2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.AlignmentSorter;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.analysis.CrossRef;
28 import jalview.analysis.NJTree;
29 import jalview.analysis.ParseProperties;
30 import jalview.analysis.SequenceIdMatcher;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.analysis.ScoreModelI;
34 import jalview.bin.Cache;
35 import jalview.commands.CommandI;
36 import jalview.commands.EditCommand;
37 import jalview.commands.OrderCommand;
38 import jalview.commands.RemoveGapColCommand;
39 import jalview.commands.RemoveGapsCommand;
40 import jalview.commands.SlideSequencesCommand;
41 import jalview.commands.TrimRegionCommand;
42 import jalview.datamodel.AlignedCodonFrame;
43 import jalview.datamodel.Alignment;
44 import jalview.datamodel.AlignmentAnnotation;
45 import jalview.datamodel.AlignmentI;
46 import jalview.datamodel.AlignmentOrder;
47 import jalview.datamodel.AlignmentView;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.PDBEntry;
50 import jalview.datamodel.SeqCigar;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AlignmentProperties;
55 import jalview.io.AnnotationFile;
56 import jalview.io.FeaturesFile;
57 import jalview.io.FileLoader;
58 import jalview.io.FormatAdapter;
59 import jalview.io.HTMLOutput;
60 import jalview.io.IdentifyFile;
61 import jalview.io.JalviewFileChooser;
62 import jalview.io.JalviewFileView;
63 import jalview.io.JnetAnnotationMaker;
64 import jalview.io.NewickFile;
65 import jalview.io.TCoffeeScoreFile;
66 import jalview.jbgui.GAlignFrame;
67 import jalview.schemes.Blosum62ColourScheme;
68 import jalview.schemes.BuriedColourScheme;
69 import jalview.schemes.ClustalxColourScheme;
70 import jalview.schemes.ColourSchemeI;
71 import jalview.schemes.ColourSchemeProperty;
72 import jalview.schemes.HelixColourScheme;
73 import jalview.schemes.HydrophobicColourScheme;
74 import jalview.schemes.NucleotideColourScheme;
75 import jalview.schemes.PIDColourScheme;
76 import jalview.schemes.PurinePyrimidineColourScheme;
77 import jalview.schemes.RNAHelicesColourChooser;
78 import jalview.schemes.ResidueProperties;
79 import jalview.schemes.StrandColourScheme;
80 import jalview.schemes.TCoffeeColourScheme;
81 import jalview.schemes.TaylorColourScheme;
82 import jalview.schemes.TurnColourScheme;
83 import jalview.schemes.UserColourScheme;
84 import jalview.schemes.ZappoColourScheme;
85 import jalview.util.MessageManager;
86 import jalview.ws.jws1.Discoverer;
87 import jalview.ws.jws2.Jws2Discoverer;
88 import jalview.ws.jws2.jabaws2.Jws2Instance;
89 import jalview.ws.seqfetcher.DbSourceProxy;
91 import java.awt.BorderLayout;
92 import java.awt.Component;
93 import java.awt.GridLayout;
94 import java.awt.Rectangle;
95 import java.awt.Toolkit;
96 import java.awt.datatransfer.Clipboard;
97 import java.awt.datatransfer.DataFlavor;
98 import java.awt.datatransfer.StringSelection;
99 import java.awt.datatransfer.Transferable;
100 import java.awt.dnd.DnDConstants;
101 import java.awt.dnd.DropTargetDragEvent;
102 import java.awt.dnd.DropTargetDropEvent;
103 import java.awt.dnd.DropTargetEvent;
104 import java.awt.dnd.DropTargetListener;
105 import java.awt.event.ActionEvent;
106 import java.awt.event.ActionListener;
107 import java.awt.event.KeyAdapter;
108 import java.awt.event.KeyEvent;
109 import java.awt.event.MouseAdapter;
110 import java.awt.event.MouseEvent;
111 import java.awt.print.PageFormat;
112 import java.awt.print.PrinterJob;
113 import java.beans.PropertyChangeEvent;
116 import java.util.ArrayList;
117 import java.util.Enumeration;
118 import java.util.Hashtable;
119 import java.util.List;
120 import java.util.Vector;
122 import javax.swing.JButton;
123 import javax.swing.JCheckBoxMenuItem;
124 import javax.swing.JEditorPane;
125 import javax.swing.JInternalFrame;
126 import javax.swing.JLabel;
127 import javax.swing.JLayeredPane;
128 import javax.swing.JMenu;
129 import javax.swing.JMenuItem;
130 import javax.swing.JOptionPane;
131 import javax.swing.JPanel;
132 import javax.swing.JProgressBar;
133 import javax.swing.JRadioButtonMenuItem;
134 import javax.swing.JScrollPane;
135 import javax.swing.SwingUtilities;
141 * @version $Revision$
143 public class AlignFrame extends GAlignFrame implements DropTargetListener,
144 IProgressIndicator, AlignViewControllerGuiI
148 public static final int DEFAULT_WIDTH = 700;
151 public static final int DEFAULT_HEIGHT = 500;
153 public AlignmentPanel alignPanel;
155 AlignViewport viewport;
157 public AlignViewControllerI avc;
159 Vector alignPanels = new Vector();
162 * Last format used to load or save alignments in this window
164 String currentFileFormat = null;
167 * Current filename for this alignment
169 String fileName = null;
172 * Creates a new AlignFrame object with specific width and height.
178 public AlignFrame(AlignmentI al, int width, int height)
180 this(al, null, width, height);
184 * Creates a new AlignFrame object with specific width, height and
190 * @param sequenceSetId
192 public AlignFrame(AlignmentI al, int width, int height,
193 String sequenceSetId)
195 this(al, null, width, height, sequenceSetId);
199 * Creates a new AlignFrame object with specific width, height and
205 * @param sequenceSetId
208 public AlignFrame(AlignmentI al, int width, int height,
209 String sequenceSetId, String viewId)
211 this(al, null, width, height, sequenceSetId, viewId);
215 * new alignment window with hidden columns
219 * @param hiddenColumns
220 * ColumnSelection or null
222 * Width of alignment frame
226 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
227 int width, int height)
229 this(al, hiddenColumns, width, height, null);
233 * Create alignment frame for al with hiddenColumns, a specific width and
234 * height, and specific sequenceId
237 * @param hiddenColumns
240 * @param sequenceSetId
243 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
244 int width, int height, String sequenceSetId)
246 this(al, hiddenColumns, width, height, sequenceSetId, null);
250 * Create alignment frame for al with hiddenColumns, a specific width and
251 * height, and specific sequenceId
254 * @param hiddenColumns
257 * @param sequenceSetId
262 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
263 int width, int height, String sequenceSetId, String viewId)
265 setSize(width, height);
267 if (al.getDataset() == null)
272 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
274 alignPanel = new AlignmentPanel(this, viewport);
277 addAlignmentPanel(alignPanel, true);
282 * Make a new AlignFrame from exisiting alignmentPanels
289 public AlignFrame(AlignmentPanel ap)
293 addAlignmentPanel(ap, false);
298 * initalise the alignframe from the underlying viewport data and the
303 avc = new jalview.controller.AlignViewController(this, viewport,
305 if (viewport.getAlignmentConservationAnnotation() == null)
307 BLOSUM62Colour.setEnabled(false);
308 conservationMenuItem.setEnabled(false);
309 modifyConservation.setEnabled(false);
310 // PIDColour.setEnabled(false);
311 // abovePIDThreshold.setEnabled(false);
312 // modifyPID.setEnabled(false);
315 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
318 if (sortby.equals("Id"))
320 sortIDMenuItem_actionPerformed(null);
322 else if (sortby.equals("Pairwise Identity"))
324 sortPairwiseMenuItem_actionPerformed(null);
327 if (Desktop.desktop != null)
329 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
330 addServiceListeners();
331 setGUINucleotide(viewport.getAlignment().isNucleotide());
334 setMenusFromViewport(viewport);
335 buildSortByAnnotationScoresMenu();
337 buildShowHideAnnotationMenus();
339 if (viewport.wrapAlignment)
341 wrapMenuItem_actionPerformed(null);
344 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
346 this.overviewMenuItem_actionPerformed(null);
354 * Change the filename and format for the alignment, and enable the 'reload'
355 * button functionality.
362 public void setFileName(String file, String format)
365 currentFileFormat = format;
366 reload.setEnabled(true);
369 void addKeyListener()
371 addKeyListener(new KeyAdapter()
374 public void keyPressed(KeyEvent evt)
376 if (viewport.cursorMode
377 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
378 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
379 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
380 && Character.isDigit(evt.getKeyChar()))
381 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
383 switch (evt.getKeyCode())
386 case 27: // escape key
387 deselectAllSequenceMenuItem_actionPerformed(null);
391 case KeyEvent.VK_DOWN:
392 if (evt.isAltDown() || !viewport.cursorMode)
393 moveSelectedSequences(false);
394 if (viewport.cursorMode)
395 alignPanel.seqPanel.moveCursor(0, 1);
399 if (evt.isAltDown() || !viewport.cursorMode)
400 moveSelectedSequences(true);
401 if (viewport.cursorMode)
402 alignPanel.seqPanel.moveCursor(0, -1);
406 case KeyEvent.VK_LEFT:
407 if (evt.isAltDown() || !viewport.cursorMode)
408 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
410 alignPanel.seqPanel.moveCursor(-1, 0);
414 case KeyEvent.VK_RIGHT:
415 if (evt.isAltDown() || !viewport.cursorMode)
416 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
418 alignPanel.seqPanel.moveCursor(1, 0);
421 case KeyEvent.VK_SPACE:
422 if (viewport.cursorMode)
424 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
425 || evt.isShiftDown() || evt.isAltDown());
429 // case KeyEvent.VK_A:
430 // if (viewport.cursorMode)
432 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
433 // //System.out.println("A");
437 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
438 * System.out.println("closing bracket"); } break;
440 case KeyEvent.VK_DELETE:
441 case KeyEvent.VK_BACK_SPACE:
442 if (!viewport.cursorMode)
444 cut_actionPerformed(null);
448 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
449 || evt.isShiftDown() || evt.isAltDown());
455 if (viewport.cursorMode)
457 alignPanel.seqPanel.setCursorRow();
461 if (viewport.cursorMode && !evt.isControlDown())
463 alignPanel.seqPanel.setCursorColumn();
467 if (viewport.cursorMode)
469 alignPanel.seqPanel.setCursorPosition();
473 case KeyEvent.VK_ENTER:
474 case KeyEvent.VK_COMMA:
475 if (viewport.cursorMode)
477 alignPanel.seqPanel.setCursorRowAndColumn();
482 if (viewport.cursorMode)
484 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
488 if (viewport.cursorMode)
490 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
495 viewport.cursorMode = !viewport.cursorMode;
496 statusBar.setText(MessageManager.formatMessage(
497 "label.keyboard_editing_mode", new String[]
498 { (viewport.cursorMode ? "on" : "off") }));
499 if (viewport.cursorMode)
501 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
502 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
504 alignPanel.seqPanel.seqCanvas.repaint();
510 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
511 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
513 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
515 javax.help.HelpBroker hb = hs.createHelpBroker();
516 hb.setCurrentID("home");
517 hb.setDisplayed(true);
518 } catch (Exception ex)
520 ex.printStackTrace();
525 boolean toggleSeqs = !evt.isControlDown();
526 boolean toggleCols = !evt.isShiftDown();
527 toggleHiddenRegions(toggleSeqs, toggleCols);
530 case KeyEvent.VK_PAGE_UP:
531 if (viewport.wrapAlignment)
533 alignPanel.scrollUp(true);
537 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
538 - viewport.endSeq + viewport.startSeq);
541 case KeyEvent.VK_PAGE_DOWN:
542 if (viewport.wrapAlignment)
544 alignPanel.scrollUp(false);
548 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
549 + viewport.endSeq - viewport.startSeq);
556 public void keyReleased(KeyEvent evt)
558 switch (evt.getKeyCode())
560 case KeyEvent.VK_LEFT:
561 if (evt.isAltDown() || !viewport.cursorMode)
562 viewport.firePropertyChange("alignment", null, viewport
563 .getAlignment().getSequences());
566 case KeyEvent.VK_RIGHT:
567 if (evt.isAltDown() || !viewport.cursorMode)
568 viewport.firePropertyChange("alignment", null, viewport
569 .getAlignment().getSequences());
576 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
578 ap.alignFrame = this;
579 avc = new jalview.controller.AlignViewController(this, viewport,
582 alignPanels.addElement(ap);
584 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
586 int aSize = alignPanels.size();
588 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
590 if (aSize == 1 && ap.av.viewName == null)
592 this.getContentPane().add(ap, BorderLayout.CENTER);
598 setInitialTabVisible();
601 expandViews.setEnabled(true);
602 gatherViews.setEnabled(true);
603 tabbedPane.addTab(ap.av.viewName, ap);
605 ap.setVisible(false);
610 if (ap.av.isPadGaps())
612 ap.av.getAlignment().padGaps();
614 ap.av.updateConservation(ap);
615 ap.av.updateConsensus(ap);
616 ap.av.updateStrucConsensus(ap);
620 public void setInitialTabVisible()
622 expandViews.setEnabled(true);
623 gatherViews.setEnabled(true);
624 tabbedPane.setVisible(true);
625 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
626 tabbedPane.addTab(first.av.viewName, first);
627 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
630 public AlignViewport getViewport()
635 /* Set up intrinsic listeners for dynamically generated GUI bits. */
636 private void addServiceListeners()
638 final java.beans.PropertyChangeListener thisListener;
639 Desktop.instance.addJalviewPropertyChangeListener("services",
640 thisListener = new java.beans.PropertyChangeListener()
643 public void propertyChange(PropertyChangeEvent evt)
645 // // System.out.println("Discoverer property change.");
646 // if (evt.getPropertyName().equals("services"))
648 SwingUtilities.invokeLater(new Runnable()
655 .println("Rebuild WS Menu for service change");
656 BuildWebServiceMenu();
663 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
666 public void internalFrameClosed(
667 javax.swing.event.InternalFrameEvent evt)
669 System.out.println("deregistering discoverer listener");
670 Desktop.instance.removeJalviewPropertyChangeListener("services",
672 closeMenuItem_actionPerformed(true);
675 // Finally, build the menu once to get current service state
676 new Thread(new Runnable()
681 BuildWebServiceMenu();
686 public void setGUINucleotide(boolean nucleotide)
688 showTranslation.setVisible(nucleotide);
689 conservationMenuItem.setEnabled(!nucleotide);
690 modifyConservation.setEnabled(!nucleotide);
691 showGroupConservation.setEnabled(!nucleotide);
692 rnahelicesColour.setEnabled(nucleotide);
693 purinePyrimidineColour.setEnabled(nucleotide);
694 // Remember AlignFrame always starts as protein
698 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
703 * set up menus for the currently viewport. This may be called after any
704 * operation that affects the data in the current view (selection changed,
705 * etc) to update the menus to reflect the new state.
