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)
1831 if (viewport.getSelectionGroup() == null)
1835 // TODO: preserve the ordering of displayed alignment annotation in any
1836 // internal paste (particularly sequence associated annotation)
1837 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1838 String[] omitHidden = null;
1840 if (viewport.hasHiddenColumns())
1842 omitHidden = viewport.getViewAsString(true);
1845 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1846 seqs, omitHidden, null);
1848 StringSelection ss = new StringSelection(output);
1852 jalview.gui.Desktop.internalCopy = true;
1853 // Its really worth setting the clipboard contents
1854 // to empty before setting the large StringSelection!!
1855 Toolkit.getDefaultToolkit().getSystemClipboard()
1856 .setContents(new StringSelection(""), null);
1858 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1860 } catch (OutOfMemoryError er)
1862 new OOMWarning("copying region", er);
1866 HiddenColumns hiddenColumns = null;
1867 if (viewport.hasHiddenColumns())
1869 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1870 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1872 // create new HiddenColumns object with copy of hidden regions
1873 // between startRes and endRes, offset by startRes
1874 hiddenColumns = new HiddenColumns(
1875 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1876 hiddenCutoff, hiddenOffset);
1879 Desktop.jalviewClipboard = new Object[] { seqs,
1880 viewport.getAlignment().getDataset(), hiddenColumns };
1881 statusBar.setText(MessageManager.formatMessage(
1882 "label.copied_sequences_to_clipboard", new Object[]
1883 { Integer.valueOf(seqs.length).toString() }));
1893 protected void pasteNew_actionPerformed(ActionEvent e)
1905 protected void pasteThis_actionPerformed(ActionEvent e)
1911 * Paste contents of Jalview clipboard
1913 * @param newAlignment
1914 * true to paste to a new alignment, otherwise add to this.
1916 void paste(boolean newAlignment)
1918 boolean externalPaste = true;
1921 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1922 Transferable contents = c.getContents(this);
1924 if (contents == null)
1933 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1934 if (str.length() < 1)
1939 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1941 } catch (OutOfMemoryError er)
1943 new OOMWarning("Out of memory pasting sequences!!", er);
1947 SequenceI[] sequences;
1948 boolean annotationAdded = false;
1949 AlignmentI alignment = null;
1951 if (Desktop.jalviewClipboard != null)
1953 // The clipboard was filled from within Jalview, we must use the
1955 // And dataset from the copied alignment
1956 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1957 // be doubly sure that we create *new* sequence objects.
1958 sequences = new SequenceI[newseq.length];
1959 for (int i = 0; i < newseq.length; i++)
1961 sequences[i] = new Sequence(newseq[i]);
1963 alignment = new Alignment(sequences);
1964 externalPaste = false;
1968 // parse the clipboard as an alignment.
1969 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1971 sequences = alignment.getSequencesArray();
1975 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1981 if (Desktop.jalviewClipboard != null)
1983 // dataset is inherited
1984 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1988 // new dataset is constructed
1989 alignment.setDataset(null);
1991 alwidth = alignment.getWidth() + 1;
1995 AlignmentI pastedal = alignment; // preserve pasted alignment object
1996 // Add pasted sequences and dataset into existing alignment.
1997 alignment = viewport.getAlignment();
1998 alwidth = alignment.getWidth() + 1;
1999 // decide if we need to import sequences from an existing dataset
2000 boolean importDs = Desktop.jalviewClipboard != null
2001 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2002 // importDs==true instructs us to copy over new dataset sequences from
2003 // an existing alignment
2004 Vector newDs = (importDs) ? new Vector() : null; // used to create
2005 // minimum dataset set
2007 for (int i = 0; i < sequences.length; i++)
2011 newDs.addElement(null);
2013 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2015 if (importDs && ds != null)
2017 if (!newDs.contains(ds))
2019 newDs.setElementAt(ds, i);
2020 ds = new Sequence(ds);
2021 // update with new dataset sequence
2022 sequences[i].setDatasetSequence(ds);
2026 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2031 // copy and derive new dataset sequence
2032 sequences[i] = sequences[i].deriveSequence();
2033 alignment.getDataset()
2034 .addSequence(sequences[i].getDatasetSequence());
2035 // TODO: avoid creation of duplicate dataset sequences with a
2036 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2038 alignment.addSequence(sequences[i]); // merges dataset
2042 newDs.clear(); // tidy up
2044 if (alignment.getAlignmentAnnotation() != null)
2046 for (AlignmentAnnotation alan : alignment
2047 .getAlignmentAnnotation())
2049 if (alan.graphGroup > fgroup)
2051 fgroup = alan.graphGroup;
2055 if (pastedal.getAlignmentAnnotation() != null)
2057 // Add any annotation attached to alignment.
2058 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2059 for (int i = 0; i < alann.length; i++)
2061 annotationAdded = true;
2062 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2064 AlignmentAnnotation newann = new AlignmentAnnotation(
2066 if (newann.graphGroup > -1)
2068 if (newGraphGroups.size() <= newann.graphGroup
2069 || newGraphGroups.get(newann.graphGroup) == null)
2071 for (int q = newGraphGroups
2072 .size(); q <= newann.graphGroup; q++)
2074 newGraphGroups.add(q, null);
2076 newGraphGroups.set(newann.graphGroup,
2077 new Integer(++fgroup));
2079 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2083 newann.padAnnotation(alwidth);
2084 alignment.addAnnotation(newann);
2094 addHistoryItem(new EditCommand(
2095 MessageManager.getString("label.add_sequences"),
2096 Action.PASTE, sequences, 0, alignment.getWidth(),
2099 // Add any annotations attached to sequences
2100 for (int i = 0; i < sequences.length; i++)
2102 if (sequences[i].getAnnotation() != null)
2104 AlignmentAnnotation newann;
2105 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2107 annotationAdded = true;
2108 newann = sequences[i].getAnnotation()[a];
2109 newann.adjustForAlignment();
2110 newann.padAnnotation(alwidth);
2111 if (newann.graphGroup > -1)
2113 if (newann.graphGroup > -1)
2115 if (newGraphGroups.size() <= newann.graphGroup
2116 || newGraphGroups.get(newann.graphGroup) == null)
2118 for (int q = newGraphGroups
2119 .size(); q <= newann.graphGroup; q++)
2121 newGraphGroups.add(q, null);
2123 newGraphGroups.set(newann.graphGroup,
2124 new Integer(++fgroup));
2126 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2130 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2134 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2142 // propagate alignment changed.
2143 viewport.getRanges().setEndSeq(alignment.getHeight());
2144 if (annotationAdded)
2146 // Duplicate sequence annotation in all views.
2147 AlignmentI[] alview = this.getViewAlignments();
2148 for (int i = 0; i < sequences.length; i++)
2150 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2155 for (int avnum = 0; avnum < alview.length; avnum++)
2157 if (alview[avnum] != alignment)
2159 // duplicate in a view other than the one with input focus
2160 int avwidth = alview[avnum].getWidth() + 1;
2161 // this relies on sann being preserved after we
2162 // modify the sequence's annotation array for each duplication
2163 for (int a = 0; a < sann.length; a++)
2165 AlignmentAnnotation newann = new AlignmentAnnotation(
2167 sequences[i].addAlignmentAnnotation(newann);
2168 newann.padAnnotation(avwidth);
2169 alview[avnum].addAnnotation(newann); // annotation was
2170 // duplicated earlier
2171 // TODO JAL-1145 graphGroups are not updated for sequence
2172 // annotation added to several views. This may cause
2174 alview[avnum].setAnnotationIndex(newann, a);
2179 buildSortByAnnotationScoresMenu();
2181 viewport.firePropertyChange("alignment", null,
2182 alignment.getSequences());
2183 if (alignPanels != null)
2185 for (AlignmentPanel ap : alignPanels)
2187 ap.validateAnnotationDimensions(false);
2192 alignPanel.validateAnnotationDimensions(false);
2198 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2200 String newtitle = new String("Copied sequences");
2202 if (Desktop.jalviewClipboard != null
2203 && Desktop.jalviewClipboard[2] != null)
2205 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2206 af.viewport.setHiddenColumns(hc);
2209 // >>>This is a fix for the moment, until a better solution is
2211 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2212 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2213 .getFeatureRenderer());
2215 // TODO: maintain provenance of an alignment, rather than just make the
2216 // title a concatenation of operations.
2219 if (title.startsWith("Copied sequences"))
2225 newtitle = newtitle.concat("- from " + title);
2230 newtitle = new String("Pasted sequences");
2233 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2238 } catch (Exception ex)
2240 ex.printStackTrace();
2241 System.out.println("Exception whilst pasting: " + ex);
2242 // could be anything being pasted in here
2248 protected void expand_newalign(ActionEvent e)
2252 AlignmentI alignment = AlignmentUtils
2253 .expandContext(getViewport().getAlignment(), -1);
2254 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2256 String newtitle = new String("Flanking alignment");
2258 if (Desktop.jalviewClipboard != null
2259 && Desktop.jalviewClipboard[2] != null)
2261 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2262 af.viewport.setHiddenColumns(hc);
2265 // >>>This is a fix for the moment, until a better solution is
2267 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2268 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2269 .getFeatureRenderer());
2271 // TODO: maintain provenance of an alignment, rather than just make the
2272 // title a concatenation of operations.
