diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index e6b7af4..aa0c392 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,5744 +1,5746 @@ /* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) * Copyright (C) 2014 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 jalview.analysis.AAFrequency; import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; import jalview.analysis.Conservation; import jalview.analysis.CrossRef; import jalview.analysis.NJTree; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.analysis.ScoreModelI; import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.commands.EditCommand; import jalview.commands.OrderCommand; import jalview.commands.RemoveGapColCommand; import jalview.commands.RemoveGapsCommand; import jalview.commands.SlideSequencesCommand; import jalview.commands.TrimRegionCommand; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SeqCigar; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.FeaturesFile; import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.io.HTMLOutput; import jalview.io.IdentifyFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.JnetAnnotationMaker; import jalview.io.NewickFile; import jalview.io.TCoffeeScoreFile; import jalview.jbgui.GAlignFrame; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; import jalview.schemes.ClustalxColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; import jalview.schemes.HelixColourScheme; import jalview.schemes.HydrophobicColourScheme; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; import jalview.schemes.RNAHelicesColourChooser; import jalview.schemes.ResidueProperties; import jalview.schemes.StrandColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; import jalview.schemes.UserColourScheme; import jalview.schemes.ZappoColourScheme; import jalview.util.MessageManager; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.seqfetcher.DbSourceProxy; import java.awt.BorderLayout; import java.awt.Component; import java.awt.GridLayout; 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.KeyAdapter; import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; 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.net.URL; import java.util.ArrayList; import java.util.Enumeration; import java.util.Hashtable; import java.util.List; import java.util.Vector; import javax.swing.JButton; import javax.swing.JCheckBoxMenuItem; 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.JOptionPane; import javax.swing.JPanel; import javax.swing.JProgressBar; import javax.swing.JRadioButtonMenuItem; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ public class AlignFrame extends GAlignFrame implements DropTargetListener, IProgressIndicator, AlignViewControllerGuiI { /** DOCUMENT ME!! */ public static final int DEFAULT_WIDTH = 700; /** DOCUMENT ME!! */ public static final int DEFAULT_HEIGHT = 500; public AlignmentPanel alignPanel; AlignViewport viewport; public AlignViewControllerI avc; Vector alignPanels = new Vector(); /** * Last format used to load or save alignments in this window */ String currentFileFormat = null; /** * Current filename for this alignment */ String fileName = null; /** * Creates a new AlignFrame object with specific width and height. * * @param al * @param width * @param height */ public AlignFrame(AlignmentI al, int width, int height) { this(al, null, width, height); } /** * Creates a new AlignFrame object with specific width, height and * sequenceSetId * * @param al * @param width * @param height * @param sequenceSetId */ public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId) { this(al, null, width, height, sequenceSetId); } /** * Creates a new AlignFrame object with specific width, height and * sequenceSetId * * @param al * @param width * @param height * @param sequenceSetId * @param viewId */ public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId, String viewId) { this(al, null, width, height, sequenceSetId, viewId); } /** * new alignment window with hidden columns * * @param al * AlignmentI * @param hiddenColumns * ColumnSelection or null * @param width * Width of alignment frame * @param height * height of frame. */ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height) { this(al, hiddenColumns, width, height, null); } /** * Create alignment frame for al with hiddenColumns, a specific width and * height, and specific sequenceId * * @param al * @param hiddenColumns * @param width * @param height * @param sequenceSetId * (may be null) */ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height, String sequenceSetId) { this(al, hiddenColumns, width, height, sequenceSetId, null); } /** * Create alignment frame for al with hiddenColumns, a specific width and * height, and specific sequenceId * * @param al * @param hiddenColumns * @param width * @param height * @param sequenceSetId * (may be null) * @param viewId * (may be null) */ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height, String sequenceSetId, String viewId) { setSize(width, height); if (al.getDataset() == null) { al.setDataset(null); } viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); alignPanel = new AlignmentPanel(this, viewport); addAlignmentPanel(alignPanel, true); init(); } /** * Make a new AlignFrame from exisiting alignmentPanels * * @param ap * AlignmentPanel * @param av * AlignViewport */ public AlignFrame(AlignmentPanel ap) { viewport = ap.av; alignPanel = ap; addAlignmentPanel(ap, false); init(); } /** * initalise the alignframe from the underlying viewport data and the * configurations */ void init() { 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 = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort"); if (sortby.equals("Id")) { sortIDMenuItem_actionPerformed(null); } else if (sortby.equals("Pairwise Identity")) { sortPairwiseMenuItem_actionPerformed(null); } if (Desktop.desktop != null) { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); addServiceListeners(); setGUINucleotide(viewport.getAlignment().isNucleotide()); } setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); buildTreeMenu(); if (viewport.wrapAlignment) { wrapMenuItem_actionPerformed(null); } if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false)) { this.overviewMenuItem_actionPerformed(null); } addKeyListener(); } /** * Change the filename and format for the alignment, and enable the 'reload' * button functionality. * * @param file * valid filename * @param format * format of file */ public void setFileName(String file, String format) { fileName = file; currentFileFormat = format; reload.setEnabled(true); } void addKeyListener() { addKeyListener(new KeyAdapter() { @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.seqPanel.numberPressed(evt.getKeyChar()); switch (evt.getKeyCode()) { case 27: // escape key deselectAllSequenceMenuItem_actionPerformed(null); break; case KeyEvent.VK_DOWN: if (evt.isAltDown() || !viewport.cursorMode) moveSelectedSequences(false); if (viewport.cursorMode) alignPanel.seqPanel.moveCursor(0, 1); break; case KeyEvent.VK_UP: if (evt.isAltDown() || !viewport.cursorMode) moveSelectedSequences(true); if (viewport.cursorMode) alignPanel.seqPanel.moveCursor(0, -1); break; case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); else alignPanel.seqPanel.moveCursor(-1, 0); break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); else alignPanel.seqPanel.moveCursor(1, 0); break; case KeyEvent.VK_SPACE: if (viewport.cursorMode) { alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() || evt.isShiftDown() || evt.isAltDown()); } break; // case KeyEvent.VK_A: // if (viewport.cursorMode) // { // alignPanel.seqPanel.insertNucAtCursor(false,"A"); // //System.out.println("A"); // } // break; /* * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) { * System.out.println("closing bracket"); } break; */ case KeyEvent.VK_DELETE: case KeyEvent.VK_BACK_SPACE: if (!viewport.cursorMode) { cut_actionPerformed(null); } else { alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown() || evt.isAltDown()); } break; case KeyEvent.VK_S: if (viewport.cursorMode) { alignPanel.seqPanel.setCursorRow(); } break; case KeyEvent.VK_C: if (viewport.cursorMode && !evt.isControlDown()) { alignPanel.seqPanel.setCursorColumn(); } break; case KeyEvent.VK_P: if (viewport.cursorMode) { alignPanel.seqPanel.setCursorPosition(); } break; case KeyEvent.VK_ENTER: case KeyEvent.VK_COMMA: if (viewport.cursorMode) { alignPanel.seqPanel.setCursorRowAndColumn(); } break; case KeyEvent.VK_Q: if (viewport.cursorMode) { alignPanel.seqPanel.setSelectionAreaAtCursor(true); } break; case KeyEvent.VK_M: if (viewport.cursorMode) { alignPanel.seqPanel.setSelectionAreaAtCursor(false); } break; case KeyEvent.VK_F2: viewport.cursorMode = !viewport.cursorMode; statusBar.setText(MessageManager.formatMessage( "label.keyboard_editing_mode", new String[] { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; } alignPanel.seqPanel.seqCanvas.repaint(); break; case KeyEvent.VK_F1: try { ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help"); javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); javax.help.HelpBroker hb = hs.createHelpBroker(); hb.setCurrentID("home"); hb.setDisplayed(true); } catch (Exception ex) { ex.printStackTrace(); } break; case KeyEvent.VK_H: { boolean toggleSeqs = !evt.isControlDown(); boolean toggleCols = !evt.isShiftDown(); toggleHiddenRegions(toggleSeqs, toggleCols); break; } case KeyEvent.VK_PAGE_UP: if (viewport.wrapAlignment) { alignPanel.scrollUp(true); } else { alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - viewport.endSeq + viewport.startSeq); } break; case KeyEvent.VK_PAGE_DOWN: if (viewport.wrapAlignment) { alignPanel.scrollUp(false); } else { alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + viewport.endSeq - viewport.startSeq); } break; } } @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.addElement(ap); PaintRefresher.Register(ap, ap.av.getSequenceSetId()); int aSize = alignPanels.size(); tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null); if (aSize == 1 && ap.av.viewName == null) { this.getContentPane().add(ap, BorderLayout.CENTER); } else { if (aSize == 2) { setInitialTabVisible(); } expandViews.setEnabled(true); gatherViews.setEnabled(true); tabbedPane.addTab(ap.av.viewName, ap); ap.setVisible(false); } if (newPanel) { if (ap.av.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 = (AlignmentPanel) alignPanels.firstElement(); tabbedPane.addTab(first.av.viewName, first); this.getContentPane().add(tabbedPane, BorderLayout.CENTER); } public AlignViewport getViewport() { return viewport; } /* Set up intrinsic listeners for dynamically generated GUI bits. */ private void addServiceListeners() { final java.beans.PropertyChangeListener thisListener; Desktop.instance.addJalviewPropertyChangeListener("services", thisListener = new java.beans.PropertyChangeListener() { @Override public void propertyChange(PropertyChangeEvent evt) { // // System.out.println("Discoverer property change."); // if (evt.getPropertyName().equals("services")) { SwingUtilities.invokeLater(new Runnable() { @Override public void run() { System.err .println("Rebuild WS Menu for service change"); BuildWebServiceMenu(); } }); } } }); addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { System.out.println("deregistering discoverer listener"); Desktop.instance.removeJalviewPropertyChangeListener("services", thisListener); closeMenuItem_actionPerformed(true); }; }); // Finally, build the menu once to get current service state new Thread(new Runnable() { @Override public void run() { BuildWebServiceMenu(); } }).start(); } public void setGUINucleotide(boolean nucleotide) { showTranslation.setVisible(nucleotide); conservationMenuItem.setEnabled(!nucleotide); modifyConservation.setEnabled(!nucleotide); showGroupConservation.setEnabled(!nucleotide); rnahelicesColour.setEnabled(nucleotide); purinePyrimidineColour.setEnabled(nucleotide); // Remember AlignFrame always starts as protein // if (!nucleotide) // { // showTr // calculateMenu.remove(calculateMenu.getItemCount() - 2); // } } /** * set up menus for the currently viewport. This may be called after any * operation that affects the data in the current view (selection changed, * etc) to update the menus to reflect the new state. */ public void setMenusForViewport() { setMenusFromViewport(viewport); } /** * Need to call this method when tabs are selected for multiple views, or when * loading from Jalview2XML.java * * @param av * AlignViewport */ void setMenusFromViewport(AlignViewport av) { padGapsMenuitem.setSelected(av.isPadGaps()); colourTextMenuItem.setSelected(av.showColourText); abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); conservationMenuItem.setSelected(av.getConservationSelected()); seqLimits.setSelected(av.getShowJVSuffix()); idRightAlign.setSelected(av.rightAlignIds); centreColumnLabelsMenuItem.setState(av.centreColumnLabels); renderGapsMenuItem.setSelected(av.renderGaps); wrapMenuItem.setSelected(av.wrapAlignment); scaleAbove.setVisible(av.wrapAlignment); scaleLeft.setVisible(av.wrapAlignment); scaleRight.setVisible(av.wrapAlignment); annotationPanelMenuItem.setState(av.showAnnotation); viewBoxesMenuItem.setSelected(av.showBoxes); viewTextMenuItem.setSelected(av.showText); showNonconservedMenuItem.setSelected(av.getShowUnconserved()); showGroupConsensus.setSelected(av.isShowGroupConsensus()); showGroupConservation.setSelected(av.isShowGroupConservation()); showConsensusHistogram.setSelected(av.isShowConsensusHistogram()); showSequenceLogo.setSelected(av.isShowSequenceLogo()); normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); setColourSelected(ColourSchemeProperty.getColourName(av .getGlobalColourScheme())); showSeqFeatures.setSelected(av.showSequenceFeatures); hiddenMarkers.setState(av.showHiddenMarkers); applyToAllGroups.setState(av.getColourAppliesToAllGroups()); showNpFeatsMenuitem.setSelected(av.isShowNpFeats()); showDbRefsMenuitem.setSelected(av.isShowDbRefs()); autoCalculate.setSelected(av.autoCalculateConsensus); sortByTree.setSelected(av.sortByTree); listenToViewSelections.setSelected(av.followSelection); rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure()); rnahelicesColour .