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.analysis.TreeModel;
30 import jalview.api.AlignExportSettingI;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.AlignViewportI;
34 import jalview.api.AlignmentViewPanel;
35 import jalview.api.FeatureSettingsControllerI;
36 import jalview.api.SplitContainerI;
37 import jalview.api.ViewStyleI;
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.jbgui.GAlignFrame;
85 import jalview.schemes.ColourSchemeI;
86 import jalview.schemes.ColourSchemes;
87 import jalview.schemes.ResidueColourScheme;
88 import jalview.schemes.TCoffeeColourScheme;
89 import jalview.util.MessageManager;
90 import jalview.viewmodel.AlignmentViewport;
91 import jalview.viewmodel.ViewportRanges;
92 import jalview.ws.DBRefFetcher;
93 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
94 import jalview.ws.jws1.Discoverer;
95 import jalview.ws.jws2.Jws2Discoverer;
96 import jalview.ws.jws2.jabaws2.Jws2Instance;
97 import jalview.ws.seqfetcher.DbSourceProxy;
99 import java.awt.BorderLayout;
100 import java.awt.Component;
101 import java.awt.Rectangle;
102 import java.awt.Toolkit;
103 import java.awt.datatransfer.Clipboard;
104 import java.awt.datatransfer.DataFlavor;
105 import java.awt.datatransfer.StringSelection;
106 import java.awt.datatransfer.Transferable;
107 import java.awt.dnd.DnDConstants;
108 import java.awt.dnd.DropTargetDragEvent;
109 import java.awt.dnd.DropTargetDropEvent;
110 import java.awt.dnd.DropTargetEvent;
111 import java.awt.dnd.DropTargetListener;
112 import java.awt.event.ActionEvent;
113 import java.awt.event.ActionListener;
114 import java.awt.event.FocusAdapter;
115 import java.awt.event.FocusEvent;
116 import java.awt.event.ItemEvent;
117 import java.awt.event.ItemListener;
118 import java.awt.event.KeyAdapter;
119 import java.awt.event.KeyEvent;
120 import java.awt.event.MouseEvent;
121 import java.awt.print.PageFormat;
122 import java.awt.print.PrinterJob;
123 import java.beans.PropertyChangeEvent;
125 import java.io.FileWriter;
126 import java.io.PrintWriter;
128 import java.util.ArrayList;
129 import java.util.Arrays;
130 import java.util.Deque;
131 import java.util.Enumeration;
132 import java.util.Hashtable;
133 import java.util.List;
134 import java.util.Vector;
136 import javax.swing.JCheckBoxMenuItem;
137 import javax.swing.JEditorPane;
138 import javax.swing.JInternalFrame;
139 import javax.swing.JLayeredPane;
140 import javax.swing.JMenu;
141 import javax.swing.JMenuItem;
142 import javax.swing.JScrollPane;
143 import javax.swing.SwingUtilities;
149 * @version $Revision$
151 public class AlignFrame extends GAlignFrame implements DropTargetListener,
152 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
155 public static final int DEFAULT_WIDTH = 700;
157 public static final int DEFAULT_HEIGHT = 500;
160 * The currently displayed panel (selected tabbed view if more than one)
162 public AlignmentPanel alignPanel;
164 AlignViewport viewport;
166 ViewportRanges vpRanges;
168 public AlignViewControllerI avc;
170 List<AlignmentPanel> alignPanels = new ArrayList<>();
173 * Last format used to load or save alignments in this window
175 FileFormatI currentFileFormat = null;
178 * Current filename for this alignment
180 String fileName = null;
183 * Creates a new AlignFrame object with specific width and height.
189 public AlignFrame(AlignmentI al, int width, int height)
191 this(al, null, width, height);
195 * Creates a new AlignFrame object with specific width, height and
201 * @param sequenceSetId
203 public AlignFrame(AlignmentI al, int width, int height,
204 String sequenceSetId)
206 this(al, null, width, height, sequenceSetId);
210 * Creates a new AlignFrame object with specific width, height and
216 * @param sequenceSetId
219 public AlignFrame(AlignmentI al, int width, int height,
220 String sequenceSetId, String viewId)
222 this(al, null, width, height, sequenceSetId, viewId);
226 * new alignment window with hidden columns
230 * @param hiddenColumns
231 * ColumnSelection or null
233 * Width of alignment frame
237 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
240 this(al, hiddenColumns, width, height, null);
244 * Create alignment frame for al with hiddenColumns, a specific width and
245 * height, and specific sequenceId
248 * @param hiddenColumns
251 * @param sequenceSetId
254 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
255 int height, String sequenceSetId)
257 this(al, hiddenColumns, width, height, sequenceSetId, null);
261 * Create alignment frame for al with hiddenColumns, a specific width and
262 * height, and specific sequenceId
265 * @param hiddenColumns
268 * @param sequenceSetId
273 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
274 int height, String sequenceSetId, String viewId)
276 setSize(width, height);
278 if (al.getDataset() == null)
283 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
285 alignPanel = new AlignmentPanel(this, viewport);
287 addAlignmentPanel(alignPanel, true);
291 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
292 HiddenColumns hiddenColumns, int width, int height)
294 setSize(width, height);
296 if (al.getDataset() == null)
301 viewport = new AlignViewport(al, hiddenColumns);
303 if (hiddenSeqs != null && hiddenSeqs.length > 0)
305 viewport.hideSequence(hiddenSeqs);
307 alignPanel = new AlignmentPanel(this, viewport);
308 addAlignmentPanel(alignPanel, true);
313 * Make a new AlignFrame from existing alignmentPanels
320 public AlignFrame(AlignmentPanel ap)
324 addAlignmentPanel(ap, false);
329 * initalise the alignframe from the underlying viewport data and the
334 if (!Jalview.isHeadlessMode())
336 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
339 vpRanges = viewport.getRanges();
340 avc = new jalview.controller.AlignViewController(this, viewport,
342 if (viewport.getAlignmentConservationAnnotation() == null)
344 // BLOSUM62Colour.setEnabled(false);
345 conservationMenuItem.setEnabled(false);
346 modifyConservation.setEnabled(false);
347 // PIDColour.setEnabled(false);
348 // abovePIDThreshold.setEnabled(false);
349 // modifyPID.setEnabled(false);
352 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
355 if (sortby.equals("Id"))
357 sortIDMenuItem_actionPerformed(null);
359 else if (sortby.equals("Pairwise Identity"))
361 sortPairwiseMenuItem_actionPerformed(null);
365 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
367 setMenusFromViewport(viewport);
368 buildSortByAnnotationScoresMenu();
369 calculateTree.addActionListener(new ActionListener()
373 public void actionPerformed(ActionEvent e)
380 if (Desktop.desktop != null)
382 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
383 addServiceListeners();
387 if (viewport.getWrapAlignment())
389 wrapMenuItem_actionPerformed(null);
392 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
394 this.overviewMenuItem_actionPerformed(null);
399 final List<AlignmentPanel> selviews = new ArrayList<>();
400 final List<AlignmentPanel> origview = new ArrayList<>();
401 final String menuLabel = MessageManager
402 .getString("label.copy_format_from");
403 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
404 new ViewSetProvider()
408 public AlignmentPanel[] getAllAlignmentPanels()
411 origview.add(alignPanel);
412 // make an array of all alignment panels except for this one
413 List<AlignmentPanel> aps = new ArrayList<>(
414 Arrays.asList(Desktop.getAlignmentPanels(null)));
415 aps.remove(AlignFrame.this.alignPanel);
416 return aps.toArray(new AlignmentPanel[aps.size()]);
418 }, selviews, new ItemListener()
422 public void itemStateChanged(ItemEvent e)
424 if (origview.size() > 0)
426 final AlignmentPanel ap = origview.get(0);
429 * Copy the ViewStyle of the selected panel to 'this one'.
430 * Don't change value of 'scaleProteinAsCdna' unless copying
433 ViewStyleI vs = selviews.get(0).getAlignViewport()
435 boolean fromSplitFrame = selviews.get(0)
436 .getAlignViewport().getCodingComplement() != null;
439 vs.setScaleProteinAsCdna(ap.getAlignViewport()
440 .getViewStyle().isScaleProteinAsCdna());
442 ap.getAlignViewport().setViewStyle(vs);
445 * Also rescale ViewStyle of SplitFrame complement if there is
446 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
447 * the whole ViewStyle (allow cDNA protein to have different
450 AlignViewportI complement = ap.getAlignViewport()
451 .getCodingComplement();
452 if (complement != null && vs.isScaleProteinAsCdna())
454 AlignFrame af = Desktop.getAlignFrameFor(complement);
455 ((SplitFrame) af.getSplitViewContainer())
457 af.setMenusForViewport();
461 ap.setSelected(true);
462 ap.alignFrame.setMenusForViewport();
467 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
468 .indexOf("devel") > -1
469 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
470 .indexOf("test") > -1)
472 formatMenu.add(vsel);
474 addFocusListener(new FocusAdapter()
477 public void focusGained(FocusEvent e)
479 Jalview.setCurrentAlignFrame(AlignFrame.this);
486 * Change the filename and format for the alignment, and enable the 'reload'
487 * button functionality.
494 public void setFileName(String file, FileFormatI format)
497 setFileFormat(format);
498 reload.setEnabled(true);
502 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
505 void addKeyListener()
507 addKeyListener(new KeyAdapter()
510 public void keyPressed(KeyEvent evt)
512 if (viewport.cursorMode
513 && ((evt.getKeyCode() >= KeyEvent.VK_0
514 && evt.getKeyCode() <= KeyEvent.VK_9)
515 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
516 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
517 && Character.isDigit(evt.getKeyChar()))
519 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
522 switch (evt.getKeyCode())
525 case 27: // escape key
526 deselectAllSequenceMenuItem_actionPerformed(null);
530 case KeyEvent.VK_DOWN:
531 if (evt.isAltDown() || !viewport.cursorMode)
533 moveSelectedSequences(false);
535 if (viewport.cursorMode)
537 alignPanel.getSeqPanel().moveCursor(0, 1);
542 if (evt.isAltDown() || !viewport.cursorMode)
544 moveSelectedSequences(true);
546 if (viewport.cursorMode)
548 alignPanel.getSeqPanel().moveCursor(0, -1);
553 case KeyEvent.VK_LEFT:
554 if (evt.isAltDown() || !viewport.cursorMode)
556 slideSequences(false,
557 alignPanel.getSeqPanel().getKeyboardNo1());
561 alignPanel.getSeqPanel().moveCursor(-1, 0);
566 case KeyEvent.VK_RIGHT:
567 if (evt.isAltDown() || !viewport.cursorMode)
569 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
573 alignPanel.getSeqPanel().moveCursor(1, 0);
577 case KeyEvent.VK_SPACE:
578 if (viewport.cursorMode)
580 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
581 || evt.isShiftDown() || evt.isAltDown());
585 // case KeyEvent.VK_A:
586 // if (viewport.cursorMode)
588 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
589 // //System.out.println("A");
593 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
594 * System.out.println("closing bracket"); } break;
596 case KeyEvent.VK_DELETE:
597 case KeyEvent.VK_BACK_SPACE:
598 if (!viewport.cursorMode)
600 cut_actionPerformed(null);
604 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
605 || evt.isShiftDown() || evt.isAltDown());
611 if (viewport.cursorMode)
613 alignPanel.getSeqPanel().setCursorRow();
617 if (viewport.cursorMode && !evt.isControlDown())
619 alignPanel.getSeqPanel().setCursorColumn();
623 if (viewport.cursorMode)
625 alignPanel.getSeqPanel().setCursorPosition();
629 case KeyEvent.VK_ENTER:
630 case KeyEvent.VK_COMMA:
631 if (viewport.cursorMode)
633 alignPanel.getSeqPanel().setCursorRowAndColumn();
638 if (viewport.cursorMode)
640 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
644 if (viewport.cursorMode)
646 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
651 viewport.cursorMode = !viewport.cursorMode;
652 statusBar.setText(MessageManager
653 .formatMessage("label.keyboard_editing_mode", new String[]
654 { (viewport.cursorMode ? "on" : "off") }));
655 if (viewport.cursorMode)
657 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
659 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
662 alignPanel.getSeqPanel().seqCanvas.repaint();
668 Help.showHelpWindow();
669 } catch (Exception ex)
671 ex.printStackTrace();
676 boolean toggleSeqs = !evt.isControlDown();
677 boolean toggleCols = !evt.isShiftDown();
678 toggleHiddenRegions(toggleSeqs, toggleCols);
683 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
684 boolean modifyExisting = true; // always modify, don't clear
685 // evt.isShiftDown();
686 boolean invertHighlighted = evt.isAltDown();
687 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
691 case KeyEvent.VK_PAGE_UP:
694 case KeyEvent.VK_PAGE_DOWN:
701 public void keyReleased(KeyEvent evt)
703 switch (evt.getKeyCode())
705 case KeyEvent.VK_LEFT:
706 if (evt.isAltDown() || !viewport.cursorMode)
708 viewport.firePropertyChange("alignment", null,
709 viewport.getAlignment().getSequences());
713 case KeyEvent.VK_RIGHT:
714 if (evt.isAltDown() || !viewport.cursorMode)
716 viewport.firePropertyChange("alignment", null,
717 viewport.getAlignment().getSequences());
725 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
727 ap.alignFrame = this;
728 avc = new jalview.controller.AlignViewController(this, viewport,
733 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
735 int aSize = alignPanels.size();
737 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
739 if (aSize == 1 && ap.av.viewName == null)
741 this.getContentPane().add(ap, BorderLayout.CENTER);
747 setInitialTabVisible();
750 expandViews.setEnabled(true);
751 gatherViews.setEnabled(true);
752 tabbedPane.addTab(ap.av.viewName, ap);
754 ap.setVisible(false);
759 if (ap.av.isPadGaps())
761 ap.av.getAlignment().padGaps();
763 ap.av.updateConservation(ap);
764 ap.av.updateConsensus(ap);
765 ap.av.updateStrucConsensus(ap);
769 public void setInitialTabVisible()
771 expandViews.setEnabled(true);
772 gatherViews.setEnabled(true);
773 tabbedPane.setVisible(true);
774 AlignmentPanel first = alignPanels.get(0);
775 tabbedPane.addTab(first.av.viewName, first);
776 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
779 public AlignViewport getViewport()
784 /* Set up intrinsic listeners for dynamically generated GUI bits. */
785 private void addServiceListeners()
787 final java.beans.PropertyChangeListener thisListener;
788 Desktop.instance.addJalviewPropertyChangeListener("services",
789 thisListener = new java.beans.PropertyChangeListener()
792 public void propertyChange(PropertyChangeEvent evt)
794 // // System.out.println("Discoverer property change.");
795 // if (evt.getPropertyName().equals("services"))
797 SwingUtilities.invokeLater(new Runnable()
804 "Rebuild WS Menu for service change");
805 BuildWebServiceMenu();
812 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
815 public void internalFrameClosed(
816 javax.swing.event.InternalFrameEvent evt)
818 // System.out.println("deregistering discoverer listener");
819 Desktop.instance.removeJalviewPropertyChangeListener("services",
821 closeMenuItem_actionPerformed(true);
824 // Finally, build the menu once to get current service state
825 new Thread(new Runnable()
830 BuildWebServiceMenu();
836 * Configure menu items that vary according to whether the alignment is
837 * nucleotide or protein
839 public void setGUINucleotide()
841 AlignmentI al = getViewport().getAlignment();
842 boolean nucleotide = al.isNucleotide();
844 showTranslation.setVisible(nucleotide);
845 showReverse.setVisible(nucleotide);
846 showReverseComplement.setVisible(nucleotide);
847 conservationMenuItem.setEnabled(!nucleotide);
849 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
850 showGroupConservation.setEnabled(!nucleotide);
852 showComplementMenuItem
853 .setText(nucleotide ? MessageManager.getString("label.protein")
854 : MessageManager.getString("label.nucleotide"));
858 * set up menus for the current viewport. This may be called after any
859 * operation that affects the data in the current view (selection changed,
860 * etc) to update the menus to reflect the new state.
