2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenColumns;
57 import jalview.datamodel.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FileParse;
74 import jalview.io.FormatAdapter;
75 import jalview.io.HtmlSvgOutput;
76 import jalview.io.IdentifyFile;
77 import jalview.io.JPredFile;
78 import jalview.io.JalviewFileChooser;
79 import jalview.io.JalviewFileView;
80 import jalview.io.JnetAnnotationMaker;
81 import jalview.io.NewickFile;
82 import jalview.io.ScoreMatrixFile;
83 import jalview.io.TCoffeeScoreFile;
84 import jalview.io.vcf.VCFLoader;
85 import jalview.jbgui.GAlignFrame;
86 import jalview.schemes.ColourSchemeI;
87 import jalview.schemes.ColourSchemes;
88 import jalview.schemes.ResidueColourScheme;
89 import jalview.schemes.TCoffeeColourScheme;
90 import jalview.util.MessageManager;
91 import jalview.viewmodel.AlignmentViewport;
92 import jalview.viewmodel.ViewportRanges;
93 import jalview.ws.DBRefFetcher;
94 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
95 import jalview.ws.jws1.Discoverer;
96 import jalview.ws.jws2.Jws2Discoverer;
97 import jalview.ws.jws2.jabaws2.Jws2Instance;
98 import jalview.ws.seqfetcher.DbSourceProxy;
100 import java.awt.BorderLayout;
101 import java.awt.Component;
102 import java.awt.Rectangle;
103 import java.awt.Toolkit;
104 import java.awt.datatransfer.Clipboard;
105 import java.awt.datatransfer.DataFlavor;
106 import java.awt.datatransfer.StringSelection;
107 import java.awt.datatransfer.Transferable;
108 import java.awt.dnd.DnDConstants;
109 import java.awt.dnd.DropTargetDragEvent;
110 import java.awt.dnd.DropTargetDropEvent;
111 import java.awt.dnd.DropTargetEvent;
112 import java.awt.dnd.DropTargetListener;
113 import java.awt.event.ActionEvent;
114 import java.awt.event.ActionListener;
115 import java.awt.event.FocusAdapter;
116 import java.awt.event.FocusEvent;
117 import java.awt.event.ItemEvent;
118 import java.awt.event.ItemListener;
119 import java.awt.event.KeyAdapter;
120 import java.awt.event.KeyEvent;
121 import java.awt.event.MouseEvent;
122 import java.awt.print.PageFormat;
123 import java.awt.print.PrinterJob;
124 import java.beans.PropertyChangeEvent;
126 import java.io.FileWriter;
127 import java.io.PrintWriter;
129 import java.util.ArrayList;
130 import java.util.Arrays;
131 import java.util.Deque;
132 import java.util.Enumeration;
133 import java.util.Hashtable;
134 import java.util.List;
135 import java.util.Vector;
137 import javax.swing.JCheckBoxMenuItem;
138 import javax.swing.JEditorPane;
139 import javax.swing.JInternalFrame;
140 import javax.swing.JLayeredPane;
141 import javax.swing.JMenu;
142 import javax.swing.JMenuItem;
143 import javax.swing.JScrollPane;
144 import javax.swing.SwingUtilities;
150 * @version $Revision$
152 public class AlignFrame extends GAlignFrame implements DropTargetListener,
153 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
156 public static final int DEFAULT_WIDTH = 700;
158 public static final int DEFAULT_HEIGHT = 500;
161 * The currently displayed panel (selected tabbed view if more than one)
163 public AlignmentPanel alignPanel;
165 AlignViewport viewport;
167 public AlignViewControllerI avc;
169 List<AlignmentPanel> alignPanels = new ArrayList<>();
172 * Last format used to load or save alignments in this window
174 FileFormatI currentFileFormat = null;
177 * Current filename for this alignment
179 String fileName = null;
182 * Creates a new AlignFrame object with specific width and height.
188 public AlignFrame(AlignmentI al, int width, int height)
190 this(al, null, width, height);
194 * Creates a new AlignFrame object with specific width, height and
200 * @param sequenceSetId
202 public AlignFrame(AlignmentI al, int width, int height,
203 String sequenceSetId)
205 this(al, null, width, height, sequenceSetId);
209 * Creates a new AlignFrame object with specific width, height and
215 * @param sequenceSetId
218 public AlignFrame(AlignmentI al, int width, int height,
219 String sequenceSetId, String viewId)
221 this(al, null, width, height, sequenceSetId, viewId);
225 * new alignment window with hidden columns
229 * @param hiddenColumns
230 * ColumnSelection or null
232 * Width of alignment frame
236 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
239 this(al, hiddenColumns, width, height, null);
243 * Create alignment frame for al with hiddenColumns, a specific width and
244 * height, and specific sequenceId
247 * @param hiddenColumns
250 * @param sequenceSetId
253 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
254 int height, String sequenceSetId)
256 this(al, hiddenColumns, width, height, sequenceSetId, null);
260 * Create alignment frame for al with hiddenColumns, a specific width and
261 * height, and specific sequenceId
264 * @param hiddenColumns
267 * @param sequenceSetId
272 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
273 int height, String sequenceSetId, String viewId)
275 setSize(width, height);
277 if (al.getDataset() == null)
282 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
284 alignPanel = new AlignmentPanel(this, viewport);
286 addAlignmentPanel(alignPanel, true);
290 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
291 HiddenColumns hiddenColumns, int width, int height)
293 setSize(width, height);
295 if (al.getDataset() == null)
300 viewport = new AlignViewport(al, hiddenColumns);
302 if (hiddenSeqs != null && hiddenSeqs.length > 0)
304 viewport.hideSequence(hiddenSeqs);
306 alignPanel = new AlignmentPanel(this, viewport);
307 addAlignmentPanel(alignPanel, true);
312 * Make a new AlignFrame from existing alignmentPanels
319 public AlignFrame(AlignmentPanel ap)
323 addAlignmentPanel(ap, false);
328 * initalise the alignframe from the underlying viewport data and the
333 if (!Jalview.isHeadlessMode())
335 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
338 avc = new jalview.controller.AlignViewController(this, viewport,
340 if (viewport.getAlignmentConservationAnnotation() == null)
342 // BLOSUM62Colour.setEnabled(false);
343 conservationMenuItem.setEnabled(false);
344 modifyConservation.setEnabled(false);
345 // PIDColour.setEnabled(false);
346 // abovePIDThreshold.setEnabled(false);
347 // modifyPID.setEnabled(false);
350 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
353 if (sortby.equals("Id"))
355 sortIDMenuItem_actionPerformed(null);
357 else if (sortby.equals("Pairwise Identity"))
359 sortPairwiseMenuItem_actionPerformed(null);
363 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
365 setMenusFromViewport(viewport);
366 buildSortByAnnotationScoresMenu();
367 calculateTree.addActionListener(new ActionListener()
371 public void actionPerformed(ActionEvent e)
378 if (Desktop.desktop != null)
380 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
381 addServiceListeners();
385 if (viewport.getWrapAlignment())
387 wrapMenuItem_actionPerformed(null);
390 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
392 this.overviewMenuItem_actionPerformed(null);
397 final List<AlignmentPanel> selviews = new ArrayList<>();
398 final List<AlignmentPanel> origview = new ArrayList<>();
399 final String menuLabel = MessageManager
400 .getString("label.copy_format_from");
401 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
402 new ViewSetProvider()
406 public AlignmentPanel[] getAllAlignmentPanels()
409 origview.add(alignPanel);
410 // make an array of all alignment panels except for this one
411 List<AlignmentPanel> aps = new ArrayList<>(
412 Arrays.asList(Desktop.getAlignmentPanels(null)));
413 aps.remove(AlignFrame.this.alignPanel);
414 return aps.toArray(new AlignmentPanel[aps.size()]);
416 }, selviews, new ItemListener()
420 public void itemStateChanged(ItemEvent e)
422 if (origview.size() > 0)
424 final AlignmentPanel ap = origview.get(0);
427 * Copy the ViewStyle of the selected panel to 'this one'.
428 * Don't change value of 'scaleProteinAsCdna' unless copying
431 ViewStyleI vs = selviews.get(0).getAlignViewport()
433 boolean fromSplitFrame = selviews.get(0)
434 .getAlignViewport().getCodingComplement() != null;
437 vs.setScaleProteinAsCdna(ap.getAlignViewport()
438 .getViewStyle().isScaleProteinAsCdna());
440 ap.getAlignViewport().setViewStyle(vs);
443 * Also rescale ViewStyle of SplitFrame complement if there is
444 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
445 * the whole ViewStyle (allow cDNA protein to have different
448 AlignViewportI complement = ap.getAlignViewport()
449 .getCodingComplement();
450 if (complement != null && vs.isScaleProteinAsCdna())
452 AlignFrame af = Desktop.getAlignFrameFor(complement);
453 ((SplitFrame) af.getSplitViewContainer())
455 af.setMenusForViewport();
459 ap.setSelected(true);
460 ap.alignFrame.setMenusForViewport();
465 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
466 .indexOf("devel") > -1
467 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
468 .indexOf("test") > -1)
470 formatMenu.add(vsel);
472 addFocusListener(new FocusAdapter()
475 public void focusGained(FocusEvent e)
477 Jalview.setCurrentAlignFrame(AlignFrame.this);
484 * Change the filename and format for the alignment, and enable the 'reload'
485 * button functionality.
492 public void setFileName(String file, FileFormatI format)
495 setFileFormat(format);
496 reload.setEnabled(true);
500 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
503 void addKeyListener()
505 addKeyListener(new KeyAdapter()
508 public void keyPressed(KeyEvent evt)
510 if (viewport.cursorMode
511 && ((evt.getKeyCode() >= KeyEvent.VK_0
512 && evt.getKeyCode() <= KeyEvent.VK_9)
513 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
514 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
515 && Character.isDigit(evt.getKeyChar()))
517 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
520 switch (evt.getKeyCode())
523 case 27: // escape key
524 deselectAllSequenceMenuItem_actionPerformed(null);
528 case KeyEvent.VK_DOWN:
529 if (evt.isAltDown() || !viewport.cursorMode)
531 moveSelectedSequences(false);
533 if (viewport.cursorMode)
535 alignPanel.getSeqPanel().moveCursor(0, 1);
540 if (evt.isAltDown() || !viewport.cursorMode)
542 moveSelectedSequences(true);
544 if (viewport.cursorMode)
546 alignPanel.getSeqPanel().moveCursor(0, -1);
551 case KeyEvent.VK_LEFT:
552 if (evt.isAltDown() || !viewport.cursorMode)
554 slideSequences(false,
555 alignPanel.getSeqPanel().getKeyboardNo1());
559 alignPanel.getSeqPanel().moveCursor(-1, 0);
564 case KeyEvent.VK_RIGHT:
565 if (evt.isAltDown() || !viewport.cursorMode)
567 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
571 alignPanel.getSeqPanel().moveCursor(1, 0);
575 case KeyEvent.VK_SPACE:
576 if (viewport.cursorMode)
578 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
579 || evt.isShiftDown() || evt.isAltDown());
583 // case KeyEvent.VK_A:
584 // if (viewport.cursorMode)
586 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
587 // //System.out.println("A");
591 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
592 * System.out.println("closing bracket"); } break;
594 case KeyEvent.VK_DELETE:
595 case KeyEvent.VK_BACK_SPACE:
596 if (!viewport.cursorMode)
598 cut_actionPerformed(null);
602 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
603 || evt.isShiftDown() || evt.isAltDown());
609 if (viewport.cursorMode)
611 alignPanel.getSeqPanel().setCursorRow();
615 if (viewport.cursorMode && !evt.isControlDown())
617 alignPanel.getSeqPanel().setCursorColumn();
621 if (viewport.cursorMode)
623 alignPanel.getSeqPanel().setCursorPosition();
627 case KeyEvent.VK_ENTER:
628 case KeyEvent.VK_COMMA:
629 if (viewport.cursorMode)
631 alignPanel.getSeqPanel().setCursorRowAndColumn();
636 if (viewport.cursorMode)
638 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
642 if (viewport.cursorMode)
644 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
649 viewport.cursorMode = !viewport.cursorMode;
650 statusBar.setText(MessageManager
651 .formatMessage("label.keyboard_editing_mode", new String[]
652 { (viewport.cursorMode ? "on" : "off") }));
653 if (viewport.cursorMode)
655 ViewportRanges ranges = viewport.getRanges();
656 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
658 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
661 alignPanel.getSeqPanel().seqCanvas.repaint();
667 Help.showHelpWindow();
668 } catch (Exception ex)
670 ex.printStackTrace();
675 boolean toggleSeqs = !evt.isControlDown();
676 boolean toggleCols = !evt.isShiftDown();
677 toggleHiddenRegions(toggleSeqs, toggleCols);
682 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
683 boolean modifyExisting = true; // always modify, don't clear
684 // evt.isShiftDown();
685 boolean invertHighlighted = evt.isAltDown();
686 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
690 case KeyEvent.VK_PAGE_UP:
691 viewport.getRanges().pageUp();
693 case KeyEvent.VK_PAGE_DOWN:
694 viewport.getRanges().pageDown();
700 public void keyReleased(KeyEvent evt)
702 switch (evt.getKeyCode())
704 case KeyEvent.VK_LEFT:
705 if (evt.isAltDown() || !viewport.cursorMode)
707 viewport.firePropertyChange("alignment", null,
708 viewport.getAlignment().getSequences());
712 case KeyEvent.VK_RIGHT:
713 if (evt.isAltDown() || !viewport.cursorMode)
715 viewport.firePropertyChange("alignment", null,
716 viewport.getAlignment().getSequences());
724 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
726 ap.alignFrame = this;
727 avc = new jalview.controller.AlignViewController(this, viewport,
732 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
734 int aSize = alignPanels.size();
736 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
738 if (aSize == 1 && ap.av.viewName == null)
740 this.getContentPane().add(ap, BorderLayout.CENTER);
746 setInitialTabVisible();
749 expandViews.setEnabled(true);
750 gatherViews.setEnabled(true);
751 tabbedPane.addTab(ap.av.viewName, ap);
753 ap.setVisible(false);
758 if (ap.av.isPadGaps())
760 ap.av.getAlignment().padGaps();
762 ap.av.updateConservation(ap);
763 ap.av.updateConsensus(ap);
764 ap.av.updateStrucConsensus(ap);
768 public void setInitialTabVisible()
770 expandViews.setEnabled(true);
771 gatherViews.setEnabled(true);
772 tabbedPane.setVisible(true);
773 AlignmentPanel first = alignPanels.get(0);
774 tabbedPane.addTab(first.av.viewName, first);
775 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
778 public AlignViewport getViewport()
783 /* Set up intrinsic listeners for dynamically generated GUI bits. */
784 private void addServiceListeners()
786 final java.beans.PropertyChangeListener thisListener;
787 Desktop.instance.addJalviewPropertyChangeListener("services",
788 thisListener = new java.beans.PropertyChangeListener()
791 public void propertyChange(PropertyChangeEvent evt)
793 // // System.out.println("Discoverer property change.");
794 // if (evt.getPropertyName().equals("services"))
796 SwingUtilities.invokeLater(new Runnable()
803 "Rebuild WS Menu for service change");
804 BuildWebServiceMenu();
811 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
814 public void internalFrameClosed(
815 javax.swing.event.InternalFrameEvent evt)
817 // System.out.println("deregistering discoverer listener");
818 Desktop.instance.removeJalviewPropertyChangeListener("services",
820 closeMenuItem_actionPerformed(true);
823 // Finally, build the menu once to get current service state
824 new Thread(new Runnable()
829 BuildWebServiceMenu();
835 * Configure menu items that vary according to whether the alignment is
836 * nucleotide or protein
838 public void setGUINucleotide()
840 AlignmentI al = getViewport().getAlignment();
841 boolean nucleotide = al.isNucleotide();
843 loadVcf.setVisible(nucleotide);
844 showTranslation.setVisible(nucleotide);
845 showReverse.setVisible(nucleotide);
846 showReverseComplement.setVisible(nucleotide);
847 conservationMenuItem.setEnabled(!nucleotide);
849 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
850 showGroupConservation.setEnabled(!nucleotide);
852 showComplementMenuItem
853 .setText(nucleotide ? MessageManager.getString("label.protein")
854 : MessageManager.getString("label.nucleotide"));
858 * set up menus for the current viewport. This may be called after any
859 * operation that affects the data in the current view (selection changed,
860 * etc) to update the menus to reflect the new state.