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); setShowProductsEnabled(); updateEditMenuBar(); } // methods for implementing IProgressIndicator // need to refactor to a reusable stub class Hashtable progressBars, progressBarHandlers; /* * (non-Javadoc) * * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ @Override public void setProgressBar(String message, long id) { if (progressBars == null) { progressBars = new Hashtable(); progressBarHandlers = new Hashtable(); } JPanel progressPanel; Long lId = new Long(id); GridLayout layout = (GridLayout) statusPanel.getLayout(); if (progressBars.get(lId) != null) { progressPanel = (JPanel) progressBars.get(new Long(id)); statusPanel.remove(progressPanel); progressBars.remove(lId); progressPanel = null; if (message != null) { statusBar.setText(message); } if (progressBarHandlers.contains(lId)) { progressBarHandlers.remove(lId); } layout.setRows(layout.getRows() - 1); } else { progressPanel = new JPanel(new BorderLayout(10, 5)); JProgressBar progressBar = new JProgressBar(); progressBar.setIndeterminate(true); progressPanel.add(new JLabel(message), BorderLayout.WEST); progressPanel.add(progressBar, BorderLayout.CENTER); layout.setRows(layout.getRows() + 1); statusPanel.add(progressPanel); progressBars.put(lId, progressPanel); } // update GUI // setMenusForViewport(); validate(); } @Override public void registerHandler(final long id, final IProgressIndicatorHandler handler) { if (progressBarHandlers == null || !progressBars.contains(new Long(id))) { throw new Error( "call setProgressBar before registering the progress bar's handler."); } progressBarHandlers.put(new Long(id), handler); final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); if (handler.canCancel()) { JButton cancel = new JButton( MessageManager.getString("action.cancel")); final IProgressIndicator us = this; cancel.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); us.setProgressBar( "Cancelled " + ((JLabel) progressPanel.getComponent(0)) .getText(), id); } }); progressPanel.add(cancel, BorderLayout.EAST); } } /** * * @return true if any progress bars are still active */ @Override public boolean operationInProgress() { if (progressBars != null && progressBars.size() > 0) { return true; } return false; } @Override public void setStatus(String text) { statusBar.setText(text); }; /* * Added so Castor Mapping file can obtain Jalview Version */ public String getVersion() { return jalview.bin.Cache.getProperty("VERSION"); } public FeatureRenderer getFeatureRenderer() { return alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); } @Override public void fetchSequence_actionPerformed(ActionEvent e) { 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 (currentFileFormat.equals("Jalview")) { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); for (int i = 0; i < frames.length; i++) { if (frames[i] instanceof AlignFrame && frames[i] != this && ((AlignFrame) frames[i]).fileName != 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(); String protocol = fileName.startsWith("http:") ? "URL" : "File"; loader.LoadFile(viewport, fileName, protocol, currentFileFormat); } else { Rectangle bounds = this.getBounds(); FileLoader loader = new FileLoader(); String protocol = fileName.startsWith("http:") ? "URL" : "File"; AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat); newframe.setBounds(bounds); if (featureSettings != null && featureSettings.isShowing()) { final Rectangle fspos = featureSettings.frame.getBounds(); // TODO: need a 'show feature settings' function that takes bounds - // need to refactor Desktop.addFrame newframe.featureSettings_actionPerformed(null); final FeatureSettings nfs = newframe.featureSettings; SwingUtilities.invokeLater(new Runnable() { @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); } @Override public void addFromURL_actionPerformed(ActionEvent e) { Desktop.instance.inputURLMenuItem_actionPerformed(viewport); } @Override public void save_actionPerformed(ActionEvent e) { if (fileName == null || (currentFileFormat == null || !jalview.io.FormatAdapter .isValidIOFormat(currentFileFormat, true)) || fileName.startsWith("http")) { saveAs_actionPerformed(null); } else { saveAlignment(fileName, currentFileFormat); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void saveAs_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS, jalview.io.AppletFormatAdapter.WRITABLE_FNAMES, currentFileFormat, false); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Save Alignment to file"); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { currentFileFormat = chooser.getSelectedFormat(); if (currentFileFormat == null) { JOptionPane .showInternalMessageDialog( Desktop.desktop, MessageManager .getString("label.select_file_format_before_saving"), MessageManager .getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE); value = chooser.showSaveDialog(this); return; } fileName = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat); jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName); if (currentFileFormat.indexOf(" ") > -1) { currentFileFormat = currentFileFormat.substring(0, currentFileFormat.indexOf(" ")); } saveAlignment(fileName, currentFileFormat); } } public boolean saveAlignment(String file, String format) { boolean success = true; if (format.equalsIgnoreCase("Jalview")) { String shortName = title; if (shortName.indexOf(java.io.File.separatorChar) > -1) { shortName = shortName.substring(shortName .lastIndexOf(java.io.File.separatorChar) + 1); } success = new Jalview2XML().SaveAlignment(this, file, shortName); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new String[] { fileName, format })); } else { if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) { warningMessage("Cannot save file " + fileName + " using format " + format, "Alignment output format not supported"); saveAs_actionPerformed(null); // JBPNote need to have a raise_gui flag here return false; } String[] omitHidden = null; if (viewport.hasHiddenColumns()) { int reply = JOptionPane .showInternalConfirmDialog( Desktop.desktop, MessageManager .getString("label.alignment_contains_hidden_columns"), MessageManager .getString("action.save_omit_hidden_columns"), JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); if (reply == JOptionPane.YES_OPTION) { omitHidden = viewport.getViewAsString(false); } } FormatAdapter f = new FormatAdapter(); String output = f.formatSequences(format, viewport.getAlignment(), // class cast exceptions will // occur in the distant future omitHidden, f.getCacheSuffixDefault(format), viewport.getColumnSelection()); if (output == null) { success = false; } else { try { java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter(file)); out.print(output); out.close(); this.setTitle(file); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new String[] { fileName, format })); } catch (Exception ex) { success = false; ex.printStackTrace(); } } } if (!success) { JOptionPane.showInternalMessageDialog(this, MessageManager .formatMessage("label.couldnt_save_file", new String[] { fileName }), MessageManager .getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE); } return success; } private void warningMessage(String warning, String title) { if (new jalview.util.Platform().isHeadless()) { System.err.println("Warning: " + title + "\nWarning: " + warning); } else { JOptionPane.showInternalMessageDialog(this, warning, title, JOptionPane.WARNING_MESSAGE); } return; } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void outputText_actionPerformed(ActionEvent e) { String[] omitHidden = null; if (viewport.hasHiddenColumns()) { int reply = JOptionPane .showInternalConfirmDialog( Desktop.desktop, MessageManager .getString("label.alignment_contains_hidden_columns"), MessageManager .getString("action.save_omit_hidden_columns"), JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); if (reply == JOptionPane.YES_OPTION) { omitHidden = viewport.getViewAsString(false); } } CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); try { cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), viewport.getAlignment(), omitHidden, viewport.getColumnSelection())); Desktop.addInternalFrame(cap, MessageManager.formatMessage( "label.alignment_output_command", new String[] { e.getActionCommand() }), 600, 500); } catch (OutOfMemoryError oom) { new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom); cap.dispose(); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); } public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void createPNG(File f) { alignPanel.makePNG(f); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void createEPS(File f) { alignPanel.makeEPS(f); } @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().exportFeatures(alignPanel); } @Override public void exportAnnotations_actionPerformed(ActionEvent e) { new AnnotationExporter().exportAnnotations(alignPanel, viewport.showAnnotation ? viewport.getAlignment() .getAlignmentAnnotation() : null, viewport .getAlignment().getGroups(), ((Alignment) viewport .getAlignment()).alignmentProperties); } @Override public void associatedData_actionPerformed(ActionEvent e) { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager .getString("label.load_jalview_annotations")); chooser.setToolTipText(MessageManager .getString("label.load_jalview_annotations")); int value = chooser.showOpenDialog(null); if (value == JalviewFileChooser.APPROVE_OPTION) { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); loadJalviewDataFile(choice, null, null, null); } } /** * 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; } try { if (alignPanels != null) { if (closeAllTabs) { if (this.isClosed()) { // really close all the windows - otherwise wait till // setClosed(true) is called for (int i = 0; i < alignPanels.size(); i++) { AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i); ap.closePanel(); } } } else { closeView(alignPanel); } } if (closeAllTabs) { this.setClosed(true); } } catch (Exception ex) { ex.printStackTrace(); } } /** * close alignPanel2 and shuffle tabs appropriately. * * @param alignPanel2 */ public void closeView(AlignmentPanel alignPanel2) { int index = tabbedPane.getSelectedIndex(); int closedindex = tabbedPane.indexOfComponent(alignPanel2); alignPanels.removeElement(alignPanel2); // Unnecessary // if (viewport == alignPanel2.av) // { // viewport = null; // } alignPanel2.closePanel(); alignPanel2 = null; tabbedPane.removeTabAt(closedindex); tabbedPane.validate(); if (index > closedindex || index == tabbedPane.getTabCount()) { // modify currently selected tab index if necessary. index--; } this.tabSelectionChanged(index); } /** * DOCUMENT ME! */ void updateEditMenuBar() { if (viewport.historyList.size() > 0) { undoMenuItem.setEnabled(true); CommandI command = (CommandI) viewport.historyList.peek(); undoMenuItem.setText(MessageManager.formatMessage( "label.undo_command", new String[] { command.getDescription() })); } else { undoMenuItem.setEnabled(false); undoMenuItem.setText(MessageManager.getString("action.undo")); } if (viewport.redoList.size() > 0) { redoMenuItem.setEnabled(true); CommandI command = (CommandI) viewport.redoList.peek(); redoMenuItem.setText(MessageManager.formatMessage( "label.redo_command", new String[] { command.getDescription() })); } else { redoMenuItem.setEnabled(false); redoMenuItem.setText(MessageManager.getString("action.redo")); } } public void addHistoryItem(CommandI command) { if (command.getSize() > 0) { viewport.historyList.push(command); viewport.redoList.clear(); updateEditMenuBar(); viewport.updateHiddenColumns(); // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null // && viewport.getColumnSelection().getHiddenColumns() != null && // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); } } /** * * @return alignment objects for all views */ AlignmentI[] getViewAlignments() { if (alignPanels != null) { Enumeration e = alignPanels.elements(); AlignmentI[] als = new AlignmentI[alignPanels.size()]; for (int i = 0; e.hasMoreElements(); i++) { als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment(); } return als; } if (viewport != null) { return new AlignmentI[] { viewport.getAlignment() }; } return null; } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void undoMenuItem_actionPerformed(ActionEvent e) { if (viewport.historyList.empty()) return; CommandI command = (CommandI) viewport.historyList.pop(); viewport.redoList.push(command); command.undoCommand(getViewAlignments()); AlignViewport originalSource = getOriginatingSource(command); updateEditMenuBar(); if (originalSource != null) { if (originalSource != viewport) { Cache.log .