2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenColumns;
57 import jalview.datamodel.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FileParse;
74 import jalview.io.FormatAdapter;
75 import jalview.io.HtmlSvgOutput;
76 import jalview.io.IdentifyFile;
77 import jalview.io.JPredFile;
78 import jalview.io.JalviewFileChooser;
79 import jalview.io.JalviewFileView;
80 import jalview.io.JnetAnnotationMaker;
81 import jalview.io.NewickFile;
82 import jalview.io.ScoreMatrixFile;
83 import jalview.io.TCoffeeScoreFile;
84 import jalview.io.vcf.VCFLoader;
85 import jalview.jbgui.GAlignFrame;
86 import jalview.schemes.ColourSchemeI;
87 import jalview.schemes.ColourSchemes;
88 import jalview.schemes.ResidueColourScheme;
89 import jalview.schemes.TCoffeeColourScheme;
90 import jalview.util.MessageManager;
91 import jalview.util.dialogrunner.RunResponse;
92 import jalview.viewmodel.AlignmentViewport;
93 import jalview.viewmodel.ViewportRanges;
94 import jalview.ws.DBRefFetcher;
95 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
96 import jalview.ws.jws1.Discoverer;
97 import jalview.ws.jws2.Jws2Discoverer;
98 import jalview.ws.jws2.jabaws2.Jws2Instance;
99 import jalview.ws.seqfetcher.DbSourceProxy;
101 import java.awt.BorderLayout;
102 import java.awt.Component;
103 import java.awt.Rectangle;
104 import java.awt.Toolkit;
105 import java.awt.datatransfer.Clipboard;
106 import java.awt.datatransfer.DataFlavor;
107 import java.awt.datatransfer.StringSelection;
108 import java.awt.datatransfer.Transferable;
109 import java.awt.dnd.DnDConstants;
110 import java.awt.dnd.DropTargetDragEvent;
111 import java.awt.dnd.DropTargetDropEvent;
112 import java.awt.dnd.DropTargetEvent;
113 import java.awt.dnd.DropTargetListener;
114 import java.awt.event.ActionEvent;
115 import java.awt.event.ActionListener;
116 import java.awt.event.FocusAdapter;
117 import java.awt.event.FocusEvent;
118 import java.awt.event.ItemEvent;
119 import java.awt.event.ItemListener;
120 import java.awt.event.KeyAdapter;
121 import java.awt.event.KeyEvent;
122 import java.awt.event.MouseEvent;
123 import java.awt.print.PageFormat;
124 import java.awt.print.PrinterJob;
125 import java.beans.PropertyChangeEvent;
126 import java.beans.PropertyChangeListener;
128 import java.io.FileWriter;
129 import java.io.PrintWriter;
131 import java.util.ArrayList;
132 import java.util.Arrays;
133 import java.util.Deque;
134 import java.util.Enumeration;
135 import java.util.Hashtable;
136 import java.util.List;
137 import java.util.Vector;
139 import javax.swing.JCheckBoxMenuItem;
140 import javax.swing.JEditorPane;
141 import javax.swing.JFileChooser;
142 import javax.swing.JInternalFrame;
143 import javax.swing.JLayeredPane;
144 import javax.swing.JMenu;
145 import javax.swing.JMenuItem;
146 import javax.swing.JScrollPane;
147 import javax.swing.SwingUtilities;
153 * @version $Revision$
155 public class AlignFrame extends GAlignFrame implements DropTargetListener,
156 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener,
157 PropertyChangeListener
160 public static final int DEFAULT_WIDTH = 700;
162 public static final int DEFAULT_HEIGHT = 500;
165 * The currently displayed panel (selected tabbed view if more than one)
167 public AlignmentPanel alignPanel;
169 AlignViewport viewport;
171 public AlignViewControllerI avc;
173 List<AlignmentPanel> alignPanels = new ArrayList<>();
176 * Last format used to load or save alignments in this window
178 FileFormatI currentFileFormat = null;
181 * Current filename for this alignment
183 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 public void propertyChange(PropertyChangeEvent evt)
336 Desktop.getDesktop().propertyChange(evt);
343 * @return true if we have any features
346 protected boolean haveAlignmentFeatures() {
347 AlignmentI alignment = getViewport().getAlignment();
349 for (int i = 0; i < alignment.getHeight(); i++)
351 SequenceI seq = alignment.getSequenceAt(i);
352 for (String group : seq.getFeatures().getFeatureGroups(true))
354 if (group != null)return true;
361 * initalise the alignframe from the underlying viewport data and the
366 if (!Jalview.isHeadlessMode())
368 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
371 avc = new jalview.controller.AlignViewController(this, viewport,
373 if (viewport.getAlignmentConservationAnnotation() == null)
375 // BLOSUM62Colour.setEnabled(false);
376 conservationMenuItem.setEnabled(false);
377 modifyConservation.setEnabled(false);
378 // PIDColour.setEnabled(false);
379 // abovePIDThreshold.setEnabled(false);
380 // modifyPID.setEnabled(false);
383 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
386 if (sortby.equals("Id"))
388 sortIDMenuItem_actionPerformed(null);
390 else if (sortby.equals("Pairwise Identity"))
392 sortPairwiseMenuItem_actionPerformed(null);
396 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
398 setMenusFromViewport(viewport);
399 buildSortByAnnotationScoresMenu();
400 calculateTree.addActionListener(new ActionListener()
404 public void actionPerformed(ActionEvent e)
411 if (Desktop.desktop != null)
413 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
415 * BH 2018 ignore service listeners
421 addServiceListeners();
426 if (viewport.getWrapAlignment())
428 wrapMenuItem_actionPerformed(null);
431 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
433 this.overviewMenuItem_actionPerformed(null);
438 final List<AlignmentPanel> selviews = new ArrayList<>();
439 final List<AlignmentPanel> origview = new ArrayList<>();
440 final String menuLabel = MessageManager
441 .getString("label.copy_format_from");
442 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
443 new ViewSetProvider()
447 public AlignmentPanel[] getAllAlignmentPanels()
450 origview.add(alignPanel);
451 // make an array of all alignment panels except for this one
452 List<AlignmentPanel> aps = new ArrayList<>(
453 Arrays.asList(Desktop.getAlignmentPanels(null)));
454 aps.remove(AlignFrame.this.alignPanel);
455 return aps.toArray(new AlignmentPanel[aps.size()]);
457 }, selviews, new ItemListener()
461 public void itemStateChanged(ItemEvent e)
463 if (origview.size() > 0)
465 final AlignmentPanel ap = origview.get(0);
468 * Copy the ViewStyle of the selected panel to 'this one'.
469 * Don't change value of 'scaleProteinAsCdna' unless copying
472 ViewStyleI vs = selviews.get(0).getAlignViewport()
474 boolean fromSplitFrame = selviews.get(0)
475 .getAlignViewport().getCodingComplement() != null;
478 vs.setScaleProteinAsCdna(ap.getAlignViewport()
479 .getViewStyle().isScaleProteinAsCdna());
481 ap.getAlignViewport().setViewStyle(vs);
484 * Also rescale ViewStyle of SplitFrame complement if there is
485 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
486 * the whole ViewStyle (allow cDNA protein to have different
489 AlignViewportI complement = ap.getAlignViewport()
490 .getCodingComplement();
491 if (complement != null && vs.isScaleProteinAsCdna())
493 AlignFrame af = Desktop.getAlignFrameFor(complement);
494 ((SplitFrame) af.getSplitViewContainer())
496 af.setMenusForViewport();
500 ap.setSelected(true);
501 ap.alignFrame.setMenusForViewport();
506 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
507 .indexOf("devel") > -1
508 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
509 .indexOf("test") > -1)
511 formatMenu.add(vsel);
513 addFocusListener(new FocusAdapter()
516 public void focusGained(FocusEvent e)
518 Jalview.setCurrentAlignFrame(AlignFrame.this);
525 * Change the filename and format for the alignment, and enable the 'reload'
526 * button functionality.
533 public void setFileName(String file, FileFormatI format)
536 setFileFormat(format);
537 reload.setEnabled(true);
541 * JavaScript will have this, maybe others. More dependable than a file name
542 * and maintains a reference to the actual bytes loaded.
546 public void setFileObject(File file) {
547 this.fileObject = file;
551 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
554 void addKeyListener()
556 addKeyListener(new KeyAdapter()
559 public void keyPressed(KeyEvent evt)
561 if (viewport.cursorMode
562 && ((evt.getKeyCode() >= KeyEvent.VK_0
563 && evt.getKeyCode() <= KeyEvent.VK_9)
564 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
565 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
566 && Character.isDigit(evt.getKeyChar()))
568 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
571 switch (evt.getKeyCode())
574 case 27: // escape key
575 deselectAllSequenceMenuItem_actionPerformed(null);
579 case KeyEvent.VK_DOWN:
580 if (evt.isAltDown() || !viewport.cursorMode)
582 moveSelectedSequences(false);
584 if (viewport.cursorMode)
586 alignPanel.getSeqPanel().moveCursor(0, 1);
591 if (evt.isAltDown() || !viewport.cursorMode)
593 moveSelectedSequences(true);
595 if (viewport.cursorMode)
597 alignPanel.getSeqPanel().moveCursor(0, -1);
602 case KeyEvent.VK_LEFT:
603 if (evt.isAltDown() || !viewport.cursorMode)
605 slideSequences(false,
606 alignPanel.getSeqPanel().getKeyboardNo1());
610 alignPanel.getSeqPanel().moveCursor(-1, 0);
615 case KeyEvent.VK_RIGHT:
616 if (evt.isAltDown() || !viewport.cursorMode)
618 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
622 alignPanel.getSeqPanel().moveCursor(1, 0);
626 case KeyEvent.VK_SPACE:
627 if (viewport.cursorMode)
629 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
630 || evt.isShiftDown() || evt.isAltDown());
634 // case KeyEvent.VK_A:
635 // if (viewport.cursorMode)
637 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
638 // //System.out.println("A");
642 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
643 * System.out.println("closing bracket"); } break;
645 case KeyEvent.VK_DELETE:
646 case KeyEvent.VK_BACK_SPACE:
647 if (!viewport.cursorMode)
649 cut_actionPerformed(null);
653 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
654 || evt.isShiftDown() || evt.isAltDown());
660 if (viewport.cursorMode)
662 alignPanel.getSeqPanel().setCursorRow();
666 if (viewport.cursorMode && !evt.isControlDown())
668 alignPanel.getSeqPanel().setCursorColumn();
672 if (viewport.cursorMode)
674 alignPanel.getSeqPanel().setCursorPosition();
678 case KeyEvent.VK_ENTER:
679 case KeyEvent.VK_COMMA:
680 if (viewport.cursorMode)
682 alignPanel.getSeqPanel().setCursorRowAndColumn();
687 if (viewport.cursorMode)
689 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
693 if (viewport.cursorMode)
695 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
700 viewport.cursorMode = !viewport.cursorMode;
701 statusBar.setText(MessageManager
702 .formatMessage("label.keyboard_editing_mode", new String[]
703 { (viewport.cursorMode ? "on" : "off") }));
704 if (viewport.cursorMode)
706 ViewportRanges ranges = viewport.getRanges();
707 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
709 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
712 alignPanel.getSeqPanel().seqCanvas.repaint();
718 Help.showHelpWindow();
719 } catch (Exception ex)
721 ex.printStackTrace();
726 boolean toggleSeqs = !evt.isControlDown();
727 boolean toggleCols = !evt.isShiftDown();
728 toggleHiddenRegions(toggleSeqs, toggleCols);
733 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
734 boolean modifyExisting = true; // always modify, don't clear
735 // evt.isShiftDown();
736 boolean invertHighlighted = evt.isAltDown();
737 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
741 case KeyEvent.VK_PAGE_UP:
742 viewport.getRanges().pageUp();
744 case KeyEvent.VK_PAGE_DOWN:
745 viewport.getRanges().pageDown();
751 public void keyReleased(KeyEvent evt)
753 switch (evt.getKeyCode())
755 case KeyEvent.VK_LEFT:
756 if (evt.isAltDown() || !viewport.cursorMode)
758 viewport.firePropertyChange("alignment", null,
759 viewport.getAlignment().getSequences());
763 case KeyEvent.VK_RIGHT:
764 if (evt.isAltDown() || !viewport.cursorMode)
766 viewport.firePropertyChange("alignment", null,
767 viewport.getAlignment().getSequences());
775 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
777 ap.alignFrame = this;
778 avc = new jalview.controller.AlignViewController(this, viewport,
783 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
785 int aSize = alignPanels.size();
787 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
789 if (aSize == 1 && ap.av.viewName == null)
791 this.getContentPane().add(ap, BorderLayout.CENTER);
797 setInitialTabVisible();
800 expandViews.setEnabled(true);
801 gatherViews.setEnabled(true);
802 tabbedPane.addTab(ap.av.viewName, ap);
804 ap.setVisible(false);
809 if (ap.av.isPadGaps())
811 ap.av.getAlignment().padGaps();
813 ap.av.updateConservation(ap);
814 ap.av.updateConsensus(ap);
815 ap.av.updateStrucConsensus(ap);
819 public void setInitialTabVisible()
821 expandViews.setEnabled(true);
822 gatherViews.setEnabled(true);
823 tabbedPane.setVisible(true);
824 AlignmentPanel first = alignPanels.get(0);
825 tabbedPane.addTab(first.av.viewName, first);
826 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
829 public AlignViewport getViewport()
834 /* Set up intrinsic listeners for dynamically generated GUI bits. */
835 private void addServiceListeners()
837 final java.beans.PropertyChangeListener thisListener;
838 Desktop.instance.addJalviewPropertyChangeListener("services",
839 thisListener = new java.beans.PropertyChangeListener()
842 public void propertyChange(PropertyChangeEvent evt)
844 // // System.out.println("Discoverer property change.");
845 // if (evt.getPropertyName().equals("services"))
847 SwingUtilities.invokeLater(new Runnable()
854 "Rebuild WS Menu for service change");
855 BuildWebServiceMenu();
862 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
865 public void internalFrameClosed(
866 javax.swing.event.InternalFrameEvent evt)
868 // System.out.println("deregistering discoverer listener");
869 Desktop.instance.removeJalviewPropertyChangeListener("services",
871 closeMenuItem_actionPerformed(true);
874 // Finally, build the menu once to get current service state
875 new Thread(new Runnable()
880 BuildWebServiceMenu();
886 * Configure menu items that vary according to whether the alignment is
887 * nucleotide or protein
889 public void setGUINucleotide()
891 AlignmentI al = getViewport().getAlignment();
892 boolean nucleotide = al.isNucleotide();
894 loadVcf.setVisible(nucleotide);
895 showTranslation.setVisible(nucleotide);
896 showReverse.setVisible(nucleotide);
897 showReverseComplement.setVisible(nucleotide);
898 conservationMenuItem.setEnabled(!nucleotide);
900 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
901 showGroupConservation.setEnabled(!nucleotide);
903 showComplementMenuItem
904 .setText(nucleotide ? MessageManager.getString("label.protein")
905 : MessageManager.getString("label.nucleotide"));
909 * set up menus for the current viewport. This may be called after any
910 * operation that affects the data in the current view (selection changed,
911 * etc) to update the menus to reflect the new state.
