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.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileLoader;
72 import jalview.io.FormatAdapter;
73 import jalview.io.HtmlSvgOutput;
74 import jalview.io.IdentifyFile;
75 import jalview.io.JPredFile;
76 import jalview.io.JalviewFileChooser;
77 import jalview.io.JalviewFileView;
78 import jalview.io.JnetAnnotationMaker;
79 import jalview.io.NewickFile;
80 import jalview.io.TCoffeeScoreFile;
81 import jalview.io.gff.SequenceOntologyI;
82 import jalview.jbgui.GAlignFrame;
83 import jalview.schemes.Blosum62ColourScheme;
84 import jalview.schemes.BuriedColourScheme;
85 import jalview.schemes.ClustalxColourScheme;
86 import jalview.schemes.ColourSchemeI;
87 import jalview.schemes.ColourSchemeProperty;
88 import jalview.schemes.HelixColourScheme;
89 import jalview.schemes.HydrophobicColourScheme;
90 import jalview.schemes.NucleotideColourScheme;
91 import jalview.schemes.PIDColourScheme;
92 import jalview.schemes.PurinePyrimidineColourScheme;
93 import jalview.schemes.RNAHelicesColourChooser;
94 import jalview.schemes.ResidueProperties;
95 import jalview.schemes.StrandColourScheme;
96 import jalview.schemes.TCoffeeColourScheme;
97 import jalview.schemes.TaylorColourScheme;
98 import jalview.schemes.TurnColourScheme;
99 import jalview.schemes.UserColourScheme;
100 import jalview.schemes.ZappoColourScheme;
101 import jalview.structure.StructureSelectionManager;
102 import jalview.util.MessageManager;
103 import jalview.viewmodel.AlignmentViewport;
104 import jalview.ws.DBRefFetcher;
105 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
106 import jalview.ws.SequenceFetcher;
107 import jalview.ws.jws1.Discoverer;
108 import jalview.ws.jws2.Jws2Discoverer;
109 import jalview.ws.jws2.jabaws2.Jws2Instance;
110 import jalview.ws.seqfetcher.DbSourceProxy;
112 import java.awt.BorderLayout;
113 import java.awt.Component;
114 import java.awt.Rectangle;
115 import java.awt.Toolkit;
116 import java.awt.datatransfer.Clipboard;
117 import java.awt.datatransfer.DataFlavor;
118 import java.awt.datatransfer.StringSelection;
119 import java.awt.datatransfer.Transferable;
120 import java.awt.dnd.DropTargetDragEvent;
121 import java.awt.dnd.DropTargetDropEvent;
122 import java.awt.dnd.DropTargetEvent;
123 import java.awt.dnd.DropTargetListener;
124 import java.awt.event.ActionEvent;
125 import java.awt.event.ActionListener;
126 import java.awt.event.FocusAdapter;
127 import java.awt.event.FocusEvent;
128 import java.awt.event.ItemEvent;
129 import java.awt.event.ItemListener;
130 import java.awt.event.KeyAdapter;
131 import java.awt.event.KeyEvent;
132 import java.awt.event.MouseAdapter;
133 import java.awt.event.MouseEvent;
134 import java.awt.print.PageFormat;
135 import java.awt.print.PrinterJob;
136 import java.beans.PropertyChangeEvent;
139 import java.util.ArrayList;
140 import java.util.Arrays;
141 import java.util.Deque;
142 import java.util.Enumeration;
143 import java.util.Hashtable;
144 import java.util.List;
145 import java.util.Vector;
147 import javax.swing.JCheckBoxMenuItem;
148 import javax.swing.JEditorPane;
149 import javax.swing.JInternalFrame;
150 import javax.swing.JLayeredPane;
151 import javax.swing.JMenu;
152 import javax.swing.JMenuItem;
153 import javax.swing.JOptionPane;
154 import javax.swing.JRadioButtonMenuItem;
155 import javax.swing.JScrollPane;
156 import javax.swing.SwingUtilities;
162 * @version $Revision$
164 public class AlignFrame extends GAlignFrame implements DropTargetListener,
165 IProgressIndicator, AlignViewControllerGuiI
168 public static final int DEFAULT_WIDTH = 700;
170 public static final int DEFAULT_HEIGHT = 500;
173 * The currently displayed panel (selected tabbed view if more than one)
175 public AlignmentPanel alignPanel;
177 AlignViewport viewport;
179 public AlignViewControllerI avc;
181 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
184 * Last format used to load or save alignments in this window
186 FileFormatI currentFileFormat = null;
189 * Current filename for this alignment
191 String fileName = null;
194 * Creates a new AlignFrame object with specific width and height.
200 public AlignFrame(AlignmentI al, int width, int height)
202 this(al, null, width, height);
206 * Creates a new AlignFrame object with specific width, height and
212 * @param sequenceSetId
214 public AlignFrame(AlignmentI al, int width, int height,
215 String sequenceSetId)
217 this(al, null, width, height, sequenceSetId);
221 * Creates a new AlignFrame object with specific width, height and
227 * @param sequenceSetId
230 public AlignFrame(AlignmentI al, int width, int height,
231 String sequenceSetId, String viewId)
233 this(al, null, width, height, sequenceSetId, viewId);
237 * new alignment window with hidden columns
241 * @param hiddenColumns
242 * ColumnSelection or null
244 * Width of alignment frame
248 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
249 int width, int height)
251 this(al, hiddenColumns, width, height, null);
255 * Create alignment frame for al with hiddenColumns, a specific width and
256 * height, and specific sequenceId
259 * @param hiddenColumns
262 * @param sequenceSetId
265 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
266 int width, int height, String sequenceSetId)
268 this(al, hiddenColumns, width, height, sequenceSetId, null);
272 * Create alignment frame for al with hiddenColumns, a specific width and
273 * height, and specific sequenceId
276 * @param hiddenColumns
279 * @param sequenceSetId
284 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
285 int width, int height, String sequenceSetId, String viewId)
287 setSize(width, height);
289 if (al.getDataset() == null)
294 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
296 alignPanel = new AlignmentPanel(this, viewport);
298 addAlignmentPanel(alignPanel, true);
302 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
303 ColumnSelection hiddenColumns, int width, int height)
305 setSize(width, height);
307 if (al.getDataset() == null)
312 viewport = new AlignViewport(al, hiddenColumns);
314 if (hiddenSeqs != null && hiddenSeqs.length > 0)
316 viewport.hideSequence(hiddenSeqs);
318 alignPanel = new AlignmentPanel(this, viewport);
319 addAlignmentPanel(alignPanel, true);
324 * Make a new AlignFrame from existing alignmentPanels
331 public AlignFrame(AlignmentPanel ap)
335 addAlignmentPanel(ap, false);
340 * initalise the alignframe from the underlying viewport data and the
345 if (!Jalview.isHeadlessMode())
347 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
350 avc = new jalview.controller.AlignViewController(this, viewport,
352 if (viewport.getAlignmentConservationAnnotation() == null)
354 BLOSUM62Colour.setEnabled(false);
355 conservationMenuItem.setEnabled(false);
356 modifyConservation.setEnabled(false);
357 // PIDColour.setEnabled(false);
358 // abovePIDThreshold.setEnabled(false);
359 // modifyPID.setEnabled(false);
362 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
365 if (sortby.equals("Id"))
367 sortIDMenuItem_actionPerformed(null);
369 else if (sortby.equals("Pairwise Identity"))
371 sortPairwiseMenuItem_actionPerformed(null);
374 if (Desktop.desktop != null)
376 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
377 addServiceListeners();
378 setGUINucleotide(viewport.getAlignment().isNucleotide());
382 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
384 setMenusFromViewport(viewport);
385 buildSortByAnnotationScoresMenu();
388 if (viewport.getWrapAlignment())
390 wrapMenuItem_actionPerformed(null);
393 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
395 this.overviewMenuItem_actionPerformed(null);
400 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
401 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
402 final String menuLabel = MessageManager
403 .getString("label.copy_format_from");
404 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
405 new ViewSetProvider()
409 public AlignmentPanel[] getAllAlignmentPanels()
412 origview.add(alignPanel);
413 // make an array of all alignment panels except for this one
414 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
415 Arrays.asList(Desktop.getAlignmentPanels(null)));
416 aps.remove(AlignFrame.this.alignPanel);
417 return aps.toArray(new AlignmentPanel[aps.size()]);
419 }, selviews, new ItemListener()
423 public void itemStateChanged(ItemEvent e)
425 if (origview.size() > 0)
427 final AlignmentPanel ap = origview.get(0);
430 * Copy the ViewStyle of the selected panel to 'this one'.
431 * Don't change value of 'scaleProteinAsCdna' unless copying
434 ViewStyleI vs = selviews.get(0).getAlignViewport()
436 boolean fromSplitFrame = selviews.get(0)
437 .getAlignViewport().getCodingComplement() != null;
440 vs.setScaleProteinAsCdna(ap.getAlignViewport()
441 .getViewStyle().isScaleProteinAsCdna());
443 ap.getAlignViewport().setViewStyle(vs);
446 * Also rescale ViewStyle of SplitFrame complement if there is
447 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
448 * the whole ViewStyle (allow cDNA protein to have different
451 AlignViewportI complement = ap.getAlignViewport()
452 .getCodingComplement();
453 if (complement != null && vs.isScaleProteinAsCdna())
455 AlignFrame af = Desktop.getAlignFrameFor(complement);
456 ((SplitFrame) af.getSplitViewContainer())
458 af.setMenusForViewport();
462 ap.setSelected(true);
463 ap.alignFrame.setMenusForViewport();
468 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
469 .indexOf("devel") > -1
470 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
471 .indexOf("test") > -1)
473 formatMenu.add(vsel);
475 addFocusListener(new FocusAdapter()
478 public void focusGained(FocusEvent e)
480 Jalview.setCurrentAlignFrame(AlignFrame.this);
487 * Change the filename and format for the alignment, and enable the 'reload'
488 * button functionality.
495 public void setFileName(String file, FileFormatI format)
498 setFileFormat(format);
499 reload.setEnabled(true);
503 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
506 void addKeyListener()
508 addKeyListener(new KeyAdapter()
511 public void keyPressed(KeyEvent evt)
513 if (viewport.cursorMode
514 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
515 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
516 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
517 && Character.isDigit(evt.getKeyChar()))
519 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
522 switch (evt.getKeyCode())
525 case 27: // escape key
526 deselectAllSequenceMenuItem_actionPerformed(null);
530 case KeyEvent.VK_DOWN:
531 if (evt.isAltDown() || !viewport.cursorMode)
533 moveSelectedSequences(false);
535 if (viewport.cursorMode)
537 alignPanel.getSeqPanel().moveCursor(0, 1);
542 if (evt.isAltDown() || !viewport.cursorMode)
544 moveSelectedSequences(true);
546 if (viewport.cursorMode)
548 alignPanel.getSeqPanel().moveCursor(0, -1);
553 case KeyEvent.VK_LEFT:
554 if (evt.isAltDown() || !viewport.cursorMode)
556 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
560 alignPanel.getSeqPanel().moveCursor(-1, 0);
565 case KeyEvent.VK_RIGHT:
566 if (evt.isAltDown() || !viewport.cursorMode)
568 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
572 alignPanel.getSeqPanel().moveCursor(1, 0);
576 case KeyEvent.VK_SPACE:
577 if (viewport.cursorMode)
579 alignPanel.getSeqPanel().insertGapAtCursor(
580 evt.isControlDown() || evt.isShiftDown()
585 // case KeyEvent.VK_A:
586 // if (viewport.cursorMode)
588 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
589 // //System.out.println("A");
593 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
594 * System.out.println("closing bracket"); } break;
596 case KeyEvent.VK_DELETE:
597 case KeyEvent.VK_BACK_SPACE:
598 if (!viewport.cursorMode)
600 cut_actionPerformed(null);
604 alignPanel.getSeqPanel().deleteGapAtCursor(
605 evt.isControlDown() || evt.isShiftDown()
612 if (viewport.cursorMode)
614 alignPanel.getSeqPanel().setCursorRow();
618 if (viewport.cursorMode && !evt.isControlDown())
620 alignPanel.getSeqPanel().setCursorColumn();
624 if (viewport.cursorMode)
626 alignPanel.getSeqPanel().setCursorPosition();
630 case KeyEvent.VK_ENTER:
631 case KeyEvent.VK_COMMA:
632 if (viewport.cursorMode)
634 alignPanel.getSeqPanel().setCursorRowAndColumn();
639 if (viewport.cursorMode)
641 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
645 if (viewport.cursorMode)
647 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
652 viewport.cursorMode = !viewport.cursorMode;
653 statusBar.setText(MessageManager.formatMessage(
654 "label.keyboard_editing_mode",
655 new String[] { (viewport.cursorMode ? "on" : "off") }));
656 if (viewport.cursorMode)
658 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
659 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
661 alignPanel.getSeqPanel().seqCanvas.repaint();
667 Help.showHelpWindow();
668 } catch (Exception ex)
670 ex.printStackTrace();
675 boolean toggleSeqs = !evt.isControlDown();
676 boolean toggleCols = !evt.isShiftDown();
677 toggleHiddenRegions(toggleSeqs, toggleCols);
680 case KeyEvent.VK_PAGE_UP:
681 if (viewport.getWrapAlignment())
683 alignPanel.scrollUp(true);
687 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
688 - viewport.endSeq + viewport.startSeq);
691 case KeyEvent.VK_PAGE_DOWN:
692 if (viewport.getWrapAlignment())
694 alignPanel.scrollUp(false);
698 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
699 + viewport.endSeq - viewport.startSeq);
706 public void keyReleased(KeyEvent evt)
708 switch (evt.getKeyCode())
710 case KeyEvent.VK_LEFT:
711 if (evt.isAltDown() || !viewport.cursorMode)
713 viewport.firePropertyChange("alignment", null, viewport
714 .getAlignment().getSequences());
718 case KeyEvent.VK_RIGHT:
719 if (evt.isAltDown() || !viewport.cursorMode)
721 viewport.firePropertyChange("alignment", null, viewport
722 .getAlignment().getSequences());
730 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
732 ap.alignFrame = this;
733 avc = new jalview.controller.AlignViewController(this, viewport,
738 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
740 int aSize = alignPanels.size();
742 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
744 if (aSize == 1 && ap.av.viewName == null)
746 this.getContentPane().add(ap, BorderLayout.CENTER);
752 setInitialTabVisible();
755 expandViews.setEnabled(true);
756 gatherViews.setEnabled(true);
757 tabbedPane.addTab(ap.av.viewName, ap);
759 ap.setVisible(false);
764 if (ap.av.isPadGaps())
766 ap.av.getAlignment().padGaps();
768 ap.av.updateConservation(ap);
769 ap.av.updateConsensus(ap);
770 ap.av.updateStrucConsensus(ap);
774 public void setInitialTabVisible()
776 expandViews.setEnabled(true);
777 gatherViews.setEnabled(true);
778 tabbedPane.setVisible(true);
779 AlignmentPanel first = alignPanels.get(0);
780 tabbedPane.addTab(first.av.viewName, first);
781 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
784 public AlignViewport getViewport()
789 /* Set up intrinsic listeners for dynamically generated GUI bits. */
790 private void addServiceListeners()
792 final java.beans.PropertyChangeListener thisListener;
793 Desktop.instance.addJalviewPropertyChangeListener("services",
794 thisListener = new java.beans.PropertyChangeListener()
797 public void propertyChange(PropertyChangeEvent evt)
799 // // System.out.println("Discoverer property change.");
800 // if (evt.getPropertyName().equals("services"))
802 SwingUtilities.invokeLater(new Runnable()
809 .println("Rebuild WS Menu for service change");
810 BuildWebServiceMenu();
817 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
820 public void internalFrameClosed(
821 javax.swing.event.InternalFrameEvent evt)
823 // System.out.println("deregistering discoverer listener");
824 Desktop.instance.removeJalviewPropertyChangeListener("services",
826 closeMenuItem_actionPerformed(true);
829 // Finally, build the menu once to get current service state
830 new Thread(new Runnable()
835 BuildWebServiceMenu();
841 * Configure menu items that vary according to whether the alignment is
842 * nucleotide or protein
846 public void setGUINucleotide(boolean nucleotide)
848 showTranslation.setVisible(nucleotide);
849 showReverse.setVisible(nucleotide);
850 showReverseComplement.setVisible(nucleotide);
851 conservationMenuItem.setEnabled(!nucleotide);
852 modifyConservation.setEnabled(!nucleotide);
853 showGroupConservation.setEnabled(!nucleotide);
854 rnahelicesColour.setEnabled(nucleotide);
855 purinePyrimidineColour.setEnabled(nucleotide);
856 showComplementMenuItem.setText(nucleotide ? MessageManager
857 .getString("label.protein") : MessageManager
858 .getString("label.nucleotide"));
859 setColourSelected(jalview.bin.Cache.getDefault(
860 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
861 : Preferences.DEFAULT_COLOUR_PROT, "None"));
865 * set up menus for the current viewport. This may be called after any
866 * operation that affects the data in the current view (selection changed,
867 * etc) to update the menus to reflect the new state.