2274 if (title.startsWith("Copied sequences"))
2280 newtitle = newtitle.concat("- from " + title);
2284 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2286 } catch (Exception ex)
2288 ex.printStackTrace();
2289 System.out.println("Exception whilst pasting: " + ex);
2290 // could be anything being pasted in here
2291 } catch (OutOfMemoryError oom)
2293 new OOMWarning("Viewing flanking region of alignment", oom);
2304 protected void cut_actionPerformed(ActionEvent e)
2306 copy_actionPerformed(null);
2307 delete_actionPerformed(null);
2317 protected void delete_actionPerformed(ActionEvent evt)
2320 SequenceGroup sg = viewport.getSelectionGroup();
2327 * If the cut affects all sequences, warn, remove highlighted columns
2329 if (sg.getSize() == viewport.getAlignment().getHeight())
2331 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2332 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2333 if (isEntireAlignWidth)
2335 int confirm = JvOptionPane.showConfirmDialog(this,
2336 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2337 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2338 JvOptionPane.OK_CANCEL_OPTION);
2340 if (confirm == JvOptionPane.CANCEL_OPTION
2341 || confirm == JvOptionPane.CLOSED_OPTION)
2346 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2347 sg.getEndRes() + 1);
2349 SequenceI[] cut = sg.getSequences()
2350 .toArray(new SequenceI[sg.getSize()]);
2352 addHistoryItem(new EditCommand(
2353 MessageManager.getString("label.cut_sequences"), Action.CUT,
2354 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2355 viewport.getAlignment()));
2357 viewport.setSelectionGroup(null);
2358 viewport.sendSelection();
2359 viewport.getAlignment().deleteGroup(sg);
2361 viewport.firePropertyChange("alignment", null,
2362 viewport.getAlignment().getSequences());
2363 if (viewport.getAlignment().getHeight() < 1)
2367 this.setClosed(true);
2368 } catch (Exception ex)
2381 protected void deleteGroups_actionPerformed(ActionEvent e)
2383 if (avc.deleteGroups())
2385 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2386 alignPanel.updateAnnotation();
2387 alignPanel.paintAlignment(true, true);
2398 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2400 SequenceGroup sg = new SequenceGroup();
2402 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2404 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2407 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2408 viewport.setSelectionGroup(sg);
2409 viewport.sendSelection();
2410 // JAL-2034 - should delegate to
2411 // alignPanel to decide if overview needs
2413 alignPanel.paintAlignment(false, false);
2414 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2424 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2426 if (viewport.cursorMode)
2428 alignPanel.getSeqPanel().keyboardNo1 = null;
2429 alignPanel.getSeqPanel().keyboardNo2 = null;
2431 viewport.setSelectionGroup(null);
2432 viewport.getColumnSelection().clear();
2433 viewport.setSelectionGroup(null);
2434 viewport.setHighlightedSeqs(null);
2435 // JAL-2034 - should delegate to
2436 // alignPanel to decide if overview needs
2438 alignPanel.paintAlignment(false, false);
2439 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2440 viewport.sendSelection();
2450 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2452 SequenceGroup sg = viewport.getSelectionGroup();
2456 selectAllSequenceMenuItem_actionPerformed(null);
2461 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2463 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2465 // JAL-2034 - should delegate to
2466 // alignPanel to decide if overview needs
2469 alignPanel.paintAlignment(true, false);
2470 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2471 viewport.sendSelection();
2475 public void invertColSel_actionPerformed(ActionEvent e)
2477 viewport.invertColumnSelection();
2478 alignPanel.paintAlignment(true, false);
2479 viewport.sendSelection();
2489 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2491 trimAlignment(true);
2501 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2503 trimAlignment(false);
2506 void trimAlignment(boolean trimLeft)
2508 ColumnSelection colSel = viewport.getColumnSelection();
2511 if (!colSel.isEmpty())
2515 column = colSel.getMin();
2519 column = colSel.getMax();
2523 if (viewport.getSelectionGroup() != null)
2525 seqs = viewport.getSelectionGroup()
2526 .getSequencesAsArray(viewport.getHiddenRepSequences());
2530 seqs = viewport.getAlignment().getSequencesArray();
2533 TrimRegionCommand trimRegion;
2536 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2537 column, viewport.getAlignment());
2538 viewport.getRanges().setStartRes(0);
2542 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2543 column, viewport.getAlignment());
2546 statusBar.setText(MessageManager
2547 .formatMessage("label.removed_columns", new String[]
2548 { Integer.valueOf(trimRegion.getSize()).toString() }));
2550 addHistoryItem(trimRegion);
2552 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2554 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2555 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2557 viewport.getAlignment().deleteGroup(sg);
2561 viewport.firePropertyChange("alignment", null,
2562 viewport.getAlignment().getSequences());
2573 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2575 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2578 if (viewport.getSelectionGroup() != null)
2580 seqs = viewport.getSelectionGroup()
2581 .getSequencesAsArray(viewport.getHiddenRepSequences());
2582 start = viewport.getSelectionGroup().getStartRes();
2583 end = viewport.getSelectionGroup().getEndRes();
2587 seqs = viewport.getAlignment().getSequencesArray();
2590 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2591 "Remove Gapped Columns", seqs, start, end,
2592 viewport.getAlignment());
2594 addHistoryItem(removeGapCols);
2596 statusBar.setText(MessageManager
2597 .formatMessage("label.removed_empty_columns", new Object[]
2598 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2600 // This is to maintain viewport position on first residue
2601 // of first sequence
2602 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2603 ViewportRanges ranges = viewport.getRanges();
2604 int startRes = seq.findPosition(ranges.getStartRes());
2605 // ShiftList shifts;
2606 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2607 // edit.alColumnChanges=shifts.getInverse();
2608 // if (viewport.hasHiddenColumns)
2609 // viewport.getColumnSelection().compensateForEdits(shifts);
2610 ranges.setStartRes(seq.findIndex(startRes) - 1);
2611 viewport.firePropertyChange("alignment", null,
2612 viewport.getAlignment().getSequences());
2623 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2625 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2628 if (viewport.getSelectionGroup() != null)
2630 seqs = viewport.getSelectionGroup()
2631 .getSequencesAsArray(viewport.getHiddenRepSequences());
2632 start = viewport.getSelectionGroup().getStartRes();
2633 end = viewport.getSelectionGroup().getEndRes();
2637 seqs = viewport.getAlignment().getSequencesArray();
2640 // This is to maintain viewport position on first residue
2641 // of first sequence
2642 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2643 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2645 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2646 viewport.getAlignment()));
2648 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2650 viewport.firePropertyChange("alignment", null,
2651 viewport.getAlignment().getSequences());
2662 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2664 viewport.setPadGaps(padGapsMenuitem.isSelected());
2665 viewport.firePropertyChange("alignment", null,
2666 viewport.getAlignment().getSequences());
2676 public void findMenuItem_actionPerformed(ActionEvent e)
2682 * Create a new view of the current alignment.
2685 public void newView_actionPerformed(ActionEvent e)
2687 newView(null, true);
2691 * Creates and shows a new view of the current alignment.
2694 * title of newly created view; if null, one will be generated
2695 * @param copyAnnotation
2696 * if true then duplicate all annnotation, groups and settings
2697 * @return new alignment panel, already displayed.
2699 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2702 * Create a new AlignmentPanel (with its own, new Viewport)
2704 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2705 if (!copyAnnotation)
2708 * remove all groups and annotation except for the automatic stuff
2710 newap.av.getAlignment().deleteAllGroups();
2711 newap.av.getAlignment().deleteAllAnnotations(false);
2714 newap.av.setGatherViewsHere(false);
2716 if (viewport.viewName == null)
2718 viewport.viewName = MessageManager
2719 .getString("label.view_name_original");
2723 * Views share the same edits undo and redo stacks
2725 newap.av.setHistoryList(viewport.getHistoryList());
2726 newap.av.setRedoList(viewport.getRedoList());
2729 * Views share the same mappings; need to deregister any new mappings
2730 * created by copyAlignPanel, and register the new reference to the shared
2733 newap.av.replaceMappings(viewport.getAlignment());
2736 * start up cDNA consensus (if applicable) now mappings are in place
2738 if (newap.av.initComplementConsensus())
2740 newap.refresh(true); // adjust layout of annotations
2743 newap.av.viewName = getNewViewName(viewTitle);
2745 addAlignmentPanel(newap, true);
2746 newap.alignmentChanged();
2748 if (alignPanels.size() == 2)
2750 viewport.setGatherViewsHere(true);
2752 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2757 * Make a new name for the view, ensuring it is unique within the current
2758 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2759 * these now use viewId. Unique view names are still desirable for usability.)
2764 protected String getNewViewName(String viewTitle)
2766 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2767 boolean addFirstIndex = false;
2768 if (viewTitle == null || viewTitle.trim().length() == 0)
2770 viewTitle = MessageManager.getString("action.view");
2771 addFirstIndex = true;
2775 index = 1;// we count from 1 if given a specific name
2777 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2779 List<Component> comps = PaintRefresher.components
2780 .get(viewport.getSequenceSetId());
2782 List<String> existingNames = getExistingViewNames(comps);
2784 while (existingNames.contains(newViewName))
2786 newViewName = viewTitle + " " + (++index);
2792 * Returns a list of distinct view names found in the given list of
2793 * components. View names are held on the viewport of an AlignmentPanel.
