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.analysis.TreeModel;
30 import jalview.api.AlignExportSettingI;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.AlignViewportI;
34 import jalview.api.AlignmentViewPanel;
35 import jalview.api.FeatureSettingsControllerI;
36 import jalview.api.SplitContainerI;
37 import jalview.api.ViewStyleI;
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.ext.forester.io.TreeParser;
64 import jalview.ext.forester.io.SupportedTreeFileFilter;
65 import jalview.ext.treeviewer.ExternalTreeParserI;
66 import jalview.gui.ColourMenuHelper.ColourChangeListener;
67 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
68 import jalview.io.AlignmentProperties;
69 import jalview.io.AnnotationFile;
70 import jalview.io.BioJsHTMLOutput;
71 import jalview.io.DataSourceType;
72 import jalview.io.FileFormat;
73 import jalview.io.FileFormatI;
74 import jalview.io.FileFormats;
75 import jalview.io.FileLoader;
76 import jalview.io.FileParse;
77 import jalview.io.FormatAdapter;
78 import jalview.io.HtmlSvgOutput;
79 import jalview.io.IdentifyFile;
80 import jalview.io.JPredFile;
81 import jalview.io.JalviewFileChooser;
82 import jalview.io.JalviewFileView;
83 import jalview.io.JnetAnnotationMaker;
84 import jalview.io.NewickFile;
85 import jalview.io.ScoreMatrixFile;
86 import jalview.io.TCoffeeScoreFile;
87 import jalview.jbgui.GAlignFrame;
88 import jalview.schemes.ColourSchemeI;
89 import jalview.schemes.ColourSchemes;
90 import jalview.schemes.ResidueColourScheme;
91 import jalview.schemes.TCoffeeColourScheme;
92 import jalview.util.MessageManager;
93 import jalview.viewmodel.AlignmentViewport;
94 import jalview.viewmodel.ViewportRanges;
95 import jalview.ws.DBRefFetcher;
96 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
97 import jalview.ws.jws1.Discoverer;
98 import jalview.ws.jws2.Jws2Discoverer;
99 import jalview.ws.jws2.jabaws2.Jws2Instance;
100 import jalview.ws.seqfetcher.DbSourceProxy;
102 import java.awt.BorderLayout;
103 import java.awt.Component;
104 import java.awt.Rectangle;
105 import java.awt.Toolkit;
106 import java.awt.datatransfer.Clipboard;
107 import java.awt.datatransfer.DataFlavor;
108 import java.awt.datatransfer.StringSelection;
109 import java.awt.datatransfer.Transferable;
110 import java.awt.dnd.DnDConstants;
111 import java.awt.dnd.DropTargetDragEvent;
112 import java.awt.dnd.DropTargetDropEvent;
113 import java.awt.dnd.DropTargetEvent;
114 import java.awt.dnd.DropTargetListener;
115 import java.awt.event.ActionEvent;
116 import java.awt.event.ActionListener;
117 import java.awt.event.FocusAdapter;
118 import java.awt.event.FocusEvent;
119 import java.awt.event.ItemEvent;
120 import java.awt.event.ItemListener;
121 import java.awt.event.KeyAdapter;
122 import java.awt.event.KeyEvent;
123 import java.awt.event.MouseEvent;
124 import java.awt.print.PageFormat;
125 import java.awt.print.PrinterJob;
126 import java.beans.PropertyChangeEvent;
128 import java.io.FileWriter;
129 import java.io.PrintWriter;
131 import java.util.ArrayList;
132 import java.util.Arrays;
133 import java.util.Deque;
134 import java.util.Enumeration;
135 import java.util.Hashtable;
136 import java.util.List;
137 import java.util.Vector;
139 import javax.swing.JCheckBoxMenuItem;
140 import javax.swing.JEditorPane;
141 import javax.swing.JInternalFrame;
142 import javax.swing.JLayeredPane;
143 import javax.swing.JMenu;
144 import javax.swing.JMenuItem;
145 import javax.swing.JScrollPane;
146 import javax.swing.SwingUtilities;
152 * @version $Revision$
154 public class AlignFrame extends GAlignFrame implements DropTargetListener,
155 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
158 public static final int DEFAULT_WIDTH = 700;
160 public static final int DEFAULT_HEIGHT = 500;
163 * The currently displayed panel (selected tabbed view if more than one)
165 public AlignmentPanel alignPanel;
167 AlignViewport viewport;
169 public AlignViewControllerI avc;
171 List<AlignmentPanel> alignPanels = new ArrayList<>();
174 * Last format used to load or save alignments in this window
176 FileFormatI currentFileFormat = null;
179 * Current filename for this alignment
181 String fileName = null;
184 * Creates a new AlignFrame object with specific width and height.
190 public AlignFrame(AlignmentI al, int width, int height)
192 this(al, null, width, height);
196 * Creates a new AlignFrame object with specific width, height and
202 * @param sequenceSetId
204 public AlignFrame(AlignmentI al, int width, int height,
205 String sequenceSetId)
207 this(al, null, width, height, sequenceSetId);
211 * Creates a new AlignFrame object with specific width, height and
217 * @param sequenceSetId
220 public AlignFrame(AlignmentI al, int width, int height,
221 String sequenceSetId, String viewId)
223 this(al, null, width, height, sequenceSetId, viewId);
227 * new alignment window with hidden columns
231 * @param hiddenColumns
232 * ColumnSelection or null
234 * Width of alignment frame
238 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
241 this(al, hiddenColumns, width, height, null);
245 * Create alignment frame for al with hiddenColumns, a specific width and
246 * height, and specific sequenceId
249 * @param hiddenColumns
252 * @param sequenceSetId
255 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
256 int height, String sequenceSetId)
258 this(al, hiddenColumns, width, height, sequenceSetId, null);
262 * Create alignment frame for al with hiddenColumns, a specific width and
263 * height, and specific sequenceId
266 * @param hiddenColumns
269 * @param sequenceSetId
274 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
275 int height, String sequenceSetId, String viewId)
277 setSize(width, height);
279 if (al.getDataset() == null)
284 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
286 alignPanel = new AlignmentPanel(this, viewport);
288 addAlignmentPanel(alignPanel, true);
292 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
293 HiddenColumns hiddenColumns, int width, int height)
295 setSize(width, height);
297 if (al.getDataset() == null)
302 viewport = new AlignViewport(al, hiddenColumns);
304 if (hiddenSeqs != null && hiddenSeqs.length > 0)
306 viewport.hideSequence(hiddenSeqs);
308 alignPanel = new AlignmentPanel(this, viewport);
309 addAlignmentPanel(alignPanel, true);
314 * Make a new AlignFrame from existing alignmentPanels
321 public AlignFrame(AlignmentPanel ap)
325 addAlignmentPanel(ap, false);
330 * initalise the alignframe from the underlying viewport data and the
335 if (!Jalview.isHeadlessMode())
337 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
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<>();
400 final List<AlignmentPanel> origview = new ArrayList<>();
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<>(
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
514 && evt.getKeyCode() <= KeyEvent.VK_9)
515 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
516 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
517 && Character.isDigit(evt.getKeyChar()))
519 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
522 switch (evt.getKeyCode())
525 case 27: // escape key
526 deselectAllSequenceMenuItem_actionPerformed(null);
530 case KeyEvent.VK_DOWN:
531 if (evt.isAltDown() || !viewport.cursorMode)
533 moveSelectedSequences(false);
535 if (viewport.cursorMode)
537 alignPanel.getSeqPanel().moveCursor(0, 1);
542 if (evt.isAltDown() || !viewport.cursorMode)
544 moveSelectedSequences(true);
546 if (viewport.cursorMode)
548 alignPanel.getSeqPanel().moveCursor(0, -1);
553 case KeyEvent.VK_LEFT:
554 if (evt.isAltDown() || !viewport.cursorMode)
556 slideSequences(false,
557 alignPanel.getSeqPanel().getKeyboardNo1());
561 alignPanel.getSeqPanel().moveCursor(-1, 0);
566 case KeyEvent.VK_RIGHT:
567 if (evt.isAltDown() || !viewport.cursorMode)
569 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
573 alignPanel.getSeqPanel().moveCursor(1, 0);
577 case KeyEvent.VK_SPACE:
578 if (viewport.cursorMode)
580 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
581 || evt.isShiftDown() || evt.isAltDown());
585 // case KeyEvent.VK_A:
586 // if (viewport.cursorMode)
588 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
589 // //System.out.println("A");
593 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
594 * System.out.println("closing bracket"); } break;
596 case KeyEvent.VK_DELETE:
597 case KeyEvent.VK_BACK_SPACE:
598 if (!viewport.cursorMode)
600 cut_actionPerformed(null);
604 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
605 || evt.isShiftDown() || evt.isAltDown());
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
653 .formatMessage("label.keyboard_editing_mode", new String[]
654 { (viewport.cursorMode ? "on" : "off") }));
655 if (viewport.cursorMode)
657 ViewportRanges ranges = viewport.getRanges();
658 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
660 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
663 alignPanel.getSeqPanel().seqCanvas.repaint();
669 Help.showHelpWindow();
670 } catch (Exception ex)
672 ex.printStackTrace();
677 boolean toggleSeqs = !evt.isControlDown();
678 boolean toggleCols = !evt.isShiftDown();
679 toggleHiddenRegions(toggleSeqs, toggleCols);
684 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
685 boolean modifyExisting = true; // always modify, don't clear
686 // evt.isShiftDown();
687 boolean invertHighlighted = evt.isAltDown();
688 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
692 case KeyEvent.VK_PAGE_UP:
693 viewport.getRanges().pageUp();
695 case KeyEvent.VK_PAGE_DOWN:
696 viewport.getRanges().pageDown();
702 public void keyReleased(KeyEvent evt)
704 switch (evt.getKeyCode())
706 case KeyEvent.VK_LEFT:
707 if (evt.isAltDown() || !viewport.cursorMode)
709 viewport.firePropertyChange("alignment", null,
710 viewport.getAlignment().getSequences());
714 case KeyEvent.VK_RIGHT:
715 if (evt.isAltDown() || !viewport.cursorMode)
717 viewport.firePropertyChange("alignment", null,
718 viewport.getAlignment().getSequences());
726 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
728 ap.alignFrame = this;
729 avc = new jalview.controller.AlignViewController(this, viewport,
734 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
736 int aSize = alignPanels.size();
738 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
740 if (aSize == 1 && ap.av.viewName == null)
742 this.getContentPane().add(ap, BorderLayout.CENTER);
748 setInitialTabVisible();
751 expandViews.setEnabled(true);
752 gatherViews.setEnabled(true);
753 tabbedPane.addTab(ap.av.viewName, ap);
755 ap.setVisible(false);
760 if (ap.av.isPadGaps())
762 ap.av.getAlignment().padGaps();
764 ap.av.updateConservation(ap);
765 ap.av.updateConsensus(ap);
766 ap.av.updateStrucConsensus(ap);
770 public void setInitialTabVisible()
772 expandViews.setEnabled(true);
773 gatherViews.setEnabled(true);
774 tabbedPane.setVisible(true);
775 AlignmentPanel first = alignPanels.get(0);
776 tabbedPane.addTab(first.av.viewName, first);
777 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
780 public AlignViewport getViewport()
785 /* Set up intrinsic listeners for dynamically generated GUI bits. */
786 private void addServiceListeners()
788 final java.beans.PropertyChangeListener thisListener;
789 Desktop.instance.addJalviewPropertyChangeListener("services",
790 thisListener = new java.beans.PropertyChangeListener()
793 public void propertyChange(PropertyChangeEvent evt)
795 // // System.out.println("Discoverer property change.");
796 // if (evt.getPropertyName().equals("services"))
798 SwingUtilities.invokeLater(new Runnable()
805 "Rebuild WS Menu for service change");
806 BuildWebServiceMenu();
813 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
816 public void internalFrameClosed(
817 javax.swing.event.InternalFrameEvent evt)
819 // System.out.println("deregistering discoverer listener");
820 Desktop.instance.removeJalviewPropertyChangeListener("services",
822 closeMenuItem_actionPerformed(true);
825 // Finally, build the menu once to get current service state
826 new Thread(new Runnable()
831 BuildWebServiceMenu();
837 * Configure menu items that vary according to whether the alignment is
838 * nucleotide or protein
840 public void setGUINucleotide()
842 AlignmentI al = getViewport().getAlignment();
843 boolean nucleotide = al.isNucleotide();
845 showTranslation.setVisible(nucleotide);
846 showReverse.setVisible(nucleotide);
847 showReverseComplement.setVisible(nucleotide);
848 conservationMenuItem.setEnabled(!nucleotide);
850 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
851 showGroupConservation.setEnabled(!nucleotide);
853 showComplementMenuItem
854 .setText(nucleotide ? MessageManager.getString("label.protein")
855 : MessageManager.getString("label.nucleotide"));
859 * set up menus for the current viewport. This may be called after any
860 * operation that affects the data in the current view (selection changed,
861 * etc) to update the menus to reflect the new state.
