2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
3 * Copyright (C) 2015 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[] { -1, -1 };
1313 int[] higestRange = new int[] { -1, -1 };
1315 for (int[] hiddenCol : hiddenCols)
1317 lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1318 higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1321 if (lowestRange[0] == -1 && lowestRange[1] == -1)
1323 startPos = aligmentStartEnd[0];
1327 startPos = lowestRange[1] + 1;
1330 if (higestRange[0] == -1 && higestRange[1] == -1)
1332 endPos = aligmentStartEnd[1];
1336 endPos = higestRange[0] - 1;
1339 // System.out.println("Export range : " + startPos + " - " + endPos);
1340 return new int[] { startPos, endPos };
1343 public static void main(String[] args)
1345 ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1346 hiddenCols.add(new int[] { 0, 0 });
1347 hiddenCols.add(new int[] { 6, 9 });
1348 hiddenCols.add(new int[] { 11, 12 });
1349 hiddenCols.add(new int[] { 33, 33 });
1350 hiddenCols.add(new int[] { 50, 50 });
1352 int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1353 // System.out.println("Export range : " + x[0] + " - " + x[1]);
1363 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1365 new HtmlSvgOutput(null, alignPanel);
1369 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1371 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1372 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1375 public void createImageMap(File file, String image)
1377 alignPanel.makePNGImageMap(file, image);
1387 public void createPNG(File f)
1389 alignPanel.makePNG(f);
1399 public void createEPS(File f)
1401 alignPanel.makeEPS(f);
1404 public void createSVG(File f)
1406 alignPanel.makeSVG(f);
1410 public void pageSetup_actionPerformed(ActionEvent e)
1412 PrinterJob printJob = PrinterJob.getPrinterJob();
1413 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1423 public void printMenuItem_actionPerformed(ActionEvent e)
1425 // Putting in a thread avoids Swing painting problems
1426 PrintThread thread = new PrintThread(alignPanel);
1431 public void exportFeatures_actionPerformed(ActionEvent e)
1433 new AnnotationExporter().exportFeatures(alignPanel);
1437 public void exportAnnotations_actionPerformed(ActionEvent e)
1439 new AnnotationExporter().exportAnnotations(alignPanel);
1443 public void associatedData_actionPerformed(ActionEvent e)
1445 // Pick the tree file
1446 JalviewFileChooser chooser = new JalviewFileChooser(
1447 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1448 chooser.setFileView(new JalviewFileView());
1449 chooser.setDialogTitle(MessageManager
1450 .getString("label.load_jalview_annotations"));
1451 chooser.setToolTipText(MessageManager
1452 .getString("label.load_jalview_annotations"));
1454 int value = chooser.showOpenDialog(null);
1456 if (value == JalviewFileChooser.APPROVE_OPTION)
1458 String choice = chooser.getSelectedFile().getPath();
1459 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1460 loadJalviewDataFile(choice, null, null, null);
1466 * Close the current view or all views in the alignment frame. If the frame
1467 * only contains one view then the alignment will be removed from memory.
1469 * @param closeAllTabs
1472 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1474 if (alignPanels != null && alignPanels.size() < 2)
1476 closeAllTabs = true;
1481 if (alignPanels != null)
1485 if (this.isClosed())
1487 // really close all the windows - otherwise wait till
1488 // setClosed(true) is called
1489 for (int i = 0; i < alignPanels.size(); i++)
1491 AlignmentPanel ap = alignPanels.get(i);
1498 closeView(alignPanel);
1505 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1506 * be called recursively, with the frame now in 'closed' state
1508 this.setClosed(true);
1510 } catch (Exception ex)
1512 ex.printStackTrace();
1517 * Close the specified panel and close up tabs appropriately.
1519 * @param panelToClose
1521 public void closeView(AlignmentPanel panelToClose)
1523 int index = tabbedPane.getSelectedIndex();
1524 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1525 alignPanels.remove(panelToClose);
1526 panelToClose.closePanel();
1527 panelToClose = null;
1529 tabbedPane.removeTabAt(closedindex);
1530 tabbedPane.validate();
1532 if (index > closedindex || index == tabbedPane.getTabCount())
1534 // modify currently selected tab index if necessary.
1538 this.tabSelectionChanged(index);
1544 void updateEditMenuBar()
1547 if (viewport.getHistoryList().size() > 0)
1549 undoMenuItem.setEnabled(true);
1550 CommandI command = viewport.getHistoryList().peek();
1551 undoMenuItem.setText(MessageManager.formatMessage(
1552 "label.undo_command",
1553 new Object[] { command.getDescription() }));
1557 undoMenuItem.setEnabled(false);
1558 undoMenuItem.setText(MessageManager.getString("action.undo"));
1561 if (viewport.getRedoList().size() > 0)
1563 redoMenuItem.setEnabled(true);
1565 CommandI command = viewport.getRedoList().peek();
1566 redoMenuItem.setText(MessageManager.formatMessage(
1567 "label.redo_command",
1568 new Object[] { command.getDescription() }));
1572 redoMenuItem.setEnabled(false);
1573 redoMenuItem.setText(MessageManager.getString("action.redo"));
1577 public void addHistoryItem(CommandI command)
1579 if (command.getSize() > 0)
1581 viewport.addToHistoryList(command);
1582 viewport.clearRedoList();
1583 updateEditMenuBar();
1584 viewport.updateHiddenColumns();
1585 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1586 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1587 // viewport.getColumnSelection()
1588 // .getHiddenColumns().size() > 0);
1594 * @return alignment objects for all views
1596 AlignmentI[] getViewAlignments()
1598 if (alignPanels != null)
1600 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1602 for (AlignmentPanel ap : alignPanels)
1604 als[i++] = ap.av.getAlignment();
1608 if (viewport != null)
1610 return new AlignmentI[] { viewport.getAlignment() };
1622 protected void undoMenuItem_actionPerformed(ActionEvent e)
1624 if (viewport.getHistoryList().isEmpty())
1628 CommandI command = viewport.getHistoryList().pop();
1629 viewport.addToRedoList(command);
1630 command.undoCommand(getViewAlignments());
1632 AlignmentViewport originalSource = getOriginatingSource(command);
1633 updateEditMenuBar();
1635 if (originalSource != null)
1637 if (originalSource != viewport)
1640 .warn("Implementation worry: mismatch of viewport origin for undo");
1642 originalSource.updateHiddenColumns();
1643 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1645 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1646 // viewport.getColumnSelection()
1647 // .getHiddenColumns().size() > 0);
1648 originalSource.firePropertyChange("alignment", null, originalSource
1649 .getAlignment().getSequences());
1660 protected void redoMenuItem_actionPerformed(ActionEvent e)
1662 if (viewport.getRedoList().size() < 1)
1667 CommandI command = viewport.getRedoList().pop();
1668 viewport.addToHistoryList(command);
1669 command.doCommand(getViewAlignments());
1671 AlignmentViewport originalSource = getOriginatingSource(command);
1672 updateEditMenuBar();
1674 if (originalSource != null)
1677 if (originalSource != viewport)
1680 .warn("Implementation worry: mismatch of viewport origin for redo");
1682 originalSource.updateHiddenColumns();
1683 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1685 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1686 // viewport.getColumnSelection()
1687 // .getHiddenColumns().size() > 0);
1688 originalSource.firePropertyChange("alignment", null, originalSource
1689 .getAlignment().getSequences());
1693 AlignmentViewport getOriginatingSource(CommandI command)
1695 AlignmentViewport originalSource = null;
1696 // For sequence removal and addition, we need to fire
1697 // the property change event FROM the viewport where the
1698 // original alignment was altered
1699 AlignmentI al = null;
1700 if (command instanceof EditCommand)
1702 EditCommand editCommand = (EditCommand) command;
1703 al = editCommand.getAlignment();
1704 List<Component> comps = PaintRefresher.components.get(viewport
1705 .getSequenceSetId());
1707 for (Component comp : comps)
1709 if (comp instanceof AlignmentPanel)
1711 if (al == ((AlignmentPanel) comp).av.getAlignment())
1713 originalSource = ((AlignmentPanel) comp).av;
1720 if (originalSource == null)
1722 // The original view is closed, we must validate
1723 // the current view against the closed view first
1726 PaintRefresher.validateSequences(al, viewport.getAlignment());
1729 originalSource = viewport;
1732 return originalSource;
1741 public void moveSelectedSequences(boolean up)
1743 SequenceGroup sg = viewport.getSelectionGroup();
1749 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1750 viewport.getHiddenRepSequences(), up);
1751 alignPanel.paintAlignment(true);
1754 synchronized void slideSequences(boolean right, int size)
1756 List<SequenceI> sg = new ArrayList<SequenceI>();
1757 if (viewport.cursorMode)
1759 sg.add(viewport.getAlignment().getSequenceAt(
1760 alignPanel.getSeqPanel().seqCanvas.cursorY));
1762 else if (viewport.getSelectionGroup() != null
1763 && viewport.getSelectionGroup().getSize() != viewport
1764 .getAlignment().getHeight())
1766 sg = viewport.getSelectionGroup().getSequences(
1767 viewport.getHiddenRepSequences());
1775 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1777 for (SequenceI seq : viewport.getAlignment().getSequences())
1779 if (!sg.contains(seq))
1781 invertGroup.add(seq);
1785 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1787 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1788 for (int i = 0; i < invertGroup.size(); i++)
1790 seqs2[i] = invertGroup.get(i);
1793 SlideSequencesCommand ssc;
1796 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1797 size, viewport.getGapCharacter());
1801 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1802 size, viewport.getGapCharacter());
1805 int groupAdjustment = 0;
1806 if (ssc.getGapsInsertedBegin() && right)
1808 if (viewport.cursorMode)
1810 alignPanel.getSeqPanel().moveCursor(size, 0);
1814 groupAdjustment = size;
1817 else if (!ssc.getGapsInsertedBegin() && !right)
1819 if (viewport.cursorMode)
1821 alignPanel.getSeqPanel().moveCursor(-size, 0);
1825 groupAdjustment = -size;
1829 if (groupAdjustment != 0)
1831 viewport.getSelectionGroup().setStartRes(
1832 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1833 viewport.getSelectionGroup().setEndRes(
1834 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1838 * just extend the last slide command if compatible; but not if in
1839 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1841 boolean appendHistoryItem = false;
1842 Deque<CommandI> historyList = viewport.getHistoryList();
1843 boolean inSplitFrame = getSplitViewContainer() != null;
1844 if (!inSplitFrame && historyList != null && historyList.size() > 0
1845 && historyList.peek() instanceof SlideSequencesCommand)
1847 appendHistoryItem = ssc
1848 .appendSlideCommand((SlideSequencesCommand) historyList
1852 if (!appendHistoryItem)
1854 addHistoryItem(ssc);
1867 protected void copy_actionPerformed(ActionEvent e)
1870 if (viewport.getSelectionGroup() == null)
1874 // TODO: preserve the ordering of displayed alignment annotation in any
1875 // internal paste (particularly sequence associated annotation)
1876 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1877 String[] omitHidden = null;
1879 if (viewport.hasHiddenColumns())
1881 omitHidden = viewport.getViewAsString(true);
1884 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1887 StringSelection ss = new StringSelection(output);
1891 jalview.gui.Desktop.internalCopy = true;
1892 // Its really worth setting the clipboard contents
1893 // to empty before setting the large StringSelection!!
