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);
245 * Create alignment frame for al with hiddenColumns, a specific width and
246 * height, and specific sequenceId
249 * @param hiddenColumns
252 * @param sequenceSetId
255 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
256 int width, int height, String sequenceSetId)
258 this(al, hiddenColumns, width, height, sequenceSetId, null);
262 * Create alignment frame for al with hiddenColumns, a specific width and
263 * height, and specific sequenceId
266 * @param hiddenColumns
269 * @param sequenceSetId
274 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
275 int width, int height, String sequenceSetId, String viewId)
277 setSize(width, height);
279 if (al.getDataset() == null)
284 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
286 alignPanel = new AlignmentPanel(this, viewport);
288 addAlignmentPanel(alignPanel, true);
292 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
293 ColumnSelection hiddenColumns, int width, int height)
295 setSize(width, height);
297 if (al.getDataset() == null)
302 viewport = new AlignViewport(al, hiddenColumns);
304 if (hiddenSeqs != null && hiddenSeqs.length > 0)
306 viewport.hideSequence(hiddenSeqs);
308 alignPanel = new AlignmentPanel(this, viewport);
309 addAlignmentPanel(alignPanel, true);
314 * Make a new AlignFrame from existing alignmentPanels
321 public AlignFrame(AlignmentPanel ap)
325 addAlignmentPanel(ap, false);
330 * initalise the alignframe from the underlying viewport data and the
335 if (!Jalview.isHeadlessMode())
337 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
340 avc = new jalview.controller.AlignViewController(this, viewport,
342 if (viewport.getAlignmentConservationAnnotation() == null)
344 BLOSUM62Colour.setEnabled(false);
345 conservationMenuItem.setEnabled(false);
346 modifyConservation.setEnabled(false);
347 // PIDColour.setEnabled(false);
348 // abovePIDThreshold.setEnabled(false);
349 // modifyPID.setEnabled(false);
352 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
355 if (sortby.equals("Id"))
357 sortIDMenuItem_actionPerformed(null);
359 else if (sortby.equals("Pairwise Identity"))
361 sortPairwiseMenuItem_actionPerformed(null);
364 if (Desktop.desktop != null)
366 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
367 addServiceListeners();
368 setGUINucleotide(viewport.getAlignment().isNucleotide());
372 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
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(
562 evt.isControlDown() || evt.isShiftDown()
567 // case KeyEvent.VK_A:
568 // if (viewport.cursorMode)
570 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
571 // //System.out.println("A");
575 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
576 * System.out.println("closing bracket"); } break;
578 case KeyEvent.VK_DELETE:
579 case KeyEvent.VK_BACK_SPACE:
580 if (!viewport.cursorMode)
582 cut_actionPerformed(null);
586 alignPanel.getSeqPanel().deleteGapAtCursor(
587 evt.isControlDown() || evt.isShiftDown()
594 if (viewport.cursorMode)
596 alignPanel.getSeqPanel().setCursorRow();
600 if (viewport.cursorMode && !evt.isControlDown())
602 alignPanel.getSeqPanel().setCursorColumn();
606 if (viewport.cursorMode)
608 alignPanel.getSeqPanel().setCursorPosition();
612 case KeyEvent.VK_ENTER:
613 case KeyEvent.VK_COMMA:
614 if (viewport.cursorMode)
616 alignPanel.getSeqPanel().setCursorRowAndColumn();
621 if (viewport.cursorMode)
623 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
627 if (viewport.cursorMode)
629 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
634 viewport.cursorMode = !viewport.cursorMode;
635 statusBar.setText(MessageManager.formatMessage(
636 "label.keyboard_editing_mode",
637 new String[] { (viewport.cursorMode ? "on" : "off") }));
638 if (viewport.cursorMode)
640 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
641 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
643 alignPanel.getSeqPanel().seqCanvas.repaint();
649 Help.showHelpWindow();
650 } catch (Exception ex)
652 ex.printStackTrace();
657 boolean toggleSeqs = !evt.isControlDown();
658 boolean toggleCols = !evt.isShiftDown();
659 toggleHiddenRegions(toggleSeqs, toggleCols);
662 case KeyEvent.VK_PAGE_UP:
663 if (viewport.getWrapAlignment())
665 alignPanel.scrollUp(true);
669 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
670 - viewport.endSeq + viewport.startSeq);
673 case KeyEvent.VK_PAGE_DOWN:
674 if (viewport.getWrapAlignment())
676 alignPanel.scrollUp(false);
680 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
681 + viewport.endSeq - viewport.startSeq);
688 public void keyReleased(KeyEvent evt)
690 switch (evt.getKeyCode())
692 case KeyEvent.VK_LEFT:
693 if (evt.isAltDown() || !viewport.cursorMode)
695 viewport.firePropertyChange("alignment", null, viewport
696 .getAlignment().getSequences());
700 case KeyEvent.VK_RIGHT:
701 if (evt.isAltDown() || !viewport.cursorMode)
703 viewport.firePropertyChange("alignment", null, viewport
704 .getAlignment().getSequences());
712 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
714 ap.alignFrame = this;
715 avc = new jalview.controller.AlignViewController(this, viewport,
720 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
722 int aSize = alignPanels.size();
724 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
726 if (aSize == 1 && ap.av.viewName == null)
728 this.getContentPane().add(ap, BorderLayout.CENTER);
734 setInitialTabVisible();
737 expandViews.setEnabled(true);
738 gatherViews.setEnabled(true);
739 tabbedPane.addTab(ap.av.viewName, ap);
741 ap.setVisible(false);
746 if (ap.av.isPadGaps())
748 ap.av.getAlignment().padGaps();
750 ap.av.updateConservation(ap);
751 ap.av.updateConsensus(ap);
752 ap.av.updateStrucConsensus(ap);
756 public void setInitialTabVisible()
758 expandViews.setEnabled(true);
759 gatherViews.setEnabled(true);
760 tabbedPane.setVisible(true);
761 AlignmentPanel first = alignPanels.get(0);
762 tabbedPane.addTab(first.av.viewName, first);
763 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
766 public AlignViewport getViewport()
771 /* Set up intrinsic listeners for dynamically generated GUI bits. */
772 private void addServiceListeners()
774 final java.beans.PropertyChangeListener thisListener;
775 Desktop.instance.addJalviewPropertyChangeListener("services",
776 thisListener = new java.beans.PropertyChangeListener()
779 public void propertyChange(PropertyChangeEvent evt)
781 // // System.out.println("Discoverer property change.");
782 // if (evt.getPropertyName().equals("services"))
784 SwingUtilities.invokeLater(new Runnable()
791 .println("Rebuild WS Menu for service change");
792 BuildWebServiceMenu();
799 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
802 public void internalFrameClosed(
803 javax.swing.event.InternalFrameEvent evt)
805 // System.out.println("deregistering discoverer listener");
806 Desktop.instance.removeJalviewPropertyChangeListener("services",
808 closeMenuItem_actionPerformed(true);
811 // Finally, build the menu once to get current service state
812 new Thread(new Runnable()
817 BuildWebServiceMenu();
823 * Configure menu items that vary according to whether the alignment is
824 * nucleotide or protein
828 public void setGUINucleotide(boolean nucleotide)
830 showTranslation.setVisible(nucleotide);
831 conservationMenuItem.setEnabled(!nucleotide);
832 modifyConservation.setEnabled(!nucleotide);
833 showGroupConservation.setEnabled(!nucleotide);
834 rnahelicesColour.setEnabled(nucleotide);
835 purinePyrimidineColour.setEnabled(nucleotide);
836 showComplementMenuItem.setText(MessageManager
837 .getString(nucleotide ? "label.protein" : "label.nucleotide"));
838 setColourSelected(jalview.bin.Cache.getDefault(
839 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
840 : Preferences.DEFAULT_COLOUR_PROT, "None"));
844 * set up menus for the current viewport. This may be called after any
845 * operation that affects the data in the current view (selection changed,
846 * etc) to update the menus to reflect the new state.
848 public void setMenusForViewport()
850 setMenusFromViewport(viewport);
854 * Need to call this method when tabs are selected for multiple views, or when
855 * loading from Jalview2XML.java
860 void setMenusFromViewport(AlignViewport av)
862 padGapsMenuitem.setSelected(av.isPadGaps());
863 colourTextMenuItem.setSelected(av.isShowColourText());
864 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
865 conservationMenuItem.setSelected(av.getConservationSelected());
866 seqLimits.setSelected(av.getShowJVSuffix());
867 idRightAlign.setSelected(av.isRightAlignIds());
868 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
869 renderGapsMenuItem.setSelected(av.isRenderGaps());
870 wrapMenuItem.setSelected(av.getWrapAlignment());
871 scaleAbove.setVisible(av.getWrapAlignment());
872 scaleLeft.setVisible(av.getWrapAlignment());
873 scaleRight.setVisible(av.getWrapAlignment());
874 annotationPanelMenuItem.setState(av.isShowAnnotation());
876 * Show/hide annotations only enabled if annotation panel is shown
878 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
879 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
880 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
881 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
882 viewBoxesMenuItem.setSelected(av.getShowBoxes());
883 viewTextMenuItem.setSelected(av.getShowText());
884 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
885 showGroupConsensus.setSelected(av.isShowGroupConsensus());
886 showGroupConservation.setSelected(av.isShowGroupConservation());
887 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
888 showSequenceLogo.setSelected(av.isShowSequenceLogo());
889 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
891 setColourSelected(ColourSchemeProperty.getColourName(av
892 .getGlobalColourScheme()));
894 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
895 hiddenMarkers.setState(av.getShowHiddenMarkers());
896 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
897 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
898 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
899 autoCalculate.setSelected(av.autoCalculateConsensus);
900 sortByTree.setSelected(av.sortByTree);
901 listenToViewSelections.setSelected(av.followSelection);
902 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
904 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
905 setShowProductsEnabled();
909 private IProgressIndicator progressBar;
914 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
917 public void setProgressBar(String message, long id)
919 progressBar.setProgressBar(message, id);
923 public void registerHandler(final long id,
924 final IProgressIndicatorHandler handler)
926 progressBar.registerHandler(id, handler);
931 * @return true if any progress bars are still active
934 public boolean operationInProgress()
936 return progressBar.operationInProgress();
940 public void setStatus(String text)
942 statusBar.setText(text);
946 * Added so Castor Mapping file can obtain Jalview Version
948 public String getVersion()
950 return jalview.bin.Cache.getProperty("VERSION");
953 public FeatureRenderer getFeatureRenderer()
955 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
959 public void fetchSequence_actionPerformed(ActionEvent e)
961 new SequenceFetcher(this);
965 public void addFromFile_actionPerformed(ActionEvent e)
967 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
971 public void reload_actionPerformed(ActionEvent e)
973 if (fileName != null)
975 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
976 // originating file's format
977 // TODO: work out how to recover feature settings for correct view(s) when
979 if (currentFileFormat.equals("Jalview"))
981 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
982 for (int i = 0; i < frames.length; i++)
984 if (frames[i] instanceof AlignFrame && frames[i] != this
985 && ((AlignFrame) frames[i]).fileName != null
986 && ((AlignFrame) frames[i]).fileName.equals(fileName))
990 frames[i].setSelected(true);
991 Desktop.instance.closeAssociatedWindows();
992 } catch (java.beans.PropertyVetoException ex)
998 Desktop.instance.closeAssociatedWindows();
1000 FileLoader loader = new FileLoader();
1001 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1002 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1006 Rectangle bounds = this.getBounds();
1008 FileLoader loader = new FileLoader();
1009 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1010 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1011 protocol, currentFileFormat);
1013 newframe.setBounds(bounds);
1014 if (featureSettings != null && featureSettings.isShowing())
1016 final Rectangle fspos = featureSettings.frame.getBounds();
1017 // TODO: need a 'show feature settings' function that takes bounds -
1018 // need to refactor Desktop.addFrame
1019 newframe.featureSettings_actionPerformed(null);
1020 final FeatureSettings nfs = newframe.featureSettings;
1021 SwingUtilities.invokeLater(new Runnable()
1026 nfs.frame.setBounds(fspos);
1029 this.featureSettings.close();
1030 this.featureSettings = null;
1032 this.closeMenuItem_actionPerformed(true);
1038 public void addFromText_actionPerformed(ActionEvent e)
1040 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1045 public void addFromURL_actionPerformed(ActionEvent e)
1047 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1051 public void save_actionPerformed(ActionEvent e)
1053 if (fileName == null
1054 || (currentFileFormat == null || !jalview.io.FormatAdapter
1055 .isValidIOFormat(currentFileFormat, true))
1056 || fileName.startsWith("http"))
1058 saveAs_actionPerformed(null);
1062 saveAlignment(fileName, currentFileFormat);
1073 public void saveAs_actionPerformed(ActionEvent e)
1075 JalviewFileChooser chooser = new JalviewFileChooser(
1076 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1077 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1078 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1079 currentFileFormat, false);
1081 chooser.setFileView(new JalviewFileView());
1082 chooser.setDialogTitle(MessageManager
1083 .getString("label.save_alignment_to_file"));
1084 chooser.setToolTipText(MessageManager.getString("action.save"));
1086 int value = chooser.showSaveDialog(this);
1088 if (value == JalviewFileChooser.APPROVE_OPTION)
1090 currentFileFormat = chooser.getSelectedFormat();
1091 while (currentFileFormat == null)
1094 .showInternalMessageDialog(
1097 .getString("label.select_file_format_before_saving"),
1099 .getString("label.file_format_not_specified"),
1100 JOptionPane.WARNING_MESSAGE);
1101 currentFileFormat = chooser.getSelectedFormat();
1102 value = chooser.showSaveDialog(this);
1103 if (value != JalviewFileChooser.APPROVE_OPTION)
1109 fileName = chooser.getSelectedFile().getPath();
