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.MessageManager;
142 import jalview.util.Platform;
143 import jalview.viewmodel.AlignmentViewport;
144 import jalview.viewmodel.ViewportRanges;
145 import jalview.ws.DBRefFetcher;
146 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
147 import jalview.ws.jws1.Discoverer;
148 import jalview.ws.jws2.Jws2Discoverer;
149 import jalview.ws.jws2.jabaws2.Jws2Instance;
150 import jalview.ws.seqfetcher.DbSourceProxy;
156 * @version $Revision$
158 public class AlignFrame extends GAlignFrame implements DropTargetListener,
159 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
162 public static final int DEFAULT_WIDTH = 700;
164 public static final int DEFAULT_HEIGHT = 500;
167 * The currently displayed panel (selected tabbed view if more than one)
169 public AlignmentPanel alignPanel;
171 AlignViewport viewport;
173 public AlignViewControllerI avc;
175 List<AlignmentPanel> alignPanels = new ArrayList<>();
178 * Last format used to load or save alignments in this window
180 FileFormatI currentFileFormat = null;
183 * Current filename for this alignment
185 String fileName = null;
188 * Creates a new AlignFrame object with specific width and height.
194 public AlignFrame(AlignmentI al, int width, int height)
196 this(al, null, width, height);
200 * Creates a new AlignFrame object with specific width, height and
206 * @param sequenceSetId
208 public AlignFrame(AlignmentI al, int width, int height,
209 String sequenceSetId)
211 this(al, null, width, height, sequenceSetId);
215 * Creates a new AlignFrame object with specific width, height and
221 * @param sequenceSetId
224 public AlignFrame(AlignmentI al, int width, int height,
225 String sequenceSetId, String viewId)
227 this(al, null, width, height, sequenceSetId, viewId);
231 * new alignment window with hidden columns
235 * @param hiddenColumns
236 * ColumnSelection or null
238 * Width of alignment frame
242 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
245 this(al, hiddenColumns, width, height, null);
249 * Create alignment frame for al with hiddenColumns, a specific width and
250 * height, and specific sequenceId
253 * @param hiddenColumns
256 * @param sequenceSetId
259 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
260 int height, String sequenceSetId)
262 this(al, hiddenColumns, width, height, sequenceSetId, null);
266 * Create alignment frame for al with hiddenColumns, a specific width and
267 * height, and specific sequenceId
270 * @param hiddenColumns
273 * @param sequenceSetId
278 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
279 int height, String sequenceSetId, String viewId)
281 setSize(width, height);
283 if (al.getDataset() == null)
288 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
290 alignPanel = new AlignmentPanel(this, viewport);
292 addAlignmentPanel(alignPanel, true);
296 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
297 HiddenColumns hiddenColumns, int width, int height)
299 setSize(width, height);
301 if (al.getDataset() == null)
306 viewport = new AlignViewport(al, hiddenColumns);
308 if (hiddenSeqs != null && hiddenSeqs.length > 0)
310 viewport.hideSequence(hiddenSeqs);
312 alignPanel = new AlignmentPanel(this, viewport);
313 addAlignmentPanel(alignPanel, true);
318 * Make a new AlignFrame from existing alignmentPanels
325 public AlignFrame(AlignmentPanel ap)
329 addAlignmentPanel(ap, false);
334 * initalise the alignframe from the underlying viewport data and the
339 if (!Jalview.isHeadlessMode())
341 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
344 avc = new jalview.controller.AlignViewController(this, viewport,
346 if (viewport.getAlignmentConservationAnnotation() == null)
348 // BLOSUM62Colour.setEnabled(false);
349 conservationMenuItem.setEnabled(false);
350 modifyConservation.setEnabled(false);
351 // PIDColour.setEnabled(false);
352 // abovePIDThreshold.setEnabled(false);
353 // modifyPID.setEnabled(false);
356 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
359 if (sortby.equals("Id"))
361 sortIDMenuItem_actionPerformed(null);
363 else if (sortby.equals("Pairwise Identity"))
365 sortPairwiseMenuItem_actionPerformed(null);
369 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
371 setMenusFromViewport(viewport);
372 buildSortByAnnotationScoresMenu();
373 calculateTree.addActionListener(new ActionListener()
377 public void actionPerformed(ActionEvent e)
384 if (Desktop.desktop != null)
386 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
387 addServiceListeners();
391 if (viewport.getWrapAlignment())
393 wrapMenuItem_actionPerformed(null);
396 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
398 this.overviewMenuItem_actionPerformed(null);
403 final List<AlignmentPanel> selviews = new ArrayList<>();
404 final List<AlignmentPanel> origview = new ArrayList<>();
405 final String menuLabel = MessageManager
406 .getString("label.copy_format_from");
407 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
408 new ViewSetProvider()
412 public AlignmentPanel[] getAllAlignmentPanels()
415 origview.add(alignPanel);
416 // make an array of all alignment panels except for this one
417 List<AlignmentPanel> aps = new ArrayList<>(
418 Arrays.asList(Desktop.getAlignmentPanels(null)));
419 aps.remove(AlignFrame.this.alignPanel);
420 return aps.toArray(new AlignmentPanel[aps.size()]);
422 }, selviews, new ItemListener()
426 public void itemStateChanged(ItemEvent e)
428 if (origview.size() > 0)
430 final AlignmentPanel ap = origview.get(0);
433 * Copy the ViewStyle of the selected panel to 'this one'.
434 * Don't change value of 'scaleProteinAsCdna' unless copying
437 ViewStyleI vs = selviews.get(0).getAlignViewport()
439 boolean fromSplitFrame = selviews.get(0)
440 .getAlignViewport().getCodingComplement() != null;
443 vs.setScaleProteinAsCdna(ap.getAlignViewport()
444 .getViewStyle().isScaleProteinAsCdna());
446 ap.getAlignViewport().setViewStyle(vs);
449 * Also rescale ViewStyle of SplitFrame complement if there is
450 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
451 * the whole ViewStyle (allow cDNA protein to have different
454 AlignViewportI complement = ap.getAlignViewport()
455 .getCodingComplement();
456 if (complement != null && vs.isScaleProteinAsCdna())
458 AlignFrame af = Desktop.getAlignFrameFor(complement);
459 ((SplitFrame) af.getSplitViewContainer())
461 af.setMenusForViewport();
465 ap.setSelected(true);
466 ap.alignFrame.setMenusForViewport();
471 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
472 .indexOf("devel") > -1
473 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
474 .indexOf("test") > -1)
476 formatMenu.add(vsel);
478 addFocusListener(new FocusAdapter()
481 public void focusGained(FocusEvent e)
483 Jalview.setCurrentAlignFrame(AlignFrame.this);
490 * Change the filename and format for the alignment, and enable the 'reload'
491 * button functionality.
498 public void setFileName(String file, FileFormatI format)
501 setFileFormat(format);
502 reload.setEnabled(true);
506 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
509 void addKeyListener()
511 addKeyListener(new KeyAdapter()
514 public void keyPressed(KeyEvent evt)
516 if (viewport.cursorMode
517 && ((evt.getKeyCode() >= KeyEvent.VK_0
518 && evt.getKeyCode() <= KeyEvent.VK_9)
519 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
520 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
521 && Character.isDigit(evt.getKeyChar()))
523 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
526 switch (evt.getKeyCode())
529 case 27: // escape key
530 deselectAllSequenceMenuItem_actionPerformed(null);
534 case KeyEvent.VK_DOWN:
535 if (evt.isAltDown() || !viewport.cursorMode)
537 moveSelectedSequences(false);
539 if (viewport.cursorMode)
541 alignPanel.getSeqPanel().moveCursor(0, 1,
542 evt.isShiftDown() && !evt.isAltDown());
547 if (evt.isAltDown() || !viewport.cursorMode)
549 moveSelectedSequences(true);
551 if (viewport.cursorMode)
553 alignPanel.getSeqPanel().moveCursor(0, -1,
554 evt.isShiftDown() && !evt.isAltDown());
558 case KeyEvent.VK_LEFT:
559 if (evt.isAltDown() || !viewport.cursorMode)
561 slideSequences(false,
562 alignPanel.getSeqPanel().getKeyboardNo1());
566 alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
571 case KeyEvent.VK_RIGHT:
572 if (evt.isAltDown() || !viewport.cursorMode)
574 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
578 alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
582 case KeyEvent.VK_SPACE:
583 if (viewport.cursorMode)
585 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
586 || evt.isShiftDown() || evt.isAltDown());
590 // case KeyEvent.VK_A:
591 // if (viewport.cursorMode)
593 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
594 // //System.out.println("A");
598 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
599 * System.out.println("closing bracket"); } break;
601 case KeyEvent.VK_DELETE:
602 case KeyEvent.VK_BACK_SPACE:
603 if (!viewport.cursorMode)
605 cut_actionPerformed(null);
609 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
610 || evt.isShiftDown() || evt.isAltDown());
616 if (viewport.cursorMode)
618 alignPanel.getSeqPanel().setCursorRow();
622 if (viewport.cursorMode && !evt.isControlDown())
624 alignPanel.getSeqPanel().setCursorColumn();
628 if (viewport.cursorMode)
630 alignPanel.getSeqPanel().setCursorPosition();
634 case KeyEvent.VK_ENTER:
635 case KeyEvent.VK_COMMA:
636 if (viewport.cursorMode)
638 alignPanel.getSeqPanel().setCursorRowAndColumn();
643 if (viewport.cursorMode)
645 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
649 if (viewport.cursorMode)
651 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
656 viewport.cursorMode = !viewport.cursorMode;
657 statusBar.setText(MessageManager
658 .formatMessage("label.keyboard_editing_mode", new String[]
659 { (viewport.cursorMode ? "on" : "off") }));
660 if (viewport.cursorMode)
662 ViewportRanges ranges = viewport.getRanges();
663 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
665 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
668 alignPanel.getSeqPanel().seqCanvas.repaint();
674 Help.showHelpWindow();
675 } catch (Exception ex)
677 ex.printStackTrace();
682 boolean toggleSeqs = !evt.isControlDown();
683 boolean toggleCols = !evt.isShiftDown();
684 toggleHiddenRegions(toggleSeqs, toggleCols);
689 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
690 boolean modifyExisting = true; // always modify, don't clear
691 // evt.isShiftDown();
692 boolean invertHighlighted = evt.isAltDown();
693 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
697 case KeyEvent.VK_PAGE_UP:
698 viewport.getRanges().pageUp();
700 case KeyEvent.VK_PAGE_DOWN:
701 viewport.getRanges().pageDown();
707 public void keyReleased(KeyEvent evt)
709 switch (evt.getKeyCode())
711 case KeyEvent.VK_LEFT:
712 if (evt.isAltDown() || !viewport.cursorMode)
714 viewport.firePropertyChange("alignment", null,
715 viewport.getAlignment().getSequences());
719 case KeyEvent.VK_RIGHT:
720 if (evt.isAltDown() || !viewport.cursorMode)
722 viewport.firePropertyChange("alignment", null,
723 viewport.getAlignment().getSequences());
731 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
733 ap.alignFrame = this;
734 avc = new jalview.controller.AlignViewController(this, viewport,
739 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
741 int aSize = alignPanels.size();
743 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
745 if (aSize == 1 && ap.av.getViewName() == null)
747 this.getContentPane().add(ap, BorderLayout.CENTER);
753 setInitialTabVisible();
756 expandViews.setEnabled(true);
757 gatherViews.setEnabled(true);
758 tabbedPane.addTab(ap.av.getViewName(), ap);
760 ap.setVisible(false);
765 if (ap.av.isPadGaps())
767 ap.av.getAlignment().padGaps();
769 ap.av.updateConservation(ap);
770 ap.av.updateConsensus(ap);
771 ap.av.updateStrucConsensus(ap);
775 public void setInitialTabVisible()
777 expandViews.setEnabled(true);
778 gatherViews.setEnabled(true);
779 tabbedPane.setVisible(true);
780 AlignmentPanel first = alignPanels.get(0);
781 tabbedPane.addTab(first.av.getViewName(), first);
782 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
785 public AlignViewport getViewport()
790 /* Set up intrinsic listeners for dynamically generated GUI bits. */
791 private void addServiceListeners()
793 final java.beans.PropertyChangeListener thisListener;
794 Desktop.instance.addJalviewPropertyChangeListener("services",
795 thisListener = new java.beans.PropertyChangeListener()
798 public void propertyChange(PropertyChangeEvent evt)
800 // // System.out.println("Discoverer property change.");
801 // if (evt.getPropertyName().equals("services"))
803 SwingUtilities.invokeLater(new Runnable()
810 "Rebuild WS Menu for service change");
811 BuildWebServiceMenu();
818 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
821 public void internalFrameClosed(
822 javax.swing.event.InternalFrameEvent evt)
824 // System.out.println("deregistering discoverer listener");
825 Desktop.instance.removeJalviewPropertyChangeListener("services",
827 closeMenuItem_actionPerformed(true);
830 // Finally, build the menu once to get current service state
831 new Thread(new Runnable()
836 BuildWebServiceMenu();
842 * Configure menu items that vary according to whether the alignment is
843 * nucleotide or protein
845 public void setGUINucleotide()
847 AlignmentI al = getViewport().getAlignment();
848 boolean nucleotide = al.isNucleotide();
850 loadVcf.setVisible(nucleotide);
851 showTranslation.setVisible(nucleotide);
852 showReverse.setVisible(nucleotide);
853 showReverseComplement.setVisible(nucleotide);
854 conservationMenuItem.setEnabled(!nucleotide);
856 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
857 showGroupConservation.setEnabled(!nucleotide);
859 showComplementMenuItem
860 .setText(nucleotide ? MessageManager.getString("label.protein")
861 : MessageManager.getString("label.nucleotide"));
865 * set up menus for the current viewport. This may be called after any
866 * operation that affects the data in the current view (selection changed,
867 * etc) to update the menus to reflect the new state.
