2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.FeatureSettingsModelI;
36 import jalview.api.SplitContainerI;
37 import jalview.api.ViewStyleI;
38 import jalview.api.analysis.ScoreModelI;
39 import jalview.bin.Cache;
40 import jalview.bin.Jalview;
41 import jalview.commands.CommandI;
42 import jalview.commands.EditCommand;
43 import jalview.commands.EditCommand.Action;
44 import jalview.commands.OrderCommand;
45 import jalview.commands.RemoveGapColCommand;
46 import jalview.commands.RemoveGapsCommand;
47 import jalview.commands.SlideSequencesCommand;
48 import jalview.commands.TrimRegionCommand;
49 import jalview.datamodel.AlignedCodonFrame;
50 import jalview.datamodel.Alignment;
51 import jalview.datamodel.AlignmentAnnotation;
52 import jalview.datamodel.AlignmentExportData;
53 import jalview.datamodel.AlignmentI;
54 import jalview.datamodel.AlignmentOrder;
55 import jalview.datamodel.AlignmentView;
56 import jalview.datamodel.ColumnSelection;
57 import jalview.datamodel.DBRefSource;
58 import jalview.datamodel.HiddenSequences;
59 import jalview.datamodel.PDBEntry;
60 import jalview.datamodel.SeqCigar;
61 import jalview.datamodel.Sequence;
62 import jalview.datamodel.SequenceGroup;
63 import jalview.datamodel.SequenceI;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileLoader;
72 import jalview.io.FormatAdapter;
73 import jalview.io.HtmlSvgOutput;
74 import jalview.io.IdentifyFile;
75 import jalview.io.JPredFile;
76 import jalview.io.JalviewFileChooser;
77 import jalview.io.JalviewFileView;
78 import jalview.io.JnetAnnotationMaker;
79 import jalview.io.NewickFile;
80 import jalview.io.TCoffeeScoreFile;
81 import jalview.io.gff.SequenceOntologyI;
82 import jalview.jbgui.GAlignFrame;
83 import jalview.schemes.Blosum62ColourScheme;
84 import jalview.schemes.BuriedColourScheme;
85 import jalview.schemes.ClustalxColourScheme;
86 import jalview.schemes.ColourSchemeI;
87 import jalview.schemes.ColourSchemeProperty;
88 import jalview.schemes.HelixColourScheme;
89 import jalview.schemes.HydrophobicColourScheme;
90 import jalview.schemes.NucleotideColourScheme;
91 import jalview.schemes.PIDColourScheme;
92 import jalview.schemes.PurinePyrimidineColourScheme;
93 import jalview.schemes.RNAHelicesColourChooser;
94 import jalview.schemes.ResidueProperties;
95 import jalview.schemes.StrandColourScheme;
96 import jalview.schemes.TCoffeeColourScheme;
97 import jalview.schemes.TaylorColourScheme;
98 import jalview.schemes.TurnColourScheme;
99 import jalview.schemes.UserColourScheme;
100 import jalview.schemes.ZappoColourScheme;
101 import jalview.structure.StructureSelectionManager;
102 import jalview.util.MessageManager;
103 import jalview.viewmodel.AlignmentViewport;
104 import jalview.ws.DBRefFetcher;
105 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
106 import jalview.ws.SequenceFetcher;
107 import jalview.ws.jws1.Discoverer;
108 import jalview.ws.jws2.Jws2Discoverer;
109 import jalview.ws.jws2.jabaws2.Jws2Instance;
110 import jalview.ws.seqfetcher.DbSourceProxy;
112 import java.awt.BorderLayout;
113 import java.awt.Component;
114 import java.awt.Rectangle;
115 import java.awt.Toolkit;
116 import java.awt.datatransfer.Clipboard;
117 import java.awt.datatransfer.DataFlavor;
118 import java.awt.datatransfer.StringSelection;
119 import java.awt.datatransfer.Transferable;
120 import java.awt.dnd.DropTargetDragEvent;
121 import java.awt.dnd.DropTargetDropEvent;
122 import java.awt.dnd.DropTargetEvent;
123 import java.awt.dnd.DropTargetListener;
124 import java.awt.event.ActionEvent;
125 import java.awt.event.ActionListener;
126 import java.awt.event.FocusAdapter;
127 import java.awt.event.FocusEvent;
128 import java.awt.event.ItemEvent;
129 import java.awt.event.ItemListener;
130 import java.awt.event.KeyAdapter;
131 import java.awt.event.KeyEvent;
132 import java.awt.event.MouseAdapter;
133 import java.awt.event.MouseEvent;
134 import java.awt.print.PageFormat;
135 import java.awt.print.PrinterJob;
136 import java.beans.PropertyChangeEvent;
139 import java.util.ArrayList;
140 import java.util.Arrays;
141 import java.util.Deque;
142 import java.util.Enumeration;
143 import java.util.Hashtable;
144 import java.util.List;
145 import java.util.Vector;
147 import javax.swing.JCheckBoxMenuItem;
148 import javax.swing.JEditorPane;
149 import javax.swing.JInternalFrame;
150 import javax.swing.JLayeredPane;
151 import javax.swing.JMenu;
152 import javax.swing.JMenuItem;
153 import javax.swing.JOptionPane;
154 import javax.swing.JRadioButtonMenuItem;
155 import javax.swing.JScrollPane;
156 import javax.swing.SwingUtilities;
162 * @version $Revision$
164 public class AlignFrame extends GAlignFrame implements DropTargetListener,
165 IProgressIndicator, AlignViewControllerGuiI
168 public static final int DEFAULT_WIDTH = 700;
170 public static final int DEFAULT_HEIGHT = 500;
173 * The currently displayed panel (selected tabbed view if more than one)
175 public AlignmentPanel alignPanel;
177 AlignViewport viewport;
179 public AlignViewControllerI avc;
181 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
184 * Last format used to load or save alignments in this window
186 FileFormatI currentFileFormat = null;
189 * Current filename for this alignment
191 String fileName = null;
194 * Creates a new AlignFrame object with specific width and height.
200 public AlignFrame(AlignmentI al, int width, int height)
202 this(al, null, width, height);
206 * Creates a new AlignFrame object with specific width, height and
212 * @param sequenceSetId
214 public AlignFrame(AlignmentI al, int width, int height,
215 String sequenceSetId)
217 this(al, null, width, height, sequenceSetId);
221 * Creates a new AlignFrame object with specific width, height and
227 * @param sequenceSetId
230 public AlignFrame(AlignmentI al, int width, int height,
231 String sequenceSetId, String viewId)
233 this(al, null, width, height, sequenceSetId, viewId);
237 * new alignment window with hidden columns
241 * @param hiddenColumns
242 * ColumnSelection or null
244 * Width of alignment frame
248 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
249 int width, int height)
251 this(al, hiddenColumns, width, height, null);
255 * Create alignment frame for al with hiddenColumns, a specific width and
256 * height, and specific sequenceId
259 * @param hiddenColumns
262 * @param sequenceSetId
265 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
266 int width, int height, String sequenceSetId)
268 this(al, hiddenColumns, width, height, sequenceSetId, null);
272 * Create alignment frame for al with hiddenColumns, a specific width and
273 * height, and specific sequenceId
276 * @param hiddenColumns
279 * @param sequenceSetId
284 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
285 int width, int height, String sequenceSetId, String viewId)
287 setSize(width, height);
289 if (al.getDataset() == null)
294 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
296 alignPanel = new AlignmentPanel(this, viewport);
298 addAlignmentPanel(alignPanel, true);
302 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
303 ColumnSelection hiddenColumns, int width, int height)
305 setSize(width, height);
307 if (al.getDataset() == null)
312 viewport = new AlignViewport(al, hiddenColumns);
314 if (hiddenSeqs != null && hiddenSeqs.length > 0)
316 viewport.hideSequence(hiddenSeqs);
318 alignPanel = new AlignmentPanel(this, viewport);
319 addAlignmentPanel(alignPanel, true);
324 * Make a new AlignFrame from existing alignmentPanels
331 public AlignFrame(AlignmentPanel ap)
335 addAlignmentPanel(ap, false);
340 * initalise the alignframe from the underlying viewport data and the
345 if (!Jalview.isHeadlessMode())
347 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
350 avc = new jalview.controller.AlignViewController(this, viewport,
352 if (viewport.getAlignmentConservationAnnotation() == null)
354 BLOSUM62Colour.setEnabled(false);
355 conservationMenuItem.setEnabled(false);
356 modifyConservation.setEnabled(false);
357 // PIDColour.setEnabled(false);
358 // abovePIDThreshold.setEnabled(false);
359 // modifyPID.setEnabled(false);
362 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
365 if (sortby.equals("Id"))
367 sortIDMenuItem_actionPerformed(null);
369 else if (sortby.equals("Pairwise Identity"))
371 sortPairwiseMenuItem_actionPerformed(null);
374 if (Desktop.desktop != null)
376 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
377 addServiceListeners();
378 setGUINucleotide(viewport.getAlignment().isNucleotide());
382 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
384 setMenusFromViewport(viewport);
385 buildSortByAnnotationScoresMenu();
388 if (viewport.getWrapAlignment())
390 wrapMenuItem_actionPerformed(null);
393 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
395 this.overviewMenuItem_actionPerformed(null);
400 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
401 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
402 final String menuLabel = MessageManager
403 .getString("label.copy_format_from");
404 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
405 new ViewSetProvider()
409 public AlignmentPanel[] getAllAlignmentPanels()
412 origview.add(alignPanel);
413 // make an array of all alignment panels except for this one
414 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
415 Arrays.asList(Desktop.getAlignmentPanels(null)));
416 aps.remove(AlignFrame.this.alignPanel);
417 return aps.toArray(new AlignmentPanel[aps.size()]);
419 }, selviews, new ItemListener()
423 public void itemStateChanged(ItemEvent e)
425 if (origview.size() > 0)
427 final AlignmentPanel ap = origview.get(0);
430 * Copy the ViewStyle of the selected panel to 'this one'.
431 * Don't change value of 'scaleProteinAsCdna' unless copying
434 ViewStyleI vs = selviews.get(0).getAlignViewport()
436 boolean fromSplitFrame = selviews.get(0)
437 .getAlignViewport().getCodingComplement() != null;
440 vs.setScaleProteinAsCdna(ap.getAlignViewport()
441 .getViewStyle().isScaleProteinAsCdna());
443 ap.getAlignViewport().setViewStyle(vs);
446 * Also rescale ViewStyle of SplitFrame complement if there is
447 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
448 * the whole ViewStyle (allow cDNA protein to have different
451 AlignViewportI complement = ap.getAlignViewport()
452 .getCodingComplement();
453 if (complement != null && vs.isScaleProteinAsCdna())
455 AlignFrame af = Desktop.getAlignFrameFor(complement);
456 ((SplitFrame) af.getSplitViewContainer())
458 af.setMenusForViewport();
462 ap.setSelected(true);
463 ap.alignFrame.setMenusForViewport();
468 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
469 .indexOf("devel") > -1
470 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
471 .indexOf("test") > -1)
473 formatMenu.add(vsel);
475 addFocusListener(new FocusAdapter()
478 public void focusGained(FocusEvent e)
480 Jalview.setCurrentAlignFrame(AlignFrame.this);
487 * Change the filename and format for the alignment, and enable the 'reload'
488 * button functionality.
