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.viewmodel.AlignmentViewport;
92 import jalview.viewmodel.ViewportRanges;
93 import jalview.ws.DBRefFetcher;
94 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
95 import jalview.ws.jws1.Discoverer;
96 import jalview.ws.jws2.Jws2Discoverer;
97 import jalview.ws.jws2.jabaws2.Jws2Instance;
98 import jalview.ws.seqfetcher.DbSourceProxy;
100 import java.awt.BorderLayout;
101 import java.awt.Component;
102 import java.awt.Rectangle;
103 import java.awt.Toolkit;
104 import java.awt.datatransfer.Clipboard;
105 import java.awt.datatransfer.DataFlavor;
106 import java.awt.datatransfer.StringSelection;
107 import java.awt.datatransfer.Transferable;
108 import java.awt.dnd.DnDConstants;
109 import java.awt.dnd.DropTargetDragEvent;
110 import java.awt.dnd.DropTargetDropEvent;
111 import java.awt.dnd.DropTargetEvent;
112 import java.awt.dnd.DropTargetListener;
113 import java.awt.event.ActionEvent;
114 import java.awt.event.ActionListener;
115 import java.awt.event.FocusAdapter;
116 import java.awt.event.FocusEvent;
117 import java.awt.event.ItemEvent;
118 import java.awt.event.ItemListener;
119 import java.awt.event.KeyAdapter;
120 import java.awt.event.KeyEvent;
121 import java.awt.event.MouseEvent;
122 import java.awt.print.PageFormat;
123 import java.awt.print.PrinterJob;
124 import java.beans.PropertyChangeEvent;
126 import java.io.FileWriter;
127 import java.io.PrintWriter;
129 import java.util.ArrayList;
130 import java.util.Arrays;
131 import java.util.Deque;
132 import java.util.Enumeration;
133 import java.util.Hashtable;
134 import java.util.List;
135 import java.util.Vector;
137 import javax.swing.JCheckBoxMenuItem;
138 import javax.swing.JEditorPane;
139 import javax.swing.JInternalFrame;
140 import javax.swing.JLayeredPane;
141 import javax.swing.JMenu;
142 import javax.swing.JMenuItem;
143 import javax.swing.JScrollPane;
144 import javax.swing.SwingUtilities;
150 * @version $Revision$
152 public class AlignFrame extends GAlignFrame implements DropTargetListener,
153 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
156 public static final int DEFAULT_WIDTH = 700;
158 public static final int DEFAULT_HEIGHT = 500;
161 * The currently displayed panel (selected tabbed view if more than one)
163 public AlignmentPanel alignPanel;
165 AlignViewport viewport;
167 ViewportRanges vpRanges;
169 public AlignViewControllerI avc;
171 List<AlignmentPanel> alignPanels = new ArrayList<>();
174 * Last format used to load or save alignments in this window
176 FileFormatI currentFileFormat = null;
179 * Current filename for this alignment
181 String fileName = null;
184 * Creates a new AlignFrame object with specific width and height.
190 public AlignFrame(AlignmentI al, int width, int height)
192 this(al, null, width, height);
196 * Creates a new AlignFrame object with specific width, height and
202 * @param sequenceSetId
204 public AlignFrame(AlignmentI al, int width, int height,
205 String sequenceSetId)
207 this(al, null, width, height, sequenceSetId);
211 * Creates a new AlignFrame object with specific width, height and
217 * @param sequenceSetId
220 public AlignFrame(AlignmentI al, int width, int height,
221 String sequenceSetId, String viewId)
223 this(al, null, width, height, sequenceSetId, viewId);
227 * new alignment window with hidden columns
231 * @param hiddenColumns
232 * ColumnSelection or null
234 * Width of alignment frame
238 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
241 this(al, hiddenColumns, width, height, null);
245 * Create alignment frame for al with hiddenColumns, a specific width and
246 * height, and specific sequenceId
249 * @param hiddenColumns
252 * @param sequenceSetId
255 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
256 int height, String sequenceSetId)
258 this(al, hiddenColumns, width, height, sequenceSetId, null);
262 * Create alignment frame for al with hiddenColumns, a specific width and
263 * height, and specific sequenceId
266 * @param hiddenColumns
269 * @param sequenceSetId
274 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
275 int height, String sequenceSetId, String viewId)
277 setSize(width, height);
279 if (al.getDataset() == null)
284 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
286 alignPanel = new AlignmentPanel(this, viewport);
288 addAlignmentPanel(alignPanel, true);
292 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
293 HiddenColumns hiddenColumns, int width, int height)
295 setSize(width, height);
297 if (al.getDataset() == null)
302 viewport = new AlignViewport(al, hiddenColumns);
304 if (hiddenSeqs != null && hiddenSeqs.length > 0)
306 viewport.hideSequence(hiddenSeqs);
308 alignPanel = new AlignmentPanel(this, viewport);
309 addAlignmentPanel(alignPanel, true);
314 * Make a new AlignFrame from existing alignmentPanels
321 public AlignFrame(AlignmentPanel ap)
325 addAlignmentPanel(ap, false);
330 * initalise the alignframe from the underlying viewport data and the
335 if (!Jalview.isHeadlessMode())
337 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
340 vpRanges = viewport.getRanges();
341 avc = new jalview.controller.AlignViewController(this, viewport,
343 if (viewport.getAlignmentConservationAnnotation() == null)
345 // BLOSUM62Colour.setEnabled(false);
346 conservationMenuItem.setEnabled(false);
347 modifyConservation.setEnabled(false);
348 // PIDColour.setEnabled(false);
349 // abovePIDThreshold.setEnabled(false);
350 // modifyPID.setEnabled(false);
353 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
356 if (sortby.equals("Id"))
358 sortIDMenuItem_actionPerformed(null);
360 else if (sortby.equals("Pairwise Identity"))
362 sortPairwiseMenuItem_actionPerformed(null);
366 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
368 setMenusFromViewport(viewport);
369 buildSortByAnnotationScoresMenu();
370 calculateTree.addActionListener(new ActionListener()
374 public void actionPerformed(ActionEvent e)
381 if (Desktop.desktop != null)
383 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
384 addServiceListeners();
388 if (viewport.getWrapAlignment())
390 wrapMenuItem_actionPerformed(null);
393 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
395 this.overviewMenuItem_actionPerformed(null);
400 final List<AlignmentPanel> selviews = new ArrayList<>();
401 final List<AlignmentPanel> origview = new ArrayList<>();
402 final String menuLabel = MessageManager
403 .getString("label.copy_format_from");
404 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
405 new ViewSetProvider()
409 public AlignmentPanel[] getAllAlignmentPanels()
412 origview.add(alignPanel);
413 // make an array of all alignment panels except for this one
414 List<AlignmentPanel> aps = new ArrayList<>(
415 Arrays.asList(Desktop.getAlignmentPanels(null)));
416 aps.remove(AlignFrame.this.alignPanel);
417 return aps.toArray(new AlignmentPanel[aps.size()]);
419 }, selviews, new ItemListener()
423 public void itemStateChanged(ItemEvent e)
425 if (origview.size() > 0)
427 final AlignmentPanel ap = origview.get(0);
430 * Copy the ViewStyle of the selected panel to 'this one'.
431 * Don't change value of 'scaleProteinAsCdna' unless copying
434 ViewStyleI vs = selviews.get(0).getAlignViewport()
436 boolean fromSplitFrame = selviews.get(0)
437 .getAlignViewport().getCodingComplement() != null;
440 vs.setScaleProteinAsCdna(ap.getAlignViewport()
441 .getViewStyle().isScaleProteinAsCdna());
443 ap.getAlignViewport().setViewStyle(vs);
446 * Also rescale ViewStyle of SplitFrame complement if there is
447 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
448 * the whole ViewStyle (allow cDNA protein to have different
451 AlignViewportI complement = ap.getAlignViewport()
452 .getCodingComplement();
453 if (complement != null && vs.isScaleProteinAsCdna())
455 AlignFrame af = Desktop.getAlignFrameFor(complement);
456 ((SplitFrame) af.getSplitViewContainer())
458 af.setMenusForViewport();
462 ap.setSelected(true);
463 ap.alignFrame.setMenusForViewport();
468 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
469 .indexOf("devel") > -1
470 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
471 .indexOf("test") > -1)
473 formatMenu.add(vsel);
475 addFocusListener(new FocusAdapter()
478 public void focusGained(FocusEvent e)
480 Jalview.setCurrentAlignFrame(AlignFrame.this);
487 * Change the filename and format for the alignment, and enable the 'reload'
488 * button functionality.
495 public void setFileName(String file, FileFormatI format)
498 setFileFormat(format);
499 reload.setEnabled(true);
503 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
506 void addKeyListener()
508 addKeyListener(new KeyAdapter()
511 public void keyPressed(KeyEvent evt)
513 if (viewport.cursorMode
514 && ((evt.getKeyCode() >= KeyEvent.VK_0
515 && evt.getKeyCode() <= KeyEvent.VK_9)
516 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
517 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
518 && Character.isDigit(evt.getKeyChar()))
520 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
523 switch (evt.getKeyCode())
526 case 27: // escape key
527 deselectAllSequenceMenuItem_actionPerformed(null);
531 case KeyEvent.VK_DOWN:
532 if (evt.isAltDown() || !viewport.cursorMode)
534 moveSelectedSequences(false);
536 if (viewport.cursorMode)
538 alignPanel.getSeqPanel().moveCursor(0, 1);
543 if (evt.isAltDown() || !viewport.cursorMode)
545 moveSelectedSequences(true);
547 if (viewport.cursorMode)
549 alignPanel.getSeqPanel().moveCursor(0, -1);
554 case KeyEvent.VK_LEFT:
555 if (evt.isAltDown() || !viewport.cursorMode)
557 slideSequences(false,
558 alignPanel.getSeqPanel().getKeyboardNo1());
562 alignPanel.getSeqPanel().moveCursor(-1, 0);
567 case KeyEvent.VK_RIGHT:
568 if (evt.isAltDown() || !viewport.cursorMode)
570 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
574 alignPanel.getSeqPanel().moveCursor(1, 0);
578 case KeyEvent.VK_SPACE:
579 if (viewport.cursorMode)
581 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
582 || evt.isShiftDown() || evt.isAltDown());
586 // case KeyEvent.VK_A:
587 // if (viewport.cursorMode)
589 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
590 // //System.out.println("A");
594 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
595 * System.out.println("closing bracket"); } break;
597 case KeyEvent.VK_DELETE:
598 case KeyEvent.VK_BACK_SPACE:
599 if (!viewport.cursorMode)
601 cut_actionPerformed(null);
605 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
606 || evt.isShiftDown() || evt.isAltDown());
612 if (viewport.cursorMode)
614 alignPanel.getSeqPanel().setCursorRow();
618 if (viewport.cursorMode && !evt.isControlDown())
620 alignPanel.getSeqPanel().setCursorColumn();
624 if (viewport.cursorMode)
626 alignPanel.getSeqPanel().setCursorPosition();
630 case KeyEvent.VK_ENTER:
631 case KeyEvent.VK_COMMA:
632 if (viewport.cursorMode)
634 alignPanel.getSeqPanel().setCursorRowAndColumn();
639 if (viewport.cursorMode)
641 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
645 if (viewport.cursorMode)
647 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
652 viewport.cursorMode = !viewport.cursorMode;
653 statusBar.setText(MessageManager
654 .formatMessage("label.keyboard_editing_mode", new String[]
655 { (viewport.cursorMode ? "on" : "off") }));
656 if (viewport.cursorMode)
658 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
660 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
663 alignPanel.getSeqPanel().seqCanvas.repaint();
669 Help.showHelpWindow();
670 } catch (Exception ex)
672 ex.printStackTrace();
677 boolean toggleSeqs = !evt.isControlDown();
678 boolean toggleCols = !evt.isShiftDown();
679 toggleHiddenRegions(toggleSeqs, toggleCols);
684 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
685 boolean modifyExisting = true; // always modify, don't clear
686 // evt.isShiftDown();
687 boolean invertHighlighted = evt.isAltDown();
688 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
692 case KeyEvent.VK_PAGE_UP:
695 case KeyEvent.VK_PAGE_DOWN:
702 public void keyReleased(KeyEvent evt)
704 switch (evt.getKeyCode())
706 case KeyEvent.VK_LEFT:
707 if (evt.isAltDown() || !viewport.cursorMode)
709 viewport.firePropertyChange("alignment", null,
710 viewport.getAlignment().getSequences());
714 case KeyEvent.VK_RIGHT:
715 if (evt.isAltDown() || !viewport.cursorMode)
717 viewport.firePropertyChange("alignment", null,
718 viewport.getAlignment().getSequences());
726 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
728 ap.alignFrame = this;
729 avc = new jalview.controller.AlignViewController(this, viewport,
734 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
736 int aSize = alignPanels.size();
738 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
740 if (aSize == 1 && ap.av.viewName == null)
742 this.getContentPane().add(ap, BorderLayout.CENTER);
748 setInitialTabVisible();
751 expandViews.setEnabled(true);
752 gatherViews.setEnabled(true);
753 tabbedPane.addTab(ap.av.viewName, ap);
755 ap.setVisible(false);
760 if (ap.av.isPadGaps())
762 ap.av.getAlignment().padGaps();
764 ap.av.updateConservation(ap);
765 ap.av.updateConsensus(ap);
766 ap.av.updateStrucConsensus(ap);
770 public void setInitialTabVisible()
772 expandViews.setEnabled(true);
773 gatherViews.setEnabled(true);
774 tabbedPane.setVisible(true);
775 AlignmentPanel first = alignPanels.get(0);
776 tabbedPane.addTab(first.av.viewName, first);
777 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
780 public AlignViewport getViewport()
785 /* Set up intrinsic listeners for dynamically generated GUI bits. */
786 private void addServiceListeners()
788 final java.beans.PropertyChangeListener thisListener;
789 Desktop.instance.addJalviewPropertyChangeListener("services",
790 thisListener = new java.beans.PropertyChangeListener()
793 public void propertyChange(PropertyChangeEvent evt)
795 // // System.out.println("Discoverer property change.");
796 // if (evt.getPropertyName().equals("services"))
798 SwingUtilities.invokeLater(new Runnable()
805 "Rebuild WS Menu for service change");
806 BuildWebServiceMenu();
813 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
816 public void internalFrameClosed(
817 javax.swing.event.InternalFrameEvent evt)
819 // System.out.println("deregistering discoverer listener");
820 Desktop.instance.removeJalviewPropertyChangeListener("services",
822 closeMenuItem_actionPerformed(true);
825 // Finally, build the menu once to get current service state
826 new Thread(new Runnable()
831 BuildWebServiceMenu();
837 * Configure menu items that vary according to whether the alignment is
838 * nucleotide or protein
840 public void setGUINucleotide()
842 AlignmentI al = getViewport().getAlignment();
843 boolean nucleotide = al.isNucleotide();
845 loadVcf.setVisible(nucleotide);
846 showTranslation.setVisible(nucleotide);
847 showReverse.setVisible(nucleotide);
848 showReverseComplement.setVisible(nucleotide);
849 conservationMenuItem.setEnabled(!nucleotide);
851 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
852 showGroupConservation.setEnabled(!nucleotide);
854 showComplementMenuItem
855 .setText(nucleotide ? MessageManager.getString("label.protein")
856 : MessageManager.getString("label.nucleotide"));
860 * set up menus for the current viewport. This may be called after any
861 * operation that affects the data in the current view (selection changed,
862 * etc) to update the menus to reflect the new state.
