2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.FeatureSettingsModelI;
36 import jalview.api.SplitContainerI;
37 import jalview.api.ViewStyleI;
38 import jalview.api.analysis.ScoreModelI;
39 import jalview.bin.Cache;
40 import jalview.bin.Jalview;
41 import jalview.commands.CommandI;
42 import jalview.commands.EditCommand;
43 import jalview.commands.EditCommand.Action;
44 import jalview.commands.OrderCommand;
45 import jalview.commands.RemoveGapColCommand;
46 import jalview.commands.RemoveGapsCommand;
47 import jalview.commands.SlideSequencesCommand;
48 import jalview.commands.TrimRegionCommand;
49 import jalview.datamodel.AlignedCodonFrame;
50 import jalview.datamodel.Alignment;
51 import jalview.datamodel.AlignmentAnnotation;
52 import jalview.datamodel.AlignmentExportData;
53 import jalview.datamodel.AlignmentI;
54 import jalview.datamodel.AlignmentOrder;
55 import jalview.datamodel.AlignmentView;
56 import jalview.datamodel.ColumnSelection;
57 import jalview.datamodel.DBRefSource;
58 import jalview.datamodel.HiddenSequences;
59 import jalview.datamodel.PDBEntry;
60 import jalview.datamodel.SeqCigar;
61 import jalview.datamodel.Sequence;
62 import jalview.datamodel.SequenceGroup;
63 import jalview.datamodel.SequenceI;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.FileLoader;
69 import jalview.io.FormatAdapter;
70 import jalview.io.HtmlSvgOutput;
71 import jalview.io.IdentifyFile;
72 import jalview.io.JalviewFileChooser;
73 import jalview.io.JalviewFileView;
74 import jalview.io.JnetAnnotationMaker;
75 import jalview.io.NewickFile;
76 import jalview.io.TCoffeeScoreFile;
77 import jalview.io.gff.SequenceOntologyI;
78 import jalview.jbgui.GAlignFrame;
79 import jalview.schemes.Blosum62ColourScheme;
80 import jalview.schemes.BuriedColourScheme;
81 import jalview.schemes.ClustalxColourScheme;
82 import jalview.schemes.ColourSchemeI;
83 import jalview.schemes.ColourSchemeProperty;
84 import jalview.schemes.HelixColourScheme;
85 import jalview.schemes.HydrophobicColourScheme;
86 import jalview.schemes.NucleotideColourScheme;
87 import jalview.schemes.PIDColourScheme;
88 import jalview.schemes.PurinePyrimidineColourScheme;
89 import jalview.schemes.RNAHelicesColourChooser;
90 import jalview.schemes.ResidueProperties;
91 import jalview.schemes.StrandColourScheme;
92 import jalview.schemes.TCoffeeColourScheme;
93 import jalview.schemes.TaylorColourScheme;
94 import jalview.schemes.TurnColourScheme;
95 import jalview.schemes.UserColourScheme;
96 import jalview.schemes.ZappoColourScheme;
97 import jalview.structure.StructureSelectionManager;
98 import jalview.util.MessageManager;
99 import jalview.viewmodel.AlignmentViewport;
100 import jalview.ws.DBRefFetcher;
101 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
102 import jalview.ws.SequenceFetcher;
103 import jalview.ws.jws1.Discoverer;
104 import jalview.ws.jws2.Jws2Discoverer;
105 import jalview.ws.jws2.jabaws2.Jws2Instance;
106 import jalview.ws.seqfetcher.DbSourceProxy;
108 import java.awt.BorderLayout;
109 import java.awt.Component;
110 import java.awt.Rectangle;
111 import java.awt.Toolkit;
112 import java.awt.datatransfer.Clipboard;
113 import java.awt.datatransfer.DataFlavor;
114 import java.awt.datatransfer.StringSelection;
115 import java.awt.datatransfer.Transferable;
116 import java.awt.dnd.DropTargetDragEvent;
117 import java.awt.dnd.DropTargetDropEvent;
118 import java.awt.dnd.DropTargetEvent;
119 import java.awt.dnd.DropTargetListener;
120 import java.awt.event.ActionEvent;
121 import java.awt.event.ActionListener;
122 import java.awt.event.FocusAdapter;
123 import java.awt.event.FocusEvent;
124 import java.awt.event.ItemEvent;
125 import java.awt.event.ItemListener;
126 import java.awt.event.KeyAdapter;
127 import java.awt.event.KeyEvent;
128 import java.awt.event.MouseAdapter;
129 import java.awt.event.MouseEvent;
130 import java.awt.print.PageFormat;
131 import java.awt.print.PrinterJob;
132 import java.beans.PropertyChangeEvent;
135 import java.util.ArrayList;
136 import java.util.Arrays;
137 import java.util.Deque;
138 import java.util.Enumeration;
139 import java.util.Hashtable;
140 import java.util.List;
141 import java.util.Vector;
143 import javax.swing.JCheckBoxMenuItem;
144 import javax.swing.JEditorPane;
145 import javax.swing.JInternalFrame;
146 import javax.swing.JLayeredPane;
147 import javax.swing.JMenu;
148 import javax.swing.JMenuItem;
149 import javax.swing.JOptionPane;
150 import javax.swing.JRadioButtonMenuItem;
151 import javax.swing.JScrollPane;
152 import javax.swing.SwingUtilities;
158 * @version $Revision$
160 public class AlignFrame extends GAlignFrame implements DropTargetListener,
161 IProgressIndicator, AlignViewControllerGuiI
164 public static final int DEFAULT_WIDTH = 700;
166 public static final int DEFAULT_HEIGHT = 500;
169 * The currently displayed panel (selected tabbed view if more than one)
171 public AlignmentPanel alignPanel;
173 AlignViewport viewport;
175 public AlignViewControllerI avc;
177 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
180 * Last format used to load or save alignments in this window
182 String currentFileFormat = null;
185 * Current filename for this alignment
187 String fileName = null;
190 * Creates a new AlignFrame object with specific width and height.
196 public AlignFrame(AlignmentI al, int width, int height)
198 this(al, null, width, height);
202 * Creates a new AlignFrame object with specific width, height and
208 * @param sequenceSetId
210 public AlignFrame(AlignmentI al, int width, int height,
211 String sequenceSetId)
213 this(al, null, width, height, sequenceSetId);
217 * Creates a new AlignFrame object with specific width, height and
223 * @param sequenceSetId
226 public AlignFrame(AlignmentI al, int width, int height,
227 String sequenceSetId, String viewId)
229 this(al, null, width, height, sequenceSetId, viewId);
233 * new alignment window with hidden columns
237 * @param hiddenColumns
238 * ColumnSelection or null
240 * Width of alignment frame
244 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
245 int width, int height)
247 this(al, hiddenColumns, width, height, null);
251 * Create alignment frame for al with hiddenColumns, a specific width and
252 * height, and specific sequenceId
255 * @param hiddenColumns
258 * @param sequenceSetId
261 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
262 int width, int height, String sequenceSetId)
264 this(al, hiddenColumns, width, height, sequenceSetId, null);
268 * Create alignment frame for al with hiddenColumns, a specific width and
269 * height, and specific sequenceId
272 * @param hiddenColumns
275 * @param sequenceSetId
280 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
281 int width, int height, String sequenceSetId, String viewId)
283 setSize(width, height);
285 if (al.getDataset() == null)
290 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
292 alignPanel = new AlignmentPanel(this, viewport);
294 addAlignmentPanel(alignPanel, true);
298 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
299 ColumnSelection hiddenColumns, int width, int height)
301 setSize(width, height);
303 if (al.getDataset() == null)
308 viewport = new AlignViewport(al, hiddenColumns);
310 if (hiddenSeqs != null && hiddenSeqs.length > 0)
312 viewport.hideSequence(hiddenSeqs);
314 alignPanel = new AlignmentPanel(this, viewport);
315 addAlignmentPanel(alignPanel, true);
320 * Make a new AlignFrame from existing alignmentPanels
327 public AlignFrame(AlignmentPanel ap)
331 addAlignmentPanel(ap, false);
336 * initalise the alignframe from the underlying viewport data and the
341 if (!Jalview.isHeadlessMode())
343 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
346 avc = new jalview.controller.AlignViewController(this, viewport,
348 if (viewport.getAlignmentConservationAnnotation() == null)
350 BLOSUM62Colour.setEnabled(false);
351 conservationMenuItem.setEnabled(false);
352 modifyConservation.setEnabled(false);
353 // PIDColour.setEnabled(false);
354 // abovePIDThreshold.setEnabled(false);
355 // modifyPID.setEnabled(false);
358 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
361 if (sortby.equals("Id"))
363 sortIDMenuItem_actionPerformed(null);
365 else if (sortby.equals("Pairwise Identity"))
367 sortPairwiseMenuItem_actionPerformed(null);
370 if (Desktop.desktop != null)
372 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
373 addServiceListeners();
374 setGUINucleotide(viewport.getAlignment().isNucleotide());
378 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
380 setMenusFromViewport(viewport);
381 buildSortByAnnotationScoresMenu();
384 if (viewport.getWrapAlignment())
386 wrapMenuItem_actionPerformed(null);
389 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
391 this.overviewMenuItem_actionPerformed(null);
396 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
397 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
398 final String menuLabel = MessageManager
399 .getString("label.copy_format_from");
400 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
401 new ViewSetProvider()
405 public AlignmentPanel[] getAllAlignmentPanels()
408 origview.add(alignPanel);
409 // make an array of all alignment panels except for this one
410 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
411 Arrays.asList(Desktop.getAlignmentPanels(null)));
412 aps.remove(AlignFrame.this.alignPanel);
413 return aps.toArray(new AlignmentPanel[aps.size()]);
415 }, selviews, new ItemListener()
419 public void itemStateChanged(ItemEvent e)
421 if (origview.size() > 0)
423 final AlignmentPanel ap = origview.get(0);
426 * Copy the ViewStyle of the selected panel to 'this one'.
427 * Don't change value of 'scaleProteinAsCdna' unless copying
430 ViewStyleI vs = selviews.get(0).getAlignViewport()
432 boolean fromSplitFrame = selviews.get(0)
433 .getAlignViewport().getCodingComplement() != null;
436 vs.setScaleProteinAsCdna(ap.getAlignViewport()
437 .getViewStyle().isScaleProteinAsCdna());
439 ap.getAlignViewport().setViewStyle(vs);
442 * Also rescale ViewStyle of SplitFrame complement if there is
443 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
444 * the whole ViewStyle (allow cDNA protein to have different
447 AlignViewportI complement = ap.getAlignViewport()
448 .getCodingComplement();
449 if (complement != null && vs.isScaleProteinAsCdna())
451 AlignFrame af = Desktop.getAlignFrameFor(complement);
452 ((SplitFrame) af.getSplitViewContainer())
454 af.setMenusForViewport();
458 ap.setSelected(true);
459 ap.alignFrame.setMenusForViewport();
464 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
465 .indexOf("devel") > -1
466 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
467 .indexOf("test") > -1)
469 formatMenu.add(vsel);
471 addFocusListener(new FocusAdapter()
474 public void focusGained(FocusEvent e)
476 Desktop.setCurrentAlignFrame(AlignFrame.this);
483 * Change the filename and format for the alignment, and enable the 'reload'
484 * button functionality.