864 public void setMenusForViewport()
866 setMenusFromViewport(viewport);
870 * Need to call this method when tabs are selected for multiple views, or when
871 * loading from Jalview2XML.java
876 void setMenusFromViewport(AlignViewport av)
878 padGapsMenuitem.setSelected(av.isPadGaps());
879 colourTextMenuItem.setSelected(av.isShowColourText());
880 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
881 modifyPID.setEnabled(abovePIDThreshold.isSelected());
882 conservationMenuItem.setSelected(av.getConservationSelected());
883 modifyConservation.setEnabled(conservationMenuItem.isSelected());
884 seqLimits.setSelected(av.getShowJVSuffix());
885 idRightAlign.setSelected(av.isRightAlignIds());
886 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
887 renderGapsMenuItem.setSelected(av.isRenderGaps());
888 wrapMenuItem.setSelected(av.getWrapAlignment());
889 scaleAbove.setVisible(av.getWrapAlignment());
890 scaleLeft.setVisible(av.getWrapAlignment());
891 scaleRight.setVisible(av.getWrapAlignment());
892 annotationPanelMenuItem.setState(av.isShowAnnotation());
894 * Show/hide annotations only enabled if annotation panel is shown
896 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
897 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
898 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
899 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
900 viewBoxesMenuItem.setSelected(av.getShowBoxes());
901 viewTextMenuItem.setSelected(av.getShowText());
902 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
903 showGroupConsensus.setSelected(av.isShowGroupConsensus());
904 showGroupConservation.setSelected(av.isShowGroupConservation());
905 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
906 showSequenceLogo.setSelected(av.isShowSequenceLogo());
907 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
909 ColourMenuHelper.setColourSelected(colourMenu,
910 av.getGlobalColourScheme());
912 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
913 hiddenMarkers.setState(av.getShowHiddenMarkers());
914 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
915 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
916 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
917 autoCalculate.setSelected(av.autoCalculateConsensus);
918 sortByTree.setSelected(av.sortByTree);
919 listenToViewSelections.setSelected(av.followSelection);
921 showProducts.setEnabled(canShowProducts());
922 setGroovyEnabled(Desktop.getGroovyConsole() != null);
928 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
932 public void setGroovyEnabled(boolean b)
934 runGroovy.setEnabled(b);
937 private IProgressIndicator progressBar;
942 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
945 public void setProgressBar(String message, long id)
947 progressBar.setProgressBar(message, id);
951 public void registerHandler(final long id,
952 final IProgressIndicatorHandler handler)
954 progressBar.registerHandler(id, handler);
959 * @return true if any progress bars are still active
962 public boolean operationInProgress()
964 return progressBar.operationInProgress();
968 public void setStatus(String text)
970 statusBar.setText(text);
974 * Added so Castor Mapping file can obtain Jalview Version
976 public String getVersion()
978 return jalview.bin.Cache.getProperty("VERSION");
981 public FeatureRenderer getFeatureRenderer()
983 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
987 public void fetchSequence_actionPerformed(ActionEvent e)
989 new jalview.gui.SequenceFetcher(this);
993 public void addFromFile_actionPerformed(ActionEvent e)
995 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
999 public void reload_actionPerformed(ActionEvent e)
1001 if (fileName != null)
1003 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1004 // originating file's format
1005 // TODO: work out how to recover feature settings for correct view(s) when
1006 // file is reloaded.
1007 if (FileFormat.Jalview.equals(currentFileFormat))
1009 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1010 for (int i = 0; i < frames.length; i++)
1012 if (frames[i] instanceof AlignFrame && frames[i] != this
1013 && ((AlignFrame) frames[i]).fileName != null
1014 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1018 frames[i].setSelected(true);
1019 Desktop.instance.closeAssociatedWindows();
1020 } catch (java.beans.PropertyVetoException ex)
1026 Desktop.instance.closeAssociatedWindows();
1028 FileLoader loader = new FileLoader();
1029 DataSourceType protocol = fileName.startsWith("http:")
1030 ? DataSourceType.URL
1031 : DataSourceType.FILE;
1032 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1036 Rectangle bounds = this.getBounds();
1038 FileLoader loader = new FileLoader();
1039 DataSourceType protocol = fileName.startsWith("http:")
1040 ? DataSourceType.URL
1041 : DataSourceType.FILE;
1042 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1043 protocol, currentFileFormat);
1045 newframe.setBounds(bounds);
1046 if (featureSettings != null && featureSettings.isShowing())
1048 final Rectangle fspos = featureSettings.frame.getBounds();
1049 // TODO: need a 'show feature settings' function that takes bounds -
1050 // need to refactor Desktop.addFrame
1051 newframe.featureSettings_actionPerformed(null);
1052 final FeatureSettings nfs = newframe.featureSettings;
1053 SwingUtilities.invokeLater(new Runnable()
1058 nfs.frame.setBounds(fspos);
1061 this.featureSettings.close();
1062 this.featureSettings = null;
1064 this.closeMenuItem_actionPerformed(true);
1070 public void addFromText_actionPerformed(ActionEvent e)
1073 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1077 public void addFromURL_actionPerformed(ActionEvent e)
1079 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1083 public void save_actionPerformed(ActionEvent e)
1085 if (fileName == null || (currentFileFormat == null)
1086 || fileName.startsWith("http"))
1088 saveAs_actionPerformed(null);
1092 saveAlignment(fileName, currentFileFormat);
1103 public void saveAs_actionPerformed(ActionEvent e)
1105 String format = currentFileFormat == null ? null
1106 : currentFileFormat.getName();
1107 JalviewFileChooser chooser = JalviewFileChooser
1108 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1110 chooser.setFileView(new JalviewFileView());
1111 chooser.setDialogTitle(
1112 MessageManager.getString("label.save_alignment_to_file"));
1113 chooser.setToolTipText(MessageManager.getString("action.save"));
1115 int value = chooser.showSaveDialog(this);
1117 if (value == JalviewFileChooser.APPROVE_OPTION)
1119 currentFileFormat = chooser.getSelectedFormat();
1120 while (currentFileFormat == null)
1122 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1123 MessageManager.getString(
1124 "label.select_file_format_before_saving"),
1125 MessageManager.getString("label.file_format_not_specified"),
1126 JvOptionPane.WARNING_MESSAGE);
1127 currentFileFormat = chooser.getSelectedFormat();
1128 value = chooser.showSaveDialog(this);
1129 if (value != JalviewFileChooser.APPROVE_OPTION)
1135 fileName = chooser.getSelectedFile().getPath();
1137 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1139 Cache.setProperty("LAST_DIRECTORY", fileName);
1140 saveAlignment(fileName, currentFileFormat);
1144 public boolean saveAlignment(String file, FileFormatI format)
1146 boolean success = true;
1148 if (FileFormat.Jalview.equals(format))
1150 String shortName = title;
1152 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1154 shortName = shortName.substring(
1155 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1158 success = new Jalview2XML().saveAlignment(this, file, shortName);
1160 statusBar.setText(MessageManager.formatMessage(
1161 "label.successfully_saved_to_file_in_format", new Object[]
1162 { fileName, format }));
1167 AlignmentExportData exportData = getAlignmentForExport(format,
1169 if (exportData.getSettings().isCancelled())
1173 FormatAdapter f = new FormatAdapter(alignPanel,
1174 exportData.getSettings());
1175 String output = f.formatSequences(format, exportData.getAlignment(), // class
1179 // occur in the distant future
1180 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1181 f.getCacheSuffixDefault(format),
1182 viewport.getAlignment().getHiddenColumns());
1192 PrintWriter out = new PrintWriter(new FileWriter(file));
1196 this.setTitle(file);
1197 statusBar.setText(MessageManager.formatMessage(
1198 "label.successfully_saved_to_file_in_format", new Object[]
1199 { fileName, format.getName() }));
1200 } catch (Exception ex)
1203 ex.printStackTrace();
1210 JvOptionPane.showInternalMessageDialog(this, MessageManager
1211 .formatMessage("label.couldnt_save_file", new Object[]
1213 MessageManager.getString("label.error_saving_file"),
1214 JvOptionPane.WARNING_MESSAGE);
1220 private void warningMessage(String warning, String title)
1222 if (new jalview.util.Platform().isHeadless())
1224 System.err.println("Warning: " + title + "\nWarning: " + warning);
1229 JvOptionPane.showInternalMessageDialog(this, warning, title,
1230 JvOptionPane.WARNING_MESSAGE);
1242 protected void outputText_actionPerformed(ActionEvent e)
1244 FileFormatI fileFormat = FileFormats.getInstance()
1245 .forName(e.getActionCommand());
1246 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1248 if (exportData.getSettings().isCancelled())
1252 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1253 cap.setForInput(null);
1256 FileFormatI format = fileFormat;
1257 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1258 .formatSequences(format, exportData.getAlignment(),
1259 exportData.getOmitHidden(),
1260 exportData.getStartEndPostions(),
1261 viewport.getAlignment().getHiddenColumns()));
1262 Desktop.addInternalFrame(cap, MessageManager
1263 .formatMessage("label.alignment_output_command", new Object[]
1264 { e.getActionCommand() }), 600, 500);
1265 } catch (OutOfMemoryError oom)
1267 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1274 public static AlignmentExportData getAlignmentForExport(
1275 FileFormatI format, AlignViewportI viewport,
1276 AlignExportSettingI exportSettings)
1278 AlignmentI alignmentToExport = null;
1279 AlignExportSettingI settings = exportSettings;
1280 String[] omitHidden = null;
1282 HiddenSequences hiddenSeqs = viewport.getAlignment()
1283 .getHiddenSequences();
1285 alignmentToExport = viewport.getAlignment();
1287 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1288 if (settings == null)
1290 settings = new AlignExportSettings(hasHiddenSeqs,
1291 viewport.hasHiddenColumns(), format);
1293 // settings.isExportAnnotations();
1295 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1297 omitHidden = viewport.getViewAsString(false,
1298 settings.isExportHiddenSequences());
1301 int[] alignmentStartEnd = new int[2];
1302 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1304 alignmentToExport = hiddenSeqs.getFullAlignment();
1308 alignmentToExport = viewport.getAlignment();
1310 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1311 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1312 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1313 omitHidden, alignmentStartEnd, settings);
1324 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1326 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1327 htmlSVG.exportHTML(null);
1331 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1333 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1334 bjs.exportHTML(null);
1337 public void createImageMap(File file, String image)
1339 alignPanel.makePNGImageMap(file, image);
1349 public void createPNG(File f)
1351 alignPanel.makePNG(f);
1361 public void createEPS(File f)
1363 alignPanel.makeEPS(f);
1367 public void createSVG(File f)
1369 alignPanel.makeSVG(f);
1373 public void pageSetup_actionPerformed(ActionEvent e)
1375 PrinterJob printJob = PrinterJob.getPrinterJob();
1376 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1386 public void printMenuItem_actionPerformed(ActionEvent e)
1388 // Putting in a thread avoids Swing painting problems
1389 PrintThread thread = new PrintThread(alignPanel);
1394 public void exportFeatures_actionPerformed(ActionEvent e)
1396 new AnnotationExporter().exportFeatures(alignPanel);
1400 public void exportAnnotations_actionPerformed(ActionEvent e)
1402 new AnnotationExporter().exportAnnotations(alignPanel);
1406 public void associatedData_actionPerformed(ActionEvent e)
1408 // Pick the tree file
1409 JalviewFileChooser chooser = new JalviewFileChooser(
1410 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1411 chooser.setFileView(new JalviewFileView());
1412 chooser.setDialogTitle(
1413 MessageManager.getString("label.load_jalview_annotations"));
1414 chooser.setToolTipText(
1415 MessageManager.getString("label.load_jalview_annotations"));
1417 int value = chooser.showOpenDialog(null);
1419 if (value == JalviewFileChooser.APPROVE_OPTION)
1421 String choice = chooser.getSelectedFile().getPath();
1422 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1423 loadJalviewDataFile(choice, null, null, null);
1429 * Close the current view or all views in the alignment frame. If the frame
1430 * only contains one view then the alignment will be removed from memory.
1432 * @param closeAllTabs
1435 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1437 if (alignPanels != null && alignPanels.size() < 2)
1439 closeAllTabs = true;
1444 if (alignPanels != null)
1448 if (this.isClosed())
1450 // really close all the windows - otherwise wait till
1451 // setClosed(true) is called
1452 for (int i = 0; i < alignPanels.size(); i++)
1454 AlignmentPanel ap = alignPanels.get(i);
1461 closeView(alignPanel);
1468 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1469 * be called recursively, with the frame now in 'closed' state
1471 this.setClosed(true);
1473 } catch (Exception ex)
1475 ex.printStackTrace();
1480 * Close the specified panel and close up tabs appropriately.
1482 * @param panelToClose
1484 public void closeView(AlignmentPanel panelToClose)
1486 int index = tabbedPane.getSelectedIndex();
1487 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1488 alignPanels.remove(panelToClose);
1489 panelToClose.closePanel();
1490 panelToClose = null;
1492 tabbedPane.removeTabAt(closedindex);
1493 tabbedPane.validate();
1495 if (index > closedindex || index == tabbedPane.getTabCount())
1497 // modify currently selected tab index if necessary.
