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.GeneticCodeI;
28 import jalview.analysis.ParseProperties;
29 import jalview.analysis.SequenceIdMatcher;
30 import jalview.api.AlignExportSettingI;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.AlignViewportI;
34 import jalview.api.AlignmentViewPanel;
35 import jalview.api.FeatureSettingsControllerI;
36 import jalview.api.SplitContainerI;
37 import jalview.api.ViewStyleI;
38 import jalview.api.analysis.SimilarityParamsI;
39 import jalview.bin.Cache;
40 import jalview.bin.Jalview;
41 import jalview.commands.CommandI;
42 import jalview.commands.EditCommand;
43 import jalview.commands.EditCommand.Action;
44 import jalview.commands.OrderCommand;
45 import jalview.commands.RemoveGapColCommand;
46 import jalview.commands.RemoveGapsCommand;
47 import jalview.commands.SlideSequencesCommand;
48 import jalview.commands.TrimRegionCommand;
49 import jalview.datamodel.AlignedCodonFrame;
50 import jalview.datamodel.Alignment;
51 import jalview.datamodel.AlignmentAnnotation;
52 import jalview.datamodel.AlignmentExportData;
53 import jalview.datamodel.AlignmentI;
54 import jalview.datamodel.AlignmentOrder;
55 import jalview.datamodel.AlignmentView;
56 import jalview.datamodel.ColumnSelection;
57 import jalview.datamodel.HiddenColumns;
58 import jalview.datamodel.HiddenSequences;
59 import jalview.datamodel.PDBEntry;
60 import jalview.datamodel.SeqCigar;
61 import jalview.datamodel.Sequence;
62 import jalview.datamodel.SequenceGroup;
63 import jalview.datamodel.SequenceI;
64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
66 import jalview.io.AlignmentProperties;
67 import jalview.io.AnnotationFile;
68 import jalview.io.BackupFiles;
69 import jalview.io.BioJsHTMLOutput;
70 import jalview.io.DataSourceType;
71 import jalview.io.FileFormat;
72 import jalview.io.FileFormatI;
73 import jalview.io.FileFormats;
74 import jalview.io.FileLoader;
75 import jalview.io.FileParse;
76 import jalview.io.FormatAdapter;
77 import jalview.io.HtmlSvgOutput;
78 import jalview.io.IdentifyFile;
79 import jalview.io.JPredFile;
80 import jalview.io.JalviewFileChooser;
81 import jalview.io.JalviewFileView;
82 import jalview.io.JnetAnnotationMaker;
83 import jalview.io.NewickFile;
84 import jalview.io.ScoreMatrixFile;
85 import jalview.io.TCoffeeScoreFile;
86 import jalview.io.vcf.VCFLoader;
87 import jalview.jbgui.GAlignFrame;
88 import jalview.schemes.ColourSchemeI;
89 import jalview.schemes.ColourSchemes;
90 import jalview.schemes.ResidueColourScheme;
91 import jalview.schemes.TCoffeeColourScheme;
92 import jalview.util.MessageManager;
93 import jalview.viewmodel.AlignmentViewport;
94 import jalview.viewmodel.ViewportRanges;
95 import jalview.ws.DBRefFetcher;
96 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
97 import jalview.ws.jws1.Discoverer;
98 import jalview.ws.jws2.Jws2Discoverer;
99 import jalview.ws.jws2.jabaws2.Jws2Instance;
100 import jalview.ws.seqfetcher.DbSourceProxy;
102 import java.awt.BorderLayout;
103 import java.awt.Component;
104 import java.awt.Rectangle;
105 import java.awt.Toolkit;
106 import java.awt.datatransfer.Clipboard;
107 import java.awt.datatransfer.DataFlavor;
108 import java.awt.datatransfer.StringSelection;
109 import java.awt.datatransfer.Transferable;
110 import java.awt.dnd.DnDConstants;
111 import java.awt.dnd.DropTargetDragEvent;
112 import java.awt.dnd.DropTargetDropEvent;
113 import java.awt.dnd.DropTargetEvent;
114 import java.awt.dnd.DropTargetListener;
115 import java.awt.event.ActionEvent;
116 import java.awt.event.ActionListener;
117 import java.awt.event.FocusAdapter;
118 import java.awt.event.FocusEvent;
119 import java.awt.event.ItemEvent;
120 import java.awt.event.ItemListener;
121 import java.awt.event.KeyAdapter;
122 import java.awt.event.KeyEvent;
123 import java.awt.event.MouseEvent;
124 import java.awt.print.PageFormat;
125 import java.awt.print.PrinterJob;
126 import java.beans.PropertyChangeEvent;
128 import java.io.FileWriter;
129 import java.io.PrintWriter;
131 import java.util.ArrayList;
132 import java.util.Arrays;
133 import java.util.Deque;
134 import java.util.Enumeration;
135 import java.util.Hashtable;
136 import java.util.List;
137 import java.util.Vector;
139 import javax.swing.ButtonGroup;
140 import javax.swing.JCheckBoxMenuItem;
141 import javax.swing.JEditorPane;
142 import javax.swing.JInternalFrame;
143 import javax.swing.JLayeredPane;
144 import javax.swing.JMenu;
145 import javax.swing.JMenuItem;
146 import javax.swing.JScrollPane;
147 import javax.swing.SwingUtilities;
153 * @version $Revision$
155 public class AlignFrame extends GAlignFrame implements DropTargetListener,
156 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
159 public static final int DEFAULT_WIDTH = 700;
161 public static final int DEFAULT_HEIGHT = 500;
164 * The currently displayed panel (selected tabbed view if more than one)
166 public AlignmentPanel alignPanel;
168 AlignViewport viewport;
170 public AlignViewControllerI avc;
172 List<AlignmentPanel> alignPanels = new ArrayList<>();
175 * Last format used to load or save alignments in this window
177 FileFormatI currentFileFormat = null;
180 * Current filename for this alignment
182 String fileName = null;
185 * Creates a new AlignFrame object with specific width and height.
191 public AlignFrame(AlignmentI al, int width, int height)
193 this(al, null, width, height);
197 * Creates a new AlignFrame object with specific width, height and
203 * @param sequenceSetId
205 public AlignFrame(AlignmentI al, int width, int height,
206 String sequenceSetId)
208 this(al, null, width, height, sequenceSetId);
212 * Creates a new AlignFrame object with specific width, height and
218 * @param sequenceSetId
221 public AlignFrame(AlignmentI al, int width, int height,
222 String sequenceSetId, String viewId)
224 this(al, null, width, height, sequenceSetId, viewId);
228 * new alignment window with hidden columns
232 * @param hiddenColumns
233 * ColumnSelection or null
235 * Width of alignment frame
239 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
242 this(al, hiddenColumns, width, height, null);
246 * Create alignment frame for al with hiddenColumns, a specific width and
247 * height, and specific sequenceId
250 * @param hiddenColumns
253 * @param sequenceSetId
256 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
257 int height, String sequenceSetId)
259 this(al, hiddenColumns, width, height, sequenceSetId, null);
263 * Create alignment frame for al with hiddenColumns, a specific width and
264 * height, and specific sequenceId
267 * @param hiddenColumns
270 * @param sequenceSetId
275 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
276 int height, String sequenceSetId, String viewId)
278 setSize(width, height);
280 if (al.getDataset() == null)
285 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
287 alignPanel = new AlignmentPanel(this, viewport);
289 addAlignmentPanel(alignPanel, true);
293 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
294 HiddenColumns hiddenColumns, int width, int height)
296 setSize(width, height);
298 if (al.getDataset() == null)
303 viewport = new AlignViewport(al, hiddenColumns);
305 if (hiddenSeqs != null && hiddenSeqs.length > 0)
307 viewport.hideSequence(hiddenSeqs);
309 alignPanel = new AlignmentPanel(this, viewport);
310 addAlignmentPanel(alignPanel, true);
315 * Make a new AlignFrame from existing alignmentPanels
322 public AlignFrame(AlignmentPanel ap)
326 addAlignmentPanel(ap, false);
331 * initalise the alignframe from the underlying viewport data and the
336 if (!Jalview.isHeadlessMode())
338 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
341 avc = new jalview.controller.AlignViewController(this, viewport,
343 if (viewport.getAlignmentConservationAnnotation() == null)
345 // BLOSUM62Colour.setEnabled(false);
346 conservationMenuItem.setEnabled(false);
347 modifyConservation.setEnabled(false);
348 // PIDColour.setEnabled(false);
349 // abovePIDThreshold.setEnabled(false);
350 // modifyPID.setEnabled(false);
353 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
356 if (sortby.equals("Id"))
358 sortIDMenuItem_actionPerformed(null);
360 else if (sortby.equals("Pairwise Identity"))
362 sortPairwiseMenuItem_actionPerformed(null);
366 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
368 setMenusFromViewport(viewport);
369 buildSortByAnnotationScoresMenu();
370 calculateTree.addActionListener(new ActionListener()
374 public void actionPerformed(ActionEvent e)
381 if (Desktop.desktop != null)
383 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
384 addServiceListeners();
388 if (viewport.getWrapAlignment())
390 wrapMenuItem_actionPerformed(null);
393 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
395 this.overviewMenuItem_actionPerformed(null);
400 final List<AlignmentPanel> selviews = new ArrayList<>();
401 final List<AlignmentPanel> origview = new ArrayList<>();
402 final String menuLabel = MessageManager
403 .getString("label.copy_format_from");
404 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
405 new ViewSetProvider()
409 public AlignmentPanel[] getAllAlignmentPanels()
412 origview.add(alignPanel);
413 // make an array of all alignment panels except for this one
414 List<AlignmentPanel> aps = new ArrayList<>(
415 Arrays.asList(Desktop.getAlignmentPanels(null)));
416 aps.remove(AlignFrame.this.alignPanel);
417 return aps.toArray(new AlignmentPanel[aps.size()]);
419 }, selviews, new ItemListener()
423 public void itemStateChanged(ItemEvent e)
425 if (origview.size() > 0)
427 final AlignmentPanel ap = origview.get(0);
430 * Copy the ViewStyle of the selected panel to 'this one'.
431 * Don't change value of 'scaleProteinAsCdna' unless copying
434 ViewStyleI vs = selviews.get(0).getAlignViewport()
436 boolean fromSplitFrame = selviews.get(0)
437 .getAlignViewport().getCodingComplement() != null;
440 vs.setScaleProteinAsCdna(ap.getAlignViewport()
441 .getViewStyle().isScaleProteinAsCdna());
443 ap.getAlignViewport().setViewStyle(vs);
446 * Also rescale ViewStyle of SplitFrame complement if there is
447 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
448 * the whole ViewStyle (allow cDNA protein to have different
451 AlignViewportI complement = ap.getAlignViewport()
452 .getCodingComplement();
453 if (complement != null && vs.isScaleProteinAsCdna())
455 AlignFrame af = Desktop.getAlignFrameFor(complement);
456 ((SplitFrame) af.getSplitViewContainer())
458 af.setMenusForViewport();
462 ap.setSelected(true);
463 ap.alignFrame.setMenusForViewport();
468 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
469 .indexOf("devel") > -1
470 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
471 .indexOf("test") > -1)
473 formatMenu.add(vsel);
475 addFocusListener(new FocusAdapter()
478 public void focusGained(FocusEvent e)
480 Jalview.setCurrentAlignFrame(AlignFrame.this);
487 * Change the filename and format for the alignment, and enable the 'reload'
488 * button functionality.