870 public void setMenusForViewport()
872 setMenusFromViewport(viewport);
876 * Need to call this method when tabs are selected for multiple views, or when
877 * loading from Jalview2XML.java
882 public void setMenusFromViewport(AlignViewport av)
884 padGapsMenuitem.setSelected(av.isPadGaps());
885 colourTextMenuItem.setSelected(av.isShowColourText());
886 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
887 modifyPID.setEnabled(abovePIDThreshold.isSelected());
888 conservationMenuItem.setSelected(av.getConservationSelected());
889 modifyConservation.setEnabled(conservationMenuItem.isSelected());
890 seqLimits.setSelected(av.getShowJVSuffix());
891 idRightAlign.setSelected(av.isRightAlignIds());
892 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
893 renderGapsMenuItem.setSelected(av.isRenderGaps());
894 wrapMenuItem.setSelected(av.getWrapAlignment());
895 scaleAbove.setVisible(av.getWrapAlignment());
896 scaleLeft.setVisible(av.getWrapAlignment());
897 scaleRight.setVisible(av.getWrapAlignment());
898 annotationPanelMenuItem.setState(av.isShowAnnotation());
900 * Show/hide annotations only enabled if annotation panel is shown
902 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
903 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
904 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
905 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
906 viewBoxesMenuItem.setSelected(av.getShowBoxes());
907 viewTextMenuItem.setSelected(av.getShowText());
908 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
909 showGroupConsensus.setSelected(av.isShowGroupConsensus());
910 showGroupConservation.setSelected(av.isShowGroupConservation());
911 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
912 showSequenceLogo.setSelected(av.isShowSequenceLogo());
913 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
915 ColourMenuHelper.setColourSelected(colourMenu,
916 av.getGlobalColourScheme());
918 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
919 hiddenMarkers.setState(av.getShowHiddenMarkers());
920 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
921 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
922 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
923 autoCalculate.setSelected(av.autoCalculateConsensus);
924 sortByTree.setSelected(av.sortByTree);
925 listenToViewSelections.setSelected(av.followSelection);
927 showProducts.setEnabled(canShowProducts());
928 setGroovyEnabled(Desktop.getGroovyConsole() != null);
934 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
938 public void setGroovyEnabled(boolean b)
940 runGroovy.setEnabled(b);
943 private IProgressIndicator progressBar;
948 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
951 public void setProgressBar(String message, long id)
953 progressBar.setProgressBar(message, id);
957 public void registerHandler(final long id,
958 final IProgressIndicatorHandler handler)
960 progressBar.registerHandler(id, handler);
965 * @return true if any progress bars are still active
968 public boolean operationInProgress()
970 return progressBar.operationInProgress();
974 * Sets the text of the status bar. Note that setting a null or empty value
975 * will cause the status bar to be hidden, with possibly undesirable flicker
976 * of the screen layout.
979 public void setStatus(String text)
981 statusBar.setText(text == null || text.isEmpty() ? " " : text);
985 * Added so Castor Mapping file can obtain Jalview Version
987 public String getVersion()
989 return jalview.bin.Cache.getProperty("VERSION");
992 public FeatureRenderer getFeatureRenderer()
994 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
998 public void fetchSequence_actionPerformed(ActionEvent e)
1000 new jalview.gui.SequenceFetcher(this);
1004 public void addFromFile_actionPerformed(ActionEvent e)
1006 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1010 public void reload_actionPerformed(ActionEvent e)
1012 if (fileName != null)
1014 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1015 // originating file's format
1016 // TODO: work out how to recover feature settings for correct view(s) when
1017 // file is reloaded.
1018 if (FileFormat.Jalview.equals(currentFileFormat))
1020 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1021 for (int i = 0; i < frames.length; i++)
1023 if (frames[i] instanceof AlignFrame && frames[i] != this
1024 && ((AlignFrame) frames[i]).fileName != null
1025 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1029 frames[i].setSelected(true);
1030 Desktop.instance.closeAssociatedWindows();
1031 } catch (java.beans.PropertyVetoException ex)
1037 Desktop.instance.closeAssociatedWindows();
1039 FileLoader loader = new FileLoader();
1040 DataSourceType protocol = fileName.startsWith("http:")
1041 ? DataSourceType.URL
1042 : DataSourceType.FILE;
1043 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1047 Rectangle bounds = this.getBounds();
1049 FileLoader loader = new FileLoader();
1050 DataSourceType protocol = fileName.startsWith("http:")
1051 ? DataSourceType.URL
1052 : DataSourceType.FILE;
1053 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1054 protocol, currentFileFormat);
1056 newframe.setBounds(bounds);
1057 if (featureSettings != null && featureSettings.isShowing())
1059 final Rectangle fspos = featureSettings.frame.getBounds();
1060 // TODO: need a 'show feature settings' function that takes bounds -
1061 // need to refactor Desktop.addFrame
1062 newframe.featureSettings_actionPerformed(null);
1063 final FeatureSettings nfs = newframe.featureSettings;
1064 SwingUtilities.invokeLater(new Runnable()
1069 nfs.frame.setBounds(fspos);
1072 this.featureSettings.close();
1073 this.featureSettings = null;
1075 this.closeMenuItem_actionPerformed(true);
1081 public void addFromText_actionPerformed(ActionEvent e)
1084 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1088 public void addFromURL_actionPerformed(ActionEvent e)
1090 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1094 public void save_actionPerformed(ActionEvent e)
1096 if (fileName == null || (currentFileFormat == null)
1097 || fileName.startsWith("http"))
1099 saveAs_actionPerformed(null);
1103 saveAlignment(fileName, currentFileFormat);
1114 public void saveAs_actionPerformed(ActionEvent e)
1116 String format = currentFileFormat == null ? null
1117 : currentFileFormat.getName();
1118 JalviewFileChooser chooser = JalviewFileChooser
1119 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1121 chooser.setFileView(new JalviewFileView());
1122 chooser.setDialogTitle(
1123 MessageManager.getString("label.save_alignment_to_file"));
1124 chooser.setToolTipText(MessageManager.getString("action.save"));
1126 int value = chooser.showSaveDialog(this);
1128 if (value == JalviewFileChooser.APPROVE_OPTION)
1130 currentFileFormat = chooser.getSelectedFormat();
1131 while (currentFileFormat == null)
1133 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1134 MessageManager.getString(
1135 "label.select_file_format_before_saving"),
1136 MessageManager.getString("label.file_format_not_specified"),
1137 JvOptionPane.WARNING_MESSAGE);
1138 currentFileFormat = chooser.getSelectedFormat();
1139 value = chooser.showSaveDialog(this);
1140 if (value != JalviewFileChooser.APPROVE_OPTION)
1146 fileName = chooser.getSelectedFile().getPath();
1148 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1150 Cache.setProperty("LAST_DIRECTORY", fileName);
1151 saveAlignment(fileName, currentFileFormat);
1155 public boolean saveAlignment(String file, FileFormatI format)
1157 boolean success = true;
1159 if (FileFormat.Jalview.equals(format))
1161 String shortName = title;
1163 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1165 shortName = shortName.substring(
1166 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1169 success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1172 statusBar.setText(MessageManager.formatMessage(
1173 "label.successfully_saved_to_file_in_format", new Object[]
1179 AlignmentExportData exportData = getAlignmentForExport(format,
1181 if (exportData.getSettings().isCancelled())
1185 FormatAdapter f = new FormatAdapter(alignPanel,
1186 exportData.getSettings());
1187 String output = f.formatSequences(format, exportData.getAlignment(), // class
1191 // occur in the distant future
1192 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1193 f.getCacheSuffixDefault(format),
1194 viewport.getAlignment().getHiddenColumns());
1202 // create backupfiles object and get new temp filename destination
1203 Cache.log.debug("ALIGNFRAME making backupfiles object for " + file);
1204 BackupFiles backupfiles = new BackupFiles(file);
1208 String tempFilePath = backupfiles.getTempFilePath();
1210 "ALIGNFRAME setting PrintWriter to " + tempFilePath);
1211 PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1214 "ALIGNFRAME about to write to temp file " + tempFilePath);
1217 Cache.log.debug("ALIGNFRAME about to close file");
1219 Cache.log.debug("ALIGNFRAME closed file");
1220 this.setTitle(file);
1221 statusBar.setText(MessageManager.formatMessage(
1222 "label.successfully_saved_to_file_in_format", new Object[]
1223 { file, format.getName() }));
1224 } catch (IOException e)
1228 "ALIGNFRAME Something happened writing the temp file");
1229 Cache.log.error(e.getMessage());
1230 Cache.log.debug(Cache.getStackTraceString(e));
1232 } catch (Exception ex)
1236 "ALIGNFRAME Something else happened writing the temp file");
1237 Cache.log.error(ex.getMessage());
1238 Cache.log.debug(Cache.getStackTraceString(ex));
1241 backupfiles.setWriteSuccess(success);
1242 Cache.log.debug("ALIGNFRAME writing temp file was "
1243 + (success ? "" : "NOT ") + "successful");
1244 // do the backup file roll and rename the temp file to actual file
1245 Cache.log.debug("ALIGNFRAME about to rollBackupsAndRenameTempFile");
1246 success = backupfiles.rollBackupsAndRenameTempFile();
1247 Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
1248 + (success ? "" : "un") + "successfully");
1255 if (!Platform.isHeadless())
1257 JvOptionPane.showInternalMessageDialog(this, MessageManager
1258 .formatMessage("label.couldnt_save_file", new Object[]
1260 MessageManager.getString("label.error_saving_file"),
1261 JvOptionPane.WARNING_MESSAGE);
1268 private void warningMessage(String warning, String title)
1270 if (new jalview.util.Platform().isHeadless())
1272 System.err.println("Warning: " + title + "\nWarning: " + warning);
1277 JvOptionPane.showInternalMessageDialog(this, warning, title,
1278 JvOptionPane.WARNING_MESSAGE);
1290 protected void outputText_actionPerformed(ActionEvent e)
1292 FileFormatI fileFormat = FileFormats.getInstance()
1293 .forName(e.getActionCommand());
1294 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1296 if (exportData.getSettings().isCancelled())
1300 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1301 cap.setForInput(null);
1304 FileFormatI format = fileFormat;
1305 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1306 .formatSequences(format, exportData.getAlignment(),
1307 exportData.getOmitHidden(),
1308 exportData.getStartEndPostions(),
1309 viewport.getAlignment().getHiddenColumns()));
1310 Desktop.addInternalFrame(cap, MessageManager
1311 .formatMessage("label.alignment_output_command", new Object[]
1312 { e.getActionCommand() }), 600, 500);
1313 } catch (OutOfMemoryError oom)
1315 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1322 public static AlignmentExportData getAlignmentForExport(
1323 FileFormatI format, AlignViewportI viewport,
1324 AlignExportSettingI exportSettings)
1326 AlignmentI alignmentToExport = null;
1327 AlignExportSettingI settings = exportSettings;
1328 String[] omitHidden = null;
1330 HiddenSequences hiddenSeqs = viewport.getAlignment()
1331 .getHiddenSequences();
1333 alignmentToExport = viewport.getAlignment();
1335 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1336 if (settings == null)
1338 settings = new AlignExportSettings(hasHiddenSeqs,
1339 viewport.hasHiddenColumns(), format);
1341 // settings.isExportAnnotations();
1343 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1345 omitHidden = viewport.getViewAsString(false,
1346 settings.isExportHiddenSequences());
1349 int[] alignmentStartEnd = new int[2];
1350 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1352 alignmentToExport = hiddenSeqs.getFullAlignment();
1356 alignmentToExport = viewport.getAlignment();
1358 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1359 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1360 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1361 omitHidden, alignmentStartEnd, settings);
1372 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1374 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1375 htmlSVG.exportHTML(null);
1379 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1381 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1382 bjs.exportHTML(null);
1385 public void createImageMap(File file, String image)
1387 alignPanel.makePNGImageMap(file, image);
1397 public void createPNG(File f)
1399 alignPanel.makePNG(f);
1409 public void createEPS(File f)
1411 alignPanel.makeEPS(f);
1415 public void createSVG(File f)
1417 alignPanel.makeSVG(f);
1421 public void pageSetup_actionPerformed(ActionEvent e)
1423 PrinterJob printJob = PrinterJob.getPrinterJob();
1424 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1434 public void printMenuItem_actionPerformed(ActionEvent e)
1436 // Putting in a thread avoids Swing painting problems
1437 PrintThread thread = new PrintThread(alignPanel);
1442 public void exportFeatures_actionPerformed(ActionEvent e)
1444 new AnnotationExporter(alignPanel).exportFeatures();
1448 public void exportAnnotations_actionPerformed(ActionEvent e)
1450 new AnnotationExporter(alignPanel).exportAnnotations();
1454 public void associatedData_actionPerformed(ActionEvent e)
1456 // Pick the tree file
1457 JalviewFileChooser chooser = new JalviewFileChooser(
1458 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1459 chooser.setFileView(new JalviewFileView());
1460 chooser.setDialogTitle(
1461 MessageManager.getString("label.load_jalview_annotations"));
1462 chooser.setToolTipText(
1463 MessageManager.getString("label.load_jalview_annotations"));
1465 int value = chooser.showOpenDialog(null);
1467 if (value == JalviewFileChooser.APPROVE_OPTION)
1469 String choice = chooser.getSelectedFile().getPath();
1470 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1471 loadJalviewDataFile(choice, null, null, null);
1477 * Close the current view or all views in the alignment frame. If the frame
1478 * only contains one view then the alignment will be removed from memory.
1480 * @param closeAllTabs
1483 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1485 if (alignPanels != null && alignPanels.size() < 2)
1487 closeAllTabs = true;
1492 if (alignPanels != null)
1496 if (this.isClosed())
1498 // really close all the windows - otherwise wait till
1499 // setClosed(true) is called
1500 for (int i = 0; i < alignPanels.size(); i++)
1502 AlignmentPanel ap = alignPanels.get(i);
1509 closeView(alignPanel);
1514 if (featureSettings != null && featureSettings.isOpen())
1516 featureSettings.close();
1517 featureSettings = null;
1520 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1521 * be called recursively, with the frame now in 'closed' state
1523 this.setClosed(true);
1525 } catch (Exception ex)
1527 ex.printStackTrace();
1532 * Close the specified panel and close up tabs appropriately.
