2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenColumns;
57 import jalview.datamodel.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FileParse;
74 import jalview.io.FormatAdapter;
75 import jalview.io.HtmlSvgOutput;
76 import jalview.io.IdentifyFile;
77 import jalview.io.JPredFile;
78 import jalview.io.JalviewFileChooser;
79 import jalview.io.JalviewFileView;
80 import jalview.io.JnetAnnotationMaker;
81 import jalview.io.NewickFile;
82 import jalview.io.ScoreMatrixFile;
83 import jalview.io.TCoffeeScoreFile;
84 import jalview.io.vcf.VCFLoader;
85 import jalview.jbgui.GAlignFrame;
86 import jalview.schemes.ColourSchemeI;
87 import jalview.schemes.ColourSchemes;
88 import jalview.schemes.ResidueColourScheme;
89 import jalview.schemes.TCoffeeColourScheme;
90 import jalview.util.MessageManager;
91 import jalview.util.dialogrunner.RunResponse;
92 import jalview.viewmodel.AlignmentViewport;
93 import jalview.viewmodel.ViewportRanges;
94 import jalview.ws.DBRefFetcher;
95 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
96 import jalview.ws.jws1.Discoverer;
97 import jalview.ws.jws2.Jws2Discoverer;
98 import jalview.ws.jws2.jabaws2.Jws2Instance;
99 import jalview.ws.seqfetcher.DbSourceProxy;
101 import java.awt.BorderLayout;
102 import java.awt.Component;
103 import java.awt.Rectangle;
104 import java.awt.Toolkit;
105 import java.awt.datatransfer.Clipboard;
106 import java.awt.datatransfer.DataFlavor;
107 import java.awt.datatransfer.StringSelection;
108 import java.awt.datatransfer.Transferable;
109 import java.awt.dnd.DnDConstants;
110 import java.awt.dnd.DropTargetDragEvent;
111 import java.awt.dnd.DropTargetDropEvent;
112 import java.awt.dnd.DropTargetEvent;
113 import java.awt.dnd.DropTargetListener;
114 import java.awt.event.ActionEvent;
115 import java.awt.event.ActionListener;
116 import java.awt.event.FocusAdapter;
117 import java.awt.event.FocusEvent;
118 import java.awt.event.ItemEvent;
119 import java.awt.event.ItemListener;
120 import java.awt.event.KeyAdapter;
121 import java.awt.event.KeyEvent;
122 import java.awt.event.MouseEvent;
123 import java.awt.print.PageFormat;
124 import java.awt.print.PrinterJob;
125 import java.beans.PropertyChangeEvent;
126 import java.beans.PropertyChangeListener;
128 import java.io.FileWriter;
129 import java.io.PrintWriter;
131 import java.util.ArrayList;
132 import java.util.Arrays;
133 import java.util.Deque;
134 import java.util.Enumeration;
135 import java.util.Hashtable;
136 import java.util.List;
137 import java.util.Vector;
139 import javax.swing.JCheckBoxMenuItem;
140 import javax.swing.JEditorPane;
141 import javax.swing.JFileChooser;
142 import javax.swing.JInternalFrame;
143 import javax.swing.JLayeredPane;
144 import javax.swing.JMenu;
145 import javax.swing.JMenuItem;
146 import javax.swing.JScrollPane;
147 import javax.swing.SwingUtilities;
153 * @version $Revision$
155 public class AlignFrame extends GAlignFrame implements DropTargetListener,
156 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener,
157 PropertyChangeListener
160 public static final int DEFAULT_WIDTH = 700;
162 public static final int DEFAULT_HEIGHT = 500;
165 * The currently displayed panel (selected tabbed view if more than one)
167 public AlignmentPanel alignPanel;
169 AlignViewport viewport;
171 public AlignViewControllerI avc;
173 List<AlignmentPanel> alignPanels = new ArrayList<>();
176 * Last format used to load or save alignments in this window
178 FileFormatI currentFileFormat = null;
181 * Current filename for this alignment
183 String fileName = null;
188 * Creates a new AlignFrame object with specific width and height.
194 public AlignFrame(AlignmentI al, int width, int height)
196 this(al, null, width, height);
200 * Creates a new AlignFrame object with specific width, height and
206 * @param sequenceSetId
208 public AlignFrame(AlignmentI al, int width, int height,
209 String sequenceSetId)
211 this(al, null, width, height, sequenceSetId);
215 * Creates a new AlignFrame object with specific width, height and
221 * @param sequenceSetId
224 public AlignFrame(AlignmentI al, int width, int height,
225 String sequenceSetId, String viewId)
227 this(al, null, width, height, sequenceSetId, viewId);
231 * new alignment window with hidden columns
235 * @param hiddenColumns
236 * ColumnSelection or null
238 * Width of alignment frame
242 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
245 this(al, hiddenColumns, width, height, null);
249 * Create alignment frame for al with hiddenColumns, a specific width and
250 * height, and specific sequenceId
253 * @param hiddenColumns
256 * @param sequenceSetId
259 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
260 int height, String sequenceSetId)
262 this(al, hiddenColumns, width, height, sequenceSetId, null);
266 * Create alignment frame for al with hiddenColumns, a specific width and
267 * height, and specific sequenceId
270 * @param hiddenColumns
273 * @param sequenceSetId
278 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
279 int height, String sequenceSetId, String viewId)
281 setSize(width, height);
283 if (al.getDataset() == null)
288 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
290 alignPanel = new AlignmentPanel(this, viewport);
292 addAlignmentPanel(alignPanel, true);
296 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
297 HiddenColumns hiddenColumns, int width, int height)
299 setSize(width, height);
301 if (al.getDataset() == null)
306 viewport = new AlignViewport(al, hiddenColumns);
308 if (hiddenSeqs != null && hiddenSeqs.length > 0)
310 viewport.hideSequence(hiddenSeqs);
312 alignPanel = new AlignmentPanel(this, viewport);
313 addAlignmentPanel(alignPanel, true);
318 * Make a new AlignFrame from existing alignmentPanels
325 public AlignFrame(AlignmentPanel ap)
329 addAlignmentPanel(ap, false);
334 public void propertyChange(PropertyChangeEvent evt)
336 Desktop.getDesktop().propertyChange(evt);
343 * @return true if we have any features
346 protected boolean haveAlignmentFeatures() {
347 AlignmentI alignment = getViewport().getAlignment();
349 for (int i = 0; i < alignment.getHeight(); i++)
351 SequenceI seq = alignment.getSequenceAt(i);
352 for (String group : seq.getFeatures().getFeatureGroups(true))
354 if (group != null)return true;
361 * initalise the alignframe from the underlying viewport data and the
366 if (!Jalview.isHeadlessMode())
368 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
371 avc = new jalview.controller.AlignViewController(this, viewport,
373 if (viewport.getAlignmentConservationAnnotation() == null)
375 // BLOSUM62Colour.setEnabled(false);
376 conservationMenuItem.setEnabled(false);
377 modifyConservation.setEnabled(false);
378 // PIDColour.setEnabled(false);
379 // abovePIDThreshold.setEnabled(false);
380 // modifyPID.setEnabled(false);
383 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
386 if (sortby.equals("Id"))
388 sortIDMenuItem_actionPerformed(null);
390 else if (sortby.equals("Pairwise Identity"))
392 sortPairwiseMenuItem_actionPerformed(null);
396 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
398 setMenusFromViewport(viewport);
399 buildSortByAnnotationScoresMenu();
400 calculateTree.addActionListener(new ActionListener()
404 public void actionPerformed(ActionEvent e)
411 if (Desktop.desktop != null)
413 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
415 * BH 2018 ignore service listeners
421 addServiceListeners();
426 if (viewport.getWrapAlignment())
428 wrapMenuItem_actionPerformed(null);
431 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
433 this.overviewMenuItem_actionPerformed(null);
438 final List<AlignmentPanel> selviews = new ArrayList<>();
439 final List<AlignmentPanel> origview = new ArrayList<>();
440 final String menuLabel = MessageManager
441 .getString("label.copy_format_from");
442 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
443 new ViewSetProvider()
447 public AlignmentPanel[] getAllAlignmentPanels()
450 origview.add(alignPanel);
451 // make an array of all alignment panels except for this one
452 List<AlignmentPanel> aps = new ArrayList<>(
453 Arrays.asList(Desktop.getAlignmentPanels(null)));
454 aps.remove(AlignFrame.this.alignPanel);
455 return aps.toArray(new AlignmentPanel[aps.size()]);
457 }, selviews, new ItemListener()
461 public void itemStateChanged(ItemEvent e)
463 if (origview.size() > 0)
465 final AlignmentPanel ap = origview.get(0);
468 * Copy the ViewStyle of the selected panel to 'this one'.
469 * Don't change value of 'scaleProteinAsCdna' unless copying
472 ViewStyleI vs = selviews.get(0).getAlignViewport()
474 boolean fromSplitFrame = selviews.get(0)
475 .getAlignViewport().getCodingComplement() != null;
478 vs.setScaleProteinAsCdna(ap.getAlignViewport()
479 .getViewStyle().isScaleProteinAsCdna());
481 ap.getAlignViewport().setViewStyle(vs);
484 * Also rescale ViewStyle of SplitFrame complement if there is
485 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
486 * the whole ViewStyle (allow cDNA protein to have different
489 AlignViewportI complement = ap.getAlignViewport()
490 .getCodingComplement();
491 if (complement != null && vs.isScaleProteinAsCdna())
493 AlignFrame af = Desktop.getAlignFrameFor(complement);
494 ((SplitFrame) af.getSplitViewContainer())
496 af.setMenusForViewport();
500 ap.setSelected(true);
501 ap.alignFrame.setMenusForViewport();
506 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
507 .indexOf("devel") > -1
508 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
509 .indexOf("test") > -1)
511 formatMenu.add(vsel);
513 addFocusListener(new FocusAdapter()
516 public void focusGained(FocusEvent e)
518 Jalview.setCurrentAlignFrame(AlignFrame.this);
525 * Change the filename and format for the alignment, and enable the 'reload'
526 * button functionality.
533 public void setFileName(String file, FileFormatI format)
536 setFileFormat(format);
537 reload.setEnabled(true);
541 * JavaScript will have this, maybe others. More dependable than a file name
542 * and maintains a reference to the actual bytes loaded.
546 public void setFileObject(File file) {
547 this.fileObject = file;
551 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
554 void addKeyListener()
556 addKeyListener(new KeyAdapter()
559 public void keyPressed(KeyEvent evt)
561 if (viewport.cursorMode
562 && ((evt.getKeyCode() >= KeyEvent.VK_0
563 && evt.getKeyCode() <= KeyEvent.VK_9)
564 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
565 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
566 && Character.isDigit(evt.getKeyChar()))
568 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
571 switch (evt.getKeyCode())
574 case 27: // escape key
575 deselectAllSequenceMenuItem_actionPerformed(null);
579 case KeyEvent.VK_DOWN:
580 if (evt.isAltDown() || !viewport.cursorMode)
582 moveSelectedSequences(false);
584 if (viewport.cursorMode)
586 alignPanel.getSeqPanel().moveCursor(0, 1);
591 if (evt.isAltDown() || !viewport.cursorMode)
593 moveSelectedSequences(true);
595 if (viewport.cursorMode)
597 alignPanel.getSeqPanel().moveCursor(0, -1);
602 case KeyEvent.VK_LEFT:
603 if (evt.isAltDown() || !viewport.cursorMode)
605 slideSequences(false,
606 alignPanel.getSeqPanel().getKeyboardNo1());
610 alignPanel.getSeqPanel().moveCursor(-1, 0);
615 case KeyEvent.VK_RIGHT:
616 if (evt.isAltDown() || !viewport.cursorMode)
618 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
622 alignPanel.getSeqPanel().moveCursor(1, 0);
626 case KeyEvent.VK_SPACE:
627 if (viewport.cursorMode)
629 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
630 || evt.isShiftDown() || evt.isAltDown());
634 // case KeyEvent.VK_A:
635 // if (viewport.cursorMode)
637 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
638 // //System.out.println("A");
642 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
643 * System.out.println("closing bracket"); } break;
645 case KeyEvent.VK_DELETE:
646 case KeyEvent.VK_BACK_SPACE:
647 if (!viewport.cursorMode)
649 cut_actionPerformed(null);
653 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
654 || evt.isShiftDown() || evt.isAltDown());
660 if (viewport.cursorMode)
662 alignPanel.getSeqPanel().setCursorRow();
666 if (viewport.cursorMode && !evt.isControlDown())
668 alignPanel.getSeqPanel().setCursorColumn();
672 if (viewport.cursorMode)
674 alignPanel.getSeqPanel().setCursorPosition();
678 case KeyEvent.VK_ENTER:
679 case KeyEvent.VK_COMMA:
680 if (viewport.cursorMode)
682 alignPanel.getSeqPanel().setCursorRowAndColumn();
687 if (viewport.cursorMode)
689 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
693 if (viewport.cursorMode)
695 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
700 viewport.cursorMode = !viewport.cursorMode;
701 statusBar.setText(MessageManager
702 .formatMessage("label.keyboard_editing_mode", new String[]
703 { (viewport.cursorMode ? "on" : "off") }));
704 if (viewport.cursorMode)
706 ViewportRanges ranges = viewport.getRanges();
707 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
709 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
712 alignPanel.getSeqPanel().seqCanvas.repaint();
718 Help.showHelpWindow();
719 } catch (Exception ex)
721 ex.printStackTrace();
726 boolean toggleSeqs = !evt.isControlDown();
727 boolean toggleCols = !evt.isShiftDown();
728 toggleHiddenRegions(toggleSeqs, toggleCols);
733 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
734 boolean modifyExisting = true; // always modify, don't clear
735 // evt.isShiftDown();
736 boolean invertHighlighted = evt.isAltDown();
737 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
741 case KeyEvent.VK_PAGE_UP:
742 viewport.getRanges().pageUp();
744 case KeyEvent.VK_PAGE_DOWN:
745 viewport.getRanges().pageDown();
751 public void keyReleased(KeyEvent evt)
753 switch (evt.getKeyCode())
755 case KeyEvent.VK_LEFT:
756 if (evt.isAltDown() || !viewport.cursorMode)
758 viewport.firePropertyChange("alignment", null,
759 viewport.getAlignment().getSequences());
763 case KeyEvent.VK_RIGHT:
764 if (evt.isAltDown() || !viewport.cursorMode)
766 viewport.firePropertyChange("alignment", null,
767 viewport.getAlignment().getSequences());
775 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
777 ap.alignFrame = this;
778 avc = new jalview.controller.AlignViewController(this, viewport,
783 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
785 int aSize = alignPanels.size();
787 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
789 if (aSize == 1 && ap.av.viewName == null)
791 this.getContentPane().add(ap, BorderLayout.CENTER);
797 setInitialTabVisible();
800 expandViews.setEnabled(true);
801 gatherViews.setEnabled(true);
802 tabbedPane.addTab(ap.av.viewName, ap);
804 ap.setVisible(false);
809 if (ap.av.isPadGaps())
811 ap.av.getAlignment().padGaps();
813 ap.av.updateConservation(ap);
814 ap.av.updateConsensus(ap);
815 ap.av.updateStrucConsensus(ap);
819 public void setInitialTabVisible()
821 expandViews.setEnabled(true);
822 gatherViews.setEnabled(true);
823 tabbedPane.setVisible(true);
824 AlignmentPanel first = alignPanels.get(0);
825 tabbedPane.addTab(first.av.viewName, first);
826 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
829 public AlignViewport getViewport()
834 /* Set up intrinsic listeners for dynamically generated GUI bits. */
835 private void addServiceListeners()
837 final java.beans.PropertyChangeListener thisListener;
838 Desktop.instance.addJalviewPropertyChangeListener("services",
839 thisListener = new java.beans.PropertyChangeListener()
842 public void propertyChange(PropertyChangeEvent evt)
844 // // System.out.println("Discoverer property change.");
845 // if (evt.getPropertyName().equals("services"))
847 SwingUtilities.invokeLater(new Runnable()
854 "Rebuild WS Menu for service change");
855 BuildWebServiceMenu();
862 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
865 public void internalFrameClosed(
866 javax.swing.event.InternalFrameEvent evt)
868 // System.out.println("deregistering discoverer listener");
869 Desktop.instance.removeJalviewPropertyChangeListener("services",
871 closeMenuItem_actionPerformed(true);
874 // Finally, build the menu once to get current service state
875 new Thread(new Runnable()
880 BuildWebServiceMenu();
886 * Configure menu items that vary according to whether the alignment is
887 * nucleotide or protein
889 public void setGUINucleotide()
891 AlignmentI al = getViewport().getAlignment();
892 boolean nucleotide = al.isNucleotide();
894 loadVcf.setVisible(nucleotide);
895 showTranslation.setVisible(nucleotide);
896 showReverse.setVisible(nucleotide);
897 showReverseComplement.setVisible(nucleotide);
898 conservationMenuItem.setEnabled(!nucleotide);
900 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
901 showGroupConservation.setEnabled(!nucleotide);
903 showComplementMenuItem
904 .setText(nucleotide ? MessageManager.getString("label.protein")
905 : MessageManager.getString("label.nucleotide"));
909 * set up menus for the current viewport. This may be called after any
910 * operation that affects the data in the current view (selection changed,
911 * etc) to update the menus to reflect the new state.
