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.FileLoader;
71 import jalview.io.FormatAdapter;
72 import jalview.io.HtmlSvgOutput;
73 import jalview.io.IdentifyFile;
74 import jalview.io.JPredFile;
75 import jalview.io.JalviewFileChooser;
76 import jalview.io.JalviewFileView;
77 import jalview.io.JnetAnnotationMaker;
78 import jalview.io.NewickFile;
79 import jalview.io.TCoffeeScoreFile;
80 import jalview.jbgui.GAlignFrame;
81 import jalview.schemes.ColourSchemeI;
82 import jalview.schemes.ColourSchemes;
83 import jalview.schemes.ResidueColourScheme;
84 import jalview.schemes.ResidueProperties;
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;
122 import java.util.ArrayList;
123 import java.util.Arrays;
124 import java.util.Deque;
125 import java.util.Enumeration;
126 import java.util.Hashtable;
127 import java.util.List;
128 import java.util.Vector;
130 import javax.swing.JCheckBoxMenuItem;
131 import javax.swing.JEditorPane;
132 import javax.swing.JInternalFrame;
133 import javax.swing.JLayeredPane;
134 import javax.swing.JMenu;
135 import javax.swing.JMenuItem;
136 import javax.swing.JScrollPane;
137 import javax.swing.SwingUtilities;
143 * @version $Revision$
145 public class AlignFrame extends GAlignFrame implements DropTargetListener,
146 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
149 public static final int DEFAULT_WIDTH = 700;
151 public static final int DEFAULT_HEIGHT = 500;
154 * The currently displayed panel (selected tabbed view if more than one)
156 public AlignmentPanel alignPanel;
158 AlignViewport viewport;
160 public AlignViewControllerI avc;
162 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
165 * Last format used to load or save alignments in this window
167 FileFormatI currentFileFormat = null;
170 * Current filename for this alignment
172 String fileName = null;
175 * Creates a new AlignFrame object with specific width and height.
181 public AlignFrame(AlignmentI al, int width, int height)
183 this(al, null, width, height);
187 * Creates a new AlignFrame object with specific width, height and
193 * @param sequenceSetId
195 public AlignFrame(AlignmentI al, int width, int height,
196 String sequenceSetId)
198 this(al, null, width, height, sequenceSetId);
202 * Creates a new AlignFrame object with specific width, height and
208 * @param sequenceSetId
211 public AlignFrame(AlignmentI al, int width, int height,
212 String sequenceSetId, String viewId)
214 this(al, null, width, height, sequenceSetId, viewId);
218 * new alignment window with hidden columns
222 * @param hiddenColumns
223 * ColumnSelection or null
225 * Width of alignment frame
229 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
230 int width, int height)
232 this(al, hiddenColumns, width, height, null);
236 * Create alignment frame for al with hiddenColumns, a specific width and
237 * height, and specific sequenceId
240 * @param hiddenColumns
243 * @param sequenceSetId
246 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
247 int width, int height, String sequenceSetId)
249 this(al, hiddenColumns, width, height, sequenceSetId, null);
253 * Create alignment frame for al with hiddenColumns, a specific width and
254 * height, and specific sequenceId
257 * @param hiddenColumns
260 * @param sequenceSetId
265 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
266 int width, int height, String sequenceSetId, String viewId)
268 setSize(width, height);
270 if (al.getDataset() == null)
275 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
277 alignPanel = new AlignmentPanel(this, viewport);
279 addAlignmentPanel(alignPanel, true);
283 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
284 ColumnSelection hiddenColumns, int width, int height)
286 setSize(width, height);
288 if (al.getDataset() == null)
293 viewport = new AlignViewport(al, hiddenColumns);
295 if (hiddenSeqs != null && hiddenSeqs.length > 0)
297 viewport.hideSequence(hiddenSeqs);
299 alignPanel = new AlignmentPanel(this, viewport);
300 addAlignmentPanel(alignPanel, true);
305 * Make a new AlignFrame from existing alignmentPanels
312 public AlignFrame(AlignmentPanel ap)
316 addAlignmentPanel(ap, false);
321 * initalise the alignframe from the underlying viewport data and the
326 if (!Jalview.isHeadlessMode())
328 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
331 avc = new jalview.controller.AlignViewController(this, viewport,
333 if (viewport.getAlignmentConservationAnnotation() == null)
335 // BLOSUM62Colour.setEnabled(false);
336 conservationMenuItem.setEnabled(false);
337 modifyConservation.setEnabled(false);
338 // PIDColour.setEnabled(false);
339 // abovePIDThreshold.setEnabled(false);
340 // modifyPID.setEnabled(false);
343 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
346 if (sortby.equals("Id"))
348 sortIDMenuItem_actionPerformed(null);
350 else if (sortby.equals("Pairwise Identity"))
352 sortPairwiseMenuItem_actionPerformed(null);
356 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
358 setMenusFromViewport(viewport);
359 buildSortByAnnotationScoresMenu();
363 if (Desktop.desktop != null)
365 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
366 addServiceListeners();
370 if (viewport.getWrapAlignment())
372 wrapMenuItem_actionPerformed(null);
375 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
377 this.overviewMenuItem_actionPerformed(null);
382 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
383 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
384 final String menuLabel = MessageManager
385 .getString("label.copy_format_from");
386 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
387 new ViewSetProvider()
391 public AlignmentPanel[] getAllAlignmentPanels()
394 origview.add(alignPanel);
395 // make an array of all alignment panels except for this one
396 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
397 Arrays.asList(Desktop.getAlignmentPanels(null)));
398 aps.remove(AlignFrame.this.alignPanel);
399 return aps.toArray(new AlignmentPanel[aps.size()]);
401 }, selviews, new ItemListener()
405 public void itemStateChanged(ItemEvent e)
407 if (origview.size() > 0)
409 final AlignmentPanel ap = origview.get(0);
412 * Copy the ViewStyle of the selected panel to 'this one'.
413 * Don't change value of 'scaleProteinAsCdna' unless copying
416 ViewStyleI vs = selviews.get(0).getAlignViewport()
418 boolean fromSplitFrame = selviews.get(0)
419 .getAlignViewport().getCodingComplement() != null;
422 vs.setScaleProteinAsCdna(ap.getAlignViewport()
423 .getViewStyle().isScaleProteinAsCdna());
425 ap.getAlignViewport().setViewStyle(vs);
428 * Also rescale ViewStyle of SplitFrame complement if there is
429 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
430 * the whole ViewStyle (allow cDNA protein to have different
433 AlignViewportI complement = ap.getAlignViewport()
434 .getCodingComplement();
435 if (complement != null && vs.isScaleProteinAsCdna())
437 AlignFrame af = Desktop.getAlignFrameFor(complement);
438 ((SplitFrame) af.getSplitViewContainer())
440 af.setMenusForViewport();
444 ap.setSelected(true);
445 ap.alignFrame.setMenusForViewport();
450 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
451 .indexOf("devel") > -1
452 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
453 .indexOf("test") > -1)
455 formatMenu.add(vsel);
457 addFocusListener(new FocusAdapter()
460 public void focusGained(FocusEvent e)
462 Jalview.setCurrentAlignFrame(AlignFrame.this);
469 * Change the filename and format for the alignment, and enable the 'reload'
470 * button functionality.
477 public void setFileName(String file, FileFormatI format)
480 setFileFormat(format);
481 reload.setEnabled(true);
485 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
488 void addKeyListener()
490 addKeyListener(new KeyAdapter()
493 public void keyPressed(KeyEvent evt)
495 if (viewport.cursorMode
496 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
497 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
498 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
499 && Character.isDigit(evt.getKeyChar()))
501 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
504 switch (evt.getKeyCode())
507 case 27: // escape key
508 deselectAllSequenceMenuItem_actionPerformed(null);
512 case KeyEvent.VK_DOWN:
513 if (evt.isAltDown() || !viewport.cursorMode)
515 moveSelectedSequences(false);
517 if (viewport.cursorMode)
519 alignPanel.getSeqPanel().moveCursor(0, 1);
524 if (evt.isAltDown() || !viewport.cursorMode)
526 moveSelectedSequences(true);
528 if (viewport.cursorMode)
530 alignPanel.getSeqPanel().moveCursor(0, -1);
535 case KeyEvent.VK_LEFT:
536 if (evt.isAltDown() || !viewport.cursorMode)
538 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
542 alignPanel.getSeqPanel().moveCursor(-1, 0);
547 case KeyEvent.VK_RIGHT:
548 if (evt.isAltDown() || !viewport.cursorMode)
550 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
554 alignPanel.getSeqPanel().moveCursor(1, 0);
558 case KeyEvent.VK_SPACE:
559 if (viewport.cursorMode)
561 alignPanel.getSeqPanel().insertGapAtCursor(
562 evt.isControlDown() || evt.isShiftDown()
567 // case KeyEvent.VK_A:
568 // if (viewport.cursorMode)
570 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
571 // //System.out.println("A");
575 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
576 * System.out.println("closing bracket"); } break;
578 case KeyEvent.VK_DELETE:
579 case KeyEvent.VK_BACK_SPACE:
580 if (!viewport.cursorMode)
582 cut_actionPerformed(null);
586 alignPanel.getSeqPanel().deleteGapAtCursor(
587 evt.isControlDown() || evt.isShiftDown()
594 if (viewport.cursorMode)
596 alignPanel.getSeqPanel().setCursorRow();
600 if (viewport.cursorMode && !evt.isControlDown())
602 alignPanel.getSeqPanel().setCursorColumn();
606 if (viewport.cursorMode)
608 alignPanel.getSeqPanel().setCursorPosition();
612 case KeyEvent.VK_ENTER:
613 case KeyEvent.VK_COMMA:
614 if (viewport.cursorMode)
616 alignPanel.getSeqPanel().setCursorRowAndColumn();
621 if (viewport.cursorMode)
623 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
627 if (viewport.cursorMode)
629 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
634 viewport.cursorMode = !viewport.cursorMode;
635 statusBar.setText(MessageManager.formatMessage(
636 "label.keyboard_editing_mode",
637 new String[] { (viewport.cursorMode ? "on" : "off") }));
638 if (viewport.cursorMode)
640 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
641 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
643 alignPanel.getSeqPanel().seqCanvas.repaint();
649 Help.showHelpWindow();
650 } catch (Exception ex)
652 ex.printStackTrace();
657 boolean toggleSeqs = !evt.isControlDown();
658 boolean toggleCols = !evt.isShiftDown();
659 toggleHiddenRegions(toggleSeqs, toggleCols);
664 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
665 boolean modifyExisting = true; // always modify, don't clear
666 // evt.isShiftDown();
667 boolean invertHighlighted = evt.isAltDown();
668 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
672 case KeyEvent.VK_PAGE_UP:
673 if (viewport.getWrapAlignment())
675 alignPanel.scrollUp(true);
679 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
680 - viewport.endSeq + viewport.startSeq);
683 case KeyEvent.VK_PAGE_DOWN:
684 if (viewport.getWrapAlignment())
686 alignPanel.scrollUp(false);
690 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
691 + viewport.endSeq - viewport.startSeq);
698 public void keyReleased(KeyEvent evt)
700 switch (evt.getKeyCode())
702 case KeyEvent.VK_LEFT:
703 if (evt.isAltDown() || !viewport.cursorMode)
705 viewport.firePropertyChange("alignment", null, viewport
706 .getAlignment().getSequences());
710 case KeyEvent.VK_RIGHT:
711 if (evt.isAltDown() || !viewport.cursorMode)
713 viewport.firePropertyChange("alignment", null, viewport
714 .getAlignment().getSequences());
722 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
724 ap.alignFrame = this;
725 avc = new jalview.controller.AlignViewController(this, viewport,
730 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
732 int aSize = alignPanels.size();
734 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
736 if (aSize == 1 && ap.av.viewName == null)
738 this.getContentPane().add(ap, BorderLayout.CENTER);
744 setInitialTabVisible();
747 expandViews.setEnabled(true);
748 gatherViews.setEnabled(true);
749 tabbedPane.addTab(ap.av.viewName, ap);
751 ap.setVisible(false);
756 if (ap.av.isPadGaps())
758 ap.av.getAlignment().padGaps();
760 ap.av.updateConservation(ap);
761 ap.av.updateConsensus(ap);
762 ap.av.updateStrucConsensus(ap);
766 public void setInitialTabVisible()
768 expandViews.setEnabled(true);
769 gatherViews.setEnabled(true);
770 tabbedPane.setVisible(true);
771 AlignmentPanel first = alignPanels.get(0);
772 tabbedPane.addTab(first.av.viewName, first);
773 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
776 public AlignViewport getViewport()
781 /* Set up intrinsic listeners for dynamically generated GUI bits. */
782 private void addServiceListeners()
784 final java.beans.PropertyChangeListener thisListener;
785 Desktop.instance.addJalviewPropertyChangeListener("services",
786 thisListener = new java.beans.PropertyChangeListener()
789 public void propertyChange(PropertyChangeEvent evt)
791 // // System.out.println("Discoverer property change.");
792 // if (evt.getPropertyName().equals("services"))
794 SwingUtilities.invokeLater(new Runnable()
801 .println("Rebuild WS Menu for service change");
802 BuildWebServiceMenu();
809 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
812 public void internalFrameClosed(
813 javax.swing.event.InternalFrameEvent evt)
815 // System.out.println("deregistering discoverer listener");
816 Desktop.instance.removeJalviewPropertyChangeListener("services",
818 closeMenuItem_actionPerformed(true);
821 // Finally, build the menu once to get current service state
822 new Thread(new Runnable()
827 BuildWebServiceMenu();
833 * Configure menu items that vary according to whether the alignment is
834 * nucleotide or protein
836 public void setGUINucleotide()
838 AlignmentI al = getViewport().getAlignment();
839 boolean nucleotide = al.isNucleotide();
841 showTranslation.setVisible(nucleotide);
842 showReverse.setVisible(nucleotide);
843 showReverseComplement.setVisible(nucleotide);
844 conservationMenuItem.setEnabled(!nucleotide);
845 modifyConservation.setEnabled(!nucleotide);
846 showGroupConservation.setEnabled(!nucleotide);
848 showComplementMenuItem.setText(nucleotide ? MessageManager
849 .getString("label.protein") : MessageManager
850 .getString("label.nucleotide"));
854 * set up menus for the current viewport. This may be called after any
855 * operation that affects the data in the current view (selection changed,
856 * etc) to update the menus to reflect the new state.
