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 Jalview.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,
1317 settings.isExportHiddenSequences());
1320 int[] alignmentStartEnd = new int[2];
1321 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1323 alignmentToExport = hiddenSeqs.getFullAlignment();
1327 alignmentToExport = viewport.getAlignment();
1329 alignmentStartEnd = alignmentToExport
1330 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1331 .getHiddenColumns());
1332 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1333 omitHidden, alignmentStartEnd, settings);
1344 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1346 new HtmlSvgOutput(null, alignPanel);
1350 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1352 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1353 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1356 public void createImageMap(File file, String image)
1358 alignPanel.makePNGImageMap(file, image);
1368 public void createPNG(File f)
1370 alignPanel.makePNG(f);
1380 public void createEPS(File f)
1382 alignPanel.makeEPS(f);
1386 public void createSVG(File f)
1388 alignPanel.makeSVG(f);
1392 public void pageSetup_actionPerformed(ActionEvent e)
1394 PrinterJob printJob = PrinterJob.getPrinterJob();
1395 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1405 public void printMenuItem_actionPerformed(ActionEvent e)
1407 // Putting in a thread avoids Swing painting problems
1408 PrintThread thread = new PrintThread(alignPanel);
1413 public void exportFeatures_actionPerformed(ActionEvent e)
1415 new AnnotationExporter().exportFeatures(alignPanel);
1419 public void exportAnnotations_actionPerformed(ActionEvent e)
1421 new AnnotationExporter().exportAnnotations(alignPanel);
1425 public void associatedData_actionPerformed(ActionEvent e)
1427 // Pick the tree file
1428 JalviewFileChooser chooser = new JalviewFileChooser(
1429 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1430 chooser.setFileView(new JalviewFileView());
1431 chooser.setDialogTitle(MessageManager
1432 .getString("label.load_jalview_annotations"));
1433 chooser.setToolTipText(MessageManager
1434 .getString("label.load_jalview_annotations"));
1436 int value = chooser.showOpenDialog(null);
1438 if (value == JalviewFileChooser.APPROVE_OPTION)
1440 String choice = chooser.getSelectedFile().getPath();
1441 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1442 loadJalviewDataFile(choice, null, null, null);
1448 * Close the current view or all views in the alignment frame. If the frame
1449 * only contains one view then the alignment will be removed from memory.
1451 * @param closeAllTabs
1454 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1456 if (alignPanels != null && alignPanels.size() < 2)
1458 closeAllTabs = true;
1463 if (alignPanels != null)
1467 if (this.isClosed())
1469 // really close all the windows - otherwise wait till
1470 // setClosed(true) is called
1471 for (int i = 0; i < alignPanels.size(); i++)
1473 AlignmentPanel ap = alignPanels.get(i);
1480 closeView(alignPanel);
1487 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1488 * be called recursively, with the frame now in 'closed' state
1490 this.setClosed(true);
1492 } catch (Exception ex)
1494 ex.printStackTrace();
1499 * Close the specified panel and close up tabs appropriately.
1501 * @param panelToClose
1503 public void closeView(AlignmentPanel panelToClose)
1505 int index = tabbedPane.getSelectedIndex();
1506 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1507 alignPanels.remove(panelToClose);
1508 panelToClose.closePanel();
1509 panelToClose = null;
1511 tabbedPane.removeTabAt(closedindex);
1512 tabbedPane.validate();
1514 if (index > closedindex || index == tabbedPane.getTabCount())
1516 // modify currently selected tab index if necessary.
1520 this.tabSelectionChanged(index);
1526 void updateEditMenuBar()
1529 if (viewport.getHistoryList().size() > 0)
1531 undoMenuItem.setEnabled(true);
1532 CommandI command = viewport.getHistoryList().peek();
1533 undoMenuItem.setText(MessageManager.formatMessage(
1534 "label.undo_command",
1535 new Object[] { command.getDescription() }));
1539 undoMenuItem.setEnabled(false);
1540 undoMenuItem.setText(MessageManager.getString("action.undo"));
1543 if (viewport.getRedoList().size() > 0)
1545 redoMenuItem.setEnabled(true);
1547 CommandI command = viewport.getRedoList().peek();
1548 redoMenuItem.setText(MessageManager.formatMessage(
1549 "label.redo_command",
1550 new Object[] { command.getDescription() }));
1554 redoMenuItem.setEnabled(false);
1555 redoMenuItem.setText(MessageManager.getString("action.redo"));
1560 public void addHistoryItem(CommandI command)
1562 if (command.getSize() > 0)
1564 viewport.addToHistoryList(command);
1565 viewport.clearRedoList();
1566 updateEditMenuBar();
1567 viewport.updateHiddenColumns();
1568 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1569 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1570 // viewport.getColumnSelection()
1571 // .getHiddenColumns().size() > 0);
1577 * @return alignment objects for all views
1579 AlignmentI[] getViewAlignments()
1581 if (alignPanels != null)
1583 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1585 for (AlignmentPanel ap : alignPanels)
1587 als[i++] = ap.av.getAlignment();
1591 if (viewport != null)
1593 return new AlignmentI[] { viewport.getAlignment() };
1605 protected void undoMenuItem_actionPerformed(ActionEvent e)
1607 if (viewport.getHistoryList().isEmpty())
1611 CommandI command = viewport.getHistoryList().pop();
1612 viewport.addToRedoList(command);
1613 command.undoCommand(getViewAlignments());
1615 AlignmentViewport originalSource = getOriginatingSource(command);
1616 updateEditMenuBar();
1618 if (originalSource != null)
1620 if (originalSource != viewport)
1623 .warn("Implementation worry: mismatch of viewport origin for undo");
1625 originalSource.updateHiddenColumns();
1626 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1628 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1629 // viewport.getColumnSelection()
1630 // .getHiddenColumns().size() > 0);
1631 originalSource.firePropertyChange("alignment", null, originalSource
1632 .getAlignment().getSequences());
1643 protected void redoMenuItem_actionPerformed(ActionEvent e)
1645 if (viewport.getRedoList().size() < 1)
1650 CommandI command = viewport.getRedoList().pop();
1651 viewport.addToHistoryList(command);
1652 command.doCommand(getViewAlignments());
1654 AlignmentViewport originalSource = getOriginatingSource(command);
1655 updateEditMenuBar();
1657 if (originalSource != null)
1660 if (originalSource != viewport)
1663 .warn("Implementation worry: mismatch of viewport origin for redo");
1665 originalSource.updateHiddenColumns();
1666 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1668 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1669 // viewport.getColumnSelection()
1670 // .getHiddenColumns().size() > 0);
1671 originalSource.firePropertyChange("alignment", null, originalSource
1672 .getAlignment().getSequences());
1676 AlignmentViewport getOriginatingSource(CommandI command)
1678 AlignmentViewport originalSource = null;
1679 // For sequence removal and addition, we need to fire
1680 // the property change event FROM the viewport where the
1681 // original alignment was altered
1682 AlignmentI al = null;
1683 if (command instanceof EditCommand)
1685 EditCommand editCommand = (EditCommand) command;
1686 al = editCommand.getAlignment();
1687 List<Component> comps = PaintRefresher.components.get(viewport
1688 .getSequenceSetId());
1690 for (Component comp : comps)
1692 if (comp instanceof AlignmentPanel)
1694 if (al == ((AlignmentPanel) comp).av.getAlignment())
1696 originalSource = ((AlignmentPanel) comp).av;
1703 if (originalSource == null)
1705 // The original view is closed, we must validate
1706 // the current view against the closed view first
1709 PaintRefresher.validateSequences(al, viewport.getAlignment());
1712 originalSource = viewport;
1715 return originalSource;
1724 public void moveSelectedSequences(boolean up)
1726 SequenceGroup sg = viewport.getSelectionGroup();
1732 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1733 viewport.getHiddenRepSequences(), up);
1734 alignPanel.paintAlignment(true);
1737 synchronized void slideSequences(boolean right, int size)
1739 List<SequenceI> sg = new ArrayList<SequenceI>();
1740 if (viewport.cursorMode)
1742 sg.add(viewport.getAlignment().getSequenceAt(
1743 alignPanel.getSeqPanel().seqCanvas.cursorY));
1745 else if (viewport.getSelectionGroup() != null
1746 && viewport.getSelectionGroup().getSize() != viewport
1747 .getAlignment().getHeight())
1749 sg = viewport.getSelectionGroup().getSequences(
1750 viewport.getHiddenRepSequences());
1758 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1760 for (SequenceI seq : viewport.getAlignment().getSequences())
1762 if (!sg.contains(seq))
1764 invertGroup.add(seq);
1768 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1770 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1771 for (int i = 0; i < invertGroup.size(); i++)
1773 seqs2[i] = invertGroup.get(i);
1776 SlideSequencesCommand ssc;
1779 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1780 size, viewport.getGapCharacter());
1784 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1785 size, viewport.getGapCharacter());
1788 int groupAdjustment = 0;
1789 if (ssc.getGapsInsertedBegin() && right)
1791 if (viewport.cursorMode)
1793 alignPanel.getSeqPanel().moveCursor(size, 0);
1797 groupAdjustment = size;
1800 else if (!ssc.getGapsInsertedBegin() && !right)
1802 if (viewport.cursorMode)
1804 alignPanel.getSeqPanel().moveCursor(-size, 0);
1808 groupAdjustment = -size;
1812 if (groupAdjustment != 0)
1814 viewport.getSelectionGroup().setStartRes(
1815 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1816 viewport.getSelectionGroup().setEndRes(
1817 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1821 * just extend the last slide command if compatible; but not if in
1822 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1824 boolean appendHistoryItem = false;
1825 Deque<CommandI> historyList = viewport.getHistoryList();
1826 boolean inSplitFrame = getSplitViewContainer() != null;
1827 if (!inSplitFrame && historyList != null && historyList.size() > 0
1828 && historyList.peek() instanceof SlideSequencesCommand)
1830 appendHistoryItem = ssc
1831 .appendSlideCommand((SlideSequencesCommand) historyList
1835 if (!appendHistoryItem)
1837 addHistoryItem(ssc);
1850 protected void copy_actionPerformed(ActionEvent e)
1853 if (viewport.getSelectionGroup() == null)
1857 // TODO: preserve the ordering of displayed alignment annotation in any
1858 // internal paste (particularly sequence associated annotation)
1859 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1860 String[] omitHidden = null;
1862 if (viewport.hasHiddenColumns())
1864 omitHidden = viewport.getViewAsString(true);
1867 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1870 StringSelection ss = new StringSelection(output);
1874 jalview.gui.Desktop.internalCopy = true;
1875 // Its really worth setting the clipboard contents
1876 // to empty before setting the large StringSelection!!
