2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.ScoreModelI;
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.HiddenSequences;
57 import jalview.datamodel.PDBEntry;
58 import jalview.datamodel.SeqCigar;
59 import jalview.datamodel.Sequence;
60 import jalview.datamodel.SequenceGroup;
61 import jalview.datamodel.SequenceI;
62 import jalview.gui.ColourMenuHelper.ColourChangeListener;
63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
64 import jalview.io.AlignmentProperties;
65 import jalview.io.AnnotationFile;
66 import jalview.io.BioJsHTMLOutput;
67 import jalview.io.DataSourceType;
68 import jalview.io.FileFormat;
69 import jalview.io.FileFormatI;
70 import jalview.io.FileFormats;
71 import jalview.io.FileLoader;
72 import jalview.io.FormatAdapter;
73 import jalview.io.HtmlSvgOutput;
74 import jalview.io.IdentifyFile;
75 import jalview.io.JPredFile;
76 import jalview.io.JalviewFileChooser;
77 import jalview.io.JalviewFileView;
78 import jalview.io.JnetAnnotationMaker;
79 import jalview.io.NewickFile;
80 import jalview.io.TCoffeeScoreFile;
81 import jalview.jbgui.GAlignFrame;
82 import jalview.schemes.ColourSchemeI;
83 import jalview.schemes.ColourSchemes;
84 import jalview.schemes.ResidueColourScheme;
85 import jalview.schemes.TCoffeeColourScheme;
86 import jalview.util.MessageManager;
87 import jalview.viewmodel.AlignmentViewport;
88 import jalview.ws.DBRefFetcher;
89 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
90 import jalview.ws.jws1.Discoverer;
91 import jalview.ws.jws2.Jws2Discoverer;
92 import jalview.ws.jws2.jabaws2.Jws2Instance;
93 import jalview.ws.seqfetcher.DbSourceProxy;
95 import java.awt.BorderLayout;
96 import java.awt.Component;
97 import java.awt.Rectangle;
98 import java.awt.Toolkit;
99 import java.awt.datatransfer.Clipboard;
100 import java.awt.datatransfer.DataFlavor;
101 import java.awt.datatransfer.StringSelection;
102 import java.awt.datatransfer.Transferable;
103 import java.awt.dnd.DnDConstants;
104 import java.awt.dnd.DropTargetDragEvent;
105 import java.awt.dnd.DropTargetDropEvent;
106 import java.awt.dnd.DropTargetEvent;
107 import java.awt.dnd.DropTargetListener;
108 import java.awt.event.ActionEvent;
109 import java.awt.event.ActionListener;
110 import java.awt.event.FocusAdapter;
111 import java.awt.event.FocusEvent;
112 import java.awt.event.ItemEvent;
113 import java.awt.event.ItemListener;
114 import java.awt.event.KeyAdapter;
115 import java.awt.event.KeyEvent;
116 import java.awt.event.MouseEvent;
117 import java.awt.print.PageFormat;
118 import java.awt.print.PrinterJob;
119 import java.beans.PropertyChangeEvent;
121 import java.io.FileWriter;
122 import java.io.PrintWriter;
124 import java.util.ArrayList;
125 import java.util.Arrays;
126 import java.util.Deque;
127 import java.util.Enumeration;
128 import java.util.Hashtable;
129 import java.util.List;
130 import java.util.Vector;
132 import javax.swing.JCheckBoxMenuItem;
133 import javax.swing.JEditorPane;
134 import javax.swing.JInternalFrame;
135 import javax.swing.JLayeredPane;
136 import javax.swing.JMenu;
137 import javax.swing.JMenuItem;
138 import javax.swing.JScrollPane;
139 import javax.swing.SwingUtilities;
145 * @version $Revision$
147 public class AlignFrame extends GAlignFrame implements DropTargetListener,
148 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
151 public static final int DEFAULT_WIDTH = 700;
153 public static final int DEFAULT_HEIGHT = 500;
156 * The currently displayed panel (selected tabbed view if more than one)
158 public AlignmentPanel alignPanel;
160 AlignViewport viewport;
162 public AlignViewControllerI avc;
164 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
167 * Last format used to load or save alignments in this window
169 FileFormatI currentFileFormat = null;
172 * Current filename for this alignment
174 String fileName = null;
177 * Creates a new AlignFrame object with specific width and height.
183 public AlignFrame(AlignmentI al, int width, int height)
185 this(al, null, width, height);
189 * Creates a new AlignFrame object with specific width, height and
195 * @param sequenceSetId
197 public AlignFrame(AlignmentI al, int width, int height,
198 String sequenceSetId)
200 this(al, null, width, height, sequenceSetId);
204 * Creates a new AlignFrame object with specific width, height and
210 * @param sequenceSetId
213 public AlignFrame(AlignmentI al, int width, int height,
214 String sequenceSetId, String viewId)
216 this(al, null, width, height, sequenceSetId, viewId);
220 * new alignment window with hidden columns
224 * @param hiddenColumns
225 * ColumnSelection or null
227 * Width of alignment frame
231 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
232 int width, int height)
234 this(al, hiddenColumns, width, height, null);
238 * Create alignment frame for al with hiddenColumns, a specific width and
239 * height, and specific sequenceId
242 * @param hiddenColumns
245 * @param sequenceSetId
248 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
249 int width, int height, String sequenceSetId)
251 this(al, hiddenColumns, width, height, sequenceSetId, null);
255 * Create alignment frame for al with hiddenColumns, a specific width and
256 * height, and specific sequenceId
259 * @param hiddenColumns
262 * @param sequenceSetId
267 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
268 int width, int height, String sequenceSetId, String viewId)
270 setSize(width, height);
272 if (al.getDataset() == null)
277 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
279 alignPanel = new AlignmentPanel(this, viewport);
281 addAlignmentPanel(alignPanel, true);
285 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
286 ColumnSelection hiddenColumns, int width, int height)
288 setSize(width, height);
290 if (al.getDataset() == null)
295 viewport = new AlignViewport(al, hiddenColumns);
297 if (hiddenSeqs != null && hiddenSeqs.length > 0)
299 viewport.hideSequence(hiddenSeqs);
301 alignPanel = new AlignmentPanel(this, viewport);
302 addAlignmentPanel(alignPanel, true);
307 * Make a new AlignFrame from existing alignmentPanels
314 public AlignFrame(AlignmentPanel ap)
318 addAlignmentPanel(ap, false);
323 * initalise the alignframe from the underlying viewport data and the
328 if (!Jalview.isHeadlessMode())
330 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
333 avc = new jalview.controller.AlignViewController(this, viewport,
335 if (viewport.getAlignmentConservationAnnotation() == null)
337 // BLOSUM62Colour.setEnabled(false);
338 conservationMenuItem.setEnabled(false);
339 modifyConservation.setEnabled(false);
340 // PIDColour.setEnabled(false);
341 // abovePIDThreshold.setEnabled(false);
342 // modifyPID.setEnabled(false);
345 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
348 if (sortby.equals("Id"))
350 sortIDMenuItem_actionPerformed(null);
352 else if (sortby.equals("Pairwise Identity"))
354 sortPairwiseMenuItem_actionPerformed(null);
358 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
360 setMenusFromViewport(viewport);
361 buildSortByAnnotationScoresMenu();
362 calculateTree.addActionListener(new ActionListener()
366 public void actionPerformed(ActionEvent e)
368 new TreeChooser(AlignFrame.this);
373 if (Desktop.desktop != null)
375 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
376 addServiceListeners();
380 if (viewport.getWrapAlignment())
382 wrapMenuItem_actionPerformed(null);
385 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
387 this.overviewMenuItem_actionPerformed(null);
392 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
393 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
394 final String menuLabel = MessageManager
395 .getString("label.copy_format_from");
396 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
397 new ViewSetProvider()
401 public AlignmentPanel[] getAllAlignmentPanels()
404 origview.add(alignPanel);
405 // make an array of all alignment panels except for this one
406 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
407 Arrays.asList(Desktop.getAlignmentPanels(null)));
408 aps.remove(AlignFrame.this.alignPanel);
409 return aps.toArray(new AlignmentPanel[aps.size()]);
411 }, selviews, new ItemListener()
415 public void itemStateChanged(ItemEvent e)
417 if (origview.size() > 0)
419 final AlignmentPanel ap = origview.get(0);
422 * Copy the ViewStyle of the selected panel to 'this one'.
423 * Don't change value of 'scaleProteinAsCdna' unless copying
426 ViewStyleI vs = selviews.get(0).getAlignViewport()
428 boolean fromSplitFrame = selviews.get(0)
429 .getAlignViewport().getCodingComplement() != null;
432 vs.setScaleProteinAsCdna(ap.getAlignViewport()
433 .getViewStyle().isScaleProteinAsCdna());
435 ap.getAlignViewport().setViewStyle(vs);
438 * Also rescale ViewStyle of SplitFrame complement if there is
439 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
440 * the whole ViewStyle (allow cDNA protein to have different
443 AlignViewportI complement = ap.getAlignViewport()
444 .getCodingComplement();
445 if (complement != null && vs.isScaleProteinAsCdna())
447 AlignFrame af = Desktop.getAlignFrameFor(complement);
448 ((SplitFrame) af.getSplitViewContainer())
450 af.setMenusForViewport();
454 ap.setSelected(true);
455 ap.alignFrame.setMenusForViewport();
460 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
461 .indexOf("devel") > -1
462 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
463 .indexOf("test") > -1)
465 formatMenu.add(vsel);
467 addFocusListener(new FocusAdapter()
470 public void focusGained(FocusEvent e)
472 Jalview.setCurrentAlignFrame(AlignFrame.this);
479 * Change the filename and format for the alignment, and enable the 'reload'
480 * button functionality.
