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.AlignExportSettingBeanI;
49 import jalview.datamodel.AlignedCodonFrame;
50 import jalview.datamodel.Alignment;
51 import jalview.datamodel.AlignmentAnnotation;
52 import jalview.datamodel.AlignmentExportData;
53 import jalview.datamodel.AlignmentI;
54 import jalview.datamodel.AlignmentOrder;
55 import jalview.datamodel.AlignmentView;
56 import jalview.datamodel.ColumnSelection;
57 import jalview.datamodel.HiddenColumns;
58 import jalview.datamodel.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 private boolean lastSaveSuccessful = false;
1205 private FileFormatI lastFormatSaved;
1207 private String lastFilenameSaved;
1210 * Raise a dialog or status message for the last call to saveAlignment.
1212 * @return true if last call to saveAlignment(file, format) was successful.
1214 public boolean isSaveAlignmentSuccessful()
1217 if (!lastSaveSuccessful)
1219 JvOptionPane.showInternalMessageDialog(this, MessageManager
1220 .formatMessage("label.couldnt_save_file", new Object[]
1221 { lastFilenameSaved }),
1222 MessageManager.getString("label.error_saving_file"),
1223 JvOptionPane.WARNING_MESSAGE);
1228 statusBar.setText(MessageManager.formatMessage(
1229 "label.successfully_saved_to_file_in_format", new Object[]
1230 { lastFilenameSaved, lastFormatSaved }));
1233 return lastSaveSuccessful;
1236 public void saveAlignment(String file, FileFormatI format)
1238 lastSaveSuccessful = false;
1239 lastFilenameSaved = file;
1240 lastFormatSaved = format;
1241 AlignFrame us = this;
1242 if (FileFormat.Jalview.equals(format))
1244 String shortName = title;
1246 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1248 shortName = shortName.substring(
1249 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1252 lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1257 AlignExportSettingI settings = getAlignmentForExport(format,
1259 settings.addActionListener(new ActionListener()
1262 public void actionPerformed(ActionEvent e)
1265 if (settings.isCancelled())
1267 lastSaveSuccessful = false;
1270 AlignmentExportData exportData = settings.getAlignExportData();
1271 FormatAdapter f = new FormatAdapter(alignPanel,
1272 exportData.getSettings());
1273 String output = f.formatSequences(format,
1274 exportData.getAlignment(), // class
1278 // occur in the distant future
1279 exportData.getOmitHidden(),
1280 exportData.getStartEndPostions(),
1281 f.getCacheSuffixDefault(format),
1282 viewport.getAlignment().getHiddenColumns());
1286 lastSaveSuccessful = false;
1292 PrintWriter out = new PrintWriter(new FileWriter(file));
1297 statusBar.setText(MessageManager.formatMessage(
1298 "label.successfully_saved_to_file_in_format",
1300 { fileName, format.getName() }));
1301 } catch (Exception ex)
1303 lastSaveSuccessful = false;
1304 ex.printStackTrace();
1310 settings.doShowSettings();
1321 protected void outputText_actionPerformed(ActionEvent e)
1323 FileFormatI fileFormat = FileFormats.getInstance()
1324 .forName(e.getActionCommand());
1325 AlignExportSettingI settings = getAlignmentForExport(fileFormat,
1327 settings.addActionListener(new ActionListener()
1330 public void actionPerformed(ActionEvent e)
1332 if (settings.isCancelled())
1336 AlignmentExportData exportData = settings.getAlignExportData();
1337 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1338 cap.setForInput(null);
1341 FileFormatI format = fileFormat;
1342 cap.setText(new FormatAdapter(alignPanel, settings)
1343 .formatSequences(format, exportData.getAlignment(),
1344 exportData.getOmitHidden(),
1345 exportData.getStartEndPostions(),
1346 viewport.getAlignment().getHiddenColumns()));
1347 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1348 "label.alignment_output_command", new Object[]
1349 { fileFormat.getName() }), 600, 500);
1350 } catch (OutOfMemoryError oom)
1352 new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1356 // TODO Auto-generated method stub
1360 settings.doShowSettings();
1363 public static AlignExportSettingI getAlignmentForExport(
1364 FileFormatI format, AlignmentPanel alignPanel,
1365 AlignExportSettingBeanI exportSettings)
1368 return new AlignExportSettings(alignPanel, format, exportSettings);
1378 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1380 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1381 htmlSVG.exportHTML(null);
1385 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1387 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1388 bjs.exportHTML(null);
1391 public void createImageMap(File file, String image)
1393 alignPanel.makePNGImageMap(file, image);
1403 public void createPNG(File f)
1405 alignPanel.makePNG(f);
1415 public void createEPS(File f)
1417 alignPanel.makeEPS(f);
1421 public void createSVG(File f)
1423 alignPanel.makeSVG(f);
1427 public void pageSetup_actionPerformed(ActionEvent e)
1429 PrinterJob printJob = PrinterJob.getPrinterJob();
1430 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1440 public void printMenuItem_actionPerformed(ActionEvent e)
1442 // Putting in a thread avoids Swing painting problems
1443 PrintThread thread = new PrintThread(alignPanel);
1448 public void exportFeatures_actionPerformed(ActionEvent e)
1450 new AnnotationExporter(alignPanel).exportFeatures();
1454 public void exportAnnotations_actionPerformed(ActionEvent e)
1456 new AnnotationExporter(alignPanel).exportAnnotations();
1460 public void associatedData_actionPerformed(ActionEvent e)
1462 final JalviewFileChooser chooser = new JalviewFileChooser(
1463 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1464 chooser.setFileView(new JalviewFileView());
1465 chooser.setDialogTitle(
1466 MessageManager.getString("label.load_jalview_annotations"));
1467 chooser.setToolTipText(
1468 MessageManager.getString("label.load_jalview_annotations"));
1469 chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
1475 String choice = chooser.getSelectedFile().getPath();
1476 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1477 loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1482 chooser.openDialog(this);
1486 * Close the current view or all views in the alignment frame. If the frame
1487 * only contains one view then the alignment will be removed from memory.
1489 * @param closeAllTabs
1492 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1494 if (alignPanels != null && alignPanels.size() < 2)
1496 closeAllTabs = true;
1501 if (alignPanels != null)
1505 if (this.isClosed())
1507 // really close all the windows - otherwise wait till
1508 // setClosed(true) is called
1509 for (int i = 0; i < alignPanels.size(); i++)
1511 AlignmentPanel ap = alignPanels.get(i);
1518 closeView(alignPanel);
1525 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1526 * be called recursively, with the frame now in 'closed' state
1528 this.setClosed(true);
1530 } catch (Exception ex)
1532 ex.printStackTrace();
1537 * Close the specified panel and close up tabs appropriately.
1539 * @param panelToClose
1541 public void closeView(AlignmentPanel panelToClose)
1543 int index = tabbedPane.getSelectedIndex();
1544 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1545 alignPanels.remove(panelToClose);
1546 panelToClose.closePanel();
1547 panelToClose = null;
1549 tabbedPane.removeTabAt(closedindex);
1550 tabbedPane.validate();
1552 if (index > closedindex || index == tabbedPane.getTabCount())
1554 // modify currently selected tab index if necessary.
1558 this.tabSelectionChanged(index);
1564 void updateEditMenuBar()
1567 if (viewport.getHistoryList().size() > 0)
1569 undoMenuItem.setEnabled(true);
1570 CommandI command = viewport.getHistoryList().peek();
1571 undoMenuItem.setText(MessageManager
1572 .formatMessage("label.undo_command", new Object[]
1573 { command.getDescription() }));
1577 undoMenuItem.setEnabled(false);
1578 undoMenuItem.setText(MessageManager.getString("action.undo"));
1581 if (viewport.getRedoList().size() > 0)
1583 redoMenuItem.setEnabled(true);
1585 CommandI command = viewport.getRedoList().peek();
1586 redoMenuItem.setText(MessageManager
1587 .formatMessage("label.redo_command", new Object[]
1588 { command.getDescription() }));
1592 redoMenuItem.setEnabled(false);
1593 redoMenuItem.setText(MessageManager.getString("action.redo"));
1598 public void addHistoryItem(CommandI command)
1600 if (command.getSize() > 0)
1602 viewport.addToHistoryList(command);
1603 viewport.clearRedoList();
1604 updateEditMenuBar();
1605 viewport.updateHiddenColumns();
1606 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1607 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1608 // viewport.getColumnSelection()
1609 // .getHiddenColumns().size() > 0);
1615 * @return alignment objects for all views
1617 AlignmentI[] getViewAlignments()
1619 if (alignPanels != null)
1621 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1623 for (AlignmentPanel ap : alignPanels)
1625 als[i++] = ap.av.getAlignment();
1629 if (viewport != null)
1631 return new AlignmentI[] { viewport.getAlignment() };
1643 protected void undoMenuItem_actionPerformed(ActionEvent e)
1645 if (viewport.getHistoryList().isEmpty())
1649 CommandI command = viewport.getHistoryList().pop();
1650 viewport.addToRedoList(command);
1651 command.undoCommand(getViewAlignments());
1653 AlignmentViewport originalSource = getOriginatingSource(command);
1654 updateEditMenuBar();
1656 if (originalSource != null)
1658 if (originalSource != viewport)
1661 "Implementation worry: mismatch of viewport origin for undo");
1663 originalSource.updateHiddenColumns();
1664 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1666 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1667 // viewport.getColumnSelection()
1668 // .getHiddenColumns().size() > 0);
1669 originalSource.firePropertyChange("alignment", null,
1670 originalSource.getAlignment().getSequences());
1681 protected void redoMenuItem_actionPerformed(ActionEvent e)
1683 if (viewport.getRedoList().size() < 1)
1688 CommandI command = viewport.getRedoList().pop();
1689 viewport.addToHistoryList(command);
1690 command.doCommand(getViewAlignments());
1692 AlignmentViewport originalSource = getOriginatingSource(command);
1693 updateEditMenuBar();
1695 if (originalSource != null)
1698 if (originalSource != viewport)
1701 "Implementation worry: mismatch of viewport origin for redo");
1703 originalSource.updateHiddenColumns();
1704 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1706 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1707 // viewport.getColumnSelection()
1708 // .getHiddenColumns().size() > 0);
1709 originalSource.firePropertyChange("alignment", null,
1710 originalSource.getAlignment().getSequences());
1714 AlignmentViewport getOriginatingSource(CommandI command)
1716 AlignmentViewport originalSource = null;
1717 // For sequence removal and addition, we need to fire
1718 // the property change event FROM the viewport where the
1719 // original alignment was altered
1720 AlignmentI al = null;
1721 if (command instanceof EditCommand)
1723 EditCommand editCommand = (EditCommand) command;
1724 al = editCommand.getAlignment();
1725 List<Component> comps = PaintRefresher.components
1726 .get(viewport.getSequenceSetId());
1728 for (Component comp : comps)
1730 if (comp instanceof AlignmentPanel)
1732 if (al == ((AlignmentPanel) comp).av.getAlignment())
1734 originalSource = ((AlignmentPanel) comp).av;
1741 if (originalSource == null)
1743 // The original view is closed, we must validate
1744 // the current view against the closed view first
1747 PaintRefresher.validateSequences(al, viewport.getAlignment());
1750 originalSource = viewport;
1753 return originalSource;
1762 public void moveSelectedSequences(boolean up)
1764 SequenceGroup sg = viewport.getSelectionGroup();
1770 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1771 viewport.getHiddenRepSequences(), up);
1772 alignPanel.paintAlignment(true, false);
1775 synchronized void slideSequences(boolean right, int size)
1777 List<SequenceI> sg = new ArrayList<>();
1778 if (viewport.cursorMode)
1780 sg.add(viewport.getAlignment()
1781 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1783 else if (viewport.getSelectionGroup() != null
1784 && viewport.getSelectionGroup().getSize() != viewport
1785 .getAlignment().getHeight())
1787 sg = viewport.getSelectionGroup()
1788 .getSequences(viewport.getHiddenRepSequences());
1796 List<SequenceI> invertGroup = new ArrayList<>();
1798 for (SequenceI seq : viewport.getAlignment().getSequences())
1800 if (!sg.contains(seq))
1802 invertGroup.add(seq);
1806 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1808 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1809 for (int i = 0; i < invertGroup.size(); i++)
1811 seqs2[i] = invertGroup.get(i);
1814 SlideSequencesCommand ssc;
1817 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1818 viewport.getGapCharacter());
1822 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1823 viewport.getGapCharacter());
1826 int groupAdjustment = 0;
1827 if (ssc.getGapsInsertedBegin() && right)
1829 if (viewport.cursorMode)
1831 alignPanel.getSeqPanel().moveCursor(size, 0);
1835 groupAdjustment = size;
1838 else if (!ssc.getGapsInsertedBegin() && !right)
1840 if (viewport.cursorMode)
1842 alignPanel.getSeqPanel().moveCursor(-size, 0);
1846 groupAdjustment = -size;
1850 if (groupAdjustment != 0)
1852 viewport.getSelectionGroup().setStartRes(
1853 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1854 viewport.getSelectionGroup().setEndRes(
1855 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1859 * just extend the last slide command if compatible; but not if in
1860 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1862 boolean appendHistoryItem = false;
1863 Deque<CommandI> historyList = viewport.getHistoryList();
1864 boolean inSplitFrame = getSplitViewContainer() != null;
1865 if (!inSplitFrame && historyList != null && historyList.size() > 0
1866 && historyList.peek() instanceof SlideSequencesCommand)
1868 appendHistoryItem = ssc.appendSlideCommand(
1869 (SlideSequencesCommand) historyList.peek());
1872 if (!appendHistoryItem)
1874 addHistoryItem(ssc);
1887 protected void copy_actionPerformed(ActionEvent e)
1889 if (viewport.getSelectionGroup() == null)
1893 // TODO: preserve the ordering of displayed alignment annotation in any
1894 // internal paste (particularly sequence associated annotation)
1895 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1896 String[] omitHidden = null;
1898 if (viewport.hasHiddenColumns())
1900 omitHidden = viewport.getViewAsString(true);
1903 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1904 seqs, omitHidden, null);
1906 StringSelection ss = new StringSelection(output);
1910 jalview.gui.Desktop.internalCopy = true;
1911 // Its really worth setting the clipboard contents
1912 // to empty before setting the large StringSelection!!
