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 java.awt.BorderLayout;
24 import java.awt.Component;
25 import java.awt.Rectangle;
26 import java.awt.Toolkit;
27 import java.awt.datatransfer.Clipboard;
28 import java.awt.datatransfer.DataFlavor;
29 import java.awt.datatransfer.StringSelection;
30 import java.awt.datatransfer.Transferable;
31 import java.awt.dnd.DnDConstants;
32 import java.awt.dnd.DropTargetDragEvent;
33 import java.awt.dnd.DropTargetDropEvent;
34 import java.awt.dnd.DropTargetEvent;
35 import java.awt.dnd.DropTargetListener;
36 import java.awt.event.ActionEvent;
37 import java.awt.event.ActionListener;
38 import java.awt.event.FocusAdapter;
39 import java.awt.event.FocusEvent;
40 import java.awt.event.ItemEvent;
41 import java.awt.event.ItemListener;
42 import java.awt.event.KeyAdapter;
43 import java.awt.event.KeyEvent;
44 import java.awt.event.MouseEvent;
45 import java.awt.print.PageFormat;
46 import java.awt.print.PrinterJob;
47 import java.beans.PropertyChangeEvent;
49 import java.io.FileWriter;
50 import java.io.IOException;
51 import java.io.PrintWriter;
53 import java.util.ArrayList;
54 import java.util.Arrays;
55 import java.util.Deque;
56 import java.util.Enumeration;
57 import java.util.Hashtable;
58 import java.util.List;
59 import java.util.Vector;
61 import javax.swing.ButtonGroup;
62 import javax.swing.JCheckBoxMenuItem;
63 import javax.swing.JEditorPane;
64 import javax.swing.JInternalFrame;
65 import javax.swing.JLayeredPane;
66 import javax.swing.JMenu;
67 import javax.swing.JMenuItem;
68 import javax.swing.JScrollPane;
69 import javax.swing.SwingUtilities;
71 import jalview.analysis.AlignmentSorter;
72 import jalview.analysis.AlignmentUtils;
73 import jalview.analysis.CrossRef;
74 import jalview.analysis.Dna;
75 import jalview.analysis.GeneticCodeI;
76 import jalview.analysis.ParseProperties;
77 import jalview.analysis.SequenceIdMatcher;
78 import jalview.api.AlignExportSettingI;
79 import jalview.api.AlignViewControllerGuiI;
80 import jalview.api.AlignViewControllerI;
81 import jalview.api.AlignViewportI;
82 import jalview.api.AlignmentViewPanel;
83 import jalview.api.FeatureSettingsControllerI;
84 import jalview.api.FeatureSettingsModelI;
85 import jalview.api.SplitContainerI;
86 import jalview.api.ViewStyleI;
87 import jalview.api.analysis.SimilarityParamsI;
88 import jalview.bin.Cache;
89 import jalview.bin.Jalview;
90 import jalview.commands.CommandI;
91 import jalview.commands.EditCommand;
92 import jalview.commands.EditCommand.Action;
93 import jalview.commands.OrderCommand;
94 import jalview.commands.RemoveGapColCommand;
95 import jalview.commands.RemoveGapsCommand;
96 import jalview.commands.SlideSequencesCommand;
97 import jalview.commands.TrimRegionCommand;
98 import jalview.datamodel.AlignedCodonFrame;
99 import jalview.datamodel.Alignment;
100 import jalview.datamodel.AlignmentAnnotation;
101 import jalview.datamodel.AlignmentExportData;
102 import jalview.datamodel.AlignmentI;
103 import jalview.datamodel.AlignmentOrder;
104 import jalview.datamodel.AlignmentView;
105 import jalview.datamodel.ColumnSelection;
106 import jalview.datamodel.HiddenColumns;
107 import jalview.datamodel.HiddenSequences;
108 import jalview.datamodel.PDBEntry;
109 import jalview.datamodel.SeqCigar;
110 import jalview.datamodel.Sequence;
111 import jalview.datamodel.SequenceGroup;
112 import jalview.datamodel.SequenceI;
113 import jalview.gui.ColourMenuHelper.ColourChangeListener;
114 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
115 import jalview.io.AlignmentProperties;
116 import jalview.io.AnnotationFile;
117 import jalview.io.BackupFiles;
118 import jalview.io.BioJsHTMLOutput;
119 import jalview.io.DataSourceType;
120 import jalview.io.FileFormat;
121 import jalview.io.FileFormatI;
122 import jalview.io.FileFormats;
123 import jalview.io.FileLoader;
124 import jalview.io.FileParse;
125 import jalview.io.FormatAdapter;
126 import jalview.io.HtmlSvgOutput;
127 import jalview.io.IdentifyFile;
128 import jalview.io.JPredFile;
129 import jalview.io.JalviewFileChooser;
130 import jalview.io.JalviewFileView;
131 import jalview.io.JnetAnnotationMaker;
132 import jalview.io.NewickFile;
133 import jalview.io.ScoreMatrixFile;
134 import jalview.io.TCoffeeScoreFile;
135 import jalview.io.vcf.VCFLoader;
136 import jalview.jbgui.GAlignFrame;
137 import jalview.schemes.ColourSchemeI;
138 import jalview.schemes.ColourSchemes;
139 import jalview.schemes.ResidueColourScheme;
140 import jalview.schemes.TCoffeeColourScheme;
141 import jalview.util.HttpUtils;
142 import jalview.util.MessageManager;
143 import jalview.util.Platform;
144 import jalview.viewmodel.AlignmentViewport;
145 import jalview.viewmodel.ViewportRanges;
146 import jalview.ws.DBRefFetcher;
147 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
148 import jalview.ws.jws1.Discoverer;
149 import jalview.ws.jws2.Jws2Discoverer;
150 import jalview.ws.jws2.jabaws2.Jws2Instance;
151 import jalview.ws.seqfetcher.DbSourceProxy;
157 * @version $Revision$
159 public class AlignFrame extends GAlignFrame implements DropTargetListener,
160 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
163 public static final int DEFAULT_WIDTH = 700;
165 public static final int DEFAULT_HEIGHT = 500;
168 * The currently displayed panel (selected tabbed view if more than one)
170 public AlignmentPanel alignPanel;
172 AlignViewport viewport;
174 public AlignViewControllerI avc;
176 List<AlignmentPanel> alignPanels = new ArrayList<>();
179 * Last format used to load or save alignments in this window
181 FileFormatI currentFileFormat = null;
184 * Current filename for this alignment
186 String fileName = null;
189 * Creates a new AlignFrame object with specific width and height.
195 public AlignFrame(AlignmentI al, int width, int height)
197 this(al, null, width, height);
201 * Creates a new AlignFrame object with specific width, height and
207 * @param sequenceSetId
209 public AlignFrame(AlignmentI al, int width, int height,
210 String sequenceSetId)
212 this(al, null, width, height, sequenceSetId);
216 * Creates a new AlignFrame object with specific width, height and
222 * @param sequenceSetId
225 public AlignFrame(AlignmentI al, int width, int height,
226 String sequenceSetId, String viewId)
228 this(al, null, width, height, sequenceSetId, viewId);
232 * new alignment window with hidden columns
236 * @param hiddenColumns
237 * ColumnSelection or null
239 * Width of alignment frame
243 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
246 this(al, hiddenColumns, width, height, null);
250 * Create alignment frame for al with hiddenColumns, a specific width and
251 * height, and specific sequenceId
254 * @param hiddenColumns
257 * @param sequenceSetId
260 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
261 int height, String sequenceSetId)
263 this(al, hiddenColumns, width, height, sequenceSetId, null);
267 * Create alignment frame for al with hiddenColumns, a specific width and
268 * height, and specific sequenceId
271 * @param hiddenColumns
274 * @param sequenceSetId
279 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
280 int height, String sequenceSetId, String viewId)
282 setSize(width, height);
284 if (al.getDataset() == null)
289 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
291 alignPanel = new AlignmentPanel(this, viewport);
293 addAlignmentPanel(alignPanel, true);
297 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
298 HiddenColumns hiddenColumns, int width, int height)
300 setSize(width, height);
302 if (al.getDataset() == null)
307 viewport = new AlignViewport(al, hiddenColumns);
309 if (hiddenSeqs != null && hiddenSeqs.length > 0)
311 viewport.hideSequence(hiddenSeqs);
313 alignPanel = new AlignmentPanel(this, viewport);
314 addAlignmentPanel(alignPanel, true);
319 * Make a new AlignFrame from existing alignmentPanels
326 public AlignFrame(AlignmentPanel ap)
330 addAlignmentPanel(ap, false);
335 * initalise the alignframe from the underlying viewport data and the
340 if (!Jalview.isHeadlessMode())
342 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
345 avc = new jalview.controller.AlignViewController(this, viewport,
347 if (viewport.getAlignmentConservationAnnotation() == null)
349 // BLOSUM62Colour.setEnabled(false);
350 conservationMenuItem.setEnabled(false);
351 modifyConservation.setEnabled(false);
352 // PIDColour.setEnabled(false);
353 // abovePIDThreshold.setEnabled(false);
354 // modifyPID.setEnabled(false);
357 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
360 if (sortby.equals("Id"))
362 sortIDMenuItem_actionPerformed(null);
364 else if (sortby.equals("Pairwise Identity"))
366 sortPairwiseMenuItem_actionPerformed(null);
370 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
372 setMenusFromViewport(viewport);
373 buildSortByAnnotationScoresMenu();
374 calculateTree.addActionListener(new ActionListener()
378 public void actionPerformed(ActionEvent e)
385 if (Desktop.desktop != null)
387 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
388 addServiceListeners();
392 if (viewport.getWrapAlignment())
394 wrapMenuItem_actionPerformed(null);
397 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
399 this.overviewMenuItem_actionPerformed(null);
404 final List<AlignmentPanel> selviews = new ArrayList<>();
405 final List<AlignmentPanel> origview = new ArrayList<>();
406 final String menuLabel = MessageManager
407 .getString("label.copy_format_from");
408 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
409 new ViewSetProvider()
413 public AlignmentPanel[] getAllAlignmentPanels()
416 origview.add(alignPanel);
417 // make an array of all alignment panels except for this one
418 List<AlignmentPanel> aps = new ArrayList<>(
419 Arrays.asList(Desktop.getAlignmentPanels(null)));
420 aps.remove(AlignFrame.this.alignPanel);
421 return aps.toArray(new AlignmentPanel[aps.size()]);
423 }, selviews, new ItemListener()
427 public void itemStateChanged(ItemEvent e)
429 if (origview.size() > 0)
431 final AlignmentPanel ap = origview.get(0);
434 * Copy the ViewStyle of the selected panel to 'this one'.
435 * Don't change value of 'scaleProteinAsCdna' unless copying
438 ViewStyleI vs = selviews.get(0).getAlignViewport()
440 boolean fromSplitFrame = selviews.get(0)
441 .getAlignViewport().getCodingComplement() != null;
444 vs.setScaleProteinAsCdna(ap.getAlignViewport()
445 .getViewStyle().isScaleProteinAsCdna());
447 ap.getAlignViewport().setViewStyle(vs);
450 * Also rescale ViewStyle of SplitFrame complement if there is
451 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
452 * the whole ViewStyle (allow cDNA protein to have different
455 AlignViewportI complement = ap.getAlignViewport()
456 .getCodingComplement();
457 if (complement != null && vs.isScaleProteinAsCdna())
459 AlignFrame af = Desktop.getAlignFrameFor(complement);
460 ((SplitFrame) af.getSplitViewContainer())
462 af.setMenusForViewport();
466 ap.setSelected(true);
467 ap.alignFrame.setMenusForViewport();
472 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
473 .indexOf("devel") > -1
474 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
475 .indexOf("test") > -1)
477 formatMenu.add(vsel);
479 addFocusListener(new FocusAdapter()
482 public void focusGained(FocusEvent e)
484 Jalview.setCurrentAlignFrame(AlignFrame.this);
491 * Change the filename and format for the alignment, and enable the 'reload'
492 * button functionality.
