2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 import jalview.analysis.AAFrequency;
21 import jalview.analysis.AlignmentSorter;
22 import jalview.analysis.Conservation;
23 import jalview.analysis.CrossRef;
24 import jalview.analysis.NJTree;
25 import jalview.analysis.ParseProperties;
26 import jalview.analysis.SequenceIdMatcher;
27 import jalview.bin.Cache;
28 import jalview.commands.CommandI;
29 import jalview.commands.EditCommand;
30 import jalview.commands.OrderCommand;
31 import jalview.commands.RemoveGapColCommand;
32 import jalview.commands.RemoveGapsCommand;
33 import jalview.commands.SlideSequencesCommand;
34 import jalview.commands.TrimRegionCommand;
35 import jalview.datamodel.AlignedCodonFrame;
36 import jalview.datamodel.Alignment;
37 import jalview.datamodel.AlignmentAnnotation;
38 import jalview.datamodel.AlignmentI;
39 import jalview.datamodel.AlignmentOrder;
40 import jalview.datamodel.AlignmentView;
41 import jalview.datamodel.ColumnSelection;
42 import jalview.datamodel.PDBEntry;
43 import jalview.datamodel.SeqCigar;
44 import jalview.datamodel.Sequence;
45 import jalview.datamodel.SequenceGroup;
46 import jalview.datamodel.SequenceI;
47 import jalview.io.AlignmentProperties;
48 import jalview.io.AnnotationFile;
49 import jalview.io.FeaturesFile;
50 import jalview.io.FileLoader;
51 import jalview.io.FormatAdapter;
52 import jalview.io.HTMLOutput;
53 import jalview.io.IdentifyFile;
54 import jalview.io.JalviewFileChooser;
55 import jalview.io.JalviewFileView;
56 import jalview.io.JnetAnnotationMaker;
57 import jalview.io.NewickFile;
58 import jalview.io.TCoffeeScoreFile;
59 import jalview.jbgui.GAlignFrame;
60 import jalview.schemes.Blosum62ColourScheme;
61 import jalview.schemes.BuriedColourScheme;
62 import jalview.schemes.ClustalxColourScheme;
63 import jalview.schemes.ColourSchemeI;
64 import jalview.schemes.ColourSchemeProperty;
65 import jalview.schemes.HelixColourScheme;
66 import jalview.schemes.HydrophobicColourScheme;
67 import jalview.schemes.NucleotideColourScheme;
68 import jalview.schemes.PIDColourScheme;
69 import jalview.schemes.PurinePyrimidineColourScheme;
70 import jalview.schemes.RNAHelicesColourChooser;
71 import jalview.schemes.ResidueProperties;
72 import jalview.schemes.StrandColourScheme;
73 import jalview.schemes.TCoffeeColourScheme;
74 import jalview.schemes.TaylorColourScheme;
75 import jalview.schemes.TurnColourScheme;
76 import jalview.schemes.UserColourScheme;
77 import jalview.schemes.ZappoColourScheme;
78 import jalview.ws.jws1.Discoverer;
79 import jalview.ws.jws2.Jws2Discoverer;
80 import jalview.ws.seqfetcher.DbSourceProxy;
82 import java.awt.BorderLayout;
83 import java.awt.Color;
84 import java.awt.Component;
85 import java.awt.GridLayout;
86 import java.awt.Rectangle;
87 import java.awt.Toolkit;
88 import java.awt.datatransfer.Clipboard;
89 import java.awt.datatransfer.DataFlavor;
90 import java.awt.datatransfer.StringSelection;
91 import java.awt.datatransfer.Transferable;
92 import java.awt.dnd.DnDConstants;
93 import java.awt.dnd.DropTargetDragEvent;
94 import java.awt.dnd.DropTargetDropEvent;
95 import java.awt.dnd.DropTargetEvent;
96 import java.awt.dnd.DropTargetListener;
97 import java.awt.event.ActionEvent;
98 import java.awt.event.ActionListener;
99 import java.awt.event.KeyAdapter;
100 import java.awt.event.KeyEvent;
101 import java.awt.event.MouseAdapter;
102 import java.awt.event.MouseEvent;
103 import java.awt.print.PageFormat;
104 import java.awt.print.PrinterJob;
105 import java.beans.PropertyChangeEvent;
108 import java.util.ArrayList;
109 import java.util.Enumeration;
110 import java.util.Hashtable;
111 import java.util.List;
112 import java.util.Vector;
114 import javax.swing.JButton;
115 import javax.swing.JEditorPane;
116 import javax.swing.JInternalFrame;
117 import javax.swing.JLabel;
118 import javax.swing.JLayeredPane;
119 import javax.swing.JMenu;
120 import javax.swing.JMenuItem;
121 import javax.swing.JOptionPane;
122 import javax.swing.JPanel;
123 import javax.swing.JProgressBar;
124 import javax.swing.JRadioButtonMenuItem;
125 import javax.swing.JScrollPane;
126 import javax.swing.SwingUtilities;
132 * @version $Revision$
134 public class AlignFrame extends GAlignFrame implements DropTargetListener,
139 public static final int DEFAULT_WIDTH = 700;
142 public static final int DEFAULT_HEIGHT = 500;
144 public AlignmentPanel alignPanel;
146 AlignViewport viewport;
148 Vector alignPanels = new Vector();
151 * Last format used to load or save alignments in this window
153 String currentFileFormat = null;
156 * Current filename for this alignment
158 String fileName = null;
161 * Creates a new AlignFrame object with specific width and height.
167 public AlignFrame(AlignmentI al, int width, int height)
169 this(al, null, width, height);
173 * Creates a new AlignFrame object with specific width, height and
179 * @param sequenceSetId
181 public AlignFrame(AlignmentI al, int width, int height,
182 String sequenceSetId)
184 this(al, null, width, height, sequenceSetId);
188 * Creates a new AlignFrame object with specific width, height and
194 * @param sequenceSetId
197 public AlignFrame(AlignmentI al, int width, int height,
198 String sequenceSetId, String viewId)
200 this(al, null, width, height, sequenceSetId, viewId);
204 * new alignment window with hidden columns
208 * @param hiddenColumns
209 * ColumnSelection or null
211 * Width of alignment frame
215 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
216 int width, int height)
218 this(al, hiddenColumns, width, height, null);
222 * Create alignment frame for al with hiddenColumns, a specific width and
223 * height, and specific sequenceId
226 * @param hiddenColumns
229 * @param sequenceSetId
232 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
233 int width, int height, String sequenceSetId)
235 this(al, hiddenColumns, width, height, sequenceSetId, null);
239 * Create alignment frame for al with hiddenColumns, a specific width and
240 * height, and specific sequenceId
243 * @param hiddenColumns
246 * @param sequenceSetId
251 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
252 int width, int height, String sequenceSetId, String viewId)
254 setSize(width, height);
255 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
257 alignPanel = new AlignmentPanel(this, viewport);
259 if (al.getDataset() == null)
264 addAlignmentPanel(alignPanel, true);
269 * Make a new AlignFrame from exisiting alignmentPanels
276 public AlignFrame(AlignmentPanel ap)
280 addAlignmentPanel(ap, false);
285 * initalise the alignframe from the underlying viewport data and the
290 if (viewport.getAlignmentConservationAnnotation() == null)
292 BLOSUM62Colour.setEnabled(false);
293 conservationMenuItem.setEnabled(false);
294 modifyConservation.setEnabled(false);
295 // PIDColour.setEnabled(false);
296 // abovePIDThreshold.setEnabled(false);
297 // modifyPID.setEnabled(false);
300 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
303 if (sortby.equals("Id"))
305 sortIDMenuItem_actionPerformed(null);
307 else if (sortby.equals("Pairwise Identity"))
309 sortPairwiseMenuItem_actionPerformed(null);
312 if (Desktop.desktop != null)
314 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
315 addServiceListeners();
316 setGUINucleotide(viewport.getAlignment().isNucleotide());
319 setMenusFromViewport(viewport);
320 buildSortByAnnotationScoresMenu();
321 if (viewport.wrapAlignment)
323 wrapMenuItem_actionPerformed(null);
326 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
328 this.overviewMenuItem_actionPerformed(null);
336 * Change the filename and format for the alignment, and enable the 'reload'
337 * button functionality.
344 public void setFileName(String file, String format)
347 currentFileFormat = format;
348 reload.setEnabled(true);
351 void addKeyListener()
353 addKeyListener(new KeyAdapter()
355 public void keyPressed(KeyEvent evt)
357 if (viewport.cursorMode
358 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
359 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
360 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
361 && Character.isDigit(evt.getKeyChar()))
362 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
364 switch (evt.getKeyCode())
367 case 27: // escape key
368 deselectAllSequenceMenuItem_actionPerformed(null);
372 case KeyEvent.VK_DOWN:
373 if (evt.isAltDown() || !viewport.cursorMode)
374 moveSelectedSequences(false);
375 if (viewport.cursorMode)
376 alignPanel.seqPanel.moveCursor(0, 1);
380 if (evt.isAltDown() || !viewport.cursorMode)
381 moveSelectedSequences(true);
382 if (viewport.cursorMode)
383 alignPanel.seqPanel.moveCursor(0, -1);
387 case KeyEvent.VK_LEFT:
388 if (evt.isAltDown() || !viewport.cursorMode)
389 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
391 alignPanel.seqPanel.moveCursor(-1, 0);
395 case KeyEvent.VK_RIGHT:
396 if (evt.isAltDown() || !viewport.cursorMode)
397 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
399 alignPanel.seqPanel.moveCursor(1, 0);
402 case KeyEvent.VK_SPACE:
403 if (viewport.cursorMode)
405 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
406 || evt.isShiftDown() || evt.isAltDown());
410 // case KeyEvent.VK_A:
411 // if (viewport.cursorMode)
413 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
414 // //System.out.println("A");
418 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
419 * System.out.println("closing bracket"); } break;
421 case KeyEvent.VK_DELETE:
422 case KeyEvent.VK_BACK_SPACE:
423 if (!viewport.cursorMode)
425 cut_actionPerformed(null);
429 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
430 || evt.isShiftDown() || evt.isAltDown());
436 if (viewport.cursorMode)
438 alignPanel.seqPanel.setCursorRow();
442 if (viewport.cursorMode && !evt.isControlDown())
444 alignPanel.seqPanel.setCursorColumn();
448 if (viewport.cursorMode)
450 alignPanel.seqPanel.setCursorPosition();
454 case KeyEvent.VK_ENTER:
455 case KeyEvent.VK_COMMA:
456 if (viewport.cursorMode)
458 alignPanel.seqPanel.setCursorRowAndColumn();
463 if (viewport.cursorMode)
465 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
469 if (viewport.cursorMode)
471 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
476 viewport.cursorMode = !viewport.cursorMode;
477 statusBar.setText("Keyboard editing mode is "
478 + (viewport.cursorMode ? "on" : "off"));
479 if (viewport.cursorMode)
481 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
482 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
484 alignPanel.seqPanel.seqCanvas.repaint();
490 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
491 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
493 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
495 javax.help.HelpBroker hb = hs.createHelpBroker();
496 hb.setCurrentID("home");
497 hb.setDisplayed(true);
498 } catch (Exception ex)
500 ex.printStackTrace();
505 boolean toggleSeqs = !evt.isControlDown();
506 boolean toggleCols = !evt.isShiftDown();
507 toggleHiddenRegions(toggleSeqs, toggleCols);
510 case KeyEvent.VK_PAGE_UP:
511 if (viewport.wrapAlignment)
513 alignPanel.scrollUp(true);
517 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
518 - viewport.endSeq + viewport.startSeq);
521 case KeyEvent.VK_PAGE_DOWN:
522 if (viewport.wrapAlignment)
524 alignPanel.scrollUp(false);
528 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
529 + viewport.endSeq - viewport.startSeq);
535 public void keyReleased(KeyEvent evt)
537 switch (evt.getKeyCode())
539 case KeyEvent.VK_LEFT:
540 if (evt.isAltDown() || !viewport.cursorMode)
541 viewport.firePropertyChange("alignment", null, viewport
542 .getAlignment().getSequences());
545 case KeyEvent.VK_RIGHT:
546 if (evt.isAltDown() || !viewport.cursorMode)
547 viewport.firePropertyChange("alignment", null, viewport
548 .getAlignment().getSequences());
555 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
557 ap.alignFrame = this;
559 alignPanels.addElement(ap);
561 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
563 int aSize = alignPanels.size();
565 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
567 if (aSize == 1 && ap.av.viewName == null)
569 this.getContentPane().add(ap, BorderLayout.CENTER);
575 setInitialTabVisible();
578 expandViews.setEnabled(true);
579 gatherViews.setEnabled(true);
580 tabbedPane.addTab(ap.av.viewName, ap);
582 ap.setVisible(false);
587 if (ap.av.isPadGaps())
589 ap.av.getAlignment().padGaps();
591 ap.av.updateConservation(ap);
592 ap.av.updateConsensus(ap);
593 ap.av.updateStrucConsensus(ap);
597 public void setInitialTabVisible()
599 expandViews.setEnabled(true);
600 gatherViews.setEnabled(true);
601 tabbedPane.setVisible(true);
602 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
603 tabbedPane.addTab(first.av.viewName, first);
604 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
607 public AlignViewport getViewport()
612 /* Set up intrinsic listeners for dynamically generated GUI bits. */
613 private void addServiceListeners()
615 final java.beans.PropertyChangeListener thisListener;
616 Desktop.instance.addJalviewPropertyChangeListener("services",
617 thisListener = new java.beans.PropertyChangeListener()
619 public void propertyChange(PropertyChangeEvent evt)
621 // // System.out.println("Discoverer property change.");
622 // if (evt.getPropertyName().equals("services"))
624 SwingUtilities.invokeLater(new Runnable()
630 .println("Rebuild WS Menu for service change");
631 BuildWebServiceMenu();
638 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
640 public void internalFrameClosed(
641 javax.swing.event.InternalFrameEvent evt)
643 System.out.println("deregistering discoverer listener");
644 Desktop.instance.removeJalviewPropertyChangeListener("services",
646 closeMenuItem_actionPerformed(true);
649 // Finally, build the menu once to get current service state
650 new Thread(new Runnable()
654 BuildWebServiceMenu();
659 public void setGUINucleotide(boolean nucleotide)
661 showTranslation.setVisible(nucleotide);
662 conservationMenuItem.setEnabled(!nucleotide);
663 modifyConservation.setEnabled(!nucleotide);
664 showGroupConservation.setEnabled(!nucleotide);
665 rnahelicesColour.setEnabled(nucleotide);
666 purinePyrimidineColour.setEnabled(nucleotide);
667 // Remember AlignFrame always starts as protein
671 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
676 * set up menus for the currently viewport. This may be called after any
677 * operation that affects the data in the current view (selection changed,
678 * etc) to update the menus to reflect the new state.