707 public void setMenusForViewport()
709 setMenusFromViewport(viewport);
713 * Need to call this method when tabs are selected for multiple views, or when
714 * loading from Jalview2XML.java
719 void setMenusFromViewport(AlignViewport av)
721 padGapsMenuitem.setSelected(av.isPadGaps());
722 colourTextMenuItem.setSelected(av.showColourText);
723 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
724 conservationMenuItem.setSelected(av.getConservationSelected());
725 seqLimits.setSelected(av.getShowJVSuffix());
726 idRightAlign.setSelected(av.rightAlignIds);
727 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
728 renderGapsMenuItem.setSelected(av.renderGaps);
729 wrapMenuItem.setSelected(av.wrapAlignment);
730 scaleAbove.setVisible(av.wrapAlignment);
731 scaleLeft.setVisible(av.wrapAlignment);
732 scaleRight.setVisible(av.wrapAlignment);
733 annotationPanelMenuItem.setState(av.showAnnotation);
734 viewBoxesMenuItem.setSelected(av.showBoxes);
735 viewTextMenuItem.setSelected(av.showText);
736 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
737 showGroupConsensus.setSelected(av.isShowGroupConsensus());
738 showGroupConservation.setSelected(av.isShowGroupConservation());
739 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
740 showSequenceLogo.setSelected(av.isShowSequenceLogo());
741 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
743 setColourSelected(ColourSchemeProperty.getColourName(av
744 .getGlobalColourScheme()));
746 showSeqFeatures.setSelected(av.showSequenceFeatures);
747 hiddenMarkers.setState(av.showHiddenMarkers);
748 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
749 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
750 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
751 autoCalculate.setSelected(av.autoCalculateConsensus);
752 sortByTree.setSelected(av.sortByTree);
753 listenToViewSelections.setSelected(av.followSelection);
754 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
756 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
757 setShowProductsEnabled();
761 // methods for implementing IProgressIndicator
762 // need to refactor to a reusable stub class
763 Hashtable progressBars, progressBarHandlers;
768 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
771 public void setProgressBar(String message, long id)
773 if (progressBars == null)
775 progressBars = new Hashtable();
776 progressBarHandlers = new Hashtable();
779 JPanel progressPanel;
780 Long lId = new Long(id);
781 GridLayout layout = (GridLayout) statusPanel.getLayout();
782 if (progressBars.get(lId) != null)
784 progressPanel = (JPanel) progressBars.get(new Long(id));
785 statusPanel.remove(progressPanel);
786 progressBars.remove(lId);
787 progressPanel = null;
790 statusBar.setText(message);
792 if (progressBarHandlers.contains(lId))
794 progressBarHandlers.remove(lId);
796 layout.setRows(layout.getRows() - 1);
800 progressPanel = new JPanel(new BorderLayout(10, 5));
802 JProgressBar progressBar = new JProgressBar();
803 progressBar.setIndeterminate(true);
805 progressPanel.add(new JLabel(message), BorderLayout.WEST);
806 progressPanel.add(progressBar, BorderLayout.CENTER);
808 layout.setRows(layout.getRows() + 1);
809 statusPanel.add(progressPanel);
811 progressBars.put(lId, progressPanel);
814 // setMenusForViewport();
819 public void registerHandler(final long id,
820 final IProgressIndicatorHandler handler)
822 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
825 "call setProgressBar before registering the progress bar's handler.");
827 progressBarHandlers.put(new Long(id), handler);
828 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
829 if (handler.canCancel())
831 JButton cancel = new JButton(
832 MessageManager.getString("action.cancel"));
833 final IProgressIndicator us = this;
834 cancel.addActionListener(new ActionListener()
838 public void actionPerformed(ActionEvent e)
840 handler.cancelActivity(id);
843 + ((JLabel) progressPanel.getComponent(0))
847 progressPanel.add(cancel, BorderLayout.EAST);
853 * @return true if any progress bars are still active
856 public boolean operationInProgress()
858 if (progressBars != null && progressBars.size() > 0)
866 public void setStatus(String text)
868 statusBar.setText(text);
872 * Added so Castor Mapping file can obtain Jalview Version
874 public String getVersion()
876 return jalview.bin.Cache.getProperty("VERSION");
879 public FeatureRenderer getFeatureRenderer()
881 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
885 public void fetchSequence_actionPerformed(ActionEvent e)
887 new SequenceFetcher(this);
891 public void addFromFile_actionPerformed(ActionEvent e)
893 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
897 public void reload_actionPerformed(ActionEvent e)
899 if (fileName != null)
901 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
902 // originating file's format
903 // TODO: work out how to recover feature settings for correct view(s) when
905 if (currentFileFormat.equals("Jalview"))
907 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
908 for (int i = 0; i < frames.length; i++)
910 if (frames[i] instanceof AlignFrame && frames[i] != this
911 && ((AlignFrame) frames[i]).fileName != null
912 && ((AlignFrame) frames[i]).fileName.equals(fileName))
916 frames[i].setSelected(true);
917 Desktop.instance.closeAssociatedWindows();
918 } catch (java.beans.PropertyVetoException ex)
924 Desktop.instance.closeAssociatedWindows();
926 FileLoader loader = new FileLoader();
927 String protocol = fileName.startsWith("http:") ? "URL" : "File";
928 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
932 Rectangle bounds = this.getBounds();
934 FileLoader loader = new FileLoader();
935 String protocol = fileName.startsWith("http:") ? "URL" : "File";
936 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
937 protocol, currentFileFormat);
939 newframe.setBounds(bounds);
940 if (featureSettings != null && featureSettings.isShowing())
942 final Rectangle fspos = featureSettings.frame.getBounds();
943 // TODO: need a 'show feature settings' function that takes bounds -
944 // need to refactor Desktop.addFrame
945 newframe.featureSettings_actionPerformed(null);
946 final FeatureSettings nfs = newframe.featureSettings;
947 SwingUtilities.invokeLater(new Runnable()
952 nfs.frame.setBounds(fspos);
955 this.featureSettings.close();
956 this.featureSettings = null;
958 this.closeMenuItem_actionPerformed(true);
964 public void addFromText_actionPerformed(ActionEvent e)
966 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
970 public void addFromURL_actionPerformed(ActionEvent e)
972 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
976 public void save_actionPerformed(ActionEvent e)
979 || (currentFileFormat == null || !jalview.io.FormatAdapter
980 .isValidIOFormat(currentFileFormat, true))
981 || fileName.startsWith("http"))
983 saveAs_actionPerformed(null);
987 saveAlignment(fileName, currentFileFormat);
998 public void saveAs_actionPerformed(ActionEvent e)
1000 JalviewFileChooser chooser = new JalviewFileChooser(
1001 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1002 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1003 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1004 currentFileFormat, false);
1006 chooser.setFileView(new JalviewFileView());
1007 chooser.setDialogTitle("Save Alignment to file");
1008 chooser.setToolTipText(MessageManager.getString("action.save"));
1010 int value = chooser.showSaveDialog(this);
1012 if (value == JalviewFileChooser.APPROVE_OPTION)
1014 currentFileFormat = chooser.getSelectedFormat();
1015 if (currentFileFormat == null)
1018 .showInternalMessageDialog(
1021 .getString("label.select_file_format_before_saving"),
1023 .getString("label.file_format_not_specified"),
1024 JOptionPane.WARNING_MESSAGE);
1025 value = chooser.showSaveDialog(this);
1029 fileName = chooser.getSelectedFile().getPath();
1031 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1034 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1035 if (currentFileFormat.indexOf(" ") > -1)
1037 currentFileFormat = currentFileFormat.substring(0,
1038 currentFileFormat.indexOf(" "));
1040 saveAlignment(fileName, currentFileFormat);
1044 public boolean saveAlignment(String file, String format)
1046 boolean success = true;
1048 if (format.equalsIgnoreCase("Jalview"))
1050 String shortName = title;
1052 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1054 shortName = shortName.substring(shortName
1055 .lastIndexOf(java.io.File.separatorChar) + 1);
1058 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1060 statusBar.setText(MessageManager.formatMessage(
1061 "label.successfully_saved_to_file_in_format", new String[]
1062 { fileName, format }));
1067 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1069 warningMessage("Cannot save file " + fileName + " using format "
1070 + format, "Alignment output format not supported");
1071 saveAs_actionPerformed(null);
1072 // JBPNote need to have a raise_gui flag here
1076 String[] omitHidden = null;
1078 if (viewport.hasHiddenColumns())
1080 int reply = JOptionPane
1081 .showInternalConfirmDialog(
1084 .getString("label.alignment_contains_hidden_columns"),
1086 .getString("action.save_omit_hidden_columns"),
1087 JOptionPane.YES_NO_OPTION,
1088 JOptionPane.QUESTION_MESSAGE);
1090 if (reply == JOptionPane.YES_OPTION)
1092 omitHidden = viewport.getViewAsString(false);
1095 FormatAdapter f = new FormatAdapter();
1096 String output = f.formatSequences(format,
1097 viewport.getAlignment(), // class cast exceptions will
1098 // occur in the distant future
1099 omitHidden, f.getCacheSuffixDefault(format),
1100 viewport.getColumnSelection());
1110 java.io.PrintWriter out = new java.io.PrintWriter(
1111 new java.io.FileWriter(file));
1115 this.setTitle(file);
1116 statusBar.setText(MessageManager.formatMessage(
1117 "label.successfully_saved_to_file_in_format",
1119 { fileName, format }));
1120 } catch (Exception ex)
1123 ex.printStackTrace();
1130 JOptionPane.showInternalMessageDialog(this, MessageManager
1131 .formatMessage("label.couldnt_save_file", new String[]
1132 { fileName }), MessageManager
1133 .getString("label.error_saving_file"),
1134 JOptionPane.WARNING_MESSAGE);
1140 private void warningMessage(String warning, String title)
1142 if (new jalview.util.Platform().isHeadless())
1144 System.err.println("Warning: " + title + "\nWarning: " + warning);
1149 JOptionPane.showInternalMessageDialog(this, warning, title,
1150 JOptionPane.WARNING_MESSAGE);
1162 protected void outputText_actionPerformed(ActionEvent e)
1164 String[] omitHidden = null;
1166 if (viewport.hasHiddenColumns())
1168 int reply = JOptionPane
1169 .showInternalConfirmDialog(
1172 .getString("label.alignment_contains_hidden_columns"),
1174 .getString("action.save_omit_hidden_columns"),
1175 JOptionPane.YES_NO_OPTION,
1176 JOptionPane.QUESTION_MESSAGE);
1178 if (reply == JOptionPane.YES_OPTION)
1180 omitHidden = viewport.getViewAsString(false);
1184 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1185 cap.setForInput(null);
1189 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1190 viewport.getAlignment(), omitHidden,
1191 viewport.getColumnSelection()));
1192 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1193 "label.alignment_output_command", new String[]
1194 { e.getActionCommand() }), 600, 500);
1195 } catch (OutOfMemoryError oom)
1197 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1210 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1212 new HTMLOutput(alignPanel,
1213 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1214 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1217 public void createImageMap(File file, String image)
1219 alignPanel.makePNGImageMap(file, image);
1229 public void createPNG(File f)
1231 alignPanel.makePNG(f);
1241 public void createEPS(File f)
1243 alignPanel.makeEPS(f);
1247 public void pageSetup_actionPerformed(ActionEvent e)
1249 PrinterJob printJob = PrinterJob.getPrinterJob();
1250 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1260 public void printMenuItem_actionPerformed(ActionEvent e)
1262 // Putting in a thread avoids Swing painting problems
1263 PrintThread thread = new PrintThread(alignPanel);
1268 public void exportFeatures_actionPerformed(ActionEvent e)
1270 new AnnotationExporter().exportFeatures(alignPanel);
1274 public void exportAnnotations_actionPerformed(ActionEvent e)
1276 new AnnotationExporter().exportAnnotations(alignPanel,
1277 viewport.showAnnotation ? viewport.getAlignment()
1278 .getAlignmentAnnotation() : null, viewport
1279 .getAlignment().getGroups(), ((Alignment) viewport
1280 .getAlignment()).alignmentProperties);
1284 public void associatedData_actionPerformed(ActionEvent e)
1286 // Pick the tree file
1287 JalviewFileChooser chooser = new JalviewFileChooser(
1288 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1289 chooser.setFileView(new JalviewFileView());
1290 chooser.setDialogTitle(MessageManager
1291 .getString("label.load_jalview_annotations"));
1292 chooser.setToolTipText(MessageManager
1293 .getString("label.load_jalview_annotations"));
1295 int value = chooser.showOpenDialog(null);
1297 if (value == JalviewFileChooser.APPROVE_OPTION)
1299 String choice = chooser.getSelectedFile().getPath();
1300 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1301 loadJalviewDataFile(choice, null, null, null);
1307 * Close the current view or all views in the alignment frame. If the frame
1308 * only contains one view then the alignment will be removed from memory.