491 public void setFileName(String file, String format)
494 setFileFormat(format);
495 reload.setEnabled(true);
499 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
502 void addKeyListener()
504 addKeyListener(new KeyAdapter()
507 public void keyPressed(KeyEvent evt)
509 if (viewport.cursorMode
510 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
511 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
512 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
513 && Character.isDigit(evt.getKeyChar()))
515 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
518 switch (evt.getKeyCode())
521 case 27: // escape key
522 deselectAllSequenceMenuItem_actionPerformed(null);
526 case KeyEvent.VK_DOWN:
527 if (evt.isAltDown() || !viewport.cursorMode)
529 moveSelectedSequences(false);
531 if (viewport.cursorMode)
533 alignPanel.getSeqPanel().moveCursor(0, 1);
538 if (evt.isAltDown() || !viewport.cursorMode)
540 moveSelectedSequences(true);
542 if (viewport.cursorMode)
544 alignPanel.getSeqPanel().moveCursor(0, -1);
549 case KeyEvent.VK_LEFT:
550 if (evt.isAltDown() || !viewport.cursorMode)
552 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
556 alignPanel.getSeqPanel().moveCursor(-1, 0);
561 case KeyEvent.VK_RIGHT:
562 if (evt.isAltDown() || !viewport.cursorMode)
564 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
568 alignPanel.getSeqPanel().moveCursor(1, 0);
572 case KeyEvent.VK_SPACE:
573 if (viewport.cursorMode)
575 alignPanel.getSeqPanel().insertGapAtCursor(
576 evt.isControlDown() || evt.isShiftDown()
581 // case KeyEvent.VK_A:
582 // if (viewport.cursorMode)
584 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
585 // //System.out.println("A");
589 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
590 * System.out.println("closing bracket"); } break;
592 case KeyEvent.VK_DELETE:
593 case KeyEvent.VK_BACK_SPACE:
594 if (!viewport.cursorMode)
596 cut_actionPerformed(null);
600 alignPanel.getSeqPanel().deleteGapAtCursor(
601 evt.isControlDown() || evt.isShiftDown()
608 if (viewport.cursorMode)
610 alignPanel.getSeqPanel().setCursorRow();
614 if (viewport.cursorMode && !evt.isControlDown())
616 alignPanel.getSeqPanel().setCursorColumn();
620 if (viewport.cursorMode)
622 alignPanel.getSeqPanel().setCursorPosition();
626 case KeyEvent.VK_ENTER:
627 case KeyEvent.VK_COMMA:
628 if (viewport.cursorMode)
630 alignPanel.getSeqPanel().setCursorRowAndColumn();
635 if (viewport.cursorMode)
637 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
641 if (viewport.cursorMode)
643 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
648 viewport.cursorMode = !viewport.cursorMode;
649 statusBar.setText(MessageManager.formatMessage(
650 "label.keyboard_editing_mode",
651 new String[] { (viewport.cursorMode ? "on" : "off") }));
652 if (viewport.cursorMode)
654 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
655 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
657 alignPanel.getSeqPanel().seqCanvas.repaint();
663 Help.showHelpWindow();
664 } catch (Exception ex)
666 ex.printStackTrace();
671 boolean toggleSeqs = !evt.isControlDown();
672 boolean toggleCols = !evt.isShiftDown();
673 toggleHiddenRegions(toggleSeqs, toggleCols);
676 case KeyEvent.VK_PAGE_UP:
677 if (viewport.getWrapAlignment())
679 alignPanel.scrollUp(true);
683 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
684 - viewport.endSeq + viewport.startSeq);
687 case KeyEvent.VK_PAGE_DOWN:
688 if (viewport.getWrapAlignment())
690 alignPanel.scrollUp(false);
694 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
695 + viewport.endSeq - viewport.startSeq);
702 public void keyReleased(KeyEvent evt)
704 switch (evt.getKeyCode())
706 case KeyEvent.VK_LEFT:
707 if (evt.isAltDown() || !viewport.cursorMode)
709 viewport.firePropertyChange("alignment", null, viewport
710 .getAlignment().getSequences());
714 case KeyEvent.VK_RIGHT:
715 if (evt.isAltDown() || !viewport.cursorMode)
717 viewport.firePropertyChange("alignment", null, viewport
718 .getAlignment().getSequences());
726 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
728 ap.alignFrame = this;
729 avc = new jalview.controller.AlignViewController(this, viewport,
734 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
736 int aSize = alignPanels.size();
738 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
740 if (aSize == 1 && ap.av.viewName == null)
742 this.getContentPane().add(ap, BorderLayout.CENTER);
748 setInitialTabVisible();
751 expandViews.setEnabled(true);
752 gatherViews.setEnabled(true);
753 tabbedPane.addTab(ap.av.viewName, ap);
755 ap.setVisible(false);
760 if (ap.av.isPadGaps())
762 ap.av.getAlignment().padGaps();
764 ap.av.updateConservation(ap);
765 ap.av.updateConsensus(ap);
766 ap.av.updateStrucConsensus(ap);
770 public void setInitialTabVisible()
772 expandViews.setEnabled(true);
773 gatherViews.setEnabled(true);
774 tabbedPane.setVisible(true);
775 AlignmentPanel first = alignPanels.get(0);
776 tabbedPane.addTab(first.av.viewName, first);
777 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
780 public AlignViewport getViewport()
785 /* Set up intrinsic listeners for dynamically generated GUI bits. */
786 private void addServiceListeners()
788 final java.beans.PropertyChangeListener thisListener;
789 Desktop.instance.addJalviewPropertyChangeListener("services",
790 thisListener = new java.beans.PropertyChangeListener()
793 public void propertyChange(PropertyChangeEvent evt)
795 // // System.out.println("Discoverer property change.");
796 // if (evt.getPropertyName().equals("services"))
798 SwingUtilities.invokeLater(new Runnable()
805 .println("Rebuild WS Menu for service change");
806 BuildWebServiceMenu();
813 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
816 public void internalFrameClosed(
817 javax.swing.event.InternalFrameEvent evt)
819 // System.out.println("deregistering discoverer listener");
820 Desktop.instance.removeJalviewPropertyChangeListener("services",
822 closeMenuItem_actionPerformed(true);
825 // Finally, build the menu once to get current service state
826 new Thread(new Runnable()
831 BuildWebServiceMenu();
837 * Configure menu items that vary according to whether the alignment is
838 * nucleotide or protein
842 public void setGUINucleotide(boolean nucleotide)
844 showTranslation.setVisible(nucleotide);
845 showReverse.setVisible(nucleotide);
846 showReverseComplement.setVisible(nucleotide);
847 conservationMenuItem.setEnabled(!nucleotide);
848 modifyConservation.setEnabled(!nucleotide);
849 showGroupConservation.setEnabled(!nucleotide);
850 rnahelicesColour.setEnabled(nucleotide);
851 purinePyrimidineColour.setEnabled(nucleotide);
852 showComplementMenuItem.setText(MessageManager
853 .getString(nucleotide ? "label.protein" : "label.nucleotide"));
854 setColourSelected(jalview.bin.Cache.getDefault(
855 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
856 : Preferences.DEFAULT_COLOUR_PROT, "None"));
860 * set up menus for the current viewport. This may be called after any
861 * operation that affects the data in the current view (selection changed,
862 * etc) to update the menus to reflect the new state.
865 public void setMenusForViewport()
867 setMenusFromViewport(viewport);
871 * Need to call this method when tabs are selected for multiple views, or when
872 * loading from Jalview2XML.java
877 void setMenusFromViewport(AlignViewport av)
879 padGapsMenuitem.setSelected(av.isPadGaps());
880 colourTextMenuItem.setSelected(av.isShowColourText());
881 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
882 conservationMenuItem.setSelected(av.getConservationSelected());
883 seqLimits.setSelected(av.getShowJVSuffix());
884 idRightAlign.setSelected(av.isRightAlignIds());
885 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
886 renderGapsMenuItem.setSelected(av.isRenderGaps());
887 wrapMenuItem.setSelected(av.getWrapAlignment());
888 scaleAbove.setVisible(av.getWrapAlignment());
889 scaleLeft.setVisible(av.getWrapAlignment());
890 scaleRight.setVisible(av.getWrapAlignment());
891 annotationPanelMenuItem.setState(av.isShowAnnotation());
893 * Show/hide annotations only enabled if annotation panel is shown
895 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
896 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
897 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
898 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
899 viewBoxesMenuItem.setSelected(av.getShowBoxes());
900 viewTextMenuItem.setSelected(av.getShowText());
901 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
902 showGroupConsensus.setSelected(av.isShowGroupConsensus());
903 showGroupConservation.setSelected(av.isShowGroupConservation());
904 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
905 showSequenceLogo.setSelected(av.isShowSequenceLogo());
906 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
908 setColourSelected(ColourSchemeProperty.getColourName(av
909 .getGlobalColourScheme()));
911 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
912 hiddenMarkers.setState(av.getShowHiddenMarkers());
913 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
914 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
915 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
916 autoCalculate.setSelected(av.autoCalculateConsensus);
917 sortByTree.setSelected(av.sortByTree);
918 listenToViewSelections.setSelected(av.followSelection);
919 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
921 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
923 showProducts.setEnabled(canShowProducts());
924 setGroovyEnabled(Desktop.getGroovyConsole() != null);
930 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
934 public void setGroovyEnabled(boolean b)
936 runGroovy.setEnabled(b);
939 private IProgressIndicator progressBar;
944 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
947 public void setProgressBar(String message, long id)
949 progressBar.setProgressBar(message, id);
953 public void registerHandler(final long id,
954 final IProgressIndicatorHandler handler)
956 progressBar.registerHandler(id, handler);
961 * @return true if any progress bars are still active
964 public boolean operationInProgress()
966 return progressBar.operationInProgress();
970 public void setStatus(String text)
972 statusBar.setText(text);
976 * Added so Castor Mapping file can obtain Jalview Version
978 public String getVersion()
980 return jalview.bin.Cache.getProperty("VERSION");
983 public FeatureRenderer getFeatureRenderer()
985 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
989 public void fetchSequence_actionPerformed(ActionEvent e)
991 new jalview.gui.SequenceFetcher(this);
995 public void addFromFile_actionPerformed(ActionEvent e)
997 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1001 public void reload_actionPerformed(ActionEvent e)
1003 if (fileName != null)
1005 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1006 // originating file's format
1007 // TODO: work out how to recover feature settings for correct view(s) when
1008 // file is reloaded.
1009 if (currentFileFormat.equals("Jalview"))
1011 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1012 for (int i = 0; i < frames.length; i++)
1014 if (frames[i] instanceof AlignFrame && frames[i] != this
1015 && ((AlignFrame) frames[i]).fileName != null
1016 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1020 frames[i].setSelected(true);
1021 Desktop.instance.closeAssociatedWindows();
1022 } catch (java.beans.PropertyVetoException ex)
1028 Desktop.instance.closeAssociatedWindows();
1030 FileLoader loader = new FileLoader();
1031 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1032 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1036 Rectangle bounds = this.getBounds();
1038 FileLoader loader = new FileLoader();
1039 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1040 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1041 protocol, currentFileFormat);
1043 newframe.setBounds(bounds);
1044 if (featureSettings != null && featureSettings.isShowing())
1046 final Rectangle fspos = featureSettings.frame.getBounds();
1047 // TODO: need a 'show feature settings' function that takes bounds -
1048 // need to refactor Desktop.addFrame
1049 newframe.featureSettings_actionPerformed(null);
1050 final FeatureSettings nfs = newframe.featureSettings;
1051 SwingUtilities.invokeLater(new Runnable()
1056 nfs.frame.setBounds(fspos);
1059 this.featureSettings.close();
1060 this.featureSettings = null;
1062 this.closeMenuItem_actionPerformed(true);
1068 public void addFromText_actionPerformed(ActionEvent e)
1070 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1075 public void addFromURL_actionPerformed(ActionEvent e)
1077 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1081 public void save_actionPerformed(ActionEvent e)
1083 if (fileName == null
1084 || (currentFileFormat == null || !jalview.io.FormatAdapter
1085 .isValidIOFormat(currentFileFormat, true))
1086 || fileName.startsWith("http"))
1088 saveAs_actionPerformed(null);
1092 saveAlignment(fileName, currentFileFormat);
1103 public void saveAs_actionPerformed(ActionEvent e)
1105 JalviewFileChooser chooser = new JalviewFileChooser(
1106 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1107 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1108 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1109 currentFileFormat, false);
1111 chooser.setFileView(new JalviewFileView());
1112 chooser.setDialogTitle(MessageManager
1113 .getString("label.save_alignment_to_file"));
1114 chooser.setToolTipText(MessageManager.getString("action.save"));
1116 int value = chooser.showSaveDialog(this);
1118 if (value == JalviewFileChooser.APPROVE_OPTION)
1120 currentFileFormat = chooser.getSelectedFormat();
1121 while (currentFileFormat == null)
1124 .showInternalMessageDialog(
1127 .getString("label.select_file_format_before_saving"),
1129 .getString("label.file_format_not_specified"),
1130 JOptionPane.WARNING_MESSAGE);
1131 currentFileFormat = chooser.getSelectedFormat();
1132 value = chooser.showSaveDialog(this);
1133 if (value != JalviewFileChooser.APPROVE_OPTION)
1139 fileName = chooser.getSelectedFile().getPath();
1141 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1144 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1145 if (currentFileFormat.indexOf(" ") > -1)
1147 currentFileFormat = currentFileFormat.substring(0,
1148 currentFileFormat.indexOf(" "));
1150 saveAlignment(fileName, currentFileFormat);
1154 public boolean saveAlignment(String file, String format)
1156 boolean success = true;
1158 if (format.equalsIgnoreCase("Jalview"))
1160 String shortName = title;
1162 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1164 shortName = shortName.substring(shortName
1165 .lastIndexOf(java.io.File.separatorChar) + 1);
1168 success = new Jalview2XML().saveAlignment(this, file, shortName);
1170 statusBar.setText(MessageManager.formatMessage(
1171 "label.successfully_saved_to_file_in_format", new Object[] {
1172 fileName, format }));
1177 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1179 warningMessage("Cannot save file " + fileName + " using format "
1180 + format, "Alignment output format not supported");
1181 if (!Jalview.isHeadlessMode())
1183 saveAs_actionPerformed(null);
1188 AlignmentExportData exportData = getAlignmentForExport(format,
1190 if (exportData.getSettings().isCancelled())
1194 FormatAdapter f = new FormatAdapter(alignPanel,
1195 exportData.getSettings());
1196 String output = f.formatSequences(
1198 exportData.getAlignment(), // class cast exceptions will
1199 // occur in the distant future
1200 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1201 f.getCacheSuffixDefault(format),
1202 viewport.getColumnSelection());
1212 java.io.PrintWriter out = new java.io.PrintWriter(
1213 new java.io.FileWriter(file));
1217 this.setTitle(file);
1218 statusBar.setText(MessageManager.formatMessage(
1219 "label.successfully_saved_to_file_in_format",
1220 new Object[] { fileName, format }));
1221 } catch (Exception ex)
1224 ex.printStackTrace();
1231 JOptionPane.showInternalMessageDialog(this, MessageManager
1232 .formatMessage("label.couldnt_save_file",
1233 new Object[] { fileName }), MessageManager
1234 .getString("label.error_saving_file"),
1235 JOptionPane.WARNING_MESSAGE);
1241 private void warningMessage(String warning, String title)
1243 if (new jalview.util.Platform().isHeadless())
1245 System.err.println("Warning: " + title + "\nWarning: " + warning);
1250 JOptionPane.showInternalMessageDialog(this, warning, title,
1251 JOptionPane.WARNING_MESSAGE);
1263 protected void outputText_actionPerformed(ActionEvent e)
1266 AlignmentExportData exportData = getAlignmentForExport(
1267 e.getActionCommand(), viewport, null);
1268 if (exportData.getSettings().isCancelled())
1272 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1273 cap.setForInput(null);
1276 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1277 .formatSequences(e.getActionCommand(),
1278 exportData.getAlignment(),
1279 exportData.getOmitHidden(),
1280 exportData.getStartEndPostions(),
1281 viewport.getColumnSelection()));
1282 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1283 "label.alignment_output_command",
1284 new Object[] { e.getActionCommand() }), 600, 500);
1285 } catch (OutOfMemoryError oom)
1287 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1293 public static AlignmentExportData getAlignmentForExport(
1294 String exportFormat, AlignViewportI viewport,
1295 AlignExportSettingI exportSettings)
1297 AlignmentI alignmentToExport = null;
1298 AlignExportSettingI settings = exportSettings;
1299 String[] omitHidden = null;
1301 HiddenSequences hiddenSeqs = viewport.getAlignment()
1302 .getHiddenSequences();
1304 alignmentToExport = viewport.getAlignment();
1306 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1307 if (settings == null)
1309 settings = new AlignExportSettings(hasHiddenSeqs,
1310 viewport.hasHiddenColumns(), exportFormat);
1312 // settings.isExportAnnotations();
1314 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1316 omitHidden = viewport.getViewAsString(false);
1319 int[] alignmentStartEnd = new int[2];
1320 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1322 alignmentToExport = hiddenSeqs.getFullAlignment();
1326 alignmentToExport = viewport.getAlignment();
1327 alignmentStartEnd = viewport.getAlignment()
1328 .getVisibleStartAndEndIndex(
1330 .getColumnSelection().getHiddenColumns());
1332 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1333 omitHidden, alignmentStartEnd, settings);
1345 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1347 new HtmlSvgOutput(null, alignPanel);
1351 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1353 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1354 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1357 public void createImageMap(File file, String image)
1359 alignPanel.makePNGImageMap(file, image);
1369 public void createPNG(File f)
1371 alignPanel.makePNG(f);
1381 public void createEPS(File f)
1383 alignPanel.makeEPS(f);
1387 public void createSVG(File f)
1389 alignPanel.makeSVG(f);
1393 public void pageSetup_actionPerformed(ActionEvent e)
1395 PrinterJob printJob = PrinterJob.getPrinterJob();
1396 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1406 public void printMenuItem_actionPerformed(ActionEvent e)
1408 // Putting in a thread avoids Swing painting problems
1409 PrintThread thread = new PrintThread(alignPanel);
1414 public void exportFeatures_actionPerformed(ActionEvent e)
1416 new AnnotationExporter().exportFeatures(alignPanel);
1420 public void exportAnnotations_actionPerformed(ActionEvent e)
1422 new AnnotationExporter().exportAnnotations(alignPanel);
1426 public void associatedData_actionPerformed(ActionEvent e)
1428 // Pick the tree file
1429 JalviewFileChooser chooser = new JalviewFileChooser(
1430 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1431 chooser.setFileView(new JalviewFileView());
1432 chooser.setDialogTitle(MessageManager
1433 .getString("label.load_jalview_annotations"));
1434 chooser.setToolTipText(MessageManager
1435 .getString("label.load_jalview_annotations"));
1437 int value = chooser.showOpenDialog(null);
1439 if (value == JalviewFileChooser.APPROVE_OPTION)
1441 String choice = chooser.getSelectedFile().getPath();
1442 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1443 loadJalviewDataFile(choice, null, null, null);
1449 * Close the current view or all views in the alignment frame. If the frame
1450 * only contains one view then the alignment will be removed from memory.