870 public void setMenusForViewport()
872 setMenusFromViewport(viewport);
876 * Need to call this method when tabs are selected for multiple views, or when
877 * loading from Jalview2XML.java
882 void setMenusFromViewport(AlignViewport av)
884 padGapsMenuitem.setSelected(av.isPadGaps());
885 colourTextMenuItem.setSelected(av.isShowColourText());
886 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
887 conservationMenuItem.setSelected(av.getConservationSelected());
888 seqLimits.setSelected(av.getShowJVSuffix());
889 idRightAlign.setSelected(av.isRightAlignIds());
890 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
891 renderGapsMenuItem.setSelected(av.isRenderGaps());
892 wrapMenuItem.setSelected(av.getWrapAlignment());
893 scaleAbove.setVisible(av.getWrapAlignment());
894 scaleLeft.setVisible(av.getWrapAlignment());
895 scaleRight.setVisible(av.getWrapAlignment());
896 annotationPanelMenuItem.setState(av.isShowAnnotation());
898 * Show/hide annotations only enabled if annotation panel is shown
900 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
901 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
902 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
903 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
904 viewBoxesMenuItem.setSelected(av.getShowBoxes());
905 viewTextMenuItem.setSelected(av.getShowText());
906 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
907 showGroupConsensus.setSelected(av.isShowGroupConsensus());
908 showGroupConservation.setSelected(av.isShowGroupConservation());
909 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
910 showSequenceLogo.setSelected(av.isShowSequenceLogo());
911 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
913 setColourSelected(ColourSchemeProperty.getColourName(av
914 .getGlobalColourScheme()));
916 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
917 hiddenMarkers.setState(av.getShowHiddenMarkers());
918 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
919 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
920 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
921 autoCalculate.setSelected(av.autoCalculateConsensus);
922 sortByTree.setSelected(av.sortByTree);
923 listenToViewSelections.setSelected(av.followSelection);
924 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
926 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
928 showProducts.setEnabled(canShowProducts());
929 setGroovyEnabled(Desktop.getGroovyConsole() != null);
935 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
939 public void setGroovyEnabled(boolean b)
941 runGroovy.setEnabled(b);
944 private IProgressIndicator progressBar;
949 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
952 public void setProgressBar(String message, long id)
954 progressBar.setProgressBar(message, id);
958 public void registerHandler(final long id,
959 final IProgressIndicatorHandler handler)
961 progressBar.registerHandler(id, handler);
966 * @return true if any progress bars are still active
969 public boolean operationInProgress()
971 return progressBar.operationInProgress();
975 public void setStatus(String text)
977 statusBar.setText(text);
981 * Added so Castor Mapping file can obtain Jalview Version
983 public String getVersion()
985 return jalview.bin.Cache.getProperty("VERSION");
988 public FeatureRenderer getFeatureRenderer()
990 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
994 public void fetchSequence_actionPerformed(ActionEvent e)
996 new jalview.gui.SequenceFetcher(this);
1000 public void addFromFile_actionPerformed(ActionEvent e)
1002 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1006 public void reload_actionPerformed(ActionEvent e)
1008 if (fileName != null)
1010 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1011 // originating file's format
1012 // TODO: work out how to recover feature settings for correct view(s) when
1013 // file is reloaded.
1014 if (currentFileFormat == FileFormat.Jalview)
1016 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1017 for (int i = 0; i < frames.length; i++)
1019 if (frames[i] instanceof AlignFrame && frames[i] != this
1020 && ((AlignFrame) frames[i]).fileName != null
1021 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1025 frames[i].setSelected(true);
1026 Desktop.instance.closeAssociatedWindows();
1027 } catch (java.beans.PropertyVetoException ex)
1033 Desktop.instance.closeAssociatedWindows();
1035 FileLoader loader = new FileLoader();
1036 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1037 : DataSourceType.FILE;
1038 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1042 Rectangle bounds = this.getBounds();
1044 FileLoader loader = new FileLoader();
1045 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1046 : DataSourceType.FILE;
1047 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1048 protocol, currentFileFormat);
1050 newframe.setBounds(bounds);
1051 if (featureSettings != null && featureSettings.isShowing())
1053 final Rectangle fspos = featureSettings.frame.getBounds();
1054 // TODO: need a 'show feature settings' function that takes bounds -
1055 // need to refactor Desktop.addFrame
1056 newframe.featureSettings_actionPerformed(null);
1057 final FeatureSettings nfs = newframe.featureSettings;
1058 SwingUtilities.invokeLater(new Runnable()
1063 nfs.frame.setBounds(fspos);
1066 this.featureSettings.close();
1067 this.featureSettings = null;
1069 this.closeMenuItem_actionPerformed(true);
1075 public void addFromText_actionPerformed(ActionEvent e)
1077 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1082 public void addFromURL_actionPerformed(ActionEvent e)
1084 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1088 public void save_actionPerformed(ActionEvent e)
1090 if (fileName == null || (currentFileFormat == null)
1091 || fileName.startsWith("http"))
1093 saveAs_actionPerformed(null);
1097 saveAlignment(fileName, currentFileFormat);
1108 public void saveAs_actionPerformed(ActionEvent e)
1110 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1111 Cache.getProperty("LAST_DIRECTORY"),
1112 // AppletFormatAdapter.WRITABLE_EXTENSIONS,
1113 // AppletFormatAdapter.WRITABLE_FNAMES,
1114 currentFileFormat.toString(), false);
1116 chooser.setFileView(new JalviewFileView());
1117 chooser.setDialogTitle(MessageManager
1118 .getString("label.save_alignment_to_file"));
1119 chooser.setToolTipText(MessageManager.getString("action.save"));
1121 int value = chooser.showSaveDialog(this);
1123 if (value == JalviewFileChooser.APPROVE_OPTION)
1125 currentFileFormat = chooser.getSelectedFormat();
1126 while (currentFileFormat == null)
1129 .showInternalMessageDialog(
1132 .getString("label.select_file_format_before_saving"),
1134 .getString("label.file_format_not_specified"),
1135 JOptionPane.WARNING_MESSAGE);
1136 currentFileFormat = chooser.getSelectedFormat();
1137 value = chooser.showSaveDialog(this);
1138 if (value != JalviewFileChooser.APPROVE_OPTION)
1144 fileName = chooser.getSelectedFile().getPath();
1146 Cache.setProperty("DEFAULT_FILE_FORMAT",
1147 currentFileFormat.toString());
1149 Cache.setProperty("LAST_DIRECTORY", fileName);
1150 saveAlignment(fileName, currentFileFormat);
1154 public boolean saveAlignment(String file, FileFormatI format)
1156 boolean success = true;
1158 if (format == FileFormat.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 FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
1267 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1269 if (exportData.getSettings().isCancelled())
1273 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1274 cap.setForInput(null);
1277 FileFormatI format = fileFormat;
1278 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1279 .formatSequences(format,
1280 exportData.getAlignment(),
1281 exportData.getOmitHidden(),
1282 exportData.getStartEndPostions(),
1283 viewport.getColumnSelection()));
1284 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1285 "label.alignment_output_command",
1286 new Object[] { e.getActionCommand() }), 600, 500);
1287 } catch (OutOfMemoryError oom)
1289 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1295 public static AlignmentExportData getAlignmentForExport(
1296 FileFormatI format, AlignViewportI viewport,
1297 AlignExportSettingI exportSettings)
1299 AlignmentI alignmentToExport = null;
1300 AlignExportSettingI settings = exportSettings;
1301 String[] omitHidden = null;
1303 HiddenSequences hiddenSeqs = viewport.getAlignment()
1304 .getHiddenSequences();
1306 alignmentToExport = viewport.getAlignment();
1308 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1309 if (settings == null)
1311 settings = new AlignExportSettings(hasHiddenSeqs,
1312 viewport.hasHiddenColumns(), format);
1314 // settings.isExportAnnotations();
1316 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1318 omitHidden = viewport.getViewAsString(false,
1319 settings.isExportHiddenSequences());
1322 int[] alignmentStartEnd = new int[2];
1323 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1325 alignmentToExport = hiddenSeqs.getFullAlignment();
1329 alignmentToExport = viewport.getAlignment();
1331 alignmentStartEnd = alignmentToExport
1332 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1333 .getHiddenColumns());
1334 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1335 omitHidden, alignmentStartEnd, settings);
1346 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1348 new HtmlSvgOutput(null, alignPanel);
1352 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1354 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1355 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1358 public void createImageMap(File file, String image)
1360 alignPanel.makePNGImageMap(file, image);
1370 public void createPNG(File f)
1372 alignPanel.makePNG(f);
1382 public void createEPS(File f)
1384 alignPanel.makeEPS(f);
1388 public void createSVG(File f)
1390 alignPanel.makeSVG(f);
1394 public void pageSetup_actionPerformed(ActionEvent e)
1396 PrinterJob printJob = PrinterJob.getPrinterJob();
1397 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1407 public void printMenuItem_actionPerformed(ActionEvent e)
1409 // Putting in a thread avoids Swing painting problems
1410 PrintThread thread = new PrintThread(alignPanel);
1415 public void exportFeatures_actionPerformed(ActionEvent e)
1417 new AnnotationExporter().exportFeatures(alignPanel);
1421 public void exportAnnotations_actionPerformed(ActionEvent e)
1423 new AnnotationExporter().exportAnnotations(alignPanel);
1427 public void associatedData_actionPerformed(ActionEvent e)
1429 // Pick the tree file
1430 JalviewFileChooser chooser = new JalviewFileChooser(
1431 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1432 chooser.setFileView(new JalviewFileView());
1433 chooser.setDialogTitle(MessageManager
1434 .getString("label.load_jalview_annotations"));
1435 chooser.setToolTipText(MessageManager
1436 .getString("label.load_jalview_annotations"));
1438 int value = chooser.showOpenDialog(null);
1440 if (value == JalviewFileChooser.APPROVE_OPTION)
1442 String choice = chooser.getSelectedFile().getPath();
1443 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1444 loadJalviewDataFile(choice, null, null, null);
1450 * Close the current view or all views in the alignment frame. If the frame
1451 * only contains one view then the alignment will be removed from memory.
1453 * @param closeAllTabs
1456 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1458 if (alignPanels != null && alignPanels.size() < 2)
1460 closeAllTabs = true;
1465 if (alignPanels != null)
1469 if (this.isClosed())
1471 // really close all the windows - otherwise wait till
1472 // setClosed(true) is called
1473 for (int i = 0; i < alignPanels.size(); i++)
1475 AlignmentPanel ap = alignPanels.get(i);
1482 closeView(alignPanel);
1489 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1490 * be called recursively, with the frame now in 'closed' state
1492 this.setClosed(true);
1494 } catch (Exception ex)
1496 ex.printStackTrace();
1501 * Close the specified panel and close up tabs appropriately.
1503 * @param panelToClose
1505 public void closeView(AlignmentPanel panelToClose)
1507 int index = tabbedPane.getSelectedIndex();
1508 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1509 alignPanels.remove(panelToClose);
1510 panelToClose.closePanel();
1511 panelToClose = null;
1513 tabbedPane.removeTabAt(closedindex);
1514 tabbedPane.validate();
1516 if (index > closedindex || index == tabbedPane.getTabCount())
1518 // modify currently selected tab index if necessary.