914 public void setMenusForViewport()
916 setMenusFromViewport(viewport);
920 * Need to call this method when tabs are selected for multiple views, or when
921 * loading from Jalview2XML.java
926 void setMenusFromViewport(AlignViewport av)
928 padGapsMenuitem.setSelected(av.isPadGaps());
929 colourTextMenuItem.setSelected(av.isShowColourText());
930 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
931 modifyPID.setEnabled(abovePIDThreshold.isSelected());
932 conservationMenuItem.setSelected(av.getConservationSelected());
933 modifyConservation.setEnabled(conservationMenuItem.isSelected());
934 seqLimits.setSelected(av.getShowJVSuffix());
935 idRightAlign.setSelected(av.isRightAlignIds());
936 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
937 renderGapsMenuItem.setSelected(av.isRenderGaps());
938 wrapMenuItem.setSelected(av.getWrapAlignment());
939 scaleAbove.setVisible(av.getWrapAlignment());
940 scaleLeft.setVisible(av.getWrapAlignment());
941 scaleRight.setVisible(av.getWrapAlignment());
942 annotationPanelMenuItem.setState(av.isShowAnnotation());
944 * Show/hide annotations only enabled if annotation panel is shown
946 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
947 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
948 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
949 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
950 viewBoxesMenuItem.setSelected(av.getShowBoxes());
951 viewTextMenuItem.setSelected(av.getShowText());
952 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
953 showGroupConsensus.setSelected(av.isShowGroupConsensus());
954 showGroupConservation.setSelected(av.isShowGroupConservation());
955 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
956 showSequenceLogo.setSelected(av.isShowSequenceLogo());
957 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
959 ColourMenuHelper.setColourSelected(colourMenu,
960 av.getGlobalColourScheme());
962 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
963 hiddenMarkers.setState(av.getShowHiddenMarkers());
964 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
965 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
966 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
967 autoCalculate.setSelected(av.autoCalculateConsensus);
968 sortByTree.setSelected(av.sortByTree);
969 listenToViewSelections.setSelected(av.followSelection);
971 showProducts.setEnabled(canShowProducts());
972 setGroovyEnabled(Desktop.getGroovyConsole() != null);
978 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
982 public void setGroovyEnabled(boolean b)
984 runGroovy.setEnabled(b);
987 private IProgressIndicator progressBar;
992 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
995 public void setProgressBar(String message, long id)
997 progressBar.setProgressBar(message, id);
1001 public void registerHandler(final long id,
1002 final IProgressIndicatorHandler handler)
1004 progressBar.registerHandler(id, handler);
1009 * @return true if any progress bars are still active
1012 public boolean operationInProgress()
1014 return progressBar.operationInProgress();
1018 public void setStatus(String text)
1020 statusBar.setText(text);
1024 * Added so Castor Mapping file can obtain Jalview Version
1026 public String getVersion()
1028 return jalview.bin.Cache.getProperty("VERSION");
1031 public FeatureRenderer getFeatureRenderer()
1033 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1037 public void fetchSequence_actionPerformed(ActionEvent e)
1039 new jalview.gui.SequenceFetcher(this);
1043 public void addFromFile_actionPerformed(ActionEvent e)
1045 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1049 public void reload_actionPerformed(ActionEvent e)
1051 if (fileName != null)
1053 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1054 // originating file's format
1055 // TODO: work out how to recover feature settings for correct view(s) when
1056 // file is reloaded.
1057 if (FileFormat.Jalview.equals(currentFileFormat))
1059 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1060 for (int i = 0; i < frames.length; i++)
1062 if (frames[i] instanceof AlignFrame && frames[i] != this
1063 && ((AlignFrame) frames[i]).fileName != null
1064 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1068 frames[i].setSelected(true);
1069 Desktop.instance.closeAssociatedWindows();
1070 } catch (java.beans.PropertyVetoException ex)
1076 Desktop.instance.closeAssociatedWindows();
1078 FileLoader loader = new FileLoader();
1079 DataSourceType protocol = fileName.startsWith("http:")
1080 ? DataSourceType.URL : DataSourceType.FILE;
1081 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1085 Rectangle bounds = this.getBounds();
1087 FileLoader loader = new FileLoader();
1089 AlignFrame newframe = null;
1091 if (fileObject == null)
1094 DataSourceType protocol = (fileName.startsWith("http:")
1095 ? DataSourceType.URL : DataSourceType.FILE);
1096 newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1101 newframe = loader.LoadFileWaitTillLoaded(fileObject, DataSourceType.FILE, currentFileFormat);
1104 newframe.setBounds(bounds);
1105 if (featureSettings != null && featureSettings.isShowing())
1107 final Rectangle fspos = featureSettings.frame.getBounds();
1108 // TODO: need a 'show feature settings' function that takes bounds -
1109 // need to refactor Desktop.addFrame
1110 newframe.featureSettings_actionPerformed(null);
1111 final FeatureSettings nfs = newframe.featureSettings;
1112 SwingUtilities.invokeLater(new Runnable()
1117 nfs.frame.setBounds(fspos);
1120 this.featureSettings.close();
1121 this.featureSettings = null;
1123 this.closeMenuItem_actionPerformed(true);
1129 public void addFromText_actionPerformed(ActionEvent e)
1132 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1136 public void addFromURL_actionPerformed(ActionEvent e)
1138 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1142 public void save_actionPerformed(ActionEvent e)
1144 if (fileName == null || (currentFileFormat == null)
1145 || fileName.startsWith("http"))
1147 saveAs_actionPerformed(null);
1151 saveAlignment(fileName, currentFileFormat);
1162 public void saveAs_actionPerformed(ActionEvent e)
1164 String format = currentFileFormat == null ? null
1165 : currentFileFormat.getName();
1166 final JalviewFileChooser chooser = JalviewFileChooser
1167 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1168 final AlignFrame us = this;
1169 chooser.setFileView(new JalviewFileView());
1170 chooser.setDialogTitle(
1171 MessageManager.getString("label.save_alignment_to_file"));
1172 chooser.setToolTipText(MessageManager.getString("action.save"));
1174 chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
1179 currentFileFormat = chooser.getSelectedFormat();
1180 while (currentFileFormat == null)
1182 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1183 MessageManager.getString(
1184 "label.select_file_format_before_saving"),
1186 .getString("label.file_format_not_specified"),
1187 JvOptionPane.WARNING_MESSAGE);
1188 currentFileFormat = chooser.getSelectedFormat();
1189 chooser.showSaveDialog(us);
1192 fileName = chooser.getSelectedFile().getPath();
1194 Cache.setProperty("DEFAULT_FILE_FORMAT",
1195 currentFileFormat.getName());
1197 Cache.setProperty("LAST_DIRECTORY", fileName);
1198 saveAlignment(fileName, currentFileFormat);
1200 }).showSaveDialog(this);
1203 public boolean saveAlignment(String file, FileFormatI format)
1205 boolean success = true;
1207 if (FileFormat.Jalview.equals(format))
1209 String shortName = title;
1211 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1213 shortName = shortName.substring(
1214 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1217 success = new Jalview2XML().saveAlignment(this, file, shortName);
1219 statusBar.setText(MessageManager.formatMessage(
1220 "label.successfully_saved_to_file_in_format", new Object[]
1221 { fileName, format }));
1226 AlignmentExportData exportData = getAlignmentForExport(format,
1228 if (exportData.getSettings().isCancelled())
1232 FormatAdapter f = new FormatAdapter(alignPanel,
1233 exportData.getSettings());
1234 String output = f.formatSequences(format, exportData.getAlignment(), // class
1238 // occur in the distant future
1239 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1240 f.getCacheSuffixDefault(format),
1241 viewport.getAlignment().getHiddenColumns());
1251 PrintWriter out = new PrintWriter(new FileWriter(file));
1255 this.setTitle(file);
1256 statusBar.setText(MessageManager.formatMessage(
1257 "label.successfully_saved_to_file_in_format", new Object[]
1258 { fileName, format.getName() }));
1259 } catch (Exception ex)
1262 ex.printStackTrace();
1269 JvOptionPane.showInternalMessageDialog(this, MessageManager
1270 .formatMessage("label.couldnt_save_file", new Object[]
1272 MessageManager.getString("label.error_saving_file"),
1273 JvOptionPane.WARNING_MESSAGE);
1279 private void warningMessage(String warning, String title)
1281 if (new jalview.util.Platform().isHeadless())
1283 System.err.println("Warning: " + title + "\nWarning: " + warning);
1288 JvOptionPane.showInternalMessageDialog(this, warning, title,
1289 JvOptionPane.WARNING_MESSAGE);
1301 protected void outputText_actionPerformed(ActionEvent e)
1303 FileFormatI fileFormat = FileFormats.getInstance()
1304 .forName(e.getActionCommand());
1305 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1307 if (exportData.getSettings().isCancelled())
1311 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1312 cap.setForInput(null);
1315 FileFormatI format = fileFormat;
1316 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1317 .formatSequences(format, exportData.getAlignment(),
1318 exportData.getOmitHidden(),
1319 exportData.getStartEndPostions(),
1320 viewport.getAlignment().getHiddenColumns()));
1321 Desktop.addInternalFrame(cap, MessageManager
1322 .formatMessage("label.alignment_output_command", new Object[]
1323 { e.getActionCommand() }), 600, 500);
1324 } catch (OutOfMemoryError oom)
1326 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1333 public static AlignmentExportData getAlignmentForExport(
1334 FileFormatI format, AlignViewportI viewport,
1335 AlignExportSettingI exportSettings)
1337 AlignmentI alignmentToExport = null;
1338 AlignExportSettingI settings = exportSettings;
1339 String[] omitHidden = null;
1341 HiddenSequences hiddenSeqs = viewport.getAlignment()
1342 .getHiddenSequences();
1344 alignmentToExport = viewport.getAlignment();
1346 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1347 if (settings == null)
1349 settings = new AlignExportSettings(hasHiddenSeqs,
1350 viewport.hasHiddenColumns(), format);
1352 // settings.isExportAnnotations();
1354 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1356 omitHidden = viewport.getViewAsString(false,
1357 settings.isExportHiddenSequences());
1360 int[] alignmentStartEnd = new int[2];
1361 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1363 alignmentToExport = hiddenSeqs.getFullAlignment();
1367 alignmentToExport = viewport.getAlignment();
1369 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1370 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1371 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1372 omitHidden, alignmentStartEnd, settings);
1383 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1385 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1386 htmlSVG.exportHTML(null);
1390 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1392 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1393 bjs.exportHTML(null);
1396 public void createImageMap(File file, String image)
1398 alignPanel.makePNGImageMap(file, image);
1408 public void createPNG(File f)
1410 alignPanel.makePNG(f);
1420 public void createEPS(File f)
1422 alignPanel.makeEPS(f);
1426 public void createSVG(File f)
1428 alignPanel.makeSVG(f);
1432 public void pageSetup_actionPerformed(ActionEvent e)
1434 PrinterJob printJob = PrinterJob.getPrinterJob();
1435 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1445 public void printMenuItem_actionPerformed(ActionEvent e)
1447 // Putting in a thread avoids Swing painting problems
1448 PrintThread thread = new PrintThread(alignPanel);
1453 public void exportFeatures_actionPerformed(ActionEvent e)
1455 new AnnotationExporter(alignPanel).exportFeatures();
1459 public void exportAnnotations_actionPerformed(ActionEvent e)
1461 new AnnotationExporter(alignPanel).exportAnnotations();
1465 public void associatedData_actionPerformed(ActionEvent e)
1467 JalviewFileChooser chooser = new JalviewFileChooser(
1468 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1469 chooser.setFileView(new JalviewFileView());
1470 chooser.setDialogTitle(
1471 MessageManager.getString("label.load_jalview_annotations"));
1472 chooser.setToolTipText(
1473 MessageManager.getString("label.load_jalview_annotations"));
1475 Desktop.getDesktop().dialogData = new Object[] { "SelectedFile",
1482 Object[] data = Desktop.getDesktop().dialogData;
1483 int value = ((Integer) data[0]).intValue();
1485 if (value == JFileChooser.APPROVE_OPTION)
1487 JalviewFileChooser chooser = (JalviewFileChooser) data[2];
1488 String choice = chooser.getSelectedFile().getPath();
1489 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1490 loadJalviewDataFile(choice, null, null, null);
1496 chooser.showOpenDialog(null);
1503 * Close the current view or all views in the alignment frame. If the frame
1504 * only contains one view then the alignment will be removed from memory.