1894 Toolkit.getDefaultToolkit().getSystemClipboard()
1895 .setContents(new StringSelection(""), null);
1897 Toolkit.getDefaultToolkit().getSystemClipboard()
1898 .setContents(ss, Desktop.instance);
1899 } catch (OutOfMemoryError er)
1901 new OOMWarning("copying region", er);
1905 ArrayList<int[]> hiddenColumns = null;
1906 if (viewport.hasHiddenColumns())
1908 hiddenColumns = new ArrayList<int[]>();
1909 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1910 .getSelectionGroup().getEndRes();
1911 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1913 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1915 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1916 region[1] - hiddenOffset });
1921 Desktop.jalviewClipboard = new Object[] { seqs,
1922 viewport.getAlignment().getDataset(), hiddenColumns };
1923 statusBar.setText(MessageManager.formatMessage(
1924 "label.copied_sequences_to_clipboard", new Object[] { Integer
1925 .valueOf(seqs.length).toString() }));
1935 protected void pasteNew_actionPerformed(ActionEvent e)
1947 protected void pasteThis_actionPerformed(ActionEvent e)
1953 * Paste contents of Jalview clipboard
1955 * @param newAlignment
1956 * true to paste to a new alignment, otherwise add to this.
1958 void paste(boolean newAlignment)
1960 boolean externalPaste = true;
1963 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1964 Transferable contents = c.getContents(this);
1966 if (contents == null)
1974 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1975 if (str.length() < 1)
1980 format = new IdentifyFile().Identify(str, "Paste");
1982 } catch (OutOfMemoryError er)
1984 new OOMWarning("Out of memory pasting sequences!!", er);
1988 SequenceI[] sequences;
1989 boolean annotationAdded = false;
1990 AlignmentI alignment = null;
1992 if (Desktop.jalviewClipboard != null)
1994 // The clipboard was filled from within Jalview, we must use the
1996 // And dataset from the copied alignment
1997 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1998 // be doubly sure that we create *new* sequence objects.
1999 sequences = new SequenceI[newseq.length];
2000 for (int i = 0; i < newseq.length; i++)
2002 sequences[i] = new Sequence(newseq[i]);
2004 alignment = new Alignment(sequences);
2005 externalPaste = false;
2009 // parse the clipboard as an alignment.
2010 alignment = new FormatAdapter().readFile(str, "Paste", format);
2011 sequences = alignment.getSequencesArray();
2015 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2021 if (Desktop.jalviewClipboard != null)
2023 // dataset is inherited
2024 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2028 // new dataset is constructed
2029 alignment.setDataset(null);
2031 alwidth = alignment.getWidth() + 1;
2035 AlignmentI pastedal = alignment; // preserve pasted alignment object
2036 // Add pasted sequences and dataset into existing alignment.
2037 alignment = viewport.getAlignment();
2038 alwidth = alignment.getWidth() + 1;
2039 // decide if we need to import sequences from an existing dataset
2040 boolean importDs = Desktop.jalviewClipboard != null
2041 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2042 // importDs==true instructs us to copy over new dataset sequences from
2043 // an existing alignment
2044 Vector newDs = (importDs) ? new Vector() : null; // used to create
2045 // minimum dataset set
2047 for (int i = 0; i < sequences.length; i++)
2051 newDs.addElement(null);
2053 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2055 if (importDs && ds != null)
2057 if (!newDs.contains(ds))
2059 newDs.setElementAt(ds, i);
2060 ds = new Sequence(ds);
2061 // update with new dataset sequence
2062 sequences[i].setDatasetSequence(ds);
2066 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2071 // copy and derive new dataset sequence
2072 sequences[i] = sequences[i].deriveSequence();
2073 alignment.getDataset().addSequence(
2074 sequences[i].getDatasetSequence());
2075 // TODO: avoid creation of duplicate dataset sequences with a
2076 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2078 alignment.addSequence(sequences[i]); // merges dataset
2082 newDs.clear(); // tidy up
2084 if (alignment.getAlignmentAnnotation() != null)
2086 for (AlignmentAnnotation alan : alignment
2087 .getAlignmentAnnotation())
2089 if (alan.graphGroup > fgroup)
2091 fgroup = alan.graphGroup;
2095 if (pastedal.getAlignmentAnnotation() != null)
2097 // Add any annotation attached to alignment.
2098 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2099 for (int i = 0; i < alann.length; i++)
2101 annotationAdded = true;
2102 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2104 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2105 if (newann.graphGroup > -1)
2107 if (newGraphGroups.size() <= newann.graphGroup
2108 || newGraphGroups.get(newann.graphGroup) == null)
2110 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2112 newGraphGroups.add(q, null);
2114 newGraphGroups.set(newann.graphGroup, new Integer(
2117 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2121 newann.padAnnotation(alwidth);
2122 alignment.addAnnotation(newann);
2132 addHistoryItem(new EditCommand(
2133 MessageManager.getString("label.add_sequences"),
2134 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2136 // Add any annotations attached to sequences
2137 for (int i = 0; i < sequences.length; i++)
2139 if (sequences[i].getAnnotation() != null)
2141 AlignmentAnnotation newann;
2142 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2144 annotationAdded = true;
2145 newann = sequences[i].getAnnotation()[a];
2146 newann.adjustForAlignment();
2147 newann.padAnnotation(alwidth);
2148 if (newann.graphGroup > -1)
2150 if (newann.graphGroup > -1)
2152 if (newGraphGroups.size() <= newann.graphGroup
2153 || newGraphGroups.get(newann.graphGroup) == null)
2155 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2157 newGraphGroups.add(q, null);
2159 newGraphGroups.set(newann.graphGroup, new Integer(
2162 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2166 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2171 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2178 // propagate alignment changed.
2179 viewport.setEndSeq(alignment.getHeight());
2180 if (annotationAdded)
2182 // Duplicate sequence annotation in all views.
2183 AlignmentI[] alview = this.getViewAlignments();
2184 for (int i = 0; i < sequences.length; i++)
2186 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2191 for (int avnum = 0; avnum < alview.length; avnum++)
2193 if (alview[avnum] != alignment)
2195 // duplicate in a view other than the one with input focus
2196 int avwidth = alview[avnum].getWidth() + 1;
2197 // this relies on sann being preserved after we
2198 // modify the sequence's annotation array for each duplication
2199 for (int a = 0; a < sann.length; a++)
2201 AlignmentAnnotation newann = new AlignmentAnnotation(
2203 sequences[i].addAlignmentAnnotation(newann);
2204 newann.padAnnotation(avwidth);
2205 alview[avnum].addAnnotation(newann); // annotation was
2206 // duplicated earlier
2207 // TODO JAL-1145 graphGroups are not updated for sequence
2208 // annotation added to several views. This may cause
2210 alview[avnum].setAnnotationIndex(newann, a);
2215 buildSortByAnnotationScoresMenu();
2217 viewport.firePropertyChange("alignment", null,
2218 alignment.getSequences());
2219 if (alignPanels != null)
2221 for (AlignmentPanel ap : alignPanels)
2223 ap.validateAnnotationDimensions(false);
2228 alignPanel.validateAnnotationDimensions(false);
2234 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2236 String newtitle = new String("Copied sequences");
2238 if (Desktop.jalviewClipboard != null
2239 && Desktop.jalviewClipboard[2] != null)
2241 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2242 for (int[] region : hc)
2244 af.viewport.hideColumns(region[0], region[1]);
2248 // >>>This is a fix for the moment, until a better solution is
2250 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2252 alignPanel.getSeqPanel().seqCanvas
2253 .getFeatureRenderer());
2255 // TODO: maintain provenance of an alignment, rather than just make the
2256 // title a concatenation of operations.
2259 if (title.startsWith("Copied sequences"))
2265 newtitle = newtitle.concat("- from " + title);
2270 newtitle = new String("Pasted sequences");
2273 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2278 } catch (Exception ex)
2280 ex.printStackTrace();
2281 System.out.println("Exception whilst pasting: " + ex);
2282 // could be anything being pasted in here
2288 protected void expand_newalign(ActionEvent e)
2292 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2293 .getAlignment(), -1);
2294 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2296 String newtitle = new String("Flanking alignment");
2298 if (Desktop.jalviewClipboard != null
2299 && Desktop.jalviewClipboard[2] != null)
2301 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2302 for (int region[] : hc)
2304 af.viewport.hideColumns(region[0], region[1]);
2308 // >>>This is a fix for the moment, until a better solution is
2310 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2312 alignPanel.getSeqPanel().seqCanvas
2313 .getFeatureRenderer());
2315 // TODO: maintain provenance of an alignment, rather than just make the
2316 // title a concatenation of operations.