1310 * @param closeAllTabs
1313 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1315 if (alignPanels != null && alignPanels.size() < 2)
1317 closeAllTabs = true;
1322 if (alignPanels != null)
1326 if (this.isClosed())
1328 // really close all the windows - otherwise wait till
1329 // setClosed(true) is called
1330 for (int i = 0; i < alignPanels.size(); i++)
1332 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1339 closeView(alignPanel);
1345 this.setClosed(true);
1347 } catch (Exception ex)
1349 ex.printStackTrace();
1354 * close alignPanel2 and shuffle tabs appropriately.
1356 * @param alignPanel2
1358 public void closeView(AlignmentPanel alignPanel2)
1360 int index = tabbedPane.getSelectedIndex();
1361 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1362 alignPanels.removeElement(alignPanel2);
1364 // if (viewport == alignPanel2.av)
1368 alignPanel2.closePanel();
1371 tabbedPane.removeTabAt(closedindex);
1372 tabbedPane.validate();
1374 if (index > closedindex || index == tabbedPane.getTabCount())
1376 // modify currently selected tab index if necessary.
1380 this.tabSelectionChanged(index);
1386 void updateEditMenuBar()
1389 if (viewport.historyList.size() > 0)
1391 undoMenuItem.setEnabled(true);
1392 CommandI command = (CommandI) viewport.historyList.peek();
1393 undoMenuItem.setText(MessageManager.formatMessage(
1394 "label.undo_command", new String[]
1395 { command.getDescription() }));
1399 undoMenuItem.setEnabled(false);
1400 undoMenuItem.setText(MessageManager.getString("action.undo"));
1403 if (viewport.redoList.size() > 0)
1405 redoMenuItem.setEnabled(true);
1407 CommandI command = (CommandI) viewport.redoList.peek();
1408 redoMenuItem.setText(MessageManager.formatMessage(
1409 "label.redo_command", new String[]
1410 { command.getDescription() }));
1414 redoMenuItem.setEnabled(false);
1415 redoMenuItem.setText(MessageManager.getString("action.redo"));
1419 public void addHistoryItem(CommandI command)
1421 if (command.getSize() > 0)
1423 viewport.historyList.push(command);
1424 viewport.redoList.clear();
1425 updateEditMenuBar();
1426 viewport.updateHiddenColumns();
1427 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1428 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1429 // viewport.getColumnSelection()
1430 // .getHiddenColumns().size() > 0);
1436 * @return alignment objects for all views
1438 AlignmentI[] getViewAlignments()
1440 if (alignPanels != null)
1442 Enumeration e = alignPanels.elements();
1443 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1444 for (int i = 0; e.hasMoreElements(); i++)
1446 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1450 if (viewport != null)
1452 return new AlignmentI[]
1453 { viewport.getAlignment() };
1465 protected void undoMenuItem_actionPerformed(ActionEvent e)
1467 if (viewport.historyList.empty())
1469 CommandI command = (CommandI) viewport.historyList.pop();
1470 viewport.redoList.push(command);
1471 command.undoCommand(getViewAlignments());
1473 AlignViewport originalSource = getOriginatingSource(command);
1474 updateEditMenuBar();
1476 if (originalSource != null)
1478 if (originalSource != viewport)
1481 .warn("Implementation worry: mismatch of viewport origin for undo");
1483 originalSource.updateHiddenColumns();
1484 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1486 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1487 // viewport.getColumnSelection()
1488 // .getHiddenColumns().size() > 0);
1489 originalSource.firePropertyChange("alignment", null, originalSource
1490 .getAlignment().getSequences());
1501 protected void redoMenuItem_actionPerformed(ActionEvent e)
1503 if (viewport.redoList.size() < 1)
1508 CommandI command = (CommandI) viewport.redoList.pop();
1509 viewport.historyList.push(command);
1510 command.doCommand(getViewAlignments());
1512 AlignViewport originalSource = getOriginatingSource(command);
1513 updateEditMenuBar();
1515 if (originalSource != null)
1518 if (originalSource != viewport)
1521 .warn("Implementation worry: mismatch of viewport origin for redo");
1523 originalSource.updateHiddenColumns();
1524 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1526 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1527 // viewport.getColumnSelection()
1528 // .getHiddenColumns().size() > 0);
1529 originalSource.firePropertyChange("alignment", null, originalSource
1530 .getAlignment().getSequences());
1534 AlignViewport getOriginatingSource(CommandI command)
1536 AlignViewport originalSource = null;
1537 // For sequence removal and addition, we need to fire
1538 // the property change event FROM the viewport where the
1539 // original alignment was altered
1540 AlignmentI al = null;
1541 if (command instanceof EditCommand)
1543 EditCommand editCommand = (EditCommand) command;
1544 al = editCommand.getAlignment();
1545 Vector comps = (Vector) PaintRefresher.components.get(viewport
1546 .getSequenceSetId());
1548 for (int i = 0; i < comps.size(); i++)
1550 if (comps.elementAt(i) instanceof AlignmentPanel)
1552 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1554 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1561 if (originalSource == null)
1563 // The original view is closed, we must validate
1564 // the current view against the closed view first
1567 PaintRefresher.validateSequences(al, viewport.getAlignment());
1570 originalSource = viewport;
1573 return originalSource;
1582 public void moveSelectedSequences(boolean up)
1584 SequenceGroup sg = viewport.getSelectionGroup();
1590 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1591 viewport.getHiddenRepSequences(), up);
1592 alignPanel.paintAlignment(true);
1595 synchronized void slideSequences(boolean right, int size)
1597 List<SequenceI> sg = new Vector();
1598 if (viewport.cursorMode)
1600 sg.add(viewport.getAlignment().getSequenceAt(
1601 alignPanel.seqPanel.seqCanvas.cursorY));
1603 else if (viewport.getSelectionGroup() != null
1604 && viewport.getSelectionGroup().getSize() != viewport
1605 .getAlignment().getHeight())
1607 sg = viewport.getSelectionGroup().getSequences(
1608 viewport.getHiddenRepSequences());
1616 Vector invertGroup = new Vector();
1618 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1620 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1621 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1624 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1626 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1627 for (int i = 0; i < invertGroup.size(); i++)
1628 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1630 SlideSequencesCommand ssc;
1632 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1633 size, viewport.getGapCharacter());
1635 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1636 size, viewport.getGapCharacter());
1638 int groupAdjustment = 0;
1639 if (ssc.getGapsInsertedBegin() && right)
1641 if (viewport.cursorMode)
1642 alignPanel.seqPanel.moveCursor(size, 0);
1644 groupAdjustment = size;
1646 else if (!ssc.getGapsInsertedBegin() && !right)
1648 if (viewport.cursorMode)
1649 alignPanel.seqPanel.moveCursor(-size, 0);
1651 groupAdjustment = -size;
1654 if (groupAdjustment != 0)
1656 viewport.getSelectionGroup().setStartRes(
1657 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1658 viewport.getSelectionGroup().setEndRes(
1659 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1662 boolean appendHistoryItem = false;
1663 if (viewport.historyList != null && viewport.historyList.size() > 0
1664 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1666 appendHistoryItem = ssc
1667 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1671 if (!appendHistoryItem)
1672 addHistoryItem(ssc);
1684 protected void copy_actionPerformed(ActionEvent e)
1687 if (viewport.getSelectionGroup() == null)
1691 // TODO: preserve the ordering of displayed alignment annotation in any
1692 // internal paste (particularly sequence associated annotation)
1693 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1694 String[] omitHidden = null;
1696 if (viewport.hasHiddenColumns())
1698 omitHidden = viewport.getViewAsString(true);
1701 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1704 StringSelection ss = new StringSelection(output);
1708 jalview.gui.Desktop.internalCopy = true;
1709 // Its really worth setting the clipboard contents
1710 // to empty before setting the large StringSelection!!
1711 Toolkit.getDefaultToolkit().getSystemClipboard()
1712 .setContents(new StringSelection(""), null);
1714 Toolkit.getDefaultToolkit().getSystemClipboard()
1715 .setContents(ss, Desktop.instance);
1716 } catch (OutOfMemoryError er)
1718 new OOMWarning("copying region", er);
1722 Vector hiddenColumns = null;
1723 if (viewport.hasHiddenColumns())
1725 hiddenColumns = new Vector();
1726 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1727 .getSelectionGroup().getEndRes();
1728 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1731 int[] region = (int[]) viewport.getColumnSelection()
1732 .getHiddenColumns().elementAt(i);
1733 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1735 hiddenColumns.addElement(new int[]
1736 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1741 Desktop.jalviewClipboard = new Object[]
1742 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1743 statusBar.setText(MessageManager.formatMessage(
1744 "label.copied_sequences_to_clipboard", new String[]
1745 { Integer.valueOf(seqs.length).toString() }));
1755 protected void pasteNew_actionPerformed(ActionEvent e)
1767 protected void pasteThis_actionPerformed(ActionEvent e)
1773 * Paste contents of Jalview clipboard
1775 * @param newAlignment
1776 * true to paste to a new alignment, otherwise add to this.
1778 void paste(boolean newAlignment)
1780 boolean externalPaste = true;
1783 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1784 Transferable contents = c.getContents(this);
1786 if (contents == null)
1794 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1795 if (str.length() < 1)
1800 format = new IdentifyFile().Identify(str, "Paste");
1802 } catch (OutOfMemoryError er)
1804 new OOMWarning("Out of memory pasting sequences!!", er);
1808 SequenceI[] sequences;
1809 boolean annotationAdded = false;
1810 AlignmentI alignment = null;
1812 if (Desktop.jalviewClipboard != null)
1814 // The clipboard was filled from within Jalview, we must use the
1816 // And dataset from the copied alignment
1817 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1818 // be doubly sure that we create *new* sequence objects.
1819 sequences = new SequenceI[newseq.length];
1820 for (int i = 0; i < newseq.length; i++)
1822 sequences[i] = new Sequence(newseq[i]);
1824 alignment = new Alignment(sequences);
1825 externalPaste = false;
1829 // parse the clipboard as an alignment.
1830 alignment = new FormatAdapter().readFile(str, "Paste", format);
1831 sequences = alignment.getSequencesArray();
1835 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1841 if (Desktop.jalviewClipboard != null)
1843 // dataset is inherited
1844 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1848 // new dataset is constructed
1849 alignment.setDataset(null);
1851 alwidth = alignment.getWidth() + 1;
1855 AlignmentI pastedal = alignment; // preserve pasted alignment object
1856 // Add pasted sequences and dataset into existing alignment.
1857 alignment = viewport.getAlignment();
1858 alwidth = alignment.getWidth() + 1;
1859 // decide if we need to import sequences from an existing dataset
1860 boolean importDs = Desktop.jalviewClipboard != null
1861 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1862 // importDs==true instructs us to copy over new dataset sequences from
1863 // an existing alignment
1864 Vector newDs = (importDs) ? new Vector() : null; // used to create
1865 // minimum dataset set
1867 for (int i = 0; i < sequences.length; i++)
1871 newDs.addElement(null);
1873 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1875 if (importDs && ds != null)
1877 if (!newDs.contains(ds))
1879 newDs.setElementAt(ds, i);
1880 ds = new Sequence(ds);
1881 // update with new dataset sequence
1882 sequences[i].setDatasetSequence(ds);
1886 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1891 // copy and derive new dataset sequence
1892 sequences[i] = sequences[i].deriveSequence();
1893 alignment.getDataset().addSequence(
1894 sequences[i].getDatasetSequence());
1895 // TODO: avoid creation of duplicate dataset sequences with a
1896 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1898 alignment.addSequence(sequences[i]); // merges dataset
1902 newDs.clear(); // tidy up
1904 if (alignment.getAlignmentAnnotation() != null)
1906 for (AlignmentAnnotation alan : alignment
1907 .getAlignmentAnnotation())
1909 if (alan.graphGroup > fgroup)
1911 fgroup = alan.graphGroup;
1915 if (pastedal.getAlignmentAnnotation() != null)
1917 // Add any annotation attached to alignment.