495 public void setFileName(String file, FileFormatI format)
498 setFileFormat(format);
499 reload.setEnabled(true);
503 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
506 void addKeyListener()
508 addKeyListener(new KeyAdapter()
511 public void keyPressed(KeyEvent evt)
513 if (viewport.cursorMode
514 && ((evt.getKeyCode() >= KeyEvent.VK_0
515 && evt.getKeyCode() <= KeyEvent.VK_9)
516 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
517 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
518 && Character.isDigit(evt.getKeyChar()))
520 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
523 switch (evt.getKeyCode())
526 case 27: // escape key
527 deselectAllSequenceMenuItem_actionPerformed(null);
531 case KeyEvent.VK_DOWN:
532 if (evt.isAltDown() || !viewport.cursorMode)
534 moveSelectedSequences(false);
536 if (viewport.cursorMode)
538 alignPanel.getSeqPanel().moveCursor(0, 1);
543 if (evt.isAltDown() || !viewport.cursorMode)
545 moveSelectedSequences(true);
547 if (viewport.cursorMode)
549 alignPanel.getSeqPanel().moveCursor(0, -1);
554 case KeyEvent.VK_LEFT:
555 if (evt.isAltDown() || !viewport.cursorMode)
557 slideSequences(false,
558 alignPanel.getSeqPanel().getKeyboardNo1());
562 alignPanel.getSeqPanel().moveCursor(-1, 0);
567 case KeyEvent.VK_RIGHT:
568 if (evt.isAltDown() || !viewport.cursorMode)
570 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
574 alignPanel.getSeqPanel().moveCursor(1, 0);
578 case KeyEvent.VK_SPACE:
579 if (viewport.cursorMode)
581 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
582 || evt.isShiftDown() || evt.isAltDown());
586 // case KeyEvent.VK_A:
587 // if (viewport.cursorMode)
589 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
590 // //System.out.println("A");
594 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
595 * System.out.println("closing bracket"); } break;
597 case KeyEvent.VK_DELETE:
598 case KeyEvent.VK_BACK_SPACE:
599 if (!viewport.cursorMode)
601 cut_actionPerformed(null);
605 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
606 || evt.isShiftDown() || evt.isAltDown());
612 if (viewport.cursorMode)
614 alignPanel.getSeqPanel().setCursorRow();
618 if (viewport.cursorMode && !evt.isControlDown())
620 alignPanel.getSeqPanel().setCursorColumn();
624 if (viewport.cursorMode)
626 alignPanel.getSeqPanel().setCursorPosition();
630 case KeyEvent.VK_ENTER:
631 case KeyEvent.VK_COMMA:
632 if (viewport.cursorMode)
634 alignPanel.getSeqPanel().setCursorRowAndColumn();
639 if (viewport.cursorMode)
641 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
645 if (viewport.cursorMode)
647 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
652 viewport.cursorMode = !viewport.cursorMode;
653 statusBar.setText(MessageManager
654 .formatMessage("label.keyboard_editing_mode", new String[]
655 { (viewport.cursorMode ? "on" : "off") }));
656 if (viewport.cursorMode)
658 ViewportRanges ranges = viewport.getRanges();
659 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
661 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
664 alignPanel.getSeqPanel().seqCanvas.repaint();
670 Help.showHelpWindow();
671 } catch (Exception ex)
673 ex.printStackTrace();
678 boolean toggleSeqs = !evt.isControlDown();
679 boolean toggleCols = !evt.isShiftDown();
680 toggleHiddenRegions(toggleSeqs, toggleCols);
685 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
686 boolean modifyExisting = true; // always modify, don't clear
687 // evt.isShiftDown();
688 boolean invertHighlighted = evt.isAltDown();
689 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
693 case KeyEvent.VK_PAGE_UP:
694 viewport.getRanges().pageUp();
696 case KeyEvent.VK_PAGE_DOWN:
697 viewport.getRanges().pageDown();
703 public void keyReleased(KeyEvent evt)
705 switch (evt.getKeyCode())
707 case KeyEvent.VK_LEFT:
708 if (evt.isAltDown() || !viewport.cursorMode)
710 viewport.firePropertyChange("alignment", null,
711 viewport.getAlignment().getSequences());
715 case KeyEvent.VK_RIGHT:
716 if (evt.isAltDown() || !viewport.cursorMode)
718 viewport.firePropertyChange("alignment", null,
719 viewport.getAlignment().getSequences());
727 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
729 ap.alignFrame = this;
730 avc = new jalview.controller.AlignViewController(this, viewport,
735 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
737 int aSize = alignPanels.size();
739 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
741 if (aSize == 1 && ap.av.getViewName() == null)
743 this.getContentPane().add(ap, BorderLayout.CENTER);
749 setInitialTabVisible();
752 expandViews.setEnabled(true);
753 gatherViews.setEnabled(true);
754 tabbedPane.addTab(ap.av.getViewName(), ap);
756 ap.setVisible(false);
761 if (ap.av.isPadGaps())
763 ap.av.getAlignment().padGaps();
765 ap.av.updateConservation(ap);
766 ap.av.updateConsensus(ap);
767 ap.av.updateStrucConsensus(ap);
771 public void setInitialTabVisible()
773 expandViews.setEnabled(true);
774 gatherViews.setEnabled(true);
775 tabbedPane.setVisible(true);
776 AlignmentPanel first = alignPanels.get(0);
777 tabbedPane.addTab(first.av.getViewName(), first);
778 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
781 public AlignViewport getViewport()
786 /* Set up intrinsic listeners for dynamically generated GUI bits. */
787 private void addServiceListeners()
789 final java.beans.PropertyChangeListener thisListener;
790 Desktop.instance.addJalviewPropertyChangeListener("services",
791 thisListener = new java.beans.PropertyChangeListener()
794 public void propertyChange(PropertyChangeEvent evt)
796 // // System.out.println("Discoverer property change.");
797 // if (evt.getPropertyName().equals("services"))
799 SwingUtilities.invokeLater(new Runnable()
806 "Rebuild WS Menu for service change");
807 BuildWebServiceMenu();
814 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
817 public void internalFrameClosed(
818 javax.swing.event.InternalFrameEvent evt)
820 // System.out.println("deregistering discoverer listener");
821 Desktop.instance.removeJalviewPropertyChangeListener("services",
823 closeMenuItem_actionPerformed(true);
826 // Finally, build the menu once to get current service state
827 new Thread(new Runnable()
832 BuildWebServiceMenu();
838 * Configure menu items that vary according to whether the alignment is
839 * nucleotide or protein
841 public void setGUINucleotide()
843 AlignmentI al = getViewport().getAlignment();
844 boolean nucleotide = al.isNucleotide();
846 loadVcf.setVisible(nucleotide);
847 showTranslation.setVisible(nucleotide);
848 showReverse.setVisible(nucleotide);
849 showReverseComplement.setVisible(nucleotide);
850 conservationMenuItem.setEnabled(!nucleotide);
852 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
853 showGroupConservation.setEnabled(!nucleotide);
855 showComplementMenuItem
856 .setText(nucleotide ? MessageManager.getString("label.protein")
857 : MessageManager.getString("label.nucleotide"));
861 * set up menus for the current viewport. This may be called after any
862 * operation that affects the data in the current view (selection changed,
863 * etc) to update the menus to reflect the new state.
866 public void setMenusForViewport()
868 setMenusFromViewport(viewport);
872 * Need to call this method when tabs are selected for multiple views, or when
873 * loading from Jalview2XML.java
878 public void setMenusFromViewport(AlignViewport av)
880 padGapsMenuitem.setSelected(av.isPadGaps());
881 colourTextMenuItem.setSelected(av.isShowColourText());
882 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
883 modifyPID.setEnabled(abovePIDThreshold.isSelected());
884 conservationMenuItem.setSelected(av.getConservationSelected());
885 modifyConservation.setEnabled(conservationMenuItem.isSelected());
886 seqLimits.setSelected(av.getShowJVSuffix());
887 idRightAlign.setSelected(av.isRightAlignIds());
888 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
889 renderGapsMenuItem.setSelected(av.isRenderGaps());
890 wrapMenuItem.setSelected(av.getWrapAlignment());
891 scaleAbove.setVisible(av.getWrapAlignment());
892 scaleLeft.setVisible(av.getWrapAlignment());
893 scaleRight.setVisible(av.getWrapAlignment());
894 annotationPanelMenuItem.setState(av.isShowAnnotation());
896 * Show/hide annotations only enabled if annotation panel is shown
898 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
899 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
900 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
901 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
902 viewBoxesMenuItem.setSelected(av.getShowBoxes());
903 viewTextMenuItem.setSelected(av.getShowText());
904 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
905 showGroupConsensus.setSelected(av.isShowGroupConsensus());
906 showGroupConservation.setSelected(av.isShowGroupConservation());
907 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
908 showSequenceLogo.setSelected(av.isShowSequenceLogo());
909 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
911 ColourMenuHelper.setColourSelected(colourMenu,
912 av.getGlobalColourScheme());
914 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
915 hiddenMarkers.setState(av.getShowHiddenMarkers());
916 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
917 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
918 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
919 autoCalculate.setSelected(av.autoCalculateConsensus);
920 sortByTree.setSelected(av.sortByTree);
921 listenToViewSelections.setSelected(av.followSelection);
923 showProducts.setEnabled(canShowProducts());
924 setGroovyEnabled(Desktop.getGroovyConsole() != null);
930 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
934 public void setGroovyEnabled(boolean b)
936 runGroovy.setEnabled(b);
939 private IProgressIndicator progressBar;
944 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
947 public void setProgressBar(String message, long id)
949 progressBar.setProgressBar(message, id);
953 public void registerHandler(final long id,
954 final IProgressIndicatorHandler handler)
956 progressBar.registerHandler(id, handler);
961 * @return true if any progress bars are still active
964 public boolean operationInProgress()
966 return progressBar.operationInProgress();
970 * Sets the text of the status bar. Note that setting a null or empty value
971 * will cause the status bar to be hidden, with possibly undesirable flicker
972 * of the screen layout.
975 public void setStatus(String text)
977 statusBar.setText(text == null || text.isEmpty() ? " " : text);
981 * Added so Castor Mapping file can obtain Jalview Version
983 public String getVersion()
985 return jalview.bin.Cache.getProperty("VERSION");
988 public FeatureRenderer getFeatureRenderer()
990 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
994 public void fetchSequence_actionPerformed(ActionEvent e)
996 new jalview.gui.SequenceFetcher(this);
1000 public void addFromFile_actionPerformed(ActionEvent e)
1002 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1006 public void reload_actionPerformed(ActionEvent e)
1008 if (fileName != null)
1010 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1011 // originating file's format
1012 // TODO: work out how to recover feature settings for correct view(s) when
1013 // file is reloaded.
1014 if (FileFormat.Jalview.equals(currentFileFormat))
1016 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1017 for (int i = 0; i < frames.length; i++)
1019 if (frames[i] instanceof AlignFrame && frames[i] != this
1020 && ((AlignFrame) frames[i]).fileName != null
1021 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1025 frames[i].setSelected(true);
1026 Desktop.instance.closeAssociatedWindows();
1027 } catch (java.beans.PropertyVetoException ex)
1033 Desktop.instance.closeAssociatedWindows();
1035 FileLoader loader = new FileLoader();
1036 DataSourceType protocol = fileName.startsWith("http:")
1037 ? DataSourceType.URL
1038 : DataSourceType.FILE;
1039 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1043 Rectangle bounds = this.getBounds();
1045 FileLoader loader = new FileLoader();
1046 DataSourceType protocol = fileName.startsWith("http:")
1047 ? DataSourceType.URL
1048 : DataSourceType.FILE;
1049 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1050 protocol, currentFileFormat);
1052 newframe.setBounds(bounds);
1053 if (featureSettings != null && featureSettings.isShowing())
1055 final Rectangle fspos = featureSettings.frame.getBounds();
1056 // TODO: need a 'show feature settings' function that takes bounds -
1057 // need to refactor Desktop.addFrame
1058 newframe.featureSettings_actionPerformed(null);
1059 final FeatureSettings nfs = newframe.featureSettings;
1060 SwingUtilities.invokeLater(new Runnable()
1065 nfs.frame.setBounds(fspos);
1068 this.featureSettings.close();
1069 this.featureSettings = null;
1071 this.closeMenuItem_actionPerformed(true);
1077 public void addFromText_actionPerformed(ActionEvent e)
1080 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1084 public void addFromURL_actionPerformed(ActionEvent e)
1086 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1090 public void save_actionPerformed(ActionEvent e)
1092 if (fileName == null || (currentFileFormat == null)
1093 || fileName.startsWith("http"))
1095 saveAs_actionPerformed(null);
1099 saveAlignment(fileName, currentFileFormat);
1110 public void saveAs_actionPerformed(ActionEvent e)
1112 String format = currentFileFormat == null ? null
1113 : currentFileFormat.getName();
1114 JalviewFileChooser chooser = JalviewFileChooser
1115 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1117 chooser.setFileView(new JalviewFileView());
1118 chooser.setDialogTitle(
1119 MessageManager.getString("label.save_alignment_to_file"));
1120 chooser.setToolTipText(MessageManager.getString("action.save"));
1122 int value = chooser.showSaveDialog(this);
1124 if (value == JalviewFileChooser.APPROVE_OPTION)
1126 currentFileFormat = chooser.getSelectedFormat();
1127 while (currentFileFormat == null)
1129 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1130 MessageManager.getString(
1131 "label.select_file_format_before_saving"),
1132 MessageManager.getString("label.file_format_not_specified"),
1133 JvOptionPane.WARNING_MESSAGE);
1134 currentFileFormat = chooser.getSelectedFormat();
1135 value = chooser.showSaveDialog(this);
1136 if (value != JalviewFileChooser.APPROVE_OPTION)
1142 fileName = chooser.getSelectedFile().getPath();
1144 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1146 Cache.setProperty("LAST_DIRECTORY", fileName);
1147 saveAlignment(fileName, currentFileFormat);
1151 public boolean saveAlignment(String file, FileFormatI format)
1153 boolean success = true;
1155 if (FileFormat.Jalview.equals(format))
1157 String shortName = title;
1159 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1161 shortName = shortName.substring(
1162 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1165 success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1168 statusBar.setText(MessageManager.formatMessage(
1169 "label.successfully_saved_to_file_in_format", new Object[]
1170 { fileName, format }));
1175 AlignmentExportData exportData = getAlignmentForExport(format,
1177 if (exportData.getSettings().isCancelled())
1181 FormatAdapter f = new FormatAdapter(alignPanel,
1182 exportData.getSettings());
1183 String output = f.formatSequences(format, exportData.getAlignment(), // class
1187 // occur in the distant future
1188 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1189 f.getCacheSuffixDefault(format),
1190 viewport.getAlignment().getHiddenColumns());
1198 // create backupfiles object and get new temp filename destination
1199 BackupFiles backupfiles = new BackupFiles(file);
1203 PrintWriter out = new PrintWriter(
1204 new FileWriter(backupfiles.getTempFilePath()));
1208 this.setTitle(file);
1209 statusBar.setText(MessageManager.formatMessage(
1210 "label.successfully_saved_to_file_in_format", new Object[]
1211 { fileName, format.getName() }));
1212 } catch (Exception ex)
1215 ex.printStackTrace();
1218 backupfiles.setWriteSuccess(success);
1219 // do the backup file roll and rename the temp file to actual file
1220 success = backupfiles.rollBackupsAndRenameTempFile();
1227 JvOptionPane.showInternalMessageDialog(this, MessageManager
1228 .formatMessage("label.couldnt_save_file", new Object[]
1230 MessageManager.getString("label.error_saving_file"),
1231 JvOptionPane.WARNING_MESSAGE);
1237 private void warningMessage(String warning, String title)
1239 if (new jalview.util.Platform().isHeadless())
1241 System.err.println("Warning: " + title + "\nWarning: " + warning);
1246 JvOptionPane.showInternalMessageDialog(this, warning, title,
1247 JvOptionPane.WARNING_MESSAGE);
1259 protected void outputText_actionPerformed(ActionEvent e)
1261 FileFormatI fileFormat = FileFormats.getInstance()
1262 .forName(e.getActionCommand());
1263 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1265 if (exportData.getSettings().isCancelled())
1269 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1270 cap.setForInput(null);
1273 FileFormatI format = fileFormat;
1274 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1275 .formatSequences(format, exportData.getAlignment(),
1276 exportData.getOmitHidden(),
1277 exportData.getStartEndPostions(),
1278 viewport.getAlignment().getHiddenColumns()));
1279 Desktop.addInternalFrame(cap, MessageManager
1280 .formatMessage("label.alignment_output_command", new Object[]
1281 { e.getActionCommand() }), 600, 500);
1282 } catch (OutOfMemoryError oom)
1284 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1291 public static AlignmentExportData getAlignmentForExport(
1292 FileFormatI format, AlignViewportI viewport,
1293 AlignExportSettingI exportSettings)
1295 AlignmentI alignmentToExport = null;
1296 AlignExportSettingI settings = exportSettings;
1297 String[] omitHidden = null;
1299 HiddenSequences hiddenSeqs = viewport.getAlignment()
1300 .getHiddenSequences();
1302 alignmentToExport = viewport.getAlignment();
1304 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1305 if (settings == null)
1307 settings = new AlignExportSettings(hasHiddenSeqs,
1308 viewport.hasHiddenColumns(), format);
1310 // settings.isExportAnnotations();
1312 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1314 omitHidden = viewport.getViewAsString(false,
1315 settings.isExportHiddenSequences());
1318 int[] alignmentStartEnd = new int[2];
1319 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1321 alignmentToExport = hiddenSeqs.getFullAlignment();
1325 alignmentToExport = viewport.getAlignment();
1327 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1328 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1329 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1330 omitHidden, alignmentStartEnd, settings);
1341 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1343 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1344 htmlSVG.exportHTML(null);
1348 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1350 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1351 bjs.exportHTML(null);
1354 public void createImageMap(File file, String image)
1356 alignPanel.makePNGImageMap(file, image);
1366 public void createPNG(File f)
1368 alignPanel.makePNG(f);
1378 public void createEPS(File f)
1380 alignPanel.makeEPS(f);
1384 public void createSVG(File f)
1386 alignPanel.makeSVG(f);
1390 public void pageSetup_actionPerformed(ActionEvent e)
1392 PrinterJob printJob = PrinterJob.getPrinterJob();
1393 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1403 public void printMenuItem_actionPerformed(ActionEvent e)
1405 // Putting in a thread avoids Swing painting problems
1406 PrintThread thread = new PrintThread(alignPanel);
1411 public void exportFeatures_actionPerformed(ActionEvent e)
1413 new AnnotationExporter(alignPanel).exportFeatures();
1417 public void exportAnnotations_actionPerformed(ActionEvent e)
1419 new AnnotationExporter(alignPanel).exportAnnotations();
1423 public void associatedData_actionPerformed(ActionEvent e)
1425 // Pick the tree file
1426 JalviewFileChooser chooser = new JalviewFileChooser(
1427 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1428 chooser.setFileView(new JalviewFileView());
1429 chooser.setDialogTitle(
1430 MessageManager.getString("label.load_jalview_annotations"));
1431 chooser.setToolTipText(
1432 MessageManager.getString("label.load_jalview_annotations"));
1434 int value = chooser.showOpenDialog(null);
1436 if (value == JalviewFileChooser.APPROVE_OPTION)
1438 String choice = chooser.getSelectedFile().getPath();
1439 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1440 loadJalviewDataFile(choice, null, null, null);
1446 * Close the current view or all views in the alignment frame. If the frame
1447 * only contains one view then the alignment will be removed from memory.