499 public void setFileName(String file, FileFormatI format)
502 setFileFormat(format);
503 reload.setEnabled(true);
507 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
510 void addKeyListener()
512 addKeyListener(new KeyAdapter()
515 public void keyPressed(KeyEvent evt)
517 if (viewport.cursorMode
518 && ((evt.getKeyCode() >= KeyEvent.VK_0
519 && evt.getKeyCode() <= KeyEvent.VK_9)
520 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
521 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
522 && Character.isDigit(evt.getKeyChar()))
524 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
527 switch (evt.getKeyCode())
530 case 27: // escape key
531 deselectAllSequenceMenuItem_actionPerformed(null);
535 case KeyEvent.VK_DOWN:
536 if (evt.isAltDown() || !viewport.cursorMode)
538 moveSelectedSequences(false);
540 if (viewport.cursorMode)
542 alignPanel.getSeqPanel().moveCursor(0, 1,
543 evt.isShiftDown() && !evt.isAltDown());
548 if (evt.isAltDown() || !viewport.cursorMode)
550 moveSelectedSequences(true);
552 if (viewport.cursorMode)
554 alignPanel.getSeqPanel().moveCursor(0, -1,
555 evt.isShiftDown() && !evt.isAltDown());
559 case KeyEvent.VK_LEFT:
560 if (evt.isAltDown() || !viewport.cursorMode)
562 slideSequences(false,
563 alignPanel.getSeqPanel().getKeyboardNo1());
567 alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
572 case KeyEvent.VK_RIGHT:
573 if (evt.isAltDown() || !viewport.cursorMode)
575 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
579 alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
583 case KeyEvent.VK_SPACE:
584 if (viewport.cursorMode)
586 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
587 || evt.isShiftDown() || evt.isAltDown());
591 // case KeyEvent.VK_A:
592 // if (viewport.cursorMode)
594 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
595 // //System.out.println("A");
599 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
600 * System.out.println("closing bracket"); } break;
602 case KeyEvent.VK_DELETE:
603 case KeyEvent.VK_BACK_SPACE:
604 if (!viewport.cursorMode)
606 cut_actionPerformed(null);
610 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
611 || evt.isShiftDown() || evt.isAltDown());
617 if (viewport.cursorMode)
619 alignPanel.getSeqPanel().setCursorRow();
623 if (viewport.cursorMode && !evt.isControlDown())
625 alignPanel.getSeqPanel().setCursorColumn();
629 if (viewport.cursorMode)
631 alignPanel.getSeqPanel().setCursorPosition();
635 case KeyEvent.VK_ENTER:
636 case KeyEvent.VK_COMMA:
637 if (viewport.cursorMode)
639 alignPanel.getSeqPanel().setCursorRowAndColumn();
644 if (viewport.cursorMode)
646 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
650 if (viewport.cursorMode)
652 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
657 viewport.cursorMode = !viewport.cursorMode;
658 statusBar.setText(MessageManager
659 .formatMessage("label.keyboard_editing_mode", new String[]
660 { (viewport.cursorMode ? "on" : "off") }));
661 if (viewport.cursorMode)
663 ViewportRanges ranges = viewport.getRanges();
664 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
666 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
669 alignPanel.getSeqPanel().seqCanvas.repaint();
675 Help.showHelpWindow();
676 } catch (Exception ex)
678 ex.printStackTrace();
683 boolean toggleSeqs = !evt.isControlDown();
684 boolean toggleCols = !evt.isShiftDown();
685 toggleHiddenRegions(toggleSeqs, toggleCols);
690 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
691 boolean modifyExisting = true; // always modify, don't clear
692 // evt.isShiftDown();
693 boolean invertHighlighted = evt.isAltDown();
694 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
698 case KeyEvent.VK_PAGE_UP:
699 viewport.getRanges().pageUp();
701 case KeyEvent.VK_PAGE_DOWN:
702 viewport.getRanges().pageDown();
708 public void keyReleased(KeyEvent evt)
710 switch (evt.getKeyCode())
712 case KeyEvent.VK_LEFT:
713 if (evt.isAltDown() || !viewport.cursorMode)
715 viewport.firePropertyChange("alignment", null,
716 viewport.getAlignment().getSequences());
720 case KeyEvent.VK_RIGHT:
721 if (evt.isAltDown() || !viewport.cursorMode)
723 viewport.firePropertyChange("alignment", null,
724 viewport.getAlignment().getSequences());
732 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
734 ap.alignFrame = this;
735 avc = new jalview.controller.AlignViewController(this, viewport,
740 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
742 int aSize = alignPanels.size();
744 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
746 if (aSize == 1 && ap.av.getViewName() == null)
748 this.getContentPane().add(ap, BorderLayout.CENTER);
754 setInitialTabVisible();
757 expandViews.setEnabled(true);
758 gatherViews.setEnabled(true);
759 tabbedPane.addTab(ap.av.getViewName(), ap);
761 ap.setVisible(false);
766 if (ap.av.isPadGaps())
768 ap.av.getAlignment().padGaps();
770 ap.av.updateConservation(ap);
771 ap.av.updateConsensus(ap);
772 ap.av.updateStrucConsensus(ap);
776 public void setInitialTabVisible()
778 expandViews.setEnabled(true);
779 gatherViews.setEnabled(true);
780 tabbedPane.setVisible(true);
781 AlignmentPanel first = alignPanels.get(0);
782 tabbedPane.addTab(first.av.getViewName(), first);
783 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
786 public AlignViewport getViewport()
791 /* Set up intrinsic listeners for dynamically generated GUI bits. */
792 private void addServiceListeners()
794 final java.beans.PropertyChangeListener thisListener;
795 Desktop.instance.addJalviewPropertyChangeListener("services",
796 thisListener = new java.beans.PropertyChangeListener()
799 public void propertyChange(PropertyChangeEvent evt)
801 // // System.out.println("Discoverer property change.");
802 // if (evt.getPropertyName().equals("services"))
804 SwingUtilities.invokeLater(new Runnable()
811 "Rebuild WS Menu for service change");
812 BuildWebServiceMenu();
819 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
822 public void internalFrameClosed(
823 javax.swing.event.InternalFrameEvent evt)
825 // System.out.println("deregistering discoverer listener");
826 Desktop.instance.removeJalviewPropertyChangeListener("services",
828 closeMenuItem_actionPerformed(true);
831 // Finally, build the menu once to get current service state
832 new Thread(new Runnable()
837 BuildWebServiceMenu();
843 * Configure menu items that vary according to whether the alignment is
844 * nucleotide or protein
846 public void setGUINucleotide()
848 AlignmentI al = getViewport().getAlignment();
849 boolean nucleotide = al.isNucleotide();
851 loadVcf.setVisible(nucleotide);
852 showTranslation.setVisible(nucleotide);
853 showReverse.setVisible(nucleotide);
854 showReverseComplement.setVisible(nucleotide);
855 conservationMenuItem.setEnabled(!nucleotide);
857 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
858 showGroupConservation.setEnabled(!nucleotide);
860 showComplementMenuItem
861 .setText(nucleotide ? MessageManager.getString("label.protein")
862 : MessageManager.getString("label.nucleotide"));
866 * set up menus for the current viewport. This may be called after any
867 * operation that affects the data in the current view (selection changed,
868 * etc) to update the menus to reflect the new state.
871 public void setMenusForViewport()
873 setMenusFromViewport(viewport);
877 * Need to call this method when tabs are selected for multiple views, or when
878 * loading from Jalview2XML.java
883 public void setMenusFromViewport(AlignViewport av)
885 padGapsMenuitem.setSelected(av.isPadGaps());
886 colourTextMenuItem.setSelected(av.isShowColourText());
887 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
888 modifyPID.setEnabled(abovePIDThreshold.isSelected());
889 conservationMenuItem.setSelected(av.getConservationSelected());
890 modifyConservation.setEnabled(conservationMenuItem.isSelected());
891 seqLimits.setSelected(av.getShowJVSuffix());
892 idRightAlign.setSelected(av.isRightAlignIds());
893 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
894 renderGapsMenuItem.setSelected(av.isRenderGaps());
895 wrapMenuItem.setSelected(av.getWrapAlignment());
896 scaleAbove.setVisible(av.getWrapAlignment());
897 scaleLeft.setVisible(av.getWrapAlignment());
898 scaleRight.setVisible(av.getWrapAlignment());
899 annotationPanelMenuItem.setState(av.isShowAnnotation());
901 * Show/hide annotations only enabled if annotation panel is shown
903 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
904 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
905 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
906 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
907 viewBoxesMenuItem.setSelected(av.getShowBoxes());
908 viewTextMenuItem.setSelected(av.getShowText());
909 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
910 showGroupConsensus.setSelected(av.isShowGroupConsensus());
911 showGroupConservation.setSelected(av.isShowGroupConservation());
912 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
913 showSequenceLogo.setSelected(av.isShowSequenceLogo());
914 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
916 ColourMenuHelper.setColourSelected(colourMenu,
917 av.getGlobalColourScheme());
919 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
920 hiddenMarkers.setState(av.getShowHiddenMarkers());
921 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
922 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
923 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
924 autoCalculate.setSelected(av.autoCalculateConsensus);
925 sortByTree.setSelected(av.sortByTree);
926 listenToViewSelections.setSelected(av.followSelection);
928 showProducts.setEnabled(canShowProducts());
929 setGroovyEnabled(Desktop.getGroovyConsole() != null);
935 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
939 public void setGroovyEnabled(boolean b)
941 runGroovy.setEnabled(b);
944 private IProgressIndicator progressBar;
949 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
952 public void setProgressBar(String message, long id)
954 progressBar.setProgressBar(message, id);
958 public void registerHandler(final long id,
959 final IProgressIndicatorHandler handler)
961 progressBar.registerHandler(id, handler);
966 * @return true if any progress bars are still active
969 public boolean operationInProgress()
971 return progressBar.operationInProgress();
975 * Sets the text of the status bar. Note that setting a null or empty value
976 * will cause the status bar to be hidden, with possibly undesirable flicker
977 * of the screen layout.
980 public void setStatus(String text)
982 statusBar.setText(text == null || text.isEmpty() ? " " : text);
986 * Added so Castor Mapping file can obtain Jalview Version
988 public String getVersion()
990 return jalview.bin.Cache.getProperty("VERSION");
993 public FeatureRenderer getFeatureRenderer()
995 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
999 public void fetchSequence_actionPerformed(ActionEvent e)
1001 new jalview.gui.SequenceFetcher(this);
1005 public void addFromFile_actionPerformed(ActionEvent e)
1007 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1011 public void reload_actionPerformed(ActionEvent e)
1013 if (fileName != null)
1015 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1016 // originating file's format
1017 // TODO: work out how to recover feature settings for correct view(s) when
1018 // file is reloaded.
1019 if (FileFormat.Jalview.equals(currentFileFormat))
1021 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1022 for (int i = 0; i < frames.length; i++)
1024 if (frames[i] instanceof AlignFrame && frames[i] != this
1025 && ((AlignFrame) frames[i]).fileName != null
1026 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1030 frames[i].setSelected(true);
1031 Desktop.instance.closeAssociatedWindows();
1032 } catch (java.beans.PropertyVetoException ex)
1038 Desktop.instance.closeAssociatedWindows();
1040 FileLoader loader = new FileLoader();
1041 DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
1042 ? DataSourceType.URL
1043 : DataSourceType.FILE;
1044 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1048 Rectangle bounds = this.getBounds();
1050 FileLoader loader = new FileLoader();
1051 DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
1052 ? DataSourceType.URL
1053 : DataSourceType.FILE;
1054 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1055 protocol, currentFileFormat);
1057 newframe.setBounds(bounds);
1058 if (featureSettings != null && featureSettings.isShowing())
1060 final Rectangle fspos = featureSettings.frame.getBounds();
1061 // TODO: need a 'show feature settings' function that takes bounds -
1062 // need to refactor Desktop.addFrame
1063 newframe.featureSettings_actionPerformed(null);
1064 final FeatureSettings nfs = newframe.featureSettings;
1065 SwingUtilities.invokeLater(new Runnable()
1070 nfs.frame.setBounds(fspos);
1073 this.featureSettings.close();
1074 this.featureSettings = null;
1076 this.closeMenuItem_actionPerformed(true);
1082 public void addFromText_actionPerformed(ActionEvent e)
1085 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1089 public void addFromURL_actionPerformed(ActionEvent e)
1091 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1095 public void save_actionPerformed(ActionEvent e)
1097 if (fileName == null || (currentFileFormat == null)
1098 || HttpUtils.startsWithHttpOrHttps(fileName))
1100 saveAs_actionPerformed(null);
1104 saveAlignment(fileName, currentFileFormat);
1115 public void saveAs_actionPerformed(ActionEvent e)
1117 String format = currentFileFormat == null ? null
1118 : currentFileFormat.getName();
1119 JalviewFileChooser chooser = JalviewFileChooser
1120 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1122 chooser.setFileView(new JalviewFileView());
1123 chooser.setDialogTitle(
1124 MessageManager.getString("label.save_alignment_to_file"));
1125 chooser.setToolTipText(MessageManager.getString("action.save"));
1127 int value = chooser.showSaveDialog(this);
1129 if (value == JalviewFileChooser.APPROVE_OPTION)
1131 currentFileFormat = chooser.getSelectedFormat();
1132 while (currentFileFormat == null)
1134 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1135 MessageManager.getString(
1136 "label.select_file_format_before_saving"),
1137 MessageManager.getString("label.file_format_not_specified"),
1138 JvOptionPane.WARNING_MESSAGE);
1139 currentFileFormat = chooser.getSelectedFormat();
1140 value = chooser.showSaveDialog(this);
1141 if (value != JalviewFileChooser.APPROVE_OPTION)
1147 fileName = chooser.getSelectedFile().getPath();
1149 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1151 Cache.setProperty("LAST_DIRECTORY", fileName);
1152 saveAlignment(fileName, currentFileFormat);
1156 public boolean saveAlignment(String file, FileFormatI format)
1158 boolean success = true;
1160 if (FileFormat.Jalview.equals(format))
1162 String shortName = title;
1164 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1166 shortName = shortName.substring(
1167 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1170 success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1173 statusBar.setText(MessageManager.formatMessage(
1174 "label.successfully_saved_to_file_in_format", new Object[]
1180 AlignmentExportData exportData = getAlignmentForExport(format,
1182 if (exportData.getSettings().isCancelled())
1186 FormatAdapter f = new FormatAdapter(alignPanel,
1187 exportData.getSettings());
1188 String output = f.formatSequences(format, exportData.getAlignment(), // class
1192 // occur in the distant future
1193 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1194 f.getCacheSuffixDefault(format),
1195 viewport.getAlignment().getHiddenColumns());
1203 // create backupfiles object and get new temp filename destination
1204 Cache.log.trace("ALIGNFRAME making backupfiles object for " + file);
1205 BackupFiles backupfiles = new BackupFiles(file);
1209 String tempFilePath = backupfiles.getTempFilePath();
1211 "ALIGNFRAME setting PrintWriter to " + tempFilePath);
1212 PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1215 "ALIGNFRAME about to write to temp file " + tempFilePath);
1218 Cache.log.trace("ALIGNFRAME about to close file");
1220 Cache.log.trace("ALIGNFRAME closed file");
1221 this.setTitle(file);
1222 statusBar.setText(MessageManager.formatMessage(
1223 "label.successfully_saved_to_file_in_format", new Object[]
1224 { file, format.getName() }));
1225 } catch (IOException e)
1229 "ALIGNFRAME Something happened writing the temp file");
1230 Cache.log.error(e.getMessage());
1231 Cache.log.debug(Cache.getStackTraceString(e));
1233 } catch (Exception ex)
1237 "ALIGNFRAME Something unexpected happened writing the temp file");
1238 Cache.log.error(ex.getMessage());
1239 Cache.log.debug(Cache.getStackTraceString(ex));
1242 backupfiles.setWriteSuccess(success);
1243 Cache.log.debug("ALIGNFRAME writing temp file was "
1244 + (success ? "" : "NOT ") + "successful");
1245 // do the backup file roll and rename the temp file to actual file
1246 Cache.log.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
1247 success = backupfiles.rollBackupsAndRenameTempFile();
1248 Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
1249 + (success ? "" : "un") + "successfully");
1256 if (!Platform.isHeadless())
1258 JvOptionPane.showInternalMessageDialog(this, MessageManager
1259 .formatMessage("label.couldnt_save_file", new Object[]
1261 MessageManager.getString("label.error_saving_file"),
1262 JvOptionPane.WARNING_MESSAGE);
1269 private void warningMessage(String warning, String title)
1271 if (new jalview.util.Platform().isHeadless())
1273 System.err.println("Warning: " + title + "\nWarning: " + warning);
1278 JvOptionPane.showInternalMessageDialog(this, warning, title,
1279 JvOptionPane.WARNING_MESSAGE);
1291 protected void outputText_actionPerformed(ActionEvent e)
1293 FileFormatI fileFormat = FileFormats.getInstance()
1294 .forName(e.getActionCommand());
1295 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1297 if (exportData.getSettings().isCancelled())
1301 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1302 cap.setForInput(null);
1305 FileFormatI format = fileFormat;
1306 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1307 .formatSequences(format, exportData.getAlignment(),
1308 exportData.getOmitHidden(),
1309 exportData.getStartEndPostions(),
1310 viewport.getAlignment().getHiddenColumns()));
1311 Desktop.addInternalFrame(cap, MessageManager
1312 .formatMessage("label.alignment_output_command", new Object[]
1313 { e.getActionCommand() }), 600, 500);
1314 } catch (OutOfMemoryError oom)
1316 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1323 public static AlignmentExportData getAlignmentForExport(
1324 FileFormatI format, AlignViewportI viewport,
1325 AlignExportSettingI exportSettings)
1327 AlignmentI alignmentToExport = null;
1328 AlignExportSettingI settings = exportSettings;
1329 String[] omitHidden = null;
1331 HiddenSequences hiddenSeqs = viewport.getAlignment()
1332 .getHiddenSequences();
1334 alignmentToExport = viewport.getAlignment();
1336 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1337 if (settings == null)
1339 settings = new AlignExportSettings(hasHiddenSeqs,
1340 viewport.hasHiddenColumns(), format);
1342 // settings.isExportAnnotations();
1344 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1346 omitHidden = viewport.getViewAsString(false,
1347 settings.isExportHiddenSequences());
1350 int[] alignmentStartEnd = new int[2];
1351 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1353 alignmentToExport = hiddenSeqs.getFullAlignment();
1357 alignmentToExport = viewport.getAlignment();
1359 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1360 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1361 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1362 omitHidden, alignmentStartEnd, settings);
1373 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1375 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1376 htmlSVG.exportHTML(null);
1380 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1382 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1383 bjs.exportHTML(null);
1386 public void createImageMap(File file, String image)
1388 alignPanel.makePNGImageMap(file, image);
1398 public void createPNG(File f)
1400 alignPanel.makePNG(f);
1410 public void createEPS(File f)
1412 alignPanel.makeEPS(f);
1416 public void createSVG(File f)
1418 alignPanel.makeSVG(f);
1422 public void pageSetup_actionPerformed(ActionEvent e)
1424 PrinterJob printJob = PrinterJob.getPrinterJob();
1425 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1435 public void printMenuItem_actionPerformed(ActionEvent e)
1437 // Putting in a thread avoids Swing painting problems
1438 PrintThread thread = new PrintThread(alignPanel);
1443 public void exportFeatures_actionPerformed(ActionEvent e)
1445 new AnnotationExporter(alignPanel).exportFeatures();
1449 public void exportAnnotations_actionPerformed(ActionEvent e)
1451 new AnnotationExporter(alignPanel).exportAnnotations();
1455 public void associatedData_actionPerformed(ActionEvent e)
1457 // Pick the tree file
1458 JalviewFileChooser chooser = new JalviewFileChooser(
1459 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1460 chooser.setFileView(new JalviewFileView());
1461 chooser.setDialogTitle(
1462 MessageManager.getString("label.load_jalview_annotations"));
1463 chooser.setToolTipText(
1464 MessageManager.getString("label.load_jalview_annotations"));
1466 int value = chooser.showOpenDialog(null);
1468 if (value == JalviewFileChooser.APPROVE_OPTION)
1470 String choice = chooser.getSelectedFile().getPath();
1471 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1472 loadJalviewDataFile(choice, null, null, null);
1478 * Close the current view or all views in the alignment frame. If the frame
1479 * only contains one view then the alignment will be removed from memory.