914 public void setMenusForViewport()
916 setMenusFromViewport(viewport);
920 * Need to call this method when tabs are selected for multiple views, or when
921 * loading from Jalview2XML.java
926 void setMenusFromViewport(AlignViewport av)
928 padGapsMenuitem.setSelected(av.isPadGaps());
929 colourTextMenuItem.setSelected(av.isShowColourText());
930 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
931 modifyPID.setEnabled(abovePIDThreshold.isSelected());
932 conservationMenuItem.setSelected(av.getConservationSelected());
933 modifyConservation.setEnabled(conservationMenuItem.isSelected());
934 seqLimits.setSelected(av.getShowJVSuffix());
935 idRightAlign.setSelected(av.isRightAlignIds());
936 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
937 renderGapsMenuItem.setSelected(av.isRenderGaps());
938 wrapMenuItem.setSelected(av.getWrapAlignment());
939 scaleAbove.setVisible(av.getWrapAlignment());
940 scaleLeft.setVisible(av.getWrapAlignment());
941 scaleRight.setVisible(av.getWrapAlignment());
942 annotationPanelMenuItem.setState(av.isShowAnnotation());
944 * Show/hide annotations only enabled if annotation panel is shown
946 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
947 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
948 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
949 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
950 viewBoxesMenuItem.setSelected(av.getShowBoxes());
951 viewTextMenuItem.setSelected(av.getShowText());
952 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
953 showGroupConsensus.setSelected(av.isShowGroupConsensus());
954 showGroupConservation.setSelected(av.isShowGroupConservation());
955 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
956 showSequenceLogo.setSelected(av.isShowSequenceLogo());
957 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
959 ColourMenuHelper.setColourSelected(colourMenu,
960 av.getGlobalColourScheme());
962 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
963 hiddenMarkers.setState(av.getShowHiddenMarkers());
964 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
965 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
966 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
967 autoCalculate.setSelected(av.autoCalculateConsensus);
968 sortByTree.setSelected(av.sortByTree);
969 listenToViewSelections.setSelected(av.followSelection);
971 showProducts.setEnabled(canShowProducts());
972 setGroovyEnabled(Desktop.getGroovyConsole() != null);
978 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
982 public void setGroovyEnabled(boolean b)
984 runGroovy.setEnabled(b);
987 private IProgressIndicator progressBar;
992 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
995 public void setProgressBar(String message, long id)
997 progressBar.setProgressBar(message, id);
1001 public void registerHandler(final long id,
1002 final IProgressIndicatorHandler handler)
1004 progressBar.registerHandler(id, handler);
1009 * @return true if any progress bars are still active
1012 public boolean operationInProgress()
1014 return progressBar.operationInProgress();
1018 public void setStatus(String text)
1020 statusBar.setText(text);
1024 * Added so Castor Mapping file can obtain Jalview Version
1026 public String getVersion()
1028 return jalview.bin.Cache.getProperty("VERSION");
1031 public FeatureRenderer getFeatureRenderer()
1033 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1037 public void fetchSequence_actionPerformed(ActionEvent e)
1039 new jalview.gui.SequenceFetcher(this);
1043 public void addFromFile_actionPerformed(ActionEvent e)
1045 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1049 public void reload_actionPerformed(ActionEvent e)
1051 if (fileName != null)
1053 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1054 // originating file's format
1055 // TODO: work out how to recover feature settings for correct view(s) when
1056 // file is reloaded.
1057 if (FileFormat.Jalview.equals(currentFileFormat))
1059 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1060 for (int i = 0; i < frames.length; i++)
1062 if (frames[i] instanceof AlignFrame && frames[i] != this
1063 && ((AlignFrame) frames[i]).fileName != null
1064 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1068 frames[i].setSelected(true);
1069 Desktop.instance.closeAssociatedWindows();
1070 } catch (java.beans.PropertyVetoException ex)
1076 Desktop.instance.closeAssociatedWindows();
1078 FileLoader loader = new FileLoader();
1079 DataSourceType protocol = fileName.startsWith("http:")
1080 ? DataSourceType.URL : DataSourceType.FILE;
1081 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1085 Rectangle bounds = this.getBounds();
1087 FileLoader loader = new FileLoader();
1089 AlignFrame newframe = null;
1091 if (fileObject == null)
1094 DataSourceType protocol = (fileName.startsWith("http:")
1095 ? DataSourceType.URL : DataSourceType.FILE);
1096 newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1101 newframe = loader.LoadFileWaitTillLoaded(fileObject, DataSourceType.FILE, currentFileFormat);
1104 newframe.setBounds(bounds);
1105 if (featureSettings != null && featureSettings.isShowing())
1107 final Rectangle fspos = featureSettings.frame.getBounds();
1108 // TODO: need a 'show feature settings' function that takes bounds -
1109 // need to refactor Desktop.addFrame
1110 newframe.featureSettings_actionPerformed(null);
1111 final FeatureSettings nfs = newframe.featureSettings;
1112 SwingUtilities.invokeLater(new Runnable()
1117 nfs.frame.setBounds(fspos);
1120 this.featureSettings.close();
1121 this.featureSettings = null;
1123 this.closeMenuItem_actionPerformed(true);
1129 public void addFromText_actionPerformed(ActionEvent e)
1132 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1136 public void addFromURL_actionPerformed(ActionEvent e)
1138 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1142 public void save_actionPerformed(ActionEvent e)
1144 if (fileName == null || (currentFileFormat == null)
1145 || fileName.startsWith("http"))
1147 saveAs_actionPerformed(null);
1151 saveAlignment(fileName, currentFileFormat);
1162 public void saveAs_actionPerformed(ActionEvent e)
1164 String format = currentFileFormat == null ? null
1165 : currentFileFormat.getName();
1166 final JalviewFileChooser chooser = JalviewFileChooser
1167 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1168 final AlignFrame us = this;
1169 chooser.setFileView(new JalviewFileView());
1170 chooser.setDialogTitle(
1171 MessageManager.getString("label.save_alignment_to_file"));
1172 chooser.setToolTipText(MessageManager.getString("action.save"));
1174 chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
1179 currentFileFormat = chooser.getSelectedFormat();
1180 while (currentFileFormat == null)
1182 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1183 MessageManager.getString(
1184 "label.select_file_format_before_saving"),
1186 .getString("label.file_format_not_specified"),
1187 JvOptionPane.WARNING_MESSAGE);
1188 currentFileFormat = chooser.getSelectedFormat();
1189 chooser.showSaveDialog(us);
1192 fileName = chooser.getSelectedFile().getPath();
1194 Cache.setProperty("DEFAULT_FILE_FORMAT",
1195 currentFileFormat.getName());
1197 Cache.setProperty("LAST_DIRECTORY", fileName);
1198 saveAlignment(fileName, currentFileFormat);
1200 }).showSaveDialog(this);
1203 public boolean saveAlignment(String file, FileFormatI format)
1205 boolean success = true;
1207 if (FileFormat.Jalview.equals(format))
1209 String shortName = title;
1211 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1213 shortName = shortName.substring(
1214 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1217 success = new Jalview2XML().saveAlignment(this, file, shortName);
1219 statusBar.setText(MessageManager.formatMessage(
1220 "label.successfully_saved_to_file_in_format", new Object[]
1221 { fileName, format }));
1226 AlignmentExportData exportData = getAlignmentForExport(format,
1228 if (exportData.getSettings().isCancelled())
1232 FormatAdapter f = new FormatAdapter(alignPanel,
1233 exportData.getSettings());
1234 String output = f.formatSequences(format, exportData.getAlignment(), // class
1238 // occur in the distant future
1239 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1240 f.getCacheSuffixDefault(format),
1241 viewport.getAlignment().getHiddenColumns());
1251 PrintWriter out = new PrintWriter(new FileWriter(file));
1255 this.setTitle(file);
1256 statusBar.setText(MessageManager.formatMessage(
1257 "label.successfully_saved_to_file_in_format", new Object[]
1258 { fileName, format.getName() }));
1259 } catch (Exception ex)
1262 ex.printStackTrace();
1269 JvOptionPane.showInternalMessageDialog(this, MessageManager
1270 .formatMessage("label.couldnt_save_file", new Object[]
1272 MessageManager.getString("label.error_saving_file"),
1273 JvOptionPane.WARNING_MESSAGE);
1279 private void warningMessage(String warning, String title)
1281 if (new jalview.util.Platform().isHeadless())
1283 System.err.println("Warning: " + title + "\nWarning: " + warning);
1288 JvOptionPane.showInternalMessageDialog(this, warning, title,
1289 JvOptionPane.WARNING_MESSAGE);
1301 protected void outputText_actionPerformed(ActionEvent e)
1303 FileFormatI fileFormat = FileFormats.getInstance()
1304 .forName(e.getActionCommand());
1305 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1307 if (exportData.getSettings().isCancelled())
1311 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1312 cap.setForInput(null);
1315 FileFormatI format = fileFormat;
1316 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1317 .formatSequences(format, exportData.getAlignment(),
1318 exportData.getOmitHidden(),
1319 exportData.getStartEndPostions(),
1320 viewport.getAlignment().getHiddenColumns()));
1321 Desktop.addInternalFrame(cap, MessageManager
1322 .formatMessage("label.alignment_output_command", new Object[]
1323 { e.getActionCommand() }), 600, 500);
1324 } catch (OutOfMemoryError oom)
1326 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1333 public static AlignmentExportData getAlignmentForExport(
1334 FileFormatI format, AlignViewportI viewport,
1335 AlignExportSettingI exportSettings)
1337 AlignmentI alignmentToExport = null;
1338 AlignExportSettingI settings = exportSettings;
1339 String[] omitHidden = null;
1341 HiddenSequences hiddenSeqs = viewport.getAlignment()
1342 .getHiddenSequences();
1344 alignmentToExport = viewport.getAlignment();
1346 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1347 if (settings == null)
1349 settings = new AlignExportSettings(hasHiddenSeqs,
1350 viewport.hasHiddenColumns(), format);
1352 // settings.isExportAnnotations();
1354 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1356 omitHidden = viewport.getViewAsString(false,
1357 settings.isExportHiddenSequences());
1360 int[] alignmentStartEnd = new int[2];
1361 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1363 alignmentToExport = hiddenSeqs.getFullAlignment();
1367 alignmentToExport = viewport.getAlignment();
1369 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1370 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1371 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1372 omitHidden, alignmentStartEnd, settings);
1383 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1385 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1386 htmlSVG.exportHTML(null);
1390 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1392 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1393 bjs.exportHTML(null);
1396 public void createImageMap(File file, String image)
1398 alignPanel.makePNGImageMap(file, image);
1408 public void createPNG(File f)
1410 alignPanel.makePNG(f);
1420 public void createEPS(File f)
1422 alignPanel.makeEPS(f);
1426 public void createSVG(File f)
1428 alignPanel.makeSVG(f);
1432 public void pageSetup_actionPerformed(ActionEvent e)
1434 PrinterJob printJob = PrinterJob.getPrinterJob();
1435 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1445 public void printMenuItem_actionPerformed(ActionEvent e)
1447 // Putting in a thread avoids Swing painting problems
1448 PrintThread thread = new PrintThread(alignPanel);
1453 public void exportFeatures_actionPerformed(ActionEvent e)
1455 new AnnotationExporter(alignPanel).exportFeatures();
1459 public void exportAnnotations_actionPerformed(ActionEvent e)
1461 new AnnotationExporter(alignPanel).exportAnnotations();
1465 public void associatedData_actionPerformed(ActionEvent e)
1467 final JalviewFileChooser chooser = new JalviewFileChooser(
1468 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1469 chooser.setFileView(new JalviewFileView());
1470 chooser.setDialogTitle(
1471 MessageManager.getString("label.load_jalview_annotations"));
1472 chooser.setToolTipText(
1473 MessageManager.getString("label.load_jalview_annotations"));
1474 chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
1480 String choice = chooser.getSelectedFile().getPath();
1481 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1482 loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1487 chooser.openDialog(this);
1491 * Close the current view or all views in the alignment frame. If the frame
1492 * only contains one view then the alignment will be removed from memory.