2798 protected List<String> getExistingViewNames(List<Component> comps)
2800 List<String> existingNames = new ArrayList<>();
2801 for (Component comp : comps)
2803 if (comp instanceof AlignmentPanel)
2805 AlignmentPanel ap = (AlignmentPanel) comp;
2806 if (!existingNames.contains(ap.av.viewName))
2808 existingNames.add(ap.av.viewName);
2812 return existingNames;
2816 * Explode tabbed views into separate windows.
2819 public void expandViews_actionPerformed(ActionEvent e)
2821 Desktop.explodeViews(this);
2825 * Gather views in separate windows back into a tabbed presentation.
2828 public void gatherViews_actionPerformed(ActionEvent e)
2830 Desktop.instance.gatherViews(this);
2840 public void font_actionPerformed(ActionEvent e)
2842 new FontChooser(alignPanel);
2852 protected void seqLimit_actionPerformed(ActionEvent e)
2854 viewport.setShowJVSuffix(seqLimits.isSelected());
2856 alignPanel.getIdPanel().getIdCanvas()
2857 .setPreferredSize(alignPanel.calculateIdWidth());
2858 alignPanel.paintAlignment(true, false);
2862 public void idRightAlign_actionPerformed(ActionEvent e)
2864 viewport.setRightAlignIds(idRightAlign.isSelected());
2865 alignPanel.paintAlignment(false, false);
2869 public void centreColumnLabels_actionPerformed(ActionEvent e)
2871 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2872 alignPanel.paintAlignment(false, false);
2878 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2881 protected void followHighlight_actionPerformed()
2884 * Set the 'follow' flag on the Viewport (and scroll to position if now
2887 final boolean state = this.followHighlightMenuItem.getState();
2888 viewport.setFollowHighlight(state);
2891 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2902 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2904 viewport.setColourText(colourTextMenuItem.isSelected());
2905 alignPanel.paintAlignment(false, false);
2915 public void wrapMenuItem_actionPerformed(ActionEvent e)
2917 scaleAbove.setVisible(wrapMenuItem.isSelected());
2918 scaleLeft.setVisible(wrapMenuItem.isSelected());
2919 scaleRight.setVisible(wrapMenuItem.isSelected());
2920 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2921 alignPanel.updateLayout();
2925 public void showAllSeqs_actionPerformed(ActionEvent e)
2927 viewport.showAllHiddenSeqs();
2931 public void showAllColumns_actionPerformed(ActionEvent e)
2933 viewport.showAllHiddenColumns();
2934 alignPanel.paintAlignment(true, true);
2935 viewport.sendSelection();
2939 public void hideSelSequences_actionPerformed(ActionEvent e)
2941 viewport.hideAllSelectedSeqs();
2945 * called by key handler and the hide all/show all menu items
2950 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2953 boolean hide = false;
2954 SequenceGroup sg = viewport.getSelectionGroup();
2955 if (!toggleSeqs && !toggleCols)
2957 // Hide everything by the current selection - this is a hack - we do the
2958 // invert and then hide
2959 // first check that there will be visible columns after the invert.
2960 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2961 && sg.getStartRes() <= sg.getEndRes()))
2963 // now invert the sequence set, if required - empty selection implies
2964 // that no hiding is required.
2967 invertSequenceMenuItem_actionPerformed(null);
2968 sg = viewport.getSelectionGroup();
2972 viewport.expandColSelection(sg, true);
2973 // finally invert the column selection and get the new sequence
2975 invertColSel_actionPerformed(null);
2982 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2984 hideSelSequences_actionPerformed(null);
2987 else if (!(toggleCols && viewport.hasSelectedColumns()))
2989 showAllSeqs_actionPerformed(null);
2995 if (viewport.hasSelectedColumns())
2997 hideSelColumns_actionPerformed(null);
3000 viewport.setSelectionGroup(sg);
3005 showAllColumns_actionPerformed(null);
3014 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3015 * event.ActionEvent)
3018 public void hideAllButSelection_actionPerformed(ActionEvent e)
3020 toggleHiddenRegions(false, false);
3021 viewport.sendSelection();
3028 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3032 public void hideAllSelection_actionPerformed(ActionEvent e)
3034 SequenceGroup sg = viewport.getSelectionGroup();
3035 viewport.expandColSelection(sg, false);
3036 viewport.hideAllSelectedSeqs();
3037 viewport.hideSelectedColumns();
3038 alignPanel.paintAlignment(true, true);
3039 viewport.sendSelection();
3046 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3050 public void showAllhidden_actionPerformed(ActionEvent e)
3052 viewport.showAllHiddenColumns();
3053 viewport.showAllHiddenSeqs();
3054 alignPanel.paintAlignment(true, true);
3055 viewport.sendSelection();
3059 public void hideSelColumns_actionPerformed(ActionEvent e)
3061 viewport.hideSelectedColumns();
3062 alignPanel.paintAlignment(true, true);
3063 viewport.sendSelection();
3067 public void hiddenMarkers_actionPerformed(ActionEvent e)
3069 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3080 protected void scaleAbove_actionPerformed(ActionEvent e)
3082 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3083 // TODO: do we actually need to update overview for scale above change ?
3084 alignPanel.paintAlignment(true, false);
3094 protected void scaleLeft_actionPerformed(ActionEvent e)
3096 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3097 alignPanel.paintAlignment(true, false);
3107 protected void scaleRight_actionPerformed(ActionEvent e)
3109 viewport.setScaleRightWrapped(scaleRight.isSelected());
3110 alignPanel.paintAlignment(true, false);
3120 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3122 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3123 alignPanel.paintAlignment(false, false);
3133 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3135 viewport.setShowText(viewTextMenuItem.isSelected());
3136 alignPanel.paintAlignment(false, false);
3146 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3148 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3149 alignPanel.paintAlignment(false, false);
3152 public FeatureSettings featureSettings;
3155 public FeatureSettingsControllerI getFeatureSettingsUI()
3157 return featureSettings;
3161 public void featureSettings_actionPerformed(ActionEvent e)
3163 if (featureSettings != null)
3165 featureSettings.close();
3166 featureSettings = null;
3168 if (!showSeqFeatures.isSelected())
3170 // make sure features are actually displayed
3171 showSeqFeatures.setSelected(true);
3172 showSeqFeatures_actionPerformed(null);
3174 featureSettings = new FeatureSettings(this);
3178 * Set or clear 'Show Sequence Features'
3184 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3186 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3187 alignPanel.paintAlignment(true, true);
3191 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3192 * the annotations panel as a whole.
3194 * The options to show/hide all annotations should be enabled when the panel
3195 * is shown, and disabled when the panel is hidden.
3200 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3202 final boolean setVisible = annotationPanelMenuItem.isSelected();
3203 viewport.setShowAnnotation(setVisible);
3204 this.showAllSeqAnnotations.setEnabled(setVisible);
3205 this.hideAllSeqAnnotations.setEnabled(setVisible);
3206 this.showAllAlAnnotations.setEnabled(setVisible);
3207 this.hideAllAlAnnotations.setEnabled(setVisible);
3208 alignPanel.updateLayout();
3212 public void alignmentProperties()
3214 JEditorPane editPane = new JEditorPane("text/html", "");
3215 editPane.setEditable(false);
3216 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3219 MessageManager.formatMessage("label.html_content", new Object[]
3220 { contents.toString() }));
3221 JInternalFrame frame = new JInternalFrame();
3222 frame.getContentPane().add(new JScrollPane(editPane));
3224 Desktop.addInternalFrame(frame, MessageManager
3225 .formatMessage("label.alignment_properties", new Object[]
3226 { getTitle() }), 500, 400);
3236 public void overviewMenuItem_actionPerformed(ActionEvent e)
3238 if (alignPanel.overviewPanel != null)
3243 JInternalFrame frame = new JInternalFrame();
3244 final OverviewPanel overview = new OverviewPanel(alignPanel);
3245 frame.setContentPane(overview);
3246 Desktop.addInternalFrame(frame, MessageManager
3247 .formatMessage("label.overview_params", new Object[]
3248 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3251 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3252 frame.addInternalFrameListener(
3253 new javax.swing.event.InternalFrameAdapter()
3256 public void internalFrameClosed(
3257 javax.swing.event.InternalFrameEvent evt)
3260 alignPanel.setOverviewPanel(null);
3263 if (getKeyListeners().length > 0)
3265 frame.addKeyListener(getKeyListeners()[0]);
3268 alignPanel.setOverviewPanel(overview);
3272 public void textColour_actionPerformed()
3274 new TextColourChooser().chooseColour(alignPanel, null);
3278 * public void covariationColour_actionPerformed() {
3280 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3284 public void annotationColour_actionPerformed()
3286 new AnnotationColourChooser(viewport, alignPanel);
3290 public void annotationColumn_actionPerformed(ActionEvent e)
3292 new AnnotationColumnChooser(viewport, alignPanel);
3296 * Action on the user checking or unchecking the option to apply the selected
3297 * colour scheme to all groups. If unchecked, groups may have their own
3298 * independent colour schemes.
