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.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenColumns;
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, HiddenColumns 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, HiddenColumns 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, HiddenColumns 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 HiddenColumns 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)
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), viewport.getAlignment()
1197 .getHiddenColumns());
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(),
1276 .getStartEndPostions(), viewport
1277 .getAlignment().getHiddenColumns()));
1278 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1279 "label.alignment_output_command",
1280 new Object[] { e.getActionCommand() }), 600, 500);
1281 } catch (OutOfMemoryError oom)
1283 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1289 public static AlignmentExportData getAlignmentForExport(
1290 FileFormatI format, AlignViewportI viewport,
1291 AlignExportSettingI exportSettings)
1293 AlignmentI alignmentToExport = null;
1294 AlignExportSettingI settings = exportSettings;
1295 String[] omitHidden = null;
1297 HiddenSequences hiddenSeqs = viewport.getAlignment()
1298 .getHiddenSequences();
1300 alignmentToExport = viewport.getAlignment();
1302 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1303 if (settings == null)
1305 settings = new AlignExportSettings(hasHiddenSeqs,
1306 viewport.hasHiddenColumns(), format);
1308 // settings.isExportAnnotations();
1310 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1312 omitHidden = viewport.getViewAsString(false,
1313 settings.isExportHiddenSequences());
1316 int[] alignmentStartEnd = new int[2];
1317 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1319 alignmentToExport = hiddenSeqs.getFullAlignment();
1323 alignmentToExport = viewport.getAlignment();
1325 alignmentStartEnd = alignmentToExport
1326 .getVisibleStartAndEndIndex(viewport.getAlignment()
1328 .getHiddenRegions());
1329 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1330 omitHidden, alignmentStartEnd, settings);
1341 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1343 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1344 htmlSVG.exportHTML(null);
1348 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1350 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1351 bjs.exportHTML(null);
1354 public void createImageMap(File file, String image)
1356 alignPanel.makePNGImageMap(file, image);
1366 public void createPNG(File f)
1368 alignPanel.makePNG(f);
1378 public void createEPS(File f)
1380 alignPanel.makeEPS(f);
1384 public void createSVG(File f)
1386 alignPanel.makeSVG(f);
1390 public void pageSetup_actionPerformed(ActionEvent e)
1392 PrinterJob printJob = PrinterJob.getPrinterJob();
1393 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1403 public void printMenuItem_actionPerformed(ActionEvent e)
1405 // Putting in a thread avoids Swing painting problems
1406 PrintThread thread = new PrintThread(alignPanel);
1411 public void exportFeatures_actionPerformed(ActionEvent e)
1413 new AnnotationExporter().exportFeatures(alignPanel);
1417 public void exportAnnotations_actionPerformed(ActionEvent e)
1419 new AnnotationExporter().exportAnnotations(alignPanel);
1423 public void associatedData_actionPerformed(ActionEvent e)
1425 // Pick the tree file
1426 JalviewFileChooser chooser = new JalviewFileChooser(
1427 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1428 chooser.setFileView(new JalviewFileView());
1429 chooser.setDialogTitle(MessageManager
1430 .getString("label.load_jalview_annotations"));
1431 chooser.setToolTipText(MessageManager
1432 .getString("label.load_jalview_annotations"));
1434 int value = chooser.showOpenDialog(null);
1436 if (value == JalviewFileChooser.APPROVE_OPTION)
1438 String choice = chooser.getSelectedFile().getPath();
1439 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1440 loadJalviewDataFile(choice, null, null, null);
1446 * Close the current view or all views in the alignment frame. If the frame
1447 * only contains one view then the alignment will be removed from memory.
1449 * @param closeAllTabs
1452 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1454 if (alignPanels != null && alignPanels.size() < 2)
1456 closeAllTabs = true;
1461 if (alignPanels != null)
1465 if (this.isClosed())
1467 // really close all the windows - otherwise wait till
1468 // setClosed(true) is called
1469 for (int i = 0; i < alignPanels.size(); i++)
1471 AlignmentPanel ap = alignPanels.get(i);
1478 closeView(alignPanel);
1485 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1486 * be called recursively, with the frame now in 'closed' state
1488 this.setClosed(true);
1490 } catch (Exception ex)
1492 ex.printStackTrace();
1497 * Close the specified panel and close up tabs appropriately.
1499 * @param panelToClose
1501 public void closeView(AlignmentPanel panelToClose)
1503 int index = tabbedPane.getSelectedIndex();
1504 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1505 alignPanels.remove(panelToClose);
1506 panelToClose.closePanel();
1507 panelToClose = null;
1509 tabbedPane.removeTabAt(closedindex);
1510 tabbedPane.validate();
1512 if (index > closedindex || index == tabbedPane.getTabCount())
1514 // modify currently selected tab index if necessary.
1518 this.tabSelectionChanged(index);
1524 void updateEditMenuBar()
1527 if (viewport.getHistoryList().size() > 0)
1529 undoMenuItem.setEnabled(true);
1530 CommandI command = viewport.getHistoryList().peek();
1531 undoMenuItem.setText(MessageManager.formatMessage(
1532 "label.undo_command",
1533 new Object[] { command.getDescription() }));
1537 undoMenuItem.setEnabled(false);
1538 undoMenuItem.setText(MessageManager.getString("action.undo"));
1541 if (viewport.getRedoList().size() > 0)
1543 redoMenuItem.setEnabled(true);
1545 CommandI command = viewport.getRedoList().peek();
1546 redoMenuItem.setText(MessageManager.formatMessage(
1547 "label.redo_command",
1548 new Object[] { command.getDescription() }));
1552 redoMenuItem.setEnabled(false);
1553 redoMenuItem.setText(MessageManager.getString("action.redo"));
1558 public void addHistoryItem(CommandI command)
1560 if (command.getSize() > 0)
1562 viewport.addToHistoryList(command);
1563 viewport.clearRedoList();
1564 updateEditMenuBar();
1565 viewport.updateHiddenColumns();
1566 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1567 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1568 // viewport.getColumnSelection()
1569 // .getHiddenColumns().size() > 0);
1575 * @return alignment objects for all views
1577 AlignmentI[] getViewAlignments()
1579 if (alignPanels != null)
1581 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1583 for (AlignmentPanel ap : alignPanels)
1585 als[i++] = ap.av.getAlignment();
1589 if (viewport != null)
1591 return new AlignmentI[] { viewport.getAlignment() };
1603 protected void undoMenuItem_actionPerformed(ActionEvent e)
1605 if (viewport.getHistoryList().isEmpty())
1609 CommandI command = viewport.getHistoryList().pop();
1610 viewport.addToRedoList(command);
1611 command.undoCommand(getViewAlignments());
1613 AlignmentViewport originalSource = getOriginatingSource(command);
1614 updateEditMenuBar();
1616 if (originalSource != null)
1618 if (originalSource != viewport)
1621 .warn("Implementation worry: mismatch of viewport origin for undo");
1623 originalSource.updateHiddenColumns();
1624 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1626 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1627 // viewport.getColumnSelection()
1628 // .getHiddenColumns().size() > 0);
1629 originalSource.firePropertyChange("alignment", null, originalSource
1630 .getAlignment().getSequences());
1641 protected void redoMenuItem_actionPerformed(ActionEvent e)
1643 if (viewport.getRedoList().size() < 1)
1648 CommandI command = viewport.getRedoList().pop();
1649 viewport.addToHistoryList(command);
1650 command.doCommand(getViewAlignments());
1652 AlignmentViewport originalSource = getOriginatingSource(command);
1653 updateEditMenuBar();
1655 if (originalSource != null)
1658 if (originalSource != viewport)
1661 .warn("Implementation worry: mismatch of viewport origin for redo");
1663 originalSource.updateHiddenColumns();
1664 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1666 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1667 // viewport.getColumnSelection()
1668 // .getHiddenColumns().size() > 0);
1669 originalSource.firePropertyChange("alignment", null, originalSource
1670 .getAlignment().getSequences());
1674 AlignmentViewport getOriginatingSource(CommandI command)
1676 AlignmentViewport originalSource = null;
1677 // For sequence removal and addition, we need to fire
1678 // the property change event FROM the viewport where the
1679 // original alignment was altered
1680 AlignmentI al = null;
1681 if (command instanceof EditCommand)
1683 EditCommand editCommand = (EditCommand) command;
1684 al = editCommand.getAlignment();
1685 List<Component> comps = PaintRefresher.components.get(viewport
1686 .getSequenceSetId());
1688 for (Component comp : comps)
1690 if (comp instanceof AlignmentPanel)
1692 if (al == ((AlignmentPanel) comp).av.getAlignment())
1694 originalSource = ((AlignmentPanel) comp).av;
1701 if (originalSource == null)
1703 // The original view is closed, we must validate
1704 // the current view against the closed view first
1707 PaintRefresher.validateSequences(al, viewport.getAlignment());
1710 originalSource = viewport;
1713 return originalSource;
1722 public void moveSelectedSequences(boolean up)
1724 SequenceGroup sg = viewport.getSelectionGroup();
1730 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1731 viewport.getHiddenRepSequences(), up);
1732 alignPanel.paintAlignment(true);
1735 synchronized void slideSequences(boolean right, int size)
1737 List<SequenceI> sg = new ArrayList<SequenceI>();
1738 if (viewport.cursorMode)
1740 sg.add(viewport.getAlignment().getSequenceAt(
1741 alignPanel.getSeqPanel().seqCanvas.cursorY));
1743 else if (viewport.getSelectionGroup() != null
1744 && viewport.getSelectionGroup().getSize() != viewport
1745 .getAlignment().getHeight())
1747 sg = viewport.getSelectionGroup().getSequences(
1748 viewport.getHiddenRepSequences());
1756 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1758 for (SequenceI seq : viewport.getAlignment().getSequences())
1760 if (!sg.contains(seq))
1762 invertGroup.add(seq);
1766 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1768 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1769 for (int i = 0; i < invertGroup.size(); i++)
1771 seqs2[i] = invertGroup.get(i);
1774 SlideSequencesCommand ssc;
1777 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1778 size, viewport.getGapCharacter());
1782 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1783 size, viewport.getGapCharacter());
1786 int groupAdjustment = 0;
1787 if (ssc.getGapsInsertedBegin() && right)
1789 if (viewport.cursorMode)
1791 alignPanel.getSeqPanel().moveCursor(size, 0);
1795 groupAdjustment = size;
1798 else if (!ssc.getGapsInsertedBegin() && !right)
1800 if (viewport.cursorMode)
1802 alignPanel.getSeqPanel().moveCursor(-size, 0);
1806 groupAdjustment = -size;
1810 if (groupAdjustment != 0)
1812 viewport.getSelectionGroup().setStartRes(
1813 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1814 viewport.getSelectionGroup().setEndRes(
1815 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1819 * just extend the last slide command if compatible; but not if in
1820 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1822 boolean appendHistoryItem = false;
1823 Deque<CommandI> historyList = viewport.getHistoryList();
1824 boolean inSplitFrame = getSplitViewContainer() != null;
1825 if (!inSplitFrame && historyList != null && historyList.size() > 0
1826 && historyList.peek() instanceof SlideSequencesCommand)
1828 appendHistoryItem = ssc
1829 .appendSlideCommand((SlideSequencesCommand) historyList
1833 if (!appendHistoryItem)
1835 addHistoryItem(ssc);
1848 protected void copy_actionPerformed(ActionEvent e)
1851 if (viewport.getSelectionGroup() == null)
1855 // TODO: preserve the ordering of displayed alignment annotation in any
1856 // internal paste (particularly sequence associated annotation)
1857 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1858 String[] omitHidden = null;
1860 if (viewport.hasHiddenColumns())
1862 omitHidden = viewport.getViewAsString(true);
1865 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1866 seqs, omitHidden, null);
1868 StringSelection ss = new StringSelection(output);
1872 jalview.gui.Desktop.internalCopy = true;
1873 // Its really worth setting the clipboard contents
1874 // to empty before setting the large StringSelection!!