495 public void setFileName(String file, FileFormatI format)
498 setFileFormat(format);
499 reload.setEnabled(true);
503 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
506 void addKeyListener()
508 addKeyListener(new KeyAdapter()
511 public void keyPressed(KeyEvent evt)
513 if (viewport.cursorMode
514 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
515 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
516 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
517 && Character.isDigit(evt.getKeyChar()))
519 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
522 switch (evt.getKeyCode())
525 case 27: // escape key
526 deselectAllSequenceMenuItem_actionPerformed(null);
530 case KeyEvent.VK_DOWN:
531 if (evt.isAltDown() || !viewport.cursorMode)
533 moveSelectedSequences(false);
535 if (viewport.cursorMode)
537 alignPanel.getSeqPanel().moveCursor(0, 1);
542 if (evt.isAltDown() || !viewport.cursorMode)
544 moveSelectedSequences(true);
546 if (viewport.cursorMode)
548 alignPanel.getSeqPanel().moveCursor(0, -1);
553 case KeyEvent.VK_LEFT:
554 if (evt.isAltDown() || !viewport.cursorMode)
556 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
560 alignPanel.getSeqPanel().moveCursor(-1, 0);
565 case KeyEvent.VK_RIGHT:
566 if (evt.isAltDown() || !viewport.cursorMode)
568 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
572 alignPanel.getSeqPanel().moveCursor(1, 0);
576 case KeyEvent.VK_SPACE:
577 if (viewport.cursorMode)
579 alignPanel.getSeqPanel().insertGapAtCursor(
580 evt.isControlDown() || evt.isShiftDown()
585 // case KeyEvent.VK_A:
586 // if (viewport.cursorMode)
588 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
589 // //System.out.println("A");
593 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
594 * System.out.println("closing bracket"); } break;
596 case KeyEvent.VK_DELETE:
597 case KeyEvent.VK_BACK_SPACE:
598 if (!viewport.cursorMode)
600 cut_actionPerformed(null);
604 alignPanel.getSeqPanel().deleteGapAtCursor(
605 evt.isControlDown() || evt.isShiftDown()
612 if (viewport.cursorMode)
614 alignPanel.getSeqPanel().setCursorRow();
618 if (viewport.cursorMode && !evt.isControlDown())
620 alignPanel.getSeqPanel().setCursorColumn();
624 if (viewport.cursorMode)
626 alignPanel.getSeqPanel().setCursorPosition();
630 case KeyEvent.VK_ENTER:
631 case KeyEvent.VK_COMMA:
632 if (viewport.cursorMode)
634 alignPanel.getSeqPanel().setCursorRowAndColumn();
639 if (viewport.cursorMode)
641 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
645 if (viewport.cursorMode)
647 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
652 viewport.cursorMode = !viewport.cursorMode;
653 statusBar.setText(MessageManager.formatMessage(
654 "label.keyboard_editing_mode",
655 new String[] { (viewport.cursorMode ? "on" : "off") }));
656 if (viewport.cursorMode)
658 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
659 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
661 alignPanel.getSeqPanel().seqCanvas.repaint();
667 Help.showHelpWindow();
668 } catch (Exception ex)
670 ex.printStackTrace();
675 boolean toggleSeqs = !evt.isControlDown();
676 boolean toggleCols = !evt.isShiftDown();
677 toggleHiddenRegions(toggleSeqs, toggleCols);
680 case KeyEvent.VK_PAGE_UP:
681 if (viewport.getWrapAlignment())
683 alignPanel.scrollUp(true);
687 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
688 - viewport.endSeq + viewport.startSeq);
691 case KeyEvent.VK_PAGE_DOWN:
692 if (viewport.getWrapAlignment())
694 alignPanel.scrollUp(false);
698 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
699 + viewport.endSeq - viewport.startSeq);
706 public void keyReleased(KeyEvent evt)
708 switch (evt.getKeyCode())
710 case KeyEvent.VK_LEFT:
711 if (evt.isAltDown() || !viewport.cursorMode)
713 viewport.firePropertyChange("alignment", null, viewport
714 .getAlignment().getSequences());
718 case KeyEvent.VK_RIGHT:
719 if (evt.isAltDown() || !viewport.cursorMode)
721 viewport.firePropertyChange("alignment", null, viewport
722 .getAlignment().getSequences());
730 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
732 ap.alignFrame = this;
733 avc = new jalview.controller.AlignViewController(this, viewport,
738 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
740 int aSize = alignPanels.size();
742 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
744 if (aSize == 1 && ap.av.viewName == null)
746 this.getContentPane().add(ap, BorderLayout.CENTER);
752 setInitialTabVisible();
755 expandViews.setEnabled(true);
756 gatherViews.setEnabled(true);
757 tabbedPane.addTab(ap.av.viewName, ap);
759 ap.setVisible(false);
764 if (ap.av.isPadGaps())
766 ap.av.getAlignment().padGaps();
768 ap.av.updateConservation(ap);
769 ap.av.updateConsensus(ap);
770 ap.av.updateStrucConsensus(ap);
774 public void setInitialTabVisible()
776 expandViews.setEnabled(true);
777 gatherViews.setEnabled(true);
778 tabbedPane.setVisible(true);
779 AlignmentPanel first = alignPanels.get(0);
780 tabbedPane.addTab(first.av.viewName, first);
781 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
784 public AlignViewport getViewport()
789 /* Set up intrinsic listeners for dynamically generated GUI bits. */
790 private void addServiceListeners()
792 final java.beans.PropertyChangeListener thisListener;
793 Desktop.instance.addJalviewPropertyChangeListener("services",
794 thisListener = new java.beans.PropertyChangeListener()
797 public void propertyChange(PropertyChangeEvent evt)
799 // // System.out.println("Discoverer property change.");
800 // if (evt.getPropertyName().equals("services"))
802 SwingUtilities.invokeLater(new Runnable()
809 .println("Rebuild WS Menu for service change");
810 BuildWebServiceMenu();
817 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
820 public void internalFrameClosed(
821 javax.swing.event.InternalFrameEvent evt)
823 // System.out.println("deregistering discoverer listener");
824 Desktop.instance.removeJalviewPropertyChangeListener("services",
826 closeMenuItem_actionPerformed(true);
829 // Finally, build the menu once to get current service state
830 new Thread(new Runnable()
835 BuildWebServiceMenu();
841 * Configure menu items that vary according to whether the alignment is
842 * nucleotide or protein
846 public void setGUINucleotide(boolean nucleotide)
848 showTranslation.setVisible(nucleotide);
849 showReverse.setVisible(nucleotide);
850 showReverseComplement.setVisible(nucleotide);
851 conservationMenuItem.setEnabled(!nucleotide);
852 modifyConservation.setEnabled(!nucleotide);
853 showGroupConservation.setEnabled(!nucleotide);
854 rnahelicesColour.setEnabled(nucleotide);
855 purinePyrimidineColour.setEnabled(nucleotide);
856 showComplementMenuItem.setText(MessageManager
857 .getString(nucleotide ? "label.protein" : "label.nucleotide"));
858 setColourSelected(jalview.bin.Cache.getDefault(
859 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
860 : Preferences.DEFAULT_COLOUR_PROT, "None"));
864 * set up menus for the current viewport. This may be called after any
865 * operation that affects the data in the current view (selection changed,
866 * etc) to update the menus to reflect the new state.
869 public void setMenusForViewport()
871 setMenusFromViewport(viewport);
875 * Need to call this method when tabs are selected for multiple views, or when
876 * loading from Jalview2XML.java
881 void setMenusFromViewport(AlignViewport av)
883 padGapsMenuitem.setSelected(av.isPadGaps());
884 colourTextMenuItem.setSelected(av.isShowColourText());
885 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
886 conservationMenuItem.setSelected(av.getConservationSelected());
887 seqLimits.setSelected(av.getShowJVSuffix());
888 idRightAlign.setSelected(av.isRightAlignIds());
889 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
890 renderGapsMenuItem.setSelected(av.isRenderGaps());
891 wrapMenuItem.setSelected(av.getWrapAlignment());
892 scaleAbove.setVisible(av.getWrapAlignment());
893 scaleLeft.setVisible(av.getWrapAlignment());
894 scaleRight.setVisible(av.getWrapAlignment());
895 annotationPanelMenuItem.setState(av.isShowAnnotation());
897 * Show/hide annotations only enabled if annotation panel is shown
899 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
900 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
901 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
902 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
903 viewBoxesMenuItem.setSelected(av.getShowBoxes());
904 viewTextMenuItem.setSelected(av.getShowText());
905 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
906 showGroupConsensus.setSelected(av.isShowGroupConsensus());
907 showGroupConservation.setSelected(av.isShowGroupConservation());
908 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
909 showSequenceLogo.setSelected(av.isShowSequenceLogo());
910 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
912 setColourSelected(ColourSchemeProperty.getColourName(av
913 .getGlobalColourScheme()));
915 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
916 hiddenMarkers.setState(av.getShowHiddenMarkers());
917 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
918 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
919 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
920 autoCalculate.setSelected(av.autoCalculateConsensus);
921 sortByTree.setSelected(av.sortByTree);
922 listenToViewSelections.setSelected(av.followSelection);
923 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
925 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
927 showProducts.setEnabled(canShowProducts());
928 setGroovyEnabled(Desktop.getGroovyConsole() != null);
934 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
938 public void setGroovyEnabled(boolean b)
940 runGroovy.setEnabled(b);
943 private IProgressIndicator progressBar;
948 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
951 public void setProgressBar(String message, long id)
953 progressBar.setProgressBar(message, id);
957 public void registerHandler(final long id,
958 final IProgressIndicatorHandler handler)
960 progressBar.registerHandler(id, handler);
965 * @return true if any progress bars are still active
968 public boolean operationInProgress()
970 return progressBar.operationInProgress();
974 public void setStatus(String text)
976 statusBar.setText(text);
980 * Added so Castor Mapping file can obtain Jalview Version
982 public String getVersion()
984 return jalview.bin.Cache.getProperty("VERSION");
987 public FeatureRenderer getFeatureRenderer()
989 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
993 public void fetchSequence_actionPerformed(ActionEvent e)
995 new jalview.gui.SequenceFetcher(this);
999 public void addFromFile_actionPerformed(ActionEvent e)
1001 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1005 public void reload_actionPerformed(ActionEvent e)
1007 if (fileName != null)
1009 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1010 // originating file's format
1011 // TODO: work out how to recover feature settings for correct view(s) when
1012 // file is reloaded.
1013 if (currentFileFormat.equals("Jalview"))
1015 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1016 for (int i = 0; i < frames.length; i++)
1018 if (frames[i] instanceof AlignFrame && frames[i] != this
1019 && ((AlignFrame) frames[i]).fileName != null
1020 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1024 frames[i].setSelected(true);
1025 Desktop.instance.closeAssociatedWindows();
1026 } catch (java.beans.PropertyVetoException ex)
1032 Desktop.instance.closeAssociatedWindows();
1034 FileLoader loader = new FileLoader();
1035 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1036 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1040 Rectangle bounds = this.getBounds();
1042 FileLoader loader = new FileLoader();
1043 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1044 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1045 protocol, currentFileFormat);
1047 newframe.setBounds(bounds);
1048 if (featureSettings != null && featureSettings.isShowing())
1050 final Rectangle fspos = featureSettings.frame.getBounds();
1051 // TODO: need a 'show feature settings' function that takes bounds -
1052 // need to refactor Desktop.addFrame
1053 newframe.featureSettings_actionPerformed(null);
1054 final FeatureSettings nfs = newframe.featureSettings;
1055 SwingUtilities.invokeLater(new Runnable()
1060 nfs.frame.setBounds(fspos);
1063 this.featureSettings.close();
1064 this.featureSettings = null;
1066 this.closeMenuItem_actionPerformed(true);
1072 public void addFromText_actionPerformed(ActionEvent e)
1074 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1079 public void addFromURL_actionPerformed(ActionEvent e)
1081 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1085 public void save_actionPerformed(ActionEvent e)
1087 if (fileName == null
1088 || (currentFileFormat == null || !jalview.io.FormatAdapter
1089 .isValidIOFormat(currentFileFormat, true))
1090 || fileName.startsWith("http"))
1092 saveAs_actionPerformed(null);
1096 saveAlignment(fileName, currentFileFormat);
1107 public void saveAs_actionPerformed(ActionEvent e)
1109 JalviewFileChooser chooser = new JalviewFileChooser(
1110 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1111 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1112 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1113 currentFileFormat, false);
1115 chooser.setFileView(new JalviewFileView());
1116 chooser.setDialogTitle(MessageManager
1117 .getString("label.save_alignment_to_file"));
1118 chooser.setToolTipText(MessageManager.getString("action.save"));
1120 int value = chooser.showSaveDialog(this);
1122 if (value == JalviewFileChooser.APPROVE_OPTION)
1124 currentFileFormat = chooser.getSelectedFormat();
1125 while (currentFileFormat == null)
1128 .showInternalMessageDialog(
1131 .getString("label.select_file_format_before_saving"),
1133 .getString("label.file_format_not_specified"),
1134 JOptionPane.WARNING_MESSAGE);
1135 currentFileFormat = chooser.getSelectedFormat();
1136 value = chooser.showSaveDialog(this);
1137 if (value != JalviewFileChooser.APPROVE_OPTION)
1143 fileName = chooser.getSelectedFile().getPath();
1145 Cache.setProperty("DEFAULT_FILE_FORMAT",
1146 currentFileFormat.toString());
1148 Cache.setProperty("LAST_DIRECTORY", fileName);
1149 if (currentFileFormat.indexOf(" ") > -1)
1151 currentFileFormat = currentFileFormat.substring(0,
1152 currentFileFormat.indexOf(" "));
1154 saveAlignment(fileName, currentFileFormat);
1158 public boolean saveAlignment(String file, FileFormatI format)
1160 boolean success = true;
1162 if (format == FileFormat.Jalview)
1164 String shortName = title;
1166 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1168 shortName = shortName.substring(shortName
1169 .lastIndexOf(java.io.File.separatorChar) + 1);
1172 success = new Jalview2XML().saveAlignment(this, file, shortName);
1174 statusBar.setText(MessageManager.formatMessage(
1175 "label.successfully_saved_to_file_in_format", new Object[] {
1176 fileName, format }));
1181 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1183 warningMessage("Cannot save file " + fileName + " using format "
1184 + format, "Alignment output format not supported");
1185 if (!Jalview.isHeadlessMode())
1187 saveAs_actionPerformed(null);
1192 AlignmentExportData exportData = getAlignmentForExport(format,
1194 if (exportData.getSettings().isCancelled())
1198 FormatAdapter f = new FormatAdapter(alignPanel,
1199 exportData.getSettings());
1200 String output = f.formatSequences(
1202 exportData.getAlignment(), // class cast exceptions will
1203 // occur in the distant future
1204 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1205 f.getCacheSuffixDefault(format),
1206 viewport.getColumnSelection());
1216 java.io.PrintWriter out = new java.io.PrintWriter(
1217 new java.io.FileWriter(file));
1221 this.setTitle(file);
1222 statusBar.setText(MessageManager.formatMessage(
1223 "label.successfully_saved_to_file_in_format",
1224 new Object[] { fileName, format }));
1225 } catch (Exception ex)
1228 ex.printStackTrace();
1235 JOptionPane.showInternalMessageDialog(this, MessageManager
1236 .formatMessage("label.couldnt_save_file",
1237 new Object[] { fileName }), MessageManager
1238 .getString("label.error_saving_file"),
1239 JOptionPane.WARNING_MESSAGE);
1245 private void warningMessage(String warning, String title)
1247 if (new jalview.util.Platform().isHeadless())
1249 System.err.println("Warning: " + title + "\nWarning: " + warning);
1254 JOptionPane.showInternalMessageDialog(this, warning, title,
1255 JOptionPane.WARNING_MESSAGE);
1267 protected void outputText_actionPerformed(ActionEvent e)
1270 AlignmentExportData exportData = getAlignmentForExport(
1271 e.getActionCommand(), viewport, null);
1272 if (exportData.getSettings().isCancelled())
1276 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1277 cap.setForInput(null);
1280 FileFormatI format = FileFormat.valueOf(e.getActionCommand());
1281 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1282 .formatSequences(format,
1283 exportData.getAlignment(),
1284 exportData.getOmitHidden(),
1285 exportData.getStartEndPostions(),
1286 viewport.getColumnSelection()));
1287 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1288 "label.alignment_output_command",
1289 new Object[] { e.getActionCommand() }), 600, 500);
1290 } catch (OutOfMemoryError oom)
1292 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1298 public static AlignmentExportData getAlignmentForExport(
1299 FileFormatI format, AlignViewportI viewport,
1300 AlignExportSettingI exportSettings)
1302 AlignmentI alignmentToExport = null;
1303 AlignExportSettingI settings = exportSettings;
1304 String[] omitHidden = null;
1306 HiddenSequences hiddenSeqs = viewport.getAlignment()
1307 .getHiddenSequences();
1309 alignmentToExport = viewport.getAlignment();
1311 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1312 if (settings == null)
1314 settings = new AlignExportSettings(hasHiddenSeqs,
1315 viewport.hasHiddenColumns(), format);
1317 // settings.isExportAnnotations();
1319 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1321 omitHidden = viewport.getViewAsString(false,
1322 settings.isExportHiddenSequences());
1325 int[] alignmentStartEnd = new int[2];
1326 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1328 alignmentToExport = hiddenSeqs.getFullAlignment();
1332 alignmentToExport = viewport.getAlignment();
1334 alignmentStartEnd = alignmentToExport
1335 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1336 .getHiddenColumns());
1337 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1338 omitHidden, alignmentStartEnd, settings);
1349 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1351 new HtmlSvgOutput(null, alignPanel);
1355 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1357 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1358 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1361 public void createImageMap(File file, String image)
1363 alignPanel.makePNGImageMap(file, image);
1373 public void createPNG(File f)
1375 alignPanel.makePNG(f);
1385 public void createEPS(File f)
1387 alignPanel.makeEPS(f);
1391 public void createSVG(File f)
1393 alignPanel.makeSVG(f);
1397 public void pageSetup_actionPerformed(ActionEvent e)
1399 PrinterJob printJob = PrinterJob.getPrinterJob();
1400 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1410 public void printMenuItem_actionPerformed(ActionEvent e)
1412 // Putting in a thread avoids Swing painting problems
1413 PrintThread thread = new PrintThread(alignPanel);
1418 public void exportFeatures_actionPerformed(ActionEvent e)
1420 new AnnotationExporter().exportFeatures(alignPanel);
1424 public void exportAnnotations_actionPerformed(ActionEvent e)
1426 new AnnotationExporter().exportAnnotations(alignPanel);
1430 public void associatedData_actionPerformed(ActionEvent e)
1432 // Pick the tree file
1433 JalviewFileChooser chooser = new JalviewFileChooser(
1434 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1435 chooser.setFileView(new JalviewFileView());
1436 chooser.setDialogTitle(MessageManager
1437 .getString("label.load_jalview_annotations"));
1438 chooser.setToolTipText(MessageManager
1439 .getString("label.load_jalview_annotations"));
1441 int value = chooser.showOpenDialog(null);
1443 if (value == JalviewFileChooser.APPROVE_OPTION)
1445 String choice = chooser.getSelectedFile().getPath();
1446 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1447 loadJalviewDataFile(choice, null, null, null);
1453 * Close the current view or all views in the alignment frame. If the frame
1454 * only contains one view then the alignment will be removed from memory.