1111 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1114 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1115 if (currentFileFormat.indexOf(" ") > -1)
1117 currentFileFormat = currentFileFormat.substring(0,
1118 currentFileFormat.indexOf(" "));
1120 saveAlignment(fileName, currentFileFormat);
1124 public boolean saveAlignment(String file, String format)
1126 boolean success = true;
1128 if (format.equalsIgnoreCase("Jalview"))
1130 String shortName = title;
1132 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1134 shortName = shortName.substring(shortName
1135 .lastIndexOf(java.io.File.separatorChar) + 1);
1138 success = new Jalview2XML().saveAlignment(this, file, shortName);
1140 statusBar.setText(MessageManager.formatMessage(
1141 "label.successfully_saved_to_file_in_format", new Object[] {
1142 fileName, format }));
1147 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1149 warningMessage("Cannot save file " + fileName + " using format "
1150 + format, "Alignment output format not supported");
1151 if (!Jalview.isHeadlessMode())
1153 saveAs_actionPerformed(null);
1158 AlignmentExportData exportData = getAlignmentForExport(format,
1160 if (exportData.getSettings().isCancelled())
1164 FormatAdapter f = new FormatAdapter(alignPanel,
1165 exportData.getSettings());
1166 String output = f.formatSequences(
1168 exportData.getAlignment(), // class cast exceptions will
1169 // occur in the distant future
1170 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1171 f.getCacheSuffixDefault(format),
1172 viewport.getColumnSelection());
1182 java.io.PrintWriter out = new java.io.PrintWriter(
1183 new java.io.FileWriter(file));
1187 this.setTitle(file);
1188 statusBar.setText(MessageManager.formatMessage(
1189 "label.successfully_saved_to_file_in_format",
1190 new Object[] { fileName, format }));
1191 } catch (Exception ex)
1194 ex.printStackTrace();
1201 JOptionPane.showInternalMessageDialog(this, MessageManager
1202 .formatMessage("label.couldnt_save_file",
1203 new Object[] { fileName }), MessageManager
1204 .getString("label.error_saving_file"),
1205 JOptionPane.WARNING_MESSAGE);
1211 private void warningMessage(String warning, String title)
1213 if (new jalview.util.Platform().isHeadless())
1215 System.err.println("Warning: " + title + "\nWarning: " + warning);
1220 JOptionPane.showInternalMessageDialog(this, warning, title,
1221 JOptionPane.WARNING_MESSAGE);
1233 protected void outputText_actionPerformed(ActionEvent e)
1236 AlignmentExportData exportData = getAlignmentForExport(
1237 e.getActionCommand(), viewport, null);
1238 if (exportData.getSettings().isCancelled())
1242 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1243 cap.setForInput(null);
1246 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1247 .formatSequences(e.getActionCommand(),
1248 exportData.getAlignment(),
1249 exportData.getOmitHidden(),
1250 exportData.getStartEndPostions(),
1251 viewport.getColumnSelection()));
1252 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1253 "label.alignment_output_command",
1254 new Object[] { e.getActionCommand() }), 600, 500);
1255 } catch (OutOfMemoryError oom)
1257 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1263 public static AlignmentExportData getAlignmentForExport(
1264 String exportFormat, AlignViewportI viewport,
1265 AlignExportSettingI exportSettings)
1267 AlignmentI alignmentToExport = null;
1268 AlignExportSettingI settings = exportSettings;
1269 String[] omitHidden = null;
1270 int[] alignmentStartEnd = new int[2];
1272 HiddenSequences hiddenSeqs = viewport.getAlignment()
1273 .getHiddenSequences();
1275 alignmentToExport = viewport.getAlignment();
1276 alignmentStartEnd = new int[] { 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,
1302 omitHidden, alignmentStartEnd, settings);
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);
1343 return new int[] { startPos, endPos };
1346 public static void main(String[] args)
1348 ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1349 hiddenCols.add(new int[] { 0, 4 });
1350 hiddenCols.add(new int[] { 6, 9 });
1351 hiddenCols.add(new int[] { 11, 12 });
1352 hiddenCols.add(new int[] { 33, 33 });
1353 hiddenCols.add(new int[] { 45, 50 });
1355 int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1356 // System.out.println("Export range : " + x[0] + " - " + x[1]);
1366 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1368 new HtmlSvgOutput(null, alignPanel);
1372 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1374 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1375 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1378 public void createImageMap(File file, String image)
1380 alignPanel.makePNGImageMap(file, image);
1390 public void createPNG(File f)
1392 alignPanel.makePNG(f);
1402 public void createEPS(File f)
1404 alignPanel.makeEPS(f);
1407 public void createSVG(File f)
1409 alignPanel.makeSVG(f);
1413 public void pageSetup_actionPerformed(ActionEvent e)
1415 PrinterJob printJob = PrinterJob.getPrinterJob();
1416 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1426 public void printMenuItem_actionPerformed(ActionEvent e)
1428 // Putting in a thread avoids Swing painting problems
1429 PrintThread thread = new PrintThread(alignPanel);
1434 public void exportFeatures_actionPerformed(ActionEvent e)
1436 new AnnotationExporter().exportFeatures(alignPanel);
1440 public void exportAnnotations_actionPerformed(ActionEvent e)
1442 new AnnotationExporter().exportAnnotations(alignPanel);
1446 public void associatedData_actionPerformed(ActionEvent e)
1448 // Pick the tree file
1449 JalviewFileChooser chooser = new JalviewFileChooser(
1450 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1451 chooser.setFileView(new JalviewFileView());
1452 chooser.setDialogTitle(MessageManager
1453 .getString("label.load_jalview_annotations"));
1454 chooser.setToolTipText(MessageManager
1455 .getString("label.load_jalview_annotations"));
1457 int value = chooser.showOpenDialog(null);
1459 if (value == JalviewFileChooser.APPROVE_OPTION)
1461 String choice = chooser.getSelectedFile().getPath();
1462 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1463 loadJalviewDataFile(choice, null, null, null);
1469 * Close the current view or all views in the alignment frame. If the frame
1470 * only contains one view then the alignment will be removed from memory.
1472 * @param closeAllTabs
1475 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1477 if (alignPanels != null && alignPanels.size() < 2)
1479 closeAllTabs = true;
1484 if (alignPanels != null)
1488 if (this.isClosed())
1490 // really close all the windows - otherwise wait till
1491 // setClosed(true) is called
1492 for (int i = 0; i < alignPanels.size(); i++)
1494 AlignmentPanel ap = alignPanels.get(i);
1501 closeView(alignPanel);
1508 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1509 * be called recursively, with the frame now in 'closed' state
1511 this.setClosed(true);
1513 } catch (Exception ex)
1515 ex.printStackTrace();
1520 * Close the specified panel and close up tabs appropriately.
1522 * @param panelToClose
1524 public void closeView(AlignmentPanel panelToClose)
1526 int index = tabbedPane.getSelectedIndex();
1527 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1528 alignPanels.remove(panelToClose);
1529 panelToClose.closePanel();
1530 panelToClose = null;
1532 tabbedPane.removeTabAt(closedindex);
1533 tabbedPane.validate();
1535 if (index > closedindex || index == tabbedPane.getTabCount())
1537 // modify currently selected tab index if necessary.
1541 this.tabSelectionChanged(index);
1547 void updateEditMenuBar()
1550 if (viewport.getHistoryList().size() > 0)
1552 undoMenuItem.setEnabled(true);
1553 CommandI command = viewport.getHistoryList().peek();
1554 undoMenuItem.setText(MessageManager.formatMessage(
1555 "label.undo_command",
1556 new Object[] { command.getDescription() }));
1560 undoMenuItem.setEnabled(false);
1561 undoMenuItem.setText(MessageManager.getString("action.undo"));
1564 if (viewport.getRedoList().size() > 0)
1566 redoMenuItem.setEnabled(true);
1568 CommandI command = viewport.getRedoList().peek();
1569 redoMenuItem.setText(MessageManager.formatMessage(
1570 "label.redo_command",
1571 new Object[] { command.getDescription() }));
1575 redoMenuItem.setEnabled(false);
1576 redoMenuItem.setText(MessageManager.getString("action.redo"));
1580 public void addHistoryItem(CommandI command)
1582 if (command.getSize() > 0)
1584 viewport.addToHistoryList(command);
1585 viewport.clearRedoList();
1586 updateEditMenuBar();
1587 viewport.updateHiddenColumns();
1588 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1589 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1590 // viewport.getColumnSelection()
1591 // .getHiddenColumns().size() > 0);
1597 * @return alignment objects for all views
1599 AlignmentI[] getViewAlignments()
1601 if (alignPanels != null)
1603 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1605 for (AlignmentPanel ap : alignPanels)
1607 als[i++] = ap.av.getAlignment();
1611 if (viewport != null)
1613 return new AlignmentI[] { viewport.getAlignment() };
1625 protected void undoMenuItem_actionPerformed(ActionEvent e)
1627 if (viewport.getHistoryList().isEmpty())
1631 CommandI command = viewport.getHistoryList().pop();
1632 viewport.addToRedoList(command);
1633 command.undoCommand(getViewAlignments());
1635 AlignmentViewport originalSource = getOriginatingSource(command);
1636 updateEditMenuBar();
1638 if (originalSource != null)
1640 if (originalSource != viewport)
1643 .warn("Implementation worry: mismatch of viewport origin for undo");
1645 originalSource.updateHiddenColumns();
1646 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1648 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1649 // viewport.getColumnSelection()
1650 // .getHiddenColumns().size() > 0);
1651 originalSource.firePropertyChange("alignment", null, originalSource
1652 .getAlignment().getSequences());
1663 protected void redoMenuItem_actionPerformed(ActionEvent e)
1665 if (viewport.getRedoList().size() < 1)
1670 CommandI command = viewport.getRedoList().pop();
1671 viewport.addToHistoryList(command);
1672 command.doCommand(getViewAlignments());
1674 AlignmentViewport originalSource = getOriginatingSource(command);
1675 updateEditMenuBar();
1677 if (originalSource != null)
1680 if (originalSource != viewport)
1683 .warn("Implementation worry: mismatch of viewport origin for redo");
1685 originalSource.updateHiddenColumns();
1686 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1688 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1689 // viewport.getColumnSelection()
1690 // .getHiddenColumns().size() > 0);
1691 originalSource.firePropertyChange("alignment", null, originalSource
1692 .getAlignment().getSequences());
1696 AlignmentViewport getOriginatingSource(CommandI command)
1698 AlignmentViewport originalSource = null;
1699 // For sequence removal and addition, we need to fire
1700 // the property change event FROM the viewport where the
1701 // original alignment was altered
1702 AlignmentI al = null;
1703 if (command instanceof EditCommand)
1705 EditCommand editCommand = (EditCommand) command;
1706 al = editCommand.getAlignment();
1707 List<Component> comps = PaintRefresher.components.get(viewport
1708 .getSequenceSetId());
1710 for (Component comp : comps)
1712 if (comp instanceof AlignmentPanel)
1714 if (al == ((AlignmentPanel) comp).av.getAlignment())
1716 originalSource = ((AlignmentPanel) comp).av;
1723 if (originalSource == null)
1725 // The original view is closed, we must validate
1726 // the current view against the closed view first
1729 PaintRefresher.validateSequences(al, viewport.getAlignment());
1732 originalSource = viewport;
1735 return originalSource;
1744 public void moveSelectedSequences(boolean up)
1746 SequenceGroup sg = viewport.getSelectionGroup();
1752 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1753 viewport.getHiddenRepSequences(), up);
1754 alignPanel.paintAlignment(true);
1757 synchronized void slideSequences(boolean right, int size)
1759 List<SequenceI> sg = new ArrayList<SequenceI>();
1760 if (viewport.cursorMode)
1762 sg.add(viewport.getAlignment().getSequenceAt(
1763 alignPanel.getSeqPanel().seqCanvas.cursorY));
1765 else if (viewport.getSelectionGroup() != null
1766 && viewport.getSelectionGroup().getSize() != viewport
1767 .getAlignment().getHeight())
1769 sg = viewport.getSelectionGroup().getSequences(
1770 viewport.getHiddenRepSequences());
1778 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1780 for (SequenceI seq : viewport.getAlignment().getSequences())
1782 if (!sg.contains(seq))
1784 invertGroup.add(seq);
1788 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1790 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1791 for (int i = 0; i < invertGroup.size(); i++)
1793 seqs2[i] = invertGroup.get(i);
1796 SlideSequencesCommand ssc;
1799 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1800 size, viewport.getGapCharacter());
1804 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1805 size, viewport.getGapCharacter());
1808 int groupAdjustment = 0;
1809 if (ssc.getGapsInsertedBegin() && right)
1811 if (viewport.cursorMode)
1813 alignPanel.getSeqPanel().moveCursor(size, 0);
1817 groupAdjustment = size;
1820 else if (!ssc.getGapsInsertedBegin() && !right)
1822 if (viewport.cursorMode)
1824 alignPanel.getSeqPanel().moveCursor(-size, 0);
1828 groupAdjustment = -size;
1832 if (groupAdjustment != 0)
1834 viewport.getSelectionGroup().setStartRes(
1835 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1836 viewport.getSelectionGroup().setEndRes(
1837 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1841 * just extend the last slide command if compatible; but not if in
1842 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1844 boolean appendHistoryItem = false;
1845 Deque<CommandI> historyList = viewport.getHistoryList();
1846 boolean inSplitFrame = getSplitViewContainer() != null;
1847 if (!inSplitFrame && historyList != null && historyList.size() > 0
1848 && historyList.peek() instanceof SlideSequencesCommand)
1850 appendHistoryItem = ssc
1851 .appendSlideCommand((SlideSequencesCommand) historyList
1855 if (!appendHistoryItem)
1857 addHistoryItem(ssc);
1870 protected void copy_actionPerformed(ActionEvent e)
1873 if (viewport.getSelectionGroup() == null)
1877 // TODO: preserve the ordering of displayed alignment annotation in any
1878 // internal paste (particularly sequence associated annotation)
1879 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1880 String[] omitHidden = null;
1882 if (viewport.hasHiddenColumns())
1884 omitHidden = viewport.getViewAsString(true);
1887 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1890 StringSelection ss = new StringSelection(output);
1894 jalview.gui.Desktop.internalCopy = true;
1895 // Its really worth setting the clipboard contents
1896 // to empty before setting the large StringSelection!!