3303 public void applyToAllGroups_actionPerformed(boolean selected)
3305 viewport.setColourAppliesToAllGroups(selected);
3309 * Action on user selecting a colour from the colour menu
3312 * the name (not the menu item label!) of the colour scheme
3315 public void changeColour_actionPerformed(String name)
3318 * 'User Defined' opens a panel to configure or load a
3319 * user-defined colour scheme
3321 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3323 new UserDefinedColours(alignPanel);
3328 * otherwise set the chosen colour scheme (or null for 'None')
3330 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3331 viewport.getAlignment(), viewport.getHiddenRepSequences());
3336 * Actions on setting or changing the alignment colour scheme
3341 public void changeColour(ColourSchemeI cs)
3343 // TODO: pull up to controller method
3344 ColourMenuHelper.setColourSelected(colourMenu, cs);
3346 viewport.setGlobalColourScheme(cs);
3348 alignPanel.paintAlignment(true, true);
3352 * Show the PID threshold slider panel
3355 protected void modifyPID_actionPerformed()
3357 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3358 alignPanel.getViewName());
3359 SliderPanel.showPIDSlider();
3363 * Show the Conservation slider panel
3366 protected void modifyConservation_actionPerformed()
3368 SliderPanel.setConservationSlider(alignPanel,
3369 viewport.getResidueShading(), alignPanel.getViewName());
3370 SliderPanel.showConservationSlider();
3374 * Action on selecting or deselecting (Colour) By Conservation
3377 public void conservationMenuItem_actionPerformed(boolean selected)
3379 modifyConservation.setEnabled(selected);
3380 viewport.setConservationSelected(selected);
3381 viewport.getResidueShading().setConservationApplied(selected);
3383 changeColour(viewport.getGlobalColourScheme());
3386 modifyConservation_actionPerformed();
3390 SliderPanel.hideConservationSlider();
3395 * Action on selecting or deselecting (Colour) Above PID Threshold
3398 public void abovePIDThreshold_actionPerformed(boolean selected)
3400 modifyPID.setEnabled(selected);
3401 viewport.setAbovePIDThreshold(selected);
3404 viewport.getResidueShading().setThreshold(0,
3405 viewport.isIgnoreGapsConsensus());
3408 changeColour(viewport.getGlobalColourScheme());
3411 modifyPID_actionPerformed();
3415 SliderPanel.hidePIDSlider();
3426 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3428 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3429 AlignmentSorter.sortByPID(viewport.getAlignment(),
3430 viewport.getAlignment().getSequenceAt(0));
3431 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3432 viewport.getAlignment()));
3433 alignPanel.paintAlignment(true, false);
3443 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3445 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3446 AlignmentSorter.sortByID(viewport.getAlignment());
3448 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3449 alignPanel.paintAlignment(true, false);
3459 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3461 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3462 AlignmentSorter.sortByLength(viewport.getAlignment());
3463 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3464 viewport.getAlignment()));
3465 alignPanel.paintAlignment(true, false);
3475 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3477 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3478 AlignmentSorter.sortByGroup(viewport.getAlignment());
3479 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3480 viewport.getAlignment()));
3482 alignPanel.paintAlignment(true, false);
3492 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3494 new RedundancyPanel(alignPanel, this);
3504 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3506 if ((viewport.getSelectionGroup() == null)
3507 || (viewport.getSelectionGroup().getSize() < 2))
3509 JvOptionPane.showInternalMessageDialog(this,
3510 MessageManager.getString(
3511 "label.you_must_select_least_two_sequences"),
3512 MessageManager.getString("label.invalid_selection"),
3513 JvOptionPane.WARNING_MESSAGE);
3517 JInternalFrame frame = new JInternalFrame();
3518 frame.setContentPane(new PairwiseAlignPanel(viewport));
3519 Desktop.addInternalFrame(frame,
3520 MessageManager.getString("action.pairwise_alignment"), 600,
3526 public void autoCalculate_actionPerformed(ActionEvent e)
3528 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3529 if (viewport.autoCalculateConsensus)
3531 viewport.firePropertyChange("alignment", null,
3532 viewport.getAlignment().getSequences());
3537 public void sortByTreeOption_actionPerformed(ActionEvent e)
3539 viewport.sortByTree = sortByTree.isSelected();
3543 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3545 viewport.followSelection = listenToViewSelections.isSelected();
3549 * Constructs a tree panel and adds it to the desktop
3552 * tree type (NJ or AV)
3554 * name of score model used to compute the tree
3556 * parameters for the distance or similarity calculation
3558 void newTreePanel(String type, String modelName,
3559 SimilarityParamsI options)
3561 String frameTitle = "";
3564 boolean onSelection = false;
3565 if (viewport.getSelectionGroup() != null
3566 && viewport.getSelectionGroup().getSize() > 0)
3568 SequenceGroup sg = viewport.getSelectionGroup();
3570 /* Decide if the selection is a column region */
3571 for (SequenceI _s : sg.getSequences())
3573 if (_s.getLength() < sg.getEndRes())
3575 JvOptionPane.showMessageDialog(Desktop.desktop,
3576 MessageManager.getString(
3577 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3578 MessageManager.getString(
3579 "label.sequences_selection_not_aligned"),
3580 JvOptionPane.WARNING_MESSAGE);
3589 if (viewport.getAlignment().getHeight() < 2)
3595 tp = new TreePanel(alignPanel, type, modelName, options);
3596 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3598 frameTitle += " from ";
3600 if (viewport.viewName != null)
3602 frameTitle += viewport.viewName + " of ";
3605 frameTitle += this.title;
3607 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3618 public void addSortByOrderMenuItem(String title,
3619 final AlignmentOrder order)
3621 final JMenuItem item = new JMenuItem(MessageManager
3622 .formatMessage("action.by_title_param", new Object[]
3625 item.addActionListener(new java.awt.event.ActionListener()
3628 public void actionPerformed(ActionEvent e)
3630 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3632 // TODO: JBPNote - have to map order entries to curent SequenceI
3634 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3636 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3637 viewport.getAlignment()));
3639 alignPanel.paintAlignment(true, false);
3645 * Add a new sort by annotation score menu item
3648 * the menu to add the option to
3650 * the label used to retrieve scores for each sequence on the
3653 public void addSortByAnnotScoreMenuItem(JMenu sort,
3654 final String scoreLabel)
3656 final JMenuItem item = new JMenuItem(scoreLabel);
3658 item.addActionListener(new java.awt.event.ActionListener()
3661 public void actionPerformed(ActionEvent e)
3663 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3664 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3665 viewport.getAlignment());// ,viewport.getSelectionGroup());
3666 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3667 viewport.getAlignment()));
3668 alignPanel.paintAlignment(true, false);
3674 * last hash for alignment's annotation array - used to minimise cost of
3677 protected int _annotationScoreVectorHash;
3680 * search the alignment and rebuild the sort by annotation score submenu the
3681 * last alignment annotation vector hash is stored to minimize cost of
3682 * rebuilding in subsequence calls.
3686 public void buildSortByAnnotationScoresMenu()
3688 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3693 if (viewport.getAlignment().getAlignmentAnnotation()
3694 .hashCode() != _annotationScoreVectorHash)
3696 sortByAnnotScore.removeAll();
3697 // almost certainly a quicker way to do this - but we keep it simple
3698 Hashtable scoreSorts = new Hashtable();
3699 AlignmentAnnotation aann[];
3700 for (SequenceI sqa : viewport.getAlignment().getSequences())
3702 aann = sqa.getAnnotation();
3703 for (int i = 0; aann != null && i < aann.length; i++)
3705 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3707 scoreSorts.put(aann[i].label, aann[i].label);
3711 Enumeration labels = scoreSorts.keys();
3712 while (labels.hasMoreElements())
3714 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3715 (String) labels.nextElement());
3717 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3720 _annotationScoreVectorHash = viewport.getAlignment()
3721 .getAlignmentAnnotation().hashCode();
3726 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3727 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3728 * call. Listeners are added to remove the menu item when the treePanel is
3729 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3733 public void buildTreeSortMenu()
3735 sortByTreeMenu.removeAll();
3737 List<Component> comps = PaintRefresher.components
3738 .get(viewport.getSequenceSetId());
3739 List<TreePanel> treePanels = new ArrayList<>();
3740 for (Component comp : comps)
3742 if (comp instanceof TreePanel)
3744 treePanels.add((TreePanel) comp);
3748 if (treePanels.size() < 1)
3750 sortByTreeMenu.setVisible(false);
3754 sortByTreeMenu.setVisible(true);
3756 for (final TreePanel tp : treePanels)
3758 final JMenuItem item = new JMenuItem(tp.getTitle());
3759 item.addActionListener(new java.awt.event.ActionListener()
3762 public void actionPerformed(ActionEvent e)
3764 tp.sortByTree_actionPerformed();
3765 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3770 sortByTreeMenu.add(item);
3774 public boolean sortBy(AlignmentOrder alorder, String undoname)
3776 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3777 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3778 if (undoname != null)
3780 addHistoryItem(new OrderCommand(undoname, oldOrder,
3781 viewport.getAlignment()));
3783 alignPanel.paintAlignment(true, false);
3788 * Work out whether the whole set of sequences or just the selected set will
3789 * be submitted for multiple alignment.
3792 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3794 // Now, check we have enough sequences
3795 AlignmentView msa = null;
3797 if ((viewport.getSelectionGroup() != null)
3798 && (viewport.getSelectionGroup().getSize() > 1))
3800 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3801 // some common interface!