1452 * @param closeAllTabs
1455 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1457 if (alignPanels != null && alignPanels.size() < 2)
1459 closeAllTabs = true;
1464 if (alignPanels != null)
1468 if (this.isClosed())
1470 // really close all the windows - otherwise wait till
1471 // setClosed(true) is called
1472 for (int i = 0; i < alignPanels.size(); i++)
1474 AlignmentPanel ap = alignPanels.get(i);
1481 closeView(alignPanel);
1488 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1489 * be called recursively, with the frame now in 'closed' state
1491 this.setClosed(true);
1493 } catch (Exception ex)
1495 ex.printStackTrace();
1500 * Close the specified panel and close up tabs appropriately.
1502 * @param panelToClose
1504 public void closeView(AlignmentPanel panelToClose)
1506 int index = tabbedPane.getSelectedIndex();
1507 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1508 alignPanels.remove(panelToClose);
1509 panelToClose.closePanel();
1510 panelToClose = null;
1512 tabbedPane.removeTabAt(closedindex);
1513 tabbedPane.validate();
1515 if (index > closedindex || index == tabbedPane.getTabCount())
1517 // modify currently selected tab index if necessary.
1521 this.tabSelectionChanged(index);
1527 void updateEditMenuBar()
1530 if (viewport.getHistoryList().size() > 0)
1532 undoMenuItem.setEnabled(true);
1533 CommandI command = viewport.getHistoryList().peek();
1534 undoMenuItem.setText(MessageManager.formatMessage(
1535 "label.undo_command",
1536 new Object[] { command.getDescription() }));
1540 undoMenuItem.setEnabled(false);
1541 undoMenuItem.setText(MessageManager.getString("action.undo"));
1544 if (viewport.getRedoList().size() > 0)
1546 redoMenuItem.setEnabled(true);
1548 CommandI command = viewport.getRedoList().peek();
1549 redoMenuItem.setText(MessageManager.formatMessage(
1550 "label.redo_command",
1551 new Object[] { command.getDescription() }));
1555 redoMenuItem.setEnabled(false);
1556 redoMenuItem.setText(MessageManager.getString("action.redo"));
1561 public void addHistoryItem(CommandI command)
1563 if (command.getSize() > 0)
1565 viewport.addToHistoryList(command);
1566 viewport.clearRedoList();
1567 updateEditMenuBar();
1568 viewport.updateHiddenColumns();
1569 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1570 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1571 // viewport.getColumnSelection()
1572 // .getHiddenColumns().size() > 0);
1578 * @return alignment objects for all views
1580 AlignmentI[] getViewAlignments()
1582 if (alignPanels != null)
1584 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1586 for (AlignmentPanel ap : alignPanels)
1588 als[i++] = ap.av.getAlignment();
1592 if (viewport != null)
1594 return new AlignmentI[] { viewport.getAlignment() };
1606 protected void undoMenuItem_actionPerformed(ActionEvent e)
1608 if (viewport.getHistoryList().isEmpty())
1612 CommandI command = viewport.getHistoryList().pop();
1613 viewport.addToRedoList(command);
1614 command.undoCommand(getViewAlignments());
1616 AlignmentViewport originalSource = getOriginatingSource(command);
1617 updateEditMenuBar();
1619 if (originalSource != null)
1621 if (originalSource != viewport)
1624 .warn("Implementation worry: mismatch of viewport origin for undo");
1626 originalSource.updateHiddenColumns();
1627 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1629 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1630 // viewport.getColumnSelection()
1631 // .getHiddenColumns().size() > 0);
1632 originalSource.firePropertyChange("alignment", null, originalSource
1633 .getAlignment().getSequences());
1644 protected void redoMenuItem_actionPerformed(ActionEvent e)
1646 if (viewport.getRedoList().size() < 1)
1651 CommandI command = viewport.getRedoList().pop();
1652 viewport.addToHistoryList(command);
1653 command.doCommand(getViewAlignments());
1655 AlignmentViewport originalSource = getOriginatingSource(command);
1656 updateEditMenuBar();
1658 if (originalSource != null)
1661 if (originalSource != viewport)
1664 .warn("Implementation worry: mismatch of viewport origin for redo");
1666 originalSource.updateHiddenColumns();
1667 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1669 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1670 // viewport.getColumnSelection()
1671 // .getHiddenColumns().size() > 0);
1672 originalSource.firePropertyChange("alignment", null, originalSource
1673 .getAlignment().getSequences());
1677 AlignmentViewport getOriginatingSource(CommandI command)
1679 AlignmentViewport originalSource = null;
1680 // For sequence removal and addition, we need to fire
1681 // the property change event FROM the viewport where the
1682 // original alignment was altered
1683 AlignmentI al = null;
1684 if (command instanceof EditCommand)
1686 EditCommand editCommand = (EditCommand) command;
1687 al = editCommand.getAlignment();
1688 List<Component> comps = PaintRefresher.components.get(viewport
1689 .getSequenceSetId());
1691 for (Component comp : comps)
1693 if (comp instanceof AlignmentPanel)
1695 if (al == ((AlignmentPanel) comp).av.getAlignment())
1697 originalSource = ((AlignmentPanel) comp).av;
1704 if (originalSource == null)
1706 // The original view is closed, we must validate
1707 // the current view against the closed view first
1710 PaintRefresher.validateSequences(al, viewport.getAlignment());
1713 originalSource = viewport;
1716 return originalSource;
1725 public void moveSelectedSequences(boolean up)
1727 SequenceGroup sg = viewport.getSelectionGroup();
1733 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1734 viewport.getHiddenRepSequences(), up);
1735 alignPanel.paintAlignment(true);
1738 synchronized void slideSequences(boolean right, int size)
1740 List<SequenceI> sg = new ArrayList<SequenceI>();
1741 if (viewport.cursorMode)
1743 sg.add(viewport.getAlignment().getSequenceAt(
1744 alignPanel.getSeqPanel().seqCanvas.cursorY));
1746 else if (viewport.getSelectionGroup() != null
1747 && viewport.getSelectionGroup().getSize() != viewport
1748 .getAlignment().getHeight())
1750 sg = viewport.getSelectionGroup().getSequences(
1751 viewport.getHiddenRepSequences());
1759 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1761 for (SequenceI seq : viewport.getAlignment().getSequences())
1763 if (!sg.contains(seq))
1765 invertGroup.add(seq);
1769 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1771 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1772 for (int i = 0; i < invertGroup.size(); i++)
1774 seqs2[i] = invertGroup.get(i);
1777 SlideSequencesCommand ssc;
1780 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1781 size, viewport.getGapCharacter());
1785 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1786 size, viewport.getGapCharacter());
1789 int groupAdjustment = 0;
1790 if (ssc.getGapsInsertedBegin() && right)
1792 if (viewport.cursorMode)
1794 alignPanel.getSeqPanel().moveCursor(size, 0);
1798 groupAdjustment = size;
1801 else if (!ssc.getGapsInsertedBegin() && !right)
1803 if (viewport.cursorMode)
1805 alignPanel.getSeqPanel().moveCursor(-size, 0);
1809 groupAdjustment = -size;
1813 if (groupAdjustment != 0)
1815 viewport.getSelectionGroup().setStartRes(
1816 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1817 viewport.getSelectionGroup().setEndRes(
1818 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1822 * just extend the last slide command if compatible; but not if in
1823 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1825 boolean appendHistoryItem = false;
1826 Deque<CommandI> historyList = viewport.getHistoryList();
1827 boolean inSplitFrame = getSplitViewContainer() != null;
1828 if (!inSplitFrame && historyList != null && historyList.size() > 0
1829 && historyList.peek() instanceof SlideSequencesCommand)
1831 appendHistoryItem = ssc
1832 .appendSlideCommand((SlideSequencesCommand) historyList
1836 if (!appendHistoryItem)
1838 addHistoryItem(ssc);
1851 protected void copy_actionPerformed(ActionEvent e)
1854 if (viewport.getSelectionGroup() == null)
1858 // TODO: preserve the ordering of displayed alignment annotation in any
1859 // internal paste (particularly sequence associated annotation)
1860 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1861 String[] omitHidden = null;
1863 if (viewport.hasHiddenColumns())
1865 omitHidden = viewport.getViewAsString(true);
1868 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1871 StringSelection ss = new StringSelection(output);
1875 jalview.gui.Desktop.internalCopy = true;
1876 // Its really worth setting the clipboard contents
1877 // to empty before setting the large StringSelection!!
1878 Toolkit.getDefaultToolkit().getSystemClipboard()
1879 .setContents(new StringSelection(""), null);
1881 Toolkit.getDefaultToolkit().getSystemClipboard()
1882 .setContents(ss, Desktop.instance);
1883 } catch (OutOfMemoryError er)
1885 new OOMWarning("copying region", er);
1889 ArrayList<int[]> hiddenColumns = null;
1890 if (viewport.hasHiddenColumns())
1892 hiddenColumns = new ArrayList<int[]>();
1893 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1894 .getSelectionGroup().getEndRes();
1895 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1897 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1899 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1900 region[1] - hiddenOffset });
1905 Desktop.jalviewClipboard = new Object[] { seqs,
1906 viewport.getAlignment().getDataset(), hiddenColumns };
1907 statusBar.setText(MessageManager.formatMessage(
1908 "label.copied_sequences_to_clipboard", new Object[] { Integer
1909 .valueOf(seqs.length).toString() }));
1919 protected void pasteNew_actionPerformed(ActionEvent e)
1931 protected void pasteThis_actionPerformed(ActionEvent e)
1937 * Paste contents of Jalview clipboard
1939 * @param newAlignment
1940 * true to paste to a new alignment, otherwise add to this.
1942 void paste(boolean newAlignment)
1944 boolean externalPaste = true;
1947 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1948 Transferable contents = c.getContents(this);
1950 if (contents == null)
1958 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1959 if (str.length() < 1)
1964 format = new IdentifyFile().identify(str, "Paste");
1966 } catch (OutOfMemoryError er)
1968 new OOMWarning("Out of memory pasting sequences!!", er);
1972 SequenceI[] sequences;
1973 boolean annotationAdded = false;
1974 AlignmentI alignment = null;
1976 if (Desktop.jalviewClipboard != null)
1978 // The clipboard was filled from within Jalview, we must use the
1980 // And dataset from the copied alignment
1981 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1982 // be doubly sure that we create *new* sequence objects.
1983 sequences = new SequenceI[newseq.length];
1984 for (int i = 0; i < newseq.length; i++)
1986 sequences[i] = new Sequence(newseq[i]);
1988 alignment = new Alignment(sequences);
1989 externalPaste = false;
1993 // parse the clipboard as an alignment.
1994 alignment = new FormatAdapter().readFile(str, "Paste", format);
1995 sequences = alignment.getSequencesArray();
1999 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2005 if (Desktop.jalviewClipboard != null)
2007 // dataset is inherited
2008 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2012 // new dataset is constructed
2013 alignment.setDataset(null);
2015 alwidth = alignment.getWidth() + 1;
2019 AlignmentI pastedal = alignment; // preserve pasted alignment object
2020 // Add pasted sequences and dataset into existing alignment.
2021 alignment = viewport.getAlignment();
2022 alwidth = alignment.getWidth() + 1;
2023 // decide if we need to import sequences from an existing dataset
2024 boolean importDs = Desktop.jalviewClipboard != null
2025 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2026 // importDs==true instructs us to copy over new dataset sequences from
2027 // an existing alignment
2028 Vector newDs = (importDs) ? new Vector() : null; // used to create
2029 // minimum dataset set
2031 for (int i = 0; i < sequences.length; i++)
2035 newDs.addElement(null);
2037 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2039 if (importDs && ds != null)
2041 if (!newDs.contains(ds))
2043 newDs.setElementAt(ds, i);
2044 ds = new Sequence(ds);
2045 // update with new dataset sequence
2046 sequences[i].setDatasetSequence(ds);
2050 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2055 // copy and derive new dataset sequence
2056 sequences[i] = sequences[i].deriveSequence();
2057 alignment.getDataset().addSequence(
2058 sequences[i].getDatasetSequence());
2059 // TODO: avoid creation of duplicate dataset sequences with a
2060 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2062 alignment.addSequence(sequences[i]); // merges dataset
2066 newDs.clear(); // tidy up
2068 if (alignment.getAlignmentAnnotation() != null)
2070 for (AlignmentAnnotation alan : alignment
2071 .getAlignmentAnnotation())
2073 if (alan.graphGroup > fgroup)
2075 fgroup = alan.graphGroup;
2079 if (pastedal.getAlignmentAnnotation() != null)
2081 // Add any annotation attached to alignment.