1897 Toolkit.getDefaultToolkit().getSystemClipboard()
1898 .setContents(new StringSelection(""), null);
1900 Toolkit.getDefaultToolkit().getSystemClipboard()
1901 .setContents(ss, Desktop.instance);
1902 } catch (OutOfMemoryError er)
1904 new OOMWarning("copying region", er);
1908 ArrayList<int[]> hiddenColumns = null;
1909 if (viewport.hasHiddenColumns())
1911 hiddenColumns = new ArrayList<int[]>();
1912 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1913 .getSelectionGroup().getEndRes();
1914 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1916 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1918 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1919 region[1] - hiddenOffset });
1924 Desktop.jalviewClipboard = new Object[] { seqs,
1925 viewport.getAlignment().getDataset(), hiddenColumns };
1926 statusBar.setText(MessageManager.formatMessage(
1927 "label.copied_sequences_to_clipboard", new Object[] { Integer
1928 .valueOf(seqs.length).toString() }));
1938 protected void pasteNew_actionPerformed(ActionEvent e)
1950 protected void pasteThis_actionPerformed(ActionEvent e)
1956 * Paste contents of Jalview clipboard
1958 * @param newAlignment
1959 * true to paste to a new alignment, otherwise add to this.
1961 void paste(boolean newAlignment)
1963 boolean externalPaste = true;
1966 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1967 Transferable contents = c.getContents(this);
1969 if (contents == null)
1977 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1978 if (str.length() < 1)
1983 format = new IdentifyFile().Identify(str, "Paste");
1985 } catch (OutOfMemoryError er)
1987 new OOMWarning("Out of memory pasting sequences!!", er);
1991 SequenceI[] sequences;
1992 boolean annotationAdded = false;
1993 AlignmentI alignment = null;
1995 if (Desktop.jalviewClipboard != null)
1997 // The clipboard was filled from within Jalview, we must use the
1999 // And dataset from the copied alignment
2000 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2001 // be doubly sure that we create *new* sequence objects.
2002 sequences = new SequenceI[newseq.length];
2003 for (int i = 0; i < newseq.length; i++)
2005 sequences[i] = new Sequence(newseq[i]);
2007 alignment = new Alignment(sequences);
2008 externalPaste = false;
2012 // parse the clipboard as an alignment.
2013 alignment = new FormatAdapter().readFile(str, "Paste", format);
2014 sequences = alignment.getSequencesArray();
2018 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2024 if (Desktop.jalviewClipboard != null)
2026 // dataset is inherited
2027 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2031 // new dataset is constructed
2032 alignment.setDataset(null);
2034 alwidth = alignment.getWidth() + 1;
2038 AlignmentI pastedal = alignment; // preserve pasted alignment object
2039 // Add pasted sequences and dataset into existing alignment.
2040 alignment = viewport.getAlignment();
2041 alwidth = alignment.getWidth() + 1;
2042 // decide if we need to import sequences from an existing dataset
2043 boolean importDs = Desktop.jalviewClipboard != null
2044 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2045 // importDs==true instructs us to copy over new dataset sequences from
2046 // an existing alignment
2047 Vector newDs = (importDs) ? new Vector() : null; // used to create
2048 // minimum dataset set
2050 for (int i = 0; i < sequences.length; i++)
2054 newDs.addElement(null);
2056 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2058 if (importDs && ds != null)
2060 if (!newDs.contains(ds))
2062 newDs.setElementAt(ds, i);
2063 ds = new Sequence(ds);
2064 // update with new dataset sequence
2065 sequences[i].setDatasetSequence(ds);
2069 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2074 // copy and derive new dataset sequence
2075 sequences[i] = sequences[i].deriveSequence();
2076 alignment.getDataset().addSequence(
2077 sequences[i].getDatasetSequence());
2078 // TODO: avoid creation of duplicate dataset sequences with a
2079 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2081 alignment.addSequence(sequences[i]); // merges dataset
2085 newDs.clear(); // tidy up
2087 if (alignment.getAlignmentAnnotation() != null)
2089 for (AlignmentAnnotation alan : alignment
2090 .getAlignmentAnnotation())
2092 if (alan.graphGroup > fgroup)
2094 fgroup = alan.graphGroup;
2098 if (pastedal.getAlignmentAnnotation() != null)
2100 // Add any annotation attached to alignment.
2101 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2102 for (int i = 0; i < alann.length; i++)
2104 annotationAdded = true;
2105 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2107 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2108 if (newann.graphGroup > -1)
2110 if (newGraphGroups.size() <= newann.graphGroup
2111 || newGraphGroups.get(newann.graphGroup) == null)
2113 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2115 newGraphGroups.add(q, null);
2117 newGraphGroups.set(newann.graphGroup, new Integer(
2120 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2124 newann.padAnnotation(alwidth);
2125 alignment.addAnnotation(newann);
2135 addHistoryItem(new EditCommand(
2136 MessageManager.getString("label.add_sequences"),
2137 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2139 // Add any annotations attached to sequences
2140 for (int i = 0; i < sequences.length; i++)
2142 if (sequences[i].getAnnotation() != null)
2144 AlignmentAnnotation newann;
2145 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2147 annotationAdded = true;
2148 newann = sequences[i].getAnnotation()[a];
2149 newann.adjustForAlignment();
2150 newann.padAnnotation(alwidth);
2151 if (newann.graphGroup > -1)
2153 if (newann.graphGroup > -1)
2155 if (newGraphGroups.size() <= newann.graphGroup
2156 || newGraphGroups.get(newann.graphGroup) == null)
2158 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2160 newGraphGroups.add(q, null);
2162 newGraphGroups.set(newann.graphGroup, new Integer(
2165 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2169 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2174 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2181 // propagate alignment changed.
2182 viewport.setEndSeq(alignment.getHeight());
2183 if (annotationAdded)
2185 // Duplicate sequence annotation in all views.
2186 AlignmentI[] alview = this.getViewAlignments();
2187 for (int i = 0; i < sequences.length; i++)
2189 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2194 for (int avnum = 0; avnum < alview.length; avnum++)
2196 if (alview[avnum] != alignment)
2198 // duplicate in a view other than the one with input focus
2199 int avwidth = alview[avnum].getWidth() + 1;
2200 // this relies on sann being preserved after we
2201 // modify the sequence's annotation array for each duplication
2202 for (int a = 0; a < sann.length; a++)
2204 AlignmentAnnotation newann = new AlignmentAnnotation(
2206 sequences[i].addAlignmentAnnotation(newann);
2207 newann.padAnnotation(avwidth);
2208 alview[avnum].addAnnotation(newann); // annotation was
2209 // duplicated earlier
2210 // TODO JAL-1145 graphGroups are not updated for sequence
2211 // annotation added to several views. This may cause
2213 alview[avnum].setAnnotationIndex(newann, a);
2218 buildSortByAnnotationScoresMenu();
2220 viewport.firePropertyChange("alignment", null,
2221 alignment.getSequences());
2222 if (alignPanels != null)
2224 for (AlignmentPanel ap : alignPanels)
2226 ap.validateAnnotationDimensions(false);
2231 alignPanel.validateAnnotationDimensions(false);
2237 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2239 String newtitle = new String("Copied sequences");
2241 if (Desktop.jalviewClipboard != null
2242 && Desktop.jalviewClipboard[2] != null)
2244 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2245 for (int[] region : hc)
2247 af.viewport.hideColumns(region[0], region[1]);
2251 // >>>This is a fix for the moment, until a better solution is
2253 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2255 alignPanel.getSeqPanel().seqCanvas
2256 .getFeatureRenderer());
2258 // TODO: maintain provenance of an alignment, rather than just make the
2259 // title a concatenation of operations.
2262 if (title.startsWith("Copied sequences"))
2268 newtitle = newtitle.concat("- from " + title);
2273 newtitle = new String("Pasted sequences");
2276 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2281 } catch (Exception ex)
2283 ex.printStackTrace();
2284 System.out.println("Exception whilst pasting: " + ex);
2285 // could be anything being pasted in here
2291 protected void expand_newalign(ActionEvent e)
2295 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2296 .getAlignment(), -1);
2297 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2299 String newtitle = new String("Flanking alignment");
2301 if (Desktop.jalviewClipboard != null
2302 && Desktop.jalviewClipboard[2] != null)
2304 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2305 for (int region[] : hc)
2307 af.viewport.hideColumns(region[0], region[1]);
2311 // >>>This is a fix for the moment, until a better solution is
2313 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2315 alignPanel.getSeqPanel().seqCanvas
2316 .getFeatureRenderer());
2318 // TODO: maintain provenance of an alignment, rather than just make the
2319 // title a concatenation of operations.