1522 this.tabSelectionChanged(index);
1528 void updateEditMenuBar()
1531 if (viewport.getHistoryList().size() > 0)
1533 undoMenuItem.setEnabled(true);
1534 CommandI command = viewport.getHistoryList().peek();
1535 undoMenuItem.setText(MessageManager.formatMessage(
1536 "label.undo_command",
1537 new Object[] { command.getDescription() }));
1541 undoMenuItem.setEnabled(false);
1542 undoMenuItem.setText(MessageManager.getString("action.undo"));
1545 if (viewport.getRedoList().size() > 0)
1547 redoMenuItem.setEnabled(true);
1549 CommandI command = viewport.getRedoList().peek();
1550 redoMenuItem.setText(MessageManager.formatMessage(
1551 "label.redo_command",
1552 new Object[] { command.getDescription() }));
1556 redoMenuItem.setEnabled(false);
1557 redoMenuItem.setText(MessageManager.getString("action.redo"));
1562 public void addHistoryItem(CommandI command)
1564 if (command.getSize() > 0)
1566 viewport.addToHistoryList(command);
1567 viewport.clearRedoList();
1568 updateEditMenuBar();
1569 viewport.updateHiddenColumns();
1570 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1571 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1572 // viewport.getColumnSelection()
1573 // .getHiddenColumns().size() > 0);
1579 * @return alignment objects for all views
1581 AlignmentI[] getViewAlignments()
1583 if (alignPanels != null)
1585 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1587 for (AlignmentPanel ap : alignPanels)
1589 als[i++] = ap.av.getAlignment();
1593 if (viewport != null)
1595 return new AlignmentI[] { viewport.getAlignment() };
1607 protected void undoMenuItem_actionPerformed(ActionEvent e)
1609 if (viewport.getHistoryList().isEmpty())
1613 CommandI command = viewport.getHistoryList().pop();
1614 viewport.addToRedoList(command);
1615 command.undoCommand(getViewAlignments());
1617 AlignmentViewport originalSource = getOriginatingSource(command);
1618 updateEditMenuBar();
1620 if (originalSource != null)
1622 if (originalSource != viewport)
1625 .warn("Implementation worry: mismatch of viewport origin for undo");
1627 originalSource.updateHiddenColumns();
1628 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1630 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1631 // viewport.getColumnSelection()
1632 // .getHiddenColumns().size() > 0);
1633 originalSource.firePropertyChange("alignment", null, originalSource
1634 .getAlignment().getSequences());
1645 protected void redoMenuItem_actionPerformed(ActionEvent e)
1647 if (viewport.getRedoList().size() < 1)
1652 CommandI command = viewport.getRedoList().pop();
1653 viewport.addToHistoryList(command);
1654 command.doCommand(getViewAlignments());
1656 AlignmentViewport originalSource = getOriginatingSource(command);
1657 updateEditMenuBar();
1659 if (originalSource != null)
1662 if (originalSource != viewport)
1665 .warn("Implementation worry: mismatch of viewport origin for redo");
1667 originalSource.updateHiddenColumns();
1668 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1670 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1671 // viewport.getColumnSelection()
1672 // .getHiddenColumns().size() > 0);
1673 originalSource.firePropertyChange("alignment", null, originalSource
1674 .getAlignment().getSequences());
1678 AlignmentViewport getOriginatingSource(CommandI command)
1680 AlignmentViewport originalSource = null;
1681 // For sequence removal and addition, we need to fire
1682 // the property change event FROM the viewport where the
1683 // original alignment was altered
1684 AlignmentI al = null;
1685 if (command instanceof EditCommand)
1687 EditCommand editCommand = (EditCommand) command;
1688 al = editCommand.getAlignment();
1689 List<Component> comps = PaintRefresher.components.get(viewport
1690 .getSequenceSetId());
1692 for (Component comp : comps)
1694 if (comp instanceof AlignmentPanel)
1696 if (al == ((AlignmentPanel) comp).av.getAlignment())
1698 originalSource = ((AlignmentPanel) comp).av;
1705 if (originalSource == null)
1707 // The original view is closed, we must validate
1708 // the current view against the closed view first
1711 PaintRefresher.validateSequences(al, viewport.getAlignment());
1714 originalSource = viewport;
1717 return originalSource;
1726 public void moveSelectedSequences(boolean up)
1728 SequenceGroup sg = viewport.getSelectionGroup();
1734 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1735 viewport.getHiddenRepSequences(), up);
1736 alignPanel.paintAlignment(true);
1739 synchronized void slideSequences(boolean right, int size)
1741 List<SequenceI> sg = new ArrayList<SequenceI>();
1742 if (viewport.cursorMode)
1744 sg.add(viewport.getAlignment().getSequenceAt(
1745 alignPanel.getSeqPanel().seqCanvas.cursorY));
1747 else if (viewport.getSelectionGroup() != null
1748 && viewport.getSelectionGroup().getSize() != viewport
1749 .getAlignment().getHeight())
1751 sg = viewport.getSelectionGroup().getSequences(
1752 viewport.getHiddenRepSequences());
1760 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1762 for (SequenceI seq : viewport.getAlignment().getSequences())
1764 if (!sg.contains(seq))
1766 invertGroup.add(seq);
1770 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1772 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1773 for (int i = 0; i < invertGroup.size(); i++)
1775 seqs2[i] = invertGroup.get(i);
1778 SlideSequencesCommand ssc;
1781 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1782 size, viewport.getGapCharacter());
1786 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1787 size, viewport.getGapCharacter());
1790 int groupAdjustment = 0;
1791 if (ssc.getGapsInsertedBegin() && right)
1793 if (viewport.cursorMode)
1795 alignPanel.getSeqPanel().moveCursor(size, 0);
1799 groupAdjustment = size;
1802 else if (!ssc.getGapsInsertedBegin() && !right)
1804 if (viewport.cursorMode)
1806 alignPanel.getSeqPanel().moveCursor(-size, 0);
1810 groupAdjustment = -size;
1814 if (groupAdjustment != 0)
1816 viewport.getSelectionGroup().setStartRes(
1817 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1818 viewport.getSelectionGroup().setEndRes(
1819 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1823 * just extend the last slide command if compatible; but not if in
1824 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1826 boolean appendHistoryItem = false;
1827 Deque<CommandI> historyList = viewport.getHistoryList();
1828 boolean inSplitFrame = getSplitViewContainer() != null;
1829 if (!inSplitFrame && historyList != null && historyList.size() > 0
1830 && historyList.peek() instanceof SlideSequencesCommand)
1832 appendHistoryItem = ssc
1833 .appendSlideCommand((SlideSequencesCommand) historyList
1837 if (!appendHistoryItem)
1839 addHistoryItem(ssc);
1852 protected void copy_actionPerformed(ActionEvent e)
1855 if (viewport.getSelectionGroup() == null)
1859 // TODO: preserve the ordering of displayed alignment annotation in any
1860 // internal paste (particularly sequence associated annotation)
1861 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1862 String[] omitHidden = null;
1864 if (viewport.hasHiddenColumns())
1866 omitHidden = viewport.getViewAsString(true);
1869 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1873 StringSelection ss = new StringSelection(output);
1877 jalview.gui.Desktop.internalCopy = true;
1878 // Its really worth setting the clipboard contents
1879 // to empty before setting the large StringSelection!!
1880 Toolkit.getDefaultToolkit().getSystemClipboard()
1881 .setContents(new StringSelection(""), null);
1883 Toolkit.getDefaultToolkit().getSystemClipboard()
1884 .setContents(ss, Desktop.instance);
1885 } catch (OutOfMemoryError er)
1887 new OOMWarning("copying region", er);
1891 ArrayList<int[]> hiddenColumns = null;
1892 if (viewport.hasHiddenColumns())
1894 hiddenColumns = new ArrayList<int[]>();
1895 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1896 .getSelectionGroup().getEndRes();
1897 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1899 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1901 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1902 region[1] - hiddenOffset });
1907 Desktop.jalviewClipboard = new Object[] { seqs,
1908 viewport.getAlignment().getDataset(), hiddenColumns };
1909 statusBar.setText(MessageManager.formatMessage(
1910 "label.copied_sequences_to_clipboard", new Object[] { Integer
1911 .valueOf(seqs.length).toString() }));
1921 protected void pasteNew_actionPerformed(ActionEvent e)
1933 protected void pasteThis_actionPerformed(ActionEvent e)
1939 * Paste contents of Jalview clipboard
1941 * @param newAlignment
1942 * true to paste to a new alignment, otherwise add to this.
1944 void paste(boolean newAlignment)
1946 boolean externalPaste = true;
1949 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1950 Transferable contents = c.getContents(this);
1952 if (contents == null)
1961 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1962 if (str.length() < 1)
1967 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1969 } catch (OutOfMemoryError er)
1971 new OOMWarning("Out of memory pasting sequences!!", er);
1975 SequenceI[] sequences;
1976 boolean annotationAdded = false;
1977 AlignmentI alignment = null;
1979 if (Desktop.jalviewClipboard != null)
1981 // The clipboard was filled from within Jalview, we must use the
1983 // And dataset from the copied alignment
1984 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1985 // be doubly sure that we create *new* sequence objects.
1986 sequences = new SequenceI[newseq.length];
1987 for (int i = 0; i < newseq.length; i++)
1989 sequences[i] = new Sequence(newseq[i]);
1991 alignment = new Alignment(sequences);
1992 externalPaste = false;
1996 // parse the clipboard as an alignment.
1997 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1999 sequences = alignment.getSequencesArray();
2003 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2009 if (Desktop.jalviewClipboard != null)
2011 // dataset is inherited
2012 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2016 // new dataset is constructed
2017 alignment.setDataset(null);
2019 alwidth = alignment.getWidth() + 1;
2023 AlignmentI pastedal = alignment; // preserve pasted alignment object
2024 // Add pasted sequences and dataset into existing alignment.
2025 alignment = viewport.getAlignment();
2026 alwidth = alignment.getWidth() + 1;
2027 // decide if we need to import sequences from an existing dataset
2028 boolean importDs = Desktop.jalviewClipboard != null
2029 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2030 // importDs==true instructs us to copy over new dataset sequences from
2031 // an existing alignment
2032 Vector newDs = (importDs) ? new Vector() : null; // used to create
2033 // minimum dataset set
2035 for (int i = 0; i < sequences.length; i++)
2039 newDs.addElement(null);
2041 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2043 if (importDs && ds != null)
2045 if (!newDs.contains(ds))
2047 newDs.setElementAt(ds, i);
2048 ds = new Sequence(ds);
2049 // update with new dataset sequence
2050 sequences[i].setDatasetSequence(ds);
2054 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2059 // copy and derive new dataset sequence
2060 sequences[i] = sequences[i].deriveSequence();
2061 alignment.getDataset().addSequence(
2062 sequences[i].getDatasetSequence());
2063 // TODO: avoid creation of duplicate dataset sequences with a
2064 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2066 alignment.addSequence(sequences[i]); // merges dataset
2070 newDs.clear(); // tidy up
2072 if (alignment.getAlignmentAnnotation() != null)
2074 for (AlignmentAnnotation alan : alignment
2075 .getAlignmentAnnotation())
2077 if (alan.graphGroup > fgroup)
2079 fgroup = alan.graphGroup;
2083 if (pastedal.getAlignmentAnnotation() != null)
2085 // Add any annotation attached to alignment.
2086 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2087 for (int i = 0; i < alann.length; i++)
2089 annotationAdded = true;
2090 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2092 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2093 if (newann.graphGroup > -1)
2095 if (newGraphGroups.size() <= newann.graphGroup
2096 || newGraphGroups.get(newann.graphGroup) == null)
2098 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2100 newGraphGroups.add(q, null);
2102 newGraphGroups.set(newann.graphGroup, new Integer(
2105 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2109 newann.padAnnotation(alwidth);
2110 alignment.addAnnotation(newann);
2120 addHistoryItem(new EditCommand(
2121 MessageManager.getString("label.add_sequences"),
2122 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2124 // Add any annotations attached to sequences
2125 for (int i = 0; i < sequences.length; i++)
2127 if (sequences[i].getAnnotation() != null)
2129 AlignmentAnnotation newann;
2130 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2132 annotationAdded = true;
2133 newann = sequences[i].getAnnotation()[a];
2134 newann.adjustForAlignment();
2135 newann.padAnnotation(alwidth);
2136 if (newann.graphGroup > -1)
2138 if (newann.graphGroup > -1)
2140 if (newGraphGroups.size() <= newann.graphGroup
2141 || newGraphGroups.get(newann.graphGroup) == null)
2143 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2145 newGraphGroups.add(q, null);
2147 newGraphGroups.set(newann.graphGroup, new Integer(
2150 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2154 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2159 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2166 // propagate alignment changed.
2167 viewport.setEndSeq(alignment.getHeight());
2168 if (annotationAdded)
2170 // Duplicate sequence annotation in all views.
2171 AlignmentI[] alview = this.getViewAlignments();
2172 for (int i = 0; i < sequences.length; i++)
2174 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2179 for (int avnum = 0; avnum < alview.length; avnum++)
2181 if (alview[avnum] != alignment)
2183 // duplicate in a view other than the one with input focus
2184 int avwidth = alview[avnum].getWidth() + 1;
2185 // this relies on sann being preserved after we
2186 // modify the sequence's annotation array for each duplication
2187 for (int a = 0; a < sann.length; a++)
2189 AlignmentAnnotation newann = new AlignmentAnnotation(
2191 sequences[i].addAlignmentAnnotation(newann);
2192 newann.padAnnotation(avwidth);
2193 alview[avnum].addAnnotation(newann); // annotation was
2194 // duplicated earlier
2195 // TODO JAL-1145 graphGroups are not updated for sequence
2196 // annotation added to several views. This may cause
2198 alview[avnum].setAnnotationIndex(newann, a);
2203 buildSortByAnnotationScoresMenu();
2205 viewport.firePropertyChange("alignment", null,
2206 alignment.getSequences());
2207 if (alignPanels != null)
2209 for (AlignmentPanel ap : alignPanels)
2211 ap.validateAnnotationDimensions(false);
2216 alignPanel.validateAnnotationDimensions(false);
2222 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2224 String newtitle = new String("Copied sequences");
2226 if (Desktop.jalviewClipboard != null
2227 && Desktop.jalviewClipboard[2] != null)
2229 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2230 for (int[] region : hc)
2232 af.viewport.hideColumns(region[0], region[1]);
2236 // >>>This is a fix for the moment, until a better solution is
2238 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2240 alignPanel.getSeqPanel().seqCanvas
2241 .getFeatureRenderer());
2243 // TODO: maintain provenance of an alignment, rather than just make the
2244 // title a concatenation of operations.