863 public void setMenusForViewport()
865 setMenusFromViewport(viewport);
869 * Need to call this method when tabs are selected for multiple views, or when
870 * loading from Jalview2XML.java
875 void setMenusFromViewport(AlignViewport av)
877 padGapsMenuitem.setSelected(av.isPadGaps());
878 colourTextMenuItem.setSelected(av.isShowColourText());
879 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
880 modifyPID.setEnabled(abovePIDThreshold.isSelected());
881 conservationMenuItem.setSelected(av.getConservationSelected());
882 modifyConservation.setEnabled(conservationMenuItem.isSelected());
883 seqLimits.setSelected(av.getShowJVSuffix());
884 idRightAlign.setSelected(av.isRightAlignIds());
885 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
886 renderGapsMenuItem.setSelected(av.isRenderGaps());
887 wrapMenuItem.setSelected(av.getWrapAlignment());
888 scaleAbove.setVisible(av.getWrapAlignment());
889 scaleLeft.setVisible(av.getWrapAlignment());
890 scaleRight.setVisible(av.getWrapAlignment());
891 annotationPanelMenuItem.setState(av.isShowAnnotation());
893 * Show/hide annotations only enabled if annotation panel is shown
895 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
896 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
897 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
898 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
899 viewBoxesMenuItem.setSelected(av.getShowBoxes());
900 viewTextMenuItem.setSelected(av.getShowText());
901 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
902 showGroupConsensus.setSelected(av.isShowGroupConsensus());
903 showGroupConservation.setSelected(av.isShowGroupConservation());
904 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
905 showSequenceLogo.setSelected(av.isShowSequenceLogo());
906 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
908 ColourMenuHelper.setColourSelected(colourMenu,
909 av.getGlobalColourScheme());
911 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
912 hiddenMarkers.setState(av.getShowHiddenMarkers());
913 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
914 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
915 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
916 autoCalculate.setSelected(av.autoCalculateConsensus);
917 sortByTree.setSelected(av.sortByTree);
918 listenToViewSelections.setSelected(av.followSelection);
920 showProducts.setEnabled(canShowProducts());
921 setGroovyEnabled(Desktop.getGroovyConsole() != null);
927 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
931 public void setGroovyEnabled(boolean b)
933 runGroovy.setEnabled(b);
936 private IProgressIndicator progressBar;
941 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
944 public void setProgressBar(String message, long id)
946 progressBar.setProgressBar(message, id);
950 public void registerHandler(final long id,
951 final IProgressIndicatorHandler handler)
953 progressBar.registerHandler(id, handler);
958 * @return true if any progress bars are still active
961 public boolean operationInProgress()
963 return progressBar.operationInProgress();
967 public void setStatus(String text)
969 statusBar.setText(text);
973 * Added so Castor Mapping file can obtain Jalview Version
975 public String getVersion()
977 return jalview.bin.Cache.getProperty("VERSION");
980 public FeatureRenderer getFeatureRenderer()
982 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
986 public void fetchSequence_actionPerformed(ActionEvent e)
988 new jalview.gui.SequenceFetcher(this);
992 public void addFromFile_actionPerformed(ActionEvent e)
994 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
998 public void reload_actionPerformed(ActionEvent e)
1000 if (fileName != null)
1002 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1003 // originating file's format
1004 // TODO: work out how to recover feature settings for correct view(s) when
1005 // file is reloaded.
1006 if (FileFormat.Jalview.equals(currentFileFormat))
1008 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1009 for (int i = 0; i < frames.length; i++)
1011 if (frames[i] instanceof AlignFrame && frames[i] != this
1012 && ((AlignFrame) frames[i]).fileName != null
1013 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1017 frames[i].setSelected(true);
1018 Desktop.instance.closeAssociatedWindows();
1019 } catch (java.beans.PropertyVetoException ex)
1025 Desktop.instance.closeAssociatedWindows();
1027 FileLoader loader = new FileLoader();
1028 DataSourceType protocol = fileName.startsWith("http:")
1029 ? DataSourceType.URL
1030 : DataSourceType.FILE;
1031 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1035 Rectangle bounds = this.getBounds();
1037 FileLoader loader = new FileLoader();
1038 DataSourceType protocol = fileName.startsWith("http:")
1039 ? DataSourceType.URL
1040 : DataSourceType.FILE;
1041 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1042 protocol, currentFileFormat);
1044 newframe.setBounds(bounds);
1045 if (featureSettings != null && featureSettings.isShowing())
1047 final Rectangle fspos = featureSettings.frame.getBounds();
1048 // TODO: need a 'show feature settings' function that takes bounds -
1049 // need to refactor Desktop.addFrame
1050 newframe.featureSettings_actionPerformed(null);
1051 final FeatureSettings nfs = newframe.featureSettings;
1052 SwingUtilities.invokeLater(new Runnable()
1057 nfs.frame.setBounds(fspos);
1060 this.featureSettings.close();
1061 this.featureSettings = null;
1063 this.closeMenuItem_actionPerformed(true);
1069 public void addFromText_actionPerformed(ActionEvent e)
1072 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1076 public void addFromURL_actionPerformed(ActionEvent e)
1078 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1082 public void save_actionPerformed(ActionEvent e)
1084 if (fileName == null || (currentFileFormat == null)
1085 || fileName.startsWith("http"))
1087 saveAs_actionPerformed(null);
1091 saveAlignment(fileName, currentFileFormat);
1102 public void saveAs_actionPerformed(ActionEvent e)
1104 String format = currentFileFormat == null ? null
1105 : currentFileFormat.getName();
1106 JalviewFileChooser chooser = JalviewFileChooser
1107 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1109 chooser.setFileView(new JalviewFileView());
1110 chooser.setDialogTitle(
1111 MessageManager.getString("label.save_alignment_to_file"));
1112 chooser.setToolTipText(MessageManager.getString("action.save"));
1114 int value = chooser.showSaveDialog(this);
1116 if (value == JalviewFileChooser.APPROVE_OPTION)
1118 currentFileFormat = chooser.getSelectedFormat();
1119 while (currentFileFormat == null)
1121 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1122 MessageManager.getString(
1123 "label.select_file_format_before_saving"),
1124 MessageManager.getString("label.file_format_not_specified"),
1125 JvOptionPane.WARNING_MESSAGE);
1126 currentFileFormat = chooser.getSelectedFormat();
1127 value = chooser.showSaveDialog(this);
1128 if (value != JalviewFileChooser.APPROVE_OPTION)
1134 fileName = chooser.getSelectedFile().getPath();
1136 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1138 Cache.setProperty("LAST_DIRECTORY", fileName);
1139 saveAlignment(fileName, currentFileFormat);
1143 public boolean saveAlignment(String file, FileFormatI format)
1145 boolean success = true;
1147 if (FileFormat.Jalview.equals(format))
1149 String shortName = title;
1151 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1153 shortName = shortName.substring(
1154 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1157 success = new Jalview2XML().saveAlignment(this, file, shortName);
1159 statusBar.setText(MessageManager.formatMessage(
1160 "label.successfully_saved_to_file_in_format", new Object[]
1161 { fileName, format }));
1166 AlignmentExportData exportData = getAlignmentForExport(format,
1168 if (exportData.getSettings().isCancelled())
1172 FormatAdapter f = new FormatAdapter(alignPanel,
1173 exportData.getSettings());
1174 String output = f.formatSequences(format, exportData.getAlignment(), // class
1178 // occur in the distant future
1179 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1180 f.getCacheSuffixDefault(format),
1181 viewport.getAlignment().getHiddenColumns());
1191 PrintWriter out = new PrintWriter(new FileWriter(file));
1195 this.setTitle(file);
1196 statusBar.setText(MessageManager.formatMessage(
1197 "label.successfully_saved_to_file_in_format", new Object[]
1198 { fileName, format.getName() }));
1199 } catch (Exception ex)
1202 ex.printStackTrace();
1209 JvOptionPane.showInternalMessageDialog(this, MessageManager
1210 .formatMessage("label.couldnt_save_file", new Object[]
1212 MessageManager.getString("label.error_saving_file"),
1213 JvOptionPane.WARNING_MESSAGE);
1219 private void warningMessage(String warning, String title)
1221 if (new jalview.util.Platform().isHeadless())
1223 System.err.println("Warning: " + title + "\nWarning: " + warning);
1228 JvOptionPane.showInternalMessageDialog(this, warning, title,
1229 JvOptionPane.WARNING_MESSAGE);
1241 protected void outputText_actionPerformed(ActionEvent e)
1243 FileFormatI fileFormat = FileFormats.getInstance()
1244 .forName(e.getActionCommand());
1245 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1247 if (exportData.getSettings().isCancelled())
1251 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1252 cap.setForInput(null);
1255 FileFormatI format = fileFormat;
1256 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1257 .formatSequences(format, exportData.getAlignment(),
1258 exportData.getOmitHidden(),
1259 exportData.getStartEndPostions(),
1260 viewport.getAlignment().getHiddenColumns()));
1261 Desktop.addInternalFrame(cap, MessageManager
1262 .formatMessage("label.alignment_output_command", new Object[]
1263 { e.getActionCommand() }), 600, 500);
1264 } catch (OutOfMemoryError oom)
1266 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1273 public static AlignmentExportData getAlignmentForExport(
1274 FileFormatI format, AlignViewportI viewport,
1275 AlignExportSettingI exportSettings)
1277 AlignmentI alignmentToExport = null;
1278 AlignExportSettingI settings = exportSettings;
1279 String[] omitHidden = null;
1281 HiddenSequences hiddenSeqs = viewport.getAlignment()
1282 .getHiddenSequences();
1284 alignmentToExport = viewport.getAlignment();
1286 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1287 if (settings == null)
1289 settings = new AlignExportSettings(hasHiddenSeqs,
1290 viewport.hasHiddenColumns(), format);
1292 // settings.isExportAnnotations();
1294 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1296 omitHidden = viewport.getViewAsString(false,
1297 settings.isExportHiddenSequences());
1300 int[] alignmentStartEnd = new int[2];
1301 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1303 alignmentToExport = hiddenSeqs.getFullAlignment();
1307 alignmentToExport = viewport.getAlignment();
1309 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1310 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1311 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1312 omitHidden, alignmentStartEnd, settings);
1323 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1325 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1326 htmlSVG.exportHTML(null);
1330 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1332 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1333 bjs.exportHTML(null);
1336 public void createImageMap(File file, String image)
1338 alignPanel.makePNGImageMap(file, image);
1348 public void createPNG(File f)
1350 alignPanel.makePNG(f);
1360 public void createEPS(File f)
1362 alignPanel.makeEPS(f);
1366 public void createSVG(File f)
1368 alignPanel.makeSVG(f);
1372 public void pageSetup_actionPerformed(ActionEvent e)
1374 PrinterJob printJob = PrinterJob.getPrinterJob();
1375 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1385 public void printMenuItem_actionPerformed(ActionEvent e)
1387 // Putting in a thread avoids Swing painting problems
1388 PrintThread thread = new PrintThread(alignPanel);
1393 public void exportFeatures_actionPerformed(ActionEvent e)
1395 new AnnotationExporter(alignPanel).exportFeatures();
1399 public void exportAnnotations_actionPerformed(ActionEvent e)
1401 new AnnotationExporter(alignPanel).exportAnnotations();
1405 public void associatedData_actionPerformed(ActionEvent e)
1407 // Pick the tree file
1408 JalviewFileChooser chooser = new JalviewFileChooser(
1409 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1410 chooser.setFileView(new JalviewFileView());
1411 chooser.setDialogTitle(
1412 MessageManager.getString("label.load_jalview_annotations"));
1413 chooser.setToolTipText(
1414 MessageManager.getString("label.load_jalview_annotations"));
1416 int value = chooser.showOpenDialog(null);
1418 if (value == JalviewFileChooser.APPROVE_OPTION)
1420 String choice = chooser.getSelectedFile().getPath();
1421 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1422 loadJalviewDataFile(choice, null, null, null);
1428 * Close the current view or all views in the alignment frame. If the frame
1429 * only contains one view then the alignment will be removed from memory.
