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);
1286 protected void outputText_actionPerformed(ActionEvent e)
1288 FileFormatI fileFormat = FileFormats.getInstance()
1289 .forName(e.getActionCommand());
1290 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1292 if (exportData.getSettings().isCancelled())
1296 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1297 cap.setForInput(null);
1300 FileFormatI format = fileFormat;
1301 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1302 .formatSequences(format, exportData.getAlignment(),
1303 exportData.getOmitHidden(),
1304 exportData.getStartEndPostions(),
1305 viewport.getAlignment().getHiddenColumns()));
1306 Desktop.addInternalFrame(cap, MessageManager
1307 .formatMessage("label.alignment_output_command", new Object[]
1308 { e.getActionCommand() }), 600, 500);
1309 } catch (OutOfMemoryError oom)
1311 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1318 public static AlignmentExportData getAlignmentForExport(
1319 FileFormatI format, AlignViewportI viewport,
1320 AlignExportSettingI exportSettings)
1322 AlignmentI alignmentToExport = null;
1323 AlignExportSettingI settings = exportSettings;
1324 String[] omitHidden = null;
1326 HiddenSequences hiddenSeqs = viewport.getAlignment()
1327 .getHiddenSequences();
1329 alignmentToExport = viewport.getAlignment();
1331 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1332 if (settings == null)
1334 settings = new AlignExportSettings(hasHiddenSeqs,
1335 viewport.hasHiddenColumns(), format);
1337 // settings.isExportAnnotations();
1339 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1341 omitHidden = viewport.getViewAsString(false,
1342 settings.isExportHiddenSequences());
1345 int[] alignmentStartEnd = new int[2];
1346 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1348 alignmentToExport = hiddenSeqs.getFullAlignment();
1352 alignmentToExport = viewport.getAlignment();
1354 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1355 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1356 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1357 omitHidden, alignmentStartEnd, settings);
1368 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1370 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1371 htmlSVG.exportHTML(null);
1375 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1377 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1378 bjs.exportHTML(null);
1381 public void createImageMap(File file, String image)
1383 alignPanel.makePNGImageMap(file, image);
1393 public void createPNG(File f)
1395 alignPanel.makePNG(f);
1405 public void createEPS(File f)
1407 alignPanel.makeEPS(f);
1411 public void createSVG(File f)
1413 alignPanel.makeSVG(f);
1417 public void pageSetup_actionPerformed(ActionEvent e)
1419 PrinterJob printJob = PrinterJob.getPrinterJob();
1420 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1430 public void printMenuItem_actionPerformed(ActionEvent e)
1432 // Putting in a thread avoids Swing painting problems
1433 PrintThread thread = new PrintThread(alignPanel);
1438 public void exportFeatures_actionPerformed(ActionEvent e)
1440 new AnnotationExporter(alignPanel).exportFeatures();
1444 public void exportAnnotations_actionPerformed(ActionEvent e)
1446 new AnnotationExporter(alignPanel).exportAnnotations();
1450 public void associatedData_actionPerformed(ActionEvent e)
1452 JalviewFileChooser chooser = new JalviewFileChooser(
1453 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1454 chooser.setFileView(new JalviewFileView());
1455 chooser.setDialogTitle(
1456 MessageManager.getString("label.load_jalview_annotations"));
1457 chooser.setToolTipText(
1458 MessageManager.getString("label.load_jalview_annotations"));
1460 Desktop.getDesktop().dialogData = new Object[] { "SelectedFile",
1467 Object[] data = Desktop.getDesktop().dialogData;
1468 int value = ((Integer) data[0]).intValue();
1470 if (value == JFileChooser.APPROVE_OPTION)
1472 JalviewFileChooser chooser = (JalviewFileChooser) data[2];
1473 String choice = chooser.getSelectedFile().getPath();
1474 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1475 loadJalviewDataFile(choice, null, null, null);
1481 chooser.showOpenDialog(null);
1488 * Close the current view or all views in the alignment frame. If the frame
1489 * only contains one view then the alignment will be removed from memory.
1491 * @param closeAllTabs
1494 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1496 if (alignPanels != null && alignPanels.size() < 2)
1498 closeAllTabs = true;
1503 if (alignPanels != null)
1507 if (this.isClosed())
1509 // really close all the windows - otherwise wait till
1510 // setClosed(true) is called
1511 for (int i = 0; i < alignPanels.size(); i++)
1513 AlignmentPanel ap = alignPanels.get(i);
1520 closeView(alignPanel);
1527 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1528 * be called recursively, with the frame now in 'closed' state
1530 this.setClosed(true);
1532 } catch (Exception ex)
1534 ex.printStackTrace();
1539 * Close the specified panel and close up tabs appropriately.
1541 * @param panelToClose
1543 public void closeView(AlignmentPanel panelToClose)
1545 int index = tabbedPane.getSelectedIndex();
1546 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1547 alignPanels.remove(panelToClose);
1548 panelToClose.closePanel();
1549 panelToClose = null;
1551 tabbedPane.removeTabAt(closedindex);
1552 tabbedPane.validate();
1554 if (index > closedindex || index == tabbedPane.getTabCount())
1556 // modify currently selected tab index if necessary.
1560 this.tabSelectionChanged(index);
1566 void updateEditMenuBar()
1569 if (viewport.getHistoryList().size() > 0)
1571 undoMenuItem.setEnabled(true);
1572 CommandI command = viewport.getHistoryList().peek();
1573 undoMenuItem.setText(MessageManager
1574 .formatMessage("label.undo_command", new Object[]
1575 { command.getDescription() }));
1579 undoMenuItem.setEnabled(false);
1580 undoMenuItem.setText(MessageManager.getString("action.undo"));
1583 if (viewport.getRedoList().size() > 0)
1585 redoMenuItem.setEnabled(true);
1587 CommandI command = viewport.getRedoList().peek();
1588 redoMenuItem.setText(MessageManager
1589 .formatMessage("label.redo_command", new Object[]
1590 { command.getDescription() }));
1594 redoMenuItem.setEnabled(false);
1595 redoMenuItem.setText(MessageManager.getString("action.redo"));
1600 public void addHistoryItem(CommandI command)
1602 if (command.getSize() > 0)
1604 viewport.addToHistoryList(command);
1605 viewport.clearRedoList();
1606 updateEditMenuBar();
1607 viewport.updateHiddenColumns();
1608 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1609 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1610 // viewport.getColumnSelection()
1611 // .getHiddenColumns().size() > 0);
1617 * @return alignment objects for all views
1619 AlignmentI[] getViewAlignments()
1621 if (alignPanels != null)
1623 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1625 for (AlignmentPanel ap : alignPanels)
1627 als[i++] = ap.av.getAlignment();
1631 if (viewport != null)
1633 return new AlignmentI[] { viewport.getAlignment() };
1645 protected void undoMenuItem_actionPerformed(ActionEvent e)
1647 if (viewport.getHistoryList().isEmpty())
1651 CommandI command = viewport.getHistoryList().pop();
1652 viewport.addToRedoList(command);
1653 command.undoCommand(getViewAlignments());
1655 AlignmentViewport originalSource = getOriginatingSource(command);
1656 updateEditMenuBar();
1658 if (originalSource != null)
1660 if (originalSource != viewport)
1663 "Implementation worry: mismatch of viewport origin for undo");
1665 originalSource.updateHiddenColumns();
1666 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1668 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1669 // viewport.getColumnSelection()
1670 // .getHiddenColumns().size() > 0);
1671 originalSource.firePropertyChange("alignment", null,
1672 originalSource.getAlignment().getSequences());
1683 protected void redoMenuItem_actionPerformed(ActionEvent e)
1685 if (viewport.getRedoList().size() < 1)
1690 CommandI command = viewport.getRedoList().pop();
1691 viewport.addToHistoryList(command);
1692 command.doCommand(getViewAlignments());
1694 AlignmentViewport originalSource = getOriginatingSource(command);
1695 updateEditMenuBar();
1697 if (originalSource != null)
1700 if (originalSource != viewport)
1703 "Implementation worry: mismatch of viewport origin for redo");
1705 originalSource.updateHiddenColumns();
1706 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1708 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1709 // viewport.getColumnSelection()
1710 // .getHiddenColumns().size() > 0);
1711 originalSource.firePropertyChange("alignment", null,
1712 originalSource.getAlignment().getSequences());
1716 AlignmentViewport getOriginatingSource(CommandI command)
1718 AlignmentViewport originalSource = null;
1719 // For sequence removal and addition, we need to fire
1720 // the property change event FROM the viewport where the
1721 // original alignment was altered
1722 AlignmentI al = null;
1723 if (command instanceof EditCommand)
1725 EditCommand editCommand = (EditCommand) command;
1726 al = editCommand.getAlignment();
1727 List<Component> comps = PaintRefresher.components
1728 .get(viewport.getSequenceSetId());
1730 for (Component comp : comps)
1732 if (comp instanceof AlignmentPanel)
1734 if (al == ((AlignmentPanel) comp).av.getAlignment())
1736 originalSource = ((AlignmentPanel) comp).av;
1743 if (originalSource == null)
1745 // The original view is closed, we must validate
1746 // the current view against the closed view first
1749 PaintRefresher.validateSequences(al, viewport.getAlignment());
1752 originalSource = viewport;
1755 return originalSource;
1764 public void moveSelectedSequences(boolean up)
1766 SequenceGroup sg = viewport.getSelectionGroup();
1772 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1773 viewport.getHiddenRepSequences(), up);
1774 alignPanel.paintAlignment(true, false);
1777 synchronized void slideSequences(boolean right, int size)
1779 List<SequenceI> sg = new ArrayList<>();
1780 if (viewport.cursorMode)
1782 sg.add(viewport.getAlignment()
1783 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1785 else if (viewport.getSelectionGroup() != null
1786 && viewport.getSelectionGroup().getSize() != viewport
1787 .getAlignment().getHeight())
1789 sg = viewport.getSelectionGroup()
1790 .getSequences(viewport.getHiddenRepSequences());
1798 List<SequenceI> invertGroup = new ArrayList<>();
1800 for (SequenceI seq : viewport.getAlignment().getSequences())
1802 if (!sg.contains(seq))
1804 invertGroup.add(seq);
1808 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1810 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1811 for (int i = 0; i < invertGroup.size(); i++)
1813 seqs2[i] = invertGroup.get(i);
1816 SlideSequencesCommand ssc;
1819 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1820 viewport.getGapCharacter());
1824 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1825 viewport.getGapCharacter());
1828 int groupAdjustment = 0;
1829 if (ssc.getGapsInsertedBegin() && right)
1831 if (viewport.cursorMode)
1833 alignPanel.getSeqPanel().moveCursor(size, 0);
1837 groupAdjustment = size;
1840 else if (!ssc.getGapsInsertedBegin() && !right)
1842 if (viewport.cursorMode)
1844 alignPanel.getSeqPanel().moveCursor(-size, 0);
1848 groupAdjustment = -size;
1852 if (groupAdjustment != 0)
1854 viewport.getSelectionGroup().setStartRes(
1855 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1856 viewport.getSelectionGroup().setEndRes(
1857 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1861 * just extend the last slide command if compatible; but not if in
1862 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1864 boolean appendHistoryItem = false;
1865 Deque<CommandI> historyList = viewport.getHistoryList();
1866 boolean inSplitFrame = getSplitViewContainer() != null;
1867 if (!inSplitFrame && historyList != null && historyList.size() > 0
1868 && historyList.peek() instanceof SlideSequencesCommand)
1870 appendHistoryItem = ssc.appendSlideCommand(
1871 (SlideSequencesCommand) historyList.peek());
1874 if (!appendHistoryItem)
1876 addHistoryItem(ssc);
1889 protected void copy_actionPerformed(ActionEvent e)
1891 if (viewport.getSelectionGroup() == null)
1895 // TODO: preserve the ordering of displayed alignment annotation in any
1896 // internal paste (particularly sequence associated annotation)
1897 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1898 String[] omitHidden = null;
1900 if (viewport.hasHiddenColumns())
1902 omitHidden = viewport.getViewAsString(true);
1905 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1906 seqs, omitHidden, null);
1908 StringSelection ss = new StringSelection(output);
1912 jalview.gui.Desktop.internalCopy = true;
1913 // Its really worth setting the clipboard contents
1914 // to empty before setting the large StringSelection!!