2082 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2083 for (int i = 0; i < alann.length; i++)
2085 annotationAdded = true;
2086 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2088 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2089 if (newann.graphGroup > -1)
2091 if (newGraphGroups.size() <= newann.graphGroup
2092 || newGraphGroups.get(newann.graphGroup) == null)
2094 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2096 newGraphGroups.add(q, null);
2098 newGraphGroups.set(newann.graphGroup, new Integer(
2101 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2105 newann.padAnnotation(alwidth);
2106 alignment.addAnnotation(newann);
2116 addHistoryItem(new EditCommand(
2117 MessageManager.getString("label.add_sequences"),
2118 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2120 // Add any annotations attached to sequences
2121 for (int i = 0; i < sequences.length; i++)
2123 if (sequences[i].getAnnotation() != null)
2125 AlignmentAnnotation newann;
2126 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2128 annotationAdded = true;
2129 newann = sequences[i].getAnnotation()[a];
2130 newann.adjustForAlignment();
2131 newann.padAnnotation(alwidth);
2132 if (newann.graphGroup > -1)
2134 if (newann.graphGroup > -1)
2136 if (newGraphGroups.size() <= newann.graphGroup
2137 || newGraphGroups.get(newann.graphGroup) == null)
2139 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2141 newGraphGroups.add(q, null);
2143 newGraphGroups.set(newann.graphGroup, new Integer(
2146 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2150 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2155 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2162 // propagate alignment changed.
2163 viewport.setEndSeq(alignment.getHeight());
2164 if (annotationAdded)
2166 // Duplicate sequence annotation in all views.
2167 AlignmentI[] alview = this.getViewAlignments();
2168 for (int i = 0; i < sequences.length; i++)
2170 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2175 for (int avnum = 0; avnum < alview.length; avnum++)
2177 if (alview[avnum] != alignment)
2179 // duplicate in a view other than the one with input focus
2180 int avwidth = alview[avnum].getWidth() + 1;
2181 // this relies on sann being preserved after we
2182 // modify the sequence's annotation array for each duplication
2183 for (int a = 0; a < sann.length; a++)
2185 AlignmentAnnotation newann = new AlignmentAnnotation(
2187 sequences[i].addAlignmentAnnotation(newann);
2188 newann.padAnnotation(avwidth);
2189 alview[avnum].addAnnotation(newann); // annotation was
2190 // duplicated earlier
2191 // TODO JAL-1145 graphGroups are not updated for sequence
2192 // annotation added to several views. This may cause
2194 alview[avnum].setAnnotationIndex(newann, a);
2199 buildSortByAnnotationScoresMenu();
2201 viewport.firePropertyChange("alignment", null,
2202 alignment.getSequences());
2203 if (alignPanels != null)
2205 for (AlignmentPanel ap : alignPanels)
2207 ap.validateAnnotationDimensions(false);
2212 alignPanel.validateAnnotationDimensions(false);
2218 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2220 String newtitle = new String("Copied sequences");
2222 if (Desktop.jalviewClipboard != null
2223 && Desktop.jalviewClipboard[2] != null)
2225 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2226 for (int[] region : hc)
2228 af.viewport.hideColumns(region[0], region[1]);
2232 // >>>This is a fix for the moment, until a better solution is
2234 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2236 alignPanel.getSeqPanel().seqCanvas
2237 .getFeatureRenderer());
2239 // TODO: maintain provenance of an alignment, rather than just make the
2240 // title a concatenation of operations.
2243 if (title.startsWith("Copied sequences"))
2249 newtitle = newtitle.concat("- from " + title);
2254 newtitle = new String("Pasted sequences");
2257 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2262 } catch (Exception ex)
2264 ex.printStackTrace();
2265 System.out.println("Exception whilst pasting: " + ex);
2266 // could be anything being pasted in here
2272 protected void expand_newalign(ActionEvent e)
2276 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2277 .getAlignment(), -1);
2278 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2280 String newtitle = new String("Flanking alignment");
2282 if (Desktop.jalviewClipboard != null
2283 && Desktop.jalviewClipboard[2] != null)
2285 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2286 for (int region[] : hc)
2288 af.viewport.hideColumns(region[0], region[1]);
2292 // >>>This is a fix for the moment, until a better solution is
2294 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2296 alignPanel.getSeqPanel().seqCanvas
2297 .getFeatureRenderer());
2299 // TODO: maintain provenance of an alignment, rather than just make the
2300 // title a concatenation of operations.
2302 if (title.startsWith("Copied sequences"))
2308 newtitle = newtitle.concat("- from " + title);
2312 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2314 } catch (Exception ex)
2316 ex.printStackTrace();
2317 System.out.println("Exception whilst pasting: " + ex);
2318 // could be anything being pasted in here
2319 } catch (OutOfMemoryError oom)
2321 new OOMWarning("Viewing flanking region of alignment", oom);
2332 protected void cut_actionPerformed(ActionEvent e)
2334 copy_actionPerformed(null);
2335 delete_actionPerformed(null);
2345 protected void delete_actionPerformed(ActionEvent evt)
2348 SequenceGroup sg = viewport.getSelectionGroup();
2355 * If the cut affects all sequences, warn, remove highlighted columns
2357 if (sg.getSize() == viewport.getAlignment().getHeight())
2359 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2360 .getAlignment().getWidth()) ? true : false;
2361 if (isEntireAlignWidth)
2363 int confirm = JOptionPane.showConfirmDialog(this,
2364 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2365 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2366 JOptionPane.OK_CANCEL_OPTION);
2368 if (confirm == JOptionPane.CANCEL_OPTION
2369 || confirm == JOptionPane.CLOSED_OPTION)
2374 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2375 sg.getEndRes() + 1);
2377 SequenceI[] cut = sg.getSequences()
2378 .toArray(new SequenceI[sg.getSize()]);
2380 addHistoryItem(new EditCommand(
2381 MessageManager.getString("label.cut_sequences"), Action.CUT,
2382 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2383 viewport.getAlignment()));
2385 viewport.setSelectionGroup(null);
2386 viewport.sendSelection();
2387 viewport.getAlignment().deleteGroup(sg);
2389 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2391 if (viewport.getAlignment().getHeight() < 1)
2395 this.setClosed(true);
2396 } catch (Exception ex)
2409 protected void deleteGroups_actionPerformed(ActionEvent e)
2411 if (avc.deleteGroups())
2413 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2414 alignPanel.updateAnnotation();
2415 alignPanel.paintAlignment(true);
2426 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2428 SequenceGroup sg = new SequenceGroup();
2430 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2432 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2435 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2436 viewport.setSelectionGroup(sg);
2437 viewport.sendSelection();
2438 alignPanel.paintAlignment(true);
2439 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2449 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2451 if (viewport.cursorMode)
2453 alignPanel.getSeqPanel().keyboardNo1 = null;
2454 alignPanel.getSeqPanel().keyboardNo2 = null;
2456 viewport.setSelectionGroup(null);
2457 viewport.getColumnSelection().clear();
2458 viewport.setSelectionGroup(null);
2459 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2460 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2461 alignPanel.paintAlignment(true);
2462 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2463 viewport.sendSelection();
2473 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2475 SequenceGroup sg = viewport.getSelectionGroup();
2479 selectAllSequenceMenuItem_actionPerformed(null);
2484 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2486 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2489 alignPanel.paintAlignment(true);
2490 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2491 viewport.sendSelection();
2495 public void invertColSel_actionPerformed(ActionEvent e)
2497 viewport.invertColumnSelection();
2498 alignPanel.paintAlignment(true);
2499 viewport.sendSelection();
2509 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2511 trimAlignment(true);
2521 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2523 trimAlignment(false);
2526 void trimAlignment(boolean trimLeft)
2528 ColumnSelection colSel = viewport.getColumnSelection();
2531 if (!colSel.isEmpty())
2535 column = colSel.getMin();
2539 column = colSel.getMax();
2543 if (viewport.getSelectionGroup() != null)
2545 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2546 viewport.getHiddenRepSequences());
2550 seqs = viewport.getAlignment().getSequencesArray();
2553 TrimRegionCommand trimRegion;
2556 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2557 column, viewport.getAlignment());
2558 viewport.setStartRes(0);
2562 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2563 column, viewport.getAlignment());
2566 statusBar.setText(MessageManager.formatMessage(
2567 "label.removed_columns",
2568 new String[] { Integer.valueOf(trimRegion.getSize())
2571 addHistoryItem(trimRegion);
2573 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2575 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2576 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2578 viewport.getAlignment().deleteGroup(sg);
2582 viewport.firePropertyChange("alignment", null, viewport
2583 .getAlignment().getSequences());
2594 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2596 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2599 if (viewport.getSelectionGroup() != null)
2601 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2602 viewport.getHiddenRepSequences());
2603 start = viewport.getSelectionGroup().getStartRes();
2604 end = viewport.getSelectionGroup().getEndRes();
2608 seqs = viewport.getAlignment().getSequencesArray();
2611 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2612 "Remove Gapped Columns", seqs, start, end,
2613 viewport.getAlignment());
2615 addHistoryItem(removeGapCols);
2617 statusBar.setText(MessageManager.formatMessage(
2618 "label.removed_empty_columns",
2619 new Object[] { Integer.valueOf(removeGapCols.getSize())
2622 // This is to maintain viewport position on first residue
2623 // of first sequence
2624 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2625 int startRes = seq.findPosition(viewport.startRes);
2626 // ShiftList shifts;
2627 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2628 // edit.alColumnChanges=shifts.getInverse();
2629 // if (viewport.hasHiddenColumns)
2630 // viewport.getColumnSelection().compensateForEdits(shifts);
2631 viewport.setStartRes(seq.findIndex(startRes) - 1);
2632 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2644 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2646 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2649 if (viewport.getSelectionGroup() != null)
2651 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2652 viewport.getHiddenRepSequences());
2653 start = viewport.getSelectionGroup().getStartRes();
2654 end = viewport.getSelectionGroup().getEndRes();
2658 seqs = viewport.getAlignment().getSequencesArray();
2661 // This is to maintain viewport position on first residue
2662 // of first sequence
2663 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2664 int startRes = seq.findPosition(viewport.startRes);
2666 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2667 viewport.getAlignment()));
2669 viewport.setStartRes(seq.findIndex(startRes) - 1);
2671 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2683 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2685 viewport.setPadGaps(padGapsMenuitem.isSelected());
2686 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2697 public void findMenuItem_actionPerformed(ActionEvent e)
2703 * Create a new view of the current alignment.
2706 public void newView_actionPerformed(ActionEvent e)
2708 newView(null, true);
2712 * Creates and shows a new view of the current alignment.
2715 * title of newly created view; if null, one will be generated
2716 * @param copyAnnotation
2717 * if true then duplicate all annnotation, groups and settings
2718 * @return new alignment panel, already displayed.
2720 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2723 * Create a new AlignmentPanel (with its own, new Viewport)
2725 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2727 if (!copyAnnotation)
2730 * remove all groups and annotation except for the automatic stuff
2732 newap.av.getAlignment().deleteAllGroups();
2733 newap.av.getAlignment().deleteAllAnnotations(false);
2736 newap.av.setGatherViewsHere(false);
2738 if (viewport.viewName == null)
2740 viewport.viewName = MessageManager
2741 .getString("label.view_name_original");
2745 * Views share the same edits undo and redo stacks
2747 newap.av.setHistoryList(viewport.getHistoryList());
2748 newap.av.setRedoList(viewport.getRedoList());
2751 * Views share the same mappings; need to deregister any new mappings
2752 * created by copyAlignPanel, and register the new reference to the shared
2755 newap.av.replaceMappings(viewport.getAlignment());
2757 newap.av.viewName = getNewViewName(viewTitle);
2759 addAlignmentPanel(newap, true);
2760 newap.alignmentChanged();
2762 if (alignPanels.size() == 2)
2764 viewport.setGatherViewsHere(true);
2766 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2771 * Make a new name for the view, ensuring it is unique within the current
2772 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2773 * these now use viewId. Unique view names are still desirable for usability.)
2778 protected String getNewViewName(String viewTitle)
2780 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2781 boolean addFirstIndex = false;
2782 if (viewTitle == null || viewTitle.trim().length() == 0)
2784 viewTitle = MessageManager.getString("action.view");
2785 addFirstIndex = true;
2789 index = 1;// we count from 1 if given a specific name
2791 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2793 List<Component> comps = PaintRefresher.components.get(viewport
2794 .getSequenceSetId());
2796 List<String> existingNames = getExistingViewNames(comps);
2798 while (existingNames.contains(newViewName))
2800 newViewName = viewTitle + " " + (++index);
2806 * Returns a list of distinct view names found in the given list of
2807 * components. View names are held on the viewport of an AlignmentPanel.
2812 protected List<String> getExistingViewNames(List<Component> comps)
2814 List<String> existingNames = new ArrayList<String>();
2815 for (Component comp : comps)
2817 if (comp instanceof AlignmentPanel)
2819 AlignmentPanel ap = (AlignmentPanel) comp;
2820 if (!existingNames.contains(ap.av.viewName))
2822 existingNames.add(ap.av.viewName);
2826 return existingNames;
2830 * Explode tabbed views into separate windows.
2833 public void expandViews_actionPerformed(ActionEvent e)
2835 Desktop.instance.explodeViews(this);
2839 * Gather views in separate windows back into a tabbed presentation.
2842 public void gatherViews_actionPerformed(ActionEvent e)
2844 Desktop.instance.gatherViews(this);
2854 public void font_actionPerformed(ActionEvent e)
2856 new FontChooser(alignPanel);
2866 protected void seqLimit_actionPerformed(ActionEvent e)
2868 viewport.setShowJVSuffix(seqLimits.isSelected());
2870 alignPanel.getIdPanel().getIdCanvas()
2871 .setPreferredSize(alignPanel.calculateIdWidth());
2872 alignPanel.paintAlignment(true);
2876 public void idRightAlign_actionPerformed(ActionEvent e)
2878 viewport.setRightAlignIds(idRightAlign.isSelected());
2879 alignPanel.paintAlignment(true);
2883 public void centreColumnLabels_actionPerformed(ActionEvent e)
2885 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2886 alignPanel.paintAlignment(true);
2892 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2895 protected void followHighlight_actionPerformed()
2898 * Set the 'follow' flag on the Viewport (and scroll to position if now
2901 final boolean state = this.followHighlightMenuItem.getState();
2902 viewport.setFollowHighlight(state);
2905 alignPanel.scrollToPosition(
2906 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2917 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2919 viewport.setColourText(colourTextMenuItem.isSelected());
2920 alignPanel.paintAlignment(true);
2930 public void wrapMenuItem_actionPerformed(ActionEvent e)
2932 scaleAbove.setVisible(wrapMenuItem.isSelected());
2933 scaleLeft.setVisible(wrapMenuItem.isSelected());
2934 scaleRight.setVisible(wrapMenuItem.isSelected());
2935 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2936 alignPanel.updateLayout();
2940 public void showAllSeqs_actionPerformed(ActionEvent e)
2942 viewport.showAllHiddenSeqs();
2946 public void showAllColumns_actionPerformed(ActionEvent e)
2948 viewport.showAllHiddenColumns();
2950 viewport.sendSelection();
2954 public void hideSelSequences_actionPerformed(ActionEvent e)
2956 viewport.hideAllSelectedSeqs();
2957 // alignPanel.paintAlignment(true);
2961 * called by key handler and the hide all/show all menu items
2966 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2969 boolean hide = false;
2970 SequenceGroup sg = viewport.getSelectionGroup();
2971 if (!toggleSeqs && !toggleCols)
2973 // Hide everything by the current selection - this is a hack - we do the
2974 // invert and then hide
2975 // first check that there will be visible columns after the invert.