1501 this.tabSelectionChanged(index);
1507 void updateEditMenuBar()
1510 if (viewport.getHistoryList().size() > 0)
1512 undoMenuItem.setEnabled(true);
1513 CommandI command = viewport.getHistoryList().peek();
1514 undoMenuItem.setText(MessageManager
1515 .formatMessage("label.undo_command", new Object[]
1516 { command.getDescription() }));
1520 undoMenuItem.setEnabled(false);
1521 undoMenuItem.setText(MessageManager.getString("action.undo"));
1524 if (viewport.getRedoList().size() > 0)
1526 redoMenuItem.setEnabled(true);
1528 CommandI command = viewport.getRedoList().peek();
1529 redoMenuItem.setText(MessageManager
1530 .formatMessage("label.redo_command", new Object[]
1531 { command.getDescription() }));
1535 redoMenuItem.setEnabled(false);
1536 redoMenuItem.setText(MessageManager.getString("action.redo"));
1541 public void addHistoryItem(CommandI command)
1543 if (command.getSize() > 0)
1545 viewport.addToHistoryList(command);
1546 viewport.clearRedoList();
1547 updateEditMenuBar();
1548 viewport.updateHiddenColumns();
1549 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1550 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1551 // viewport.getColumnSelection()
1552 // .getHiddenColumns().size() > 0);
1558 * @return alignment objects for all views
1560 AlignmentI[] getViewAlignments()
1562 if (alignPanels != null)
1564 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1566 for (AlignmentPanel ap : alignPanels)
1568 als[i++] = ap.av.getAlignment();
1572 if (viewport != null)
1574 return new AlignmentI[] { viewport.getAlignment() };
1586 protected void undoMenuItem_actionPerformed(ActionEvent e)
1588 if (viewport.getHistoryList().isEmpty())
1592 CommandI command = viewport.getHistoryList().pop();
1593 viewport.addToRedoList(command);
1594 command.undoCommand(getViewAlignments());
1596 AlignmentViewport originalSource = getOriginatingSource(command);
1597 updateEditMenuBar();
1599 if (originalSource != null)
1601 if (originalSource != viewport)
1604 "Implementation worry: mismatch of viewport origin for undo");
1606 originalSource.updateHiddenColumns();
1607 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1609 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1610 // viewport.getColumnSelection()
1611 // .getHiddenColumns().size() > 0);
1612 originalSource.firePropertyChange("alignment", null,
1613 originalSource.getAlignment().getSequences());
1624 protected void redoMenuItem_actionPerformed(ActionEvent e)
1626 if (viewport.getRedoList().size() < 1)
1631 CommandI command = viewport.getRedoList().pop();
1632 viewport.addToHistoryList(command);
1633 command.doCommand(getViewAlignments());
1635 AlignmentViewport originalSource = getOriginatingSource(command);
1636 updateEditMenuBar();
1638 if (originalSource != null)
1641 if (originalSource != viewport)
1644 "Implementation worry: mismatch of viewport origin for redo");
1646 originalSource.updateHiddenColumns();
1647 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1649 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1650 // viewport.getColumnSelection()
1651 // .getHiddenColumns().size() > 0);
1652 originalSource.firePropertyChange("alignment", null,
1653 originalSource.getAlignment().getSequences());
1657 AlignmentViewport getOriginatingSource(CommandI command)
1659 AlignmentViewport originalSource = null;
1660 // For sequence removal and addition, we need to fire
1661 // the property change event FROM the viewport where the
1662 // original alignment was altered
1663 AlignmentI al = null;
1664 if (command instanceof EditCommand)
1666 EditCommand editCommand = (EditCommand) command;
1667 al = editCommand.getAlignment();
1668 List<Component> comps = PaintRefresher.components
1669 .get(viewport.getSequenceSetId());
1671 for (Component comp : comps)
1673 if (comp instanceof AlignmentPanel)
1675 if (al == ((AlignmentPanel) comp).av.getAlignment())
1677 originalSource = ((AlignmentPanel) comp).av;
1684 if (originalSource == null)
1686 // The original view is closed, we must validate
1687 // the current view against the closed view first
1690 PaintRefresher.validateSequences(al, viewport.getAlignment());
1693 originalSource = viewport;
1696 return originalSource;
1705 public void moveSelectedSequences(boolean up)
1707 SequenceGroup sg = viewport.getSelectionGroup();
1713 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1714 viewport.getHiddenRepSequences(), up);
1715 alignPanel.paintAlignment(true, false);
1718 synchronized void slideSequences(boolean right, int size)
1720 List<SequenceI> sg = new ArrayList<>();
1721 if (viewport.cursorMode)
1723 sg.add(viewport.getAlignment()
1724 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1726 else if (viewport.getSelectionGroup() != null
1727 && viewport.getSelectionGroup().getSize() != viewport
1728 .getAlignment().getHeight())
1730 sg = viewport.getSelectionGroup()
1731 .getSequences(viewport.getHiddenRepSequences());
1739 List<SequenceI> invertGroup = new ArrayList<>();
1741 for (SequenceI seq : viewport.getAlignment().getSequences())
1743 if (!sg.contains(seq))
1745 invertGroup.add(seq);
1749 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1751 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1752 for (int i = 0; i < invertGroup.size(); i++)
1754 seqs2[i] = invertGroup.get(i);
1757 SlideSequencesCommand ssc;
1760 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1761 viewport.getGapCharacter());
1765 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1766 viewport.getGapCharacter());
1769 int groupAdjustment = 0;
1770 if (ssc.getGapsInsertedBegin() && right)
1772 if (viewport.cursorMode)
1774 alignPanel.getSeqPanel().moveCursor(size, 0);
1778 groupAdjustment = size;
1781 else if (!ssc.getGapsInsertedBegin() && !right)
1783 if (viewport.cursorMode)
1785 alignPanel.getSeqPanel().moveCursor(-size, 0);
1789 groupAdjustment = -size;
1793 if (groupAdjustment != 0)
1795 viewport.getSelectionGroup().setStartRes(
1796 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1797 viewport.getSelectionGroup().setEndRes(
1798 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1802 * just extend the last slide command if compatible; but not if in
1803 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1805 boolean appendHistoryItem = false;
1806 Deque<CommandI> historyList = viewport.getHistoryList();
1807 boolean inSplitFrame = getSplitViewContainer() != null;
1808 if (!inSplitFrame && historyList != null && historyList.size() > 0
1809 && historyList.peek() instanceof SlideSequencesCommand)
1811 appendHistoryItem = ssc.appendSlideCommand(
1812 (SlideSequencesCommand) historyList.peek());
1815 if (!appendHistoryItem)
1817 addHistoryItem(ssc);
1830 protected void copy_actionPerformed(ActionEvent e)
1833 if (viewport.getSelectionGroup() == null)
1837 // TODO: preserve the ordering of displayed alignment annotation in any
1838 // internal paste (particularly sequence associated annotation)
1839 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1840 String[] omitHidden = null;
1842 if (viewport.hasHiddenColumns())
1844 omitHidden = viewport.getViewAsString(true);
1847 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1848 seqs, omitHidden, null);
1850 StringSelection ss = new StringSelection(output);
1854 jalview.gui.Desktop.internalCopy = true;
1855 // Its really worth setting the clipboard contents
1856 // to empty before setting the large StringSelection!!
1857 Toolkit.getDefaultToolkit().getSystemClipboard()
1858 .setContents(new StringSelection(""), null);
1860 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1862 } catch (OutOfMemoryError er)
1864 new OOMWarning("copying region", er);
1868 ArrayList<int[]> hiddenColumns = null;
1869 if (viewport.hasHiddenColumns())
1871 hiddenColumns = new ArrayList<>();
1872 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1873 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1874 ArrayList<int[]> hiddenRegions = viewport.getAlignment()
1875 .getHiddenColumns().getHiddenColumnsCopy();
1876 for (int[] region : hiddenRegions)
1878 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1882 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1887 Desktop.jalviewClipboard = new Object[] { seqs,
1888 viewport.getAlignment().getDataset(), hiddenColumns };
1889 statusBar.setText(MessageManager.formatMessage(
1890 "label.copied_sequences_to_clipboard", new Object[]
1891 { Integer.valueOf(seqs.length).toString() }));
1901 protected void pasteNew_actionPerformed(ActionEvent e)
1913 protected void pasteThis_actionPerformed(ActionEvent e)
1919 * Paste contents of Jalview clipboard
1921 * @param newAlignment
1922 * true to paste to a new alignment, otherwise add to this.
1924 void paste(boolean newAlignment)
1926 boolean externalPaste = true;
1929 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1930 Transferable contents = c.getContents(this);
1932 if (contents == null)
1941 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1942 if (str.length() < 1)
1947 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1949 } catch (OutOfMemoryError er)
1951 new OOMWarning("Out of memory pasting sequences!!", er);
1955 SequenceI[] sequences;
1956 boolean annotationAdded = false;
1957 AlignmentI alignment = null;
1959 if (Desktop.jalviewClipboard != null)
1961 // The clipboard was filled from within Jalview, we must use the
1963 // And dataset from the copied alignment
1964 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1965 // be doubly sure that we create *new* sequence objects.
1966 sequences = new SequenceI[newseq.length];
1967 for (int i = 0; i < newseq.length; i++)
1969 sequences[i] = new Sequence(newseq[i]);
1971 alignment = new Alignment(sequences);
1972 externalPaste = false;
1976 // parse the clipboard as an alignment.
1977 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1979 sequences = alignment.getSequencesArray();
1983 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1989 if (Desktop.jalviewClipboard != null)
1991 // dataset is inherited
1992 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1996 // new dataset is constructed
1997 alignment.setDataset(null);
1999 alwidth = alignment.getWidth() + 1;
2003 AlignmentI pastedal = alignment; // preserve pasted alignment object
2004 // Add pasted sequences and dataset into existing alignment.
2005 alignment = viewport.getAlignment();
2006 alwidth = alignment.getWidth() + 1;
2007 // decide if we need to import sequences from an existing dataset
2008 boolean importDs = Desktop.jalviewClipboard != null
2009 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2010 // importDs==true instructs us to copy over new dataset sequences from
2011 // an existing alignment
2012 Vector newDs = (importDs) ? new Vector() : null; // used to create
2013 // minimum dataset set
2015 for (int i = 0; i < sequences.length; i++)
2019 newDs.addElement(null);
2021 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2023 if (importDs && ds != null)
2025 if (!newDs.contains(ds))
2027 newDs.setElementAt(ds, i);
2028 ds = new Sequence(ds);
2029 // update with new dataset sequence
2030 sequences[i].setDatasetSequence(ds);
2034 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2039 // copy and derive new dataset sequence
2040 sequences[i] = sequences[i].deriveSequence();
2041 alignment.getDataset()
2042 .addSequence(sequences[i].getDatasetSequence());
2043 // TODO: avoid creation of duplicate dataset sequences with a
2044 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2046 alignment.addSequence(sequences[i]); // merges dataset
2050 newDs.clear(); // tidy up
2052 if (alignment.getAlignmentAnnotation() != null)
2054 for (AlignmentAnnotation alan : alignment
2055 .getAlignmentAnnotation())
2057 if (alan.graphGroup > fgroup)
2059 fgroup = alan.graphGroup;
2063 if (pastedal.getAlignmentAnnotation() != null)
2065 // Add any annotation attached to alignment.
2066 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2067 for (int i = 0; i < alann.length; i++)
2069 annotationAdded = true;
2070 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2072 AlignmentAnnotation newann = new AlignmentAnnotation(
2074 if (newann.graphGroup > -1)
2076 if (newGraphGroups.size() <= newann.graphGroup
2077 || newGraphGroups.get(newann.graphGroup) == null)
2079 for (int q = newGraphGroups
2080 .size(); q <= newann.graphGroup; q++)
2082 newGraphGroups.add(q, null);
2084 newGraphGroups.set(newann.graphGroup,
2085 new Integer(++fgroup));
2087 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2091 newann.padAnnotation(alwidth);
2092 alignment.addAnnotation(newann);
2102 addHistoryItem(new EditCommand(
2103 MessageManager.getString("label.add_sequences"),
2104 Action.PASTE, sequences, 0, alignment.getWidth(),
2107 // Add any annotations attached to sequences
2108 for (int i = 0; i < sequences.length; i++)
2110 if (sequences[i].getAnnotation() != null)
2112 AlignmentAnnotation newann;
2113 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2115 annotationAdded = true;
2116 newann = sequences[i].getAnnotation()[a];
2117 newann.adjustForAlignment();
2118 newann.padAnnotation(alwidth);
2119 if (newann.graphGroup > -1)
2121 if (newann.graphGroup > -1)
2123 if (newGraphGroups.size() <= newann.graphGroup
2124 || newGraphGroups.get(newann.graphGroup) == null)
2126 for (int q = newGraphGroups
2127 .size(); q <= newann.graphGroup; q++)
2129 newGraphGroups.add(q, null);
2131 newGraphGroups.set(newann.graphGroup,
2132 new Integer(++fgroup));
2134 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2138 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2142 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2150 // propagate alignment changed.
2151 viewport.getRanges().setEndSeq(alignment.getHeight());
2152 if (annotationAdded)
2154 // Duplicate sequence annotation in all views.