863 public void setMenusForViewport()
865 setMenusFromViewport(viewport);
869 * Need to call this method when tabs are selected for multiple views, or when
870 * loading from Jalview2XML.java
875 void setMenusFromViewport(AlignViewport av)
877 padGapsMenuitem.setSelected(av.isPadGaps());
878 colourTextMenuItem.setSelected(av.isShowColourText());
879 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
880 modifyPID.setEnabled(abovePIDThreshold.isSelected());
881 conservationMenuItem.setSelected(av.getConservationSelected());
882 modifyConservation.setEnabled(conservationMenuItem.isSelected());
883 seqLimits.setSelected(av.getShowJVSuffix());
884 idRightAlign.setSelected(av.isRightAlignIds());
885 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
886 renderGapsMenuItem.setSelected(av.isRenderGaps());
887 wrapMenuItem.setSelected(av.getWrapAlignment());
888 scaleAbove.setVisible(av.getWrapAlignment());
889 scaleLeft.setVisible(av.getWrapAlignment());
890 scaleRight.setVisible(av.getWrapAlignment());
891 annotationPanelMenuItem.setState(av.isShowAnnotation());
893 * Show/hide annotations only enabled if annotation panel is shown
895 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
896 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
897 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
898 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
899 viewBoxesMenuItem.setSelected(av.getShowBoxes());
900 viewTextMenuItem.setSelected(av.getShowText());
901 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
902 showGroupConsensus.setSelected(av.isShowGroupConsensus());
903 showGroupConservation.setSelected(av.isShowGroupConservation());
904 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
905 showSequenceLogo.setSelected(av.isShowSequenceLogo());
906 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
908 ColourMenuHelper.setColourSelected(colourMenu,
909 av.getGlobalColourScheme());
911 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
912 hiddenMarkers.setState(av.getShowHiddenMarkers());
913 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
914 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
915 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
916 autoCalculate.setSelected(av.autoCalculateConsensus);
917 sortByTree.setSelected(av.sortByTree);
918 listenToViewSelections.setSelected(av.followSelection);
920 showProducts.setEnabled(canShowProducts());
921 setGroovyEnabled(Desktop.getGroovyConsole() != null);
927 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
931 public void setGroovyEnabled(boolean b)
933 runGroovy.setEnabled(b);
936 private IProgressIndicator progressBar;
941 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
944 public void setProgressBar(String message, long id)
946 progressBar.setProgressBar(message, id);
950 public void registerHandler(final long id,
951 final IProgressIndicatorHandler handler)
953 progressBar.registerHandler(id, handler);
958 * @return true if any progress bars are still active
961 public boolean operationInProgress()
963 return progressBar.operationInProgress();
967 public void setStatus(String text)
969 statusBar.setText(text);
973 * Added so Castor Mapping file can obtain Jalview Version
975 public String getVersion()
977 return jalview.bin.Cache.getProperty("VERSION");
980 public FeatureRenderer getFeatureRenderer()
982 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
986 public void fetchSequence_actionPerformed(ActionEvent e)
988 new jalview.gui.SequenceFetcher(this);
992 public void addFromFile_actionPerformed(ActionEvent e)
994 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
998 public void reload_actionPerformed(ActionEvent e)
1000 if (fileName != null)
1002 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1003 // originating file's format
1004 // TODO: work out how to recover feature settings for correct view(s) when
1005 // file is reloaded.
1006 if (FileFormat.Jalview.equals(currentFileFormat))
1008 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1009 for (int i = 0; i < frames.length; i++)
1011 if (frames[i] instanceof AlignFrame && frames[i] != this
1012 && ((AlignFrame) frames[i]).fileName != null
1013 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1017 frames[i].setSelected(true);
1018 Desktop.instance.closeAssociatedWindows();
1019 } catch (java.beans.PropertyVetoException ex)
1025 Desktop.instance.closeAssociatedWindows();
1027 FileLoader loader = new FileLoader();
1028 DataSourceType protocol = fileName.startsWith("http:")
1029 ? DataSourceType.URL
1030 : DataSourceType.FILE;
1031 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1035 Rectangle bounds = this.getBounds();
1037 FileLoader loader = new FileLoader();
1038 DataSourceType protocol = fileName.startsWith("http:")
1039 ? DataSourceType.URL
1040 : DataSourceType.FILE;
1041 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1042 protocol, currentFileFormat);
1044 newframe.setBounds(bounds);
1045 if (featureSettings != null && featureSettings.isShowing())
1047 final Rectangle fspos = featureSettings.frame.getBounds();
1048 // TODO: need a 'show feature settings' function that takes bounds -
1049 // need to refactor Desktop.addFrame
1050 newframe.featureSettings_actionPerformed(null);
1051 final FeatureSettings nfs = newframe.featureSettings;
1052 SwingUtilities.invokeLater(new Runnable()
1057 nfs.frame.setBounds(fspos);
1060 this.featureSettings.close();
1061 this.featureSettings = null;
1063 this.closeMenuItem_actionPerformed(true);
1069 public void addFromText_actionPerformed(ActionEvent e)
1072 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1076 public void addFromURL_actionPerformed(ActionEvent e)
1078 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1082 public void save_actionPerformed(ActionEvent e)
1084 if (fileName == null || (currentFileFormat == null)
1085 || fileName.startsWith("http"))
1087 saveAs_actionPerformed(null);
1091 saveAlignment(fileName, currentFileFormat);
1102 public void saveAs_actionPerformed(ActionEvent e)
1104 String format = currentFileFormat == null ? null
1105 : currentFileFormat.getName();
1106 JalviewFileChooser chooser = JalviewFileChooser
1107 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1109 chooser.setFileView(new JalviewFileView());
1110 chooser.setDialogTitle(
1111 MessageManager.getString("label.save_alignment_to_file"));
1112 chooser.setToolTipText(MessageManager.getString("action.save"));
1114 int value = chooser.showSaveDialog(this);
1116 if (value == JalviewFileChooser.APPROVE_OPTION)
1118 currentFileFormat = chooser.getSelectedFormat();
1119 while (currentFileFormat == null)
1121 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1122 MessageManager.getString(
1123 "label.select_file_format_before_saving"),
1124 MessageManager.getString("label.file_format_not_specified"),
1125 JvOptionPane.WARNING_MESSAGE);
1126 currentFileFormat = chooser.getSelectedFormat();
1127 value = chooser.showSaveDialog(this);
1128 if (value != JalviewFileChooser.APPROVE_OPTION)
1134 fileName = chooser.getSelectedFile().getPath();
1136 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1138 Cache.setProperty("LAST_DIRECTORY", fileName);
1139 saveAlignment(fileName, currentFileFormat);
1143 public boolean saveAlignment(String file, FileFormatI format)
1145 boolean success = true;
1147 if (FileFormat.Jalview.equals(format))
1149 String shortName = title;
1151 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1153 shortName = shortName.substring(
1154 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1157 success = new Jalview2XML().saveAlignment(this, file, shortName);
1159 statusBar.setText(MessageManager.formatMessage(
1160 "label.successfully_saved_to_file_in_format", new Object[]
1161 { fileName, format }));
1166 AlignmentExportData exportData = getAlignmentForExport(format,
1168 if (exportData.getSettings().isCancelled())
1172 FormatAdapter f = new FormatAdapter(alignPanel,
1173 exportData.getSettings());
1174 String output = f.formatSequences(format, exportData.getAlignment(), // class
1178 // occur in the distant future
1179 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1180 f.getCacheSuffixDefault(format),
1181 viewport.getAlignment().getHiddenColumns());
1191 PrintWriter out = new PrintWriter(new FileWriter(file));
1195 this.setTitle(file);
1196 statusBar.setText(MessageManager.formatMessage(
1197 "label.successfully_saved_to_file_in_format", new Object[]
1198 { fileName, format.getName() }));
1199 } catch (Exception ex)
1202 ex.printStackTrace();
1209 JvOptionPane.showInternalMessageDialog(this, MessageManager
1210 .formatMessage("label.couldnt_save_file", new Object[]
1212 MessageManager.getString("label.error_saving_file"),
1213 JvOptionPane.WARNING_MESSAGE);
1219 private void warningMessage(String warning, String title)
1221 if (new jalview.util.Platform().isHeadless())
1223 System.err.println("Warning: " + title + "\nWarning: " + warning);
1228 JvOptionPane.showInternalMessageDialog(this, warning, title,
1229 JvOptionPane.WARNING_MESSAGE);
1241 protected void outputText_actionPerformed(ActionEvent e)
1243 FileFormatI fileFormat = FileFormats.getInstance()
1244 .forName(e.getActionCommand());
1245 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1247 if (exportData.getSettings().isCancelled())
1251 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1252 cap.setForInput(null);
1255 FileFormatI format = fileFormat;
1256 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1257 .formatSequences(format, exportData.getAlignment(),
1258 exportData.getOmitHidden(),
1259 exportData.getStartEndPostions(),
1260 viewport.getAlignment().getHiddenColumns()));
1261 Desktop.addInternalFrame(cap, MessageManager
1262 .formatMessage("label.alignment_output_command", new Object[]
1263 { e.getActionCommand() }), 600, 500);
1264 } catch (OutOfMemoryError oom)
1266 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1273 public static AlignmentExportData getAlignmentForExport(
1274 FileFormatI format, AlignViewportI viewport,
1275 AlignExportSettingI exportSettings)
1277 AlignmentI alignmentToExport = null;
1278 AlignExportSettingI settings = exportSettings;
1279 String[] omitHidden = null;
1281 HiddenSequences hiddenSeqs = viewport.getAlignment()
1282 .getHiddenSequences();
1284 alignmentToExport = viewport.getAlignment();
1286 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1287 if (settings == null)
1289 settings = new AlignExportSettings(hasHiddenSeqs,
1290 viewport.hasHiddenColumns(), format);
1292 // settings.isExportAnnotations();
1294 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1296 omitHidden = viewport.getViewAsString(false,
1297 settings.isExportHiddenSequences());
1300 int[] alignmentStartEnd = new int[2];
1301 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1303 alignmentToExport = hiddenSeqs.getFullAlignment();
1307 alignmentToExport = viewport.getAlignment();
1309 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1310 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1311 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1312 omitHidden, alignmentStartEnd, settings);
1323 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1325 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1326 htmlSVG.exportHTML(null);
1330 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1332 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1333 bjs.exportHTML(null);
1336 public void createImageMap(File file, String image)
1338 alignPanel.makePNGImageMap(file, image);
1348 public void createPNG(File f)
1350 alignPanel.makePNG(f);
1360 public void createEPS(File f)
1362 alignPanel.makeEPS(f);
1366 public void createSVG(File f)
1368 alignPanel.makeSVG(f);
1372 public void pageSetup_actionPerformed(ActionEvent e)
1374 PrinterJob printJob = PrinterJob.getPrinterJob();
1375 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1385 public void printMenuItem_actionPerformed(ActionEvent e)
1387 // Putting in a thread avoids Swing painting problems
1388 PrintThread thread = new PrintThread(alignPanel);
1393 public void exportFeatures_actionPerformed(ActionEvent e)
1395 new AnnotationExporter().exportFeatures(alignPanel);
1399 public void exportAnnotations_actionPerformed(ActionEvent e)
1401 new AnnotationExporter().exportAnnotations(alignPanel);
1405 public void associatedData_actionPerformed(ActionEvent e)
1407 // Pick the tree file
1408 JalviewFileChooser chooser = new JalviewFileChooser(
1409 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1410 chooser.setFileView(new JalviewFileView());
1411 chooser.setDialogTitle(
1412 MessageManager.getString("label.load_jalview_annotations"));
1413 chooser.setToolTipText(
1414 MessageManager.getString("label.load_jalview_annotations"));
1416 int value = chooser.showOpenDialog(null);
1418 if (value == JalviewFileChooser.APPROVE_OPTION)
1420 String choice = chooser.getSelectedFile().getPath();
1421 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1422 loadJalviewDataFile(choice, null, null, null);
1428 * Close the current view or all views in the alignment frame. If the frame
1429 * only contains one view then the alignment will be removed from memory.