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.redoList.size() < 1) { return; } CommandI command = (CommandI) viewport.redoList.pop(); viewport.historyList.push(command); command.doCommand(getViewAlignments()); AlignViewport originalSource = getOriginatingSource(command); updateEditMenuBar(); if (originalSource != null) { if (originalSource != viewport) { Cache.log .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()); } } AlignViewport getOriginatingSource(CommandI command) { AlignViewport originalSource = null; // For sequence removal and addition, we need to fire // the property change event FROM the viewport where the // original alignment was altered AlignmentI al = null; if (command instanceof EditCommand) { EditCommand editCommand = (EditCommand) command; al = editCommand.getAlignment(); Vector comps = (Vector) PaintRefresher.components.get(viewport .getSequenceSetId()); for (int i = 0; i < comps.size(); i++) { if (comps.elementAt(i) instanceof AlignmentPanel) { if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment()) { originalSource = ((AlignmentPanel) comps.elementAt(i)).av; break; } } } } if (originalSource == null) { // The original view is closed, we must validate // the current view against the closed view first if (al != null) { PaintRefresher.validateSequences(al, viewport.getAlignment()); } originalSource = viewport; } return originalSource; } /** * DOCUMENT ME! * * @param up * DOCUMENT ME! */ public void moveSelectedSequences(boolean up) { SequenceGroup sg = viewport.getSelectionGroup(); if (sg == null) { return; } viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up); alignPanel.paintAlignment(true); } synchronized void slideSequences(boolean right, int size) { List sg = new Vector(); if (viewport.cursorMode) { sg.add(viewport.getAlignment().getSequenceAt( alignPanel.seqPanel.seqCanvas.cursorY)); } else if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() != viewport .getAlignment().getHeight()) { sg = viewport.getSelectionGroup().getSequences( viewport.getHiddenRepSequences()); } if (sg.size() < 1) { return; } Vector invertGroup = new Vector(); for (int i = 0; i < viewport.getAlignment().getHeight(); i++) { if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) invertGroup.add(viewport.getAlignment().getSequenceAt(i)); } SequenceI[] seqs1 = sg.toArray(new SequenceI[0]); SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; for (int i = 0; i < invertGroup.size(); i++) seqs2[i] = (SequenceI) invertGroup.elementAt(i); SlideSequencesCommand ssc; if (right) ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, viewport.getGapCharacter()); else ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, viewport.getGapCharacter()); int groupAdjustment = 0; if (ssc.getGapsInsertedBegin() && right) { if (viewport.cursorMode) alignPanel.seqPanel.moveCursor(size, 0); else groupAdjustment = size; } else if (!ssc.getGapsInsertedBegin() && !right) { if (viewport.cursorMode) alignPanel.seqPanel.moveCursor(-size, 0); else groupAdjustment = -size; } if (groupAdjustment != 0) { viewport.getSelectionGroup().setStartRes( viewport.getSelectionGroup().getStartRes() + groupAdjustment); viewport.getSelectionGroup().setEndRes( viewport.getSelectionGroup().getEndRes() + groupAdjustment); } boolean appendHistoryItem = false; if (viewport.historyList != null && viewport.historyList.size() > 0 && viewport.historyList.peek() instanceof SlideSequencesCommand) { appendHistoryItem = ssc .appendSlideCommand((SlideSequencesCommand) viewport.historyList .peek()); } if (!appendHistoryItem) addHistoryItem(ssc); repaint(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void copy_actionPerformed(ActionEvent e) { System.gc(); if (viewport.getSelectionGroup() == null) { return; } // TODO: preserve the ordering of displayed alignment annotation in any // internal paste (particularly sequence associated annotation) SequenceI[] seqs = viewport.getSelectionAsNewSequence(); String[] omitHidden = null; if (viewport.hasHiddenColumns()) { omitHidden = viewport.getViewAsString(true); } String output = new FormatAdapter().formatSequences("Fasta", seqs, omitHidden); StringSelection ss = new StringSelection(output); try { jalview.gui.Desktop.internalCopy = true; // Its really worth setting the clipboard contents // to empty before setting the large StringSelection!! Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(""), null); Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(ss, Desktop.instance); } catch (OutOfMemoryError er) { new OOMWarning("copying region", er); return; } Vector hiddenColumns = null; if (viewport.hasHiddenColumns()) { hiddenColumns = new Vector(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport .getSelectionGroup().getEndRes(); for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() .size(); i++) { int[] region = (int[]) viewport.getColumnSelection() .getHiddenColumns().elementAt(i); if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) { hiddenColumns.addElement(new int[] { region[0] - hiddenOffset, region[1] - hiddenOffset }); } } } Desktop.jalviewClipboard = new Object[] { seqs, viewport.getAlignment().getDataset(), hiddenColumns }; statusBar.setText(MessageManager.formatMessage( "label.copied_sequences_to_clipboard", new String[] { 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, format; try { str = (String) contents.getTransferData(DataFlavor.stringFlavor); if (str.length() < 1) { return; } format = new IdentifyFile().Identify(str, "Paste"); } catch (OutOfMemoryError er) { new OOMWarning("Out of memory pasting sequences!!", er); return; } SequenceI[] sequences; boolean annotationAdded = false; AlignmentI alignment = null; if (Desktop.jalviewClipboard != null) { // The clipboard was filled from within Jalview, we must use the // sequences // And dataset from the copied alignment SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0]; // be doubly sure that we create *new* sequence objects. sequences = new SequenceI[newseq.length]; for (int i = 0; i < newseq.length; i++) { sequences[i] = new Sequence(newseq[i]); } alignment = new Alignment(sequences); externalPaste = false; } else { // parse the clipboard as an alignment. alignment = new FormatAdapter().readFile(str, "Paste", format); sequences = alignment.getSequencesArray(); } int alwidth = 0; 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, new Integer( ++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); } newann.padAnnotation(alwidth); alignment.addAnnotation(newann); } } } } if (!newAlignment) { // ///// // ADD HISTORY ITEM // addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment)); } // Add any annotations attached to sequences for (int i = 0; i < sequences.length; i++) { if (sequences[i].getAnnotation() != null) { 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, new Integer( ++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); } } alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation // was // duplicated // earlier alignment .setAnnotationIndex(sequences[i].getAnnotation()[a], a); } } } if (!newAlignment) { // propagate alignment changed. viewport.setEndSeq(alignment.getHeight()); if (annotationAdded) { // Duplicate sequence annotation in all views. AlignmentI[] alview = this.getViewAlignments(); for (int i = 0; i < sequences.length; i++) { AlignmentAnnotation sann[] = sequences[i].getAnnotation(); if (sann == null) continue; for (int avnum = 0; avnum < alview.length; avnum++) { if (alview[avnum] != alignment) { // duplicate in a view other than the one with input focus int avwidth = alview[avnum].getWidth() + 1; // this relies on sann being preserved after we // modify the sequence's annotation array for each duplication for (int a = 0; a < sann.length; a++) { AlignmentAnnotation newann = new AlignmentAnnotation( sann[a]); sequences[i].addAlignmentAnnotation(newann); newann.padAnnotation(avwidth); alview[avnum].addAnnotation(newann); // annotation was // duplicated earlier // 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 : ((Vector) 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) { Vector hc = (Vector) Desktop.jalviewClipboard[2]; for (int i = 0; i < hc.size(); i++) { int[] region = (int[]) hc.elementAt(i); af.viewport.hideColumns(region[0], region[1]); } } // >>>This is a fix for the moment, until a better solution is // found!!<<< af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() .transferSettings( alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. if (!externalPaste) { if (title.startsWith("Copied sequences")) { newtitle = title; } else { newtitle = newtitle.concat("- from " + title); } } else { newtitle = new String("Pasted sequences"); } Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); } } catch (Exception ex) { ex.printStackTrace(); System.out.println("Exception whilst pasting: " + ex); // could be anything being pasted in here } } @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) { Vector hc = (Vector) Desktop.jalviewClipboard[2]; for (int i = 0; i < hc.size(); i++) { int[] region = (int[]) hc.elementAt(i); af.viewport.hideColumns(region[0], region[1]); } } // >>>This is a fix for the moment, until a better solution is // found!!