); } 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.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer .getServiceClient(sh); impl.attachWSMenuEntry(secstrmenu, me); } 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.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer .getServiceClient(sh); impl.attachWSMenuEntry(seqsrchmenu, me); } wsmenu.add(seqsrchmenu); } } // TODO: move into separate menu builder class. if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); if (jws2servs != null) { if (jws2servs.hasServices()) { JMenu jws2men = new JMenu("Jaba Web Services"); jws2servs.attachWSMenuEntry(jws2men, me); for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++) { wsmenu.add(jws2men.getMenuComponent(i)); } } } } javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { try { resetWebServiceMenu(); // finally, add the whole shebang onto the webservices menu if (wsmenu.size() > 0) { for (int i = 0, j = wsmenu.size(); i < j; i++) { webService.add((JMenu) wsmenu.get(i)); } } else { me.webService.add(me.webServiceNoServices); } } catch (Exception e) { } ; } }); } catch (Exception e) { } ; buildingMenu = false; } }).start(); } /** * empty the web service menu and add any ad-hoc functions not dynamically * discovered. * */ private void resetWebServiceMenu() { webService.removeAll(); build_fetchdbmenu(webService); build_urlServiceMenu(webService); } /** * construct any groupURL type service menu entries. * * @param webService */ private void build_urlServiceMenu(JMenu webService) { if (Cache.getDefault("SHOW_ENFIN_SERVICES", true)) { jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry( webService, this); } } /* * 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 = (selection == null || selection.length == 0) ? null : 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 < ptypes.length; t++) { showp = true; final boolean isRegSel = isRegionSelection; final AlignFrame af = this; final String source = ptypes[t]; JMenuItem xtype = new JMenuItem(ptypes[t]); xtype.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { // TODO: new thread for this call with vis-delay af.showProductsFor(af.viewport.getSequenceSelection(), ds, isRegSel, dna, source); } }); showProducts.add(xtype); } showProducts.setVisible(showp); showProducts.setEnabled(showp); } catch (Exception e) { jalview.bin.Cache.log .warn("canTranslate threw an exception - please report to help@jalview.org", e); return false; } return showp; } protected void showProductsFor(SequenceI[] sel, Alignment ds, boolean isRegSel, boolean dna, String source) { final boolean fisRegSel = isRegSel; final boolean fdna = dna; final String fsrc = source; final AlignFrame ths = this; final SequenceI[] fsel = sel; Runnable foo = new Runnable() { public void run() { final long sttime = System.currentTimeMillis(); ths.setProgressBar("Searching for sequences from " + fsrc, sttime); try { Alignment ds = ths.getViewport().alignment.getDataset(); // update // our local // dataset // reference Alignment prods = CrossRef .findXrefSequences(fsel, fdna, fsrc, ds); if (prods != null) { SequenceI[] sprods = new SequenceI[prods.getHeight()]; for (int s = 0; s < sprods.length; s++) { sprods[s] = (prods.getSequenceAt(s)).deriveSequence(); if (ds.getSequences() == null || !ds.getSequences().contains( sprods[s].getDatasetSequence())) ds.addSequence(sprods[s].getDatasetSequence()); sprods[s].updatePDBIds(); } Alignment al = new Alignment(sprods); AlignedCodonFrame[] cf = prods.getCodonFrames(); al.setDataset(ds); for (int s = 0; cf != null && s < cf.length; s++) { al.addCodonFrame(cf[s]); cf[s] = null; } AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ") + " for " + ((fisRegSel) ? "selected region of " : "") + getTitle(); Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); } else { System.err.println("No Sequences generated for xRef type " + fsrc); } } catch (Exception e) { jalview.bin.Cache.log.error( "Exception when finding crossreferences", e); } catch (OutOfMemoryError e) { new OOMWarning("whilst fetching crossreferences", e); } catch (Error e) { jalview.bin.Cache.log.error("Error when finding crossreferences", e); } ths.setProgressBar("Finished searching for sequences from " + fsrc, sttime); } }; Thread frunner = new Thread(foo); frunner.start(); } public boolean canShowTranslationProducts(SequenceI[] selection, AlignmentI alignment) { // old way try { return (jalview.analysis.Dna.canTranslate(selection, viewport.getViewAsVisibleContigs(true))); } catch (Exception e) { jalview.bin.Cache.log .warn("canTranslate threw an exception - please report to help@jalview.org", e); return false; } } public void showProducts_actionPerformed(ActionEvent e) { // ///////////////////////////// // Collect Data to be translated/transferred SequenceI[] selection = viewport.getSequenceSelection(); AlignmentI al = null; try { al = jalview.analysis.Dna.CdnaTranslate(selection, viewport .getViewAsVisibleContigs(true), viewport.getGapCharacter(), viewport.getAlignment().getDataset()); } catch (Exception ex) { al = null; jalview.bin.Cache.log.debug("Exception