2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.FeatureSettingsModelI;
36 import jalview.api.SplitContainerI;
37 import jalview.api.ViewStyleI;
38 import jalview.api.analysis.ScoreModelI;
39 import jalview.bin.Cache;
40 import jalview.bin.Jalview;
41 import jalview.commands.CommandI;
42 import jalview.commands.EditCommand;
43 import jalview.commands.EditCommand.Action;
44 import jalview.commands.OrderCommand;
45 import jalview.commands.RemoveGapColCommand;
46 import jalview.commands.RemoveGapsCommand;
47 import jalview.commands.SlideSequencesCommand;
48 import jalview.commands.TrimRegionCommand;
49 import jalview.datamodel.AlignedCodonFrame;
50 import jalview.datamodel.Alignment;
51 import jalview.datamodel.AlignmentAnnotation;
52 import jalview.datamodel.AlignmentExportData;
53 import jalview.datamodel.AlignmentI;
54 import jalview.datamodel.AlignmentOrder;
55 import jalview.datamodel.AlignmentView;
56 import jalview.datamodel.ColumnSelection;
57 import jalview.datamodel.DBRefSource;
58 import jalview.datamodel.HiddenSequences;
59 import jalview.datamodel.PDBEntry;
60 import jalview.datamodel.SeqCigar;
61 import jalview.datamodel.Sequence;
62 import jalview.datamodel.SequenceGroup;
63 import jalview.datamodel.SequenceI;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.FileLoader;
69 import jalview.io.FormatAdapter;
70 import jalview.io.HtmlSvgOutput;
71 import jalview.io.IdentifyFile;
72 import jalview.io.JalviewFileChooser;
73 import jalview.io.JalviewFileView;
74 import jalview.io.JnetAnnotationMaker;
75 import jalview.io.NewickFile;
76 import jalview.io.TCoffeeScoreFile;
77 import jalview.io.gff.SequenceOntologyI;
78 import jalview.jbgui.GAlignFrame;
79 import jalview.schemes.Blosum62ColourScheme;
80 import jalview.schemes.BuriedColourScheme;
81 import jalview.schemes.ClustalxColourScheme;
82 import jalview.schemes.ColourSchemeI;
83 import jalview.schemes.ColourSchemeProperty;
84 import jalview.schemes.HelixColourScheme;
85 import jalview.schemes.HydrophobicColourScheme;
86 import jalview.schemes.NucleotideColourScheme;
87 import jalview.schemes.PIDColourScheme;
88 import jalview.schemes.PurinePyrimidineColourScheme;
89 import jalview.schemes.RNAHelicesColourChooser;
90 import jalview.schemes.ResidueProperties;
91 import jalview.schemes.StrandColourScheme;
92 import jalview.schemes.TCoffeeColourScheme;
93 import jalview.schemes.TaylorColourScheme;
94 import jalview.schemes.TurnColourScheme;
95 import jalview.schemes.UserColourScheme;
96 import jalview.schemes.ZappoColourScheme;
97 import jalview.structure.StructureSelectionManager;
98 import jalview.util.MessageManager;
99 import jalview.viewmodel.AlignmentViewport;
100 import jalview.ws.DBRefFetcher;
101 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
102 import jalview.ws.SequenceFetcher;
103 import jalview.ws.jws1.Discoverer;
104 import jalview.ws.jws2.Jws2Discoverer;
105 import jalview.ws.jws2.jabaws2.Jws2Instance;
106 import jalview.ws.seqfetcher.DbSourceProxy;
108 import java.awt.BorderLayout;
109 import java.awt.Component;
110 import java.awt.Rectangle;
111 import java.awt.Toolkit;
112 import java.awt.datatransfer.Clipboard;
113 import java.awt.datatransfer.DataFlavor;
114 import java.awt.datatransfer.StringSelection;
115 import java.awt.datatransfer.Transferable;
116 import java.awt.dnd.DropTargetDragEvent;
117 import java.awt.dnd.DropTargetDropEvent;
118 import java.awt.dnd.DropTargetEvent;
119 import java.awt.dnd.DropTargetListener;
120 import java.awt.event.ActionEvent;
121 import java.awt.event.ActionListener;
122 import java.awt.event.FocusAdapter;
123 import java.awt.event.FocusEvent;
124 import java.awt.event.ItemEvent;
125 import java.awt.event.ItemListener;
126 import java.awt.event.KeyAdapter;
127 import java.awt.event.KeyEvent;
128 import java.awt.event.MouseAdapter;
129 import java.awt.event.MouseEvent;
130 import java.awt.print.PageFormat;
131 import java.awt.print.PrinterJob;
132 import java.beans.PropertyChangeEvent;
135 import java.util.ArrayList;
136 import java.util.Arrays;
137 import java.util.Deque;
138 import java.util.Enumeration;
139 import java.util.Hashtable;
140 import java.util.List;
141 import java.util.Vector;
143 import javax.swing.JCheckBoxMenuItem;
144 import javax.swing.JEditorPane;
145 import javax.swing.JInternalFrame;
146 import javax.swing.JLayeredPane;
147 import javax.swing.JMenu;
148 import javax.swing.JMenuItem;
149 import javax.swing.JOptionPane;
150 import javax.swing.JRadioButtonMenuItem;
151 import javax.swing.JScrollPane;
152 import javax.swing.SwingUtilities;
158 * @version $Revision$
160 public class AlignFrame extends GAlignFrame implements DropTargetListener,
161 IProgressIndicator, AlignViewControllerGuiI
164 public static final int DEFAULT_WIDTH = 700;
166 public static final int DEFAULT_HEIGHT = 500;
169 * The currently displayed panel (selected tabbed view if more than one)
171 public AlignmentPanel alignPanel;
173 AlignViewport viewport;
175 public AlignViewControllerI avc;
177 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
180 * Last format used to load or save alignments in this window
182 String currentFileFormat = null;
185 * Current filename for this alignment
187 String fileName = null;
190 * Creates a new AlignFrame object with specific width and height.
196 public AlignFrame(AlignmentI al, int width, int height)
198 this(al, null, width, height);
202 * Creates a new AlignFrame object with specific width, height and
208 * @param sequenceSetId
210 public AlignFrame(AlignmentI al, int width, int height,
211 String sequenceSetId)
213 this(al, null, width, height, sequenceSetId);
217 * Creates a new AlignFrame object with specific width, height and
223 * @param sequenceSetId
226 public AlignFrame(AlignmentI al, int width, int height,
227 String sequenceSetId, String viewId)
229 this(al, null, width, height, sequenceSetId, viewId);
233 * new alignment window with hidden columns
237 * @param hiddenColumns
238 * ColumnSelection or null
240 * Width of alignment frame
244 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
245 int width, int height)
247 this(al, hiddenColumns, width, height, null);
251 * Create alignment frame for al with hiddenColumns, a specific width and
252 * height, and specific sequenceId
255 * @param hiddenColumns
258 * @param sequenceSetId
261 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
262 int width, int height, String sequenceSetId)
264 this(al, hiddenColumns, width, height, sequenceSetId, null);
268 * Create alignment frame for al with hiddenColumns, a specific width and
269 * height, and specific sequenceId
272 * @param hiddenColumns
275 * @param sequenceSetId
280 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
281 int width, int height, String sequenceSetId, String viewId)
283 setSize(width, height);
285 if (al.getDataset() == null)
290 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
292 alignPanel = new AlignmentPanel(this, viewport);
294 addAlignmentPanel(alignPanel, true);
298 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
299 ColumnSelection hiddenColumns, int width, int height)
301 setSize(width, height);
303 if (al.getDataset() == null)
308 viewport = new AlignViewport(al, hiddenColumns);
310 if (hiddenSeqs != null && hiddenSeqs.length > 0)
312 viewport.hideSequence(hiddenSeqs);
314 alignPanel = new AlignmentPanel(this, viewport);
315 addAlignmentPanel(alignPanel, true);
320 * Make a new AlignFrame from existing alignmentPanels
327 public AlignFrame(AlignmentPanel ap)
331 addAlignmentPanel(ap, false);
336 * initalise the alignframe from the underlying viewport data and the
341 if (!Jalview.isHeadlessMode())
343 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
346 avc = new jalview.controller.AlignViewController(this, viewport,
348 if (viewport.getAlignmentConservationAnnotation() == null)
350 BLOSUM62Colour.setEnabled(false);
351 conservationMenuItem.setEnabled(false);
352 modifyConservation.setEnabled(false);
353 // PIDColour.setEnabled(false);
354 // abovePIDThreshold.setEnabled(false);
355 // modifyPID.setEnabled(false);
358 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
361 if (sortby.equals("Id"))
363 sortIDMenuItem_actionPerformed(null);
365 else if (sortby.equals("Pairwise Identity"))
367 sortPairwiseMenuItem_actionPerformed(null);
370 if (Desktop.desktop != null)
372 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
373 addServiceListeners();
374 setGUINucleotide(viewport.getAlignment().isNucleotide());
378 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
380 setMenusFromViewport(viewport);
381 buildSortByAnnotationScoresMenu();
384 if (viewport.getWrapAlignment())
386 wrapMenuItem_actionPerformed(null);
389 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
391 this.overviewMenuItem_actionPerformed(null);
396 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
397 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
398 final String menuLabel = MessageManager
399 .getString("label.copy_format_from");
400 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
401 new ViewSetProvider()
405 public AlignmentPanel[] getAllAlignmentPanels()
408 origview.add(alignPanel);
409 // make an array of all alignment panels except for this one
410 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
411 Arrays.asList(Desktop.getAlignmentPanels(null)));
412 aps.remove(AlignFrame.this.alignPanel);
413 return aps.toArray(new AlignmentPanel[aps.size()]);
415 }, selviews, new ItemListener()
419 public void itemStateChanged(ItemEvent e)
421 if (origview.size() > 0)
423 final AlignmentPanel ap = origview.get(0);
426 * Copy the ViewStyle of the selected panel to 'this one'.
427 * Don't change value of 'scaleProteinAsCdna' unless copying
430 ViewStyleI vs = selviews.get(0).getAlignViewport()
432 boolean fromSplitFrame = selviews.get(0)
433 .getAlignViewport().getCodingComplement() != null;
436 vs.setScaleProteinAsCdna(ap.getAlignViewport()
437 .getViewStyle().isScaleProteinAsCdna());
439 ap.getAlignViewport().setViewStyle(vs);
442 * Also rescale ViewStyle of SplitFrame complement if there is
443 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
444 * the whole ViewStyle (allow cDNA protein to have different
447 AlignViewportI complement = ap.getAlignViewport()
448 .getCodingComplement();
449 if (complement != null && vs.isScaleProteinAsCdna())
451 AlignFrame af = Desktop.getAlignFrameFor(complement);
452 ((SplitFrame) af.getSplitViewContainer())
454 af.setMenusForViewport();
458 ap.setSelected(true);
459 ap.alignFrame.setMenusForViewport();
464 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
465 .indexOf("devel") > -1
466 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
467 .indexOf("test") > -1)
469 formatMenu.add(vsel);
471 addFocusListener(new FocusAdapter()
474 public void focusGained(FocusEvent e)
476 Desktop.setCurrentAlignFrame(AlignFrame.this);
483 * Change the filename and format for the alignment, and enable the 'reload'
484 * button functionality.