3803 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3804 * SequenceI[sz = seqs.getSize(false)];
3806 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3807 * seqs.getSequenceAt(i); }
3809 msa = viewport.getAlignmentView(true);
3811 else if (viewport.getSelectionGroup() != null
3812 && viewport.getSelectionGroup().getSize() == 1)
3814 int option = JvOptionPane.showConfirmDialog(this,
3815 MessageManager.getString("warn.oneseq_msainput_selection"),
3816 MessageManager.getString("label.invalid_selection"),
3817 JvOptionPane.OK_CANCEL_OPTION);
3818 if (option == JvOptionPane.OK_OPTION)
3820 msa = viewport.getAlignmentView(false);
3825 msa = viewport.getAlignmentView(false);
3831 * Decides what is submitted to a secondary structure prediction service: the
3832 * first sequence in the alignment, or in the current selection, or, if the
3833 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3834 * region or the whole alignment. (where the first sequence in the set is the
3835 * one that the prediction will be for).
3837 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3839 AlignmentView seqs = null;
3841 if ((viewport.getSelectionGroup() != null)
3842 && (viewport.getSelectionGroup().getSize() > 0))
3844 seqs = viewport.getAlignmentView(true);
3848 seqs = viewport.getAlignmentView(false);
3850 // limit sequences - JBPNote in future - could spawn multiple prediction
3852 // TODO: viewport.getAlignment().isAligned is a global state - the local
3853 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3854 if (!viewport.getAlignment().isAligned(false))
3856 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3857 // TODO: if seqs.getSequences().length>1 then should really have warned
3871 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3873 // Pick the tree file
3874 JalviewFileChooser chooser = new JalviewFileChooser(
3875 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3876 chooser.setFileView(new JalviewFileView());
3877 chooser.setDialogTitle(
3878 MessageManager.getString("label.select_newick_like_tree_file"));
3879 chooser.setToolTipText(
3880 MessageManager.getString("label.load_tree_file"));
3882 int value = chooser.showOpenDialog(null);
3884 if (value == JalviewFileChooser.APPROVE_OPTION)
3886 String filePath = chooser.getSelectedFile().getPath();
3887 Cache.setProperty("LAST_DIRECTORY", filePath);
3888 NewickFile fin = null;
3891 fin = new NewickFile(filePath, DataSourceType.FILE);
3892 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3893 } catch (Exception ex)
3895 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3896 MessageManager.getString("label.problem_reading_tree_file"),
3897 JvOptionPane.WARNING_MESSAGE);
3898 ex.printStackTrace();
3900 if (fin != null && fin.hasWarningMessage())
3902 JvOptionPane.showMessageDialog(Desktop.desktop,
3903 fin.getWarningMessage(),
3905 .getString("label.possible_problem_with_tree_file"),
3906 JvOptionPane.WARNING_MESSAGE);
3911 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3913 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3916 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3917 int h, int x, int y)
3919 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3923 * Add a treeviewer for the tree extracted from a Newick file object to the
3924 * current alignment view
3931 * Associated alignment input data (or null)
3940 * @return TreePanel handle
3942 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3943 AlignmentView input, int w, int h, int x, int y)
3945 TreePanel tp = null;
3951 if (nf.getTree() != null)
3953 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3959 tp.setLocation(x, y);
3962 Desktop.addInternalFrame(tp, treeTitle, w, h);
3964 } catch (Exception ex)
3966 ex.printStackTrace();
3972 private boolean buildingMenu = false;
3975 * Generates menu items and listener event actions for web service clients
3978 public void BuildWebServiceMenu()
3980 while (buildingMenu)
3984 System.err.println("Waiting for building menu to finish.");
3986 } catch (Exception e)
3990 final AlignFrame me = this;
3991 buildingMenu = true;
3992 new Thread(new Runnable()
3997 final List<JMenuItem> legacyItems = new ArrayList<>();
4000 // System.err.println("Building ws menu again "
4001 // + Thread.currentThread());
4002 // TODO: add support for context dependent disabling of services based
4004 // alignment and current selection
4005 // TODO: add additional serviceHandle parameter to specify abstract
4007 // class independently of AbstractName
4008 // TODO: add in rediscovery GUI function to restart discoverer
4009 // TODO: group services by location as well as function and/or
4011 // object broker mechanism.
4012 final Vector<JMenu> wsmenu = new Vector<>();
4013 final IProgressIndicator af = me;
4016 * do not i18n these strings - they are hard-coded in class
4017 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4018 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4020 final JMenu msawsmenu = new JMenu("Alignment");
4021 final JMenu secstrmenu = new JMenu(
4022 "Secondary Structure Prediction");
4023 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4024 final JMenu analymenu = new JMenu("Analysis");
4025 final JMenu dismenu = new JMenu("Protein Disorder");
4026 // JAL-940 - only show secondary structure prediction services from
4027 // the legacy server
4028 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4030 Discoverer.services != null && (Discoverer.services.size() > 0))
4032 // TODO: refactor to allow list of AbstractName/Handler bindings to
4034 // stored or retrieved from elsewhere
4035 // No MSAWS used any more:
4036 // Vector msaws = null; // (Vector)
4037 // Discoverer.services.get("MsaWS");
4038 Vector secstrpr = (Vector) Discoverer.services
4040 if (secstrpr != null)
4042 // Add any secondary structure prediction services
4043 for (int i = 0, j = secstrpr.size(); i < j; i++)
4045 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4047 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4048 .getServiceClient(sh);
4049 int p = secstrmenu.getItemCount();
4050 impl.attachWSMenuEntry(secstrmenu, me);
4051 int q = secstrmenu.getItemCount();
4052 for (int litm = p; litm < q; litm++)
4054 legacyItems.add(secstrmenu.getItem(litm));
4060 // Add all submenus in the order they should appear on the web
4062 wsmenu.add(msawsmenu);
4063 wsmenu.add(secstrmenu);
4064 wsmenu.add(dismenu);
4065 wsmenu.add(analymenu);
4066 // No search services yet
4067 // wsmenu.add(seqsrchmenu);
4069 javax.swing.SwingUtilities.invokeLater(new Runnable()
4076 webService.removeAll();
4077 // first, add discovered services onto the webservices menu
4078 if (wsmenu.size() > 0)
4080 for (int i = 0, j = wsmenu.size(); i < j; i++)
4082 webService.add(wsmenu.get(i));
4087 webService.add(me.webServiceNoServices);
4089 // TODO: move into separate menu builder class.
4090 boolean new_sspred = false;
4091 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4093 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4094 if (jws2servs != null)
4096 if (jws2servs.hasServices())
4098 jws2servs.attachWSMenuEntry(webService, me);
4099 for (Jws2Instance sv : jws2servs.getServices())
4101 if (sv.description.toLowerCase().contains("jpred"))
4103 for (JMenuItem jmi : legacyItems)
4105 jmi.setVisible(false);
4111 if (jws2servs.isRunning())
4113 JMenuItem tm = new JMenuItem(
4114 "Still discovering JABA Services");
4115 tm.setEnabled(false);
4120 build_urlServiceMenu(me.webService);
4121 build_fetchdbmenu(webService);
4122 for (JMenu item : wsmenu)
4124 if (item.getItemCount() == 0)
4126 item.setEnabled(false);
4130 item.setEnabled(true);
4133 } catch (Exception e)
4136 "Exception during web service menu building process.",
4141 } catch (Exception e)
4144 buildingMenu = false;
4151 * construct any groupURL type service menu entries.
4155 private void build_urlServiceMenu(JMenu webService)
4157 // TODO: remove this code when 2.7 is released
4158 // DEBUG - alignmentView
4160 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4161 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4163 * @Override public void actionPerformed(ActionEvent e) {
4164 * jalview.datamodel.AlignmentView
4165 * .testSelectionViews(af.viewport.getAlignment(),
4166 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4168 * }); webService.add(testAlView);
4170 // TODO: refactor to RestClient discoverer and merge menu entries for
4171 // rest-style services with other types of analysis/calculation service
4172 // SHmmr test client - still being implemented.
4173 // DEBUG - alignmentView
4175 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4178 client.attachWSMenuEntry(
4179 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4185 * Searches the alignment sequences for xRefs and builds the Show
4186 * Cross-References menu (formerly called Show Products), with database
4187 * sources for which cross-references are found (protein sources for a
4188 * nucleotide alignment and vice versa)
4190 * @return true if Show Cross-references menu should be enabled
4192 public boolean canShowProducts()
4194 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4195 AlignmentI dataset = viewport.getAlignment().getDataset();
4197 showProducts.removeAll();
4198 final boolean dna = viewport.getAlignment().isNucleotide();
4200 if (seqs == null || seqs.length == 0)
4202 // nothing to see here.
4206 boolean showp = false;
4209 List<String> ptypes = new CrossRef(seqs, dataset)
4210 .findXrefSourcesForSequences(dna);
4212 for (final String source : ptypes)
4215 final AlignFrame af = this;
4216 JMenuItem xtype = new JMenuItem(source);
4217 xtype.addActionListener(new ActionListener()
4220 public void actionPerformed(ActionEvent e)
4222 showProductsFor(af.viewport.getSequenceSelection(), dna,
4226 showProducts.add(xtype);
4228 showProducts.setVisible(showp);
4229 showProducts.setEnabled(showp);
4230 } catch (Exception e)
4233 "canShowProducts threw an exception - please report to help@jalview.org",
4241 * Finds and displays cross-references for the selected sequences (protein
4242 * products for nucleotide sequences, dna coding sequences for peptides).
