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.ViewSelectionMenu.ViewSetProvider;
63 import jalview.io.AlignmentProperties;
64 import jalview.io.AnnotationFile;
65 import jalview.io.BioJsHTMLOutput;
66 import jalview.io.FileLoader;
67 import jalview.io.FormatAdapter;
68 import jalview.io.HtmlSvgOutput;
69 import jalview.io.IdentifyFile;
70 import jalview.io.JalviewFileChooser;
71 import jalview.io.JalviewFileView;
72 import jalview.io.JnetAnnotationMaker;
73 import jalview.io.NewickFile;
74 import jalview.io.TCoffeeScoreFile;
75 import jalview.jbgui.GAlignFrame;
76 import jalview.schemes.Blosum62ColourScheme;
77 import jalview.schemes.BuriedColourScheme;
78 import jalview.schemes.ClustalxColourScheme;
79 import jalview.schemes.ColourSchemeI;
80 import jalview.schemes.ColourSchemeProperty;
81 import jalview.schemes.HelixColourScheme;
82 import jalview.schemes.HydrophobicColourScheme;
83 import jalview.schemes.NucleotideColourScheme;
84 import jalview.schemes.PIDColourScheme;
85 import jalview.schemes.PurinePyrimidineColourScheme;
86 import jalview.schemes.RNAHelicesColourChooser;
87 import jalview.schemes.ResidueProperties;
88 import jalview.schemes.StrandColourScheme;
89 import jalview.schemes.TCoffeeColourScheme;
90 import jalview.schemes.TaylorColourScheme;
91 import jalview.schemes.TurnColourScheme;
92 import jalview.schemes.UserColourScheme;
93 import jalview.schemes.ZappoColourScheme;
94 import jalview.structure.StructureSelectionManager;
95 import jalview.util.MessageManager;
96 import jalview.viewmodel.AlignmentViewport;
97 import jalview.ws.jws1.Discoverer;
98 import jalview.ws.jws2.Jws2Discoverer;
99 import jalview.ws.jws2.jabaws2.Jws2Instance;
100 import jalview.ws.seqfetcher.DbSourceProxy;
102 import java.awt.BorderLayout;
103 import java.awt.Component;
104 import java.awt.Rectangle;
105 import java.awt.Toolkit;
106 import java.awt.datatransfer.Clipboard;
107 import java.awt.datatransfer.DataFlavor;
108 import java.awt.datatransfer.StringSelection;
109 import java.awt.datatransfer.Transferable;
110 import java.awt.dnd.DnDConstants;
111 import java.awt.dnd.DropTargetDragEvent;
112 import java.awt.dnd.DropTargetDropEvent;
113 import java.awt.dnd.DropTargetEvent;
114 import java.awt.dnd.DropTargetListener;
115 import java.awt.event.ActionEvent;
116 import java.awt.event.ActionListener;
117 import java.awt.event.ItemEvent;
118 import java.awt.event.ItemListener;
119 import java.awt.event.KeyAdapter;
120 import java.awt.event.KeyEvent;
121 import java.awt.event.MouseAdapter;
122 import java.awt.event.MouseEvent;
123 import java.awt.print.PageFormat;
124 import java.awt.print.PrinterJob;
125 import java.beans.PropertyChangeEvent;
128 import java.util.ArrayList;
129 import java.util.Arrays;
130 import java.util.Deque;
131 import java.util.Enumeration;
132 import java.util.Hashtable;
133 import java.util.List;
134 import java.util.Vector;
136 import javax.swing.JCheckBoxMenuItem;
137 import javax.swing.JEditorPane;
138 import javax.swing.JInternalFrame;
139 import javax.swing.JLayeredPane;
140 import javax.swing.JMenu;
141 import javax.swing.JMenuItem;
142 import javax.swing.JOptionPane;
143 import javax.swing.JRadioButtonMenuItem;
144 import javax.swing.JScrollPane;
145 import javax.swing.SwingUtilities;
151 * @version $Revision$
153 public class AlignFrame extends GAlignFrame implements DropTargetListener,
154 IProgressIndicator, AlignViewControllerGuiI
157 public static final int DEFAULT_WIDTH = 700;
159 public static final int DEFAULT_HEIGHT = 500;
162 * The currently displayed panel (selected tabbed view if more than one)
164 public AlignmentPanel alignPanel;
166 AlignViewport viewport;
168 public AlignViewControllerI avc;
170 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
173 * Last format used to load or save alignments in this window
175 String currentFileFormat = null;
178 * Current filename for this alignment
180 String fileName = null;
183 * Creates a new AlignFrame object with specific width and height.
189 public AlignFrame(AlignmentI al, int width, int height)
191 this(al, null, width, height);
195 * Creates a new AlignFrame object with specific width, height and
201 * @param sequenceSetId
203 public AlignFrame(AlignmentI al, int width, int height,
204 String sequenceSetId)
206 this(al, null, width, height, sequenceSetId);
210 * Creates a new AlignFrame object with specific width, height and
216 * @param sequenceSetId
219 public AlignFrame(AlignmentI al, int width, int height,
220 String sequenceSetId, String viewId)
222 this(al, null, width, height, sequenceSetId, viewId);
226 * new alignment window with hidden columns
230 * @param hiddenColumns
231 * ColumnSelection or null
233 * Width of alignment frame
237 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
238 int width, int height)
240 this(al, hiddenColumns, width, height, null);
244 * Create alignment frame for al with hiddenColumns, a specific width and
245 * height, and specific sequenceId
248 * @param hiddenColumns
251 * @param sequenceSetId
254 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
255 int width, int height, String sequenceSetId)
257 this(al, hiddenColumns, width, height, sequenceSetId, null);
261 * Create alignment frame for al with hiddenColumns, a specific width and
262 * height, and specific sequenceId
265 * @param hiddenColumns
268 * @param sequenceSetId
273 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
274 int width, int height, String sequenceSetId, String viewId)
276 setSize(width, height);
278 if (al.getDataset() == null)
283 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
285 alignPanel = new AlignmentPanel(this, viewport);
287 addAlignmentPanel(alignPanel, true);
291 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
292 ColumnSelection hiddenColumns, int width, int height)
294 setSize(width, height);
296 if (al.getDataset() == null)
301 viewport = new AlignViewport(al, hiddenColumns);
303 if (hiddenSeqs != null && hiddenSeqs.length > 0)
305 viewport.hideSequence(hiddenSeqs);
307 alignPanel = new AlignmentPanel(this, viewport);
308 addAlignmentPanel(alignPanel, true);
313 * Make a new AlignFrame from existing alignmentPanels
320 public AlignFrame(AlignmentPanel ap)
324 addAlignmentPanel(ap, false);
329 * initalise the alignframe from the underlying viewport data and the
334 if (!Jalview.isHeadlessMode())
336 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
339 avc = new jalview.controller.AlignViewController(this, viewport,
341 if (viewport.getAlignmentConservationAnnotation() == null)
343 BLOSUM62Colour.setEnabled(false);
344 conservationMenuItem.setEnabled(false);
345 modifyConservation.setEnabled(false);
346 // PIDColour.setEnabled(false);
347 // abovePIDThreshold.setEnabled(false);
348 // modifyPID.setEnabled(false);
351 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
354 if (sortby.equals("Id"))
356 sortIDMenuItem_actionPerformed(null);
358 else if (sortby.equals("Pairwise Identity"))
360 sortPairwiseMenuItem_actionPerformed(null);
363 if (Desktop.desktop != null)
365 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
366 addServiceListeners();
367 setGUINucleotide(viewport.getAlignment().isNucleotide());
371 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
373 setMenusFromViewport(viewport);
374 buildSortByAnnotationScoresMenu();
377 if (viewport.getWrapAlignment())
379 wrapMenuItem_actionPerformed(null);
382 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
384 this.overviewMenuItem_actionPerformed(null);
389 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
390 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
391 final String menuLabel = MessageManager
392 .getString("label.copy_format_from");
393 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
394 new ViewSetProvider()
398 public AlignmentPanel[] getAllAlignmentPanels()
401 origview.add(alignPanel);
402 // make an array of all alignment panels except for this one
403 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
404 Arrays.asList(Desktop.getAlignmentPanels(null)));
405 aps.remove(AlignFrame.this.alignPanel);
406 return aps.toArray(new AlignmentPanel[aps.size()]);
408 }, selviews, new ItemListener()
412 public void itemStateChanged(ItemEvent e)
414 if (origview.size() > 0)
416 final AlignmentPanel ap = origview.get(0);
419 * Copy the ViewStyle of the selected panel to 'this one'.
420 * Don't change value of 'scaleProteinAsCdna' unless copying
423 ViewStyleI vs = selviews.get(0).getAlignViewport()
425 boolean fromSplitFrame = selviews.get(0)
426 .getAlignViewport().getCodingComplement() != null;
429 vs.setScaleProteinAsCdna(ap.getAlignViewport()
430 .getViewStyle().isScaleProteinAsCdna());
432 ap.getAlignViewport().setViewStyle(vs);
435 * Also rescale ViewStyle of SplitFrame complement if there is
436 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
437 * the whole ViewStyle (allow cDNA protein to have different
440 AlignViewportI complement = ap.getAlignViewport()
441 .getCodingComplement();
442 if (complement != null && vs.isScaleProteinAsCdna())
444 AlignFrame af = Desktop.getAlignFrameFor(complement);
445 ((SplitFrame) af.getSplitViewContainer())
447 af.setMenusForViewport();
451 ap.setSelected(true);
452 ap.alignFrame.setMenusForViewport();
457 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
458 .indexOf("devel") > -1
459 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
460 .indexOf("test") > -1)
462 formatMenu.add(vsel);
468 * Change the filename and format for the alignment, and enable the 'reload'
469 * button functionality.
476 public void setFileName(String file, String format)
479 setFileFormat(format);
480 reload.setEnabled(true);
484 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
487 void addKeyListener()
489 addKeyListener(new KeyAdapter()
492 public void keyPressed(KeyEvent evt)
494 if (viewport.cursorMode
495 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
496 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
497 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
498 && Character.isDigit(evt.getKeyChar()))
500 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
503 switch (evt.getKeyCode())
506 case 27: // escape key
507 deselectAllSequenceMenuItem_actionPerformed(null);
511 case KeyEvent.VK_DOWN:
512 if (evt.isAltDown() || !viewport.cursorMode)
514 moveSelectedSequences(false);
516 if (viewport.cursorMode)
518 alignPanel.getSeqPanel().moveCursor(0, 1);
523 if (evt.isAltDown() || !viewport.cursorMode)
525 moveSelectedSequences(true);
527 if (viewport.cursorMode)
529 alignPanel.getSeqPanel().moveCursor(0, -1);
534 case KeyEvent.VK_LEFT:
535 if (evt.isAltDown() || !viewport.cursorMode)
537 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
541 alignPanel.getSeqPanel().moveCursor(-1, 0);
546 case KeyEvent.VK_RIGHT:
547 if (evt.isAltDown() || !viewport.cursorMode)
549 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
553 alignPanel.getSeqPanel().moveCursor(1, 0);
557 case KeyEvent.VK_SPACE:
558 if (viewport.cursorMode)
560 alignPanel.getSeqPanel().insertGapAtCursor(
561 evt.isControlDown() || evt.isShiftDown()
566 // case KeyEvent.VK_A:
567 // if (viewport.cursorMode)
569 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
570 // //System.out.println("A");
574 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
575 * System.out.println("closing bracket"); } break;
577 case KeyEvent.VK_DELETE:
578 case KeyEvent.VK_BACK_SPACE:
579 if (!viewport.cursorMode)
581 cut_actionPerformed(null);
585 alignPanel.getSeqPanel().deleteGapAtCursor(
586 evt.isControlDown() || evt.isShiftDown()
593 if (viewport.cursorMode)
595 alignPanel.getSeqPanel().setCursorRow();
599 if (viewport.cursorMode && !evt.isControlDown())
601 alignPanel.getSeqPanel().setCursorColumn();
605 if (viewport.cursorMode)
607 alignPanel.getSeqPanel().setCursorPosition();
611 case KeyEvent.VK_ENTER:
612 case KeyEvent.VK_COMMA:
613 if (viewport.cursorMode)
615 alignPanel.getSeqPanel().setCursorRowAndColumn();
620 if (viewport.cursorMode)
622 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
626 if (viewport.cursorMode)
628 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
633 viewport.cursorMode = !viewport.cursorMode;
634 statusBar.setText(MessageManager.formatMessage(
635 "label.keyboard_editing_mode",
636 new String[] { (viewport.cursorMode ? "on" : "off") }));
637 if (viewport.cursorMode)
639 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
640 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
642 alignPanel.getSeqPanel().seqCanvas.repaint();
648 Help.showHelpWindow();
649 } catch (Exception ex)
651 ex.printStackTrace();
656 boolean toggleSeqs = !evt.isControlDown();
657 boolean toggleCols = !evt.isShiftDown();
658 toggleHiddenRegions(toggleSeqs, toggleCols);
661 case KeyEvent.VK_PAGE_UP:
662 if (viewport.getWrapAlignment())
664 alignPanel.scrollUp(true);
668 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
669 - viewport.endSeq + viewport.startSeq);
672 case KeyEvent.VK_PAGE_DOWN:
673 if (viewport.getWrapAlignment())
675 alignPanel.scrollUp(false);
679 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
680 + viewport.endSeq - viewport.startSeq);
687 public void keyReleased(KeyEvent evt)
689 switch (evt.getKeyCode())
691 case KeyEvent.VK_LEFT:
692 if (evt.isAltDown() || !viewport.cursorMode)
694 viewport.firePropertyChange("alignment", null, viewport
695 .getAlignment().getSequences());
699 case KeyEvent.VK_RIGHT:
700 if (evt.isAltDown() || !viewport.cursorMode)
702 viewport.firePropertyChange("alignment", null, viewport
703 .getAlignment().getSequences());
711 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
713 ap.alignFrame = this;
714 avc = new jalview.controller.AlignViewController(this, viewport,
719 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
721 int aSize = alignPanels.size();
723 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
725 if (aSize == 1 && ap.av.viewName == null)
727 this.getContentPane().add(ap, BorderLayout.CENTER);
733 setInitialTabVisible();
736 expandViews.setEnabled(true);
737 gatherViews.setEnabled(true);
738 tabbedPane.addTab(ap.av.viewName, ap);
740 ap.setVisible(false);
745 if (ap.av.isPadGaps())
747 ap.av.getAlignment().padGaps();
749 ap.av.updateConservation(ap);
750 ap.av.updateConsensus(ap);
751 ap.av.updateStrucConsensus(ap);
755 public void setInitialTabVisible()
757 expandViews.setEnabled(true);
758 gatherViews.setEnabled(true);
759 tabbedPane.setVisible(true);
760 AlignmentPanel first = alignPanels.get(0);
761 tabbedPane.addTab(first.av.viewName, first);
762 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
765 public AlignViewport getViewport()
770 /* Set up intrinsic listeners for dynamically generated GUI bits. */
771 private void addServiceListeners()
773 final java.beans.PropertyChangeListener thisListener;
774 Desktop.instance.addJalviewPropertyChangeListener("services",
775 thisListener = new java.beans.PropertyChangeListener()
778 public void propertyChange(PropertyChangeEvent evt)
780 // // System.out.println("Discoverer property change.");
781 // if (evt.getPropertyName().equals("services"))
783 SwingUtilities.invokeLater(new Runnable()
790 .println("Rebuild WS Menu for service change");
791 BuildWebServiceMenu();
798 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
801 public void internalFrameClosed(
802 javax.swing.event.InternalFrameEvent evt)
804 // System.out.println("deregistering discoverer listener");
805 Desktop.instance.removeJalviewPropertyChangeListener("services",
807 closeMenuItem_actionPerformed(true);
810 // Finally, build the menu once to get current service state
811 new Thread(new Runnable()
816 BuildWebServiceMenu();
822 * Configure menu items that vary according to whether the alignment is
823 * nucleotide or protein
827 public void setGUINucleotide(boolean nucleotide)
829 showTranslation.setVisible(nucleotide);
830 showReverse.setVisible(nucleotide);
831 showReverseComplement.setVisible(nucleotide);
832 conservationMenuItem.setEnabled(!nucleotide);
833 modifyConservation.setEnabled(!nucleotide);
834 showGroupConservation.setEnabled(!nucleotide);
835 rnahelicesColour.setEnabled(nucleotide);
836 purinePyrimidineColour.setEnabled(nucleotide);
837 showComplementMenuItem.setText(MessageManager
838 .getString(nucleotide ? "label.protein" : "label.nucleotide"));
839 setColourSelected(jalview.bin.Cache.getDefault(
840 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
841 : Preferences.DEFAULT_COLOUR_PROT, "None"));
845 * set up menus for the current viewport. This may be called after any
846 * operation that affects the data in the current view (selection changed,
847 * etc) to update the menus to reflect the new state.