1456 * @param closeAllTabs
1459 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1461 if (alignPanels != null && alignPanels.size() < 2)
1463 closeAllTabs = true;
1468 if (alignPanels != null)
1472 if (this.isClosed())
1474 // really close all the windows - otherwise wait till
1475 // setClosed(true) is called
1476 for (int i = 0; i < alignPanels.size(); i++)
1478 AlignmentPanel ap = alignPanels.get(i);
1485 closeView(alignPanel);
1492 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1493 * be called recursively, with the frame now in 'closed' state
1495 this.setClosed(true);
1497 } catch (Exception ex)
1499 ex.printStackTrace();
1504 * Close the specified panel and close up tabs appropriately.
1506 * @param panelToClose
1508 public void closeView(AlignmentPanel panelToClose)
1510 int index = tabbedPane.getSelectedIndex();
1511 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1512 alignPanels.remove(panelToClose);
1513 panelToClose.closePanel();
1514 panelToClose = null;
1516 tabbedPane.removeTabAt(closedindex);
1517 tabbedPane.validate();
1519 if (index > closedindex || index == tabbedPane.getTabCount())
1521 // modify currently selected tab index if necessary.
1525 this.tabSelectionChanged(index);
1531 void updateEditMenuBar()
1534 if (viewport.getHistoryList().size() > 0)
1536 undoMenuItem.setEnabled(true);
1537 CommandI command = viewport.getHistoryList().peek();
1538 undoMenuItem.setText(MessageManager.formatMessage(
1539 "label.undo_command",
1540 new Object[] { command.getDescription() }));
1544 undoMenuItem.setEnabled(false);
1545 undoMenuItem.setText(MessageManager.getString("action.undo"));
1548 if (viewport.getRedoList().size() > 0)
1550 redoMenuItem.setEnabled(true);
1552 CommandI command = viewport.getRedoList().peek();
1553 redoMenuItem.setText(MessageManager.formatMessage(
1554 "label.redo_command",
1555 new Object[] { command.getDescription() }));
1559 redoMenuItem.setEnabled(false);
1560 redoMenuItem.setText(MessageManager.getString("action.redo"));
1565 public void addHistoryItem(CommandI command)
1567 if (command.getSize() > 0)
1569 viewport.addToHistoryList(command);
1570 viewport.clearRedoList();
1571 updateEditMenuBar();
1572 viewport.updateHiddenColumns();
1573 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1574 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1575 // viewport.getColumnSelection()
1576 // .getHiddenColumns().size() > 0);
1582 * @return alignment objects for all views
1584 AlignmentI[] getViewAlignments()
1586 if (alignPanels != null)
1588 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1590 for (AlignmentPanel ap : alignPanels)
1592 als[i++] = ap.av.getAlignment();
1596 if (viewport != null)
1598 return new AlignmentI[] { viewport.getAlignment() };
1610 protected void undoMenuItem_actionPerformed(ActionEvent e)
1612 if (viewport.getHistoryList().isEmpty())
1616 CommandI command = viewport.getHistoryList().pop();
1617 viewport.addToRedoList(command);
1618 command.undoCommand(getViewAlignments());
1620 AlignmentViewport originalSource = getOriginatingSource(command);
1621 updateEditMenuBar();
1623 if (originalSource != null)
1625 if (originalSource != viewport)
1628 .warn("Implementation worry: mismatch of viewport origin for undo");
1630 originalSource.updateHiddenColumns();
1631 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1633 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1634 // viewport.getColumnSelection()
1635 // .getHiddenColumns().size() > 0);
1636 originalSource.firePropertyChange("alignment", null, originalSource
1637 .getAlignment().getSequences());
1648 protected void redoMenuItem_actionPerformed(ActionEvent e)
1650 if (viewport.getRedoList().size() < 1)
1655 CommandI command = viewport.getRedoList().pop();
1656 viewport.addToHistoryList(command);
1657 command.doCommand(getViewAlignments());
1659 AlignmentViewport originalSource = getOriginatingSource(command);
1660 updateEditMenuBar();
1662 if (originalSource != null)
1665 if (originalSource != viewport)
1668 .warn("Implementation worry: mismatch of viewport origin for redo");
1670 originalSource.updateHiddenColumns();
1671 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1673 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1674 // viewport.getColumnSelection()
1675 // .getHiddenColumns().size() > 0);
1676 originalSource.firePropertyChange("alignment", null, originalSource
1677 .getAlignment().getSequences());
1681 AlignmentViewport getOriginatingSource(CommandI command)
1683 AlignmentViewport originalSource = null;
1684 // For sequence removal and addition, we need to fire
1685 // the property change event FROM the viewport where the
1686 // original alignment was altered
1687 AlignmentI al = null;
1688 if (command instanceof EditCommand)
1690 EditCommand editCommand = (EditCommand) command;
1691 al = editCommand.getAlignment();
1692 List<Component> comps = PaintRefresher.components.get(viewport
1693 .getSequenceSetId());
1695 for (Component comp : comps)
1697 if (comp instanceof AlignmentPanel)
1699 if (al == ((AlignmentPanel) comp).av.getAlignment())
1701 originalSource = ((AlignmentPanel) comp).av;
1708 if (originalSource == null)
1710 // The original view is closed, we must validate
1711 // the current view against the closed view first
1714 PaintRefresher.validateSequences(al, viewport.getAlignment());
1717 originalSource = viewport;
1720 return originalSource;
1729 public void moveSelectedSequences(boolean up)
1731 SequenceGroup sg = viewport.getSelectionGroup();
1737 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1738 viewport.getHiddenRepSequences(), up);
1739 alignPanel.paintAlignment(true);
1742 synchronized void slideSequences(boolean right, int size)
1744 List<SequenceI> sg = new ArrayList<SequenceI>();
1745 if (viewport.cursorMode)
1747 sg.add(viewport.getAlignment().getSequenceAt(
1748 alignPanel.getSeqPanel().seqCanvas.cursorY));
1750 else if (viewport.getSelectionGroup() != null
1751 && viewport.getSelectionGroup().getSize() != viewport
1752 .getAlignment().getHeight())
1754 sg = viewport.getSelectionGroup().getSequences(
1755 viewport.getHiddenRepSequences());
1763 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1765 for (SequenceI seq : viewport.getAlignment().getSequences())
1767 if (!sg.contains(seq))
1769 invertGroup.add(seq);
1773 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1775 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1776 for (int i = 0; i < invertGroup.size(); i++)
1778 seqs2[i] = invertGroup.get(i);
1781 SlideSequencesCommand ssc;
1784 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1785 size, viewport.getGapCharacter());
1789 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1790 size, viewport.getGapCharacter());
1793 int groupAdjustment = 0;
1794 if (ssc.getGapsInsertedBegin() && right)
1796 if (viewport.cursorMode)
1798 alignPanel.getSeqPanel().moveCursor(size, 0);
1802 groupAdjustment = size;
1805 else if (!ssc.getGapsInsertedBegin() && !right)
1807 if (viewport.cursorMode)
1809 alignPanel.getSeqPanel().moveCursor(-size, 0);
1813 groupAdjustment = -size;
1817 if (groupAdjustment != 0)
1819 viewport.getSelectionGroup().setStartRes(
1820 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1821 viewport.getSelectionGroup().setEndRes(
1822 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1826 * just extend the last slide command if compatible; but not if in
1827 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1829 boolean appendHistoryItem = false;
1830 Deque<CommandI> historyList = viewport.getHistoryList();
1831 boolean inSplitFrame = getSplitViewContainer() != null;
1832 if (!inSplitFrame && historyList != null && historyList.size() > 0
1833 && historyList.peek() instanceof SlideSequencesCommand)
1835 appendHistoryItem = ssc
1836 .appendSlideCommand((SlideSequencesCommand) historyList
1840 if (!appendHistoryItem)
1842 addHistoryItem(ssc);
1855 protected void copy_actionPerformed(ActionEvent e)
1858 if (viewport.getSelectionGroup() == null)
1862 // TODO: preserve the ordering of displayed alignment annotation in any
1863 // internal paste (particularly sequence associated annotation)
1864 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1865 String[] omitHidden = null;
1867 if (viewport.hasHiddenColumns())
1869 omitHidden = viewport.getViewAsString(true);
1872 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1875 StringSelection ss = new StringSelection(output);
1879 jalview.gui.Desktop.internalCopy = true;
1880 // Its really worth setting the clipboard contents
1881 // to empty before setting the large StringSelection!!
1882 Toolkit.getDefaultToolkit().getSystemClipboard()
1883 .setContents(new StringSelection(""), null);
1885 Toolkit.getDefaultToolkit().getSystemClipboard()
1886 .setContents(ss, Desktop.instance);
1887 } catch (OutOfMemoryError er)
1889 new OOMWarning("copying region", er);
1893 ArrayList<int[]> hiddenColumns = null;
1894 if (viewport.hasHiddenColumns())
1896 hiddenColumns = new ArrayList<int[]>();
1897 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1898 .getSelectionGroup().getEndRes();
1899 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1901 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1903 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1904 region[1] - hiddenOffset });
1909 Desktop.jalviewClipboard = new Object[] { seqs,
1910 viewport.getAlignment().getDataset(), hiddenColumns };
1911 statusBar.setText(MessageManager.formatMessage(
1912 "label.copied_sequences_to_clipboard", new Object[] { Integer
1913 .valueOf(seqs.length).toString() }));
1923 protected void pasteNew_actionPerformed(ActionEvent e)
1935 protected void pasteThis_actionPerformed(ActionEvent e)
1941 * Paste contents of Jalview clipboard
1943 * @param newAlignment
1944 * true to paste to a new alignment, otherwise add to this.
1946 void paste(boolean newAlignment)
1948 boolean externalPaste = true;
1951 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1952 Transferable contents = c.getContents(this);
1954 if (contents == null)
1962 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1963 if (str.length() < 1)
1968 format = new IdentifyFile().identify(str, "Paste");
1970 } catch (OutOfMemoryError er)
1972 new OOMWarning("Out of memory pasting sequences!!", er);
1976 SequenceI[] sequences;
1977 boolean annotationAdded = false;
1978 AlignmentI alignment = null;
1980 if (Desktop.jalviewClipboard != null)
1982 // The clipboard was filled from within Jalview, we must use the
1984 // And dataset from the copied alignment
1985 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1986 // be doubly sure that we create *new* sequence objects.
1987 sequences = new SequenceI[newseq.length];
1988 for (int i = 0; i < newseq.length; i++)
1990 sequences[i] = new Sequence(newseq[i]);
1992 alignment = new Alignment(sequences);
1993 externalPaste = false;
1997 // parse the clipboard as an alignment.
1998 alignment = new FormatAdapter().readFile(str, "Paste", format);
1999 sequences = alignment.getSequencesArray();
2003 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2009 if (Desktop.jalviewClipboard != null)
2011 // dataset is inherited
2012 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2016 // new dataset is constructed
2017 alignment.setDataset(null);
2019 alwidth = alignment.getWidth() + 1;
2023 AlignmentI pastedal = alignment; // preserve pasted alignment object
2024 // Add pasted sequences and dataset into existing alignment.
2025 alignment = viewport.getAlignment();
2026 alwidth = alignment.getWidth() + 1;
2027 // decide if we need to import sequences from an existing dataset
2028 boolean importDs = Desktop.jalviewClipboard != null
2029 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2030 // importDs==true instructs us to copy over new dataset sequences from
2031 // an existing alignment
2032 Vector newDs = (importDs) ? new Vector() : null; // used to create
2033 // minimum dataset set
2035 for (int i = 0; i < sequences.length; i++)
2039 newDs.addElement(null);
2041 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2043 if (importDs && ds != null)
2045 if (!newDs.contains(ds))
2047 newDs.setElementAt(ds, i);
2048 ds = new Sequence(ds);
2049 // update with new dataset sequence
2050 sequences[i].setDatasetSequence(ds);
2054 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2059 // copy and derive new dataset sequence
2060 sequences[i] = sequences[i].deriveSequence();
2061 alignment.getDataset().addSequence(
2062 sequences[i].getDatasetSequence());
2063 // TODO: avoid creation of duplicate dataset sequences with a
2064 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2066 alignment.addSequence(sequences[i]); // merges dataset
2070 newDs.clear(); // tidy up
2072 if (alignment.getAlignmentAnnotation() != null)
2074 for (AlignmentAnnotation alan : alignment
2075 .getAlignmentAnnotation())
2077 if (alan.graphGroup > fgroup)
2079 fgroup = alan.graphGroup;
2083 if (pastedal.getAlignmentAnnotation() != null)
2085 // Add any annotation attached to alignment.
2086 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2087 for (int i = 0; i < alann.length; i++)
2089 annotationAdded = true;
2090 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2092 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2093 if (newann.graphGroup > -1)
2095 if (newGraphGroups.size() <= newann.graphGroup
2096 || newGraphGroups.get(newann.graphGroup) == null)
2098 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2100 newGraphGroups.add(q, null);
2102 newGraphGroups.set(newann.graphGroup, new Integer(
2105 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2109 newann.padAnnotation(alwidth);
2110 alignment.addAnnotation(newann);
2120 addHistoryItem(new EditCommand(
2121 MessageManager.getString("label.add_sequences"),
2122 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2124 // Add any annotations attached to sequences
2125 for (int i = 0; i < sequences.length; i++)
2127 if (sequences[i].getAnnotation() != null)
2129 AlignmentAnnotation newann;
2130 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2132 annotationAdded = true;
2133 newann = sequences[i].getAnnotation()[a];
2134 newann.adjustForAlignment();
2135 newann.padAnnotation(alwidth);
2136 if (newann.graphGroup > -1)
2138 if (newann.graphGroup > -1)
2140 if (newGraphGroups.size() <= newann.graphGroup
2141 || newGraphGroups.get(newann.graphGroup) == null)
2143 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2145 newGraphGroups.add(q, null);
2147 newGraphGroups.set(newann.graphGroup, new Integer(
2150 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2154 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2159 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2166 // propagate alignment changed.