1915 Toolkit.getDefaultToolkit().getSystemClipboard()
1916 .setContents(new StringSelection(""), null);
1918 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1920 } catch (OutOfMemoryError er)
1922 new OOMWarning("copying region", er);
1926 HiddenColumns hiddenColumns = null;
1927 if (viewport.hasHiddenColumns())
1929 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1930 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1932 // create new HiddenColumns object with copy of hidden regions
1933 // between startRes and endRes, offset by startRes
1934 hiddenColumns = new HiddenColumns(
1935 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1936 hiddenCutoff, hiddenOffset);
1939 Desktop.jalviewClipboard = new Object[] { seqs,
1940 viewport.getAlignment().getDataset(), hiddenColumns };
1941 statusBar.setText(MessageManager.formatMessage(
1942 "label.copied_sequences_to_clipboard", new Object[]
1943 { Integer.valueOf(seqs.length).toString() }));
1953 protected void pasteNew_actionPerformed(ActionEvent e)
1965 protected void pasteThis_actionPerformed(ActionEvent e)
1971 * Paste contents of Jalview clipboard
1973 * @param newAlignment
1974 * true to paste to a new alignment, otherwise add to this.
1976 void paste(boolean newAlignment)
1978 boolean externalPaste = true;
1981 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1982 Transferable contents = c.getContents(this);
1984 if (contents == null)
1993 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1994 if (str.length() < 1)
1999 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2001 } catch (OutOfMemoryError er)
2003 new OOMWarning("Out of memory pasting sequences!!", er);
2007 SequenceI[] sequences;
2008 boolean annotationAdded = false;
2009 AlignmentI alignment = null;
2011 if (Desktop.jalviewClipboard != null)
2013 // The clipboard was filled from within Jalview, we must use the
2015 // And dataset from the copied alignment
2016 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2017 // be doubly sure that we create *new* sequence objects.
2018 sequences = new SequenceI[newseq.length];
2019 for (int i = 0; i < newseq.length; i++)
2021 sequences[i] = new Sequence(newseq[i]);
2023 alignment = new Alignment(sequences);
2024 externalPaste = false;
2028 // parse the clipboard as an alignment.
2029 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2031 sequences = alignment.getSequencesArray();
2035 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2041 if (Desktop.jalviewClipboard != null)
2043 // dataset is inherited
2044 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2048 // new dataset is constructed
2049 alignment.setDataset(null);
2051 alwidth = alignment.getWidth() + 1;
2055 AlignmentI pastedal = alignment; // preserve pasted alignment object
2056 // Add pasted sequences and dataset into existing alignment.
2057 alignment = viewport.getAlignment();
2058 alwidth = alignment.getWidth() + 1;
2059 // decide if we need to import sequences from an existing dataset
2060 boolean importDs = Desktop.jalviewClipboard != null
2061 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2062 // importDs==true instructs us to copy over new dataset sequences from
2063 // an existing alignment
2064 Vector newDs = (importDs) ? new Vector() : null; // used to create
2065 // minimum dataset set
2067 for (int i = 0; i < sequences.length; i++)
2071 newDs.addElement(null);
2073 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2075 if (importDs && ds != null)
2077 if (!newDs.contains(ds))
2079 newDs.setElementAt(ds, i);
2080 ds = new Sequence(ds);
2081 // update with new dataset sequence
2082 sequences[i].setDatasetSequence(ds);
2086 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2091 // copy and derive new dataset sequence
2092 sequences[i] = sequences[i].deriveSequence();
2093 alignment.getDataset()
2094 .addSequence(sequences[i].getDatasetSequence());
2095 // TODO: avoid creation of duplicate dataset sequences with a
2096 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2098 alignment.addSequence(sequences[i]); // merges dataset
2102 newDs.clear(); // tidy up
2104 if (alignment.getAlignmentAnnotation() != null)
2106 for (AlignmentAnnotation alan : alignment
2107 .getAlignmentAnnotation())
2109 if (alan.graphGroup > fgroup)
2111 fgroup = alan.graphGroup;
2115 if (pastedal.getAlignmentAnnotation() != null)
2117 // Add any annotation attached to alignment.
2118 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2119 for (int i = 0; i < alann.length; i++)
2121 annotationAdded = true;
2122 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2124 AlignmentAnnotation newann = new AlignmentAnnotation(
2126 if (newann.graphGroup > -1)
2128 if (newGraphGroups.size() <= newann.graphGroup
2129 || newGraphGroups.get(newann.graphGroup) == null)
2131 for (int q = newGraphGroups
2132 .size(); q <= newann.graphGroup; q++)
2134 newGraphGroups.add(q, null);
2136 newGraphGroups.set(newann.graphGroup,
2137 new Integer(++fgroup));
2139 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2143 newann.padAnnotation(alwidth);
2144 alignment.addAnnotation(newann);
2154 addHistoryItem(new EditCommand(
2155 MessageManager.getString("label.add_sequences"),
2156 Action.PASTE, sequences, 0, alignment.getWidth(),
2159 // Add any annotations attached to sequences
2160 for (int i = 0; i < sequences.length; i++)
2162 if (sequences[i].getAnnotation() != null)
2164 AlignmentAnnotation newann;
2165 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2167 annotationAdded = true;
2168 newann = sequences[i].getAnnotation()[a];
2169 newann.adjustForAlignment();
2170 newann.padAnnotation(alwidth);
2171 if (newann.graphGroup > -1)
2173 if (newann.graphGroup > -1)
2175 if (newGraphGroups.size() <= newann.graphGroup
2176 || newGraphGroups.get(newann.graphGroup) == null)
2178 for (int q = newGraphGroups
2179 .size(); q <= newann.graphGroup; q++)
2181 newGraphGroups.add(q, null);
2183 newGraphGroups.set(newann.graphGroup,
2184 new Integer(++fgroup));
2186 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2190 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2194 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2202 // propagate alignment changed.
2203 viewport.getRanges().setEndSeq(alignment.getHeight());
2204 if (annotationAdded)
2206 // Duplicate sequence annotation in all views.
2207 AlignmentI[] alview = this.getViewAlignments();
2208 for (int i = 0; i < sequences.length; i++)
2210 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2215 for (int avnum = 0; avnum < alview.length; avnum++)
2217 if (alview[avnum] != alignment)
2219 // duplicate in a view other than the one with input focus
2220 int avwidth = alview[avnum].getWidth() + 1;
2221 // this relies on sann being preserved after we
2222 // modify the sequence's annotation array for each duplication
2223 for (int a = 0; a < sann.length; a++)
2225 AlignmentAnnotation newann = new AlignmentAnnotation(
2227 sequences[i].addAlignmentAnnotation(newann);
2228 newann.padAnnotation(avwidth);
2229 alview[avnum].addAnnotation(newann); // annotation was
2230 // duplicated earlier
2231 // TODO JAL-1145 graphGroups are not updated for sequence
2232 // annotation added to several views. This may cause
2234 alview[avnum].setAnnotationIndex(newann, a);
2239 buildSortByAnnotationScoresMenu();
2241 viewport.firePropertyChange("alignment", null,
2242 alignment.getSequences());
2243 if (alignPanels != null)
2245 for (AlignmentPanel ap : alignPanels)
2247 ap.validateAnnotationDimensions(false);
2252 alignPanel.validateAnnotationDimensions(false);
2258 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2260 String newtitle = new String("Copied sequences");
2262 if (Desktop.jalviewClipboard != null
2263 && Desktop.jalviewClipboard[2] != null)
2265 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2266 af.viewport.setHiddenColumns(hc);
2269 // >>>This is a fix for the moment, until a better solution is
2271 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2272 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2273 .getFeatureRenderer());
2275 // TODO: maintain provenance of an alignment, rather than just make the
2276 // title a concatenation of operations.
2279 if (title.startsWith("Copied sequences"))
2285 newtitle = newtitle.concat("- from " + title);
2290 newtitle = new String("Pasted sequences");
2293 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2298 } catch (Exception ex)
2300 ex.printStackTrace();
2301 System.out.println("Exception whilst pasting: " + ex);
2302 // could be anything being pasted in here
2308 protected void expand_newalign(ActionEvent e)
2312 AlignmentI alignment = AlignmentUtils
2313 .expandContext(getViewport().getAlignment(), -1);
2314 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2316 String newtitle = new String("Flanking alignment");
2318 if (Desktop.jalviewClipboard != null
2319 && Desktop.jalviewClipboard[2] != null)
2321 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2322 af.viewport.setHiddenColumns(hc);
2325 // >>>This is a fix for the moment, until a better solution is
2327 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2328 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2329 .getFeatureRenderer());
2331 // TODO: maintain provenance of an alignment, rather than just make the
2332 // title a concatenation of operations.