1913 Toolkit.getDefaultToolkit().getSystemClipboard()
1914 .setContents(new StringSelection(""), null);
1916 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1918 } catch (OutOfMemoryError er)
1920 new OOMWarning("copying region", er);
1924 HiddenColumns hiddenColumns = null;
1925 if (viewport.hasHiddenColumns())
1927 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1928 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1930 // create new HiddenColumns object with copy of hidden regions
1931 // between startRes and endRes, offset by startRes
1932 hiddenColumns = new HiddenColumns(
1933 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1934 hiddenCutoff, hiddenOffset);
1937 Desktop.jalviewClipboard = new Object[] { seqs,
1938 viewport.getAlignment().getDataset(), hiddenColumns };
1939 statusBar.setText(MessageManager.formatMessage(
1940 "label.copied_sequences_to_clipboard", new Object[]
1941 { Integer.valueOf(seqs.length).toString() }));
1951 protected void pasteNew_actionPerformed(ActionEvent e)
1963 protected void pasteThis_actionPerformed(ActionEvent e)
1969 * Paste contents of Jalview clipboard
1971 * @param newAlignment
1972 * true to paste to a new alignment, otherwise add to this.
1974 void paste(boolean newAlignment)
1976 boolean externalPaste = true;
1979 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1980 Transferable contents = c.getContents(this);
1982 if (contents == null)
1991 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1992 if (str.length() < 1)
1997 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1999 } catch (OutOfMemoryError er)
2001 new OOMWarning("Out of memory pasting sequences!!", er);
2005 SequenceI[] sequences;
2006 boolean annotationAdded = false;
2007 AlignmentI alignment = null;
2009 if (Desktop.jalviewClipboard != null)
2011 // The clipboard was filled from within Jalview, we must use the
2013 // And dataset from the copied alignment
2014 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2015 // be doubly sure that we create *new* sequence objects.
2016 sequences = new SequenceI[newseq.length];
2017 for (int i = 0; i < newseq.length; i++)
2019 sequences[i] = new Sequence(newseq[i]);
2021 alignment = new Alignment(sequences);
2022 externalPaste = false;
2026 // parse the clipboard as an alignment.
2027 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2029 sequences = alignment.getSequencesArray();
2033 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2039 if (Desktop.jalviewClipboard != null)
2041 // dataset is inherited
2042 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2046 // new dataset is constructed
2047 alignment.setDataset(null);
2049 alwidth = alignment.getWidth() + 1;
2053 AlignmentI pastedal = alignment; // preserve pasted alignment object
2054 // Add pasted sequences and dataset into existing alignment.
2055 alignment = viewport.getAlignment();
2056 alwidth = alignment.getWidth() + 1;
2057 // decide if we need to import sequences from an existing dataset
2058 boolean importDs = Desktop.jalviewClipboard != null
2059 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2060 // importDs==true instructs us to copy over new dataset sequences from
2061 // an existing alignment
2062 Vector newDs = (importDs) ? new Vector() : null; // used to create
2063 // minimum dataset set
2065 for (int i = 0; i < sequences.length; i++)
2069 newDs.addElement(null);
2071 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2073 if (importDs && ds != null)
2075 if (!newDs.contains(ds))
2077 newDs.setElementAt(ds, i);
2078 ds = new Sequence(ds);
2079 // update with new dataset sequence
2080 sequences[i].setDatasetSequence(ds);
2084 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2089 // copy and derive new dataset sequence
2090 sequences[i] = sequences[i].deriveSequence();
2091 alignment.getDataset()
2092 .addSequence(sequences[i].getDatasetSequence());
2093 // TODO: avoid creation of duplicate dataset sequences with a
2094 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2096 alignment.addSequence(sequences[i]); // merges dataset
2100 newDs.clear(); // tidy up
2102 if (alignment.getAlignmentAnnotation() != null)
2104 for (AlignmentAnnotation alan : alignment
2105 .getAlignmentAnnotation())
2107 if (alan.graphGroup > fgroup)
2109 fgroup = alan.graphGroup;
2113 if (pastedal.getAlignmentAnnotation() != null)
2115 // Add any annotation attached to alignment.
2116 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2117 for (int i = 0; i < alann.length; i++)
2119 annotationAdded = true;
2120 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2122 AlignmentAnnotation newann = new AlignmentAnnotation(
2124 if (newann.graphGroup > -1)
2126 if (newGraphGroups.size() <= newann.graphGroup
2127 || newGraphGroups.get(newann.graphGroup) == null)
2129 for (int q = newGraphGroups
2130 .size(); q <= newann.graphGroup; q++)
2132 newGraphGroups.add(q, null);
2134 newGraphGroups.set(newann.graphGroup,
2135 new Integer(++fgroup));
2137 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2141 newann.padAnnotation(alwidth);
2142 alignment.addAnnotation(newann);
2152 addHistoryItem(new EditCommand(
2153 MessageManager.getString("label.add_sequences"),
2154 Action.PASTE, sequences, 0, alignment.getWidth(),
2157 // Add any annotations attached to sequences
2158 for (int i = 0; i < sequences.length; i++)
2160 if (sequences[i].getAnnotation() != null)
2162 AlignmentAnnotation newann;
2163 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2165 annotationAdded = true;
2166 newann = sequences[i].getAnnotation()[a];
2167 newann.adjustForAlignment();
2168 newann.padAnnotation(alwidth);
2169 if (newann.graphGroup > -1)
2171 if (newann.graphGroup > -1)
2173 if (newGraphGroups.size() <= newann.graphGroup
2174 || newGraphGroups.get(newann.graphGroup) == null)
2176 for (int q = newGraphGroups
2177 .size(); q <= newann.graphGroup; q++)
2179 newGraphGroups.add(q, null);
2181 newGraphGroups.set(newann.graphGroup,
2182 new Integer(++fgroup));
2184 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2188 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2192 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2200 // propagate alignment changed.
2201 viewport.getRanges().setEndSeq(alignment.getHeight());
2202 if (annotationAdded)
2204 // Duplicate sequence annotation in all views.
2205 AlignmentI[] alview = this.getViewAlignments();
2206 for (int i = 0; i < sequences.length; i++)
2208 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2213 for (int avnum = 0; avnum < alview.length; avnum++)
2215 if (alview[avnum] != alignment)
2217 // duplicate in a view other than the one with input focus
2218 int avwidth = alview[avnum].getWidth() + 1;
2219 // this relies on sann being preserved after we
2220 // modify the sequence's annotation array for each duplication
2221 for (int a = 0; a < sann.length; a++)
2223 AlignmentAnnotation newann = new AlignmentAnnotation(
2225 sequences[i].addAlignmentAnnotation(newann);
2226 newann.padAnnotation(avwidth);
2227 alview[avnum].addAnnotation(newann); // annotation was
2228 // duplicated earlier
2229 // TODO JAL-1145 graphGroups are not updated for sequence
2230 // annotation added to several views. This may cause
2232 alview[avnum].setAnnotationIndex(newann, a);
2237 buildSortByAnnotationScoresMenu();
2239 viewport.firePropertyChange("alignment", null,
2240 alignment.getSequences());
2241 if (alignPanels != null)
2243 for (AlignmentPanel ap : alignPanels)
2245 ap.validateAnnotationDimensions(false);
2250 alignPanel.validateAnnotationDimensions(false);
2256 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2258 String newtitle = new String("Copied sequences");
2260 if (Desktop.jalviewClipboard != null
2261 && Desktop.jalviewClipboard[2] != null)
2263 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2264 af.viewport.setHiddenColumns(hc);
2267 // >>>This is a fix for the moment, until a better solution is
2269 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2270 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2271 .getFeatureRenderer());
2273 // TODO: maintain provenance of an alignment, rather than just make the
2274 // title a concatenation of operations.