487 public void setFileName(String file, FileFormatI format)
490 setFileFormat(format);
491 reload.setEnabled(true);
495 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
498 void addKeyListener()
500 addKeyListener(new KeyAdapter()
503 public void keyPressed(KeyEvent evt)
505 if (viewport.cursorMode
506 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
507 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
508 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
509 && Character.isDigit(evt.getKeyChar()))
511 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
514 switch (evt.getKeyCode())
517 case 27: // escape key
518 deselectAllSequenceMenuItem_actionPerformed(null);
522 case KeyEvent.VK_DOWN:
523 if (evt.isAltDown() || !viewport.cursorMode)
525 moveSelectedSequences(false);
527 if (viewport.cursorMode)
529 alignPanel.getSeqPanel().moveCursor(0, 1);
534 if (evt.isAltDown() || !viewport.cursorMode)
536 moveSelectedSequences(true);
538 if (viewport.cursorMode)
540 alignPanel.getSeqPanel().moveCursor(0, -1);
545 case KeyEvent.VK_LEFT:
546 if (evt.isAltDown() || !viewport.cursorMode)
548 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
552 alignPanel.getSeqPanel().moveCursor(-1, 0);
557 case KeyEvent.VK_RIGHT:
558 if (evt.isAltDown() || !viewport.cursorMode)
560 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
564 alignPanel.getSeqPanel().moveCursor(1, 0);
568 case KeyEvent.VK_SPACE:
569 if (viewport.cursorMode)
571 alignPanel.getSeqPanel().insertGapAtCursor(
572 evt.isControlDown() || evt.isShiftDown()
577 // case KeyEvent.VK_A:
578 // if (viewport.cursorMode)
580 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
581 // //System.out.println("A");
585 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
586 * System.out.println("closing bracket"); } break;
588 case KeyEvent.VK_DELETE:
589 case KeyEvent.VK_BACK_SPACE:
590 if (!viewport.cursorMode)
592 cut_actionPerformed(null);
596 alignPanel.getSeqPanel().deleteGapAtCursor(
597 evt.isControlDown() || evt.isShiftDown()
604 if (viewport.cursorMode)
606 alignPanel.getSeqPanel().setCursorRow();
610 if (viewport.cursorMode && !evt.isControlDown())
612 alignPanel.getSeqPanel().setCursorColumn();
616 if (viewport.cursorMode)
618 alignPanel.getSeqPanel().setCursorPosition();
622 case KeyEvent.VK_ENTER:
623 case KeyEvent.VK_COMMA:
624 if (viewport.cursorMode)
626 alignPanel.getSeqPanel().setCursorRowAndColumn();
631 if (viewport.cursorMode)
633 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
637 if (viewport.cursorMode)
639 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
644 viewport.cursorMode = !viewport.cursorMode;
645 statusBar.setText(MessageManager.formatMessage(
646 "label.keyboard_editing_mode",
647 new String[] { (viewport.cursorMode ? "on" : "off") }));
648 if (viewport.cursorMode)
650 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
651 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
653 alignPanel.getSeqPanel().seqCanvas.repaint();
659 Help.showHelpWindow();
660 } catch (Exception ex)
662 ex.printStackTrace();
667 boolean toggleSeqs = !evt.isControlDown();
668 boolean toggleCols = !evt.isShiftDown();
669 toggleHiddenRegions(toggleSeqs, toggleCols);
674 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
675 boolean modifyExisting = true; // always modify, don't clear
676 // evt.isShiftDown();
677 boolean invertHighlighted = evt.isAltDown();
678 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
682 case KeyEvent.VK_PAGE_UP:
683 if (viewport.getWrapAlignment())
685 alignPanel.scrollUp(true);
689 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
690 - viewport.endSeq + viewport.startSeq);
693 case KeyEvent.VK_PAGE_DOWN:
694 if (viewport.getWrapAlignment())
696 alignPanel.scrollUp(false);
700 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
701 + viewport.endSeq - viewport.startSeq);
708 public void keyReleased(KeyEvent evt)
710 switch (evt.getKeyCode())
712 case KeyEvent.VK_LEFT:
713 if (evt.isAltDown() || !viewport.cursorMode)
715 viewport.firePropertyChange("alignment", null, viewport
716 .getAlignment().getSequences());
720 case KeyEvent.VK_RIGHT:
721 if (evt.isAltDown() || !viewport.cursorMode)
723 viewport.firePropertyChange("alignment", null, viewport
724 .getAlignment().getSequences());
732 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
734 ap.alignFrame = this;
735 avc = new jalview.controller.AlignViewController(this, viewport,
740 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
742 int aSize = alignPanels.size();
744 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
746 if (aSize == 1 && ap.av.viewName == null)
748 this.getContentPane().add(ap, BorderLayout.CENTER);
754 setInitialTabVisible();
757 expandViews.setEnabled(true);
758 gatherViews.setEnabled(true);
759 tabbedPane.addTab(ap.av.viewName, ap);
761 ap.setVisible(false);
766 if (ap.av.isPadGaps())
768 ap.av.getAlignment().padGaps();
770 ap.av.updateConservation(ap);
771 ap.av.updateConsensus(ap);
772 ap.av.updateStrucConsensus(ap);
776 public void setInitialTabVisible()
778 expandViews.setEnabled(true);
779 gatherViews.setEnabled(true);
780 tabbedPane.setVisible(true);
781 AlignmentPanel first = alignPanels.get(0);
782 tabbedPane.addTab(first.av.viewName, first);
783 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
786 public AlignViewport getViewport()
791 /* Set up intrinsic listeners for dynamically generated GUI bits. */
792 private void addServiceListeners()
794 final java.beans.PropertyChangeListener thisListener;
795 Desktop.instance.addJalviewPropertyChangeListener("services",
796 thisListener = new java.beans.PropertyChangeListener()
799 public void propertyChange(PropertyChangeEvent evt)
801 // // System.out.println("Discoverer property change.");
802 // if (evt.getPropertyName().equals("services"))
804 SwingUtilities.invokeLater(new Runnable()
811 .println("Rebuild WS Menu for service change");
812 BuildWebServiceMenu();
819 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
822 public void internalFrameClosed(
823 javax.swing.event.InternalFrameEvent evt)
825 // System.out.println("deregistering discoverer listener");
826 Desktop.instance.removeJalviewPropertyChangeListener("services",
828 closeMenuItem_actionPerformed(true);
831 // Finally, build the menu once to get current service state
832 new Thread(new Runnable()
837 BuildWebServiceMenu();
843 * Configure menu items that vary according to whether the alignment is
844 * nucleotide or protein
846 public void setGUINucleotide()
848 AlignmentI al = getViewport().getAlignment();
849 boolean nucleotide = al.isNucleotide();
851 showTranslation.setVisible(nucleotide);
852 showReverse.setVisible(nucleotide);
853 showReverseComplement.setVisible(nucleotide);
854 conservationMenuItem.setEnabled(!nucleotide);
855 modifyConservation.setEnabled(!nucleotide
856 && conservationMenuItem.isSelected());
857 showGroupConservation.setEnabled(!nucleotide);
859 showComplementMenuItem.setText(nucleotide ? MessageManager
860 .getString("label.protein") : MessageManager
861 .getString("label.nucleotide"));
865 * set up menus for the current viewport. This may be called after any
866 * operation that affects the data in the current view (selection changed,
867 * etc) to update the menus to reflect the new state.
870 public void setMenusForViewport()
872 setMenusFromViewport(viewport);
876 * Need to call this method when tabs are selected for multiple views, or when
877 * loading from Jalview2XML.java
882 void setMenusFromViewport(AlignViewport av)
884 padGapsMenuitem.setSelected(av.isPadGaps());
885 colourTextMenuItem.setSelected(av.isShowColourText());
886 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
887 modifyPID.setEnabled(abovePIDThreshold.isSelected());
888 conservationMenuItem.setSelected(av.getConservationSelected());
889 modifyConservation.setEnabled(conservationMenuItem.isSelected());
890 seqLimits.setSelected(av.getShowJVSuffix());
891 idRightAlign.setSelected(av.isRightAlignIds());
892 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
893 renderGapsMenuItem.setSelected(av.isRenderGaps());
894 wrapMenuItem.setSelected(av.getWrapAlignment());
895 scaleAbove.setVisible(av.getWrapAlignment());
896 scaleLeft.setVisible(av.getWrapAlignment());
897 scaleRight.setVisible(av.getWrapAlignment());
898 annotationPanelMenuItem.setState(av.isShowAnnotation());
900 * Show/hide annotations only enabled if annotation panel is shown
902 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
903 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
904 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
905 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
906 viewBoxesMenuItem.setSelected(av.getShowBoxes());
907 viewTextMenuItem.setSelected(av.getShowText());
908 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
909 showGroupConsensus.setSelected(av.isShowGroupConsensus());
910 showGroupConservation.setSelected(av.isShowGroupConservation());
911 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
912 showSequenceLogo.setSelected(av.isShowSequenceLogo());
913 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
915 ColourMenuHelper.setColourSelected(colourMenu,
916 av.getGlobalColourScheme());
918 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
919 hiddenMarkers.setState(av.getShowHiddenMarkers());
920 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
921 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
922 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
923 autoCalculate.setSelected(av.autoCalculateConsensus);
924 sortByTree.setSelected(av.sortByTree);
925 listenToViewSelections.setSelected(av.followSelection);
927 showProducts.setEnabled(canShowProducts());
928 setGroovyEnabled(Desktop.getGroovyConsole() != null);
934 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
938 public void setGroovyEnabled(boolean b)
940 runGroovy.setEnabled(b);
943 private IProgressIndicator progressBar;
948 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
951 public void setProgressBar(String message, long id)
953 progressBar.setProgressBar(message, id);
957 public void registerHandler(final long id,
958 final IProgressIndicatorHandler handler)
960 progressBar.registerHandler(id, handler);
965 * @return true if any progress bars are still active
968 public boolean operationInProgress()
970 return progressBar.operationInProgress();
974 public void setStatus(String text)
976 statusBar.setText(text);
980 * Added so Castor Mapping file can obtain Jalview Version
982 public String getVersion()
984 return jalview.bin.Cache.getProperty("VERSION");
987 public FeatureRenderer getFeatureRenderer()
989 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
993 public void fetchSequence_actionPerformed(ActionEvent e)
995 new jalview.gui.SequenceFetcher(this);
999 public void addFromFile_actionPerformed(ActionEvent e)
1001 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1005 public void reload_actionPerformed(ActionEvent e)
1007 if (fileName != null)
1009 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1010 // originating file's format
1011 // TODO: work out how to recover feature settings for correct view(s) when
1012 // file is reloaded.
1013 if (FileFormat.Jalview.equals(currentFileFormat))
1015 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1016 for (int i = 0; i < frames.length; i++)
1018 if (frames[i] instanceof AlignFrame && frames[i] != this
1019 && ((AlignFrame) frames[i]).fileName != null
1020 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1024 frames[i].setSelected(true);
1025 Desktop.instance.closeAssociatedWindows();
1026 } catch (java.beans.PropertyVetoException ex)
1032 Desktop.instance.closeAssociatedWindows();
1034 FileLoader loader = new FileLoader();
1035 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1036 : DataSourceType.FILE;
1037 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1041 Rectangle bounds = this.getBounds();
1043 FileLoader loader = new FileLoader();
1044 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1045 : DataSourceType.FILE;
1046 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1047 protocol, currentFileFormat);
1049 newframe.setBounds(bounds);
1050 if (featureSettings != null && featureSettings.isShowing())
1052 final Rectangle fspos = featureSettings.frame.getBounds();
1053 // TODO: need a 'show feature settings' function that takes bounds -
1054 // need to refactor Desktop.addFrame
1055 newframe.featureSettings_actionPerformed(null);
1056 final FeatureSettings nfs = newframe.featureSettings;
1057 SwingUtilities.invokeLater(new Runnable()
1062 nfs.frame.setBounds(fspos);
1065 this.featureSettings.close();
1066 this.featureSettings = null;
1068 this.closeMenuItem_actionPerformed(true);
1074 public void addFromText_actionPerformed(ActionEvent e)
1076 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1081 public void addFromURL_actionPerformed(ActionEvent e)
1083 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1087 public void save_actionPerformed(ActionEvent e)
1089 if (fileName == null || (currentFileFormat == null)
1090 || fileName.startsWith("http"))
1092 saveAs_actionPerformed(null);
1096 saveAlignment(fileName, currentFileFormat);
1107 public void saveAs_actionPerformed(ActionEvent e)
1109 String format = currentFileFormat == null ? null : currentFileFormat
1111 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1112 Cache.getProperty("LAST_DIRECTORY"), format);
1114 chooser.setFileView(new JalviewFileView());
1115 chooser.setDialogTitle(MessageManager
1116 .getString("label.save_alignment_to_file"));
1117 chooser.setToolTipText(MessageManager.getString("action.save"));
1119 int value = chooser.showSaveDialog(this);
1121 if (value == JalviewFileChooser.APPROVE_OPTION)
1123 currentFileFormat = chooser.getSelectedFormat();
1124 while (currentFileFormat == null)
1127 .showInternalMessageDialog(
1130 .getString("label.select_file_format_before_saving"),
1132 .getString("label.file_format_not_specified"),
1133 JvOptionPane.WARNING_MESSAGE);
1134 currentFileFormat = chooser.getSelectedFormat();
1135 value = chooser.showSaveDialog(this);
1136 if (value != JalviewFileChooser.APPROVE_OPTION)
1142 fileName = chooser.getSelectedFile().getPath();
1144 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1146 Cache.setProperty("LAST_DIRECTORY", fileName);
1147 saveAlignment(fileName, currentFileFormat);
1151 public boolean saveAlignment(String file, FileFormatI format)
1153 boolean success = true;
1155 if (FileFormat.Jalview.equals(format))
1157 String shortName = title;
1159 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1161 shortName = shortName.substring(shortName
1162 .lastIndexOf(java.io.File.separatorChar) + 1);
1165 success = new Jalview2XML().saveAlignment(this, file, shortName);
1167 statusBar.setText(MessageManager.formatMessage(
1168 "label.successfully_saved_to_file_in_format", new Object[] {
1169 fileName, format }));
1174 AlignmentExportData exportData = getAlignmentForExport(format,
1176 if (exportData.getSettings().isCancelled())
1180 FormatAdapter f = new FormatAdapter(alignPanel,
1181 exportData.getSettings());
1182 String output = f.formatSequences(
1184 exportData.getAlignment(), // class cast exceptions will
1185 // occur in the distant future
1186 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1187 f.getCacheSuffixDefault(format),
1188 viewport.getColumnSelection());
1198 PrintWriter out = new PrintWriter(new FileWriter(file));
1202 this.setTitle(file);
1203 statusBar.setText(MessageManager.formatMessage(
1204 "label.successfully_saved_to_file_in_format",
1205 new Object[] { fileName, format.getName() }));
1206 } catch (Exception ex)
1209 ex.printStackTrace();
1216 JvOptionPane.showInternalMessageDialog(this, MessageManager
1217 .formatMessage("label.couldnt_save_file",
1218 new Object[] { fileName }), MessageManager
1219 .getString("label.error_saving_file"),
1220 JvOptionPane.WARNING_MESSAGE);
1226 private void warningMessage(String warning, String title)
1228 if (new jalview.util.Platform().isHeadless())
1230 System.err.println("Warning: " + title + "\nWarning: " + warning);
1235 JvOptionPane.showInternalMessageDialog(this, warning, title,
1236 JvOptionPane.WARNING_MESSAGE);
1248 protected void outputText_actionPerformed(ActionEvent e)
1250 FileFormatI fileFormat = FileFormats.getInstance().forName(
1251 e.getActionCommand());
1252 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1254 if (exportData.getSettings().isCancelled())
1258 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1259 cap.setForInput(null);
1262 FileFormatI format = fileFormat;
1263 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1264 .formatSequences(format, exportData.getAlignment(),
1265 exportData.getOmitHidden(),
1266 exportData.getStartEndPostions(),
1267 viewport.getColumnSelection()));
1268 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1269 "label.alignment_output_command",
1270 new Object[] { e.getActionCommand() }), 600, 500);
1271 } catch (OutOfMemoryError oom)
1273 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1279 public static AlignmentExportData getAlignmentForExport(
1280 FileFormatI format, AlignViewportI viewport,
1281 AlignExportSettingI exportSettings)
1283 AlignmentI alignmentToExport = null;
1284 AlignExportSettingI settings = exportSettings;
1285 String[] omitHidden = null;
1287 HiddenSequences hiddenSeqs = viewport.getAlignment()
1288 .getHiddenSequences();
1290 alignmentToExport = viewport.getAlignment();
1292 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1293 if (settings == null)
1295 settings = new AlignExportSettings(hasHiddenSeqs,
1296 viewport.hasHiddenColumns(), format);
1298 // settings.isExportAnnotations();
1300 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1302 omitHidden = viewport.getViewAsString(false,
1303 settings.isExportHiddenSequences());
1306 int[] alignmentStartEnd = new int[2];
1307 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1309 alignmentToExport = hiddenSeqs.getFullAlignment();
1313 alignmentToExport = viewport.getAlignment();
1315 alignmentStartEnd = alignmentToExport
1316 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1317 .getHiddenColumns());
1318 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1319 omitHidden, alignmentStartEnd, settings);
1330 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1332 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1333 htmlSVG.exportHTML(null);
1337 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1339 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1340 bjs.exportHTML(null);
1343 public void createImageMap(File file, String image)
1345 alignPanel.makePNGImageMap(file, image);
1355 public void createPNG(File f)
1357 alignPanel.makePNG(f);
1367 public void createEPS(File f)
1369 alignPanel.makeEPS(f);
1373 public void createSVG(File f)
1375 alignPanel.makeSVG(f);
1379 public void pageSetup_actionPerformed(ActionEvent e)
1381 PrinterJob printJob = PrinterJob.getPrinterJob();
1382 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1392 public void printMenuItem_actionPerformed(ActionEvent e)
1394 // Putting in a thread avoids Swing painting problems
1395 PrintThread thread = new PrintThread(alignPanel);
1400 public void exportFeatures_actionPerformed(ActionEvent e)
1402 new AnnotationExporter().exportFeatures(alignPanel);
1406 public void exportAnnotations_actionPerformed(ActionEvent e)
1408 new AnnotationExporter().exportAnnotations(alignPanel);
1412 public void associatedData_actionPerformed(ActionEvent e)
1414 // Pick the tree file
1415 JalviewFileChooser chooser = new JalviewFileChooser(
1416 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1417 chooser.setFileView(new JalviewFileView());
1418 chooser.setDialogTitle(MessageManager
1419 .getString("label.load_jalview_annotations"));
1420 chooser.setToolTipText(MessageManager
1421 .getString("label.load_jalview_annotations"));
1423 int value = chooser.showOpenDialog(null);
1425 if (value == JalviewFileChooser.APPROVE_OPTION)
1427 String choice = chooser.getSelectedFile().getPath();
1428 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1429 loadJalviewDataFile(choice, null, null, null);
1435 * Close the current view or all views in the alignment frame. If the frame
1436 * only contains one view then the alignment will be removed from memory.