2334 if (title.startsWith("Copied sequences"))
2340 newtitle = newtitle.concat("- from " + title);
2344 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2346 } catch (Exception ex)
2348 ex.printStackTrace();
2349 System.out.println("Exception whilst pasting: " + ex);
2350 // could be anything being pasted in here
2351 } catch (OutOfMemoryError oom)
2353 new OOMWarning("Viewing flanking region of alignment", oom);
2364 protected void cut_actionPerformed(ActionEvent e)
2366 copy_actionPerformed(null);
2367 delete_actionPerformed(null);
2377 protected void delete_actionPerformed(ActionEvent evt)
2380 SequenceGroup sg = viewport.getSelectionGroup();
2387 * If the cut affects all sequences, warn, remove highlighted columns
2389 if (sg.getSize() == viewport.getAlignment().getHeight())
2391 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2392 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2393 if (isEntireAlignWidth)
2395 int confirm = JvOptionPane.showConfirmDialog(this,
2396 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2397 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2398 JvOptionPane.OK_CANCEL_OPTION);
2400 if (confirm == JvOptionPane.CANCEL_OPTION
2401 || confirm == JvOptionPane.CLOSED_OPTION)
2406 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2407 sg.getEndRes() + 1);
2409 SequenceI[] cut = sg.getSequences()
2410 .toArray(new SequenceI[sg.getSize()]);
2412 addHistoryItem(new EditCommand(
2413 MessageManager.getString("label.cut_sequences"), Action.CUT,
2414 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2415 viewport.getAlignment()));
2417 viewport.setSelectionGroup(null);
2418 viewport.sendSelection();
2419 viewport.getAlignment().deleteGroup(sg);
2421 viewport.firePropertyChange("alignment", null,
2422 viewport.getAlignment().getSequences());
2423 if (viewport.getAlignment().getHeight() < 1)
2427 this.setClosed(true);
2428 } catch (Exception ex)
2441 protected void deleteGroups_actionPerformed(ActionEvent e)
2443 if (avc.deleteGroups())
2445 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2446 alignPanel.updateAnnotation();
2447 alignPanel.paintAlignment(true, true);
2458 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2460 SequenceGroup sg = new SequenceGroup();
2462 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2464 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2467 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2468 viewport.setSelectionGroup(sg);
2469 viewport.sendSelection();
2470 // JAL-2034 - should delegate to
2471 // alignPanel to decide if overview needs
2473 alignPanel.paintAlignment(false, false);
2474 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2484 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2486 if (viewport.cursorMode)
2488 alignPanel.getSeqPanel().keyboardNo1 = null;
2489 alignPanel.getSeqPanel().keyboardNo2 = null;
2491 viewport.setSelectionGroup(null);
2492 viewport.getColumnSelection().clear();
2493 viewport.setSelectionGroup(null);
2494 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2495 // JAL-2034 - should delegate to
2496 // alignPanel to decide if overview needs
2498 alignPanel.paintAlignment(false, false);
2499 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2500 viewport.sendSelection();
2510 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2512 SequenceGroup sg = viewport.getSelectionGroup();
2516 selectAllSequenceMenuItem_actionPerformed(null);
2521 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2523 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2525 // JAL-2034 - should delegate to
2526 // alignPanel to decide if overview needs
2529 alignPanel.paintAlignment(true, false);
2530 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2531 viewport.sendSelection();
2535 public void invertColSel_actionPerformed(ActionEvent e)
2537 viewport.invertColumnSelection();
2538 alignPanel.paintAlignment(true, false);
2539 viewport.sendSelection();
2549 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2551 trimAlignment(true);
2561 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2563 trimAlignment(false);
2566 void trimAlignment(boolean trimLeft)
2568 ColumnSelection colSel = viewport.getColumnSelection();
2571 if (!colSel.isEmpty())
2575 column = colSel.getMin();
2579 column = colSel.getMax();
2583 if (viewport.getSelectionGroup() != null)
2585 seqs = viewport.getSelectionGroup()
2586 .getSequencesAsArray(viewport.getHiddenRepSequences());
2590 seqs = viewport.getAlignment().getSequencesArray();
2593 TrimRegionCommand trimRegion;
2596 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2597 column, viewport.getAlignment());
2598 viewport.getRanges().setStartRes(0);
2602 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2603 column, viewport.getAlignment());
2606 statusBar.setText(MessageManager
2607 .formatMessage("label.removed_columns", new String[]
2608 { Integer.valueOf(trimRegion.getSize()).toString() }));
2610 addHistoryItem(trimRegion);
2612 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2614 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2615 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2617 viewport.getAlignment().deleteGroup(sg);
2621 viewport.firePropertyChange("alignment", null,
2622 viewport.getAlignment().getSequences());
2633 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2635 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2638 if (viewport.getSelectionGroup() != null)
2640 seqs = viewport.getSelectionGroup()
2641 .getSequencesAsArray(viewport.getHiddenRepSequences());
2642 start = viewport.getSelectionGroup().getStartRes();
2643 end = viewport.getSelectionGroup().getEndRes();
2647 seqs = viewport.getAlignment().getSequencesArray();
2650 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2651 "Remove Gapped Columns", seqs, start, end,
2652 viewport.getAlignment());
2654 addHistoryItem(removeGapCols);
2656 statusBar.setText(MessageManager
2657 .formatMessage("label.removed_empty_columns", new Object[]
2658 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2660 // This is to maintain viewport position on first residue
2661 // of first sequence
2662 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2663 ViewportRanges ranges = viewport.getRanges();
2664 int startRes = seq.findPosition(ranges.getStartRes());
2665 // ShiftList shifts;
2666 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2667 // edit.alColumnChanges=shifts.getInverse();
2668 // if (viewport.hasHiddenColumns)
2669 // viewport.getColumnSelection().compensateForEdits(shifts);
2670 ranges.setStartRes(seq.findIndex(startRes) - 1);
2671 viewport.firePropertyChange("alignment", null,
2672 viewport.getAlignment().getSequences());
2683 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2685 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2688 if (viewport.getSelectionGroup() != null)
2690 seqs = viewport.getSelectionGroup()
2691 .getSequencesAsArray(viewport.getHiddenRepSequences());
2692 start = viewport.getSelectionGroup().getStartRes();
2693 end = viewport.getSelectionGroup().getEndRes();
2697 seqs = viewport.getAlignment().getSequencesArray();
2700 // This is to maintain viewport position on first residue
2701 // of first sequence
2702 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2703 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2705 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2706 viewport.getAlignment()));
2708 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2710 viewport.firePropertyChange("alignment", null,
2711 viewport.getAlignment().getSequences());
2722 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2724 viewport.setPadGaps(padGapsMenuitem.isSelected());
2725 viewport.firePropertyChange("alignment", null,
2726 viewport.getAlignment().getSequences());
2736 public void findMenuItem_actionPerformed(ActionEvent e)
2742 * Create a new view of the current alignment.
2745 public void newView_actionPerformed(ActionEvent e)
2747 newView(null, true);
2751 * Creates and shows a new view of the current alignment.
2754 * title of newly created view; if null, one will be generated
2755 * @param copyAnnotation
2756 * if true then duplicate all annnotation, groups and settings
2757 * @return new alignment panel, already displayed.
2759 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2762 * Create a new AlignmentPanel (with its own, new Viewport)
2764 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2765 if (!copyAnnotation)
2768 * remove all groups and annotation except for the automatic stuff
2770 newap.av.getAlignment().deleteAllGroups();
2771 newap.av.getAlignment().deleteAllAnnotations(false);
2774 newap.av.setGatherViewsHere(false);
2776 if (viewport.viewName == null)
2778 viewport.viewName = MessageManager
2779 .getString("label.view_name_original");
2783 * Views share the same edits undo and redo stacks
2785 newap.av.setHistoryList(viewport.getHistoryList());
2786 newap.av.setRedoList(viewport.getRedoList());
2789 * Views share the same mappings; need to deregister any new mappings
2790 * created by copyAlignPanel, and register the new reference to the shared
2793 newap.av.replaceMappings(viewport.getAlignment());
2796 * start up cDNA consensus (if applicable) now mappings are in place
2798 if (newap.av.initComplementConsensus())
2800 newap.refresh(true); // adjust layout of annotations
2803 newap.av.viewName = getNewViewName(viewTitle);
2805 addAlignmentPanel(newap, true);
2806 newap.alignmentChanged();
2808 if (alignPanels.size() == 2)
2810 viewport.setGatherViewsHere(true);
2812 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2817 * Make a new name for the view, ensuring it is unique within the current
2818 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2819 * these now use viewId. Unique view names are still desirable for usability.)
2824 protected String getNewViewName(String viewTitle)
2826 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2827 boolean addFirstIndex = false;
2828 if (viewTitle == null || viewTitle.trim().length() == 0)
2830 viewTitle = MessageManager.getString("action.view");
2831 addFirstIndex = true;
2835 index = 1;// we count from 1 if given a specific name
2837 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2839 List<Component> comps = PaintRefresher.components
2840 .get(viewport.getSequenceSetId());
2842 List<String> existingNames = getExistingViewNames(comps);
2844 while (existingNames.contains(newViewName))
2846 newViewName = viewTitle + " " + (++index);
2852 * Returns a list of distinct view names found in the given list of
2853 * components. View names are held on the viewport of an AlignmentPanel.
2858 protected List<String> getExistingViewNames(List<Component> comps)
2860 List<String> existingNames = new ArrayList<>();
2861 for (Component comp : comps)
2863 if (comp instanceof AlignmentPanel)
2865 AlignmentPanel ap = (AlignmentPanel) comp;
2866 if (!existingNames.contains(ap.av.viewName))
2868 existingNames.add(ap.av.viewName);
2872 return existingNames;
2876 * Explode tabbed views into separate windows.
2879 public void expandViews_actionPerformed(ActionEvent e)
2881 Desktop.explodeViews(this);
2885 * Gather views in separate windows back into a tabbed presentation.
2888 public void gatherViews_actionPerformed(ActionEvent e)
2890 Desktop.instance.gatherViews(this);
2900 public void font_actionPerformed(ActionEvent e)
2902 new FontChooser(alignPanel);
2912 protected void seqLimit_actionPerformed(ActionEvent e)
2914 viewport.setShowJVSuffix(seqLimits.isSelected());
2916 alignPanel.getIdPanel().getIdCanvas()
2917 .setPreferredSize(alignPanel.calculateIdWidth());
2918 alignPanel.paintAlignment(true, false);
2922 public void idRightAlign_actionPerformed(ActionEvent e)
2924 viewport.setRightAlignIds(idRightAlign.isSelected());
2925 alignPanel.paintAlignment(false, false);
2929 public void centreColumnLabels_actionPerformed(ActionEvent e)
2931 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2932 alignPanel.paintAlignment(false, false);
2938 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2941 protected void followHighlight_actionPerformed()
2944 * Set the 'follow' flag on the Viewport (and scroll to position if now
2947 final boolean state = this.followHighlightMenuItem.getState();
2948 viewport.setFollowHighlight(state);
2951 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2962 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2964 viewport.setColourText(colourTextMenuItem.isSelected());
2965 alignPanel.paintAlignment(false, false);
2975 public void wrapMenuItem_actionPerformed(ActionEvent e)
2977 scaleAbove.setVisible(wrapMenuItem.isSelected());
2978 scaleLeft.setVisible(wrapMenuItem.isSelected());
2979 scaleRight.setVisible(wrapMenuItem.isSelected());
2980 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2981 alignPanel.updateLayout();
2985 public void showAllSeqs_actionPerformed(ActionEvent e)
2987 viewport.showAllHiddenSeqs();
2991 public void showAllColumns_actionPerformed(ActionEvent e)
2993 viewport.showAllHiddenColumns();
2994 alignPanel.paintAlignment(true, true);
2995 viewport.sendSelection();
2999 public void hideSelSequences_actionPerformed(ActionEvent e)
3001 viewport.hideAllSelectedSeqs();
3005 * called by key handler and the hide all/show all menu items
3010 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3013 boolean hide = false;
3014 SequenceGroup sg = viewport.getSelectionGroup();
3015 if (!toggleSeqs && !toggleCols)
3017 // Hide everything by the current selection - this is a hack - we do the
3018 // invert and then hide
3019 // first check that there will be visible columns after the invert.
