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.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.ScoreModelI;
38 import jalview.api.analysis.SimilarityParamsI;
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.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
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.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FileParse;
74 import jalview.io.FormatAdapter;
75 import jalview.io.HtmlSvgOutput;
76 import jalview.io.IdentifyFile;
77 import jalview.io.JPredFile;
78 import jalview.io.JalviewFileChooser;
79 import jalview.io.JalviewFileView;
80 import jalview.io.JnetAnnotationMaker;
81 import jalview.io.NewickFile;
82 import jalview.io.ScoreMatrixFile;
83 import jalview.io.TCoffeeScoreFile;
84 import jalview.jbgui.GAlignFrame;
85 import jalview.schemes.ColourSchemeI;
86 import jalview.schemes.ColourSchemes;
87 import jalview.schemes.ResidueColourScheme;
88 import jalview.schemes.TCoffeeColourScheme;
89 import jalview.util.MessageManager;
90 import jalview.viewmodel.AlignmentViewport;
91 import jalview.viewmodel.ViewportRanges;
92 import jalview.ws.DBRefFetcher;
93 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
94 import jalview.ws.jws1.Discoverer;
95 import jalview.ws.jws2.Jws2Discoverer;
96 import jalview.ws.jws2.jabaws2.Jws2Instance;
97 import jalview.ws.seqfetcher.DbSourceProxy;
99 import java.awt.BorderLayout;
100 import java.awt.Component;
101 import java.awt.Rectangle;
102 import java.awt.Toolkit;
103 import java.awt.datatransfer.Clipboard;
104 import java.awt.datatransfer.DataFlavor;
105 import java.awt.datatransfer.StringSelection;
106 import java.awt.datatransfer.Transferable;
107 import java.awt.dnd.DnDConstants;
108 import java.awt.dnd.DropTargetDragEvent;
109 import java.awt.dnd.DropTargetDropEvent;
110 import java.awt.dnd.DropTargetEvent;
111 import java.awt.dnd.DropTargetListener;
112 import java.awt.event.ActionEvent;
113 import java.awt.event.ActionListener;
114 import java.awt.event.FocusAdapter;
115 import java.awt.event.FocusEvent;
116 import java.awt.event.ItemEvent;
117 import java.awt.event.ItemListener;
118 import java.awt.event.KeyAdapter;
119 import java.awt.event.KeyEvent;
120 import java.awt.event.MouseEvent;
121 import java.awt.print.PageFormat;
122 import java.awt.print.PrinterJob;
123 import java.beans.PropertyChangeEvent;
125 import java.io.FileWriter;
126 import java.io.PrintWriter;
128 import java.util.ArrayList;
129 import java.util.Arrays;
130 import java.util.Deque;
131 import java.util.Enumeration;
132 import java.util.Hashtable;
133 import java.util.List;
134 import java.util.Vector;
136 import javax.swing.JCheckBoxMenuItem;
137 import javax.swing.JEditorPane;
138 import javax.swing.JInternalFrame;
139 import javax.swing.JLayeredPane;
140 import javax.swing.JMenu;
141 import javax.swing.JMenuItem;
142 import javax.swing.JScrollPane;
143 import javax.swing.SwingUtilities;
149 * @version $Revision$
151 public class AlignFrame extends GAlignFrame implements DropTargetListener,
152 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
155 public static final int DEFAULT_WIDTH = 700;
157 public static final int DEFAULT_HEIGHT = 500;
160 * The currently displayed panel (selected tabbed view if more than one)
162 public AlignmentPanel alignPanel;
164 AlignViewport viewport;
166 ViewportRanges vpRanges;
168 public AlignViewControllerI avc;
170 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
173 * Last format used to load or save alignments in this window
175 FileFormatI currentFileFormat = null;
178 * Current filename for this alignment
180 String fileName = null;
183 * Creates a new AlignFrame object with specific width and height.
189 public AlignFrame(AlignmentI al, int width, int height)
191 this(al, null, width, height);
195 * Creates a new AlignFrame object with specific width, height and
201 * @param sequenceSetId
203 public AlignFrame(AlignmentI al, int width, int height,
204 String sequenceSetId)
206 this(al, null, width, height, sequenceSetId);
210 * Creates a new AlignFrame object with specific width, height and
216 * @param sequenceSetId
219 public AlignFrame(AlignmentI al, int width, int height,
220 String sequenceSetId, String viewId)
222 this(al, null, width, height, sequenceSetId, viewId);
226 * new alignment window with hidden columns
230 * @param hiddenColumns
231 * ColumnSelection or null
233 * Width of alignment frame
237 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
238 int width, int height)
240 this(al, hiddenColumns, width, height, null);
244 * Create alignment frame for al with hiddenColumns, a specific width and
245 * height, and specific sequenceId
248 * @param hiddenColumns
251 * @param sequenceSetId
254 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
255 int width, int height, String sequenceSetId)
257 this(al, hiddenColumns, width, height, sequenceSetId, null);
261 * Create alignment frame for al with hiddenColumns, a specific width and
262 * height, and specific sequenceId
265 * @param hiddenColumns
268 * @param sequenceSetId
273 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
274 int width, int height, String sequenceSetId, String viewId)
276 setSize(width, height);
278 if (al.getDataset() == null)
283 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
285 alignPanel = new AlignmentPanel(this, viewport);
287 addAlignmentPanel(alignPanel, true);
291 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
292 ColumnSelection hiddenColumns, int width, int height)
294 setSize(width, height);
296 if (al.getDataset() == null)
301 viewport = new AlignViewport(al, hiddenColumns);
303 if (hiddenSeqs != null && hiddenSeqs.length > 0)
305 viewport.hideSequence(hiddenSeqs);
307 alignPanel = new AlignmentPanel(this, viewport);
308 addAlignmentPanel(alignPanel, true);
313 * Make a new AlignFrame from existing alignmentPanels
320 public AlignFrame(AlignmentPanel ap)
324 addAlignmentPanel(ap, false);
329 * initalise the alignframe from the underlying viewport data and the
334 if (!Jalview.isHeadlessMode())
336 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
339 vpRanges = viewport.getRanges();
340 avc = new jalview.controller.AlignViewController(this, viewport,
342 if (viewport.getAlignmentConservationAnnotation() == null)
344 // BLOSUM62Colour.setEnabled(false);
345 conservationMenuItem.setEnabled(false);
346 modifyConservation.setEnabled(false);
347 // PIDColour.setEnabled(false);
348 // abovePIDThreshold.setEnabled(false);
349 // modifyPID.setEnabled(false);
352 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
355 if (sortby.equals("Id"))
357 sortIDMenuItem_actionPerformed(null);
359 else if (sortby.equals("Pairwise Identity"))
361 sortPairwiseMenuItem_actionPerformed(null);
365 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
367 setMenusFromViewport(viewport);
368 buildSortByAnnotationScoresMenu();
369 calculateTree.addActionListener(new ActionListener()
373 public void actionPerformed(ActionEvent e)
375 new TreeChooser(AlignFrame.this);
380 if (Desktop.desktop != null)
382 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
383 addServiceListeners();
387 if (viewport.getWrapAlignment())
389 wrapMenuItem_actionPerformed(null);
392 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
394 this.overviewMenuItem_actionPerformed(null);
399 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
400 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
401 final String menuLabel = MessageManager
402 .getString("label.copy_format_from");
403 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
404 new ViewSetProvider()
408 public AlignmentPanel[] getAllAlignmentPanels()
411 origview.add(alignPanel);
412 // make an array of all alignment panels except for this one
413 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
414 Arrays.asList(Desktop.getAlignmentPanels(null)));
415 aps.remove(AlignFrame.this.alignPanel);
416 return aps.toArray(new AlignmentPanel[aps.size()]);
418 }, selviews, new ItemListener()
422 public void itemStateChanged(ItemEvent e)
424 if (origview.size() > 0)
426 final AlignmentPanel ap = origview.get(0);
429 * Copy the ViewStyle of the selected panel to 'this one'.
430 * Don't change value of 'scaleProteinAsCdna' unless copying
433 ViewStyleI vs = selviews.get(0).getAlignViewport()
435 boolean fromSplitFrame = selviews.get(0)
436 .getAlignViewport().getCodingComplement() != null;
439 vs.setScaleProteinAsCdna(ap.getAlignViewport()
440 .getViewStyle().isScaleProteinAsCdna());
442 ap.getAlignViewport().setViewStyle(vs);
445 * Also rescale ViewStyle of SplitFrame complement if there is
446 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
447 * the whole ViewStyle (allow cDNA protein to have different
450 AlignViewportI complement = ap.getAlignViewport()
451 .getCodingComplement();
452 if (complement != null && vs.isScaleProteinAsCdna())
454 AlignFrame af = Desktop.getAlignFrameFor(complement);
455 ((SplitFrame) af.getSplitViewContainer())
457 af.setMenusForViewport();
461 ap.setSelected(true);
462 ap.alignFrame.setMenusForViewport();
467 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
468 .indexOf("devel") > -1
469 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
470 .indexOf("test") > -1)
472 formatMenu.add(vsel);
474 addFocusListener(new FocusAdapter()
477 public void focusGained(FocusEvent e)
479 Jalview.setCurrentAlignFrame(AlignFrame.this);
486 * Change the filename and format for the alignment, and enable the 'reload'
487 * button functionality.
494 public void setFileName(String file, FileFormatI format)
497 setFileFormat(format);
498 reload.setEnabled(true);
502 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
505 void addKeyListener()
507 addKeyListener(new KeyAdapter()
510 public void keyPressed(KeyEvent evt)
512 if (viewport.cursorMode
513 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
514 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
515 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
516 && Character.isDigit(evt.getKeyChar()))
518 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
521 switch (evt.getKeyCode())
524 case 27: // escape key
525 deselectAllSequenceMenuItem_actionPerformed(null);
529 case KeyEvent.VK_DOWN:
530 if (evt.isAltDown() || !viewport.cursorMode)
532 moveSelectedSequences(false);
534 if (viewport.cursorMode)
536 alignPanel.getSeqPanel().moveCursor(0, 1);
541 if (evt.isAltDown() || !viewport.cursorMode)
543 moveSelectedSequences(true);
545 if (viewport.cursorMode)
547 alignPanel.getSeqPanel().moveCursor(0, -1);
552 case KeyEvent.VK_LEFT:
553 if (evt.isAltDown() || !viewport.cursorMode)
555 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
559 alignPanel.getSeqPanel().moveCursor(-1, 0);
564 case KeyEvent.VK_RIGHT:
565 if (evt.isAltDown() || !viewport.cursorMode)
567 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
571 alignPanel.getSeqPanel().moveCursor(1, 0);
575 case KeyEvent.VK_SPACE:
576 if (viewport.cursorMode)
578 alignPanel.getSeqPanel().insertGapAtCursor(
579 evt.isControlDown() || evt.isShiftDown()
584 // case KeyEvent.VK_A:
585 // if (viewport.cursorMode)
587 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
588 // //System.out.println("A");
592 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
593 * System.out.println("closing bracket"); } break;
595 case KeyEvent.VK_DELETE:
596 case KeyEvent.VK_BACK_SPACE:
597 if (!viewport.cursorMode)
599 cut_actionPerformed(null);
603 alignPanel.getSeqPanel().deleteGapAtCursor(
604 evt.isControlDown() || evt.isShiftDown()
611 if (viewport.cursorMode)
613 alignPanel.getSeqPanel().setCursorRow();
617 if (viewport.cursorMode && !evt.isControlDown())
619 alignPanel.getSeqPanel().setCursorColumn();
623 if (viewport.cursorMode)
625 alignPanel.getSeqPanel().setCursorPosition();
629 case KeyEvent.VK_ENTER:
630 case KeyEvent.VK_COMMA:
631 if (viewport.cursorMode)
633 alignPanel.getSeqPanel().setCursorRowAndColumn();
638 if (viewport.cursorMode)
640 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
644 if (viewport.cursorMode)
646 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
651 viewport.cursorMode = !viewport.cursorMode;
652 statusBar.setText(MessageManager.formatMessage(
653 "label.keyboard_editing_mode",
654 new String[] { (viewport.cursorMode ? "on" : "off") }));
655 if (viewport.cursorMode)
657 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
659 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
662 alignPanel.getSeqPanel().seqCanvas.repaint();
668 Help.showHelpWindow();
669 } catch (Exception ex)
671 ex.printStackTrace();
676 boolean toggleSeqs = !evt.isControlDown();
677 boolean toggleCols = !evt.isShiftDown();
678 toggleHiddenRegions(toggleSeqs, toggleCols);
683 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
684 boolean modifyExisting = true; // always modify, don't clear
685 // evt.isShiftDown();
686 boolean invertHighlighted = evt.isAltDown();
687 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
691 case KeyEvent.VK_PAGE_UP:
692 if (viewport.getWrapAlignment())
694 alignPanel.scrollUp(true);
698 alignPanel.setScrollValues(vpRanges.getStartRes(),
699 2 * vpRanges.getStartSeq() - vpRanges.getEndSeq());
702 case KeyEvent.VK_PAGE_DOWN:
703 if (viewport.getWrapAlignment())
705 alignPanel.scrollUp(false);
709 alignPanel.setScrollValues(vpRanges.getStartRes(),
710 vpRanges.getEndSeq());
717 public void keyReleased(KeyEvent evt)
719 switch (evt.getKeyCode())
721 case KeyEvent.VK_LEFT:
722 if (evt.isAltDown() || !viewport.cursorMode)
724 viewport.firePropertyChange("alignment", null, viewport
725 .getAlignment().getSequences());
729 case KeyEvent.VK_RIGHT:
730 if (evt.isAltDown() || !viewport.cursorMode)
732 viewport.firePropertyChange("alignment", null, viewport
733 .getAlignment().getSequences());
741 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
743 ap.alignFrame = this;
744 avc = new jalview.controller.AlignViewController(this, viewport,
749 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
751 int aSize = alignPanels.size();
753 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
755 if (aSize == 1 && ap.av.viewName == null)
757 this.getContentPane().add(ap, BorderLayout.CENTER);
763 setInitialTabVisible();
766 expandViews.setEnabled(true);
767 gatherViews.setEnabled(true);
768 tabbedPane.addTab(ap.av.viewName, ap);
770 ap.setVisible(false);
775 if (ap.av.isPadGaps())
777 ap.av.getAlignment().padGaps();
779 ap.av.updateConservation(ap);
780 ap.av.updateConsensus(ap);
781 ap.av.updateStrucConsensus(ap);
785 public void setInitialTabVisible()
787 expandViews.setEnabled(true);
788 gatherViews.setEnabled(true);
789 tabbedPane.setVisible(true);
790 AlignmentPanel first = alignPanels.get(0);
791 tabbedPane.addTab(first.av.viewName, first);
792 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
795 public AlignViewport getViewport()
800 /* Set up intrinsic listeners for dynamically generated GUI bits. */
801 private void addServiceListeners()
803 final java.beans.PropertyChangeListener thisListener;
804 Desktop.instance.addJalviewPropertyChangeListener("services",
805 thisListener = new java.beans.PropertyChangeListener()
808 public void propertyChange(PropertyChangeEvent evt)
810 // // System.out.println("Discoverer property change.");
811 // if (evt.getPropertyName().equals("services"))
813 SwingUtilities.invokeLater(new Runnable()
820 .println("Rebuild WS Menu for service change");
821 BuildWebServiceMenu();
828 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
831 public void internalFrameClosed(
832 javax.swing.event.InternalFrameEvent evt)
834 // System.out.println("deregistering discoverer listener");
835 Desktop.instance.removeJalviewPropertyChangeListener("services",
837 closeMenuItem_actionPerformed(true);
840 // Finally, build the menu once to get current service state
841 new Thread(new Runnable()
846 BuildWebServiceMenu();
852 * Configure menu items that vary according to whether the alignment is
853 * nucleotide or protein
855 public void setGUINucleotide()
857 AlignmentI al = getViewport().getAlignment();
858 boolean nucleotide = al.isNucleotide();
860 showTranslation.setVisible(nucleotide);
861 showReverse.setVisible(nucleotide);
862 showReverseComplement.setVisible(nucleotide);
863 conservationMenuItem.setEnabled(!nucleotide);
864 modifyConservation.setEnabled(!nucleotide
865 && conservationMenuItem.isSelected());
866 showGroupConservation.setEnabled(!nucleotide);
868 showComplementMenuItem.setText(nucleotide ? MessageManager
869 .getString("label.protein") : MessageManager
870 .getString("label.nucleotide"));
874 * set up menus for the current viewport. This may be called after any
875 * operation that affects the data in the current view (selection changed,
876 * etc) to update the menus to reflect the new state.