1431 * @param closeAllTabs
1434 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1436 if (alignPanels != null && alignPanels.size() < 2)
1438 closeAllTabs = true;
1443 if (alignPanels != null)
1447 if (this.isClosed())
1449 // really close all the windows - otherwise wait till
1450 // setClosed(true) is called
1451 for (int i = 0; i < alignPanels.size(); i++)
1453 AlignmentPanel ap = alignPanels.get(i);
1460 closeView(alignPanel);
1467 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1468 * be called recursively, with the frame now in 'closed' state
1470 this.setClosed(true);
1472 } catch (Exception ex)
1474 ex.printStackTrace();
1479 * Close the specified panel and close up tabs appropriately.
1481 * @param panelToClose
1483 public void closeView(AlignmentPanel panelToClose)
1485 int index = tabbedPane.getSelectedIndex();
1486 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1487 alignPanels.remove(panelToClose);
1488 panelToClose.closePanel();
1489 panelToClose = null;
1491 tabbedPane.removeTabAt(closedindex);
1492 tabbedPane.validate();
1494 if (index > closedindex || index == tabbedPane.getTabCount())
1496 // modify currently selected tab index if necessary.
1500 this.tabSelectionChanged(index);
1506 void updateEditMenuBar()
1509 if (viewport.getHistoryList().size() > 0)
1511 undoMenuItem.setEnabled(true);
1512 CommandI command = viewport.getHistoryList().peek();
1513 undoMenuItem.setText(MessageManager
1514 .formatMessage("label.undo_command", new Object[]
1515 { command.getDescription() }));
1519 undoMenuItem.setEnabled(false);
1520 undoMenuItem.setText(MessageManager.getString("action.undo"));
1523 if (viewport.getRedoList().size() > 0)
1525 redoMenuItem.setEnabled(true);
1527 CommandI command = viewport.getRedoList().peek();
1528 redoMenuItem.setText(MessageManager
1529 .formatMessage("label.redo_command", new Object[]
1530 { command.getDescription() }));
1534 redoMenuItem.setEnabled(false);
1535 redoMenuItem.setText(MessageManager.getString("action.redo"));
1540 public void addHistoryItem(CommandI command)
1542 if (command.getSize() > 0)
1544 viewport.addToHistoryList(command);
1545 viewport.clearRedoList();
1546 updateEditMenuBar();
1547 viewport.updateHiddenColumns();
1548 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1549 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1550 // viewport.getColumnSelection()
1551 // .getHiddenColumns().size() > 0);
1557 * @return alignment objects for all views
1559 AlignmentI[] getViewAlignments()
1561 if (alignPanels != null)
1563 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1565 for (AlignmentPanel ap : alignPanels)
1567 als[i++] = ap.av.getAlignment();
1571 if (viewport != null)
1573 return new AlignmentI[] { viewport.getAlignment() };
1585 protected void undoMenuItem_actionPerformed(ActionEvent e)
1587 if (viewport.getHistoryList().isEmpty())
1591 CommandI command = viewport.getHistoryList().pop();
1592 viewport.addToRedoList(command);
1593 command.undoCommand(getViewAlignments());
1595 AlignmentViewport originalSource = getOriginatingSource(command);
1596 updateEditMenuBar();
1598 if (originalSource != null)
1600 if (originalSource != viewport)
1603 "Implementation worry: mismatch of viewport origin for undo");
1605 originalSource.updateHiddenColumns();
1606 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1608 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1609 // viewport.getColumnSelection()
1610 // .getHiddenColumns().size() > 0);
1611 originalSource.firePropertyChange("alignment", null,
1612 originalSource.getAlignment().getSequences());
1623 protected void redoMenuItem_actionPerformed(ActionEvent e)
1625 if (viewport.getRedoList().size() < 1)
1630 CommandI command = viewport.getRedoList().pop();
1631 viewport.addToHistoryList(command);
1632 command.doCommand(getViewAlignments());
1634 AlignmentViewport originalSource = getOriginatingSource(command);
1635 updateEditMenuBar();
1637 if (originalSource != null)
1640 if (originalSource != viewport)
1643 "Implementation worry: mismatch of viewport origin for redo");
1645 originalSource.updateHiddenColumns();
1646 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1648 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1649 // viewport.getColumnSelection()
1650 // .getHiddenColumns().size() > 0);
1651 originalSource.firePropertyChange("alignment", null,
1652 originalSource.getAlignment().getSequences());
1656 AlignmentViewport getOriginatingSource(CommandI command)
1658 AlignmentViewport originalSource = null;
1659 // For sequence removal and addition, we need to fire
1660 // the property change event FROM the viewport where the
1661 // original alignment was altered
1662 AlignmentI al = null;
1663 if (command instanceof EditCommand)
1665 EditCommand editCommand = (EditCommand) command;
1666 al = editCommand.getAlignment();
1667 List<Component> comps = PaintRefresher.components
1668 .get(viewport.getSequenceSetId());
1670 for (Component comp : comps)
1672 if (comp instanceof AlignmentPanel)
1674 if (al == ((AlignmentPanel) comp).av.getAlignment())
1676 originalSource = ((AlignmentPanel) comp).av;
1683 if (originalSource == null)
1685 // The original view is closed, we must validate
1686 // the current view against the closed view first
1689 PaintRefresher.validateSequences(al, viewport.getAlignment());
1692 originalSource = viewport;
1695 return originalSource;
1704 public void moveSelectedSequences(boolean up)
1706 SequenceGroup sg = viewport.getSelectionGroup();
1712 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1713 viewport.getHiddenRepSequences(), up);
1714 alignPanel.paintAlignment(true);
1717 synchronized void slideSequences(boolean right, int size)
1719 List<SequenceI> sg = new ArrayList<>();
1720 if (viewport.cursorMode)
1722 sg.add(viewport.getAlignment()
1723 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1725 else if (viewport.getSelectionGroup() != null
1726 && viewport.getSelectionGroup().getSize() != viewport
1727 .getAlignment().getHeight())
1729 sg = viewport.getSelectionGroup()
1730 .getSequences(viewport.getHiddenRepSequences());
1738 List<SequenceI> invertGroup = new ArrayList<>();
1740 for (SequenceI seq : viewport.getAlignment().getSequences())
1742 if (!sg.contains(seq))
1744 invertGroup.add(seq);
1748 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1750 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1751 for (int i = 0; i < invertGroup.size(); i++)
1753 seqs2[i] = invertGroup.get(i);
1756 SlideSequencesCommand ssc;
1759 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1760 viewport.getGapCharacter());
1764 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1765 viewport.getGapCharacter());
1768 int groupAdjustment = 0;
1769 if (ssc.getGapsInsertedBegin() && right)
1771 if (viewport.cursorMode)
1773 alignPanel.getSeqPanel().moveCursor(size, 0);
1777 groupAdjustment = size;
1780 else if (!ssc.getGapsInsertedBegin() && !right)
1782 if (viewport.cursorMode)
1784 alignPanel.getSeqPanel().moveCursor(-size, 0);
1788 groupAdjustment = -size;
1792 if (groupAdjustment != 0)
1794 viewport.getSelectionGroup().setStartRes(
1795 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1796 viewport.getSelectionGroup().setEndRes(
1797 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1801 * just extend the last slide command if compatible; but not if in
1802 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1804 boolean appendHistoryItem = false;
1805 Deque<CommandI> historyList = viewport.getHistoryList();
1806 boolean inSplitFrame = getSplitViewContainer() != null;
1807 if (!inSplitFrame && historyList != null && historyList.size() > 0
1808 && historyList.peek() instanceof SlideSequencesCommand)
1810 appendHistoryItem = ssc.appendSlideCommand(
1811 (SlideSequencesCommand) historyList.peek());
1814 if (!appendHistoryItem)
1816 addHistoryItem(ssc);
1829 protected void copy_actionPerformed(ActionEvent e)
1832 if (viewport.getSelectionGroup() == null)
1836 // TODO: preserve the ordering of displayed alignment annotation in any
1837 // internal paste (particularly sequence associated annotation)
1838 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1839 String[] omitHidden = null;
1841 if (viewport.hasHiddenColumns())
1843 omitHidden = viewport.getViewAsString(true);
1846 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1847 seqs, omitHidden, null);
1849 StringSelection ss = new StringSelection(output);
1853 jalview.gui.Desktop.internalCopy = true;
1854 // Its really worth setting the clipboard contents
1855 // to empty before setting the large StringSelection!!
1856 Toolkit.getDefaultToolkit().getSystemClipboard()
1857 .setContents(new StringSelection(""), null);
1859 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1861 } catch (OutOfMemoryError er)
1863 new OOMWarning("copying region", er);
1867 ArrayList<int[]> hiddenColumns = null;
1868 if (viewport.hasHiddenColumns())
1870 hiddenColumns = new ArrayList<>();
1871 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1872 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1873 ArrayList<int[]> hiddenRegions = viewport.getAlignment()
1874 .getHiddenColumns().getHiddenColumnsCopy();
1875 for (int[] region : hiddenRegions)
1877 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1881 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1886 Desktop.jalviewClipboard = new Object[] { seqs,
1887 viewport.getAlignment().getDataset(), hiddenColumns };
1888 statusBar.setText(MessageManager.formatMessage(
1889 "label.copied_sequences_to_clipboard", new Object[]
1890 { Integer.valueOf(seqs.length).toString() }));
1900 protected void pasteNew_actionPerformed(ActionEvent e)
1912 protected void pasteThis_actionPerformed(ActionEvent e)
1918 * Paste contents of Jalview clipboard
1920 * @param newAlignment
1921 * true to paste to a new alignment, otherwise add to this.
1923 void paste(boolean newAlignment)
1925 boolean externalPaste = true;
1928 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1929 Transferable contents = c.getContents(this);
1931 if (contents == null)
1940 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1941 if (str.length() < 1)
1946 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1948 } catch (OutOfMemoryError er)
1950 new OOMWarning("Out of memory pasting sequences!!", er);
1954 SequenceI[] sequences;
1955 boolean annotationAdded = false;
1956 AlignmentI alignment = null;
1958 if (Desktop.jalviewClipboard != null)
1960 // The clipboard was filled from within Jalview, we must use the
1962 // And dataset from the copied alignment
1963 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1964 // be doubly sure that we create *new* sequence objects.
1965 sequences = new SequenceI[newseq.length];
1966 for (int i = 0; i < newseq.length; i++)
1968 sequences[i] = new Sequence(newseq[i]);
1970 alignment = new Alignment(sequences);
1971 externalPaste = false;
1975 // parse the clipboard as an alignment.
1976 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1978 sequences = alignment.getSequencesArray();
1982 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1988 if (Desktop.jalviewClipboard != null)
1990 // dataset is inherited
1991 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1995 // new dataset is constructed
1996 alignment.setDataset(null);
1998 alwidth = alignment.getWidth() + 1;
2002 AlignmentI pastedal = alignment; // preserve pasted alignment object
2003 // Add pasted sequences and dataset into existing alignment.
2004 alignment = viewport.getAlignment();
2005 alwidth = alignment.getWidth() + 1;
2006 // decide if we need to import sequences from an existing dataset
2007 boolean importDs = Desktop.jalviewClipboard != null
2008 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2009 // importDs==true instructs us to copy over new dataset sequences from
2010 // an existing alignment
2011 Vector newDs = (importDs) ? new Vector() : null; // used to create
2012 // minimum dataset set
2014 for (int i = 0; i < sequences.length; i++)
2018 newDs.addElement(null);
2020 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2022 if (importDs && ds != null)
2024 if (!newDs.contains(ds))
2026 newDs.setElementAt(ds, i);
2027 ds = new Sequence(ds);
2028 // update with new dataset sequence
2029 sequences[i].setDatasetSequence(ds);
2033 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2038 // copy and derive new dataset sequence
2039 sequences[i] = sequences[i].deriveSequence();
2040 alignment.getDataset()
2041 .addSequence(sequences[i].getDatasetSequence());
2042 // TODO: avoid creation of duplicate dataset sequences with a
2043 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2045 alignment.addSequence(sequences[i]); // merges dataset
2049 newDs.clear(); // tidy up
2051 if (alignment.getAlignmentAnnotation() != null)
2053 for (AlignmentAnnotation alan : alignment
2054 .getAlignmentAnnotation())
2056 if (alan.graphGroup > fgroup)
2058 fgroup = alan.graphGroup;
2062 if (pastedal.getAlignmentAnnotation() != null)
2064 // Add any annotation attached to alignment.