1438 * @param closeAllTabs
1441 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1443 if (alignPanels != null && alignPanels.size() < 2)
1445 closeAllTabs = true;
1450 if (alignPanels != null)
1454 if (this.isClosed())
1456 // really close all the windows - otherwise wait till
1457 // setClosed(true) is called
1458 for (int i = 0; i < alignPanels.size(); i++)
1460 AlignmentPanel ap = alignPanels.get(i);
1467 closeView(alignPanel);
1474 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1475 * be called recursively, with the frame now in 'closed' state
1477 this.setClosed(true);
1479 } catch (Exception ex)
1481 ex.printStackTrace();
1486 * Close the specified panel and close up tabs appropriately.
1488 * @param panelToClose
1490 public void closeView(AlignmentPanel panelToClose)
1492 int index = tabbedPane.getSelectedIndex();
1493 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1494 alignPanels.remove(panelToClose);
1495 panelToClose.closePanel();
1496 panelToClose = null;
1498 tabbedPane.removeTabAt(closedindex);
1499 tabbedPane.validate();
1501 if (index > closedindex || index == tabbedPane.getTabCount())
1503 // modify currently selected tab index if necessary.
1507 this.tabSelectionChanged(index);
1513 void updateEditMenuBar()
1516 if (viewport.getHistoryList().size() > 0)
1518 undoMenuItem.setEnabled(true);
1519 CommandI command = viewport.getHistoryList().peek();
1520 undoMenuItem.setText(MessageManager.formatMessage(
1521 "label.undo_command",
1522 new Object[] { command.getDescription() }));
1526 undoMenuItem.setEnabled(false);
1527 undoMenuItem.setText(MessageManager.getString("action.undo"));
1530 if (viewport.getRedoList().size() > 0)
1532 redoMenuItem.setEnabled(true);
1534 CommandI command = viewport.getRedoList().peek();
1535 redoMenuItem.setText(MessageManager.formatMessage(
1536 "label.redo_command",
1537 new Object[] { command.getDescription() }));
1541 redoMenuItem.setEnabled(false);
1542 redoMenuItem.setText(MessageManager.getString("action.redo"));
1547 public void addHistoryItem(CommandI command)
1549 if (command.getSize() > 0)
1551 viewport.addToHistoryList(command);
1552 viewport.clearRedoList();
1553 updateEditMenuBar();
1554 viewport.updateHiddenColumns();
1555 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1556 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1557 // viewport.getColumnSelection()
1558 // .getHiddenColumns().size() > 0);
1564 * @return alignment objects for all views
1566 AlignmentI[] getViewAlignments()
1568 if (alignPanels != null)
1570 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1572 for (AlignmentPanel ap : alignPanels)
1574 als[i++] = ap.av.getAlignment();
1578 if (viewport != null)
1580 return new AlignmentI[] { viewport.getAlignment() };
1592 protected void undoMenuItem_actionPerformed(ActionEvent e)
1594 if (viewport.getHistoryList().isEmpty())
1598 CommandI command = viewport.getHistoryList().pop();
1599 viewport.addToRedoList(command);
1600 command.undoCommand(getViewAlignments());
1602 AlignmentViewport originalSource = getOriginatingSource(command);
1603 updateEditMenuBar();
1605 if (originalSource != null)
1607 if (originalSource != viewport)
1610 .warn("Implementation worry: mismatch of viewport origin for undo");
1612 originalSource.updateHiddenColumns();
1613 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1615 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1616 // viewport.getColumnSelection()
1617 // .getHiddenColumns().size() > 0);
1618 originalSource.firePropertyChange("alignment", null, originalSource
1619 .getAlignment().getSequences());
1630 protected void redoMenuItem_actionPerformed(ActionEvent e)
1632 if (viewport.getRedoList().size() < 1)
1637 CommandI command = viewport.getRedoList().pop();
1638 viewport.addToHistoryList(command);
1639 command.doCommand(getViewAlignments());
1641 AlignmentViewport originalSource = getOriginatingSource(command);
1642 updateEditMenuBar();
1644 if (originalSource != null)
1647 if (originalSource != viewport)
1650 .warn("Implementation worry: mismatch of viewport origin for redo");
1652 originalSource.updateHiddenColumns();
1653 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1655 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1656 // viewport.getColumnSelection()
1657 // .getHiddenColumns().size() > 0);
1658 originalSource.firePropertyChange("alignment", null, originalSource
1659 .getAlignment().getSequences());
1663 AlignmentViewport getOriginatingSource(CommandI command)
1665 AlignmentViewport originalSource = null;
1666 // For sequence removal and addition, we need to fire
1667 // the property change event FROM the viewport where the
1668 // original alignment was altered
1669 AlignmentI al = null;
1670 if (command instanceof EditCommand)
1672 EditCommand editCommand = (EditCommand) command;
1673 al = editCommand.getAlignment();
1674 List<Component> comps = PaintRefresher.components.get(viewport
1675 .getSequenceSetId());
1677 for (Component comp : comps)
1679 if (comp instanceof AlignmentPanel)
1681 if (al == ((AlignmentPanel) comp).av.getAlignment())
1683 originalSource = ((AlignmentPanel) comp).av;
1690 if (originalSource == null)
1692 // The original view is closed, we must validate
1693 // the current view against the closed view first
1696 PaintRefresher.validateSequences(al, viewport.getAlignment());
1699 originalSource = viewport;
1702 return originalSource;
1711 public void moveSelectedSequences(boolean up)
1713 SequenceGroup sg = viewport.getSelectionGroup();
1719 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1720 viewport.getHiddenRepSequences(), up);
1721 alignPanel.paintAlignment(true);
1724 synchronized void slideSequences(boolean right, int size)
1726 List<SequenceI> sg = new ArrayList<SequenceI>();
1727 if (viewport.cursorMode)
1729 sg.add(viewport.getAlignment().getSequenceAt(
1730 alignPanel.getSeqPanel().seqCanvas.cursorY));
1732 else if (viewport.getSelectionGroup() != null
1733 && viewport.getSelectionGroup().getSize() != viewport
1734 .getAlignment().getHeight())
1736 sg = viewport.getSelectionGroup().getSequences(
1737 viewport.getHiddenRepSequences());
1745 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1747 for (SequenceI seq : viewport.getAlignment().getSequences())
1749 if (!sg.contains(seq))
1751 invertGroup.add(seq);
1755 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1757 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1758 for (int i = 0; i < invertGroup.size(); i++)
1760 seqs2[i] = invertGroup.get(i);
1763 SlideSequencesCommand ssc;
1766 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1767 size, viewport.getGapCharacter());
1771 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1772 size, viewport.getGapCharacter());
1775 int groupAdjustment = 0;
1776 if (ssc.getGapsInsertedBegin() && right)
1778 if (viewport.cursorMode)
1780 alignPanel.getSeqPanel().moveCursor(size, 0);
1784 groupAdjustment = size;
1787 else if (!ssc.getGapsInsertedBegin() && !right)
1789 if (viewport.cursorMode)
1791 alignPanel.getSeqPanel().moveCursor(-size, 0);
1795 groupAdjustment = -size;
1799 if (groupAdjustment != 0)
1801 viewport.getSelectionGroup().setStartRes(
1802 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1803 viewport.getSelectionGroup().setEndRes(
1804 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1808 * just extend the last slide command if compatible; but not if in
1809 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1811 boolean appendHistoryItem = false;
1812 Deque<CommandI> historyList = viewport.getHistoryList();
1813 boolean inSplitFrame = getSplitViewContainer() != null;
1814 if (!inSplitFrame && historyList != null && historyList.size() > 0
1815 && historyList.peek() instanceof SlideSequencesCommand)
1817 appendHistoryItem = ssc
1818 .appendSlideCommand((SlideSequencesCommand) historyList
1822 if (!appendHistoryItem)
1824 addHistoryItem(ssc);
1837 protected void copy_actionPerformed(ActionEvent e)
1840 if (viewport.getSelectionGroup() == null)
1844 // TODO: preserve the ordering of displayed alignment annotation in any
1845 // internal paste (particularly sequence associated annotation)
1846 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1847 String[] omitHidden = null;
1849 if (viewport.hasHiddenColumns())
1851 omitHidden = viewport.getViewAsString(true);
1854 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1855 seqs, omitHidden, null);
1857 StringSelection ss = new StringSelection(output);
1861 jalview.gui.Desktop.internalCopy = true;
1862 // Its really worth setting the clipboard contents
1863 // to empty before setting the large StringSelection!!
1864 Toolkit.getDefaultToolkit().getSystemClipboard()
1865 .setContents(new StringSelection(""), null);
1867 Toolkit.getDefaultToolkit().getSystemClipboard()
1868 .setContents(ss, Desktop.instance);
1869 } catch (OutOfMemoryError er)
1871 new OOMWarning("copying region", er);
1875 ArrayList<int[]> hiddenColumns = null;
1876 if (viewport.hasHiddenColumns())
1878 hiddenColumns = new ArrayList<int[]>();
1879 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1880 .getSelectionGroup().getEndRes();
1881 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1883 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1885 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1886 region[1] - hiddenOffset });
1891 Desktop.jalviewClipboard = new Object[] { seqs,
1892 viewport.getAlignment().getDataset(), hiddenColumns };
1893 statusBar.setText(MessageManager.formatMessage(
1894 "label.copied_sequences_to_clipboard", new Object[] { Integer
1895 .valueOf(seqs.length).toString() }));
1905 protected void pasteNew_actionPerformed(ActionEvent e)
1917 protected void pasteThis_actionPerformed(ActionEvent e)
1923 * Paste contents of Jalview clipboard
1925 * @param newAlignment
1926 * true to paste to a new alignment, otherwise add to this.
1928 void paste(boolean newAlignment)
1930 boolean externalPaste = true;
1933 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1934 Transferable contents = c.getContents(this);
1936 if (contents == null)
1945 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1946 if (str.length() < 1)
1951 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1953 } catch (OutOfMemoryError er)
1955 new OOMWarning("Out of memory pasting sequences!!", er);
1959 SequenceI[] sequences;
1960 boolean annotationAdded = false;
1961 AlignmentI alignment = null;
1963 if (Desktop.jalviewClipboard != null)
1965 // The clipboard was filled from within Jalview, we must use the
1967 // And dataset from the copied alignment
1968 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1969 // be doubly sure that we create *new* sequence objects.