865 public void setMenusForViewport()
867 setMenusFromViewport(viewport);
871 * Need to call this method when tabs are selected for multiple views, or when
872 * loading from Jalview2XML.java
877 void setMenusFromViewport(AlignViewport av)
879 padGapsMenuitem.setSelected(av.isPadGaps());
880 colourTextMenuItem.setSelected(av.isShowColourText());
881 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
882 modifyPID.setEnabled(abovePIDThreshold.isSelected());
883 conservationMenuItem.setSelected(av.getConservationSelected());
884 modifyConservation.setEnabled(conservationMenuItem.isSelected());
885 seqLimits.setSelected(av.getShowJVSuffix());
886 idRightAlign.setSelected(av.isRightAlignIds());
887 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
888 renderGapsMenuItem.setSelected(av.isRenderGaps());
889 wrapMenuItem.setSelected(av.getWrapAlignment());
890 scaleAbove.setVisible(av.getWrapAlignment());
891 scaleLeft.setVisible(av.getWrapAlignment());
892 scaleRight.setVisible(av.getWrapAlignment());
893 annotationPanelMenuItem.setState(av.isShowAnnotation());
895 * Show/hide annotations only enabled if annotation panel is shown
897 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
898 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
899 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
900 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
901 viewBoxesMenuItem.setSelected(av.getShowBoxes());
902 viewTextMenuItem.setSelected(av.getShowText());
903 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
904 showGroupConsensus.setSelected(av.isShowGroupConsensus());
905 showGroupConservation.setSelected(av.isShowGroupConservation());
906 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
907 showSequenceLogo.setSelected(av.isShowSequenceLogo());
908 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
910 ColourMenuHelper.setColourSelected(colourMenu,
911 av.getGlobalColourScheme());
913 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
914 hiddenMarkers.setState(av.getShowHiddenMarkers());
915 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
916 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
917 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
918 autoCalculate.setSelected(av.autoCalculateConsensus);
919 sortByTree.setSelected(av.sortByTree);
920 listenToViewSelections.setSelected(av.followSelection);
922 showProducts.setEnabled(canShowProducts());
923 setGroovyEnabled(Desktop.getGroovyConsole() != null);
929 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
933 public void setGroovyEnabled(boolean b)
935 runGroovy.setEnabled(b);
938 private IProgressIndicator progressBar;
943 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
946 public void setProgressBar(String message, long id)
948 progressBar.setProgressBar(message, id);
952 public void registerHandler(final long id,
953 final IProgressIndicatorHandler handler)
955 progressBar.registerHandler(id, handler);
960 * @return true if any progress bars are still active
963 public boolean operationInProgress()
965 return progressBar.operationInProgress();
969 public void setStatus(String text)
971 statusBar.setText(text);
975 * Added so Castor Mapping file can obtain Jalview Version
977 public String getVersion()
979 return jalview.bin.Cache.getProperty("VERSION");
982 public FeatureRenderer getFeatureRenderer()
984 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
988 public void fetchSequence_actionPerformed(ActionEvent e)
990 new jalview.gui.SequenceFetcher(this);
994 public void addFromFile_actionPerformed(ActionEvent e)
996 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1000 public void reload_actionPerformed(ActionEvent e)
1002 if (fileName != null)
1004 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1005 // originating file's format
1006 // TODO: work out how to recover feature settings for correct view(s) when
1007 // file is reloaded.
1008 if (FileFormat.Jalview.equals(currentFileFormat))
1010 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1011 for (int i = 0; i < frames.length; i++)
1013 if (frames[i] instanceof AlignFrame && frames[i] != this
1014 && ((AlignFrame) frames[i]).fileName != null
1015 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1019 frames[i].setSelected(true);
1020 Desktop.instance.closeAssociatedWindows();
1021 } catch (java.beans.PropertyVetoException ex)
1027 Desktop.instance.closeAssociatedWindows();
1029 FileLoader loader = new FileLoader();
1030 DataSourceType protocol = fileName.startsWith("http:")
1031 ? DataSourceType.URL
1032 : DataSourceType.FILE;
1033 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1037 Rectangle bounds = this.getBounds();
1039 FileLoader loader = new FileLoader();
1040 DataSourceType protocol = fileName.startsWith("http:")
1041 ? DataSourceType.URL
1042 : DataSourceType.FILE;
1043 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1044 protocol, currentFileFormat);
1046 newframe.setBounds(bounds);
1047 if (featureSettings != null && featureSettings.isShowing())
1049 final Rectangle fspos = featureSettings.frame.getBounds();
1050 // TODO: need a 'show feature settings' function that takes bounds -
1051 // need to refactor Desktop.addFrame
1052 newframe.featureSettings_actionPerformed(null);
1053 final FeatureSettings nfs = newframe.featureSettings;
1054 SwingUtilities.invokeLater(new Runnable()
1059 nfs.frame.setBounds(fspos);
1062 this.featureSettings.close();
1063 this.featureSettings = null;
1065 this.closeMenuItem_actionPerformed(true);
1071 public void addFromText_actionPerformed(ActionEvent e)
1074 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1078 public void addFromURL_actionPerformed(ActionEvent e)
1080 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1084 public void save_actionPerformed(ActionEvent e)
1086 if (fileName == null || (currentFileFormat == null)
1087 || fileName.startsWith("http"))
1089 saveAs_actionPerformed(null);
1093 saveAlignment(fileName, currentFileFormat);
1104 public void saveAs_actionPerformed(ActionEvent e)
1106 String format = currentFileFormat == null ? null
1107 : currentFileFormat.getName();
1108 JalviewFileChooser chooser = JalviewFileChooser
1109 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1111 chooser.setFileView(new JalviewFileView());
1112 chooser.setDialogTitle(
1113 MessageManager.getString("label.save_alignment_to_file"));
1114 chooser.setToolTipText(MessageManager.getString("action.save"));
1116 int value = chooser.showSaveDialog(this);
1118 if (value == JalviewFileChooser.APPROVE_OPTION)
1120 currentFileFormat = chooser.getSelectedFormat();
1121 while (currentFileFormat == null)
1123 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1124 MessageManager.getString(
1125 "label.select_file_format_before_saving"),
1126 MessageManager.getString("label.file_format_not_specified"),
1127 JvOptionPane.WARNING_MESSAGE);
1128 currentFileFormat = chooser.getSelectedFormat();
1129 value = chooser.showSaveDialog(this);
1130 if (value != JalviewFileChooser.APPROVE_OPTION)
1136 fileName = chooser.getSelectedFile().getPath();
1138 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1140 Cache.setProperty("LAST_DIRECTORY", fileName);
1141 saveAlignment(fileName, currentFileFormat);
1145 public boolean saveAlignment(String file, FileFormatI format)
1147 boolean success = true;
1149 if (FileFormat.Jalview.equals(format))
1151 String shortName = title;
1153 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1155 shortName = shortName.substring(
1156 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1159 success = new Jalview2XML().saveAlignment(this, file, shortName);
1161 statusBar.setText(MessageManager.formatMessage(
1162 "label.successfully_saved_to_file_in_format", new Object[]
1163 { fileName, format }));
1168 AlignmentExportData exportData = getAlignmentForExport(format,
1170 if (exportData.getSettings().isCancelled())
1174 FormatAdapter f = new FormatAdapter(alignPanel,
1175 exportData.getSettings());
1176 String output = f.formatSequences(format, exportData.getAlignment(), // class
1180 // occur in the distant future
1181 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1182 f.getCacheSuffixDefault(format),
1183 viewport.getAlignment().getHiddenColumns());
1193 PrintWriter out = new PrintWriter(new FileWriter(file));
1197 this.setTitle(file);
1198 statusBar.setText(MessageManager.formatMessage(
1199 "label.successfully_saved_to_file_in_format", new Object[]
1200 { fileName, format.getName() }));
1201 } catch (Exception ex)
1204 ex.printStackTrace();
1211 JvOptionPane.showInternalMessageDialog(this, MessageManager
1212 .formatMessage("label.couldnt_save_file", new Object[]
1214 MessageManager.getString("label.error_saving_file"),
1215 JvOptionPane.WARNING_MESSAGE);
1221 private void warningMessage(String warning, String title)
1223 if (new jalview.util.Platform().isHeadless())
1225 System.err.println("Warning: " + title + "\nWarning: " + warning);
1230 JvOptionPane.showInternalMessageDialog(this, warning, title,
1231 JvOptionPane.WARNING_MESSAGE);
1243 protected void outputText_actionPerformed(ActionEvent e)
1245 FileFormatI fileFormat = FileFormats.getInstance()
1246 .forName(e.getActionCommand());
1247 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1249 if (exportData.getSettings().isCancelled())
1253 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1254 cap.setForInput(null);
1257 FileFormatI format = fileFormat;
1258 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1259 .formatSequences(format, exportData.getAlignment(),
1260 exportData.getOmitHidden(),
1261 exportData.getStartEndPostions(),
1262 viewport.getAlignment().getHiddenColumns()));
1263 Desktop.addInternalFrame(cap, MessageManager
1264 .formatMessage("label.alignment_output_command", new Object[]
1265 { e.getActionCommand() }), 600, 500);
1266 } catch (OutOfMemoryError oom)
1268 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1275 public static AlignmentExportData getAlignmentForExport(
1276 FileFormatI format, AlignViewportI viewport,
1277 AlignExportSettingI exportSettings)
1279 AlignmentI alignmentToExport = null;
1280 AlignExportSettingI settings = exportSettings;
1281 String[] omitHidden = null;
1283 HiddenSequences hiddenSeqs = viewport.getAlignment()
1284 .getHiddenSequences();
1286 alignmentToExport = viewport.getAlignment();
1288 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1289 if (settings == null)
1291 settings = new AlignExportSettings(hasHiddenSeqs,
1292 viewport.hasHiddenColumns(), format);
1294 // settings.isExportAnnotations();
1296 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1298 omitHidden = viewport.getViewAsString(false,
1299 settings.isExportHiddenSequences());
1302 int[] alignmentStartEnd = new int[2];
1303 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1305 alignmentToExport = hiddenSeqs.getFullAlignment();
1309 alignmentToExport = viewport.getAlignment();
1311 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1312 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1313 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1314 omitHidden, alignmentStartEnd, settings);
1325 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1327 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1328 htmlSVG.exportHTML(null);
1332 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1334 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1335 bjs.exportHTML(null);
1338 public void createImageMap(File file, String image)
1340 alignPanel.makePNGImageMap(file, image);
1350 public void createPNG(File f)
1352 alignPanel.makePNG(f);
1362 public void createEPS(File f)
1364 alignPanel.makeEPS(f);
1368 public void createSVG(File f)
1370 alignPanel.makeSVG(f);
1374 public void pageSetup_actionPerformed(ActionEvent e)
1376 PrinterJob printJob = PrinterJob.getPrinterJob();
1377 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1387 public void printMenuItem_actionPerformed(ActionEvent e)
1389 // Putting in a thread avoids Swing painting problems
1390 PrintThread thread = new PrintThread(alignPanel);
1395 public void exportFeatures_actionPerformed(ActionEvent e)
1397 new AnnotationExporter().exportFeatures(alignPanel);
1401 public void exportAnnotations_actionPerformed(ActionEvent e)
1403 new AnnotationExporter().exportAnnotations(alignPanel);
1407 public void associatedData_actionPerformed(ActionEvent e)
1409 // Pick the tree file
1410 JalviewFileChooser chooser = new JalviewFileChooser(
1411 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1412 chooser.setFileView(new JalviewFileView());
1413 chooser.setDialogTitle(
1414 MessageManager.getString("label.load_jalview_annotations"));
1415 chooser.setToolTipText(
1416 MessageManager.getString("label.load_jalview_annotations"));
1418 int value = chooser.showOpenDialog(null);
1420 if (value == JalviewFileChooser.APPROVE_OPTION)
1422 String choice = chooser.getSelectedFile().getPath();
1423 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1424 loadJalviewDataFile(choice, null, null, null);
1430 * Close the current view or all views in the alignment frame. If the frame
1431 * only contains one view then the alignment will be removed from memory.