2065 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2066 for (int i = 0; i < alann.length; i++)
2068 annotationAdded = true;
2069 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2071 AlignmentAnnotation newann = new AlignmentAnnotation(
2073 if (newann.graphGroup > -1)
2075 if (newGraphGroups.size() <= newann.graphGroup
2076 || newGraphGroups.get(newann.graphGroup) == null)
2078 for (int q = newGraphGroups
2079 .size(); q <= newann.graphGroup; q++)
2081 newGraphGroups.add(q, null);
2083 newGraphGroups.set(newann.graphGroup,
2084 new Integer(++fgroup));
2086 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2090 newann.padAnnotation(alwidth);
2091 alignment.addAnnotation(newann);
2101 addHistoryItem(new EditCommand(
2102 MessageManager.getString("label.add_sequences"),
2103 Action.PASTE, sequences, 0, alignment.getWidth(),
2106 // Add any annotations attached to sequences
2107 for (int i = 0; i < sequences.length; i++)
2109 if (sequences[i].getAnnotation() != null)
2111 AlignmentAnnotation newann;
2112 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2114 annotationAdded = true;
2115 newann = sequences[i].getAnnotation()[a];
2116 newann.adjustForAlignment();
2117 newann.padAnnotation(alwidth);
2118 if (newann.graphGroup > -1)
2120 if (newann.graphGroup > -1)
2122 if (newGraphGroups.size() <= newann.graphGroup
2123 || newGraphGroups.get(newann.graphGroup) == null)
2125 for (int q = newGraphGroups
2126 .size(); q <= newann.graphGroup; q++)
2128 newGraphGroups.add(q, null);
2130 newGraphGroups.set(newann.graphGroup,
2131 new Integer(++fgroup));
2133 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2137 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2141 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2149 // propagate alignment changed.
2150 vpRanges.setEndSeq(alignment.getHeight());
2151 if (annotationAdded)
2153 // Duplicate sequence annotation in all views.
2154 AlignmentI[] alview = this.getViewAlignments();
2155 for (int i = 0; i < sequences.length; i++)
2157 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2162 for (int avnum = 0; avnum < alview.length; avnum++)
2164 if (alview[avnum] != alignment)
2166 // duplicate in a view other than the one with input focus
2167 int avwidth = alview[avnum].getWidth() + 1;
2168 // this relies on sann being preserved after we
2169 // modify the sequence's annotation array for each duplication
2170 for (int a = 0; a < sann.length; a++)
2172 AlignmentAnnotation newann = new AlignmentAnnotation(
2174 sequences[i].addAlignmentAnnotation(newann);
2175 newann.padAnnotation(avwidth);
2176 alview[avnum].addAnnotation(newann); // annotation was
2177 // duplicated earlier
2178 // TODO JAL-1145 graphGroups are not updated for sequence
2179 // annotation added to several views. This may cause
2181 alview[avnum].setAnnotationIndex(newann, a);
2186 buildSortByAnnotationScoresMenu();
2188 viewport.firePropertyChange("alignment", null,
2189 alignment.getSequences());
2190 if (alignPanels != null)
2192 for (AlignmentPanel ap : alignPanels)
2194 ap.validateAnnotationDimensions(false);
2199 alignPanel.validateAnnotationDimensions(false);
2205 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2207 String newtitle = new String("Copied sequences");
2209 if (Desktop.jalviewClipboard != null
2210 && Desktop.jalviewClipboard[2] != null)
2212 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2213 for (int[] region : hc)
2215 af.viewport.hideColumns(region[0], region[1]);
2219 // >>>This is a fix for the moment, until a better solution is
2221 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2222 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2223 .getFeatureRenderer());
2225 // TODO: maintain provenance of an alignment, rather than just make the
2226 // title a concatenation of operations.
2229 if (title.startsWith("Copied sequences"))
2235 newtitle = newtitle.concat("- from " + title);
2240 newtitle = new String("Pasted sequences");
2243 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2248 } catch (Exception ex)
2250 ex.printStackTrace();
2251 System.out.println("Exception whilst pasting: " + ex);
2252 // could be anything being pasted in here
2258 protected void expand_newalign(ActionEvent e)
2262 AlignmentI alignment = AlignmentUtils
2263 .expandContext(getViewport().getAlignment(), -1);
2264 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2266 String newtitle = new String("Flanking alignment");
2268 if (Desktop.jalviewClipboard != null
2269 && Desktop.jalviewClipboard[2] != null)
2271 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2272 for (int region[] : hc)
2274 af.viewport.hideColumns(region[0], region[1]);
2278 // >>>This is a fix for the moment, until a better solution is
2280 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2281 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2282 .getFeatureRenderer());
2284 // TODO: maintain provenance of an alignment, rather than just make the
2285 // title a concatenation of operations.
2287 if (title.startsWith("Copied sequences"))
2293 newtitle = newtitle.concat("- from " + title);
2297 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2299 } catch (Exception ex)
2301 ex.printStackTrace();
2302 System.out.println("Exception whilst pasting: " + ex);
2303 // could be anything being pasted in here
2304 } catch (OutOfMemoryError oom)
2306 new OOMWarning("Viewing flanking region of alignment", oom);
2317 protected void cut_actionPerformed(ActionEvent e)
2319 copy_actionPerformed(null);
2320 delete_actionPerformed(null);
2330 protected void delete_actionPerformed(ActionEvent evt)
2333 SequenceGroup sg = viewport.getSelectionGroup();
2340 * If the cut affects all sequences, warn, remove highlighted columns
2342 if (sg.getSize() == viewport.getAlignment().getHeight())
2344 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2345 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2346 if (isEntireAlignWidth)
2348 int confirm = JvOptionPane.showConfirmDialog(this,
2349 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2350 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2351 JvOptionPane.OK_CANCEL_OPTION);
2353 if (confirm == JvOptionPane.CANCEL_OPTION
2354 || confirm == JvOptionPane.CLOSED_OPTION)
2359 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2360 sg.getEndRes() + 1);
2362 SequenceI[] cut = sg.getSequences()
2363 .toArray(new SequenceI[sg.getSize()]);
2365 addHistoryItem(new EditCommand(
2366 MessageManager.getString("label.cut_sequences"), Action.CUT,
2367 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2368 viewport.getAlignment()));
2370 viewport.setSelectionGroup(null);
2371 viewport.sendSelection();
2372 viewport.getAlignment().deleteGroup(sg);
2374 viewport.firePropertyChange("alignment", null,
2375 viewport.getAlignment().getSequences());
2376 if (viewport.getAlignment().getHeight() < 1)
2380 this.setClosed(true);
2381 } catch (Exception ex)
2394 protected void deleteGroups_actionPerformed(ActionEvent e)
2396 if (avc.deleteGroups())
2398 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2399 alignPanel.updateAnnotation();
2400 alignPanel.paintAlignment(true);
2411 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2413 SequenceGroup sg = new SequenceGroup();
2415 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2417 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2420 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2421 viewport.setSelectionGroup(sg);
2422 viewport.sendSelection();
2423 // JAL-2034 - should delegate to
2424 // alignPanel to decide if overview needs
2426 alignPanel.paintAlignment(false);
2427 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2437 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2439 if (viewport.cursorMode)
2441 alignPanel.getSeqPanel().keyboardNo1 = null;
2442 alignPanel.getSeqPanel().keyboardNo2 = null;
2444 viewport.setSelectionGroup(null);
2445 viewport.getColumnSelection().clear();
2446 viewport.setSelectionGroup(null);
2447 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2448 // JAL-2034 - should delegate to
2449 // alignPanel to decide if overview needs
2451 alignPanel.paintAlignment(false);
2452 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2453 viewport.sendSelection();
2463 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2465 SequenceGroup sg = viewport.getSelectionGroup();
2469 selectAllSequenceMenuItem_actionPerformed(null);
2474 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2476 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2478 // JAL-2034 - should delegate to
2479 // alignPanel to decide if overview needs
2482 alignPanel.paintAlignment(true);
2483 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2484 viewport.sendSelection();
2488 public void invertColSel_actionPerformed(ActionEvent e)
2490 viewport.invertColumnSelection();
2491 alignPanel.paintAlignment(true);
2492 viewport.sendSelection();
2502 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2504 trimAlignment(true);
2514 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2516 trimAlignment(false);
2519 void trimAlignment(boolean trimLeft)
2521 ColumnSelection colSel = viewport.getColumnSelection();
2524 if (!colSel.isEmpty())
2528 column = colSel.getMin();
2532 column = colSel.getMax();
2536 if (viewport.getSelectionGroup() != null)
2538 seqs = viewport.getSelectionGroup()
2539 .getSequencesAsArray(viewport.getHiddenRepSequences());
2543 seqs = viewport.getAlignment().getSequencesArray();
2546 TrimRegionCommand trimRegion;
2549 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2550 column, viewport.getAlignment());
2551 vpRanges.setStartRes(0);
2555 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2556 column, viewport.getAlignment());
2559 statusBar.setText(MessageManager
2560 .formatMessage("label.removed_columns", new String[]
2561 { Integer.valueOf(trimRegion.getSize()).toString() }));
2563 addHistoryItem(trimRegion);
2565 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2567 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2568 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2570 viewport.getAlignment().deleteGroup(sg);
2574 viewport.firePropertyChange("alignment", null,
2575 viewport.getAlignment().getSequences());
2586 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2588 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2591 if (viewport.getSelectionGroup() != null)
2593 seqs = viewport.getSelectionGroup()
2594 .getSequencesAsArray(viewport.getHiddenRepSequences());
2595 start = viewport.getSelectionGroup().getStartRes();
2596 end = viewport.getSelectionGroup().getEndRes();
2600 seqs = viewport.getAlignment().getSequencesArray();
2603 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2604 "Remove Gapped Columns", seqs, start, end,
2605 viewport.getAlignment());
2607 addHistoryItem(removeGapCols);
2609 statusBar.setText(MessageManager
2610 .formatMessage("label.removed_empty_columns", new Object[]
2611 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2613 // This is to maintain viewport position on first residue
2614 // of first sequence
2615 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2616 int startRes = seq.findPosition(vpRanges.getStartRes());
2617 // ShiftList shifts;
2618 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2619 // edit.alColumnChanges=shifts.getInverse();
2620 // if (viewport.hasHiddenColumns)
2621 // viewport.getColumnSelection().compensateForEdits(shifts);
2622 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2623 viewport.firePropertyChange("alignment", null,
2624 viewport.getAlignment().getSequences());
2635 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2637 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2640 if (viewport.getSelectionGroup() != null)
2642 seqs = viewport.getSelectionGroup()
2643 .getSequencesAsArray(viewport.getHiddenRepSequences());
2644 start = viewport.getSelectionGroup().getStartRes();
2645 end = viewport.getSelectionGroup().getEndRes();
2649 seqs = viewport.getAlignment().getSequencesArray();
2652 // This is to maintain viewport position on first residue
2653 // of first sequence
2654 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2655 int startRes = seq.findPosition(vpRanges.getStartRes());
2657 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2658 viewport.getAlignment()));
2660 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2662 viewport.firePropertyChange("alignment", null,
2663 viewport.getAlignment().getSequences());
2674 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2676 viewport.setPadGaps(padGapsMenuitem.isSelected());
2677 viewport.firePropertyChange("alignment", null,
2678 viewport.getAlignment().getSequences());
2688 public void findMenuItem_actionPerformed(ActionEvent e)
2694 * Create a new view of the current alignment.
2697 public void newView_actionPerformed(ActionEvent e)
2699 newView(null, true);
2703 * Creates and shows a new view of the current alignment.
2706 * title of newly created view; if null, one will be generated
2707 * @param copyAnnotation
2708 * if true then duplicate all annnotation, groups and settings
2709 * @return new alignment panel, already displayed.
2711 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2714 * Create a new AlignmentPanel (with its own, new Viewport)
2716 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2718 if (!copyAnnotation)
2721 * remove all groups and annotation except for the automatic stuff
2723 newap.av.getAlignment().deleteAllGroups();
2724 newap.av.getAlignment().deleteAllAnnotations(false);
2727 newap.av.setGatherViewsHere(false);
2729 if (viewport.viewName == null)
2731 viewport.viewName = MessageManager
2732 .getString("label.view_name_original");
2736 * Views share the same edits undo and redo stacks
2738 newap.av.setHistoryList(viewport.getHistoryList());
2739 newap.av.setRedoList(viewport.getRedoList());
2742 * Views share the same mappings; need to deregister any new mappings
2743 * created by copyAlignPanel, and register the new reference to the shared
2746 newap.av.replaceMappings(viewport.getAlignment());
2749 * start up cDNA consensus (if applicable) now mappings are in place
2751 if (newap.av.initComplementConsensus())
2753 newap.refresh(true); // adjust layout of annotations
2756 newap.av.viewName = getNewViewName(viewTitle);
2758 addAlignmentPanel(newap, true);
2759 newap.alignmentChanged();
2761 if (alignPanels.size() == 2)
2763 viewport.setGatherViewsHere(true);
2765 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2770 * Make a new name for the view, ensuring it is unique within the current
2771 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2772 * these now use viewId. Unique view names are still desirable for usability.)
2777 protected String getNewViewName(String viewTitle)
2779 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2780 boolean addFirstIndex = false;
2781 if (viewTitle == null || viewTitle.trim().length() == 0)
2783 viewTitle = MessageManager.getString("action.view");
2784 addFirstIndex = true;
2788 index = 1;// we count from 1 if given a specific name
2790 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2792 List<Component> comps = PaintRefresher.components
2793 .get(viewport.getSequenceSetId());
2795 List<String> existingNames = getExistingViewNames(comps);
2797 while (existingNames.contains(newViewName))
2799 newViewName = viewTitle + " " + (++index);
2805 * Returns a list of distinct view names found in the given list of
2806 * components. View names are held on the viewport of an AlignmentPanel.
2811 protected List<String> getExistingViewNames(List<Component> comps)
2813 List<String> existingNames = new ArrayList<>();
2814 for (Component comp : comps)
2816 if (comp instanceof AlignmentPanel)
2818 AlignmentPanel ap = (AlignmentPanel) comp;
2819 if (!existingNames.contains(ap.av.viewName))
2821 existingNames.add(ap.av.viewName);
2825 return existingNames;
2829 * Explode tabbed views into separate windows.