2247 if (title.startsWith("Copied sequences"))
2253 newtitle = newtitle.concat("- from " + title);
2258 newtitle = new String("Pasted sequences");
2261 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2266 } catch (Exception ex)
2268 ex.printStackTrace();
2269 System.out.println("Exception whilst pasting: " + ex);
2270 // could be anything being pasted in here
2276 protected void expand_newalign(ActionEvent e)
2280 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2281 .getAlignment(), -1);
2282 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2284 String newtitle = new String("Flanking alignment");
2286 if (Desktop.jalviewClipboard != null
2287 && Desktop.jalviewClipboard[2] != null)
2289 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2290 for (int region[] : hc)
2292 af.viewport.hideColumns(region[0], region[1]);
2296 // >>>This is a fix for the moment, until a better solution is
2298 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2300 alignPanel.getSeqPanel().seqCanvas
2301 .getFeatureRenderer());
2303 // TODO: maintain provenance of an alignment, rather than just make the
2304 // title a concatenation of operations.
2306 if (title.startsWith("Copied sequences"))
2312 newtitle = newtitle.concat("- from " + title);
2316 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2318 } catch (Exception ex)
2320 ex.printStackTrace();
2321 System.out.println("Exception whilst pasting: " + ex);
2322 // could be anything being pasted in here
2323 } catch (OutOfMemoryError oom)
2325 new OOMWarning("Viewing flanking region of alignment", oom);
2336 protected void cut_actionPerformed(ActionEvent e)
2338 copy_actionPerformed(null);
2339 delete_actionPerformed(null);
2349 protected void delete_actionPerformed(ActionEvent evt)
2352 SequenceGroup sg = viewport.getSelectionGroup();
2359 * If the cut affects all sequences, warn, remove highlighted columns
2361 if (sg.getSize() == viewport.getAlignment().getHeight())
2363 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2364 .getAlignment().getWidth()) ? true : false;
2365 if (isEntireAlignWidth)
2367 int confirm = JOptionPane.showConfirmDialog(this,
2368 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2369 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2370 JOptionPane.OK_CANCEL_OPTION);
2372 if (confirm == JOptionPane.CANCEL_OPTION
2373 || confirm == JOptionPane.CLOSED_OPTION)
2378 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2379 sg.getEndRes() + 1);
2381 SequenceI[] cut = sg.getSequences()
2382 .toArray(new SequenceI[sg.getSize()]);
2384 addHistoryItem(new EditCommand(
2385 MessageManager.getString("label.cut_sequences"), Action.CUT,
2386 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2387 viewport.getAlignment()));
2389 viewport.setSelectionGroup(null);
2390 viewport.sendSelection();
2391 viewport.getAlignment().deleteGroup(sg);
2393 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2395 if (viewport.getAlignment().getHeight() < 1)
2399 this.setClosed(true);
2400 } catch (Exception ex)
2413 protected void deleteGroups_actionPerformed(ActionEvent e)
2415 if (avc.deleteGroups())
2417 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2418 alignPanel.updateAnnotation();
2419 alignPanel.paintAlignment(true);
2430 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2432 SequenceGroup sg = new SequenceGroup();
2434 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2436 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2439 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2440 viewport.setSelectionGroup(sg);
2441 viewport.sendSelection();
2442 // JAL-2034 - should delegate to
2443 // alignPanel to decide if overview needs
2445 alignPanel.paintAlignment(false);
2446 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2456 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2458 if (viewport.cursorMode)
2460 alignPanel.getSeqPanel().keyboardNo1 = null;
2461 alignPanel.getSeqPanel().keyboardNo2 = null;
2463 viewport.setSelectionGroup(null);
2464 viewport.getColumnSelection().clear();
2465 viewport.setSelectionGroup(null);
2466 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2467 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2468 // JAL-2034 - should delegate to
2469 // alignPanel to decide if overview needs
2471 alignPanel.paintAlignment(false);
2472 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2473 viewport.sendSelection();
2483 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2485 SequenceGroup sg = viewport.getSelectionGroup();
2489 selectAllSequenceMenuItem_actionPerformed(null);
2494 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2496 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2498 // JAL-2034 - should delegate to
2499 // alignPanel to decide if overview needs
2502 alignPanel.paintAlignment(true);
2503 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2504 viewport.sendSelection();
2508 public void invertColSel_actionPerformed(ActionEvent e)
2510 viewport.invertColumnSelection();
2511 alignPanel.paintAlignment(true);
2512 viewport.sendSelection();
2522 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2524 trimAlignment(true);
2534 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2536 trimAlignment(false);
2539 void trimAlignment(boolean trimLeft)
2541 ColumnSelection colSel = viewport.getColumnSelection();
2544 if (!colSel.isEmpty())
2548 column = colSel.getMin();
2552 column = colSel.getMax();
2556 if (viewport.getSelectionGroup() != null)
2558 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2559 viewport.getHiddenRepSequences());
2563 seqs = viewport.getAlignment().getSequencesArray();
2566 TrimRegionCommand trimRegion;
2569 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2570 column, viewport.getAlignment());
2571 viewport.setStartRes(0);
2575 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2576 column, viewport.getAlignment());
2579 statusBar.setText(MessageManager.formatMessage(
2580 "label.removed_columns",
2581 new String[] { Integer.valueOf(trimRegion.getSize())
2584 addHistoryItem(trimRegion);
2586 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2588 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2589 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2591 viewport.getAlignment().deleteGroup(sg);
2595 viewport.firePropertyChange("alignment", null, viewport
2596 .getAlignment().getSequences());
2607 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2609 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2612 if (viewport.getSelectionGroup() != null)
2614 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2615 viewport.getHiddenRepSequences());
2616 start = viewport.getSelectionGroup().getStartRes();
2617 end = viewport.getSelectionGroup().getEndRes();
2621 seqs = viewport.getAlignment().getSequencesArray();
2624 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2625 "Remove Gapped Columns", seqs, start, end,
2626 viewport.getAlignment());
2628 addHistoryItem(removeGapCols);
2630 statusBar.setText(MessageManager.formatMessage(
2631 "label.removed_empty_columns",
2632 new Object[] { Integer.valueOf(removeGapCols.getSize())
2635 // This is to maintain viewport position on first residue
2636 // of first sequence
2637 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2638 int startRes = seq.findPosition(viewport.startRes);
2639 // ShiftList shifts;
2640 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2641 // edit.alColumnChanges=shifts.getInverse();
2642 // if (viewport.hasHiddenColumns)
2643 // viewport.getColumnSelection().compensateForEdits(shifts);
2644 viewport.setStartRes(seq.findIndex(startRes) - 1);
2645 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2657 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2659 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2662 if (viewport.getSelectionGroup() != null)
2664 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2665 viewport.getHiddenRepSequences());
2666 start = viewport.getSelectionGroup().getStartRes();
2667 end = viewport.getSelectionGroup().getEndRes();
2671 seqs = viewport.getAlignment().getSequencesArray();
2674 // This is to maintain viewport position on first residue
2675 // of first sequence
2676 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2677 int startRes = seq.findPosition(viewport.startRes);
2679 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2680 viewport.getAlignment()));
2682 viewport.setStartRes(seq.findIndex(startRes) - 1);
2684 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2696 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2698 viewport.setPadGaps(padGapsMenuitem.isSelected());
2699 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2710 public void findMenuItem_actionPerformed(ActionEvent e)
2716 * Create a new view of the current alignment.
2719 public void newView_actionPerformed(ActionEvent e)
2721 newView(null, true);
2725 * Creates and shows a new view of the current alignment.
2728 * title of newly created view; if null, one will be generated
2729 * @param copyAnnotation
2730 * if true then duplicate all annnotation, groups and settings
2731 * @return new alignment panel, already displayed.
2733 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2736 * Create a new AlignmentPanel (with its own, new Viewport)
2738 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2740 if (!copyAnnotation)
2743 * remove all groups and annotation except for the automatic stuff
2745 newap.av.getAlignment().deleteAllGroups();
2746 newap.av.getAlignment().deleteAllAnnotations(false);
2749 newap.av.setGatherViewsHere(false);
2751 if (viewport.viewName == null)
2753 viewport.viewName = MessageManager
2754 .getString("label.view_name_original");
2758 * Views share the same edits undo and redo stacks
2760 newap.av.setHistoryList(viewport.getHistoryList());
2761 newap.av.setRedoList(viewport.getRedoList());
2764 * Views share the same mappings; need to deregister any new mappings
2765 * created by copyAlignPanel, and register the new reference to the shared
2768 newap.av.replaceMappings(viewport.getAlignment());
2770 newap.av.viewName = getNewViewName(viewTitle);
2772 addAlignmentPanel(newap, true);
2773 newap.alignmentChanged();
2775 if (alignPanels.size() == 2)
2777 viewport.setGatherViewsHere(true);
2779 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2784 * Make a new name for the view, ensuring it is unique within the current
2785 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2786 * these now use viewId. Unique view names are still desirable for usability.)
2791 protected String getNewViewName(String viewTitle)
2793 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2794 boolean addFirstIndex = false;
2795 if (viewTitle == null || viewTitle.trim().length() == 0)
2797 viewTitle = MessageManager.getString("action.view");
2798 addFirstIndex = true;
2802 index = 1;// we count from 1 if given a specific name
2804 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2806 List<Component> comps = PaintRefresher.components.get(viewport
2807 .getSequenceSetId());
2809 List<String> existingNames = getExistingViewNames(comps);
2811 while (existingNames.contains(newViewName))
2813 newViewName = viewTitle + " " + (++index);
2819 * Returns a list of distinct view names found in the given list of
2820 * components. View names are held on the viewport of an AlignmentPanel.
2825 protected List<String> getExistingViewNames(List<Component> comps)
2827 List<String> existingNames = new ArrayList<String>();
2828 for (Component comp : comps)
2830 if (comp instanceof AlignmentPanel)
2832 AlignmentPanel ap = (AlignmentPanel) comp;
2833 if (!existingNames.contains(ap.av.viewName))
2835 existingNames.add(ap.av.viewName);
2839 return existingNames;
2843 * Explode tabbed views into separate windows.
2846 public void expandViews_actionPerformed(ActionEvent e)
2848 Desktop.explodeViews(this);
2852 * Gather views in separate windows back into a tabbed presentation.
2855 public void gatherViews_actionPerformed(ActionEvent e)
2857 Desktop.instance.gatherViews(this);
2867 public void font_actionPerformed(ActionEvent e)
2869 new FontChooser(alignPanel);
2879 protected void seqLimit_actionPerformed(ActionEvent e)
2881 viewport.setShowJVSuffix(seqLimits.isSelected());
2883 alignPanel.getIdPanel().getIdCanvas()
2884 .setPreferredSize(alignPanel.calculateIdWidth());
2885 alignPanel.paintAlignment(true);
2889 public void idRightAlign_actionPerformed(ActionEvent e)
2891 viewport.setRightAlignIds(idRightAlign.isSelected());
2892 alignPanel.paintAlignment(true);
2896 public void centreColumnLabels_actionPerformed(ActionEvent e)
2898 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2899 alignPanel.paintAlignment(true);
2905 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2908 protected void followHighlight_actionPerformed()
2911 * Set the 'follow' flag on the Viewport (and scroll to position if now
2914 final boolean state = this.followHighlightMenuItem.getState();
2915 viewport.setFollowHighlight(state);
2918 alignPanel.scrollToPosition(
2919 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2930 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2932 viewport.setColourText(colourTextMenuItem.isSelected());
2933 alignPanel.paintAlignment(true);
2943 public void wrapMenuItem_actionPerformed(ActionEvent e)
2945 scaleAbove.setVisible(wrapMenuItem.isSelected());
2946 scaleLeft.setVisible(wrapMenuItem.isSelected());
2947 scaleRight.setVisible(wrapMenuItem.isSelected());
2948 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2949 alignPanel.updateLayout();
2953 public void showAllSeqs_actionPerformed(ActionEvent e)
2955 viewport.showAllHiddenSeqs();
2959 public void showAllColumns_actionPerformed(ActionEvent e)
2961 viewport.showAllHiddenColumns();
2963 viewport.sendSelection();
2967 public void hideSelSequences_actionPerformed(ActionEvent e)
2969 viewport.hideAllSelectedSeqs();
2970 // alignPanel.paintAlignment(true);
2974 * called by key handler and the hide all/show all menu items
2979 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2982 boolean hide = false;
2983 SequenceGroup sg = viewport.getSelectionGroup();
2984 if (!toggleSeqs && !toggleCols)
2986 // Hide everything by the current selection - this is a hack - we do the
2987 // invert and then hide
2988 // first check that there will be visible columns after the invert.
2989 if ((viewport.getColumnSelection() != null
2990 && viewport.getColumnSelection().getSelected() != null && viewport
2991 .getColumnSelection().getSelected().size() > 0)
2992 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2995 // now invert the sequence set, if required - empty selection implies
2996 // that no hiding is required.