1433 * @param closeAllTabs
1436 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1438 if (alignPanels != null && alignPanels.size() < 2)
1440 closeAllTabs = true;
1445 if (alignPanels != null)
1449 if (this.isClosed())
1451 // really close all the windows - otherwise wait till
1452 // setClosed(true) is called
1453 for (int i = 0; i < alignPanels.size(); i++)
1455 AlignmentPanel ap = alignPanels.get(i);
1462 closeView(alignPanel);
1469 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1470 * be called recursively, with the frame now in 'closed' state
1472 this.setClosed(true);
1474 } catch (Exception ex)
1476 ex.printStackTrace();
1481 * Close the specified panel and close up tabs appropriately.
1483 * @param panelToClose
1485 public void closeView(AlignmentPanel panelToClose)
1487 int index = tabbedPane.getSelectedIndex();
1488 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1489 alignPanels.remove(panelToClose);
1490 panelToClose.closePanel();
1491 panelToClose = null;
1493 tabbedPane.removeTabAt(closedindex);
1494 tabbedPane.validate();
1496 if (index > closedindex || index == tabbedPane.getTabCount())
1498 // modify currently selected tab index if necessary.
1502 this.tabSelectionChanged(index);
1508 void updateEditMenuBar()
1511 if (viewport.getHistoryList().size() > 0)
1513 undoMenuItem.setEnabled(true);
1514 CommandI command = viewport.getHistoryList().peek();
1515 undoMenuItem.setText(MessageManager
1516 .formatMessage("label.undo_command", new Object[]
1517 { command.getDescription() }));
1521 undoMenuItem.setEnabled(false);
1522 undoMenuItem.setText(MessageManager.getString("action.undo"));
1525 if (viewport.getRedoList().size() > 0)
1527 redoMenuItem.setEnabled(true);
1529 CommandI command = viewport.getRedoList().peek();
1530 redoMenuItem.setText(MessageManager
1531 .formatMessage("label.redo_command", new Object[]
1532 { command.getDescription() }));
1536 redoMenuItem.setEnabled(false);
1537 redoMenuItem.setText(MessageManager.getString("action.redo"));
1542 public void addHistoryItem(CommandI command)
1544 if (command.getSize() > 0)
1546 viewport.addToHistoryList(command);
1547 viewport.clearRedoList();
1548 updateEditMenuBar();
1549 viewport.updateHiddenColumns();
1550 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1551 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1552 // viewport.getColumnSelection()
1553 // .getHiddenColumns().size() > 0);
1559 * @return alignment objects for all views
1561 AlignmentI[] getViewAlignments()
1563 if (alignPanels != null)
1565 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1567 for (AlignmentPanel ap : alignPanels)
1569 als[i++] = ap.av.getAlignment();
1573 if (viewport != null)
1575 return new AlignmentI[] { viewport.getAlignment() };
1587 protected void undoMenuItem_actionPerformed(ActionEvent e)
1589 if (viewport.getHistoryList().isEmpty())
1593 CommandI command = viewport.getHistoryList().pop();
1594 viewport.addToRedoList(command);
1595 command.undoCommand(getViewAlignments());
1597 AlignmentViewport originalSource = getOriginatingSource(command);
1598 updateEditMenuBar();
1600 if (originalSource != null)
1602 if (originalSource != viewport)
1605 "Implementation worry: mismatch of viewport origin for undo");
1607 originalSource.updateHiddenColumns();
1608 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1610 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1611 // viewport.getColumnSelection()
1612 // .getHiddenColumns().size() > 0);
1613 originalSource.firePropertyChange("alignment", null,
1614 originalSource.getAlignment().getSequences());
1625 protected void redoMenuItem_actionPerformed(ActionEvent e)
1627 if (viewport.getRedoList().size() < 1)
1632 CommandI command = viewport.getRedoList().pop();
1633 viewport.addToHistoryList(command);
1634 command.doCommand(getViewAlignments());
1636 AlignmentViewport originalSource = getOriginatingSource(command);
1637 updateEditMenuBar();
1639 if (originalSource != null)
1642 if (originalSource != viewport)
1645 "Implementation worry: mismatch of viewport origin for redo");
1647 originalSource.updateHiddenColumns();
1648 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1650 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1651 // viewport.getColumnSelection()
1652 // .getHiddenColumns().size() > 0);
1653 originalSource.firePropertyChange("alignment", null,
1654 originalSource.getAlignment().getSequences());
1658 AlignmentViewport getOriginatingSource(CommandI command)
1660 AlignmentViewport originalSource = null;
1661 // For sequence removal and addition, we need to fire
1662 // the property change event FROM the viewport where the
1663 // original alignment was altered
1664 AlignmentI al = null;
1665 if (command instanceof EditCommand)
1667 EditCommand editCommand = (EditCommand) command;
1668 al = editCommand.getAlignment();
1669 List<Component> comps = PaintRefresher.components
1670 .get(viewport.getSequenceSetId());
1672 for (Component comp : comps)
1674 if (comp instanceof AlignmentPanel)
1676 if (al == ((AlignmentPanel) comp).av.getAlignment())
1678 originalSource = ((AlignmentPanel) comp).av;
1685 if (originalSource == null)
1687 // The original view is closed, we must validate
1688 // the current view against the closed view first
1691 PaintRefresher.validateSequences(al, viewport.getAlignment());
1694 originalSource = viewport;
1697 return originalSource;
1706 public void moveSelectedSequences(boolean up)
1708 SequenceGroup sg = viewport.getSelectionGroup();
1714 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1715 viewport.getHiddenRepSequences(), up);
1716 alignPanel.paintAlignment(true);
1719 synchronized void slideSequences(boolean right, int size)
1721 List<SequenceI> sg = new ArrayList<>();
1722 if (viewport.cursorMode)
1724 sg.add(viewport.getAlignment()
1725 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1727 else if (viewport.getSelectionGroup() != null
1728 && viewport.getSelectionGroup().getSize() != viewport
1729 .getAlignment().getHeight())
1731 sg = viewport.getSelectionGroup()
1732 .getSequences(viewport.getHiddenRepSequences());
1740 List<SequenceI> invertGroup = new ArrayList<>();
1742 for (SequenceI seq : viewport.getAlignment().getSequences())
1744 if (!sg.contains(seq))
1746 invertGroup.add(seq);
1750 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1752 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1753 for (int i = 0; i < invertGroup.size(); i++)
1755 seqs2[i] = invertGroup.get(i);
1758 SlideSequencesCommand ssc;
1761 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1762 viewport.getGapCharacter());
1766 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1767 viewport.getGapCharacter());
1770 int groupAdjustment = 0;
1771 if (ssc.getGapsInsertedBegin() && right)
1773 if (viewport.cursorMode)
1775 alignPanel.getSeqPanel().moveCursor(size, 0);
1779 groupAdjustment = size;
1782 else if (!ssc.getGapsInsertedBegin() && !right)
1784 if (viewport.cursorMode)
1786 alignPanel.getSeqPanel().moveCursor(-size, 0);
1790 groupAdjustment = -size;
1794 if (groupAdjustment != 0)
1796 viewport.getSelectionGroup().setStartRes(
1797 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1798 viewport.getSelectionGroup().setEndRes(
1799 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1803 * just extend the last slide command if compatible; but not if in
1804 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1806 boolean appendHistoryItem = false;
1807 Deque<CommandI> historyList = viewport.getHistoryList();
1808 boolean inSplitFrame = getSplitViewContainer() != null;
1809 if (!inSplitFrame && historyList != null && historyList.size() > 0
1810 && historyList.peek() instanceof SlideSequencesCommand)
1812 appendHistoryItem = ssc.appendSlideCommand(
1813 (SlideSequencesCommand) historyList.peek());
1816 if (!appendHistoryItem)
1818 addHistoryItem(ssc);
1831 protected void copy_actionPerformed(ActionEvent e)
1834 if (viewport.getSelectionGroup() == null)
1838 // TODO: preserve the ordering of displayed alignment annotation in any
1839 // internal paste (particularly sequence associated annotation)
1840 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1841 String[] omitHidden = null;
1843 if (viewport.hasHiddenColumns())
1845 omitHidden = viewport.getViewAsString(true);
1848 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1849 seqs, omitHidden, null);
1851 StringSelection ss = new StringSelection(output);
1855 jalview.gui.Desktop.internalCopy = true;
1856 // Its really worth setting the clipboard contents
1857 // to empty before setting the large StringSelection!!
1858 Toolkit.getDefaultToolkit().getSystemClipboard()
1859 .setContents(new StringSelection(""), null);
1861 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1863 } catch (OutOfMemoryError er)
1865 new OOMWarning("copying region", er);
1869 ArrayList<int[]> hiddenColumns = null;
1870 if (viewport.hasHiddenColumns())
1872 hiddenColumns = new ArrayList<>();
1873 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1874 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1875 ArrayList<int[]> hiddenRegions = viewport.getAlignment()
1876 .getHiddenColumns().getHiddenColumnsCopy();
1877 for (int[] region : hiddenRegions)
1879 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1883 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1888 Desktop.jalviewClipboard = new Object[] { seqs,
1889 viewport.getAlignment().getDataset(), hiddenColumns };
1890 statusBar.setText(MessageManager.formatMessage(
1891 "label.copied_sequences_to_clipboard", new Object[]
1892 { Integer.valueOf(seqs.length).toString() }));
1902 protected void pasteNew_actionPerformed(ActionEvent e)
1914 protected void pasteThis_actionPerformed(ActionEvent e)
1920 * Paste contents of Jalview clipboard
1922 * @param newAlignment
1923 * true to paste to a new alignment, otherwise add to this.
1925 void paste(boolean newAlignment)
1927 boolean externalPaste = true;
1930 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1931 Transferable contents = c.getContents(this);
1933 if (contents == null)
1942 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1943 if (str.length() < 1)
1948 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1950 } catch (OutOfMemoryError er)
1952 new OOMWarning("Out of memory pasting sequences!!", er);
1956 SequenceI[] sequences;
1957 boolean annotationAdded = false;
1958 AlignmentI alignment = null;
1960 if (Desktop.jalviewClipboard != null)
1962 // The clipboard was filled from within Jalview, we must use the
1964 // And dataset from the copied alignment
1965 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1966 // be doubly sure that we create *new* sequence objects.
1967 sequences = new SequenceI[newseq.length];
1968 for (int i = 0; i < newseq.length; i++)
1970 sequences[i] = new Sequence(newseq[i]);
1972 alignment = new Alignment(sequences);
1973 externalPaste = false;
1977 // parse the clipboard as an alignment.
1978 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1980 sequences = alignment.getSequencesArray();
1984 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1990 if (Desktop.jalviewClipboard != null)
1992 // dataset is inherited
1993 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1997 // new dataset is constructed
1998 alignment.setDataset(null);
2000 alwidth = alignment.getWidth() + 1;
2004 AlignmentI pastedal = alignment; // preserve pasted alignment object
2005 // Add pasted sequences and dataset into existing alignment.
2006 alignment = viewport.getAlignment();
2007 alwidth = alignment.getWidth() + 1;
2008 // decide if we need to import sequences from an existing dataset
2009 boolean importDs = Desktop.jalviewClipboard != null
2010 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2011 // importDs==true instructs us to copy over new dataset sequences from
2012 // an existing alignment
2013 Vector newDs = (importDs) ? new Vector() : null; // used to create
2014 // minimum dataset set
2016 for (int i = 0; i < sequences.length; i++)
2020 newDs.addElement(null);
2022 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2024 if (importDs && ds != null)
2026 if (!newDs.contains(ds))
2028 newDs.setElementAt(ds, i);
2029 ds = new Sequence(ds);
2030 // update with new dataset sequence
2031 sequences[i].setDatasetSequence(ds);
2035 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2040 // copy and derive new dataset sequence
2041 sequences[i] = sequences[i].deriveSequence();
2042 alignment.getDataset()
2043 .addSequence(sequences[i].getDatasetSequence());
2044 // TODO: avoid creation of duplicate dataset sequences with a
2045 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2047 alignment.addSequence(sequences[i]); // merges dataset
2051 newDs.clear(); // tidy up
2053 if (alignment.getAlignmentAnnotation() != null)
2055 for (AlignmentAnnotation alan : alignment
2056 .getAlignmentAnnotation())
2058 if (alan.graphGroup > fgroup)
2060 fgroup = alan.graphGroup;
2064 if (pastedal.getAlignmentAnnotation() != null)
2066 // Add any annotation attached to alignment.
2067 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2068 for (int i = 0; i < alann.length; i++)
2070 annotationAdded = true;
2071 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2073 AlignmentAnnotation newann = new AlignmentAnnotation(
2075 if (newann.graphGroup > -1)
2077 if (newGraphGroups.size() <= newann.graphGroup
2078 || newGraphGroups.get(newann.graphGroup) == null)
2080 for (int q = newGraphGroups
2081 .size(); q <= newann.graphGroup; q++)
2083 newGraphGroups.add(q, null);
2085 newGraphGroups.set(newann.graphGroup,
2086 new Integer(++fgroup));
2088 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2092 newann.padAnnotation(alwidth);
2093 alignment.addAnnotation(newann);
2103 addHistoryItem(new EditCommand(
2104 MessageManager.getString("label.add_sequences"),
2105 Action.PASTE, sequences, 0, alignment.getWidth(),
2108 // Add any annotations attached to sequences
2109 for (int i = 0; i < sequences.length; i++)
2111 if (sequences[i].getAnnotation() != null)
2113 AlignmentAnnotation newann;
2114 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2116 annotationAdded = true;
2117 newann = sequences[i].getAnnotation()[a];
2118 newann.adjustForAlignment();
2119 newann.padAnnotation(alwidth);
2120 if (newann.graphGroup > -1)
2122 if (newann.graphGroup > -1)
2124 if (newGraphGroups.size() <= newann.graphGroup
2125 || newGraphGroups.get(newann.graphGroup) == null)
2127 for (int q = newGraphGroups
2128 .size(); q <= newann.graphGroup; q++)
2130 newGraphGroups.add(q, null);
2132 newGraphGroups.set(newann.graphGroup,
2133 new Integer(++fgroup));
2135 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2139 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2143 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2151 // propagate alignment changed.