1875 Toolkit.getDefaultToolkit().getSystemClipboard()
1876 .setContents(new StringSelection(""), null);
1878 Toolkit.getDefaultToolkit().getSystemClipboard()
1879 .setContents(ss, Desktop.instance);
1880 } catch (OutOfMemoryError er)
1882 new OOMWarning("copying region", er);
1886 ArrayList<int[]> hiddenColumns = null;
1887 if (viewport.hasHiddenColumns())
1889 hiddenColumns = new ArrayList<int[]>();
1890 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1891 .getSelectionGroup().getEndRes();
1892 for (int[] region : viewport.getAlignment().getHiddenColumns()
1893 .getHiddenRegions())
1895 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1897 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1898 region[1] - hiddenOffset });
1903 Desktop.jalviewClipboard = new Object[] { seqs,
1904 viewport.getAlignment().getDataset(), hiddenColumns };
1905 statusBar.setText(MessageManager.formatMessage(
1906 "label.copied_sequences_to_clipboard", new Object[] { Integer
1907 .valueOf(seqs.length).toString() }));
1917 protected void pasteNew_actionPerformed(ActionEvent e)
1929 protected void pasteThis_actionPerformed(ActionEvent e)
1935 * Paste contents of Jalview clipboard
1937 * @param newAlignment
1938 * true to paste to a new alignment, otherwise add to this.
1940 void paste(boolean newAlignment)
1942 boolean externalPaste = true;
1945 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1946 Transferable contents = c.getContents(this);
1948 if (contents == null)
1957 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1958 if (str.length() < 1)
1963 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1965 } catch (OutOfMemoryError er)
1967 new OOMWarning("Out of memory pasting sequences!!", er);
1971 SequenceI[] sequences;
1972 boolean annotationAdded = false;
1973 AlignmentI alignment = null;
1975 if (Desktop.jalviewClipboard != null)
1977 // The clipboard was filled from within Jalview, we must use the
1979 // And dataset from the copied alignment
1980 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1981 // be doubly sure that we create *new* sequence objects.
1982 sequences = new SequenceI[newseq.length];
1983 for (int i = 0; i < newseq.length; i++)
1985 sequences[i] = new Sequence(newseq[i]);
1987 alignment = new Alignment(sequences);
1988 externalPaste = false;
1992 // parse the clipboard as an alignment.
1993 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1995 sequences = alignment.getSequencesArray();
1999 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2005 if (Desktop.jalviewClipboard != null)
2007 // dataset is inherited
2008 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2012 // new dataset is constructed
2013 alignment.setDataset(null);
2015 alwidth = alignment.getWidth() + 1;
2019 AlignmentI pastedal = alignment; // preserve pasted alignment object
2020 // Add pasted sequences and dataset into existing alignment.
2021 alignment = viewport.getAlignment();
2022 alwidth = alignment.getWidth() + 1;
2023 // decide if we need to import sequences from an existing dataset
2024 boolean importDs = Desktop.jalviewClipboard != null
2025 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2026 // importDs==true instructs us to copy over new dataset sequences from
2027 // an existing alignment
2028 Vector newDs = (importDs) ? new Vector() : null; // used to create
2029 // minimum dataset set
2031 for (int i = 0; i < sequences.length; i++)
2035 newDs.addElement(null);
2037 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2039 if (importDs && ds != null)
2041 if (!newDs.contains(ds))
2043 newDs.setElementAt(ds, i);
2044 ds = new Sequence(ds);
2045 // update with new dataset sequence
2046 sequences[i].setDatasetSequence(ds);
2050 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2055 // copy and derive new dataset sequence
2056 sequences[i] = sequences[i].deriveSequence();
2057 alignment.getDataset().addSequence(
2058 sequences[i].getDatasetSequence());
2059 // TODO: avoid creation of duplicate dataset sequences with a
2060 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2062 alignment.addSequence(sequences[i]); // merges dataset
2066 newDs.clear(); // tidy up
2068 if (alignment.getAlignmentAnnotation() != null)
2070 for (AlignmentAnnotation alan : alignment
2071 .getAlignmentAnnotation())
2073 if (alan.graphGroup > fgroup)
2075 fgroup = alan.graphGroup;
2079 if (pastedal.getAlignmentAnnotation() != null)
2081 // Add any annotation attached to alignment.
2082 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2083 for (int i = 0; i < alann.length; i++)
2085 annotationAdded = true;
2086 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2088 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2089 if (newann.graphGroup > -1)
2091 if (newGraphGroups.size() <= newann.graphGroup
2092 || newGraphGroups.get(newann.graphGroup) == null)
2094 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2096 newGraphGroups.add(q, null);
2098 newGraphGroups.set(newann.graphGroup, new Integer(
2101 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2105 newann.padAnnotation(alwidth);
2106 alignment.addAnnotation(newann);
2116 addHistoryItem(new EditCommand(
2117 MessageManager.getString("label.add_sequences"),
2118 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2120 // Add any annotations attached to sequences
2121 for (int i = 0; i < sequences.length; i++)
2123 if (sequences[i].getAnnotation() != null)
2125 AlignmentAnnotation newann;
2126 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2128 annotationAdded = true;
2129 newann = sequences[i].getAnnotation()[a];
2130 newann.adjustForAlignment();
2131 newann.padAnnotation(alwidth);
2132 if (newann.graphGroup > -1)
2134 if (newann.graphGroup > -1)
2136 if (newGraphGroups.size() <= newann.graphGroup
2137 || newGraphGroups.get(newann.graphGroup) == null)
2139 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2141 newGraphGroups.add(q, null);
2143 newGraphGroups.set(newann.graphGroup, new Integer(
2146 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2150 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2155 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2162 // propagate alignment changed.
2163 vpRanges.setEndSeq(alignment.getHeight());
2164 if (annotationAdded)
2166 // Duplicate sequence annotation in all views.
2167 AlignmentI[] alview = this.getViewAlignments();
2168 for (int i = 0; i < sequences.length; i++)
2170 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2175 for (int avnum = 0; avnum < alview.length; avnum++)
2177 if (alview[avnum] != alignment)
2179 // duplicate in a view other than the one with input focus
2180 int avwidth = alview[avnum].getWidth() + 1;
2181 // this relies on sann being preserved after we
2182 // modify the sequence's annotation array for each duplication
2183 for (int a = 0; a < sann.length; a++)
2185 AlignmentAnnotation newann = new AlignmentAnnotation(
2187 sequences[i].addAlignmentAnnotation(newann);
2188 newann.padAnnotation(avwidth);
2189 alview[avnum].addAnnotation(newann); // annotation was
2190 // duplicated earlier
2191 // TODO JAL-1145 graphGroups are not updated for sequence
2192 // annotation added to several views. This may cause
2194 alview[avnum].setAnnotationIndex(newann, a);
2199 buildSortByAnnotationScoresMenu();
2201 viewport.firePropertyChange("alignment", null,
2202 alignment.getSequences());
2203 if (alignPanels != null)
2205 for (AlignmentPanel ap : alignPanels)
2207 ap.validateAnnotationDimensions(false);
2212 alignPanel.validateAnnotationDimensions(false);
2218 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2220 String newtitle = new String("Copied sequences");
2222 if (Desktop.jalviewClipboard != null
2223 && Desktop.jalviewClipboard[2] != null)
2225 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2226 for (int[] region : hc)
2228 af.viewport.hideColumns(region[0], region[1]);
2232 // >>>This is a fix for the moment, until a better solution is
2234 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2236 alignPanel.getSeqPanel().seqCanvas
2237 .getFeatureRenderer());
2239 // TODO: maintain provenance of an alignment, rather than just make the
2240 // title a concatenation of operations.
2243 if (title.startsWith("Copied sequences"))
2249 newtitle = newtitle.concat("- from " + title);
2254 newtitle = new String("Pasted sequences");
2257 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2262 } catch (Exception ex)
2264 ex.printStackTrace();
2265 System.out.println("Exception whilst pasting: " + ex);
2266 // could be anything being pasted in here
2272 protected void expand_newalign(ActionEvent e)
2276 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2277 .getAlignment(), -1);
2278 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2280 String newtitle = new String("Flanking alignment");
2282 if (Desktop.jalviewClipboard != null
2283 && Desktop.jalviewClipboard[2] != null)
2285 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2286 for (int region[] : hc)
2288 af.viewport.hideColumns(region[0], region[1]);
2292 // >>>This is a fix for the moment, until a better solution is
2294 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2296 alignPanel.getSeqPanel().seqCanvas
2297 .getFeatureRenderer());
2299 // TODO: maintain provenance of an alignment, rather than just make the
2300 // title a concatenation of operations.