1918 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1919 for (int i = 0; i < alann.length; i++)
1921 annotationAdded = true;
1922 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1924 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1925 if (newann.graphGroup > -1)
1927 if (newGraphGroups.size() <= newann.graphGroup
1928 || newGraphGroups.get(newann.graphGroup) == null)
1930 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1932 newGraphGroups.add(q, null);
1934 newGraphGroups.set(newann.graphGroup, new Integer(
1937 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1941 newann.padAnnotation(alwidth);
1942 alignment.addAnnotation(newann);
1952 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1953 sequences, 0, alignment.getWidth(), alignment));
1955 // Add any annotations attached to sequences
1956 for (int i = 0; i < sequences.length; i++)
1958 if (sequences[i].getAnnotation() != null)
1960 AlignmentAnnotation newann;
1961 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1963 annotationAdded = true;
1964 newann = sequences[i].getAnnotation()[a];
1965 newann.adjustForAlignment();
1966 newann.padAnnotation(alwidth);
1967 if (newann.graphGroup > -1)
1969 if (newann.graphGroup > -1)
1971 if (newGraphGroups.size() <= newann.graphGroup
1972 || newGraphGroups.get(newann.graphGroup) == null)
1974 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1976 newGraphGroups.add(q, null);
1978 newGraphGroups.set(newann.graphGroup, new Integer(
1981 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1985 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1990 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1997 // propagate alignment changed.
1998 viewport.setEndSeq(alignment.getHeight());
1999 if (annotationAdded)
2001 // Duplicate sequence annotation in all views.
2002 AlignmentI[] alview = this.getViewAlignments();
2003 for (int i = 0; i < sequences.length; i++)
2005 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2008 for (int avnum = 0; avnum < alview.length; avnum++)
2010 if (alview[avnum] != alignment)
2012 // duplicate in a view other than the one with input focus
2013 int avwidth = alview[avnum].getWidth() + 1;
2014 // this relies on sann being preserved after we
2015 // modify the sequence's annotation array for each duplication
2016 for (int a = 0; a < sann.length; a++)
2018 AlignmentAnnotation newann = new AlignmentAnnotation(
2020 sequences[i].addAlignmentAnnotation(newann);
2021 newann.padAnnotation(avwidth);
2022 alview[avnum].addAnnotation(newann); // annotation was
2023 // duplicated earlier
2024 // TODO JAL-1145 graphGroups are not updated for sequence
2025 // annotation added to several views. This may cause
2027 alview[avnum].setAnnotationIndex(newann, a);
2032 buildSortByAnnotationScoresMenu();
2034 viewport.firePropertyChange("alignment", null,
2035 alignment.getSequences());
2036 if (alignPanels != null)
2038 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2040 ap.validateAnnotationDimensions(false);
2045 alignPanel.validateAnnotationDimensions(false);
2051 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2053 String newtitle = new String("Copied sequences");
2055 if (Desktop.jalviewClipboard != null
2056 && Desktop.jalviewClipboard[2] != null)
2058 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2059 for (int i = 0; i < hc.size(); i++)
2061 int[] region = (int[]) hc.elementAt(i);
2062 af.viewport.hideColumns(region[0], region[1]);
2066 // >>>This is a fix for the moment, until a better solution is
2068 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2070 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2072 // TODO: maintain provenance of an alignment, rather than just make the
2073 // title a concatenation of operations.
2076 if (title.startsWith("Copied sequences"))
2082 newtitle = newtitle.concat("- from " + title);
2087 newtitle = new String("Pasted sequences");
2090 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2095 } catch (Exception ex)
2097 ex.printStackTrace();
2098 System.out.println("Exception whilst pasting: " + ex);
2099 // could be anything being pasted in here
2105 protected void expand_newalign(ActionEvent e)
2109 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2110 .getAlignment(), -1);
2111 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2113 String newtitle = new String("Flanking alignment");
2115 if (Desktop.jalviewClipboard != null
2116 && Desktop.jalviewClipboard[2] != null)
2118 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2119 for (int i = 0; i < hc.size(); i++)
2121 int[] region = (int[]) hc.elementAt(i);
2122 af.viewport.hideColumns(region[0], region[1]);
2126 // >>>This is a fix for the moment, until a better solution is
2128 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2130 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2132 // TODO: maintain provenance of an alignment, rather than just make the
2133 // title a concatenation of operations.
2135 if (title.startsWith("Copied sequences"))
2141 newtitle = newtitle.concat("- from " + title);
2145 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2147 } catch (Exception ex)
2149 ex.printStackTrace();
2150 System.out.println("Exception whilst pasting: " + ex);
2151 // could be anything being pasted in here
2152 } catch (OutOfMemoryError oom)
2154 new OOMWarning("Viewing flanking region of alignment", oom);
2165 protected void cut_actionPerformed(ActionEvent e)
2167 copy_actionPerformed(null);
2168 delete_actionPerformed(null);
2178 protected void delete_actionPerformed(ActionEvent evt)
2181 SequenceGroup sg = viewport.getSelectionGroup();
2187 Vector seqs = new Vector();
2189 for (int i = 0; i < sg.getSize(); i++)
2191 seq = sg.getSequenceAt(i);
2192 seqs.addElement(seq);
2195 // If the cut affects all sequences, remove highlighted columns
2196 if (sg.getSize() == viewport.getAlignment().getHeight())
2198 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2199 sg.getEndRes() + 1);
2202 SequenceI[] cut = new SequenceI[seqs.size()];
2203 for (int i = 0; i < seqs.size(); i++)
2205 cut[i] = (SequenceI) seqs.elementAt(i);
2209 * //ADD HISTORY ITEM
2211 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2212 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2213 viewport.getAlignment()));
2215 viewport.setSelectionGroup(null);
2216 viewport.sendSelection();
2217 viewport.getAlignment().deleteGroup(sg);
2219 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2221 if (viewport.getAlignment().getHeight() < 1)
2225 this.setClosed(true);
2226 } catch (Exception ex)
2239 protected void deleteGroups_actionPerformed(ActionEvent e)
2241 if (avc.deleteGroups())
2243 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2244 alignPanel.updateAnnotation();
2245 alignPanel.paintAlignment(true);
2256 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2258 SequenceGroup sg = new SequenceGroup();
2260 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2262 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2265 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2266 viewport.setSelectionGroup(sg);
2267 viewport.sendSelection();
2268 alignPanel.paintAlignment(true);
2269 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2279 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2281 if (viewport.cursorMode)
2283 alignPanel.seqPanel.keyboardNo1 = null;
2284 alignPanel.seqPanel.keyboardNo2 = null;
2286 viewport.setSelectionGroup(null);
2287 viewport.getColumnSelection().clear();
2288 viewport.setSelectionGroup(null);
2289 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2290 alignPanel.idPanel.idCanvas.searchResults = null;
2291 alignPanel.paintAlignment(true);
2292 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2293 viewport.sendSelection();
2303 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2305 SequenceGroup sg = viewport.getSelectionGroup();
2309 selectAllSequenceMenuItem_actionPerformed(null);
2314 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2316 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2319 alignPanel.paintAlignment(true);
2320 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2321 viewport.sendSelection();
2325 public void invertColSel_actionPerformed(ActionEvent e)
2327 viewport.invertColumnSelection();
2328 alignPanel.paintAlignment(true);
2329 viewport.sendSelection();
2339 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2341 trimAlignment(true);
2351 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2353 trimAlignment(false);
2356 void trimAlignment(boolean trimLeft)
2358 ColumnSelection colSel = viewport.getColumnSelection();
2361 if (colSel.size() > 0)
2365 column = colSel.getMin();
2369 column = colSel.getMax();
2373 if (viewport.getSelectionGroup() != null)
2375 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2376 viewport.getHiddenRepSequences());
2380 seqs = viewport.getAlignment().getSequencesArray();
2383 TrimRegionCommand trimRegion;
2386 trimRegion = new TrimRegionCommand("Remove Left",
2387 TrimRegionCommand.TRIM_LEFT, seqs, column,
2388 viewport.getAlignment(), viewport.getColumnSelection(),
2389 viewport.getSelectionGroup());
2390 viewport.setStartRes(0);
2394 trimRegion = new TrimRegionCommand("Remove Right",
2395 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2396 viewport.getAlignment(), viewport.getColumnSelection(),
2397 viewport.getSelectionGroup());
2400 statusBar.setText(MessageManager.formatMessage(
2401 "label.removed_columns", new String[]
2402 { Integer.valueOf(trimRegion.getSize()).toString() }));
2404 addHistoryItem(trimRegion);
2406 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2408 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2409 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2411 viewport.getAlignment().deleteGroup(sg);
2415 viewport.firePropertyChange("alignment", null, viewport
2416 .getAlignment().getSequences());
2427 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2429 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2432 if (viewport.getSelectionGroup() != null)
2434 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2435 viewport.getHiddenRepSequences());
2436 start = viewport.getSelectionGroup().getStartRes();
2437 end = viewport.getSelectionGroup().getEndRes();
2441 seqs = viewport.getAlignment().getSequencesArray();
2444 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2445 "Remove Gapped Columns", seqs, start, end,
2446 viewport.getAlignment());
2448 addHistoryItem(removeGapCols);
2450 statusBar.setText(MessageManager.formatMessage(
2451 "label.removed_empty_columns", new String[]
2452 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2454 // This is to maintain viewport position on first residue
2455 // of first sequence
2456 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2457 int startRes = seq.findPosition(viewport.startRes);
2458 // ShiftList shifts;
2459 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2460 // edit.alColumnChanges=shifts.getInverse();
2461 // if (viewport.hasHiddenColumns)
2462 // viewport.getColumnSelection().compensateForEdits(shifts);
2463 viewport.setStartRes(seq.findIndex(startRes) - 1);
2464 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2476 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2478 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2481 if (viewport.getSelectionGroup() != null)
2483 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2484 viewport.getHiddenRepSequences());
2485 start = viewport.getSelectionGroup().getStartRes();
2486 end = viewport.getSelectionGroup().getEndRes();
2490 seqs = viewport.getAlignment().getSequencesArray();
2493 // This is to maintain viewport position on first residue
2494 // of first sequence
2495 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2496 int startRes = seq.findPosition(viewport.startRes);
2498 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2499 viewport.getAlignment()));
2501 viewport.setStartRes(seq.findIndex(startRes) - 1);
2503 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2515 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2517 viewport.setPadGaps(padGapsMenuitem.isSelected());
2518 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2524 // if (justifySeqs>0)
2526 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2539 public void findMenuItem_actionPerformed(ActionEvent e)
2545 public void newView_actionPerformed(ActionEvent e)
2552 * @param copyAnnotation
2553 * if true then duplicate all annnotation, groups and settings
2554 * @return new alignment panel, already displayed.
2556 public AlignmentPanel newView(boolean copyAnnotation)
2558 return newView(null, copyAnnotation);
2564 * title of newly created view
2565 * @return new alignment panel, already displayed.
2567 public AlignmentPanel newView(String viewTitle)
2569 return newView(viewTitle, true);
2575 * title of newly created view
2576 * @param copyAnnotation
2577 * if true then duplicate all annnotation, groups and settings
2578 * @return new alignment panel, already displayed.
2580 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2582 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2584 if (!copyAnnotation)
2586 // just remove all the current annotation except for the automatic stuff
2587 newap.av.getAlignment().deleteAllGroups();
2588 for (AlignmentAnnotation alan : newap.av.getAlignment()
2589 .getAlignmentAnnotation())
2591 if (!alan.autoCalculated)
2593 newap.av.getAlignment().deleteAnnotation(alan);
2599 newap.av.gatherViewsHere = false;
2601 if (viewport.viewName == null)
2603 viewport.viewName = "Original";
2606 newap.av.historyList = viewport.historyList;
2607 newap.av.redoList = viewport.redoList;
2609 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2610 // make sure the new view has a unique name - this is essential for Jalview
2612 boolean addFirstIndex = false;
2613 if (viewTitle == null || viewTitle.trim().length() == 0)
2616 addFirstIndex = true;
2620 index = 1;// we count from 1 if given a specific name
2622 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2623 Vector comps = (Vector) PaintRefresher.components.get(viewport
2624 .getSequenceSetId());
2625 Vector existingNames = new Vector();
2626 for (int i = 0; i < comps.size(); i++)
2628 if (comps.elementAt(i) instanceof AlignmentPanel)
2630 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2631 if (!existingNames.contains(ap.av.viewName))
2633 existingNames.addElement(ap.av.viewName);
2638 while (existingNames.contains(newViewName))
2640 newViewName = viewTitle + " " + (++index);
2643 newap.av.viewName = newViewName;
2645 addAlignmentPanel(newap, true);
2646 newap.alignmentChanged();
2648 if (alignPanels.size() == 2)
2650 viewport.gatherViewsHere = true;
2652 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2657 public void expandViews_actionPerformed(ActionEvent e)
2659 Desktop.instance.explodeViews(this);
2663 public void gatherViews_actionPerformed(ActionEvent e)
2665 Desktop.instance.gatherViews(this);
2675 public void font_actionPerformed(ActionEvent e)
2677 new FontChooser(alignPanel);
2687 protected void seqLimit_actionPerformed(ActionEvent e)
2689 viewport.setShowJVSuffix(seqLimits.isSelected());
2691 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2692 .calculateIdWidth());
2693 alignPanel.paintAlignment(true);
2697 public void idRightAlign_actionPerformed(ActionEvent e)
2699 viewport.rightAlignIds = idRightAlign.isSelected();
2700 alignPanel.paintAlignment(true);
2704 public void centreColumnLabels_actionPerformed(ActionEvent e)
2706 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2707 alignPanel.paintAlignment(true);
2713 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2716 protected void followHighlight_actionPerformed()
2718 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2720 alignPanel.scrollToPosition(
2721 alignPanel.seqPanel.seqCanvas.searchResults, false);
2732 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2734 viewport.setColourText(colourTextMenuItem.isSelected());
2735 alignPanel.paintAlignment(true);
2745 public void wrapMenuItem_actionPerformed(ActionEvent e)
2747 scaleAbove.setVisible(wrapMenuItem.isSelected());
2748 scaleLeft.setVisible(wrapMenuItem.isSelected());
2749 scaleRight.setVisible(wrapMenuItem.isSelected());
2750 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2751 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2755 public void showAllSeqs_actionPerformed(ActionEvent e)
2757 viewport.showAllHiddenSeqs();
2761 public void showAllColumns_actionPerformed(ActionEvent e)
2763 viewport.showAllHiddenColumns();
2768 public void hideSelSequences_actionPerformed(ActionEvent e)
2770 viewport.hideAllSelectedSeqs();
2771 alignPanel.paintAlignment(true);
2775 * called by key handler and the hide all/show all menu items
2780 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2783 boolean hide = false;
2784 SequenceGroup sg = viewport.getSelectionGroup();
2785 if (!toggleSeqs && !toggleCols)
2787 // Hide everything by the current selection - this is a hack - we do the
2788 // invert and then hide
2789 // first check that there will be visible columns after the invert.