2976 if ((viewport.getColumnSelection() != null
2977 && viewport.getColumnSelection().getSelected() != null && viewport
2978 .getColumnSelection().getSelected().size() > 0)
2979 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2982 // now invert the sequence set, if required - empty selection implies
2983 // that no hiding is required.
2986 invertSequenceMenuItem_actionPerformed(null);
2987 sg = viewport.getSelectionGroup();
2991 viewport.expandColSelection(sg, true);
2992 // finally invert the column selection and get the new sequence
2994 invertColSel_actionPerformed(null);
3001 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3003 hideSelSequences_actionPerformed(null);
3006 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3009 showAllSeqs_actionPerformed(null);
3015 if (viewport.getColumnSelection().getSelected().size() > 0)
3017 hideSelColumns_actionPerformed(null);
3020 viewport.setSelectionGroup(sg);
3025 showAllColumns_actionPerformed(null);
3034 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3035 * event.ActionEvent)
3038 public void hideAllButSelection_actionPerformed(ActionEvent e)
3040 toggleHiddenRegions(false, false);
3041 viewport.sendSelection();
3048 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3052 public void hideAllSelection_actionPerformed(ActionEvent e)
3054 SequenceGroup sg = viewport.getSelectionGroup();
3055 viewport.expandColSelection(sg, false);
3056 viewport.hideAllSelectedSeqs();
3057 viewport.hideSelectedColumns();
3058 alignPanel.paintAlignment(true);
3059 viewport.sendSelection();
3066 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3070 public void showAllhidden_actionPerformed(ActionEvent e)
3072 viewport.showAllHiddenColumns();
3073 viewport.showAllHiddenSeqs();
3074 alignPanel.paintAlignment(true);
3075 viewport.sendSelection();
3079 public void hideSelColumns_actionPerformed(ActionEvent e)
3081 viewport.hideSelectedColumns();
3082 alignPanel.paintAlignment(true);
3083 viewport.sendSelection();
3087 public void hiddenMarkers_actionPerformed(ActionEvent e)
3089 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3100 protected void scaleAbove_actionPerformed(ActionEvent e)
3102 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3103 alignPanel.paintAlignment(true);
3113 protected void scaleLeft_actionPerformed(ActionEvent e)
3115 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3116 alignPanel.paintAlignment(true);
3126 protected void scaleRight_actionPerformed(ActionEvent e)
3128 viewport.setScaleRightWrapped(scaleRight.isSelected());
3129 alignPanel.paintAlignment(true);
3139 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3141 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3142 alignPanel.paintAlignment(true);
3152 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3154 viewport.setShowText(viewTextMenuItem.isSelected());
3155 alignPanel.paintAlignment(true);
3165 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3167 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3168 alignPanel.paintAlignment(true);
3171 public FeatureSettings featureSettings;
3174 public FeatureSettingsControllerI getFeatureSettingsUI()
3176 return featureSettings;
3180 public void featureSettings_actionPerformed(ActionEvent e)
3182 if (featureSettings != null)
3184 featureSettings.close();
3185 featureSettings = null;
3187 if (!showSeqFeatures.isSelected())
3189 // make sure features are actually displayed
3190 showSeqFeatures.setSelected(true);
3191 showSeqFeatures_actionPerformed(null);
3193 featureSettings = new FeatureSettings(this);
3197 * Set or clear 'Show Sequence Features'
3203 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3205 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3206 alignPanel.paintAlignment(true);
3207 if (alignPanel.getOverviewPanel() != null)
3209 alignPanel.getOverviewPanel().updateOverviewImage();
3214 * Set or clear 'Show Sequence Features'
3220 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3222 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3224 if (viewport.isShowSequenceFeaturesHeight())
3226 // ensure we're actually displaying features
3227 viewport.setShowSequenceFeatures(true);
3228 showSeqFeatures.setSelected(true);
3230 alignPanel.paintAlignment(true);
3231 if (alignPanel.getOverviewPanel() != null)
3233 alignPanel.getOverviewPanel().updateOverviewImage();
3238 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3239 * the annotations panel as a whole.
3241 * The options to show/hide all annotations should be enabled when the panel
3242 * is shown, and disabled when the panel is hidden.
3247 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3249 final boolean setVisible = annotationPanelMenuItem.isSelected();
3250 viewport.setShowAnnotation(setVisible);
3251 this.showAllSeqAnnotations.setEnabled(setVisible);
3252 this.hideAllSeqAnnotations.setEnabled(setVisible);
3253 this.showAllAlAnnotations.setEnabled(setVisible);
3254 this.hideAllAlAnnotations.setEnabled(setVisible);
3255 alignPanel.updateLayout();
3259 public void alignmentProperties()
3261 JEditorPane editPane = new JEditorPane("text/html", "");
3262 editPane.setEditable(false);
3263 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3265 editPane.setText(MessageManager.formatMessage("label.html_content",
3266 new Object[] { contents.toString() }));
3267 JInternalFrame frame = new JInternalFrame();
3268 frame.getContentPane().add(new JScrollPane(editPane));
3270 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3271 "label.alignment_properties", new Object[] { getTitle() }),
3282 public void overviewMenuItem_actionPerformed(ActionEvent e)
3284 if (alignPanel.overviewPanel != null)
3289 JInternalFrame frame = new JInternalFrame();
3290 OverviewPanel overview = new OverviewPanel(alignPanel);
3291 frame.setContentPane(overview);
3292 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3293 "label.overview_params", new Object[] { this.getTitle() }),
3294 frame.getWidth(), frame.getHeight());
3296 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3297 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3300 public void internalFrameClosed(
3301 javax.swing.event.InternalFrameEvent evt)
3303 alignPanel.setOverviewPanel(null);
3307 alignPanel.setOverviewPanel(overview);
3311 public void textColour_actionPerformed(ActionEvent e)
3313 new TextColourChooser().chooseColour(alignPanel, null);
3323 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3335 public void clustalColour_actionPerformed(ActionEvent e)
3337 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3338 viewport.getHiddenRepSequences()));
3348 public void zappoColour_actionPerformed(ActionEvent e)
3350 changeColour(new ZappoColourScheme());
3360 public void taylorColour_actionPerformed(ActionEvent e)
3362 changeColour(new TaylorColourScheme());
3372 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3374 changeColour(new HydrophobicColourScheme());
3384 public void helixColour_actionPerformed(ActionEvent e)
3386 changeColour(new HelixColourScheme());
3396 public void strandColour_actionPerformed(ActionEvent e)
3398 changeColour(new StrandColourScheme());
3408 public void turnColour_actionPerformed(ActionEvent e)
3410 changeColour(new TurnColourScheme());
3420 public void buriedColour_actionPerformed(ActionEvent e)
3422 changeColour(new BuriedColourScheme());
3432 public void nucleotideColour_actionPerformed(ActionEvent e)
3434 changeColour(new NucleotideColourScheme());
3438 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3440 changeColour(new PurinePyrimidineColourScheme());
3444 * public void covariationColour_actionPerformed(ActionEvent e) {
3446 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3450 public void annotationColour_actionPerformed(ActionEvent e)
3452 new AnnotationColourChooser(viewport, alignPanel);
3456 public void annotationColumn_actionPerformed(ActionEvent e)
3458 new AnnotationColumnChooser(viewport, alignPanel);
3462 public void rnahelicesColour_actionPerformed(ActionEvent e)
3464 new RNAHelicesColourChooser(viewport, alignPanel);
3474 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3476 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3486 public void changeColour(ColourSchemeI cs)
3488 // TODO: pull up to controller method
3492 // Make sure viewport is up to date w.r.t. any sliders
3493 if (viewport.getAbovePIDThreshold())
3495 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3497 viewport.setThreshold(threshold);
3500 if (viewport.getConservationSelected())
3502 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3505 if (cs instanceof TCoffeeColourScheme)
3507 tcoffeeColour.setEnabled(true);
3508 tcoffeeColour.setSelected(true);
3512 viewport.setGlobalColourScheme(cs);
3514 alignPanel.paintAlignment(true);
3524 protected void modifyPID_actionPerformed(ActionEvent e)
3526 if (viewport.getAbovePIDThreshold()
3527 && viewport.getGlobalColourScheme() != null)
3529 SliderPanel.setPIDSliderSource(alignPanel,
3530 viewport.getGlobalColourScheme(), "Background");
3531 SliderPanel.showPIDSlider();
3542 protected void modifyConservation_actionPerformed(ActionEvent e)
3544 if (viewport.getConservationSelected()
3545 && viewport.getGlobalColourScheme() != null)
3547 SliderPanel.setConservationSlider(alignPanel,
3548 viewport.getGlobalColourScheme(), "Background");
3549 SliderPanel.showConservationSlider();
3560 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3562 viewport.setConservationSelected(conservationMenuItem.isSelected());
3564 viewport.setAbovePIDThreshold(false);
3565 abovePIDThreshold.setSelected(false);
3567 changeColour(viewport.getGlobalColourScheme());
3569 modifyConservation_actionPerformed(null);
3579 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3581 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3583 conservationMenuItem.setSelected(false);
3584 viewport.setConservationSelected(false);
3586 changeColour(viewport.getGlobalColourScheme());
3588 modifyPID_actionPerformed(null);
3598 public void userDefinedColour_actionPerformed(ActionEvent e)
3600 if (e.getActionCommand().equals(
3601 MessageManager.getString("action.user_defined")))
3603 new UserDefinedColours(alignPanel, null);
3607 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3608 .getUserColourSchemes().get(e.getActionCommand());
3614 public void updateUserColourMenu()
3617 Component[] menuItems = colourMenu.getMenuComponents();
3618 int iSize = menuItems.length;
3619 for (int i = 0; i < iSize; i++)
3621 if (menuItems[i].getName() != null
3622 && menuItems[i].getName().equals("USER_DEFINED"))
3624 colourMenu.remove(menuItems[i]);
3628 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3630 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3631 .getUserColourSchemes().keys();
3633 while (userColours.hasMoreElements())
3635 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3636 userColours.nextElement().toString());
3637 radioItem.setName("USER_DEFINED");
3638 radioItem.addMouseListener(new MouseAdapter()
3641 public void mousePressed(MouseEvent evt)
3643 if (evt.isPopupTrigger())
3645 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3647 int option = JOptionPane.showInternalConfirmDialog(
3648 jalview.gui.Desktop.desktop,
3650 .getString("label.remove_from_default_list"),
3652 .getString("label.remove_user_defined_colour"),
3653 JOptionPane.YES_NO_OPTION);
3654 if (option == JOptionPane.YES_OPTION)
3656 jalview.gui.UserDefinedColours
3657 .removeColourFromDefaults(radioItem.getText());
3658 colourMenu.remove(radioItem);
3662 radioItem.addActionListener(new ActionListener()
3665 public void actionPerformed(ActionEvent evt)
3667 userDefinedColour_actionPerformed(evt);
3674 radioItem.addActionListener(new ActionListener()
3677 public void actionPerformed(ActionEvent evt)
3679 userDefinedColour_actionPerformed(evt);
3683 colourMenu.insert(radioItem, 15);
3684 colours.add(radioItem);
3696 public void PIDColour_actionPerformed(ActionEvent e)
3698 changeColour(new PIDColourScheme());
3708 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3710 changeColour(new Blosum62ColourScheme());
3720 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3722 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3723 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3724 .getAlignment().getSequenceAt(0), null);
3725 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3726 viewport.getAlignment()));
3727 alignPanel.paintAlignment(true);
3737 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3739 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3740 AlignmentSorter.sortByID(viewport.getAlignment());
3741 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3742 viewport.getAlignment()));
3743 alignPanel.paintAlignment(true);
3753 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3755 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3756 AlignmentSorter.sortByLength(viewport.getAlignment());
3757 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3758 viewport.getAlignment()));
3759 alignPanel.paintAlignment(true);
3769 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3771 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3772 AlignmentSorter.sortByGroup(viewport.getAlignment());
3773 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3774 viewport.getAlignment()));
3776 alignPanel.paintAlignment(true);
3786 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3788 new RedundancyPanel(alignPanel, this);
3798 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3800 if ((viewport.getSelectionGroup() == null)
3801 || (viewport.getSelectionGroup().getSize() < 2))
3803 JOptionPane.showInternalMessageDialog(this, MessageManager
3804 .getString("label.you_must_select_least_two_sequences"),
3805 MessageManager.getString("label.invalid_selection"),
3806 JOptionPane.WARNING_MESSAGE);
3810 JInternalFrame frame = new JInternalFrame();
3811 frame.setContentPane(new PairwiseAlignPanel(viewport));
3812 Desktop.addInternalFrame(frame,
3813 MessageManager.getString("action.pairwise_alignment"), 600,
3825 public void PCAMenuItem_actionPerformed(ActionEvent e)
3827 if (((viewport.getSelectionGroup() != null)
3828 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3829 .getSelectionGroup().getSize() > 0))
3830 || (viewport.getAlignment().getHeight() < 4))
3833 .showInternalMessageDialog(
3836 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3838 .getString("label.sequence_selection_insufficient"),
3839 JOptionPane.WARNING_MESSAGE);
3844 new PCAPanel(alignPanel);
3848 public void autoCalculate_actionPerformed(ActionEvent e)
3850 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3851 if (viewport.autoCalculateConsensus)
3853 viewport.firePropertyChange("alignment", null, viewport
3854 .getAlignment().getSequences());
3859 public void sortByTreeOption_actionPerformed(ActionEvent e)
3861 viewport.sortByTree = sortByTree.isSelected();
3865 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3867 viewport.followSelection = listenToViewSelections.isSelected();
3877 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3879 newTreePanel("AV", "PID", "Average distance tree using PID");
3889 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3891 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3901 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3903 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3913 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3915 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3928 void newTreePanel(String type, String pwType, String title)
3932 if (viewport.getSelectionGroup() != null
3933 && viewport.getSelectionGroup().getSize() > 0)
3935 if (viewport.getSelectionGroup().getSize() < 3)
3941 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3943 .getString("label.not_enough_sequences"),
3944 JOptionPane.WARNING_MESSAGE);
3948 SequenceGroup sg = viewport.getSelectionGroup();
3950 /* Decide if the selection is a column region */
3951 for (SequenceI _s : sg.getSequences())
3953 if (_s.getLength() < sg.getEndRes())
3959 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3961 .getString("label.sequences_selection_not_aligned"),
3962 JOptionPane.WARNING_MESSAGE);
3968 title = title + " on region";
3969 tp = new TreePanel(alignPanel, type, pwType);
3973 // are the visible sequences aligned?