2302 if (title.startsWith("Copied sequences"))
2308 newtitle = newtitle.concat("- from " + title);
2312 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2314 } catch (Exception ex)
2316 ex.printStackTrace();
2317 System.out.println("Exception whilst pasting: " + ex);
2318 // could be anything being pasted in here
2319 } catch (OutOfMemoryError oom)
2321 new OOMWarning("Viewing flanking region of alignment", oom);
2332 protected void cut_actionPerformed(ActionEvent e)
2334 copy_actionPerformed(null);
2335 delete_actionPerformed(null);
2345 protected void delete_actionPerformed(ActionEvent evt)
2348 SequenceGroup sg = viewport.getSelectionGroup();
2355 * If the cut affects all sequences, warn, remove highlighted columns
2357 if (sg.getSize() == viewport.getAlignment().getHeight())
2359 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2360 .getAlignment().getWidth()) ? true : false;
2361 if (isEntireAlignWidth)
2363 int confirm = JvOptionPane.showConfirmDialog(this,
2364 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2365 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2366 JvOptionPane.OK_CANCEL_OPTION);
2368 if (confirm == JvOptionPane.CANCEL_OPTION
2369 || confirm == JvOptionPane.CLOSED_OPTION)
2374 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2375 sg.getEndRes() + 1);
2377 SequenceI[] cut = sg.getSequences()
2378 .toArray(new SequenceI[sg.getSize()]);
2380 addHistoryItem(new EditCommand(
2381 MessageManager.getString("label.cut_sequences"), Action.CUT,
2382 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2383 viewport.getAlignment()));
2385 viewport.setSelectionGroup(null);
2386 viewport.sendSelection();
2387 viewport.getAlignment().deleteGroup(sg);
2389 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2391 if (viewport.getAlignment().getHeight() < 1)
2395 this.setClosed(true);
2396 } catch (Exception ex)
2409 protected void deleteGroups_actionPerformed(ActionEvent e)
2411 if (avc.deleteGroups())
2413 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2414 alignPanel.updateAnnotation();
2415 alignPanel.paintAlignment(true);
2426 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2428 SequenceGroup sg = new SequenceGroup();
2430 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2432 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2435 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2436 viewport.setSelectionGroup(sg);
2437 viewport.sendSelection();
2438 // JAL-2034 - should delegate to
2439 // alignPanel to decide if overview needs
2441 alignPanel.paintAlignment(false);
2442 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2452 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2454 if (viewport.cursorMode)
2456 alignPanel.getSeqPanel().keyboardNo1 = null;
2457 alignPanel.getSeqPanel().keyboardNo2 = null;
2459 viewport.setSelectionGroup(null);
2460 viewport.getColumnSelection().clear();
2461 viewport.setSelectionGroup(null);
2462 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2463 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2464 // JAL-2034 - should delegate to
2465 // alignPanel to decide if overview needs
2467 alignPanel.paintAlignment(false);
2468 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2469 viewport.sendSelection();
2479 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2481 SequenceGroup sg = viewport.getSelectionGroup();
2485 selectAllSequenceMenuItem_actionPerformed(null);
2490 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2492 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2494 // JAL-2034 - should delegate to
2495 // alignPanel to decide if overview needs
2498 alignPanel.paintAlignment(true);
2499 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2500 viewport.sendSelection();
2504 public void invertColSel_actionPerformed(ActionEvent e)
2506 viewport.invertColumnSelection();
2507 alignPanel.paintAlignment(true);
2508 viewport.sendSelection();
2518 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2520 trimAlignment(true);
2530 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2532 trimAlignment(false);
2535 void trimAlignment(boolean trimLeft)
2537 ColumnSelection colSel = viewport.getColumnSelection();
2540 if (!colSel.isEmpty())
2544 column = colSel.getMin();
2548 column = colSel.getMax();
2552 if (viewport.getSelectionGroup() != null)
2554 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2555 viewport.getHiddenRepSequences());
2559 seqs = viewport.getAlignment().getSequencesArray();
2562 TrimRegionCommand trimRegion;
2565 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2566 column, viewport.getAlignment());
2567 vpRanges.setStartRes(0);
2571 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2572 column, viewport.getAlignment());
2575 statusBar.setText(MessageManager.formatMessage(
2576 "label.removed_columns",
2577 new String[] { Integer.valueOf(trimRegion.getSize())
2580 addHistoryItem(trimRegion);
2582 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2584 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2585 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2587 viewport.getAlignment().deleteGroup(sg);
2591 viewport.firePropertyChange("alignment", null, viewport
2592 .getAlignment().getSequences());
2603 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2605 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2608 if (viewport.getSelectionGroup() != null)
2610 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2611 viewport.getHiddenRepSequences());
2612 start = viewport.getSelectionGroup().getStartRes();
2613 end = viewport.getSelectionGroup().getEndRes();
2617 seqs = viewport.getAlignment().getSequencesArray();
2620 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2621 "Remove Gapped Columns", seqs, start, end,
2622 viewport.getAlignment());
2624 addHistoryItem(removeGapCols);
2626 statusBar.setText(MessageManager.formatMessage(
2627 "label.removed_empty_columns",
2628 new Object[] { Integer.valueOf(removeGapCols.getSize())
2631 // This is to maintain viewport position on first residue
2632 // of first sequence
2633 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2634 int startRes = seq.findPosition(vpRanges.getStartRes());
2635 // ShiftList shifts;
2636 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2637 // edit.alColumnChanges=shifts.getInverse();
2638 // if (viewport.hasHiddenColumns)
2639 // viewport.getColumnSelection().compensateForEdits(shifts);
2640 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2641 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2653 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2655 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2658 if (viewport.getSelectionGroup() != null)
2660 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2661 viewport.getHiddenRepSequences());
2662 start = viewport.getSelectionGroup().getStartRes();
2663 end = viewport.getSelectionGroup().getEndRes();
2667 seqs = viewport.getAlignment().getSequencesArray();
2670 // This is to maintain viewport position on first residue
2671 // of first sequence
2672 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2673 int startRes = seq.findPosition(vpRanges.getStartRes());
2675 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2676 viewport.getAlignment()));
2678 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2680 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2692 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2694 viewport.setPadGaps(padGapsMenuitem.isSelected());
2695 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2706 public void findMenuItem_actionPerformed(ActionEvent e)
2712 * Create a new view of the current alignment.
2715 public void newView_actionPerformed(ActionEvent e)
2717 newView(null, true);
2721 * Creates and shows a new view of the current alignment.
2724 * title of newly created view; if null, one will be generated
2725 * @param copyAnnotation
2726 * if true then duplicate all annnotation, groups and settings
2727 * @return new alignment panel, already displayed.
2729 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2732 * Create a new AlignmentPanel (with its own, new Viewport)
2734 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2736 if (!copyAnnotation)
2739 * remove all groups and annotation except for the automatic stuff
2741 newap.av.getAlignment().deleteAllGroups();
2742 newap.av.getAlignment().deleteAllAnnotations(false);
2745 newap.av.setGatherViewsHere(false);
2747 if (viewport.viewName == null)
2749 viewport.viewName = MessageManager
2750 .getString("label.view_name_original");
2754 * Views share the same edits undo and redo stacks
2756 newap.av.setHistoryList(viewport.getHistoryList());
2757 newap.av.setRedoList(viewport.getRedoList());
2760 * Views share the same mappings; need to deregister any new mappings
2761 * created by copyAlignPanel, and register the new reference to the shared
2764 newap.av.replaceMappings(viewport.getAlignment());
2767 * start up cDNA consensus (if applicable) now mappings are in place
2769 if (newap.av.initComplementConsensus())
2771 newap.refresh(true); // adjust layout of annotations
2774 newap.av.viewName = getNewViewName(viewTitle);
2776 addAlignmentPanel(newap, true);
2777 newap.alignmentChanged();
2779 if (alignPanels.size() == 2)
2781 viewport.setGatherViewsHere(true);
2783 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2788 * Make a new name for the view, ensuring it is unique within the current
2789 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2790 * these now use viewId. Unique view names are still desirable for usability.)
2795 protected String getNewViewName(String viewTitle)
2797 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2798 boolean addFirstIndex = false;
2799 if (viewTitle == null || viewTitle.trim().length() == 0)
2801 viewTitle = MessageManager.getString("action.view");
2802 addFirstIndex = true;
2806 index = 1;// we count from 1 if given a specific name
2808 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2810 List<Component> comps = PaintRefresher.components.get(viewport
2811 .getSequenceSetId());
2813 List<String> existingNames = getExistingViewNames(comps);
2815 while (existingNames.contains(newViewName))
2817 newViewName = viewTitle + " " + (++index);
2823 * Returns a list of distinct view names found in the given list of
2824 * components. View names are held on the viewport of an AlignmentPanel.
2829 protected List<String> getExistingViewNames(List<Component> comps)
2831 List<String> existingNames = new ArrayList<String>();
2832 for (Component comp : comps)
2834 if (comp instanceof AlignmentPanel)
2836 AlignmentPanel ap = (AlignmentPanel) comp;
2837 if (!existingNames.contains(ap.av.viewName))
2839 existingNames.add(ap.av.viewName);
2843 return existingNames;
2847 * Explode tabbed views into separate windows.
2850 public void expandViews_actionPerformed(ActionEvent e)
2852 Desktop.explodeViews(this);
2856 * Gather views in separate windows back into a tabbed presentation.