2155 AlignmentI[] alview = this.getViewAlignments();
2156 for (int i = 0; i < sequences.length; i++)
2158 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2163 for (int avnum = 0; avnum < alview.length; avnum++)
2165 if (alview[avnum] != alignment)
2167 // duplicate in a view other than the one with input focus
2168 int avwidth = alview[avnum].getWidth() + 1;
2169 // this relies on sann being preserved after we
2170 // modify the sequence's annotation array for each duplication
2171 for (int a = 0; a < sann.length; a++)
2173 AlignmentAnnotation newann = new AlignmentAnnotation(
2175 sequences[i].addAlignmentAnnotation(newann);
2176 newann.padAnnotation(avwidth);
2177 alview[avnum].addAnnotation(newann); // annotation was
2178 // duplicated earlier
2179 // TODO JAL-1145 graphGroups are not updated for sequence
2180 // annotation added to several views. This may cause
2182 alview[avnum].setAnnotationIndex(newann, a);
2187 buildSortByAnnotationScoresMenu();
2189 viewport.firePropertyChange("alignment", null,
2190 alignment.getSequences());
2191 if (alignPanels != null)
2193 for (AlignmentPanel ap : alignPanels)
2195 ap.validateAnnotationDimensions(false);
2200 alignPanel.validateAnnotationDimensions(false);
2206 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2208 String newtitle = new String("Copied sequences");
2210 if (Desktop.jalviewClipboard != null
2211 && Desktop.jalviewClipboard[2] != null)
2213 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2214 for (int[] region : hc)
2216 af.viewport.hideColumns(region[0], region[1]);
2220 // >>>This is a fix for the moment, until a better solution is
2222 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2223 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2224 .getFeatureRenderer());
2226 // TODO: maintain provenance of an alignment, rather than just make the
2227 // title a concatenation of operations.
2230 if (title.startsWith("Copied sequences"))
2236 newtitle = newtitle.concat("- from " + title);
2241 newtitle = new String("Pasted sequences");
2244 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2249 } catch (Exception ex)
2251 ex.printStackTrace();
2252 System.out.println("Exception whilst pasting: " + ex);
2253 // could be anything being pasted in here
2259 protected void expand_newalign(ActionEvent e)
2263 AlignmentI alignment = AlignmentUtils
2264 .expandContext(getViewport().getAlignment(), -1);
2265 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2267 String newtitle = new String("Flanking alignment");
2269 if (Desktop.jalviewClipboard != null
2270 && Desktop.jalviewClipboard[2] != null)
2272 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2273 for (int region[] : hc)
2275 af.viewport.hideColumns(region[0], region[1]);
2279 // >>>This is a fix for the moment, until a better solution is
2281 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2282 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2283 .getFeatureRenderer());
2285 // TODO: maintain provenance of an alignment, rather than just make the
2286 // title a concatenation of operations.
2288 if (title.startsWith("Copied sequences"))
2294 newtitle = newtitle.concat("- from " + title);
2298 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2300 } catch (Exception ex)
2302 ex.printStackTrace();
2303 System.out.println("Exception whilst pasting: " + ex);
2304 // could be anything being pasted in here
2305 } catch (OutOfMemoryError oom)
2307 new OOMWarning("Viewing flanking region of alignment", oom);
2318 protected void cut_actionPerformed(ActionEvent e)
2320 copy_actionPerformed(null);
2321 delete_actionPerformed(null);
2331 protected void delete_actionPerformed(ActionEvent evt)
2334 SequenceGroup sg = viewport.getSelectionGroup();
2341 * If the cut affects all sequences, warn, remove highlighted columns
2343 if (sg.getSize() == viewport.getAlignment().getHeight())
2345 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2346 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2347 if (isEntireAlignWidth)
2349 int confirm = JvOptionPane.showConfirmDialog(this,
2350 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2351 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2352 JvOptionPane.OK_CANCEL_OPTION);
2354 if (confirm == JvOptionPane.CANCEL_OPTION
2355 || confirm == JvOptionPane.CLOSED_OPTION)
2360 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2361 sg.getEndRes() + 1);
2363 SequenceI[] cut = sg.getSequences()
2364 .toArray(new SequenceI[sg.getSize()]);
2366 addHistoryItem(new EditCommand(
2367 MessageManager.getString("label.cut_sequences"), Action.CUT,
2368 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2369 viewport.getAlignment()));
2371 viewport.setSelectionGroup(null);
2372 viewport.sendSelection();
2373 viewport.getAlignment().deleteGroup(sg);
2375 viewport.firePropertyChange("alignment", null,
2376 viewport.getAlignment().getSequences());
2377 if (viewport.getAlignment().getHeight() < 1)
2381 this.setClosed(true);
2382 } catch (Exception ex)
2395 protected void deleteGroups_actionPerformed(ActionEvent e)
2397 if (avc.deleteGroups())
2399 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2400 alignPanel.updateAnnotation();
2401 alignPanel.paintAlignment(true, true);
2412 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2414 SequenceGroup sg = new SequenceGroup();
2416 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2418 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2421 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2422 viewport.setSelectionGroup(sg);
2423 viewport.sendSelection();
2424 // JAL-2034 - should delegate to
2425 // alignPanel to decide if overview needs
2427 alignPanel.paintAlignment(false, false);
2428 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2438 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2440 if (viewport.cursorMode)
2442 alignPanel.getSeqPanel().keyboardNo1 = null;
2443 alignPanel.getSeqPanel().keyboardNo2 = null;
2445 viewport.setSelectionGroup(null);
2446 viewport.getColumnSelection().clear();
2447 viewport.setSelectionGroup(null);
2448 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2449 // JAL-2034 - should delegate to
2450 // alignPanel to decide if overview needs
2452 alignPanel.paintAlignment(false, false);
2453 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2454 viewport.sendSelection();
2464 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2466 SequenceGroup sg = viewport.getSelectionGroup();
2470 selectAllSequenceMenuItem_actionPerformed(null);
2475 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2477 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2479 // JAL-2034 - should delegate to
2480 // alignPanel to decide if overview needs
2483 alignPanel.paintAlignment(true, false);
2484 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2485 viewport.sendSelection();
2489 public void invertColSel_actionPerformed(ActionEvent e)
2491 viewport.invertColumnSelection();
2492 alignPanel.paintAlignment(true, false);
2493 viewport.sendSelection();
2503 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2505 trimAlignment(true);
2515 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2517 trimAlignment(false);
2520 void trimAlignment(boolean trimLeft)
2522 ColumnSelection colSel = viewport.getColumnSelection();
2525 if (!colSel.isEmpty())
2529 column = colSel.getMin();
2533 column = colSel.getMax();
2537 if (viewport.getSelectionGroup() != null)
2539 seqs = viewport.getSelectionGroup()
2540 .getSequencesAsArray(viewport.getHiddenRepSequences());
2544 seqs = viewport.getAlignment().getSequencesArray();
2547 TrimRegionCommand trimRegion;
2550 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2551 column, viewport.getAlignment());
2552 viewport.getRanges().setStartRes(0);
2556 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2557 column, viewport.getAlignment());
2560 statusBar.setText(MessageManager
2561 .formatMessage("label.removed_columns", new String[]
2562 { Integer.valueOf(trimRegion.getSize()).toString() }));
2564 addHistoryItem(trimRegion);
2566 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2568 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2569 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2571 viewport.getAlignment().deleteGroup(sg);
2575 viewport.firePropertyChange("alignment", null,
2576 viewport.getAlignment().getSequences());
2587 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2589 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2592 if (viewport.getSelectionGroup() != null)
2594 seqs = viewport.getSelectionGroup()
2595 .getSequencesAsArray(viewport.getHiddenRepSequences());
2596 start = viewport.getSelectionGroup().getStartRes();
2597 end = viewport.getSelectionGroup().getEndRes();
2601 seqs = viewport.getAlignment().getSequencesArray();
2604 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2605 "Remove Gapped Columns", seqs, start, end,
2606 viewport.getAlignment());
2608 addHistoryItem(removeGapCols);
2610 statusBar.setText(MessageManager
2611 .formatMessage("label.removed_empty_columns", new Object[]
2612 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2614 // This is to maintain viewport position on first residue
2615 // of first sequence
2616 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2617 ViewportRanges ranges = viewport.getRanges();
2618 int startRes = seq.findPosition(ranges.getStartRes());
2619 // ShiftList shifts;
2620 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2621 // edit.alColumnChanges=shifts.getInverse();
2622 // if (viewport.hasHiddenColumns)
2623 // viewport.getColumnSelection().compensateForEdits(shifts);
2624 ranges.setStartRes(seq.findIndex(startRes) - 1);
2625 viewport.firePropertyChange("alignment", null,
2626 viewport.getAlignment().getSequences());
2637 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2639 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2642 if (viewport.getSelectionGroup() != null)
2644 seqs = viewport.getSelectionGroup()
2645 .getSequencesAsArray(viewport.getHiddenRepSequences());
2646 start = viewport.getSelectionGroup().getStartRes();
2647 end = viewport.getSelectionGroup().getEndRes();
2651 seqs = viewport.getAlignment().getSequencesArray();
2654 // This is to maintain viewport position on first residue
2655 // of first sequence
2656 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2657 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2659 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2660 viewport.getAlignment()));
2662 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2664 viewport.firePropertyChange("alignment", null,
2665 viewport.getAlignment().getSequences());
2676 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2678 viewport.setPadGaps(padGapsMenuitem.isSelected());
2679 viewport.firePropertyChange("alignment", null,
2680 viewport.getAlignment().getSequences());
2690 public void findMenuItem_actionPerformed(ActionEvent e)
2696 * Create a new view of the current alignment.
2699 public void newView_actionPerformed(ActionEvent e)
2701 newView(null, true);
2705 * Creates and shows a new view of the current alignment.
2708 * title of newly created view; if null, one will be generated
2709 * @param copyAnnotation
2710 * if true then duplicate all annnotation, groups and settings
2711 * @return new alignment panel, already displayed.
2713 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2716 * Create a new AlignmentPanel (with its own, new Viewport)
2718 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2719 if (!copyAnnotation)
2722 * remove all groups and annotation except for the automatic stuff
2724 newap.av.getAlignment().deleteAllGroups();
2725 newap.av.getAlignment().deleteAllAnnotations(false);
2728 newap.av.setGatherViewsHere(false);
2730 if (viewport.viewName == null)
2732 viewport.viewName = MessageManager
2733 .getString("label.view_name_original");
2737 * Views share the same edits undo and redo stacks
2739 newap.av.setHistoryList(viewport.getHistoryList());
2740 newap.av.setRedoList(viewport.getRedoList());
2743 * Views share the same mappings; need to deregister any new mappings
2744 * created by copyAlignPanel, and register the new reference to the shared
2747 newap.av.replaceMappings(viewport.getAlignment());
2750 * start up cDNA consensus (if applicable) now mappings are in place
2752 if (newap.av.initComplementConsensus())
2754 newap.refresh(true); // adjust layout of annotations
2757 newap.av.viewName = getNewViewName(viewTitle);
2759 addAlignmentPanel(newap, true);
2760 newap.alignmentChanged();
2762 if (alignPanels.size() == 2)
2764 viewport.setGatherViewsHere(true);
2766 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2771 * Make a new name for the view, ensuring it is unique within the current
2772 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2773 * these now use viewId. Unique view names are still desirable for usability.)
2778 protected String getNewViewName(String viewTitle)
2780 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2781 boolean addFirstIndex = false;
2782 if (viewTitle == null || viewTitle.trim().length() == 0)
2784 viewTitle = MessageManager.getString("action.view");
2785 addFirstIndex = true;
2789 index = 1;// we count from 1 if given a specific name
2791 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2793 List<Component> comps = PaintRefresher.components
2794 .get(viewport.getSequenceSetId());
2796 List<String> existingNames = getExistingViewNames(comps);
2798 while (existingNames.contains(newViewName))
2800 newViewName = viewTitle + " " + (++index);
2806 * Returns a list of distinct view names found in the given list of
2807 * components. View names are held on the viewport of an AlignmentPanel.
2812 protected List<String> getExistingViewNames(List<Component> comps)
2814 List<String> existingNames = new ArrayList<>();
2815 for (Component comp : comps)
2817 if (comp instanceof AlignmentPanel)
2819 AlignmentPanel ap = (AlignmentPanel) comp;
2820 if (!existingNames.contains(ap.av.viewName))
2822 existingNames.add(ap.av.viewName);
2826 return existingNames;
2830 * Explode tabbed views into separate windows.
2833 public void expandViews_actionPerformed(ActionEvent e)
2835 Desktop.explodeViews(this);
2839 * Gather views in separate windows back into a tabbed presentation.
2842 public void gatherViews_actionPerformed(ActionEvent e)
2844 Desktop.instance.gatherViews(this);
2854 public void font_actionPerformed(ActionEvent e)
2856 new FontChooser(alignPanel);
2866 protected void seqLimit_actionPerformed(ActionEvent e)
2868 viewport.setShowJVSuffix(seqLimits.isSelected());
2870 alignPanel.getIdPanel().getIdCanvas()
2871 .setPreferredSize(alignPanel.calculateIdWidth());
2872 alignPanel.paintAlignment(true, false);
2876 public void idRightAlign_actionPerformed(ActionEvent e)
2878 viewport.setRightAlignIds(idRightAlign.isSelected());
2879 alignPanel.paintAlignment(false, false);
2883 public void centreColumnLabels_actionPerformed(ActionEvent e)
2885 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2886 alignPanel.paintAlignment(false, false);
2892 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2895 protected void followHighlight_actionPerformed()
2898 * Set the 'follow' flag on the Viewport (and scroll to position if now
2901 final boolean state = this.followHighlightMenuItem.getState();
2902 viewport.setFollowHighlight(state);
2905 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2916 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2918 viewport.setColourText(colourTextMenuItem.isSelected());
2919 alignPanel.paintAlignment(false, false);
2929 public void wrapMenuItem_actionPerformed(ActionEvent e)
2931 scaleAbove.setVisible(wrapMenuItem.isSelected());
2932 scaleLeft.setVisible(wrapMenuItem.isSelected());
2933 scaleRight.setVisible(wrapMenuItem.isSelected());
2934 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2935 alignPanel.updateLayout();
2939 public void showAllSeqs_actionPerformed(ActionEvent e)
2941 viewport.showAllHiddenSeqs();
2945 public void showAllColumns_actionPerformed(ActionEvent e)
2947 viewport.showAllHiddenColumns();
2948 alignPanel.paintAlignment(true, true);
2949 viewport.sendSelection();
2953 public void hideSelSequences_actionPerformed(ActionEvent e)
2955 viewport.hideAllSelectedSeqs();
2959 * called by key handler and the hide all/show all menu items
2964 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2967 boolean hide = false;
2968 SequenceGroup sg = viewport.getSelectionGroup();
2969 if (!toggleSeqs && !toggleCols)
2971 // Hide everything by the current selection - this is a hack - we do the
2972 // invert and then hide
2973 // first check that there will be visible columns after the invert.
