2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.ScoreModelI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenSequences;
57 import jalview.datamodel.PDBEntry;
58 import jalview.datamodel.SeqCigar;
59 import jalview.datamodel.Sequence;
60 import jalview.datamodel.SequenceGroup;
61 import jalview.datamodel.SequenceI;
62 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
63 import jalview.io.AlignmentProperties;
64 import jalview.io.AnnotationFile;
65 import jalview.io.BioJsHTMLOutput;
66 import jalview.io.FileLoader;
67 import jalview.io.FormatAdapter;
68 import jalview.io.HtmlSvgOutput;
69 import jalview.io.IdentifyFile;
70 import jalview.io.JalviewFileChooser;
71 import jalview.io.JalviewFileView;
72 import jalview.io.JnetAnnotationMaker;
73 import jalview.io.NewickFile;
74 import jalview.io.TCoffeeScoreFile;
75 import jalview.jbgui.GAlignFrame;
76 import jalview.schemes.Blosum62ColourScheme;
77 import jalview.schemes.BuriedColourScheme;
78 import jalview.schemes.ClustalxColourScheme;
79 import jalview.schemes.ColourSchemeI;
80 import jalview.schemes.ColourSchemeProperty;
81 import jalview.schemes.HelixColourScheme;
82 import jalview.schemes.HydrophobicColourScheme;
83 import jalview.schemes.NucleotideColourScheme;
84 import jalview.schemes.PIDColourScheme;
85 import jalview.schemes.PurinePyrimidineColourScheme;
86 import jalview.schemes.RNAHelicesColourChooser;
87 import jalview.schemes.ResidueProperties;
88 import jalview.schemes.StrandColourScheme;
89 import jalview.schemes.TCoffeeColourScheme;
90 import jalview.schemes.TaylorColourScheme;
91 import jalview.schemes.TurnColourScheme;
92 import jalview.schemes.UserColourScheme;
93 import jalview.schemes.ZappoColourScheme;
94 import jalview.structure.StructureSelectionManager;
95 import jalview.util.MessageManager;
96 import jalview.viewmodel.AlignmentViewport;
97 import jalview.ws.jws1.Discoverer;
98 import jalview.ws.jws2.Jws2Discoverer;
99 import jalview.ws.jws2.jabaws2.Jws2Instance;
100 import jalview.ws.seqfetcher.DbSourceProxy;
102 import java.awt.BorderLayout;
103 import java.awt.Component;
104 import java.awt.Rectangle;
105 import java.awt.Toolkit;
106 import java.awt.datatransfer.Clipboard;
107 import java.awt.datatransfer.DataFlavor;
108 import java.awt.datatransfer.StringSelection;
109 import java.awt.datatransfer.Transferable;
110 import java.awt.dnd.DnDConstants;
111 import java.awt.dnd.DropTargetDragEvent;
112 import java.awt.dnd.DropTargetDropEvent;
113 import java.awt.dnd.DropTargetEvent;
114 import java.awt.dnd.DropTargetListener;
115 import java.awt.event.ActionEvent;
116 import java.awt.event.ActionListener;
117 import java.awt.event.ItemEvent;
118 import java.awt.event.ItemListener;
119 import java.awt.event.KeyAdapter;
120 import java.awt.event.KeyEvent;
121 import java.awt.event.MouseAdapter;
122 import java.awt.event.MouseEvent;
123 import java.awt.print.PageFormat;
124 import java.awt.print.PrinterJob;
125 import java.beans.PropertyChangeEvent;
128 import java.util.ArrayList;
129 import java.util.Arrays;
130 import java.util.Deque;
131 import java.util.Enumeration;
132 import java.util.Hashtable;
133 import java.util.List;
134 import java.util.Set;
135 import java.util.Vector;
137 import javax.swing.JCheckBoxMenuItem;
138 import javax.swing.JEditorPane;
139 import javax.swing.JInternalFrame;
140 import javax.swing.JLayeredPane;
141 import javax.swing.JMenu;
142 import javax.swing.JMenuItem;
143 import javax.swing.JOptionPane;
144 import javax.swing.JRadioButtonMenuItem;
145 import javax.swing.JScrollPane;
146 import javax.swing.SwingUtilities;
152 * @version $Revision$
154 public class AlignFrame extends GAlignFrame implements DropTargetListener,
155 IProgressIndicator, AlignViewControllerGuiI
158 public static final int DEFAULT_WIDTH = 700;
160 public static final int DEFAULT_HEIGHT = 500;
163 * The currently displayed panel (selected tabbed view if more than one)
165 public AlignmentPanel alignPanel;
167 AlignViewport viewport;
169 public AlignViewControllerI avc;
171 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
174 * Last format used to load or save alignments in this window
176 String currentFileFormat = null;
179 * Current filename for this alignment
181 String fileName = null;
184 * Creates a new AlignFrame object with specific width and height.
190 public AlignFrame(AlignmentI al, int width, int height)
192 this(al, null, width, height);
196 * Creates a new AlignFrame object with specific width, height and
202 * @param sequenceSetId
204 public AlignFrame(AlignmentI al, int width, int height,
205 String sequenceSetId)
207 this(al, null, width, height, sequenceSetId);
211 * Creates a new AlignFrame object with specific width, height and
217 * @param sequenceSetId
220 public AlignFrame(AlignmentI al, int width, int height,
221 String sequenceSetId, String viewId)
223 this(al, null, width, height, sequenceSetId, viewId);
227 * new alignment window with hidden columns
231 * @param hiddenColumns
232 * ColumnSelection or null
234 * Width of alignment frame
238 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
239 int width, int height)
241 this(al, hiddenColumns, width, height, null);
246 * Create alignment frame for al with hiddenColumns, a specific width and
247 * height, and specific sequenceId
250 * @param hiddenColumns
253 * @param sequenceSetId
256 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
257 int width, int height, String sequenceSetId)
259 this(al, hiddenColumns, width, height, sequenceSetId, null);
263 * Create alignment frame for al with hiddenColumns, a specific width and
264 * height, and specific sequenceId
267 * @param hiddenColumns
270 * @param sequenceSetId
275 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
276 int width, int height, String sequenceSetId, String viewId)
278 setSize(width, height);
280 if (al.getDataset() == null)
285 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
287 alignPanel = new AlignmentPanel(this, viewport);
290 addAlignmentPanel(alignPanel, true);
294 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
295 ColumnSelection hiddenColumns, int width, int height)
297 setSize(width, height);
299 if (al.getDataset() == null)
304 viewport = new AlignViewport(al, hiddenColumns);
306 if (hiddenSeqs != null && hiddenSeqs.length > 0)
308 viewport.hideSequence(hiddenSeqs);
310 alignPanel = new AlignmentPanel(this, viewport);
311 addAlignmentPanel(alignPanel, true);
317 * Make a new AlignFrame from existing alignmentPanels
324 public AlignFrame(AlignmentPanel ap)
328 addAlignmentPanel(ap, false);
333 * initalise the alignframe from the underlying viewport data and the
338 if (!Jalview.isHeadlessMode())
340 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
343 avc = new jalview.controller.AlignViewController(this, viewport,
345 if (viewport.getAlignmentConservationAnnotation() == null)
347 BLOSUM62Colour.setEnabled(false);
348 conservationMenuItem.setEnabled(false);
349 modifyConservation.setEnabled(false);
350 // PIDColour.setEnabled(false);
351 // abovePIDThreshold.setEnabled(false);
352 // modifyPID.setEnabled(false);
355 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
358 if (sortby.equals("Id"))
360 sortIDMenuItem_actionPerformed(null);
362 else if (sortby.equals("Pairwise Identity"))
364 sortPairwiseMenuItem_actionPerformed(null);
367 if (Desktop.desktop != null)
369 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
370 addServiceListeners();
371 setGUINucleotide(viewport.getAlignment().isNucleotide());
374 setMenusFromViewport(viewport);
375 buildSortByAnnotationScoresMenu();
378 if (viewport.getWrapAlignment())
380 wrapMenuItem_actionPerformed(null);
383 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
385 this.overviewMenuItem_actionPerformed(null);
390 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
391 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
392 final String menuLabel = MessageManager
393 .getString("label.copy_format_from");
394 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
395 new ViewSetProvider()
399 public AlignmentPanel[] getAllAlignmentPanels()
402 origview.add(alignPanel);
403 // make an array of all alignment panels except for this one
404 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
405 Arrays.asList(Desktop.getAlignmentPanels(null)));
406 aps.remove(AlignFrame.this.alignPanel);
407 return aps.toArray(new AlignmentPanel[aps.size()]);
409 }, selviews, new ItemListener()
413 public void itemStateChanged(ItemEvent e)
415 if (origview.size() > 0)
417 final AlignmentPanel ap = origview.get(0);
420 * Copy the ViewStyle of the selected panel to 'this one'.
421 * Don't change value of 'scaleProteinAsCdna' unless copying
424 ViewStyleI vs = selviews.get(0).getAlignViewport()
426 boolean fromSplitFrame = selviews.get(0)
427 .getAlignViewport().getCodingComplement() != null;
430 vs.setScaleProteinAsCdna(ap.getAlignViewport()
431 .getViewStyle().isScaleProteinAsCdna());
433 ap.getAlignViewport().setViewStyle(vs);
436 * Also rescale ViewStyle of SplitFrame complement if there is
437 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
438 * the whole ViewStyle (allow cDNA protein to have different
441 AlignViewportI complement = ap.getAlignViewport()
442 .getCodingComplement();
443 if (complement != null && vs.isScaleProteinAsCdna())
445 AlignFrame af = Desktop.getAlignFrameFor(complement);
446 ((SplitFrame) af.getSplitViewContainer())
448 af.setMenusForViewport();
452 ap.setSelected(true);
453 ap.alignFrame.setMenusForViewport();
458 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
459 .indexOf("devel") > -1
460 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
461 .indexOf("test") > -1)
463 formatMenu.add(vsel);
469 * Change the filename and format for the alignment, and enable the 'reload'
470 * button functionality.
477 public void setFileName(String file, String format)
480 setFileFormat(format);
481 reload.setEnabled(true);
485 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
488 void addKeyListener()
490 addKeyListener(new KeyAdapter()
493 public void keyPressed(KeyEvent evt)
495 if (viewport.cursorMode
496 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
497 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
498 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
499 && Character.isDigit(evt.getKeyChar()))
501 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
504 switch (evt.getKeyCode())
507 case 27: // escape key
508 deselectAllSequenceMenuItem_actionPerformed(null);
512 case KeyEvent.VK_DOWN:
513 if (evt.isAltDown() || !viewport.cursorMode)
515 moveSelectedSequences(false);
517 if (viewport.cursorMode)
519 alignPanel.getSeqPanel().moveCursor(0, 1);
524 if (evt.isAltDown() || !viewport.cursorMode)
526 moveSelectedSequences(true);
528 if (viewport.cursorMode)
530 alignPanel.getSeqPanel().moveCursor(0, -1);
535 case KeyEvent.VK_LEFT:
536 if (evt.isAltDown() || !viewport.cursorMode)
538 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
542 alignPanel.getSeqPanel().moveCursor(-1, 0);
547 case KeyEvent.VK_RIGHT:
548 if (evt.isAltDown() || !viewport.cursorMode)
550 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
554 alignPanel.getSeqPanel().moveCursor(1, 0);
558 case KeyEvent.VK_SPACE:
559 if (viewport.cursorMode)
561 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
562 || evt.isShiftDown() || evt.isAltDown());
566 // case KeyEvent.VK_A:
567 // if (viewport.cursorMode)
569 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
570 // //System.out.println("A");
574 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
575 * System.out.println("closing bracket"); } break;
577 case KeyEvent.VK_DELETE:
578 case KeyEvent.VK_BACK_SPACE:
579 if (!viewport.cursorMode)
581 cut_actionPerformed(null);
585 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
586 || evt.isShiftDown() || evt.isAltDown());
592 if (viewport.cursorMode)
594 alignPanel.getSeqPanel().setCursorRow();
598 if (viewport.cursorMode && !evt.isControlDown())
600 alignPanel.getSeqPanel().setCursorColumn();
604 if (viewport.cursorMode)
606 alignPanel.getSeqPanel().setCursorPosition();
610 case KeyEvent.VK_ENTER:
611 case KeyEvent.VK_COMMA:
612 if (viewport.cursorMode)
614 alignPanel.getSeqPanel().setCursorRowAndColumn();
619 if (viewport.cursorMode)
621 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
625 if (viewport.cursorMode)
627 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
632 viewport.cursorMode = !viewport.cursorMode;
633 statusBar.setText(MessageManager.formatMessage(
634 "label.keyboard_editing_mode", new String[]
635 { (viewport.cursorMode ? "on" : "off") }));
636 if (viewport.cursorMode)
638 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
639 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
641 alignPanel.getSeqPanel().seqCanvas.repaint();
647 Help.showHelpWindow();
648 } catch (Exception ex)
650 ex.printStackTrace();
655 boolean toggleSeqs = !evt.isControlDown();
656 boolean toggleCols = !evt.isShiftDown();
657 toggleHiddenRegions(toggleSeqs, toggleCols);
660 case KeyEvent.VK_PAGE_UP:
661 if (viewport.getWrapAlignment())
663 alignPanel.scrollUp(true);
667 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
668 - viewport.endSeq + viewport.startSeq);
671 case KeyEvent.VK_PAGE_DOWN:
672 if (viewport.getWrapAlignment())
674 alignPanel.scrollUp(false);
678 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
679 + viewport.endSeq - viewport.startSeq);
686 public void keyReleased(KeyEvent evt)
688 switch (evt.getKeyCode())
690 case KeyEvent.VK_LEFT:
691 if (evt.isAltDown() || !viewport.cursorMode)
693 viewport.firePropertyChange("alignment", null, viewport
694 .getAlignment().getSequences());
698 case KeyEvent.VK_RIGHT:
699 if (evt.isAltDown() || !viewport.cursorMode)
701 viewport.firePropertyChange("alignment", null, viewport
702 .getAlignment().getSequences());
710 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
712 ap.alignFrame = this;
713 avc = new jalview.controller.AlignViewController(this, viewport,
718 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
720 int aSize = alignPanels.size();
722 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
724 if (aSize == 1 && ap.av.viewName == null)
726 this.getContentPane().add(ap, BorderLayout.CENTER);
732 setInitialTabVisible();
735 expandViews.setEnabled(true);
736 gatherViews.setEnabled(true);
737 tabbedPane.addTab(ap.av.viewName, ap);
739 ap.setVisible(false);
744 if (ap.av.isPadGaps())
746 ap.av.getAlignment().padGaps();
748 ap.av.updateConservation(ap);
749 ap.av.updateConsensus(ap);
750 ap.av.updateStrucConsensus(ap);
754 public void setInitialTabVisible()
756 expandViews.setEnabled(true);
757 gatherViews.setEnabled(true);
758 tabbedPane.setVisible(true);
759 AlignmentPanel first = alignPanels.get(0);
760 tabbedPane.addTab(first.av.viewName, first);
761 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
764 public AlignViewport getViewport()
769 /* Set up intrinsic listeners for dynamically generated GUI bits. */
770 private void addServiceListeners()
772 final java.beans.PropertyChangeListener thisListener;
773 Desktop.instance.addJalviewPropertyChangeListener("services",
774 thisListener = new java.beans.PropertyChangeListener()
777 public void propertyChange(PropertyChangeEvent evt)
779 // // System.out.println("Discoverer property change.");
780 // if (evt.getPropertyName().equals("services"))
782 SwingUtilities.invokeLater(new Runnable()
789 .println("Rebuild WS Menu for service change");
790 BuildWebServiceMenu();
797 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
800 public void internalFrameClosed(
801 javax.swing.event.InternalFrameEvent evt)
803 // System.out.println("deregistering discoverer listener");
804 Desktop.instance.removeJalviewPropertyChangeListener("services",
806 closeMenuItem_actionPerformed(true);
809 // Finally, build the menu once to get current service state
810 new Thread(new Runnable()
815 BuildWebServiceMenu();
821 * Configure menu items that vary according to whether the alignment is
822 * nucleotide or protein
826 public void setGUINucleotide(boolean nucleotide)
828 showTranslation.setVisible(nucleotide);
829 conservationMenuItem.setEnabled(!nucleotide);
830 modifyConservation.setEnabled(!nucleotide);
831 showGroupConservation.setEnabled(!nucleotide);
832 rnahelicesColour.setEnabled(nucleotide);
833 purinePyrimidineColour.setEnabled(nucleotide);
834 showComplementMenuItem.setText(MessageManager
835 .getString(nucleotide ? "label.protein" : "label.nucleotide"));
836 setColourSelected(jalview.bin.Cache.getDefault(
837 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
838 : Preferences.DEFAULT_COLOUR_PROT, "None"));
842 * set up menus for the current viewport. This may be called after any
843 * operation that affects the data in the current view (selection changed,
844 * etc) to update the menus to reflect the new state.