2999 invertSequenceMenuItem_actionPerformed(null);
3000 sg = viewport.getSelectionGroup();
3004 viewport.expandColSelection(sg, true);
3005 // finally invert the column selection and get the new sequence
3007 invertColSel_actionPerformed(null);
3014 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3016 hideSelSequences_actionPerformed(null);
3019 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3022 showAllSeqs_actionPerformed(null);
3028 if (viewport.getColumnSelection().getSelected().size() > 0)
3030 hideSelColumns_actionPerformed(null);
3033 viewport.setSelectionGroup(sg);
3038 showAllColumns_actionPerformed(null);
3047 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3048 * event.ActionEvent)
3051 public void hideAllButSelection_actionPerformed(ActionEvent e)
3053 toggleHiddenRegions(false, false);
3054 viewport.sendSelection();
3061 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3065 public void hideAllSelection_actionPerformed(ActionEvent e)
3067 SequenceGroup sg = viewport.getSelectionGroup();
3068 viewport.expandColSelection(sg, false);
3069 viewport.hideAllSelectedSeqs();
3070 viewport.hideSelectedColumns();
3071 alignPanel.paintAlignment(true);
3072 viewport.sendSelection();
3079 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3083 public void showAllhidden_actionPerformed(ActionEvent e)
3085 viewport.showAllHiddenColumns();
3086 viewport.showAllHiddenSeqs();
3087 alignPanel.paintAlignment(true);
3088 viewport.sendSelection();
3092 public void hideSelColumns_actionPerformed(ActionEvent e)
3094 viewport.hideSelectedColumns();
3095 alignPanel.paintAlignment(true);
3096 viewport.sendSelection();
3100 public void hiddenMarkers_actionPerformed(ActionEvent e)
3102 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3113 protected void scaleAbove_actionPerformed(ActionEvent e)
3115 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3116 alignPanel.paintAlignment(true);
3126 protected void scaleLeft_actionPerformed(ActionEvent e)
3128 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3129 alignPanel.paintAlignment(true);
3139 protected void scaleRight_actionPerformed(ActionEvent e)
3141 viewport.setScaleRightWrapped(scaleRight.isSelected());
3142 alignPanel.paintAlignment(true);
3152 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3154 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3155 alignPanel.paintAlignment(true);
3165 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3167 viewport.setShowText(viewTextMenuItem.isSelected());
3168 alignPanel.paintAlignment(true);
3178 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3180 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3181 alignPanel.paintAlignment(true);
3184 public FeatureSettings featureSettings;
3187 public FeatureSettingsControllerI getFeatureSettingsUI()
3189 return featureSettings;
3193 public void featureSettings_actionPerformed(ActionEvent e)
3195 if (featureSettings != null)
3197 featureSettings.close();
3198 featureSettings = null;
3200 if (!showSeqFeatures.isSelected())
3202 // make sure features are actually displayed
3203 showSeqFeatures.setSelected(true);
3204 showSeqFeatures_actionPerformed(null);
3206 featureSettings = new FeatureSettings(this);
3210 * Set or clear 'Show Sequence Features'
3216 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3218 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3219 alignPanel.paintAlignment(true);
3220 if (alignPanel.getOverviewPanel() != null)
3222 alignPanel.getOverviewPanel().updateOverviewImage();
3227 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3228 * the annotations panel as a whole.
3230 * The options to show/hide all annotations should be enabled when the panel
3231 * is shown, and disabled when the panel is hidden.
3236 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3238 final boolean setVisible = annotationPanelMenuItem.isSelected();
3239 viewport.setShowAnnotation(setVisible);
3240 this.showAllSeqAnnotations.setEnabled(setVisible);
3241 this.hideAllSeqAnnotations.setEnabled(setVisible);
3242 this.showAllAlAnnotations.setEnabled(setVisible);
3243 this.hideAllAlAnnotations.setEnabled(setVisible);
3244 alignPanel.updateLayout();
3248 public void alignmentProperties()
3250 JEditorPane editPane = new JEditorPane("text/html", "");
3251 editPane.setEditable(false);
3252 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3254 editPane.setText(MessageManager.formatMessage("label.html_content",
3255 new Object[] { contents.toString() }));
3256 JInternalFrame frame = new JInternalFrame();
3257 frame.getContentPane().add(new JScrollPane(editPane));
3259 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3260 "label.alignment_properties", new Object[] { getTitle() }),
3271 public void overviewMenuItem_actionPerformed(ActionEvent e)
3273 if (alignPanel.overviewPanel != null)
3278 JInternalFrame frame = new JInternalFrame();
3279 OverviewPanel overview = new OverviewPanel(alignPanel);
3280 frame.setContentPane(overview);
3281 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3282 "label.overview_params", new Object[] { this.getTitle() }),
3283 frame.getWidth(), frame.getHeight());
3285 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3286 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3289 public void internalFrameClosed(
3290 javax.swing.event.InternalFrameEvent evt)
3292 alignPanel.setOverviewPanel(null);
3296 alignPanel.setOverviewPanel(overview);
3300 public void textColour_actionPerformed(ActionEvent e)
3302 new TextColourChooser().chooseColour(alignPanel, null);
3312 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3324 public void clustalColour_actionPerformed(ActionEvent e)
3326 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3327 viewport.getHiddenRepSequences()));
3337 public void zappoColour_actionPerformed(ActionEvent e)
3339 changeColour(new ZappoColourScheme());
3349 public void taylorColour_actionPerformed(ActionEvent e)
3351 changeColour(new TaylorColourScheme());
3361 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3363 changeColour(new HydrophobicColourScheme());
3373 public void helixColour_actionPerformed(ActionEvent e)
3375 changeColour(new HelixColourScheme());
3385 public void strandColour_actionPerformed(ActionEvent e)
3387 changeColour(new StrandColourScheme());
3397 public void turnColour_actionPerformed(ActionEvent e)
3399 changeColour(new TurnColourScheme());
3409 public void buriedColour_actionPerformed(ActionEvent e)
3411 changeColour(new BuriedColourScheme());
3421 public void nucleotideColour_actionPerformed(ActionEvent e)
3423 changeColour(new NucleotideColourScheme());
3427 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3429 changeColour(new PurinePyrimidineColourScheme());
3433 * public void covariationColour_actionPerformed(ActionEvent e) {
3435 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3439 public void annotationColour_actionPerformed(ActionEvent e)
3441 new AnnotationColourChooser(viewport, alignPanel);
3445 public void annotationColumn_actionPerformed(ActionEvent e)
3447 new AnnotationColumnChooser(viewport, alignPanel);
3451 public void rnahelicesColour_actionPerformed(ActionEvent e)
3453 new RNAHelicesColourChooser(viewport, alignPanel);
3463 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3465 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3475 public void changeColour(ColourSchemeI cs)
3477 // TODO: pull up to controller method
3481 // Make sure viewport is up to date w.r.t. any sliders
3482 if (viewport.getAbovePIDThreshold())
3484 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3486 viewport.setThreshold(threshold);
3489 if (viewport.getConservationSelected())
3491 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3494 if (cs instanceof TCoffeeColourScheme)
3496 tcoffeeColour.setEnabled(true);
3497 tcoffeeColour.setSelected(true);
3501 viewport.setGlobalColourScheme(cs);
3503 alignPanel.paintAlignment(true);
3513 protected void modifyPID_actionPerformed(ActionEvent e)
3515 if (viewport.getAbovePIDThreshold()
3516 && viewport.getGlobalColourScheme() != null)
3518 SliderPanel.setPIDSliderSource(alignPanel,
3519 viewport.getGlobalColourScheme(), "Background");
3520 SliderPanel.showPIDSlider();
3531 protected void modifyConservation_actionPerformed(ActionEvent e)
3533 if (viewport.getConservationSelected()
3534 && viewport.getGlobalColourScheme() != null)
3536 SliderPanel.setConservationSlider(alignPanel,
3537 viewport.getGlobalColourScheme(), "Background");
3538 SliderPanel.showConservationSlider();
3549 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3551 viewport.setConservationSelected(conservationMenuItem.isSelected());
3553 viewport.setAbovePIDThreshold(false);
3554 abovePIDThreshold.setSelected(false);
3556 changeColour(viewport.getGlobalColourScheme());
3558 modifyConservation_actionPerformed(null);
3568 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3570 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3572 conservationMenuItem.setSelected(false);
3573 viewport.setConservationSelected(false);
3575 changeColour(viewport.getGlobalColourScheme());
3577 modifyPID_actionPerformed(null);
3587 public void userDefinedColour_actionPerformed(ActionEvent e)
3589 if (e.getActionCommand().equals(
3590 MessageManager.getString("action.user_defined")))
3592 new UserDefinedColours(alignPanel, null);
3596 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3597 .getUserColourSchemes().get(e.getActionCommand());
3603 public void updateUserColourMenu()
3606 Component[] menuItems = colourMenu.getMenuComponents();
3607 int iSize = menuItems.length;
3608 for (int i = 0; i < iSize; i++)
3610 if (menuItems[i].getName() != null
3611 && menuItems[i].getName().equals("USER_DEFINED"))
3613 colourMenu.remove(menuItems[i]);
3617 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3619 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3620 .getUserColourSchemes().keys();
3622 while (userColours.hasMoreElements())
3624 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3625 userColours.nextElement().toString());
3626 radioItem.setName("USER_DEFINED");
3627 radioItem.addMouseListener(new MouseAdapter()
3630 public void mousePressed(MouseEvent evt)
3632 if (evt.isPopupTrigger())
3634 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3636 int option = JOptionPane.showInternalConfirmDialog(
3637 jalview.gui.Desktop.desktop,
3639 .getString("label.remove_from_default_list"),
3641 .getString("label.remove_user_defined_colour"),
3642 JOptionPane.YES_NO_OPTION);
3643 if (option == JOptionPane.YES_OPTION)
3645 jalview.gui.UserDefinedColours
3646 .removeColourFromDefaults(radioItem.getText());
3647 colourMenu.remove(radioItem);
3651 radioItem.addActionListener(new ActionListener()
3654 public void actionPerformed(ActionEvent evt)
3656 userDefinedColour_actionPerformed(evt);
3663 radioItem.addActionListener(new ActionListener()
3666 public void actionPerformed(ActionEvent evt)
3668 userDefinedColour_actionPerformed(evt);
3672 colourMenu.insert(radioItem, 15);
3673 colours.add(radioItem);
3685 public void PIDColour_actionPerformed(ActionEvent e)
3687 changeColour(new PIDColourScheme());
3697 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3699 changeColour(new Blosum62ColourScheme());
3709 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3711 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3712 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3713 .getAlignment().getSequenceAt(0), null);
3714 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3715 viewport.getAlignment()));
3716 alignPanel.paintAlignment(true);
3726 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3728 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3729 AlignmentSorter.sortByID(viewport.getAlignment());
3730 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3731 viewport.getAlignment()));
3732 alignPanel.paintAlignment(true);
3742 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3744 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3745 AlignmentSorter.sortByLength(viewport.getAlignment());
3746 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3747 viewport.getAlignment()));
3748 alignPanel.paintAlignment(true);
3758 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3760 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3761 AlignmentSorter.sortByGroup(viewport.getAlignment());
3762 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3763 viewport.getAlignment()));
3765 alignPanel.paintAlignment(true);
3775 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3777 new RedundancyPanel(alignPanel, this);
3787 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3789 if ((viewport.getSelectionGroup() == null)
3790 || (viewport.getSelectionGroup().getSize() < 2))
3792 JOptionPane.showInternalMessageDialog(this, MessageManager
3793 .getString("label.you_must_select_least_two_sequences"),
3794 MessageManager.getString("label.invalid_selection"),
3795 JOptionPane.WARNING_MESSAGE);
3799 JInternalFrame frame = new JInternalFrame();
3800 frame.setContentPane(new PairwiseAlignPanel(viewport));
3801 Desktop.addInternalFrame(frame,
3802 MessageManager.getString("action.pairwise_alignment"), 600,
3814 public void PCAMenuItem_actionPerformed(ActionEvent e)
3816 if (((viewport.getSelectionGroup() != null)
3817 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3818 .getSelectionGroup().getSize() > 0))
3819 || (viewport.getAlignment().getHeight() < 4))
3822 .showInternalMessageDialog(
3825 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3827 .getString("label.sequence_selection_insufficient"),
3828 JOptionPane.WARNING_MESSAGE);
3833 new PCAPanel(alignPanel);
3837 public void autoCalculate_actionPerformed(ActionEvent e)
3839 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3840 if (viewport.autoCalculateConsensus)
3842 viewport.firePropertyChange("alignment", null, viewport
3843 .getAlignment().getSequences());
3848 public void sortByTreeOption_actionPerformed(ActionEvent e)
3850 viewport.sortByTree = sortByTree.isSelected();
3854 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3856 viewport.followSelection = listenToViewSelections.isSelected();
3866 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3868 newTreePanel("AV", "PID", "Average distance tree using PID");
3878 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3880 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3890 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3892 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3902 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3904 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3917 void newTreePanel(String type, String pwType, String title)
3921 if (viewport.getSelectionGroup() != null
3922 && viewport.getSelectionGroup().getSize() > 0)
3924 if (viewport.getSelectionGroup().getSize() < 3)
3930 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3932 .getString("label.not_enough_sequences"),
3933 JOptionPane.WARNING_MESSAGE);
3937 SequenceGroup sg = viewport.getSelectionGroup();
3939 /* Decide if the selection is a column region */
3940 for (SequenceI _s : sg.getSequences())
3942 if (_s.getLength() < sg.getEndRes())
3948 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3950 .getString("label.sequences_selection_not_aligned"),
3951 JOptionPane.WARNING_MESSAGE);
3957 title = title + " on region";
3958 tp = new TreePanel(alignPanel, type, pwType);
3962 // are the visible sequences aligned?
3963 if (!viewport.getAlignment().isAligned(false))
3969 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3971 .getString("label.sequences_not_aligned"),
3972 JOptionPane.WARNING_MESSAGE);
3977 if (viewport.getAlignment().getHeight() < 2)
3982 tp = new TreePanel(alignPanel, type, pwType);
3987 if (viewport.viewName != null)
3989 title += viewport.viewName + " of ";
3992 title += this.title;
3994 Desktop.addInternalFrame(tp, title, 600, 500);
4005 public void addSortByOrderMenuItem(String title,
4006 final AlignmentOrder order)
4008 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4009 "action.by_title_param", new Object[] { title }));
4011 item.addActionListener(new java.awt.event.ActionListener()
4014 public void actionPerformed(ActionEvent e)
4016 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4018 // TODO: JBPNote - have to map order entries to curent SequenceI
4020 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4022 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4025 alignPanel.paintAlignment(true);
4031 * Add a new sort by annotation score menu item
4034 * the menu to add the option to
4036 * the label used to retrieve scores for each sequence on the
4039 public void addSortByAnnotScoreMenuItem(JMenu sort,
4040 final String scoreLabel)
4042 final JMenuItem item = new JMenuItem(scoreLabel);
4044 item.addActionListener(new java.awt.event.ActionListener()
4047 public void actionPerformed(ActionEvent e)
4049 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4050 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4051 viewport.getAlignment());// ,viewport.getSelectionGroup());
4052 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4053 viewport.getAlignment()));
4054 alignPanel.paintAlignment(true);
4060 * last hash for alignment's annotation array - used to minimise cost of
4063 protected int _annotationScoreVectorHash;
4066 * search the alignment and rebuild the sort by annotation score submenu the
4067 * last alignment annotation vector hash is stored to minimize cost of
4068 * rebuilding in subsequence calls.