2321 if (title.startsWith("Copied sequences"))
2327 newtitle = newtitle.concat("- from " + title);
2331 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2333 } catch (Exception ex)
2335 ex.printStackTrace();
2336 System.out.println("Exception whilst pasting: " + ex);
2337 // could be anything being pasted in here
2338 } catch (OutOfMemoryError oom)
2340 new OOMWarning("Viewing flanking region of alignment", oom);
2351 protected void cut_actionPerformed(ActionEvent e)
2353 copy_actionPerformed(null);
2354 delete_actionPerformed(null);
2364 protected void delete_actionPerformed(ActionEvent evt)
2367 SequenceGroup sg = viewport.getSelectionGroup();
2374 * If the cut affects all sequences, warn, remove highlighted columns
2376 if (sg.getSize() == viewport.getAlignment().getHeight())
2378 int confirm = JOptionPane.showConfirmDialog(this,
2379 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2380 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2381 JOptionPane.OK_CANCEL_OPTION);
2383 if (confirm == JOptionPane.CANCEL_OPTION
2384 || confirm == JOptionPane.CLOSED_OPTION)
2388 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2389 sg.getEndRes() + 1);
2392 SequenceI[] cut = sg.getSequences()
2393 .toArray(new SequenceI[sg.getSize()]);
2395 addHistoryItem(new EditCommand(
2396 MessageManager.getString("label.cut_sequences"), Action.CUT,
2397 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2398 viewport.getAlignment()));
2400 viewport.setSelectionGroup(null);
2401 viewport.sendSelection();
2402 viewport.getAlignment().deleteGroup(sg);
2404 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2406 if (viewport.getAlignment().getHeight() < 1)
2410 this.setClosed(true);
2411 } catch (Exception ex)
2424 protected void deleteGroups_actionPerformed(ActionEvent e)
2426 if (avc.deleteGroups())
2428 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2429 alignPanel.updateAnnotation();
2430 alignPanel.paintAlignment(true);
2441 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2443 SequenceGroup sg = new SequenceGroup();
2445 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2447 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2450 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2451 viewport.setSelectionGroup(sg);
2452 viewport.sendSelection();
2453 alignPanel.paintAlignment(true);
2454 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2464 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2466 if (viewport.cursorMode)
2468 alignPanel.getSeqPanel().keyboardNo1 = null;
2469 alignPanel.getSeqPanel().keyboardNo2 = null;
2471 viewport.setSelectionGroup(null);
2472 viewport.getColumnSelection().clear();
2473 viewport.setSelectionGroup(null);
2474 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2475 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2476 alignPanel.paintAlignment(true);
2477 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2478 viewport.sendSelection();
2488 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2490 SequenceGroup sg = viewport.getSelectionGroup();
2494 selectAllSequenceMenuItem_actionPerformed(null);
2499 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2501 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2504 alignPanel.paintAlignment(true);
2505 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2506 viewport.sendSelection();
2510 public void invertColSel_actionPerformed(ActionEvent e)
2512 viewport.invertColumnSelection();
2513 alignPanel.paintAlignment(true);
2514 viewport.sendSelection();
2524 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2526 trimAlignment(true);
2536 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2538 trimAlignment(false);
2541 void trimAlignment(boolean trimLeft)
2543 ColumnSelection colSel = viewport.getColumnSelection();
2546 if (colSel.size() > 0)
2550 column = colSel.getMin();
2554 column = colSel.getMax();
2558 if (viewport.getSelectionGroup() != null)
2560 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2561 viewport.getHiddenRepSequences());
2565 seqs = viewport.getAlignment().getSequencesArray();
2568 TrimRegionCommand trimRegion;
2571 trimRegion = new TrimRegionCommand("Remove Left",
2572 TrimRegionCommand.TRIM_LEFT, seqs, column,
2573 viewport.getAlignment(), viewport.getColumnSelection(),
2574 viewport.getSelectionGroup());
2575 viewport.setStartRes(0);
2579 trimRegion = new TrimRegionCommand("Remove Right",
2580 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2581 viewport.getAlignment(), viewport.getColumnSelection(),
2582 viewport.getSelectionGroup());
2585 statusBar.setText(MessageManager.formatMessage(
2586 "label.removed_columns",
2587 new String[] { Integer.valueOf(trimRegion.getSize())
2590 addHistoryItem(trimRegion);
2592 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2594 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2595 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2597 viewport.getAlignment().deleteGroup(sg);
2601 viewport.firePropertyChange("alignment", null, viewport
2602 .getAlignment().getSequences());
2613 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2615 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2618 if (viewport.getSelectionGroup() != null)
2620 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2621 viewport.getHiddenRepSequences());
2622 start = viewport.getSelectionGroup().getStartRes();
2623 end = viewport.getSelectionGroup().getEndRes();
2627 seqs = viewport.getAlignment().getSequencesArray();
2630 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2631 "Remove Gapped Columns", seqs, start, end,
2632 viewport.getAlignment());
2634 addHistoryItem(removeGapCols);
2636 statusBar.setText(MessageManager.formatMessage(
2637 "label.removed_empty_columns",
2638 new Object[] { Integer.valueOf(removeGapCols.getSize())
2641 // This is to maintain viewport position on first residue
2642 // of first sequence
2643 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2644 int startRes = seq.findPosition(viewport.startRes);
2645 // ShiftList shifts;
2646 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2647 // edit.alColumnChanges=shifts.getInverse();
2648 // if (viewport.hasHiddenColumns)
2649 // viewport.getColumnSelection().compensateForEdits(shifts);
2650 viewport.setStartRes(seq.findIndex(startRes) - 1);
2651 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2663 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2665 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2668 if (viewport.getSelectionGroup() != null)
2670 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2671 viewport.getHiddenRepSequences());
2672 start = viewport.getSelectionGroup().getStartRes();
2673 end = viewport.getSelectionGroup().getEndRes();
2677 seqs = viewport.getAlignment().getSequencesArray();
2680 // This is to maintain viewport position on first residue
2681 // of first sequence
2682 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2683 int startRes = seq.findPosition(viewport.startRes);
2685 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2686 viewport.getAlignment()));
2688 viewport.setStartRes(seq.findIndex(startRes) - 1);
2690 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2702 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2704 viewport.setPadGaps(padGapsMenuitem.isSelected());
2705 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2716 public void findMenuItem_actionPerformed(ActionEvent e)
2722 * Create a new view of the current alignment.
2725 public void newView_actionPerformed(ActionEvent e)
2727 newView(null, true);
2731 * Creates and shows a new view of the current alignment.
2734 * title of newly created view; if null, one will be generated
2735 * @param copyAnnotation
2736 * if true then duplicate all annnotation, groups and settings
2737 * @return new alignment panel, already displayed.
2739 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2742 * Create a new AlignmentPanel (with its own, new Viewport)
2744 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2746 if (!copyAnnotation)
2749 * remove all groups and annotation except for the automatic stuff
2751 newap.av.getAlignment().deleteAllGroups();
2752 newap.av.getAlignment().deleteAllAnnotations(false);
2755 newap.av.setGatherViewsHere(false);
2757 if (viewport.viewName == null)
2759 viewport.viewName = MessageManager
2760 .getString("label.view_name_original");
2764 * Views share the same edits undo and redo stacks
2766 newap.av.setHistoryList(viewport.getHistoryList());
2767 newap.av.setRedoList(viewport.getRedoList());
2770 * Views share the same mappings; need to deregister any new mappings
2771 * created by copyAlignPanel, and register the new reference to the shared
2774 newap.av.replaceMappings(viewport.getAlignment());
2776 newap.av.viewName = getNewViewName(viewTitle);
2778 addAlignmentPanel(newap, true);
2779 newap.alignmentChanged();
2781 if (alignPanels.size() == 2)
2783 viewport.setGatherViewsHere(true);
2785 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2790 * Make a new name for the view, ensuring it is unique within the current
2791 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2792 * these now use viewId. Unique view names are still desirable for usability.)
2797 protected String getNewViewName(String viewTitle)
2799 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2800 boolean addFirstIndex = false;
2801 if (viewTitle == null || viewTitle.trim().length() == 0)
2803 viewTitle = MessageManager.getString("action.view");
2804 addFirstIndex = true;
2808 index = 1;// we count from 1 if given a specific name
2810 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2812 List<Component> comps = PaintRefresher.components.get(viewport
2813 .getSequenceSetId());
2815 List<String> existingNames = getExistingViewNames(comps);
2817 while (existingNames.contains(newViewName))
2819 newViewName = viewTitle + " " + (++index);
2825 * Returns a list of distinct view names found in the given list of
2826 * components. View names are held on the viewport of an AlignmentPanel.
2831 protected List<String> getExistingViewNames(List<Component> comps)
2833 List<String> existingNames = new ArrayList<String>();
2834 for (Component comp : comps)
2836 if (comp instanceof AlignmentPanel)
2838 AlignmentPanel ap = (AlignmentPanel) comp;
2839 if (!existingNames.contains(ap.av.viewName))
2841 existingNames.add(ap.av.viewName);
2845 return existingNames;
2849 * Explode tabbed views into separate windows.
2852 public void expandViews_actionPerformed(ActionEvent e)
2854 Desktop.instance.explodeViews(this);
2858 * Gather views in separate windows back into a tabbed presentation.
2861 public void gatherViews_actionPerformed(ActionEvent e)
2863 Desktop.instance.gatherViews(this);
2873 public void font_actionPerformed(ActionEvent e)
2875 new FontChooser(alignPanel);
2885 protected void seqLimit_actionPerformed(ActionEvent e)
2887 viewport.setShowJVSuffix(seqLimits.isSelected());
2889 alignPanel.getIdPanel().getIdCanvas()
2890 .setPreferredSize(alignPanel.calculateIdWidth());
2891 alignPanel.paintAlignment(true);
2895 public void idRightAlign_actionPerformed(ActionEvent e)
2897 viewport.setRightAlignIds(idRightAlign.isSelected());
2898 alignPanel.paintAlignment(true);
2902 public void centreColumnLabels_actionPerformed(ActionEvent e)
2904 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2905 alignPanel.paintAlignment(true);
2911 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2914 protected void followHighlight_actionPerformed()
2917 * Set the 'follow' flag on the Viewport (and scroll to position if now
2920 final boolean state = this.followHighlightMenuItem.getState();
2921 viewport.setFollowHighlight(state);
2924 alignPanel.scrollToPosition(
2925 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2936 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2938 viewport.setColourText(colourTextMenuItem.isSelected());
2939 alignPanel.paintAlignment(true);
2949 public void wrapMenuItem_actionPerformed(ActionEvent e)
2951 scaleAbove.setVisible(wrapMenuItem.isSelected());
2952 scaleLeft.setVisible(wrapMenuItem.isSelected());
2953 scaleRight.setVisible(wrapMenuItem.isSelected());
2954 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2955 alignPanel.updateLayout();
2959 public void showAllSeqs_actionPerformed(ActionEvent e)
2961 viewport.showAllHiddenSeqs();
2965 public void showAllColumns_actionPerformed(ActionEvent e)
2967 viewport.showAllHiddenColumns();
2972 public void hideSelSequences_actionPerformed(ActionEvent e)
2974 viewport.hideAllSelectedSeqs();
2975 // alignPanel.paintAlignment(true);
2979 * called by key handler and the hide all/show all menu items
2984 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2987 boolean hide = false;
2988 SequenceGroup sg = viewport.getSelectionGroup();
2989 if (!toggleSeqs && !toggleCols)
2991 // Hide everything by the current selection - this is a hack - we do the
2992 // invert and then hide
2993 // first check that there will be visible columns after the invert.
2994 if ((viewport.getColumnSelection() != null
2995 && viewport.getColumnSelection().getSelected() != null && viewport
2996 .getColumnSelection().getSelected().size() > 0)
2997 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3000 // now invert the sequence set, if required - empty selection implies
3001 // that no hiding is required.
3004 invertSequenceMenuItem_actionPerformed(null);
3005 sg = viewport.getSelectionGroup();
3009 viewport.expandColSelection(sg, true);
3010 // finally invert the column selection and get the new sequence
3012 invertColSel_actionPerformed(null);
3019 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3021 hideSelSequences_actionPerformed(null);
3024 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3027 showAllSeqs_actionPerformed(null);
3033 if (viewport.getColumnSelection().getSelected().size() > 0)
3035 hideSelColumns_actionPerformed(null);
3038 viewport.setSelectionGroup(sg);
3043 showAllColumns_actionPerformed(null);
3052 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3053 * event.ActionEvent)
3056 public void hideAllButSelection_actionPerformed(ActionEvent e)
3058 toggleHiddenRegions(false, false);
3065 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3069 public void hideAllSelection_actionPerformed(ActionEvent e)
3071 SequenceGroup sg = viewport.getSelectionGroup();
3072 viewport.expandColSelection(sg, false);
3073 viewport.hideAllSelectedSeqs();
3074 viewport.hideSelectedColumns();
3075 alignPanel.paintAlignment(true);
3082 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3086 public void showAllhidden_actionPerformed(ActionEvent e)
3088 viewport.showAllHiddenColumns();
3089 viewport.showAllHiddenSeqs();
3090 alignPanel.paintAlignment(true);
3094 public void hideSelColumns_actionPerformed(ActionEvent e)
3096 viewport.hideSelectedColumns();
3097 alignPanel.paintAlignment(true);
3101 public void hiddenMarkers_actionPerformed(ActionEvent e)
3103 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3114 protected void scaleAbove_actionPerformed(ActionEvent e)
3116 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3117 alignPanel.paintAlignment(true);
3127 protected void scaleLeft_actionPerformed(ActionEvent e)
3129 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3130 alignPanel.paintAlignment(true);
3140 protected void scaleRight_actionPerformed(ActionEvent e)
3142 viewport.setScaleRightWrapped(scaleRight.isSelected());
3143 alignPanel.paintAlignment(true);
3153 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3155 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3156 alignPanel.paintAlignment(true);
3166 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3168 viewport.setShowText(viewTextMenuItem.isSelected());
3169 alignPanel.paintAlignment(true);
3179 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3181 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3182 alignPanel.paintAlignment(true);
3185 public FeatureSettings featureSettings;
3188 public FeatureSettingsControllerI getFeatureSettingsUI()
3190 return featureSettings;
3194 public void featureSettings_actionPerformed(ActionEvent e)
3196 if (featureSettings != null)
3198 featureSettings.close();
3199 featureSettings = null;
3201 if (!showSeqFeatures.isSelected())
3203 // make sure features are actually displayed
3204 showSeqFeatures.setSelected(true);
3205 showSeqFeatures_actionPerformed(null);
3207 featureSettings = new FeatureSettings(this);
3211 * Set or clear 'Show Sequence Features'
3217 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3219 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3220 alignPanel.paintAlignment(true);
3221 if (alignPanel.getOverviewPanel() != null)
3223 alignPanel.getOverviewPanel().updateOverviewImage();
3228 * Set or clear 'Show Sequence Features'
3234 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3236 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3238 if (viewport.isShowSequenceFeaturesHeight())
3240 // ensure we're actually displaying features
3241 viewport.setShowSequenceFeatures(true);
3242 showSeqFeatures.setSelected(true);
3244 alignPanel.paintAlignment(true);
3245 if (alignPanel.getOverviewPanel() != null)
3247 alignPanel.getOverviewPanel().updateOverviewImage();
3252 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3253 * the annotations panel as a whole.