491 public void setFileName(String file, String format)
494 setFileFormat(format);
495 reload.setEnabled(true);
499 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
502 void addKeyListener()
504 addKeyListener(new KeyAdapter()
507 public void keyPressed(KeyEvent evt)
509 if (viewport.cursorMode
510 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
511 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
512 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
513 && Character.isDigit(evt.getKeyChar()))
515 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
518 switch (evt.getKeyCode())
521 case 27: // escape key
522 deselectAllSequenceMenuItem_actionPerformed(null);
526 case KeyEvent.VK_DOWN:
527 if (evt.isAltDown() || !viewport.cursorMode)
529 moveSelectedSequences(false);
531 if (viewport.cursorMode)
533 alignPanel.getSeqPanel().moveCursor(0, 1);
538 if (evt.isAltDown() || !viewport.cursorMode)
540 moveSelectedSequences(true);
542 if (viewport.cursorMode)
544 alignPanel.getSeqPanel().moveCursor(0, -1);
549 case KeyEvent.VK_LEFT:
550 if (evt.isAltDown() || !viewport.cursorMode)
552 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
556 alignPanel.getSeqPanel().moveCursor(-1, 0);
561 case KeyEvent.VK_RIGHT:
562 if (evt.isAltDown() || !viewport.cursorMode)
564 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
568 alignPanel.getSeqPanel().moveCursor(1, 0);
572 case KeyEvent.VK_SPACE:
573 if (viewport.cursorMode)
575 alignPanel.getSeqPanel().insertGapAtCursor(
576 evt.isControlDown() || evt.isShiftDown()
581 // case KeyEvent.VK_A:
582 // if (viewport.cursorMode)
584 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
585 // //System.out.println("A");
589 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
590 * System.out.println("closing bracket"); } break;
592 case KeyEvent.VK_DELETE:
593 case KeyEvent.VK_BACK_SPACE:
594 if (!viewport.cursorMode)
596 cut_actionPerformed(null);
600 alignPanel.getSeqPanel().deleteGapAtCursor(
601 evt.isControlDown() || evt.isShiftDown()
608 if (viewport.cursorMode)
610 alignPanel.getSeqPanel().setCursorRow();
614 if (viewport.cursorMode && !evt.isControlDown())
616 alignPanel.getSeqPanel().setCursorColumn();
620 if (viewport.cursorMode)
622 alignPanel.getSeqPanel().setCursorPosition();
626 case KeyEvent.VK_ENTER:
627 case KeyEvent.VK_COMMA:
628 if (viewport.cursorMode)
630 alignPanel.getSeqPanel().setCursorRowAndColumn();
635 if (viewport.cursorMode)
637 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
641 if (viewport.cursorMode)
643 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
648 viewport.cursorMode = !viewport.cursorMode;
649 statusBar.setText(MessageManager.formatMessage(
650 "label.keyboard_editing_mode",
651 new String[] { (viewport.cursorMode ? "on" : "off") }));
652 if (viewport.cursorMode)
654 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
655 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
657 alignPanel.getSeqPanel().seqCanvas.repaint();
663 Help.showHelpWindow();
664 } catch (Exception ex)
666 ex.printStackTrace();
671 boolean toggleSeqs = !evt.isControlDown();
672 boolean toggleCols = !evt.isShiftDown();
673 toggleHiddenRegions(toggleSeqs, toggleCols);
676 case KeyEvent.VK_PAGE_UP:
677 if (viewport.getWrapAlignment())
679 alignPanel.scrollUp(true);
683 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
684 - viewport.endSeq + viewport.startSeq);
687 case KeyEvent.VK_PAGE_DOWN:
688 if (viewport.getWrapAlignment())
690 alignPanel.scrollUp(false);
694 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
695 + viewport.endSeq - viewport.startSeq);
702 public void keyReleased(KeyEvent evt)
704 switch (evt.getKeyCode())
706 case KeyEvent.VK_LEFT:
707 if (evt.isAltDown() || !viewport.cursorMode)
709 viewport.firePropertyChange("alignment", null, viewport
710 .getAlignment().getSequences());
714 case KeyEvent.VK_RIGHT:
715 if (evt.isAltDown() || !viewport.cursorMode)
717 viewport.firePropertyChange("alignment", null, viewport
718 .getAlignment().getSequences());
726 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
728 ap.alignFrame = this;
729 avc = new jalview.controller.AlignViewController(this, viewport,
734 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
736 int aSize = alignPanels.size();
738 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
740 if (aSize == 1 && ap.av.viewName == null)
742 this.getContentPane().add(ap, BorderLayout.CENTER);
748 setInitialTabVisible();
751 expandViews.setEnabled(true);
752 gatherViews.setEnabled(true);
753 tabbedPane.addTab(ap.av.viewName, ap);
755 ap.setVisible(false);
760 if (ap.av.isPadGaps())
762 ap.av.getAlignment().padGaps();
764 ap.av.updateConservation(ap);
765 ap.av.updateConsensus(ap);
766 ap.av.updateStrucConsensus(ap);
770 public void setInitialTabVisible()
772 expandViews.setEnabled(true);
773 gatherViews.setEnabled(true);
774 tabbedPane.setVisible(true);
775 AlignmentPanel first = alignPanels.get(0);
776 tabbedPane.addTab(first.av.viewName, first);
777 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
780 public AlignViewport getViewport()
785 /* Set up intrinsic listeners for dynamically generated GUI bits. */
786 private void addServiceListeners()
788 final java.beans.PropertyChangeListener thisListener;
789 Desktop.instance.addJalviewPropertyChangeListener("services",
790 thisListener = new java.beans.PropertyChangeListener()
793 public void propertyChange(PropertyChangeEvent evt)
795 // // System.out.println("Discoverer property change.");
796 // if (evt.getPropertyName().equals("services"))
798 SwingUtilities.invokeLater(new Runnable()
805 .println("Rebuild WS Menu for service change");
806 BuildWebServiceMenu();
813 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
816 public void internalFrameClosed(
817 javax.swing.event.InternalFrameEvent evt)
819 // System.out.println("deregistering discoverer listener");
820 Desktop.instance.removeJalviewPropertyChangeListener("services",
822 closeMenuItem_actionPerformed(true);
825 // Finally, build the menu once to get current service state
826 new Thread(new Runnable()
831 BuildWebServiceMenu();
837 * Configure menu items that vary according to whether the alignment is
838 * nucleotide or protein
842 public void setGUINucleotide(boolean nucleotide)
844 showTranslation.setVisible(nucleotide);
845 showReverse.setVisible(nucleotide);
846 showReverseComplement.setVisible(nucleotide);
847 conservationMenuItem.setEnabled(!nucleotide);
848 modifyConservation.setEnabled(!nucleotide);
849 showGroupConservation.setEnabled(!nucleotide);
850 rnahelicesColour.setEnabled(nucleotide);
851 purinePyrimidineColour.setEnabled(nucleotide);
852 showComplementMenuItem.setText(MessageManager
853 .getString(nucleotide ? "label.protein" : "label.nucleotide"));
854 setColourSelected(jalview.bin.Cache.getDefault(
855 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
856 : Preferences.DEFAULT_COLOUR_PROT, "None"));
860 * set up menus for the current viewport. This may be called after any
861 * operation that affects the data in the current view (selection changed,
862 * etc) to update the menus to reflect the new state.
865 public void setMenusForViewport()
867 setMenusFromViewport(viewport);
871 * Need to call this method when tabs are selected for multiple views, or when
872 * loading from Jalview2XML.java
877 void setMenusFromViewport(AlignViewport av)
879 padGapsMenuitem.setSelected(av.isPadGaps());
880 colourTextMenuItem.setSelected(av.isShowColourText());
881 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
882 conservationMenuItem.setSelected(av.getConservationSelected());
883 seqLimits.setSelected(av.getShowJVSuffix());
884 idRightAlign.setSelected(av.isRightAlignIds());
885 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
886 renderGapsMenuItem.setSelected(av.isRenderGaps());
887 wrapMenuItem.setSelected(av.getWrapAlignment());
888 scaleAbove.setVisible(av.getWrapAlignment());
889 scaleLeft.setVisible(av.getWrapAlignment());
890 scaleRight.setVisible(av.getWrapAlignment());
891 annotationPanelMenuItem.setState(av.isShowAnnotation());
893 * Show/hide annotations only enabled if annotation panel is shown
895 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
896 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
897 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
898 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
899 viewBoxesMenuItem.setSelected(av.getShowBoxes());
900 viewTextMenuItem.setSelected(av.getShowText());
901 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
902 showGroupConsensus.setSelected(av.isShowGroupConsensus());
903 showGroupConservation.setSelected(av.isShowGroupConservation());
904 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
905 showSequenceLogo.setSelected(av.isShowSequenceLogo());
906 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
908 setColourSelected(ColourSchemeProperty.getColourName(av
909 .getGlobalColourScheme()));
911 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
912 hiddenMarkers.setState(av.getShowHiddenMarkers());
913 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
914 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
915 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
916 autoCalculate.setSelected(av.autoCalculateConsensus);
917 sortByTree.setSelected(av.sortByTree);
918 listenToViewSelections.setSelected(av.followSelection);
919 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
921 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
923 showProducts.setEnabled(canShowProducts());
924 setGroovyEnabled(Desktop.getGroovyConsole() != null);
930 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
934 public void setGroovyEnabled(boolean b)
936 runGroovy.setEnabled(b);
939 private IProgressIndicator progressBar;
944 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
947 public void setProgressBar(String message, long id)
949 progressBar.setProgressBar(message, id);
953 public void registerHandler(final long id,
954 final IProgressIndicatorHandler handler)
956 progressBar.registerHandler(id, handler);
961 * @return true if any progress bars are still active
964 public boolean operationInProgress()
966 return progressBar.operationInProgress();
970 public void setStatus(String text)
972 statusBar.setText(text);
976 * Added so Castor Mapping file can obtain Jalview Version
978 public String getVersion()
980 return jalview.bin.Cache.getProperty("VERSION");
983 public FeatureRenderer getFeatureRenderer()
985 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
989 public void fetchSequence_actionPerformed(ActionEvent e)
991 new jalview.gui.SequenceFetcher(this);
995 public void addFromFile_actionPerformed(ActionEvent e)
997 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1001 public void reload_actionPerformed(ActionEvent e)
1003 if (fileName != null)
1005 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1006 // originating file's format
1007 // TODO: work out how to recover feature settings for correct view(s) when
1008 // file is reloaded.
1009 if (currentFileFormat.equals("Jalview"))
1011 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1012 for (int i = 0; i < frames.length; i++)
1014 if (frames[i] instanceof AlignFrame && frames[i] != this
1015 && ((AlignFrame) frames[i]).fileName != null
1016 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1020 frames[i].setSelected(true);
1021 Desktop.instance.closeAssociatedWindows();
1022 } catch (java.beans.PropertyVetoException ex)
1028 Desktop.instance.closeAssociatedWindows();
1030 FileLoader loader = new FileLoader();
1031 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1032 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1036 Rectangle bounds = this.getBounds();
1038 FileLoader loader = new FileLoader();
1039 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1040 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1041 protocol, currentFileFormat);
1043 newframe.setBounds(bounds);
1044 if (featureSettings != null && featureSettings.isShowing())
1046 final Rectangle fspos = featureSettings.frame.getBounds();
1047 // TODO: need a 'show feature settings' function that takes bounds -
1048 // need to refactor Desktop.addFrame
1049 newframe.featureSettings_actionPerformed(null);
1050 final FeatureSettings nfs = newframe.featureSettings;
1051 SwingUtilities.invokeLater(new Runnable()
1056 nfs.frame.setBounds(fspos);
1059 this.featureSettings.close();
1060 this.featureSettings = null;
1062 this.closeMenuItem_actionPerformed(true);
1068 public void addFromText_actionPerformed(ActionEvent e)
1070 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1075 public void addFromURL_actionPerformed(ActionEvent e)
1077 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1081 public void save_actionPerformed(ActionEvent e)
1083 if (fileName == null
1084 || (currentFileFormat == null || !jalview.io.FormatAdapter
1085 .isValidIOFormat(currentFileFormat, true))
1086 || fileName.startsWith("http"))
1088 saveAs_actionPerformed(null);
1092 saveAlignment(fileName, currentFileFormat);
1103 public void saveAs_actionPerformed(ActionEvent e)
1105 JalviewFileChooser chooser = new JalviewFileChooser(
1106 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1107 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1108 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1109 currentFileFormat, false);
1111 chooser.setFileView(new JalviewFileView());
1112 chooser.setDialogTitle(MessageManager
1113 .getString("label.save_alignment_to_file"));
1114 chooser.setToolTipText(MessageManager.getString("action.save"));
1116 int value = chooser.showSaveDialog(this);
1118 if (value == JalviewFileChooser.APPROVE_OPTION)
1120 currentFileFormat = chooser.getSelectedFormat();
1121 while (currentFileFormat == null)
1124 .showInternalMessageDialog(
1127 .getString("label.select_file_format_before_saving"),
1129 .getString("label.file_format_not_specified"),
1130 JOptionPane.WARNING_MESSAGE);
1131 currentFileFormat = chooser.getSelectedFormat();
1132 value = chooser.showSaveDialog(this);
1133 if (value != JalviewFileChooser.APPROVE_OPTION)
1139 fileName = chooser.getSelectedFile().getPath();
1141 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1144 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1145 if (currentFileFormat.indexOf(" ") > -1)
1147 currentFileFormat = currentFileFormat.substring(0,
1148 currentFileFormat.indexOf(" "));
1150 saveAlignment(fileName, currentFileFormat);
1154 public boolean saveAlignment(String file, String format)
1156 boolean success = true;
1158 if (format.equalsIgnoreCase("Jalview"))
1160 String shortName = title;
1162 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1164 shortName = shortName.substring(shortName
1165 .lastIndexOf(java.io.File.separatorChar) + 1);
1168 success = new Jalview2XML().saveAlignment(this, file, shortName);
1170 statusBar.setText(MessageManager.formatMessage(
1171 "label.successfully_saved_to_file_in_format", new Object[] {
1172 fileName, format }));
1177 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1179 warningMessage("Cannot save file " + fileName + " using format "
1180 + format, "Alignment output format not supported");
1181 if (!Jalview.isHeadlessMode())
1183 saveAs_actionPerformed(null);
1188 AlignmentExportData exportData = getAlignmentForExport(format,
1190 if (exportData.getSettings().isCancelled())
1194 FormatAdapter f = new FormatAdapter(alignPanel,
1195 exportData.getSettings());
1196 String output = f.formatSequences(
1198 exportData.getAlignment(), // class cast exceptions will
1199 // occur in the distant future
1200 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1201 f.getCacheSuffixDefault(format),
1202 viewport.getColumnSelection());
1212 java.io.PrintWriter out = new java.io.PrintWriter(
1213 new java.io.FileWriter(file));
1217 this.setTitle(file);
1218 statusBar.setText(MessageManager.formatMessage(
1219 "label.successfully_saved_to_file_in_format",
1220 new Object[] { fileName, format }));
1221 } catch (Exception ex)
1224 ex.printStackTrace();
1231 JOptionPane.showInternalMessageDialog(this, MessageManager
1232 .formatMessage("label.couldnt_save_file",
1233 new Object[] { fileName }), MessageManager
1234 .getString("label.error_saving_file"),
1235 JOptionPane.WARNING_MESSAGE);
1241 private void warningMessage(String warning, String title)
1243 if (new jalview.util.Platform().isHeadless())
1245 System.err.println("Warning: " + title + "\nWarning: " + warning);
1250 JOptionPane.showInternalMessageDialog(this, warning, title,
1251 JOptionPane.WARNING_MESSAGE);
1263 protected void outputText_actionPerformed(ActionEvent e)
1266 AlignmentExportData exportData = getAlignmentForExport(
1267 e.getActionCommand(), viewport, null);
1268 if (exportData.getSettings().isCancelled())
1272 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1273 cap.setForInput(null);
1276 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1277 .formatSequences(e.getActionCommand(),
1278 exportData.getAlignment(),
1279 exportData.getOmitHidden(),
1280 exportData.getStartEndPostions(),
1281 viewport.getColumnSelection()));
1282 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1283 "label.alignment_output_command",
1284 new Object[] { e.getActionCommand() }), 600, 500);
1285 } catch (OutOfMemoryError oom)
1287 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1293 public static AlignmentExportData getAlignmentForExport(
1294 String exportFormat, AlignViewportI viewport,
1295 AlignExportSettingI exportSettings)
1297 AlignmentI alignmentToExport = null;
1298 AlignExportSettingI settings = exportSettings;
1299 String[] omitHidden = null;
1301 HiddenSequences hiddenSeqs = viewport.getAlignment()
1302 .getHiddenSequences();
1304 alignmentToExport = viewport.getAlignment();
1306 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1307 if (settings == null)
1309 settings = new AlignExportSettings(hasHiddenSeqs,
1310 viewport.hasHiddenColumns(), exportFormat);
1312 // settings.isExportAnnotations();
1314 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1316 omitHidden = viewport.getViewAsString(false);
1319 int[] alignmentStartEnd = new int[2];
1320 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1322 alignmentToExport = hiddenSeqs.getFullAlignment();
1326 alignmentToExport = viewport.getAlignment();
1327 alignmentStartEnd = viewport.getAlignment()
1328 .getVisibleStartAndEndIndex(
1329 viewport.getColumnSelection().getHiddenColumns());
1331 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1332 omitHidden, alignmentStartEnd, settings);
1343 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1345 new HtmlSvgOutput(null, alignPanel);
1349 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1351 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1352 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1355 public void createImageMap(File file, String image)
1357 alignPanel.makePNGImageMap(file, image);
1367 public void createPNG(File f)
1369 alignPanel.makePNG(f);
1379 public void createEPS(File f)
1381 alignPanel.makeEPS(f);
1385 public void createSVG(File f)
1387 alignPanel.makeSVG(f);
1391 public void pageSetup_actionPerformed(ActionEvent e)
1393 PrinterJob printJob = PrinterJob.getPrinterJob();
1394 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1404 public void printMenuItem_actionPerformed(ActionEvent e)
1406 // Putting in a thread avoids Swing painting problems
1407 PrintThread thread = new PrintThread(alignPanel);
1412 public void exportFeatures_actionPerformed(ActionEvent e)
1414 new AnnotationExporter().exportFeatures(alignPanel);
1418 public void exportAnnotations_actionPerformed(ActionEvent e)
1420 new AnnotationExporter().exportAnnotations(alignPanel);
1424 public void associatedData_actionPerformed(ActionEvent e)
1426 // Pick the tree file
1427 JalviewFileChooser chooser = new JalviewFileChooser(
1428 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1429 chooser.setFileView(new JalviewFileView());
1430 chooser.setDialogTitle(MessageManager
1431 .getString("label.load_jalview_annotations"));
1432 chooser.setToolTipText(MessageManager
1433 .getString("label.load_jalview_annotations"));
1435 int value = chooser.showOpenDialog(null);
1437 if (value == JalviewFileChooser.APPROVE_OPTION)
1439 String choice = chooser.getSelectedFile().getPath();
1440 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1441 loadJalviewDataFile(choice, null, null, null);
1447 * Close the current view or all views in the alignment frame. If the frame
1448 * only contains one view then the alignment will be removed from memory.