4072 public void buildSortByAnnotationScoresMenu()
4074 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4079 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4081 sortByAnnotScore.removeAll();
4082 // almost certainly a quicker way to do this - but we keep it simple
4083 Hashtable scoreSorts = new Hashtable();
4084 AlignmentAnnotation aann[];
4085 for (SequenceI sqa : viewport.getAlignment().getSequences())
4087 aann = sqa.getAnnotation();
4088 for (int i = 0; aann != null && i < aann.length; i++)
4090 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4092 scoreSorts.put(aann[i].label, aann[i].label);
4096 Enumeration labels = scoreSorts.keys();
4097 while (labels.hasMoreElements())
4099 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4100 (String) labels.nextElement());
4102 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4105 _annotationScoreVectorHash = viewport.getAlignment()
4106 .getAlignmentAnnotation().hashCode();
4111 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4112 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4113 * call. Listeners are added to remove the menu item when the treePanel is
4114 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4118 * Displayed tree window.
4120 * SortBy menu item title.
4123 public void buildTreeMenu()
4125 calculateTree.removeAll();
4126 // build the calculate menu
4128 for (final String type : new String[] { "NJ", "AV" })
4130 String treecalcnm = MessageManager.getString("label.tree_calc_"
4131 + type.toLowerCase());
4132 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4134 JMenuItem tm = new JMenuItem();
4135 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4136 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4137 || sm.isProtein() == !viewport.getAlignment()
4140 String smn = MessageManager.getStringOrReturn(
4141 "label.score_model_", sm.getName());
4142 final String title = MessageManager.formatMessage(
4143 "label.treecalc_title", treecalcnm, smn);
4144 tm.setText(title);//
4145 tm.addActionListener(new java.awt.event.ActionListener()
4148 public void actionPerformed(ActionEvent e)
4150 newTreePanel(type, pwtype, title);
4153 calculateTree.add(tm);
4158 sortByTreeMenu.removeAll();
4160 List<Component> comps = PaintRefresher.components.get(viewport
4161 .getSequenceSetId());
4162 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4163 for (Component comp : comps)
4165 if (comp instanceof TreePanel)
4167 treePanels.add((TreePanel) comp);
4171 if (treePanels.size() < 1)
4173 sortByTreeMenu.setVisible(false);
4177 sortByTreeMenu.setVisible(true);
4179 for (final TreePanel tp : treePanels)
4181 final JMenuItem item = new JMenuItem(tp.getTitle());
4182 item.addActionListener(new java.awt.event.ActionListener()
4185 public void actionPerformed(ActionEvent e)
4187 tp.sortByTree_actionPerformed();
4188 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4193 sortByTreeMenu.add(item);
4197 public boolean sortBy(AlignmentOrder alorder, String undoname)
4199 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4200 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4201 if (undoname != null)
4203 addHistoryItem(new OrderCommand(undoname, oldOrder,
4204 viewport.getAlignment()));
4206 alignPanel.paintAlignment(true);
4211 * Work out whether the whole set of sequences or just the selected set will
4212 * be submitted for multiple alignment.
4215 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4217 // Now, check we have enough sequences
4218 AlignmentView msa = null;
4220 if ((viewport.getSelectionGroup() != null)
4221 && (viewport.getSelectionGroup().getSize() > 1))
4223 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4224 // some common interface!
4226 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4227 * SequenceI[sz = seqs.getSize(false)];
4229 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4230 * seqs.getSequenceAt(i); }
4232 msa = viewport.getAlignmentView(true);
4234 else if (viewport.getSelectionGroup() != null
4235 && viewport.getSelectionGroup().getSize() == 1)
4237 int option = JOptionPane.showConfirmDialog(this,
4238 MessageManager.getString("warn.oneseq_msainput_selection"),
4239 MessageManager.getString("label.invalid_selection"),
4240 JOptionPane.OK_CANCEL_OPTION);
4241 if (option == JOptionPane.OK_OPTION)
4243 msa = viewport.getAlignmentView(false);
4248 msa = viewport.getAlignmentView(false);
4254 * Decides what is submitted to a secondary structure prediction service: the
4255 * first sequence in the alignment, or in the current selection, or, if the
4256 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4257 * region or the whole alignment. (where the first sequence in the set is the
4258 * one that the prediction will be for).
4260 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4262 AlignmentView seqs = null;
4264 if ((viewport.getSelectionGroup() != null)
4265 && (viewport.getSelectionGroup().getSize() > 0))
4267 seqs = viewport.getAlignmentView(true);
4271 seqs = viewport.getAlignmentView(false);
4273 // limit sequences - JBPNote in future - could spawn multiple prediction
4275 // TODO: viewport.getAlignment().isAligned is a global state - the local
4276 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4277 if (!viewport.getAlignment().isAligned(false))
4279 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4280 // TODO: if seqs.getSequences().length>1 then should really have warned
4294 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4296 // Pick the tree file
4297 JalviewFileChooser chooser = new JalviewFileChooser(
4298 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4299 chooser.setFileView(new JalviewFileView());
4300 chooser.setDialogTitle(MessageManager
4301 .getString("label.select_newick_like_tree_file"));
4302 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4304 int value = chooser.showOpenDialog(null);
4306 if (value == JalviewFileChooser.APPROVE_OPTION)
4308 String choice = chooser.getSelectedFile().getPath();
4309 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4310 jalview.io.NewickFile fin = null;
4313 fin = new NewickFile(choice, DataSourceType.FILE);
4314 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4315 } catch (Exception ex)
4322 .getString("label.problem_reading_tree_file"),
4323 JOptionPane.WARNING_MESSAGE);
4324 ex.printStackTrace();
4326 if (fin != null && fin.hasWarningMessage())
4328 JOptionPane.showMessageDialog(Desktop.desktop, fin
4329 .getWarningMessage(), MessageManager
4330 .getString("label.possible_problem_with_tree_file"),
4331 JOptionPane.WARNING_MESSAGE);
4337 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4339 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4342 public TreePanel ShowNewickTree(NewickFile nf, String title)
4344 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4347 public TreePanel ShowNewickTree(NewickFile nf, String title,
4348 AlignmentView input)
4350 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4353 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4354 int h, int x, int y)
4356 return ShowNewickTree(nf, title, null, w, h, x, y);
4360 * Add a treeviewer for the tree extracted from a newick file object to the
4361 * current alignment view
4368 * Associated alignment input data (or null)
4377 * @return TreePanel handle
4379 public TreePanel ShowNewickTree(NewickFile nf, String title,
4380 AlignmentView input, int w, int h, int x, int y)
4382 TreePanel tp = null;
4388 if (nf.getTree() != null)
4390 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4396 tp.setLocation(x, y);
4399 Desktop.addInternalFrame(tp, title, w, h);
4401 } catch (Exception ex)
4403 ex.printStackTrace();
4409 private boolean buildingMenu = false;
4412 * Generates menu items and listener event actions for web service clients
4415 public void BuildWebServiceMenu()
4417 while (buildingMenu)
4421 System.err.println("Waiting for building menu to finish.");
4423 } catch (Exception e)
4427 final AlignFrame me = this;
4428 buildingMenu = true;
4429 new Thread(new Runnable()
4434 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4437 // System.err.println("Building ws menu again "
4438 // + Thread.currentThread());
4439 // TODO: add support for context dependent disabling of services based
4441 // alignment and current selection
4442 // TODO: add additional serviceHandle parameter to specify abstract
4444 // class independently of AbstractName
4445 // TODO: add in rediscovery GUI function to restart discoverer
4446 // TODO: group services by location as well as function and/or
4448 // object broker mechanism.
4449 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4450 final IProgressIndicator af = me;
4453 * do not i18n these strings - they are hard-coded in class
4454 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4455 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4457 final JMenu msawsmenu = new JMenu("Alignment");
4458 final JMenu secstrmenu = new JMenu(
4459 "Secondary Structure Prediction");
4460 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4461 final JMenu analymenu = new JMenu("Analysis");
4462 final JMenu dismenu = new JMenu("Protein Disorder");
4463 // JAL-940 - only show secondary structure prediction services from
4464 // the legacy server
4465 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4467 Discoverer.services != null && (Discoverer.services.size() > 0))
4469 // TODO: refactor to allow list of AbstractName/Handler bindings to
4471 // stored or retrieved from elsewhere
4472 // No MSAWS used any more:
4473 // Vector msaws = null; // (Vector)
4474 // Discoverer.services.get("MsaWS");
4475 Vector secstrpr = (Vector) Discoverer.services
4477 if (secstrpr != null)
4479 // Add any secondary structure prediction services
4480 for (int i = 0, j = secstrpr.size(); i < j; i++)
4482 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4484 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4485 .getServiceClient(sh);
4486 int p = secstrmenu.getItemCount();
4487 impl.attachWSMenuEntry(secstrmenu, me);
4488 int q = secstrmenu.getItemCount();
4489 for (int litm = p; litm < q; litm++)
4491 legacyItems.add(secstrmenu.getItem(litm));
4497 // Add all submenus in the order they should appear on the web
4499 wsmenu.add(msawsmenu);
4500 wsmenu.add(secstrmenu);
4501 wsmenu.add(dismenu);
4502 wsmenu.add(analymenu);
4503 // No search services yet
4504 // wsmenu.add(seqsrchmenu);
4506 javax.swing.SwingUtilities.invokeLater(new Runnable()
4513 webService.removeAll();
4514 // first, add discovered services onto the webservices menu
4515 if (wsmenu.size() > 0)
4517 for (int i = 0, j = wsmenu.size(); i < j; i++)
4519 webService.add(wsmenu.get(i));
4524 webService.add(me.webServiceNoServices);
4526 // TODO: move into separate menu builder class.
4527 boolean new_sspred = false;
4528 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4530 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4531 if (jws2servs != null)
4533 if (jws2servs.hasServices())
4535 jws2servs.attachWSMenuEntry(webService, me);
4536 for (Jws2Instance sv : jws2servs.getServices())
4538 if (sv.description.toLowerCase().contains("jpred"))
4540 for (JMenuItem jmi : legacyItems)
4542 jmi.setVisible(false);
4548 if (jws2servs.isRunning())
4550 JMenuItem tm = new JMenuItem(
4551 "Still discovering JABA Services");
4552 tm.setEnabled(false);
4557 build_urlServiceMenu(me.webService);
4558 build_fetchdbmenu(webService);
4559 for (JMenu item : wsmenu)
4561 if (item.getItemCount() == 0)
4563 item.setEnabled(false);
4567 item.setEnabled(true);
4570 } catch (Exception e)
4573 .debug("Exception during web service menu building process.",
4578 } catch (Exception e)
4581 buildingMenu = false;
4588 * construct any groupURL type service menu entries.
4592 private void build_urlServiceMenu(JMenu webService)
4594 // TODO: remove this code when 2.7 is released
4595 // DEBUG - alignmentView
4597 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4598 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4600 * @Override public void actionPerformed(ActionEvent e) {
4601 * jalview.datamodel.AlignmentView
4602 * .testSelectionViews(af.viewport.getAlignment(),
4603 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4605 * }); webService.add(testAlView);
4607 // TODO: refactor to RestClient discoverer and merge menu entries for
4608 // rest-style services with other types of analysis/calculation service
4609 // SHmmr test client - still being implemented.
4610 // DEBUG - alignmentView
4612 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4615 client.attachWSMenuEntry(
4616 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4622 * Searches the alignment sequences for xRefs and builds the Show
4623 * Cross-References menu (formerly called Show Products), with database
4624 * sources for which cross-references are found (protein sources for a
4625 * nucleotide alignment and vice versa)
4627 * @return true if Show Cross-references menu should be enabled
4629 public boolean canShowProducts()
4631 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4632 AlignmentI dataset = viewport.getAlignment().getDataset();
4633 boolean showp = false;
4636 showProducts.removeAll();
4637 final boolean dna = viewport.getAlignment().isNucleotide();
4638 List<String> ptypes = (seqs == null || seqs.length == 0) ? null
4639 : new CrossRef(seqs, dataset)
4640 .findXrefSourcesForSequences(dna);
4642 for (final String source : ptypes)
4645 final AlignFrame af = this;
4646 JMenuItem xtype = new JMenuItem(source);
4647 xtype.addActionListener(new ActionListener()
4650 public void actionPerformed(ActionEvent e)
4652 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4655 showProducts.add(xtype);
4657 showProducts.setVisible(showp);
4658 showProducts.setEnabled(showp);
4659 } catch (Exception e)
4662 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4670 * Finds and displays cross-references for the selected sequences (protein
4671 * products for nucleotide sequences, dna coding sequences for peptides).