1481 * @param closeAllTabs
1484 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1486 if (alignPanels != null && alignPanels.size() < 2)
1488 closeAllTabs = true;
1493 if (alignPanels != null)
1497 if (this.isClosed())
1499 // really close all the windows - otherwise wait till
1500 // setClosed(true) is called
1501 for (int i = 0; i < alignPanels.size(); i++)
1503 AlignmentPanel ap = alignPanels.get(i);
1510 closeView(alignPanel);
1515 if (featureSettings != null && featureSettings.isOpen())
1517 featureSettings.close();
1518 featureSettings = null;
1521 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1522 * be called recursively, with the frame now in 'closed' state
1524 this.setClosed(true);
1526 } catch (Exception ex)
1528 ex.printStackTrace();
1533 * Close the specified panel and close up tabs appropriately.
1535 * @param panelToClose
1537 public void closeView(AlignmentPanel panelToClose)
1539 int index = tabbedPane.getSelectedIndex();
1540 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1541 alignPanels.remove(panelToClose);
1542 panelToClose.closePanel();
1543 panelToClose = null;
1545 tabbedPane.removeTabAt(closedindex);
1546 tabbedPane.validate();
1548 if (index > closedindex || index == tabbedPane.getTabCount())
1550 // modify currently selected tab index if necessary.
1554 this.tabSelectionChanged(index);
1560 void updateEditMenuBar()
1563 if (viewport.getHistoryList().size() > 0)
1565 undoMenuItem.setEnabled(true);
1566 CommandI command = viewport.getHistoryList().peek();
1567 undoMenuItem.setText(MessageManager
1568 .formatMessage("label.undo_command", new Object[]
1569 { command.getDescription() }));
1573 undoMenuItem.setEnabled(false);
1574 undoMenuItem.setText(MessageManager.getString("action.undo"));
1577 if (viewport.getRedoList().size() > 0)
1579 redoMenuItem.setEnabled(true);
1581 CommandI command = viewport.getRedoList().peek();
1582 redoMenuItem.setText(MessageManager
1583 .formatMessage("label.redo_command", new Object[]
1584 { command.getDescription() }));
1588 redoMenuItem.setEnabled(false);
1589 redoMenuItem.setText(MessageManager.getString("action.redo"));
1594 public void addHistoryItem(CommandI command)
1596 if (command.getSize() > 0)
1598 viewport.addToHistoryList(command);
1599 viewport.clearRedoList();
1600 updateEditMenuBar();
1601 viewport.updateHiddenColumns();
1602 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1603 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1604 // viewport.getColumnSelection()
1605 // .getHiddenColumns().size() > 0);
1611 * @return alignment objects for all views
1613 AlignmentI[] getViewAlignments()
1615 if (alignPanels != null)
1617 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1619 for (AlignmentPanel ap : alignPanels)
1621 als[i++] = ap.av.getAlignment();
1625 if (viewport != null)
1627 return new AlignmentI[] { viewport.getAlignment() };
1639 protected void undoMenuItem_actionPerformed(ActionEvent e)
1641 if (viewport.getHistoryList().isEmpty())
1645 CommandI command = viewport.getHistoryList().pop();
1646 viewport.addToRedoList(command);
1647 command.undoCommand(getViewAlignments());
1649 AlignmentViewport originalSource = getOriginatingSource(command);
1650 updateEditMenuBar();
1652 if (originalSource != null)
1654 if (originalSource != viewport)
1657 "Implementation worry: mismatch of viewport origin for undo");
1659 originalSource.updateHiddenColumns();
1660 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1662 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1663 // viewport.getColumnSelection()
1664 // .getHiddenColumns().size() > 0);
1665 originalSource.firePropertyChange("alignment", null,
1666 originalSource.getAlignment().getSequences());
1677 protected void redoMenuItem_actionPerformed(ActionEvent e)
1679 if (viewport.getRedoList().size() < 1)
1684 CommandI command = viewport.getRedoList().pop();
1685 viewport.addToHistoryList(command);
1686 command.doCommand(getViewAlignments());
1688 AlignmentViewport originalSource = getOriginatingSource(command);
1689 updateEditMenuBar();
1691 if (originalSource != null)
1694 if (originalSource != viewport)
1697 "Implementation worry: mismatch of viewport origin for redo");
1699 originalSource.updateHiddenColumns();
1700 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1702 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1703 // viewport.getColumnSelection()
1704 // .getHiddenColumns().size() > 0);
1705 originalSource.firePropertyChange("alignment", null,
1706 originalSource.getAlignment().getSequences());
1710 AlignmentViewport getOriginatingSource(CommandI command)
1712 AlignmentViewport originalSource = null;
1713 // For sequence removal and addition, we need to fire
1714 // the property change event FROM the viewport where the
1715 // original alignment was altered
1716 AlignmentI al = null;
1717 if (command instanceof EditCommand)
1719 EditCommand editCommand = (EditCommand) command;
1720 al = editCommand.getAlignment();
1721 List<Component> comps = PaintRefresher.components
1722 .get(viewport.getSequenceSetId());
1724 for (Component comp : comps)
1726 if (comp instanceof AlignmentPanel)
1728 if (al == ((AlignmentPanel) comp).av.getAlignment())
1730 originalSource = ((AlignmentPanel) comp).av;
1737 if (originalSource == null)
1739 // The original view is closed, we must validate
1740 // the current view against the closed view first
1743 PaintRefresher.validateSequences(al, viewport.getAlignment());
1746 originalSource = viewport;
1749 return originalSource;
1753 * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
1754 * or the sequence under cursor in keyboard mode
1759 public void moveSelectedSequences(boolean up)
1761 SequenceGroup sg = viewport.getSelectionGroup();
1765 if (viewport.cursorMode)
1767 sg = new SequenceGroup();
1768 sg.addSequence(viewport.getAlignment().getSequenceAt(
1769 alignPanel.getSeqPanel().seqCanvas.cursorY), false);
1777 if (sg.getSize() < 1)
1782 // TODO: JAL-3733 - add an event to the undo buffer for this !
1784 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1785 viewport.getHiddenRepSequences(), up);
1786 alignPanel.paintAlignment(true, false);
1789 synchronized void slideSequences(boolean right, int size)
1791 List<SequenceI> sg = new ArrayList<>();
1792 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup()
1793 .getSize() != viewport.getAlignment().getHeight())
1795 sg = viewport.getSelectionGroup()
1796 .getSequences(viewport.getHiddenRepSequences());
1799 if (sg.size() == 0 && viewport.cursorMode)
1801 sg.add(viewport.getAlignment()
1802 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1810 List<SequenceI> invertGroup = new ArrayList<>();
1812 for (SequenceI seq : viewport.getAlignment().getSequences())
1814 if (!sg.contains(seq))
1816 invertGroup.add(seq);
1820 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1822 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1823 for (int i = 0; i < invertGroup.size(); i++)
1825 seqs2[i] = invertGroup.get(i);
1828 SlideSequencesCommand ssc;
1831 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1832 viewport.getGapCharacter());
1836 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1837 viewport.getGapCharacter());
1840 int groupAdjustment = 0;
1841 if (ssc.getGapsInsertedBegin() && right)
1843 if (viewport.cursorMode)
1845 alignPanel.getSeqPanel().moveCursor(size, 0);
1849 groupAdjustment = size;
1852 else if (!ssc.getGapsInsertedBegin() && !right)
1854 if (viewport.cursorMode)
1856 alignPanel.getSeqPanel().moveCursor(-size, 0);
1860 groupAdjustment = -size;
1864 if (groupAdjustment != 0)
1866 viewport.getSelectionGroup().setStartRes(
1867 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1868 viewport.getSelectionGroup().setEndRes(
1869 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1873 * just extend the last slide command if compatible; but not if in
1874 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1876 boolean appendHistoryItem = false;
1877 Deque<CommandI> historyList = viewport.getHistoryList();
1878 boolean inSplitFrame = getSplitViewContainer() != null;
1879 if (!inSplitFrame && historyList != null && historyList.size() > 0
1880 && historyList.peek() instanceof SlideSequencesCommand)
1882 appendHistoryItem = ssc.appendSlideCommand(
1883 (SlideSequencesCommand) historyList.peek());
1886 if (!appendHistoryItem)
1888 addHistoryItem(ssc);
1901 protected void copy_actionPerformed(ActionEvent e)
1903 if (viewport.getSelectionGroup() == null)
1907 // TODO: preserve the ordering of displayed alignment annotation in any
1908 // internal paste (particularly sequence associated annotation)
1909 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1910 String[] omitHidden = null;
1912 if (viewport.hasHiddenColumns())
1914 omitHidden = viewport.getViewAsString(true);
1917 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1918 seqs, omitHidden, null);
1920 StringSelection ss = new StringSelection(output);
1924 jalview.gui.Desktop.internalCopy = true;
1925 // Its really worth setting the clipboard contents
1926 // to empty before setting the large StringSelection!!
1927 Toolkit.getDefaultToolkit().getSystemClipboard()
1928 .setContents(new StringSelection(""), null);
1930 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1932 } catch (OutOfMemoryError er)
1934 new OOMWarning("copying region", er);
1938 HiddenColumns hiddenColumns = null;
1939 if (viewport.hasHiddenColumns())
1941 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1942 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1944 // create new HiddenColumns object with copy of hidden regions
1945 // between startRes and endRes, offset by startRes
1946 hiddenColumns = new HiddenColumns(
1947 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1948 hiddenCutoff, hiddenOffset);
1951 Desktop.jalviewClipboard = new Object[] { seqs,
1952 viewport.getAlignment().getDataset(), hiddenColumns };
1953 statusBar.setText(MessageManager.formatMessage(
1954 "label.copied_sequences_to_clipboard", new Object[]
1955 { Integer.valueOf(seqs.length).toString() }));
1965 protected void pasteNew_actionPerformed(ActionEvent e)
1977 protected void pasteThis_actionPerformed(ActionEvent e)
1983 * Paste contents of Jalview clipboard
1985 * @param newAlignment
1986 * true to paste to a new alignment, otherwise add to this.
1988 void paste(boolean newAlignment)
1990 boolean externalPaste = true;
1993 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1994 Transferable contents = c.getContents(this);
1996 if (contents == null)
2005 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2006 if (str.length() < 1)
2011 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2013 } catch (OutOfMemoryError er)
2015 new OOMWarning("Out of memory pasting sequences!!", er);
2019 SequenceI[] sequences;
2020 boolean annotationAdded = false;
2021 AlignmentI alignment = null;
2023 if (Desktop.jalviewClipboard != null)
2025 // The clipboard was filled from within Jalview, we must use the
2027 // And dataset from the copied alignment
2028 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2029 // be doubly sure that we create *new* sequence objects.
2030 sequences = new SequenceI[newseq.length];
2031 for (int i = 0; i < newseq.length; i++)
2033 sequences[i] = new Sequence(newseq[i]);
2035 alignment = new Alignment(sequences);
2036 externalPaste = false;
2040 // parse the clipboard as an alignment.
2041 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2043 sequences = alignment.getSequencesArray();
2047 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2053 if (Desktop.jalviewClipboard != null)
2055 // dataset is inherited
2056 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2060 // new dataset is constructed
2061 alignment.setDataset(null);
2063 alwidth = alignment.getWidth() + 1;
2067 AlignmentI pastedal = alignment; // preserve pasted alignment object
2068 // Add pasted sequences and dataset into existing alignment.