1877 Toolkit.getDefaultToolkit().getSystemClipboard()
1878 .setContents(new StringSelection(""), null);
1880 Toolkit.getDefaultToolkit().getSystemClipboard()
1881 .setContents(ss, Desktop.instance);
1882 } catch (OutOfMemoryError er)
1884 new OOMWarning("copying region", er);
1888 ArrayList<int[]> hiddenColumns = null;
1889 if (viewport.hasHiddenColumns())
1891 hiddenColumns = new ArrayList<int[]>();
1892 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1893 .getSelectionGroup().getEndRes();
1894 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1896 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1898 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1899 region[1] - hiddenOffset });
1904 Desktop.jalviewClipboard = new Object[] { seqs,
1905 viewport.getAlignment().getDataset(), hiddenColumns };
1906 statusBar.setText(MessageManager.formatMessage(
1907 "label.copied_sequences_to_clipboard", new Object[] { Integer
1908 .valueOf(seqs.length).toString() }));
1918 protected void pasteNew_actionPerformed(ActionEvent e)
1930 protected void pasteThis_actionPerformed(ActionEvent e)
1936 * Paste contents of Jalview clipboard
1938 * @param newAlignment
1939 * true to paste to a new alignment, otherwise add to this.
1941 void paste(boolean newAlignment)
1943 boolean externalPaste = true;
1946 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1947 Transferable contents = c.getContents(this);
1949 if (contents == null)
1957 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1958 if (str.length() < 1)
1963 format = new IdentifyFile().identify(str, "Paste");
1965 } catch (OutOfMemoryError er)
1967 new OOMWarning("Out of memory pasting sequences!!", er);
1971 SequenceI[] sequences;
1972 boolean annotationAdded = false;
1973 AlignmentI alignment = null;
1975 if (Desktop.jalviewClipboard != null)
1977 // The clipboard was filled from within Jalview, we must use the
1979 // And dataset from the copied alignment
1980 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1981 // be doubly sure that we create *new* sequence objects.
1982 sequences = new SequenceI[newseq.length];
1983 for (int i = 0; i < newseq.length; i++)
1985 sequences[i] = new Sequence(newseq[i]);
1987 alignment = new Alignment(sequences);
1988 externalPaste = false;
1992 // parse the clipboard as an alignment.
1993 alignment = new FormatAdapter().readFile(str, "Paste", format);
1994 sequences = alignment.getSequencesArray();
1998 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2004 if (Desktop.jalviewClipboard != null)
2006 // dataset is inherited
2007 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2011 // new dataset is constructed
2012 alignment.setDataset(null);
2014 alwidth = alignment.getWidth() + 1;
2018 AlignmentI pastedal = alignment; // preserve pasted alignment object
2019 // Add pasted sequences and dataset into existing alignment.
2020 alignment = viewport.getAlignment();
2021 alwidth = alignment.getWidth() + 1;
2022 // decide if we need to import sequences from an existing dataset
2023 boolean importDs = Desktop.jalviewClipboard != null
2024 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2025 // importDs==true instructs us to copy over new dataset sequences from
2026 // an existing alignment
2027 Vector newDs = (importDs) ? new Vector() : null; // used to create
2028 // minimum dataset set
2030 for (int i = 0; i < sequences.length; i++)
2034 newDs.addElement(null);
2036 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2038 if (importDs && ds != null)
2040 if (!newDs.contains(ds))
2042 newDs.setElementAt(ds, i);
2043 ds = new Sequence(ds);
2044 // update with new dataset sequence
2045 sequences[i].setDatasetSequence(ds);
2049 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2054 // copy and derive new dataset sequence
2055 sequences[i] = sequences[i].deriveSequence();
2056 alignment.getDataset().addSequence(
2057 sequences[i].getDatasetSequence());
2058 // TODO: avoid creation of duplicate dataset sequences with a
2059 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2061 alignment.addSequence(sequences[i]); // merges dataset
2065 newDs.clear(); // tidy up
2067 if (alignment.getAlignmentAnnotation() != null)
2069 for (AlignmentAnnotation alan : alignment
2070 .getAlignmentAnnotation())
2072 if (alan.graphGroup > fgroup)
2074 fgroup = alan.graphGroup;
2078 if (pastedal.getAlignmentAnnotation() != null)
2080 // Add any annotation attached to alignment.
2081 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2082 for (int i = 0; i < alann.length; i++)
2084 annotationAdded = true;
2085 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2087 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2088 if (newann.graphGroup > -1)
2090 if (newGraphGroups.size() <= newann.graphGroup
2091 || newGraphGroups.get(newann.graphGroup) == null)
2093 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2095 newGraphGroups.add(q, null);
2097 newGraphGroups.set(newann.graphGroup, new Integer(
2100 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2104 newann.padAnnotation(alwidth);
2105 alignment.addAnnotation(newann);
2115 addHistoryItem(new EditCommand(
2116 MessageManager.getString("label.add_sequences"),
2117 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2119 // Add any annotations attached to sequences
2120 for (int i = 0; i < sequences.length; i++)
2122 if (sequences[i].getAnnotation() != null)
2124 AlignmentAnnotation newann;
2125 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2127 annotationAdded = true;
2128 newann = sequences[i].getAnnotation()[a];
2129 newann.adjustForAlignment();
2130 newann.padAnnotation(alwidth);
2131 if (newann.graphGroup > -1)
2133 if (newann.graphGroup > -1)
2135 if (newGraphGroups.size() <= newann.graphGroup
2136 || newGraphGroups.get(newann.graphGroup) == null)
2138 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2140 newGraphGroups.add(q, null);
2142 newGraphGroups.set(newann.graphGroup, new Integer(
2145 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2149 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2154 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2161 // propagate alignment changed.
2162 viewport.setEndSeq(alignment.getHeight());
2163 if (annotationAdded)
2165 // Duplicate sequence annotation in all views.
2166 AlignmentI[] alview = this.getViewAlignments();
2167 for (int i = 0; i < sequences.length; i++)
2169 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2174 for (int avnum = 0; avnum < alview.length; avnum++)
2176 if (alview[avnum] != alignment)
2178 // duplicate in a view other than the one with input focus
2179 int avwidth = alview[avnum].getWidth() + 1;
2180 // this relies on sann being preserved after we
2181 // modify the sequence's annotation array for each duplication
2182 for (int a = 0; a < sann.length; a++)
2184 AlignmentAnnotation newann = new AlignmentAnnotation(
2186 sequences[i].addAlignmentAnnotation(newann);
2187 newann.padAnnotation(avwidth);
2188 alview[avnum].addAnnotation(newann); // annotation was
2189 // duplicated earlier
2190 // TODO JAL-1145 graphGroups are not updated for sequence
2191 // annotation added to several views. This may cause
2193 alview[avnum].setAnnotationIndex(newann, a);
2198 buildSortByAnnotationScoresMenu();
2200 viewport.firePropertyChange("alignment", null,
2201 alignment.getSequences());
2202 if (alignPanels != null)
2204 for (AlignmentPanel ap : alignPanels)
2206 ap.validateAnnotationDimensions(false);
2211 alignPanel.validateAnnotationDimensions(false);
2217 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2219 String newtitle = new String("Copied sequences");
2221 if (Desktop.jalviewClipboard != null
2222 && Desktop.jalviewClipboard[2] != null)
2224 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2225 for (int[] region : hc)
2227 af.viewport.hideColumns(region[0], region[1]);
2231 // >>>This is a fix for the moment, until a better solution is
2233 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2235 alignPanel.getSeqPanel().seqCanvas
2236 .getFeatureRenderer());
2238 // TODO: maintain provenance of an alignment, rather than just make the
2239 // title a concatenation of operations.
2242 if (title.startsWith("Copied sequences"))
2248 newtitle = newtitle.concat("- from " + title);
2253 newtitle = new String("Pasted sequences");
2256 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2261 } catch (Exception ex)
2263 ex.printStackTrace();
2264 System.out.println("Exception whilst pasting: " + ex);
2265 // could be anything being pasted in here
2271 protected void expand_newalign(ActionEvent e)
2275 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2276 .getAlignment(), -1);
2277 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2279 String newtitle = new String("Flanking alignment");
2281 if (Desktop.jalviewClipboard != null
2282 && Desktop.jalviewClipboard[2] != null)
2284 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2285 for (int region[] : hc)
2287 af.viewport.hideColumns(region[0], region[1]);
2291 // >>>This is a fix for the moment, until a better solution is
2293 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2295 alignPanel.getSeqPanel().seqCanvas
2296 .getFeatureRenderer());
2298 // TODO: maintain provenance of an alignment, rather than just make the
2299 // title a concatenation of operations.
2301 if (title.startsWith("Copied sequences"))
2307 newtitle = newtitle.concat("- from " + title);
2311 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2313 } catch (Exception ex)
2315 ex.printStackTrace();
2316 System.out.println("Exception whilst pasting: " + ex);
2317 // could be anything being pasted in here
2318 } catch (OutOfMemoryError oom)
2320 new OOMWarning("Viewing flanking region of alignment", oom);
2331 protected void cut_actionPerformed(ActionEvent e)
2333 copy_actionPerformed(null);
2334 delete_actionPerformed(null);
2344 protected void delete_actionPerformed(ActionEvent evt)
2347 SequenceGroup sg = viewport.getSelectionGroup();
2354 * If the cut affects all sequences, warn, remove highlighted columns
2356 if (sg.getSize() == viewport.getAlignment().getHeight())
2358 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2359 .getAlignment().getWidth()) ? true : false;
2360 if (isEntireAlignWidth)
2362 int confirm = JOptionPane.showConfirmDialog(this,
2363 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2364 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2365 JOptionPane.OK_CANCEL_OPTION);
2367 if (confirm == JOptionPane.CANCEL_OPTION
2368 || confirm == JOptionPane.CLOSED_OPTION)
2373 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2374 sg.getEndRes() + 1);
2376 SequenceI[] cut = sg.getSequences()
2377 .toArray(new SequenceI[sg.getSize()]);
2379 addHistoryItem(new EditCommand(
2380 MessageManager.getString("label.cut_sequences"), Action.CUT,
2381 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2382 viewport.getAlignment()));
2384 viewport.setSelectionGroup(null);
2385 viewport.sendSelection();
2386 viewport.getAlignment().deleteGroup(sg);
2388 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2390 if (viewport.getAlignment().getHeight() < 1)
2394 this.setClosed(true);
2395 } catch (Exception ex)
2408 protected void deleteGroups_actionPerformed(ActionEvent e)
2410 if (avc.deleteGroups())
2412 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2413 alignPanel.updateAnnotation();
2414 alignPanel.paintAlignment(true);
2425 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2427 SequenceGroup sg = new SequenceGroup();
2429 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2431 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2434 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2435 viewport.setSelectionGroup(sg);
2436 viewport.sendSelection();
2437 // JAL-2034 - should delegate to
2438 // alignPanel to decide if overview needs
2440 alignPanel.paintAlignment(false);
2441 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2451 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2453 if (viewport.cursorMode)
2455 alignPanel.getSeqPanel().keyboardNo1 = null;
2456 alignPanel.getSeqPanel().keyboardNo2 = null;
2458 viewport.setSelectionGroup(null);
2459 viewport.getColumnSelection().clear();
2460 viewport.setSelectionGroup(null);
2461 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2462 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2463 // JAL-2034 - should delegate to
2464 // alignPanel to decide if overview needs
2466 alignPanel.paintAlignment(false);
2467 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2468 viewport.sendSelection();
2478 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2480 SequenceGroup sg = viewport.getSelectionGroup();
2484 selectAllSequenceMenuItem_actionPerformed(null);
2489 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2491 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2493 // JAL-2034 - should delegate to
2494 // alignPanel to decide if overview needs
2497 alignPanel.paintAlignment(true);
2498 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2499 viewport.sendSelection();
2503 public void invertColSel_actionPerformed(ActionEvent e)
2505 viewport.invertColumnSelection();
2506 alignPanel.paintAlignment(true);
2507 viewport.sendSelection();
2517 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2519 trimAlignment(true);
2529 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2531 trimAlignment(false);
2534 void trimAlignment(boolean trimLeft)
2536 ColumnSelection colSel = viewport.getColumnSelection();
2539 if (!colSel.isEmpty())
2543 column = colSel.getMin();
2547 column = colSel.getMax();
2551 if (viewport.getSelectionGroup() != null)
2553 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2554 viewport.getHiddenRepSequences());
2558 seqs = viewport.getAlignment().getSequencesArray();
2561 TrimRegionCommand trimRegion;
2564 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2565 column, viewport.getAlignment());
2566 viewport.setStartRes(0);
2570 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2571 column, viewport.getAlignment());
2574 statusBar.setText(MessageManager.formatMessage(
2575 "label.removed_columns",
2576 new String[] { Integer.valueOf(trimRegion.getSize())
2579 addHistoryItem(trimRegion);
2581 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2583 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2584 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2586 viewport.getAlignment().deleteGroup(sg);
2590 viewport.firePropertyChange("alignment", null, viewport
2591 .getAlignment().getSequences());
2602 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2604 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2607 if (viewport.getSelectionGroup() != null)
2609 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2610 viewport.getHiddenRepSequences());
2611 start = viewport.getSelectionGroup().getStartRes();
2612 end = viewport.getSelectionGroup().getEndRes();
2616 seqs = viewport.getAlignment().getSequencesArray();
2619 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2620 "Remove Gapped Columns", seqs, start, end,
2621 viewport.getAlignment());
2623 addHistoryItem(removeGapCols);
2625 statusBar.setText(MessageManager.formatMessage(
2626 "label.removed_empty_columns",
2627 new Object[] { Integer.valueOf(removeGapCols.getSize())
2630 // This is to maintain viewport position on first residue
2631 // of first sequence
2632 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2633 int startRes = seq.findPosition(viewport.startRes);
2634 // ShiftList shifts;
2635 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2636 // edit.alColumnChanges=shifts.getInverse();
2637 // if (viewport.hasHiddenColumns)
2638 // viewport.getColumnSelection().compensateForEdits(shifts);
2639 viewport.setStartRes(seq.findIndex(startRes) - 1);
2640 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2652 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2654 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2657 if (viewport.getSelectionGroup() != null)
2659 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2660 viewport.getHiddenRepSequences());
2661 start = viewport.getSelectionGroup().getStartRes();
2662 end = viewport.getSelectionGroup().getEndRes();
2666 seqs = viewport.getAlignment().getSequencesArray();
2669 // This is to maintain viewport position on first residue
2670 // of first sequence
2671 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2672 int startRes = seq.findPosition(viewport.startRes);
2674 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2675 viewport.getAlignment()));
2677 viewport.setStartRes(seq.findIndex(startRes) - 1);
2679 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2691 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2693 viewport.setPadGaps(padGapsMenuitem.isSelected());
2694 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2705 public void findMenuItem_actionPerformed(ActionEvent e)
2711 * Create a new view of the current alignment.