2277 if (title.startsWith("Copied sequences"))
2283 newtitle = newtitle.concat("- from " + title);
2288 newtitle = new String("Pasted sequences");
2291 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2296 } catch (Exception ex)
2298 ex.printStackTrace();
2299 System.out.println("Exception whilst pasting: " + ex);
2300 // could be anything being pasted in here
2306 protected void expand_newalign(ActionEvent e)
2310 AlignmentI alignment = AlignmentUtils
2311 .expandContext(getViewport().getAlignment(), -1);
2312 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2314 String newtitle = new String("Flanking alignment");
2316 if (Desktop.jalviewClipboard != null
2317 && Desktop.jalviewClipboard[2] != null)
2319 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2320 af.viewport.setHiddenColumns(hc);
2323 // >>>This is a fix for the moment, until a better solution is
2325 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2326 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2327 .getFeatureRenderer());
2329 // TODO: maintain provenance of an alignment, rather than just make the
2330 // title a concatenation of operations.
2332 if (title.startsWith("Copied sequences"))
2338 newtitle = newtitle.concat("- from " + title);
2342 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2344 } catch (Exception ex)
2346 ex.printStackTrace();
2347 System.out.println("Exception whilst pasting: " + ex);
2348 // could be anything being pasted in here
2349 } catch (OutOfMemoryError oom)
2351 new OOMWarning("Viewing flanking region of alignment", oom);
2362 protected void cut_actionPerformed(ActionEvent e)
2364 copy_actionPerformed(null);
2365 delete_actionPerformed(null);
2375 protected void delete_actionPerformed(ActionEvent evt)
2378 SequenceGroup sg = viewport.getSelectionGroup();
2385 * If the cut affects all sequences, warn, remove highlighted columns
2387 if (sg.getSize() == viewport.getAlignment().getHeight())
2389 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2390 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2391 if (isEntireAlignWidth)
2393 int confirm = JvOptionPane.showConfirmDialog(this,
2394 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2395 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2396 JvOptionPane.OK_CANCEL_OPTION);
2398 if (confirm == JvOptionPane.CANCEL_OPTION
2399 || confirm == JvOptionPane.CLOSED_OPTION)
2404 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2405 sg.getEndRes() + 1);
2407 SequenceI[] cut = sg.getSequences()
2408 .toArray(new SequenceI[sg.getSize()]);
2410 addHistoryItem(new EditCommand(
2411 MessageManager.getString("label.cut_sequences"), Action.CUT,
2412 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2413 viewport.getAlignment()));
2415 viewport.setSelectionGroup(null);
2416 viewport.sendSelection();
2417 viewport.getAlignment().deleteGroup(sg);
2419 viewport.firePropertyChange("alignment", null,
2420 viewport.getAlignment().getSequences());
2421 if (viewport.getAlignment().getHeight() < 1)
2425 this.setClosed(true);
2426 } catch (Exception ex)
2439 protected void deleteGroups_actionPerformed(ActionEvent e)
2441 if (avc.deleteGroups())
2443 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2444 alignPanel.updateAnnotation();
2445 alignPanel.paintAlignment(true, true);
2456 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2458 SequenceGroup sg = new SequenceGroup();
2460 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2462 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2465 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2466 viewport.setSelectionGroup(sg);
2467 viewport.sendSelection();
2468 // JAL-2034 - should delegate to
2469 // alignPanel to decide if overview needs
2471 alignPanel.paintAlignment(false, false);
2472 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2482 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2484 if (viewport.cursorMode)
2486 alignPanel.getSeqPanel().keyboardNo1 = null;
2487 alignPanel.getSeqPanel().keyboardNo2 = null;
2489 viewport.setSelectionGroup(null);
2490 viewport.getColumnSelection().clear();
2491 viewport.setSelectionGroup(null);
2492 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2493 // JAL-2034 - should delegate to
2494 // alignPanel to decide if overview needs
2496 alignPanel.paintAlignment(false, false);
2497 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2498 viewport.sendSelection();
2508 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2510 SequenceGroup sg = viewport.getSelectionGroup();
2514 selectAllSequenceMenuItem_actionPerformed(null);
2519 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2521 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2523 // JAL-2034 - should delegate to
2524 // alignPanel to decide if overview needs
2527 alignPanel.paintAlignment(true, false);
2528 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2529 viewport.sendSelection();
2533 public void invertColSel_actionPerformed(ActionEvent e)
2535 viewport.invertColumnSelection();
2536 alignPanel.paintAlignment(true, false);
2537 viewport.sendSelection();
2547 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2549 trimAlignment(true);
2559 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2561 trimAlignment(false);
2564 void trimAlignment(boolean trimLeft)
2566 ColumnSelection colSel = viewport.getColumnSelection();
2569 if (!colSel.isEmpty())
2573 column = colSel.getMin();
2577 column = colSel.getMax();
2581 if (viewport.getSelectionGroup() != null)
2583 seqs = viewport.getSelectionGroup()
2584 .getSequencesAsArray(viewport.getHiddenRepSequences());
2588 seqs = viewport.getAlignment().getSequencesArray();
2591 TrimRegionCommand trimRegion;
2594 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2595 column, viewport.getAlignment());
2596 viewport.getRanges().setStartRes(0);
2600 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2601 column, viewport.getAlignment());
2604 statusBar.setText(MessageManager
2605 .formatMessage("label.removed_columns", new String[]
2606 { Integer.valueOf(trimRegion.getSize()).toString() }));
2608 addHistoryItem(trimRegion);
2610 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2612 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2613 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2615 viewport.getAlignment().deleteGroup(sg);
2619 viewport.firePropertyChange("alignment", null,
2620 viewport.getAlignment().getSequences());
2631 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2633 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2636 if (viewport.getSelectionGroup() != null)
2638 seqs = viewport.getSelectionGroup()
2639 .getSequencesAsArray(viewport.getHiddenRepSequences());
2640 start = viewport.getSelectionGroup().getStartRes();
2641 end = viewport.getSelectionGroup().getEndRes();
2645 seqs = viewport.getAlignment().getSequencesArray();
2648 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2649 "Remove Gapped Columns", seqs, start, end,
2650 viewport.getAlignment());
2652 addHistoryItem(removeGapCols);
2654 statusBar.setText(MessageManager
2655 .formatMessage("label.removed_empty_columns", new Object[]
2656 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2658 // This is to maintain viewport position on first residue
2659 // of first sequence
2660 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2661 ViewportRanges ranges = viewport.getRanges();
2662 int startRes = seq.findPosition(ranges.getStartRes());
2663 // ShiftList shifts;
2664 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2665 // edit.alColumnChanges=shifts.getInverse();
2666 // if (viewport.hasHiddenColumns)
2667 // viewport.getColumnSelection().compensateForEdits(shifts);
2668 ranges.setStartRes(seq.findIndex(startRes) - 1);
2669 viewport.firePropertyChange("alignment", null,
2670 viewport.getAlignment().getSequences());
2681 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2683 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2686 if (viewport.getSelectionGroup() != null)
2688 seqs = viewport.getSelectionGroup()
2689 .getSequencesAsArray(viewport.getHiddenRepSequences());
2690 start = viewport.getSelectionGroup().getStartRes();
2691 end = viewport.getSelectionGroup().getEndRes();
2695 seqs = viewport.getAlignment().getSequencesArray();
2698 // This is to maintain viewport position on first residue
2699 // of first sequence
2700 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2701 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2703 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2704 viewport.getAlignment()));
2706 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2708 viewport.firePropertyChange("alignment", null,
2709 viewport.getAlignment().getSequences());
2720 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2722 viewport.setPadGaps(padGapsMenuitem.isSelected());
2723 viewport.firePropertyChange("alignment", null,
2724 viewport.getAlignment().getSequences());
2734 public void findMenuItem_actionPerformed(ActionEvent e)
2740 * Create a new view of the current alignment.
2743 public void newView_actionPerformed(ActionEvent e)
2745 newView(null, true);
2749 * Creates and shows a new view of the current alignment.
2752 * title of newly created view; if null, one will be generated
2753 * @param copyAnnotation
2754 * if true then duplicate all annnotation, groups and settings
2755 * @return new alignment panel, already displayed.
2757 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2760 * Create a new AlignmentPanel (with its own, new Viewport)
2762 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2763 if (!copyAnnotation)
2766 * remove all groups and annotation except for the automatic stuff
2768 newap.av.getAlignment().deleteAllGroups();
2769 newap.av.getAlignment().deleteAllAnnotations(false);
2772 newap.av.setGatherViewsHere(false);
2774 if (viewport.viewName == null)
2776 viewport.viewName = MessageManager
2777 .getString("label.view_name_original");
2781 * Views share the same edits undo and redo stacks
2783 newap.av.setHistoryList(viewport.getHistoryList());
2784 newap.av.setRedoList(viewport.getRedoList());
2787 * Views share the same mappings; need to deregister any new mappings
2788 * created by copyAlignPanel, and register the new reference to the shared
2791 newap.av.replaceMappings(viewport.getAlignment());
2794 * start up cDNA consensus (if applicable) now mappings are in place
2796 if (newap.av.initComplementConsensus())
2798 newap.refresh(true); // adjust layout of annotations
2801 newap.av.viewName = getNewViewName(viewTitle);
2803 addAlignmentPanel(newap, true);
2804 newap.alignmentChanged();
2806 if (alignPanels.size() == 2)
2808 viewport.setGatherViewsHere(true);
2810 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2815 * Make a new name for the view, ensuring it is unique within the current
2816 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2817 * these now use viewId. Unique view names are still desirable for usability.)
2822 protected String getNewViewName(String viewTitle)
2824 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2825 boolean addFirstIndex = false;
2826 if (viewTitle == null || viewTitle.trim().length() == 0)
2828 viewTitle = MessageManager.getString("action.view");
2829 addFirstIndex = true;
2833 index = 1;// we count from 1 if given a specific name
2835 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2837 List<Component> comps = PaintRefresher.components
2838 .get(viewport.getSequenceSetId());
2840 List<String> existingNames = getExistingViewNames(comps);
2842 while (existingNames.contains(newViewName))
2844 newViewName = viewTitle + " " + (++index);
2850 * Returns a list of distinct view names found in the given list of
2851 * components. View names are held on the viewport of an AlignmentPanel.
2856 protected List<String> getExistingViewNames(List<Component> comps)
2858 List<String> existingNames = new ArrayList<>();
2859 for (Component comp : comps)
2861 if (comp instanceof AlignmentPanel)
2863 AlignmentPanel ap = (AlignmentPanel) comp;
2864 if (!existingNames.contains(ap.av.viewName))
2866 existingNames.add(ap.av.viewName);
2870 return existingNames;
2874 * Explode tabbed views into separate windows.
2877 public void expandViews_actionPerformed(ActionEvent e)
2879 Desktop.explodeViews(this);
2883 * Gather views in separate windows back into a tabbed presentation.