1431 * @param closeAllTabs
1434 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1436 if (alignPanels != null && alignPanels.size() < 2)
1438 closeAllTabs = true;
1443 if (alignPanels != null)
1447 if (this.isClosed())
1449 // really close all the windows - otherwise wait till
1450 // setClosed(true) is called
1451 for (int i = 0; i < alignPanels.size(); i++)
1453 AlignmentPanel ap = alignPanels.get(i);
1460 closeView(alignPanel);
1467 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1468 * be called recursively, with the frame now in 'closed' state
1470 this.setClosed(true);
1472 } catch (Exception ex)
1474 ex.printStackTrace();
1479 * Close the specified panel and close up tabs appropriately.
1481 * @param panelToClose
1483 public void closeView(AlignmentPanel panelToClose)
1485 int index = tabbedPane.getSelectedIndex();
1486 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1487 alignPanels.remove(panelToClose);
1488 panelToClose.closePanel();
1489 panelToClose = null;
1491 tabbedPane.removeTabAt(closedindex);
1492 tabbedPane.validate();
1494 if (index > closedindex || index == tabbedPane.getTabCount())
1496 // modify currently selected tab index if necessary.
1500 this.tabSelectionChanged(index);
1506 void updateEditMenuBar()
1509 if (viewport.getHistoryList().size() > 0)
1511 undoMenuItem.setEnabled(true);
1512 CommandI command = viewport.getHistoryList().peek();
1513 undoMenuItem.setText(MessageManager
1514 .formatMessage("label.undo_command", new Object[]
1515 { command.getDescription() }));
1519 undoMenuItem.setEnabled(false);
1520 undoMenuItem.setText(MessageManager.getString("action.undo"));
1523 if (viewport.getRedoList().size() > 0)
1525 redoMenuItem.setEnabled(true);
1527 CommandI command = viewport.getRedoList().peek();
1528 redoMenuItem.setText(MessageManager
1529 .formatMessage("label.redo_command", new Object[]
1530 { command.getDescription() }));
1534 redoMenuItem.setEnabled(false);
1535 redoMenuItem.setText(MessageManager.getString("action.redo"));
1540 public void addHistoryItem(CommandI command)
1542 if (command.getSize() > 0)
1544 viewport.addToHistoryList(command);
1545 viewport.clearRedoList();
1546 updateEditMenuBar();
1547 viewport.updateHiddenColumns();
1548 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1549 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1550 // viewport.getColumnSelection()
1551 // .getHiddenColumns().size() > 0);
1557 * @return alignment objects for all views
1559 AlignmentI[] getViewAlignments()
1561 if (alignPanels != null)
1563 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1565 for (AlignmentPanel ap : alignPanels)
1567 als[i++] = ap.av.getAlignment();
1571 if (viewport != null)
1573 return new AlignmentI[] { viewport.getAlignment() };
1585 protected void undoMenuItem_actionPerformed(ActionEvent e)
1587 if (viewport.getHistoryList().isEmpty())
1591 CommandI command = viewport.getHistoryList().pop();
1592 viewport.addToRedoList(command);
1593 command.undoCommand(getViewAlignments());
1595 AlignmentViewport originalSource = getOriginatingSource(command);
1596 updateEditMenuBar();
1598 if (originalSource != null)
1600 if (originalSource != viewport)
1603 "Implementation worry: mismatch of viewport origin for undo");
1605 originalSource.updateHiddenColumns();
1606 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1608 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1609 // viewport.getColumnSelection()
1610 // .getHiddenColumns().size() > 0);
1611 originalSource.firePropertyChange("alignment", null,
1612 originalSource.getAlignment().getSequences());
1623 protected void redoMenuItem_actionPerformed(ActionEvent e)
1625 if (viewport.getRedoList().size() < 1)
1630 CommandI command = viewport.getRedoList().pop();
1631 viewport.addToHistoryList(command);
1632 command.doCommand(getViewAlignments());
1634 AlignmentViewport originalSource = getOriginatingSource(command);
1635 updateEditMenuBar();
1637 if (originalSource != null)
1640 if (originalSource != viewport)
1643 "Implementation worry: mismatch of viewport origin for redo");
1645 originalSource.updateHiddenColumns();
1646 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1648 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1649 // viewport.getColumnSelection()
1650 // .getHiddenColumns().size() > 0);
1651 originalSource.firePropertyChange("alignment", null,
1652 originalSource.getAlignment().getSequences());
1656 AlignmentViewport getOriginatingSource(CommandI command)
1658 AlignmentViewport originalSource = null;
1659 // For sequence removal and addition, we need to fire
1660 // the property change event FROM the viewport where the
1661 // original alignment was altered
1662 AlignmentI al = null;
1663 if (command instanceof EditCommand)
1665 EditCommand editCommand = (EditCommand) command;
1666 al = editCommand.getAlignment();
1667 List<Component> comps = PaintRefresher.components
1668 .get(viewport.getSequenceSetId());
1670 for (Component comp : comps)
1672 if (comp instanceof AlignmentPanel)
1674 if (al == ((AlignmentPanel) comp).av.getAlignment())
1676 originalSource = ((AlignmentPanel) comp).av;
1683 if (originalSource == null)
1685 // The original view is closed, we must validate
1686 // the current view against the closed view first
1689 PaintRefresher.validateSequences(al, viewport.getAlignment());
1692 originalSource = viewport;
1695 return originalSource;
1704 public void moveSelectedSequences(boolean up)
1706 SequenceGroup sg = viewport.getSelectionGroup();
1712 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1713 viewport.getHiddenRepSequences(), up);
1714 alignPanel.paintAlignment(true, false);
1717 synchronized void slideSequences(boolean right, int size)
1719 List<SequenceI> sg = new ArrayList<>();
1720 if (viewport.cursorMode)
1722 sg.add(viewport.getAlignment()
1723 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1725 else if (viewport.getSelectionGroup() != null
1726 && viewport.getSelectionGroup().getSize() != viewport
1727 .getAlignment().getHeight())
1729 sg = viewport.getSelectionGroup()
1730 .getSequences(viewport.getHiddenRepSequences());
1738 List<SequenceI> invertGroup = new ArrayList<>();
1740 for (SequenceI seq : viewport.getAlignment().getSequences())
1742 if (!sg.contains(seq))
1744 invertGroup.add(seq);
1748 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1750 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1751 for (int i = 0; i < invertGroup.size(); i++)
1753 seqs2[i] = invertGroup.get(i);
1756 SlideSequencesCommand ssc;
1759 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1760 viewport.getGapCharacter());
1764 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1765 viewport.getGapCharacter());
1768 int groupAdjustment = 0;
1769 if (ssc.getGapsInsertedBegin() && right)
1771 if (viewport.cursorMode)
1773 alignPanel.getSeqPanel().moveCursor(size, 0);
1777 groupAdjustment = size;
1780 else if (!ssc.getGapsInsertedBegin() && !right)
1782 if (viewport.cursorMode)
1784 alignPanel.getSeqPanel().moveCursor(-size, 0);
1788 groupAdjustment = -size;
1792 if (groupAdjustment != 0)
1794 viewport.getSelectionGroup().setStartRes(
1795 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1796 viewport.getSelectionGroup().setEndRes(
1797 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1801 * just extend the last slide command if compatible; but not if in
1802 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1804 boolean appendHistoryItem = false;
1805 Deque<CommandI> historyList = viewport.getHistoryList();
1806 boolean inSplitFrame = getSplitViewContainer() != null;
1807 if (!inSplitFrame && historyList != null && historyList.size() > 0
1808 && historyList.peek() instanceof SlideSequencesCommand)
1810 appendHistoryItem = ssc.appendSlideCommand(
1811 (SlideSequencesCommand) historyList.peek());
1814 if (!appendHistoryItem)
1816 addHistoryItem(ssc);
1829 protected void copy_actionPerformed(ActionEvent e)
1832 if (viewport.getSelectionGroup() == null)
1836 // TODO: preserve the ordering of displayed alignment annotation in any
1837 // internal paste (particularly sequence associated annotation)
1838 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1839 String[] omitHidden = null;
1841 if (viewport.hasHiddenColumns())
1843 omitHidden = viewport.getViewAsString(true);
1846 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1847 seqs, omitHidden, null);
1849 StringSelection ss = new StringSelection(output);
1853 jalview.gui.Desktop.internalCopy = true;
1854 // Its really worth setting the clipboard contents
1855 // to empty before setting the large StringSelection!!
1856 Toolkit.getDefaultToolkit().getSystemClipboard()
1857 .setContents(new StringSelection(""), null);
1859 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1861 } catch (OutOfMemoryError er)
1863 new OOMWarning("copying region", er);
1867 HiddenColumns hiddenColumns = null;
1868 if (viewport.hasHiddenColumns())
1870 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1871 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1873 // create new HiddenColumns object with copy of hidden regions
1874 // between startRes and endRes, offset by startRes
1875 hiddenColumns = new HiddenColumns(
1876 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1877 hiddenCutoff, hiddenOffset);
1880 Desktop.jalviewClipboard = new Object[] { seqs,
1881 viewport.getAlignment().getDataset(), hiddenColumns };
1882 statusBar.setText(MessageManager.formatMessage(
1883 "label.copied_sequences_to_clipboard", new Object[]
1884 { Integer.valueOf(seqs.length).toString() }));
1894 protected void pasteNew_actionPerformed(ActionEvent e)
1906 protected void pasteThis_actionPerformed(ActionEvent e)
1912 * Paste contents of Jalview clipboard
1914 * @param newAlignment
1915 * true to paste to a new alignment, otherwise add to this.
1917 void paste(boolean newAlignment)
1919 boolean externalPaste = true;
1922 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1923 Transferable contents = c.getContents(this);
1925 if (contents == null)
1934 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1935 if (str.length() < 1)
1940 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1942 } catch (OutOfMemoryError er)
1944 new OOMWarning("Out of memory pasting sequences!!", er);
1948 SequenceI[] sequences;
1949 boolean annotationAdded = false;
1950 AlignmentI alignment = null;
1952 if (Desktop.jalviewClipboard != null)
1954 // The clipboard was filled from within Jalview, we must use the
1956 // And dataset from the copied alignment
1957 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1958 // be doubly sure that we create *new* sequence objects.
1959 sequences = new SequenceI[newseq.length];
1960 for (int i = 0; i < newseq.length; i++)
1962 sequences[i] = new Sequence(newseq[i]);
1964 alignment = new Alignment(sequences);
1965 externalPaste = false;
1969 // parse the clipboard as an alignment.
1970 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1972 sequences = alignment.getSequencesArray();
1976 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1982 if (Desktop.jalviewClipboard != null)
1984 // dataset is inherited
1985 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1989 // new dataset is constructed
1990 alignment.setDataset(null);
1992 alwidth = alignment.getWidth() + 1;
1996 AlignmentI pastedal = alignment; // preserve pasted alignment object
1997 // Add pasted sequences and dataset into existing alignment.
1998 alignment = viewport.getAlignment();
1999 alwidth = alignment.getWidth() + 1;
2000 // decide if we need to import sequences from an existing dataset
2001 boolean importDs = Desktop.jalviewClipboard != null
2002 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2003 // importDs==true instructs us to copy over new dataset sequences from
2004 // an existing alignment
2005 Vector newDs = (importDs) ? new Vector() : null; // used to create
2006 // minimum dataset set
2008 for (int i = 0; i < sequences.length; i++)
2012 newDs.addElement(null);
2014 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2016 if (importDs && ds != null)
2018 if (!newDs.contains(ds))
2020 newDs.setElementAt(ds, i);
2021 ds = new Sequence(ds);
2022 // update with new dataset sequence
2023 sequences[i].setDatasetSequence(ds);
2027 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2032 // copy and derive new dataset sequence
2033 sequences[i] = sequences[i].deriveSequence();
2034 alignment.getDataset()
2035 .addSequence(sequences[i].getDatasetSequence());
2036 // TODO: avoid creation of duplicate dataset sequences with a
2037 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2039 alignment.addSequence(sequences[i]); // merges dataset
2043 newDs.clear(); // tidy up
2045 if (alignment.getAlignmentAnnotation() != null)
2047 for (AlignmentAnnotation alan : alignment
2048 .getAlignmentAnnotation())
2050 if (alan.graphGroup > fgroup)
2052 fgroup = alan.graphGroup;
2056 if (pastedal.getAlignmentAnnotation() != null)
2058 // Add any annotation attached to alignment.