1506 * @param closeAllTabs
1509 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1511 if (alignPanels != null && alignPanels.size() < 2)
1513 closeAllTabs = true;
1518 if (alignPanels != null)
1522 if (this.isClosed())
1524 // really close all the windows - otherwise wait till
1525 // setClosed(true) is called
1526 for (int i = 0; i < alignPanels.size(); i++)
1528 AlignmentPanel ap = alignPanels.get(i);
1535 closeView(alignPanel);
1542 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1543 * be called recursively, with the frame now in 'closed' state
1545 this.setClosed(true);
1547 } catch (Exception ex)
1549 ex.printStackTrace();
1554 * Close the specified panel and close up tabs appropriately.
1556 * @param panelToClose
1558 public void closeView(AlignmentPanel panelToClose)
1560 int index = tabbedPane.getSelectedIndex();
1561 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1562 alignPanels.remove(panelToClose);
1563 panelToClose.closePanel();
1564 panelToClose = null;
1566 tabbedPane.removeTabAt(closedindex);
1567 tabbedPane.validate();
1569 if (index > closedindex || index == tabbedPane.getTabCount())
1571 // modify currently selected tab index if necessary.
1575 this.tabSelectionChanged(index);
1581 void updateEditMenuBar()
1584 if (viewport.getHistoryList().size() > 0)
1586 undoMenuItem.setEnabled(true);
1587 CommandI command = viewport.getHistoryList().peek();
1588 undoMenuItem.setText(MessageManager
1589 .formatMessage("label.undo_command", new Object[]
1590 { command.getDescription() }));
1594 undoMenuItem.setEnabled(false);
1595 undoMenuItem.setText(MessageManager.getString("action.undo"));
1598 if (viewport.getRedoList().size() > 0)
1600 redoMenuItem.setEnabled(true);
1602 CommandI command = viewport.getRedoList().peek();
1603 redoMenuItem.setText(MessageManager
1604 .formatMessage("label.redo_command", new Object[]
1605 { command.getDescription() }));
1609 redoMenuItem.setEnabled(false);
1610 redoMenuItem.setText(MessageManager.getString("action.redo"));
1615 public void addHistoryItem(CommandI command)
1617 if (command.getSize() > 0)
1619 viewport.addToHistoryList(command);
1620 viewport.clearRedoList();
1621 updateEditMenuBar();
1622 viewport.updateHiddenColumns();
1623 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1624 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1625 // viewport.getColumnSelection()
1626 // .getHiddenColumns().size() > 0);
1632 * @return alignment objects for all views
1634 AlignmentI[] getViewAlignments()
1636 if (alignPanels != null)
1638 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1640 for (AlignmentPanel ap : alignPanels)
1642 als[i++] = ap.av.getAlignment();
1646 if (viewport != null)
1648 return new AlignmentI[] { viewport.getAlignment() };
1660 protected void undoMenuItem_actionPerformed(ActionEvent e)
1662 if (viewport.getHistoryList().isEmpty())
1666 CommandI command = viewport.getHistoryList().pop();
1667 viewport.addToRedoList(command);
1668 command.undoCommand(getViewAlignments());
1670 AlignmentViewport originalSource = getOriginatingSource(command);
1671 updateEditMenuBar();
1673 if (originalSource != null)
1675 if (originalSource != viewport)
1678 "Implementation worry: mismatch of viewport origin for undo");
1680 originalSource.updateHiddenColumns();
1681 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1683 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1684 // viewport.getColumnSelection()
1685 // .getHiddenColumns().size() > 0);
1686 originalSource.firePropertyChange("alignment", null,
1687 originalSource.getAlignment().getSequences());
1698 protected void redoMenuItem_actionPerformed(ActionEvent e)
1700 if (viewport.getRedoList().size() < 1)
1705 CommandI command = viewport.getRedoList().pop();
1706 viewport.addToHistoryList(command);
1707 command.doCommand(getViewAlignments());
1709 AlignmentViewport originalSource = getOriginatingSource(command);
1710 updateEditMenuBar();
1712 if (originalSource != null)
1715 if (originalSource != viewport)
1718 "Implementation worry: mismatch of viewport origin for redo");
1720 originalSource.updateHiddenColumns();
1721 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1723 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1724 // viewport.getColumnSelection()
1725 // .getHiddenColumns().size() > 0);
1726 originalSource.firePropertyChange("alignment", null,
1727 originalSource.getAlignment().getSequences());
1731 AlignmentViewport getOriginatingSource(CommandI command)
1733 AlignmentViewport originalSource = null;
1734 // For sequence removal and addition, we need to fire
1735 // the property change event FROM the viewport where the
1736 // original alignment was altered
1737 AlignmentI al = null;
1738 if (command instanceof EditCommand)
1740 EditCommand editCommand = (EditCommand) command;
1741 al = editCommand.getAlignment();
1742 List<Component> comps = PaintRefresher.components
1743 .get(viewport.getSequenceSetId());
1745 for (Component comp : comps)
1747 if (comp instanceof AlignmentPanel)
1749 if (al == ((AlignmentPanel) comp).av.getAlignment())
1751 originalSource = ((AlignmentPanel) comp).av;
1758 if (originalSource == null)
1760 // The original view is closed, we must validate
1761 // the current view against the closed view first
1764 PaintRefresher.validateSequences(al, viewport.getAlignment());
1767 originalSource = viewport;
1770 return originalSource;
1779 public void moveSelectedSequences(boolean up)
1781 SequenceGroup sg = viewport.getSelectionGroup();
1787 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1788 viewport.getHiddenRepSequences(), up);
1789 alignPanel.paintAlignment(true, false);
1792 synchronized void slideSequences(boolean right, int size)
1794 List<SequenceI> sg = new ArrayList<>();
1795 if (viewport.cursorMode)
1797 sg.add(viewport.getAlignment()
1798 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1800 else if (viewport.getSelectionGroup() != null
1801 && viewport.getSelectionGroup().getSize() != viewport
1802 .getAlignment().getHeight())
1804 sg = viewport.getSelectionGroup()
1805 .getSequences(viewport.getHiddenRepSequences());
1813 List<SequenceI> invertGroup = new ArrayList<>();
1815 for (SequenceI seq : viewport.getAlignment().getSequences())
1817 if (!sg.contains(seq))
1819 invertGroup.add(seq);
1823 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1825 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1826 for (int i = 0; i < invertGroup.size(); i++)
1828 seqs2[i] = invertGroup.get(i);
1831 SlideSequencesCommand ssc;
1834 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1835 viewport.getGapCharacter());
1839 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1840 viewport.getGapCharacter());
1843 int groupAdjustment = 0;
1844 if (ssc.getGapsInsertedBegin() && right)
1846 if (viewport.cursorMode)
1848 alignPanel.getSeqPanel().moveCursor(size, 0);
1852 groupAdjustment = size;
1855 else if (!ssc.getGapsInsertedBegin() && !right)
1857 if (viewport.cursorMode)
1859 alignPanel.getSeqPanel().moveCursor(-size, 0);
1863 groupAdjustment = -size;
1867 if (groupAdjustment != 0)
1869 viewport.getSelectionGroup().setStartRes(
1870 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1871 viewport.getSelectionGroup().setEndRes(
1872 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1876 * just extend the last slide command if compatible; but not if in
1877 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1879 boolean appendHistoryItem = false;
1880 Deque<CommandI> historyList = viewport.getHistoryList();
1881 boolean inSplitFrame = getSplitViewContainer() != null;
1882 if (!inSplitFrame && historyList != null && historyList.size() > 0
1883 && historyList.peek() instanceof SlideSequencesCommand)
1885 appendHistoryItem = ssc.appendSlideCommand(
1886 (SlideSequencesCommand) historyList.peek());
1889 if (!appendHistoryItem)
1891 addHistoryItem(ssc);
1904 protected void copy_actionPerformed(ActionEvent e)
1906 if (viewport.getSelectionGroup() == null)
1910 // TODO: preserve the ordering of displayed alignment annotation in any
1911 // internal paste (particularly sequence associated annotation)
1912 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1913 String[] omitHidden = null;
1915 if (viewport.hasHiddenColumns())
1917 omitHidden = viewport.getViewAsString(true);
1920 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1921 seqs, omitHidden, null);
1923 StringSelection ss = new StringSelection(output);
1927 jalview.gui.Desktop.internalCopy = true;
1928 // Its really worth setting the clipboard contents
1929 // to empty before setting the large StringSelection!!
1930 Toolkit.getDefaultToolkit().getSystemClipboard()
1931 .setContents(new StringSelection(""), null);
1933 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1935 } catch (OutOfMemoryError er)
1937 new OOMWarning("copying region", er);
1941 HiddenColumns hiddenColumns = null;
1942 if (viewport.hasHiddenColumns())
1944 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1945 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1947 // create new HiddenColumns object with copy of hidden regions
1948 // between startRes and endRes, offset by startRes
1949 hiddenColumns = new HiddenColumns(
1950 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1951 hiddenCutoff, hiddenOffset);
1954 Desktop.jalviewClipboard = new Object[] { seqs,
1955 viewport.getAlignment().getDataset(), hiddenColumns };
1956 statusBar.setText(MessageManager.formatMessage(
1957 "label.copied_sequences_to_clipboard", new Object[]
1958 { Integer.valueOf(seqs.length).toString() }));
1968 protected void pasteNew_actionPerformed(ActionEvent e)
1980 protected void pasteThis_actionPerformed(ActionEvent e)
1986 * Paste contents of Jalview clipboard
1988 * @param newAlignment
1989 * true to paste to a new alignment, otherwise add to this.
1991 void paste(boolean newAlignment)
1993 boolean externalPaste = true;
1996 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1997 Transferable contents = c.getContents(this);
1999 if (contents == null)
2008 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2009 if (str.length() < 1)
2014 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2016 } catch (OutOfMemoryError er)
2018 new OOMWarning("Out of memory pasting sequences!!", er);
2022 SequenceI[] sequences;
2023 boolean annotationAdded = false;
2024 AlignmentI alignment = null;
2026 if (Desktop.jalviewClipboard != null)
2028 // The clipboard was filled from within Jalview, we must use the
2030 // And dataset from the copied alignment
2031 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2032 // be doubly sure that we create *new* sequence objects.
2033 sequences = new SequenceI[newseq.length];
2034 for (int i = 0; i < newseq.length; i++)
2036 sequences[i] = new Sequence(newseq[i]);
2038 alignment = new Alignment(sequences);
2039 externalPaste = false;
2043 // parse the clipboard as an alignment.
2044 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2046 sequences = alignment.getSequencesArray();
2050 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2056 if (Desktop.jalviewClipboard != null)
2058 // dataset is inherited
2059 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2063 // new dataset is constructed
2064 alignment.setDataset(null);
2066 alwidth = alignment.getWidth() + 1;
2070 AlignmentI pastedal = alignment; // preserve pasted alignment object
2071 // Add pasted sequences and dataset into existing alignment.
2072 alignment = viewport.getAlignment();
2073 alwidth = alignment.getWidth() + 1;
2074 // decide if we need to import sequences from an existing dataset
2075 boolean importDs = Desktop.jalviewClipboard != null
2076 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2077 // importDs==true instructs us to copy over new dataset sequences from
2078 // an existing alignment
2079 Vector newDs = (importDs) ? new Vector() : null; // used to create
2080 // minimum dataset set
2082 for (int i = 0; i < sequences.length; i++)
2086 newDs.addElement(null);
2088 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2090 if (importDs && ds != null)
2092 if (!newDs.contains(ds))
2094 newDs.setElementAt(ds, i);
2095 ds = new Sequence(ds);
2096 // update with new dataset sequence
2097 sequences[i].setDatasetSequence(ds);
2101 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2106 // copy and derive new dataset sequence
2107 sequences[i] = sequences[i].deriveSequence();
2108 alignment.getDataset()
2109 .addSequence(sequences[i].getDatasetSequence());
2110 // TODO: avoid creation of duplicate dataset sequences with a
2111 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2113 alignment.addSequence(sequences[i]); // merges dataset
2117 newDs.clear(); // tidy up
2119 if (alignment.getAlignmentAnnotation() != null)
2121 for (AlignmentAnnotation alan : alignment
2122 .getAlignmentAnnotation())
2124 if (alan.graphGroup > fgroup)
2126 fgroup = alan.graphGroup;
2130 if (pastedal.getAlignmentAnnotation() != null)
2132 // Add any annotation attached to alignment.