<<< af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() .transferSettings( alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. { if (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(); System.out.println("Exception whilst pasting: " + ex); // could be anything being pasted in here } catch (OutOfMemoryError oom) { new OOMWarning("Viewing flanking region of alignment", oom); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void cut_actionPerformed(ActionEvent e) { copy_actionPerformed(null); delete_actionPerformed(null); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void delete_actionPerformed(ActionEvent evt) { SequenceGroup sg = viewport.getSelectionGroup(); if (sg == null) { return; } Vector seqs = new Vector(); SequenceI seq; for (int i = 0; i < sg.getSize(); i++) { seq = sg.getSequenceAt(i); seqs.addElement(seq); } // If the cut affects all sequences, remove highlighted columns if (sg.getSize() == viewport.getAlignment().getHeight()) { viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); } SequenceI[] cut = new SequenceI[seqs.size()]; for (int i = 0; i < seqs.size(); i++) { cut[i] = (SequenceI) seqs.elementAt(i); } /* * //ADD HISTORY ITEM */ addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, viewport.getAlignment())); viewport.setSelectionGroup(null); viewport.sendSelection(); viewport.getAlignment().deleteGroup(sg); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); if (viewport.getAlignment().getHeight() < 1) { try { this.setClosed(true); } catch (Exception ex) { } } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void deleteGroups_actionPerformed(ActionEvent e) { if (avc.deleteGroups()) { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); alignPanel.paintAlignment(true); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = new SequenceGroup(); for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); } sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); viewport.sendSelection(); alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { if (viewport.cursorMode) { alignPanel.seqPanel.keyboardNo1 = null; alignPanel.seqPanel.keyboardNo2 = null; } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); alignPanel.idPanel.idCanvas.searchResults = null; alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); 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); } alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @Override public void invertColSel_actionPerformed(ActionEvent e) { viewport.invertColumnSelection(); alignPanel.paintAlignment(true); 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.size() > 0) { 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", TrimRegionCommand.TRIM_LEFT, seqs, column, viewport.getAlignment(), viewport.getColumnSelection(), viewport.getSelectionGroup()); viewport.setStartRes(0); } else { trimRegion = new TrimRegionCommand("Remove Right", TrimRegionCommand.TRIM_RIGHT, seqs, column, viewport.getAlignment(), viewport.getColumnSelection(), viewport.getSelectionGroup()); } statusBar.setText(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); statusBar.setText(MessageManager.formatMessage( "label.removed_empty_columns", new String[] { Integer.valueOf(removeGapCols.getSize()).toString() })); // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); viewport.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @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.startRes); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, viewport.getAlignment())); viewport.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()); } // else { // if (justifySeqs>0) { // alignment.justify(justifySeqs!=RIGHT_JUSTIFY); } } // } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void findMenuItem_actionPerformed(ActionEvent e) { new Finder(); } @Override public void newView_actionPerformed(ActionEvent e) { newView(true); } /** * * @param copyAnnotation * if true then duplicate all annnotation, groups and settings * @return new alignment panel, already displayed. */ public AlignmentPanel newView(boolean copyAnnotation) { return newView(null, copyAnnotation); } /** * * @param viewTitle * title of newly created view * @return new alignment panel, already displayed. */ public AlignmentPanel newView(String viewTitle) { return newView(viewTitle, true); } /** * * @param viewTitle * title of newly created view * @param copyAnnotation * if true then duplicate all annnotation, groups and settings * @return new alignment panel, already displayed. */ public AlignmentPanel newView(String viewTitle, boolean copyAnnotation) { AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel, true); if (!copyAnnotation) { // just remove all the current annotation except for the automatic stuff newap.av.getAlignment().deleteAllGroups(); for (AlignmentAnnotation alan : newap.av.getAlignment() .getAlignmentAnnotation()) { if (!alan.autoCalculated) { newap.av.getAlignment().deleteAnnotation(alan); } ; } } newap.av.gatherViewsHere = false; if (viewport.viewName == null) { viewport.viewName = "Original"; } newap.av.historyList = viewport.historyList; newap.av.redoList = viewport.redoList; int index = Desktop.getViewCount(viewport.getSequenceSetId()); // make sure the new view has a unique name - this is essential for Jalview // 2 archives boolean addFirstIndex = false; if (viewTitle == null || viewTitle.trim().length() == 0) { viewTitle = "View"; addFirstIndex = true; } else { index = 1;// we count from 1 if given a specific name } String newViewName = viewTitle + ((addFirstIndex) ? " " + index : ""); Vector comps = (Vector) PaintRefresher.components.get(viewport .getSequenceSetId()); Vector existingNames = new Vector(); for (int i = 0; i < comps.size(); i++) { if (comps.elementAt(i) instanceof AlignmentPanel) { AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i); if (!existingNames.contains(ap.av.viewName)) { existingNames.addElement(ap.av.viewName); } } } while (existingNames.contains(newViewName)) { newViewName = viewTitle + " " + (++index); } newap.av.viewName = newViewName; addAlignmentPanel(newap, true); newap.alignmentChanged(); if (alignPanels.size() == 2) { viewport.gatherViewsHere = true; } tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); return newap; } @Override public void expandViews_actionPerformed(ActionEvent e) { Desktop.instance.explodeViews(this); } @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.idPanel.idCanvas.setPreferredSize(alignPanel .calculateIdWidth()); alignPanel.paintAlignment(true); } @Override public void idRightAlign_actionPerformed(ActionEvent e) { viewport.rightAlignIds = idRightAlign.isSelected(); alignPanel.paintAlignment(true); } @Override public void centreColumnLabels_actionPerformed(ActionEvent e) { viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState(); alignPanel.paintAlignment(true); } /* * (non-Javadoc) * * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() */ @Override protected void followHighlight_actionPerformed() { if (viewport.followHighlight = this.followHighlightMenuItem.getState()) { alignPanel.scrollToPosition( alignPanel.seqPanel.seqCanvas.searchResults, false); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void colourTextMenuItem_actionPerformed(ActionEvent e) { viewport.setColourText(colourTextMenuItem.isSelected()); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void wrapMenuItem_actionPerformed(ActionEvent e) { scaleAbove.setVisible(wrapMenuItem.isSelected()); scaleLeft.setVisible(wrapMenuItem.isSelected()); scaleRight.setVisible(wrapMenuItem.isSelected()); viewport.setWrapAlignment(wrapMenuItem.isSelected()); alignPanel.setWrapAlignment(wrapMenuItem.isSelected()); } @Override public void showAllSeqs_actionPerformed(ActionEvent e) { viewport.showAllHiddenSeqs(); } @Override public void showAllColumns_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); repaint(); } @Override public void hideSelSequences_actionPerformed(ActionEvent e) { viewport.hideAllSelectedSeqs(); alignPanel.paintAlignment(true); } /** * called by key handler and the hide all/show all menu items * * @param toggleSeqs * @param toggleCols */ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) { boolean hide = false; SequenceGroup sg = viewport.getSelectionGroup(); if (!toggleSeqs && !toggleCols) { // Hide everything by the current selection - this is a hack - we do the // invert and then hide // first check that there will be visible columns after the invert. if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport .getColumnSelection().getSelected().size() > 0) || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg .getEndRes())) { // now invert the sequence set, if required - empty selection implies // that no hiding is required. if (sg != null) { invertSequenceMenuItem_actionPerformed(null); sg = viewport.getSelectionGroup(); toggleSeqs = true; } viewport.expandColSelection(sg, true); // finally invert the column selection and get the new sequence // selection. invertColSel_actionPerformed(null); toggleCols = true; } } if (toggleSeqs) { if (sg != null && sg.getSize() != viewport.getAlignment().getHeight()) { hideSelSequences_actionPerformed(null); hide = true; } else if (!(toggleCols && viewport.getColumnSelection().getSelected() .size() > 0)) { showAllSeqs_actionPerformed(null); } } if (toggleCols) { if (viewport.getColumnSelection().getSelected().size() > 0) { 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); } /* * (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.paintAlignment(true); } /* * (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); } @Override public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); } @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.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void viewTextMenuItem_actionPerformed(ActionEvent e) { viewport.setShowText(viewTextMenuItem.isSelected()); alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { viewport.setRenderGaps(renderGapsMenuItem.isSelected()); alignPanel.paintAlignment(true); } public FeatureSettings featureSettings; @Override public void featureSettings_actionPerformed(ActionEvent e) { if (featureSettings != null) { featureSettings.close(); featureSettings = null; } if (!showSeqFeatures.isSelected()) { // make sure features are actually displayed showSeqFeatures.setSelected(true); showSeqFeatures_actionPerformed(null); } featureSettings = new FeatureSettings(this); } /** * Set or clear 'Show Sequence Features' * * @param evt * DOCUMENT ME! */ @Override public void showSeqFeatures_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); alignPanel.paintAlignment(true); if (alignPanel.getOverviewPanel() != null) { alignPanel.getOverviewPanel().updateOverviewImage(); } } /** * Set or clear 'Show Sequence Features' * * @param evt * DOCUMENT ME! */ @Override public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight .isSelected()); if (viewport.getShowSequenceFeaturesHeight()) { // ensure we're actually displaying features viewport.setShowSequenceFeatures(true); showSeqFeatures.setSelected(true); } alignPanel.paintAlignment(true); if (alignPanel.getOverviewPanel() != null) { alignPanel.getOverviewPanel().updateOverviewImage(); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { viewport.setShowAnnotation(annotationPanelMenuItem.isSelected()); alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected()); } @Override public void alignmentProperties() { JEditorPane editPane = new JEditorPane("text/html", ""); editPane.setEditable(false); StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) .formatAsHtml(); editPane.setText(MessageManager.formatMessage("label.html_content", new String[] { contents.toString() })); JInternalFrame frame = new JInternalFrame(); frame.getContentPane().add(new JScrollPane(editPane)); Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage( "label.alignment_properties", new String[] { getTitle() }), 500, 400); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { if (alignPanel.overviewPanel != null) { return; } JInternalFrame frame = new JInternalFrame(); OverviewPanel overview = new OverviewPanel(alignPanel); frame.setContentPane(overview); Desktop.addInternalFrame(frame, MessageManager.formatMessage( "label.overview_params", new String[] { this.getTitle() }), frame.getWidth(), frame.getHeight()); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { alignPanel.setOverviewPanel(null); }; }); alignPanel.setOverviewPanel(overview); } @Override public void textColour_actionPerformed(ActionEvent e) { new TextColourChooser().chooseColour(alignPanel, null); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void noColourmenuItem_actionPerformed(ActionEvent e) { changeColour(null); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void clustalColour_actionPerformed(ActionEvent e) { changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences())); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void zappoColour_actionPerformed(ActionEvent e) { changeColour(new ZappoColourScheme()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void taylorColour_actionPerformed(ActionEvent e) { changeColour(new TaylorColourScheme()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void hydrophobicityColour_actionPerformed(ActionEvent e) { changeColour(new HydrophobicColourScheme()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void helixColour_actionPerformed(ActionEvent e) { changeColour(new HelixColourScheme()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void strandColour_actionPerformed(ActionEvent e) { changeColour(new StrandColourScheme()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void turnColour_actionPerformed(ActionEvent e) { changeColour(new TurnColourScheme()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void buriedColour_actionPerformed(ActionEvent e) { changeColour(new BuriedColourScheme()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void nucleotideColour_actionPerformed(ActionEvent