2886 public void gatherViews_actionPerformed(ActionEvent e)
2888 Desktop.instance.gatherViews(this);
2898 public void font_actionPerformed(ActionEvent e)
2900 new FontChooser(alignPanel);
2910 protected void seqLimit_actionPerformed(ActionEvent e)
2912 viewport.setShowJVSuffix(seqLimits.isSelected());
2914 alignPanel.getIdPanel().getIdCanvas()
2915 .setPreferredSize(alignPanel.calculateIdWidth());
2916 alignPanel.paintAlignment(true, false);
2920 public void idRightAlign_actionPerformed(ActionEvent e)
2922 viewport.setRightAlignIds(idRightAlign.isSelected());
2923 alignPanel.paintAlignment(false, false);
2927 public void centreColumnLabels_actionPerformed(ActionEvent e)
2929 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2930 alignPanel.paintAlignment(false, false);
2936 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2939 protected void followHighlight_actionPerformed()
2942 * Set the 'follow' flag on the Viewport (and scroll to position if now
2945 final boolean state = this.followHighlightMenuItem.getState();
2946 viewport.setFollowHighlight(state);
2949 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2960 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2962 viewport.setColourText(colourTextMenuItem.isSelected());
2963 alignPanel.paintAlignment(false, false);
2973 public void wrapMenuItem_actionPerformed(ActionEvent e)
2975 scaleAbove.setVisible(wrapMenuItem.isSelected());
2976 scaleLeft.setVisible(wrapMenuItem.isSelected());
2977 scaleRight.setVisible(wrapMenuItem.isSelected());
2978 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2979 alignPanel.updateLayout();
2983 public void showAllSeqs_actionPerformed(ActionEvent e)
2985 viewport.showAllHiddenSeqs();
2989 public void showAllColumns_actionPerformed(ActionEvent e)
2991 viewport.showAllHiddenColumns();
2992 alignPanel.paintAlignment(true, true);
2993 viewport.sendSelection();
2997 public void hideSelSequences_actionPerformed(ActionEvent e)
2999 viewport.hideAllSelectedSeqs();
3003 * called by key handler and the hide all/show all menu items
3008 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3011 boolean hide = false;
3012 SequenceGroup sg = viewport.getSelectionGroup();
3013 if (!toggleSeqs && !toggleCols)
3015 // Hide everything by the current selection - this is a hack - we do the
3016 // invert and then hide
3017 // first check that there will be visible columns after the invert.
3018 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3019 && sg.getStartRes() <= sg.getEndRes()))
3021 // now invert the sequence set, if required - empty selection implies
3022 // that no hiding is required.
3025 invertSequenceMenuItem_actionPerformed(null);
3026 sg = viewport.getSelectionGroup();
3030 viewport.expandColSelection(sg, true);
3031 // finally invert the column selection and get the new sequence
3033 invertColSel_actionPerformed(null);
3040 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3042 hideSelSequences_actionPerformed(null);
3045 else if (!(toggleCols && viewport.hasSelectedColumns()))
3047 showAllSeqs_actionPerformed(null);
3053 if (viewport.hasSelectedColumns())
3055 hideSelColumns_actionPerformed(null);
3058 viewport.setSelectionGroup(sg);
3063 showAllColumns_actionPerformed(null);
3072 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3073 * event.ActionEvent)
3076 public void hideAllButSelection_actionPerformed(ActionEvent e)
3078 toggleHiddenRegions(false, false);
3079 viewport.sendSelection();
3086 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3090 public void hideAllSelection_actionPerformed(ActionEvent e)
3092 SequenceGroup sg = viewport.getSelectionGroup();
3093 viewport.expandColSelection(sg, false);
3094 viewport.hideAllSelectedSeqs();
3095 viewport.hideSelectedColumns();
3096 alignPanel.paintAlignment(true, true);
3097 viewport.sendSelection();
3104 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3108 public void showAllhidden_actionPerformed(ActionEvent e)
3110 viewport.showAllHiddenColumns();
3111 viewport.showAllHiddenSeqs();
3112 alignPanel.paintAlignment(true, true);
3113 viewport.sendSelection();
3117 public void hideSelColumns_actionPerformed(ActionEvent e)
3119 viewport.hideSelectedColumns();
3120 alignPanel.paintAlignment(true, true);
3121 viewport.sendSelection();
3125 public void hiddenMarkers_actionPerformed(ActionEvent e)
3127 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3138 protected void scaleAbove_actionPerformed(ActionEvent e)
3140 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3141 // TODO: do we actually need to update overview for scale above change ?
3142 alignPanel.paintAlignment(true, false);
3152 protected void scaleLeft_actionPerformed(ActionEvent e)
3154 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3155 alignPanel.paintAlignment(true, false);
3165 protected void scaleRight_actionPerformed(ActionEvent e)
3167 viewport.setScaleRightWrapped(scaleRight.isSelected());
3168 alignPanel.paintAlignment(true, false);
3178 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3180 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3181 alignPanel.paintAlignment(false, false);
3191 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3193 viewport.setShowText(viewTextMenuItem.isSelected());
3194 alignPanel.paintAlignment(false, false);
3204 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3206 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3207 alignPanel.paintAlignment(false, false);
3210 public FeatureSettings featureSettings;
3213 public FeatureSettingsControllerI getFeatureSettingsUI()
3215 return featureSettings;
3219 public void featureSettings_actionPerformed(ActionEvent e)
3221 if (featureSettings != null)
3223 featureSettings.close();
3224 featureSettings = null;
3226 if (!showSeqFeatures.isSelected())
3228 // make sure features are actually displayed
3229 showSeqFeatures.setSelected(true);
3230 showSeqFeatures_actionPerformed(null);
3232 featureSettings = new FeatureSettings(this);
3236 * Set or clear 'Show Sequence Features'
3242 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3244 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3245 alignPanel.paintAlignment(true, true);
3249 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3250 * the annotations panel as a whole.
3252 * The options to show/hide all annotations should be enabled when the panel
3253 * is shown, and disabled when the panel is hidden.
3258 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3260 final boolean setVisible = annotationPanelMenuItem.isSelected();
3261 viewport.setShowAnnotation(setVisible);
3262 this.showAllSeqAnnotations.setEnabled(setVisible);
3263 this.hideAllSeqAnnotations.setEnabled(setVisible);
3264 this.showAllAlAnnotations.setEnabled(setVisible);
3265 this.hideAllAlAnnotations.setEnabled(setVisible);
3266 alignPanel.updateLayout();
3270 public void alignmentProperties()
3272 JEditorPane editPane = new JEditorPane("text/html", "");
3273 editPane.setEditable(false);
3274 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3277 MessageManager.formatMessage("label.html_content", new Object[]
3278 { contents.toString() }));
3279 JInternalFrame frame = new JInternalFrame();
3280 frame.getContentPane().add(new JScrollPane(editPane));
3282 Desktop.addInternalFrame(frame, MessageManager
3283 .formatMessage("label.alignment_properties", new Object[]
3284 { getTitle() }), 500, 400);
3294 public void overviewMenuItem_actionPerformed(ActionEvent e)
3296 if (alignPanel.overviewPanel != null)
3301 JInternalFrame frame = new JInternalFrame();
3302 final OverviewPanel overview = new OverviewPanel(alignPanel);
3303 frame.setContentPane(overview);
3304 Desktop.addInternalFrame(frame, MessageManager
3305 .formatMessage("label.overview_params", new Object[]
3306 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3309 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3310 frame.addInternalFrameListener(
3311 new javax.swing.event.InternalFrameAdapter()
3314 public void internalFrameClosed(
3315 javax.swing.event.InternalFrameEvent evt)
3318 alignPanel.setOverviewPanel(null);
3321 if (getKeyListeners().length > 0)
3323 frame.addKeyListener(getKeyListeners()[0]);
3326 alignPanel.setOverviewPanel(overview);
3330 public void textColour_actionPerformed()
3332 new TextColourChooser().chooseColour(alignPanel, null);
3336 * public void covariationColour_actionPerformed() {
3338 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3342 public void annotationColour_actionPerformed()
3344 new AnnotationColourChooser(viewport, alignPanel);
3348 public void annotationColumn_actionPerformed(ActionEvent e)
3350 new AnnotationColumnChooser(viewport, alignPanel);
3354 * Action on the user checking or unchecking the option to apply the selected
3355 * colour scheme to all groups. If unchecked, groups may have their own
3356 * independent colour schemes.