1494 * @param closeAllTabs
1497 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1499 if (alignPanels != null && alignPanels.size() < 2)
1501 closeAllTabs = true;
1506 if (alignPanels != null)
1510 if (this.isClosed())
1512 // really close all the windows - otherwise wait till
1513 // setClosed(true) is called
1514 for (int i = 0; i < alignPanels.size(); i++)
1516 AlignmentPanel ap = alignPanels.get(i);
1523 closeView(alignPanel);
1530 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1531 * be called recursively, with the frame now in 'closed' state
1533 this.setClosed(true);
1535 } catch (Exception ex)
1537 ex.printStackTrace();
1542 * Close the specified panel and close up tabs appropriately.
1544 * @param panelToClose
1546 public void closeView(AlignmentPanel panelToClose)
1548 int index = tabbedPane.getSelectedIndex();
1549 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1550 alignPanels.remove(panelToClose);
1551 panelToClose.closePanel();
1552 panelToClose = null;
1554 tabbedPane.removeTabAt(closedindex);
1555 tabbedPane.validate();
1557 if (index > closedindex || index == tabbedPane.getTabCount())
1559 // modify currently selected tab index if necessary.
1563 this.tabSelectionChanged(index);
1569 void updateEditMenuBar()
1572 if (viewport.getHistoryList().size() > 0)
1574 undoMenuItem.setEnabled(true);
1575 CommandI command = viewport.getHistoryList().peek();
1576 undoMenuItem.setText(MessageManager
1577 .formatMessage("label.undo_command", new Object[]
1578 { command.getDescription() }));
1582 undoMenuItem.setEnabled(false);
1583 undoMenuItem.setText(MessageManager.getString("action.undo"));
1586 if (viewport.getRedoList().size() > 0)
1588 redoMenuItem.setEnabled(true);
1590 CommandI command = viewport.getRedoList().peek();
1591 redoMenuItem.setText(MessageManager
1592 .formatMessage("label.redo_command", new Object[]
1593 { command.getDescription() }));
1597 redoMenuItem.setEnabled(false);
1598 redoMenuItem.setText(MessageManager.getString("action.redo"));
1603 public void addHistoryItem(CommandI command)
1605 if (command.getSize() > 0)
1607 viewport.addToHistoryList(command);
1608 viewport.clearRedoList();
1609 updateEditMenuBar();
1610 viewport.updateHiddenColumns();
1611 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1612 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1613 // viewport.getColumnSelection()
1614 // .getHiddenColumns().size() > 0);
1620 * @return alignment objects for all views
1622 AlignmentI[] getViewAlignments()
1624 if (alignPanels != null)
1626 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1628 for (AlignmentPanel ap : alignPanels)
1630 als[i++] = ap.av.getAlignment();
1634 if (viewport != null)
1636 return new AlignmentI[] { viewport.getAlignment() };
1648 protected void undoMenuItem_actionPerformed(ActionEvent e)
1650 if (viewport.getHistoryList().isEmpty())
1654 CommandI command = viewport.getHistoryList().pop();
1655 viewport.addToRedoList(command);
1656 command.undoCommand(getViewAlignments());
1658 AlignmentViewport originalSource = getOriginatingSource(command);
1659 updateEditMenuBar();
1661 if (originalSource != null)
1663 if (originalSource != viewport)
1666 "Implementation worry: mismatch of viewport origin for undo");
1668 originalSource.updateHiddenColumns();
1669 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1671 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1672 // viewport.getColumnSelection()
1673 // .getHiddenColumns().size() > 0);
1674 originalSource.firePropertyChange("alignment", null,
1675 originalSource.getAlignment().getSequences());
1686 protected void redoMenuItem_actionPerformed(ActionEvent e)
1688 if (viewport.getRedoList().size() < 1)
1693 CommandI command = viewport.getRedoList().pop();
1694 viewport.addToHistoryList(command);
1695 command.doCommand(getViewAlignments());
1697 AlignmentViewport originalSource = getOriginatingSource(command);
1698 updateEditMenuBar();
1700 if (originalSource != null)
1703 if (originalSource != viewport)
1706 "Implementation worry: mismatch of viewport origin for redo");
1708 originalSource.updateHiddenColumns();
1709 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1711 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1712 // viewport.getColumnSelection()
1713 // .getHiddenColumns().size() > 0);
1714 originalSource.firePropertyChange("alignment", null,
1715 originalSource.getAlignment().getSequences());
1719 AlignmentViewport getOriginatingSource(CommandI command)
1721 AlignmentViewport originalSource = null;
1722 // For sequence removal and addition, we need to fire
1723 // the property change event FROM the viewport where the
1724 // original alignment was altered
1725 AlignmentI al = null;
1726 if (command instanceof EditCommand)
1728 EditCommand editCommand = (EditCommand) command;
1729 al = editCommand.getAlignment();
1730 List<Component> comps = PaintRefresher.components
1731 .get(viewport.getSequenceSetId());
1733 for (Component comp : comps)
1735 if (comp instanceof AlignmentPanel)
1737 if (al == ((AlignmentPanel) comp).av.getAlignment())
1739 originalSource = ((AlignmentPanel) comp).av;
1746 if (originalSource == null)
1748 // The original view is closed, we must validate
1749 // the current view against the closed view first
1752 PaintRefresher.validateSequences(al, viewport.getAlignment());
1755 originalSource = viewport;
1758 return originalSource;
1767 public void moveSelectedSequences(boolean up)
1769 SequenceGroup sg = viewport.getSelectionGroup();
1775 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1776 viewport.getHiddenRepSequences(), up);
1777 alignPanel.paintAlignment(true, false);
1780 synchronized void slideSequences(boolean right, int size)
1782 List<SequenceI> sg = new ArrayList<>();
1783 if (viewport.cursorMode)
1785 sg.add(viewport.getAlignment()
1786 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1788 else if (viewport.getSelectionGroup() != null
1789 && viewport.getSelectionGroup().getSize() != viewport
1790 .getAlignment().getHeight())
1792 sg = viewport.getSelectionGroup()
1793 .getSequences(viewport.getHiddenRepSequences());
1801 List<SequenceI> invertGroup = new ArrayList<>();
1803 for (SequenceI seq : viewport.getAlignment().getSequences())
1805 if (!sg.contains(seq))
1807 invertGroup.add(seq);
1811 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1813 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1814 for (int i = 0; i < invertGroup.size(); i++)
1816 seqs2[i] = invertGroup.get(i);
1819 SlideSequencesCommand ssc;
1822 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1823 viewport.getGapCharacter());
1827 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1828 viewport.getGapCharacter());
1831 int groupAdjustment = 0;
1832 if (ssc.getGapsInsertedBegin() && right)
1834 if (viewport.cursorMode)
1836 alignPanel.getSeqPanel().moveCursor(size, 0);
1840 groupAdjustment = size;
1843 else if (!ssc.getGapsInsertedBegin() && !right)
1845 if (viewport.cursorMode)
1847 alignPanel.getSeqPanel().moveCursor(-size, 0);
1851 groupAdjustment = -size;
1855 if (groupAdjustment != 0)
1857 viewport.getSelectionGroup().setStartRes(
1858 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1859 viewport.getSelectionGroup().setEndRes(
1860 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1864 * just extend the last slide command if compatible; but not if in
1865 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1867 boolean appendHistoryItem = false;
1868 Deque<CommandI> historyList = viewport.getHistoryList();
1869 boolean inSplitFrame = getSplitViewContainer() != null;
1870 if (!inSplitFrame && historyList != null && historyList.size() > 0
1871 && historyList.peek() instanceof SlideSequencesCommand)
1873 appendHistoryItem = ssc.appendSlideCommand(
1874 (SlideSequencesCommand) historyList.peek());
1877 if (!appendHistoryItem)
1879 addHistoryItem(ssc);
1892 protected void copy_actionPerformed(ActionEvent e)
1894 if (viewport.getSelectionGroup() == null)
1898 // TODO: preserve the ordering of displayed alignment annotation in any
1899 // internal paste (particularly sequence associated annotation)
1900 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1901 String[] omitHidden = null;
1903 if (viewport.hasHiddenColumns())
1905 omitHidden = viewport.getViewAsString(true);
1908 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1909 seqs, omitHidden, null);
1911 StringSelection ss = new StringSelection(output);
1915 jalview.gui.Desktop.internalCopy = true;
1916 // Its really worth setting the clipboard contents
1917 // to empty before setting the large StringSelection!!
1918 Toolkit.getDefaultToolkit().getSystemClipboard()
1919 .setContents(new StringSelection(""), null);
1921 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1923 } catch (OutOfMemoryError er)
1925 new OOMWarning("copying region", er);
1929 HiddenColumns hiddenColumns = null;
1930 if (viewport.hasHiddenColumns())
1932 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1933 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1935 // create new HiddenColumns object with copy of hidden regions
1936 // between startRes and endRes, offset by startRes
1937 hiddenColumns = new HiddenColumns(
1938 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1939 hiddenCutoff, hiddenOffset);
1942 Desktop.jalviewClipboard = new Object[] { seqs,
1943 viewport.getAlignment().getDataset(), hiddenColumns };
1944 statusBar.setText(MessageManager.formatMessage(
1945 "label.copied_sequences_to_clipboard", new Object[]
1946 { Integer.valueOf(seqs.length).toString() }));
1956 protected void pasteNew_actionPerformed(ActionEvent e)
1968 protected void pasteThis_actionPerformed(ActionEvent e)
1974 * Paste contents of Jalview clipboard
1976 * @param newAlignment
1977 * true to paste to a new alignment, otherwise add to this.
1979 void paste(boolean newAlignment)
1981 boolean externalPaste = true;
1984 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1985 Transferable contents = c.getContents(this);
1987 if (contents == null)
1996 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1997 if (str.length() < 1)
2002 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2004 } catch (OutOfMemoryError er)
2006 new OOMWarning("Out of memory pasting sequences!!", er);
2010 SequenceI[] sequences;
2011 boolean annotationAdded = false;
2012 AlignmentI alignment = null;
2014 if (Desktop.jalviewClipboard != null)
2016 // The clipboard was filled from within Jalview, we must use the
2018 // And dataset from the copied alignment
2019 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2020 // be doubly sure that we create *new* sequence objects.
2021 sequences = new SequenceI[newseq.length];
2022 for (int i = 0; i < newseq.length; i++)
2024 sequences[i] = new Sequence(newseq[i]);
2026 alignment = new Alignment(sequences);
2027 externalPaste = false;
2031 // parse the clipboard as an alignment.
2032 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2034 sequences = alignment.getSequencesArray();
2038 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2044 if (Desktop.jalviewClipboard != null)
2046 // dataset is inherited
2047 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2051 // new dataset is constructed
2052 alignment.setDataset(null);
2054 alwidth = alignment.getWidth() + 1;
2058 AlignmentI pastedal = alignment; // preserve pasted alignment object
2059 // Add pasted sequences and dataset into existing alignment.
2060 alignment = viewport.getAlignment();
2061 alwidth = alignment.getWidth() + 1;
2062 // decide if we need to import sequences from an existing dataset
2063 boolean importDs = Desktop.jalviewClipboard != null
2064 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2065 // importDs==true instructs us to copy over new dataset sequences from
2066 // an existing alignment
2067 Vector newDs = (importDs) ? new Vector() : null; // used to create
2068 // minimum dataset set
2070 for (int i = 0; i < sequences.length; i++)
2074 newDs.addElement(null);
2076 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2078 if (importDs && ds != null)
2080 if (!newDs.contains(ds))
2082 newDs.setElementAt(ds, i);
2083 ds = new Sequence(ds);
2084 // update with new dataset sequence
2085 sequences[i].setDatasetSequence(ds);
2089 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2094 // copy and derive new dataset sequence
2095 sequences[i] = sequences[i].deriveSequence();
2096 alignment.getDataset()
2097 .addSequence(sequences[i].getDatasetSequence());
2098 // TODO: avoid creation of duplicate dataset sequences with a
2099 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2101 alignment.addSequence(sequences[i]); // merges dataset
2105 newDs.clear(); // tidy up
2107 if (alignment.getAlignmentAnnotation() != null)
2109 for (AlignmentAnnotation alan : alignment
2110 .getAlignmentAnnotation())
2112 if (alan.graphGroup > fgroup)
2114 fgroup = alan.graphGroup;
2118 if (pastedal.getAlignmentAnnotation() != null)
2120 // Add any annotation attached to alignment.
2121 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2122 for (int i = 0; i < alann.length; i++)
2124 annotationAdded = true;
2125 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2127 AlignmentAnnotation newann = new AlignmentAnnotation(
2129 if (newann.graphGroup > -1)
2131 if (newGraphGroups.size() <= newann.graphGroup
2132 || newGraphGroups.get(newann.graphGroup) == null)
2134 for (int q = newGraphGroups
2135 .size(); q <= newann.graphGroup; q++)
2137 newGraphGroups.add(q, null);
2139 newGraphGroups.set(newann.graphGroup,
2140 new Integer(++fgroup));
2142 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2146 newann.padAnnotation(alwidth);
2147 alignment.addAnnotation(newann);
2157 addHistoryItem(new EditCommand(
2158 MessageManager.getString("label.add_sequences"),
2159 Action.PASTE, sequences, 0, alignment.getWidth(),
2162 // Add any annotations attached to sequences
2163 for (int i = 0; i < sequences.length; i++)
2165 if (sequences[i].getAnnotation() != null)
2167 AlignmentAnnotation newann;
2168 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2170 annotationAdded = true;
2171 newann = sequences[i].getAnnotation()[a];
2172 newann.adjustForAlignment();
2173 newann.padAnnotation(alwidth);
2174 if (newann.graphGroup > -1)
2176 if (newann.graphGroup > -1)
2178 if (newGraphGroups.size() <= newann.graphGroup
2179 || newGraphGroups.get(newann.graphGroup) == null)
2181 for (int q = newGraphGroups
2182 .size(); q <= newann.graphGroup; q++)
2184 newGraphGroups.add(q, null);
2186 newGraphGroups.set(newann.graphGroup,
2187 new Integer(++fgroup));
2189 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2193 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2197 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2205 // propagate alignment changed.