1450 * @param closeAllTabs
1453 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1455 if (alignPanels != null && alignPanels.size() < 2)
1457 closeAllTabs = true;
1462 if (alignPanels != null)
1466 if (this.isClosed())
1468 // really close all the windows - otherwise wait till
1469 // setClosed(true) is called
1470 for (int i = 0; i < alignPanels.size(); i++)
1472 AlignmentPanel ap = alignPanels.get(i);
1479 closeView(alignPanel);
1486 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1487 * be called recursively, with the frame now in 'closed' state
1489 this.setClosed(true);
1491 } catch (Exception ex)
1493 ex.printStackTrace();
1498 * Close the specified panel and close up tabs appropriately.
1500 * @param panelToClose
1502 public void closeView(AlignmentPanel panelToClose)
1504 int index = tabbedPane.getSelectedIndex();
1505 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1506 alignPanels.remove(panelToClose);
1507 panelToClose.closePanel();
1508 panelToClose = null;
1510 tabbedPane.removeTabAt(closedindex);
1511 tabbedPane.validate();
1513 if (index > closedindex || index == tabbedPane.getTabCount())
1515 // modify currently selected tab index if necessary.
1519 this.tabSelectionChanged(index);
1525 void updateEditMenuBar()
1528 if (viewport.getHistoryList().size() > 0)
1530 undoMenuItem.setEnabled(true);
1531 CommandI command = viewport.getHistoryList().peek();
1532 undoMenuItem.setText(MessageManager.formatMessage(
1533 "label.undo_command",
1534 new Object[] { command.getDescription() }));
1538 undoMenuItem.setEnabled(false);
1539 undoMenuItem.setText(MessageManager.getString("action.undo"));
1542 if (viewport.getRedoList().size() > 0)
1544 redoMenuItem.setEnabled(true);
1546 CommandI command = viewport.getRedoList().peek();
1547 redoMenuItem.setText(MessageManager.formatMessage(
1548 "label.redo_command",
1549 new Object[] { command.getDescription() }));
1553 redoMenuItem.setEnabled(false);
1554 redoMenuItem.setText(MessageManager.getString("action.redo"));
1559 public void addHistoryItem(CommandI command)
1561 if (command.getSize() > 0)
1563 viewport.addToHistoryList(command);
1564 viewport.clearRedoList();
1565 updateEditMenuBar();
1566 viewport.updateHiddenColumns();
1567 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1568 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1569 // viewport.getColumnSelection()
1570 // .getHiddenColumns().size() > 0);
1576 * @return alignment objects for all views
1578 AlignmentI[] getViewAlignments()
1580 if (alignPanels != null)
1582 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1584 for (AlignmentPanel ap : alignPanels)
1586 als[i++] = ap.av.getAlignment();
1590 if (viewport != null)
1592 return new AlignmentI[] { viewport.getAlignment() };
1604 protected void undoMenuItem_actionPerformed(ActionEvent e)
1606 if (viewport.getHistoryList().isEmpty())
1610 CommandI command = viewport.getHistoryList().pop();
1611 viewport.addToRedoList(command);
1612 command.undoCommand(getViewAlignments());
1614 AlignmentViewport originalSource = getOriginatingSource(command);
1615 updateEditMenuBar();
1617 if (originalSource != null)
1619 if (originalSource != viewport)
1622 .warn("Implementation worry: mismatch of viewport origin for undo");
1624 originalSource.updateHiddenColumns();
1625 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1627 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1628 // viewport.getColumnSelection()
1629 // .getHiddenColumns().size() > 0);
1630 originalSource.firePropertyChange("alignment", null, originalSource
1631 .getAlignment().getSequences());
1642 protected void redoMenuItem_actionPerformed(ActionEvent e)
1644 if (viewport.getRedoList().size() < 1)
1649 CommandI command = viewport.getRedoList().pop();
1650 viewport.addToHistoryList(command);
1651 command.doCommand(getViewAlignments());
1653 AlignmentViewport originalSource = getOriginatingSource(command);
1654 updateEditMenuBar();
1656 if (originalSource != null)
1659 if (originalSource != viewport)
1662 .warn("Implementation worry: mismatch of viewport origin for redo");
1664 originalSource.updateHiddenColumns();
1665 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1667 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1668 // viewport.getColumnSelection()
1669 // .getHiddenColumns().size() > 0);
1670 originalSource.firePropertyChange("alignment", null, originalSource
1671 .getAlignment().getSequences());
1675 AlignmentViewport getOriginatingSource(CommandI command)
1677 AlignmentViewport originalSource = null;
1678 // For sequence removal and addition, we need to fire
1679 // the property change event FROM the viewport where the
1680 // original alignment was altered
1681 AlignmentI al = null;
1682 if (command instanceof EditCommand)
1684 EditCommand editCommand = (EditCommand) command;
1685 al = editCommand.getAlignment();
1686 List<Component> comps = PaintRefresher.components.get(viewport
1687 .getSequenceSetId());
1689 for (Component comp : comps)
1691 if (comp instanceof AlignmentPanel)
1693 if (al == ((AlignmentPanel) comp).av.getAlignment())
1695 originalSource = ((AlignmentPanel) comp).av;
1702 if (originalSource == null)
1704 // The original view is closed, we must validate
1705 // the current view against the closed view first
1708 PaintRefresher.validateSequences(al, viewport.getAlignment());
1711 originalSource = viewport;
1714 return originalSource;
1723 public void moveSelectedSequences(boolean up)
1725 SequenceGroup sg = viewport.getSelectionGroup();
1731 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1732 viewport.getHiddenRepSequences(), up);
1733 alignPanel.paintAlignment(true);
1736 synchronized void slideSequences(boolean right, int size)
1738 List<SequenceI> sg = new ArrayList<SequenceI>();
1739 if (viewport.cursorMode)
1741 sg.add(viewport.getAlignment().getSequenceAt(
1742 alignPanel.getSeqPanel().seqCanvas.cursorY));
1744 else if (viewport.getSelectionGroup() != null
1745 && viewport.getSelectionGroup().getSize() != viewport
1746 .getAlignment().getHeight())
1748 sg = viewport.getSelectionGroup().getSequences(
1749 viewport.getHiddenRepSequences());
1757 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1759 for (SequenceI seq : viewport.getAlignment().getSequences())
1761 if (!sg.contains(seq))
1763 invertGroup.add(seq);
1767 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1769 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1770 for (int i = 0; i < invertGroup.size(); i++)
1772 seqs2[i] = invertGroup.get(i);
1775 SlideSequencesCommand ssc;
1778 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1779 size, viewport.getGapCharacter());
1783 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1784 size, viewport.getGapCharacter());
1787 int groupAdjustment = 0;
1788 if (ssc.getGapsInsertedBegin() && right)
1790 if (viewport.cursorMode)
1792 alignPanel.getSeqPanel().moveCursor(size, 0);
1796 groupAdjustment = size;
1799 else if (!ssc.getGapsInsertedBegin() && !right)
1801 if (viewport.cursorMode)
1803 alignPanel.getSeqPanel().moveCursor(-size, 0);
1807 groupAdjustment = -size;
1811 if (groupAdjustment != 0)
1813 viewport.getSelectionGroup().setStartRes(
1814 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1815 viewport.getSelectionGroup().setEndRes(
1816 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1820 * just extend the last slide command if compatible; but not if in
1821 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1823 boolean appendHistoryItem = false;
1824 Deque<CommandI> historyList = viewport.getHistoryList();
1825 boolean inSplitFrame = getSplitViewContainer() != null;
1826 if (!inSplitFrame && historyList != null && historyList.size() > 0
1827 && historyList.peek() instanceof SlideSequencesCommand)
1829 appendHistoryItem = ssc
1830 .appendSlideCommand((SlideSequencesCommand) historyList
1834 if (!appendHistoryItem)
1836 addHistoryItem(ssc);
1849 protected void copy_actionPerformed(ActionEvent e)
1852 if (viewport.getSelectionGroup() == null)
1856 // TODO: preserve the ordering of displayed alignment annotation in any
1857 // internal paste (particularly sequence associated annotation)
1858 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1859 String[] omitHidden = null;
1861 if (viewport.hasHiddenColumns())
1863 omitHidden = viewport.getViewAsString(true);
1866 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1869 StringSelection ss = new StringSelection(output);
1873 jalview.gui.Desktop.internalCopy = true;
1874 // Its really worth setting the clipboard contents
1875 // to empty before setting the large StringSelection!!
1876 Toolkit.getDefaultToolkit().getSystemClipboard()
1877 .setContents(new StringSelection(""), null);
1879 Toolkit.getDefaultToolkit().getSystemClipboard()
1880 .setContents(ss, Desktop.instance);
1881 } catch (OutOfMemoryError er)
1883 new OOMWarning("copying region", er);
1887 ArrayList<int[]> hiddenColumns = null;
1888 if (viewport.hasHiddenColumns())
1890 hiddenColumns = new ArrayList<int[]>();
1891 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1892 .getSelectionGroup().getEndRes();
1893 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1895 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1897 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1898 region[1] - hiddenOffset });
1903 Desktop.jalviewClipboard = new Object[] { seqs,
1904 viewport.getAlignment().getDataset(), hiddenColumns };
1905 statusBar.setText(MessageManager.formatMessage(
1906 "label.copied_sequences_to_clipboard", new Object[] { Integer
1907 .valueOf(seqs.length).toString() }));
1917 protected void pasteNew_actionPerformed(ActionEvent e)
1929 protected void pasteThis_actionPerformed(ActionEvent e)
1935 * Paste contents of Jalview clipboard
1937 * @param newAlignment
1938 * true to paste to a new alignment, otherwise add to this.
1940 void paste(boolean newAlignment)
1942 boolean externalPaste = true;
1945 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1946 Transferable contents = c.getContents(this);
1948 if (contents == null)
1956 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1957 if (str.length() < 1)
1962 format = new IdentifyFile().identify(str, "Paste");
1964 } catch (OutOfMemoryError er)
1966 new OOMWarning("Out of memory pasting sequences!!", er);
1970 SequenceI[] sequences;
1971 boolean annotationAdded = false;
1972 AlignmentI alignment = null;
1974 if (Desktop.jalviewClipboard != null)
1976 // The clipboard was filled from within Jalview, we must use the
1978 // And dataset from the copied alignment
1979 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1980 // be doubly sure that we create *new* sequence objects.
1981 sequences = new SequenceI[newseq.length];
1982 for (int i = 0; i < newseq.length; i++)
1984 sequences[i] = new Sequence(newseq[i]);
1986 alignment = new Alignment(sequences);
1987 externalPaste = false;
1991 // parse the clipboard as an alignment.
1992 alignment = new FormatAdapter().readFile(str, "Paste", format);
1993 sequences = alignment.getSequencesArray();
1997 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2003 if (Desktop.jalviewClipboard != null)
2005 // dataset is inherited
2006 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2010 // new dataset is constructed
2011 alignment.setDataset(null);
2013 alwidth = alignment.getWidth() + 1;
2017 AlignmentI pastedal = alignment; // preserve pasted alignment object
2018 // Add pasted sequences and dataset into existing alignment.
2019 alignment = viewport.getAlignment();
2020 alwidth = alignment.getWidth() + 1;
2021 // decide if we need to import sequences from an existing dataset
2022 boolean importDs = Desktop.jalviewClipboard != null
2023 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2024 // importDs==true instructs us to copy over new dataset sequences from
2025 // an existing alignment
2026 Vector newDs = (importDs) ? new Vector() : null; // used to create
2027 // minimum dataset set
2029 for (int i = 0; i < sequences.length; i++)
2033 newDs.addElement(null);
2035 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2037 if (importDs && ds != null)
2039 if (!newDs.contains(ds))
2041 newDs.setElementAt(ds, i);
2042 ds = new Sequence(ds);
2043 // update with new dataset sequence
2044 sequences[i].setDatasetSequence(ds);
2048 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2053 // copy and derive new dataset sequence
2054 sequences[i] = sequences[i].deriveSequence();
2055 alignment.getDataset().addSequence(
2056 sequences[i].getDatasetSequence());
2057 // TODO: avoid creation of duplicate dataset sequences with a
2058 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2060 alignment.addSequence(sequences[i]); // merges dataset
2064 newDs.clear(); // tidy up
2066 if (alignment.getAlignmentAnnotation() != null)
2068 for (AlignmentAnnotation alan : alignment
2069 .getAlignmentAnnotation())
2071 if (alan.graphGroup > fgroup)
2073 fgroup = alan.graphGroup;
2077 if (pastedal.getAlignmentAnnotation() != null)
2079 // Add any annotation attached to alignment.