2069 alignment = viewport.getAlignment();
2070 alwidth = alignment.getWidth() + 1;
2071 // decide if we need to import sequences from an existing dataset
2072 boolean importDs = Desktop.jalviewClipboard != null
2073 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2074 // importDs==true instructs us to copy over new dataset sequences from
2075 // an existing alignment
2076 Vector newDs = (importDs) ? new Vector() : null; // used to create
2077 // minimum dataset set
2079 for (int i = 0; i < sequences.length; i++)
2083 newDs.addElement(null);
2085 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2087 if (importDs && ds != null)
2089 if (!newDs.contains(ds))
2091 newDs.setElementAt(ds, i);
2092 ds = new Sequence(ds);
2093 // update with new dataset sequence
2094 sequences[i].setDatasetSequence(ds);
2098 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2103 // copy and derive new dataset sequence
2104 sequences[i] = sequences[i].deriveSequence();
2105 alignment.getDataset()
2106 .addSequence(sequences[i].getDatasetSequence());
2107 // TODO: avoid creation of duplicate dataset sequences with a
2108 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2110 alignment.addSequence(sequences[i]); // merges dataset
2114 newDs.clear(); // tidy up
2116 if (alignment.getAlignmentAnnotation() != null)
2118 for (AlignmentAnnotation alan : alignment
2119 .getAlignmentAnnotation())
2121 if (alan.graphGroup > fgroup)
2123 fgroup = alan.graphGroup;
2127 if (pastedal.getAlignmentAnnotation() != null)
2129 // Add any annotation attached to alignment.
2130 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2131 for (int i = 0; i < alann.length; i++)
2133 annotationAdded = true;
2134 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2136 AlignmentAnnotation newann = new AlignmentAnnotation(
2138 if (newann.graphGroup > -1)
2140 if (newGraphGroups.size() <= newann.graphGroup
2141 || newGraphGroups.get(newann.graphGroup) == null)
2143 for (int q = newGraphGroups
2144 .size(); q <= newann.graphGroup; q++)
2146 newGraphGroups.add(q, null);
2148 newGraphGroups.set(newann.graphGroup,
2149 Integer.valueOf(++fgroup));
2151 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2155 newann.padAnnotation(alwidth);
2156 alignment.addAnnotation(newann);
2166 addHistoryItem(new EditCommand(
2167 MessageManager.getString("label.add_sequences"),
2168 Action.PASTE, sequences, 0, alignment.getWidth(),
2171 // Add any annotations attached to sequences
2172 for (int i = 0; i < sequences.length; i++)
2174 if (sequences[i].getAnnotation() != null)
2176 AlignmentAnnotation newann;
2177 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2179 annotationAdded = true;
2180 newann = sequences[i].getAnnotation()[a];
2181 newann.adjustForAlignment();
2182 newann.padAnnotation(alwidth);
2183 if (newann.graphGroup > -1)
2185 if (newann.graphGroup > -1)
2187 if (newGraphGroups.size() <= newann.graphGroup
2188 || newGraphGroups.get(newann.graphGroup) == null)
2190 for (int q = newGraphGroups
2191 .size(); q <= newann.graphGroup; q++)
2193 newGraphGroups.add(q, null);
2195 newGraphGroups.set(newann.graphGroup,
2196 Integer.valueOf(++fgroup));
2198 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2202 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2206 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2214 // propagate alignment changed.
2215 viewport.getRanges().setEndSeq(alignment.getHeight());
2216 if (annotationAdded)
2218 // Duplicate sequence annotation in all views.
2219 AlignmentI[] alview = this.getViewAlignments();
2220 for (int i = 0; i < sequences.length; i++)
2222 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2227 for (int avnum = 0; avnum < alview.length; avnum++)
2229 if (alview[avnum] != alignment)
2231 // duplicate in a view other than the one with input focus
2232 int avwidth = alview[avnum].getWidth() + 1;
2233 // this relies on sann being preserved after we
2234 // modify the sequence's annotation array for each duplication
2235 for (int a = 0; a < sann.length; a++)
2237 AlignmentAnnotation newann = new AlignmentAnnotation(
2239 sequences[i].addAlignmentAnnotation(newann);
2240 newann.padAnnotation(avwidth);
2241 alview[avnum].addAnnotation(newann); // annotation was
2242 // duplicated earlier
2243 // TODO JAL-1145 graphGroups are not updated for sequence
2244 // annotation added to several views. This may cause
2246 alview[avnum].setAnnotationIndex(newann, a);
2251 buildSortByAnnotationScoresMenu();
2253 viewport.firePropertyChange("alignment", null,
2254 alignment.getSequences());
2255 if (alignPanels != null)
2257 for (AlignmentPanel ap : alignPanels)
2259 ap.validateAnnotationDimensions(false);
2264 alignPanel.validateAnnotationDimensions(false);
2270 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2272 String newtitle = new String("Copied sequences");
2274 if (Desktop.jalviewClipboard != null
2275 && Desktop.jalviewClipboard[2] != null)
2277 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2278 af.viewport.setHiddenColumns(hc);
2281 // >>>This is a fix for the moment, until a better solution is
2283 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2284 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2285 .getFeatureRenderer());
2287 // TODO: maintain provenance of an alignment, rather than just make the
2288 // title a concatenation of operations.
2291 if (title.startsWith("Copied sequences"))
2297 newtitle = newtitle.concat("- from " + title);
2302 newtitle = new String("Pasted sequences");
2305 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2310 } catch (Exception ex)
2312 ex.printStackTrace();
2313 System.out.println("Exception whilst pasting: " + ex);
2314 // could be anything being pasted in here
2320 protected void expand_newalign(ActionEvent e)
2324 AlignmentI alignment = AlignmentUtils
2325 .expandContext(getViewport().getAlignment(), -1);
2326 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2328 String newtitle = new String("Flanking alignment");
2330 if (Desktop.jalviewClipboard != null
2331 && Desktop.jalviewClipboard[2] != null)
2333 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2334 af.viewport.setHiddenColumns(hc);
2337 // >>>This is a fix for the moment, until a better solution is
2339 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2340 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2341 .getFeatureRenderer());
2343 // TODO: maintain provenance of an alignment, rather than just make the
2344 // title a concatenation of operations.
2346 if (title.startsWith("Copied sequences"))
2352 newtitle = newtitle.concat("- from " + title);
2356 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2358 } catch (Exception ex)
2360 ex.printStackTrace();
2361 System.out.println("Exception whilst pasting: " + ex);
2362 // could be anything being pasted in here
2363 } catch (OutOfMemoryError oom)
2365 new OOMWarning("Viewing flanking region of alignment", oom);
2376 protected void cut_actionPerformed(ActionEvent e)
2378 copy_actionPerformed(null);
2379 delete_actionPerformed(null);
2389 protected void delete_actionPerformed(ActionEvent evt)
2392 SequenceGroup sg = viewport.getSelectionGroup();
2399 * If the cut affects all sequences, warn, remove highlighted columns
2401 if (sg.getSize() == viewport.getAlignment().getHeight())
2403 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2404 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2405 if (isEntireAlignWidth)
2407 int confirm = JvOptionPane.showConfirmDialog(this,
2408 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2409 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2410 JvOptionPane.OK_CANCEL_OPTION);
2412 if (confirm == JvOptionPane.CANCEL_OPTION
2413 || confirm == JvOptionPane.CLOSED_OPTION)
2418 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2419 sg.getEndRes() + 1);
2421 SequenceI[] cut = sg.getSequences()
2422 .toArray(new SequenceI[sg.getSize()]);
2424 addHistoryItem(new EditCommand(
2425 MessageManager.getString("label.cut_sequences"), Action.CUT,
2426 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2427 viewport.getAlignment()));
2429 viewport.setSelectionGroup(null);
2430 viewport.sendSelection();
2431 viewport.getAlignment().deleteGroup(sg);
2433 viewport.firePropertyChange("alignment", null,
2434 viewport.getAlignment().getSequences());
2435 if (viewport.getAlignment().getHeight() < 1)
2439 this.setClosed(true);
2440 } catch (Exception ex)
2453 protected void deleteGroups_actionPerformed(ActionEvent e)
2455 if (avc.deleteGroups())
2457 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2458 alignPanel.updateAnnotation();
2459 alignPanel.paintAlignment(true, true);
2470 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2472 SequenceGroup sg = new SequenceGroup(
2473 viewport.getAlignment().getSequences());
2475 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2476 viewport.setSelectionGroup(sg);
2477 viewport.isSelectionGroupChanged(true);
2478 viewport.sendSelection();
2479 // JAL-2034 - should delegate to
2480 // alignPanel to decide if overview needs
2482 alignPanel.paintAlignment(false, false);
2483 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2493 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2495 if (viewport.cursorMode)
2497 alignPanel.getSeqPanel().keyboardNo1 = null;
2498 alignPanel.getSeqPanel().keyboardNo2 = null;
2500 viewport.setSelectionGroup(null);
2501 viewport.getColumnSelection().clear();
2502 viewport.setSearchResults(null);
2503 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2504 // JAL-2034 - should delegate to
2505 // alignPanel to decide if overview needs
2507 alignPanel.paintAlignment(false, false);
2508 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2509 viewport.sendSelection();
2519 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2521 SequenceGroup sg = viewport.getSelectionGroup();
2525 selectAllSequenceMenuItem_actionPerformed(null);
2530 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2532 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2534 // JAL-2034 - should delegate to
2535 // alignPanel to decide if overview needs
2538 alignPanel.paintAlignment(true, false);
2539 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2540 viewport.sendSelection();
2544 public void invertColSel_actionPerformed(ActionEvent e)
2546 viewport.invertColumnSelection();
2547 alignPanel.paintAlignment(true, false);
2548 viewport.sendSelection();
2558 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2560 trimAlignment(true);
2570 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2572 trimAlignment(false);
2575 void trimAlignment(boolean trimLeft)
2577 ColumnSelection colSel = viewport.getColumnSelection();
2580 if (!colSel.isEmpty())
2584 column = colSel.getMin();
2588 column = colSel.getMax();
2592 if (viewport.getSelectionGroup() != null)
2594 seqs = viewport.getSelectionGroup()
2595 .getSequencesAsArray(viewport.getHiddenRepSequences());
2599 seqs = viewport.getAlignment().getSequencesArray();
2602 TrimRegionCommand trimRegion;
2605 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2606 column, viewport.getAlignment());
2607 viewport.getRanges().setStartRes(0);
2611 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2612 column, viewport.getAlignment());
2615 statusBar.setText(MessageManager
2616 .formatMessage("label.removed_columns", new String[]
2617 { Integer.valueOf(trimRegion.getSize()).toString() }));
2619 addHistoryItem(trimRegion);
2621 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2623 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2624 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2626 viewport.getAlignment().deleteGroup(sg);
2630 viewport.firePropertyChange("alignment", null,
2631 viewport.getAlignment().getSequences());
2642 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2644 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2647 if (viewport.getSelectionGroup() != null)
2649 seqs = viewport.getSelectionGroup()
2650 .getSequencesAsArray(viewport.getHiddenRepSequences());
2651 start = viewport.getSelectionGroup().getStartRes();
2652 end = viewport.getSelectionGroup().getEndRes();
2656 seqs = viewport.getAlignment().getSequencesArray();
2659 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2660 "Remove Gapped Columns", seqs, start, end,
2661 viewport.getAlignment());
2663 addHistoryItem(removeGapCols);
2665 statusBar.setText(MessageManager
2666 .formatMessage("label.removed_empty_columns", new Object[]
2667 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2669 // This is to maintain viewport position on first residue
2670 // of first sequence
2671 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2672 ViewportRanges ranges = viewport.getRanges();
2673 int startRes = seq.findPosition(ranges.getStartRes());
2674 // ShiftList shifts;
2675 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2676 // edit.alColumnChanges=shifts.getInverse();
2677 // if (viewport.hasHiddenColumns)
2678 // viewport.getColumnSelection().compensateForEdits(shifts);
2679 ranges.setStartRes(seq.findIndex(startRes) - 1);
2680 viewport.firePropertyChange("alignment", null,
2681 viewport.getAlignment().getSequences());
2692 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2694 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2697 if (viewport.getSelectionGroup() != null)
2699 seqs = viewport.getSelectionGroup()
2700 .getSequencesAsArray(viewport.getHiddenRepSequences());
2701 start = viewport.getSelectionGroup().getStartRes();
2702 end = viewport.getSelectionGroup().getEndRes();
2706 seqs = viewport.getAlignment().getSequencesArray();
2709 // This is to maintain viewport position on first residue
2710 // of first sequence
2711 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2712 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2714 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2715 viewport.getAlignment()));
2717 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2719 viewport.firePropertyChange("alignment", null,
2720 viewport.getAlignment().getSequences());
2731 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2733 viewport.setPadGaps(padGapsMenuitem.isSelected());
2734 viewport.firePropertyChange("alignment", null,
2735 viewport.getAlignment().getSequences());
2739 * Opens a Finder dialog
2744 public void findMenuItem_actionPerformed(ActionEvent e)
2746 new Finder(alignPanel);
2750 * Create a new view of the current alignment.
2753 public void newView_actionPerformed(ActionEvent e)
2755 newView(null, true);
2759 * Creates and shows a new view of the current alignment.
2762 * title of newly created view; if null, one will be generated
2763 * @param copyAnnotation
2764 * if true then duplicate all annnotation, groups and settings
2765 * @return new alignment panel, already displayed.
2767 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2770 * Create a new AlignmentPanel (with its own, new Viewport)
2772 AlignmentPanel newap = new jalview.project.Jalview2XML()
2773 .copyAlignPanel(alignPanel);
2774 if (!copyAnnotation)
2777 * remove all groups and annotation except for the automatic stuff
2779 newap.av.getAlignment().deleteAllGroups();
2780 newap.av.getAlignment().deleteAllAnnotations(false);
2783 newap.av.setGatherViewsHere(false);
2785 if (viewport.getViewName() == null)
2787 viewport.setViewName(
2788 MessageManager.getString("label.view_name_original"));
2792 * Views share the same edits undo and redo stacks
2794 newap.av.setHistoryList(viewport.getHistoryList());
2795 newap.av.setRedoList(viewport.getRedoList());
2798 * copy any visualisation settings that are not saved in the project
2800 newap.av.setColourAppliesToAllGroups(
2801 viewport.getColourAppliesToAllGroups());
2804 * Views share the same mappings; need to deregister any new mappings
2805 * created by copyAlignPanel, and register the new reference to the shared
2808 newap.av.replaceMappings(viewport.getAlignment());
2811 * start up cDNA consensus (if applicable) now mappings are in place
2813 if (newap.av.initComplementConsensus())
2815 newap.refresh(true); // adjust layout of annotations
2818 newap.av.setViewName(getNewViewName(viewTitle));
2820 addAlignmentPanel(newap, true);
2821 newap.alignmentChanged();
2823 if (alignPanels.size() == 2)
2825 viewport.setGatherViewsHere(true);
2827 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2832 * Make a new name for the view, ensuring it is unique within the current
2833 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2834 * these now use viewId. Unique view names are still desirable for usability.)