2133 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2134 for (int i = 0; i < alann.length; i++)
2136 annotationAdded = true;
2137 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2139 AlignmentAnnotation newann = new AlignmentAnnotation(
2141 if (newann.graphGroup > -1)
2143 if (newGraphGroups.size() <= newann.graphGroup
2144 || newGraphGroups.get(newann.graphGroup) == null)
2146 for (int q = newGraphGroups
2147 .size(); q <= newann.graphGroup; q++)
2149 newGraphGroups.add(q, null);
2151 newGraphGroups.set(newann.graphGroup,
2152 new Integer(++fgroup));
2154 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2158 newann.padAnnotation(alwidth);
2159 alignment.addAnnotation(newann);
2169 addHistoryItem(new EditCommand(
2170 MessageManager.getString("label.add_sequences"),
2171 Action.PASTE, sequences, 0, alignment.getWidth(),
2174 // Add any annotations attached to sequences
2175 for (int i = 0; i < sequences.length; i++)
2177 if (sequences[i].getAnnotation() != null)
2179 AlignmentAnnotation newann;
2180 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2182 annotationAdded = true;
2183 newann = sequences[i].getAnnotation()[a];
2184 newann.adjustForAlignment();
2185 newann.padAnnotation(alwidth);
2186 if (newann.graphGroup > -1)
2188 if (newann.graphGroup > -1)
2190 if (newGraphGroups.size() <= newann.graphGroup
2191 || newGraphGroups.get(newann.graphGroup) == null)
2193 for (int q = newGraphGroups
2194 .size(); q <= newann.graphGroup; q++)
2196 newGraphGroups.add(q, null);
2198 newGraphGroups.set(newann.graphGroup,
2199 new Integer(++fgroup));
2201 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2205 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2209 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2217 // propagate alignment changed.
2218 viewport.getRanges().setEndSeq(alignment.getHeight());
2219 if (annotationAdded)
2221 // Duplicate sequence annotation in all views.
2222 AlignmentI[] alview = this.getViewAlignments();
2223 for (int i = 0; i < sequences.length; i++)
2225 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2230 for (int avnum = 0; avnum < alview.length; avnum++)
2232 if (alview[avnum] != alignment)
2234 // duplicate in a view other than the one with input focus
2235 int avwidth = alview[avnum].getWidth() + 1;
2236 // this relies on sann being preserved after we
2237 // modify the sequence's annotation array for each duplication
2238 for (int a = 0; a < sann.length; a++)
2240 AlignmentAnnotation newann = new AlignmentAnnotation(
2242 sequences[i].addAlignmentAnnotation(newann);
2243 newann.padAnnotation(avwidth);
2244 alview[avnum].addAnnotation(newann); // annotation was
2245 // duplicated earlier
2246 // TODO JAL-1145 graphGroups are not updated for sequence
2247 // annotation added to several views. This may cause
2249 alview[avnum].setAnnotationIndex(newann, a);
2254 buildSortByAnnotationScoresMenu();
2256 viewport.firePropertyChange("alignment", null,
2257 alignment.getSequences());
2258 if (alignPanels != null)
2260 for (AlignmentPanel ap : alignPanels)
2262 ap.validateAnnotationDimensions(false);
2267 alignPanel.validateAnnotationDimensions(false);
2273 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2275 String newtitle = new String("Copied sequences");
2277 if (Desktop.jalviewClipboard != null
2278 && Desktop.jalviewClipboard[2] != null)
2280 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2281 af.viewport.setHiddenColumns(hc);
2284 // >>>This is a fix for the moment, until a better solution is
2286 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2287 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2288 .getFeatureRenderer());
2290 // TODO: maintain provenance of an alignment, rather than just make the
2291 // title a concatenation of operations.
2294 if (title.startsWith("Copied sequences"))
2300 newtitle = newtitle.concat("- from " + title);
2305 newtitle = new String("Pasted sequences");
2308 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2313 } catch (Exception ex)
2315 ex.printStackTrace();
2316 System.out.println("Exception whilst pasting: " + ex);
2317 // could be anything being pasted in here
2323 protected void expand_newalign(ActionEvent e)
2327 AlignmentI alignment = AlignmentUtils
2328 .expandContext(getViewport().getAlignment(), -1);
2329 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2331 String newtitle = new String("Flanking alignment");
2333 if (Desktop.jalviewClipboard != null
2334 && Desktop.jalviewClipboard[2] != null)
2336 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2337 af.viewport.setHiddenColumns(hc);
2340 // >>>This is a fix for the moment, until a better solution is
2342 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2343 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2344 .getFeatureRenderer());
2346 // TODO: maintain provenance of an alignment, rather than just make the
2347 // title a concatenation of operations.
2349 if (title.startsWith("Copied sequences"))
2355 newtitle = newtitle.concat("- from " + title);
2359 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2361 } catch (Exception ex)
2363 ex.printStackTrace();
2364 System.out.println("Exception whilst pasting: " + ex);
2365 // could be anything being pasted in here
2366 } catch (OutOfMemoryError oom)
2368 new OOMWarning("Viewing flanking region of alignment", oom);
2379 protected void cut_actionPerformed(ActionEvent e)
2381 copy_actionPerformed(null);
2382 delete_actionPerformed(null);
2392 protected void delete_actionPerformed(ActionEvent evt)
2395 SequenceGroup sg = viewport.getSelectionGroup();
2402 * If the cut affects all sequences, warn, remove highlighted columns
2404 if (sg.getSize() == viewport.getAlignment().getHeight())
2406 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2407 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2408 if (isEntireAlignWidth)
2410 int confirm = JvOptionPane.showConfirmDialog(this,
2411 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2412 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2413 JvOptionPane.OK_CANCEL_OPTION);
2415 if (confirm == JvOptionPane.CANCEL_OPTION
2416 || confirm == JvOptionPane.CLOSED_OPTION)
2421 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2422 sg.getEndRes() + 1);
2424 SequenceI[] cut = sg.getSequences()
2425 .toArray(new SequenceI[sg.getSize()]);
2427 addHistoryItem(new EditCommand(
2428 MessageManager.getString("label.cut_sequences"), Action.CUT,
2429 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2430 viewport.getAlignment()));
2432 viewport.setSelectionGroup(null);
2433 viewport.sendSelection();
2434 viewport.getAlignment().deleteGroup(sg);
2436 viewport.firePropertyChange("alignment", null,
2437 viewport.getAlignment().getSequences());
2438 if (viewport.getAlignment().getHeight() < 1)
2442 this.setClosed(true);
2443 } catch (Exception ex)
2456 protected void deleteGroups_actionPerformed(ActionEvent e)
2458 if (avc.deleteGroups())
2460 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2461 alignPanel.updateAnnotation();
2462 alignPanel.paintAlignment(true, true);
2473 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2475 SequenceGroup sg = new SequenceGroup();
2477 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2479 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2482 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2483 viewport.setSelectionGroup(sg);
2484 viewport.sendSelection();
2485 // JAL-2034 - should delegate to
2486 // alignPanel to decide if overview needs
2488 alignPanel.paintAlignment(false, false);
2489 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2499 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2501 if (viewport.cursorMode)
2503 alignPanel.getSeqPanel().keyboardNo1 = null;
2504 alignPanel.getSeqPanel().keyboardNo2 = null;
2506 viewport.setSelectionGroup(null);
2507 viewport.getColumnSelection().clear();
2508 viewport.setSelectionGroup(null);
2509 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2510 // JAL-2034 - should delegate to
2511 // alignPanel to decide if overview needs
2513 alignPanel.paintAlignment(false, false);
2514 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2515 viewport.sendSelection();
2525 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2527 SequenceGroup sg = viewport.getSelectionGroup();
2531 selectAllSequenceMenuItem_actionPerformed(null);
2536 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2538 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2540 // JAL-2034 - should delegate to
2541 // alignPanel to decide if overview needs
2544 alignPanel.paintAlignment(true, false);
2545 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2546 viewport.sendSelection();
2550 public void invertColSel_actionPerformed(ActionEvent e)
2552 viewport.invertColumnSelection();
2553 alignPanel.paintAlignment(true, false);
2554 viewport.sendSelection();
2564 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2566 trimAlignment(true);
2576 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2578 trimAlignment(false);
2581 void trimAlignment(boolean trimLeft)
2583 ColumnSelection colSel = viewport.getColumnSelection();
2586 if (!colSel.isEmpty())
2590 column = colSel.getMin();
2594 column = colSel.getMax();
2598 if (viewport.getSelectionGroup() != null)
2600 seqs = viewport.getSelectionGroup()
2601 .getSequencesAsArray(viewport.getHiddenRepSequences());
2605 seqs = viewport.getAlignment().getSequencesArray();
2608 TrimRegionCommand trimRegion;
2611 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2612 column, viewport.getAlignment());
2613 viewport.getRanges().setStartRes(0);
2617 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2618 column, viewport.getAlignment());
2621 statusBar.setText(MessageManager
2622 .formatMessage("label.removed_columns", new String[]
2623 { Integer.valueOf(trimRegion.getSize()).toString() }));
2625 addHistoryItem(trimRegion);
2627 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2629 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2630 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2632 viewport.getAlignment().deleteGroup(sg);
2636 viewport.firePropertyChange("alignment", null,
2637 viewport.getAlignment().getSequences());
2648 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2650 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2653 if (viewport.getSelectionGroup() != null)
2655 seqs = viewport.getSelectionGroup()
2656 .getSequencesAsArray(viewport.getHiddenRepSequences());
2657 start = viewport.getSelectionGroup().getStartRes();
2658 end = viewport.getSelectionGroup().getEndRes();
2662 seqs = viewport.getAlignment().getSequencesArray();
2665 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2666 "Remove Gapped Columns", seqs, start, end,
2667 viewport.getAlignment());
2669 addHistoryItem(removeGapCols);
2671 statusBar.setText(MessageManager
2672 .formatMessage("label.removed_empty_columns", new Object[]
2673 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2675 // This is to maintain viewport position on first residue
2676 // of first sequence
2677 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2678 ViewportRanges ranges = viewport.getRanges();
2679 int startRes = seq.findPosition(ranges.getStartRes());
2680 // ShiftList shifts;
2681 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2682 // edit.alColumnChanges=shifts.getInverse();
2683 // if (viewport.hasHiddenColumns)
2684 // viewport.getColumnSelection().compensateForEdits(shifts);
2685 ranges.setStartRes(seq.findIndex(startRes) - 1);
2686 viewport.firePropertyChange("alignment", null,
2687 viewport.getAlignment().getSequences());
2698 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2700 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2703 if (viewport.getSelectionGroup() != null)
2705 seqs = viewport.getSelectionGroup()
2706 .getSequencesAsArray(viewport.getHiddenRepSequences());
2707 start = viewport.getSelectionGroup().getStartRes();
2708 end = viewport.getSelectionGroup().getEndRes();
2712 seqs = viewport.getAlignment().getSequencesArray();
2715 // This is to maintain viewport position on first residue
2716 // of first sequence
2717 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2718 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2720 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2721 viewport.getAlignment()));
2723 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2725 viewport.firePropertyChange("alignment", null,
2726 viewport.getAlignment().getSequences());
2737 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2739 viewport.setPadGaps(padGapsMenuitem.isSelected());
2740 viewport.firePropertyChange("alignment", null,
2741 viewport.getAlignment().getSequences());
2751 public void findMenuItem_actionPerformed(ActionEvent e)
2757 * Create a new view of the current alignment.
2760 public void newView_actionPerformed(ActionEvent e)
2762 newView(null, true);
2766 * Creates and shows a new view of the current alignment.
2769 * title of newly created view; if null, one will be generated
2770 * @param copyAnnotation
2771 * if true then duplicate all annnotation, groups and settings
2772 * @return new alignment panel, already displayed.
2774 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2777 * Create a new AlignmentPanel (with its own, new Viewport)
2779 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2780 if (!copyAnnotation)
2783 * remove all groups and annotation except for the automatic stuff
2785 newap.av.getAlignment().deleteAllGroups();
2786 newap.av.getAlignment().deleteAllAnnotations(false);
2789 newap.av.setGatherViewsHere(false);
2791 if (viewport.viewName == null)
2793 viewport.viewName = MessageManager
2794 .getString("label.view_name_original");
2798 * Views share the same edits undo and redo stacks
2800 newap.av.setHistoryList(viewport.getHistoryList());
2801 newap.av.setRedoList(viewport.getRedoList());
2804 * Views share the same mappings; need to deregister any new mappings
2805 * created by copyAlignPanel, and register the new reference to the shared
2808 newap.av.replaceMappings(viewport.getAlignment());
2811 * start up cDNA consensus (if applicable) now mappings are in place
2813 if (newap.av.initComplementConsensus())
2815 newap.refresh(true); // adjust layout of annotations
2818 newap.av.viewName = getNewViewName(viewTitle);
2820 addAlignmentPanel(newap, true);
2821 newap.alignmentChanged();
2823 if (alignPanels.size() == 2)
2825 viewport.setGatherViewsHere(true);
2827 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2832 * Make a new name for the view, ensuring it is unique within the current
2833 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2834 * these now use viewId. Unique view names are still desirable for usability.)
2839 protected String getNewViewName(String viewTitle)
2841 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2842 boolean addFirstIndex = false;
2843 if (viewTitle == null || viewTitle.trim().length() == 0)
2845 viewTitle = MessageManager.getString("action.view");
2846 addFirstIndex = true;
2850 index = 1;// we count from 1 if given a specific name
2852 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2854 List<Component> comps = PaintRefresher.components
2855 .get(viewport.getSequenceSetId());
2857 List<String> existingNames = getExistingViewNames(comps);
2859 while (existingNames.contains(newViewName))
2861 newViewName = viewTitle + " " + (++index);
2867 * Returns a list of distinct view names found in the given list of
2868 * components. View names are held on the viewport of an AlignmentPanel.