879 public void setMenusForViewport()
881 setMenusFromViewport(viewport);
885 * Need to call this method when tabs are selected for multiple views, or when
886 * loading from Jalview2XML.java
891 void setMenusFromViewport(AlignViewport av)
893 padGapsMenuitem.setSelected(av.isPadGaps());
894 colourTextMenuItem.setSelected(av.isShowColourText());
895 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
896 modifyPID.setEnabled(abovePIDThreshold.isSelected());
897 conservationMenuItem.setSelected(av.getConservationSelected());
898 modifyConservation.setEnabled(conservationMenuItem.isSelected());
899 seqLimits.setSelected(av.getShowJVSuffix());
900 idRightAlign.setSelected(av.isRightAlignIds());
901 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
902 renderGapsMenuItem.setSelected(av.isRenderGaps());
903 wrapMenuItem.setSelected(av.getWrapAlignment());
904 scaleAbove.setVisible(av.getWrapAlignment());
905 scaleLeft.setVisible(av.getWrapAlignment());
906 scaleRight.setVisible(av.getWrapAlignment());
907 annotationPanelMenuItem.setState(av.isShowAnnotation());
909 * Show/hide annotations only enabled if annotation panel is shown
911 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
912 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
913 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
914 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
915 viewBoxesMenuItem.setSelected(av.getShowBoxes());
916 viewTextMenuItem.setSelected(av.getShowText());
917 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
918 showGroupConsensus.setSelected(av.isShowGroupConsensus());
919 showGroupConservation.setSelected(av.isShowGroupConservation());
920 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
921 showSequenceLogo.setSelected(av.isShowSequenceLogo());
922 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
924 ColourMenuHelper.setColourSelected(colourMenu,
925 av.getGlobalColourScheme());
927 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
928 hiddenMarkers.setState(av.getShowHiddenMarkers());
929 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
930 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
931 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
932 autoCalculate.setSelected(av.autoCalculateConsensus);
933 sortByTree.setSelected(av.sortByTree);
934 listenToViewSelections.setSelected(av.followSelection);
936 showProducts.setEnabled(canShowProducts());
937 setGroovyEnabled(Desktop.getGroovyConsole() != null);
943 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
947 public void setGroovyEnabled(boolean b)
949 runGroovy.setEnabled(b);
952 private IProgressIndicator progressBar;
957 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
960 public void setProgressBar(String message, long id)
962 progressBar.setProgressBar(message, id);
966 public void registerHandler(final long id,
967 final IProgressIndicatorHandler handler)
969 progressBar.registerHandler(id, handler);
974 * @return true if any progress bars are still active
977 public boolean operationInProgress()
979 return progressBar.operationInProgress();
983 public void setStatus(String text)
985 statusBar.setText(text);
989 * Added so Castor Mapping file can obtain Jalview Version
991 public String getVersion()
993 return jalview.bin.Cache.getProperty("VERSION");
996 public FeatureRenderer getFeatureRenderer()
998 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1002 public void fetchSequence_actionPerformed(ActionEvent e)
1004 new jalview.gui.SequenceFetcher(this);
1008 public void addFromFile_actionPerformed(ActionEvent e)
1010 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1014 public void reload_actionPerformed(ActionEvent e)
1016 if (fileName != null)
1018 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1019 // originating file's format
1020 // TODO: work out how to recover feature settings for correct view(s) when
1021 // file is reloaded.
1022 if (FileFormat.Jalview.equals(currentFileFormat))
1024 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1025 for (int i = 0; i < frames.length; i++)
1027 if (frames[i] instanceof AlignFrame && frames[i] != this
1028 && ((AlignFrame) frames[i]).fileName != null
1029 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1033 frames[i].setSelected(true);
1034 Desktop.instance.closeAssociatedWindows();
1035 } catch (java.beans.PropertyVetoException ex)
1041 Desktop.instance.closeAssociatedWindows();
1043 FileLoader loader = new FileLoader();
1044 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1045 : DataSourceType.FILE;
1046 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1050 Rectangle bounds = this.getBounds();
1052 FileLoader loader = new FileLoader();
1053 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1054 : DataSourceType.FILE;
1055 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1056 protocol, currentFileFormat);
1058 newframe.setBounds(bounds);
1059 if (featureSettings != null && featureSettings.isShowing())
1061 final Rectangle fspos = featureSettings.frame.getBounds();
1062 // TODO: need a 'show feature settings' function that takes bounds -
1063 // need to refactor Desktop.addFrame
1064 newframe.featureSettings_actionPerformed(null);
1065 final FeatureSettings nfs = newframe.featureSettings;
1066 SwingUtilities.invokeLater(new Runnable()
1071 nfs.frame.setBounds(fspos);
1074 this.featureSettings.close();
1075 this.featureSettings = null;
1077 this.closeMenuItem_actionPerformed(true);
1083 public void addFromText_actionPerformed(ActionEvent e)
1085 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1090 public void addFromURL_actionPerformed(ActionEvent e)
1092 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1096 public void save_actionPerformed(ActionEvent e)
1098 if (fileName == null || (currentFileFormat == null)
1099 || fileName.startsWith("http"))
1101 saveAs_actionPerformed(null);
1105 saveAlignment(fileName, currentFileFormat);
1116 public void saveAs_actionPerformed(ActionEvent e)
1118 String format = currentFileFormat == null ? null : currentFileFormat
1120 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1121 Cache.getProperty("LAST_DIRECTORY"), format);
1123 chooser.setFileView(new JalviewFileView());
1124 chooser.setDialogTitle(MessageManager
1125 .getString("label.save_alignment_to_file"));
1126 chooser.setToolTipText(MessageManager.getString("action.save"));
1128 int value = chooser.showSaveDialog(this);
1130 if (value == JalviewFileChooser.APPROVE_OPTION)
1132 currentFileFormat = chooser.getSelectedFormat();
1133 while (currentFileFormat == null)
1136 .showInternalMessageDialog(
1139 .getString("label.select_file_format_before_saving"),
1141 .getString("label.file_format_not_specified"),
1142 JvOptionPane.WARNING_MESSAGE);
1143 currentFileFormat = chooser.getSelectedFormat();
1144 value = chooser.showSaveDialog(this);
1145 if (value != JalviewFileChooser.APPROVE_OPTION)
1151 fileName = chooser.getSelectedFile().getPath();
1153 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1155 Cache.setProperty("LAST_DIRECTORY", fileName);
1156 saveAlignment(fileName, currentFileFormat);
1160 public boolean saveAlignment(String file, FileFormatI format)
1162 boolean success = true;
1164 if (FileFormat.Jalview.equals(format))
1166 String shortName = title;
1168 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1170 shortName = shortName.substring(shortName
1171 .lastIndexOf(java.io.File.separatorChar) + 1);
1174 success = new Jalview2XML().saveAlignment(this, file, shortName);
1176 statusBar.setText(MessageManager.formatMessage(
1177 "label.successfully_saved_to_file_in_format", new Object[] {
1178 fileName, format }));
1183 AlignmentExportData exportData = getAlignmentForExport(format,
1185 if (exportData.getSettings().isCancelled())
1189 FormatAdapter f = new FormatAdapter(alignPanel,
1190 exportData.getSettings());
1191 String output = f.formatSequences(
1193 exportData.getAlignment(), // class cast exceptions will
1194 // occur in the distant future
1195 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1196 f.getCacheSuffixDefault(format),
1197 viewport.getColumnSelection());
1207 PrintWriter out = new PrintWriter(new FileWriter(file));
1211 this.setTitle(file);
1212 statusBar.setText(MessageManager.formatMessage(
1213 "label.successfully_saved_to_file_in_format",
1214 new Object[] { fileName, format.getName() }));
1215 } catch (Exception ex)
1218 ex.printStackTrace();
1225 JvOptionPane.showInternalMessageDialog(this, MessageManager
1226 .formatMessage("label.couldnt_save_file",
1227 new Object[] { fileName }), MessageManager
1228 .getString("label.error_saving_file"),
1229 JvOptionPane.WARNING_MESSAGE);
1235 private void warningMessage(String warning, String title)
1237 if (new jalview.util.Platform().isHeadless())
1239 System.err.println("Warning: " + title + "\nWarning: " + warning);
1244 JvOptionPane.showInternalMessageDialog(this, warning, title,
1245 JvOptionPane.WARNING_MESSAGE);
1257 protected void outputText_actionPerformed(ActionEvent e)
1259 FileFormatI fileFormat = FileFormats.getInstance().forName(
1260 e.getActionCommand());
1261 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1263 if (exportData.getSettings().isCancelled())
1267 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1268 cap.setForInput(null);
1271 FileFormatI format = fileFormat;
1272 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1273 .formatSequences(format, exportData.getAlignment(),
1274 exportData.getOmitHidden(),
1275 exportData.getStartEndPostions(),
1276 viewport.getColumnSelection()));
1277 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1278 "label.alignment_output_command",
1279 new Object[] { e.getActionCommand() }), 600, 500);
1280 } catch (OutOfMemoryError oom)
1282 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1288 public static AlignmentExportData getAlignmentForExport(
1289 FileFormatI format, AlignViewportI viewport,
1290 AlignExportSettingI exportSettings)
1292 AlignmentI alignmentToExport = null;
1293 AlignExportSettingI settings = exportSettings;
1294 String[] omitHidden = null;
1296 HiddenSequences hiddenSeqs = viewport.getAlignment()
1297 .getHiddenSequences();
1299 alignmentToExport = viewport.getAlignment();
1301 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1302 if (settings == null)
1304 settings = new AlignExportSettings(hasHiddenSeqs,
1305 viewport.hasHiddenColumns(), format);
1307 // settings.isExportAnnotations();
1309 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1311 omitHidden = viewport.getViewAsString(false,
1312 settings.isExportHiddenSequences());
1315 int[] alignmentStartEnd = new int[2];
1316 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1318 alignmentToExport = hiddenSeqs.getFullAlignment();
1322 alignmentToExport = viewport.getAlignment();
1324 alignmentStartEnd = alignmentToExport
1325 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1326 .getHiddenColumns());
1327 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1328 omitHidden, alignmentStartEnd, settings);
1339 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1341 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1342 htmlSVG.exportHTML(null);
1346 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1348 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1349 bjs.exportHTML(null);
1352 public void createImageMap(File file, String image)
1354 alignPanel.makePNGImageMap(file, image);
1364 public void createPNG(File f)
1366 alignPanel.makePNG(f);
1376 public void createEPS(File f)
1378 alignPanel.makeEPS(f);
1382 public void createSVG(File f)
1384 alignPanel.makeSVG(f);
1388 public void pageSetup_actionPerformed(ActionEvent e)
1390 PrinterJob printJob = PrinterJob.getPrinterJob();
1391 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1401 public void printMenuItem_actionPerformed(ActionEvent e)
1403 // Putting in a thread avoids Swing painting problems
1404 PrintThread thread = new PrintThread(alignPanel);
1409 public void exportFeatures_actionPerformed(ActionEvent e)
1411 new AnnotationExporter().exportFeatures(alignPanel);
1415 public void exportAnnotations_actionPerformed(ActionEvent e)
1417 new AnnotationExporter().exportAnnotations(alignPanel);
1421 public void associatedData_actionPerformed(ActionEvent e)
1423 // Pick the tree file
1424 JalviewFileChooser chooser = new JalviewFileChooser(
1425 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1426 chooser.setFileView(new JalviewFileView());
1427 chooser.setDialogTitle(MessageManager
1428 .getString("label.load_jalview_annotations"));
1429 chooser.setToolTipText(MessageManager
1430 .getString("label.load_jalview_annotations"));
1432 int value = chooser.showOpenDialog(null);
1434 if (value == JalviewFileChooser.APPROVE_OPTION)
1436 String choice = chooser.getSelectedFile().getPath();
1437 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1438 loadJalviewDataFile(choice, null, null, null);
1444 * Close the current view or all views in the alignment frame. If the frame
1445 * only contains one view then the alignment will be removed from memory.