2080 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2081 for (int i = 0; i < alann.length; i++)
2083 annotationAdded = true;
2084 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2086 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2087 if (newann.graphGroup > -1)
2089 if (newGraphGroups.size() <= newann.graphGroup
2090 || newGraphGroups.get(newann.graphGroup) == null)
2092 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2094 newGraphGroups.add(q, null);
2096 newGraphGroups.set(newann.graphGroup, new Integer(
2099 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2103 newann.padAnnotation(alwidth);
2104 alignment.addAnnotation(newann);
2114 addHistoryItem(new EditCommand(
2115 MessageManager.getString("label.add_sequences"),
2116 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2118 // Add any annotations attached to sequences
2119 for (int i = 0; i < sequences.length; i++)
2121 if (sequences[i].getAnnotation() != null)
2123 AlignmentAnnotation newann;
2124 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2126 annotationAdded = true;
2127 newann = sequences[i].getAnnotation()[a];
2128 newann.adjustForAlignment();
2129 newann.padAnnotation(alwidth);
2130 if (newann.graphGroup > -1)
2132 if (newann.graphGroup > -1)
2134 if (newGraphGroups.size() <= newann.graphGroup
2135 || newGraphGroups.get(newann.graphGroup) == null)
2137 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2139 newGraphGroups.add(q, null);
2141 newGraphGroups.set(newann.graphGroup, new Integer(
2144 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2148 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2153 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2160 // propagate alignment changed.
2161 viewport.setEndSeq(alignment.getHeight());
2162 if (annotationAdded)
2164 // Duplicate sequence annotation in all views.
2165 AlignmentI[] alview = this.getViewAlignments();
2166 for (int i = 0; i < sequences.length; i++)
2168 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2173 for (int avnum = 0; avnum < alview.length; avnum++)
2175 if (alview[avnum] != alignment)
2177 // duplicate in a view other than the one with input focus
2178 int avwidth = alview[avnum].getWidth() + 1;
2179 // this relies on sann being preserved after we
2180 // modify the sequence's annotation array for each duplication
2181 for (int a = 0; a < sann.length; a++)
2183 AlignmentAnnotation newann = new AlignmentAnnotation(
2185 sequences[i].addAlignmentAnnotation(newann);
2186 newann.padAnnotation(avwidth);
2187 alview[avnum].addAnnotation(newann); // annotation was
2188 // duplicated earlier
2189 // TODO JAL-1145 graphGroups are not updated for sequence
2190 // annotation added to several views. This may cause
2192 alview[avnum].setAnnotationIndex(newann, a);
2197 buildSortByAnnotationScoresMenu();
2199 viewport.firePropertyChange("alignment", null,
2200 alignment.getSequences());
2201 if (alignPanels != null)
2203 for (AlignmentPanel ap : alignPanels)
2205 ap.validateAnnotationDimensions(false);
2210 alignPanel.validateAnnotationDimensions(false);
2216 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2218 String newtitle = new String("Copied sequences");
2220 if (Desktop.jalviewClipboard != null
2221 && Desktop.jalviewClipboard[2] != null)
2223 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2224 for (int[] region : hc)
2226 af.viewport.hideColumns(region[0], region[1]);
2230 // >>>This is a fix for the moment, until a better solution is
2232 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2234 alignPanel.getSeqPanel().seqCanvas
2235 .getFeatureRenderer());
2237 // TODO: maintain provenance of an alignment, rather than just make the
2238 // title a concatenation of operations.
2241 if (title.startsWith("Copied sequences"))
2247 newtitle = newtitle.concat("- from " + title);
2252 newtitle = new String("Pasted sequences");
2255 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2260 } catch (Exception ex)
2262 ex.printStackTrace();
2263 System.out.println("Exception whilst pasting: " + ex);
2264 // could be anything being pasted in here
2270 protected void expand_newalign(ActionEvent e)
2274 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2275 .getAlignment(), -1);
2276 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2278 String newtitle = new String("Flanking alignment");
2280 if (Desktop.jalviewClipboard != null
2281 && Desktop.jalviewClipboard[2] != null)
2283 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2284 for (int region[] : hc)
2286 af.viewport.hideColumns(region[0], region[1]);
2290 // >>>This is a fix for the moment, until a better solution is
2292 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2294 alignPanel.getSeqPanel().seqCanvas
2295 .getFeatureRenderer());
2297 // TODO: maintain provenance of an alignment, rather than just make the
2298 // title a concatenation of operations.
2300 if (title.startsWith("Copied sequences"))
2306 newtitle = newtitle.concat("- from " + title);
2310 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2312 } catch (Exception ex)
2314 ex.printStackTrace();
2315 System.out.println("Exception whilst pasting: " + ex);
2316 // could be anything being pasted in here
2317 } catch (OutOfMemoryError oom)
2319 new OOMWarning("Viewing flanking region of alignment", oom);
2330 protected void cut_actionPerformed(ActionEvent e)
2332 copy_actionPerformed(null);
2333 delete_actionPerformed(null);
2343 protected void delete_actionPerformed(ActionEvent evt)
2346 SequenceGroup sg = viewport.getSelectionGroup();
2353 * If the cut affects all sequences, warn, remove highlighted columns
2355 if (sg.getSize() == viewport.getAlignment().getHeight())
2357 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2358 .getAlignment().getWidth()) ? true : false;
2359 if (isEntireAlignWidth)
2361 int confirm = JOptionPane.showConfirmDialog(this,
2362 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2363 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2364 JOptionPane.OK_CANCEL_OPTION);
2366 if (confirm == JOptionPane.CANCEL_OPTION
2367 || confirm == JOptionPane.CLOSED_OPTION)
2372 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2373 sg.getEndRes() + 1);
2375 SequenceI[] cut = sg.getSequences()
2376 .toArray(new SequenceI[sg.getSize()]);
2378 addHistoryItem(new EditCommand(
2379 MessageManager.getString("label.cut_sequences"), Action.CUT,
2380 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2381 viewport.getAlignment()));
2383 viewport.setSelectionGroup(null);
2384 viewport.sendSelection();
2385 viewport.getAlignment().deleteGroup(sg);
2387 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2389 if (viewport.getAlignment().getHeight() < 1)
2393 this.setClosed(true);
2394 } catch (Exception ex)
2407 protected void deleteGroups_actionPerformed(ActionEvent e)
2409 if (avc.deleteGroups())
2411 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2412 alignPanel.updateAnnotation();
2413 alignPanel.paintAlignment(true);
2424 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2426 SequenceGroup sg = new SequenceGroup();
2428 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2430 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2433 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2434 viewport.setSelectionGroup(sg);
2435 viewport.sendSelection();
2436 alignPanel.paintAlignment(true);
2437 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2447 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2449 if (viewport.cursorMode)
2451 alignPanel.getSeqPanel().keyboardNo1 = null;
2452 alignPanel.getSeqPanel().keyboardNo2 = null;
2454 viewport.setSelectionGroup(null);
2455 viewport.getColumnSelection().clear();
2456 viewport.setSelectionGroup(null);
2457 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2458 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2459 alignPanel.paintAlignment(true);
2460 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2461 viewport.sendSelection();
2471 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2473 SequenceGroup sg = viewport.getSelectionGroup();
2477 selectAllSequenceMenuItem_actionPerformed(null);
2482 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2484 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2487 alignPanel.paintAlignment(true);
2488 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2489 viewport.sendSelection();
2493 public void invertColSel_actionPerformed(ActionEvent e)
2495 viewport.invertColumnSelection();
2496 alignPanel.paintAlignment(true);
2497 viewport.sendSelection();
2507 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2509 trimAlignment(true);
2519 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2521 trimAlignment(false);
2524 void trimAlignment(boolean trimLeft)
2526 ColumnSelection colSel = viewport.getColumnSelection();
2529 if (!colSel.isEmpty())
2533 column = colSel.getMin();
2537 column = colSel.getMax();
2541 if (viewport.getSelectionGroup() != null)
2543 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2544 viewport.getHiddenRepSequences());
2548 seqs = viewport.getAlignment().getSequencesArray();
2551 TrimRegionCommand trimRegion;
2554 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2555 column, viewport.getAlignment());
2556 viewport.setStartRes(0);
2560 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2561 column, viewport.getAlignment());
2564 statusBar.setText(MessageManager.formatMessage(
2565 "label.removed_columns",
2566 new String[] { Integer.valueOf(trimRegion.getSize())
2569 addHistoryItem(trimRegion);
2571 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2573 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2574 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2576 viewport.getAlignment().deleteGroup(sg);
2580 viewport.firePropertyChange("alignment", null, viewport
2581 .getAlignment().getSequences());
2592 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2594 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2597 if (viewport.getSelectionGroup() != null)
2599 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2600 viewport.getHiddenRepSequences());
2601 start = viewport.getSelectionGroup().getStartRes();
2602 end = viewport.getSelectionGroup().getEndRes();
2606 seqs = viewport.getAlignment().getSequencesArray();
2609 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2610 "Remove Gapped Columns", seqs, start, end,
2611 viewport.getAlignment());
2613 addHistoryItem(removeGapCols);
2615 statusBar.setText(MessageManager.formatMessage(
2616 "label.removed_empty_columns",
2617 new Object[] { Integer.valueOf(removeGapCols.getSize())
2620 // This is to maintain viewport position on first residue
2621 // of first sequence
2622 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2623 int startRes = seq.findPosition(viewport.startRes);
2624 // ShiftList shifts;
2625 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2626 // edit.alColumnChanges=shifts.getInverse();
2627 // if (viewport.hasHiddenColumns)
2628 // viewport.getColumnSelection().compensateForEdits(shifts);
2629 viewport.setStartRes(seq.findIndex(startRes) - 1);
2630 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2642 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2644 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2647 if (viewport.getSelectionGroup() != null)
2649 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2650 viewport.getHiddenRepSequences());
2651 start = viewport.getSelectionGroup().getStartRes();
2652 end = viewport.getSelectionGroup().getEndRes();
2656 seqs = viewport.getAlignment().getSequencesArray();
2659 // This is to maintain viewport position on first residue
2660 // of first sequence
2661 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2662 int startRes = seq.findPosition(viewport.startRes);
2664 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2665 viewport.getAlignment()));
2667 viewport.setStartRes(seq.findIndex(startRes) - 1);
2669 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2681 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2683 viewport.setPadGaps(padGapsMenuitem.isSelected());
2684 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2695 public void findMenuItem_actionPerformed(ActionEvent e)
2701 * Create a new view of the current alignment.
2704 public void newView_actionPerformed(ActionEvent e)
2706 newView(null, true);
2710 * Creates and shows a new view of the current alignment.
2713 * title of newly created view; if null, one will be generated
2714 * @param copyAnnotation
2715 * if true then duplicate all annnotation, groups and settings
2716 * @return new alignment panel, already displayed.
2718 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2721 * Create a new AlignmentPanel (with its own, new Viewport)
2723 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2725 if (!copyAnnotation)
2728 * remove all groups and annotation except for the automatic stuff
2730 newap.av.getAlignment().deleteAllGroups();
2731 newap.av.getAlignment().deleteAllAnnotations(false);
2734 newap.av.setGatherViewsHere(false);
2736 if (viewport.viewName == null)
2738 viewport.viewName = MessageManager
2739 .getString("label.view_name_original");
2743 * Views share the same edits undo and redo stacks
2745 newap.av.setHistoryList(viewport.getHistoryList());
2746 newap.av.setRedoList(viewport.getRedoList());
2749 * Views share the same mappings; need to deregister any new mappings
2750 * created by copyAlignPanel, and register the new reference to the shared
2753 newap.av.replaceMappings(viewport.getAlignment());
2755 newap.av.viewName = getNewViewName(viewTitle);
2757 addAlignmentPanel(newap, true);
2758 newap.alignmentChanged();
2760 if (alignPanels.size() == 2)
2762 viewport.setGatherViewsHere(true);
2764 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2769 * Make a new name for the view, ensuring it is unique within the current
2770 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2771 * these now use viewId. Unique view names are still desirable for usability.)
2776 protected String getNewViewName(String viewTitle)
2778 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2779 boolean addFirstIndex = false;
2780 if (viewTitle == null || viewTitle.trim().length() == 0)
2782 viewTitle = MessageManager.getString("action.view");
2783 addFirstIndex = true;
2787 index = 1;// we count from 1 if given a specific name
2789 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2791 List<Component> comps = PaintRefresher.components.get(viewport
2792 .getSequenceSetId());
2794 List<String> existingNames = getExistingViewNames(comps);
2796 while (existingNames.contains(newViewName))
2798 newViewName = viewTitle + " " + (++index);
2804 * Returns a list of distinct view names found in the given list of
2805 * components. View names are held on the viewport of an AlignmentPanel.
2810 protected List<String> getExistingViewNames(List<Component> comps)
2812 List<String> existingNames = new ArrayList<String>();
2813 for (Component comp : comps)
2815 if (comp instanceof AlignmentPanel)
2817 AlignmentPanel ap = (AlignmentPanel) comp;
2818 if (!existingNames.contains(ap.av.viewName))
2820 existingNames.add(ap.av.viewName);
2824 return existingNames;
2828 * Explode tabbed views into separate windows.
2831 public void expandViews_actionPerformed(ActionEvent e)
2833 Desktop.instance.explodeViews(this);
2837 * Gather views in separate windows back into a tabbed presentation.
2840 public void gatherViews_actionPerformed(ActionEvent e)
2842 Desktop.instance.gatherViews(this);
2852 public void font_actionPerformed(ActionEvent e)
2854 new FontChooser(alignPanel);
2864 protected void seqLimit_actionPerformed(ActionEvent e)
2866 viewport.setShowJVSuffix(seqLimits.isSelected());
2868 alignPanel.getIdPanel().getIdCanvas()
2869 .setPreferredSize(alignPanel.calculateIdWidth());
2870 alignPanel.paintAlignment(true);
2874 public void idRightAlign_actionPerformed(ActionEvent e)
2876 viewport.setRightAlignIds(idRightAlign.isSelected());
2877 alignPanel.paintAlignment(true);
2881 public void centreColumnLabels_actionPerformed(ActionEvent e)
2883 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2884 alignPanel.paintAlignment(true);
2890 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2893 protected void followHighlight_actionPerformed()
2896 * Set the 'follow' flag on the Viewport (and scroll to position if now
2899 final boolean state = this.followHighlightMenuItem.getState();
2900 viewport.setFollowHighlight(state);
2903 alignPanel.scrollToPosition(
2904 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2915 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2917 viewport.setColourText(colourTextMenuItem.isSelected());
2918 alignPanel.paintAlignment(true);
2928 public void wrapMenuItem_actionPerformed(ActionEvent e)
2930 scaleAbove.setVisible(wrapMenuItem.isSelected());
2931 scaleLeft.setVisible(wrapMenuItem.isSelected());
2932 scaleRight.setVisible(wrapMenuItem.isSelected());
2933 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2934 alignPanel.updateLayout();
2938 public void showAllSeqs_actionPerformed(ActionEvent e)
2940 viewport.showAllHiddenSeqs();
2944 public void showAllColumns_actionPerformed(ActionEvent e)
2946 viewport.showAllHiddenColumns();
2948 viewport.sendSelection();
2952 public void hideSelSequences_actionPerformed(ActionEvent e)
2954 viewport.hideAllSelectedSeqs();
2955 // alignPanel.paintAlignment(true);
2959 * called by key handler and the hide all/show all menu items
2964 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2967 boolean hide = false;
2968 SequenceGroup sg = viewport.getSelectionGroup();
2969 if (!toggleSeqs && !toggleCols)
2971 // Hide everything by the current selection - this is a hack - we do the
2972 // invert and then hide
2973 // first check that there will be visible columns after the invert.