1534 * @param panelToClose
1536 public void closeView(AlignmentPanel panelToClose)
1538 int index = tabbedPane.getSelectedIndex();
1539 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1540 alignPanels.remove(panelToClose);
1541 panelToClose.closePanel();
1542 panelToClose = null;
1544 tabbedPane.removeTabAt(closedindex);
1545 tabbedPane.validate();
1547 if (index > closedindex || index == tabbedPane.getTabCount())
1549 // modify currently selected tab index if necessary.
1553 this.tabSelectionChanged(index);
1559 void updateEditMenuBar()
1562 if (viewport.getHistoryList().size() > 0)
1564 undoMenuItem.setEnabled(true);
1565 CommandI command = viewport.getHistoryList().peek();
1566 undoMenuItem.setText(MessageManager
1567 .formatMessage("label.undo_command", new Object[]
1568 { command.getDescription() }));
1572 undoMenuItem.setEnabled(false);
1573 undoMenuItem.setText(MessageManager.getString("action.undo"));
1576 if (viewport.getRedoList().size() > 0)
1578 redoMenuItem.setEnabled(true);
1580 CommandI command = viewport.getRedoList().peek();
1581 redoMenuItem.setText(MessageManager
1582 .formatMessage("label.redo_command", new Object[]
1583 { command.getDescription() }));
1587 redoMenuItem.setEnabled(false);
1588 redoMenuItem.setText(MessageManager.getString("action.redo"));
1593 public void addHistoryItem(CommandI command)
1595 if (command.getSize() > 0)
1597 viewport.addToHistoryList(command);
1598 viewport.clearRedoList();
1599 updateEditMenuBar();
1600 viewport.updateHiddenColumns();
1601 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1602 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1603 // viewport.getColumnSelection()
1604 // .getHiddenColumns().size() > 0);
1610 * @return alignment objects for all views
1612 AlignmentI[] getViewAlignments()
1614 if (alignPanels != null)
1616 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1618 for (AlignmentPanel ap : alignPanels)
1620 als[i++] = ap.av.getAlignment();
1624 if (viewport != null)
1626 return new AlignmentI[] { viewport.getAlignment() };
1638 protected void undoMenuItem_actionPerformed(ActionEvent e)
1640 if (viewport.getHistoryList().isEmpty())
1644 CommandI command = viewport.getHistoryList().pop();
1645 viewport.addToRedoList(command);
1646 command.undoCommand(getViewAlignments());
1648 AlignmentViewport originalSource = getOriginatingSource(command);
1649 updateEditMenuBar();
1651 if (originalSource != null)
1653 if (originalSource != viewport)
1656 "Implementation worry: mismatch of viewport origin for undo");
1658 originalSource.updateHiddenColumns();
1659 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1661 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1662 // viewport.getColumnSelection()
1663 // .getHiddenColumns().size() > 0);
1664 originalSource.firePropertyChange("alignment", null,
1665 originalSource.getAlignment().getSequences());
1676 protected void redoMenuItem_actionPerformed(ActionEvent e)
1678 if (viewport.getRedoList().size() < 1)
1683 CommandI command = viewport.getRedoList().pop();
1684 viewport.addToHistoryList(command);
1685 command.doCommand(getViewAlignments());
1687 AlignmentViewport originalSource = getOriginatingSource(command);
1688 updateEditMenuBar();
1690 if (originalSource != null)
1693 if (originalSource != viewport)
1696 "Implementation worry: mismatch of viewport origin for redo");
1698 originalSource.updateHiddenColumns();
1699 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1701 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1702 // viewport.getColumnSelection()
1703 // .getHiddenColumns().size() > 0);
1704 originalSource.firePropertyChange("alignment", null,
1705 originalSource.getAlignment().getSequences());
1709 AlignmentViewport getOriginatingSource(CommandI command)
1711 AlignmentViewport originalSource = null;
1712 // For sequence removal and addition, we need to fire
1713 // the property change event FROM the viewport where the
1714 // original alignment was altered
1715 AlignmentI al = null;
1716 if (command instanceof EditCommand)
1718 EditCommand editCommand = (EditCommand) command;
1719 al = editCommand.getAlignment();
1720 List<Component> comps = PaintRefresher.components
1721 .get(viewport.getSequenceSetId());
1723 for (Component comp : comps)
1725 if (comp instanceof AlignmentPanel)
1727 if (al == ((AlignmentPanel) comp).av.getAlignment())
1729 originalSource = ((AlignmentPanel) comp).av;
1736 if (originalSource == null)
1738 // The original view is closed, we must validate
1739 // the current view against the closed view first
1742 PaintRefresher.validateSequences(al, viewport.getAlignment());
1745 originalSource = viewport;
1748 return originalSource;
1757 public void moveSelectedSequences(boolean up)
1759 SequenceGroup sg = viewport.getSelectionGroup();
1765 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1766 viewport.getHiddenRepSequences(), up);
1767 alignPanel.paintAlignment(true, false);
1770 synchronized void slideSequences(boolean right, int size)
1772 List<SequenceI> sg = new ArrayList<>();
1773 if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup()
1774 .getSize() != viewport.getAlignment().getHeight())
1776 sg = viewport.getSelectionGroup()
1777 .getSequences(viewport.getHiddenRepSequences());
1780 if (sg.size() == 0 && viewport.cursorMode)
1782 sg.add(viewport.getAlignment()
1783 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1791 List<SequenceI> invertGroup = new ArrayList<>();
1793 for (SequenceI seq : viewport.getAlignment().getSequences())
1795 if (!sg.contains(seq))
1797 invertGroup.add(seq);
1801 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1803 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1804 for (int i = 0; i < invertGroup.size(); i++)
1806 seqs2[i] = invertGroup.get(i);
1809 SlideSequencesCommand ssc;
1812 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1813 viewport.getGapCharacter());
1817 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1818 viewport.getGapCharacter());
1821 int groupAdjustment = 0;
1822 if (ssc.getGapsInsertedBegin() && right)
1824 if (viewport.cursorMode)
1826 alignPanel.getSeqPanel().moveCursor(size, 0);
1830 groupAdjustment = size;
1833 else if (!ssc.getGapsInsertedBegin() && !right)
1835 if (viewport.cursorMode)
1837 alignPanel.getSeqPanel().moveCursor(-size, 0);
1841 groupAdjustment = -size;
1845 if (groupAdjustment != 0)
1847 viewport.getSelectionGroup().setStartRes(
1848 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1849 viewport.getSelectionGroup().setEndRes(
1850 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1854 * just extend the last slide command if compatible; but not if in
1855 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1857 boolean appendHistoryItem = false;
1858 Deque<CommandI> historyList = viewport.getHistoryList();
1859 boolean inSplitFrame = getSplitViewContainer() != null;
1860 if (!inSplitFrame && historyList != null && historyList.size() > 0
1861 && historyList.peek() instanceof SlideSequencesCommand)
1863 appendHistoryItem = ssc.appendSlideCommand(
1864 (SlideSequencesCommand) historyList.peek());
1867 if (!appendHistoryItem)
1869 addHistoryItem(ssc);
1882 protected void copy_actionPerformed(ActionEvent e)
1884 if (viewport.getSelectionGroup() == null)
1888 // TODO: preserve the ordering of displayed alignment annotation in any
1889 // internal paste (particularly sequence associated annotation)
1890 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1891 String[] omitHidden = null;
1893 if (viewport.hasHiddenColumns())
1895 omitHidden = viewport.getViewAsString(true);
1898 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1899 seqs, omitHidden, null);
1901 StringSelection ss = new StringSelection(output);
1905 jalview.gui.Desktop.internalCopy = true;
1906 // Its really worth setting the clipboard contents
1907 // to empty before setting the large StringSelection!!
1908 Toolkit.getDefaultToolkit().getSystemClipboard()
1909 .setContents(new StringSelection(""), null);
1911 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1913 } catch (OutOfMemoryError er)
1915 new OOMWarning("copying region", er);
1919 HiddenColumns hiddenColumns = null;
1920 if (viewport.hasHiddenColumns())
1922 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1923 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1925 // create new HiddenColumns object with copy of hidden regions
1926 // between startRes and endRes, offset by startRes
1927 hiddenColumns = new HiddenColumns(
1928 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1929 hiddenCutoff, hiddenOffset);
1932 Desktop.jalviewClipboard = new Object[] { seqs,
1933 viewport.getAlignment().getDataset(), hiddenColumns };
1934 statusBar.setText(MessageManager.formatMessage(
1935 "label.copied_sequences_to_clipboard", new Object[]
1936 { Integer.valueOf(seqs.length).toString() }));
1946 protected void pasteNew_actionPerformed(ActionEvent e)
1958 protected void pasteThis_actionPerformed(ActionEvent e)
1964 * Paste contents of Jalview clipboard
1966 * @param newAlignment
1967 * true to paste to a new alignment, otherwise add to this.
1969 void paste(boolean newAlignment)
1971 boolean externalPaste = true;
1974 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1975 Transferable contents = c.getContents(this);
1977 if (contents == null)
1986 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1987 if (str.length() < 1)
1992 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1994 } catch (OutOfMemoryError er)
1996 new OOMWarning("Out of memory pasting sequences!!", er);
2000 SequenceI[] sequences;
2001 boolean annotationAdded = false;
2002 AlignmentI alignment = null;
2004 if (Desktop.jalviewClipboard != null)
2006 // The clipboard was filled from within Jalview, we must use the
2008 // And dataset from the copied alignment
2009 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2010 // be doubly sure that we create *new* sequence objects.
2011 sequences = new SequenceI[newseq.length];
2012 for (int i = 0; i < newseq.length; i++)
2014 sequences[i] = new Sequence(newseq[i]);
2016 alignment = new Alignment(sequences);
2017 externalPaste = false;
2021 // parse the clipboard as an alignment.
2022 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2024 sequences = alignment.getSequencesArray();
2028 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2034 if (Desktop.jalviewClipboard != null)
2036 // dataset is inherited
2037 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2041 // new dataset is constructed
2042 alignment.setDataset(null);
2044 alwidth = alignment.getWidth() + 1;
2048 AlignmentI pastedal = alignment; // preserve pasted alignment object
2049 // Add pasted sequences and dataset into existing alignment.
2050 alignment = viewport.getAlignment();
2051 alwidth = alignment.getWidth() + 1;
2052 // decide if we need to import sequences from an existing dataset
2053 boolean importDs = Desktop.jalviewClipboard != null
2054 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2055 // importDs==true instructs us to copy over new dataset sequences from
2056 // an existing alignment
2057 Vector newDs = (importDs) ? new Vector() : null; // used to create
2058 // minimum dataset set
2060 for (int i = 0; i < sequences.length; i++)
2064 newDs.addElement(null);
2066 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2068 if (importDs && ds != null)
2070 if (!newDs.contains(ds))
2072 newDs.setElementAt(ds, i);
2073 ds = new Sequence(ds);
2074 // update with new dataset sequence
2075 sequences[i].setDatasetSequence(ds);
2079 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2084 // copy and derive new dataset sequence
2085 sequences[i] = sequences[i].deriveSequence();
2086 alignment.getDataset()
2087 .addSequence(sequences[i].getDatasetSequence());
2088 // TODO: avoid creation of duplicate dataset sequences with a
2089 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2091 alignment.addSequence(sequences[i]); // merges dataset
2095 newDs.clear(); // tidy up
2097 if (alignment.getAlignmentAnnotation() != null)
2099 for (AlignmentAnnotation alan : alignment
2100 .getAlignmentAnnotation())
2102 if (alan.graphGroup > fgroup)
2104 fgroup = alan.graphGroup;
2108 if (pastedal.getAlignmentAnnotation() != null)
2110 // Add any annotation attached to alignment.
2111 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2112 for (int i = 0; i < alann.length; i++)
2114 annotationAdded = true;
2115 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2117 AlignmentAnnotation newann = new AlignmentAnnotation(
2119 if (newann.graphGroup > -1)
2121 if (newGraphGroups.size() <= newann.graphGroup
2122 || newGraphGroups.get(newann.graphGroup) == null)
2124 for (int q = newGraphGroups
2125 .size(); q <= newann.graphGroup; q++)
2127 newGraphGroups.add(q, null);
2129 newGraphGroups.set(newann.graphGroup,
2130 Integer.valueOf(++fgroup));
2132 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2136 newann.padAnnotation(alwidth);
2137 alignment.addAnnotation(newann);
2147 addHistoryItem(new EditCommand(
2148 MessageManager.getString("label.add_sequences"),
2149 Action.PASTE, sequences, 0, alignment.getWidth(),
2152 // Add any annotations attached to sequences
2153 for (int i = 0; i < sequences.length; i++)
2155 if (sequences[i].getAnnotation() != null)
2157 AlignmentAnnotation newann;
2158 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2160 annotationAdded = true;
2161 newann = sequences[i].getAnnotation()[a];
2162 newann.adjustForAlignment();
2163 newann.padAnnotation(alwidth);
2164 if (newann.graphGroup > -1)
2166 if (newann.graphGroup > -1)
2168 if (newGraphGroups.size() <= newann.graphGroup
2169 || newGraphGroups.get(newann.graphGroup) == null)
2171 for (int q = newGraphGroups
2172 .size(); q <= newann.graphGroup; q++)
2174 newGraphGroups.add(q, null);
2176 newGraphGroups.set(newann.graphGroup,
2177 Integer.valueOf(++fgroup));
2179 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2183 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2187 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2195 // propagate alignment changed.
2196 viewport.getRanges().setEndSeq(alignment.getHeight());
2197 if (annotationAdded)
2199 // Duplicate sequence annotation in all views.