4674 * the sequences to show cross-references for
4676 * true if from a nucleotide alignment (so showing proteins)
4678 * the database to show cross-references for
4680 protected void showProductsFor(final SequenceI[] sel,
4681 final boolean _odna, final String source)
4683 Runnable foo = new Runnable()
4689 final long sttime = System.currentTimeMillis();
4690 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4691 "status.searching_for_sequences_from",
4692 new Object[] { source }), sttime);
4695 AlignmentI alignment = AlignFrame.this.getViewport()
4697 AlignmentI dataset = alignment.getDataset() == null ? alignment
4698 : alignment.getDataset();
4699 boolean dna = alignment.isNucleotide();
4703 .println("Conflict: showProducts for alignment originally "
4705 + (_odna ? "DNA" : "Protein")
4706 + " now searching for "
4707 + (dna ? "DNA" : "Protein") + " Context.");
4709 AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences(
4716 * get display scheme (if any) to apply to features
4718 FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
4719 .getFeatureColourScheme(source);
4721 AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
4725 xrefsAlignment = AlignmentUtils.makeCdsAlignment(
4726 xrefsAlignment.getSequencesArray(), dataset, sel);
4727 xrefsAlignment.alignAs(alignment);
4731 * If we are opening a splitframe, make a copy of this alignment (sharing the same dataset
4732 * sequences). If we are DNA, drop introns and update mappings
4734 AlignmentI copyAlignment = null;
4736 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4738 boolean copyAlignmentIsAligned = false;
4741 copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
4742 xrefsAlignment.getSequencesArray());
4743 if (copyAlignment.getHeight() == 0)
4745 JOptionPane.showMessageDialog(AlignFrame.this,
4746 MessageManager.getString("label.cant_map_cds"),
4747 MessageManager.getString("label.operation_failed"),
4748 JOptionPane.OK_OPTION);
4749 System.err.println("Failed to make CDS alignment");
4753 * pending getting Embl transcripts to 'align',
4754 * we are only doing this for Ensembl
4756 // TODO proper criteria for 'can align as cdna'
4757 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
4758 || AlignmentUtils.looksLikeEnsembl(alignment))
4760 copyAlignment.alignAs(alignment);
4761 copyAlignmentIsAligned = true;
4766 copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
4767 xrefs.getSequencesArray(), dataset);
4769 copyAlignment.setGapCharacter(AlignFrame.this.viewport
4770 .getGapCharacter());
4772 StructureSelectionManager ssm = StructureSelectionManager
4773 .getStructureSelectionManager(Desktop.instance);
4776 * register any new mappings for sequence mouseover etc
4777 * (will not duplicate any previously registered mappings)
4779 ssm.registerMappings(dataset.getCodonFrames());
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 xrefsAlignment.alignAs(copyAlignment);
4797 * align cdna to protein - currently only if
4798 * fetching and aligning Ensembl transcripts!
4800 // TODO: generalise for other sources of locus/transcript/cds data
4801 if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4803 copyAlignment.alignAs(xrefsAlignment);
4808 * build AlignFrame(s) according to available alignment data
4810 AlignFrame newFrame = new AlignFrame(xrefsAlignment,
4811 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4812 if (Cache.getDefault("HIDE_INTRONS", true))
4814 newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
4816 String newtitle = String.format("%s %s %s",
4817 dna ? MessageManager.getString("label.proteins")
4818 : MessageManager.getString("label.nucleotides"),
4819 MessageManager.getString("label.for"), getTitle());
4820 newFrame.setTitle(newtitle);
4822 if (copyAlignment == null)
4825 * split frame display is turned off in preferences file
4827 Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4829 return; // via finally clause
4831 AlignFrame copyThis = new AlignFrame(copyAlignment,
4832 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4833 copyThis.setTitle(AlignFrame.this.getTitle());
4835 boolean showSequenceFeatures = viewport.isShowSequenceFeatures();
4836 newFrame.setShowSeqFeatures(showSequenceFeatures);
4837 copyThis.setShowSeqFeatures(showSequenceFeatures);
4838 FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4839 .getFeatureRenderer();
4842 * copy feature rendering settings to split frame
4844 newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
4845 .transferSettings(myFeatureStyling);
4846 copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
4847 .transferSettings(myFeatureStyling);
4850 * apply 'database source' feature configuration
4853 // TODO is this the feature colouring for the original
4854 // alignment or the fetched xrefs? either could be Ensembl
4855 newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
4856 copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
4858 SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4859 dna ? newFrame : copyThis);
4860 newFrame.setVisible(true);
4861 copyThis.setVisible(true);
4862 String linkedTitle = MessageManager
4863 .getString("label.linked_view_title");
4864 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4866 } catch (OutOfMemoryError e)
4868 new OOMWarning("whilst fetching crossreferences", e);
4869 } catch (Throwable e)
4871 Cache.log.error("Error when finding crossreferences", e);
4874 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4875 "status.finished_searching_for_sequences_from",
4876 new Object[] { source }), sttime);
4881 * Makes an alignment containing the given sequences, and adds them to the
4882 * given dataset, which is also set as the dataset for the new alignment
4884 * TODO: refactor to DatasetI method
4890 protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
4893 SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4894 for (int s = 0; s < sprods.length; s++)
4896 sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4897 if (dataset.getSequences() == null
4898 || !dataset.getSequences().contains(
4899 sprods[s].getDatasetSequence()))
4901 dataset.addSequence(sprods[s].getDatasetSequence());
4903 sprods[s].updatePDBIds();
4905 Alignment al = new Alignment(sprods);
4906 al.setDataset(dataset);
4911 Thread frunner = new Thread(foo);
4916 * Construct and display a new frame containing the translation of this
4917 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4920 public void showTranslation_actionPerformed(ActionEvent e)
4922 AlignmentI al = null;
4925 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4927 al = dna.translateCdna();
4928 } catch (Exception ex)
4930 jalview.bin.Cache.log.error(
4931 "Exception during translation. Please report this !", ex);
4932 final String msg = MessageManager
4933 .getString("label.error_when_translating_sequences_submit_bug_report");
4934 final String errorTitle = MessageManager
4935 .getString("label.implementation_error")
4936 + MessageManager.getString("label.translation_failed");
4937 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4938 JOptionPane.ERROR_MESSAGE);
4941 if (al == null || al.getHeight() == 0)
4943 final String msg = MessageManager
4944 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4945 final String errorTitle = MessageManager
4946 .getString("label.translation_failed");
4947 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4948 JOptionPane.WARNING_MESSAGE);
4952 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4953 af.setFileFormat(this.currentFileFormat);
4954 final String newTitle = MessageManager.formatMessage(
4955 "label.translation_of_params",
4956 new Object[] { this.getTitle() });
4957 af.setTitle(newTitle);
4958 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4960 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4961 viewport.openSplitFrame(af, new Alignment(seqs));
4965 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4972 * Set the file format
4976 public void setFileFormat(FileFormatI format)
4978 this.currentFileFormat = format;
4982 * Try to load a features file onto the alignment.
4985 * contents or path to retrieve file
4987 * access mode of file (see jalview.io.AlignFile)
4988 * @return true if features file was parsed correctly.
4990 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4992 return avc.parseFeaturesFile(file, sourceType,
4993 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4998 public void refreshFeatureUI(boolean enableIfNecessary)
5000 // note - currently this is only still here rather than in the controller
5001 // because of the featureSettings hard reference that is yet to be
5003 if (enableIfNecessary)
5005 viewport.setShowSequenceFeatures(true);
5006 showSeqFeatures.setSelected(true);
5012 public void dragEnter(DropTargetDragEvent evt)
5017 public void dragExit(DropTargetEvent evt)
5022 public void dragOver(DropTargetDragEvent evt)
5027 public void dropActionChanged(DropTargetDragEvent evt)
5032 public void drop(DropTargetDropEvent evt)
5034 Transferable t = evt.getTransferable();
5035 List<String> files = new ArrayList<String>();
5036 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
5040 Desktop.transferFromDropTarget(files, protocols, evt, t);
5041 } catch (Exception e)
5043 e.printStackTrace();
5049 // check to see if any of these files have names matching sequences in
5051 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5052 .getAlignment().getSequencesArray());
5054 * Object[] { String,SequenceI}
5056 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5057 ArrayList<String> filesnotmatched = new ArrayList<String>();
5058 for (int i = 0; i < files.size(); i++)
5060 String file = files.get(i).toString();
5062 DataSourceType protocol = FormatAdapter.checkProtocol(file);
5063 if (protocol == DataSourceType.FILE)
5065 File fl = new File(file);
5066 pdbfn = fl.getName();
5068 else if (protocol == DataSourceType.URL)
5070 URL url = new URL(file);
5071 pdbfn = url.getFile();
5073 if (pdbfn.length() > 0)
5075 // attempt to find a match in the alignment
5076 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5077 int l = 0, c = pdbfn.indexOf(".");
5078 while (mtch == null && c != -1)
5083 } while ((c = pdbfn.indexOf(".", l)) > l);
5086 pdbfn = pdbfn.substring(0, l);
5088 mtch = idm.findAllIdMatches(pdbfn);
5092 FileFormatI type = null;
5095 type = new IdentifyFile().identify(file, protocol);
5096 } catch (Exception ex)
5102 if (type == FileFormat.PDB)
5104 filesmatched.add(new Object[] { file, protocol, mtch });
5109 // File wasn't named like one of the sequences or wasn't a PDB file.
5110 filesnotmatched.add(file);
5114 if (filesmatched.size() > 0)
5116 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5122 "label.automatically_associate_pdb_files_with_sequences_same_name",
5123 new Object[] { Integer
5129 .getString("label.automatically_associate_pdb_files_by_name"),
5130 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5133 for (Object[] fm : filesmatched)
5135 // try and associate
5136 // TODO: may want to set a standard ID naming formalism for
5137 // associating PDB files which have no IDs.
5138 for (SequenceI toassoc : (SequenceI[]) fm[2])
5140 PDBEntry pe = new AssociatePdbFileWithSeq()
5141 .associatePdbWithSeq((String) fm[0],
5142 (DataSourceType) fm[1], toassoc, false,
5146 System.err.println("Associated file : "
5147 + ((String) fm[0]) + " with "
5148 + toassoc.getDisplayId(true));
5152 alignPanel.paintAlignment(true);
5156 if (filesnotmatched.size() > 0)
5159 && (Cache.getDefault(
5160 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5166 "label.ignore_unmatched_dropped_files_info",
5167 new Object[] { Integer
5174 .getString("label.ignore_unmatched_dropped_files"),
5175 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5179 for (String fn : filesnotmatched)
5181 loadJalviewDataFile(fn, null, null, null);
5185 } catch (Exception ex)
5187 ex.printStackTrace();
5193 * Attempt to load a "dropped" file or URL string: First by testing whether
5194 * it's an Annotation file, then a JNet file, and finally a features file. If
5195 * all are false then the user may have dropped an alignment file onto this
5199 * either a filename or a URL string.
5201 public void loadJalviewDataFile(String file, DataSourceType sourceType,
5202 FileFormatI format, SequenceI assocSeq)
5206 if (sourceType == null)
5208 sourceType = FormatAdapter.checkProtocol(file);
5210 // if the file isn't identified, or not positively identified as some
5211 // other filetype (PFAM is default unidentified alignment file type) then
5212 // try to parse as annotation.
5213 boolean isAnnotation = (format == null || format == FileFormat.Pfam) ? new AnnotationFile()
5214 .annotateAlignmentView(viewport, file, sourceType) : false;
5218 // first see if its a T-COFFEE score file
5219 TCoffeeScoreFile tcf = null;
5222 tcf = new TCoffeeScoreFile(file, sourceType);
5225 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5227 tcoffeeColour.setEnabled(true);
5228 tcoffeeColour.setSelected(true);
5229 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5230 isAnnotation = true;
5232 .setText(MessageManager
5233 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5237 // some problem - if no warning its probable that the ID matching
5238 // process didn't work
5242 tcf.getWarningMessage() == null ? MessageManager
5243 .getString("label.check_file_matches_sequence_ids_alignment")
5244 : tcf.getWarningMessage(),
5246 .getString("label.problem_reading_tcoffee_score_file"),
5247 JOptionPane.WARNING_MESSAGE);
5254 } catch (Exception x)
5257 .debug("Exception when processing data source as T-COFFEE score file",
5263 // try to see if its a JNet 'concise' style annotation file *before*
5265 // try to parse it as a features file
5268 format = new IdentifyFile().identify(file, sourceType);
5270 if (format == FileFormat.Jnet)
5272 JPredFile predictions = new JPredFile(
5274 new JnetAnnotationMaker();
5275 JnetAnnotationMaker.add_annotation(predictions,
5276 viewport.getAlignment(), 0, false);
5277 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5278 viewport.getAlignment().setSeqrep(repseq);
5279 ColumnSelection cs = new ColumnSelection();
5280 cs.hideInsertionsFor(repseq);
5281 viewport.setColumnSelection(cs);
5282 isAnnotation = true;
5284 // else if (IdentifyFile.FeaturesFile.equals(format))
5285 else if (format == FileFormat.Features)
5287 if (parseFeaturesFile(file, sourceType))
5289 alignPanel.paintAlignment(true);
5294 new FileLoader().LoadFile(viewport, file, sourceType, format);
5301 alignPanel.adjustAnnotationHeight();
5302 viewport.updateSequenceIdColours();
5303 buildSortByAnnotationScoresMenu();
5304 alignPanel.paintAlignment(true);
5306 } catch (Exception ex)
5308 ex.printStackTrace();
5309 } catch (OutOfMemoryError oom)
5314 } catch (Exception x)
5319 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
5320 : "using " + sourceType + " from " + file)
5322 + (format != null ? "(parsing as '" + format
5323 + "' file)" : ""), oom, Desktop.desktop);
5328 * Method invoked by the ChangeListener on the tabbed pane, in other words
5329 * when a different tabbed pane is selected by the user or programmatically.
5332 public void tabSelectionChanged(int index)
5336 alignPanel = alignPanels.get(index);
5337 viewport = alignPanel.av;
5338 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5339 setMenusFromViewport(viewport);
5343 * If there is a frame linked to this one in a SplitPane, switch it to the
5344 * same view tab index. No infinite recursion of calls should happen, since
5345 * tabSelectionChanged() should not get invoked on setting the selected
5346 * index to an unchanged value. Guard against setting an invalid index
5347 * before the new view peer tab has been created.
5349 final AlignViewportI peer = viewport.getCodingComplement();
5352 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5353 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5355 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5361 * On right mouse click on view tab, prompt for and set new view name.
5364 public void tabbedPane_mousePressed(MouseEvent e)
5366 if (e.isPopupTrigger())
5368 String msg = MessageManager.getString("label.enter_view_name");
5369 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5370 JOptionPane.QUESTION_MESSAGE);
5374 viewport.viewName = reply;
5375 // TODO warn if reply is in getExistingViewNames()?
5376 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5381 public AlignViewport getCurrentView()
5387 * Open the dialog for regex description parsing.