2059 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2060 for (int i = 0; i < alann.length; i++)
2062 annotationAdded = true;
2063 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2065 AlignmentAnnotation newann = new AlignmentAnnotation(
2067 if (newann.graphGroup > -1)
2069 if (newGraphGroups.size() <= newann.graphGroup
2070 || newGraphGroups.get(newann.graphGroup) == null)
2072 for (int q = newGraphGroups
2073 .size(); q <= newann.graphGroup; q++)
2075 newGraphGroups.add(q, null);
2077 newGraphGroups.set(newann.graphGroup,
2078 new Integer(++fgroup));
2080 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2084 newann.padAnnotation(alwidth);
2085 alignment.addAnnotation(newann);
2095 addHistoryItem(new EditCommand(
2096 MessageManager.getString("label.add_sequences"),
2097 Action.PASTE, sequences, 0, alignment.getWidth(),
2100 // Add any annotations attached to sequences
2101 for (int i = 0; i < sequences.length; i++)
2103 if (sequences[i].getAnnotation() != null)
2105 AlignmentAnnotation newann;
2106 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2108 annotationAdded = true;
2109 newann = sequences[i].getAnnotation()[a];
2110 newann.adjustForAlignment();
2111 newann.padAnnotation(alwidth);
2112 if (newann.graphGroup > -1)
2114 if (newann.graphGroup > -1)
2116 if (newGraphGroups.size() <= newann.graphGroup
2117 || newGraphGroups.get(newann.graphGroup) == null)
2119 for (int q = newGraphGroups
2120 .size(); q <= newann.graphGroup; q++)
2122 newGraphGroups.add(q, null);
2124 newGraphGroups.set(newann.graphGroup,
2125 new Integer(++fgroup));
2127 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2131 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2135 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2143 // propagate alignment changed.
2144 viewport.getRanges().setEndSeq(alignment.getHeight());
2145 if (annotationAdded)
2147 // Duplicate sequence annotation in all views.
2148 AlignmentI[] alview = this.getViewAlignments();
2149 for (int i = 0; i < sequences.length; i++)
2151 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2156 for (int avnum = 0; avnum < alview.length; avnum++)
2158 if (alview[avnum] != alignment)
2160 // duplicate in a view other than the one with input focus
2161 int avwidth = alview[avnum].getWidth() + 1;
2162 // this relies on sann being preserved after we
2163 // modify the sequence's annotation array for each duplication
2164 for (int a = 0; a < sann.length; a++)
2166 AlignmentAnnotation newann = new AlignmentAnnotation(
2168 sequences[i].addAlignmentAnnotation(newann);
2169 newann.padAnnotation(avwidth);
2170 alview[avnum].addAnnotation(newann); // annotation was
2171 // duplicated earlier
2172 // TODO JAL-1145 graphGroups are not updated for sequence
2173 // annotation added to several views. This may cause
2175 alview[avnum].setAnnotationIndex(newann, a);
2180 buildSortByAnnotationScoresMenu();
2182 viewport.firePropertyChange("alignment", null,
2183 alignment.getSequences());
2184 if (alignPanels != null)
2186 for (AlignmentPanel ap : alignPanels)
2188 ap.validateAnnotationDimensions(false);
2193 alignPanel.validateAnnotationDimensions(false);
2199 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2201 String newtitle = new String("Copied sequences");
2203 if (Desktop.jalviewClipboard != null
2204 && Desktop.jalviewClipboard[2] != null)
2206 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2207 af.viewport.setHiddenColumns(hc);
2210 // >>>This is a fix for the moment, until a better solution is
2212 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2213 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2214 .getFeatureRenderer());
2216 // TODO: maintain provenance of an alignment, rather than just make the
2217 // title a concatenation of operations.
2220 if (title.startsWith("Copied sequences"))
2226 newtitle = newtitle.concat("- from " + title);
2231 newtitle = new String("Pasted sequences");
2234 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2239 } catch (Exception ex)
2241 ex.printStackTrace();
2242 System.out.println("Exception whilst pasting: " + ex);
2243 // could be anything being pasted in here
2249 protected void expand_newalign(ActionEvent e)
2253 AlignmentI alignment = AlignmentUtils
2254 .expandContext(getViewport().getAlignment(), -1);
2255 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2257 String newtitle = new String("Flanking alignment");
2259 if (Desktop.jalviewClipboard != null
2260 && Desktop.jalviewClipboard[2] != null)
2262 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2263 af.viewport.setHiddenColumns(hc);
2266 // >>>This is a fix for the moment, until a better solution is
2268 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2269 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2270 .getFeatureRenderer());
2272 // TODO: maintain provenance of an alignment, rather than just make the
2273 // title a concatenation of operations.
2275 if (title.startsWith("Copied sequences"))
2281 newtitle = newtitle.concat("- from " + title);
2285 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2287 } catch (Exception ex)
2289 ex.printStackTrace();
2290 System.out.println("Exception whilst pasting: " + ex);
2291 // could be anything being pasted in here
2292 } catch (OutOfMemoryError oom)
2294 new OOMWarning("Viewing flanking region of alignment", oom);
2305 protected void cut_actionPerformed(ActionEvent e)
2307 copy_actionPerformed(null);
2308 delete_actionPerformed(null);
2318 protected void delete_actionPerformed(ActionEvent evt)
2321 SequenceGroup sg = viewport.getSelectionGroup();
2328 * If the cut affects all sequences, warn, remove highlighted columns
2330 if (sg.getSize() == viewport.getAlignment().getHeight())
2332 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2333 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2334 if (isEntireAlignWidth)
2336 int confirm = JvOptionPane.showConfirmDialog(this,
2337 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2338 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2339 JvOptionPane.OK_CANCEL_OPTION);
2341 if (confirm == JvOptionPane.CANCEL_OPTION
2342 || confirm == JvOptionPane.CLOSED_OPTION)
2347 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2348 sg.getEndRes() + 1);
2350 SequenceI[] cut = sg.getSequences()
2351 .toArray(new SequenceI[sg.getSize()]);
2353 addHistoryItem(new EditCommand(
2354 MessageManager.getString("label.cut_sequences"), Action.CUT,
2355 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2356 viewport.getAlignment()));
2358 viewport.setSelectionGroup(null);
2359 viewport.sendSelection();
2360 viewport.getAlignment().deleteGroup(sg);
2362 viewport.firePropertyChange("alignment", null,
2363 viewport.getAlignment().getSequences());
2364 if (viewport.getAlignment().getHeight() < 1)
2368 this.setClosed(true);
2369 } catch (Exception ex)
2382 protected void deleteGroups_actionPerformed(ActionEvent e)
2384 if (avc.deleteGroups())
2386 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2387 alignPanel.updateAnnotation();
2388 alignPanel.paintAlignment(true, true);
2399 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2401 SequenceGroup sg = new SequenceGroup();
2403 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2405 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2408 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2409 viewport.setSelectionGroup(sg);
2410 viewport.sendSelection();
2411 // JAL-2034 - should delegate to
2412 // alignPanel to decide if overview needs
2414 alignPanel.paintAlignment(false, false);
2415 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2425 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2427 if (viewport.cursorMode)
2429 alignPanel.getSeqPanel().keyboardNo1 = null;
2430 alignPanel.getSeqPanel().keyboardNo2 = null;
2432 viewport.setSelectionGroup(null);
2433 viewport.getColumnSelection().clear();
2434 viewport.setSelectionGroup(null);
2435 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2436 // JAL-2034 - should delegate to
2437 // alignPanel to decide if overview needs
2439 alignPanel.paintAlignment(false, false);
2440 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2441 viewport.sendSelection();
2451 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2453 SequenceGroup sg = viewport.getSelectionGroup();
2457 selectAllSequenceMenuItem_actionPerformed(null);
2462 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2464 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2466 // JAL-2034 - should delegate to
2467 // alignPanel to decide if overview needs
2470 alignPanel.paintAlignment(true, false);
2471 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2472 viewport.sendSelection();
2476 public void invertColSel_actionPerformed(ActionEvent e)
2478 viewport.invertColumnSelection();
2479 alignPanel.paintAlignment(true, false);
2480 viewport.sendSelection();
2490 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2492 trimAlignment(true);
2502 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2504 trimAlignment(false);
2507 void trimAlignment(boolean trimLeft)
2509 ColumnSelection colSel = viewport.getColumnSelection();
2512 if (!colSel.isEmpty())
2516 column = colSel.getMin();
2520 column = colSel.getMax();
2524 if (viewport.getSelectionGroup() != null)
2526 seqs = viewport.getSelectionGroup()
2527 .getSequencesAsArray(viewport.getHiddenRepSequences());
2531 seqs = viewport.getAlignment().getSequencesArray();
2534 TrimRegionCommand trimRegion;
2537 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2538 column, viewport.getAlignment());
2539 viewport.getRanges().setStartRes(0);
2543 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2544 column, viewport.getAlignment());
2547 statusBar.setText(MessageManager
2548 .formatMessage("label.removed_columns", new String[]
2549 { Integer.valueOf(trimRegion.getSize()).toString() }));
2551 addHistoryItem(trimRegion);
2553 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2555 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2556 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2558 viewport.getAlignment().deleteGroup(sg);
2562 viewport.firePropertyChange("alignment", null,
2563 viewport.getAlignment().getSequences());
2574 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2576 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2579 if (viewport.getSelectionGroup() != null)
2581 seqs = viewport.getSelectionGroup()
2582 .getSequencesAsArray(viewport.getHiddenRepSequences());
2583 start = viewport.getSelectionGroup().getStartRes();
2584 end = viewport.getSelectionGroup().getEndRes();
2588 seqs = viewport.getAlignment().getSequencesArray();
2591 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2592 "Remove Gapped Columns", seqs, start, end,
2593 viewport.getAlignment());
2595 addHistoryItem(removeGapCols);
2597 statusBar.setText(MessageManager
2598 .formatMessage("label.removed_empty_columns", new Object[]
2599 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2601 // This is to maintain viewport position on first residue
2602 // of first sequence
2603 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2604 ViewportRanges ranges = viewport.getRanges();
2605 int startRes = seq.findPosition(ranges.getStartRes());
2606 // ShiftList shifts;
2607 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2608 // edit.alColumnChanges=shifts.getInverse();
2609 // if (viewport.hasHiddenColumns)
2610 // viewport.getColumnSelection().compensateForEdits(shifts);
2611 ranges.setStartRes(seq.findIndex(startRes) - 1);
2612 viewport.firePropertyChange("alignment", null,
2613 viewport.getAlignment().getSequences());
2624 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2626 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2629 if (viewport.getSelectionGroup() != null)
2631 seqs = viewport.getSelectionGroup()
2632 .getSequencesAsArray(viewport.getHiddenRepSequences());
2633 start = viewport.getSelectionGroup().getStartRes();
2634 end = viewport.getSelectionGroup().getEndRes();
2638 seqs = viewport.getAlignment().getSequencesArray();
2641 // This is to maintain viewport position on first residue
2642 // of first sequence
2643 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2644 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2646 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2647 viewport.getAlignment()));
2649 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2651 viewport.firePropertyChange("alignment", null,
2652 viewport.getAlignment().getSequences());
2663 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2665 viewport.setPadGaps(padGapsMenuitem.isSelected());
2666 viewport.firePropertyChange("alignment", null,
2667 viewport.getAlignment().getSequences());
2677 public void findMenuItem_actionPerformed(ActionEvent e)
2683 * Create a new view of the current alignment.
2686 public void newView_actionPerformed(ActionEvent e)
2688 newView(null, true);
2692 * Creates and shows a new view of the current alignment.
2695 * title of newly created view; if null, one will be generated
2696 * @param copyAnnotation
2697 * if true then duplicate all annnotation, groups and settings
2698 * @return new alignment panel, already displayed.
2700 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2703 * Create a new AlignmentPanel (with its own, new Viewport)
2705 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2706 if (!copyAnnotation)
2709 * remove all groups and annotation except for the automatic stuff
2711 newap.av.getAlignment().deleteAllGroups();
2712 newap.av.getAlignment().deleteAllAnnotations(false);
2715 newap.av.setGatherViewsHere(false);
2717 if (viewport.viewName == null)
2719 viewport.viewName = MessageManager
2720 .getString("label.view_name_original");
2724 * Views share the same edits undo and redo stacks
2726 newap.av.setHistoryList(viewport.getHistoryList());
2727 newap.av.setRedoList(viewport.getRedoList());
2730 * Views share the same mappings; need to deregister any new mappings
2731 * created by copyAlignPanel, and register the new reference to the shared
2734 newap.av.replaceMappings(viewport.getAlignment());
2737 * start up cDNA consensus (if applicable) now mappings are in place
2739 if (newap.av.initComplementConsensus())
2741 newap.refresh(true); // adjust layout of annotations
2744 newap.av.viewName = getNewViewName(viewTitle);
2746 addAlignmentPanel(newap, true);
2747 newap.alignmentChanged();
2749 if (alignPanels.size() == 2)
2751 viewport.setGatherViewsHere(true);
2753 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2758 * Make a new name for the view, ensuring it is unique within the current
2759 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2760 * these now use viewId. Unique view names are still desirable for usability.)
2765 protected String getNewViewName(String viewTitle)
2767 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2768 boolean addFirstIndex = false;
2769 if (viewTitle == null || viewTitle.trim().length() == 0)
2771 viewTitle = MessageManager.getString("action.view");
2772 addFirstIndex = true;
2776 index = 1;// we count from 1 if given a specific name
2778 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2780 List<Component> comps = PaintRefresher.components
2781 .get(viewport.getSequenceSetId());
2783 List<String> existingNames = getExistingViewNames(comps);
2785 while (existingNames.contains(newViewName))
2787 newViewName = viewTitle + " " + (++index);
2793 * Returns a list of distinct view names found in the given list of
2794 * components. View names are held on the viewport of an AlignmentPanel.
2799 protected List<String> getExistingViewNames(List<Component> comps)
2801 List<String> existingNames = new ArrayList<>();
2802 for (Component comp : comps)
2804 if (comp instanceof AlignmentPanel)
2806 AlignmentPanel ap = (AlignmentPanel) comp;
2807 if (!existingNames.contains(ap.av.viewName))
2809 existingNames.add(ap.av.viewName);
2813 return existingNames;
2817 * Explode tabbed views into separate windows.