3361 public void applyToAllGroups_actionPerformed(boolean selected)
3363 viewport.setColourAppliesToAllGroups(selected);
3367 * Action on user selecting a colour from the colour menu
3370 * the name (not the menu item label!) of the colour scheme
3373 public void changeColour_actionPerformed(String name)
3376 * 'User Defined' opens a panel to configure or load a
3377 * user-defined colour scheme
3379 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3381 new UserDefinedColours(alignPanel);
3386 * otherwise set the chosen colour scheme (or null for 'None')
3388 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3389 viewport.getAlignment(), viewport.getHiddenRepSequences());
3394 * Actions on setting or changing the alignment colour scheme
3399 public void changeColour(ColourSchemeI cs)
3401 // TODO: pull up to controller method
3402 ColourMenuHelper.setColourSelected(colourMenu, cs);
3404 viewport.setGlobalColourScheme(cs);
3406 alignPanel.paintAlignment(true, true);
3410 * Show the PID threshold slider panel
3413 protected void modifyPID_actionPerformed()
3415 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3416 alignPanel.getViewName());
3417 SliderPanel.showPIDSlider();
3421 * Show the Conservation slider panel
3424 protected void modifyConservation_actionPerformed()
3426 SliderPanel.setConservationSlider(alignPanel,
3427 viewport.getResidueShading(), alignPanel.getViewName());
3428 SliderPanel.showConservationSlider();
3432 * Action on selecting or deselecting (Colour) By Conservation
3435 public void conservationMenuItem_actionPerformed(boolean selected)
3437 modifyConservation.setEnabled(selected);
3438 viewport.setConservationSelected(selected);
3439 viewport.getResidueShading().setConservationApplied(selected);
3441 changeColour(viewport.getGlobalColourScheme());
3444 modifyConservation_actionPerformed();
3448 SliderPanel.hideConservationSlider();
3453 * Action on selecting or deselecting (Colour) Above PID Threshold
3456 public void abovePIDThreshold_actionPerformed(boolean selected)
3458 modifyPID.setEnabled(selected);
3459 viewport.setAbovePIDThreshold(selected);
3462 viewport.getResidueShading().setThreshold(0,
3463 viewport.isIgnoreGapsConsensus());
3466 changeColour(viewport.getGlobalColourScheme());
3469 modifyPID_actionPerformed();
3473 SliderPanel.hidePIDSlider();
3484 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3486 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3487 AlignmentSorter.sortByPID(viewport.getAlignment(),
3488 viewport.getAlignment().getSequenceAt(0));
3489 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3490 viewport.getAlignment()));
3491 alignPanel.paintAlignment(true, false);
3501 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3503 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3504 AlignmentSorter.sortByID(viewport.getAlignment());
3506 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3507 alignPanel.paintAlignment(true, false);
3517 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3519 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3520 AlignmentSorter.sortByLength(viewport.getAlignment());
3521 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3522 viewport.getAlignment()));
3523 alignPanel.paintAlignment(true, false);
3533 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3535 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3536 AlignmentSorter.sortByGroup(viewport.getAlignment());
3537 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3538 viewport.getAlignment()));
3540 alignPanel.paintAlignment(true, false);
3550 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3552 new RedundancyPanel(alignPanel, this);
3562 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3564 if ((viewport.getSelectionGroup() == null)
3565 || (viewport.getSelectionGroup().getSize() < 2))
3567 JvOptionPane.showInternalMessageDialog(this,
3568 MessageManager.getString(
3569 "label.you_must_select_least_two_sequences"),
3570 MessageManager.getString("label.invalid_selection"),
3571 JvOptionPane.WARNING_MESSAGE);
3575 JInternalFrame frame = new JInternalFrame();
3576 frame.setContentPane(new PairwiseAlignPanel(viewport));
3577 Desktop.addInternalFrame(frame,
3578 MessageManager.getString("action.pairwise_alignment"), 600,
3584 public void autoCalculate_actionPerformed(ActionEvent e)
3586 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3587 if (viewport.autoCalculateConsensus)
3589 viewport.firePropertyChange("alignment", null,
3590 viewport.getAlignment().getSequences());
3595 public void sortByTreeOption_actionPerformed(ActionEvent e)
3597 viewport.sortByTree = sortByTree.isSelected();
3601 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3603 viewport.followSelection = listenToViewSelections.isSelected();
3607 * Constructs a tree panel and adds it to the desktop
3610 * tree type (NJ or AV)
3612 * name of score model used to compute the tree
3614 * parameters for the distance or similarity calculation
3616 void newTreePanel(String type, String modelName,
3617 SimilarityParamsI options)
3619 String frameTitle = "";
3622 boolean onSelection = false;
3623 if (viewport.getSelectionGroup() != null
3624 && viewport.getSelectionGroup().getSize() > 0)
3626 SequenceGroup sg = viewport.getSelectionGroup();
3628 /* Decide if the selection is a column region */
3629 for (SequenceI _s : sg.getSequences())
3631 if (_s.getLength() < sg.getEndRes())
3633 JvOptionPane.showMessageDialog(Desktop.desktop,
3634 MessageManager.getString(
3635 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3636 MessageManager.getString(
3637 "label.sequences_selection_not_aligned"),
3638 JvOptionPane.WARNING_MESSAGE);
3647 if (viewport.getAlignment().getHeight() < 2)
3653 tp = new TreePanel(alignPanel, type, modelName, options);
3654 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3656 frameTitle += " from ";
3658 if (viewport.viewName != null)
3660 frameTitle += viewport.viewName + " of ";
3663 frameTitle += this.title;
3665 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3676 public void addSortByOrderMenuItem(String title,
3677 final AlignmentOrder order)
3679 final JMenuItem item = new JMenuItem(MessageManager
3680 .formatMessage("action.by_title_param", new Object[]
3683 item.addActionListener(new java.awt.event.ActionListener()
3686 public void actionPerformed(ActionEvent e)
3688 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3690 // TODO: JBPNote - have to map order entries to curent SequenceI
3692 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3694 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3695 viewport.getAlignment()));
3697 alignPanel.paintAlignment(true, false);
3703 * Add a new sort by annotation score menu item
3706 * the menu to add the option to
3708 * the label used to retrieve scores for each sequence on the
3711 public void addSortByAnnotScoreMenuItem(JMenu sort,
3712 final String scoreLabel)
3714 final JMenuItem item = new JMenuItem(scoreLabel);
3716 item.addActionListener(new java.awt.event.ActionListener()
3719 public void actionPerformed(ActionEvent e)
3721 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3722 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3723 viewport.getAlignment());// ,viewport.getSelectionGroup());
3724 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3725 viewport.getAlignment()));
3726 alignPanel.paintAlignment(true, false);
3732 * last hash for alignment's annotation array - used to minimise cost of
3735 protected int _annotationScoreVectorHash;
3738 * search the alignment and rebuild the sort by annotation score submenu the
3739 * last alignment annotation vector hash is stored to minimize cost of
3740 * rebuilding in subsequence calls.
3744 public void buildSortByAnnotationScoresMenu()
3746 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3751 if (viewport.getAlignment().getAlignmentAnnotation()
3752 .hashCode() != _annotationScoreVectorHash)
3754 sortByAnnotScore.removeAll();
3755 // almost certainly a quicker way to do this - but we keep it simple
3756 Hashtable scoreSorts = new Hashtable();
3757 AlignmentAnnotation aann[];
3758 for (SequenceI sqa : viewport.getAlignment().getSequences())
3760 aann = sqa.getAnnotation();
3761 for (int i = 0; aann != null && i < aann.length; i++)
3763 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3765 scoreSorts.put(aann[i].label, aann[i].label);
3769 Enumeration labels = scoreSorts.keys();
3770 while (labels.hasMoreElements())
3772 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3773 (String) labels.nextElement());
3775 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3778 _annotationScoreVectorHash = viewport.getAlignment()
3779 .getAlignmentAnnotation().hashCode();
3784 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3785 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3786 * call. Listeners are added to remove the menu item when the treePanel is
3787 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3791 public void buildTreeSortMenu()
3793 sortByTreeMenu.removeAll();
3795 List<Component> comps = PaintRefresher.components
3796 .get(viewport.getSequenceSetId());
3797 List<TreePanel> treePanels = new ArrayList<>();
3798 for (Component comp : comps)
3800 if (comp instanceof TreePanel)
3802 treePanels.add((TreePanel) comp);
3806 if (treePanels.size() < 1)
3808 sortByTreeMenu.setVisible(false);
3812 sortByTreeMenu.setVisible(true);
3814 for (final TreePanel tp : treePanels)
3816 final JMenuItem item = new JMenuItem(tp.getTitle());
3817 item.addActionListener(new java.awt.event.ActionListener()
3820 public void actionPerformed(ActionEvent e)
3822 tp.sortByTree_actionPerformed();
3823 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3828 sortByTreeMenu.add(item);
3832 public boolean sortBy(AlignmentOrder alorder, String undoname)
3834 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3835 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3836 if (undoname != null)
3838 addHistoryItem(new OrderCommand(undoname, oldOrder,
3839 viewport.getAlignment()));
3841 alignPanel.paintAlignment(true, false);
3846 * Work out whether the whole set of sequences or just the selected set will
3847 * be submitted for multiple alignment.
3850 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3852 // Now, check we have enough sequences
3853 AlignmentView msa = null;
3855 if ((viewport.getSelectionGroup() != null)
3856 && (viewport.getSelectionGroup().getSize() > 1))
3858 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3859 // some common interface!
3861 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3862 * SequenceI[sz = seqs.getSize(false)];
3864 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3865 * seqs.getSequenceAt(i); }
3867 msa = viewport.getAlignmentView(true);
3869 else if (viewport.getSelectionGroup() != null
3870 && viewport.getSelectionGroup().getSize() == 1)
3872 int option = JvOptionPane.showConfirmDialog(this,
3873 MessageManager.getString("warn.oneseq_msainput_selection"),
3874 MessageManager.getString("label.invalid_selection"),
3875 JvOptionPane.OK_CANCEL_OPTION);
3876 if (option == JvOptionPane.OK_OPTION)
3878 msa = viewport.getAlignmentView(false);
3883 msa = viewport.getAlignmentView(false);
3889 * Decides what is submitted to a secondary structure prediction service: the
3890 * first sequence in the alignment, or in the current selection, or, if the
3891 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3892 * region or the whole alignment. (where the first sequence in the set is the
3893 * one that the prediction will be for).
3895 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3897 AlignmentView seqs = null;
3899 if ((viewport.getSelectionGroup() != null)
3900 && (viewport.getSelectionGroup().getSize() > 0))
3902 seqs = viewport.getAlignmentView(true);
3906 seqs = viewport.getAlignmentView(false);
3908 // limit sequences - JBPNote in future - could spawn multiple prediction
3910 // TODO: viewport.getAlignment().isAligned is a global state - the local
3911 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3912 if (!viewport.getAlignment().isAligned(false))
3914 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3915 // TODO: if seqs.getSequences().length>1 then should really have warned
3929 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3931 // Pick the tree file
3932 JalviewFileChooser chooser = new JalviewFileChooser(
3933 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3934 chooser.setFileView(new JalviewFileView());
3935 chooser.setDialogTitle(
3936 MessageManager.getString("label.select_newick_like_tree_file"));
3937 chooser.setToolTipText(
3938 MessageManager.getString("label.load_tree_file"));
3941 new jalview.util.dialogrunner.RunResponse(JalviewFileChooser.APPROVE_OPTION)
3946 String filePath = chooser.getSelectedFile().getPath();
3947 Cache.setProperty("LAST_DIRECTORY", filePath);
3948 NewickFile fin = null;
3951 fin = new NewickFile(new FileParse(
3952 chooser.getSelectedFile(), DataSourceType.FILE));
3953 viewport.setCurrentTree(
3954 showNewickTree(fin, filePath).getTree());
3955 } catch (Exception ex)
3957 JvOptionPane.showMessageDialog(Desktop.desktop,
3959 MessageManager.getString(
3960 "label.problem_reading_tree_file"),
3961 JvOptionPane.WARNING_MESSAGE);
3962 ex.printStackTrace();
3964 if (fin != null && fin.hasWarningMessage())
3966 JvOptionPane.showMessageDialog(Desktop.desktop,
3967 fin.getWarningMessage(),
3968 MessageManager.getString(
3969 "label.possible_problem_with_tree_file"),
3970 JvOptionPane.WARNING_MESSAGE);
3973 }).openDialog(this);
3976 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3978 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3981 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3982 int h, int x, int y)
3984 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3988 * Add a treeviewer for the tree extracted from a Newick file object to the
3989 * current alignment view
3996 * Associated alignment input data (or null)
4005 * @return TreePanel handle
4007 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4008 AlignmentView input, int w, int h, int x, int y)
4010 TreePanel tp = null;
4016 if (nf.getTree() != null)
4018 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4024 tp.setLocation(x, y);
4027 Desktop.addInternalFrame(tp, treeTitle, w, h);
4029 } catch (Exception ex)
4031 ex.printStackTrace();
4037 private boolean buildingMenu = false;
4040 * Generates menu items and listener event actions for web service clients
4043 public void BuildWebServiceMenu()
4045 while (buildingMenu)
4049 System.err.println("Waiting for building menu to finish.");
4051 } catch (Exception e)
4055 final AlignFrame me = this;
4056 buildingMenu = true;
4057 new Thread(new Runnable()
4062 final List<JMenuItem> legacyItems = new ArrayList<>();
4065 // System.err.println("Building ws menu again "
4066 // + Thread.currentThread());
4067 // TODO: add support for context dependent disabling of services based
4069 // alignment and current selection
4070 // TODO: add additional serviceHandle parameter to specify abstract
4072 // class independently of AbstractName
4073 // TODO: add in rediscovery GUI function to restart discoverer
4074 // TODO: group services by location as well as function and/or
4076 // object broker mechanism.