2873 protected List<String> getExistingViewNames(List<Component> comps)
2875 List<String> existingNames = new ArrayList<>();
2876 for (Component comp : comps)
2878 if (comp instanceof AlignmentPanel)
2880 AlignmentPanel ap = (AlignmentPanel) comp;
2881 if (!existingNames.contains(ap.av.viewName))
2883 existingNames.add(ap.av.viewName);
2887 return existingNames;
2891 * Explode tabbed views into separate windows.
2894 public void expandViews_actionPerformed(ActionEvent e)
2896 Desktop.explodeViews(this);
2900 * Gather views in separate windows back into a tabbed presentation.
2903 public void gatherViews_actionPerformed(ActionEvent e)
2905 Desktop.instance.gatherViews(this);
2915 public void font_actionPerformed(ActionEvent e)
2917 new FontChooser(alignPanel);
2927 protected void seqLimit_actionPerformed(ActionEvent e)
2929 viewport.setShowJVSuffix(seqLimits.isSelected());
2931 alignPanel.getIdPanel().getIdCanvas()
2932 .setPreferredSize(alignPanel.calculateIdWidth());
2933 alignPanel.paintAlignment(true, false);
2937 public void idRightAlign_actionPerformed(ActionEvent e)
2939 viewport.setRightAlignIds(idRightAlign.isSelected());
2940 alignPanel.paintAlignment(false, false);
2944 public void centreColumnLabels_actionPerformed(ActionEvent e)
2946 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2947 alignPanel.paintAlignment(false, false);
2953 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2956 protected void followHighlight_actionPerformed()
2959 * Set the 'follow' flag on the Viewport (and scroll to position if now
2962 final boolean state = this.followHighlightMenuItem.getState();
2963 viewport.setFollowHighlight(state);
2966 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2977 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2979 viewport.setColourText(colourTextMenuItem.isSelected());
2980 alignPanel.paintAlignment(false, false);
2990 public void wrapMenuItem_actionPerformed(ActionEvent e)
2992 scaleAbove.setVisible(wrapMenuItem.isSelected());
2993 scaleLeft.setVisible(wrapMenuItem.isSelected());
2994 scaleRight.setVisible(wrapMenuItem.isSelected());
2995 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2996 alignPanel.updateLayout();
3000 public void showAllSeqs_actionPerformed(ActionEvent e)
3002 viewport.showAllHiddenSeqs();
3006 public void showAllColumns_actionPerformed(ActionEvent e)
3008 viewport.showAllHiddenColumns();
3009 alignPanel.paintAlignment(true, true);
3010 viewport.sendSelection();
3014 public void hideSelSequences_actionPerformed(ActionEvent e)
3016 viewport.hideAllSelectedSeqs();
3020 * called by key handler and the hide all/show all menu items
3025 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3028 boolean hide = false;
3029 SequenceGroup sg = viewport.getSelectionGroup();
3030 if (!toggleSeqs && !toggleCols)
3032 // Hide everything by the current selection - this is a hack - we do the
3033 // invert and then hide
3034 // first check that there will be visible columns after the invert.
3035 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3036 && sg.getStartRes() <= sg.getEndRes()))
3038 // now invert the sequence set, if required - empty selection implies
3039 // that no hiding is required.
3042 invertSequenceMenuItem_actionPerformed(null);
3043 sg = viewport.getSelectionGroup();
3047 viewport.expandColSelection(sg, true);
3048 // finally invert the column selection and get the new sequence
3050 invertColSel_actionPerformed(null);
3057 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3059 hideSelSequences_actionPerformed(null);
3062 else if (!(toggleCols && viewport.hasSelectedColumns()))
3064 showAllSeqs_actionPerformed(null);
3070 if (viewport.hasSelectedColumns())
3072 hideSelColumns_actionPerformed(null);
3075 viewport.setSelectionGroup(sg);
3080 showAllColumns_actionPerformed(null);
3089 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3090 * event.ActionEvent)
3093 public void hideAllButSelection_actionPerformed(ActionEvent e)
3095 toggleHiddenRegions(false, false);
3096 viewport.sendSelection();
3103 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3107 public void hideAllSelection_actionPerformed(ActionEvent e)
3109 SequenceGroup sg = viewport.getSelectionGroup();
3110 viewport.expandColSelection(sg, false);
3111 viewport.hideAllSelectedSeqs();
3112 viewport.hideSelectedColumns();
3113 alignPanel.paintAlignment(true, true);
3114 viewport.sendSelection();
3121 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3125 public void showAllhidden_actionPerformed(ActionEvent e)
3127 viewport.showAllHiddenColumns();
3128 viewport.showAllHiddenSeqs();
3129 alignPanel.paintAlignment(true, true);
3130 viewport.sendSelection();
3134 public void hideSelColumns_actionPerformed(ActionEvent e)
3136 viewport.hideSelectedColumns();
3137 alignPanel.paintAlignment(true, true);
3138 viewport.sendSelection();
3142 public void hiddenMarkers_actionPerformed(ActionEvent e)
3144 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3155 protected void scaleAbove_actionPerformed(ActionEvent e)
3157 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3158 // TODO: do we actually need to update overview for scale above change ?
3159 alignPanel.paintAlignment(true, false);
3169 protected void scaleLeft_actionPerformed(ActionEvent e)
3171 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3172 alignPanel.paintAlignment(true, false);
3182 protected void scaleRight_actionPerformed(ActionEvent e)
3184 viewport.setScaleRightWrapped(scaleRight.isSelected());
3185 alignPanel.paintAlignment(true, false);
3195 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3197 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3198 alignPanel.paintAlignment(false, false);
3208 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3210 viewport.setShowText(viewTextMenuItem.isSelected());
3211 alignPanel.paintAlignment(false, false);
3221 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3223 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3224 alignPanel.paintAlignment(false, false);
3227 public FeatureSettings featureSettings;
3230 public FeatureSettingsControllerI getFeatureSettingsUI()
3232 return featureSettings;
3236 public void featureSettings_actionPerformed(ActionEvent e)
3238 if (featureSettings != null)
3240 featureSettings.close();
3241 featureSettings = null;
3243 if (!showSeqFeatures.isSelected())
3245 // make sure features are actually displayed
3246 showSeqFeatures.setSelected(true);
3247 showSeqFeatures_actionPerformed(null);
3249 featureSettings = new FeatureSettings(this);
3253 * Set or clear 'Show Sequence Features'
3259 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3261 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3262 alignPanel.paintAlignment(true, true);
3266 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3267 * the annotations panel as a whole.
3269 * The options to show/hide all annotations should be enabled when the panel
3270 * is shown, and disabled when the panel is hidden.
3275 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3277 final boolean setVisible = annotationPanelMenuItem.isSelected();
3278 viewport.setShowAnnotation(setVisible);
3279 this.showAllSeqAnnotations.setEnabled(setVisible);
3280 this.hideAllSeqAnnotations.setEnabled(setVisible);
3281 this.showAllAlAnnotations.setEnabled(setVisible);
3282 this.hideAllAlAnnotations.setEnabled(setVisible);
3283 alignPanel.updateLayout();
3287 public void alignmentProperties()
3289 JEditorPane editPane = new JEditorPane("text/html", "");
3290 editPane.setEditable(false);
3291 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3294 MessageManager.formatMessage("label.html_content", new Object[]
3295 { contents.toString() }));
3296 JInternalFrame frame = new JInternalFrame();
3297 frame.getContentPane().add(new JScrollPane(editPane));
3299 Desktop.addInternalFrame(frame, MessageManager
3300 .formatMessage("label.alignment_properties", new Object[]
3301 { getTitle() }), 500, 400);
3311 public void overviewMenuItem_actionPerformed(ActionEvent e)
3313 if (alignPanel.overviewPanel != null)
3318 JInternalFrame frame = new JInternalFrame();
3319 final OverviewPanel overview = new OverviewPanel(alignPanel);
3320 frame.setContentPane(overview);
3321 Desktop.addInternalFrame(frame, MessageManager
3322 .formatMessage("label.overview_params", new Object[]
3323 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3326 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3327 frame.addInternalFrameListener(
3328 new javax.swing.event.InternalFrameAdapter()
3331 public void internalFrameClosed(
3332 javax.swing.event.InternalFrameEvent evt)
3335 alignPanel.setOverviewPanel(null);
3338 if (getKeyListeners().length > 0)
3340 frame.addKeyListener(getKeyListeners()[0]);
3343 alignPanel.setOverviewPanel(overview);
3347 public void textColour_actionPerformed()
3349 new TextColourChooser().chooseColour(alignPanel, null);
3353 * public void covariationColour_actionPerformed() {
3355 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3359 public void annotationColour_actionPerformed()
3361 new AnnotationColourChooser(viewport, alignPanel);
3365 public void annotationColumn_actionPerformed(ActionEvent e)
3367 new AnnotationColumnChooser(viewport, alignPanel);
3371 * Action on the user checking or unchecking the option to apply the selected
3372 * colour scheme to all groups. If unchecked, groups may have their own
3373 * independent colour schemes.
3378 public void applyToAllGroups_actionPerformed(boolean selected)
3380 viewport.setColourAppliesToAllGroups(selected);
3384 * Action on user selecting a colour from the colour menu
3387 * the name (not the menu item label!) of the colour scheme
3390 public void changeColour_actionPerformed(String name)
3393 * 'User Defined' opens a panel to configure or load a
3394 * user-defined colour scheme
3396 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3398 new UserDefinedColours(alignPanel);
3403 * otherwise set the chosen colour scheme (or null for 'None')
3405 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3406 viewport.getAlignment(), viewport.getHiddenRepSequences());
3411 * Actions on setting or changing the alignment colour scheme
3416 public void changeColour(ColourSchemeI cs)
3418 // TODO: pull up to controller method
3419 ColourMenuHelper.setColourSelected(colourMenu, cs);
3421 viewport.setGlobalColourScheme(cs);
3423 alignPanel.paintAlignment(true, true);
3427 * Show the PID threshold slider panel
3430 protected void modifyPID_actionPerformed()
3432 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3433 alignPanel.getViewName());
3434 SliderPanel.showPIDSlider();
3438 * Show the Conservation slider panel
3441 protected void modifyConservation_actionPerformed()
3443 SliderPanel.setConservationSlider(alignPanel,
3444 viewport.getResidueShading(), alignPanel.getViewName());
3445 SliderPanel.showConservationSlider();
3449 * Action on selecting or deselecting (Colour) By Conservation
3452 public void conservationMenuItem_actionPerformed(boolean selected)
3454 modifyConservation.setEnabled(selected);
3455 viewport.setConservationSelected(selected);
3456 viewport.getResidueShading().setConservationApplied(selected);
3458 changeColour(viewport.getGlobalColourScheme());
3461 modifyConservation_actionPerformed();
3465 SliderPanel.hideConservationSlider();
3470 * Action on selecting or deselecting (Colour) Above PID Threshold
3473 public void abovePIDThreshold_actionPerformed(boolean selected)
3475 modifyPID.setEnabled(selected);
3476 viewport.setAbovePIDThreshold(selected);
3479 viewport.getResidueShading().setThreshold(0,
3480 viewport.isIgnoreGapsConsensus());
3483 changeColour(viewport.getGlobalColourScheme());
3486 modifyPID_actionPerformed();
3490 SliderPanel.hidePIDSlider();
3501 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3503 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3504 AlignmentSorter.sortByPID(viewport.getAlignment(),
3505 viewport.getAlignment().getSequenceAt(0));
3506 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3507 viewport.getAlignment()));
3508 alignPanel.paintAlignment(true, false);
3518 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3520 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3521 AlignmentSorter.sortByID(viewport.getAlignment());
3523 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3524 alignPanel.paintAlignment(true, false);
3534 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3536 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3537 AlignmentSorter.sortByLength(viewport.getAlignment());
3538 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3539 viewport.getAlignment()));
3540 alignPanel.paintAlignment(true, false);
3550 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3552 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3553 AlignmentSorter.sortByGroup(viewport.getAlignment());
3554 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3555 viewport.getAlignment()));
3557 alignPanel.paintAlignment(true, false);
3567 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3569 new RedundancyPanel(alignPanel, this);
3579 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3581 if ((viewport.getSelectionGroup() == null)
3582 || (viewport.getSelectionGroup().getSize() < 2))
3584 JvOptionPane.showInternalMessageDialog(this,
3585 MessageManager.getString(
3586 "label.you_must_select_least_two_sequences"),
3587 MessageManager.getString("label.invalid_selection"),
3588 JvOptionPane.WARNING_MESSAGE);
3592 JInternalFrame frame = new JInternalFrame();
3593 frame.setContentPane(new PairwiseAlignPanel(viewport));
3594 Desktop.addInternalFrame(frame,
3595 MessageManager.getString("action.pairwise_alignment"), 600,
3601 public void autoCalculate_actionPerformed(ActionEvent e)
3603 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3604 if (viewport.autoCalculateConsensus)
3606 viewport.firePropertyChange("alignment", null,
3607 viewport.getAlignment().getSequences());
3612 public void sortByTreeOption_actionPerformed(ActionEvent e)
3614 viewport.sortByTree = sortByTree.isSelected();
3618 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3620 viewport.followSelection = listenToViewSelections.isSelected();
3624 * Constructs a tree panel and adds it to the desktop
3627 * tree type (NJ or AV)
3629 * name of score model used to compute the tree
3631 * parameters for the distance or similarity calculation
3633 void newTreePanel(String type, String modelName,
3634 SimilarityParamsI options)
3636 String frameTitle = "";
3639 boolean onSelection = false;
3640 if (viewport.getSelectionGroup() != null
3641 && viewport.getSelectionGroup().getSize() > 0)
3643 SequenceGroup sg = viewport.getSelectionGroup();
3645 /* Decide if the selection is a column region */
3646 for (SequenceI _s : sg.getSequences())
3648 if (_s.getLength() < sg.getEndRes())
3650 JvOptionPane.showMessageDialog(Desktop.desktop,
3651 MessageManager.getString(
3652 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3653 MessageManager.getString(
3654 "label.sequences_selection_not_aligned"),
3655 JvOptionPane.WARNING_MESSAGE);
3664 if (viewport.getAlignment().getHeight() < 2)
3670 tp = new TreePanel(alignPanel, type, modelName, options);
3671 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3673 frameTitle += " from ";
3675 if (viewport.viewName != null)
3677 frameTitle += viewport.viewName + " of ";
3680 frameTitle += this.title;
3682 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3693 public void addSortByOrderMenuItem(String title,
3694 final AlignmentOrder order)
3696 final JMenuItem item = new JMenuItem(MessageManager
3697 .formatMessage("action.by_title_param", new Object[]
3700 item.addActionListener(new java.awt.event.ActionListener()
3703 public void actionPerformed(ActionEvent e)
3705 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3707 // TODO: JBPNote - have to map order entries to curent SequenceI
3709 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3711 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3712 viewport.getAlignment()));
3714 alignPanel.paintAlignment(true, false);
3720 * Add a new sort by annotation score menu item
3723 * the menu to add the option to
3725 * the label used to retrieve scores for each sequence on the
3728 public void addSortByAnnotScoreMenuItem(JMenu sort,
3729 final String scoreLabel)
3731 final JMenuItem item = new JMenuItem(scoreLabel);
3733 item.addActionListener(new java.awt.event.ActionListener()
3736 public void actionPerformed(ActionEvent e)
3738 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3739 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3740 viewport.getAlignment());// ,viewport.getSelectionGroup());
3741 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3742 viewport.getAlignment()));
3743 alignPanel.paintAlignment(true, false);
3749 * last hash for alignment's annotation array - used to minimise cost of
3752 protected int _annotationScoreVectorHash;
3755 * search the alignment and rebuild the sort by annotation score submenu the
3756 * last alignment annotation vector hash is stored to minimize cost of
3757 * rebuilding in subsequence calls.
