/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * 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 . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Rectangle; import java.awt.Toolkit; import java.awt.datatransfer.Clipboard; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.StringSelection; import java.awt.datatransfer.Transferable; import java.awt.dnd.DnDConstants; import java.awt.dnd.DropTargetDragEvent; import java.awt.dnd.DropTargetDropEvent; import java.awt.dnd.DropTargetEvent; import java.awt.dnd.DropTargetListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusAdapter; import java.awt.event.FocusEvent; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.KeyAdapter; import java.awt.event.KeyEvent; import java.awt.event.MouseEvent; import java.awt.print.PageFormat; import java.awt.print.PrinterJob; import java.beans.PropertyChangeEvent; import java.io.File; import java.io.FileWriter; import java.io.IOException; import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; import java.util.Deque; import java.util.Enumeration; import java.util.Hashtable; import java.util.List; import java.util.Locale; import java.util.Vector; import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; import javax.swing.JComponent; import javax.swing.JEditorPane; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JLayeredPane; import javax.swing.JMenu; import javax.swing.JMenuItem; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; import ext.vamsas.ServiceHandle; import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; import jalview.analysis.CrossRef; import jalview.analysis.Dna; import jalview.analysis.GeneticCodeI; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignExportSettingsI; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureSettingsControllerI; import jalview.api.FeatureSettingsModelI; import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; import jalview.bin.Console; import jalview.bin.Jalview; import jalview.bin.groovy.JalviewObjectI; import jalview.commands.CommandI; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.commands.OrderCommand; import jalview.commands.RemoveGapColCommand; import jalview.commands.RemoveGapsCommand; import jalview.commands.SlideSequencesCommand; import jalview.commands.TrimRegionCommand; import jalview.datamodel.AlignExportSettingsAdapter; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentExportData; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; import jalview.datamodel.ColumnSelection; import jalview.datamodel.ContactMatrixI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SeqCigar; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.BackupFiles; import jalview.io.BioJsHTMLOutput; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatI; import jalview.io.FileFormats; import jalview.io.FileLoader; import jalview.io.FileParse; import jalview.io.FormatAdapter; import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; import jalview.io.JPredFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.JnetAnnotationMaker; import jalview.io.NewickFile; import jalview.io.ScoreMatrixFile; import jalview.io.TCoffeeScoreFile; import jalview.io.exceptions.ImageOutputException; import jalview.io.vcf.VCFLoader; import jalview.jbgui.GAlignFrame; import jalview.project.Jalview2XML; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.schemes.ResidueColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.util.HttpUtils; import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.imagemaker.BitmapImageSizing; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.seqfetcher.DbSourceProxy; /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ @SuppressWarnings("serial") public class AlignFrame extends GAlignFrame implements DropTargetListener, IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener { public static final int DEFAULT_WIDTH = 700; public static final int DEFAULT_HEIGHT = 500; /* * The currently displayed panel (selected tabbed view if more than one) */ public AlignmentPanel alignPanel; AlignViewport viewport; public AlignViewControllerI avc; List alignPanels = new ArrayList<>(); /** * Last format used to load or save alignments in this window */ FileFormatI currentFileFormat = null; /** * Current filename for this alignment */ String fileName = null; File fileObject; /** * 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, HiddenColumns 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, HiddenColumns 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, HiddenColumns hiddenColumns, int width, int height, String sequenceSetId, String viewId) { setSize(width, height); if (al.getDataset() == null) { al.setDataset(null); } viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); alignPanel = new AlignmentPanel(this, viewport); addAlignmentPanel(alignPanel, true); init(); } public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, HiddenColumns hiddenColumns, int width, int height) { setSize(width, height); if (al.getDataset() == null) { al.setDataset(null); } viewport = new AlignViewport(al, hiddenColumns); if (hiddenSeqs != null && hiddenSeqs.length > 0) { viewport.hideSequence(hiddenSeqs); } alignPanel = new AlignmentPanel(this, viewport); addAlignmentPanel(alignPanel, true); init(); } /** * Make a new AlignFrame from existing 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() { setFrameIcon(null); // setBackground(Color.white); // BH 2019 if (!Jalview.isHeadlessMode()) { progressBar = new ProgressBar(this.statusPanel, this.statusBar); } avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) { // BLOSUM62Colour.setEnabled(false); conservationMenuItem.setEnabled(false); modifyConservation.setEnabled(false); // PIDColour.setEnabled(false); // abovePIDThreshold.setEnabled(false); // modifyPID.setEnabled(false); } String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort"); if (sortby.equals("Id")) { sortIDMenuItem_actionPerformed(null); } else if (sortby.equals("Pairwise Identity")) { sortPairwiseMenuItem_actionPerformed(null); } this.alignPanel.av .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); calculateTree.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { openTreePcaDialog(); } }); buildColourMenu(); if (Desktop.desktop != null) { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); if (!Platform.isJS()) { addServiceListeners(); } setGUINucleotide(); } if (viewport.getWrapAlignment()) { wrapMenuItem_actionPerformed(null); } if (Cache.getDefault("SHOW_OVERVIEW", false)) { this.overviewMenuItem_actionPerformed(null); } addKeyListener(); final List selviews = new ArrayList<>(); final List origview = new ArrayList<>(); final String menuLabel = MessageManager .getString("label.copy_format_from"); ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel, new ViewSetProvider() { @Override public AlignmentPanel[] getAllAlignmentPanels() { origview.clear(); origview.add(alignPanel); // make an array of all alignment panels except for this one List aps = new ArrayList<>( Arrays.asList(Desktop.getAlignmentPanels(null))); aps.remove(AlignFrame.this.alignPanel); return aps.toArray(new AlignmentPanel[aps.size()]); } }, selviews, new ItemListener() { @Override public void itemStateChanged(ItemEvent e) { if (origview.size() > 0) { final AlignmentPanel ap = origview.get(0); /* * Copy the ViewStyle of the selected panel to 'this one'. * Don't change value of 'scaleProteinAsCdna' unless copying * from a SplitFrame. */ ViewStyleI vs = selviews.get(0).getAlignViewport() .getViewStyle(); boolean fromSplitFrame = selviews.get(0) .getAlignViewport().getCodingComplement() != null; if (!fromSplitFrame) { vs.setScaleProteinAsCdna(ap.getAlignViewport() .getViewStyle().isScaleProteinAsCdna()); } ap.getAlignViewport().setViewStyle(vs); /* * Also rescale ViewStyle of SplitFrame complement if there is * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy * the whole ViewStyle (allow cDNA protein to have different * fonts) */ AlignViewportI complement = ap.getAlignViewport() .getCodingComplement(); if (complement != null && vs.isScaleProteinAsCdna()) { AlignFrame af = Desktop.getAlignFrameFor(complement); ((SplitFrame) af.getSplitViewContainer()) .adjustLayout(); af.setMenusForViewport(); } ap.updateLayout(); ap.setSelected(true); ap.alignFrame.setMenusForViewport(); } } }); if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT) .indexOf("devel") > -1 || Cache.getDefault("VERSION", "DEVELOPMENT") .toLowerCase(Locale.ROOT).indexOf("test") > -1) { formatMenu.add(vsel); } addFocusListener(new FocusAdapter() { @Override public void focusGained(FocusEvent e) { Jalview.getInstance().setCurrentAlignFrame(AlignFrame.this); } }); } /** * 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, FileFormatI format) { fileName = file; setFileFormat(format); reload.setEnabled(true); } /** * JavaScript will have this, maybe others. More dependable than a file name * and maintains a reference to the actual bytes loaded. * * @param file */ public void setFileObject(File file) { this.fileObject = file; } /** * Add a KeyListener with handlers for various KeyPressed and KeyReleased * events */ void addKeyListener() { addKeyListener(new KeyAdapter() { @Override 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.getSeqPanel().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.getSeqPanel().moveCursor(0, 1, evt.isShiftDown()); } break; case KeyEvent.VK_UP: if (evt.isAltDown() || !viewport.cursorMode) { moveSelectedSequences(true); } if (viewport.cursorMode) { alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown()); } break; case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) { slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1()); } else { alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown()); } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) { slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1()); } else { alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown()); } break; case KeyEvent.VK_SPACE: if (viewport.cursorMode) { alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown() || evt.isShiftDown() || evt.isAltDown()); } break; // case KeyEvent.VK_A: // if (viewport.cursorMode) // { // alignPanel.seqPanel.insertNucAtCursor(false,"A"); // //jalview.bin.Console.outPrintln("A"); // } // break; /* * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) { * jalview.bin.Console.outPrintln("closing bracket"); } break; */ case KeyEvent.VK_DELETE: case KeyEvent.VK_BACK_SPACE: if (!viewport.cursorMode) { cut_actionPerformed(); } else { alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown() || evt.isAltDown()); } break; case KeyEvent.VK_S: if (viewport.cursorMode) { alignPanel.getSeqPanel().setCursorRow(); } break; case KeyEvent.VK_C: if (viewport.cursorMode && !evt.isControlDown()) { alignPanel.getSeqPanel().setCursorColumn(); } break; case KeyEvent.VK_P: if (viewport.cursorMode) { alignPanel.getSeqPanel().setCursorPosition(); } break; case KeyEvent.VK_ENTER: case KeyEvent.VK_COMMA: if (viewport.cursorMode) { alignPanel.getSeqPanel().setCursorRowAndColumn(); } break; case KeyEvent.VK_Q: if (viewport.cursorMode) { alignPanel.getSeqPanel().setSelectionAreaAtCursor(true); } break; case KeyEvent.VK_M: if (viewport.cursorMode) { alignPanel.getSeqPanel().setSelectionAreaAtCursor(false); } break; case KeyEvent.VK_F2: viewport.cursorMode = !viewport.cursorMode; setStatus(MessageManager .formatMessage("label.keyboard_editing_mode", new String[] { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { ViewportRanges ranges = viewport.getRanges(); alignPanel.getSeqPanel().seqCanvas.cursorX = ranges .getStartRes(); alignPanel.getSeqPanel().seqCanvas.cursorY = ranges .getStartSeq(); } alignPanel.getSeqPanel().seqCanvas.repaint(); break; case KeyEvent.VK_F1: try { Help.showHelpWindow(); } 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_B: { boolean toggleSel = evt.isControlDown() || evt.isMetaDown(); boolean modifyExisting = true; // always modify, don't clear // evt.isShiftDown(); boolean invertHighlighted = evt.isAltDown(); avc.markHighlightedColumns(invertHighlighted, modifyExisting, toggleSel); break; } case KeyEvent.VK_PAGE_UP: viewport.getRanges().pageUp(); break; case KeyEvent.VK_PAGE_DOWN: viewport.getRanges().pageDown(); break; } } @Override 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; avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); alignPanels.add(ap); PaintRefresher.Register(ap, ap.av.getSequenceSetId()); int aSize = alignPanels.size(); tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null); if (aSize == 1 && ap.av.getViewName() == null) { this.getContentPane().add(ap, BorderLayout.CENTER); } else { if (aSize == 2) { setInitialTabVisible(); } expandViews.setEnabled(true); gatherViews.setEnabled(true); tabbedPane.addTab(ap.av.getViewName(), ap); ap.setVisible(false); } if (newPanel) { if (ap.av.isPadGaps()) { ap.av.getAlignment().padGaps(); } ap.av.updateConservation(ap); ap.av.updateConsensus(ap); ap.av.updateStrucConsensus(ap); } } public void setInitialTabVisible() { expandViews.setEnabled(true); gatherViews.setEnabled(true); tabbedPane.setVisible(true); AlignmentPanel first = alignPanels.get(0); tabbedPane.addTab(first.av.getViewName(), 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() { @Override public void propertyChange(PropertyChangeEvent evt) { // // jalview.bin.Console.outPrintln("Discoverer property // change."); // if (evt.getPropertyName().equals("services")) { SwingUtilities.invokeLater(new Runnable() { @Override public void run() { jalview.bin.Console.errPrintln( "Rebuild WS Menu for service change"); BuildWebServiceMenu(); } }); } } }); addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { // jalview.bin.Console.outPrintln("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() { @Override public void run() { BuildWebServiceMenu(); } }).start(); } /** * Configure menu items that vary according