2974 if ((viewport.getColumnSelection() != null
2975 && viewport.getColumnSelection().getSelected() != null && viewport
2976 .getColumnSelection().getSelected().size() > 0)
2977 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2980 // now invert the sequence set, if required - empty selection implies
2981 // that no hiding is required.
2984 invertSequenceMenuItem_actionPerformed(null);
2985 sg = viewport.getSelectionGroup();
2989 viewport.expandColSelection(sg, true);
2990 // finally invert the column selection and get the new sequence
2992 invertColSel_actionPerformed(null);
2999 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3001 hideSelSequences_actionPerformed(null);
3004 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3007 showAllSeqs_actionPerformed(null);
3013 if (viewport.getColumnSelection().getSelected().size() > 0)
3015 hideSelColumns_actionPerformed(null);
3018 viewport.setSelectionGroup(sg);
3023 showAllColumns_actionPerformed(null);
3032 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3033 * event.ActionEvent)
3036 public void hideAllButSelection_actionPerformed(ActionEvent e)
3038 toggleHiddenRegions(false, false);
3039 viewport.sendSelection();
3046 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3050 public void hideAllSelection_actionPerformed(ActionEvent e)
3052 SequenceGroup sg = viewport.getSelectionGroup();
3053 viewport.expandColSelection(sg, false);
3054 viewport.hideAllSelectedSeqs();
3055 viewport.hideSelectedColumns();
3056 alignPanel.paintAlignment(true);
3057 viewport.sendSelection();
3064 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3068 public void showAllhidden_actionPerformed(ActionEvent e)
3070 viewport.showAllHiddenColumns();
3071 viewport.showAllHiddenSeqs();
3072 alignPanel.paintAlignment(true);
3073 viewport.sendSelection();
3077 public void hideSelColumns_actionPerformed(ActionEvent e)
3079 viewport.hideSelectedColumns();
3080 alignPanel.paintAlignment(true);
3081 viewport.sendSelection();
3085 public void hiddenMarkers_actionPerformed(ActionEvent e)
3087 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3098 protected void scaleAbove_actionPerformed(ActionEvent e)
3100 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3101 alignPanel.paintAlignment(true);
3111 protected void scaleLeft_actionPerformed(ActionEvent e)
3113 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3114 alignPanel.paintAlignment(true);
3124 protected void scaleRight_actionPerformed(ActionEvent e)
3126 viewport.setScaleRightWrapped(scaleRight.isSelected());
3127 alignPanel.paintAlignment(true);
3137 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3139 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3140 alignPanel.paintAlignment(true);
3150 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3152 viewport.setShowText(viewTextMenuItem.isSelected());
3153 alignPanel.paintAlignment(true);
3163 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3165 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3166 alignPanel.paintAlignment(true);
3169 public FeatureSettings featureSettings;
3172 public FeatureSettingsControllerI getFeatureSettingsUI()
3174 return featureSettings;
3178 public void featureSettings_actionPerformed(ActionEvent e)
3180 if (featureSettings != null)
3182 featureSettings.close();
3183 featureSettings = null;
3185 if (!showSeqFeatures.isSelected())
3187 // make sure features are actually displayed
3188 showSeqFeatures.setSelected(true);
3189 showSeqFeatures_actionPerformed(null);
3191 featureSettings = new FeatureSettings(this);
3195 * Set or clear 'Show Sequence Features'
3201 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3203 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3204 alignPanel.paintAlignment(true);
3205 if (alignPanel.getOverviewPanel() != null)
3207 alignPanel.getOverviewPanel().updateOverviewImage();
3212 * Set or clear 'Show Sequence Features'
3218 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3220 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3222 if (viewport.isShowSequenceFeaturesHeight())
3224 // ensure we're actually displaying features
3225 viewport.setShowSequenceFeatures(true);
3226 showSeqFeatures.setSelected(true);
3228 alignPanel.paintAlignment(true);
3229 if (alignPanel.getOverviewPanel() != null)
3231 alignPanel.getOverviewPanel().updateOverviewImage();
3236 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3237 * the annotations panel as a whole.
3239 * The options to show/hide all annotations should be enabled when the panel
3240 * is shown, and disabled when the panel is hidden.
3245 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3247 final boolean setVisible = annotationPanelMenuItem.isSelected();
3248 viewport.setShowAnnotation(setVisible);
3249 this.showAllSeqAnnotations.setEnabled(setVisible);
3250 this.hideAllSeqAnnotations.setEnabled(setVisible);
3251 this.showAllAlAnnotations.setEnabled(setVisible);
3252 this.hideAllAlAnnotations.setEnabled(setVisible);
3253 alignPanel.updateLayout();
3257 public void alignmentProperties()
3259 JEditorPane editPane = new JEditorPane("text/html", "");
3260 editPane.setEditable(false);
3261 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3263 editPane.setText(MessageManager.formatMessage("label.html_content",
3264 new Object[] { contents.toString() }));
3265 JInternalFrame frame = new JInternalFrame();
3266 frame.getContentPane().add(new JScrollPane(editPane));
3268 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3269 "label.alignment_properties", new Object[] { getTitle() }),
3280 public void overviewMenuItem_actionPerformed(ActionEvent e)
3282 if (alignPanel.overviewPanel != null)
3287 JInternalFrame frame = new JInternalFrame();
3288 OverviewPanel overview = new OverviewPanel(alignPanel);
3289 frame.setContentPane(overview);
3290 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3291 "label.overview_params", new Object[] { this.getTitle() }),
3292 frame.getWidth(), frame.getHeight());
3294 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3295 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3298 public void internalFrameClosed(
3299 javax.swing.event.InternalFrameEvent evt)
3301 alignPanel.setOverviewPanel(null);
3305 alignPanel.setOverviewPanel(overview);
3309 public void textColour_actionPerformed(ActionEvent e)
3311 new TextColourChooser().chooseColour(alignPanel, null);
3321 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3333 public void clustalColour_actionPerformed(ActionEvent e)
3335 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3336 viewport.getHiddenRepSequences()));
3346 public void zappoColour_actionPerformed(ActionEvent e)
3348 changeColour(new ZappoColourScheme());
3358 public void taylorColour_actionPerformed(ActionEvent e)
3360 changeColour(new TaylorColourScheme());
3370 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3372 changeColour(new HydrophobicColourScheme());
3382 public void helixColour_actionPerformed(ActionEvent e)
3384 changeColour(new HelixColourScheme());
3394 public void strandColour_actionPerformed(ActionEvent e)
3396 changeColour(new StrandColourScheme());
3406 public void turnColour_actionPerformed(ActionEvent e)
3408 changeColour(new TurnColourScheme());
3418 public void buriedColour_actionPerformed(ActionEvent e)
3420 changeColour(new BuriedColourScheme());
3430 public void nucleotideColour_actionPerformed(ActionEvent e)
3432 changeColour(new NucleotideColourScheme());
3436 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3438 changeColour(new PurinePyrimidineColourScheme());
3442 * public void covariationColour_actionPerformed(ActionEvent e) {
3444 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3448 public void annotationColour_actionPerformed(ActionEvent e)
3450 new AnnotationColourChooser(viewport, alignPanel);
3454 public void annotationColumn_actionPerformed(ActionEvent e)
3456 new AnnotationColumnChooser(viewport, alignPanel);
3460 public void rnahelicesColour_actionPerformed(ActionEvent e)
3462 new RNAHelicesColourChooser(viewport, alignPanel);
3472 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3474 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3484 public void changeColour(ColourSchemeI cs)
3486 // TODO: pull up to controller method
3490 // Make sure viewport is up to date w.r.t. any sliders
3491 if (viewport.getAbovePIDThreshold())
3493 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3495 viewport.setThreshold(threshold);
3498 if (viewport.getConservationSelected())
3500 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3503 if (cs instanceof TCoffeeColourScheme)
3505 tcoffeeColour.setEnabled(true);
3506 tcoffeeColour.setSelected(true);
3510 viewport.setGlobalColourScheme(cs);
3512 alignPanel.paintAlignment(true);
3522 protected void modifyPID_actionPerformed(ActionEvent e)
3524 if (viewport.getAbovePIDThreshold()
3525 && viewport.getGlobalColourScheme() != null)
3527 SliderPanel.setPIDSliderSource(alignPanel,
3528 viewport.getGlobalColourScheme(), "Background");
3529 SliderPanel.showPIDSlider();
3540 protected void modifyConservation_actionPerformed(ActionEvent e)
3542 if (viewport.getConservationSelected()
3543 && viewport.getGlobalColourScheme() != null)
3545 SliderPanel.setConservationSlider(alignPanel,
3546 viewport.getGlobalColourScheme(), "Background");
3547 SliderPanel.showConservationSlider();
3558 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3560 viewport.setConservationSelected(conservationMenuItem.isSelected());
3562 viewport.setAbovePIDThreshold(false);
3563 abovePIDThreshold.setSelected(false);
3565 changeColour(viewport.getGlobalColourScheme());
3567 modifyConservation_actionPerformed(null);
3577 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3579 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3581 conservationMenuItem.setSelected(false);
3582 viewport.setConservationSelected(false);
3584 changeColour(viewport.getGlobalColourScheme());
3586 modifyPID_actionPerformed(null);
3596 public void userDefinedColour_actionPerformed(ActionEvent e)
3598 if (e.getActionCommand().equals(
3599 MessageManager.getString("action.user_defined")))
3601 new UserDefinedColours(alignPanel, null);
3605 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3606 .getUserColourSchemes().get(e.getActionCommand());
3612 public void updateUserColourMenu()
3615 Component[] menuItems = colourMenu.getMenuComponents();
3616 int iSize = menuItems.length;
3617 for (int i = 0; i < iSize; i++)
3619 if (menuItems[i].getName() != null
3620 && menuItems[i].getName().equals("USER_DEFINED"))
3622 colourMenu.remove(menuItems[i]);
3626 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3628 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3629 .getUserColourSchemes().keys();
3631 while (userColours.hasMoreElements())
3633 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3634 userColours.nextElement().toString());
3635 radioItem.setName("USER_DEFINED");
3636 radioItem.addMouseListener(new MouseAdapter()
3639 public void mousePressed(MouseEvent evt)
3641 if (evt.isPopupTrigger())
3643 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3645 int option = JOptionPane.showInternalConfirmDialog(
3646 jalview.gui.Desktop.desktop,
3648 .getString("label.remove_from_default_list"),
3650 .getString("label.remove_user_defined_colour"),
3651 JOptionPane.YES_NO_OPTION);
3652 if (option == JOptionPane.YES_OPTION)
3654 jalview.gui.UserDefinedColours
3655 .removeColourFromDefaults(radioItem.getText());
3656 colourMenu.remove(radioItem);
3660 radioItem.addActionListener(new ActionListener()
3663 public void actionPerformed(ActionEvent evt)
3665 userDefinedColour_actionPerformed(evt);
3672 radioItem.addActionListener(new ActionListener()
3675 public void actionPerformed(ActionEvent evt)
3677 userDefinedColour_actionPerformed(evt);
3681 colourMenu.insert(radioItem, 15);
3682 colours.add(radioItem);
3694 public void PIDColour_actionPerformed(ActionEvent e)
3696 changeColour(new PIDColourScheme());
3706 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3708 changeColour(new Blosum62ColourScheme());
3718 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3720 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3721 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3722 .getAlignment().getSequenceAt(0), null);
3723 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3724 viewport.getAlignment()));
3725 alignPanel.paintAlignment(true);
3735 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3737 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3738 AlignmentSorter.sortByID(viewport.getAlignment());
3739 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3740 viewport.getAlignment()));
3741 alignPanel.paintAlignment(true);
3751 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3753 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3754 AlignmentSorter.sortByLength(viewport.getAlignment());
3755 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3756 viewport.getAlignment()));
3757 alignPanel.paintAlignment(true);
3767 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3769 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3770 AlignmentSorter.sortByGroup(viewport.getAlignment());
3771 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3772 viewport.getAlignment()));
3774 alignPanel.paintAlignment(true);
3784 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3786 new RedundancyPanel(alignPanel, this);
3796 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3798 if ((viewport.getSelectionGroup() == null)
3799 || (viewport.getSelectionGroup().getSize() < 2))
3801 JOptionPane.showInternalMessageDialog(this, MessageManager
3802 .getString("label.you_must_select_least_two_sequences"),
3803 MessageManager.getString("label.invalid_selection"),
3804 JOptionPane.WARNING_MESSAGE);
3808 JInternalFrame frame = new JInternalFrame();
3809 frame.setContentPane(new PairwiseAlignPanel(viewport));
3810 Desktop.addInternalFrame(frame,
3811 MessageManager.getString("action.pairwise_alignment"), 600,
3823 public void PCAMenuItem_actionPerformed(ActionEvent e)
3825 if (((viewport.getSelectionGroup() != null)
3826 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3827 .getSelectionGroup().getSize() > 0))
3828 || (viewport.getAlignment().getHeight() < 4))
3831 .showInternalMessageDialog(
3834 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3836 .getString("label.sequence_selection_insufficient"),
3837 JOptionPane.WARNING_MESSAGE);
3842 new PCAPanel(alignPanel);
3846 public void autoCalculate_actionPerformed(ActionEvent e)
3848 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3849 if (viewport.autoCalculateConsensus)
3851 viewport.firePropertyChange("alignment", null, viewport
3852 .getAlignment().getSequences());
3857 public void sortByTreeOption_actionPerformed(ActionEvent e)
3859 viewport.sortByTree = sortByTree.isSelected();
3863 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3865 viewport.followSelection = listenToViewSelections.isSelected();
3875 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3877 newTreePanel("AV", "PID", "Average distance tree using PID");
3887 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3889 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3899 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3901 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3911 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3913 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3926 void newTreePanel(String type, String pwType, String title)
3930 if (viewport.getSelectionGroup() != null
3931 && viewport.getSelectionGroup().getSize() > 0)
3933 if (viewport.getSelectionGroup().getSize() < 3)
3939 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3941 .getString("label.not_enough_sequences"),
3942 JOptionPane.WARNING_MESSAGE);
3946 SequenceGroup sg = viewport.getSelectionGroup();
3948 /* Decide if the selection is a column region */
3949 for (SequenceI _s : sg.getSequences())
3951 if (_s.getLength() < sg.getEndRes())
3957 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3959 .getString("label.sequences_selection_not_aligned"),
3960 JOptionPane.WARNING_MESSAGE);
3966 title = title + " on region";
3967 tp = new TreePanel(alignPanel, type, pwType);
3971 // are the visible sequences aligned?