e) { changeColour(new NucleotideColourScheme()); } @Override public void purinePyrimidineColour_actionPerformed(ActionEvent e) { changeColour(new PurinePyrimidineColourScheme()); } /* * public void covariationColour_actionPerformed(ActionEvent e) { * changeColour(new * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation * ()[0])); } */ @Override public void annotationColour_actionPerformed(ActionEvent e) { new AnnotationColourChooser(viewport, alignPanel); } @Override public void rnahelicesColour_actionPerformed(ActionEvent e) { new RNAHelicesColourChooser(viewport, alignPanel); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void applyToAllGroups_actionPerformed(ActionEvent e) { viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); } /** * DOCUMENT ME! * * @param cs * DOCUMENT ME! */ public void changeColour(ColourSchemeI cs) { // TODO: compare with applet and pull up to model method int threshold = 0; if (cs != null) { if (viewport.getAbovePIDThreshold()) { threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); } else { cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); } if (viewport.getConservationSelected()) { Alignment al = (Alignment) viewport.getAlignment(); Conservation c = new Conservation("All", ResidueProperties.propHash, 3, al.getSequences(), 0, al.getWidth() - 1); c.calculate(); c.verdict(false, viewport.getConsPercGaps()); cs.setConservation(c); cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs, "Background")); } else { cs.setConservation(null); } cs.setConsensus(viewport.getSequenceConsensusHash()); } viewport.setGlobalColourScheme(cs); if (viewport.getColourAppliesToAllGroups()) { for (SequenceGroup sg : viewport.getAlignment().getGroups()) { if (cs == null) { sg.cs = null; continue; } if (cs instanceof ClustalxColourScheme) { sg.cs = new ClustalxColourScheme(sg, viewport.getHiddenRepSequences()); } else if (cs instanceof UserColourScheme) { sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours()); } else { try { sg.cs = cs.getClass().newInstance(); } catch (Exception ex) { } } if (viewport.getAbovePIDThreshold() || cs instanceof PIDColourScheme || cs instanceof Blosum62ColourScheme) { sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); sg.cs.setConsensus(AAFrequency.calculate( sg.getSequences(viewport.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); } else { sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); } if (viewport.getConservationSelected()) { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, sg.getSequences(viewport .getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); c.verdict(false, viewport.getConsPercGaps()); sg.cs.setConservation(c); } else { sg.cs.setConservation(null); } } } if (alignPanel.getOverviewPanel() != null) { alignPanel.getOverviewPanel().updateOverviewImage(); } alignPanel.paintAlignment(true); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void modifyPID_actionPerformed(ActionEvent e) { if (viewport.getAbovePIDThreshold() && viewport.getGlobalColourScheme() != null) { SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background"); SliderPanel.showPIDSlider(); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void modifyConservation_actionPerformed(ActionEvent e) { if (viewport.getConservationSelected() && viewport.getGlobalColourScheme() != null) { SliderPanel.setConservationSlider(alignPanel, viewport.getGlobalColourScheme(), "Background"); SliderPanel.showConservationSlider(); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void conservationMenuItem_actionPerformed(ActionEvent e) { viewport.setConservationSelected(conservationMenuItem.isSelected()); viewport.setAbovePIDThreshold(false); abovePIDThreshold.setSelected(false); changeColour(viewport.getGlobalColourScheme()); modifyConservation_actionPerformed(null); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void abovePIDThreshold_actionPerformed(ActionEvent e) { viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); conservationMenuItem.setSelected(false); viewport.setConservationSelected(false); changeColour(viewport.getGlobalColourScheme()); modifyPID_actionPerformed(null); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void userDefinedColour_actionPerformed(ActionEvent e) { if (e.getActionCommand().equals( MessageManager.getString("action.user_defined"))) { new UserDefinedColours(alignPanel, null); } else { UserColourScheme udc = (UserColourScheme) UserDefinedColours .getUserColourSchemes().get(e.getActionCommand()); changeColour(udc); } } public void updateUserColourMenu() { Component[] menuItems = colourMenu.getMenuComponents(); int i, iSize = menuItems.length; for (i = 0; i < iSize; i++) { if (menuItems[i].getName() != null && menuItems[i].getName().equals("USER_DEFINED")) { colourMenu.remove(menuItems[i]); iSize--; } } if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) { java.util.Enumeration userColours = jalview.gui.UserDefinedColours .getUserColourSchemes().keys(); while (userColours.hasMoreElements()) { final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( userColours.nextElement().toString()); radioItem.setName("USER_DEFINED"); radioItem.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent evt) { if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) { radioItem.removeActionListener(radioItem.getActionListeners()[0]); int option = JOptionPane.showInternalConfirmDialog( jalview.gui.Desktop.desktop, MessageManager .getString("label.remove_from_default_list"), MessageManager .getString("label.remove_user_defined_colour"), JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { jalview.gui.UserDefinedColours .removeColourFromDefaults(radioItem.getText()); colourMenu.remove(radioItem); } else { radioItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); } }); } } } }); radioItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); } }); colourMenu.insert(radioItem, 15); colours.add(radioItem); } } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void PIDColour_actionPerformed(ActionEvent e) { changeColour(new PIDColourScheme()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void BLOSUM62Colour_actionPerformed(ActionEvent e) { changeColour(new Blosum62ColourScheme()); } /** * 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), null); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.getAlignment())); alignPanel.paintAlignment(true); } /** * 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); } /** * 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); } /** * 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); } /** * 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)) { JOptionPane.showInternalMessageDialog(this, MessageManager .getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"), JOptionPane.WARNING_MESSAGE); } else { JInternalFrame frame = new JInternalFrame(); frame.setContentPane(new PairwiseAlignPanel(viewport)); Desktop.addInternalFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void PCAMenuItem_actionPerformed(ActionEvent e) { if (((viewport.getSelectionGroup() != null) && (viewport.getSelectionGroup().getSize() < 4) && (viewport .getSelectionGroup().getSize() > 0)) || (viewport.getAlignment().getHeight() < 4)) { JOptionPane .showInternalMessageDialog( this, MessageManager .getString("label.principal_component_analysis_must_take_least_four_input_sequences"), MessageManager .getString("label.sequence_selection_insufficient"), JOptionPane.WARNING_MESSAGE); return; } new PCAPanel(alignPanel); } @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(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("AV", "PID", "Average distance tree using PID"); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); } /** * DOCUMENT ME! * * @param type * DOCUMENT ME! * @param pwType * DOCUMENT ME! * @param title * DOCUMENT ME! */ void NewTreePanel(String type, String pwType, String title) { TreePanel tp; if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 0) { if (viewport.getSelectionGroup().getSize() < 3) { JOptionPane .showMessageDialog( Desktop.desktop, MessageManager .getString("label.you_need_more_two_sequences_selected_build_tree"), MessageManager .getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE); return; } SequenceGroup sg = viewport.getSelectionGroup(); /* Decide if the selection is a column region */ for (SequenceI _s : sg.getSequences()) { if (_s.getLength() < sg.getEndRes()) { JOptionPane .showMessageDialog( Desktop.desktop, MessageManager .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"), MessageManager .getString("label.sequences_selection_not_aligned"), JOptionPane.WARNING_MESSAGE); return; } } title = title + " on region"; tp = new TreePanel(alignPanel, type, pwType); } else { // are the visible sequences aligned? if (!viewport.getAlignment().isAligned(false)) { JOptionPane .showMessageDialog( Desktop.desktop, MessageManager .getString("label.sequences_must_be_aligned_before_creating_tree"), MessageManager .getString("label.sequences_not_aligned"), JOptionPane.WARNING_MESSAGE); return; } if (viewport.getAlignment().getHeight() < 2) { return; } tp = new TreePanel(alignPanel, type, pwType); } title += " from "; if (viewport.viewName != null) { title += viewport.viewName + " of "; } title += this.title; Desktop.addInternalFrame(tp, title, 600, 500); } /** * DOCUMENT ME! * * @param title * DOCUMENT ME! * @param order * DOCUMENT ME! */ public void addSortByOrderMenuItem(String title, final AlignmentOrder order) { final JMenuItem item = new JMenuItem("by " + title); sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { @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); } }); } /** * 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); } }); } /** * 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, (String) 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. * * @param treePanel * Displayed tree window. * @param title * SortBy menu item title. */ @Override public void buildTreeMenu() { calculateTree.removeAll(); // build the calculate menu for (final String type : new String[] { "NJ", "AV" }) { String treecalcnm = MessageManager.getString("label.tree_calc_" + type.toLowerCase()); for (final Object pwtype : ResidueProperties.scoreMatrices.keySet()) { JMenuItem tm = new JMenuItem(); ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype); if (sm.isProtein() == !viewport.getAlignment().isNucleotide()) { String smn = MessageManager.getStringOrReturn( "label.score_model_", sm.getName()); final String title = MessageManager.formatMessage( "label.treecalc_title", treecalcnm, smn); tm.setText(title);// tm.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { NewTreePanel(type, (String) pwtype, title); } }); calculateTree.add(tm); } } } sortByTreeMenu.removeAll(); Vector comps = (Vector) PaintRefresher.components.get(viewport .getSequenceSetId()); Vector treePanels = new Vector(); int i, iSize = comps.size(); for (i = 0; i < iSize; i++) { if (comps.elementAt(i) instanceof TreePanel) { treePanels.add(comps.elementAt(i)); } } iSize = treePanels.size(); if (iSize < 1) { sortByTreeMenu.setVisible(false); return; } sortByTreeMenu.setVisible(true); for (i = 0; i < treePanels.size(); i++) { final TreePanel tp = (TreePanel) treePanels.elementAt(i); final JMenuItem item = new JMenuItem(tp.getTitle()); final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree(); item.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { tp.sortByTree_actionPerformed(null); 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); 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 { /* * Vector seqs = viewport.getAlignment().getSequences(); * * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()]; * * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI) * seqs.elementAt(i); } } */ msa = viewport.getAlignmentView(false); } return msa; } /** * Decides what is submitted to a secondary structure prediction service: the * first sequence in the alignment, or in the current selection, or, if the * alignment is 'aligned' (ie padded with gaps), then the currently selected * region or the whole alignment. (where the first sequence in the set is the * one that the prediction will be for). */ public AlignmentView gatherSeqOrMsaForSecStrPrediction() { AlignmentView seqs = null; if ((viewport.getSelectionGroup() != null) && (viewport.getSelectionGroup().getSize() > 0)) { seqs = viewport.getAlignmentView(true); } else { seqs = viewport.getAlignmentView(false); } // limit sequences - JBPNote in future - could spawn multiple prediction // jobs // TODO: viewport.