1449 * @param closeAllTabs
1452 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1454 if (alignPanels != null && alignPanels.size() < 2)
1456 closeAllTabs = true;
1461 if (alignPanels != null)
1465 if (this.isClosed())
1467 // really close all the windows - otherwise wait till
1468 // setClosed(true) is called
1469 for (int i = 0; i < alignPanels.size(); i++)
1471 AlignmentPanel ap = alignPanels.get(i);
1478 closeView(alignPanel);
1485 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1486 * be called recursively, with the frame now in 'closed' state
1488 this.setClosed(true);
1490 } catch (Exception ex)
1492 ex.printStackTrace();
1497 * Close the specified panel and close up tabs appropriately.
1499 * @param panelToClose
1501 public void closeView(AlignmentPanel panelToClose)
1503 int index = tabbedPane.getSelectedIndex();
1504 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1505 alignPanels.remove(panelToClose);
1506 panelToClose.closePanel();
1507 panelToClose = null;
1509 tabbedPane.removeTabAt(closedindex);
1510 tabbedPane.validate();
1512 if (index > closedindex || index == tabbedPane.getTabCount())
1514 // modify currently selected tab index if necessary.
1518 this.tabSelectionChanged(index);
1524 void updateEditMenuBar()
1527 if (viewport.getHistoryList().size() > 0)
1529 undoMenuItem.setEnabled(true);
1530 CommandI command = viewport.getHistoryList().peek();
1531 undoMenuItem.setText(MessageManager
1532 .formatMessage("label.undo_command", new Object[]
1533 { command.getDescription() }));
1537 undoMenuItem.setEnabled(false);
1538 undoMenuItem.setText(MessageManager.getString("action.undo"));
1541 if (viewport.getRedoList().size() > 0)
1543 redoMenuItem.setEnabled(true);
1545 CommandI command = viewport.getRedoList().peek();
1546 redoMenuItem.setText(MessageManager
1547 .formatMessage("label.redo_command", new Object[]
1548 { command.getDescription() }));
1552 redoMenuItem.setEnabled(false);
1553 redoMenuItem.setText(MessageManager.getString("action.redo"));
1558 public void addHistoryItem(CommandI command)
1560 if (command.getSize() > 0)
1562 viewport.addToHistoryList(command);
1563 viewport.clearRedoList();
1564 updateEditMenuBar();
1565 viewport.updateHiddenColumns();
1566 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1567 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1568 // viewport.getColumnSelection()
1569 // .getHiddenColumns().size() > 0);
1575 * @return alignment objects for all views
1577 AlignmentI[] getViewAlignments()
1579 if (alignPanels != null)
1581 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1583 for (AlignmentPanel ap : alignPanels)
1585 als[i++] = ap.av.getAlignment();
1589 if (viewport != null)
1591 return new AlignmentI[] { viewport.getAlignment() };
1603 protected void undoMenuItem_actionPerformed(ActionEvent e)
1605 if (viewport.getHistoryList().isEmpty())
1609 CommandI command = viewport.getHistoryList().pop();
1610 viewport.addToRedoList(command);
1611 command.undoCommand(getViewAlignments());
1613 AlignmentViewport originalSource = getOriginatingSource(command);
1614 updateEditMenuBar();
1616 if (originalSource != null)
1618 if (originalSource != viewport)
1621 "Implementation worry: mismatch of viewport origin for undo");
1623 originalSource.updateHiddenColumns();
1624 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1626 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1627 // viewport.getColumnSelection()
1628 // .getHiddenColumns().size() > 0);
1629 originalSource.firePropertyChange("alignment", null,
1630 originalSource.getAlignment().getSequences());
1641 protected void redoMenuItem_actionPerformed(ActionEvent e)
1643 if (viewport.getRedoList().size() < 1)
1648 CommandI command = viewport.getRedoList().pop();
1649 viewport.addToHistoryList(command);
1650 command.doCommand(getViewAlignments());
1652 AlignmentViewport originalSource = getOriginatingSource(command);
1653 updateEditMenuBar();
1655 if (originalSource != null)
1658 if (originalSource != viewport)
1661 "Implementation worry: mismatch of viewport origin for redo");
1663 originalSource.updateHiddenColumns();
1664 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1666 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1667 // viewport.getColumnSelection()
1668 // .getHiddenColumns().size() > 0);
1669 originalSource.firePropertyChange("alignment", null,
1670 originalSource.getAlignment().getSequences());
1674 AlignmentViewport getOriginatingSource(CommandI command)
1676 AlignmentViewport originalSource = null;
1677 // For sequence removal and addition, we need to fire
1678 // the property change event FROM the viewport where the
1679 // original alignment was altered
1680 AlignmentI al = null;
1681 if (command instanceof EditCommand)
1683 EditCommand editCommand = (EditCommand) command;
1684 al = editCommand.getAlignment();
1685 List<Component> comps = PaintRefresher.components
1686 .get(viewport.getSequenceSetId());
1688 for (Component comp : comps)
1690 if (comp instanceof AlignmentPanel)
1692 if (al == ((AlignmentPanel) comp).av.getAlignment())
1694 originalSource = ((AlignmentPanel) comp).av;
1701 if (originalSource == null)
1703 // The original view is closed, we must validate
1704 // the current view against the closed view first
1707 PaintRefresher.validateSequences(al, viewport.getAlignment());
1710 originalSource = viewport;
1713 return originalSource;
1722 public void moveSelectedSequences(boolean up)
1724 SequenceGroup sg = viewport.getSelectionGroup();
1730 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1731 viewport.getHiddenRepSequences(), up);
1732 alignPanel.paintAlignment(true, false);
1735 synchronized void slideSequences(boolean right, int size)
1737 List<SequenceI> sg = new ArrayList<>();
1738 if (viewport.cursorMode)
1740 sg.add(viewport.getAlignment()
1741 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1743 else if (viewport.getSelectionGroup() != null
1744 && viewport.getSelectionGroup().getSize() != viewport
1745 .getAlignment().getHeight())
1747 sg = viewport.getSelectionGroup()
1748 .getSequences(viewport.getHiddenRepSequences());
1756 List<SequenceI> invertGroup = new ArrayList<>();
1758 for (SequenceI seq : viewport.getAlignment().getSequences())
1760 if (!sg.contains(seq))
1762 invertGroup.add(seq);
1766 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1768 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1769 for (int i = 0; i < invertGroup.size(); i++)
1771 seqs2[i] = invertGroup.get(i);
1774 SlideSequencesCommand ssc;
1777 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1778 viewport.getGapCharacter());
1782 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1783 viewport.getGapCharacter());
1786 int groupAdjustment = 0;
1787 if (ssc.getGapsInsertedBegin() && right)
1789 if (viewport.cursorMode)
1791 alignPanel.getSeqPanel().moveCursor(size, 0);
1795 groupAdjustment = size;
1798 else if (!ssc.getGapsInsertedBegin() && !right)
1800 if (viewport.cursorMode)
1802 alignPanel.getSeqPanel().moveCursor(-size, 0);
1806 groupAdjustment = -size;
1810 if (groupAdjustment != 0)
1812 viewport.getSelectionGroup().setStartRes(
1813 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1814 viewport.getSelectionGroup().setEndRes(
1815 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1819 * just extend the last slide command if compatible; but not if in
1820 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1822 boolean appendHistoryItem = false;
1823 Deque<CommandI> historyList = viewport.getHistoryList();
1824 boolean inSplitFrame = getSplitViewContainer() != null;
1825 if (!inSplitFrame && historyList != null && historyList.size() > 0
1826 && historyList.peek() instanceof SlideSequencesCommand)
1828 appendHistoryItem = ssc.appendSlideCommand(
1829 (SlideSequencesCommand) historyList.peek());
1832 if (!appendHistoryItem)
1834 addHistoryItem(ssc);
1847 protected void copy_actionPerformed(ActionEvent e)
1849 if (viewport.getSelectionGroup() == null)
1853 // TODO: preserve the ordering of displayed alignment annotation in any
1854 // internal paste (particularly sequence associated annotation)
1855 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1856 String[] omitHidden = null;
1858 if (viewport.hasHiddenColumns())
1860 omitHidden = viewport.getViewAsString(true);
1863 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1864 seqs, omitHidden, null);
1866 StringSelection ss = new StringSelection(output);
1870 jalview.gui.Desktop.internalCopy = true;
1871 // Its really worth setting the clipboard contents
1872 // to empty before setting the large StringSelection!!
1873 Toolkit.getDefaultToolkit().getSystemClipboard()
1874 .setContents(new StringSelection(""), null);
1876 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1878 } catch (OutOfMemoryError er)
1880 new OOMWarning("copying region", er);
1884 HiddenColumns hiddenColumns = null;
1885 if (viewport.hasHiddenColumns())
1887 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1888 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1890 // create new HiddenColumns object with copy of hidden regions
1891 // between startRes and endRes, offset by startRes
1892 hiddenColumns = new HiddenColumns(
1893 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1894 hiddenCutoff, hiddenOffset);
1897 Desktop.jalviewClipboard = new Object[] { seqs,
1898 viewport.getAlignment().getDataset(), hiddenColumns };
1899 statusBar.setText(MessageManager.formatMessage(
1900 "label.copied_sequences_to_clipboard", new Object[]
1901 { Integer.valueOf(seqs.length).toString() }));
1911 protected void pasteNew_actionPerformed(ActionEvent e)
1923 protected void pasteThis_actionPerformed(ActionEvent e)
1929 * Paste contents of Jalview clipboard
1931 * @param newAlignment
1932 * true to paste to a new alignment, otherwise add to this.
1934 void paste(boolean newAlignment)
1936 boolean externalPaste = true;
1939 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1940 Transferable contents = c.getContents(this);
1942 if (contents == null)
1951 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1952 if (str.length() < 1)
1957 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1959 } catch (OutOfMemoryError er)
1961 new OOMWarning("Out of memory pasting sequences!!", er);
1965 SequenceI[] sequences;
1966 boolean annotationAdded = false;
1967 AlignmentI alignment = null;
1969 if (Desktop.jalviewClipboard != null)
1971 // The clipboard was filled from within Jalview, we must use the
1973 // And dataset from the copied alignment
1974 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1975 // be doubly sure that we create *new* sequence objects.
1976 sequences = new SequenceI[newseq.length];
1977 for (int i = 0; i < newseq.length; i++)
1979 sequences[i] = new Sequence(newseq[i]);
1981 alignment = new Alignment(sequences);
1982 externalPaste = false;
1986 // parse the clipboard as an alignment.
1987 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1989 sequences = alignment.getSequencesArray();
1993 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1999 if (Desktop.jalviewClipboard != null)
2001 // dataset is inherited
2002 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2006 // new dataset is constructed
2007 alignment.setDataset(null);
2009 alwidth = alignment.getWidth() + 1;
2013 AlignmentI pastedal = alignment; // preserve pasted alignment object
2014 // Add pasted sequences and dataset into existing alignment.
2015 alignment = viewport.getAlignment();
2016 alwidth = alignment.getWidth() + 1;
2017 // decide if we need to import sequences from an existing dataset
2018 boolean importDs = Desktop.jalviewClipboard != null
2019 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2020 // importDs==true instructs us to copy over new dataset sequences from
2021 // an existing alignment
2022 Vector newDs = (importDs) ? new Vector() : null; // used to create
2023 // minimum dataset set
2025 for (int i = 0; i < sequences.length; i++)
2029 newDs.addElement(null);
2031 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2033 if (importDs && ds != null)
2035 if (!newDs.contains(ds))
2037 newDs.setElementAt(ds, i);
2038 ds = new Sequence(ds);
2039 // update with new dataset sequence
2040 sequences[i].setDatasetSequence(ds);
2044 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2049 // copy and derive new dataset sequence
2050 sequences[i] = sequences[i].deriveSequence();
2051 alignment.getDataset()
2052 .addSequence(sequences[i].getDatasetSequence());
2053 // TODO: avoid creation of duplicate dataset sequences with a
2054 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2056 alignment.addSequence(sequences[i]); // merges dataset
2060 newDs.clear(); // tidy up
2062 if (alignment.getAlignmentAnnotation() != null)
2064 for (AlignmentAnnotation alan : alignment
2065 .getAlignmentAnnotation())
2067 if (alan.graphGroup > fgroup)
2069 fgroup = alan.graphGroup;
2073 if (pastedal.getAlignmentAnnotation() != null)
2075 // Add any annotation attached to alignment.