2839 protected String getNewViewName(String viewTitle)
2841 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2842 boolean addFirstIndex = false;
2843 if (viewTitle == null || viewTitle.trim().length() == 0)
2845 viewTitle = MessageManager.getString("action.view");
2846 addFirstIndex = true;
2850 index = 1;// we count from 1 if given a specific name
2852 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2854 List<Component> comps = PaintRefresher.components
2855 .get(viewport.getSequenceSetId());
2857 List<String> existingNames = getExistingViewNames(comps);
2859 while (existingNames.contains(newViewName))
2861 newViewName = viewTitle + " " + (++index);
2867 * Returns a list of distinct view names found in the given list of
2868 * components. View names are held on the viewport of an AlignmentPanel.
2873 protected List<String> getExistingViewNames(List<Component> comps)
2875 List<String> existingNames = new ArrayList<>();
2876 for (Component comp : comps)
2878 if (comp instanceof AlignmentPanel)
2880 AlignmentPanel ap = (AlignmentPanel) comp;
2881 if (!existingNames.contains(ap.av.getViewName()))
2883 existingNames.add(ap.av.getViewName());
2887 return existingNames;
2891 * Explode tabbed views into separate windows.
2894 public void expandViews_actionPerformed(ActionEvent e)
2896 Desktop.explodeViews(this);
2900 * Gather views in separate windows back into a tabbed presentation.
2903 public void gatherViews_actionPerformed(ActionEvent e)
2905 Desktop.instance.gatherViews(this);
2915 public void font_actionPerformed(ActionEvent e)
2917 new FontChooser(alignPanel);
2927 protected void seqLimit_actionPerformed(ActionEvent e)
2929 viewport.setShowJVSuffix(seqLimits.isSelected());
2931 alignPanel.getIdPanel().getIdCanvas()
2932 .setPreferredSize(alignPanel.calculateIdWidth());
2933 alignPanel.paintAlignment(true, false);
2937 public void idRightAlign_actionPerformed(ActionEvent e)
2939 viewport.setRightAlignIds(idRightAlign.isSelected());
2940 alignPanel.paintAlignment(false, false);
2944 public void centreColumnLabels_actionPerformed(ActionEvent e)
2946 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2947 alignPanel.paintAlignment(false, false);
2953 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2956 protected void followHighlight_actionPerformed()
2959 * Set the 'follow' flag on the Viewport (and scroll to position if now
2962 final boolean state = this.followHighlightMenuItem.getState();
2963 viewport.setFollowHighlight(state);
2966 alignPanel.scrollToPosition(viewport.getSearchResults());
2977 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2979 viewport.setColourText(colourTextMenuItem.isSelected());
2980 alignPanel.paintAlignment(false, false);
2990 public void wrapMenuItem_actionPerformed(ActionEvent e)
2992 scaleAbove.setVisible(wrapMenuItem.isSelected());
2993 scaleLeft.setVisible(wrapMenuItem.isSelected());
2994 scaleRight.setVisible(wrapMenuItem.isSelected());
2995 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2996 alignPanel.updateLayout();
3000 public void showAllSeqs_actionPerformed(ActionEvent e)
3002 viewport.showAllHiddenSeqs();
3006 public void showAllColumns_actionPerformed(ActionEvent e)
3008 viewport.showAllHiddenColumns();
3009 alignPanel.paintAlignment(true, true);
3010 viewport.sendSelection();
3014 public void hideSelSequences_actionPerformed(ActionEvent e)
3016 viewport.hideAllSelectedSeqs();
3020 * called by key handler and the hide all/show all menu items
3025 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3028 boolean hide = false;
3029 SequenceGroup sg = viewport.getSelectionGroup();
3030 if (!toggleSeqs && !toggleCols)
3032 // Hide everything by the current selection - this is a hack - we do the
3033 // invert and then hide
3034 // first check that there will be visible columns after the invert.
3035 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3036 && sg.getStartRes() <= sg.getEndRes()))
3038 // now invert the sequence set, if required - empty selection implies
3039 // that no hiding is required.
3042 invertSequenceMenuItem_actionPerformed(null);
3043 sg = viewport.getSelectionGroup();
3047 viewport.expandColSelection(sg, true);
3048 // finally invert the column selection and get the new sequence
3050 invertColSel_actionPerformed(null);
3057 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3059 hideSelSequences_actionPerformed(null);
3062 else if (!(toggleCols && viewport.hasSelectedColumns()))
3064 showAllSeqs_actionPerformed(null);
3070 if (viewport.hasSelectedColumns())
3072 hideSelColumns_actionPerformed(null);
3075 viewport.setSelectionGroup(sg);
3080 showAllColumns_actionPerformed(null);
3089 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3090 * event.ActionEvent)
3093 public void hideAllButSelection_actionPerformed(ActionEvent e)
3095 toggleHiddenRegions(false, false);
3096 viewport.sendSelection();
3103 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3107 public void hideAllSelection_actionPerformed(ActionEvent e)
3109 SequenceGroup sg = viewport.getSelectionGroup();
3110 viewport.expandColSelection(sg, false);
3111 viewport.hideAllSelectedSeqs();
3112 viewport.hideSelectedColumns();
3113 alignPanel.updateLayout();
3114 alignPanel.paintAlignment(true, true);
3115 viewport.sendSelection();
3122 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3126 public void showAllhidden_actionPerformed(ActionEvent e)
3128 viewport.showAllHiddenColumns();
3129 viewport.showAllHiddenSeqs();
3130 alignPanel.paintAlignment(true, true);
3131 viewport.sendSelection();
3135 public void hideSelColumns_actionPerformed(ActionEvent e)
3137 viewport.hideSelectedColumns();
3138 alignPanel.updateLayout();
3139 alignPanel.paintAlignment(true, true);
3140 viewport.sendSelection();
3144 public void hiddenMarkers_actionPerformed(ActionEvent e)
3146 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3157 protected void scaleAbove_actionPerformed(ActionEvent e)
3159 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3160 alignPanel.updateLayout();
3161 alignPanel.paintAlignment(true, false);
3171 protected void scaleLeft_actionPerformed(ActionEvent e)
3173 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3174 alignPanel.updateLayout();
3175 alignPanel.paintAlignment(true, false);
3185 protected void scaleRight_actionPerformed(ActionEvent e)
3187 viewport.setScaleRightWrapped(scaleRight.isSelected());
3188 alignPanel.updateLayout();
3189 alignPanel.paintAlignment(true, false);
3199 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3201 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3202 alignPanel.paintAlignment(false, false);
3212 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3214 viewport.setShowText(viewTextMenuItem.isSelected());
3215 alignPanel.paintAlignment(false, false);
3225 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3227 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3228 alignPanel.paintAlignment(false, false);
3231 public FeatureSettings featureSettings;
3234 public FeatureSettingsControllerI getFeatureSettingsUI()
3236 return featureSettings;
3240 public void featureSettings_actionPerformed(ActionEvent e)
3242 showFeatureSettingsUI();
3246 public FeatureSettingsControllerI showFeatureSettingsUI()
3248 if (featureSettings != null)
3250 featureSettings.closeOldSettings();
3251 featureSettings = null;
3253 if (!showSeqFeatures.isSelected())
3255 // make sure features are actually displayed
3256 showSeqFeatures.setSelected(true);
3257 showSeqFeatures_actionPerformed(null);
3259 featureSettings = new FeatureSettings(this);
3260 return featureSettings;
3264 * Set or clear 'Show Sequence Features'
3270 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3272 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3273 alignPanel.paintAlignment(true, true);
3277 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3278 * the annotations panel as a whole.
3280 * The options to show/hide all annotations should be enabled when the panel
3281 * is shown, and disabled when the panel is hidden.
3286 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3288 final boolean setVisible = annotationPanelMenuItem.isSelected();
3289 viewport.setShowAnnotation(setVisible);
3290 this.showAllSeqAnnotations.setEnabled(setVisible);
3291 this.hideAllSeqAnnotations.setEnabled(setVisible);
3292 this.showAllAlAnnotations.setEnabled(setVisible);
3293 this.hideAllAlAnnotations.setEnabled(setVisible);
3294 alignPanel.updateLayout();
3298 public void alignmentProperties()
3300 JEditorPane editPane = new JEditorPane("text/html", "");
3301 editPane.setEditable(false);
3302 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3305 MessageManager.formatMessage("label.html_content", new Object[]
3306 { contents.toString() }));
3307 JInternalFrame frame = new JInternalFrame();
3308 frame.getContentPane().add(new JScrollPane(editPane));
3310 Desktop.addInternalFrame(frame, MessageManager
3311 .formatMessage("label.alignment_properties", new Object[]
3312 { getTitle() }), 500, 400);
3322 public void overviewMenuItem_actionPerformed(ActionEvent e)
3324 if (alignPanel.overviewPanel != null)
3329 JInternalFrame frame = new JInternalFrame();
3330 final OverviewPanel overview = new OverviewPanel(alignPanel);
3331 frame.setContentPane(overview);
3332 Desktop.addInternalFrame(frame, MessageManager
3333 .formatMessage("label.overview_params", new Object[]
3334 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3337 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3338 frame.addInternalFrameListener(
3339 new javax.swing.event.InternalFrameAdapter()
3342 public void internalFrameClosed(
3343 javax.swing.event.InternalFrameEvent evt)
3346 alignPanel.setOverviewPanel(null);
3349 if (getKeyListeners().length > 0)
3351 frame.addKeyListener(getKeyListeners()[0]);
3354 alignPanel.setOverviewPanel(overview);
3358 public void textColour_actionPerformed()
3360 new TextColourChooser().chooseColour(alignPanel, null);
3364 * public void covariationColour_actionPerformed() {
3366 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3370 public void annotationColour_actionPerformed()
3372 new AnnotationColourChooser(viewport, alignPanel);
3376 public void annotationColumn_actionPerformed(ActionEvent e)
3378 new AnnotationColumnChooser(viewport, alignPanel);
3382 * Action on the user checking or unchecking the option to apply the selected
3383 * colour scheme to all groups. If unchecked, groups may have their own
3384 * independent colour schemes.
3389 public void applyToAllGroups_actionPerformed(boolean selected)
3391 viewport.setColourAppliesToAllGroups(selected);
3395 * Action on user selecting a colour from the colour menu
3398 * the name (not the menu item label!) of the colour scheme
3401 public void changeColour_actionPerformed(String name)
3404 * 'User Defined' opens a panel to configure or load a
3405 * user-defined colour scheme
3407 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3409 new UserDefinedColours(alignPanel);
3414 * otherwise set the chosen colour scheme (or null for 'None')
3416 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3417 viewport, viewport.getAlignment(),
3418 viewport.getHiddenRepSequences());
3423 * Actions on setting or changing the alignment colour scheme
3428 public void changeColour(ColourSchemeI cs)
3430 // TODO: pull up to controller method
3431 ColourMenuHelper.setColourSelected(colourMenu, cs);
3433 viewport.setGlobalColourScheme(cs);
3435 alignPanel.paintAlignment(true, true);
3439 * Show the PID threshold slider panel
3442 protected void modifyPID_actionPerformed()
3444 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3445 alignPanel.getViewName());
3446 SliderPanel.showPIDSlider();
3450 * Show the Conservation slider panel
3453 protected void modifyConservation_actionPerformed()
3455 SliderPanel.setConservationSlider(alignPanel,
3456 viewport.getResidueShading(), alignPanel.getViewName());
3457 SliderPanel.showConservationSlider();
3461 * Action on selecting or deselecting (Colour) By Conservation
3464 public void conservationMenuItem_actionPerformed(boolean selected)
3466 modifyConservation.setEnabled(selected);
3467 viewport.setConservationSelected(selected);
3468 viewport.getResidueShading().setConservationApplied(selected);
3470 changeColour(viewport.getGlobalColourScheme());
3473 modifyConservation_actionPerformed();
3477 SliderPanel.hideConservationSlider();
3482 * Action on selecting or deselecting (Colour) Above PID Threshold
3485 public void abovePIDThreshold_actionPerformed(boolean selected)
3487 modifyPID.setEnabled(selected);
3488 viewport.setAbovePIDThreshold(selected);
3491 viewport.getResidueShading().setThreshold(0,
3492 viewport.isIgnoreGapsConsensus());
3495 changeColour(viewport.getGlobalColourScheme());
3498 modifyPID_actionPerformed();
3502 SliderPanel.hidePIDSlider();
3513 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3515 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3516 AlignmentSorter.sortByPID(viewport.getAlignment(),
3517 viewport.getAlignment().getSequenceAt(0));
3518 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3519 viewport.getAlignment()));
3520 alignPanel.paintAlignment(true, false);
3530 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3532 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3533 AlignmentSorter.sortByID(viewport.getAlignment());
3535 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3536 alignPanel.paintAlignment(true, false);
3546 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3548 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3549 AlignmentSorter.sortByLength(viewport.getAlignment());
3550 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3551 viewport.getAlignment()));
3552 alignPanel.paintAlignment(true, false);
3562 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3564 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3565 AlignmentSorter.sortByGroup(viewport.getAlignment());
3566 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3567 viewport.getAlignment()));
3569 alignPanel.paintAlignment(true, false);
3579 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3581 new RedundancyPanel(alignPanel, this);
3591 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3593 if ((viewport.getSelectionGroup() == null)
3594 || (viewport.getSelectionGroup().getSize() < 2))
3596 JvOptionPane.showInternalMessageDialog(this,
3597 MessageManager.getString(
3598 "label.you_must_select_least_two_sequences"),
3599 MessageManager.getString("label.invalid_selection"),
3600 JvOptionPane.WARNING_MESSAGE);
3604 JInternalFrame frame = new JInternalFrame();
3605 frame.setContentPane(new PairwiseAlignPanel(viewport));
3606 Desktop.addInternalFrame(frame,
3607 MessageManager.getString("action.pairwise_alignment"), 600,
3613 public void autoCalculate_actionPerformed(ActionEvent e)
3615 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3616 if (viewport.autoCalculateConsensus)
3618 viewport.firePropertyChange("alignment", null,
3619 viewport.getAlignment().getSequences());
3624 public void sortByTreeOption_actionPerformed(ActionEvent e)
3626 viewport.sortByTree = sortByTree.isSelected();
3630 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3632 viewport.followSelection = listenToViewSelections.isSelected();
3636 * Constructs a tree panel and adds it to the desktop
3639 * tree type (NJ or AV)
3641 * name of score model used to compute the tree
3643 * parameters for the distance or similarity calculation
3645 void newTreePanel(String type, String modelName,
3646 SimilarityParamsI options)
3648 String frameTitle = "";
3651 boolean onSelection = false;
3652 if (viewport.getSelectionGroup() != null
3653 && viewport.getSelectionGroup().getSize() > 0)
3655 SequenceGroup sg = viewport.getSelectionGroup();
3657 /* Decide if the selection is a column region */
3658 for (SequenceI _s : sg.getSequences())
3660 if (_s.getLength() < sg.getEndRes())
3662 JvOptionPane.showMessageDialog(Desktop.desktop,
3663 MessageManager.getString(
3664 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3665 MessageManager.getString(
3666 "label.sequences_selection_not_aligned"),
3667 JvOptionPane.WARNING_MESSAGE);
3676 if (viewport.getAlignment().getHeight() < 2)
3682 tp = new TreePanel(alignPanel, type, modelName, options);
3683 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3685 frameTitle += " from ";
3687 if (viewport.getViewName() != null)
3689 frameTitle += viewport.getViewName() + " of ";
3692 frameTitle += this.title;
3694 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3705 public void addSortByOrderMenuItem(String title,
3706 final AlignmentOrder order)
3708 final JMenuItem item = new JMenuItem(MessageManager
3709 .formatMessage("action.by_title_param", new Object[]
3712 item.addActionListener(new java.awt.event.ActionListener()
3715 public void actionPerformed(ActionEvent e)
3717 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3719 // TODO: JBPNote - have to map order entries to curent SequenceI
3721 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3723 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3724 viewport.getAlignment()));
3726 alignPanel.paintAlignment(true, false);
3732 * Add a new sort by annotation score menu item
3735 * the menu to add the option to
3737 * the label used to retrieve scores for each sequence on the
3740 public void addSortByAnnotScoreMenuItem(JMenu sort,
3741 final String scoreLabel)
3743 final JMenuItem item = new JMenuItem(scoreLabel);
3745 item.addActionListener(new java.awt.event.ActionListener()
3748 public void actionPerformed(ActionEvent e)
3750 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3751 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3752 viewport.getAlignment());// ,viewport.getSelectionGroup());
3753 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3754 viewport.getAlignment()));
3755 alignPanel.paintAlignment(true, false);
3761 * last hash for alignment's annotation array - used to minimise cost of
3764 protected int _annotationScoreVectorHash;
3767 * search the alignment and rebuild the sort by annotation score submenu the
3768 * last alignment annotation vector hash is stored to minimize cost of
3769 * rebuilding in subsequence calls.