1447 * @param closeAllTabs
1450 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1452 if (alignPanels != null && alignPanels.size() < 2)
1454 closeAllTabs = true;
1459 if (alignPanels != null)
1463 if (this.isClosed())
1465 // really close all the windows - otherwise wait till
1466 // setClosed(true) is called
1467 for (int i = 0; i < alignPanels.size(); i++)
1469 AlignmentPanel ap = alignPanels.get(i);
1476 closeView(alignPanel);
1483 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1484 * be called recursively, with the frame now in 'closed' state
1486 this.setClosed(true);
1488 } catch (Exception ex)
1490 ex.printStackTrace();
1495 * Close the specified panel and close up tabs appropriately.
1497 * @param panelToClose
1499 public void closeView(AlignmentPanel panelToClose)
1501 int index = tabbedPane.getSelectedIndex();
1502 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1503 alignPanels.remove(panelToClose);
1504 panelToClose.closePanel();
1505 panelToClose = null;
1507 tabbedPane.removeTabAt(closedindex);
1508 tabbedPane.validate();
1510 if (index > closedindex || index == tabbedPane.getTabCount())
1512 // modify currently selected tab index if necessary.
1516 this.tabSelectionChanged(index);
1522 void updateEditMenuBar()
1525 if (viewport.getHistoryList().size() > 0)
1527 undoMenuItem.setEnabled(true);
1528 CommandI command = viewport.getHistoryList().peek();
1529 undoMenuItem.setText(MessageManager.formatMessage(
1530 "label.undo_command",
1531 new Object[] { command.getDescription() }));
1535 undoMenuItem.setEnabled(false);
1536 undoMenuItem.setText(MessageManager.getString("action.undo"));
1539 if (viewport.getRedoList().size() > 0)
1541 redoMenuItem.setEnabled(true);
1543 CommandI command = viewport.getRedoList().peek();
1544 redoMenuItem.setText(MessageManager.formatMessage(
1545 "label.redo_command",
1546 new Object[] { command.getDescription() }));
1550 redoMenuItem.setEnabled(false);
1551 redoMenuItem.setText(MessageManager.getString("action.redo"));
1556 public void addHistoryItem(CommandI command)
1558 if (command.getSize() > 0)
1560 viewport.addToHistoryList(command);
1561 viewport.clearRedoList();
1562 updateEditMenuBar();
1563 viewport.updateHiddenColumns();
1564 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1565 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1566 // viewport.getColumnSelection()
1567 // .getHiddenColumns().size() > 0);
1573 * @return alignment objects for all views
1575 AlignmentI[] getViewAlignments()
1577 if (alignPanels != null)
1579 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1581 for (AlignmentPanel ap : alignPanels)
1583 als[i++] = ap.av.getAlignment();
1587 if (viewport != null)
1589 return new AlignmentI[] { viewport.getAlignment() };
1601 protected void undoMenuItem_actionPerformed(ActionEvent e)
1603 if (viewport.getHistoryList().isEmpty())
1607 CommandI command = viewport.getHistoryList().pop();
1608 viewport.addToRedoList(command);
1609 command.undoCommand(getViewAlignments());
1611 AlignmentViewport originalSource = getOriginatingSource(command);
1612 updateEditMenuBar();
1614 if (originalSource != null)
1616 if (originalSource != viewport)
1619 .warn("Implementation worry: mismatch of viewport origin for undo");
1621 originalSource.updateHiddenColumns();
1622 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1624 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1625 // viewport.getColumnSelection()
1626 // .getHiddenColumns().size() > 0);
1627 originalSource.firePropertyChange("alignment", null, originalSource
1628 .getAlignment().getSequences());
1639 protected void redoMenuItem_actionPerformed(ActionEvent e)
1641 if (viewport.getRedoList().size() < 1)
1646 CommandI command = viewport.getRedoList().pop();
1647 viewport.addToHistoryList(command);
1648 command.doCommand(getViewAlignments());
1650 AlignmentViewport originalSource = getOriginatingSource(command);
1651 updateEditMenuBar();
1653 if (originalSource != null)
1656 if (originalSource != viewport)
1659 .warn("Implementation worry: mismatch of viewport origin for redo");
1661 originalSource.updateHiddenColumns();
1662 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1664 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1665 // viewport.getColumnSelection()
1666 // .getHiddenColumns().size() > 0);
1667 originalSource.firePropertyChange("alignment", null, originalSource
1668 .getAlignment().getSequences());
1672 AlignmentViewport getOriginatingSource(CommandI command)
1674 AlignmentViewport originalSource = null;
1675 // For sequence removal and addition, we need to fire
1676 // the property change event FROM the viewport where the
1677 // original alignment was altered
1678 AlignmentI al = null;
1679 if (command instanceof EditCommand)
1681 EditCommand editCommand = (EditCommand) command;
1682 al = editCommand.getAlignment();
1683 List<Component> comps = PaintRefresher.components.get(viewport
1684 .getSequenceSetId());
1686 for (Component comp : comps)
1688 if (comp instanceof AlignmentPanel)
1690 if (al == ((AlignmentPanel) comp).av.getAlignment())
1692 originalSource = ((AlignmentPanel) comp).av;
1699 if (originalSource == null)
1701 // The original view is closed, we must validate
1702 // the current view against the closed view first
1705 PaintRefresher.validateSequences(al, viewport.getAlignment());
1708 originalSource = viewport;
1711 return originalSource;
1720 public void moveSelectedSequences(boolean up)
1722 SequenceGroup sg = viewport.getSelectionGroup();
1728 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1729 viewport.getHiddenRepSequences(), up);
1730 alignPanel.paintAlignment(true);
1733 synchronized void slideSequences(boolean right, int size)
1735 List<SequenceI> sg = new ArrayList<SequenceI>();
1736 if (viewport.cursorMode)
1738 sg.add(viewport.getAlignment().getSequenceAt(
1739 alignPanel.getSeqPanel().seqCanvas.cursorY));
1741 else if (viewport.getSelectionGroup() != null
1742 && viewport.getSelectionGroup().getSize() != viewport
1743 .getAlignment().getHeight())
1745 sg = viewport.getSelectionGroup().getSequences(
1746 viewport.getHiddenRepSequences());
1754 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1756 for (SequenceI seq : viewport.getAlignment().getSequences())
1758 if (!sg.contains(seq))
1760 invertGroup.add(seq);
1764 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1766 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1767 for (int i = 0; i < invertGroup.size(); i++)
1769 seqs2[i] = invertGroup.get(i);
1772 SlideSequencesCommand ssc;
1775 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1776 size, viewport.getGapCharacter());
1780 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1781 size, viewport.getGapCharacter());
1784 int groupAdjustment = 0;
1785 if (ssc.getGapsInsertedBegin() && right)
1787 if (viewport.cursorMode)
1789 alignPanel.getSeqPanel().moveCursor(size, 0);
1793 groupAdjustment = size;
1796 else if (!ssc.getGapsInsertedBegin() && !right)
1798 if (viewport.cursorMode)
1800 alignPanel.getSeqPanel().moveCursor(-size, 0);
1804 groupAdjustment = -size;
1808 if (groupAdjustment != 0)
1810 viewport.getSelectionGroup().setStartRes(
1811 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1812 viewport.getSelectionGroup().setEndRes(
1813 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1817 * just extend the last slide command if compatible; but not if in
1818 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1820 boolean appendHistoryItem = false;
1821 Deque<CommandI> historyList = viewport.getHistoryList();
1822 boolean inSplitFrame = getSplitViewContainer() != null;
1823 if (!inSplitFrame && historyList != null && historyList.size() > 0
1824 && historyList.peek() instanceof SlideSequencesCommand)
1826 appendHistoryItem = ssc
1827 .appendSlideCommand((SlideSequencesCommand) historyList
1831 if (!appendHistoryItem)
1833 addHistoryItem(ssc);
1846 protected void copy_actionPerformed(ActionEvent e)
1849 if (viewport.getSelectionGroup() == null)
1853 // TODO: preserve the ordering of displayed alignment annotation in any
1854 // internal paste (particularly sequence associated annotation)
1855 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1856 String[] omitHidden = null;
1858 if (viewport.hasHiddenColumns())
1860 omitHidden = viewport.getViewAsString(true);
1863 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1864 seqs, omitHidden, null);
1866 StringSelection ss = new StringSelection(output);
1870 jalview.gui.Desktop.internalCopy = true;
1871 // Its really worth setting the clipboard contents
1872 // to empty before setting the large StringSelection!!
1873 Toolkit.getDefaultToolkit().getSystemClipboard()
1874 .setContents(new StringSelection(""), null);
1876 Toolkit.getDefaultToolkit().getSystemClipboard()
1877 .setContents(ss, Desktop.instance);
1878 } catch (OutOfMemoryError er)
1880 new OOMWarning("copying region", er);
1884 ArrayList<int[]> hiddenColumns = null;
1885 if (viewport.hasHiddenColumns())
1887 hiddenColumns = new ArrayList<int[]>();
1888 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1889 .getSelectionGroup().getEndRes();
1890 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1892 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1894 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1895 region[1] - hiddenOffset });
1900 Desktop.jalviewClipboard = new Object[] { seqs,
1901 viewport.getAlignment().getDataset(), hiddenColumns };
1902 statusBar.setText(MessageManager.formatMessage(
1903 "label.copied_sequences_to_clipboard", new Object[] { Integer
1904 .valueOf(seqs.length).toString() }));
1914 protected void pasteNew_actionPerformed(ActionEvent e)
1926 protected void pasteThis_actionPerformed(ActionEvent e)
1932 * Paste contents of Jalview clipboard
1934 * @param newAlignment
1935 * true to paste to a new alignment, otherwise add to this.
1937 void paste(boolean newAlignment)
1939 boolean externalPaste = true;
1942 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1943 Transferable contents = c.getContents(this);
1945 if (contents == null)
1954 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1955 if (str.length() < 1)
1960 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1962 } catch (OutOfMemoryError er)
1964 new OOMWarning("Out of memory pasting sequences!!", er);
1968 SequenceI[] sequences;
1969 boolean annotationAdded = false;
1970 AlignmentI alignment = null;
1972 if (Desktop.jalviewClipboard != null)
1974 // The clipboard was filled from within Jalview, we must use the
1976 // And dataset from the copied alignment
1977 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1978 // be doubly sure that we create *new* sequence objects.
1979 sequences = new SequenceI[newseq.length];
1980 for (int i = 0; i < newseq.length; i++)
1982 sequences[i] = new Sequence(newseq[i]);
1984 alignment = new Alignment(sequences);
1985 externalPaste = false;
1989 // parse the clipboard as an alignment.
1990 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1992 sequences = alignment.getSequencesArray();
1996 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2002 if (Desktop.jalviewClipboard != null)
2004 // dataset is inherited
2005 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2009 // new dataset is constructed
2010 alignment.setDataset(null);
2012 alwidth = alignment.getWidth() + 1;
2016 AlignmentI pastedal = alignment; // preserve pasted alignment object
2017 // Add pasted sequences and dataset into existing alignment.
2018 alignment = viewport.getAlignment();
2019 alwidth = alignment.getWidth() + 1;
2020 // decide if we need to import sequences from an existing dataset
2021 boolean importDs = Desktop.jalviewClipboard != null
2022 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2023 // importDs==true instructs us to copy over new dataset sequences from
2024 // an existing alignment
2025 Vector newDs = (importDs) ? new Vector() : null; // used to create
2026 // minimum dataset set
2028 for (int i = 0; i < sequences.length; i++)
2032 newDs.addElement(null);
2034 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2036 if (importDs && ds != null)
2038 if (!newDs.contains(ds))
2040 newDs.setElementAt(ds, i);
2041 ds = new Sequence(ds);
2042 // update with new dataset sequence
2043 sequences[i].setDatasetSequence(ds);
2047 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2052 // copy and derive new dataset sequence
2053 sequences[i] = sequences[i].deriveSequence();
2054 alignment.getDataset().addSequence(
2055 sequences[i].getDatasetSequence());
2056 // TODO: avoid creation of duplicate dataset sequences with a
2057 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2059 alignment.addSequence(sequences[i]); // merges dataset
2063 newDs.clear(); // tidy up
2065 if (alignment.getAlignmentAnnotation() != null)
2067 for (AlignmentAnnotation alan : alignment
2068 .getAlignmentAnnotation())
2070 if (alan.graphGroup > fgroup)
2072 fgroup = alan.graphGroup;
2076 if (pastedal.getAlignmentAnnotation() != null)
2078 // Add any annotation attached to alignment.