2790 if ((viewport.getColumnSelection() != null
2791 && viewport.getColumnSelection().getSelected() != null && viewport
2792 .getColumnSelection().getSelected().size() > 0)
2793 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2796 // now invert the sequence set, if required - empty selection implies
2797 // that no hiding is required.
2800 invertSequenceMenuItem_actionPerformed(null);
2801 sg = viewport.getSelectionGroup();
2805 viewport.expandColSelection(sg, true);
2806 // finally invert the column selection and get the new sequence
2808 invertColSel_actionPerformed(null);
2815 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2817 hideSelSequences_actionPerformed(null);
2820 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2823 showAllSeqs_actionPerformed(null);
2829 if (viewport.getColumnSelection().getSelected().size() > 0)
2831 hideSelColumns_actionPerformed(null);
2834 viewport.setSelectionGroup(sg);
2839 showAllColumns_actionPerformed(null);
2848 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2849 * event.ActionEvent)
2852 public void hideAllButSelection_actionPerformed(ActionEvent e)
2854 toggleHiddenRegions(false, false);
2861 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2865 public void hideAllSelection_actionPerformed(ActionEvent e)
2867 SequenceGroup sg = viewport.getSelectionGroup();
2868 viewport.expandColSelection(sg, false);
2869 viewport.hideAllSelectedSeqs();
2870 viewport.hideSelectedColumns();
2871 alignPanel.paintAlignment(true);
2878 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2882 public void showAllhidden_actionPerformed(ActionEvent e)
2884 viewport.showAllHiddenColumns();
2885 viewport.showAllHiddenSeqs();
2886 alignPanel.paintAlignment(true);
2890 public void hideSelColumns_actionPerformed(ActionEvent e)
2892 viewport.hideSelectedColumns();
2893 alignPanel.paintAlignment(true);
2897 public void hiddenMarkers_actionPerformed(ActionEvent e)
2899 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2910 protected void scaleAbove_actionPerformed(ActionEvent e)
2912 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2913 alignPanel.paintAlignment(true);
2923 protected void scaleLeft_actionPerformed(ActionEvent e)
2925 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2926 alignPanel.paintAlignment(true);
2936 protected void scaleRight_actionPerformed(ActionEvent e)
2938 viewport.setScaleRightWrapped(scaleRight.isSelected());
2939 alignPanel.paintAlignment(true);
2949 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2951 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2952 alignPanel.paintAlignment(true);
2962 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2964 viewport.setShowText(viewTextMenuItem.isSelected());
2965 alignPanel.paintAlignment(true);
2975 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2977 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2978 alignPanel.paintAlignment(true);
2981 public FeatureSettings featureSettings;
2984 public void featureSettings_actionPerformed(ActionEvent e)
2986 if (featureSettings != null)
2988 featureSettings.close();
2989 featureSettings = null;
2991 if (!showSeqFeatures.isSelected())
2993 // make sure features are actually displayed
2994 showSeqFeatures.setSelected(true);
2995 showSeqFeatures_actionPerformed(null);
2997 featureSettings = new FeatureSettings(this);
3001 * Set or clear 'Show Sequence Features'
3007 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3009 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3010 alignPanel.paintAlignment(true);
3011 if (alignPanel.getOverviewPanel() != null)
3013 alignPanel.getOverviewPanel().updateOverviewImage();
3018 * Set or clear 'Show Sequence Features'
3024 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3026 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3028 if (viewport.getShowSequenceFeaturesHeight())
3030 // ensure we're actually displaying features
3031 viewport.setShowSequenceFeatures(true);
3032 showSeqFeatures.setSelected(true);
3034 alignPanel.paintAlignment(true);
3035 if (alignPanel.getOverviewPanel() != null)
3037 alignPanel.getOverviewPanel().updateOverviewImage();
3048 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3050 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
3051 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
3055 public void alignmentProperties()
3057 JEditorPane editPane = new JEditorPane("text/html", "");
3058 editPane.setEditable(false);
3059 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3061 editPane.setText(MessageManager.formatMessage("label.html_content",
3063 { contents.toString() }));
3064 JInternalFrame frame = new JInternalFrame();
3065 frame.getContentPane().add(new JScrollPane(editPane));
3067 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3068 "label.alignment_properties", new String[]
3069 { getTitle() }), 500, 400);
3079 public void overviewMenuItem_actionPerformed(ActionEvent e)
3081 if (alignPanel.overviewPanel != null)
3086 JInternalFrame frame = new JInternalFrame();
3087 OverviewPanel overview = new OverviewPanel(alignPanel);
3088 frame.setContentPane(overview);
3089 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3090 "label.overview_params", new String[]
3091 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3093 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3094 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3097 public void internalFrameClosed(
3098 javax.swing.event.InternalFrameEvent evt)
3100 alignPanel.setOverviewPanel(null);
3104 alignPanel.setOverviewPanel(overview);
3108 public void textColour_actionPerformed(ActionEvent e)
3110 new TextColourChooser().chooseColour(alignPanel, null);
3120 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3132 public void clustalColour_actionPerformed(ActionEvent e)
3134 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3135 viewport.getHiddenRepSequences()));
3145 public void zappoColour_actionPerformed(ActionEvent e)
3147 changeColour(new ZappoColourScheme());
3157 public void taylorColour_actionPerformed(ActionEvent e)
3159 changeColour(new TaylorColourScheme());
3169 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3171 changeColour(new HydrophobicColourScheme());
3181 public void helixColour_actionPerformed(ActionEvent e)
3183 changeColour(new HelixColourScheme());
3193 public void strandColour_actionPerformed(ActionEvent e)
3195 changeColour(new StrandColourScheme());
3205 public void turnColour_actionPerformed(ActionEvent e)
3207 changeColour(new TurnColourScheme());
3217 public void buriedColour_actionPerformed(ActionEvent e)
3219 changeColour(new BuriedColourScheme());
3229 public void nucleotideColour_actionPerformed(ActionEvent e)
3231 changeColour(new NucleotideColourScheme());
3235 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3237 changeColour(new PurinePyrimidineColourScheme());
3241 * public void covariationColour_actionPerformed(ActionEvent e) {
3243 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3247 public void annotationColour_actionPerformed(ActionEvent e)
3249 new AnnotationColourChooser(viewport, alignPanel);
3253 public void rnahelicesColour_actionPerformed(ActionEvent e)
3255 new RNAHelicesColourChooser(viewport, alignPanel);
3265 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3267 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3276 public void changeColour(ColourSchemeI cs)
3278 // TODO: compare with applet and pull up to model method
3283 if (viewport.getAbovePIDThreshold())
3285 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3287 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3291 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3294 if (viewport.getConservationSelected())
3297 Alignment al = (Alignment) viewport.getAlignment();
3298 Conservation c = new Conservation("All",
3299 ResidueProperties.propHash, 3, al.getSequences(), 0,
3303 c.verdict(false, viewport.getConsPercGaps());
3305 cs.setConservation(c);
3307 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3312 cs.setConservation(null);
3315 cs.setConsensus(viewport.getSequenceConsensusHash());
3318 viewport.setGlobalColourScheme(cs);
3320 if (viewport.getColourAppliesToAllGroups())
3323 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3331 if (cs instanceof ClustalxColourScheme)
3333 sg.cs = new ClustalxColourScheme(sg,
3334 viewport.getHiddenRepSequences());
3336 else if (cs instanceof UserColourScheme)
3338 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3344 sg.cs = cs.getClass().newInstance();
3345 } catch (Exception ex)
3350 if (viewport.getAbovePIDThreshold()
3351 || cs instanceof PIDColourScheme
3352 || cs instanceof Blosum62ColourScheme)
3354 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3356 sg.cs.setConsensus(AAFrequency.calculate(
3357 sg.getSequences(viewport.getHiddenRepSequences()),
3358 sg.getStartRes(), sg.getEndRes() + 1));
3362 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3365 if (viewport.getConservationSelected())
3367 Conservation c = new Conservation("Group",
3368 ResidueProperties.propHash, 3, sg.getSequences(viewport
3369 .getHiddenRepSequences()), sg.getStartRes(),
3370 sg.getEndRes() + 1);
3372 c.verdict(false, viewport.getConsPercGaps());
3373 sg.cs.setConservation(c);
3377 sg.cs.setConservation(null);
3382 if (alignPanel.getOverviewPanel() != null)
3384 alignPanel.getOverviewPanel().updateOverviewImage();
3387 alignPanel.paintAlignment(true);
3397 protected void modifyPID_actionPerformed(ActionEvent e)
3399 if (viewport.getAbovePIDThreshold()
3400 && viewport.getGlobalColourScheme() != null)
3402 SliderPanel.setPIDSliderSource(alignPanel,
3403 viewport.getGlobalColourScheme(), "Background");
3404 SliderPanel.showPIDSlider();
3415 protected void modifyConservation_actionPerformed(ActionEvent e)
3417 if (viewport.getConservationSelected()
3418 && viewport.getGlobalColourScheme() != null)
3420 SliderPanel.setConservationSlider(alignPanel,
3421 viewport.getGlobalColourScheme(), "Background");
3422 SliderPanel.showConservationSlider();
3433 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3435 viewport.setConservationSelected(conservationMenuItem.isSelected());
3437 viewport.setAbovePIDThreshold(false);
3438 abovePIDThreshold.setSelected(false);
3440 changeColour(viewport.getGlobalColourScheme());
3442 modifyConservation_actionPerformed(null);
3452 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3454 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3456 conservationMenuItem.setSelected(false);
3457 viewport.setConservationSelected(false);
3459 changeColour(viewport.getGlobalColourScheme());
3461 modifyPID_actionPerformed(null);
3471 public void userDefinedColour_actionPerformed(ActionEvent e)
3473 if (e.getActionCommand().equals(
3474 MessageManager.getString("action.user_defined")))
3476 new UserDefinedColours(alignPanel, null);
3480 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3481 .getUserColourSchemes().get(e.getActionCommand());
3487 public void updateUserColourMenu()
3490 Component[] menuItems = colourMenu.getMenuComponents();
3491 int i, iSize = menuItems.length;
3492 for (i = 0; i < iSize; i++)
3494 if (menuItems[i].getName() != null
3495 && menuItems[i].getName().equals("USER_DEFINED"))
3497 colourMenu.remove(menuItems[i]);
3501 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3503 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3504 .getUserColourSchemes().keys();
3506 while (userColours.hasMoreElements())
3508 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3509 userColours.nextElement().toString());
3510 radioItem.setName("USER_DEFINED");
3511 radioItem.addMouseListener(new MouseAdapter()
3514 public void mousePressed(MouseEvent evt)
3516 if (evt.isControlDown()
3517 || SwingUtilities.isRightMouseButton(evt))
3519 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3521 int option = JOptionPane.showInternalConfirmDialog(
3522 jalview.gui.Desktop.desktop,
3524 .getString("label.remove_from_default_list"),
3526 .getString("label.remove_user_defined_colour"),
3527 JOptionPane.YES_NO_OPTION);
3528 if (option == JOptionPane.YES_OPTION)
3530 jalview.gui.UserDefinedColours
3531 .removeColourFromDefaults(radioItem.getText());
3532 colourMenu.remove(radioItem);
3536 radioItem.addActionListener(new ActionListener()
3539 public void actionPerformed(ActionEvent evt)
3541 userDefinedColour_actionPerformed(evt);
3548 radioItem.addActionListener(new ActionListener()
3551 public void actionPerformed(ActionEvent evt)
3553 userDefinedColour_actionPerformed(evt);
3557 colourMenu.insert(radioItem, 15);
3558 colours.add(radioItem);
3570 public void PIDColour_actionPerformed(ActionEvent e)
3572 changeColour(new PIDColourScheme());
3582 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3584 changeColour(new Blosum62ColourScheme());
3594 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3596 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3597 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3598 .getAlignment().getSequenceAt(0), null);
3599 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3600 viewport.getAlignment()));
3601 alignPanel.paintAlignment(true);
3611 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3613 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3614 AlignmentSorter.sortByID(viewport.getAlignment());
3615 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3616 viewport.getAlignment()));
3617 alignPanel.paintAlignment(true);
3627 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3629 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3630 AlignmentSorter.sortByLength(viewport.getAlignment());
3631 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3632 viewport.getAlignment()));
3633 alignPanel.paintAlignment(true);
3643 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3645 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3646 AlignmentSorter.sortByGroup(viewport.getAlignment());
3647 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3648 viewport.getAlignment()));
3650 alignPanel.paintAlignment(true);
3660 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3662 new RedundancyPanel(alignPanel, this);
3672 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3674 if ((viewport.getSelectionGroup() == null)
3675 || (viewport.getSelectionGroup().getSize() < 2))
3677 JOptionPane.showInternalMessageDialog(this, MessageManager
3678 .getString("label.you_must_select_least_two_sequences"),
3679 MessageManager.getString("label.invalid_selection"),
3680 JOptionPane.WARNING_MESSAGE);
3684 JInternalFrame frame = new JInternalFrame();
3685 frame.setContentPane(new PairwiseAlignPanel(viewport));
3686 Desktop.addInternalFrame(frame,
3687 MessageManager.getString("action.pairwise_alignment"), 600,
3699 public void PCAMenuItem_actionPerformed(ActionEvent e)
3701 if (((viewport.getSelectionGroup() != null)
3702 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3703 .getSelectionGroup().getSize() > 0))
3704 || (viewport.getAlignment().getHeight() < 4))
3707 .showInternalMessageDialog(
3710 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3712 .getString("label.sequence_selection_insufficient"),
3713 JOptionPane.WARNING_MESSAGE);
3718 new PCAPanel(alignPanel);
3722 public void autoCalculate_actionPerformed(ActionEvent e)
3724 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3725 if (viewport.autoCalculateConsensus)
3727 viewport.firePropertyChange("alignment", null, viewport
3728 .getAlignment().getSequences());
3733 public void sortByTreeOption_actionPerformed(ActionEvent e)
3735 viewport.sortByTree = sortByTree.isSelected();
3739 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3741 viewport.followSelection = listenToViewSelections.isSelected();
3751 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3753 NewTreePanel("AV", "PID", "Average distance tree using PID");
3763 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3765 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3775 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3777 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3787 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3789 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3802 void NewTreePanel(String type, String pwType, String title)
3806 if (viewport.getSelectionGroup() != null
3807 && viewport.getSelectionGroup().getSize() > 0)
3809 if (viewport.getSelectionGroup().getSize() < 3)
3815 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3817 .getString("label.not_enough_sequences"),
3818 JOptionPane.WARNING_MESSAGE);
3822 SequenceGroup sg = viewport.getSelectionGroup();
3824 /* Decide if the selection is a column region */
3825 for (SequenceI _s : sg.getSequences())
3827 if (_s.getLength() < sg.getEndRes())
3833 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3835 .getString("label.sequences_selection_not_aligned"),
3836 JOptionPane.WARNING_MESSAGE);
3842 title = title + " on region";
3843 tp = new TreePanel(alignPanel, type, pwType);
3847 // are the visible sequences aligned?