to whether the alignment is * nucleotide or protein */ public void setGUINucleotide() { AlignmentI al = getViewport().getAlignment(); boolean nucleotide = al.isNucleotide(); loadVcf.setVisible(nucleotide); showTranslation.setVisible(nucleotide); showReverse.setVisible(nucleotide); showReverseComplement.setVisible(nucleotide); conservationMenuItem.setEnabled(!nucleotide); modifyConservation .setEnabled(!nucleotide && conservationMenuItem.isSelected()); showGroupConservation.setEnabled(!nucleotide); showComplementMenuItem .setText(nucleotide ? MessageManager.getString("label.protein") : MessageManager.getString("label.nucleotide")); } /** * set up menus for the current 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. */ @Override 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 */ public void setMenusFromViewport(AlignViewport av) { padGapsMenuitem.setSelected(av.isPadGaps()); colourTextMenuItem.setSelected(av.isShowColourText()); abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); modifyPID.setEnabled(abovePIDThreshold.isSelected()); conservationMenuItem.setSelected(av.getConservationSelected()); modifyConservation.setEnabled(conservationMenuItem.isSelected()); seqLimits.setSelected(av.getShowJVSuffix()); idRightAlign.setSelected(av.isRightAlignIds()); centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels()); renderGapsMenuItem.setSelected(av.isRenderGaps()); wrapMenuItem.setSelected(av.getWrapAlignment()); scaleAbove.setVisible(av.getWrapAlignment()); scaleLeft.setVisible(av.getWrapAlignment()); scaleRight.setVisible(av.getWrapAlignment()); annotationPanelMenuItem.setState(av.isShowAnnotation()); /* * Show/hide annotations only enabled if annotation panel is shown */ showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); viewBoxesMenuItem.setSelected(av.getShowBoxes()); viewTextMenuItem.setSelected(av.getShowText()); showNonconservedMenuItem.setSelected(av.getShowUnconserved()); showGroupConsensus.setSelected(av.isShowGroupConsensus()); showGroupConservation.setSelected(av.isShowGroupConservation()); showConsensusHistogram.setSelected(av.isShowConsensusHistogram()); showSequenceLogo.setSelected(av.isShowSequenceLogo()); normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); ColourMenuHelper.setColourSelected(colourMenu, av.getGlobalColourScheme()); showSeqFeatures.setSelected(av.isShowSequenceFeatures()); hiddenMarkers.setState(av.getShowHiddenMarkers()); applyToAllGroups.setState(av.getColourAppliesToAllGroups()); showNpFeatsMenuitem.setSelected(av.isShowNPFeats()); showDbRefsMenuitem.setSelected(av.isShowDBRefs()); autoCalculate.setSelected(av.autoCalculateConsensus); sortByTree.setSelected(av.sortByTree); listenToViewSelections.setSelected(av.followSelection); showProducts.setEnabled(canShowProducts()); setGroovyEnabled(Desktop.getGroovyConsole() != null); updateEditMenuBar(); } /** * Set the enabled state of the 'Run Groovy' option in the Calculate menu * * @param b */ public void setGroovyEnabled(boolean b) { runGroovy.setEnabled(b); } private IProgressIndicator progressBar; /* * (non-Javadoc) * * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ @Override public void setProgressBar(String message, long id) { if (!Platform.isHeadless() && progressBar != null) progressBar.setProgressBar(message, id); } @Override public void registerHandler(final long id, final IProgressIndicatorHandler handler) { if (progressBar != null) progressBar.registerHandler(id, handler); } /** * * @return true if any progress bars are still active */ @Override public boolean operationInProgress() { return progressBar == null ? false : progressBar.operationInProgress(); } /** * Sets the text of the status bar. Note that setting a null or empty value * will cause the status bar to be hidden, with possibly undesirable flicker * of the screen layout. */ @Override public void setStatus(String text) { statusBar.setText(text == null || text.isEmpty() ? " " : text); } /* * Added so Castor Mapping file can obtain Jalview Version */ public String getVersion() { return Cache.getProperty("VERSION"); } public FeatureRenderer getFeatureRenderer() { return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer(); } @Override public void fetchSequence_actionPerformed() { new SequenceFetcher(this); } @Override public void addFromFile_actionPerformed(ActionEvent e) { Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); } @Override public void reload_actionPerformed(ActionEvent e) { if (fileName != null) { // TODO: JAL-1108 - ensure all associated frames are closed regardless of // originating file's format // TODO: work out how to recover feature settings for correct view(s) when // file is reloaded. if (FileFormat.Jalview.equals(currentFileFormat)) { 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 != null && ((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(); DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName) ? DataSourceType.URL : DataSourceType.FILE; loader.LoadFile(viewport, fileName, protocol, currentFileFormat); } else { Rectangle bounds = this.getBounds(); FileLoader loader = new FileLoader(); AlignFrame newframe = null; if (fileObject == null) { DataSourceType protocol = HttpUtils.startsWithHttpOrHttps( fileName) ? DataSourceType.URL : DataSourceType.FILE; newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat); } else { newframe = loader.LoadFileWaitTillLoaded(fileObject, DataSourceType.FILE, 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() { @Override public void run() { nfs.frame.setBounds(fspos); } }); this.featureSettings.close(); this.featureSettings = null; } this.closeMenuItem_actionPerformed(true); } } } @Override public void addFromText_actionPerformed(ActionEvent e) { Desktop.instance .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel()); } @Override public void addFromURL_actionPerformed(ActionEvent e) { Desktop.instance.inputURLMenuItem_actionPerformed(viewport); } @Override public void save_actionPerformed(ActionEvent e) { if (fileName == null || (currentFileFormat == null) || HttpUtils.startsWithHttpOrHttps(fileName)) { saveAs_actionPerformed(); } else { saveAlignment(fileName, currentFileFormat); } } /** * Saves the alignment to a file with a name chosen by the user, if necessary * warning if a file would be overwritten */ @Override public void saveAs_actionPerformed() { String format = currentFileFormat == null ? null : currentFileFormat.getName(); JalviewFileChooser chooser = JalviewFileChooser .forWrite(Cache.getProperty("LAST_DIRECTORY"), format); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.save_alignment_to_file")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); if (value != JalviewFileChooser.APPROVE_OPTION) { return; } currentFileFormat = chooser.getSelectedFormat(); // todo is this (2005) test now obsolete - value is never null? while (currentFileFormat == null) { JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.select_file_format_before_saving"), MessageManager.getString("label.file_format_not_specified"), JvOptionPane.WARNING_MESSAGE); currentFileFormat = chooser.getSelectedFormat(); value = chooser.showSaveDialog(this); if (value != JalviewFileChooser.APPROVE_OPTION) { return; } } fileName = chooser.getSelectedFile().getPath(); Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName()); Cache.setProperty("LAST_DIRECTORY", fileName); saveAlignment(fileName, currentFileFormat); } boolean lastSaveSuccessful = false; FileFormatI lastFormatSaved; String lastFilenameSaved; /** * Raise a dialog or status message for the last call to saveAlignment. * * @return true if last call to saveAlignment(file, format) was successful. */ public boolean isSaveAlignmentSuccessful() { if (!lastSaveSuccessful) { if (!Platform.isHeadless()) { JvOptionPane.showInternalMessageDialog(this, MessageManager .formatMessage("label.couldnt_save_file", new Object[] { lastFilenameSaved }), MessageManager.getString("label.error_saving_file"), JvOptionPane.WARNING_MESSAGE); } else { Console.error(MessageManager .formatMessage("label.couldnt_save_file", new Object[] { lastFilenameSaved })); } } else { setStatus(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new Object[] { lastFilenameSaved, lastFormatSaved })); } return lastSaveSuccessful; } /** * Saves the alignment to the specified file path, in the specified format, * which may be an alignment format, or Jalview project format. If the * alignment has hidden regions, or the format is one capable of including * non-sequence data (features, annotations, groups), then the user may be * prompted to specify what to include in the output. * * @param file * @param format */ public void saveAlignment(String file, FileFormatI format) { saveAlignment(file, format, false, false); } public void saveAlignment(String file, FileFormatI format, boolean stdout, boolean forceBackup) { lastSaveSuccessful = true; if (!stdout) { lastFilenameSaved = file; } lastFormatSaved = format; if (FileFormat.Jalview.equals(format)) { String shortName = title; if (shortName.indexOf(File.separatorChar) > -1) { shortName = shortName .substring(shortName.lastIndexOf(File.separatorChar) + 1); } // TODO deal with stdout=true lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName); Console.debug("lastSaveSuccessful=" + lastSaveSuccessful); if (lastSaveSuccessful) { this.getViewport().setSavedUpToDate(true); } statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new Object[] { file, format })); return; } AlignExportSettingsI options = new AlignExportSettingsAdapter(false); Runnable cancelAction = () -> { lastSaveSuccessful = false; }; Runnable outputAction = () -> { // todo defer this to inside formatSequences (or later) AlignmentExportData exportData = viewport.getAlignExportData(options); String output = new FormatAdapter(alignPanel, options) .formatSequences(format, exportData.getAlignment(), exportData.getOmitHidden(), exportData.getStartEndPostions(), viewport.getAlignment().getHiddenColumns()); if (output == null) { lastSaveSuccessful = false; } else { // create backupfiles object and get new temp filename destination boolean doBackup = forceBackup || (BackupFiles.getEnabled() && !stdout); BackupFiles backupfiles = null; if (doBackup) { Console.trace("ALIGNFRAME making backupfiles object for " + file); backupfiles = new BackupFiles(file); } try { String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file; Console.trace("ALIGNFRAME setting PrintWriter"); PrintWriter out = stdout ? new PrintWriter(new OutputStreamWriter(System.out)) : new PrintWriter(new FileWriter(tempFilePath)); if (backupfiles != null) { Console.trace("ALIGNFRAME about to write to temp file " + backupfiles.getTempFilePath()); } out.print(output); out.flush(); if (!stdout) { Console.trace("ALIGNFRAME about to close file"); out.close(); Console.trace("ALIGNFRAME closed file"); } AlignFrame.this.setTitle(stdout ? "STDOUT" : file); if (stdout) { statusBar.setText(MessageManager.formatMessage( "label.successfully_printed_to_stdout_in_format", new Object[] { format.getName() })); } else { statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new Object[] { fileName, format.getName() })); } lastSaveSuccessful = true; } catch (IOException e) { lastSaveSuccessful = false; Console.error( "ALIGNFRAME Something happened writing the temp file"); Console.error(e.getMessage()); Console.debug(Cache.getStackTraceString(e)); } catch (Exception ex) { lastSaveSuccessful = false; Console.error( "ALIGNFRAME Something unexpected happened writing the temp file"); Console.error(ex.getMessage()); Console.debug(Cache.getStackTraceString(ex)); } if (doBackup) { backupfiles.setWriteSuccess(lastSaveSuccessful); Console.debug("ALIGNFRAME writing temp file was " + (lastSaveSuccessful ? "" : "NOT ") + "successful"); // do the backup file roll and rename the temp file to actual file Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile"); lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile " + (lastSaveSuccessful ? "" : "un") + "successfully"); } Console.debug("lastSaveSuccessful=" + lastSaveSuccessful); if (lastSaveSuccessful) { AlignFrame.this.getViewport().setSavedUpToDate(true); } } }; /* * show dialog with export options if applicable; else just do it */ if (AlignExportOptions.isNeeded(viewport, format)) { AlignExportOptions choices = new AlignExportOptions( alignPanel.getAlignViewport(), format, options); choices.setResponseAction(0, outputAction); choices.setResponseAction(1, cancelAction); choices.showDialog(); } else { try { outputAction.run(); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } } /** * Outputs the alignment to textbox in the requested format, if necessary * first prompting the user for whether to include hidden regions or * non-sequence data * * @param fileFormatName */ @Override protected void outputText_actionPerformed(String fileFormatName) { FileFormatI fileFormat = FileFormats.getInstance() .forName(fileFormatName); AlignExportSettingsI options = new AlignExportSettingsAdapter(false); Runnable outputAction = () -> { // todo defer this to inside formatSequences (or later) AlignmentExportData exportData = viewport.getAlignExportData(options); CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); try { FileFormatI format = fileFormat; cap.setText(new FormatAdapter(alignPanel, options).formatSequences( format, exportData.getAlignment(), exportData.getOmitHidden(), exportData.getStartEndPostions(), viewport.getAlignment().getHiddenColumns())); Desktop.addInternalFrame(cap, MessageManager.formatMessage( "label.alignment_output_command", new Object[] { fileFormat.getName() }), 600, 500); } catch (OutOfMemoryError oom) { new OOMWarning("Outputting alignment as " + fileFormat.getName(), oom); cap.dispose(); } }; /* * show dialog with export options if applicable; else just do it */ if (AlignExportOptions.isNeeded(viewport, fileFormat)) { AlignExportOptions choices = new