3972 if (!viewport.getAlignment().isAligned(false))
3978 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3980 .getString("label.sequences_not_aligned"),
3981 JOptionPane.WARNING_MESSAGE);
3986 if (viewport.getAlignment().getHeight() < 2)
3991 tp = new TreePanel(alignPanel, type, pwType);
3996 if (viewport.viewName != null)
3998 title += viewport.viewName + " of ";
4001 title += this.title;
4003 Desktop.addInternalFrame(tp, title, 600, 500);
4014 public void addSortByOrderMenuItem(String title,
4015 final AlignmentOrder order)
4017 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4018 "action.by_title_param", new Object[] { title }));
4020 item.addActionListener(new java.awt.event.ActionListener()
4023 public void actionPerformed(ActionEvent e)
4025 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4027 // TODO: JBPNote - have to map order entries to curent SequenceI
4029 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4031 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4034 alignPanel.paintAlignment(true);
4040 * Add a new sort by annotation score menu item
4043 * the menu to add the option to
4045 * the label used to retrieve scores for each sequence on the
4048 public void addSortByAnnotScoreMenuItem(JMenu sort,
4049 final String scoreLabel)
4051 final JMenuItem item = new JMenuItem(scoreLabel);
4053 item.addActionListener(new java.awt.event.ActionListener()
4056 public void actionPerformed(ActionEvent e)
4058 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4059 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4060 viewport.getAlignment());// ,viewport.getSelectionGroup());
4061 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4062 viewport.getAlignment()));
4063 alignPanel.paintAlignment(true);
4069 * last hash for alignment's annotation array - used to minimise cost of
4072 protected int _annotationScoreVectorHash;
4075 * search the alignment and rebuild the sort by annotation score submenu the
4076 * last alignment annotation vector hash is stored to minimize cost of
4077 * rebuilding in subsequence calls.
4081 public void buildSortByAnnotationScoresMenu()
4083 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4088 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4090 sortByAnnotScore.removeAll();
4091 // almost certainly a quicker way to do this - but we keep it simple
4092 Hashtable scoreSorts = new Hashtable();
4093 AlignmentAnnotation aann[];
4094 for (SequenceI sqa : viewport.getAlignment().getSequences())
4096 aann = sqa.getAnnotation();
4097 for (int i = 0; aann != null && i < aann.length; i++)
4099 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4101 scoreSorts.put(aann[i].label, aann[i].label);
4105 Enumeration labels = scoreSorts.keys();
4106 while (labels.hasMoreElements())
4108 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4109 (String) labels.nextElement());
4111 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4114 _annotationScoreVectorHash = viewport.getAlignment()
4115 .getAlignmentAnnotation().hashCode();
4120 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4121 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4122 * call. Listeners are added to remove the menu item when the treePanel is
4123 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4127 * Displayed tree window.
4129 * SortBy menu item title.
4132 public void buildTreeMenu()
4134 calculateTree.removeAll();
4135 // build the calculate menu
4137 for (final String type : new String[] { "NJ", "AV" })
4139 String treecalcnm = MessageManager.getString("label.tree_calc_"
4140 + type.toLowerCase());
4141 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4143 JMenuItem tm = new JMenuItem();
4144 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4145 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4146 || sm.isProtein() == !viewport.getAlignment()
4149 String smn = MessageManager.getStringOrReturn(
4150 "label.score_model_", sm.getName());
4151 final String title = MessageManager.formatMessage(
4152 "label.treecalc_title", treecalcnm, smn);
4153 tm.setText(title);//
4154 tm.addActionListener(new java.awt.event.ActionListener()
4157 public void actionPerformed(ActionEvent e)
4159 newTreePanel(type, pwtype, title);
4162 calculateTree.add(tm);
4167 sortByTreeMenu.removeAll();
4169 List<Component> comps = PaintRefresher.components.get(viewport
4170 .getSequenceSetId());
4171 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4172 for (Component comp : comps)
4174 if (comp instanceof TreePanel)
4176 treePanels.add((TreePanel) comp);
4180 if (treePanels.size() < 1)
4182 sortByTreeMenu.setVisible(false);
4186 sortByTreeMenu.setVisible(true);
4188 for (final TreePanel tp : treePanels)
4190 final JMenuItem item = new JMenuItem(tp.getTitle());
4191 item.addActionListener(new java.awt.event.ActionListener()
4194 public void actionPerformed(ActionEvent e)
4196 tp.sortByTree_actionPerformed();
4197 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4202 sortByTreeMenu.add(item);
4206 public boolean sortBy(AlignmentOrder alorder, String undoname)
4208 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4209 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4210 if (undoname != null)
4212 addHistoryItem(new OrderCommand(undoname, oldOrder,
4213 viewport.getAlignment()));
4215 alignPanel.paintAlignment(true);
4220 * Work out whether the whole set of sequences or just the selected set will
4221 * be submitted for multiple alignment.
4224 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4226 // Now, check we have enough sequences
4227 AlignmentView msa = null;
4229 if ((viewport.getSelectionGroup() != null)
4230 && (viewport.getSelectionGroup().getSize() > 1))
4232 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4233 // some common interface!
4235 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4236 * SequenceI[sz = seqs.getSize(false)];
4238 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4239 * seqs.getSequenceAt(i); }
4241 msa = viewport.getAlignmentView(true);
4243 else if (viewport.getSelectionGroup() != null
4244 && viewport.getSelectionGroup().getSize() == 1)
4246 int option = JOptionPane.showConfirmDialog(this,
4247 MessageManager.getString("warn.oneseq_msainput_selection"),
4248 MessageManager.getString("label.invalid_selection"),
4249 JOptionPane.OK_CANCEL_OPTION);
4250 if (option == JOptionPane.OK_OPTION)
4252 msa = viewport.getAlignmentView(false);
4257 msa = viewport.getAlignmentView(false);
4263 * Decides what is submitted to a secondary structure prediction service: the
4264 * first sequence in the alignment, or in the current selection, or, if the
4265 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4266 * region or the whole alignment. (where the first sequence in the set is the
4267 * one that the prediction will be for).
4269 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4271 AlignmentView seqs = null;
4273 if ((viewport.getSelectionGroup() != null)
4274 && (viewport.getSelectionGroup().getSize() > 0))
4276 seqs = viewport.getAlignmentView(true);
4280 seqs = viewport.getAlignmentView(false);
4282 // limit sequences - JBPNote in future - could spawn multiple prediction
4284 // TODO: viewport.getAlignment().isAligned is a global state - the local
4285 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4286 if (!viewport.getAlignment().isAligned(false))
4288 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4289 // TODO: if seqs.getSequences().length>1 then should really have warned
4303 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4305 // Pick the tree file
4306 JalviewFileChooser chooser = new JalviewFileChooser(
4307 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4308 chooser.setFileView(new JalviewFileView());
4309 chooser.setDialogTitle(MessageManager
4310 .getString("label.select_newick_like_tree_file"));
4311 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4313 int value = chooser.showOpenDialog(null);
4315 if (value == JalviewFileChooser.APPROVE_OPTION)
4317 String choice = chooser.getSelectedFile().getPath();
4318 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4319 jalview.io.NewickFile fin = null;
4322 fin = new jalview.io.NewickFile(choice, "File");
4323 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4324 } catch (Exception ex)
4331 .getString("label.problem_reading_tree_file"),
4332 JOptionPane.WARNING_MESSAGE);
4333 ex.printStackTrace();
4335 if (fin != null && fin.hasWarningMessage())
4337 JOptionPane.showMessageDialog(Desktop.desktop, fin
4338 .getWarningMessage(), MessageManager
4339 .getString("label.possible_problem_with_tree_file"),
4340 JOptionPane.WARNING_MESSAGE);
4346 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4348 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4351 public TreePanel ShowNewickTree(NewickFile nf, String title)
4353 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4356 public TreePanel ShowNewickTree(NewickFile nf, String title,
4357 AlignmentView input)
4359 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4362 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4363 int h, int x, int y)
4365 return ShowNewickTree(nf, title, null, w, h, x, y);
4369 * Add a treeviewer for the tree extracted from a newick file object to the
4370 * current alignment view
4377 * Associated alignment input data (or null)
4386 * @return TreePanel handle
4388 public TreePanel ShowNewickTree(NewickFile nf, String title,
4389 AlignmentView input, int w, int h, int x, int y)
4391 TreePanel tp = null;
4397 if (nf.getTree() != null)
4399 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4405 tp.setLocation(x, y);
4408 Desktop.addInternalFrame(tp, title, w, h);
4410 } catch (Exception ex)
4412 ex.printStackTrace();
4418 private boolean buildingMenu = false;
4421 * Generates menu items and listener event actions for web service clients
4424 public void BuildWebServiceMenu()
4426 while (buildingMenu)
4430 System.err.println("Waiting for building menu to finish.");
4432 } catch (Exception e)
4436 final AlignFrame me = this;
4437 buildingMenu = true;
4438 new Thread(new Runnable()
4443 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4446 // System.err.println("Building ws menu again "
4447 // + Thread.currentThread());
4448 // TODO: add support for context dependent disabling of services based
4450 // alignment and current selection
4451 // TODO: add additional serviceHandle parameter to specify abstract
4453 // class independently of AbstractName
4454 // TODO: add in rediscovery GUI function to restart discoverer
4455 // TODO: group services by location as well as function and/or
4457 // object broker mechanism.
4458 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4459 final IProgressIndicator af = me;
4460 final JMenu msawsmenu = new JMenu("Alignment");
4461 final JMenu secstrmenu = new JMenu(
4462 "Secondary Structure Prediction");
4463 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4464 final JMenu analymenu = new JMenu("Analysis");
4465 final JMenu dismenu = new JMenu("Protein Disorder");
4466 // final JMenu msawsmenu = new
4467 // JMenu(MessageManager.getString("label.alignment"));
4468 // final JMenu secstrmenu = new
4469 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4470 // final JMenu seqsrchmenu = new
4471 // JMenu(MessageManager.getString("label.sequence_database_search"));
4472 // final JMenu analymenu = new
4473 // JMenu(MessageManager.getString("label.analysis"));
4474 // final JMenu dismenu = new
4475 // JMenu(MessageManager.getString("label.protein_disorder"));
4476 // JAL-940 - only show secondary structure prediction services from
4477 // the legacy server
4478 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4480 Discoverer.services != null && (Discoverer.services.size() > 0))
4482 // TODO: refactor to allow list of AbstractName/Handler bindings to
4484 // stored or retrieved from elsewhere
4485 // No MSAWS used any more:
4486 // Vector msaws = null; // (Vector)
4487 // Discoverer.services.get("MsaWS");
4488 Vector secstrpr = (Vector) Discoverer.services
4490 if (secstrpr != null)
4492 // Add any secondary structure prediction services
4493 for (int i = 0, j = secstrpr.size(); i < j; i++)
4495 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4497 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4498 .getServiceClient(sh);
4499 int p = secstrmenu.getItemCount();
4500 impl.attachWSMenuEntry(secstrmenu, me);
4501 int q = secstrmenu.getItemCount();
4502 for (int litm = p; litm < q; litm++)
4504 legacyItems.add(secstrmenu.getItem(litm));
4510 // Add all submenus in the order they should appear on the web
4512 wsmenu.add(msawsmenu);
4513 wsmenu.add(secstrmenu);
4514 wsmenu.add(dismenu);
4515 wsmenu.add(analymenu);
4516 // No search services yet
4517 // wsmenu.add(seqsrchmenu);
4519 javax.swing.SwingUtilities.invokeLater(new Runnable()
4526 webService.removeAll();
4527 // first, add discovered services onto the webservices menu
4528 if (wsmenu.size() > 0)
4530 for (int i = 0, j = wsmenu.size(); i < j; i++)
4532 webService.add(wsmenu.get(i));
4537 webService.add(me.webServiceNoServices);
4539 // TODO: move into separate menu builder class.
4540 boolean new_sspred = false;
4541 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4543 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4544 if (jws2servs != null)
4546 if (jws2servs.hasServices())
4548 jws2servs.attachWSMenuEntry(webService, me);
4549 for (Jws2Instance sv : jws2servs.getServices())
4551 if (sv.description.toLowerCase().contains("jpred"))
4553 for (JMenuItem jmi : legacyItems)
4555 jmi.setVisible(false);
4561 if (jws2servs.isRunning())
4563 JMenuItem tm = new JMenuItem(
4564 "Still discovering JABA Services");
4565 tm.setEnabled(false);
4570 build_urlServiceMenu(me.webService);
4571 build_fetchdbmenu(webService);
4572 for (JMenu item : wsmenu)
4574 if (item.getItemCount() == 0)
4576 item.setEnabled(false);
4580 item.setEnabled(true);
4583 } catch (Exception e)
4586 .debug("Exception during web service menu building process.",
4591 } catch (Exception e)
4594 buildingMenu = false;
4601 * construct any groupURL type service menu entries.
4605 private void build_urlServiceMenu(JMenu webService)
4607 // TODO: remove this code when 2.7 is released
4608 // DEBUG - alignmentView
4610 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4611 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4613 * @Override public void actionPerformed(ActionEvent e) {
4614 * jalview.datamodel.AlignmentView
4615 * .testSelectionViews(af.viewport.getAlignment(),
4616 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4618 * }); webService.add(testAlView);
4620 // TODO: refactor to RestClient discoverer and merge menu entries for
4621 // rest-style services with other types of analysis/calculation service
4622 // SHmmr test client - still being implemented.
4623 // DEBUG - alignmentView
4625 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4628 client.attachWSMenuEntry(
4629 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4635 * Searches selected sequences for xRef products and builds the Show
4636 * Cross-References menu (formerly called Show Products)
4638 * @return true if Show Cross-references menu should be enabled.