2079 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2080 for (int i = 0; i < alann.length; i++)
2082 annotationAdded = true;
2083 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2085 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2086 if (newann.graphGroup > -1)
2088 if (newGraphGroups.size() <= newann.graphGroup
2089 || newGraphGroups.get(newann.graphGroup) == null)
2091 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2093 newGraphGroups.add(q, null);
2095 newGraphGroups.set(newann.graphGroup, new Integer(
2098 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2102 newann.padAnnotation(alwidth);
2103 alignment.addAnnotation(newann);
2113 addHistoryItem(new EditCommand(
2114 MessageManager.getString("label.add_sequences"),
2115 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2117 // Add any annotations attached to sequences
2118 for (int i = 0; i < sequences.length; i++)
2120 if (sequences[i].getAnnotation() != null)
2122 AlignmentAnnotation newann;
2123 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2125 annotationAdded = true;
2126 newann = sequences[i].getAnnotation()[a];
2127 newann.adjustForAlignment();
2128 newann.padAnnotation(alwidth);
2129 if (newann.graphGroup > -1)
2131 if (newann.graphGroup > -1)
2133 if (newGraphGroups.size() <= newann.graphGroup
2134 || newGraphGroups.get(newann.graphGroup) == null)
2136 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2138 newGraphGroups.add(q, null);
2140 newGraphGroups.set(newann.graphGroup, new Integer(
2143 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2147 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2152 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2159 // propagate alignment changed.
2160 vpRanges.setEndSeq(alignment.getHeight());
2161 if (annotationAdded)
2163 // Duplicate sequence annotation in all views.
2164 AlignmentI[] alview = this.getViewAlignments();
2165 for (int i = 0; i < sequences.length; i++)
2167 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2172 for (int avnum = 0; avnum < alview.length; avnum++)
2174 if (alview[avnum] != alignment)
2176 // duplicate in a view other than the one with input focus
2177 int avwidth = alview[avnum].getWidth() + 1;
2178 // this relies on sann being preserved after we
2179 // modify the sequence's annotation array for each duplication
2180 for (int a = 0; a < sann.length; a++)
2182 AlignmentAnnotation newann = new AlignmentAnnotation(
2184 sequences[i].addAlignmentAnnotation(newann);
2185 newann.padAnnotation(avwidth);
2186 alview[avnum].addAnnotation(newann); // annotation was
2187 // duplicated earlier
2188 // TODO JAL-1145 graphGroups are not updated for sequence
2189 // annotation added to several views. This may cause
2191 alview[avnum].setAnnotationIndex(newann, a);
2196 buildSortByAnnotationScoresMenu();
2198 viewport.firePropertyChange("alignment", null,
2199 alignment.getSequences());
2200 if (alignPanels != null)
2202 for (AlignmentPanel ap : alignPanels)
2204 ap.validateAnnotationDimensions(false);
2209 alignPanel.validateAnnotationDimensions(false);
2215 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2217 String newtitle = new String("Copied sequences");
2219 if (Desktop.jalviewClipboard != null
2220 && Desktop.jalviewClipboard[2] != null)
2222 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2223 for (int[] region : hc)
2225 af.viewport.hideColumns(region[0], region[1]);
2229 // >>>This is a fix for the moment, until a better solution is
2231 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2233 alignPanel.getSeqPanel().seqCanvas
2234 .getFeatureRenderer());
2236 // TODO: maintain provenance of an alignment, rather than just make the
2237 // title a concatenation of operations.
2240 if (title.startsWith("Copied sequences"))
2246 newtitle = newtitle.concat("- from " + title);
2251 newtitle = new String("Pasted sequences");
2254 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2259 } catch (Exception ex)
2261 ex.printStackTrace();
2262 System.out.println("Exception whilst pasting: " + ex);
2263 // could be anything being pasted in here
2269 protected void expand_newalign(ActionEvent e)
2273 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2274 .getAlignment(), -1);
2275 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2277 String newtitle = new String("Flanking alignment");
2279 if (Desktop.jalviewClipboard != null
2280 && Desktop.jalviewClipboard[2] != null)
2282 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2283 for (int region[] : hc)
2285 af.viewport.hideColumns(region[0], region[1]);
2289 // >>>This is a fix for the moment, until a better solution is
2291 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2293 alignPanel.getSeqPanel().seqCanvas
2294 .getFeatureRenderer());
2296 // TODO: maintain provenance of an alignment, rather than just make the
2297 // title a concatenation of operations.
2299 if (title.startsWith("Copied sequences"))
2305 newtitle = newtitle.concat("- from " + title);
2309 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2311 } catch (Exception ex)
2313 ex.printStackTrace();
2314 System.out.println("Exception whilst pasting: " + ex);
2315 // could be anything being pasted in here
2316 } catch (OutOfMemoryError oom)
2318 new OOMWarning("Viewing flanking region of alignment", oom);
2329 protected void cut_actionPerformed(ActionEvent e)
2331 copy_actionPerformed(null);
2332 delete_actionPerformed(null);
2342 protected void delete_actionPerformed(ActionEvent evt)
2345 SequenceGroup sg = viewport.getSelectionGroup();
2352 * If the cut affects all sequences, warn, remove highlighted columns
2354 if (sg.getSize() == viewport.getAlignment().getHeight())
2356 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2357 .getAlignment().getWidth()) ? true : false;
2358 if (isEntireAlignWidth)
2360 int confirm = JvOptionPane.showConfirmDialog(this,
2361 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2362 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2363 JvOptionPane.OK_CANCEL_OPTION);
2365 if (confirm == JvOptionPane.CANCEL_OPTION
2366 || confirm == JvOptionPane.CLOSED_OPTION)
2371 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2372 sg.getEndRes() + 1);
2374 SequenceI[] cut = sg.getSequences()
2375 .toArray(new SequenceI[sg.getSize()]);
2377 addHistoryItem(new EditCommand(
2378 MessageManager.getString("label.cut_sequences"), Action.CUT,
2379 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2380 viewport.getAlignment()));
2382 viewport.setSelectionGroup(null);
2383 viewport.sendSelection();
2384 viewport.getAlignment().deleteGroup(sg);
2386 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2388 if (viewport.getAlignment().getHeight() < 1)
2392 this.setClosed(true);
2393 } catch (Exception ex)
2406 protected void deleteGroups_actionPerformed(ActionEvent e)
2408 if (avc.deleteGroups())
2410 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2411 alignPanel.updateAnnotation();
2412 alignPanel.paintAlignment(true);
2423 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2425 SequenceGroup sg = new SequenceGroup();
2427 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2429 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2432 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2433 viewport.setSelectionGroup(sg);
2434 viewport.sendSelection();
2435 // JAL-2034 - should delegate to
2436 // alignPanel to decide if overview needs
2438 alignPanel.paintAlignment(false);
2439 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2449 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2451 if (viewport.cursorMode)
2453 alignPanel.getSeqPanel().keyboardNo1 = null;
2454 alignPanel.getSeqPanel().keyboardNo2 = null;
2456 viewport.setSelectionGroup(null);
2457 viewport.getColumnSelection().clear();
2458 viewport.setSelectionGroup(null);
2459 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2460 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2461 // JAL-2034 - should delegate to
2462 // alignPanel to decide if overview needs
2464 alignPanel.paintAlignment(false);
2465 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2466 viewport.sendSelection();
2476 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2478 SequenceGroup sg = viewport.getSelectionGroup();
2482 selectAllSequenceMenuItem_actionPerformed(null);
2487 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2489 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2491 // JAL-2034 - should delegate to
2492 // alignPanel to decide if overview needs
2495 alignPanel.paintAlignment(true);
2496 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2497 viewport.sendSelection();
2501 public void invertColSel_actionPerformed(ActionEvent e)
2503 viewport.invertColumnSelection();
2504 alignPanel.paintAlignment(true);
2505 viewport.sendSelection();
2515 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2517 trimAlignment(true);
2527 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2529 trimAlignment(false);
2532 void trimAlignment(boolean trimLeft)
2534 ColumnSelection colSel = viewport.getColumnSelection();
2537 if (!colSel.isEmpty())
2541 column = colSel.getMin();
2545 column = colSel.getMax();
2549 if (viewport.getSelectionGroup() != null)
2551 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2552 viewport.getHiddenRepSequences());
2556 seqs = viewport.getAlignment().getSequencesArray();
2559 TrimRegionCommand trimRegion;
2562 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2563 column, viewport.getAlignment());
2564 vpRanges.setStartRes(0);
2568 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2569 column, viewport.getAlignment());
2572 statusBar.setText(MessageManager.formatMessage(
2573 "label.removed_columns",
2574 new String[] { Integer.valueOf(trimRegion.getSize())
2577 addHistoryItem(trimRegion);
2579 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2581 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2582 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2584 viewport.getAlignment().deleteGroup(sg);
2588 viewport.firePropertyChange("alignment", null, viewport
2589 .getAlignment().getSequences());
2600 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2602 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2605 if (viewport.getSelectionGroup() != null)
2607 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2608 viewport.getHiddenRepSequences());
2609 start = viewport.getSelectionGroup().getStartRes();
2610 end = viewport.getSelectionGroup().getEndRes();
2614 seqs = viewport.getAlignment().getSequencesArray();
2617 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2618 "Remove Gapped Columns", seqs, start, end,
2619 viewport.getAlignment());
2621 addHistoryItem(removeGapCols);
2623 statusBar.setText(MessageManager.formatMessage(
2624 "label.removed_empty_columns",
2625 new Object[] { Integer.valueOf(removeGapCols.getSize())
2628 // This is to maintain viewport position on first residue
2629 // of first sequence
2630 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2631 int startRes = seq.findPosition(vpRanges.getStartRes());
2632 // ShiftList shifts;
2633 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2634 // edit.alColumnChanges=shifts.getInverse();
2635 // if (viewport.hasHiddenColumns)
2636 // viewport.getColumnSelection().compensateForEdits(shifts);
2637 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2638 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2650 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2652 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2655 if (viewport.getSelectionGroup() != null)
2657 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2658 viewport.getHiddenRepSequences());
2659 start = viewport.getSelectionGroup().getStartRes();
2660 end = viewport.getSelectionGroup().getEndRes();
2664 seqs = viewport.getAlignment().getSequencesArray();
2667 // This is to maintain viewport position on first residue
2668 // of first sequence
2669 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2670 int startRes = seq.findPosition(vpRanges.getStartRes());
2672 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2673 viewport.getAlignment()));
2675 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2677 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2689 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2691 viewport.setPadGaps(padGapsMenuitem.isSelected());
2692 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2703 public void findMenuItem_actionPerformed(ActionEvent e)
2709 * Create a new view of the current alignment.
2712 public void newView_actionPerformed(ActionEvent e)
2714 newView(null, true);
2718 * Creates and shows a new view of the current alignment.
2721 * title of newly created view; if null, one will be generated
2722 * @param copyAnnotation
2723 * if true then duplicate all annnotation, groups and settings
2724 * @return new alignment panel, already displayed.
2726 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2729 * Create a new AlignmentPanel (with its own, new Viewport)
2731 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2733 if (!copyAnnotation)
2736 * remove all groups and annotation except for the automatic stuff
2738 newap.av.getAlignment().deleteAllGroups();
2739 newap.av.getAlignment().deleteAllAnnotations(false);
2742 newap.av.setGatherViewsHere(false);
2744 if (viewport.viewName == null)
2746 viewport.viewName = MessageManager
2747 .getString("label.view_name_original");
2751 * Views share the same edits undo and redo stacks
2753 newap.av.setHistoryList(viewport.getHistoryList());
2754 newap.av.setRedoList(viewport.getRedoList());
2757 * Views share the same mappings; need to deregister any new mappings
2758 * created by copyAlignPanel, and register the new reference to the shared
2761 newap.av.replaceMappings(viewport.getAlignment());
2763 newap.av.viewName = getNewViewName(viewTitle);
2765 addAlignmentPanel(newap, true);
2766 newap.alignmentChanged();
2768 if (alignPanels.size() == 2)
2770 viewport.setGatherViewsHere(true);
2772 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2777 * Make a new name for the view, ensuring it is unique within the current
2778 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2779 * these now use viewId. Unique view names are still desirable for usability.)
2784 protected String getNewViewName(String viewTitle)
2786 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2787 boolean addFirstIndex = false;
2788 if (viewTitle == null || viewTitle.trim().length() == 0)
2790 viewTitle = MessageManager.getString("action.view");
2791 addFirstIndex = true;
2795 index = 1;// we count from 1 if given a specific name
2797 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2799 List<Component> comps = PaintRefresher.components.get(viewport
2800 .getSequenceSetId());
2802 List<String> existingNames = getExistingViewNames(comps);
2804 while (existingNames.contains(newViewName))
2806 newViewName = viewTitle + " " + (++index);
2812 * Returns a list of distinct view names found in the given list of
2813 * components. View names are held on the viewport of an AlignmentPanel.