2206 viewport.getRanges().setEndSeq(alignment.getHeight());
2207 if (annotationAdded)
2209 // Duplicate sequence annotation in all views.
2210 AlignmentI[] alview = this.getViewAlignments();
2211 for (int i = 0; i < sequences.length; i++)
2213 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2218 for (int avnum = 0; avnum < alview.length; avnum++)
2220 if (alview[avnum] != alignment)
2222 // duplicate in a view other than the one with input focus
2223 int avwidth = alview[avnum].getWidth() + 1;
2224 // this relies on sann being preserved after we
2225 // modify the sequence's annotation array for each duplication
2226 for (int a = 0; a < sann.length; a++)
2228 AlignmentAnnotation newann = new AlignmentAnnotation(
2230 sequences[i].addAlignmentAnnotation(newann);
2231 newann.padAnnotation(avwidth);
2232 alview[avnum].addAnnotation(newann); // annotation was
2233 // duplicated earlier
2234 // TODO JAL-1145 graphGroups are not updated for sequence
2235 // annotation added to several views. This may cause
2237 alview[avnum].setAnnotationIndex(newann, a);
2242 buildSortByAnnotationScoresMenu();
2244 viewport.firePropertyChange("alignment", null,
2245 alignment.getSequences());
2246 if (alignPanels != null)
2248 for (AlignmentPanel ap : alignPanels)
2250 ap.validateAnnotationDimensions(false);
2255 alignPanel.validateAnnotationDimensions(false);
2261 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2263 String newtitle = new String("Copied sequences");
2265 if (Desktop.jalviewClipboard != null
2266 && Desktop.jalviewClipboard[2] != null)
2268 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2269 af.viewport.setHiddenColumns(hc);
2272 // >>>This is a fix for the moment, until a better solution is
2274 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2275 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2276 .getFeatureRenderer());
2278 // TODO: maintain provenance of an alignment, rather than just make the
2279 // title a concatenation of operations.
2282 if (title.startsWith("Copied sequences"))
2288 newtitle = newtitle.concat("- from " + title);
2293 newtitle = new String("Pasted sequences");
2296 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2301 } catch (Exception ex)
2303 ex.printStackTrace();
2304 System.out.println("Exception whilst pasting: " + ex);
2305 // could be anything being pasted in here
2311 protected void expand_newalign(ActionEvent e)
2315 AlignmentI alignment = AlignmentUtils
2316 .expandContext(getViewport().getAlignment(), -1);
2317 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2319 String newtitle = new String("Flanking alignment");
2321 if (Desktop.jalviewClipboard != null
2322 && Desktop.jalviewClipboard[2] != null)
2324 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2325 af.viewport.setHiddenColumns(hc);
2328 // >>>This is a fix for the moment, until a better solution is
2330 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2331 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2332 .getFeatureRenderer());
2334 // TODO: maintain provenance of an alignment, rather than just make the
2335 // title a concatenation of operations.
2337 if (title.startsWith("Copied sequences"))
2343 newtitle = newtitle.concat("- from " + title);
2347 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2349 } catch (Exception ex)
2351 ex.printStackTrace();
2352 System.out.println("Exception whilst pasting: " + ex);
2353 // could be anything being pasted in here
2354 } catch (OutOfMemoryError oom)
2356 new OOMWarning("Viewing flanking region of alignment", oom);
2367 protected void cut_actionPerformed(ActionEvent e)
2369 copy_actionPerformed(null);
2370 delete_actionPerformed(null);
2380 protected void delete_actionPerformed(ActionEvent evt)
2383 SequenceGroup sg = viewport.getSelectionGroup();
2390 * If the cut affects all sequences, warn, remove highlighted columns
2392 if (sg.getSize() == viewport.getAlignment().getHeight())
2394 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2395 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2396 if (isEntireAlignWidth)
2398 int confirm = JvOptionPane.showConfirmDialog(this,
2399 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2400 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2401 JvOptionPane.OK_CANCEL_OPTION);
2403 if (confirm == JvOptionPane.CANCEL_OPTION
2404 || confirm == JvOptionPane.CLOSED_OPTION)
2409 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2410 sg.getEndRes() + 1);
2412 SequenceI[] cut = sg.getSequences()
2413 .toArray(new SequenceI[sg.getSize()]);
2415 addHistoryItem(new EditCommand(
2416 MessageManager.getString("label.cut_sequences"), Action.CUT,
2417 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2418 viewport.getAlignment()));
2420 viewport.setSelectionGroup(null);
2421 viewport.sendSelection();
2422 viewport.getAlignment().deleteGroup(sg);
2424 viewport.firePropertyChange("alignment", null,
2425 viewport.getAlignment().getSequences());
2426 if (viewport.getAlignment().getHeight() < 1)
2430 this.setClosed(true);
2431 } catch (Exception ex)
2444 protected void deleteGroups_actionPerformed(ActionEvent e)
2446 if (avc.deleteGroups())
2448 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2449 alignPanel.updateAnnotation();
2450 alignPanel.paintAlignment(true, true);
2461 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2463 SequenceGroup sg = new SequenceGroup();
2465 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2467 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2470 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2471 viewport.setSelectionGroup(sg);
2472 viewport.sendSelection();
2473 // JAL-2034 - should delegate to
2474 // alignPanel to decide if overview needs
2476 alignPanel.paintAlignment(false, false);
2477 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2487 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2489 if (viewport.cursorMode)
2491 alignPanel.getSeqPanel().keyboardNo1 = null;
2492 alignPanel.getSeqPanel().keyboardNo2 = null;
2494 viewport.setSelectionGroup(null);
2495 viewport.getColumnSelection().clear();
2496 viewport.setSelectionGroup(null);
2497 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2498 // JAL-2034 - should delegate to
2499 // alignPanel to decide if overview needs
2501 alignPanel.paintAlignment(false, false);
2502 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2503 viewport.sendSelection();
2513 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2515 SequenceGroup sg = viewport.getSelectionGroup();
2519 selectAllSequenceMenuItem_actionPerformed(null);
2524 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2526 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2528 // JAL-2034 - should delegate to
2529 // alignPanel to decide if overview needs
2532 alignPanel.paintAlignment(true, false);
2533 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2534 viewport.sendSelection();
2538 public void invertColSel_actionPerformed(ActionEvent e)
2540 viewport.invertColumnSelection();
2541 alignPanel.paintAlignment(true, false);
2542 viewport.sendSelection();
2552 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2554 trimAlignment(true);
2564 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2566 trimAlignment(false);
2569 void trimAlignment(boolean trimLeft)
2571 ColumnSelection colSel = viewport.getColumnSelection();
2574 if (!colSel.isEmpty())
2578 column = colSel.getMin();
2582 column = colSel.getMax();
2586 if (viewport.getSelectionGroup() != null)
2588 seqs = viewport.getSelectionGroup()
2589 .getSequencesAsArray(viewport.getHiddenRepSequences());
2593 seqs = viewport.getAlignment().getSequencesArray();
2596 TrimRegionCommand trimRegion;
2599 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2600 column, viewport.getAlignment());
2601 viewport.getRanges().setStartRes(0);
2605 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2606 column, viewport.getAlignment());
2609 statusBar.setText(MessageManager
2610 .formatMessage("label.removed_columns", new String[]
2611 { Integer.valueOf(trimRegion.getSize()).toString() }));
2613 addHistoryItem(trimRegion);
2615 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2617 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2618 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2620 viewport.getAlignment().deleteGroup(sg);
2624 viewport.firePropertyChange("alignment", null,
2625 viewport.getAlignment().getSequences());
2636 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2638 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2641 if (viewport.getSelectionGroup() != null)
2643 seqs = viewport.getSelectionGroup()
2644 .getSequencesAsArray(viewport.getHiddenRepSequences());
2645 start = viewport.getSelectionGroup().getStartRes();
2646 end = viewport.getSelectionGroup().getEndRes();
2650 seqs = viewport.getAlignment().getSequencesArray();
2653 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2654 "Remove Gapped Columns", seqs, start, end,
2655 viewport.getAlignment());
2657 addHistoryItem(removeGapCols);
2659 statusBar.setText(MessageManager
2660 .formatMessage("label.removed_empty_columns", new Object[]
2661 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2663 // This is to maintain viewport position on first residue
2664 // of first sequence
2665 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2666 ViewportRanges ranges = viewport.getRanges();
2667 int startRes = seq.findPosition(ranges.getStartRes());
2668 // ShiftList shifts;
2669 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2670 // edit.alColumnChanges=shifts.getInverse();
2671 // if (viewport.hasHiddenColumns)
2672 // viewport.getColumnSelection().compensateForEdits(shifts);
2673 ranges.setStartRes(seq.findIndex(startRes) - 1);
2674 viewport.firePropertyChange("alignment", null,
2675 viewport.getAlignment().getSequences());
2686 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2688 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2691 if (viewport.getSelectionGroup() != null)
2693 seqs = viewport.getSelectionGroup()
2694 .getSequencesAsArray(viewport.getHiddenRepSequences());
2695 start = viewport.getSelectionGroup().getStartRes();
2696 end = viewport.getSelectionGroup().getEndRes();
2700 seqs = viewport.getAlignment().getSequencesArray();
2703 // This is to maintain viewport position on first residue
2704 // of first sequence
2705 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2706 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2708 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2709 viewport.getAlignment()));
2711 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2713 viewport.firePropertyChange("alignment", null,
2714 viewport.getAlignment().getSequences());
2725 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2727 viewport.setPadGaps(padGapsMenuitem.isSelected());
2728 viewport.firePropertyChange("alignment", null,
2729 viewport.getAlignment().getSequences());
2739 public void findMenuItem_actionPerformed(ActionEvent e)
2745 * Create a new view of the current alignment.
2748 public void newView_actionPerformed(ActionEvent e)
2750 newView(null, true);
2754 * Creates and shows a new view of the current alignment.
2757 * title of newly created view; if null, one will be generated
2758 * @param copyAnnotation
2759 * if true then duplicate all annnotation, groups and settings
2760 * @return new alignment panel, already displayed.
2762 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2765 * Create a new AlignmentPanel (with its own, new Viewport)
2767 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2768 if (!copyAnnotation)
2771 * remove all groups and annotation except for the automatic stuff
2773 newap.av.getAlignment().deleteAllGroups();
2774 newap.av.getAlignment().deleteAllAnnotations(false);
2777 newap.av.setGatherViewsHere(false);
2779 if (viewport.viewName == null)
2781 viewport.viewName = MessageManager
2782 .getString("label.view_name_original");
2786 * Views share the same edits undo and redo stacks
2788 newap.av.setHistoryList(viewport.getHistoryList());
2789 newap.av.setRedoList(viewport.getRedoList());
2792 * Views share the same mappings; need to deregister any new mappings
2793 * created by copyAlignPanel, and register the new reference to the shared
2796 newap.av.replaceMappings(viewport.getAlignment());
2799 * start up cDNA consensus (if applicable) now mappings are in place
2801 if (newap.av.initComplementConsensus())
2803 newap.refresh(true); // adjust layout of annotations
2806 newap.av.viewName = getNewViewName(viewTitle);
2808 addAlignmentPanel(newap, true);
2809 newap.alignmentChanged();
2811 if (alignPanels.size() == 2)
2813 viewport.setGatherViewsHere(true);
2815 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2820 * Make a new name for the view, ensuring it is unique within the current
2821 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2822 * these now use viewId. Unique view names are still desirable for usability.)
2827 protected String getNewViewName(String viewTitle)
2829 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2830 boolean addFirstIndex = false;
2831 if (viewTitle == null || viewTitle.trim().length() == 0)
2833 viewTitle = MessageManager.getString("action.view");
2834 addFirstIndex = true;
2838 index = 1;// we count from 1 if given a specific name
2840 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2842 List<Component> comps = PaintRefresher.components
2843 .get(viewport.getSequenceSetId());
2845 List<String> existingNames = getExistingViewNames(comps);
2847 while (existingNames.contains(newViewName))
2849 newViewName = viewTitle + " " + (++index);
2855 * Returns a list of distinct view names found in the given list of
2856 * components. View names are held on the viewport of an AlignmentPanel.
2861 protected List<String> getExistingViewNames(List<Component> comps)
2863 List<String> existingNames = new ArrayList<>();
2864 for (Component comp : comps)
2866 if (comp instanceof AlignmentPanel)
2868 AlignmentPanel ap = (AlignmentPanel) comp;
2869 if (!existingNames.contains(ap.av.viewName))
2871 existingNames.add(ap.av.viewName);
2875 return existingNames;
2879 * Explode tabbed views into separate windows.
2882 public void expandViews_actionPerformed(ActionEvent e)
2884 Desktop.explodeViews(this);
2888 * Gather views in separate windows back into a tabbed presentation.