846 public void setMenusForViewport()
848 setMenusFromViewport(viewport);
852 * Need to call this method when tabs are selected for multiple views, or when
853 * loading from Jalview2XML.java
858 void setMenusFromViewport(AlignViewport av)
860 padGapsMenuitem.setSelected(av.isPadGaps());
861 colourTextMenuItem.setSelected(av.isShowColourText());
862 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
863 conservationMenuItem.setSelected(av.getConservationSelected());
864 seqLimits.setSelected(av.getShowJVSuffix());
865 idRightAlign.setSelected(av.isRightAlignIds());
866 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
867 renderGapsMenuItem.setSelected(av.isRenderGaps());
868 wrapMenuItem.setSelected(av.getWrapAlignment());
869 scaleAbove.setVisible(av.getWrapAlignment());
870 scaleLeft.setVisible(av.getWrapAlignment());
871 scaleRight.setVisible(av.getWrapAlignment());
872 annotationPanelMenuItem.setState(av.isShowAnnotation());
874 * Show/hide annotations only enabled if annotation panel is shown
876 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
877 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
878 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
879 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
880 viewBoxesMenuItem.setSelected(av.getShowBoxes());
881 viewTextMenuItem.setSelected(av.getShowText());
882 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
883 showGroupConsensus.setSelected(av.isShowGroupConsensus());
884 showGroupConservation.setSelected(av.isShowGroupConservation());
885 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
886 showSequenceLogo.setSelected(av.isShowSequenceLogo());
887 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
889 setColourSelected(ColourSchemeProperty.getColourName(av
890 .getGlobalColourScheme()));
892 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
893 hiddenMarkers.setState(av.getShowHiddenMarkers());
894 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
895 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
896 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
897 autoCalculate.setSelected(av.autoCalculateConsensus);
898 sortByTree.setSelected(av.sortByTree);
899 listenToViewSelections.setSelected(av.followSelection);
900 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
902 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
903 setShowProductsEnabled();
907 private IProgressIndicator progressBar;
912 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
915 public void setProgressBar(String message, long id)
917 progressBar.setProgressBar(message, id);
921 public void registerHandler(final long id,
922 final IProgressIndicatorHandler handler)
924 progressBar.registerHandler(id, handler);
929 * @return true if any progress bars are still active
932 public boolean operationInProgress()
934 return progressBar.operationInProgress();
938 public void setStatus(String text)
940 statusBar.setText(text);
944 * Added so Castor Mapping file can obtain Jalview Version
946 public String getVersion()
948 return jalview.bin.Cache.getProperty("VERSION");
951 public FeatureRenderer getFeatureRenderer()
953 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
957 public void fetchSequence_actionPerformed(ActionEvent e)
959 new SequenceFetcher(this);
963 public void addFromFile_actionPerformed(ActionEvent e)
965 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
969 public void reload_actionPerformed(ActionEvent e)
971 if (fileName != null)
973 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
974 // originating file's format
975 // TODO: work out how to recover feature settings for correct view(s) when
977 if (currentFileFormat.equals("Jalview"))
979 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
980 for (int i = 0; i < frames.length; i++)
982 if (frames[i] instanceof AlignFrame && frames[i] != this
983 && ((AlignFrame) frames[i]).fileName != null
984 && ((AlignFrame) frames[i]).fileName.equals(fileName))
988 frames[i].setSelected(true);
989 Desktop.instance.closeAssociatedWindows();
990 } catch (java.beans.PropertyVetoException ex)
996 Desktop.instance.closeAssociatedWindows();
998 FileLoader loader = new FileLoader();
999 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1000 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1004 Rectangle bounds = this.getBounds();
1006 FileLoader loader = new FileLoader();
1007 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1008 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1009 protocol, currentFileFormat);
1011 newframe.setBounds(bounds);
1012 if (featureSettings != null && featureSettings.isShowing())
1014 final Rectangle fspos = featureSettings.frame.getBounds();
1015 // TODO: need a 'show feature settings' function that takes bounds -
1016 // need to refactor Desktop.addFrame
1017 newframe.featureSettings_actionPerformed(null);
1018 final FeatureSettings nfs = newframe.featureSettings;
1019 SwingUtilities.invokeLater(new Runnable()
1024 nfs.frame.setBounds(fspos);
1027 this.featureSettings.close();
1028 this.featureSettings = null;
1030 this.closeMenuItem_actionPerformed(true);
1036 public void addFromText_actionPerformed(ActionEvent e)
1038 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1043 public void addFromURL_actionPerformed(ActionEvent e)
1045 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1049 public void save_actionPerformed(ActionEvent e)
1051 if (fileName == null
1052 || (currentFileFormat == null || !jalview.io.FormatAdapter
1053 .isValidIOFormat(currentFileFormat, true))
1054 || fileName.startsWith("http"))
1056 saveAs_actionPerformed(null);
1060 saveAlignment(fileName, currentFileFormat);
1071 public void saveAs_actionPerformed(ActionEvent e)
1073 JalviewFileChooser chooser = new JalviewFileChooser(
1074 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1075 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1076 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1077 currentFileFormat, false);
1079 chooser.setFileView(new JalviewFileView());
1080 chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1081 chooser.setToolTipText(MessageManager.getString("action.save"));
1083 int value = chooser.showSaveDialog(this);
1085 if (value == JalviewFileChooser.APPROVE_OPTION)
1087 currentFileFormat = chooser.getSelectedFormat();
1088 while (currentFileFormat == null)
1091 .showInternalMessageDialog(
1094 .getString("label.select_file_format_before_saving"),
1096 .getString("label.file_format_not_specified"),
1097 JOptionPane.WARNING_MESSAGE);
1098 currentFileFormat = chooser.getSelectedFormat();
1099 value = chooser.showSaveDialog(this);
1100 if (value != JalviewFileChooser.APPROVE_OPTION)
1106 fileName = chooser.getSelectedFile().getPath();
1108 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1111 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1112 if (currentFileFormat.indexOf(" ") > -1)
1114 currentFileFormat = currentFileFormat.substring(0,
1115 currentFileFormat.indexOf(" "));
1117 saveAlignment(fileName, currentFileFormat);
1121 public boolean saveAlignment(String file, String format)
1123 boolean success = true;
1125 if (format.equalsIgnoreCase("Jalview"))
1127 String shortName = title;
1129 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1131 shortName = shortName.substring(shortName
1132 .lastIndexOf(java.io.File.separatorChar) + 1);
1135 success = new Jalview2XML().saveAlignment(this, file, shortName);
1137 statusBar.setText(MessageManager.formatMessage(
1138 "label.successfully_saved_to_file_in_format", new Object[]
1139 { fileName, format }));
1144 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1146 warningMessage("Cannot save file " + fileName + " using format "
1147 + format, "Alignment output format not supported");
1148 if (!Jalview.isHeadlessMode())
1150 saveAs_actionPerformed(null);
1155 AlignmentExportData exportData = getAlignmentForExport(format,
1157 if (exportData.getSettings().isCancelled())
1161 FormatAdapter f = new FormatAdapter(alignPanel,
1162 exportData.getSettings());
1163 String output = f.formatSequences(format,
1164 exportData.getAlignment(), // class cast exceptions will
1165 // occur in the distant future
1166 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1167 f.getCacheSuffixDefault(format),
1168 viewport.getColumnSelection());
1178 java.io.PrintWriter out = new java.io.PrintWriter(
1179 new java.io.FileWriter(file));
1183 this.setTitle(file);
1184 statusBar.setText(MessageManager.formatMessage(
1185 "label.successfully_saved_to_file_in_format",
1187 { fileName, format }));
1188 } catch (Exception ex)
1191 ex.printStackTrace();
1198 JOptionPane.showInternalMessageDialog(this, MessageManager
1199 .formatMessage("label.couldnt_save_file", new Object[]
1200 { fileName }), MessageManager
1201 .getString("label.error_saving_file"),
1202 JOptionPane.WARNING_MESSAGE);
1209 private void warningMessage(String warning, String title)
1211 if (new jalview.util.Platform().isHeadless())
1213 System.err.println("Warning: " + title + "\nWarning: " + warning);
1218 JOptionPane.showInternalMessageDialog(this, warning, title,
1219 JOptionPane.WARNING_MESSAGE);
1231 protected void outputText_actionPerformed(ActionEvent e)
1234 AlignmentExportData exportData = getAlignmentForExport(
1235 e.getActionCommand(), viewport, null);
1236 if (exportData.getSettings().isCancelled())
1240 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1241 cap.setForInput(null);
1244 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1246 e.getActionCommand(),
1247 exportData.getAlignment(),
1248 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1249 viewport.getColumnSelection()));
1250 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1251 "label.alignment_output_command", new Object[]
1252 { e.getActionCommand() }), 600, 500);
1253 } catch (OutOfMemoryError oom)
1255 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1261 public static AlignmentExportData getAlignmentForExport(String exportFormat,
1262 AlignViewportI viewport,
1263 AlignExportSettingI exportSettings)
1265 AlignmentI alignmentToExport = null;
1266 AlignExportSettingI settings = exportSettings;
1267 String[] omitHidden = null;
1268 int[] alignmentStartEnd = new int[2];
1270 HiddenSequences hiddenSeqs = viewport.getAlignment()
1271 .getHiddenSequences();
1274 alignmentToExport = viewport.getAlignment();
1275 alignmentStartEnd = new int[]
1276 { 0, alignmentToExport.getWidth() - 1 };
1278 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1279 if (settings == null)
1281 settings = new AlignExportSettings(hasHiddenSeqs,
1282 viewport.hasHiddenColumns(), exportFormat);
1284 // settings.isExportAnnotations();
1286 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1288 omitHidden = viewport.getViewAsString(false);
1291 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1293 alignmentToExport = hiddenSeqs.getFullAlignment();
1297 alignmentToExport = viewport.getAlignment();
1298 alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1299 .getColumnSelection().getHiddenColumns());
1301 AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd,
1306 public static int[] getStartEnd(int[] aligmentStartEnd,
1307 List<int[]> hiddenCols)
1309 int startPos = aligmentStartEnd[0];
1310 int endPos = aligmentStartEnd[1];
1312 int[] lowestRange = new int[2];
1313 int[] higestRange = new int[2];
1315 for (int[] hiddenCol : hiddenCols)
1317 // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
1318 lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1319 higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1321 // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
1322 // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
1324 if (lowestRange[0] == 0 && lowestRange[1] == 0)
1326 startPos = aligmentStartEnd[0];
1330 startPos = lowestRange[1] + 1;
1333 if (higestRange[0] == 0 && higestRange[1] == 0)
1335 endPos = aligmentStartEnd[1];
1339 endPos = higestRange[0];
1342 // System.out.println("Export range : " + minPos + " - " + maxPos);
1344 { startPos, endPos };
1347 public static void main(String[] args)
1349 ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1350 hiddenCols.add(new int[]
1352 hiddenCols.add(new int[]
1354 hiddenCols.add(new int[]
1356 hiddenCols.add(new int[]
1358 hiddenCols.add(new int[]
1361 int[] x = getStartEnd(new int[]
1362 { 0, 50 }, hiddenCols);
1363 // System.out.println("Export range : " + x[0] + " - " + x[1]);
1373 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1375 new HtmlSvgOutput(null, alignPanel);
1379 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1381 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1382 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1384 public void createImageMap(File file, String image)
1386 alignPanel.makePNGImageMap(file, image);
1396 public void createPNG(File f)
1398 alignPanel.makePNG(f);
1408 public void createEPS(File f)
1410 alignPanel.makeEPS(f);
1413 public void createSVG(File f)
1415 alignPanel.makeSVG(f);
1418 public void pageSetup_actionPerformed(ActionEvent e)
1420 PrinterJob printJob = PrinterJob.getPrinterJob();
1421 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1431 public void printMenuItem_actionPerformed(ActionEvent e)
1433 // Putting in a thread avoids Swing painting problems
1434 PrintThread thread = new PrintThread(alignPanel);
1439 public void exportFeatures_actionPerformed(ActionEvent e)
1441 new AnnotationExporter().exportFeatures(alignPanel);
1445 public void exportAnnotations_actionPerformed(ActionEvent e)
1447 new AnnotationExporter().exportAnnotations(alignPanel);
1451 public void associatedData_actionPerformed(ActionEvent e)
1453 // Pick the tree file
1454 JalviewFileChooser chooser = new JalviewFileChooser(
1455 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1456 chooser.setFileView(new JalviewFileView());
1457 chooser.setDialogTitle(MessageManager
1458 .getString("label.load_jalview_annotations"));
1459 chooser.setToolTipText(MessageManager
1460 .getString("label.load_jalview_annotations"));
1462 int value = chooser.showOpenDialog(null);
1464 if (value == JalviewFileChooser.APPROVE_OPTION)
1466 String choice = chooser.getSelectedFile().getPath();
1467 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1468 loadJalviewDataFile(choice, null, null, null);
1474 * Close the current view or all views in the alignment frame. If the frame
1475 * only contains one view then the alignment will be removed from memory.