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( jalview.bin.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")); int value = chooser.showOpenDialog(null); if (value == JalviewFileChooser.APPROVE_OPTION) { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); jalview.io.NewickFile fin = null; try { fin = new jalview.io.NewickFile(choice, "File"); viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); } catch (Exception ex) { JOptionPane .showMessageDialog( Desktop.desktop, ex.getMessage(), MessageManager .getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } if (fin != null && fin.hasWarningMessage()) { JOptionPane.showMessageDialog(Desktop.desktop, fin .getWarningMessage(), MessageManager .getString("label.possible_problem_with_tree_file"), JOptionPane.WARNING_MESSAGE); } } } @Override protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) { changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); } public TreePanel ShowNewickTree(NewickFile nf, String title) { return ShowNewickTree(nf, title, 600, 500, 4, 5); } public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input) { return ShowNewickTree(nf, title, input, 600, 500, 4, 5); } public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h, int x, int y) { return ShowNewickTree(nf, title, null, w, h, x, y); } /** * Add a treeviewer for the tree extracted from a newick file object to the * current alignment view * * @param nf * the tree * @param title * tree viewer title * @param input * Associated alignment input data (or null) * @param w * width * @param h * height * @param x * position * @param y * position * @return TreePanel handle */ public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w, int h, int x, int y) { TreePanel tp = null; try { nf.parse(); if (nf.getTree() != null) { tp = new TreePanel(alignPanel, "FromFile", title, nf, input); tp.setSize(w, h); if (x > 0 && y > 0) { tp.setLocation(x, y); } Desktop.addInternalFrame(tp, title, w, h); } } catch (Exception ex) { ex.printStackTrace(); } return tp; } private boolean buildingMenu = false; /** * Generates menu items and listener event actions for web service clients * */ public void BuildWebServiceMenu() { while (buildingMenu) { try { System.err.println("Waiting for building menu to finish."); Thread.sleep(10); } catch (Exception e) { } ; } final AlignFrame me = this; buildingMenu = true; new Thread(new Runnable() { @Override public void run() { final List legacyItems = new ArrayList(); try { System.err.println("Building ws menu again " + Thread.currentThread()); // TODO: add support for context dependent disabling of services based // on // alignment and current selection // TODO: add additional serviceHandle parameter to specify abstract // handler // class independently of AbstractName // TODO: add in rediscovery GUI function to restart discoverer // TODO: group services by location as well as function and/or // introduce // object broker mechanism. final Vector wsmenu = new Vector(); final IProgressIndicator af = me; 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"); + final JMenu d2p2menu = new JMenu("Database of Disordered Protein Predictions"); // 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 = (Vector) 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 = (ext.vamsas.ServiceHandle) 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(d2p2menu); 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. boolean new_sspred = false; if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); if (jws2servs != null) { if (jws2servs.hasServices()) { jws2servs.attachWSMenuEntry(webService, me); for (Jws2Instance sv : jws2servs.getServices()) { if (sv.description.toLowerCase().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); } } } 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) { Cache.log .debug("Exception during web service menu building process.", e); } ; } }); } catch (Exception e) { } ; buildingMenu = false; } }).start(); } /** * construct any groupURL type service menu entries. * * @param webService */ private 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); } } /* * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser * chooser = new JalviewFileChooser(jalview.bin.Cache. * getProperty("LAST_DIRECTORY")); * * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export * to Vamsas file"); chooser.setToolTipText("Export"); * * int value = chooser.showSaveDialog(this); * * if (value == JalviewFileChooser.APPROVE_OPTION) { * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport); * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview( * chooser.getSelectedFile().getAbsolutePath(), this); } } */ /** * prototype of an automatically enabled/disabled analysis function * */ protected void setShowProductsEnabled() { SequenceI[] selection = viewport.getSequenceSelection(); if (canShowProducts(selection, viewport.getSelectionGroup() != null, viewport.getAlignment().getDataset())) { showProducts.setEnabled(true); } else { showProducts.setEnabled(false); } } /** * search selection for sequence xRef products and build the show products * menu. * * @param selection * @param dataset * @return true if showProducts menu should be enabled. */ public boolean canShowProducts(SequenceI[] selection, boolean isRegionSelection, Alignment dataset) { boolean showp = false; try { showProducts.removeAll(); final boolean dna = viewport.getAlignment().isNucleotide(); final Alignment ds = dataset; String[] ptypes = (selection == null || selection.length == 0) ? null : CrossRef.findSequenceXrefTypes(dna, selection, dataset); // Object[] prods = // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(), // selection, dataset, true); final SequenceI[] sel = selection; for (int t = 0; ptypes != null && t < ptypes.length; t++) { showp = true; final boolean isRegSel = isRegionSelection; final AlignFrame af = this; final String source = ptypes[t]; JMenuItem xtype = new JMenuItem(ptypes[t]); xtype.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { // TODO: new thread for this call with vis-delay af.showProductsFor(af.viewport.getSequenceSelection(), ds, isRegSel, dna, source); } }); showProducts.add(xtype); } showProducts.setVisible(showp); showProducts.setEnabled(showp); } catch (Exception e) { jalview.bin.Cache.log .warn("canTranslate threw an exception - please report to help@jalview.org", e); return false; } return showp; } protected void showProductsFor(SequenceI[] sel, Alignment ds, boolean isRegSel, boolean dna, String source) { final boolean fisRegSel = isRegSel; final boolean fdna = dna; final String fsrc = source; final AlignFrame ths = this; final SequenceI[] fsel = sel; Runnable foo = new Runnable() { @Override public void run() { final long sttime = System.currentTimeMillis(); ths.setProgressBar("Searching for sequences from " + fsrc, sttime); try { Alignment ds = ths.getViewport().getAlignment().getDataset(); // update // our local // dataset // reference Alignment prods = CrossRef .findXrefSequences(fsel, fdna, fsrc, ds); if (prods != null) { SequenceI[] sprods = new SequenceI[prods.getHeight()]; for (int s = 0; s < sprods.length; s++) { sprods[s] = (prods.getSequenceAt(s)).deriveSequence(); if (ds.getSequences() == null || !ds.getSequences().contains( sprods[s].getDatasetSequence())) ds.addSequence(sprods[s].getDatasetSequence()); sprods[s].updatePDBIds(); } Alignment al = new Alignment(sprods); AlignedCodonFrame[] cf = prods.getCodonFrames(); al.setDataset(ds); for (int s = 0; cf != null && s < cf.length; s++) { al.addCodonFrame(cf[s]); cf[s] = null; } AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ") + " for " + ((fisRegSel) ? "selected region of " : "") + getTitle(); Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); } else { System.err.println("No Sequences generated for xRef type " + fsrc); } } catch (Exception e) { jalview.bin.Cache.log.error( "Exception when finding crossreferences", e); } catch (OutOfMemoryError e) { new OOMWarning("whilst fetching crossreferences", e); } catch (Error e) { jalview.bin.Cache.log.error("Error when finding crossreferences", e); } ths.setProgressBar("Finished searching for sequences from " + fsrc, sttime); } }; Thread frunner = new Thread(foo); frunner.start(); } public boolean canShowTranslationProducts(SequenceI[] selection, AlignmentI alignment) { // old way try { return (jalview.analysis.Dna.canTranslate(selection, viewport.getViewAsVisibleContigs(true))); } catch (Exception e) { jalview.bin.Cache.log .warn("canTranslate threw an exception - please report to help@jalview.org", e); return false; } } @Override public void showProducts_actionPerformed(ActionEvent e) { // ///////////////////////////// // Collect Data to be translated/transferred SequenceI[] selection = viewport.getSequenceSelection(); AlignmentI al = null; try { al = jalview.analysis.Dna.CdnaTranslate(selection, viewport .getViewAsVisibleContigs(true), viewport.getGapCharacter(), viewport.getAlignment().getDataset()); } catch (Exception ex) { al = null; jalview.bin.Cache.log.debug("Exception during translation.", ex); } if (al == null) { JOptionPane .showMessageDialog( Desktop.desktop, MessageManager .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"), MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE); } else { AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); Desktop.addInternalFrame(af, MessageManager.formatMessage( "label.translation_of_params", new String[] { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT); } } @Override public void showTranslation_actionPerformed(ActionEvent e) { // ///////////////////////////// // Collect Data to be translated/transferred SequenceI[] selection = viewport.getSequenceSelection(); String[] seqstring = viewport.getViewAsString(true); AlignmentI al = null; try { al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true), viewport .getGapCharacter(), viewport.getAlignment() .getAlignmentAnnotation(), viewport.getAlignment() .getWidth(), viewport.getAlignment().getDataset()); } catch (Exception ex) { al = null; jalview.bin.Cache.log.error( "Exception during translation. Please report this !", ex); JOptionPane .showMessageDialog( Desktop.desktop, MessageManager .getString("label.error_when_translating_sequences_submit_bug_report"), MessageManager .getString("label.implementation_error") + MessageManager .getString("translation_failed"), JOptionPane.ERROR_MESSAGE); return; } if (al == null) { JOptionPane .showMessageDialog( Desktop.desktop, MessageManager .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"), MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE); } else { AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); Desktop.addInternalFrame(af, MessageManager.formatMessage( "label.translation_of_params", new String[] { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT); } } /** * Try to load a features file onto the alignment. * * @param file * contents or path to retrieve file * @param type * access mode of file (see jalview.io.AlignFile) * @return true if features file was parsed corectly. */ public boolean parseFeaturesFile(String file, String type) { boolean featuresFile = false; try { featuresFile = new FeaturesFile(file, type).parse(viewport .