3773 public void buildSortByAnnotationScoresMenu()
3775 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3780 if (viewport.getAlignment().getAlignmentAnnotation()
3781 .hashCode() != _annotationScoreVectorHash)
3783 sortByAnnotScore.removeAll();
3784 // almost certainly a quicker way to do this - but we keep it simple
3785 Hashtable scoreSorts = new Hashtable();
3786 AlignmentAnnotation aann[];
3787 for (SequenceI sqa : viewport.getAlignment().getSequences())
3789 aann = sqa.getAnnotation();
3790 for (int i = 0; aann != null && i < aann.length; i++)
3792 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3794 scoreSorts.put(aann[i].label, aann[i].label);
3798 Enumeration labels = scoreSorts.keys();
3799 while (labels.hasMoreElements())
3801 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3802 (String) labels.nextElement());
3804 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3807 _annotationScoreVectorHash = viewport.getAlignment()
3808 .getAlignmentAnnotation().hashCode();
3813 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3814 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3815 * call. Listeners are added to remove the menu item when the treePanel is
3816 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3820 public void buildTreeSortMenu()
3822 sortByTreeMenu.removeAll();
3824 List<Component> comps = PaintRefresher.components
3825 .get(viewport.getSequenceSetId());
3826 List<TreePanel> treePanels = new ArrayList<>();
3827 for (Component comp : comps)
3829 if (comp instanceof TreePanel)
3831 treePanels.add((TreePanel) comp);
3835 if (treePanels.size() < 1)
3837 sortByTreeMenu.setVisible(false);
3841 sortByTreeMenu.setVisible(true);
3843 for (final TreePanel tp : treePanels)
3845 final JMenuItem item = new JMenuItem(tp.getTitle());
3846 item.addActionListener(new java.awt.event.ActionListener()
3849 public void actionPerformed(ActionEvent e)
3851 tp.sortByTree_actionPerformed();
3852 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3857 sortByTreeMenu.add(item);
3861 public boolean sortBy(AlignmentOrder alorder, String undoname)
3863 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3864 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3865 if (undoname != null)
3867 addHistoryItem(new OrderCommand(undoname, oldOrder,
3868 viewport.getAlignment()));
3870 alignPanel.paintAlignment(true, false);
3875 * Work out whether the whole set of sequences or just the selected set will
3876 * be submitted for multiple alignment.
3879 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3881 // Now, check we have enough sequences
3882 AlignmentView msa = null;
3884 if ((viewport.getSelectionGroup() != null)
3885 && (viewport.getSelectionGroup().getSize() > 1))
3887 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3888 // some common interface!
3890 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3891 * SequenceI[sz = seqs.getSize(false)];
3893 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3894 * seqs.getSequenceAt(i); }
3896 msa = viewport.getAlignmentView(true);
3898 else if (viewport.getSelectionGroup() != null
3899 && viewport.getSelectionGroup().getSize() == 1)
3901 int option = JvOptionPane.showConfirmDialog(this,
3902 MessageManager.getString("warn.oneseq_msainput_selection"),
3903 MessageManager.getString("label.invalid_selection"),
3904 JvOptionPane.OK_CANCEL_OPTION);
3905 if (option == JvOptionPane.OK_OPTION)
3907 msa = viewport.getAlignmentView(false);
3912 msa = viewport.getAlignmentView(false);
3918 * Decides what is submitted to a secondary structure prediction service: the
3919 * first sequence in the alignment, or in the current selection, or, if the
3920 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3921 * region or the whole alignment. (where the first sequence in the set is the
3922 * one that the prediction will be for).
3924 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3926 AlignmentView seqs = null;
3928 if ((viewport.getSelectionGroup() != null)
3929 && (viewport.getSelectionGroup().getSize() > 0))
3931 seqs = viewport.getAlignmentView(true);
3935 seqs = viewport.getAlignmentView(false);
3937 // limit sequences - JBPNote in future - could spawn multiple prediction
3939 // TODO: viewport.getAlignment().isAligned is a global state - the local
3940 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3941 if (!viewport.getAlignment().isAligned(false))
3943 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3944 // TODO: if seqs.getSequences().length>1 then should really have warned
3958 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3960 // Pick the tree file
3961 JalviewFileChooser chooser = new JalviewFileChooser(
3962 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3963 chooser.setFileView(new JalviewFileView());
3964 chooser.setDialogTitle(
3965 MessageManager.getString("label.select_newick_like_tree_file"));
3966 chooser.setToolTipText(
3967 MessageManager.getString("label.load_tree_file"));
3969 int value = chooser.showOpenDialog(null);
3971 if (value == JalviewFileChooser.APPROVE_OPTION)
3973 String filePath = chooser.getSelectedFile().getPath();
3974 Cache.setProperty("LAST_DIRECTORY", filePath);
3975 NewickFile fin = null;
3978 fin = new NewickFile(filePath, DataSourceType.FILE);
3979 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3980 } catch (Exception ex)
3982 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3983 MessageManager.getString("label.problem_reading_tree_file"),
3984 JvOptionPane.WARNING_MESSAGE);
3985 ex.printStackTrace();
3987 if (fin != null && fin.hasWarningMessage())
3989 JvOptionPane.showMessageDialog(Desktop.desktop,
3990 fin.getWarningMessage(),
3992 .getString("label.possible_problem_with_tree_file"),
3993 JvOptionPane.WARNING_MESSAGE);
3998 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4000 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4003 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4004 int h, int x, int y)
4006 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4010 * Add a treeviewer for the tree extracted from a Newick file object to the
4011 * current alignment view
4018 * Associated alignment input data (or null)
4027 * @return TreePanel handle
4029 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4030 AlignmentView input, int w, int h, int x, int y)
4032 TreePanel tp = null;
4038 if (nf.getTree() != null)
4040 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4046 tp.setLocation(x, y);
4049 Desktop.addInternalFrame(tp, treeTitle, w, h);
4051 } catch (Exception ex)
4053 ex.printStackTrace();
4059 private boolean buildingMenu = false;
4062 * Generates menu items and listener event actions for web service clients
4065 public void BuildWebServiceMenu()
4067 while (buildingMenu)
4071 System.err.println("Waiting for building menu to finish.");
4073 } catch (Exception e)
4077 final AlignFrame me = this;
4078 buildingMenu = true;
4079 new Thread(new Runnable()
4084 final List<JMenuItem> legacyItems = new ArrayList<>();
4087 // System.err.println("Building ws menu again "
4088 // + Thread.currentThread());
4089 // TODO: add support for context dependent disabling of services based
4091 // alignment and current selection
4092 // TODO: add additional serviceHandle parameter to specify abstract
4094 // class independently of AbstractName
4095 // TODO: add in rediscovery GUI function to restart discoverer
4096 // TODO: group services by location as well as function and/or
4098 // object broker mechanism.
4099 final Vector<JMenu> wsmenu = new Vector<>();
4100 final IProgressIndicator af = me;
4103 * do not i18n these strings - they are hard-coded in class
4104 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4105 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4107 final JMenu msawsmenu = new JMenu("Alignment");
4108 final JMenu secstrmenu = new JMenu(
4109 "Secondary Structure Prediction");
4110 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4111 final JMenu analymenu = new JMenu("Analysis");
4112 final JMenu dismenu = new JMenu("Protein Disorder");
4113 // JAL-940 - only show secondary structure prediction services from
4114 // the legacy server
4115 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4117 Discoverer.services != null && (Discoverer.services.size() > 0))
4119 // TODO: refactor to allow list of AbstractName/Handler bindings to
4121 // stored or retrieved from elsewhere
4122 // No MSAWS used any more:
4123 // Vector msaws = null; // (Vector)
4124 // Discoverer.services.get("MsaWS");
4125 Vector secstrpr = (Vector) Discoverer.services
4127 if (secstrpr != null)
4129 // Add any secondary structure prediction services
4130 for (int i = 0, j = secstrpr.size(); i < j; i++)
4132 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4134 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4135 .getServiceClient(sh);
4136 int p = secstrmenu.getItemCount();
4137 impl.attachWSMenuEntry(secstrmenu, me);
4138 int q = secstrmenu.getItemCount();
4139 for (int litm = p; litm < q; litm++)
4141 legacyItems.add(secstrmenu.getItem(litm));
4147 // Add all submenus in the order they should appear on the web
4149 wsmenu.add(msawsmenu);
4150 wsmenu.add(secstrmenu);
4151 wsmenu.add(dismenu);
4152 wsmenu.add(analymenu);
4153 // No search services yet
4154 // wsmenu.add(seqsrchmenu);
4156 javax.swing.SwingUtilities.invokeLater(new Runnable()
4163 webService.removeAll();
4164 // first, add discovered services onto the webservices menu
4165 if (wsmenu.size() > 0)
4167 for (int i = 0, j = wsmenu.size(); i < j; i++)
4169 webService.add(wsmenu.get(i));
4174 webService.add(me.webServiceNoServices);
4176 // TODO: move into separate menu builder class.
4177 boolean new_sspred = false;
4178 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4180 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4181 if (jws2servs != null)
4183 if (jws2servs.hasServices())
4185 jws2servs.attachWSMenuEntry(webService, me);
4186 for (Jws2Instance sv : jws2servs.getServices())
4188 if (sv.description.toLowerCase().contains("jpred"))
4190 for (JMenuItem jmi : legacyItems)
4192 jmi.setVisible(false);
4198 if (jws2servs.isRunning())
4200 JMenuItem tm = new JMenuItem(
4201 "Still discovering JABA Services");
4202 tm.setEnabled(false);
4207 build_urlServiceMenu(me.webService);
4208 build_fetchdbmenu(webService);
4209 for (JMenu item : wsmenu)
4211 if (item.getItemCount() == 0)
4213 item.setEnabled(false);
4217 item.setEnabled(true);
4220 } catch (Exception e)
4223 "Exception during web service menu building process.",
4228 } catch (Exception e)
4231 buildingMenu = false;
4238 * construct any groupURL type service menu entries.
4242 private void build_urlServiceMenu(JMenu webService)
4244 // TODO: remove this code when 2.7 is released
4245 // DEBUG - alignmentView
4247 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4248 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4250 * @Override public void actionPerformed(ActionEvent e) {
4251 * jalview.datamodel.AlignmentView
4252 * .testSelectionViews(af.viewport.getAlignment(),
4253 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4255 * }); webService.add(testAlView);
4257 // TODO: refactor to RestClient discoverer and merge menu entries for
4258 // rest-style services with other types of analysis/calculation service
4259 // SHmmr test client - still being implemented.
4260 // DEBUG - alignmentView
4262 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4265 client.attachWSMenuEntry(
4266 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4272 * Searches the alignment sequences for xRefs and builds the Show
4273 * Cross-References menu (formerly called Show Products), with database
4274 * sources for which cross-references are found (protein sources for a
4275 * nucleotide alignment and vice versa)
4277 * @return true if Show Cross-references menu should be enabled
4279 public boolean canShowProducts()
4281 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4282 AlignmentI dataset = viewport.getAlignment().getDataset();
4284 showProducts.removeAll();
4285 final boolean dna = viewport.getAlignment().isNucleotide();
4287 if (seqs == null || seqs.length == 0)
4289 // nothing to see here.
4293 boolean showp = false;
4296 List<String> ptypes = new CrossRef(seqs, dataset)
4297 .findXrefSourcesForSequences(dna);
4299 for (final String source : ptypes)
4302 final AlignFrame af = this;
4303 JMenuItem xtype = new JMenuItem(source);
4304 xtype.addActionListener(new ActionListener()
4307 public void actionPerformed(ActionEvent e)
4309 showProductsFor(af.viewport.getSequenceSelection(), dna,
4313 showProducts.add(xtype);
4315 showProducts.setVisible(showp);
4316 showProducts.setEnabled(showp);
4317 } catch (Exception e)
4320 "canShowProducts threw an exception - please report to help@jalview.org",
4328 * Finds and displays cross-references for the selected sequences (protein
4329 * products for nucleotide sequences, dna coding sequences for peptides).