1477 * @param closeAllTabs
1480 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1482 if (alignPanels != null && alignPanels.size() < 2)
1484 closeAllTabs = true;
1489 if (alignPanels != null)
1493 if (this.isClosed())
1495 // really close all the windows - otherwise wait till
1496 // setClosed(true) is called
1497 for (int i = 0; i < alignPanels.size(); i++)
1499 AlignmentPanel ap = alignPanels.get(i);
1506 closeView(alignPanel);
1513 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1514 * be called recursively, with the frame now in 'closed' state
1516 this.setClosed(true);
1518 } catch (Exception ex)
1520 ex.printStackTrace();
1525 * Close the specified panel and close up tabs appropriately.
1527 * @param panelToClose
1529 public void closeView(AlignmentPanel panelToClose)
1531 int index = tabbedPane.getSelectedIndex();
1532 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1533 alignPanels.remove(panelToClose);
1534 panelToClose.closePanel();
1535 panelToClose = null;
1537 tabbedPane.removeTabAt(closedindex);
1538 tabbedPane.validate();
1540 if (index > closedindex || index == tabbedPane.getTabCount())
1542 // modify currently selected tab index if necessary.
1546 this.tabSelectionChanged(index);
1552 void updateEditMenuBar()
1555 if (viewport.getHistoryList().size() > 0)
1557 undoMenuItem.setEnabled(true);
1558 CommandI command = viewport.getHistoryList().peek();
1559 undoMenuItem.setText(MessageManager.formatMessage(
1560 "label.undo_command", new Object[]
1561 { command.getDescription() }));
1565 undoMenuItem.setEnabled(false);
1566 undoMenuItem.setText(MessageManager.getString("action.undo"));
1569 if (viewport.getRedoList().size() > 0)
1571 redoMenuItem.setEnabled(true);
1573 CommandI command = viewport.getRedoList().peek();
1574 redoMenuItem.setText(MessageManager.formatMessage(
1575 "label.redo_command", new Object[]
1576 { command.getDescription() }));
1580 redoMenuItem.setEnabled(false);
1581 redoMenuItem.setText(MessageManager.getString("action.redo"));
1585 public void addHistoryItem(CommandI command)
1587 if (command.getSize() > 0)
1589 viewport.addToHistoryList(command);
1590 viewport.clearRedoList();
1591 updateEditMenuBar();
1592 viewport.updateHiddenColumns();
1593 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1594 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1595 // viewport.getColumnSelection()
1596 // .getHiddenColumns().size() > 0);
1602 * @return alignment objects for all views
1604 AlignmentI[] getViewAlignments()
1606 if (alignPanels != null)
1608 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1610 for (AlignmentPanel ap : alignPanels)
1612 als[i++] = ap.av.getAlignment();
1616 if (viewport != null)
1618 return new AlignmentI[]
1619 { viewport.getAlignment() };
1631 protected void undoMenuItem_actionPerformed(ActionEvent e)
1633 if (viewport.getHistoryList().isEmpty())
1637 CommandI command = viewport.getHistoryList().pop();
1638 viewport.addToRedoList(command);
1639 command.undoCommand(getViewAlignments());
1641 AlignmentViewport originalSource = getOriginatingSource(command);
1642 updateEditMenuBar();
1644 if (originalSource != null)
1646 if (originalSource != viewport)
1649 .warn("Implementation worry: mismatch of viewport origin for undo");
1651 originalSource.updateHiddenColumns();
1652 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1654 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1655 // viewport.getColumnSelection()
1656 // .getHiddenColumns().size() > 0);
1657 originalSource.firePropertyChange("alignment", null, originalSource
1658 .getAlignment().getSequences());
1669 protected void redoMenuItem_actionPerformed(ActionEvent e)
1671 if (viewport.getRedoList().size() < 1)
1676 CommandI command = viewport.getRedoList().pop();
1677 viewport.addToHistoryList(command);
1678 command.doCommand(getViewAlignments());
1680 AlignmentViewport originalSource = getOriginatingSource(command);
1681 updateEditMenuBar();
1683 if (originalSource != null)
1686 if (originalSource != viewport)
1689 .warn("Implementation worry: mismatch of viewport origin for redo");
1691 originalSource.updateHiddenColumns();
1692 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1694 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1695 // viewport.getColumnSelection()
1696 // .getHiddenColumns().size() > 0);
1697 originalSource.firePropertyChange("alignment", null, originalSource
1698 .getAlignment().getSequences());
1702 AlignmentViewport getOriginatingSource(CommandI command)
1704 AlignmentViewport originalSource = null;
1705 // For sequence removal and addition, we need to fire
1706 // the property change event FROM the viewport where the
1707 // original alignment was altered
1708 AlignmentI al = null;
1709 if (command instanceof EditCommand)
1711 EditCommand editCommand = (EditCommand) command;
1712 al = editCommand.getAlignment();
1713 List<Component> comps = PaintRefresher.components.get(viewport
1714 .getSequenceSetId());
1716 for (Component comp : comps)
1718 if (comp instanceof AlignmentPanel)
1720 if (al == ((AlignmentPanel) comp).av.getAlignment())
1722 originalSource = ((AlignmentPanel) comp).av;
1729 if (originalSource == null)
1731 // The original view is closed, we must validate
1732 // the current view against the closed view first
1735 PaintRefresher.validateSequences(al, viewport.getAlignment());
1738 originalSource = viewport;
1741 return originalSource;
1750 public void moveSelectedSequences(boolean up)
1752 SequenceGroup sg = viewport.getSelectionGroup();
1758 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1759 viewport.getHiddenRepSequences(), up);
1760 alignPanel.paintAlignment(true);
1763 synchronized void slideSequences(boolean right, int size)
1765 List<SequenceI> sg = new ArrayList<SequenceI>();
1766 if (viewport.cursorMode)
1768 sg.add(viewport.getAlignment().getSequenceAt(
1769 alignPanel.getSeqPanel().seqCanvas.cursorY));
1771 else if (viewport.getSelectionGroup() != null
1772 && viewport.getSelectionGroup().getSize() != viewport
1773 .getAlignment().getHeight())
1775 sg = viewport.getSelectionGroup().getSequences(
1776 viewport.getHiddenRepSequences());
1784 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1786 for (SequenceI seq : viewport.getAlignment().getSequences())
1788 if (!sg.contains(seq))
1790 invertGroup.add(seq);
1794 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1796 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1797 for (int i = 0; i < invertGroup.size(); i++)
1799 seqs2[i] = invertGroup.get(i);
1802 SlideSequencesCommand ssc;
1805 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1806 size, viewport.getGapCharacter());
1810 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1811 size, viewport.getGapCharacter());
1814 int groupAdjustment = 0;
1815 if (ssc.getGapsInsertedBegin() && right)
1817 if (viewport.cursorMode)
1819 alignPanel.getSeqPanel().moveCursor(size, 0);
1823 groupAdjustment = size;
1826 else if (!ssc.getGapsInsertedBegin() && !right)
1828 if (viewport.cursorMode)
1830 alignPanel.getSeqPanel().moveCursor(-size, 0);
1834 groupAdjustment = -size;
1838 if (groupAdjustment != 0)
1840 viewport.getSelectionGroup().setStartRes(
1841 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1842 viewport.getSelectionGroup().setEndRes(
1843 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1847 * just extend the last slide command if compatible; but not if in
1848 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1850 boolean appendHistoryItem = false;
1851 Deque<CommandI> historyList = viewport.getHistoryList();
1852 boolean inSplitFrame = getSplitViewContainer() != null;
1853 if (!inSplitFrame && historyList != null
1854 && historyList.size() > 0
1855 && historyList.peek() instanceof SlideSequencesCommand)
1857 appendHistoryItem = ssc
1858 .appendSlideCommand((SlideSequencesCommand) historyList
1862 if (!appendHistoryItem)
1864 addHistoryItem(ssc);
1877 protected void copy_actionPerformed(ActionEvent e)
1880 if (viewport.getSelectionGroup() == null)
1884 // TODO: preserve the ordering of displayed alignment annotation in any
1885 // internal paste (particularly sequence associated annotation)
1886 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1887 String[] omitHidden = null;
1889 if (viewport.hasHiddenColumns())
1891 omitHidden = viewport.getViewAsString(true);
1894 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1897 StringSelection ss = new StringSelection(output);
1901 jalview.gui.Desktop.internalCopy = true;
1902 // Its really worth setting the clipboard contents
1903 // to empty before setting the large StringSelection!!
1904 Toolkit.getDefaultToolkit().getSystemClipboard()
1905 .setContents(new StringSelection(""), null);
1907 Toolkit.getDefaultToolkit().getSystemClipboard()
1908 .setContents(ss, Desktop.instance);
1909 } catch (OutOfMemoryError er)
1911 new OOMWarning("copying region", er);
1915 ArrayList<int[]> hiddenColumns = null;
1916 if (viewport.hasHiddenColumns())
1918 hiddenColumns = new ArrayList<int[]>();
1919 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1920 .getSelectionGroup().getEndRes();
1921 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1923 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1925 hiddenColumns.add(new int[]
1926 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1931 Desktop.jalviewClipboard = new Object[]
1932 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1933 statusBar.setText(MessageManager.formatMessage(
1934 "label.copied_sequences_to_clipboard", new Object[]
1935 { Integer.valueOf(seqs.length).toString() }));
1945 protected void pasteNew_actionPerformed(ActionEvent e)
1957 protected void pasteThis_actionPerformed(ActionEvent e)
1963 * Paste contents of Jalview clipboard
1965 * @param newAlignment
1966 * true to paste to a new alignment, otherwise add to this.
1968 void paste(boolean newAlignment)
1970 boolean externalPaste = true;
1973 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1974 Transferable contents = c.getContents(this);
1976 if (contents == null)
1984 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1985 if (str.length() < 1)
1990 format = new IdentifyFile().Identify(str, "Paste");
1992 } catch (OutOfMemoryError er)
1994 new OOMWarning("Out of memory pasting sequences!!", er);
1998 SequenceI[] sequences;
1999 boolean annotationAdded = false;
2000 AlignmentI alignment = null;
2002 if (Desktop.jalviewClipboard != null)
2004 // The clipboard was filled from within Jalview, we must use the
2006 // And dataset from the copied alignment
2007 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2008 // be doubly sure that we create *new* sequence objects.
2009 sequences = new SequenceI[newseq.length];
2010 for (int i = 0; i < newseq.length; i++)
2012 sequences[i] = new Sequence(newseq[i]);
2014 alignment = new Alignment(sequences);
2015 externalPaste = false;
2019 // parse the clipboard as an alignment.
2020 alignment = new FormatAdapter().readFile(str, "Paste", format);
2021 sequences = alignment.getSequencesArray();
2025 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2031 if (Desktop.jalviewClipboard != null)
2033 // dataset is inherited
2034 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2038 // new dataset is constructed
2039 alignment.setDataset(null);
2041 alwidth = alignment.getWidth() + 1;
2045 AlignmentI pastedal = alignment; // preserve pasted alignment object
2046 // Add pasted sequences and dataset into existing alignment.
2047 alignment = viewport.getAlignment();
2048 alwidth = alignment.getWidth() + 1;
2049 // decide if we need to import sequences from an existing dataset
2050 boolean importDs = Desktop.jalviewClipboard != null
2051 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2052 // importDs==true instructs us to copy over new dataset sequences from
2053 // an existing alignment
2054 Vector newDs = (importDs) ? new Vector() : null; // used to create
2055 // minimum dataset set
2057 for (int i = 0; i < sequences.length; i++)
2061 newDs.addElement(null);
2063 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2065 if (importDs && ds != null)
2067 if (!newDs.contains(ds))
2069 newDs.setElementAt(ds, i);
2070 ds = new Sequence(ds);
2071 // update with new dataset sequence
2072 sequences[i].setDatasetSequence(ds);
2076 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2081 // copy and derive new dataset sequence
2082 sequences[i] = sequences[i].deriveSequence();
2083 alignment.getDataset().addSequence(
2084 sequences[i].getDatasetSequence());
2085 // TODO: avoid creation of duplicate dataset sequences with a
2086 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2088 alignment.addSequence(sequences[i]); // merges dataset
2092 newDs.clear(); // tidy up
2094 if (alignment.getAlignmentAnnotation() != null)
2096 for (AlignmentAnnotation alan : alignment
2097 .getAlignmentAnnotation())
2099 if (alan.graphGroup > fgroup)
2101 fgroup = alan.graphGroup;
2105 if (pastedal.getAlignmentAnnotation() != null)
2107 // Add any annotation attached to alignment.