3020 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3021 && sg.getStartRes() <= sg.getEndRes()))
3023 // now invert the sequence set, if required - empty selection implies
3024 // that no hiding is required.
3027 invertSequenceMenuItem_actionPerformed(null);
3028 sg = viewport.getSelectionGroup();
3032 viewport.expandColSelection(sg, true);
3033 // finally invert the column selection and get the new sequence
3035 invertColSel_actionPerformed(null);
3042 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3044 hideSelSequences_actionPerformed(null);
3047 else if (!(toggleCols && viewport.hasSelectedColumns()))
3049 showAllSeqs_actionPerformed(null);
3055 if (viewport.hasSelectedColumns())
3057 hideSelColumns_actionPerformed(null);
3060 viewport.setSelectionGroup(sg);
3065 showAllColumns_actionPerformed(null);
3074 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3075 * event.ActionEvent)
3078 public void hideAllButSelection_actionPerformed(ActionEvent e)
3080 toggleHiddenRegions(false, false);
3081 viewport.sendSelection();
3088 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3092 public void hideAllSelection_actionPerformed(ActionEvent e)
3094 SequenceGroup sg = viewport.getSelectionGroup();
3095 viewport.expandColSelection(sg, false);
3096 viewport.hideAllSelectedSeqs();
3097 viewport.hideSelectedColumns();
3098 alignPanel.paintAlignment(true, true);
3099 viewport.sendSelection();
3106 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3110 public void showAllhidden_actionPerformed(ActionEvent e)
3112 viewport.showAllHiddenColumns();
3113 viewport.showAllHiddenSeqs();
3114 alignPanel.paintAlignment(true, true);
3115 viewport.sendSelection();
3119 public void hideSelColumns_actionPerformed(ActionEvent e)
3121 viewport.hideSelectedColumns();
3122 alignPanel.paintAlignment(true, true);
3123 viewport.sendSelection();
3127 public void hiddenMarkers_actionPerformed(ActionEvent e)
3129 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3140 protected void scaleAbove_actionPerformed(ActionEvent e)
3142 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3143 // TODO: do we actually need to update overview for scale above change ?
3144 alignPanel.paintAlignment(true, false);
3154 protected void scaleLeft_actionPerformed(ActionEvent e)
3156 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3157 alignPanel.paintAlignment(true, false);
3167 protected void scaleRight_actionPerformed(ActionEvent e)
3169 viewport.setScaleRightWrapped(scaleRight.isSelected());
3170 alignPanel.paintAlignment(true, false);
3180 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3182 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3183 alignPanel.paintAlignment(false, false);
3193 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3195 viewport.setShowText(viewTextMenuItem.isSelected());
3196 alignPanel.paintAlignment(false, false);
3206 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3208 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3209 alignPanel.paintAlignment(false, false);
3212 public FeatureSettings featureSettings;
3215 public FeatureSettingsControllerI getFeatureSettingsUI()
3217 return featureSettings;
3221 public void featureSettings_actionPerformed(ActionEvent e)
3223 if (featureSettings != null)
3225 featureSettings.close();
3226 featureSettings = null;
3228 if (!showSeqFeatures.isSelected())
3230 // make sure features are actually displayed
3231 showSeqFeatures.setSelected(true);
3232 showSeqFeatures_actionPerformed(null);
3234 featureSettings = new FeatureSettings(this);
3238 * Set or clear 'Show Sequence Features'
3244 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3246 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3247 alignPanel.paintAlignment(true, true);
3251 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3252 * the annotations panel as a whole.
3254 * The options to show/hide all annotations should be enabled when the panel
3255 * is shown, and disabled when the panel is hidden.
3260 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3262 final boolean setVisible = annotationPanelMenuItem.isSelected();
3263 viewport.setShowAnnotation(setVisible);
3264 this.showAllSeqAnnotations.setEnabled(setVisible);
3265 this.hideAllSeqAnnotations.setEnabled(setVisible);
3266 this.showAllAlAnnotations.setEnabled(setVisible);
3267 this.hideAllAlAnnotations.setEnabled(setVisible);
3268 alignPanel.updateLayout();
3272 public void alignmentProperties()
3274 JEditorPane editPane = new JEditorPane("text/html", "");
3275 editPane.setEditable(false);
3276 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3279 MessageManager.formatMessage("label.html_content", new Object[]
3280 { contents.toString() }));
3281 JInternalFrame frame = new JInternalFrame();
3282 frame.getContentPane().add(new JScrollPane(editPane));
3284 Desktop.addInternalFrame(frame, MessageManager
3285 .formatMessage("label.alignment_properties", new Object[]
3286 { getTitle() }), 500, 400);
3296 public void overviewMenuItem_actionPerformed(ActionEvent e)
3298 if (alignPanel.overviewPanel != null)
3303 JInternalFrame frame = new JInternalFrame();
3304 final OverviewPanel overview = new OverviewPanel(alignPanel);
3305 frame.setContentPane(overview);
3306 Desktop.addInternalFrame(frame, MessageManager
3307 .formatMessage("label.overview_params", new Object[]
3308 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3311 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3312 frame.addInternalFrameListener(
3313 new javax.swing.event.InternalFrameAdapter()
3316 public void internalFrameClosed(
3317 javax.swing.event.InternalFrameEvent evt)
3320 alignPanel.setOverviewPanel(null);
3323 if (getKeyListeners().length > 0)
3325 frame.addKeyListener(getKeyListeners()[0]);
3328 alignPanel.setOverviewPanel(overview);
3332 public void textColour_actionPerformed()
3334 new TextColourChooser().chooseColour(alignPanel, null);
3338 * public void covariationColour_actionPerformed() {
3340 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3344 public void annotationColour_actionPerformed()
3346 new AnnotationColourChooser(viewport, alignPanel);
3350 public void annotationColumn_actionPerformed(ActionEvent e)
3352 new AnnotationColumnChooser(viewport, alignPanel);
3356 * Action on the user checking or unchecking the option to apply the selected
3357 * colour scheme to all groups. If unchecked, groups may have their own
3358 * independent colour schemes.
3363 public void applyToAllGroups_actionPerformed(boolean selected)
3365 viewport.setColourAppliesToAllGroups(selected);
3369 * Action on user selecting a colour from the colour menu
3372 * the name (not the menu item label!) of the colour scheme
3375 public void changeColour_actionPerformed(String name)
3378 * 'User Defined' opens a panel to configure or load a
3379 * user-defined colour scheme
3381 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3383 new UserDefinedColours(alignPanel);
3388 * otherwise set the chosen colour scheme (or null for 'None')
3390 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3391 viewport.getAlignment(), viewport.getHiddenRepSequences());
3396 * Actions on setting or changing the alignment colour scheme
3401 public void changeColour(ColourSchemeI cs)
3403 // TODO: pull up to controller method
3404 ColourMenuHelper.setColourSelected(colourMenu, cs);
3406 viewport.setGlobalColourScheme(cs);
3408 alignPanel.paintAlignment(true, true);
3412 * Show the PID threshold slider panel
3415 protected void modifyPID_actionPerformed()
3417 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3418 alignPanel.getViewName());
3419 SliderPanel.showPIDSlider();
3423 * Show the Conservation slider panel
3426 protected void modifyConservation_actionPerformed()
3428 SliderPanel.setConservationSlider(alignPanel,
3429 viewport.getResidueShading(), alignPanel.getViewName());
3430 SliderPanel.showConservationSlider();
3434 * Action on selecting or deselecting (Colour) By Conservation
3437 public void conservationMenuItem_actionPerformed(boolean selected)
3439 modifyConservation.setEnabled(selected);
3440 viewport.setConservationSelected(selected);
3441 viewport.getResidueShading().setConservationApplied(selected);
3443 changeColour(viewport.getGlobalColourScheme());
3446 modifyConservation_actionPerformed();
3450 SliderPanel.hideConservationSlider();
3455 * Action on selecting or deselecting (Colour) Above PID Threshold
3458 public void abovePIDThreshold_actionPerformed(boolean selected)
3460 modifyPID.setEnabled(selected);
3461 viewport.setAbovePIDThreshold(selected);
3464 viewport.getResidueShading().setThreshold(0,
3465 viewport.isIgnoreGapsConsensus());
3468 changeColour(viewport.getGlobalColourScheme());
3471 modifyPID_actionPerformed();
3475 SliderPanel.hidePIDSlider();
3486 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3488 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3489 AlignmentSorter.sortByPID(viewport.getAlignment(),
3490 viewport.getAlignment().getSequenceAt(0));
3491 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3492 viewport.getAlignment()));
3493 alignPanel.paintAlignment(true, false);
3503 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3505 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3506 AlignmentSorter.sortByID(viewport.getAlignment());
3508 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3509 alignPanel.paintAlignment(true, false);
3519 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3521 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3522 AlignmentSorter.sortByLength(viewport.getAlignment());
3523 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3524 viewport.getAlignment()));
3525 alignPanel.paintAlignment(true, false);
3535 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3537 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3538 AlignmentSorter.sortByGroup(viewport.getAlignment());
3539 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3540 viewport.getAlignment()));
3542 alignPanel.paintAlignment(true, false);
3552 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3554 new RedundancyPanel(alignPanel, this);
3564 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3566 if ((viewport.getSelectionGroup() == null)
3567 || (viewport.getSelectionGroup().getSize() < 2))
3569 JvOptionPane.showInternalMessageDialog(this,
3570 MessageManager.getString(
3571 "label.you_must_select_least_two_sequences"),
3572 MessageManager.getString("label.invalid_selection"),
3573 JvOptionPane.WARNING_MESSAGE);
3577 JInternalFrame frame = new JInternalFrame();
3578 frame.setContentPane(new PairwiseAlignPanel(viewport));
3579 Desktop.addInternalFrame(frame,
3580 MessageManager.getString("action.pairwise_alignment"), 600,
3586 public void autoCalculate_actionPerformed(ActionEvent e)
3588 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3589 if (viewport.autoCalculateConsensus)
3591 viewport.firePropertyChange("alignment", null,
3592 viewport.getAlignment().getSequences());
3597 public void sortByTreeOption_actionPerformed(ActionEvent e)
3599 viewport.sortByTree = sortByTree.isSelected();
3603 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3605 viewport.followSelection = listenToViewSelections.isSelected();
3609 * Constructs a tree panel and adds it to the desktop
3612 * tree type (NJ or AV)
3614 * name of score model used to compute the tree
3616 * parameters for the distance or similarity calculation
3618 void newTreePanel(String type, String modelName,
3619 SimilarityParamsI options)
3621 String frameTitle = "";
3624 boolean onSelection = false;
3625 if (viewport.getSelectionGroup() != null
3626 && viewport.getSelectionGroup().getSize() > 0)
3628 SequenceGroup sg = viewport.getSelectionGroup();
3630 /* Decide if the selection is a column region */
3631 for (SequenceI _s : sg.getSequences())
3633 if (_s.getLength() < sg.getEndRes())
3635 JvOptionPane.showMessageDialog(Desktop.desktop,
3636 MessageManager.getString(
3637 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3638 MessageManager.getString(
3639 "label.sequences_selection_not_aligned"),
3640 JvOptionPane.WARNING_MESSAGE);
3649 if (viewport.getAlignment().getHeight() < 2)
3655 tp = new TreePanel(alignPanel, type, modelName, options);
3656 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3658 frameTitle += " from ";
3660 if (viewport.viewName != null)
3662 frameTitle += viewport.viewName + " of ";
3665 frameTitle += this.title;
3667 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3678 public void addSortByOrderMenuItem(String title,
3679 final AlignmentOrder order)
3681 final JMenuItem item = new JMenuItem(MessageManager
3682 .formatMessage("action.by_title_param", new Object[]
3685 item.addActionListener(new java.awt.event.ActionListener()
3688 public void actionPerformed(ActionEvent e)
3690 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3692 // TODO: JBPNote - have to map order entries to curent SequenceI
3694 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3696 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3697 viewport.getAlignment()));
3699 alignPanel.paintAlignment(true, false);
3705 * Add a new sort by annotation score menu item
3708 * the menu to add the option to
3710 * the label used to retrieve scores for each sequence on the
3713 public void addSortByAnnotScoreMenuItem(JMenu sort,
3714 final String scoreLabel)
3716 final JMenuItem item = new JMenuItem(scoreLabel);
3718 item.addActionListener(new java.awt.event.ActionListener()
3721 public void actionPerformed(ActionEvent e)
3723 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3724 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3725 viewport.getAlignment());// ,viewport.getSelectionGroup());
3726 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3727 viewport.getAlignment()));
3728 alignPanel.paintAlignment(true, false);
3734 * last hash for alignment's annotation array - used to minimise cost of
3737 protected int _annotationScoreVectorHash;
3740 * search the alignment and rebuild the sort by annotation score submenu the
3741 * last alignment annotation vector hash is stored to minimize cost of
3742 * rebuilding in subsequence calls.