2891 public void gatherViews_actionPerformed(ActionEvent e)
2893 Desktop.instance.gatherViews(this);
2903 public void font_actionPerformed(ActionEvent e)
2905 new FontChooser(alignPanel);
2915 protected void seqLimit_actionPerformed(ActionEvent e)
2917 viewport.setShowJVSuffix(seqLimits.isSelected());
2919 alignPanel.getIdPanel().getIdCanvas()
2920 .setPreferredSize(alignPanel.calculateIdWidth());
2921 alignPanel.paintAlignment(true, false);
2925 public void idRightAlign_actionPerformed(ActionEvent e)
2927 viewport.setRightAlignIds(idRightAlign.isSelected());
2928 alignPanel.paintAlignment(false, false);
2932 public void centreColumnLabels_actionPerformed(ActionEvent e)
2934 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2935 alignPanel.paintAlignment(false, false);
2941 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2944 protected void followHighlight_actionPerformed()
2947 * Set the 'follow' flag on the Viewport (and scroll to position if now
2950 final boolean state = this.followHighlightMenuItem.getState();
2951 viewport.setFollowHighlight(state);
2954 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2965 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2967 viewport.setColourText(colourTextMenuItem.isSelected());
2968 alignPanel.paintAlignment(false, false);
2978 public void wrapMenuItem_actionPerformed(ActionEvent e)
2980 scaleAbove.setVisible(wrapMenuItem.isSelected());
2981 scaleLeft.setVisible(wrapMenuItem.isSelected());
2982 scaleRight.setVisible(wrapMenuItem.isSelected());
2983 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2984 alignPanel.updateLayout();
2988 public void showAllSeqs_actionPerformed(ActionEvent e)
2990 viewport.showAllHiddenSeqs();
2994 public void showAllColumns_actionPerformed(ActionEvent e)
2996 viewport.showAllHiddenColumns();
2997 alignPanel.paintAlignment(true, true);
2998 viewport.sendSelection();
3002 public void hideSelSequences_actionPerformed(ActionEvent e)
3004 viewport.hideAllSelectedSeqs();
3008 * called by key handler and the hide all/show all menu items
3013 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3016 boolean hide = false;
3017 SequenceGroup sg = viewport.getSelectionGroup();
3018 if (!toggleSeqs && !toggleCols)
3020 // Hide everything by the current selection - this is a hack - we do the
3021 // invert and then hide
3022 // first check that there will be visible columns after the invert.
3023 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3024 && sg.getStartRes() <= sg.getEndRes()))
3026 // now invert the sequence set, if required - empty selection implies
3027 // that no hiding is required.
3030 invertSequenceMenuItem_actionPerformed(null);
3031 sg = viewport.getSelectionGroup();
3035 viewport.expandColSelection(sg, true);
3036 // finally invert the column selection and get the new sequence
3038 invertColSel_actionPerformed(null);
3045 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3047 hideSelSequences_actionPerformed(null);
3050 else if (!(toggleCols && viewport.hasSelectedColumns()))
3052 showAllSeqs_actionPerformed(null);
3058 if (viewport.hasSelectedColumns())
3060 hideSelColumns_actionPerformed(null);
3063 viewport.setSelectionGroup(sg);
3068 showAllColumns_actionPerformed(null);
3077 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3078 * event.ActionEvent)
3081 public void hideAllButSelection_actionPerformed(ActionEvent e)
3083 toggleHiddenRegions(false, false);
3084 viewport.sendSelection();
3091 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3095 public void hideAllSelection_actionPerformed(ActionEvent e)
3097 SequenceGroup sg = viewport.getSelectionGroup();
3098 viewport.expandColSelection(sg, false);
3099 viewport.hideAllSelectedSeqs();
3100 viewport.hideSelectedColumns();
3101 alignPanel.paintAlignment(true, true);
3102 viewport.sendSelection();
3109 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3113 public void showAllhidden_actionPerformed(ActionEvent e)
3115 viewport.showAllHiddenColumns();
3116 viewport.showAllHiddenSeqs();
3117 alignPanel.paintAlignment(true, true);
3118 viewport.sendSelection();
3122 public void hideSelColumns_actionPerformed(ActionEvent e)
3124 viewport.hideSelectedColumns();
3125 alignPanel.paintAlignment(true, true);
3126 viewport.sendSelection();
3130 public void hiddenMarkers_actionPerformed(ActionEvent e)
3132 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3143 protected void scaleAbove_actionPerformed(ActionEvent e)
3145 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3146 // TODO: do we actually need to update overview for scale above change ?
3147 alignPanel.paintAlignment(true, false);
3157 protected void scaleLeft_actionPerformed(ActionEvent e)
3159 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3160 alignPanel.paintAlignment(true, false);
3170 protected void scaleRight_actionPerformed(ActionEvent e)
3172 viewport.setScaleRightWrapped(scaleRight.isSelected());
3173 alignPanel.paintAlignment(true, false);
3183 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3185 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3186 alignPanel.paintAlignment(false, false);
3196 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3198 viewport.setShowText(viewTextMenuItem.isSelected());
3199 alignPanel.paintAlignment(false, false);
3209 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3211 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3212 alignPanel.paintAlignment(false, false);
3215 public FeatureSettings featureSettings;
3218 public FeatureSettingsControllerI getFeatureSettingsUI()
3220 return featureSettings;
3224 public void featureSettings_actionPerformed(ActionEvent e)
3226 if (featureSettings != null)
3228 featureSettings.close();
3229 featureSettings = null;
3231 if (!showSeqFeatures.isSelected())
3233 // make sure features are actually displayed
3234 showSeqFeatures.setSelected(true);
3235 showSeqFeatures_actionPerformed(null);
3237 featureSettings = new FeatureSettings(this);
3241 * Set or clear 'Show Sequence Features'
3247 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3249 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3250 alignPanel.paintAlignment(true, true);
3254 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3255 * the annotations panel as a whole.
3257 * The options to show/hide all annotations should be enabled when the panel
3258 * is shown, and disabled when the panel is hidden.
3263 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3265 final boolean setVisible = annotationPanelMenuItem.isSelected();
3266 viewport.setShowAnnotation(setVisible);
3267 this.showAllSeqAnnotations.setEnabled(setVisible);
3268 this.hideAllSeqAnnotations.setEnabled(setVisible);
3269 this.showAllAlAnnotations.setEnabled(setVisible);
3270 this.hideAllAlAnnotations.setEnabled(setVisible);
3271 alignPanel.updateLayout();
3275 public void alignmentProperties()
3277 JEditorPane editPane = new JEditorPane("text/html", "");
3278 editPane.setEditable(false);
3279 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3282 MessageManager.formatMessage("label.html_content", new Object[]
3283 { contents.toString() }));
3284 JInternalFrame frame = new JInternalFrame();
3285 frame.getContentPane().add(new JScrollPane(editPane));
3287 Desktop.addInternalFrame(frame, MessageManager
3288 .formatMessage("label.alignment_properties", new Object[]
3289 { getTitle() }), 500, 400);
3299 public void overviewMenuItem_actionPerformed(ActionEvent e)
3301 if (alignPanel.overviewPanel != null)
3306 JInternalFrame frame = new JInternalFrame();
3307 final OverviewPanel overview = new OverviewPanel(alignPanel);
3308 frame.setContentPane(overview);
3309 Desktop.addInternalFrame(frame, MessageManager
3310 .formatMessage("label.overview_params", new Object[]
3311 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3314 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3315 frame.addInternalFrameListener(
3316 new javax.swing.event.InternalFrameAdapter()
3319 public void internalFrameClosed(
3320 javax.swing.event.InternalFrameEvent evt)
3323 alignPanel.setOverviewPanel(null);
3326 if (getKeyListeners().length > 0)
3328 frame.addKeyListener(getKeyListeners()[0]);
3331 alignPanel.setOverviewPanel(overview);
3335 public void textColour_actionPerformed()
3337 new TextColourChooser().chooseColour(alignPanel, null);
3341 * public void covariationColour_actionPerformed() {
3343 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3347 public void annotationColour_actionPerformed()
3349 new AnnotationColourChooser(viewport, alignPanel);
3353 public void annotationColumn_actionPerformed(ActionEvent e)
3355 new AnnotationColumnChooser(viewport, alignPanel);
3359 * Action on the user checking or unchecking the option to apply the selected
3360 * colour scheme to all groups. If unchecked, groups may have their own
3361 * independent colour schemes.
3366 public void applyToAllGroups_actionPerformed(boolean selected)
3368 viewport.setColourAppliesToAllGroups(selected);
3372 * Action on user selecting a colour from the colour menu
3375 * the name (not the menu item label!) of the colour scheme
3378 public void changeColour_actionPerformed(String name)
3381 * 'User Defined' opens a panel to configure or load a
3382 * user-defined colour scheme
3384 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3386 new UserDefinedColours(alignPanel);
3391 * otherwise set the chosen colour scheme (or null for 'None')
3393 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3394 viewport.getAlignment(), viewport.getHiddenRepSequences());
3399 * Actions on setting or changing the alignment colour scheme
3404 public void changeColour(ColourSchemeI cs)
3406 // TODO: pull up to controller method
3407 ColourMenuHelper.setColourSelected(colourMenu, cs);
3409 viewport.setGlobalColourScheme(cs);
3411 alignPanel.paintAlignment(true, true);
3415 * Show the PID threshold slider panel
3418 protected void modifyPID_actionPerformed()
3420 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3421 alignPanel.getViewName());
3422 SliderPanel.showPIDSlider();
3426 * Show the Conservation slider panel
3429 protected void modifyConservation_actionPerformed()
3431 SliderPanel.setConservationSlider(alignPanel,
3432 viewport.getResidueShading(), alignPanel.getViewName());
3433 SliderPanel.showConservationSlider();
3437 * Action on selecting or deselecting (Colour) By Conservation
3440 public void conservationMenuItem_actionPerformed(boolean selected)
3442 modifyConservation.setEnabled(selected);
3443 viewport.setConservationSelected(selected);
3444 viewport.getResidueShading().setConservationApplied(selected);
3446 changeColour(viewport.getGlobalColourScheme());
3449 modifyConservation_actionPerformed();
3453 SliderPanel.hideConservationSlider();
3458 * Action on selecting or deselecting (Colour) Above PID Threshold
3461 public void abovePIDThreshold_actionPerformed(boolean selected)
3463 modifyPID.setEnabled(selected);
3464 viewport.setAbovePIDThreshold(selected);
3467 viewport.getResidueShading().setThreshold(0,
3468 viewport.isIgnoreGapsConsensus());
3471 changeColour(viewport.getGlobalColourScheme());
3474 modifyPID_actionPerformed();
3478 SliderPanel.hidePIDSlider();
3489 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3491 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3492 AlignmentSorter.sortByPID(viewport.getAlignment(),
3493 viewport.getAlignment().getSequenceAt(0));
3494 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3495 viewport.getAlignment()));
3496 alignPanel.paintAlignment(true, false);
3506 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3508 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3509 AlignmentSorter.sortByID(viewport.getAlignment());
3511 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3512 alignPanel.paintAlignment(true, false);
3522 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3524 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3525 AlignmentSorter.sortByLength(viewport.getAlignment());
3526 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3527 viewport.getAlignment()));
3528 alignPanel.paintAlignment(true, false);
3538 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3540 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3541 AlignmentSorter.sortByGroup(viewport.getAlignment());
3542 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3543 viewport.getAlignment()));
3545 alignPanel.paintAlignment(true, false);
3555 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3557 new RedundancyPanel(alignPanel, this);
3567 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3569 if ((viewport.getSelectionGroup() == null)
3570 || (viewport.getSelectionGroup().getSize() < 2))
3572 JvOptionPane.showInternalMessageDialog(this,
3573 MessageManager.getString(
3574 "label.you_must_select_least_two_sequences"),
3575 MessageManager.getString("label.invalid_selection"),
3576 JvOptionPane.WARNING_MESSAGE);
3580 JInternalFrame frame = new JInternalFrame();
3581 frame.setContentPane(new PairwiseAlignPanel(viewport));
3582 Desktop.addInternalFrame(frame,
3583 MessageManager.getString("action.pairwise_alignment"), 600,
3589 public void autoCalculate_actionPerformed(ActionEvent e)
3591 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3592 if (viewport.autoCalculateConsensus)
3594 viewport.firePropertyChange("alignment", null,
3595 viewport.getAlignment().getSequences());
3600 public void sortByTreeOption_actionPerformed(ActionEvent e)
3602 viewport.sortByTree = sortByTree.isSelected();
3606 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3608 viewport.followSelection = listenToViewSelections.isSelected();
3612 * Constructs a tree panel and adds it to the desktop
3615 * tree type (NJ or AV)
3617 * name of score model used to compute the tree
3619 * parameters for the distance or similarity calculation
3621 void newTreePanel(String type, String modelName,
3622 SimilarityParamsI options)
3624 String frameTitle = "";
3627 boolean onSelection = false;
3628 if (viewport.getSelectionGroup() != null
3629 && viewport.getSelectionGroup().getSize() > 0)
3631 SequenceGroup sg = viewport.getSelectionGroup();
3633 /* Decide if the selection is a column region */
3634 for (SequenceI _s : sg.getSequences())
3636 if (_s.getLength() < sg.getEndRes())
3638 JvOptionPane.showMessageDialog(Desktop.desktop,
3639 MessageManager.getString(
3640 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3641 MessageManager.getString(
3642 "label.sequences_selection_not_aligned"),
3643 JvOptionPane.WARNING_MESSAGE);
3652 if (viewport.getAlignment().getHeight() < 2)
3658 tp = new TreePanel(alignPanel, type, modelName, options);
3659 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3661 frameTitle += " from ";
3663 if (viewport.viewName != null)
3665 frameTitle += viewport.viewName + " of ";
3668 frameTitle += this.title;
3670 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3681 public void addSortByOrderMenuItem(String title,
3682 final AlignmentOrder order)
3684 final JMenuItem item = new JMenuItem(MessageManager
3685 .formatMessage("action.by_title_param", new Object[]
3688 item.addActionListener(new java.awt.event.ActionListener()
3691 public void actionPerformed(ActionEvent e)
3693 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3695 // TODO: JBPNote - have to map order entries to curent SequenceI
3697 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3699 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3700 viewport.getAlignment()));
3702 alignPanel.paintAlignment(true, false);
3708 * Add a new sort by annotation score menu item
3711 * the menu to add the option to
3713 * the label used to retrieve scores for each sequence on the
3716 public void addSortByAnnotScoreMenuItem(JMenu sort,
3717 final String scoreLabel)
3719 final JMenuItem item = new JMenuItem(scoreLabel);
3721 item.addActionListener(new java.awt.event.ActionListener()
3724 public void actionPerformed(ActionEvent e)
3726 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3727 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3728 viewport.getAlignment());// ,viewport.getSelectionGroup());
3729 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3730 viewport.getAlignment()));
3731 alignPanel.paintAlignment(true, false);
3737 * last hash for alignment's annotation array - used to minimise cost of
3740 protected int _annotationScoreVectorHash;
3743 * search the alignment and rebuild the sort by annotation score submenu the
3744 * last alignment annotation vector hash is stored to minimize cost of
3745 * rebuilding in subsequence calls.