680 public void setMenusForViewport()
682 setMenusFromViewport(viewport);
686 * Need to call this method when tabs are selected for multiple views, or when
687 * loading from Jalview2XML.java
692 void setMenusFromViewport(AlignViewport av)
694 padGapsMenuitem.setSelected(av.isPadGaps());
695 colourTextMenuItem.setSelected(av.showColourText);
696 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
697 conservationMenuItem.setSelected(av.getConservationSelected());
698 seqLimits.setSelected(av.getShowJVSuffix());
699 idRightAlign.setSelected(av.rightAlignIds);
700 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
701 renderGapsMenuItem.setSelected(av.renderGaps);
702 wrapMenuItem.setSelected(av.wrapAlignment);
703 scaleAbove.setVisible(av.wrapAlignment);
704 scaleLeft.setVisible(av.wrapAlignment);
705 scaleRight.setVisible(av.wrapAlignment);
706 annotationPanelMenuItem.setState(av.showAnnotation);
707 viewBoxesMenuItem.setSelected(av.showBoxes);
708 viewTextMenuItem.setSelected(av.showText);
709 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
710 showGroupConsensus.setSelected(av.isShowGroupConsensus());
711 showGroupConservation.setSelected(av.isShowGroupConservation());
712 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
713 showSequenceLogo.setSelected(av.isShowSequenceLogo());
714 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
716 setColourSelected(ColourSchemeProperty.getColourName(av
717 .getGlobalColourScheme()));
719 showSeqFeatures.setSelected(av.showSequenceFeatures);
720 hiddenMarkers.setState(av.showHiddenMarkers);
721 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
722 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
723 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
724 autoCalculate.setSelected(av.autoCalculateConsensus);
725 sortByTree.setSelected(av.sortByTree);
726 listenToViewSelections.setSelected(av.followSelection);
727 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
729 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
730 setShowProductsEnabled();
735 Hashtable progressBars, progressBarHandlers;
740 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
742 public void setProgressBar(String message, long id)
744 if (progressBars == null)
746 progressBars = new Hashtable();
747 progressBarHandlers = new Hashtable();
750 JPanel progressPanel;
751 Long lId = new Long(id);
752 GridLayout layout = (GridLayout) statusPanel.getLayout();
753 if (progressBars.get(lId) != null)
755 progressPanel = (JPanel) progressBars.get(new Long(id));
756 statusPanel.remove(progressPanel);
757 progressBars.remove(lId);
758 progressPanel = null;
761 statusBar.setText(message);
763 if (progressBarHandlers.contains(lId))
765 progressBarHandlers.remove(lId);
767 layout.setRows(layout.getRows() - 1);
771 progressPanel = new JPanel(new BorderLayout(10, 5));
773 JProgressBar progressBar = new JProgressBar();
774 progressBar.setIndeterminate(true);
776 progressPanel.add(new JLabel(message), BorderLayout.WEST);
777 progressPanel.add(progressBar, BorderLayout.CENTER);
779 layout.setRows(layout.getRows() + 1);
780 statusPanel.add(progressPanel);
782 progressBars.put(lId, progressPanel);
785 // setMenusForViewport();
789 public void registerHandler(final long id,
790 final IProgressIndicatorHandler handler)
792 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
795 "call setProgressBar before registering the progress bar's handler.");
797 progressBarHandlers.put(new Long(id), handler);
798 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
799 if (handler.canCancel())
801 JButton cancel = new JButton("Cancel");
802 final IProgressIndicator us = this;
803 cancel.addActionListener(new ActionListener()
806 public void actionPerformed(ActionEvent e)
808 handler.cancelActivity(id);
811 + ((JLabel) progressPanel.getComponent(0))
815 progressPanel.add(cancel, BorderLayout.EAST);
821 * @return true if any progress bars are still active
823 public boolean operationInProgress()
825 if (progressBars != null && progressBars.size() > 0)
833 * Added so Castor Mapping file can obtain Jalview Version
835 public String getVersion()
837 return jalview.bin.Cache.getProperty("VERSION");
840 public FeatureRenderer getFeatureRenderer()
842 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
845 public void fetchSequence_actionPerformed(ActionEvent e)
847 new SequenceFetcher(this);
850 public void addFromFile_actionPerformed(ActionEvent e)
852 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
855 public void reload_actionPerformed(ActionEvent e)
857 if (fileName != null)
859 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
860 // originating file's format
861 // TODO: work out how to recover feature settings for correct view(s) when
863 if (currentFileFormat.equals("Jalview"))
865 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
866 for (int i = 0; i < frames.length; i++)
868 if (frames[i] instanceof AlignFrame && frames[i] != this
869 && ((AlignFrame) frames[i]).fileName.equals(fileName))
873 frames[i].setSelected(true);
874 Desktop.instance.closeAssociatedWindows();
875 } catch (java.beans.PropertyVetoException ex)
881 Desktop.instance.closeAssociatedWindows();
883 FileLoader loader = new FileLoader();
884 String protocol = fileName.startsWith("http:") ? "URL" : "File";
885 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
889 Rectangle bounds = this.getBounds();
891 FileLoader loader = new FileLoader();
892 String protocol = fileName.startsWith("http:") ? "URL" : "File";
893 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
894 protocol, currentFileFormat);
896 newframe.setBounds(bounds);
897 if (featureSettings != null && featureSettings.isShowing())
899 final Rectangle fspos = featureSettings.frame.getBounds();
900 // TODO: need a 'show feature settings' function that takes bounds -
901 // need to refactor Desktop.addFrame
902 newframe.featureSettings_actionPerformed(null);
903 final FeatureSettings nfs = newframe.featureSettings;
904 SwingUtilities.invokeLater(new Runnable()
908 nfs.frame.setBounds(fspos);
911 this.featureSettings.close();
912 this.featureSettings = null;
914 this.closeMenuItem_actionPerformed(true);
919 public void addFromText_actionPerformed(ActionEvent e)
921 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
924 public void addFromURL_actionPerformed(ActionEvent e)
926 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
929 public void save_actionPerformed(ActionEvent e)
932 || (currentFileFormat == null || !jalview.io.FormatAdapter
933 .isValidIOFormat(currentFileFormat, true))
934 || fileName.startsWith("http"))
936 saveAs_actionPerformed(null);
940 saveAlignment(fileName, currentFileFormat);
950 public void saveAs_actionPerformed(ActionEvent e)
952 JalviewFileChooser chooser = new JalviewFileChooser(
953 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
954 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
955 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
956 currentFileFormat, false);
958 chooser.setFileView(new JalviewFileView());
959 chooser.setDialogTitle("Save Alignment to file");
960 chooser.setToolTipText("Save");
962 int value = chooser.showSaveDialog(this);
964 if (value == JalviewFileChooser.APPROVE_OPTION)
966 currentFileFormat = chooser.getSelectedFormat();
967 if (currentFileFormat == null)
969 JOptionPane.showInternalMessageDialog(Desktop.desktop,
970 "You must select a file format before saving!",
971 "File format not specified", JOptionPane.WARNING_MESSAGE);
972 value = chooser.showSaveDialog(this);
976 fileName = chooser.getSelectedFile().getPath();
978 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
981 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
982 if (currentFileFormat.indexOf(" ") > -1)
984 currentFileFormat = currentFileFormat.substring(0,
985 currentFileFormat.indexOf(" "));
987 saveAlignment(fileName, currentFileFormat);
991 public boolean saveAlignment(String file, String format)
993 boolean success = true;
995 if (format.equalsIgnoreCase("Jalview"))
997 String shortName = title;
999 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1001 shortName = shortName.substring(shortName
1002 .lastIndexOf(java.io.File.separatorChar) + 1);
1005 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1007 statusBar.setText("Successfully saved to file: " + fileName + " in "
1008 + format + " format.");
1013 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1015 warningMessage("Cannot save file " + fileName + " using format "
1016 + format, "Alignment output format not supported");
1017 saveAs_actionPerformed(null);
1018 // JBPNote need to have a raise_gui flag here
1022 String[] omitHidden = null;
1024 if (viewport.hasHiddenColumns())
1026 int reply = JOptionPane
1027 .showInternalConfirmDialog(
1029 "The Alignment contains hidden columns."
1030 + "\nDo you want to save only the visible alignment?",
1031 "Save / Omit Hidden Columns",
1032 JOptionPane.YES_NO_OPTION,
1033 JOptionPane.QUESTION_MESSAGE);
1035 if (reply == JOptionPane.YES_OPTION)
1037 omitHidden = viewport.getViewAsString(false);
1040 FormatAdapter f = new FormatAdapter();
1041 String output = f.formatSequences(
1043 (Alignment) viewport.getAlignment(), // class cast exceptions will
1044 // occur in the distant future
1045 omitHidden, f.getCacheSuffixDefault(format),
1046 viewport.getColumnSelection());
1056 java.io.PrintWriter out = new java.io.PrintWriter(
1057 new java.io.FileWriter(file));
1061 this.setTitle(file);
1062 statusBar.setText("Successfully saved to file: " + fileName
1063 + " in " + format + " format.");
1064 } catch (Exception ex)
1067 ex.printStackTrace();
1074 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
1075 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
1081 private void warningMessage(String warning, String title)
1083 if (new jalview.util.Platform().isHeadless())
1085 System.err.println("Warning: " + title + "\nWarning: " + warning);
1090 JOptionPane.showInternalMessageDialog(this, warning, title,
1091 JOptionPane.WARNING_MESSAGE);
1102 protected void outputText_actionPerformed(ActionEvent e)
1104 String[] omitHidden = null;
1106 if (viewport.hasHiddenColumns())
1108 int reply = JOptionPane
1109 .showInternalConfirmDialog(
1111 "The Alignment contains hidden columns."