4245 * the sequences to show cross-references for
4247 * true if from a nucleotide alignment (so showing proteins)
4249 * the database to show cross-references for
4251 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4252 final String source)
4254 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4259 * Construct and display a new frame containing the translation of this
4260 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4263 public void showTranslation_actionPerformed(ActionEvent e)
4265 AlignmentI al = null;
4268 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4270 al = dna.translateCdna();
4271 } catch (Exception ex)
4273 jalview.bin.Cache.log.error(
4274 "Exception during translation. Please report this !", ex);
4275 final String msg = MessageManager.getString(
4276 "label.error_when_translating_sequences_submit_bug_report");
4277 final String errorTitle = MessageManager
4278 .getString("label.implementation_error")
4279 + MessageManager.getString("label.translation_failed");
4280 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4281 JvOptionPane.ERROR_MESSAGE);
4284 if (al == null || al.getHeight() == 0)
4286 final String msg = MessageManager.getString(
4287 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4288 final String errorTitle = MessageManager
4289 .getString("label.translation_failed");
4290 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4291 JvOptionPane.WARNING_MESSAGE);
4295 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4296 af.setFileFormat(this.currentFileFormat);
4297 final String newTitle = MessageManager
4298 .formatMessage("label.translation_of_params", new Object[]
4299 { this.getTitle() });
4300 af.setTitle(newTitle);
4301 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4303 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4304 viewport.openSplitFrame(af, new Alignment(seqs));
4308 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4315 * Set the file format
4319 public void setFileFormat(FileFormatI format)
4321 this.currentFileFormat = format;
4325 * Try to load a features file onto the alignment.
4328 * contents or path to retrieve file
4330 * access mode of file (see jalview.io.AlignFile)
4331 * @return true if features file was parsed correctly.
4333 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4335 return avc.parseFeaturesFile(file, sourceType,
4336 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4341 public void refreshFeatureUI(boolean enableIfNecessary)
4343 // note - currently this is only still here rather than in the controller
4344 // because of the featureSettings hard reference that is yet to be
4346 if (enableIfNecessary)
4348 viewport.setShowSequenceFeatures(true);
4349 showSeqFeatures.setSelected(true);
4355 public void dragEnter(DropTargetDragEvent evt)
4360 public void dragExit(DropTargetEvent evt)
4365 public void dragOver(DropTargetDragEvent evt)
4370 public void dropActionChanged(DropTargetDragEvent evt)
4375 public void drop(DropTargetDropEvent evt)
4377 // JAL-1552 - acceptDrop required before getTransferable call for
4378 // Java's Transferable for native dnd
4379 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4380 Transferable t = evt.getTransferable();
4381 final AlignFrame thisaf = this;
4382 final List<String> files = new ArrayList<>();
4383 List<DataSourceType> protocols = new ArrayList<>();
4387 Desktop.transferFromDropTarget(files, protocols, evt, t);
4388 } catch (Exception e)
4390 e.printStackTrace();
4394 new Thread(new Runnable()
4401 // check to see if any of these files have names matching sequences
4404 SequenceIdMatcher idm = new SequenceIdMatcher(
4405 viewport.getAlignment().getSequencesArray());
4407 * Object[] { String,SequenceI}
4409 ArrayList<Object[]> filesmatched = new ArrayList<>();
4410 ArrayList<String> filesnotmatched = new ArrayList<>();
4411 for (int i = 0; i < files.size(); i++)
4413 String file = files.get(i).toString();
4415 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4416 if (protocol == DataSourceType.FILE)
4418 File fl = new File(file);
4419 pdbfn = fl.getName();
4421 else if (protocol == DataSourceType.URL)
4423 URL url = new URL(file);
4424 pdbfn = url.getFile();
4426 if (pdbfn.length() > 0)
4428 // attempt to find a match in the alignment
4429 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4430 int l = 0, c = pdbfn.indexOf(".");
4431 while (mtch == null && c != -1)
4436 } while ((c = pdbfn.indexOf(".", l)) > l);
4439 pdbfn = pdbfn.substring(0, l);
4441 mtch = idm.findAllIdMatches(pdbfn);
4445 FileFormatI type = null;
4448 type = new IdentifyFile().identify(file, protocol);
4449 } catch (Exception ex)
4453 if (type != null && type.isStructureFile())
4455 filesmatched.add(new Object[] { file, protocol, mtch });
4459 // File wasn't named like one of the sequences or wasn't a PDB
4461 filesnotmatched.add(file);
4465 if (filesmatched.size() > 0)
4467 boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4470 String msg = MessageManager.formatMessage(
4471 "label.automatically_associate_structure_files_with_sequences_same_name",
4473 { Integer.valueOf(filesmatched.size())
4475 String ttl = MessageManager.getString(
4476 "label.automatically_associate_structure_files_by_name");
4477 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4478 ttl, JvOptionPane.YES_NO_OPTION);
4479 autoAssociate = choice == JvOptionPane.YES_OPTION;
4483 for (Object[] fm : filesmatched)
4485 // try and associate
4486 // TODO: may want to set a standard ID naming formalism for
4487 // associating PDB files which have no IDs.
4488 for (SequenceI toassoc : (SequenceI[]) fm[2])
4490 PDBEntry pe = new AssociatePdbFileWithSeq()
4491 .associatePdbWithSeq((String) fm[0],
4492 (DataSourceType) fm[1], toassoc, false,
4496 System.err.println("Associated file : "
4497 + ((String) fm[0]) + " with "
4498 + toassoc.getDisplayId(true));
4502 // TODO: do we need to update overview ? only if features are
4504 alignPanel.paintAlignment(true, false);
4510 * add declined structures as sequences
4512 for (Object[] o : filesmatched)
4514 filesnotmatched.add((String) o[0]);
4518 if (filesnotmatched.size() > 0)
4520 if (assocfiles > 0 && (Cache.getDefault(
4521 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4522 || JvOptionPane.showConfirmDialog(thisaf,
4523 "<html>" + MessageManager.formatMessage(
4524 "label.ignore_unmatched_dropped_files_info",
4527 filesnotmatched.size())
4530 MessageManager.getString(
4531 "label.ignore_unmatched_dropped_files"),
4532 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4536 for (String fn : filesnotmatched)
4538 loadJalviewDataFile(fn, null, null, null);
4542 } catch (Exception ex)
4544 ex.printStackTrace();
4552 * Attempt to load a "dropped" file or URL string, by testing in turn for
4554 * <li>an Annotation file</li>
4555 * <li>a JNet file</li>
4556 * <li>a features file</li>
4557 * <li>else try to interpret as an alignment file</li>
4561 * either a filename or a URL string.
4563 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4564 FileFormatI format, SequenceI assocSeq)
4568 if (sourceType == null)
4570 sourceType = FormatAdapter.checkProtocol(file);
4572 // if the file isn't identified, or not positively identified as some
4573 // other filetype (PFAM is default unidentified alignment file type) then
4574 // try to parse as annotation.
4575 boolean isAnnotation = (format == null
4576 || FileFormat.Pfam.equals(format))
4577 ? new AnnotationFile().annotateAlignmentView(viewport,
4583 // first see if its a T-COFFEE score file
4584 TCoffeeScoreFile tcf = null;
4587 tcf = new TCoffeeScoreFile(file, sourceType);
4590 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4594 new TCoffeeColourScheme(viewport.getAlignment()));
4595 isAnnotation = true;
4596 statusBar.setText(MessageManager.getString(
4597 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4601 // some problem - if no warning its probable that the ID matching
4602 // process didn't work
4603 JvOptionPane.showMessageDialog(Desktop.desktop,
4604 tcf.getWarningMessage() == null
4605 ? MessageManager.getString(
4606 "label.check_file_matches_sequence_ids_alignment")
4607 : tcf.getWarningMessage(),
4608 MessageManager.getString(
4609 "label.problem_reading_tcoffee_score_file"),
4610 JvOptionPane.WARNING_MESSAGE);
4617 } catch (Exception x)
4620 "Exception when processing data source as T-COFFEE score file",
4626 // try to see if its a JNet 'concise' style annotation file *before*
4628 // try to parse it as a features file
4631 format = new IdentifyFile().identify(file, sourceType);
4633 if (FileFormat.ScoreMatrix == format)
4635 ScoreMatrixFile sm = new ScoreMatrixFile(
4636 new FileParse(file, sourceType));
4638 // todo: i18n this message
4639 statusBar.setText(MessageManager.formatMessage(
4640 "label.successfully_loaded_matrix",
4641 sm.getMatrixName()));
4643 else if (FileFormat.Jnet.equals(format))
4645 JPredFile predictions = new JPredFile(file, sourceType);
4646 new JnetAnnotationMaker();
4647 JnetAnnotationMaker.add_annotation(predictions,
4648 viewport.getAlignment(), 0, false);
4649 viewport.getAlignment().setupJPredAlignment();
4650 isAnnotation = true;
4652 // else if (IdentifyFile.FeaturesFile.equals(format))
4653 else if (FileFormat.Features.equals(format))
4655 if (parseFeaturesFile(file, sourceType))
4657 alignPanel.paintAlignment(true, true);
4662 new FileLoader().LoadFile(viewport, file, sourceType, format);
4669 alignPanel.adjustAnnotationHeight();
4670 viewport.updateSequenceIdColours();
4671 buildSortByAnnotationScoresMenu();
4672 alignPanel.paintAlignment(true, true);
4674 } catch (Exception ex)
4676 ex.printStackTrace();
4677 } catch (OutOfMemoryError oom)
4682 } catch (Exception x)
4687 + (sourceType != null
4688 ? (sourceType == DataSourceType.PASTE
4690 : "using " + sourceType + " from "
4694 ? "(parsing as '" + format + "' file)"
4696 oom, Desktop.desktop);
4701 * Method invoked by the ChangeListener on the tabbed pane, in other words
4702 * when a different tabbed pane is selected by the user or programmatically.