5390 protected void extractScores_actionPerformed(ActionEvent e)
5392 ParseProperties pp = new jalview.analysis.ParseProperties(
5393 viewport.getAlignment());
5394 // TODO: verify regex and introduce GUI dialog for version 2.5
5395 // if (pp.getScoresFromDescription("col", "score column ",
5396 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5398 if (pp.getScoresFromDescription("description column",
5399 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5401 buildSortByAnnotationScoresMenu();
5409 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5413 protected void showDbRefs_actionPerformed(ActionEvent e)
5415 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5421 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5425 protected void showNpFeats_actionPerformed(ActionEvent e)
5427 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5431 * find the viewport amongst the tabs in this alignment frame and close that
5436 public boolean closeView(AlignViewportI av)
5440 this.closeMenuItem_actionPerformed(false);
5443 Component[] comp = tabbedPane.getComponents();
5444 for (int i = 0; comp != null && i < comp.length; i++)
5446 if (comp[i] instanceof AlignmentPanel)
5448 if (((AlignmentPanel) comp[i]).av == av)
5451 closeView((AlignmentPanel) comp[i]);
5459 protected void build_fetchdbmenu(JMenu webService)
5461 // Temporary hack - DBRef Fetcher always top level ws entry.
5462 // TODO We probably want to store a sequence database checklist in
5463 // preferences and have checkboxes.. rather than individual sources selected
5465 final JMenu rfetch = new JMenu(
5466 MessageManager.getString("action.fetch_db_references"));
5467 rfetch.setToolTipText(MessageManager
5468 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5469 webService.add(rfetch);
5471 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5472 MessageManager.getString("option.trim_retrieved_seqs"));
5473 trimrs.setToolTipText(MessageManager
5474 .getString("label.trim_retrieved_sequences"));
5475 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5476 trimrs.addActionListener(new ActionListener()
5479 public void actionPerformed(ActionEvent e)
5481 trimrs.setSelected(trimrs.isSelected());
5482 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5483 Boolean.valueOf(trimrs.isSelected()).toString());
5487 JMenuItem fetchr = new JMenuItem(
5488 MessageManager.getString("label.standard_databases"));
5489 fetchr.setToolTipText(MessageManager
5490 .getString("label.fetch_embl_uniprot"));
5491 fetchr.addActionListener(new ActionListener()
5495 public void actionPerformed(ActionEvent e)
5497 new Thread(new Runnable()
5502 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5503 .getAlignment().isNucleotide();
5504 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5505 .getSequenceSelection(), alignPanel.alignFrame, null,
5506 alignPanel.alignFrame.featureSettings, isNucleotide);
5507 dbRefFetcher.addListener(new FetchFinishedListenerI()
5510 public void finished()
5512 AlignFrame.this.setMenusForViewport();
5515 dbRefFetcher.fetchDBRefs(false);
5523 final AlignFrame me = this;
5524 new Thread(new Runnable()
5529 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5530 .getSequenceFetcherSingleton(me);
5531 javax.swing.SwingUtilities.invokeLater(new Runnable()
5536 String[] dbclasses = sf.getOrderedSupportedSources();
5537 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5538 // jalview.util.QuickSort.sort(otherdb, otherdb);
5539 List<DbSourceProxy> otherdb;
5540 JMenu dfetch = new JMenu();
5541 JMenu ifetch = new JMenu();
5542 JMenuItem fetchr = null;
5543 int comp = 0, icomp = 0, mcomp = 15;
5544 String mname = null;
5546 for (String dbclass : dbclasses)
5548 otherdb = sf.getSourceProxy(dbclass);
5549 // add a single entry for this class, or submenu allowing 'fetch
5551 if (otherdb == null || otherdb.size() < 1)
5555 // List<DbSourceProxy> dbs=otherdb;
5556 // otherdb=new ArrayList<DbSourceProxy>();
5557 // for (DbSourceProxy db:dbs)
5559 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5563 mname = "From " + dbclass;
5565 if (otherdb.size() == 1)
5567 final DbSourceProxy[] dassource = otherdb
5568 .toArray(new DbSourceProxy[0]);
5569 DbSourceProxy src = otherdb.get(0);
5570 fetchr = new JMenuItem(src.getDbSource());
5571 fetchr.addActionListener(new ActionListener()
5575 public void actionPerformed(ActionEvent e)
5577 new Thread(new Runnable()
5583 boolean isNucleotide = alignPanel.alignFrame
5584 .getViewport().getAlignment()
5586 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5587 alignPanel.av.getSequenceSelection(),
5588 alignPanel.alignFrame, dassource,
5589 alignPanel.alignFrame.featureSettings,
5592 .addListener(new FetchFinishedListenerI()
5595 public void finished()
5597 AlignFrame.this.setMenusForViewport();
5600 dbRefFetcher.fetchDBRefs(false);
5606 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5607 MessageManager.formatMessage(
5608 "label.fetch_retrieve_from",
5609 new Object[] { src.getDbName() })));
5615 final DbSourceProxy[] dassource = otherdb
5616 .toArray(new DbSourceProxy[0]);
5618 DbSourceProxy src = otherdb.get(0);
5619 fetchr = new JMenuItem(MessageManager.formatMessage(
5620 "label.fetch_all_param",
5621 new Object[] { src.getDbSource() }));
5622 fetchr.addActionListener(new ActionListener()
5625 public void actionPerformed(ActionEvent e)
5627 new Thread(new Runnable()
5633 boolean isNucleotide = alignPanel.alignFrame
5634 .getViewport().getAlignment()
5636 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5637 alignPanel.av.getSequenceSelection(),
5638 alignPanel.alignFrame, dassource,
5639 alignPanel.alignFrame.featureSettings,
5642 .addListener(new FetchFinishedListenerI()
5645 public void finished()
5647 AlignFrame.this.setMenusForViewport();
5650 dbRefFetcher.fetchDBRefs(false);
5656 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5657 MessageManager.formatMessage(
5658 "label.fetch_retrieve_from_all_sources",
5660 Integer.valueOf(otherdb.size())
5661 .toString(), src.getDbSource(),
5662 src.getDbName() })));
5665 // and then build the rest of the individual menus
5666 ifetch = new JMenu(MessageManager.formatMessage(
5667 "label.source_from_db_source",
5668 new Object[] { src.getDbSource() }));
5670 String imname = null;
5672 for (DbSourceProxy sproxy : otherdb)
5674 String dbname = sproxy.getDbName();
5675 String sname = dbname.length() > 5 ? dbname.substring(0,
5676 5) + "..." : dbname;
5677 String msname = dbname.length() > 10 ? dbname.substring(
5678 0, 10) + "..." : dbname;
5681 imname = MessageManager.formatMessage(
5682 "label.from_msname", new Object[] { sname });
5684 fetchr = new JMenuItem(msname);
5685 final DbSourceProxy[] dassrc = { sproxy };
5686 fetchr.addActionListener(new ActionListener()
5690 public void actionPerformed(ActionEvent e)
5692 new Thread(new Runnable()
5698 boolean isNucleotide = alignPanel.alignFrame
5699 .getViewport().getAlignment()
5701 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5702 alignPanel.av.getSequenceSelection(),
5703 alignPanel.alignFrame, dassrc,
5704 alignPanel.alignFrame.featureSettings,
5707 .addListener(new FetchFinishedListenerI()
5710 public void finished()
5712 AlignFrame.this.setMenusForViewport();
5715 dbRefFetcher.fetchDBRefs(false);
5721 fetchr.setToolTipText("<html>"
5722 + MessageManager.formatMessage(
5723 "label.fetch_retrieve_from", new Object[]
5727 if (++icomp >= mcomp || i == (otherdb.size()))
5729 ifetch.setText(MessageManager.formatMessage(
5730 "label.source_to_target", imname, sname));
5732 ifetch = new JMenu();
5740 if (comp >= mcomp || dbi >= (dbclasses.length))
5742 dfetch.setText(MessageManager.formatMessage(
5743 "label.source_to_target", mname, dbclass));
5745 dfetch = new JMenu();
5758 * Left justify the whole alignment.
5761 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5763 AlignmentI al = viewport.getAlignment();
5765 viewport.firePropertyChange("alignment", null, al);
5769 * Right justify the whole alignment.
5772 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5774 AlignmentI al = viewport.getAlignment();
5776 viewport.firePropertyChange("alignment", null, al);
5780 public void setShowSeqFeatures(boolean b)
5782 showSeqFeatures.setSelected(b);
5783 viewport.setShowSequenceFeatures(b);
5790 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5791 * awt.event.ActionEvent)
5794 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5796 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5797 alignPanel.paintAlignment(true);
5804 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5808 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5810 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5811 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5819 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5820 * .event.ActionEvent)
5823 protected void showGroupConservation_actionPerformed(ActionEvent e)
5825 viewport.setShowGroupConservation(showGroupConservation.getState());
5826 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5833 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5834 * .event.ActionEvent)
5837 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5839 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5840 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5847 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5848 * .event.ActionEvent)
5851 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5853 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5854 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5858 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5860 showSequenceLogo.setState(true);
5861 viewport.setShowSequenceLogo(true);
5862 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5863 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5867 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5869 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5876 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5877 * .event.ActionEvent)
5880 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5882 if (avc.makeGroupsFromSelection())
5884 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5885 alignPanel.updateAnnotation();
5886 alignPanel.paintAlignment(true);
5890 public void clearAlignmentSeqRep()
5892 // TODO refactor alignmentseqrep to controller
5893 if (viewport.getAlignment().hasSeqrep())
5895 viewport.getAlignment().setSeqrep(null);
5896 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5897 alignPanel.updateAnnotation();
5898 alignPanel.paintAlignment(true);
5903 protected void createGroup_actionPerformed(ActionEvent e)
5905 if (avc.createGroup())
5907 alignPanel.alignmentChanged();
5912 protected void unGroup_actionPerformed(ActionEvent e)
5916 alignPanel.alignmentChanged();
5921 * make the given alignmentPanel the currently selected tab
5923 * @param alignmentPanel
5925 public void setDisplayedView(AlignmentPanel alignmentPanel)
5927 if (!viewport.getSequenceSetId().equals(
5928 alignmentPanel.av.getSequenceSetId()))
5932 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5934 if (tabbedPane != null
5935 && tabbedPane.getTabCount() > 0
5936 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5937 .getSelectedIndex())
5939 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5944 * Action on selection of menu options to Show or Hide annotations.
5947 * @param forSequences
5948 * update sequence-related annotations
5949 * @param forAlignment
5950 * update non-sequence-related annotations
5953 protected void setAnnotationsVisibility(boolean visible,
5954 boolean forSequences, boolean forAlignment)
5956 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5957 .getAlignmentAnnotation();
5962 for (AlignmentAnnotation aa : anns)
5965 * don't display non-positional annotations on an alignment
5967 if (aa.annotations == null)
5971 boolean apply = (aa.sequenceRef == null && forAlignment)
5972 || (aa.sequenceRef != null && forSequences);
5975 aa.visible = visible;
5978 alignPanel.validateAnnotationDimensions(true);
5979 alignPanel.alignmentChanged();
5983 * Store selected annotation sort order for the view and repaint.
5986 protected void sortAnnotations_actionPerformed()
5988 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5990 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5991 alignPanel.paintAlignment(true);
5996 * @return alignment panels in this alignment frame
5998 public List<? extends AlignmentViewPanel> getAlignPanels()
6000 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6004 * Open a new alignment window, with the cDNA associated with this (protein)
6005 * alignment, aligned as is the protein.
6007 protected void viewAsCdna_actionPerformed()
6009 // TODO no longer a menu action - refactor as required
6010 final AlignmentI alignment = getViewport().getAlignment();
6011 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6012 if (mappings == null)
6016 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6017 for (SequenceI aaSeq : alignment.getSequences())
6019 for (AlignedCodonFrame acf : mappings)
6021 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6025 * There is a cDNA mapping for this protein sequence - add to new
6026 * alignment. It will share the same dataset sequence as other mapped
6027 * cDNA (no new mappings need to be created).
6029 final Sequence newSeq = new Sequence(dnaSeq);
6030 newSeq.setDatasetSequence(dnaSeq);
6031 cdnaSeqs.add(newSeq);
6035 if (cdnaSeqs.size() == 0)
6037 // show a warning dialog no mapped cDNA
6040 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6042 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6043 AlignFrame.DEFAULT_HEIGHT);
6044 cdna.alignAs(alignment);
6045 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6047 Desktop.addInternalFrame(alignFrame, newtitle,
6048 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6052 * Set visibility of dna/protein complement view (available when shown in a
6058 protected void showComplement_actionPerformed(boolean show)
6060 SplitContainerI sf = getSplitViewContainer();
6063 sf.setComplementVisible(this, show);
6068 * Generate the reverse (optionally complemented) of the selected sequences,
6069 * and add them to the alignment
6072 protected void showReverse_actionPerformed(boolean complement)
6074 AlignmentI al = null;
6077 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6078 al = dna.reverseCdna(complement);
6079 viewport.addAlignment(al, "");
6080 addHistoryItem(new EditCommand(
6081 MessageManager.getString("label.add_sequences"),
6082 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
6083 viewport.getAlignment()));
6084 } catch (Exception ex)
6086 System.err.println(ex.getMessage());
6092 * Try to run a script in the Groovy console, having first ensured that this
6093 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
6094 * be targeted at this alignment.
6097 protected void runGroovy_actionPerformed()
6099 Jalview.setCurrentAlignFrame(this);
6100 groovy.ui.Console console = Desktop.getGroovyConsole();
6101 if (console != null)
6105 console.runScript();
6106 } catch (Exception ex)
6108 System.err.println((ex.toString()));
6110 .showInternalMessageDialog(Desktop.desktop, MessageManager
6111 .getString("label.couldnt_run_groovy_script"),
6113 .getString("label.groovy_support_failed"),
6114 JOptionPane.ERROR_MESSAGE);
6119 System.err.println("Can't run Groovy script as console not found");
6124 * Hides columns containing (or not containing) a specified feature, provided
6125 * that would not leave all columns hidden
6127 * @param featureType
6128 * @param columnsContaining
6131 public boolean hideFeatureColumns(String featureType,
6132 boolean columnsContaining)
6134 boolean notForHiding = avc.markColumnsContainingFeatures(
6135 columnsContaining, false, false, featureType);
6138 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
6139 false, featureType))
6141 getViewport().hideSelectedColumns();
6149 class PrintThread extends Thread
6153 public PrintThread(AlignmentPanel ap)
6158 static PageFormat pf;
6163 PrinterJob printJob = PrinterJob.getPrinterJob();
6167 printJob.setPrintable(ap, pf);
6171 printJob.setPrintable(ap);
6174 if (printJob.printDialog())
6179 } catch (Exception PrintException)
6181 PrintException.printStackTrace();