2076 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2077 for (int i = 0; i < alann.length; i++)
2079 annotationAdded = true;
2080 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2082 AlignmentAnnotation newann = new AlignmentAnnotation(
2084 if (newann.graphGroup > -1)
2086 if (newGraphGroups.size() <= newann.graphGroup
2087 || newGraphGroups.get(newann.graphGroup) == null)
2089 for (int q = newGraphGroups
2090 .size(); q <= newann.graphGroup; q++)
2092 newGraphGroups.add(q, null);
2094 newGraphGroups.set(newann.graphGroup,
2095 new Integer(++fgroup));
2097 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2101 newann.padAnnotation(alwidth);
2102 alignment.addAnnotation(newann);
2112 addHistoryItem(new EditCommand(
2113 MessageManager.getString("label.add_sequences"),
2114 Action.PASTE, sequences, 0, alignment.getWidth(),
2117 // Add any annotations attached to sequences
2118 for (int i = 0; i < sequences.length; i++)
2120 if (sequences[i].getAnnotation() != null)
2122 AlignmentAnnotation newann;
2123 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2125 annotationAdded = true;
2126 newann = sequences[i].getAnnotation()[a];
2127 newann.adjustForAlignment();
2128 newann.padAnnotation(alwidth);
2129 if (newann.graphGroup > -1)
2131 if (newann.graphGroup > -1)
2133 if (newGraphGroups.size() <= newann.graphGroup
2134 || newGraphGroups.get(newann.graphGroup) == null)
2136 for (int q = newGraphGroups
2137 .size(); q <= newann.graphGroup; q++)
2139 newGraphGroups.add(q, null);
2141 newGraphGroups.set(newann.graphGroup,
2142 new Integer(++fgroup));
2144 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2148 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2152 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2160 // propagate alignment changed.
2161 viewport.getRanges().setEndSeq(alignment.getHeight());
2162 if (annotationAdded)
2164 // Duplicate sequence annotation in all views.
2165 AlignmentI[] alview = this.getViewAlignments();
2166 for (int i = 0; i < sequences.length; i++)
2168 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2173 for (int avnum = 0; avnum < alview.length; avnum++)
2175 if (alview[avnum] != alignment)
2177 // duplicate in a view other than the one with input focus
2178 int avwidth = alview[avnum].getWidth() + 1;
2179 // this relies on sann being preserved after we
2180 // modify the sequence's annotation array for each duplication
2181 for (int a = 0; a < sann.length; a++)
2183 AlignmentAnnotation newann = new AlignmentAnnotation(
2185 sequences[i].addAlignmentAnnotation(newann);
2186 newann.padAnnotation(avwidth);
2187 alview[avnum].addAnnotation(newann); // annotation was
2188 // duplicated earlier
2189 // TODO JAL-1145 graphGroups are not updated for sequence
2190 // annotation added to several views. This may cause
2192 alview[avnum].setAnnotationIndex(newann, a);
2197 buildSortByAnnotationScoresMenu();
2199 viewport.firePropertyChange("alignment", null,
2200 alignment.getSequences());
2201 if (alignPanels != null)
2203 for (AlignmentPanel ap : alignPanels)
2205 ap.validateAnnotationDimensions(false);
2210 alignPanel.validateAnnotationDimensions(false);
2216 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2218 String newtitle = new String("Copied sequences");
2220 if (Desktop.jalviewClipboard != null
2221 && Desktop.jalviewClipboard[2] != null)
2223 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2224 af.viewport.setHiddenColumns(hc);
2227 // >>>This is a fix for the moment, until a better solution is
2229 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2230 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2231 .getFeatureRenderer());
2233 // TODO: maintain provenance of an alignment, rather than just make the
2234 // title a concatenation of operations.
2237 if (title.startsWith("Copied sequences"))
2243 newtitle = newtitle.concat("- from " + title);
2248 newtitle = new String("Pasted sequences");
2251 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2256 } catch (Exception ex)
2258 ex.printStackTrace();
2259 System.out.println("Exception whilst pasting: " + ex);
2260 // could be anything being pasted in here
2266 protected void expand_newalign(ActionEvent e)
2270 AlignmentI alignment = AlignmentUtils
2271 .expandContext(getViewport().getAlignment(), -1);
2272 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2274 String newtitle = new String("Flanking alignment");
2276 if (Desktop.jalviewClipboard != null
2277 && Desktop.jalviewClipboard[2] != null)
2279 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2280 af.viewport.setHiddenColumns(hc);
2283 // >>>This is a fix for the moment, until a better solution is
2285 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2286 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2287 .getFeatureRenderer());
2289 // TODO: maintain provenance of an alignment, rather than just make the
2290 // title a concatenation of operations.
2292 if (title.startsWith("Copied sequences"))
2298 newtitle = newtitle.concat("- from " + title);
2302 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2304 } catch (Exception ex)
2306 ex.printStackTrace();
2307 System.out.println("Exception whilst pasting: " + ex);
2308 // could be anything being pasted in here
2309 } catch (OutOfMemoryError oom)
2311 new OOMWarning("Viewing flanking region of alignment", oom);
2322 protected void cut_actionPerformed(ActionEvent e)
2324 copy_actionPerformed(null);
2325 delete_actionPerformed(null);
2335 protected void delete_actionPerformed(ActionEvent evt)
2338 SequenceGroup sg = viewport.getSelectionGroup();
2345 * If the cut affects all sequences, warn, remove highlighted columns
2347 if (sg.getSize() == viewport.getAlignment().getHeight())
2349 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2350 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2351 if (isEntireAlignWidth)
2353 int confirm = JvOptionPane.showConfirmDialog(this,
2354 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2355 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2356 JvOptionPane.OK_CANCEL_OPTION);
2358 if (confirm == JvOptionPane.CANCEL_OPTION
2359 || confirm == JvOptionPane.CLOSED_OPTION)
2364 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2365 sg.getEndRes() + 1);
2367 SequenceI[] cut = sg.getSequences()
2368 .toArray(new SequenceI[sg.getSize()]);
2370 addHistoryItem(new EditCommand(
2371 MessageManager.getString("label.cut_sequences"), Action.CUT,
2372 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2373 viewport.getAlignment()));
2375 viewport.setSelectionGroup(null);
2376 viewport.sendSelection();
2377 viewport.getAlignment().deleteGroup(sg);
2379 viewport.firePropertyChange("alignment", null,
2380 viewport.getAlignment().getSequences());
2381 if (viewport.getAlignment().getHeight() < 1)
2385 this.setClosed(true);
2386 } catch (Exception ex)
2399 protected void deleteGroups_actionPerformed(ActionEvent e)
2401 if (avc.deleteGroups())
2403 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2404 alignPanel.updateAnnotation();
2405 alignPanel.paintAlignment(true, true);
2416 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2418 SequenceGroup sg = new SequenceGroup(
2419 viewport.getAlignment().getSequences());
2421 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2422 viewport.setSelectionGroup(sg);
2423 viewport.isSelectionGroupChanged(true);
2424 viewport.sendSelection();
2425 // JAL-2034 - should delegate to
2426 // alignPanel to decide if overview needs
2428 alignPanel.paintAlignment(false, false);
2429 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2439 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2441 if (viewport.cursorMode)
2443 alignPanel.getSeqPanel().keyboardNo1 = null;
2444 alignPanel.getSeqPanel().keyboardNo2 = null;
2446 viewport.setSelectionGroup(null);
2447 viewport.getColumnSelection().clear();
2448 viewport.setSelectionGroup(null);
2449 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2450 // JAL-2034 - should delegate to
2451 // alignPanel to decide if overview needs
2453 alignPanel.paintAlignment(false, false);
2454 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2455 viewport.sendSelection();
2465 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2467 SequenceGroup sg = viewport.getSelectionGroup();
2471 selectAllSequenceMenuItem_actionPerformed(null);
2476 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2478 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2480 // JAL-2034 - should delegate to
2481 // alignPanel to decide if overview needs
2484 alignPanel.paintAlignment(true, false);
2485 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2486 viewport.sendSelection();
2490 public void invertColSel_actionPerformed(ActionEvent e)
2492 viewport.invertColumnSelection();
2493 alignPanel.paintAlignment(true, false);
2494 viewport.sendSelection();
2504 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2506 trimAlignment(true);
2516 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2518 trimAlignment(false);
2521 void trimAlignment(boolean trimLeft)
2523 ColumnSelection colSel = viewport.getColumnSelection();
2526 if (!colSel.isEmpty())
2530 column = colSel.getMin();
2534 column = colSel.getMax();
2538 if (viewport.getSelectionGroup() != null)
2540 seqs = viewport.getSelectionGroup()
2541 .getSequencesAsArray(viewport.getHiddenRepSequences());
2545 seqs = viewport.getAlignment().getSequencesArray();
2548 TrimRegionCommand trimRegion;
2551 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2552 column, viewport.getAlignment());
2553 viewport.getRanges().setStartRes(0);
2557 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2558 column, viewport.getAlignment());
2561 statusBar.setText(MessageManager
2562 .formatMessage("label.removed_columns", new String[]
2563 { Integer.valueOf(trimRegion.getSize()).toString() }));
2565 addHistoryItem(trimRegion);
2567 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2569 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2570 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2572 viewport.getAlignment().deleteGroup(sg);
2576 viewport.firePropertyChange("alignment", null,
2577 viewport.getAlignment().getSequences());
2588 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2590 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2593 if (viewport.getSelectionGroup() != null)
2595 seqs = viewport.getSelectionGroup()
2596 .getSequencesAsArray(viewport.getHiddenRepSequences());
2597 start = viewport.getSelectionGroup().getStartRes();
2598 end = viewport.getSelectionGroup().getEndRes();
2602 seqs = viewport.getAlignment().getSequencesArray();
2605 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2606 "Remove Gapped Columns", seqs, start, end,
2607 viewport.getAlignment());
2609 addHistoryItem(removeGapCols);
2611 statusBar.setText(MessageManager
2612 .formatMessage("label.removed_empty_columns", new Object[]
2613 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2615 // This is to maintain viewport position on first residue
2616 // of first sequence
2617 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2618 ViewportRanges ranges = viewport.getRanges();
2619 int startRes = seq.findPosition(ranges.getStartRes());
2620 // ShiftList shifts;
2621 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2622 // edit.alColumnChanges=shifts.getInverse();
2623 // if (viewport.hasHiddenColumns)
2624 // viewport.getColumnSelection().compensateForEdits(shifts);
2625 ranges.setStartRes(seq.findIndex(startRes) - 1);
2626 viewport.firePropertyChange("alignment", null,
2627 viewport.getAlignment().getSequences());
2638 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2640 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2643 if (viewport.getSelectionGroup() != null)
2645 seqs = viewport.getSelectionGroup()
2646 .getSequencesAsArray(viewport.getHiddenRepSequences());
2647 start = viewport.getSelectionGroup().getStartRes();
2648 end = viewport.getSelectionGroup().getEndRes();
2652 seqs = viewport.getAlignment().getSequencesArray();
2655 // This is to maintain viewport position on first residue
2656 // of first sequence
2657 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2658 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2660 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2661 viewport.getAlignment()));
2663 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2665 viewport.firePropertyChange("alignment", null,
2666 viewport.getAlignment().getSequences());
2677 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2679 viewport.setPadGaps(padGapsMenuitem.isSelected());
2680 viewport.firePropertyChange("alignment", null,
2681 viewport.getAlignment().getSequences());
2691 public void findMenuItem_actionPerformed(ActionEvent e)
2697 * Create a new view of the current alignment.
2700 public void newView_actionPerformed(ActionEvent e)
2702 newView(null, true);
2706 * Creates and shows a new view of the current alignment.
2709 * title of newly created view; if null, one will be generated
2710 * @param copyAnnotation
2711 * if true then duplicate all annnotation, groups and settings
2712 * @return new alignment panel, already displayed.
2714 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2717 * Create a new AlignmentPanel (with its own, new Viewport)
2719 AlignmentPanel newap = new jalview.project.Jalview2XML()
2720 .copyAlignPanel(alignPanel);
2721 if (!copyAnnotation)
2724 * remove all groups and annotation except for the automatic stuff
2726 newap.av.getAlignment().deleteAllGroups();
2727 newap.av.getAlignment().deleteAllAnnotations(false);
2730 newap.av.setGatherViewsHere(false);
2732 if (viewport.getViewName() == null)
2734 viewport.setViewName(MessageManager
2735 .getString("label.view_name_original"));
2739 * Views share the same edits undo and redo stacks
2741 newap.av.setHistoryList(viewport.getHistoryList());
2742 newap.av.setRedoList(viewport.getRedoList());
2745 * copy any visualisation settings that are not saved in the project
2747 newap.av.setColourAppliesToAllGroups(
2748 viewport.getColourAppliesToAllGroups());
2751 * Views share the same mappings; need to deregister any new mappings
2752 * created by copyAlignPanel, and register the new reference to the shared
2755 newap.av.replaceMappings(viewport.getAlignment());
2758 * start up cDNA consensus (if applicable) now mappings are in place
2760 if (newap.av.initComplementConsensus())
2762 newap.refresh(true); // adjust layout of annotations
2765 newap.av.setViewName(getNewViewName(viewTitle));
2767 addAlignmentPanel(newap, true);
2768 newap.alignmentChanged();
2770 if (alignPanels.size() == 2)
2772 viewport.setGatherViewsHere(true);
2774 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2779 * Make a new name for the view, ensuring it is unique within the current
2780 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2781 * these now use viewId. Unique view names are still desirable for usability.)