3974 if (!viewport.getAlignment().isAligned(false))
3980 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3982 .getString("label.sequences_not_aligned"),
3983 JOptionPane.WARNING_MESSAGE);
3988 if (viewport.getAlignment().getHeight() < 2)
3993 tp = new TreePanel(alignPanel, type, pwType);
3998 if (viewport.viewName != null)
4000 title += viewport.viewName + " of ";
4003 title += this.title;
4005 Desktop.addInternalFrame(tp, title, 600, 500);
4016 public void addSortByOrderMenuItem(String title,
4017 final AlignmentOrder order)
4019 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4020 "action.by_title_param", new Object[] { title }));
4022 item.addActionListener(new java.awt.event.ActionListener()
4025 public void actionPerformed(ActionEvent e)
4027 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4029 // TODO: JBPNote - have to map order entries to curent SequenceI
4031 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4033 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4036 alignPanel.paintAlignment(true);
4042 * Add a new sort by annotation score menu item
4045 * the menu to add the option to
4047 * the label used to retrieve scores for each sequence on the
4050 public void addSortByAnnotScoreMenuItem(JMenu sort,
4051 final String scoreLabel)
4053 final JMenuItem item = new JMenuItem(scoreLabel);
4055 item.addActionListener(new java.awt.event.ActionListener()
4058 public void actionPerformed(ActionEvent e)
4060 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4061 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4062 viewport.getAlignment());// ,viewport.getSelectionGroup());
4063 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4064 viewport.getAlignment()));
4065 alignPanel.paintAlignment(true);
4071 * last hash for alignment's annotation array - used to minimise cost of
4074 protected int _annotationScoreVectorHash;
4077 * search the alignment and rebuild the sort by annotation score submenu the
4078 * last alignment annotation vector hash is stored to minimize cost of
4079 * rebuilding in subsequence calls.
4083 public void buildSortByAnnotationScoresMenu()
4085 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4090 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4092 sortByAnnotScore.removeAll();
4093 // almost certainly a quicker way to do this - but we keep it simple
4094 Hashtable scoreSorts = new Hashtable();
4095 AlignmentAnnotation aann[];
4096 for (SequenceI sqa : viewport.getAlignment().getSequences())
4098 aann = sqa.getAnnotation();
4099 for (int i = 0; aann != null && i < aann.length; i++)
4101 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4103 scoreSorts.put(aann[i].label, aann[i].label);
4107 Enumeration labels = scoreSorts.keys();
4108 while (labels.hasMoreElements())
4110 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4111 (String) labels.nextElement());
4113 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4116 _annotationScoreVectorHash = viewport.getAlignment()
4117 .getAlignmentAnnotation().hashCode();
4122 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4123 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4124 * call. Listeners are added to remove the menu item when the treePanel is
4125 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4129 * Displayed tree window.
4131 * SortBy menu item title.
4134 public void buildTreeMenu()
4136 calculateTree.removeAll();
4137 // build the calculate menu
4139 for (final String type : new String[] { "NJ", "AV" })
4141 String treecalcnm = MessageManager.getString("label.tree_calc_"
4142 + type.toLowerCase());
4143 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4145 JMenuItem tm = new JMenuItem();
4146 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4147 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4148 || sm.isProtein() == !viewport.getAlignment()
4151 String smn = MessageManager.getStringOrReturn(
4152 "label.score_model_", sm.getName());
4153 final String title = MessageManager.formatMessage(
4154 "label.treecalc_title", treecalcnm, smn);
4155 tm.setText(title);//
4156 tm.addActionListener(new java.awt.event.ActionListener()
4159 public void actionPerformed(ActionEvent e)
4161 newTreePanel(type, pwtype, title);
4164 calculateTree.add(tm);
4169 sortByTreeMenu.removeAll();
4171 List<Component> comps = PaintRefresher.components.get(viewport
4172 .getSequenceSetId());
4173 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4174 for (Component comp : comps)
4176 if (comp instanceof TreePanel)
4178 treePanels.add((TreePanel) comp);
4182 if (treePanels.size() < 1)
4184 sortByTreeMenu.setVisible(false);
4188 sortByTreeMenu.setVisible(true);
4190 for (final TreePanel tp : treePanels)
4192 final JMenuItem item = new JMenuItem(tp.getTitle());
4193 item.addActionListener(new java.awt.event.ActionListener()
4196 public void actionPerformed(ActionEvent e)
4198 tp.sortByTree_actionPerformed();
4199 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4204 sortByTreeMenu.add(item);
4208 public boolean sortBy(AlignmentOrder alorder, String undoname)
4210 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4211 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4212 if (undoname != null)
4214 addHistoryItem(new OrderCommand(undoname, oldOrder,
4215 viewport.getAlignment()));
4217 alignPanel.paintAlignment(true);
4222 * Work out whether the whole set of sequences or just the selected set will
4223 * be submitted for multiple alignment.
4226 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4228 // Now, check we have enough sequences
4229 AlignmentView msa = null;
4231 if ((viewport.getSelectionGroup() != null)
4232 && (viewport.getSelectionGroup().getSize() > 1))
4234 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4235 // some common interface!
4237 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4238 * SequenceI[sz = seqs.getSize(false)];
4240 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4241 * seqs.getSequenceAt(i); }
4243 msa = viewport.getAlignmentView(true);
4245 else if (viewport.getSelectionGroup() != null
4246 && viewport.getSelectionGroup().getSize() == 1)
4248 int option = JOptionPane.showConfirmDialog(this,
4249 MessageManager.getString("warn.oneseq_msainput_selection"),
4250 MessageManager.getString("label.invalid_selection"),
4251 JOptionPane.OK_CANCEL_OPTION);
4252 if (option == JOptionPane.OK_OPTION)
4254 msa = viewport.getAlignmentView(false);
4259 msa = viewport.getAlignmentView(false);
4265 * Decides what is submitted to a secondary structure prediction service: the
4266 * first sequence in the alignment, or in the current selection, or, if the
4267 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4268 * region or the whole alignment. (where the first sequence in the set is the
4269 * one that the prediction will be for).
4271 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4273 AlignmentView seqs = null;
4275 if ((viewport.getSelectionGroup() != null)
4276 && (viewport.getSelectionGroup().getSize() > 0))
4278 seqs = viewport.getAlignmentView(true);
4282 seqs = viewport.getAlignmentView(false);
4284 // limit sequences - JBPNote in future - could spawn multiple prediction
4286 // TODO: viewport.getAlignment().isAligned is a global state - the local
4287 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4288 if (!viewport.getAlignment().isAligned(false))
4290 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4291 // TODO: if seqs.getSequences().length>1 then should really have warned
4305 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4307 // Pick the tree file
4308 JalviewFileChooser chooser = new JalviewFileChooser(
4309 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4310 chooser.setFileView(new JalviewFileView());
4311 chooser.setDialogTitle(MessageManager
4312 .getString("label.select_newick_like_tree_file"));
4313 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4315 int value = chooser.showOpenDialog(null);
4317 if (value == JalviewFileChooser.APPROVE_OPTION)
4319 String choice = chooser.getSelectedFile().getPath();
4320 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4321 jalview.io.NewickFile fin = null;
4324 fin = new jalview.io.NewickFile(choice, "File");
4325 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4326 } catch (Exception ex)
4333 .getString("label.problem_reading_tree_file"),
4334 JOptionPane.WARNING_MESSAGE);
4335 ex.printStackTrace();
4337 if (fin != null && fin.hasWarningMessage())
4339 JOptionPane.showMessageDialog(Desktop.desktop, fin
4340 .getWarningMessage(), MessageManager
4341 .getString("label.possible_problem_with_tree_file"),
4342 JOptionPane.WARNING_MESSAGE);
4348 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4350 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4353 public TreePanel ShowNewickTree(NewickFile nf, String title)
4355 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4358 public TreePanel ShowNewickTree(NewickFile nf, String title,
4359 AlignmentView input)
4361 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4364 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4365 int h, int x, int y)
4367 return ShowNewickTree(nf, title, null, w, h, x, y);
4371 * Add a treeviewer for the tree extracted from a newick file object to the
4372 * current alignment view
4379 * Associated alignment input data (or null)
4388 * @return TreePanel handle
4390 public TreePanel ShowNewickTree(NewickFile nf, String title,
4391 AlignmentView input, int w, int h, int x, int y)
4393 TreePanel tp = null;
4399 if (nf.getTree() != null)
4401 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4407 tp.setLocation(x, y);
4410 Desktop.addInternalFrame(tp, title, w, h);
4412 } catch (Exception ex)
4414 ex.printStackTrace();
4420 private boolean buildingMenu = false;
4423 * Generates menu items and listener event actions for web service clients
4426 public void BuildWebServiceMenu()
4428 while (buildingMenu)
4432 System.err.println("Waiting for building menu to finish.");
4434 } catch (Exception e)
4438 final AlignFrame me = this;
4439 buildingMenu = true;
4440 new Thread(new Runnable()
4445 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4448 // System.err.println("Building ws menu again "
4449 // + Thread.currentThread());
4450 // TODO: add support for context dependent disabling of services based
4452 // alignment and current selection
4453 // TODO: add additional serviceHandle parameter to specify abstract
4455 // class independently of AbstractName
4456 // TODO: add in rediscovery GUI function to restart discoverer
4457 // TODO: group services by location as well as function and/or
4459 // object broker mechanism.
4460 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4461 final IProgressIndicator af = me;
4462 final JMenu msawsmenu = new JMenu("Alignment");
4463 final JMenu secstrmenu = new JMenu(
4464 "Secondary Structure Prediction");
4465 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4466 final JMenu analymenu = new JMenu("Analysis");
4467 final JMenu dismenu = new JMenu("Protein Disorder");
4468 // final JMenu msawsmenu = new
4469 // JMenu(MessageManager.getString("label.alignment"));
4470 // final JMenu secstrmenu = new
4471 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4472 // final JMenu seqsrchmenu = new
4473 // JMenu(MessageManager.getString("label.sequence_database_search"));
4474 // final JMenu analymenu = new
4475 // JMenu(MessageManager.getString("label.analysis"));
4476 // final JMenu dismenu = new
4477 // JMenu(MessageManager.getString("label.protein_disorder"));
4478 // JAL-940 - only show secondary structure prediction services from
4479 // the legacy server
4480 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4482 Discoverer.services != null && (Discoverer.services.size() > 0))
4484 // TODO: refactor to allow list of AbstractName/Handler bindings to
4486 // stored or retrieved from elsewhere
4487 // No MSAWS used any more:
4488 // Vector msaws = null; // (Vector)
4489 // Discoverer.services.get("MsaWS");
4490 Vector secstrpr = (Vector) Discoverer.services
4492 if (secstrpr != null)
4494 // Add any secondary structure prediction services
4495 for (int i = 0, j = secstrpr.size(); i < j; i++)
4497 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4499 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4500 .getServiceClient(sh);
4501 int p = secstrmenu.getItemCount();
4502 impl.attachWSMenuEntry(secstrmenu, me);
4503 int q = secstrmenu.getItemCount();
4504 for (int litm = p; litm < q; litm++)
4506 legacyItems.add(secstrmenu.getItem(litm));
4512 // Add all submenus in the order they should appear on the web
4514 wsmenu.add(msawsmenu);
4515 wsmenu.add(secstrmenu);
4516 wsmenu.add(dismenu);
4517 wsmenu.add(analymenu);
4518 // No search services yet
4519 // wsmenu.add(seqsrchmenu);
4521 javax.swing.SwingUtilities.invokeLater(new Runnable()
4528 webService.removeAll();
4529 // first, add discovered services onto the webservices menu
4530 if (wsmenu.size() > 0)
4532 for (int i = 0, j = wsmenu.size(); i < j; i++)
4534 webService.add(wsmenu.get(i));
4539 webService.add(me.webServiceNoServices);
4541 // TODO: move into separate menu builder class.
4542 boolean new_sspred = false;
4543 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4545 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4546 if (jws2servs != null)
4548 if (jws2servs.hasServices())
4550 jws2servs.attachWSMenuEntry(webService, me);
4551 for (Jws2Instance sv : jws2servs.getServices())
4553 if (sv.description.toLowerCase().contains("jpred"))
4555 for (JMenuItem jmi : legacyItems)
4557 jmi.setVisible(false);
4563 if (jws2servs.isRunning())
4565 JMenuItem tm = new JMenuItem(
4566 "Still discovering JABA Services");
4567 tm.setEnabled(false);
4572 build_urlServiceMenu(me.webService);
4573 build_fetchdbmenu(webService);
4574 for (JMenu item : wsmenu)
4576 if (item.getItemCount() == 0)
4578 item.setEnabled(false);
4582 item.setEnabled(true);
4585 } catch (Exception e)
4588 .debug("Exception during web service menu building process.",
4593 } catch (Exception e)
4596 buildingMenu = false;
4603 * construct any groupURL type service menu entries.
4607 private void build_urlServiceMenu(JMenu webService)
4609 // TODO: remove this code when 2.7 is released
4610 // DEBUG - alignmentView
4612 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4613 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4615 * @Override public void actionPerformed(ActionEvent e) {
4616 * jalview.datamodel.AlignmentView
4617 * .testSelectionViews(af.viewport.getAlignment(),
4618 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4620 * }); webService.add(testAlView);
4622 // TODO: refactor to RestClient discoverer and merge menu entries for
4623 // rest-style services with other types of analysis/calculation service
4624 // SHmmr test client - still being implemented.
4625 // DEBUG - alignmentView
4627 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4630 client.attachWSMenuEntry(
4631 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4637 * Searches selected sequences for xRef products and builds the Show
4638 * Cross-References menu (formerly called Show Products)
4640 * @return true if Show Cross-references menu should be enabled.