2152 vpRanges.setEndSeq(alignment.getHeight());
2153 if (annotationAdded)
2155 // Duplicate sequence annotation in all views.
2156 AlignmentI[] alview = this.getViewAlignments();
2157 for (int i = 0; i < sequences.length; i++)
2159 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2164 for (int avnum = 0; avnum < alview.length; avnum++)
2166 if (alview[avnum] != alignment)
2168 // duplicate in a view other than the one with input focus
2169 int avwidth = alview[avnum].getWidth() + 1;
2170 // this relies on sann being preserved after we
2171 // modify the sequence's annotation array for each duplication
2172 for (int a = 0; a < sann.length; a++)
2174 AlignmentAnnotation newann = new AlignmentAnnotation(
2176 sequences[i].addAlignmentAnnotation(newann);
2177 newann.padAnnotation(avwidth);
2178 alview[avnum].addAnnotation(newann); // annotation was
2179 // duplicated earlier
2180 // TODO JAL-1145 graphGroups are not updated for sequence
2181 // annotation added to several views. This may cause
2183 alview[avnum].setAnnotationIndex(newann, a);
2188 buildSortByAnnotationScoresMenu();
2190 viewport.firePropertyChange("alignment", null,
2191 alignment.getSequences());
2192 if (alignPanels != null)
2194 for (AlignmentPanel ap : alignPanels)
2196 ap.validateAnnotationDimensions(false);
2201 alignPanel.validateAnnotationDimensions(false);
2207 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2209 String newtitle = new String("Copied sequences");
2211 if (Desktop.jalviewClipboard != null
2212 && Desktop.jalviewClipboard[2] != null)
2214 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2215 for (int[] region : hc)
2217 af.viewport.hideColumns(region[0], region[1]);
2221 // >>>This is a fix for the moment, until a better solution is
2223 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2224 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2225 .getFeatureRenderer());
2227 // TODO: maintain provenance of an alignment, rather than just make the
2228 // title a concatenation of operations.
2231 if (title.startsWith("Copied sequences"))
2237 newtitle = newtitle.concat("- from " + title);
2242 newtitle = new String("Pasted sequences");
2245 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2250 } catch (Exception ex)
2252 ex.printStackTrace();
2253 System.out.println("Exception whilst pasting: " + ex);
2254 // could be anything being pasted in here
2260 protected void expand_newalign(ActionEvent e)
2264 AlignmentI alignment = AlignmentUtils
2265 .expandContext(getViewport().getAlignment(), -1);
2266 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2268 String newtitle = new String("Flanking alignment");
2270 if (Desktop.jalviewClipboard != null
2271 && Desktop.jalviewClipboard[2] != null)
2273 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2274 for (int region[] : hc)
2276 af.viewport.hideColumns(region[0], region[1]);
2280 // >>>This is a fix for the moment, until a better solution is
2282 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2283 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2284 .getFeatureRenderer());
2286 // TODO: maintain provenance of an alignment, rather than just make the
2287 // title a concatenation of operations.
2289 if (title.startsWith("Copied sequences"))
2295 newtitle = newtitle.concat("- from " + title);
2299 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2301 } catch (Exception ex)
2303 ex.printStackTrace();
2304 System.out.println("Exception whilst pasting: " + ex);
2305 // could be anything being pasted in here
2306 } catch (OutOfMemoryError oom)
2308 new OOMWarning("Viewing flanking region of alignment", oom);
2319 protected void cut_actionPerformed(ActionEvent e)
2321 copy_actionPerformed(null);
2322 delete_actionPerformed(null);
2332 protected void delete_actionPerformed(ActionEvent evt)
2335 SequenceGroup sg = viewport.getSelectionGroup();
2342 * If the cut affects all sequences, warn, remove highlighted columns
2344 if (sg.getSize() == viewport.getAlignment().getHeight())
2346 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2347 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2348 if (isEntireAlignWidth)
2350 int confirm = JvOptionPane.showConfirmDialog(this,
2351 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2352 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2353 JvOptionPane.OK_CANCEL_OPTION);
2355 if (confirm == JvOptionPane.CANCEL_OPTION
2356 || confirm == JvOptionPane.CLOSED_OPTION)
2361 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2362 sg.getEndRes() + 1);
2364 SequenceI[] cut = sg.getSequences()
2365 .toArray(new SequenceI[sg.getSize()]);
2367 addHistoryItem(new EditCommand(
2368 MessageManager.getString("label.cut_sequences"), Action.CUT,
2369 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2370 viewport.getAlignment()));
2372 viewport.setSelectionGroup(null);
2373 viewport.sendSelection();
2374 viewport.getAlignment().deleteGroup(sg);
2376 viewport.firePropertyChange("alignment", null,
2377 viewport.getAlignment().getSequences());
2378 if (viewport.getAlignment().getHeight() < 1)
2382 this.setClosed(true);
2383 } catch (Exception ex)
2396 protected void deleteGroups_actionPerformed(ActionEvent e)
2398 if (avc.deleteGroups())
2400 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2401 alignPanel.updateAnnotation();
2402 alignPanel.paintAlignment(true);
2413 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2415 SequenceGroup sg = new SequenceGroup();
2417 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2419 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2422 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2423 viewport.setSelectionGroup(sg);
2424 viewport.sendSelection();
2425 // JAL-2034 - should delegate to
2426 // alignPanel to decide if overview needs
2428 alignPanel.paintAlignment(false);
2429 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2439 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2441 if (viewport.cursorMode)
2443 alignPanel.getSeqPanel().keyboardNo1 = null;
2444 alignPanel.getSeqPanel().keyboardNo2 = null;
2446 viewport.setSelectionGroup(null);
2447 viewport.getColumnSelection().clear();
2448 viewport.setSelectionGroup(null);
2449 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2450 // JAL-2034 - should delegate to
2451 // alignPanel to decide if overview needs
2453 alignPanel.paintAlignment(false);
2454 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2455 viewport.sendSelection();
2465 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2467 SequenceGroup sg = viewport.getSelectionGroup();
2471 selectAllSequenceMenuItem_actionPerformed(null);
2476 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2478 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2480 // JAL-2034 - should delegate to
2481 // alignPanel to decide if overview needs
2484 alignPanel.paintAlignment(true);
2485 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2486 viewport.sendSelection();
2490 public void invertColSel_actionPerformed(ActionEvent e)
2492 viewport.invertColumnSelection();
2493 alignPanel.paintAlignment(true);
2494 viewport.sendSelection();
2504 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2506 trimAlignment(true);
2516 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2518 trimAlignment(false);
2521 void trimAlignment(boolean trimLeft)
2523 ColumnSelection colSel = viewport.getColumnSelection();
2526 if (!colSel.isEmpty())
2530 column = colSel.getMin();
2534 column = colSel.getMax();
2538 if (viewport.getSelectionGroup() != null)
2540 seqs = viewport.getSelectionGroup()
2541 .getSequencesAsArray(viewport.getHiddenRepSequences());
2545 seqs = viewport.getAlignment().getSequencesArray();
2548 TrimRegionCommand trimRegion;
2551 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2552 column, viewport.getAlignment());
2553 vpRanges.setStartRes(0);
2557 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2558 column, viewport.getAlignment());
2561 statusBar.setText(MessageManager
2562 .formatMessage("label.removed_columns", new String[]
2563 { Integer.valueOf(trimRegion.getSize()).toString() }));
2565 addHistoryItem(trimRegion);
2567 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2569 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2570 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2572 viewport.getAlignment().deleteGroup(sg);
2576 viewport.firePropertyChange("alignment", null,
2577 viewport.getAlignment().getSequences());
2588 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2590 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2593 if (viewport.getSelectionGroup() != null)
2595 seqs = viewport.getSelectionGroup()
2596 .getSequencesAsArray(viewport.getHiddenRepSequences());
2597 start = viewport.getSelectionGroup().getStartRes();
2598 end = viewport.getSelectionGroup().getEndRes();
2602 seqs = viewport.getAlignment().getSequencesArray();
2605 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2606 "Remove Gapped Columns", seqs, start, end,
2607 viewport.getAlignment());
2609 addHistoryItem(removeGapCols);
2611 statusBar.setText(MessageManager
2612 .formatMessage("label.removed_empty_columns", new Object[]
2613 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2615 // This is to maintain viewport position on first residue
2616 // of first sequence
2617 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2618 int startRes = seq.findPosition(vpRanges.getStartRes());
2619 // ShiftList shifts;
2620 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2621 // edit.alColumnChanges=shifts.getInverse();
2622 // if (viewport.hasHiddenColumns)
2623 // viewport.getColumnSelection().compensateForEdits(shifts);
2624 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2625 viewport.firePropertyChange("alignment", null,
2626 viewport.getAlignment().getSequences());
2637 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2639 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2642 if (viewport.getSelectionGroup() != null)
2644 seqs = viewport.getSelectionGroup()
2645 .getSequencesAsArray(viewport.getHiddenRepSequences());
2646 start = viewport.getSelectionGroup().getStartRes();
2647 end = viewport.getSelectionGroup().getEndRes();
2651 seqs = viewport.getAlignment().getSequencesArray();
2654 // This is to maintain viewport position on first residue
2655 // of first sequence
2656 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2657 int startRes = seq.findPosition(vpRanges.getStartRes());
2659 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2660 viewport.getAlignment()));
2662 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2664 viewport.firePropertyChange("alignment", null,
2665 viewport.getAlignment().getSequences());
2676 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2678 viewport.setPadGaps(padGapsMenuitem.isSelected());
2679 viewport.firePropertyChange("alignment", null,
2680 viewport.getAlignment().getSequences());
2690 public void findMenuItem_actionPerformed(ActionEvent e)
2696 * Create a new view of the current alignment.
2699 public void newView_actionPerformed(ActionEvent e)
2701 newView(null, true);
2705 * Creates and shows a new view of the current alignment.
2708 * title of newly created view; if null, one will be generated
2709 * @param copyAnnotation
2710 * if true then duplicate all annnotation, groups and settings
2711 * @return new alignment panel, already displayed.
2713 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2716 * Create a new AlignmentPanel (with its own, new Viewport)
2718 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2720 if (!copyAnnotation)
2723 * remove all groups and annotation except for the automatic stuff
2725 newap.av.getAlignment().deleteAllGroups();
2726 newap.av.getAlignment().deleteAllAnnotations(false);
2729 newap.av.setGatherViewsHere(false);
2731 if (viewport.viewName == null)
2733 viewport.viewName = MessageManager
2734 .getString("label.view_name_original");
2738 * Views share the same edits undo and redo stacks
2740 newap.av.setHistoryList(viewport.getHistoryList());
2741 newap.av.setRedoList(viewport.getRedoList());
2744 * Views share the same mappings; need to deregister any new mappings
2745 * created by copyAlignPanel, and register the new reference to the shared
2748 newap.av.replaceMappings(viewport.getAlignment());
2751 * start up cDNA consensus (if applicable) now mappings are in place
2753 if (newap.av.initComplementConsensus())
2755 newap.refresh(true); // adjust layout of annotations
2758 newap.av.viewName = getNewViewName(viewTitle);
2760 addAlignmentPanel(newap, true);
2761 newap.alignmentChanged();
2763 if (alignPanels.size() == 2)
2765 viewport.setGatherViewsHere(true);
2767 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2772 * Make a new name for the view, ensuring it is unique within the current
2773 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2774 * these now use viewId. Unique view names are still desirable for usability.)
2779 protected String getNewViewName(String viewTitle)
2781 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2782 boolean addFirstIndex = false;
2783 if (viewTitle == null || viewTitle.trim().length() == 0)
2785 viewTitle = MessageManager.getString("action.view");
2786 addFirstIndex = true;
2790 index = 1;// we count from 1 if given a specific name
2792 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2794 List<Component> comps = PaintRefresher.components
2795 .get(viewport.getSequenceSetId());
2797 List<String> existingNames = getExistingViewNames(comps);
2799 while (existingNames.contains(newViewName))
2801 newViewName = viewTitle + " " + (++index);
2807 * Returns a list of distinct view names found in the given list of
2808 * components. View names are held on the viewport of an AlignmentPanel.
2813 protected List<String> getExistingViewNames(List<Component> comps)
2815 List<String> existingNames = new ArrayList<>();
2816 for (Component comp : comps)
2818 if (comp instanceof AlignmentPanel)
2820 AlignmentPanel ap = (AlignmentPanel) comp;
2821 if (!existingNames.contains(ap.av.viewName))
2823 existingNames.add(ap.av.viewName);
2827 return existingNames;
2831 * Explode tabbed views into separate windows.
2834 public void expandViews_actionPerformed(ActionEvent e)
2836 Desktop.explodeViews(this);
2840 * Gather views in separate windows back into a tabbed presentation.