2974 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2975 && sg.getStartRes() <= sg.getEndRes()))
2977 // now invert the sequence set, if required - empty selection implies
2978 // that no hiding is required.
2981 invertSequenceMenuItem_actionPerformed(null);
2982 sg = viewport.getSelectionGroup();
2986 viewport.expandColSelection(sg, true);
2987 // finally invert the column selection and get the new sequence
2989 invertColSel_actionPerformed(null);
2996 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2998 hideSelSequences_actionPerformed(null);
3001 else if (!(toggleCols && viewport.hasSelectedColumns()))
3003 showAllSeqs_actionPerformed(null);
3009 if (viewport.hasSelectedColumns())
3011 hideSelColumns_actionPerformed(null);
3014 viewport.setSelectionGroup(sg);
3019 showAllColumns_actionPerformed(null);
3028 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3029 * event.ActionEvent)
3032 public void hideAllButSelection_actionPerformed(ActionEvent e)
3034 toggleHiddenRegions(false, false);
3035 viewport.sendSelection();
3042 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3046 public void hideAllSelection_actionPerformed(ActionEvent e)
3048 SequenceGroup sg = viewport.getSelectionGroup();
3049 viewport.expandColSelection(sg, false);
3050 viewport.hideAllSelectedSeqs();
3051 viewport.hideSelectedColumns();
3052 alignPanel.paintAlignment(true, true);
3053 viewport.sendSelection();
3060 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3064 public void showAllhidden_actionPerformed(ActionEvent e)
3066 viewport.showAllHiddenColumns();
3067 viewport.showAllHiddenSeqs();
3068 alignPanel.paintAlignment(true, true);
3069 viewport.sendSelection();
3073 public void hideSelColumns_actionPerformed(ActionEvent e)
3075 viewport.hideSelectedColumns();
3076 alignPanel.paintAlignment(true, true);
3077 viewport.sendSelection();
3081 public void hiddenMarkers_actionPerformed(ActionEvent e)
3083 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3094 protected void scaleAbove_actionPerformed(ActionEvent e)
3096 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3097 // TODO: do we actually need to update overview for scale above change ?
3098 alignPanel.paintAlignment(true, false);
3108 protected void scaleLeft_actionPerformed(ActionEvent e)
3110 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3111 alignPanel.paintAlignment(true, false);
3121 protected void scaleRight_actionPerformed(ActionEvent e)
3123 viewport.setScaleRightWrapped(scaleRight.isSelected());
3124 alignPanel.paintAlignment(true, false);
3134 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3136 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3137 alignPanel.paintAlignment(false, false);
3147 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3149 viewport.setShowText(viewTextMenuItem.isSelected());
3150 alignPanel.paintAlignment(false, false);
3160 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3162 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3163 alignPanel.paintAlignment(false, false);
3166 public FeatureSettings featureSettings;
3169 public FeatureSettingsControllerI getFeatureSettingsUI()
3171 return featureSettings;
3175 public void featureSettings_actionPerformed(ActionEvent e)
3177 if (featureSettings != null)
3179 featureSettings.close();
3180 featureSettings = null;
3182 if (!showSeqFeatures.isSelected())
3184 // make sure features are actually displayed
3185 showSeqFeatures.setSelected(true);
3186 showSeqFeatures_actionPerformed(null);
3188 featureSettings = new FeatureSettings(this);
3192 * Set or clear 'Show Sequence Features'
3198 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3200 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3201 alignPanel.paintAlignment(true, true);
3205 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3206 * the annotations panel as a whole.
3208 * The options to show/hide all annotations should be enabled when the panel
3209 * is shown, and disabled when the panel is hidden.
3214 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3216 final boolean setVisible = annotationPanelMenuItem.isSelected();
3217 viewport.setShowAnnotation(setVisible);
3218 this.showAllSeqAnnotations.setEnabled(setVisible);
3219 this.hideAllSeqAnnotations.setEnabled(setVisible);
3220 this.showAllAlAnnotations.setEnabled(setVisible);
3221 this.hideAllAlAnnotations.setEnabled(setVisible);
3222 alignPanel.updateLayout();
3226 public void alignmentProperties()
3228 JEditorPane editPane = new JEditorPane("text/html", "");
3229 editPane.setEditable(false);
3230 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3233 MessageManager.formatMessage("label.html_content", new Object[]
3234 { contents.toString() }));
3235 JInternalFrame frame = new JInternalFrame();
3236 frame.getContentPane().add(new JScrollPane(editPane));
3238 Desktop.addInternalFrame(frame, MessageManager
3239 .formatMessage("label.alignment_properties", new Object[]
3240 { getTitle() }), 500, 400);
3250 public void overviewMenuItem_actionPerformed(ActionEvent e)
3252 if (alignPanel.overviewPanel != null)
3257 JInternalFrame frame = new JInternalFrame();
3258 final OverviewPanel overview = new OverviewPanel(alignPanel);
3259 frame.setContentPane(overview);
3260 Desktop.addInternalFrame(frame, MessageManager
3261 .formatMessage("label.overview_params", new Object[]
3262 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3265 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3266 frame.addInternalFrameListener(
3267 new javax.swing.event.InternalFrameAdapter()
3270 public void internalFrameClosed(
3271 javax.swing.event.InternalFrameEvent evt)
3274 alignPanel.setOverviewPanel(null);
3278 alignPanel.setOverviewPanel(overview);
3282 public void textColour_actionPerformed()
3284 new TextColourChooser().chooseColour(alignPanel, null);
3288 * public void covariationColour_actionPerformed() {
3290 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3294 public void annotationColour_actionPerformed()
3296 new AnnotationColourChooser(viewport, alignPanel);
3300 public void annotationColumn_actionPerformed(ActionEvent e)
3302 new AnnotationColumnChooser(viewport, alignPanel);
3306 * Action on the user checking or unchecking the option to apply the selected
3307 * colour scheme to all groups. If unchecked, groups may have their own
3308 * independent colour schemes.
3313 public void applyToAllGroups_actionPerformed(boolean selected)
3315 viewport.setColourAppliesToAllGroups(selected);
3319 * Action on user selecting a colour from the colour menu
3322 * the name (not the menu item label!) of the colour scheme
3325 public void changeColour_actionPerformed(String name)
3328 * 'User Defined' opens a panel to configure or load a
3329 * user-defined colour scheme
3331 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3333 new UserDefinedColours(alignPanel);
3338 * otherwise set the chosen colour scheme (or null for 'None')
3340 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3341 viewport.getAlignment(), viewport.getHiddenRepSequences());
3346 * Actions on setting or changing the alignment colour scheme
3351 public void changeColour(ColourSchemeI cs)
3353 // TODO: pull up to controller method
3354 ColourMenuHelper.setColourSelected(colourMenu, cs);
3356 viewport.setGlobalColourScheme(cs);
3358 alignPanel.paintAlignment(true, true);
3362 * Show the PID threshold slider panel
3365 protected void modifyPID_actionPerformed()
3367 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3368 alignPanel.getViewName());
3369 SliderPanel.showPIDSlider();
3373 * Show the Conservation slider panel
3376 protected void modifyConservation_actionPerformed()
3378 SliderPanel.setConservationSlider(alignPanel,
3379 viewport.getResidueShading(), alignPanel.getViewName());
3380 SliderPanel.showConservationSlider();
3384 * Action on selecting or deselecting (Colour) By Conservation
3387 public void conservationMenuItem_actionPerformed(boolean selected)
3389 modifyConservation.setEnabled(selected);
3390 viewport.setConservationSelected(selected);
3391 viewport.getResidueShading().setConservationApplied(selected);
3393 changeColour(viewport.getGlobalColourScheme());
3396 modifyConservation_actionPerformed();
3400 SliderPanel.hideConservationSlider();
3405 * Action on selecting or deselecting (Colour) Above PID Threshold
3408 public void abovePIDThreshold_actionPerformed(boolean selected)
3410 modifyPID.setEnabled(selected);
3411 viewport.setAbovePIDThreshold(selected);
3414 viewport.getResidueShading().setThreshold(0,
3415 viewport.isIgnoreGapsConsensus());
3418 changeColour(viewport.getGlobalColourScheme());
3421 modifyPID_actionPerformed();
3425 SliderPanel.hidePIDSlider();
3436 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3438 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3439 AlignmentSorter.sortByPID(viewport.getAlignment(),
3440 viewport.getAlignment().getSequenceAt(0));
3441 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3442 viewport.getAlignment()));
3443 alignPanel.paintAlignment(true, false);
3453 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3455 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3456 AlignmentSorter.sortByID(viewport.getAlignment());
3458 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3459 alignPanel.paintAlignment(true, false);
3469 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3471 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3472 AlignmentSorter.sortByLength(viewport.getAlignment());
3473 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3474 viewport.getAlignment()));
3475 alignPanel.paintAlignment(true, false);
3485 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3487 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3488 AlignmentSorter.sortByGroup(viewport.getAlignment());
3489 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3490 viewport.getAlignment()));
3492 alignPanel.paintAlignment(true, false);
3502 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3504 new RedundancyPanel(alignPanel, this);
3514 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3516 if ((viewport.getSelectionGroup() == null)
3517 || (viewport.getSelectionGroup().getSize() < 2))
3519 JvOptionPane.showInternalMessageDialog(this,
3520 MessageManager.getString(
3521 "label.you_must_select_least_two_sequences"),
3522 MessageManager.getString("label.invalid_selection"),
3523 JvOptionPane.WARNING_MESSAGE);
3527 JInternalFrame frame = new JInternalFrame();
3528 frame.setContentPane(new PairwiseAlignPanel(viewport));
3529 Desktop.addInternalFrame(frame,
3530 MessageManager.getString("action.pairwise_alignment"), 600,
3536 public void autoCalculate_actionPerformed(ActionEvent e)
3538 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3539 if (viewport.autoCalculateConsensus)
3541 viewport.firePropertyChange("alignment", null,
3542 viewport.getAlignment().getSequences());
3547 public void sortByTreeOption_actionPerformed(ActionEvent e)
3549 viewport.sortByTree = sortByTree.isSelected();
3553 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3555 viewport.followSelection = listenToViewSelections.isSelected();
3559 * Constructs a tree panel and adds it to the desktop
3568 void newTreePanel(TreeModel tree, String treeAlgo,
3569 String substitutionMatrix)
3571 String frameTitle = "";
3574 boolean onSelection = false;
3575 if (viewport.getSelectionGroup() != null
3576 && viewport.getSelectionGroup().getSize() > 0)
3578 SequenceGroup sg = viewport.getSelectionGroup();
3580 /* Decide if the selection is a column region */
3581 for (SequenceI _s : sg.getSequences()) // port this to Archaeopteryx?
3583 if (_s.getLength() < sg.getEndRes())
3585 JvOptionPane.showMessageDialog(Desktop.desktop,
3586 MessageManager.getString(
3587 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3588 MessageManager.getString(
3589 "label.sequences_selection_not_aligned"),
3590 JvOptionPane.WARNING_MESSAGE);
3599 if (viewport.getAlignment().getHeight() < 2)
3605 tp = new TreePanel(alignPanel, tree, treeAlgo, substitutionMatrix);
3606 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3608 frameTitle += " from ";
3610 if (viewport.viewName != null)
3612 frameTitle += viewport.viewName + " of ";
3615 frameTitle += this.title;
3617 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3628 public void addSortByOrderMenuItem(String title,
3629 final AlignmentOrder order)
3631 final JMenuItem item = new JMenuItem(MessageManager
3632 .formatMessage("action.by_title_param", new Object[]
3635 item.addActionListener(new java.awt.event.ActionListener()
3638 public void actionPerformed(ActionEvent e)
3640 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3642 // TODO: JBPNote - have to map order entries to curent SequenceI
3644 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3646 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3647 viewport.getAlignment()));
3649 alignPanel.paintAlignment(true, false);
3655 * Add a new sort by annotation score menu item
3658 * the menu to add the option to
3660 * the label used to retrieve scores for each sequence on the
3663 public void addSortByAnnotScoreMenuItem(JMenu sort,
3664 final String scoreLabel)
3666 final JMenuItem item = new JMenuItem(scoreLabel);
3668 item.addActionListener(new java.awt.event.ActionListener()
3671 public void actionPerformed(ActionEvent e)
3673 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3674 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3675 viewport.getAlignment());// ,viewport.getSelectionGroup());
3676 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3677 viewport.getAlignment()));
3678 alignPanel.paintAlignment(true, false);
3684 * last hash for alignment's annotation array - used to minimise cost of
3687 protected int _annotationScoreVectorHash;
3690 * search the alignment and rebuild the sort by annotation score submenu the
3691 * last alignment annotation vector hash is stored to minimize cost of
3692 * rebuilding in subsequence calls.