1112 + "\nDo you want to output only the visible alignment?",
1113 "Save / Omit Hidden Columns",
1114 JOptionPane.YES_NO_OPTION,
1115 JOptionPane.QUESTION_MESSAGE);
1117 if (reply == JOptionPane.YES_OPTION)
1119 omitHidden = viewport.getViewAsString(false);
1123 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1124 cap.setForInput(null);
1128 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1129 viewport.getAlignment(), omitHidden,
1130 viewport.getColumnSelection()));
1131 Desktop.addInternalFrame(cap,
1132 "Alignment output - " + e.getActionCommand(), 600, 500);
1133 } catch (OutOfMemoryError oom)
1135 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1147 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1149 new HTMLOutput(alignPanel,
1150 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1151 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1154 public void createImageMap(File file, String image)
1156 alignPanel.makePNGImageMap(file, image);
1165 public void createPNG(File f)
1167 alignPanel.makePNG(f);
1176 public void createEPS(File f)
1178 alignPanel.makeEPS(f);
1181 public void pageSetup_actionPerformed(ActionEvent e)
1183 PrinterJob printJob = PrinterJob.getPrinterJob();
1184 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1193 public void printMenuItem_actionPerformed(ActionEvent e)
1195 // Putting in a thread avoids Swing painting problems
1196 PrintThread thread = new PrintThread(alignPanel);
1200 public void exportFeatures_actionPerformed(ActionEvent e)
1202 new AnnotationExporter().exportFeatures(alignPanel);
1205 public void exportAnnotations_actionPerformed(ActionEvent e)
1207 new AnnotationExporter().exportAnnotations(alignPanel,
1208 viewport.showAnnotation ? viewport.getAlignment()
1209 .getAlignmentAnnotation() : null, viewport
1210 .getAlignment().getGroups(), ((Alignment) viewport
1211 .getAlignment()).alignmentProperties);
1214 public void associatedData_actionPerformed(ActionEvent e)
1216 // Pick the tree file
1217 JalviewFileChooser chooser = new JalviewFileChooser(
1218 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1219 chooser.setFileView(new JalviewFileView());
1220 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1221 chooser.setToolTipText("Load Jalview Annotations / Features file");
1223 int value = chooser.showOpenDialog(null);
1225 if (value == JalviewFileChooser.APPROVE_OPTION)
1227 String choice = chooser.getSelectedFile().getPath();
1228 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1229 loadJalviewDataFile(choice, null, null, null);
1235 * Close the current view or all views in the alignment frame. If the frame
1236 * only contains one view then the alignment will be removed from memory.
1238 * @param closeAllTabs
1240 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1242 if (alignPanels != null && alignPanels.size() < 2)
1244 closeAllTabs = true;
1249 if (alignPanels != null)
1253 if (this.isClosed())
1255 // really close all the windows - otherwise wait till
1256 // setClosed(true) is called
1257 for (int i = 0; i < alignPanels.size(); i++)
1259 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1266 closeView(alignPanel);
1272 this.setClosed(true);
1274 } catch (Exception ex)
1276 ex.printStackTrace();
1281 * close alignPanel2 and shuffle tabs appropriately.
1283 * @param alignPanel2
1285 public void closeView(AlignmentPanel alignPanel2)
1287 int index = tabbedPane.getSelectedIndex();
1288 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1289 alignPanels.removeElement(alignPanel2);
1291 // if (viewport == alignPanel2.av)
1295 alignPanel2.closePanel();
1298 tabbedPane.removeTabAt(closedindex);
1299 tabbedPane.validate();
1301 if (index > closedindex || index == tabbedPane.getTabCount())
1303 // modify currently selected tab index if necessary.
1307 this.tabSelectionChanged(index);
1313 void updateEditMenuBar()
1316 if (viewport.historyList.size() > 0)
1318 undoMenuItem.setEnabled(true);
1319 CommandI command = (CommandI) viewport.historyList.peek();
1320 undoMenuItem.setText("Undo " + command.getDescription());
1324 undoMenuItem.setEnabled(false);
1325 undoMenuItem.setText("Undo");
1328 if (viewport.redoList.size() > 0)
1330 redoMenuItem.setEnabled(true);
1332 CommandI command = (CommandI) viewport.redoList.peek();
1333 redoMenuItem.setText("Redo " + command.getDescription());
1337 redoMenuItem.setEnabled(false);
1338 redoMenuItem.setText("Redo");
1342 public void addHistoryItem(CommandI command)
1344 if (command.getSize() > 0)
1346 viewport.historyList.push(command);
1347 viewport.redoList.clear();
1348 updateEditMenuBar();
1349 viewport.updateHiddenColumns();
1350 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1351 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1352 // viewport.getColumnSelection()
1353 // .getHiddenColumns().size() > 0);
1359 * @return alignment objects for all views
1361 AlignmentI[] getViewAlignments()
1363 if (alignPanels != null)
1365 Enumeration e = alignPanels.elements();
1366 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1367 for (int i = 0; e.hasMoreElements(); i++)
1369 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1373 if (viewport != null)
1375 return new AlignmentI[]
1376 { viewport.getAlignment() };
1387 protected void undoMenuItem_actionPerformed(ActionEvent e)
1389 if (viewport.historyList.empty())
1391 CommandI command = (CommandI) viewport.historyList.pop();
1392 viewport.redoList.push(command);
1393 command.undoCommand(getViewAlignments());
1395 AlignViewport originalSource = getOriginatingSource(command);
1396 updateEditMenuBar();
1398 if (originalSource != null)
1400 if (originalSource != viewport)
1403 .warn("Implementation worry: mismatch of viewport origin for undo");
1405 originalSource.updateHiddenColumns();
1406 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1408 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1409 // viewport.getColumnSelection()
1410 // .getHiddenColumns().size() > 0);
1411 originalSource.firePropertyChange("alignment", null, originalSource
1412 .getAlignment().getSequences());
1422 protected void redoMenuItem_actionPerformed(ActionEvent e)
1424 if (viewport.redoList.size() < 1)
1429 CommandI command = (CommandI) viewport.redoList.pop();
1430 viewport.historyList.push(command);
1431 command.doCommand(getViewAlignments());
1433 AlignViewport originalSource = getOriginatingSource(command);
1434 updateEditMenuBar();
1436 if (originalSource != null)
1439 if (originalSource != viewport)
1442 .warn("Implementation worry: mismatch of viewport origin for redo");
1444 originalSource.updateHiddenColumns();
1445 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1447 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1448 // viewport.getColumnSelection()
1449 // .getHiddenColumns().size() > 0);
1450 originalSource.firePropertyChange("alignment", null, originalSource
1451 .getAlignment().getSequences());
1455 AlignViewport getOriginatingSource(CommandI command)
1457 AlignViewport originalSource = null;
1458 // For sequence removal and addition, we need to fire
1459 // the property change event FROM the viewport where the
1460 // original alignment was altered
1461 AlignmentI al = null;
1462 if (command instanceof EditCommand)
1464 EditCommand editCommand = (EditCommand) command;
1465 al = editCommand.getAlignment();
1466 Vector comps = (Vector) PaintRefresher.components.get(viewport
1467 .getSequenceSetId());
1469 for (int i = 0; i < comps.size(); i++)
1471 if (comps.elementAt(i) instanceof AlignmentPanel)
1473 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1475 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1482 if (originalSource == null)
1484 // The original view is closed, we must validate
1485 // the current view against the closed view first
1488 PaintRefresher.validateSequences(al, viewport.getAlignment());
1491 originalSource = viewport;
1494 return originalSource;
1503 public void moveSelectedSequences(boolean up)
1505 SequenceGroup sg = viewport.getSelectionGroup();
1514 for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
1516 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
1518 if (!sg.getSequences(null).contains(seq))
1523 SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
1525 if (sg.getSequences(null).contains(temp))
1530 viewport.getAlignment().getSequences().setElementAt(temp, i);
1531 viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
1536 for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
1538 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
1540 if (!sg.getSequences(null).contains(seq))
1545 SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
1547 if (sg.getSequences(null).contains(temp))
1552 viewport.getAlignment().getSequences().setElementAt(temp, i);
1553 viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
1557 alignPanel.paintAlignment(true);
1560 synchronized void slideSequences(boolean right, int size)
1562 List<SequenceI> sg = new Vector();
1563 if (viewport.cursorMode)
1565 sg.add(viewport.getAlignment().getSequenceAt(
1566 alignPanel.seqPanel.seqCanvas.cursorY));
1568 else if (viewport.getSelectionGroup() != null
1569 && viewport.getSelectionGroup().getSize() != viewport
1570 .getAlignment().getHeight())
1572 sg = viewport.getSelectionGroup().getSequences(
1573 viewport.getHiddenRepSequences());
1581 Vector invertGroup = new Vector();
1583 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1585 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1586 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1589 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1591 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1592 for (int i = 0; i < invertGroup.size(); i++)
1593 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1595 SlideSequencesCommand ssc;
1597 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1598 size, viewport.getGapCharacter());
1600 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1601 size, viewport.getGapCharacter());
1603 int groupAdjustment = 0;
1604 if (ssc.getGapsInsertedBegin() && right)
1606 if (viewport.cursorMode)
1607 alignPanel.seqPanel.moveCursor(size, 0);
1609 groupAdjustment = size;
1611 else if (!ssc.getGapsInsertedBegin() && !right)
1613 if (viewport.cursorMode)
1614 alignPanel.seqPanel.moveCursor(-size, 0);
1616 groupAdjustment = -size;
1619 if (groupAdjustment != 0)
1621 viewport.getSelectionGroup().setStartRes(
1622 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1623 viewport.getSelectionGroup().setEndRes(
1624 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1627 boolean appendHistoryItem = false;
1628 if (viewport.historyList != null && viewport.historyList.size() > 0
1629 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1631 appendHistoryItem = ssc
1632 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1636 if (!appendHistoryItem)
1637 addHistoryItem(ssc);
1648 protected void copy_actionPerformed(ActionEvent e)
1651 if (viewport.getSelectionGroup() == null)
1655 // TODO: preserve the ordering of displayed alignment annotation in any
1656 // internal paste (particularly sequence associated annotation)
1657 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1658 String[] omitHidden = null;
1660 if (viewport.hasHiddenColumns())
1662 omitHidden = viewport.getViewAsString(true);
1665 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1668 StringSelection ss = new StringSelection(output);
1672 jalview.gui.Desktop.internalCopy = true;
1673 // Its really worth setting the clipboard contents
1674 // to empty before setting the large StringSelection!!
1675 Toolkit.getDefaultToolkit().getSystemClipboard()
1676 .setContents(new StringSelection(""), null);
1678 Toolkit.getDefaultToolkit().getSystemClipboard()
1679 .setContents(ss, Desktop.instance);
1680 } catch (OutOfMemoryError er)
1682 new OOMWarning("copying region", er);
1686 Vector hiddenColumns = null;
1687 if (viewport.hasHiddenColumns())
1689 hiddenColumns = new Vector();
1690 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1691 .getSelectionGroup().getEndRes();
1692 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1695 int[] region = (int[]) viewport.getColumnSelection()
1696 .getHiddenColumns().elementAt(i);
1697 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1699 hiddenColumns.addElement(new int[]
1700 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1705 Desktop.jalviewClipboard = new Object[]
1706 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1707 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1716 protected void pasteNew_actionPerformed(ActionEvent e)
1727 protected void pasteThis_actionPerformed(ActionEvent e)
1733 * Paste contents of Jalview clipboard
1735 * @param newAlignment
1736 * true to paste to a new alignment, otherwise add to this.
1738 void paste(boolean newAlignment)
1740 boolean externalPaste = true;
1743 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1744 Transferable contents = c.getContents(this);
1746 if (contents == null)
1754 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1755 if (str.length() < 1)
1760 format = new IdentifyFile().Identify(str, "Paste");
1762 } catch (OutOfMemoryError er)
1764 new OOMWarning("Out of memory pasting sequences!!", er);
1768 SequenceI[] sequences;
1769 boolean annotationAdded = false;
1770 AlignmentI alignment = null;
1772 if (Desktop.jalviewClipboard != null)
1774 // The clipboard was filled from within Jalview, we must use the
1776 // And dataset from the copied alignment
1777 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1778 // be doubly sure that we create *new* sequence objects.
1779 sequences = new SequenceI[newseq.length];
1780 for (int i = 0; i < newseq.length; i++)
1782 sequences[i] = new Sequence(newseq[i]);
1784 alignment = new Alignment(sequences);
1785 externalPaste = false;
1789 // parse the clipboard as an alignment.
1790 alignment = new FormatAdapter().readFile(str, "Paste", format);
1791 sequences = alignment.getSequencesArray();
1799 if (Desktop.jalviewClipboard != null)
1801 // dataset is inherited
1802 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1806 // new dataset is constructed
1807 alignment.setDataset(null);
1809 alwidth = alignment.getWidth() + 1;
1813 AlignmentI pastedal = alignment; // preserve pasted alignment object
1814 // Add pasted sequences and dataset into existing alignment.