4640 public boolean canShowProducts()
4642 SequenceI[] selection = viewport.getSequenceSelection();
4643 AlignmentI dataset = viewport.getAlignment().getDataset();
4644 boolean showp = false;
4647 showProducts.removeAll();
4648 final boolean dna = viewport.getAlignment().isNucleotide();
4649 String[] ptypes = (selection == null || selection.length == 0) ? null
4650 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4652 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4655 final AlignFrame af = this;
4656 final String source = ptypes[t];
4657 JMenuItem xtype = new JMenuItem(ptypes[t]);
4658 xtype.addActionListener(new ActionListener()
4662 public void actionPerformed(ActionEvent e)
4664 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4668 showProducts.add(xtype);
4670 showProducts.setVisible(showp);
4671 showProducts.setEnabled(showp);
4672 } catch (Exception e)
4674 jalview.bin.Cache.log
4675 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4682 protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4683 final String source)
4685 Runnable foo = new Runnable()
4691 final long sttime = System.currentTimeMillis();
4692 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4693 "status.searching_for_sequences_from",
4694 new Object[] { source }), sttime);
4697 AlignmentI alignment = AlignFrame.this.getViewport()
4699 AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
4704 * get display scheme (if any) to apply to features
4706 FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
4707 .getFeatureColourScheme(source);
4709 AlignmentI al = makeCrossReferencesAlignment(
4710 alignment.getDataset(), xrefs);
4712 AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4714 if (Cache.getDefault("HIDE_INTRONS", true))
4716 newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
4718 String newtitle = String.format("%s %s %s",
4719 MessageManager.getString(dna ? "label.proteins"
4720 : "label.nucleotides"), MessageManager
4721 .getString("label.for"), getTitle());
4722 newFrame.setTitle(newtitle);
4724 if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4727 * split frame display is turned off in preferences file
4729 Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4731 return; // via finally clause
4735 * Make a copy of this alignment (sharing the same dataset
4736 * sequences). If we are DNA, drop introns and update mappings
4738 AlignmentI copyAlignment = null;
4739 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4740 .getSequenceSelection();
4741 List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4742 boolean copyAlignmentIsAligned = false;
4745 copyAlignment = AlignmentUtils.makeCdsAlignment(
4746 sequenceSelection, cf, alignment);
4747 if (copyAlignment.getHeight() == 0)
4749 System.err.println("Failed to make CDS alignment");
4751 al.getCodonFrames().clear();
4752 al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
4755 * pending getting Embl transcripts to 'align',
4756 * we are only doing this for Ensembl
4758 // TODO proper criteria for 'can align as cdna'
4759 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
4760 || AlignmentUtils.looksLikeEnsembl(alignment))
4762 copyAlignment.alignAs(alignment);
4763 copyAlignmentIsAligned = true;
4768 copyAlignment = AlignmentUtils.makeCopyAlignment(
4769 sequenceSelection, xrefs.getSequencesArray());
4770 copyAlignment.getCodonFrames().addAll(cf);
4772 copyAlignment.setGapCharacter(AlignFrame.this.viewport
4773 .getGapCharacter());
4775 StructureSelectionManager ssm = StructureSelectionManager
4776 .getStructureSelectionManager(Desktop.instance);
4777 ssm.registerMappings(cf);
4779 if (copyAlignment.getHeight() <= 0)
4781 System.err.println("No Sequences generated for xRef type "
4786 * align protein to dna
4788 if (dna && copyAlignmentIsAligned)
4790 al.alignAs(copyAlignment);
4795 * align cdna to protein - currently only if
4796 * fetching and aligning Ensembl transcripts!
4798 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4800 copyAlignment.alignAs(al);
4804 AlignFrame copyThis = new AlignFrame(copyAlignment,
4805 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4806 copyThis.setTitle(AlignFrame.this.getTitle());
4808 boolean showSequenceFeatures = viewport
4809 .isShowSequenceFeatures();
4810 newFrame.setShowSeqFeatures(showSequenceFeatures);
4811 copyThis.setShowSeqFeatures(showSequenceFeatures);
4812 FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4813 .getFeatureRenderer();
4816 * copy feature rendering settings to split frame
4818 newFrame.alignPanel.getSeqPanel().seqCanvas
4819 .getFeatureRenderer()
4820 .transferSettings(myFeatureStyling);
4821 copyThis.alignPanel.getSeqPanel().seqCanvas
4822 .getFeatureRenderer()
4823 .transferSettings(myFeatureStyling);
4826 * apply 'database source' feature configuration
4829 // TODO is this the feature colouring for the original
4830 // alignment or the fetched xrefs? either could be Ensembl
4831 newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
4832 copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
4834 SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4835 dna ? newFrame : copyThis);
4836 newFrame.setVisible(true);
4837 copyThis.setVisible(true);
4838 String linkedTitle = MessageManager
4839 .getString("label.linked_view_title");
4840 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4843 } catch (Exception e)
4845 Cache.log.error("Exception when finding crossreferences", e);
4846 } catch (OutOfMemoryError e)
4848 new OOMWarning("whilst fetching crossreferences", e);
4849 } catch (Throwable e)
4851 Cache.log.error("Error when finding crossreferences", e);
4854 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4855 "status.finished_searching_for_sequences_from",
4856 new Object[] { source }), sttime);
4861 * Makes an alignment containing the given sequences. If this is of the
4862 * same type as the given dataset (nucleotide/protein), then the new
4863 * alignment shares the same dataset, and its dataset sequences are added
4864 * to it. Otherwise a new dataset sequence is created for the
4871 protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
4874 boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
4876 SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4877 for (int s = 0; s < sprods.length; s++)
4879 sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4882 if (dataset.getSequences() == null
4883 || !dataset.getSequences().contains(
4884 sprods[s].getDatasetSequence()))
4886 dataset.addSequence(sprods[s].getDatasetSequence());
4889 sprods[s].updatePDBIds();
4891 Alignment al = new Alignment(sprods);
4894 al.setDataset((Alignment) dataset);
4898 al.createDatasetAlignment();
4904 Thread frunner = new Thread(foo);
4909 * Construct and display a new frame containing the translation of this
4910 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4913 public void showTranslation_actionPerformed(ActionEvent e)
4915 AlignmentI al = null;
4918 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4920 al = dna.translateCdna();
4921 } catch (Exception ex)
4923 jalview.bin.Cache.log.error(
4924 "Exception during translation. Please report this !", ex);
4925 final String msg = MessageManager
4926 .getString("label.error_when_translating_sequences_submit_bug_report");
4927 final String errorTitle = MessageManager
4928 .getString("label.implementation_error")
4929 + MessageManager.getString("translation_failed");
4930 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4931 JOptionPane.ERROR_MESSAGE);
4934 if (al == null || al.getHeight() == 0)
4936 final String msg = MessageManager
4937 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4938 final String errorTitle = MessageManager
4939 .getString("label.translation_failed");
4940 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4941 JOptionPane.WARNING_MESSAGE);
4945 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4946 af.setFileFormat(this.currentFileFormat);
4947 final String newTitle = MessageManager.formatMessage(
4948 "label.translation_of_params",
4949 new Object[] { this.getTitle() });
4950 af.setTitle(newTitle);
4951 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4953 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4954 viewport.openSplitFrame(af, new Alignment(seqs));
4958 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4965 * Set the file format
4969 public void setFileFormat(String fileFormat)
4971 this.currentFileFormat = fileFormat;
4975 * Try to load a features file onto the alignment.
4978 * contents or path to retrieve file
4980 * access mode of file (see jalview.io.AlignFile)
4981 * @return true if features file was parsed correctly.
4983 public boolean parseFeaturesFile(String file, String type)
4985 return avc.parseFeaturesFile(file, type,
4986 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4991 public void refreshFeatureUI(boolean enableIfNecessary)
4993 // note - currently this is only still here rather than in the controller
4994 // because of the featureSettings hard reference that is yet to be
4996 if (enableIfNecessary)
4998 viewport.setShowSequenceFeatures(true);
4999 showSeqFeatures.setSelected(true);
5005 public void dragEnter(DropTargetDragEvent evt)
5010 public void dragExit(DropTargetEvent evt)
5015 public void dragOver(DropTargetDragEvent evt)
5020 public void dropActionChanged(DropTargetDragEvent evt)
5025 public void drop(DropTargetDropEvent evt)
5027 Transferable t = evt.getTransferable();
5028 java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
5032 Desktop.transferFromDropTarget(files, protocols, evt, t);
5033 } catch (Exception e)
5035 e.printStackTrace();
5041 // check to see if any of these files have names matching sequences in
5043 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5044 .getAlignment().getSequencesArray());
5046 * Object[] { String,SequenceI}
5048 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5049 ArrayList<String> filesnotmatched = new ArrayList<String>();
5050 for (int i = 0; i < files.size(); i++)
5052 String file = files.get(i).toString();
5054 String protocol = FormatAdapter.checkProtocol(file);
5055 if (protocol == jalview.io.FormatAdapter.FILE)
5057 File fl = new File(file);
5058 pdbfn = fl.getName();
5060 else if (protocol == jalview.io.FormatAdapter.URL)
5062 URL url = new URL(file);
5063 pdbfn = url.getFile();
5065 if (pdbfn.length() > 0)
5067 // attempt to find a match in the alignment
5068 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5069 int l = 0, c = pdbfn.indexOf(".");
5070 while (mtch == null && c != -1)
5075 } while ((c = pdbfn.indexOf(".", l)) > l);
5078 pdbfn = pdbfn.substring(0, l);
5080 mtch = idm.findAllIdMatches(pdbfn);
5087 type = new IdentifyFile().identify(file, protocol);
5088 } catch (Exception ex)
5094 if (type.equalsIgnoreCase("PDB"))
5096 filesmatched.add(new Object[] { file, protocol, mtch });
5101 // File wasn't named like one of the sequences or wasn't a PDB file.
5102 filesnotmatched.add(file);
5106 if (filesmatched.size() > 0)
5108 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5114 "label.automatically_associate_pdb_files_with_sequences_same_name",
5115 new Object[] { Integer
5121 .getString("label.automatically_associate_pdb_files_by_name"),
5122 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5125 for (Object[] fm : filesmatched)
5127 // try and associate
5128 // TODO: may want to set a standard ID naming formalism for
5129 // associating PDB files which have no IDs.
5130 for (SequenceI toassoc : (SequenceI[]) fm[2])
5132 PDBEntry pe = new AssociatePdbFileWithSeq()
5133 .associatePdbWithSeq((String) fm[0],
5134 (String) fm[1], toassoc, false,
5138 System.err.println("Associated file : "
5139 + ((String) fm[0]) + " with "
5140 + toassoc.getDisplayId(true));
5144 alignPanel.paintAlignment(true);
5148 if (filesnotmatched.size() > 0)
5151 && (Cache.getDefault(
5152 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5158 "label.ignore_unmatched_dropped_files_info",
5159 new Object[] { Integer
5166 .getString("label.ignore_unmatched_dropped_files"),
5167 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5171 for (String fn : filesnotmatched)
5173 loadJalviewDataFile(fn, null, null, null);
5177 } catch (Exception ex)
5179 ex.printStackTrace();
5185 * Attempt to load a "dropped" file or URL string: First by testing whether
5186 * it's an Annotation file, then a JNet file, and finally a features file. If
5187 * all are false then the user may have dropped an alignment file onto this
5191 * either a filename or a URL string.
5193 public void loadJalviewDataFile(String file, String protocol,
5194 String format, SequenceI assocSeq)
5198 if (protocol == null)
5200 protocol = FormatAdapter.checkProtocol(file);
5202 // if the file isn't identified, or not positively identified as some
5203 // other filetype (PFAM is default unidentified alignment file type) then
5204 // try to parse as annotation.
5205 boolean isAnnotation = (format == null || format
5206 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5207 .annotateAlignmentView(viewport, file, protocol) : false;
5211 // first see if its a T-COFFEE score file
5212 TCoffeeScoreFile tcf = null;
5215 tcf = new TCoffeeScoreFile(file, protocol);
5218 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5220 tcoffeeColour.setEnabled(true);
5221 tcoffeeColour.setSelected(true);
5222 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5223 isAnnotation = true;
5225 .setText(MessageManager
5226 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5230 // some problem - if no warning its probable that the ID matching
5231 // process didn't work
5235 tcf.getWarningMessage() == null ? MessageManager
5236 .getString("label.check_file_matches_sequence_ids_alignment")
5237 : tcf.getWarningMessage(),
5239 .getString("label.problem_reading_tcoffee_score_file"),
5240 JOptionPane.WARNING_MESSAGE);
5247 } catch (Exception x)
5250 .debug("Exception when processing data source as T-COFFEE score file",
5256 // try to see if its a JNet 'concise' style annotation file *before*
5258 // try to parse it as a features file
5261 format = new IdentifyFile().identify(file, protocol);
5263 if (format.equalsIgnoreCase("JnetFile"))
5265 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5267 new JnetAnnotationMaker();
5268 JnetAnnotationMaker.add_annotation(predictions,
5269 viewport.getAlignment(), 0, false);
5270 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5271 viewport.getAlignment().setSeqrep(repseq);
5272 ColumnSelection cs = new ColumnSelection();
5273 cs.hideInsertionsFor(repseq);
5274 viewport.setColumnSelection(cs);
5275 isAnnotation = true;
5277 else if (IdentifyFile.FeaturesFile.equals(format))
5279 if (parseFeaturesFile(file, protocol))
5281 alignPanel.paintAlignment(true);
5286 new FileLoader().LoadFile(viewport, file, protocol, format);
5293 alignPanel.adjustAnnotationHeight();
5294 viewport.updateSequenceIdColours();
5295 buildSortByAnnotationScoresMenu();
5296 alignPanel.paintAlignment(true);
5298 } catch (Exception ex)
5300 ex.printStackTrace();
5301 } catch (OutOfMemoryError oom)
5306 } catch (Exception x)
5311 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5312 : "using " + protocol + " from " + file)
5314 + (format != null ? "(parsing as '" + format
5315 + "' file)" : ""), oom, Desktop.desktop);
5320 * Method invoked by the ChangeListener on the tabbed pane, in other words
5321 * when a different tabbed pane is selected by the user or programmatically.
5324 public void tabSelectionChanged(int index)
5328 alignPanel = alignPanels.get(index);
5329 viewport = alignPanel.av;
5330 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5331 setMenusFromViewport(viewport);
5335 * If there is a frame linked to this one in a SplitPane, switch it to the
5336 * same view tab index. No infinite recursion of calls should happen, since
5337 * tabSelectionChanged() should not get invoked on setting the selected
5338 * index to an unchanged value. Guard against setting an invalid index
5339 * before the new view peer tab has been created.
5341 final AlignViewportI peer = viewport.getCodingComplement();
5344 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5345 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5347 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5353 * On right mouse click on view tab, prompt for and set new view name.
5356 public void tabbedPane_mousePressed(MouseEvent e)
5358 if (e.isPopupTrigger())
5360 String msg = MessageManager.getString("label.enter_view_name");
5361 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5362 JOptionPane.QUESTION_MESSAGE);
5366 viewport.viewName = reply;
5367 // TODO warn if reply is in getExistingViewNames()?
5368 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5373 public AlignViewport getCurrentView()
5379 * Open the dialog for regex description parsing.