3761 public void buildSortByAnnotationScoresMenu()
3763 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3768 if (viewport.getAlignment().getAlignmentAnnotation()
3769 .hashCode() != _annotationScoreVectorHash)
3771 sortByAnnotScore.removeAll();
3772 // almost certainly a quicker way to do this - but we keep it simple
3773 Hashtable scoreSorts = new Hashtable();
3774 AlignmentAnnotation aann[];
3775 for (SequenceI sqa : viewport.getAlignment().getSequences())
3777 aann = sqa.getAnnotation();
3778 for (int i = 0; aann != null && i < aann.length; i++)
3780 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3782 scoreSorts.put(aann[i].label, aann[i].label);
3786 Enumeration labels = scoreSorts.keys();
3787 while (labels.hasMoreElements())
3789 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3790 (String) labels.nextElement());
3792 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3795 _annotationScoreVectorHash = viewport.getAlignment()
3796 .getAlignmentAnnotation().hashCode();
3801 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3802 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3803 * call. Listeners are added to remove the menu item when the treePanel is
3804 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3808 public void buildTreeSortMenu()
3810 sortByTreeMenu.removeAll();
3812 List<Component> comps = PaintRefresher.components
3813 .get(viewport.getSequenceSetId());
3814 List<TreePanel> treePanels = new ArrayList<>();
3815 for (Component comp : comps)
3817 if (comp instanceof TreePanel)
3819 treePanels.add((TreePanel) comp);
3823 if (treePanels.size() < 1)
3825 sortByTreeMenu.setVisible(false);
3829 sortByTreeMenu.setVisible(true);
3831 for (final TreePanel tp : treePanels)
3833 final JMenuItem item = new JMenuItem(tp.getTitle());
3834 item.addActionListener(new java.awt.event.ActionListener()
3837 public void actionPerformed(ActionEvent e)
3839 tp.sortByTree_actionPerformed();
3840 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3845 sortByTreeMenu.add(item);
3849 public boolean sortBy(AlignmentOrder alorder, String undoname)
3851 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3852 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3853 if (undoname != null)
3855 addHistoryItem(new OrderCommand(undoname, oldOrder,
3856 viewport.getAlignment()));
3858 alignPanel.paintAlignment(true, false);
3863 * Work out whether the whole set of sequences or just the selected set will
3864 * be submitted for multiple alignment.
3867 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3869 // Now, check we have enough sequences
3870 AlignmentView msa = null;
3872 if ((viewport.getSelectionGroup() != null)
3873 && (viewport.getSelectionGroup().getSize() > 1))
3875 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3876 // some common interface!
3878 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3879 * SequenceI[sz = seqs.getSize(false)];
3881 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3882 * seqs.getSequenceAt(i); }
3884 msa = viewport.getAlignmentView(true);
3886 else if (viewport.getSelectionGroup() != null
3887 && viewport.getSelectionGroup().getSize() == 1)
3889 int option = JvOptionPane.showConfirmDialog(this,
3890 MessageManager.getString("warn.oneseq_msainput_selection"),
3891 MessageManager.getString("label.invalid_selection"),
3892 JvOptionPane.OK_CANCEL_OPTION);
3893 if (option == JvOptionPane.OK_OPTION)
3895 msa = viewport.getAlignmentView(false);
3900 msa = viewport.getAlignmentView(false);
3906 * Decides what is submitted to a secondary structure prediction service: the
3907 * first sequence in the alignment, or in the current selection, or, if the
3908 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3909 * region or the whole alignment. (where the first sequence in the set is the
3910 * one that the prediction will be for).
3912 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3914 AlignmentView seqs = null;
3916 if ((viewport.getSelectionGroup() != null)
3917 && (viewport.getSelectionGroup().getSize() > 0))
3919 seqs = viewport.getAlignmentView(true);
3923 seqs = viewport.getAlignmentView(false);
3925 // limit sequences - JBPNote in future - could spawn multiple prediction
3927 // TODO: viewport.getAlignment().isAligned is a global state - the local
3928 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3929 if (!viewport.getAlignment().isAligned(false))
3931 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3932 // TODO: if seqs.getSequences().length>1 then should really have warned
3946 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3948 // Pick the tree file
3949 JalviewFileChooser chooser = new JalviewFileChooser(
3950 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3951 chooser.setFileView(new JalviewFileView());
3952 chooser.setDialogTitle(
3953 MessageManager.getString("label.select_newick_like_tree_file"));
3954 chooser.setToolTipText(
3955 MessageManager.getString("label.load_tree_file"));
3958 new jalview.util.dialogrunner.RunResponse(JalviewFileChooser.APPROVE_OPTION)
3963 String filePath = chooser.getSelectedFile().getPath();
3964 Cache.setProperty("LAST_DIRECTORY", filePath);
3965 NewickFile fin = null;
3968 fin = new NewickFile(new FileParse(
3969 chooser.getSelectedFile(), DataSourceType.FILE));
3970 viewport.setCurrentTree(
3971 showNewickTree(fin, filePath).getTree());
3972 } catch (Exception ex)
3974 JvOptionPane.showMessageDialog(Desktop.desktop,
3976 MessageManager.getString(
3977 "label.problem_reading_tree_file"),
3978 JvOptionPane.WARNING_MESSAGE);
3979 ex.printStackTrace();
3981 if (fin != null && fin.hasWarningMessage())
3983 JvOptionPane.showMessageDialog(Desktop.desktop,
3984 fin.getWarningMessage(),
3985 MessageManager.getString(
3986 "label.possible_problem_with_tree_file"),
3987 JvOptionPane.WARNING_MESSAGE);
3990 }).openDialog(this);
3993 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3995 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3998 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3999 int h, int x, int y)
4001 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4005 * Add a treeviewer for the tree extracted from a Newick file object to the
4006 * current alignment view
4013 * Associated alignment input data (or null)
4022 * @return TreePanel handle
4024 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4025 AlignmentView input, int w, int h, int x, int y)
4027 TreePanel tp = null;
4033 if (nf.getTree() != null)
4035 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4041 tp.setLocation(x, y);
4044 Desktop.addInternalFrame(tp, treeTitle, w, h);
4046 } catch (Exception ex)
4048 ex.printStackTrace();
4054 private boolean buildingMenu = false;
4057 * Generates menu items and listener event actions for web service clients
4060 public void BuildWebServiceMenu()
4062 while (buildingMenu)
4066 System.err.println("Waiting for building menu to finish.");
4068 } catch (Exception e)
4072 final AlignFrame me = this;
4073 buildingMenu = true;
4074 new Thread(new Runnable()
4079 final List<JMenuItem> legacyItems = new ArrayList<>();
4082 // System.err.println("Building ws menu again "
4083 // + Thread.currentThread());
4084 // TODO: add support for context dependent disabling of services based
4086 // alignment and current selection
4087 // TODO: add additional serviceHandle parameter to specify abstract
4089 // class independently of AbstractName
4090 // TODO: add in rediscovery GUI function to restart discoverer
4091 // TODO: group services by location as well as function and/or
4093 // object broker mechanism.
4094 final Vector<JMenu> wsmenu = new Vector<>();
4095 final IProgressIndicator af = me;
4098 * do not i18n these strings - they are hard-coded in class
4099 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4100 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4102 final JMenu msawsmenu = new JMenu("Alignment");
4103 final JMenu secstrmenu = new JMenu(
4104 "Secondary Structure Prediction");
4105 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4106 final JMenu analymenu = new JMenu("Analysis");
4107 final JMenu dismenu = new JMenu("Protein Disorder");
4108 // JAL-940 - only show secondary structure prediction services from
4109 // the legacy server
4110 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4112 Discoverer.services != null && (Discoverer.services.size() > 0))
4114 // TODO: refactor to allow list of AbstractName/Handler bindings to
4116 // stored or retrieved from elsewhere
4117 // No MSAWS used any more:
4118 // Vector msaws = null; // (Vector)
4119 // Discoverer.services.get("MsaWS");
4120 Vector secstrpr = (Vector) Discoverer.services
4122 if (secstrpr != null)
4124 // Add any secondary structure prediction services
4125 for (int i = 0, j = secstrpr.size(); i < j; i++)
4127 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4129 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4130 .getServiceClient(sh);
4131 int p = secstrmenu.getItemCount();
4132 impl.attachWSMenuEntry(secstrmenu, me);
4133 int q = secstrmenu.getItemCount();
4134 for (int litm = p; litm < q; litm++)
4136 legacyItems.add(secstrmenu.getItem(litm));
4142 // Add all submenus in the order they should appear on the web
4144 wsmenu.add(msawsmenu);
4145 wsmenu.add(secstrmenu);
4146 wsmenu.add(dismenu);
4147 wsmenu.add(analymenu);
4148 // No search services yet
4149 // wsmenu.add(seqsrchmenu);
4151 javax.swing.SwingUtilities.invokeLater(new Runnable()
4158 webService.removeAll();
4159 // first, add discovered services onto the webservices menu
4160 if (wsmenu.size() > 0)
4162 for (int i = 0, j = wsmenu.size(); i < j; i++)
4164 webService.add(wsmenu.get(i));
4169 webService.add(me.webServiceNoServices);
4171 // TODO: move into separate menu builder class.
4172 boolean new_sspred = false;
4173 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4175 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4176 if (jws2servs != null)
4178 if (jws2servs.hasServices())
4180 jws2servs.attachWSMenuEntry(webService, me);
4181 for (Jws2Instance sv : jws2servs.getServices())
4183 if (sv.description.toLowerCase().contains("jpred"))
4185 for (JMenuItem jmi : legacyItems)
4187 jmi.setVisible(false);
4193 if (jws2servs.isRunning())
4195 JMenuItem tm = new JMenuItem(
4196 "Still discovering JABA Services");
4197 tm.setEnabled(false);
4202 build_urlServiceMenu(me.webService);
4203 build_fetchdbmenu(webService);
4204 for (JMenu item : wsmenu)
4206 if (item.getItemCount() == 0)
4208 item.setEnabled(false);
4212 item.setEnabled(true);
4215 } catch (Exception e)
4218 "Exception during web service menu building process.",
4223 } catch (Exception e)
4226 buildingMenu = false;
4233 * construct any groupURL type service menu entries.
4237 private void build_urlServiceMenu(JMenu webService)
4239 // TODO: remove this code when 2.7 is released
4240 // DEBUG - alignmentView
4242 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4243 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4245 * @Override public void actionPerformed(ActionEvent e) {
4246 * jalview.datamodel.AlignmentView
4247 * .testSelectionViews(af.viewport.getAlignment(),
4248 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4250 * }); webService.add(testAlView);
4252 // TODO: refactor to RestClient discoverer and merge menu entries for
4253 // rest-style services with other types of analysis/calculation service
4254 // SHmmr test client - still being implemented.
4255 // DEBUG - alignmentView
4257 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4260 client.attachWSMenuEntry(
4261 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4267 * Searches the alignment sequences for xRefs and builds the Show
4268 * Cross-References menu (formerly called Show Products), with database
4269 * sources for which cross-references are found (protein sources for a
4270 * nucleotide alignment and vice versa)
4272 * @return true if Show Cross-references menu should be enabled
4274 public boolean canShowProducts()
4276 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4277 AlignmentI dataset = viewport.getAlignment().getDataset();
4279 showProducts.removeAll();
4280 final boolean dna = viewport.getAlignment().isNucleotide();
4282 if (seqs == null || seqs.length == 0)
4284 // nothing to see here.
4288 boolean showp = false;
4291 List<String> ptypes = new CrossRef(seqs, dataset)
4292 .findXrefSourcesForSequences(dna);
4294 for (final String source : ptypes)
4297 final AlignFrame af = this;
4298 JMenuItem xtype = new JMenuItem(source);
4299 xtype.addActionListener(new ActionListener()
4302 public void actionPerformed(ActionEvent e)
4304 showProductsFor(af.viewport.getSequenceSelection(), dna,
4308 showProducts.add(xtype);
4310 showProducts.setVisible(showp);
4311 showProducts.setEnabled(showp);
4312 } catch (Exception e)
4315 "canShowProducts threw an exception - please report to help@jalview.org",
4323 * Finds and displays cross-references for the selected sequences (protein
4324 * products for nucleotide sequences, dna coding sequences for peptides).