3696 public void buildSortByAnnotationScoresMenu()
3698 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3703 if (viewport.getAlignment().getAlignmentAnnotation()
3704 .hashCode() != _annotationScoreVectorHash)
3706 sortByAnnotScore.removeAll();
3707 // almost certainly a quicker way to do this - but we keep it simple
3708 Hashtable scoreSorts = new Hashtable();
3709 AlignmentAnnotation aann[];
3710 for (SequenceI sqa : viewport.getAlignment().getSequences())
3712 aann = sqa.getAnnotation();
3713 for (int i = 0; aann != null && i < aann.length; i++)
3715 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3717 scoreSorts.put(aann[i].label, aann[i].label);
3721 Enumeration labels = scoreSorts.keys();
3722 while (labels.hasMoreElements())
3724 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3725 (String) labels.nextElement());
3727 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3730 _annotationScoreVectorHash = viewport.getAlignment()
3731 .getAlignmentAnnotation().hashCode();
3736 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3737 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3738 * call. Listeners are added to remove the menu item when the treePanel is
3739 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3743 public void buildTreeSortMenu()
3745 sortByTreeMenu.removeAll();
3747 List<Component> comps = PaintRefresher.components
3748 .get(viewport.getSequenceSetId());
3749 List<TreePanel> treePanels = new ArrayList<>();
3750 for (Component comp : comps)
3752 if (comp instanceof TreePanel)
3754 treePanels.add((TreePanel) comp);
3758 if (treePanels.size() < 1)
3760 sortByTreeMenu.setVisible(false);
3764 sortByTreeMenu.setVisible(true);
3766 for (final TreePanel tp : treePanels)
3768 final JMenuItem item = new JMenuItem(tp.getTitle());
3769 item.addActionListener(new java.awt.event.ActionListener()
3772 public void actionPerformed(ActionEvent e)
3775 tp.sortByTree_actionPerformed();
3776 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3781 sortByTreeMenu.add(item);
3785 public boolean sortBy(AlignmentOrder alorder, String undoname)
3787 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3788 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3789 if (undoname != null)
3791 addHistoryItem(new OrderCommand(undoname, oldOrder,
3792 viewport.getAlignment()));
3794 alignPanel.paintAlignment(true, false);
3799 * Work out whether the whole set of sequences or just the selected set will
3800 * be submitted for multiple alignment.
3803 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3805 // Now, check we have enough sequences
3806 AlignmentView msa = null;
3808 if ((viewport.getSelectionGroup() != null)
3809 && (viewport.getSelectionGroup().getSize() > 1))
3811 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3812 // some common interface!
3814 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3815 * SequenceI[sz = seqs.getSize(false)];
3817 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3818 * seqs.getSequenceAt(i); }
3820 msa = viewport.getAlignmentView(true);
3822 else if (viewport.getSelectionGroup() != null
3823 && viewport.getSelectionGroup().getSize() == 1)
3825 int option = JvOptionPane.showConfirmDialog(this,
3826 MessageManager.getString("warn.oneseq_msainput_selection"),
3827 MessageManager.getString("label.invalid_selection"),
3828 JvOptionPane.OK_CANCEL_OPTION);
3829 if (option == JvOptionPane.OK_OPTION)
3831 msa = viewport.getAlignmentView(false);
3836 msa = viewport.getAlignmentView(false);
3842 * Decides what is submitted to a secondary structure prediction service: the
3843 * first sequence in the alignment, or in the current selection, or, if the
3844 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3845 * region or the whole alignment. (where the first sequence in the set is the
3846 * one that the prediction will be for).
3848 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3850 AlignmentView seqs = null;
3852 if ((viewport.getSelectionGroup() != null)
3853 && (viewport.getSelectionGroup().getSize() > 0))
3855 seqs = viewport.getAlignmentView(true);
3859 seqs = viewport.getAlignmentView(false);
3861 // limit sequences - JBPNote in future - could spawn multiple prediction
3863 // TODO: viewport.getAlignment().isAligned is a global state - the local
3864 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3865 if (!viewport.getAlignment().isAligned(false))
3867 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3868 // TODO: if seqs.getSequences().length>1 then should really have warned
3882 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3884 // Pick the tree file
3885 JalviewFileChooser chooser = new JalviewFileChooser(
3886 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3887 chooser.setFileView(new JalviewFileView());
3888 chooser.setDialogTitle(
3889 MessageManager.getString("label.select_newick_like_tree_file")); // modify
3890 chooser.setToolTipText(
3891 MessageManager.getString("label.load_tree_file"));
3892 for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter.values())
3894 chooser.setFileFilter(treeFormat.getTreeFilter());
3897 int value = chooser.showOpenDialog(null);
3899 if (value == JalviewFileChooser.APPROVE_OPTION)
3901 String filePath = chooser.getSelectedFile().getPath();
3902 Cache.setProperty("LAST_DIRECTORY", filePath);
3904 NewickFile fin = null;
3907 ExternalTreeParserI<?> treeParser = new TreeParser(
3909 treeParser.loadTree(viewport);
3913 fin = new NewickFile(filePath, DataSourceType.FILE);
3914 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3915 } catch (Exception ex)
3917 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3918 MessageManager.getString("label.problem_reading_tree_file"),
3919 JvOptionPane.WARNING_MESSAGE);
3920 ex.printStackTrace();
3922 if (fin != null && fin.hasWarningMessage())
3924 JvOptionPane.showMessageDialog(Desktop.desktop,
3925 fin.getWarningMessage(),
3927 .getString("label.possible_problem_with_tree_file"),
3928 JvOptionPane.WARNING_MESSAGE);
3933 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3935 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3938 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3939 int h, int x, int y)
3941 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3945 * Add a treeviewer for the tree extracted from a Newick file object to the
3946 * current alignment view
3953 * Associated alignment input data (or null)
3962 * @return TreePanel handle
3964 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3965 AlignmentView input, int w, int h, int x, int y)
3967 TreePanel tp = null;
3973 if (nf.getTree() != null)
3975 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3981 tp.setLocation(x, y);
3984 Desktop.addInternalFrame(tp, treeTitle, w, h);
3986 } catch (Exception ex)
3988 ex.printStackTrace();
3994 private boolean buildingMenu = false;
3997 * Generates menu items and listener event actions for web service clients
4000 public void BuildWebServiceMenu()
4002 while (buildingMenu)
4006 System.err.println("Waiting for building menu to finish.");
4008 } catch (Exception e)
4012 final AlignFrame me = this;
4013 buildingMenu = true;
4014 new Thread(new Runnable()
4019 final List<JMenuItem> legacyItems = new ArrayList<>();
4022 // System.err.println("Building ws menu again "
4023 // + Thread.currentThread());
4024 // TODO: add support for context dependent disabling of services based
4026 // alignment and current selection
4027 // TODO: add additional serviceHandle parameter to specify abstract
4029 // class independently of AbstractName
4030 // TODO: add in rediscovery GUI function to restart discoverer
4031 // TODO: group services by location as well as function and/or
4033 // object broker mechanism.
4034 final Vector<JMenu> wsmenu = new Vector<>();
4035 final IProgressIndicator af = me;
4038 * do not i18n these strings - they are hard-coded in class
4039 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4040 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4042 final JMenu msawsmenu = new JMenu("Alignment");
4043 final JMenu secstrmenu = new JMenu(
4044 "Secondary Structure Prediction");
4045 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4046 final JMenu analymenu = new JMenu("Analysis");
4047 final JMenu dismenu = new JMenu("Protein Disorder");
4048 final JMenu phylogenmenu = new JMenu("Phylogenetic inference");
4050 // JAL-940 - only show secondary structure prediction services from
4051 // the legacy server
4052 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4054 Discoverer.services != null && (Discoverer.services.size() > 0))
4056 // TODO: refactor to allow list of AbstractName/Handler bindings to
4058 // stored or retrieved from elsewhere
4059 // No MSAWS used any more:
4060 // Vector msaws = null; // (Vector)
4061 // Discoverer.services.get("MsaWS");
4062 Vector secstrpr = (Vector) Discoverer.services
4064 if (secstrpr != null)
4066 // Add any secondary structure prediction services
4067 for (int i = 0, j = secstrpr.size(); i < j; i++)
4069 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4071 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4072 .getServiceClient(sh);
4073 int p = secstrmenu.getItemCount();
4074 impl.attachWSMenuEntry(secstrmenu, me);
4075 int q = secstrmenu.getItemCount();
4076 for (int litm = p; litm < q; litm++)
4078 legacyItems.add(secstrmenu.getItem(litm));
4084 // Add all submenus in the order they should appear on the web
4086 wsmenu.add(msawsmenu);
4087 wsmenu.add(secstrmenu);
4088 wsmenu.add(dismenu);
4089 wsmenu.add(analymenu);
4090 wsmenu.add(phylogenmenu);
4091 // No search services yet
4092 // wsmenu.add(seqsrchmenu);
4094 javax.swing.SwingUtilities.invokeLater(new Runnable()
4101 webService.removeAll();
4102 // first, add discovered services onto the webservices menu
4103 if (wsmenu.size() > 0)
4105 for (int i = 0, j = wsmenu.size(); i < j; i++)
4107 webService.add(wsmenu.get(i));
4112 webService.add(me.webServiceNoServices);
4114 // TODO: move into separate menu builder class.
4115 boolean new_sspred = false;
4116 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4118 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4119 if (jws2servs != null)
4121 if (jws2servs.hasServices())
4123 jws2servs.attachWSMenuEntry(webService, me);
4124 for (Jws2Instance sv : jws2servs.getServices())
4126 if (sv.description.toLowerCase().contains("jpred"))
4128 for (JMenuItem jmi : legacyItems)
4130 jmi.setVisible(false);
4136 if (jws2servs.isRunning())
4138 JMenuItem tm = new JMenuItem(
4139 "Still discovering JABA Services");
4140 tm.setEnabled(false);
4145 build_urlServiceMenu(me.webService);
4146 build_fetchdbmenu(webService);
4147 for (JMenu item : wsmenu)
4149 if (item.getItemCount() == 0)
4151 item.setEnabled(false);
4155 item.setEnabled(true);
4158 } catch (Exception e)
4161 "Exception during web service menu building process.",
4166 } catch (Exception e)
4169 buildingMenu = false;
4171 }, "BuildWebServiceThread").start();
4176 * construct any groupURL type service menu entries.
4180 private void build_urlServiceMenu(JMenu webService)
4182 // TODO: remove this code when 2.7 is released
4183 // DEBUG - alignmentView
4185 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4186 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4188 * @Override public void actionPerformed(ActionEvent e) {
4189 * jalview.datamodel.AlignmentView
4190 * .testSelectionViews(af.viewport.getAlignment(),
4191 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4193 * }); webService.add(testAlView);
4195 // TODO: refactor to RestClient discoverer and merge menu entries for
4196 // rest-style services with other types of analysis/calculation service
4197 // SHmmr test client - still being implemented.
4198 // DEBUG - alignmentView
4200 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4203 client.attachWSMenuEntry(
4204 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4210 * Searches the alignment sequences for xRefs and builds the Show
4211 * Cross-References menu (formerly called Show Products), with database
4212 * sources for which cross-references are found (protein sources for a
4213 * nucleotide alignment and vice versa)
4215 * @return true if Show Cross-references menu should be enabled
4217 public boolean canShowProducts()
4219 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4220 AlignmentI dataset = viewport.getAlignment().getDataset();
4222 showProducts.removeAll();
4223 final boolean dna = viewport.getAlignment().isNucleotide();
4225 if (seqs == null || seqs.length == 0)
4227 // nothing to see here.
4231 boolean showp = false;
4234 List<String> ptypes = new CrossRef(seqs, dataset)
4235 .findXrefSourcesForSequences(dna);
4237 for (final String source : ptypes)
4240 final AlignFrame af = this;
4241 JMenuItem xtype = new JMenuItem(source);
4242 xtype.addActionListener(new ActionListener()
4245 public void actionPerformed(ActionEvent e)
4247 showProductsFor(af.viewport.getSequenceSelection(), dna,
4251 showProducts.add(xtype);
4253 showProducts.setVisible(showp);
4254 showProducts.setEnabled(showp);
4255 } catch (Exception e)
4258 "canShowProducts threw an exception - please report to help@jalview.org",
4266 * Finds and displays cross-references for the selected sequences (protein
4267 * products for nucleotide sequences, dna coding sequences for peptides).
4270 * the sequences to show cross-references for
4272 * true if from a nucleotide alignment (so showing proteins)
4274 * the database to show cross-references for
4276 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4277 final String source)
4279 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this),
4280 "CrossReferencesThread")
4285 * Construct and display a new frame containing the translation of this
4286 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4289 public void showTranslation_actionPerformed(ActionEvent e)
4291 AlignmentI al = null;
4294 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4296 al = dna.translateCdna();
4297 } catch (Exception ex)
4299 jalview.bin.Cache.log.error(
4300 "Exception during translation. Please report this !", ex);
4301 final String msg = MessageManager.getString(
4302 "label.error_when_translating_sequences_submit_bug_report");
4303 final String errorTitle = MessageManager
4304 .getString("label.implementation_error")
4305 + MessageManager.getString("label.translation_failed");
4306 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4307 JvOptionPane.ERROR_MESSAGE);
4310 if (al == null || al.getHeight() == 0)
4312 final String msg = MessageManager.getString(
4313 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4314 final String errorTitle = MessageManager
4315 .getString("label.translation_failed");
4316 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4317 JvOptionPane.WARNING_MESSAGE);
4321 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4322 af.setFileFormat(this.currentFileFormat);
4323 final String newTitle = MessageManager
4324 .formatMessage("label.translation_of_params", new Object[]
4325 { this.getTitle() });
4326 af.setTitle(newTitle);
4327 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4329 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4330 viewport.openSplitFrame(af, new Alignment(seqs));
4334 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4341 * Set the file format
4345 public void setFileFormat(FileFormatI format)
4347 this.currentFileFormat = format;
4351 * Try to load a features file onto the alignment.