2818 protected List<String> getExistingViewNames(List<Component> comps)
2820 List<String> existingNames = new ArrayList<String>();
2821 for (Component comp : comps)
2823 if (comp instanceof AlignmentPanel)
2825 AlignmentPanel ap = (AlignmentPanel) comp;
2826 if (!existingNames.contains(ap.av.viewName))
2828 existingNames.add(ap.av.viewName);
2832 return existingNames;
2836 * Explode tabbed views into separate windows.
2839 public void expandViews_actionPerformed(ActionEvent e)
2841 Desktop.explodeViews(this);
2845 * Gather views in separate windows back into a tabbed presentation.
2848 public void gatherViews_actionPerformed(ActionEvent e)
2850 Desktop.instance.gatherViews(this);
2860 public void font_actionPerformed(ActionEvent e)
2862 new FontChooser(alignPanel);
2872 protected void seqLimit_actionPerformed(ActionEvent e)
2874 viewport.setShowJVSuffix(seqLimits.isSelected());
2876 alignPanel.getIdPanel().getIdCanvas()
2877 .setPreferredSize(alignPanel.calculateIdWidth());
2878 alignPanel.paintAlignment(true);
2882 public void idRightAlign_actionPerformed(ActionEvent e)
2884 viewport.setRightAlignIds(idRightAlign.isSelected());
2885 alignPanel.paintAlignment(true);
2889 public void centreColumnLabels_actionPerformed(ActionEvent e)
2891 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2892 alignPanel.paintAlignment(true);
2898 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2901 protected void followHighlight_actionPerformed()
2904 * Set the 'follow' flag on the Viewport (and scroll to position if now
2907 final boolean state = this.followHighlightMenuItem.getState();
2908 viewport.setFollowHighlight(state);
2911 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2922 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2924 viewport.setColourText(colourTextMenuItem.isSelected());
2925 alignPanel.paintAlignment(true);
2935 public void wrapMenuItem_actionPerformed(ActionEvent e)
2937 scaleAbove.setVisible(wrapMenuItem.isSelected());
2938 scaleLeft.setVisible(wrapMenuItem.isSelected());
2939 scaleRight.setVisible(wrapMenuItem.isSelected());
2940 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2941 alignPanel.updateLayout();
2945 public void showAllSeqs_actionPerformed(ActionEvent e)
2947 viewport.showAllHiddenSeqs();
2951 public void showAllColumns_actionPerformed(ActionEvent e)
2953 viewport.showAllHiddenColumns();
2955 viewport.sendSelection();
2959 public void hideSelSequences_actionPerformed(ActionEvent e)
2961 viewport.hideAllSelectedSeqs();
2962 // alignPanel.paintAlignment(true);
2966 * called by key handler and the hide all/show all menu items
2971 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2974 boolean hide = false;
2975 SequenceGroup sg = viewport.getSelectionGroup();
2976 if (!toggleSeqs && !toggleCols)
2978 // Hide everything by the current selection - this is a hack - we do the
2979 // invert and then hide
2980 // first check that there will be visible columns after the invert.
2981 if (viewport.hasSelectedColumns()
2982 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2985 // now invert the sequence set, if required - empty selection implies
2986 // that no hiding is required.
2989 invertSequenceMenuItem_actionPerformed(null);
2990 sg = viewport.getSelectionGroup();
2994 viewport.expandColSelection(sg, true);
2995 // finally invert the column selection and get the new sequence
2997 invertColSel_actionPerformed(null);
3004 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3006 hideSelSequences_actionPerformed(null);
3009 else if (!(toggleCols && viewport.hasSelectedColumns()))
3011 showAllSeqs_actionPerformed(null);
3017 if (viewport.hasSelectedColumns())
3019 hideSelColumns_actionPerformed(null);
3022 viewport.setSelectionGroup(sg);
3027 showAllColumns_actionPerformed(null);
3036 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3037 * event.ActionEvent)
3040 public void hideAllButSelection_actionPerformed(ActionEvent e)
3042 toggleHiddenRegions(false, false);
3043 viewport.sendSelection();
3050 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3054 public void hideAllSelection_actionPerformed(ActionEvent e)
3056 SequenceGroup sg = viewport.getSelectionGroup();
3057 viewport.expandColSelection(sg, false);
3058 viewport.hideAllSelectedSeqs();
3059 viewport.hideSelectedColumns();
3060 alignPanel.paintAlignment(true);
3061 viewport.sendSelection();
3068 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3072 public void showAllhidden_actionPerformed(ActionEvent e)
3074 viewport.showAllHiddenColumns();
3075 viewport.showAllHiddenSeqs();
3076 alignPanel.paintAlignment(true);
3077 viewport.sendSelection();
3081 public void hideSelColumns_actionPerformed(ActionEvent e)
3083 viewport.hideSelectedColumns();
3084 alignPanel.paintAlignment(true);
3085 viewport.sendSelection();
3089 public void hiddenMarkers_actionPerformed(ActionEvent e)
3091 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3102 protected void scaleAbove_actionPerformed(ActionEvent e)
3104 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3105 alignPanel.paintAlignment(true);
3115 protected void scaleLeft_actionPerformed(ActionEvent e)
3117 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3118 alignPanel.paintAlignment(true);
3128 protected void scaleRight_actionPerformed(ActionEvent e)
3130 viewport.setScaleRightWrapped(scaleRight.isSelected());
3131 alignPanel.paintAlignment(true);
3141 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3143 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3144 alignPanel.paintAlignment(true);
3154 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3156 viewport.setShowText(viewTextMenuItem.isSelected());
3157 alignPanel.paintAlignment(true);
3167 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3169 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3170 alignPanel.paintAlignment(true);
3173 public FeatureSettings featureSettings;
3176 public FeatureSettingsControllerI getFeatureSettingsUI()
3178 return featureSettings;
3182 public void featureSettings_actionPerformed(ActionEvent e)
3184 if (featureSettings != null)
3186 featureSettings.close();
3187 featureSettings = null;
3189 if (!showSeqFeatures.isSelected())
3191 // make sure features are actually displayed
3192 showSeqFeatures.setSelected(true);
3193 showSeqFeatures_actionPerformed(null);
3195 featureSettings = new FeatureSettings(this);
3199 * Set or clear 'Show Sequence Features'
3205 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3207 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3208 alignPanel.paintAlignment(true);
3209 if (alignPanel.getOverviewPanel() != null)
3211 alignPanel.getOverviewPanel().updateOverviewImage();
3216 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3217 * the annotations panel as a whole.
3219 * The options to show/hide all annotations should be enabled when the panel
3220 * is shown, and disabled when the panel is hidden.
3225 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3227 final boolean setVisible = annotationPanelMenuItem.isSelected();
3228 viewport.setShowAnnotation(setVisible);
3229 this.showAllSeqAnnotations.setEnabled(setVisible);
3230 this.hideAllSeqAnnotations.setEnabled(setVisible);
3231 this.showAllAlAnnotations.setEnabled(setVisible);
3232 this.hideAllAlAnnotations.setEnabled(setVisible);
3233 alignPanel.updateLayout();
3237 public void alignmentProperties()
3239 JEditorPane editPane = new JEditorPane("text/html", "");
3240 editPane.setEditable(false);
3241 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3243 editPane.setText(MessageManager.formatMessage("label.html_content",
3244 new Object[] { contents.toString() }));
3245 JInternalFrame frame = new JInternalFrame();
3246 frame.getContentPane().add(new JScrollPane(editPane));
3248 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3249 "label.alignment_properties", new Object[] { getTitle() }),
3260 public void overviewMenuItem_actionPerformed(ActionEvent e)
3262 if (alignPanel.overviewPanel != null)
3267 JInternalFrame frame = new JInternalFrame();
3268 OverviewPanel overview = new OverviewPanel(alignPanel);
3269 frame.setContentPane(overview);
3270 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3271 "label.overview_params", new Object[] { this.getTitle() }),
3272 frame.getWidth(), frame.getHeight());
3274 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3275 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3278 public void internalFrameClosed(
3279 javax.swing.event.InternalFrameEvent evt)
3281 alignPanel.setOverviewPanel(null);
3285 alignPanel.setOverviewPanel(overview);
3289 public void textColour_actionPerformed()
3291 new TextColourChooser().chooseColour(alignPanel, null);
3295 * public void covariationColour_actionPerformed() {
3297 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3301 public void annotationColour_actionPerformed()
3303 new AnnotationColourChooser(viewport, alignPanel);
3307 public void annotationColumn_actionPerformed(ActionEvent e)
3309 new AnnotationColumnChooser(viewport, alignPanel);
3313 * Action on the user checking or unchecking the option to apply the selected
3314 * colour scheme to all groups. If unchecked, groups may have their own
3315 * independent colour schemes.
3320 public void applyToAllGroups_actionPerformed(boolean selected)
3322 viewport.setColourAppliesToAllGroups(selected);
3326 * Action on user selecting a colour from the colour menu
3329 * the name (not the menu item label!) of the colour scheme
3332 public void changeColour_actionPerformed(String name)
3335 * 'User Defined' opens a panel to configure or load a
3336 * user-defined colour scheme
3338 if (ResidueColourScheme.USER_DEFINED.equals(name))
3340 new UserDefinedColours(alignPanel, null);
3345 * otherwise set the chosen colour scheme (or null for 'None')
3347 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3348 viewport.getAlignment(), viewport.getHiddenRepSequences());
3353 * Actions on setting or changing the alignment colour scheme
3358 public void changeColour(ColourSchemeI cs)
3360 // TODO: pull up to controller method
3363 ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3366 viewport.setGlobalColourScheme(cs);
3368 alignPanel.paintAlignment(true);
3372 * Show the PID threshold slider panel
3375 protected void modifyPID_actionPerformed()
3377 SliderPanel.setPIDSliderSource(alignPanel,
3378 viewport.getResidueShading(), alignPanel.getViewName());
3379 SliderPanel.showPIDSlider();
3383 * Show the Conservation slider panel
3386 protected void modifyConservation_actionPerformed()
3388 SliderPanel.setConservationSlider(alignPanel,
3389 viewport.getResidueShading(), alignPanel.getViewName());
3390 SliderPanel.showConservationSlider();
3394 * Action on selecting or deselecting (Colour) By Conservation
3397 public void conservationMenuItem_actionPerformed(boolean selected)
3399 modifyConservation.setEnabled(selected);
3400 viewport.setConservationSelected(selected);
3401 viewport.getResidueShading().setConservationApplied(selected);
3403 changeColour(viewport.getGlobalColourScheme());
3406 modifyConservation_actionPerformed();
3410 SliderPanel.hideConservationSlider();
3415 * Action on selecting or deselecting (Colour) Above PID Threshold
3418 public void abovePIDThreshold_actionPerformed(boolean selected)
3420 modifyPID.setEnabled(selected);
3421 viewport.setAbovePIDThreshold(selected);
3424 viewport.getResidueShading().setThreshold(0,
3425 viewport.isIgnoreGapsConsensus());
3428 changeColour(viewport.getGlobalColourScheme());
3431 modifyPID_actionPerformed();
3435 SliderPanel.hidePIDSlider();
3446 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3448 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3449 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3450 .getAlignment().getSequenceAt(0));
3451 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3452 viewport.getAlignment()));
3453 alignPanel.paintAlignment(true);
3463 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3465 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3466 AlignmentSorter.sortByID(viewport.getAlignment());
3467 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3468 viewport.getAlignment()));
3469 alignPanel.paintAlignment(true);
3479 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3481 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3482 AlignmentSorter.sortByLength(viewport.getAlignment());
3483 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3484 viewport.getAlignment()));
3485 alignPanel.paintAlignment(true);
3495 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3497 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3498 AlignmentSorter.sortByGroup(viewport.getAlignment());
3499 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3500 viewport.getAlignment()));
3502 alignPanel.paintAlignment(true);
3512 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3514 new RedundancyPanel(alignPanel, this);
3524 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3526 if ((viewport.getSelectionGroup() == null)
3527 || (viewport.getSelectionGroup().getSize() < 2))
3529 JvOptionPane.showInternalMessageDialog(this, MessageManager
3530 .getString("label.you_must_select_least_two_sequences"),
3531 MessageManager.getString("label.invalid_selection"),
3532 JvOptionPane.WARNING_MESSAGE);
3536 JInternalFrame frame = new JInternalFrame();
3537 frame.setContentPane(new PairwiseAlignPanel(viewport));
3538 Desktop.addInternalFrame(frame,
3539 MessageManager.getString("action.pairwise_alignment"), 600,
3551 public void PCAMenuItem_actionPerformed(ActionEvent e)
3553 if (((viewport.getSelectionGroup() != null)
3554 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3555 .getSelectionGroup().getSize() > 0))
3556 || (viewport.getAlignment().getHeight() < 4))
3559 .showInternalMessageDialog(
3562 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3564 .getString("label.sequence_selection_insufficient"),
3565 JvOptionPane.WARNING_MESSAGE);
3570 new PCAPanel(alignPanel);
3574 public void autoCalculate_actionPerformed(ActionEvent e)
3576 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3577 if (viewport.autoCalculateConsensus)
3579 viewport.firePropertyChange("alignment", null, viewport
3580 .getAlignment().getSequences());
3585 public void sortByTreeOption_actionPerformed(ActionEvent e)
3587 viewport.sortByTree = sortByTree.isSelected();
3591 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3593 viewport.followSelection = listenToViewSelections.isSelected();
3597 * Constructs a tree panel and adds it to the desktop
3600 * tree type (NJ or AV)
3602 * distance or similarity score model used to compute the tree
3604 * parameters for the distance or similarity calculation
3606 void newTreePanel(String type, ScoreModelI sm, SimilarityParamsI options)
3608 String frameTitle = "";
3611 if (viewport.getSelectionGroup() != null
3612 && viewport.getSelectionGroup().getSize() > 0)
3614 if (viewport.getSelectionGroup().getSize() < 3)
3620 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3622 .getString("label.not_enough_sequences"),
3623 JvOptionPane.WARNING_MESSAGE);
3627 SequenceGroup sg = viewport.getSelectionGroup();
3629 /* Decide if the selection is a column region */
3630 for (SequenceI _s : sg.getSequences())
3632 if (_s.getLength() < sg.getEndRes())
3638 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3640 .getString("label.sequences_selection_not_aligned"),
3641 JvOptionPane.WARNING_MESSAGE);
3647 tp = new TreePanel(alignPanel, type, sm, options);
3648 frameTitle = tp.getPanelTitle() + " on region";
3652 // are the visible sequences aligned?