1815 alignment = viewport.getAlignment();
1816 alwidth = alignment.getWidth() + 1;
1817 // decide if we need to import sequences from an existing dataset
1818 boolean importDs = Desktop.jalviewClipboard != null
1819 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1820 // importDs==true instructs us to copy over new dataset sequences from
1821 // an existing alignment
1822 Vector newDs = (importDs) ? new Vector() : null; // used to create
1823 // minimum dataset set
1825 for (int i = 0; i < sequences.length; i++)
1829 newDs.addElement(null);
1831 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1833 if (importDs && ds != null)
1835 if (!newDs.contains(ds))
1837 newDs.setElementAt(ds, i);
1838 ds = new Sequence(ds);
1839 // update with new dataset sequence
1840 sequences[i].setDatasetSequence(ds);
1844 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1849 // copy and derive new dataset sequence
1850 sequences[i] = sequences[i].deriveSequence();
1851 alignment.getDataset().addSequence(
1852 sequences[i].getDatasetSequence());
1853 // TODO: avoid creation of duplicate dataset sequences with a
1854 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1856 alignment.addSequence(sequences[i]); // merges dataset
1860 newDs.clear(); // tidy up
1862 if (pastedal.getAlignmentAnnotation() != null)
1864 // Add any annotation attached to alignment.
1865 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1866 for (int i = 0; i < alann.length; i++)
1868 annotationAdded = true;
1869 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1871 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1872 newann.padAnnotation(alwidth);
1873 alignment.addAnnotation(newann);
1883 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1884 sequences, 0, alignment.getWidth(), alignment));
1886 // Add any annotations attached to sequences
1887 for (int i = 0; i < sequences.length; i++)
1889 if (sequences[i].getAnnotation() != null)
1891 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1893 annotationAdded = true;
1894 sequences[i].getAnnotation()[a].adjustForAlignment();
1895 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1896 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1901 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1908 // propagate alignment changed.
1909 viewport.setEndSeq(alignment.getHeight());
1910 if (annotationAdded)
1912 // Duplicate sequence annotation in all views.
1913 AlignmentI[] alview = this.getViewAlignments();
1914 for (int i = 0; i < sequences.length; i++)
1916 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1919 for (int avnum = 0; avnum < alview.length; avnum++)
1921 if (alview[avnum] != alignment)
1923 // duplicate in a view other than the one with input focus
1924 int avwidth = alview[avnum].getWidth() + 1;
1925 // this relies on sann being preserved after we
1926 // modify the sequence's annotation array for each duplication
1927 for (int a = 0; a < sann.length; a++)
1929 AlignmentAnnotation newann = new AlignmentAnnotation(
1931 sequences[i].addAlignmentAnnotation(newann);
1932 newann.padAnnotation(avwidth);
1933 alview[avnum].addAnnotation(newann); // annotation was
1934 // duplicated earlier
1935 alview[avnum].setAnnotationIndex(newann, a);
1940 buildSortByAnnotationScoresMenu();
1942 viewport.firePropertyChange("alignment", null,
1943 alignment.getSequences());
1948 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1950 String newtitle = new String("Copied sequences");
1952 if (Desktop.jalviewClipboard != null
1953 && Desktop.jalviewClipboard[2] != null)
1955 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1956 for (int i = 0; i < hc.size(); i++)
1958 int[] region = (int[]) hc.elementAt(i);
1959 af.viewport.hideColumns(region[0], region[1]);
1963 // >>>This is a fix for the moment, until a better solution is
1965 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1967 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1969 // TODO: maintain provenance of an alignment, rather than just make the
1970 // title a concatenation of operations.
1973 if (title.startsWith("Copied sequences"))
1979 newtitle = newtitle.concat("- from " + title);
1984 newtitle = new String("Pasted sequences");
1987 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1992 } catch (Exception ex)
1994 ex.printStackTrace();
1995 System.out.println("Exception whilst pasting: " + ex);
1996 // could be anything being pasted in here
2007 protected void cut_actionPerformed(ActionEvent e)
2009 copy_actionPerformed(null);
2010 delete_actionPerformed(null);
2019 protected void delete_actionPerformed(ActionEvent evt)
2022 SequenceGroup sg = viewport.getSelectionGroup();
2028 Vector seqs = new Vector();
2030 for (int i = 0; i < sg.getSize(); i++)
2032 seq = sg.getSequenceAt(i);
2033 seqs.addElement(seq);
2036 // If the cut affects all sequences, remove highlighted columns
2037 if (sg.getSize() == viewport.getAlignment().getHeight())
2039 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2040 sg.getEndRes() + 1);
2043 SequenceI[] cut = new SequenceI[seqs.size()];
2044 for (int i = 0; i < seqs.size(); i++)
2046 cut[i] = (SequenceI) seqs.elementAt(i);
2050 * //ADD HISTORY ITEM
2052 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2053 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2054 viewport.getAlignment()));
2056 viewport.setSelectionGroup(null);
2057 viewport.sendSelection();
2058 viewport.getAlignment().deleteGroup(sg);
2060 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2062 if (viewport.getAlignment().getHeight() < 1)
2066 this.setClosed(true);
2067 } catch (Exception ex)
2079 protected void deleteGroups_actionPerformed(ActionEvent e)
2081 viewport.getAlignment().deleteAllGroups();
2082 viewport.sequenceColours = null;
2083 viewport.setSelectionGroup(null);
2084 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2085 alignPanel.updateAnnotation();
2086 alignPanel.paintAlignment(true);
2095 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2097 SequenceGroup sg = new SequenceGroup();
2099 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2101 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2104 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2105 viewport.setSelectionGroup(sg);
2106 viewport.sendSelection();
2107 alignPanel.paintAlignment(true);
2108 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2117 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2119 if (viewport.cursorMode)
2121 alignPanel.seqPanel.keyboardNo1 = null;
2122 alignPanel.seqPanel.keyboardNo2 = null;
2124 viewport.setSelectionGroup(null);
2125 viewport.getColumnSelection().clear();
2126 viewport.setSelectionGroup(null);
2127 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2128 alignPanel.idPanel.idCanvas.searchResults = null;
2129 alignPanel.paintAlignment(true);
2130 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2131 viewport.sendSelection();
2140 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2142 SequenceGroup sg = viewport.getSelectionGroup();
2146 selectAllSequenceMenuItem_actionPerformed(null);
2151 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2153 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2156 alignPanel.paintAlignment(true);
2157 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2158 viewport.sendSelection();
2161 public void invertColSel_actionPerformed(ActionEvent e)
2163 viewport.invertColumnSelection();
2164 alignPanel.paintAlignment(true);
2165 viewport.sendSelection();
2174 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2176 trimAlignment(true);
2185 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2187 trimAlignment(false);
2190 void trimAlignment(boolean trimLeft)
2192 ColumnSelection colSel = viewport.getColumnSelection();
2195 if (colSel.size() > 0)
2199 column = colSel.getMin();
2203 column = colSel.getMax();
2207 if (viewport.getSelectionGroup() != null)
2209 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2210 viewport.getHiddenRepSequences());
2214 seqs = viewport.getAlignment().getSequencesArray();
2217 TrimRegionCommand trimRegion;
2220 trimRegion = new TrimRegionCommand("Remove Left",
2221 TrimRegionCommand.TRIM_LEFT, seqs, column,
2222 viewport.getAlignment(), viewport.getColumnSelection(),
2223 viewport.getSelectionGroup());
2224 viewport.setStartRes(0);
2228 trimRegion = new TrimRegionCommand("Remove Right",
2229 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2230 viewport.getAlignment(), viewport.getColumnSelection(),
2231 viewport.getSelectionGroup());
2234 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2236 addHistoryItem(trimRegion);
2238 for (SequenceGroup sg :viewport.getAlignment().getGroups())
2240 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2241 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2243 viewport.getAlignment().deleteGroup(sg);
2247 viewport.firePropertyChange("alignment", null, viewport
2248 .getAlignment().getSequences());
2258 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2260 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2263 if (viewport.getSelectionGroup() != null)
2265 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2266 viewport.getHiddenRepSequences());
2267 start = viewport.getSelectionGroup().getStartRes();
2268 end = viewport.getSelectionGroup().getEndRes();
2272 seqs = viewport.getAlignment().getSequencesArray();
2275 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2276 "Remove Gapped Columns", seqs, start, end,
2277 viewport.getAlignment());
2279 addHistoryItem(removeGapCols);
2281 statusBar.setText("Removed " + removeGapCols.getSize()
2282 + " empty columns.");
2284 // This is to maintain viewport position on first residue
2285 // of first sequence
2286 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2287 int startRes = seq.findPosition(viewport.startRes);
2288 // ShiftList shifts;
2289 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2290 // edit.alColumnChanges=shifts.getInverse();
2291 // if (viewport.hasHiddenColumns)
2292 // viewport.getColumnSelection().compensateForEdits(shifts);
2293 viewport.setStartRes(seq.findIndex(startRes) - 1);
2294 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2305 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2307 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2310 if (viewport.getSelectionGroup() != null)
2312 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2313 viewport.getHiddenRepSequences());
2314 start = viewport.getSelectionGroup().getStartRes();
2315 end = viewport.getSelectionGroup().getEndRes();
2319 seqs = viewport.getAlignment().getSequencesArray();
2322 // This is to maintain viewport position on first residue
2323 // of first sequence
2324 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2325 int startRes = seq.findPosition(viewport.startRes);
2327 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2328 viewport.getAlignment()));
2330 viewport.setStartRes(seq.findIndex(startRes) - 1);
2332 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2343 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2345 viewport.setPadGaps(padGapsMenuitem.isSelected());
2346 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2352 // if (justifySeqs>0)
2354 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2366 public void findMenuItem_actionPerformed(ActionEvent e)
2371 public void newView_actionPerformed(ActionEvent e)
2378 * @param copyAnnotation
2379 * if true then duplicate all annnotation, groups and settings
2380 * @return new alignment panel, already displayed.
2382 public AlignmentPanel newView(boolean copyAnnotation)
2384 return newView(null, copyAnnotation);
2390 * title of newly created view
2391 * @return new alignment panel, already displayed.
2393 public AlignmentPanel newView(String viewTitle)
2395 return newView(viewTitle, true);
2401 * title of newly created view
2402 * @param copyAnnotation
2403 * if true then duplicate all annnotation, groups and settings
2404 * @return new alignment panel, already displayed.
2406 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2408 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2410 if (!copyAnnotation)
2412 // just remove all the current annotation except for the automatic stuff
2413 newap.av.getAlignment().deleteAllGroups();
2414 for (AlignmentAnnotation alan : newap.av.getAlignment()
2415 .getAlignmentAnnotation())
2417 if (!alan.autoCalculated)
2419 newap.av.getAlignment().deleteAnnotation(alan);
2425 newap.av.gatherViewsHere = false;
2427 if (viewport.viewName == null)
2429 viewport.viewName = "Original";
2432 newap.av.historyList = viewport.historyList;
2433 newap.av.redoList = viewport.redoList;
2435 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2436 // make sure the new view has a unique name - this is essential for Jalview
2438 boolean addFirstIndex = false;
2439 if (viewTitle == null || viewTitle.trim().length() == 0)
2442 addFirstIndex = true;
2446 index = 1;// we count from 1 if given a specific name
2448 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2449 Vector comps = (Vector) PaintRefresher.components.get(viewport
2450 .getSequenceSetId());
2451 Vector existingNames = new Vector();
2452 for (int i = 0; i < comps.size(); i++)
2454 if (comps.elementAt(i) instanceof AlignmentPanel)
2456 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2457 if (!existingNames.contains(ap.av.viewName))
2459 existingNames.addElement(ap.av.viewName);
2464 while (existingNames.contains(newViewName))
2466 newViewName = viewTitle + " " + (++index);
2469 newap.av.viewName = newViewName;
2471 addAlignmentPanel(newap, true);
2473 if (alignPanels.size() == 2)
2475 viewport.gatherViewsHere = true;
2477 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2481 public void expandViews_actionPerformed(ActionEvent e)
2483 Desktop.instance.explodeViews(this);
2486 public void gatherViews_actionPerformed(ActionEvent e)
2488 Desktop.instance.gatherViews(this);
2497 public void font_actionPerformed(ActionEvent e)
2499 new FontChooser(alignPanel);
2508 protected void seqLimit_actionPerformed(ActionEvent e)
2510 viewport.setShowJVSuffix(seqLimits.isSelected());
2512 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2513 .calculateIdWidth());
2514 alignPanel.paintAlignment(true);
2517 public void idRightAlign_actionPerformed(ActionEvent e)
2519 viewport.rightAlignIds = idRightAlign.isSelected();
2520 alignPanel.paintAlignment(true);
2523 public void centreColumnLabels_actionPerformed(ActionEvent e)
2525 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2526 alignPanel.paintAlignment(true);
2532 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2534 protected void followHighlight_actionPerformed()
2536 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2538 alignPanel.scrollToPosition(
2539 alignPanel.seqPanel.seqCanvas.searchResults, false);
2549 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2551 viewport.setColourText(colourTextMenuItem.isSelected());
2552 alignPanel.paintAlignment(true);
2561 public void wrapMenuItem_actionPerformed(ActionEvent e)
2563 scaleAbove.setVisible(wrapMenuItem.isSelected());
2564 scaleLeft.setVisible(wrapMenuItem.isSelected());
2565 scaleRight.setVisible(wrapMenuItem.isSelected());
2566 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2567 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2570 public void showAllSeqs_actionPerformed(ActionEvent e)
2572 viewport.showAllHiddenSeqs();
2575 public void showAllColumns_actionPerformed(ActionEvent e)
2577 viewport.showAllHiddenColumns();
2581 public void hideSelSequences_actionPerformed(ActionEvent e)
2583 viewport.hideAllSelectedSeqs();
2584 alignPanel.paintAlignment(true);
2588 * called by key handler and the hide all/show all menu items
2593 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2596 boolean hide = false;
2597 SequenceGroup sg = viewport.getSelectionGroup();
2598 if (!toggleSeqs && !toggleCols)
2600 // Hide everything by the current selection - this is a hack - we do the
2601 // invert and then hide
2602 // first check that there will be visible columns after the invert.