4327 * the sequences to show cross-references for
4329 * true if from a nucleotide alignment (so showing proteins)
4331 * the database to show cross-references for
4333 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4334 final String source)
4336 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4341 * Construct and display a new frame containing the translation of this
4342 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4345 public void showTranslation_actionPerformed(ActionEvent e)
4347 AlignmentI al = null;
4350 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4352 al = dna.translateCdna();
4353 } catch (Exception ex)
4355 jalview.bin.Cache.log.error(
4356 "Exception during translation. Please report this !", ex);
4357 final String msg = MessageManager.getString(
4358 "label.error_when_translating_sequences_submit_bug_report");
4359 final String errorTitle = MessageManager
4360 .getString("label.implementation_error")
4361 + MessageManager.getString("label.translation_failed");
4362 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4363 JvOptionPane.ERROR_MESSAGE);
4366 if (al == null || al.getHeight() == 0)
4368 final String msg = MessageManager.getString(
4369 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4370 final String errorTitle = MessageManager
4371 .getString("label.translation_failed");
4372 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4373 JvOptionPane.WARNING_MESSAGE);
4377 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4378 af.setFileFormat(this.currentFileFormat);
4379 final String newTitle = MessageManager
4380 .formatMessage("label.translation_of_params", new Object[]
4381 { this.getTitle() });
4382 af.setTitle(newTitle);
4383 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4385 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4386 viewport.openSplitFrame(af, new Alignment(seqs));
4390 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4397 * Set the file format
4401 public void setFileFormat(FileFormatI format)
4403 this.currentFileFormat = format;
4407 * Try to load a features file onto the alignment.
4410 * contents or path to retrieve file or a File object
4412 * access mode of file (see jalview.io.AlignFile)
4413 * @return true if features file was parsed correctly.
4415 public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4418 return avc.parseFeaturesFile(file, sourceType,
4419 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4424 public void refreshFeatureUI(boolean enableIfNecessary)
4426 // note - currently this is only still here rather than in the controller
4427 // because of the featureSettings hard reference that is yet to be
4429 if (enableIfNecessary)
4431 viewport.setShowSequenceFeatures(true);
4432 showSeqFeatures.setSelected(true);
4438 public void dragEnter(DropTargetDragEvent evt)
4443 public void dragExit(DropTargetEvent evt)
4448 public void dragOver(DropTargetDragEvent evt)
4453 public void dropActionChanged(DropTargetDragEvent evt)
4458 public void drop(DropTargetDropEvent evt)
4460 // JAL-1552 - acceptDrop required before getTransferable call for
4461 // Java's Transferable for native dnd
4462 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4463 Transferable t = evt.getTransferable();
4466 final AlignFrame thisaf = this;
4467 final List<Object> files = new ArrayList<>();
4468 List<DataSourceType> protocols = new ArrayList<>();
4472 Desktop.transferFromDropTarget(files, protocols, evt, t);
4473 } catch (Exception e)
4475 e.printStackTrace();
4479 new Thread(new Runnable()
4486 // check to see if any of these files have names matching sequences
4489 SequenceIdMatcher idm = new SequenceIdMatcher(
4490 viewport.getAlignment().getSequencesArray());
4492 * Object[] { String,SequenceI}
4494 ArrayList<Object[]> filesmatched = new ArrayList<>();
4495 ArrayList<Object> filesnotmatched = new ArrayList<>();
4496 for (int i = 0; i < files.size(); i++)
4499 Object file = files.get(i);
4500 String fileName = file.toString();
4502 DataSourceType protocol = (file instanceof File ? DataSourceType.FILE : FormatAdapter.checkProtocol(fileName));
4503 if (protocol == DataSourceType.FILE)
4505 File fl = (file instanceof File ? (File) file : new File(fileName));
4506 pdbfn = fl.getName();
4508 else if (protocol == DataSourceType.URL)
4510 URL url = new URL(fileName);
4511 pdbfn = url.getFile();
4513 if (pdbfn.length() > 0)
4515 // attempt to find a match in the alignment
4516 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4517 int l = 0, c = pdbfn.indexOf(".");
4518 while (mtch == null && c != -1)
4523 } while ((c = pdbfn.indexOf(".", l)) > l);
4526 pdbfn = pdbfn.substring(0, l);
4528 mtch = idm.findAllIdMatches(pdbfn);
4535 type = new IdentifyFile().identify(file, protocol);
4536 } catch (Exception ex)
4540 if (type != null && type.isStructureFile())
4542 filesmatched.add(new Object[] { file, protocol, mtch });
4546 // File wasn't named like one of the sequences or wasn't a PDB
4548 filesnotmatched.add(file);
4552 if (filesmatched.size() > 0)
4554 boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4557 String msg = MessageManager.formatMessage(
4558 "label.automatically_associate_structure_files_with_sequences_same_name",
4560 { Integer.valueOf(filesmatched.size())
4562 String ttl = MessageManager.getString(
4563 "label.automatically_associate_structure_files_by_name");
4564 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4565 ttl, JvOptionPane.YES_NO_OPTION);
4566 autoAssociate = choice == JvOptionPane.YES_OPTION;
4570 for (Object[] fm : filesmatched)
4572 // try and associate
4573 // TODO: may want to set a standard ID naming formalism for
4574 // associating PDB files which have no IDs.
4575 for (SequenceI toassoc : (SequenceI[]) fm[2])
4577 PDBEntry pe = new AssociatePdbFileWithSeq()
4578 .associatePdbWithSeq((String) fm[0],
4579 (DataSourceType) fm[1], toassoc, false,
4583 System.err.println("Associated file : "
4584 + ((String) fm[0]) + " with "
4585 + toassoc.getDisplayId(true));
4589 // TODO: do we need to update overview ? only if features are
4591 alignPanel.paintAlignment(true, false);
4597 * add declined structures as sequences
4599 for (Object[] o : filesmatched)
4601 filesnotmatched.add(o[0]);
4605 if (filesnotmatched.size() > 0)
4607 if (assocfiles > 0 && (Cache.getDefault(
4608 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4609 || JvOptionPane.showConfirmDialog(thisaf,
4610 "<html>" + MessageManager.formatMessage(
4611 "label.ignore_unmatched_dropped_files_info",
4614 filesnotmatched.size())
4617 MessageManager.getString(
4618 "label.ignore_unmatched_dropped_files"),
4619 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4623 for (Object fn : filesnotmatched)
4625 loadJalviewDataFile(fn, null, null, null);
4629 } catch (Exception ex)
4631 ex.printStackTrace();
4639 * Attempt to load a "dropped" file or URL string, by testing in turn for
4641 * <li>an Annotation file</li>
4642 * <li>a JNet file</li>
4643 * <li>a features file</li>
4644 * <li>else try to interpret as an alignment file</li>
4648 * either a filename or a URL string.
4650 public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4651 FileFormatI format, SequenceI assocSeq)
4653 // BH 2018 was String file
4656 if (sourceType == null)
4658 sourceType = FormatAdapter.checkProtocol(file);
4660 // if the file isn't identified, or not positively identified as some
4661 // other filetype (PFAM is default unidentified alignment file type) then
4662 // try to parse as annotation.
4663 boolean isAnnotation = (format == null
4664 || FileFormat.Pfam.equals(format))
4665 ? new AnnotationFile().annotateAlignmentView(viewport,
4671 // first see if its a T-COFFEE score file
4672 TCoffeeScoreFile tcf = null;
4675 tcf = new TCoffeeScoreFile(file, sourceType);
4678 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4682 new TCoffeeColourScheme(viewport.getAlignment()));
4683 isAnnotation = true;
4684 statusBar.setText(MessageManager.getString(
4685 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4689 // some problem - if no warning its probable that the ID matching
4690 // process didn't work
4691 JvOptionPane.showMessageDialog(Desktop.desktop,
4692 tcf.getWarningMessage() == null
4693 ? MessageManager.getString(
4694 "label.check_file_matches_sequence_ids_alignment")
4695 : tcf.getWarningMessage(),
4696 MessageManager.getString(
4697 "label.problem_reading_tcoffee_score_file"),
4698 JvOptionPane.WARNING_MESSAGE);
4705 } catch (Exception x)
4708 "Exception when processing data source as T-COFFEE score file",
4714 // try to see if its a JNet 'concise' style annotation file *before*
4716 // try to parse it as a features file
4719 format = new IdentifyFile().identify(file, sourceType);
4721 if (FileFormat.ScoreMatrix == format)
4723 ScoreMatrixFile sm = new ScoreMatrixFile(
4724 new FileParse(file, sourceType));
4726 // todo: i18n this message
4727 statusBar.setText(MessageManager.formatMessage(
4728 "label.successfully_loaded_matrix",
4729 sm.getMatrixName()));
4731 else if (FileFormat.Jnet.equals(format))
4733 JPredFile predictions = new JPredFile(file, sourceType);
4734 new JnetAnnotationMaker();
4735 JnetAnnotationMaker.add_annotation(predictions,
4736 viewport.getAlignment(), 0, false);
4737 viewport.getAlignment().setupJPredAlignment();
4738 isAnnotation = true;
4740 // else if (IdentifyFile.FeaturesFile.equals(format))
4741 else if (FileFormat.Features.equals(format))
4743 if (parseFeaturesFile(file, sourceType))
4745 alignPanel.paintAlignment(true, true);
4750 new FileLoader().LoadFile(viewport, file, sourceType, format);
4757 alignPanel.adjustAnnotationHeight();
4758 viewport.updateSequenceIdColours();
4759 buildSortByAnnotationScoresMenu();
4760 alignPanel.paintAlignment(true, true);
4762 } catch (Exception ex)
4764 ex.printStackTrace();
4765 } catch (OutOfMemoryError oom)
4770 } catch (Exception x)
4775 + (sourceType != null
4776 ? (sourceType == DataSourceType.PASTE
4778 : "using " + sourceType + " from "
4782 ? "(parsing as '" + format + "' file)"
4784 oom, Desktop.desktop);
4789 * Method invoked by the ChangeListener on the tabbed pane, in other words
4790 * when a different tabbed pane is selected by the user or programmatically.
4793 public void tabSelectionChanged(int index)
4797 alignPanel = alignPanels.get(index);
4798 viewport = alignPanel.av;
4799 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4800 setMenusFromViewport(viewport);
4804 * 'focus' any colour slider that is open to the selected viewport
4806 if (viewport.getConservationSelected())
4808 SliderPanel.setConservationSlider(alignPanel,
4809 viewport.getResidueShading(), alignPanel.getViewName());
4813 SliderPanel.hideConservationSlider();
4815 if (viewport.getAbovePIDThreshold())
4817 SliderPanel.setPIDSliderSource(alignPanel,
4818 viewport.getResidueShading(), alignPanel.getViewName());
4822 SliderPanel.hidePIDSlider();
4826 * If there is a frame linked to this one in a SplitPane, switch it to the
4827 * same view tab index. No infinite recursion of calls should happen, since
4828 * tabSelectionChanged() should not get invoked on setting the selected
4829 * index to an unchanged value. Guard against setting an invalid index
4830 * before the new view peer tab has been created.
4832 final AlignViewportI peer = viewport.getCodingComplement();
4835 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4836 .getAlignPanel().alignFrame;
4837 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4839 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4845 * On right mouse click on view tab, prompt for and set new view name.
4848 public void tabbedPane_mousePressed(MouseEvent e)
4850 if (e.isPopupTrigger())
4852 String msg = MessageManager.getString("label.enter_view_name");
4853 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4854 JvOptionPane.QUESTION_MESSAGE);
4858 viewport.viewName = reply;
4859 // TODO warn if reply is in getExistingViewNames()?
4860 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4865 public AlignViewport getCurrentView()
4871 * Open the dialog for regex description parsing.
4874 protected void extractScores_actionPerformed(ActionEvent e)
4876 ParseProperties pp = new jalview.analysis.ParseProperties(
4877 viewport.getAlignment());
4878 // TODO: verify regex and introduce GUI dialog for version 2.5
4879 // if (pp.getScoresFromDescription("col", "score column ",
4880 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4882 if (pp.getScoresFromDescription("description column",
4883 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4885 buildSortByAnnotationScoresMenu();
4893 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4897 protected void showDbRefs_actionPerformed(ActionEvent e)
4899 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4905 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4909 protected void showNpFeats_actionPerformed(ActionEvent e)
4911 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4915 * find the viewport amongst the tabs in this alignment frame and close that
4920 public boolean closeView(AlignViewportI av)
4924 this.closeMenuItem_actionPerformed(false);
4927 Component[] comp = tabbedPane.getComponents();
4928 for (int i = 0; comp != null && i < comp.length; i++)
4930 if (comp[i] instanceof AlignmentPanel)
4932 if (((AlignmentPanel) comp[i]).av == av)
4935 closeView((AlignmentPanel) comp[i]);
4943 protected void build_fetchdbmenu(JMenu webService)
4945 // Temporary hack - DBRef Fetcher always top level ws entry.