2786 protected String getNewViewName(String viewTitle)
2788 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2789 boolean addFirstIndex = false;
2790 if (viewTitle == null || viewTitle.trim().length() == 0)
2792 viewTitle = MessageManager.getString("action.view");
2793 addFirstIndex = true;
2797 index = 1;// we count from 1 if given a specific name
2799 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2801 List<Component> comps = PaintRefresher.components
2802 .get(viewport.getSequenceSetId());
2804 List<String> existingNames = getExistingViewNames(comps);
2806 while (existingNames.contains(newViewName))
2808 newViewName = viewTitle + " " + (++index);
2814 * Returns a list of distinct view names found in the given list of
2815 * components. View names are held on the viewport of an AlignmentPanel.
2820 protected List<String> getExistingViewNames(List<Component> comps)
2822 List<String> existingNames = new ArrayList<>();
2823 for (Component comp : comps)
2825 if (comp instanceof AlignmentPanel)
2827 AlignmentPanel ap = (AlignmentPanel) comp;
2828 if (!existingNames.contains(ap.av.getViewName()))
2830 existingNames.add(ap.av.getViewName());
2834 return existingNames;
2838 * Explode tabbed views into separate windows.
2841 public void expandViews_actionPerformed(ActionEvent e)
2843 Desktop.explodeViews(this);
2847 * Gather views in separate windows back into a tabbed presentation.
2850 public void gatherViews_actionPerformed(ActionEvent e)
2852 Desktop.instance.gatherViews(this);
2862 public void font_actionPerformed(ActionEvent e)
2864 new FontChooser(alignPanel);
2874 protected void seqLimit_actionPerformed(ActionEvent e)
2876 viewport.setShowJVSuffix(seqLimits.isSelected());
2878 alignPanel.getIdPanel().getIdCanvas()
2879 .setPreferredSize(alignPanel.calculateIdWidth());
2880 alignPanel.paintAlignment(true, false);
2884 public void idRightAlign_actionPerformed(ActionEvent e)
2886 viewport.setRightAlignIds(idRightAlign.isSelected());
2887 alignPanel.paintAlignment(false, false);
2891 public void centreColumnLabels_actionPerformed(ActionEvent e)
2893 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2894 alignPanel.paintAlignment(false, false);
2900 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2903 protected void followHighlight_actionPerformed()
2906 * Set the 'follow' flag on the Viewport (and scroll to position if now
2909 final boolean state = this.followHighlightMenuItem.getState();
2910 viewport.setFollowHighlight(state);
2913 alignPanel.scrollToPosition(viewport.getSearchResults());
2924 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2926 viewport.setColourText(colourTextMenuItem.isSelected());
2927 alignPanel.paintAlignment(false, false);
2937 public void wrapMenuItem_actionPerformed(ActionEvent e)
2939 scaleAbove.setVisible(wrapMenuItem.isSelected());
2940 scaleLeft.setVisible(wrapMenuItem.isSelected());
2941 scaleRight.setVisible(wrapMenuItem.isSelected());
2942 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2943 alignPanel.updateLayout();
2947 public void showAllSeqs_actionPerformed(ActionEvent e)
2949 viewport.showAllHiddenSeqs();
2953 public void showAllColumns_actionPerformed(ActionEvent e)
2955 viewport.showAllHiddenColumns();
2956 alignPanel.paintAlignment(true, true);
2957 viewport.sendSelection();
2961 public void hideSelSequences_actionPerformed(ActionEvent e)
2963 viewport.hideAllSelectedSeqs();
2967 * called by key handler and the hide all/show all menu items
2972 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2975 boolean hide = false;
2976 SequenceGroup sg = viewport.getSelectionGroup();
2977 if (!toggleSeqs && !toggleCols)
2979 // Hide everything by the current selection - this is a hack - we do the
2980 // invert and then hide
2981 // first check that there will be visible columns after the invert.
2982 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2983 && sg.getStartRes() <= sg.getEndRes()))
2985 // now invert the sequence set, if required - empty selection implies
2986 // that no hiding is required.
2989 invertSequenceMenuItem_actionPerformed(null);
2990 sg = viewport.getSelectionGroup();
2994 viewport.expandColSelection(sg, true);
2995 // finally invert the column selection and get the new sequence
2997 invertColSel_actionPerformed(null);
3004 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3006 hideSelSequences_actionPerformed(null);
3009 else if (!(toggleCols && viewport.hasSelectedColumns()))
3011 showAllSeqs_actionPerformed(null);
3017 if (viewport.hasSelectedColumns())
3019 hideSelColumns_actionPerformed(null);
3022 viewport.setSelectionGroup(sg);
3027 showAllColumns_actionPerformed(null);
3036 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3037 * event.ActionEvent)
3040 public void hideAllButSelection_actionPerformed(ActionEvent e)
3042 toggleHiddenRegions(false, false);
3043 viewport.sendSelection();
3050 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3054 public void hideAllSelection_actionPerformed(ActionEvent e)
3056 SequenceGroup sg = viewport.getSelectionGroup();
3057 viewport.expandColSelection(sg, false);
3058 viewport.hideAllSelectedSeqs();
3059 viewport.hideSelectedColumns();
3060 alignPanel.updateLayout();
3061 alignPanel.paintAlignment(true, true);
3062 viewport.sendSelection();
3069 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3073 public void showAllhidden_actionPerformed(ActionEvent e)
3075 viewport.showAllHiddenColumns();
3076 viewport.showAllHiddenSeqs();
3077 alignPanel.paintAlignment(true, true);
3078 viewport.sendSelection();
3082 public void hideSelColumns_actionPerformed(ActionEvent e)
3084 viewport.hideSelectedColumns();
3085 alignPanel.updateLayout();
3086 alignPanel.paintAlignment(true, true);
3087 viewport.sendSelection();
3091 public void hiddenMarkers_actionPerformed(ActionEvent e)
3093 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3104 protected void scaleAbove_actionPerformed(ActionEvent e)
3106 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3107 alignPanel.updateLayout();
3108 alignPanel.paintAlignment(true, false);
3118 protected void scaleLeft_actionPerformed(ActionEvent e)
3120 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3121 alignPanel.updateLayout();
3122 alignPanel.paintAlignment(true, false);
3132 protected void scaleRight_actionPerformed(ActionEvent e)
3134 viewport.setScaleRightWrapped(scaleRight.isSelected());
3135 alignPanel.updateLayout();
3136 alignPanel.paintAlignment(true, false);
3146 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3148 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3149 alignPanel.paintAlignment(false, false);
3159 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3161 viewport.setShowText(viewTextMenuItem.isSelected());
3162 alignPanel.paintAlignment(false, false);
3172 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3174 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3175 alignPanel.paintAlignment(false, false);
3178 public FeatureSettings featureSettings;
3181 public FeatureSettingsControllerI getFeatureSettingsUI()
3183 return featureSettings;
3187 public void featureSettings_actionPerformed(ActionEvent e)
3189 if (featureSettings != null)
3191 featureSettings.close();
3192 featureSettings = null;
3194 if (!showSeqFeatures.isSelected())
3196 // make sure features are actually displayed
3197 showSeqFeatures.setSelected(true);
3198 showSeqFeatures_actionPerformed(null);
3200 featureSettings = new FeatureSettings(this);
3204 * Set or clear 'Show Sequence Features'
3210 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3212 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3213 alignPanel.paintAlignment(true, true);
3217 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3218 * the annotations panel as a whole.
3220 * The options to show/hide all annotations should be enabled when the panel
3221 * is shown, and disabled when the panel is hidden.
3226 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3228 final boolean setVisible = annotationPanelMenuItem.isSelected();
3229 viewport.setShowAnnotation(setVisible);
3230 this.showAllSeqAnnotations.setEnabled(setVisible);
3231 this.hideAllSeqAnnotations.setEnabled(setVisible);
3232 this.showAllAlAnnotations.setEnabled(setVisible);
3233 this.hideAllAlAnnotations.setEnabled(setVisible);
3234 alignPanel.updateLayout();
3238 public void alignmentProperties()
3240 JEditorPane editPane = new JEditorPane("text/html", "");
3241 editPane.setEditable(false);
3242 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3245 MessageManager.formatMessage("label.html_content", new Object[]
3246 { contents.toString() }));
3247 JInternalFrame frame = new JInternalFrame();
3248 frame.getContentPane().add(new JScrollPane(editPane));
3250 Desktop.addInternalFrame(frame, MessageManager
3251 .formatMessage("label.alignment_properties", new Object[]
3252 { getTitle() }), 500, 400);
3262 public void overviewMenuItem_actionPerformed(ActionEvent e)
3264 if (alignPanel.overviewPanel != null)
3269 JInternalFrame frame = new JInternalFrame();
3270 final OverviewPanel overview = new OverviewPanel(alignPanel);
3271 frame.setContentPane(overview);
3272 Desktop.addInternalFrame(frame, MessageManager
3273 .formatMessage("label.overview_params", new Object[]
3274 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3277 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3278 frame.addInternalFrameListener(
3279 new javax.swing.event.InternalFrameAdapter()
3282 public void internalFrameClosed(
3283 javax.swing.event.InternalFrameEvent evt)
3286 alignPanel.setOverviewPanel(null);
3289 if (getKeyListeners().length > 0)
3291 frame.addKeyListener(getKeyListeners()[0]);
3294 alignPanel.setOverviewPanel(overview);
3298 public void textColour_actionPerformed()
3300 new TextColourChooser().chooseColour(alignPanel, null);
3304 * public void covariationColour_actionPerformed() {
3306 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3310 public void annotationColour_actionPerformed()
3312 new AnnotationColourChooser(viewport, alignPanel);
3316 public void annotationColumn_actionPerformed(ActionEvent e)
3318 new AnnotationColumnChooser(viewport, alignPanel);
3322 * Action on the user checking or unchecking the option to apply the selected
3323 * colour scheme to all groups. If unchecked, groups may have their own
3324 * independent colour schemes.
3329 public void applyToAllGroups_actionPerformed(boolean selected)
3331 viewport.setColourAppliesToAllGroups(selected);
3335 * Action on user selecting a colour from the colour menu
3338 * the name (not the menu item label!) of the colour scheme
3341 public void changeColour_actionPerformed(String name)
3344 * 'User Defined' opens a panel to configure or load a
3345 * user-defined colour scheme
3347 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3349 new UserDefinedColours(alignPanel);
3354 * otherwise set the chosen colour scheme (or null for 'None')
3356 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3358 viewport.getAlignment(), viewport.getHiddenRepSequences());
3363 * Actions on setting or changing the alignment colour scheme
3368 public void changeColour(ColourSchemeI cs)
3370 // TODO: pull up to controller method
3371 ColourMenuHelper.setColourSelected(colourMenu, cs);
3373 viewport.setGlobalColourScheme(cs);
3375 alignPanel.paintAlignment(true, true);
3379 * Show the PID threshold slider panel
3382 protected void modifyPID_actionPerformed()
3384 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3385 alignPanel.getViewName());
3386 SliderPanel.showPIDSlider();
3390 * Show the Conservation slider panel
3393 protected void modifyConservation_actionPerformed()
3395 SliderPanel.setConservationSlider(alignPanel,
3396 viewport.getResidueShading(), alignPanel.getViewName());
3397 SliderPanel.showConservationSlider();
3401 * Action on selecting or deselecting (Colour) By Conservation
3404 public void conservationMenuItem_actionPerformed(boolean selected)
3406 modifyConservation.setEnabled(selected);
3407 viewport.setConservationSelected(selected);
3408 viewport.getResidueShading().setConservationApplied(selected);
3410 changeColour(viewport.getGlobalColourScheme());
3413 modifyConservation_actionPerformed();
3417 SliderPanel.hideConservationSlider();
3422 * Action on selecting or deselecting (Colour) Above PID Threshold
3425 public void abovePIDThreshold_actionPerformed(boolean selected)
3427 modifyPID.setEnabled(selected);
3428 viewport.setAbovePIDThreshold(selected);
3431 viewport.getResidueShading().setThreshold(0,
3432 viewport.isIgnoreGapsConsensus());
3435 changeColour(viewport.getGlobalColourScheme());
3438 modifyPID_actionPerformed();
3442 SliderPanel.hidePIDSlider();
3453 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3455 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3456 AlignmentSorter.sortByPID(viewport.getAlignment(),
3457 viewport.getAlignment().getSequenceAt(0));
3458 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3459 viewport.getAlignment()));
3460 alignPanel.paintAlignment(true, false);
3470 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3472 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3473 AlignmentSorter.sortByID(viewport.getAlignment());
3475 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3476 alignPanel.paintAlignment(true, false);
3486 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3488 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3489 AlignmentSorter.sortByLength(viewport.getAlignment());
3490 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3491 viewport.getAlignment()));
3492 alignPanel.paintAlignment(true, false);
3502 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3504 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3505 AlignmentSorter.sortByGroup(viewport.getAlignment());
3506 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3507 viewport.getAlignment()));
3509 alignPanel.paintAlignment(true, false);
3519 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3521 new RedundancyPanel(alignPanel, this);
3531 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3533 if ((viewport.getSelectionGroup() == null)
3534 || (viewport.getSelectionGroup().getSize() < 2))
3536 JvOptionPane.showInternalMessageDialog(this,
3537 MessageManager.getString(
3538 "label.you_must_select_least_two_sequences"),
3539 MessageManager.getString("label.invalid_selection"),
3540 JvOptionPane.WARNING_MESSAGE);
3544 JInternalFrame frame = new JInternalFrame();
3545 frame.setContentPane(new PairwiseAlignPanel(viewport));
3546 Desktop.addInternalFrame(frame,
3547 MessageManager.getString("action.pairwise_alignment"), 600,
3553 public void autoCalculate_actionPerformed(ActionEvent e)
3555 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3556 if (viewport.autoCalculateConsensus)
3558 viewport.firePropertyChange("alignment", null,
3559 viewport.getAlignment().getSequences());
3564 public void sortByTreeOption_actionPerformed(ActionEvent e)
3566 viewport.sortByTree = sortByTree.isSelected();
3570 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3572 viewport.followSelection = listenToViewSelections.isSelected();
3576 * Constructs a tree panel and adds it to the desktop
3579 * tree type (NJ or AV)
3581 * name of score model used to compute the tree
3583 * parameters for the distance or similarity calculation
3585 void newTreePanel(String type, String modelName,
3586 SimilarityParamsI options)
3588 String frameTitle = "";
3591 boolean onSelection = false;
3592 if (viewport.getSelectionGroup() != null
3593 && viewport.getSelectionGroup().getSize() > 0)
3595 SequenceGroup sg = viewport.getSelectionGroup();
3597 /* Decide if the selection is a column region */
3598 for (SequenceI _s : sg.getSequences())
3600 if (_s.getLength() < sg.getEndRes())
3602 JvOptionPane.showMessageDialog(Desktop.desktop,
3603 MessageManager.getString(
3604 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3605 MessageManager.getString(
3606 "label.sequences_selection_not_aligned"),
3607 JvOptionPane.WARNING_MESSAGE);
3616 if (viewport.getAlignment().getHeight() < 2)
3622 tp = new TreePanel(alignPanel, type, modelName, options);
3623 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3625 frameTitle += " from ";
3627 if (viewport.getViewName() != null)
3629 frameTitle += viewport.getViewName() + " of ";
3632 frameTitle += this.title;
3634 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3645 public void addSortByOrderMenuItem(String title,
3646 final AlignmentOrder order)
3648 final JMenuItem item = new JMenuItem(MessageManager
3649 .formatMessage("action.by_title_param", new Object[]
3652 item.addActionListener(new java.awt.event.ActionListener()
3655 public void actionPerformed(ActionEvent e)
3657 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3659 // TODO: JBPNote - have to map order entries to curent SequenceI
3661 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3663 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3664 viewport.getAlignment()));
3666 alignPanel.paintAlignment(true, false);
3672 * Add a new sort by annotation score menu item
3675 * the menu to add the option to
3677 * the label used to retrieve scores for each sequence on the
3680 public void addSortByAnnotScoreMenuItem(JMenu sort,
3681 final String scoreLabel)
3683 final JMenuItem item = new JMenuItem(scoreLabel);
3685 item.addActionListener(new java.awt.event.ActionListener()
3688 public void actionPerformed(ActionEvent e)
3690 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3691 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3692 viewport.getAlignment());// ,viewport.getSelectionGroup());
3693 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3694 viewport.getAlignment()));
3695 alignPanel.paintAlignment(true, false);
3701 * last hash for alignment's annotation array - used to minimise cost of
3704 protected int _annotationScoreVectorHash;
3707 * search the alignment and rebuild the sort by annotation score submenu the
3708 * last alignment annotation vector hash is stored to minimize cost of
3709 * rebuilding in subsequence calls.