4354 * contents or path to retrieve file
4356 * access mode of file (see jalview.io.AlignFile)
4357 * @return true if features file was parsed correctly.
4359 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4361 return avc.parseFeaturesFile(file, sourceType,
4362 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4367 public void refreshFeatureUI(boolean enableIfNecessary)
4369 // note - currently this is only still here rather than in the controller
4370 // because of the featureSettings hard reference that is yet to be
4372 if (enableIfNecessary)
4374 viewport.setShowSequenceFeatures(true);
4375 showSeqFeatures.setSelected(true);
4381 public void dragEnter(DropTargetDragEvent evt)
4386 public void dragExit(DropTargetEvent evt)
4391 public void dragOver(DropTargetDragEvent evt)
4396 public void dropActionChanged(DropTargetDragEvent evt)
4401 public void drop(DropTargetDropEvent evt)
4403 // JAL-1552 - acceptDrop required before getTransferable call for
4404 // Java's Transferable for native dnd
4405 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4406 Transferable t = evt.getTransferable();
4407 final AlignFrame thisaf = this;
4408 final List<String> files = new ArrayList<>();
4409 List<DataSourceType> protocols = new ArrayList<>();
4413 Desktop.transferFromDropTarget(files, protocols, evt, t);
4414 } catch (Exception e)
4416 e.printStackTrace();
4420 new Thread(new Runnable()
4427 // check to see if any of these files have names matching sequences
4430 SequenceIdMatcher idm = new SequenceIdMatcher(
4431 viewport.getAlignment().getSequencesArray());
4433 * Object[] { String,SequenceI}
4435 ArrayList<Object[]> filesmatched = new ArrayList<>();
4436 ArrayList<String> filesnotmatched = new ArrayList<>();
4437 for (int i = 0; i < files.size(); i++)
4439 String file = files.get(i).toString();
4441 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4442 if (protocol == DataSourceType.FILE)
4444 File fl = new File(file);
4445 pdbfn = fl.getName();
4447 else if (protocol == DataSourceType.URL)
4449 URL url = new URL(file);
4450 pdbfn = url.getFile();
4452 if (pdbfn.length() > 0)
4454 // attempt to find a match in the alignment
4455 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4456 int l = 0, c = pdbfn.indexOf(".");
4457 while (mtch == null && c != -1)
4462 } while ((c = pdbfn.indexOf(".", l)) > l);
4465 pdbfn = pdbfn.substring(0, l);
4467 mtch = idm.findAllIdMatches(pdbfn);
4471 FileFormatI type = null;
4474 type = new IdentifyFile().identify(file, protocol);
4475 } catch (Exception ex)
4479 if (type != null && type.isStructureFile())
4481 filesmatched.add(new Object[] { file, protocol, mtch });
4485 // File wasn't named like one of the sequences or wasn't a PDB
4487 filesnotmatched.add(file);
4491 if (filesmatched.size() > 0)
4493 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4494 || JvOptionPane.showConfirmDialog(thisaf,
4495 MessageManager.formatMessage(
4496 "label.automatically_associate_structure_files_with_sequences_same_name",
4498 { Integer.valueOf(filesmatched.size())
4500 MessageManager.getString(
4501 "label.automatically_associate_structure_files_by_name"),
4502 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4505 for (Object[] fm : filesmatched)
4507 // try and associate
4508 // TODO: may want to set a standard ID naming formalism for
4509 // associating PDB files which have no IDs.
4510 for (SequenceI toassoc : (SequenceI[]) fm[2])
4512 PDBEntry pe = new AssociatePdbFileWithSeq()
4513 .associatePdbWithSeq((String) fm[0],
4514 (DataSourceType) fm[1], toassoc, false,
4518 System.err.println("Associated file : "
4519 + ((String) fm[0]) + " with "
4520 + toassoc.getDisplayId(true));
4524 // TODO: do we need to update overview ? only if features are
4526 alignPanel.paintAlignment(true, false);
4530 if (filesnotmatched.size() > 0)
4532 if (assocfiles > 0 && (Cache.getDefault(
4533 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4534 || JvOptionPane.showConfirmDialog(thisaf,
4535 "<html>" + MessageManager.formatMessage(
4536 "label.ignore_unmatched_dropped_files_info",
4539 filesnotmatched.size())
4542 MessageManager.getString(
4543 "label.ignore_unmatched_dropped_files"),
4544 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4548 for (String fn : filesnotmatched)
4550 loadJalviewDataFile(fn, null, null, null);
4554 } catch (Exception ex)
4556 ex.printStackTrace();
4559 }, "DropFileThread").start();
4564 * Attempt to load a "dropped" file or URL string, by testing in turn for
4566 * <li>an Annotation file</li>
4567 * <li>a JNet file</li>
4568 * <li>a features file</li>
4569 * <li>else try to interpret as an alignment file</li>
4573 * either a filename or a URL string.
4575 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4576 FileFormatI format, SequenceI assocSeq)
4580 if (sourceType == null)
4582 sourceType = FormatAdapter.checkProtocol(file);
4584 // if the file isn't identified, or not positively identified as some
4585 // other filetype (PFAM is default unidentified alignment file type) then
4586 // try to parse as annotation.
4587 boolean isAnnotation = (format == null
4588 || FileFormat.Pfam.equals(format))
4589 ? new AnnotationFile().annotateAlignmentView(viewport,
4595 // first see if its a T-COFFEE score file
4596 TCoffeeScoreFile tcf = null;
4599 tcf = new TCoffeeScoreFile(file, sourceType);
4602 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4606 new TCoffeeColourScheme(viewport.getAlignment()));
4607 isAnnotation = true;
4608 statusBar.setText(MessageManager.getString(
4609 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4613 // some problem - if no warning its probable that the ID matching
4614 // process didn't work
4615 JvOptionPane.showMessageDialog(Desktop.desktop,
4616 tcf.getWarningMessage() == null
4617 ? MessageManager.getString(
4618 "label.check_file_matches_sequence_ids_alignment")
4619 : tcf.getWarningMessage(),
4620 MessageManager.getString(
4621 "label.problem_reading_tcoffee_score_file"),
4622 JvOptionPane.WARNING_MESSAGE);
4629 } catch (Exception x)
4632 "Exception when processing data source as T-COFFEE score file",
4638 // try to see if its a JNet 'concise' style annotation file *before*
4640 // try to parse it as a features file
4643 format = new IdentifyFile().identify(file, sourceType);
4645 if (FileFormat.ScoreMatrix == format)
4647 ScoreMatrixFile sm = new ScoreMatrixFile(
4648 new FileParse(file, sourceType));
4650 // todo: i18n this message
4651 statusBar.setText(MessageManager.formatMessage(
4652 "label.successfully_loaded_matrix",
4653 sm.getMatrixName()));
4655 else if (FileFormat.Jnet.equals(format))
4657 JPredFile predictions = new JPredFile(file, sourceType);
4658 new JnetAnnotationMaker();
4659 JnetAnnotationMaker.add_annotation(predictions,
4660 viewport.getAlignment(), 0, false);
4661 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4662 viewport.getAlignment().setSeqrep(repseq);
4663 HiddenColumns cs = new HiddenColumns();
4664 cs.hideInsertionsFor(repseq);
4665 viewport.getAlignment().setHiddenColumns(cs);
4666 isAnnotation = true;
4668 // else if (IdentifyFile.FeaturesFile.equals(format))
4669 else if (FileFormat.Features.equals(format))
4671 if (parseFeaturesFile(file, sourceType))
4673 alignPanel.paintAlignment(true, true);
4678 new FileLoader().LoadFile(viewport, file, sourceType, format);
4685 alignPanel.adjustAnnotationHeight();
4686 viewport.updateSequenceIdColours();
4687 buildSortByAnnotationScoresMenu();
4688 alignPanel.paintAlignment(true, true);
4690 } catch (Exception ex)
4692 ex.printStackTrace();
4693 } catch (OutOfMemoryError oom)
4698 } catch (Exception x)
4703 + (sourceType != null
4704 ? (sourceType == DataSourceType.PASTE
4706 : "using " + sourceType + " from "
4710 ? "(parsing as '" + format + "' file)"
4712 oom, Desktop.desktop);
4717 * Method invoked by the ChangeListener on the tabbed pane, in other words
4718 * when a different tabbed pane is selected by the user or programmatically.
4721 public void tabSelectionChanged(int index)
4725 alignPanel = alignPanels.get(index);
4726 viewport = alignPanel.av;
4727 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4728 setMenusFromViewport(viewport);
4732 * 'focus' any colour slider that is open to the selected viewport
4734 if (viewport.getConservationSelected())
4736 SliderPanel.setConservationSlider(alignPanel,
4737 viewport.getResidueShading(), alignPanel.getViewName());
4741 SliderPanel.hideConservationSlider();
4743 if (viewport.getAbovePIDThreshold())
4745 SliderPanel.setPIDSliderSource(alignPanel,
4746 viewport.getResidueShading(), alignPanel.getViewName());
4750 SliderPanel.hidePIDSlider();
4754 * If there is a frame linked to this one in a SplitPane, switch it to the
4755 * same view tab index. No infinite recursion of calls should happen, since
4756 * tabSelectionChanged() should not get invoked on setting the selected
4757 * index to an unchanged value. Guard against setting an invalid index
4758 * before the new view peer tab has been created.
4760 final AlignViewportI peer = viewport.getCodingComplement();
4763 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4764 .getAlignPanel().alignFrame;
4765 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4767 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4773 * On right mouse click on view tab, prompt for and set new view name.
4776 public void tabbedPane_mousePressed(MouseEvent e)
4778 if (e.isPopupTrigger())
4780 String msg = MessageManager.getString("label.enter_view_name");
4781 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4782 JvOptionPane.QUESTION_MESSAGE);
4786 viewport.viewName = reply;
4787 // TODO warn if reply is in getExistingViewNames()?
4788 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4793 public AlignViewport getCurrentView()
4799 * Open the dialog for regex description parsing.
4802 protected void extractScores_actionPerformed(ActionEvent e)
4804 ParseProperties pp = new jalview.analysis.ParseProperties(
4805 viewport.getAlignment());
4806 // TODO: verify regex and introduce GUI dialog for version 2.5
4807 // if (pp.getScoresFromDescription("col", "score column ",
4808 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4810 if (pp.getScoresFromDescription("description column",
4811 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4813 buildSortByAnnotationScoresMenu();
4821 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4825 protected void showDbRefs_actionPerformed(ActionEvent e)
4827 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4833 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4837 protected void showNpFeats_actionPerformed(ActionEvent e)
4839 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4843 * find the viewport amongst the tabs in this alignment frame and close that
4848 public boolean closeView(AlignViewportI av)
4852 this.closeMenuItem_actionPerformed(false);
4855 Component[] comp = tabbedPane.getComponents();
4856 for (int i = 0; comp != null && i < comp.length; i++)
4858 if (comp[i] instanceof AlignmentPanel)
4860 if (((AlignmentPanel) comp[i]).av == av)
4863 closeView((AlignmentPanel) comp[i]);
4871 protected void build_fetchdbmenu(JMenu webService)
4873 // Temporary hack - DBRef Fetcher always top level ws entry.