1970 sequences = new SequenceI[newseq.length];
1971 for (int i = 0; i < newseq.length; i++)
1973 sequences[i] = new Sequence(newseq[i]);
1975 alignment = new Alignment(sequences);
1976 externalPaste = false;
1980 // parse the clipboard as an alignment.
1981 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1983 sequences = alignment.getSequencesArray();
1987 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1993 if (Desktop.jalviewClipboard != null)
1995 // dataset is inherited
1996 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2000 // new dataset is constructed
2001 alignment.setDataset(null);
2003 alwidth = alignment.getWidth() + 1;
2007 AlignmentI pastedal = alignment; // preserve pasted alignment object
2008 // Add pasted sequences and dataset into existing alignment.
2009 alignment = viewport.getAlignment();
2010 alwidth = alignment.getWidth() + 1;
2011 // decide if we need to import sequences from an existing dataset
2012 boolean importDs = Desktop.jalviewClipboard != null
2013 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2014 // importDs==true instructs us to copy over new dataset sequences from
2015 // an existing alignment
2016 Vector newDs = (importDs) ? new Vector() : null; // used to create
2017 // minimum dataset set
2019 for (int i = 0; i < sequences.length; i++)
2023 newDs.addElement(null);
2025 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2027 if (importDs && ds != null)
2029 if (!newDs.contains(ds))
2031 newDs.setElementAt(ds, i);
2032 ds = new Sequence(ds);
2033 // update with new dataset sequence
2034 sequences[i].setDatasetSequence(ds);
2038 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2043 // copy and derive new dataset sequence
2044 sequences[i] = sequences[i].deriveSequence();
2045 alignment.getDataset().addSequence(
2046 sequences[i].getDatasetSequence());
2047 // TODO: avoid creation of duplicate dataset sequences with a
2048 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2050 alignment.addSequence(sequences[i]); // merges dataset
2054 newDs.clear(); // tidy up
2056 if (alignment.getAlignmentAnnotation() != null)
2058 for (AlignmentAnnotation alan : alignment
2059 .getAlignmentAnnotation())
2061 if (alan.graphGroup > fgroup)
2063 fgroup = alan.graphGroup;
2067 if (pastedal.getAlignmentAnnotation() != null)
2069 // Add any annotation attached to alignment.
2070 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2071 for (int i = 0; i < alann.length; i++)
2073 annotationAdded = true;
2074 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2076 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2077 if (newann.graphGroup > -1)
2079 if (newGraphGroups.size() <= newann.graphGroup
2080 || newGraphGroups.get(newann.graphGroup) == null)
2082 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2084 newGraphGroups.add(q, null);
2086 newGraphGroups.set(newann.graphGroup, new Integer(
2089 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2093 newann.padAnnotation(alwidth);
2094 alignment.addAnnotation(newann);
2104 addHistoryItem(new EditCommand(
2105 MessageManager.getString("label.add_sequences"),
2106 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2108 // Add any annotations attached to sequences
2109 for (int i = 0; i < sequences.length; i++)
2111 if (sequences[i].getAnnotation() != null)
2113 AlignmentAnnotation newann;
2114 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2116 annotationAdded = true;
2117 newann = sequences[i].getAnnotation()[a];
2118 newann.adjustForAlignment();
2119 newann.padAnnotation(alwidth);
2120 if (newann.graphGroup > -1)
2122 if (newann.graphGroup > -1)
2124 if (newGraphGroups.size() <= newann.graphGroup
2125 || newGraphGroups.get(newann.graphGroup) == null)
2127 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2129 newGraphGroups.add(q, null);
2131 newGraphGroups.set(newann.graphGroup, new Integer(
2134 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2138 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2143 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2150 // propagate alignment changed.
2151 viewport.setEndSeq(alignment.getHeight());
2152 if (annotationAdded)
2154 // Duplicate sequence annotation in all views.
2155 AlignmentI[] alview = this.getViewAlignments();
2156 for (int i = 0; i < sequences.length; i++)
2158 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2163 for (int avnum = 0; avnum < alview.length; avnum++)
2165 if (alview[avnum] != alignment)
2167 // duplicate in a view other than the one with input focus
2168 int avwidth = alview[avnum].getWidth() + 1;
2169 // this relies on sann being preserved after we
2170 // modify the sequence's annotation array for each duplication
2171 for (int a = 0; a < sann.length; a++)
2173 AlignmentAnnotation newann = new AlignmentAnnotation(
2175 sequences[i].addAlignmentAnnotation(newann);
2176 newann.padAnnotation(avwidth);
2177 alview[avnum].addAnnotation(newann); // annotation was
2178 // duplicated earlier
2179 // TODO JAL-1145 graphGroups are not updated for sequence
2180 // annotation added to several views. This may cause
2182 alview[avnum].setAnnotationIndex(newann, a);
2187 buildSortByAnnotationScoresMenu();
2189 viewport.firePropertyChange("alignment", null,
2190 alignment.getSequences());
2191 if (alignPanels != null)
2193 for (AlignmentPanel ap : alignPanels)
2195 ap.validateAnnotationDimensions(false);
2200 alignPanel.validateAnnotationDimensions(false);
2206 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2208 String newtitle = new String("Copied sequences");
2210 if (Desktop.jalviewClipboard != null
2211 && Desktop.jalviewClipboard[2] != null)
2213 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2214 for (int[] region : hc)
2216 af.viewport.hideColumns(region[0], region[1]);
2220 // >>>This is a fix for the moment, until a better solution is
2222 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2224 alignPanel.getSeqPanel().seqCanvas
2225 .getFeatureRenderer());
2227 // TODO: maintain provenance of an alignment, rather than just make the
2228 // title a concatenation of operations.
2231 if (title.startsWith("Copied sequences"))
2237 newtitle = newtitle.concat("- from " + title);
2242 newtitle = new String("Pasted sequences");
2245 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2250 } catch (Exception ex)
2252 ex.printStackTrace();
2253 System.out.println("Exception whilst pasting: " + ex);
2254 // could be anything being pasted in here
2260 protected void expand_newalign(ActionEvent e)
2264 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2265 .getAlignment(), -1);
2266 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2268 String newtitle = new String("Flanking alignment");
2270 if (Desktop.jalviewClipboard != null
2271 && Desktop.jalviewClipboard[2] != null)
2273 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2274 for (int region[] : hc)
2276 af.viewport.hideColumns(region[0], region[1]);
2280 // >>>This is a fix for the moment, until a better solution is
2282 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2284 alignPanel.getSeqPanel().seqCanvas
2285 .getFeatureRenderer());
2287 // TODO: maintain provenance of an alignment, rather than just make the
2288 // title a concatenation of operations.
2290 if (title.startsWith("Copied sequences"))
2296 newtitle = newtitle.concat("- from " + title);
2300 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2302 } catch (Exception ex)
2304 ex.printStackTrace();
2305 System.out.println("Exception whilst pasting: " + ex);
2306 // could be anything being pasted in here
2307 } catch (OutOfMemoryError oom)
2309 new OOMWarning("Viewing flanking region of alignment", oom);
2320 protected void cut_actionPerformed(ActionEvent e)
2322 copy_actionPerformed(null);
2323 delete_actionPerformed(null);
2333 protected void delete_actionPerformed(ActionEvent evt)
2336 SequenceGroup sg = viewport.getSelectionGroup();
2343 * If the cut affects all sequences, warn, remove highlighted columns
2345 if (sg.getSize() == viewport.getAlignment().getHeight())
2347 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2348 .getAlignment().getWidth()) ? true : false;
2349 if (isEntireAlignWidth)
2351 int confirm = JvOptionPane.showConfirmDialog(this,
2352 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2353 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2354 JvOptionPane.OK_CANCEL_OPTION);
2356 if (confirm == JvOptionPane.CANCEL_OPTION
2357 || confirm == JvOptionPane.CLOSED_OPTION)
2362 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2363 sg.getEndRes() + 1);
2365 SequenceI[] cut = sg.getSequences()
2366 .toArray(new SequenceI[sg.getSize()]);
2368 addHistoryItem(new EditCommand(
2369 MessageManager.getString("label.cut_sequences"), Action.CUT,
2370 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2371 viewport.getAlignment()));
2373 viewport.setSelectionGroup(null);
2374 viewport.sendSelection();
2375 viewport.getAlignment().deleteGroup(sg);
2377 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2379 if (viewport.getAlignment().getHeight() < 1)
2383 this.setClosed(true);
2384 } catch (Exception ex)
2397 protected void deleteGroups_actionPerformed(ActionEvent e)
2399 if (avc.deleteGroups())
2401 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2402 alignPanel.updateAnnotation();
2403 alignPanel.paintAlignment(true);
2414 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2416 SequenceGroup sg = new SequenceGroup();
2418 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2420 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2423 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2424 viewport.setSelectionGroup(sg);
2425 viewport.sendSelection();
2426 // JAL-2034 - should delegate to
2427 // alignPanel to decide if overview needs
2429 alignPanel.paintAlignment(false);
2430 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2440 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2442 if (viewport.cursorMode)
2444 alignPanel.getSeqPanel().keyboardNo1 = null;
2445 alignPanel.getSeqPanel().keyboardNo2 = null;
2447 viewport.setSelectionGroup(null);
2448 viewport.getColumnSelection().clear();
2449 viewport.setSelectionGroup(null);
2450 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2451 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2452 // JAL-2034 - should delegate to
2453 // alignPanel to decide if overview needs
2455 alignPanel.paintAlignment(false);
2456 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2457 viewport.sendSelection();
2467 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2469 SequenceGroup sg = viewport.getSelectionGroup();
2473 selectAllSequenceMenuItem_actionPerformed(null);
2478 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2480 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2482 // JAL-2034 - should delegate to
2483 // alignPanel to decide if overview needs
2486 alignPanel.paintAlignment(true);
2487 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2488 viewport.sendSelection();
2492 public void invertColSel_actionPerformed(ActionEvent e)
2494 viewport.invertColumnSelection();
2495 alignPanel.paintAlignment(true);
2496 viewport.sendSelection();
2506 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2508 trimAlignment(true);
2518 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2520 trimAlignment(false);
2523 void trimAlignment(boolean trimLeft)
2525 ColumnSelection colSel = viewport.getColumnSelection();
2528 if (!colSel.isEmpty())
2532 column = colSel.getMin();
2536 column = colSel.getMax();
2540 if (viewport.getSelectionGroup() != null)
2542 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2543 viewport.getHiddenRepSequences());
2547 seqs = viewport.getAlignment().getSequencesArray();
2550 TrimRegionCommand trimRegion;
2553 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2554 column, viewport.getAlignment());
2555 viewport.setStartRes(0);
2559 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2560 column, viewport.getAlignment());
2563 statusBar.setText(MessageManager.formatMessage(
2564 "label.removed_columns",
2565 new String[] { Integer.valueOf(trimRegion.getSize())
2568 addHistoryItem(trimRegion);
2570 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2572 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2573 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2575 viewport.getAlignment().deleteGroup(sg);
2579 viewport.firePropertyChange("alignment", null, viewport
2580 .getAlignment().getSequences());
2591 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2593 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2596 if (viewport.getSelectionGroup() != null)
2598 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2599 viewport.getHiddenRepSequences());
2600 start = viewport.getSelectionGroup().getStartRes();
2601 end = viewport.getSelectionGroup().getEndRes();
2605 seqs = viewport.getAlignment().getSequencesArray();
2608 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2609 "Remove Gapped Columns", seqs, start, end,
2610 viewport.getAlignment());
2612 addHistoryItem(removeGapCols);
2614 statusBar.setText(MessageManager.formatMessage(
2615 "label.removed_empty_columns",
2616 new Object[] { Integer.valueOf(removeGapCols.getSize())
2619 // This is to maintain viewport position on first residue
2620 // of first sequence
2621 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2622 int startRes = seq.findPosition(viewport.startRes);
2623 // ShiftList shifts;
2624 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2625 // edit.alColumnChanges=shifts.getInverse();
2626 // if (viewport.hasHiddenColumns)
2627 // viewport.getColumnSelection().compensateForEdits(shifts);
2628 viewport.setStartRes(seq.findIndex(startRes) - 1);
2629 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2641 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2643 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2646 if (viewport.getSelectionGroup() != null)
2648 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2649 viewport.getHiddenRepSequences());
2650 start = viewport.getSelectionGroup().getStartRes();
2651 end = viewport.getSelectionGroup().getEndRes();
2655 seqs = viewport.getAlignment().getSequencesArray();
2658 // This is to maintain viewport position on first residue
2659 // of first sequence
2660 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2661 int startRes = seq.findPosition(viewport.startRes);
2663 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2664 viewport.getAlignment()));
2666 viewport.setStartRes(seq.findIndex(startRes) - 1);
2668 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2680 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2682 viewport.setPadGaps(padGapsMenuitem.isSelected());
2683 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2694 public void findMenuItem_actionPerformed(ActionEvent e)
2700 * Create a new view of the current alignment.