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas .getFeatureRenderer().featureColours, false, jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); } catch (Exception ex) { ex.printStackTrace(); } if (featuresFile) { viewport.showSequenceFeatures = true; showSeqFeatures.setSelected(true); if (alignPanel.seqPanel.seqCanvas.fr != null) { // update the min/max ranges where necessary alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); } if (featureSettings != null) { featureSettings.setTableData(); } alignPanel.paintAlignment(true); } return featuresFile; } @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) { Transferable t = evt.getTransferable(); java.util.List files = null; try { DataFlavor uriListFlavor = new DataFlavor( "text/uri-list;class=java.lang.String"); if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) { // Works on Windows and MacOSX evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); files = (java.util.List) t .getTransferData(DataFlavor.javaFileListFlavor); } else if (t.isDataFlavorSupported(uriListFlavor)) { // This is used by Unix drag system evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); String data = (String) t.getTransferData(uriListFlavor); files = new java.util.ArrayList(1); for (java.util.StringTokenizer st = new java.util.StringTokenizer( data, "\r\n"); st.hasMoreTokens();) { String s = st.nextToken(); if (s.startsWith("#")) { // the line is a comment (as per the RFC 2483) continue; } java.net.URI uri = new java.net.URI(s); // check to see if we can handle this kind of URI if (uri.getScheme().toLowerCase().startsWith("http")) { files.add(uri.toString()); } else { // otherwise preserve old behaviour: catch all for file objects java.io.File file = new java.io.File(uri); files.add(file.toString()); } } } } catch (Exception e) { e.printStackTrace(); } if (files != null) { try { // 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++) { String file = files.get(i).toString(); String pdbfn = ""; String protocol = FormatAdapter.checkProtocol(file); if (protocol == jalview.io.FormatAdapter.FILE) { File fl = new File(file); pdbfn = fl.getName(); } else if (protocol == jalview.io.FormatAdapter.URL) { URL url = new URL(file); 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); } if (mtch != null) { String type = null; try { type = new IdentifyFile().Identify(file, protocol); } catch (Exception ex) { type = null; } if (type != null) { if (type.equalsIgnoreCase("PDB")) { 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(file); } } int assocfiles = 0; if (filesmatched.size() > 0) { if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) || JOptionPane .showConfirmDialog( this, MessageManager .formatMessage( "label.automatically_associate_pdb_files_with_sequences_same_name", new String[] { Integer.valueOf( filesmatched .size()) .toString() }), MessageManager .getString("label.automatically_associate_pdb_files_by_name"), JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) { 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((String) fm[0], (String) fm[1], toassoc, false); if (pe != null) { System.err.println("Associated file : " + ((String) fm[0]) + " with " + toassoc.getDisplayId(true)); assocfiles++; } } alignPanel.paintAlignment(true); } } } if (filesnotmatched.size() > 0) { if (assocfiles > 0 && (Cache.getDefault( "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane .showConfirmDialog( this, MessageManager .formatMessage( "label.ignore_unmatched_dropped_files_info", new String[] { Integer.valueOf( filesnotmatched .size()) .toString() }), MessageManager .getString("label.ignore_unmatched_dropped_files"), JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)) { return; } for (String fn : filesnotmatched) { loadJalviewDataFile(fn, null, null, null); } } } catch (Exception ex) { ex.printStackTrace(); } } } /** * Attempt to load a "dropped" file or URL string: First by testing whether * it's and Annotation file, then a JNet file, and finally a features file. If * all are false then the user may have dropped an alignment file onto this * AlignFrame. * * @param file * either a filename or a URL string. */ public void loadJalviewDataFile(String file, String protocol, String format, SequenceI assocSeq) { try { if (protocol == null) { protocol = jalview.io.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 || format .equalsIgnoreCase("PFAM")) ? new AnnotationFile() .readAnnotationFile(viewport.getAlignment(), file, protocol) : false; if (!isAnnotation) { // first see if its a T-COFFEE score file TCoffeeScoreFile tcf = null; try { tcf = new TCoffeeScoreFile(file, protocol); if (tcf.isValid()) { if (tcf.annotateAlignment(viewport.getAlignment(), true)) { tcoffeeColour.setEnabled(true); tcoffeeColour.setSelected(true); changeColour(new TCoffeeColourScheme(viewport.getAlignment())); isAnnotation = true; statusBar .setText(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 JOptionPane .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"), JOptionPane.WARNING_MESSAGE); } } else { tcf = null; } } catch (Exception x) { Cache.log .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, protocol); } if (format.equalsIgnoreCase("JnetFile")) { jalview.io.JPredFile predictions = new jalview.io.JPredFile( file, protocol); new JnetAnnotationMaker().add_annotation(predictions, viewport.getAlignment(), 0, false); isAnnotation = true; } else { /* * if (format.equalsIgnoreCase("PDB")) { * * String pdbfn = ""; // try to match up filename with sequence id * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = * new File(file); pdbfn = fl.getName(); } else if (protocol == * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn = * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { * // attempt to find a match in the alignment SequenceI mtch = * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq() * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) * { System.err.println("Associated file : " + file + " with " + * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } // * TODO: maybe need to load as normal otherwise return; } } */ // try to parse it as a features file boolean isGroupsFile = parseFeaturesFile(file, protocol); // if it wasn't a features file then we just treat it as a general // alignment file to load into the current view. if (!isGroupsFile) { new FileLoader().LoadFile(viewport, file, protocol, format); } else { alignPanel.paintAlignment(true); } } } } if (isAnnotation) { alignPanel.adjustAnnotationHeight(); viewport.updateSequenceIdColours(); buildSortByAnnotationScoresMenu(); alignPanel.paintAlignment(true); } } catch (Exception ex) { ex.printStackTrace(); } catch (OutOfMemoryError oom) { try { System.gc(); } catch (Exception x) { } ; new OOMWarning( "loading data " + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard." : "using " + protocol + " from " + file) : ".") + (format != null ? "(parsing as '" + format + "' file)" : ""), oom, Desktop.desktop); } } @Override public void tabSelectionChanged(int index) { if (index > -1) { alignPanel = (AlignmentPanel) alignPanels.elementAt(index); viewport = alignPanel.av; avc.setViewportAndAlignmentPanel(viewport, alignPanel); setMenusFromViewport(viewport); } } @Override public void tabbedPane_mousePressed(MouseEvent e) { if (SwingUtilities.isRightMouseButton(e)) { String reply = JOptionPane.showInternalInputDialog(this, MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name"), JOptionPane.QUESTION_MESSAGE); if (reply != null) { viewport.viewName = reply; tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); } } } public AlignViewport getCurrentView() { return viewport; } /** * Open the dialog for regex description parsing. */ @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(AlignViewport av) { if (viewport == av) { this.closeMenuItem_actionPerformed(false); return true; } Component[] comp = tabbedPane.getComponents(); for (int i = 0; comp != null && i < comp.length; i++) { if (comp[i] instanceof AlignmentPanel) { if (((AlignmentPanel) comp[i]).av == av) { // close the view. closeView((AlignmentPanel) comp[i]); return true; } } } return false; } protected void build_fetchdbmenu(JMenu webService) { // Temporary hack - DBRef Fetcher always top level ws entry. // TODO We probably want to store a sequence database checklist in // preferences and have checkboxes.. rather than individual sources selected // here final JMenu rfetch = new JMenu( 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("TRIM_FETCHED_DATASET_SEQS", true)); trimrs.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { trimrs.setSelected(trimrs.isSelected()); Cache.setProperty("TRIM_FETCHED_DATASET_SEQS", 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() { new jalview.ws.DBRefFetcher(alignPanel.av .getSequenceSelection(), alignPanel.alignFrame) .fetchDBRefs(false); } }).start(); } }); rfetch.add(fetchr); final AlignFrame me = this; new Thread(new Runnable() { @Override public void run() { final jalview.ws.SequenceFetcher sf = SequenceFetcher .getSequenceFetcherSingleton(me); javax.swing.SwingUtilities.invokeLater(new Runnable() { @Override public void run() { String[] dbclasses = sf.getOrderedSupportedSources(); // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); // jalview.util.QuickSort.sort(otherdb, otherdb); 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; } // List dbs=otherdb; // otherdb=new ArrayList(); // for (DbSourceProxy db:dbs) // { // if (!db.isA(DBRefSource.ALIGNMENTDB) // } 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() { new jalview.ws.DBRefFetcher(alignPanel.av .getSequenceSelection(), alignPanel.alignFrame, dassource) .fetchDBRefs(false); } }).start(); } }); fetchr.setToolTipText("" + JvSwingUtils.wrapTooltip("Retrieve from " + 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 String[] { src.getDbSource() })); fetchr.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { @Override public void run() { new jalview.ws.DBRefFetcher(alignPanel.av .getSequenceSelection(), alignPanel.alignFrame, dassource) .fetchDBRefs(false); } }).start(); } }); fetchr.setToolTipText("" + JvSwingUtils.wrapTooltip("Retrieve from all " + otherdb.size() + " sources in " + src.getDbSource() + "
First is :" + src.getDbName()) + ""); dfetch.add(fetchr); comp++; // and then build the rest of the individual menus ifetch = new JMenu("Sources from " + 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 = "from '" + 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() { new jalview.ws.DBRefFetcher(alignPanel.av .getSequenceSelection(), alignPanel.alignFrame, dassrc) .fetchDBRefs(false); } }).start(); } }); fetchr.setToolTipText("" + JvSwingUtils.wrapTooltip("Retrieve from " + 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); } public void setShowSeqFeatures(boolean b) { showSeqFeatures.setSelected(true); viewport.setShowSequenceFeatures(true); } /* * (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(true); } /* * (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); } } @Override protected void createGroup_actionPerformed(ActionEvent e) { if (avc.createGroup()) { 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( "Implementation error: cannot show a view from another alignment in an AlignFrame."); } if (tabbedPane != null & alignPanels.indexOf(alignmentPanel) != tabbedPane .getSelectedIndex()) { tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); } } } 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(); } } } } diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java index 3229cdc..7852121 100644 --- a/src/jalview/ws/jws1/Discoverer.java +++ b/src/jalview/ws/jws1/Discoverer.java @@ -1,436 +1,447 @@ /* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) * Copyright (C) 2014 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.ws.jws1; +import jalview.ws.jws2.D2P2WSClient; + import java.util.*; import javax.swing.*; import ext.vamsas.