2200 AlignmentI[] alview = this.getViewAlignments();
2201 for (int i = 0; i < sequences.length; i++)
2203 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2208 for (int avnum = 0; avnum < alview.length; avnum++)
2210 if (alview[avnum] != alignment)
2212 // duplicate in a view other than the one with input focus
2213 int avwidth = alview[avnum].getWidth() + 1;
2214 // this relies on sann being preserved after we
2215 // modify the sequence's annotation array for each duplication
2216 for (int a = 0; a < sann.length; a++)
2218 AlignmentAnnotation newann = new AlignmentAnnotation(
2220 sequences[i].addAlignmentAnnotation(newann);
2221 newann.padAnnotation(avwidth);
2222 alview[avnum].addAnnotation(newann); // annotation was
2223 // duplicated earlier
2224 // TODO JAL-1145 graphGroups are not updated for sequence
2225 // annotation added to several views. This may cause
2227 alview[avnum].setAnnotationIndex(newann, a);
2232 buildSortByAnnotationScoresMenu();
2234 viewport.firePropertyChange("alignment", null,
2235 alignment.getSequences());
2236 if (alignPanels != null)
2238 for (AlignmentPanel ap : alignPanels)
2240 ap.validateAnnotationDimensions(false);
2245 alignPanel.validateAnnotationDimensions(false);
2251 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2253 String newtitle = new String("Copied sequences");
2255 if (Desktop.jalviewClipboard != null
2256 && Desktop.jalviewClipboard[2] != null)
2258 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2259 af.viewport.setHiddenColumns(hc);
2262 // >>>This is a fix for the moment, until a better solution is
2264 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2265 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2266 .getFeatureRenderer());
2268 // TODO: maintain provenance of an alignment, rather than just make the
2269 // title a concatenation of operations.
2272 if (title.startsWith("Copied sequences"))
2278 newtitle = newtitle.concat("- from " + title);
2283 newtitle = new String("Pasted sequences");
2286 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2291 } catch (Exception ex)
2293 ex.printStackTrace();
2294 System.out.println("Exception whilst pasting: " + ex);
2295 // could be anything being pasted in here
2301 protected void expand_newalign(ActionEvent e)
2305 AlignmentI alignment = AlignmentUtils
2306 .expandContext(getViewport().getAlignment(), -1);
2307 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2309 String newtitle = new String("Flanking alignment");
2311 if (Desktop.jalviewClipboard != null
2312 && Desktop.jalviewClipboard[2] != null)
2314 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2315 af.viewport.setHiddenColumns(hc);
2318 // >>>This is a fix for the moment, until a better solution is
2320 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2321 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2322 .getFeatureRenderer());
2324 // TODO: maintain provenance of an alignment, rather than just make the
2325 // title a concatenation of operations.
2327 if (title.startsWith("Copied sequences"))
2333 newtitle = newtitle.concat("- from " + title);
2337 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2339 } catch (Exception ex)
2341 ex.printStackTrace();
2342 System.out.println("Exception whilst pasting: " + ex);
2343 // could be anything being pasted in here
2344 } catch (OutOfMemoryError oom)
2346 new OOMWarning("Viewing flanking region of alignment", oom);
2357 protected void cut_actionPerformed(ActionEvent e)
2359 copy_actionPerformed(null);
2360 delete_actionPerformed(null);
2370 protected void delete_actionPerformed(ActionEvent evt)
2373 SequenceGroup sg = viewport.getSelectionGroup();
2380 * If the cut affects all sequences, warn, remove highlighted columns
2382 if (sg.getSize() == viewport.getAlignment().getHeight())
2384 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2385 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2386 if (isEntireAlignWidth)
2388 int confirm = JvOptionPane.showConfirmDialog(this,
2389 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2390 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2391 JvOptionPane.OK_CANCEL_OPTION);
2393 if (confirm == JvOptionPane.CANCEL_OPTION
2394 || confirm == JvOptionPane.CLOSED_OPTION)
2399 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2400 sg.getEndRes() + 1);
2402 SequenceI[] cut = sg.getSequences()
2403 .toArray(new SequenceI[sg.getSize()]);
2405 addHistoryItem(new EditCommand(
2406 MessageManager.getString("label.cut_sequences"), Action.CUT,
2407 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2408 viewport.getAlignment()));
2410 viewport.setSelectionGroup(null);
2411 viewport.sendSelection();
2412 viewport.getAlignment().deleteGroup(sg);
2414 viewport.firePropertyChange("alignment", null,
2415 viewport.getAlignment().getSequences());
2416 if (viewport.getAlignment().getHeight() < 1)
2420 this.setClosed(true);
2421 } catch (Exception ex)
2434 protected void deleteGroups_actionPerformed(ActionEvent e)
2436 if (avc.deleteGroups())
2438 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2439 alignPanel.updateAnnotation();
2440 alignPanel.paintAlignment(true, true);
2451 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2453 SequenceGroup sg = new SequenceGroup(
2454 viewport.getAlignment().getSequences());
2456 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2457 viewport.setSelectionGroup(sg);
2458 viewport.isSelectionGroupChanged(true);
2459 viewport.sendSelection();
2460 // JAL-2034 - should delegate to
2461 // alignPanel to decide if overview needs
2463 alignPanel.paintAlignment(false, false);
2464 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2474 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2476 if (viewport.cursorMode)
2478 alignPanel.getSeqPanel().keyboardNo1 = null;
2479 alignPanel.getSeqPanel().keyboardNo2 = null;
2481 viewport.setSelectionGroup(null);
2482 viewport.getColumnSelection().clear();
2483 viewport.setSearchResults(null);
2484 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2485 // JAL-2034 - should delegate to
2486 // alignPanel to decide if overview needs
2488 alignPanel.paintAlignment(false, false);
2489 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2490 viewport.sendSelection();
2500 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2502 SequenceGroup sg = viewport.getSelectionGroup();
2506 selectAllSequenceMenuItem_actionPerformed(null);
2511 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2513 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2515 // JAL-2034 - should delegate to
2516 // alignPanel to decide if overview needs
2519 alignPanel.paintAlignment(true, false);
2520 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2521 viewport.sendSelection();
2525 public void invertColSel_actionPerformed(ActionEvent e)
2527 viewport.invertColumnSelection();
2528 alignPanel.paintAlignment(true, false);
2529 viewport.sendSelection();
2539 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2541 trimAlignment(true);
2551 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2553 trimAlignment(false);
2556 void trimAlignment(boolean trimLeft)
2558 ColumnSelection colSel = viewport.getColumnSelection();
2561 if (!colSel.isEmpty())
2565 column = colSel.getMin();
2569 column = colSel.getMax();
2573 if (viewport.getSelectionGroup() != null)
2575 seqs = viewport.getSelectionGroup()
2576 .getSequencesAsArray(viewport.getHiddenRepSequences());
2580 seqs = viewport.getAlignment().getSequencesArray();
2583 TrimRegionCommand trimRegion;
2586 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2587 column, viewport.getAlignment());
2588 viewport.getRanges().setStartRes(0);
2592 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2593 column, viewport.getAlignment());
2596 statusBar.setText(MessageManager
2597 .formatMessage("label.removed_columns", new String[]
2598 { Integer.valueOf(trimRegion.getSize()).toString() }));
2600 addHistoryItem(trimRegion);
2602 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2604 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2605 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2607 viewport.getAlignment().deleteGroup(sg);
2611 viewport.firePropertyChange("alignment", null,
2612 viewport.getAlignment().getSequences());
2623 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2625 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2628 if (viewport.getSelectionGroup() != null)
2630 seqs = viewport.getSelectionGroup()
2631 .getSequencesAsArray(viewport.getHiddenRepSequences());
2632 start = viewport.getSelectionGroup().getStartRes();
2633 end = viewport.getSelectionGroup().getEndRes();
2637 seqs = viewport.getAlignment().getSequencesArray();
2640 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2641 "Remove Gapped Columns", seqs, start, end,
2642 viewport.getAlignment());
2644 addHistoryItem(removeGapCols);
2646 statusBar.setText(MessageManager
2647 .formatMessage("label.removed_empty_columns", new Object[]
2648 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2650 // This is to maintain viewport position on first residue
2651 // of first sequence
2652 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2653 ViewportRanges ranges = viewport.getRanges();
2654 int startRes = seq.findPosition(ranges.getStartRes());
2655 // ShiftList shifts;
2656 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2657 // edit.alColumnChanges=shifts.getInverse();
2658 // if (viewport.hasHiddenColumns)
2659 // viewport.getColumnSelection().compensateForEdits(shifts);
2660 ranges.setStartRes(seq.findIndex(startRes) - 1);
2661 viewport.firePropertyChange("alignment", null,
2662 viewport.getAlignment().getSequences());
2673 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2675 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2678 if (viewport.getSelectionGroup() != null)
2680 seqs = viewport.getSelectionGroup()
2681 .getSequencesAsArray(viewport.getHiddenRepSequences());
2682 start = viewport.getSelectionGroup().getStartRes();
2683 end = viewport.getSelectionGroup().getEndRes();
2687 seqs = viewport.getAlignment().getSequencesArray();
2690 // This is to maintain viewport position on first residue
2691 // of first sequence
2692 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2693 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2695 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2696 viewport.getAlignment()));
2698 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2700 viewport.firePropertyChange("alignment", null,
2701 viewport.getAlignment().getSequences());
2712 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2714 viewport.setPadGaps(padGapsMenuitem.isSelected());
2715 viewport.firePropertyChange("alignment", null,
2716 viewport.getAlignment().getSequences());
2726 public void findMenuItem_actionPerformed(ActionEvent e)
2732 * Create a new view of the current alignment.
2735 public void newView_actionPerformed(ActionEvent e)
2737 newView(null, true);
2741 * Creates and shows a new view of the current alignment.
2744 * title of newly created view; if null, one will be generated
2745 * @param copyAnnotation
2746 * if true then duplicate all annnotation, groups and settings
2747 * @return new alignment panel, already displayed.
2749 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2752 * Create a new AlignmentPanel (with its own, new Viewport)
2754 AlignmentPanel newap = new jalview.project.Jalview2XML()
2755 .copyAlignPanel(alignPanel);
2756 if (!copyAnnotation)
2759 * remove all groups and annotation except for the automatic stuff
2761 newap.av.getAlignment().deleteAllGroups();
2762 newap.av.getAlignment().deleteAllAnnotations(false);
2765 newap.av.setGatherViewsHere(false);
2767 if (viewport.getViewName() == null)
2769 viewport.setViewName(
2770 MessageManager.getString("label.view_name_original"));
2774 * Views share the same edits undo and redo stacks
2776 newap.av.setHistoryList(viewport.getHistoryList());
2777 newap.av.setRedoList(viewport.getRedoList());
2780 * copy any visualisation settings that are not saved in the project
2782 newap.av.setColourAppliesToAllGroups(
2783 viewport.getColourAppliesToAllGroups());
2786 * Views share the same mappings; need to deregister any new mappings
2787 * created by copyAlignPanel, and register the new reference to the shared
2790 newap.av.replaceMappings(viewport.getAlignment());
2793 * start up cDNA consensus (if applicable) now mappings are in place
2795 if (newap.av.initComplementConsensus())
2797 newap.refresh(true); // adjust layout of annotations
2800 newap.av.setViewName(getNewViewName(viewTitle));
2802 addAlignmentPanel(newap, true);
2803 newap.alignmentChanged();
2805 if (alignPanels.size() == 2)
2807 viewport.setGatherViewsHere(true);
2809 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2814 * Make a new name for the view, ensuring it is unique within the current
2815 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2816 * these now use viewId. Unique view names are still desirable for usability.)
2821 protected String getNewViewName(String viewTitle)
2823 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2824 boolean addFirstIndex = false;
2825 if (viewTitle == null || viewTitle.trim().length() == 0)
2827 viewTitle = MessageManager.getString("action.view");
2828 addFirstIndex = true;
2832 index = 1;// we count from 1 if given a specific name
2834 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2836 List<Component> comps = PaintRefresher.components
2837 .get(viewport.getSequenceSetId());
2839 List<String> existingNames = getExistingViewNames(comps);
2841 while (existingNames.contains(newViewName))
2843 newViewName = viewTitle + " " + (++index);
2849 * Returns a list of distinct view names found in the given list of
2850 * components. View names are held on the viewport of an AlignmentPanel.
2855 protected List<String> getExistingViewNames(List<Component> comps)
2857 List<String> existingNames = new ArrayList<>();
2858 for (Component comp : comps)
2860 if (comp instanceof AlignmentPanel)
2862 AlignmentPanel ap = (AlignmentPanel) comp;
2863 if (!existingNames.contains(ap.av.getViewName()))
2865 existingNames.add(ap.av.getViewName());
2869 return existingNames;
2873 * Explode tabbed views into separate windows.
2876 public void expandViews_actionPerformed(ActionEvent e)
2878 Desktop.explodeViews(this);
2882 * Gather views in separate windows back into a tabbed presentation.