850 public void setMenusForViewport()
852 setMenusFromViewport(viewport);
856 * Need to call this method when tabs are selected for multiple views, or when
857 * loading from Jalview2XML.java
862 void setMenusFromViewport(AlignViewport av)
864 padGapsMenuitem.setSelected(av.isPadGaps());
865 colourTextMenuItem.setSelected(av.isShowColourText());
866 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
867 conservationMenuItem.setSelected(av.getConservationSelected());
868 seqLimits.setSelected(av.getShowJVSuffix());
869 idRightAlign.setSelected(av.isRightAlignIds());
870 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
871 renderGapsMenuItem.setSelected(av.isRenderGaps());
872 wrapMenuItem.setSelected(av.getWrapAlignment());
873 scaleAbove.setVisible(av.getWrapAlignment());
874 scaleLeft.setVisible(av.getWrapAlignment());
875 scaleRight.setVisible(av.getWrapAlignment());
876 annotationPanelMenuItem.setState(av.isShowAnnotation());
878 * Show/hide annotations only enabled if annotation panel is shown
880 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
881 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
882 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
883 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
884 viewBoxesMenuItem.setSelected(av.getShowBoxes());
885 viewTextMenuItem.setSelected(av.getShowText());
886 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
887 showGroupConsensus.setSelected(av.isShowGroupConsensus());
888 showGroupConservation.setSelected(av.isShowGroupConservation());
889 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
890 showSequenceLogo.setSelected(av.isShowSequenceLogo());
891 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
893 setColourSelected(ColourSchemeProperty.getColourName(av
894 .getGlobalColourScheme()));
896 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
897 hiddenMarkers.setState(av.getShowHiddenMarkers());
898 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
899 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
900 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
901 autoCalculate.setSelected(av.autoCalculateConsensus);
902 sortByTree.setSelected(av.sortByTree);
903 listenToViewSelections.setSelected(av.followSelection);
904 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
906 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
908 showProducts.setEnabled(canShowProducts());
913 private IProgressIndicator progressBar;
918 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
921 public void setProgressBar(String message, long id)
923 progressBar.setProgressBar(message, id);
927 public void registerHandler(final long id,
928 final IProgressIndicatorHandler handler)
930 progressBar.registerHandler(id, handler);
935 * @return true if any progress bars are still active
938 public boolean operationInProgress()
940 return progressBar.operationInProgress();
944 public void setStatus(String text)
946 statusBar.setText(text);
950 * Added so Castor Mapping file can obtain Jalview Version
952 public String getVersion()
954 return jalview.bin.Cache.getProperty("VERSION");
957 public FeatureRenderer getFeatureRenderer()
959 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
963 public void fetchSequence_actionPerformed(ActionEvent e)
965 new SequenceFetcher(this);
969 public void addFromFile_actionPerformed(ActionEvent e)
971 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
975 public void reload_actionPerformed(ActionEvent e)
977 if (fileName != null)
979 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
980 // originating file's format
981 // TODO: work out how to recover feature settings for correct view(s) when
983 if (currentFileFormat.equals("Jalview"))
985 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
986 for (int i = 0; i < frames.length; i++)
988 if (frames[i] instanceof AlignFrame && frames[i] != this
989 && ((AlignFrame) frames[i]).fileName != null
990 && ((AlignFrame) frames[i]).fileName.equals(fileName))
994 frames[i].setSelected(true);
995 Desktop.instance.closeAssociatedWindows();
996 } catch (java.beans.PropertyVetoException ex)
1002 Desktop.instance.closeAssociatedWindows();
1004 FileLoader loader = new FileLoader();
1005 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1006 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1010 Rectangle bounds = this.getBounds();
1012 FileLoader loader = new FileLoader();
1013 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1014 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1015 protocol, currentFileFormat);
1017 newframe.setBounds(bounds);
1018 if (featureSettings != null && featureSettings.isShowing())
1020 final Rectangle fspos = featureSettings.frame.getBounds();
1021 // TODO: need a 'show feature settings' function that takes bounds -
1022 // need to refactor Desktop.addFrame
1023 newframe.featureSettings_actionPerformed(null);
1024 final FeatureSettings nfs = newframe.featureSettings;
1025 SwingUtilities.invokeLater(new Runnable()
1030 nfs.frame.setBounds(fspos);
1033 this.featureSettings.close();
1034 this.featureSettings = null;
1036 this.closeMenuItem_actionPerformed(true);
1042 public void addFromText_actionPerformed(ActionEvent e)
1044 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1049 public void addFromURL_actionPerformed(ActionEvent e)
1051 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1055 public void save_actionPerformed(ActionEvent e)
1057 if (fileName == null
1058 || (currentFileFormat == null || !jalview.io.FormatAdapter
1059 .isValidIOFormat(currentFileFormat, true))
1060 || fileName.startsWith("http"))
1062 saveAs_actionPerformed(null);
1066 saveAlignment(fileName, currentFileFormat);
1077 public void saveAs_actionPerformed(ActionEvent e)
1079 JalviewFileChooser chooser = new JalviewFileChooser(
1080 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1081 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1082 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1083 currentFileFormat, false);
1085 chooser.setFileView(new JalviewFileView());
1086 chooser.setDialogTitle(MessageManager
1087 .getString("label.save_alignment_to_file"));
1088 chooser.setToolTipText(MessageManager.getString("action.save"));
1090 int value = chooser.showSaveDialog(this);
1092 if (value == JalviewFileChooser.APPROVE_OPTION)
1094 currentFileFormat = chooser.getSelectedFormat();
1095 while (currentFileFormat == null)
1098 .showInternalMessageDialog(
1101 .getString("label.select_file_format_before_saving"),
1103 .getString("label.file_format_not_specified"),
1104 JOptionPane.WARNING_MESSAGE);
1105 currentFileFormat = chooser.getSelectedFormat();
1106 value = chooser.showSaveDialog(this);
1107 if (value != JalviewFileChooser.APPROVE_OPTION)
1113 fileName = chooser.getSelectedFile().getPath();
1115 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1118 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1119 if (currentFileFormat.indexOf(" ") > -1)
1121 currentFileFormat = currentFileFormat.substring(0,
1122 currentFileFormat.indexOf(" "));
1124 saveAlignment(fileName, currentFileFormat);
1128 public boolean saveAlignment(String file, String format)
1130 boolean success = true;
1132 if (format.equalsIgnoreCase("Jalview"))
1134 String shortName = title;
1136 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1138 shortName = shortName.substring(shortName
1139 .lastIndexOf(java.io.File.separatorChar) + 1);
1142 success = new Jalview2XML().saveAlignment(this, file, shortName);
1144 statusBar.setText(MessageManager.formatMessage(
1145 "label.successfully_saved_to_file_in_format", new Object[] {
1146 fileName, format }));
1151 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1153 warningMessage("Cannot save file " + fileName + " using format "
1154 + format, "Alignment output format not supported");
1155 if (!Jalview.isHeadlessMode())
1157 saveAs_actionPerformed(null);
1162 AlignmentExportData exportData = getAlignmentForExport(format,
1164 if (exportData.getSettings().isCancelled())
1168 FormatAdapter f = new FormatAdapter(alignPanel,
1169 exportData.getSettings());
1170 String output = f.formatSequences(
1172 exportData.getAlignment(), // class cast exceptions will
1173 // occur in the distant future
1174 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1175 f.getCacheSuffixDefault(format),
1176 viewport.getColumnSelection());
1186 java.io.PrintWriter out = new java.io.PrintWriter(
1187 new java.io.FileWriter(file));
1191 this.setTitle(file);
1192 statusBar.setText(MessageManager.formatMessage(
1193 "label.successfully_saved_to_file_in_format",
1194 new Object[] { fileName, format }));
1195 } catch (Exception ex)
1198 ex.printStackTrace();
1205 JOptionPane.showInternalMessageDialog(this, MessageManager
1206 .formatMessage("label.couldnt_save_file",
1207 new Object[] { fileName }), MessageManager
1208 .getString("label.error_saving_file"),
1209 JOptionPane.WARNING_MESSAGE);
1215 private void warningMessage(String warning, String title)
1217 if (new jalview.util.Platform().isHeadless())
1219 System.err.println("Warning: " + title + "\nWarning: " + warning);
1224 JOptionPane.showInternalMessageDialog(this, warning, title,
1225 JOptionPane.WARNING_MESSAGE);
1237 protected void outputText_actionPerformed(ActionEvent e)
1240 AlignmentExportData exportData = getAlignmentForExport(
1241 e.getActionCommand(), viewport, null);
1242 if (exportData.getSettings().isCancelled())
1246 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1247 cap.setForInput(null);
1250 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1251 .formatSequences(e.getActionCommand(),
1252 exportData.getAlignment(),
1253 exportData.getOmitHidden(),
1254 exportData.getStartEndPostions(),
1255 viewport.getColumnSelection()));
1256 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1257 "label.alignment_output_command",
1258 new Object[] { e.getActionCommand() }), 600, 500);
1259 } catch (OutOfMemoryError oom)
1261 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1267 public static AlignmentExportData getAlignmentForExport(
1268 String exportFormat, AlignViewportI viewport,
1269 AlignExportSettingI exportSettings)
1271 AlignmentI alignmentToExport = null;
1272 AlignExportSettingI settings = exportSettings;
1273 String[] omitHidden = null;
1274 int[] alignmentStartEnd = new int[2];
1276 HiddenSequences hiddenSeqs = viewport.getAlignment()
1277 .getHiddenSequences();
1279 alignmentToExport = viewport.getAlignment();
1280 alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
1282 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1283 if (settings == null)
1285 settings = new AlignExportSettings(hasHiddenSeqs,
1286 viewport.hasHiddenColumns(), exportFormat);
1288 // settings.isExportAnnotations();
1290 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1292 omitHidden = viewport.getViewAsString(false);
1295 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1297 alignmentToExport = hiddenSeqs.getFullAlignment();
1301 alignmentToExport = viewport.getAlignment();
1302 alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1303 .getColumnSelection().getHiddenColumns());
1305 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1306 omitHidden, alignmentStartEnd, settings);
1310 public static int[] getStartEnd(int[] aligmentStartEnd,
1311 List<int[]> hiddenCols)
1313 int startPos = aligmentStartEnd[0];
1314 int endPos = aligmentStartEnd[1];
1316 int[] lowestRange = new int[] { -1, -1 };
1317 int[] higestRange = new int[] { -1, -1 };
1319 for (int[] hiddenCol : hiddenCols)
1321 lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1322 higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1325 if (lowestRange[0] == -1 && lowestRange[1] == -1)
1327 startPos = aligmentStartEnd[0];
1331 startPos = lowestRange[1] + 1;
1334 if (higestRange[0] == -1 && higestRange[1] == -1)
1336 endPos = aligmentStartEnd[1];
1340 endPos = higestRange[0] - 1;
1343 // System.out.println("Export range : " + startPos + " - " + endPos);
1344 return new int[] { startPos, endPos };
1347 public static void main(String[] args)
1349 ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1350 hiddenCols.add(new int[] { 0, 0 });
1351 hiddenCols.add(new int[] { 6, 9 });
1352 hiddenCols.add(new int[] { 11, 12 });
1353 hiddenCols.add(new int[] { 33, 33 });
1354 hiddenCols.add(new int[] { 50, 50 });
1356 int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1357 // System.out.println("Export range : " + x[0] + " - " + x[1]);
1367 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1369 new HtmlSvgOutput(null, alignPanel);
1373 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1375 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
1376 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1379 public void createImageMap(File file, String image)
1381 alignPanel.makePNGImageMap(file, image);
1391 public void createPNG(File f)
1393 alignPanel.makePNG(f);
1403 public void createEPS(File f)
1405 alignPanel.makeEPS(f);
1409 public void createSVG(File f)
1411 alignPanel.makeSVG(f);
1415 public void pageSetup_actionPerformed(ActionEvent e)
1417 PrinterJob printJob = PrinterJob.getPrinterJob();
1418 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1428 public void printMenuItem_actionPerformed(ActionEvent e)
1430 // Putting in a thread avoids Swing painting problems
1431 PrintThread thread = new PrintThread(alignPanel);
1436 public void exportFeatures_actionPerformed(ActionEvent e)
1438 new AnnotationExporter().exportFeatures(alignPanel);
1442 public void exportAnnotations_actionPerformed(ActionEvent e)
1444 new AnnotationExporter().exportAnnotations(alignPanel);
1448 public void associatedData_actionPerformed(ActionEvent e)
1450 // Pick the tree file
1451 JalviewFileChooser chooser = new JalviewFileChooser(
1452 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1453 chooser.setFileView(new JalviewFileView());
1454 chooser.setDialogTitle(MessageManager
1455 .getString("label.load_jalview_annotations"));
1456 chooser.setToolTipText(MessageManager
1457 .getString("label.load_jalview_annotations"));
1459 int value = chooser.showOpenDialog(null);
1461 if (value == JalviewFileChooser.APPROVE_OPTION)
1463 String choice = chooser.getSelectedFile().getPath();
1464 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1465 loadJalviewDataFile(choice, null, null, null);
1471 * Close the current view or all views in the alignment frame. If the frame
1472 * only contains one view then the alignment will be removed from memory.