2603 if ((viewport.getColumnSelection() != null
2604 && viewport.getColumnSelection().getSelected() != null && viewport
2605 .getColumnSelection().getSelected().size() > 0)
2606 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2609 // now invert the sequence set, if required - empty selection implies
2610 // that no hiding is required.
2613 invertSequenceMenuItem_actionPerformed(null);
2614 sg = viewport.getSelectionGroup();
2618 viewport.expandColSelection(sg, true);
2619 // finally invert the column selection and get the new sequence
2621 invertColSel_actionPerformed(null);
2628 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2630 hideSelSequences_actionPerformed(null);
2633 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2636 showAllSeqs_actionPerformed(null);
2642 if (viewport.getColumnSelection().getSelected().size() > 0)
2644 hideSelColumns_actionPerformed(null);
2647 viewport.setSelectionGroup(sg);
2652 showAllColumns_actionPerformed(null);
2661 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2662 * event.ActionEvent)
2664 public void hideAllButSelection_actionPerformed(ActionEvent e)
2666 toggleHiddenRegions(false, false);
2673 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2676 public void hideAllSelection_actionPerformed(ActionEvent e)
2678 SequenceGroup sg = viewport.getSelectionGroup();
2679 viewport.expandColSelection(sg, false);
2680 viewport.hideAllSelectedSeqs();
2681 viewport.hideSelectedColumns();
2682 alignPanel.paintAlignment(true);
2689 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2692 public void showAllhidden_actionPerformed(ActionEvent e)
2694 viewport.showAllHiddenColumns();
2695 viewport.showAllHiddenSeqs();
2696 alignPanel.paintAlignment(true);
2699 public void hideSelColumns_actionPerformed(ActionEvent e)
2701 viewport.hideSelectedColumns();
2702 alignPanel.paintAlignment(true);
2705 public void hiddenMarkers_actionPerformed(ActionEvent e)
2707 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2717 protected void scaleAbove_actionPerformed(ActionEvent e)
2719 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2720 alignPanel.paintAlignment(true);
2729 protected void scaleLeft_actionPerformed(ActionEvent e)
2731 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2732 alignPanel.paintAlignment(true);
2741 protected void scaleRight_actionPerformed(ActionEvent e)
2743 viewport.setScaleRightWrapped(scaleRight.isSelected());
2744 alignPanel.paintAlignment(true);
2753 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2755 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2756 alignPanel.paintAlignment(true);
2765 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2767 viewport.setShowText(viewTextMenuItem.isSelected());
2768 alignPanel.paintAlignment(true);
2777 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2779 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2780 alignPanel.paintAlignment(true);
2783 public FeatureSettings featureSettings;
2785 public void featureSettings_actionPerformed(ActionEvent e)
2787 if (featureSettings != null)
2789 featureSettings.close();
2790 featureSettings = null;
2792 if (!showSeqFeatures.isSelected())
2794 // make sure features are actually displayed
2795 showSeqFeatures.setSelected(true);
2796 showSeqFeatures_actionPerformed(null);
2798 featureSettings = new FeatureSettings(this);
2802 * Set or clear 'Show Sequence Features'
2807 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2809 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2810 alignPanel.paintAlignment(true);
2811 if (alignPanel.getOverviewPanel() != null)
2813 alignPanel.getOverviewPanel().updateOverviewImage();
2818 * Set or clear 'Show Sequence Features'
2823 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2825 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2827 if (viewport.getShowSequenceFeaturesHeight())
2829 // ensure we're actually displaying features
2830 viewport.setShowSequenceFeatures(true);
2831 showSeqFeatures.setSelected(true);
2833 alignPanel.paintAlignment(true);
2834 if (alignPanel.getOverviewPanel() != null)
2836 alignPanel.getOverviewPanel().updateOverviewImage();
2846 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2848 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2849 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2852 public void alignmentProperties()
2854 JEditorPane editPane = new JEditorPane("text/html", "");
2855 editPane.setEditable(false);
2856 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
2858 editPane.setText("<html>" + contents.toString() + "</html>");
2859 JInternalFrame frame = new JInternalFrame();
2860 frame.getContentPane().add(new JScrollPane(editPane));
2862 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2863 + getTitle(), 500, 400);
2872 public void overviewMenuItem_actionPerformed(ActionEvent e)
2874 if (alignPanel.overviewPanel != null)
2879 JInternalFrame frame = new JInternalFrame();
2880 OverviewPanel overview = new OverviewPanel(alignPanel);
2881 frame.setContentPane(overview);
2882 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2883 frame.getWidth(), frame.getHeight());
2885 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2886 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2888 public void internalFrameClosed(
2889 javax.swing.event.InternalFrameEvent evt)
2891 alignPanel.setOverviewPanel(null);
2895 alignPanel.setOverviewPanel(overview);
2898 public void textColour_actionPerformed(ActionEvent e)
2900 new TextColourChooser().chooseColour(alignPanel, null);
2909 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2920 public void clustalColour_actionPerformed(ActionEvent e)
2922 changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences()));
2931 public void zappoColour_actionPerformed(ActionEvent e)
2933 changeColour(new ZappoColourScheme());
2942 public void taylorColour_actionPerformed(ActionEvent e)
2944 changeColour(new TaylorColourScheme());
2953 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2955 changeColour(new HydrophobicColourScheme());
2964 public void helixColour_actionPerformed(ActionEvent e)
2966 changeColour(new HelixColourScheme());
2975 public void strandColour_actionPerformed(ActionEvent e)
2977 changeColour(new StrandColourScheme());
2986 public void turnColour_actionPerformed(ActionEvent e)
2988 changeColour(new TurnColourScheme());
2997 public void buriedColour_actionPerformed(ActionEvent e)
2999 changeColour(new BuriedColourScheme());
3008 public void nucleotideColour_actionPerformed(ActionEvent e)
3010 changeColour(new NucleotideColourScheme());
3013 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3015 changeColour(new PurinePyrimidineColourScheme());
3019 * public void covariationColour_actionPerformed(ActionEvent e) {
3021 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3024 public void annotationColour_actionPerformed(ActionEvent e)
3026 new AnnotationColourChooser(viewport, alignPanel);
3029 public void rnahelicesColour_actionPerformed(ActionEvent e)
3031 new RNAHelicesColourChooser(viewport, alignPanel);
3040 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3042 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3051 public void changeColour(ColourSchemeI cs)
3053 // TODO: compare with applet and pull up to model method
3058 if (viewport.getAbovePIDThreshold())
3060 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3063 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3065 viewport.setGlobalColourScheme(cs);
3069 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3072 if (viewport.getConservationSelected())
3075 Alignment al = (Alignment) viewport.getAlignment();
3076 Conservation c = new Conservation("All",
3077 ResidueProperties.propHash, 3, al.getSequences(), 0,
3081 c.verdict(false, viewport.getConsPercGaps());
3083 cs.setConservation(c);
3085 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3090 cs.setConservation(null);
3093 cs.setConsensus(viewport.getSequenceConsensusHash());
3096 viewport.setGlobalColourScheme(cs);
3098 if (viewport.getColourAppliesToAllGroups())
3102 for (SequenceGroup sg:viewport.getAlignment().getGroups())
3110 if (cs instanceof ClustalxColourScheme)
3112 sg.cs = new ClustalxColourScheme(sg, viewport
3113 .getHiddenRepSequences());
3115 else if (cs instanceof UserColourScheme)
3117 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3123 sg.cs = cs.getClass().newInstance();
3124 } catch (Exception ex)
3129 if (viewport.getAbovePIDThreshold()
3130 || cs instanceof PIDColourScheme
3131 || cs instanceof Blosum62ColourScheme)
3133 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3135 sg.cs.setConsensus(AAFrequency.calculate(
3136 sg.getSequences(viewport.getHiddenRepSequences()),
3137 sg.getStartRes(), sg.getEndRes() + 1));
3141 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3144 if (viewport.getConservationSelected())
3146 Conservation c = new Conservation("Group",
3147 ResidueProperties.propHash, 3, sg.getSequences(viewport
3148 .getHiddenRepSequences()), sg.getStartRes(),
3149 sg.getEndRes() + 1);
3151 c.verdict(false, viewport.getConsPercGaps());
3152 sg.cs.setConservation(c);
3156 sg.cs.setConservation(null);
3161 if (alignPanel.getOverviewPanel() != null)
3163 alignPanel.getOverviewPanel().updateOverviewImage();
3166 alignPanel.paintAlignment(true);
3175 protected void modifyPID_actionPerformed(ActionEvent e)
3177 if (viewport.getAbovePIDThreshold()
3178 && viewport.getGlobalColourScheme() != null)
3180 SliderPanel.setPIDSliderSource(alignPanel,
3181 viewport.getGlobalColourScheme(), "Background");
3182 SliderPanel.showPIDSlider();
3192 protected void modifyConservation_actionPerformed(ActionEvent e)
3194 if (viewport.getConservationSelected()
3195 && viewport.getGlobalColourScheme() != null)
3197 SliderPanel.setConservationSlider(alignPanel,
3198 viewport.getGlobalColourScheme(), "Background");
3199 SliderPanel.showConservationSlider();
3209 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3211 viewport.setConservationSelected(conservationMenuItem.isSelected());
3213 viewport.setAbovePIDThreshold(false);
3214 abovePIDThreshold.setSelected(false);
3216 changeColour(viewport.getGlobalColourScheme());
3218 modifyConservation_actionPerformed(null);
3227 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3229 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3231 conservationMenuItem.setSelected(false);
3232 viewport.setConservationSelected(false);
3234 changeColour(viewport.getGlobalColourScheme());
3236 modifyPID_actionPerformed(null);
3245 public void userDefinedColour_actionPerformed(ActionEvent e)
3247 if (e.getActionCommand().equals("User Defined..."))