2885 public void gatherViews_actionPerformed(ActionEvent e)
2887 Desktop.instance.gatherViews(this);
2897 public void font_actionPerformed(ActionEvent e)
2899 new FontChooser(alignPanel);
2909 protected void seqLimit_actionPerformed(ActionEvent e)
2911 viewport.setShowJVSuffix(seqLimits.isSelected());
2913 alignPanel.getIdPanel().getIdCanvas()
2914 .setPreferredSize(alignPanel.calculateIdWidth());
2915 alignPanel.paintAlignment(true, false);
2919 public void idRightAlign_actionPerformed(ActionEvent e)
2921 viewport.setRightAlignIds(idRightAlign.isSelected());
2922 alignPanel.paintAlignment(false, false);
2926 public void centreColumnLabels_actionPerformed(ActionEvent e)
2928 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2929 alignPanel.paintAlignment(false, false);
2935 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2938 protected void followHighlight_actionPerformed()
2941 * Set the 'follow' flag on the Viewport (and scroll to position if now
2944 final boolean state = this.followHighlightMenuItem.getState();
2945 viewport.setFollowHighlight(state);
2948 alignPanel.scrollToPosition(viewport.getSearchResults());
2959 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2961 viewport.setColourText(colourTextMenuItem.isSelected());
2962 alignPanel.paintAlignment(false, false);
2972 public void wrapMenuItem_actionPerformed(ActionEvent e)
2974 scaleAbove.setVisible(wrapMenuItem.isSelected());
2975 scaleLeft.setVisible(wrapMenuItem.isSelected());
2976 scaleRight.setVisible(wrapMenuItem.isSelected());
2977 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2978 alignPanel.updateLayout();
2982 public void showAllSeqs_actionPerformed(ActionEvent e)
2984 viewport.showAllHiddenSeqs();
2988 public void showAllColumns_actionPerformed(ActionEvent e)
2990 viewport.showAllHiddenColumns();
2991 alignPanel.paintAlignment(true, true);
2992 viewport.sendSelection();
2996 public void hideSelSequences_actionPerformed(ActionEvent e)
2998 viewport.hideAllSelectedSeqs();
3002 * called by key handler and the hide all/show all menu items
3007 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3010 boolean hide = false;
3011 SequenceGroup sg = viewport.getSelectionGroup();
3012 if (!toggleSeqs && !toggleCols)
3014 // Hide everything by the current selection - this is a hack - we do the
3015 // invert and then hide
3016 // first check that there will be visible columns after the invert.
3017 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3018 && sg.getStartRes() <= sg.getEndRes()))
3020 // now invert the sequence set, if required - empty selection implies
3021 // that no hiding is required.
3024 invertSequenceMenuItem_actionPerformed(null);
3025 sg = viewport.getSelectionGroup();
3029 viewport.expandColSelection(sg, true);
3030 // finally invert the column selection and get the new sequence
3032 invertColSel_actionPerformed(null);
3039 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3041 hideSelSequences_actionPerformed(null);
3044 else if (!(toggleCols && viewport.hasSelectedColumns()))
3046 showAllSeqs_actionPerformed(null);
3052 if (viewport.hasSelectedColumns())
3054 hideSelColumns_actionPerformed(null);
3057 viewport.setSelectionGroup(sg);
3062 showAllColumns_actionPerformed(null);
3071 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3072 * event.ActionEvent)
3075 public void hideAllButSelection_actionPerformed(ActionEvent e)
3077 toggleHiddenRegions(false, false);
3078 viewport.sendSelection();
3085 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3089 public void hideAllSelection_actionPerformed(ActionEvent e)
3091 SequenceGroup sg = viewport.getSelectionGroup();
3092 viewport.expandColSelection(sg, false);
3093 viewport.hideAllSelectedSeqs();
3094 viewport.hideSelectedColumns();
3095 alignPanel.updateLayout();
3096 alignPanel.paintAlignment(true, true);
3097 viewport.sendSelection();
3104 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3108 public void showAllhidden_actionPerformed(ActionEvent e)
3110 viewport.showAllHiddenColumns();
3111 viewport.showAllHiddenSeqs();
3112 alignPanel.paintAlignment(true, true);
3113 viewport.sendSelection();
3117 public void hideSelColumns_actionPerformed(ActionEvent e)
3119 viewport.hideSelectedColumns();
3120 alignPanel.updateLayout();
3121 alignPanel.paintAlignment(true, true);
3122 viewport.sendSelection();
3126 public void hiddenMarkers_actionPerformed(ActionEvent e)
3128 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3139 protected void scaleAbove_actionPerformed(ActionEvent e)
3141 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3142 alignPanel.updateLayout();
3143 alignPanel.paintAlignment(true, false);
3153 protected void scaleLeft_actionPerformed(ActionEvent e)
3155 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3156 alignPanel.updateLayout();
3157 alignPanel.paintAlignment(true, false);
3167 protected void scaleRight_actionPerformed(ActionEvent e)
3169 viewport.setScaleRightWrapped(scaleRight.isSelected());
3170 alignPanel.updateLayout();
3171 alignPanel.paintAlignment(true, false);
3181 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3183 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3184 alignPanel.paintAlignment(false, false);
3194 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3196 viewport.setShowText(viewTextMenuItem.isSelected());
3197 alignPanel.paintAlignment(false, false);
3207 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3209 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3210 alignPanel.paintAlignment(false, false);
3213 public FeatureSettings featureSettings;
3216 public FeatureSettingsControllerI getFeatureSettingsUI()
3218 return featureSettings;
3222 public void featureSettings_actionPerformed(ActionEvent e)
3224 showFeatureSettingsUI();
3228 public FeatureSettingsControllerI showFeatureSettingsUI()
3230 if (featureSettings != null)
3232 featureSettings.closeOldSettings();
3233 featureSettings = null;
3235 if (!showSeqFeatures.isSelected())
3237 // make sure features are actually displayed
3238 showSeqFeatures.setSelected(true);
3239 showSeqFeatures_actionPerformed(null);
3241 featureSettings = new FeatureSettings(this);
3242 return featureSettings;
3246 * Set or clear 'Show Sequence Features'
3252 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3254 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3255 alignPanel.paintAlignment(true, true);
3259 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3260 * the annotations panel as a whole.
3262 * The options to show/hide all annotations should be enabled when the panel
3263 * is shown, and disabled when the panel is hidden.
3268 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3270 final boolean setVisible = annotationPanelMenuItem.isSelected();
3271 viewport.setShowAnnotation(setVisible);
3272 this.showAllSeqAnnotations.setEnabled(setVisible);
3273 this.hideAllSeqAnnotations.setEnabled(setVisible);
3274 this.showAllAlAnnotations.setEnabled(setVisible);
3275 this.hideAllAlAnnotations.setEnabled(setVisible);
3276 alignPanel.updateLayout();
3280 public void alignmentProperties()
3282 JEditorPane editPane = new JEditorPane("text/html", "");
3283 editPane.setEditable(false);
3284 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3287 MessageManager.formatMessage("label.html_content", new Object[]
3288 { contents.toString() }));
3289 JInternalFrame frame = new JInternalFrame();
3290 frame.getContentPane().add(new JScrollPane(editPane));
3292 Desktop.addInternalFrame(frame, MessageManager
3293 .formatMessage("label.alignment_properties", new Object[]
3294 { getTitle() }), 500, 400);
3304 public void overviewMenuItem_actionPerformed(ActionEvent e)
3306 if (alignPanel.overviewPanel != null)
3311 JInternalFrame frame = new JInternalFrame();
3312 final OverviewPanel overview = new OverviewPanel(alignPanel);
3313 frame.setContentPane(overview);
3314 Desktop.addInternalFrame(frame, MessageManager
3315 .formatMessage("label.overview_params", new Object[]
3316 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3319 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3320 frame.addInternalFrameListener(
3321 new javax.swing.event.InternalFrameAdapter()
3324 public void internalFrameClosed(
3325 javax.swing.event.InternalFrameEvent evt)
3328 alignPanel.setOverviewPanel(null);
3331 if (getKeyListeners().length > 0)
3333 frame.addKeyListener(getKeyListeners()[0]);
3336 alignPanel.setOverviewPanel(overview);
3340 public void textColour_actionPerformed()
3342 new TextColourChooser().chooseColour(alignPanel, null);
3346 * public void covariationColour_actionPerformed() {
3348 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3352 public void annotationColour_actionPerformed()
3354 new AnnotationColourChooser(viewport, alignPanel);
3358 public void annotationColumn_actionPerformed(ActionEvent e)
3360 new AnnotationColumnChooser(viewport, alignPanel);
3364 * Action on the user checking or unchecking the option to apply the selected
3365 * colour scheme to all groups. If unchecked, groups may have their own
3366 * independent colour schemes.
3371 public void applyToAllGroups_actionPerformed(boolean selected)
3373 viewport.setColourAppliesToAllGroups(selected);
3377 * Action on user selecting a colour from the colour menu
3380 * the name (not the menu item label!) of the colour scheme
3383 public void changeColour_actionPerformed(String name)
3386 * 'User Defined' opens a panel to configure or load a
3387 * user-defined colour scheme
3389 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3391 new UserDefinedColours(alignPanel);
3396 * otherwise set the chosen colour scheme (or null for 'None')
3398 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3399 viewport, viewport.getAlignment(),
3400 viewport.getHiddenRepSequences());
3405 * Actions on setting or changing the alignment colour scheme
3410 public void changeColour(ColourSchemeI cs)
3412 // TODO: pull up to controller method
3413 ColourMenuHelper.setColourSelected(colourMenu, cs);
3415 viewport.setGlobalColourScheme(cs);
3417 alignPanel.paintAlignment(true, true);
3421 * Show the PID threshold slider panel
3424 protected void modifyPID_actionPerformed()
3426 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3427 alignPanel.getViewName());
3428 SliderPanel.showPIDSlider();
3432 * Show the Conservation slider panel
3435 protected void modifyConservation_actionPerformed()
3437 SliderPanel.setConservationSlider(alignPanel,
3438 viewport.getResidueShading(), alignPanel.getViewName());
3439 SliderPanel.showConservationSlider();
3443 * Action on selecting or deselecting (Colour) By Conservation
3446 public void conservationMenuItem_actionPerformed(boolean selected)
3448 modifyConservation.setEnabled(selected);
3449 viewport.setConservationSelected(selected);
3450 viewport.getResidueShading().setConservationApplied(selected);
3452 changeColour(viewport.getGlobalColourScheme());
3455 modifyConservation_actionPerformed();
3459 SliderPanel.hideConservationSlider();
3464 * Action on selecting or deselecting (Colour) Above PID Threshold
3467 public void abovePIDThreshold_actionPerformed(boolean selected)
3469 modifyPID.setEnabled(selected);
3470 viewport.setAbovePIDThreshold(selected);
3473 viewport.getResidueShading().setThreshold(0,
3474 viewport.isIgnoreGapsConsensus());
3477 changeColour(viewport.getGlobalColourScheme());
3480 modifyPID_actionPerformed();
3484 SliderPanel.hidePIDSlider();
3495 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3497 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3498 AlignmentSorter.sortByPID(viewport.getAlignment(),
3499 viewport.getAlignment().getSequenceAt(0));
3500 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3501 viewport.getAlignment()));
3502 alignPanel.paintAlignment(true, false);
3512 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3514 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3515 AlignmentSorter.sortByID(viewport.getAlignment());
3517 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3518 alignPanel.paintAlignment(true, false);
3528 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3530 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3531 AlignmentSorter.sortByLength(viewport.getAlignment());
3532 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3533 viewport.getAlignment()));
3534 alignPanel.paintAlignment(true, false);
3544 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3546 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3547 AlignmentSorter.sortByGroup(viewport.getAlignment());
3548 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3549 viewport.getAlignment()));
3551 alignPanel.paintAlignment(true, false);
3561 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3563 new RedundancyPanel(alignPanel, this);
3573 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3575 if ((viewport.getSelectionGroup() == null)
3576 || (viewport.getSelectionGroup().getSize() < 2))
3578 JvOptionPane.showInternalMessageDialog(this,
3579 MessageManager.getString(
3580 "label.you_must_select_least_two_sequences"),
3581 MessageManager.getString("label.invalid_selection"),
3582 JvOptionPane.WARNING_MESSAGE);
3586 JInternalFrame frame = new JInternalFrame();
3587 frame.setContentPane(new PairwiseAlignPanel(viewport));
3588 Desktop.addInternalFrame(frame,
3589 MessageManager.getString("action.pairwise_alignment"), 600,
3595 public void autoCalculate_actionPerformed(ActionEvent e)
3597 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3598 if (viewport.autoCalculateConsensus)
3600 viewport.firePropertyChange("alignment", null,
3601 viewport.getAlignment().getSequences());
3606 public void sortByTreeOption_actionPerformed(ActionEvent e)
3608 viewport.sortByTree = sortByTree.isSelected();
3612 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3614 viewport.followSelection = listenToViewSelections.isSelected();
3618 * Constructs a tree panel and adds it to the desktop
3621 * tree type (NJ or AV)
3623 * name of score model used to compute the tree
3625 * parameters for the distance or similarity calculation
3627 void newTreePanel(String type, String modelName,
3628 SimilarityParamsI options)
3630 String frameTitle = "";
3633 boolean onSelection = false;
3634 if (viewport.getSelectionGroup() != null
3635 && viewport.getSelectionGroup().getSize() > 0)
3637 SequenceGroup sg = viewport.getSelectionGroup();
3639 /* Decide if the selection is a column region */
3640 for (SequenceI _s : sg.getSequences())
3642 if (_s.getLength() < sg.getEndRes())
3644 JvOptionPane.showMessageDialog(Desktop.desktop,
3645 MessageManager.getString(
3646 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3647 MessageManager.getString(
3648 "label.sequences_selection_not_aligned"),
3649 JvOptionPane.WARNING_MESSAGE);
3658 if (viewport.getAlignment().getHeight() < 2)
3664 tp = new TreePanel(alignPanel, type, modelName, options);
3665 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3667 frameTitle += " from ";
3669 if (viewport.getViewName() != null)
3671 frameTitle += viewport.getViewName() + " of ";
3674 frameTitle += this.title;
3676 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3687 public void addSortByOrderMenuItem(String title,
3688 final AlignmentOrder order)
3690 final JMenuItem item = new JMenuItem(MessageManager
3691 .formatMessage("action.by_title_param", new Object[]
3694 item.addActionListener(new java.awt.event.ActionListener()
3697 public void actionPerformed(ActionEvent e)
3699 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3701 // TODO: JBPNote - have to map order entries to curent SequenceI
3703 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3705 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3706 viewport.getAlignment()));
3708 alignPanel.paintAlignment(true, false);
3714 * Add a new sort by annotation score menu item
3717 * the menu to add the option to
3719 * the label used to retrieve scores for each sequence on the
3722 public void addSortByAnnotScoreMenuItem(JMenu sort,
3723 final String scoreLabel)
3725 final JMenuItem item = new JMenuItem(scoreLabel);
3727 item.addActionListener(new java.awt.event.ActionListener()
3730 public void actionPerformed(ActionEvent e)
3732 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3733 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3734 viewport.getAlignment());// ,viewport.getSelectionGroup());
3735 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3736 viewport.getAlignment()));
3737 alignPanel.paintAlignment(true, false);
3743 * last hash for alignment's annotation array - used to minimise cost of
3746 protected int _annotationScoreVectorHash;
3749 * search the alignment and rebuild the sort by annotation score submenu the
3750 * last alignment annotation vector hash is stored to minimize cost of
3751 * rebuilding in subsequence calls.