2703 public void newView_actionPerformed(ActionEvent e)
2705 newView(null, true);
2709 * Creates and shows a new view of the current alignment.
2712 * title of newly created view; if null, one will be generated
2713 * @param copyAnnotation
2714 * if true then duplicate all annnotation, groups and settings
2715 * @return new alignment panel, already displayed.
2717 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2720 * Create a new AlignmentPanel (with its own, new Viewport)
2722 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2724 if (!copyAnnotation)
2727 * remove all groups and annotation except for the automatic stuff
2729 newap.av.getAlignment().deleteAllGroups();
2730 newap.av.getAlignment().deleteAllAnnotations(false);
2733 newap.av.setGatherViewsHere(false);
2735 if (viewport.viewName == null)
2737 viewport.viewName = MessageManager
2738 .getString("label.view_name_original");
2742 * Views share the same edits undo and redo stacks
2744 newap.av.setHistoryList(viewport.getHistoryList());
2745 newap.av.setRedoList(viewport.getRedoList());
2748 * Views share the same mappings; need to deregister any new mappings
2749 * created by copyAlignPanel, and register the new reference to the shared
2752 newap.av.replaceMappings(viewport.getAlignment());
2754 newap.av.viewName = getNewViewName(viewTitle);
2756 addAlignmentPanel(newap, true);
2757 newap.alignmentChanged();
2759 if (alignPanels.size() == 2)
2761 viewport.setGatherViewsHere(true);
2763 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2768 * Make a new name for the view, ensuring it is unique within the current
2769 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2770 * these now use viewId. Unique view names are still desirable for usability.)
2775 protected String getNewViewName(String viewTitle)
2777 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2778 boolean addFirstIndex = false;
2779 if (viewTitle == null || viewTitle.trim().length() == 0)
2781 viewTitle = MessageManager.getString("action.view");
2782 addFirstIndex = true;
2786 index = 1;// we count from 1 if given a specific name
2788 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2790 List<Component> comps = PaintRefresher.components.get(viewport
2791 .getSequenceSetId());
2793 List<String> existingNames = getExistingViewNames(comps);
2795 while (existingNames.contains(newViewName))
2797 newViewName = viewTitle + " " + (++index);
2803 * Returns a list of distinct view names found in the given list of
2804 * components. View names are held on the viewport of an AlignmentPanel.
2809 protected List<String> getExistingViewNames(List<Component> comps)
2811 List<String> existingNames = new ArrayList<String>();
2812 for (Component comp : comps)
2814 if (comp instanceof AlignmentPanel)
2816 AlignmentPanel ap = (AlignmentPanel) comp;
2817 if (!existingNames.contains(ap.av.viewName))
2819 existingNames.add(ap.av.viewName);
2823 return existingNames;
2827 * Explode tabbed views into separate windows.
2830 public void expandViews_actionPerformed(ActionEvent e)
2832 Desktop.explodeViews(this);
2836 * Gather views in separate windows back into a tabbed presentation.
2839 public void gatherViews_actionPerformed(ActionEvent e)
2841 Desktop.instance.gatherViews(this);
2851 public void font_actionPerformed(ActionEvent e)
2853 new FontChooser(alignPanel);
2863 protected void seqLimit_actionPerformed(ActionEvent e)
2865 viewport.setShowJVSuffix(seqLimits.isSelected());
2867 alignPanel.getIdPanel().getIdCanvas()
2868 .setPreferredSize(alignPanel.calculateIdWidth());
2869 alignPanel.paintAlignment(true);
2873 public void idRightAlign_actionPerformed(ActionEvent e)
2875 viewport.setRightAlignIds(idRightAlign.isSelected());
2876 alignPanel.paintAlignment(true);
2880 public void centreColumnLabels_actionPerformed(ActionEvent e)
2882 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2883 alignPanel.paintAlignment(true);
2889 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2892 protected void followHighlight_actionPerformed()
2895 * Set the 'follow' flag on the Viewport (and scroll to position if now
2898 final boolean state = this.followHighlightMenuItem.getState();
2899 viewport.setFollowHighlight(state);
2902 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2913 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2915 viewport.setColourText(colourTextMenuItem.isSelected());
2916 alignPanel.paintAlignment(true);
2926 public void wrapMenuItem_actionPerformed(ActionEvent e)
2928 scaleAbove.setVisible(wrapMenuItem.isSelected());
2929 scaleLeft.setVisible(wrapMenuItem.isSelected());
2930 scaleRight.setVisible(wrapMenuItem.isSelected());
2931 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2932 alignPanel.updateLayout();
2936 public void showAllSeqs_actionPerformed(ActionEvent e)
2938 viewport.showAllHiddenSeqs();
2942 public void showAllColumns_actionPerformed(ActionEvent e)
2944 viewport.showAllHiddenColumns();
2946 viewport.sendSelection();
2950 public void hideSelSequences_actionPerformed(ActionEvent e)
2952 viewport.hideAllSelectedSeqs();
2953 // alignPanel.paintAlignment(true);
2957 * called by key handler and the hide all/show all menu items
2962 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2965 boolean hide = false;
2966 SequenceGroup sg = viewport.getSelectionGroup();
2967 if (!toggleSeqs && !toggleCols)
2969 // Hide everything by the current selection - this is a hack - we do the
2970 // invert and then hide
2971 // first check that there will be visible columns after the invert.
2972 if (viewport.hasSelectedColumns()
2973 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
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);
3200 if (alignPanel.getOverviewPanel() != null)
3202 alignPanel.getOverviewPanel().updateOverviewImage();
3207 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3208 * the annotations panel as a whole.
3210 * The options to show/hide all annotations should be enabled when the panel
3211 * is shown, and disabled when the panel is hidden.
3216 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3218 final boolean setVisible = annotationPanelMenuItem.isSelected();
3219 viewport.setShowAnnotation(setVisible);
3220 this.showAllSeqAnnotations.setEnabled(setVisible);
3221 this.hideAllSeqAnnotations.setEnabled(setVisible);
3222 this.showAllAlAnnotations.setEnabled(setVisible);
3223 this.hideAllAlAnnotations.setEnabled(setVisible);
3224 alignPanel.updateLayout();
3228 public void alignmentProperties()
3230 JEditorPane editPane = new JEditorPane("text/html", "");
3231 editPane.setEditable(false);
3232 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3234 editPane.setText(MessageManager.formatMessage("label.html_content",
3235 new Object[] { contents.toString() }));
3236 JInternalFrame frame = new JInternalFrame();
3237 frame.getContentPane().add(new JScrollPane(editPane));
3239 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3240 "label.alignment_properties", new Object[] { getTitle() }),
3251 public void overviewMenuItem_actionPerformed(ActionEvent e)
3253 if (alignPanel.overviewPanel != null)
3258 JInternalFrame frame = new JInternalFrame();
3259 OverviewPanel overview = new OverviewPanel(alignPanel);
3260 frame.setContentPane(overview);
3261 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3262 "label.overview_params", new Object[] { this.getTitle() }),
3263 frame.getWidth(), frame.getHeight());
3265 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3266 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3269 public void internalFrameClosed(
3270 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.equals(name))
3331 new UserDefinedColours(alignPanel, null);
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
3354 ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3357 viewport.setGlobalColourScheme(cs);
3359 alignPanel.paintAlignment(true);
3363 * Show the PID threshold slider panel
3366 protected void modifyPID_actionPerformed()
3368 SliderPanel.setPIDSliderSource(alignPanel,
3369 viewport.getResidueShading(), alignPanel.getViewName());
3370 SliderPanel.showPIDSlider();
3374 * Show the Conservation slider panel
3377 protected void modifyConservation_actionPerformed()
3379 SliderPanel.setConservationSlider(alignPanel,
3380 viewport.getResidueShading(), alignPanel.getViewName());
3381 SliderPanel.showConservationSlider();
3385 * Action on selecting or deselecting (Colour) By Conservation
3388 public void conservationMenuItem_actionPerformed(boolean selected)
3390 modifyConservation.setEnabled(selected);
3391 viewport.setConservationSelected(selected);
3392 viewport.getResidueShading().setConservationApplied(selected);
3394 changeColour(viewport.getGlobalColourScheme());
3397 modifyConservation_actionPerformed();
3401 SliderPanel.hideConservationSlider();
3406 * Action on selecting or deselecting (Colour) Above PID Threshold
3409 public void abovePIDThreshold_actionPerformed(boolean selected)
3411 modifyPID.setEnabled(selected);
3412 viewport.setAbovePIDThreshold(selected);
3415 viewport.getResidueShading().setThreshold(0,
3416 viewport.isIgnoreGapsConsensus());
3419 changeColour(viewport.getGlobalColourScheme());
3422 modifyPID_actionPerformed();
3426 SliderPanel.hidePIDSlider();
3437 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3439 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3440 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3441 .getAlignment().getSequenceAt(0), null);
3442 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3443 viewport.getAlignment()));
3444 alignPanel.paintAlignment(true);
3454 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3456 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3457 AlignmentSorter.sortByID(viewport.getAlignment());
3458 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3459 viewport.getAlignment()));
3460 alignPanel.paintAlignment(true);
3470 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3472 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3473 AlignmentSorter.sortByLength(viewport.getAlignment());
3474 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3475 viewport.getAlignment()));
3476 alignPanel.paintAlignment(true);
3486 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3488 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3489 AlignmentSorter.sortByGroup(viewport.getAlignment());
3490 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3491 viewport.getAlignment()));
3493 alignPanel.paintAlignment(true);
3503 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3505 new RedundancyPanel(alignPanel, this);
3515 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3517 if ((viewport.getSelectionGroup() == null)
3518 || (viewport.getSelectionGroup().getSize() < 2))
3520 JvOptionPane.showInternalMessageDialog(this, MessageManager
3521 .getString("label.you_must_select_least_two_sequences"),
3522 MessageManager.getString("label.invalid_selection"),
3523 JvOptionPane.WARNING_MESSAGE);
3527 JInternalFrame frame = new JInternalFrame();
3528 frame.setContentPane(new PairwiseAlignPanel(viewport));
3529 Desktop.addInternalFrame(frame,
3530 MessageManager.getString("action.pairwise_alignment"), 600,
3542 public void PCAMenuItem_actionPerformed(ActionEvent e)
3544 if (((viewport.getSelectionGroup() != null)
3545 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3546 .getSelectionGroup().getSize() > 0))
3547 || (viewport.getAlignment().getHeight() < 4))
3550 .showInternalMessageDialog(
3553 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3555 .getString("label.sequence_selection_insufficient"),
3556 JvOptionPane.WARNING_MESSAGE);
3561 new PCAPanel(alignPanel);
3565 public void autoCalculate_actionPerformed(ActionEvent e)
3567 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3568 if (viewport.autoCalculateConsensus)
3570 viewport.firePropertyChange("alignment", null, viewport
3571 .getAlignment().getSequences());
3576 public void sortByTreeOption_actionPerformed(ActionEvent e)
3578 viewport.sortByTree = sortByTree.isSelected();
3582 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3584 viewport.followSelection = listenToViewSelections.isSelected();
3597 void newTreePanel(String type, String pwType, String title)
3601 if (viewport.getSelectionGroup() != null
3602 && viewport.getSelectionGroup().getSize() > 0)
3604 if (viewport.getSelectionGroup().getSize() < 3)
3610 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3612 .getString("label.not_enough_sequences"),
3613 JvOptionPane.WARNING_MESSAGE);
3617 SequenceGroup sg = viewport.getSelectionGroup();
3619 /* Decide if the selection is a column region */
3620 for (SequenceI _s : sg.getSequences())
3622 if (_s.getLength() < sg.getEndRes())
3628 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3630 .getString("label.sequences_selection_not_aligned"),
3631 JvOptionPane.WARNING_MESSAGE);
3637 title = title + " on region";
3638 tp = new TreePanel(alignPanel, type, pwType);
3642 // are the visible sequences aligned?
3643 if (!viewport.getAlignment().isAligned(false))
3649 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3651 .getString("label.sequences_not_aligned"),
3652 JvOptionPane.WARNING_MESSAGE);
3657 if (viewport.getAlignment().getHeight() < 2)
3662 tp = new TreePanel(alignPanel, type, pwType);
3667 if (viewport.viewName != null)
3669 title += viewport.viewName + " of ";
3672 title += this.title;
3674 Desktop.addInternalFrame(tp, title, 600, 500);
3685 public void addSortByOrderMenuItem(String title,
3686 final AlignmentOrder order)
3688 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3689 "action.by_title_param", new Object[] { title }));
3691 item.addActionListener(new java.awt.event.ActionListener()
3694 public void actionPerformed(ActionEvent e)
3696 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3698 // TODO: JBPNote - have to map order entries to curent SequenceI
3700 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3702 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3705 alignPanel.paintAlignment(true);
3711 * Add a new sort by annotation score menu item
3714 * the menu to add the option to
3716 * the label used to retrieve scores for each sequence on the
3719 public void addSortByAnnotScoreMenuItem(JMenu sort,
3720 final String scoreLabel)
3722 final JMenuItem item = new JMenuItem(scoreLabel);
3724 item.addActionListener(new java.awt.event.ActionListener()
3727 public void actionPerformed(ActionEvent e)
3729 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3730 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3731 viewport.getAlignment());// ,viewport.getSelectionGroup());
3732 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3733 viewport.getAlignment()));
3734 alignPanel.paintAlignment(true);
3740 * last hash for alignment's annotation array - used to minimise cost of
3743 protected int _annotationScoreVectorHash;
3746 * search the alignment and rebuild the sort by annotation score submenu the
3747 * last alignment annotation vector hash is stored to minimize cost of
3748 * rebuilding in subsequence calls.