2843 public void gatherViews_actionPerformed(ActionEvent e)
2845 Desktop.instance.gatherViews(this);
2855 public void font_actionPerformed(ActionEvent e)
2857 new FontChooser(alignPanel);
2867 protected void seqLimit_actionPerformed(ActionEvent e)
2869 viewport.setShowJVSuffix(seqLimits.isSelected());
2871 alignPanel.getIdPanel().getIdCanvas()
2872 .setPreferredSize(alignPanel.calculateIdWidth());
2873 alignPanel.paintAlignment(true);
2877 public void idRightAlign_actionPerformed(ActionEvent e)
2879 viewport.setRightAlignIds(idRightAlign.isSelected());
2880 alignPanel.paintAlignment(true);
2884 public void centreColumnLabels_actionPerformed(ActionEvent e)
2886 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2887 alignPanel.paintAlignment(true);
2893 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2896 protected void followHighlight_actionPerformed()
2899 * Set the 'follow' flag on the Viewport (and scroll to position if now
2902 final boolean state = this.followHighlightMenuItem.getState();
2903 viewport.setFollowHighlight(state);
2906 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2917 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2919 viewport.setColourText(colourTextMenuItem.isSelected());
2920 alignPanel.paintAlignment(true);
2930 public void wrapMenuItem_actionPerformed(ActionEvent e)
2932 scaleAbove.setVisible(wrapMenuItem.isSelected());
2933 scaleLeft.setVisible(wrapMenuItem.isSelected());
2934 scaleRight.setVisible(wrapMenuItem.isSelected());
2935 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2936 alignPanel.updateLayout();
2940 public void showAllSeqs_actionPerformed(ActionEvent e)
2942 viewport.showAllHiddenSeqs();
2946 public void showAllColumns_actionPerformed(ActionEvent e)
2948 viewport.showAllHiddenColumns();
2949 alignPanel.paintAlignment(true);
2950 viewport.sendSelection();
2954 public void hideSelSequences_actionPerformed(ActionEvent e)
2956 viewport.hideAllSelectedSeqs();
2960 * called by key handler and the hide all/show all menu items
2965 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2968 boolean hide = false;
2969 SequenceGroup sg = viewport.getSelectionGroup();
2970 if (!toggleSeqs && !toggleCols)
2972 // Hide everything by the current selection - this is a hack - we do the
2973 // invert and then hide
2974 // first check that there will be visible columns after the invert.
2975 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2976 && sg.getStartRes() <= sg.getEndRes()))
2978 // now invert the sequence set, if required - empty selection implies
2979 // that no hiding is required.
2982 invertSequenceMenuItem_actionPerformed(null);
2983 sg = viewport.getSelectionGroup();
2987 viewport.expandColSelection(sg, true);
2988 // finally invert the column selection and get the new sequence
2990 invertColSel_actionPerformed(null);
2997 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2999 hideSelSequences_actionPerformed(null);
3002 else if (!(toggleCols && viewport.hasSelectedColumns()))
3004 showAllSeqs_actionPerformed(null);
3010 if (viewport.hasSelectedColumns())
3012 hideSelColumns_actionPerformed(null);
3015 viewport.setSelectionGroup(sg);
3020 showAllColumns_actionPerformed(null);
3029 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3030 * event.ActionEvent)
3033 public void hideAllButSelection_actionPerformed(ActionEvent e)
3035 toggleHiddenRegions(false, false);
3036 viewport.sendSelection();
3043 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3047 public void hideAllSelection_actionPerformed(ActionEvent e)
3049 SequenceGroup sg = viewport.getSelectionGroup();
3050 viewport.expandColSelection(sg, false);
3051 viewport.hideAllSelectedSeqs();
3052 viewport.hideSelectedColumns();
3053 alignPanel.paintAlignment(true);
3054 viewport.sendSelection();
3061 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3065 public void showAllhidden_actionPerformed(ActionEvent e)
3067 viewport.showAllHiddenColumns();
3068 viewport.showAllHiddenSeqs();
3069 alignPanel.paintAlignment(true);
3070 viewport.sendSelection();
3074 public void hideSelColumns_actionPerformed(ActionEvent e)
3076 viewport.hideSelectedColumns();
3077 alignPanel.paintAlignment(true);
3078 viewport.sendSelection();
3082 public void hiddenMarkers_actionPerformed(ActionEvent e)
3084 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3095 protected void scaleAbove_actionPerformed(ActionEvent e)
3097 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3098 alignPanel.paintAlignment(true);
3108 protected void scaleLeft_actionPerformed(ActionEvent e)
3110 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3111 alignPanel.paintAlignment(true);
3121 protected void scaleRight_actionPerformed(ActionEvent e)
3123 viewport.setScaleRightWrapped(scaleRight.isSelected());
3124 alignPanel.paintAlignment(true);
3134 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3136 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3137 alignPanel.paintAlignment(true);
3147 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3149 viewport.setShowText(viewTextMenuItem.isSelected());
3150 alignPanel.paintAlignment(true);
3160 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3162 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3163 alignPanel.paintAlignment(true);
3166 public FeatureSettings featureSettings;
3169 public FeatureSettingsControllerI getFeatureSettingsUI()
3171 return featureSettings;
3175 public void featureSettings_actionPerformed(ActionEvent e)
3177 if (featureSettings != null)
3179 featureSettings.close();
3180 featureSettings = null;
3182 if (!showSeqFeatures.isSelected())
3184 // make sure features are actually displayed
3185 showSeqFeatures.setSelected(true);
3186 showSeqFeatures_actionPerformed(null);
3188 featureSettings = new FeatureSettings(this);
3192 * Set or clear 'Show Sequence Features'
3198 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3200 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3201 alignPanel.paintAlignment(true);
3205 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3206 * the annotations panel as a whole.
3208 * The options to show/hide all annotations should be enabled when the panel
3209 * is shown, and disabled when the panel is hidden.
3214 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3216 final boolean setVisible = annotationPanelMenuItem.isSelected();
3217 viewport.setShowAnnotation(setVisible);
3218 this.showAllSeqAnnotations.setEnabled(setVisible);
3219 this.hideAllSeqAnnotations.setEnabled(setVisible);
3220 this.showAllAlAnnotations.setEnabled(setVisible);
3221 this.hideAllAlAnnotations.setEnabled(setVisible);
3222 alignPanel.updateLayout();
3226 public void alignmentProperties()
3228 JEditorPane editPane = new JEditorPane("text/html", "");
3229 editPane.setEditable(false);
3230 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3233 MessageManager.formatMessage("label.html_content", new Object[]
3234 { contents.toString() }));
3235 JInternalFrame frame = new JInternalFrame();
3236 frame.getContentPane().add(new JScrollPane(editPane));
3238 Desktop.addInternalFrame(frame, MessageManager
3239 .formatMessage("label.alignment_properties", new Object[]
3240 { getTitle() }), 500, 400);
3250 public void overviewMenuItem_actionPerformed(ActionEvent e)
3252 if (alignPanel.overviewPanel != null)
3257 JInternalFrame frame = new JInternalFrame();
3258 final OverviewPanel overview = new OverviewPanel(alignPanel);
3259 frame.setContentPane(overview);
3260 Desktop.addInternalFrame(frame, MessageManager
3261 .formatMessage("label.overview_params", new Object[]
3262 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3265 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3266 frame.addInternalFrameListener(
3267 new javax.swing.event.InternalFrameAdapter()
3270 public void internalFrameClosed(
3271 javax.swing.event.InternalFrameEvent evt)
3274 alignPanel.setOverviewPanel(null);
3278 alignPanel.setOverviewPanel(overview);
3282 public void textColour_actionPerformed()
3284 new TextColourChooser().chooseColour(alignPanel, null);
3288 * public void covariationColour_actionPerformed() {
3290 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3294 public void annotationColour_actionPerformed()
3296 new AnnotationColourChooser(viewport, alignPanel);
3300 public void annotationColumn_actionPerformed(ActionEvent e)
3302 new AnnotationColumnChooser(viewport, alignPanel);
3306 * Action on the user checking or unchecking the option to apply the selected
3307 * colour scheme to all groups. If unchecked, groups may have their own
3308 * independent colour schemes.
3313 public void applyToAllGroups_actionPerformed(boolean selected)
3315 viewport.setColourAppliesToAllGroups(selected);
3319 * Action on user selecting a colour from the colour menu
3322 * the name (not the menu item label!) of the colour scheme
3325 public void changeColour_actionPerformed(String name)
3328 * 'User Defined' opens a panel to configure or load a
3329 * user-defined colour scheme
3331 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3333 new UserDefinedColours(alignPanel);
3338 * otherwise set the chosen colour scheme (or null for 'None')
3340 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3341 viewport.getAlignment(), viewport.getHiddenRepSequences());
3346 * Actions on setting or changing the alignment colour scheme
3351 public void changeColour(ColourSchemeI cs)
3353 // TODO: pull up to controller method
3354 ColourMenuHelper.setColourSelected(colourMenu, cs);
3356 viewport.setGlobalColourScheme(cs);
3358 alignPanel.paintAlignment(true);
3362 * Show the PID threshold slider panel
3365 protected void modifyPID_actionPerformed()
3367 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3368 alignPanel.getViewName());
3369 SliderPanel.showPIDSlider();
3373 * Show the Conservation slider panel
3376 protected void modifyConservation_actionPerformed()
3378 SliderPanel.setConservationSlider(alignPanel,
3379 viewport.getResidueShading(), alignPanel.getViewName());
3380 SliderPanel.showConservationSlider();
3384 * Action on selecting or deselecting (Colour) By Conservation
3387 public void conservationMenuItem_actionPerformed(boolean selected)
3389 modifyConservation.setEnabled(selected);
3390 viewport.setConservationSelected(selected);
3391 viewport.getResidueShading().setConservationApplied(selected);
3393 changeColour(viewport.getGlobalColourScheme());
3396 modifyConservation_actionPerformed();
3400 SliderPanel.hideConservationSlider();
3405 * Action on selecting or deselecting (Colour) Above PID Threshold
3408 public void abovePIDThreshold_actionPerformed(boolean selected)
3410 modifyPID.setEnabled(selected);
3411 viewport.setAbovePIDThreshold(selected);
3414 viewport.getResidueShading().setThreshold(0,
3415 viewport.isIgnoreGapsConsensus());
3418 changeColour(viewport.getGlobalColourScheme());
3421 modifyPID_actionPerformed();
3425 SliderPanel.hidePIDSlider();
3436 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3438 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3439 AlignmentSorter.sortByPID(viewport.getAlignment(),
3440 viewport.getAlignment().getSequenceAt(0));
3441 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3442 viewport.getAlignment()));
3443 alignPanel.paintAlignment(true);
3453 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3455 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3456 AlignmentSorter.sortByID(viewport.getAlignment());
3458 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3459 alignPanel.paintAlignment(true);
3469 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3471 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3472 AlignmentSorter.sortByLength(viewport.getAlignment());
3473 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3474 viewport.getAlignment()));
3475 alignPanel.paintAlignment(true);
3485 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3487 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3488 AlignmentSorter.sortByGroup(viewport.getAlignment());
3489 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3490 viewport.getAlignment()));
3492 alignPanel.paintAlignment(true);
3502 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3504 new RedundancyPanel(alignPanel, this);
3514 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3516 if ((viewport.getSelectionGroup() == null)
3517 || (viewport.getSelectionGroup().getSize() < 2))
3519 JvOptionPane.showInternalMessageDialog(this,
3520 MessageManager.getString(
3521 "label.you_must_select_least_two_sequences"),
3522 MessageManager.getString("label.invalid_selection"),
3523 JvOptionPane.WARNING_MESSAGE);
3527 JInternalFrame frame = new JInternalFrame();
3528 frame.setContentPane(new PairwiseAlignPanel(viewport));
3529 Desktop.addInternalFrame(frame,
3530 MessageManager.getString("action.pairwise_alignment"), 600,
3536 public void autoCalculate_actionPerformed(ActionEvent e)
3538 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3539 if (viewport.autoCalculateConsensus)
3541 viewport.firePropertyChange("alignment", null,
3542 viewport.getAlignment().getSequences());
3547 public void sortByTreeOption_actionPerformed(ActionEvent e)
3549 viewport.sortByTree = sortByTree.isSelected();
3553 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3555 viewport.followSelection = listenToViewSelections.isSelected();
3559 * Constructs a tree panel and adds it to the desktop
3562 * tree type (NJ or AV)
3564 * name of score model used to compute the tree
3566 * parameters for the distance or similarity calculation
3568 void newTreePanel(String type, String modelName,
3569 SimilarityParamsI options)
3571 String frameTitle = "";
3574 boolean onSelection = false;
3575 if (viewport.getSelectionGroup() != null
3576 && viewport.getSelectionGroup().getSize() > 0)
3578 SequenceGroup sg = viewport.getSelectionGroup();
3580 /* Decide if the selection is a column region */
3581 for (SequenceI _s : sg.getSequences())
3583 if (_s.getLength() < sg.getEndRes())
3585 JvOptionPane.showMessageDialog(Desktop.desktop,
3586 MessageManager.getString(
3587 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3588 MessageManager.getString(
3589 "label.sequences_selection_not_aligned"),
3590 JvOptionPane.WARNING_MESSAGE);
3599 if (viewport.getAlignment().getHeight() < 2)
3605 tp = new TreePanel(alignPanel, type, modelName, options);
3606 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3608 frameTitle += " from ";
3610 if (viewport.viewName != null)
3612 frameTitle += viewport.viewName + " of ";
3615 frameTitle += this.title;
3617 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3628 public void addSortByOrderMenuItem(String title,
3629 final AlignmentOrder order)
3631 final JMenuItem item = new JMenuItem(MessageManager
3632 .formatMessage("action.by_title_param", new Object[]
3635 item.addActionListener(new java.awt.event.ActionListener()
3638 public void actionPerformed(ActionEvent e)
3640 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3642 // TODO: JBPNote - have to map order entries to curent SequenceI
3644 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3646 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3647 viewport.getAlignment()));
3649 alignPanel.paintAlignment(true);
3655 * Add a new sort by annotation score menu item
3658 * the menu to add the option to
3660 * the label used to retrieve scores for each sequence on the
3663 public void addSortByAnnotScoreMenuItem(JMenu sort,
3664 final String scoreLabel)
3666 final JMenuItem item = new JMenuItem(scoreLabel);
3668 item.addActionListener(new java.awt.event.ActionListener()
3671 public void actionPerformed(ActionEvent e)
3673 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3674 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3675 viewport.getAlignment());// ,viewport.getSelectionGroup());
3676 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3677 viewport.getAlignment()));
3678 alignPanel.paintAlignment(true);
3684 * last hash for alignment's annotation array - used to minimise cost of
3687 protected int _annotationScoreVectorHash;
3690 * search the alignment and rebuild the sort by annotation score submenu the
3691 * last alignment annotation vector hash is stored to minimize cost of
3692 * rebuilding in subsequence calls.