2859 public void gatherViews_actionPerformed(ActionEvent e)
2861 Desktop.instance.gatherViews(this);
2871 public void font_actionPerformed(ActionEvent e)
2873 new FontChooser(alignPanel);
2883 protected void seqLimit_actionPerformed(ActionEvent e)
2885 viewport.setShowJVSuffix(seqLimits.isSelected());
2887 alignPanel.getIdPanel().getIdCanvas()
2888 .setPreferredSize(alignPanel.calculateIdWidth());
2889 alignPanel.paintAlignment(true);
2893 public void idRightAlign_actionPerformed(ActionEvent e)
2895 viewport.setRightAlignIds(idRightAlign.isSelected());
2896 alignPanel.paintAlignment(true);
2900 public void centreColumnLabels_actionPerformed(ActionEvent e)
2902 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2903 alignPanel.paintAlignment(true);
2909 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2912 protected void followHighlight_actionPerformed()
2915 * Set the 'follow' flag on the Viewport (and scroll to position if now
2918 final boolean state = this.followHighlightMenuItem.getState();
2919 viewport.setFollowHighlight(state);
2922 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2933 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2935 viewport.setColourText(colourTextMenuItem.isSelected());
2936 alignPanel.paintAlignment(true);
2946 public void wrapMenuItem_actionPerformed(ActionEvent e)
2948 scaleAbove.setVisible(wrapMenuItem.isSelected());
2949 scaleLeft.setVisible(wrapMenuItem.isSelected());
2950 scaleRight.setVisible(wrapMenuItem.isSelected());
2951 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2952 alignPanel.updateLayout();
2956 public void showAllSeqs_actionPerformed(ActionEvent e)
2958 viewport.showAllHiddenSeqs();
2962 public void showAllColumns_actionPerformed(ActionEvent e)
2964 viewport.showAllHiddenColumns();
2966 viewport.sendSelection();
2970 public void hideSelSequences_actionPerformed(ActionEvent e)
2972 viewport.hideAllSelectedSeqs();
2973 // alignPanel.paintAlignment(true);
2977 * called by key handler and the hide all/show all menu items
2982 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2985 boolean hide = false;
2986 SequenceGroup sg = viewport.getSelectionGroup();
2987 if (!toggleSeqs && !toggleCols)
2989 // Hide everything by the current selection - this is a hack - we do the
2990 // invert and then hide
2991 // first check that there will be visible columns after the invert.
2992 if (viewport.hasSelectedColumns()
2993 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2996 // now invert the sequence set, if required - empty selection implies
2997 // that no hiding is required.
3000 invertSequenceMenuItem_actionPerformed(null);
3001 sg = viewport.getSelectionGroup();
3005 viewport.expandColSelection(sg, true);
3006 // finally invert the column selection and get the new sequence
3008 invertColSel_actionPerformed(null);
3015 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3017 hideSelSequences_actionPerformed(null);
3020 else if (!(toggleCols && viewport.hasSelectedColumns()))
3022 showAllSeqs_actionPerformed(null);
3028 if (viewport.hasSelectedColumns())
3030 hideSelColumns_actionPerformed(null);
3033 viewport.setSelectionGroup(sg);
3038 showAllColumns_actionPerformed(null);
3047 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3048 * event.ActionEvent)
3051 public void hideAllButSelection_actionPerformed(ActionEvent e)
3053 toggleHiddenRegions(false, false);
3054 viewport.sendSelection();
3061 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3065 public void hideAllSelection_actionPerformed(ActionEvent e)
3067 SequenceGroup sg = viewport.getSelectionGroup();
3068 viewport.expandColSelection(sg, false);
3069 viewport.hideAllSelectedSeqs();
3070 viewport.hideSelectedColumns();
3071 alignPanel.paintAlignment(true);
3072 viewport.sendSelection();
3079 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3083 public void showAllhidden_actionPerformed(ActionEvent e)
3085 viewport.showAllHiddenColumns();
3086 viewport.showAllHiddenSeqs();
3087 alignPanel.paintAlignment(true);
3088 viewport.sendSelection();
3092 public void hideSelColumns_actionPerformed(ActionEvent e)
3094 viewport.hideSelectedColumns();
3095 alignPanel.paintAlignment(true);
3096 viewport.sendSelection();
3100 public void hiddenMarkers_actionPerformed(ActionEvent e)
3102 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3113 protected void scaleAbove_actionPerformed(ActionEvent e)
3115 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3116 alignPanel.paintAlignment(true);
3126 protected void scaleLeft_actionPerformed(ActionEvent e)
3128 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3129 alignPanel.paintAlignment(true);
3139 protected void scaleRight_actionPerformed(ActionEvent e)
3141 viewport.setScaleRightWrapped(scaleRight.isSelected());
3142 alignPanel.paintAlignment(true);
3152 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3154 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3155 alignPanel.paintAlignment(true);
3165 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3167 viewport.setShowText(viewTextMenuItem.isSelected());
3168 alignPanel.paintAlignment(true);
3178 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3180 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3181 alignPanel.paintAlignment(true);
3184 public FeatureSettings featureSettings;
3187 public FeatureSettingsControllerI getFeatureSettingsUI()
3189 return featureSettings;
3193 public void featureSettings_actionPerformed(ActionEvent e)
3195 if (featureSettings != null)
3197 featureSettings.close();
3198 featureSettings = null;
3200 if (!showSeqFeatures.isSelected())
3202 // make sure features are actually displayed
3203 showSeqFeatures.setSelected(true);
3204 showSeqFeatures_actionPerformed(null);
3206 featureSettings = new FeatureSettings(this);
3210 * Set or clear 'Show Sequence Features'
3216 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3218 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3219 alignPanel.paintAlignment(true);
3220 if (alignPanel.getOverviewPanel() != null)
3222 alignPanel.getOverviewPanel().updateOverviewImage();
3227 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3228 * the annotations panel as a whole.
3230 * The options to show/hide all annotations should be enabled when the panel
3231 * is shown, and disabled when the panel is hidden.
3236 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3238 final boolean setVisible = annotationPanelMenuItem.isSelected();
3239 viewport.setShowAnnotation(setVisible);
3240 this.showAllSeqAnnotations.setEnabled(setVisible);
3241 this.hideAllSeqAnnotations.setEnabled(setVisible);
3242 this.showAllAlAnnotations.setEnabled(setVisible);
3243 this.hideAllAlAnnotations.setEnabled(setVisible);
3244 alignPanel.updateLayout();
3248 public void alignmentProperties()
3250 JEditorPane editPane = new JEditorPane("text/html", "");
3251 editPane.setEditable(false);
3252 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3254 editPane.setText(MessageManager.formatMessage("label.html_content",
3255 new Object[] { contents.toString() }));
3256 JInternalFrame frame = new JInternalFrame();
3257 frame.getContentPane().add(new JScrollPane(editPane));
3259 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3260 "label.alignment_properties", new Object[] { getTitle() }),
3271 public void overviewMenuItem_actionPerformed(ActionEvent e)
3273 if (alignPanel.overviewPanel != null)
3278 JInternalFrame frame = new JInternalFrame();
3279 OverviewPanel overview = new OverviewPanel(alignPanel);
3280 frame.setContentPane(overview);
3281 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3282 "label.overview_params", new Object[] { this.getTitle() }),
3283 frame.getWidth(), frame.getHeight());
3285 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3286 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3289 public void internalFrameClosed(
3290 javax.swing.event.InternalFrameEvent evt)
3292 alignPanel.setOverviewPanel(null);
3296 alignPanel.setOverviewPanel(overview);
3300 public void textColour_actionPerformed()
3302 new TextColourChooser().chooseColour(alignPanel, null);
3306 * public void covariationColour_actionPerformed() {
3308 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3312 public void annotationColour_actionPerformed()
3314 new AnnotationColourChooser(viewport, alignPanel);
3318 public void annotationColumn_actionPerformed(ActionEvent e)
3320 new AnnotationColumnChooser(viewport, alignPanel);
3324 * Action on the user checking or unchecking the option to apply the selected
3325 * colour scheme to all groups. If unchecked, groups may have their own
3326 * independent colour schemes.
3331 public void applyToAllGroups_actionPerformed(boolean selected)
3333 viewport.setColourAppliesToAllGroups(selected);
3337 * Action on user selecting a colour from the colour menu
3340 * the name (not the menu item label!) of the colour scheme
3343 public void changeColour_actionPerformed(String name)
3346 * 'User Defined' opens a panel to configure or load a
3347 * user-defined colour scheme
3349 if (ResidueColourScheme.USER_DEFINED.equals(name))
3351 new UserDefinedColours(alignPanel);
3356 * otherwise set the chosen colour scheme (or null for 'None')
3358 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3359 viewport.getAlignment(), viewport.getHiddenRepSequences());
3364 * Actions on setting or changing the alignment colour scheme
3369 public void changeColour(ColourSchemeI cs)
3371 // TODO: pull up to controller method
3372 ColourMenuHelper.setColourSelected(colourMenu, cs);
3374 viewport.setGlobalColourScheme(cs);
3376 alignPanel.paintAlignment(true);
3380 * Show the PID threshold slider panel
3383 protected void modifyPID_actionPerformed()
3385 SliderPanel.setPIDSliderSource(alignPanel,
3386 viewport.getResidueShading(), alignPanel.getViewName());
3387 SliderPanel.showPIDSlider();
3391 * Show the Conservation slider panel
3394 protected void modifyConservation_actionPerformed()
3396 SliderPanel.setConservationSlider(alignPanel,
3397 viewport.getResidueShading(), alignPanel.getViewName());
3398 SliderPanel.showConservationSlider();
3402 * Action on selecting or deselecting (Colour) By Conservation
3405 public void conservationMenuItem_actionPerformed(boolean selected)
3407 modifyConservation.setEnabled(selected);
3408 viewport.setConservationSelected(selected);
3409 viewport.getResidueShading().setConservationApplied(selected);
3411 changeColour(viewport.getGlobalColourScheme());
3414 modifyConservation_actionPerformed();
3418 SliderPanel.hideConservationSlider();
3423 * Action on selecting or deselecting (Colour) Above PID Threshold
3426 public void abovePIDThreshold_actionPerformed(boolean selected)
3428 modifyPID.setEnabled(selected);
3429 viewport.setAbovePIDThreshold(selected);
3432 viewport.getResidueShading().setThreshold(0,
3433 viewport.isIgnoreGapsConsensus());
3436 changeColour(viewport.getGlobalColourScheme());
3439 modifyPID_actionPerformed();
3443 SliderPanel.hidePIDSlider();
3454 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3456 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3457 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3458 .getAlignment().getSequenceAt(0));
3459 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3460 viewport.getAlignment()));
3461 alignPanel.paintAlignment(true);
3471 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3473 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3474 AlignmentSorter.sortByID(viewport.getAlignment());
3475 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3476 viewport.getAlignment()));
3477 alignPanel.paintAlignment(true);
3487 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3489 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3490 AlignmentSorter.sortByLength(viewport.getAlignment());