859 public void setMenusForViewport()
861 setMenusFromViewport(viewport);
865 * Need to call this method when tabs are selected for multiple views, or when
866 * loading from Jalview2XML.java
871 void setMenusFromViewport(AlignViewport av)
873 padGapsMenuitem.setSelected(av.isPadGaps());
874 colourTextMenuItem.setSelected(av.isShowColourText());
875 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
876 conservationMenuItem.setSelected(av.getConservationSelected());
877 seqLimits.setSelected(av.getShowJVSuffix());
878 idRightAlign.setSelected(av.isRightAlignIds());
879 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
880 renderGapsMenuItem.setSelected(av.isRenderGaps());
881 wrapMenuItem.setSelected(av.getWrapAlignment());
882 scaleAbove.setVisible(av.getWrapAlignment());
883 scaleLeft.setVisible(av.getWrapAlignment());
884 scaleRight.setVisible(av.getWrapAlignment());
885 annotationPanelMenuItem.setState(av.isShowAnnotation());
887 * Show/hide annotations only enabled if annotation panel is shown
889 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
890 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
891 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
892 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
893 viewBoxesMenuItem.setSelected(av.getShowBoxes());
894 viewTextMenuItem.setSelected(av.getShowText());
895 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
896 showGroupConsensus.setSelected(av.isShowGroupConsensus());
897 showGroupConservation.setSelected(av.isShowGroupConservation());
898 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
899 showSequenceLogo.setSelected(av.isShowSequenceLogo());
900 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
902 ColourMenuHelper.setColourSelected(colourMenu,
903 av.getGlobalColourScheme());
905 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
906 hiddenMarkers.setState(av.getShowHiddenMarkers());
907 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
908 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
909 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
910 autoCalculate.setSelected(av.autoCalculateConsensus);
911 sortByTree.setSelected(av.sortByTree);
912 listenToViewSelections.setSelected(av.followSelection);
914 showProducts.setEnabled(canShowProducts());
915 setGroovyEnabled(Desktop.getGroovyConsole() != null);
921 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
925 public void setGroovyEnabled(boolean b)
927 runGroovy.setEnabled(b);
930 private IProgressIndicator progressBar;
935 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
938 public void setProgressBar(String message, long id)
940 progressBar.setProgressBar(message, id);
944 public void registerHandler(final long id,
945 final IProgressIndicatorHandler handler)
947 progressBar.registerHandler(id, handler);
952 * @return true if any progress bars are still active
955 public boolean operationInProgress()
957 return progressBar.operationInProgress();
961 public void setStatus(String text)
963 statusBar.setText(text);
967 * Added so Castor Mapping file can obtain Jalview Version
969 public String getVersion()
971 return jalview.bin.Cache.getProperty("VERSION");
974 public FeatureRenderer getFeatureRenderer()
976 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
980 public void fetchSequence_actionPerformed(ActionEvent e)
982 new jalview.gui.SequenceFetcher(this);
986 public void addFromFile_actionPerformed(ActionEvent e)
988 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
992 public void reload_actionPerformed(ActionEvent e)
994 if (fileName != null)
996 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
997 // originating file's format
998 // TODO: work out how to recover feature settings for correct view(s) when
1000 if (FileFormat.Jalview.equals(currentFileFormat))
1002 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1003 for (int i = 0; i < frames.length; i++)
1005 if (frames[i] instanceof AlignFrame && frames[i] != this
1006 && ((AlignFrame) frames[i]).fileName != null
1007 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1011 frames[i].setSelected(true);
1012 Desktop.instance.closeAssociatedWindows();
1013 } catch (java.beans.PropertyVetoException ex)
1019 Desktop.instance.closeAssociatedWindows();
1021 FileLoader loader = new FileLoader();
1022 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1023 : DataSourceType.FILE;
1024 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1028 Rectangle bounds = this.getBounds();
1030 FileLoader loader = new FileLoader();
1031 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1032 : DataSourceType.FILE;
1033 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1034 protocol, currentFileFormat);
1036 newframe.setBounds(bounds);
1037 if (featureSettings != null && featureSettings.isShowing())
1039 final Rectangle fspos = featureSettings.frame.getBounds();
1040 // TODO: need a 'show feature settings' function that takes bounds -
1041 // need to refactor Desktop.addFrame
1042 newframe.featureSettings_actionPerformed(null);
1043 final FeatureSettings nfs = newframe.featureSettings;
1044 SwingUtilities.invokeLater(new Runnable()
1049 nfs.frame.setBounds(fspos);
1052 this.featureSettings.close();
1053 this.featureSettings = null;
1055 this.closeMenuItem_actionPerformed(true);
1061 public void addFromText_actionPerformed(ActionEvent e)
1063 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1068 public void addFromURL_actionPerformed(ActionEvent e)
1070 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1074 public void save_actionPerformed(ActionEvent e)
1076 if (fileName == null || (currentFileFormat == null)
1077 || fileName.startsWith("http"))
1079 saveAs_actionPerformed(null);
1083 saveAlignment(fileName, currentFileFormat);
1094 public void saveAs_actionPerformed(ActionEvent e)
1096 String format = currentFileFormat == null ? null : currentFileFormat
1098 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1099 Cache.getProperty("LAST_DIRECTORY"), format);
1101 chooser.setFileView(new JalviewFileView());
1102 chooser.setDialogTitle(MessageManager
1103 .getString("label.save_alignment_to_file"));
1104 chooser.setToolTipText(MessageManager.getString("action.save"));
1106 int value = chooser.showSaveDialog(this);
1108 if (value == JalviewFileChooser.APPROVE_OPTION)
1110 currentFileFormat = chooser.getSelectedFormat();
1111 while (currentFileFormat == null)
1114 .showInternalMessageDialog(
1117 .getString("label.select_file_format_before_saving"),
1119 .getString("label.file_format_not_specified"),
1120 JvOptionPane.WARNING_MESSAGE);
1121 currentFileFormat = chooser.getSelectedFormat();
1122 value = chooser.showSaveDialog(this);
1123 if (value != JalviewFileChooser.APPROVE_OPTION)
1129 fileName = chooser.getSelectedFile().getPath();
1131 Cache.setProperty("DEFAULT_FILE_FORMAT",
1132 currentFileFormat.toString());
1134 Cache.setProperty("LAST_DIRECTORY", fileName);
1135 saveAlignment(fileName, currentFileFormat);
1139 public boolean saveAlignment(String file, FileFormatI format)
1141 boolean success = true;
1143 if (FileFormat.Jalview.equals(format))
1145 String shortName = title;
1147 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1149 shortName = shortName.substring(shortName
1150 .lastIndexOf(java.io.File.separatorChar) + 1);
1153 success = new Jalview2XML().saveAlignment(this, file, shortName);
1155 statusBar.setText(MessageManager.formatMessage(
1156 "label.successfully_saved_to_file_in_format", new Object[] {
1157 fileName, format }));
1162 // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1164 // warningMessage("Cannot save file " + fileName + " using format "
1165 // + format, "Alignment output format not supported");
1166 // if (!Jalview.isHeadlessMode())
1168 // saveAs_actionPerformed(null);
1173 AlignmentExportData exportData = getAlignmentForExport(format,
1175 if (exportData.getSettings().isCancelled())
1179 FormatAdapter f = new FormatAdapter(alignPanel,
1180 exportData.getSettings());
1181 String output = f.formatSequences(
1183 exportData.getAlignment(), // class cast exceptions will
1184 // occur in the distant future
1185 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1186 f.getCacheSuffixDefault(format),
1187 viewport.getColumnSelection());
1197 java.io.PrintWriter out = new java.io.PrintWriter(
1198 new java.io.FileWriter(file));
1202 this.setTitle(file);
1203 statusBar.setText(MessageManager.formatMessage(
1204 "label.successfully_saved_to_file_in_format",
1205 new Object[] { fileName, format }));
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)
1251 FileFormatI fileFormat = FileFormat.forName(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,
1265 exportData.getAlignment(),
1266 exportData.getOmitHidden(),
1267 exportData.getStartEndPostions(),
1268 viewport.getColumnSelection()));
1269 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1270 "label.alignment_output_command",
1271 new Object[] { e.getActionCommand() }), 600, 500);
1272 } catch (OutOfMemoryError oom)
1274 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1280 public static AlignmentExportData getAlignmentForExport(
1281 FileFormatI format, AlignViewportI viewport,
1282 AlignExportSettingI exportSettings)
1284 AlignmentI alignmentToExport = null;
1285 AlignExportSettingI settings = exportSettings;
1286 String[] omitHidden = null;
1288 HiddenSequences hiddenSeqs = viewport.getAlignment()
1289 .getHiddenSequences();
1291 alignmentToExport = viewport.getAlignment();
1293 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1294 if (settings == null)
1296 settings = new AlignExportSettings(hasHiddenSeqs,
1297 viewport.hasHiddenColumns(), format);
1299 // settings.isExportAnnotations();
1301 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1303 omitHidden = viewport.getViewAsString(false,
1304 settings.isExportHiddenSequences());
1307 int[] alignmentStartEnd = new int[2];
1308 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1310 alignmentToExport = hiddenSeqs.getFullAlignment();
1314 alignmentToExport = viewport.getAlignment();
1316 alignmentStartEnd = alignmentToExport
1317 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1318 .getHiddenColumns());
1319 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1320 omitHidden, alignmentStartEnd, settings);
1331 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1333 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1334 htmlSVG.exportHTML(null);
1338 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1340 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1341 bjs.exportHTML(null);
1344 public void createImageMap(File file, String image)
1346 alignPanel.makePNGImageMap(file, image);
1356 public void createPNG(File f)
1358 alignPanel.makePNG(f);
1368 public void createEPS(File f)
1370 alignPanel.makeEPS(f);
1374 public void createSVG(File f)
1376 alignPanel.makeSVG(f);
1380 public void pageSetup_actionPerformed(ActionEvent e)
1382 PrinterJob printJob = PrinterJob.getPrinterJob();
1383 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1393 public void printMenuItem_actionPerformed(ActionEvent e)
1395 // Putting in a thread avoids Swing painting problems
1396 PrintThread thread = new PrintThread(alignPanel);
1401 public void exportFeatures_actionPerformed(ActionEvent e)
1403 new AnnotationExporter().exportFeatures(alignPanel);
1407 public void exportAnnotations_actionPerformed(ActionEvent e)
1409 new AnnotationExporter().exportAnnotations(alignPanel);
1413 public void associatedData_actionPerformed(ActionEvent e)
1415 // Pick the tree file
1416 JalviewFileChooser chooser = new JalviewFileChooser(
1417 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1418 chooser.setFileView(new JalviewFileView());
1419 chooser.setDialogTitle(MessageManager
1420 .getString("label.load_jalview_annotations"));
1421 chooser.setToolTipText(MessageManager
1422 .getString("label.load_jalview_annotations"));
1424 int value = chooser.showOpenDialog(null);
1426 if (value == JalviewFileChooser.APPROVE_OPTION)
1428 String choice = chooser.getSelectedFile().getPath();
1429 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1430 loadJalviewDataFile(choice, null, null, null);
1436 * Close the current view or all views in the alignment frame. If the frame
1437 * only contains one view then the alignment will be removed from memory.
1439 * @param closeAllTabs
1442 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1444 if (alignPanels != null && alignPanels.size() < 2)
1446 closeAllTabs = true;
1451 if (alignPanels != null)
1455 if (this.isClosed())
1457 // really close all the windows - otherwise wait till
1458 // setClosed(true) is called
1459 for (int i = 0; i < alignPanels.size(); i++)
1461 AlignmentPanel ap = alignPanels.get(i);
1468 closeView(alignPanel);
1475 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1476 * be called recursively, with the frame now in 'closed' state
1478 this.setClosed(true);
1480 } catch (Exception ex)
1482 ex.printStackTrace();
1487 * Close the specified panel and close up tabs appropriately.