5382 protected void extractScores_actionPerformed(ActionEvent e)
5384 ParseProperties pp = new jalview.analysis.ParseProperties(
5385 viewport.getAlignment());
5386 // TODO: verify regex and introduce GUI dialog for version 2.5
5387 // if (pp.getScoresFromDescription("col", "score column ",
5388 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5390 if (pp.getScoresFromDescription("description column",
5391 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5393 buildSortByAnnotationScoresMenu();
5401 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5405 protected void showDbRefs_actionPerformed(ActionEvent e)
5407 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5413 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5417 protected void showNpFeats_actionPerformed(ActionEvent e)
5419 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5423 * find the viewport amongst the tabs in this alignment frame and close that
5428 public boolean closeView(AlignViewportI av)
5432 this.closeMenuItem_actionPerformed(false);
5435 Component[] comp = tabbedPane.getComponents();
5436 for (int i = 0; comp != null && i < comp.length; i++)
5438 if (comp[i] instanceof AlignmentPanel)
5440 if (((AlignmentPanel) comp[i]).av == av)
5443 closeView((AlignmentPanel) comp[i]);
5451 protected void build_fetchdbmenu(JMenu webService)
5453 // Temporary hack - DBRef Fetcher always top level ws entry.
5454 // TODO We probably want to store a sequence database checklist in
5455 // preferences and have checkboxes.. rather than individual sources selected
5457 final JMenu rfetch = new JMenu(
5458 MessageManager.getString("action.fetch_db_references"));
5459 rfetch.setToolTipText(MessageManager
5460 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5461 webService.add(rfetch);
5463 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5464 MessageManager.getString("option.trim_retrieved_seqs"));
5465 trimrs.setToolTipText(MessageManager
5466 .getString("label.trim_retrieved_sequences"));
5467 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5468 trimrs.addActionListener(new ActionListener()
5471 public void actionPerformed(ActionEvent e)
5473 trimrs.setSelected(trimrs.isSelected());
5474 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5475 Boolean.valueOf(trimrs.isSelected()).toString());
5479 JMenuItem fetchr = new JMenuItem(
5480 MessageManager.getString("label.standard_databases"));
5481 fetchr.setToolTipText(MessageManager
5482 .getString("label.fetch_embl_uniprot"));
5483 fetchr.addActionListener(new ActionListener()
5487 public void actionPerformed(ActionEvent e)
5489 new Thread(new Runnable()
5494 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5495 .getAlignment().isNucleotide();
5496 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5497 .getSequenceSelection(), alignPanel.alignFrame, null,
5498 alignPanel.alignFrame.featureSettings, isNucleotide);
5499 dbRefFetcher.addListener(new FetchFinishedListenerI()
5502 public void finished()
5504 AlignFrame.this.setMenusForViewport();
5507 dbRefFetcher.fetchDBRefs(false);
5515 final AlignFrame me = this;
5516 new Thread(new Runnable()
5521 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5522 .getSequenceFetcherSingleton(me);
5523 javax.swing.SwingUtilities.invokeLater(new Runnable()
5528 String[] dbclasses = sf.getOrderedSupportedSources();
5529 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5530 // jalview.util.QuickSort.sort(otherdb, otherdb);
5531 List<DbSourceProxy> otherdb;
5532 JMenu dfetch = new JMenu();
5533 JMenu ifetch = new JMenu();
5534 JMenuItem fetchr = null;
5535 int comp = 0, icomp = 0, mcomp = 15;
5536 String mname = null;
5538 for (String dbclass : dbclasses)
5540 otherdb = sf.getSourceProxy(dbclass);
5541 // add a single entry for this class, or submenu allowing 'fetch
5543 if (otherdb == null || otherdb.size() < 1)
5547 // List<DbSourceProxy> dbs=otherdb;
5548 // otherdb=new ArrayList<DbSourceProxy>();
5549 // for (DbSourceProxy db:dbs)
5551 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5555 mname = "From " + dbclass;
5557 if (otherdb.size() == 1)
5559 final DbSourceProxy[] dassource = otherdb
5560 .toArray(new DbSourceProxy[0]);
5561 DbSourceProxy src = otherdb.get(0);
5562 fetchr = new JMenuItem(src.getDbSource());
5563 fetchr.addActionListener(new ActionListener()
5567 public void actionPerformed(ActionEvent e)
5569 new Thread(new Runnable()
5575 boolean isNucleotide = alignPanel.alignFrame
5576 .getViewport().getAlignment()
5578 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5579 alignPanel.av.getSequenceSelection(),
5580 alignPanel.alignFrame, dassource,
5581 alignPanel.alignFrame.featureSettings,
5584 .addListener(new FetchFinishedListenerI()
5587 public void finished()
5589 AlignFrame.this.setMenusForViewport();
5592 dbRefFetcher.fetchDBRefs(false);
5598 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5599 MessageManager.formatMessage(
5600 "label.fetch_retrieve_from",
5601 new Object[] { src.getDbName() })));
5607 final DbSourceProxy[] dassource = otherdb
5608 .toArray(new DbSourceProxy[0]);
5610 DbSourceProxy src = otherdb.get(0);
5611 fetchr = new JMenuItem(MessageManager.formatMessage(
5612 "label.fetch_all_param",
5613 new Object[] { src.getDbSource() }));
5614 fetchr.addActionListener(new ActionListener()
5617 public void actionPerformed(ActionEvent e)
5619 new Thread(new Runnable()
5625 boolean isNucleotide = alignPanel.alignFrame
5626 .getViewport().getAlignment()
5628 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5629 alignPanel.av.getSequenceSelection(),
5630 alignPanel.alignFrame, dassource,
5631 alignPanel.alignFrame.featureSettings,
5634 .addListener(new FetchFinishedListenerI()
5637 public void finished()
5639 AlignFrame.this.setMenusForViewport();
5642 dbRefFetcher.fetchDBRefs(false);
5648 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5649 MessageManager.formatMessage(
5650 "label.fetch_retrieve_from_all_sources",
5652 Integer.valueOf(otherdb.size())
5653 .toString(), src.getDbSource(),
5654 src.getDbName() })));
5657 // and then build the rest of the individual menus
5658 ifetch = new JMenu(MessageManager.formatMessage(
5659 "label.source_from_db_source",
5660 new Object[] { src.getDbSource() }));
5662 String imname = null;
5664 for (DbSourceProxy sproxy : otherdb)
5666 String dbname = sproxy.getDbName();
5667 String sname = dbname.length() > 5 ? dbname.substring(0,
5668 5) + "..." : dbname;
5669 String msname = dbname.length() > 10 ? dbname.substring(
5670 0, 10) + "..." : dbname;
5673 imname = MessageManager.formatMessage(
5674 "label.from_msname", new Object[] { sname });
5676 fetchr = new JMenuItem(msname);
5677 final DbSourceProxy[] dassrc = { sproxy };
5678 fetchr.addActionListener(new ActionListener()
5682 public void actionPerformed(ActionEvent e)
5684 new Thread(new Runnable()
5690 boolean isNucleotide = alignPanel.alignFrame
5691 .getViewport().getAlignment()
5693 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5694 alignPanel.av.getSequenceSelection(),
5695 alignPanel.alignFrame, dassrc,
5696 alignPanel.alignFrame.featureSettings,
5699 .addListener(new FetchFinishedListenerI()
5702 public void finished()
5704 AlignFrame.this.setMenusForViewport();
5707 dbRefFetcher.fetchDBRefs(false);
5713 fetchr.setToolTipText("<html>"
5714 + MessageManager.formatMessage(
5715 "label.fetch_retrieve_from", new Object[]
5719 if (++icomp >= mcomp || i == (otherdb.size()))
5721 ifetch.setText(MessageManager.formatMessage(
5722 "label.source_to_target", imname, sname));
5724 ifetch = new JMenu();
5732 if (comp >= mcomp || dbi >= (dbclasses.length))
5734 dfetch.setText(MessageManager.formatMessage(
5735 "label.source_to_target", mname, dbclass));
5737 dfetch = new JMenu();
5750 * Left justify the whole alignment.
5753 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5755 AlignmentI al = viewport.getAlignment();
5757 viewport.firePropertyChange("alignment", null, al);
5761 * Right justify the whole alignment.
5764 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5766 AlignmentI al = viewport.getAlignment();
5768 viewport.firePropertyChange("alignment", null, al);
5772 public void setShowSeqFeatures(boolean b)
5774 showSeqFeatures.setSelected(b);
5775 viewport.setShowSequenceFeatures(b);
5782 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5783 * awt.event.ActionEvent)
5786 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5788 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5789 alignPanel.paintAlignment(true);
5796 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5800 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5802 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5803 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5811 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5812 * .event.ActionEvent)
5815 protected void showGroupConservation_actionPerformed(ActionEvent e)
5817 viewport.setShowGroupConservation(showGroupConservation.getState());
5818 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5825 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5826 * .event.ActionEvent)
5829 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5831 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5832 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5839 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5840 * .event.ActionEvent)
5843 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5845 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5846 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5850 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5852 showSequenceLogo.setState(true);
5853 viewport.setShowSequenceLogo(true);
5854 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5855 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5859 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5861 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5868 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5869 * .event.ActionEvent)
5872 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5874 if (avc.makeGroupsFromSelection())
5876 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5877 alignPanel.updateAnnotation();
5878 alignPanel.paintAlignment(true);
5882 public void clearAlignmentSeqRep()
5884 // TODO refactor alignmentseqrep to controller
5885 if (viewport.getAlignment().hasSeqrep())
5887 viewport.getAlignment().setSeqrep(null);
5888 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5889 alignPanel.updateAnnotation();
5890 alignPanel.paintAlignment(true);
5895 protected void createGroup_actionPerformed(ActionEvent e)
5897 if (avc.createGroup())
5899 alignPanel.alignmentChanged();
5904 protected void unGroup_actionPerformed(ActionEvent e)
5908 alignPanel.alignmentChanged();
5913 * make the given alignmentPanel the currently selected tab
5915 * @param alignmentPanel
5917 public void setDisplayedView(AlignmentPanel alignmentPanel)
5919 if (!viewport.getSequenceSetId().equals(
5920 alignmentPanel.av.getSequenceSetId()))
5924 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5926 if (tabbedPane != null
5927 && tabbedPane.getTabCount() > 0
5928 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5929 .getSelectedIndex())
5931 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5936 * Action on selection of menu options to Show or Hide annotations.
5939 * @param forSequences
5940 * update sequence-related annotations
5941 * @param forAlignment
5942 * update non-sequence-related annotations
5945 protected void setAnnotationsVisibility(boolean visible,
5946 boolean forSequences, boolean forAlignment)
5948 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5949 .getAlignmentAnnotation())
5952 * don't display non-positional annotations on an alignment
5954 if (aa.annotations == null)
5958 boolean apply = (aa.sequenceRef == null && forAlignment)
5959 || (aa.sequenceRef != null && forSequences);
5962 aa.visible = visible;
5965 alignPanel.validateAnnotationDimensions(true);
5966 alignPanel.alignmentChanged();
5970 * Store selected annotation sort order for the view and repaint.
5973 protected void sortAnnotations_actionPerformed()
5975 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5977 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5978 alignPanel.paintAlignment(true);
5983 * @return alignment panels in this alignment frame
5985 public List<? extends AlignmentViewPanel> getAlignPanels()
5987 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5991 * Open a new alignment window, with the cDNA associated with this (protein)
5992 * alignment, aligned as is the protein.
5994 protected void viewAsCdna_actionPerformed()
5996 // TODO no longer a menu action - refactor as required
5997 final AlignmentI alignment = getViewport().getAlignment();
5998 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5999 if (mappings == null)
6003 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6004 for (SequenceI aaSeq : alignment.getSequences())
6006 for (AlignedCodonFrame acf : mappings)
6008 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6012 * There is a cDNA mapping for this protein sequence - add to new
6013 * alignment. It will share the same dataset sequence as other mapped
6014 * cDNA (no new mappings need to be created).
6016 final Sequence newSeq = new Sequence(dnaSeq);
6017 newSeq.setDatasetSequence(dnaSeq);
6018 cdnaSeqs.add(newSeq);
6022 if (cdnaSeqs.size() == 0)
6024 // show a warning dialog no mapped cDNA
6027 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6029 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6030 AlignFrame.DEFAULT_HEIGHT);
6031 cdna.alignAs(alignment);
6032 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6034 Desktop.addInternalFrame(alignFrame, newtitle,
6035 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6039 * Set visibility of dna/protein complement view (available when shown in a
6045 protected void showComplement_actionPerformed(boolean show)
6047 SplitContainerI sf = getSplitViewContainer();
6050 sf.setComplementVisible(this, show);
6055 * Generate the reverse (optionally complemented) of the selected sequences,
6056 * and add them to the alignment
6059 protected void showReverse_actionPerformed(boolean complement)
6061 AlignmentI al = null;
6064 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6066 al = dna.reverseCdna(complement);
6067 viewport.addAlignment(al, "");
6068 } catch (Exception ex)
6070 System.err.println(ex.getMessage());
6076 * Try to run a script in the Groovy console, having first ensured that this
6077 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
6078 * be targeted at this alignment.
6081 protected void runGroovy_actionPerformed()
6083 Desktop.setCurrentAlignFrame(this);
6084 groovy.ui.Console console = Desktop.getGroovyConsole();
6085 if (console != null)
6089 console.runScript();
6090 } catch (Exception ex)
6092 System.err.println((ex.toString()));
6094 .showInternalMessageDialog(Desktop.desktop, MessageManager
6095 .getString("label.couldnt_run_groovy_script"),
6097 .getString("label.groovy_support_failed"),
6098 JOptionPane.ERROR_MESSAGE);
6103 System.err.println("Can't run Groovy script as console not found");
6108 * Hides columns containing (or not containing) a specified feature, provided
6109 * that would not leave all columns hidden
6111 * @param featureType
6112 * @param columnsContaining
6115 public boolean hideFeatureColumns(String featureType,
6116 boolean columnsContaining)
6118 boolean notForHiding = avc.markColumnsContainingFeatures(
6119 columnsContaining, false, false, featureType);
6122 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
6123 false, featureType))
6125 getViewport().hideSelectedColumns();
6133 class PrintThread extends Thread
6137 public PrintThread(AlignmentPanel ap)
6142 static PageFormat pf;
6147 PrinterJob printJob = PrinterJob.getPrinterJob();
6151 printJob.setPrintable(ap, pf);
6155 printJob.setPrintable(ap);
6158 if (printJob.printDialog())
6163 } catch (Exception PrintException)
6165 PrintException.printStackTrace();