1474 * @param closeAllTabs
1477 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1479 if (alignPanels != null && alignPanels.size() < 2)
1481 closeAllTabs = true;
1486 if (alignPanels != null)
1490 if (this.isClosed())
1492 // really close all the windows - otherwise wait till
1493 // setClosed(true) is called
1494 for (int i = 0; i < alignPanels.size(); i++)
1496 AlignmentPanel ap = alignPanels.get(i);
1503 closeView(alignPanel);
1510 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1511 * be called recursively, with the frame now in 'closed' state
1513 this.setClosed(true);
1515 } catch (Exception ex)
1517 ex.printStackTrace();
1522 * Close the specified panel and close up tabs appropriately.
1524 * @param panelToClose
1526 public void closeView(AlignmentPanel panelToClose)
1528 int index = tabbedPane.getSelectedIndex();
1529 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1530 alignPanels.remove(panelToClose);
1531 panelToClose.closePanel();
1532 panelToClose = null;
1534 tabbedPane.removeTabAt(closedindex);
1535 tabbedPane.validate();
1537 if (index > closedindex || index == tabbedPane.getTabCount())
1539 // modify currently selected tab index if necessary.
1543 this.tabSelectionChanged(index);
1549 void updateEditMenuBar()
1552 if (viewport.getHistoryList().size() > 0)
1554 undoMenuItem.setEnabled(true);
1555 CommandI command = viewport.getHistoryList().peek();
1556 undoMenuItem.setText(MessageManager.formatMessage(
1557 "label.undo_command",
1558 new Object[] { command.getDescription() }));
1562 undoMenuItem.setEnabled(false);
1563 undoMenuItem.setText(MessageManager.getString("action.undo"));
1566 if (viewport.getRedoList().size() > 0)
1568 redoMenuItem.setEnabled(true);
1570 CommandI command = viewport.getRedoList().peek();
1571 redoMenuItem.setText(MessageManager.formatMessage(
1572 "label.redo_command",
1573 new Object[] { command.getDescription() }));
1577 redoMenuItem.setEnabled(false);
1578 redoMenuItem.setText(MessageManager.getString("action.redo"));
1583 public void addHistoryItem(CommandI command)
1585 if (command.getSize() > 0)
1587 viewport.addToHistoryList(command);
1588 viewport.clearRedoList();
1589 updateEditMenuBar();
1590 viewport.updateHiddenColumns();
1591 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1592 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1593 // viewport.getColumnSelection()
1594 // .getHiddenColumns().size() > 0);
1600 * @return alignment objects for all views
1602 AlignmentI[] getViewAlignments()
1604 if (alignPanels != null)
1606 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1608 for (AlignmentPanel ap : alignPanels)
1610 als[i++] = ap.av.getAlignment();
1614 if (viewport != null)
1616 return new AlignmentI[] { viewport.getAlignment() };
1628 protected void undoMenuItem_actionPerformed(ActionEvent e)
1630 if (viewport.getHistoryList().isEmpty())
1634 CommandI command = viewport.getHistoryList().pop();
1635 viewport.addToRedoList(command);
1636 command.undoCommand(getViewAlignments());
1638 AlignmentViewport originalSource = getOriginatingSource(command);
1639 updateEditMenuBar();
1641 if (originalSource != null)
1643 if (originalSource != viewport)
1646 .warn("Implementation worry: mismatch of viewport origin for undo");
1648 originalSource.updateHiddenColumns();
1649 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1651 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1652 // viewport.getColumnSelection()
1653 // .getHiddenColumns().size() > 0);
1654 originalSource.firePropertyChange("alignment", null, originalSource
1655 .getAlignment().getSequences());
1666 protected void redoMenuItem_actionPerformed(ActionEvent e)
1668 if (viewport.getRedoList().size() < 1)
1673 CommandI command = viewport.getRedoList().pop();
1674 viewport.addToHistoryList(command);
1675 command.doCommand(getViewAlignments());
1677 AlignmentViewport originalSource = getOriginatingSource(command);
1678 updateEditMenuBar();
1680 if (originalSource != null)
1683 if (originalSource != viewport)
1686 .warn("Implementation worry: mismatch of viewport origin for redo");
1688 originalSource.updateHiddenColumns();
1689 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1691 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1692 // viewport.getColumnSelection()
1693 // .getHiddenColumns().size() > 0);
1694 originalSource.firePropertyChange("alignment", null, originalSource
1695 .getAlignment().getSequences());
1699 AlignmentViewport getOriginatingSource(CommandI command)
1701 AlignmentViewport originalSource = null;
1702 // For sequence removal and addition, we need to fire
1703 // the property change event FROM the viewport where the
1704 // original alignment was altered
1705 AlignmentI al = null;
1706 if (command instanceof EditCommand)
1708 EditCommand editCommand = (EditCommand) command;
1709 al = editCommand.getAlignment();
1710 List<Component> comps = PaintRefresher.components.get(viewport
1711 .getSequenceSetId());
1713 for (Component comp : comps)
1715 if (comp instanceof AlignmentPanel)
1717 if (al == ((AlignmentPanel) comp).av.getAlignment())
1719 originalSource = ((AlignmentPanel) comp).av;
1726 if (originalSource == null)
1728 // The original view is closed, we must validate
1729 // the current view against the closed view first
1732 PaintRefresher.validateSequences(al, viewport.getAlignment());
1735 originalSource = viewport;
1738 return originalSource;
1747 public void moveSelectedSequences(boolean up)
1749 SequenceGroup sg = viewport.getSelectionGroup();
1755 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1756 viewport.getHiddenRepSequences(), up);
1757 alignPanel.paintAlignment(true);
1760 synchronized void slideSequences(boolean right, int size)
1762 List<SequenceI> sg = new ArrayList<SequenceI>();
1763 if (viewport.cursorMode)
1765 sg.add(viewport.getAlignment().getSequenceAt(
1766 alignPanel.getSeqPanel().seqCanvas.cursorY));
1768 else if (viewport.getSelectionGroup() != null
1769 && viewport.getSelectionGroup().getSize() != viewport
1770 .getAlignment().getHeight())
1772 sg = viewport.getSelectionGroup().getSequences(
1773 viewport.getHiddenRepSequences());
1781 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1783 for (SequenceI seq : viewport.getAlignment().getSequences())
1785 if (!sg.contains(seq))
1787 invertGroup.add(seq);
1791 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1793 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1794 for (int i = 0; i < invertGroup.size(); i++)
1796 seqs2[i] = invertGroup.get(i);
1799 SlideSequencesCommand ssc;
1802 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1803 size, viewport.getGapCharacter());
1807 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1808 size, viewport.getGapCharacter());
1811 int groupAdjustment = 0;
1812 if (ssc.getGapsInsertedBegin() && right)
1814 if (viewport.cursorMode)
1816 alignPanel.getSeqPanel().moveCursor(size, 0);
1820 groupAdjustment = size;
1823 else if (!ssc.getGapsInsertedBegin() && !right)
1825 if (viewport.cursorMode)
1827 alignPanel.getSeqPanel().moveCursor(-size, 0);
1831 groupAdjustment = -size;
1835 if (groupAdjustment != 0)
1837 viewport.getSelectionGroup().setStartRes(
1838 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1839 viewport.getSelectionGroup().setEndRes(
1840 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1844 * just extend the last slide command if compatible; but not if in
1845 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1847 boolean appendHistoryItem = false;
1848 Deque<CommandI> historyList = viewport.getHistoryList();
1849 boolean inSplitFrame = getSplitViewContainer() != null;
1850 if (!inSplitFrame && historyList != null && historyList.size() > 0
1851 && historyList.peek() instanceof SlideSequencesCommand)
1853 appendHistoryItem = ssc
1854 .appendSlideCommand((SlideSequencesCommand) historyList
1858 if (!appendHistoryItem)
1860 addHistoryItem(ssc);
1873 protected void copy_actionPerformed(ActionEvent e)
1876 if (viewport.getSelectionGroup() == null)
1880 // TODO: preserve the ordering of displayed alignment annotation in any
1881 // internal paste (particularly sequence associated annotation)
1882 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1883 String[] omitHidden = null;
1885 if (viewport.hasHiddenColumns())
1887 omitHidden = viewport.getViewAsString(true);
1890 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1893 StringSelection ss = new StringSelection(output);
1897 jalview.gui.Desktop.internalCopy = true;
1898 // Its really worth setting the clipboard contents
1899 // to empty before setting the large StringSelection!!
1900 Toolkit.getDefaultToolkit().getSystemClipboard()
1901 .setContents(new StringSelection(""), null);
1903 Toolkit.getDefaultToolkit().getSystemClipboard()
1904 .setContents(ss, Desktop.instance);
1905 } catch (OutOfMemoryError er)
1907 new OOMWarning("copying region", er);
1911 ArrayList<int[]> hiddenColumns = null;
1912 if (viewport.hasHiddenColumns())
1914 hiddenColumns = new ArrayList<int[]>();
1915 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1916 .getSelectionGroup().getEndRes();
1917 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1919 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1921 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1922 region[1] - hiddenOffset });
1927 Desktop.jalviewClipboard = new Object[] { seqs,
1928 viewport.getAlignment().getDataset(), hiddenColumns };
1929 statusBar.setText(MessageManager.formatMessage(
1930 "label.copied_sequences_to_clipboard", new Object[] { Integer
1931 .valueOf(seqs.length).toString() }));
1941 protected void pasteNew_actionPerformed(ActionEvent e)
1953 protected void pasteThis_actionPerformed(ActionEvent e)
1959 * Paste contents of Jalview clipboard
1961 * @param newAlignment
1962 * true to paste to a new alignment, otherwise add to this.
1964 void paste(boolean newAlignment)
1966 boolean externalPaste = true;
1969 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1970 Transferable contents = c.getContents(this);
1972 if (contents == null)
1980 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1981 if (str.length() < 1)
1986 format = new IdentifyFile().identify(str, "Paste");
1988 } catch (OutOfMemoryError er)
1990 new OOMWarning("Out of memory pasting sequences!!", er);
1994 SequenceI[] sequences;
1995 boolean annotationAdded = false;
1996 AlignmentI alignment = null;
1998 if (Desktop.jalviewClipboard != null)
2000 // The clipboard was filled from within Jalview, we must use the
2002 // And dataset from the copied alignment
2003 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2004 // be doubly sure that we create *new* sequence objects.
2005 sequences = new SequenceI[newseq.length];
2006 for (int i = 0; i < newseq.length; i++)
2008 sequences[i] = new Sequence(newseq[i]);
2010 alignment = new Alignment(sequences);
2011 externalPaste = false;
2015 // parse the clipboard as an alignment.
2016 alignment = new FormatAdapter().readFile(str, "Paste", format);
2017 sequences = alignment.getSequencesArray();
2021 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2027 if (Desktop.jalviewClipboard != null)
2029 // dataset is inherited
2030 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2034 // new dataset is constructed
2035 alignment.setDataset(null);
2037 alwidth = alignment.getWidth() + 1;
2041 AlignmentI pastedal = alignment; // preserve pasted alignment object
2042 // Add pasted sequences and dataset into existing alignment.
2043 alignment = viewport.getAlignment();
2044 alwidth = alignment.getWidth() + 1;
2045 // decide if we need to import sequences from an existing dataset
2046 boolean importDs = Desktop.jalviewClipboard != null
2047 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2048 // importDs==true instructs us to copy over new dataset sequences from
2049 // an existing alignment
2050 Vector newDs = (importDs) ? new Vector() : null; // used to create
2051 // minimum dataset set
2053 for (int i = 0; i < sequences.length; i++)
2057 newDs.addElement(null);
2059 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2061 if (importDs && ds != null)
2063 if (!newDs.contains(ds))
2065 newDs.setElementAt(ds, i);
2066 ds = new Sequence(ds);
2067 // update with new dataset sequence
2068 sequences[i].setDatasetSequence(ds);
2072 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2077 // copy and derive new dataset sequence
2078 sequences[i] = sequences[i].deriveSequence();
2079 alignment.getDataset().addSequence(
2080 sequences[i].getDatasetSequence());
2081 // TODO: avoid creation of duplicate dataset sequences with a
2082 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2084 alignment.addSequence(sequences[i]); // merges dataset
2088 newDs.clear(); // tidy up
2090 if (alignment.getAlignmentAnnotation() != null)
2092 for (AlignmentAnnotation alan : alignment
2093 .getAlignmentAnnotation())
2095 if (alan.graphGroup > fgroup)
2097 fgroup = alan.graphGroup;
2101 if (pastedal.getAlignmentAnnotation() != null)
2103 // Add any annotation attached to alignment.