2714 public void newView_actionPerformed(ActionEvent e)
2716 newView(null, true);
2720 * Creates and shows a new view of the current alignment.
2723 * title of newly created view; if null, one will be generated
2724 * @param copyAnnotation
2725 * if true then duplicate all annnotation, groups and settings
2726 * @return new alignment panel, already displayed.
2728 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2731 * Create a new AlignmentPanel (with its own, new Viewport)
2733 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2735 if (!copyAnnotation)
2738 * remove all groups and annotation except for the automatic stuff
2740 newap.av.getAlignment().deleteAllGroups();
2741 newap.av.getAlignment().deleteAllAnnotations(false);
2744 newap.av.setGatherViewsHere(false);
2746 if (viewport.viewName == null)
2748 viewport.viewName = MessageManager
2749 .getString("label.view_name_original");
2753 * Views share the same edits undo and redo stacks
2755 newap.av.setHistoryList(viewport.getHistoryList());
2756 newap.av.setRedoList(viewport.getRedoList());
2759 * Views share the same mappings; need to deregister any new mappings
2760 * created by copyAlignPanel, and register the new reference to the shared
2763 newap.av.replaceMappings(viewport.getAlignment());
2765 newap.av.viewName = getNewViewName(viewTitle);
2767 addAlignmentPanel(newap, true);
2768 newap.alignmentChanged();
2770 if (alignPanels.size() == 2)
2772 viewport.setGatherViewsHere(true);
2774 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2779 * Make a new name for the view, ensuring it is unique within the current
2780 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2781 * these now use viewId. Unique view names are still desirable for usability.)
2786 protected String getNewViewName(String viewTitle)
2788 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2789 boolean addFirstIndex = false;
2790 if (viewTitle == null || viewTitle.trim().length() == 0)
2792 viewTitle = MessageManager.getString("action.view");
2793 addFirstIndex = true;
2797 index = 1;// we count from 1 if given a specific name
2799 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2801 List<Component> comps = PaintRefresher.components.get(viewport
2802 .getSequenceSetId());
2804 List<String> existingNames = getExistingViewNames(comps);
2806 while (existingNames.contains(newViewName))
2808 newViewName = viewTitle + " " + (++index);
2814 * Returns a list of distinct view names found in the given list of
2815 * components. View names are held on the viewport of an AlignmentPanel.
2820 protected List<String> getExistingViewNames(List<Component> comps)
2822 List<String> existingNames = new ArrayList<String>();
2823 for (Component comp : comps)
2825 if (comp instanceof AlignmentPanel)
2827 AlignmentPanel ap = (AlignmentPanel) comp;
2828 if (!existingNames.contains(ap.av.viewName))
2830 existingNames.add(ap.av.viewName);
2834 return existingNames;
2838 * Explode tabbed views into separate windows.
2841 public void expandViews_actionPerformed(ActionEvent e)
2843 Desktop.explodeViews(this);
2847 * Gather views in separate windows back into a tabbed presentation.
2850 public void gatherViews_actionPerformed(ActionEvent e)
2852 Desktop.instance.gatherViews(this);
2862 public void font_actionPerformed(ActionEvent e)
2864 new FontChooser(alignPanel);
2874 protected void seqLimit_actionPerformed(ActionEvent e)
2876 viewport.setShowJVSuffix(seqLimits.isSelected());
2878 alignPanel.getIdPanel().getIdCanvas()
2879 .setPreferredSize(alignPanel.calculateIdWidth());
2880 alignPanel.paintAlignment(true);
2884 public void idRightAlign_actionPerformed(ActionEvent e)
2886 viewport.setRightAlignIds(idRightAlign.isSelected());
2887 alignPanel.paintAlignment(true);
2891 public void centreColumnLabels_actionPerformed(ActionEvent e)
2893 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2894 alignPanel.paintAlignment(true);
2900 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2903 protected void followHighlight_actionPerformed()
2906 * Set the 'follow' flag on the Viewport (and scroll to position if now
2909 final boolean state = this.followHighlightMenuItem.getState();
2910 viewport.setFollowHighlight(state);
2913 alignPanel.scrollToPosition(
2914 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2925 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2927 viewport.setColourText(colourTextMenuItem.isSelected());
2928 alignPanel.paintAlignment(true);
2938 public void wrapMenuItem_actionPerformed(ActionEvent e)
2940 scaleAbove.setVisible(wrapMenuItem.isSelected());
2941 scaleLeft.setVisible(wrapMenuItem.isSelected());
2942 scaleRight.setVisible(wrapMenuItem.isSelected());
2943 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2944 alignPanel.updateLayout();
2948 public void showAllSeqs_actionPerformed(ActionEvent e)
2950 viewport.showAllHiddenSeqs();
2954 public void showAllColumns_actionPerformed(ActionEvent e)
2956 viewport.showAllHiddenColumns();
2958 viewport.sendSelection();
2962 public void hideSelSequences_actionPerformed(ActionEvent e)
2964 viewport.hideAllSelectedSeqs();
2965 // alignPanel.paintAlignment(true);
2969 * called by key handler and the hide all/show all menu items
2974 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2977 boolean hide = false;
2978 SequenceGroup sg = viewport.getSelectionGroup();
2979 if (!toggleSeqs && !toggleCols)
2981 // Hide everything by the current selection - this is a hack - we do the
2982 // invert and then hide
2983 // first check that there will be visible columns after the invert.
2984 if ((viewport.getColumnSelection() != null
2985 && viewport.getColumnSelection().getSelected() != null && viewport
2986 .getColumnSelection().getSelected().size() > 0)
2987 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2990 // now invert the sequence set, if required - empty selection implies
2991 // that no hiding is required.
2994 invertSequenceMenuItem_actionPerformed(null);
2995 sg = viewport.getSelectionGroup();
2999 viewport.expandColSelection(sg, true);
3000 // finally invert the column selection and get the new sequence
3002 invertColSel_actionPerformed(null);
3009 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3011 hideSelSequences_actionPerformed(null);
3014 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3017 showAllSeqs_actionPerformed(null);
3023 if (viewport.getColumnSelection().getSelected().size() > 0)
3025 hideSelColumns_actionPerformed(null);
3028 viewport.setSelectionGroup(sg);
3033 showAllColumns_actionPerformed(null);
3042 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3043 * event.ActionEvent)
3046 public void hideAllButSelection_actionPerformed(ActionEvent e)
3048 toggleHiddenRegions(false, false);
3049 viewport.sendSelection();
3056 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3060 public void hideAllSelection_actionPerformed(ActionEvent e)
3062 SequenceGroup sg = viewport.getSelectionGroup();
3063 viewport.expandColSelection(sg, false);
3064 viewport.hideAllSelectedSeqs();
3065 viewport.hideSelectedColumns();
3066 alignPanel.paintAlignment(true);
3067 viewport.sendSelection();
3074 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3078 public void showAllhidden_actionPerformed(ActionEvent e)
3080 viewport.showAllHiddenColumns();
3081 viewport.showAllHiddenSeqs();
3082 alignPanel.paintAlignment(true);
3083 viewport.sendSelection();
3087 public void hideSelColumns_actionPerformed(ActionEvent e)
3089 viewport.hideSelectedColumns();
3090 alignPanel.paintAlignment(true);
3091 viewport.sendSelection();
3095 public void hiddenMarkers_actionPerformed(ActionEvent e)
3097 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3108 protected void scaleAbove_actionPerformed(ActionEvent e)
3110 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3111 alignPanel.paintAlignment(true);
3121 protected void scaleLeft_actionPerformed(ActionEvent e)
3123 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3124 alignPanel.paintAlignment(true);
3134 protected void scaleRight_actionPerformed(ActionEvent e)
3136 viewport.setScaleRightWrapped(scaleRight.isSelected());
3137 alignPanel.paintAlignment(true);
3147 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3149 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3150 alignPanel.paintAlignment(true);
3160 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3162 viewport.setShowText(viewTextMenuItem.isSelected());
3163 alignPanel.paintAlignment(true);
3173 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3175 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3176 alignPanel.paintAlignment(true);
3179 public FeatureSettings featureSettings;
3182 public FeatureSettingsControllerI getFeatureSettingsUI()
3184 return featureSettings;
3188 public void featureSettings_actionPerformed(ActionEvent e)
3190 if (featureSettings != null)
3192 featureSettings.close();
3193 featureSettings = null;
3195 if (!showSeqFeatures.isSelected())
3197 // make sure features are actually displayed
3198 showSeqFeatures.setSelected(true);
3199 showSeqFeatures_actionPerformed(null);
3201 featureSettings = new FeatureSettings(this);
3205 * Set or clear 'Show Sequence Features'
3211 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3213 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3214 alignPanel.paintAlignment(true);
3215 if (alignPanel.getOverviewPanel() != null)
3217 alignPanel.getOverviewPanel().updateOverviewImage();
3222 * Set or clear 'Show Sequence Features'
3228 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3230 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3232 if (viewport.isShowSequenceFeaturesHeight())
3234 // ensure we're actually displaying features
3235 viewport.setShowSequenceFeatures(true);
3236 showSeqFeatures.setSelected(true);
3238 alignPanel.paintAlignment(true);
3239 if (alignPanel.getOverviewPanel() != null)
3241 alignPanel.getOverviewPanel().updateOverviewImage();
3246 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3247 * the annotations panel as a whole.