2318 if (title.startsWith("Copied sequences"))
2324 newtitle = newtitle.concat("- from " + title);
2328 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2330 } catch (Exception ex)
2332 ex.printStackTrace();
2333 System.out.println("Exception whilst pasting: " + ex);
2334 // could be anything being pasted in here
2335 } catch (OutOfMemoryError oom)
2337 new OOMWarning("Viewing flanking region of alignment", oom);
2348 protected void cut_actionPerformed(ActionEvent e)
2350 copy_actionPerformed(null);
2351 delete_actionPerformed(null);
2361 protected void delete_actionPerformed(ActionEvent evt)
2364 SequenceGroup sg = viewport.getSelectionGroup();
2371 * If the cut affects all sequences, warn, remove highlighted columns
2373 if (sg.getSize() == viewport.getAlignment().getHeight())
2375 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2376 .getAlignment().getWidth()) ? true : false;
2377 if (isEntireAlignWidth)
2379 int confirm = JOptionPane.showConfirmDialog(this,
2380 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2381 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2382 JOptionPane.OK_CANCEL_OPTION);
2384 if (confirm == JOptionPane.CANCEL_OPTION
2385 || confirm == JOptionPane.CLOSED_OPTION)
2390 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2391 sg.getEndRes() + 1);
2393 SequenceI[] cut = sg.getSequences()
2394 .toArray(new SequenceI[sg.getSize()]);
2396 addHistoryItem(new EditCommand(
2397 MessageManager.getString("label.cut_sequences"), Action.CUT,
2398 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2399 viewport.getAlignment()));
2401 viewport.setSelectionGroup(null);
2402 viewport.sendSelection();
2403 viewport.getAlignment().deleteGroup(sg);
2405 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2407 if (viewport.getAlignment().getHeight() < 1)
2411 this.setClosed(true);
2412 } catch (Exception ex)
2425 protected void deleteGroups_actionPerformed(ActionEvent e)
2427 if (avc.deleteGroups())
2429 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2430 alignPanel.updateAnnotation();
2431 alignPanel.paintAlignment(true);
2442 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2444 SequenceGroup sg = new SequenceGroup();
2446 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2448 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2451 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2452 viewport.setSelectionGroup(sg);
2453 viewport.sendSelection();
2454 alignPanel.paintAlignment(true);
2455 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2465 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2467 if (viewport.cursorMode)
2469 alignPanel.getSeqPanel().keyboardNo1 = null;
2470 alignPanel.getSeqPanel().keyboardNo2 = null;
2472 viewport.setSelectionGroup(null);
2473 viewport.getColumnSelection().clear();
2474 viewport.setSelectionGroup(null);
2475 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2476 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2477 alignPanel.paintAlignment(true);
2478 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2479 viewport.sendSelection();
2489 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2491 SequenceGroup sg = viewport.getSelectionGroup();
2495 selectAllSequenceMenuItem_actionPerformed(null);
2500 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2502 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2505 alignPanel.paintAlignment(true);
2506 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2507 viewport.sendSelection();
2511 public void invertColSel_actionPerformed(ActionEvent e)
2513 viewport.invertColumnSelection();
2514 alignPanel.paintAlignment(true);
2515 viewport.sendSelection();
2525 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2527 trimAlignment(true);
2537 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2539 trimAlignment(false);
2542 void trimAlignment(boolean trimLeft)
2544 ColumnSelection colSel = viewport.getColumnSelection();
2547 if (colSel.size() > 0)
2551 column = colSel.getMin();
2555 column = colSel.getMax();
2559 if (viewport.getSelectionGroup() != null)
2561 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2562 viewport.getHiddenRepSequences());
2566 seqs = viewport.getAlignment().getSequencesArray();
2569 TrimRegionCommand trimRegion;
2572 trimRegion = new TrimRegionCommand("Remove Left",
2573 TrimRegionCommand.TRIM_LEFT, seqs, column,
2574 viewport.getAlignment(), viewport.getColumnSelection(),
2575 viewport.getSelectionGroup());
2576 viewport.setStartRes(0);
2580 trimRegion = new TrimRegionCommand("Remove Right",
2581 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2582 viewport.getAlignment(), viewport.getColumnSelection(),
2583 viewport.getSelectionGroup());
2586 statusBar.setText(MessageManager.formatMessage(
2587 "label.removed_columns",
2588 new String[] { Integer.valueOf(trimRegion.getSize())
2591 addHistoryItem(trimRegion);
2593 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2595 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2596 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2598 viewport.getAlignment().deleteGroup(sg);
2602 viewport.firePropertyChange("alignment", null, viewport
2603 .getAlignment().getSequences());
2614 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2616 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2619 if (viewport.getSelectionGroup() != null)
2621 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2622 viewport.getHiddenRepSequences());
2623 start = viewport.getSelectionGroup().getStartRes();
2624 end = viewport.getSelectionGroup().getEndRes();
2628 seqs = viewport.getAlignment().getSequencesArray();
2631 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2632 "Remove Gapped Columns", seqs, start, end,
2633 viewport.getAlignment());
2635 addHistoryItem(removeGapCols);
2637 statusBar.setText(MessageManager.formatMessage(
2638 "label.removed_empty_columns",
2639 new Object[] { Integer.valueOf(removeGapCols.getSize())
2642 // This is to maintain viewport position on first residue
2643 // of first sequence
2644 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2645 int startRes = seq.findPosition(viewport.startRes);
2646 // ShiftList shifts;
2647 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2648 // edit.alColumnChanges=shifts.getInverse();
2649 // if (viewport.hasHiddenColumns)
2650 // viewport.getColumnSelection().compensateForEdits(shifts);
2651 viewport.setStartRes(seq.findIndex(startRes) - 1);
2652 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2664 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2666 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2669 if (viewport.getSelectionGroup() != null)
2671 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2672 viewport.getHiddenRepSequences());
2673 start = viewport.getSelectionGroup().getStartRes();
2674 end = viewport.getSelectionGroup().getEndRes();
2678 seqs = viewport.getAlignment().getSequencesArray();
2681 // This is to maintain viewport position on first residue
2682 // of first sequence
2683 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2684 int startRes = seq.findPosition(viewport.startRes);
2686 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2687 viewport.getAlignment()));
2689 viewport.setStartRes(seq.findIndex(startRes) - 1);
2691 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2703 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2705 viewport.setPadGaps(padGapsMenuitem.isSelected());
2706 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2717 public void findMenuItem_actionPerformed(ActionEvent e)
2723 * Create a new view of the current alignment.
2726 public void newView_actionPerformed(ActionEvent e)
2728 newView(null, true);
2732 * Creates and shows a new view of the current alignment.
2735 * title of newly created view; if null, one will be generated
2736 * @param copyAnnotation
2737 * if true then duplicate all annnotation, groups and settings
2738 * @return new alignment panel, already displayed.
2740 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2743 * Create a new AlignmentPanel (with its own, new Viewport)
2745 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2747 if (!copyAnnotation)
2750 * remove all groups and annotation except for the automatic stuff
2752 newap.av.getAlignment().deleteAllGroups();
2753 newap.av.getAlignment().deleteAllAnnotations(false);
2756 newap.av.setGatherViewsHere(false);
2758 if (viewport.viewName == null)
2760 viewport.viewName = MessageManager
2761 .getString("label.view_name_original");
2765 * Views share the same edits undo and redo stacks
2767 newap.av.setHistoryList(viewport.getHistoryList());
2768 newap.av.setRedoList(viewport.getRedoList());
2771 * Views share the same mappings; need to deregister any new mappings
2772 * created by copyAlignPanel, and register the new reference to the shared
2775 newap.av.replaceMappings(viewport.getAlignment());
2777 newap.av.viewName = getNewViewName(viewTitle);
2779 addAlignmentPanel(newap, true);
2780 newap.alignmentChanged();
2782 if (alignPanels.size() == 2)
2784 viewport.setGatherViewsHere(true);
2786 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2791 * Make a new name for the view, ensuring it is unique within the current
2792 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2793 * these now use viewId. Unique view names are still desirable for usability.)
2798 protected String getNewViewName(String viewTitle)
2800 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2801 boolean addFirstIndex = false;
2802 if (viewTitle == null || viewTitle.trim().length() == 0)
2804 viewTitle = MessageManager.getString("action.view");
2805 addFirstIndex = true;
2809 index = 1;// we count from 1 if given a specific name
2811 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2813 List<Component> comps = PaintRefresher.components.get(viewport
2814 .getSequenceSetId());
2816 List<String> existingNames = getExistingViewNames(comps);
2818 while (existingNames.contains(newViewName))
2820 newViewName = viewTitle + " " + (++index);
2826 * Returns a list of distinct view names found in the given list of
2827 * components. View names are held on the viewport of an AlignmentPanel.
2832 protected List<String> getExistingViewNames(List<Component> comps)
2834 List<String> existingNames = new ArrayList<String>();
2835 for (Component comp : comps)
2837 if (comp instanceof AlignmentPanel)
2839 AlignmentPanel ap = (AlignmentPanel) comp;
2840 if (!existingNames.contains(ap.av.viewName))
2842 existingNames.add(ap.av.viewName);
2846 return existingNames;
2850 * Explode tabbed views into separate windows.
2853 public void expandViews_actionPerformed(ActionEvent e)
2855 Desktop.instance.explodeViews(this);
2859 * Gather views in separate windows back into a tabbed presentation.
2862 public void gatherViews_actionPerformed(ActionEvent e)
2864 Desktop.instance.gatherViews(this);
2874 public void font_actionPerformed(ActionEvent e)
2876 new FontChooser(alignPanel);
2886 protected void seqLimit_actionPerformed(ActionEvent e)
2888 viewport.setShowJVSuffix(seqLimits.isSelected());
2890 alignPanel.getIdPanel().getIdCanvas()
2891 .setPreferredSize(alignPanel.calculateIdWidth());
2892 alignPanel.paintAlignment(true);
2896 public void idRightAlign_actionPerformed(ActionEvent e)
2898 viewport.setRightAlignIds(idRightAlign.isSelected());
2899 alignPanel.paintAlignment(true);
2903 public void centreColumnLabels_actionPerformed(ActionEvent e)
2905 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2906 alignPanel.paintAlignment(true);
2912 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2915 protected void followHighlight_actionPerformed()
2918 * Set the 'follow' flag on the Viewport (and scroll to position if now
2921 final boolean state = this.followHighlightMenuItem.getState();
2922 viewport.setFollowHighlight(state);
2925 alignPanel.scrollToPosition(
2926 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2937 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2939 viewport.setColourText(colourTextMenuItem.isSelected());
2940 alignPanel.paintAlignment(true);
2950 public void wrapMenuItem_actionPerformed(ActionEvent e)
2952 scaleAbove.setVisible(wrapMenuItem.isSelected());
2953 scaleLeft.setVisible(wrapMenuItem.isSelected());
2954 scaleRight.setVisible(wrapMenuItem.isSelected());
2955 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2956 alignPanel.updateLayout();
2960 public void showAllSeqs_actionPerformed(ActionEvent e)
2962 viewport.showAllHiddenSeqs();
2966 public void showAllColumns_actionPerformed(ActionEvent e)
2968 viewport.showAllHiddenColumns();
2973 public void hideSelSequences_actionPerformed(ActionEvent e)
2975 viewport.hideAllSelectedSeqs();
2976 // alignPanel.paintAlignment(true);
2980 * called by key handler and the hide all/show all menu items
2985 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2988 boolean hide = false;
2989 SequenceGroup sg = viewport.getSelectionGroup();
2990 if (!toggleSeqs && !toggleCols)
2992 // Hide everything by the current selection - this is a hack - we do the
2993 // invert and then hide
2994 // first check that there will be visible columns after the invert.
2995 if ((viewport.getColumnSelection() != null
2996 && viewport.getColumnSelection().getSelected() != null && viewport
2997 .getColumnSelection().getSelected().size() > 0)
2998 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3001 // now invert the sequence set, if required - empty selection implies
3002 // that no hiding is required.