4332 * the sequences to show cross-references for
4334 * true if from a nucleotide alignment (so showing proteins)
4336 * the database to show cross-references for
4338 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4339 final String source)
4341 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4346 * Construct and display a new frame containing the translation of this
4347 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4350 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4352 AlignmentI al = null;
4355 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4357 al = dna.translateCdna(codeTable);
4358 } catch (Exception ex)
4360 jalview.bin.Cache.log.error(
4361 "Exception during translation. Please report this !", ex);
4362 final String msg = MessageManager.getString(
4363 "label.error_when_translating_sequences_submit_bug_report");
4364 final String errorTitle = MessageManager
4365 .getString("label.implementation_error")
4366 + MessageManager.getString("label.translation_failed");
4367 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4368 JvOptionPane.ERROR_MESSAGE);
4371 if (al == null || al.getHeight() == 0)
4373 final String msg = MessageManager.getString(
4374 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4375 final String errorTitle = MessageManager
4376 .getString("label.translation_failed");
4377 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4378 JvOptionPane.WARNING_MESSAGE);
4382 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4383 af.setFileFormat(this.currentFileFormat);
4384 final String newTitle = MessageManager
4385 .formatMessage("label.translation_of_params", new Object[]
4386 { this.getTitle(), codeTable.getId() });
4387 af.setTitle(newTitle);
4388 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4390 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4391 viewport.openSplitFrame(af, new Alignment(seqs));
4395 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4402 * Set the file format
4406 public void setFileFormat(FileFormatI format)
4408 this.currentFileFormat = format;
4412 * Try to load a features file onto the alignment.
4415 * contents or path to retrieve file
4417 * access mode of file (see jalview.io.AlignFile)
4418 * @return true if features file was parsed correctly.
4420 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4422 return avc.parseFeaturesFile(file, sourceType,
4423 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4428 public void refreshFeatureUI(boolean enableIfNecessary)
4430 // note - currently this is only still here rather than in the controller
4431 // because of the featureSettings hard reference that is yet to be
4433 if (enableIfNecessary)
4435 viewport.setShowSequenceFeatures(true);
4436 showSeqFeatures.setSelected(true);
4442 public void dragEnter(DropTargetDragEvent evt)
4447 public void dragExit(DropTargetEvent evt)
4452 public void dragOver(DropTargetDragEvent evt)
4457 public void dropActionChanged(DropTargetDragEvent evt)
4462 public void drop(DropTargetDropEvent evt)
4464 // JAL-1552 - acceptDrop required before getTransferable call for
4465 // Java's Transferable for native dnd
4466 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4467 Transferable t = evt.getTransferable();
4468 final AlignFrame thisaf = this;
4469 final List<String> files = new ArrayList<>();
4470 List<DataSourceType> protocols = new ArrayList<>();
4474 Desktop.transferFromDropTarget(files, protocols, evt, t);
4475 } catch (Exception e)
4477 e.printStackTrace();
4481 new Thread(new Runnable()
4488 // check to see if any of these files have names matching sequences
4491 SequenceIdMatcher idm = new SequenceIdMatcher(
4492 viewport.getAlignment().getSequencesArray());
4494 * Object[] { String,SequenceI}
4496 ArrayList<Object[]> filesmatched = new ArrayList<>();
4497 ArrayList<String> filesnotmatched = new ArrayList<>();
4498 for (int i = 0; i < files.size(); i++)
4500 String file = files.get(i).toString();
4502 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4503 if (protocol == DataSourceType.FILE)
4505 File fl = new File(file);
4506 pdbfn = fl.getName();
4508 else if (protocol == DataSourceType.URL)
4510 URL url = new URL(file);
4511 pdbfn = url.getFile();
4513 if (pdbfn.length() > 0)
4515 // attempt to find a match in the alignment
4516 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4517 int l = 0, c = pdbfn.indexOf(".");
4518 while (mtch == null && c != -1)
4523 } while ((c = pdbfn.indexOf(".", l)) > l);
4526 pdbfn = pdbfn.substring(0, l);
4528 mtch = idm.findAllIdMatches(pdbfn);
4532 FileFormatI type = null;
4535 type = new IdentifyFile().identify(file, protocol);
4536 } catch (Exception ex)
4540 if (type != null && type.isStructureFile())
4542 filesmatched.add(new Object[] { file, protocol, mtch });
4546 // File wasn't named like one of the sequences or wasn't a PDB
4548 filesnotmatched.add(file);
4552 if (filesmatched.size() > 0)
4554 boolean autoAssociate = Cache
4555 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4558 String msg = MessageManager.formatMessage(
4559 "label.automatically_associate_structure_files_with_sequences_same_name",
4561 { Integer.valueOf(filesmatched.size())
4563 String ttl = MessageManager.getString(
4564 "label.automatically_associate_structure_files_by_name");
4565 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4566 ttl, JvOptionPane.YES_NO_OPTION);
4567 autoAssociate = choice == JvOptionPane.YES_OPTION;
4571 for (Object[] fm : filesmatched)
4573 // try and associate
4574 // TODO: may want to set a standard ID naming formalism for
4575 // associating PDB files which have no IDs.
4576 for (SequenceI toassoc : (SequenceI[]) fm[2])
4578 PDBEntry pe = new AssociatePdbFileWithSeq()
4579 .associatePdbWithSeq((String) fm[0],
4580 (DataSourceType) fm[1], toassoc, false,
4584 System.err.println("Associated file : "
4585 + ((String) fm[0]) + " with "
4586 + toassoc.getDisplayId(true));
4590 // TODO: do we need to update overview ? only if features are
4592 alignPanel.paintAlignment(true, false);
4598 * add declined structures as sequences
4600 for (Object[] o : filesmatched)
4602 filesnotmatched.add((String) o[0]);
4606 if (filesnotmatched.size() > 0)
4608 if (assocfiles > 0 && (Cache.getDefault(
4609 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4610 || JvOptionPane.showConfirmDialog(thisaf,
4611 "<html>" + MessageManager.formatMessage(
4612 "label.ignore_unmatched_dropped_files_info",
4615 filesnotmatched.size())
4618 MessageManager.getString(
4619 "label.ignore_unmatched_dropped_files"),
4620 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4624 for (String fn : filesnotmatched)
4626 loadJalviewDataFile(fn, null, null, null);
4630 } catch (Exception ex)
4632 ex.printStackTrace();
4640 * Attempt to load a "dropped" file or URL string, by testing in turn for
4642 * <li>an Annotation file</li>
4643 * <li>a JNet file</li>
4644 * <li>a features file</li>
4645 * <li>else try to interpret as an alignment file</li>
4649 * either a filename or a URL string.
4651 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4652 FileFormatI format, SequenceI assocSeq)
4656 if (sourceType == null)
4658 sourceType = FormatAdapter.checkProtocol(file);
4660 // if the file isn't identified, or not positively identified as some
4661 // other filetype (PFAM is default unidentified alignment file type) then
4662 // try to parse as annotation.
4663 boolean isAnnotation = (format == null
4664 || FileFormat.Pfam.equals(format))
4665 ? new AnnotationFile().annotateAlignmentView(viewport,
4671 // first see if its a T-COFFEE score file
4672 TCoffeeScoreFile tcf = null;
4675 tcf = new TCoffeeScoreFile(file, sourceType);
4678 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4682 new TCoffeeColourScheme(viewport.getAlignment()));
4683 isAnnotation = true;
4684 statusBar.setText(MessageManager.getString(
4685 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4689 // some problem - if no warning its probable that the ID matching
4690 // process didn't work
4691 JvOptionPane.showMessageDialog(Desktop.desktop,
4692 tcf.getWarningMessage() == null
4693 ? MessageManager.getString(
4694 "label.check_file_matches_sequence_ids_alignment")
4695 : tcf.getWarningMessage(),
4696 MessageManager.getString(
4697 "label.problem_reading_tcoffee_score_file"),
4698 JvOptionPane.WARNING_MESSAGE);
4705 } catch (Exception x)
4708 "Exception when processing data source as T-COFFEE score file",
4714 // try to see if its a JNet 'concise' style annotation file *before*
4716 // try to parse it as a features file
4719 format = new IdentifyFile().identify(file, sourceType);
4721 if (FileFormat.ScoreMatrix == format)
4723 ScoreMatrixFile sm = new ScoreMatrixFile(
4724 new FileParse(file, sourceType));
4726 // todo: i18n this message
4727 statusBar.setText(MessageManager.formatMessage(
4728 "label.successfully_loaded_matrix",
4729 sm.getMatrixName()));
4731 else if (FileFormat.Jnet.equals(format))
4733 JPredFile predictions = new JPredFile(file, sourceType);
4734 new JnetAnnotationMaker();
4735 JnetAnnotationMaker.add_annotation(predictions,
4736 viewport.getAlignment(), 0, false);
4737 viewport.getAlignment().setupJPredAlignment();
4738 isAnnotation = true;
4740 // else if (IdentifyFile.FeaturesFile.equals(format))
4741 else if (FileFormat.Features.equals(format))
4743 if (parseFeaturesFile(file, sourceType))
4745 SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4746 if (splitFrame != null)
4748 splitFrame.repaint();
4752 alignPanel.paintAlignment(true, true);
4758 new FileLoader().LoadFile(viewport, file, sourceType, format);
4765 alignPanel.adjustAnnotationHeight();
4766 viewport.updateSequenceIdColours();
4767 buildSortByAnnotationScoresMenu();
4768 alignPanel.paintAlignment(true, true);
4770 } catch (Exception ex)
4772 ex.printStackTrace();
4773 } catch (OutOfMemoryError oom)
4778 } catch (Exception x)
4783 + (sourceType != null
4784 ? (sourceType == DataSourceType.PASTE
4786 : "using " + sourceType + " from "
4790 ? "(parsing as '" + format + "' file)"
4792 oom, Desktop.desktop);
4797 * Method invoked by the ChangeListener on the tabbed pane, in other words
4798 * when a different tabbed pane is selected by the user or programmatically.
4801 public void tabSelectionChanged(int index)
4805 alignPanel = alignPanels.get(index);
4806 viewport = alignPanel.av;
4807 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4808 setMenusFromViewport(viewport);
4809 if (featureSettings != null && featureSettings.isOpen()
4810 && featureSettings.fr.getViewport() != viewport)
4812 if (viewport.isShowSequenceFeatures())
4814 // refresh the featureSettings to reflect UI change
4815 showFeatureSettingsUI();
4819 // close feature settings for this view.
4820 featureSettings.close();
4827 * 'focus' any colour slider that is open to the selected viewport
4829 if (viewport.getConservationSelected())
4831 SliderPanel.setConservationSlider(alignPanel,
4832 viewport.getResidueShading(), alignPanel.getViewName());
4836 SliderPanel.hideConservationSlider();
4838 if (viewport.getAbovePIDThreshold())
4840 SliderPanel.setPIDSliderSource(alignPanel,
4841 viewport.getResidueShading(), alignPanel.getViewName());
4845 SliderPanel.hidePIDSlider();
4849 * If there is a frame linked to this one in a SplitPane, switch it to the
4850 * same view tab index. No infinite recursion of calls should happen, since
4851 * tabSelectionChanged() should not get invoked on setting the selected
4852 * index to an unchanged value. Guard against setting an invalid index
4853 * before the new view peer tab has been created.
4855 final AlignViewportI peer = viewport.getCodingComplement();
4858 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4859 .getAlignPanel().alignFrame;
4860 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4862 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4868 * On right mouse click on view tab, prompt for and set new view name.
4871 public void tabbedPane_mousePressed(MouseEvent e)
4873 if (e.isPopupTrigger())
4875 String msg = MessageManager.getString("label.enter_view_name");
4876 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4877 JvOptionPane.QUESTION_MESSAGE);
4881 viewport.setViewName(reply);
4882 // TODO warn if reply is in getExistingViewNames()?
4883 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4888 public AlignViewport getCurrentView()
4894 * Open the dialog for regex description parsing.
4897 protected void extractScores_actionPerformed(ActionEvent e)
4899 ParseProperties pp = new jalview.analysis.ParseProperties(
4900 viewport.getAlignment());
4901 // TODO: verify regex and introduce GUI dialog for version 2.5
4902 // if (pp.getScoresFromDescription("col", "score column ",
4903 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4905 if (pp.getScoresFromDescription("description column",
4906 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4908 buildSortByAnnotationScoresMenu();
4916 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4920 protected void showDbRefs_actionPerformed(ActionEvent e)
4922 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4928 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4932 protected void showNpFeats_actionPerformed(ActionEvent e)
4934 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4938 * find the viewport amongst the tabs in this alignment frame and close that
4943 public boolean closeView(AlignViewportI av)
4947 this.closeMenuItem_actionPerformed(false);
4950 Component[] comp = tabbedPane.getComponents();
4951 for (int i = 0; comp != null && i < comp.length; i++)
4953 if (comp[i] instanceof AlignmentPanel)
4955 if (((AlignmentPanel) comp[i]).av == av)
4958 closeView((AlignmentPanel) comp[i]);
4966 protected void build_fetchdbmenu(JMenu webService)
4968 // Temporary hack - DBRef Fetcher always top level ws entry.