2167 viewport.setEndSeq(alignment.getHeight());
2168 if (annotationAdded)
2170 // Duplicate sequence annotation in all views.
2171 AlignmentI[] alview = this.getViewAlignments();
2172 for (int i = 0; i < sequences.length; i++)
2174 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2179 for (int avnum = 0; avnum < alview.length; avnum++)
2181 if (alview[avnum] != alignment)
2183 // duplicate in a view other than the one with input focus
2184 int avwidth = alview[avnum].getWidth() + 1;
2185 // this relies on sann being preserved after we
2186 // modify the sequence's annotation array for each duplication
2187 for (int a = 0; a < sann.length; a++)
2189 AlignmentAnnotation newann = new AlignmentAnnotation(
2191 sequences[i].addAlignmentAnnotation(newann);
2192 newann.padAnnotation(avwidth);
2193 alview[avnum].addAnnotation(newann); // annotation was
2194 // duplicated earlier
2195 // TODO JAL-1145 graphGroups are not updated for sequence
2196 // annotation added to several views. This may cause
2198 alview[avnum].setAnnotationIndex(newann, a);
2203 buildSortByAnnotationScoresMenu();
2205 viewport.firePropertyChange("alignment", null,
2206 alignment.getSequences());
2207 if (alignPanels != null)
2209 for (AlignmentPanel ap : alignPanels)
2211 ap.validateAnnotationDimensions(false);
2216 alignPanel.validateAnnotationDimensions(false);
2222 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2224 String newtitle = new String("Copied sequences");
2226 if (Desktop.jalviewClipboard != null
2227 && Desktop.jalviewClipboard[2] != null)
2229 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2230 for (int[] region : hc)
2232 af.viewport.hideColumns(region[0], region[1]);
2236 // >>>This is a fix for the moment, until a better solution is
2238 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2240 alignPanel.getSeqPanel().seqCanvas
2241 .getFeatureRenderer());
2243 // TODO: maintain provenance of an alignment, rather than just make the
2244 // title a concatenation of operations.
2247 if (title.startsWith("Copied sequences"))
2253 newtitle = newtitle.concat("- from " + title);
2258 newtitle = new String("Pasted sequences");
2261 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2266 } catch (Exception ex)
2268 ex.printStackTrace();
2269 System.out.println("Exception whilst pasting: " + ex);
2270 // could be anything being pasted in here
2276 protected void expand_newalign(ActionEvent e)
2280 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2281 .getAlignment(), -1);
2282 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2284 String newtitle = new String("Flanking alignment");
2286 if (Desktop.jalviewClipboard != null
2287 && Desktop.jalviewClipboard[2] != null)
2289 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2290 for (int region[] : hc)
2292 af.viewport.hideColumns(region[0], region[1]);
2296 // >>>This is a fix for the moment, until a better solution is
2298 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2300 alignPanel.getSeqPanel().seqCanvas
2301 .getFeatureRenderer());
2303 // TODO: maintain provenance of an alignment, rather than just make the
2304 // title a concatenation of operations.
2306 if (title.startsWith("Copied sequences"))
2312 newtitle = newtitle.concat("- from " + title);
2316 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2318 } catch (Exception ex)
2320 ex.printStackTrace();
2321 System.out.println("Exception whilst pasting: " + ex);
2322 // could be anything being pasted in here
2323 } catch (OutOfMemoryError oom)
2325 new OOMWarning("Viewing flanking region of alignment", oom);
2336 protected void cut_actionPerformed(ActionEvent e)
2338 copy_actionPerformed(null);
2339 delete_actionPerformed(null);
2349 protected void delete_actionPerformed(ActionEvent evt)
2352 SequenceGroup sg = viewport.getSelectionGroup();
2359 * If the cut affects all sequences, warn, remove highlighted columns
2361 if (sg.getSize() == viewport.getAlignment().getHeight())
2363 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2364 .getAlignment().getWidth()) ? true : false;
2365 if (isEntireAlignWidth)
2367 int confirm = JOptionPane.showConfirmDialog(this,
2368 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2369 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2370 JOptionPane.OK_CANCEL_OPTION);
2372 if (confirm == JOptionPane.CANCEL_OPTION
2373 || confirm == JOptionPane.CLOSED_OPTION)
2378 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2379 sg.getEndRes() + 1);
2381 SequenceI[] cut = sg.getSequences()
2382 .toArray(new SequenceI[sg.getSize()]);
2384 addHistoryItem(new EditCommand(
2385 MessageManager.getString("label.cut_sequences"), Action.CUT,
2386 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2387 viewport.getAlignment()));
2389 viewport.setSelectionGroup(null);
2390 viewport.sendSelection();
2391 viewport.getAlignment().deleteGroup(sg);
2393 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2395 if (viewport.getAlignment().getHeight() < 1)
2399 this.setClosed(true);
2400 } catch (Exception ex)
2413 protected void deleteGroups_actionPerformed(ActionEvent e)
2415 if (avc.deleteGroups())
2417 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2418 alignPanel.updateAnnotation();
2419 alignPanel.paintAlignment(true);
2430 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2432 SequenceGroup sg = new SequenceGroup();
2434 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2436 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2439 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2440 viewport.setSelectionGroup(sg);
2441 viewport.sendSelection();
2442 alignPanel.paintAlignment(true);
2443 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2453 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2455 if (viewport.cursorMode)
2457 alignPanel.getSeqPanel().keyboardNo1 = null;
2458 alignPanel.getSeqPanel().keyboardNo2 = null;
2460 viewport.setSelectionGroup(null);
2461 viewport.getColumnSelection().clear();
2462 viewport.setSelectionGroup(null);
2463 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2464 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2465 alignPanel.paintAlignment(true);
2466 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2467 viewport.sendSelection();
2477 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2479 SequenceGroup sg = viewport.getSelectionGroup();
2483 selectAllSequenceMenuItem_actionPerformed(null);
2488 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2490 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2493 alignPanel.paintAlignment(true);
2494 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2495 viewport.sendSelection();
2499 public void invertColSel_actionPerformed(ActionEvent e)
2501 viewport.invertColumnSelection();
2502 alignPanel.paintAlignment(true);
2503 viewport.sendSelection();
2513 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2515 trimAlignment(true);
2525 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2527 trimAlignment(false);
2530 void trimAlignment(boolean trimLeft)
2532 ColumnSelection colSel = viewport.getColumnSelection();
2535 if (!colSel.isEmpty())
2539 column = colSel.getMin();
2543 column = colSel.getMax();
2547 if (viewport.getSelectionGroup() != null)
2549 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2550 viewport.getHiddenRepSequences());
2554 seqs = viewport.getAlignment().getSequencesArray();
2557 TrimRegionCommand trimRegion;
2560 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2561 column, viewport.getAlignment());
2562 viewport.setStartRes(0);
2566 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2567 column, viewport.getAlignment());
2570 statusBar.setText(MessageManager.formatMessage(
2571 "label.removed_columns",
2572 new String[] { Integer.valueOf(trimRegion.getSize())
2575 addHistoryItem(trimRegion);
2577 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2579 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2580 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2582 viewport.getAlignment().deleteGroup(sg);
2586 viewport.firePropertyChange("alignment", null, viewport
2587 .getAlignment().getSequences());
2598 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2600 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2603 if (viewport.getSelectionGroup() != null)
2605 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2606 viewport.getHiddenRepSequences());
2607 start = viewport.getSelectionGroup().getStartRes();
2608 end = viewport.getSelectionGroup().getEndRes();
2612 seqs = viewport.getAlignment().getSequencesArray();
2615 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2616 "Remove Gapped Columns", seqs, start, end,
2617 viewport.getAlignment());
2619 addHistoryItem(removeGapCols);
2621 statusBar.setText(MessageManager.formatMessage(
2622 "label.removed_empty_columns",
2623 new Object[] { Integer.valueOf(removeGapCols.getSize())
2626 // This is to maintain viewport position on first residue
2627 // of first sequence
2628 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2629 int startRes = seq.findPosition(viewport.startRes);
2630 // ShiftList shifts;
2631 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2632 // edit.alColumnChanges=shifts.getInverse();
2633 // if (viewport.hasHiddenColumns)
2634 // viewport.getColumnSelection().compensateForEdits(shifts);
2635 viewport.setStartRes(seq.findIndex(startRes) - 1);
2636 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2648 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2650 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2653 if (viewport.getSelectionGroup() != null)
2655 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2656 viewport.getHiddenRepSequences());
2657 start = viewport.getSelectionGroup().getStartRes();
2658 end = viewport.getSelectionGroup().getEndRes();
2662 seqs = viewport.getAlignment().getSequencesArray();
2665 // This is to maintain viewport position on first residue
2666 // of first sequence
2667 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2668 int startRes = seq.findPosition(viewport.startRes);
2670 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2671 viewport.getAlignment()));
2673 viewport.setStartRes(seq.findIndex(startRes) - 1);
2675 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2687 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2689 viewport.setPadGaps(padGapsMenuitem.isSelected());
2690 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2701 public void findMenuItem_actionPerformed(ActionEvent e)
2707 * Create a new view of the current alignment.
2710 public void newView_actionPerformed(ActionEvent e)
2712 newView(null, true);
2716 * Creates and shows a new view of the current alignment.
2719 * title of newly created view; if null, one will be generated
2720 * @param copyAnnotation
2721 * if true then duplicate all annnotation, groups and settings
2722 * @return new alignment panel, already displayed.
2724 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2727 * Create a new AlignmentPanel (with its own, new Viewport)
2729 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2731 if (!copyAnnotation)
2734 * remove all groups and annotation except for the automatic stuff
2736 newap.av.getAlignment().deleteAllGroups();
2737 newap.av.getAlignment().deleteAllAnnotations(false);
2740 newap.av.setGatherViewsHere(false);
2742 if (viewport.viewName == null)
2744 viewport.viewName = MessageManager
2745 .getString("label.view_name_original");
2749 * Views share the same edits undo and redo stacks
2751 newap.av.setHistoryList(viewport.getHistoryList());
2752 newap.av.setRedoList(viewport.getRedoList());
2755 * Views share the same mappings; need to deregister any new mappings
2756 * created by copyAlignPanel, and register the new reference to the shared
2759 newap.av.replaceMappings(viewport.getAlignment());
2761 newap.av.viewName = getNewViewName(viewTitle);
2763 addAlignmentPanel(newap, true);
2764 newap.alignmentChanged();
2766 if (alignPanels.size() == 2)
2768 viewport.setGatherViewsHere(true);
2770 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2775 * Make a new name for the view, ensuring it is unique within the current
2776 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2777 * these now use viewId. Unique view names are still desirable for usability.)
2782 protected String getNewViewName(String viewTitle)
2784 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2785 boolean addFirstIndex = false;
2786 if (viewTitle == null || viewTitle.trim().length() == 0)
2788 viewTitle = MessageManager.getString("action.view");
2789 addFirstIndex = true;
2793 index = 1;// we count from 1 if given a specific name
2795 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2797 List<Component> comps = PaintRefresher.components.get(viewport
2798 .getSequenceSetId());
2800 List<String> existingNames = getExistingViewNames(comps);
2802 while (existingNames.contains(newViewName))
2804 newViewName = viewTitle + " " + (++index);
2810 * Returns a list of distinct view names found in the given list of
2811 * components. View names are held on the viewport of an AlignmentPanel.
2816 protected List<String> getExistingViewNames(List<Component> comps)
2818 List<String> existingNames = new ArrayList<String>();
2819 for (Component comp : comps)
2821 if (comp instanceof AlignmentPanel)
2823 AlignmentPanel ap = (AlignmentPanel) comp;
2824 if (!existingNames.contains(ap.av.viewName))
2826 existingNames.add(ap.av.viewName);
2830 return existingNames;
2834 * Explode tabbed views into separate windows.
2837 public void expandViews_actionPerformed(ActionEvent e)
2839 Desktop.instance.explodeViews(this);
2843 * Gather views in separate windows back into a tabbed presentation.
2846 public void gatherViews_actionPerformed(ActionEvent e)
2848 Desktop.instance.gatherViews(this);
2858 public void font_actionPerformed(ActionEvent e)
2860 new FontChooser(alignPanel);
2870 protected void seqLimit_actionPerformed(ActionEvent e)
2872 viewport.setShowJVSuffix(seqLimits.isSelected());
2874 alignPanel.getIdPanel().getIdCanvas()
2875 .setPreferredSize(alignPanel.calculateIdWidth());
2876 alignPanel.paintAlignment(true);
2880 public void idRightAlign_actionPerformed(ActionEvent e)
2882 viewport.setRightAlignIds(idRightAlign.isSelected());
2883 alignPanel.paintAlignment(true);
2887 public void centreColumnLabels_actionPerformed(ActionEvent e)
2889 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2890 alignPanel.paintAlignment(true);
2896 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2899 protected void followHighlight_actionPerformed()
2902 * Set the 'follow' flag on the Viewport (and scroll to position if now
2905 final boolean state = this.followHighlightMenuItem.getState();
2906 viewport.setFollowHighlight(state);
2909 alignPanel.scrollToPosition(
2910 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2921 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2923 viewport.setColourText(colourTextMenuItem.isSelected());
2924 alignPanel.paintAlignment(true);
2934 public void wrapMenuItem_actionPerformed(ActionEvent e)
2936 scaleAbove.setVisible(wrapMenuItem.isSelected());
2937 scaleLeft.setVisible(wrapMenuItem.isSelected());
2938 scaleRight.setVisible(wrapMenuItem.isSelected());
2939 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2940 alignPanel.updateLayout();
2944 public void showAllSeqs_actionPerformed(ActionEvent e)
2946 viewport.showAllHiddenSeqs();
2950 public void showAllColumns_actionPerformed(ActionEvent e)
2952 viewport.showAllHiddenColumns();
2954 viewport.sendSelection();
2958 public void hideSelSequences_actionPerformed(ActionEvent e)
2960 viewport.hideAllSelectedSeqs();
2961 // alignPanel.paintAlignment(true);
2965 * called by key handler and the hide all/show all menu items
2970 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2973 boolean hide = false;
2974 SequenceGroup sg = viewport.getSelectionGroup();
2975 if (!toggleSeqs && !toggleCols)
2977 // Hide everything by the current selection - this is a hack - we do the
2978 // invert and then hide
2979 // first check that there will be visible columns after the invert.