3848 if (!viewport.getAlignment().isAligned(false))
3854 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3856 .getString("label.sequences_not_aligned"),
3857 JOptionPane.WARNING_MESSAGE);
3862 if (viewport.getAlignment().getHeight() < 2)
3867 tp = new TreePanel(alignPanel, type, pwType);
3872 if (viewport.viewName != null)
3874 title += viewport.viewName + " of ";
3877 title += this.title;
3879 Desktop.addInternalFrame(tp, title, 600, 500);
3890 public void addSortByOrderMenuItem(String title,
3891 final AlignmentOrder order)
3893 final JMenuItem item = new JMenuItem("by " + title);
3895 item.addActionListener(new java.awt.event.ActionListener()
3898 public void actionPerformed(ActionEvent e)
3900 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3902 // TODO: JBPNote - have to map order entries to curent SequenceI
3904 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3906 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3909 alignPanel.paintAlignment(true);
3915 * Add a new sort by annotation score menu item
3918 * the menu to add the option to
3920 * the label used to retrieve scores for each sequence on the
3923 public void addSortByAnnotScoreMenuItem(JMenu sort,
3924 final String scoreLabel)
3926 final JMenuItem item = new JMenuItem(scoreLabel);
3928 item.addActionListener(new java.awt.event.ActionListener()
3931 public void actionPerformed(ActionEvent e)
3933 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3934 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3935 viewport.getAlignment());// ,viewport.getSelectionGroup());
3936 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3937 viewport.getAlignment()));
3938 alignPanel.paintAlignment(true);
3944 * last hash for alignment's annotation array - used to minimise cost of
3947 protected int _annotationScoreVectorHash;
3950 * search the alignment and rebuild the sort by annotation score submenu the
3951 * last alignment annotation vector hash is stored to minimize cost of
3952 * rebuilding in subsequence calls.
3956 public void buildSortByAnnotationScoresMenu()
3958 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3963 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3965 sortByAnnotScore.removeAll();
3966 // almost certainly a quicker way to do this - but we keep it simple
3967 Hashtable scoreSorts = new Hashtable();
3968 AlignmentAnnotation aann[];
3969 for (SequenceI sqa : viewport.getAlignment().getSequences())
3971 aann = sqa.getAnnotation();
3972 for (int i = 0; aann != null && i < aann.length; i++)
3974 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3976 scoreSorts.put(aann[i].label, aann[i].label);
3980 Enumeration labels = scoreSorts.keys();
3981 while (labels.hasMoreElements())
3983 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3984 (String) labels.nextElement());
3986 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3989 _annotationScoreVectorHash = viewport.getAlignment()
3990 .getAlignmentAnnotation().hashCode();
3995 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3996 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3997 * call. Listeners are added to remove the menu item when the treePanel is
3998 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4002 * Displayed tree window.
4004 * SortBy menu item title.
4007 public void buildTreeMenu()
4009 calculateTree.removeAll();
4010 // build the calculate menu
4012 for (final String type : new String[]
4015 String treecalcnm = MessageManager.getString("label.tree_calc_"
4016 + type.toLowerCase());
4017 for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4019 JMenuItem tm = new JMenuItem();
4020 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4021 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4023 String smn = MessageManager.getStringOrReturn(
4024 "label.score_model_", sm.getName());
4025 final String title = MessageManager.formatMessage(
4026 "label.treecalc_title", treecalcnm, smn);
4027 tm.setText(title);//
4028 tm.addActionListener(new java.awt.event.ActionListener()
4031 public void actionPerformed(ActionEvent e)
4033 NewTreePanel(type, (String) pwtype, title);
4036 calculateTree.add(tm);
4041 sortByTreeMenu.removeAll();
4043 Vector comps = (Vector) PaintRefresher.components.get(viewport
4044 .getSequenceSetId());
4045 Vector treePanels = new Vector();
4046 int i, iSize = comps.size();
4047 for (i = 0; i < iSize; i++)
4049 if (comps.elementAt(i) instanceof TreePanel)
4051 treePanels.add(comps.elementAt(i));
4055 iSize = treePanels.size();
4059 sortByTreeMenu.setVisible(false);
4063 sortByTreeMenu.setVisible(true);
4065 for (i = 0; i < treePanels.size(); i++)
4067 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4068 final JMenuItem item = new JMenuItem(tp.getTitle());
4069 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4070 item.addActionListener(new java.awt.event.ActionListener()
4073 public void actionPerformed(ActionEvent e)
4075 tp.sortByTree_actionPerformed(null);
4076 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4081 sortByTreeMenu.add(item);
4085 public boolean sortBy(AlignmentOrder alorder, String undoname)
4087 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4088 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4089 if (undoname != null)
4091 addHistoryItem(new OrderCommand(undoname, oldOrder,
4092 viewport.getAlignment()));
4094 alignPanel.paintAlignment(true);
4099 * Work out whether the whole set of sequences or just the selected set will
4100 * be submitted for multiple alignment.
4103 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4105 // Now, check we have enough sequences
4106 AlignmentView msa = null;
4108 if ((viewport.getSelectionGroup() != null)
4109 && (viewport.getSelectionGroup().getSize() > 1))
4111 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4112 // some common interface!
4114 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4115 * SequenceI[sz = seqs.getSize(false)];
4117 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4118 * seqs.getSequenceAt(i); }
4120 msa = viewport.getAlignmentView(true);
4125 * Vector seqs = viewport.getAlignment().getSequences();
4127 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
4129 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
4130 * seqs.elementAt(i); } }
4132 msa = viewport.getAlignmentView(false);
4138 * Decides what is submitted to a secondary structure prediction service: the
4139 * first sequence in the alignment, or in the current selection, or, if the
4140 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4141 * region or the whole alignment. (where the first sequence in the set is the
4142 * one that the prediction will be for).
4144 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4146 AlignmentView seqs = null;
4148 if ((viewport.getSelectionGroup() != null)
4149 && (viewport.getSelectionGroup().getSize() > 0))
4151 seqs = viewport.getAlignmentView(true);
4155 seqs = viewport.getAlignmentView(false);
4157 // limit sequences - JBPNote in future - could spawn multiple prediction
4159 // TODO: viewport.getAlignment().isAligned is a global state - the local
4160 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4161 if (!viewport.getAlignment().isAligned(false))
4163 seqs.setSequences(new SeqCigar[]
4164 { seqs.getSequences()[0] });
4165 // TODO: if seqs.getSequences().length>1 then should really have warned
4179 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4181 // Pick the tree file
4182 JalviewFileChooser chooser = new JalviewFileChooser(
4183 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4184 chooser.setFileView(new JalviewFileView());
4185 chooser.setDialogTitle(MessageManager
4186 .getString("label.select_newick_like_tree_file"));
4187 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4189 int value = chooser.showOpenDialog(null);
4191 if (value == JalviewFileChooser.APPROVE_OPTION)
4193 String choice = chooser.getSelectedFile().getPath();
4194 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4195 jalview.io.NewickFile fin = null;
4198 fin = new jalview.io.NewickFile(choice, "File");
4199 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4200 } catch (Exception ex)
4207 .getString("label.problem_reading_tree_file"),
4208 JOptionPane.WARNING_MESSAGE);
4209 ex.printStackTrace();
4211 if (fin != null && fin.hasWarningMessage())
4213 JOptionPane.showMessageDialog(Desktop.desktop, fin
4214 .getWarningMessage(), MessageManager
4215 .getString("label.possible_problem_with_tree_file"),
4216 JOptionPane.WARNING_MESSAGE);
4222 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4224 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4227 public TreePanel ShowNewickTree(NewickFile nf, String title)
4229 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4232 public TreePanel ShowNewickTree(NewickFile nf, String title,
4233 AlignmentView input)
4235 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4238 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4239 int h, int x, int y)
4241 return ShowNewickTree(nf, title, null, w, h, x, y);
4245 * Add a treeviewer for the tree extracted from a newick file object to the
4246 * current alignment view
4253 * Associated alignment input data (or null)
4262 * @return TreePanel handle
4264 public TreePanel ShowNewickTree(NewickFile nf, String title,
4265 AlignmentView input, int w, int h, int x, int y)
4267 TreePanel tp = null;
4273 if (nf.getTree() != null)
4275 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4281 tp.setLocation(x, y);
4284 Desktop.addInternalFrame(tp, title, w, h);
4286 } catch (Exception ex)
4288 ex.printStackTrace();
4294 private boolean buildingMenu = false;
4297 * Generates menu items and listener event actions for web service clients
4300 public void BuildWebServiceMenu()
4302 while (buildingMenu)
4306 System.err.println("Waiting for building menu to finish.");
4308 } catch (Exception e)
4313 final AlignFrame me = this;
4314 buildingMenu = true;
4315 new Thread(new Runnable()
4320 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4323 System.err.println("Building ws menu again "
4324 + Thread.currentThread());
4325 // TODO: add support for context dependent disabling of services based
4327 // alignment and current selection
4328 // TODO: add additional serviceHandle parameter to specify abstract
4330 // class independently of AbstractName
4331 // TODO: add in rediscovery GUI function to restart discoverer
4332 // TODO: group services by location as well as function and/or
4334 // object broker mechanism.
4335 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4336 final IProgressIndicator af = me;
4337 final JMenu msawsmenu = new JMenu("Alignment");
4338 final JMenu secstrmenu = new JMenu(
4339 "Secondary Structure Prediction");
4340 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4341 final JMenu analymenu = new JMenu("Analysis");
4342 final JMenu dismenu = new JMenu("Protein Disorder");
4343 // JAL-940 - only show secondary structure prediction services from
4344 // the legacy server
4345 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4347 Discoverer.services != null && (Discoverer.services.size() > 0))
4349 // TODO: refactor to allow list of AbstractName/Handler bindings to
4351 // stored or retrieved from elsewhere
4352 // No MSAWS used any more:
4353 // Vector msaws = null; // (Vector)
4354 // Discoverer.services.get("MsaWS");
4355 Vector secstrpr = (Vector) Discoverer.services
4357 if (secstrpr != null)
4359 // Add any secondary structure prediction services
4360 for (int i = 0, j = secstrpr.size(); i < j; i++)
4362 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4364 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4365 .getServiceClient(sh);
4366 int p = secstrmenu.getItemCount();
4367 impl.attachWSMenuEntry(secstrmenu, me);
4368 int q = secstrmenu.getItemCount();
4369 for (int litm = p; litm < q; litm++)
4371 legacyItems.add(secstrmenu.getItem(litm));
4377 // Add all submenus in the order they should appear on the web
4379 wsmenu.add(msawsmenu);
4380 wsmenu.add(secstrmenu);
4381 wsmenu.add(dismenu);
4382 wsmenu.add(analymenu);
4383 // No search services yet
4384 // wsmenu.add(seqsrchmenu);
4386 javax.swing.SwingUtilities.invokeLater(new Runnable()
4393 webService.removeAll();
4394 // first, add discovered services onto the webservices menu
4395 if (wsmenu.size() > 0)
4397 for (int i = 0, j = wsmenu.size(); i < j; i++)
4399 webService.add(wsmenu.get(i));
4404 webService.add(me.webServiceNoServices);
4406 // TODO: move into separate menu builder class.