3653 if (!viewport.getAlignment().isAligned(false))
3659 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3661 .getString("label.sequences_not_aligned"),
3662 JvOptionPane.WARNING_MESSAGE);
3667 if (viewport.getAlignment().getHeight() < 2)
3672 tp = new TreePanel(alignPanel, type, sm, options);
3673 frameTitle = tp.getPanelTitle();
3676 frameTitle += " from ";
3678 if (viewport.viewName != null)
3680 frameTitle += viewport.viewName + " of ";
3683 frameTitle += this.title;
3685 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3696 public void addSortByOrderMenuItem(String title,
3697 final AlignmentOrder order)
3699 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3700 "action.by_title_param", new Object[] { title }));
3702 item.addActionListener(new java.awt.event.ActionListener()
3705 public void actionPerformed(ActionEvent e)
3707 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3709 // TODO: JBPNote - have to map order entries to curent SequenceI
3711 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3713 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3716 alignPanel.paintAlignment(true);
3722 * Add a new sort by annotation score menu item
3725 * the menu to add the option to
3727 * the label used to retrieve scores for each sequence on the
3730 public void addSortByAnnotScoreMenuItem(JMenu sort,
3731 final String scoreLabel)
3733 final JMenuItem item = new JMenuItem(scoreLabel);
3735 item.addActionListener(new java.awt.event.ActionListener()
3738 public void actionPerformed(ActionEvent e)
3740 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3741 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3742 viewport.getAlignment());// ,viewport.getSelectionGroup());
3743 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3744 viewport.getAlignment()));
3745 alignPanel.paintAlignment(true);
3751 * last hash for alignment's annotation array - used to minimise cost of
3754 protected int _annotationScoreVectorHash;
3757 * search the alignment and rebuild the sort by annotation score submenu the
3758 * last alignment annotation vector hash is stored to minimize cost of
3759 * rebuilding in subsequence calls.
3763 public void buildSortByAnnotationScoresMenu()
3765 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3770 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3772 sortByAnnotScore.removeAll();
3773 // almost certainly a quicker way to do this - but we keep it simple
3774 Hashtable scoreSorts = new Hashtable();
3775 AlignmentAnnotation aann[];
3776 for (SequenceI sqa : viewport.getAlignment().getSequences())
3778 aann = sqa.getAnnotation();
3779 for (int i = 0; aann != null && i < aann.length; i++)
3781 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3783 scoreSorts.put(aann[i].label, aann[i].label);
3787 Enumeration labels = scoreSorts.keys();
3788 while (labels.hasMoreElements())
3790 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3791 (String) labels.nextElement());
3793 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3796 _annotationScoreVectorHash = viewport.getAlignment()
3797 .getAlignmentAnnotation().hashCode();
3802 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3803 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3804 * call. Listeners are added to remove the menu item when the treePanel is
3805 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3809 public void buildTreeSortMenu()
3811 sortByTreeMenu.removeAll();
3813 List<Component> comps = PaintRefresher.components.get(viewport
3814 .getSequenceSetId());
3815 List<TreePanel> treePanels = new ArrayList<TreePanel>();
3816 for (Component comp : comps)
3818 if (comp instanceof TreePanel)
3820 treePanels.add((TreePanel) comp);
3824 if (treePanels.size() < 1)
3826 sortByTreeMenu.setVisible(false);
3830 sortByTreeMenu.setVisible(true);
3832 for (final TreePanel tp : treePanels)
3834 final JMenuItem item = new JMenuItem(tp.getTitle());
3835 item.addActionListener(new java.awt.event.ActionListener()
3838 public void actionPerformed(ActionEvent e)
3840 tp.sortByTree_actionPerformed();
3841 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3846 sortByTreeMenu.add(item);
3850 public boolean sortBy(AlignmentOrder alorder, String undoname)
3852 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3853 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3854 if (undoname != null)
3856 addHistoryItem(new OrderCommand(undoname, oldOrder,
3857 viewport.getAlignment()));
3859 alignPanel.paintAlignment(true);
3864 * Work out whether the whole set of sequences or just the selected set will
3865 * be submitted for multiple alignment.
3868 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3870 // Now, check we have enough sequences
3871 AlignmentView msa = null;
3873 if ((viewport.getSelectionGroup() != null)
3874 && (viewport.getSelectionGroup().getSize() > 1))
3876 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3877 // some common interface!
3879 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3880 * SequenceI[sz = seqs.getSize(false)];
3882 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3883 * seqs.getSequenceAt(i); }
3885 msa = viewport.getAlignmentView(true);
3887 else if (viewport.getSelectionGroup() != null
3888 && viewport.getSelectionGroup().getSize() == 1)
3890 int option = JvOptionPane.showConfirmDialog(this,
3891 MessageManager.getString("warn.oneseq_msainput_selection"),
3892 MessageManager.getString("label.invalid_selection"),
3893 JvOptionPane.OK_CANCEL_OPTION);
3894 if (option == JvOptionPane.OK_OPTION)
3896 msa = viewport.getAlignmentView(false);
3901 msa = viewport.getAlignmentView(false);
3907 * Decides what is submitted to a secondary structure prediction service: the
3908 * first sequence in the alignment, or in the current selection, or, if the
3909 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3910 * region or the whole alignment. (where the first sequence in the set is the
3911 * one that the prediction will be for).
3913 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3915 AlignmentView seqs = null;
3917 if ((viewport.getSelectionGroup() != null)
3918 && (viewport.getSelectionGroup().getSize() > 0))
3920 seqs = viewport.getAlignmentView(true);
3924 seqs = viewport.getAlignmentView(false);
3926 // limit sequences - JBPNote in future - could spawn multiple prediction
3928 // TODO: viewport.getAlignment().isAligned is a global state - the local
3929 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3930 if (!viewport.getAlignment().isAligned(false))
3932 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3933 // TODO: if seqs.getSequences().length>1 then should really have warned
3947 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3949 // Pick the tree file
3950 JalviewFileChooser chooser = new JalviewFileChooser(
3951 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3952 chooser.setFileView(new JalviewFileView());
3953 chooser.setDialogTitle(MessageManager
3954 .getString("label.select_newick_like_tree_file"));
3955 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3957 int value = chooser.showOpenDialog(null);
3959 if (value == JalviewFileChooser.APPROVE_OPTION)
3961 String filePath = chooser.getSelectedFile().getPath();
3962 Cache.setProperty("LAST_DIRECTORY", filePath);
3963 NewickFile fin = null;
3966 fin = new NewickFile(filePath, DataSourceType.FILE);
3967 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3968 } catch (Exception ex)
3975 .getString("label.problem_reading_tree_file"),
3976 JvOptionPane.WARNING_MESSAGE);
3977 ex.printStackTrace();
3979 if (fin != null && fin.hasWarningMessage())
3981 JvOptionPane.showMessageDialog(Desktop.desktop, fin
3982 .getWarningMessage(), MessageManager
3983 .getString("label.possible_problem_with_tree_file"),
3984 JvOptionPane.WARNING_MESSAGE);
3989 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3991 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3994 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3995 int h, int x, int y)
3997 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4001 * Add a treeviewer for the tree extracted from a Newick file object to the
4002 * current alignment view
4009 * Associated alignment input data (or null)
4018 * @return TreePanel handle
4020 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4021 AlignmentView input, int w, int h, int x, int y)
4023 TreePanel tp = null;
4029 if (nf.getTree() != null)
4031 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4037 tp.setLocation(x, y);
4040 Desktop.addInternalFrame(tp, treeTitle, w, h);
4042 } catch (Exception ex)
4044 ex.printStackTrace();
4050 private boolean buildingMenu = false;
4053 * Generates menu items and listener event actions for web service clients
4056 public void BuildWebServiceMenu()
4058 while (buildingMenu)
4062 System.err.println("Waiting for building menu to finish.");
4064 } catch (Exception e)
4068 final AlignFrame me = this;
4069 buildingMenu = true;
4070 new Thread(new Runnable()
4075 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4078 // System.err.println("Building ws menu again "
4079 // + Thread.currentThread());
4080 // TODO: add support for context dependent disabling of services based
4082 // alignment and current selection
4083 // TODO: add additional serviceHandle parameter to specify abstract
4085 // class independently of AbstractName
4086 // TODO: add in rediscovery GUI function to restart discoverer
4087 // TODO: group services by location as well as function and/or
4089 // object broker mechanism.
4090 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4091 final IProgressIndicator af = me;
4094 * do not i18n these strings - they are hard-coded in class
4095 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4096 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4098 final JMenu msawsmenu = new JMenu("Alignment");
4099 final JMenu secstrmenu = new JMenu(
4100 "Secondary Structure Prediction");
4101 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4102 final JMenu analymenu = new JMenu("Analysis");
4103 final JMenu dismenu = new JMenu("Protein Disorder");
4104 // JAL-940 - only show secondary structure prediction services from
4105 // the legacy server
4106 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4108 Discoverer.services != null && (Discoverer.services.size() > 0))
4110 // TODO: refactor to allow list of AbstractName/Handler bindings to
4112 // stored or retrieved from elsewhere
4113 // No MSAWS used any more:
4114 // Vector msaws = null; // (Vector)
4115 // Discoverer.services.get("MsaWS");
4116 Vector secstrpr = (Vector) Discoverer.services
4118 if (secstrpr != null)
4120 // Add any secondary structure prediction services
4121 for (int i = 0, j = secstrpr.size(); i < j; i++)
4123 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4125 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4126 .getServiceClient(sh);
4127 int p = secstrmenu.getItemCount();
4128 impl.attachWSMenuEntry(secstrmenu, me);
4129 int q = secstrmenu.getItemCount();
4130 for (int litm = p; litm < q; litm++)
4132 legacyItems.add(secstrmenu.getItem(litm));
4138 // Add all submenus in the order they should appear on the web
4140 wsmenu.add(msawsmenu);
4141 wsmenu.add(secstrmenu);
4142 wsmenu.add(dismenu);
4143 wsmenu.add(analymenu);
4144 // No search services yet
4145 // wsmenu.add(seqsrchmenu);
4147 javax.swing.SwingUtilities.invokeLater(new Runnable()
4154 webService.removeAll();
4155 // first, add discovered services onto the webservices menu
4156 if (wsmenu.size() > 0)
4158 for (int i = 0, j = wsmenu.size(); i < j; i++)
4160 webService.add(wsmenu.get(i));
4165 webService.add(me.webServiceNoServices);
4167 // TODO: move into separate menu builder class.
4168 boolean new_sspred = false;
4169 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4171 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4172 if (jws2servs != null)
4174 if (jws2servs.hasServices())
4176 jws2servs.attachWSMenuEntry(webService, me);
4177 for (Jws2Instance sv : jws2servs.getServices())
4179 if (sv.description.toLowerCase().contains("jpred"))
4181 for (JMenuItem jmi : legacyItems)
4183 jmi.setVisible(false);
4189 if (jws2servs.isRunning())
4191 JMenuItem tm = new JMenuItem(
4192 "Still discovering JABA Services");
4193 tm.setEnabled(false);
4198 build_urlServiceMenu(me.webService);
4199 build_fetchdbmenu(webService);
4200 for (JMenu item : wsmenu)
4202 if (item.getItemCount() == 0)
4204 item.setEnabled(false);
4208 item.setEnabled(true);
4211 } catch (Exception e)
4214 .debug("Exception during web service menu building process.",
4219 } catch (Exception e)
4222 buildingMenu = false;
4229 * construct any groupURL type service menu entries.
4233 private void build_urlServiceMenu(JMenu webService)
4235 // TODO: remove this code when 2.7 is released
4236 // DEBUG - alignmentView
4238 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4239 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4241 * @Override public void actionPerformed(ActionEvent e) {
4242 * jalview.datamodel.AlignmentView
4243 * .testSelectionViews(af.viewport.getAlignment(),
4244 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4246 * }); webService.add(testAlView);
4248 // TODO: refactor to RestClient discoverer and merge menu entries for
4249 // rest-style services with other types of analysis/calculation service
4250 // SHmmr test client - still being implemented.
4251 // DEBUG - alignmentView
4253 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4256 client.attachWSMenuEntry(
4257 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4263 * Searches the alignment sequences for xRefs and builds the Show
4264 * Cross-References menu (formerly called Show Products), with database
4265 * sources for which cross-references are found (protein sources for a
4266 * nucleotide alignment and vice versa)
4268 * @return true if Show Cross-references menu should be enabled
4270 public boolean canShowProducts()
4272 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4273 AlignmentI dataset = viewport.getAlignment().getDataset();
4275 showProducts.removeAll();
4276 final boolean dna = viewport.getAlignment().isNucleotide();
4278 if (seqs == null || seqs.length == 0)
4280 // nothing to see here.