2980 if ((viewport.getColumnSelection() != null
2981 && viewport.getColumnSelection().getSelected() != null && viewport
2982 .getColumnSelection().getSelected().size() > 0)
2983 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2986 // now invert the sequence set, if required - empty selection implies
2987 // that no hiding is required.
2990 invertSequenceMenuItem_actionPerformed(null);
2991 sg = viewport.getSelectionGroup();
2995 viewport.expandColSelection(sg, true);
2996 // finally invert the column selection and get the new sequence
2998 invertColSel_actionPerformed(null);
3005 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3007 hideSelSequences_actionPerformed(null);
3010 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3013 showAllSeqs_actionPerformed(null);
3019 if (viewport.getColumnSelection().getSelected().size() > 0)
3021 hideSelColumns_actionPerformed(null);
3024 viewport.setSelectionGroup(sg);
3029 showAllColumns_actionPerformed(null);
3038 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3039 * event.ActionEvent)
3042 public void hideAllButSelection_actionPerformed(ActionEvent e)
3044 toggleHiddenRegions(false, false);
3045 viewport.sendSelection();
3052 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3056 public void hideAllSelection_actionPerformed(ActionEvent e)
3058 SequenceGroup sg = viewport.getSelectionGroup();
3059 viewport.expandColSelection(sg, false);
3060 viewport.hideAllSelectedSeqs();
3061 viewport.hideSelectedColumns();
3062 alignPanel.paintAlignment(true);
3063 viewport.sendSelection();
3070 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3074 public void showAllhidden_actionPerformed(ActionEvent e)
3076 viewport.showAllHiddenColumns();
3077 viewport.showAllHiddenSeqs();
3078 alignPanel.paintAlignment(true);
3079 viewport.sendSelection();
3083 public void hideSelColumns_actionPerformed(ActionEvent e)
3085 viewport.hideSelectedColumns();
3086 alignPanel.paintAlignment(true);
3087 viewport.sendSelection();
3091 public void hiddenMarkers_actionPerformed(ActionEvent e)
3093 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3104 protected void scaleAbove_actionPerformed(ActionEvent e)
3106 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3107 alignPanel.paintAlignment(true);
3117 protected void scaleLeft_actionPerformed(ActionEvent e)
3119 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3120 alignPanel.paintAlignment(true);
3130 protected void scaleRight_actionPerformed(ActionEvent e)
3132 viewport.setScaleRightWrapped(scaleRight.isSelected());
3133 alignPanel.paintAlignment(true);
3143 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3145 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3146 alignPanel.paintAlignment(true);
3156 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3158 viewport.setShowText(viewTextMenuItem.isSelected());
3159 alignPanel.paintAlignment(true);
3169 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3171 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3172 alignPanel.paintAlignment(true);
3175 public FeatureSettings featureSettings;
3178 public FeatureSettingsControllerI getFeatureSettingsUI()
3180 return featureSettings;
3184 public void featureSettings_actionPerformed(ActionEvent e)
3186 if (featureSettings != null)
3188 featureSettings.close();
3189 featureSettings = null;
3191 if (!showSeqFeatures.isSelected())
3193 // make sure features are actually displayed
3194 showSeqFeatures.setSelected(true);
3195 showSeqFeatures_actionPerformed(null);
3197 featureSettings = new FeatureSettings(this);
3201 * Set or clear 'Show Sequence Features'
3207 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3209 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3210 alignPanel.paintAlignment(true);
3211 if (alignPanel.getOverviewPanel() != null)
3213 alignPanel.getOverviewPanel().updateOverviewImage();
3218 * Set or clear 'Show Sequence Features'
3224 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3226 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3228 if (viewport.isShowSequenceFeaturesHeight())
3230 // ensure we're actually displaying features
3231 viewport.setShowSequenceFeatures(true);
3232 showSeqFeatures.setSelected(true);
3234 alignPanel.paintAlignment(true);
3235 if (alignPanel.getOverviewPanel() != null)
3237 alignPanel.getOverviewPanel().updateOverviewImage();
3242 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3243 * the annotations panel as a whole.
3245 * The options to show/hide all annotations should be enabled when the panel
3246 * is shown, and disabled when the panel is hidden.
3251 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3253 final boolean setVisible = annotationPanelMenuItem.isSelected();
3254 viewport.setShowAnnotation(setVisible);
3255 this.showAllSeqAnnotations.setEnabled(setVisible);
3256 this.hideAllSeqAnnotations.setEnabled(setVisible);
3257 this.showAllAlAnnotations.setEnabled(setVisible);
3258 this.hideAllAlAnnotations.setEnabled(setVisible);
3259 alignPanel.updateLayout();
3263 public void alignmentProperties()
3265 JEditorPane editPane = new JEditorPane("text/html", "");
3266 editPane.setEditable(false);
3267 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3269 editPane.setText(MessageManager.formatMessage("label.html_content",
3270 new Object[] { contents.toString() }));
3271 JInternalFrame frame = new JInternalFrame();
3272 frame.getContentPane().add(new JScrollPane(editPane));
3274 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3275 "label.alignment_properties", new Object[] { getTitle() }),
3286 public void overviewMenuItem_actionPerformed(ActionEvent e)
3288 if (alignPanel.overviewPanel != null)
3293 JInternalFrame frame = new JInternalFrame();
3294 OverviewPanel overview = new OverviewPanel(alignPanel);
3295 frame.setContentPane(overview);
3296 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3297 "label.overview_params", new Object[] { this.getTitle() }),
3298 frame.getWidth(), frame.getHeight());
3300 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3301 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3304 public void internalFrameClosed(
3305 javax.swing.event.InternalFrameEvent evt)
3307 alignPanel.setOverviewPanel(null);
3311 alignPanel.setOverviewPanel(overview);
3315 public void textColour_actionPerformed(ActionEvent e)
3317 new TextColourChooser().chooseColour(alignPanel, null);
3327 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3339 public void clustalColour_actionPerformed(ActionEvent e)
3341 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3342 viewport.getHiddenRepSequences()));
3352 public void zappoColour_actionPerformed(ActionEvent e)
3354 changeColour(new ZappoColourScheme());
3364 public void taylorColour_actionPerformed(ActionEvent e)
3366 changeColour(new TaylorColourScheme());
3376 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3378 changeColour(new HydrophobicColourScheme());
3388 public void helixColour_actionPerformed(ActionEvent e)
3390 changeColour(new HelixColourScheme());
3400 public void strandColour_actionPerformed(ActionEvent e)
3402 changeColour(new StrandColourScheme());
3412 public void turnColour_actionPerformed(ActionEvent e)
3414 changeColour(new TurnColourScheme());
3424 public void buriedColour_actionPerformed(ActionEvent e)
3426 changeColour(new BuriedColourScheme());
3436 public void nucleotideColour_actionPerformed(ActionEvent e)
3438 changeColour(new NucleotideColourScheme());
3442 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3444 changeColour(new PurinePyrimidineColourScheme());
3448 * public void covariationColour_actionPerformed(ActionEvent e) {
3450 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3454 public void annotationColour_actionPerformed(ActionEvent e)
3456 new AnnotationColourChooser(viewport, alignPanel);
3460 public void annotationColumn_actionPerformed(ActionEvent e)
3462 new AnnotationColumnChooser(viewport, alignPanel);
3466 public void rnahelicesColour_actionPerformed(ActionEvent e)
3468 new RNAHelicesColourChooser(viewport, alignPanel);
3478 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3480 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3490 public void changeColour(ColourSchemeI cs)
3492 // TODO: pull up to controller method
3496 // Make sure viewport is up to date w.r.t. any sliders
3497 if (viewport.getAbovePIDThreshold())
3499 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3501 viewport.setThreshold(threshold);
3504 if (viewport.getConservationSelected())
3506 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3509 if (cs instanceof TCoffeeColourScheme)
3511 tcoffeeColour.setEnabled(true);
3512 tcoffeeColour.setSelected(true);
3516 viewport.setGlobalColourScheme(cs);
3518 alignPanel.paintAlignment(true);
3528 protected void modifyPID_actionPerformed(ActionEvent e)
3530 if (viewport.getAbovePIDThreshold()
3531 && viewport.getGlobalColourScheme() != null)
3533 SliderPanel.setPIDSliderSource(alignPanel,
3534 viewport.getGlobalColourScheme(), "Background");
3535 SliderPanel.showPIDSlider();
3546 protected void modifyConservation_actionPerformed(ActionEvent e)
3548 if (viewport.getConservationSelected()
3549 && viewport.getGlobalColourScheme() != null)
3551 SliderPanel.setConservationSlider(alignPanel,
3552 viewport.getGlobalColourScheme(), "Background");
3553 SliderPanel.showConservationSlider();
3564 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3566 viewport.setConservationSelected(conservationMenuItem.isSelected());
3568 viewport.setAbovePIDThreshold(false);
3569 abovePIDThreshold.setSelected(false);
3571 changeColour(viewport.getGlobalColourScheme());
3573 modifyConservation_actionPerformed(null);
3583 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3585 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3587 conservationMenuItem.setSelected(false);
3588 viewport.setConservationSelected(false);
3590 changeColour(viewport.getGlobalColourScheme());
3592 modifyPID_actionPerformed(null);
3602 public void userDefinedColour_actionPerformed(ActionEvent e)
3604 if (e.getActionCommand().equals(
3605 MessageManager.getString("action.user_defined")))
3607 new UserDefinedColours(alignPanel, null);
3611 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3612 .getUserColourSchemes().get(e.getActionCommand());
3618 public void updateUserColourMenu()
3621 Component[] menuItems = colourMenu.getMenuComponents();
3622 int iSize = menuItems.length;
3623 for (int i = 0; i < iSize; i++)
3625 if (menuItems[i].getName() != null
3626 && menuItems[i].getName().equals("USER_DEFINED"))
3628 colourMenu.remove(menuItems[i]);
3632 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3634 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3635 .getUserColourSchemes().keys();
3637 while (userColours.hasMoreElements())
3639 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3640 userColours.nextElement().toString());
3641 radioItem.setName("USER_DEFINED");
3642 radioItem.addMouseListener(new MouseAdapter()
3645 public void mousePressed(MouseEvent evt)
3647 if (evt.isPopupTrigger())
3649 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3651 int option = JOptionPane.showInternalConfirmDialog(
3652 jalview.gui.Desktop.desktop,
3654 .getString("label.remove_from_default_list"),
3656 .getString("label.remove_user_defined_colour"),
3657 JOptionPane.YES_NO_OPTION);
3658 if (option == JOptionPane.YES_OPTION)
3660 jalview.gui.UserDefinedColours
3661 .removeColourFromDefaults(radioItem.getText());
3662 colourMenu.remove(radioItem);
3666 radioItem.addActionListener(new ActionListener()
3669 public void actionPerformed(ActionEvent evt)
3671 userDefinedColour_actionPerformed(evt);
3678 radioItem.addActionListener(new ActionListener()
3681 public void actionPerformed(ActionEvent evt)
3683 userDefinedColour_actionPerformed(evt);
3687 colourMenu.insert(radioItem, 15);
3688 colours.add(radioItem);
3700 public void PIDColour_actionPerformed(ActionEvent e)
3702 changeColour(new PIDColourScheme());
3712 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3714 changeColour(new Blosum62ColourScheme());
3724 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3726 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3727 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3728 .getAlignment().getSequenceAt(0), null);
3729 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3730 viewport.getAlignment()));
3731 alignPanel.paintAlignment(true);
3741 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3743 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3744 AlignmentSorter.sortByID(viewport.getAlignment());
3745 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3746 viewport.getAlignment()));
3747 alignPanel.paintAlignment(true);
3757 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3759 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3760 AlignmentSorter.sortByLength(viewport.getAlignment());
3761 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3762 viewport.getAlignment()));
3763 alignPanel.paintAlignment(true);
3773 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3775 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3776 AlignmentSorter.sortByGroup(viewport.getAlignment());
3777 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3778 viewport.getAlignment()));
3780 alignPanel.paintAlignment(true);
3790 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3792 new RedundancyPanel(alignPanel, this);
3802 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3804 if ((viewport.getSelectionGroup() == null)
3805 || (viewport.getSelectionGroup().getSize() < 2))
3807 JOptionPane.showInternalMessageDialog(this, MessageManager
3808 .getString("label.you_must_select_least_two_sequences"),
3809 MessageManager.getString("label.invalid_selection"),
3810 JOptionPane.WARNING_MESSAGE);
3814 JInternalFrame frame = new JInternalFrame();
3815 frame.setContentPane(new PairwiseAlignPanel(viewport));
3816 Desktop.addInternalFrame(frame,
3817 MessageManager.getString("action.pairwise_alignment"), 600,
3829 public void PCAMenuItem_actionPerformed(ActionEvent e)
3831 if (((viewport.getSelectionGroup() != null)
3832 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3833 .getSelectionGroup().getSize() > 0))
3834 || (viewport.getAlignment().getHeight() < 4))
3837 .showInternalMessageDialog(
3840 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3842 .getString("label.sequence_selection_insufficient"),
3843 JOptionPane.WARNING_MESSAGE);
3848 new PCAPanel(alignPanel);
3852 public void autoCalculate_actionPerformed(ActionEvent e)
3854 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3855 if (viewport.autoCalculateConsensus)
3857 viewport.firePropertyChange("alignment", null, viewport
3858 .getAlignment().getSequences());
3863 public void sortByTreeOption_actionPerformed(ActionEvent e)
3865 viewport.sortByTree = sortByTree.isSelected();
3869 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3871 viewport.followSelection = listenToViewSelections.isSelected();
3881 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3883 newTreePanel("AV", "PID", "Average distance tree using PID");
3893 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3895 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3905 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3907 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3917 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3919 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3932 void newTreePanel(String type, String pwType, String title)
3936 if (viewport.getSelectionGroup() != null
3937 && viewport.getSelectionGroup().getSize() > 0)
3939 if (viewport.getSelectionGroup().getSize() < 3)
3945 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3947 .getString("label.not_enough_sequences"),
3948 JOptionPane.WARNING_MESSAGE);
3952 SequenceGroup sg = viewport.getSelectionGroup();
3954 /* Decide if the selection is a column region */
3955 for (SequenceI _s : sg.getSequences())
3957 if (_s.getLength() < sg.getEndRes())
3963 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3965 .getString("label.sequences_selection_not_aligned"),
3966 JOptionPane.WARNING_MESSAGE);
3972 title = title + " on region";
3973 tp = new TreePanel(alignPanel, type, pwType);
3977 // are the visible sequences aligned?