AlignExportOptions( alignPanel.getAlignViewport(), fileFormat, options); choices.setResponseAction(0, outputAction); choices.showDialog(); } else { try { outputAction.run(); } catch (Exception e) { e.printStackTrace(); } } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel); try { htmlSVG.exportHTML(null); } catch (ImageOutputException x) { // report problem to console and raise dialog } } @Override public void bioJSMenuItem_actionPerformed(ActionEvent e) { BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel); try { bjs.exportHTML(null); } catch (ImageOutputException x) { // report problem to console and raise dialog } } public void createImageMap(File file, String image) { try { alignPanel.makePNGImageMap(file, image); } catch (ImageOutputException x) { // report problem to console and raise dialog } } @Override public void createPNG_actionPerformed(ActionEvent e) { try { createPNG(null); } catch (ImageOutputException ioex) { // raise dialog, and report via console } } @Override public void createEPS_actionPerformed(ActionEvent e) { try { createEPS(null); } catch (ImageOutputException ioex) { // raise dialog, and report via console } } @Override public void createSVG_actionPerformed(ActionEvent e) { try { createSVG(null); } catch (ImageOutputException ioex) { // raise dialog, and report via console } } /** * Creates a PNG image of the alignment and writes it to the given file. If * the file is null, the user is prompted to choose a file. * * @param f */ public void createPNG(File f) throws ImageOutputException { createPNG(f, null, BitmapImageSizing.defaultBitmapImageSizing()); } public void createPNG(File f, String renderer, BitmapImageSizing userBis) throws ImageOutputException { alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis); } /** * Creates an EPS image of the alignment and writes it to the given file. If * the file is null, the user is prompted to choose a file. * * @param f */ public void createEPS(File f) throws ImageOutputException { createEPS(f, null); } public void createEPS(File f, String renderer) throws ImageOutputException { alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer); } /** * Creates an SVG image of the alignment and writes it to the given file. If * the file is null, the user is prompted to choose a file. * * @param f */ public void createSVG(File f) throws ImageOutputException { createSVG(f, null); } public void createSVG(File f, String renderer) throws ImageOutputException { alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer); } @Override public void pageSetup_actionPerformed(ActionEvent e) { PrinterJob printJob = PrinterJob.getPrinterJob(); PrintThread.pf = printJob.pageDialog(printJob.defaultPage()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void printMenuItem_actionPerformed(ActionEvent e) { // Putting in a thread avoids Swing painting problems PrintThread thread = new PrintThread(alignPanel); thread.start(); } @Override public void exportFeatures_actionPerformed(ActionEvent e) { new AnnotationExporter(alignPanel).exportFeatures(); } @Override public void exportAnnotations_actionPerformed(ActionEvent e) { new AnnotationExporter(alignPanel).exportAnnotations(); } @Override public void associatedData_actionPerformed(ActionEvent e) { final JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); String tooltip = MessageManager .getString("label.load_jalview_annotations"); chooser.setDialogTitle(tooltip); chooser.setToolTipText(tooltip); chooser.setResponseHandler(0, () -> { String choice = chooser.getSelectedFile().getPath(); Cache.setProperty("LAST_DIRECTORY", choice); loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); }); chooser.showOpenDialog(this); } /** * 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 */ @Override public void closeMenuItem_actionPerformed(boolean closeAllTabs) { if (alignPanels != null && alignPanels.size() < 2) { closeAllTabs = true; } Desktop.closeModal(this); 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 = alignPanels.get(i); ap.closePanel(); } } } else { closeView(alignPanel); } } if (closeAllTabs) { if (featureSettings != null && featureSettings.isOpen()) { featureSettings.close(); featureSettings = null; } /* * this will raise an INTERNAL_FRAME_CLOSED event and this method will * be called recursively, with the frame now in 'closed' state */ this.setClosed(true); } } catch (Exception ex) { ex.printStackTrace(); } } /** * Close the specified panel and close up tabs appropriately. * * @param panelToClose */ public void closeView(AlignmentPanel panelToClose) { int index = tabbedPane.getSelectedIndex(); int closedindex = tabbedPane.indexOfComponent(panelToClose); alignPanels.remove(panelToClose); panelToClose.closePanel(); panelToClose = 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.getHistoryList().size() > 0) { undoMenuItem.setEnabled(true); CommandI command = viewport.getHistoryList().peek(); undoMenuItem.setText(MessageManager .formatMessage("label.undo_command", new Object[] { command.getDescription() })); } else { undoMenuItem.setEnabled(false); undoMenuItem.setText(MessageManager.getString("action.undo")); } if (viewport.getRedoList().size() > 0) { redoMenuItem.setEnabled(true); CommandI command = viewport.getRedoList().peek(); redoMenuItem.setText(MessageManager .formatMessage("label.redo_command", new Object[] { command.getDescription() })); } else { redoMenuItem.setEnabled(false); redoMenuItem.setText(MessageManager.getString("action.redo")); } } @Override public void addHistoryItem(CommandI command) { if (command.getSize() > 0) { viewport.addToHistoryList(command); viewport.clearRedoList(); updateEditMenuBar(); viewport.updateHiddenColumns(); // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null // && viewport.getColumnSelection().getHiddenColumns() != null && // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); } } /** * * @return alignment objects for all views */ public AlignmentI[] getViewAlignments() { if (alignPanels != null) { AlignmentI[] als = new AlignmentI[alignPanels.size()]; int i = 0; for (AlignmentPanel ap : alignPanels) { als[i++] = ap.av.getAlignment(); } return als; } if (viewport != null) { return new AlignmentI[] { viewport.getAlignment() }; } return null; } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void undoMenuItem_actionPerformed(ActionEvent e) { if (viewport.getHistoryList().isEmpty()) { return; } CommandI command = viewport.getHistoryList().pop(); viewport.addToRedoList(command); command.undoCommand(getViewAlignments()); AlignmentViewport originalSource = getOriginatingSource(command); updateEditMenuBar(); if (originalSource != null) { if (originalSource != viewport) { Console.warn( "Implementation worry: mismatch of viewport origin for undo"); } originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != // null // && viewport.getColumnSelection().getHiddenColumns() != null && // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); originalSource.firePropertyChange("alignment", null, originalSource.getAlignment().getSequences()); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void redoMenuItem_actionPerformed(ActionEvent e) { if (viewport.getRedoList().size() < 1) { return; } CommandI command = viewport.getRedoList().pop(); viewport.addToHistoryList(command); command.doCommand(getViewAlignments()); AlignmentViewport originalSource = getOriginatingSource(command); updateEditMenuBar(); if (originalSource != null) { if (originalSource != viewport) { Console.warn( "Implementation worry: mismatch of viewport origin for redo"); } originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != // null // && viewport.getColumnSelection().getHiddenColumns() != null && // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); originalSource.firePropertyChange("alignment", null, originalSource.getAlignment().getSequences()); } } AlignmentViewport getOriginatingSource(CommandI command) { AlignmentViewport 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(); List comps = PaintRefresher.components .get(viewport.getSequenceSetId()); for (Component comp : comps) { if (comp instanceof AlignmentPanel) { if (al == ((AlignmentPanel) comp).av.getAlignment()) { originalSource = ((AlignmentPanel) comp).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.getAlignment()); } originalSource = viewport; } return originalSource; } /** * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection * or the sequence under cursor in keyboard mode * * @param up * or down (if !up) */ public void moveSelectedSequences(boolean up) { SequenceGroup sg = viewport.getSelectionGroup(); if (sg == null) { if (viewport.cursorMode) { sg = new SequenceGroup(); sg.addSequence(viewport.getAlignment().getSequenceAt( alignPanel.getSeqPanel().seqCanvas.cursorY), false); } else { return; } } if (sg.getSize() < 1) { return; } // TODO: JAL-3733 - add an event to the undo buffer for this ! viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up); alignPanel.paintAlignment(true, false); } synchronized void slideSequences(boolean right, int size) { List sg = new ArrayList<>(); if (viewport.cursorMode) { sg.add(viewport.getAlignment() .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY)); } else if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() != viewport .getAlignment().getHeight()) { sg = viewport.getSelectionGroup() .getSequences(viewport.getHiddenRepSequences()); } if (sg.size() < 1) { return; } List invertGroup = new ArrayList<>(); for (SequenceI seq : viewport.getAlignment().getSequences()) { if (!sg.contains(seq)) { invertGroup.add(seq); } } SequenceI[] seqs1 = sg.toArray(new SequenceI[0]); SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; for (int i = 0; i < invertGroup.size(); i++) { seqs2[i] = invertGroup.get(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.getSeqPanel().moveCursor(size, 0); } else { groupAdjustment = size; } } else if (!ssc.getGapsInsertedBegin() && !right) { if (viewport.cursorMode) { alignPanel.getSeqPanel().moveCursor(-size, 0); } else { groupAdjustment = -size; } } if (groupAdjustment != 0) { viewport.getSelectionGroup().setStartRes( viewport.getSelectionGroup().getStartRes() + groupAdjustment); viewport.getSelectionGroup().setEndRes( viewport.getSelectionGroup().getEndRes() + groupAdjustment); } /* * just extend the last slide command if compatible; but not if in * SplitFrame mode (to ensure all edits are broadcast - JAL-1802) */ boolean appendHistoryItem = false; Deque historyList = viewport.getHistoryList(); boolean inSplitFrame = getSplitViewContainer() != null; if (!inSplitFrame && historyList != null && historyList.size() > 0 && historyList.peek() instanceof SlideSequencesCommand) { appendHistoryItem = ssc.appendSlideCommand( (SlideSequencesCommand) historyList.peek()); } if (!appendHistoryItem) { addHistoryItem(ssc); } repaint(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void copy_actionPerformed() { 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(FileFormat.Fasta, seqs, omitHidden, null); 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; } HiddenColumns hiddenColumns = null; if (viewport.hasHiddenColumns()) { int hiddenOffset = viewport.getSelectionGroup().getStartRes(); int hiddenCutoff = viewport.getSelectionGroup().getEndRes(); // create new HiddenColumns object with copy of hidden regions // between startRes and endRes, offset by startRes hiddenColumns = new HiddenColumns( viewport.getAlignment().getHiddenColumns(), hiddenOffset, hiddenCutoff, hiddenOffset); } Desktop.jalviewClipboard = new Object[] { seqs, viewport.getAlignment().getDataset(), hiddenColumns }; setStatus(MessageManager.formatMessage( "label.copied_sequences_to_clipboard", new Object[] { Integer.valueOf(seqs.length).toString() })); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void pasteNew_actionPerformed(ActionEvent e) { paste(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override 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; FileFormatI format; try { str = (String) contents.getTransferData(DataFlavor.stringFlavor); if (str.length() < 1) { return; } format = new IdentifyFile().identify(str, DataSourceType.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, DataSourceType.PASTE, format); sequences = alignment.getSequencesArray(); } int alwidth = 0; ArrayList newGraphGroups = new ArrayList<>(); int fgroup = -1; 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 (alignment.getAlignmentAnnotation() != null) { for (AlignmentAnnotation alan : alignment .getAlignmentAnnotation()) { if (alan.graphGroup > fgroup) { fgroup = alan.graphGroup; } } } 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]); if (newann.graphGroup > -1) { if (newGraphGroups.size() <= newann.graphGroup || newGraphGroups.get(newann.graphGroup) == null) { for (int q = newGraphGroups .size(); q <= newann.graphGroup; q++) { newGraphGroups.add(q, null); } newGraphGroups.set(newann.graphGroup, Integer.valueOf(++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); } newann.padAnnotation(alwidth); alignment.addAnnotation(newann); } } } } if (!newAlignment) { // ///// // ADD HISTORY ITEM // addHistoryItem(new EditCommand( MessageManager.getString("label.add_sequences"), Action.