3005 invertSequenceMenuItem_actionPerformed(null);
3006 sg = viewport.getSelectionGroup();
3010 viewport.expandColSelection(sg, true);
3011 // finally invert the column selection and get the new sequence
3013 invertColSel_actionPerformed(null);
3020 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3022 hideSelSequences_actionPerformed(null);
3025 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3028 showAllSeqs_actionPerformed(null);
3034 if (viewport.getColumnSelection().getSelected().size() > 0)
3036 hideSelColumns_actionPerformed(null);
3039 viewport.setSelectionGroup(sg);
3044 showAllColumns_actionPerformed(null);
3053 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3054 * event.ActionEvent)
3057 public void hideAllButSelection_actionPerformed(ActionEvent e)
3059 toggleHiddenRegions(false, false);
3066 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3070 public void hideAllSelection_actionPerformed(ActionEvent e)
3072 SequenceGroup sg = viewport.getSelectionGroup();
3073 viewport.expandColSelection(sg, false);
3074 viewport.hideAllSelectedSeqs();
3075 viewport.hideSelectedColumns();
3076 alignPanel.paintAlignment(true);
3083 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3087 public void showAllhidden_actionPerformed(ActionEvent e)
3089 viewport.showAllHiddenColumns();
3090 viewport.showAllHiddenSeqs();
3091 alignPanel.paintAlignment(true);
3095 public void hideSelColumns_actionPerformed(ActionEvent e)
3097 viewport.hideSelectedColumns();
3098 alignPanel.paintAlignment(true);
3102 public void hiddenMarkers_actionPerformed(ActionEvent e)
3104 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3115 protected void scaleAbove_actionPerformed(ActionEvent e)
3117 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3118 alignPanel.paintAlignment(true);
3128 protected void scaleLeft_actionPerformed(ActionEvent e)
3130 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3131 alignPanel.paintAlignment(true);
3141 protected void scaleRight_actionPerformed(ActionEvent e)
3143 viewport.setScaleRightWrapped(scaleRight.isSelected());
3144 alignPanel.paintAlignment(true);
3154 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3156 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3157 alignPanel.paintAlignment(true);
3167 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3169 viewport.setShowText(viewTextMenuItem.isSelected());
3170 alignPanel.paintAlignment(true);
3180 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3182 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3183 alignPanel.paintAlignment(true);
3186 public FeatureSettings featureSettings;
3189 public FeatureSettingsControllerI getFeatureSettingsUI()
3191 return featureSettings;
3195 public void featureSettings_actionPerformed(ActionEvent e)
3197 if (featureSettings != null)
3199 featureSettings.close();
3200 featureSettings = null;
3202 if (!showSeqFeatures.isSelected())
3204 // make sure features are actually displayed
3205 showSeqFeatures.setSelected(true);
3206 showSeqFeatures_actionPerformed(null);
3208 featureSettings = new FeatureSettings(this);
3212 * Set or clear 'Show Sequence Features'
3218 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3220 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3221 alignPanel.paintAlignment(true);
3222 if (alignPanel.getOverviewPanel() != null)
3224 alignPanel.getOverviewPanel().updateOverviewImage();
3229 * Set or clear 'Show Sequence Features'
3235 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3237 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3239 if (viewport.isShowSequenceFeaturesHeight())
3241 // ensure we're actually displaying features
3242 viewport.setShowSequenceFeatures(true);
3243 showSeqFeatures.setSelected(true);
3245 alignPanel.paintAlignment(true);
3246 if (alignPanel.getOverviewPanel() != null)
3248 alignPanel.getOverviewPanel().updateOverviewImage();
3253 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3254 * the annotations panel as a whole.
3256 * The options to show/hide all annotations should be enabled when the panel
3257 * is shown, and disabled when the panel is hidden.
3262 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3264 final boolean setVisible = annotationPanelMenuItem.isSelected();
3265 viewport.setShowAnnotation(setVisible);
3266 this.showAllSeqAnnotations.setEnabled(setVisible);
3267 this.hideAllSeqAnnotations.setEnabled(setVisible);
3268 this.showAllAlAnnotations.setEnabled(setVisible);
3269 this.hideAllAlAnnotations.setEnabled(setVisible);
3270 alignPanel.updateLayout();
3274 public void alignmentProperties()
3276 JEditorPane editPane = new JEditorPane("text/html", "");
3277 editPane.setEditable(false);
3278 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3280 editPane.setText(MessageManager.formatMessage("label.html_content",
3281 new Object[] { contents.toString() }));
3282 JInternalFrame frame = new JInternalFrame();
3283 frame.getContentPane().add(new JScrollPane(editPane));
3285 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3286 "label.alignment_properties", new Object[] { getTitle() }),
3297 public void overviewMenuItem_actionPerformed(ActionEvent e)
3299 if (alignPanel.overviewPanel != null)
3304 JInternalFrame frame = new JInternalFrame();
3305 OverviewPanel overview = new OverviewPanel(alignPanel);
3306 frame.setContentPane(overview);
3307 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3308 "label.overview_params", new Object[] { this.getTitle() }),
3309 frame.getWidth(), frame.getHeight());
3311 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3312 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3315 public void internalFrameClosed(
3316 javax.swing.event.InternalFrameEvent evt)
3318 alignPanel.setOverviewPanel(null);
3322 alignPanel.setOverviewPanel(overview);
3326 public void textColour_actionPerformed(ActionEvent e)
3328 new TextColourChooser().chooseColour(alignPanel, null);
3338 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3350 public void clustalColour_actionPerformed(ActionEvent e)
3352 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3353 viewport.getHiddenRepSequences()));
3363 public void zappoColour_actionPerformed(ActionEvent e)
3365 changeColour(new ZappoColourScheme());
3375 public void taylorColour_actionPerformed(ActionEvent e)
3377 changeColour(new TaylorColourScheme());
3387 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3389 changeColour(new HydrophobicColourScheme());
3399 public void helixColour_actionPerformed(ActionEvent e)
3401 changeColour(new HelixColourScheme());
3411 public void strandColour_actionPerformed(ActionEvent e)
3413 changeColour(new StrandColourScheme());
3423 public void turnColour_actionPerformed(ActionEvent e)
3425 changeColour(new TurnColourScheme());
3435 public void buriedColour_actionPerformed(ActionEvent e)
3437 changeColour(new BuriedColourScheme());
3447 public void nucleotideColour_actionPerformed(ActionEvent e)
3449 changeColour(new NucleotideColourScheme());
3453 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3455 changeColour(new PurinePyrimidineColourScheme());
3459 * public void covariationColour_actionPerformed(ActionEvent e) {
3461 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3465 public void annotationColour_actionPerformed(ActionEvent e)
3467 new AnnotationColourChooser(viewport, alignPanel);
3471 public void annotationColumn_actionPerformed(ActionEvent e)
3473 new AnnotationColumnChooser(viewport, alignPanel);
3477 public void rnahelicesColour_actionPerformed(ActionEvent e)
3479 new RNAHelicesColourChooser(viewport, alignPanel);
3489 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3491 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3500 public void changeColour(ColourSchemeI cs)
3502 // TODO: pull up to controller method
3506 // Make sure viewport is up to date w.r.t. any sliders
3507 if (viewport.getAbovePIDThreshold())
3509 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3511 viewport.setThreshold(threshold);
3514 if (viewport.getConservationSelected())
3516 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3519 if (cs instanceof TCoffeeColourScheme)
3521 tcoffeeColour.setEnabled(true);
3522 tcoffeeColour.setSelected(true);
3526 viewport.setGlobalColourScheme(cs);
3528 alignPanel.paintAlignment(true);
3538 protected void modifyPID_actionPerformed(ActionEvent e)
3540 if (viewport.getAbovePIDThreshold()
3541 && viewport.getGlobalColourScheme() != null)
3543 SliderPanel.setPIDSliderSource(alignPanel,
3544 viewport.getGlobalColourScheme(), "Background");
3545 SliderPanel.showPIDSlider();
3556 protected void modifyConservation_actionPerformed(ActionEvent e)
3558 if (viewport.getConservationSelected()
3559 && viewport.getGlobalColourScheme() != null)
3561 SliderPanel.setConservationSlider(alignPanel,
3562 viewport.getGlobalColourScheme(), "Background");
3563 SliderPanel.showConservationSlider();
3574 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3576 viewport.setConservationSelected(conservationMenuItem.isSelected());
3578 viewport.setAbovePIDThreshold(false);
3579 abovePIDThreshold.setSelected(false);
3581 changeColour(viewport.getGlobalColourScheme());
3583 modifyConservation_actionPerformed(null);
3593 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3595 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3597 conservationMenuItem.setSelected(false);
3598 viewport.setConservationSelected(false);
3600 changeColour(viewport.getGlobalColourScheme());
3602 modifyPID_actionPerformed(null);
3612 public void userDefinedColour_actionPerformed(ActionEvent e)
3614 if (e.getActionCommand().equals(
3615 MessageManager.getString("action.user_defined")))
3617 new UserDefinedColours(alignPanel, null);
3621 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3622 .getUserColourSchemes().get(e.getActionCommand());
3628 public void updateUserColourMenu()
3631 Component[] menuItems = colourMenu.getMenuComponents();
3632 int iSize = menuItems.length;
3633 for (int i = 0; i < iSize; i++)
3635 if (menuItems[i].getName() != null
3636 && menuItems[i].getName().equals("USER_DEFINED"))
3638 colourMenu.remove(menuItems[i]);
3642 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3644 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3645 .getUserColourSchemes().keys();
3647 while (userColours.hasMoreElements())
3649 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3650 userColours.nextElement().toString());
3651 radioItem.setName("USER_DEFINED");
3652 radioItem.addMouseListener(new MouseAdapter()
3655 public void mousePressed(MouseEvent evt)
3657 if (evt.isControlDown()
3658 || SwingUtilities.isRightMouseButton(evt))
3660 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3662 int option = JOptionPane.showInternalConfirmDialog(
3663 jalview.gui.Desktop.desktop,
3665 .getString("label.remove_from_default_list"),
3667 .getString("label.remove_user_defined_colour"),
3668 JOptionPane.YES_NO_OPTION);
3669 if (option == JOptionPane.YES_OPTION)
3671 jalview.gui.UserDefinedColours
3672 .removeColourFromDefaults(radioItem.getText());
3673 colourMenu.remove(radioItem);
3677 radioItem.addActionListener(new ActionListener()
3680 public void actionPerformed(ActionEvent evt)
3682 userDefinedColour_actionPerformed(evt);
3689 radioItem.addActionListener(new ActionListener()
3692 public void actionPerformed(ActionEvent evt)
3694 userDefinedColour_actionPerformed(evt);
3698 colourMenu.insert(radioItem, 15);
3699 colours.add(radioItem);
3711 public void PIDColour_actionPerformed(ActionEvent e)
3713 changeColour(new PIDColourScheme());
3723 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3725 changeColour(new Blosum62ColourScheme());
3735 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3737 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3738 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3739 .getAlignment().getSequenceAt(0), null);
3740 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3741 viewport.getAlignment()));
3742 alignPanel.paintAlignment(true);
3752 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3754 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3755 AlignmentSorter.sortByID(viewport.getAlignment());
3756 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3757 viewport.getAlignment()));
3758 alignPanel.paintAlignment(true);
3768 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3770 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3771 AlignmentSorter.sortByLength(viewport.getAlignment());
3772 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3773 viewport.getAlignment()));
3774 alignPanel.paintAlignment(true);
3784 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3786 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3787 AlignmentSorter.sortByGroup(viewport.getAlignment());
3788 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3789 viewport.getAlignment()));
3791 alignPanel.paintAlignment(true);
3801 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3803 new RedundancyPanel(alignPanel, this);
3813 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3815 if ((viewport.getSelectionGroup() == null)
3816 || (viewport.getSelectionGroup().getSize() < 2))
3818 JOptionPane.showInternalMessageDialog(this, MessageManager
3819 .getString("label.you_must_select_least_two_sequences"),
3820 MessageManager.getString("label.invalid_selection"),
3821 JOptionPane.WARNING_MESSAGE);
3825 JInternalFrame frame = new JInternalFrame();
3826 frame.setContentPane(new PairwiseAlignPanel(viewport));
3827 Desktop.addInternalFrame(frame,
3828 MessageManager.getString("action.pairwise_alignment"), 600,
3840 public void PCAMenuItem_actionPerformed(ActionEvent e)
3842 if (((viewport.getSelectionGroup() != null)
3843 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3844 .getSelectionGroup().getSize() > 0))
3845 || (viewport.getAlignment().getHeight() < 4))
3848 .showInternalMessageDialog(
3851 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3853 .getString("label.sequence_selection_insufficient"),
3854 JOptionPane.WARNING_MESSAGE);
3859 new PCAPanel(alignPanel);
3863 public void autoCalculate_actionPerformed(ActionEvent e)
3865 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3866 if (viewport.autoCalculateConsensus)
3868 viewport.firePropertyChange("alignment", null, viewport
3869 .getAlignment().getSequences());
3874 public void sortByTreeOption_actionPerformed(ActionEvent e)
3876 viewport.sortByTree = sortByTree.isSelected();
3880 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3882 viewport.followSelection = listenToViewSelections.isSelected();
3892 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3894 newTreePanel("AV", "PID", "Average distance tree using PID");
3904 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3906 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3916 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3918 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3928 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3930 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3943 void newTreePanel(String type, String pwType, String title)
3947 if (viewport.getSelectionGroup() != null
3948 && viewport.getSelectionGroup().getSize() > 0)
3950 if (viewport.getSelectionGroup().getSize() < 3)
3956 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3958 .getString("label.not_enough_sequences"),
3959 JOptionPane.WARNING_MESSAGE);
3963 SequenceGroup sg = viewport.getSelectionGroup();
3965 /* Decide if the selection is a column region */
3966 for (SequenceI _s : sg.getSequences())
3968 if (_s.getLength() < sg.getEndRes())
3974 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3976 .getString("label.sequences_selection_not_aligned"),
3977 JOptionPane.WARNING_MESSAGE);
3983 title = title + " on region";
3984 tp = new TreePanel(alignPanel, type, pwType);
3988 // are the visible sequences aligned?