3249 new UserDefinedColours(alignPanel, null);
3253 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3254 .getUserColourSchemes().get(e.getActionCommand());
3260 public void updateUserColourMenu()
3263 Component[] menuItems = colourMenu.getMenuComponents();
3264 int i, iSize = menuItems.length;
3265 for (i = 0; i < iSize; i++)
3267 if (menuItems[i].getName() != null
3268 && menuItems[i].getName().equals("USER_DEFINED"))
3270 colourMenu.remove(menuItems[i]);
3274 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3276 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3277 .getUserColourSchemes().keys();
3279 while (userColours.hasMoreElements())
3281 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3282 userColours.nextElement().toString());
3283 radioItem.setName("USER_DEFINED");
3284 radioItem.addMouseListener(new MouseAdapter()
3286 public void mousePressed(MouseEvent evt)
3288 if (evt.isControlDown()
3289 || SwingUtilities.isRightMouseButton(evt))
3291 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3293 int option = JOptionPane.showInternalConfirmDialog(
3294 jalview.gui.Desktop.desktop,
3295 "Remove from default list?",
3296 "Remove user defined colour",
3297 JOptionPane.YES_NO_OPTION);
3298 if (option == JOptionPane.YES_OPTION)
3300 jalview.gui.UserDefinedColours
3301 .removeColourFromDefaults(radioItem.getText());
3302 colourMenu.remove(radioItem);
3306 radioItem.addActionListener(new ActionListener()
3308 public void actionPerformed(ActionEvent evt)
3310 userDefinedColour_actionPerformed(evt);
3317 radioItem.addActionListener(new ActionListener()
3319 public void actionPerformed(ActionEvent evt)
3321 userDefinedColour_actionPerformed(evt);
3325 colourMenu.insert(radioItem, 15);
3326 colours.add(radioItem);
3337 public void PIDColour_actionPerformed(ActionEvent e)
3339 changeColour(new PIDColourScheme());
3348 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3350 changeColour(new Blosum62ColourScheme());
3359 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3361 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3362 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3363 .getAlignment().getSequenceAt(0), null);
3364 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3365 viewport.getAlignment()));
3366 alignPanel.paintAlignment(true);
3375 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3377 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3378 AlignmentSorter.sortByID(viewport.getAlignment());
3379 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3380 viewport.getAlignment()));
3381 alignPanel.paintAlignment(true);
3390 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3392 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3393 AlignmentSorter.sortByLength(viewport.getAlignment());
3394 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3395 viewport.getAlignment()));
3396 alignPanel.paintAlignment(true);
3405 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3407 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3408 AlignmentSorter.sortByGroup(viewport.getAlignment());
3409 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3410 viewport.getAlignment()));
3412 alignPanel.paintAlignment(true);
3421 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3423 new RedundancyPanel(alignPanel, this);
3432 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3434 if ((viewport.getSelectionGroup() == null)
3435 || (viewport.getSelectionGroup().getSize() < 2))
3437 JOptionPane.showInternalMessageDialog(this,
3438 "You must select at least 2 sequences.", "Invalid Selection",
3439 JOptionPane.WARNING_MESSAGE);
3443 JInternalFrame frame = new JInternalFrame();
3444 frame.setContentPane(new PairwiseAlignPanel(viewport));
3445 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3455 public void PCAMenuItem_actionPerformed(ActionEvent e)
3457 if (((viewport.getSelectionGroup() != null)
3458 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3459 .getSelectionGroup().getSize() > 0))
3460 || (viewport.getAlignment().getHeight() < 4))
3462 JOptionPane.showInternalMessageDialog(this,
3463 "Principal component analysis must take\n"
3464 + "at least 4 input sequences.",
3465 "Sequence selection insufficient",
3466 JOptionPane.WARNING_MESSAGE);
3471 new PCAPanel(alignPanel);
3474 public void autoCalculate_actionPerformed(ActionEvent e)
3476 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3477 if (viewport.autoCalculateConsensus)
3479 viewport.firePropertyChange("alignment", null, viewport
3480 .getAlignment().getSequences());
3484 public void sortByTreeOption_actionPerformed(ActionEvent e)
3486 viewport.sortByTree = sortByTree.isSelected();
3490 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3492 viewport.followSelection = listenToViewSelections.isSelected();
3501 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3503 NewTreePanel("AV", "PID", "Average distance tree using PID");
3512 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3514 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3523 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3525 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3534 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3536 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3549 void NewTreePanel(String type, String pwType, String title)
3553 if (viewport.getSelectionGroup() != null)
3555 if (viewport.getSelectionGroup().getSize() < 3)
3560 "You need to have more than two sequences selected to build a tree!",
3561 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3565 SequenceGroup sg = viewport.getSelectionGroup();
3567 /* Decide if the selection is a column region */
3568 for (SequenceI _s:sg.getSequences())
3570 if (_s.getLength() < sg
3576 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3577 + "Try using the Pad function in the edit menu,\n"
3578 + "or one of the multiple sequence alignment web services.",
3579 "Sequences in selection are not aligned",
3580 JOptionPane.WARNING_MESSAGE);
3586 title = title + " on region";
3587 tp = new TreePanel(alignPanel, type, pwType);
3591 // are the visible sequences aligned?
3592 if (!viewport.getAlignment().isAligned(false))
3597 "The sequences must be aligned before creating a tree.\n"
3598 + "Try using the Pad function in the edit menu,\n"
3599 + "or one of the multiple sequence alignment web services.",
3600 "Sequences not aligned",
3601 JOptionPane.WARNING_MESSAGE);
3606 if (viewport.getAlignment().getHeight() < 2)
3611 tp = new TreePanel(alignPanel, type, pwType);
3616 if (viewport.viewName != null)
3618 title += viewport.viewName + " of ";
3621 title += this.title;
3623 Desktop.addInternalFrame(tp, title, 600, 500);
3634 public void addSortByOrderMenuItem(String title,
3635 final AlignmentOrder order)
3637 final JMenuItem item = new JMenuItem("by " + title);
3639 item.addActionListener(new java.awt.event.ActionListener()
3641 public void actionPerformed(ActionEvent e)
3643 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3645 // TODO: JBPNote - have to map order entries to curent SequenceI
3647 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3649 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3652 alignPanel.paintAlignment(true);
3658 * Add a new sort by annotation score menu item
3661 * the menu to add the option to
3663 * the label used to retrieve scores for each sequence on the
3666 public void addSortByAnnotScoreMenuItem(JMenu sort,
3667 final String scoreLabel)
3669 final JMenuItem item = new JMenuItem(scoreLabel);
3671 item.addActionListener(new java.awt.event.ActionListener()
3673 public void actionPerformed(ActionEvent e)
3675 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3676 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3677 viewport.getAlignment());// ,viewport.getSelectionGroup());
3678 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3679 viewport.getAlignment()));
3680 alignPanel.paintAlignment(true);
3686 * last hash for alignment's annotation array - used to minimise cost of
3689 protected int _annotationScoreVectorHash;
3692 * search the alignment and rebuild the sort by annotation score submenu the
3693 * last alignment annotation vector hash is stored to minimize cost of
3694 * rebuilding in subsequence calls.
3697 public void buildSortByAnnotationScoresMenu()
3699 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3704 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3706 sortByAnnotScore.removeAll();
3707 // almost certainly a quicker way to do this - but we keep it simple
3708 Hashtable scoreSorts = new Hashtable();
3709 AlignmentAnnotation aann[];
3710 Enumeration sq = viewport.getAlignment().getSequences().elements();
3711 while (sq.hasMoreElements())
3713 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3714 for (int i = 0; aann != null && i < aann.length; i++)
3716 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3718 scoreSorts.put(aann[i].label, aann[i].label);
3722 Enumeration labels = scoreSorts.keys();
3723 while (labels.hasMoreElements())
3725 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3726 (String) labels.nextElement());
3728 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3731 _annotationScoreVectorHash = viewport.getAlignment()
3732 .getAlignmentAnnotation().hashCode();
3737 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3738 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3739 * call. Listeners are added to remove the menu item when the treePanel is
3740 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3744 * Displayed tree window.
3746 * SortBy menu item title.
3748 public void buildTreeMenu()
3750 sortByTreeMenu.removeAll();
3752 Vector comps = (Vector) PaintRefresher.components.get(viewport
3753 .getSequenceSetId());
3754 Vector treePanels = new Vector();
3755 int i, iSize = comps.size();
3756 for (i = 0; i < iSize; i++)
3758 if (comps.elementAt(i) instanceof TreePanel)
3760 treePanels.add(comps.elementAt(i));
3764 iSize = treePanels.size();
3768 sortByTreeMenu.setVisible(false);
3772 sortByTreeMenu.setVisible(true);
3774 for (i = 0; i < treePanels.size(); i++)
3776 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3777 final JMenuItem item = new JMenuItem(tp.getTitle());
3778 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3779 item.addActionListener(new java.awt.event.ActionListener()
3781 public void actionPerformed(ActionEvent e)
3783 tp.sortByTree_actionPerformed(null);
3784 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3789 sortByTreeMenu.add(item);
3793 public boolean sortBy(AlignmentOrder alorder, String undoname)
3795 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3796 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3797 if (undoname != null)
3799 addHistoryItem(new OrderCommand(undoname, oldOrder,
3800 viewport.getAlignment()));
3802 alignPanel.paintAlignment(true);
3807 * Work out whether the whole set of sequences or just the selected set will
3808 * be submitted for multiple alignment.
3811 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3813 // Now, check we have enough sequences
3814 AlignmentView msa = null;
3816 if ((viewport.getSelectionGroup() != null)
3817 && (viewport.getSelectionGroup().getSize() > 1))
3819 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3820 // some common interface!
3822 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3823 * SequenceI[sz = seqs.getSize(false)];
3825 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3826 * seqs.getSequenceAt(i); }
3828 msa = viewport.getAlignmentView(true);
3833 * Vector seqs = viewport.getAlignment().getSequences();
3835 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3837 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3838 * seqs.elementAt(i); } }
3840 msa = viewport.getAlignmentView(false);
3846 * Decides what is submitted to a secondary structure prediction service: the
3847 * first sequence in the alignment, or in the current selection, or, if the
3848 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3849 * region or the whole alignment. (where the first sequence in the set is the
3850 * one that the prediction will be for).
3852 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3854 AlignmentView seqs = null;
3856 if ((viewport.getSelectionGroup() != null)
3857 && (viewport.getSelectionGroup().getSize() > 0))
3859 seqs = viewport.getAlignmentView(true);
3863 seqs = viewport.getAlignmentView(false);
3865 // limit sequences - JBPNote in future - could spawn multiple prediction
3867 // TODO: viewport.getAlignment().isAligned is a global state - the local
3868 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3869 if (!viewport.getAlignment().isAligned(false))
3871 seqs.setSequences(new SeqCigar[]
3872 { seqs.getSequences()[0] });
3873 // TODO: if seqs.getSequences().length>1 then should really have warned
3886 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3888 // Pick the tree file
3889 JalviewFileChooser chooser = new JalviewFileChooser(
3890 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3891 chooser.setFileView(new JalviewFileView());
3892 chooser.setDialogTitle("Select a newick-like tree file");
3893 chooser.setToolTipText("Load a tree file");
3895 int value = chooser.showOpenDialog(null);
3897 if (value == JalviewFileChooser.APPROVE_OPTION)
3899 String choice = chooser.getSelectedFile().getPath();
3900 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3901 jalview.io.NewickFile fin = null;
3904 fin = new jalview.io.NewickFile(choice, "File");
3905 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3906 } catch (Exception ex)
3908 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3909 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3910 ex.printStackTrace();
3912 if (fin != null && fin.hasWarningMessage())
3914 JOptionPane.showMessageDialog(Desktop.desktop,
3915 fin.getWarningMessage(), "Possible problem with tree file",
3916 JOptionPane.WARNING_MESSAGE);
3922 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
3924 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3927 public TreePanel ShowNewickTree(NewickFile nf, String title)
3929 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3932 public TreePanel ShowNewickTree(NewickFile nf, String title,
3933 AlignmentView input)
3935 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3938 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3939 int h, int x, int y)
3941 return ShowNewickTree(nf, title, null, w, h, x, y);
3945 * Add a treeviewer for the tree extracted from a newick file object to the
3946 * current alignment view
3953 * Associated alignment input data (or null)
3962 * @return TreePanel handle
3964 public TreePanel ShowNewickTree(NewickFile nf, String title,
3965 AlignmentView input, int w, int h, int x, int y)
3967 TreePanel tp = null;
3973 if (nf.getTree() != null)
3975 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3981 tp.setLocation(x, y);
3984 Desktop.addInternalFrame(tp, title, w, h);
3986 } catch (Exception ex)
3988 ex.printStackTrace();
3994 private boolean buildingMenu = false;
3997 * Generates menu items and listener event actions for web service clients
4000 public void BuildWebServiceMenu()
4002 while (buildingMenu)
4006 System.err.println("Waiting for building menu to finish.");
4008 } catch (Exception e)
4013 final AlignFrame me = this;
4014 buildingMenu = true;
4015 new Thread(new Runnable()
4021 System.err.println("Building ws menu again "
4022 + Thread.currentThread());
4023 // TODO: add support for context dependent disabling of services based
4025 // alignment and current selection
4026 // TODO: add additional serviceHandle parameter to specify abstract
4028 // class independently of AbstractName
4029 // TODO: add in rediscovery GUI function to restart discoverer
4030 // TODO: group services by location as well as function and/or
4032 // object broker mechanism.