1489 * @param panelToClose
1491 public void closeView(AlignmentPanel panelToClose)
1493 int index = tabbedPane.getSelectedIndex();
1494 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1495 alignPanels.remove(panelToClose);
1496 panelToClose.closePanel();
1497 panelToClose = null;
1499 tabbedPane.removeTabAt(closedindex);
1500 tabbedPane.validate();
1502 if (index > closedindex || index == tabbedPane.getTabCount())
1504 // modify currently selected tab index if necessary.
1508 this.tabSelectionChanged(index);
1514 void updateEditMenuBar()
1517 if (viewport.getHistoryList().size() > 0)
1519 undoMenuItem.setEnabled(true);
1520 CommandI command = viewport.getHistoryList().peek();
1521 undoMenuItem.setText(MessageManager.formatMessage(
1522 "label.undo_command",
1523 new Object[] { command.getDescription() }));
1527 undoMenuItem.setEnabled(false);
1528 undoMenuItem.setText(MessageManager.getString("action.undo"));
1531 if (viewport.getRedoList().size() > 0)
1533 redoMenuItem.setEnabled(true);
1535 CommandI command = viewport.getRedoList().peek();
1536 redoMenuItem.setText(MessageManager.formatMessage(
1537 "label.redo_command",
1538 new Object[] { command.getDescription() }));
1542 redoMenuItem.setEnabled(false);
1543 redoMenuItem.setText(MessageManager.getString("action.redo"));
1548 public void addHistoryItem(CommandI command)
1550 if (command.getSize() > 0)
1552 viewport.addToHistoryList(command);
1553 viewport.clearRedoList();
1554 updateEditMenuBar();
1555 viewport.updateHiddenColumns();
1556 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1557 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1558 // viewport.getColumnSelection()
1559 // .getHiddenColumns().size() > 0);
1565 * @return alignment objects for all views
1567 AlignmentI[] getViewAlignments()
1569 if (alignPanels != null)
1571 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1573 for (AlignmentPanel ap : alignPanels)
1575 als[i++] = ap.av.getAlignment();
1579 if (viewport != null)
1581 return new AlignmentI[] { viewport.getAlignment() };
1593 protected void undoMenuItem_actionPerformed(ActionEvent e)
1595 if (viewport.getHistoryList().isEmpty())
1599 CommandI command = viewport.getHistoryList().pop();
1600 viewport.addToRedoList(command);
1601 command.undoCommand(getViewAlignments());
1603 AlignmentViewport originalSource = getOriginatingSource(command);
1604 updateEditMenuBar();
1606 if (originalSource != null)
1608 if (originalSource != viewport)
1611 .warn("Implementation worry: mismatch of viewport origin for undo");
1613 originalSource.updateHiddenColumns();
1614 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1616 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1617 // viewport.getColumnSelection()
1618 // .getHiddenColumns().size() > 0);
1619 originalSource.firePropertyChange("alignment", null, originalSource
1620 .getAlignment().getSequences());
1631 protected void redoMenuItem_actionPerformed(ActionEvent e)
1633 if (viewport.getRedoList().size() < 1)
1638 CommandI command = viewport.getRedoList().pop();
1639 viewport.addToHistoryList(command);
1640 command.doCommand(getViewAlignments());
1642 AlignmentViewport originalSource = getOriginatingSource(command);
1643 updateEditMenuBar();
1645 if (originalSource != null)
1648 if (originalSource != viewport)
1651 .warn("Implementation worry: mismatch of viewport origin for redo");
1653 originalSource.updateHiddenColumns();
1654 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1656 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1657 // viewport.getColumnSelection()
1658 // .getHiddenColumns().size() > 0);
1659 originalSource.firePropertyChange("alignment", null, originalSource
1660 .getAlignment().getSequences());
1664 AlignmentViewport getOriginatingSource(CommandI command)
1666 AlignmentViewport originalSource = null;
1667 // For sequence removal and addition, we need to fire
1668 // the property change event FROM the viewport where the
1669 // original alignment was altered
1670 AlignmentI al = null;
1671 if (command instanceof EditCommand)
1673 EditCommand editCommand = (EditCommand) command;
1674 al = editCommand.getAlignment();
1675 List<Component> comps = PaintRefresher.components.get(viewport
1676 .getSequenceSetId());
1678 for (Component comp : comps)
1680 if (comp instanceof AlignmentPanel)
1682 if (al == ((AlignmentPanel) comp).av.getAlignment())
1684 originalSource = ((AlignmentPanel) comp).av;
1691 if (originalSource == null)
1693 // The original view is closed, we must validate
1694 // the current view against the closed view first
1697 PaintRefresher.validateSequences(al, viewport.getAlignment());
1700 originalSource = viewport;
1703 return originalSource;
1712 public void moveSelectedSequences(boolean up)
1714 SequenceGroup sg = viewport.getSelectionGroup();
1720 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1721 viewport.getHiddenRepSequences(), up);
1722 alignPanel.paintAlignment(true);
1725 synchronized void slideSequences(boolean right, int size)
1727 List<SequenceI> sg = new ArrayList<SequenceI>();
1728 if (viewport.cursorMode)
1730 sg.add(viewport.getAlignment().getSequenceAt(
1731 alignPanel.getSeqPanel().seqCanvas.cursorY));
1733 else if (viewport.getSelectionGroup() != null
1734 && viewport.getSelectionGroup().getSize() != viewport
1735 .getAlignment().getHeight())
1737 sg = viewport.getSelectionGroup().getSequences(
1738 viewport.getHiddenRepSequences());
1746 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1748 for (SequenceI seq : viewport.getAlignment().getSequences())
1750 if (!sg.contains(seq))
1752 invertGroup.add(seq);
1756 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1758 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1759 for (int i = 0; i < invertGroup.size(); i++)
1761 seqs2[i] = invertGroup.get(i);
1764 SlideSequencesCommand ssc;
1767 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1768 size, viewport.getGapCharacter());
1772 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1773 size, viewport.getGapCharacter());
1776 int groupAdjustment = 0;
1777 if (ssc.getGapsInsertedBegin() && right)
1779 if (viewport.cursorMode)
1781 alignPanel.getSeqPanel().moveCursor(size, 0);
1785 groupAdjustment = size;
1788 else if (!ssc.getGapsInsertedBegin() && !right)
1790 if (viewport.cursorMode)
1792 alignPanel.getSeqPanel().moveCursor(-size, 0);
1796 groupAdjustment = -size;
1800 if (groupAdjustment != 0)
1802 viewport.getSelectionGroup().setStartRes(
1803 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1804 viewport.getSelectionGroup().setEndRes(
1805 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1809 * just extend the last slide command if compatible; but not if in
1810 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1812 boolean appendHistoryItem = false;
1813 Deque<CommandI> historyList = viewport.getHistoryList();
1814 boolean inSplitFrame = getSplitViewContainer() != null;
1815 if (!inSplitFrame && historyList != null && historyList.size() > 0
1816 && historyList.peek() instanceof SlideSequencesCommand)
1818 appendHistoryItem = ssc
1819 .appendSlideCommand((SlideSequencesCommand) historyList
1823 if (!appendHistoryItem)
1825 addHistoryItem(ssc);
1838 protected void copy_actionPerformed(ActionEvent e)
1841 if (viewport.getSelectionGroup() == null)
1845 // TODO: preserve the ordering of displayed alignment annotation in any
1846 // internal paste (particularly sequence associated annotation)
1847 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1848 String[] omitHidden = null;
1850 if (viewport.hasHiddenColumns())
1852 omitHidden = viewport.getViewAsString(true);
1855 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1859 StringSelection ss = new StringSelection(output);
1863 jalview.gui.Desktop.internalCopy = true;
1864 // Its really worth setting the clipboard contents
1865 // to empty before setting the large StringSelection!!
1866 Toolkit.getDefaultToolkit().getSystemClipboard()
1867 .setContents(new StringSelection(""), null);
1869 Toolkit.getDefaultToolkit().getSystemClipboard()
1870 .setContents(ss, Desktop.instance);
1871 } catch (OutOfMemoryError er)
1873 new OOMWarning("copying region", er);
1877 ArrayList<int[]> hiddenColumns = null;
1878 if (viewport.hasHiddenColumns())
1880 hiddenColumns = new ArrayList<int[]>();
1881 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1882 .getSelectionGroup().getEndRes();
1883 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1885 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1887 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1888 region[1] - hiddenOffset });
1893 Desktop.jalviewClipboard = new Object[] { seqs,
1894 viewport.getAlignment().getDataset(), hiddenColumns };
1895 statusBar.setText(MessageManager.formatMessage(
1896 "label.copied_sequences_to_clipboard", new Object[] { Integer
1897 .valueOf(seqs.length).toString() }));
1907 protected void pasteNew_actionPerformed(ActionEvent e)
1919 protected void pasteThis_actionPerformed(ActionEvent e)
1925 * Paste contents of Jalview clipboard
1927 * @param newAlignment
1928 * true to paste to a new alignment, otherwise add to this.
1930 void paste(boolean newAlignment)
1932 boolean externalPaste = true;
1935 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1936 Transferable contents = c.getContents(this);
1938 if (contents == null)
1947 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1948 if (str.length() < 1)
1953 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1955 } catch (OutOfMemoryError er)
1957 new OOMWarning("Out of memory pasting sequences!!", er);
1961 SequenceI[] sequences;
1962 boolean annotationAdded = false;
1963 AlignmentI alignment = null;
1965 if (Desktop.jalviewClipboard != null)
1967 // The clipboard was filled from within Jalview, we must use the
1969 // And dataset from the copied alignment
1970 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1971 // be doubly sure that we create *new* sequence objects.
1972 sequences = new SequenceI[newseq.length];
1973 for (int i = 0; i < newseq.length; i++)
1975 sequences[i] = new Sequence(newseq[i]);
1977 alignment = new Alignment(sequences);
1978 externalPaste = false;
1982 // parse the clipboard as an alignment.
1983 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1985 sequences = alignment.getSequencesArray();
1989 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1995 if (Desktop.jalviewClipboard != null)
1997 // dataset is inherited
1998 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2002 // new dataset is constructed
2003 alignment.setDataset(null);
2005 alwidth = alignment.getWidth() + 1;
2009 AlignmentI pastedal = alignment; // preserve pasted alignment object
2010 // Add pasted sequences and dataset into existing alignment.
2011 alignment = viewport.getAlignment();
2012 alwidth = alignment.getWidth() + 1;
2013 // decide if we need to import sequences from an existing dataset
2014 boolean importDs = Desktop.jalviewClipboard != null
2015 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2016 // importDs==true instructs us to copy over new dataset sequences from
2017 // an existing alignment
2018 Vector newDs = (importDs) ? new Vector() : null; // used to create
2019 // minimum dataset set
2021 for (int i = 0; i < sequences.length; i++)
2025 newDs.addElement(null);
2027 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2029 if (importDs && ds != null)
2031 if (!newDs.contains(ds))
2033 newDs.setElementAt(ds, i);
2034 ds = new Sequence(ds);
2035 // update with new dataset sequence
2036 sequences[i].setDatasetSequence(ds);
2040 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2045 // copy and derive new dataset sequence
2046 sequences[i] = sequences[i].deriveSequence();
2047 alignment.getDataset().addSequence(
2048 sequences[i].getDatasetSequence());
2049 // TODO: avoid creation of duplicate dataset sequences with a
2050 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2052 alignment.addSequence(sequences[i]); // merges dataset
2056 newDs.clear(); // tidy up
2058 if (alignment.getAlignmentAnnotation() != null)
2060 for (AlignmentAnnotation alan : alignment
2061 .getAlignmentAnnotation())
2063 if (alan.graphGroup > fgroup)
2065 fgroup = alan.graphGroup;
2069 if (pastedal.getAlignmentAnnotation() != null)
2071 // Add any annotation attached to alignment.
2072 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2073 for (int i = 0; i < alann.length; i++)
2075 annotationAdded = true;
2076 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2078 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2079 if (newann.graphGroup > -1)
2081 if (newGraphGroups.size() <= newann.graphGroup
2082 || newGraphGroups.get(newann.graphGroup) == null)
2084 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2086 newGraphGroups.add(q, null);
2088 newGraphGroups.set(newann.graphGroup, new Integer(
2091 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2095 newann.padAnnotation(alwidth);
2096 alignment.addAnnotation(newann);
2106 addHistoryItem(new EditCommand(
2107 MessageManager.getString("label.add_sequences"),
2108 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2110 // Add any annotations attached to sequences
2111 for (int i = 0; i < sequences.length; i++)
2113 if (sequences[i].getAnnotation() != null)
2115 AlignmentAnnotation newann;
2116 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2118 annotationAdded = true;
2119 newann = sequences[i].getAnnotation()[a];
2120 newann.adjustForAlignment();
2121 newann.padAnnotation(alwidth);
2122 if (newann.graphGroup > -1)
2124 if (newann.graphGroup > -1)
2126 if (newGraphGroups.size() <= newann.graphGroup
2127 || newGraphGroups.get(newann.graphGroup) == null)
2129 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2131 newGraphGroups.add(q, null);
2133 newGraphGroups.set(newann.graphGroup, new Integer(
2136 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2140 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2145 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2152 // propagate alignment changed.
2153 viewport.setEndSeq(alignment.getHeight());
2154 if (annotationAdded)
2156 // Duplicate sequence annotation in all views.