4407 boolean new_sspred = false;
4408 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4410 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4411 if (jws2servs != null)
4413 if (jws2servs.hasServices())
4415 jws2servs.attachWSMenuEntry(webService, me);
4416 for (Jws2Instance sv : jws2servs.getServices())
4418 if (sv.description.toLowerCase().contains("jpred"))
4420 for (JMenuItem jmi : legacyItems)
4422 jmi.setVisible(false);
4428 if (jws2servs.isRunning())
4430 JMenuItem tm = new JMenuItem(
4431 "Still discovering JABA Services");
4432 tm.setEnabled(false);
4437 build_urlServiceMenu(me.webService);
4438 build_fetchdbmenu(webService);
4439 for (JMenu item : wsmenu)
4441 if (item.getItemCount() == 0)
4443 item.setEnabled(false);
4447 item.setEnabled(true);
4450 } catch (Exception e)
4453 .debug("Exception during web service menu building process.",
4459 } catch (Exception e)
4464 buildingMenu = false;
4471 * construct any groupURL type service menu entries.
4475 private void build_urlServiceMenu(JMenu webService)
4477 // TODO: remove this code when 2.7 is released
4478 // DEBUG - alignmentView
4480 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4481 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4483 * @Override public void actionPerformed(ActionEvent e) {
4484 * jalview.datamodel.AlignmentView
4485 * .testSelectionViews(af.viewport.getAlignment(),
4486 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4488 * }); webService.add(testAlView);
4490 // TODO: refactor to RestClient discoverer and merge menu entries for
4491 // rest-style services with other types of analysis/calculation service
4492 // SHmmr test client - still being implemented.
4493 // DEBUG - alignmentView
4495 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4498 client.attachWSMenuEntry(
4499 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4505 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4506 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4507 * getProperty("LAST_DIRECTORY"));
4509 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4510 * to Vamsas file"); chooser.setToolTipText("Export");
4512 * int value = chooser.showSaveDialog(this);
4514 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4515 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4516 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4517 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4520 * prototype of an automatically enabled/disabled analysis function
4523 protected void setShowProductsEnabled()
4525 SequenceI[] selection = viewport.getSequenceSelection();
4526 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4527 viewport.getAlignment().getDataset()))
4529 showProducts.setEnabled(true);
4534 showProducts.setEnabled(false);
4539 * search selection for sequence xRef products and build the show products
4544 * @return true if showProducts menu should be enabled.
4546 public boolean canShowProducts(SequenceI[] selection,
4547 boolean isRegionSelection, Alignment dataset)
4549 boolean showp = false;
4552 showProducts.removeAll();
4553 final boolean dna = viewport.getAlignment().isNucleotide();
4554 final Alignment ds = dataset;
4555 String[] ptypes = (selection == null || selection.length == 0) ? null
4556 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4558 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4559 // selection, dataset, true);
4560 final SequenceI[] sel = selection;
4561 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4564 final boolean isRegSel = isRegionSelection;
4565 final AlignFrame af = this;
4566 final String source = ptypes[t];
4567 JMenuItem xtype = new JMenuItem(ptypes[t]);
4568 xtype.addActionListener(new ActionListener()
4572 public void actionPerformed(ActionEvent e)
4574 // TODO: new thread for this call with vis-delay
4575 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4576 isRegSel, dna, source);
4580 showProducts.add(xtype);
4582 showProducts.setVisible(showp);
4583 showProducts.setEnabled(showp);
4584 } catch (Exception e)
4586 jalview.bin.Cache.log
4587 .warn("canTranslate threw an exception - please report to help@jalview.org",
4594 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4595 boolean isRegSel, boolean dna, String source)
4597 final boolean fisRegSel = isRegSel;
4598 final boolean fdna = dna;
4599 final String fsrc = source;
4600 final AlignFrame ths = this;
4601 final SequenceI[] fsel = sel;
4602 Runnable foo = new Runnable()
4608 final long sttime = System.currentTimeMillis();
4609 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4612 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4616 Alignment prods = CrossRef
4617 .findXrefSequences(fsel, fdna, fsrc, ds);
4620 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4621 for (int s = 0; s < sprods.length; s++)
4623 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4624 if (ds.getSequences() == null
4625 || !ds.getSequences().contains(
4626 sprods[s].getDatasetSequence()))
4627 ds.addSequence(sprods[s].getDatasetSequence());
4628 sprods[s].updatePDBIds();
4630 Alignment al = new Alignment(sprods);
4631 AlignedCodonFrame[] cf = prods.getCodonFrames();
4633 for (int s = 0; cf != null && s < cf.length; s++)
4635 al.addCodonFrame(cf[s]);
4638 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4640 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4641 + " for " + ((fisRegSel) ? "selected region of " : "")
4643 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4648 System.err.println("No Sequences generated for xRef type "
4651 } catch (Exception e)
4653 jalview.bin.Cache.log.error(
4654 "Exception when finding crossreferences", e);
4655 } catch (OutOfMemoryError e)
4657 new OOMWarning("whilst fetching crossreferences", e);
4660 jalview.bin.Cache.log.error("Error when finding crossreferences",
4663 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4668 Thread frunner = new Thread(foo);
4672 public boolean canShowTranslationProducts(SequenceI[] selection,
4673 AlignmentI alignment)
4678 return (jalview.analysis.Dna.canTranslate(selection,
4679 viewport.getViewAsVisibleContigs(true)));
4680 } catch (Exception e)
4682 jalview.bin.Cache.log
4683 .warn("canTranslate threw an exception - please report to help@jalview.org",
4690 public void showProducts_actionPerformed(ActionEvent e)
4692 // /////////////////////////////
4693 // Collect Data to be translated/transferred
4695 SequenceI[] selection = viewport.getSequenceSelection();
4696 AlignmentI al = null;
4699 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4700 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4701 viewport.getAlignment().getDataset());
4702 } catch (Exception ex)
4705 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4713 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4714 MessageManager.getString("label.translation_failed"),
4715 JOptionPane.WARNING_MESSAGE);
4719 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4720 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4721 "label.translation_of_params", new String[]
4722 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4727 public void showTranslation_actionPerformed(ActionEvent e)
4729 // /////////////////////////////
4730 // Collect Data to be translated/transferred
4732 SequenceI[] selection = viewport.getSequenceSelection();
4733 String[] seqstring = viewport.getViewAsString(true);
4734 AlignmentI al = null;
4737 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4738 viewport.getViewAsVisibleContigs(true), viewport
4739 .getGapCharacter(), viewport.getAlignment()
4740 .getAlignmentAnnotation(), viewport.getAlignment()
4741 .getWidth(), viewport.getAlignment().getDataset());
4742 } catch (Exception ex)
4745 jalview.bin.Cache.log.error(
4746 "Exception during translation. Please report this !", ex);
4751 .getString("label.error_when_translating_sequences_submit_bug_report"),
4753 .getString("label.implementation_error")
4755 .getString("translation_failed"),
4756 JOptionPane.ERROR_MESSAGE);
4765 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4766 MessageManager.getString("label.translation_failed"),
4767 JOptionPane.WARNING_MESSAGE);
4771 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4772 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4773 "label.translation_of_params", new String[]
4774 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4779 * Try to load a features file onto the alignment.
4782 * contents or path to retrieve file
4784 * access mode of file (see jalview.io.AlignFile)
4785 * @return true if features file was parsed corectly.
4787 public boolean parseFeaturesFile(String file, String type)
4789 boolean featuresFile = false;
4792 featuresFile = new FeaturesFile(file, type).parse(viewport
4793 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4794 .getFeatureRenderer().featureColours, false,
4795 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4796 } catch (Exception ex)
4798 ex.printStackTrace();
4803 viewport.showSequenceFeatures = true;
4804 showSeqFeatures.setSelected(true);
4805 if (alignPanel.seqPanel.seqCanvas.fr != null)
4807 // update the min/max ranges where necessary
4808 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4810 if (featureSettings != null)
4812 featureSettings.setTableData();
4814 alignPanel.paintAlignment(true);
4817 return featuresFile;
4821 public void dragEnter(DropTargetDragEvent evt)
4826 public void dragExit(DropTargetEvent evt)
4831 public void dragOver(DropTargetDragEvent evt)
4836 public void dropActionChanged(DropTargetDragEvent evt)
4841 public void drop(DropTargetDropEvent evt)
4843 Transferable t = evt.getTransferable();
4844 java.util.List files = null;
4848 DataFlavor uriListFlavor = new DataFlavor(
4849 "text/uri-list;class=java.lang.String");
4850 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4852 // Works on Windows and MacOSX
4853 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4854 files = (java.util.List) t
4855 .getTransferData(DataFlavor.javaFileListFlavor);
4857 else if (t.isDataFlavorSupported(uriListFlavor))
4859 // This is used by Unix drag system
4860 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4861 String data = (String) t.getTransferData(uriListFlavor);
4862 files = new java.util.ArrayList(1);
4863 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4864 data, "\r\n"); st.hasMoreTokens();)
4866 String s = st.nextToken();
4867 if (s.startsWith("#"))
4869 // the line is a comment (as per the RFC 2483)
4873 java.net.URI uri = new java.net.URI(s);
4874 // check to see if we can handle this kind of URI
4875 if (uri.getScheme().toLowerCase().startsWith("http"))
4877 files.add(uri.toString());
4881 // otherwise preserve old behaviour: catch all for file objects
4882 java.io.File file = new java.io.File(uri);
4883 files.add(file.toString());
4887 } catch (Exception e)
4889 e.printStackTrace();
4895 // check to see if any of these files have names matching sequences in
4897 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4898 .getAlignment().getSequencesArray());
4900 * Object[] { String,SequenceI}
4902 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4903 ArrayList<String> filesnotmatched = new ArrayList<String>();
4904 for (int i = 0; i < files.size(); i++)
4906 String file = files.get(i).toString();
4908 String protocol = FormatAdapter.checkProtocol(file);
4909 if (protocol == jalview.io.FormatAdapter.FILE)
4911 File fl = new File(file);
4912 pdbfn = fl.getName();
4914 else if (protocol == jalview.io.FormatAdapter.URL)
4916 URL url = new URL(file);
4917 pdbfn = url.getFile();
4919 if (pdbfn.length() > 0)
4921 // attempt to find a match in the alignment
4922 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4923 int l = 0, c = pdbfn.indexOf(".");
4924 while (mtch == null && c != -1)
4929 } while ((c = pdbfn.indexOf(".", l)) > l);
4932 pdbfn = pdbfn.substring(0, l);
4934 mtch = idm.findAllIdMatches(pdbfn);
4941 type = new IdentifyFile().Identify(file, protocol);
4942 } catch (Exception ex)
4948 if (type.equalsIgnoreCase("PDB"))
4950 filesmatched.add(new Object[]
4951 { file, protocol, mtch });
4956 // File wasn't named like one of the sequences or wasn't a PDB file.
4957 filesnotmatched.add(file);
4961 if (filesmatched.size() > 0)
4963 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4969 "label.automatically_associate_pdb_files_with_sequences_same_name",
4976 .getString("label.automatically_associate_pdb_files_by_name"),
4977 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4980 for (Object[] fm : filesmatched)
4982 // try and associate
4983 // TODO: may want to set a standard ID naming formalism for
4984 // associating PDB files which have no IDs.
4985 for (SequenceI toassoc : (SequenceI[]) fm[2])
4987 PDBEntry pe = new AssociatePdbFileWithSeq()
4988 .associatePdbWithSeq((String) fm[0],
4989 (String) fm[1], toassoc, false);
4992 System.err.println("Associated file : "
4993 + ((String) fm[0]) + " with "
4994 + toassoc.getDisplayId(true));
4998 alignPanel.paintAlignment(true);
5002 if (filesnotmatched.size() > 0)
5005 && (Cache.getDefault(
5006 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5011 "label.ignore_unmatched_dropped_files_info",
5018 .getString("label.ignore_unmatched_dropped_files"),
5019 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5023 for (String fn : filesnotmatched)
5025 loadJalviewDataFile(fn, null, null, null);
5029 } catch (Exception ex)
5031 ex.printStackTrace();
5037 * Attempt to load a "dropped" file or URL string: First by testing whether
5038 * it's and Annotation file, then a JNet file, and finally a features file. If
5039 * all are false then the user may have dropped an alignment file onto this
5043 * either a filename or a URL string.
5045 public void loadJalviewDataFile(String file, String protocol,
5046 String format, SequenceI assocSeq)
5050 if (protocol == null)
5052 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5054 // if the file isn't identified, or not positively identified as some
5055 // other filetype (PFAM is default unidentified alignment file type) then
5056 // try to parse as annotation.