4705 public void tabSelectionChanged(int index)
4709 alignPanel = alignPanels.get(index);
4710 viewport = alignPanel.av;
4711 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4712 setMenusFromViewport(viewport);
4716 * 'focus' any colour slider that is open to the selected viewport
4718 if (viewport.getConservationSelected())
4720 SliderPanel.setConservationSlider(alignPanel,
4721 viewport.getResidueShading(), alignPanel.getViewName());
4725 SliderPanel.hideConservationSlider();
4727 if (viewport.getAbovePIDThreshold())
4729 SliderPanel.setPIDSliderSource(alignPanel,
4730 viewport.getResidueShading(), alignPanel.getViewName());
4734 SliderPanel.hidePIDSlider();
4738 * If there is a frame linked to this one in a SplitPane, switch it to the
4739 * same view tab index. No infinite recursion of calls should happen, since
4740 * tabSelectionChanged() should not get invoked on setting the selected
4741 * index to an unchanged value. Guard against setting an invalid index
4742 * before the new view peer tab has been created.
4744 final AlignViewportI peer = viewport.getCodingComplement();
4747 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4748 .getAlignPanel().alignFrame;
4749 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4751 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4757 * On right mouse click on view tab, prompt for and set new view name.
4760 public void tabbedPane_mousePressed(MouseEvent e)
4762 if (e.isPopupTrigger())
4764 String msg = MessageManager.getString("label.enter_view_name");
4765 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4766 JvOptionPane.QUESTION_MESSAGE);
4770 viewport.viewName = reply;
4771 // TODO warn if reply is in getExistingViewNames()?
4772 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4777 public AlignViewport getCurrentView()
4783 * Open the dialog for regex description parsing.
4786 protected void extractScores_actionPerformed(ActionEvent e)
4788 ParseProperties pp = new jalview.analysis.ParseProperties(
4789 viewport.getAlignment());
4790 // TODO: verify regex and introduce GUI dialog for version 2.5
4791 // if (pp.getScoresFromDescription("col", "score column ",
4792 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4794 if (pp.getScoresFromDescription("description column",
4795 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4797 buildSortByAnnotationScoresMenu();
4805 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4809 protected void showDbRefs_actionPerformed(ActionEvent e)
4811 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4817 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4821 protected void showNpFeats_actionPerformed(ActionEvent e)
4823 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4827 * find the viewport amongst the tabs in this alignment frame and close that
4832 public boolean closeView(AlignViewportI av)
4836 this.closeMenuItem_actionPerformed(false);
4839 Component[] comp = tabbedPane.getComponents();
4840 for (int i = 0; comp != null && i < comp.length; i++)
4842 if (comp[i] instanceof AlignmentPanel)
4844 if (((AlignmentPanel) comp[i]).av == av)
4847 closeView((AlignmentPanel) comp[i]);
4855 protected void build_fetchdbmenu(JMenu webService)
4857 // Temporary hack - DBRef Fetcher always top level ws entry.
4858 // TODO We probably want to store a sequence database checklist in
4859 // preferences and have checkboxes.. rather than individual sources selected
4861 final JMenu rfetch = new JMenu(
4862 MessageManager.getString("action.fetch_db_references"));
4863 rfetch.setToolTipText(MessageManager.getString(
4864 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4865 webService.add(rfetch);
4867 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4868 MessageManager.getString("option.trim_retrieved_seqs"));
4869 trimrs.setToolTipText(
4870 MessageManager.getString("label.trim_retrieved_sequences"));
4872 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4873 trimrs.addActionListener(new ActionListener()
4876 public void actionPerformed(ActionEvent e)
4878 trimrs.setSelected(trimrs.isSelected());
4879 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4880 Boolean.valueOf(trimrs.isSelected()).toString());
4884 JMenuItem fetchr = new JMenuItem(
4885 MessageManager.getString("label.standard_databases"));
4886 fetchr.setToolTipText(
4887 MessageManager.getString("label.fetch_embl_uniprot"));
4888 fetchr.addActionListener(new ActionListener()
4892 public void actionPerformed(ActionEvent e)
4894 new Thread(new Runnable()
4899 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4900 .getAlignment().isNucleotide();
4901 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4902 alignPanel.av.getSequenceSelection(),
4903 alignPanel.alignFrame, null,
4904 alignPanel.alignFrame.featureSettings, isNucleotide);
4905 dbRefFetcher.addListener(new FetchFinishedListenerI()
4908 public void finished()
4910 AlignFrame.this.setMenusForViewport();
4913 dbRefFetcher.fetchDBRefs(false);
4921 final AlignFrame me = this;
4922 new Thread(new Runnable()
4927 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4928 .getSequenceFetcherSingleton(me);
4929 javax.swing.SwingUtilities.invokeLater(new Runnable()
4934 String[] dbclasses = sf.getOrderedSupportedSources();
4935 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4936 // jalview.util.QuickSort.sort(otherdb, otherdb);
4937 List<DbSourceProxy> otherdb;
4938 JMenu dfetch = new JMenu();
4939 JMenu ifetch = new JMenu();
4940 JMenuItem fetchr = null;
4941 int comp = 0, icomp = 0, mcomp = 15;
4942 String mname = null;
4944 for (String dbclass : dbclasses)
4946 otherdb = sf.getSourceProxy(dbclass);
4947 // add a single entry for this class, or submenu allowing 'fetch
4949 if (otherdb == null || otherdb.size() < 1)
4953 // List<DbSourceProxy> dbs=otherdb;
4954 // otherdb=new ArrayList<DbSourceProxy>();
4955 // for (DbSourceProxy db:dbs)
4957 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4961 mname = "From " + dbclass;
4963 if (otherdb.size() == 1)
4965 final DbSourceProxy[] dassource = otherdb
4966 .toArray(new DbSourceProxy[0]);
4967 DbSourceProxy src = otherdb.get(0);
4968 fetchr = new JMenuItem(src.getDbSource());
4969 fetchr.addActionListener(new ActionListener()
4973 public void actionPerformed(ActionEvent e)
4975 new Thread(new Runnable()
4981 boolean isNucleotide = alignPanel.alignFrame
4982 .getViewport().getAlignment()
4984 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4985 alignPanel.av.getSequenceSelection(),
4986 alignPanel.alignFrame, dassource,
4987 alignPanel.alignFrame.featureSettings,
4990 .addListener(new FetchFinishedListenerI()
4993 public void finished()
4995 AlignFrame.this.setMenusForViewport();
4998 dbRefFetcher.fetchDBRefs(false);
5004 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5005 MessageManager.formatMessage(
5006 "label.fetch_retrieve_from", new Object[]
5007 { src.getDbName() })));
5013 final DbSourceProxy[] dassource = otherdb
5014 .toArray(new DbSourceProxy[0]);
5016 DbSourceProxy src = otherdb.get(0);
5017 fetchr = new JMenuItem(MessageManager
5018 .formatMessage("label.fetch_all_param", new Object[]
5019 { src.getDbSource() }));
5020 fetchr.addActionListener(new ActionListener()
5023 public void actionPerformed(ActionEvent e)
5025 new Thread(new Runnable()
5031 boolean isNucleotide = alignPanel.alignFrame
5032 .getViewport().getAlignment()
5034 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5035 alignPanel.av.getSequenceSelection(),
5036 alignPanel.alignFrame, dassource,
5037 alignPanel.alignFrame.featureSettings,
5040 .addListener(new FetchFinishedListenerI()
5043 public void finished()
5045 AlignFrame.this.setMenusForViewport();
5048 dbRefFetcher.fetchDBRefs(false);
5054 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5055 MessageManager.formatMessage(
5056 "label.fetch_retrieve_from_all_sources",
5058 { Integer.valueOf(otherdb.size())
5060 src.getDbSource(), src.getDbName() })));
5063 // and then build the rest of the individual menus
5064 ifetch = new JMenu(MessageManager.formatMessage(
5065 "label.source_from_db_source", new Object[]
5066 { src.getDbSource() }));
5068 String imname = null;
5070 for (DbSourceProxy sproxy : otherdb)
5072 String dbname = sproxy.getDbName();
5073 String sname = dbname.length() > 5
5074 ? dbname.substring(0, 5) + "..."
5076 String msname = dbname.length() > 10
5077 ? dbname.substring(0, 10) + "..."
5081 imname = MessageManager
5082 .formatMessage("label.from_msname", new Object[]
5085 fetchr = new JMenuItem(msname);
5086 final DbSourceProxy[] dassrc = { sproxy };
5087 fetchr.addActionListener(new ActionListener()
5091 public void actionPerformed(ActionEvent e)
5093 new Thread(new Runnable()
5099 boolean isNucleotide = alignPanel.alignFrame
5100 .getViewport().getAlignment()
5102 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5103 alignPanel.av.getSequenceSelection(),
5104 alignPanel.alignFrame, dassrc,
5105 alignPanel.alignFrame.featureSettings,
5108 .addListener(new FetchFinishedListenerI()
5111 public void finished()
5113 AlignFrame.this.setMenusForViewport();
5116 dbRefFetcher.fetchDBRefs(false);
5122 fetchr.setToolTipText(
5123 "<html>" + MessageManager.formatMessage(
5124 "label.fetch_retrieve_from", new Object[]
5128 if (++icomp >= mcomp || i == (otherdb.size()))
5130 ifetch.setText(MessageManager.formatMessage(
5131 "label.source_to_target", imname, sname));
5133 ifetch = new JMenu();
5141 if (comp >= mcomp || dbi >= (dbclasses.length))
5143 dfetch.setText(MessageManager.formatMessage(
5144 "label.source_to_target", mname, dbclass));
5146 dfetch = new JMenu();
5159 * Left justify the whole alignment.