3978 if (!viewport.getAlignment().isAligned(false))
3984 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3986 .getString("label.sequences_not_aligned"),
3987 JOptionPane.WARNING_MESSAGE);
3992 if (viewport.getAlignment().getHeight() < 2)
3997 tp = new TreePanel(alignPanel, type, pwType);
4002 if (viewport.viewName != null)
4004 title += viewport.viewName + " of ";
4007 title += this.title;
4009 Desktop.addInternalFrame(tp, title, 600, 500);
4020 public void addSortByOrderMenuItem(String title,
4021 final AlignmentOrder order)
4023 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4024 "action.by_title_param", new Object[] { title }));
4026 item.addActionListener(new java.awt.event.ActionListener()
4029 public void actionPerformed(ActionEvent e)
4031 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4033 // TODO: JBPNote - have to map order entries to curent SequenceI
4035 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4037 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4040 alignPanel.paintAlignment(true);
4046 * Add a new sort by annotation score menu item
4049 * the menu to add the option to
4051 * the label used to retrieve scores for each sequence on the
4054 public void addSortByAnnotScoreMenuItem(JMenu sort,
4055 final String scoreLabel)
4057 final JMenuItem item = new JMenuItem(scoreLabel);
4059 item.addActionListener(new java.awt.event.ActionListener()
4062 public void actionPerformed(ActionEvent e)
4064 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4065 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4066 viewport.getAlignment());// ,viewport.getSelectionGroup());
4067 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4068 viewport.getAlignment()));
4069 alignPanel.paintAlignment(true);
4075 * last hash for alignment's annotation array - used to minimise cost of
4078 protected int _annotationScoreVectorHash;
4081 * search the alignment and rebuild the sort by annotation score submenu the
4082 * last alignment annotation vector hash is stored to minimize cost of
4083 * rebuilding in subsequence calls.
4087 public void buildSortByAnnotationScoresMenu()
4089 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4094 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4096 sortByAnnotScore.removeAll();
4097 // almost certainly a quicker way to do this - but we keep it simple
4098 Hashtable scoreSorts = new Hashtable();
4099 AlignmentAnnotation aann[];
4100 for (SequenceI sqa : viewport.getAlignment().getSequences())
4102 aann = sqa.getAnnotation();
4103 for (int i = 0; aann != null && i < aann.length; i++)
4105 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4107 scoreSorts.put(aann[i].label, aann[i].label);
4111 Enumeration labels = scoreSorts.keys();
4112 while (labels.hasMoreElements())
4114 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4115 (String) labels.nextElement());
4117 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4120 _annotationScoreVectorHash = viewport.getAlignment()
4121 .getAlignmentAnnotation().hashCode();
4126 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4127 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4128 * call. Listeners are added to remove the menu item when the treePanel is
4129 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4133 * Displayed tree window.
4135 * SortBy menu item title.
4138 public void buildTreeMenu()
4140 calculateTree.removeAll();
4141 // build the calculate menu
4143 for (final String type : new String[] { "NJ", "AV" })
4145 String treecalcnm = MessageManager.getString("label.tree_calc_"
4146 + type.toLowerCase());
4147 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4149 JMenuItem tm = new JMenuItem();
4150 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4151 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4152 || sm.isProtein() == !viewport.getAlignment()
4155 String smn = MessageManager.getStringOrReturn(
4156 "label.score_model_", sm.getName());
4157 final String title = MessageManager.formatMessage(
4158 "label.treecalc_title", treecalcnm, smn);
4159 tm.setText(title);//
4160 tm.addActionListener(new java.awt.event.ActionListener()
4163 public void actionPerformed(ActionEvent e)
4165 newTreePanel(type, pwtype, title);
4168 calculateTree.add(tm);
4173 sortByTreeMenu.removeAll();
4175 List<Component> comps = PaintRefresher.components.get(viewport
4176 .getSequenceSetId());
4177 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4178 for (Component comp : comps)
4180 if (comp instanceof TreePanel)
4182 treePanels.add((TreePanel) comp);
4186 if (treePanels.size() < 1)
4188 sortByTreeMenu.setVisible(false);
4192 sortByTreeMenu.setVisible(true);
4194 for (final TreePanel tp : treePanels)
4196 final JMenuItem item = new JMenuItem(tp.getTitle());
4197 item.addActionListener(new java.awt.event.ActionListener()
4200 public void actionPerformed(ActionEvent e)
4202 tp.sortByTree_actionPerformed();
4203 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4208 sortByTreeMenu.add(item);
4212 public boolean sortBy(AlignmentOrder alorder, String undoname)
4214 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4215 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4216 if (undoname != null)
4218 addHistoryItem(new OrderCommand(undoname, oldOrder,
4219 viewport.getAlignment()));
4221 alignPanel.paintAlignment(true);
4226 * Work out whether the whole set of sequences or just the selected set will
4227 * be submitted for multiple alignment.
4230 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4232 // Now, check we have enough sequences
4233 AlignmentView msa = null;
4235 if ((viewport.getSelectionGroup() != null)
4236 && (viewport.getSelectionGroup().getSize() > 1))
4238 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4239 // some common interface!
4241 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4242 * SequenceI[sz = seqs.getSize(false)];
4244 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4245 * seqs.getSequenceAt(i); }
4247 msa = viewport.getAlignmentView(true);
4249 else if (viewport.getSelectionGroup() != null
4250 && viewport.getSelectionGroup().getSize() == 1)
4252 int option = JOptionPane.showConfirmDialog(this,
4253 MessageManager.getString("warn.oneseq_msainput_selection"),
4254 MessageManager.getString("label.invalid_selection"),
4255 JOptionPane.OK_CANCEL_OPTION);
4256 if (option == JOptionPane.OK_OPTION)
4258 msa = viewport.getAlignmentView(false);
4263 msa = viewport.getAlignmentView(false);
4269 * Decides what is submitted to a secondary structure prediction service: the
4270 * first sequence in the alignment, or in the current selection, or, if the
4271 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4272 * region or the whole alignment. (where the first sequence in the set is the
4273 * one that the prediction will be for).
4275 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4277 AlignmentView seqs = null;
4279 if ((viewport.getSelectionGroup() != null)
4280 && (viewport.getSelectionGroup().getSize() > 0))
4282 seqs = viewport.getAlignmentView(true);
4286 seqs = viewport.getAlignmentView(false);
4288 // limit sequences - JBPNote in future - could spawn multiple prediction
4290 // TODO: viewport.getAlignment().isAligned is a global state - the local
4291 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4292 if (!viewport.getAlignment().isAligned(false))
4294 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4295 // TODO: if seqs.getSequences().length>1 then should really have warned
4309 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4311 // Pick the tree file
4312 JalviewFileChooser chooser = new JalviewFileChooser(
4313 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4314 chooser.setFileView(new JalviewFileView());
4315 chooser.setDialogTitle(MessageManager
4316 .getString("label.select_newick_like_tree_file"));
4317 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4319 int value = chooser.showOpenDialog(null);
4321 if (value == JalviewFileChooser.APPROVE_OPTION)
4323 String choice = chooser.getSelectedFile().getPath();
4324 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4325 jalview.io.NewickFile fin = null;
4328 fin = new NewickFile(choice, DataSourceType.FILE);
4329 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4330 } catch (Exception ex)
4337 .getString("label.problem_reading_tree_file"),
4338 JOptionPane.WARNING_MESSAGE);
4339 ex.printStackTrace();
4341 if (fin != null && fin.hasWarningMessage())
4343 JOptionPane.showMessageDialog(Desktop.desktop, fin
4344 .getWarningMessage(), MessageManager
4345 .getString("label.possible_problem_with_tree_file"),
4346 JOptionPane.WARNING_MESSAGE);
4352 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4354 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4357 public TreePanel ShowNewickTree(NewickFile nf, String title)
4359 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4362 public TreePanel ShowNewickTree(NewickFile nf, String title,
4363 AlignmentView input)
4365 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4368 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4369 int h, int x, int y)
4371 return ShowNewickTree(nf, title, null, w, h, x, y);
4375 * Add a treeviewer for the tree extracted from a newick file object to the
4376 * current alignment view
4383 * Associated alignment input data (or null)
4392 * @return TreePanel handle
4394 public TreePanel ShowNewickTree(NewickFile nf, String title,
4395 AlignmentView input, int w, int h, int x, int y)
4397 TreePanel tp = null;
4403 if (nf.getTree() != null)
4405 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4411 tp.setLocation(x, y);
4414 Desktop.addInternalFrame(tp, title, w, h);
4416 } catch (Exception ex)
4418 ex.printStackTrace();
4424 private boolean buildingMenu = false;
4427 * Generates menu items and listener event actions for web service clients
4430 public void BuildWebServiceMenu()
4432 while (buildingMenu)
4436 System.err.println("Waiting for building menu to finish.");
4438 } catch (Exception e)
4442 final AlignFrame me = this;
4443 buildingMenu = true;
4444 new Thread(new Runnable()
4449 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4452 // System.err.println("Building ws menu again "
4453 // + Thread.currentThread());
4454 // TODO: add support for context dependent disabling of services based
4456 // alignment and current selection
4457 // TODO: add additional serviceHandle parameter to specify abstract
4459 // class independently of AbstractName
4460 // TODO: add in rediscovery GUI function to restart discoverer
4461 // TODO: group services by location as well as function and/or
4463 // object broker mechanism.
4464 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4465 final IProgressIndicator af = me;
4466 final JMenu msawsmenu = new JMenu("Alignment");
4467 final JMenu secstrmenu = new JMenu(
4468 "Secondary Structure Prediction");
4469 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4470 final JMenu analymenu = new JMenu("Analysis");
4471 final JMenu dismenu = new JMenu("Protein Disorder");
4472 // final JMenu msawsmenu = new
4473 // JMenu(MessageManager.getString("label.alignment"));
4474 // final JMenu secstrmenu = new
4475 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4476 // final JMenu seqsrchmenu = new
4477 // JMenu(MessageManager.getString("label.sequence_database_search"));
4478 // final JMenu analymenu = new
4479 // JMenu(MessageManager.getString("label.analysis"));
4480 // final JMenu dismenu = new
4481 // JMenu(MessageManager.getString("label.protein_disorder"));
4482 // JAL-940 - only show secondary structure prediction services from
4483 // the legacy server
4484 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4486 Discoverer.services != null && (Discoverer.services.size() > 0))
4488 // TODO: refactor to allow list of AbstractName/Handler bindings to
4490 // stored or retrieved from elsewhere
4491 // No MSAWS used any more:
4492 // Vector msaws = null; // (Vector)
4493 // Discoverer.services.get("MsaWS");
4494 Vector secstrpr = (Vector) Discoverer.services
4496 if (secstrpr != null)
4498 // Add any secondary structure prediction services
4499 for (int i = 0, j = secstrpr.size(); i < j; i++)
4501 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4503 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4504 .getServiceClient(sh);
4505 int p = secstrmenu.getItemCount();
4506 impl.attachWSMenuEntry(secstrmenu, me);
4507 int q = secstrmenu.getItemCount();
4508 for (int litm = p; litm < q; litm++)
4510 legacyItems.add(secstrmenu.getItem(litm));
4516 // Add all submenus in the order they should appear on the web
4518 wsmenu.add(msawsmenu);
4519 wsmenu.add(secstrmenu);
4520 wsmenu.add(dismenu);
4521 wsmenu.add(analymenu);
4522 // No search services yet
4523 // wsmenu.add(seqsrchmenu);
4525 javax.swing.SwingUtilities.invokeLater(new Runnable()
4532 webService.removeAll();
4533 // first, add discovered services onto the webservices menu
4534 if (wsmenu.size() > 0)
4536 for (int i = 0, j = wsmenu.size(); i < j; i++)
4538 webService.add(wsmenu.get(i));
4543 webService.add(me.webServiceNoServices);
4545 // TODO: move into separate menu builder class.
4546 boolean new_sspred = false;
4547 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4549 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4550 if (jws2servs != null)
4552 if (jws2servs.hasServices())
4554 jws2servs.attachWSMenuEntry(webService, me);
4555 for (Jws2Instance sv : jws2servs.getServices())
4557 if (sv.description.toLowerCase().contains("jpred"))
4559 for (JMenuItem jmi : legacyItems)
4561 jmi.setVisible(false);
4567 if (jws2servs.isRunning())
4569 JMenuItem tm = new JMenuItem(
4570 "Still discovering JABA Services");
4571 tm.setEnabled(false);
4576 build_urlServiceMenu(me.webService);
4577 build_fetchdbmenu(webService);
4578 for (JMenu item : wsmenu)
4580 if (item.getItemCount() == 0)
4582 item.setEnabled(false);
4586 item.setEnabled(true);
4589 } catch (Exception e)
4592 .debug("Exception during web service menu building process.",
4597 } catch (Exception e)
4600 buildingMenu = false;
4607 * construct any groupURL type service menu entries.
4611 private void build_urlServiceMenu(JMenu webService)
4613 // TODO: remove this code when 2.7 is released
4614 // DEBUG - alignmentView
4616 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4617 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4619 * @Override public void actionPerformed(ActionEvent e) {
4620 * jalview.datamodel.AlignmentView
4621 * .testSelectionViews(af.viewport.getAlignment(),
4622 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4624 * }); webService.add(testAlView);
4626 // TODO: refactor to RestClient discoverer and merge menu entries for
4627 // rest-style services with other types of analysis/calculation service
4628 // SHmmr test client - still being implemented.
4629 // DEBUG - alignmentView
4631 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4634 client.attachWSMenuEntry(
4635 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4641 * Searches selected sequences for xRef products and builds the Show
4642 * Cross-References menu (formerly called Show Products)
4644 * @return true if Show Cross-references menu should be enabled.
4646 public boolean canShowProducts()
4648 SequenceI[] selection = viewport.getSequenceSelection();
4649 AlignmentI dataset = viewport.getAlignment().getDataset();
4650 boolean showp = false;
4653 showProducts.removeAll();
4654 final boolean dna = viewport.getAlignment().isNucleotide();
4655 String[] ptypes = (selection == null || selection.length == 0) ? null
4656 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4658 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4661 final AlignFrame af = this;
4662 final String source = ptypes[t];
4663 JMenuItem xtype = new JMenuItem(ptypes[t]);
4664 xtype.addActionListener(new ActionListener()
4668 public void actionPerformed(ActionEvent e)
4670 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4674 showProducts.add(xtype);
4676 showProducts.setVisible(showp);
4677 showProducts.setEnabled(showp);
4678 } catch (Exception e)
4680 jalview.bin.Cache.log
4681 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4689 * Finds and displays cross-references for the selected sequences (protein
4690 * products for nucleotide sequences, dna coding sequences for peptides).