3491 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3492 viewport.getAlignment()));
3493 alignPanel.paintAlignment(true);
3503 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3505 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3506 AlignmentSorter.sortByGroup(viewport.getAlignment());
3507 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3508 viewport.getAlignment()));
3510 alignPanel.paintAlignment(true);
3520 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3522 new RedundancyPanel(alignPanel, this);
3532 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3534 if ((viewport.getSelectionGroup() == null)
3535 || (viewport.getSelectionGroup().getSize() < 2))
3537 JvOptionPane.showInternalMessageDialog(this, MessageManager
3538 .getString("label.you_must_select_least_two_sequences"),
3539 MessageManager.getString("label.invalid_selection"),
3540 JvOptionPane.WARNING_MESSAGE);
3544 JInternalFrame frame = new JInternalFrame();
3545 frame.setContentPane(new PairwiseAlignPanel(viewport));
3546 Desktop.addInternalFrame(frame,
3547 MessageManager.getString("action.pairwise_alignment"), 600,
3553 public void autoCalculate_actionPerformed(ActionEvent e)
3555 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3556 if (viewport.autoCalculateConsensus)
3558 viewport.firePropertyChange("alignment", null, viewport
3559 .getAlignment().getSequences());
3564 public void sortByTreeOption_actionPerformed(ActionEvent e)
3566 viewport.sortByTree = sortByTree.isSelected();
3570 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3572 viewport.followSelection = listenToViewSelections.isSelected();
3576 * Constructs a tree panel and adds it to the desktop
3579 * tree type (NJ or AV)
3581 * name of score model used to compute the tree
3583 * parameters for the distance or similarity calculation
3585 void newTreePanel(String type, String modelName, SimilarityParamsI options)
3587 String frameTitle = "";
3590 boolean onSelection = false;
3591 if (viewport.getSelectionGroup() != null
3592 && viewport.getSelectionGroup().getSize() > 0)
3594 SequenceGroup sg = viewport.getSelectionGroup();
3596 /* Decide if the selection is a column region */
3597 for (SequenceI _s : sg.getSequences())
3599 if (_s.getLength() < sg.getEndRes())
3605 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3607 .getString("label.sequences_selection_not_aligned"),
3608 JvOptionPane.WARNING_MESSAGE);
3617 if (viewport.getAlignment().getHeight() < 2)
3623 tp = new TreePanel(alignPanel, type, modelName, options);
3624 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3626 frameTitle += " from ";
3628 if (viewport.viewName != null)
3630 frameTitle += viewport.viewName + " of ";
3633 frameTitle += this.title;
3635 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3646 public void addSortByOrderMenuItem(String title,
3647 final AlignmentOrder order)
3649 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3650 "action.by_title_param", new Object[] { title }));
3652 item.addActionListener(new java.awt.event.ActionListener()
3655 public void actionPerformed(ActionEvent e)
3657 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3659 // TODO: JBPNote - have to map order entries to curent SequenceI
3661 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3663 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3666 alignPanel.paintAlignment(true);
3672 * Add a new sort by annotation score menu item
3675 * the menu to add the option to
3677 * the label used to retrieve scores for each sequence on the
3680 public void addSortByAnnotScoreMenuItem(JMenu sort,
3681 final String scoreLabel)
3683 final JMenuItem item = new JMenuItem(scoreLabel);
3685 item.addActionListener(new java.awt.event.ActionListener()
3688 public void actionPerformed(ActionEvent e)
3690 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3691 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3692 viewport.getAlignment());// ,viewport.getSelectionGroup());
3693 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3694 viewport.getAlignment()));
3695 alignPanel.paintAlignment(true);
3701 * last hash for alignment's annotation array - used to minimise cost of
3704 protected int _annotationScoreVectorHash;
3707 * search the alignment and rebuild the sort by annotation score submenu the
3708 * last alignment annotation vector hash is stored to minimize cost of
3709 * rebuilding in subsequence calls.
3713 public void buildSortByAnnotationScoresMenu()
3715 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3720 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3722 sortByAnnotScore.removeAll();
3723 // almost certainly a quicker way to do this - but we keep it simple
3724 Hashtable scoreSorts = new Hashtable();
3725 AlignmentAnnotation aann[];
3726 for (SequenceI sqa : viewport.getAlignment().getSequences())
3728 aann = sqa.getAnnotation();
3729 for (int i = 0; aann != null && i < aann.length; i++)
3731 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3733 scoreSorts.put(aann[i].label, aann[i].label);
3737 Enumeration labels = scoreSorts.keys();
3738 while (labels.hasMoreElements())
3740 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3741 (String) labels.nextElement());
3743 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3746 _annotationScoreVectorHash = viewport.getAlignment()
3747 .getAlignmentAnnotation().hashCode();
3752 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3753 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3754 * call. Listeners are added to remove the menu item when the treePanel is
3755 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3759 public void buildTreeSortMenu()
3761 sortByTreeMenu.removeAll();
3763 List<Component> comps = PaintRefresher.components.get(viewport
3764 .getSequenceSetId());
3765 List<TreePanel> treePanels = new ArrayList<TreePanel>();
3766 for (Component comp : comps)
3768 if (comp instanceof TreePanel)
3770 treePanels.add((TreePanel) comp);
3774 if (treePanels.size() < 1)
3776 sortByTreeMenu.setVisible(false);
3780 sortByTreeMenu.setVisible(true);
3782 for (final TreePanel tp : treePanels)
3784 final JMenuItem item = new JMenuItem(tp.getTitle());
3785 item.addActionListener(new java.awt.event.ActionListener()
3788 public void actionPerformed(ActionEvent e)
3790 tp.sortByTree_actionPerformed();
3791 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3796 sortByTreeMenu.add(item);
3800 public boolean sortBy(AlignmentOrder alorder, String undoname)
3802 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3803 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3804 if (undoname != null)
3806 addHistoryItem(new OrderCommand(undoname, oldOrder,
3807 viewport.getAlignment()));
3809 alignPanel.paintAlignment(true);
3814 * Work out whether the whole set of sequences or just the selected set will
3815 * be submitted for multiple alignment.
3818 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3820 // Now, check we have enough sequences
3821 AlignmentView msa = null;
3823 if ((viewport.getSelectionGroup() != null)
3824 && (viewport.getSelectionGroup().getSize() > 1))
3826 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3827 // some common interface!
3829 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3830 * SequenceI[sz = seqs.getSize(false)];
3832 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3833 * seqs.getSequenceAt(i); }
3835 msa = viewport.getAlignmentView(true);
3837 else if (viewport.getSelectionGroup() != null
3838 && viewport.getSelectionGroup().getSize() == 1)
3840 int option = JvOptionPane.showConfirmDialog(this,
3841 MessageManager.getString("warn.oneseq_msainput_selection"),
3842 MessageManager.getString("label.invalid_selection"),
3843 JvOptionPane.OK_CANCEL_OPTION);
3844 if (option == JvOptionPane.OK_OPTION)
3846 msa = viewport.getAlignmentView(false);
3851 msa = viewport.getAlignmentView(false);
3857 * Decides what is submitted to a secondary structure prediction service: the
3858 * first sequence in the alignment, or in the current selection, or, if the
3859 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3860 * region or the whole alignment. (where the first sequence in the set is the
3861 * one that the prediction will be for).
3863 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3865 AlignmentView seqs = null;
3867 if ((viewport.getSelectionGroup() != null)
3868 && (viewport.getSelectionGroup().getSize() > 0))
3870 seqs = viewport.getAlignmentView(true);
3874 seqs = viewport.getAlignmentView(false);
3876 // limit sequences - JBPNote in future - could spawn multiple prediction
3878 // TODO: viewport.getAlignment().isAligned is a global state - the local
3879 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3880 if (!viewport.getAlignment().isAligned(false))
3882 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3883 // TODO: if seqs.getSequences().length>1 then should really have warned
3897 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3899 // Pick the tree file
3900 JalviewFileChooser chooser = new JalviewFileChooser(
3901 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3902 chooser.setFileView(new JalviewFileView());
3903 chooser.setDialogTitle(MessageManager
3904 .getString("label.select_newick_like_tree_file"));
3905 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3907 int value = chooser.showOpenDialog(null);
3909 if (value == JalviewFileChooser.APPROVE_OPTION)
3911 String filePath = chooser.getSelectedFile().getPath();
3912 Cache.setProperty("LAST_DIRECTORY", filePath);
3913 NewickFile fin = null;
3916 fin = new NewickFile(filePath, DataSourceType.FILE);
3917 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3918 } catch (Exception ex)
3925 .getString("label.problem_reading_tree_file"),
3926 JvOptionPane.WARNING_MESSAGE);
3927 ex.printStackTrace();
3929 if (fin != null && fin.hasWarningMessage())
3931 JvOptionPane.showMessageDialog(Desktop.desktop, fin
3932 .getWarningMessage(), MessageManager
3933 .getString("label.possible_problem_with_tree_file"),
3934 JvOptionPane.WARNING_MESSAGE);
3939 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3941 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3944 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3945 int h, int x, int y)
3947 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3951 * Add a treeviewer for the tree extracted from a Newick file object to the
3952 * current alignment view
3959 * Associated alignment input data (or null)
3968 * @return TreePanel handle
3970 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3971 AlignmentView input, int w, int h, int x, int y)
3973 TreePanel tp = null;
3979 if (nf.getTree() != null)
3981 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3987 tp.setLocation(x, y);
3990 Desktop.addInternalFrame(tp, treeTitle, w, h);
3992 } catch (Exception ex)
3994 ex.printStackTrace();
4000 private boolean buildingMenu = false;
4003 * Generates menu items and listener event actions for web service clients
4006 public void BuildWebServiceMenu()
4008 while (buildingMenu)
4012 System.err.println("Waiting for building menu to finish.");
4014 } catch (Exception e)
4018 final AlignFrame me = this;
4019 buildingMenu = true;
4020 new Thread(new Runnable()
4025 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4028 // System.err.println("Building ws menu again "
4029 // + Thread.currentThread());
4030 // TODO: add support for context dependent disabling of services based
4032 // alignment and current selection
4033 // TODO: add additional serviceHandle parameter to specify abstract
4035 // class independently of AbstractName
4036 // TODO: add in rediscovery GUI function to restart discoverer
4037 // TODO: group services by location as well as function and/or
4039 // object broker mechanism.