4874 // TODO We probably want to store a sequence database checklist in
4875 // preferences and have checkboxes.. rather than individual sources selected
4877 final JMenu rfetch = new JMenu(
4878 MessageManager.getString("action.fetch_db_references"));
4879 rfetch.setToolTipText(MessageManager.getString(
4880 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4881 webService.add(rfetch);
4883 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4884 MessageManager.getString("option.trim_retrieved_seqs"));
4885 trimrs.setToolTipText(
4886 MessageManager.getString("label.trim_retrieved_sequences"));
4887 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4888 trimrs.addActionListener(new ActionListener()
4891 public void actionPerformed(ActionEvent e)
4893 trimrs.setSelected(trimrs.isSelected());
4894 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4895 Boolean.valueOf(trimrs.isSelected()).toString());
4899 JMenuItem fetchr = new JMenuItem(
4900 MessageManager.getString("label.standard_databases"));
4901 fetchr.setToolTipText(
4902 MessageManager.getString("label.fetch_embl_uniprot"));
4903 fetchr.addActionListener(new ActionListener()
4907 public void actionPerformed(ActionEvent e)
4909 new Thread(new Runnable()
4914 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4915 .getAlignment().isNucleotide();
4916 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4917 alignPanel.av.getSequenceSelection(),
4918 alignPanel.alignFrame, null,
4919 alignPanel.alignFrame.featureSettings, isNucleotide);
4920 dbRefFetcher.addListener(new FetchFinishedListenerI()
4923 public void finished()
4925 AlignFrame.this.setMenusForViewport();
4928 dbRefFetcher.fetchDBRefs(false);
4930 }, "BuildFetchDBMenuThread").start();
4936 final AlignFrame me = this;
4937 new Thread(new Runnable()
4942 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4943 .getSequenceFetcherSingleton(me);
4944 javax.swing.SwingUtilities.invokeLater(new Runnable()
4949 String[] dbclasses = sf.getOrderedSupportedSources();
4950 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4951 // jalview.util.QuickSort.sort(otherdb, otherdb);
4952 List<DbSourceProxy> otherdb;
4953 JMenu dfetch = new JMenu();
4954 JMenu ifetch = new JMenu();
4955 JMenuItem fetchr = null;
4956 int comp = 0, icomp = 0, mcomp = 15;
4957 String mname = null;
4959 for (String dbclass : dbclasses)
4961 otherdb = sf.getSourceProxy(dbclass);
4962 // add a single entry for this class, or submenu allowing 'fetch
4964 if (otherdb == null || otherdb.size() < 1)
4968 // List<DbSourceProxy> dbs=otherdb;
4969 // otherdb=new ArrayList<DbSourceProxy>();
4970 // for (DbSourceProxy db:dbs)
4972 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4976 mname = "From " + dbclass;
4978 if (otherdb.size() == 1)
4980 final DbSourceProxy[] dassource = otherdb
4981 .toArray(new DbSourceProxy[0]);
4982 DbSourceProxy src = otherdb.get(0);
4983 fetchr = new JMenuItem(src.getDbSource());
4984 fetchr.addActionListener(new ActionListener()
4988 public void actionPerformed(ActionEvent e)
4990 new Thread(new Runnable()
4996 boolean isNucleotide = alignPanel.alignFrame
4997 .getViewport().getAlignment()
4999 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5000 alignPanel.av.getSequenceSelection(),
5001 alignPanel.alignFrame, dassource,
5002 alignPanel.alignFrame.featureSettings,
5005 .addListener(new FetchFinishedListenerI()
5008 public void finished()
5010 AlignFrame.this.setMenusForViewport();
5013 dbRefFetcher.fetchDBRefs(false);
5019 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5020 MessageManager.formatMessage(
5021 "label.fetch_retrieve_from", new Object[]
5022 { src.getDbName() })));
5028 final DbSourceProxy[] dassource = otherdb
5029 .toArray(new DbSourceProxy[0]);
5031 DbSourceProxy src = otherdb.get(0);
5032 fetchr = new JMenuItem(MessageManager
5033 .formatMessage("label.fetch_all_param", new Object[]
5034 { src.getDbSource() }));
5035 fetchr.addActionListener(new ActionListener()
5038 public void actionPerformed(ActionEvent e)
5040 new Thread(new Runnable()
5046 boolean isNucleotide = alignPanel.alignFrame
5047 .getViewport().getAlignment()
5049 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5050 alignPanel.av.getSequenceSelection(),
5051 alignPanel.alignFrame, dassource,
5052 alignPanel.alignFrame.featureSettings,
5055 .addListener(new FetchFinishedListenerI()
5058 public void finished()
5060 AlignFrame.this.setMenusForViewport();
5063 dbRefFetcher.fetchDBRefs(false);
5069 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5070 MessageManager.formatMessage(
5071 "label.fetch_retrieve_from_all_sources",
5073 { Integer.valueOf(otherdb.size())
5075 src.getDbSource(), src.getDbName() })));
5078 // and then build the rest of the individual menus
5079 ifetch = new JMenu(MessageManager.formatMessage(
5080 "label.source_from_db_source", new Object[]
5081 { src.getDbSource() }));
5083 String imname = null;
5085 for (DbSourceProxy sproxy : otherdb)
5087 String dbname = sproxy.getDbName();
5088 String sname = dbname.length() > 5
5089 ? dbname.substring(0, 5) + "..."
5091 String msname = dbname.length() > 10
5092 ? dbname.substring(0, 10) + "..."
5096 imname = MessageManager
5097 .formatMessage("label.from_msname", new Object[]
5100 fetchr = new JMenuItem(msname);
5101 final DbSourceProxy[] dassrc = { sproxy };
5102 fetchr.addActionListener(new ActionListener()
5106 public void actionPerformed(ActionEvent e)
5108 new Thread(new Runnable()
5114 boolean isNucleotide = alignPanel.alignFrame
5115 .getViewport().getAlignment()
5117 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5118 alignPanel.av.getSequenceSelection(),
5119 alignPanel.alignFrame, dassrc,
5120 alignPanel.alignFrame.featureSettings,
5123 .addListener(new FetchFinishedListenerI()
5126 public void finished()
5128 AlignFrame.this.setMenusForViewport();
5131 dbRefFetcher.fetchDBRefs(false);
5137 fetchr.setToolTipText(
5138 "<html>" + MessageManager.formatMessage(
5139 "label.fetch_retrieve_from", new Object[]
5143 if (++icomp >= mcomp || i == (otherdb.size()))
5145 ifetch.setText(MessageManager.formatMessage(
5146 "label.source_to_target", imname, sname));
5148 ifetch = new JMenu();
5156 if (comp >= mcomp || dbi >= (dbclasses.length))
5158 dfetch.setText(MessageManager.formatMessage(
5159 "label.source_to_target", mname, dbclass));
5161 dfetch = new JMenu();
5174 * Left justify the whole alignment.
5177 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5179 AlignmentI al = viewport.getAlignment();
5181 viewport.firePropertyChange("alignment", null, al);
5185 * Right justify the whole alignment.
5188 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5190 AlignmentI al = viewport.getAlignment();
5192 viewport.firePropertyChange("alignment", null, al);
5196 public void setShowSeqFeatures(boolean b)
5198 showSeqFeatures.setSelected(b);
5199 viewport.setShowSequenceFeatures(b);
5206 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5207 * awt.event.ActionEvent)
5210 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5212 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5213 alignPanel.paintAlignment(false, false);
5220 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5224 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5226 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5227 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5235 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5236 * .event.ActionEvent)
5239 protected void showGroupConservation_actionPerformed(ActionEvent e)
5241 viewport.setShowGroupConservation(showGroupConservation.getState());
5242 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5249 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5250 * .event.ActionEvent)
5253 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5255 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5256 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5263 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5264 * .event.ActionEvent)
5267 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5269 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5270 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5274 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5276 showSequenceLogo.setState(true);
5277 viewport.setShowSequenceLogo(true);
5278 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5279 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5283 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5285 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5292 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5293 * .event.ActionEvent)
5296 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5298 if (avc.makeGroupsFromSelection())
5300 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5301 alignPanel.updateAnnotation();
5302 alignPanel.paintAlignment(true, true);
5306 public void clearAlignmentSeqRep()
5308 // TODO refactor alignmentseqrep to controller
5309 if (viewport.getAlignment().hasSeqrep())
5311 viewport.getAlignment().setSeqrep(null);
5312 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5313 alignPanel.updateAnnotation();
5314 alignPanel.paintAlignment(true, true);
5319 protected void createGroup_actionPerformed(ActionEvent e)
5321 if (avc.createGroup())
5323 alignPanel.alignmentChanged();
5328 protected void unGroup_actionPerformed(ActionEvent e)
5332 alignPanel.alignmentChanged();
5337 * make the given alignmentPanel the currently selected tab
5339 * @param alignmentPanel
5341 public void setDisplayedView(AlignmentPanel alignmentPanel)
5343 if (!viewport.getSequenceSetId()
5344 .equals(alignmentPanel.av.getSequenceSetId()))
5346 throw new Error(MessageManager.getString(
5347 "error.implementation_error_cannot_show_view_alignment_frame"));
5349 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5350 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5352 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5357 * Action on selection of menu options to Show or Hide annotations.
5360 * @param forSequences
5361 * update sequence-related annotations
5362 * @param forAlignment
5363 * update non-sequence-related annotations
5366 protected void setAnnotationsVisibility(boolean visible,
5367 boolean forSequences, boolean forAlignment)
5369 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5370 .getAlignmentAnnotation();
5375 for (AlignmentAnnotation aa : anns)
5378 * don't display non-positional annotations on an alignment
5380 if (aa.annotations == null)
5384 boolean apply = (aa.sequenceRef == null && forAlignment)
5385 || (aa.sequenceRef != null && forSequences);
5388 aa.visible = visible;
5391 alignPanel.validateAnnotationDimensions(true);
5392 alignPanel.alignmentChanged();
5396 * Store selected annotation sort order for the view and repaint.
5399 protected void sortAnnotations_actionPerformed()
5401 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5403 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5404 alignPanel.paintAlignment(false, false);
5409 * @return alignment panels in this alignment frame
5411 public List<? extends AlignmentViewPanel> getAlignPanels()
5413 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5417 * Open a new alignment window, with the cDNA associated with this (protein)
5418 * alignment, aligned as is the protein.
5420 protected void viewAsCdna_actionPerformed()
5422 // TODO no longer a menu action - refactor as required
5423 final AlignmentI alignment = getViewport().getAlignment();
5424 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5425 if (mappings == null)
5429 List<SequenceI> cdnaSeqs = new ArrayList<>();
5430 for (SequenceI aaSeq : alignment.getSequences())
5432 for (AlignedCodonFrame acf : mappings)
5434 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5438 * There is a cDNA mapping for this protein sequence - add to new
5439 * alignment. It will share the same dataset sequence as other mapped
5440 * cDNA (no new mappings need to be created).
5442 final Sequence newSeq = new Sequence(dnaSeq);
5443 newSeq.setDatasetSequence(dnaSeq);
5444 cdnaSeqs.add(newSeq);
5448 if (cdnaSeqs.size() == 0)
5450 // show a warning dialog no mapped cDNA
5453 AlignmentI cdna = new Alignment(
5454 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5455 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5456 AlignFrame.DEFAULT_HEIGHT);
5457 cdna.alignAs(alignment);
5458 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5460 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5461 AlignFrame.DEFAULT_HEIGHT);
5465 * Set visibility of dna/protein complement view (available when shown in a
5471 protected void showComplement_actionPerformed(boolean show)
5473 SplitContainerI sf = getSplitViewContainer();
5476 sf.setComplementVisible(this, show);
5481 * Generate the reverse (optionally complemented) of the selected sequences,
5482 * and add them to the alignment
5485 protected void showReverse_actionPerformed(boolean complement)
5487 AlignmentI al = null;
5490 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5491 al = dna.reverseCdna(complement);
5492 viewport.addAlignment(al, "");
5493 addHistoryItem(new EditCommand(
5494 MessageManager.getString("label.add_sequences"), Action.PASTE,
5495 al.getSequencesArray(), 0, al.getWidth(),
5496 viewport.getAlignment()));
5497 } catch (Exception ex)
5499 System.err.println(ex.getMessage());
5505 * Try to run a script in the Groovy console, having first ensured that this
5506 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5507 * be targeted at this alignment.
5510 protected void runGroovy_actionPerformed()
5512 Jalview.setCurrentAlignFrame(this);
5513 groovy.ui.Console console = Desktop.getGroovyConsole();
5514 if (console != null)
5518 console.runScript();
5519 } catch (Exception ex)
5521 System.err.println((ex.toString()));
5522 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5523 MessageManager.getString("label.couldnt_run_groovy_script"),
5524 MessageManager.getString("label.groovy_support_failed"),
5525 JvOptionPane.ERROR_MESSAGE);
5530 System.err.println("Can't run Groovy script as console not found");
5535 * Hides columns containing (or not containing) a specified feature, provided
5536 * that would not leave all columns hidden
5538 * @param featureType
5539 * @param columnsContaining
5542 public boolean hideFeatureColumns(String featureType,
5543 boolean columnsContaining)
5545 boolean notForHiding = avc.markColumnsContainingFeatures(
5546 columnsContaining, false, false, featureType);
5549 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5550 false, featureType))
5552 getViewport().hideSelectedColumns();
5560 protected void selectHighlightedColumns_actionPerformed(
5561 ActionEvent actionEvent)
5563 // include key modifier check in case user selects from menu
5564 avc.markHighlightedColumns(
5565 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5566 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5567 | ActionEvent.CTRL_MASK)) != 0);
5571 * Rebuilds the Colour menu, including any user-defined colours which have
5572 * been loaded either on startup or during the session
5574 public void buildColourMenu()
5576 colourMenu.removeAll();
5578 colourMenu.add(applyToAllGroups);
5579 colourMenu.add(textColour);
5580 colourMenu.addSeparator();
5582 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5585 colourMenu.addSeparator();
5586 colourMenu.add(conservationMenuItem);
5587 colourMenu.add(modifyConservation);
5588 colourMenu.add(abovePIDThreshold);
5589 colourMenu.add(modifyPID);
5590 colourMenu.add(annotationColour);
5592 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5593 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5597 * Open a dialog (if not already open) that allows the user to select and
5598 * calculate PCA or Tree analysis
5600 protected void openTreePcaDialog()
5602 if (alignPanel.getCalculationDialog() == null)
5604 new CalculationChooser(AlignFrame.this);
5609 class PrintThread extends Thread
5613 public PrintThread(AlignmentPanel ap)
5618 static PageFormat pf;
5623 PrinterJob printJob = PrinterJob.getPrinterJob();
5627 printJob.setPrintable(ap, pf);
5631 printJob.setPrintable(ap);
5634 if (printJob.printDialog())
5639 } catch (Exception PrintException)
5641 PrintException.printStackTrace();