4077 final Vector<JMenu> wsmenu = new Vector<>();
4078 final IProgressIndicator af = me;
4081 * do not i18n these strings - they are hard-coded in class
4082 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4083 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4085 final JMenu msawsmenu = new JMenu("Alignment");
4086 final JMenu secstrmenu = new JMenu(
4087 "Secondary Structure Prediction");
4088 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4089 final JMenu analymenu = new JMenu("Analysis");
4090 final JMenu dismenu = new JMenu("Protein Disorder");
4091 // JAL-940 - only show secondary structure prediction services from
4092 // the legacy server
4093 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4095 Discoverer.services != null && (Discoverer.services.size() > 0))
4097 // TODO: refactor to allow list of AbstractName/Handler bindings to
4099 // stored or retrieved from elsewhere
4100 // No MSAWS used any more:
4101 // Vector msaws = null; // (Vector)
4102 // Discoverer.services.get("MsaWS");
4103 Vector secstrpr = (Vector) Discoverer.services
4105 if (secstrpr != null)
4107 // Add any secondary structure prediction services
4108 for (int i = 0, j = secstrpr.size(); i < j; i++)
4110 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4112 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4113 .getServiceClient(sh);
4114 int p = secstrmenu.getItemCount();
4115 impl.attachWSMenuEntry(secstrmenu, me);
4116 int q = secstrmenu.getItemCount();
4117 for (int litm = p; litm < q; litm++)
4119 legacyItems.add(secstrmenu.getItem(litm));
4125 // Add all submenus in the order they should appear on the web
4127 wsmenu.add(msawsmenu);
4128 wsmenu.add(secstrmenu);
4129 wsmenu.add(dismenu);
4130 wsmenu.add(analymenu);
4131 // No search services yet
4132 // wsmenu.add(seqsrchmenu);
4134 javax.swing.SwingUtilities.invokeLater(new Runnable()
4141 webService.removeAll();
4142 // first, add discovered services onto the webservices menu
4143 if (wsmenu.size() > 0)
4145 for (int i = 0, j = wsmenu.size(); i < j; i++)
4147 webService.add(wsmenu.get(i));
4152 webService.add(me.webServiceNoServices);
4154 // TODO: move into separate menu builder class.
4155 boolean new_sspred = false;
4156 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4158 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4159 if (jws2servs != null)
4161 if (jws2servs.hasServices())
4163 jws2servs.attachWSMenuEntry(webService, me);
4164 for (Jws2Instance sv : jws2servs.getServices())
4166 if (sv.description.toLowerCase().contains("jpred"))
4168 for (JMenuItem jmi : legacyItems)
4170 jmi.setVisible(false);
4176 if (jws2servs.isRunning())
4178 JMenuItem tm = new JMenuItem(
4179 "Still discovering JABA Services");
4180 tm.setEnabled(false);
4185 build_urlServiceMenu(me.webService);
4186 build_fetchdbmenu(webService);
4187 for (JMenu item : wsmenu)
4189 if (item.getItemCount() == 0)
4191 item.setEnabled(false);
4195 item.setEnabled(true);
4198 } catch (Exception e)
4201 "Exception during web service menu building process.",
4206 } catch (Exception e)
4209 buildingMenu = false;
4216 * construct any groupURL type service menu entries.
4220 private void build_urlServiceMenu(JMenu webService)
4222 // TODO: remove this code when 2.7 is released
4223 // DEBUG - alignmentView
4225 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4226 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4228 * @Override public void actionPerformed(ActionEvent e) {
4229 * jalview.datamodel.AlignmentView
4230 * .testSelectionViews(af.viewport.getAlignment(),
4231 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4233 * }); webService.add(testAlView);
4235 // TODO: refactor to RestClient discoverer and merge menu entries for
4236 // rest-style services with other types of analysis/calculation service
4237 // SHmmr test client - still being implemented.
4238 // DEBUG - alignmentView
4240 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4243 client.attachWSMenuEntry(
4244 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4250 * Searches the alignment sequences for xRefs and builds the Show
4251 * Cross-References menu (formerly called Show Products), with database
4252 * sources for which cross-references are found (protein sources for a
4253 * nucleotide alignment and vice versa)
4255 * @return true if Show Cross-references menu should be enabled
4257 public boolean canShowProducts()
4259 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4260 AlignmentI dataset = viewport.getAlignment().getDataset();
4262 showProducts.removeAll();
4263 final boolean dna = viewport.getAlignment().isNucleotide();
4265 if (seqs == null || seqs.length == 0)
4267 // nothing to see here.
4271 boolean showp = false;
4274 List<String> ptypes = new CrossRef(seqs, dataset)
4275 .findXrefSourcesForSequences(dna);
4277 for (final String source : ptypes)
4280 final AlignFrame af = this;
4281 JMenuItem xtype = new JMenuItem(source);
4282 xtype.addActionListener(new ActionListener()
4285 public void actionPerformed(ActionEvent e)
4287 showProductsFor(af.viewport.getSequenceSelection(), dna,
4291 showProducts.add(xtype);
4293 showProducts.setVisible(showp);
4294 showProducts.setEnabled(showp);
4295 } catch (Exception e)
4298 "canShowProducts threw an exception - please report to help@jalview.org",
4306 * Finds and displays cross-references for the selected sequences (protein
4307 * products for nucleotide sequences, dna coding sequences for peptides).
4310 * the sequences to show cross-references for
4312 * true if from a nucleotide alignment (so showing proteins)
4314 * the database to show cross-references for
4316 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4317 final String source)
4319 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4324 * Construct and display a new frame containing the translation of this
4325 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4328 public void showTranslation_actionPerformed(ActionEvent e)
4330 AlignmentI al = null;
4333 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4335 al = dna.translateCdna();
4336 } catch (Exception ex)
4338 jalview.bin.Cache.log.error(
4339 "Exception during translation. Please report this !", ex);
4340 final String msg = MessageManager.getString(
4341 "label.error_when_translating_sequences_submit_bug_report");
4342 final String errorTitle = MessageManager
4343 .getString("label.implementation_error")
4344 + MessageManager.getString("label.translation_failed");
4345 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4346 JvOptionPane.ERROR_MESSAGE);
4349 if (al == null || al.getHeight() == 0)
4351 final String msg = MessageManager.getString(
4352 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4353 final String errorTitle = MessageManager
4354 .getString("label.translation_failed");
4355 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4356 JvOptionPane.WARNING_MESSAGE);
4360 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4361 af.setFileFormat(this.currentFileFormat);
4362 final String newTitle = MessageManager
4363 .formatMessage("label.translation_of_params", new Object[]
4364 { this.getTitle() });
4365 af.setTitle(newTitle);
4366 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4368 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4369 viewport.openSplitFrame(af, new Alignment(seqs));
4373 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4380 * Set the file format
4384 public void setFileFormat(FileFormatI format)
4386 this.currentFileFormat = format;
4390 * Try to load a features file onto the alignment.
4393 * contents or path to retrieve file or a File object
4395 * access mode of file (see jalview.io.AlignFile)
4396 * @return true if features file was parsed correctly.
4398 public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4401 return avc.parseFeaturesFile(file, sourceType,
4402 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4407 public void refreshFeatureUI(boolean enableIfNecessary)
4409 // note - currently this is only still here rather than in the controller
4410 // because of the featureSettings hard reference that is yet to be
4412 if (enableIfNecessary)
4414 viewport.setShowSequenceFeatures(true);
4415 showSeqFeatures.setSelected(true);
4421 public void dragEnter(DropTargetDragEvent evt)
4426 public void dragExit(DropTargetEvent evt)
4431 public void dragOver(DropTargetDragEvent evt)
4436 public void dropActionChanged(DropTargetDragEvent evt)
4441 public void drop(DropTargetDropEvent evt)
4443 // JAL-1552 - acceptDrop required before getTransferable call for
4444 // Java's Transferable for native dnd
4445 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4446 Transferable t = evt.getTransferable();
4449 final AlignFrame thisaf = this;
4450 final List<Object> files = new ArrayList<>();
4451 List<DataSourceType> protocols = new ArrayList<>();
4455 Desktop.transferFromDropTarget(files, protocols, evt, t);
4456 } catch (Exception e)
4458 e.printStackTrace();
4462 new Thread(new Runnable()
4469 // check to see if any of these files have names matching sequences
4472 SequenceIdMatcher idm = new SequenceIdMatcher(
4473 viewport.getAlignment().getSequencesArray());
4475 * Object[] { String,SequenceI}
4477 ArrayList<Object[]> filesmatched = new ArrayList<>();
4478 ArrayList<Object> filesnotmatched = new ArrayList<>();
4479 for (int i = 0; i < files.size(); i++)
4482 Object file = files.get(i);
4483 String fileName = file.toString();
4485 DataSourceType protocol = (file instanceof File ? DataSourceType.FILE : FormatAdapter.checkProtocol(fileName));
4486 if (protocol == DataSourceType.FILE)
4488 File fl = (file instanceof File ? (File) file : new File(fileName));
4489 pdbfn = fl.getName();
4491 else if (protocol == DataSourceType.URL)
4493 URL url = new URL(fileName);
4494 pdbfn = url.getFile();
4496 if (pdbfn.length() > 0)
4498 // attempt to find a match in the alignment
4499 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4500 int l = 0, c = pdbfn.indexOf(".");
4501 while (mtch == null && c != -1)
4506 } while ((c = pdbfn.indexOf(".", l)) > l);
4509 pdbfn = pdbfn.substring(0, l);
4511 mtch = idm.findAllIdMatches(pdbfn);
4518 type = new IdentifyFile().identify(file, protocol);
4519 } catch (Exception ex)
4523 if (type != null && type.isStructureFile())
4525 filesmatched.add(new Object[] { file, protocol, mtch });
4529 // File wasn't named like one of the sequences or wasn't a PDB
4531 filesnotmatched.add(file);
4535 if (filesmatched.size() > 0)
4537 boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4540 String msg = MessageManager.formatMessage(
4541 "label.automatically_associate_structure_files_with_sequences_same_name",
4543 { Integer.valueOf(filesmatched.size())
4545 String ttl = MessageManager.getString(
4546 "label.automatically_associate_structure_files_by_name");
4547 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4548 ttl, JvOptionPane.YES_NO_OPTION);
4549 autoAssociate = choice == JvOptionPane.YES_OPTION;
4553 for (Object[] fm : filesmatched)
4555 // try and associate
4556 // TODO: may want to set a standard ID naming formalism for
4557 // associating PDB files which have no IDs.
4558 for (SequenceI toassoc : (SequenceI[]) fm[2])
4560 PDBEntry pe = new AssociatePdbFileWithSeq()
4561 .associatePdbWithSeq((String) fm[0],
4562 (DataSourceType) fm[1], toassoc, false,
4566 System.err.println("Associated file : "
4567 + ((String) fm[0]) + " with "
4568 + toassoc.getDisplayId(true));
4572 // TODO: do we need to update overview ? only if features are
4574 alignPanel.paintAlignment(true, false);
4580 * add declined structures as sequences
4582 for (Object[] o : filesmatched)
4584 filesnotmatched.add(o[0]);
4588 if (filesnotmatched.size() > 0)
4590 if (assocfiles > 0 && (Cache.getDefault(
4591 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4592 || JvOptionPane.showConfirmDialog(thisaf,
4593 "<html>" + MessageManager.formatMessage(
4594 "label.ignore_unmatched_dropped_files_info",
4597 filesnotmatched.size())
4600 MessageManager.getString(
4601 "label.ignore_unmatched_dropped_files"),
4602 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4606 for (Object fn : filesnotmatched)
4608 loadJalviewDataFile(fn, null, null, null);
4612 } catch (Exception ex)
4614 ex.printStackTrace();
4622 * Attempt to load a "dropped" file or URL string, by testing in turn for
4624 * <li>an Annotation file</li>
4625 * <li>a JNet file</li>
4626 * <li>a features file</li>
4627 * <li>else try to interpret as an alignment file</li>
4631 * either a filename or a URL string.