4040 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4041 final IProgressIndicator af = me;
4044 * do not i18n these strings - they are hard-coded in class
4045 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4046 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4048 final JMenu msawsmenu = new JMenu("Alignment");
4049 final JMenu secstrmenu = new JMenu(
4050 "Secondary Structure Prediction");
4051 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4052 final JMenu analymenu = new JMenu("Analysis");
4053 final JMenu dismenu = new JMenu("Protein Disorder");
4054 // JAL-940 - only show secondary structure prediction services from
4055 // the legacy server
4056 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4058 Discoverer.services != null && (Discoverer.services.size() > 0))
4060 // TODO: refactor to allow list of AbstractName/Handler bindings to
4062 // stored or retrieved from elsewhere
4063 // No MSAWS used any more:
4064 // Vector msaws = null; // (Vector)
4065 // Discoverer.services.get("MsaWS");
4066 Vector secstrpr = (Vector) Discoverer.services
4068 if (secstrpr != null)
4070 // Add any secondary structure prediction services
4071 for (int i = 0, j = secstrpr.size(); i < j; i++)
4073 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4075 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4076 .getServiceClient(sh);
4077 int p = secstrmenu.getItemCount();
4078 impl.attachWSMenuEntry(secstrmenu, me);
4079 int q = secstrmenu.getItemCount();
4080 for (int litm = p; litm < q; litm++)
4082 legacyItems.add(secstrmenu.getItem(litm));
4088 // Add all submenus in the order they should appear on the web
4090 wsmenu.add(msawsmenu);
4091 wsmenu.add(secstrmenu);
4092 wsmenu.add(dismenu);
4093 wsmenu.add(analymenu);
4094 // No search services yet
4095 // wsmenu.add(seqsrchmenu);
4097 javax.swing.SwingUtilities.invokeLater(new Runnable()
4104 webService.removeAll();
4105 // first, add discovered services onto the webservices menu
4106 if (wsmenu.size() > 0)
4108 for (int i = 0, j = wsmenu.size(); i < j; i++)
4110 webService.add(wsmenu.get(i));
4115 webService.add(me.webServiceNoServices);
4117 // TODO: move into separate menu builder class.
4118 boolean new_sspred = false;
4119 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4121 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4122 if (jws2servs != null)
4124 if (jws2servs.hasServices())
4126 jws2servs.attachWSMenuEntry(webService, me);
4127 for (Jws2Instance sv : jws2servs.getServices())
4129 if (sv.description.toLowerCase().contains("jpred"))
4131 for (JMenuItem jmi : legacyItems)
4133 jmi.setVisible(false);
4139 if (jws2servs.isRunning())
4141 JMenuItem tm = new JMenuItem(
4142 "Still discovering JABA Services");
4143 tm.setEnabled(false);
4148 build_urlServiceMenu(me.webService);
4149 build_fetchdbmenu(webService);
4150 for (JMenu item : wsmenu)
4152 if (item.getItemCount() == 0)
4154 item.setEnabled(false);
4158 item.setEnabled(true);
4161 } catch (Exception e)
4164 .debug("Exception during web service menu building process.",
4169 } catch (Exception e)
4172 buildingMenu = false;
4179 * construct any groupURL type service menu entries.
4183 private void build_urlServiceMenu(JMenu webService)
4185 // TODO: remove this code when 2.7 is released
4186 // DEBUG - alignmentView
4188 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4189 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4191 * @Override public void actionPerformed(ActionEvent e) {
4192 * jalview.datamodel.AlignmentView
4193 * .testSelectionViews(af.viewport.getAlignment(),
4194 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4196 * }); webService.add(testAlView);
4198 // TODO: refactor to RestClient discoverer and merge menu entries for
4199 // rest-style services with other types of analysis/calculation service
4200 // SHmmr test client - still being implemented.
4201 // DEBUG - alignmentView
4203 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4206 client.attachWSMenuEntry(
4207 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4213 * Searches the alignment sequences for xRefs and builds the Show
4214 * Cross-References menu (formerly called Show Products), with database
4215 * sources for which cross-references are found (protein sources for a
4216 * nucleotide alignment and vice versa)
4218 * @return true if Show Cross-references menu should be enabled
4220 public boolean canShowProducts()
4222 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4223 AlignmentI dataset = viewport.getAlignment().getDataset();
4225 showProducts.removeAll();
4226 final boolean dna = viewport.getAlignment().isNucleotide();
4228 if (seqs == null || seqs.length == 0)
4230 // nothing to see here.
4234 boolean showp = false;
4237 List<String> ptypes = new CrossRef(seqs, dataset)
4238 .findXrefSourcesForSequences(dna);
4240 for (final String source : ptypes)
4243 final AlignFrame af = this;
4244 JMenuItem xtype = new JMenuItem(source);
4245 xtype.addActionListener(new ActionListener()
4248 public void actionPerformed(ActionEvent e)
4250 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4253 showProducts.add(xtype);
4255 showProducts.setVisible(showp);
4256 showProducts.setEnabled(showp);
4257 } catch (Exception e)
4260 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4268 * Finds and displays cross-references for the selected sequences (protein
4269 * products for nucleotide sequences, dna coding sequences for peptides).
4272 * the sequences to show cross-references for
4274 * true if from a nucleotide alignment (so showing proteins)
4276 * the database to show cross-references for
4278 protected void showProductsFor(final SequenceI[] sel,
4279 final boolean _odna, final String source)
4281 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4286 * Construct and display a new frame containing the translation of this
4287 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4290 public void showTranslation_actionPerformed(ActionEvent e)
4292 AlignmentI al = null;
4295 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4297 al = dna.translateCdna();
4298 } catch (Exception ex)
4300 jalview.bin.Cache.log.error(
4301 "Exception during translation. Please report this !", ex);
4302 final String msg = MessageManager
4303 .getString("label.error_when_translating_sequences_submit_bug_report");
4304 final String errorTitle = MessageManager
4305 .getString("label.implementation_error")
4306 + MessageManager.getString("label.translation_failed");
4307 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4308 JvOptionPane.ERROR_MESSAGE);
4311 if (al == null || al.getHeight() == 0)
4313 final String msg = MessageManager
4314 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4315 final String errorTitle = MessageManager
4316 .getString("label.translation_failed");
4317 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4318 JvOptionPane.WARNING_MESSAGE);
4322 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4323 af.setFileFormat(this.currentFileFormat);
4324 final String newTitle = MessageManager.formatMessage(
4325 "label.translation_of_params",
4326 new Object[] { this.getTitle() });
4327 af.setTitle(newTitle);
4328 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4330 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4331 viewport.openSplitFrame(af, new Alignment(seqs));
4335 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4342 * Set the file format
4346 public void setFileFormat(FileFormatI format)
4348 this.currentFileFormat = format;
4352 * Try to load a features file onto the alignment.
4355 * contents or path to retrieve file
4357 * access mode of file (see jalview.io.AlignFile)
4358 * @return true if features file was parsed correctly.
4360 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4362 return avc.parseFeaturesFile(file, sourceType,
4363 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4368 public void refreshFeatureUI(boolean enableIfNecessary)
4370 // note - currently this is only still here rather than in the controller
4371 // because of the featureSettings hard reference that is yet to be
4373 if (enableIfNecessary)
4375 viewport.setShowSequenceFeatures(true);
4376 showSeqFeatures.setSelected(true);
4382 public void dragEnter(DropTargetDragEvent evt)
4387 public void dragExit(DropTargetEvent evt)
4392 public void dragOver(DropTargetDragEvent evt)
4397 public void dropActionChanged(DropTargetDragEvent evt)
4402 public void drop(DropTargetDropEvent evt)
4404 // JAL-1552 - acceptDrop required before getTransferable call for
4405 // Java's Transferable for native dnd
4406 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4407 Transferable t = evt.getTransferable();
4408 List<String> files = new ArrayList<String>();
4409 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4413 Desktop.transferFromDropTarget(files, protocols, evt, t);
4414 } catch (Exception e)
4416 e.printStackTrace();
4422 // check to see if any of these files have names matching sequences in
4424 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4425 .getAlignment().getSequencesArray());
4427 * Object[] { String,SequenceI}
4429 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4430 ArrayList<String> filesnotmatched = new ArrayList<String>();
4431 for (int i = 0; i < files.size(); i++)
4433 String file = files.get(i).toString();
4435 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4436 if (protocol == DataSourceType.FILE)
4438 File fl = new File(file);
4439 pdbfn = fl.getName();
4441 else if (protocol == DataSourceType.URL)
4443 URL url = new URL(file);
4444 pdbfn = url.getFile();
4446 if (pdbfn.length() > 0)
4448 // attempt to find a match in the alignment
4449 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4450 int l = 0, c = pdbfn.indexOf(".");
4451 while (mtch == null && c != -1)
4456 } while ((c = pdbfn.indexOf(".", l)) > l);
4459 pdbfn = pdbfn.substring(0, l);
4461 mtch = idm.findAllIdMatches(pdbfn);
4465 FileFormatI type = null;
4468 type = new IdentifyFile().identify(file, protocol);
4469 } catch (Exception ex)
4473 if (type != null && type.isStructureFile())
4475 filesmatched.add(new Object[] { file, protocol, mtch });
4479 // File wasn't named like one of the sequences or wasn't a PDB file.
4480 filesnotmatched.add(file);
4484 if (filesmatched.size() > 0)
4486 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4492 "label.automatically_associate_structure_files_with_sequences_same_name",
4493 new Object[] { Integer
4499 .getString("label.automatically_associate_structure_files_by_name"),
4500 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4503 for (Object[] fm : filesmatched)
4505 // try and associate
4506 // TODO: may want to set a standard ID naming formalism for
4507 // associating PDB files which have no IDs.
4508 for (SequenceI toassoc : (SequenceI[]) fm[2])
4510 PDBEntry pe = new AssociatePdbFileWithSeq()
4511 .associatePdbWithSeq((String) fm[0],
4512 (DataSourceType) fm[1], toassoc, false,
4516 System.err.println("Associated file : "
4517 + ((String) fm[0]) + " with "
4518 + toassoc.getDisplayId(true));
4522 alignPanel.paintAlignment(true);
4526 if (filesnotmatched.size() > 0)
4529 && (Cache.getDefault(
4530 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4536 "label.ignore_unmatched_dropped_files_info",
4537 new Object[] { Integer
4544 .getString("label.ignore_unmatched_dropped_files"),
4545 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4549 for (String fn : filesnotmatched)
4551 loadJalviewDataFile(fn, null, null, null);
4555 } catch (Exception ex)
4557 ex.printStackTrace();
4563 * Attempt to load a "dropped" file or URL string, by testing in turn for
4565 * <li>an Annotation file</li>
4566 * <li>a JNet file</li>
4567 * <li>a features file</li>
4568 * <li>else try to interpret as an alignment file</li>
4572 * either a filename or a URL string.