4946 // TODO We probably want to store a sequence database checklist in
4947 // preferences and have checkboxes.. rather than individual sources selected
4949 final JMenu rfetch = new JMenu(
4950 MessageManager.getString("action.fetch_db_references"));
4951 rfetch.setToolTipText(MessageManager.getString(
4952 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4953 webService.add(rfetch);
4955 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4956 MessageManager.getString("option.trim_retrieved_seqs"));
4957 trimrs.setToolTipText(
4958 MessageManager.getString("label.trim_retrieved_sequences"));
4960 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4961 trimrs.addActionListener(new ActionListener()
4964 public void actionPerformed(ActionEvent e)
4966 trimrs.setSelected(trimrs.isSelected());
4967 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4968 Boolean.valueOf(trimrs.isSelected()).toString());
4972 JMenuItem fetchr = new JMenuItem(
4973 MessageManager.getString("label.standard_databases"));
4974 fetchr.setToolTipText(
4975 MessageManager.getString("label.fetch_embl_uniprot"));
4976 fetchr.addActionListener(new ActionListener()
4980 public void actionPerformed(ActionEvent e)
4982 new Thread(new Runnable()
4987 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4988 .getAlignment().isNucleotide();
4989 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4990 alignPanel.av.getSequenceSelection(),
4991 alignPanel.alignFrame, null,
4992 alignPanel.alignFrame.featureSettings, isNucleotide);
4993 dbRefFetcher.addListener(new FetchFinishedListenerI()
4996 public void finished()
4998 AlignFrame.this.setMenusForViewport();
5001 dbRefFetcher.fetchDBRefs(false);
5009 final AlignFrame me = this;
5010 new Thread(new Runnable()
5015 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5016 .getSequenceFetcherSingleton(me);
5017 javax.swing.SwingUtilities.invokeLater(new Runnable()
5022 String[] dbclasses = sf.getOrderedSupportedSources();
5023 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5024 // jalview.util.QuickSort.sort(otherdb, otherdb);
5025 List<DbSourceProxy> otherdb;
5026 JMenu dfetch = new JMenu();
5027 JMenu ifetch = new JMenu();
5028 JMenuItem fetchr = null;
5029 int comp = 0, icomp = 0, mcomp = 15;
5030 String mname = null;
5032 for (String dbclass : dbclasses)
5034 otherdb = sf.getSourceProxy(dbclass);
5035 // add a single entry for this class, or submenu allowing 'fetch
5037 if (otherdb == null || otherdb.size() < 1)
5041 // List<DbSourceProxy> dbs=otherdb;
5042 // otherdb=new ArrayList<DbSourceProxy>();
5043 // for (DbSourceProxy db:dbs)
5045 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5049 mname = "From " + dbclass;
5051 if (otherdb.size() == 1)
5053 final DbSourceProxy[] dassource = otherdb
5054 .toArray(new DbSourceProxy[0]);
5055 DbSourceProxy src = otherdb.get(0);
5056 fetchr = new JMenuItem(src.getDbSource());
5057 fetchr.addActionListener(new ActionListener()
5061 public void actionPerformed(ActionEvent e)
5063 new Thread(new Runnable()
5069 boolean isNucleotide = alignPanel.alignFrame
5070 .getViewport().getAlignment()
5072 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5073 alignPanel.av.getSequenceSelection(),
5074 alignPanel.alignFrame, dassource,
5075 alignPanel.alignFrame.featureSettings,
5078 .addListener(new FetchFinishedListenerI()
5081 public void finished()
5083 AlignFrame.this.setMenusForViewport();
5086 dbRefFetcher.fetchDBRefs(false);
5092 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5093 MessageManager.formatMessage(
5094 "label.fetch_retrieve_from", new Object[]
5095 { src.getDbName() })));
5101 final DbSourceProxy[] dassource = otherdb
5102 .toArray(new DbSourceProxy[0]);
5104 DbSourceProxy src = otherdb.get(0);
5105 fetchr = new JMenuItem(MessageManager
5106 .formatMessage("label.fetch_all_param", new Object[]
5107 { src.getDbSource() }));
5108 fetchr.addActionListener(new ActionListener()
5111 public void actionPerformed(ActionEvent e)
5113 new Thread(new Runnable()
5119 boolean isNucleotide = alignPanel.alignFrame
5120 .getViewport().getAlignment()
5122 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5123 alignPanel.av.getSequenceSelection(),
5124 alignPanel.alignFrame, dassource,
5125 alignPanel.alignFrame.featureSettings,
5128 .addListener(new FetchFinishedListenerI()
5131 public void finished()
5133 AlignFrame.this.setMenusForViewport();
5136 dbRefFetcher.fetchDBRefs(false);
5142 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5143 MessageManager.formatMessage(
5144 "label.fetch_retrieve_from_all_sources",
5146 { Integer.valueOf(otherdb.size())
5148 src.getDbSource(), src.getDbName() })));
5151 // and then build the rest of the individual menus
5152 ifetch = new JMenu(MessageManager.formatMessage(
5153 "label.source_from_db_source", new Object[]
5154 { src.getDbSource() }));
5156 String imname = null;
5158 for (DbSourceProxy sproxy : otherdb)
5160 String dbname = sproxy.getDbName();
5161 String sname = dbname.length() > 5
5162 ? dbname.substring(0, 5) + "..."
5164 String msname = dbname.length() > 10
5165 ? dbname.substring(0, 10) + "..."
5169 imname = MessageManager
5170 .formatMessage("label.from_msname", new Object[]
5173 fetchr = new JMenuItem(msname);
5174 final DbSourceProxy[] dassrc = { sproxy };
5175 fetchr.addActionListener(new ActionListener()
5179 public void actionPerformed(ActionEvent e)
5181 new Thread(new Runnable()
5187 boolean isNucleotide = alignPanel.alignFrame
5188 .getViewport().getAlignment()
5190 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5191 alignPanel.av.getSequenceSelection(),
5192 alignPanel.alignFrame, dassrc,
5193 alignPanel.alignFrame.featureSettings,
5196 .addListener(new FetchFinishedListenerI()
5199 public void finished()
5201 AlignFrame.this.setMenusForViewport();
5204 dbRefFetcher.fetchDBRefs(false);
5210 fetchr.setToolTipText(
5211 "<html>" + MessageManager.formatMessage(
5212 "label.fetch_retrieve_from", new Object[]
5216 if (++icomp >= mcomp || i == (otherdb.size()))
5218 ifetch.setText(MessageManager.formatMessage(
5219 "label.source_to_target", imname, sname));
5221 ifetch = new JMenu();
5229 if (comp >= mcomp || dbi >= (dbclasses.length))
5231 dfetch.setText(MessageManager.formatMessage(
5232 "label.source_to_target", mname, dbclass));
5234 dfetch = new JMenu();
5247 * Left justify the whole alignment.
5250 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5252 AlignmentI al = viewport.getAlignment();
5254 viewport.firePropertyChange("alignment", null, al);
5258 * Right justify the whole alignment.
5261 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5263 AlignmentI al = viewport.getAlignment();
5265 viewport.firePropertyChange("alignment", null, al);
5269 public void setShowSeqFeatures(boolean b)
5271 showSeqFeatures.setSelected(b);
5272 viewport.setShowSequenceFeatures(b);
5279 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5280 * awt.event.ActionEvent)
5283 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5285 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5286 alignPanel.paintAlignment(false, false);
5293 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5297 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5299 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5300 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5308 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5309 * .event.ActionEvent)
5312 protected void showGroupConservation_actionPerformed(ActionEvent e)
5314 viewport.setShowGroupConservation(showGroupConservation.getState());
5315 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5322 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5323 * .event.ActionEvent)
5326 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5328 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5329 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5336 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5337 * .event.ActionEvent)
5340 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5342 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5343 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5347 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5349 showSequenceLogo.setState(true);
5350 viewport.setShowSequenceLogo(true);
5351 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5352 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5356 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5358 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5365 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5366 * .event.ActionEvent)
5369 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5371 if (avc.makeGroupsFromSelection())
5373 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5374 alignPanel.updateAnnotation();
5375 alignPanel.paintAlignment(true, true);
5379 public void clearAlignmentSeqRep()
5381 // TODO refactor alignmentseqrep to controller
5382 if (viewport.getAlignment().hasSeqrep())
5384 viewport.getAlignment().setSeqrep(null);
5385 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5386 alignPanel.updateAnnotation();
5387 alignPanel.paintAlignment(true, true);
5392 protected void createGroup_actionPerformed(ActionEvent e)
5394 if (avc.createGroup())
5396 alignPanel.alignmentChanged();
5401 protected void unGroup_actionPerformed(ActionEvent e)
5405 alignPanel.alignmentChanged();
5410 * make the given alignmentPanel the currently selected tab
5412 * @param alignmentPanel
5414 public void setDisplayedView(AlignmentPanel alignmentPanel)
5416 if (!viewport.getSequenceSetId()
5417 .equals(alignmentPanel.av.getSequenceSetId()))
5419 throw new Error(MessageManager.getString(
5420 "error.implementation_error_cannot_show_view_alignment_frame"));
5422 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5423 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5425 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5430 * Action on selection of menu options to Show or Hide annotations.
5433 * @param forSequences
5434 * update sequence-related annotations
5435 * @param forAlignment
5436 * update non-sequence-related annotations
5439 protected void setAnnotationsVisibility(boolean visible,
5440 boolean forSequences, boolean forAlignment)
5442 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5443 .getAlignmentAnnotation();
5448 for (AlignmentAnnotation aa : anns)
5451 * don't display non-positional annotations on an alignment
5453 if (aa.annotations == null)
5457 boolean apply = (aa.sequenceRef == null && forAlignment)
5458 || (aa.sequenceRef != null && forSequences);
5461 aa.visible = visible;
5464 alignPanel.validateAnnotationDimensions(true);
5465 alignPanel.alignmentChanged();
5469 * Store selected annotation sort order for the view and repaint.
5472 protected void sortAnnotations_actionPerformed()
5474 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5476 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5477 alignPanel.paintAlignment(false, false);
5482 * @return alignment panels in this alignment frame
5484 public List<? extends AlignmentViewPanel> getAlignPanels()
5486 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5490 * Open a new alignment window, with the cDNA associated with this (protein)
5491 * alignment, aligned as is the protein.
5493 protected void viewAsCdna_actionPerformed()
5495 // TODO no longer a menu action - refactor as required
5496 final AlignmentI alignment = getViewport().getAlignment();
5497 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5498 if (mappings == null)
5502 List<SequenceI> cdnaSeqs = new ArrayList<>();
5503 for (SequenceI aaSeq : alignment.getSequences())
5505 for (AlignedCodonFrame acf : mappings)
5507 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5511 * There is a cDNA mapping for this protein sequence - add to new
5512 * alignment. It will share the same dataset sequence as other mapped
5513 * cDNA (no new mappings need to be created).
5515 final Sequence newSeq = new Sequence(dnaSeq);
5516 newSeq.setDatasetSequence(dnaSeq);
5517 cdnaSeqs.add(newSeq);
5521 if (cdnaSeqs.size() == 0)
5523 // show a warning dialog no mapped cDNA
5526 AlignmentI cdna = new Alignment(
5527 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5528 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5529 AlignFrame.DEFAULT_HEIGHT);
5530 cdna.alignAs(alignment);
5531 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5533 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5534 AlignFrame.DEFAULT_HEIGHT);
5538 * Set visibility of dna/protein complement view (available when shown in a
5544 protected void showComplement_actionPerformed(boolean show)
5546 SplitContainerI sf = getSplitViewContainer();
5549 sf.setComplementVisible(this, show);
5554 * Generate the reverse (optionally complemented) of the selected sequences,
5555 * and add them to the alignment
5558 protected void showReverse_actionPerformed(boolean complement)
5560 AlignmentI al = null;
5563 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5564 al = dna.reverseCdna(complement);
5565 viewport.addAlignment(al, "");
5566 addHistoryItem(new EditCommand(
5567 MessageManager.getString("label.add_sequences"), Action.PASTE,
5568 al.getSequencesArray(), 0, al.getWidth(),
5569 viewport.getAlignment()));
5570 } catch (Exception ex)
5572 System.err.println(ex.getMessage());
5578 * Try to run a script in the Groovy console, having first ensured that this
5579 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5580 * be targeted at this alignment.
5583 protected void runGroovy_actionPerformed()
5585 Jalview.setCurrentAlignFrame(this);
5586 groovy.ui.Console console = Desktop.getGroovyConsole();
5587 if (console != null)
5591 console.runScript();
5592 } catch (Exception ex)
5594 System.err.println((ex.toString()));
5595 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5596 MessageManager.getString("label.couldnt_run_groovy_script"),
5597 MessageManager.getString("label.groovy_support_failed"),
5598 JvOptionPane.ERROR_MESSAGE);
5603 System.err.println("Can't run Groovy script as console not found");
5608 * Hides columns containing (or not containing) a specified feature, provided
5609 * that would not leave all columns hidden
5611 * @param featureType
5612 * @param columnsContaining
5615 public boolean hideFeatureColumns(String featureType,
5616 boolean columnsContaining)
5618 boolean notForHiding = avc.markColumnsContainingFeatures(
5619 columnsContaining, false, false, featureType);
5622 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5623 false, featureType))
5625 getViewport().hideSelectedColumns();
5633 protected void selectHighlightedColumns_actionPerformed(
5634 ActionEvent actionEvent)
5636 // include key modifier check in case user selects from menu
5637 avc.markHighlightedColumns(
5638 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5639 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5640 | ActionEvent.CTRL_MASK)) != 0);
5644 * Rebuilds the Colour menu, including any user-defined colours which have
5645 * been loaded either on startup or during the session
5647 public void buildColourMenu()
5649 colourMenu.removeAll();
5651 colourMenu.add(applyToAllGroups);
5652 colourMenu.add(textColour);
5653 colourMenu.addSeparator();
5655 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5658 colourMenu.addSeparator();
5659 colourMenu.add(conservationMenuItem);
5660 colourMenu.add(modifyConservation);
5661 colourMenu.add(abovePIDThreshold);
5662 colourMenu.add(modifyPID);
5663 colourMenu.add(annotationColour);
5665 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5666 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5670 * Open a dialog (if not already open) that allows the user to select and
5671 * calculate PCA or Tree analysis
5673 protected void openTreePcaDialog()
5675 if (alignPanel.getCalculationDialog() == null)
5677 new CalculationChooser(AlignFrame.this);
5682 protected void loadVcf_actionPerformed()
5684 JalviewFileChooser chooser = new JalviewFileChooser(
5685 Cache.getProperty("LAST_DIRECTORY"));
5686 chooser.setFileView(new JalviewFileView());
5687 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5688 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5689 final AlignFrame us = this;
5690 chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
5697 String choice = chooser.getSelectedFile().getPath();
5698 Cache.setProperty("LAST_DIRECTORY", choice);
5699 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5700 new VCFLoader(choice).loadVCF(seqs, us);
5704 }).openDialog(null);
5710 class PrintThread extends Thread
5714 public PrintThread(AlignmentPanel ap)
5719 static PageFormat pf;
5724 PrinterJob printJob = PrinterJob.getPrinterJob();
5728 printJob.setPrintable(ap, pf);
5732 printJob.setPrintable(ap);
5735 if (printJob.printDialog())
5740 } catch (Exception PrintException)
5742 PrintException.printStackTrace();