2832 public void expandViews_actionPerformed(ActionEvent e)
2834 Desktop.explodeViews(this);
2838 * Gather views in separate windows back into a tabbed presentation.
2841 public void gatherViews_actionPerformed(ActionEvent e)
2843 Desktop.instance.gatherViews(this);
2853 public void font_actionPerformed(ActionEvent e)
2855 new FontChooser(alignPanel);
2865 protected void seqLimit_actionPerformed(ActionEvent e)
2867 viewport.setShowJVSuffix(seqLimits.isSelected());
2869 alignPanel.getIdPanel().getIdCanvas()
2870 .setPreferredSize(alignPanel.calculateIdWidth());
2871 alignPanel.paintAlignment(true);
2875 public void idRightAlign_actionPerformed(ActionEvent e)
2877 viewport.setRightAlignIds(idRightAlign.isSelected());
2878 alignPanel.paintAlignment(true);
2882 public void centreColumnLabels_actionPerformed(ActionEvent e)
2884 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2885 alignPanel.paintAlignment(true);
2891 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2894 protected void followHighlight_actionPerformed()
2897 * Set the 'follow' flag on the Viewport (and scroll to position if now
2900 final boolean state = this.followHighlightMenuItem.getState();
2901 viewport.setFollowHighlight(state);
2904 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2915 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2917 viewport.setColourText(colourTextMenuItem.isSelected());
2918 alignPanel.paintAlignment(true);
2928 public void wrapMenuItem_actionPerformed(ActionEvent e)
2930 scaleAbove.setVisible(wrapMenuItem.isSelected());
2931 scaleLeft.setVisible(wrapMenuItem.isSelected());
2932 scaleRight.setVisible(wrapMenuItem.isSelected());
2933 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2934 alignPanel.updateLayout();
2938 public void showAllSeqs_actionPerformed(ActionEvent e)
2940 viewport.showAllHiddenSeqs();
2944 public void showAllColumns_actionPerformed(ActionEvent e)
2946 viewport.showAllHiddenColumns();
2947 alignPanel.paintAlignment(true);
2948 viewport.sendSelection();
2952 public void hideSelSequences_actionPerformed(ActionEvent e)
2954 viewport.hideAllSelectedSeqs();
2958 * called by key handler and the hide all/show all menu items
2963 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2966 boolean hide = false;
2967 SequenceGroup sg = viewport.getSelectionGroup();
2968 if (!toggleSeqs && !toggleCols)
2970 // Hide everything by the current selection - this is a hack - we do the
2971 // invert and then hide
2972 // first check that there will be visible columns after the invert.
2973 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2974 && sg.getStartRes() <= sg.getEndRes()))
2976 // now invert the sequence set, if required - empty selection implies
2977 // that no hiding is required.
2980 invertSequenceMenuItem_actionPerformed(null);
2981 sg = viewport.getSelectionGroup();
2985 viewport.expandColSelection(sg, true);
2986 // finally invert the column selection and get the new sequence
2988 invertColSel_actionPerformed(null);
2995 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2997 hideSelSequences_actionPerformed(null);
3000 else if (!(toggleCols && viewport.hasSelectedColumns()))
3002 showAllSeqs_actionPerformed(null);
3008 if (viewport.hasSelectedColumns())
3010 hideSelColumns_actionPerformed(null);
3013 viewport.setSelectionGroup(sg);
3018 showAllColumns_actionPerformed(null);
3027 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3028 * event.ActionEvent)
3031 public void hideAllButSelection_actionPerformed(ActionEvent e)
3033 toggleHiddenRegions(false, false);
3034 viewport.sendSelection();
3041 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3045 public void hideAllSelection_actionPerformed(ActionEvent e)
3047 SequenceGroup sg = viewport.getSelectionGroup();
3048 viewport.expandColSelection(sg, false);
3049 viewport.hideAllSelectedSeqs();
3050 viewport.hideSelectedColumns();
3051 alignPanel.paintAlignment(true);
3052 viewport.sendSelection();
3059 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3063 public void showAllhidden_actionPerformed(ActionEvent e)
3065 viewport.showAllHiddenColumns();
3066 viewport.showAllHiddenSeqs();
3067 alignPanel.paintAlignment(true);
3068 viewport.sendSelection();
3072 public void hideSelColumns_actionPerformed(ActionEvent e)
3074 viewport.hideSelectedColumns();
3075 alignPanel.paintAlignment(true);
3076 viewport.sendSelection();
3080 public void hiddenMarkers_actionPerformed(ActionEvent e)
3082 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3093 protected void scaleAbove_actionPerformed(ActionEvent e)
3095 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3096 alignPanel.paintAlignment(true);
3106 protected void scaleLeft_actionPerformed(ActionEvent e)
3108 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3109 alignPanel.paintAlignment(true);
3119 protected void scaleRight_actionPerformed(ActionEvent e)
3121 viewport.setScaleRightWrapped(scaleRight.isSelected());
3122 alignPanel.paintAlignment(true);
3132 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3134 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3135 alignPanel.paintAlignment(true);
3145 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3147 viewport.setShowText(viewTextMenuItem.isSelected());
3148 alignPanel.paintAlignment(true);
3158 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3160 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3161 alignPanel.paintAlignment(true);
3164 public FeatureSettings featureSettings;
3167 public FeatureSettingsControllerI getFeatureSettingsUI()
3169 return featureSettings;
3173 public void featureSettings_actionPerformed(ActionEvent e)
3175 if (featureSettings != null)
3177 featureSettings.close();
3178 featureSettings = null;
3180 if (!showSeqFeatures.isSelected())
3182 // make sure features are actually displayed
3183 showSeqFeatures.setSelected(true);
3184 showSeqFeatures_actionPerformed(null);
3186 featureSettings = new FeatureSettings(this);
3190 * Set or clear 'Show Sequence Features'
3196 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3198 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3199 alignPanel.paintAlignment(true);
3203 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3204 * the annotations panel as a whole.
3206 * The options to show/hide all annotations should be enabled when the panel
3207 * is shown, and disabled when the panel is hidden.
3212 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3214 final boolean setVisible = annotationPanelMenuItem.isSelected();
3215 viewport.setShowAnnotation(setVisible);
3216 this.showAllSeqAnnotations.setEnabled(setVisible);
3217 this.hideAllSeqAnnotations.setEnabled(setVisible);
3218 this.showAllAlAnnotations.setEnabled(setVisible);
3219 this.hideAllAlAnnotations.setEnabled(setVisible);
3220 alignPanel.updateLayout();
3224 public void alignmentProperties()
3226 JEditorPane editPane = new JEditorPane("text/html", "");
3227 editPane.setEditable(false);
3228 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3231 MessageManager.formatMessage("label.html_content", new Object[]
3232 { contents.toString() }));
3233 JInternalFrame frame = new JInternalFrame();
3234 frame.getContentPane().add(new JScrollPane(editPane));
3236 Desktop.addInternalFrame(frame, MessageManager
3237 .formatMessage("label.alignment_properties", new Object[]
3238 { getTitle() }), 500, 400);
3248 public void overviewMenuItem_actionPerformed(ActionEvent e)
3250 if (alignPanel.overviewPanel != null)
3255 JInternalFrame frame = new JInternalFrame();
3256 final OverviewPanel overview = new OverviewPanel(alignPanel);
3257 frame.setContentPane(overview);
3258 Desktop.addInternalFrame(frame, MessageManager
3259 .formatMessage("label.overview_params", new Object[]
3260 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3263 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3264 frame.addInternalFrameListener(
3265 new javax.swing.event.InternalFrameAdapter()
3268 public void internalFrameClosed(
3269 javax.swing.event.InternalFrameEvent evt)
3272 alignPanel.setOverviewPanel(null);
3276 alignPanel.setOverviewPanel(overview);
3280 public void textColour_actionPerformed()
3282 new TextColourChooser().chooseColour(alignPanel, null);
3286 * public void covariationColour_actionPerformed() {
3288 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3292 public void annotationColour_actionPerformed()
3294 new AnnotationColourChooser(viewport, alignPanel);
3298 public void annotationColumn_actionPerformed(ActionEvent e)
3300 new AnnotationColumnChooser(viewport, alignPanel);
3304 * Action on the user checking or unchecking the option to apply the selected
3305 * colour scheme to all groups. If unchecked, groups may have their own
3306 * independent colour schemes.
3311 public void applyToAllGroups_actionPerformed(boolean selected)
3313 viewport.setColourAppliesToAllGroups(selected);
3317 * Action on user selecting a colour from the colour menu
3320 * the name (not the menu item label!) of the colour scheme
3323 public void changeColour_actionPerformed(String name)
3326 * 'User Defined' opens a panel to configure or load a
3327 * user-defined colour scheme
3329 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3331 new UserDefinedColours(alignPanel);
3336 * otherwise set the chosen colour scheme (or null for 'None')
3338 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3339 viewport.getAlignment(), viewport.getHiddenRepSequences());
3344 * Actions on setting or changing the alignment colour scheme
3349 public void changeColour(ColourSchemeI cs)
3351 // TODO: pull up to controller method
3352 ColourMenuHelper.setColourSelected(colourMenu, cs);
3354 viewport.setGlobalColourScheme(cs);
3356 alignPanel.paintAlignment(true);
3360 * Show the PID threshold slider panel
3363 protected void modifyPID_actionPerformed()
3365 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3366 alignPanel.getViewName());
3367 SliderPanel.showPIDSlider();
3371 * Show the Conservation slider panel
3374 protected void modifyConservation_actionPerformed()
3376 SliderPanel.setConservationSlider(alignPanel,
3377 viewport.getResidueShading(), alignPanel.getViewName());
3378 SliderPanel.showConservationSlider();
3382 * Action on selecting or deselecting (Colour) By Conservation
3385 public void conservationMenuItem_actionPerformed(boolean selected)
3387 modifyConservation.setEnabled(selected);
3388 viewport.setConservationSelected(selected);
3389 viewport.getResidueShading().setConservationApplied(selected);
3391 changeColour(viewport.getGlobalColourScheme());
3394 modifyConservation_actionPerformed();
3398 SliderPanel.hideConservationSlider();
3403 * Action on selecting or deselecting (Colour) Above PID Threshold
3406 public void abovePIDThreshold_actionPerformed(boolean selected)
3408 modifyPID.setEnabled(selected);
3409 viewport.setAbovePIDThreshold(selected);
3412 viewport.getResidueShading().setThreshold(0,
3413 viewport.isIgnoreGapsConsensus());
3416 changeColour(viewport.getGlobalColourScheme());
3419 modifyPID_actionPerformed();
3423 SliderPanel.hidePIDSlider();
3434 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3436 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3437 AlignmentSorter.sortByPID(viewport.getAlignment(),
3438 viewport.getAlignment().getSequenceAt(0));
3439 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3440 viewport.getAlignment()));
3441 alignPanel.paintAlignment(true);
3451 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3453 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3454 AlignmentSorter.sortByID(viewport.getAlignment());
3456 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3457 alignPanel.paintAlignment(true);
3467 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3469 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3470 AlignmentSorter.sortByLength(viewport.getAlignment());
3471 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3472 viewport.getAlignment()));
3473 alignPanel.paintAlignment(true);
3483 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3485 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3486 AlignmentSorter.sortByGroup(viewport.getAlignment());
3487 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3488 viewport.getAlignment()));
3490 alignPanel.paintAlignment(true);
3500 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3502 new RedundancyPanel(alignPanel, this);
3512 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3514 if ((viewport.getSelectionGroup() == null)
3515 || (viewport.getSelectionGroup().getSize() < 2))
3517 JvOptionPane.showInternalMessageDialog(this,
3518 MessageManager.getString(
3519 "label.you_must_select_least_two_sequences"),
3520 MessageManager.getString("label.invalid_selection"),
3521 JvOptionPane.WARNING_MESSAGE);
3525 JInternalFrame frame = new JInternalFrame();
3526 frame.setContentPane(new PairwiseAlignPanel(viewport));
3527 Desktop.addInternalFrame(frame,
3528 MessageManager.getString("action.pairwise_alignment"), 600,
3534 public void autoCalculate_actionPerformed(ActionEvent e)
3536 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3537 if (viewport.autoCalculateConsensus)
3539 viewport.firePropertyChange("alignment", null,
3540 viewport.getAlignment().getSequences());
3545 public void sortByTreeOption_actionPerformed(ActionEvent e)
3547 viewport.sortByTree = sortByTree.isSelected();
3551 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3553 viewport.followSelection = listenToViewSelections.isSelected();
3558 * Constructs a tree panel and adds it to the desktop
3567 void newTreePanel(TreeModel tree, String treeAlgo,
3568 String substitutionMatrix)
3570 String frameTitle = "";
3573 boolean onSelection = false;
3574 if (viewport.getSelectionGroup() != null
3575 && viewport.getSelectionGroup().getSize() > 0)
3577 SequenceGroup sg = viewport.getSelectionGroup();
3579 /* Decide if the selection is a column region */
3580 for (SequenceI _s : sg.getSequences())
3582 if (_s.getLength() < sg.getEndRes())
3584 JvOptionPane.showMessageDialog(Desktop.desktop,
3585 MessageManager.getString(
3586 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3587 MessageManager.getString(
3588 "label.sequences_selection_not_aligned"),
3589 JvOptionPane.WARNING_MESSAGE);
3598 if (viewport.getAlignment().getHeight() < 2)
3604 tp = new TreePanel(alignPanel, tree, treeAlgo, substitutionMatrix);
3605 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3607 frameTitle += " from ";
3609 if (viewport.viewName != null)
3611 frameTitle += viewport.viewName + " of ";
3614 frameTitle += this.title;
3616 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3627 public void addSortByOrderMenuItem(String title,
3628 final AlignmentOrder order)
3630 final JMenuItem item = new JMenuItem(MessageManager
3631 .formatMessage("action.by_title_param", new Object[]
3634 item.addActionListener(new java.awt.event.ActionListener()
3637 public void actionPerformed(ActionEvent e)
3639 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3641 // TODO: JBPNote - have to map order entries to curent SequenceI
3643 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3645 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3646 viewport.getAlignment()));
3648 alignPanel.paintAlignment(true);
3654 * Add a new sort by annotation score menu item
3657 * the menu to add the option to
3659 * the label used to retrieve scores for each sequence on the
3662 public void addSortByAnnotScoreMenuItem(JMenu sort,
3663 final String scoreLabel)
3665 final JMenuItem item = new JMenuItem(scoreLabel);
3667 item.addActionListener(new java.awt.event.ActionListener()
3670 public void actionPerformed(ActionEvent e)
3672 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3673 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3674 viewport.getAlignment());// ,viewport.getSelectionGroup());
3675 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3676 viewport.getAlignment()));
3677 alignPanel.paintAlignment(true);
3683 * last hash for alignment's annotation array - used to minimise cost of
3686 protected int _annotationScoreVectorHash;
3689 * search the alignment and rebuild the sort by annotation score submenu the
3690 * last alignment annotation vector hash is stored to minimize cost of
3691 * rebuilding in subsequence calls.