4693 * the sequences to show cross-references for
4695 * true if from a nucleotide alignment (so showing proteins)
4697 * the database to show cross-references for
4699 protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4700 final String source)
4702 Runnable foo = new Runnable()
4708 final long sttime = System.currentTimeMillis();
4709 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4710 "status.searching_for_sequences_from",
4711 new Object[] { source }), sttime);
4714 AlignmentI alignment = AlignFrame.this.getViewport()
4716 AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
4721 * get display scheme (if any) to apply to features
4723 FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
4724 .getFeatureColourScheme(source);
4726 AlignmentI al = makeCrossReferencesAlignment(
4727 alignment.getDataset(), xrefs);
4729 AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4731 if (Cache.getDefault("HIDE_INTRONS", true))
4733 newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
4735 String newtitle = String.format("%s %s %s",
4736 MessageManager.getString(dna ? "label.proteins"
4737 : "label.nucleotides"), MessageManager
4738 .getString("label.for"), getTitle());
4739 newFrame.setTitle(newtitle);
4741 if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4744 * split frame display is turned off in preferences file
4746 Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4748 return; // via finally clause
4752 * Make a copy of this alignment (sharing the same dataset
4753 * sequences). If we are DNA, drop introns and update mappings
4755 AlignmentI copyAlignment = null;
4756 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4757 .getSequenceSelection();
4758 List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4759 boolean copyAlignmentIsAligned = false;
4762 copyAlignment = AlignmentUtils.makeCdsAlignment(
4763 sequenceSelection, cf, alignment);
4764 if (copyAlignment.getHeight() == 0)
4766 System.err.println("Failed to make CDS alignment");
4768 al.getCodonFrames().clear();
4769 al.addCodonFrames(copyAlignment.getCodonFrames());
4770 al.addCodonFrames(cf);
4773 * pending getting Embl transcripts to 'align',
4774 * we are only doing this for Ensembl
4776 // TODO proper criteria for 'can align as cdna'
4777 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
4778 || AlignmentUtils.looksLikeEnsembl(alignment))
4780 copyAlignment.alignAs(alignment);
4781 copyAlignmentIsAligned = true;
4786 copyAlignment = AlignmentUtils.makeCopyAlignment(
4787 sequenceSelection, xrefs.getSequencesArray());
4788 copyAlignment.addCodonFrames(cf);
4789 al.addCodonFrames(copyAlignment.getCodonFrames());
4790 al.addCodonFrames(cf);
4792 copyAlignment.setGapCharacter(AlignFrame.this.viewport
4793 .getGapCharacter());
4795 StructureSelectionManager ssm = StructureSelectionManager
4796 .getStructureSelectionManager(Desktop.instance);
4797 ssm.registerMappings(cf);
4799 if (copyAlignment.getHeight() <= 0)
4801 System.err.println("No Sequences generated for xRef type "
4806 * align protein to dna
4808 if (dna && copyAlignmentIsAligned)
4810 al.alignAs(copyAlignment);
4815 * align cdna to protein - currently only if
4816 * fetching and aligning Ensembl transcripts!
4818 if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
4820 copyAlignment.alignAs(al);
4824 AlignFrame copyThis = new AlignFrame(copyAlignment,
4825 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4826 copyThis.setTitle(AlignFrame.this.getTitle());
4828 boolean showSequenceFeatures = viewport
4829 .isShowSequenceFeatures();
4830 newFrame.setShowSeqFeatures(showSequenceFeatures);
4831 copyThis.setShowSeqFeatures(showSequenceFeatures);
4832 FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4833 .getFeatureRenderer();
4836 * copy feature rendering settings to split frame
4838 newFrame.alignPanel.getSeqPanel().seqCanvas
4839 .getFeatureRenderer()
4840 .transferSettings(myFeatureStyling);
4841 copyThis.alignPanel.getSeqPanel().seqCanvas
4842 .getFeatureRenderer()
4843 .transferSettings(myFeatureStyling);
4846 * apply 'database source' feature configuration
4849 // TODO is this the feature colouring for the original
4850 // alignment or the fetched xrefs? either could be Ensembl
4851 newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
4852 copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
4854 SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4855 dna ? newFrame : copyThis);
4856 newFrame.setVisible(true);
4857 copyThis.setVisible(true);
4858 String linkedTitle = MessageManager
4859 .getString("label.linked_view_title");
4860 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4863 } catch (Exception e)
4865 Cache.log.error("Exception when finding crossreferences", e);
4866 } catch (OutOfMemoryError e)
4868 new OOMWarning("whilst fetching crossreferences", e);
4869 } catch (Throwable e)
4871 Cache.log.error("Error when finding crossreferences", e);
4874 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4875 "status.finished_searching_for_sequences_from",
4876 new Object[] { source }), sttime);
4881 * Makes an alignment containing the given sequences. If this is of the
4882 * same type as the given dataset (nucleotide/protein), then the new
4883 * alignment shares the same dataset, and its dataset sequences are added
4884 * to it. Otherwise a new dataset sequence is created for the
4891 protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
4894 boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
4896 SequenceI[] sprods = new SequenceI[seqs.getHeight()];
4897 for (int s = 0; s < sprods.length; s++)
4899 sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
4902 if (dataset.getSequences() == null
4903 || !dataset.getSequences().contains(
4904 sprods[s].getDatasetSequence()))
4906 dataset.addSequence(sprods[s].getDatasetSequence());
4909 sprods[s].updatePDBIds();
4911 Alignment al = new Alignment(sprods);
4914 al.setDataset((Alignment) dataset);
4918 al.createDatasetAlignment();
4924 Thread frunner = new Thread(foo);
4929 * Construct and display a new frame containing the translation of this
4930 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4933 public void showTranslation_actionPerformed(ActionEvent e)
4935 AlignmentI al = null;
4938 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4940 al = dna.translateCdna();
4941 } catch (Exception ex)
4943 jalview.bin.Cache.log.error(
4944 "Exception during translation. Please report this !", ex);
4945 final String msg = MessageManager
4946 .getString("label.error_when_translating_sequences_submit_bug_report");
4947 final String errorTitle = MessageManager
4948 .getString("label.implementation_error")
4949 + MessageManager.getString("label.translation_failed");
4950 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4951 JOptionPane.ERROR_MESSAGE);
4954 if (al == null || al.getHeight() == 0)
4956 final String msg = MessageManager
4957 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4958 final String errorTitle = MessageManager
4959 .getString("label.translation_failed");
4960 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4961 JOptionPane.WARNING_MESSAGE);
4965 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4966 af.setFileFormat(this.currentFileFormat);
4967 final String newTitle = MessageManager.formatMessage(
4968 "label.translation_of_params",
4969 new Object[] { this.getTitle() });
4970 af.setTitle(newTitle);
4971 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4973 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4974 viewport.openSplitFrame(af, new Alignment(seqs));
4978 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4985 * Set the file format
4989 public void setFileFormat(FileFormatI format)
4991 this.currentFileFormat = format;
4995 * Try to load a features file onto the alignment.
4998 * contents or path to retrieve file
5000 * access mode of file (see jalview.io.AlignFile)
5001 * @return true if features file was parsed correctly.
5003 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
5005 return avc.parseFeaturesFile(file, sourceType,
5006 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5011 public void refreshFeatureUI(boolean enableIfNecessary)
5013 // note - currently this is only still here rather than in the controller
5014 // because of the featureSettings hard reference that is yet to be
5016 if (enableIfNecessary)
5018 viewport.setShowSequenceFeatures(true);
5019 showSeqFeatures.setSelected(true);
5025 public void dragEnter(DropTargetDragEvent evt)
5030 public void dragExit(DropTargetEvent evt)
5035 public void dragOver(DropTargetDragEvent evt)
5040 public void dropActionChanged(DropTargetDragEvent evt)
5045 public void drop(DropTargetDropEvent evt)
5047 Transferable t = evt.getTransferable();
5048 List<String> files = new ArrayList<String>();
5049 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
5053 Desktop.transferFromDropTarget(files, protocols, evt, t);
5054 } catch (Exception e)
5056 e.printStackTrace();
5062 // check to see if any of these files have names matching sequences in
5064 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5065 .getAlignment().getSequencesArray());
5067 * Object[] { String,SequenceI}
5069 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5070 ArrayList<String> filesnotmatched = new ArrayList<String>();
5071 for (int i = 0; i < files.size(); i++)
5073 String file = files.get(i).toString();
5075 DataSourceType protocol = FormatAdapter.checkProtocol(file);
5076 if (protocol == DataSourceType.FILE)
5078 File fl = new File(file);
5079 pdbfn = fl.getName();
5081 else if (protocol == DataSourceType.URL)
5083 URL url = new URL(file);
5084 pdbfn = url.getFile();
5086 if (pdbfn.length() > 0)
5088 // attempt to find a match in the alignment
5089 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5090 int l = 0, c = pdbfn.indexOf(".");
5091 while (mtch == null && c != -1)
5096 } while ((c = pdbfn.indexOf(".", l)) > l);
5099 pdbfn = pdbfn.substring(0, l);
5101 mtch = idm.findAllIdMatches(pdbfn);
5108 type = new IdentifyFile().identify(file, protocol);
5109 } catch (Exception ex)
5115 if (type.equalsIgnoreCase("PDB"))
5117 filesmatched.add(new Object[] { file, protocol, mtch });
5122 // File wasn't named like one of the sequences or wasn't a PDB file.
5123 filesnotmatched.add(file);
5127 if (filesmatched.size() > 0)
5129 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5135 "label.automatically_associate_pdb_files_with_sequences_same_name",
5136 new Object[] { Integer
5142 .getString("label.automatically_associate_pdb_files_by_name"),
5143 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5146 for (Object[] fm : filesmatched)
5148 // try and associate
5149 // TODO: may want to set a standard ID naming formalism for
5150 // associating PDB files which have no IDs.
5151 for (SequenceI toassoc : (SequenceI[]) fm[2])
5153 PDBEntry pe = new AssociatePdbFileWithSeq()
5154 .associatePdbWithSeq((String) fm[0],
5155 (String) fm[1], toassoc, false,
5159 System.err.println("Associated file : "
5160 + ((String) fm[0]) + " with "
5161 + toassoc.getDisplayId(true));
5165 alignPanel.paintAlignment(true);
5169 if (filesnotmatched.size() > 0)
5172 && (Cache.getDefault(
5173 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5179 "label.ignore_unmatched_dropped_files_info",
5180 new Object[] { Integer
5187 .getString("label.ignore_unmatched_dropped_files"),
5188 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5192 for (String fn : filesnotmatched)
5194 loadJalviewDataFile(fn, null, null, null);
5198 } catch (Exception ex)
5200 ex.printStackTrace();
5206 * Attempt to load a "dropped" file or URL string: First by testing whether
5207 * it's an Annotation file, then a JNet file, and finally a features file. If
5208 * all are false then the user may have dropped an alignment file onto this
5212 * either a filename or a URL string.
5214 public void loadJalviewDataFile(String file, DataSourceType sourceType,
5215 FileFormatI format, SequenceI assocSeq)
5219 if (sourceType == null)
5221 sourceType = FormatAdapter.checkProtocol(file);
5223 // if the file isn't identified, or not positively identified as some
5224 // other filetype (PFAM is default unidentified alignment file type) then
5225 // try to parse as annotation.
5226 boolean isAnnotation = (format == null || format == FileFormat.Pfam) ? new AnnotationFile()
5227 .annotateAlignmentView(viewport, file, sourceType) : false;
5231 // first see if its a T-COFFEE score file
5232 TCoffeeScoreFile tcf = null;
5235 tcf = new TCoffeeScoreFile(file, sourceType);
5238 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5240 tcoffeeColour.setEnabled(true);
5241 tcoffeeColour.setSelected(true);
5242 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5243 isAnnotation = true;
5245 .setText(MessageManager
5246 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5250 // some problem - if no warning its probable that the ID matching
5251 // process didn't work
5255 tcf.getWarningMessage() == null ? MessageManager
5256 .getString("label.check_file_matches_sequence_ids_alignment")
5257 : tcf.getWarningMessage(),
5259 .getString("label.problem_reading_tcoffee_score_file"),
5260 JOptionPane.WARNING_MESSAGE);
5267 } catch (Exception x)
5270 .debug("Exception when processing data source as T-COFFEE score file",
5276 // try to see if its a JNet 'concise' style annotation file *before*
5278 // try to parse it as a features file
5281 format = new IdentifyFile().identify(file, sourceType);
5283 if (format == FileFormat.Jnet)
5285 JPredFile predictions = new JPredFile(
5287 new JnetAnnotationMaker();
5288 JnetAnnotationMaker.add_annotation(predictions,
5289 viewport.getAlignment(), 0, false);
5290 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5291 viewport.getAlignment().setSeqrep(repseq);
5292 ColumnSelection cs = new ColumnSelection();
5293 cs.hideInsertionsFor(repseq);
5294 viewport.setColumnSelection(cs);
5295 isAnnotation = true;
5297 else if (IdentifyFile.FeaturesFile.equals(format))
5299 if (parseFeaturesFile(file, sourceType))
5301 alignPanel.paintAlignment(true);
5306 new FileLoader().LoadFile(viewport, file, sourceType, format);
5313 alignPanel.adjustAnnotationHeight();
5314 viewport.updateSequenceIdColours();
5315 buildSortByAnnotationScoresMenu();
5316 alignPanel.paintAlignment(true);
5318 } catch (Exception ex)
5320 ex.printStackTrace();
5321 } catch (OutOfMemoryError oom)
5326 } catch (Exception x)
5331 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
5332 : "using " + sourceType + " from " + file)
5334 + (format != null ? "(parsing as '" + format
5335 + "' file)" : ""), oom, Desktop.desktop);
5340 * Method invoked by the ChangeListener on the tabbed pane, in other words
5341 * when a different tabbed pane is selected by the user or programmatically.
5344 public void tabSelectionChanged(int index)
5348 alignPanel = alignPanels.get(index);
5349 viewport = alignPanel.av;
5350 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5351 setMenusFromViewport(viewport);
5355 * If there is a frame linked to this one in a SplitPane, switch it to the
5356 * same view tab index. No infinite recursion of calls should happen, since
5357 * tabSelectionChanged() should not get invoked on setting the selected
5358 * index to an unchanged value. Guard against setting an invalid index
5359 * before the new view peer tab has been created.
5361 final AlignViewportI peer = viewport.getCodingComplement();
5364 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5365 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5367 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5373 * On right mouse click on view tab, prompt for and set new view name.
5376 public void tabbedPane_mousePressed(MouseEvent e)
5378 if (e.isPopupTrigger())
5380 String msg = MessageManager.getString("label.enter_view_name");
5381 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5382 JOptionPane.QUESTION_MESSAGE);
5386 viewport.viewName = reply;
5387 // TODO warn if reply is in getExistingViewNames()?
5388 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5393 public AlignViewport getCurrentView()
5399 * Open the dialog for regex description parsing.