2157 AlignmentI[] alview = this.getViewAlignments();
2158 for (int i = 0; i < sequences.length; i++)
2160 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2165 for (int avnum = 0; avnum < alview.length; avnum++)
2167 if (alview[avnum] != alignment)
2169 // duplicate in a view other than the one with input focus
2170 int avwidth = alview[avnum].getWidth() + 1;
2171 // this relies on sann being preserved after we
2172 // modify the sequence's annotation array for each duplication
2173 for (int a = 0; a < sann.length; a++)
2175 AlignmentAnnotation newann = new AlignmentAnnotation(
2177 sequences[i].addAlignmentAnnotation(newann);
2178 newann.padAnnotation(avwidth);
2179 alview[avnum].addAnnotation(newann); // annotation was
2180 // duplicated earlier
2181 // TODO JAL-1145 graphGroups are not updated for sequence
2182 // annotation added to several views. This may cause
2184 alview[avnum].setAnnotationIndex(newann, a);
2189 buildSortByAnnotationScoresMenu();
2191 viewport.firePropertyChange("alignment", null,
2192 alignment.getSequences());
2193 if (alignPanels != null)
2195 for (AlignmentPanel ap : alignPanels)
2197 ap.validateAnnotationDimensions(false);
2202 alignPanel.validateAnnotationDimensions(false);
2208 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2210 String newtitle = new String("Copied sequences");
2212 if (Desktop.jalviewClipboard != null
2213 && Desktop.jalviewClipboard[2] != null)
2215 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2216 for (int[] region : hc)
2218 af.viewport.hideColumns(region[0], region[1]);
2222 // >>>This is a fix for the moment, until a better solution is
2224 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2226 alignPanel.getSeqPanel().seqCanvas
2227 .getFeatureRenderer());
2229 // TODO: maintain provenance of an alignment, rather than just make the
2230 // title a concatenation of operations.
2233 if (title.startsWith("Copied sequences"))
2239 newtitle = newtitle.concat("- from " + title);
2244 newtitle = new String("Pasted sequences");
2247 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2252 } catch (Exception ex)
2254 ex.printStackTrace();
2255 System.out.println("Exception whilst pasting: " + ex);
2256 // could be anything being pasted in here
2262 protected void expand_newalign(ActionEvent e)
2266 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2267 .getAlignment(), -1);
2268 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2270 String newtitle = new String("Flanking alignment");
2272 if (Desktop.jalviewClipboard != null
2273 && Desktop.jalviewClipboard[2] != null)
2275 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2276 for (int region[] : hc)
2278 af.viewport.hideColumns(region[0], region[1]);
2282 // >>>This is a fix for the moment, until a better solution is
2284 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2286 alignPanel.getSeqPanel().seqCanvas
2287 .getFeatureRenderer());
2289 // TODO: maintain provenance of an alignment, rather than just make the
2290 // title a concatenation of operations.
2292 if (title.startsWith("Copied sequences"))
2298 newtitle = newtitle.concat("- from " + title);
2302 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2304 } catch (Exception ex)
2306 ex.printStackTrace();
2307 System.out.println("Exception whilst pasting: " + ex);
2308 // could be anything being pasted in here
2309 } catch (OutOfMemoryError oom)
2311 new OOMWarning("Viewing flanking region of alignment", oom);
2322 protected void cut_actionPerformed(ActionEvent e)
2324 copy_actionPerformed(null);
2325 delete_actionPerformed(null);
2335 protected void delete_actionPerformed(ActionEvent evt)
2338 SequenceGroup sg = viewport.getSelectionGroup();
2345 * If the cut affects all sequences, warn, remove highlighted columns
2347 if (sg.getSize() == viewport.getAlignment().getHeight())
2349 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2350 .getAlignment().getWidth()) ? true : false;
2351 if (isEntireAlignWidth)
2353 int confirm = JvOptionPane.showConfirmDialog(this,
2354 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2355 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2356 JvOptionPane.OK_CANCEL_OPTION);
2358 if (confirm == JvOptionPane.CANCEL_OPTION
2359 || confirm == JvOptionPane.CLOSED_OPTION)
2364 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2365 sg.getEndRes() + 1);
2367 SequenceI[] cut = sg.getSequences()
2368 .toArray(new SequenceI[sg.getSize()]);
2370 addHistoryItem(new EditCommand(
2371 MessageManager.getString("label.cut_sequences"), Action.CUT,
2372 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2373 viewport.getAlignment()));
2375 viewport.setSelectionGroup(null);
2376 viewport.sendSelection();
2377 viewport.getAlignment().deleteGroup(sg);
2379 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2381 if (viewport.getAlignment().getHeight() < 1)
2385 this.setClosed(true);
2386 } catch (Exception ex)
2399 protected void deleteGroups_actionPerformed(ActionEvent e)
2401 if (avc.deleteGroups())
2403 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2404 alignPanel.updateAnnotation();
2405 alignPanel.paintAlignment(true);
2416 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2418 SequenceGroup sg = new SequenceGroup();
2420 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2422 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2425 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2426 viewport.setSelectionGroup(sg);
2427 viewport.sendSelection();
2428 // JAL-2034 - should delegate to
2429 // alignPanel to decide if overview needs
2431 alignPanel.paintAlignment(false);
2432 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2442 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2444 if (viewport.cursorMode)
2446 alignPanel.getSeqPanel().keyboardNo1 = null;
2447 alignPanel.getSeqPanel().keyboardNo2 = null;
2449 viewport.setSelectionGroup(null);
2450 viewport.getColumnSelection().clear();
2451 viewport.setSelectionGroup(null);
2452 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2453 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2454 // JAL-2034 - should delegate to
2455 // alignPanel to decide if overview needs
2457 alignPanel.paintAlignment(false);
2458 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2459 viewport.sendSelection();
2469 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2471 SequenceGroup sg = viewport.getSelectionGroup();
2475 selectAllSequenceMenuItem_actionPerformed(null);
2480 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2482 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2484 // JAL-2034 - should delegate to
2485 // alignPanel to decide if overview needs
2488 alignPanel.paintAlignment(true);
2489 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2490 viewport.sendSelection();
2494 public void invertColSel_actionPerformed(ActionEvent e)
2496 viewport.invertColumnSelection();
2497 alignPanel.paintAlignment(true);
2498 viewport.sendSelection();
2508 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2510 trimAlignment(true);
2520 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2522 trimAlignment(false);
2525 void trimAlignment(boolean trimLeft)
2527 ColumnSelection colSel = viewport.getColumnSelection();
2530 if (!colSel.isEmpty())
2534 column = colSel.getMin();
2538 column = colSel.getMax();
2542 if (viewport.getSelectionGroup() != null)
2544 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2545 viewport.getHiddenRepSequences());
2549 seqs = viewport.getAlignment().getSequencesArray();
2552 TrimRegionCommand trimRegion;
2555 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2556 column, viewport.getAlignment());
2557 viewport.setStartRes(0);
2561 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2562 column, viewport.getAlignment());
2565 statusBar.setText(MessageManager.formatMessage(
2566 "label.removed_columns",
2567 new String[] { Integer.valueOf(trimRegion.getSize())
2570 addHistoryItem(trimRegion);
2572 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2574 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2575 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2577 viewport.getAlignment().deleteGroup(sg);
2581 viewport.firePropertyChange("alignment", null, viewport
2582 .getAlignment().getSequences());
2593 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2595 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2598 if (viewport.getSelectionGroup() != null)
2600 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2601 viewport.getHiddenRepSequences());
2602 start = viewport.getSelectionGroup().getStartRes();
2603 end = viewport.getSelectionGroup().getEndRes();
2607 seqs = viewport.getAlignment().getSequencesArray();
2610 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2611 "Remove Gapped Columns", seqs, start, end,
2612 viewport.getAlignment());
2614 addHistoryItem(removeGapCols);
2616 statusBar.setText(MessageManager.formatMessage(
2617 "label.removed_empty_columns",
2618 new Object[] { Integer.valueOf(removeGapCols.getSize())
2621 // This is to maintain viewport position on first residue
2622 // of first sequence
2623 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2624 int startRes = seq.findPosition(viewport.startRes);
2625 // ShiftList shifts;
2626 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2627 // edit.alColumnChanges=shifts.getInverse();
2628 // if (viewport.hasHiddenColumns)
2629 // viewport.getColumnSelection().compensateForEdits(shifts);
2630 viewport.setStartRes(seq.findIndex(startRes) - 1);
2631 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2643 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2645 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2648 if (viewport.getSelectionGroup() != null)
2650 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2651 viewport.getHiddenRepSequences());
2652 start = viewport.getSelectionGroup().getStartRes();
2653 end = viewport.getSelectionGroup().getEndRes();
2657 seqs = viewport.getAlignment().getSequencesArray();
2660 // This is to maintain viewport position on first residue
2661 // of first sequence
2662 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2663 int startRes = seq.findPosition(viewport.startRes);
2665 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2666 viewport.getAlignment()));
2668 viewport.setStartRes(seq.findIndex(startRes) - 1);
2670 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2682 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2684 viewport.setPadGaps(padGapsMenuitem.isSelected());
2685 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2696 public void findMenuItem_actionPerformed(ActionEvent e)
2702 * Create a new view of the current alignment.
2705 public void newView_actionPerformed(ActionEvent e)
2707 newView(null, true);
2711 * Creates and shows a new view of the current alignment.
2714 * title of newly created view; if null, one will be generated
2715 * @param copyAnnotation
2716 * if true then duplicate all annnotation, groups and settings
2717 * @return new alignment panel, already displayed.
2719 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2722 * Create a new AlignmentPanel (with its own, new Viewport)
2724 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2726 if (!copyAnnotation)
2729 * remove all groups and annotation except for the automatic stuff
2731 newap.av.getAlignment().deleteAllGroups();
2732 newap.av.getAlignment().deleteAllAnnotations(false);
2735 newap.av.setGatherViewsHere(false);
2737 if (viewport.viewName == null)
2739 viewport.viewName = MessageManager
2740 .getString("label.view_name_original");
2744 * Views share the same edits undo and redo stacks
2746 newap.av.setHistoryList(viewport.getHistoryList());
2747 newap.av.setRedoList(viewport.getRedoList());
2750 * Views share the same mappings; need to deregister any new mappings
2751 * created by copyAlignPanel, and register the new reference to the shared
2754 newap.av.replaceMappings(viewport.getAlignment());
2756 newap.av.viewName = getNewViewName(viewTitle);
2758 addAlignmentPanel(newap, true);
2759 newap.alignmentChanged();
2761 if (alignPanels.size() == 2)
2763 viewport.setGatherViewsHere(true);
2765 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2770 * Make a new name for the view, ensuring it is unique within the current
2771 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2772 * these now use viewId. Unique view names are still desirable for usability.)
2777 protected String getNewViewName(String viewTitle)
2779 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2780 boolean addFirstIndex = false;
2781 if (viewTitle == null || viewTitle.trim().length() == 0)
2783 viewTitle = MessageManager.getString("action.view");
2784 addFirstIndex = true;
2788 index = 1;// we count from 1 if given a specific name
2790 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2792 List<Component> comps = PaintRefresher.components.get(viewport
2793 .getSequenceSetId());
2795 List<String> existingNames = getExistingViewNames(comps);
2797 while (existingNames.contains(newViewName))
2799 newViewName = viewTitle + " " + (++index);
2805 * Returns a list of distinct view names found in the given list of
2806 * components. View names are held on the viewport of an AlignmentPanel.
2811 protected List<String> getExistingViewNames(List<Component> comps)
2813 List<String> existingNames = new ArrayList<String>();
2814 for (Component comp : comps)
2816 if (comp instanceof AlignmentPanel)
2818 AlignmentPanel ap = (AlignmentPanel) comp;
2819 if (!existingNames.contains(ap.av.viewName))
2821 existingNames.add(ap.av.viewName);
2825 return existingNames;
2829 * Explode tabbed views into separate windows.
2832 public void expandViews_actionPerformed(ActionEvent e)
2834 Desktop.explodeViews(this);
2838 * Gather views in separate windows back into a tabbed presentation.