3695 public void buildSortByAnnotationScoresMenu()
3697 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3702 if (viewport.getAlignment().getAlignmentAnnotation()
3703 .hashCode() != _annotationScoreVectorHash)
3705 sortByAnnotScore.removeAll();
3706 // almost certainly a quicker way to do this - but we keep it simple
3707 Hashtable scoreSorts = new Hashtable();
3708 AlignmentAnnotation aann[];
3709 for (SequenceI sqa : viewport.getAlignment().getSequences())
3711 aann = sqa.getAnnotation();
3712 for (int i = 0; aann != null && i < aann.length; i++)
3714 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3716 scoreSorts.put(aann[i].label, aann[i].label);
3720 Enumeration labels = scoreSorts.keys();
3721 while (labels.hasMoreElements())
3723 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3724 (String) labels.nextElement());
3726 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3729 _annotationScoreVectorHash = viewport.getAlignment()
3730 .getAlignmentAnnotation().hashCode();
3735 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3736 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3737 * call. Listeners are added to remove the menu item when the treePanel is
3738 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3742 public void buildTreeSortMenu()
3744 sortByTreeMenu.removeAll();
3746 List<Component> comps = PaintRefresher.components
3747 .get(viewport.getSequenceSetId());
3748 List<TreePanel> treePanels = new ArrayList<>();
3749 for (Component comp : comps)
3751 if (comp instanceof TreePanel)
3753 treePanels.add((TreePanel) comp);
3757 if (treePanels.size() < 1)
3759 sortByTreeMenu.setVisible(false);
3763 sortByTreeMenu.setVisible(true);
3765 for (final TreePanel tp : treePanels)
3767 final JMenuItem item = new JMenuItem(tp.getTitle());
3768 item.addActionListener(new java.awt.event.ActionListener()
3771 public void actionPerformed(ActionEvent e)
3773 tp.sortByTree_actionPerformed();
3774 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3779 sortByTreeMenu.add(item);
3783 public boolean sortBy(AlignmentOrder alorder, String undoname)
3785 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3786 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3787 if (undoname != null)
3789 addHistoryItem(new OrderCommand(undoname, oldOrder,
3790 viewport.getAlignment()));
3792 alignPanel.paintAlignment(true);
3797 * Work out whether the whole set of sequences or just the selected set will
3798 * be submitted for multiple alignment.
3801 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3803 // Now, check we have enough sequences
3804 AlignmentView msa = null;
3806 if ((viewport.getSelectionGroup() != null)
3807 && (viewport.getSelectionGroup().getSize() > 1))
3809 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3810 // some common interface!
3812 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3813 * SequenceI[sz = seqs.getSize(false)];
3815 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3816 * seqs.getSequenceAt(i); }
3818 msa = viewport.getAlignmentView(true);
3820 else if (viewport.getSelectionGroup() != null
3821 && viewport.getSelectionGroup().getSize() == 1)
3823 int option = JvOptionPane.showConfirmDialog(this,
3824 MessageManager.getString("warn.oneseq_msainput_selection"),
3825 MessageManager.getString("label.invalid_selection"),
3826 JvOptionPane.OK_CANCEL_OPTION);
3827 if (option == JvOptionPane.OK_OPTION)
3829 msa = viewport.getAlignmentView(false);
3834 msa = viewport.getAlignmentView(false);
3840 * Decides what is submitted to a secondary structure prediction service: the
3841 * first sequence in the alignment, or in the current selection, or, if the
3842 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3843 * region or the whole alignment. (where the first sequence in the set is the
3844 * one that the prediction will be for).
3846 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3848 AlignmentView seqs = null;
3850 if ((viewport.getSelectionGroup() != null)
3851 && (viewport.getSelectionGroup().getSize() > 0))
3853 seqs = viewport.getAlignmentView(true);
3857 seqs = viewport.getAlignmentView(false);
3859 // limit sequences - JBPNote in future - could spawn multiple prediction
3861 // TODO: viewport.getAlignment().isAligned is a global state - the local
3862 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3863 if (!viewport.getAlignment().isAligned(false))
3865 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3866 // TODO: if seqs.getSequences().length>1 then should really have warned
3880 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3882 // Pick the tree file
3883 JalviewFileChooser chooser = new JalviewFileChooser(
3884 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3885 chooser.setFileView(new JalviewFileView());
3886 chooser.setDialogTitle(
3887 MessageManager.getString("label.select_newick_like_tree_file"));
3888 chooser.setToolTipText(
3889 MessageManager.getString("label.load_tree_file"));
3891 int value = chooser.showOpenDialog(null);
3893 if (value == JalviewFileChooser.APPROVE_OPTION)
3895 String filePath = chooser.getSelectedFile().getPath();
3896 Cache.setProperty("LAST_DIRECTORY", filePath);
3897 NewickFile fin = null;
3900 fin = new NewickFile(filePath, DataSourceType.FILE);
3901 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3902 } catch (Exception ex)
3904 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3905 MessageManager.getString("label.problem_reading_tree_file"),
3906 JvOptionPane.WARNING_MESSAGE);
3907 ex.printStackTrace();
3909 if (fin != null && fin.hasWarningMessage())
3911 JvOptionPane.showMessageDialog(Desktop.desktop,
3912 fin.getWarningMessage(),
3914 .getString("label.possible_problem_with_tree_file"),
3915 JvOptionPane.WARNING_MESSAGE);
3920 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3922 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3925 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3926 int h, int x, int y)
3928 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3932 * Add a treeviewer for the tree extracted from a Newick file object to the
3933 * current alignment view
3940 * Associated alignment input data (or null)
3949 * @return TreePanel handle
3951 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3952 AlignmentView input, int w, int h, int x, int y)
3954 TreePanel tp = null;
3960 if (nf.getTree() != null)
3962 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3968 tp.setLocation(x, y);
3971 Desktop.addInternalFrame(tp, treeTitle, w, h);
3973 } catch (Exception ex)
3975 ex.printStackTrace();
3981 private boolean buildingMenu = false;
3984 * Generates menu items and listener event actions for web service clients
3987 public void BuildWebServiceMenu()
3989 while (buildingMenu)
3993 System.err.println("Waiting for building menu to finish.");
3995 } catch (Exception e)
3999 final AlignFrame me = this;
4000 buildingMenu = true;
4001 new Thread(new Runnable()
4006 final List<JMenuItem> legacyItems = new ArrayList<>();
4009 // System.err.println("Building ws menu again "
4010 // + Thread.currentThread());
4011 // TODO: add support for context dependent disabling of services based
4013 // alignment and current selection
4014 // TODO: add additional serviceHandle parameter to specify abstract
4016 // class independently of AbstractName
4017 // TODO: add in rediscovery GUI function to restart discoverer
4018 // TODO: group services by location as well as function and/or
4020 // object broker mechanism.
4021 final Vector<JMenu> wsmenu = new Vector<>();
4022 final IProgressIndicator af = me;
4025 * do not i18n these strings - they are hard-coded in class
4026 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4027 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4029 final JMenu msawsmenu = new JMenu("Alignment");
4030 final JMenu secstrmenu = new JMenu(
4031 "Secondary Structure Prediction");
4032 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4033 final JMenu analymenu = new JMenu("Analysis");
4034 final JMenu dismenu = new JMenu("Protein Disorder");
4035 final JMenu phylogenmenu = new JMenu("Phylogenetic inference");
4037 // JAL-940 - only show secondary structure prediction services from
4038 // the legacy server
4039 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4041 Discoverer.services != null && (Discoverer.services.size() > 0))
4043 // TODO: refactor to allow list of AbstractName/Handler bindings to
4045 // stored or retrieved from elsewhere
4046 // No MSAWS used any more:
4047 // Vector msaws = null; // (Vector)
4048 // Discoverer.services.get("MsaWS");
4049 Vector secstrpr = (Vector) Discoverer.services
4051 if (secstrpr != null)
4053 // Add any secondary structure prediction services
4054 for (int i = 0, j = secstrpr.size(); i < j; i++)
4056 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4058 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4059 .getServiceClient(sh);
4060 int p = secstrmenu.getItemCount();
4061 impl.attachWSMenuEntry(secstrmenu, me);
4062 int q = secstrmenu.getItemCount();
4063 for (int litm = p; litm < q; litm++)
4065 legacyItems.add(secstrmenu.getItem(litm));
4071 // Add all submenus in the order they should appear on the web
4073 wsmenu.add(msawsmenu);
4074 wsmenu.add(secstrmenu);
4075 wsmenu.add(dismenu);
4076 wsmenu.add(analymenu);
4077 wsmenu.add(phylogenmenu);
4078 // No search services yet
4079 // wsmenu.add(seqsrchmenu);
4081 javax.swing.SwingUtilities.invokeLater(new Runnable()
4088 webService.removeAll();
4089 // first, add discovered services onto the webservices menu
4090 if (wsmenu.size() > 0)
4092 for (int i = 0, j = wsmenu.size(); i < j; i++)
4094 webService.add(wsmenu.get(i));
4099 webService.add(me.webServiceNoServices);
4101 // TODO: move into separate menu builder class.
4102 boolean new_sspred = false;
4103 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4105 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4106 if (jws2servs != null)
4108 if (jws2servs.hasServices())
4110 jws2servs.attachWSMenuEntry(webService, me);
4111 for (Jws2Instance sv : jws2servs.getServices())
4113 if (sv.description.toLowerCase().contains("jpred"))
4115 for (JMenuItem jmi : legacyItems)
4117 jmi.setVisible(false);
4123 if (jws2servs.isRunning())
4125 JMenuItem tm = new JMenuItem(
4126 "Still discovering JABA Services");
4127 tm.setEnabled(false);
4132 build_urlServiceMenu(me.webService);
4133 build_fetchdbmenu(webService);
4134 for (JMenu item : wsmenu)
4136 if (item.getItemCount() == 0)
4138 item.setEnabled(false);
4142 item.setEnabled(true);
4145 } catch (Exception e)
4148 "Exception during web service menu building process.",
4153 } catch (Exception e)
4156 buildingMenu = false;
4163 * construct any groupURL type service menu entries.
4167 private void build_urlServiceMenu(JMenu webService)
4169 // TODO: remove this code when 2.7 is released
4170 // DEBUG - alignmentView
4172 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4173 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4175 * @Override public void actionPerformed(ActionEvent e) {
4176 * jalview.datamodel.AlignmentView
4177 * .testSelectionViews(af.viewport.getAlignment(),
4178 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4180 * }); webService.add(testAlView);
4182 // TODO: refactor to RestClient discoverer and merge menu entries for
4183 // rest-style services with other types of analysis/calculation service
4184 // SHmmr test client - still being implemented.
4185 // DEBUG - alignmentView
4187 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4190 client.attachWSMenuEntry(
4191 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4197 * Searches the alignment sequences for xRefs and builds the Show
4198 * Cross-References menu (formerly called Show Products), with database
4199 * sources for which cross-references are found (protein sources for a
4200 * nucleotide alignment and vice versa)
4202 * @return true if Show Cross-references menu should be enabled
4204 public boolean canShowProducts()
4206 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4207 AlignmentI dataset = viewport.getAlignment().getDataset();
4209 showProducts.removeAll();
4210 final boolean dna = viewport.getAlignment().isNucleotide();
4212 if (seqs == null || seqs.length == 0)
4214 // nothing to see here.
4218 boolean showp = false;
4221 List<String> ptypes = new CrossRef(seqs, dataset)
4222 .findXrefSourcesForSequences(dna);
4224 for (final String source : ptypes)
4227 final AlignFrame af = this;
4228 JMenuItem xtype = new JMenuItem(source);
4229 xtype.addActionListener(new ActionListener()
4232 public void actionPerformed(ActionEvent e)
4234 showProductsFor(af.viewport.getSequenceSelection(), dna,
4238 showProducts.add(xtype);
4240 showProducts.setVisible(showp);
4241 showProducts.setEnabled(showp);
4242 } catch (Exception e)
4245 "canShowProducts threw an exception - please report to help@jalview.org",
4253 * Finds and displays cross-references for the selected sequences (protein
4254 * products for nucleotide sequences, dna coding sequences for peptides).