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) { AlignmentAnnotation newann; for (int a = 0; a < sequences[i].getAnnotation().length; a++) { annotationAdded = true; newann = sequences[i].getAnnotation()[a]; newann.adjustForAlignment(); newann.padAnnotation(alwidth); if (newann.graphGroup > -1) { if (newann.graphGroup > -1) { if (newGraphGroups.size() <= newann.graphGroup || newGraphGroups.get(newann.graphGroup) == null) { for (int q = newGraphGroups .size(); q <= newann.graphGroup; q++) { newGraphGroups.add(q, null); } newGraphGroups.set(newann.graphGroup, Integer.valueOf(++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); } } // annotation was duplicated earlier alignment.addAnnotation(sequences[i].getAnnotation()[a]); // take care of contact matrix too ContactMatrixI cm = sequences[i] .getContactMatrixFor(sequences[i].getAnnotation()[a]); if (cm != null) { alignment.addContactListFor(sequences[i].getAnnotation()[a], cm); } alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], a); } } } if (!newAlignment) { // propagate alignment changed. viewport.getRanges().setEndSeq(alignment.getHeight() - 1); 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 // TODO JAL-1145 graphGroups are not updated for sequence // annotation added to several views. This may cause // strangeness alview[avnum].setAnnotationIndex(newann, a); } } } } buildSortByAnnotationScoresMenu(); } viewport.firePropertyChange("alignment", null, alignment.getSequences()); if (alignPanels != null) { for (AlignmentPanel ap : alignPanels) { ap.validateAnnotationDimensions(false); } } else { alignPanel.validateAnnotationDimensions(false); } } else { AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT); String newtitle = new String("Copied sequences"); if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; af.viewport.setHiddenColumns(hc); } // >>>This is a fix for the moment, until a better solution is // found!!<<< af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() .transferSettings(alignPanel.getSeqPanel().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(); jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex); // could be anything being pasted in here } } @Override protected void expand_newalign(ActionEvent e) { try { AlignmentI alignment = AlignmentUtils .expandContext(getViewport().getAlignment(), -1); AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT); String newtitle = new String("Flanking alignment"); if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; af.viewport.setHiddenColumns(hc); } // >>>This is a fix for the moment, until a better solution is // found!!<<< af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() .transferSettings(alignPanel.getSeqPanel().seqCanvas .getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. { if (title.startsWith("Copied sequences")) { newtitle = title; } else { newtitle = newtitle.concat("- from " + title); } } Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); } catch (Exception ex) { ex.printStackTrace(); jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex); // could be anything being pasted in here } catch (OutOfMemoryError oom) { new OOMWarning("Viewing flanking region of alignment", oom); } } /** * Action Cut (delete and copy) the selected region */ @Override protected void cut_actionPerformed() { copy_actionPerformed(); delete_actionPerformed(); } /** * Performs menu option to Delete the currently selected region */ @Override protected void delete_actionPerformed() { SequenceGroup sg = viewport.getSelectionGroup(); if (sg == null) { return; } Runnable okAction = () -> { SequenceI[] cut = sg.getSequences() .toArray(new SequenceI[sg.getSize()]); addHistoryItem(new EditCommand( MessageManager.getString("label.cut_sequences"), Action.CUT, cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, viewport.getAlignment())); viewport.setSelectionGroup(null); viewport.sendSelection(); viewport.getAlignment().deleteGroup(sg); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); if (viewport.getAlignment().getHeight() < 1) { try { AlignFrame.this.setClosed(true); } catch (Exception ex) { } } }; /* * If the cut affects all sequences, prompt for confirmation */ boolean wholeHeight = sg.getSize() == viewport.getAlignment() .getHeight(); boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport.getAlignment().getWidth()) ? true : false; if (wholeHeight && wholeWidth) { JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop); dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION Object[] options = new Object[] { MessageManager.getString("action.ok"), MessageManager.getString("action.cancel") }; dialog.showDialog(MessageManager.getString("warn.delete_all"), MessageManager.getString("label.delete_all"), JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options, options[0]); } else { try { okAction.run(); } catch (Exception e) { e.printStackTrace(); } } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void deleteGroups_actionPerformed(ActionEvent e) { if (avc.deleteGroups()) { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); alignPanel.paintAlignment(true, true); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = new SequenceGroup( viewport.getAlignment().getSequences()); sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); viewport.isSelectionGroupChanged(true); viewport.sendSelection(); // JAL-2034 - should delegate to // alignPanel to decide if overview needs // updating. alignPanel.paintAlignment(false, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { if (viewport.cursorMode) { alignPanel.getSeqPanel().keyboardNo1 = null; alignPanel.getSeqPanel().keyboardNo2 = null; } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSearchResults(null); alignPanel.getIdPanel().getIdCanvas().searchResults = null; // JAL-2034 - should delegate to // alignPanel to decide if overview needs // updating. alignPanel.paintAlignment(false, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override 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); } // JAL-2034 - should delegate to // alignPanel to decide if overview needs // updating. alignPanel.paintAlignment(true, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @Override public void invertColSel_actionPerformed(ActionEvent e) { viewport.invertColumnSelection(); alignPanel.paintAlignment(true, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void remove2LeftMenuItem_actionPerformed(ActionEvent e) { trimAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void remove2RightMenuItem_actionPerformed(ActionEvent e) { trimAlignment(false); } void trimAlignment(boolean trimLeft) { ColumnSelection colSel = viewport.getColumnSelection(); int column; if (!colSel.isEmpty()) { if (trimLeft) { column = colSel.getMin(); } else { column = colSel.getMax(); } SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup() .getSequencesAsArray(viewport.getHiddenRepSequences()); } else { seqs = viewport.getAlignment().getSequencesArray(); } TrimRegionCommand trimRegion; if (trimLeft) { trimRegion = new TrimRegionCommand("Remove Left", true, seqs, column, viewport.getAlignment()); viewport.getRanges().setStartRes(0); } else { trimRegion = new TrimRegionCommand("Remove Right", false, seqs, column, viewport.getAlignment()); } setStatus(MessageManager.formatMessage("label.removed_columns", new String[] { Integer.valueOf(trimRegion.getSize()).toString() })); addHistoryItem(trimRegion); for (SequenceGroup sg : viewport.getAlignment().getGroups()) { if ((trimLeft && !sg.adjustForRemoveLeft(column)) || (!trimLeft && !sg.adjustForRemoveRight(column))) { viewport.getAlignment().deleteGroup(sg); } } viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { int start = 0, end = viewport.getAlignment().getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup() .getSequencesAsArray(viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else { seqs = viewport.getAlignment().getSequencesArray(); } RemoveGapColCommand removeGapCols = new RemoveGapColCommand( "Remove Gapped Columns", seqs, start, end, viewport.getAlignment()); addHistoryItem(removeGapCols); setStatus(MessageManager.formatMessage("label.removed_empty_columns", new Object[] { Integer.valueOf(removeGapCols.getSize()).toString() })); // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); ViewportRanges ranges = viewport.getRanges(); int startRes = seq.findPosition(ranges.getStartRes()); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); ranges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { int start = 0, end = viewport.getAlignment().getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup() .getSequencesAsArray(viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else { seqs = viewport.getAlignment().getSequencesArray(); } // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); int startRes = seq.findPosition(viewport.getRanges().getStartRes()); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, viewport.getAlignment())); viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void padGapsMenuitem_actionPerformed(ActionEvent e) { viewport.setPadGaps(padGapsMenuitem.isSelected()); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } /** * Opens a Finder dialog * * @param e */ @Override public void findMenuItem_actionPerformed(ActionEvent e) { new Finder(alignPanel, false, null); } /** * Create a new view of the current alignment. */ @Override public void newView_actionPerformed(ActionEvent e) { newView(null, true); } /** * Creates and shows a new view of the current alignment. * * @param viewTitle * title of newly created view; if null, one will be generated * @param copyAnnotation * if true then duplicate all annnotation, groups and settings * @return new alignment panel, already displayed. */ public AlignmentPanel newView(String viewTitle, boolean copyAnnotation) { /* * Create a new AlignmentPanel (with its own, new Viewport) */ AlignmentPanel newap = new jalview.project.Jalview2XML() .copyAlignPanel(alignPanel); if (!copyAnnotation) { /* * remove all groups and annotation except for the automatic stuff */ newap.av.getAlignment().deleteAllGroups(); newap.av.getAlignment().deleteAllAnnotations(false); } newap.av.setGatherViewsHere(false); if (viewport.getViewName() == null) { viewport.setViewName( MessageManager.getString("label.view_name_original")); } /* * Views share the same edits undo and redo stacks */ newap.av.setHistoryList(viewport.getHistoryList()); newap.av.setRedoList(viewport.getRedoList()); /* * copy any visualisation settings that are not saved in the project */ newap.av.setColourAppliesToAllGroups( viewport.getColourAppliesToAllGroups()); /* * Views share the same mappings; need to deregister any new mappings * created by copyAlignPanel, and register the new reference to the shared * mappings */ newap.av.replaceMappings(viewport.getAlignment()); /* * start up cDNA consensus (if applicable) now mappings are in place */ if (newap.av.initComplementConsensus()) { newap.refresh(true); // adjust layout of annotations } newap.av.setViewName(getNewViewName(viewTitle)); addAlignmentPanel(newap, true); newap.alignmentChanged(); if (alignPanels.size() == 2) { viewport.setGatherViewsHere(true); } tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); return newap; } /** * Make a new name for the view, ensuring it is unique within the current * sequenceSetId. (This used to be essential for Jalview Project archives, but * these now use viewId. Unique view names are still desirable for usability.) * * @param viewTitle * @return */ protected String getNewViewName(String viewTitle) { int index = Desktop.getViewCount(viewport.getSequenceSetId()); boolean addFirstIndex = false; if (viewTitle == null || viewTitle.trim().length() == 0) { viewTitle = MessageManager.getString("action.view"); addFirstIndex = true; } else { index = 1;// we count from 1 if given a specific name } String newViewName = viewTitle + ((addFirstIndex) ? " " + index : ""); List comps = PaintRefresher.components .get(viewport.getSequenceSetId()); List existingNames = getExistingViewNames(comps); while (existingNames.contains(newViewName)) { newViewName = viewTitle + " " + (++index); } return newViewName; } /** * Returns a list of distinct view names found in the given list of * components. View names are held on the viewport of an AlignmentPanel. * * @param comps * @return */ protected List getExistingViewNames(List comps) { List existingNames = new ArrayList<>(); for (Component comp : comps) { if (comp instanceof AlignmentPanel) { AlignmentPanel ap = (AlignmentPanel) comp; if (!existingNames.contains(ap.av.getViewName())) { existingNames.add(ap.av.getViewName()); } } } return existingNames; } /** * Explode tabbed views into separate windows. */ @Override public void expandViews_actionPerformed(ActionEvent e) { Desktop.explodeViews(this); } /** * Gather views in separate windows back into a tabbed presentation. */ @Override public void gatherViews_actionPerformed(ActionEvent e) { Desktop.instance.gatherViews(this); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void font_actionPerformed(ActionEvent e) { new FontChooser(alignPanel); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void seqLimit_actionPerformed(ActionEvent e) { viewport.setShowJVSuffix(seqLimits.isSelected()); alignPanel.getIdPanel().getIdCanvas() .setPreferredSize(alignPanel.calculateIdWidth()); alignPanel.paintAlignment(true, false); } @Override public void idRightAlign_actionPerformed(ActionEvent e) { viewport.setRightAlignIds(idRightAlign.isSelected()); alignPanel.paintAlignment(false, false); } @Override public void centreColumnLabels_actionPerformed(ActionEvent e) { viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState()); alignPanel.paintAlignment(false, false); } /* * (non-Javadoc) * * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() */ @Override protected void followHighlight_actionPerformed() { /* * Set the 'follow' flag on the Viewport (and scroll to position if now * true). */ final boolean state = this.followHighlightMenuItem.getState(); viewport.setFollowHighlight(state); if (state) { alignPanel.scrollToPosition(viewport.getSearchResults()); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void colourTextMenuItem_actionPerformed(ActionEvent e) { viewport.setColourText(colourTextMenuItem.isSelected()); alignPanel.paintAlignment(false, false); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void wrapMenuItem_actionPerformed(ActionEvent e) { setWrapFormat(wrapMenuItem.isSelected(), false); } public void setWrapFormat(boolean b, boolean setMenuItem) { scaleAbove.setVisible(b); scaleLeft.setVisible(b); scaleRight.setVisible(b); viewport.setWrapAlignment(b); alignPanel.updateLayout(); if (setMenuItem) { wrapMenuItem.setSelected(b); } } @Override public void showAllSeqs_actionPerformed(ActionEvent e) { viewport.showAllHiddenSeqs(); } @Override public void showAllColumns_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @Override public void hideSelSequences_actionPerformed(ActionEvent e) { viewport.hideAllSelectedSeqs(); } /** * called by key handler and the hide all/show all menu items * * @param toggleSeqs * @param toggleCols */ protected 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.hasSelectedColumns() || (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.getAlignment().getHeight()) { hideSelSequences_actionPerformed(null); hide = true; } else if (!