2104 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2105 for (int i = 0; i < alann.length; i++)
2107 annotationAdded = true;
2108 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2110 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2111 if (newann.graphGroup > -1)
2113 if (newGraphGroups.size() <= newann.graphGroup
2114 || newGraphGroups.get(newann.graphGroup) == null)
2116 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2118 newGraphGroups.add(q, null);
2120 newGraphGroups.set(newann.graphGroup, new Integer(
2123 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2127 newann.padAnnotation(alwidth);
2128 alignment.addAnnotation(newann);
2138 addHistoryItem(new EditCommand(
2139 MessageManager.getString("label.add_sequences"),
2140 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2142 // Add any annotations attached to sequences
2143 for (int i = 0; i < sequences.length; i++)
2145 if (sequences[i].getAnnotation() != null)
2147 AlignmentAnnotation newann;
2148 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2150 annotationAdded = true;
2151 newann = sequences[i].getAnnotation()[a];
2152 newann.adjustForAlignment();
2153 newann.padAnnotation(alwidth);
2154 if (newann.graphGroup > -1)
2156 if (newann.graphGroup > -1)
2158 if (newGraphGroups.size() <= newann.graphGroup
2159 || newGraphGroups.get(newann.graphGroup) == null)
2161 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2163 newGraphGroups.add(q, null);
2165 newGraphGroups.set(newann.graphGroup, new Integer(
2168 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2172 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2177 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2184 // propagate alignment changed.
2185 viewport.setEndSeq(alignment.getHeight());
2186 if (annotationAdded)
2188 // Duplicate sequence annotation in all views.
2189 AlignmentI[] alview = this.getViewAlignments();
2190 for (int i = 0; i < sequences.length; i++)
2192 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2197 for (int avnum = 0; avnum < alview.length; avnum++)
2199 if (alview[avnum] != alignment)
2201 // duplicate in a view other than the one with input focus
2202 int avwidth = alview[avnum].getWidth() + 1;
2203 // this relies on sann being preserved after we
2204 // modify the sequence's annotation array for each duplication
2205 for (int a = 0; a < sann.length; a++)
2207 AlignmentAnnotation newann = new AlignmentAnnotation(
2209 sequences[i].addAlignmentAnnotation(newann);
2210 newann.padAnnotation(avwidth);
2211 alview[avnum].addAnnotation(newann); // annotation was
2212 // duplicated earlier
2213 // TODO JAL-1145 graphGroups are not updated for sequence
2214 // annotation added to several views. This may cause
2216 alview[avnum].setAnnotationIndex(newann, a);
2221 buildSortByAnnotationScoresMenu();
2223 viewport.firePropertyChange("alignment", null,
2224 alignment.getSequences());
2225 if (alignPanels != null)
2227 for (AlignmentPanel ap : alignPanels)
2229 ap.validateAnnotationDimensions(false);
2234 alignPanel.validateAnnotationDimensions(false);
2240 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2242 String newtitle = new String("Copied sequences");
2244 if (Desktop.jalviewClipboard != null
2245 && Desktop.jalviewClipboard[2] != null)
2247 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2248 for (int[] region : hc)
2250 af.viewport.hideColumns(region[0], region[1]);
2254 // >>>This is a fix for the moment, until a better solution is
2256 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2258 alignPanel.getSeqPanel().seqCanvas
2259 .getFeatureRenderer());
2261 // TODO: maintain provenance of an alignment, rather than just make the
2262 // title a concatenation of operations.
2265 if (title.startsWith("Copied sequences"))
2271 newtitle = newtitle.concat("- from " + title);
2276 newtitle = new String("Pasted sequences");
2279 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2284 } catch (Exception ex)
2286 ex.printStackTrace();
2287 System.out.println("Exception whilst pasting: " + ex);
2288 // could be anything being pasted in here
2294 protected void expand_newalign(ActionEvent e)
2298 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2299 .getAlignment(), -1);
2300 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2302 String newtitle = new String("Flanking alignment");
2304 if (Desktop.jalviewClipboard != null
2305 && Desktop.jalviewClipboard[2] != null)
2307 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2308 for (int region[] : hc)
2310 af.viewport.hideColumns(region[0], region[1]);
2314 // >>>This is a fix for the moment, until a better solution is
2316 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2318 alignPanel.getSeqPanel().seqCanvas
2319 .getFeatureRenderer());
2321 // TODO: maintain provenance of an alignment, rather than just make the
2322 // title a concatenation of operations.
2324 if (title.startsWith("Copied sequences"))
2330 newtitle = newtitle.concat("- from " + title);
2334 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2336 } catch (Exception ex)
2338 ex.printStackTrace();
2339 System.out.println("Exception whilst pasting: " + ex);
2340 // could be anything being pasted in here
2341 } catch (OutOfMemoryError oom)
2343 new OOMWarning("Viewing flanking region of alignment", oom);
2354 protected void cut_actionPerformed(ActionEvent e)
2356 copy_actionPerformed(null);
2357 delete_actionPerformed(null);
2367 protected void delete_actionPerformed(ActionEvent evt)
2370 SequenceGroup sg = viewport.getSelectionGroup();
2377 * If the cut affects all sequences, warn, remove highlighted columns
2379 if (sg.getSize() == viewport.getAlignment().getHeight())
2381 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2382 .getAlignment().getWidth()) ? true : false;
2383 if (isEntireAlignWidth)
2385 int confirm = JOptionPane.showConfirmDialog(this,
2386 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2387 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2388 JOptionPane.OK_CANCEL_OPTION);
2390 if (confirm == JOptionPane.CANCEL_OPTION
2391 || confirm == JOptionPane.CLOSED_OPTION)
2396 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2397 sg.getEndRes() + 1);
2399 SequenceI[] cut = sg.getSequences()
2400 .toArray(new SequenceI[sg.getSize()]);
2402 addHistoryItem(new EditCommand(
2403 MessageManager.getString("label.cut_sequences"), Action.CUT,
2404 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2405 viewport.getAlignment()));
2407 viewport.setSelectionGroup(null);
2408 viewport.sendSelection();
2409 viewport.getAlignment().deleteGroup(sg);
2411 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2413 if (viewport.getAlignment().getHeight() < 1)
2417 this.setClosed(true);
2418 } catch (Exception ex)
2431 protected void deleteGroups_actionPerformed(ActionEvent e)
2433 if (avc.deleteGroups())
2435 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2436 alignPanel.updateAnnotation();
2437 alignPanel.paintAlignment(true);
2448 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2450 SequenceGroup sg = new SequenceGroup();
2452 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2454 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2457 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2458 viewport.setSelectionGroup(sg);
2459 viewport.sendSelection();
2460 alignPanel.paintAlignment(true);
2461 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2471 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2473 if (viewport.cursorMode)
2475 alignPanel.getSeqPanel().keyboardNo1 = null;
2476 alignPanel.getSeqPanel().keyboardNo2 = null;
2478 viewport.setSelectionGroup(null);
2479 viewport.getColumnSelection().clear();
2480 viewport.setSelectionGroup(null);
2481 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2482 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2483 alignPanel.paintAlignment(true);
2484 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2485 viewport.sendSelection();
2495 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2497 SequenceGroup sg = viewport.getSelectionGroup();
2501 selectAllSequenceMenuItem_actionPerformed(null);
2506 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2508 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2511 alignPanel.paintAlignment(true);
2512 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2513 viewport.sendSelection();
2517 public void invertColSel_actionPerformed(ActionEvent e)
2519 viewport.invertColumnSelection();
2520 alignPanel.paintAlignment(true);
2521 viewport.sendSelection();
2531 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2533 trimAlignment(true);
2543 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2545 trimAlignment(false);
2548 void trimAlignment(boolean trimLeft)
2550 ColumnSelection colSel = viewport.getColumnSelection();
2553 if (!colSel.isEmpty())
2557 column = colSel.getMin();
2561 column = colSel.getMax();
2565 if (viewport.getSelectionGroup() != null)
2567 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2568 viewport.getHiddenRepSequences());
2572 seqs = viewport.getAlignment().getSequencesArray();
2575 TrimRegionCommand trimRegion;
2578 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2579 column, viewport.getAlignment());
2580 viewport.setStartRes(0);
2584 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2585 column, viewport.getAlignment());
2588 statusBar.setText(MessageManager.formatMessage(
2589 "label.removed_columns",
2590 new String[] { Integer.valueOf(trimRegion.getSize())
2593 addHistoryItem(trimRegion);
2595 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2597 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2598 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2600 viewport.getAlignment().deleteGroup(sg);
2604 viewport.firePropertyChange("alignment", null, viewport
2605 .getAlignment().getSequences());
2616 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2618 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2621 if (viewport.getSelectionGroup() != null)
2623 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2624 viewport.getHiddenRepSequences());
2625 start = viewport.getSelectionGroup().getStartRes();
2626 end = viewport.getSelectionGroup().getEndRes();
2630 seqs = viewport.getAlignment().getSequencesArray();
2633 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2634 "Remove Gapped Columns", seqs, start, end,
2635 viewport.getAlignment());
2637 addHistoryItem(removeGapCols);
2639 statusBar.setText(MessageManager.formatMessage(
2640 "label.removed_empty_columns",
2641 new Object[] { Integer.valueOf(removeGapCols.getSize())
2644 // This is to maintain viewport position on first residue
2645 // of first sequence
2646 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2647 int startRes = seq.findPosition(viewport.startRes);
2648 // ShiftList shifts;
2649 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2650 // edit.alColumnChanges=shifts.getInverse();
2651 // if (viewport.hasHiddenColumns)
2652 // viewport.getColumnSelection().compensateForEdits(shifts);
2653 viewport.setStartRes(seq.findIndex(startRes) - 1);
2654 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2666 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2668 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2671 if (viewport.getSelectionGroup() != null)
2673 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2674 viewport.getHiddenRepSequences());
2675 start = viewport.getSelectionGroup().getStartRes();
2676 end = viewport.getSelectionGroup().getEndRes();
2680 seqs = viewport.getAlignment().getSequencesArray();
2683 // This is to maintain viewport position on first residue
2684 // of first sequence
2685 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2686 int startRes = seq.findPosition(viewport.startRes);
2688 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2689 viewport.getAlignment()));
2691 viewport.setStartRes(seq.findIndex(startRes) - 1);
2693 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2705 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2707 viewport.setPadGaps(padGapsMenuitem.isSelected());
2708 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2719 public void findMenuItem_actionPerformed(ActionEvent e)
2725 * Create a new view of the current alignment.
2728 public void newView_actionPerformed(ActionEvent e)
2730 newView(null, true);
2734 * Creates and shows a new view of the current alignment.
2737 * title of newly created view; if null, one will be generated
2738 * @param copyAnnotation
2739 * if true then duplicate all annnotation, groups and settings
2740 * @return new alignment panel, already displayed.
2742 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2745 * Create a new AlignmentPanel (with its own, new Viewport)
2747 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2749 if (!copyAnnotation)
2752 * remove all groups and annotation except for the automatic stuff
2754 newap.av.getAlignment().deleteAllGroups();
2755 newap.av.getAlignment().deleteAllAnnotations(false);
2758 newap.av.setGatherViewsHere(false);
2760 if (viewport.viewName == null)
2762 viewport.viewName = MessageManager
2763 .getString("label.view_name_original");
2767 * Views share the same edits undo and redo stacks
2769 newap.av.setHistoryList(viewport.getHistoryList());
2770 newap.av.setRedoList(viewport.getRedoList());
2773 * Views share the same mappings; need to deregister any new mappings
2774 * created by copyAlignPanel, and register the new reference to the shared
2777 newap.av.replaceMappings(viewport.getAlignment());
2779 newap.av.viewName = getNewViewName(viewTitle);
2781 addAlignmentPanel(newap, true);
2782 newap.alignmentChanged();
2784 if (alignPanels.size() == 2)
2786 viewport.setGatherViewsHere(true);
2788 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2793 * Make a new name for the view, ensuring it is unique within the current
2794 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2795 * these now use viewId. Unique view names are still desirable for usability.)
2800 protected String getNewViewName(String viewTitle)
2802 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2803 boolean addFirstIndex = false;
2804 if (viewTitle == null || viewTitle.trim().length() == 0)
2806 viewTitle = MessageManager.getString("action.view");
2807 addFirstIndex = true;
2811 index = 1;// we count from 1 if given a specific name
2813 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2815 List<Component> comps = PaintRefresher.components.get(viewport
2816 .getSequenceSetId());
2818 List<String> existingNames = getExistingViewNames(comps);
2820 while (existingNames.contains(newViewName))
2822 newViewName = viewTitle + " " + (++index);
2828 * Returns a list of distinct view names found in the given list of
2829 * components. View names are held on the viewport of an AlignmentPanel.
2834 protected List<String> getExistingViewNames(List<Component> comps)
2836 List<String> existingNames = new ArrayList<String>();
2837 for (Component comp : comps)
2839 if (comp instanceof AlignmentPanel)
2841 AlignmentPanel ap = (AlignmentPanel) comp;
2842 if (!existingNames.contains(ap.av.viewName))
2844 existingNames.add(ap.av.viewName);
2848 return existingNames;
2852 * Explode tabbed views into separate windows.
2855 public void expandViews_actionPerformed(ActionEvent e)
2857 Desktop.instance.explodeViews(this);
2861 * Gather views in separate windows back into a tabbed presentation.