3989 if (!viewport.getAlignment().isAligned(false))
3995 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3997 .getString("label.sequences_not_aligned"),
3998 JOptionPane.WARNING_MESSAGE);
4003 if (viewport.getAlignment().getHeight() < 2)
4008 tp = new TreePanel(alignPanel, type, pwType);
4013 if (viewport.viewName != null)
4015 title += viewport.viewName + " of ";
4018 title += this.title;
4020 Desktop.addInternalFrame(tp, title, 600, 500);
4031 public void addSortByOrderMenuItem(String title,
4032 final AlignmentOrder order)
4034 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4035 "action.by_title_param", new Object[] { title }));
4037 item.addActionListener(new java.awt.event.ActionListener()
4040 public void actionPerformed(ActionEvent e)
4042 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4044 // TODO: JBPNote - have to map order entries to curent SequenceI
4046 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4048 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4051 alignPanel.paintAlignment(true);
4057 * Add a new sort by annotation score menu item
4060 * the menu to add the option to
4062 * the label used to retrieve scores for each sequence on the
4065 public void addSortByAnnotScoreMenuItem(JMenu sort,
4066 final String scoreLabel)
4068 final JMenuItem item = new JMenuItem(scoreLabel);
4070 item.addActionListener(new java.awt.event.ActionListener()
4073 public void actionPerformed(ActionEvent e)
4075 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4076 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4077 viewport.getAlignment());// ,viewport.getSelectionGroup());
4078 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4079 viewport.getAlignment()));
4080 alignPanel.paintAlignment(true);
4086 * last hash for alignment's annotation array - used to minimise cost of
4089 protected int _annotationScoreVectorHash;
4092 * search the alignment and rebuild the sort by annotation score submenu the
4093 * last alignment annotation vector hash is stored to minimize cost of
4094 * rebuilding in subsequence calls.
4098 public void buildSortByAnnotationScoresMenu()
4100 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4105 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4107 sortByAnnotScore.removeAll();
4108 // almost certainly a quicker way to do this - but we keep it simple
4109 Hashtable scoreSorts = new Hashtable();
4110 AlignmentAnnotation aann[];
4111 for (SequenceI sqa : viewport.getAlignment().getSequences())
4113 aann = sqa.getAnnotation();
4114 for (int i = 0; aann != null && i < aann.length; i++)
4116 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4118 scoreSorts.put(aann[i].label, aann[i].label);
4122 Enumeration labels = scoreSorts.keys();
4123 while (labels.hasMoreElements())
4125 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4126 (String) labels.nextElement());
4128 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4131 _annotationScoreVectorHash = viewport.getAlignment()
4132 .getAlignmentAnnotation().hashCode();
4137 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4138 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4139 * call. Listeners are added to remove the menu item when the treePanel is
4140 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4144 * Displayed tree window.
4146 * SortBy menu item title.
4149 public void buildTreeMenu()
4151 calculateTree.removeAll();
4152 // build the calculate menu
4154 for (final String type : new String[] { "NJ", "AV" })
4156 String treecalcnm = MessageManager.getString("label.tree_calc_"
4157 + type.toLowerCase());
4158 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4160 JMenuItem tm = new JMenuItem();
4161 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4162 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4164 String smn = MessageManager.getStringOrReturn(
4165 "label.score_model_", sm.getName());
4166 final String title = MessageManager.formatMessage(
4167 "label.treecalc_title", treecalcnm, smn);
4168 tm.setText(title);//
4169 tm.addActionListener(new java.awt.event.ActionListener()
4172 public void actionPerformed(ActionEvent e)
4174 newTreePanel(type, pwtype, title);
4177 calculateTree.add(tm);
4182 sortByTreeMenu.removeAll();
4184 List<Component> comps = PaintRefresher.components.get(viewport
4185 .getSequenceSetId());
4186 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4187 for (Component comp : comps)
4189 if (comp instanceof TreePanel)
4191 treePanels.add((TreePanel) comp);
4195 if (treePanels.size() < 1)
4197 sortByTreeMenu.setVisible(false);
4201 sortByTreeMenu.setVisible(true);
4203 for (final TreePanel tp : treePanels)
4205 final JMenuItem item = new JMenuItem(tp.getTitle());
4206 item.addActionListener(new java.awt.event.ActionListener()
4209 public void actionPerformed(ActionEvent e)
4211 tp.sortByTree_actionPerformed();
4212 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4217 sortByTreeMenu.add(item);
4221 public boolean sortBy(AlignmentOrder alorder, String undoname)
4223 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4224 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4225 if (undoname != null)
4227 addHistoryItem(new OrderCommand(undoname, oldOrder,
4228 viewport.getAlignment()));
4230 alignPanel.paintAlignment(true);
4235 * Work out whether the whole set of sequences or just the selected set will
4236 * be submitted for multiple alignment.
4239 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4241 // Now, check we have enough sequences
4242 AlignmentView msa = null;
4244 if ((viewport.getSelectionGroup() != null)
4245 && (viewport.getSelectionGroup().getSize() > 1))
4247 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4248 // some common interface!
4250 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4251 * SequenceI[sz = seqs.getSize(false)];
4253 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4254 * seqs.getSequenceAt(i); }
4256 msa = viewport.getAlignmentView(true);
4258 else if (viewport.getSelectionGroup() != null
4259 && viewport.getSelectionGroup().getSize() == 1)
4261 int option = JOptionPane.showConfirmDialog(this,
4262 MessageManager.getString("warn.oneseq_msainput_selection"),
4263 MessageManager.getString("label.invalid_selection"),
4264 JOptionPane.OK_CANCEL_OPTION);
4265 if (option == JOptionPane.OK_OPTION)
4267 msa = viewport.getAlignmentView(false);
4272 msa = viewport.getAlignmentView(false);
4278 * Decides what is submitted to a secondary structure prediction service: the
4279 * first sequence in the alignment, or in the current selection, or, if the
4280 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4281 * region or the whole alignment. (where the first sequence in the set is the
4282 * one that the prediction will be for).
4284 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4286 AlignmentView seqs = null;
4288 if ((viewport.getSelectionGroup() != null)
4289 && (viewport.getSelectionGroup().getSize() > 0))
4291 seqs = viewport.getAlignmentView(true);
4295 seqs = viewport.getAlignmentView(false);
4297 // limit sequences - JBPNote in future - could spawn multiple prediction
4299 // TODO: viewport.getAlignment().isAligned is a global state - the local
4300 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4301 if (!viewport.getAlignment().isAligned(false))
4303 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4304 // TODO: if seqs.getSequences().length>1 then should really have warned
4318 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4320 // Pick the tree file
4321 JalviewFileChooser chooser = new JalviewFileChooser(
4322 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4323 chooser.setFileView(new JalviewFileView());
4324 chooser.setDialogTitle(MessageManager
4325 .getString("label.select_newick_like_tree_file"));
4326 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4328 int value = chooser.showOpenDialog(null);
4330 if (value == JalviewFileChooser.APPROVE_OPTION)
4332 String choice = chooser.getSelectedFile().getPath();
4333 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4334 jalview.io.NewickFile fin = null;
4337 fin = new jalview.io.NewickFile(choice, "File");
4338 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4339 } catch (Exception ex)
4346 .getString("label.problem_reading_tree_file"),
4347 JOptionPane.WARNING_MESSAGE);
4348 ex.printStackTrace();
4350 if (fin != null && fin.hasWarningMessage())
4352 JOptionPane.showMessageDialog(Desktop.desktop, fin
4353 .getWarningMessage(), MessageManager
4354 .getString("label.possible_problem_with_tree_file"),
4355 JOptionPane.WARNING_MESSAGE);
4361 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4363 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4366 public TreePanel ShowNewickTree(NewickFile nf, String title)
4368 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4371 public TreePanel ShowNewickTree(NewickFile nf, String title,
4372 AlignmentView input)
4374 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4377 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4378 int h, int x, int y)
4380 return ShowNewickTree(nf, title, null, w, h, x, y);
4384 * Add a treeviewer for the tree extracted from a newick file object to the
4385 * current alignment view
4392 * Associated alignment input data (or null)
4401 * @return TreePanel handle
4403 public TreePanel ShowNewickTree(NewickFile nf, String title,
4404 AlignmentView input, int w, int h, int x, int y)
4406 TreePanel tp = null;
4412 if (nf.getTree() != null)
4414 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4420 tp.setLocation(x, y);
4423 Desktop.addInternalFrame(tp, title, w, h);
4425 } catch (Exception ex)
4427 ex.printStackTrace();
4433 private boolean buildingMenu = false;
4436 * Generates menu items and listener event actions for web service clients
4439 public void BuildWebServiceMenu()
4441 while (buildingMenu)
4445 System.err.println("Waiting for building menu to finish.");
4447 } catch (Exception e)
4451 final AlignFrame me = this;
4452 buildingMenu = true;
4453 new Thread(new Runnable()
4458 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4461 // System.err.println("Building ws menu again "
4462 // + Thread.currentThread());
4463 // TODO: add support for context dependent disabling of services based
4465 // alignment and current selection
4466 // TODO: add additional serviceHandle parameter to specify abstract
4468 // class independently of AbstractName
4469 // TODO: add in rediscovery GUI function to restart discoverer
4470 // TODO: group services by location as well as function and/or
4472 // object broker mechanism.