4642 public boolean canShowProducts()
4644 SequenceI[] selection = viewport.getSequenceSelection();
4645 AlignmentI dataset = viewport.getAlignment().getDataset();
4646 boolean showp = false;
4649 showProducts.removeAll();
4650 final boolean dna = viewport.getAlignment().isNucleotide();
4651 String[] ptypes = (selection == null || selection.length == 0) ? null
4652 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4654 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4657 final AlignFrame af = this;
4658 final String source = ptypes[t];
4659 JMenuItem xtype = new JMenuItem(ptypes[t]);
4660 xtype.addActionListener(new ActionListener()
4664 public void actionPerformed(ActionEvent e)
4666 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4670 showProducts.add(xtype);
4672 showProducts.setVisible(showp);
4673 showProducts.setEnabled(showp);
4674 } catch (Exception e)
4676 jalview.bin.Cache.log
4677 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4684 protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4685 final String source)
4687 Runnable foo = new Runnable()
4693 final long sttime = System.currentTimeMillis();
4694 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4695 "status.searching_for_sequences_from",
4696 new Object[] { source }), sttime);
4699 AlignmentI alignment = AlignFrame.this.getViewport()
4701 AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
4706 * get display scheme (if any) to apply to features
4708 FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
4709 .getFeatureColourScheme(source);
4711 AlignmentI al = makeCrossReferencesAlignment(
4712 alignment.getDataset(), xrefs);
4714 AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4716 if (Cache.getDefault("HIDE_INTRONS", true))
4718 newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
4720 String newtitle = String.format("%s %s %s",
4721 MessageManager.getString(dna ? "label.proteins"
4722 : "label.nucleotides"), MessageManager
4723 .getString("label.for"), getTitle());
4724 newFrame.setTitle(newtitle);
4726 if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4729 * split frame display is turned off in preferences file
4731 Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4733 return; // via finally clause
4737 * Make a copy of this alignment (sharing the same dataset
4738 * sequences). If we are DNA, drop introns and update mappings
4740 AlignmentI copyAlignment = null;
4741 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4742 .getSequenceSelection();
4743 List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4744 boolean copyAlignmentIsAligned = false;
4747 copyAlignment = AlignmentUtils.makeCdsAlignment(
4748 sequenceSelection, cf, alignment);
4749 if (copyAlignment.getHeight() == 0)
4751 System.err.println("Failed to make CDS alignment");
4753 al.getCodonFrames().clear();
4754 al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
4757 * pending getting Embl transcripts to 'align',
4758 * we are only doing this for Ensembl
4760 // TODO proper criteria for 'can align as cdna'
4761 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
4762 || AlignmentUtils.looksLikeEnsembl(alignment))
4764 copyAlignment.alignAs(alignment);
4765 copyAlignmentIsAligned = true;
4770 copyAlignment = AlignmentUtils.makeCopyAlignment(
4771 sequenceSelection, xrefs.getSequencesArray());
4772 copyAlignment.getCodonFrames().addAll(cf);
4774 copyAlignment.setGapCharacter(AlignFrame.this.viewport
4775 .getGapCharacter());
4777 StructureSelectionManager ssm = StructureSelectionManager
4778 .getStructureSelectionManager(Desktop.instance);
4779 ssm.registerMappings(cf);
4781 if (copyAlignment.getHeight() <= 0)
4783 System.err.println("No Sequences generated for xRef type "
4788 * align protein to dna
4790 if (dna && copyAlignmentIsAligned)
4792 al.alignAs(copyAlignment);
4797 * align cdna to protein - currently only if
4798 * fetching and aligning Ensembl transcripts!
4800 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4802 copyAlignment.alignAs(al);
4806 AlignFrame copyThis = new AlignFrame(copyAlignment,
4807 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4808 copyThis.setTitle(AlignFrame.this.getTitle());
4810 boolean showSequenceFeatures = viewport
4811 .isShowSequenceFeatures();
4812 newFrame.setShowSeqFeatures(showSequenceFeatures);
4813 copyThis.setShowSeqFeatures(showSequenceFeatures);
4814 FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4815 .getFeatureRenderer();
4818 * copy feature rendering settings to split frame
4820 newFrame.alignPanel.getSeqPanel().seqCanvas
4821 .getFeatureRenderer()
4822 .transferSettings(myFeatureStyling);
4823 copyThis.alignPanel.getSeqPanel().seqCanvas
4824 .getFeatureRenderer()
4825 .transferSettings(myFeatureStyling);
4828 * apply 'database source' feature configuration
4831 // TODO is this the feature colouring for the original
4832 // alignment or the fetched xrefs? either could be Ensembl
4833 newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
4834 copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
4836 SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4837 dna ? newFrame : copyThis);
4838 newFrame.setVisible(true);
4839 copyThis.setVisible(true);
4840 String linkedTitle = MessageManager
4841 .getString("label.linked_view_title");
4842 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4845 } catch (Exception e)
4848 "Exception when finding crossreferences", e);
4849 } catch (OutOfMemoryError e)
4851 new OOMWarning("whilst fetching crossreferences", e);
4852 } catch (Throwable e)
4854 Cache.log.error("Error when finding crossreferences",
4858 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4859 "status.finished_searching_for_sequences_from",
4860 new Object[] { source }), sttime);
4865 * Makes an alignment containing the given sequences. If this is of the
4866 * same type as the given dataset (nucleotide/protein), then the new
4867 * alignment shares the same dataset, and its dataset sequences are added
4868 * to it. Otherwise a new dataset sequence is created for the
4875 protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
4878 boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
4880 SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4881 for (int s = 0; s < sprods.length; s++)
4883 sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4886 if (dataset.getSequences() == null
4887 || !dataset.getSequences().contains(
4888 sprods[s].getDatasetSequence()))
4890 dataset.addSequence(sprods[s].getDatasetSequence());
4893 sprods[s].updatePDBIds();
4895 Alignment al = new Alignment(sprods);
4898 al.setDataset((Alignment) dataset);
4902 al.createDatasetAlignment();
4908 Thread frunner = new Thread(foo);
4913 * Construct and display a new frame containing the translation of this
4914 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4917 public void showTranslation_actionPerformed(ActionEvent e)
4919 AlignmentI al = null;
4922 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4924 al = dna.translateCdna();
4925 } catch (Exception ex)
4927 jalview.bin.Cache.log.error(
4928 "Exception during translation. Please report this !", ex);
4929 final String msg = MessageManager
4930 .getString("label.error_when_translating_sequences_submit_bug_report");
4931 final String errorTitle = MessageManager
4932 .getString("label.implementation_error")
4933 + MessageManager.getString("translation_failed");
4934 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4935 JOptionPane.ERROR_MESSAGE);
4938 if (al == null || al.getHeight() == 0)
4940 final String msg = MessageManager
4941 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4942 final String errorTitle = MessageManager
4943 .getString("label.translation_failed");
4944 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4945 JOptionPane.WARNING_MESSAGE);
4949 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4950 af.setFileFormat(this.currentFileFormat);
4951 final String newTitle = MessageManager.formatMessage(
4952 "label.translation_of_params",
4953 new Object[] { this.getTitle() });
4954 af.setTitle(newTitle);
4955 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4957 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4958 viewport.openSplitFrame(af, new Alignment(seqs));
4962 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4969 * Set the file format
4973 public void setFileFormat(String fileFormat)
4975 this.currentFileFormat = fileFormat;
4979 * Try to load a features file onto the alignment.
4982 * contents or path to retrieve file
4984 * access mode of file (see jalview.io.AlignFile)
4985 * @return true if features file was parsed correctly.
4987 public boolean parseFeaturesFile(String file, String type)
4989 return avc.parseFeaturesFile(file, type,
4990 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4995 public void refreshFeatureUI(boolean enableIfNecessary)
4997 // note - currently this is only still here rather than in the controller
4998 // because of the featureSettings hard reference that is yet to be
5000 if (enableIfNecessary)
5002 viewport.setShowSequenceFeatures(true);
5003 showSeqFeatures.setSelected(true);
5009 public void dragEnter(DropTargetDragEvent evt)
5014 public void dragExit(DropTargetEvent evt)
5019 public void dragOver(DropTargetDragEvent evt)
5024 public void dropActionChanged(DropTargetDragEvent evt)
5029 public void drop(DropTargetDropEvent evt)
5031 Transferable t = evt.getTransferable();
5032 java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
5036 Desktop.transferFromDropTarget(files, protocols, evt, t);
5037 } catch (Exception e)
5039 e.printStackTrace();
5045 // check to see if any of these files have names matching sequences in
5047 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5048 .getAlignment().getSequencesArray());
5050 * Object[] { String,SequenceI}
5052 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5053 ArrayList<String> filesnotmatched = new ArrayList<String>();
5054 for (int i = 0; i < files.size(); i++)
5056 String file = files.get(i).toString();
5058 String protocol = FormatAdapter.checkProtocol(file);
5059 if (protocol == jalview.io.FormatAdapter.FILE)
5061 File fl = new File(file);
5062 pdbfn = fl.getName();
5064 else if (protocol == jalview.io.FormatAdapter.URL)
5066 URL url = new URL(file);
5067 pdbfn = url.getFile();
5069 if (pdbfn.length() > 0)
5071 // attempt to find a match in the alignment
5072 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5073 int l = 0, c = pdbfn.indexOf(".");
5074 while (mtch == null && c != -1)
5079 } while ((c = pdbfn.indexOf(".", l)) > l);
5082 pdbfn = pdbfn.substring(0, l);
5084 mtch = idm.findAllIdMatches(pdbfn);
5091 type = new IdentifyFile().identify(file, protocol);
5092 } catch (Exception ex)
5098 if (type.equalsIgnoreCase("PDB"))
5100 filesmatched.add(new Object[] { file, protocol, mtch });
5105 // File wasn't named like one of the sequences or wasn't a PDB file.
5106 filesnotmatched.add(file);
5110 if (filesmatched.size() > 0)
5112 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5118 "label.automatically_associate_pdb_files_with_sequences_same_name",
5119 new Object[] { Integer
5125 .getString("label.automatically_associate_pdb_files_by_name"),
5126 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5129 for (Object[] fm : filesmatched)
5131 // try and associate
5132 // TODO: may want to set a standard ID naming formalism for
5133 // associating PDB files which have no IDs.
5134 for (SequenceI toassoc : (SequenceI[]) fm[2])
5136 PDBEntry pe = new AssociatePdbFileWithSeq()
5137 .associatePdbWithSeq((String) fm[0],
5138 (String) fm[1], toassoc, false,
5142 System.err.println("Associated file : "
5143 + ((String) fm[0]) + " with "
5144 + toassoc.getDisplayId(true));
5148 alignPanel.paintAlignment(true);
5152 if (filesnotmatched.size() > 0)
5155 && (Cache.getDefault(
5156 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5162 "label.ignore_unmatched_dropped_files_info",
5163 new Object[] { Integer
5170 .getString("label.ignore_unmatched_dropped_files"),
5171 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5175 for (String fn : filesnotmatched)
5177 loadJalviewDataFile(fn, null, null, null);
5181 } catch (Exception ex)
5183 ex.printStackTrace();
5189 * Attempt to load a "dropped" file or URL string: First by testing whether
5190 * it's an Annotation file, then a JNet file, and finally a features file. If
5191 * all are false then the user may have dropped an alignment file onto this
5195 * either a filename or a URL string.
5197 public void loadJalviewDataFile(String file, String protocol,
5198 String format, SequenceI assocSeq)
5202 if (protocol == null)
5204 protocol = FormatAdapter.checkProtocol(file);
5206 // if the file isn't identified, or not positively identified as some
5207 // other filetype (PFAM is default unidentified alignment file type) then
5208 // try to parse as annotation.
5209 boolean isAnnotation = (format == null || format
5210 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5211 .annotateAlignmentView(viewport, file, protocol) : false;
5215 // first see if its a T-COFFEE score file
5216 TCoffeeScoreFile tcf = null;
5219 tcf = new TCoffeeScoreFile(file, protocol);
5222 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5224 tcoffeeColour.setEnabled(true);
5225 tcoffeeColour.setSelected(true);
5226 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5227 isAnnotation = true;
5229 .setText(MessageManager
5230 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5234 // some problem - if no warning its probable that the ID matching
5235 // process didn't work
5239 tcf.getWarningMessage() == null ? MessageManager
5240 .getString("label.check_file_matches_sequence_ids_alignment")
5241 : tcf.getWarningMessage(),
5243 .getString("label.problem_reading_tcoffee_score_file"),
5244 JOptionPane.WARNING_MESSAGE);
5251 } catch (Exception x)
5254 .debug("Exception when processing data source as T-COFFEE score file",
5260 // try to see if its a JNet 'concise' style annotation file *before*
5262 // try to parse it as a features file
5265 format = new IdentifyFile().identify(file, protocol);
5267 if (format.equalsIgnoreCase("JnetFile"))
5269 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5271 new JnetAnnotationMaker();
5272 JnetAnnotationMaker.add_annotation(predictions,
5273 viewport.getAlignment(), 0, false);
5274 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5275 viewport.getAlignment().setSeqrep(repseq);
5276 ColumnSelection cs = new ColumnSelection();
5277 cs.hideInsertionsFor(repseq);
5278 viewport.setColumnSelection(cs);
5279 isAnnotation = true;
5281 else if (IdentifyFile.FeaturesFile.equals(format))
5283 if (parseFeaturesFile(file, protocol))
5285 alignPanel.paintAlignment(true);
5290 new FileLoader().LoadFile(viewport, file, protocol, format);
5297 alignPanel.adjustAnnotationHeight();
5298 viewport.updateSequenceIdColours();
5299 buildSortByAnnotationScoresMenu();
5300 alignPanel.paintAlignment(true);
5302 } catch (Exception ex)
5304 ex.printStackTrace();
5305 } catch (OutOfMemoryError oom)
5310 } catch (Exception x)
5315 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5316 : "using " + protocol + " from " + file)
5318 + (format != null ? "(parsing as '" + format
5319 + "' file)" : ""), oom, Desktop.desktop);
5324 * Method invoked by the ChangeListener on the tabbed pane, in other words
5325 * when a different tabbed pane is selected by the user or programmatically.
5328 public void tabSelectionChanged(int index)
5332 alignPanel = alignPanels.get(index);
5333 viewport = alignPanel.av;
5334 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5335 setMenusFromViewport(viewport);
5339 * If there is a frame linked to this one in a SplitPane, switch it to the
5340 * same view tab index. No infinite recursion of calls should happen, since
5341 * tabSelectionChanged() should not get invoked on setting the selected
5342 * index to an unchanged value. Guard against setting an invalid index
5343 * before the new view peer tab has been created.
5345 final AlignViewportI peer = viewport.getCodingComplement();
5348 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5349 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5351 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5357 * On right mouse click on view tab, prompt for and set new view name.
5360 public void tabbedPane_mousePressed(MouseEvent e)
5362 if (e.isPopupTrigger())
5364 String msg = MessageManager.getString("label.enter_view_name");
5365 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5366 JOptionPane.QUESTION_MESSAGE);
5370 viewport.viewName = reply;
5371 // TODO warn if reply is in getExistingViewNames()?