4284 boolean showp = false;
4287 List<String> ptypes = new CrossRef(seqs, dataset)
4288 .findXrefSourcesForSequences(dna);
4290 for (final String source : ptypes)
4293 final AlignFrame af = this;
4294 JMenuItem xtype = new JMenuItem(source);
4295 xtype.addActionListener(new ActionListener()
4298 public void actionPerformed(ActionEvent e)
4300 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4303 showProducts.add(xtype);
4305 showProducts.setVisible(showp);
4306 showProducts.setEnabled(showp);
4307 } catch (Exception e)
4310 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4318 * Finds and displays cross-references for the selected sequences (protein
4319 * products for nucleotide sequences, dna coding sequences for peptides).
4322 * the sequences to show cross-references for
4324 * true if from a nucleotide alignment (so showing proteins)
4326 * the database to show cross-references for
4328 protected void showProductsFor(final SequenceI[] sel,
4329 final boolean _odna, final String source)
4331 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4336 * Construct and display a new frame containing the translation of this
4337 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4340 public void showTranslation_actionPerformed(ActionEvent e)
4342 AlignmentI al = null;
4345 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4347 al = dna.translateCdna();
4348 } catch (Exception ex)
4350 jalview.bin.Cache.log.error(
4351 "Exception during translation. Please report this !", ex);
4352 final String msg = MessageManager
4353 .getString("label.error_when_translating_sequences_submit_bug_report");
4354 final String errorTitle = MessageManager
4355 .getString("label.implementation_error")
4356 + MessageManager.getString("label.translation_failed");
4357 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4358 JvOptionPane.ERROR_MESSAGE);
4361 if (al == null || al.getHeight() == 0)
4363 final String msg = MessageManager
4364 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4365 final String errorTitle = MessageManager
4366 .getString("label.translation_failed");
4367 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4368 JvOptionPane.WARNING_MESSAGE);
4372 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4373 af.setFileFormat(this.currentFileFormat);
4374 final String newTitle = MessageManager.formatMessage(
4375 "label.translation_of_params",
4376 new Object[] { this.getTitle() });
4377 af.setTitle(newTitle);
4378 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4380 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4381 viewport.openSplitFrame(af, new Alignment(seqs));
4385 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4392 * Set the file format
4396 public void setFileFormat(FileFormatI format)
4398 this.currentFileFormat = format;
4402 * Try to load a features file onto the alignment.
4405 * contents or path to retrieve file
4407 * access mode of file (see jalview.io.AlignFile)
4408 * @return true if features file was parsed correctly.
4410 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4412 return avc.parseFeaturesFile(file, sourceType,
4413 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4418 public void refreshFeatureUI(boolean enableIfNecessary)
4420 // note - currently this is only still here rather than in the controller
4421 // because of the featureSettings hard reference that is yet to be
4423 if (enableIfNecessary)
4425 viewport.setShowSequenceFeatures(true);
4426 showSeqFeatures.setSelected(true);
4432 public void dragEnter(DropTargetDragEvent evt)
4437 public void dragExit(DropTargetEvent evt)
4442 public void dragOver(DropTargetDragEvent evt)
4447 public void dropActionChanged(DropTargetDragEvent evt)
4452 public void drop(DropTargetDropEvent evt)
4454 // JAL-1552 - acceptDrop required before getTransferable call for
4455 // Java's Transferable for native dnd
4456 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4457 Transferable t = evt.getTransferable();
4458 List<String> files = new ArrayList<String>();
4459 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4463 Desktop.transferFromDropTarget(files, protocols, evt, t);
4464 } catch (Exception e)
4466 e.printStackTrace();
4472 // check to see if any of these files have names matching sequences in
4474 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4475 .getAlignment().getSequencesArray());
4477 * Object[] { String,SequenceI}
4479 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4480 ArrayList<String> filesnotmatched = new ArrayList<String>();
4481 for (int i = 0; i < files.size(); i++)
4483 String file = files.get(i).toString();
4485 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4486 if (protocol == DataSourceType.FILE)
4488 File fl = new File(file);
4489 pdbfn = fl.getName();
4491 else if (protocol == DataSourceType.URL)
4493 URL url = new URL(file);
4494 pdbfn = url.getFile();
4496 if (pdbfn.length() > 0)
4498 // attempt to find a match in the alignment
4499 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4500 int l = 0, c = pdbfn.indexOf(".");
4501 while (mtch == null && c != -1)
4506 } while ((c = pdbfn.indexOf(".", l)) > l);
4509 pdbfn = pdbfn.substring(0, l);
4511 mtch = idm.findAllIdMatches(pdbfn);
4515 FileFormatI type = null;
4518 type = new IdentifyFile().identify(file, protocol);
4519 } catch (Exception ex)
4523 if (type != null && type.isStructureFile())
4525 filesmatched.add(new Object[] { file, protocol, mtch });
4529 // File wasn't named like one of the sequences or wasn't a PDB file.
4530 filesnotmatched.add(file);
4534 if (filesmatched.size() > 0)
4536 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4542 "label.automatically_associate_structure_files_with_sequences_same_name",
4543 new Object[] { Integer
4549 .getString("label.automatically_associate_structure_files_by_name"),
4550 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4553 for (Object[] fm : filesmatched)
4555 // try and associate
4556 // TODO: may want to set a standard ID naming formalism for
4557 // associating PDB files which have no IDs.
4558 for (SequenceI toassoc : (SequenceI[]) fm[2])
4560 PDBEntry pe = new AssociatePdbFileWithSeq()
4561 .associatePdbWithSeq((String) fm[0],
4562 (DataSourceType) fm[1], toassoc, false,
4566 System.err.println("Associated file : "
4567 + ((String) fm[0]) + " with "
4568 + toassoc.getDisplayId(true));
4572 alignPanel.paintAlignment(true);
4576 if (filesnotmatched.size() > 0)
4579 && (Cache.getDefault(
4580 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4586 "label.ignore_unmatched_dropped_files_info",
4587 new Object[] { Integer
4594 .getString("label.ignore_unmatched_dropped_files"),
4595 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4599 for (String fn : filesnotmatched)
4601 loadJalviewDataFile(fn, null, null, null);
4605 } catch (Exception ex)
4607 ex.printStackTrace();
4613 * Attempt to load a "dropped" file or URL string, by testing in turn for
4615 * <li>an Annotation file</li>
4616 * <li>a JNet file</li>
4617 * <li>a features file</li>
4618 * <li>else try to interpret as an alignment file</li>
4622 * either a filename or a URL string.
4624 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4625 FileFormatI format, SequenceI assocSeq)
4629 if (sourceType == null)
4631 sourceType = FormatAdapter.checkProtocol(file);
4633 // if the file isn't identified, or not positively identified as some
4634 // other filetype (PFAM is default unidentified alignment file type) then
4635 // try to parse as annotation.
4636 boolean isAnnotation = (format == null || FileFormat.Pfam
4637 .equals(format)) ? new AnnotationFile()
4638 .annotateAlignmentView(viewport, file, sourceType) : false;
4642 // first see if its a T-COFFEE score file
4643 TCoffeeScoreFile tcf = null;
4646 tcf = new TCoffeeScoreFile(file, sourceType);
4649 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4652 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4653 isAnnotation = true;
4655 .setText(MessageManager
4656 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4660 // some problem - if no warning its probable that the ID matching
4661 // process didn't work
4665 tcf.getWarningMessage() == null ? MessageManager
4666 .getString("label.check_file_matches_sequence_ids_alignment")
4667 : tcf.getWarningMessage(),
4669 .getString("label.problem_reading_tcoffee_score_file"),
4670 JvOptionPane.WARNING_MESSAGE);
4677 } catch (Exception x)
4680 .debug("Exception when processing data source as T-COFFEE score file",
4686 // try to see if its a JNet 'concise' style annotation file *before*
4688 // try to parse it as a features file
4691 format = new IdentifyFile().identify(file, sourceType);
4693 if (FileFormat.ScoreMatrix == format)
4695 ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4698 // todo: i18n this message
4700 .setText(MessageManager.formatMessage(
4701 "label.successfully_loaded_matrix",
4702 sm.getMatrixName()));
4704 else if (FileFormat.Jnet.equals(format))
4706 JPredFile predictions = new JPredFile(file, sourceType);
4707 new JnetAnnotationMaker();
4708 JnetAnnotationMaker.add_annotation(predictions,
4709 viewport.getAlignment(), 0, false);
4710 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4711 viewport.getAlignment().setSeqrep(repseq);
4712 ColumnSelection cs = new ColumnSelection();
4713 cs.hideInsertionsFor(repseq);
4714 viewport.setColumnSelection(cs);
4715 isAnnotation = true;
4717 // else if (IdentifyFile.FeaturesFile.equals(format))
4718 else if (FileFormat.Features.equals(format))
4720 if (parseFeaturesFile(file, sourceType))
4722 alignPanel.paintAlignment(true);
4727 new FileLoader().LoadFile(viewport, file, sourceType, format);
4734 alignPanel.adjustAnnotationHeight();
4735 viewport.updateSequenceIdColours();
4736 buildSortByAnnotationScoresMenu();
4737 alignPanel.paintAlignment(true);
4739 } catch (Exception ex)
4741 ex.printStackTrace();
4742 } catch (OutOfMemoryError oom)
4747 } catch (Exception x)
4752 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4753 : "using " + sourceType + " from " + file)
4755 + (format != null ? "(parsing as '" + format
4756 + "' file)" : ""), oom, Desktop.desktop);
4761 * Method invoked by the ChangeListener on the tabbed pane, in other words
4762 * when a different tabbed pane is selected by the user or programmatically.
4765 public void tabSelectionChanged(int index)
4769 alignPanel = alignPanels.get(index);
4770 viewport = alignPanel.av;
4771 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4772 setMenusFromViewport(viewport);
4776 * 'focus' any colour slider that is open to the selected viewport
4778 if (viewport.getConservationSelected())
4780 SliderPanel.setConservationSlider(alignPanel,
4781 viewport.getResidueShading(), alignPanel.getViewName());
4785 SliderPanel.hideConservationSlider();
4787 if (viewport.getAbovePIDThreshold())
4789 SliderPanel.setPIDSliderSource(alignPanel,
4790 viewport.getResidueShading(), alignPanel.getViewName());
4794 SliderPanel.hidePIDSlider();
4798 * If there is a frame linked to this one in a SplitPane, switch it to the
4799 * same view tab index. No infinite recursion of calls should happen, since
4800 * tabSelectionChanged() should not get invoked on setting the selected
4801 * index to an unchanged value. Guard against setting an invalid index
4802 * before the new view peer tab has been created.
4804 final AlignViewportI peer = viewport.getCodingComplement();
4807 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4808 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4810 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4816 * On right mouse click on view tab, prompt for and set new view name.
4819 public void tabbedPane_mousePressed(MouseEvent e)
4821 if (e.isPopupTrigger())
4823 String msg = MessageManager.getString("label.enter_view_name");
4824 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4825 JvOptionPane.QUESTION_MESSAGE);
4829 viewport.viewName = reply;
4830 // TODO warn if reply is in getExistingViewNames()?
4831 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4836 public AlignViewport getCurrentView()
4842 * Open the dialog for regex description parsing.
4845 protected void extractScores_actionPerformed(ActionEvent e)
4847 ParseProperties pp = new jalview.analysis.ParseProperties(
4848 viewport.getAlignment());
4849 // TODO: verify regex and introduce GUI dialog for version 2.5
4850 // if (pp.getScoresFromDescription("col", "score column ",
4851 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4853 if (pp.getScoresFromDescription("description column",
4854 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4856 buildSortByAnnotationScoresMenu();
4864 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4868 protected void showDbRefs_actionPerformed(ActionEvent e)
4870 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4876 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4880 protected void showNpFeats_actionPerformed(ActionEvent e)
4882 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4886 * find the viewport amongst the tabs in this alignment frame and close that
4891 public boolean closeView(AlignViewportI av)
4895 this.closeMenuItem_actionPerformed(false);
4898 Component[] comp = tabbedPane.getComponents();
4899 for (int i = 0; comp != null && i < comp.length; i++)
4901 if (comp[i] instanceof AlignmentPanel)
4903 if (((AlignmentPanel) comp[i]).av == av)
4906 closeView((AlignmentPanel) comp[i]);
4914 protected void build_fetchdbmenu(JMenu webService)
4916 // Temporary hack - DBRef Fetcher always top level ws entry.