2864 public void gatherViews_actionPerformed(ActionEvent e)
2866 Desktop.instance.gatherViews(this);
2876 public void font_actionPerformed(ActionEvent e)
2878 new FontChooser(alignPanel);
2888 protected void seqLimit_actionPerformed(ActionEvent e)
2890 viewport.setShowJVSuffix(seqLimits.isSelected());
2892 alignPanel.getIdPanel().getIdCanvas()
2893 .setPreferredSize(alignPanel.calculateIdWidth());
2894 alignPanel.paintAlignment(true);
2898 public void idRightAlign_actionPerformed(ActionEvent e)
2900 viewport.setRightAlignIds(idRightAlign.isSelected());
2901 alignPanel.paintAlignment(true);
2905 public void centreColumnLabels_actionPerformed(ActionEvent e)
2907 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2908 alignPanel.paintAlignment(true);
2914 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2917 protected void followHighlight_actionPerformed()
2920 * Set the 'follow' flag on the Viewport (and scroll to position if now
2923 final boolean state = this.followHighlightMenuItem.getState();
2924 viewport.setFollowHighlight(state);
2927 alignPanel.scrollToPosition(
2928 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2939 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2941 viewport.setColourText(colourTextMenuItem.isSelected());
2942 alignPanel.paintAlignment(true);
2952 public void wrapMenuItem_actionPerformed(ActionEvent e)
2954 scaleAbove.setVisible(wrapMenuItem.isSelected());
2955 scaleLeft.setVisible(wrapMenuItem.isSelected());
2956 scaleRight.setVisible(wrapMenuItem.isSelected());
2957 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2958 alignPanel.updateLayout();
2962 public void showAllSeqs_actionPerformed(ActionEvent e)
2964 viewport.showAllHiddenSeqs();
2968 public void showAllColumns_actionPerformed(ActionEvent e)
2970 viewport.showAllHiddenColumns();
2972 viewport.sendSelection();
2976 public void hideSelSequences_actionPerformed(ActionEvent e)
2978 viewport.hideAllSelectedSeqs();
2979 // alignPanel.paintAlignment(true);
2983 * called by key handler and the hide all/show all menu items
2988 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2991 boolean hide = false;
2992 SequenceGroup sg = viewport.getSelectionGroup();
2993 if (!toggleSeqs && !toggleCols)
2995 // Hide everything by the current selection - this is a hack - we do the
2996 // invert and then hide
2997 // first check that there will be visible columns after the invert.
2998 if ((viewport.getColumnSelection() != null
2999 && viewport.getColumnSelection().getSelected() != null && viewport
3000 .getColumnSelection().getSelected().size() > 0)
3001 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3004 // now invert the sequence set, if required - empty selection implies
3005 // that no hiding is required.
3008 invertSequenceMenuItem_actionPerformed(null);
3009 sg = viewport.getSelectionGroup();
3013 viewport.expandColSelection(sg, true);
3014 // finally invert the column selection and get the new sequence
3016 invertColSel_actionPerformed(null);
3023 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3025 hideSelSequences_actionPerformed(null);
3028 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3031 showAllSeqs_actionPerformed(null);
3037 if (viewport.getColumnSelection().getSelected().size() > 0)
3039 hideSelColumns_actionPerformed(null);
3042 viewport.setSelectionGroup(sg);
3047 showAllColumns_actionPerformed(null);
3056 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3057 * event.ActionEvent)
3060 public void hideAllButSelection_actionPerformed(ActionEvent e)
3062 toggleHiddenRegions(false, false);
3063 viewport.sendSelection();
3070 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3074 public void hideAllSelection_actionPerformed(ActionEvent e)
3076 SequenceGroup sg = viewport.getSelectionGroup();
3077 viewport.expandColSelection(sg, false);
3078 viewport.hideAllSelectedSeqs();
3079 viewport.hideSelectedColumns();
3080 alignPanel.paintAlignment(true);
3081 viewport.sendSelection();
3088 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3092 public void showAllhidden_actionPerformed(ActionEvent e)
3094 viewport.showAllHiddenColumns();
3095 viewport.showAllHiddenSeqs();
3096 alignPanel.paintAlignment(true);
3097 viewport.sendSelection();
3101 public void hideSelColumns_actionPerformed(ActionEvent e)
3103 viewport.hideSelectedColumns();
3104 alignPanel.paintAlignment(true);
3105 viewport.sendSelection();
3109 public void hiddenMarkers_actionPerformed(ActionEvent e)
3111 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3122 protected void scaleAbove_actionPerformed(ActionEvent e)
3124 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3125 alignPanel.paintAlignment(true);
3135 protected void scaleLeft_actionPerformed(ActionEvent e)
3137 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3138 alignPanel.paintAlignment(true);
3148 protected void scaleRight_actionPerformed(ActionEvent e)
3150 viewport.setScaleRightWrapped(scaleRight.isSelected());
3151 alignPanel.paintAlignment(true);
3161 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3163 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3164 alignPanel.paintAlignment(true);
3174 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3176 viewport.setShowText(viewTextMenuItem.isSelected());
3177 alignPanel.paintAlignment(true);
3187 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3189 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3190 alignPanel.paintAlignment(true);
3193 public FeatureSettings featureSettings;
3196 public FeatureSettingsControllerI getFeatureSettingsUI()
3198 return featureSettings;
3202 public void featureSettings_actionPerformed(ActionEvent e)
3204 if (featureSettings != null)
3206 featureSettings.close();
3207 featureSettings = null;
3209 if (!showSeqFeatures.isSelected())
3211 // make sure features are actually displayed
3212 showSeqFeatures.setSelected(true);
3213 showSeqFeatures_actionPerformed(null);
3215 featureSettings = new FeatureSettings(this);
3219 * Set or clear 'Show Sequence Features'
3225 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3227 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3228 alignPanel.paintAlignment(true);
3229 if (alignPanel.getOverviewPanel() != null)
3231 alignPanel.getOverviewPanel().updateOverviewImage();
3236 * Set or clear 'Show Sequence Features'
3242 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3244 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3246 if (viewport.isShowSequenceFeaturesHeight())
3248 // ensure we're actually displaying features
3249 viewport.setShowSequenceFeatures(true);
3250 showSeqFeatures.setSelected(true);
3252 alignPanel.paintAlignment(true);
3253 if (alignPanel.getOverviewPanel() != null)
3255 alignPanel.getOverviewPanel().updateOverviewImage();
3260 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3261 * the annotations panel as a whole.
3263 * The options to show/hide all annotations should be enabled when the panel
3264 * is shown, and disabled when the panel is hidden.
3269 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3271 final boolean setVisible = annotationPanelMenuItem.isSelected();
3272 viewport.setShowAnnotation(setVisible);
3273 this.showAllSeqAnnotations.setEnabled(setVisible);
3274 this.hideAllSeqAnnotations.setEnabled(setVisible);
3275 this.showAllAlAnnotations.setEnabled(setVisible);
3276 this.hideAllAlAnnotations.setEnabled(setVisible);
3277 alignPanel.updateLayout();
3281 public void alignmentProperties()
3283 JEditorPane editPane = new JEditorPane("text/html", "");
3284 editPane.setEditable(false);
3285 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3287 editPane.setText(MessageManager.formatMessage("label.html_content",
3288 new Object[] { contents.toString() }));
3289 JInternalFrame frame = new JInternalFrame();
3290 frame.getContentPane().add(new JScrollPane(editPane));
3292 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3293 "label.alignment_properties", new Object[] { getTitle() }),
3304 public void overviewMenuItem_actionPerformed(ActionEvent e)
3306 if (alignPanel.overviewPanel != null)
3311 JInternalFrame frame = new JInternalFrame();
3312 OverviewPanel overview = new OverviewPanel(alignPanel);
3313 frame.setContentPane(overview);
3314 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3315 "label.overview_params", new Object[] { this.getTitle() }),
3316 frame.getWidth(), frame.getHeight());
3318 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3319 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3322 public void internalFrameClosed(
3323 javax.swing.event.InternalFrameEvent evt)
3325 alignPanel.setOverviewPanel(null);
3329 alignPanel.setOverviewPanel(overview);
3333 public void textColour_actionPerformed(ActionEvent e)
3335 new TextColourChooser().chooseColour(alignPanel, null);
3345 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3357 public void clustalColour_actionPerformed(ActionEvent e)
3359 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3360 viewport.getHiddenRepSequences()));
3370 public void zappoColour_actionPerformed(ActionEvent e)
3372 changeColour(new ZappoColourScheme());
3382 public void taylorColour_actionPerformed(ActionEvent e)
3384 changeColour(new TaylorColourScheme());
3394 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3396 changeColour(new HydrophobicColourScheme());
3406 public void helixColour_actionPerformed(ActionEvent e)
3408 changeColour(new HelixColourScheme());
3418 public void strandColour_actionPerformed(ActionEvent e)
3420 changeColour(new StrandColourScheme());
3430 public void turnColour_actionPerformed(ActionEvent e)
3432 changeColour(new TurnColourScheme());
3442 public void buriedColour_actionPerformed(ActionEvent e)
3444 changeColour(new BuriedColourScheme());
3454 public void nucleotideColour_actionPerformed(ActionEvent e)
3456 changeColour(new NucleotideColourScheme());
3460 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3462 changeColour(new PurinePyrimidineColourScheme());
3466 * public void covariationColour_actionPerformed(ActionEvent e) {
3468 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3472 public void annotationColour_actionPerformed(ActionEvent e)
3474 new AnnotationColourChooser(viewport, alignPanel);
3478 public void annotationColumn_actionPerformed(ActionEvent e)
3480 new AnnotationColumnChooser(viewport, alignPanel);
3484 public void rnahelicesColour_actionPerformed(ActionEvent e)
3486 new RNAHelicesColourChooser(viewport, alignPanel);
3496 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3498 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3508 public void changeColour(ColourSchemeI cs)
3510 // TODO: pull up to controller method
3514 // Make sure viewport is up to date w.r.t. any sliders
3515 if (viewport.getAbovePIDThreshold())
3517 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3519 viewport.setThreshold(threshold);
3522 if (viewport.getConservationSelected())
3524 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3527 if (cs instanceof TCoffeeColourScheme)
3529 tcoffeeColour.setEnabled(true);
3530 tcoffeeColour.setSelected(true);
3534 viewport.setGlobalColourScheme(cs);
3536 alignPanel.paintAlignment(true);
3546 protected void modifyPID_actionPerformed(ActionEvent e)
3548 if (viewport.getAbovePIDThreshold()
3549 && viewport.getGlobalColourScheme() != null)
3551 SliderPanel.setPIDSliderSource(alignPanel,
3552 viewport.getGlobalColourScheme(), "Background");
3553 SliderPanel.showPIDSlider();
3564 protected void modifyConservation_actionPerformed(ActionEvent e)
3566 if (viewport.getConservationSelected()
3567 && viewport.getGlobalColourScheme() != null)
3569 SliderPanel.setConservationSlider(alignPanel,
3570 viewport.getGlobalColourScheme(), "Background");
3571 SliderPanel.showConservationSlider();
3582 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3584 viewport.setConservationSelected(conservationMenuItem.isSelected());
3586 viewport.setAbovePIDThreshold(false);
3587 abovePIDThreshold.setSelected(false);
3589 changeColour(viewport.getGlobalColourScheme());
3591 modifyConservation_actionPerformed(null);
3601 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3603 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3605 conservationMenuItem.setSelected(false);
3606 viewport.setConservationSelected(false);
3608 changeColour(viewport.getGlobalColourScheme());
3610 modifyPID_actionPerformed(null);
3620 public void userDefinedColour_actionPerformed(ActionEvent e)
3622 if (e.getActionCommand().equals(
3623 MessageManager.getString("action.user_defined")))
3625 new UserDefinedColours(alignPanel, null);
3629 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3630 .getUserColourSchemes().get(e.getActionCommand());
3636 public void updateUserColourMenu()
3639 Component[] menuItems = colourMenu.getMenuComponents();
3640 int iSize = menuItems.length;
3641 for (int i = 0; i < iSize; i++)
3643 if (menuItems[i].getName() != null
3644 && menuItems[i].getName().equals("USER_DEFINED"))
3646 colourMenu.remove(menuItems[i]);
3650 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3652 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3653 .getUserColourSchemes().keys();
3655 while (userColours.hasMoreElements())
3657 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3658 userColours.nextElement().toString());
3659 radioItem.setName("USER_DEFINED");
3660 radioItem.addMouseListener(new MouseAdapter()
3663 public void mousePressed(MouseEvent evt)
3665 if (evt.isControlDown()
3666 || SwingUtilities.isRightMouseButton(evt))
3668 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3670 int option = JOptionPane.showInternalConfirmDialog(
3671 jalview.gui.Desktop.desktop,
3673 .getString("label.remove_from_default_list"),
3675 .getString("label.remove_user_defined_colour"),
3676 JOptionPane.YES_NO_OPTION);
3677 if (option == JOptionPane.YES_OPTION)
3679 jalview.gui.UserDefinedColours
3680 .removeColourFromDefaults(radioItem.getText());
3681 colourMenu.remove(radioItem);
3685 radioItem.addActionListener(new ActionListener()
3688 public void actionPerformed(ActionEvent evt)
3690 userDefinedColour_actionPerformed(evt);
3697 radioItem.addActionListener(new ActionListener()
3700 public void actionPerformed(ActionEvent evt)
3702 userDefinedColour_actionPerformed(evt);
3706 colourMenu.insert(radioItem, 15);
3707 colours.add(radioItem);
3719 public void PIDColour_actionPerformed(ActionEvent e)
3721 changeColour(new PIDColourScheme());
3731 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3733 changeColour(new Blosum62ColourScheme());
3743 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3745 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3746 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3747 .getAlignment().getSequenceAt(0), null);
3748 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3749 viewport.getAlignment()));
3750 alignPanel.paintAlignment(true);
3760 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3762 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3763 AlignmentSorter.sortByID(viewport.getAlignment());
3764 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3765 viewport.getAlignment()));
3766 alignPanel.paintAlignment(true);
3776 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3778 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3779 AlignmentSorter.sortByLength(viewport.getAlignment());
3780 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3781 viewport.getAlignment()));
3782 alignPanel.paintAlignment(true);
3792 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3794 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3795 AlignmentSorter.sortByGroup(viewport.getAlignment());
3796 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3797 viewport.getAlignment()));
3799 alignPanel.paintAlignment(true);
3809 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3811 new RedundancyPanel(alignPanel, this);
3821 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3823 if ((viewport.getSelectionGroup() == null)
3824 || (viewport.getSelectionGroup().getSize() < 2))
3826 JOptionPane.showInternalMessageDialog(this, MessageManager
3827 .getString("label.you_must_select_least_two_sequences"),
3828 MessageManager.getString("label.invalid_selection"),
3829 JOptionPane.WARNING_MESSAGE);
3833 JInternalFrame frame = new JInternalFrame();
3834 frame.setContentPane(new PairwiseAlignPanel(viewport));
3835 Desktop.addInternalFrame(frame,
3836 MessageManager.getString("action.pairwise_alignment"), 600,
3848 public void PCAMenuItem_actionPerformed(ActionEvent e)
3850 if (((viewport.getSelectionGroup() != null)
3851 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3852 .getSelectionGroup().getSize() > 0))
3853 || (viewport.getAlignment().getHeight() < 4))
3856 .showInternalMessageDialog(
3859 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3861 .getString("label.sequence_selection_insufficient"),
3862 JOptionPane.WARNING_MESSAGE);
3867 new PCAPanel(alignPanel);
3871 public void autoCalculate_actionPerformed(ActionEvent e)
3873 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3874 if (viewport.autoCalculateConsensus)
3876 viewport.firePropertyChange("alignment", null, viewport
3877 .getAlignment().getSequences());
3882 public void sortByTreeOption_actionPerformed(ActionEvent e)
3884 viewport.sortByTree = sortByTree.isSelected();
3888 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3890 viewport.followSelection = listenToViewSelections.isSelected();
3900 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3902 newTreePanel("AV", "PID", "Average distance tree using PID");
3912 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3914 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3924 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3926 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3936 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3938 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3951 void newTreePanel(String type, String pwType, String title)
3955 if (viewport.getSelectionGroup() != null
3956 && viewport.getSelectionGroup().getSize() > 0)
3958 if (viewport.getSelectionGroup().getSize() < 3)
3964 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3966 .getString("label.not_enough_sequences"),
3967 JOptionPane.WARNING_MESSAGE);
3971 SequenceGroup sg = viewport.getSelectionGroup();
3973 /* Decide if the selection is a column region */
3974 for (SequenceI _s : sg.getSequences())
3976 if (_s.getLength() < sg.getEndRes())
3982 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3984 .getString("label.sequences_selection_not_aligned"),
3985 JOptionPane.WARNING_MESSAGE);
3991 title = title + " on region";
3992 tp = new TreePanel(alignPanel, type, pwType);
3996 // are the visible sequences aligned?