3749 public void buildSortByAnnotationScoresMenu()
3751 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3756 if (viewport.getAlignment().getAlignmentAnnotation()
3757 .hashCode() != _annotationScoreVectorHash)
3759 sortByAnnotScore.removeAll();
3760 // almost certainly a quicker way to do this - but we keep it simple
3761 Hashtable scoreSorts = new Hashtable();
3762 AlignmentAnnotation aann[];
3763 for (SequenceI sqa : viewport.getAlignment().getSequences())
3765 aann = sqa.getAnnotation();
3766 for (int i = 0; aann != null && i < aann.length; i++)
3768 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3770 scoreSorts.put(aann[i].label, aann[i].label);
3774 Enumeration labels = scoreSorts.keys();
3775 while (labels.hasMoreElements())
3777 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3778 (String) labels.nextElement());
3780 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3783 _annotationScoreVectorHash = viewport.getAlignment()
3784 .getAlignmentAnnotation().hashCode();
3789 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3790 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3791 * call. Listeners are added to remove the menu item when the treePanel is
3792 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3796 public void buildTreeSortMenu()
3798 sortByTreeMenu.removeAll();
3800 List<Component> comps = PaintRefresher.components
3801 .get(viewport.getSequenceSetId());
3802 List<TreePanel> treePanels = new ArrayList<>();
3803 for (Component comp : comps)
3805 if (comp instanceof TreePanel)
3807 treePanels.add((TreePanel) comp);
3811 if (treePanels.size() < 1)
3813 sortByTreeMenu.setVisible(false);
3817 sortByTreeMenu.setVisible(true);
3819 for (final TreePanel tp : treePanels)
3821 final JMenuItem item = new JMenuItem(tp.getTitle());
3822 item.addActionListener(new java.awt.event.ActionListener()
3825 public void actionPerformed(ActionEvent e)
3827 tp.sortByTree_actionPerformed();
3828 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3833 sortByTreeMenu.add(item);
3837 public boolean sortBy(AlignmentOrder alorder, String undoname)
3839 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3840 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3841 if (undoname != null)
3843 addHistoryItem(new OrderCommand(undoname, oldOrder,
3844 viewport.getAlignment()));
3846 alignPanel.paintAlignment(true, false);
3851 * Work out whether the whole set of sequences or just the selected set will
3852 * be submitted for multiple alignment.
3855 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3857 // Now, check we have enough sequences
3858 AlignmentView msa = null;
3860 if ((viewport.getSelectionGroup() != null)
3861 && (viewport.getSelectionGroup().getSize() > 1))
3863 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3864 // some common interface!
3866 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3867 * SequenceI[sz = seqs.getSize(false)];
3869 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3870 * seqs.getSequenceAt(i); }
3872 msa = viewport.getAlignmentView(true);
3874 else if (viewport.getSelectionGroup() != null
3875 && viewport.getSelectionGroup().getSize() == 1)
3877 int option = JvOptionPane.showConfirmDialog(this,
3878 MessageManager.getString("warn.oneseq_msainput_selection"),
3879 MessageManager.getString("label.invalid_selection"),
3880 JvOptionPane.OK_CANCEL_OPTION);
3881 if (option == JvOptionPane.OK_OPTION)
3883 msa = viewport.getAlignmentView(false);
3888 msa = viewport.getAlignmentView(false);
3894 * Decides what is submitted to a secondary structure prediction service: the
3895 * first sequence in the alignment, or in the current selection, or, if the
3896 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3897 * region or the whole alignment. (where the first sequence in the set is the
3898 * one that the prediction will be for).
3900 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3902 AlignmentView seqs = null;
3904 if ((viewport.getSelectionGroup() != null)
3905 && (viewport.getSelectionGroup().getSize() > 0))
3907 seqs = viewport.getAlignmentView(true);
3911 seqs = viewport.getAlignmentView(false);
3913 // limit sequences - JBPNote in future - could spawn multiple prediction
3915 // TODO: viewport.getAlignment().isAligned is a global state - the local
3916 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3917 if (!viewport.getAlignment().isAligned(false))
3919 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3920 // TODO: if seqs.getSequences().length>1 then should really have warned
3934 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3936 // Pick the tree file
3937 JalviewFileChooser chooser = new JalviewFileChooser(
3938 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3939 chooser.setFileView(new JalviewFileView());
3940 chooser.setDialogTitle(
3941 MessageManager.getString("label.select_newick_like_tree_file"));
3942 chooser.setToolTipText(
3943 MessageManager.getString("label.load_tree_file"));
3946 new jalview.util.dialogrunner.RunResponse(JalviewFileChooser.APPROVE_OPTION)
3951 String filePath = chooser.getSelectedFile().getPath();
3952 Cache.setProperty("LAST_DIRECTORY", filePath);
3953 NewickFile fin = null;
3956 fin = new NewickFile(new FileParse(
3957 chooser.getSelectedFile(), DataSourceType.FILE));
3958 viewport.setCurrentTree(
3959 showNewickTree(fin, filePath).getTree());
3960 } catch (Exception ex)
3962 JvOptionPane.showMessageDialog(Desktop.desktop,
3964 MessageManager.getString(
3965 "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(),
3973 MessageManager.getString(
3974 "label.possible_problem_with_tree_file"),
3975 JvOptionPane.WARNING_MESSAGE);
3978 }).openDialog(this);
3981 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3983 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3986 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3987 int h, int x, int y)
3989 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3993 * Add a treeviewer for the tree extracted from a Newick file object to the
3994 * current alignment view
4001 * Associated alignment input data (or null)
4010 * @return TreePanel handle
4012 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4013 AlignmentView input, int w, int h, int x, int y)
4015 TreePanel tp = null;
4021 if (nf.getTree() != null)
4023 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4029 tp.setLocation(x, y);
4032 Desktop.addInternalFrame(tp, treeTitle, w, h);
4034 } catch (Exception ex)
4036 ex.printStackTrace();
4042 private boolean buildingMenu = false;
4045 * Generates menu items and listener event actions for web service clients
4048 public void BuildWebServiceMenu()
4050 while (buildingMenu)
4054 System.err.println("Waiting for building menu to finish.");
4056 } catch (Exception e)
4060 final AlignFrame me = this;
4061 buildingMenu = true;
4062 new Thread(new Runnable()
4067 final List<JMenuItem> legacyItems = new ArrayList<>();
4070 // System.err.println("Building ws menu again "
4071 // + Thread.currentThread());
4072 // TODO: add support for context dependent disabling of services based
4074 // alignment and current selection
4075 // TODO: add additional serviceHandle parameter to specify abstract
4077 // class independently of AbstractName
4078 // TODO: add in rediscovery GUI function to restart discoverer
4079 // TODO: group services by location as well as function and/or
4081 // object broker mechanism.
4082 final Vector<JMenu> wsmenu = new Vector<>();
4083 final IProgressIndicator af = me;
4086 * do not i18n these strings - they are hard-coded in class
4087 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4088 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4090 final JMenu msawsmenu = new JMenu("Alignment");
4091 final JMenu secstrmenu = new JMenu(
4092 "Secondary Structure Prediction");
4093 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4094 final JMenu analymenu = new JMenu("Analysis");
4095 final JMenu dismenu = new JMenu("Protein Disorder");
4096 // JAL-940 - only show secondary structure prediction services from
4097 // the legacy server
4098 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4100 Discoverer.services != null && (Discoverer.services.size() > 0))
4102 // TODO: refactor to allow list of AbstractName/Handler bindings to
4104 // stored or retrieved from elsewhere
4105 // No MSAWS used any more:
4106 // Vector msaws = null; // (Vector)
4107 // Discoverer.services.get("MsaWS");
4108 Vector secstrpr = (Vector) Discoverer.services
4110 if (secstrpr != null)
4112 // Add any secondary structure prediction services
4113 for (int i = 0, j = secstrpr.size(); i < j; i++)
4115 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4117 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4118 .getServiceClient(sh);
4119 int p = secstrmenu.getItemCount();
4120 impl.attachWSMenuEntry(secstrmenu, me);
4121 int q = secstrmenu.getItemCount();
4122 for (int litm = p; litm < q; litm++)
4124 legacyItems.add(secstrmenu.getItem(litm));
4130 // Add all submenus in the order they should appear on the web
4132 wsmenu.add(msawsmenu);
4133 wsmenu.add(secstrmenu);
4134 wsmenu.add(dismenu);
4135 wsmenu.add(analymenu);
4136 // No search services yet
4137 // wsmenu.add(seqsrchmenu);
4139 javax.swing.SwingUtilities.invokeLater(new Runnable()
4146 webService.removeAll();
4147 // first, add discovered services onto the webservices menu
4148 if (wsmenu.size() > 0)
4150 for (int i = 0, j = wsmenu.size(); i < j; i++)
4152 webService.add(wsmenu.get(i));
4157 webService.add(me.webServiceNoServices);
4159 // TODO: move into separate menu builder class.
4160 boolean new_sspred = false;
4161 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4163 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4164 if (jws2servs != null)
4166 if (jws2servs.hasServices())
4168 jws2servs.attachWSMenuEntry(webService, me);
4169 for (Jws2Instance sv : jws2servs.getServices())
4171 if (sv.description.toLowerCase().contains("jpred"))
4173 for (JMenuItem jmi : legacyItems)
4175 jmi.setVisible(false);
4181 if (jws2servs.isRunning())
4183 JMenuItem tm = new JMenuItem(
4184 "Still discovering JABA Services");
4185 tm.setEnabled(false);
4190 build_urlServiceMenu(me.webService);
4191 build_fetchdbmenu(webService);
4192 for (JMenu item : wsmenu)
4194 if (item.getItemCount() == 0)
4196 item.setEnabled(false);
4200 item.setEnabled(true);
4203 } catch (Exception e)
4206 "Exception during web service menu building process.",
4211 } catch (Exception e)
4214 buildingMenu = false;
4221 * construct any groupURL type service menu entries.
4225 private void build_urlServiceMenu(JMenu webService)
4227 // TODO: remove this code when 2.7 is released
4228 // DEBUG - alignmentView
4230 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4231 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4233 * @Override public void actionPerformed(ActionEvent e) {
4234 * jalview.datamodel.AlignmentView
4235 * .testSelectionViews(af.viewport.getAlignment(),
4236 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4238 * }); webService.add(testAlView);
4240 // TODO: refactor to RestClient discoverer and merge menu entries for
4241 // rest-style services with other types of analysis/calculation service
4242 // SHmmr test client - still being implemented.
4243 // DEBUG - alignmentView
4245 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4248 client.attachWSMenuEntry(
4249 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4255 * Searches the alignment sequences for xRefs and builds the Show
4256 * Cross-References menu (formerly called Show Products), with database
4257 * sources for which cross-references are found (protein sources for a
4258 * nucleotide alignment and vice versa)
4260 * @return true if Show Cross-references menu should be enabled
4262 public boolean canShowProducts()
4264 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4265 AlignmentI dataset = viewport.getAlignment().getDataset();
4267 showProducts.removeAll();
4268 final boolean dna = viewport.getAlignment().isNucleotide();
4270 if (seqs == null || seqs.length == 0)
4272 // nothing to see here.
4276 boolean showp = false;
4279 List<String> ptypes = new CrossRef(seqs, dataset)
4280 .findXrefSourcesForSequences(dna);
4282 for (final String source : ptypes)
4285 final AlignFrame af = this;
4286 JMenuItem xtype = new JMenuItem(source);
4287 xtype.addActionListener(new ActionListener()
4290 public void actionPerformed(ActionEvent e)
4292 showProductsFor(af.viewport.getSequenceSelection(), dna,
4296 showProducts.add(xtype);
4298 showProducts.setVisible(showp);
4299 showProducts.setEnabled(showp);
4300 } catch (Exception e)
4303 "canShowProducts threw an exception - please report to help@jalview.org",
4311 * Finds and displays cross-references for the selected sequences (protein
4312 * products for nucleotide sequences, dna coding sequences for peptides).
4315 * the sequences to show cross-references for
4317 * true if from a nucleotide alignment (so showing proteins)
4319 * the database to show cross-references for
4321 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4322 final String source)
4324 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4329 * Construct and display a new frame containing the translation of this
4330 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4333 public void showTranslation_actionPerformed(ActionEvent e)
4335 AlignmentI al = null;
4338 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4340 al = dna.translateCdna();
4341 } catch (Exception ex)
4343 jalview.bin.Cache.log.error(
4344 "Exception during translation. Please report this !", ex);
4345 final String msg = MessageManager.getString(
4346 "label.error_when_translating_sequences_submit_bug_report");
4347 final String errorTitle = MessageManager
4348 .getString("label.implementation_error")
4349 + MessageManager.getString("label.translation_failed");
4350 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4351 JvOptionPane.ERROR_MESSAGE);
4354 if (al == null || al.getHeight() == 0)
4356 final String msg = MessageManager.getString(
4357 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4358 final String errorTitle = MessageManager
4359 .getString("label.translation_failed");
4360 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4361 JvOptionPane.WARNING_MESSAGE);
4365 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4366 af.setFileFormat(this.currentFileFormat);
4367 final String newTitle = MessageManager
4368 .formatMessage("label.translation_of_params", new Object[]
4369 { this.getTitle() });
4370 af.setTitle(newTitle);
4371 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4373 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4374 viewport.openSplitFrame(af, new Alignment(seqs));
4378 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4385 * Set the file format
4389 public void setFileFormat(FileFormatI format)
4391 this.currentFileFormat = format;
4395 * Try to load a features file onto the alignment.