3696 public void buildSortByAnnotationScoresMenu()
3698 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3703 if (viewport.getAlignment().getAlignmentAnnotation()
3704 .hashCode() != _annotationScoreVectorHash)
3706 sortByAnnotScore.removeAll();
3707 // almost certainly a quicker way to do this - but we keep it simple
3708 Hashtable scoreSorts = new Hashtable();
3709 AlignmentAnnotation aann[];
3710 for (SequenceI sqa : viewport.getAlignment().getSequences())
3712 aann = sqa.getAnnotation();
3713 for (int i = 0; aann != null && i < aann.length; i++)
3715 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3717 scoreSorts.put(aann[i].label, aann[i].label);
3721 Enumeration labels = scoreSorts.keys();
3722 while (labels.hasMoreElements())
3724 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3725 (String) labels.nextElement());
3727 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3730 _annotationScoreVectorHash = viewport.getAlignment()
3731 .getAlignmentAnnotation().hashCode();
3736 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3737 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3738 * call. Listeners are added to remove the menu item when the treePanel is
3739 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3743 public void buildTreeSortMenu()
3745 sortByTreeMenu.removeAll();
3747 List<Component> comps = PaintRefresher.components
3748 .get(viewport.getSequenceSetId());
3749 List<TreePanel> treePanels = new ArrayList<>();
3750 for (Component comp : comps)
3752 if (comp instanceof TreePanel)
3754 treePanels.add((TreePanel) comp);
3758 if (treePanels.size() < 1)
3760 sortByTreeMenu.setVisible(false);
3764 sortByTreeMenu.setVisible(true);
3766 for (final TreePanel tp : treePanels)
3768 final JMenuItem item = new JMenuItem(tp.getTitle());
3769 item.addActionListener(new java.awt.event.ActionListener()
3772 public void actionPerformed(ActionEvent e)
3774 tp.sortByTree_actionPerformed();
3775 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3780 sortByTreeMenu.add(item);
3784 public boolean sortBy(AlignmentOrder alorder, String undoname)
3786 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3787 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3788 if (undoname != null)
3790 addHistoryItem(new OrderCommand(undoname, oldOrder,
3791 viewport.getAlignment()));
3793 alignPanel.paintAlignment(true);
3798 * Work out whether the whole set of sequences or just the selected set will
3799 * be submitted for multiple alignment.
3802 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3804 // Now, check we have enough sequences
3805 AlignmentView msa = null;
3807 if ((viewport.getSelectionGroup() != null)
3808 && (viewport.getSelectionGroup().getSize() > 1))
3810 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3811 // some common interface!
3813 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3814 * SequenceI[sz = seqs.getSize(false)];
3816 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3817 * seqs.getSequenceAt(i); }
3819 msa = viewport.getAlignmentView(true);
3821 else if (viewport.getSelectionGroup() != null
3822 && viewport.getSelectionGroup().getSize() == 1)
3824 int option = JvOptionPane.showConfirmDialog(this,
3825 MessageManager.getString("warn.oneseq_msainput_selection"),
3826 MessageManager.getString("label.invalid_selection"),
3827 JvOptionPane.OK_CANCEL_OPTION);
3828 if (option == JvOptionPane.OK_OPTION)
3830 msa = viewport.getAlignmentView(false);
3835 msa = viewport.getAlignmentView(false);
3841 * Decides what is submitted to a secondary structure prediction service: the
3842 * first sequence in the alignment, or in the current selection, or, if the
3843 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3844 * region or the whole alignment. (where the first sequence in the set is the
3845 * one that the prediction will be for).
3847 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3849 AlignmentView seqs = null;
3851 if ((viewport.getSelectionGroup() != null)
3852 && (viewport.getSelectionGroup().getSize() > 0))
3854 seqs = viewport.getAlignmentView(true);
3858 seqs = viewport.getAlignmentView(false);
3860 // limit sequences - JBPNote in future - could spawn multiple prediction
3862 // TODO: viewport.getAlignment().isAligned is a global state - the local
3863 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3864 if (!viewport.getAlignment().isAligned(false))
3866 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3867 // TODO: if seqs.getSequences().length>1 then should really have warned
3881 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3883 // Pick the tree file
3884 JalviewFileChooser chooser = new JalviewFileChooser(
3885 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3886 chooser.setFileView(new JalviewFileView());
3887 chooser.setDialogTitle(
3888 MessageManager.getString("label.select_newick_like_tree_file"));
3889 chooser.setToolTipText(
3890 MessageManager.getString("label.load_tree_file"));
3892 int value = chooser.showOpenDialog(null);
3894 if (value == JalviewFileChooser.APPROVE_OPTION)
3896 String filePath = chooser.getSelectedFile().getPath();
3897 Cache.setProperty("LAST_DIRECTORY", filePath);
3898 NewickFile fin = null;
3901 fin = new NewickFile(filePath, DataSourceType.FILE);
3902 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3903 } catch (Exception ex)
3905 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3906 MessageManager.getString("label.problem_reading_tree_file"),
3907 JvOptionPane.WARNING_MESSAGE);
3908 ex.printStackTrace();
3910 if (fin != null && fin.hasWarningMessage())
3912 JvOptionPane.showMessageDialog(Desktop.desktop,
3913 fin.getWarningMessage(),
3915 .getString("label.possible_problem_with_tree_file"),
3916 JvOptionPane.WARNING_MESSAGE);
3921 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3923 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3926 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3927 int h, int x, int y)
3929 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3933 * Add a treeviewer for the tree extracted from a Newick file object to the
3934 * current alignment view
3941 * Associated alignment input data (or null)
3950 * @return TreePanel handle
3952 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3953 AlignmentView input, int w, int h, int x, int y)
3955 TreePanel tp = null;
3961 if (nf.getTree() != null)
3963 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3969 tp.setLocation(x, y);
3972 Desktop.addInternalFrame(tp, treeTitle, w, h);
3974 } catch (Exception ex)
3976 ex.printStackTrace();
3982 private boolean buildingMenu = false;
3985 * Generates menu items and listener event actions for web service clients
3988 public void BuildWebServiceMenu()
3990 while (buildingMenu)
3994 System.err.println("Waiting for building menu to finish.");
3996 } catch (Exception e)
4000 final AlignFrame me = this;
4001 buildingMenu = true;
4002 new Thread(new Runnable()
4007 final List<JMenuItem> legacyItems = new ArrayList<>();
4010 // System.err.println("Building ws menu again "
4011 // + Thread.currentThread());
4012 // TODO: add support for context dependent disabling of services based
4014 // alignment and current selection
4015 // TODO: add additional serviceHandle parameter to specify abstract
4017 // class independently of AbstractName
4018 // TODO: add in rediscovery GUI function to restart discoverer
4019 // TODO: group services by location as well as function and/or
4021 // object broker mechanism.
4022 final Vector<JMenu> wsmenu = new Vector<>();
4023 final IProgressIndicator af = me;
4026 * do not i18n these strings - they are hard-coded in class
4027 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4028 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4030 final JMenu msawsmenu = new JMenu("Alignment");
4031 final JMenu secstrmenu = new JMenu(
4032 "Secondary Structure Prediction");
4033 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4034 final JMenu analymenu = new JMenu("Analysis");
4035 final JMenu dismenu = new JMenu("Protein Disorder");
4036 // JAL-940 - only show secondary structure prediction services from
4037 // the legacy server
4038 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4040 Discoverer.services != null && (Discoverer.services.size() > 0))
4042 // TODO: refactor to allow list of AbstractName/Handler bindings to
4044 // stored or retrieved from elsewhere
4045 // No MSAWS used any more:
4046 // Vector msaws = null; // (Vector)
4047 // Discoverer.services.get("MsaWS");
4048 Vector secstrpr = (Vector) Discoverer.services
4050 if (secstrpr != null)
4052 // Add any secondary structure prediction services
4053 for (int i = 0, j = secstrpr.size(); i < j; i++)
4055 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4057 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4058 .getServiceClient(sh);
4059 int p = secstrmenu.getItemCount();
4060 impl.attachWSMenuEntry(secstrmenu, me);
4061 int q = secstrmenu.getItemCount();
4062 for (int litm = p; litm < q; litm++)
4064 legacyItems.add(secstrmenu.getItem(litm));
4070 // Add all submenus in the order they should appear on the web
4072 wsmenu.add(msawsmenu);
4073 wsmenu.add(secstrmenu);
4074 wsmenu.add(dismenu);
4075 wsmenu.add(analymenu);
4076 // No search services yet
4077 // wsmenu.add(seqsrchmenu);
4079 javax.swing.SwingUtilities.invokeLater(new Runnable()
4086 webService.removeAll();
4087 // first, add discovered services onto the webservices menu
4088 if (wsmenu.size() > 0)
4090 for (int i = 0, j = wsmenu.size(); i < j; i++)
4092 webService.add(wsmenu.get(i));
4097 webService.add(me.webServiceNoServices);
4099 // TODO: move into separate menu builder class.
4100 boolean new_sspred = false;
4101 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4103 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4104 if (jws2servs != null)
4106 if (jws2servs.hasServices())
4108 jws2servs.attachWSMenuEntry(webService, me);
4109 for (Jws2Instance sv : jws2servs.getServices())
4111 if (sv.description.toLowerCase().contains("jpred"))
4113 for (JMenuItem jmi : legacyItems)
4115 jmi.setVisible(false);
4121 if (jws2servs.isRunning())
4123 JMenuItem tm = new JMenuItem(
4124 "Still discovering JABA Services");
4125 tm.setEnabled(false);
4130 build_urlServiceMenu(me.webService);
4131 build_fetchdbmenu(webService);
4132 for (JMenu item : wsmenu)
4134 if (item.getItemCount() == 0)
4136 item.setEnabled(false);
4140 item.setEnabled(true);
4143 } catch (Exception e)
4146 "Exception during web service menu building process.",
4151 } catch (Exception e)
4154 buildingMenu = false;
4161 * construct any groupURL type service menu entries.
4165 private void build_urlServiceMenu(JMenu webService)
4167 // TODO: remove this code when 2.7 is released
4168 // DEBUG - alignmentView
4170 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4171 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4173 * @Override public void actionPerformed(ActionEvent e) {
4174 * jalview.datamodel.AlignmentView
4175 * .testSelectionViews(af.viewport.getAlignment(),
4176 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4178 * }); webService.add(testAlView);
4180 // TODO: refactor to RestClient discoverer and merge menu entries for
4181 // rest-style services with other types of analysis/calculation service
4182 // SHmmr test client - still being implemented.
4183 // DEBUG - alignmentView
4185 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4188 client.attachWSMenuEntry(
4189 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4195 * Searches the alignment sequences for xRefs and builds the Show
4196 * Cross-References menu (formerly called Show Products), with database
4197 * sources for which cross-references are found (protein sources for a
4198 * nucleotide alignment and vice versa)
4200 * @return true if Show Cross-references menu should be enabled
4202 public boolean canShowProducts()
4204 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4205 AlignmentI dataset = viewport.getAlignment().getDataset();
4207 showProducts.removeAll();
4208 final boolean dna = viewport.getAlignment().isNucleotide();
4210 if (seqs == null || seqs.length == 0)
4212 // nothing to see here.
4216 boolean showp = false;
4219 List<String> ptypes = new CrossRef(seqs, dataset)
4220 .findXrefSourcesForSequences(dna);
4222 for (final String source : ptypes)
4225 final AlignFrame af = this;
4226 JMenuItem xtype = new JMenuItem(source);
4227 xtype.addActionListener(new ActionListener()
4230 public void actionPerformed(ActionEvent e)
4232 showProductsFor(af.viewport.getSequenceSelection(), dna,
4236 showProducts.add(xtype);
4238 showProducts.setVisible(showp);
4239 showProducts.setEnabled(showp);
4240 } catch (Exception e)
4243 "canShowProducts threw an exception - please report to help@jalview.org",
4251 * Finds and displays cross-references for the selected sequences (protein
4252 * products for nucleotide sequences, dna coding sequences for peptides).