2108 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2109 for (int i = 0; i < alann.length; i++)
2111 annotationAdded = true;
2112 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2114 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2115 if (newann.graphGroup > -1)
2117 if (newGraphGroups.size() <= newann.graphGroup
2118 || newGraphGroups.get(newann.graphGroup) == null)
2120 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2122 newGraphGroups.add(q, null);
2124 newGraphGroups.set(newann.graphGroup, new Integer(
2127 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2131 newann.padAnnotation(alwidth);
2132 alignment.addAnnotation(newann);
2142 addHistoryItem(new EditCommand(
2143 MessageManager.getString("label.add_sequences"),
2145 sequences, 0, alignment.getWidth(), alignment));
2147 // Add any annotations attached to sequences
2148 for (int i = 0; i < sequences.length; i++)
2150 if (sequences[i].getAnnotation() != null)
2152 AlignmentAnnotation newann;
2153 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2155 annotationAdded = true;
2156 newann = sequences[i].getAnnotation()[a];
2157 newann.adjustForAlignment();
2158 newann.padAnnotation(alwidth);
2159 if (newann.graphGroup > -1)
2161 if (newann.graphGroup > -1)
2163 if (newGraphGroups.size() <= newann.graphGroup
2164 || newGraphGroups.get(newann.graphGroup) == null)
2166 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2168 newGraphGroups.add(q, null);
2170 newGraphGroups.set(newann.graphGroup, new Integer(
2173 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2177 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2182 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2189 // propagate alignment changed.
2190 viewport.setEndSeq(alignment.getHeight());
2191 if (annotationAdded)
2193 // Duplicate sequence annotation in all views.
2194 AlignmentI[] alview = this.getViewAlignments();
2195 for (int i = 0; i < sequences.length; i++)
2197 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2202 for (int avnum = 0; avnum < alview.length; avnum++)
2204 if (alview[avnum] != alignment)
2206 // duplicate in a view other than the one with input focus
2207 int avwidth = alview[avnum].getWidth() + 1;
2208 // this relies on sann being preserved after we
2209 // modify the sequence's annotation array for each duplication
2210 for (int a = 0; a < sann.length; a++)
2212 AlignmentAnnotation newann = new AlignmentAnnotation(
2214 sequences[i].addAlignmentAnnotation(newann);
2215 newann.padAnnotation(avwidth);
2216 alview[avnum].addAnnotation(newann); // annotation was
2217 // duplicated earlier
2218 // TODO JAL-1145 graphGroups are not updated for sequence
2219 // annotation added to several views. This may cause
2221 alview[avnum].setAnnotationIndex(newann, a);
2226 buildSortByAnnotationScoresMenu();
2228 viewport.firePropertyChange("alignment", null,
2229 alignment.getSequences());
2230 if (alignPanels != null)
2232 for (AlignmentPanel ap : alignPanels)
2234 ap.validateAnnotationDimensions(false);
2239 alignPanel.validateAnnotationDimensions(false);
2245 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2247 String newtitle = new String("Copied sequences");
2249 if (Desktop.jalviewClipboard != null
2250 && Desktop.jalviewClipboard[2] != null)
2252 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2253 for (int[] region : hc)
2255 af.viewport.hideColumns(region[0], region[1]);
2259 // >>>This is a fix for the moment, until a better solution is
2261 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2263 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2265 // TODO: maintain provenance of an alignment, rather than just make the
2266 // title a concatenation of operations.
2269 if (title.startsWith("Copied sequences"))
2275 newtitle = newtitle.concat("- from " + title);
2280 newtitle = new String("Pasted sequences");
2283 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2288 } catch (Exception ex)
2290 ex.printStackTrace();
2291 System.out.println("Exception whilst pasting: " + ex);
2292 // could be anything being pasted in here
2298 protected void expand_newalign(ActionEvent e)
2302 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2303 .getAlignment(), -1);
2304 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2306 String newtitle = new String("Flanking alignment");
2308 if (Desktop.jalviewClipboard != null
2309 && Desktop.jalviewClipboard[2] != null)
2311 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2312 for (int region[] : hc)
2314 af.viewport.hideColumns(region[0], region[1]);
2318 // >>>This is a fix for the moment, until a better solution is
2320 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2322 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2324 // TODO: maintain provenance of an alignment, rather than just make the
2325 // title a concatenation of operations.
2327 if (title.startsWith("Copied sequences"))
2333 newtitle = newtitle.concat("- from " + title);
2337 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2339 } catch (Exception ex)
2341 ex.printStackTrace();
2342 System.out.println("Exception whilst pasting: " + ex);
2343 // could be anything being pasted in here
2344 } catch (OutOfMemoryError oom)
2346 new OOMWarning("Viewing flanking region of alignment", oom);
2357 protected void cut_actionPerformed(ActionEvent e)
2359 copy_actionPerformed(null);
2360 delete_actionPerformed(null);
2370 protected void delete_actionPerformed(ActionEvent evt)
2373 SequenceGroup sg = viewport.getSelectionGroup();
2380 * If the cut affects all sequences, warn, remove highlighted columns
2382 if (sg.getSize() == viewport.getAlignment().getHeight())
2384 int confirm = JOptionPane.showConfirmDialog(this,
2385 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2386 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2387 JOptionPane.OK_CANCEL_OPTION);
2389 if (confirm == JOptionPane.CANCEL_OPTION
2390 || confirm == JOptionPane.CLOSED_OPTION)
2394 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2395 sg.getEndRes() + 1);
2398 SequenceI[] cut = sg.getSequences()
2399 .toArray(new SequenceI[sg.getSize()]);
2401 addHistoryItem(new EditCommand(
2402 MessageManager.getString("label.cut_sequences"), Action.CUT,
2403 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2404 viewport.getAlignment()));
2406 viewport.setSelectionGroup(null);
2407 viewport.sendSelection();
2408 viewport.getAlignment().deleteGroup(sg);
2410 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2412 if (viewport.getAlignment().getHeight() < 1)
2416 this.setClosed(true);
2417 } catch (Exception ex)
2430 protected void deleteGroups_actionPerformed(ActionEvent e)
2432 if (avc.deleteGroups())
2434 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2435 alignPanel.updateAnnotation();
2436 alignPanel.paintAlignment(true);
2447 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2449 SequenceGroup sg = new SequenceGroup();
2451 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2453 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2456 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2457 viewport.setSelectionGroup(sg);
2458 viewport.sendSelection();
2459 alignPanel.paintAlignment(true);
2460 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2470 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2472 if (viewport.cursorMode)
2474 alignPanel.getSeqPanel().keyboardNo1 = null;
2475 alignPanel.getSeqPanel().keyboardNo2 = null;
2477 viewport.setSelectionGroup(null);
2478 viewport.getColumnSelection().clear();
2479 viewport.setSelectionGroup(null);
2480 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2481 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2482 alignPanel.paintAlignment(true);
2483 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2484 viewport.sendSelection();
2494 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2496 SequenceGroup sg = viewport.getSelectionGroup();
2500 selectAllSequenceMenuItem_actionPerformed(null);
2505 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2507 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2510 alignPanel.paintAlignment(true);
2511 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2512 viewport.sendSelection();
2516 public void invertColSel_actionPerformed(ActionEvent e)
2518 viewport.invertColumnSelection();
2519 alignPanel.paintAlignment(true);
2520 viewport.sendSelection();
2530 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2532 trimAlignment(true);
2542 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2544 trimAlignment(false);
2547 void trimAlignment(boolean trimLeft)
2549 ColumnSelection colSel = viewport.getColumnSelection();
2552 if (colSel.size() > 0)
2556 column = colSel.getMin();
2560 column = colSel.getMax();
2564 if (viewport.getSelectionGroup() != null)
2566 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2567 viewport.getHiddenRepSequences());
2571 seqs = viewport.getAlignment().getSequencesArray();
2574 TrimRegionCommand trimRegion;
2577 trimRegion = new TrimRegionCommand("Remove Left",
2578 TrimRegionCommand.TRIM_LEFT, seqs, column,
2579 viewport.getAlignment(), viewport.getColumnSelection(),
2580 viewport.getSelectionGroup());
2581 viewport.setStartRes(0);
2585 trimRegion = new TrimRegionCommand("Remove Right",
2586 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2587 viewport.getAlignment(), viewport.getColumnSelection(),
2588 viewport.getSelectionGroup());
2591 statusBar.setText(MessageManager.formatMessage(
2592 "label.removed_columns", new String[]
2593 { Integer.valueOf(trimRegion.getSize()).toString() }));
2595 addHistoryItem(trimRegion);
2597 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2599 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2600 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2602 viewport.getAlignment().deleteGroup(sg);
2606 viewport.firePropertyChange("alignment", null, viewport
2607 .getAlignment().getSequences());
2618 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2620 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2623 if (viewport.getSelectionGroup() != null)
2625 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2626 viewport.getHiddenRepSequences());
2627 start = viewport.getSelectionGroup().getStartRes();
2628 end = viewport.getSelectionGroup().getEndRes();
2632 seqs = viewport.getAlignment().getSequencesArray();
2635 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2636 "Remove Gapped Columns", seqs, start, end,
2637 viewport.getAlignment());
2639 addHistoryItem(removeGapCols);
2641 statusBar.setText(MessageManager.formatMessage(
2642 "label.removed_empty_columns", new Object[]
2643 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2645 // This is to maintain viewport position on first residue
2646 // of first sequence
2647 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2648 int startRes = seq.findPosition(viewport.startRes);
2649 // ShiftList shifts;
2650 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2651 // edit.alColumnChanges=shifts.getInverse();
2652 // if (viewport.hasHiddenColumns)
2653 // viewport.getColumnSelection().compensateForEdits(shifts);
2654 viewport.setStartRes(seq.findIndex(startRes) - 1);
2655 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2667 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2669 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2672 if (viewport.getSelectionGroup() != null)
2674 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2675 viewport.getHiddenRepSequences());
2676 start = viewport.getSelectionGroup().getStartRes();
2677 end = viewport.getSelectionGroup().getEndRes();
2681 seqs = viewport.getAlignment().getSequencesArray();
2684 // This is to maintain viewport position on first residue
2685 // of first sequence
2686 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2687 int startRes = seq.findPosition(viewport.startRes);
2689 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2690 viewport.getAlignment()));
2692 viewport.setStartRes(seq.findIndex(startRes) - 1);
2694 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2706 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2708 viewport.setPadGaps(padGapsMenuitem.isSelected());
2709 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2720 public void findMenuItem_actionPerformed(ActionEvent e)
2726 * Create a new view of the current alignment.
2729 public void newView_actionPerformed(ActionEvent e)
2731 newView(null, true);
2735 * Creates and shows a new view of the current alignment.
2738 * title of newly created view; if null, one will be generated
2739 * @param copyAnnotation
2740 * if true then duplicate all annnotation, groups and settings
2741 * @return new alignment panel, already displayed.
2743 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2746 * Create a new AlignmentPanel (with its own, new Viewport)
2748 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2750 if (!copyAnnotation)
2753 * remove all groups and annotation except for the automatic stuff
2755 newap.av.getAlignment().deleteAllGroups();
2756 newap.av.getAlignment().deleteAllAnnotations(false);
2759 newap.av.setGatherViewsHere(false);
2761 if (viewport.viewName == null)
2763 viewport.viewName = MessageManager
2764 .getString("label.view_name_original");
2768 * Views share the same edits undo and redo stacks
2770 newap.av.setHistoryList(viewport.getHistoryList());
2771 newap.av.setRedoList(viewport.getRedoList());
2774 * Views share the same mappings; need to deregister any new mappings
2775 * created by copyAlignPanel, and register the new reference to the shared
2778 newap.av.replaceMappings(viewport.getAlignment());
2780 newap.av.viewName = getNewViewName(viewTitle);
2782 addAlignmentPanel(newap, true);
2783 newap.alignmentChanged();
2785 if (alignPanels.size() == 2)
2787 viewport.setGatherViewsHere(true);
2789 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2794 * Make a new name for the view, ensuring it is unique within the current
2795 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2796 * these now use viewId. Unique view names are still desirable for usability.)
2801 protected String getNewViewName(String viewTitle)
2803 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2804 boolean addFirstIndex = false;
2805 if (viewTitle == null || viewTitle.trim().length() == 0)
2807 viewTitle = MessageManager.getString("action.view");
2808 addFirstIndex = true;
2812 index = 1;// we count from 1 if given a specific name
2814 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2816 List<Component> comps = PaintRefresher.components.get(viewport
2817 .getSequenceSetId());
2819 List<String> existingNames = getExistingViewNames(comps);
2821 while (existingNames.contains(newViewName))
2823 newViewName = viewTitle + " " + (++index);
2829 * Returns a list of distinct view names found in the given list of
2830 * components. View names are held on the viewport of an AlignmentPanel.
2835 protected List<String> getExistingViewNames(List<Component> comps)
2837 List<String> existingNames = new ArrayList<String>();
2838 for (Component comp : comps)
2840 if (comp instanceof AlignmentPanel)
2842 AlignmentPanel ap = (AlignmentPanel) comp;
2843 if (!existingNames.contains(ap.av.viewName))
2845 existingNames.add(ap.av.viewName);
2849 return existingNames;
2853 * Explode tabbed views into separate windows.
2856 public void expandViews_actionPerformed(ActionEvent e)
2858 Desktop.instance.explodeViews(this);
2862 * Gather views in separate windows back into a tabbed presentation.