4033 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4034 final IProgressIndicator af = me;
4035 final JMenu msawsmenu = new JMenu("Alignment");
4036 final JMenu secstrmenu = new JMenu(
4037 "Secondary Structure Prediction");
4038 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4039 final JMenu analymenu = new JMenu("Analysis");
4040 final JMenu dismenu = new JMenu("Disorder");
4041 // JAL-940 - only show secondary structure prediction services from
4042 // the legacy server
4043 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4045 Discoverer.services != null && (Discoverer.services.size() > 0))
4047 // TODO: refactor to allow list of AbstractName/Handler bindings to
4049 // stored or retrieved from elsewhere
4050 Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4051 Vector secstrpr = (Vector) Discoverer.services
4053 Vector seqsrch = null; // (Vector)
4054 // Discoverer.services.get("SeqSearch");
4055 // TODO: move GUI generation code onto service implementation - so a
4056 // client instance attaches itself to the GUI with method call like
4057 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
4061 // Add any Multiple Sequence Alignment Services
4062 for (int i = 0, j = msaws.size(); i < j; i++)
4064 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
4066 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4067 .getServiceClient(sh);
4068 impl.attachWSMenuEntry(msawsmenu, me);
4072 if (secstrpr != null)
4074 // Add any secondary structure prediction services
4075 for (int i = 0, j = secstrpr.size(); i < j; i++)
4077 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4079 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4080 .getServiceClient(sh);
4081 impl.attachWSMenuEntry(secstrmenu, me);
4084 if (seqsrch != null)
4086 // Add any sequence search services
4087 for (int i = 0, j = seqsrch.size(); i < j; i++)
4089 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
4091 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4092 .getServiceClient(sh);
4093 impl.attachWSMenuEntry(seqsrchmenu, me);
4098 // Add all submenus in the order they should appear on the web
4100 wsmenu.add(msawsmenu);
4101 wsmenu.add(secstrmenu);
4102 wsmenu.add(dismenu);
4103 wsmenu.add(analymenu);
4104 // final ArrayList<JMenu> submens=new ArrayList<JMenu>();
4105 // submens.add(msawsmenu);
4106 // submens.add(secstrmenu);
4107 // submens.add(dismenu);
4108 // submens.add(analymenu);
4110 // No search services yet
4111 // wsmenu.add(seqsrchmenu);
4113 javax.swing.SwingUtilities.invokeLater(new Runnable()
4119 webService.removeAll();
4120 // first, add discovered services onto the webservices menu
4121 if (wsmenu.size() > 0)
4123 for (int i = 0, j = wsmenu.size(); i < j; i++)
4125 webService.add((JMenu) wsmenu.get(i));
4130 webService.add(me.webServiceNoServices);
4132 // TODO: move into separate menu builder class.
4133 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4135 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4136 if (jws2servs != null)
4138 if (jws2servs.hasServices())
4140 jws2servs.attachWSMenuEntry(webService, me);
4142 if (jws2servs.isRunning())
4144 JMenuItem tm = new JMenuItem(
4145 "Still discovering JABA Services");
4146 tm.setEnabled(false);
4152 build_urlServiceMenu(me.webService);
4153 build_fetchdbmenu(webService);
4154 for (JMenu item : wsmenu)
4156 if (item.getItemCount() == 0)
4158 item.setEnabled(false);
4162 item.setEnabled(true);
4165 } catch (Exception e)
4171 } catch (Exception e)
4176 buildingMenu = false;
4183 * construct any groupURL type service menu entries.
4187 private void build_urlServiceMenu(JMenu webService)
4189 // TODO: remove this code when 2.7 is released
4190 // DEBUG - alignmentView
4192 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4193 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4195 * @Override public void actionPerformed(ActionEvent e) {
4196 * jalview.datamodel.AlignmentView
4197 * .testSelectionViews(af.viewport.getAlignment(),
4198 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4200 * }); webService.add(testAlView);
4202 // TODO: refactor to RestClient discoverer and merge menu entries for
4203 // rest-style services with other types of analysis/calculation service
4204 // SHmmr test client - still being implemented.
4205 // DEBUG - alignmentView
4207 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4210 client.attachWSMenuEntry(
4211 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4215 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4217 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4223 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4224 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4225 * getProperty("LAST_DIRECTORY"));
4227 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4228 * to Vamsas file"); chooser.setToolTipText("Export");
4230 * int value = chooser.showSaveDialog(this);
4232 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4233 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4234 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4235 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4238 * prototype of an automatically enabled/disabled analysis function
4241 protected void setShowProductsEnabled()
4243 SequenceI[] selection = viewport.getSequenceSelection();
4244 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4245 viewport.getAlignment().getDataset()))
4247 showProducts.setEnabled(true);
4252 showProducts.setEnabled(false);
4257 * search selection for sequence xRef products and build the show products
4262 * @return true if showProducts menu should be enabled.
4264 public boolean canShowProducts(SequenceI[] selection,
4265 boolean isRegionSelection, Alignment dataset)
4267 boolean showp = false;
4270 showProducts.removeAll();
4271 final boolean dna = viewport.getAlignment().isNucleotide();
4272 final Alignment ds = dataset;
4273 String[] ptypes = (selection == null || selection.length == 0) ? null
4274 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4276 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4277 // selection, dataset, true);
4278 final SequenceI[] sel = selection;
4279 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4282 final boolean isRegSel = isRegionSelection;
4283 final AlignFrame af = this;
4284 final String source = ptypes[t];
4285 JMenuItem xtype = new JMenuItem(ptypes[t]);
4286 xtype.addActionListener(new ActionListener()
4289 public void actionPerformed(ActionEvent e)
4291 // TODO: new thread for this call with vis-delay
4292 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4293 isRegSel, dna, source);
4297 showProducts.add(xtype);
4299 showProducts.setVisible(showp);
4300 showProducts.setEnabled(showp);
4301 } catch (Exception e)
4303 jalview.bin.Cache.log
4304 .warn("canTranslate threw an exception - please report to help@jalview.org",
4311 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4312 boolean isRegSel, boolean dna, String source)
4314 final boolean fisRegSel = isRegSel;
4315 final boolean fdna = dna;
4316 final String fsrc = source;
4317 final AlignFrame ths = this;
4318 final SequenceI[] fsel = sel;
4319 Runnable foo = new Runnable()
4324 final long sttime = System.currentTimeMillis();
4325 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4328 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4332 Alignment prods = CrossRef
4333 .findXrefSequences(fsel, fdna, fsrc, ds);
4336 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4337 for (int s = 0; s < sprods.length; s++)
4339 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4340 if (ds.getSequences() == null
4341 || !ds.getSequences().contains(
4342 sprods[s].getDatasetSequence()))
4343 ds.addSequence(sprods[s].getDatasetSequence());
4344 sprods[s].updatePDBIds();
4346 Alignment al = new Alignment(sprods);
4347 AlignedCodonFrame[] cf = prods.getCodonFrames();
4349 for (int s = 0; cf != null && s < cf.length; s++)
4351 al.addCodonFrame(cf[s]);
4354 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4356 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4357 + " for " + ((fisRegSel) ? "selected region of " : "")
4359 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4364 System.err.println("No Sequences generated for xRef type "
4367 } catch (Exception e)
4369 jalview.bin.Cache.log.error(
4370 "Exception when finding crossreferences", e);
4371 } catch (OutOfMemoryError e)
4373 new OOMWarning("whilst fetching crossreferences", e);
4376 jalview.bin.Cache.log.error("Error when finding crossreferences",
4379 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4384 Thread frunner = new Thread(foo);
4388 public boolean canShowTranslationProducts(SequenceI[] selection,
4389 AlignmentI alignment)
4394 return (jalview.analysis.Dna.canTranslate(selection,
4395 viewport.getViewAsVisibleContigs(true)));
4396 } catch (Exception e)
4398 jalview.bin.Cache.log
4399 .warn("canTranslate threw an exception - please report to help@jalview.org",
4405 public void showProducts_actionPerformed(ActionEvent e)
4407 // /////////////////////////////
4408 // Collect Data to be translated/transferred
4410 SequenceI[] selection = viewport.getSequenceSelection();
4411 AlignmentI al = null;
4414 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4415 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4416 viewport.getAlignment().getDataset());
4417 } catch (Exception ex)
4420 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4427 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4428 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4432 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4433 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4434 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4438 public void showTranslation_actionPerformed(ActionEvent e)
4440 // /////////////////////////////
4441 // Collect Data to be translated/transferred
4443 SequenceI[] selection = viewport.getSequenceSelection();
4444 String[] seqstring = viewport.getViewAsString(true);
4445 AlignmentI al = null;
4448 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4449 viewport.getViewAsVisibleContigs(true), viewport
4450 .getGapCharacter(), viewport.getAlignment()
4451 .getAlignmentAnnotation(), viewport.getAlignment()
4452 .getWidth(), viewport.getAlignment().getDataset());
4453 } catch (Exception ex)
4456 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4463 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4464 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4468 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4469 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4470 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4475 * Try to load a features file onto the alignment.
4478 * contents or path to retrieve file
4480 * access mode of file (see jalview.io.AlignFile)
4481 * @return true if features file was parsed corectly.
4483 public boolean parseFeaturesFile(String file, String type)
4485 boolean featuresFile = false;
4488 featuresFile = new FeaturesFile(file, type).parse(viewport
4489 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4490 .getFeatureRenderer().featureColours, false,
4491 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4492 } catch (Exception ex)
4494 ex.printStackTrace();
4499 viewport.showSequenceFeatures = true;
4500 showSeqFeatures.setSelected(true);
4501 if (alignPanel.seqPanel.seqCanvas.fr != null)
4503 // update the min/max ranges where necessary
4504 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4506 if (featureSettings != null)
4508 featureSettings.setTableData();
4510 alignPanel.paintAlignment(true);
4513 return featuresFile;
4516 public void dragEnter(DropTargetDragEvent evt)
4520 public void dragExit(DropTargetEvent evt)
4524 public void dragOver(DropTargetDragEvent evt)
4528 public void dropActionChanged(DropTargetDragEvent evt)
4532 public void drop(DropTargetDropEvent evt)
4534 Transferable t = evt.getTransferable();
4535 java.util.List files = null;
4539 DataFlavor uriListFlavor = new DataFlavor(
4540 "text/uri-list;class=java.lang.String");
4541 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4543 // Works on Windows and MacOSX
4544 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4545 files = (java.util.List) t
4546 .getTransferData(DataFlavor.javaFileListFlavor);
4548 else if (t.isDataFlavorSupported(uriListFlavor))
4550 // This is used by Unix drag system
4551 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4552 String data = (String) t.getTransferData(uriListFlavor);
4553 files = new java.util.ArrayList(1);
4554 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4555 data, "\r\n"); st.hasMoreTokens();)
4557 String s = st.nextToken();
4558 if (s.startsWith("#"))
4560 // the line is a comment (as per the RFC 2483)
4564 java.net.URI uri = new java.net.URI(s);
4565 // check to see if we can handle this kind of URI
4566 if (uri.getScheme().toLowerCase().startsWith("http"))
4568 files.add(uri.toString());
4572 // otherwise preserve old behaviour: catch all for file objects
4573 java.io.File file = new java.io.File(uri);
4574 files.add(file.toString());
4578 } catch (Exception e)
4580 e.printStackTrace();
4586 // check to see if any of these files have names matching sequences in
4588 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4589 .getAlignment().getSequencesArray());
4591 * Object[] { String,SequenceI}
4593 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4594 ArrayList<String> filesnotmatched = new ArrayList<String>();
4595 for (int i = 0; i < files.size(); i++)
4597 String file = files.get(i).toString();
4599 String protocol = FormatAdapter.checkProtocol(file);
4600 if (protocol == jalview.io.FormatAdapter.FILE)
4602 File fl = new File(file);
4603 pdbfn = fl.getName();
4605 else if (protocol == jalview.io.FormatAdapter.URL)
4607 URL url = new URL(file);
4608 pdbfn = url.getFile();
4610 if (pdbfn.length() > 0)
4612 // attempt to find a match in the alignment
4613 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4614 int l = 0, c = pdbfn.indexOf(".");
4615 while (mtch == null && c != -1)
4620 } while ((c = pdbfn.indexOf(".", l)) > l);
4623 pdbfn = pdbfn.substring(0, l);
4625 mtch = idm.findAllIdMatches(pdbfn);
4632 type = new IdentifyFile().Identify(file, protocol);
4633 } catch (Exception ex)
4639 if (type.equalsIgnoreCase("PDB"))
4641 filesmatched.add(new Object[]
4642 { file, protocol, mtch });
4647 // File wasn't named like one of the sequences or wasn't a PDB file.
4648 filesnotmatched.add(file);
4652 if (filesmatched.size() > 0)
4654 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4658 "Do you want to automatically associate the "
4659 + filesmatched.size()
4660 + " PDB files with sequences in the alignment that have the same name ?",
4661 "Automatically Associate PDB files by name",
4662 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4665 for (Object[] fm : filesmatched)
4667 // try and associate
4668 // TODO: may want to set a standard ID naming formalism for
4669 // associating PDB files which have no IDs.