3249 * The options to show/hide all annotations should be enabled when the panel
3250 * is shown, and disabled when the panel is hidden.
3255 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3257 final boolean setVisible = annotationPanelMenuItem.isSelected();
3258 viewport.setShowAnnotation(setVisible);
3259 this.showAllSeqAnnotations.setEnabled(setVisible);
3260 this.hideAllSeqAnnotations.setEnabled(setVisible);
3261 this.showAllAlAnnotations.setEnabled(setVisible);
3262 this.hideAllAlAnnotations.setEnabled(setVisible);
3263 alignPanel.updateLayout();
3267 public void alignmentProperties()
3269 JEditorPane editPane = new JEditorPane("text/html", "");
3270 editPane.setEditable(false);
3271 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3273 editPane.setText(MessageManager.formatMessage("label.html_content",
3274 new Object[] { contents.toString() }));
3275 JInternalFrame frame = new JInternalFrame();
3276 frame.getContentPane().add(new JScrollPane(editPane));
3278 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3279 "label.alignment_properties", new Object[] { getTitle() }),
3290 public void overviewMenuItem_actionPerformed(ActionEvent e)
3292 if (alignPanel.overviewPanel != null)
3297 JInternalFrame frame = new JInternalFrame();
3298 OverviewPanel overview = new OverviewPanel(alignPanel);
3299 frame.setContentPane(overview);
3300 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3301 "label.overview_params", new Object[] { this.getTitle() }),
3302 frame.getWidth(), frame.getHeight());
3304 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3305 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3308 public void internalFrameClosed(
3309 javax.swing.event.InternalFrameEvent evt)
3311 alignPanel.setOverviewPanel(null);
3315 alignPanel.setOverviewPanel(overview);
3319 public void textColour_actionPerformed(ActionEvent e)
3321 new TextColourChooser().chooseColour(alignPanel, null);
3331 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3343 public void clustalColour_actionPerformed(ActionEvent e)
3345 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3346 viewport.getHiddenRepSequences()));
3356 public void zappoColour_actionPerformed(ActionEvent e)
3358 changeColour(new ZappoColourScheme());
3368 public void taylorColour_actionPerformed(ActionEvent e)
3370 changeColour(new TaylorColourScheme());
3380 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3382 changeColour(new HydrophobicColourScheme());
3392 public void helixColour_actionPerformed(ActionEvent e)
3394 changeColour(new HelixColourScheme());
3404 public void strandColour_actionPerformed(ActionEvent e)
3406 changeColour(new StrandColourScheme());
3416 public void turnColour_actionPerformed(ActionEvent e)
3418 changeColour(new TurnColourScheme());
3428 public void buriedColour_actionPerformed(ActionEvent e)
3430 changeColour(new BuriedColourScheme());
3440 public void nucleotideColour_actionPerformed(ActionEvent e)
3442 changeColour(new NucleotideColourScheme());
3446 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3448 changeColour(new PurinePyrimidineColourScheme());
3452 * public void covariationColour_actionPerformed(ActionEvent e) {
3454 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3458 public void annotationColour_actionPerformed(ActionEvent e)
3460 new AnnotationColourChooser(viewport, alignPanel);
3464 public void annotationColumn_actionPerformed(ActionEvent e)
3466 new AnnotationColumnChooser(viewport, alignPanel);
3470 public void rnahelicesColour_actionPerformed(ActionEvent e)
3472 new RNAHelicesColourChooser(viewport, alignPanel);
3482 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3484 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3494 public void changeColour(ColourSchemeI cs)
3496 // TODO: pull up to controller method
3500 // Make sure viewport is up to date w.r.t. any sliders
3501 if (viewport.getAbovePIDThreshold())
3503 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3505 viewport.setThreshold(threshold);
3508 if (viewport.getConservationSelected())
3510 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3513 if (cs instanceof TCoffeeColourScheme)
3515 tcoffeeColour.setEnabled(true);
3516 tcoffeeColour.setSelected(true);
3520 viewport.setGlobalColourScheme(cs);
3522 alignPanel.paintAlignment(true);
3532 protected void modifyPID_actionPerformed(ActionEvent e)
3534 if (viewport.getAbovePIDThreshold()
3535 && viewport.getGlobalColourScheme() != null)
3537 SliderPanel.setPIDSliderSource(alignPanel,
3538 viewport.getGlobalColourScheme(), "Background");
3539 SliderPanel.showPIDSlider();
3550 protected void modifyConservation_actionPerformed(ActionEvent e)
3552 if (viewport.getConservationSelected()
3553 && viewport.getGlobalColourScheme() != null)
3555 SliderPanel.setConservationSlider(alignPanel,
3556 viewport.getGlobalColourScheme(), "Background");
3557 SliderPanel.showConservationSlider();
3568 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3570 viewport.setConservationSelected(conservationMenuItem.isSelected());
3572 viewport.setAbovePIDThreshold(false);
3573 abovePIDThreshold.setSelected(false);
3575 changeColour(viewport.getGlobalColourScheme());
3577 modifyConservation_actionPerformed(null);
3587 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3589 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3591 conservationMenuItem.setSelected(false);
3592 viewport.setConservationSelected(false);
3594 changeColour(viewport.getGlobalColourScheme());
3596 modifyPID_actionPerformed(null);
3606 public void userDefinedColour_actionPerformed(ActionEvent e)
3608 if (e.getActionCommand().equals(
3609 MessageManager.getString("action.user_defined")))
3611 new UserDefinedColours(alignPanel, null);
3615 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3616 .getUserColourSchemes().get(e.getActionCommand());
3622 public void updateUserColourMenu()
3625 Component[] menuItems = colourMenu.getMenuComponents();
3626 int iSize = menuItems.length;
3627 for (int i = 0; i < iSize; i++)
3629 if (menuItems[i].getName() != null
3630 && menuItems[i].getName().equals("USER_DEFINED"))
3632 colourMenu.remove(menuItems[i]);
3636 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3638 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3639 .getUserColourSchemes().keys();
3641 while (userColours.hasMoreElements())
3643 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3644 userColours.nextElement().toString());
3645 radioItem.setName("USER_DEFINED");
3646 radioItem.addMouseListener(new MouseAdapter()
3649 public void mousePressed(MouseEvent evt)
3651 if (evt.isPopupTrigger())
3653 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3655 int option = JOptionPane.showInternalConfirmDialog(
3656 jalview.gui.Desktop.desktop,
3658 .getString("label.remove_from_default_list"),
3660 .getString("label.remove_user_defined_colour"),
3661 JOptionPane.YES_NO_OPTION);
3662 if (option == JOptionPane.YES_OPTION)
3664 jalview.gui.UserDefinedColours
3665 .removeColourFromDefaults(radioItem.getText());
3666 colourMenu.remove(radioItem);
3670 radioItem.addActionListener(new ActionListener()
3673 public void actionPerformed(ActionEvent evt)
3675 userDefinedColour_actionPerformed(evt);
3682 radioItem.addActionListener(new ActionListener()
3685 public void actionPerformed(ActionEvent evt)
3687 userDefinedColour_actionPerformed(evt);
3691 colourMenu.insert(radioItem, 15);
3692 colours.add(radioItem);
3704 public void PIDColour_actionPerformed(ActionEvent e)
3706 changeColour(new PIDColourScheme());
3716 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3718 changeColour(new Blosum62ColourScheme());
3728 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3730 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3731 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3732 .getAlignment().getSequenceAt(0), null);
3733 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3734 viewport.getAlignment()));
3735 alignPanel.paintAlignment(true);
3745 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3747 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3748 AlignmentSorter.sortByID(viewport.getAlignment());
3749 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3750 viewport.getAlignment()));
3751 alignPanel.paintAlignment(true);
3761 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3763 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3764 AlignmentSorter.sortByLength(viewport.getAlignment());
3765 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3766 viewport.getAlignment()));
3767 alignPanel.paintAlignment(true);
3777 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3779 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3780 AlignmentSorter.sortByGroup(viewport.getAlignment());
3781 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3782 viewport.getAlignment()));
3784 alignPanel.paintAlignment(true);
3794 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3796 new RedundancyPanel(alignPanel, this);
3806 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3808 if ((viewport.getSelectionGroup() == null)
3809 || (viewport.getSelectionGroup().getSize() < 2))
3811 JOptionPane.showInternalMessageDialog(this, MessageManager
3812 .getString("label.you_must_select_least_two_sequences"),
3813 MessageManager.getString("label.invalid_selection"),
3814 JOptionPane.WARNING_MESSAGE);
3818 JInternalFrame frame = new JInternalFrame();
3819 frame.setContentPane(new PairwiseAlignPanel(viewport));
3820 Desktop.addInternalFrame(frame,
3821 MessageManager.getString("action.pairwise_alignment"), 600,
3833 public void PCAMenuItem_actionPerformed(ActionEvent e)
3835 if (((viewport.getSelectionGroup() != null)
3836 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3837 .getSelectionGroup().getSize() > 0))
3838 || (viewport.getAlignment().getHeight() < 4))
3841 .showInternalMessageDialog(
3844 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3846 .getString("label.sequence_selection_insufficient"),
3847 JOptionPane.WARNING_MESSAGE);
3852 new PCAPanel(alignPanel);
3856 public void autoCalculate_actionPerformed(ActionEvent e)
3858 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3859 if (viewport.autoCalculateConsensus)
3861 viewport.firePropertyChange("alignment", null, viewport
3862 .getAlignment().getSequences());
3867 public void sortByTreeOption_actionPerformed(ActionEvent e)
3869 viewport.sortByTree = sortByTree.isSelected();
3873 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3875 viewport.followSelection = listenToViewSelections.isSelected();
3885 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3887 newTreePanel("AV", "PID", "Average distance tree using PID");
3897 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3899 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3909 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3911 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3921 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3923 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3936 void newTreePanel(String type, String pwType, String title)
3940 if (viewport.getSelectionGroup() != null
3941 && viewport.getSelectionGroup().getSize() > 0)
3943 if (viewport.getSelectionGroup().getSize() < 3)
3949 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3951 .getString("label.not_enough_sequences"),
3952 JOptionPane.WARNING_MESSAGE);
3956 SequenceGroup sg = viewport.getSelectionGroup();
3958 /* Decide if the selection is a column region */
3959 for (SequenceI _s : sg.getSequences())
3961 if (_s.getLength() < sg.getEndRes())
3967 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3969 .getString("label.sequences_selection_not_aligned"),
3970 JOptionPane.WARNING_MESSAGE);
3976 title = title + " on region";
3977 tp = new TreePanel(alignPanel, type, pwType);
3981 // are the visible sequences aligned?