4257 * the sequences to show cross-references for
4259 * true if from a nucleotide alignment (so showing proteins)
4261 * the database to show cross-references for
4263 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4264 final String source)
4266 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4271 * Construct and display a new frame containing the translation of this
4272 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4275 public void showTranslation_actionPerformed(ActionEvent e)
4277 AlignmentI al = null;
4280 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4282 al = dna.translateCdna();
4283 } catch (Exception ex)
4285 jalview.bin.Cache.log.error(
4286 "Exception during translation. Please report this !", ex);
4287 final String msg = MessageManager.getString(
4288 "label.error_when_translating_sequences_submit_bug_report");
4289 final String errorTitle = MessageManager
4290 .getString("label.implementation_error")
4291 + MessageManager.getString("label.translation_failed");
4292 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4293 JvOptionPane.ERROR_MESSAGE);
4296 if (al == null || al.getHeight() == 0)
4298 final String msg = MessageManager.getString(
4299 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4300 final String errorTitle = MessageManager
4301 .getString("label.translation_failed");
4302 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4303 JvOptionPane.WARNING_MESSAGE);
4307 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4308 af.setFileFormat(this.currentFileFormat);
4309 final String newTitle = MessageManager
4310 .formatMessage("label.translation_of_params", new Object[]
4311 { this.getTitle() });
4312 af.setTitle(newTitle);
4313 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4315 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4316 viewport.openSplitFrame(af, new Alignment(seqs));
4320 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4327 * Set the file format
4331 public void setFileFormat(FileFormatI format)
4333 this.currentFileFormat = format;
4337 * Try to load a features file onto the alignment.
4340 * contents or path to retrieve file
4342 * access mode of file (see jalview.io.AlignFile)
4343 * @return true if features file was parsed correctly.
4345 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4347 return avc.parseFeaturesFile(file, sourceType,
4348 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4353 public void refreshFeatureUI(boolean enableIfNecessary)
4355 // note - currently this is only still here rather than in the controller
4356 // because of the featureSettings hard reference that is yet to be
4358 if (enableIfNecessary)
4360 viewport.setShowSequenceFeatures(true);
4361 showSeqFeatures.setSelected(true);
4367 public void dragEnter(DropTargetDragEvent evt)
4372 public void dragExit(DropTargetEvent evt)
4377 public void dragOver(DropTargetDragEvent evt)
4382 public void dropActionChanged(DropTargetDragEvent evt)
4387 public void drop(DropTargetDropEvent evt)
4389 // JAL-1552 - acceptDrop required before getTransferable call for
4390 // Java's Transferable for native dnd
4391 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4392 Transferable t = evt.getTransferable();
4393 final AlignFrame thisaf = this;
4394 final List<String> files = new ArrayList<>();
4395 List<DataSourceType> protocols = new ArrayList<>();
4399 Desktop.transferFromDropTarget(files, protocols, evt, t);
4400 } catch (Exception e)
4402 e.printStackTrace();
4406 new Thread(new Runnable()
4413 // check to see if any of these files have names matching sequences
4416 SequenceIdMatcher idm = new SequenceIdMatcher(
4417 viewport.getAlignment().getSequencesArray());
4419 * Object[] { String,SequenceI}
4421 ArrayList<Object[]> filesmatched = new ArrayList<>();
4422 ArrayList<String> filesnotmatched = new ArrayList<>();
4423 for (int i = 0; i < files.size(); i++)
4425 String file = files.get(i).toString();
4427 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4428 if (protocol == DataSourceType.FILE)
4430 File fl = new File(file);
4431 pdbfn = fl.getName();
4433 else if (protocol == DataSourceType.URL)
4435 URL url = new URL(file);
4436 pdbfn = url.getFile();
4438 if (pdbfn.length() > 0)
4440 // attempt to find a match in the alignment
4441 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4442 int l = 0, c = pdbfn.indexOf(".");
4443 while (mtch == null && c != -1)
4448 } while ((c = pdbfn.indexOf(".", l)) > l);
4451 pdbfn = pdbfn.substring(0, l);
4453 mtch = idm.findAllIdMatches(pdbfn);
4457 FileFormatI type = null;
4460 type = new IdentifyFile().identify(file, protocol);
4461 } catch (Exception ex)
4465 if (type != null && type.isStructureFile())
4467 filesmatched.add(new Object[] { file, protocol, mtch });
4471 // File wasn't named like one of the sequences or wasn't a PDB
4473 filesnotmatched.add(file);
4477 if (filesmatched.size() > 0)
4479 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4480 || JvOptionPane.showConfirmDialog(thisaf,
4481 MessageManager.formatMessage(
4482 "label.automatically_associate_structure_files_with_sequences_same_name",
4484 { Integer.valueOf(filesmatched.size())
4486 MessageManager.getString(
4487 "label.automatically_associate_structure_files_by_name"),
4488 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4491 for (Object[] fm : filesmatched)
4493 // try and associate
4494 // TODO: may want to set a standard ID naming formalism for
4495 // associating PDB files which have no IDs.
4496 for (SequenceI toassoc : (SequenceI[]) fm[2])
4498 PDBEntry pe = new AssociatePdbFileWithSeq()
4499 .associatePdbWithSeq((String) fm[0],
4500 (DataSourceType) fm[1], toassoc, false,
4504 System.err.println("Associated file : "
4505 + ((String) fm[0]) + " with "
4506 + toassoc.getDisplayId(true));
4510 alignPanel.paintAlignment(true);
4514 if (filesnotmatched.size() > 0)
4516 if (assocfiles > 0 && (Cache.getDefault(
4517 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4518 || JvOptionPane.showConfirmDialog(thisaf,
4519 "<html>" + MessageManager.formatMessage(
4520 "label.ignore_unmatched_dropped_files_info",
4523 filesnotmatched.size())
4526 MessageManager.getString(
4527 "label.ignore_unmatched_dropped_files"),
4528 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4532 for (String fn : filesnotmatched)
4534 loadJalviewDataFile(fn, null, null, null);
4538 } catch (Exception ex)
4540 ex.printStackTrace();
4548 * Attempt to load a "dropped" file or URL string, by testing in turn for
4550 * <li>an Annotation file</li>
4551 * <li>a JNet file</li>
4552 * <li>a features file</li>
4553 * <li>else try to interpret as an alignment file</li>
4557 * either a filename or a URL string.
4559 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4560 FileFormatI format, SequenceI assocSeq)
4564 if (sourceType == null)
4566 sourceType = FormatAdapter.checkProtocol(file);
4568 // if the file isn't identified, or not positively identified as some
4569 // other filetype (PFAM is default unidentified alignment file type) then
4570 // try to parse as annotation.
4571 boolean isAnnotation = (format == null
4572 || FileFormat.Pfam.equals(format))
4573 ? new AnnotationFile().annotateAlignmentView(viewport,
4579 // first see if its a T-COFFEE score file
4580 TCoffeeScoreFile tcf = null;
4583 tcf = new TCoffeeScoreFile(file, sourceType);
4586 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4590 new TCoffeeColourScheme(viewport.getAlignment()));
4591 isAnnotation = true;
4592 statusBar.setText(MessageManager.getString(
4593 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4597 // some problem - if no warning its probable that the ID matching
4598 // process didn't work
4599 JvOptionPane.showMessageDialog(Desktop.desktop,
4600 tcf.getWarningMessage() == null
4601 ? MessageManager.getString(
4602 "label.check_file_matches_sequence_ids_alignment")
4603 : tcf.getWarningMessage(),
4604 MessageManager.getString(
4605 "label.problem_reading_tcoffee_score_file"),
4606 JvOptionPane.WARNING_MESSAGE);
4613 } catch (Exception x)
4616 "Exception when processing data source as T-COFFEE score file",
4622 // try to see if its a JNet 'concise' style annotation file *before*
4624 // try to parse it as a features file
4627 format = new IdentifyFile().identify(file, sourceType);
4629 if (FileFormat.ScoreMatrix == format)
4631 ScoreMatrixFile sm = new ScoreMatrixFile(
4632 new FileParse(file, sourceType));
4634 // todo: i18n this message
4635 statusBar.setText(MessageManager.formatMessage(
4636 "label.successfully_loaded_matrix",
4637 sm.getMatrixName()));
4639 else if (FileFormat.Jnet.equals(format))
4641 JPredFile predictions = new JPredFile(file, sourceType);
4642 new JnetAnnotationMaker();
4643 JnetAnnotationMaker.add_annotation(predictions,
4644 viewport.getAlignment(), 0, false);
4645 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4646 viewport.getAlignment().setSeqrep(repseq);
4647 HiddenColumns cs = new HiddenColumns();
4648 cs.hideInsertionsFor(repseq);
4649 viewport.getAlignment().setHiddenColumns(cs);
4650 isAnnotation = true;
4652 // else if (IdentifyFile.FeaturesFile.equals(format))
4653 else if (FileFormat.Features.equals(format))
4655 if (parseFeaturesFile(file, sourceType))
4657 alignPanel.paintAlignment(true);
4662 new FileLoader().LoadFile(viewport, file, sourceType, format);
4669 alignPanel.adjustAnnotationHeight();
4670 viewport.updateSequenceIdColours();
4671 buildSortByAnnotationScoresMenu();
4672 alignPanel.paintAlignment(true);
4674 } catch (Exception ex)
4676 ex.printStackTrace();
4677 } catch (OutOfMemoryError oom)
4682 } catch (Exception x)
4687 + (sourceType != null
4688 ? (sourceType == DataSourceType.PASTE
4690 : "using " + sourceType + " from "
4694 ? "(parsing as '" + format + "' file)"
4696 oom, Desktop.desktop);
4701 * Method invoked by the ChangeListener on the tabbed pane, in other words
4702 * when a different tabbed pane is selected by the user or programmatically.
4705 public void tabSelectionChanged(int index)
4709 alignPanel = alignPanels.get(index);
4710 viewport = alignPanel.av;
4711 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4712 setMenusFromViewport(viewport);
4716 * 'focus' any colour slider that is open to the selected viewport
4718 if (viewport.getConservationSelected())
4720 SliderPanel.setConservationSlider(alignPanel,
4721 viewport.getResidueShading(), alignPanel.getViewName());
4725 SliderPanel.hideConservationSlider();
4727 if (viewport.getAbovePIDThreshold())
4729 SliderPanel.setPIDSliderSource(alignPanel,
4730 viewport.getResidueShading(), alignPanel.getViewName());
4734 SliderPanel.hidePIDSlider();
4738 * If there is a frame linked to this one in a SplitPane, switch it to the
4739 * same view tab index. No infinite recursion of calls should happen, since
4740 * tabSelectionChanged() should not get invoked on setting the selected
4741 * index to an unchanged value. Guard against setting an invalid index
4742 * before the new view peer tab has been created.
4744 final AlignViewportI peer = viewport.getCodingComplement();
4747 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4748 .getAlignPanel().alignFrame;
4749 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4751 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4757 * On right mouse click on view tab, prompt for and set new view name.
4760 public void tabbedPane_mousePressed(MouseEvent e)
4762 if (e.isPopupTrigger())
4764 String msg = MessageManager.getString("label.enter_view_name");
4765 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4766 JvOptionPane.QUESTION_MESSAGE);
4770 viewport.viewName = reply;
4771 // TODO warn if reply is in getExistingViewNames()?
4772 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4777 public AlignViewport getCurrentView()
4783 * Open the dialog for regex description parsing.
4786 protected void extractScores_actionPerformed(ActionEvent e)
4788 ParseProperties pp = new jalview.analysis.ParseProperties(
4789 viewport.getAlignment());
4790 // TODO: verify regex and introduce GUI dialog for version 2.5
4791 // if (pp.getScoresFromDescription("col", "score column ",
4792 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4794 if (pp.getScoresFromDescription("description column",
4795 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4797 buildSortByAnnotationScoresMenu();
4805 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4809 protected void showDbRefs_actionPerformed(ActionEvent e)
4811 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4817 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4821 protected void showNpFeats_actionPerformed(ActionEvent e)
4823 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4827 * find the viewport amongst the tabs in this alignment frame and close that
4832 public boolean closeView(AlignViewportI av)
4836 this.closeMenuItem_actionPerformed(false);
4839 Component[] comp = tabbedPane.getComponents();
4840 for (int i = 0; comp != null && i < comp.length; i++)
4842 if (comp[i] instanceof AlignmentPanel)
4844 if (((AlignmentPanel) comp[i]).av == av)
4847 closeView((AlignmentPanel) comp[i]);
4855 protected void build_fetchdbmenu(JMenu webService)
4857 // Temporary hack - DBRef Fetcher always top level ws entry.