3752 public void buildSortByAnnotationScoresMenu()
3754 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3759 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3761 sortByAnnotScore.removeAll();
3762 // almost certainly a quicker way to do this - but we keep it simple
3763 Hashtable scoreSorts = new Hashtable();
3764 AlignmentAnnotation aann[];
3765 for (SequenceI sqa : viewport.getAlignment().getSequences())
3767 aann = sqa.getAnnotation();
3768 for (int i = 0; aann != null && i < aann.length; i++)
3770 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3772 scoreSorts.put(aann[i].label, aann[i].label);
3776 Enumeration labels = scoreSorts.keys();
3777 while (labels.hasMoreElements())
3779 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3780 (String) labels.nextElement());
3782 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3785 _annotationScoreVectorHash = viewport.getAlignment()
3786 .getAlignmentAnnotation().hashCode();
3791 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3792 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3793 * call. Listeners are added to remove the menu item when the treePanel is
3794 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3798 public void buildTreeSortMenu()
3800 sortByTreeMenu.removeAll();
3802 List<Component> comps = PaintRefresher.components.get(viewport
3803 .getSequenceSetId());
3804 List<TreePanel> treePanels = new ArrayList<TreePanel>();
3805 for (Component comp : comps)
3807 if (comp instanceof TreePanel)
3809 treePanels.add((TreePanel) comp);
3813 if (treePanels.size() < 1)
3815 sortByTreeMenu.setVisible(false);
3819 sortByTreeMenu.setVisible(true);
3821 for (final TreePanel tp : treePanels)
3823 final JMenuItem item = new JMenuItem(tp.getTitle());
3824 item.addActionListener(new java.awt.event.ActionListener()
3827 public void actionPerformed(ActionEvent e)
3829 tp.sortByTree_actionPerformed();
3830 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3835 sortByTreeMenu.add(item);
3839 public boolean sortBy(AlignmentOrder alorder, String undoname)
3841 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3842 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3843 if (undoname != null)
3845 addHistoryItem(new OrderCommand(undoname, oldOrder,
3846 viewport.getAlignment()));
3848 alignPanel.paintAlignment(true);
3853 * Work out whether the whole set of sequences or just the selected set will
3854 * be submitted for multiple alignment.
3857 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3859 // Now, check we have enough sequences
3860 AlignmentView msa = null;
3862 if ((viewport.getSelectionGroup() != null)
3863 && (viewport.getSelectionGroup().getSize() > 1))
3865 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3866 // some common interface!
3868 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3869 * SequenceI[sz = seqs.getSize(false)];
3871 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3872 * seqs.getSequenceAt(i); }
3874 msa = viewport.getAlignmentView(true);
3876 else if (viewport.getSelectionGroup() != null
3877 && viewport.getSelectionGroup().getSize() == 1)
3879 int option = JvOptionPane.showConfirmDialog(this,
3880 MessageManager.getString("warn.oneseq_msainput_selection"),
3881 MessageManager.getString("label.invalid_selection"),
3882 JvOptionPane.OK_CANCEL_OPTION);
3883 if (option == JvOptionPane.OK_OPTION)
3885 msa = viewport.getAlignmentView(false);
3890 msa = viewport.getAlignmentView(false);
3896 * Decides what is submitted to a secondary structure prediction service: the
3897 * first sequence in the alignment, or in the current selection, or, if the
3898 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3899 * region or the whole alignment. (where the first sequence in the set is the
3900 * one that the prediction will be for).
3902 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3904 AlignmentView seqs = null;
3906 if ((viewport.getSelectionGroup() != null)
3907 && (viewport.getSelectionGroup().getSize() > 0))
3909 seqs = viewport.getAlignmentView(true);
3913 seqs = viewport.getAlignmentView(false);
3915 // limit sequences - JBPNote in future - could spawn multiple prediction
3917 // TODO: viewport.getAlignment().isAligned is a global state - the local
3918 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3919 if (!viewport.getAlignment().isAligned(false))
3921 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3922 // TODO: if seqs.getSequences().length>1 then should really have warned
3936 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3938 // Pick the tree file
3939 JalviewFileChooser chooser = new JalviewFileChooser(
3940 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3941 chooser.setFileView(new JalviewFileView());
3942 chooser.setDialogTitle(MessageManager
3943 .getString("label.select_newick_like_tree_file"));
3944 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3946 int value = chooser.showOpenDialog(null);
3948 if (value == JalviewFileChooser.APPROVE_OPTION)
3950 String choice = chooser.getSelectedFile().getPath();
3951 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3952 jalview.io.NewickFile fin = null;
3955 fin = new NewickFile(choice, DataSourceType.FILE);
3956 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3957 } catch (Exception ex)
3964 .getString("label.problem_reading_tree_file"),
3965 JvOptionPane.WARNING_MESSAGE);
3966 ex.printStackTrace();
3968 if (fin != null && fin.hasWarningMessage())
3970 JvOptionPane.showMessageDialog(Desktop.desktop, fin
3971 .getWarningMessage(), MessageManager
3972 .getString("label.possible_problem_with_tree_file"),
3973 JvOptionPane.WARNING_MESSAGE);
3978 public TreePanel ShowNewickTree(NewickFile nf, String title)
3980 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3983 public TreePanel ShowNewickTree(NewickFile nf, String title,
3984 AlignmentView input)
3986 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3989 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3990 int h, int x, int y)
3992 return ShowNewickTree(nf, title, null, w, h, x, y);
3996 * Add a treeviewer for the tree extracted from a newick file object to the
3997 * current alignment view
4004 * Associated alignment input data (or null)
4013 * @return TreePanel handle
4015 public TreePanel ShowNewickTree(NewickFile nf, String title,
4016 AlignmentView input, int w, int h, int x, int y)
4018 TreePanel tp = null;
4024 if (nf.getTree() != null)
4026 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4032 tp.setLocation(x, y);
4035 Desktop.addInternalFrame(tp, title, w, h);
4037 } catch (Exception ex)
4039 ex.printStackTrace();
4045 private boolean buildingMenu = false;
4048 * Generates menu items and listener event actions for web service clients
4051 public void BuildWebServiceMenu()
4053 while (buildingMenu)
4057 System.err.println("Waiting for building menu to finish.");
4059 } catch (Exception e)
4063 final AlignFrame me = this;
4064 buildingMenu = true;
4065 new Thread(new Runnable()
4070 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4073 // System.err.println("Building ws menu again "
4074 // + Thread.currentThread());
4075 // TODO: add support for context dependent disabling of services based
4077 // alignment and current selection
4078 // TODO: add additional serviceHandle parameter to specify abstract
4080 // class independently of AbstractName
4081 // TODO: add in rediscovery GUI function to restart discoverer
4082 // TODO: group services by location as well as function and/or
4084 // object broker mechanism.
4085 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4086 final IProgressIndicator af = me;
4089 * do not i18n these strings - they are hard-coded in class
4090 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4091 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4093 final JMenu msawsmenu = new JMenu("Alignment");
4094 final JMenu secstrmenu = new JMenu(
4095 "Secondary Structure Prediction");
4096 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4097 final JMenu analymenu = new JMenu("Analysis");
4098 final JMenu dismenu = new JMenu("Protein Disorder");
4099 // JAL-940 - only show secondary structure prediction services from
4100 // the legacy server
4101 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4103 Discoverer.services != null && (Discoverer.services.size() > 0))
4105 // TODO: refactor to allow list of AbstractName/Handler bindings to
4107 // stored or retrieved from elsewhere
4108 // No MSAWS used any more:
4109 // Vector msaws = null; // (Vector)
4110 // Discoverer.services.get("MsaWS");
4111 Vector secstrpr = (Vector) Discoverer.services
4113 if (secstrpr != null)
4115 // Add any secondary structure prediction services
4116 for (int i = 0, j = secstrpr.size(); i < j; i++)
4118 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4120 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4121 .getServiceClient(sh);
4122 int p = secstrmenu.getItemCount();
4123 impl.attachWSMenuEntry(secstrmenu, me);
4124 int q = secstrmenu.getItemCount();
4125 for (int litm = p; litm < q; litm++)
4127 legacyItems.add(secstrmenu.getItem(litm));
4133 // Add all submenus in the order they should appear on the web
4135 wsmenu.add(msawsmenu);
4136 wsmenu.add(secstrmenu);
4137 wsmenu.add(dismenu);
4138 wsmenu.add(analymenu);
4139 // No search services yet
4140 // wsmenu.add(seqsrchmenu);
4142 javax.swing.SwingUtilities.invokeLater(new Runnable()
4149 webService.removeAll();
4150 // first, add discovered services onto the webservices menu
4151 if (wsmenu.size() > 0)
4153 for (int i = 0, j = wsmenu.size(); i < j; i++)
4155 webService.add(wsmenu.get(i));
4160 webService.add(me.webServiceNoServices);
4162 // TODO: move into separate menu builder class.
4163 boolean new_sspred = false;
4164 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4166 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4167 if (jws2servs != null)
4169 if (jws2servs.hasServices())
4171 jws2servs.attachWSMenuEntry(webService, me);
4172 for (Jws2Instance sv : jws2servs.getServices())
4174 if (sv.description.toLowerCase().contains("jpred"))
4176 for (JMenuItem jmi : legacyItems)
4178 jmi.setVisible(false);
4184 if (jws2servs.isRunning())
4186 JMenuItem tm = new JMenuItem(
4187 "Still discovering JABA Services");
4188 tm.setEnabled(false);
4193 build_urlServiceMenu(me.webService);
4194 build_fetchdbmenu(webService);
4195 for (JMenu item : wsmenu)
4197 if (item.getItemCount() == 0)
4199 item.setEnabled(false);
4203 item.setEnabled(true);
4206 } catch (Exception e)
4209 .debug("Exception during web service menu building process.",
4214 } catch (Exception e)
4217 buildingMenu = false;
4224 * construct any groupURL type service menu entries.
4228 private void build_urlServiceMenu(JMenu webService)
4230 // TODO: remove this code when 2.7 is released
4231 // DEBUG - alignmentView
4233 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4234 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4236 * @Override public void actionPerformed(ActionEvent e) {
4237 * jalview.datamodel.AlignmentView
4238 * .testSelectionViews(af.viewport.getAlignment(),
4239 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4241 * }); webService.add(testAlView);
4243 // TODO: refactor to RestClient discoverer and merge menu entries for
4244 // rest-style services with other types of analysis/calculation service
4245 // SHmmr test client - still being implemented.
4246 // DEBUG - alignmentView
4248 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4251 client.attachWSMenuEntry(
4252 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4258 * Searches the alignment sequences for xRefs and builds the Show
4259 * Cross-References menu (formerly called Show Products), with database
4260 * sources for which cross-references are found (protein sources for a
4261 * nucleotide alignment and vice versa)
4263 * @return true if Show Cross-references menu should be enabled
4265 public boolean canShowProducts()
4267 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4268 AlignmentI dataset = viewport.getAlignment().getDataset();
4270 showProducts.removeAll();
4271 final boolean dna = viewport.getAlignment().isNucleotide();
4273 if (seqs == null || seqs.length == 0)
4275 // nothing to see here.
4279 boolean showp = false;
4282 List<String> ptypes = new CrossRef(seqs, dataset)
4283 .findXrefSourcesForSequences(dna);
4285 for (final String source : ptypes)
4288 final AlignFrame af = this;
4289 JMenuItem xtype = new JMenuItem(source);
4290 xtype.addActionListener(new ActionListener()
4293 public void actionPerformed(ActionEvent e)
4295 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4298 showProducts.add(xtype);
4300 showProducts.setVisible(showp);
4301 showProducts.setEnabled(showp);
4302 } catch (Exception e)
4305 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4313 * Finds and displays cross-references for the selected sequences (protein
4314 * products for nucleotide sequences, dna coding sequences for peptides).