3713 public void buildSortByAnnotationScoresMenu()
3715 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3720 if (viewport.getAlignment().getAlignmentAnnotation()
3721 .hashCode() != _annotationScoreVectorHash)
3723 sortByAnnotScore.removeAll();
3724 // almost certainly a quicker way to do this - but we keep it simple
3725 Hashtable scoreSorts = new Hashtable();
3726 AlignmentAnnotation aann[];
3727 for (SequenceI sqa : viewport.getAlignment().getSequences())
3729 aann = sqa.getAnnotation();
3730 for (int i = 0; aann != null && i < aann.length; i++)
3732 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3734 scoreSorts.put(aann[i].label, aann[i].label);
3738 Enumeration labels = scoreSorts.keys();
3739 while (labels.hasMoreElements())
3741 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3742 (String) labels.nextElement());
3744 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3747 _annotationScoreVectorHash = viewport.getAlignment()
3748 .getAlignmentAnnotation().hashCode();
3753 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3754 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3755 * call. Listeners are added to remove the menu item when the treePanel is
3756 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3760 public void buildTreeSortMenu()
3762 sortByTreeMenu.removeAll();
3764 List<Component> comps = PaintRefresher.components
3765 .get(viewport.getSequenceSetId());
3766 List<TreePanel> treePanels = new ArrayList<>();
3767 for (Component comp : comps)
3769 if (comp instanceof TreePanel)
3771 treePanels.add((TreePanel) comp);
3775 if (treePanels.size() < 1)
3777 sortByTreeMenu.setVisible(false);
3781 sortByTreeMenu.setVisible(true);
3783 for (final TreePanel tp : treePanels)
3785 final JMenuItem item = new JMenuItem(tp.getTitle());
3786 item.addActionListener(new java.awt.event.ActionListener()
3789 public void actionPerformed(ActionEvent e)
3791 tp.sortByTree_actionPerformed();
3792 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3797 sortByTreeMenu.add(item);
3801 public boolean sortBy(AlignmentOrder alorder, String undoname)
3803 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3804 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3805 if (undoname != null)
3807 addHistoryItem(new OrderCommand(undoname, oldOrder,
3808 viewport.getAlignment()));
3810 alignPanel.paintAlignment(true, false);
3815 * Work out whether the whole set of sequences or just the selected set will
3816 * be submitted for multiple alignment.
3819 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3821 // Now, check we have enough sequences
3822 AlignmentView msa = null;
3824 if ((viewport.getSelectionGroup() != null)
3825 && (viewport.getSelectionGroup().getSize() > 1))
3827 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3828 // some common interface!
3830 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3831 * SequenceI[sz = seqs.getSize(false)];
3833 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3834 * seqs.getSequenceAt(i); }
3836 msa = viewport.getAlignmentView(true);
3838 else if (viewport.getSelectionGroup() != null
3839 && viewport.getSelectionGroup().getSize() == 1)
3841 int option = JvOptionPane.showConfirmDialog(this,
3842 MessageManager.getString("warn.oneseq_msainput_selection"),
3843 MessageManager.getString("label.invalid_selection"),
3844 JvOptionPane.OK_CANCEL_OPTION);
3845 if (option == JvOptionPane.OK_OPTION)
3847 msa = viewport.getAlignmentView(false);
3852 msa = viewport.getAlignmentView(false);
3858 * Decides what is submitted to a secondary structure prediction service: the
3859 * first sequence in the alignment, or in the current selection, or, if the
3860 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3861 * region or the whole alignment. (where the first sequence in the set is the
3862 * one that the prediction will be for).
3864 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3866 AlignmentView seqs = null;
3868 if ((viewport.getSelectionGroup() != null)
3869 && (viewport.getSelectionGroup().getSize() > 0))
3871 seqs = viewport.getAlignmentView(true);
3875 seqs = viewport.getAlignmentView(false);
3877 // limit sequences - JBPNote in future - could spawn multiple prediction
3879 // TODO: viewport.getAlignment().isAligned is a global state - the local
3880 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3881 if (!viewport.getAlignment().isAligned(false))
3883 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3884 // TODO: if seqs.getSequences().length>1 then should really have warned
3898 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3900 // Pick the tree file
3901 JalviewFileChooser chooser = new JalviewFileChooser(
3902 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3903 chooser.setFileView(new JalviewFileView());
3904 chooser.setDialogTitle(
3905 MessageManager.getString("label.select_newick_like_tree_file"));
3906 chooser.setToolTipText(
3907 MessageManager.getString("label.load_tree_file"));
3909 int value = chooser.showOpenDialog(null);
3911 if (value == JalviewFileChooser.APPROVE_OPTION)
3913 String filePath = chooser.getSelectedFile().getPath();
3914 Cache.setProperty("LAST_DIRECTORY", filePath);
3915 NewickFile fin = null;
3918 fin = new NewickFile(filePath, DataSourceType.FILE);
3919 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3920 } catch (Exception ex)
3922 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3923 MessageManager.getString("label.problem_reading_tree_file"),
3924 JvOptionPane.WARNING_MESSAGE);
3925 ex.printStackTrace();
3927 if (fin != null && fin.hasWarningMessage())
3929 JvOptionPane.showMessageDialog(Desktop.desktop,
3930 fin.getWarningMessage(),
3932 .getString("label.possible_problem_with_tree_file"),
3933 JvOptionPane.WARNING_MESSAGE);
3938 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3940 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3943 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3944 int h, int x, int y)
3946 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3950 * Add a treeviewer for the tree extracted from a Newick file object to the
3951 * current alignment view
3958 * Associated alignment input data (or null)
3967 * @return TreePanel handle
3969 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3970 AlignmentView input, int w, int h, int x, int y)
3972 TreePanel tp = null;
3978 if (nf.getTree() != null)
3980 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3986 tp.setLocation(x, y);
3989 Desktop.addInternalFrame(tp, treeTitle, w, h);
3991 } catch (Exception ex)
3993 ex.printStackTrace();
3999 private boolean buildingMenu = false;
4002 * Generates menu items and listener event actions for web service clients
4005 public void BuildWebServiceMenu()
4007 while (buildingMenu)
4011 System.err.println("Waiting for building menu to finish.");
4013 } catch (Exception e)
4017 final AlignFrame me = this;
4018 buildingMenu = true;
4019 new Thread(new Runnable()
4024 final List<JMenuItem> legacyItems = new ArrayList<>();
4027 // System.err.println("Building ws menu again "
4028 // + Thread.currentThread());
4029 // TODO: add support for context dependent disabling of services based
4031 // alignment and current selection
4032 // TODO: add additional serviceHandle parameter to specify abstract
4034 // class independently of AbstractName
4035 // TODO: add in rediscovery GUI function to restart discoverer
4036 // TODO: group services by location as well as function and/or
4038 // object broker mechanism.
4039 final Vector<JMenu> wsmenu = new Vector<>();
4040 final IProgressIndicator af = me;
4043 * do not i18n these strings - they are hard-coded in class
4044 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4045 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4047 final JMenu msawsmenu = new JMenu("Alignment");
4048 final JMenu secstrmenu = new JMenu(
4049 "Secondary Structure Prediction");
4050 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4051 final JMenu analymenu = new JMenu("Analysis");
4052 final JMenu dismenu = new JMenu("Protein Disorder");
4053 // JAL-940 - only show secondary structure prediction services from
4054 // the legacy server
4055 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4057 Discoverer.services != null && (Discoverer.services.size() > 0))
4059 // TODO: refactor to allow list of AbstractName/Handler bindings to
4061 // stored or retrieved from elsewhere
4062 // No MSAWS used any more:
4063 // Vector msaws = null; // (Vector)
4064 // Discoverer.services.get("MsaWS");
4065 Vector secstrpr = (Vector) Discoverer.services
4067 if (secstrpr != null)
4069 // Add any secondary structure prediction services
4070 for (int i = 0, j = secstrpr.size(); i < j; i++)
4072 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4074 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4075 .getServiceClient(sh);
4076 int p = secstrmenu.getItemCount();
4077 impl.attachWSMenuEntry(secstrmenu, me);
4078 int q = secstrmenu.getItemCount();
4079 for (int litm = p; litm < q; litm++)
4081 legacyItems.add(secstrmenu.getItem(litm));
4087 // Add all submenus in the order they should appear on the web
4089 wsmenu.add(msawsmenu);
4090 wsmenu.add(secstrmenu);
4091 wsmenu.add(dismenu);
4092 wsmenu.add(analymenu);
4093 // No search services yet
4094 // wsmenu.add(seqsrchmenu);
4096 javax.swing.SwingUtilities.invokeLater(new Runnable()
4103 webService.removeAll();
4104 // first, add discovered services onto the webservices menu
4105 if (wsmenu.size() > 0)
4107 for (int i = 0, j = wsmenu.size(); i < j; i++)
4109 webService.add(wsmenu.get(i));
4114 webService.add(me.webServiceNoServices);
4116 // TODO: move into separate menu builder class.
4117 boolean new_sspred = false;
4118 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4120 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4121 if (jws2servs != null)
4123 if (jws2servs.hasServices())
4125 jws2servs.attachWSMenuEntry(webService, me);
4126 for (Jws2Instance sv : jws2servs.getServices())
4128 if (sv.description.toLowerCase().contains("jpred"))
4130 for (JMenuItem jmi : legacyItems)
4132 jmi.setVisible(false);
4138 if (jws2servs.isRunning())
4140 JMenuItem tm = new JMenuItem(
4141 "Still discovering JABA Services");
4142 tm.setEnabled(false);
4147 build_urlServiceMenu(me.webService);
4148 build_fetchdbmenu(webService);
4149 for (JMenu item : wsmenu)
4151 if (item.getItemCount() == 0)
4153 item.setEnabled(false);
4157 item.setEnabled(true);
4160 } catch (Exception e)
4163 "Exception during web service menu building process.",
4168 } catch (Exception e)
4171 buildingMenu = false;
4178 * construct any groupURL type service menu entries.
4182 private void build_urlServiceMenu(JMenu webService)
4184 // TODO: remove this code when 2.7 is released
4185 // DEBUG - alignmentView
4187 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4188 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4190 * @Override public void actionPerformed(ActionEvent e) {
4191 * jalview.datamodel.AlignmentView
4192 * .testSelectionViews(af.viewport.getAlignment(),
4193 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4195 * }); webService.add(testAlView);
4197 // TODO: refactor to RestClient discoverer and merge menu entries for
4198 // rest-style services with other types of analysis/calculation service
4199 // SHmmr test client - still being implemented.
4200 // DEBUG - alignmentView
4202 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4205 client.attachWSMenuEntry(
4206 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4212 * Searches the alignment sequences for xRefs and builds the Show
4213 * Cross-References menu (formerly called Show Products), with database
4214 * sources for which cross-references are found (protein sources for a
4215 * nucleotide alignment and vice versa)
4217 * @return true if Show Cross-references menu should be enabled
4219 public boolean canShowProducts()
4221 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4222 AlignmentI dataset = viewport.getAlignment().getDataset();
4224 showProducts.removeAll();
4225 final boolean dna = viewport.getAlignment().isNucleotide();
4227 if (seqs == null || seqs.length == 0)
4229 // nothing to see here.
4233 boolean showp = false;
4236 List<String> ptypes = new CrossRef(seqs, dataset)
4237 .findXrefSourcesForSequences(dna);
4239 for (final String source : ptypes)
4242 final AlignFrame af = this;
4243 JMenuItem xtype = new JMenuItem(source);
4244 xtype.addActionListener(new ActionListener()
4247 public void actionPerformed(ActionEvent e)
4249 showProductsFor(af.viewport.getSequenceSelection(), dna,
4253 showProducts.add(xtype);
4255 showProducts.setVisible(showp);
4256 showProducts.setEnabled(showp);
4257 } catch (Exception e)
4260 "canShowProducts threw an exception - please report to help@jalview.org",
4268 * Finds and displays cross-references for the selected sequences (protein
4269 * products for nucleotide sequences, dna coding sequences for peptides).