3746 public void buildSortByAnnotationScoresMenu()
3748 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3753 if (viewport.getAlignment().getAlignmentAnnotation()
3754 .hashCode() != _annotationScoreVectorHash)
3756 sortByAnnotScore.removeAll();
3757 // almost certainly a quicker way to do this - but we keep it simple
3758 Hashtable scoreSorts = new Hashtable();
3759 AlignmentAnnotation aann[];
3760 for (SequenceI sqa : viewport.getAlignment().getSequences())
3762 aann = sqa.getAnnotation();
3763 for (int i = 0; aann != null && i < aann.length; i++)
3765 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3767 scoreSorts.put(aann[i].label, aann[i].label);
3771 Enumeration labels = scoreSorts.keys();
3772 while (labels.hasMoreElements())
3774 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3775 (String) labels.nextElement());
3777 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3780 _annotationScoreVectorHash = viewport.getAlignment()
3781 .getAlignmentAnnotation().hashCode();
3786 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3787 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3788 * call. Listeners are added to remove the menu item when the treePanel is
3789 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3793 public void buildTreeSortMenu()
3795 sortByTreeMenu.removeAll();
3797 List<Component> comps = PaintRefresher.components
3798 .get(viewport.getSequenceSetId());
3799 List<TreePanel> treePanels = new ArrayList<>();
3800 for (Component comp : comps)
3802 if (comp instanceof TreePanel)
3804 treePanels.add((TreePanel) comp);
3808 if (treePanels.size() < 1)
3810 sortByTreeMenu.setVisible(false);
3814 sortByTreeMenu.setVisible(true);
3816 for (final TreePanel tp : treePanels)
3818 final JMenuItem item = new JMenuItem(tp.getTitle());
3819 item.addActionListener(new java.awt.event.ActionListener()
3822 public void actionPerformed(ActionEvent e)
3824 tp.sortByTree_actionPerformed();
3825 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3830 sortByTreeMenu.add(item);
3834 public boolean sortBy(AlignmentOrder alorder, String undoname)
3836 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3837 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3838 if (undoname != null)
3840 addHistoryItem(new OrderCommand(undoname, oldOrder,
3841 viewport.getAlignment()));
3843 alignPanel.paintAlignment(true, false);
3848 * Work out whether the whole set of sequences or just the selected set will
3849 * be submitted for multiple alignment.
3852 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3854 // Now, check we have enough sequences
3855 AlignmentView msa = null;
3857 if ((viewport.getSelectionGroup() != null)
3858 && (viewport.getSelectionGroup().getSize() > 1))
3860 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3861 // some common interface!
3863 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3864 * SequenceI[sz = seqs.getSize(false)];
3866 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3867 * seqs.getSequenceAt(i); }
3869 msa = viewport.getAlignmentView(true);
3871 else if (viewport.getSelectionGroup() != null
3872 && viewport.getSelectionGroup().getSize() == 1)
3874 int option = JvOptionPane.showConfirmDialog(this,
3875 MessageManager.getString("warn.oneseq_msainput_selection"),
3876 MessageManager.getString("label.invalid_selection"),
3877 JvOptionPane.OK_CANCEL_OPTION);
3878 if (option == JvOptionPane.OK_OPTION)
3880 msa = viewport.getAlignmentView(false);
3885 msa = viewport.getAlignmentView(false);
3891 * Decides what is submitted to a secondary structure prediction service: the
3892 * first sequence in the alignment, or in the current selection, or, if the
3893 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3894 * region or the whole alignment. (where the first sequence in the set is the
3895 * one that the prediction will be for).
3897 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3899 AlignmentView seqs = null;
3901 if ((viewport.getSelectionGroup() != null)
3902 && (viewport.getSelectionGroup().getSize() > 0))
3904 seqs = viewport.getAlignmentView(true);
3908 seqs = viewport.getAlignmentView(false);
3910 // limit sequences - JBPNote in future - could spawn multiple prediction
3912 // TODO: viewport.getAlignment().isAligned is a global state - the local
3913 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3914 if (!viewport.getAlignment().isAligned(false))
3916 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3917 // TODO: if seqs.getSequences().length>1 then should really have warned
3931 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3933 // Pick the tree file
3934 JalviewFileChooser chooser = new JalviewFileChooser(
3935 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3936 chooser.setFileView(new JalviewFileView());
3937 chooser.setDialogTitle(
3938 MessageManager.getString("label.select_newick_like_tree_file"));
3939 chooser.setToolTipText(
3940 MessageManager.getString("label.load_tree_file"));
3943 new jalview.util.dialogrunner.RunResponse(JalviewFileChooser.APPROVE_OPTION)
3948 String filePath = chooser.getSelectedFile().getPath();
3949 Cache.setProperty("LAST_DIRECTORY", filePath);
3950 NewickFile fin = null;
3953 fin = new NewickFile(new FileParse(
3954 chooser.getSelectedFile(), DataSourceType.FILE));
3955 viewport.setCurrentTree(
3956 showNewickTree(fin, filePath).getTree());
3957 } catch (Exception ex)
3959 JvOptionPane.showMessageDialog(Desktop.desktop,
3961 MessageManager.getString(
3962 "label.problem_reading_tree_file"),
3963 JvOptionPane.WARNING_MESSAGE);
3964 ex.printStackTrace();
3966 if (fin != null && fin.hasWarningMessage())
3968 JvOptionPane.showMessageDialog(Desktop.desktop,
3969 fin.getWarningMessage(),
3970 MessageManager.getString(
3971 "label.possible_problem_with_tree_file"),
3972 JvOptionPane.WARNING_MESSAGE);
3975 }).openDialog(this);
3978 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3980 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3983 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3984 int h, int x, int y)
3986 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3990 * Add a treeviewer for the tree extracted from a Newick file object to the
3991 * current alignment view
3998 * Associated alignment input data (or null)
4007 * @return TreePanel handle
4009 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4010 AlignmentView input, int w, int h, int x, int y)
4012 TreePanel tp = null;
4018 if (nf.getTree() != null)
4020 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4026 tp.setLocation(x, y);
4029 Desktop.addInternalFrame(tp, treeTitle, w, h);
4031 } catch (Exception ex)
4033 ex.printStackTrace();
4039 private boolean buildingMenu = false;
4042 * Generates menu items and listener event actions for web service clients
4045 public void BuildWebServiceMenu()
4047 while (buildingMenu)
4051 System.err.println("Waiting for building menu to finish.");
4053 } catch (Exception e)
4057 final AlignFrame me = this;
4058 buildingMenu = true;
4059 new Thread(new Runnable()
4064 final List<JMenuItem> legacyItems = new ArrayList<>();
4067 // System.err.println("Building ws menu again "
4068 // + Thread.currentThread());
4069 // TODO: add support for context dependent disabling of services based
4071 // alignment and current selection
4072 // TODO: add additional serviceHandle parameter to specify abstract
4074 // class independently of AbstractName
4075 // TODO: add in rediscovery GUI function to restart discoverer
4076 // TODO: group services by location as well as function and/or
4078 // object broker mechanism.
4079 final Vector<JMenu> wsmenu = new Vector<>();
4080 final IProgressIndicator af = me;
4083 * do not i18n these strings - they are hard-coded in class
4084 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4085 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4087 final JMenu msawsmenu = new JMenu("Alignment");
4088 final JMenu secstrmenu = new JMenu(
4089 "Secondary Structure Prediction");
4090 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4091 final JMenu analymenu = new JMenu("Analysis");
4092 final JMenu dismenu = new JMenu("Protein Disorder");
4093 // JAL-940 - only show secondary structure prediction services from
4094 // the legacy server
4095 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4097 Discoverer.services != null && (Discoverer.services.size() > 0))
4099 // TODO: refactor to allow list of AbstractName/Handler bindings to
4101 // stored or retrieved from elsewhere
4102 // No MSAWS used any more:
4103 // Vector msaws = null; // (Vector)
4104 // Discoverer.services.get("MsaWS");
4105 Vector secstrpr = (Vector) Discoverer.services
4107 if (secstrpr != null)
4109 // Add any secondary structure prediction services
4110 for (int i = 0, j = secstrpr.size(); i < j; i++)
4112 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4114 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4115 .getServiceClient(sh);
4116 int p = secstrmenu.getItemCount();
4117 impl.attachWSMenuEntry(secstrmenu, me);
4118 int q = secstrmenu.getItemCount();
4119 for (int litm = p; litm < q; litm++)
4121 legacyItems.add(secstrmenu.getItem(litm));
4127 // Add all submenus in the order they should appear on the web
4129 wsmenu.add(msawsmenu);
4130 wsmenu.add(secstrmenu);
4131 wsmenu.add(dismenu);
4132 wsmenu.add(analymenu);
4133 // No search services yet
4134 // wsmenu.add(seqsrchmenu);
4136 javax.swing.SwingUtilities.invokeLater(new Runnable()
4143 webService.removeAll();
4144 // first, add discovered services onto the webservices menu
4145 if (wsmenu.size() > 0)
4147 for (int i = 0, j = wsmenu.size(); i < j; i++)
4149 webService.add(wsmenu.get(i));
4154 webService.add(me.webServiceNoServices);
4156 // TODO: move into separate menu builder class.