4255 * the sequences to show cross-references for
4257 * true if from a nucleotide alignment (so showing proteins)
4259 * the database to show cross-references for
4261 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4262 final String source)
4264 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4269 * Construct and display a new frame containing the translation of this
4270 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4273 public void showTranslation_actionPerformed(ActionEvent e)
4275 AlignmentI al = null;
4278 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4280 al = dna.translateCdna();
4281 } catch (Exception ex)
4283 jalview.bin.Cache.log.error(
4284 "Exception during translation. Please report this !", ex);
4285 final String msg = MessageManager.getString(
4286 "label.error_when_translating_sequences_submit_bug_report");
4287 final String errorTitle = MessageManager
4288 .getString("label.implementation_error")
4289 + MessageManager.getString("label.translation_failed");
4290 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4291 JvOptionPane.ERROR_MESSAGE);
4294 if (al == null || al.getHeight() == 0)
4296 final String msg = MessageManager.getString(
4297 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4298 final String errorTitle = MessageManager
4299 .getString("label.translation_failed");
4300 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4301 JvOptionPane.WARNING_MESSAGE);
4305 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4306 af.setFileFormat(this.currentFileFormat);
4307 final String newTitle = MessageManager
4308 .formatMessage("label.translation_of_params", new Object[]
4309 { this.getTitle() });
4310 af.setTitle(newTitle);
4311 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4313 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4314 viewport.openSplitFrame(af, new Alignment(seqs));
4318 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4325 * Set the file format
4329 public void setFileFormat(FileFormatI format)
4331 this.currentFileFormat = format;
4335 * Try to load a features file onto the alignment.
4338 * contents or path to retrieve file
4340 * access mode of file (see jalview.io.AlignFile)
4341 * @return true if features file was parsed correctly.
4343 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4345 return avc.parseFeaturesFile(file, sourceType,
4346 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4351 public void refreshFeatureUI(boolean enableIfNecessary)
4353 // note - currently this is only still here rather than in the controller
4354 // because of the featureSettings hard reference that is yet to be
4356 if (enableIfNecessary)
4358 viewport.setShowSequenceFeatures(true);
4359 showSeqFeatures.setSelected(true);
4365 public void dragEnter(DropTargetDragEvent evt)
4370 public void dragExit(DropTargetEvent evt)
4375 public void dragOver(DropTargetDragEvent evt)
4380 public void dropActionChanged(DropTargetDragEvent evt)
4385 public void drop(DropTargetDropEvent evt)
4387 // JAL-1552 - acceptDrop required before getTransferable call for
4388 // Java's Transferable for native dnd
4389 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4390 Transferable t = evt.getTransferable();
4391 final AlignFrame thisaf = this;
4392 final List<String> files = new ArrayList<>();
4393 List<DataSourceType> protocols = new ArrayList<>();
4397 Desktop.transferFromDropTarget(files, protocols, evt, t);
4398 } catch (Exception e)
4400 e.printStackTrace();
4404 new Thread(new Runnable()
4411 // check to see if any of these files have names matching sequences
4414 SequenceIdMatcher idm = new SequenceIdMatcher(
4415 viewport.getAlignment().getSequencesArray());
4417 * Object[] { String,SequenceI}
4419 ArrayList<Object[]> filesmatched = new ArrayList<>();
4420 ArrayList<String> filesnotmatched = new ArrayList<>();
4421 for (int i = 0; i < files.size(); i++)
4423 String file = files.get(i).toString();
4425 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4426 if (protocol == DataSourceType.FILE)
4428 File fl = new File(file);
4429 pdbfn = fl.getName();
4431 else if (protocol == DataSourceType.URL)
4433 URL url = new URL(file);
4434 pdbfn = url.getFile();
4436 if (pdbfn.length() > 0)
4438 // attempt to find a match in the alignment
4439 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4440 int l = 0, c = pdbfn.indexOf(".");
4441 while (mtch == null && c != -1)
4446 } while ((c = pdbfn.indexOf(".", l)) > l);
4449 pdbfn = pdbfn.substring(0, l);
4451 mtch = idm.findAllIdMatches(pdbfn);
4455 FileFormatI type = null;
4458 type = new IdentifyFile().identify(file, protocol);
4459 } catch (Exception ex)
4463 if (type != null && type.isStructureFile())
4465 filesmatched.add(new Object[] { file, protocol, mtch });
4469 // File wasn't named like one of the sequences or wasn't a PDB
4471 filesnotmatched.add(file);
4475 if (filesmatched.size() > 0)
4477 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4478 || JvOptionPane.showConfirmDialog(thisaf,
4479 MessageManager.formatMessage(
4480 "label.automatically_associate_structure_files_with_sequences_same_name",
4482 { Integer.valueOf(filesmatched.size())
4484 MessageManager.getString(
4485 "label.automatically_associate_structure_files_by_name"),
4486 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4489 for (Object[] fm : filesmatched)
4491 // try and associate
4492 // TODO: may want to set a standard ID naming formalism for
4493 // associating PDB files which have no IDs.
4494 for (SequenceI toassoc : (SequenceI[]) fm[2])
4496 PDBEntry pe = new AssociatePdbFileWithSeq()
4497 .associatePdbWithSeq((String) fm[0],
4498 (DataSourceType) fm[1], toassoc, false,
4502 System.err.println("Associated file : "
4503 + ((String) fm[0]) + " with "
4504 + toassoc.getDisplayId(true));
4508 alignPanel.paintAlignment(true);
4512 if (filesnotmatched.size() > 0)
4514 if (assocfiles > 0 && (Cache.getDefault(
4515 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4516 || JvOptionPane.showConfirmDialog(thisaf,
4517 "<html>" + MessageManager.formatMessage(
4518 "label.ignore_unmatched_dropped_files_info",
4521 filesnotmatched.size())
4524 MessageManager.getString(
4525 "label.ignore_unmatched_dropped_files"),
4526 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4530 for (String fn : filesnotmatched)
4532 loadJalviewDataFile(fn, null, null, null);
4536 } catch (Exception ex)
4538 ex.printStackTrace();
4546 * Attempt to load a "dropped" file or URL string, by testing in turn for
4548 * <li>an Annotation file</li>
4549 * <li>a JNet file</li>
4550 * <li>a features file</li>
4551 * <li>else try to interpret as an alignment file</li>
4555 * either a filename or a URL string.
4557 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4558 FileFormatI format, SequenceI assocSeq)
4562 if (sourceType == null)
4564 sourceType = FormatAdapter.checkProtocol(file);
4566 // if the file isn't identified, or not positively identified as some
4567 // other filetype (PFAM is default unidentified alignment file type) then
4568 // try to parse as annotation.
4569 boolean isAnnotation = (format == null
4570 || FileFormat.Pfam.equals(format))
4571 ? new AnnotationFile().annotateAlignmentView(viewport,
4577 // first see if its a T-COFFEE score file
4578 TCoffeeScoreFile tcf = null;
4581 tcf = new TCoffeeScoreFile(file, sourceType);
4584 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4588 new TCoffeeColourScheme(viewport.getAlignment()));
4589 isAnnotation = true;
4590 statusBar.setText(MessageManager.getString(
4591 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4595 // some problem - if no warning its probable that the ID matching
4596 // process didn't work
4597 JvOptionPane.showMessageDialog(Desktop.desktop,
4598 tcf.getWarningMessage() == null
4599 ? MessageManager.getString(
4600 "label.check_file_matches_sequence_ids_alignment")
4601 : tcf.getWarningMessage(),
4602 MessageManager.getString(
4603 "label.problem_reading_tcoffee_score_file"),
4604 JvOptionPane.WARNING_MESSAGE);
4611 } catch (Exception x)
4614 "Exception when processing data source as T-COFFEE score file",
4620 // try to see if its a JNet 'concise' style annotation file *before*
4622 // try to parse it as a features file
4625 format = new IdentifyFile().identify(file, sourceType);
4627 if (FileFormat.ScoreMatrix == format)
4629 ScoreMatrixFile sm = new ScoreMatrixFile(
4630 new FileParse(file, sourceType));
4632 // todo: i18n this message
4633 statusBar.setText(MessageManager.formatMessage(
4634 "label.successfully_loaded_matrix",
4635 sm.getMatrixName()));
4637 else if (FileFormat.Jnet.equals(format))
4639 JPredFile predictions = new JPredFile(file, sourceType);
4640 new JnetAnnotationMaker();
4641 JnetAnnotationMaker.add_annotation(predictions,
4642 viewport.getAlignment(), 0, false);
4643 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4644 viewport.getAlignment().setSeqrep(repseq);
4645 HiddenColumns cs = new HiddenColumns();
4646 cs.hideInsertionsFor(repseq);
4647 viewport.getAlignment().setHiddenColumns(cs);
4648 isAnnotation = true;
4650 // else if (IdentifyFile.FeaturesFile.equals(format))
4651 else if (FileFormat.Features.equals(format))
4653 if (parseFeaturesFile(file, sourceType))
4655 alignPanel.paintAlignment(true);
4660 new FileLoader().LoadFile(viewport, file, sourceType, format);
4667 alignPanel.adjustAnnotationHeight();
4668 viewport.updateSequenceIdColours();
4669 buildSortByAnnotationScoresMenu();
4670 alignPanel.paintAlignment(true);
4672 } catch (Exception ex)
4674 ex.printStackTrace();
4675 } catch (OutOfMemoryError oom)
4680 } catch (Exception x)
4685 + (sourceType != null
4686 ? (sourceType == DataSourceType.PASTE
4688 : "using " + sourceType + " from "
4692 ? "(parsing as '" + format + "' file)"
4694 oom, Desktop.desktop);
4699 * Method invoked by the ChangeListener on the tabbed pane, in other words
4700 * when a different tabbed pane is selected by the user or programmatically.
4703 public void tabSelectionChanged(int index)
4707 alignPanel = alignPanels.get(index);
4708 viewport = alignPanel.av;
4709 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4710 setMenusFromViewport(viewport);
4714 * 'focus' any colour slider that is open to the selected viewport
4716 if (viewport.getConservationSelected())
4718 SliderPanel.setConservationSlider(alignPanel,
4719 viewport.getResidueShading(), alignPanel.getViewName());
4723 SliderPanel.hideConservationSlider();
4725 if (viewport.getAbovePIDThreshold())
4727 SliderPanel.setPIDSliderSource(alignPanel,
4728 viewport.getResidueShading(), alignPanel.getViewName());
4732 SliderPanel.hidePIDSlider();
4736 * If there is a frame linked to this one in a SplitPane, switch it to the
4737 * same view tab index. No infinite recursion of calls should happen, since
4738 * tabSelectionChanged() should not get invoked on setting the selected
4739 * index to an unchanged value. Guard against setting an invalid index
4740 * before the new view peer tab has been created.
4742 final AlignViewportI peer = viewport.getCodingComplement();
4745 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4746 .getAlignPanel().alignFrame;
4747 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4749 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4755 * On right mouse click on view tab, prompt for and set new view name.
4758 public void tabbedPane_mousePressed(MouseEvent e)
4760 if (e.isPopupTrigger())
4762 String msg = MessageManager.getString("label.enter_view_name");
4763 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4764 JvOptionPane.QUESTION_MESSAGE);
4768 viewport.viewName = reply;
4769 // TODO warn if reply is in getExistingViewNames()?
4770 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4775 public AlignViewport getCurrentView()
4781 * Open the dialog for regex description parsing.
4784 protected void extractScores_actionPerformed(ActionEvent e)
4786 ParseProperties pp = new jalview.analysis.ParseProperties(
4787 viewport.getAlignment());
4788 // TODO: verify regex and introduce GUI dialog for version 2.5
4789 // if (pp.getScoresFromDescription("col", "score column ",
4790 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4792 if (pp.getScoresFromDescription("description column",
4793 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4795 buildSortByAnnotationScoresMenu();
4803 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4807 protected void showDbRefs_actionPerformed(ActionEvent e)
4809 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4815 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4819 protected void showNpFeats_actionPerformed(ActionEvent e)
4821 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4825 * find the viewport amongst the tabs in this alignment frame and close that
4830 public boolean closeView(AlignViewportI av)
4834 this.closeMenuItem_actionPerformed(false);
4837 Component[] comp = tabbedPane.getComponents();
4838 for (int i = 0; comp != null && i < comp.length; i++)
4840 if (comp[i] instanceof AlignmentPanel)
4842 if (((AlignmentPanel) comp[i]).av == av)
4845 closeView((AlignmentPanel) comp[i]);
4853 protected void build_fetchdbmenu(JMenu webService)
4855 // Temporary hack - DBRef Fetcher always top level ws entry.