2841 public void gatherViews_actionPerformed(ActionEvent e)
2843 Desktop.instance.gatherViews(this);
2853 public void font_actionPerformed(ActionEvent e)
2855 new FontChooser(alignPanel);
2865 protected void seqLimit_actionPerformed(ActionEvent e)
2867 viewport.setShowJVSuffix(seqLimits.isSelected());
2869 alignPanel.getIdPanel().getIdCanvas()
2870 .setPreferredSize(alignPanel.calculateIdWidth());
2871 alignPanel.paintAlignment(true);
2875 public void idRightAlign_actionPerformed(ActionEvent e)
2877 viewport.setRightAlignIds(idRightAlign.isSelected());
2878 alignPanel.paintAlignment(true);
2882 public void centreColumnLabels_actionPerformed(ActionEvent e)
2884 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2885 alignPanel.paintAlignment(true);
2891 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2894 protected void followHighlight_actionPerformed()
2897 * Set the 'follow' flag on the Viewport (and scroll to position if now
2900 final boolean state = this.followHighlightMenuItem.getState();
2901 viewport.setFollowHighlight(state);
2904 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2915 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2917 viewport.setColourText(colourTextMenuItem.isSelected());
2918 alignPanel.paintAlignment(true);
2928 public void wrapMenuItem_actionPerformed(ActionEvent e)
2930 scaleAbove.setVisible(wrapMenuItem.isSelected());
2931 scaleLeft.setVisible(wrapMenuItem.isSelected());
2932 scaleRight.setVisible(wrapMenuItem.isSelected());
2933 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2934 alignPanel.updateLayout();
2938 public void showAllSeqs_actionPerformed(ActionEvent e)
2940 viewport.showAllHiddenSeqs();
2944 public void showAllColumns_actionPerformed(ActionEvent e)
2946 viewport.showAllHiddenColumns();
2948 viewport.sendSelection();
2952 public void hideSelSequences_actionPerformed(ActionEvent e)
2954 viewport.hideAllSelectedSeqs();
2955 // alignPanel.paintAlignment(true);
2959 * called by key handler and the hide all/show all menu items
2964 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2967 boolean hide = false;
2968 SequenceGroup sg = viewport.getSelectionGroup();
2969 if (!toggleSeqs && !toggleCols)
2971 // Hide everything by the current selection - this is a hack - we do the
2972 // invert and then hide
2973 // first check that there will be visible columns after the invert.
2974 if (viewport.hasSelectedColumns()
2975 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2978 // now invert the sequence set, if required - empty selection implies
2979 // that no hiding is required.
2982 invertSequenceMenuItem_actionPerformed(null);
2983 sg = viewport.getSelectionGroup();
2987 viewport.expandColSelection(sg, true);
2988 // finally invert the column selection and get the new sequence
2990 invertColSel_actionPerformed(null);
2997 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2999 hideSelSequences_actionPerformed(null);
3002 else if (!(toggleCols && viewport.hasSelectedColumns()))
3004 showAllSeqs_actionPerformed(null);
3010 if (viewport.hasSelectedColumns())
3012 hideSelColumns_actionPerformed(null);
3015 viewport.setSelectionGroup(sg);
3020 showAllColumns_actionPerformed(null);
3029 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3030 * event.ActionEvent)
3033 public void hideAllButSelection_actionPerformed(ActionEvent e)
3035 toggleHiddenRegions(false, false);
3036 viewport.sendSelection();
3043 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3047 public void hideAllSelection_actionPerformed(ActionEvent e)
3049 SequenceGroup sg = viewport.getSelectionGroup();
3050 viewport.expandColSelection(sg, false);
3051 viewport.hideAllSelectedSeqs();
3052 viewport.hideSelectedColumns();
3053 alignPanel.paintAlignment(true);
3054 viewport.sendSelection();
3061 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3065 public void showAllhidden_actionPerformed(ActionEvent e)
3067 viewport.showAllHiddenColumns();
3068 viewport.showAllHiddenSeqs();
3069 alignPanel.paintAlignment(true);
3070 viewport.sendSelection();
3074 public void hideSelColumns_actionPerformed(ActionEvent e)
3076 viewport.hideSelectedColumns();
3077 alignPanel.paintAlignment(true);
3078 viewport.sendSelection();
3082 public void hiddenMarkers_actionPerformed(ActionEvent e)
3084 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3095 protected void scaleAbove_actionPerformed(ActionEvent e)
3097 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3098 alignPanel.paintAlignment(true);
3108 protected void scaleLeft_actionPerformed(ActionEvent e)
3110 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3111 alignPanel.paintAlignment(true);
3121 protected void scaleRight_actionPerformed(ActionEvent e)
3123 viewport.setScaleRightWrapped(scaleRight.isSelected());
3124 alignPanel.paintAlignment(true);
3134 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3136 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3137 alignPanel.paintAlignment(true);
3147 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3149 viewport.setShowText(viewTextMenuItem.isSelected());
3150 alignPanel.paintAlignment(true);
3160 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3162 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3163 alignPanel.paintAlignment(true);
3166 public FeatureSettings featureSettings;
3169 public FeatureSettingsControllerI getFeatureSettingsUI()
3171 return featureSettings;
3175 public void featureSettings_actionPerformed(ActionEvent e)
3177 if (featureSettings != null)
3179 featureSettings.close();
3180 featureSettings = null;
3182 if (!showSeqFeatures.isSelected())
3184 // make sure features are actually displayed
3185 showSeqFeatures.setSelected(true);
3186 showSeqFeatures_actionPerformed(null);
3188 featureSettings = new FeatureSettings(this);
3192 * Set or clear 'Show Sequence Features'
3198 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3200 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3201 alignPanel.paintAlignment(true);
3202 if (alignPanel.getOverviewPanel() != null)
3204 alignPanel.getOverviewPanel().updateOverviewImage();
3209 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3210 * the annotations panel as a whole.
3212 * The options to show/hide all annotations should be enabled when the panel
3213 * is shown, and disabled when the panel is hidden.
3218 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3220 final boolean setVisible = annotationPanelMenuItem.isSelected();
3221 viewport.setShowAnnotation(setVisible);
3222 this.showAllSeqAnnotations.setEnabled(setVisible);
3223 this.hideAllSeqAnnotations.setEnabled(setVisible);
3224 this.showAllAlAnnotations.setEnabled(setVisible);
3225 this.hideAllAlAnnotations.setEnabled(setVisible);
3226 alignPanel.updateLayout();
3230 public void alignmentProperties()
3232 JEditorPane editPane = new JEditorPane("text/html", "");
3233 editPane.setEditable(false);
3234 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3236 editPane.setText(MessageManager.formatMessage("label.html_content",
3237 new Object[] { contents.toString() }));
3238 JInternalFrame frame = new JInternalFrame();
3239 frame.getContentPane().add(new JScrollPane(editPane));
3241 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3242 "label.alignment_properties", new Object[] { getTitle() }),
3253 public void overviewMenuItem_actionPerformed(ActionEvent e)
3255 if (alignPanel.overviewPanel != null)
3260 JInternalFrame frame = new JInternalFrame();
3261 OverviewPanel overview = new OverviewPanel(alignPanel);
3262 frame.setContentPane(overview);
3263 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3264 "label.overview_params", new Object[] { this.getTitle() }),
3265 frame.getWidth(), frame.getHeight());
3267 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3268 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3271 public void internalFrameClosed(
3272 javax.swing.event.InternalFrameEvent evt)
3274 alignPanel.setOverviewPanel(null);
3278 alignPanel.setOverviewPanel(overview);
3282 public void textColour_actionPerformed()
3284 new TextColourChooser().chooseColour(alignPanel, null);
3288 * public void covariationColour_actionPerformed() {
3290 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3294 public void annotationColour_actionPerformed()
3296 new AnnotationColourChooser(viewport, alignPanel);
3300 public void annotationColumn_actionPerformed(ActionEvent e)
3302 new AnnotationColumnChooser(viewport, alignPanel);
3306 * Action on the user checking or unchecking the option to apply the selected
3307 * colour scheme to all groups. If unchecked, groups may have their own
3308 * independent colour schemes.
3312 protected void applyToAllGroups_actionPerformed()
3314 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3318 * Action on user selecting a colour from the colour menu
3321 * the name (not the menu item label!) of the colour scheme
3324 public void changeColour_actionPerformed(String name)
3327 * 'User Defined' opens a panel to configure or load a
3328 * user-defined colour scheme
3330 if (ResidueColourScheme.USER_DEFINED.equals(name))
3332 new UserDefinedColours(alignPanel, null);
3337 * otherwise set the chosen colour scheme (or null for 'None')
3339 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3340 viewport.getAlignment(), viewport.getHiddenRepSequences());
3345 * Actions on setting or changing the alignment colour scheme
3350 public void changeColour(ColourSchemeI cs)
3352 // TODO: pull up to controller method
3355 ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3356 // Make sure viewport is up to date w.r.t. any sliders
3357 // ? not needed as handled by SliderPanel.valueChanged?
3358 // if (viewport.getAbovePIDThreshold())
3360 // int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3362 //todo is threshold held in viewport style or in colour scheme?
3363 // viewport.setThreshold(threshold);
3366 // if (viewport.getConservationSelected())
3368 // cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3369 // cs, "Background"));
3373 viewport.setGlobalColourScheme(cs);
3374 if (viewport.getConservationSelected())
3376 int conservationInc = SliderPanel.getConservationValue();
3377 viewport.getViewportColourScheme()
3378 .setConservationInc(conservationInc);
3381 alignPanel.paintAlignment(true);
3391 protected void modifyPID_actionPerformed()
3393 if (viewport.getAbovePIDThreshold())
3395 SliderPanel.setPIDSliderSource(alignPanel,
3396 viewport.getViewportColourScheme(), "Background");
3397 SliderPanel.showPIDSlider();
3408 protected void modifyConservation_actionPerformed()
3410 if (viewport.getConservationSelected()
3411 && viewport.getGlobalColourScheme() != null)
3413 SliderPanel.setConservationSlider(alignPanel,
3414 viewport.getViewportColourScheme(), "Background");
3415 SliderPanel.showConservationSlider();
3426 protected void conservationMenuItem_actionPerformed()
3428 viewport.setConservationSelected(conservationMenuItem.isSelected());
3430 viewport.setAbovePIDThreshold(false);
3431 abovePIDThreshold.setSelected(false);
3433 changeColour(viewport.getGlobalColourScheme());
3435 modifyConservation_actionPerformed();
3445 public void abovePIDThreshold_actionPerformed()
3447 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3449 conservationMenuItem.setSelected(false);
3450 viewport.setConservationSelected(false);
3452 changeColour(viewport.getGlobalColourScheme());
3454 modifyPID_actionPerformed();
3464 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3466 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3467 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3468 .getAlignment().getSequenceAt(0), null);
3469 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3470 viewport.getAlignment()));
3471 alignPanel.paintAlignment(true);
3481 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3483 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3484 AlignmentSorter.sortByID(viewport.getAlignment());
3485 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3486 viewport.getAlignment()));
3487 alignPanel.paintAlignment(true);
3497 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3499 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3500 AlignmentSorter.sortByLength(viewport.getAlignment());
3501 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3502 viewport.getAlignment()));
3503 alignPanel.paintAlignment(true);
3513 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3515 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3516 AlignmentSorter.sortByGroup(viewport.getAlignment());
3517 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3518 viewport.getAlignment()));
3520 alignPanel.paintAlignment(true);
3530 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3532 new RedundancyPanel(alignPanel, this);
3542 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3544 if ((viewport.getSelectionGroup() == null)
3545 || (viewport.getSelectionGroup().getSize() < 2))
3547 JvOptionPane.showInternalMessageDialog(this, MessageManager
3548 .getString("label.you_must_select_least_two_sequences"),
3549 MessageManager.getString("label.invalid_selection"),
3550 JvOptionPane.WARNING_MESSAGE);
3554 JInternalFrame frame = new JInternalFrame();
3555 frame.setContentPane(new PairwiseAlignPanel(viewport));
3556 Desktop.addInternalFrame(frame,
3557 MessageManager.getString("action.pairwise_alignment"), 600,
3569 public void PCAMenuItem_actionPerformed(ActionEvent e)
3571 if (((viewport.getSelectionGroup() != null)
3572 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3573 .getSelectionGroup().getSize() > 0))
3574 || (viewport.getAlignment().getHeight() < 4))
3577 .showInternalMessageDialog(
3580 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3582 .getString("label.sequence_selection_insufficient"),
3583 JvOptionPane.WARNING_MESSAGE);
3588 new PCAPanel(alignPanel);
3592 public void autoCalculate_actionPerformed(ActionEvent e)
3594 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3595 if (viewport.autoCalculateConsensus)
3597 viewport.firePropertyChange("alignment", null, viewport
3598 .getAlignment().getSequences());
3603 public void sortByTreeOption_actionPerformed(ActionEvent e)
3605 viewport.sortByTree = sortByTree.isSelected();
3609 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3611 viewport.followSelection = listenToViewSelections.isSelected();
3621 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3623 newTreePanel("AV", "PID", "Average distance tree using PID");
3633 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3635 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3645 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3647 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3657 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3659 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3672 void newTreePanel(String type, String pwType, String title)
3676 if (viewport.getSelectionGroup() != null
3677 && viewport.getSelectionGroup().getSize() > 0)
3679 if (viewport.getSelectionGroup().getSize() < 3)
3685 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3687 .getString("label.not_enough_sequences"),
3688 JvOptionPane.WARNING_MESSAGE);
3692 SequenceGroup sg = viewport.getSelectionGroup();
3694 /* Decide if the selection is a column region */
3695 for (SequenceI _s : sg.getSequences())
3697 if (_s.getLength() < sg.getEndRes())
3703 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3705 .getString("label.sequences_selection_not_aligned"),
3706 JvOptionPane.WARNING_MESSAGE);
3712 title = title + " on region";
3713 tp = new TreePanel(alignPanel, type, pwType);
3717 // are the visible sequences aligned?