4317 * the sequences to show cross-references for
4319 * true if from a nucleotide alignment (so showing proteins)
4321 * the database to show cross-references for
4323 protected void showProductsFor(final SequenceI[] sel,
4324 final boolean _odna, final String source)
4326 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4331 * Construct and display a new frame containing the translation of this
4332 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4335 public void showTranslation_actionPerformed(ActionEvent e)
4337 AlignmentI al = null;
4340 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4342 al = dna.translateCdna();
4343 } catch (Exception ex)
4345 jalview.bin.Cache.log.error(
4346 "Exception during translation. Please report this !", ex);
4347 final String msg = MessageManager
4348 .getString("label.error_when_translating_sequences_submit_bug_report");
4349 final String errorTitle = MessageManager
4350 .getString("label.implementation_error")
4351 + MessageManager.getString("label.translation_failed");
4352 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4353 JvOptionPane.ERROR_MESSAGE);
4356 if (al == null || al.getHeight() == 0)
4358 final String msg = MessageManager
4359 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4360 final String errorTitle = MessageManager
4361 .getString("label.translation_failed");
4362 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4363 JvOptionPane.WARNING_MESSAGE);
4367 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4368 af.setFileFormat(this.currentFileFormat);
4369 final String newTitle = MessageManager.formatMessage(
4370 "label.translation_of_params",
4371 new Object[] { this.getTitle() });
4372 af.setTitle(newTitle);
4373 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4375 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4376 viewport.openSplitFrame(af, new Alignment(seqs));
4380 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4387 * Set the file format
4391 public void setFileFormat(FileFormatI format)
4393 this.currentFileFormat = format;
4397 * Try to load a features file onto the alignment.
4400 * contents or path to retrieve file
4402 * access mode of file (see jalview.io.AlignFile)
4403 * @return true if features file was parsed correctly.
4405 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4407 return avc.parseFeaturesFile(file, sourceType,
4408 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4413 public void refreshFeatureUI(boolean enableIfNecessary)
4415 // note - currently this is only still here rather than in the controller
4416 // because of the featureSettings hard reference that is yet to be
4418 if (enableIfNecessary)
4420 viewport.setShowSequenceFeatures(true);
4421 showSeqFeatures.setSelected(true);
4427 public void dragEnter(DropTargetDragEvent evt)
4432 public void dragExit(DropTargetEvent evt)
4437 public void dragOver(DropTargetDragEvent evt)
4442 public void dropActionChanged(DropTargetDragEvent evt)
4447 public void drop(DropTargetDropEvent evt)
4449 // JAL-1552 - acceptDrop required before getTransferable call for
4450 // Java's Transferable for native dnd
4451 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4452 Transferable t = evt.getTransferable();
4453 List<String> files = new ArrayList<String>();
4454 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4458 Desktop.transferFromDropTarget(files, protocols, evt, t);
4459 } catch (Exception e)
4461 e.printStackTrace();
4467 // check to see if any of these files have names matching sequences in
4469 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4470 .getAlignment().getSequencesArray());
4472 * Object[] { String,SequenceI}
4474 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4475 ArrayList<String> filesnotmatched = new ArrayList<String>();
4476 for (int i = 0; i < files.size(); i++)
4478 String file = files.get(i).toString();
4480 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4481 if (protocol == DataSourceType.FILE)
4483 File fl = new File(file);
4484 pdbfn = fl.getName();
4486 else if (protocol == DataSourceType.URL)
4488 URL url = new URL(file);
4489 pdbfn = url.getFile();
4491 if (pdbfn.length() > 0)
4493 // attempt to find a match in the alignment
4494 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4495 int l = 0, c = pdbfn.indexOf(".");
4496 while (mtch == null && c != -1)
4501 } while ((c = pdbfn.indexOf(".", l)) > l);
4504 pdbfn = pdbfn.substring(0, l);
4506 mtch = idm.findAllIdMatches(pdbfn);
4510 FileFormatI type = null;
4513 type = new IdentifyFile().identify(file, protocol);
4514 } catch (Exception ex)
4518 if (type != null && type.isStructureFile())
4520 filesmatched.add(new Object[] { file, protocol, mtch });
4524 // File wasn't named like one of the sequences or wasn't a PDB file.
4525 filesnotmatched.add(file);
4529 if (filesmatched.size() > 0)
4531 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4537 "label.automatically_associate_structure_files_with_sequences_same_name",
4538 new Object[] { Integer
4544 .getString("label.automatically_associate_structure_files_by_name"),
4545 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4548 for (Object[] fm : filesmatched)
4550 // try and associate
4551 // TODO: may want to set a standard ID naming formalism for
4552 // associating PDB files which have no IDs.
4553 for (SequenceI toassoc : (SequenceI[]) fm[2])
4555 PDBEntry pe = new AssociatePdbFileWithSeq()
4556 .associatePdbWithSeq((String) fm[0],
4557 (DataSourceType) fm[1], toassoc, false,
4561 System.err.println("Associated file : "
4562 + ((String) fm[0]) + " with "
4563 + toassoc.getDisplayId(true));
4567 alignPanel.paintAlignment(true);
4571 if (filesnotmatched.size() > 0)
4574 && (Cache.getDefault(
4575 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4581 "label.ignore_unmatched_dropped_files_info",
4582 new Object[] { Integer
4589 .getString("label.ignore_unmatched_dropped_files"),
4590 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4594 for (String fn : filesnotmatched)
4596 loadJalviewDataFile(fn, null, null, null);
4600 } catch (Exception ex)
4602 ex.printStackTrace();
4608 * Attempt to load a "dropped" file or URL string: First by testing whether
4609 * it's an Annotation file, then a JNet file, and finally a features file. If
4610 * all are false then the user may have dropped an alignment file onto this
4614 * either a filename or a URL string.
4616 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4617 FileFormatI format, SequenceI assocSeq)
4621 if (sourceType == null)
4623 sourceType = FormatAdapter.checkProtocol(file);
4625 // if the file isn't identified, or not positively identified as some
4626 // other filetype (PFAM is default unidentified alignment file type) then
4627 // try to parse as annotation.
4628 boolean isAnnotation = (format == null || FileFormat.Pfam
4629 .equals(format)) ? new AnnotationFile()
4630 .annotateAlignmentView(viewport, file, sourceType) : false;
4634 // first see if its a T-COFFEE score file
4635 TCoffeeScoreFile tcf = null;
4638 tcf = new TCoffeeScoreFile(file, sourceType);
4641 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4644 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4645 isAnnotation = true;
4647 .setText(MessageManager
4648 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4652 // some problem - if no warning its probable that the ID matching
4653 // process didn't work
4657 tcf.getWarningMessage() == null ? MessageManager
4658 .getString("label.check_file_matches_sequence_ids_alignment")
4659 : tcf.getWarningMessage(),
4661 .getString("label.problem_reading_tcoffee_score_file"),
4662 JvOptionPane.WARNING_MESSAGE);
4669 } catch (Exception x)
4672 .debug("Exception when processing data source as T-COFFEE score file",
4678 // try to see if its a JNet 'concise' style annotation file *before*
4680 // try to parse it as a features file
4683 format = new IdentifyFile().identify(file, sourceType);
4685 if (FileFormat.Jnet.equals(format))
4687 JPredFile predictions = new JPredFile(file, sourceType);
4688 new JnetAnnotationMaker();
4689 JnetAnnotationMaker.add_annotation(predictions,
4690 viewport.getAlignment(), 0, false);
4691 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4692 viewport.getAlignment().setSeqrep(repseq);
4693 ColumnSelection cs = new ColumnSelection();
4694 cs.hideInsertionsFor(repseq);
4695 viewport.setColumnSelection(cs);
4696 isAnnotation = true;
4698 // else if (IdentifyFile.FeaturesFile.equals(format))
4699 else if (FileFormat.Features.equals(format))
4701 if (parseFeaturesFile(file, sourceType))
4703 alignPanel.paintAlignment(true);
4708 new FileLoader().LoadFile(viewport, file, sourceType, format);
4715 alignPanel.adjustAnnotationHeight();
4716 viewport.updateSequenceIdColours();
4717 buildSortByAnnotationScoresMenu();
4718 alignPanel.paintAlignment(true);
4720 } catch (Exception ex)
4722 ex.printStackTrace();
4723 } catch (OutOfMemoryError oom)
4728 } catch (Exception x)
4733 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4734 : "using " + sourceType + " from " + file)
4736 + (format != null ? "(parsing as '" + format
4737 + "' file)" : ""), oom, Desktop.desktop);
4742 * Method invoked by the ChangeListener on the tabbed pane, in other words
4743 * when a different tabbed pane is selected by the user or programmatically.
4746 public void tabSelectionChanged(int index)
4750 alignPanel = alignPanels.get(index);
4751 viewport = alignPanel.av;
4752 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4753 setMenusFromViewport(viewport);
4757 * 'focus' any colour slider that is open to the selected viewport
4759 if (viewport.getConservationSelected())
4761 SliderPanel.setConservationSlider(alignPanel,
4762 viewport.getResidueShading(), alignPanel.getViewName());
4766 SliderPanel.hideConservationSlider();
4768 if (viewport.getAbovePIDThreshold())
4770 SliderPanel.setPIDSliderSource(alignPanel,
4771 viewport.getResidueShading(), alignPanel.getViewName());
4775 SliderPanel.hidePIDSlider();
4779 * If there is a frame linked to this one in a SplitPane, switch it to the
4780 * same view tab index. No infinite recursion of calls should happen, since
4781 * tabSelectionChanged() should not get invoked on setting the selected
4782 * index to an unchanged value. Guard against setting an invalid index
4783 * before the new view peer tab has been created.
4785 final AlignViewportI peer = viewport.getCodingComplement();
4788 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4789 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4791 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4797 * On right mouse click on view tab, prompt for and set new view name.
4800 public void tabbedPane_mousePressed(MouseEvent e)
4802 if (e.isPopupTrigger())
4804 String msg = MessageManager.getString("label.enter_view_name");
4805 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4806 JvOptionPane.QUESTION_MESSAGE);
4810 viewport.viewName = reply;
4811 // TODO warn if reply is in getExistingViewNames()?
4812 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4817 public AlignViewport getCurrentView()
4823 * Open the dialog for regex description parsing.
4826 protected void extractScores_actionPerformed(ActionEvent e)
4828 ParseProperties pp = new jalview.analysis.ParseProperties(
4829 viewport.getAlignment());
4830 // TODO: verify regex and introduce GUI dialog for version 2.5
4831 // if (pp.getScoresFromDescription("col", "score column ",
4832 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4834 if (pp.getScoresFromDescription("description column",
4835 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4837 buildSortByAnnotationScoresMenu();
4845 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4849 protected void showDbRefs_actionPerformed(ActionEvent e)
4851 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4857 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4861 protected void showNpFeats_actionPerformed(ActionEvent e)
4863 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4867 * find the viewport amongst the tabs in this alignment frame and close that
4872 public boolean closeView(AlignViewportI av)
4876 this.closeMenuItem_actionPerformed(false);
4879 Component[] comp = tabbedPane.getComponents();
4880 for (int i = 0; comp != null && i < comp.length; i++)
4882 if (comp[i] instanceof AlignmentPanel)
4884 if (((AlignmentPanel) comp[i]).av == av)
4887 closeView((AlignmentPanel) comp[i]);
4895 protected void build_fetchdbmenu(JMenu webService)
4897 // Temporary hack - DBRef Fetcher always top level ws entry.