4858 // TODO We probably want to store a sequence database checklist in
4859 // preferences and have checkboxes.. rather than individual sources selected
4861 final JMenu rfetch = new JMenu(
4862 MessageManager.getString("action.fetch_db_references"));
4863 rfetch.setToolTipText(MessageManager.getString(
4864 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4865 webService.add(rfetch);
4867 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4868 MessageManager.getString("option.trim_retrieved_seqs"));
4869 trimrs.setToolTipText(
4870 MessageManager.getString("label.trim_retrieved_sequences"));
4871 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4872 trimrs.addActionListener(new ActionListener()
4875 public void actionPerformed(ActionEvent e)
4877 trimrs.setSelected(trimrs.isSelected());
4878 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4879 Boolean.valueOf(trimrs.isSelected()).toString());
4883 JMenuItem fetchr = new JMenuItem(
4884 MessageManager.getString("label.standard_databases"));
4885 fetchr.setToolTipText(
4886 MessageManager.getString("label.fetch_embl_uniprot"));
4887 fetchr.addActionListener(new ActionListener()
4891 public void actionPerformed(ActionEvent e)
4893 new Thread(new Runnable()
4898 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4899 .getAlignment().isNucleotide();
4900 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4901 alignPanel.av.getSequenceSelection(),
4902 alignPanel.alignFrame, null,
4903 alignPanel.alignFrame.featureSettings, isNucleotide);
4904 dbRefFetcher.addListener(new FetchFinishedListenerI()
4907 public void finished()
4909 AlignFrame.this.setMenusForViewport();
4912 dbRefFetcher.fetchDBRefs(false);
4920 final AlignFrame me = this;
4921 new Thread(new Runnable()
4926 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4927 .getSequenceFetcherSingleton(me);
4928 javax.swing.SwingUtilities.invokeLater(new Runnable()
4933 String[] dbclasses = sf.getOrderedSupportedSources();
4934 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4935 // jalview.util.QuickSort.sort(otherdb, otherdb);
4936 List<DbSourceProxy> otherdb;
4937 JMenu dfetch = new JMenu();
4938 JMenu ifetch = new JMenu();
4939 JMenuItem fetchr = null;
4940 int comp = 0, icomp = 0, mcomp = 15;
4941 String mname = null;
4943 for (String dbclass : dbclasses)
4945 otherdb = sf.getSourceProxy(dbclass);
4946 // add a single entry for this class, or submenu allowing 'fetch
4948 if (otherdb == null || otherdb.size() < 1)
4952 // List<DbSourceProxy> dbs=otherdb;
4953 // otherdb=new ArrayList<DbSourceProxy>();
4954 // for (DbSourceProxy db:dbs)
4956 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4960 mname = "From " + dbclass;
4962 if (otherdb.size() == 1)
4964 final DbSourceProxy[] dassource = otherdb
4965 .toArray(new DbSourceProxy[0]);
4966 DbSourceProxy src = otherdb.get(0);
4967 fetchr = new JMenuItem(src.getDbSource());
4968 fetchr.addActionListener(new ActionListener()
4972 public void actionPerformed(ActionEvent e)
4974 new Thread(new Runnable()
4980 boolean isNucleotide = alignPanel.alignFrame
4981 .getViewport().getAlignment()
4983 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4984 alignPanel.av.getSequenceSelection(),
4985 alignPanel.alignFrame, dassource,
4986 alignPanel.alignFrame.featureSettings,
4989 .addListener(new FetchFinishedListenerI()
4992 public void finished()
4994 AlignFrame.this.setMenusForViewport();
4997 dbRefFetcher.fetchDBRefs(false);
5003 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5004 MessageManager.formatMessage(
5005 "label.fetch_retrieve_from", new Object[]
5006 { src.getDbName() })));
5012 final DbSourceProxy[] dassource = otherdb
5013 .toArray(new DbSourceProxy[0]);
5015 DbSourceProxy src = otherdb.get(0);
5016 fetchr = new JMenuItem(MessageManager
5017 .formatMessage("label.fetch_all_param", new Object[]
5018 { src.getDbSource() }));
5019 fetchr.addActionListener(new ActionListener()
5022 public void actionPerformed(ActionEvent e)
5024 new Thread(new Runnable()
5030 boolean isNucleotide = alignPanel.alignFrame
5031 .getViewport().getAlignment()
5033 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5034 alignPanel.av.getSequenceSelection(),
5035 alignPanel.alignFrame, dassource,
5036 alignPanel.alignFrame.featureSettings,
5039 .addListener(new FetchFinishedListenerI()
5042 public void finished()
5044 AlignFrame.this.setMenusForViewport();
5047 dbRefFetcher.fetchDBRefs(false);
5053 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5054 MessageManager.formatMessage(
5055 "label.fetch_retrieve_from_all_sources",
5057 { Integer.valueOf(otherdb.size())
5059 src.getDbSource(), src.getDbName() })));
5062 // and then build the rest of the individual menus
5063 ifetch = new JMenu(MessageManager.formatMessage(
5064 "label.source_from_db_source", new Object[]
5065 { src.getDbSource() }));
5067 String imname = null;
5069 for (DbSourceProxy sproxy : otherdb)
5071 String dbname = sproxy.getDbName();
5072 String sname = dbname.length() > 5
5073 ? dbname.substring(0, 5) + "..."
5075 String msname = dbname.length() > 10
5076 ? dbname.substring(0, 10) + "..."
5080 imname = MessageManager
5081 .formatMessage("label.from_msname", new Object[]
5084 fetchr = new JMenuItem(msname);
5085 final DbSourceProxy[] dassrc = { sproxy };
5086 fetchr.addActionListener(new ActionListener()
5090 public void actionPerformed(ActionEvent e)
5092 new Thread(new Runnable()
5098 boolean isNucleotide = alignPanel.alignFrame
5099 .getViewport().getAlignment()
5101 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5102 alignPanel.av.getSequenceSelection(),
5103 alignPanel.alignFrame, dassrc,
5104 alignPanel.alignFrame.featureSettings,
5107 .addListener(new FetchFinishedListenerI()
5110 public void finished()
5112 AlignFrame.this.setMenusForViewport();
5115 dbRefFetcher.fetchDBRefs(false);
5121 fetchr.setToolTipText(
5122 "<html>" + MessageManager.formatMessage(
5123 "label.fetch_retrieve_from", new Object[]
5127 if (++icomp >= mcomp || i == (otherdb.size()))
5129 ifetch.setText(MessageManager.formatMessage(
5130 "label.source_to_target", imname, sname));
5132 ifetch = new JMenu();
5140 if (comp >= mcomp || dbi >= (dbclasses.length))
5142 dfetch.setText(MessageManager.formatMessage(
5143 "label.source_to_target", mname, dbclass));
5145 dfetch = new JMenu();
5158 * Left justify the whole alignment.
5161 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5163 AlignmentI al = viewport.getAlignment();
5165 viewport.firePropertyChange("alignment", null, al);
5169 * Right justify the whole alignment.
5172 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5174 AlignmentI al = viewport.getAlignment();
5176 viewport.firePropertyChange("alignment", null, al);
5180 public void setShowSeqFeatures(boolean b)
5182 showSeqFeatures.setSelected(b);
5183 viewport.setShowSequenceFeatures(b);
5190 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5191 * awt.event.ActionEvent)
5194 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5196 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5197 alignPanel.paintAlignment(true);
5204 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5208 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5210 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5211 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5219 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5220 * .event.ActionEvent)
5223 protected void showGroupConservation_actionPerformed(ActionEvent e)
5225 viewport.setShowGroupConservation(showGroupConservation.getState());
5226 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5233 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5234 * .event.ActionEvent)
5237 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5239 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5240 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5247 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5248 * .event.ActionEvent)
5251 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5253 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5254 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5258 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5260 showSequenceLogo.setState(true);
5261 viewport.setShowSequenceLogo(true);
5262 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5263 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5267 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5269 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5276 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5277 * .event.ActionEvent)
5280 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5282 if (avc.makeGroupsFromSelection())
5284 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5285 alignPanel.updateAnnotation();
5286 alignPanel.paintAlignment(true);
5290 public void clearAlignmentSeqRep()
5292 // TODO refactor alignmentseqrep to controller
5293 if (viewport.getAlignment().hasSeqrep())
5295 viewport.getAlignment().setSeqrep(null);
5296 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5297 alignPanel.updateAnnotation();
5298 alignPanel.paintAlignment(true);
5303 protected void createGroup_actionPerformed(ActionEvent e)
5305 if (avc.createGroup())
5307 alignPanel.alignmentChanged();
5312 protected void unGroup_actionPerformed(ActionEvent e)
5316 alignPanel.alignmentChanged();
5321 * make the given alignmentPanel the currently selected tab
5323 * @param alignmentPanel
5325 public void setDisplayedView(AlignmentPanel alignmentPanel)
5327 if (!viewport.getSequenceSetId()
5328 .equals(alignmentPanel.av.getSequenceSetId()))
5330 throw new Error(MessageManager.getString(
5331 "error.implementation_error_cannot_show_view_alignment_frame"));
5333 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5334 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5336 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5341 * Action on selection of menu options to Show or Hide annotations.
5344 * @param forSequences
5345 * update sequence-related annotations
5346 * @param forAlignment
5347 * update non-sequence-related annotations
5350 protected void setAnnotationsVisibility(boolean visible,
5351 boolean forSequences, boolean forAlignment)
5353 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5354 .getAlignmentAnnotation();
5359 for (AlignmentAnnotation aa : anns)
5362 * don't display non-positional annotations on an alignment
5364 if (aa.annotations == null)
5368 boolean apply = (aa.sequenceRef == null && forAlignment)
5369 || (aa.sequenceRef != null && forSequences);
5372 aa.visible = visible;
5375 alignPanel.validateAnnotationDimensions(true);
5376 alignPanel.alignmentChanged();
5380 * Store selected annotation sort order for the view and repaint.
5383 protected void sortAnnotations_actionPerformed()
5385 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5387 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5388 alignPanel.paintAlignment(true);
5393 * @return alignment panels in this alignment frame
5395 public List<? extends AlignmentViewPanel> getAlignPanels()
5397 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5401 * Open a new alignment window, with the cDNA associated with this (protein)
5402 * alignment, aligned as is the protein.
5404 protected void viewAsCdna_actionPerformed()
5406 // TODO no longer a menu action - refactor as required
5407 final AlignmentI alignment = getViewport().getAlignment();
5408 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5409 if (mappings == null)
5413 List<SequenceI> cdnaSeqs = new ArrayList<>();
5414 for (SequenceI aaSeq : alignment.getSequences())
5416 for (AlignedCodonFrame acf : mappings)
5418 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5422 * There is a cDNA mapping for this protein sequence - add to new
5423 * alignment. It will share the same dataset sequence as other mapped
5424 * cDNA (no new mappings need to be created).
5426 final Sequence newSeq = new Sequence(dnaSeq);
5427 newSeq.setDatasetSequence(dnaSeq);
5428 cdnaSeqs.add(newSeq);
5432 if (cdnaSeqs.size() == 0)
5434 // show a warning dialog no mapped cDNA
5437 AlignmentI cdna = new Alignment(
5438 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5439 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5440 AlignFrame.DEFAULT_HEIGHT);
5441 cdna.alignAs(alignment);
5442 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5444 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5445 AlignFrame.DEFAULT_HEIGHT);
5449 * Set visibility of dna/protein complement view (available when shown in a
5455 protected void showComplement_actionPerformed(boolean show)
5457 SplitContainerI sf = getSplitViewContainer();
5460 sf.setComplementVisible(this, show);
5465 * Generate the reverse (optionally complemented) of the selected sequences,
5466 * and add them to the alignment
5469 protected void showReverse_actionPerformed(boolean complement)
5471 AlignmentI al = null;
5474 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5475 al = dna.reverseCdna(complement);
5476 viewport.addAlignment(al, "");
5477 addHistoryItem(new EditCommand(
5478 MessageManager.getString("label.add_sequences"), Action.PASTE,
5479 al.getSequencesArray(), 0, al.getWidth(),
5480 viewport.getAlignment()));
5481 } catch (Exception ex)
5483 System.err.println(ex.getMessage());
5489 * Try to run a script in the Groovy console, having first ensured that this
5490 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5491 * be targeted at this alignment.
5494 protected void runGroovy_actionPerformed()
5496 Jalview.setCurrentAlignFrame(this);
5497 groovy.ui.Console console = Desktop.getGroovyConsole();
5498 if (console != null)
5502 console.runScript();
5503 } catch (Exception ex)
5505 System.err.println((ex.toString()));
5506 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5507 MessageManager.getString("label.couldnt_run_groovy_script"),
5508 MessageManager.getString("label.groovy_support_failed"),
5509 JvOptionPane.ERROR_MESSAGE);
5514 System.err.println("Can't run Groovy script as console not found");
5519 * Hides columns containing (or not containing) a specified feature, provided
5520 * that would not leave all columns hidden
5522 * @param featureType
5523 * @param columnsContaining
5526 public boolean hideFeatureColumns(String featureType,
5527 boolean columnsContaining)
5529 boolean notForHiding = avc.markColumnsContainingFeatures(
5530 columnsContaining, false, false, featureType);
5533 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5534 false, featureType))
5536 getViewport().hideSelectedColumns();
5544 protected void selectHighlightedColumns_actionPerformed(
5545 ActionEvent actionEvent)
5547 // include key modifier check in case user selects from menu
5548 avc.markHighlightedColumns(
5549 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5550 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5551 | ActionEvent.CTRL_MASK)) != 0);
5555 * Rebuilds the Colour menu, including any user-defined colours which have
5556 * been loaded either on startup or during the session
5558 public void buildColourMenu()
5560 colourMenu.removeAll();
5562 colourMenu.add(applyToAllGroups);
5563 colourMenu.add(textColour);
5564 colourMenu.addSeparator();
5566 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5569 colourMenu.addSeparator();
5570 colourMenu.add(conservationMenuItem);
5571 colourMenu.add(modifyConservation);
5572 colourMenu.add(abovePIDThreshold);
5573 colourMenu.add(modifyPID);
5574 colourMenu.add(annotationColour);
5576 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5577 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5581 * Open a dialog (if not already open) that allows the user to select and
5582 * calculate PCA or Tree analysis
5584 protected void openTreePcaDialog()
5586 if (alignPanel.getCalculationDialog() == null)
5588 new CalculationChooser(AlignFrame.this);
5593 class PrintThread extends Thread
5597 public PrintThread(AlignmentPanel ap)
5602 static PageFormat pf;
5607 PrinterJob printJob = PrinterJob.getPrinterJob();
5611 printJob.setPrintable(ap, pf);
5615 printJob.setPrintable(ap);
5618 if (printJob.printDialog())
5623 } catch (Exception PrintException)
5625 PrintException.printStackTrace();