3982 if (!viewport.getAlignment().isAligned(false))
3988 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3990 .getString("label.sequences_not_aligned"),
3991 JOptionPane.WARNING_MESSAGE);
3996 if (viewport.getAlignment().getHeight() < 2)
4001 tp = new TreePanel(alignPanel, type, pwType);
4006 if (viewport.viewName != null)
4008 title += viewport.viewName + " of ";
4011 title += this.title;
4013 Desktop.addInternalFrame(tp, title, 600, 500);
4024 public void addSortByOrderMenuItem(String title,
4025 final AlignmentOrder order)
4027 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4028 "action.by_title_param", new Object[] { title }));
4030 item.addActionListener(new java.awt.event.ActionListener()
4033 public void actionPerformed(ActionEvent e)
4035 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4037 // TODO: JBPNote - have to map order entries to curent SequenceI
4039 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4041 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4044 alignPanel.paintAlignment(true);
4050 * Add a new sort by annotation score menu item
4053 * the menu to add the option to
4055 * the label used to retrieve scores for each sequence on the
4058 public void addSortByAnnotScoreMenuItem(JMenu sort,
4059 final String scoreLabel)
4061 final JMenuItem item = new JMenuItem(scoreLabel);
4063 item.addActionListener(new java.awt.event.ActionListener()
4066 public void actionPerformed(ActionEvent e)
4068 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4069 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4070 viewport.getAlignment());// ,viewport.getSelectionGroup());
4071 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4072 viewport.getAlignment()));
4073 alignPanel.paintAlignment(true);
4079 * last hash for alignment's annotation array - used to minimise cost of
4082 protected int _annotationScoreVectorHash;
4085 * search the alignment and rebuild the sort by annotation score submenu the
4086 * last alignment annotation vector hash is stored to minimize cost of
4087 * rebuilding in subsequence calls.
4091 public void buildSortByAnnotationScoresMenu()
4093 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4098 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4100 sortByAnnotScore.removeAll();
4101 // almost certainly a quicker way to do this - but we keep it simple
4102 Hashtable scoreSorts = new Hashtable();
4103 AlignmentAnnotation aann[];
4104 for (SequenceI sqa : viewport.getAlignment().getSequences())
4106 aann = sqa.getAnnotation();
4107 for (int i = 0; aann != null && i < aann.length; i++)
4109 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4111 scoreSorts.put(aann[i].label, aann[i].label);
4115 Enumeration labels = scoreSorts.keys();
4116 while (labels.hasMoreElements())
4118 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4119 (String) labels.nextElement());
4121 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4124 _annotationScoreVectorHash = viewport.getAlignment()
4125 .getAlignmentAnnotation().hashCode();
4130 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4131 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4132 * call. Listeners are added to remove the menu item when the treePanel is
4133 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4137 * Displayed tree window.
4139 * SortBy menu item title.
4142 public void buildTreeMenu()
4144 calculateTree.removeAll();
4145 // build the calculate menu
4147 for (final String type : new String[] { "NJ", "AV" })
4149 String treecalcnm = MessageManager.getString("label.tree_calc_"
4150 + type.toLowerCase());
4151 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4153 JMenuItem tm = new JMenuItem();
4154 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4155 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4156 || sm.isProtein() == !viewport.getAlignment()
4159 String smn = MessageManager.getStringOrReturn(
4160 "label.score_model_", sm.getName());
4161 final String title = MessageManager.formatMessage(
4162 "label.treecalc_title", treecalcnm, smn);
4163 tm.setText(title);//
4164 tm.addActionListener(new java.awt.event.ActionListener()
4167 public void actionPerformed(ActionEvent e)
4169 newTreePanel(type, pwtype, title);
4172 calculateTree.add(tm);
4177 sortByTreeMenu.removeAll();
4179 List<Component> comps = PaintRefresher.components.get(viewport
4180 .getSequenceSetId());
4181 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4182 for (Component comp : comps)
4184 if (comp instanceof TreePanel)
4186 treePanels.add((TreePanel) comp);
4190 if (treePanels.size() < 1)
4192 sortByTreeMenu.setVisible(false);
4196 sortByTreeMenu.setVisible(true);
4198 for (final TreePanel tp : treePanels)
4200 final JMenuItem item = new JMenuItem(tp.getTitle());
4201 item.addActionListener(new java.awt.event.ActionListener()
4204 public void actionPerformed(ActionEvent e)
4206 tp.sortByTree_actionPerformed();
4207 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4212 sortByTreeMenu.add(item);
4216 public boolean sortBy(AlignmentOrder alorder, String undoname)
4218 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4219 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4220 if (undoname != null)
4222 addHistoryItem(new OrderCommand(undoname, oldOrder,
4223 viewport.getAlignment()));
4225 alignPanel.paintAlignment(true);
4230 * Work out whether the whole set of sequences or just the selected set will
4231 * be submitted for multiple alignment.
4234 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4236 // Now, check we have enough sequences
4237 AlignmentView msa = null;
4239 if ((viewport.getSelectionGroup() != null)
4240 && (viewport.getSelectionGroup().getSize() > 1))
4242 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4243 // some common interface!
4245 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4246 * SequenceI[sz = seqs.getSize(false)];
4248 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4249 * seqs.getSequenceAt(i); }
4251 msa = viewport.getAlignmentView(true);
4253 else if (viewport.getSelectionGroup() != null
4254 && viewport.getSelectionGroup().getSize() == 1)
4256 int option = JOptionPane.showConfirmDialog(this,
4257 MessageManager.getString("warn.oneseq_msainput_selection"),
4258 MessageManager.getString("label.invalid_selection"),
4259 JOptionPane.OK_CANCEL_OPTION);
4260 if (option == JOptionPane.OK_OPTION)
4262 msa = viewport.getAlignmentView(false);
4267 msa = viewport.getAlignmentView(false);
4273 * Decides what is submitted to a secondary structure prediction service: the
4274 * first sequence in the alignment, or in the current selection, or, if the
4275 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4276 * region or the whole alignment. (where the first sequence in the set is the
4277 * one that the prediction will be for).
4279 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4281 AlignmentView seqs = null;
4283 if ((viewport.getSelectionGroup() != null)
4284 && (viewport.getSelectionGroup().getSize() > 0))
4286 seqs = viewport.getAlignmentView(true);
4290 seqs = viewport.getAlignmentView(false);
4292 // limit sequences - JBPNote in future - could spawn multiple prediction
4294 // TODO: viewport.getAlignment().isAligned is a global state - the local
4295 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4296 if (!viewport.getAlignment().isAligned(false))
4298 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4299 // TODO: if seqs.getSequences().length>1 then should really have warned
4313 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4315 // Pick the tree file
4316 JalviewFileChooser chooser = new JalviewFileChooser(
4317 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4318 chooser.setFileView(new JalviewFileView());
4319 chooser.setDialogTitle(MessageManager
4320 .getString("label.select_newick_like_tree_file"));
4321 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4323 int value = chooser.showOpenDialog(null);
4325 if (value == JalviewFileChooser.APPROVE_OPTION)
4327 String choice = chooser.getSelectedFile().getPath();
4328 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4329 jalview.io.NewickFile fin = null;
4332 fin = new jalview.io.NewickFile(choice, "File");
4333 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4334 } catch (Exception ex)
4341 .getString("label.problem_reading_tree_file"),
4342 JOptionPane.WARNING_MESSAGE);
4343 ex.printStackTrace();
4345 if (fin != null && fin.hasWarningMessage())
4347 JOptionPane.showMessageDialog(Desktop.desktop, fin
4348 .getWarningMessage(), MessageManager
4349 .getString("label.possible_problem_with_tree_file"),
4350 JOptionPane.WARNING_MESSAGE);
4356 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4358 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4361 public TreePanel ShowNewickTree(NewickFile nf, String title)
4363 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4366 public TreePanel ShowNewickTree(NewickFile nf, String title,
4367 AlignmentView input)
4369 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4372 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4373 int h, int x, int y)
4375 return ShowNewickTree(nf, title, null, w, h, x, y);
4379 * Add a treeviewer for the tree extracted from a newick file object to the
4380 * current alignment view
4387 * Associated alignment input data (or null)
4396 * @return TreePanel handle
4398 public TreePanel ShowNewickTree(NewickFile nf, String title,
4399 AlignmentView input, int w, int h, int x, int y)
4401 TreePanel tp = null;
4407 if (nf.getTree() != null)
4409 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4415 tp.setLocation(x, y);
4418 Desktop.addInternalFrame(tp, title, w, h);
4420 } catch (Exception ex)
4422 ex.printStackTrace();
4428 private boolean buildingMenu = false;
4431 * Generates menu items and listener event actions for web service clients
4434 public void BuildWebServiceMenu()
4436 while (buildingMenu)
4440 System.err.println("Waiting for building menu to finish.");
4442 } catch (Exception e)
4446 final AlignFrame me = this;
4447 buildingMenu = true;
4448 new Thread(new Runnable()
4453 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4456 // System.err.println("Building ws menu again "
4457 // + Thread.currentThread());
4458 // TODO: add support for context dependent disabling of services based
4460 // alignment and current selection
4461 // TODO: add additional serviceHandle parameter to specify abstract
4463 // class independently of AbstractName
4464 // TODO: add in rediscovery GUI function to restart discoverer
4465 // TODO: group services by location as well as function and/or
4467 // object broker mechanism.
4468 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4469 final IProgressIndicator af = me;
4470 final JMenu msawsmenu = new JMenu("Alignment");
4471 final JMenu secstrmenu = new JMenu(
4472 "Secondary Structure Prediction");
4473 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4474 final JMenu analymenu = new JMenu("Analysis");
4475 final JMenu dismenu = new JMenu("Protein Disorder");
4476 // final JMenu msawsmenu = new
4477 // JMenu(MessageManager.getString("label.alignment"));
4478 // final JMenu secstrmenu = new
4479 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4480 // final JMenu seqsrchmenu = new
4481 // JMenu(MessageManager.getString("label.sequence_database_search"));
4482 // final JMenu analymenu = new
4483 // JMenu(MessageManager.getString("label.analysis"));
4484 // final JMenu dismenu = new
4485 // JMenu(MessageManager.getString("label.protein_disorder"));
4486 // JAL-940 - only show secondary structure prediction services from
4487 // the legacy server
4488 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4490 Discoverer.services != null && (Discoverer.services.size() > 0))
4492 // TODO: refactor to allow list of AbstractName/Handler bindings to
4494 // stored or retrieved from elsewhere
4495 // No MSAWS used any more:
4496 // Vector msaws = null; // (Vector)
4497 // Discoverer.services.get("MsaWS");
4498 Vector secstrpr = (Vector) Discoverer.services
4500 if (secstrpr != null)
4502 // Add any secondary structure prediction services
4503 for (int i = 0, j = secstrpr.size(); i < j; i++)
4505 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4507 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4508 .getServiceClient(sh);
4509 int p = secstrmenu.getItemCount();
4510 impl.attachWSMenuEntry(secstrmenu, me);
4511 int q = secstrmenu.getItemCount();
4512 for (int litm = p; litm < q; litm++)
4514 legacyItems.add(secstrmenu.getItem(litm));
4520 // Add all submenus in the order they should appear on the web
4522 wsmenu.add(msawsmenu);
4523 wsmenu.add(secstrmenu);
4524 wsmenu.add(dismenu);
4525 wsmenu.add(analymenu);
4526 // No search services yet
4527 // wsmenu.add(seqsrchmenu);
4529 javax.swing.SwingUtilities.invokeLater(new Runnable()
4536 webService.removeAll();
4537 // first, add discovered services onto the webservices menu
4538 if (wsmenu.size() > 0)
4540 for (int i = 0, j = wsmenu.size(); i < j; i++)
4542 webService.add(wsmenu.get(i));
4547 webService.add(me.webServiceNoServices);
4549 // TODO: move into separate menu builder class.