4898 // TODO We probably want to store a sequence database checklist in
4899 // preferences and have checkboxes.. rather than individual sources selected
4901 final JMenu rfetch = new JMenu(
4902 MessageManager.getString("action.fetch_db_references"));
4903 rfetch.setToolTipText(MessageManager
4904 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4905 webService.add(rfetch);
4907 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4908 MessageManager.getString("option.trim_retrieved_seqs"));
4909 trimrs.setToolTipText(MessageManager
4910 .getString("label.trim_retrieved_sequences"));
4911 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4912 trimrs.addActionListener(new ActionListener()
4915 public void actionPerformed(ActionEvent e)
4917 trimrs.setSelected(trimrs.isSelected());
4918 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4919 Boolean.valueOf(trimrs.isSelected()).toString());
4923 JMenuItem fetchr = new JMenuItem(
4924 MessageManager.getString("label.standard_databases"));
4925 fetchr.setToolTipText(MessageManager
4926 .getString("label.fetch_embl_uniprot"));
4927 fetchr.addActionListener(new ActionListener()
4931 public void actionPerformed(ActionEvent e)
4933 new Thread(new Runnable()
4938 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4939 .getAlignment().isNucleotide();
4940 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4941 .getSequenceSelection(), alignPanel.alignFrame, null,
4942 alignPanel.alignFrame.featureSettings, isNucleotide);
4943 dbRefFetcher.addListener(new FetchFinishedListenerI()
4946 public void finished()
4948 AlignFrame.this.setMenusForViewport();
4951 dbRefFetcher.fetchDBRefs(false);
4959 final AlignFrame me = this;
4960 new Thread(new Runnable()
4965 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4966 .getSequenceFetcherSingleton(me);
4967 javax.swing.SwingUtilities.invokeLater(new Runnable()
4972 String[] dbclasses = sf.getOrderedSupportedSources();
4973 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4974 // jalview.util.QuickSort.sort(otherdb, otherdb);
4975 List<DbSourceProxy> otherdb;
4976 JMenu dfetch = new JMenu();
4977 JMenu ifetch = new JMenu();
4978 JMenuItem fetchr = null;
4979 int comp = 0, icomp = 0, mcomp = 15;
4980 String mname = null;
4982 for (String dbclass : dbclasses)
4984 otherdb = sf.getSourceProxy(dbclass);
4985 // add a single entry for this class, or submenu allowing 'fetch
4987 if (otherdb == null || otherdb.size() < 1)
4991 // List<DbSourceProxy> dbs=otherdb;
4992 // otherdb=new ArrayList<DbSourceProxy>();
4993 // for (DbSourceProxy db:dbs)
4995 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4999 mname = "From " + dbclass;
5001 if (otherdb.size() == 1)
5003 final DbSourceProxy[] dassource = otherdb
5004 .toArray(new DbSourceProxy[0]);
5005 DbSourceProxy src = otherdb.get(0);
5006 fetchr = new JMenuItem(src.getDbSource());
5007 fetchr.addActionListener(new ActionListener()
5011 public void actionPerformed(ActionEvent e)
5013 new Thread(new Runnable()
5019 boolean isNucleotide = alignPanel.alignFrame
5020 .getViewport().getAlignment()
5022 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5023 alignPanel.av.getSequenceSelection(),
5024 alignPanel.alignFrame, dassource,
5025 alignPanel.alignFrame.featureSettings,
5028 .addListener(new FetchFinishedListenerI()
5031 public void finished()
5033 AlignFrame.this.setMenusForViewport();
5036 dbRefFetcher.fetchDBRefs(false);
5042 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5043 MessageManager.formatMessage(
5044 "label.fetch_retrieve_from",
5045 new Object[] { src.getDbName() })));
5051 final DbSourceProxy[] dassource = otherdb
5052 .toArray(new DbSourceProxy[0]);
5054 DbSourceProxy src = otherdb.get(0);
5055 fetchr = new JMenuItem(MessageManager.formatMessage(
5056 "label.fetch_all_param",
5057 new Object[] { src.getDbSource() }));
5058 fetchr.addActionListener(new ActionListener()
5061 public void actionPerformed(ActionEvent e)
5063 new Thread(new Runnable()
5069 boolean isNucleotide = alignPanel.alignFrame
5070 .getViewport().getAlignment()
5072 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5073 alignPanel.av.getSequenceSelection(),
5074 alignPanel.alignFrame, dassource,
5075 alignPanel.alignFrame.featureSettings,
5078 .addListener(new FetchFinishedListenerI()
5081 public void finished()
5083 AlignFrame.this.setMenusForViewport();
5086 dbRefFetcher.fetchDBRefs(false);
5092 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5093 MessageManager.formatMessage(
5094 "label.fetch_retrieve_from_all_sources",
5096 Integer.valueOf(otherdb.size())
5097 .toString(), src.getDbSource(),
5098 src.getDbName() })));
5101 // and then build the rest of the individual menus
5102 ifetch = new JMenu(MessageManager.formatMessage(
5103 "label.source_from_db_source",
5104 new Object[] { src.getDbSource() }));
5106 String imname = null;
5108 for (DbSourceProxy sproxy : otherdb)
5110 String dbname = sproxy.getDbName();
5111 String sname = dbname.length() > 5 ? dbname.substring(0,
5112 5) + "..." : dbname;
5113 String msname = dbname.length() > 10 ? dbname.substring(
5114 0, 10) + "..." : dbname;
5117 imname = MessageManager.formatMessage(
5118 "label.from_msname", new Object[] { sname });
5120 fetchr = new JMenuItem(msname);
5121 final DbSourceProxy[] dassrc = { sproxy };
5122 fetchr.addActionListener(new ActionListener()
5126 public void actionPerformed(ActionEvent e)
5128 new Thread(new Runnable()
5134 boolean isNucleotide = alignPanel.alignFrame
5135 .getViewport().getAlignment()
5137 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5138 alignPanel.av.getSequenceSelection(),
5139 alignPanel.alignFrame, dassrc,
5140 alignPanel.alignFrame.featureSettings,
5143 .addListener(new FetchFinishedListenerI()
5146 public void finished()
5148 AlignFrame.this.setMenusForViewport();
5151 dbRefFetcher.fetchDBRefs(false);
5157 fetchr.setToolTipText("<html>"
5158 + MessageManager.formatMessage(
5159 "label.fetch_retrieve_from", new Object[]
5163 if (++icomp >= mcomp || i == (otherdb.size()))
5165 ifetch.setText(MessageManager.formatMessage(
5166 "label.source_to_target", imname, sname));
5168 ifetch = new JMenu();
5176 if (comp >= mcomp || dbi >= (dbclasses.length))
5178 dfetch.setText(MessageManager.formatMessage(
5179 "label.source_to_target", mname, dbclass));
5181 dfetch = new JMenu();
5194 * Left justify the whole alignment.
5197 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5199 AlignmentI al = viewport.getAlignment();
5201 viewport.firePropertyChange("alignment", null, al);
5205 * Right justify the whole alignment.
5208 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5210 AlignmentI al = viewport.getAlignment();
5212 viewport.firePropertyChange("alignment", null, al);
5216 public void setShowSeqFeatures(boolean b)
5218 showSeqFeatures.setSelected(b);
5219 viewport.setShowSequenceFeatures(b);
5226 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5227 * awt.event.ActionEvent)
5230 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5232 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5233 alignPanel.paintAlignment(true);
5240 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5244 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5246 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5247 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5255 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5256 * .event.ActionEvent)
5259 protected void showGroupConservation_actionPerformed(ActionEvent e)
5261 viewport.setShowGroupConservation(showGroupConservation.getState());
5262 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5269 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5270 * .event.ActionEvent)
5273 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5275 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5276 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5283 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5284 * .event.ActionEvent)
5287 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5289 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5290 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5294 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5296 showSequenceLogo.setState(true);
5297 viewport.setShowSequenceLogo(true);
5298 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5299 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5303 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5305 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5312 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5313 * .event.ActionEvent)
5316 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5318 if (avc.makeGroupsFromSelection())
5320 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5321 alignPanel.updateAnnotation();
5322 alignPanel.paintAlignment(true);
5326 public void clearAlignmentSeqRep()
5328 // TODO refactor alignmentseqrep to controller
5329 if (viewport.getAlignment().hasSeqrep())
5331 viewport.getAlignment().setSeqrep(null);
5332 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5333 alignPanel.updateAnnotation();
5334 alignPanel.paintAlignment(true);
5339 protected void createGroup_actionPerformed(ActionEvent e)
5341 if (avc.createGroup())
5343 alignPanel.alignmentChanged();
5348 protected void unGroup_actionPerformed(ActionEvent e)
5352 alignPanel.alignmentChanged();
5357 * make the given alignmentPanel the currently selected tab
5359 * @param alignmentPanel
5361 public void setDisplayedView(AlignmentPanel alignmentPanel)
5363 if (!viewport.getSequenceSetId().equals(
5364 alignmentPanel.av.getSequenceSetId()))
5368 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5370 if (tabbedPane != null
5371 && tabbedPane.getTabCount() > 0
5372 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5373 .getSelectedIndex())
5375 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5380 * Action on selection of menu options to Show or Hide annotations.
5383 * @param forSequences
5384 * update sequence-related annotations
5385 * @param forAlignment
5386 * update non-sequence-related annotations
5389 protected void setAnnotationsVisibility(boolean visible,
5390 boolean forSequences, boolean forAlignment)
5392 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5393 .getAlignmentAnnotation();
5398 for (AlignmentAnnotation aa : anns)
5401 * don't display non-positional annotations on an alignment
5403 if (aa.annotations == null)
5407 boolean apply = (aa.sequenceRef == null && forAlignment)
5408 || (aa.sequenceRef != null && forSequences);
5411 aa.visible = visible;
5414 alignPanel.validateAnnotationDimensions(true);
5415 alignPanel.alignmentChanged();
5419 * Store selected annotation sort order for the view and repaint.
5422 protected void sortAnnotations_actionPerformed()
5424 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5426 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5427 alignPanel.paintAlignment(true);
5432 * @return alignment panels in this alignment frame
5434 public List<? extends AlignmentViewPanel> getAlignPanels()
5436 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5440 * Open a new alignment window, with the cDNA associated with this (protein)
5441 * alignment, aligned as is the protein.
5443 protected void viewAsCdna_actionPerformed()
5445 // TODO no longer a menu action - refactor as required
5446 final AlignmentI alignment = getViewport().getAlignment();
5447 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5448 if (mappings == null)
5452 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5453 for (SequenceI aaSeq : alignment.getSequences())
5455 for (AlignedCodonFrame acf : mappings)
5457 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5461 * There is a cDNA mapping for this protein sequence - add to new
5462 * alignment. It will share the same dataset sequence as other mapped
5463 * cDNA (no new mappings need to be created).
5465 final Sequence newSeq = new Sequence(dnaSeq);
5466 newSeq.setDatasetSequence(dnaSeq);
5467 cdnaSeqs.add(newSeq);
5471 if (cdnaSeqs.size() == 0)
5473 // show a warning dialog no mapped cDNA
5476 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5478 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5479 AlignFrame.DEFAULT_HEIGHT);
5480 cdna.alignAs(alignment);
5481 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5483 Desktop.addInternalFrame(alignFrame, newtitle,
5484 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5488 * Set visibility of dna/protein complement view (available when shown in a
5494 protected void showComplement_actionPerformed(boolean show)
5496 SplitContainerI sf = getSplitViewContainer();
5499 sf.setComplementVisible(this, show);
5504 * Generate the reverse (optionally complemented) of the selected sequences,
5505 * and add them to the alignment
5508 protected void showReverse_actionPerformed(boolean complement)
5510 AlignmentI al = null;
5513 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5514 al = dna.reverseCdna(complement);
5515 viewport.addAlignment(al, "");
5516 addHistoryItem(new EditCommand(
5517 MessageManager.getString("label.add_sequences"),
5518 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5519 viewport.getAlignment()));
5520 } catch (Exception ex)
5522 System.err.println(ex.getMessage());
5528 * Try to run a script in the Groovy console, having first ensured that this
5529 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5530 * be targeted at this alignment.
5533 protected void runGroovy_actionPerformed()
5535 Jalview.setCurrentAlignFrame(this);
5536 groovy.ui.Console console = Desktop.getGroovyConsole();
5537 if (console != null)
5541 console.runScript();
5542 } catch (Exception ex)
5544 System.err.println((ex.toString()));
5546 .showInternalMessageDialog(Desktop.desktop, MessageManager
5547 .getString("label.couldnt_run_groovy_script"),
5549 .getString("label.groovy_support_failed"),
5550 JvOptionPane.ERROR_MESSAGE);
5555 System.err.println("Can't run Groovy script as console not found");
5560 * Hides columns containing (or not containing) a specified feature, provided
5561 * that would not leave all columns hidden
5563 * @param featureType
5564 * @param columnsContaining
5567 public boolean hideFeatureColumns(String featureType,
5568 boolean columnsContaining)
5570 boolean notForHiding = avc.markColumnsContainingFeatures(
5571 columnsContaining, false, false, featureType);
5574 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5575 false, featureType))
5577 getViewport().hideSelectedColumns();
5585 protected void selectHighlightedColumns_actionPerformed(
5586 ActionEvent actionEvent)
5588 // include key modifier check in case user selects from menu
5589 avc.markHighlightedColumns(
5590 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5592 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5596 * Rebuilds the Colour menu, including any user-defined colours which have
5597 * been loaded either on startup or during the session
5599 public void buildColourMenu()
5601 colourMenu.removeAll();
5603 colourMenu.add(applyToAllGroups);
5604 colourMenu.add(textColour);
5605 colourMenu.addSeparator();
5607 ColourMenuHelper.addMenuItems(colourMenu, this,
5608 viewport.getAlignment(), false);
5610 colourMenu.addSeparator();
5611 colourMenu.add(conservationMenuItem);
5612 colourMenu.add(modifyConservation);
5613 colourMenu.add(abovePIDThreshold);
5614 colourMenu.add(modifyPID);
5615 colourMenu.add(annotationColour);
5617 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5618 String schemeName = colourScheme == null ? null : colourScheme
5621 ColourMenuHelper.setColourSelected(colourMenu, schemeName);
5624 public void newTreePanel(String treeType, ScoreModelI sm)
5626 String treecalcnm = MessageManager.getString("label.tree_calc_"
5627 + treeType.toLowerCase());
5628 String smn = MessageManager.getStringOrReturn("label.score_model_",
5630 final String ttl = MessageManager.formatMessage("label.treecalc_title",
5632 newTreePanel(treeType, sm.getName(), ttl);
5636 class PrintThread extends Thread
5640 public PrintThread(AlignmentPanel ap)
5645 static PageFormat pf;
5650 PrinterJob printJob = PrinterJob.getPrinterJob();
5654 printJob.setPrintable(ap, pf);
5658 printJob.setPrintable(ap);
5661 if (printJob.printDialog())
5666 } catch (Exception PrintException)
5668 PrintException.printStackTrace();