4574 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4575 FileFormatI format, SequenceI assocSeq)
4579 if (sourceType == null)
4581 sourceType = FormatAdapter.checkProtocol(file);
4583 // if the file isn't identified, or not positively identified as some
4584 // other filetype (PFAM is default unidentified alignment file type) then
4585 // try to parse as annotation.
4586 boolean isAnnotation = (format == null || FileFormat.Pfam
4587 .equals(format)) ? new AnnotationFile()
4588 .annotateAlignmentView(viewport, file, sourceType) : false;
4592 // first see if its a T-COFFEE score file
4593 TCoffeeScoreFile tcf = null;
4596 tcf = new TCoffeeScoreFile(file, sourceType);
4599 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4602 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4603 isAnnotation = true;
4605 .setText(MessageManager
4606 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4610 // some problem - if no warning its probable that the ID matching
4611 // process didn't work
4615 tcf.getWarningMessage() == null ? MessageManager
4616 .getString("label.check_file_matches_sequence_ids_alignment")
4617 : tcf.getWarningMessage(),
4619 .getString("label.problem_reading_tcoffee_score_file"),
4620 JvOptionPane.WARNING_MESSAGE);
4627 } catch (Exception x)
4630 .debug("Exception when processing data source as T-COFFEE score file",
4636 // try to see if its a JNet 'concise' style annotation file *before*
4638 // try to parse it as a features file
4641 format = new IdentifyFile().identify(file, sourceType);
4643 if (FileFormat.ScoreMatrix == format)
4645 ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4648 // todo: i18n this message
4650 .setText(MessageManager.formatMessage(
4651 "label.successfully_loaded_matrix",
4652 sm.getMatrixName()));
4654 else if (FileFormat.Jnet.equals(format))
4656 JPredFile predictions = new JPredFile(file, sourceType);
4657 new JnetAnnotationMaker();
4658 JnetAnnotationMaker.add_annotation(predictions,
4659 viewport.getAlignment(), 0, false);
4660 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4661 viewport.getAlignment().setSeqrep(repseq);
4662 HiddenColumns cs = new HiddenColumns();
4663 cs.hideInsertionsFor(repseq);
4664 viewport.getAlignment().setHiddenColumns(cs);
4665 isAnnotation = true;
4667 // else if (IdentifyFile.FeaturesFile.equals(format))
4668 else if (FileFormat.Features.equals(format))
4670 if (parseFeaturesFile(file, sourceType))
4672 alignPanel.paintAlignment(true);
4677 new FileLoader().LoadFile(viewport, file, sourceType, format);
4684 alignPanel.adjustAnnotationHeight();
4685 viewport.updateSequenceIdColours();
4686 buildSortByAnnotationScoresMenu();
4687 alignPanel.paintAlignment(true);
4689 } catch (Exception ex)
4691 ex.printStackTrace();
4692 } catch (OutOfMemoryError oom)
4697 } catch (Exception x)
4702 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4703 : "using " + sourceType + " from " + file)
4705 + (format != null ? "(parsing as '" + format
4706 + "' file)" : ""), oom, Desktop.desktop);
4711 * Method invoked by the ChangeListener on the tabbed pane, in other words
4712 * when a different tabbed pane is selected by the user or programmatically.
4715 public void tabSelectionChanged(int index)
4719 alignPanel = alignPanels.get(index);
4720 viewport = alignPanel.av;
4721 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4722 setMenusFromViewport(viewport);
4726 * 'focus' any colour slider that is open to the selected viewport
4728 if (viewport.getConservationSelected())
4730 SliderPanel.setConservationSlider(alignPanel,
4731 viewport.getResidueShading(), alignPanel.getViewName());
4735 SliderPanel.hideConservationSlider();
4737 if (viewport.getAbovePIDThreshold())
4739 SliderPanel.setPIDSliderSource(alignPanel,
4740 viewport.getResidueShading(), alignPanel.getViewName());
4744 SliderPanel.hidePIDSlider();
4748 * If there is a frame linked to this one in a SplitPane, switch it to the
4749 * same view tab index. No infinite recursion of calls should happen, since
4750 * tabSelectionChanged() should not get invoked on setting the selected
4751 * index to an unchanged value. Guard against setting an invalid index
4752 * before the new view peer tab has been created.
4754 final AlignViewportI peer = viewport.getCodingComplement();
4757 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4758 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4760 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4766 * On right mouse click on view tab, prompt for and set new view name.
4769 public void tabbedPane_mousePressed(MouseEvent e)
4771 if (e.isPopupTrigger())
4773 String msg = MessageManager.getString("label.enter_view_name");
4774 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4775 JvOptionPane.QUESTION_MESSAGE);
4779 viewport.viewName = reply;
4780 // TODO warn if reply is in getExistingViewNames()?
4781 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4786 public AlignViewport getCurrentView()
4792 * Open the dialog for regex description parsing.
4795 protected void extractScores_actionPerformed(ActionEvent e)
4797 ParseProperties pp = new jalview.analysis.ParseProperties(
4798 viewport.getAlignment());
4799 // TODO: verify regex and introduce GUI dialog for version 2.5
4800 // if (pp.getScoresFromDescription("col", "score column ",
4801 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4803 if (pp.getScoresFromDescription("description column",
4804 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4806 buildSortByAnnotationScoresMenu();
4814 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4818 protected void showDbRefs_actionPerformed(ActionEvent e)
4820 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4826 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4830 protected void showNpFeats_actionPerformed(ActionEvent e)
4832 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4836 * find the viewport amongst the tabs in this alignment frame and close that
4841 public boolean closeView(AlignViewportI av)
4845 this.closeMenuItem_actionPerformed(false);
4848 Component[] comp = tabbedPane.getComponents();
4849 for (int i = 0; comp != null && i < comp.length; i++)
4851 if (comp[i] instanceof AlignmentPanel)
4853 if (((AlignmentPanel) comp[i]).av == av)
4856 closeView((AlignmentPanel) comp[i]);
4864 protected void build_fetchdbmenu(JMenu webService)
4866 // Temporary hack - DBRef Fetcher always top level ws entry.
4867 // TODO We probably want to store a sequence database checklist in
4868 // preferences and have checkboxes.. rather than individual sources selected
4870 final JMenu rfetch = new JMenu(
4871 MessageManager.getString("action.fetch_db_references"));
4872 rfetch.setToolTipText(MessageManager
4873 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4874 webService.add(rfetch);
4876 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4877 MessageManager.getString("option.trim_retrieved_seqs"));
4878 trimrs.setToolTipText(MessageManager
4879 .getString("label.trim_retrieved_sequences"));
4880 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4881 trimrs.addActionListener(new ActionListener()
4884 public void actionPerformed(ActionEvent e)
4886 trimrs.setSelected(trimrs.isSelected());
4887 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4888 Boolean.valueOf(trimrs.isSelected()).toString());
4892 JMenuItem fetchr = new JMenuItem(
4893 MessageManager.getString("label.standard_databases"));
4894 fetchr.setToolTipText(MessageManager
4895 .getString("label.fetch_embl_uniprot"));
4896 fetchr.addActionListener(new ActionListener()
4900 public void actionPerformed(ActionEvent e)
4902 new Thread(new Runnable()
4907 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4908 .getAlignment().isNucleotide();
4909 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4910 .getSequenceSelection(), alignPanel.alignFrame, null,
4911 alignPanel.alignFrame.featureSettings, isNucleotide);
4912 dbRefFetcher.addListener(new FetchFinishedListenerI()
4915 public void finished()
4917 AlignFrame.this.setMenusForViewport();
4920 dbRefFetcher.fetchDBRefs(false);
4928 final AlignFrame me = this;
4929 new Thread(new Runnable()
4934 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4935 .getSequenceFetcherSingleton(me);
4936 javax.swing.SwingUtilities.invokeLater(new Runnable()
4941 String[] dbclasses = sf.getOrderedSupportedSources();
4942 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4943 // jalview.util.QuickSort.sort(otherdb, otherdb);
4944 List<DbSourceProxy> otherdb;
4945 JMenu dfetch = new JMenu();
4946 JMenu ifetch = new JMenu();
4947 JMenuItem fetchr = null;
4948 int comp = 0, icomp = 0, mcomp = 15;
4949 String mname = null;
4951 for (String dbclass : dbclasses)
4953 otherdb = sf.getSourceProxy(dbclass);
4954 // add a single entry for this class, or submenu allowing 'fetch
4956 if (otherdb == null || otherdb.size() < 1)
4960 // List<DbSourceProxy> dbs=otherdb;
4961 // otherdb=new ArrayList<DbSourceProxy>();
4962 // for (DbSourceProxy db:dbs)
4964 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4968 mname = "From " + dbclass;
4970 if (otherdb.size() == 1)
4972 final DbSourceProxy[] dassource = otherdb
4973 .toArray(new DbSourceProxy[0]);
4974 DbSourceProxy src = otherdb.get(0);
4975 fetchr = new JMenuItem(src.getDbSource());
4976 fetchr.addActionListener(new ActionListener()
4980 public void actionPerformed(ActionEvent e)
4982 new Thread(new Runnable()
4988 boolean isNucleotide = alignPanel.alignFrame
4989 .getViewport().getAlignment()
4991 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4992 alignPanel.av.getSequenceSelection(),
4993 alignPanel.alignFrame, dassource,
4994 alignPanel.alignFrame.featureSettings,
4997 .addListener(new FetchFinishedListenerI()
5000 public void finished()
5002 AlignFrame.this.setMenusForViewport();
5005 dbRefFetcher.fetchDBRefs(false);
5011 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5012 MessageManager.formatMessage(
5013 "label.fetch_retrieve_from",
5014 new Object[] { src.getDbName() })));
5020 final DbSourceProxy[] dassource = otherdb
5021 .toArray(new DbSourceProxy[0]);
5023 DbSourceProxy src = otherdb.get(0);
5024 fetchr = new JMenuItem(MessageManager.formatMessage(
5025 "label.fetch_all_param",
5026 new Object[] { src.getDbSource() }));
5027 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_all_sources",
5065 Integer.valueOf(otherdb.size())
5066 .toString(), src.getDbSource(),
5067 src.getDbName() })));
5070 // and then build the rest of the individual menus
5071 ifetch = new JMenu(MessageManager.formatMessage(
5072 "label.source_from_db_source",
5073 new Object[] { src.getDbSource() }));
5075 String imname = null;
5077 for (DbSourceProxy sproxy : otherdb)
5079 String dbname = sproxy.getDbName();
5080 String sname = dbname.length() > 5 ? dbname.substring(0,
5081 5) + "..." : dbname;
5082 String msname = dbname.length() > 10 ? dbname.substring(
5083 0, 10) + "..." : dbname;
5086 imname = MessageManager.formatMessage(
5087 "label.from_msname", new Object[] { sname });
5089 fetchr = new JMenuItem(msname);
5090 final DbSourceProxy[] dassrc = { sproxy };
5091 fetchr.addActionListener(new ActionListener()
5095 public void actionPerformed(ActionEvent e)
5097 new Thread(new Runnable()
5103 boolean isNucleotide = alignPanel.alignFrame
5104 .getViewport().getAlignment()
5106 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5107 alignPanel.av.getSequenceSelection(),
5108 alignPanel.alignFrame, dassrc,
5109 alignPanel.alignFrame.featureSettings,
5112 .addListener(new FetchFinishedListenerI()
5115 public void finished()
5117 AlignFrame.this.setMenusForViewport();
5120 dbRefFetcher.fetchDBRefs(false);
5126 fetchr.setToolTipText("<html>"
5127 + MessageManager.formatMessage(
5128 "label.fetch_retrieve_from", new Object[]
5132 if (++icomp >= mcomp || i == (otherdb.size()))
5134 ifetch.setText(MessageManager.formatMessage(
5135 "label.source_to_target", imname, sname));
5137 ifetch = new JMenu();
5145 if (comp >= mcomp || dbi >= (dbclasses.length))
5147 dfetch.setText(MessageManager.formatMessage(
5148 "label.source_to_target", mname, dbclass));
5150 dfetch = new JMenu();
5163 * Left justify the whole alignment.