3997 if (!viewport.getAlignment().isAligned(false))
4003 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4005 .getString("label.sequences_not_aligned"),
4006 JOptionPane.WARNING_MESSAGE);
4011 if (viewport.getAlignment().getHeight() < 2)
4016 tp = new TreePanel(alignPanel, type, pwType);
4021 if (viewport.viewName != null)
4023 title += viewport.viewName + " of ";
4026 title += this.title;
4028 Desktop.addInternalFrame(tp, title, 600, 500);
4039 public void addSortByOrderMenuItem(String title,
4040 final AlignmentOrder order)
4042 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4043 "action.by_title_param", new Object[] { title }));
4045 item.addActionListener(new java.awt.event.ActionListener()
4048 public void actionPerformed(ActionEvent e)
4050 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4052 // TODO: JBPNote - have to map order entries to curent SequenceI
4054 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4056 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4059 alignPanel.paintAlignment(true);
4065 * Add a new sort by annotation score menu item
4068 * the menu to add the option to
4070 * the label used to retrieve scores for each sequence on the
4073 public void addSortByAnnotScoreMenuItem(JMenu sort,
4074 final String scoreLabel)
4076 final JMenuItem item = new JMenuItem(scoreLabel);
4078 item.addActionListener(new java.awt.event.ActionListener()
4081 public void actionPerformed(ActionEvent e)
4083 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4084 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4085 viewport.getAlignment());// ,viewport.getSelectionGroup());
4086 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4087 viewport.getAlignment()));
4088 alignPanel.paintAlignment(true);
4094 * last hash for alignment's annotation array - used to minimise cost of
4097 protected int _annotationScoreVectorHash;
4100 * search the alignment and rebuild the sort by annotation score submenu the
4101 * last alignment annotation vector hash is stored to minimize cost of
4102 * rebuilding in subsequence calls.
4106 public void buildSortByAnnotationScoresMenu()
4108 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4113 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4115 sortByAnnotScore.removeAll();
4116 // almost certainly a quicker way to do this - but we keep it simple
4117 Hashtable scoreSorts = new Hashtable();
4118 AlignmentAnnotation aann[];
4119 for (SequenceI sqa : viewport.getAlignment().getSequences())
4121 aann = sqa.getAnnotation();
4122 for (int i = 0; aann != null && i < aann.length; i++)
4124 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4126 scoreSorts.put(aann[i].label, aann[i].label);
4130 Enumeration labels = scoreSorts.keys();
4131 while (labels.hasMoreElements())
4133 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4134 (String) labels.nextElement());
4136 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4139 _annotationScoreVectorHash = viewport.getAlignment()
4140 .getAlignmentAnnotation().hashCode();
4145 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4146 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4147 * call. Listeners are added to remove the menu item when the treePanel is
4148 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4152 * Displayed tree window.
4154 * SortBy menu item title.
4157 public void buildTreeMenu()
4159 calculateTree.removeAll();
4160 // build the calculate menu
4162 for (final String type : new String[] { "NJ", "AV" })
4164 String treecalcnm = MessageManager.getString("label.tree_calc_"
4165 + type.toLowerCase());
4166 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4168 JMenuItem tm = new JMenuItem();
4169 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4170 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4172 String smn = MessageManager.getStringOrReturn(
4173 "label.score_model_", sm.getName());
4174 final String title = MessageManager.formatMessage(
4175 "label.treecalc_title", treecalcnm, smn);
4176 tm.setText(title);//
4177 tm.addActionListener(new java.awt.event.ActionListener()
4180 public void actionPerformed(ActionEvent e)
4182 newTreePanel(type, pwtype, title);
4185 calculateTree.add(tm);
4190 sortByTreeMenu.removeAll();
4192 List<Component> comps = PaintRefresher.components.get(viewport
4193 .getSequenceSetId());
4194 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4195 for (Component comp : comps)
4197 if (comp instanceof TreePanel)
4199 treePanels.add((TreePanel) comp);
4203 if (treePanels.size() < 1)
4205 sortByTreeMenu.setVisible(false);
4209 sortByTreeMenu.setVisible(true);
4211 for (final TreePanel tp : treePanels)
4213 final JMenuItem item = new JMenuItem(tp.getTitle());
4214 item.addActionListener(new java.awt.event.ActionListener()
4217 public void actionPerformed(ActionEvent e)
4219 tp.sortByTree_actionPerformed();
4220 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4225 sortByTreeMenu.add(item);
4229 public boolean sortBy(AlignmentOrder alorder, String undoname)
4231 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4232 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4233 if (undoname != null)
4235 addHistoryItem(new OrderCommand(undoname, oldOrder,
4236 viewport.getAlignment()));
4238 alignPanel.paintAlignment(true);
4243 * Work out whether the whole set of sequences or just the selected set will
4244 * be submitted for multiple alignment.
4247 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4249 // Now, check we have enough sequences
4250 AlignmentView msa = null;
4252 if ((viewport.getSelectionGroup() != null)
4253 && (viewport.getSelectionGroup().getSize() > 1))
4255 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4256 // some common interface!
4258 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4259 * SequenceI[sz = seqs.getSize(false)];
4261 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4262 * seqs.getSequenceAt(i); }
4264 msa = viewport.getAlignmentView(true);
4266 else if (viewport.getSelectionGroup() != null
4267 && viewport.getSelectionGroup().getSize() == 1)
4269 int option = JOptionPane.showConfirmDialog(this,
4270 MessageManager.getString("warn.oneseq_msainput_selection"),
4271 MessageManager.getString("label.invalid_selection"),
4272 JOptionPane.OK_CANCEL_OPTION);
4273 if (option == JOptionPane.OK_OPTION)
4275 msa = viewport.getAlignmentView(false);
4280 msa = viewport.getAlignmentView(false);
4286 * Decides what is submitted to a secondary structure prediction service: the
4287 * first sequence in the alignment, or in the current selection, or, if the
4288 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4289 * region or the whole alignment. (where the first sequence in the set is the
4290 * one that the prediction will be for).
4292 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4294 AlignmentView seqs = null;
4296 if ((viewport.getSelectionGroup() != null)
4297 && (viewport.getSelectionGroup().getSize() > 0))
4299 seqs = viewport.getAlignmentView(true);
4303 seqs = viewport.getAlignmentView(false);
4305 // limit sequences - JBPNote in future - could spawn multiple prediction
4307 // TODO: viewport.getAlignment().isAligned is a global state - the local
4308 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4309 if (!viewport.getAlignment().isAligned(false))
4311 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4312 // TODO: if seqs.getSequences().length>1 then should really have warned
4326 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4328 // Pick the tree file
4329 JalviewFileChooser chooser = new JalviewFileChooser(
4330 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4331 chooser.setFileView(new JalviewFileView());
4332 chooser.setDialogTitle(MessageManager
4333 .getString("label.select_newick_like_tree_file"));
4334 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4336 int value = chooser.showOpenDialog(null);
4338 if (value == JalviewFileChooser.APPROVE_OPTION)
4340 String choice = chooser.getSelectedFile().getPath();
4341 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4342 jalview.io.NewickFile fin = null;
4345 fin = new jalview.io.NewickFile(choice, "File");
4346 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4347 } catch (Exception ex)
4354 .getString("label.problem_reading_tree_file"),
4355 JOptionPane.WARNING_MESSAGE);
4356 ex.printStackTrace();
4358 if (fin != null && fin.hasWarningMessage())
4360 JOptionPane.showMessageDialog(Desktop.desktop, fin
4361 .getWarningMessage(), MessageManager
4362 .getString("label.possible_problem_with_tree_file"),
4363 JOptionPane.WARNING_MESSAGE);
4369 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4371 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4374 public TreePanel ShowNewickTree(NewickFile nf, String title)
4376 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4379 public TreePanel ShowNewickTree(NewickFile nf, String title,
4380 AlignmentView input)
4382 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4385 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4386 int h, int x, int y)
4388 return ShowNewickTree(nf, title, null, w, h, x, y);
4392 * Add a treeviewer for the tree extracted from a newick file object to the
4393 * current alignment view
4400 * Associated alignment input data (or null)
4409 * @return TreePanel handle
4411 public TreePanel ShowNewickTree(NewickFile nf, String title,
4412 AlignmentView input, int w, int h, int x, int y)
4414 TreePanel tp = null;
4420 if (nf.getTree() != null)
4422 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4428 tp.setLocation(x, y);
4431 Desktop.addInternalFrame(tp, title, w, h);
4433 } catch (Exception ex)
4435 ex.printStackTrace();
4441 private boolean buildingMenu = false;
4444 * Generates menu items and listener event actions for web service clients
4447 public void BuildWebServiceMenu()
4449 while (buildingMenu)
4453 System.err.println("Waiting for building menu to finish.");
4455 } catch (Exception e)
4459 final AlignFrame me = this;
4460 buildingMenu = true;
4461 new Thread(new Runnable()
4466 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4469 // System.err.println("Building ws menu again "
4470 // + Thread.currentThread());
4471 // TODO: add support for context dependent disabling of services based
4473 // alignment and current selection
4474 // TODO: add additional serviceHandle parameter to specify abstract
4476 // class independently of AbstractName
4477 // TODO: add in rediscovery GUI function to restart discoverer
4478 // TODO: group services by location as well as function and/or
4480 // object broker mechanism.
4481 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4482 final IProgressIndicator af = me;
4483 final JMenu msawsmenu = new JMenu("Alignment");
4484 final JMenu secstrmenu = new JMenu(
4485 "Secondary Structure Prediction");
4486 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4487 final JMenu analymenu = new JMenu("Analysis");
4488 final JMenu dismenu = new JMenu("Protein Disorder");
4489 // final JMenu msawsmenu = new
4490 // JMenu(MessageManager.getString("label.alignment"));
4491 // final JMenu secstrmenu = new
4492 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4493 // final JMenu seqsrchmenu = new
4494 // JMenu(MessageManager.getString("label.sequence_database_search"));
4495 // final JMenu analymenu = new
4496 // JMenu(MessageManager.getString("label.analysis"));
4497 // final JMenu dismenu = new
4498 // JMenu(MessageManager.getString("label.protein_disorder"));
4499 // JAL-940 - only show secondary structure prediction services from
4500 // the legacy server
4501 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4503 Discoverer.services != null && (Discoverer.services.size() > 0))
4505 // TODO: refactor to allow list of AbstractName/Handler bindings to
4507 // stored or retrieved from elsewhere
4508 // No MSAWS used any more:
4509 // Vector msaws = null; // (Vector)
4510 // Discoverer.services.get("MsaWS");
4511 Vector secstrpr = (Vector) Discoverer.services
4513 if (secstrpr != null)
4515 // Add any secondary structure prediction services
4516 for (int i = 0, j = secstrpr.size(); i < j; i++)
4518 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4520 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4521 .getServiceClient(sh);
4522 int p = secstrmenu.getItemCount();
4523 impl.attachWSMenuEntry(secstrmenu, me);
4524 int q = secstrmenu.getItemCount();
4525 for (int litm = p; litm < q; litm++)
4527 legacyItems.add(secstrmenu.getItem(litm));
4533 // Add all submenus in the order they should appear on the web
4535 wsmenu.add(msawsmenu);
4536 wsmenu.add(secstrmenu);
4537 wsmenu.add(dismenu);
4538 wsmenu.add(analymenu);
4539 // No search services yet
4540 // wsmenu.add(seqsrchmenu);
4542 javax.swing.SwingUtilities.invokeLater(new Runnable()
4549 webService.removeAll();
4550 // first, add discovered services onto the webservices menu
4551 if (wsmenu.size() > 0)
4553 for (int i = 0, j = wsmenu.size(); i < j; i++)
4555 webService.add(wsmenu.get(i));
4560 webService.add(me.webServiceNoServices);
4562 // TODO: move into separate menu builder class.