during translation.", ex); } if (al == null) { JOptionPane .showMessageDialog( Desktop.desktop, "Please select at least three bases in at least one sequence in order to perform a cDNA translation.", "Translation Failed", JOptionPane.WARNING_MESSAGE); } else { AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); Desktop.addInternalFrame(af, "Translation of " + this.getTitle(), DEFAULT_WIDTH, DEFAULT_HEIGHT); } } public void showTranslation_actionPerformed(ActionEvent e) { // ///////////////////////////// // Collect Data to be translated/transferred SequenceI[] selection = viewport.getSequenceSelection(); String[] seqstring = viewport.getViewAsString(true); AlignmentI al = null; try { al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true), viewport .getGapCharacter(), viewport.alignment .getAlignmentAnnotation(), viewport.alignment .getWidth(), viewport.getAlignment().getDataset()); } catch (Exception ex) { al = null; jalview.bin.Cache.log.debug("Exception during translation.", ex); } if (al == null) { JOptionPane .showMessageDialog( Desktop.desktop, "Please select at least three bases in at least one sequence in order to perform a cDNA translation.", "Translation Failed", JOptionPane.WARNING_MESSAGE); } else { AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); Desktop.addInternalFrame(af, "Translation of " + this.getTitle(), DEFAULT_WIDTH, DEFAULT_HEIGHT); } } /** * Try to load a features file onto the alignment. * * @param file * contents or path to retrieve file * @param type * access mode of file (see jalview.io.AlignFile) * @return true if features file was parsed corectly. */ public boolean parseFeaturesFile(String file, String type) { boolean featuresFile = false; try { featuresFile = new FeaturesFile(file, type) .parse(viewport.alignment.getDataset(), alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours, false); } catch (Exception ex) { ex.printStackTrace(); } if (featuresFile) { viewport.showSequenceFeatures = true; showSeqFeatures.setSelected(true); if (alignPanel.seqPanel.seqCanvas.fr != null) { // update the min/max ranges where necessary alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); } if (featureSettings != null) { featureSettings.setTableData(); } alignPanel.paintAlignment(true); } return featuresFile; } public void dragEnter(DropTargetDragEvent evt) { } public void dragExit(DropTargetEvent evt) { } public void dragOver(DropTargetDragEvent evt) { } public void dropActionChanged(DropTargetDragEvent evt) { } public void drop(DropTargetDropEvent evt) { Transferable t = evt.getTransferable(); java.util.List files = null; try { DataFlavor uriListFlavor = new DataFlavor( "text/uri-list;class=java.lang.String"); if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) { // Works on Windows and MacOSX evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); files = (java.util.List) t .getTransferData(DataFlavor.javaFileListFlavor); } else if (t.isDataFlavorSupported(uriListFlavor)) { // This is used by Unix drag system evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); String data = (String) t.getTransferData(uriListFlavor); files = new java.util.ArrayList(1); for (java.util.StringTokenizer st = new java.util.StringTokenizer( data, "\r\n"); st.hasMoreTokens();) { String s = st.nextToken(); if (s.startsWith("#")) { // the line is a comment (as per the RFC 2483) continue; } java.net.URI uri = new java.net.URI(s); // check to see if we can handle this kind of URI if (uri.getScheme().toLowerCase().startsWith("http")) { files.add(uri.toString()); } else { // otherwise preserve old behaviour: catch all for file objects java.io.File file = new java.io.File(uri); files.add(file.toString()); } } } } catch (Exception e) { e.printStackTrace(); } if (files != null) { try { for (int i = 0; i < files.size(); i++) { loadJalviewDataFile(files.get(i).toString()); } } catch (Exception ex) { ex.printStackTrace(); } } } /** * Attempt to load a "dropped" file or URL string: First by testing whether * it's and Annotation file, then a JNet file, and finally a features file. If * all are false then the user may have dropped an alignment file onto this * AlignFrame. * * @param file * either a filename or a URL string. */ public void loadJalviewDataFile(String file) { try { String protocol = jalview.io.FormatAdapter.FILE; String f = file.toLowerCase(); if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0 || f.indexOf("file:") == 0) { protocol = jalview.io.FormatAdapter.