5162 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5164 AlignmentI al = viewport.getAlignment();
5166 viewport.firePropertyChange("alignment", null, al);
5170 * Right justify the whole alignment.
5173 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5175 AlignmentI al = viewport.getAlignment();
5177 viewport.firePropertyChange("alignment", null, al);
5181 public void setShowSeqFeatures(boolean b)
5183 showSeqFeatures.setSelected(b);
5184 viewport.setShowSequenceFeatures(b);
5191 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5192 * awt.event.ActionEvent)
5195 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5197 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5198 alignPanel.paintAlignment(false, false);
5205 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5209 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5211 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5212 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5220 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5221 * .event.ActionEvent)
5224 protected void showGroupConservation_actionPerformed(ActionEvent e)
5226 viewport.setShowGroupConservation(showGroupConservation.getState());
5227 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5234 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5235 * .event.ActionEvent)
5238 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5240 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5241 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5248 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5249 * .event.ActionEvent)
5252 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5254 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5255 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5259 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5261 showSequenceLogo.setState(true);
5262 viewport.setShowSequenceLogo(true);
5263 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5264 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5268 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5270 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5277 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5278 * .event.ActionEvent)
5281 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5283 if (avc.makeGroupsFromSelection())
5285 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5286 alignPanel.updateAnnotation();
5287 alignPanel.paintAlignment(true, true);
5291 public void clearAlignmentSeqRep()
5293 // TODO refactor alignmentseqrep to controller
5294 if (viewport.getAlignment().hasSeqrep())
5296 viewport.getAlignment().setSeqrep(null);
5297 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5298 alignPanel.updateAnnotation();
5299 alignPanel.paintAlignment(true, true);
5304 protected void createGroup_actionPerformed(ActionEvent e)
5306 if (avc.createGroup())
5308 if (applyAutoAnnotationSettings.isSelected())
5310 alignPanel.updateAnnotation(true, false);
5312 alignPanel.alignmentChanged();
5317 protected void unGroup_actionPerformed(ActionEvent e)
5321 alignPanel.alignmentChanged();
5326 * make the given alignmentPanel the currently selected tab
5328 * @param alignmentPanel
5330 public void setDisplayedView(AlignmentPanel alignmentPanel)
5332 if (!viewport.getSequenceSetId()
5333 .equals(alignmentPanel.av.getSequenceSetId()))
5335 throw new Error(MessageManager.getString(
5336 "error.implementation_error_cannot_show_view_alignment_frame"));
5338 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5339 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5341 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5346 * Action on selection of menu options to Show or Hide annotations.
5349 * @param forSequences
5350 * update sequence-related annotations
5351 * @param forAlignment
5352 * update non-sequence-related annotations
5355 protected void setAnnotationsVisibility(boolean visible,
5356 boolean forSequences, boolean forAlignment)
5358 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5359 .getAlignmentAnnotation();
5364 for (AlignmentAnnotation aa : anns)
5367 * don't display non-positional annotations on an alignment
5369 if (aa.annotations == null)
5373 boolean apply = (aa.sequenceRef == null && forAlignment)
5374 || (aa.sequenceRef != null && forSequences);
5377 aa.visible = visible;
5380 alignPanel.validateAnnotationDimensions(true);
5381 alignPanel.alignmentChanged();
5385 * Store selected annotation sort order for the view and repaint.
5388 protected void sortAnnotations_actionPerformed()
5390 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5392 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5393 alignPanel.paintAlignment(false, false);
5398 * @return alignment panels in this alignment frame
5400 public List<? extends AlignmentViewPanel> getAlignPanels()
5402 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5406 * Open a new alignment window, with the cDNA associated with this (protein)
5407 * alignment, aligned as is the protein.
5409 protected void viewAsCdna_actionPerformed()
5411 // TODO no longer a menu action - refactor as required
5412 final AlignmentI alignment = getViewport().getAlignment();
5413 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5414 if (mappings == null)
5418 List<SequenceI> cdnaSeqs = new ArrayList<>();
5419 for (SequenceI aaSeq : alignment.getSequences())
5421 for (AlignedCodonFrame acf : mappings)
5423 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5427 * There is a cDNA mapping for this protein sequence - add to new
5428 * alignment. It will share the same dataset sequence as other mapped
5429 * cDNA (no new mappings need to be created).
5431 final Sequence newSeq = new Sequence(dnaSeq);
5432 newSeq.setDatasetSequence(dnaSeq);
5433 cdnaSeqs.add(newSeq);
5437 if (cdnaSeqs.size() == 0)
5439 // show a warning dialog no mapped cDNA
5442 AlignmentI cdna = new Alignment(
5443 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5444 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5445 AlignFrame.DEFAULT_HEIGHT);
5446 cdna.alignAs(alignment);
5447 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5449 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5450 AlignFrame.DEFAULT_HEIGHT);
5454 * Set visibility of dna/protein complement view (available when shown in a
5460 protected void showComplement_actionPerformed(boolean show)
5462 SplitContainerI sf = getSplitViewContainer();
5465 sf.setComplementVisible(this, show);
5470 * Generate the reverse (optionally complemented) of the selected sequences,
5471 * and add them to the alignment
5474 protected void showReverse_actionPerformed(boolean complement)
5476 AlignmentI al = null;
5479 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5480 al = dna.reverseCdna(complement);
5481 viewport.addAlignment(al, "");
5482 addHistoryItem(new EditCommand(
5483 MessageManager.getString("label.add_sequences"), Action.PASTE,
5484 al.getSequencesArray(), 0, al.getWidth(),
5485 viewport.getAlignment()));
5486 } catch (Exception ex)
5488 System.err.println(ex.getMessage());
5494 * Try to run a script in the Groovy console, having first ensured that this
5495 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5496 * be targeted at this alignment.
5499 protected void runGroovy_actionPerformed()
5501 Jalview.setCurrentAlignFrame(this);
5502 groovy.ui.Console console = Desktop.getGroovyConsole();
5503 if (console != null)
5507 console.runScript();
5508 } catch (Exception ex)
5510 System.err.println((ex.toString()));
5511 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5512 MessageManager.getString("label.couldnt_run_groovy_script"),
5513 MessageManager.getString("label.groovy_support_failed"),
5514 JvOptionPane.ERROR_MESSAGE);
5519 System.err.println("Can't run Groovy script as console not found");
5524 * Hides columns containing (or not containing) a specified feature, provided
5525 * that would not leave all columns hidden
5527 * @param featureType
5528 * @param columnsContaining
5531 public boolean hideFeatureColumns(String featureType,
5532 boolean columnsContaining)
5534 boolean notForHiding = avc.markColumnsContainingFeatures(
5535 columnsContaining, false, false, featureType);
5538 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5539 false, featureType))
5541 getViewport().hideSelectedColumns();
5549 protected void selectHighlightedColumns_actionPerformed(
5550 ActionEvent actionEvent)
5552 // include key modifier check in case user selects from menu
5553 avc.markHighlightedColumns(
5554 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5555 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5556 | ActionEvent.CTRL_MASK)) != 0);
5560 * Rebuilds the Colour menu, including any user-defined colours which have
5561 * been loaded either on startup or during the session
5563 public void buildColourMenu()
5565 colourMenu.removeAll();
5567 colourMenu.add(applyToAllGroups);
5568 colourMenu.add(textColour);
5569 colourMenu.addSeparator();
5571 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5574 colourMenu.addSeparator();
5575 colourMenu.add(conservationMenuItem);
5576 colourMenu.add(modifyConservation);
5577 colourMenu.add(abovePIDThreshold);
5578 colourMenu.add(modifyPID);
5579 colourMenu.add(annotationColour);
5581 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5582 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5586 * Open a dialog (if not already open) that allows the user to select and
5587 * calculate PCA or Tree analysis
5589 protected void openTreePcaDialog()
5591 if (alignPanel.getCalculationDialog() == null)
5593 new CalculationChooser(AlignFrame.this);
5598 protected void loadVcf_actionPerformed()
5600 JalviewFileChooser chooser = new JalviewFileChooser(
5601 Cache.getProperty("LAST_DIRECTORY"));
5602 chooser.setFileView(new JalviewFileView());
5603 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5604 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5606 int value = chooser.showOpenDialog(null);
5608 if (value == JalviewFileChooser.APPROVE_OPTION)
5610 String choice = chooser.getSelectedFile().getPath();
5611 Cache.setProperty("LAST_DIRECTORY", choice);
5612 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5613 new VCFLoader(choice).loadVCF(seqs, this);
5619 class PrintThread extends Thread
5623 public PrintThread(AlignmentPanel ap)
5628 static PageFormat pf;
5633 PrinterJob printJob = PrinterJob.getPrinterJob();
5637 printJob.setPrintable(ap, pf);
5641 printJob.setPrintable(ap);
5644 if (printJob.printDialog())
5649 } catch (Exception PrintException)
5651 PrintException.printStackTrace();