(toggleCols && viewport.hasSelectedColumns())) { showAllSeqs_actionPerformed(null); } } if (toggleCols) { if (viewport.hasSelectedColumns()) { hideSelColumns_actionPerformed(null); if (!toggleSeqs) { viewport.setSelectionGroup(sg); } } else if (!hide) { showAllColumns_actionPerformed(null); } } } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. * event.ActionEvent) */ @Override public void hideAllButSelection_actionPerformed(ActionEvent e) { toggleHiddenRegions(false, false); viewport.sendSelection(); } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event * .ActionEvent) */ @Override public void hideAllSelection_actionPerformed(ActionEvent e) { SequenceGroup sg = viewport.getSelectionGroup(); viewport.expandColSelection(sg, false); viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); alignPanel.updateLayout(); alignPanel.paintAlignment(true, true); viewport.sendSelection(); } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. * ActionEvent) */ @Override public void showAllhidden_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); viewport.showAllHiddenSeqs(); alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @Override public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); alignPanel.updateLayout(); alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @Override public void hiddenMarkers_actionPerformed(ActionEvent e) { viewport.setShowHiddenMarkers(hiddenMarkers.isSelected()); repaint(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void scaleAbove_actionPerformed(ActionEvent e) { viewport.setScaleAboveWrapped(scaleAbove.isSelected()); alignPanel.updateLayout(); alignPanel.paintAlignment(true, false); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); alignPanel.updateLayout(); alignPanel.paintAlignment(true, false); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); alignPanel.updateLayout(); alignPanel.paintAlignment(true, false); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); alignPanel.paintAlignment(false, false); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void viewTextMenuItem_actionPerformed(ActionEvent e) { viewport.setShowText(viewTextMenuItem.isSelected()); alignPanel.paintAlignment(false, false); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { viewport.setRenderGaps(renderGapsMenuItem.isSelected()); alignPanel.paintAlignment(false, false); } public FeatureSettings featureSettings; @Override public FeatureSettingsControllerI getFeatureSettingsUI() { return featureSettings; } @Override public void featureSettings_actionPerformed(ActionEvent e) { showFeatureSettingsUI(); } @Override public FeatureSettingsControllerI showFeatureSettingsUI() { if (featureSettings != null) { featureSettings.closeOldSettings(); featureSettings = null; } if (!showSeqFeatures.isSelected()) { // make sure features are actually displayed showSeqFeatures.setSelected(true); showSeqFeatures_actionPerformed(null); } featureSettings = new FeatureSettings(this); return featureSettings; } /** * Set or clear 'Show Sequence Features' * * @param evt * DOCUMENT ME! */ @Override public void showSeqFeatures_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); alignPanel.paintAlignment(true, true); } /** * Action on toggle of the 'Show annotations' menu item. This shows or hides * the annotations panel as a whole. * * The options to show/hide all annotations should be enabled when the panel * is shown, and disabled when the panel is hidden. * * @param e */ @Override public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { final boolean setVisible = annotationPanelMenuItem.isSelected(); viewport.setShowAnnotation(setVisible); this.showAllSeqAnnotations.setEnabled(setVisible); this.hideAllSeqAnnotations.setEnabled(setVisible); this.showAllAlAnnotations.setEnabled(setVisible); this.hideAllAlAnnotations.setEnabled(setVisible); alignPanel.updateLayout(); } @Override public void alignmentProperties() { JComponent pane; StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) .formatAsHtml(); String content = MessageManager.formatMessage("label.html_content", new Object[] { contents.toString() }); contents = null; if (Platform.isJS()) { JLabel textLabel = new JLabel(); textLabel.setText(content); textLabel.setBackground(Color.WHITE); pane = new JPanel(new BorderLayout()); ((JPanel) pane).setOpaque(true); pane.setBackground(Color.WHITE); ((JPanel) pane).add(textLabel, BorderLayout.NORTH); } else /** * Java only * * @j2sIgnore */ { JEditorPane editPane = new JEditorPane("text/html", ""); editPane.setEditable(false); editPane.setText(content); pane = editPane; } JInternalFrame frame = new JInternalFrame(); frame.setFrameIcon(null); frame.getContentPane().add(new JScrollPane(pane)); Desktop.addInternalFrame(frame, MessageManager .formatMessage("label.alignment_properties", new Object[] { getTitle() }), 500, 400); } /** * Opens an Overview panel for the alignment, unless one is open already * * @param e */ @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { boolean showHiddenRegions = Cache .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false); openOverviewPanel(showHiddenRegions); } public OverviewPanel openOverviewPanel(boolean showHidden) { if (alignPanel.overviewPanel != null) { return alignPanel.overviewPanel; } JInternalFrame frame = new JInternalFrame(); frame.setFrameIcon(null); final OverviewPanel overview = new OverviewPanel(alignPanel, frame, showHidden); frame.setContentPane(overview); alignPanel.setOverviewPanel(overview); alignPanel.setOverviewTitle(this); Desktop.addInternalFrame(frame, overview.getTitle(), true, frame.getWidth(), frame.getHeight(), true, true); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); final AlignmentPanel thePanel = this.alignPanel; frame.addInternalFrameListener( new javax.swing.event.InternalFrameAdapter() { @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { overview.dispose(); thePanel.setOverviewPanel(null); } }); if (getKeyListeners().length > 0) { frame.addKeyListener(getKeyListeners()[0]); } return overview; } @Override public void textColour_actionPerformed() { new TextColourChooser().chooseColour(alignPanel, null); } /* * public void covariationColour_actionPerformed() { * changeColour(new * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation * ()[0])); } */ @Override public void annotationColour_actionPerformed() { new AnnotationColourChooser(viewport, alignPanel); } @Override public void annotationColumn_actionPerformed(ActionEvent e) { new AnnotationColumnChooser(viewport, alignPanel); } /** * Action on the user checking or unchecking the option to apply the selected * colour scheme to all groups. If unchecked, groups may have their own * independent colour schemes. * * @param selected */ @Override public void applyToAllGroups_actionPerformed(boolean selected) { viewport.setColourAppliesToAllGroups(selected); } /** * Action on user selecting a colour from the colour menu * * @param name * the name (not the menu item label!) of the colour scheme */ @Override public void changeColour_actionPerformed(String name) { /* * 'User Defined' opens a panel to configure or load a * user-defined colour scheme */ if (ResidueColourScheme.USER_DEFINED_MENU.equals(name)) { new UserDefinedColours(alignPanel); return; } /* * otherwise set the chosen colour scheme (or null for 'None') */ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name, viewport, viewport.getAlignment(), viewport.getHiddenRepSequences()); changeColour(cs); } /** * Actions on setting or changing the alignment colour scheme * * @param cs */ @Override public void changeColour(ColourSchemeI cs) { // TODO: pull up to controller method ColourMenuHelper.setColourSelected(colourMenu, cs); viewport.setGlobalColourScheme(cs); alignPanel.paintAlignment(true, true); } /** * Show the PID threshold slider panel */ @Override protected void modifyPID_actionPerformed() { SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(), alignPanel.getViewName()); SliderPanel.showPIDSlider(); } /** * Show the Conservation slider panel */ @Override protected void modifyConservation_actionPerformed() { SliderPanel.setConservationSlider(alignPanel, viewport.getResidueShading(), alignPanel.getViewName()); SliderPanel.showConservationSlider(); } /** * Action on selecting or deselecting (Colour) By Conservation */ @Override public void conservationMenuItem_actionPerformed(boolean selected) { modifyConservation.setEnabled(selected); viewport.setConservationSelected(selected); viewport.getResidueShading().setConservationApplied(selected); changeColour(viewport.getGlobalColourScheme()); if (selected) { modifyConservation_actionPerformed(); } else { SliderPanel.hideConservationSlider(); } } /** * Action on selecting or deselecting (Colour) Above PID Threshold */ @Override public void abovePIDThreshold_actionPerformed(boolean selected) { modifyPID.setEnabled(selected); viewport.setAbovePIDThreshold(selected); if (!selected) { viewport.getResidueShading().setThreshold(0, viewport.isIgnoreGapsConsensus()); } changeColour(viewport.getGlobalColourScheme()); if (selected) { modifyPID_actionPerformed(); } else { SliderPanel.hidePIDSlider(); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0)); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.getAlignment())); alignPanel.paintAlignment(true, false); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void sortIDMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); addHistoryItem( new OrderCommand("ID Sort", oldOrder, viewport.getAlignment())); alignPanel.paintAlignment(true, false); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void sortLengthMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByLength(viewport.getAlignment()); addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.getAlignment())); alignPanel.paintAlignment(true, false); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void sortGroupMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByGroup(viewport.getAlignment()); addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.getAlignment())); alignPanel.paintAlignment(true, false); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { new RedundancyPanel(alignPanel, this); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { if ((viewport.getSelectionGroup() == null) || (viewport.getSelectionGroup().getSize() < 2)) { JvOptionPane.showInternalMessageDialog(this, MessageManager.getString( "label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"), JvOptionPane.WARNING_MESSAGE); } else { JInternalFrame frame = new JInternalFrame(); frame.setFrameIcon(null); frame.setContentPane(new PairwiseAlignPanel(viewport)); Desktop.addInternalFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500); } } @Override public void autoCalculate_actionPerformed(ActionEvent e) { viewport.autoCalculateConsensus = autoCalculate.isSelected(); if (viewport.autoCalculateConsensus) { viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } @Override public void sortByTreeOption_actionPerformed(ActionEvent e) { viewport.sortByTree = sortByTree.isSelected(); } @Override protected void listenToViewSelections_actionPerformed(ActionEvent e) { viewport.followSelection = listenToViewSelections.isSelected(); } /** * Constructs a tree panel and adds it to the desktop * * @param type * tree type (NJ or AV) * @param modelName * name of score model used to compute the tree * @param options * parameters for the distance or similarity calculation */ void newTreePanel(String type, String modelName, SimilarityParamsI options) { String frameTitle = ""; TreePanel tp; boolean onSelection = false; if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 0) { SequenceGroup sg = viewport.getSelectionGroup(); /* Decide if the selection is a column region */ for (SequenceI _s : sg.getSequences()) { if (_s.getLength() < sg.getEndRes()) { JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager.getString( "label.selected_region_to_tree_may_only_contain_residues_or_gaps"), MessageManager.getString( "label.sequences_selection_not_aligned"), JvOptionPane.WARNING_MESSAGE); return; } } onSelection = true; } else { if (viewport.getAlignment().getHeight() < 2) { return; } } tp = new TreePanel(alignPanel, type, modelName, options); frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : ""); frameTitle += " from "; if (viewport.getViewName() != null) { frameTitle += viewport.getViewName() + " of "; } frameTitle += this.title; Desktop.addInternalFrame(tp, frameTitle, 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(MessageManager .formatMessage("action.by_title_param", new Object[] { title })); sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { @Override 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.getAlignment())); alignPanel.paintAlignment(true, false); } }); } /** * 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() { @Override 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.getAlignment())); alignPanel.paintAlignment(true, false); } }); } /** * 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. * */ @Override public void buildSortByAnnotationScoresMenu() { if (viewport.getAlignment().getAlignmentAnnotation() == null) { return; } if (viewport.getAlignment().getAlignmentAnnotation() .hashCode() != _annotationScoreVectorHash) { sortByAnnotScore.removeAll(); // almost certainly a quicker way to do this - but we keep it simple Hashtable scoreSorts = new Hashtable<>(); AlignmentAnnotation aann[]; for (SequenceI sqa : viewport.getAlignment().getSequences()) { aann = sqa.