2865 public void gatherViews_actionPerformed(ActionEvent e)
2867 Desktop.instance.gatherViews(this);
2877 public void font_actionPerformed(ActionEvent e)
2879 new FontChooser(alignPanel);
2889 protected void seqLimit_actionPerformed(ActionEvent e)
2891 viewport.setShowJVSuffix(seqLimits.isSelected());
2893 alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
2894 .calculateIdWidth());
2895 alignPanel.paintAlignment(true);
2899 public void idRightAlign_actionPerformed(ActionEvent e)
2901 viewport.setRightAlignIds(idRightAlign.isSelected());
2902 alignPanel.paintAlignment(true);
2906 public void centreColumnLabels_actionPerformed(ActionEvent e)
2908 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2909 alignPanel.paintAlignment(true);
2915 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2918 protected void followHighlight_actionPerformed()
2921 * Set the 'follow' flag on the Viewport (and scroll to position if now
2924 final boolean state = this.followHighlightMenuItem.getState();
2925 viewport.setFollowHighlight(state);
2928 alignPanel.scrollToPosition(
2929 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2940 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2942 viewport.setColourText(colourTextMenuItem.isSelected());
2943 alignPanel.paintAlignment(true);
2953 public void wrapMenuItem_actionPerformed(ActionEvent e)
2955 scaleAbove.setVisible(wrapMenuItem.isSelected());
2956 scaleLeft.setVisible(wrapMenuItem.isSelected());
2957 scaleRight.setVisible(wrapMenuItem.isSelected());
2958 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2959 alignPanel.updateLayout();
2963 public void showAllSeqs_actionPerformed(ActionEvent e)
2965 viewport.showAllHiddenSeqs();
2969 public void showAllColumns_actionPerformed(ActionEvent e)
2971 viewport.showAllHiddenColumns();
2976 public void hideSelSequences_actionPerformed(ActionEvent e)
2978 viewport.hideAllSelectedSeqs();
2979 // alignPanel.paintAlignment(true);
2983 * called by key handler and the hide all/show all menu items
2988 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2991 boolean hide = false;
2992 SequenceGroup sg = viewport.getSelectionGroup();
2993 if (!toggleSeqs && !toggleCols)
2995 // Hide everything by the current selection - this is a hack - we do the
2996 // invert and then hide
2997 // first check that there will be visible columns after the invert.
2998 if ((viewport.getColumnSelection() != null
2999 && viewport.getColumnSelection().getSelected() != null && viewport
3000 .getColumnSelection().getSelected().size() > 0)
3001 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3004 // now invert the sequence set, if required - empty selection implies
3005 // that no hiding is required.
3008 invertSequenceMenuItem_actionPerformed(null);
3009 sg = viewport.getSelectionGroup();
3013 viewport.expandColSelection(sg, true);
3014 // finally invert the column selection and get the new sequence
3016 invertColSel_actionPerformed(null);
3023 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3025 hideSelSequences_actionPerformed(null);
3028 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3031 showAllSeqs_actionPerformed(null);
3037 if (viewport.getColumnSelection().getSelected().size() > 0)
3039 hideSelColumns_actionPerformed(null);
3042 viewport.setSelectionGroup(sg);
3047 showAllColumns_actionPerformed(null);
3056 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3057 * event.ActionEvent)
3060 public void hideAllButSelection_actionPerformed(ActionEvent e)
3062 toggleHiddenRegions(false, false);
3069 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3073 public void hideAllSelection_actionPerformed(ActionEvent e)
3075 SequenceGroup sg = viewport.getSelectionGroup();
3076 viewport.expandColSelection(sg, false);
3077 viewport.hideAllSelectedSeqs();
3078 viewport.hideSelectedColumns();
3079 alignPanel.paintAlignment(true);
3086 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3090 public void showAllhidden_actionPerformed(ActionEvent e)
3092 viewport.showAllHiddenColumns();
3093 viewport.showAllHiddenSeqs();
3094 alignPanel.paintAlignment(true);
3098 public void hideSelColumns_actionPerformed(ActionEvent e)
3100 viewport.hideSelectedColumns();
3101 alignPanel.paintAlignment(true);
3105 public void hiddenMarkers_actionPerformed(ActionEvent e)
3107 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3118 protected void scaleAbove_actionPerformed(ActionEvent e)
3120 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3121 alignPanel.paintAlignment(true);
3131 protected void scaleLeft_actionPerformed(ActionEvent e)
3133 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3134 alignPanel.paintAlignment(true);
3144 protected void scaleRight_actionPerformed(ActionEvent e)
3146 viewport.setScaleRightWrapped(scaleRight.isSelected());
3147 alignPanel.paintAlignment(true);
3157 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3159 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3160 alignPanel.paintAlignment(true);
3170 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3172 viewport.setShowText(viewTextMenuItem.isSelected());
3173 alignPanel.paintAlignment(true);
3183 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3185 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3186 alignPanel.paintAlignment(true);
3189 public FeatureSettings featureSettings;
3192 public FeatureSettingsControllerI getFeatureSettingsUI()
3194 return featureSettings;
3198 public void featureSettings_actionPerformed(ActionEvent e)
3200 if (featureSettings != null)
3202 featureSettings.close();
3203 featureSettings = null;
3205 if (!showSeqFeatures.isSelected())
3207 // make sure features are actually displayed
3208 showSeqFeatures.setSelected(true);
3209 showSeqFeatures_actionPerformed(null);
3211 featureSettings = new FeatureSettings(this);
3215 * Set or clear 'Show Sequence Features'
3221 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3223 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3224 alignPanel.paintAlignment(true);
3225 if (alignPanel.getOverviewPanel() != null)
3227 alignPanel.getOverviewPanel().updateOverviewImage();
3232 * Set or clear 'Show Sequence Features'
3238 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3240 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3242 if (viewport.isShowSequenceFeaturesHeight())
3244 // ensure we're actually displaying features
3245 viewport.setShowSequenceFeatures(true);
3246 showSeqFeatures.setSelected(true);
3248 alignPanel.paintAlignment(true);
3249 if (alignPanel.getOverviewPanel() != null)
3251 alignPanel.getOverviewPanel().updateOverviewImage();
3256 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3257 * the annotations panel as a whole.
3259 * The options to show/hide all annotations should be enabled when the panel
3260 * is shown, and disabled when the panel is hidden.
3265 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3267 final boolean setVisible = annotationPanelMenuItem.isSelected();
3268 viewport.setShowAnnotation(setVisible);
3269 this.showAllSeqAnnotations.setEnabled(setVisible);
3270 this.hideAllSeqAnnotations.setEnabled(setVisible);
3271 this.showAllAlAnnotations.setEnabled(setVisible);
3272 this.hideAllAlAnnotations.setEnabled(setVisible);
3273 alignPanel.updateLayout();
3277 public void alignmentProperties()
3279 JEditorPane editPane = new JEditorPane("text/html", "");
3280 editPane.setEditable(false);
3281 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3283 editPane.setText(MessageManager.formatMessage("label.html_content",
3285 { contents.toString() }));
3286 JInternalFrame frame = new JInternalFrame();
3287 frame.getContentPane().add(new JScrollPane(editPane));
3289 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3290 "label.alignment_properties", new Object[]
3291 { getTitle() }), 500, 400);
3301 public void overviewMenuItem_actionPerformed(ActionEvent e)
3303 if (alignPanel.overviewPanel != null)
3308 JInternalFrame frame = new JInternalFrame();
3309 OverviewPanel overview = new OverviewPanel(alignPanel);
3310 frame.setContentPane(overview);
3311 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3312 "label.overview_params", new Object[]
3313 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3315 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3316 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3319 public void internalFrameClosed(
3320 javax.swing.event.InternalFrameEvent evt)
3322 alignPanel.setOverviewPanel(null);
3326 alignPanel.setOverviewPanel(overview);
3330 public void textColour_actionPerformed(ActionEvent e)
3332 new TextColourChooser().chooseColour(alignPanel, null);
3342 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3354 public void clustalColour_actionPerformed(ActionEvent e)
3356 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3357 viewport.getHiddenRepSequences()));
3367 public void zappoColour_actionPerformed(ActionEvent e)
3369 changeColour(new ZappoColourScheme());
3379 public void taylorColour_actionPerformed(ActionEvent e)
3381 changeColour(new TaylorColourScheme());
3391 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3393 changeColour(new HydrophobicColourScheme());
3403 public void helixColour_actionPerformed(ActionEvent e)
3405 changeColour(new HelixColourScheme());
3415 public void strandColour_actionPerformed(ActionEvent e)
3417 changeColour(new StrandColourScheme());
3427 public void turnColour_actionPerformed(ActionEvent e)
3429 changeColour(new TurnColourScheme());
3439 public void buriedColour_actionPerformed(ActionEvent e)
3441 changeColour(new BuriedColourScheme());
3451 public void nucleotideColour_actionPerformed(ActionEvent e)
3453 changeColour(new NucleotideColourScheme());
3457 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3459 changeColour(new PurinePyrimidineColourScheme());
3463 * public void covariationColour_actionPerformed(ActionEvent e) {
3465 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3469 public void annotationColour_actionPerformed(ActionEvent e)
3471 new AnnotationColourChooser(viewport, alignPanel);
3475 public void annotationColumn_actionPerformed(ActionEvent e)
3477 new AnnotationColumnChooser(viewport, alignPanel);
3481 public void rnahelicesColour_actionPerformed(ActionEvent e)
3483 new RNAHelicesColourChooser(viewport, alignPanel);
3493 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3495 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3504 public void changeColour(ColourSchemeI cs)
3506 // TODO: pull up to controller method
3510 // Make sure viewport is up to date w.r.t. any sliders
3511 if (viewport.getAbovePIDThreshold())
3513 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3515 viewport.setThreshold(threshold);
3518 if (viewport.getConservationSelected())
3520 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3525 viewport.setGlobalColourScheme(cs);
3527 alignPanel.paintAlignment(true);
3537 protected void modifyPID_actionPerformed(ActionEvent e)
3539 if (viewport.getAbovePIDThreshold()
3540 && viewport.getGlobalColourScheme() != null)
3542 SliderPanel.setPIDSliderSource(alignPanel,
3543 viewport.getGlobalColourScheme(), "Background");
3544 SliderPanel.showPIDSlider();
3555 protected void modifyConservation_actionPerformed(ActionEvent e)
3557 if (viewport.getConservationSelected()
3558 && viewport.getGlobalColourScheme() != null)
3560 SliderPanel.setConservationSlider(alignPanel,
3561 viewport.getGlobalColourScheme(), "Background");
3562 SliderPanel.showConservationSlider();
3573 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3575 viewport.setConservationSelected(conservationMenuItem.isSelected());
3577 viewport.setAbovePIDThreshold(false);
3578 abovePIDThreshold.setSelected(false);
3580 changeColour(viewport.getGlobalColourScheme());
3582 modifyConservation_actionPerformed(null);
3592 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3594 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3596 conservationMenuItem.setSelected(false);
3597 viewport.setConservationSelected(false);
3599 changeColour(viewport.getGlobalColourScheme());
3601 modifyPID_actionPerformed(null);
3611 public void userDefinedColour_actionPerformed(ActionEvent e)
3613 if (e.getActionCommand().equals(
3614 MessageManager.getString("action.user_defined")))
3616 new UserDefinedColours(alignPanel, null);
3620 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3621 .getUserColourSchemes().get(e.getActionCommand());
3627 public void updateUserColourMenu()
3630 Component[] menuItems = colourMenu.getMenuComponents();
3631 int iSize = menuItems.length;
3632 for (int i = 0; i < iSize; i++)
3634 if (menuItems[i].getName() != null
3635 && menuItems[i].getName().equals("USER_DEFINED"))
3637 colourMenu.remove(menuItems[i]);
3641 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3643 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3644 .getUserColourSchemes().keys();
3646 while (userColours.hasMoreElements())
3648 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3649 userColours.nextElement().toString());
3650 radioItem.setName("USER_DEFINED");
3651 radioItem.addMouseListener(new MouseAdapter()
3654 public void mousePressed(MouseEvent evt)
3656 if (evt.isControlDown()
3657 || SwingUtilities.isRightMouseButton(evt))
3659 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3661 int option = JOptionPane.showInternalConfirmDialog(
3662 jalview.gui.Desktop.desktop,
3664 .getString("label.remove_from_default_list"),
3666 .getString("label.remove_user_defined_colour"),
3667 JOptionPane.YES_NO_OPTION);
3668 if (option == JOptionPane.YES_OPTION)
3670 jalview.gui.UserDefinedColours
3671 .removeColourFromDefaults(radioItem.getText());
3672 colourMenu.remove(radioItem);
3676 radioItem.addActionListener(new ActionListener()
3679 public void actionPerformed(ActionEvent evt)
3681 userDefinedColour_actionPerformed(evt);
3688 radioItem.addActionListener(new ActionListener()
3691 public void actionPerformed(ActionEvent evt)
3693 userDefinedColour_actionPerformed(evt);
3697 colourMenu.insert(radioItem, 15);
3698 colours.add(radioItem);
3710 public void PIDColour_actionPerformed(ActionEvent e)
3712 changeColour(new PIDColourScheme());
3722 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3724 changeColour(new Blosum62ColourScheme());
3734 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3736 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3737 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3738 .getAlignment().getSequenceAt(0), null);
3739 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3740 viewport.getAlignment()));
3741 alignPanel.paintAlignment(true);
3751 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3753 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3754 AlignmentSorter.sortByID(viewport.getAlignment());
3755 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3756 viewport.getAlignment()));
3757 alignPanel.paintAlignment(true);
3767 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3769 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3770 AlignmentSorter.sortByLength(viewport.getAlignment());
3771 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3772 viewport.getAlignment()));
3773 alignPanel.paintAlignment(true);
3783 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3785 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3786 AlignmentSorter.sortByGroup(viewport.getAlignment());
3787 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3788 viewport.getAlignment()));
3790 alignPanel.paintAlignment(true);
3800 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3802 new RedundancyPanel(alignPanel, this);
3812 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3814 if ((viewport.getSelectionGroup() == null)
3815 || (viewport.getSelectionGroup().getSize() < 2))
3817 JOptionPane.showInternalMessageDialog(this, MessageManager
3818 .getString("label.you_must_select_least_two_sequences"),
3819 MessageManager.getString("label.invalid_selection"),
3820 JOptionPane.WARNING_MESSAGE);
3824 JInternalFrame frame = new JInternalFrame();
3825 frame.setContentPane(new PairwiseAlignPanel(viewport));
3826 Desktop.addInternalFrame(frame,
3827 MessageManager.getString("action.pairwise_alignment"), 600,
3839 public void PCAMenuItem_actionPerformed(ActionEvent e)
3841 if (((viewport.getSelectionGroup() != null)
3842 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3843 .getSelectionGroup().getSize() > 0))
3844 || (viewport.getAlignment().getHeight() < 4))
3847 .showInternalMessageDialog(
3850 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3852 .getString("label.sequence_selection_insufficient"),
3853 JOptionPane.WARNING_MESSAGE);
3858 new PCAPanel(alignPanel);
3862 public void autoCalculate_actionPerformed(ActionEvent e)
3864 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3865 if (viewport.autoCalculateConsensus)
3867 viewport.firePropertyChange("alignment", null, viewport
3868 .getAlignment().getSequences());
3873 public void sortByTreeOption_actionPerformed(ActionEvent e)
3875 viewport.sortByTree = sortByTree.isSelected();
3879 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3881 viewport.followSelection = listenToViewSelections.isSelected();
3891 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3893 newTreePanel("AV", "PID", "Average distance tree using PID");
3903 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3905 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3915 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3917 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3927 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3929 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3942 void newTreePanel(String type, String pwType, String title)
3946 if (viewport.getSelectionGroup() != null
3947 && viewport.getSelectionGroup().getSize() > 0)
3949 if (viewport.getSelectionGroup().getSize() < 3)
3955 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3957 .getString("label.not_enough_sequences"),
3958 JOptionPane.WARNING_MESSAGE);
3962 SequenceGroup sg = viewport.getSelectionGroup();
3964 /* Decide if the selection is a column region */
3965 for (SequenceI _s : sg.getSequences())
3967 if (_s.getLength() < sg.getEndRes())
3973 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3975 .getString("label.sequences_selection_not_aligned"),
3976 JOptionPane.WARNING_MESSAGE);
3982 title = title + " on region";
3983 tp = new TreePanel(alignPanel, type, pwType);
3987 // are the visible sequences aligned?