4157 boolean new_sspred = false;
4158 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4160 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4161 if (jws2servs != null)
4163 if (jws2servs.hasServices())
4165 jws2servs.attachWSMenuEntry(webService, me);
4166 for (Jws2Instance sv : jws2servs.getServices())
4168 if (sv.description.toLowerCase().contains("jpred"))
4170 for (JMenuItem jmi : legacyItems)
4172 jmi.setVisible(false);
4178 if (jws2servs.isRunning())
4180 JMenuItem tm = new JMenuItem(
4181 "Still discovering JABA Services");
4182 tm.setEnabled(false);
4187 build_urlServiceMenu(me.webService);
4188 build_fetchdbmenu(webService);
4189 for (JMenu item : wsmenu)
4191 if (item.getItemCount() == 0)
4193 item.setEnabled(false);
4197 item.setEnabled(true);
4200 } catch (Exception e)
4203 "Exception during web service menu building process.",
4208 } catch (Exception e)
4211 buildingMenu = false;
4218 * construct any groupURL type service menu entries.
4222 private void build_urlServiceMenu(JMenu webService)
4224 // TODO: remove this code when 2.7 is released
4225 // DEBUG - alignmentView
4227 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4228 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4230 * @Override public void actionPerformed(ActionEvent e) {
4231 * jalview.datamodel.AlignmentView
4232 * .testSelectionViews(af.viewport.getAlignment(),
4233 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4235 * }); webService.add(testAlView);
4237 // TODO: refactor to RestClient discoverer and merge menu entries for
4238 // rest-style services with other types of analysis/calculation service
4239 // SHmmr test client - still being implemented.
4240 // DEBUG - alignmentView
4242 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4245 client.attachWSMenuEntry(
4246 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4252 * Searches the alignment sequences for xRefs and builds the Show
4253 * Cross-References menu (formerly called Show Products), with database
4254 * sources for which cross-references are found (protein sources for a
4255 * nucleotide alignment and vice versa)
4257 * @return true if Show Cross-references menu should be enabled
4259 public boolean canShowProducts()
4261 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4262 AlignmentI dataset = viewport.getAlignment().getDataset();
4264 showProducts.removeAll();
4265 final boolean dna = viewport.getAlignment().isNucleotide();
4267 if (seqs == null || seqs.length == 0)
4269 // nothing to see here.
4273 boolean showp = false;
4276 List<String> ptypes = new CrossRef(seqs, dataset)
4277 .findXrefSourcesForSequences(dna);
4279 for (final String source : ptypes)
4282 final AlignFrame af = this;
4283 JMenuItem xtype = new JMenuItem(source);
4284 xtype.addActionListener(new ActionListener()
4287 public void actionPerformed(ActionEvent e)
4289 showProductsFor(af.viewport.getSequenceSelection(), dna,
4293 showProducts.add(xtype);
4295 showProducts.setVisible(showp);
4296 showProducts.setEnabled(showp);
4297 } catch (Exception e)
4300 "canShowProducts threw an exception - please report to help@jalview.org",
4308 * Finds and displays cross-references for the selected sequences (protein
4309 * products for nucleotide sequences, dna coding sequences for peptides).
4312 * the sequences to show cross-references for
4314 * true if from a nucleotide alignment (so showing proteins)
4316 * the database to show cross-references for
4318 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4319 final String source)
4321 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4326 * Construct and display a new frame containing the translation of this
4327 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4330 public void showTranslation_actionPerformed(ActionEvent e)
4332 AlignmentI al = null;
4335 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4337 al = dna.translateCdna();
4338 } catch (Exception ex)
4340 jalview.bin.Cache.log.error(
4341 "Exception during translation. Please report this !", ex);
4342 final String msg = MessageManager.getString(
4343 "label.error_when_translating_sequences_submit_bug_report");
4344 final String errorTitle = MessageManager
4345 .getString("label.implementation_error")
4346 + MessageManager.getString("label.translation_failed");
4347 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4348 JvOptionPane.ERROR_MESSAGE);
4351 if (al == null || al.getHeight() == 0)
4353 final String msg = MessageManager.getString(
4354 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4355 final String errorTitle = MessageManager
4356 .getString("label.translation_failed");
4357 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4358 JvOptionPane.WARNING_MESSAGE);
4362 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4363 af.setFileFormat(this.currentFileFormat);
4364 final String newTitle = MessageManager
4365 .formatMessage("label.translation_of_params", new Object[]
4366 { this.getTitle() });
4367 af.setTitle(newTitle);
4368 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4370 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4371 viewport.openSplitFrame(af, new Alignment(seqs));
4375 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4382 * Set the file format
4386 public void setFileFormat(FileFormatI format)
4388 this.currentFileFormat = format;
4392 * Try to load a features file onto the alignment.
4395 * contents or path to retrieve file or a File object
4397 * access mode of file (see jalview.io.AlignFile)
4398 * @return true if features file was parsed correctly.
4400 public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4403 return avc.parseFeaturesFile(file, sourceType,
4404 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4409 public void refreshFeatureUI(boolean enableIfNecessary)
4411 // note - currently this is only still here rather than in the controller
4412 // because of the featureSettings hard reference that is yet to be
4414 if (enableIfNecessary)
4416 viewport.setShowSequenceFeatures(true);
4417 showSeqFeatures.setSelected(true);
4423 public void dragEnter(DropTargetDragEvent evt)
4428 public void dragExit(DropTargetEvent evt)
4433 public void dragOver(DropTargetDragEvent evt)
4438 public void dropActionChanged(DropTargetDragEvent evt)
4443 public void drop(DropTargetDropEvent evt)
4445 // JAL-1552 - acceptDrop required before getTransferable call for
4446 // Java's Transferable for native dnd
4447 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4448 Transferable t = evt.getTransferable();
4451 final AlignFrame thisaf = this;
4452 final List<Object> files = new ArrayList<>();
4453 List<DataSourceType> protocols = new ArrayList<>();
4457 Desktop.transferFromDropTarget(files, protocols, evt, t);
4458 } catch (Exception e)
4460 e.printStackTrace();
4464 new Thread(new Runnable()
4471 // check to see if any of these files have names matching sequences
4474 SequenceIdMatcher idm = new SequenceIdMatcher(
4475 viewport.getAlignment().getSequencesArray());
4477 * Object[] { String,SequenceI}
4479 ArrayList<Object[]> filesmatched = new ArrayList<>();
4480 ArrayList<Object> filesnotmatched = new ArrayList<>();
4481 for (int i = 0; i < files.size(); i++)
4484 Object file = files.get(i);
4485 String fileName = file.toString();
4487 DataSourceType protocol = (file instanceof File ? DataSourceType.FILE : FormatAdapter.checkProtocol(fileName));
4488 if (protocol == DataSourceType.FILE)
4490 File fl = (file instanceof File ? (File) file : new File(fileName));
4491 pdbfn = fl.getName();
4493 else if (protocol == DataSourceType.URL)
4495 URL url = new URL(fileName);
4496 pdbfn = url.getFile();
4498 if (pdbfn.length() > 0)
4500 // attempt to find a match in the alignment
4501 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4502 int l = 0, c = pdbfn.indexOf(".");
4503 while (mtch == null && c != -1)
4508 } while ((c = pdbfn.indexOf(".", l)) > l);
4511 pdbfn = pdbfn.substring(0, l);
4513 mtch = idm.findAllIdMatches(pdbfn);
4520 type = new IdentifyFile().identify(file, protocol);
4521 } catch (Exception ex)
4525 if (type != null && type.isStructureFile())
4527 filesmatched.add(new Object[] { file, protocol, mtch });
4531 // File wasn't named like one of the sequences or wasn't a PDB
4533 filesnotmatched.add(file);
4537 if (filesmatched.size() > 0)
4539 boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4542 String msg = MessageManager.formatMessage(
4543 "label.automatically_associate_structure_files_with_sequences_same_name",
4545 { Integer.valueOf(filesmatched.size())
4547 String ttl = MessageManager.getString(
4548 "label.automatically_associate_structure_files_by_name");
4549 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4550 ttl, JvOptionPane.YES_NO_OPTION);
4551 autoAssociate = choice == JvOptionPane.YES_OPTION;
4555 for (Object[] fm : filesmatched)
4557 // try and associate
4558 // TODO: may want to set a standard ID naming formalism for
4559 // associating PDB files which have no IDs.
4560 for (SequenceI toassoc : (SequenceI[]) fm[2])
4562 PDBEntry pe = new AssociatePdbFileWithSeq()
4563 .associatePdbWithSeq((String) fm[0],
4564 (DataSourceType) fm[1], toassoc, false,
4568 System.err.println("Associated file : "
4569 + ((String) fm[0]) + " with "
4570 + toassoc.getDisplayId(true));
4574 // TODO: do we need to update overview ? only if features are
4576 alignPanel.paintAlignment(true, false);
4582 * add declined structures as sequences
4584 for (Object[] o : filesmatched)
4586 filesnotmatched.add(o[0]);
4590 if (filesnotmatched.size() > 0)
4592 if (assocfiles > 0 && (Cache.getDefault(
4593 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4594 || JvOptionPane.showConfirmDialog(thisaf,
4595 "<html>" + MessageManager.formatMessage(
4596 "label.ignore_unmatched_dropped_files_info",
4599 filesnotmatched.size())
4602 MessageManager.getString(
4603 "label.ignore_unmatched_dropped_files"),
4604 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4608 for (Object fn : filesnotmatched)
4610 loadJalviewDataFile(fn, null, null, null);
4614 } catch (Exception ex)
4616 ex.printStackTrace();
4624 * Attempt to load a "dropped" file or URL string, by testing in turn for
4626 * <li>an Annotation file</li>
4627 * <li>a JNet file</li>
4628 * <li>a features file</li>
4629 * <li>else try to interpret as an alignment file</li>
4633 * either a filename or a URL string.