2820 public void expandViews_actionPerformed(ActionEvent e)
2822 Desktop.explodeViews(this);
2826 * Gather views in separate windows back into a tabbed presentation.
2829 public void gatherViews_actionPerformed(ActionEvent e)
2831 Desktop.instance.gatherViews(this);
2841 public void font_actionPerformed(ActionEvent e)
2843 new FontChooser(alignPanel);
2853 protected void seqLimit_actionPerformed(ActionEvent e)
2855 viewport.setShowJVSuffix(seqLimits.isSelected());
2857 alignPanel.getIdPanel().getIdCanvas()
2858 .setPreferredSize(alignPanel.calculateIdWidth());
2859 alignPanel.paintAlignment(true, false);
2863 public void idRightAlign_actionPerformed(ActionEvent e)
2865 viewport.setRightAlignIds(idRightAlign.isSelected());
2866 alignPanel.paintAlignment(false, false);
2870 public void centreColumnLabels_actionPerformed(ActionEvent e)
2872 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2873 alignPanel.paintAlignment(false, false);
2879 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2882 protected void followHighlight_actionPerformed()
2885 * Set the 'follow' flag on the Viewport (and scroll to position if now
2888 final boolean state = this.followHighlightMenuItem.getState();
2889 viewport.setFollowHighlight(state);
2892 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2903 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2905 viewport.setColourText(colourTextMenuItem.isSelected());
2906 alignPanel.paintAlignment(false, false);
2916 public void wrapMenuItem_actionPerformed(ActionEvent e)
2918 scaleAbove.setVisible(wrapMenuItem.isSelected());
2919 scaleLeft.setVisible(wrapMenuItem.isSelected());
2920 scaleRight.setVisible(wrapMenuItem.isSelected());
2921 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2922 alignPanel.updateLayout();
2926 public void showAllSeqs_actionPerformed(ActionEvent e)
2928 viewport.showAllHiddenSeqs();
2932 public void showAllColumns_actionPerformed(ActionEvent e)
2934 viewport.showAllHiddenColumns();
2935 alignPanel.paintAlignment(true, true);
2936 viewport.sendSelection();
2940 public void hideSelSequences_actionPerformed(ActionEvent e)
2942 viewport.hideAllSelectedSeqs();
2946 * called by key handler and the hide all/show all menu items
2951 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2954 boolean hide = false;
2955 SequenceGroup sg = viewport.getSelectionGroup();
2956 if (!toggleSeqs && !toggleCols)
2958 // Hide everything by the current selection - this is a hack - we do the
2959 // invert and then hide
2960 // first check that there will be visible columns after the invert.
2961 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2962 && sg.getStartRes() <= sg.getEndRes()))
2964 // now invert the sequence set, if required - empty selection implies
2965 // that no hiding is required.
2968 invertSequenceMenuItem_actionPerformed(null);
2969 sg = viewport.getSelectionGroup();
2973 viewport.expandColSelection(sg, true);
2974 // finally invert the column selection and get the new sequence
2976 invertColSel_actionPerformed(null);
2983 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2985 hideSelSequences_actionPerformed(null);
2988 else if (!(toggleCols && viewport.hasSelectedColumns()))
2990 showAllSeqs_actionPerformed(null);
2996 if (viewport.hasSelectedColumns())
2998 hideSelColumns_actionPerformed(null);
3001 viewport.setSelectionGroup(sg);
3006 showAllColumns_actionPerformed(null);
3015 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3016 * event.ActionEvent)
3019 public void hideAllButSelection_actionPerformed(ActionEvent e)
3021 toggleHiddenRegions(false, false);
3022 viewport.sendSelection();
3029 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3033 public void hideAllSelection_actionPerformed(ActionEvent e)
3035 SequenceGroup sg = viewport.getSelectionGroup();
3036 viewport.expandColSelection(sg, false);
3037 viewport.hideAllSelectedSeqs();
3038 viewport.hideSelectedColumns();
3039 alignPanel.paintAlignment(true, true);
3040 viewport.sendSelection();
3047 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3051 public void showAllhidden_actionPerformed(ActionEvent e)
3053 viewport.showAllHiddenColumns();
3054 viewport.showAllHiddenSeqs();
3055 alignPanel.paintAlignment(true, true);
3056 viewport.sendSelection();
3060 public void hideSelColumns_actionPerformed(ActionEvent e)
3062 viewport.hideSelectedColumns();
3063 alignPanel.paintAlignment(true, true);
3064 viewport.sendSelection();
3068 public void hiddenMarkers_actionPerformed(ActionEvent e)
3070 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3081 protected void scaleAbove_actionPerformed(ActionEvent e)
3083 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3084 // TODO: do we actually need to update overview for scale above change ?
3085 alignPanel.paintAlignment(true, false);
3095 protected void scaleLeft_actionPerformed(ActionEvent e)
3097 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3098 alignPanel.paintAlignment(true, false);
3108 protected void scaleRight_actionPerformed(ActionEvent e)
3110 viewport.setScaleRightWrapped(scaleRight.isSelected());
3111 alignPanel.paintAlignment(true, false);
3121 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3123 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3124 alignPanel.paintAlignment(false, false);
3134 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3136 viewport.setShowText(viewTextMenuItem.isSelected());
3137 alignPanel.paintAlignment(false, false);
3147 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3149 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3150 alignPanel.paintAlignment(false, false);
3153 public FeatureSettings featureSettings;
3156 public FeatureSettingsControllerI getFeatureSettingsUI()
3158 return featureSettings;
3162 public void featureSettings_actionPerformed(ActionEvent e)
3164 if (featureSettings != null)
3166 featureSettings.close();
3167 featureSettings = null;
3169 if (!showSeqFeatures.isSelected())
3171 // make sure features are actually displayed
3172 showSeqFeatures.setSelected(true);
3173 showSeqFeatures_actionPerformed(null);
3175 featureSettings = new FeatureSettings(this);
3179 * Set or clear 'Show Sequence Features'
3185 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3187 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3188 alignPanel.paintAlignment(true, true);
3192 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3193 * the annotations panel as a whole.
3195 * The options to show/hide all annotations should be enabled when the panel
3196 * is shown, and disabled when the panel is hidden.
3201 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3203 final boolean setVisible = annotationPanelMenuItem.isSelected();
3204 viewport.setShowAnnotation(setVisible);
3205 this.showAllSeqAnnotations.setEnabled(setVisible);
3206 this.hideAllSeqAnnotations.setEnabled(setVisible);
3207 this.showAllAlAnnotations.setEnabled(setVisible);
3208 this.hideAllAlAnnotations.setEnabled(setVisible);
3209 alignPanel.updateLayout();
3213 public void alignmentProperties()
3215 JEditorPane editPane = new JEditorPane("text/html", "");
3216 editPane.setEditable(false);
3217 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3220 MessageManager.formatMessage("label.html_content", new Object[]
3221 { contents.toString() }));
3222 JInternalFrame frame = new JInternalFrame();
3223 frame.getContentPane().add(new JScrollPane(editPane));
3225 Desktop.addInternalFrame(frame, MessageManager
3226 .formatMessage("label.alignment_properties", new Object[]
3227 { getTitle() }), 500, 400);
3237 public void overviewMenuItem_actionPerformed(ActionEvent e)
3239 if (alignPanel.overviewPanel != null)
3244 JInternalFrame frame = new JInternalFrame();
3245 final OverviewPanel overview = new OverviewPanel(alignPanel);
3246 frame.setContentPane(overview);
3247 Desktop.addInternalFrame(frame, MessageManager
3248 .formatMessage("label.overview_params", new Object[]
3249 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3252 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3253 frame.addInternalFrameListener(
3254 new javax.swing.event.InternalFrameAdapter()
3257 public void internalFrameClosed(
3258 javax.swing.event.InternalFrameEvent evt)
3261 alignPanel.setOverviewPanel(null);
3265 alignPanel.setOverviewPanel(overview);
3269 public void textColour_actionPerformed()
3271 new TextColourChooser().chooseColour(alignPanel, null);
3275 * public void covariationColour_actionPerformed() {
3277 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3281 public void annotationColour_actionPerformed()
3283 new AnnotationColourChooser(viewport, alignPanel);
3287 public void annotationColumn_actionPerformed(ActionEvent e)
3289 new AnnotationColumnChooser(viewport, alignPanel);
3293 * Action on the user checking or unchecking the option to apply the selected
3294 * colour scheme to all groups. If unchecked, groups may have their own
3295 * independent colour schemes.
3300 public void applyToAllGroups_actionPerformed(boolean selected)
3302 viewport.setColourAppliesToAllGroups(selected);
3306 * Action on user selecting a colour from the colour menu
3309 * the name (not the menu item label!) of the colour scheme
3312 public void changeColour_actionPerformed(String name)
3315 * 'User Defined' opens a panel to configure or load a
3316 * user-defined colour scheme
3318 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3320 new UserDefinedColours(alignPanel);
3325 * otherwise set the chosen colour scheme (or null for 'None')
3327 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3328 viewport.getAlignment(), viewport.getHiddenRepSequences());
3333 * Actions on setting or changing the alignment colour scheme
3338 public void changeColour(ColourSchemeI cs)
3340 // TODO: pull up to controller method
3341 ColourMenuHelper.setColourSelected(colourMenu, cs);
3343 viewport.setGlobalColourScheme(cs);
3345 alignPanel.paintAlignment(true, true);
3349 * Show the PID threshold slider panel
3352 protected void modifyPID_actionPerformed()
3354 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3355 alignPanel.getViewName());
3356 SliderPanel.showPIDSlider();
3360 * Show the Conservation slider panel
3363 protected void modifyConservation_actionPerformed()
3365 SliderPanel.setConservationSlider(alignPanel,
3366 viewport.getResidueShading(), alignPanel.getViewName());
3367 SliderPanel.showConservationSlider();
3371 * Action on selecting or deselecting (Colour) By Conservation
3374 public void conservationMenuItem_actionPerformed(boolean selected)
3376 modifyConservation.setEnabled(selected);
3377 viewport.setConservationSelected(selected);
3378 viewport.getResidueShading().setConservationApplied(selected);
3380 changeColour(viewport.getGlobalColourScheme());
3383 modifyConservation_actionPerformed();
3387 SliderPanel.hideConservationSlider();
3392 * Action on selecting or deselecting (Colour) Above PID Threshold
3395 public void abovePIDThreshold_actionPerformed(boolean selected)
3397 modifyPID.setEnabled(selected);
3398 viewport.setAbovePIDThreshold(selected);
3401 viewport.getResidueShading().setThreshold(0,
3402 viewport.isIgnoreGapsConsensus());
3405 changeColour(viewport.getGlobalColourScheme());
3408 modifyPID_actionPerformed();
3412 SliderPanel.hidePIDSlider();
3423 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3425 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3426 AlignmentSorter.sortByPID(viewport.getAlignment(),
3427 viewport.getAlignment().getSequenceAt(0));
3428 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3429 viewport.getAlignment()));
3430 alignPanel.paintAlignment(true, false);
3440 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3442 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3443 AlignmentSorter.sortByID(viewport.getAlignment());
3445 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3446 alignPanel.paintAlignment(true, false);
3456 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3458 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3459 AlignmentSorter.sortByLength(viewport.getAlignment());
3460 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3461 viewport.getAlignment()));
3462 alignPanel.paintAlignment(true, false);
3472 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3474 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3475 AlignmentSorter.sortByGroup(viewport.getAlignment());
3476 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3477 viewport.getAlignment()));
3479 alignPanel.paintAlignment(true, false);
3489 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3491 new RedundancyPanel(alignPanel, this);
3501 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3503 if ((viewport.getSelectionGroup() == null)
3504 || (viewport.getSelectionGroup().getSize() < 2))
3506 JvOptionPane.showInternalMessageDialog(this,
3507 MessageManager.getString(
3508 "label.you_must_select_least_two_sequences"),
3509 MessageManager.getString("label.invalid_selection"),
3510 JvOptionPane.WARNING_MESSAGE);
3514 JInternalFrame frame = new JInternalFrame();
3515 frame.setContentPane(new PairwiseAlignPanel(viewport));
3516 Desktop.addInternalFrame(frame,
3517 MessageManager.getString("action.pairwise_alignment"), 600,
3523 public void autoCalculate_actionPerformed(ActionEvent e)
3525 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3526 if (viewport.autoCalculateConsensus)
3528 viewport.firePropertyChange("alignment", null,
3529 viewport.getAlignment().getSequences());
3534 public void sortByTreeOption_actionPerformed(ActionEvent e)
3536 viewport.sortByTree = sortByTree.isSelected();
3540 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3542 viewport.followSelection = listenToViewSelections.isSelected();
3546 * Constructs a tree panel and adds it to the desktop
3549 * tree type (NJ or AV)
3551 * name of score model used to compute the tree
3553 * parameters for the distance or similarity calculation
3555 void newTreePanel(String type, String modelName,
3556 SimilarityParamsI options)
3558 String frameTitle = "";
3561 boolean onSelection = false;
3562 if (viewport.getSelectionGroup() != null
3563 && viewport.getSelectionGroup().getSize() > 0)
3565 SequenceGroup sg = viewport.getSelectionGroup();
3567 /* Decide if the selection is a column region */
3568 for (SequenceI _s : sg.getSequences())
3570 if (_s.getLength() < sg.getEndRes())
3572 JvOptionPane.showMessageDialog(Desktop.desktop,
3573 MessageManager.getString(
3574 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3575 MessageManager.getString(
3576 "label.sequences_selection_not_aligned"),
3577 JvOptionPane.WARNING_MESSAGE);
3586 if (viewport.getAlignment().getHeight() < 2)
3592 tp = new TreePanel(alignPanel, type, modelName, options);
3593 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3595 frameTitle += " from ";
3597 if (viewport.viewName != null)
3599 frameTitle += viewport.viewName + " of ";
3602 frameTitle += this.title;
3604 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3615 public void addSortByOrderMenuItem(String title,
3616 final AlignmentOrder order)
3618 final JMenuItem item = new JMenuItem(MessageManager
3619 .formatMessage("action.by_title_param", new Object[]
3622 item.addActionListener(new java.awt.event.ActionListener()
3625 public void actionPerformed(ActionEvent e)
3627 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3629 // TODO: JBPNote - have to map order entries to curent SequenceI
3631 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3633 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3634 viewport.getAlignment()));
3636 alignPanel.paintAlignment(true, false);
3642 * Add a new sort by annotation score menu item
3645 * the menu to add the option to
3647 * the label used to retrieve scores for each sequence on the
3650 public void addSortByAnnotScoreMenuItem(JMenu sort,
3651 final String scoreLabel)
3653 final JMenuItem item = new JMenuItem(scoreLabel);
3655 item.addActionListener(new java.awt.event.ActionListener()
3658 public void actionPerformed(ActionEvent e)
3660 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3661 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3662 viewport.getAlignment());// ,viewport.getSelectionGroup());
3663 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3664 viewport.getAlignment()));
3665 alignPanel.paintAlignment(true, false);
3671 * last hash for alignment's annotation array - used to minimise cost of
3674 protected int _annotationScoreVectorHash;
3677 * search the alignment and rebuild the sort by annotation score submenu the
3678 * last alignment annotation vector hash is stored to minimize cost of
3679 * rebuilding in subsequence calls.