3755 public void buildSortByAnnotationScoresMenu()
3757 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3762 if (viewport.getAlignment().getAlignmentAnnotation()
3763 .hashCode() != _annotationScoreVectorHash)
3765 sortByAnnotScore.removeAll();
3766 // almost certainly a quicker way to do this - but we keep it simple
3767 Hashtable scoreSorts = new Hashtable();
3768 AlignmentAnnotation aann[];
3769 for (SequenceI sqa : viewport.getAlignment().getSequences())
3771 aann = sqa.getAnnotation();
3772 for (int i = 0; aann != null && i < aann.length; i++)
3774 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3776 scoreSorts.put(aann[i].label, aann[i].label);
3780 Enumeration labels = scoreSorts.keys();
3781 while (labels.hasMoreElements())
3783 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3784 (String) labels.nextElement());
3786 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3789 _annotationScoreVectorHash = viewport.getAlignment()
3790 .getAlignmentAnnotation().hashCode();
3795 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3796 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3797 * call. Listeners are added to remove the menu item when the treePanel is
3798 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3802 public void buildTreeSortMenu()
3804 sortByTreeMenu.removeAll();
3806 List<Component> comps = PaintRefresher.components
3807 .get(viewport.getSequenceSetId());
3808 List<TreePanel> treePanels = new ArrayList<>();
3809 for (Component comp : comps)
3811 if (comp instanceof TreePanel)
3813 treePanels.add((TreePanel) comp);
3817 if (treePanels.size() < 1)
3819 sortByTreeMenu.setVisible(false);
3823 sortByTreeMenu.setVisible(true);
3825 for (final TreePanel tp : treePanels)
3827 final JMenuItem item = new JMenuItem(tp.getTitle());
3828 item.addActionListener(new java.awt.event.ActionListener()
3831 public void actionPerformed(ActionEvent e)
3833 tp.sortByTree_actionPerformed();
3834 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3839 sortByTreeMenu.add(item);
3843 public boolean sortBy(AlignmentOrder alorder, String undoname)
3845 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3846 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3847 if (undoname != null)
3849 addHistoryItem(new OrderCommand(undoname, oldOrder,
3850 viewport.getAlignment()));
3852 alignPanel.paintAlignment(true, false);
3857 * Work out whether the whole set of sequences or just the selected set will
3858 * be submitted for multiple alignment.
3861 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3863 // Now, check we have enough sequences
3864 AlignmentView msa = null;
3866 if ((viewport.getSelectionGroup() != null)
3867 && (viewport.getSelectionGroup().getSize() > 1))
3869 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3870 // some common interface!
3872 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3873 * SequenceI[sz = seqs.getSize(false)];
3875 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3876 * seqs.getSequenceAt(i); }
3878 msa = viewport.getAlignmentView(true);
3880 else if (viewport.getSelectionGroup() != null
3881 && viewport.getSelectionGroup().getSize() == 1)
3883 int option = JvOptionPane.showConfirmDialog(this,
3884 MessageManager.getString("warn.oneseq_msainput_selection"),
3885 MessageManager.getString("label.invalid_selection"),
3886 JvOptionPane.OK_CANCEL_OPTION);
3887 if (option == JvOptionPane.OK_OPTION)
3889 msa = viewport.getAlignmentView(false);
3894 msa = viewport.getAlignmentView(false);
3900 * Decides what is submitted to a secondary structure prediction service: the
3901 * first sequence in the alignment, or in the current selection, or, if the
3902 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3903 * region or the whole alignment. (where the first sequence in the set is the
3904 * one that the prediction will be for).
3906 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3908 AlignmentView seqs = null;
3910 if ((viewport.getSelectionGroup() != null)
3911 && (viewport.getSelectionGroup().getSize() > 0))
3913 seqs = viewport.getAlignmentView(true);
3917 seqs = viewport.getAlignmentView(false);
3919 // limit sequences - JBPNote in future - could spawn multiple prediction
3921 // TODO: viewport.getAlignment().isAligned is a global state - the local
3922 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3923 if (!viewport.getAlignment().isAligned(false))
3925 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3926 // TODO: if seqs.getSequences().length>1 then should really have warned
3940 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3942 // Pick the tree file
3943 JalviewFileChooser chooser = new JalviewFileChooser(
3944 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3945 chooser.setFileView(new JalviewFileView());
3946 chooser.setDialogTitle(
3947 MessageManager.getString("label.select_newick_like_tree_file"));
3948 chooser.setToolTipText(
3949 MessageManager.getString("label.load_tree_file"));
3951 int value = chooser.showOpenDialog(null);
3953 if (value == JalviewFileChooser.APPROVE_OPTION)
3955 String filePath = chooser.getSelectedFile().getPath();
3956 Cache.setProperty("LAST_DIRECTORY", filePath);
3957 NewickFile fin = null;
3960 fin = new NewickFile(filePath, DataSourceType.FILE);
3961 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3962 } catch (Exception ex)
3964 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3965 MessageManager.getString("label.problem_reading_tree_file"),
3966 JvOptionPane.WARNING_MESSAGE);
3967 ex.printStackTrace();
3969 if (fin != null && fin.hasWarningMessage())
3971 JvOptionPane.showMessageDialog(Desktop.desktop,
3972 fin.getWarningMessage(),
3974 .getString("label.possible_problem_with_tree_file"),
3975 JvOptionPane.WARNING_MESSAGE);
3980 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3982 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3985 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3986 int h, int x, int y)
3988 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3992 * Add a treeviewer for the tree extracted from a Newick file object to the
3993 * current alignment view
4000 * Associated alignment input data (or null)
4009 * @return TreePanel handle
4011 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4012 AlignmentView input, int w, int h, int x, int y)
4014 TreePanel tp = null;
4020 if (nf.getTree() != null)
4022 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4028 tp.setLocation(x, y);
4031 Desktop.addInternalFrame(tp, treeTitle, w, h);
4033 } catch (Exception ex)
4035 ex.printStackTrace();
4041 private boolean buildingMenu = false;
4044 * Generates menu items and listener event actions for web service clients
4047 public void BuildWebServiceMenu()
4049 while (buildingMenu)
4053 System.err.println("Waiting for building menu to finish.");
4055 } catch (Exception e)
4059 final AlignFrame me = this;
4060 buildingMenu = true;
4061 new Thread(new Runnable()
4066 final List<JMenuItem> legacyItems = new ArrayList<>();
4069 // System.err.println("Building ws menu again "
4070 // + Thread.currentThread());
4071 // TODO: add support for context dependent disabling of services based
4073 // alignment and current selection
4074 // TODO: add additional serviceHandle parameter to specify abstract
4076 // class independently of AbstractName
4077 // TODO: add in rediscovery GUI function to restart discoverer
4078 // TODO: group services by location as well as function and/or
4080 // object broker mechanism.
4081 final Vector<JMenu> wsmenu = new Vector<>();
4082 final IProgressIndicator af = me;
4085 * do not i18n these strings - they are hard-coded in class
4086 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4087 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4089 final JMenu msawsmenu = new JMenu("Alignment");
4090 final JMenu secstrmenu = new JMenu(
4091 "Secondary Structure Prediction");
4092 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4093 final JMenu analymenu = new JMenu("Analysis");
4094 final JMenu dismenu = new JMenu("Protein Disorder");
4095 // JAL-940 - only show secondary structure prediction services from
4096 // the legacy server
4097 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4099 Discoverer.services != null && (Discoverer.services.size() > 0))
4101 // TODO: refactor to allow list of AbstractName/Handler bindings to
4103 // stored or retrieved from elsewhere
4104 // No MSAWS used any more:
4105 // Vector msaws = null; // (Vector)
4106 // Discoverer.services.get("MsaWS");
4107 Vector secstrpr = (Vector) Discoverer.services
4109 if (secstrpr != null)
4111 // Add any secondary structure prediction services
4112 for (int i = 0, j = secstrpr.size(); i < j; i++)
4114 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4116 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4117 .getServiceClient(sh);
4118 int p = secstrmenu.getItemCount();
4119 impl.attachWSMenuEntry(secstrmenu, me);
4120 int q = secstrmenu.getItemCount();
4121 for (int litm = p; litm < q; litm++)
4123 legacyItems.add(secstrmenu.getItem(litm));
4129 // Add all submenus in the order they should appear on the web
4131 wsmenu.add(msawsmenu);
4132 wsmenu.add(secstrmenu);
4133 wsmenu.add(dismenu);
4134 wsmenu.add(analymenu);
4135 // No search services yet
4136 // wsmenu.add(seqsrchmenu);
4138 javax.swing.SwingUtilities.invokeLater(new Runnable()
4145 webService.removeAll();
4146 // first, add discovered services onto the webservices menu
4147 if (wsmenu.size() > 0)
4149 for (int i = 0, j = wsmenu.size(); i < j; i++)
4151 webService.add(wsmenu.get(i));
4156 webService.add(me.webServiceNoServices);
4158 // TODO: move into separate menu builder class.
4159 boolean new_sspred = false;
4160 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4162 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4163 if (jws2servs != null)
4165 if (jws2servs.hasServices())
4167 jws2servs.attachWSMenuEntry(webService, me);
4168 for (Jws2Instance sv : jws2servs.getServices())
4170 if (sv.description.toLowerCase().contains("jpred"))
4172 for (JMenuItem jmi : legacyItems)
4174 jmi.setVisible(false);
4180 if (jws2servs.isRunning())
4182 JMenuItem tm = new JMenuItem(
4183 "Still discovering JABA Services");
4184 tm.setEnabled(false);
4189 build_urlServiceMenu(me.webService);
4190 build_fetchdbmenu(webService);
4191 for (JMenu item : wsmenu)
4193 if (item.getItemCount() == 0)
4195 item.setEnabled(false);
4199 item.setEnabled(true);
4202 } catch (Exception e)
4205 "Exception during web service menu building process.",
4210 } catch (Exception e)
4213 buildingMenu = false;
4220 * construct any groupURL type service menu entries.
4224 private void build_urlServiceMenu(JMenu webService)
4226 // TODO: remove this code when 2.7 is released
4227 // DEBUG - alignmentView
4229 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4230 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4232 * @Override public void actionPerformed(ActionEvent e) {
4233 * jalview.datamodel.AlignmentView
4234 * .testSelectionViews(af.viewport.getAlignment(),
4235 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4237 * }); webService.add(testAlView);
4239 // TODO: refactor to RestClient discoverer and merge menu entries for
4240 // rest-style services with other types of analysis/calculation service
4241 // SHmmr test client - still being implemented.
4242 // DEBUG - alignmentView
4244 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4247 client.attachWSMenuEntry(
4248 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4254 * Searches the alignment sequences for xRefs and builds the Show
4255 * Cross-References menu (formerly called Show Products), with database
4256 * sources for which cross-references are found (protein sources for a
4257 * nucleotide alignment and vice versa)
4259 * @return true if Show Cross-references menu should be enabled
4261 public boolean canShowProducts()
4263 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4264 AlignmentI dataset = viewport.getAlignment().getDataset();
4266 showProducts.removeAll();
4267 final boolean dna = viewport.getAlignment().isNucleotide();
4269 if (seqs == null || seqs.length == 0)
4271 // nothing to see here.
4275 boolean showp = false;
4278 List<String> ptypes = new CrossRef(seqs, dataset)
4279 .findXrefSourcesForSequences(dna);
4281 for (final String source : ptypes)
4284 final AlignFrame af = this;
4285 JMenuItem xtype = new JMenuItem(source);
4286 xtype.addActionListener(new ActionListener()
4289 public void actionPerformed(ActionEvent e)
4291 showProductsFor(af.viewport.getSequenceSelection(), dna,
4295 showProducts.add(xtype);
4297 showProducts.setVisible(showp);
4298 showProducts.setEnabled(showp);
4299 } catch (Exception e)
4302 "canShowProducts threw an exception - please report to help@jalview.org",
4310 * Finds and displays cross-references for the selected sequences (protein
4311 * products for nucleotide sequences, dna coding sequences for peptides).
4314 * the sequences to show cross-references for
4316 * true if from a nucleotide alignment (so showing proteins)
4318 * the database to show cross-references for
4320 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4321 final String source)
4323 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4328 * Construct and display a new frame containing the translation of this
4329 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4332 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4334 AlignmentI al = null;
4337 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4339 al = dna.translateCdna(codeTable);
4340 } catch (Exception ex)
4342 jalview.bin.Cache.log.error(
4343 "Exception during translation. Please report this !", ex);
4344 final String msg = MessageManager.getString(
4345 "label.error_when_translating_sequences_submit_bug_report");
4346 final String errorTitle = MessageManager
4347 .getString("label.implementation_error")
4348 + MessageManager.getString("label.translation_failed");
4349 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4350 JvOptionPane.ERROR_MESSAGE);
4353 if (al == null || al.getHeight() == 0)
4355 final String msg = MessageManager.getString(
4356 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4357 final String errorTitle = MessageManager
4358 .getString("label.translation_failed");
4359 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4360 JvOptionPane.WARNING_MESSAGE);
4364 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4365 af.setFileFormat(this.currentFileFormat);
4366 final String newTitle = MessageManager
4367 .formatMessage("label.translation_of_params", new Object[]
4368 { this.getTitle(), codeTable.getId() });
4369 af.setTitle(newTitle);
4370 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4372 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4373 viewport.openSplitFrame(af, new Alignment(seqs));
4377 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4384 * Set the file format
4388 public void setFileFormat(FileFormatI format)
4390 this.currentFileFormat = format;
4394 * Try to load a features file onto the alignment.