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, labels.nextElement()); } sortByAnnotScore.setVisible(scoreSorts.size() > 0); scoreSorts.clear(); _annotationScoreVectorHash = viewport.getAlignment() .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. */ @Override public void buildTreeSortMenu() { sortByTreeMenu.removeAll(); List comps = PaintRefresher.components .get(viewport.getSequenceSetId()); List treePanels = new ArrayList<>(); for (Component comp : comps) { if (comp instanceof TreePanel) { treePanels.add((TreePanel) comp); } } if (treePanels.size() < 1) { sortByTreeMenu.setVisible(false); return; } sortByTreeMenu.setVisible(true); for (final TreePanel tp : treePanels) { final JMenuItem item = new JMenuItem(tp.getTitle()); item.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { tp.sortByTree_actionPerformed(); addHistoryItem(tp.sortAlignmentIn(alignPanel)); } }); sortByTreeMenu.add(item); } } public boolean sortBy(AlignmentOrder alorder, String undoname) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortBy(viewport.getAlignment(), alorder); if (undoname != null) { addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment())); } alignPanel.paintAlignment(true, false); return true; } /** * 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 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() == 1) { int option = JvOptionPane.showConfirmDialog(this, MessageManager.getString("warn.oneseq_msainput_selection"), MessageManager.getString("label.invalid_selection"), JvOptionPane.OK_CANCEL_OPTION); if (option == JvOptionPane.OK_OPTION) { msa = viewport.getAlignmentView(false); } } else { 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.getAlignment().isAligned is a global state - the local // selection may well be aligned - we preserve 2.0.8 behaviour for moment. if (!viewport.getAlignment().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! */ @Override protected void loadTreeMenuItem_actionPerformed(ActionEvent e) { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.select_newick_like_tree_file")); chooser.setToolTipText( MessageManager.getString("label.load_tree_file")); chooser.setResponseHandler(0, () -> { String filePath = chooser.getSelectedFile().getPath(); Cache.setProperty("LAST_DIRECTORY", filePath); NewickFile fin = null; try { fin = new NewickFile(new FileParse(chooser.getSelectedFile(), DataSourceType.FILE)); viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); } catch (Exception ex) { JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), MessageManager.getString("label.problem_reading_tree_file"), JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } if (fin != null && fin.hasWarningMessage()) { JvOptionPane.showMessageDialog(Desktop.desktop, fin.getWarningMessage(), MessageManager .getString("label.possible_problem_with_tree_file"), JvOptionPane.WARNING_MESSAGE); } }); chooser.showOpenDialog(this); } public TreePanel showNewickTree(NewickFile nf, String treeTitle) { return showNewickTree(nf, treeTitle, 600, 500, 4, 5); } public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w, int h, int x, int y) { return showNewickTree(nf, treeTitle, 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 treeTitle, AlignmentView input, int w, int h, int x, int y) { TreePanel tp = null; try { nf.parse(); if (nf.getTree() != null) { tp = new TreePanel(alignPanel, nf, treeTitle, input); tp.setSize(w, h); if (x > 0 && y > 0) { tp.setLocation(x, y); } Desktop.addInternalFrame(tp, treeTitle, w, h); } } catch (Exception ex) { ex.printStackTrace(); } return tp; } public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm) { int x = 4, y = 5; int w = 400, h = 500; try { NewickFile fin = new NewickFile( new FileParse(cm.getNewick(), DataSourceType.PASTE)); String title = aa.label + " " + cm.getTreeMethod() + " tree" + (aa.sequenceRef != null ? (" for " + aa.sequenceRef.getDisplayId(false)) : ""); showColumnWiseTree(fin, aa, title, w, h, x, y); } catch (Throwable xx) { Console.error("Unexpected exception showing tree for contact matrix", xx); } } public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa, String treeTitle, int w, int h, int x, int y) { try { nf.parse(); if (nf.getTree() == null) { return null; } TreePanel tp = new TreePanel(alignPanel, nf, aa, treeTitle); tp.setSize(w, h); if (x > 0 && y > 0) { tp.setLocation(x, y); } Desktop.addInternalFrame(tp, treeTitle, w, h); return tp; } catch (Throwable xx) { Console.error("Unexpected exception showing tree for contact matrix", xx); } return null; } private boolean buildingMenu = false; /** * Generates menu items and listener event actions for web service clients * */ public void BuildWebServiceMenu() { while (buildingMenu) { try { jalview.bin.Console .errPrintln("Waiting for building menu to finish."); Thread.sleep(10); } catch (Exception e) { } } final AlignFrame me = this; buildingMenu = true; new Thread(new Runnable() { @Override public void run() { final List legacyItems = new ArrayList<>(); try { // jalview.bin.Console.errPrintln("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; /* * do not i18n these strings - they are hard-coded in class * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and * SequenceAnnotationWSClient.initSequenceAnnotationWSClient() */ final JMenu msawsmenu = new JMenu("Alignment"); final JMenu secstrmenu = new JMenu( "Secondary Structure Prediction"); final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); final JMenu analymenu = new JMenu("Analysis"); final JMenu dismenu = new JMenu("Protein Disorder"); // JAL-940 - only show secondary structure prediction services from // the legacy server 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 // No MSAWS used any more: // Vector msaws = null; // (Vector) // Discoverer.services.get("MsaWS"); Vector secstrpr = Discoverer.services .get("SecStrPred"); if (secstrpr != null) { // Add any secondary structure prediction services for (int i = 0, j = secstrpr.size(); i < j; i++) { final ext.vamsas.ServiceHandle sh = secstrpr.get(i); jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer .getServiceClient(sh); int p = secstrmenu.getItemCount(); impl.attachWSMenuEntry(secstrmenu, me); int q = secstrmenu.getItemCount(); for (int litm = p; litm < q; litm++) { legacyItems.add(secstrmenu.getItem(litm)); } } } } // Add all submenus in the order they should appear on the web // services menu wsmenu.add(msawsmenu); wsmenu.add(secstrmenu); wsmenu.add(dismenu); wsmenu.add(analymenu); // No search services yet // wsmenu.add(seqsrchmenu); javax.swing.SwingUtilities.invokeLater(new Runnable() { @Override public void run() { try { webService.removeAll(); // first, add discovered services onto the webservices menu if (wsmenu.size() > 0) { for (int i = 0, j = wsmenu.size(); i < j; i++) { webService.add(wsmenu.get(i)); } } else { webService.add(me.webServiceNoServices); } // TODO: move into separate menu builder class. { // logic for 2.11.1.4 is // always look to see if there is a discover. if there isn't // we can't show any Jws2 services // if there are services available, show them - regardless of // the 'show JWS2 preference' // if the discoverer is running then say so // otherwise offer to trigger discovery if 'show JWS2' is not // enabled Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); if (jws2servs != null) { if (jws2servs.hasServices()) { jws2servs.attachWSMenuEntry(webService, me); for (Jws2Instance sv : jws2servs.getServices()) { if (sv.description.toLowerCase(Locale.ROOT) .contains("jpred")) { for (JMenuItem jmi : legacyItems) { jmi.setVisible(false); } } } } if (jws2servs.isRunning()) { JMenuItem tm = new JMenuItem( "Still discovering JABA Services"); tm.setEnabled(false); webService.add(tm); } else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true)) { JMenuItem enableJws2 = new JMenuItem( "Discover Web Services"); enableJws2.setToolTipText( "Select to start JABA Web Service discovery (or enable option in Web Service preferences)"); enableJws2.setEnabled(true); enableJws2.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { // start service discoverer, but ignore preference Desktop.instance.startServiceDiscovery(false, true); } }); webService.add(enableJws2); } } } build_urlServiceMenu(me.webService); build_fetchdbmenu(webService); for (JMenu item : wsmenu) { if (item.getItemCount() == 0) { item.setEnabled(false); } else { item.setEnabled(true); } } } catch (Exception e) { Console.debug( "Exception during web service menu building process.", e); } } }); } catch (Exception e) { } buildingMenu = false; } }).start(); } /** * construct any groupURL type service menu entries. * * @param webService */ protected void build_urlServiceMenu(JMenu webService) { // TODO: remove this code when 2.7 is released // DEBUG - alignmentView /* * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final * AlignFrame af = this; testAlView.addActionListener(new ActionListener() { * * @Override public void actionPerformed(ActionEvent e) { * jalview.datamodel.AlignmentView * .testSelectionViews(af.viewport.getAlignment(), * af.viewport.getColumnSelection(), af.viewport.selectionGroup); } * * }); webService.add(testAlView); */ // TODO: refactor to RestClient discoverer and merge menu entries for // rest-style services with other types of analysis/calculation service // SHmmr test client - still being implemented. // DEBUG - alignmentView for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient .getRestClients()) { client.attachWSMenuEntry( JvSwingUtils.findOrCreateMenu(webService, client.getAction()), this); } } /** * Searches the alignment sequences for xRefs and builds the Show * Cross-References menu (formerly called Show Products), with database * sources for which cross-references are found (protein sources for a * nucleotide alignment and vice versa) * * @return true if Show Cross-references menu should be enabled */ public boolean canShowProducts() { SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); AlignmentI dataset = viewport.getAlignment().getDataset(); showProducts.removeAll(); final boolean dna = viewport.getAlignment().isNucleotide(); if (seqs == null || seqs.length == 0) { // nothing to see here. return false; } boolean showp = false; try { List ptypes = new CrossRef(seqs, dataset) .findXrefSourcesForSequences(dna); for (final String source : ptypes) { showp = true; final AlignFrame af = this; JMenuItem xtype = new JMenuItem(source); xtype.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { showProductsFor(af.viewport.getSequenceSelection(), dna, source); } }); showProducts.add(xtype); } showProducts.setVisible(showp); showProducts.setEnabled(showp); } catch (Exception e) { Console.warn( "canShowProducts threw an exception - please report to help@jalview.org", e); return false; } return showp; } /** * Finds and displays cross-references for the selected sequences (protein * products for nucleotide sequences, dna coding sequences for peptides). * * @param sel * the sequences to show cross-references for * @param dna * true if from a nucleotide alignment (so showing proteins) * @param source * the database to show cross-references for */ protected void showProductsFor(final SequenceI[] sel, final boolean _odna, final String source) { new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this)) .start(); } /** * Construct and display a new frame containing the translation of this * frame's DNA sequences to their aligned protein (amino acid) equivalents. */ @Override public void showTranslation_actionPerformed(GeneticCodeI codeTable) { AlignmentI al = null; try { Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); al = dna.translateCdna(codeTable); } catch (Exception ex) { Console.error("Exception during translation. Please report this !", ex); final String msg = MessageManager.getString( "label.error_when_translating_sequences_submit_bug_report"); final String errorTitle = MessageManager .getString("label.implementation_error") + MessageManager.getString("label.translation_failed"); JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, JvOptionPane.ERROR_MESSAGE); return; } if (al == null || al.getHeight() == 0) { final String msg = MessageManager.getString( "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); final String errorTitle = MessageManager .getString("label.translation_failed"); JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, JvOptionPane.WARNING_MESSAGE); } else { AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); af.setFileFormat(this.currentFileFormat); final String newTitle = MessageManager .formatMessage("label.translation_of_params", new Object[] { this.getTitle(), codeTable.getId() }); af.setTitle(newTitle); if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) { final SequenceI[] seqs = viewport.getSelectionAsNewSequence(); viewport.openSplitFrame(af, new Alignment(seqs)); } else { Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); } } } /** * Set the file format * * @param format */ public void setFileFormat(FileFormatI format) { this.currentFileFormat = format; } /** * Try to load a features file onto the alignment. * * @param file * contents or path to retrieve file or a File object * @param sourceType * access mode of file (see jalview.io.AlignFile) * @return true if features file was parsed correctly. */ public boolean parseFeaturesFile(Object file, DataSourceType sourceType) { // BH 2018 return avc.parseFeaturesFile(file, sourceType, Cache.getDefault("RELAXEDSEQIDMATCHING", false)); } @Override public void refreshFeatureUI(boolean enableIfNecessary) { // note - currently this is only still here rather than in