3683 public void buildSortByAnnotationScoresMenu()
3685 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3690 if (viewport.getAlignment().getAlignmentAnnotation()
3691 .hashCode() != _annotationScoreVectorHash)
3693 sortByAnnotScore.removeAll();
3694 // almost certainly a quicker way to do this - but we keep it simple
3695 Hashtable scoreSorts = new Hashtable();
3696 AlignmentAnnotation aann[];
3697 for (SequenceI sqa : viewport.getAlignment().getSequences())
3699 aann = sqa.getAnnotation();
3700 for (int i = 0; aann != null && i < aann.length; i++)
3702 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3704 scoreSorts.put(aann[i].label, aann[i].label);
3708 Enumeration labels = scoreSorts.keys();
3709 while (labels.hasMoreElements())
3711 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3712 (String) labels.nextElement());
3714 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3717 _annotationScoreVectorHash = viewport.getAlignment()
3718 .getAlignmentAnnotation().hashCode();
3723 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3724 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3725 * call. Listeners are added to remove the menu item when the treePanel is
3726 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3730 public void buildTreeSortMenu()
3732 sortByTreeMenu.removeAll();
3734 List<Component> comps = PaintRefresher.components
3735 .get(viewport.getSequenceSetId());
3736 List<TreePanel> treePanels = new ArrayList<>();
3737 for (Component comp : comps)
3739 if (comp instanceof TreePanel)
3741 treePanels.add((TreePanel) comp);
3745 if (treePanels.size() < 1)
3747 sortByTreeMenu.setVisible(false);
3751 sortByTreeMenu.setVisible(true);
3753 for (final TreePanel tp : treePanels)
3755 final JMenuItem item = new JMenuItem(tp.getTitle());
3756 item.addActionListener(new java.awt.event.ActionListener()
3759 public void actionPerformed(ActionEvent e)
3761 tp.sortByTree_actionPerformed();
3762 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3767 sortByTreeMenu.add(item);
3771 public boolean sortBy(AlignmentOrder alorder, String undoname)
3773 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3774 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3775 if (undoname != null)
3777 addHistoryItem(new OrderCommand(undoname, oldOrder,
3778 viewport.getAlignment()));
3780 alignPanel.paintAlignment(true, false);
3785 * Work out whether the whole set of sequences or just the selected set will
3786 * be submitted for multiple alignment.
3789 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3791 // Now, check we have enough sequences
3792 AlignmentView msa = null;
3794 if ((viewport.getSelectionGroup() != null)
3795 && (viewport.getSelectionGroup().getSize() > 1))
3797 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3798 // some common interface!
3800 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3801 * SequenceI[sz = seqs.getSize(false)];
3803 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3804 * seqs.getSequenceAt(i); }
3806 msa = viewport.getAlignmentView(true);
3808 else if (viewport.getSelectionGroup() != null
3809 && viewport.getSelectionGroup().getSize() == 1)
3811 int option = JvOptionPane.showConfirmDialog(this,
3812 MessageManager.getString("warn.oneseq_msainput_selection"),
3813 MessageManager.getString("label.invalid_selection"),
3814 JvOptionPane.OK_CANCEL_OPTION);
3815 if (option == JvOptionPane.OK_OPTION)
3817 msa = viewport.getAlignmentView(false);
3822 msa = viewport.getAlignmentView(false);
3828 * Decides what is submitted to a secondary structure prediction service: the
3829 * first sequence in the alignment, or in the current selection, or, if the
3830 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3831 * region or the whole alignment. (where the first sequence in the set is the
3832 * one that the prediction will be for).
3834 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3836 AlignmentView seqs = null;
3838 if ((viewport.getSelectionGroup() != null)
3839 && (viewport.getSelectionGroup().getSize() > 0))
3841 seqs = viewport.getAlignmentView(true);
3845 seqs = viewport.getAlignmentView(false);
3847 // limit sequences - JBPNote in future - could spawn multiple prediction
3849 // TODO: viewport.getAlignment().isAligned is a global state - the local
3850 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3851 if (!viewport.getAlignment().isAligned(false))
3853 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3854 // TODO: if seqs.getSequences().length>1 then should really have warned
3868 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3870 // Pick the tree file
3871 JalviewFileChooser chooser = new JalviewFileChooser(
3872 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3873 chooser.setFileView(new JalviewFileView());
3874 chooser.setDialogTitle(
3875 MessageManager.getString("label.select_newick_like_tree_file"));
3876 chooser.setToolTipText(
3877 MessageManager.getString("label.load_tree_file"));
3879 int value = chooser.showOpenDialog(null);
3881 if (value == JalviewFileChooser.APPROVE_OPTION)
3883 String filePath = chooser.getSelectedFile().getPath();
3884 Cache.setProperty("LAST_DIRECTORY", filePath);
3885 NewickFile fin = null;
3888 fin = new NewickFile(filePath, DataSourceType.FILE);
3889 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3890 } catch (Exception ex)
3892 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3893 MessageManager.getString("label.problem_reading_tree_file"),
3894 JvOptionPane.WARNING_MESSAGE);
3895 ex.printStackTrace();
3897 if (fin != null && fin.hasWarningMessage())
3899 JvOptionPane.showMessageDialog(Desktop.desktop,
3900 fin.getWarningMessage(),
3902 .getString("label.possible_problem_with_tree_file"),
3903 JvOptionPane.WARNING_MESSAGE);
3908 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3910 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3913 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3914 int h, int x, int y)
3916 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3920 * Add a treeviewer for the tree extracted from a Newick file object to the
3921 * current alignment view
3928 * Associated alignment input data (or null)
3937 * @return TreePanel handle
3939 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3940 AlignmentView input, int w, int h, int x, int y)
3942 TreePanel tp = null;
3948 if (nf.getTree() != null)
3950 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3956 tp.setLocation(x, y);
3959 Desktop.addInternalFrame(tp, treeTitle, w, h);
3961 } catch (Exception ex)
3963 ex.printStackTrace();
3969 private boolean buildingMenu = false;
3972 * Generates menu items and listener event actions for web service clients
3975 public void BuildWebServiceMenu()
3977 while (buildingMenu)
3981 System.err.println("Waiting for building menu to finish.");
3983 } catch (Exception e)
3987 final AlignFrame me = this;
3988 buildingMenu = true;
3989 new Thread(new Runnable()
3994 final List<JMenuItem> legacyItems = new ArrayList<>();
3997 // System.err.println("Building ws menu again "
3998 // + Thread.currentThread());
3999 // TODO: add support for context dependent disabling of services based
4001 // alignment and current selection
4002 // TODO: add additional serviceHandle parameter to specify abstract
4004 // class independently of AbstractName
4005 // TODO: add in rediscovery GUI function to restart discoverer
4006 // TODO: group services by location as well as function and/or
4008 // object broker mechanism.
4009 final Vector<JMenu> wsmenu = new Vector<>();
4010 final IProgressIndicator af = me;
4013 * do not i18n these strings - they are hard-coded in class
4014 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4015 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4017 final JMenu msawsmenu = new JMenu("Alignment");
4018 final JMenu secstrmenu = new JMenu(
4019 "Secondary Structure Prediction");
4020 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4021 final JMenu analymenu = new JMenu("Analysis");
4022 final JMenu dismenu = new JMenu("Protein Disorder");
4023 // JAL-940 - only show secondary structure prediction services from
4024 // the legacy server
4025 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4027 Discoverer.services != null && (Discoverer.services.size() > 0))
4029 // TODO: refactor to allow list of AbstractName/Handler bindings to
4031 // stored or retrieved from elsewhere
4032 // No MSAWS used any more:
4033 // Vector msaws = null; // (Vector)
4034 // Discoverer.services.get("MsaWS");
4035 Vector secstrpr = (Vector) Discoverer.services
4037 if (secstrpr != null)
4039 // Add any secondary structure prediction services
4040 for (int i = 0, j = secstrpr.size(); i < j; i++)
4042 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4044 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4045 .getServiceClient(sh);
4046 int p = secstrmenu.getItemCount();
4047 impl.attachWSMenuEntry(secstrmenu, me);
4048 int q = secstrmenu.getItemCount();
4049 for (int litm = p; litm < q; litm++)
4051 legacyItems.add(secstrmenu.getItem(litm));
4057 // Add all submenus in the order they should appear on the web
4059 wsmenu.add(msawsmenu);
4060 wsmenu.add(secstrmenu);
4061 wsmenu.add(dismenu);
4062 wsmenu.add(analymenu);
4063 // No search services yet
4064 // wsmenu.add(seqsrchmenu);
4066 javax.swing.SwingUtilities.invokeLater(new Runnable()
4073 webService.removeAll();
4074 // first, add discovered services onto the webservices menu
4075 if (wsmenu.size() > 0)
4077 for (int i = 0, j = wsmenu.size(); i < j; i++)
4079 webService.add(wsmenu.get(i));
4084 webService.add(me.webServiceNoServices);
4086 // TODO: move into separate menu builder class.
4087 boolean new_sspred = false;
4088 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4090 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4091 if (jws2servs != null)
4093 if (jws2servs.hasServices())
4095 jws2servs.attachWSMenuEntry(webService, me);
4096 for (Jws2Instance sv : jws2servs.getServices())
4098 if (sv.description.toLowerCase().contains("jpred"))
4100 for (JMenuItem jmi : legacyItems)
4102 jmi.setVisible(false);
4108 if (jws2servs.isRunning())
4110 JMenuItem tm = new JMenuItem(
4111 "Still discovering JABA Services");
4112 tm.setEnabled(false);
4117 build_urlServiceMenu(me.webService);
4118 build_fetchdbmenu(webService);
4119 for (JMenu item : wsmenu)
4121 if (item.getItemCount() == 0)
4123 item.setEnabled(false);
4127 item.setEnabled(true);
4130 } catch (Exception e)
4133 "Exception during web service menu building process.",
4138 } catch (Exception e)
4141 buildingMenu = false;
4148 * construct any groupURL type service menu entries.
4152 private void build_urlServiceMenu(JMenu webService)
4154 // TODO: remove this code when 2.7 is released
4155 // DEBUG - alignmentView
4157 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4158 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4160 * @Override public void actionPerformed(ActionEvent e) {
4161 * jalview.datamodel.AlignmentView
4162 * .testSelectionViews(af.viewport.getAlignment(),
4163 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4165 * }); webService.add(testAlView);
4167 // TODO: refactor to RestClient discoverer and merge menu entries for
4168 // rest-style services with other types of analysis/calculation service
4169 // SHmmr test client - still being implemented.
4170 // DEBUG - alignmentView
4172 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4175 client.attachWSMenuEntry(
4176 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4182 * Searches the alignment sequences for xRefs and builds the Show
4183 * Cross-References menu (formerly called Show Products), with database
4184 * sources for which cross-references are found (protein sources for a
4185 * nucleotide alignment and vice versa)
4187 * @return true if Show Cross-references menu should be enabled
4189 public boolean canShowProducts()
4191 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4192 AlignmentI dataset = viewport.getAlignment().getDataset();
4194 showProducts.removeAll();
4195 final boolean dna = viewport.getAlignment().isNucleotide();
4197 if (seqs == null || seqs.length == 0)
4199 // nothing to see here.
4203 boolean showp = false;
4206 List<String> ptypes = new CrossRef(seqs, dataset)
4207 .findXrefSourcesForSequences(dna);
4209 for (final String source : ptypes)
4212 final AlignFrame af = this;
4213 JMenuItem xtype = new JMenuItem(source);
4214 xtype.addActionListener(new ActionListener()
4217 public void actionPerformed(ActionEvent e)
4219 showProductsFor(af.viewport.getSequenceSelection(), dna,
4223 showProducts.add(xtype);
4225 showProducts.setVisible(showp);
4226 showProducts.setEnabled(showp);
4227 } catch (Exception e)
4230 "canShowProducts threw an exception - please report to help@jalview.org",
4238 * Finds and displays cross-references for the selected sequences (protein
4239 * products for nucleotide sequences, dna coding sequences for peptides).