4397 * contents or path to retrieve file
4399 * access mode of file (see jalview.io.AlignFile)
4400 * @return true if features file was parsed correctly.
4402 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4404 return avc.parseFeaturesFile(file, sourceType,
4405 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4410 public void refreshFeatureUI(boolean enableIfNecessary)
4412 // note - currently this is only still here rather than in the controller
4413 // because of the featureSettings hard reference that is yet to be
4415 if (enableIfNecessary)
4417 viewport.setShowSequenceFeatures(true);
4418 showSeqFeatures.setSelected(true);
4424 public void dragEnter(DropTargetDragEvent evt)
4429 public void dragExit(DropTargetEvent evt)
4434 public void dragOver(DropTargetDragEvent evt)
4439 public void dropActionChanged(DropTargetDragEvent evt)
4444 public void drop(DropTargetDropEvent evt)
4446 // JAL-1552 - acceptDrop required before getTransferable call for
4447 // Java's Transferable for native dnd
4448 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4449 Transferable t = evt.getTransferable();
4450 final AlignFrame thisaf = this;
4451 final List<String> files = new ArrayList<>();
4452 List<DataSourceType> protocols = new ArrayList<>();
4456 Desktop.transferFromDropTarget(files, protocols, evt, t);
4457 } catch (Exception e)
4459 e.printStackTrace();
4463 new Thread(new Runnable()
4470 // check to see if any of these files have names matching sequences
4473 SequenceIdMatcher idm = new SequenceIdMatcher(
4474 viewport.getAlignment().getSequencesArray());
4476 * Object[] { String,SequenceI}
4478 ArrayList<Object[]> filesmatched = new ArrayList<>();
4479 ArrayList<String> filesnotmatched = new ArrayList<>();
4480 for (int i = 0; i < files.size(); i++)
4482 String file = files.get(i).toString();
4484 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4485 if (protocol == DataSourceType.FILE)
4487 File fl = new File(file);
4488 pdbfn = fl.getName();
4490 else if (protocol == DataSourceType.URL)
4492 URL url = new URL(file);
4493 pdbfn = url.getFile();
4495 if (pdbfn.length() > 0)
4497 // attempt to find a match in the alignment
4498 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4499 int l = 0, c = pdbfn.indexOf(".");
4500 while (mtch == null && c != -1)
4505 } while ((c = pdbfn.indexOf(".", l)) > l);
4508 pdbfn = pdbfn.substring(0, l);
4510 mtch = idm.findAllIdMatches(pdbfn);
4514 FileFormatI type = null;
4517 type = new IdentifyFile().identify(file, protocol);
4518 } catch (Exception ex)
4522 if (type != null && type.isStructureFile())
4524 filesmatched.add(new Object[] { file, protocol, mtch });
4528 // File wasn't named like one of the sequences or wasn't a PDB
4530 filesnotmatched.add(file);
4534 if (filesmatched.size() > 0)
4536 boolean autoAssociate = Cache
4537 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4540 String msg = MessageManager.formatMessage(
4541 "label.automatically_associate_structure_files_with_sequences_same_name",
4543 { Integer.valueOf(filesmatched.size())
4545 String ttl = MessageManager.getString(
4546 "label.automatically_associate_structure_files_by_name");
4547 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4548 ttl, JvOptionPane.YES_NO_OPTION);
4549 autoAssociate = choice == JvOptionPane.YES_OPTION;
4553 for (Object[] fm : filesmatched)
4555 // try and associate
4556 // TODO: may want to set a standard ID naming formalism for
4557 // associating PDB files which have no IDs.
4558 for (SequenceI toassoc : (SequenceI[]) fm[2])
4560 PDBEntry pe = new AssociatePdbFileWithSeq()
4561 .associatePdbWithSeq((String) fm[0],
4562 (DataSourceType) fm[1], toassoc, false,
4566 System.err.println("Associated file : "
4567 + ((String) fm[0]) + " with "
4568 + toassoc.getDisplayId(true));
4572 // TODO: do we need to update overview ? only if features are
4574 alignPanel.paintAlignment(true, false);
4580 * add declined structures as sequences
4582 for (Object[] o : filesmatched)
4584 filesnotmatched.add((String) o[0]);
4588 if (filesnotmatched.size() > 0)
4590 if (assocfiles > 0 && (Cache.getDefault(
4591 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4592 || JvOptionPane.showConfirmDialog(thisaf,
4593 "<html>" + MessageManager.formatMessage(
4594 "label.ignore_unmatched_dropped_files_info",
4597 filesnotmatched.size())
4600 MessageManager.getString(
4601 "label.ignore_unmatched_dropped_files"),
4602 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4606 for (String fn : filesnotmatched)
4608 loadJalviewDataFile(fn, null, null, null);
4612 } catch (Exception ex)
4614 ex.printStackTrace();
4622 * Attempt to load a "dropped" file or URL string, by testing in turn for
4624 * <li>an Annotation file</li>
4625 * <li>a JNet file</li>
4626 * <li>a features file</li>
4627 * <li>else try to interpret as an alignment file</li>
4631 * either a filename or a URL string.
4633 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4634 FileFormatI format, SequenceI assocSeq)
4638 if (sourceType == null)
4640 sourceType = FormatAdapter.checkProtocol(file);
4642 // if the file isn't identified, or not positively identified as some
4643 // other filetype (PFAM is default unidentified alignment file type) then
4644 // try to parse as annotation.
4645 boolean isAnnotation = (format == null
4646 || FileFormat.Pfam.equals(format))
4647 ? new AnnotationFile().annotateAlignmentView(viewport,
4653 // first see if its a T-COFFEE score file
4654 TCoffeeScoreFile tcf = null;
4657 tcf = new TCoffeeScoreFile(file, sourceType);
4660 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4664 new TCoffeeColourScheme(viewport.getAlignment()));
4665 isAnnotation = true;
4666 statusBar.setText(MessageManager.getString(
4667 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4671 // some problem - if no warning its probable that the ID matching
4672 // process didn't work
4673 JvOptionPane.showMessageDialog(Desktop.desktop,
4674 tcf.getWarningMessage() == null
4675 ? MessageManager.getString(
4676 "label.check_file_matches_sequence_ids_alignment")
4677 : tcf.getWarningMessage(),
4678 MessageManager.getString(
4679 "label.problem_reading_tcoffee_score_file"),
4680 JvOptionPane.WARNING_MESSAGE);
4687 } catch (Exception x)
4690 "Exception when processing data source as T-COFFEE score file",
4696 // try to see if its a JNet 'concise' style annotation file *before*
4698 // try to parse it as a features file
4701 format = new IdentifyFile().identify(file, sourceType);
4703 if (FileFormat.ScoreMatrix == format)
4705 ScoreMatrixFile sm = new ScoreMatrixFile(
4706 new FileParse(file, sourceType));
4708 // todo: i18n this message
4709 statusBar.setText(MessageManager.formatMessage(
4710 "label.successfully_loaded_matrix",
4711 sm.getMatrixName()));
4713 else if (FileFormat.Jnet.equals(format))
4715 JPredFile predictions = new JPredFile(file, sourceType);
4716 new JnetAnnotationMaker();
4717 JnetAnnotationMaker.add_annotation(predictions,
4718 viewport.getAlignment(), 0, false);
4719 viewport.getAlignment().setupJPredAlignment();
4720 isAnnotation = true;
4722 // else if (IdentifyFile.FeaturesFile.equals(format))
4723 else if (FileFormat.Features.equals(format))
4725 if (parseFeaturesFile(file, sourceType))
4727 SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4728 if (splitFrame != null)
4730 splitFrame.repaint();
4734 alignPanel.paintAlignment(true, true);
4740 new FileLoader().LoadFile(viewport, file, sourceType, format);
4747 alignPanel.adjustAnnotationHeight();
4748 viewport.updateSequenceIdColours();
4749 buildSortByAnnotationScoresMenu();
4750 alignPanel.paintAlignment(true, true);
4752 } catch (Exception ex)
4754 ex.printStackTrace();
4755 } catch (OutOfMemoryError oom)
4760 } catch (Exception x)
4765 + (sourceType != null
4766 ? (sourceType == DataSourceType.PASTE
4768 : "using " + sourceType + " from "
4772 ? "(parsing as '" + format + "' file)"
4774 oom, Desktop.desktop);
4779 * Method invoked by the ChangeListener on the tabbed pane, in other words
4780 * when a different tabbed pane is selected by the user or programmatically.
4783 public void tabSelectionChanged(int index)
4787 alignPanel = alignPanels.get(index);
4788 viewport = alignPanel.av;
4789 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4790 setMenusFromViewport(viewport);
4791 if (featureSettings != null && featureSettings.isOpen()
4792 && featureSettings.fr.getViewport() != viewport)
4794 if (viewport.isShowSequenceFeatures())
4796 // refresh the featureSettings to reflect UI change
4797 showFeatureSettingsUI();
4801 // close feature settings for this view.
4802 featureSettings.close();
4809 * 'focus' any colour slider that is open to the selected viewport
4811 if (viewport.getConservationSelected())
4813 SliderPanel.setConservationSlider(alignPanel,
4814 viewport.getResidueShading(), alignPanel.getViewName());
4818 SliderPanel.hideConservationSlider();
4820 if (viewport.getAbovePIDThreshold())
4822 SliderPanel.setPIDSliderSource(alignPanel,
4823 viewport.getResidueShading(), alignPanel.getViewName());
4827 SliderPanel.hidePIDSlider();
4831 * If there is a frame linked to this one in a SplitPane, switch it to the
4832 * same view tab index. No infinite recursion of calls should happen, since
4833 * tabSelectionChanged() should not get invoked on setting the selected
4834 * index to an unchanged value. Guard against setting an invalid index
4835 * before the new view peer tab has been created.
4837 final AlignViewportI peer = viewport.getCodingComplement();
4840 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4841 .getAlignPanel().alignFrame;
4842 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4844 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4850 * On right mouse click on view tab, prompt for and set new view name.
4853 public void tabbedPane_mousePressed(MouseEvent e)
4855 if (e.isPopupTrigger())
4857 String msg = MessageManager.getString("label.enter_view_name");
4858 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4859 JvOptionPane.QUESTION_MESSAGE);
4863 viewport.setViewName(reply);
4864 // TODO warn if reply is in getExistingViewNames()?
4865 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4870 public AlignViewport getCurrentView()
4876 * Open the dialog for regex description parsing.
4879 protected void extractScores_actionPerformed(ActionEvent e)
4881 ParseProperties pp = new jalview.analysis.ParseProperties(
4882 viewport.getAlignment());
4883 // TODO: verify regex and introduce GUI dialog for version 2.5
4884 // if (pp.getScoresFromDescription("col", "score column ",
4885 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4887 if (pp.getScoresFromDescription("description column",
4888 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4890 buildSortByAnnotationScoresMenu();
4898 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4902 protected void showDbRefs_actionPerformed(ActionEvent e)
4904 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4910 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4914 protected void showNpFeats_actionPerformed(ActionEvent e)
4916 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4920 * find the viewport amongst the tabs in this alignment frame and close that
4925 public boolean closeView(AlignViewportI av)
4929 this.closeMenuItem_actionPerformed(false);
4932 Component[] comp = tabbedPane.getComponents();
4933 for (int i = 0; comp != null && i < comp.length; i++)
4935 if (comp[i] instanceof AlignmentPanel)
4937 if (((AlignmentPanel) comp[i]).av == av)
4940 closeView((AlignmentPanel) comp[i]);
4948 protected void build_fetchdbmenu(JMenu webService)
4950 // Temporary hack - DBRef Fetcher always top level ws entry.