4398 * contents or path to retrieve file or a File object
4400 * access mode of file (see jalview.io.AlignFile)
4401 * @return true if features file was parsed correctly.
4403 public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4406 return avc.parseFeaturesFile(file, sourceType,
4407 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4412 public void refreshFeatureUI(boolean enableIfNecessary)
4414 // note - currently this is only still here rather than in the controller
4415 // because of the featureSettings hard reference that is yet to be
4417 if (enableIfNecessary)
4419 viewport.setShowSequenceFeatures(true);
4420 showSeqFeatures.setSelected(true);
4426 public void dragEnter(DropTargetDragEvent evt)
4431 public void dragExit(DropTargetEvent evt)
4436 public void dragOver(DropTargetDragEvent evt)
4441 public void dropActionChanged(DropTargetDragEvent evt)
4446 public void drop(DropTargetDropEvent evt)
4448 // JAL-1552 - acceptDrop required before getTransferable call for
4449 // Java's Transferable for native dnd
4450 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4451 Transferable t = evt.getTransferable();
4454 final AlignFrame thisaf = this;
4455 final List<Object> files = new ArrayList<>();
4456 List<DataSourceType> protocols = new ArrayList<>();
4460 Desktop.transferFromDropTarget(files, protocols, evt, t);
4461 } catch (Exception e)
4463 e.printStackTrace();
4467 new Thread(new Runnable()
4474 // check to see if any of these files have names matching sequences
4477 SequenceIdMatcher idm = new SequenceIdMatcher(
4478 viewport.getAlignment().getSequencesArray());
4480 * Object[] { String,SequenceI}
4482 ArrayList<Object[]> filesmatched = new ArrayList<>();
4483 ArrayList<Object> filesnotmatched = new ArrayList<>();
4484 for (int i = 0; i < files.size(); i++)
4487 Object file = files.get(i);
4488 String fileName = file.toString();
4490 DataSourceType protocol = (file instanceof File ? DataSourceType.FILE : FormatAdapter.checkProtocol(fileName));
4491 if (protocol == DataSourceType.FILE)
4493 File fl = (file instanceof File ? (File) file : new File(fileName));
4494 pdbfn = fl.getName();
4496 else if (protocol == DataSourceType.URL)
4498 URL url = new URL(fileName);
4499 pdbfn = url.getFile();
4501 if (pdbfn.length() > 0)
4503 // attempt to find a match in the alignment
4504 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4505 int l = 0, c = pdbfn.indexOf(".");
4506 while (mtch == null && c != -1)
4511 } while ((c = pdbfn.indexOf(".", l)) > l);
4514 pdbfn = pdbfn.substring(0, l);
4516 mtch = idm.findAllIdMatches(pdbfn);
4523 type = new IdentifyFile().identify(file, protocol);
4524 } catch (Exception ex)
4528 if (type != null && type.isStructureFile())
4530 filesmatched.add(new Object[] { file, protocol, mtch });
4534 // File wasn't named like one of the sequences or wasn't a PDB
4536 filesnotmatched.add(file);
4540 if (filesmatched.size() > 0)
4542 boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4545 String msg = MessageManager.formatMessage(
4546 "label.automatically_associate_structure_files_with_sequences_same_name",
4548 { Integer.valueOf(filesmatched.size())
4550 String ttl = MessageManager.getString(
4551 "label.automatically_associate_structure_files_by_name");
4552 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4553 ttl, JvOptionPane.YES_NO_OPTION);
4554 autoAssociate = choice == JvOptionPane.YES_OPTION;
4558 for (Object[] fm : filesmatched)
4560 // try and associate
4561 // TODO: may want to set a standard ID naming formalism for
4562 // associating PDB files which have no IDs.
4563 for (SequenceI toassoc : (SequenceI[]) fm[2])
4565 PDBEntry pe = new AssociatePdbFileWithSeq()
4566 .associatePdbWithSeq((String) fm[0],
4567 (DataSourceType) fm[1], toassoc, false,
4571 System.err.println("Associated file : "
4572 + ((String) fm[0]) + " with "
4573 + toassoc.getDisplayId(true));
4577 // TODO: do we need to update overview ? only if features are
4579 alignPanel.paintAlignment(true, false);
4585 * add declined structures as sequences
4587 for (Object[] o : filesmatched)
4589 filesnotmatched.add(o[0]);
4593 if (filesnotmatched.size() > 0)
4595 if (assocfiles > 0 && (Cache.getDefault(
4596 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4597 || JvOptionPane.showConfirmDialog(thisaf,
4598 "<html>" + MessageManager.formatMessage(
4599 "label.ignore_unmatched_dropped_files_info",
4602 filesnotmatched.size())
4605 MessageManager.getString(
4606 "label.ignore_unmatched_dropped_files"),
4607 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4611 for (Object fn : filesnotmatched)
4613 loadJalviewDataFile(fn, null, null, null);
4617 } catch (Exception ex)
4619 ex.printStackTrace();
4627 * Attempt to load a "dropped" file or URL string, by testing in turn for
4629 * <li>an Annotation file</li>
4630 * <li>a JNet file</li>
4631 * <li>a features file</li>
4632 * <li>else try to interpret as an alignment file</li>
4636 * either a filename or a URL string.
4638 public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4639 FileFormatI format, SequenceI assocSeq)
4641 // BH 2018 was String file
4644 if (sourceType == null)
4646 sourceType = FormatAdapter.checkProtocol(file);
4648 // if the file isn't identified, or not positively identified as some
4649 // other filetype (PFAM is default unidentified alignment file type) then
4650 // try to parse as annotation.
4651 boolean isAnnotation = (format == null
4652 || FileFormat.Pfam.equals(format))
4653 ? new AnnotationFile().annotateAlignmentView(viewport,
4659 // first see if its a T-COFFEE score file
4660 TCoffeeScoreFile tcf = null;
4663 tcf = new TCoffeeScoreFile(file, sourceType);
4666 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4670 new TCoffeeColourScheme(viewport.getAlignment()));
4671 isAnnotation = true;
4672 statusBar.setText(MessageManager.getString(
4673 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4677 // some problem - if no warning its probable that the ID matching
4678 // process didn't work
4679 JvOptionPane.showMessageDialog(Desktop.desktop,
4680 tcf.getWarningMessage() == null
4681 ? MessageManager.getString(
4682 "label.check_file_matches_sequence_ids_alignment")
4683 : tcf.getWarningMessage(),
4684 MessageManager.getString(
4685 "label.problem_reading_tcoffee_score_file"),
4686 JvOptionPane.WARNING_MESSAGE);
4693 } catch (Exception x)
4696 "Exception when processing data source as T-COFFEE score file",
4702 // try to see if its a JNet 'concise' style annotation file *before*
4704 // try to parse it as a features file
4707 format = new IdentifyFile().identify(file, sourceType);
4709 if (FileFormat.ScoreMatrix == format)
4711 ScoreMatrixFile sm = new ScoreMatrixFile(
4712 new FileParse(file, sourceType));
4714 // todo: i18n this message
4715 statusBar.setText(MessageManager.formatMessage(
4716 "label.successfully_loaded_matrix",
4717 sm.getMatrixName()));
4719 else if (FileFormat.Jnet.equals(format))
4721 JPredFile predictions = new JPredFile(file, sourceType);
4722 new JnetAnnotationMaker();
4723 JnetAnnotationMaker.add_annotation(predictions,
4724 viewport.getAlignment(), 0, false);
4725 viewport.getAlignment().setupJPredAlignment();
4726 isAnnotation = true;
4728 // else if (IdentifyFile.FeaturesFile.equals(format))
4729 else if (FileFormat.Features.equals(format))
4731 if (parseFeaturesFile(file, sourceType))
4733 alignPanel.paintAlignment(true, true);
4738 new FileLoader().LoadFile(viewport, file, sourceType, format);
4745 alignPanel.adjustAnnotationHeight();
4746 viewport.updateSequenceIdColours();
4747 buildSortByAnnotationScoresMenu();
4748 alignPanel.paintAlignment(true, true);
4750 } catch (Exception ex)
4752 ex.printStackTrace();
4753 } catch (OutOfMemoryError oom)
4758 } catch (Exception x)
4763 + (sourceType != null
4764 ? (sourceType == DataSourceType.PASTE
4766 : "using " + sourceType + " from "
4770 ? "(parsing as '" + format + "' file)"
4772 oom, Desktop.desktop);
4777 * Method invoked by the ChangeListener on the tabbed pane, in other words
4778 * when a different tabbed pane is selected by the user or programmatically.
4781 public void tabSelectionChanged(int index)
4785 alignPanel = alignPanels.get(index);
4786 viewport = alignPanel.av;
4787 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4788 setMenusFromViewport(viewport);
4792 * 'focus' any colour slider that is open to the selected viewport
4794 if (viewport.getConservationSelected())
4796 SliderPanel.setConservationSlider(alignPanel,
4797 viewport.getResidueShading(), alignPanel.getViewName());
4801 SliderPanel.hideConservationSlider();
4803 if (viewport.getAbovePIDThreshold())
4805 SliderPanel.setPIDSliderSource(alignPanel,
4806 viewport.getResidueShading(), alignPanel.getViewName());
4810 SliderPanel.hidePIDSlider();
4814 * If there is a frame linked to this one in a SplitPane, switch it to the
4815 * same view tab index. No infinite recursion of calls should happen, since
4816 * tabSelectionChanged() should not get invoked on setting the selected
4817 * index to an unchanged value. Guard against setting an invalid index
4818 * before the new view peer tab has been created.
4820 final AlignViewportI peer = viewport.getCodingComplement();
4823 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4824 .getAlignPanel().alignFrame;
4825 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4827 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4833 * On right mouse click on view tab, prompt for and set new view name.
4836 public void tabbedPane_mousePressed(MouseEvent e)
4838 if (e.isPopupTrigger())
4840 String msg = MessageManager.getString("label.enter_view_name");
4841 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4842 JvOptionPane.QUESTION_MESSAGE);
4846 viewport.viewName = reply;
4847 // TODO warn if reply is in getExistingViewNames()?
4848 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4853 public AlignViewport getCurrentView()
4859 * Open the dialog for regex description parsing.
4862 protected void extractScores_actionPerformed(ActionEvent e)
4864 ParseProperties pp = new jalview.analysis.ParseProperties(
4865 viewport.getAlignment());
4866 // TODO: verify regex and introduce GUI dialog for version 2.5
4867 // if (pp.getScoresFromDescription("col", "score column ",
4868 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4870 if (pp.getScoresFromDescription("description column",
4871 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4873 buildSortByAnnotationScoresMenu();
4881 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4885 protected void showDbRefs_actionPerformed(ActionEvent e)
4887 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4893 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4897 protected void showNpFeats_actionPerformed(ActionEvent e)
4899 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4903 * find the viewport amongst the tabs in this alignment frame and close that
4908 public boolean closeView(AlignViewportI av)
4912 this.closeMenuItem_actionPerformed(false);
4915 Component[] comp = tabbedPane.getComponents();
4916 for (int i = 0; comp != null && i < comp.length; i++)
4918 if (comp[i] instanceof AlignmentPanel)
4920 if (((AlignmentPanel) comp[i]).av == av)
4923 closeView((AlignmentPanel) comp[i]);
4931 protected void build_fetchdbmenu(JMenu webService)
4933 // Temporary hack - DBRef Fetcher always top level ws entry.