5372 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5377 public AlignViewport getCurrentView()
5383 * Open the dialog for regex description parsing.
5386 protected void extractScores_actionPerformed(ActionEvent e)
5388 ParseProperties pp = new jalview.analysis.ParseProperties(
5389 viewport.getAlignment());
5390 // TODO: verify regex and introduce GUI dialog for version 2.5
5391 // if (pp.getScoresFromDescription("col", "score column ",
5392 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5394 if (pp.getScoresFromDescription("description column",
5395 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5397 buildSortByAnnotationScoresMenu();
5405 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5409 protected void showDbRefs_actionPerformed(ActionEvent e)
5411 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5417 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5421 protected void showNpFeats_actionPerformed(ActionEvent e)
5423 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5427 * find the viewport amongst the tabs in this alignment frame and close that
5432 public boolean closeView(AlignViewportI av)
5436 this.closeMenuItem_actionPerformed(false);
5439 Component[] comp = tabbedPane.getComponents();
5440 for (int i = 0; comp != null && i < comp.length; i++)
5442 if (comp[i] instanceof AlignmentPanel)
5444 if (((AlignmentPanel) comp[i]).av == av)
5447 closeView((AlignmentPanel) comp[i]);
5455 protected void build_fetchdbmenu(JMenu webService)
5457 // Temporary hack - DBRef Fetcher always top level ws entry.
5458 // TODO We probably want to store a sequence database checklist in
5459 // preferences and have checkboxes.. rather than individual sources selected
5461 final JMenu rfetch = new JMenu(
5462 MessageManager.getString("action.fetch_db_references"));
5463 rfetch.setToolTipText(MessageManager
5464 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5465 webService.add(rfetch);
5467 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5468 MessageManager.getString("option.trim_retrieved_seqs"));
5469 trimrs.setToolTipText(MessageManager
5470 .getString("label.trim_retrieved_sequences"));
5471 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5472 trimrs.addActionListener(new ActionListener()
5475 public void actionPerformed(ActionEvent e)
5477 trimrs.setSelected(trimrs.isSelected());
5478 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5479 Boolean.valueOf(trimrs.isSelected()).toString());
5483 JMenuItem fetchr = new JMenuItem(
5484 MessageManager.getString("label.standard_databases"));
5485 fetchr.setToolTipText(MessageManager
5486 .getString("label.fetch_embl_uniprot"));
5487 fetchr.addActionListener(new ActionListener()
5491 public void actionPerformed(ActionEvent e)
5493 new Thread(new Runnable()
5498 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5499 .getAlignment().isNucleotide();
5500 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5501 .getSequenceSelection(), alignPanel.alignFrame, null,
5502 alignPanel.alignFrame.featureSettings, isNucleotide);
5503 dbRefFetcher.addListener(new FetchFinishedListenerI()
5506 public void finished()
5508 AlignFrame.this.setMenusForViewport();
5512 .fetchDBRefs(false);
5520 final AlignFrame me = this;
5521 new Thread(new Runnable()
5526 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5527 .getSequenceFetcherSingleton(me);
5528 javax.swing.SwingUtilities.invokeLater(new Runnable()
5533 String[] dbclasses = sf.getOrderedSupportedSources();
5534 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5535 // jalview.util.QuickSort.sort(otherdb, otherdb);
5536 List<DbSourceProxy> otherdb;
5537 JMenu dfetch = new JMenu();
5538 JMenu ifetch = new JMenu();
5539 JMenuItem fetchr = null;
5540 int comp = 0, icomp = 0, mcomp = 15;
5541 String mname = null;
5543 for (String dbclass : dbclasses)
5545 otherdb = sf.getSourceProxy(dbclass);
5546 // add a single entry for this class, or submenu allowing 'fetch
5548 if (otherdb == null || otherdb.size() < 1)
5552 // List<DbSourceProxy> dbs=otherdb;
5553 // otherdb=new ArrayList<DbSourceProxy>();
5554 // for (DbSourceProxy db:dbs)
5556 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5560 mname = "From " + dbclass;
5562 if (otherdb.size() == 1)
5564 final DbSourceProxy[] dassource = otherdb
5565 .toArray(new DbSourceProxy[0]);
5566 DbSourceProxy src = otherdb.get(0);
5567 fetchr = new JMenuItem(src.getDbSource());
5568 fetchr.addActionListener(new ActionListener()
5572 public void actionPerformed(ActionEvent e)
5574 new Thread(new Runnable()
5580 boolean isNucleotide = alignPanel.alignFrame
5581 .getViewport().getAlignment()
5583 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5584 alignPanel.av.getSequenceSelection(),
5585 alignPanel.alignFrame, dassource,
5586 alignPanel.alignFrame.featureSettings,
5589 .addListener(new FetchFinishedListenerI()
5592 public void finished()
5594 AlignFrame.this.setMenusForViewport();
5597 dbRefFetcher.fetchDBRefs(false);
5603 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5604 MessageManager.formatMessage(
5605 "label.fetch_retrieve_from",
5606 new Object[] { src.getDbName() })));
5612 final DbSourceProxy[] dassource = otherdb
5613 .toArray(new DbSourceProxy[0]);
5615 DbSourceProxy src = otherdb.get(0);
5616 fetchr = new JMenuItem(MessageManager.formatMessage(
5617 "label.fetch_all_param",
5618 new Object[] { src.getDbSource() }));
5619 fetchr.addActionListener(new ActionListener()
5622 public void actionPerformed(ActionEvent e)
5624 new Thread(new Runnable()
5630 boolean isNucleotide = alignPanel.alignFrame
5631 .getViewport().getAlignment()
5633 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5634 alignPanel.av.getSequenceSelection(),
5635 alignPanel.alignFrame, dassource,
5636 alignPanel.alignFrame.featureSettings,
5639 .addListener(new FetchFinishedListenerI()
5642 public void finished()
5644 AlignFrame.this.setMenusForViewport();
5647 dbRefFetcher.fetchDBRefs(false);
5653 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5654 MessageManager.formatMessage(
5655 "label.fetch_retrieve_from_all_sources",
5657 Integer.valueOf(otherdb.size())
5658 .toString(), src.getDbSource(),
5659 src.getDbName() })));
5662 // and then build the rest of the individual menus
5663 ifetch = new JMenu(MessageManager.formatMessage(
5664 "label.source_from_db_source",
5665 new Object[] { src.getDbSource() }));
5667 String imname = null;
5669 for (DbSourceProxy sproxy : otherdb)
5671 String dbname = sproxy.getDbName();
5672 String sname = dbname.length() > 5 ? dbname.substring(0,
5673 5) + "..." : dbname;
5674 String msname = dbname.length() > 10 ? dbname.substring(
5675 0, 10) + "..." : dbname;
5678 imname = MessageManager.formatMessage(
5679 "label.from_msname", new Object[] { sname });
5681 fetchr = new JMenuItem(msname);
5682 final DbSourceProxy[] dassrc = { sproxy };
5683 fetchr.addActionListener(new ActionListener()
5687 public void actionPerformed(ActionEvent e)
5689 new Thread(new Runnable()
5695 boolean isNucleotide = alignPanel.alignFrame
5696 .getViewport().getAlignment()
5698 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5699 alignPanel.av.getSequenceSelection(),
5700 alignPanel.alignFrame, dassrc,
5701 alignPanel.alignFrame.featureSettings,
5704 .addListener(new FetchFinishedListenerI()
5707 public void finished()
5709 AlignFrame.this.setMenusForViewport();
5712 dbRefFetcher.fetchDBRefs(false);
5718 fetchr.setToolTipText("<html>"
5719 + MessageManager.formatMessage(
5720 "label.fetch_retrieve_from", new Object[]
5724 if (++icomp >= mcomp || i == (otherdb.size()))
5726 ifetch.setText(MessageManager.formatMessage(
5727 "label.source_to_target", imname, sname));
5729 ifetch = new JMenu();
5737 if (comp >= mcomp || dbi >= (dbclasses.length))
5739 dfetch.setText(MessageManager.formatMessage(
5740 "label.source_to_target", mname, dbclass));
5742 dfetch = new JMenu();
5755 * Left justify the whole alignment.
5758 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5760 AlignmentI al = viewport.getAlignment();
5762 viewport.firePropertyChange("alignment", null, al);
5766 * Right justify the whole alignment.
5769 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5771 AlignmentI al = viewport.getAlignment();
5773 viewport.firePropertyChange("alignment", null, al);
5777 public void setShowSeqFeatures(boolean b)
5779 showSeqFeatures.setSelected(b);
5780 viewport.setShowSequenceFeatures(b);
5787 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5788 * awt.event.ActionEvent)
5791 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5793 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5794 alignPanel.paintAlignment(true);
5801 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5805 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5807 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5808 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5816 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5817 * .event.ActionEvent)
5820 protected void showGroupConservation_actionPerformed(ActionEvent e)
5822 viewport.setShowGroupConservation(showGroupConservation.getState());
5823 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5830 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5831 * .event.ActionEvent)
5834 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5836 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5837 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5844 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5845 * .event.ActionEvent)
5848 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5850 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5851 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5855 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5857 showSequenceLogo.setState(true);
5858 viewport.setShowSequenceLogo(true);
5859 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5860 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5864 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5866 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5873 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5874 * .event.ActionEvent)
5877 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5879 if (avc.makeGroupsFromSelection())
5881 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5882 alignPanel.updateAnnotation();
5883 alignPanel.paintAlignment(true);
5887 public void clearAlignmentSeqRep()
5889 // TODO refactor alignmentseqrep to controller
5890 if (viewport.getAlignment().hasSeqrep())
5892 viewport.getAlignment().setSeqrep(null);
5893 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5894 alignPanel.updateAnnotation();
5895 alignPanel.paintAlignment(true);
5900 protected void createGroup_actionPerformed(ActionEvent e)
5902 if (avc.createGroup())
5904 alignPanel.alignmentChanged();
5909 protected void unGroup_actionPerformed(ActionEvent e)
5913 alignPanel.alignmentChanged();
5918 * make the given alignmentPanel the currently selected tab
5920 * @param alignmentPanel
5922 public void setDisplayedView(AlignmentPanel alignmentPanel)
5924 if (!viewport.getSequenceSetId().equals(
5925 alignmentPanel.av.getSequenceSetId()))
5929 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5931 if (tabbedPane != null
5932 && tabbedPane.getTabCount() > 0
5933 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5934 .getSelectedIndex())
5936 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5941 * Action on selection of menu options to Show or Hide annotations.
5944 * @param forSequences
5945 * update sequence-related annotations
5946 * @param forAlignment
5947 * update non-sequence-related annotations
5950 protected void setAnnotationsVisibility(boolean visible,
5951 boolean forSequences, boolean forAlignment)
5953 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5954 .getAlignmentAnnotation())
5957 * don't display non-positional annotations on an alignment
5959 if (aa.annotations == null)
5963 boolean apply = (aa.sequenceRef == null && forAlignment)
5964 || (aa.sequenceRef != null && forSequences);
5967 aa.visible = visible;
5970 alignPanel.validateAnnotationDimensions(true);
5971 alignPanel.alignmentChanged();
5975 * Store selected annotation sort order for the view and repaint.
5978 protected void sortAnnotations_actionPerformed()
5980 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5982 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5983 alignPanel.paintAlignment(true);
5988 * @return alignment panels in this alignment frame
5990 public List<? extends AlignmentViewPanel> getAlignPanels()
5992 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5996 * Open a new alignment window, with the cDNA associated with this (protein)
5997 * alignment, aligned as is the protein.
5999 protected void viewAsCdna_actionPerformed()
6001 // TODO no longer a menu action - refactor as required
6002 final AlignmentI alignment = getViewport().getAlignment();
6003 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6004 if (mappings == null)
6008 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6009 for (SequenceI aaSeq : alignment.getSequences())
6011 for (AlignedCodonFrame acf : mappings)
6013 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6017 * There is a cDNA mapping for this protein sequence - add to new
6018 * alignment. It will share the same dataset sequence as other mapped
6019 * cDNA (no new mappings need to be created).
6021 final Sequence newSeq = new Sequence(dnaSeq);
6022 newSeq.setDatasetSequence(dnaSeq);
6023 cdnaSeqs.add(newSeq);
6027 if (cdnaSeqs.size() == 0)
6029 // show a warning dialog no mapped cDNA
6032 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6034 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6035 AlignFrame.DEFAULT_HEIGHT);
6036 cdna.alignAs(alignment);
6037 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6039 Desktop.addInternalFrame(alignFrame, newtitle,
6040 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6044 * Set visibility of dna/protein complement view (available when shown in a
6050 protected void showComplement_actionPerformed(boolean show)
6052 SplitContainerI sf = getSplitViewContainer();
6055 sf.setComplementVisible(this, show);
6060 * Generate the reverse (optionally complemented) of the selected sequences,
6061 * and add them to the alignment
6064 protected void showReverse_actionPerformed(boolean complement)
6066 AlignmentI al = null;
6069 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6071 al = dna.reverseCdna(complement);
6072 viewport.addAlignment(al, "");
6073 } catch (Exception ex)
6075 System.err.println(ex.getMessage());
6081 * Try to run a script in the Groovy console, having first ensured that this
6082 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
6083 * be targeted at this alignment.
6086 protected void runGroovy_actionPerformed()
6088 Desktop.setCurrentAlignFrame(this);
6089 groovy.ui.Console console = Desktop.getGroovyConsole();
6090 if (console != null)
6094 console.runScript();
6095 } catch (Exception ex)
6097 System.err.println((ex.toString()));
6099 .showInternalMessageDialog(Desktop.desktop, MessageManager
6100 .getString("label.couldnt_run_groovy_script"),
6102 .getString("label.groovy_support_failed"),
6103 JOptionPane.ERROR_MESSAGE);
6108 System.err.println("Can't run Groovy script as console not found");
6113 * Hides columns containing (or not containing) a specified feature, provided
6114 * that would not leave all columns hidden
6116 * @param featureType
6117 * @param columnsContaining
6120 public boolean hideFeatureColumns(String featureType,
6121 boolean columnsContaining)
6123 boolean notForHiding = avc.markColumnsContainingFeatures(
6124 columnsContaining, false, false, featureType);
6127 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
6128 false, featureType))
6130 getViewport().hideSelectedColumns();
6138 class PrintThread extends Thread
6142 public PrintThread(AlignmentPanel ap)
6147 static PageFormat pf;
6152 PrinterJob printJob = PrinterJob.getPrinterJob();
6156 printJob.setPrintable(ap, pf);
6160 printJob.setPrintable(ap);
6163 if (printJob.printDialog())
6168 } catch (Exception PrintException)
6170 PrintException.printStackTrace();