4635 public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4636 FileFormatI format, SequenceI assocSeq)
4638 // BH 2018 was String file
4641 if (sourceType == null)
4643 sourceType = FormatAdapter.checkProtocol(file);
4645 // if the file isn't identified, or not positively identified as some
4646 // other filetype (PFAM is default unidentified alignment file type) then
4647 // try to parse as annotation.
4648 boolean isAnnotation = (format == null
4649 || FileFormat.Pfam.equals(format))
4650 ? new AnnotationFile().annotateAlignmentView(viewport,
4656 // first see if its a T-COFFEE score file
4657 TCoffeeScoreFile tcf = null;
4660 tcf = new TCoffeeScoreFile(file, sourceType);
4663 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4667 new TCoffeeColourScheme(viewport.getAlignment()));
4668 isAnnotation = true;
4669 statusBar.setText(MessageManager.getString(
4670 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4674 // some problem - if no warning its probable that the ID matching
4675 // process didn't work
4676 JvOptionPane.showMessageDialog(Desktop.desktop,
4677 tcf.getWarningMessage() == null
4678 ? MessageManager.getString(
4679 "label.check_file_matches_sequence_ids_alignment")
4680 : tcf.getWarningMessage(),
4681 MessageManager.getString(
4682 "label.problem_reading_tcoffee_score_file"),
4683 JvOptionPane.WARNING_MESSAGE);
4690 } catch (Exception x)
4693 "Exception when processing data source as T-COFFEE score file",
4699 // try to see if its a JNet 'concise' style annotation file *before*
4701 // try to parse it as a features file
4704 format = new IdentifyFile().identify(file, sourceType);
4706 if (FileFormat.ScoreMatrix == format)
4708 ScoreMatrixFile sm = new ScoreMatrixFile(
4709 new FileParse(file, sourceType));
4711 // todo: i18n this message
4712 statusBar.setText(MessageManager.formatMessage(
4713 "label.successfully_loaded_matrix",
4714 sm.getMatrixName()));
4716 else if (FileFormat.Jnet.equals(format))
4718 JPredFile predictions = new JPredFile(file, sourceType);
4719 new JnetAnnotationMaker();
4720 JnetAnnotationMaker.add_annotation(predictions,
4721 viewport.getAlignment(), 0, false);
4722 viewport.getAlignment().setupJPredAlignment();
4723 isAnnotation = true;
4725 // else if (IdentifyFile.FeaturesFile.equals(format))
4726 else if (FileFormat.Features.equals(format))
4728 if (parseFeaturesFile(file, sourceType))
4730 alignPanel.paintAlignment(true, true);
4735 new FileLoader().LoadFile(viewport, file, sourceType, format);
4742 alignPanel.adjustAnnotationHeight();
4743 viewport.updateSequenceIdColours();
4744 buildSortByAnnotationScoresMenu();
4745 alignPanel.paintAlignment(true, true);
4747 } catch (Exception ex)
4749 ex.printStackTrace();
4750 } catch (OutOfMemoryError oom)
4755 } catch (Exception x)
4760 + (sourceType != null
4761 ? (sourceType == DataSourceType.PASTE
4763 : "using " + sourceType + " from "
4767 ? "(parsing as '" + format + "' file)"
4769 oom, Desktop.desktop);
4774 * Method invoked by the ChangeListener on the tabbed pane, in other words
4775 * when a different tabbed pane is selected by the user or programmatically.
4778 public void tabSelectionChanged(int index)
4782 alignPanel = alignPanels.get(index);
4783 viewport = alignPanel.av;
4784 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4785 setMenusFromViewport(viewport);
4789 * 'focus' any colour slider that is open to the selected viewport
4791 if (viewport.getConservationSelected())
4793 SliderPanel.setConservationSlider(alignPanel,
4794 viewport.getResidueShading(), alignPanel.getViewName());
4798 SliderPanel.hideConservationSlider();
4800 if (viewport.getAbovePIDThreshold())
4802 SliderPanel.setPIDSliderSource(alignPanel,
4803 viewport.getResidueShading(), alignPanel.getViewName());
4807 SliderPanel.hidePIDSlider();
4811 * If there is a frame linked to this one in a SplitPane, switch it to the
4812 * same view tab index. No infinite recursion of calls should happen, since
4813 * tabSelectionChanged() should not get invoked on setting the selected
4814 * index to an unchanged value. Guard against setting an invalid index
4815 * before the new view peer tab has been created.
4817 final AlignViewportI peer = viewport.getCodingComplement();
4820 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4821 .getAlignPanel().alignFrame;
4822 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4824 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4830 * On right mouse click on view tab, prompt for and set new view name.
4833 public void tabbedPane_mousePressed(MouseEvent e)
4835 if (e.isPopupTrigger())
4837 String msg = MessageManager.getString("label.enter_view_name");
4838 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4839 JvOptionPane.QUESTION_MESSAGE);
4843 viewport.viewName = reply;
4844 // TODO warn if reply is in getExistingViewNames()?
4845 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4850 public AlignViewport getCurrentView()
4856 * Open the dialog for regex description parsing.
4859 protected void extractScores_actionPerformed(ActionEvent e)
4861 ParseProperties pp = new jalview.analysis.ParseProperties(
4862 viewport.getAlignment());
4863 // TODO: verify regex and introduce GUI dialog for version 2.5
4864 // if (pp.getScoresFromDescription("col", "score column ",
4865 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4867 if (pp.getScoresFromDescription("description column",
4868 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4870 buildSortByAnnotationScoresMenu();
4878 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4882 protected void showDbRefs_actionPerformed(ActionEvent e)
4884 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4890 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4894 protected void showNpFeats_actionPerformed(ActionEvent e)
4896 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4900 * find the viewport amongst the tabs in this alignment frame and close that
4905 public boolean closeView(AlignViewportI av)
4909 this.closeMenuItem_actionPerformed(false);
4912 Component[] comp = tabbedPane.getComponents();
4913 for (int i = 0; comp != null && i < comp.length; i++)
4915 if (comp[i] instanceof AlignmentPanel)
4917 if (((AlignmentPanel) comp[i]).av == av)
4920 closeView((AlignmentPanel) comp[i]);
4928 protected void build_fetchdbmenu(JMenu webService)
4930 // Temporary hack - DBRef Fetcher always top level ws entry.
4931 // TODO We probably want to store a sequence database checklist in
4932 // preferences and have checkboxes.. rather than individual sources selected
4934 final JMenu rfetch = new JMenu(
4935 MessageManager.getString("action.fetch_db_references"));
4936 rfetch.setToolTipText(MessageManager.getString(
4937 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4938 webService.add(rfetch);
4940 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4941 MessageManager.getString("option.trim_retrieved_seqs"));
4942 trimrs.setToolTipText(
4943 MessageManager.getString("label.trim_retrieved_sequences"));
4945 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4946 trimrs.addActionListener(new ActionListener()
4949 public void actionPerformed(ActionEvent e)
4951 trimrs.setSelected(trimrs.isSelected());
4952 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4953 Boolean.valueOf(trimrs.isSelected()).toString());
4957 JMenuItem fetchr = new JMenuItem(
4958 MessageManager.getString("label.standard_databases"));
4959 fetchr.setToolTipText(
4960 MessageManager.getString("label.fetch_embl_uniprot"));
4961 fetchr.addActionListener(new ActionListener()
4965 public void actionPerformed(ActionEvent e)
4967 new Thread(new Runnable()
4972 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4973 .getAlignment().isNucleotide();
4974 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4975 alignPanel.av.getSequenceSelection(),
4976 alignPanel.alignFrame, null,
4977 alignPanel.alignFrame.featureSettings, isNucleotide);
4978 dbRefFetcher.addListener(new FetchFinishedListenerI()
4981 public void finished()
4983 AlignFrame.this.setMenusForViewport();
4986 dbRefFetcher.fetchDBRefs(false);
4994 final AlignFrame me = this;
4995 new Thread(new Runnable()
5000 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5001 .getSequenceFetcherSingleton(me);
5002 javax.swing.SwingUtilities.invokeLater(new Runnable()
5007 String[] dbclasses = sf.getOrderedSupportedSources();
5008 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5009 // jalview.util.QuickSort.sort(otherdb, otherdb);
5010 List<DbSourceProxy> otherdb;
5011 JMenu dfetch = new JMenu();
5012 JMenu ifetch = new JMenu();
5013 JMenuItem fetchr = null;
5014 int comp = 0, icomp = 0, mcomp = 15;
5015 String mname = null;
5017 for (String dbclass : dbclasses)
5019 otherdb = sf.getSourceProxy(dbclass);
5020 // add a single entry for this class, or submenu allowing 'fetch
5022 if (otherdb == null || otherdb.size() < 1)
5026 // List<DbSourceProxy> dbs=otherdb;
5027 // otherdb=new ArrayList<DbSourceProxy>();
5028 // for (DbSourceProxy db:dbs)
5030 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5034 mname = "From " + dbclass;
5036 if (otherdb.size() == 1)
5038 final DbSourceProxy[] dassource = otherdb
5039 .toArray(new DbSourceProxy[0]);
5040 DbSourceProxy src = otherdb.get(0);
5041 fetchr = new JMenuItem(src.getDbSource());
5042 fetchr.addActionListener(new ActionListener()
5046 public void actionPerformed(ActionEvent e)
5048 new Thread(new Runnable()
5054 boolean isNucleotide = alignPanel.alignFrame
5055 .getViewport().getAlignment()
5057 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5058 alignPanel.av.getSequenceSelection(),
5059 alignPanel.alignFrame, dassource,
5060 alignPanel.alignFrame.featureSettings,
5063 .addListener(new FetchFinishedListenerI()
5066 public void finished()
5068 AlignFrame.this.setMenusForViewport();
5071 dbRefFetcher.fetchDBRefs(false);
5077 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5078 MessageManager.formatMessage(
5079 "label.fetch_retrieve_from", new Object[]
5080 { src.getDbName() })));
5086 final DbSourceProxy[] dassource = otherdb
5087 .toArray(new DbSourceProxy[0]);
5089 DbSourceProxy src = otherdb.get(0);
5090 fetchr = new JMenuItem(MessageManager
5091 .formatMessage("label.fetch_all_param", new Object[]
5092 { src.getDbSource() }));
5093 fetchr.addActionListener(new ActionListener()
5096 public void actionPerformed(ActionEvent e)
5098 new Thread(new Runnable()
5104 boolean isNucleotide = alignPanel.alignFrame
5105 .getViewport().getAlignment()
5107 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5108 alignPanel.av.getSequenceSelection(),
5109 alignPanel.alignFrame, dassource,
5110 alignPanel.alignFrame.featureSettings,
5113 .addListener(new FetchFinishedListenerI()
5116 public void finished()
5118 AlignFrame.this.setMenusForViewport();
5121 dbRefFetcher.fetchDBRefs(false);
5127 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5128 MessageManager.formatMessage(
5129 "label.fetch_retrieve_from_all_sources",
5131 { Integer.valueOf(otherdb.size())
5133 src.getDbSource(), src.getDbName() })));
5136 // and then build the rest of the individual menus
5137 ifetch = new JMenu(MessageManager.formatMessage(
5138 "label.source_from_db_source", new Object[]
5139 { src.getDbSource() }));
5141 String imname = null;
5143 for (DbSourceProxy sproxy : otherdb)
5145 String dbname = sproxy.getDbName();
5146 String sname = dbname.length() > 5
5147 ? dbname.substring(0, 5) + "..."