4934 // TODO We probably want to store a sequence database checklist in
4935 // preferences and have checkboxes.. rather than individual sources selected
4937 final JMenu rfetch = new JMenu(
4938 MessageManager.getString("action.fetch_db_references"));
4939 rfetch.setToolTipText(MessageManager.getString(
4940 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4941 webService.add(rfetch);
4943 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4944 MessageManager.getString("option.trim_retrieved_seqs"));
4945 trimrs.setToolTipText(
4946 MessageManager.getString("label.trim_retrieved_sequences"));
4948 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4949 trimrs.addActionListener(new ActionListener()
4952 public void actionPerformed(ActionEvent e)
4954 trimrs.setSelected(trimrs.isSelected());
4955 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4956 Boolean.valueOf(trimrs.isSelected()).toString());
4960 JMenuItem fetchr = new JMenuItem(
4961 MessageManager.getString("label.standard_databases"));
4962 fetchr.setToolTipText(
4963 MessageManager.getString("label.fetch_embl_uniprot"));
4964 fetchr.addActionListener(new ActionListener()
4968 public void actionPerformed(ActionEvent e)
4970 new Thread(new Runnable()
4975 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4976 .getAlignment().isNucleotide();
4977 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4978 alignPanel.av.getSequenceSelection(),
4979 alignPanel.alignFrame, null,
4980 alignPanel.alignFrame.featureSettings, isNucleotide);
4981 dbRefFetcher.addListener(new FetchFinishedListenerI()
4984 public void finished()
4986 AlignFrame.this.setMenusForViewport();
4989 dbRefFetcher.fetchDBRefs(false);
4997 final AlignFrame me = this;
4998 new Thread(new Runnable()
5003 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5004 .getSequenceFetcherSingleton(me);
5005 javax.swing.SwingUtilities.invokeLater(new Runnable()
5010 String[] dbclasses = sf.getOrderedSupportedSources();
5011 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5012 // jalview.util.QuickSort.sort(otherdb, otherdb);
5013 List<DbSourceProxy> otherdb;
5014 JMenu dfetch = new JMenu();
5015 JMenu ifetch = new JMenu();
5016 JMenuItem fetchr = null;
5017 int comp = 0, icomp = 0, mcomp = 15;
5018 String mname = null;
5020 for (String dbclass : dbclasses)
5022 otherdb = sf.getSourceProxy(dbclass);
5023 // add a single entry for this class, or submenu allowing 'fetch
5025 if (otherdb == null || otherdb.size() < 1)
5029 // List<DbSourceProxy> dbs=otherdb;
5030 // otherdb=new ArrayList<DbSourceProxy>();
5031 // for (DbSourceProxy db:dbs)
5033 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5037 mname = "From " + dbclass;
5039 if (otherdb.size() == 1)
5041 final DbSourceProxy[] dassource = otherdb
5042 .toArray(new DbSourceProxy[0]);
5043 DbSourceProxy src = otherdb.get(0);
5044 fetchr = new JMenuItem(src.getDbSource());
5045 fetchr.addActionListener(new ActionListener()
5049 public void actionPerformed(ActionEvent e)
5051 new Thread(new Runnable()
5057 boolean isNucleotide = alignPanel.alignFrame
5058 .getViewport().getAlignment()
5060 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5061 alignPanel.av.getSequenceSelection(),
5062 alignPanel.alignFrame, dassource,
5063 alignPanel.alignFrame.featureSettings,
5066 .addListener(new FetchFinishedListenerI()
5069 public void finished()
5071 AlignFrame.this.setMenusForViewport();
5074 dbRefFetcher.fetchDBRefs(false);
5080 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5081 MessageManager.formatMessage(
5082 "label.fetch_retrieve_from", new Object[]
5083 { src.getDbName() })));
5089 final DbSourceProxy[] dassource = otherdb
5090 .toArray(new DbSourceProxy[0]);
5092 DbSourceProxy src = otherdb.get(0);
5093 fetchr = new JMenuItem(MessageManager
5094 .formatMessage("label.fetch_all_param", new Object[]
5095 { src.getDbSource() }));
5096 fetchr.addActionListener(new ActionListener()
5099 public void actionPerformed(ActionEvent e)
5101 new Thread(new Runnable()
5107 boolean isNucleotide = alignPanel.alignFrame
5108 .getViewport().getAlignment()
5110 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5111 alignPanel.av.getSequenceSelection(),
5112 alignPanel.alignFrame, dassource,
5113 alignPanel.alignFrame.featureSettings,
5116 .addListener(new FetchFinishedListenerI()
5119 public void finished()
5121 AlignFrame.this.setMenusForViewport();
5124 dbRefFetcher.fetchDBRefs(false);
5130 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5131 MessageManager.formatMessage(
5132 "label.fetch_retrieve_from_all_sources",
5134 { Integer.valueOf(otherdb.size())
5136 src.getDbSource(), src.getDbName() })));
5139 // and then build the rest of the individual menus
5140 ifetch = new JMenu(MessageManager.formatMessage(
5141 "label.source_from_db_source", new Object[]
5142 { src.getDbSource() }));
5144 String imname = null;
5146 for (DbSourceProxy sproxy : otherdb)
5148 String dbname = sproxy.getDbName();
5149 String sname = dbname.length() > 5
5150 ? dbname.substring(0, 5) + "..."
5152 String msname = dbname.length() > 10
5153 ? dbname.substring(0, 10) + "..."
5157 imname = MessageManager
5158 .formatMessage("label.from_msname", new Object[]
5161 fetchr = new JMenuItem(msname);
5162 final DbSourceProxy[] dassrc = { sproxy };
5163 fetchr.addActionListener(new ActionListener()
5167 public void actionPerformed(ActionEvent e)
5169 new Thread(new Runnable()
5175 boolean isNucleotide = alignPanel.alignFrame
5176 .getViewport().getAlignment()
5178 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5179 alignPanel.av.getSequenceSelection(),
5180 alignPanel.alignFrame, dassrc,
5181 alignPanel.alignFrame.featureSettings,
5184 .addListener(new FetchFinishedListenerI()
5187 public void finished()
5189 AlignFrame.this.setMenusForViewport();
5192 dbRefFetcher.fetchDBRefs(false);
5198 fetchr.setToolTipText(
5199 "<html>" + MessageManager.formatMessage(
5200 "label.fetch_retrieve_from", new Object[]
5204 if (++icomp >= mcomp || i == (otherdb.size()))
5206 ifetch.setText(MessageManager.formatMessage(
5207 "label.source_to_target", imname, sname));
5209 ifetch = new JMenu();
5217 if (comp >= mcomp || dbi >= (dbclasses.length))
5219 dfetch.setText(MessageManager.formatMessage(
5220 "label.source_to_target", mname, dbclass));
5222 dfetch = new JMenu();
5235 * Left justify the whole alignment.
5238 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5240 AlignmentI al = viewport.getAlignment();
5242 viewport.firePropertyChange("alignment", null, al);
5246 * Right justify the whole alignment.
5249 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5251 AlignmentI al = viewport.getAlignment();
5253 viewport.firePropertyChange("alignment", null, al);
5257 public void setShowSeqFeatures(boolean b)
5259 showSeqFeatures.setSelected(b);
5260 viewport.setShowSequenceFeatures(b);
5267 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5268 * awt.event.ActionEvent)
5271 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5273 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5274 alignPanel.paintAlignment(false, false);
5281 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5285 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5287 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5288 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5296 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5297 * .event.ActionEvent)
5300 protected void showGroupConservation_actionPerformed(ActionEvent e)
5302 viewport.setShowGroupConservation(showGroupConservation.getState());
5303 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5310 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5311 * .event.ActionEvent)
5314 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5316 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5317 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5324 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5325 * .event.ActionEvent)
5328 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5330 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5331 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5335 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5337 showSequenceLogo.setState(true);
5338 viewport.setShowSequenceLogo(true);
5339 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5340 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5344 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5346 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5353 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5354 * .event.ActionEvent)
5357 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5359 if (avc.makeGroupsFromSelection())
5361 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5362 alignPanel.updateAnnotation();
5363 alignPanel.paintAlignment(true, true);
5367 public void clearAlignmentSeqRep()
5369 // TODO refactor alignmentseqrep to controller
5370 if (viewport.getAlignment().hasSeqrep())
5372 viewport.getAlignment().setSeqrep(null);
5373 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5374 alignPanel.updateAnnotation();
5375 alignPanel.paintAlignment(true, true);
5380 protected void createGroup_actionPerformed(ActionEvent e)
5382 if (avc.createGroup())
5384 alignPanel.alignmentChanged();
5389 protected void unGroup_actionPerformed(ActionEvent e)
5393 alignPanel.alignmentChanged();
5398 * make the given alignmentPanel the currently selected tab
5400 * @param alignmentPanel
5402 public void setDisplayedView(AlignmentPanel alignmentPanel)
5404 if (!viewport.getSequenceSetId()
5405 .equals(alignmentPanel.av.getSequenceSetId()))
5407 throw new Error(MessageManager.getString(
5408 "error.implementation_error_cannot_show_view_alignment_frame"));
5410 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5411 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5413 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5418 * Action on selection of menu options to Show or Hide annotations.
5421 * @param forSequences
5422 * update sequence-related annotations
5423 * @param forAlignment
5424 * update non-sequence-related annotations
5427 protected void setAnnotationsVisibility(boolean visible,
5428 boolean forSequences, boolean forAlignment)
5430 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5431 .getAlignmentAnnotation();
5436 for (AlignmentAnnotation aa : anns)
5439 * don't display non-positional annotations on an alignment
5441 if (aa.annotations == null)
5445 boolean apply = (aa.sequenceRef == null && forAlignment)
5446 || (aa.sequenceRef != null && forSequences);
5449 aa.visible = visible;
5452 alignPanel.validateAnnotationDimensions(true);
5453 alignPanel.alignmentChanged();
5457 * Store selected annotation sort order for the view and repaint.
5460 protected void sortAnnotations_actionPerformed()
5462 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5464 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5465 alignPanel.paintAlignment(false, false);
5470 * @return alignment panels in this alignment frame
5472 public List<? extends AlignmentViewPanel> getAlignPanels()
5474 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5478 * Open a new alignment window, with the cDNA associated with this (protein)
5479 * alignment, aligned as is the protein.
5481 protected void viewAsCdna_actionPerformed()
5483 // TODO no longer a menu action - refactor as required
5484 final AlignmentI alignment = getViewport().getAlignment();
5485 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5486 if (mappings == null)
5490 List<SequenceI> cdnaSeqs = new ArrayList<>();
5491 for (SequenceI aaSeq : alignment.getSequences())
5493 for (AlignedCodonFrame acf : mappings)
5495 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5499 * There is a cDNA mapping for this protein sequence - add to new
5500 * alignment. It will share the same dataset sequence as other mapped
5501 * cDNA (no new mappings need to be created).
5503 final Sequence newSeq = new Sequence(dnaSeq);
5504 newSeq.setDatasetSequence(dnaSeq);
5505 cdnaSeqs.add(newSeq);
5509 if (cdnaSeqs.size() == 0)
5511 // show a warning dialog no mapped cDNA
5514 AlignmentI cdna = new Alignment(
5515 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5516 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5517 AlignFrame.DEFAULT_HEIGHT);
5518 cdna.alignAs(alignment);
5519 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5521 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5522 AlignFrame.DEFAULT_HEIGHT);
5526 * Set visibility of dna/protein complement view (available when shown in a
5532 protected void showComplement_actionPerformed(boolean show)
5534 SplitContainerI sf = getSplitViewContainer();
5537 sf.setComplementVisible(this, show);
5542 * Generate the reverse (optionally complemented) of the selected sequences,
5543 * and add them to the alignment
5546 protected void showReverse_actionPerformed(boolean complement)
5548 AlignmentI al = null;
5551 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5552 al = dna.reverseCdna(complement);
5553 viewport.addAlignment(al, "");
5554 addHistoryItem(new EditCommand(
5555 MessageManager.getString("label.add_sequences"), Action.PASTE,
5556 al.getSequencesArray(), 0, al.getWidth(),
5557 viewport.getAlignment()));
5558 } catch (Exception ex)
5560 System.err.println(ex.getMessage());
5566 * Try to run a script in the Groovy console, having first ensured that this
5567 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5568 * be targeted at this alignment.
5571 protected void runGroovy_actionPerformed()
5573 Jalview.setCurrentAlignFrame(this);
5574 groovy.ui.Console console = Desktop.getGroovyConsole();
5575 if (console != null)
5579 console.runScript();
5580 } catch (Exception ex)
5582 System.err.println((ex.toString()));
5583 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5584 MessageManager.getString("label.couldnt_run_groovy_script"),
5585 MessageManager.getString("label.groovy_support_failed"),
5586 JvOptionPane.ERROR_MESSAGE);
5591 System.err.println("Can't run Groovy script as console not found");
5596 * Hides columns containing (or not containing) a specified feature, provided
5597 * that would not leave all columns hidden
5599 * @param featureType
5600 * @param columnsContaining
5603 public boolean hideFeatureColumns(String featureType,
5604 boolean columnsContaining)
5606 boolean notForHiding = avc.markColumnsContainingFeatures(
5607 columnsContaining, false, false, featureType);
5610 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5611 false, featureType))
5613 getViewport().hideSelectedColumns();
5621 protected void selectHighlightedColumns_actionPerformed(
5622 ActionEvent actionEvent)
5624 // include key modifier check in case user selects from menu
5625 avc.markHighlightedColumns(
5626 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5627 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5628 | ActionEvent.CTRL_MASK)) != 0);
5632 * Rebuilds the Colour menu, including any user-defined colours which have
5633 * been loaded either on startup or during the session
5635 public void buildColourMenu()
5637 colourMenu.removeAll();
5639 colourMenu.add(applyToAllGroups);
5640 colourMenu.add(textColour);
5641 colourMenu.addSeparator();
5643 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5646 colourMenu.addSeparator();
5647 colourMenu.add(conservationMenuItem);
5648 colourMenu.add(modifyConservation);
5649 colourMenu.add(abovePIDThreshold);
5650 colourMenu.add(modifyPID);
5651 colourMenu.add(annotationColour);
5653 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5654 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5658 * Open a dialog (if not already open) that allows the user to select and
5659 * calculate PCA or Tree analysis
5661 protected void openTreePcaDialog()
5663 if (alignPanel.getCalculationDialog() == null)
5665 new CalculationChooser(AlignFrame.this);
5670 protected void loadVcf_actionPerformed()
5672 JalviewFileChooser chooser = new JalviewFileChooser(
5673 Cache.getProperty("LAST_DIRECTORY"));
5674 chooser.setFileView(new JalviewFileView());
5675 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5676 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5677 final AlignFrame us = this;
5678 chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
5685 String choice = chooser.getSelectedFile().getPath();
5686 Cache.setProperty("LAST_DIRECTORY", choice);
5687 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5688 new VCFLoader(choice).loadVCF(seqs, us);
5692 }).openDialog(null);
5698 class PrintThread extends Thread
5702 public PrintThread(AlignmentPanel ap)
5707 static PageFormat pf;
5712 PrinterJob printJob = PrinterJob.getPrinterJob();
5716 printJob.setPrintable(ap, pf);
5720 printJob.setPrintable(ap);
5723 if (printJob.printDialog())
5728 } catch (Exception PrintException)
5730 PrintException.printStackTrace();