4951 // TODO We probably want to store a sequence database checklist in
4952 // preferences and have checkboxes.. rather than individual sources selected
4954 final JMenu rfetch = new JMenu(
4955 MessageManager.getString("action.fetch_db_references"));
4956 rfetch.setToolTipText(MessageManager.getString(
4957 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4958 webService.add(rfetch);
4960 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4961 MessageManager.getString("option.trim_retrieved_seqs"));
4962 trimrs.setToolTipText(
4963 MessageManager.getString("label.trim_retrieved_sequences"));
4965 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4966 trimrs.addActionListener(new ActionListener()
4969 public void actionPerformed(ActionEvent e)
4971 trimrs.setSelected(trimrs.isSelected());
4972 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4973 Boolean.valueOf(trimrs.isSelected()).toString());
4977 JMenuItem fetchr = new JMenuItem(
4978 MessageManager.getString("label.standard_databases"));
4979 fetchr.setToolTipText(
4980 MessageManager.getString("label.fetch_embl_uniprot"));
4981 fetchr.addActionListener(new ActionListener()
4985 public void actionPerformed(ActionEvent e)
4987 new Thread(new Runnable()
4992 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4993 .getAlignment().isNucleotide();
4994 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4995 alignPanel.av.getSequenceSelection(),
4996 alignPanel.alignFrame, null,
4997 alignPanel.alignFrame.featureSettings, isNucleotide);
4998 dbRefFetcher.addListener(new FetchFinishedListenerI()
5001 public void finished()
5004 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5005 .getFeatureSettingsModels())
5008 alignPanel.av.mergeFeaturesStyle(srcSettings);
5010 AlignFrame.this.setMenusForViewport();
5013 dbRefFetcher.fetchDBRefs(false);
5021 final AlignFrame me = this;
5022 new Thread(new Runnable()
5027 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5028 .getSequenceFetcherSingleton(me);
5029 javax.swing.SwingUtilities.invokeLater(new Runnable()
5034 String[] dbclasses = sf.getOrderedSupportedSources();
5035 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5036 // jalview.util.QuickSort.sort(otherdb, otherdb);
5037 List<DbSourceProxy> otherdb;
5038 JMenu dfetch = new JMenu();
5039 JMenu ifetch = new JMenu();
5040 JMenuItem fetchr = null;
5041 int comp = 0, icomp = 0, mcomp = 15;
5042 String mname = null;
5044 for (String dbclass : dbclasses)
5046 otherdb = sf.getSourceProxy(dbclass);
5047 // add a single entry for this class, or submenu allowing 'fetch
5049 if (otherdb == null || otherdb.size() < 1)
5053 // List<DbSourceProxy> dbs=otherdb;
5054 // otherdb=new ArrayList<DbSourceProxy>();
5055 // for (DbSourceProxy db:dbs)
5057 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5061 mname = "From " + dbclass;
5063 if (otherdb.size() == 1)
5065 final DbSourceProxy[] dassource = otherdb
5066 .toArray(new DbSourceProxy[0]);
5067 DbSourceProxy src = otherdb.get(0);
5068 fetchr = new JMenuItem(src.getDbSource());
5069 fetchr.addActionListener(new ActionListener()
5073 public void actionPerformed(ActionEvent e)
5075 new Thread(new Runnable()
5081 boolean isNucleotide = alignPanel.alignFrame
5082 .getViewport().getAlignment()
5084 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5085 alignPanel.av.getSequenceSelection(),
5086 alignPanel.alignFrame, dassource,
5087 alignPanel.alignFrame.featureSettings,
5090 .addListener(new FetchFinishedListenerI()
5093 public void finished()
5095 FeatureSettingsModelI srcSettings = dassource[0]
5096 .getFeatureColourScheme();
5097 alignPanel.av.mergeFeaturesStyle(
5099 AlignFrame.this.setMenusForViewport();
5102 dbRefFetcher.fetchDBRefs(false);
5108 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5109 MessageManager.formatMessage(
5110 "label.fetch_retrieve_from", new Object[]
5111 { src.getDbName() })));
5117 final DbSourceProxy[] dassource = otherdb
5118 .toArray(new DbSourceProxy[0]);
5120 DbSourceProxy src = otherdb.get(0);
5121 fetchr = new JMenuItem(MessageManager
5122 .formatMessage("label.fetch_all_param", new Object[]
5123 { src.getDbSource() }));
5124 fetchr.addActionListener(new ActionListener()
5127 public void actionPerformed(ActionEvent e)
5129 new Thread(new Runnable()
5135 boolean isNucleotide = alignPanel.alignFrame
5136 .getViewport().getAlignment()
5138 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5139 alignPanel.av.getSequenceSelection(),
5140 alignPanel.alignFrame, dassource,
5141 alignPanel.alignFrame.featureSettings,
5144 .addListener(new FetchFinishedListenerI()
5147 public void finished()
5149 AlignFrame.this.setMenusForViewport();
5152 dbRefFetcher.fetchDBRefs(false);
5158 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5159 MessageManager.formatMessage(
5160 "label.fetch_retrieve_from_all_sources",
5162 { Integer.valueOf(otherdb.size())
5164 src.getDbSource(), src.getDbName() })));
5167 // and then build the rest of the individual menus
5168 ifetch = new JMenu(MessageManager.formatMessage(
5169 "label.source_from_db_source", new Object[]
5170 { src.getDbSource() }));
5172 String imname = null;
5174 for (DbSourceProxy sproxy : otherdb)
5176 String dbname = sproxy.getDbName();
5177 String sname = dbname.length() > 5
5178 ? dbname.substring(0, 5) + "..."
5180 String msname = dbname.length() > 10
5181 ? dbname.substring(0, 10) + "..."
5185 imname = MessageManager
5186 .formatMessage("label.from_msname", new Object[]
5189 fetchr = new JMenuItem(msname);
5190 final DbSourceProxy[] dassrc = { sproxy };
5191 fetchr.addActionListener(new ActionListener()
5195 public void actionPerformed(ActionEvent e)
5197 new Thread(new Runnable()
5203 boolean isNucleotide = alignPanel.alignFrame
5204 .getViewport().getAlignment()
5206 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5207 alignPanel.av.getSequenceSelection(),
5208 alignPanel.alignFrame, dassrc,
5209 alignPanel.alignFrame.featureSettings,
5212 .addListener(new FetchFinishedListenerI()
5215 public void finished()
5217 AlignFrame.this.setMenusForViewport();
5220 dbRefFetcher.fetchDBRefs(false);
5226 fetchr.setToolTipText(
5227 "<html>" + MessageManager.formatMessage(
5228 "label.fetch_retrieve_from", new Object[]
5232 if (++icomp >= mcomp || i == (otherdb.size()))
5234 ifetch.setText(MessageManager.formatMessage(
5235 "label.source_to_target", imname, sname));
5237 ifetch = new JMenu();
5245 if (comp >= mcomp || dbi >= (dbclasses.length))
5247 dfetch.setText(MessageManager.formatMessage(
5248 "label.source_to_target", mname, dbclass));
5250 dfetch = new JMenu();
5263 * Left justify the whole alignment.
5266 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5268 AlignmentI al = viewport.getAlignment();
5270 viewport.firePropertyChange("alignment", null, al);
5274 * Right justify the whole alignment.
5277 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5279 AlignmentI al = viewport.getAlignment();
5281 viewport.firePropertyChange("alignment", null, al);
5285 public void setShowSeqFeatures(boolean b)
5287 showSeqFeatures.setSelected(b);
5288 viewport.setShowSequenceFeatures(b);
5295 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5296 * awt.event.ActionEvent)
5299 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5301 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5302 alignPanel.paintAlignment(false, false);
5309 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5313 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5315 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5316 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5324 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5325 * .event.ActionEvent)
5328 protected void showGroupConservation_actionPerformed(ActionEvent e)
5330 viewport.setShowGroupConservation(showGroupConservation.getState());
5331 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5338 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5339 * .event.ActionEvent)
5342 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5344 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5345 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5352 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5353 * .event.ActionEvent)
5356 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5358 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5359 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5363 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5365 showSequenceLogo.setState(true);
5366 viewport.setShowSequenceLogo(true);
5367 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5368 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5372 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5374 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5381 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5382 * .event.ActionEvent)
5385 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5387 if (avc.makeGroupsFromSelection())
5389 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5390 alignPanel.updateAnnotation();
5391 alignPanel.paintAlignment(true,
5392 viewport.needToUpdateStructureViews());
5396 public void clearAlignmentSeqRep()
5398 // TODO refactor alignmentseqrep to controller
5399 if (viewport.getAlignment().hasSeqrep())
5401 viewport.getAlignment().setSeqrep(null);
5402 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5403 alignPanel.updateAnnotation();
5404 alignPanel.paintAlignment(true, true);
5409 protected void createGroup_actionPerformed(ActionEvent e)
5411 if (avc.createGroup())
5413 if (applyAutoAnnotationSettings.isSelected())
5415 alignPanel.updateAnnotation(true, false);
5417 alignPanel.alignmentChanged();
5422 protected void unGroup_actionPerformed(ActionEvent e)
5426 alignPanel.alignmentChanged();
5431 * make the given alignmentPanel the currently selected tab
5433 * @param alignmentPanel
5435 public void setDisplayedView(AlignmentPanel alignmentPanel)
5437 if (!viewport.getSequenceSetId()
5438 .equals(alignmentPanel.av.getSequenceSetId()))
5440 throw new Error(MessageManager.getString(
5441 "error.implementation_error_cannot_show_view_alignment_frame"));
5443 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5444 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5446 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5451 * Action on selection of menu options to Show or Hide annotations.
5454 * @param forSequences
5455 * update sequence-related annotations
5456 * @param forAlignment
5457 * update non-sequence-related annotations
5460 protected void setAnnotationsVisibility(boolean visible,
5461 boolean forSequences, boolean forAlignment)
5463 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5464 .getAlignmentAnnotation();
5469 for (AlignmentAnnotation aa : anns)
5472 * don't display non-positional annotations on an alignment
5474 if (aa.annotations == null)
5478 boolean apply = (aa.sequenceRef == null && forAlignment)
5479 || (aa.sequenceRef != null && forSequences);
5482 aa.visible = visible;
5485 alignPanel.validateAnnotationDimensions(true);
5486 alignPanel.alignmentChanged();
5490 * Store selected annotation sort order for the view and repaint.
5493 protected void sortAnnotations_actionPerformed()
5495 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5497 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5498 alignPanel.paintAlignment(false, false);
5503 * @return alignment panels in this alignment frame
5505 public List<? extends AlignmentViewPanel> getAlignPanels()
5507 // alignPanels is never null
5508 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5513 * Open a new alignment window, with the cDNA associated with this (protein)
5514 * alignment, aligned as is the protein.
5516 protected void viewAsCdna_actionPerformed()
5518 // TODO no longer a menu action - refactor as required
5519 final AlignmentI alignment = getViewport().getAlignment();
5520 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5521 if (mappings == null)
5525 List<SequenceI> cdnaSeqs = new ArrayList<>();
5526 for (SequenceI aaSeq : alignment.getSequences())
5528 for (AlignedCodonFrame acf : mappings)
5530 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5534 * There is a cDNA mapping for this protein sequence - add to new
5535 * alignment. It will share the same dataset sequence as other mapped
5536 * cDNA (no new mappings need to be created).
5538 final Sequence newSeq = new Sequence(dnaSeq);
5539 newSeq.setDatasetSequence(dnaSeq);
5540 cdnaSeqs.add(newSeq);
5544 if (cdnaSeqs.size() == 0)
5546 // show a warning dialog no mapped cDNA
5549 AlignmentI cdna = new Alignment(
5550 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5551 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5552 AlignFrame.DEFAULT_HEIGHT);
5553 cdna.alignAs(alignment);
5554 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5556 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5557 AlignFrame.DEFAULT_HEIGHT);
5561 * Set visibility of dna/protein complement view (available when shown in a
5567 protected void showComplement_actionPerformed(boolean show)
5569 SplitContainerI sf = getSplitViewContainer();
5572 sf.setComplementVisible(this, show);
5577 * Generate the reverse (optionally complemented) of the selected sequences,
5578 * and add them to the alignment
5581 protected void showReverse_actionPerformed(boolean complement)
5583 AlignmentI al = null;
5586 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5587 al = dna.reverseCdna(complement);
5588 viewport.addAlignment(al, "");
5589 addHistoryItem(new EditCommand(
5590 MessageManager.getString("label.add_sequences"), Action.PASTE,
5591 al.getSequencesArray(), 0, al.getWidth(),
5592 viewport.getAlignment()));
5593 } catch (Exception ex)
5595 System.err.println(ex.getMessage());
5601 * Try to run a script in the Groovy console, having first ensured that this
5602 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5603 * be targeted at this alignment.
5606 protected void runGroovy_actionPerformed()
5608 Jalview.setCurrentAlignFrame(this);
5609 groovy.ui.Console console = Desktop.getGroovyConsole();
5610 if (console != null)
5614 console.runScript();
5615 } catch (Exception ex)
5617 System.err.println((ex.toString()));
5618 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5619 MessageManager.getString("label.couldnt_run_groovy_script"),
5620 MessageManager.getString("label.groovy_support_failed"),
5621 JvOptionPane.ERROR_MESSAGE);
5626 System.err.println("Can't run Groovy script as console not found");
5631 * Hides columns containing (or not containing) a specified feature, provided
5632 * that would not leave all columns hidden
5634 * @param featureType
5635 * @param columnsContaining
5638 public boolean hideFeatureColumns(String featureType,
5639 boolean columnsContaining)
5641 boolean notForHiding = avc.markColumnsContainingFeatures(
5642 columnsContaining, false, false, featureType);
5645 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5646 false, featureType))
5648 getViewport().hideSelectedColumns();
5656 protected void selectHighlightedColumns_actionPerformed(
5657 ActionEvent actionEvent)
5659 // include key modifier check in case user selects from menu
5660 avc.markHighlightedColumns(
5661 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5662 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5663 | ActionEvent.CTRL_MASK)) != 0);
5667 * Rebuilds the Colour menu, including any user-defined colours which have
5668 * been loaded either on startup or during the session
5670 public void buildColourMenu()
5672 colourMenu.removeAll();
5674 colourMenu.add(applyToAllGroups);
5675 colourMenu.add(textColour);
5676 colourMenu.addSeparator();
5678 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5679 viewport.getAlignment(), false);
5681 colourMenu.add(annotationColour);
5682 bg.add(annotationColour);
5683 colourMenu.addSeparator();
5684 colourMenu.add(conservationMenuItem);
5685 colourMenu.add(modifyConservation);
5686 colourMenu.add(abovePIDThreshold);
5687 colourMenu.add(modifyPID);
5689 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5690 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5694 * Open a dialog (if not already open) that allows the user to select and
5695 * calculate PCA or Tree analysis
5697 protected void openTreePcaDialog()
5699 if (alignPanel.getCalculationDialog() == null)
5701 new CalculationChooser(AlignFrame.this);
5706 protected void loadVcf_actionPerformed()
5708 JalviewFileChooser chooser = new JalviewFileChooser(
5709 Cache.getProperty("LAST_DIRECTORY"));
5710 chooser.setFileView(new JalviewFileView());
5711 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5712 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5714 int value = chooser.showOpenDialog(null);
5716 if (value == JalviewFileChooser.APPROVE_OPTION)
5718 String choice = chooser.getSelectedFile().getPath();
5719 Cache.setProperty("LAST_DIRECTORY", choice);
5720 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5721 new VCFLoader(choice).loadVCF(seqs, this);
5726 private Rectangle lastFeatureSettingsBounds = null;
5729 public void setFeatureSettingsGeometry(Rectangle bounds)
5731 lastFeatureSettingsBounds = bounds;
5735 public Rectangle getFeatureSettingsGeometry()
5737 return lastFeatureSettingsBounds;
5741 class PrintThread extends Thread
5745 public PrintThread(AlignmentPanel ap)
5750 static PageFormat pf;
5755 PrinterJob printJob = PrinterJob.getPrinterJob();
5759 printJob.setPrintable(ap, pf);
5763 printJob.setPrintable(ap);
5766 if (printJob.printDialog())
5771 } catch (Exception PrintException)
5773 PrintException.printStackTrace();