4563 boolean new_sspred = false;
4564 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4566 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4567 if (jws2servs != null)
4569 if (jws2servs.hasServices())
4571 jws2servs.attachWSMenuEntry(webService, me);
4572 for (Jws2Instance sv : jws2servs.getServices())
4574 if (sv.description.toLowerCase().contains("jpred"))
4576 for (JMenuItem jmi : legacyItems)
4578 jmi.setVisible(false);
4584 if (jws2servs.isRunning())
4586 JMenuItem tm = new JMenuItem(
4587 "Still discovering JABA Services");
4588 tm.setEnabled(false);
4593 build_urlServiceMenu(me.webService);
4594 build_fetchdbmenu(webService);
4595 for (JMenu item : wsmenu)
4597 if (item.getItemCount() == 0)
4599 item.setEnabled(false);
4603 item.setEnabled(true);
4606 } catch (Exception e)
4609 .debug("Exception during web service menu building process.",
4614 } catch (Exception e)
4617 buildingMenu = false;
4624 * construct any groupURL type service menu entries.
4628 private void build_urlServiceMenu(JMenu webService)
4630 // TODO: remove this code when 2.7 is released
4631 // DEBUG - alignmentView
4633 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4634 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4636 * @Override public void actionPerformed(ActionEvent e) {
4637 * jalview.datamodel.AlignmentView
4638 * .testSelectionViews(af.viewport.getAlignment(),
4639 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4641 * }); webService.add(testAlView);
4643 // TODO: refactor to RestClient discoverer and merge menu entries for
4644 // rest-style services with other types of analysis/calculation service
4645 // SHmmr test client - still being implemented.
4646 // DEBUG - alignmentView
4648 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4651 client.attachWSMenuEntry(
4652 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4658 * Searches selected sequences for xRef products and builds the Show
4659 * Cross-References menu (formerly called Show Products)
4661 * @return true if Show Cross-references menu should be enabled.
4663 public boolean canShowProducts()
4665 SequenceI[] selection = viewport.getSequenceSelection();
4666 AlignmentI dataset = viewport.getAlignment().getDataset();
4667 boolean showp = false;
4670 showProducts.removeAll();
4671 final boolean dna = viewport.getAlignment().isNucleotide();
4672 String[] ptypes = (selection == null || selection.length == 0) ? null
4673 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4675 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4678 final AlignFrame af = this;
4679 final String source = ptypes[t];
4680 JMenuItem xtype = new JMenuItem(ptypes[t]);
4681 xtype.addActionListener(new ActionListener()
4685 public void actionPerformed(ActionEvent e)
4687 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4691 showProducts.add(xtype);
4693 showProducts.setVisible(showp);
4694 showProducts.setEnabled(showp);
4695 } catch (Exception e)
4697 jalview.bin.Cache.log
4698 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4705 protected void showProductsFor(final SequenceI[] sel, final boolean dna,
4706 final String source)
4708 Runnable foo = new Runnable()
4714 final long sttime = System.currentTimeMillis();
4715 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4716 "status.searching_for_sequences_from",
4717 new Object[] { source }), sttime);
4721 * 'peer' sequences are any to add to this alignment, for example
4722 * alternative protein products for my protein's gene
4724 List<SequenceI> addedPeers = new ArrayList<SequenceI>();
4725 AlignmentI alignment = AlignFrame.this.getViewport().getAlignment();
4726 Alignment xrefs = CrossRef.findXrefSequences(sel, dna, source,
4727 alignment, addedPeers);
4730 Alignment al = makeCrossReferencesAlignment(
4731 alignment.getDataset(), xrefs);
4734 * Copy dna-to-protein mappings to new alignment
4736 // TODO 1: no mappings are set up for EMBL product
4737 // TODO 2: if they were, should add them to protein alignment, not
4739 // List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4740 // for (AlignedCodonFrame acf : cf)
4742 // al.addCodonFrame(acf);
4744 AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4746 String newtitle = String.format("%s %s %s",
4747 MessageManager.getString(dna ? "label.proteins"
4748 : "label.nucleotides"), MessageManager
4749 .getString("label.for"), getTitle());
4750 newFrame.setTitle(newtitle);
4752 boolean asSplitFrame = Cache.getDefault(
4753 Preferences.ENABLE_SPLIT_FRAME, true);
4757 * Make a copy of this alignment (sharing the same dataset
4758 * sequences). If we are DNA, drop introns and update mappings
4760 AlignmentI copyAlignment = null;
4761 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4762 .getSequenceSelection();
4763 List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
4766 copyAlignment = AlignmentUtils.makeCdsAlignment(
4767 sequenceSelection, cf);
4768 al.getCodonFrames().clear();
4769 al.getCodonFrames().addAll(cf);
4773 copyAlignment = new Alignment(new Alignment(
4774 sequenceSelection));
4775 copyAlignment.getCodonFrames().addAll(cf);
4777 StructureSelectionManager ssm = StructureSelectionManager
4778 .getStructureSelectionManager(Desktop.instance);
4779 ssm.registerMappings(cf);
4782 * add in any extra 'peer' sequences discovered
4783 * (e.g. alternative protein products)
4785 for (SequenceI peer : addedPeers)
4787 copyAlignment.addSequence(peer);
4791 * align protein to dna
4793 // TODO needs debugging
4796 // al.alignAs(copyAlignment);
4800 // copyAlignment.alignAs(al);
4803 AlignFrame copyThis = new AlignFrame(copyAlignment,
4804 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4805 copyThis.setTitle(AlignFrame.this.getTitle());
4807 boolean showSequenceFeatures = viewport
4808 .isShowSequenceFeatures();
4809 newFrame.setShowSeqFeatures(showSequenceFeatures);
4810 copyThis.setShowSeqFeatures(showSequenceFeatures);
4811 FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4812 .getFeatureRenderer();
4814 * copy feature rendering settings to split frame
4816 newFrame.alignPanel.getSeqPanel().seqCanvas
4817 .getFeatureRenderer().transferSettings(
4819 copyThis.alignPanel.getSeqPanel().seqCanvas
4820 .getFeatureRenderer().transferSettings(
4822 SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4823 dna ? newFrame : copyThis);
4824 newFrame.setVisible(true);
4825 copyThis.setVisible(true);
4826 String linkedTitle = MessageManager
4827 .getString("label.linked_view_title");
4828 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4833 Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4839 System.err.println("No Sequences generated for xRef type "
4842 } catch (Exception e)
4844 jalview.bin.Cache.log.error(
4845 "Exception when finding crossreferences", e);
4846 } catch (OutOfMemoryError e)
4848 new OOMWarning("whilst fetching crossreferences", e);
4851 jalview.bin.Cache.log.error("Error when finding crossreferences",
4854 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4855 "status.finished_searching_for_sequences_from",
4856 new Object[] { source }), sttime);
4864 protected Alignment makeCrossReferencesAlignment(
4868 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4869 for (int s = 0; s < sprods.length; s++)
4871 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4872 if (dataset.getSequences() == null
4873 || !dataset.getSequences().contains(
4874 sprods[s].getDatasetSequence()))
4876 dataset.addSequence(sprods[s].getDatasetSequence());
4878 sprods[s].updatePDBIds();
4880 Alignment al = new Alignment(sprods);
4881 al.setDataset(dataset);
4886 Thread frunner = new Thread(foo);
4890 public boolean canShowTranslationProducts(SequenceI[] selection,
4891 AlignmentI alignment)
4896 return (jalview.analysis.Dna.canTranslate(selection,
4897 viewport.getViewAsVisibleContigs(true)));
4898 } catch (Exception e)
4900 jalview.bin.Cache.log
4901 .warn("canTranslate threw an exception - please report to help@jalview.org",
4908 * Construct and display a new frame containing the translation of this
4909 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4912 public void showTranslation_actionPerformed(ActionEvent e)
4914 AlignmentI al = null;
4917 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4919 al = dna.translateCdna();
4920 } catch (Exception ex)
4922 jalview.bin.Cache.log.error(
4923 "Exception during translation. Please report this !", ex);
4924 final String msg = MessageManager
4925 .getString("label.error_when_translating_sequences_submit_bug_report");
4926 final String errorTitle = MessageManager
4927 .getString("label.implementation_error")
4928 + MessageManager.getString("translation_failed");
4929 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4930 JOptionPane.ERROR_MESSAGE);
4933 if (al == null || al.getHeight() == 0)
4935 final String msg = MessageManager
4936 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4937 final String errorTitle = MessageManager
4938 .getString("label.translation_failed");
4939 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4940 JOptionPane.WARNING_MESSAGE);
4944 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4945 af.setFileFormat(this.currentFileFormat);
4946 final String newTitle = MessageManager.formatMessage(
4947 "label.translation_of_params",
4948 new Object[] { this.getTitle() });
4949 af.setTitle(newTitle);
4950 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4952 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4953 viewport.openSplitFrame(af, new Alignment(seqs));
4957 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4964 * Set the file format
4968 public void setFileFormat(String fileFormat)
4970 this.currentFileFormat = fileFormat;
4974 * Try to load a features file onto the alignment.
4977 * contents or path to retrieve file
4979 * access mode of file (see jalview.io.AlignFile)
4980 * @return true if features file was parsed correctly.
4982 public boolean parseFeaturesFile(String file, String type)
4984 return avc.parseFeaturesFile(file, type,
4985 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4990 public void refreshFeatureUI(boolean enableIfNecessary)
4992 // note - currently this is only still here rather than in the controller
4993 // because of the featureSettings hard reference that is yet to be
4995 if (enableIfNecessary)
4997 viewport.setShowSequenceFeatures(true);
4998 showSeqFeatures.setSelected(true);
5004 public void dragEnter(DropTargetDragEvent evt)
5009 public void dragExit(DropTargetEvent evt)
5014 public void dragOver(DropTargetDragEvent evt)
5019 public void dropActionChanged(DropTargetDragEvent evt)
5024 public void drop(DropTargetDropEvent evt)
5026 Transferable t = evt.getTransferable();
5027 java.util.List files = null;
5031 DataFlavor uriListFlavor = new DataFlavor(
5032 "text/uri-list;class=java.lang.String");
5033 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5035 // Works on Windows and MacOSX
5036 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5037 files = (java.util.List) t
5038 .getTransferData(DataFlavor.javaFileListFlavor);
5040 else if (t.isDataFlavorSupported(uriListFlavor))
5042 // This is used by Unix drag system
5043 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5044 String data = (String) t.getTransferData(uriListFlavor);
5045 files = new java.util.ArrayList(1);
5046 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5047 data, "\r\n"); st.hasMoreTokens();)
5049 String s = st.nextToken();
5050 if (s.startsWith("#"))
5052 // the line is a comment (as per the RFC 2483)
5056 java.net.URI uri = new java.net.URI(s);
5057 // check to see if we can handle this kind of URI
5058 if (uri.getScheme().toLowerCase().startsWith("http"))
5060 files.add(uri.toString());
5064 // otherwise preserve old behaviour: catch all for file objects
5065 java.io.File file = new java.io.File(uri);
5066 files.add(file.toString());
5070 } catch (Exception e)
5072 e.printStackTrace();
5078 // check to see if any of these files have names matching sequences in
5080 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5081 .getAlignment().getSequencesArray());
5083 * Object[] { String,SequenceI}
5085 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5086 ArrayList<String> filesnotmatched = new ArrayList<String>();
5087 for (int i = 0; i < files.size(); i++)
5089 String file = files.get(i).toString();
5091 String protocol = FormatAdapter.checkProtocol(file);
5092 if (protocol == jalview.io.FormatAdapter.FILE)
5094 File fl = new File(file);
5095 pdbfn = fl.getName();
5097 else if (protocol == jalview.io.FormatAdapter.URL)
5099 URL url = new URL(file);
5100 pdbfn = url.getFile();
5102 if (pdbfn.length() > 0)
5104 // attempt to find a match in the alignment
5105 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5106 int l = 0, c = pdbfn.indexOf(".");
5107 while (mtch == null && c != -1)
5112 } while ((c = pdbfn.indexOf(".", l)) > l);
5115 pdbfn = pdbfn.substring(0, l);
5117 mtch = idm.findAllIdMatches(pdbfn);
5124 type = new IdentifyFile().identify(file, protocol);
5125 } catch (Exception ex)
5131 if (type.equalsIgnoreCase("PDB"))
5133 filesmatched.add(new Object[] { file, protocol, mtch });
5138 // File wasn't named like one of the sequences or wasn't a PDB file.
5139 filesnotmatched.add(file);
5143 if (filesmatched.size() > 0)
5145 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5151 "label.automatically_associate_pdb_files_with_sequences_same_name",
5152 new Object[] { Integer
5158 .getString("label.automatically_associate_pdb_files_by_name"),
5159 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5162 for (Object[] fm : filesmatched)
5164 // try and associate
5165 // TODO: may want to set a standard ID naming formalism for
5166 // associating PDB files which have no IDs.