*; public class Discoverer implements Runnable { ext.vamsas.IRegistry registry; // the root registry service. private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( this); /** * change listeners are notified of "services" property changes * * @param listener * to be added that consumes new services Hashtable object. */ public void addPropertyChangeListener( java.beans.PropertyChangeListener listener) { changeSupport.addPropertyChangeListener(listener); } /** * * * @param listener * to be removed */ public void removePropertyChangeListener( java.beans.PropertyChangeListener listener) { changeSupport.removePropertyChangeListener(listener); } /** * Property change listener firing routine * * @param prop * services * @param oldvalue * old services hash * @param newvalue * new services hash */ public void firePropertyChange(String prop, Object oldvalue, Object newvalue) { changeSupport.firePropertyChange(prop, oldvalue, newvalue); } /** * Initializes the server field with a valid service implementation. * * @return true if service was located. */ private IRegistry locateWebService(java.net.URL WsURL) { IRegistryServiceLocator loc = new IRegistryServiceLocator(); // Default IRegistry server = null; try { server = loc.getRegistryService(WsURL); ((RegistryServiceSoapBindingStub) server).setTimeout(60000); // One // minute // timeout } catch (Exception ex) { jalview.bin.Cache.log .error("Serious! Service location failed\nfor URL :" + WsURL + "\n", ex); return null; } loc.getEngine().setOption("axis", "1"); return server; } static private java.net.URL RootServiceURL = null; static public Vector ServiceURLList = null; static private boolean reallyDiscoverServices = true; public static java.util.Hashtable services = null; // vectors of services // stored by // abstractServiceType // string public static java.util.Vector serviceList = null; // flat list of services static private Vector getDiscoveryURLS() { Vector urls = new Vector(); String RootServiceURLs = jalview.bin.Cache .getDefault("DISCOVERY_URLS", "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry"); try { StringTokenizer st = new StringTokenizer(RootServiceURLs, ","); while (st.hasMoreElements()) { String url = null; try { java.net.URL u = new java.net.URL(url = st.nextToken()); if (!urls.contains(u)) { urls.add(u); } else { jalview.bin.Cache.log .info("Ignoring duplicate url in DISCOVERY_URLS list"); } } catch (Exception ex) { jalview.bin.Cache.log .warn("Problem whilst trying to make a URL from '" + ((url != null) ? url : "") + "'"); jalview.bin.Cache.log .warn("This was probably due to a malformed comma separated list" + " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)"); jalview.bin.Cache.log.debug("Exception was ", ex); } } } catch (Exception ex) { jalview.bin.Cache.log .warn("Error parsing comma separated list of urls in DISCOVERY_URLS.", ex); } if (urls.size() > 0) { return urls; } return null; } /** * fetch new services or reset to hardwired defaults depending on preferences. */ static public void doDiscovery() { jalview.bin.Cache.log .debug("(Re)-Initialising the discovery URL list."); try { reallyDiscoverServices = jalview.bin.Cache.getDefault( "DISCOVERY_START", false); if (reallyDiscoverServices) { ServiceURLList = getDiscoveryURLS(); } else { jalview.bin.Cache.log.debug("Setting default services"); services = new Hashtable(); // Muscle, Clustal and JPred. ServiceHandle[] defServices = { new ServiceHandle( "MsaWS", "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.", "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS", "Muscle Multiple Protein Sequence Alignment"), new ServiceHandle( "MsaWS", "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) " + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\"" + " Nucleic Acids Research, 33 511-518", "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS", "MAFFT Multiple Sequence Alignment"), new ServiceHandle( "MsaWS", "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." + " Nucleic Acids Research, 22 4673-4680", "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS", "ClustalW Multiple Sequence Alignment"), new ServiceHandle( "SecStrPred", "Cole C., Barber J. D., Barton G.J (2008) " + "The Jpred 3 secondary structure prediction server " + "Nucleic Acids Research, 36 W197-W201", "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred", - "JNet Secondary Structure Prediction") }; + "JNet Secondary Structure Prediction"), + new ServiceHandle( + "D2P2Pred", + "Oates,M.E., Romero,P., Ishida,T., Ghalwash,M., Mizianty,M.J., Xue,B., Dosztányi,S., Uversky,V.N., Obradovic,Z., Kurgan,L., Dunker,A.K., Gough,J. (2013)" + + "D2P2: Database of Disordered Protein Predictions. " + + "Nucleic Acids Research 41(D1):D508-D516", + "http://d2p2.pro/api/seqid", + "Database of Disordered Protein Predictions") + }; services = new Hashtable(); serviceList = new Vector(); buildServiceLists(defServices, serviceList, services); } } catch (Exception e) { System.err .println("jalview.rootRegistry is not a proper url!\nWas set to " + RootServiceURL + "\n" + e); } } // TODO: JBPNote : make this discover more services based on list of // discovery service urls, break cyclic references to the same url and // duplicate service entries (same endpoint *and* same interface) private ServiceHandle[] getServices(java.net.URL location) { ServiceHandles shs = null; try { jalview.bin.Cache.log.debug("Discovering services using " + location); shs = locateWebService(location).getServices(); } catch (org.apache.axis.AxisFault f) { // JBPNote - should do this a better way! if (f.getFaultReason().indexOf("(407)") > -1) { if (jalview.gui.Desktop.desktop != null) { JOptionPane .showMessageDialog( jalview.gui.Desktop.desktop, "Please set up your proxy settings in the 'Connections' tab of the Preferences window", "Proxy Authorization Failed", JOptionPane.WARNING_MESSAGE); } } else { jalview.bin.Cache.log.warn("No Discovery service at " + location); jalview.bin.Cache.log.debug("Axis Fault", f); } } catch (Exception e) { jalview.bin.Cache.log.warn("No Discovery service at " + location); jalview.bin.Cache.log.debug("Discovery Service General Exception", e); } if ((shs != null) && shs.getServices().length > 0) { return shs.getServices(); } return null; } /** * Adds a list of services to the service catalog and categorised catalog * returns true if ServiceURLList was modified with a new DiscoveryService URL * * @param sh * ServiceHandle[] * @param cat * Vector * @param sscat * Hashtable * @return boolean */ static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat, Hashtable sscat) { boolean seenNewDiscovery = false; for (int i = 0, j = sh.length; i < j; i++) { if (!cat.contains(sh[i])) { jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName() + " service called " + sh[i].getName() + " exists at " + sh[i].getEndpointURL() + "\n"); if (!sscat.containsKey(sh[i].getAbstractName())) { sscat.put(sh[i].getAbstractName(), cat = new Vector()); } else { cat = (Vector) sscat.get(sh[i].getAbstractName()); } cat.add(sh[i]); if (sh[i].getAbstractName().equals("Registry")) { for (int s = 0, sUrls = ServiceURLList.size(); s < sUrls; s++) { java.net.URL disc_serv = null; try { disc_serv = new java.net.URL(sh[i].getEndpointURL()); if (!ServiceURLList.contains(disc_serv)) { jalview.bin.Cache.log .debug("Adding new discovery service at " + disc_serv); ServiceURLList.add(disc_serv); seenNewDiscovery = true; } } catch (Exception e) { jalview.bin.Cache.log.debug( "Ignoring bad discovery service URL " + sh[i].getEndpointURL(), e); } } } } } return seenNewDiscovery; } public void discoverServices() { Hashtable sscat = new Hashtable(); Vector cat = new Vector(); ServiceHandle sh[] = null; int s_url = 0; if (ServiceURLList == null) { jalview.bin.Cache.log .debug("No service endpoints to use for service discovery."); return; } while (s_url < ServiceURLList.size()) { if ((sh = getServices((java.net.URL) ServiceURLList.get(s_url))) != null) { buildServiceLists(sh, cat, sscat); } else { jalview.bin.Cache.log .warn("No services at " + ((java.net.URL) ServiceURLList.get(s_url)) + " - check DISCOVERY_URLS property in .jalview_properties"); } s_url++; } // TODO: decide on correct semantics for services list - PropertyChange // provides a way of passing the new object around // so no need to access original discovery thread. // Curent decision is to change properties then notify listeners with old // and new values. Hashtable oldServices = services; // Vector oldServicelist = serviceList; services = sscat; serviceList = cat; changeSupport.firePropertyChange("services", oldServices, services); } /** * creates a new thread to call discoverServices() */ public void run() { final Discoverer discoverer = this; Thread discoverThread = new Thread() { public void run() { discoverer.doDiscovery(); discoverer.discoverServices(); } }; discoverThread.start(); } /** * binding service abstract name to handler class */ private static Hashtable serviceClientBindings; public static WS1Client getServiceClient(ServiceHandle sh) { if (serviceClientBindings == null) { // get a list from Config or create below serviceClientBindings = new Hashtable(); serviceClientBindings.put("MsaWS", new MsaWSClient()); serviceClientBindings.put("SecStrPred", new JPredClient()); serviceClientBindings.put("SeqSearch", new SeqSearchWSClient()); + serviceClientBindings.put("D2P2Pred", new D2P2WSClient()); } WS1Client instance = (WS1Client) serviceClientBindings.get(sh .getAbstractName()); if (instance == null) { System.err .println("WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for " + sh.getAbstractName()); } else { instance.serviceHandle = sh; } return instance; } /** * notes on discovery service 1. need to allow multiple discovery source urls. * 2. user interface to add/control list of urls in preferences notes on * wsclient discovery 1. need a classpath property with list of additional * plugin directories 2. optional config to cite specific bindings between * class name and Abstract service name. 3. precedence for automatic discovery * by using getAbstractName for WSClient - user added plugins override default * plugins ? notes on wsclient gui code for gui attachment now moved to * wsclient implementation. Needs more abstraction but approach seems to work. * is it possible to 'generalise' the data retrieval calls further ? current * methods are very specific (gatherForMSA or gatherForSeqOrMsaSecStrPred), * new methods for conservation (group or alignment), treecalc (aligned * profile), seqannot (sequences selected from dataset, annotation back to * dataset). * */ } diff --git a/src/jalview/ws/jws2/D2P2WSClient.java b/src/jalview/ws/jws2/D2P2WSClient.java new file mode 100644 index 0000000..9a600f9 --- /dev/null +++ b/src/jalview/ws/jws2/D2P2WSClient.java @@ -0,0 +1,131 @@ +package jalview.ws.jws2; + +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.params.WsParamSetI; + +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.io.IOException; +import java.io.InputStreamReader; +import java.net.MalformedURLException; +import java.net.URL; +import java.net.URLConnection; +import java.util.ArrayList; +import java.util.List; + +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; + +import org.json.simple.JSONObject; +import org.json.simple.parser.ParseException; + +import compbio.metadata.Argument; + +public class D2P2WSClient extends Jws2Client { + private static String d2p2URL = "http://d2p2.pro/api/seqid/"; + private URL url = null; + private URLConnection con = null; + public D2P2WSClient() { + super(); + } + + public D2P2WSClient(Jws2Instance sh, AlignFrame alignFrame, + WsParamSetI preset, List arguments) { + super(alignFrame, preset, arguments); + + if ((wsInfo = setWebService(sh, false)) == null) + { + JOptionPane.showMessageDialog(Desktop.desktop, + "The D2P2 Service named " + + sh.serviceType + " is unknown", + "Internal Jalview Error", JOptionPane.WARNING_MESSAGE); + + return; + } + List seqsToQuery = new ArrayList(); + seqsToQuery.add("P04637"); + this.getResults(seqsToQuery); + + } + + private void buildURL(List ids) { + StringBuilder built_url = new StringBuilder(d2p2URL).append("["); + for (String id : ids) { + built_url.append("\""); + built_url.append(id); + built_url.append("\","); + } + built_url.replace(built_url.lastIndexOf(","), + built_url.lastIndexOf(",") + 1, "]"); + try { + url = new URL(built_url.toString()); + } catch (MalformedURLException e) { + JOptionPane.showMessageDialog(Desktop.desktop, + "D2P2 request URL was malformed.", "Internal Jalview Error",JOptionPane.WARNING_MESSAGE); + } + } + + private void connect() { + try { + con = url.openConnection(); + con.setDoInput(true); + } catch (IOException e) { + JOptionPane.showMessageDialog(Desktop.desktop, + "Couldn't connect to the D2P2 service.", "Internal Jalview Error", JOptionPane.WARNING_MESSAGE); + } + } + + public String getResults(List ids) { + JSONObject results = null; + buildURL(ids); + connect(); + + org.json.simple.parser.JSONParser jp = new org.json.simple.parser.JSONParser(); + try { + results = (JSONObject) jp.parse(new InputStreamReader(con.getInputStream())); + } catch (IOException e) { + e.printStackTrace(); + JOptionPane.showMessageDialog(Desktop.desktop, + "Error parsing the response", "Internal Jalview Error", JOptionPane.WARNING_MESSAGE); + } catch (ParseException e) { + e.printStackTrace(); + JOptionPane.showMessageDialog(Desktop.desktop, + "Error parsing the response", "Internal Jalview Error", JOptionPane.WARNING_MESSAGE); + } + return results.toJSONString(); + } + + @Override + void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service, final AlignFrame alignFrame) { + setWebService(service, true); + JMenu p2s2menu = wsmenu; + p2s2menu = new JMenu(WebServiceName); + wsmenu.add(p2s2menu); + JMenuItem method = new JMenuItem("Invoke"); + method.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + new D2P2WSClient(service, alignFrame, null, null); + } + }); + p2s2menu.add(method); + + } + + /** + * @param args + */ + public static void main(String[] args) { + // TODO Auto-generated method stub + D2P2WSClient client = new D2P2WSClient(); + List seqsToQuery = new ArrayList(); + seqsToQuery.add("P04637"); + System.out.println(client.getResults(seqsToQuery)); + + } + +}