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(); } } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent * ) */ protected void showDbRefs_actionPerformed(ActionEvent e) { viewport.setShowDbRefs(showDbRefsMenuitem.isSelected()); } /* * (non-Javadoc) * * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. * ActionEvent) */ protected void showNpFeats_actionPerformed(ActionEvent e) { viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected()); } /** * find the viewport amongst the tabs in this alignment frame and close that * tab * * @param av */ public boolean closeView(AlignViewport av) { if (viewport == av) { this.closeMenuItem_actionPerformed(false); return true; } Component[] comp = tabbedPane.getComponents(); for (int i = 0; comp != null && i < comp.length; i++) { if (comp[i] instanceof AlignmentPanel) { if (((AlignmentPanel) comp[i]).av == av) { // close the view. closeView((AlignmentPanel) comp[i]); return true; } } } return false; } protected void build_fetchdbmenu(JMenu webService) { // Temporary hack - DBRef Fetcher always top level ws entry. // TODO We probably want to store a sequence database checklist in // preferences and have checkboxes.. rather than individual sources selected // here final JMenu rfetch = new JMenu("Fetch DB References"); rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences"); webService.add(rfetch); JMenuItem fetchr = new JMenuItem("Standard Databases"); fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources"); fetchr.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(); } }); rfetch.add(fetchr); final AlignFrame me = this; new Thread(new Runnable() { public void run() { final jalview.ws.SequenceFetcher sf = SequenceFetcher .getSequenceFetcherSingleton(me); final String[] otherdb = sf.getOrderedSupportedSources(); // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); // jalview.util.QuickSort.sort(otherdb, otherdb); javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { JMenu dfetch = new JMenu(); JMenuItem fetchr; rfetch.add(dfetch); int comp = 0, mcomp = 15; String mname = null; if (otherdb != null && otherdb.length > 0) { for (int i = 0; i < otherdb.length; i++) { String dbname = sf.getSourceProxy(otherdb[i]).getDbName(); if (mname == null) { mname = "from '" + dbname + "'"; } fetchr = new JMenuItem(otherdb[i]); final String[] dassource = new String[] { otherdb[i] }; fetchr.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { public void run() { new jalview.ws.DBRefFetcher(alignPanel.av .getSequenceSelection(), alignPanel.alignFrame, dassource) .fetchDBRefs(false); } }).start(); } }); fetchr.setToolTipText("Retrieve from " + dbname); dfetch.add(fetchr); if (comp++ == mcomp || i == (otherdb.length - 1)) { dfetch.setText(mname + " to '" + dbname + "'"); rfetch.add(dfetch); dfetch = new JMenu(); mname = null; comp = 0; } } } } }); } }).start(); } /** * Left justify the whole alignment. */ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) { AlignmentI al = viewport.getAlignment(); al.justify(false); viewport.firePropertyChange("alignment", null, al); } /** * Right justify the whole alignment. */ protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { AlignmentI al = viewport.getAlignment(); al.justify(true); viewport.firePropertyChange("alignment", null, al); } public void setShowSeqFeatures(boolean b) { showSeqFeatures.setSelected(true); viewport.setShowSequenceFeatures(true); } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. * awt.event.ActionEvent) */ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { viewport.setShowUnconserved(showNonconservedMenuItem.getState()); alignPanel.paintAlignment(true); } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event * .ActionEvent) */ protected void showGroupConsensus_actionPerformed(ActionEvent e) { viewport.setShowGroupConsensus(showGroupConsensus.getState()); alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt * .event.ActionEvent) */ protected void showGroupConservation_actionPerformed(ActionEvent e) { viewport.setShowGroupConservation(showGroupConservation.getState()); alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt * .event.ActionEvent) */ protected void showConsensusHistogram_actionPerformed(ActionEvent e) { viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt * .event.ActionEvent) */ protected void showSequenceLogo_actionPerformed(ActionEvent e) { viewport.setShowSequenceLogo(showSequenceLogo.getState()); alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) { alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt * .event.ActionEvent) */ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) { if (viewport.getSelectionGroup() != null) { SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom( viewport.getSequenceSelection(), viewport.getAlignmentView(true).getSequenceStrings( viewport.getGapCharacter()), viewport.alignment.getGroups()); viewport.alignment.deleteAllGroups(); viewport.sequenceColours = null; viewport.setSelectionGroup(null); // set view properties for each group for (int g = 0; g < gps.length; g++) { gps[g].setShowNonconserved(viewport.getShowUnconserved()); gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); viewport.alignment.addGroup(gps[g]); Color col = new Color((int) (Math.random() * 255), (int) (Math.random() * 255), (int) (Math.random() * 255)); col = col.brighter(); for (Enumeration sq = gps[g].getSequences(null).elements(); sq .hasMoreElements(); viewport.setSequenceColour( (SequenceI) sq.nextElement(), col)) ; } PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); alignPanel.paintAlignment(true); } } } 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(); } } } }