5057 boolean isAnnotation = (format == null || format
5058 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5059 .readAnnotationFile(viewport.getAlignment(), file, protocol)
5064 // first see if its a T-COFFEE score file
5065 TCoffeeScoreFile tcf = null;
5068 tcf = new TCoffeeScoreFile(file, protocol);
5071 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5073 tcoffeeColour.setEnabled(true);
5074 tcoffeeColour.setSelected(true);
5075 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5076 isAnnotation = true;
5078 .setText(MessageManager
5079 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5083 // some problem - if no warning its probable that the ID matching
5084 // process didn't work
5088 tcf.getWarningMessage() == null ? MessageManager
5089 .getString("label.check_file_matches_sequence_ids_alignment")
5090 : tcf.getWarningMessage(),
5092 .getString("label.problem_reading_tcoffee_score_file"),
5093 JOptionPane.WARNING_MESSAGE);
5100 } catch (Exception x)
5103 .debug("Exception when processing data source as T-COFFEE score file",
5109 // try to see if its a JNet 'concise' style annotation file *before*
5111 // try to parse it as a features file
5114 format = new IdentifyFile().Identify(file, protocol);
5116 if (format.equalsIgnoreCase("JnetFile"))
5118 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5120 new JnetAnnotationMaker().add_annotation(predictions,
5121 viewport.getAlignment(), 0, false);
5122 isAnnotation = true;
5127 * if (format.equalsIgnoreCase("PDB")) {
5129 * String pdbfn = ""; // try to match up filename with sequence id
5130 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5131 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5132 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5133 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5134 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5135 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5136 * // attempt to find a match in the alignment SequenceI mtch =
5137 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5138 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5139 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5140 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5141 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5142 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5143 * { System.err.println("Associated file : " + file + " with " +
5144 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5145 * TODO: maybe need to load as normal otherwise return; } }
5147 // try to parse it as a features file
5148 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5149 // if it wasn't a features file then we just treat it as a general
5150 // alignment file to load into the current view.
5153 new FileLoader().LoadFile(viewport, file, protocol, format);
5157 alignPanel.paintAlignment(true);
5165 alignPanel.adjustAnnotationHeight();
5166 viewport.updateSequenceIdColours();
5167 buildSortByAnnotationScoresMenu();
5168 alignPanel.paintAlignment(true);
5170 } catch (Exception ex)
5172 ex.printStackTrace();
5173 } catch (OutOfMemoryError oom)
5178 } catch (Exception x)
5184 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5185 : "using " + protocol + " from " + file)
5187 + (format != null ? "(parsing as '" + format
5188 + "' file)" : ""), oom, Desktop.desktop);
5193 public void tabSelectionChanged(int index)
5197 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5198 viewport = alignPanel.av;
5199 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5200 setMenusFromViewport(viewport);
5205 public void tabbedPane_mousePressed(MouseEvent e)
5207 if (SwingUtilities.isRightMouseButton(e))
5209 String reply = JOptionPane.showInternalInputDialog(this,
5210 MessageManager.getString("label.enter_view_name"),
5211 MessageManager.getString("label.enter_view_name"),
5212 JOptionPane.QUESTION_MESSAGE);
5216 viewport.viewName = reply;
5217 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5222 public AlignViewport getCurrentView()
5228 * Open the dialog for regex description parsing.
5231 protected void extractScores_actionPerformed(ActionEvent e)
5233 ParseProperties pp = new jalview.analysis.ParseProperties(
5234 viewport.getAlignment());
5235 // TODO: verify regex and introduce GUI dialog for version 2.5
5236 // if (pp.getScoresFromDescription("col", "score column ",
5237 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5239 if (pp.getScoresFromDescription("description column",
5240 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5242 buildSortByAnnotationScoresMenu();
5250 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5254 protected void showDbRefs_actionPerformed(ActionEvent e)
5256 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5262 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5266 protected void showNpFeats_actionPerformed(ActionEvent e)
5268 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5272 * find the viewport amongst the tabs in this alignment frame and close that
5277 public boolean closeView(AlignViewport av)
5281 this.closeMenuItem_actionPerformed(false);
5284 Component[] comp = tabbedPane.getComponents();
5285 for (int i = 0; comp != null && i < comp.length; i++)
5287 if (comp[i] instanceof AlignmentPanel)
5289 if (((AlignmentPanel) comp[i]).av == av)
5292 closeView((AlignmentPanel) comp[i]);
5300 protected void build_fetchdbmenu(JMenu webService)
5302 // Temporary hack - DBRef Fetcher always top level ws entry.
5303 // TODO We probably want to store a sequence database checklist in
5304 // preferences and have checkboxes.. rather than individual sources selected
5306 final JMenu rfetch = new JMenu(
5307 MessageManager.getString("action.fetch_db_references"));
5308 rfetch.setToolTipText(MessageManager
5309 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5310 webService.add(rfetch);
5312 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5313 MessageManager.getString("option.trim_retrieved_seqs"));
5314 trimrs.setToolTipText(MessageManager
5315 .getString("label.trim_retrieved_sequences"));
5316 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5317 trimrs.addActionListener(new ActionListener()
5320 public void actionPerformed(ActionEvent e)
5322 trimrs.setSelected(trimrs.isSelected());
5323 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5324 Boolean.valueOf(trimrs.isSelected()).toString());
5328 JMenuItem fetchr = new JMenuItem(
5329 MessageManager.getString("label.standard_databases"));
5330 fetchr.setToolTipText(MessageManager
5331 .getString("label.fetch_embl_uniprot"));
5332 fetchr.addActionListener(new ActionListener()
5336 public void actionPerformed(ActionEvent e)
5338 new Thread(new Runnable()
5344 new jalview.ws.DBRefFetcher(alignPanel.av
5345 .getSequenceSelection(), alignPanel.alignFrame)
5346 .fetchDBRefs(false);
5354 final AlignFrame me = this;
5355 new Thread(new Runnable()
5360 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5361 .getSequenceFetcherSingleton(me);
5362 javax.swing.SwingUtilities.invokeLater(new Runnable()
5367 String[] dbclasses = sf.getOrderedSupportedSources();
5368 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5369 // jalview.util.QuickSort.sort(otherdb, otherdb);
5370 List<DbSourceProxy> otherdb;
5371 JMenu dfetch = new JMenu();
5372 JMenu ifetch = new JMenu();
5373 JMenuItem fetchr = null;
5374 int comp = 0, icomp = 0, mcomp = 15;
5375 String mname = null;
5377 for (String dbclass : dbclasses)
5379 otherdb = sf.getSourceProxy(dbclass);
5380 // add a single entry for this class, or submenu allowing 'fetch
5382 if (otherdb == null || otherdb.size() < 1)
5386 // List<DbSourceProxy> dbs=otherdb;
5387 // otherdb=new ArrayList<DbSourceProxy>();
5388 // for (DbSourceProxy db:dbs)
5390 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5394 mname = "From " + dbclass;
5396 if (otherdb.size() == 1)
5398 final DbSourceProxy[] dassource = otherdb
5399 .toArray(new DbSourceProxy[0]);
5400 DbSourceProxy src = otherdb.get(0);
5401 fetchr = new JMenuItem(src.getDbSource());
5402 fetchr.addActionListener(new ActionListener()
5406 public void actionPerformed(ActionEvent e)
5408 new Thread(new Runnable()
5414 new jalview.ws.DBRefFetcher(alignPanel.av
5415 .getSequenceSelection(),
5416 alignPanel.alignFrame, dassource)
5417 .fetchDBRefs(false);
5423 fetchr.setToolTipText("<html>"
5424 + JvSwingUtils.wrapTooltip("Retrieve from "
5425 + src.getDbName()) + "<html>");
5431 final DbSourceProxy[] dassource = otherdb
5432 .toArray(new DbSourceProxy[0]);
5434 DbSourceProxy src = otherdb.get(0);
5435 fetchr = new JMenuItem(MessageManager.formatMessage(
5436 "label.fetch_all_param", new String[]
5437 { src.getDbSource() }));
5438 fetchr.addActionListener(new ActionListener()
5441 public void actionPerformed(ActionEvent e)
5443 new Thread(new Runnable()
5449 new jalview.ws.DBRefFetcher(alignPanel.av
5450 .getSequenceSelection(),
5451 alignPanel.alignFrame, dassource)
5452 .fetchDBRefs(false);
5458 fetchr.setToolTipText("<html>"
5459 + JvSwingUtils.wrapTooltip("Retrieve from all "
5460 + otherdb.size() + " sources in "
5461 + src.getDbSource() + "<br>First is :"
5462 + src.getDbName()) + "<html>");
5465 // and then build the rest of the individual menus
5466 ifetch = new JMenu("Sources from " + src.getDbSource());
5468 String imname = null;
5470 for (DbSourceProxy sproxy : otherdb)
5472 String dbname = sproxy.getDbName();
5473 String sname = dbname.length() > 5 ? dbname.substring(0,
5474 5) + "..." : dbname;
5475 String msname = dbname.length() > 10 ? dbname.substring(
5476 0, 10) + "..." : dbname;
5479 imname = "from '" + sname + "'";
5481 fetchr = new JMenuItem(msname);
5482 final DbSourceProxy[] dassrc =
5484 fetchr.addActionListener(new ActionListener()
5488 public void actionPerformed(ActionEvent e)
5490 new Thread(new Runnable()
5496 new jalview.ws.DBRefFetcher(alignPanel.av
5497 .getSequenceSelection(),
5498 alignPanel.alignFrame, dassrc)
5499 .fetchDBRefs(false);
5505 fetchr.setToolTipText("<html>"
5506 + JvSwingUtils.wrapTooltip("Retrieve from "
5507 + dbname) + "</html>");
5510 if (++icomp >= mcomp || i == (otherdb.size()))
5512 ifetch.setText(MessageManager.formatMessage(
5513 "label.source_to_target", imname, sname));
5515 ifetch = new JMenu();
5523 if (comp >= mcomp || dbi >= (dbclasses.length))
5525 dfetch.setText(MessageManager.formatMessage(
5526 "label.source_to_target", mname, dbclass));
5528 dfetch = new JMenu();
5541 * Left justify the whole alignment.
5544 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5546 AlignmentI al = viewport.getAlignment();
5548 viewport.firePropertyChange("alignment", null, al);
5552 * Right justify the whole alignment.
5555 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5557 AlignmentI al = viewport.getAlignment();
5559 viewport.firePropertyChange("alignment", null, al);
5562 public void setShowSeqFeatures(boolean b)
5564 showSeqFeatures.setSelected(true);
5565 viewport.setShowSequenceFeatures(true);
5572 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5573 * awt.event.ActionEvent)
5576 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5578 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5579 alignPanel.paintAlignment(true);
5586 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5590 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5592 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5593 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5601 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5602 * .event.ActionEvent)
5605 protected void showGroupConservation_actionPerformed(ActionEvent e)
5607 viewport.setShowGroupConservation(showGroupConservation.getState());
5608 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5615 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5616 * .event.ActionEvent)
5619 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5621 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5622 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5629 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5630 * .event.ActionEvent)
5633 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5635 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5636 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5640 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5642 showSequenceLogo.setState(true);
5643 viewport.setShowSequenceLogo(true);
5644 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5645 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5649 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5651 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5658 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5659 * .event.ActionEvent)
5662 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5664 if (avc.makeGroupsFromSelection())
5666 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5667 alignPanel.updateAnnotation();
5668 alignPanel.paintAlignment(true);
5673 protected void createGroup_actionPerformed(ActionEvent e)
5675 if (avc.createGroup())
5677 alignPanel.alignmentChanged();
5682 protected void unGroup_actionPerformed(ActionEvent e)
5686 alignPanel.alignmentChanged();
5691 * make the given alignmentPanel the currently selected tab
5693 * @param alignmentPanel
5695 public void setDisplayedView(AlignmentPanel alignmentPanel)
5697 if (!viewport.getSequenceSetId().equals(
5698 alignmentPanel.av.getSequenceSetId()))
5701 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5703 if (tabbedPane != null
5704 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5705 .getSelectedIndex())
5707 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5712 * On menu option, open a panel to allow choice of annotation types to
5716 protected void chooseAnnotations_actionPerformed()
5718 new AnnotationChooser(this.alignPanel);
5722 * Get a list of unique annotation types for the alignment, optionally
5723 * restricted to sequence-specific annotations.
5725 protected List<String> getAnnotationTypes(boolean sequenceSpecificOnly)
5727 // TODO move this to an AlignmentUtils class or similar
5728 List<String> types = new ArrayList<String>();
5729 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5730 .getAlignmentAnnotation())
5732 if (sequenceSpecificOnly && aa.sequenceRef == null)
5736 String type = aa.label;
5737 if (!types.contains(type))
5746 * Action on selection of an annotation type to Show or Hide.
5752 protected void showHideAnnotation_actionPerformed(String type, boolean doShow)
5754 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5755 .getAlignmentAnnotation())
5757 if (type.equals(aa.label))
5759 aa.visible = doShow;
5762 this.alignPanel.paintAlignment(true);
5766 * Dynamically build the list of annotation types to show or hide.
5769 protected void buildShowHideAnnotationMenus()
5771 showAnnotations.removeAll();
5772 hideAnnotations.removeAll();
5774 List<String> types = getAnnotationTypes(false);
5775 for (final String type : types)
5777 final JMenuItem showitem = new JMenuItem(type);
5778 showitem.addActionListener(new java.awt.event.ActionListener()
5781 public void actionPerformed(ActionEvent e)
5783 showHideAnnotation_actionPerformed(type, true);
5786 showAnnotations.add(showitem);
5787 final JMenuItem hideitem = new JMenuItem(type);
5788 hideitem.addActionListener(new java.awt.event.ActionListener()
5791 public void actionPerformed(ActionEvent e)
5793 showHideAnnotation_actionPerformed(type, false);
5796 hideAnnotations.add(hideitem);
5801 class PrintThread extends Thread
5805 public PrintThread(AlignmentPanel ap)
5810 static PageFormat pf;
5815 PrinterJob printJob = PrinterJob.getPrinterJob();
5819 printJob.setPrintable(ap, pf);
5823 printJob.setPrintable(ap);
5826 if (printJob.printDialog())
5831 } catch (Exception PrintException)
5833 PrintException.printStackTrace();