4670 for (SequenceI toassoc : (SequenceI[]) fm[2])
4672 PDBEntry pe = new AssociatePdbFileWithSeq()
4673 .associatePdbWithSeq((String) fm[0],
4674 (String) fm[1], toassoc, false);
4677 System.err.println("Associated file : "
4678 + ((String) fm[0]) + " with "
4679 + toassoc.getDisplayId(true));
4683 alignPanel.paintAlignment(true);
4687 if (filesnotmatched.size() > 0)
4690 && (Cache.getDefault(
4691 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4694 "<html>Do you want to <em>ignore</em> the "
4695 + filesnotmatched.size()
4696 + " files whose names did not match any sequence IDs ?</html>",
4697 "Ignore unmatched dropped files ?",
4698 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4702 for (String fn : filesnotmatched)
4704 loadJalviewDataFile(fn, null, null, null);
4708 } catch (Exception ex)
4710 ex.printStackTrace();
4716 * Attempt to load a "dropped" file or URL string: First by testing whether
4717 * it's and Annotation file, then a JNet file, and finally a features file. If
4718 * all are false then the user may have dropped an alignment file onto this
4722 * either a filename or a URL string.
4724 public void loadJalviewDataFile(String file, String protocol,
4725 String format, SequenceI assocSeq)
4729 if (protocol == null)
4731 protocol = jalview.io.FormatAdapter.checkProtocol(file);
4733 // if the file isn't identified, or not positively identified as some
4734 // other filetype (PFAM is default unidentified alignment file type) then
4735 // try to parse as annotation.
4736 boolean isAnnotation = (format == null || format
4737 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4738 .readAnnotationFile(viewport.getAlignment(), file, protocol)
4743 // first see if its a T-COFFEE score file
4744 TCoffeeScoreFile tcf = null;
4747 tcf = new TCoffeeScoreFile(file, protocol);
4750 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4752 tcoffeeColour.setEnabled(true);
4753 tcoffeeColour.setSelected(true);
4754 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4755 isAnnotation = true;
4757 .setText("Successfully pasted T-Coffee scores to alignment.");
4761 // some problem - if no warning its probable that the ID matching process didn't work
4762 JOptionPane.showMessageDialog(Desktop.desktop,
4763 tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(),
4764 "Problem reading T-COFFEE score file",
4765 JOptionPane.WARNING_MESSAGE);
4772 } catch (Exception x)
4774 Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
4779 // try to see if its a JNet 'concise' style annotation file *before*
4781 // try to parse it as a features file
4784 format = new IdentifyFile().Identify(file, protocol);
4786 if (format.equalsIgnoreCase("JnetFile"))
4788 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
4790 new JnetAnnotationMaker().add_annotation(predictions,
4791 viewport.getAlignment(), 0, false);
4792 isAnnotation = true;
4797 * if (format.equalsIgnoreCase("PDB")) {
4799 * String pdbfn = ""; // try to match up filename with sequence id
4800 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
4801 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
4802 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4803 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
4804 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4805 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
4806 * // attempt to find a match in the alignment SequenceI mtch =
4807 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4808 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
4809 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
4810 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
4811 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4812 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
4813 * { System.err.println("Associated file : " + file + " with " +
4814 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4815 * TODO: maybe need to load as normal otherwise return; } }
4817 // try to parse it as a features file
4818 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4819 // if it wasn't a features file then we just treat it as a general
4820 // alignment file to load into the current view.
4823 new FileLoader().LoadFile(viewport, file, protocol, format);
4827 alignPanel.paintAlignment(true);
4835 alignPanel.adjustAnnotationHeight();
4836 viewport.updateSequenceIdColours();
4837 buildSortByAnnotationScoresMenu();
4838 alignPanel.paintAlignment(true);
4840 } catch (Exception ex)
4842 ex.printStackTrace();
4846 public void tabSelectionChanged(int index)
4850 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4851 viewport = alignPanel.av;
4852 setMenusFromViewport(viewport);
4856 public void tabbedPane_mousePressed(MouseEvent e)
4858 if (SwingUtilities.isRightMouseButton(e))
4860 String reply = JOptionPane.showInternalInputDialog(this,
4861 "Enter View Name", "Edit View Name",
4862 JOptionPane.QUESTION_MESSAGE);
4866 viewport.viewName = reply;
4867 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4872 public AlignViewport getCurrentView()
4878 * Open the dialog for regex description parsing.
4880 protected void extractScores_actionPerformed(ActionEvent e)
4882 ParseProperties pp = new jalview.analysis.ParseProperties(
4883 viewport.getAlignment());
4884 // TODO: verify regex and introduce GUI dialog for version 2.5
4885 // if (pp.getScoresFromDescription("col", "score column ",
4886 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4888 if (pp.getScoresFromDescription("description column",
4889 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4891 buildSortByAnnotationScoresMenu();
4899 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4902 protected void showDbRefs_actionPerformed(ActionEvent e)
4904 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4910 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4913 protected void showNpFeats_actionPerformed(ActionEvent e)
4915 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4919 * find the viewport amongst the tabs in this alignment frame and close that
4924 public boolean closeView(AlignViewport av)
4928 this.closeMenuItem_actionPerformed(false);
4931 Component[] comp = tabbedPane.getComponents();
4932 for (int i = 0; comp != null && i < comp.length; i++)
4934 if (comp[i] instanceof AlignmentPanel)
4936 if (((AlignmentPanel) comp[i]).av == av)
4939 closeView((AlignmentPanel) comp[i]);
4947 protected void build_fetchdbmenu(JMenu webService)
4949 // Temporary hack - DBRef Fetcher always top level ws entry.
4950 // TODO We probably want to store a sequence database checklist in
4951 // preferences and have checkboxes.. rather than individual sources selected
4953 final JMenu rfetch = new JMenu("Fetch DB References");
4954 rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4955 webService.add(rfetch);
4957 JMenuItem fetchr = new JMenuItem("Standard Databases");
4958 fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4959 fetchr.addActionListener(new ActionListener()
4962 public void actionPerformed(ActionEvent e)
4964 new Thread(new Runnable()
4969 new jalview.ws.DBRefFetcher(alignPanel.av
4970 .getSequenceSelection(), alignPanel.alignFrame)
4971 .fetchDBRefs(false);
4979 final AlignFrame me = this;
4980 new Thread(new Runnable()
4984 final jalview.ws.SequenceFetcher sf = SequenceFetcher
4985 .getSequenceFetcherSingleton(me);
4986 javax.swing.SwingUtilities.invokeLater(new Runnable()
4990 String[] dbclasses = sf.getOrderedSupportedSources();
4991 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4992 // jalview.util.QuickSort.sort(otherdb, otherdb);
4993 List<DbSourceProxy> otherdb;
4994 JMenu dfetch = new JMenu();
4995 JMenu ifetch = new JMenu();
4996 JMenuItem fetchr = null;
4997 int comp = 0, icomp = 0, mcomp = 15;
4998 String mname = null;
5000 for (String dbclass : dbclasses)
5002 otherdb = sf.getSourceProxy(dbclass);
5003 // add a single entry for this class, or submenu allowing 'fetch
5005 if (otherdb == null || otherdb.size() < 1)
5009 // List<DbSourceProxy> dbs=otherdb;
5010 // otherdb=new ArrayList<DbSourceProxy>();
5011 // for (DbSourceProxy db:dbs)
5013 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5017 mname = "From " + dbclass;
5019 if (otherdb.size() == 1)
5021 final DbSourceProxy[] dassource = otherdb
5022 .toArray(new DbSourceProxy[0]);
5023 DbSourceProxy src = otherdb.get(0);
5024 fetchr = new JMenuItem(src.getDbSource());
5025 fetchr.addActionListener(new ActionListener()
5028 public void actionPerformed(ActionEvent e)
5030 new Thread(new Runnable()
5035 new jalview.ws.DBRefFetcher(alignPanel.av
5036 .getSequenceSelection(),
5037 alignPanel.alignFrame, dassource)
5038 .fetchDBRefs(false);
5044 fetchr.setToolTipText("<html>"
5045 + JvSwingUtils.wrapTooltip("Retrieve from "
5046 + src.getDbName()) + "<html>");
5052 final DbSourceProxy[] dassource = otherdb
5053 .toArray(new DbSourceProxy[0]);
5055 DbSourceProxy src = otherdb.get(0);
5056 fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
5058 fetchr.addActionListener(new ActionListener()
5060 public void actionPerformed(ActionEvent e)
5062 new Thread(new Runnable()
5067 new jalview.ws.DBRefFetcher(alignPanel.av
5068 .getSequenceSelection(),
5069 alignPanel.alignFrame, dassource)
5070 .fetchDBRefs(false);
5076 fetchr.setToolTipText("<html>"
5077 + JvSwingUtils.wrapTooltip("Retrieve from all "
5078 + otherdb.size() + " sources in "
5079 + src.getDbSource() + "<br>First is :"
5080 + src.getDbName()) + "<html>");
5083 // and then build the rest of the individual menus
5084 ifetch = new JMenu("Sources from " + src.getDbSource());
5086 String imname = null;
5088 for (DbSourceProxy sproxy : otherdb)
5090 String dbname = sproxy.getDbName();
5091 String sname = dbname.length() > 5 ? dbname.substring(0,
5092 5) + "..." : dbname;
5093 String msname = dbname.length() > 10 ? dbname.substring(
5094 0, 10) + "..." : dbname;
5097 imname = "from '" + sname + "'";
5099 fetchr = new JMenuItem(msname);
5100 final DbSourceProxy[] dassrc =
5102 fetchr.addActionListener(new ActionListener()
5105 public void actionPerformed(ActionEvent e)
5107 new Thread(new Runnable()
5112 new jalview.ws.DBRefFetcher(alignPanel.av
5113 .getSequenceSelection(),
5114 alignPanel.alignFrame, dassrc)
5115 .fetchDBRefs(false);
5121 fetchr.setToolTipText("<html>"
5122 + JvSwingUtils.wrapTooltip("Retrieve from "
5123 + dbname) + "</html>");
5126 if (++icomp >= mcomp || i == (otherdb.size()))
5128 ifetch.setText(imname + " to '" + sname + "'");
5130 ifetch = new JMenu();
5138 if (comp >= mcomp || dbi >= (dbclasses.length))
5140 dfetch.setText(mname + " to '" + dbclass + "'");
5142 dfetch = new JMenu();
5155 * Left justify the whole alignment.
5157 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5159 AlignmentI al = viewport.getAlignment();
5161 viewport.firePropertyChange("alignment", null, al);
5165 * Right justify the whole alignment.
5167 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5169 AlignmentI al = viewport.getAlignment();
5171 viewport.firePropertyChange("alignment", null, al);
5174 public void setShowSeqFeatures(boolean b)
5176 showSeqFeatures.setSelected(true);
5177 viewport.setShowSequenceFeatures(true);
5184 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5185 * awt.event.ActionEvent)
5187 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5189 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5190 alignPanel.paintAlignment(true);
5197 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5200 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5202 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5203 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5211 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5212 * .event.ActionEvent)
5214 protected void showGroupConservation_actionPerformed(ActionEvent e)
5216 viewport.setShowGroupConservation(showGroupConservation.getState());
5217 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5224 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5225 * .event.ActionEvent)
5227 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5229 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5230 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5237 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5238 * .event.ActionEvent)
5240 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5242 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5243 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5246 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5248 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5249 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5252 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5254 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5261 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5262 * .event.ActionEvent)
5264 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5266 if (viewport.getSelectionGroup() != null)
5268 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
5269 viewport.getSequenceSelection(),
5270 viewport.getAlignmentView(true).getSequenceStrings(
5271 viewport.getGapCharacter()), viewport.getAlignment()
5273 viewport.getAlignment().deleteAllGroups();
5274 viewport.sequenceColours = null;
5275 viewport.setSelectionGroup(null);
5276 // set view properties for each group
5277 for (int g = 0; g < gps.length; g++)
5279 gps[g].setShowNonconserved(viewport.getShowUnconserved());
5280 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
5281 viewport.getAlignment().addGroup(gps[g]);
5282 Color col = new Color((int) (Math.random() * 255),
5283 (int) (Math.random() * 255), (int) (Math.random() * 255));
5284 col = col.brighter();
5285 for (SequenceI s:gps[g].getSequences())
5286 viewport.setSequenceColour(
5290 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5291 alignPanel.updateAnnotation();
5292 alignPanel.paintAlignment(true);
5297 * make the given alignmentPanel the currently selected tab
5299 * @param alignmentPanel
5301 public void setDisplayedView(AlignmentPanel alignmentPanel)
5303 if (!viewport.getSequenceSetId().equals(
5304 alignmentPanel.av.getSequenceSetId()))
5307 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5309 if (tabbedPane != null
5310 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5311 .getSelectedIndex())
5313 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5318 class PrintThread extends Thread
5322 public PrintThread(AlignmentPanel ap)
5327 static PageFormat pf;
5331 PrinterJob printJob = PrinterJob.getPrinterJob();
5335 printJob.setPrintable(ap, pf);
5339 printJob.setPrintable(ap);
5342 if (printJob.printDialog())
5347 } catch (Exception PrintException)
5349 PrintException.printStackTrace();