4633 public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4634 FileFormatI format, SequenceI assocSeq)
4636 // BH 2018 was String file
4639 if (sourceType == null)
4641 sourceType = FormatAdapter.checkProtocol(file);
4643 // if the file isn't identified, or not positively identified as some
4644 // other filetype (PFAM is default unidentified alignment file type) then
4645 // try to parse as annotation.
4646 boolean isAnnotation = (format == null
4647 || FileFormat.Pfam.equals(format))
4648 ? new AnnotationFile().annotateAlignmentView(viewport,
4654 // first see if its a T-COFFEE score file
4655 TCoffeeScoreFile tcf = null;
4658 tcf = new TCoffeeScoreFile(file, sourceType);
4661 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4665 new TCoffeeColourScheme(viewport.getAlignment()));
4666 isAnnotation = true;
4667 statusBar.setText(MessageManager.getString(
4668 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4672 // some problem - if no warning its probable that the ID matching
4673 // process didn't work
4674 JvOptionPane.showMessageDialog(Desktop.desktop,
4675 tcf.getWarningMessage() == null
4676 ? MessageManager.getString(
4677 "label.check_file_matches_sequence_ids_alignment")
4678 : tcf.getWarningMessage(),
4679 MessageManager.getString(
4680 "label.problem_reading_tcoffee_score_file"),
4681 JvOptionPane.WARNING_MESSAGE);
4688 } catch (Exception x)
4691 "Exception when processing data source as T-COFFEE score file",
4697 // try to see if its a JNet 'concise' style annotation file *before*
4699 // try to parse it as a features file
4702 format = new IdentifyFile().identify(file, sourceType);
4704 if (FileFormat.ScoreMatrix == format)
4706 ScoreMatrixFile sm = new ScoreMatrixFile(
4707 new FileParse(file, sourceType));
4709 // todo: i18n this message
4710 statusBar.setText(MessageManager.formatMessage(
4711 "label.successfully_loaded_matrix",
4712 sm.getMatrixName()));
4714 else if (FileFormat.Jnet.equals(format))
4716 JPredFile predictions = new JPredFile(file, sourceType);
4717 new JnetAnnotationMaker();
4718 JnetAnnotationMaker.add_annotation(predictions,
4719 viewport.getAlignment(), 0, false);
4720 viewport.getAlignment().setupJPredAlignment();
4721 isAnnotation = true;
4723 // else if (IdentifyFile.FeaturesFile.equals(format))
4724 else if (FileFormat.Features.equals(format))
4726 if (parseFeaturesFile(file, sourceType))
4728 alignPanel.paintAlignment(true, true);
4733 new FileLoader().LoadFile(viewport, file, sourceType, format);
4740 alignPanel.adjustAnnotationHeight();
4741 viewport.updateSequenceIdColours();
4742 buildSortByAnnotationScoresMenu();
4743 alignPanel.paintAlignment(true, true);
4745 } catch (Exception ex)
4747 ex.printStackTrace();
4748 } catch (OutOfMemoryError oom)
4753 } catch (Exception x)
4758 + (sourceType != null
4759 ? (sourceType == DataSourceType.PASTE
4761 : "using " + sourceType + " from "
4765 ? "(parsing as '" + format + "' file)"
4767 oom, Desktop.desktop);
4772 * Method invoked by the ChangeListener on the tabbed pane, in other words
4773 * when a different tabbed pane is selected by the user or programmatically.
4776 public void tabSelectionChanged(int index)
4780 alignPanel = alignPanels.get(index);
4781 viewport = alignPanel.av;
4782 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4783 setMenusFromViewport(viewport);
4787 * 'focus' any colour slider that is open to the selected viewport
4789 if (viewport.getConservationSelected())
4791 SliderPanel.setConservationSlider(alignPanel,
4792 viewport.getResidueShading(), alignPanel.getViewName());
4796 SliderPanel.hideConservationSlider();
4798 if (viewport.getAbovePIDThreshold())
4800 SliderPanel.setPIDSliderSource(alignPanel,
4801 viewport.getResidueShading(), alignPanel.getViewName());
4805 SliderPanel.hidePIDSlider();
4809 * If there is a frame linked to this one in a SplitPane, switch it to the
4810 * same view tab index. No infinite recursion of calls should happen, since
4811 * tabSelectionChanged() should not get invoked on setting the selected
4812 * index to an unchanged value. Guard against setting an invalid index
4813 * before the new view peer tab has been created.
4815 final AlignViewportI peer = viewport.getCodingComplement();
4818 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4819 .getAlignPanel().alignFrame;
4820 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4822 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4828 * On right mouse click on view tab, prompt for and set new view name.
4831 public void tabbedPane_mousePressed(MouseEvent e)
4833 if (e.isPopupTrigger())
4835 String msg = MessageManager.getString("label.enter_view_name");
4836 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4837 JvOptionPane.QUESTION_MESSAGE);
4841 viewport.viewName = reply;
4842 // TODO warn if reply is in getExistingViewNames()?
4843 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4848 public AlignViewport getCurrentView()
4854 * Open the dialog for regex description parsing.
4857 protected void extractScores_actionPerformed(ActionEvent e)
4859 ParseProperties pp = new jalview.analysis.ParseProperties(
4860 viewport.getAlignment());
4861 // TODO: verify regex and introduce GUI dialog for version 2.5
4862 // if (pp.getScoresFromDescription("col", "score column ",
4863 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4865 if (pp.getScoresFromDescription("description column",
4866 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4868 buildSortByAnnotationScoresMenu();
4876 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4880 protected void showDbRefs_actionPerformed(ActionEvent e)
4882 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4888 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4892 protected void showNpFeats_actionPerformed(ActionEvent e)
4894 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4898 * find the viewport amongst the tabs in this alignment frame and close that
4903 public boolean closeView(AlignViewportI av)
4907 this.closeMenuItem_actionPerformed(false);
4910 Component[] comp = tabbedPane.getComponents();
4911 for (int i = 0; comp != null && i < comp.length; i++)
4913 if (comp[i] instanceof AlignmentPanel)
4915 if (((AlignmentPanel) comp[i]).av == av)
4918 closeView((AlignmentPanel) comp[i]);
4926 protected void build_fetchdbmenu(JMenu webService)
4928 // Temporary hack - DBRef Fetcher always top level ws entry.
4929 // TODO We probably want to store a sequence database checklist in
4930 // preferences and have checkboxes.. rather than individual sources selected
4932 final JMenu rfetch = new JMenu(
4933 MessageManager.getString("action.fetch_db_references"));
4934 rfetch.setToolTipText(MessageManager.getString(
4935 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4936 webService.add(rfetch);
4938 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4939 MessageManager.getString("option.trim_retrieved_seqs"));
4940 trimrs.setToolTipText(
4941 MessageManager.getString("label.trim_retrieved_sequences"));
4943 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4944 trimrs.addActionListener(new ActionListener()
4947 public void actionPerformed(ActionEvent e)
4949 trimrs.setSelected(trimrs.isSelected());
4950 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4951 Boolean.valueOf(trimrs.isSelected()).toString());
4955 JMenuItem fetchr = new JMenuItem(
4956 MessageManager.getString("label.standard_databases"));
4957 fetchr.setToolTipText(
4958 MessageManager.getString("label.fetch_embl_uniprot"));
4959 fetchr.addActionListener(new ActionListener()
4963 public void actionPerformed(ActionEvent e)
4965 new Thread(new Runnable()
4970 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4971 .getAlignment().isNucleotide();
4972 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4973 alignPanel.av.getSequenceSelection(),
4974 alignPanel.alignFrame, null,
4975 alignPanel.alignFrame.featureSettings, isNucleotide);
4976 dbRefFetcher.addListener(new FetchFinishedListenerI()
4979 public void finished()
4981 AlignFrame.this.setMenusForViewport();
4984 dbRefFetcher.fetchDBRefs(false);
4992 final AlignFrame me = this;
4993 new Thread(new Runnable()
4998 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4999 .getSequenceFetcherSingleton(me);
5000 javax.swing.SwingUtilities.invokeLater(new Runnable()
5005 String[] dbclasses = sf.getOrderedSupportedSources();
5006 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5007 // jalview.util.QuickSort.sort(otherdb, otherdb);
5008 List<DbSourceProxy> otherdb;
5009 JMenu dfetch = new JMenu();
5010 JMenu ifetch = new JMenu();
5011 JMenuItem fetchr = null;
5012 int comp = 0, icomp = 0, mcomp = 15;
5013 String mname = null;
5015 for (String dbclass : dbclasses)
5017 otherdb = sf.getSourceProxy(dbclass);
5018 // add a single entry for this class, or submenu allowing 'fetch
5020 if (otherdb == null || otherdb.size() < 1)
5024 // List<DbSourceProxy> dbs=otherdb;
5025 // otherdb=new ArrayList<DbSourceProxy>();
5026 // for (DbSourceProxy db:dbs)
5028 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5032 mname = "From " + dbclass;
5034 if (otherdb.size() == 1)
5036 final DbSourceProxy[] dassource = otherdb
5037 .toArray(new DbSourceProxy[0]);
5038 DbSourceProxy src = otherdb.get(0);
5039 fetchr = new JMenuItem(src.getDbSource());
5040 fetchr.addActionListener(new ActionListener()
5044 public void actionPerformed(ActionEvent e)
5046 new Thread(new Runnable()
5052 boolean isNucleotide = alignPanel.alignFrame
5053 .getViewport().getAlignment()
5055 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5056 alignPanel.av.getSequenceSelection(),
5057 alignPanel.alignFrame, dassource,
5058 alignPanel.alignFrame.featureSettings,
5061 .addListener(new FetchFinishedListenerI()
5064 public void finished()
5066 AlignFrame.this.setMenusForViewport();
5069 dbRefFetcher.fetchDBRefs(false);
5075 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5076 MessageManager.formatMessage(
5077 "label.fetch_retrieve_from", new Object[]
5078 { src.getDbName() })));
5084 final DbSourceProxy[] dassource = otherdb
5085 .toArray(new DbSourceProxy[0]);
5087 DbSourceProxy src = otherdb.get(0);
5088 fetchr = new JMenuItem(MessageManager
5089 .formatMessage("label.fetch_all_param", new Object[]
5090 { src.getDbSource() }));
5091 fetchr.addActionListener(new ActionListener()
5094 public void actionPerformed(ActionEvent e)
5096 new Thread(new Runnable()
5102 boolean isNucleotide = alignPanel.alignFrame
5103 .getViewport().getAlignment()
5105 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5106 alignPanel.av.getSequenceSelection(),
5107 alignPanel.alignFrame, dassource,
5108 alignPanel.alignFrame.featureSettings,
5111 .addListener(new FetchFinishedListenerI()
5114 public void finished()
5116 AlignFrame.this.setMenusForViewport();
5119 dbRefFetcher.fetchDBRefs(false);
5125 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5126 MessageManager.formatMessage(
5127 "label.fetch_retrieve_from_all_sources",
5129 { Integer.valueOf(otherdb.size())
5131 src.getDbSource(), src.getDbName() })));
5134 // and then build the rest of the individual menus
5135 ifetch = new JMenu(MessageManager.formatMessage(
5136 "label.source_from_db_source", new Object[]
5137 { src.getDbSource() }));
5139 String imname = null;
5141 for (DbSourceProxy sproxy : otherdb)
5143 String dbname = sproxy.getDbName();
5144 String sname = dbname.length() > 5
5145 ? dbname.substring(0, 5) + "..."