3255 * The options to show/hide all annotations should be enabled when the panel
3256 * is shown, and disabled when the panel is hidden.
3261 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3263 final boolean setVisible = annotationPanelMenuItem.isSelected();
3264 viewport.setShowAnnotation(setVisible);
3265 this.showAllSeqAnnotations.setEnabled(setVisible);
3266 this.hideAllSeqAnnotations.setEnabled(setVisible);
3267 this.showAllAlAnnotations.setEnabled(setVisible);
3268 this.hideAllAlAnnotations.setEnabled(setVisible);
3269 alignPanel.updateLayout();
3273 public void alignmentProperties()
3275 JEditorPane editPane = new JEditorPane("text/html", "");
3276 editPane.setEditable(false);
3277 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3279 editPane.setText(MessageManager.formatMessage("label.html_content",
3280 new Object[] { contents.toString() }));
3281 JInternalFrame frame = new JInternalFrame();
3282 frame.getContentPane().add(new JScrollPane(editPane));
3284 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3285 "label.alignment_properties", new Object[] { getTitle() }),
3296 public void overviewMenuItem_actionPerformed(ActionEvent e)
3298 if (alignPanel.overviewPanel != null)
3303 JInternalFrame frame = new JInternalFrame();
3304 OverviewPanel overview = new OverviewPanel(alignPanel);
3305 frame.setContentPane(overview);
3306 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3307 "label.overview_params", new Object[] { this.getTitle() }),
3308 frame.getWidth(), frame.getHeight());
3310 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3311 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3314 public void internalFrameClosed(
3315 javax.swing.event.InternalFrameEvent evt)
3317 alignPanel.setOverviewPanel(null);
3321 alignPanel.setOverviewPanel(overview);
3325 public void textColour_actionPerformed(ActionEvent e)
3327 new TextColourChooser().chooseColour(alignPanel, null);
3337 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3349 public void clustalColour_actionPerformed(ActionEvent e)
3351 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3352 viewport.getHiddenRepSequences()));
3362 public void zappoColour_actionPerformed(ActionEvent e)
3364 changeColour(new ZappoColourScheme());
3374 public void taylorColour_actionPerformed(ActionEvent e)
3376 changeColour(new TaylorColourScheme());
3386 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3388 changeColour(new HydrophobicColourScheme());
3398 public void helixColour_actionPerformed(ActionEvent e)
3400 changeColour(new HelixColourScheme());
3410 public void strandColour_actionPerformed(ActionEvent e)
3412 changeColour(new StrandColourScheme());
3422 public void turnColour_actionPerformed(ActionEvent e)
3424 changeColour(new TurnColourScheme());
3434 public void buriedColour_actionPerformed(ActionEvent e)
3436 changeColour(new BuriedColourScheme());
3446 public void nucleotideColour_actionPerformed(ActionEvent e)
3448 changeColour(new NucleotideColourScheme());
3452 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3454 changeColour(new PurinePyrimidineColourScheme());
3458 * public void covariationColour_actionPerformed(ActionEvent e) {
3460 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3464 public void annotationColour_actionPerformed(ActionEvent e)
3466 new AnnotationColourChooser(viewport, alignPanel);
3470 public void annotationColumn_actionPerformed(ActionEvent e)
3472 new AnnotationColumnChooser(viewport, alignPanel);
3476 public void rnahelicesColour_actionPerformed(ActionEvent e)
3478 new RNAHelicesColourChooser(viewport, alignPanel);
3488 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3490 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3499 public void changeColour(ColourSchemeI cs)
3501 // TODO: pull up to controller method
3505 // Make sure viewport is up to date w.r.t. any sliders
3506 if (viewport.getAbovePIDThreshold())
3508 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3510 viewport.setThreshold(threshold);
3513 if (viewport.getConservationSelected())
3515 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3520 viewport.setGlobalColourScheme(cs);
3522 alignPanel.paintAlignment(true);
3532 protected void modifyPID_actionPerformed(ActionEvent e)
3534 if (viewport.getAbovePIDThreshold()
3535 && viewport.getGlobalColourScheme() != null)
3537 SliderPanel.setPIDSliderSource(alignPanel,
3538 viewport.getGlobalColourScheme(), "Background");
3539 SliderPanel.showPIDSlider();
3550 protected void modifyConservation_actionPerformed(ActionEvent e)
3552 if (viewport.getConservationSelected()
3553 && viewport.getGlobalColourScheme() != null)
3555 SliderPanel.setConservationSlider(alignPanel,
3556 viewport.getGlobalColourScheme(), "Background");
3557 SliderPanel.showConservationSlider();
3568 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3570 viewport.setConservationSelected(conservationMenuItem.isSelected());
3572 viewport.setAbovePIDThreshold(false);
3573 abovePIDThreshold.setSelected(false);
3575 changeColour(viewport.getGlobalColourScheme());
3577 modifyConservation_actionPerformed(null);
3587 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3589 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3591 conservationMenuItem.setSelected(false);
3592 viewport.setConservationSelected(false);
3594 changeColour(viewport.getGlobalColourScheme());
3596 modifyPID_actionPerformed(null);
3606 public void userDefinedColour_actionPerformed(ActionEvent e)
3608 if (e.getActionCommand().equals(
3609 MessageManager.getString("action.user_defined")))
3611 new UserDefinedColours(alignPanel, null);
3615 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3616 .getUserColourSchemes().get(e.getActionCommand());
3622 public void updateUserColourMenu()
3625 Component[] menuItems = colourMenu.getMenuComponents();
3626 int iSize = menuItems.length;
3627 for (int i = 0; i < iSize; i++)
3629 if (menuItems[i].getName() != null
3630 && menuItems[i].getName().equals("USER_DEFINED"))
3632 colourMenu.remove(menuItems[i]);
3636 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3638 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3639 .getUserColourSchemes().keys();
3641 while (userColours.hasMoreElements())
3643 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3644 userColours.nextElement().toString());
3645 radioItem.setName("USER_DEFINED");
3646 radioItem.addMouseListener(new MouseAdapter()
3649 public void mousePressed(MouseEvent evt)
3651 if (evt.isControlDown()
3652 || SwingUtilities.isRightMouseButton(evt))
3654 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3656 int option = JOptionPane.showInternalConfirmDialog(
3657 jalview.gui.Desktop.desktop,
3659 .getString("label.remove_from_default_list"),
3661 .getString("label.remove_user_defined_colour"),
3662 JOptionPane.YES_NO_OPTION);
3663 if (option == JOptionPane.YES_OPTION)
3665 jalview.gui.UserDefinedColours
3666 .removeColourFromDefaults(radioItem.getText());
3667 colourMenu.remove(radioItem);
3671 radioItem.addActionListener(new ActionListener()
3674 public void actionPerformed(ActionEvent evt)
3676 userDefinedColour_actionPerformed(evt);
3683 radioItem.addActionListener(new ActionListener()
3686 public void actionPerformed(ActionEvent evt)
3688 userDefinedColour_actionPerformed(evt);
3692 colourMenu.insert(radioItem, 15);
3693 colours.add(radioItem);
3705 public void PIDColour_actionPerformed(ActionEvent e)
3707 changeColour(new PIDColourScheme());
3717 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3719 changeColour(new Blosum62ColourScheme());
3729 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3731 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3732 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3733 .getAlignment().getSequenceAt(0), null);
3734 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3735 viewport.getAlignment()));
3736 alignPanel.paintAlignment(true);
3746 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3748 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3749 AlignmentSorter.sortByID(viewport.getAlignment());
3750 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3751 viewport.getAlignment()));
3752 alignPanel.paintAlignment(true);
3762 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3764 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3765 AlignmentSorter.sortByLength(viewport.getAlignment());
3766 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3767 viewport.getAlignment()));
3768 alignPanel.paintAlignment(true);
3778 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3780 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3781 AlignmentSorter.sortByGroup(viewport.getAlignment());
3782 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3783 viewport.getAlignment()));
3785 alignPanel.paintAlignment(true);
3795 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3797 new RedundancyPanel(alignPanel, this);
3807 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3809 if ((viewport.getSelectionGroup() == null)
3810 || (viewport.getSelectionGroup().getSize() < 2))
3812 JOptionPane.showInternalMessageDialog(this, MessageManager
3813 .getString("label.you_must_select_least_two_sequences"),
3814 MessageManager.getString("label.invalid_selection"),
3815 JOptionPane.WARNING_MESSAGE);
3819 JInternalFrame frame = new JInternalFrame();
3820 frame.setContentPane(new PairwiseAlignPanel(viewport));
3821 Desktop.addInternalFrame(frame,
3822 MessageManager.getString("action.pairwise_alignment"), 600,
3834 public void PCAMenuItem_actionPerformed(ActionEvent e)
3836 if (((viewport.getSelectionGroup() != null)
3837 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3838 .getSelectionGroup().getSize() > 0))
3839 || (viewport.getAlignment().getHeight() < 4))
3842 .showInternalMessageDialog(
3845 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3847 .getString("label.sequence_selection_insufficient"),
3848 JOptionPane.WARNING_MESSAGE);
3853 new PCAPanel(alignPanel);
3857 public void autoCalculate_actionPerformed(ActionEvent e)
3859 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3860 if (viewport.autoCalculateConsensus)
3862 viewport.firePropertyChange("alignment", null, viewport
3863 .getAlignment().getSequences());
3868 public void sortByTreeOption_actionPerformed(ActionEvent e)
3870 viewport.sortByTree = sortByTree.isSelected();
3874 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3876 viewport.followSelection = listenToViewSelections.isSelected();
3886 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3888 newTreePanel("AV", "PID", "Average distance tree using PID");
3898 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3900 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3910 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3912 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3922 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3924 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3937 void newTreePanel(String type, String pwType, String title)
3941 if (viewport.getSelectionGroup() != null
3942 && viewport.getSelectionGroup().getSize() > 0)
3944 if (viewport.getSelectionGroup().getSize() < 3)
3950 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3952 .getString("label.not_enough_sequences"),
3953 JOptionPane.WARNING_MESSAGE);
3957 SequenceGroup sg = viewport.getSelectionGroup();
3959 /* Decide if the selection is a column region */
3960 for (SequenceI _s : sg.getSequences())
3962 if (_s.getLength() < sg.getEndRes())
3968 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3970 .getString("label.sequences_selection_not_aligned"),
3971 JOptionPane.WARNING_MESSAGE);
3977 title = title + " on region";
3978 tp = new TreePanel(alignPanel, type, pwType);
3982 // are the visible sequences aligned?
3983 if (!viewport.getAlignment().isAligned(false))
3989 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3991 .getString("label.sequences_not_aligned"),
3992 JOptionPane.WARNING_MESSAGE);
3997 if (viewport.getAlignment().getHeight() < 2)
4002 tp = new TreePanel(alignPanel, type, pwType);
4007 if (viewport.viewName != null)
4009 title += viewport.viewName + " of ";
4012 title += this.title;
4014 Desktop.addInternalFrame(tp, title, 600, 500);
4025 public void addSortByOrderMenuItem(String title,
4026 final AlignmentOrder order)
4028 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4029 "action.by_title_param", new Object[] { title }));
4031 item.addActionListener(new java.awt.event.ActionListener()
4034 public void actionPerformed(ActionEvent e)
4036 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4038 // TODO: JBPNote - have to map order entries to curent SequenceI
4040 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4042 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4045 alignPanel.paintAlignment(true);
4051 * Add a new sort by annotation score menu item
4054 * the menu to add the option to
4056 * the label used to retrieve scores for each sequence on the
4059 public void addSortByAnnotScoreMenuItem(JMenu sort,
4060 final String scoreLabel)
4062 final JMenuItem item = new JMenuItem(scoreLabel);
4064 item.addActionListener(new java.awt.event.ActionListener()
4067 public void actionPerformed(ActionEvent e)
4069 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4070 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4071 viewport.getAlignment());// ,viewport.getSelectionGroup());
4072 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4073 viewport.getAlignment()));
4074 alignPanel.paintAlignment(true);
4080 * last hash for alignment's annotation array - used to minimise cost of
4083 protected int _annotationScoreVectorHash;
4086 * search the alignment and rebuild the sort by annotation score submenu the
4087 * last alignment annotation vector hash is stored to minimize cost of
4088 * rebuilding in subsequence calls.
4092 public void buildSortByAnnotationScoresMenu()
4094 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4099 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4101 sortByAnnotScore.removeAll();
4102 // almost certainly a quicker way to do this - but we keep it simple
4103 Hashtable scoreSorts = new Hashtable();
4104 AlignmentAnnotation aann[];
4105 for (SequenceI sqa : viewport.getAlignment().getSequences())
4107 aann = sqa.getAnnotation();
4108 for (int i = 0; aann != null && i < aann.length; i++)
4110 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4112 scoreSorts.put(aann[i].label, aann[i].label);
4116 Enumeration labels = scoreSorts.keys();
4117 while (labels.hasMoreElements())
4119 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4120 (String) labels.nextElement());
4122 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4125 _annotationScoreVectorHash = viewport.getAlignment()
4126 .getAlignmentAnnotation().hashCode();
4131 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4132 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4133 * call. Listeners are added to remove the menu item when the treePanel is
4134 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4138 * Displayed tree window.