4917 // TODO We probably want to store a sequence database checklist in
4918 // preferences and have checkboxes.. rather than individual sources selected
4920 final JMenu rfetch = new JMenu(
4921 MessageManager.getString("action.fetch_db_references"));
4922 rfetch.setToolTipText(MessageManager
4923 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4924 webService.add(rfetch);
4926 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4927 MessageManager.getString("option.trim_retrieved_seqs"));
4928 trimrs.setToolTipText(MessageManager
4929 .getString("label.trim_retrieved_sequences"));
4930 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4931 trimrs.addActionListener(new ActionListener()
4934 public void actionPerformed(ActionEvent e)
4936 trimrs.setSelected(trimrs.isSelected());
4937 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4938 Boolean.valueOf(trimrs.isSelected()).toString());
4942 JMenuItem fetchr = new JMenuItem(
4943 MessageManager.getString("label.standard_databases"));
4944 fetchr.setToolTipText(MessageManager
4945 .getString("label.fetch_embl_uniprot"));
4946 fetchr.addActionListener(new ActionListener()
4950 public void actionPerformed(ActionEvent e)
4952 new Thread(new Runnable()
4957 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4958 .getAlignment().isNucleotide();
4959 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4960 .getSequenceSelection(), alignPanel.alignFrame, null,
4961 alignPanel.alignFrame.featureSettings, isNucleotide);
4962 dbRefFetcher.addListener(new FetchFinishedListenerI()
4965 public void finished()
4967 AlignFrame.this.setMenusForViewport();
4970 dbRefFetcher.fetchDBRefs(false);
4978 final AlignFrame me = this;
4979 new Thread(new Runnable()
4984 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4985 .getSequenceFetcherSingleton(me);
4986 javax.swing.SwingUtilities.invokeLater(new Runnable()
4991 String[] dbclasses = sf.getOrderedSupportedSources();
4992 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4993 // jalview.util.QuickSort.sort(otherdb, otherdb);
4994 List<DbSourceProxy> otherdb;
4995 JMenu dfetch = new JMenu();
4996 JMenu ifetch = new JMenu();
4997 JMenuItem fetchr = null;
4998 int comp = 0, icomp = 0, mcomp = 15;
4999 String mname = null;
5001 for (String dbclass : dbclasses)
5003 otherdb = sf.getSourceProxy(dbclass);
5004 // add a single entry for this class, or submenu allowing 'fetch
5006 if (otherdb == null || otherdb.size() < 1)
5010 // List<DbSourceProxy> dbs=otherdb;
5011 // otherdb=new ArrayList<DbSourceProxy>();
5012 // for (DbSourceProxy db:dbs)
5014 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5018 mname = "From " + dbclass;
5020 if (otherdb.size() == 1)
5022 final DbSourceProxy[] dassource = otherdb
5023 .toArray(new DbSourceProxy[0]);
5024 DbSourceProxy src = otherdb.get(0);
5025 fetchr = new JMenuItem(src.getDbSource());
5026 fetchr.addActionListener(new ActionListener()
5030 public void actionPerformed(ActionEvent e)
5032 new Thread(new Runnable()
5038 boolean isNucleotide = alignPanel.alignFrame
5039 .getViewport().getAlignment()
5041 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5042 alignPanel.av.getSequenceSelection(),
5043 alignPanel.alignFrame, dassource,
5044 alignPanel.alignFrame.featureSettings,
5047 .addListener(new FetchFinishedListenerI()
5050 public void finished()
5052 AlignFrame.this.setMenusForViewport();
5055 dbRefFetcher.fetchDBRefs(false);
5061 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5062 MessageManager.formatMessage(
5063 "label.fetch_retrieve_from",
5064 new Object[] { src.getDbName() })));
5070 final DbSourceProxy[] dassource = otherdb
5071 .toArray(new DbSourceProxy[0]);
5073 DbSourceProxy src = otherdb.get(0);
5074 fetchr = new JMenuItem(MessageManager.formatMessage(
5075 "label.fetch_all_param",
5076 new Object[] { src.getDbSource() }));
5077 fetchr.addActionListener(new ActionListener()
5080 public void actionPerformed(ActionEvent e)
5082 new Thread(new Runnable()
5088 boolean isNucleotide = alignPanel.alignFrame
5089 .getViewport().getAlignment()
5091 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5092 alignPanel.av.getSequenceSelection(),
5093 alignPanel.alignFrame, dassource,
5094 alignPanel.alignFrame.featureSettings,
5097 .addListener(new FetchFinishedListenerI()
5100 public void finished()
5102 AlignFrame.this.setMenusForViewport();
5105 dbRefFetcher.fetchDBRefs(false);
5111 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5112 MessageManager.formatMessage(
5113 "label.fetch_retrieve_from_all_sources",
5115 Integer.valueOf(otherdb.size())
5116 .toString(), src.getDbSource(),
5117 src.getDbName() })));
5120 // and then build the rest of the individual menus
5121 ifetch = new JMenu(MessageManager.formatMessage(
5122 "label.source_from_db_source",
5123 new Object[] { src.getDbSource() }));
5125 String imname = null;
5127 for (DbSourceProxy sproxy : otherdb)
5129 String dbname = sproxy.getDbName();
5130 String sname = dbname.length() > 5 ? dbname.substring(0,
5131 5) + "..." : dbname;
5132 String msname = dbname.length() > 10 ? dbname.substring(
5133 0, 10) + "..." : dbname;
5136 imname = MessageManager.formatMessage(
5137 "label.from_msname", new Object[] { sname });
5139 fetchr = new JMenuItem(msname);
5140 final DbSourceProxy[] dassrc = { sproxy };
5141 fetchr.addActionListener(new ActionListener()
5145 public void actionPerformed(ActionEvent e)
5147 new Thread(new Runnable()
5153 boolean isNucleotide = alignPanel.alignFrame
5154 .getViewport().getAlignment()
5156 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5157 alignPanel.av.getSequenceSelection(),
5158 alignPanel.alignFrame, dassrc,
5159 alignPanel.alignFrame.featureSettings,
5162 .addListener(new FetchFinishedListenerI()
5165 public void finished()
5167 AlignFrame.this.setMenusForViewport();
5170 dbRefFetcher.fetchDBRefs(false);
5176 fetchr.setToolTipText("<html>"
5177 + MessageManager.formatMessage(
5178 "label.fetch_retrieve_from", new Object[]
5182 if (++icomp >= mcomp || i == (otherdb.size()))
5184 ifetch.setText(MessageManager.formatMessage(
5185 "label.source_to_target", imname, sname));
5187 ifetch = new JMenu();
5195 if (comp >= mcomp || dbi >= (dbclasses.length))
5197 dfetch.setText(MessageManager.formatMessage(
5198 "label.source_to_target", mname, dbclass));
5200 dfetch = new JMenu();
5213 * Left justify the whole alignment.
5216 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5218 AlignmentI al = viewport.getAlignment();
5220 viewport.firePropertyChange("alignment", null, al);
5224 * Right justify the whole alignment.
5227 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5229 AlignmentI al = viewport.getAlignment();
5231 viewport.firePropertyChange("alignment", null, al);
5235 public void setShowSeqFeatures(boolean b)
5237 showSeqFeatures.setSelected(b);
5238 viewport.setShowSequenceFeatures(b);
5245 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5246 * awt.event.ActionEvent)
5249 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5251 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5252 alignPanel.paintAlignment(true);
5259 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5263 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5265 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5266 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5274 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5275 * .event.ActionEvent)
5278 protected void showGroupConservation_actionPerformed(ActionEvent e)
5280 viewport.setShowGroupConservation(showGroupConservation.getState());
5281 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5288 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5289 * .event.ActionEvent)
5292 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5294 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5295 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5302 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5303 * .event.ActionEvent)
5306 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5308 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5309 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5313 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5315 showSequenceLogo.setState(true);
5316 viewport.setShowSequenceLogo(true);
5317 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5318 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5322 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5324 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5331 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5332 * .event.ActionEvent)
5335 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5337 if (avc.makeGroupsFromSelection())
5339 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5340 alignPanel.updateAnnotation();
5341 alignPanel.paintAlignment(true);
5345 public void clearAlignmentSeqRep()
5347 // TODO refactor alignmentseqrep to controller
5348 if (viewport.getAlignment().hasSeqrep())
5350 viewport.getAlignment().setSeqrep(null);
5351 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5352 alignPanel.updateAnnotation();
5353 alignPanel.paintAlignment(true);
5358 protected void createGroup_actionPerformed(ActionEvent e)
5360 if (avc.createGroup())
5362 alignPanel.alignmentChanged();
5367 protected void unGroup_actionPerformed(ActionEvent e)
5371 alignPanel.alignmentChanged();
5376 * make the given alignmentPanel the currently selected tab
5378 * @param alignmentPanel
5380 public void setDisplayedView(AlignmentPanel alignmentPanel)
5382 if (!viewport.getSequenceSetId().equals(
5383 alignmentPanel.av.getSequenceSetId()))
5387 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5389 if (tabbedPane != null
5390 && tabbedPane.getTabCount() > 0
5391 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5392 .getSelectedIndex())
5394 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5399 * Action on selection of menu options to Show or Hide annotations.
5402 * @param forSequences
5403 * update sequence-related annotations
5404 * @param forAlignment
5405 * update non-sequence-related annotations
5408 protected void setAnnotationsVisibility(boolean visible,
5409 boolean forSequences, boolean forAlignment)
5411 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5412 .getAlignmentAnnotation();
5417 for (AlignmentAnnotation aa : anns)
5420 * don't display non-positional annotations on an alignment
5422 if (aa.annotations == null)
5426 boolean apply = (aa.sequenceRef == null && forAlignment)
5427 || (aa.sequenceRef != null && forSequences);
5430 aa.visible = visible;
5433 alignPanel.validateAnnotationDimensions(true);
5434 alignPanel.alignmentChanged();
5438 * Store selected annotation sort order for the view and repaint.
5441 protected void sortAnnotations_actionPerformed()
5443 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5445 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5446 alignPanel.paintAlignment(true);
5451 * @return alignment panels in this alignment frame
5453 public List<? extends AlignmentViewPanel> getAlignPanels()
5455 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5459 * Open a new alignment window, with the cDNA associated with this (protein)
5460 * alignment, aligned as is the protein.
5462 protected void viewAsCdna_actionPerformed()
5464 // TODO no longer a menu action - refactor as required
5465 final AlignmentI alignment = getViewport().getAlignment();
5466 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5467 if (mappings == null)
5471 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5472 for (SequenceI aaSeq : alignment.getSequences())
5474 for (AlignedCodonFrame acf : mappings)
5476 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5480 * There is a cDNA mapping for this protein sequence - add to new
5481 * alignment. It will share the same dataset sequence as other mapped
5482 * cDNA (no new mappings need to be created).
5484 final Sequence newSeq = new Sequence(dnaSeq);
5485 newSeq.setDatasetSequence(dnaSeq);
5486 cdnaSeqs.add(newSeq);
5490 if (cdnaSeqs.size() == 0)
5492 // show a warning dialog no mapped cDNA
5495 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5497 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5498 AlignFrame.DEFAULT_HEIGHT);
5499 cdna.alignAs(alignment);
5500 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5502 Desktop.addInternalFrame(alignFrame, newtitle,
5503 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5507 * Set visibility of dna/protein complement view (available when shown in a
5513 protected void showComplement_actionPerformed(boolean show)
5515 SplitContainerI sf = getSplitViewContainer();
5518 sf.setComplementVisible(this, show);
5523 * Generate the reverse (optionally complemented) of the selected sequences,
5524 * and add them to the alignment
5527 protected void showReverse_actionPerformed(boolean complement)
5529 AlignmentI al = null;
5532 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5533 al = dna.reverseCdna(complement);
5534 viewport.addAlignment(al, "");
5535 addHistoryItem(new EditCommand(
5536 MessageManager.getString("label.add_sequences"),
5537 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5538 viewport.getAlignment()));
5539 } catch (Exception ex)
5541 System.err.println(ex.getMessage());
5547 * Try to run a script in the Groovy console, having first ensured that this
5548 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5549 * be targeted at this alignment.
5552 protected void runGroovy_actionPerformed()
5554 Jalview.setCurrentAlignFrame(this);
5555 groovy.ui.Console console = Desktop.getGroovyConsole();
5556 if (console != null)
5560 console.runScript();
5561 } catch (Exception ex)
5563 System.err.println((ex.toString()));
5565 .showInternalMessageDialog(Desktop.desktop, MessageManager
5566 .getString("label.couldnt_run_groovy_script"),
5568 .getString("label.groovy_support_failed"),
5569 JvOptionPane.ERROR_MESSAGE);
5574 System.err.println("Can't run Groovy script as console not found");
5579 * Hides columns containing (or not containing) a specified feature, provided
5580 * that would not leave all columns hidden
5582 * @param featureType
5583 * @param columnsContaining
5586 public boolean hideFeatureColumns(String featureType,
5587 boolean columnsContaining)
5589 boolean notForHiding = avc.markColumnsContainingFeatures(
5590 columnsContaining, false, false, featureType);
5593 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5594 false, featureType))
5596 getViewport().hideSelectedColumns();
5604 protected void selectHighlightedColumns_actionPerformed(
5605 ActionEvent actionEvent)
5607 // include key modifier check in case user selects from menu
5608 avc.markHighlightedColumns(
5609 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5611 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5615 * Rebuilds the Colour menu, including any user-defined colours which have
5616 * been loaded either on startup or during the session
5618 public void buildColourMenu()
5620 colourMenu.removeAll();
5622 colourMenu.add(applyToAllGroups);
5623 colourMenu.add(textColour);
5624 colourMenu.addSeparator();
5626 ColourMenuHelper.addMenuItems(colourMenu, this,
5627 viewport.getAlignment(), false);
5629 colourMenu.addSeparator();
5630 colourMenu.add(conservationMenuItem);
5631 colourMenu.add(modifyConservation);
5632 colourMenu.add(abovePIDThreshold);
5633 colourMenu.add(modifyPID);
5634 colourMenu.add(annotationColour);
5636 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5637 String schemeName = colourScheme == null ? null : colourScheme
5640 ColourMenuHelper.setColourSelected(colourMenu, schemeName);
5644 class PrintThread extends Thread
5648 public PrintThread(AlignmentPanel ap)
5653 static PageFormat pf;
5658 PrinterJob printJob = PrinterJob.getPrinterJob();
5662 printJob.setPrintable(ap, pf);
5666 printJob.setPrintable(ap);
5669 if (printJob.printDialog())
5674 } catch (Exception PrintException)
5676 PrintException.printStackTrace();