5147 String msname = dbname.length() > 10
5148 ? dbname.substring(0, 10) + "..."
5152 imname = MessageManager
5153 .formatMessage("label.from_msname", new Object[]
5156 fetchr = new JMenuItem(msname);
5157 final DbSourceProxy[] dassrc = { sproxy };
5158 fetchr.addActionListener(new ActionListener()
5162 public void actionPerformed(ActionEvent e)
5164 new Thread(new Runnable()
5170 boolean isNucleotide = alignPanel.alignFrame
5171 .getViewport().getAlignment()
5173 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5174 alignPanel.av.getSequenceSelection(),
5175 alignPanel.alignFrame, dassrc,
5176 alignPanel.alignFrame.featureSettings,
5179 .addListener(new FetchFinishedListenerI()
5182 public void finished()
5184 AlignFrame.this.setMenusForViewport();
5187 dbRefFetcher.fetchDBRefs(false);
5193 fetchr.setToolTipText(
5194 "<html>" + MessageManager.formatMessage(
5195 "label.fetch_retrieve_from", new Object[]
5199 if (++icomp >= mcomp || i == (otherdb.size()))
5201 ifetch.setText(MessageManager.formatMessage(
5202 "label.source_to_target", imname, sname));
5204 ifetch = new JMenu();
5212 if (comp >= mcomp || dbi >= (dbclasses.length))
5214 dfetch.setText(MessageManager.formatMessage(
5215 "label.source_to_target", mname, dbclass));
5217 dfetch = new JMenu();
5230 * Left justify the whole alignment.
5233 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5235 AlignmentI al = viewport.getAlignment();
5237 viewport.firePropertyChange("alignment", null, al);
5241 * Right justify the whole alignment.
5244 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5246 AlignmentI al = viewport.getAlignment();
5248 viewport.firePropertyChange("alignment", null, al);
5252 public void setShowSeqFeatures(boolean b)
5254 showSeqFeatures.setSelected(b);
5255 viewport.setShowSequenceFeatures(b);
5262 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5263 * awt.event.ActionEvent)
5266 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5268 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5269 alignPanel.paintAlignment(false, false);
5276 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5280 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5282 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5283 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5291 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5292 * .event.ActionEvent)
5295 protected void showGroupConservation_actionPerformed(ActionEvent e)
5297 viewport.setShowGroupConservation(showGroupConservation.getState());
5298 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5305 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5306 * .event.ActionEvent)
5309 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5311 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5312 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5319 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5320 * .event.ActionEvent)
5323 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5325 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5326 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5330 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5332 showSequenceLogo.setState(true);
5333 viewport.setShowSequenceLogo(true);
5334 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5335 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5339 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5341 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5348 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5349 * .event.ActionEvent)
5352 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5354 if (avc.makeGroupsFromSelection())
5356 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5357 alignPanel.updateAnnotation();
5358 alignPanel.paintAlignment(true, true);
5362 public void clearAlignmentSeqRep()
5364 // TODO refactor alignmentseqrep to controller
5365 if (viewport.getAlignment().hasSeqrep())
5367 viewport.getAlignment().setSeqrep(null);
5368 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5369 alignPanel.updateAnnotation();
5370 alignPanel.paintAlignment(true, true);
5375 protected void createGroup_actionPerformed(ActionEvent e)
5377 if (avc.createGroup())
5379 alignPanel.alignmentChanged();
5384 protected void unGroup_actionPerformed(ActionEvent e)
5388 alignPanel.alignmentChanged();
5393 * make the given alignmentPanel the currently selected tab
5395 * @param alignmentPanel
5397 public void setDisplayedView(AlignmentPanel alignmentPanel)
5399 if (!viewport.getSequenceSetId()
5400 .equals(alignmentPanel.av.getSequenceSetId()))
5402 throw new Error(MessageManager.getString(
5403 "error.implementation_error_cannot_show_view_alignment_frame"));
5405 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5406 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5408 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5413 * Action on selection of menu options to Show or Hide annotations.
5416 * @param forSequences
5417 * update sequence-related annotations
5418 * @param forAlignment
5419 * update non-sequence-related annotations
5422 protected void setAnnotationsVisibility(boolean visible,
5423 boolean forSequences, boolean forAlignment)
5425 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5426 .getAlignmentAnnotation();
5431 for (AlignmentAnnotation aa : anns)
5434 * don't display non-positional annotations on an alignment
5436 if (aa.annotations == null)
5440 boolean apply = (aa.sequenceRef == null && forAlignment)
5441 || (aa.sequenceRef != null && forSequences);
5444 aa.visible = visible;
5447 alignPanel.validateAnnotationDimensions(true);
5448 alignPanel.alignmentChanged();
5452 * Store selected annotation sort order for the view and repaint.
5455 protected void sortAnnotations_actionPerformed()
5457 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5459 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5460 alignPanel.paintAlignment(false, false);
5465 * @return alignment panels in this alignment frame
5467 public List<? extends AlignmentViewPanel> getAlignPanels()
5469 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5473 * Open a new alignment window, with the cDNA associated with this (protein)
5474 * alignment, aligned as is the protein.
5476 protected void viewAsCdna_actionPerformed()
5478 // TODO no longer a menu action - refactor as required
5479 final AlignmentI alignment = getViewport().getAlignment();
5480 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5481 if (mappings == null)
5485 List<SequenceI> cdnaSeqs = new ArrayList<>();
5486 for (SequenceI aaSeq : alignment.getSequences())
5488 for (AlignedCodonFrame acf : mappings)
5490 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5494 * There is a cDNA mapping for this protein sequence - add to new
5495 * alignment. It will share the same dataset sequence as other mapped
5496 * cDNA (no new mappings need to be created).
5498 final Sequence newSeq = new Sequence(dnaSeq);
5499 newSeq.setDatasetSequence(dnaSeq);
5500 cdnaSeqs.add(newSeq);
5504 if (cdnaSeqs.size() == 0)
5506 // show a warning dialog no mapped cDNA
5509 AlignmentI cdna = new Alignment(
5510 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5511 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5512 AlignFrame.DEFAULT_HEIGHT);
5513 cdna.alignAs(alignment);
5514 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5516 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5517 AlignFrame.DEFAULT_HEIGHT);
5521 * Set visibility of dna/protein complement view (available when shown in a
5527 protected void showComplement_actionPerformed(boolean show)
5529 SplitContainerI sf = getSplitViewContainer();
5532 sf.setComplementVisible(this, show);
5537 * Generate the reverse (optionally complemented) of the selected sequences,
5538 * and add them to the alignment
5541 protected void showReverse_actionPerformed(boolean complement)
5543 AlignmentI al = null;
5546 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5547 al = dna.reverseCdna(complement);
5548 viewport.addAlignment(al, "");
5549 addHistoryItem(new EditCommand(
5550 MessageManager.getString("label.add_sequences"), Action.PASTE,
5551 al.getSequencesArray(), 0, al.getWidth(),
5552 viewport.getAlignment()));
5553 } catch (Exception ex)
5555 System.err.println(ex.getMessage());
5561 * Try to run a script in the Groovy console, having first ensured that this
5562 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5563 * be targeted at this alignment.
5566 protected void runGroovy_actionPerformed()
5568 Jalview.setCurrentAlignFrame(this);
5569 groovy.ui.Console console = Desktop.getGroovyConsole();
5570 if (console != null)
5574 console.runScript();
5575 } catch (Exception ex)
5577 System.err.println((ex.toString()));
5578 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5579 MessageManager.getString("label.couldnt_run_groovy_script"),
5580 MessageManager.getString("label.groovy_support_failed"),
5581 JvOptionPane.ERROR_MESSAGE);
5586 System.err.println("Can't run Groovy script as console not found");
5591 * Hides columns containing (or not containing) a specified feature, provided
5592 * that would not leave all columns hidden
5594 * @param featureType
5595 * @param columnsContaining
5598 public boolean hideFeatureColumns(String featureType,
5599 boolean columnsContaining)
5601 boolean notForHiding = avc.markColumnsContainingFeatures(
5602 columnsContaining, false, false, featureType);
5605 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5606 false, featureType))
5608 getViewport().hideSelectedColumns();
5616 protected void selectHighlightedColumns_actionPerformed(
5617 ActionEvent actionEvent)
5619 // include key modifier check in case user selects from menu
5620 avc.markHighlightedColumns(
5621 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5622 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5623 | ActionEvent.CTRL_MASK)) != 0);
5627 * Rebuilds the Colour menu, including any user-defined colours which have
5628 * been loaded either on startup or during the session
5630 public void buildColourMenu()
5632 colourMenu.removeAll();
5634 colourMenu.add(applyToAllGroups);
5635 colourMenu.add(textColour);
5636 colourMenu.addSeparator();
5638 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5641 colourMenu.addSeparator();
5642 colourMenu.add(conservationMenuItem);
5643 colourMenu.add(modifyConservation);
5644 colourMenu.add(abovePIDThreshold);
5645 colourMenu.add(modifyPID);
5646 colourMenu.add(annotationColour);
5648 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5649 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5653 * Open a dialog (if not already open) that allows the user to select and
5654 * calculate PCA or Tree analysis
5656 protected void openTreePcaDialog()
5658 if (alignPanel.getCalculationDialog() == null)
5660 new CalculationChooser(AlignFrame.this);
5665 protected void loadVcf_actionPerformed()
5667 JalviewFileChooser chooser = new JalviewFileChooser(
5668 Cache.getProperty("LAST_DIRECTORY"));
5669 chooser.setFileView(new JalviewFileView());
5670 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5671 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5672 final AlignFrame us = this;
5673 chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
5680 String choice = chooser.getSelectedFile().getPath();
5681 Cache.setProperty("LAST_DIRECTORY", choice);
5682 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5683 new VCFLoader(choice).loadVCF(seqs, us);
5687 }).openDialog(null);
5693 class PrintThread extends Thread
5697 public PrintThread(AlignmentPanel ap)
5702 static PageFormat pf;
5707 PrinterJob printJob = PrinterJob.getPrinterJob();
5711 printJob.setPrintable(ap, pf);
5715 printJob.setPrintable(ap);
5718 if (printJob.printDialog())
5723 } catch (Exception PrintException)
5725 PrintException.printStackTrace();