4856 // TODO We probably want to store a sequence database checklist in
4857 // preferences and have checkboxes.. rather than individual sources selected
4859 final JMenu rfetch = new JMenu(
4860 MessageManager.getString("action.fetch_db_references"));
4861 rfetch.setToolTipText(MessageManager.getString(
4862 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4863 webService.add(rfetch);
4865 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4866 MessageManager.getString("option.trim_retrieved_seqs"));
4867 trimrs.setToolTipText(
4868 MessageManager.getString("label.trim_retrieved_sequences"));
4869 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4870 trimrs.addActionListener(new ActionListener()
4873 public void actionPerformed(ActionEvent e)
4875 trimrs.setSelected(trimrs.isSelected());
4876 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4877 Boolean.valueOf(trimrs.isSelected()).toString());
4881 JMenuItem fetchr = new JMenuItem(
4882 MessageManager.getString("label.standard_databases"));
4883 fetchr.setToolTipText(
4884 MessageManager.getString("label.fetch_embl_uniprot"));
4885 fetchr.addActionListener(new ActionListener()
4889 public void actionPerformed(ActionEvent e)
4891 new Thread(new Runnable()
4896 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4897 .getAlignment().isNucleotide();
4898 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4899 alignPanel.av.getSequenceSelection(),
4900 alignPanel.alignFrame, null,
4901 alignPanel.alignFrame.featureSettings, isNucleotide);
4902 dbRefFetcher.addListener(new FetchFinishedListenerI()
4905 public void finished()
4907 AlignFrame.this.setMenusForViewport();
4910 dbRefFetcher.fetchDBRefs(false);
4918 final AlignFrame me = this;
4919 new Thread(new Runnable()
4924 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4925 .getSequenceFetcherSingleton(me);
4926 javax.swing.SwingUtilities.invokeLater(new Runnable()
4931 String[] dbclasses = sf.getOrderedSupportedSources();
4932 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4933 // jalview.util.QuickSort.sort(otherdb, otherdb);
4934 List<DbSourceProxy> otherdb;
4935 JMenu dfetch = new JMenu();
4936 JMenu ifetch = new JMenu();
4937 JMenuItem fetchr = null;
4938 int comp = 0, icomp = 0, mcomp = 15;
4939 String mname = null;
4941 for (String dbclass : dbclasses)
4943 otherdb = sf.getSourceProxy(dbclass);
4944 // add a single entry for this class, or submenu allowing 'fetch
4946 if (otherdb == null || otherdb.size() < 1)
4950 // List<DbSourceProxy> dbs=otherdb;
4951 // otherdb=new ArrayList<DbSourceProxy>();
4952 // for (DbSourceProxy db:dbs)
4954 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4958 mname = "From " + dbclass;
4960 if (otherdb.size() == 1)
4962 final DbSourceProxy[] dassource = otherdb
4963 .toArray(new DbSourceProxy[0]);
4964 DbSourceProxy src = otherdb.get(0);
4965 fetchr = new JMenuItem(src.getDbSource());
4966 fetchr.addActionListener(new ActionListener()
4970 public void actionPerformed(ActionEvent e)
4972 new Thread(new Runnable()
4978 boolean isNucleotide = alignPanel.alignFrame
4979 .getViewport().getAlignment()
4981 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4982 alignPanel.av.getSequenceSelection(),
4983 alignPanel.alignFrame, dassource,
4984 alignPanel.alignFrame.featureSettings,
4987 .addListener(new FetchFinishedListenerI()
4990 public void finished()
4992 AlignFrame.this.setMenusForViewport();
4995 dbRefFetcher.fetchDBRefs(false);
5001 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5002 MessageManager.formatMessage(
5003 "label.fetch_retrieve_from", new Object[]
5004 { src.getDbName() })));
5010 final DbSourceProxy[] dassource = otherdb
5011 .toArray(new DbSourceProxy[0]);
5013 DbSourceProxy src = otherdb.get(0);
5014 fetchr = new JMenuItem(MessageManager
5015 .formatMessage("label.fetch_all_param", new Object[]
5016 { src.getDbSource() }));
5017 fetchr.addActionListener(new ActionListener()
5020 public void actionPerformed(ActionEvent e)
5022 new Thread(new Runnable()
5028 boolean isNucleotide = alignPanel.alignFrame
5029 .getViewport().getAlignment()
5031 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5032 alignPanel.av.getSequenceSelection(),
5033 alignPanel.alignFrame, dassource,
5034 alignPanel.alignFrame.featureSettings,
5037 .addListener(new FetchFinishedListenerI()
5040 public void finished()
5042 AlignFrame.this.setMenusForViewport();
5045 dbRefFetcher.fetchDBRefs(false);
5051 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5052 MessageManager.formatMessage(
5053 "label.fetch_retrieve_from_all_sources",
5055 { Integer.valueOf(otherdb.size())
5057 src.getDbSource(), src.getDbName() })));
5060 // and then build the rest of the individual menus
5061 ifetch = new JMenu(MessageManager.formatMessage(
5062 "label.source_from_db_source", new Object[]
5063 { src.getDbSource() }));
5065 String imname = null;
5067 for (DbSourceProxy sproxy : otherdb)
5069 String dbname = sproxy.getDbName();
5070 String sname = dbname.length() > 5
5071 ? dbname.substring(0, 5) + "..."
5073 String msname = dbname.length() > 10
5074 ? dbname.substring(0, 10) + "..."
5078 imname = MessageManager
5079 .formatMessage("label.from_msname", new Object[]
5082 fetchr = new JMenuItem(msname);
5083 final DbSourceProxy[] dassrc = { sproxy };
5084 fetchr.addActionListener(new ActionListener()
5088 public void actionPerformed(ActionEvent e)
5090 new Thread(new Runnable()
5096 boolean isNucleotide = alignPanel.alignFrame
5097 .getViewport().getAlignment()
5099 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5100 alignPanel.av.getSequenceSelection(),
5101 alignPanel.alignFrame, dassrc,
5102 alignPanel.alignFrame.featureSettings,
5105 .addListener(new FetchFinishedListenerI()
5108 public void finished()
5110 AlignFrame.this.setMenusForViewport();
5113 dbRefFetcher.fetchDBRefs(false);
5119 fetchr.setToolTipText(
5120 "<html>" + MessageManager.formatMessage(
5121 "label.fetch_retrieve_from", new Object[]
5125 if (++icomp >= mcomp || i == (otherdb.size()))
5127 ifetch.setText(MessageManager.formatMessage(
5128 "label.source_to_target", imname, sname));
5130 ifetch = new JMenu();
5138 if (comp >= mcomp || dbi >= (dbclasses.length))
5140 dfetch.setText(MessageManager.formatMessage(
5141 "label.source_to_target", mname, dbclass));
5143 dfetch = new JMenu();
5156 * Left justify the whole alignment.
5159 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5161 AlignmentI al = viewport.getAlignment();
5163 viewport.firePropertyChange("alignment", null, al);
5167 * Right justify the whole alignment.
5170 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5172 AlignmentI al = viewport.getAlignment();
5174 viewport.firePropertyChange("alignment", null, al);
5178 public void setShowSeqFeatures(boolean b)
5180 showSeqFeatures.setSelected(b);
5181 viewport.setShowSequenceFeatures(b);
5188 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5189 * awt.event.ActionEvent)
5192 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5194 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5195 alignPanel.paintAlignment(true);
5202 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5206 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5208 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5209 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5217 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5218 * .event.ActionEvent)
5221 protected void showGroupConservation_actionPerformed(ActionEvent e)
5223 viewport.setShowGroupConservation(showGroupConservation.getState());
5224 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5231 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5232 * .event.ActionEvent)
5235 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5237 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5238 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5245 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5246 * .event.ActionEvent)
5249 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5251 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5252 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5256 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5258 showSequenceLogo.setState(true);
5259 viewport.setShowSequenceLogo(true);
5260 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5261 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5265 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5267 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5274 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5275 * .event.ActionEvent)
5278 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5280 if (avc.makeGroupsFromSelection())
5282 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5283 alignPanel.updateAnnotation();
5284 alignPanel.paintAlignment(true);
5288 public void clearAlignmentSeqRep()
5290 // TODO refactor alignmentseqrep to controller
5291 if (viewport.getAlignment().hasSeqrep())
5293 viewport.getAlignment().setSeqrep(null);
5294 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5295 alignPanel.updateAnnotation();
5296 alignPanel.paintAlignment(true);
5301 protected void createGroup_actionPerformed(ActionEvent e)
5303 if (avc.createGroup())
5305 alignPanel.alignmentChanged();
5310 protected void unGroup_actionPerformed(ActionEvent e)
5314 alignPanel.alignmentChanged();
5319 * make the given alignmentPanel the currently selected tab
5321 * @param alignmentPanel
5323 public void setDisplayedView(AlignmentPanel alignmentPanel)
5325 if (!viewport.getSequenceSetId()
5326 .equals(alignmentPanel.av.getSequenceSetId()))
5328 throw new Error(MessageManager.getString(
5329 "error.implementation_error_cannot_show_view_alignment_frame"));
5331 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5332 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5334 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5339 * Action on selection of menu options to Show or Hide annotations.
5342 * @param forSequences
5343 * update sequence-related annotations
5344 * @param forAlignment
5345 * update non-sequence-related annotations
5348 protected void setAnnotationsVisibility(boolean visible,
5349 boolean forSequences, boolean forAlignment)
5351 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5352 .getAlignmentAnnotation();
5357 for (AlignmentAnnotation aa : anns)
5360 * don't display non-positional annotations on an alignment
5362 if (aa.annotations == null)
5366 boolean apply = (aa.sequenceRef == null && forAlignment)
5367 || (aa.sequenceRef != null && forSequences);
5370 aa.visible = visible;
5373 alignPanel.validateAnnotationDimensions(true);
5374 alignPanel.alignmentChanged();
5378 * Store selected annotation sort order for the view and repaint.
5381 protected void sortAnnotations_actionPerformed()
5383 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5385 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5386 alignPanel.paintAlignment(true);
5391 * @return alignment panels in this alignment frame
5393 public List<? extends AlignmentViewPanel> getAlignPanels()
5395 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5399 * Open a new alignment window, with the cDNA associated with this (protein)
5400 * alignment, aligned as is the protein.
5402 protected void viewAsCdna_actionPerformed()
5404 // TODO no longer a menu action - refactor as required
5405 final AlignmentI alignment = getViewport().getAlignment();
5406 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5407 if (mappings == null)
5411 List<SequenceI> cdnaSeqs = new ArrayList<>();
5412 for (SequenceI aaSeq : alignment.getSequences())
5414 for (AlignedCodonFrame acf : mappings)
5416 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5420 * There is a cDNA mapping for this protein sequence - add to new
5421 * alignment. It will share the same dataset sequence as other mapped
5422 * cDNA (no new mappings need to be created).
5424 final Sequence newSeq = new Sequence(dnaSeq);
5425 newSeq.setDatasetSequence(dnaSeq);
5426 cdnaSeqs.add(newSeq);
5430 if (cdnaSeqs.size() == 0)
5432 // show a warning dialog no mapped cDNA
5435 AlignmentI cdna = new Alignment(
5436 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5437 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5438 AlignFrame.DEFAULT_HEIGHT);
5439 cdna.alignAs(alignment);
5440 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5442 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5443 AlignFrame.DEFAULT_HEIGHT);
5447 * Set visibility of dna/protein complement view (available when shown in a
5453 protected void showComplement_actionPerformed(boolean show)
5455 SplitContainerI sf = getSplitViewContainer();
5458 sf.setComplementVisible(this, show);
5463 * Generate the reverse (optionally complemented) of the selected sequences,
5464 * and add them to the alignment
5467 protected void showReverse_actionPerformed(boolean complement)
5469 AlignmentI al = null;
5472 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5473 al = dna.reverseCdna(complement);
5474 viewport.addAlignment(al, "");
5475 addHistoryItem(new EditCommand(
5476 MessageManager.getString("label.add_sequences"), Action.PASTE,
5477 al.getSequencesArray(), 0, al.getWidth(),
5478 viewport.getAlignment()));
5479 } catch (Exception ex)
5481 System.err.println(ex.getMessage());
5487 * Try to run a script in the Groovy console, having first ensured that this
5488 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5489 * be targeted at this alignment.
5492 protected void runGroovy_actionPerformed()
5494 Jalview.setCurrentAlignFrame(this);
5495 groovy.ui.Console console = Desktop.getGroovyConsole();
5496 if (console != null)
5500 console.runScript();
5501 } catch (Exception ex)
5503 System.err.println((ex.toString()));
5504 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5505 MessageManager.getString("label.couldnt_run_groovy_script"),
5506 MessageManager.getString("label.groovy_support_failed"),
5507 JvOptionPane.ERROR_MESSAGE);
5512 System.err.println("Can't run Groovy script as console not found");
5517 * Hides columns containing (or not containing) a specified feature, provided
5518 * that would not leave all columns hidden
5520 * @param featureType
5521 * @param columnsContaining
5524 public boolean hideFeatureColumns(String featureType,
5525 boolean columnsContaining)
5527 boolean notForHiding = avc.markColumnsContainingFeatures(
5528 columnsContaining, false, false, featureType);
5531 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5532 false, featureType))
5534 getViewport().hideSelectedColumns();
5542 protected void selectHighlightedColumns_actionPerformed(
5543 ActionEvent actionEvent)
5545 // include key modifier check in case user selects from menu
5546 avc.markHighlightedColumns(
5547 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5548 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5549 | ActionEvent.CTRL_MASK)) != 0);
5553 * Rebuilds the Colour menu, including any user-defined colours which have
5554 * been loaded either on startup or during the session
5556 public void buildColourMenu()
5558 colourMenu.removeAll();
5560 colourMenu.add(applyToAllGroups);
5561 colourMenu.add(textColour);
5562 colourMenu.addSeparator();
5564 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5567 colourMenu.addSeparator();
5568 colourMenu.add(conservationMenuItem);
5569 colourMenu.add(modifyConservation);
5570 colourMenu.add(abovePIDThreshold);
5571 colourMenu.add(modifyPID);
5572 colourMenu.add(annotationColour);
5574 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5575 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5579 * Open a dialog (if not already open) that allows the user to select and
5580 * calculate PCA or Tree analysis
5582 protected void openTreePcaDialog()
5584 if (alignPanel.getCalculationDialog() == null)
5586 new CalculationChooser(AlignFrame.this);
5591 protected void loadVcf_actionPerformed()
5593 JalviewFileChooser chooser = new JalviewFileChooser(
5594 Cache.getProperty("LAST_DIRECTORY"));
5595 chooser.setFileView(new JalviewFileView());
5596 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5597 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5599 int value = chooser.showOpenDialog(null);
5601 if (value == JalviewFileChooser.APPROVE_OPTION)
5603 String choice = chooser.getSelectedFile().getPath();
5604 Cache.setProperty("LAST_DIRECTORY", choice);
5605 new VCFLoader(viewport.getAlignment()).loadVCF(choice, this);
5611 class PrintThread extends Thread
5615 public PrintThread(AlignmentPanel ap)
5620 static PageFormat pf;
5625 PrinterJob printJob = PrinterJob.getPrinterJob();
5629 printJob.setPrintable(ap, pf);
5633 printJob.setPrintable(ap);
5636 if (printJob.printDialog())
5641 } catch (Exception PrintException)
5643 PrintException.printStackTrace();