4550 boolean new_sspred = false;
4551 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4553 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4554 if (jws2servs != null)
4556 if (jws2servs.hasServices())
4558 jws2servs.attachWSMenuEntry(webService, me);
4559 for (Jws2Instance sv : jws2servs.getServices())
4561 if (sv.description.toLowerCase().contains("jpred"))
4563 for (JMenuItem jmi : legacyItems)
4565 jmi.setVisible(false);
4571 if (jws2servs.isRunning())
4573 JMenuItem tm = new JMenuItem(
4574 "Still discovering JABA Services");
4575 tm.setEnabled(false);
4580 build_urlServiceMenu(me.webService);
4581 build_fetchdbmenu(webService);
4582 for (JMenu item : wsmenu)
4584 if (item.getItemCount() == 0)
4586 item.setEnabled(false);
4590 item.setEnabled(true);
4593 } catch (Exception e)
4596 .debug("Exception during web service menu building process.",
4601 } catch (Exception e)
4604 buildingMenu = false;
4611 * construct any groupURL type service menu entries.
4615 private void build_urlServiceMenu(JMenu webService)
4617 // TODO: remove this code when 2.7 is released
4618 // DEBUG - alignmentView
4620 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4621 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4623 * @Override public void actionPerformed(ActionEvent e) {
4624 * jalview.datamodel.AlignmentView
4625 * .testSelectionViews(af.viewport.getAlignment(),
4626 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4628 * }); webService.add(testAlView);
4630 // TODO: refactor to RestClient discoverer and merge menu entries for
4631 // rest-style services with other types of analysis/calculation service
4632 // SHmmr test client - still being implemented.
4633 // DEBUG - alignmentView
4635 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4638 client.attachWSMenuEntry(
4639 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4645 * Searches the alignment sequences for xRefs and builds the Show
4646 * Cross-References menu (formerly called Show Products), with database
4647 * sources for which cross-references are found (protein sources for a
4648 * nucleotide alignment and vice versa)
4650 * @return true if Show Cross-references menu should be enabled
4652 public boolean canShowProducts()
4654 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4655 AlignmentI dataset = viewport.getAlignment().getDataset();
4656 boolean showp = false;
4659 showProducts.removeAll();
4660 final boolean dna = viewport.getAlignment().isNucleotide();
4661 List<String> ptypes = (seqs == null || seqs.length == 0) ? null
4662 : new CrossRef(seqs, dataset)
4663 .findXrefSourcesForSequences(dna);
4665 for (final String source : ptypes)
4668 final AlignFrame af = this;
4669 JMenuItem xtype = new JMenuItem(source);
4670 xtype.addActionListener(new ActionListener()
4673 public void actionPerformed(ActionEvent e)
4675 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4678 showProducts.add(xtype);
4680 showProducts.setVisible(showp);
4681 showProducts.setEnabled(showp);
4682 } catch (Exception e)
4685 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4693 * Finds and displays cross-references for the selected sequences (protein
4694 * products for nucleotide sequences, dna coding sequences for peptides).
4697 * the sequences to show cross-references for
4699 * true if from a nucleotide alignment (so showing proteins)
4701 * the database to show cross-references for
4703 protected void showProductsFor(final SequenceI[] sel,
4704 final boolean _odna, final String source)
4706 Runnable foo = new Runnable()
4712 final long sttime = System.currentTimeMillis();
4713 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4714 "status.searching_for_sequences_from",
4715 new Object[] { source }), sttime);
4718 AlignmentI alignment = AlignFrame.this.getViewport()
4720 AlignmentI dataset = alignment.getDataset() == null ? alignment
4721 : alignment.getDataset();
4722 boolean dna = alignment.isNucleotide();
4726 .println("Conflict: showProducts for alignment originally "
4728 + (_odna ? "DNA" : "Protein")
4729 + " now searching for "
4730 + (dna ? "DNA" : "Protein") + " Context.");
4732 AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences(
4739 * get display scheme (if any) to apply to features
4741 FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
4742 .getFeatureColourScheme(source);
4744 AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
4748 xrefsAlignment = AlignmentUtils.makeCdsAlignment(
4749 xrefsAlignment.getSequencesArray(), dataset, sel);
4750 xrefsAlignment.alignAs(alignment);
4754 * If we are opening a splitframe, make a copy of this alignment (sharing the same dataset
4755 * sequences). If we are DNA, drop introns and update mappings
4757 AlignmentI copyAlignment = null;
4759 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4761 boolean copyAlignmentIsAligned = false;
4764 copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
4765 xrefsAlignment.getSequencesArray());
4766 if (copyAlignment.getHeight() == 0)
4768 System.err.println("Failed to make CDS alignment");
4772 * pending getting Embl transcripts to 'align',
4773 * we are only doing this for Ensembl
4775 // TODO proper criteria for 'can align as cdna'
4776 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
4777 || AlignmentUtils.looksLikeEnsembl(alignment))
4779 copyAlignment.alignAs(alignment);
4780 copyAlignmentIsAligned = true;
4785 copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
4786 xrefs.getSequencesArray(), dataset);
4788 copyAlignment.setGapCharacter(AlignFrame.this.viewport
4789 .getGapCharacter());
4791 StructureSelectionManager ssm = StructureSelectionManager
4792 .getStructureSelectionManager(Desktop.instance);
4795 * register any new mappings for sequence mouseover etc
4796 * (will not duplicate any previously registered mappings)
4798 ssm.registerMappings(dataset.getCodonFrames());
4800 if (copyAlignment.getHeight() <= 0)
4802 System.err.println("No Sequences generated for xRef type "
4807 * align protein to dna
4809 if (dna && copyAlignmentIsAligned)
4811 xrefsAlignment.alignAs(copyAlignment);
4816 * align cdna to protein - currently only if
4817 * fetching and aligning Ensembl transcripts!
4819 // TODO: generalise for other sources of locus/transcript/cds data
4820 if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4822 copyAlignment.alignAs(xrefsAlignment);
4827 * build AlignFrame(s) according to available alignment data
4829 AlignFrame newFrame = new AlignFrame(xrefsAlignment,
4830 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4831 if (Cache.getDefault("HIDE_INTRONS", true))
4833 newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
4835 String newtitle = String.format("%s %s %s", MessageManager
4836 .getString(dna ? "label.proteins" : "label.nucleotides"),
4837 MessageManager.getString("label.for"), getTitle());
4838 newFrame.setTitle(newtitle);
4840 if (copyAlignment == null)
4843 * split frame display is turned off in preferences file
4845 Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4847 return; // via finally clause
4849 AlignFrame copyThis = new AlignFrame(copyAlignment,
4850 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4851 copyThis.setTitle(AlignFrame.this.getTitle());
4853 boolean showSequenceFeatures = viewport.isShowSequenceFeatures();
4854 newFrame.setShowSeqFeatures(showSequenceFeatures);
4855 copyThis.setShowSeqFeatures(showSequenceFeatures);
4856 FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4857 .getFeatureRenderer();
4860 * copy feature rendering settings to split frame
4862 newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
4863 .transferSettings(myFeatureStyling);
4864 copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
4865 .transferSettings(myFeatureStyling);
4868 * apply 'database source' feature configuration
4871 // TODO is this the feature colouring for the original
4872 // alignment or the fetched xrefs? either could be Ensembl
4873 newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
4874 copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
4876 SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4877 dna ? newFrame : copyThis);
4878 newFrame.setVisible(true);
4879 copyThis.setVisible(true);
4880 String linkedTitle = MessageManager
4881 .getString("label.linked_view_title");
4882 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4884 } catch (OutOfMemoryError e)
4886 new OOMWarning("whilst fetching crossreferences", e);
4887 } catch (Throwable e)
4889 Cache.log.error("Error when finding crossreferences", e);
4892 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4893 "status.finished_searching_for_sequences_from",
4894 new Object[] { source }), sttime);
4899 * Makes an alignment containing the given sequences, and adds them to the
4900 * given dataset, which is also set as the dataset for the new alignment
4902 * TODO: refactor to DatasetI method
4908 protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
4911 SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4912 for (int s = 0; s < sprods.length; s++)
4914 sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4915 if (dataset.getSequences() == null
4916 || !dataset.getSequences().contains(
4917 sprods[s].getDatasetSequence()))
4919 dataset.addSequence(sprods[s].getDatasetSequence());
4921 sprods[s].updatePDBIds();
4923 Alignment al = new Alignment(sprods);
4924 al.setDataset(dataset);
4929 Thread frunner = new Thread(foo);
4934 * Construct and display a new frame containing the translation of this
4935 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4938 public void showTranslation_actionPerformed(ActionEvent e)
4940 AlignmentI al = null;
4943 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4945 al = dna.translateCdna();
4946 } catch (Exception ex)
4948 jalview.bin.Cache.log.error(
4949 "Exception during translation. Please report this !", ex);
4950 final String msg = MessageManager
4951 .getString("label.error_when_translating_sequences_submit_bug_report");
4952 final String errorTitle = MessageManager
4953 .getString("label.implementation_error")
4954 + MessageManager.getString("label.translation_failed");
4955 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4956 JOptionPane.ERROR_MESSAGE);
4959 if (al == null || al.getHeight() == 0)
4961 final String msg = MessageManager
4962 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4963 final String errorTitle = MessageManager
4964 .getString("label.translation_failed");
4965 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4966 JOptionPane.WARNING_MESSAGE);
4970 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4971 af.setFileFormat(this.currentFileFormat);
4972 final String newTitle = MessageManager.formatMessage(
4973 "label.translation_of_params",
4974 new Object[] { this.getTitle() });
4975 af.setTitle(newTitle);
4976 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4978 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4979 viewport.openSplitFrame(af, new Alignment(seqs));
4983 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4990 * Set the file format
4994 public void setFileFormat(String fileFormat)
4996 this.currentFileFormat = fileFormat;
5000 * Try to load a features file onto the alignment.
5003 * contents or path to retrieve file
5005 * access mode of file (see jalview.io.AlignFile)
5006 * @return true if features file was parsed correctly.