the controller // because of the featureSettings hard reference that is yet to be // abstracted if (enableIfNecessary) { viewport.setShowSequenceFeatures(true); showSeqFeatures.setSelected(true); } } @Override public void dragEnter(DropTargetDragEvent evt) { } @Override public void dragExit(DropTargetEvent evt) { } @Override public void dragOver(DropTargetDragEvent evt) { } @Override public void dropActionChanged(DropTargetDragEvent evt) { } @Override public void drop(DropTargetDropEvent evt) { // JAL-1552 - acceptDrop required before getTransferable call for // Java's Transferable for native dnd evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); final AlignFrame thisaf = this; final List files = new ArrayList<>(); List protocols = new ArrayList<>(); try { Desktop.transferFromDropTarget(files, protocols, evt, t); } catch (Exception e) { e.printStackTrace(); } if (files != null) { new Thread(new Runnable() { @Override public void run() { try { // check to see if any of these files have names matching sequences // in // the alignment SequenceIdMatcher idm = new SequenceIdMatcher( viewport.getAlignment().getSequencesArray()); /** * Object[] { String,SequenceI} */ ArrayList filesmatched = new ArrayList<>(); ArrayList filesnotmatched = new ArrayList<>(); for (int i = 0; i < files.size(); i++) { // BH 2018 Object file = files.get(i); String fileName = file.toString(); String pdbfn = ""; DataSourceType protocol = (file instanceof File ? DataSourceType.FILE : FormatAdapter.checkProtocol(fileName)); if (protocol == DataSourceType.FILE) { File fl; if (file instanceof File) { fl = (File) file; Platform.cacheFileData(fl); } else { fl = new File(fileName); } pdbfn = fl.getName(); } else if (protocol == DataSourceType.URL) { URL url = new URL(fileName); pdbfn = url.getFile(); } if (pdbfn.length() > 0) { // attempt to find a match in the alignment SequenceI[] mtch = idm.findAllIdMatches(pdbfn); int l = 0, c = pdbfn.indexOf("."); while (mtch == null && c != -1) { do { l = c; } while ((c = pdbfn.indexOf(".", l)) > l); if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch = idm.findAllIdMatches(pdbfn); } FileFormatI type = null; if (mtch != null) { try { type = new IdentifyFile().identify(file, protocol); } catch (Exception ex) { type = null; } if (type != null && type.isStructureFile()) { filesmatched.add(new Object[] { file, protocol, mtch }); continue; } } // File wasn't named like one of the sequences or wasn't a PDB // file. filesnotmatched.add(new Object[] { file, protocol, type }); } } int assocfiles = 0; if (filesmatched.size() > 0) { boolean autoAssociate = Cache .getDefault("AUTOASSOCIATE_PDBANDSEQS", false); if (!autoAssociate) { String msg = MessageManager.formatMessage( "label.automatically_associate_structure_files_with_sequences_same_name", new Object[] { Integer.valueOf(filesmatched.size()) .toString() }); String ttl = MessageManager.getString( "label.automatically_associate_structure_files_by_name"); int choice = JvOptionPane.showConfirmDialog(thisaf, msg, ttl, JvOptionPane.YES_NO_OPTION); autoAssociate = choice == JvOptionPane.YES_OPTION; } if (autoAssociate) { for (Object[] fm : filesmatched) { // try and associate // TODO: may want to set a standard ID naming formalism for // associating PDB files which have no IDs. for (SequenceI toassoc : (SequenceI[]) fm[2]) { PDBEntry pe = new AssociatePdbFileWithSeq() .associatePdbWithSeq(fm[0].toString(), (DataSourceType) fm[1], toassoc, false, Desktop.instance); if (pe != null) { jalview.bin.Console.errPrintln("Associated file : " + (fm[0].toString()) + " with " + toassoc.getDisplayId(true)); assocfiles++; } } // TODO: do we need to update overview ? only if features are // shown I guess alignPanel.paintAlignment(true, false); } } else { /* * add declined structures as sequences */ for (Object[] o : filesmatched) { filesnotmatched.add(new Object[] { o[0], o[1] }); } } } if (filesnotmatched.size() > 0) { if (assocfiles > 0 && (Cache.getDefault( "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane.showConfirmDialog(thisaf, "" + MessageManager.formatMessage( "label.ignore_unmatched_dropped_files_info", new Object[] { Integer.valueOf( filesnotmatched.size()) .toString() }) + "", MessageManager.getString( "label.ignore_unmatched_dropped_files"), JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) { return; } for (Object[] fn : filesnotmatched) { loadJalviewDataFile(fn[0], (DataSourceType) fn[1], (FileFormatI) fn[2], null); } } } catch (Exception ex) { ex.printStackTrace(); } } }).start(); } } /** * Attempt to load a "dropped" file or URL string, by testing in turn for *
    *
  • an Annotation file
  • *
  • a JNet file
  • *
  • a features file
  • *
  • else try to interpret as an alignment file
  • *
* * @param file * either a filename or a URL string. */ public void loadJalviewDataFile(Object file, DataSourceType sourceType, FileFormatI format, SequenceI assocSeq) { // BH 2018 was String file try { if (sourceType == null) { sourceType = FormatAdapter.checkProtocol(file); } // if the file isn't identified, or not positively identified as some // other filetype (PFAM is default unidentified alignment file type) then // try to parse as annotation. boolean isAnnotation = (format == null || FileFormat.Pfam.equals(format)) ? new AnnotationFile().annotateAlignmentView(viewport, file, sourceType) : false; if (!isAnnotation) { // first see if its a T-COFFEE score file TCoffeeScoreFile tcf = null; try { tcf = new TCoffeeScoreFile(file, sourceType); if (tcf.isValid()) { if (tcf.annotateAlignment(viewport.getAlignment(), true)) { buildColourMenu(); changeColour( new TCoffeeColourScheme(viewport.getAlignment())); isAnnotation = true; setStatus(MessageManager.getString( "label.successfully_pasted_tcoffee_scores_to_alignment")); } else { // some problem - if no warning its probable that the ID matching // process didn't work JvOptionPane.showMessageDialog(Desktop.desktop, tcf.getWarningMessage() == null ? MessageManager.getString( "label.check_file_matches_sequence_ids_alignment") : tcf.getWarningMessage(), MessageManager.getString( "label.problem_reading_tcoffee_score_file"), JvOptionPane.WARNING_MESSAGE); } } else { tcf = null; } } catch (Exception x) { Console.debug( "Exception when processing data source as T-COFFEE score file", x); tcf = null; } if (tcf == null) { // try to see if its a JNet 'concise' style annotation file *before* // we // try to parse it as a features file if (format == null) { format = new IdentifyFile().identify(file, sourceType); } if (FileFormat.FeatureSettings == format) { if (featureSettings != null) { featureSettings.load(file, sourceType); } else { FeatureSettings.loadFeatureSettingsFile(getFeatureRenderer(), fileObject, sourceType); } } else if (FileFormat.ScoreMatrix == format) { ScoreMatrixFile sm = new ScoreMatrixFile( new FileParse(file, sourceType)); sm.parse(); // todo: i18n this message setStatus(MessageManager.formatMessage( "label.successfully_loaded_matrix", sm.getMatrixName())); } else if (FileFormat.Jnet.equals(format)) { JPredFile predictions = new JPredFile(file, sourceType); new JnetAnnotationMaker(); JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); viewport.getAlignment().setupJPredAlignment(); isAnnotation = true; } // else if (IdentifyFile.FeaturesFile.equals(format)) else if (FileFormat.Features.equals(format)) { if (parseFeaturesFile(file, sourceType)) { SplitFrame splitFrame = (SplitFrame) getSplitViewContainer(); if (splitFrame != null) { splitFrame.repaint(); } else { alignPanel.paintAlignment(true, true); } } } else { new FileLoader().LoadFile(viewport, file, sourceType, format); } } } if (isAnnotation) { alignPanel.adjustAnnotationHeight(); viewport.updateSequenceIdColours(); buildSortByAnnotationScoresMenu(); alignPanel.paintAlignment(true, true); } } catch (Exception ex) { ex.printStackTrace(); } catch (OutOfMemoryError oom) { try { System.gc(); } catch (Exception x) { } new OOMWarning( "loading data " + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard." : "using " + sourceType + " from " + file) : ".") + (format != null ? "(parsing as '" + format + "' file)" : ""), oom, Desktop.desktop); } } /** * Method invoked by the ChangeListener on the tabbed pane, in other words * when a different tabbed pane is selected by the user or programmatically. */ @Override public void tabSelectionChanged(int index) { if (index > -1) { /* * update current Overview window title (if there is one) * to add view name "Original" if necessary */ alignPanel.setOverviewTitle(this); /* * switch panels and set Overview title (if there is one * because it was opened automatically) */ alignPanel = alignPanels.get(index); alignPanel.setOverviewTitle(this); viewport = alignPanel.av; avc.setViewportAndAlignmentPanel(viewport, alignPanel); setMenusFromViewport(viewport); if (featureSettings != null && featureSettings.isOpen() && featureSettings.fr.getViewport() != viewport) { if (viewport.isShowSequenceFeatures()) { // refresh the featureSettings to reflect UI change showFeatureSettingsUI(); } else { // close feature settings for this view. featureSettings.close(); } } } /* * 'focus' any colour slider that is open to the selected viewport */ if (viewport.getConservationSelected()) { SliderPanel.setConservationSlider(alignPanel, viewport.getResidueShading(), alignPanel.getViewName()); } else { SliderPanel.hideConservationSlider(); } if (viewport.getAbovePIDThreshold()) { SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(), alignPanel.getViewName()); } else { SliderPanel.hidePIDSlider(); } /* * If there is a frame linked to this one in a SplitPane, switch it to the * same view tab index. No infinite recursion of calls should happen, since * tabSelectionChanged() should not get invoked on setting the selected * index to an unchanged value. Guard against setting an invalid index * before the new view peer tab has been created. */ final AlignViewportI peer = viewport.getCodingComplement(); if (peer != null) { AlignFrame linkedAlignFrame = ((AlignViewport) peer) .getAlignPanel().alignFrame; if (linkedAlignFrame.tabbedPane.getTabCount() > index) { linkedAlignFrame.tabbedPane.setSelectedIndex(index); } } } /** * On right mouse click on view tab, prompt for and set new view name. */ @Override public void tabbedPane_mousePressed(MouseEvent e) { if (e.isPopupTrigger()) { String msg = MessageManager.getString("label.enter_view_name"); String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex()); String reply = JvOptionPane.showInputDialog(msg, ttl); if (reply != null) { viewport.setViewName(reply); // TODO warn if reply is in getExistingViewNames()? tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); } } } public AlignViewport getCurrentView() { return viewport; } /** * Open the dialog for regex description parsing. */ @Override protected void extractScores_actionPerformed(ActionEvent e) { ParseProperties pp = new jalview.analysis.ParseProperties( viewport.getAlignment()); // 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 * ) */ @Override protected void showDbRefs_actionPerformed(ActionEvent e) { viewport.setShowDBRefs(showDbRefsMenuitem.isSelected()); } /* * (non-Javadoc) * * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. * ActionEvent) */ @Override 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(AlignViewportI 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( MessageManager.getString("action.fetch_db_references")); rfetch.setToolTipText(MessageManager.getString( "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences")); webService.add(rfetch); final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem( MessageManager.getString("option.trim_retrieved_seqs")); trimrs.setToolTipText( MessageManager.getString("label.trim_retrieved_sequences")); trimrs.setSelected( Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); trimrs.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { trimrs.setSelected(trimrs.isSelected()); Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, Boolean.valueOf(trimrs.isSelected()).toString()); } }); rfetch.add(trimrs); JMenuItem fetchr = new JMenuItem( MessageManager.getString("label.standard_databases")); fetchr.setToolTipText( MessageManager.getString("label.fetch_embl_uniprot")); fetchr.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { @Override public void run() { boolean isNucleotide = alignPanel.alignFrame.getViewport() .getAlignment().isNucleotide(); DBRefFetcher dbRefFetcher = new DBRefFetcher( alignPanel.av.getSequenceSelection(), alignPanel.alignFrame, null, alignPanel.alignFrame.featureSettings, isNucleotide); dbRefFetcher.addListener(new FetchFinishedListenerI() { @Override public void finished() { for (FeatureSettingsModelI srcSettings : dbRefFetcher .getFeatureSettingsModels()) { alignPanel.av.mergeFeaturesStyle(srcSettings); } AlignFrame.this.setMenusForViewport(); } }); dbRefFetcher.fetchDBRefs(false); } }).start(); } }); rfetch.add(fetchr); new Thread(new Runnable() { @Override public void run() { final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher .getSequenceFetcherSingleton(); javax.swing.SwingUtilities.invokeLater(new Runnable() { @Override public void run() { String[] dbclasses = sf.getNonAlignmentSources(); List otherdb; JMenu dfetch = new JMenu(); JMenu ifetch = new JMenu(); JMenuItem fetchr = null; int comp = 0, icomp = 0, mcomp = 15; String mname = null; int dbi = 0; for (String dbclass : dbclasses) { otherdb = sf.getSourceProxy(dbclass); // add a single entry for this class, or submenu allowing 'fetch // all' or pick one if (otherdb == null || otherdb.size() < 1) { continue; } if (mname == null) { mname = "From " + dbclass; } if (otherdb.size() == 1) { final DbSourceProxy[] dassource = otherdb .toArray(new DbSourceProxy[0]); DbSourceProxy src = otherdb.get(0); fetchr = new JMenuItem(src.getDbSource()); fetchr.