4140 * SortBy menu item title.
4143 public void buildTreeMenu()
4145 calculateTree.removeAll();
4146 // build the calculate menu
4148 for (final String type : new String[] { "NJ", "AV" })
4150 String treecalcnm = MessageManager.getString("label.tree_calc_"
4151 + type.toLowerCase());
4152 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4154 JMenuItem tm = new JMenuItem();
4155 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4156 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4158 String smn = MessageManager.getStringOrReturn(
4159 "label.score_model_", sm.getName());
4160 final String title = MessageManager.formatMessage(
4161 "label.treecalc_title", treecalcnm, smn);
4162 tm.setText(title);//
4163 tm.addActionListener(new java.awt.event.ActionListener()
4166 public void actionPerformed(ActionEvent e)
4168 newTreePanel(type, pwtype, title);
4171 calculateTree.add(tm);
4176 sortByTreeMenu.removeAll();
4178 List<Component> comps = PaintRefresher.components.get(viewport
4179 .getSequenceSetId());
4180 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4181 for (Component comp : comps)
4183 if (comp instanceof TreePanel)
4185 treePanels.add((TreePanel) comp);
4189 if (treePanels.size() < 1)
4191 sortByTreeMenu.setVisible(false);
4195 sortByTreeMenu.setVisible(true);
4197 for (final TreePanel tp : treePanels)
4199 final JMenuItem item = new JMenuItem(tp.getTitle());
4200 item.addActionListener(new java.awt.event.ActionListener()
4203 public void actionPerformed(ActionEvent e)
4205 tp.sortByTree_actionPerformed();
4206 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4211 sortByTreeMenu.add(item);
4215 public boolean sortBy(AlignmentOrder alorder, String undoname)
4217 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4218 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4219 if (undoname != null)
4221 addHistoryItem(new OrderCommand(undoname, oldOrder,
4222 viewport.getAlignment()));
4224 alignPanel.paintAlignment(true);
4229 * Work out whether the whole set of sequences or just the selected set will
4230 * be submitted for multiple alignment.
4233 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4235 // Now, check we have enough sequences
4236 AlignmentView msa = null;
4238 if ((viewport.getSelectionGroup() != null)
4239 && (viewport.getSelectionGroup().getSize() > 1))
4241 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4242 // some common interface!
4244 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4245 * SequenceI[sz = seqs.getSize(false)];
4247 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4248 * seqs.getSequenceAt(i); }
4250 msa = viewport.getAlignmentView(true);
4252 else if (viewport.getSelectionGroup() != null
4253 && viewport.getSelectionGroup().getSize() == 1)
4255 int option = JOptionPane.showConfirmDialog(this,
4256 MessageManager.getString("warn.oneseq_msainput_selection"),
4257 MessageManager.getString("label.invalid_selection"),
4258 JOptionPane.OK_CANCEL_OPTION);
4259 if (option == JOptionPane.OK_OPTION)
4261 msa = viewport.getAlignmentView(false);
4266 msa = viewport.getAlignmentView(false);
4272 * Decides what is submitted to a secondary structure prediction service: the
4273 * first sequence in the alignment, or in the current selection, or, if the
4274 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4275 * region or the whole alignment. (where the first sequence in the set is the
4276 * one that the prediction will be for).
4278 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4280 AlignmentView seqs = null;
4282 if ((viewport.getSelectionGroup() != null)
4283 && (viewport.getSelectionGroup().getSize() > 0))
4285 seqs = viewport.getAlignmentView(true);
4289 seqs = viewport.getAlignmentView(false);
4291 // limit sequences - JBPNote in future - could spawn multiple prediction
4293 // TODO: viewport.getAlignment().isAligned is a global state - the local
4294 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4295 if (!viewport.getAlignment().isAligned(false))
4297 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4298 // TODO: if seqs.getSequences().length>1 then should really have warned
4312 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4314 // Pick the tree file
4315 JalviewFileChooser chooser = new JalviewFileChooser(
4316 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4317 chooser.setFileView(new JalviewFileView());
4318 chooser.setDialogTitle(MessageManager
4319 .getString("label.select_newick_like_tree_file"));
4320 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4322 int value = chooser.showOpenDialog(null);
4324 if (value == JalviewFileChooser.APPROVE_OPTION)
4326 String choice = chooser.getSelectedFile().getPath();
4327 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4328 jalview.io.NewickFile fin = null;
4331 fin = new jalview.io.NewickFile(choice, "File");
4332 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4333 } catch (Exception ex)
4340 .getString("label.problem_reading_tree_file"),
4341 JOptionPane.WARNING_MESSAGE);
4342 ex.printStackTrace();
4344 if (fin != null && fin.hasWarningMessage())
4346 JOptionPane.showMessageDialog(Desktop.desktop, fin
4347 .getWarningMessage(), MessageManager
4348 .getString("label.possible_problem_with_tree_file"),
4349 JOptionPane.WARNING_MESSAGE);
4355 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4357 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4360 public TreePanel ShowNewickTree(NewickFile nf, String title)
4362 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4365 public TreePanel ShowNewickTree(NewickFile nf, String title,
4366 AlignmentView input)
4368 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4371 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4372 int h, int x, int y)
4374 return ShowNewickTree(nf, title, null, w, h, x, y);
4378 * Add a treeviewer for the tree extracted from a newick file object to the
4379 * current alignment view
4386 * Associated alignment input data (or null)
4395 * @return TreePanel handle
4397 public TreePanel ShowNewickTree(NewickFile nf, String title,
4398 AlignmentView input, int w, int h, int x, int y)
4400 TreePanel tp = null;
4406 if (nf.getTree() != null)
4408 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4414 tp.setLocation(x, y);
4417 Desktop.addInternalFrame(tp, title, w, h);
4419 } catch (Exception ex)
4421 ex.printStackTrace();
4427 private boolean buildingMenu = false;
4430 * Generates menu items and listener event actions for web service clients
4433 public void BuildWebServiceMenu()
4435 while (buildingMenu)
4439 System.err.println("Waiting for building menu to finish.");
4441 } catch (Exception e)
4445 final AlignFrame me = this;
4446 buildingMenu = true;
4447 new Thread(new Runnable()
4452 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4455 // System.err.println("Building ws menu again "
4456 // + Thread.currentThread());
4457 // TODO: add support for context dependent disabling of services based
4459 // alignment and current selection
4460 // TODO: add additional serviceHandle parameter to specify abstract
4462 // class independently of AbstractName
4463 // TODO: add in rediscovery GUI function to restart discoverer
4464 // TODO: group services by location as well as function and/or
4466 // object broker mechanism.
4467 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4468 final IProgressIndicator af = me;
4469 final JMenu msawsmenu = new JMenu("Alignment");
4470 final JMenu secstrmenu = new JMenu(
4471 "Secondary Structure Prediction");
4472 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4473 final JMenu analymenu = new JMenu("Analysis");
4474 final JMenu dismenu = new JMenu("Protein Disorder");
4475 // final JMenu msawsmenu = new
4476 // JMenu(MessageManager.getString("label.alignment"));
4477 // final JMenu secstrmenu = new
4478 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4479 // final JMenu seqsrchmenu = new
4480 // JMenu(MessageManager.getString("label.sequence_database_search"));
4481 // final JMenu analymenu = new
4482 // JMenu(MessageManager.getString("label.analysis"));
4483 // final JMenu dismenu = new
4484 // JMenu(MessageManager.getString("label.protein_disorder"));
4485 // JAL-940 - only show secondary structure prediction services from
4486 // the legacy server
4487 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4489 Discoverer.services != null && (Discoverer.services.size() > 0))
4491 // TODO: refactor to allow list of AbstractName/Handler bindings to
4493 // stored or retrieved from elsewhere
4494 // No MSAWS used any more:
4495 // Vector msaws = null; // (Vector)
4496 // Discoverer.services.get("MsaWS");
4497 Vector secstrpr = (Vector) Discoverer.services
4499 if (secstrpr != null)
4501 // Add any secondary structure prediction services
4502 for (int i = 0, j = secstrpr.size(); i < j; i++)
4504 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4506 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4507 .getServiceClient(sh);
4508 int p = secstrmenu.getItemCount();
4509 impl.attachWSMenuEntry(secstrmenu, me);
4510 int q = secstrmenu.getItemCount();
4511 for (int litm = p; litm < q; litm++)
4513 legacyItems.add(secstrmenu.getItem(litm));
4519 // Add all submenus in the order they should appear on the web
4521 wsmenu.add(msawsmenu);
4522 wsmenu.add(secstrmenu);
4523 wsmenu.add(dismenu);
4524 wsmenu.add(analymenu);
4525 // No search services yet
4526 // wsmenu.add(seqsrchmenu);
4528 javax.swing.SwingUtilities.invokeLater(new Runnable()
4535 webService.removeAll();
4536 // first, add discovered services onto the webservices menu
4537 if (wsmenu.size() > 0)
4539 for (int i = 0, j = wsmenu.size(); i < j; i++)
4541 webService.add(wsmenu.get(i));
4546 webService.add(me.webServiceNoServices);
4548 // TODO: move into separate menu builder class.
4549 boolean new_sspred = false;
4550 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4552 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4553 if (jws2servs != null)
4555 if (jws2servs.hasServices())
4557 jws2servs.attachWSMenuEntry(webService, me);
4558 for (Jws2Instance sv : jws2servs.getServices())
4560 if (sv.description.toLowerCase().contains("jpred"))
4562 for (JMenuItem jmi : legacyItems)
4564 jmi.setVisible(false);
4570 if (jws2servs.isRunning())
4572 JMenuItem tm = new JMenuItem(
4573 "Still discovering JABA Services");
4574 tm.setEnabled(false);
4579 build_urlServiceMenu(me.webService);
4580 build_fetchdbmenu(webService);
4581 for (JMenu item : wsmenu)
4583 if (item.getItemCount() == 0)
4585 item.setEnabled(false);
4589 item.setEnabled(true);
4592 } catch (Exception e)
4595 .debug("Exception during web service menu building process.",
4600 } catch (Exception e)
4603 buildingMenu = false;
4610 * construct any groupURL type service menu entries.
4614 private void build_urlServiceMenu(JMenu webService)
4616 // TODO: remove this code when 2.7 is released
4617 // DEBUG - alignmentView
4619 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4620 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4622 * @Override public void actionPerformed(ActionEvent e) {
4623 * jalview.datamodel.AlignmentView
4624 * .testSelectionViews(af.viewport.getAlignment(),
4625 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4627 * }); webService.add(testAlView);
4629 // TODO: refactor to RestClient discoverer and merge menu entries for
4630 // rest-style services with other types of analysis/calculation service
4631 // SHmmr test client - still being implemented.
4632 // DEBUG - alignmentView
4634 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4637 client.attachWSMenuEntry(
4638 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4644 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4645 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4646 * getProperty("LAST_DIRECTORY"));
4648 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4649 * to Vamsas file"); chooser.setToolTipText("Export");
4651 * int value = chooser.showSaveDialog(this);
4653 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4654 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4655 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4656 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4659 * prototype of an automatically enabled/disabled analysis function
4662 protected void setShowProductsEnabled()
4664 SequenceI[] selection = viewport.getSequenceSelection();
4665 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4666 viewport.getAlignment().getDataset()))
4668 showProducts.setEnabled(true);
4673 showProducts.setEnabled(false);
4678 * search selection for sequence xRef products and build the show products
4683 * @return true if showProducts menu should be enabled.