3718 if (!viewport.getAlignment().isAligned(false))
3724 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3726 .getString("label.sequences_not_aligned"),
3727 JvOptionPane.WARNING_MESSAGE);
3732 if (viewport.getAlignment().getHeight() < 2)
3737 tp = new TreePanel(alignPanel, type, pwType);
3742 if (viewport.viewName != null)
3744 title += viewport.viewName + " of ";
3747 title += this.title;
3749 Desktop.addInternalFrame(tp, title, 600, 500);
3760 public void addSortByOrderMenuItem(String title,
3761 final AlignmentOrder order)
3763 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3764 "action.by_title_param", new Object[] { title }));
3766 item.addActionListener(new java.awt.event.ActionListener()
3769 public void actionPerformed(ActionEvent e)
3771 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3773 // TODO: JBPNote - have to map order entries to curent SequenceI
3775 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3777 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3780 alignPanel.paintAlignment(true);
3786 * Add a new sort by annotation score menu item
3789 * the menu to add the option to
3791 * the label used to retrieve scores for each sequence on the
3794 public void addSortByAnnotScoreMenuItem(JMenu sort,
3795 final String scoreLabel)
3797 final JMenuItem item = new JMenuItem(scoreLabel);
3799 item.addActionListener(new java.awt.event.ActionListener()
3802 public void actionPerformed(ActionEvent e)
3804 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3805 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3806 viewport.getAlignment());// ,viewport.getSelectionGroup());
3807 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3808 viewport.getAlignment()));
3809 alignPanel.paintAlignment(true);
3815 * last hash for alignment's annotation array - used to minimise cost of
3818 protected int _annotationScoreVectorHash;
3821 * search the alignment and rebuild the sort by annotation score submenu the
3822 * last alignment annotation vector hash is stored to minimize cost of
3823 * rebuilding in subsequence calls.
3827 public void buildSortByAnnotationScoresMenu()
3829 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3834 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3836 sortByAnnotScore.removeAll();
3837 // almost certainly a quicker way to do this - but we keep it simple
3838 Hashtable scoreSorts = new Hashtable();
3839 AlignmentAnnotation aann[];
3840 for (SequenceI sqa : viewport.getAlignment().getSequences())
3842 aann = sqa.getAnnotation();
3843 for (int i = 0; aann != null && i < aann.length; i++)
3845 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3847 scoreSorts.put(aann[i].label, aann[i].label);
3851 Enumeration labels = scoreSorts.keys();
3852 while (labels.hasMoreElements())
3854 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3855 (String) labels.nextElement());
3857 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3860 _annotationScoreVectorHash = viewport.getAlignment()
3861 .getAlignmentAnnotation().hashCode();
3866 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3867 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3868 * call. Listeners are added to remove the menu item when the treePanel is
3869 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3873 * Displayed tree window.
3875 * SortBy menu item title.
3878 public void buildTreeMenu()
3880 calculateTree.removeAll();
3881 // build the calculate menu
3883 for (final String type : new String[] { "NJ", "AV" })
3885 String treecalcnm = MessageManager.getString("label.tree_calc_"
3886 + type.toLowerCase());
3887 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3889 JMenuItem tm = new JMenuItem();
3890 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3891 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3892 || sm.isProtein() == !viewport.getAlignment()
3895 String smn = MessageManager.getStringOrReturn(
3896 "label.score_model_", sm.getName());
3897 final String title = MessageManager.formatMessage(
3898 "label.treecalc_title", treecalcnm, smn);
3899 tm.setText(title);//
3900 tm.addActionListener(new java.awt.event.ActionListener()
3903 public void actionPerformed(ActionEvent e)
3905 newTreePanel(type, pwtype, title);
3908 calculateTree.add(tm);
3913 sortByTreeMenu.removeAll();
3915 List<Component> comps = PaintRefresher.components.get(viewport
3916 .getSequenceSetId());
3917 List<TreePanel> treePanels = new ArrayList<TreePanel>();
3918 for (Component comp : comps)
3920 if (comp instanceof TreePanel)
3922 treePanels.add((TreePanel) comp);
3926 if (treePanels.size() < 1)
3928 sortByTreeMenu.setVisible(false);
3932 sortByTreeMenu.setVisible(true);
3934 for (final TreePanel tp : treePanels)
3936 final JMenuItem item = new JMenuItem(tp.getTitle());
3937 item.addActionListener(new java.awt.event.ActionListener()
3940 public void actionPerformed(ActionEvent e)
3942 tp.sortByTree_actionPerformed();
3943 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3948 sortByTreeMenu.add(item);
3952 public boolean sortBy(AlignmentOrder alorder, String undoname)
3954 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3955 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3956 if (undoname != null)
3958 addHistoryItem(new OrderCommand(undoname, oldOrder,
3959 viewport.getAlignment()));
3961 alignPanel.paintAlignment(true);
3966 * Work out whether the whole set of sequences or just the selected set will
3967 * be submitted for multiple alignment.
3970 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3972 // Now, check we have enough sequences
3973 AlignmentView msa = null;
3975 if ((viewport.getSelectionGroup() != null)
3976 && (viewport.getSelectionGroup().getSize() > 1))
3978 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3979 // some common interface!
3981 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3982 * SequenceI[sz = seqs.getSize(false)];
3984 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3985 * seqs.getSequenceAt(i); }
3987 msa = viewport.getAlignmentView(true);
3989 else if (viewport.getSelectionGroup() != null
3990 && viewport.getSelectionGroup().getSize() == 1)
3992 int option = JvOptionPane.showConfirmDialog(this,
3993 MessageManager.getString("warn.oneseq_msainput_selection"),
3994 MessageManager.getString("label.invalid_selection"),
3995 JvOptionPane.OK_CANCEL_OPTION);
3996 if (option == JvOptionPane.OK_OPTION)
3998 msa = viewport.getAlignmentView(false);
4003 msa = viewport.getAlignmentView(false);
4009 * Decides what is submitted to a secondary structure prediction service: the
4010 * first sequence in the alignment, or in the current selection, or, if the
4011 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4012 * region or the whole alignment. (where the first sequence in the set is the
4013 * one that the prediction will be for).
4015 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4017 AlignmentView seqs = null;
4019 if ((viewport.getSelectionGroup() != null)
4020 && (viewport.getSelectionGroup().getSize() > 0))
4022 seqs = viewport.getAlignmentView(true);
4026 seqs = viewport.getAlignmentView(false);
4028 // limit sequences - JBPNote in future - could spawn multiple prediction
4030 // TODO: viewport.getAlignment().isAligned is a global state - the local
4031 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4032 if (!viewport.getAlignment().isAligned(false))
4034 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4035 // TODO: if seqs.getSequences().length>1 then should really have warned
4049 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4051 // Pick the tree file
4052 JalviewFileChooser chooser = new JalviewFileChooser(
4053 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4054 chooser.setFileView(new JalviewFileView());
4055 chooser.setDialogTitle(MessageManager
4056 .getString("label.select_newick_like_tree_file"));
4057 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4059 int value = chooser.showOpenDialog(null);
4061 if (value == JalviewFileChooser.APPROVE_OPTION)
4063 String choice = chooser.getSelectedFile().getPath();
4064 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4065 jalview.io.NewickFile fin = null;
4068 fin = new NewickFile(choice, DataSourceType.FILE);
4069 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4070 } catch (Exception ex)
4077 .getString("label.problem_reading_tree_file"),
4078 JvOptionPane.WARNING_MESSAGE);
4079 ex.printStackTrace();
4081 if (fin != null && fin.hasWarningMessage())
4083 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4084 .getWarningMessage(), MessageManager
4085 .getString("label.possible_problem_with_tree_file"),
4086 JvOptionPane.WARNING_MESSAGE);
4091 public TreePanel ShowNewickTree(NewickFile nf, String title)
4093 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4096 public TreePanel ShowNewickTree(NewickFile nf, String title,
4097 AlignmentView input)
4099 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4102 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4103 int h, int x, int y)
4105 return ShowNewickTree(nf, title, null, w, h, x, y);
4109 * Add a treeviewer for the tree extracted from a newick file object to the
4110 * current alignment view
4117 * Associated alignment input data (or null)
4126 * @return TreePanel handle
4128 public TreePanel ShowNewickTree(NewickFile nf, String title,
4129 AlignmentView input, int w, int h, int x, int y)
4131 TreePanel tp = null;
4137 if (nf.getTree() != null)
4139 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4145 tp.setLocation(x, y);
4148 Desktop.addInternalFrame(tp, title, w, h);
4150 } catch (Exception ex)
4152 ex.printStackTrace();
4158 private boolean buildingMenu = false;
4161 * Generates menu items and listener event actions for web service clients
4164 public void BuildWebServiceMenu()
4166 while (buildingMenu)
4170 System.err.println("Waiting for building menu to finish.");
4172 } catch (Exception e)
4176 final AlignFrame me = this;
4177 buildingMenu = true;
4178 new Thread(new Runnable()
4183 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4186 // System.err.println("Building ws menu again "
4187 // + Thread.currentThread());
4188 // TODO: add support for context dependent disabling of services based
4190 // alignment and current selection
4191 // TODO: add additional serviceHandle parameter to specify abstract
4193 // class independently of AbstractName
4194 // TODO: add in rediscovery GUI function to restart discoverer
4195 // TODO: group services by location as well as function and/or
4197 // object broker mechanism.
4198 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4199 final IProgressIndicator af = me;
4202 * do not i18n these strings - they are hard-coded in class
4203 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4204 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4206 final JMenu msawsmenu = new JMenu("Alignment");
4207 final JMenu secstrmenu = new JMenu(
4208 "Secondary Structure Prediction");
4209 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4210 final JMenu analymenu = new JMenu("Analysis");
4211 final JMenu dismenu = new JMenu("Protein Disorder");
4212 // JAL-940 - only show secondary structure prediction services from
4213 // the legacy server
4214 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4216 Discoverer.services != null && (Discoverer.services.size() > 0))
4218 // TODO: refactor to allow list of AbstractName/Handler bindings to
4220 // stored or retrieved from elsewhere
4221 // No MSAWS used any more:
4222 // Vector msaws = null; // (Vector)
4223 // Discoverer.services.get("MsaWS");
4224 Vector secstrpr = (Vector) Discoverer.services
4226 if (secstrpr != null)
4228 // Add any secondary structure prediction services
4229 for (int i = 0, j = secstrpr.size(); i < j; i++)
4231 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4233 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4234 .getServiceClient(sh);
4235 int p = secstrmenu.getItemCount();
4236 impl.attachWSMenuEntry(secstrmenu, me);
4237 int q = secstrmenu.getItemCount();
4238 for (int litm = p; litm < q; litm++)
4240 legacyItems.add(secstrmenu.getItem(litm));
4246 // Add all submenus in the order they should appear on the web
4248 wsmenu.add(msawsmenu);
4249 wsmenu.add(secstrmenu);
4250 wsmenu.add(dismenu);
4251 wsmenu.add(analymenu);
4252 // No search services yet
4253 // wsmenu.add(seqsrchmenu);
4255 javax.swing.SwingUtilities.invokeLater(new Runnable()
4262 webService.removeAll();
4263 // first, add discovered services onto the webservices menu
4264 if (wsmenu.size() > 0)
4266 for (int i = 0, j = wsmenu.size(); i < j; i++)
4268 webService.add(wsmenu.get(i));
4273 webService.add(me.webServiceNoServices);
4275 // TODO: move into separate menu builder class.
4276 boolean new_sspred = false;
4277 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4279 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4280 if (jws2servs != null)
4282 if (jws2servs.hasServices())
4284 jws2servs.attachWSMenuEntry(webService, me);
4285 for (Jws2Instance sv : jws2servs.getServices())
4287 if (sv.description.toLowerCase().contains("jpred"))
4289 for (JMenuItem jmi : legacyItems)
4291 jmi.setVisible(false);
4297 if (jws2servs.isRunning())
4299 JMenuItem tm = new JMenuItem(
4300 "Still discovering JABA Services");
4301 tm.setEnabled(false);
4306 build_urlServiceMenu(me.webService);
4307 build_fetchdbmenu(webService);
4308 for (JMenu item : wsmenu)
4310 if (item.getItemCount() == 0)
4312 item.setEnabled(false);
4316 item.setEnabled(true);
4319 } catch (Exception e)
4322 .debug("Exception during web service menu building process.",
4327 } catch (Exception e)
4330 buildingMenu = false;
4337 * construct any groupURL type service menu entries.
4341 private void build_urlServiceMenu(JMenu webService)
4343 // TODO: remove this code when 2.7 is released
4344 // DEBUG - alignmentView
4346 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4347 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4349 * @Override public void actionPerformed(ActionEvent e) {
4350 * jalview.datamodel.AlignmentView
4351 * .testSelectionViews(af.viewport.getAlignment(),
4352 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4354 * }); webService.add(testAlView);
4356 // TODO: refactor to RestClient discoverer and merge menu entries for
4357 // rest-style services with other types of analysis/calculation service
4358 // SHmmr test client - still being implemented.
4359 // DEBUG - alignmentView
4361 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4364 client.attachWSMenuEntry(
4365 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4371 * Searches the alignment sequences for xRefs and builds the Show
4372 * Cross-References menu (formerly called Show Products), with database
4373 * sources for which cross-references are found (protein sources for a
4374 * nucleotide alignment and vice versa)
4376 * @return true if Show Cross-references menu should be enabled
4378 public boolean canShowProducts()
4380 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4381 AlignmentI dataset = viewport.getAlignment().getDataset();
4383 showProducts.removeAll();
4384 final boolean dna = viewport.getAlignment().isNucleotide();
4386 if (seqs == null || seqs.length == 0)
4388 // nothing to see here.