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { @Override public void run() { boolean isNucleotide = alignPanel.alignFrame .getViewport().getAlignment() .isNucleotide(); DBRefFetcher dbRefFetcher = new DBRefFetcher( alignPanel.av.getSequenceSelection(), alignPanel.alignFrame, dassource, alignPanel.alignFrame.featureSettings, isNucleotide); dbRefFetcher .addListener(new FetchFinishedListenerI() { @Override public void finished() { FeatureSettingsModelI srcSettings = dassource[0] .getFeatureColourScheme(); alignPanel.av.mergeFeaturesStyle( srcSettings); AlignFrame.this.setMenusForViewport(); } }); dbRefFetcher.fetchDBRefs(false); } }).start(); } }); fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage( "label.fetch_retrieve_from", new Object[] { src.getDbName() }))); dfetch.add(fetchr); comp++; } else { final DbSourceProxy[] dassource = otherdb .toArray(new DbSourceProxy[0]); // fetch all entry DbSourceProxy src = otherdb.get(0); fetchr = new JMenuItem(MessageManager .formatMessage("label.fetch_all_param", new Object[] { src.getDbSource() })); fetchr.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { @Override public void run() { boolean isNucleotide = alignPanel.alignFrame .getViewport().getAlignment() .isNucleotide(); DBRefFetcher dbRefFetcher = new DBRefFetcher( alignPanel.av.getSequenceSelection(), alignPanel.alignFrame, dassource, alignPanel.alignFrame.featureSettings, isNucleotide); dbRefFetcher .addListener(new FetchFinishedListenerI() { @Override public void finished() { AlignFrame.this.setMenusForViewport(); } }); dbRefFetcher.fetchDBRefs(false); } }).start(); } }); fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage( "label.fetch_retrieve_from_all_sources", new Object[] { Integer.valueOf(otherdb.size()) .toString(), src.getDbSource(), src.getDbName() }))); dfetch.add(fetchr); comp++; // and then build the rest of the individual menus ifetch = new JMenu(MessageManager.formatMessage( "label.source_from_db_source", new Object[] { src.getDbSource() })); icomp = 0; String imname = null; int i = 0; for (DbSourceProxy sproxy : otherdb) { String dbname = sproxy.getDbName(); String sname = dbname.length() > 5 ? dbname.substring(0, 5) + "..." : dbname; String msname = dbname.length() > 10 ? dbname.substring(0, 10) + "..." : dbname; if (imname == null) { imname = MessageManager .formatMessage("label.from_msname", new Object[] { sname }); } fetchr = new JMenuItem(msname); final DbSourceProxy[] dassrc = { sproxy }; fetchr.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { @Override public void run() { boolean isNucleotide = alignPanel.alignFrame .getViewport().getAlignment() .isNucleotide(); DBRefFetcher dbRefFetcher = new DBRefFetcher( alignPanel.av.getSequenceSelection(), alignPanel.alignFrame, dassrc, alignPanel.alignFrame.featureSettings, isNucleotide); dbRefFetcher .addListener(new FetchFinishedListenerI() { @Override public void finished() { AlignFrame.this.setMenusForViewport(); } }); dbRefFetcher.fetchDBRefs(false); } }).start(); } }); fetchr.setToolTipText( "" + MessageManager.formatMessage( "label.fetch_retrieve_from", new Object[] { dbname })); ifetch.add(fetchr); ++i; if (++icomp >= mcomp || i == (otherdb.size())) { ifetch.setText(MessageManager.formatMessage( "label.source_to_target", imname, sname)); dfetch.add(ifetch); ifetch = new JMenu(); imname = null; icomp = 0; comp++; } } } ++dbi; if (comp >= mcomp || dbi >= (dbclasses.length)) { dfetch.setText(MessageManager.formatMessage( "label.source_to_target", mname, dbclass)); rfetch.add(dfetch); dfetch = new JMenu(); mname = null; comp = 0; } } } }); } }).start(); } /** * Left justify the whole alignment. */ @Override protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) { AlignmentI al = viewport.getAlignment(); al.justify(false); viewport.firePropertyChange("alignment", null, al); } /** * Right justify the whole alignment. */ @Override protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { AlignmentI al = viewport.getAlignment(); al.justify(true); viewport.firePropertyChange("alignment", null, al); } @Override public void setShowSeqFeatures(boolean b) { showSeqFeatures.setSelected(b); viewport.setShowSequenceFeatures(b); } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. * awt.event.ActionEvent) */ @Override protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { viewport.setShowUnconserved(showNonconservedMenuItem.getState()); alignPanel.paintAlignment(false, false); } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event * .ActionEvent) */ @Override 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) */ @Override 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) */ @Override 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) */ @Override protected void showSequenceLogo_actionPerformed(ActionEvent e) { viewport.setShowSequenceLogo(showSequenceLogo.getState()); alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } @Override protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) { showSequenceLogo.setState(true); viewport.setShowSequenceLogo(true); viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState()); alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } @Override protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) { alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } /* * (non-Javadoc) * * @see * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt * .event.ActionEvent) */ @Override protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) { if (avc.makeGroupsFromSelection()) { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); alignPanel.paintAlignment(true, viewport.needToUpdateStructureViews()); } } public void clearAlignmentSeqRep() { // TODO refactor alignmentseqrep to controller if (viewport.getAlignment().hasSeqrep()) { viewport.getAlignment().setSeqrep(null); PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); alignPanel.paintAlignment(true, true); } } @Override protected void createGroup_actionPerformed(ActionEvent e) { if (avc.createGroup()) { if (applyAutoAnnotationSettings.isSelected()) { alignPanel.updateAnnotation(true, false); } alignPanel.alignmentChanged(); } } @Override protected void unGroup_actionPerformed(ActionEvent e) { if (avc.unGroup()) { alignPanel.alignmentChanged(); } } /** * make the given alignmentPanel the currently selected tab * * @param alignmentPanel */ public void setDisplayedView(AlignmentPanel alignmentPanel) { if (!viewport.getSequenceSetId() .equals(alignmentPanel.av.getSequenceSetId())) { throw new Error(MessageManager.getString( "error.implementation_error_cannot_show_view_alignment_frame")); } if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex()) { tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); } } /** * Action on selection of menu options to Show or Hide annotations. * * @param visible * @param forSequences * update sequence-related annotations * @param forAlignment * update non-sequence-related annotations */ @Override public void setAnnotationsVisibility(boolean visible, boolean forSequences, boolean forAlignment) { AlignmentAnnotation[] anns = alignPanel.getAlignment() .getAlignmentAnnotation(); if (anns == null) { return; } for (AlignmentAnnotation aa : anns) { /* * don't display non-positional annotations on an alignment */ if (aa.annotations == null) { continue; } boolean apply = (aa.sequenceRef == null && forAlignment) || (aa.sequenceRef != null && forSequences); if (apply) { aa.visible = visible; } } alignPanel.validateAnnotationDimensions(true); // TODO this triggers relayout of annotation panel - otherwise annotation // label height is different to panel height alignPanel.fontChanged(); alignPanel.alignmentChanged(); } /** * Store selected annotation sort order for the view and repaint. */ @Override protected void sortAnnotations_actionPerformed() { this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder()); this.alignPanel.av .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); alignPanel.paintAlignment(false, false); } /** * * @return alignment panels in this alignment frame */ public List getAlignPanels() { // alignPanels is never null // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; return alignPanels; } /** * Open a new alignment window, with the cDNA associated with this (protein) * alignment, aligned as is the protein. */ protected void viewAsCdna_actionPerformed() { // TODO no longer a menu action - refactor as required final AlignmentI alignment = getViewport().getAlignment(); List mappings = alignment.getCodonFrames(); if (mappings == null) { return; } List cdnaSeqs = new ArrayList<>(); for (SequenceI aaSeq : alignment.getSequences()) { for (AlignedCodonFrame acf : mappings) { SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence()); if (dnaSeq != null) { /* * There is a cDNA mapping for this protein sequence - add to new * alignment. It will share the same dataset sequence as other mapped * cDNA (no new mappings need to be created). */ final Sequence newSeq = new Sequence(dnaSeq); newSeq.setDatasetSequence(dnaSeq); cdnaSeqs.add(newSeq); } } } if (cdnaSeqs.size() == 0) { // show a warning dialog no mapped cDNA return; } AlignmentI cdna = new Alignment( cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()])); GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); cdna.alignAs(alignment); String newtitle = "cDNA " + MessageManager.getString("label.for") + " " + this.title; Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } /** * Set visibility of dna/protein complement view (available when shown in a * split frame). * * @param show */ @Override protected void showComplement_actionPerformed(boolean show) { SplitContainerI sf = getSplitViewContainer(); if (sf != null) { sf.setComplementVisible(this, show); } } /** * Generate the reverse (optionally complemented) of the selected sequences, * and add them to the alignment */ @Override protected void showReverse_actionPerformed(boolean complement) { AlignmentI al = null; try { Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); al = dna.reverseCdna(complement); viewport.addAlignment(al, ""); addHistoryItem(new EditCommand( MessageManager.getString("label.add_sequences"), Action.PASTE, al.getSequencesArray(), 0, al.getWidth(), viewport.getAlignment())); } catch (Exception ex) { jalview.bin.Console.errPrintln(ex.getMessage()); return; } } /** * Try to run a script in the Groovy console, having first ensured that this * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to * be targeted at this alignment. */ @Override protected void runGroovy_actionPerformed() { Jalview.getInstance().setCurrentAlignFrame(this); groovy.console.ui.Console console = Desktop.getGroovyConsole(); if (console != null) { try { console.setVariable(JalviewObjectI.currentAlFrameName, this); console.runScript(); } catch (Exception ex) { jalview.bin.Console.errPrintln((ex.toString())); JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.couldnt_run_groovy_script"), MessageManager.getString("label.groovy_support_failed"), JvOptionPane.ERROR_MESSAGE); } } else { jalview.bin.Console .errPrintln("Can't run Groovy script as console not found"); } } /** * Hides columns containing (or not containing) a specified feature, provided * that would not leave all columns hidden * * @param featureType * @param columnsContaining * @return */ public boolean hideFeatureColumns(String featureType, boolean columnsContaining) { boolean notForHiding = avc.markColumnsContainingFeatures( columnsContaining, false, false, featureType); if (notForHiding) { if (avc.markColumnsContainingFeatures(!columnsContaining, false, false, featureType)) { getViewport().hideSelectedColumns(); return true; } } return false; } @Override protected void selectHighlightedColumns_actionPerformed( ActionEvent actionEvent) { // include key modifier check in case user selects from menu avc.markHighlightedColumns( (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true, (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0); } @Override protected void copyHighlightedColumns_actionPerformed( ActionEvent actionEvent) { avc.copyHighlightedRegionsToClipboard(); } /** * Rebuilds the Colour menu, including any user-defined colours which have * been loaded either on startup or during the session */ public void buildColourMenu() { colourMenu.removeAll(); colourMenu.add(applyToAllGroups); colourMenu.add(textColour); colourMenu.addSeparator(); ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(), false); colourMenu.add(annotationColour); bg.add(annotationColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); colourMenu.add(modifyConservation); colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); ColourSchemeI colourScheme = viewport.getGlobalColourScheme(); ColourMenuHelper.setColourSelected(colourMenu, colourScheme); } /** * Open a dialog (if not already open) that allows the user to select and * calculate PCA or Tree analysis */ protected void openTreePcaDialog() { if (alignPanel.getCalculationDialog() == null) { new CalculationChooser(AlignFrame.this); } } @Override protected void loadVcf_actionPerformed() { JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file")); chooser.setToolTipText(MessageManager.getString("label.load_vcf_file")); final AlignFrame us = this; chooser.setResponseHandler(0, () -> { String choice = chooser.getSelectedFile().getPath(); Cache.setProperty("LAST_DIRECTORY", choice); SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); new VCFLoader(choice).loadVCF(seqs, us); }); chooser.showOpenDialog(null); } private Rectangle lastFeatureSettingsBounds = null; @Override public void setFeatureSettingsGeometry(Rectangle bounds) { lastFeatureSettingsBounds = bounds; } @Override public Rectangle getFeatureSettingsGeometry() { return lastFeatureSettingsBounds; } } class PrintThread extends Thread { AlignmentPanel ap; public PrintThread(AlignmentPanel ap) { this.ap = ap; } static PageFormat pf; @Override 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(); } } } }