4242 * the sequences to show cross-references for
4244 * true if from a nucleotide alignment (so showing proteins)
4246 * the database to show cross-references for
4248 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4249 final String source)
4251 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4256 * Construct and display a new frame containing the translation of this
4257 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4260 public void showTranslation_actionPerformed(ActionEvent e)
4262 AlignmentI al = null;
4265 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4267 al = dna.translateCdna();
4268 } catch (Exception ex)
4270 jalview.bin.Cache.log.error(
4271 "Exception during translation. Please report this !", ex);
4272 final String msg = MessageManager.getString(
4273 "label.error_when_translating_sequences_submit_bug_report");
4274 final String errorTitle = MessageManager
4275 .getString("label.implementation_error")
4276 + MessageManager.getString("label.translation_failed");
4277 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4278 JvOptionPane.ERROR_MESSAGE);
4281 if (al == null || al.getHeight() == 0)
4283 final String msg = MessageManager.getString(
4284 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4285 final String errorTitle = MessageManager
4286 .getString("label.translation_failed");
4287 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4288 JvOptionPane.WARNING_MESSAGE);
4292 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4293 af.setFileFormat(this.currentFileFormat);
4294 final String newTitle = MessageManager
4295 .formatMessage("label.translation_of_params", new Object[]
4296 { this.getTitle() });
4297 af.setTitle(newTitle);
4298 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4300 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4301 viewport.openSplitFrame(af, new Alignment(seqs));
4305 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4312 * Set the file format
4316 public void setFileFormat(FileFormatI format)
4318 this.currentFileFormat = format;
4322 * Try to load a features file onto the alignment.
4325 * contents or path to retrieve file
4327 * access mode of file (see jalview.io.AlignFile)
4328 * @return true if features file was parsed correctly.
4330 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4332 return avc.parseFeaturesFile(file, sourceType,
4333 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4338 public void refreshFeatureUI(boolean enableIfNecessary)
4340 // note - currently this is only still here rather than in the controller
4341 // because of the featureSettings hard reference that is yet to be
4343 if (enableIfNecessary)
4345 viewport.setShowSequenceFeatures(true);
4346 showSeqFeatures.setSelected(true);
4352 public void dragEnter(DropTargetDragEvent evt)
4357 public void dragExit(DropTargetEvent evt)
4362 public void dragOver(DropTargetDragEvent evt)
4367 public void dropActionChanged(DropTargetDragEvent evt)
4372 public void drop(DropTargetDropEvent evt)
4374 // JAL-1552 - acceptDrop required before getTransferable call for
4375 // Java's Transferable for native dnd
4376 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4377 Transferable t = evt.getTransferable();
4378 final AlignFrame thisaf = this;
4379 final List<String> files = new ArrayList<>();
4380 List<DataSourceType> protocols = new ArrayList<>();
4384 Desktop.transferFromDropTarget(files, protocols, evt, t);
4385 } catch (Exception e)
4387 e.printStackTrace();
4391 new Thread(new Runnable()
4398 // check to see if any of these files have names matching sequences
4401 SequenceIdMatcher idm = new SequenceIdMatcher(
4402 viewport.getAlignment().getSequencesArray());
4404 * Object[] { String,SequenceI}
4406 ArrayList<Object[]> filesmatched = new ArrayList<>();
4407 ArrayList<String> filesnotmatched = new ArrayList<>();
4408 for (int i = 0; i < files.size(); i++)
4410 String file = files.get(i).toString();
4412 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4413 if (protocol == DataSourceType.FILE)
4415 File fl = new File(file);
4416 pdbfn = fl.getName();
4418 else if (protocol == DataSourceType.URL)
4420 URL url = new URL(file);
4421 pdbfn = url.getFile();
4423 if (pdbfn.length() > 0)
4425 // attempt to find a match in the alignment
4426 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4427 int l = 0, c = pdbfn.indexOf(".");
4428 while (mtch == null && c != -1)
4433 } while ((c = pdbfn.indexOf(".", l)) > l);
4436 pdbfn = pdbfn.substring(0, l);
4438 mtch = idm.findAllIdMatches(pdbfn);
4442 FileFormatI type = null;
4445 type = new IdentifyFile().identify(file, protocol);
4446 } catch (Exception ex)
4450 if (type != null && type.isStructureFile())
4452 filesmatched.add(new Object[] { file, protocol, mtch });
4456 // File wasn't named like one of the sequences or wasn't a PDB
4458 filesnotmatched.add(file);
4462 if (filesmatched.size() > 0)
4464 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4465 || JvOptionPane.showConfirmDialog(thisaf,
4466 MessageManager.formatMessage(
4467 "label.automatically_associate_structure_files_with_sequences_same_name",
4469 { Integer.valueOf(filesmatched.size())
4471 MessageManager.getString(
4472 "label.automatically_associate_structure_files_by_name"),
4473 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4476 for (Object[] fm : filesmatched)
4478 // try and associate
4479 // TODO: may want to set a standard ID naming formalism for
4480 // associating PDB files which have no IDs.
4481 for (SequenceI toassoc : (SequenceI[]) fm[2])
4483 PDBEntry pe = new AssociatePdbFileWithSeq()
4484 .associatePdbWithSeq((String) fm[0],
4485 (DataSourceType) fm[1], toassoc, false,
4489 System.err.println("Associated file : "
4490 + ((String) fm[0]) + " with "
4491 + toassoc.getDisplayId(true));
4495 // TODO: do we need to update overview ? only if features are
4497 alignPanel.paintAlignment(true, false);
4501 if (filesnotmatched.size() > 0)
4503 if (assocfiles > 0 && (Cache.getDefault(
4504 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4505 || JvOptionPane.showConfirmDialog(thisaf,
4506 "<html>" + MessageManager.formatMessage(
4507 "label.ignore_unmatched_dropped_files_info",
4510 filesnotmatched.size())
4513 MessageManager.getString(
4514 "label.ignore_unmatched_dropped_files"),
4515 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4519 for (String fn : filesnotmatched)
4521 loadJalviewDataFile(fn, null, null, null);
4525 } catch (Exception ex)
4527 ex.printStackTrace();
4535 * Attempt to load a "dropped" file or URL string, by testing in turn for
4537 * <li>an Annotation file</li>
4538 * <li>a JNet file</li>
4539 * <li>a features file</li>
4540 * <li>else try to interpret as an alignment file</li>
4544 * either a filename or a URL string.
4546 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4547 FileFormatI format, SequenceI assocSeq)
4551 if (sourceType == null)
4553 sourceType = FormatAdapter.checkProtocol(file);
4555 // if the file isn't identified, or not positively identified as some
4556 // other filetype (PFAM is default unidentified alignment file type) then
4557 // try to parse as annotation.
4558 boolean isAnnotation = (format == null
4559 || FileFormat.Pfam.equals(format))
4560 ? new AnnotationFile().annotateAlignmentView(viewport,
4566 // first see if its a T-COFFEE score file
4567 TCoffeeScoreFile tcf = null;
4570 tcf = new TCoffeeScoreFile(file, sourceType);
4573 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4577 new TCoffeeColourScheme(viewport.getAlignment()));
4578 isAnnotation = true;
4579 statusBar.setText(MessageManager.getString(
4580 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4584 // some problem - if no warning its probable that the ID matching
4585 // process didn't work
4586 JvOptionPane.showMessageDialog(Desktop.desktop,
4587 tcf.getWarningMessage() == null
4588 ? MessageManager.getString(
4589 "label.check_file_matches_sequence_ids_alignment")
4590 : tcf.getWarningMessage(),
4591 MessageManager.getString(
4592 "label.problem_reading_tcoffee_score_file"),
4593 JvOptionPane.WARNING_MESSAGE);
4600 } catch (Exception x)
4603 "Exception when processing data source as T-COFFEE score file",
4609 // try to see if its a JNet 'concise' style annotation file *before*
4611 // try to parse it as a features file
4614 format = new IdentifyFile().identify(file, sourceType);
4616 if (FileFormat.ScoreMatrix == format)
4618 ScoreMatrixFile sm = new ScoreMatrixFile(
4619 new FileParse(file, sourceType));
4621 // todo: i18n this message
4622 statusBar.setText(MessageManager.formatMessage(
4623 "label.successfully_loaded_matrix",
4624 sm.getMatrixName()));
4626 else if (FileFormat.Jnet.equals(format))
4628 JPredFile predictions = new JPredFile(file, sourceType);
4629 new JnetAnnotationMaker();
4630 JnetAnnotationMaker.add_annotation(predictions,
4631 viewport.getAlignment(), 0, false);
4632 viewport.getAlignment().setupJPredAlignment();
4633 isAnnotation = true;
4635 // else if (IdentifyFile.FeaturesFile.equals(format))
4636 else if (FileFormat.Features.equals(format))
4638 if (parseFeaturesFile(file, sourceType))
4640 alignPanel.paintAlignment(true, true);
4645 new FileLoader().LoadFile(viewport, file, sourceType, format);
4652 alignPanel.adjustAnnotationHeight();
4653 viewport.updateSequenceIdColours();
4654 buildSortByAnnotationScoresMenu();
4655 alignPanel.paintAlignment(true, true);
4657 } catch (Exception ex)
4659 ex.printStackTrace();
4660 } catch (OutOfMemoryError oom)
4665 } catch (Exception x)
4670 + (sourceType != null
4671 ? (sourceType == DataSourceType.PASTE
4673 : "using " + sourceType + " from "
4677 ? "(parsing as '" + format + "' file)"
4679 oom, Desktop.desktop);
4684 * Method invoked by the ChangeListener on the tabbed pane, in other words
4685 * when a different tabbed pane is selected by the user or programmatically.
4688 public void tabSelectionChanged(int index)
4692 alignPanel = alignPanels.get(index);
4693 viewport = alignPanel.av;
4694 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4695 setMenusFromViewport(viewport);
4699 * 'focus' any colour slider that is open to the selected viewport
4701 if (viewport.getConservationSelected())
4703 SliderPanel.setConservationSlider(alignPanel,
4704 viewport.getResidueShading(), alignPanel.getViewName());
4708 SliderPanel.hideConservationSlider();
4710 if (viewport.getAbovePIDThreshold())
4712 SliderPanel.setPIDSliderSource(alignPanel,
4713 viewport.getResidueShading(), alignPanel.getViewName());
4717 SliderPanel.hidePIDSlider();
4721 * If there is a frame linked to this one in a SplitPane, switch it to the
4722 * same view tab index. No infinite recursion of calls should happen, since
4723 * tabSelectionChanged() should not get invoked on setting the selected
4724 * index to an unchanged value. Guard against setting an invalid index
4725 * before the new view peer tab has been created.
4727 final AlignViewportI peer = viewport.getCodingComplement();
4730 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4731 .getAlignPanel().alignFrame;
4732 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4734 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4740 * On right mouse click on view tab, prompt for and set new view name.
4743 public void tabbedPane_mousePressed(MouseEvent e)
4745 if (e.isPopupTrigger())
4747 String msg = MessageManager.getString("label.enter_view_name");
4748 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4749 JvOptionPane.QUESTION_MESSAGE);
4753 viewport.viewName = reply;
4754 // TODO warn if reply is in getExistingViewNames()?
4755 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4760 public AlignViewport getCurrentView()
4766 * Open the dialog for regex description parsing.
4769 protected void extractScores_actionPerformed(ActionEvent e)
4771 ParseProperties pp = new jalview.analysis.ParseProperties(
4772 viewport.getAlignment());
4773 // TODO: verify regex and introduce GUI dialog for version 2.5
4774 // if (pp.getScoresFromDescription("col", "score column ",
4775 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4777 if (pp.getScoresFromDescription("description column",
4778 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4780 buildSortByAnnotationScoresMenu();
4788 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4792 protected void showDbRefs_actionPerformed(ActionEvent e)
4794 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4800 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4804 protected void showNpFeats_actionPerformed(ActionEvent e)
4806 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4810 * find the viewport amongst the tabs in this alignment frame and close that
4815 public boolean closeView(AlignViewportI av)
4819 this.closeMenuItem_actionPerformed(false);
4822 Component[] comp = tabbedPane.getComponents();
4823 for (int i = 0; comp != null && i < comp.length; i++)
4825 if (comp[i] instanceof AlignmentPanel)
4827 if (((AlignmentPanel) comp[i]).av == av)
4830 closeView((AlignmentPanel) comp[i]);
4838 protected void build_fetchdbmenu(JMenu webService)
4840 // Temporary hack - DBRef Fetcher always top level ws entry.