3988 if (!viewport.getAlignment().isAligned(false))
3994 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3996 .getString("label.sequences_not_aligned"),
3997 JOptionPane.WARNING_MESSAGE);
4002 if (viewport.getAlignment().getHeight() < 2)
4007 tp = new TreePanel(alignPanel, type, pwType);
4012 if (viewport.viewName != null)
4014 title += viewport.viewName + " of ";
4017 title += this.title;
4019 Desktop.addInternalFrame(tp, title, 600, 500);
4030 public void addSortByOrderMenuItem(String title,
4031 final AlignmentOrder order)
4033 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title}));
4035 item.addActionListener(new java.awt.event.ActionListener()
4038 public void actionPerformed(ActionEvent e)
4040 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4042 // TODO: JBPNote - have to map order entries to curent SequenceI
4044 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4046 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4049 alignPanel.paintAlignment(true);
4055 * Add a new sort by annotation score menu item
4058 * the menu to add the option to
4060 * the label used to retrieve scores for each sequence on the
4063 public void addSortByAnnotScoreMenuItem(JMenu sort,
4064 final String scoreLabel)
4066 final JMenuItem item = new JMenuItem(scoreLabel);
4068 item.addActionListener(new java.awt.event.ActionListener()
4071 public void actionPerformed(ActionEvent e)
4073 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4074 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4075 viewport.getAlignment());// ,viewport.getSelectionGroup());
4076 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4077 viewport.getAlignment()));
4078 alignPanel.paintAlignment(true);
4084 * last hash for alignment's annotation array - used to minimise cost of
4087 protected int _annotationScoreVectorHash;
4090 * search the alignment and rebuild the sort by annotation score submenu the
4091 * last alignment annotation vector hash is stored to minimize cost of
4092 * rebuilding in subsequence calls.
4096 public void buildSortByAnnotationScoresMenu()
4098 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4103 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4105 sortByAnnotScore.removeAll();
4106 // almost certainly a quicker way to do this - but we keep it simple
4107 Hashtable scoreSorts = new Hashtable();
4108 AlignmentAnnotation aann[];
4109 for (SequenceI sqa : viewport.getAlignment().getSequences())
4111 aann = sqa.getAnnotation();
4112 for (int i = 0; aann != null && i < aann.length; i++)
4114 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4116 scoreSorts.put(aann[i].label, aann[i].label);
4120 Enumeration labels = scoreSorts.keys();
4121 while (labels.hasMoreElements())
4123 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4124 (String) labels.nextElement());
4126 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4129 _annotationScoreVectorHash = viewport.getAlignment()
4130 .getAlignmentAnnotation().hashCode();
4135 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4136 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4137 * call. Listeners are added to remove the menu item when the treePanel is
4138 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4142 * Displayed tree window.
4144 * SortBy menu item title.
4147 public void buildTreeMenu()
4149 calculateTree.removeAll();
4150 // build the calculate menu
4152 for (final String type : new String[]
4155 String treecalcnm = MessageManager.getString("label.tree_calc_"
4156 + type.toLowerCase());
4157 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4159 JMenuItem tm = new JMenuItem();
4160 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4161 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4163 String smn = MessageManager.getStringOrReturn(
4164 "label.score_model_", sm.getName());
4165 final String title = MessageManager.formatMessage(
4166 "label.treecalc_title", treecalcnm, smn);
4167 tm.setText(title);//
4168 tm.addActionListener(new java.awt.event.ActionListener()
4171 public void actionPerformed(ActionEvent e)
4173 newTreePanel(type, pwtype, title);
4176 calculateTree.add(tm);
4181 sortByTreeMenu.removeAll();
4183 List<Component> comps = PaintRefresher.components.get(viewport
4184 .getSequenceSetId());
4185 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4186 for (Component comp : comps)
4188 if (comp instanceof TreePanel)
4190 treePanels.add((TreePanel) comp);
4194 if (treePanels.size() < 1)
4196 sortByTreeMenu.setVisible(false);
4200 sortByTreeMenu.setVisible(true);
4202 for (final TreePanel tp : treePanels)
4204 final JMenuItem item = new JMenuItem(tp.getTitle());
4205 item.addActionListener(new java.awt.event.ActionListener()
4208 public void actionPerformed(ActionEvent e)
4210 tp.sortByTree_actionPerformed();
4211 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4216 sortByTreeMenu.add(item);
4220 public boolean sortBy(AlignmentOrder alorder, String undoname)
4222 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4223 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4224 if (undoname != null)
4226 addHistoryItem(new OrderCommand(undoname, oldOrder,
4227 viewport.getAlignment()));
4229 alignPanel.paintAlignment(true);
4234 * Work out whether the whole set of sequences or just the selected set will
4235 * be submitted for multiple alignment.
4238 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4240 // Now, check we have enough sequences
4241 AlignmentView msa = null;
4243 if ((viewport.getSelectionGroup() != null)
4244 && (viewport.getSelectionGroup().getSize() > 1))
4246 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4247 // some common interface!
4249 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4250 * SequenceI[sz = seqs.getSize(false)];
4252 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4253 * seqs.getSequenceAt(i); }
4255 msa = viewport.getAlignmentView(true);
4257 else if (viewport.getSelectionGroup() != null
4258 && viewport.getSelectionGroup().getSize() == 1)
4260 int option = JOptionPane.showConfirmDialog(this,
4261 MessageManager.getString("warn.oneseq_msainput_selection"),
4262 MessageManager.getString("label.invalid_selection"),
4263 JOptionPane.OK_CANCEL_OPTION);
4264 if (option == JOptionPane.OK_OPTION)
4266 msa = viewport.getAlignmentView(false);
4271 msa = viewport.getAlignmentView(false);
4277 * Decides what is submitted to a secondary structure prediction service: the
4278 * first sequence in the alignment, or in the current selection, or, if the
4279 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4280 * region or the whole alignment. (where the first sequence in the set is the
4281 * one that the prediction will be for).
4283 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4285 AlignmentView seqs = null;
4287 if ((viewport.getSelectionGroup() != null)
4288 && (viewport.getSelectionGroup().getSize() > 0))
4290 seqs = viewport.getAlignmentView(true);
4294 seqs = viewport.getAlignmentView(false);
4296 // limit sequences - JBPNote in future - could spawn multiple prediction
4298 // TODO: viewport.getAlignment().isAligned is a global state - the local
4299 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4300 if (!viewport.getAlignment().isAligned(false))
4302 seqs.setSequences(new SeqCigar[]
4303 { seqs.getSequences()[0] });
4304 // TODO: if seqs.getSequences().length>1 then should really have warned
4318 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4320 // Pick the tree file
4321 JalviewFileChooser chooser = new JalviewFileChooser(
4322 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4323 chooser.setFileView(new JalviewFileView());
4324 chooser.setDialogTitle(MessageManager
4325 .getString("label.select_newick_like_tree_file"));
4326 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4328 int value = chooser.showOpenDialog(null);
4330 if (value == JalviewFileChooser.APPROVE_OPTION)
4332 String choice = chooser.getSelectedFile().getPath();
4333 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4334 jalview.io.NewickFile fin = null;
4337 fin = new jalview.io.NewickFile(choice, "File");
4338 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4339 } catch (Exception ex)
4346 .getString("label.problem_reading_tree_file"),
4347 JOptionPane.WARNING_MESSAGE);
4348 ex.printStackTrace();
4350 if (fin != null && fin.hasWarningMessage())
4352 JOptionPane.showMessageDialog(Desktop.desktop, fin
4353 .getWarningMessage(), MessageManager
4354 .getString("label.possible_problem_with_tree_file"),
4355 JOptionPane.WARNING_MESSAGE);
4361 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4363 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4366 public TreePanel ShowNewickTree(NewickFile nf, String title)
4368 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4371 public TreePanel ShowNewickTree(NewickFile nf, String title,
4372 AlignmentView input)
4374 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4377 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4378 int h, int x, int y)
4380 return ShowNewickTree(nf, title, null, w, h, x, y);
4384 * Add a treeviewer for the tree extracted from a newick file object to the
4385 * current alignment view
4392 * Associated alignment input data (or null)
4401 * @return TreePanel handle
4403 public TreePanel ShowNewickTree(NewickFile nf, String title,
4404 AlignmentView input, int w, int h, int x, int y)
4406 TreePanel tp = null;
4412 if (nf.getTree() != null)
4414 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4420 tp.setLocation(x, y);
4423 Desktop.addInternalFrame(tp, title, w, h);
4425 } catch (Exception ex)
4427 ex.printStackTrace();
4433 private boolean buildingMenu = false;
4436 * Generates menu items and listener event actions for web service clients
4439 public void BuildWebServiceMenu()
4441 while (buildingMenu)
4445 System.err.println("Waiting for building menu to finish.");
4447 } catch (Exception e)
4451 final AlignFrame me = this;
4452 buildingMenu = true;
4453 new Thread(new Runnable()
4458 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4461 // System.err.println("Building ws menu again "
4462 // + Thread.currentThread());
4463 // TODO: add support for context dependent disabling of services based
4465 // alignment and current selection
4466 // TODO: add additional serviceHandle parameter to specify abstract
4468 // class independently of AbstractName
4469 // TODO: add in rediscovery GUI function to restart discoverer
4470 // TODO: group services by location as well as function and/or
4472 // object broker mechanism.
4473 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4474 final IProgressIndicator af = me;
4475 final JMenu msawsmenu = new JMenu("Alignment");
4476 final JMenu secstrmenu = new JMenu(
4477 "Secondary Structure Prediction");
4478 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4479 final JMenu analymenu = new JMenu("Analysis");
4480 final JMenu dismenu = new JMenu("Protein Disorder");
4481 // final JMenu msawsmenu = new
4482 // JMenu(MessageManager.getString("label.alignment"));
4483 // final JMenu secstrmenu = new
4484 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4485 // final JMenu seqsrchmenu = new
4486 // JMenu(MessageManager.getString("label.sequence_database_search"));
4487 // final JMenu analymenu = new
4488 // JMenu(MessageManager.getString("label.analysis"));
4489 // final JMenu dismenu = new
4490 // JMenu(MessageManager.getString("label.protein_disorder"));
4491 // JAL-940 - only show secondary structure prediction services from
4492 // the legacy server
4493 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4495 Discoverer.services != null && (Discoverer.services.size() > 0))
4497 // TODO: refactor to allow list of AbstractName/Handler bindings to
4499 // stored or retrieved from elsewhere
4500 // No MSAWS used any more:
4501 // Vector msaws = null; // (Vector)
4502 // Discoverer.services.get("MsaWS");
4503 Vector secstrpr = (Vector) Discoverer.services
4505 if (secstrpr != null)
4507 // Add any secondary structure prediction services
4508 for (int i = 0, j = secstrpr.size(); i < j; i++)
4510 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4512 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4513 .getServiceClient(sh);
4514 int p = secstrmenu.getItemCount();
4515 impl.attachWSMenuEntry(secstrmenu, me);
4516 int q = secstrmenu.getItemCount();
4517 for (int litm = p; litm < q; litm++)
4519 legacyItems.add(secstrmenu.getItem(litm));
4525 // Add all submenus in the order they should appear on the web
4527 wsmenu.add(msawsmenu);
4528 wsmenu.add(secstrmenu);
4529 wsmenu.add(dismenu);
4530 wsmenu.add(analymenu);
4531 // No search services yet
4532 // wsmenu.add(seqsrchmenu);
4534 javax.swing.SwingUtilities.invokeLater(new Runnable()
4541 webService.removeAll();
4542 // first, add discovered services onto the webservices menu
4543 if (wsmenu.size() > 0)
4545 for (int i = 0, j = wsmenu.size(); i < j; i++)
4547 webService.add(wsmenu.get(i));
4552 webService.add(me.webServiceNoServices);
4554 // TODO: move into separate menu builder class.
4555 boolean new_sspred = false;
4556 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4558 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4559 if (jws2servs != null)
4561 if (jws2servs.hasServices())
4563 jws2servs.attachWSMenuEntry(webService, me);
4564 for (Jws2Instance sv : jws2servs.getServices())
4566 if (sv.description.toLowerCase().contains("jpred"))
4568 for (JMenuItem jmi : legacyItems)
4570 jmi.setVisible(false);
4576 if (jws2servs.isRunning())
4578 JMenuItem tm = new JMenuItem(
4579 "Still discovering JABA Services");
4580 tm.setEnabled(false);
4585 build_urlServiceMenu(me.webService);
4586 build_fetchdbmenu(webService);
4587 for (JMenu item : wsmenu)
4589 if (item.getItemCount() == 0)
4591 item.setEnabled(false);
4595 item.setEnabled(true);
4598 } catch (Exception e)
4601 .debug("Exception during web service menu building process.",
4606 } catch (Exception e)
4609 buildingMenu = false;
4616 * construct any groupURL type service menu entries.