4473 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4474 final IProgressIndicator af = me;
4475 final JMenu msawsmenu = new JMenu("Alignment");
4476 final JMenu secstrmenu = new JMenu(
4477 "Secondary Structure Prediction");
4478 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4479 final JMenu analymenu = new JMenu("Analysis");
4480 final JMenu dismenu = new JMenu("Protein Disorder");
4481 // final JMenu msawsmenu = new
4482 // JMenu(MessageManager.getString("label.alignment"));
4483 // final JMenu secstrmenu = new
4484 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4485 // final JMenu seqsrchmenu = new
4486 // JMenu(MessageManager.getString("label.sequence_database_search"));
4487 // final JMenu analymenu = new
4488 // JMenu(MessageManager.getString("label.analysis"));
4489 // final JMenu dismenu = new
4490 // JMenu(MessageManager.getString("label.protein_disorder"));
4491 // JAL-940 - only show secondary structure prediction services from
4492 // the legacy server
4493 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4495 Discoverer.services != null && (Discoverer.services.size() > 0))
4497 // TODO: refactor to allow list of AbstractName/Handler bindings to
4499 // stored or retrieved from elsewhere
4500 // No MSAWS used any more:
4501 // Vector msaws = null; // (Vector)
4502 // Discoverer.services.get("MsaWS");
4503 Vector secstrpr = (Vector) Discoverer.services
4505 if (secstrpr != null)
4507 // Add any secondary structure prediction services
4508 for (int i = 0, j = secstrpr.size(); i < j; i++)
4510 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4512 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4513 .getServiceClient(sh);
4514 int p = secstrmenu.getItemCount();
4515 impl.attachWSMenuEntry(secstrmenu, me);
4516 int q = secstrmenu.getItemCount();
4517 for (int litm = p; litm < q; litm++)
4519 legacyItems.add(secstrmenu.getItem(litm));
4525 // Add all submenus in the order they should appear on the web
4527 wsmenu.add(msawsmenu);
4528 wsmenu.add(secstrmenu);
4529 wsmenu.add(dismenu);
4530 wsmenu.add(analymenu);
4531 // No search services yet
4532 // wsmenu.add(seqsrchmenu);
4534 javax.swing.SwingUtilities.invokeLater(new Runnable()
4541 webService.removeAll();
4542 // first, add discovered services onto the webservices menu
4543 if (wsmenu.size() > 0)
4545 for (int i = 0, j = wsmenu.size(); i < j; i++)
4547 webService.add(wsmenu.get(i));
4552 webService.add(me.webServiceNoServices);
4554 // TODO: move into separate menu builder class.
4555 boolean new_sspred = false;
4556 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4558 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4559 if (jws2servs != null)
4561 if (jws2servs.hasServices())
4563 jws2servs.attachWSMenuEntry(webService, me);
4564 for (Jws2Instance sv : jws2servs.getServices())
4566 if (sv.description.toLowerCase().contains("jpred"))
4568 for (JMenuItem jmi : legacyItems)
4570 jmi.setVisible(false);
4576 if (jws2servs.isRunning())
4578 JMenuItem tm = new JMenuItem(
4579 "Still discovering JABA Services");
4580 tm.setEnabled(false);
4585 build_urlServiceMenu(me.webService);
4586 build_fetchdbmenu(webService);
4587 for (JMenu item : wsmenu)
4589 if (item.getItemCount() == 0)
4591 item.setEnabled(false);
4595 item.setEnabled(true);
4598 } catch (Exception e)
4601 .debug("Exception during web service menu building process.",
4606 } catch (Exception e)
4609 buildingMenu = false;
4616 * construct any groupURL type service menu entries.
4620 private void build_urlServiceMenu(JMenu webService)
4622 // TODO: remove this code when 2.7 is released
4623 // DEBUG - alignmentView
4625 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4626 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4628 * @Override public void actionPerformed(ActionEvent e) {
4629 * jalview.datamodel.AlignmentView
4630 * .testSelectionViews(af.viewport.getAlignment(),
4631 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4633 * }); webService.add(testAlView);
4635 // TODO: refactor to RestClient discoverer and merge menu entries for
4636 // rest-style services with other types of analysis/calculation service
4637 // SHmmr test client - still being implemented.
4638 // DEBUG - alignmentView
4640 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4643 client.attachWSMenuEntry(
4644 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4650 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4651 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4652 * getProperty("LAST_DIRECTORY"));
4654 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4655 * to Vamsas file"); chooser.setToolTipText("Export");
4657 * int value = chooser.showSaveDialog(this);
4659 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4660 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4661 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4662 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4665 * prototype of an automatically enabled/disabled analysis function
4668 protected void setShowProductsEnabled()
4670 SequenceI[] selection = viewport.getSequenceSelection();
4671 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4672 viewport.getAlignment().getDataset()))
4674 showProducts.setEnabled(true);
4679 showProducts.setEnabled(false);
4684 * search selection for sequence xRef products and build the show products
4689 * @return true if showProducts menu should be enabled.
4691 public boolean canShowProducts(SequenceI[] selection,
4692 boolean isRegionSelection, Alignment dataset)
4694 boolean showp = false;
4697 showProducts.removeAll();
4698 final boolean dna = viewport.getAlignment().isNucleotide();
4699 final Alignment ds = dataset;
4700 String[] ptypes = (selection == null || selection.length == 0) ? null
4701 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4703 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4704 // selection, dataset, true);
4705 final SequenceI[] sel = selection;
4706 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4709 final boolean isRegSel = isRegionSelection;
4710 final AlignFrame af = this;
4711 final String source = ptypes[t];
4712 JMenuItem xtype = new JMenuItem(ptypes[t]);
4713 xtype.addActionListener(new ActionListener()
4717 public void actionPerformed(ActionEvent e)
4719 // TODO: new thread for this call with vis-delay
4720 af.showProductsFor(af.viewport.getSequenceSelection(),
4721 isRegSel, dna, source);
4725 showProducts.add(xtype);
4727 showProducts.setVisible(showp);
4728 showProducts.setEnabled(showp);
4729 } catch (Exception e)
4731 jalview.bin.Cache.log
4732 .warn("canTranslate threw an exception - please report to help@jalview.org",
4739 protected void showProductsFor(final SequenceI[] sel,
4740 final boolean isRegSel, final boolean dna, final String source)
4742 Runnable foo = new Runnable()
4748 final long sttime = System.currentTimeMillis();
4749 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4750 "status.searching_for_sequences_from",
4751 new Object[] { source }), sttime);
4754 // update our local dataset reference
4755 Alignment ds = AlignFrame.this.getViewport().getAlignment()
4757 Alignment prods = CrossRef
4758 .findXrefSequences(sel, dna, source, ds);
4761 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4762 for (int s = 0; s < sprods.length; s++)
4764 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4765 if (ds.getSequences() == null
4766 || !ds.getSequences().contains(
4767 sprods[s].getDatasetSequence()))
4769 ds.addSequence(sprods[s].getDatasetSequence());
4771 sprods[s].updatePDBIds();
4773 Alignment al = new Alignment(sprods);
4777 * Copy dna-to-protein mappings to new alignment
4779 // TODO 1: no mappings are set up for EMBL product
4780 // TODO 2: if they were, should add them to protein alignment, not
4782 Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4783 for (AlignedCodonFrame acf : cf)
4785 al.addCodonFrame(acf);
4787 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4789 String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4790 + " for " + ((isRegSel) ? "selected region of " : "")
4792 naf.setTitle(newtitle);
4794 // temporary flag until SplitFrame is released
4795 boolean asSplitFrame = Cache.getDefault(
4796 Preferences.ENABLE_SPLIT_FRAME, true);
4800 * Make a copy of this alignment (sharing the same dataset
4801 * sequences). If we are DNA, drop introns and update mappings
4803 AlignmentI copyAlignment = null;
4804 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4805 .getSequenceSelection();
4808 copyAlignment = AlignmentUtils.makeExonAlignment(
4809 sequenceSelection, cf);
4810 al.getCodonFrames().clear();
4811 al.getCodonFrames().addAll(cf);
4812 final StructureSelectionManager ssm = StructureSelectionManager
4813 .getStructureSelectionManager(Desktop.instance);
4814 ssm.registerMappings(cf);
4818 copyAlignment = new Alignment(new Alignment(
4819 sequenceSelection));
4821 AlignFrame copyThis = new AlignFrame(copyAlignment,
4822 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4823 copyThis.setTitle(AlignFrame.this.getTitle());
4824 // SplitFrame with dna above, protein below
4825 SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4826 dna ? naf : copyThis);
4827 naf.setVisible(true);
4828 copyThis.setVisible(true);
4829 String linkedTitle = MessageManager
4830 .getString("label.linked_view_title");
4831 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4835 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4841 System.err.println("No Sequences generated for xRef type "
4844 } catch (Exception e)
4846 jalview.bin.Cache.log.error(
4847 "Exception when finding crossreferences", e);
4848 } catch (OutOfMemoryError e)
4850 new OOMWarning("whilst fetching crossreferences", e);
4853 jalview.bin.Cache.log.error("Error when finding crossreferences",
4856 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4857 "status.finished_searching_for_sequences_from",
4858 new Object[] { source }), sttime);
4862 Thread frunner = new Thread(foo);
4866 public boolean canShowTranslationProducts(SequenceI[] selection,
4867 AlignmentI alignment)
4872 return (jalview.analysis.Dna.canTranslate(selection,
4873 viewport.getViewAsVisibleContigs(true)));
4874 } catch (Exception e)
4876 jalview.bin.Cache.log
4877 .warn("canTranslate threw an exception - please report to help@jalview.org",
4884 * Construct and display a new frame containing the translation of this
4885 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4888 public void showTranslation_actionPerformed(ActionEvent e)
4890 AlignmentI al = null;
4893 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4895 al = dna.translateCdna();
4896 } catch (Exception ex)
4898 jalview.bin.Cache.log.error(
4899 "Exception during translation. Please report this !", ex);
4900 final String msg = MessageManager
4901 .getString("label.error_when_translating_sequences_submit_bug_report");
4902 final String errorTitle = MessageManager
4903 .getString("label.implementation_error")
4904 + MessageManager.getString("translation_failed");
4905 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4906 JOptionPane.ERROR_MESSAGE);
4909 if (al == null || al.getHeight() == 0)
4911 final String msg = MessageManager
4912 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4913 final String errorTitle = MessageManager
4914 .getString("label.translation_failed");
4915 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4916 JOptionPane.WARNING_MESSAGE);
4920 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4921 af.setFileFormat(this.currentFileFormat);
4922 final String newTitle = MessageManager.formatMessage(
4923 "label.translation_of_params",
4924 new Object[] { this.getTitle() });
4925 af.setTitle(newTitle);
4926 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4928 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4929 viewport.openSplitFrame(af, new Alignment(seqs));
4933 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4940 * Set the file format
4944 public void setFileFormat(String fileFormat)
4946 this.currentFileFormat = fileFormat;
4950 * Try to load a features file onto the alignment.