4841 // TODO We probably want to store a sequence database checklist in
4842 // preferences and have checkboxes.. rather than individual sources selected
4844 final JMenu rfetch = new JMenu(
4845 MessageManager.getString("action.fetch_db_references"));
4846 rfetch.setToolTipText(MessageManager.getString(
4847 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4848 webService.add(rfetch);
4850 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4851 MessageManager.getString("option.trim_retrieved_seqs"));
4852 trimrs.setToolTipText(
4853 MessageManager.getString("label.trim_retrieved_sequences"));
4855 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4856 trimrs.addActionListener(new ActionListener()
4859 public void actionPerformed(ActionEvent e)
4861 trimrs.setSelected(trimrs.isSelected());
4862 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4863 Boolean.valueOf(trimrs.isSelected()).toString());
4867 JMenuItem fetchr = new JMenuItem(
4868 MessageManager.getString("label.standard_databases"));
4869 fetchr.setToolTipText(
4870 MessageManager.getString("label.fetch_embl_uniprot"));
4871 fetchr.addActionListener(new ActionListener()
4875 public void actionPerformed(ActionEvent e)
4877 new Thread(new Runnable()
4882 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4883 .getAlignment().isNucleotide();
4884 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4885 alignPanel.av.getSequenceSelection(),
4886 alignPanel.alignFrame, null,
4887 alignPanel.alignFrame.featureSettings, isNucleotide);
4888 dbRefFetcher.addListener(new FetchFinishedListenerI()
4891 public void finished()
4893 AlignFrame.this.setMenusForViewport();
4896 dbRefFetcher.fetchDBRefs(false);
4904 final AlignFrame me = this;
4905 new Thread(new Runnable()
4910 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4911 .getSequenceFetcherSingleton(me);
4912 javax.swing.SwingUtilities.invokeLater(new Runnable()
4917 String[] dbclasses = sf.getOrderedSupportedSources();
4918 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4919 // jalview.util.QuickSort.sort(otherdb, otherdb);
4920 List<DbSourceProxy> otherdb;
4921 JMenu dfetch = new JMenu();
4922 JMenu ifetch = new JMenu();
4923 JMenuItem fetchr = null;
4924 int comp = 0, icomp = 0, mcomp = 15;
4925 String mname = null;
4927 for (String dbclass : dbclasses)
4929 otherdb = sf.getSourceProxy(dbclass);
4930 // add a single entry for this class, or submenu allowing 'fetch
4932 if (otherdb == null || otherdb.size() < 1)
4936 // List<DbSourceProxy> dbs=otherdb;
4937 // otherdb=new ArrayList<DbSourceProxy>();
4938 // for (DbSourceProxy db:dbs)
4940 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4944 mname = "From " + dbclass;
4946 if (otherdb.size() == 1)
4948 final DbSourceProxy[] dassource = otherdb
4949 .toArray(new DbSourceProxy[0]);
4950 DbSourceProxy src = otherdb.get(0);
4951 fetchr = new JMenuItem(src.getDbSource());
4952 fetchr.addActionListener(new ActionListener()
4956 public void actionPerformed(ActionEvent e)
4958 new Thread(new Runnable()
4964 boolean isNucleotide = alignPanel.alignFrame
4965 .getViewport().getAlignment()
4967 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4968 alignPanel.av.getSequenceSelection(),
4969 alignPanel.alignFrame, dassource,
4970 alignPanel.alignFrame.featureSettings,
4973 .addListener(new FetchFinishedListenerI()
4976 public void finished()
4978 AlignFrame.this.setMenusForViewport();
4981 dbRefFetcher.fetchDBRefs(false);
4987 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
4988 MessageManager.formatMessage(
4989 "label.fetch_retrieve_from", new Object[]
4990 { src.getDbName() })));
4996 final DbSourceProxy[] dassource = otherdb
4997 .toArray(new DbSourceProxy[0]);
4999 DbSourceProxy src = otherdb.get(0);
5000 fetchr = new JMenuItem(MessageManager
5001 .formatMessage("label.fetch_all_param", new Object[]
5002 { src.getDbSource() }));
5003 fetchr.addActionListener(new ActionListener()
5006 public void actionPerformed(ActionEvent e)
5008 new Thread(new Runnable()
5014 boolean isNucleotide = alignPanel.alignFrame
5015 .getViewport().getAlignment()
5017 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5018 alignPanel.av.getSequenceSelection(),
5019 alignPanel.alignFrame, dassource,
5020 alignPanel.alignFrame.featureSettings,
5023 .addListener(new FetchFinishedListenerI()
5026 public void finished()
5028 AlignFrame.this.setMenusForViewport();
5031 dbRefFetcher.fetchDBRefs(false);
5037 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5038 MessageManager.formatMessage(
5039 "label.fetch_retrieve_from_all_sources",
5041 { Integer.valueOf(otherdb.size())
5043 src.getDbSource(), src.getDbName() })));
5046 // and then build the rest of the individual menus
5047 ifetch = new JMenu(MessageManager.formatMessage(
5048 "label.source_from_db_source", new Object[]
5049 { src.getDbSource() }));
5051 String imname = null;
5053 for (DbSourceProxy sproxy : otherdb)
5055 String dbname = sproxy.getDbName();
5056 String sname = dbname.length() > 5
5057 ? dbname.substring(0, 5) + "..."
5059 String msname = dbname.length() > 10
5060 ? dbname.substring(0, 10) + "..."
5064 imname = MessageManager
5065 .formatMessage("label.from_msname", new Object[]
5068 fetchr = new JMenuItem(msname);
5069 final DbSourceProxy[] dassrc = { sproxy };
5070 fetchr.addActionListener(new ActionListener()
5074 public void actionPerformed(ActionEvent e)
5076 new Thread(new Runnable()
5082 boolean isNucleotide = alignPanel.alignFrame
5083 .getViewport().getAlignment()
5085 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5086 alignPanel.av.getSequenceSelection(),
5087 alignPanel.alignFrame, dassrc,
5088 alignPanel.alignFrame.featureSettings,
5091 .addListener(new FetchFinishedListenerI()
5094 public void finished()
5096 AlignFrame.this.setMenusForViewport();
5099 dbRefFetcher.fetchDBRefs(false);
5105 fetchr.setToolTipText(
5106 "<html>" + MessageManager.formatMessage(
5107 "label.fetch_retrieve_from", new Object[]
5111 if (++icomp >= mcomp || i == (otherdb.size()))
5113 ifetch.setText(MessageManager.formatMessage(
5114 "label.source_to_target", imname, sname));
5116 ifetch = new JMenu();
5124 if (comp >= mcomp || dbi >= (dbclasses.length))
5126 dfetch.setText(MessageManager.formatMessage(
5127 "label.source_to_target", mname, dbclass));
5129 dfetch = new JMenu();
5142 * Left justify the whole alignment.
5145 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5147 AlignmentI al = viewport.getAlignment();
5149 viewport.firePropertyChange("alignment", null, al);
5153 * Right justify the whole alignment.
5156 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5158 AlignmentI al = viewport.getAlignment();
5160 viewport.firePropertyChange("alignment", null, al);
5164 public void setShowSeqFeatures(boolean b)
5166 showSeqFeatures.setSelected(b);
5167 viewport.setShowSequenceFeatures(b);
5174 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5175 * awt.event.ActionEvent)
5178 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5180 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5181 alignPanel.paintAlignment(false, false);
5188 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5192 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5194 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5195 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5203 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5204 * .event.ActionEvent)
5207 protected void showGroupConservation_actionPerformed(ActionEvent e)
5209 viewport.setShowGroupConservation(showGroupConservation.getState());
5210 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5217 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5218 * .event.ActionEvent)
5221 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5223 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5224 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5231 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5232 * .event.ActionEvent)
5235 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5237 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5238 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5242 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5244 showSequenceLogo.setState(true);
5245 viewport.setShowSequenceLogo(true);
5246 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5247 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5251 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5253 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5260 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5261 * .event.ActionEvent)
5264 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5266 if (avc.makeGroupsFromSelection())
5268 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5269 alignPanel.updateAnnotation();
5270 alignPanel.paintAlignment(true, true);
5274 public void clearAlignmentSeqRep()
5276 // TODO refactor alignmentseqrep to controller
5277 if (viewport.getAlignment().hasSeqrep())
5279 viewport.getAlignment().setSeqrep(null);
5280 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5281 alignPanel.updateAnnotation();
5282 alignPanel.paintAlignment(true, true);
5287 protected void createGroup_actionPerformed(ActionEvent e)
5289 if (avc.createGroup())
5291 alignPanel.alignmentChanged();
5296 protected void unGroup_actionPerformed(ActionEvent e)
5300 alignPanel.alignmentChanged();
5305 * make the given alignmentPanel the currently selected tab
5307 * @param alignmentPanel
5309 public void setDisplayedView(AlignmentPanel alignmentPanel)
5311 if (!viewport.getSequenceSetId()
5312 .equals(alignmentPanel.av.getSequenceSetId()))
5314 throw new Error(MessageManager.getString(
5315 "error.implementation_error_cannot_show_view_alignment_frame"));
5317 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5318 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5320 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5325 * Action on selection of menu options to Show or Hide annotations.
5328 * @param forSequences
5329 * update sequence-related annotations
5330 * @param forAlignment
5331 * update non-sequence-related annotations
5334 protected void setAnnotationsVisibility(boolean visible,
5335 boolean forSequences, boolean forAlignment)
5337 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5338 .getAlignmentAnnotation();
5343 for (AlignmentAnnotation aa : anns)
5346 * don't display non-positional annotations on an alignment
5348 if (aa.annotations == null)
5352 boolean apply = (aa.sequenceRef == null && forAlignment)
5353 || (aa.sequenceRef != null && forSequences);
5356 aa.visible = visible;
5359 alignPanel.validateAnnotationDimensions(true);
5360 alignPanel.alignmentChanged();
5364 * Store selected annotation sort order for the view and repaint.
5367 protected void sortAnnotations_actionPerformed()
5369 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5371 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5372 alignPanel.paintAlignment(false, false);
5377 * @return alignment panels in this alignment frame
5379 public List<? extends AlignmentViewPanel> getAlignPanels()
5381 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5385 * Open a new alignment window, with the cDNA associated with this (protein)
5386 * alignment, aligned as is the protein.
5388 protected void viewAsCdna_actionPerformed()
5390 // TODO no longer a menu action - refactor as required
5391 final AlignmentI alignment = getViewport().getAlignment();
5392 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5393 if (mappings == null)
5397 List<SequenceI> cdnaSeqs = new ArrayList<>();
5398 for (SequenceI aaSeq : alignment.getSequences())
5400 for (AlignedCodonFrame acf : mappings)
5402 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5406 * There is a cDNA mapping for this protein sequence - add to new
5407 * alignment. It will share the same dataset sequence as other mapped
5408 * cDNA (no new mappings need to be created).
5410 final Sequence newSeq = new Sequence(dnaSeq);
5411 newSeq.setDatasetSequence(dnaSeq);
5412 cdnaSeqs.add(newSeq);
5416 if (cdnaSeqs.size() == 0)
5418 // show a warning dialog no mapped cDNA
5421 AlignmentI cdna = new Alignment(
5422 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5423 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5424 AlignFrame.DEFAULT_HEIGHT);
5425 cdna.alignAs(alignment);
5426 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5428 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5429 AlignFrame.DEFAULT_HEIGHT);
5433 * Set visibility of dna/protein complement view (available when shown in a
5439 protected void showComplement_actionPerformed(boolean show)
5441 SplitContainerI sf = getSplitViewContainer();
5444 sf.setComplementVisible(this, show);
5449 * Generate the reverse (optionally complemented) of the selected sequences,
5450 * and add them to the alignment
5453 protected void showReverse_actionPerformed(boolean complement)
5455 AlignmentI al = null;
5458 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5459 al = dna.reverseCdna(complement);
5460 viewport.addAlignment(al, "");
5461 addHistoryItem(new EditCommand(
5462 MessageManager.getString("label.add_sequences"), Action.PASTE,
5463 al.getSequencesArray(), 0, al.getWidth(),
5464 viewport.getAlignment()));
5465 } catch (Exception ex)
5467 System.err.println(ex.getMessage());
5473 * Try to run a script in the Groovy console, having first ensured that this
5474 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5475 * be targeted at this alignment.
5478 protected void runGroovy_actionPerformed()
5480 Jalview.setCurrentAlignFrame(this);
5481 groovy.ui.Console console = Desktop.getGroovyConsole();
5482 if (console != null)
5486 console.runScript();
5487 } catch (Exception ex)
5489 System.err.println((ex.toString()));
5490 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5491 MessageManager.getString("label.couldnt_run_groovy_script"),
5492 MessageManager.getString("label.groovy_support_failed"),
5493 JvOptionPane.ERROR_MESSAGE);
5498 System.err.println("Can't run Groovy script as console not found");
5503 * Hides columns containing (or not containing) a specified feature, provided
5504 * that would not leave all columns hidden
5506 * @param featureType
5507 * @param columnsContaining
5510 public boolean hideFeatureColumns(String featureType,
5511 boolean columnsContaining)
5513 boolean notForHiding = avc.markColumnsContainingFeatures(
5514 columnsContaining, false, false, featureType);
5517 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5518 false, featureType))
5520 getViewport().hideSelectedColumns();
5528 protected void selectHighlightedColumns_actionPerformed(
5529 ActionEvent actionEvent)
5531 // include key modifier check in case user selects from menu
5532 avc.markHighlightedColumns(
5533 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5534 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5535 | ActionEvent.CTRL_MASK)) != 0);
5539 * Rebuilds the Colour menu, including any user-defined colours which have
5540 * been loaded either on startup or during the session
5542 public void buildColourMenu()
5544 colourMenu.removeAll();
5546 colourMenu.add(applyToAllGroups);
5547 colourMenu.add(textColour);
5548 colourMenu.addSeparator();
5550 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5553 colourMenu.addSeparator();
5554 colourMenu.add(conservationMenuItem);
5555 colourMenu.add(modifyConservation);
5556 colourMenu.add(abovePIDThreshold);
5557 colourMenu.add(modifyPID);
5558 colourMenu.add(annotationColour);
5560 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5561 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5565 * Open a dialog (if not already open) that allows the user to select and
5566 * calculate PCA or Tree analysis
5568 protected void openTreePcaDialog()
5570 if (alignPanel.getCalculationDialog() == null)
5572 new CalculationChooser(AlignFrame.this);
5577 protected void loadVcf_actionPerformed()
5579 JalviewFileChooser chooser = new JalviewFileChooser(
5580 Cache.getProperty("LAST_DIRECTORY"));
5581 chooser.setFileView(new JalviewFileView());
5582 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5583 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5585 int value = chooser.showOpenDialog(null);
5587 if (value == JalviewFileChooser.APPROVE_OPTION)
5589 String choice = chooser.getSelectedFile().getPath();
5590 Cache.setProperty("LAST_DIRECTORY", choice);
5591 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5592 new VCFLoader(choice).loadVCF(seqs, this);
5598 class PrintThread extends Thread
5602 public PrintThread(AlignmentPanel ap)
5607 static PageFormat pf;
5612 PrinterJob printJob = PrinterJob.getPrinterJob();
5616 printJob.setPrintable(ap, pf);
5620 printJob.setPrintable(ap);
5623 if (printJob.printDialog())
5628 } catch (Exception PrintException)
5630 PrintException.printStackTrace();