4392 boolean showp = false;
4395 List<String> ptypes = new CrossRef(seqs, dataset)
4396 .findXrefSourcesForSequences(dna);
4398 for (final String source : ptypes)
4401 final AlignFrame af = this;
4402 JMenuItem xtype = new JMenuItem(source);
4403 xtype.addActionListener(new ActionListener()
4406 public void actionPerformed(ActionEvent e)
4408 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4411 showProducts.add(xtype);
4413 showProducts.setVisible(showp);
4414 showProducts.setEnabled(showp);
4415 } catch (Exception e)
4418 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4426 * Finds and displays cross-references for the selected sequences (protein
4427 * products for nucleotide sequences, dna coding sequences for peptides).
4430 * the sequences to show cross-references for
4432 * true if from a nucleotide alignment (so showing proteins)
4434 * the database to show cross-references for
4436 protected void showProductsFor(final SequenceI[] sel,
4437 final boolean _odna, final String source)
4439 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4444 * Construct and display a new frame containing the translation of this
4445 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4448 public void showTranslation_actionPerformed(ActionEvent e)
4450 AlignmentI al = null;
4453 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4455 al = dna.translateCdna();
4456 } catch (Exception ex)
4458 jalview.bin.Cache.log.error(
4459 "Exception during translation. Please report this !", ex);
4460 final String msg = MessageManager
4461 .getString("label.error_when_translating_sequences_submit_bug_report");
4462 final String errorTitle = MessageManager
4463 .getString("label.implementation_error")
4464 + MessageManager.getString("label.translation_failed");
4465 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4466 JvOptionPane.ERROR_MESSAGE);
4469 if (al == null || al.getHeight() == 0)
4471 final String msg = MessageManager
4472 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4473 final String errorTitle = MessageManager
4474 .getString("label.translation_failed");
4475 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4476 JvOptionPane.WARNING_MESSAGE);
4480 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4481 af.setFileFormat(this.currentFileFormat);
4482 final String newTitle = MessageManager.formatMessage(
4483 "label.translation_of_params",
4484 new Object[] { this.getTitle() });
4485 af.setTitle(newTitle);
4486 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4488 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4489 viewport.openSplitFrame(af, new Alignment(seqs));
4493 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4500 * Set the file format
4504 public void setFileFormat(FileFormatI format)
4506 this.currentFileFormat = format;
4510 * Try to load a features file onto the alignment.
4513 * contents or path to retrieve file
4515 * access mode of file (see jalview.io.AlignFile)
4516 * @return true if features file was parsed correctly.
4518 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4520 return avc.parseFeaturesFile(file, sourceType,
4521 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4526 public void refreshFeatureUI(boolean enableIfNecessary)
4528 // note - currently this is only still here rather than in the controller
4529 // because of the featureSettings hard reference that is yet to be
4531 if (enableIfNecessary)
4533 viewport.setShowSequenceFeatures(true);
4534 showSeqFeatures.setSelected(true);
4540 public void dragEnter(DropTargetDragEvent evt)
4545 public void dragExit(DropTargetEvent evt)
4550 public void dragOver(DropTargetDragEvent evt)
4555 public void dropActionChanged(DropTargetDragEvent evt)
4560 public void drop(DropTargetDropEvent evt)
4562 // JAL-1552 - acceptDrop required before getTransferable call for
4563 // Java's Transferable for native dnd
4564 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4565 Transferable t = evt.getTransferable();
4566 List<String> files = new ArrayList<String>();
4567 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4571 Desktop.transferFromDropTarget(files, protocols, evt, t);
4572 } catch (Exception e)
4574 e.printStackTrace();
4580 // check to see if any of these files have names matching sequences in
4582 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4583 .getAlignment().getSequencesArray());
4585 * Object[] { String,SequenceI}
4587 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4588 ArrayList<String> filesnotmatched = new ArrayList<String>();
4589 for (int i = 0; i < files.size(); i++)
4591 String file = files.get(i).toString();
4593 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4594 if (protocol == DataSourceType.FILE)
4596 File fl = new File(file);
4597 pdbfn = fl.getName();
4599 else if (protocol == DataSourceType.URL)
4601 URL url = new URL(file);
4602 pdbfn = url.getFile();
4604 if (pdbfn.length() > 0)
4606 // attempt to find a match in the alignment
4607 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4608 int l = 0, c = pdbfn.indexOf(".");
4609 while (mtch == null && c != -1)
4614 } while ((c = pdbfn.indexOf(".", l)) > l);
4617 pdbfn = pdbfn.substring(0, l);
4619 mtch = idm.findAllIdMatches(pdbfn);
4623 FileFormatI type = null;
4626 type = new IdentifyFile().identify(file, protocol);
4627 } catch (Exception ex)
4631 if (type != null && type.isStructureFile())
4633 filesmatched.add(new Object[] { file, protocol, mtch });
4637 // File wasn't named like one of the sequences or wasn't a PDB file.
4638 filesnotmatched.add(file);
4642 if (filesmatched.size() > 0)
4644 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4650 "label.automatically_associate_structure_files_with_sequences_same_name",
4651 new Object[] { Integer
4657 .getString("label.automatically_associate_structure_files_by_name"),
4658 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4661 for (Object[] fm : filesmatched)
4663 // try and associate
4664 // TODO: may want to set a standard ID naming formalism for
4665 // associating PDB files which have no IDs.
4666 for (SequenceI toassoc : (SequenceI[]) fm[2])
4668 PDBEntry pe = new AssociatePdbFileWithSeq()
4669 .associatePdbWithSeq((String) fm[0],
4670 (DataSourceType) fm[1], toassoc, false,
4674 System.err.println("Associated file : "
4675 + ((String) fm[0]) + " with "
4676 + toassoc.getDisplayId(true));
4680 alignPanel.paintAlignment(true);
4684 if (filesnotmatched.size() > 0)
4687 && (Cache.getDefault(
4688 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4694 "label.ignore_unmatched_dropped_files_info",
4695 new Object[] { Integer
4702 .getString("label.ignore_unmatched_dropped_files"),
4703 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4707 for (String fn : filesnotmatched)
4709 loadJalviewDataFile(fn, null, null, null);
4713 } catch (Exception ex)
4715 ex.printStackTrace();
4721 * Attempt to load a "dropped" file or URL string: First by testing whether
4722 * it's an Annotation file, then a JNet file, and finally a features file. If
4723 * all are false then the user may have dropped an alignment file onto this
4727 * either a filename or a URL string.
4729 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4730 FileFormatI format, SequenceI assocSeq)
4734 if (sourceType == null)
4736 sourceType = FormatAdapter.checkProtocol(file);
4738 // if the file isn't identified, or not positively identified as some
4739 // other filetype (PFAM is default unidentified alignment file type) then
4740 // try to parse as annotation.
4741 boolean isAnnotation = (format == null || FileFormat.Pfam
4742 .equals(format)) ? new AnnotationFile()
4743 .annotateAlignmentView(viewport, file, sourceType) : false;
4747 // first see if its a T-COFFEE score file
4748 TCoffeeScoreFile tcf = null;
4751 tcf = new TCoffeeScoreFile(file, sourceType);
4754 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4757 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4758 isAnnotation = true;
4760 .setText(MessageManager
4761 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4765 // some problem - if no warning its probable that the ID matching
4766 // process didn't work
4770 tcf.getWarningMessage() == null ? MessageManager
4771 .getString("label.check_file_matches_sequence_ids_alignment")
4772 : tcf.getWarningMessage(),
4774 .getString("label.problem_reading_tcoffee_score_file"),
4775 JvOptionPane.WARNING_MESSAGE);
4782 } catch (Exception x)
4785 .debug("Exception when processing data source as T-COFFEE score file",
4791 // try to see if its a JNet 'concise' style annotation file *before*
4793 // try to parse it as a features file
4796 format = new IdentifyFile().identify(file, sourceType);
4798 if (FileFormat.Jnet.equals(format))
4800 JPredFile predictions = new JPredFile(
4802 new JnetAnnotationMaker();
4803 JnetAnnotationMaker.add_annotation(predictions,
4804 viewport.getAlignment(), 0, false);
4805 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4806 viewport.getAlignment().setSeqrep(repseq);
4807 ColumnSelection cs = new ColumnSelection();
4808 cs.hideInsertionsFor(repseq);
4809 viewport.setColumnSelection(cs);
4810 isAnnotation = true;
4812 // else if (IdentifyFile.FeaturesFile.equals(format))
4813 else if (FileFormat.Features.equals(format))
4815 if (parseFeaturesFile(file, sourceType))
4817 alignPanel.paintAlignment(true);
4822 new FileLoader().LoadFile(viewport, file, sourceType, format);
4829 alignPanel.adjustAnnotationHeight();
4830 viewport.updateSequenceIdColours();
4831 buildSortByAnnotationScoresMenu();
4832 alignPanel.paintAlignment(true);
4834 } catch (Exception ex)
4836 ex.printStackTrace();
4837 } catch (OutOfMemoryError oom)
4842 } catch (Exception x)
4847 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4848 : "using " + sourceType + " from " + file)
4850 + (format != null ? "(parsing as '" + format
4851 + "' file)" : ""), oom, Desktop.desktop);
4856 * Method invoked by the ChangeListener on the tabbed pane, in other words
4857 * when a different tabbed pane is selected by the user or programmatically.
4860 public void tabSelectionChanged(int index)
4864 alignPanel = alignPanels.get(index);
4865 viewport = alignPanel.av;
4866 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4867 setMenusFromViewport(viewport);
4871 * If there is a frame linked to this one in a SplitPane, switch it to the
4872 * same view tab index. No infinite recursion of calls should happen, since
4873 * tabSelectionChanged() should not get invoked on setting the selected
4874 * index to an unchanged value. Guard against setting an invalid index
4875 * before the new view peer tab has been created.
4877 final AlignViewportI peer = viewport.getCodingComplement();
4880 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4881 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4883 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4889 * On right mouse click on view tab, prompt for and set new view name.
4892 public void tabbedPane_mousePressed(MouseEvent e)
4894 if (e.isPopupTrigger())
4896 String msg = MessageManager.getString("label.enter_view_name");
4897 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4898 JvOptionPane.QUESTION_MESSAGE);
4902 viewport.viewName = reply;
4903 // TODO warn if reply is in getExistingViewNames()?
4904 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4909 public AlignViewport getCurrentView()
4915 * Open the dialog for regex description parsing.
4918 protected void extractScores_actionPerformed(ActionEvent e)
4920 ParseProperties pp = new jalview.analysis.ParseProperties(
4921 viewport.getAlignment());
4922 // TODO: verify regex and introduce GUI dialog for version 2.5
4923 // if (pp.getScoresFromDescription("col", "score column ",
4924 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4926 if (pp.getScoresFromDescription("description column",
4927 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4929 buildSortByAnnotationScoresMenu();
4937 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4941 protected void showDbRefs_actionPerformed(ActionEvent e)
4943 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4949 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4953 protected void showNpFeats_actionPerformed(ActionEvent e)
4955 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4959 * find the viewport amongst the tabs in this alignment frame and close that
4964 public boolean closeView(AlignViewportI av)
4968 this.closeMenuItem_actionPerformed(false);
4971 Component[] comp = tabbedPane.getComponents();
4972 for (int i = 0; comp != null && i < comp.length; i++)
4974 if (comp[i] instanceof AlignmentPanel)
4976 if (((AlignmentPanel) comp[i]).av == av)
4979 closeView((AlignmentPanel) comp[i]);
4987 protected void build_fetchdbmenu(JMenu webService)
4989 // Temporary hack - DBRef Fetcher always top level ws entry.