4685 public boolean canShowProducts(SequenceI[] selection,
4686 boolean isRegionSelection, Alignment dataset)
4688 boolean showp = false;
4691 showProducts.removeAll();
4692 final boolean dna = viewport.getAlignment().isNucleotide();
4693 final Alignment ds = dataset;
4694 String[] ptypes = (selection == null || selection.length == 0) ? null
4695 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4697 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4698 // selection, dataset, true);
4699 final SequenceI[] sel = selection;
4700 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4703 final boolean isRegSel = isRegionSelection;
4704 final AlignFrame af = this;
4705 final String source = ptypes[t];
4706 JMenuItem xtype = new JMenuItem(ptypes[t]);
4707 xtype.addActionListener(new ActionListener()
4711 public void actionPerformed(ActionEvent e)
4713 // TODO: new thread for this call with vis-delay
4714 af.showProductsFor(af.viewport.getSequenceSelection(),
4715 isRegSel, dna, source);
4719 showProducts.add(xtype);
4721 showProducts.setVisible(showp);
4722 showProducts.setEnabled(showp);
4723 } catch (Exception e)
4725 jalview.bin.Cache.log
4726 .warn("canTranslate threw an exception - please report to help@jalview.org",
4733 protected void showProductsFor(final SequenceI[] sel,
4734 final boolean isRegSel, final boolean dna, final String source)
4736 Runnable foo = new Runnable()
4742 final long sttime = System.currentTimeMillis();
4743 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4744 "status.searching_for_sequences_from",
4745 new Object[] { source }), sttime);
4748 // update our local dataset reference
4749 Alignment ds = AlignFrame.this.getViewport().getAlignment()
4751 Alignment prods = CrossRef
4752 .findXrefSequences(sel, dna, source, ds);
4755 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4756 for (int s = 0; s < sprods.length; s++)
4758 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4759 if (ds.getSequences() == null
4760 || !ds.getSequences().contains(
4761 sprods[s].getDatasetSequence()))
4763 ds.addSequence(sprods[s].getDatasetSequence());
4765 sprods[s].updatePDBIds();
4767 Alignment al = new Alignment(sprods);
4771 * Copy dna-to-protein mappings to new alignment
4773 // TODO 1: no mappings are set up for EMBL product
4774 // TODO 2: if they were, should add them to protein alignment, not
4776 Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4777 for (AlignedCodonFrame acf : cf)
4779 al.addCodonFrame(acf);
4781 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4783 String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4784 + " for " + ((isRegSel) ? "selected region of " : "")
4786 naf.setTitle(newtitle);
4788 // temporary flag until SplitFrame is released
4789 boolean asSplitFrame = Cache.getDefault(
4790 Preferences.ENABLE_SPLIT_FRAME, true);
4794 * Make a copy of this alignment (sharing the same dataset
4795 * sequences). If we are DNA, drop introns and update mappings
4797 AlignmentI copyAlignment = null;
4798 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4799 .getSequenceSelection();
4802 copyAlignment = AlignmentUtils.makeExonAlignment(
4803 sequenceSelection, cf);
4804 al.getCodonFrames().clear();
4805 al.getCodonFrames().addAll(cf);
4806 final StructureSelectionManager ssm = StructureSelectionManager
4807 .getStructureSelectionManager(Desktop.instance);
4808 ssm.registerMappings(cf);
4812 copyAlignment = new Alignment(new Alignment(
4813 sequenceSelection));
4815 AlignFrame copyThis = new AlignFrame(copyAlignment,
4816 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4817 copyThis.setTitle(AlignFrame.this.getTitle());
4818 // SplitFrame with dna above, protein below
4819 SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4820 dna ? naf : copyThis);
4821 naf.setVisible(true);
4822 copyThis.setVisible(true);
4823 String linkedTitle = MessageManager
4824 .getString("label.linked_view_title");
4825 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4829 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4835 System.err.println("No Sequences generated for xRef type "
4838 } catch (Exception e)
4840 jalview.bin.Cache.log.error(
4841 "Exception when finding crossreferences", e);
4842 } catch (OutOfMemoryError e)
4844 new OOMWarning("whilst fetching crossreferences", e);
4847 jalview.bin.Cache.log.error("Error when finding crossreferences",
4850 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4851 "status.finished_searching_for_sequences_from",
4852 new Object[] { source }), sttime);
4856 Thread frunner = new Thread(foo);
4860 public boolean canShowTranslationProducts(SequenceI[] selection,
4861 AlignmentI alignment)
4866 return (jalview.analysis.Dna.canTranslate(selection,
4867 viewport.getViewAsVisibleContigs(true)));
4868 } catch (Exception e)
4870 jalview.bin.Cache.log
4871 .warn("canTranslate threw an exception - please report to help@jalview.org",
4878 * Construct and display a new frame containing the translation of this
4879 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4882 public void showTranslation_actionPerformed(ActionEvent e)
4884 AlignmentI al = null;
4887 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4889 al = dna.translateCdna();
4890 } catch (Exception ex)
4892 jalview.bin.Cache.log.error(
4893 "Exception during translation. Please report this !", ex);
4894 final String msg = MessageManager
4895 .getString("label.error_when_translating_sequences_submit_bug_report");
4896 final String errorTitle = MessageManager
4897 .getString("label.implementation_error")
4898 + MessageManager.getString("translation_failed");
4899 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4900 JOptionPane.ERROR_MESSAGE);
4903 if (al == null || al.getHeight() == 0)
4905 final String msg = MessageManager
4906 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4907 final String errorTitle = MessageManager
4908 .getString("label.translation_failed");
4909 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4910 JOptionPane.WARNING_MESSAGE);
4914 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4915 af.setFileFormat(this.currentFileFormat);
4916 final String newTitle = MessageManager.formatMessage(
4917 "label.translation_of_params",
4918 new Object[] { this.getTitle() });
4919 af.setTitle(newTitle);
4920 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4922 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4923 viewport.openSplitFrame(af, new Alignment(seqs));
4927 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4934 * Set the file format
4938 public void setFileFormat(String fileFormat)
4940 this.currentFileFormat = fileFormat;
4944 * Try to load a features file onto the alignment.
4947 * contents or path to retrieve file
4949 * access mode of file (see jalview.io.AlignFile)
4950 * @return true if features file was parsed correctly.
4952 public boolean parseFeaturesFile(String file, String type)
4954 return avc.parseFeaturesFile(file, type,
4955 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4960 public void refreshFeatureUI(boolean enableIfNecessary)
4962 // note - currently this is only still here rather than in the controller
4963 // because of the featureSettings hard reference that is yet to be
4965 if (enableIfNecessary)
4967 viewport.setShowSequenceFeatures(true);
4968 showSeqFeatures.setSelected(true);
4974 public void dragEnter(DropTargetDragEvent evt)
4979 public void dragExit(DropTargetEvent evt)
4984 public void dragOver(DropTargetDragEvent evt)
4989 public void dropActionChanged(DropTargetDragEvent evt)
4994 public void drop(DropTargetDropEvent evt)
4996 Transferable t = evt.getTransferable();
4997 java.util.List files = null;
5001 DataFlavor uriListFlavor = new DataFlavor(
5002 "text/uri-list;class=java.lang.String");
5003 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5005 // Works on Windows and MacOSX
5006 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5007 files = (java.util.List) t
5008 .getTransferData(DataFlavor.javaFileListFlavor);
5010 else if (t.isDataFlavorSupported(uriListFlavor))
5012 // This is used by Unix drag system
5013 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5014 String data = (String) t.getTransferData(uriListFlavor);
5015 files = new java.util.ArrayList(1);
5016 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5017 data, "\r\n"); st.hasMoreTokens();)
5019 String s = st.nextToken();
5020 if (s.startsWith("#"))
5022 // the line is a comment (as per the RFC 2483)
5026 java.net.URI uri = new java.net.URI(s);
5027 // check to see if we can handle this kind of URI
5028 if (uri.getScheme().toLowerCase().startsWith("http"))
5030 files.add(uri.toString());
5034 // otherwise preserve old behaviour: catch all for file objects
5035 java.io.File file = new java.io.File(uri);
5036 files.add(file.toString());
5040 } catch (Exception e)
5042 e.printStackTrace();
5048 // check to see if any of these files have names matching sequences in
5050 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5051 .getAlignment().getSequencesArray());
5053 * Object[] { String,SequenceI}
5055 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5056 ArrayList<String> filesnotmatched = new ArrayList<String>();
5057 for (int i = 0; i < files.size(); i++)
5059 String file = files.get(i).toString();
5061 String protocol = FormatAdapter.checkProtocol(file);
5062 if (protocol == jalview.io.FormatAdapter.FILE)
5064 File fl = new File(file);
5065 pdbfn = fl.getName();
5067 else if (protocol == jalview.io.FormatAdapter.URL)
5069 URL url = new URL(file);
5070 pdbfn = url.getFile();
5072 if (pdbfn.length() > 0)
5074 // attempt to find a match in the alignment
5075 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5076 int l = 0, c = pdbfn.indexOf(".");
5077 while (mtch == null && c != -1)
5082 } while ((c = pdbfn.indexOf(".", l)) > l);
5085 pdbfn = pdbfn.substring(0, l);
5087 mtch = idm.findAllIdMatches(pdbfn);
5094 type = new IdentifyFile().Identify(file, protocol);
5095 } catch (Exception ex)
5101 if (type.equalsIgnoreCase("PDB"))
5103 filesmatched.add(new Object[] { file, protocol, mtch });
5108 // File wasn't named like one of the sequences or wasn't a PDB file.
5109 filesnotmatched.add(file);
5113 if (filesmatched.size() > 0)
5115 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5121 "label.automatically_associate_pdb_files_with_sequences_same_name",
5122 new Object[] { Integer
5128 .getString("label.automatically_associate_pdb_files_by_name"),
5129 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5132 for (Object[] fm : filesmatched)
5134 // try and associate
5135 // TODO: may want to set a standard ID naming formalism for
5136 // associating PDB files which have no IDs.
5137 for (SequenceI toassoc : (SequenceI[]) fm[2])
5139 PDBEntry pe = new AssociatePdbFileWithSeq()
5140 .associatePdbWithSeq((String) fm[0],
5141 (String) fm[1], toassoc, false,
5145 System.err.println("Associated file : "
5146 + ((String) fm[0]) + " with "
5147 + toassoc.getDisplayId(true));
5151 alignPanel.paintAlignment(true);
5155 if (filesnotmatched.size() > 0)
5158 && (Cache.getDefault(
5159 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5165 "label.ignore_unmatched_dropped_files_info",
5166 new Object[] { Integer
5173 .getString("label.ignore_unmatched_dropped_files"),
5174 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5178 for (String fn : filesnotmatched)
5180 loadJalviewDataFile(fn, null, null, null);
5184 } catch (Exception ex)
5186 ex.printStackTrace();
5192 * Attempt to load a "dropped" file or URL string: First by testing whether
5193 * it's and Annotation file, then a JNet file, and finally a features file. If
5194 * all are false then the user may have dropped an alignment file onto this
5198 * either a filename or a URL string.
5200 public void loadJalviewDataFile(String file, String protocol,
5201 String format, SequenceI assocSeq)
5205 if (protocol == null)
5207 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5209 // if the file isn't identified, or not positively identified as some
5210 // other filetype (PFAM is default unidentified alignment file type) then
5211 // try to parse as annotation.
5212 boolean isAnnotation = (format == null || format
5213 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5214 .annotateAlignmentView(viewport, file, protocol) : false;
5218 // first see if its a T-COFFEE score file
5219 TCoffeeScoreFile tcf = null;
5222 tcf = new TCoffeeScoreFile(file, protocol);
5225 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5227 tcoffeeColour.setEnabled(true);
5228 tcoffeeColour.setSelected(true);
5229 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5230 isAnnotation = true;
5232 .setText(MessageManager
5233 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5237 // some problem - if no warning its probable that the ID matching
5238 // process didn't work
5242 tcf.getWarningMessage() == null ? MessageManager
5243 .getString("label.check_file_matches_sequence_ids_alignment")
5244 : tcf.getWarningMessage(),
5246 .getString("label.problem_reading_tcoffee_score_file"),
5247 JOptionPane.WARNING_MESSAGE);
5254 } catch (Exception x)
5257 .debug("Exception when processing data source as T-COFFEE score file",
5263 // try to see if its a JNet 'concise' style annotation file *before*
5265 // try to parse it as a features file
5268 format = new IdentifyFile().Identify(file, protocol);
5270 if (format.equalsIgnoreCase("JnetFile"))
5272 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5274 new JnetAnnotationMaker();
5275 JnetAnnotationMaker.add_annotation(predictions,
5276 viewport.getAlignment(), 0, false);
5277 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5278 viewport.getAlignment().setSeqrep(repseq);
5279 ColumnSelection cs = new ColumnSelection();
5280 cs.hideInsertionsFor(repseq);
5281 viewport.setColumnSelection(cs);
5282 isAnnotation = true;
5287 * if (format.equalsIgnoreCase("PDB")) {
5289 * String pdbfn = ""; // try to match up filename with sequence id
5290 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5291 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5292 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5293 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5294 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5295 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5296 * // attempt to find a match in the alignment SequenceI mtch =
5297 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5298 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5299 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5300 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5301 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5302 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5303 * { System.err.println("Associated file : " + file + " with " +
5304 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5305 * TODO: maybe need to load as normal otherwise return; } }
5307 // try to parse it as a features file
5308 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5309 // if it wasn't a features file then we just treat it as a general
5310 // alignment file to load into the current view.
5313 new FileLoader().LoadFile(viewport, file, protocol, format);
5317 alignPanel.paintAlignment(true);
5325 alignPanel.adjustAnnotationHeight();
5326 viewport.updateSequenceIdColours();
5327 buildSortByAnnotationScoresMenu();
5328 alignPanel.paintAlignment(true);
5330 } catch (Exception ex)
5332 ex.printStackTrace();
5333 } catch (OutOfMemoryError oom)
5338 } catch (Exception x)
5344 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5345 : "using " + protocol + " from " + file)
5347 + (format != null ? "(parsing as '" + format
5348 + "' file)" : ""), oom, Desktop.desktop);
5353 * Method invoked by the ChangeListener on the tabbed pane, in other words
5354 * when a different tabbed pane is selected by the user or programmatically.