5402 protected void extractScores_actionPerformed(ActionEvent e)
5404 ParseProperties pp = new jalview.analysis.ParseProperties(
5405 viewport.getAlignment());
5406 // TODO: verify regex and introduce GUI dialog for version 2.5
5407 // if (pp.getScoresFromDescription("col", "score column ",
5408 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5410 if (pp.getScoresFromDescription("description column",
5411 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5413 buildSortByAnnotationScoresMenu();
5421 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5425 protected void showDbRefs_actionPerformed(ActionEvent e)
5427 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5433 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5437 protected void showNpFeats_actionPerformed(ActionEvent e)
5439 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5443 * find the viewport amongst the tabs in this alignment frame and close that
5448 public boolean closeView(AlignViewportI av)
5452 this.closeMenuItem_actionPerformed(false);
5455 Component[] comp = tabbedPane.getComponents();
5456 for (int i = 0; comp != null && i < comp.length; i++)
5458 if (comp[i] instanceof AlignmentPanel)
5460 if (((AlignmentPanel) comp[i]).av == av)
5463 closeView((AlignmentPanel) comp[i]);
5471 protected void build_fetchdbmenu(JMenu webService)
5473 // Temporary hack - DBRef Fetcher always top level ws entry.
5474 // TODO We probably want to store a sequence database checklist in
5475 // preferences and have checkboxes.. rather than individual sources selected
5477 final JMenu rfetch = new JMenu(
5478 MessageManager.getString("action.fetch_db_references"));
5479 rfetch.setToolTipText(MessageManager
5480 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5481 webService.add(rfetch);
5483 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5484 MessageManager.getString("option.trim_retrieved_seqs"));
5485 trimrs.setToolTipText(MessageManager
5486 .getString("label.trim_retrieved_sequences"));
5487 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5488 trimrs.addActionListener(new ActionListener()
5491 public void actionPerformed(ActionEvent e)
5493 trimrs.setSelected(trimrs.isSelected());
5494 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5495 Boolean.valueOf(trimrs.isSelected()).toString());
5499 JMenuItem fetchr = new JMenuItem(
5500 MessageManager.getString("label.standard_databases"));
5501 fetchr.setToolTipText(MessageManager
5502 .getString("label.fetch_embl_uniprot"));
5503 fetchr.addActionListener(new ActionListener()
5507 public void actionPerformed(ActionEvent e)
5509 new Thread(new Runnable()
5514 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5515 .getAlignment().isNucleotide();
5516 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5517 .getSequenceSelection(), alignPanel.alignFrame, null,
5518 alignPanel.alignFrame.featureSettings, isNucleotide);
5519 dbRefFetcher.addListener(new FetchFinishedListenerI()
5522 public void finished()
5524 AlignFrame.this.setMenusForViewport();
5527 dbRefFetcher.fetchDBRefs(false);
5535 final AlignFrame me = this;
5536 new Thread(new Runnable()
5541 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5542 .getSequenceFetcherSingleton(me);
5543 javax.swing.SwingUtilities.invokeLater(new Runnable()
5548 String[] dbclasses = sf.getOrderedSupportedSources();
5549 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5550 // jalview.util.QuickSort.sort(otherdb, otherdb);
5551 List<DbSourceProxy> otherdb;
5552 JMenu dfetch = new JMenu();
5553 JMenu ifetch = new JMenu();
5554 JMenuItem fetchr = null;
5555 int comp = 0, icomp = 0, mcomp = 15;
5556 String mname = null;
5558 for (String dbclass : dbclasses)
5560 otherdb = sf.getSourceProxy(dbclass);
5561 // add a single entry for this class, or submenu allowing 'fetch
5563 if (otherdb == null || otherdb.size() < 1)
5567 // List<DbSourceProxy> dbs=otherdb;
5568 // otherdb=new ArrayList<DbSourceProxy>();
5569 // for (DbSourceProxy db:dbs)
5571 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5575 mname = "From " + dbclass;
5577 if (otherdb.size() == 1)
5579 final DbSourceProxy[] dassource = otherdb
5580 .toArray(new DbSourceProxy[0]);
5581 DbSourceProxy src = otherdb.get(0);
5582 fetchr = new JMenuItem(src.getDbSource());
5583 fetchr.addActionListener(new ActionListener()
5587 public void actionPerformed(ActionEvent e)
5589 new Thread(new Runnable()
5595 boolean isNucleotide = alignPanel.alignFrame
5596 .getViewport().getAlignment()
5598 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5599 alignPanel.av.getSequenceSelection(),
5600 alignPanel.alignFrame, dassource,
5601 alignPanel.alignFrame.featureSettings,
5604 .addListener(new FetchFinishedListenerI()
5607 public void finished()
5609 AlignFrame.this.setMenusForViewport();
5612 dbRefFetcher.fetchDBRefs(false);
5618 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5619 MessageManager.formatMessage(
5620 "label.fetch_retrieve_from",
5621 new Object[] { src.getDbName() })));
5627 final DbSourceProxy[] dassource = otherdb
5628 .toArray(new DbSourceProxy[0]);
5630 DbSourceProxy src = otherdb.get(0);
5631 fetchr = new JMenuItem(MessageManager.formatMessage(
5632 "label.fetch_all_param",
5633 new Object[] { src.getDbSource() }));
5634 fetchr.addActionListener(new ActionListener()
5637 public void actionPerformed(ActionEvent e)
5639 new Thread(new Runnable()
5645 boolean isNucleotide = alignPanel.alignFrame
5646 .getViewport().getAlignment()
5648 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5649 alignPanel.av.getSequenceSelection(),
5650 alignPanel.alignFrame, dassource,
5651 alignPanel.alignFrame.featureSettings,
5654 .addListener(new FetchFinishedListenerI()
5657 public void finished()
5659 AlignFrame.this.setMenusForViewport();
5662 dbRefFetcher.fetchDBRefs(false);
5668 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5669 MessageManager.formatMessage(
5670 "label.fetch_retrieve_from_all_sources",
5672 Integer.valueOf(otherdb.size())
5673 .toString(), src.getDbSource(),
5674 src.getDbName() })));
5677 // and then build the rest of the individual menus
5678 ifetch = new JMenu(MessageManager.formatMessage(
5679 "label.source_from_db_source",
5680 new Object[] { src.getDbSource() }));
5682 String imname = null;
5684 for (DbSourceProxy sproxy : otherdb)
5686 String dbname = sproxy.getDbName();
5687 String sname = dbname.length() > 5 ? dbname.substring(0,
5688 5) + "..." : dbname;
5689 String msname = dbname.length() > 10 ? dbname.substring(
5690 0, 10) + "..." : dbname;
5693 imname = MessageManager.formatMessage(
5694 "label.from_msname", new Object[] { sname });
5696 fetchr = new JMenuItem(msname);
5697 final DbSourceProxy[] dassrc = { sproxy };
5698 fetchr.addActionListener(new ActionListener()
5702 public void actionPerformed(ActionEvent e)
5704 new Thread(new Runnable()
5710 boolean isNucleotide = alignPanel.alignFrame
5711 .getViewport().getAlignment()
5713 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5714 alignPanel.av.getSequenceSelection(),
5715 alignPanel.alignFrame, dassrc,
5716 alignPanel.alignFrame.featureSettings,
5719 .addListener(new FetchFinishedListenerI()
5722 public void finished()
5724 AlignFrame.this.setMenusForViewport();
5727 dbRefFetcher.fetchDBRefs(false);
5733 fetchr.setToolTipText("<html>"
5734 + MessageManager.formatMessage(
5735 "label.fetch_retrieve_from", new Object[]
5739 if (++icomp >= mcomp || i == (otherdb.size()))
5741 ifetch.setText(MessageManager.formatMessage(
5742 "label.source_to_target", imname, sname));
5744 ifetch = new JMenu();
5752 if (comp >= mcomp || dbi >= (dbclasses.length))
5754 dfetch.setText(MessageManager.formatMessage(
5755 "label.source_to_target", mname, dbclass));
5757 dfetch = new JMenu();
5770 * Left justify the whole alignment.
5773 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5775 AlignmentI al = viewport.getAlignment();
5777 viewport.firePropertyChange("alignment", null, al);
5781 * Right justify the whole alignment.
5784 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5786 AlignmentI al = viewport.getAlignment();
5788 viewport.firePropertyChange("alignment", null, al);
5792 public void setShowSeqFeatures(boolean b)
5794 showSeqFeatures.setSelected(b);
5795 viewport.setShowSequenceFeatures(b);
5802 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5803 * awt.event.ActionEvent)
5806 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5808 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5809 alignPanel.paintAlignment(true);
5816 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5820 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5822 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5823 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5831 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5832 * .event.ActionEvent)
5835 protected void showGroupConservation_actionPerformed(ActionEvent e)
5837 viewport.setShowGroupConservation(showGroupConservation.getState());
5838 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5845 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5846 * .event.ActionEvent)
5849 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5851 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5852 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5859 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5860 * .event.ActionEvent)
5863 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5865 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5866 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5870 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5872 showSequenceLogo.setState(true);
5873 viewport.setShowSequenceLogo(true);
5874 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5875 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5879 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5881 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5888 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5889 * .event.ActionEvent)
5892 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5894 if (avc.makeGroupsFromSelection())
5896 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5897 alignPanel.updateAnnotation();
5898 alignPanel.paintAlignment(true);
5902 public void clearAlignmentSeqRep()
5904 // TODO refactor alignmentseqrep to controller
5905 if (viewport.getAlignment().hasSeqrep())
5907 viewport.getAlignment().setSeqrep(null);
5908 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5909 alignPanel.updateAnnotation();
5910 alignPanel.paintAlignment(true);
5915 protected void createGroup_actionPerformed(ActionEvent e)
5917 if (avc.createGroup())
5919 alignPanel.alignmentChanged();
5924 protected void unGroup_actionPerformed(ActionEvent e)
5928 alignPanel.alignmentChanged();
5933 * make the given alignmentPanel the currently selected tab
5935 * @param alignmentPanel
5937 public void setDisplayedView(AlignmentPanel alignmentPanel)
5939 if (!viewport.getSequenceSetId().equals(
5940 alignmentPanel.av.getSequenceSetId()))
5944 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5946 if (tabbedPane != null
5947 && tabbedPane.getTabCount() > 0
5948 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5949 .getSelectedIndex())
5951 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5956 * Action on selection of menu options to Show or Hide annotations.
5959 * @param forSequences
5960 * update sequence-related annotations
5961 * @param forAlignment
5962 * update non-sequence-related annotations
5965 protected void setAnnotationsVisibility(boolean visible,
5966 boolean forSequences, boolean forAlignment)
5968 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5969 .getAlignmentAnnotation();
5974 for (AlignmentAnnotation aa : anns)
5977 * don't display non-positional annotations on an alignment
5979 if (aa.annotations == null)
5983 boolean apply = (aa.sequenceRef == null && forAlignment)
5984 || (aa.sequenceRef != null && forSequences);
5987 aa.visible = visible;
5990 alignPanel.validateAnnotationDimensions(true);
5991 alignPanel.alignmentChanged();
5995 * Store selected annotation sort order for the view and repaint.
5998 protected void sortAnnotations_actionPerformed()
6000 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6002 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6003 alignPanel.paintAlignment(true);
6008 * @return alignment panels in this alignment frame
6010 public List<? extends AlignmentViewPanel> getAlignPanels()
6012 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
6016 * Open a new alignment window, with the cDNA associated with this (protein)
6017 * alignment, aligned as is the protein.
6019 protected void viewAsCdna_actionPerformed()
6021 // TODO no longer a menu action - refactor as required
6022 final AlignmentI alignment = getViewport().getAlignment();
6023 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6024 if (mappings == null)
6028 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6029 for (SequenceI aaSeq : alignment.getSequences())
6031 for (AlignedCodonFrame acf : mappings)
6033 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6037 * There is a cDNA mapping for this protein sequence - add to new
6038 * alignment. It will share the same dataset sequence as other mapped
6039 * cDNA (no new mappings need to be created).
6041 final Sequence newSeq = new Sequence(dnaSeq);
6042 newSeq.setDatasetSequence(dnaSeq);
6043 cdnaSeqs.add(newSeq);
6047 if (cdnaSeqs.size() == 0)
6049 // show a warning dialog no mapped cDNA
6052 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6054 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6055 AlignFrame.DEFAULT_HEIGHT);
6056 cdna.alignAs(alignment);
6057 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6059 Desktop.addInternalFrame(alignFrame, newtitle,
6060 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6064 * Set visibility of dna/protein complement view (available when shown in a
6070 protected void showComplement_actionPerformed(boolean show)
6072 SplitContainerI sf = getSplitViewContainer();
6075 sf.setComplementVisible(this, show);
6080 * Generate the reverse (optionally complemented) of the selected sequences,
6081 * and add them to the alignment
6084 protected void showReverse_actionPerformed(boolean complement)
6086 AlignmentI al = null;
6089 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6090 al = dna.reverseCdna(complement);
6091 viewport.addAlignment(al, "");
6092 addHistoryItem(new EditCommand(
6093 MessageManager.getString("label.add_sequences"),
6094 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
6095 viewport.getAlignment()));
6096 } catch (Exception ex)
6098 System.err.println(ex.getMessage());
6104 * Try to run a script in the Groovy console, having first ensured that this
6105 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
6106 * be targeted at this alignment.
6109 protected void runGroovy_actionPerformed()
6111 Jalview.setCurrentAlignFrame(this);
6112 groovy.ui.Console console = Desktop.getGroovyConsole();
6113 if (console != null)
6117 console.runScript();
6118 } catch (Exception ex)
6120 System.err.println((ex.toString()));
6122 .showInternalMessageDialog(Desktop.desktop, MessageManager
6123 .getString("label.couldnt_run_groovy_script"),
6125 .getString("label.groovy_support_failed"),
6126 JOptionPane.ERROR_MESSAGE);
6131 System.err.println("Can't run Groovy script as console not found");
6136 * Hides columns containing (or not containing) a specified feature, provided
6137 * that would not leave all columns hidden
6139 * @param featureType
6140 * @param columnsContaining
6143 public boolean hideFeatureColumns(String featureType,
6144 boolean columnsContaining)
6146 boolean notForHiding = avc.markColumnsContainingFeatures(
6147 columnsContaining, false, false, featureType);
6150 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
6151 false, featureType))
6153 getViewport().hideSelectedColumns();
6161 class PrintThread extends Thread
6165 public PrintThread(AlignmentPanel ap)
6170 static PageFormat pf;
6175 PrinterJob printJob = PrinterJob.getPrinterJob();
6179 printJob.setPrintable(ap, pf);
6183 printJob.setPrintable(ap);
6186 if (printJob.printDialog())
6191 } catch (Exception PrintException)
6193 PrintException.printStackTrace();