4990 // TODO We probably want to store a sequence database checklist in
4991 // preferences and have checkboxes.. rather than individual sources selected
4993 final JMenu rfetch = new JMenu(
4994 MessageManager.getString("action.fetch_db_references"));
4995 rfetch.setToolTipText(MessageManager
4996 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4997 webService.add(rfetch);
4999 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5000 MessageManager.getString("option.trim_retrieved_seqs"));
5001 trimrs.setToolTipText(MessageManager
5002 .getString("label.trim_retrieved_sequences"));
5003 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5004 trimrs.addActionListener(new ActionListener()
5007 public void actionPerformed(ActionEvent e)
5009 trimrs.setSelected(trimrs.isSelected());
5010 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5011 Boolean.valueOf(trimrs.isSelected()).toString());
5015 JMenuItem fetchr = new JMenuItem(
5016 MessageManager.getString("label.standard_databases"));
5017 fetchr.setToolTipText(MessageManager
5018 .getString("label.fetch_embl_uniprot"));
5019 fetchr.addActionListener(new ActionListener()
5023 public void actionPerformed(ActionEvent e)
5025 new Thread(new Runnable()
5030 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5031 .getAlignment().isNucleotide();
5032 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5033 .getSequenceSelection(), alignPanel.alignFrame, null,
5034 alignPanel.alignFrame.featureSettings, isNucleotide);
5035 dbRefFetcher.addListener(new FetchFinishedListenerI()
5038 public void finished()
5040 AlignFrame.this.setMenusForViewport();
5043 dbRefFetcher.fetchDBRefs(false);
5051 final AlignFrame me = this;
5052 new Thread(new Runnable()
5057 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5058 .getSequenceFetcherSingleton(me);
5059 javax.swing.SwingUtilities.invokeLater(new Runnable()
5064 String[] dbclasses = sf.getOrderedSupportedSources();
5065 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5066 // jalview.util.QuickSort.sort(otherdb, otherdb);
5067 List<DbSourceProxy> otherdb;
5068 JMenu dfetch = new JMenu();
5069 JMenu ifetch = new JMenu();
5070 JMenuItem fetchr = null;
5071 int comp = 0, icomp = 0, mcomp = 15;
5072 String mname = null;
5074 for (String dbclass : dbclasses)
5076 otherdb = sf.getSourceProxy(dbclass);
5077 // add a single entry for this class, or submenu allowing 'fetch
5079 if (otherdb == null || otherdb.size() < 1)
5083 // List<DbSourceProxy> dbs=otherdb;
5084 // otherdb=new ArrayList<DbSourceProxy>();
5085 // for (DbSourceProxy db:dbs)
5087 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5091 mname = "From " + dbclass;
5093 if (otherdb.size() == 1)
5095 final DbSourceProxy[] dassource = otherdb
5096 .toArray(new DbSourceProxy[0]);
5097 DbSourceProxy src = otherdb.get(0);
5098 fetchr = new JMenuItem(src.getDbSource());
5099 fetchr.addActionListener(new ActionListener()
5103 public void actionPerformed(ActionEvent e)
5105 new Thread(new Runnable()
5111 boolean isNucleotide = alignPanel.alignFrame
5112 .getViewport().getAlignment()
5114 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5115 alignPanel.av.getSequenceSelection(),
5116 alignPanel.alignFrame, dassource,
5117 alignPanel.alignFrame.featureSettings,
5120 .addListener(new FetchFinishedListenerI()
5123 public void finished()
5125 AlignFrame.this.setMenusForViewport();
5128 dbRefFetcher.fetchDBRefs(false);
5134 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5135 MessageManager.formatMessage(
5136 "label.fetch_retrieve_from",
5137 new Object[] { src.getDbName() })));
5143 final DbSourceProxy[] dassource = otherdb
5144 .toArray(new DbSourceProxy[0]);
5146 DbSourceProxy src = otherdb.get(0);
5147 fetchr = new JMenuItem(MessageManager.formatMessage(
5148 "label.fetch_all_param",
5149 new Object[] { src.getDbSource() }));
5150 fetchr.addActionListener(new ActionListener()
5153 public void actionPerformed(ActionEvent e)
5155 new Thread(new Runnable()
5161 boolean isNucleotide = alignPanel.alignFrame
5162 .getViewport().getAlignment()
5164 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5165 alignPanel.av.getSequenceSelection(),
5166 alignPanel.alignFrame, dassource,
5167 alignPanel.alignFrame.featureSettings,
5170 .addListener(new FetchFinishedListenerI()
5173 public void finished()
5175 AlignFrame.this.setMenusForViewport();
5178 dbRefFetcher.fetchDBRefs(false);
5184 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5185 MessageManager.formatMessage(
5186 "label.fetch_retrieve_from_all_sources",
5188 Integer.valueOf(otherdb.size())
5189 .toString(), src.getDbSource(),
5190 src.getDbName() })));
5193 // and then build the rest of the individual menus
5194 ifetch = new JMenu(MessageManager.formatMessage(
5195 "label.source_from_db_source",
5196 new Object[] { src.getDbSource() }));
5198 String imname = null;
5200 for (DbSourceProxy sproxy : otherdb)
5202 String dbname = sproxy.getDbName();
5203 String sname = dbname.length() > 5 ? dbname.substring(0,
5204 5) + "..." : dbname;
5205 String msname = dbname.length() > 10 ? dbname.substring(
5206 0, 10) + "..." : dbname;
5209 imname = MessageManager.formatMessage(
5210 "label.from_msname", new Object[] { sname });
5212 fetchr = new JMenuItem(msname);
5213 final DbSourceProxy[] dassrc = { sproxy };
5214 fetchr.addActionListener(new ActionListener()
5218 public void actionPerformed(ActionEvent e)
5220 new Thread(new Runnable()
5226 boolean isNucleotide = alignPanel.alignFrame
5227 .getViewport().getAlignment()
5229 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5230 alignPanel.av.getSequenceSelection(),
5231 alignPanel.alignFrame, dassrc,
5232 alignPanel.alignFrame.featureSettings,
5235 .addListener(new FetchFinishedListenerI()
5238 public void finished()
5240 AlignFrame.this.setMenusForViewport();
5243 dbRefFetcher.fetchDBRefs(false);
5249 fetchr.setToolTipText("<html>"
5250 + MessageManager.formatMessage(
5251 "label.fetch_retrieve_from", new Object[]
5255 if (++icomp >= mcomp || i == (otherdb.size()))
5257 ifetch.setText(MessageManager.formatMessage(
5258 "label.source_to_target", imname, sname));
5260 ifetch = new JMenu();
5268 if (comp >= mcomp || dbi >= (dbclasses.length))
5270 dfetch.setText(MessageManager.formatMessage(
5271 "label.source_to_target", mname, dbclass));
5273 dfetch = new JMenu();
5286 * Left justify the whole alignment.
5289 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5291 AlignmentI al = viewport.getAlignment();
5293 viewport.firePropertyChange("alignment", null, al);
5297 * Right justify the whole alignment.
5300 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5302 AlignmentI al = viewport.getAlignment();
5304 viewport.firePropertyChange("alignment", null, al);
5308 public void setShowSeqFeatures(boolean b)
5310 showSeqFeatures.setSelected(b);
5311 viewport.setShowSequenceFeatures(b);
5318 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5319 * awt.event.ActionEvent)
5322 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5324 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5325 alignPanel.paintAlignment(true);
5332 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5336 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5338 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5339 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5347 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5348 * .event.ActionEvent)
5351 protected void showGroupConservation_actionPerformed(ActionEvent e)
5353 viewport.setShowGroupConservation(showGroupConservation.getState());
5354 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5361 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5362 * .event.ActionEvent)
5365 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5367 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5368 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5375 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5376 * .event.ActionEvent)
5379 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5381 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5382 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5386 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5388 showSequenceLogo.setState(true);
5389 viewport.setShowSequenceLogo(true);
5390 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5391 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5395 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5397 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5404 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5405 * .event.ActionEvent)
5408 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5410 if (avc.makeGroupsFromSelection())
5412 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5413 alignPanel.updateAnnotation();
5414 alignPanel.paintAlignment(true);
5418 public void clearAlignmentSeqRep()
5420 // TODO refactor alignmentseqrep to controller
5421 if (viewport.getAlignment().hasSeqrep())
5423 viewport.getAlignment().setSeqrep(null);
5424 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5425 alignPanel.updateAnnotation();
5426 alignPanel.paintAlignment(true);
5431 protected void createGroup_actionPerformed(ActionEvent e)
5433 if (avc.createGroup())
5435 alignPanel.alignmentChanged();
5440 protected void unGroup_actionPerformed(ActionEvent e)
5444 alignPanel.alignmentChanged();
5449 * make the given alignmentPanel the currently selected tab
5451 * @param alignmentPanel
5453 public void setDisplayedView(AlignmentPanel alignmentPanel)
5455 if (!viewport.getSequenceSetId().equals(
5456 alignmentPanel.av.getSequenceSetId()))
5460 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5462 if (tabbedPane != null
5463 && tabbedPane.getTabCount() > 0
5464 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5465 .getSelectedIndex())
5467 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5472 * Action on selection of menu options to Show or Hide annotations.
5475 * @param forSequences
5476 * update sequence-related annotations
5477 * @param forAlignment
5478 * update non-sequence-related annotations
5481 protected void setAnnotationsVisibility(boolean visible,
5482 boolean forSequences, boolean forAlignment)
5484 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5485 .getAlignmentAnnotation();
5490 for (AlignmentAnnotation aa : anns)
5493 * don't display non-positional annotations on an alignment
5495 if (aa.annotations == null)
5499 boolean apply = (aa.sequenceRef == null && forAlignment)
5500 || (aa.sequenceRef != null && forSequences);
5503 aa.visible = visible;
5506 alignPanel.validateAnnotationDimensions(true);
5507 alignPanel.alignmentChanged();
5511 * Store selected annotation sort order for the view and repaint.
5514 protected void sortAnnotations_actionPerformed()
5516 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5518 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5519 alignPanel.paintAlignment(true);
5524 * @return alignment panels in this alignment frame
5526 public List<? extends AlignmentViewPanel> getAlignPanels()
5528 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5532 * Open a new alignment window, with the cDNA associated with this (protein)
5533 * alignment, aligned as is the protein.
5535 protected void viewAsCdna_actionPerformed()
5537 // TODO no longer a menu action - refactor as required
5538 final AlignmentI alignment = getViewport().getAlignment();
5539 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5540 if (mappings == null)
5544 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5545 for (SequenceI aaSeq : alignment.getSequences())
5547 for (AlignedCodonFrame acf : mappings)
5549 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5553 * There is a cDNA mapping for this protein sequence - add to new
5554 * alignment. It will share the same dataset sequence as other mapped
5555 * cDNA (no new mappings need to be created).
5557 final Sequence newSeq = new Sequence(dnaSeq);
5558 newSeq.setDatasetSequence(dnaSeq);
5559 cdnaSeqs.add(newSeq);
5563 if (cdnaSeqs.size() == 0)
5565 // show a warning dialog no mapped cDNA
5568 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5570 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5571 AlignFrame.DEFAULT_HEIGHT);
5572 cdna.alignAs(alignment);
5573 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5575 Desktop.addInternalFrame(alignFrame, newtitle,
5576 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5580 * Set visibility of dna/protein complement view (available when shown in a
5586 protected void showComplement_actionPerformed(boolean show)
5588 SplitContainerI sf = getSplitViewContainer();
5591 sf.setComplementVisible(this, show);
5596 * Generate the reverse (optionally complemented) of the selected sequences,
5597 * and add them to the alignment
5600 protected void showReverse_actionPerformed(boolean complement)
5602 AlignmentI al = null;
5605 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5606 al = dna.reverseCdna(complement);
5607 viewport.addAlignment(al, "");
5608 addHistoryItem(new EditCommand(
5609 MessageManager.getString("label.add_sequences"),
5610 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5611 viewport.getAlignment()));
5612 } catch (Exception ex)
5614 System.err.println(ex.getMessage());
5620 * Try to run a script in the Groovy console, having first ensured that this
5621 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5622 * be targeted at this alignment.
5625 protected void runGroovy_actionPerformed()
5627 Jalview.setCurrentAlignFrame(this);
5628 groovy.ui.Console console = Desktop.getGroovyConsole();
5629 if (console != null)
5633 console.runScript();
5634 } catch (Exception ex)
5636 System.err.println((ex.toString()));
5638 .showInternalMessageDialog(Desktop.desktop, MessageManager
5639 .getString("label.couldnt_run_groovy_script"),
5641 .getString("label.groovy_support_failed"),
5642 JvOptionPane.ERROR_MESSAGE);
5647 System.err.println("Can't run Groovy script as console not found");
5652 * Hides columns containing (or not containing) a specified feature, provided
5653 * that would not leave all columns hidden
5655 * @param featureType
5656 * @param columnsContaining
5659 public boolean hideFeatureColumns(String featureType,
5660 boolean columnsContaining)
5662 boolean notForHiding = avc.markColumnsContainingFeatures(
5663 columnsContaining, false, false, featureType);
5666 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5667 false, featureType))
5669 getViewport().hideSelectedColumns();
5677 protected void selectHighlightedColumns_actionPerformed(
5678 ActionEvent actionEvent)
5680 // include key modifier check in case user selects from menu
5681 avc.markHighlightedColumns(
5682 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5684 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5688 * Rebuilds the Colour menu, including any user-defined colours which have
5689 * been loaded either on startup or during the session
5691 public void buildColourMenu()
5693 colourMenu.removeAll();
5695 colourMenu.add(applyToAllGroups);
5696 colourMenu.add(textColour);
5697 colourMenu.addSeparator();
5699 ColourMenuHelper.addMenuItems(colourMenu, this,
5700 viewport.getAlignment(), false);
5702 colourMenu.addSeparator();
5703 colourMenu.add(conservationMenuItem);
5704 colourMenu.add(modifyConservation);
5705 colourMenu.add(abovePIDThreshold);
5706 colourMenu.add(modifyPID);
5707 colourMenu.add(annotationColour);
5709 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5710 String schemeName = colourScheme == null ? null : colourScheme
5713 ColourMenuHelper.setColourSelected(colourMenu, schemeName);
5717 class PrintThread extends Thread
5721 public PrintThread(AlignmentPanel ap)
5726 static PageFormat pf;
5731 PrinterJob printJob = PrinterJob.getPrinterJob();
5735 printJob.setPrintable(ap, pf);
5739 printJob.setPrintable(ap);
5742 if (printJob.printDialog())
5747 } catch (Exception PrintException)
5749 PrintException.printStackTrace();