4953 * contents or path to retrieve file
4955 * access mode of file (see jalview.io.AlignFile)
4956 * @return true if features file was parsed correctly.
4958 public boolean parseFeaturesFile(String file, String type)
4960 return avc.parseFeaturesFile(file, type,
4961 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4966 public void refreshFeatureUI(boolean enableIfNecessary)
4968 // note - currently this is only still here rather than in the controller
4969 // because of the featureSettings hard reference that is yet to be
4971 if (enableIfNecessary)
4973 viewport.setShowSequenceFeatures(true);
4974 showSeqFeatures.setSelected(true);
4980 public void dragEnter(DropTargetDragEvent evt)
4985 public void dragExit(DropTargetEvent evt)
4990 public void dragOver(DropTargetDragEvent evt)
4995 public void dropActionChanged(DropTargetDragEvent evt)
5000 public void drop(DropTargetDropEvent evt)
5002 Transferable t = evt.getTransferable();
5003 java.util.List files = null;
5007 DataFlavor uriListFlavor = new DataFlavor(
5008 "text/uri-list;class=java.lang.String");
5009 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5011 // Works on Windows and MacOSX
5012 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5013 files = (java.util.List) t
5014 .getTransferData(DataFlavor.javaFileListFlavor);
5016 else if (t.isDataFlavorSupported(uriListFlavor))
5018 // This is used by Unix drag system
5019 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5020 String data = (String) t.getTransferData(uriListFlavor);
5021 files = new java.util.ArrayList(1);
5022 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5023 data, "\r\n"); st.hasMoreTokens();)
5025 String s = st.nextToken();
5026 if (s.startsWith("#"))
5028 // the line is a comment (as per the RFC 2483)
5032 java.net.URI uri = new java.net.URI(s);
5033 // check to see if we can handle this kind of URI
5034 if (uri.getScheme().toLowerCase().startsWith("http"))
5036 files.add(uri.toString());
5040 // otherwise preserve old behaviour: catch all for file objects
5041 java.io.File file = new java.io.File(uri);
5042 files.add(file.toString());
5046 } catch (Exception e)
5048 e.printStackTrace();
5054 // check to see if any of these files have names matching sequences in
5056 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5057 .getAlignment().getSequencesArray());
5059 * Object[] { String,SequenceI}
5061 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5062 ArrayList<String> filesnotmatched = new ArrayList<String>();
5063 for (int i = 0; i < files.size(); i++)
5065 String file = files.get(i).toString();
5067 String protocol = FormatAdapter.checkProtocol(file);
5068 if (protocol == jalview.io.FormatAdapter.FILE)
5070 File fl = new File(file);
5071 pdbfn = fl.getName();
5073 else if (protocol == jalview.io.FormatAdapter.URL)
5075 URL url = new URL(file);
5076 pdbfn = url.getFile();
5078 if (pdbfn.length() > 0)
5080 // attempt to find a match in the alignment
5081 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5082 int l = 0, c = pdbfn.indexOf(".");
5083 while (mtch == null && c != -1)
5088 } while ((c = pdbfn.indexOf(".", l)) > l);
5091 pdbfn = pdbfn.substring(0, l);
5093 mtch = idm.findAllIdMatches(pdbfn);
5100 type = new IdentifyFile().Identify(file, protocol);
5101 } catch (Exception ex)
5107 if (type.equalsIgnoreCase("PDB"))
5109 filesmatched.add(new Object[] { file, protocol, mtch });
5114 // File wasn't named like one of the sequences or wasn't a PDB file.
5115 filesnotmatched.add(file);
5119 if (filesmatched.size() > 0)
5121 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5127 "label.automatically_associate_pdb_files_with_sequences_same_name",
5128 new Object[] { Integer
5134 .getString("label.automatically_associate_pdb_files_by_name"),
5135 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5138 for (Object[] fm : filesmatched)
5140 // try and associate
5141 // TODO: may want to set a standard ID naming formalism for
5142 // associating PDB files which have no IDs.
5143 for (SequenceI toassoc : (SequenceI[]) fm[2])
5145 PDBEntry pe = new AssociatePdbFileWithSeq()
5146 .associatePdbWithSeq((String) fm[0],
5147 (String) fm[1], toassoc, false,
5151 System.err.println("Associated file : "
5152 + ((String) fm[0]) + " with "
5153 + toassoc.getDisplayId(true));
5157 alignPanel.paintAlignment(true);
5161 if (filesnotmatched.size() > 0)
5164 && (Cache.getDefault(
5165 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5171 "label.ignore_unmatched_dropped_files_info",
5172 new Object[] { Integer
5179 .getString("label.ignore_unmatched_dropped_files"),
5180 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5184 for (String fn : filesnotmatched)
5186 loadJalviewDataFile(fn, null, null, null);
5190 } catch (Exception ex)
5192 ex.printStackTrace();
5198 * Attempt to load a "dropped" file or URL string: First by testing whether
5199 * it's and Annotation file, then a JNet file, and finally a features file. If
5200 * all are false then the user may have dropped an alignment file onto this
5204 * either a filename or a URL string.
5206 public void loadJalviewDataFile(String file, String protocol,
5207 String format, SequenceI assocSeq)
5211 if (protocol == null)
5213 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5215 // if the file isn't identified, or not positively identified as some
5216 // other filetype (PFAM is default unidentified alignment file type) then
5217 // try to parse as annotation.
5218 boolean isAnnotation = (format == null || format
5219 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5220 .annotateAlignmentView(viewport, file, protocol) : false;
5224 // first see if its a T-COFFEE score file
5225 TCoffeeScoreFile tcf = null;
5228 tcf = new TCoffeeScoreFile(file, protocol);
5231 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5233 tcoffeeColour.setEnabled(true);
5234 tcoffeeColour.setSelected(true);
5235 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5236 isAnnotation = true;
5238 .setText(MessageManager
5239 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5243 // some problem - if no warning its probable that the ID matching
5244 // process didn't work
5248 tcf.getWarningMessage() == null ? MessageManager
5249 .getString("label.check_file_matches_sequence_ids_alignment")
5250 : tcf.getWarningMessage(),
5252 .getString("label.problem_reading_tcoffee_score_file"),
5253 JOptionPane.WARNING_MESSAGE);
5260 } catch (Exception x)
5263 .debug("Exception when processing data source as T-COFFEE score file",
5269 // try to see if its a JNet 'concise' style annotation file *before*
5271 // try to parse it as a features file
5274 format = new IdentifyFile().Identify(file, protocol);
5276 if (format.equalsIgnoreCase("JnetFile"))
5278 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5280 new JnetAnnotationMaker();
5281 JnetAnnotationMaker.add_annotation(predictions,
5282 viewport.getAlignment(), 0, false);
5283 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5284 viewport.getAlignment().setSeqrep(repseq);
5285 ColumnSelection cs = new ColumnSelection();
5286 cs.hideInsertionsFor(repseq);
5287 viewport.setColumnSelection(cs);
5288 isAnnotation = true;
5293 * if (format.equalsIgnoreCase("PDB")) {
5295 * String pdbfn = ""; // try to match up filename with sequence id
5296 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5297 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5298 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5299 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5300 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5301 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5302 * // attempt to find a match in the alignment SequenceI mtch =
5303 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5304 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5305 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5306 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5307 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5308 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5309 * { System.err.println("Associated file : " + file + " with " +
5310 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5311 * TODO: maybe need to load as normal otherwise return; } }
5313 // try to parse it as a features file
5314 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5315 // if it wasn't a features file then we just treat it as a general
5316 // alignment file to load into the current view.
5319 new FileLoader().LoadFile(viewport, file, protocol, format);
5323 alignPanel.paintAlignment(true);
5331 alignPanel.adjustAnnotationHeight();
5332 viewport.updateSequenceIdColours();
5333 buildSortByAnnotationScoresMenu();
5334 alignPanel.paintAlignment(true);
5336 } catch (Exception ex)
5338 ex.printStackTrace();
5339 } catch (OutOfMemoryError oom)
5344 } catch (Exception x)
5350 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5351 : "using " + protocol + " from " + file)
5353 + (format != null ? "(parsing as '" + format
5354 + "' file)" : ""), oom, Desktop.desktop);
5359 * Method invoked by the ChangeListener on the tabbed pane, in other words
5360 * when a different tabbed pane is selected by the user or programmatically.
5363 public void tabSelectionChanged(int index)
5367 alignPanel = alignPanels.get(index);
5368 viewport = alignPanel.av;
5369 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5370 setMenusFromViewport(viewport);
5374 * If there is a frame linked to this one in a SplitPane, switch it to the
5375 * same view tab index. No infinite recursion of calls should happen, since
5376 * tabSelectionChanged() should not get invoked on setting the selected
5377 * index to an unchanged value. Guard against setting an invalid index
5378 * before the new view peer tab has been created.
5380 final AlignViewportI peer = viewport.getCodingComplement();
5383 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5384 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5386 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5392 * On right mouse click on view tab, prompt for and set new view name.
5395 public void tabbedPane_mousePressed(MouseEvent e)
5397 if (SwingUtilities.isRightMouseButton(e))
5399 String msg = MessageManager.getString("label.enter_view_name");
5400 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5401 JOptionPane.QUESTION_MESSAGE);
5405 viewport.viewName = reply;
5406 // TODO warn if reply is in getExistingViewNames()?
5407 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5412 public AlignViewport getCurrentView()
5418 * Open the dialog for regex description parsing.
5421 protected void extractScores_actionPerformed(ActionEvent e)
5423 ParseProperties pp = new jalview.analysis.ParseProperties(
5424 viewport.getAlignment());
5425 // TODO: verify regex and introduce GUI dialog for version 2.5
5426 // if (pp.getScoresFromDescription("col", "score column ",
5427 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5429 if (pp.getScoresFromDescription("description column",
5430 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5432 buildSortByAnnotationScoresMenu();
5440 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5444 protected void showDbRefs_actionPerformed(ActionEvent e)
5446 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5452 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5456 protected void showNpFeats_actionPerformed(ActionEvent e)
5458 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5462 * find the viewport amongst the tabs in this alignment frame and close that
5467 public boolean closeView(AlignViewportI av)
5471 this.closeMenuItem_actionPerformed(false);
5474 Component[] comp = tabbedPane.getComponents();
5475 for (int i = 0; comp != null && i < comp.length; i++)
5477 if (comp[i] instanceof AlignmentPanel)
5479 if (((AlignmentPanel) comp[i]).av == av)
5482 closeView((AlignmentPanel) comp[i]);
5490 protected void build_fetchdbmenu(JMenu webService)
5492 // Temporary hack - DBRef Fetcher always top level ws entry.