5357 public void tabSelectionChanged(int index)
5361 alignPanel = alignPanels.get(index);
5362 viewport = alignPanel.av;
5363 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5364 setMenusFromViewport(viewport);
5368 * If there is a frame linked to this one in a SplitPane, switch it to the
5369 * same view tab index. No infinite recursion of calls should happen, since
5370 * tabSelectionChanged() should not get invoked on setting the selected
5371 * index to an unchanged value. Guard against setting an invalid index
5372 * before the new view peer tab has been created.
5374 final AlignViewportI peer = viewport.getCodingComplement();
5377 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5378 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5380 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5386 * On right mouse click on view tab, prompt for and set new view name.
5389 public void tabbedPane_mousePressed(MouseEvent e)
5391 if (SwingUtilities.isRightMouseButton(e))
5393 String msg = MessageManager.getString("label.enter_view_name");
5394 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5395 JOptionPane.QUESTION_MESSAGE);
5399 viewport.viewName = reply;
5400 // TODO warn if reply is in getExistingViewNames()?
5401 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5406 public AlignViewport getCurrentView()
5412 * Open the dialog for regex description parsing.
5415 protected void extractScores_actionPerformed(ActionEvent e)
5417 ParseProperties pp = new jalview.analysis.ParseProperties(
5418 viewport.getAlignment());
5419 // TODO: verify regex and introduce GUI dialog for version 2.5
5420 // if (pp.getScoresFromDescription("col", "score column ",
5421 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5423 if (pp.getScoresFromDescription("description column",
5424 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5426 buildSortByAnnotationScoresMenu();
5434 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5438 protected void showDbRefs_actionPerformed(ActionEvent e)
5440 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5446 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5450 protected void showNpFeats_actionPerformed(ActionEvent e)
5452 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5456 * find the viewport amongst the tabs in this alignment frame and close that
5461 public boolean closeView(AlignViewportI av)
5465 this.closeMenuItem_actionPerformed(false);
5468 Component[] comp = tabbedPane.getComponents();
5469 for (int i = 0; comp != null && i < comp.length; i++)
5471 if (comp[i] instanceof AlignmentPanel)
5473 if (((AlignmentPanel) comp[i]).av == av)
5476 closeView((AlignmentPanel) comp[i]);
5484 protected void build_fetchdbmenu(JMenu webService)
5486 // Temporary hack - DBRef Fetcher always top level ws entry.
5487 // TODO We probably want to store a sequence database checklist in
5488 // preferences and have checkboxes.. rather than individual sources selected
5490 final JMenu rfetch = new JMenu(
5491 MessageManager.getString("action.fetch_db_references"));
5492 rfetch.setToolTipText(MessageManager
5493 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5494 webService.add(rfetch);
5496 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5497 MessageManager.getString("option.trim_retrieved_seqs"));
5498 trimrs.setToolTipText(MessageManager
5499 .getString("label.trim_retrieved_sequences"));
5500 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5501 trimrs.addActionListener(new ActionListener()
5504 public void actionPerformed(ActionEvent e)
5506 trimrs.setSelected(trimrs.isSelected());
5507 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5508 Boolean.valueOf(trimrs.isSelected()).toString());
5512 JMenuItem fetchr = new JMenuItem(
5513 MessageManager.getString("label.standard_databases"));
5514 fetchr.setToolTipText(MessageManager
5515 .getString("label.fetch_embl_uniprot"));
5516 fetchr.addActionListener(new ActionListener()
5520 public void actionPerformed(ActionEvent e)
5522 new Thread(new Runnable()
5528 new jalview.ws.DBRefFetcher(alignPanel.av
5529 .getSequenceSelection(), alignPanel.alignFrame)
5530 .fetchDBRefs(false);
5538 final AlignFrame me = this;
5539 new Thread(new Runnable()
5544 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5545 .getSequenceFetcherSingleton(me);
5546 javax.swing.SwingUtilities.invokeLater(new Runnable()
5551 String[] dbclasses = sf.getOrderedSupportedSources();
5552 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5553 // jalview.util.QuickSort.sort(otherdb, otherdb);
5554 List<DbSourceProxy> otherdb;
5555 JMenu dfetch = new JMenu();
5556 JMenu ifetch = new JMenu();
5557 JMenuItem fetchr = null;
5558 int comp = 0, icomp = 0, mcomp = 15;
5559 String mname = null;
5561 for (String dbclass : dbclasses)
5563 otherdb = sf.getSourceProxy(dbclass);
5564 // add a single entry for this class, or submenu allowing 'fetch
5566 if (otherdb == null || otherdb.size() < 1)
5570 // List<DbSourceProxy> dbs=otherdb;
5571 // otherdb=new ArrayList<DbSourceProxy>();
5572 // for (DbSourceProxy db:dbs)
5574 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5578 mname = "From " + dbclass;
5580 if (otherdb.size() == 1)
5582 final DbSourceProxy[] dassource = otherdb
5583 .toArray(new DbSourceProxy[0]);
5584 DbSourceProxy src = otherdb.get(0);
5585 fetchr = new JMenuItem(src.getDbSource());
5586 fetchr.addActionListener(new ActionListener()
5590 public void actionPerformed(ActionEvent e)
5592 new Thread(new Runnable()
5598 new jalview.ws.DBRefFetcher(alignPanel.av
5599 .getSequenceSelection(),
5600 alignPanel.alignFrame, dassource)
5601 .fetchDBRefs(false);
5607 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5608 MessageManager.formatMessage(
5609 "label.fetch_retrieve_from",
5610 new Object[] { src.getDbName() })));
5616 final DbSourceProxy[] dassource = otherdb
5617 .toArray(new DbSourceProxy[0]);
5619 DbSourceProxy src = otherdb.get(0);
5620 fetchr = new JMenuItem(MessageManager.formatMessage(
5621 "label.fetch_all_param",
5622 new Object[] { src.getDbSource() }));
5623 fetchr.addActionListener(new ActionListener()
5626 public void actionPerformed(ActionEvent e)
5628 new Thread(new Runnable()
5634 new jalview.ws.DBRefFetcher(alignPanel.av
5635 .getSequenceSelection(),
5636 alignPanel.alignFrame, dassource)
5637 .fetchDBRefs(false);
5643 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5644 MessageManager.formatMessage(
5645 "label.fetch_retrieve_from_all_sources",
5647 Integer.valueOf(otherdb.size())
5648 .toString(), src.getDbSource(),
5649 src.getDbName() })));
5652 // and then build the rest of the individual menus
5653 ifetch = new JMenu(MessageManager.formatMessage(
5654 "label.source_from_db_source",
5655 new Object[] { src.getDbSource() }));
5657 String imname = null;
5659 for (DbSourceProxy sproxy : otherdb)
5661 String dbname = sproxy.getDbName();
5662 String sname = dbname.length() > 5 ? dbname.substring(0,
5663 5) + "..." : dbname;
5664 String msname = dbname.length() > 10 ? dbname.substring(
5665 0, 10) + "..." : dbname;
5668 imname = MessageManager.formatMessage(
5669 "label.from_msname", new Object[] { sname });
5671 fetchr = new JMenuItem(msname);
5672 final DbSourceProxy[] dassrc = { sproxy };
5673 fetchr.addActionListener(new ActionListener()
5677 public void actionPerformed(ActionEvent e)
5679 new Thread(new Runnable()
5685 new jalview.ws.DBRefFetcher(alignPanel.av
5686 .getSequenceSelection(),
5687 alignPanel.alignFrame, dassrc)
5688 .fetchDBRefs(false);
5694 fetchr.setToolTipText("<html>"
5695 + MessageManager.formatMessage(
5696 "label.fetch_retrieve_from", new Object[]
5700 if (++icomp >= mcomp || i == (otherdb.size()))
5702 ifetch.setText(MessageManager.formatMessage(
5703 "label.source_to_target", imname, sname));
5705 ifetch = new JMenu();
5713 if (comp >= mcomp || dbi >= (dbclasses.length))
5715 dfetch.setText(MessageManager.formatMessage(
5716 "label.source_to_target", mname, dbclass));
5718 dfetch = new JMenu();
5731 * Left justify the whole alignment.
5734 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5736 AlignmentI al = viewport.getAlignment();
5738 viewport.firePropertyChange("alignment", null, al);
5742 * Right justify the whole alignment.
5745 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5747 AlignmentI al = viewport.getAlignment();
5749 viewport.firePropertyChange("alignment", null, al);
5752 public void setShowSeqFeatures(boolean b)
5754 showSeqFeatures.setSelected(b);
5755 viewport.setShowSequenceFeatures(b);
5762 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5763 * awt.event.ActionEvent)
5766 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5768 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5769 alignPanel.paintAlignment(true);
5776 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5780 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5782 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5783 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5791 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5792 * .event.ActionEvent)
5795 protected void showGroupConservation_actionPerformed(ActionEvent e)
5797 viewport.setShowGroupConservation(showGroupConservation.getState());
5798 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5805 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5806 * .event.ActionEvent)
5809 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5811 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5812 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5819 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5820 * .event.ActionEvent)
5823 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5825 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5826 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5830 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5832 showSequenceLogo.setState(true);
5833 viewport.setShowSequenceLogo(true);
5834 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5835 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5839 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5841 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5848 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5849 * .event.ActionEvent)
5852 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5854 if (avc.makeGroupsFromSelection())
5856 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5857 alignPanel.updateAnnotation();
5858 alignPanel.paintAlignment(true);
5862 public void clearAlignmentSeqRep()
5864 // TODO refactor alignmentseqrep to controller
5865 if (viewport.getAlignment().hasSeqrep())
5867 viewport.getAlignment().setSeqrep(null);
5868 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5869 alignPanel.updateAnnotation();
5870 alignPanel.paintAlignment(true);
5875 protected void createGroup_actionPerformed(ActionEvent e)
5877 if (avc.createGroup())
5879 alignPanel.alignmentChanged();
5884 protected void unGroup_actionPerformed(ActionEvent e)
5888 alignPanel.alignmentChanged();
5893 * make the given alignmentPanel the currently selected tab
5895 * @param alignmentPanel
5897 public void setDisplayedView(AlignmentPanel alignmentPanel)
5899 if (!viewport.getSequenceSetId().equals(
5900 alignmentPanel.av.getSequenceSetId()))
5904 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5906 if (tabbedPane != null
5907 && tabbedPane.getTabCount() > 0
5908 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5909 .getSelectedIndex())
5911 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5916 * Action on selection of menu options to Show or Hide annotations.
5919 * @param forSequences
5920 * update sequence-related annotations
5921 * @param forAlignment
5922 * update non-sequence-related annotations
5925 protected void setAnnotationsVisibility(boolean visible,
5926 boolean forSequences, boolean forAlignment)
5928 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5929 .getAlignmentAnnotation())
5932 * don't display non-positional annotations on an alignment
5934 if (aa.annotations == null)
5938 boolean apply = (aa.sequenceRef == null && forAlignment)
5939 || (aa.sequenceRef != null && forSequences);
5942 aa.visible = visible;
5945 alignPanel.validateAnnotationDimensions(true);
5946 alignPanel.alignmentChanged();
5950 * Store selected annotation sort order for the view and repaint.
5953 protected void sortAnnotations_actionPerformed()
5955 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5957 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5958 alignPanel.paintAlignment(true);
5963 * @return alignment panels in this alignment frame
5965 public List<? extends AlignmentViewPanel> getAlignPanels()
5967 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5971 * Open a new alignment window, with the cDNA associated with this (protein)
5972 * alignment, aligned as is the protein.
5974 protected void viewAsCdna_actionPerformed()
5976 // TODO no longer a menu action - refactor as required
5977 final AlignmentI alignment = getViewport().getAlignment();
5978 Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5979 if (mappings == null)
5983 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5984 for (SequenceI aaSeq : alignment.getSequences())
5986 for (AlignedCodonFrame acf : mappings)
5988 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5992 * There is a cDNA mapping for this protein sequence - add to new
5993 * alignment. It will share the same dataset sequence as other mapped
5994 * cDNA (no new mappings need to be created).
5996 final Sequence newSeq = new Sequence(dnaSeq);
5997 newSeq.setDatasetSequence(dnaSeq);
5998 cdnaSeqs.add(newSeq);
6002 if (cdnaSeqs.size() == 0)
6004 // show a warning dialog no mapped cDNA
6007 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6009 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6010 AlignFrame.DEFAULT_HEIGHT);
6011 cdna.alignAs(alignment);
6012 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6014 Desktop.addInternalFrame(alignFrame, newtitle,
6015 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6019 * Set visibility of dna/protein complement view (available when shown in a
6025 protected void showComplement_actionPerformed(boolean show)
6027 SplitContainerI sf = getSplitViewContainer();
6030 sf.setComplementVisible(this, show);
6035 class PrintThread extends Thread
6039 public PrintThread(AlignmentPanel ap)
6044 static PageFormat pf;
6049 PrinterJob printJob = PrinterJob.getPrinterJob();
6053 printJob.setPrintable(ap, pf);
6057 printJob.setPrintable(ap);
6060 if (printJob.printDialog())
6065 } catch (Exception PrintException)
6067 PrintException.printStackTrace();