4272 * the sequences to show cross-references for
4274 * true if from a nucleotide alignment (so showing proteins)
4276 * the database to show cross-references for
4278 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4279 final String source)
4281 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4286 * Construct and display a new frame containing the translation of this
4287 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4290 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4292 AlignmentI al = null;
4295 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4297 al = dna.translateCdna(codeTable);
4298 } catch (Exception ex)
4300 jalview.bin.Cache.log.error(
4301 "Exception during translation. Please report this !", ex);
4302 final String msg = MessageManager.getString(
4303 "label.error_when_translating_sequences_submit_bug_report");
4304 final String errorTitle = MessageManager
4305 .getString("label.implementation_error")
4306 + MessageManager.getString("label.translation_failed");
4307 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4308 JvOptionPane.ERROR_MESSAGE);
4311 if (al == null || al.getHeight() == 0)
4313 final String msg = MessageManager.getString(
4314 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4315 final String errorTitle = MessageManager
4316 .getString("label.translation_failed");
4317 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4318 JvOptionPane.WARNING_MESSAGE);
4322 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4323 af.setFileFormat(this.currentFileFormat);
4324 final String newTitle = MessageManager
4325 .formatMessage("label.translation_of_params", new Object[]
4326 { this.getTitle(), codeTable.getId() });
4327 af.setTitle(newTitle);
4328 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4330 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4331 viewport.openSplitFrame(af, new Alignment(seqs));
4335 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4342 * Set the file format
4346 public void setFileFormat(FileFormatI format)
4348 this.currentFileFormat = format;
4352 * Try to load a features file onto the alignment.
4355 * contents or path to retrieve file
4357 * access mode of file (see jalview.io.AlignFile)
4358 * @return true if features file was parsed correctly.
4360 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4362 return avc.parseFeaturesFile(file, sourceType,
4363 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4368 public void refreshFeatureUI(boolean enableIfNecessary)
4370 // note - currently this is only still here rather than in the controller
4371 // because of the featureSettings hard reference that is yet to be
4373 if (enableIfNecessary)
4375 viewport.setShowSequenceFeatures(true);
4376 showSeqFeatures.setSelected(true);
4382 public void dragEnter(DropTargetDragEvent evt)
4387 public void dragExit(DropTargetEvent evt)
4392 public void dragOver(DropTargetDragEvent evt)
4397 public void dropActionChanged(DropTargetDragEvent evt)
4402 public void drop(DropTargetDropEvent evt)
4404 // JAL-1552 - acceptDrop required before getTransferable call for
4405 // Java's Transferable for native dnd
4406 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4407 Transferable t = evt.getTransferable();
4408 final AlignFrame thisaf = this;
4409 final List<String> files = new ArrayList<>();
4410 List<DataSourceType> protocols = new ArrayList<>();
4414 Desktop.transferFromDropTarget(files, protocols, evt, t);
4415 } catch (Exception e)
4417 e.printStackTrace();
4421 new Thread(new Runnable()
4428 // check to see if any of these files have names matching sequences
4431 SequenceIdMatcher idm = new SequenceIdMatcher(
4432 viewport.getAlignment().getSequencesArray());
4434 * Object[] { String,SequenceI}
4436 ArrayList<Object[]> filesmatched = new ArrayList<>();
4437 ArrayList<String> filesnotmatched = new ArrayList<>();
4438 for (int i = 0; i < files.size(); i++)
4440 String file = files.get(i).toString();
4442 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4443 if (protocol == DataSourceType.FILE)
4445 File fl = new File(file);
4446 pdbfn = fl.getName();
4448 else if (protocol == DataSourceType.URL)
4450 URL url = new URL(file);
4451 pdbfn = url.getFile();
4453 if (pdbfn.length() > 0)
4455 // attempt to find a match in the alignment
4456 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4457 int l = 0, c = pdbfn.indexOf(".");
4458 while (mtch == null && c != -1)
4463 } while ((c = pdbfn.indexOf(".", l)) > l);
4466 pdbfn = pdbfn.substring(0, l);
4468 mtch = idm.findAllIdMatches(pdbfn);
4472 FileFormatI type = null;
4475 type = new IdentifyFile().identify(file, protocol);
4476 } catch (Exception ex)
4480 if (type != null && type.isStructureFile())
4482 filesmatched.add(new Object[] { file, protocol, mtch });
4486 // File wasn't named like one of the sequences or wasn't a PDB
4488 filesnotmatched.add(file);
4492 if (filesmatched.size() > 0)
4494 boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4497 String msg = MessageManager.formatMessage(
4498 "label.automatically_associate_structure_files_with_sequences_same_name",
4500 { Integer.valueOf(filesmatched.size())
4502 String ttl = MessageManager.getString(
4503 "label.automatically_associate_structure_files_by_name");
4504 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4505 ttl, JvOptionPane.YES_NO_OPTION);
4506 autoAssociate = choice == JvOptionPane.YES_OPTION;
4510 for (Object[] fm : filesmatched)
4512 // try and associate
4513 // TODO: may want to set a standard ID naming formalism for
4514 // associating PDB files which have no IDs.
4515 for (SequenceI toassoc : (SequenceI[]) fm[2])
4517 PDBEntry pe = new AssociatePdbFileWithSeq()
4518 .associatePdbWithSeq((String) fm[0],
4519 (DataSourceType) fm[1], toassoc, false,
4523 System.err.println("Associated file : "
4524 + ((String) fm[0]) + " with "
4525 + toassoc.getDisplayId(true));
4529 // TODO: do we need to update overview ? only if features are
4531 alignPanel.paintAlignment(true, false);
4537 * add declined structures as sequences
4539 for (Object[] o : filesmatched)
4541 filesnotmatched.add((String) o[0]);
4545 if (filesnotmatched.size() > 0)
4547 if (assocfiles > 0 && (Cache.getDefault(
4548 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4549 || JvOptionPane.showConfirmDialog(thisaf,
4550 "<html>" + MessageManager.formatMessage(
4551 "label.ignore_unmatched_dropped_files_info",
4554 filesnotmatched.size())
4557 MessageManager.getString(
4558 "label.ignore_unmatched_dropped_files"),
4559 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4563 for (String fn : filesnotmatched)
4565 loadJalviewDataFile(fn, null, null, null);
4569 } catch (Exception ex)
4571 ex.printStackTrace();
4579 * Attempt to load a "dropped" file or URL string, by testing in turn for
4581 * <li>an Annotation file</li>
4582 * <li>a JNet file</li>
4583 * <li>a features file</li>
4584 * <li>else try to interpret as an alignment file</li>
4588 * either a filename or a URL string.
4590 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4591 FileFormatI format, SequenceI assocSeq)
4595 if (sourceType == null)
4597 sourceType = FormatAdapter.checkProtocol(file);
4599 // if the file isn't identified, or not positively identified as some
4600 // other filetype (PFAM is default unidentified alignment file type) then
4601 // try to parse as annotation.
4602 boolean isAnnotation = (format == null
4603 || FileFormat.Pfam.equals(format))
4604 ? new AnnotationFile().annotateAlignmentView(viewport,
4610 // first see if its a T-COFFEE score file
4611 TCoffeeScoreFile tcf = null;
4614 tcf = new TCoffeeScoreFile(file, sourceType);
4617 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4621 new TCoffeeColourScheme(viewport.getAlignment()));
4622 isAnnotation = true;
4623 statusBar.setText(MessageManager.getString(
4624 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4628 // some problem - if no warning its probable that the ID matching
4629 // process didn't work
4630 JvOptionPane.showMessageDialog(Desktop.desktop,
4631 tcf.getWarningMessage() == null
4632 ? MessageManager.getString(
4633 "label.check_file_matches_sequence_ids_alignment")
4634 : tcf.getWarningMessage(),
4635 MessageManager.getString(
4636 "label.problem_reading_tcoffee_score_file"),
4637 JvOptionPane.WARNING_MESSAGE);
4644 } catch (Exception x)
4647 "Exception when processing data source as T-COFFEE score file",
4653 // try to see if its a JNet 'concise' style annotation file *before*
4655 // try to parse it as a features file
4658 format = new IdentifyFile().identify(file, sourceType);
4660 if (FileFormat.ScoreMatrix == format)
4662 ScoreMatrixFile sm = new ScoreMatrixFile(
4663 new FileParse(file, sourceType));
4665 // todo: i18n this message
4666 statusBar.setText(MessageManager.formatMessage(
4667 "label.successfully_loaded_matrix",
4668 sm.getMatrixName()));
4670 else if (FileFormat.Jnet.equals(format))
4672 JPredFile predictions = new JPredFile(file, sourceType);
4673 new JnetAnnotationMaker();
4674 JnetAnnotationMaker.add_annotation(predictions,
4675 viewport.getAlignment(), 0, false);
4676 viewport.getAlignment().setupJPredAlignment();
4677 isAnnotation = true;
4679 // else if (IdentifyFile.FeaturesFile.equals(format))
4680 else if (FileFormat.Features.equals(format))
4682 if (parseFeaturesFile(file, sourceType))
4684 alignPanel.paintAlignment(true, true);
4689 new FileLoader().LoadFile(viewport, file, sourceType, format);
4696 alignPanel.adjustAnnotationHeight();
4697 viewport.updateSequenceIdColours();
4698 buildSortByAnnotationScoresMenu();
4699 alignPanel.paintAlignment(true, true);
4701 } catch (Exception ex)
4703 ex.printStackTrace();
4704 } catch (OutOfMemoryError oom)
4709 } catch (Exception x)
4714 + (sourceType != null
4715 ? (sourceType == DataSourceType.PASTE
4717 : "using " + sourceType + " from "
4721 ? "(parsing as '" + format + "' file)"
4723 oom, Desktop.desktop);
4728 * Method invoked by the ChangeListener on the tabbed pane, in other words
4729 * when a different tabbed pane is selected by the user or programmatically.
4732 public void tabSelectionChanged(int index)
4736 alignPanel = alignPanels.get(index);
4737 viewport = alignPanel.av;
4738 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4739 setMenusFromViewport(viewport);
4743 * 'focus' any colour slider that is open to the selected viewport
4745 if (viewport.getConservationSelected())
4747 SliderPanel.setConservationSlider(alignPanel,
4748 viewport.getResidueShading(), alignPanel.getViewName());
4752 SliderPanel.hideConservationSlider();
4754 if (viewport.getAbovePIDThreshold())
4756 SliderPanel.setPIDSliderSource(alignPanel,
4757 viewport.getResidueShading(), alignPanel.getViewName());
4761 SliderPanel.hidePIDSlider();
4765 * If there is a frame linked to this one in a SplitPane, switch it to the
4766 * same view tab index. No infinite recursion of calls should happen, since
4767 * tabSelectionChanged() should not get invoked on setting the selected
4768 * index to an unchanged value. Guard against setting an invalid index
4769 * before the new view peer tab has been created.
4771 final AlignViewportI peer = viewport.getCodingComplement();
4774 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4775 .getAlignPanel().alignFrame;
4776 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4778 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4784 * On right mouse click on view tab, prompt for and set new view name.
4787 public void tabbedPane_mousePressed(MouseEvent e)
4789 if (e.isPopupTrigger())
4791 String msg = MessageManager.getString("label.enter_view_name");
4792 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4793 JvOptionPane.QUESTION_MESSAGE);
4797 viewport.setViewName(reply);
4798 // TODO warn if reply is in getExistingViewNames()?
4799 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4804 public AlignViewport getCurrentView()
4810 * Open the dialog for regex description parsing.
4813 protected void extractScores_actionPerformed(ActionEvent e)
4815 ParseProperties pp = new jalview.analysis.ParseProperties(
4816 viewport.getAlignment());
4817 // TODO: verify regex and introduce GUI dialog for version 2.5
4818 // if (pp.getScoresFromDescription("col", "score column ",
4819 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4821 if (pp.getScoresFromDescription("description column",
4822 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4824 buildSortByAnnotationScoresMenu();
4832 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4836 protected void showDbRefs_actionPerformed(ActionEvent e)
4838 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4844 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4848 protected void showNpFeats_actionPerformed(ActionEvent e)
4850 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4854 * find the viewport amongst the tabs in this alignment frame and close that
4859 public boolean closeView(AlignViewportI av)
4863 this.closeMenuItem_actionPerformed(false);
4866 Component[] comp = tabbedPane.getComponents();
4867 for (int i = 0; comp != null && i < comp.length; i++)
4869 if (comp[i] instanceof AlignmentPanel)
4871 if (((AlignmentPanel) comp[i]).av == av)
4874 closeView((AlignmentPanel) comp[i]);
4882 protected void build_fetchdbmenu(JMenu webService)
4884 // Temporary hack - DBRef Fetcher always top level ws entry.