5166 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5168 AlignmentI al = viewport.getAlignment();
5170 viewport.firePropertyChange("alignment", null, al);
5174 * Right justify the whole alignment.
5177 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5179 AlignmentI al = viewport.getAlignment();
5181 viewport.firePropertyChange("alignment", null, al);
5185 public void setShowSeqFeatures(boolean b)
5187 showSeqFeatures.setSelected(b);
5188 viewport.setShowSequenceFeatures(b);
5195 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5196 * awt.event.ActionEvent)
5199 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5201 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5202 alignPanel.paintAlignment(true);
5209 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5213 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5215 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5216 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5224 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5225 * .event.ActionEvent)
5228 protected void showGroupConservation_actionPerformed(ActionEvent e)
5230 viewport.setShowGroupConservation(showGroupConservation.getState());
5231 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5238 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5239 * .event.ActionEvent)
5242 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5244 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5245 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5252 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5253 * .event.ActionEvent)
5256 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5258 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5259 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5263 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5265 showSequenceLogo.setState(true);
5266 viewport.setShowSequenceLogo(true);
5267 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5268 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5272 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5274 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5281 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5282 * .event.ActionEvent)
5285 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5287 if (avc.makeGroupsFromSelection())
5289 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5290 alignPanel.updateAnnotation();
5291 alignPanel.paintAlignment(true);
5295 public void clearAlignmentSeqRep()
5297 // TODO refactor alignmentseqrep to controller
5298 if (viewport.getAlignment().hasSeqrep())
5300 viewport.getAlignment().setSeqrep(null);
5301 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5302 alignPanel.updateAnnotation();
5303 alignPanel.paintAlignment(true);
5308 protected void createGroup_actionPerformed(ActionEvent e)
5310 if (avc.createGroup())
5312 alignPanel.alignmentChanged();
5317 protected void unGroup_actionPerformed(ActionEvent e)
5321 alignPanel.alignmentChanged();
5326 * make the given alignmentPanel the currently selected tab
5328 * @param alignmentPanel
5330 public void setDisplayedView(AlignmentPanel alignmentPanel)
5332 if (!viewport.getSequenceSetId().equals(
5333 alignmentPanel.av.getSequenceSetId()))
5337 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5339 if (tabbedPane != null
5340 && tabbedPane.getTabCount() > 0
5341 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5342 .getSelectedIndex())
5344 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5349 * Action on selection of menu options to Show or Hide annotations.
5352 * @param forSequences
5353 * update sequence-related annotations
5354 * @param forAlignment
5355 * update non-sequence-related annotations
5358 protected void setAnnotationsVisibility(boolean visible,
5359 boolean forSequences, boolean forAlignment)
5361 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5362 .getAlignmentAnnotation();
5367 for (AlignmentAnnotation aa : anns)
5370 * don't display non-positional annotations on an alignment
5372 if (aa.annotations == null)
5376 boolean apply = (aa.sequenceRef == null && forAlignment)
5377 || (aa.sequenceRef != null && forSequences);
5380 aa.visible = visible;
5383 alignPanel.validateAnnotationDimensions(true);
5384 alignPanel.alignmentChanged();
5388 * Store selected annotation sort order for the view and repaint.
5391 protected void sortAnnotations_actionPerformed()
5393 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5395 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5396 alignPanel.paintAlignment(true);
5401 * @return alignment panels in this alignment frame
5403 public List<? extends AlignmentViewPanel> getAlignPanels()
5405 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5409 * Open a new alignment window, with the cDNA associated with this (protein)
5410 * alignment, aligned as is the protein.
5412 protected void viewAsCdna_actionPerformed()
5414 // TODO no longer a menu action - refactor as required
5415 final AlignmentI alignment = getViewport().getAlignment();
5416 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5417 if (mappings == null)
5421 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5422 for (SequenceI aaSeq : alignment.getSequences())
5424 for (AlignedCodonFrame acf : mappings)
5426 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5430 * There is a cDNA mapping for this protein sequence - add to new
5431 * alignment. It will share the same dataset sequence as other mapped
5432 * cDNA (no new mappings need to be created).
5434 final Sequence newSeq = new Sequence(dnaSeq);
5435 newSeq.setDatasetSequence(dnaSeq);
5436 cdnaSeqs.add(newSeq);
5440 if (cdnaSeqs.size() == 0)
5442 // show a warning dialog no mapped cDNA
5445 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5447 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5448 AlignFrame.DEFAULT_HEIGHT);
5449 cdna.alignAs(alignment);
5450 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5452 Desktop.addInternalFrame(alignFrame, newtitle,
5453 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5457 * Set visibility of dna/protein complement view (available when shown in a
5463 protected void showComplement_actionPerformed(boolean show)
5465 SplitContainerI sf = getSplitViewContainer();
5468 sf.setComplementVisible(this, show);
5473 * Generate the reverse (optionally complemented) of the selected sequences,
5474 * and add them to the alignment
5477 protected void showReverse_actionPerformed(boolean complement)
5479 AlignmentI al = null;
5482 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5483 al = dna.reverseCdna(complement);
5484 viewport.addAlignment(al, "");
5485 addHistoryItem(new EditCommand(
5486 MessageManager.getString("label.add_sequences"),
5487 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5488 viewport.getAlignment()));
5489 } catch (Exception ex)
5491 System.err.println(ex.getMessage());
5497 * Try to run a script in the Groovy console, having first ensured that this
5498 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5499 * be targeted at this alignment.
5502 protected void runGroovy_actionPerformed()
5504 Jalview.setCurrentAlignFrame(this);
5505 groovy.ui.Console console = Desktop.getGroovyConsole();
5506 if (console != null)
5510 console.runScript();
5511 } catch (Exception ex)
5513 System.err.println((ex.toString()));
5515 .showInternalMessageDialog(Desktop.desktop, MessageManager
5516 .getString("label.couldnt_run_groovy_script"),
5518 .getString("label.groovy_support_failed"),
5519 JvOptionPane.ERROR_MESSAGE);
5524 System.err.println("Can't run Groovy script as console not found");
5529 * Hides columns containing (or not containing) a specified feature, provided
5530 * that would not leave all columns hidden
5532 * @param featureType
5533 * @param columnsContaining
5536 public boolean hideFeatureColumns(String featureType,
5537 boolean columnsContaining)
5539 boolean notForHiding = avc.markColumnsContainingFeatures(
5540 columnsContaining, false, false, featureType);
5543 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5544 false, featureType))
5546 getViewport().hideSelectedColumns();
5554 protected void selectHighlightedColumns_actionPerformed(
5555 ActionEvent actionEvent)
5557 // include key modifier check in case user selects from menu
5558 avc.markHighlightedColumns(
5559 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5561 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5565 * Rebuilds the Colour menu, including any user-defined colours which have
5566 * been loaded either on startup or during the session
5568 public void buildColourMenu()
5570 colourMenu.removeAll();
5572 colourMenu.add(applyToAllGroups);
5573 colourMenu.add(textColour);
5574 colourMenu.addSeparator();
5576 ColourMenuHelper.addMenuItems(colourMenu, this,
5577 viewport.getAlignment(), false);
5579 colourMenu.addSeparator();
5580 colourMenu.add(conservationMenuItem);
5581 colourMenu.add(modifyConservation);
5582 colourMenu.add(abovePIDThreshold);
5583 colourMenu.add(modifyPID);
5584 colourMenu.add(annotationColour);
5586 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5587 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5591 * Open a dialog (if not already open) that allows the user to select and
5592 * calculate PCA or Tree analysis
5594 protected void openTreePcaDialog()
5596 if (alignPanel.getCalculationDialog() == null)
5598 new CalculationChooser(AlignFrame.this);
5603 class PrintThread extends Thread
5607 public PrintThread(AlignmentPanel ap)
5612 static PageFormat pf;
5617 PrinterJob printJob = PrinterJob.getPrinterJob();
5621 printJob.setPrintable(ap, pf);
5625 printJob.setPrintable(ap);
5628 if (printJob.printDialog())
5633 } catch (Exception PrintException)
5635 PrintException.printStackTrace();