5149 String msname = dbname.length() > 10
5150 ? dbname.substring(0, 10) + "..."
5154 imname = MessageManager
5155 .formatMessage("label.from_msname", new Object[]
5158 fetchr = new JMenuItem(msname);
5159 final DbSourceProxy[] dassrc = { sproxy };
5160 fetchr.addActionListener(new ActionListener()
5164 public void actionPerformed(ActionEvent e)
5166 new Thread(new Runnable()
5172 boolean isNucleotide = alignPanel.alignFrame
5173 .getViewport().getAlignment()
5175 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5176 alignPanel.av.getSequenceSelection(),
5177 alignPanel.alignFrame, dassrc,
5178 alignPanel.alignFrame.featureSettings,
5181 .addListener(new FetchFinishedListenerI()
5184 public void finished()
5186 AlignFrame.this.setMenusForViewport();
5189 dbRefFetcher.fetchDBRefs(false);
5195 fetchr.setToolTipText(
5196 "<html>" + MessageManager.formatMessage(
5197 "label.fetch_retrieve_from", new Object[]
5201 if (++icomp >= mcomp || i == (otherdb.size()))
5203 ifetch.setText(MessageManager.formatMessage(
5204 "label.source_to_target", imname, sname));
5206 ifetch = new JMenu();
5214 if (comp >= mcomp || dbi >= (dbclasses.length))
5216 dfetch.setText(MessageManager.formatMessage(
5217 "label.source_to_target", mname, dbclass));
5219 dfetch = new JMenu();
5232 * Left justify the whole alignment.
5235 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5237 AlignmentI al = viewport.getAlignment();
5239 viewport.firePropertyChange("alignment", null, al);
5243 * Right justify the whole alignment.
5246 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5248 AlignmentI al = viewport.getAlignment();
5250 viewport.firePropertyChange("alignment", null, al);
5254 public void setShowSeqFeatures(boolean b)
5256 showSeqFeatures.setSelected(b);
5257 viewport.setShowSequenceFeatures(b);
5264 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5265 * awt.event.ActionEvent)
5268 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5270 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5271 alignPanel.paintAlignment(false, false);
5278 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5282 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5284 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5285 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5293 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5294 * .event.ActionEvent)
5297 protected void showGroupConservation_actionPerformed(ActionEvent e)
5299 viewport.setShowGroupConservation(showGroupConservation.getState());
5300 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5307 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5308 * .event.ActionEvent)
5311 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5313 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5314 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5321 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5322 * .event.ActionEvent)
5325 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5327 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5328 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5332 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5334 showSequenceLogo.setState(true);
5335 viewport.setShowSequenceLogo(true);
5336 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5337 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5341 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5343 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5350 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5351 * .event.ActionEvent)
5354 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5356 if (avc.makeGroupsFromSelection())
5358 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5359 alignPanel.updateAnnotation();
5360 alignPanel.paintAlignment(true, true);
5364 public void clearAlignmentSeqRep()
5366 // TODO refactor alignmentseqrep to controller
5367 if (viewport.getAlignment().hasSeqrep())
5369 viewport.getAlignment().setSeqrep(null);
5370 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5371 alignPanel.updateAnnotation();
5372 alignPanel.paintAlignment(true, true);
5377 protected void createGroup_actionPerformed(ActionEvent e)
5379 if (avc.createGroup())
5381 alignPanel.alignmentChanged();
5386 protected void unGroup_actionPerformed(ActionEvent e)
5390 alignPanel.alignmentChanged();
5395 * make the given alignmentPanel the currently selected tab
5397 * @param alignmentPanel
5399 public void setDisplayedView(AlignmentPanel alignmentPanel)
5401 if (!viewport.getSequenceSetId()
5402 .equals(alignmentPanel.av.getSequenceSetId()))
5404 throw new Error(MessageManager.getString(
5405 "error.implementation_error_cannot_show_view_alignment_frame"));
5407 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5408 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5410 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5415 * Action on selection of menu options to Show or Hide annotations.
5418 * @param forSequences
5419 * update sequence-related annotations
5420 * @param forAlignment
5421 * update non-sequence-related annotations
5424 protected void setAnnotationsVisibility(boolean visible,
5425 boolean forSequences, boolean forAlignment)
5427 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5428 .getAlignmentAnnotation();
5433 for (AlignmentAnnotation aa : anns)
5436 * don't display non-positional annotations on an alignment
5438 if (aa.annotations == null)
5442 boolean apply = (aa.sequenceRef == null && forAlignment)
5443 || (aa.sequenceRef != null && forSequences);
5446 aa.visible = visible;
5449 alignPanel.validateAnnotationDimensions(true);
5450 alignPanel.alignmentChanged();
5454 * Store selected annotation sort order for the view and repaint.
5457 protected void sortAnnotations_actionPerformed()
5459 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5461 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5462 alignPanel.paintAlignment(false, false);
5467 * @return alignment panels in this alignment frame
5469 public List<? extends AlignmentViewPanel> getAlignPanels()
5471 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5475 * Open a new alignment window, with the cDNA associated with this (protein)
5476 * alignment, aligned as is the protein.
5478 protected void viewAsCdna_actionPerformed()
5480 // TODO no longer a menu action - refactor as required
5481 final AlignmentI alignment = getViewport().getAlignment();
5482 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5483 if (mappings == null)
5487 List<SequenceI> cdnaSeqs = new ArrayList<>();
5488 for (SequenceI aaSeq : alignment.getSequences())
5490 for (AlignedCodonFrame acf : mappings)
5492 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5496 * There is a cDNA mapping for this protein sequence - add to new
5497 * alignment. It will share the same dataset sequence as other mapped
5498 * cDNA (no new mappings need to be created).
5500 final Sequence newSeq = new Sequence(dnaSeq);
5501 newSeq.setDatasetSequence(dnaSeq);
5502 cdnaSeqs.add(newSeq);
5506 if (cdnaSeqs.size() == 0)
5508 // show a warning dialog no mapped cDNA
5511 AlignmentI cdna = new Alignment(
5512 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5513 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5514 AlignFrame.DEFAULT_HEIGHT);
5515 cdna.alignAs(alignment);
5516 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5518 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5519 AlignFrame.DEFAULT_HEIGHT);
5523 * Set visibility of dna/protein complement view (available when shown in a
5529 protected void showComplement_actionPerformed(boolean show)
5531 SplitContainerI sf = getSplitViewContainer();
5534 sf.setComplementVisible(this, show);
5539 * Generate the reverse (optionally complemented) of the selected sequences,
5540 * and add them to the alignment
5543 protected void showReverse_actionPerformed(boolean complement)
5545 AlignmentI al = null;
5548 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5549 al = dna.reverseCdna(complement);
5550 viewport.addAlignment(al, "");
5551 addHistoryItem(new EditCommand(
5552 MessageManager.getString("label.add_sequences"), Action.PASTE,
5553 al.getSequencesArray(), 0, al.getWidth(),
5554 viewport.getAlignment()));
5555 } catch (Exception ex)
5557 System.err.println(ex.getMessage());
5563 * Try to run a script in the Groovy console, having first ensured that this
5564 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5565 * be targeted at this alignment.
5568 protected void runGroovy_actionPerformed()
5570 Jalview.setCurrentAlignFrame(this);
5571 groovy.ui.Console console = Desktop.getGroovyConsole();
5572 if (console != null)
5576 console.runScript();
5577 } catch (Exception ex)
5579 System.err.println((ex.toString()));
5580 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5581 MessageManager.getString("label.couldnt_run_groovy_script"),
5582 MessageManager.getString("label.groovy_support_failed"),
5583 JvOptionPane.ERROR_MESSAGE);
5588 System.err.println("Can't run Groovy script as console not found");
5593 * Hides columns containing (or not containing) a specified feature, provided
5594 * that would not leave all columns hidden
5596 * @param featureType
5597 * @param columnsContaining
5600 public boolean hideFeatureColumns(String featureType,
5601 boolean columnsContaining)
5603 boolean notForHiding = avc.markColumnsContainingFeatures(
5604 columnsContaining, false, false, featureType);
5607 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5608 false, featureType))
5610 getViewport().hideSelectedColumns();
5618 protected void selectHighlightedColumns_actionPerformed(
5619 ActionEvent actionEvent)
5621 // include key modifier check in case user selects from menu
5622 avc.markHighlightedColumns(
5623 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5624 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5625 | ActionEvent.CTRL_MASK)) != 0);
5629 * Rebuilds the Colour menu, including any user-defined colours which have
5630 * been loaded either on startup or during the session
5632 public void buildColourMenu()
5634 colourMenu.removeAll();
5636 colourMenu.add(applyToAllGroups);
5637 colourMenu.add(textColour);
5638 colourMenu.addSeparator();
5640 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5643 colourMenu.addSeparator();
5644 colourMenu.add(conservationMenuItem);
5645 colourMenu.add(modifyConservation);
5646 colourMenu.add(abovePIDThreshold);
5647 colourMenu.add(modifyPID);
5648 colourMenu.add(annotationColour);
5650 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5651 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5655 * Open a dialog (if not already open) that allows the user to select and
5656 * calculate PCA or Tree analysis
5658 protected void openTreePcaDialog()
5660 if (alignPanel.getCalculationDialog() == null)
5662 new CalculationChooser(AlignFrame.this);
5667 protected void loadVcf_actionPerformed()
5669 JalviewFileChooser chooser = new JalviewFileChooser(
5670 Cache.getProperty("LAST_DIRECTORY"));
5671 chooser.setFileView(new JalviewFileView());
5672 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5673 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5674 final AlignFrame us = this;
5675 chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
5682 String choice = chooser.getSelectedFile().getPath();
5683 Cache.setProperty("LAST_DIRECTORY", choice);
5684 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5685 new VCFLoader(choice).loadVCF(seqs, us);
5689 }).openDialog(null);
5695 class PrintThread extends Thread
5699 public PrintThread(AlignmentPanel ap)
5704 static PageFormat pf;
5709 PrinterJob printJob = PrinterJob.getPrinterJob();
5713 printJob.setPrintable(ap, pf);
5717 printJob.setPrintable(ap);
5720 if (printJob.printDialog())
5725 } catch (Exception PrintException)
5727 PrintException.printStackTrace();