4885 // TODO We probably want to store a sequence database checklist in
4886 // preferences and have checkboxes.. rather than individual sources selected
4888 final JMenu rfetch = new JMenu(
4889 MessageManager.getString("action.fetch_db_references"));
4890 rfetch.setToolTipText(MessageManager.getString(
4891 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4892 webService.add(rfetch);
4894 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4895 MessageManager.getString("option.trim_retrieved_seqs"));
4896 trimrs.setToolTipText(
4897 MessageManager.getString("label.trim_retrieved_sequences"));
4899 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4900 trimrs.addActionListener(new ActionListener()
4903 public void actionPerformed(ActionEvent e)
4905 trimrs.setSelected(trimrs.isSelected());
4906 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4907 Boolean.valueOf(trimrs.isSelected()).toString());
4911 JMenuItem fetchr = new JMenuItem(
4912 MessageManager.getString("label.standard_databases"));
4913 fetchr.setToolTipText(
4914 MessageManager.getString("label.fetch_embl_uniprot"));
4915 fetchr.addActionListener(new ActionListener()
4919 public void actionPerformed(ActionEvent e)
4921 new Thread(new Runnable()
4926 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4927 .getAlignment().isNucleotide();
4928 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4929 alignPanel.av.getSequenceSelection(),
4930 alignPanel.alignFrame, null,
4931 alignPanel.alignFrame.featureSettings, isNucleotide);
4932 dbRefFetcher.addListener(new FetchFinishedListenerI()
4935 public void finished()
4937 AlignFrame.this.setMenusForViewport();
4940 dbRefFetcher.fetchDBRefs(false);
4948 final AlignFrame me = this;
4949 new Thread(new Runnable()
4954 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4955 .getSequenceFetcherSingleton(me);
4956 javax.swing.SwingUtilities.invokeLater(new Runnable()
4961 String[] dbclasses = sf.getOrderedSupportedSources();
4962 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4963 // jalview.util.QuickSort.sort(otherdb, otherdb);
4964 List<DbSourceProxy> otherdb;
4965 JMenu dfetch = new JMenu();
4966 JMenu ifetch = new JMenu();
4967 JMenuItem fetchr = null;
4968 int comp = 0, icomp = 0, mcomp = 15;
4969 String mname = null;
4971 for (String dbclass : dbclasses)
4973 otherdb = sf.getSourceProxy(dbclass);
4974 // add a single entry for this class, or submenu allowing 'fetch
4976 if (otherdb == null || otherdb.size() < 1)
4980 // List<DbSourceProxy> dbs=otherdb;
4981 // otherdb=new ArrayList<DbSourceProxy>();
4982 // for (DbSourceProxy db:dbs)
4984 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4988 mname = "From " + dbclass;
4990 if (otherdb.size() == 1)
4992 final DbSourceProxy[] dassource = otherdb
4993 .toArray(new DbSourceProxy[0]);
4994 DbSourceProxy src = otherdb.get(0);
4995 fetchr = new JMenuItem(src.getDbSource());
4996 fetchr.addActionListener(new ActionListener()
5000 public void actionPerformed(ActionEvent e)
5002 new Thread(new Runnable()
5008 boolean isNucleotide = alignPanel.alignFrame
5009 .getViewport().getAlignment()
5011 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5012 alignPanel.av.getSequenceSelection(),
5013 alignPanel.alignFrame, dassource,
5014 alignPanel.alignFrame.featureSettings,
5017 .addListener(new FetchFinishedListenerI()
5020 public void finished()
5022 AlignFrame.this.setMenusForViewport();
5025 dbRefFetcher.fetchDBRefs(false);
5031 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5032 MessageManager.formatMessage(
5033 "label.fetch_retrieve_from", new Object[]
5034 { src.getDbName() })));
5040 final DbSourceProxy[] dassource = otherdb
5041 .toArray(new DbSourceProxy[0]);
5043 DbSourceProxy src = otherdb.get(0);
5044 fetchr = new JMenuItem(MessageManager
5045 .formatMessage("label.fetch_all_param", new Object[]
5046 { src.getDbSource() }));
5047 fetchr.addActionListener(new ActionListener()
5050 public void actionPerformed(ActionEvent e)
5052 new Thread(new Runnable()
5058 boolean isNucleotide = alignPanel.alignFrame
5059 .getViewport().getAlignment()
5061 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5062 alignPanel.av.getSequenceSelection(),
5063 alignPanel.alignFrame, dassource,
5064 alignPanel.alignFrame.featureSettings,
5067 .addListener(new FetchFinishedListenerI()
5070 public void finished()
5072 AlignFrame.this.setMenusForViewport();
5075 dbRefFetcher.fetchDBRefs(false);
5081 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5082 MessageManager.formatMessage(
5083 "label.fetch_retrieve_from_all_sources",
5085 { Integer.valueOf(otherdb.size())
5087 src.getDbSource(), src.getDbName() })));
5090 // and then build the rest of the individual menus
5091 ifetch = new JMenu(MessageManager.formatMessage(
5092 "label.source_from_db_source", new Object[]
5093 { src.getDbSource() }));
5095 String imname = null;
5097 for (DbSourceProxy sproxy : otherdb)
5099 String dbname = sproxy.getDbName();
5100 String sname = dbname.length() > 5
5101 ? dbname.substring(0, 5) + "..."
5103 String msname = dbname.length() > 10
5104 ? dbname.substring(0, 10) + "..."
5108 imname = MessageManager
5109 .formatMessage("label.from_msname", new Object[]
5112 fetchr = new JMenuItem(msname);
5113 final DbSourceProxy[] dassrc = { sproxy };
5114 fetchr.addActionListener(new ActionListener()
5118 public void actionPerformed(ActionEvent e)
5120 new Thread(new Runnable()
5126 boolean isNucleotide = alignPanel.alignFrame
5127 .getViewport().getAlignment()
5129 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5130 alignPanel.av.getSequenceSelection(),
5131 alignPanel.alignFrame, dassrc,
5132 alignPanel.alignFrame.featureSettings,
5135 .addListener(new FetchFinishedListenerI()
5138 public void finished()
5140 AlignFrame.this.setMenusForViewport();
5143 dbRefFetcher.fetchDBRefs(false);
5149 fetchr.setToolTipText(
5150 "<html>" + MessageManager.formatMessage(
5151 "label.fetch_retrieve_from", new Object[]
5155 if (++icomp >= mcomp || i == (otherdb.size()))
5157 ifetch.setText(MessageManager.formatMessage(
5158 "label.source_to_target", imname, sname));
5160 ifetch = new JMenu();
5168 if (comp >= mcomp || dbi >= (dbclasses.length))
5170 dfetch.setText(MessageManager.formatMessage(
5171 "label.source_to_target", mname, dbclass));
5173 dfetch = new JMenu();
5186 * Left justify the whole alignment.
5189 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5191 AlignmentI al = viewport.getAlignment();
5193 viewport.firePropertyChange("alignment", null, al);
5197 * Right justify the whole alignment.
5200 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5202 AlignmentI al = viewport.getAlignment();
5204 viewport.firePropertyChange("alignment", null, al);
5208 public void setShowSeqFeatures(boolean b)
5210 showSeqFeatures.setSelected(b);
5211 viewport.setShowSequenceFeatures(b);
5218 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5219 * awt.event.ActionEvent)
5222 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5224 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5225 alignPanel.paintAlignment(false, false);
5232 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5236 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5238 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5239 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5247 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5248 * .event.ActionEvent)
5251 protected void showGroupConservation_actionPerformed(ActionEvent e)
5253 viewport.setShowGroupConservation(showGroupConservation.getState());
5254 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5261 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5262 * .event.ActionEvent)
5265 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5267 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5268 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5275 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5276 * .event.ActionEvent)
5279 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5281 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5282 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5286 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5288 showSequenceLogo.setState(true);
5289 viewport.setShowSequenceLogo(true);
5290 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5291 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5295 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5297 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5304 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5305 * .event.ActionEvent)
5308 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5310 if (avc.makeGroupsFromSelection())
5312 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5313 alignPanel.updateAnnotation();
5314 alignPanel.paintAlignment(true,
5315 viewport.needToUpdateStructureViews());
5319 public void clearAlignmentSeqRep()
5321 // TODO refactor alignmentseqrep to controller
5322 if (viewport.getAlignment().hasSeqrep())
5324 viewport.getAlignment().setSeqrep(null);
5325 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5326 alignPanel.updateAnnotation();
5327 alignPanel.paintAlignment(true, true);
5332 protected void createGroup_actionPerformed(ActionEvent e)
5334 if (avc.createGroup())
5336 if (applyAutoAnnotationSettings.isSelected())
5338 alignPanel.updateAnnotation(true, false);
5340 alignPanel.alignmentChanged();
5345 protected void unGroup_actionPerformed(ActionEvent e)
5349 alignPanel.alignmentChanged();
5354 * make the given alignmentPanel the currently selected tab
5356 * @param alignmentPanel
5358 public void setDisplayedView(AlignmentPanel alignmentPanel)
5360 if (!viewport.getSequenceSetId()
5361 .equals(alignmentPanel.av.getSequenceSetId()))
5363 throw new Error(MessageManager.getString(
5364 "error.implementation_error_cannot_show_view_alignment_frame"));
5366 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5367 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5369 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5374 * Action on selection of menu options to Show or Hide annotations.
5377 * @param forSequences
5378 * update sequence-related annotations
5379 * @param forAlignment
5380 * update non-sequence-related annotations
5383 protected void setAnnotationsVisibility(boolean visible,
5384 boolean forSequences, boolean forAlignment)
5386 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5387 .getAlignmentAnnotation();
5392 for (AlignmentAnnotation aa : anns)
5395 * don't display non-positional annotations on an alignment
5397 if (aa.annotations == null)
5401 boolean apply = (aa.sequenceRef == null && forAlignment)
5402 || (aa.sequenceRef != null && forSequences);
5405 aa.visible = visible;
5408 alignPanel.validateAnnotationDimensions(true);
5409 alignPanel.alignmentChanged();
5413 * Store selected annotation sort order for the view and repaint.
5416 protected void sortAnnotations_actionPerformed()
5418 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5420 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5421 alignPanel.paintAlignment(false, false);
5426 * @return alignment panels in this alignment frame
5428 public List<? extends AlignmentViewPanel> getAlignPanels()
5430 // alignPanels is never null
5431 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5436 * Open a new alignment window, with the cDNA associated with this (protein)
5437 * alignment, aligned as is the protein.
5439 protected void viewAsCdna_actionPerformed()
5441 // TODO no longer a menu action - refactor as required
5442 final AlignmentI alignment = getViewport().getAlignment();
5443 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5444 if (mappings == null)
5448 List<SequenceI> cdnaSeqs = new ArrayList<>();
5449 for (SequenceI aaSeq : alignment.getSequences())
5451 for (AlignedCodonFrame acf : mappings)
5453 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5457 * There is a cDNA mapping for this protein sequence - add to new
5458 * alignment. It will share the same dataset sequence as other mapped
5459 * cDNA (no new mappings need to be created).
5461 final Sequence newSeq = new Sequence(dnaSeq);
5462 newSeq.setDatasetSequence(dnaSeq);
5463 cdnaSeqs.add(newSeq);
5467 if (cdnaSeqs.size() == 0)
5469 // show a warning dialog no mapped cDNA
5472 AlignmentI cdna = new Alignment(
5473 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5474 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5475 AlignFrame.DEFAULT_HEIGHT);
5476 cdna.alignAs(alignment);
5477 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5479 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5480 AlignFrame.DEFAULT_HEIGHT);
5484 * Set visibility of dna/protein complement view (available when shown in a
5490 protected void showComplement_actionPerformed(boolean show)
5492 SplitContainerI sf = getSplitViewContainer();
5495 sf.setComplementVisible(this, show);
5500 * Generate the reverse (optionally complemented) of the selected sequences,
5501 * and add them to the alignment
5504 protected void showReverse_actionPerformed(boolean complement)
5506 AlignmentI al = null;
5509 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5510 al = dna.reverseCdna(complement);
5511 viewport.addAlignment(al, "");
5512 addHistoryItem(new EditCommand(
5513 MessageManager.getString("label.add_sequences"), Action.PASTE,
5514 al.getSequencesArray(), 0, al.getWidth(),
5515 viewport.getAlignment()));
5516 } catch (Exception ex)
5518 System.err.println(ex.getMessage());
5524 * Try to run a script in the Groovy console, having first ensured that this
5525 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5526 * be targeted at this alignment.
5529 protected void runGroovy_actionPerformed()
5531 Jalview.setCurrentAlignFrame(this);
5532 groovy.ui.Console console = Desktop.getGroovyConsole();
5533 if (console != null)
5537 console.runScript();
5538 } catch (Exception ex)
5540 System.err.println((ex.toString()));
5541 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5542 MessageManager.getString("label.couldnt_run_groovy_script"),
5543 MessageManager.getString("label.groovy_support_failed"),
5544 JvOptionPane.ERROR_MESSAGE);
5549 System.err.println("Can't run Groovy script as console not found");
5554 * Hides columns containing (or not containing) a specified feature, provided
5555 * that would not leave all columns hidden
5557 * @param featureType
5558 * @param columnsContaining
5561 public boolean hideFeatureColumns(String featureType,
5562 boolean columnsContaining)
5564 boolean notForHiding = avc.markColumnsContainingFeatures(
5565 columnsContaining, false, false, featureType);
5568 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5569 false, featureType))
5571 getViewport().hideSelectedColumns();
5579 protected void selectHighlightedColumns_actionPerformed(
5580 ActionEvent actionEvent)
5582 // include key modifier check in case user selects from menu
5583 avc.markHighlightedColumns(
5584 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5585 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5586 | ActionEvent.CTRL_MASK)) != 0);
5590 * Rebuilds the Colour menu, including any user-defined colours which have
5591 * been loaded either on startup or during the session
5593 public void buildColourMenu()
5595 colourMenu.removeAll();
5597 colourMenu.add(applyToAllGroups);
5598 colourMenu.add(textColour);
5599 colourMenu.addSeparator();
5601 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5602 viewport.getAlignment(), false);
5604 colourMenu.add(annotationColour);
5605 bg.add(annotationColour);
5606 colourMenu.addSeparator();
5607 colourMenu.add(conservationMenuItem);
5608 colourMenu.add(modifyConservation);
5609 colourMenu.add(abovePIDThreshold);
5610 colourMenu.add(modifyPID);
5612 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5613 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5617 * Open a dialog (if not already open) that allows the user to select and
5618 * calculate PCA or Tree analysis
5620 protected void openTreePcaDialog()
5622 if (alignPanel.getCalculationDialog() == null)
5624 new CalculationChooser(AlignFrame.this);
5629 protected void loadVcf_actionPerformed()
5631 JalviewFileChooser chooser = new JalviewFileChooser(
5632 Cache.getProperty("LAST_DIRECTORY"));
5633 chooser.setFileView(new JalviewFileView());
5634 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5635 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5637 int value = chooser.showOpenDialog(null);
5639 if (value == JalviewFileChooser.APPROVE_OPTION)
5641 String choice = chooser.getSelectedFile().getPath();
5642 Cache.setProperty("LAST_DIRECTORY", choice);
5643 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5644 new VCFLoader(choice).loadVCF(seqs, this);
5650 class PrintThread extends Thread
5654 public PrintThread(AlignmentPanel ap)
5659 static PageFormat pf;
5664 PrinterJob printJob = PrinterJob.getPrinterJob();
5668 printJob.setPrintable(ap, pf);
5672 printJob.setPrintable(ap);
5675 if (printJob.printDialog())
5680 } catch (Exception PrintException)
5682 PrintException.printStackTrace();