5008 public boolean parseFeaturesFile(String file, String type)
5010 return avc.parseFeaturesFile(file, type,
5011 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5016 public void refreshFeatureUI(boolean enableIfNecessary)
5018 // note - currently this is only still here rather than in the controller
5019 // because of the featureSettings hard reference that is yet to be
5021 if (enableIfNecessary)
5023 viewport.setShowSequenceFeatures(true);
5024 showSeqFeatures.setSelected(true);
5030 public void dragEnter(DropTargetDragEvent evt)
5035 public void dragExit(DropTargetEvent evt)
5040 public void dragOver(DropTargetDragEvent evt)
5045 public void dropActionChanged(DropTargetDragEvent evt)
5050 public void drop(DropTargetDropEvent evt)
5052 Transferable t = evt.getTransferable();
5053 java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
5057 Desktop.transferFromDropTarget(files, protocols, evt, t);
5058 } catch (Exception e)
5060 e.printStackTrace();
5066 // check to see if any of these files have names matching sequences in
5068 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5069 .getAlignment().getSequencesArray());
5071 * Object[] { String,SequenceI}
5073 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5074 ArrayList<String> filesnotmatched = new ArrayList<String>();
5075 for (int i = 0; i < files.size(); i++)
5077 String file = files.get(i).toString();
5079 String protocol = FormatAdapter.checkProtocol(file);
5080 if (protocol == jalview.io.FormatAdapter.FILE)
5082 File fl = new File(file);
5083 pdbfn = fl.getName();
5085 else if (protocol == jalview.io.FormatAdapter.URL)
5087 URL url = new URL(file);
5088 pdbfn = url.getFile();
5090 if (pdbfn.length() > 0)
5092 // attempt to find a match in the alignment
5093 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5094 int l = 0, c = pdbfn.indexOf(".");
5095 while (mtch == null && c != -1)
5100 } while ((c = pdbfn.indexOf(".", l)) > l);
5103 pdbfn = pdbfn.substring(0, l);
5105 mtch = idm.findAllIdMatches(pdbfn);
5112 type = new IdentifyFile().identify(file, protocol);
5113 } catch (Exception ex)
5119 if (type.equalsIgnoreCase("PDB"))
5121 filesmatched.add(new Object[] { file, protocol, mtch });
5126 // File wasn't named like one of the sequences or wasn't a PDB file.
5127 filesnotmatched.add(file);
5131 if (filesmatched.size() > 0)
5133 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5139 "label.automatically_associate_pdb_files_with_sequences_same_name",
5140 new Object[] { Integer
5146 .getString("label.automatically_associate_pdb_files_by_name"),
5147 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5150 for (Object[] fm : filesmatched)
5152 // try and associate
5153 // TODO: may want to set a standard ID naming formalism for
5154 // associating PDB files which have no IDs.
5155 for (SequenceI toassoc : (SequenceI[]) fm[2])
5157 PDBEntry pe = new AssociatePdbFileWithSeq()
5158 .associatePdbWithSeq((String) fm[0],
5159 (String) fm[1], toassoc, false,
5163 System.err.println("Associated file : "
5164 + ((String) fm[0]) + " with "
5165 + toassoc.getDisplayId(true));
5169 alignPanel.paintAlignment(true);
5173 if (filesnotmatched.size() > 0)
5176 && (Cache.getDefault(
5177 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5183 "label.ignore_unmatched_dropped_files_info",
5184 new Object[] { Integer
5191 .getString("label.ignore_unmatched_dropped_files"),
5192 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5196 for (String fn : filesnotmatched)
5198 loadJalviewDataFile(fn, null, null, null);
5202 } catch (Exception ex)
5204 ex.printStackTrace();
5210 * Attempt to load a "dropped" file or URL string: First by testing whether
5211 * it's an Annotation file, then a JNet file, and finally a features file. If
5212 * all are false then the user may have dropped an alignment file onto this
5216 * either a filename or a URL string.
5218 public void loadJalviewDataFile(String file, String protocol,
5219 String format, SequenceI assocSeq)
5223 if (protocol == null)
5225 protocol = FormatAdapter.checkProtocol(file);
5227 // if the file isn't identified, or not positively identified as some
5228 // other filetype (PFAM is default unidentified alignment file type) then
5229 // try to parse as annotation.
5230 boolean isAnnotation = (format == null || format
5231 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5232 .annotateAlignmentView(viewport, file, protocol) : false;
5236 // first see if its a T-COFFEE score file
5237 TCoffeeScoreFile tcf = null;
5240 tcf = new TCoffeeScoreFile(file, protocol);
5243 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5245 tcoffeeColour.setEnabled(true);
5246 tcoffeeColour.setSelected(true);
5247 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5248 isAnnotation = true;
5250 .setText(MessageManager
5251 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5255 // some problem - if no warning its probable that the ID matching
5256 // process didn't work
5260 tcf.getWarningMessage() == null ? MessageManager
5261 .getString("label.check_file_matches_sequence_ids_alignment")
5262 : tcf.getWarningMessage(),
5264 .getString("label.problem_reading_tcoffee_score_file"),
5265 JOptionPane.WARNING_MESSAGE);
5272 } catch (Exception x)
5275 .debug("Exception when processing data source as T-COFFEE score file",
5281 // try to see if its a JNet 'concise' style annotation file *before*
5283 // try to parse it as a features file
5286 format = new IdentifyFile().identify(file, protocol);
5288 if (format.equalsIgnoreCase("JnetFile"))
5290 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5292 new JnetAnnotationMaker();
5293 JnetAnnotationMaker.add_annotation(predictions,
5294 viewport.getAlignment(), 0, false);
5295 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5296 viewport.getAlignment().setSeqrep(repseq);
5297 ColumnSelection cs = new ColumnSelection();
5298 cs.hideInsertionsFor(repseq);
5299 viewport.setColumnSelection(cs);
5300 isAnnotation = true;
5302 else if (IdentifyFile.FeaturesFile.equals(format))
5304 if (parseFeaturesFile(file, protocol))
5306 alignPanel.paintAlignment(true);
5311 new FileLoader().LoadFile(viewport, file, protocol, format);
5318 alignPanel.adjustAnnotationHeight();
5319 viewport.updateSequenceIdColours();
5320 buildSortByAnnotationScoresMenu();
5321 alignPanel.paintAlignment(true);
5323 } catch (Exception ex)
5325 ex.printStackTrace();
5326 } catch (OutOfMemoryError oom)
5331 } catch (Exception x)
5336 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5337 : "using " + protocol + " from " + file)
5339 + (format != null ? "(parsing as '" + format
5340 + "' file)" : ""), oom, Desktop.desktop);
5345 * Method invoked by the ChangeListener on the tabbed pane, in other words
5346 * when a different tabbed pane is selected by the user or programmatically.
5349 public void tabSelectionChanged(int index)
5353 alignPanel = alignPanels.get(index);
5354 viewport = alignPanel.av;
5355 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5356 setMenusFromViewport(viewport);
5360 * If there is a frame linked to this one in a SplitPane, switch it to the
5361 * same view tab index. No infinite recursion of calls should happen, since
5362 * tabSelectionChanged() should not get invoked on setting the selected
5363 * index to an unchanged value. Guard against setting an invalid index
5364 * before the new view peer tab has been created.
5366 final AlignViewportI peer = viewport.getCodingComplement();
5369 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5370 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5372 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5378 * On right mouse click on view tab, prompt for and set new view name.
5381 public void tabbedPane_mousePressed(MouseEvent e)
5383 if (e.isPopupTrigger())
5385 String msg = MessageManager.getString("label.enter_view_name");
5386 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5387 JOptionPane.QUESTION_MESSAGE);
5391 viewport.viewName = reply;
5392 // TODO warn if reply is in getExistingViewNames()?
5393 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5398 public AlignViewport getCurrentView()
5404 * Open the dialog for regex description parsing.
5407 protected void extractScores_actionPerformed(ActionEvent e)
5409 ParseProperties pp = new jalview.analysis.ParseProperties(
5410 viewport.getAlignment());
5411 // TODO: verify regex and introduce GUI dialog for version 2.5
5412 // if (pp.getScoresFromDescription("col", "score column ",
5413 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5415 if (pp.getScoresFromDescription("description column",
5416 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5418 buildSortByAnnotationScoresMenu();
5426 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5430 protected void showDbRefs_actionPerformed(ActionEvent e)
5432 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5438 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5442 protected void showNpFeats_actionPerformed(ActionEvent e)
5444 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5448 * find the viewport amongst the tabs in this alignment frame and close that
5453 public boolean closeView(AlignViewportI av)
5457 this.closeMenuItem_actionPerformed(false);
5460 Component[] comp = tabbedPane.getComponents();
5461 for (int i = 0; comp != null && i < comp.length; i++)
5463 if (comp[i] instanceof AlignmentPanel)
5465 if (((AlignmentPanel) comp[i]).av == av)
5468 closeView((AlignmentPanel) comp[i]);
5476 protected void build_fetchdbmenu(JMenu webService)
5478 // Temporary hack - DBRef Fetcher always top level ws entry.