4620 private void build_urlServiceMenu(JMenu webService)
4622 // TODO: remove this code when 2.7 is released
4623 // DEBUG - alignmentView
4625 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4626 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4628 * @Override public void actionPerformed(ActionEvent e) {
4629 * jalview.datamodel.AlignmentView
4630 * .testSelectionViews(af.viewport.getAlignment(),
4631 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4633 * }); webService.add(testAlView);
4635 // TODO: refactor to RestClient discoverer and merge menu entries for
4636 // rest-style services with other types of analysis/calculation service
4637 // SHmmr test client - still being implemented.
4638 // DEBUG - alignmentView
4640 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4643 client.attachWSMenuEntry(
4644 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4650 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4651 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4652 * getProperty("LAST_DIRECTORY"));
4654 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4655 * to Vamsas file"); chooser.setToolTipText("Export");
4657 * int value = chooser.showSaveDialog(this);
4659 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4660 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4661 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4662 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4665 * prototype of an automatically enabled/disabled analysis function
4668 protected void setShowProductsEnabled()
4670 SequenceI[] selection = viewport.getSequenceSelection();
4671 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4672 viewport.getAlignment().getDataset()))
4674 showProducts.setEnabled(true);
4679 showProducts.setEnabled(false);
4684 * search selection for sequence xRef products and build the show products
4689 * @return true if showProducts menu should be enabled.
4691 public boolean canShowProducts(SequenceI[] selection,
4692 boolean isRegionSelection, Alignment dataset)
4694 boolean showp = false;
4697 showProducts.removeAll();
4698 final boolean dna = viewport.getAlignment().isNucleotide();
4699 final Alignment ds = dataset;
4700 String[] ptypes = (selection == null || selection.length == 0) ? null
4701 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4703 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4704 // selection, dataset, true);
4705 final SequenceI[] sel = selection;
4706 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4709 final boolean isRegSel = isRegionSelection;
4710 final AlignFrame af = this;
4711 final String source = ptypes[t];
4712 JMenuItem xtype = new JMenuItem(ptypes[t]);
4713 xtype.addActionListener(new ActionListener()
4717 public void actionPerformed(ActionEvent e)
4719 // TODO: new thread for this call with vis-delay
4720 af.showProductsFor(af.viewport.getSequenceSelection(),
4721 isRegSel, dna, source);
4725 showProducts.add(xtype);
4727 showProducts.setVisible(showp);
4728 showProducts.setEnabled(showp);
4729 } catch (Exception e)
4731 jalview.bin.Cache.log
4732 .warn("canTranslate threw an exception - please report to help@jalview.org",
4739 protected void showProductsFor(final SequenceI[] sel,
4740 final boolean isRegSel, final boolean dna, final String source)
4742 Runnable foo = new Runnable()
4748 final long sttime = System.currentTimeMillis();
4749 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4750 "status.searching_for_sequences_from", new Object[]
4751 { source }), sttime);
4754 // update our local dataset reference
4755 Alignment ds = AlignFrame.this.getViewport().getAlignment()
4757 Alignment prods = CrossRef
4758 .findXrefSequences(sel, dna, source, ds);
4761 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4762 for (int s = 0; s < sprods.length; s++)
4764 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4765 if (ds.getSequences() == null
4766 || !ds.getSequences().contains(
4767 sprods[s].getDatasetSequence()))
4769 ds.addSequence(sprods[s].getDatasetSequence());
4771 sprods[s].updatePDBIds();
4773 Alignment al = new Alignment(sprods);
4777 * Copy dna-to-protein mappings to new alignment
4779 // TODO 1: no mappings are set up for EMBL product
4780 // TODO 2: if they were, should add them to protein alignment, not
4782 Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4783 for (AlignedCodonFrame acf : cf)
4785 al.addCodonFrame(acf);
4787 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4789 String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4790 + " for " + ((isRegSel) ? "selected region of " : "")
4792 naf.setTitle(newtitle);
4794 // temporary flag until SplitFrame is released
4795 boolean asSplitFrame = Cache.getDefault(
4796 Preferences.ENABLE_SPLIT_FRAME, true);
4800 * Make a copy of this alignment (sharing the same dataset
4801 * sequences). If we are DNA, drop introns and update mappings
4803 AlignmentI copyAlignment = null;
4804 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4805 .getSequenceSelection();
4808 copyAlignment = AlignmentUtils.makeExonAlignment(
4809 sequenceSelection, cf);
4810 al.getCodonFrames().clear();
4811 al.getCodonFrames().addAll(cf);
4812 final StructureSelectionManager ssm = StructureSelectionManager
4813 .getStructureSelectionManager(Desktop.instance);
4814 ssm.registerMappings(cf);
4818 copyAlignment = new Alignment(new Alignment(
4819 sequenceSelection));
4821 AlignFrame copyThis = new AlignFrame(copyAlignment,
4822 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4823 copyThis.setTitle(AlignFrame.this.getTitle());
4824 // SplitFrame with dna above, protein below
4825 SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4826 dna ? naf : copyThis);
4827 naf.setVisible(true);
4828 copyThis.setVisible(true);
4829 String linkedTitle = MessageManager
4830 .getString("label.linked_view_title");
4831 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4835 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4841 System.err.println("No Sequences generated for xRef type "
4844 } catch (Exception e)
4846 jalview.bin.Cache.log.error(
4847 "Exception when finding crossreferences", e);
4848 } catch (OutOfMemoryError e)
4850 new OOMWarning("whilst fetching crossreferences", e);
4853 jalview.bin.Cache.log.error("Error when finding crossreferences",
4856 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4857 "status.finished_searching_for_sequences_from",
4864 Thread frunner = new Thread(foo);
4868 public boolean canShowTranslationProducts(SequenceI[] selection,
4869 AlignmentI alignment)
4874 return (jalview.analysis.Dna.canTranslate(selection,
4875 viewport.getViewAsVisibleContigs(true)));
4876 } catch (Exception e)
4878 jalview.bin.Cache.log
4879 .warn("canTranslate threw an exception - please report to help@jalview.org",
4886 * Construct and display a new frame containing the translation of this
4887 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4890 public void showTranslation_actionPerformed(ActionEvent e)
4892 AlignmentI al = null;
4895 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4897 al = dna.translateCdna();
4898 } catch (Exception ex)
4900 jalview.bin.Cache.log.error(
4901 "Exception during translation. Please report this !", ex);
4902 final String msg = MessageManager
4903 .getString("label.error_when_translating_sequences_submit_bug_report");
4904 final String errorTitle = MessageManager
4905 .getString("label.implementation_error")
4906 + MessageManager.getString("translation_failed");
4907 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4908 JOptionPane.ERROR_MESSAGE);
4911 if (al == null || al.getHeight() == 0)
4913 final String msg = MessageManager
4914 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4915 final String errorTitle = MessageManager
4916 .getString("label.translation_failed");
4917 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4918 JOptionPane.WARNING_MESSAGE);
4922 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4923 af.setFileFormat(this.currentFileFormat);
4924 final String newTitle = MessageManager.formatMessage(
4925 "label.translation_of_params", new Object[]
4926 { this.getTitle() });
4927 af.setTitle(newTitle);
4928 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4930 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4931 viewport.openSplitFrame(af, new Alignment(seqs));
4935 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4942 * Set the file format
4946 public void setFileFormat(String fileFormat)
4948 this.currentFileFormat = fileFormat;
4952 * Try to load a features file onto the alignment.
4955 * contents or path to retrieve file
4957 * access mode of file (see jalview.io.AlignFile)
4958 * @return true if features file was parsed correctly.
4960 public boolean parseFeaturesFile(String file, String type)
4962 return avc.parseFeaturesFile(file, type,
4963 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4968 public void refreshFeatureUI(boolean enableIfNecessary)
4970 // note - currently this is only still here rather than in the controller
4971 // because of the featureSettings hard reference that is yet to be
4973 if (enableIfNecessary)
4975 viewport.setShowSequenceFeatures(true);
4976 showSeqFeatures.setSelected(true);
4982 public void dragEnter(DropTargetDragEvent evt)
4987 public void dragExit(DropTargetEvent evt)
4992 public void dragOver(DropTargetDragEvent evt)
4997 public void dropActionChanged(DropTargetDragEvent evt)
5002 public void drop(DropTargetDropEvent evt)
5004 Transferable t = evt.getTransferable();
5005 java.util.List files = null;
5009 DataFlavor uriListFlavor = new DataFlavor(
5010 "text/uri-list;class=java.lang.String");
5011 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5013 // Works on Windows and MacOSX
5014 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5015 files = (java.util.List) t
5016 .getTransferData(DataFlavor.javaFileListFlavor);
5018 else if (t.isDataFlavorSupported(uriListFlavor))
5020 // This is used by Unix drag system
5021 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5022 String data = (String) t.getTransferData(uriListFlavor);
5023 files = new java.util.ArrayList(1);
5024 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5025 data, "\r\n"); st.hasMoreTokens();)
5027 String s = st.nextToken();
5028 if (s.startsWith("#"))
5030 // the line is a comment (as per the RFC 2483)
5034 java.net.URI uri = new java.net.URI(s);
5035 // check to see if we can handle this kind of URI
5036 if (uri.getScheme().toLowerCase().startsWith("http"))
5038 files.add(uri.toString());
5042 // otherwise preserve old behaviour: catch all for file objects
5043 java.io.File file = new java.io.File(uri);
5044 files.add(file.toString());
5048 } catch (Exception e)
5050 e.printStackTrace();
5056 // check to see if any of these files have names matching sequences in
5058 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5059 .getAlignment().getSequencesArray());
5061 * Object[] { String,SequenceI}
5063 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5064 ArrayList<String> filesnotmatched = new ArrayList<String>();
5065 for (int i = 0; i < files.size(); i++)
5067 String file = files.get(i).toString();
5069 String protocol = FormatAdapter.checkProtocol(file);
5070 if (protocol == jalview.io.FormatAdapter.FILE)
5072 File fl = new File(file);
5073 pdbfn = fl.getName();
5075 else if (protocol == jalview.io.FormatAdapter.URL)
5077 URL url = new URL(file);
5078 pdbfn = url.getFile();
5080 if (pdbfn.length() > 0)
5082 // attempt to find a match in the alignment
5083 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5084 int l = 0, c = pdbfn.indexOf(".");
5085 while (mtch == null && c != -1)
5090 } while ((c = pdbfn.indexOf(".", l)) > l);
5093 pdbfn = pdbfn.substring(0, l);
5095 mtch = idm.findAllIdMatches(pdbfn);
5102 type = new IdentifyFile().Identify(file, protocol);
5103 } catch (Exception ex)
5109 if (type.equalsIgnoreCase("PDB"))
5111 filesmatched.add(new Object[]
5112 { file, protocol, mtch });
5117 // File wasn't named like one of the sequences or wasn't a PDB file.
5118 filesnotmatched.add(file);
5122 if (filesmatched.size() > 0)
5124 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5130 "label.automatically_associate_pdb_files_with_sequences_same_name",
5137 .getString("label.automatically_associate_pdb_files_by_name"),
5138 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5141 for (Object[] fm : filesmatched)
5143 // try and associate
5144 // TODO: may want to set a standard ID naming formalism for
5145 // associating PDB files which have no IDs.
5146 for (SequenceI toassoc : (SequenceI[]) fm[2])
5148 PDBEntry pe = new AssociatePdbFileWithSeq()
5149 .associatePdbWithSeq((String) fm[0],
5150 (String) fm[1], toassoc, false,
5154 System.err.println("Associated file : "
5155 + ((String) fm[0]) + " with "
5156 + toassoc.getDisplayId(true));
5160 alignPanel.paintAlignment(true);
5164 if (filesnotmatched.size() > 0)
5167 && (Cache.getDefault(
5168 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5171 "<html>"+MessageManager
5173 "label.ignore_unmatched_dropped_files_info",
5178 .toString() })+"</html>",
5180 .getString("label.ignore_unmatched_dropped_files"),
5181 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5185 for (String fn : filesnotmatched)
5187 loadJalviewDataFile(fn, null, null, null);
5191 } catch (Exception ex)
5193 ex.printStackTrace();
5199 * Attempt to load a "dropped" file or URL string: First by testing whether
5200 * it's and Annotation file, then a JNet file, and finally a features file. If
5201 * all are false then the user may have dropped an alignment file onto this
5205 * either a filename or a URL string.
5207 public void loadJalviewDataFile(String file, String protocol,
5208 String format, SequenceI assocSeq)
5212 if (protocol == null)
5214 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5216 // if the file isn't identified, or not positively identified as some
5217 // other filetype (PFAM is default unidentified alignment file type) then
5218 // try to parse as annotation.
5219 boolean isAnnotation = (format == null || format
5220 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5221 .annotateAlignmentView(viewport, file, protocol)
5226 // first see if its a T-COFFEE score file
5227 TCoffeeScoreFile tcf = null;
5230 tcf = new TCoffeeScoreFile(file, protocol);
5233 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5235 tcoffeeColour.setEnabled(true);
5236 tcoffeeColour.setSelected(true);
5237 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5238 isAnnotation = true;
5240 .setText(MessageManager
5241 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5245 // some problem - if no warning its probable that the ID matching
5246 // process didn't work
5250 tcf.getWarningMessage() == null ? MessageManager
5251 .getString("label.check_file_matches_sequence_ids_alignment")
5252 : tcf.getWarningMessage(),
5254 .getString("label.problem_reading_tcoffee_score_file"),
5255 JOptionPane.WARNING_MESSAGE);
5262 } catch (Exception x)
5265 .debug("Exception when processing data source as T-COFFEE score file",
5271 // try to see if its a JNet 'concise' style annotation file *before*
5273 // try to parse it as a features file
5276 format = new IdentifyFile().Identify(file, protocol);
5278 if (format.equalsIgnoreCase("JnetFile"))
5280 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5282 new JnetAnnotationMaker();
5283 JnetAnnotationMaker.add_annotation(predictions,
5284 viewport.getAlignment(), 0, false);
5285 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5286 viewport.getAlignment().setSeqrep(repseq);
5287 ColumnSelection cs = new ColumnSelection();
5288 cs.hideInsertionsFor(repseq);
5289 viewport.setColumnSelection(cs);
5290 isAnnotation = true;
5295 * if (format.equalsIgnoreCase("PDB")) {
5297 * String pdbfn = ""; // try to match up filename with sequence id
5298 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5299 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5300 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5301 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5302 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5303 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5304 * // attempt to find a match in the alignment SequenceI mtch =
5305 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5306 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5307 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5308 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5309 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5310 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5311 * { System.err.println("Associated file : " + file + " with " +
5312 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5313 * TODO: maybe need to load as normal otherwise return; } }
5315 // try to parse it as a features file
5316 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5317 // if it wasn't a features file then we just treat it as a general
5318 // alignment file to load into the current view.