4969 // TODO We probably want to store a sequence database checklist in
4970 // preferences and have checkboxes.. rather than individual sources selected
4972 final JMenu rfetch = new JMenu(
4973 MessageManager.getString("action.fetch_db_references"));
4974 rfetch.setToolTipText(MessageManager.getString(
4975 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4976 webService.add(rfetch);
4978 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4979 MessageManager.getString("option.trim_retrieved_seqs"));
4980 trimrs.setToolTipText(
4981 MessageManager.getString("label.trim_retrieved_sequences"));
4983 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4984 trimrs.addActionListener(new ActionListener()
4987 public void actionPerformed(ActionEvent e)
4989 trimrs.setSelected(trimrs.isSelected());
4990 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4991 Boolean.valueOf(trimrs.isSelected()).toString());
4995 JMenuItem fetchr = new JMenuItem(
4996 MessageManager.getString("label.standard_databases"));
4997 fetchr.setToolTipText(
4998 MessageManager.getString("label.fetch_embl_uniprot"));
4999 fetchr.addActionListener(new ActionListener()
5003 public void actionPerformed(ActionEvent e)
5005 new Thread(new Runnable()
5010 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5011 .getAlignment().isNucleotide();
5012 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5013 alignPanel.av.getSequenceSelection(),
5014 alignPanel.alignFrame, null,
5015 alignPanel.alignFrame.featureSettings, isNucleotide);
5016 dbRefFetcher.addListener(new FetchFinishedListenerI()
5019 public void finished()
5022 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5023 .getFeatureSettingsModels())
5026 alignPanel.av.mergeFeaturesStyle(srcSettings);
5028 AlignFrame.this.setMenusForViewport();
5031 dbRefFetcher.fetchDBRefs(false);
5039 final AlignFrame me = this;
5040 new Thread(new Runnable()
5045 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5046 .getSequenceFetcherSingleton(me);
5047 javax.swing.SwingUtilities.invokeLater(new Runnable()
5052 String[] dbclasses = sf.getOrderedSupportedSources();
5053 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5054 // jalview.util.QuickSort.sort(otherdb, otherdb);
5055 List<DbSourceProxy> otherdb;
5056 JMenu dfetch = new JMenu();
5057 JMenu ifetch = new JMenu();
5058 JMenuItem fetchr = null;
5059 int comp = 0, icomp = 0, mcomp = 15;
5060 String mname = null;
5062 for (String dbclass : dbclasses)
5064 otherdb = sf.getSourceProxy(dbclass);
5065 // add a single entry for this class, or submenu allowing 'fetch
5067 if (otherdb == null || otherdb.size() < 1)
5071 // List<DbSourceProxy> dbs=otherdb;
5072 // otherdb=new ArrayList<DbSourceProxy>();
5073 // for (DbSourceProxy db:dbs)
5075 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5079 mname = "From " + dbclass;
5081 if (otherdb.size() == 1)
5083 final DbSourceProxy[] dassource = otherdb
5084 .toArray(new DbSourceProxy[0]);
5085 DbSourceProxy src = otherdb.get(0);
5086 fetchr = new JMenuItem(src.getDbSource());
5087 fetchr.addActionListener(new ActionListener()
5091 public void actionPerformed(ActionEvent e)
5093 new Thread(new Runnable()
5099 boolean isNucleotide = alignPanel.alignFrame
5100 .getViewport().getAlignment()
5102 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5103 alignPanel.av.getSequenceSelection(),
5104 alignPanel.alignFrame, dassource,
5105 alignPanel.alignFrame.featureSettings,
5108 .addListener(new FetchFinishedListenerI()
5111 public void finished()
5113 FeatureSettingsModelI srcSettings = dassource[0]
5114 .getFeatureColourScheme();
5115 alignPanel.av.mergeFeaturesStyle(
5117 AlignFrame.this.setMenusForViewport();
5120 dbRefFetcher.fetchDBRefs(false);
5126 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5127 MessageManager.formatMessage(
5128 "label.fetch_retrieve_from", new Object[]
5129 { src.getDbName() })));
5135 final DbSourceProxy[] dassource = otherdb
5136 .toArray(new DbSourceProxy[0]);
5138 DbSourceProxy src = otherdb.get(0);
5139 fetchr = new JMenuItem(MessageManager
5140 .formatMessage("label.fetch_all_param", new Object[]
5141 { src.getDbSource() }));
5142 fetchr.addActionListener(new ActionListener()
5145 public void actionPerformed(ActionEvent e)
5147 new Thread(new Runnable()
5153 boolean isNucleotide = alignPanel.alignFrame
5154 .getViewport().getAlignment()
5156 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5157 alignPanel.av.getSequenceSelection(),
5158 alignPanel.alignFrame, dassource,
5159 alignPanel.alignFrame.featureSettings,
5162 .addListener(new FetchFinishedListenerI()
5165 public void finished()
5167 AlignFrame.this.setMenusForViewport();
5170 dbRefFetcher.fetchDBRefs(false);
5176 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5177 MessageManager.formatMessage(
5178 "label.fetch_retrieve_from_all_sources",
5180 { Integer.valueOf(otherdb.size())
5182 src.getDbSource(), src.getDbName() })));
5185 // and then build the rest of the individual menus
5186 ifetch = new JMenu(MessageManager.formatMessage(
5187 "label.source_from_db_source", new Object[]
5188 { src.getDbSource() }));
5190 String imname = null;
5192 for (DbSourceProxy sproxy : otherdb)
5194 String dbname = sproxy.getDbName();
5195 String sname = dbname.length() > 5
5196 ? dbname.substring(0, 5) + "..."
5198 String msname = dbname.length() > 10
5199 ? dbname.substring(0, 10) + "..."
5203 imname = MessageManager
5204 .formatMessage("label.from_msname", new Object[]
5207 fetchr = new JMenuItem(msname);
5208 final DbSourceProxy[] dassrc = { sproxy };
5209 fetchr.addActionListener(new ActionListener()
5213 public void actionPerformed(ActionEvent e)
5215 new Thread(new Runnable()
5221 boolean isNucleotide = alignPanel.alignFrame
5222 .getViewport().getAlignment()
5224 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5225 alignPanel.av.getSequenceSelection(),
5226 alignPanel.alignFrame, dassrc,
5227 alignPanel.alignFrame.featureSettings,
5230 .addListener(new FetchFinishedListenerI()
5233 public void finished()
5235 AlignFrame.this.setMenusForViewport();
5238 dbRefFetcher.fetchDBRefs(false);
5244 fetchr.setToolTipText(
5245 "<html>" + MessageManager.formatMessage(
5246 "label.fetch_retrieve_from", new Object[]
5250 if (++icomp >= mcomp || i == (otherdb.size()))
5252 ifetch.setText(MessageManager.formatMessage(
5253 "label.source_to_target", imname, sname));
5255 ifetch = new JMenu();
5263 if (comp >= mcomp || dbi >= (dbclasses.length))
5265 dfetch.setText(MessageManager.formatMessage(
5266 "label.source_to_target", mname, dbclass));
5268 dfetch = new JMenu();
5281 * Left justify the whole alignment.
5284 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5286 AlignmentI al = viewport.getAlignment();
5288 viewport.firePropertyChange("alignment", null, al);
5292 * Right justify the whole alignment.
5295 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5297 AlignmentI al = viewport.getAlignment();
5299 viewport.firePropertyChange("alignment", null, al);
5303 public void setShowSeqFeatures(boolean b)
5305 showSeqFeatures.setSelected(b);
5306 viewport.setShowSequenceFeatures(b);
5313 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5314 * awt.event.ActionEvent)
5317 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5319 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5320 alignPanel.paintAlignment(false, false);
5327 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5331 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5333 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5334 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5342 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5343 * .event.ActionEvent)
5346 protected void showGroupConservation_actionPerformed(ActionEvent e)
5348 viewport.setShowGroupConservation(showGroupConservation.getState());
5349 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5356 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5357 * .event.ActionEvent)
5360 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5362 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5363 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5370 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5371 * .event.ActionEvent)
5374 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5376 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5377 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5381 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5383 showSequenceLogo.setState(true);
5384 viewport.setShowSequenceLogo(true);
5385 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5386 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5390 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5392 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5399 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5400 * .event.ActionEvent)
5403 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5405 if (avc.makeGroupsFromSelection())
5407 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5408 alignPanel.updateAnnotation();
5409 alignPanel.paintAlignment(true,
5410 viewport.needToUpdateStructureViews());
5414 public void clearAlignmentSeqRep()
5416 // TODO refactor alignmentseqrep to controller
5417 if (viewport.getAlignment().hasSeqrep())
5419 viewport.getAlignment().setSeqrep(null);
5420 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5421 alignPanel.updateAnnotation();
5422 alignPanel.paintAlignment(true, true);
5427 protected void createGroup_actionPerformed(ActionEvent e)
5429 if (avc.createGroup())
5431 if (applyAutoAnnotationSettings.isSelected())
5433 alignPanel.updateAnnotation(true, false);
5435 alignPanel.alignmentChanged();
5440 protected void unGroup_actionPerformed(ActionEvent e)
5444 alignPanel.alignmentChanged();
5449 * make the given alignmentPanel the currently selected tab
5451 * @param alignmentPanel
5453 public void setDisplayedView(AlignmentPanel alignmentPanel)
5455 if (!viewport.getSequenceSetId()
5456 .equals(alignmentPanel.av.getSequenceSetId()))
5458 throw new Error(MessageManager.getString(
5459 "error.implementation_error_cannot_show_view_alignment_frame"));
5461 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5462 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5464 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5469 * Action on selection of menu options to Show or Hide annotations.
5472 * @param forSequences
5473 * update sequence-related annotations
5474 * @param forAlignment
5475 * update non-sequence-related annotations
5478 protected void setAnnotationsVisibility(boolean visible,
5479 boolean forSequences, boolean forAlignment)
5481 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5482 .getAlignmentAnnotation();
5487 for (AlignmentAnnotation aa : anns)
5490 * don't display non-positional annotations on an alignment
5492 if (aa.annotations == null)
5496 boolean apply = (aa.sequenceRef == null && forAlignment)
5497 || (aa.sequenceRef != null && forSequences);
5500 aa.visible = visible;
5503 alignPanel.validateAnnotationDimensions(true);
5504 alignPanel.alignmentChanged();
5508 * Store selected annotation sort order for the view and repaint.
5511 protected void sortAnnotations_actionPerformed()
5513 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5515 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5516 alignPanel.paintAlignment(false, false);
5521 * @return alignment panels in this alignment frame
5523 public List<? extends AlignmentViewPanel> getAlignPanels()
5525 // alignPanels is never null
5526 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5531 * Open a new alignment window, with the cDNA associated with this (protein)
5532 * alignment, aligned as is the protein.
5534 protected void viewAsCdna_actionPerformed()
5536 // TODO no longer a menu action - refactor as required
5537 final AlignmentI alignment = getViewport().getAlignment();
5538 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5539 if (mappings == null)
5543 List<SequenceI> cdnaSeqs = new ArrayList<>();
5544 for (SequenceI aaSeq : alignment.getSequences())
5546 for (AlignedCodonFrame acf : mappings)
5548 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5552 * There is a cDNA mapping for this protein sequence - add to new
5553 * alignment. It will share the same dataset sequence as other mapped
5554 * cDNA (no new mappings need to be created).
5556 final Sequence newSeq = new Sequence(dnaSeq);
5557 newSeq.setDatasetSequence(dnaSeq);
5558 cdnaSeqs.add(newSeq);
5562 if (cdnaSeqs.size() == 0)
5564 // show a warning dialog no mapped cDNA
5567 AlignmentI cdna = new Alignment(
5568 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5569 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5570 AlignFrame.DEFAULT_HEIGHT);
5571 cdna.alignAs(alignment);
5572 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5574 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5575 AlignFrame.DEFAULT_HEIGHT);
5579 * Set visibility of dna/protein complement view (available when shown in a
5585 protected void showComplement_actionPerformed(boolean show)
5587 SplitContainerI sf = getSplitViewContainer();
5590 sf.setComplementVisible(this, show);
5595 * Generate the reverse (optionally complemented) of the selected sequences,
5596 * and add them to the alignment
5599 protected void showReverse_actionPerformed(boolean complement)
5601 AlignmentI al = null;
5604 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5605 al = dna.reverseCdna(complement);
5606 viewport.addAlignment(al, "");
5607 addHistoryItem(new EditCommand(
5608 MessageManager.getString("label.add_sequences"), Action.PASTE,
5609 al.getSequencesArray(), 0, al.getWidth(),
5610 viewport.getAlignment()));
5611 } catch (Exception ex)
5613 System.err.println(ex.getMessage());
5619 * Try to run a script in the Groovy console, having first ensured that this
5620 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5621 * be targeted at this alignment.
5624 protected void runGroovy_actionPerformed()
5626 Jalview.setCurrentAlignFrame(this);
5627 groovy.ui.Console console = Desktop.getGroovyConsole();
5628 if (console != null)
5632 console.runScript();
5633 } catch (Exception ex)
5635 System.err.println((ex.toString()));
5636 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5637 MessageManager.getString("label.couldnt_run_groovy_script"),
5638 MessageManager.getString("label.groovy_support_failed"),
5639 JvOptionPane.ERROR_MESSAGE);
5644 System.err.println("Can't run Groovy script as console not found");
5649 * Hides columns containing (or not containing) a specified feature, provided
5650 * that would not leave all columns hidden
5652 * @param featureType
5653 * @param columnsContaining
5656 public boolean hideFeatureColumns(String featureType,
5657 boolean columnsContaining)
5659 boolean notForHiding = avc.markColumnsContainingFeatures(
5660 columnsContaining, false, false, featureType);
5663 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5664 false, featureType))
5666 getViewport().hideSelectedColumns();
5674 protected void selectHighlightedColumns_actionPerformed(
5675 ActionEvent actionEvent)
5677 // include key modifier check in case user selects from menu
5678 avc.markHighlightedColumns(
5679 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5680 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5681 | ActionEvent.CTRL_MASK)) != 0);
5685 * Rebuilds the Colour menu, including any user-defined colours which have
5686 * been loaded either on startup or during the session
5688 public void buildColourMenu()
5690 colourMenu.removeAll();
5692 colourMenu.add(applyToAllGroups);
5693 colourMenu.add(textColour);
5694 colourMenu.addSeparator();
5696 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5697 viewport.getAlignment(), false);
5699 colourMenu.add(annotationColour);
5700 bg.add(annotationColour);
5701 colourMenu.addSeparator();
5702 colourMenu.add(conservationMenuItem);
5703 colourMenu.add(modifyConservation);
5704 colourMenu.add(abovePIDThreshold);
5705 colourMenu.add(modifyPID);
5707 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5708 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5712 * Open a dialog (if not already open) that allows the user to select and
5713 * calculate PCA or Tree analysis
5715 protected void openTreePcaDialog()
5717 if (alignPanel.getCalculationDialog() == null)
5719 new CalculationChooser(AlignFrame.this);
5724 protected void loadVcf_actionPerformed()
5726 JalviewFileChooser chooser = new JalviewFileChooser(
5727 Cache.getProperty("LAST_DIRECTORY"));
5728 chooser.setFileView(new JalviewFileView());
5729 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5730 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5732 int value = chooser.showOpenDialog(null);
5734 if (value == JalviewFileChooser.APPROVE_OPTION)
5736 String choice = chooser.getSelectedFile().getPath();
5737 Cache.setProperty("LAST_DIRECTORY", choice);
5738 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5739 new VCFLoader(choice).loadVCF(seqs, this);
5744 private Rectangle lastFeatureSettingsBounds = null;
5747 public void setFeatureSettingsGeometry(Rectangle bounds)
5749 lastFeatureSettingsBounds = bounds;
5753 public Rectangle getFeatureSettingsGeometry()
5755 return lastFeatureSettingsBounds;
5759 class PrintThread extends Thread
5763 public PrintThread(AlignmentPanel ap)
5768 static PageFormat pf;
5773 PrinterJob printJob = PrinterJob.getPrinterJob();
5777 printJob.setPrintable(ap, pf);
5781 printJob.setPrintable(ap);
5784 if (printJob.printDialog())
5789 } catch (Exception PrintException)
5791 PrintException.printStackTrace();