5479 // TODO We probably want to store a sequence database checklist in
5480 // preferences and have checkboxes.. rather than individual sources selected
5482 final JMenu rfetch = new JMenu(
5483 MessageManager.getString("action.fetch_db_references"));
5484 rfetch.setToolTipText(MessageManager
5485 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5486 webService.add(rfetch);
5488 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5489 MessageManager.getString("option.trim_retrieved_seqs"));
5490 trimrs.setToolTipText(MessageManager
5491 .getString("label.trim_retrieved_sequences"));
5492 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5493 trimrs.addActionListener(new ActionListener()
5496 public void actionPerformed(ActionEvent e)
5498 trimrs.setSelected(trimrs.isSelected());
5499 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5500 Boolean.valueOf(trimrs.isSelected()).toString());
5504 JMenuItem fetchr = new JMenuItem(
5505 MessageManager.getString("label.standard_databases"));
5506 fetchr.setToolTipText(MessageManager
5507 .getString("label.fetch_embl_uniprot"));
5508 fetchr.addActionListener(new ActionListener()
5512 public void actionPerformed(ActionEvent e)
5514 new Thread(new Runnable()
5519 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5520 .getAlignment().isNucleotide();
5521 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5522 .getSequenceSelection(), alignPanel.alignFrame, null,
5523 alignPanel.alignFrame.featureSettings, isNucleotide);
5524 dbRefFetcher.addListener(new FetchFinishedListenerI()
5527 public void finished()
5529 AlignFrame.this.setMenusForViewport();
5532 dbRefFetcher.fetchDBRefs(false);
5540 final AlignFrame me = this;
5541 new Thread(new Runnable()
5546 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5547 .getSequenceFetcherSingleton(me);
5548 javax.swing.SwingUtilities.invokeLater(new Runnable()
5553 String[] dbclasses = sf.getOrderedSupportedSources();
5554 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5555 // jalview.util.QuickSort.sort(otherdb, otherdb);
5556 List<DbSourceProxy> otherdb;
5557 JMenu dfetch = new JMenu();
5558 JMenu ifetch = new JMenu();
5559 JMenuItem fetchr = null;
5560 int comp = 0, icomp = 0, mcomp = 15;
5561 String mname = null;
5563 for (String dbclass : dbclasses)
5565 otherdb = sf.getSourceProxy(dbclass);
5566 // add a single entry for this class, or submenu allowing 'fetch
5568 if (otherdb == null || otherdb.size() < 1)
5572 // List<DbSourceProxy> dbs=otherdb;
5573 // otherdb=new ArrayList<DbSourceProxy>();
5574 // for (DbSourceProxy db:dbs)
5576 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5580 mname = "From " + dbclass;
5582 if (otherdb.size() == 1)
5584 final DbSourceProxy[] dassource = otherdb
5585 .toArray(new DbSourceProxy[0]);
5586 DbSourceProxy src = otherdb.get(0);
5587 fetchr = new JMenuItem(src.getDbSource());
5588 fetchr.addActionListener(new ActionListener()
5592 public void actionPerformed(ActionEvent e)
5594 new Thread(new Runnable()
5600 boolean isNucleotide = alignPanel.alignFrame
5601 .getViewport().getAlignment()
5603 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5604 alignPanel.av.getSequenceSelection(),
5605 alignPanel.alignFrame, dassource,
5606 alignPanel.alignFrame.featureSettings,
5609 .addListener(new FetchFinishedListenerI()
5612 public void finished()
5614 AlignFrame.this.setMenusForViewport();
5617 dbRefFetcher.fetchDBRefs(false);
5623 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5624 MessageManager.formatMessage(
5625 "label.fetch_retrieve_from",
5626 new Object[] { src.getDbName() })));
5632 final DbSourceProxy[] dassource = otherdb
5633 .toArray(new DbSourceProxy[0]);
5635 DbSourceProxy src = otherdb.get(0);
5636 fetchr = new JMenuItem(MessageManager.formatMessage(
5637 "label.fetch_all_param",
5638 new Object[] { src.getDbSource() }));
5639 fetchr.addActionListener(new ActionListener()
5642 public void actionPerformed(ActionEvent e)
5644 new Thread(new Runnable()
5650 boolean isNucleotide = alignPanel.alignFrame
5651 .getViewport().getAlignment()
5653 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5654 alignPanel.av.getSequenceSelection(),
5655 alignPanel.alignFrame, dassource,
5656 alignPanel.alignFrame.featureSettings,
5659 .addListener(new FetchFinishedListenerI()
5662 public void finished()
5664 AlignFrame.this.setMenusForViewport();
5667 dbRefFetcher.fetchDBRefs(false);
5673 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5674 MessageManager.formatMessage(
5675 "label.fetch_retrieve_from_all_sources",
5677 Integer.valueOf(otherdb.size())
5678 .toString(), src.getDbSource(),
5679 src.getDbName() })));
5682 // and then build the rest of the individual menus
5683 ifetch = new JMenu(MessageManager.formatMessage(
5684 "label.source_from_db_source",
5685 new Object[] { src.getDbSource() }));
5687 String imname = null;
5689 for (DbSourceProxy sproxy : otherdb)
5691 String dbname = sproxy.getDbName();
5692 String sname = dbname.length() > 5 ? dbname.substring(0,
5693 5) + "..." : dbname;
5694 String msname = dbname.length() > 10 ? dbname.substring(
5695 0, 10) + "..." : dbname;
5698 imname = MessageManager.formatMessage(
5699 "label.from_msname", new Object[] { sname });
5701 fetchr = new JMenuItem(msname);
5702 final DbSourceProxy[] dassrc = { sproxy };
5703 fetchr.addActionListener(new ActionListener()
5707 public void actionPerformed(ActionEvent e)
5709 new Thread(new Runnable()
5715 boolean isNucleotide = alignPanel.alignFrame
5716 .getViewport().getAlignment()
5718 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5719 alignPanel.av.getSequenceSelection(),
5720 alignPanel.alignFrame, dassrc,
5721 alignPanel.alignFrame.featureSettings,
5724 .addListener(new FetchFinishedListenerI()
5727 public void finished()
5729 AlignFrame.this.setMenusForViewport();
5732 dbRefFetcher.fetchDBRefs(false);
5738 fetchr.setToolTipText("<html>"
5739 + MessageManager.formatMessage(
5740 "label.fetch_retrieve_from", new Object[]
5744 if (++icomp >= mcomp || i == (otherdb.size()))
5746 ifetch.setText(MessageManager.formatMessage(
5747 "label.source_to_target", imname, sname));
5749 ifetch = new JMenu();
5757 if (comp >= mcomp || dbi >= (dbclasses.length))
5759 dfetch.setText(MessageManager.formatMessage(
5760 "label.source_to_target", mname, dbclass));
5762 dfetch = new JMenu();
5775 * Left justify the whole alignment.
5778 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5780 AlignmentI al = viewport.getAlignment();
5782 viewport.firePropertyChange("alignment", null, al);
5786 * Right justify the whole alignment.
5789 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5791 AlignmentI al = viewport.getAlignment();
5793 viewport.firePropertyChange("alignment", null, al);
5797 public void setShowSeqFeatures(boolean b)
5799 showSeqFeatures.setSelected(b);
5800 viewport.setShowSequenceFeatures(b);
5807 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5808 * awt.event.ActionEvent)
5811 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5813 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5814 alignPanel.paintAlignment(true);
5821 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5825 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5827 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5828 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5836 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5837 * .event.ActionEvent)
5840 protected void showGroupConservation_actionPerformed(ActionEvent e)
5842 viewport.setShowGroupConservation(showGroupConservation.getState());
5843 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5850 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5851 * .event.ActionEvent)
5854 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5856 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5857 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5864 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5865 * .event.ActionEvent)
5868 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5870 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5871 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5875 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5877 showSequenceLogo.setState(true);
5878 viewport.setShowSequenceLogo(true);
5879 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5880 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5884 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5886 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5893 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5894 * .event.ActionEvent)
5897 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5899 if (avc.makeGroupsFromSelection())
5901 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5902 alignPanel.updateAnnotation();
5903 alignPanel.paintAlignment(true);
5907 public void clearAlignmentSeqRep()
5909 // TODO refactor alignmentseqrep to controller
5910 if (viewport.getAlignment().hasSeqrep())
5912 viewport.getAlignment().setSeqrep(null);
5913 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5914 alignPanel.updateAnnotation();
5915 alignPanel.paintAlignment(true);
5920 protected void createGroup_actionPerformed(ActionEvent e)
5922 if (avc.createGroup())
5924 alignPanel.alignmentChanged();
5929 protected void unGroup_actionPerformed(ActionEvent e)
5933 alignPanel.alignmentChanged();
5938 * make the given alignmentPanel the currently selected tab
5940 * @param alignmentPanel
5942 public void setDisplayedView(AlignmentPanel alignmentPanel)
5944 if (!viewport.getSequenceSetId().equals(
5945 alignmentPanel.av.getSequenceSetId()))
5949 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5951 if (tabbedPane != null
5952 && tabbedPane.getTabCount() > 0
5953 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5954 .getSelectedIndex())
5956 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5961 * Action on selection of menu options to Show or Hide annotations.
5964 * @param forSequences
5965 * update sequence-related annotations
5966 * @param forAlignment
5967 * update non-sequence-related annotations
5970 protected void setAnnotationsVisibility(boolean visible,
5971 boolean forSequences, boolean forAlignment)
5973 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5974 .getAlignmentAnnotation();
5979 for (AlignmentAnnotation aa : anns)
5982 * don't display non-positional annotations on an alignment
5984 if (aa.annotations == null)
5988 boolean apply = (aa.sequenceRef == null && forAlignment)
5989 || (aa.sequenceRef != null && forSequences);
5992 aa.visible = visible;
5995 alignPanel.validateAnnotationDimensions(true);
5996 alignPanel.alignmentChanged();
6000 * Store selected annotation sort order for the view and repaint.
6003 protected void sortAnnotations_actionPerformed()
6005 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6007 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6008 alignPanel.paintAlignment(true);
6013 * @return alignment panels in this alignment frame
6015 public List<? extends AlignmentViewPanel> getAlignPanels()
6017 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6021 * Open a new alignment window, with the cDNA associated with this (protein)
6022 * alignment, aligned as is the protein.
6024 protected void viewAsCdna_actionPerformed()
6026 // TODO no longer a menu action - refactor as required
6027 final AlignmentI alignment = getViewport().getAlignment();
6028 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6029 if (mappings == null)
6033 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6034 for (SequenceI aaSeq : alignment.getSequences())
6036 for (AlignedCodonFrame acf : mappings)
6038 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6042 * There is a cDNA mapping for this protein sequence - add to new
6043 * alignment. It will share the same dataset sequence as other mapped
6044 * cDNA (no new mappings need to be created).
6046 final Sequence newSeq = new Sequence(dnaSeq);
6047 newSeq.setDatasetSequence(dnaSeq);
6048 cdnaSeqs.add(newSeq);
6052 if (cdnaSeqs.size() == 0)
6054 // show a warning dialog no mapped cDNA
6057 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6059 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6060 AlignFrame.DEFAULT_HEIGHT);
6061 cdna.alignAs(alignment);
6062 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6064 Desktop.addInternalFrame(alignFrame, newtitle,
6065 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6069 * Set visibility of dna/protein complement view (available when shown in a
6075 protected void showComplement_actionPerformed(boolean show)
6077 SplitContainerI sf = getSplitViewContainer();
6080 sf.setComplementVisible(this, show);
6085 * Generate the reverse (optionally complemented) of the selected sequences,
6086 * and add them to the alignment
6089 protected void showReverse_actionPerformed(boolean complement)
6091 AlignmentI al = null;
6094 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6095 al = dna.reverseCdna(complement);
6096 viewport.addAlignment(al, "");
6097 addHistoryItem(new EditCommand(
6098 MessageManager.getString("label.add_sequences"),
6099 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
6100 viewport.getAlignment()));
6101 } catch (Exception ex)
6103 System.err.println(ex.getMessage());
6109 * Try to run a script in the Groovy console, having first ensured that this
6110 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
6111 * be targeted at this alignment.
6114 protected void runGroovy_actionPerformed()
6116 Jalview.setCurrentAlignFrame(this);
6117 groovy.ui.Console console = Desktop.getGroovyConsole();
6118 if (console != null)
6122 console.runScript();
6123 } catch (Exception ex)
6125 System.err.println((ex.toString()));
6127 .showInternalMessageDialog(Desktop.desktop, MessageManager
6128 .getString("label.couldnt_run_groovy_script"),
6130 .getString("label.groovy_support_failed"),
6131 JOptionPane.ERROR_MESSAGE);
6136 System.err.println("Can't run Groovy script as console not found");
6141 * Hides columns containing (or not containing) a specified feature, provided
6142 * that would not leave all columns hidden
6144 * @param featureType
6145 * @param columnsContaining
6148 public boolean hideFeatureColumns(String featureType,
6149 boolean columnsContaining)
6151 boolean notForHiding = avc.markColumnsContainingFeatures(
6152 columnsContaining, false, false, featureType);
6155 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
6156 false, featureType))
6158 getViewport().hideSelectedColumns();
6166 class PrintThread extends Thread
6170 public PrintThread(AlignmentPanel ap)
6175 static PageFormat pf;
6180 PrinterJob printJob = PrinterJob.getPrinterJob();
6184 printJob.setPrintable(ap, pf);
6188 printJob.setPrintable(ap);
6191 if (printJob.printDialog())
6196 } catch (Exception PrintException)
6198 PrintException.printStackTrace();