5321 new FileLoader().LoadFile(viewport, file, protocol, format);
5325 alignPanel.paintAlignment(true);
5333 alignPanel.adjustAnnotationHeight();
5334 viewport.updateSequenceIdColours();
5335 buildSortByAnnotationScoresMenu();
5336 alignPanel.paintAlignment(true);
5338 } catch (Exception ex)
5340 ex.printStackTrace();
5341 } catch (OutOfMemoryError oom)
5346 } catch (Exception x)
5352 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5353 : "using " + protocol + " from " + file)
5355 + (format != null ? "(parsing as '" + format
5356 + "' file)" : ""), oom, Desktop.desktop);
5361 * Method invoked by the ChangeListener on the tabbed pane, in other words
5362 * when a different tabbed pane is selected by the user or programmatically.
5365 public void tabSelectionChanged(int index)
5369 alignPanel = alignPanels.get(index);
5370 viewport = alignPanel.av;
5371 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5372 setMenusFromViewport(viewport);
5376 * If there is a frame linked to this one in a SplitPane, switch it to the
5377 * same view tab index. No infinite recursion of calls should happen, since
5378 * tabSelectionChanged() should not get invoked on setting the selected
5379 * index to an unchanged value. Guard against setting an invalid index
5380 * before the new view peer tab has been created.
5382 final AlignViewportI peer = viewport.getCodingComplement();
5385 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5386 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5388 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5394 * On right mouse click on view tab, prompt for and set new view name.
5397 public void tabbedPane_mousePressed(MouseEvent e)
5399 if (SwingUtilities.isRightMouseButton(e))
5401 String msg = MessageManager.getString("label.enter_view_name");
5402 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5403 JOptionPane.QUESTION_MESSAGE);
5407 viewport.viewName = reply;
5408 // TODO warn if reply is in getExistingViewNames()?
5409 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5414 public AlignViewport getCurrentView()
5420 * Open the dialog for regex description parsing.
5423 protected void extractScores_actionPerformed(ActionEvent e)
5425 ParseProperties pp = new jalview.analysis.ParseProperties(
5426 viewport.getAlignment());
5427 // TODO: verify regex and introduce GUI dialog for version 2.5
5428 // if (pp.getScoresFromDescription("col", "score column ",
5429 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5431 if (pp.getScoresFromDescription("description column",
5432 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5434 buildSortByAnnotationScoresMenu();
5442 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5446 protected void showDbRefs_actionPerformed(ActionEvent e)
5448 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5454 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5458 protected void showNpFeats_actionPerformed(ActionEvent e)
5460 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5464 * find the viewport amongst the tabs in this alignment frame and close that
5469 public boolean closeView(AlignViewportI av)
5473 this.closeMenuItem_actionPerformed(false);
5476 Component[] comp = tabbedPane.getComponents();
5477 for (int i = 0; comp != null && i < comp.length; i++)
5479 if (comp[i] instanceof AlignmentPanel)
5481 if (((AlignmentPanel) comp[i]).av == av)
5484 closeView((AlignmentPanel) comp[i]);
5492 protected void build_fetchdbmenu(JMenu webService)
5494 // Temporary hack - DBRef Fetcher always top level ws entry.
5495 // TODO We probably want to store a sequence database checklist in
5496 // preferences and have checkboxes.. rather than individual sources selected
5498 final JMenu rfetch = new JMenu(
5499 MessageManager.getString("action.fetch_db_references"));
5500 rfetch.setToolTipText(MessageManager
5501 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5502 webService.add(rfetch);
5504 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5505 MessageManager.getString("option.trim_retrieved_seqs"));
5506 trimrs.setToolTipText(MessageManager
5507 .getString("label.trim_retrieved_sequences"));
5508 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5509 trimrs.addActionListener(new ActionListener()
5512 public void actionPerformed(ActionEvent e)
5514 trimrs.setSelected(trimrs.isSelected());
5515 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5516 Boolean.valueOf(trimrs.isSelected()).toString());
5520 JMenuItem fetchr = new JMenuItem(
5521 MessageManager.getString("label.standard_databases"));
5522 fetchr.setToolTipText(MessageManager
5523 .getString("label.fetch_embl_uniprot"));
5524 fetchr.addActionListener(new ActionListener()
5528 public void actionPerformed(ActionEvent e)
5530 new Thread(new Runnable()
5536 new jalview.ws.DBRefFetcher(alignPanel.av
5537 .getSequenceSelection(), alignPanel.alignFrame)
5538 .fetchDBRefs(false);
5546 final AlignFrame me = this;
5547 new Thread(new Runnable()
5552 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5553 .getSequenceFetcherSingleton(me);
5554 javax.swing.SwingUtilities.invokeLater(new Runnable()
5559 String[] dbclasses = sf.getOrderedSupportedSources();
5560 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5561 // jalview.util.QuickSort.sort(otherdb, otherdb);
5562 List<DbSourceProxy> otherdb;
5563 JMenu dfetch = new JMenu();
5564 JMenu ifetch = new JMenu();
5565 JMenuItem fetchr = null;
5566 int comp = 0, icomp = 0, mcomp = 15;
5567 String mname = null;
5569 for (String dbclass : dbclasses)
5571 otherdb = sf.getSourceProxy(dbclass);
5572 // add a single entry for this class, or submenu allowing 'fetch
5574 if (otherdb == null || otherdb.size() < 1)
5578 // List<DbSourceProxy> dbs=otherdb;
5579 // otherdb=new ArrayList<DbSourceProxy>();
5580 // for (DbSourceProxy db:dbs)
5582 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5586 mname = "From " + dbclass;
5588 if (otherdb.size() == 1)
5590 final DbSourceProxy[] dassource = otherdb
5591 .toArray(new DbSourceProxy[0]);
5592 DbSourceProxy src = otherdb.get(0);
5593 fetchr = new JMenuItem(src.getDbSource());
5594 fetchr.addActionListener(new ActionListener()
5598 public void actionPerformed(ActionEvent e)
5600 new Thread(new Runnable()
5606 new jalview.ws.DBRefFetcher(alignPanel.av
5607 .getSequenceSelection(),
5608 alignPanel.alignFrame, dassource)
5609 .fetchDBRefs(false);
5615 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()})));
5621 final DbSourceProxy[] dassource = otherdb
5622 .toArray(new DbSourceProxy[0]);
5624 DbSourceProxy src = otherdb.get(0);
5625 fetchr = new JMenuItem(MessageManager.formatMessage(
5626 "label.fetch_all_param", new Object[]
5627 { src.getDbSource() }));
5628 fetchr.addActionListener(new ActionListener()
5631 public void actionPerformed(ActionEvent e)
5633 new Thread(new Runnable()
5639 new jalview.ws.DBRefFetcher(alignPanel.av
5640 .getSequenceSelection(),
5641 alignPanel.alignFrame, dassource)
5642 .fetchDBRefs(false);
5648 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new Object[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5651 // and then build the rest of the individual menus
5652 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()}));
5654 String imname = null;
5656 for (DbSourceProxy sproxy : otherdb)
5658 String dbname = sproxy.getDbName();
5659 String sname = dbname.length() > 5 ? dbname.substring(0,
5660 5) + "..." : dbname;
5661 String msname = dbname.length() > 10 ? dbname.substring(
5662 0, 10) + "..." : dbname;
5665 imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname});
5667 fetchr = new JMenuItem(msname);
5668 final DbSourceProxy[] dassrc =
5670 fetchr.addActionListener(new ActionListener()
5674 public void actionPerformed(ActionEvent e)
5676 new Thread(new Runnable()
5682 new jalview.ws.DBRefFetcher(alignPanel.av
5683 .getSequenceSelection(),
5684 alignPanel.alignFrame, dassrc)
5685 .fetchDBRefs(false);
5691 fetchr.setToolTipText("<html>"
5692 + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname}));
5695 if (++icomp >= mcomp || i == (otherdb.size()))
5697 ifetch.setText(MessageManager.formatMessage(
5698 "label.source_to_target", imname, sname));
5700 ifetch = new JMenu();
5708 if (comp >= mcomp || dbi >= (dbclasses.length))
5710 dfetch.setText(MessageManager.formatMessage(
5711 "label.source_to_target", mname, dbclass));
5713 dfetch = new JMenu();
5726 * Left justify the whole alignment.
5729 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5731 AlignmentI al = viewport.getAlignment();
5733 viewport.firePropertyChange("alignment", null, al);
5737 * Right justify the whole alignment.
5740 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5742 AlignmentI al = viewport.getAlignment();
5744 viewport.firePropertyChange("alignment", null, al);
5747 public void setShowSeqFeatures(boolean b)
5749 showSeqFeatures.setSelected(b);
5750 viewport.setShowSequenceFeatures(b);
5757 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5758 * awt.event.ActionEvent)
5761 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5763 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5764 alignPanel.paintAlignment(true);
5771 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5775 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5777 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5778 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5786 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5787 * .event.ActionEvent)
5790 protected void showGroupConservation_actionPerformed(ActionEvent e)
5792 viewport.setShowGroupConservation(showGroupConservation.getState());
5793 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5800 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5801 * .event.ActionEvent)
5804 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5806 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5807 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5814 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5815 * .event.ActionEvent)
5818 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5820 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5821 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5825 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5827 showSequenceLogo.setState(true);
5828 viewport.setShowSequenceLogo(true);
5829 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5830 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5834 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5836 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5843 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5844 * .event.ActionEvent)
5847 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5849 if (avc.makeGroupsFromSelection())
5851 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5852 alignPanel.updateAnnotation();
5853 alignPanel.paintAlignment(true);
5856 public void clearAlignmentSeqRep()
5858 // TODO refactor alignmentseqrep to controller
5859 if (viewport.getAlignment().hasSeqrep()) {
5860 viewport.getAlignment().setSeqrep(null);
5861 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5862 alignPanel.updateAnnotation();
5863 alignPanel.paintAlignment(true);
5868 protected void createGroup_actionPerformed(ActionEvent e)
5870 if (avc.createGroup())
5872 alignPanel.alignmentChanged();
5877 protected void unGroup_actionPerformed(ActionEvent e)
5881 alignPanel.alignmentChanged();
5886 * make the given alignmentPanel the currently selected tab
5888 * @param alignmentPanel
5890 public void setDisplayedView(AlignmentPanel alignmentPanel)
5892 if (!viewport.getSequenceSetId().equals(
5893 alignmentPanel.av.getSequenceSetId()))
5895 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5897 if (tabbedPane != null
5898 && tabbedPane.getTabCount() > 0
5899 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5900 .getSelectedIndex())
5902 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5907 * Action on selection of menu options to Show or Hide annotations.
5910 * @param forSequences
5911 * update sequence-related annotations
5912 * @param forAlignment
5913 * update non-sequence-related annotations
5916 protected void setAnnotationsVisibility(boolean visible,
5917 boolean forSequences, boolean forAlignment)
5919 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5920 .getAlignmentAnnotation())
5923 * don't display non-positional annotations on an alignment
5925 if (aa.annotations == null)
5929 boolean apply = (aa.sequenceRef == null && forAlignment)
5930 || (aa.sequenceRef != null && forSequences);
5933 aa.visible = visible;
5936 alignPanel.validateAnnotationDimensions(true);
5937 alignPanel.alignmentChanged();
5941 * Store selected annotation sort order for the view and repaint.
5944 protected void sortAnnotations_actionPerformed()
5946 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5948 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5949 alignPanel.paintAlignment(true);
5954 * @return alignment panels in this alignment frame
5956 public List<? extends AlignmentViewPanel> getAlignPanels()
5958 return alignPanels == null ? Arrays.asList(alignPanel)
5963 * Open a new alignment window, with the cDNA associated with this (protein)
5964 * alignment, aligned as is the protein.
5966 protected void viewAsCdna_actionPerformed()
5968 // TODO no longer a menu action - refactor as required
5969 final AlignmentI alignment = getViewport().getAlignment();
5970 Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5971 if (mappings == null)
5975 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5976 for (SequenceI aaSeq : alignment.getSequences()) {
5977 for (AlignedCodonFrame acf : mappings) {
5978 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5982 * There is a cDNA mapping for this protein sequence - add to new
5983 * alignment. It will share the same dataset sequence as other mapped
5984 * cDNA (no new mappings need to be created).
5986 final Sequence newSeq = new Sequence(dnaSeq);
5987 newSeq.setDatasetSequence(dnaSeq);
5988 cdnaSeqs.add(newSeq);
5992 if (cdnaSeqs.size() == 0)
5994 // show a warning dialog no mapped cDNA
5997 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5999 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6000 AlignFrame.DEFAULT_HEIGHT);
6001 cdna.alignAs(alignment);
6002 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6004 Desktop.addInternalFrame(alignFrame, newtitle,
6005 AlignFrame.DEFAULT_WIDTH,
6006 AlignFrame.DEFAULT_HEIGHT);
6010 * Set visibility of dna/protein complement view (available when shown in a
6016 protected void showComplement_actionPerformed(boolean show)
6018 SplitContainerI sf = getSplitViewContainer();
6020 sf.setComplementVisible(this, show);
6025 class PrintThread extends Thread
6029 public PrintThread(AlignmentPanel ap)
6034 static PageFormat pf;
6039 PrinterJob printJob = PrinterJob.getPrinterJob();
6043 printJob.setPrintable(ap, pf);
6047 printJob.setPrintable(ap);
6050 if (printJob.printDialog())
6055 } catch (Exception PrintException)
6057 PrintException.printStackTrace();