5493 // TODO We probably want to store a sequence database checklist in
5494 // preferences and have checkboxes.. rather than individual sources selected
5496 final JMenu rfetch = new JMenu(
5497 MessageManager.getString("action.fetch_db_references"));
5498 rfetch.setToolTipText(MessageManager
5499 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5500 webService.add(rfetch);
5502 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5503 MessageManager.getString("option.trim_retrieved_seqs"));
5504 trimrs.setToolTipText(MessageManager
5505 .getString("label.trim_retrieved_sequences"));
5506 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5507 trimrs.addActionListener(new ActionListener()
5510 public void actionPerformed(ActionEvent e)
5512 trimrs.setSelected(trimrs.isSelected());
5513 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5514 Boolean.valueOf(trimrs.isSelected()).toString());
5518 JMenuItem fetchr = new JMenuItem(
5519 MessageManager.getString("label.standard_databases"));
5520 fetchr.setToolTipText(MessageManager
5521 .getString("label.fetch_embl_uniprot"));
5522 fetchr.addActionListener(new ActionListener()
5526 public void actionPerformed(ActionEvent e)
5528 new Thread(new Runnable()
5534 new jalview.ws.DBRefFetcher(alignPanel.av
5535 .getSequenceSelection(), alignPanel.alignFrame)
5536 .fetchDBRefs(false);
5544 final AlignFrame me = this;
5545 new Thread(new Runnable()
5550 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5551 .getSequenceFetcherSingleton(me);
5552 javax.swing.SwingUtilities.invokeLater(new Runnable()
5557 String[] dbclasses = sf.getOrderedSupportedSources();
5558 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5559 // jalview.util.QuickSort.sort(otherdb, otherdb);
5560 List<DbSourceProxy> otherdb;
5561 JMenu dfetch = new JMenu();
5562 JMenu ifetch = new JMenu();
5563 JMenuItem fetchr = null;
5564 int comp = 0, icomp = 0, mcomp = 15;
5565 String mname = null;
5567 for (String dbclass : dbclasses)
5569 otherdb = sf.getSourceProxy(dbclass);
5570 // add a single entry for this class, or submenu allowing 'fetch
5572 if (otherdb == null || otherdb.size() < 1)
5576 // List<DbSourceProxy> dbs=otherdb;
5577 // otherdb=new ArrayList<DbSourceProxy>();
5578 // for (DbSourceProxy db:dbs)
5580 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5584 mname = "From " + dbclass;
5586 if (otherdb.size() == 1)
5588 final DbSourceProxy[] dassource = otherdb
5589 .toArray(new DbSourceProxy[0]);
5590 DbSourceProxy src = otherdb.get(0);
5591 fetchr = new JMenuItem(src.getDbSource());
5592 fetchr.addActionListener(new ActionListener()
5596 public void actionPerformed(ActionEvent e)
5598 new Thread(new Runnable()
5604 new jalview.ws.DBRefFetcher(alignPanel.av
5605 .getSequenceSelection(),
5606 alignPanel.alignFrame, dassource)
5607 .fetchDBRefs(false);
5613 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5614 MessageManager.formatMessage(
5615 "label.fetch_retrieve_from",
5616 new Object[] { src.getDbName() })));
5622 final DbSourceProxy[] dassource = otherdb
5623 .toArray(new DbSourceProxy[0]);
5625 DbSourceProxy src = otherdb.get(0);
5626 fetchr = new JMenuItem(MessageManager.formatMessage(
5627 "label.fetch_all_param",
5628 new Object[] { src.getDbSource() }));
5629 fetchr.addActionListener(new ActionListener()
5632 public void actionPerformed(ActionEvent e)
5634 new Thread(new Runnable()
5640 new jalview.ws.DBRefFetcher(alignPanel.av
5641 .getSequenceSelection(),
5642 alignPanel.alignFrame, dassource)
5643 .fetchDBRefs(false);
5649 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5650 MessageManager.formatMessage(
5651 "label.fetch_retrieve_from_all_sources",
5653 Integer.valueOf(otherdb.size())
5654 .toString(), src.getDbSource(),
5655 src.getDbName() })));
5658 // and then build the rest of the individual menus
5659 ifetch = new JMenu(MessageManager.formatMessage(
5660 "label.source_from_db_source",
5661 new Object[] { src.getDbSource() }));
5663 String imname = null;
5665 for (DbSourceProxy sproxy : otherdb)
5667 String dbname = sproxy.getDbName();
5668 String sname = dbname.length() > 5 ? dbname.substring(0,
5669 5) + "..." : dbname;
5670 String msname = dbname.length() > 10 ? dbname.substring(
5671 0, 10) + "..." : dbname;
5674 imname = MessageManager.formatMessage(
5675 "label.from_msname", new Object[] { sname });
5677 fetchr = new JMenuItem(msname);
5678 final DbSourceProxy[] dassrc = { sproxy };
5679 fetchr.addActionListener(new ActionListener()
5683 public void actionPerformed(ActionEvent e)
5685 new Thread(new Runnable()
5691 new jalview.ws.DBRefFetcher(alignPanel.av
5692 .getSequenceSelection(),
5693 alignPanel.alignFrame, dassrc)
5694 .fetchDBRefs(false);
5700 fetchr.setToolTipText("<html>"
5701 + MessageManager.formatMessage(
5702 "label.fetch_retrieve_from", new Object[]
5706 if (++icomp >= mcomp || i == (otherdb.size()))
5708 ifetch.setText(MessageManager.formatMessage(
5709 "label.source_to_target", imname, sname));
5711 ifetch = new JMenu();
5719 if (comp >= mcomp || dbi >= (dbclasses.length))
5721 dfetch.setText(MessageManager.formatMessage(
5722 "label.source_to_target", mname, dbclass));
5724 dfetch = new JMenu();
5737 * Left justify the whole alignment.
5740 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5742 AlignmentI al = viewport.getAlignment();
5744 viewport.firePropertyChange("alignment", null, al);
5748 * Right justify the whole alignment.
5751 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5753 AlignmentI al = viewport.getAlignment();
5755 viewport.firePropertyChange("alignment", null, al);
5758 public void setShowSeqFeatures(boolean b)
5760 showSeqFeatures.setSelected(b);
5761 viewport.setShowSequenceFeatures(b);
5768 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5769 * awt.event.ActionEvent)
5772 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5774 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5775 alignPanel.paintAlignment(true);
5782 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5786 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5788 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5789 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5797 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5798 * .event.ActionEvent)
5801 protected void showGroupConservation_actionPerformed(ActionEvent e)
5803 viewport.setShowGroupConservation(showGroupConservation.getState());
5804 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5811 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5812 * .event.ActionEvent)
5815 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5817 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5818 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5825 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5826 * .event.ActionEvent)
5829 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5831 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5832 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5836 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5838 showSequenceLogo.setState(true);
5839 viewport.setShowSequenceLogo(true);
5840 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5841 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5845 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5847 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5854 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5855 * .event.ActionEvent)
5858 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5860 if (avc.makeGroupsFromSelection())
5862 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5863 alignPanel.updateAnnotation();
5864 alignPanel.paintAlignment(true);
5868 public void clearAlignmentSeqRep()
5870 // TODO refactor alignmentseqrep to controller
5871 if (viewport.getAlignment().hasSeqrep())
5873 viewport.getAlignment().setSeqrep(null);
5874 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5875 alignPanel.updateAnnotation();
5876 alignPanel.paintAlignment(true);
5881 protected void createGroup_actionPerformed(ActionEvent e)
5883 if (avc.createGroup())
5885 alignPanel.alignmentChanged();
5890 protected void unGroup_actionPerformed(ActionEvent e)
5894 alignPanel.alignmentChanged();
5899 * make the given alignmentPanel the currently selected tab
5901 * @param alignmentPanel
5903 public void setDisplayedView(AlignmentPanel alignmentPanel)
5905 if (!viewport.getSequenceSetId().equals(
5906 alignmentPanel.av.getSequenceSetId()))
5910 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5912 if (tabbedPane != null
5913 && tabbedPane.getTabCount() > 0
5914 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5915 .getSelectedIndex())
5917 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5922 * Action on selection of menu options to Show or Hide annotations.
5925 * @param forSequences
5926 * update sequence-related annotations
5927 * @param forAlignment
5928 * update non-sequence-related annotations
5931 protected void setAnnotationsVisibility(boolean visible,
5932 boolean forSequences, boolean forAlignment)
5934 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5935 .getAlignmentAnnotation())
5938 * don't display non-positional annotations on an alignment
5940 if (aa.annotations == null)
5944 boolean apply = (aa.sequenceRef == null && forAlignment)
5945 || (aa.sequenceRef != null && forSequences);
5948 aa.visible = visible;
5951 alignPanel.validateAnnotationDimensions(true);
5952 alignPanel.alignmentChanged();
5956 * Store selected annotation sort order for the view and repaint.
5959 protected void sortAnnotations_actionPerformed()
5961 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5963 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5964 alignPanel.paintAlignment(true);
5969 * @return alignment panels in this alignment frame
5971 public List<? extends AlignmentViewPanel> getAlignPanels()
5973 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5977 * Open a new alignment window, with the cDNA associated with this (protein)
5978 * alignment, aligned as is the protein.
5980 protected void viewAsCdna_actionPerformed()
5982 // TODO no longer a menu action - refactor as required
5983 final AlignmentI alignment = getViewport().getAlignment();
5984 Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5985 if (mappings == null)
5989 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5990 for (SequenceI aaSeq : alignment.getSequences())
5992 for (AlignedCodonFrame acf : mappings)
5994 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5998 * There is a cDNA mapping for this protein sequence - add to new
5999 * alignment. It will share the same dataset sequence as other mapped
6000 * cDNA (no new mappings need to be created).
6002 final Sequence newSeq = new Sequence(dnaSeq);
6003 newSeq.setDatasetSequence(dnaSeq);
6004 cdnaSeqs.add(newSeq);
6008 if (cdnaSeqs.size() == 0)
6010 // show a warning dialog no mapped cDNA
6013 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6015 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6016 AlignFrame.DEFAULT_HEIGHT);
6017 cdna.alignAs(alignment);
6018 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6020 Desktop.addInternalFrame(alignFrame, newtitle,
6021 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6025 * Set visibility of dna/protein complement view (available when shown in a
6031 protected void showComplement_actionPerformed(boolean show)
6033 SplitContainerI sf = getSplitViewContainer();
6036 sf.setComplementVisible(this, show);
6041 class PrintThread extends Thread
6045 public PrintThread(AlignmentPanel ap)
6050 static PageFormat pf;
6055 PrinterJob printJob = PrinterJob.getPrinterJob();
6059 printJob.setPrintable(ap, pf);
6063 printJob.setPrintable(ap);
6066 if (printJob.printDialog())
6071 } catch (Exception PrintException)
6073 PrintException.printStackTrace();