5167 for (SequenceI toassoc : (SequenceI[]) fm[2])
5169 PDBEntry pe = new AssociatePdbFileWithSeq()
5170 .associatePdbWithSeq((String) fm[0],
5171 (String) fm[1], toassoc, false,
5175 System.err.println("Associated file : "
5176 + ((String) fm[0]) + " with "
5177 + toassoc.getDisplayId(true));
5181 alignPanel.paintAlignment(true);
5185 if (filesnotmatched.size() > 0)
5188 && (Cache.getDefault(
5189 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5195 "label.ignore_unmatched_dropped_files_info",
5196 new Object[] { Integer
5203 .getString("label.ignore_unmatched_dropped_files"),
5204 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5208 for (String fn : filesnotmatched)
5210 loadJalviewDataFile(fn, null, null, null);
5214 } catch (Exception ex)
5216 ex.printStackTrace();
5222 * Attempt to load a "dropped" file or URL string: First by testing whether
5223 * it's an Annotation file, then a JNet file, and finally a features file. If
5224 * all are false then the user may have dropped an alignment file onto this
5228 * either a filename or a URL string.
5230 public void loadJalviewDataFile(String file, String protocol,
5231 String format, SequenceI assocSeq)
5235 if (protocol == null)
5237 protocol = FormatAdapter.checkProtocol(file);
5239 // if the file isn't identified, or not positively identified as some
5240 // other filetype (PFAM is default unidentified alignment file type) then
5241 // try to parse as annotation.
5242 boolean isAnnotation = (format == null || format
5243 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5244 .annotateAlignmentView(viewport, file, protocol) : false;
5248 // first see if its a T-COFFEE score file
5249 TCoffeeScoreFile tcf = null;
5252 tcf = new TCoffeeScoreFile(file, protocol);
5255 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5257 tcoffeeColour.setEnabled(true);
5258 tcoffeeColour.setSelected(true);
5259 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5260 isAnnotation = true;
5262 .setText(MessageManager
5263 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5267 // some problem - if no warning its probable that the ID matching
5268 // process didn't work
5272 tcf.getWarningMessage() == null ? MessageManager
5273 .getString("label.check_file_matches_sequence_ids_alignment")
5274 : tcf.getWarningMessage(),
5276 .getString("label.problem_reading_tcoffee_score_file"),
5277 JOptionPane.WARNING_MESSAGE);
5284 } catch (Exception x)
5287 .debug("Exception when processing data source as T-COFFEE score file",
5293 // try to see if its a JNet 'concise' style annotation file *before*
5295 // try to parse it as a features file
5298 format = new IdentifyFile().identify(file, protocol);
5300 if (format.equalsIgnoreCase("JnetFile"))
5302 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5304 new JnetAnnotationMaker();
5305 JnetAnnotationMaker.add_annotation(predictions,
5306 viewport.getAlignment(), 0, false);
5307 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5308 viewport.getAlignment().setSeqrep(repseq);
5309 ColumnSelection cs = new ColumnSelection();
5310 cs.hideInsertionsFor(repseq);
5311 viewport.setColumnSelection(cs);
5312 isAnnotation = true;
5314 else if (IdentifyFile.FeaturesFile.equals(format))
5316 if (parseFeaturesFile(file, protocol))
5318 alignPanel.paintAlignment(true);
5323 new FileLoader().LoadFile(viewport, file, protocol, format);
5330 alignPanel.adjustAnnotationHeight();
5331 viewport.updateSequenceIdColours();
5332 buildSortByAnnotationScoresMenu();
5333 alignPanel.paintAlignment(true);
5335 } catch (Exception ex)
5337 ex.printStackTrace();
5338 } catch (OutOfMemoryError oom)
5343 } catch (Exception x)
5348 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5349 : "using " + protocol + " from " + file)
5351 + (format != null ? "(parsing as '" + format
5352 + "' file)" : ""), oom, Desktop.desktop);
5357 * Method invoked by the ChangeListener on the tabbed pane, in other words
5358 * when a different tabbed pane is selected by the user or programmatically.
5361 public void tabSelectionChanged(int index)
5365 alignPanel = alignPanels.get(index);
5366 viewport = alignPanel.av;
5367 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5368 setMenusFromViewport(viewport);
5372 * If there is a frame linked to this one in a SplitPane, switch it to the
5373 * same view tab index. No infinite recursion of calls should happen, since
5374 * tabSelectionChanged() should not get invoked on setting the selected
5375 * index to an unchanged value. Guard against setting an invalid index
5376 * before the new view peer tab has been created.
5378 final AlignViewportI peer = viewport.getCodingComplement();
5381 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5382 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5384 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5390 * On right mouse click on view tab, prompt for and set new view name.
5393 public void tabbedPane_mousePressed(MouseEvent e)
5395 if (SwingUtilities.isRightMouseButton(e))
5397 String msg = MessageManager.getString("label.enter_view_name");
5398 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5399 JOptionPane.QUESTION_MESSAGE);
5403 viewport.viewName = reply;
5404 // TODO warn if reply is in getExistingViewNames()?
5405 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5410 public AlignViewport getCurrentView()
5416 * Open the dialog for regex description parsing.
5419 protected void extractScores_actionPerformed(ActionEvent e)
5421 ParseProperties pp = new jalview.analysis.ParseProperties(
5422 viewport.getAlignment());
5423 // TODO: verify regex and introduce GUI dialog for version 2.5
5424 // if (pp.getScoresFromDescription("col", "score column ",
5425 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5427 if (pp.getScoresFromDescription("description column",
5428 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5430 buildSortByAnnotationScoresMenu();
5438 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5442 protected void showDbRefs_actionPerformed(ActionEvent e)
5444 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5450 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5454 protected void showNpFeats_actionPerformed(ActionEvent e)
5456 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5460 * find the viewport amongst the tabs in this alignment frame and close that
5465 public boolean closeView(AlignViewportI av)
5469 this.closeMenuItem_actionPerformed(false);
5472 Component[] comp = tabbedPane.getComponents();
5473 for (int i = 0; comp != null && i < comp.length; i++)
5475 if (comp[i] instanceof AlignmentPanel)
5477 if (((AlignmentPanel) comp[i]).av == av)
5480 closeView((AlignmentPanel) comp[i]);
5488 protected void build_fetchdbmenu(JMenu webService)
5490 // Temporary hack - DBRef Fetcher always top level ws entry.
5491 // TODO We probably want to store a sequence database checklist in
5492 // preferences and have checkboxes.. rather than individual sources selected
5494 final JMenu rfetch = new JMenu(
5495 MessageManager.getString("action.fetch_db_references"));
5496 rfetch.setToolTipText(MessageManager
5497 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5498 webService.add(rfetch);
5500 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5501 MessageManager.getString("option.trim_retrieved_seqs"));
5502 trimrs.setToolTipText(MessageManager
5503 .getString("label.trim_retrieved_sequences"));
5504 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5505 trimrs.addActionListener(new ActionListener()
5508 public void actionPerformed(ActionEvent e)
5510 trimrs.setSelected(trimrs.isSelected());
5511 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5512 Boolean.valueOf(trimrs.isSelected()).toString());
5516 JMenuItem fetchr = new JMenuItem(
5517 MessageManager.getString("label.standard_databases"));
5518 fetchr.setToolTipText(MessageManager
5519 .getString("label.fetch_embl_uniprot"));
5520 fetchr.addActionListener(new ActionListener()
5524 public void actionPerformed(ActionEvent e)
5526 new Thread(new Runnable()
5532 boolean isNuclueotide = alignPanel.alignFrame
5533 .getViewport().getAlignment()
5535 new jalview.ws.DBRefFetcher(alignPanel.av
5536 .getSequenceSelection(),
5537 alignPanel.alignFrame, null,
5538 alignPanel.alignFrame.featureSettings,
5540 .fetchDBRefs(false);
5548 final AlignFrame me = this;
5549 new Thread(new Runnable()
5554 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5555 .getSequenceFetcherSingleton(me);
5556 javax.swing.SwingUtilities.invokeLater(new Runnable()
5561 String[] dbclasses = sf.getOrderedSupportedSources();
5562 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5563 // jalview.util.QuickSort.sort(otherdb, otherdb);
5564 List<DbSourceProxy> otherdb;
5565 JMenu dfetch = new JMenu();
5566 JMenu ifetch = new JMenu();
5567 JMenuItem fetchr = null;
5568 int comp = 0, icomp = 0, mcomp = 15;
5569 String mname = null;
5571 for (String dbclass : dbclasses)
5573 otherdb = sf.getSourceProxy(dbclass);
5574 // add a single entry for this class, or submenu allowing 'fetch
5576 if (otherdb == null || otherdb.size() < 1)
5580 // List<DbSourceProxy> dbs=otherdb;
5581 // otherdb=new ArrayList<DbSourceProxy>();
5582 // for (DbSourceProxy db:dbs)
5584 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5588 mname = "From " + dbclass;
5590 if (otherdb.size() == 1)
5592 final DbSourceProxy[] dassource = otherdb
5593 .toArray(new DbSourceProxy[0]);
5594 DbSourceProxy src = otherdb.get(0);
5595 fetchr = new JMenuItem(src.getDbSource());
5596 fetchr.addActionListener(new ActionListener()
5600 public void actionPerformed(ActionEvent e)
5602 new Thread(new Runnable()
5608 boolean isNuclueotide = alignPanel.alignFrame
5609 .getViewport().getAlignment()
5611 new jalview.ws.DBRefFetcher(alignPanel.av
5612 .getSequenceSelection(),
5613 alignPanel.alignFrame, dassource,
5614 alignPanel.alignFrame.featureSettings,
5616 .fetchDBRefs(false);
5622 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5623 MessageManager.formatMessage(
5624 "label.fetch_retrieve_from",
5625 new Object[] { src.getDbName() })));
5631 final DbSourceProxy[] dassource = otherdb
5632 .toArray(new DbSourceProxy[0]);
5634 DbSourceProxy src = otherdb.get(0);
5635 fetchr = new JMenuItem(MessageManager.formatMessage(
5636 "label.fetch_all_param",
5637 new Object[] { src.getDbSource() }));
5638 fetchr.addActionListener(new ActionListener()
5641 public void actionPerformed(ActionEvent e)
5643 new Thread(new Runnable()
5649 boolean isNuclueotide = alignPanel.alignFrame
5650 .getViewport().getAlignment()
5652 new jalview.ws.DBRefFetcher(alignPanel.av
5653 .getSequenceSelection(),
5654 alignPanel.alignFrame, dassource,
5655 alignPanel.alignFrame.featureSettings,
5657 .fetchDBRefs(false);
5663 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5664 MessageManager.formatMessage(
5665 "label.fetch_retrieve_from_all_sources",
5667 Integer.valueOf(otherdb.size())
5668 .toString(), src.getDbSource(),
5669 src.getDbName() })));
5672 // and then build the rest of the individual menus
5673 ifetch = new JMenu(MessageManager.formatMessage(
5674 "label.source_from_db_source",
5675 new Object[] { src.getDbSource() }));
5677 String imname = null;
5679 for (DbSourceProxy sproxy : otherdb)
5681 String dbname = sproxy.getDbName();
5682 String sname = dbname.length() > 5 ? dbname.substring(0,
5683 5) + "..." : dbname;
5684 String msname = dbname.length() > 10 ? dbname.substring(
5685 0, 10) + "..." : dbname;
5688 imname = MessageManager.formatMessage(
5689 "label.from_msname", new Object[] { sname });
5691 fetchr = new JMenuItem(msname);
5692 final DbSourceProxy[] dassrc = { sproxy };
5693 fetchr.addActionListener(new ActionListener()
5697 public void actionPerformed(ActionEvent e)
5699 new Thread(new Runnable()
5705 boolean isNuclueotide = alignPanel.alignFrame
5706 .getViewport().getAlignment()
5708 new jalview.ws.DBRefFetcher(alignPanel.av
5709 .getSequenceSelection(),
5710 alignPanel.alignFrame, dassrc,
5711 alignPanel.alignFrame.featureSettings,
5713 .fetchDBRefs(false);
5719 fetchr.setToolTipText("<html>"
5720 + MessageManager.formatMessage(
5721 "label.fetch_retrieve_from", new Object[]
5725 if (++icomp >= mcomp || i == (otherdb.size()))
5727 ifetch.setText(MessageManager.formatMessage(
5728 "label.source_to_target", imname, sname));
5730 ifetch = new JMenu();
5738 if (comp >= mcomp || dbi >= (dbclasses.length))
5740 dfetch.setText(MessageManager.formatMessage(
5741 "label.source_to_target", mname, dbclass));
5743 dfetch = new JMenu();
5756 * Left justify the whole alignment.
5759 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5761 AlignmentI al = viewport.getAlignment();
5763 viewport.firePropertyChange("alignment", null, al);
5767 * Right justify the whole alignment.
5770 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5772 AlignmentI al = viewport.getAlignment();
5774 viewport.firePropertyChange("alignment", null, al);
5778 public void setShowSeqFeatures(boolean b)
5780 showSeqFeatures.setSelected(b);
5781 viewport.setShowSequenceFeatures(b);
5788 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5789 * awt.event.ActionEvent)
5792 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5794 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5795 alignPanel.paintAlignment(true);
5802 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5806 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5808 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5809 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5817 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5818 * .event.ActionEvent)
5821 protected void showGroupConservation_actionPerformed(ActionEvent e)
5823 viewport.setShowGroupConservation(showGroupConservation.getState());
5824 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5831 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5832 * .event.ActionEvent)
5835 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5837 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5838 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5845 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5846 * .event.ActionEvent)
5849 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5851 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5852 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5856 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5858 showSequenceLogo.setState(true);
5859 viewport.setShowSequenceLogo(true);
5860 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5861 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5865 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5867 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5874 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5875 * .event.ActionEvent)
5878 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5880 if (avc.makeGroupsFromSelection())
5882 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5883 alignPanel.updateAnnotation();
5884 alignPanel.paintAlignment(true);
5888 public void clearAlignmentSeqRep()
5890 // TODO refactor alignmentseqrep to controller
5891 if (viewport.getAlignment().hasSeqrep())
5893 viewport.getAlignment().setSeqrep(null);
5894 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5895 alignPanel.updateAnnotation();
5896 alignPanel.paintAlignment(true);
5901 protected void createGroup_actionPerformed(ActionEvent e)
5903 if (avc.createGroup())
5905 alignPanel.alignmentChanged();
5910 protected void unGroup_actionPerformed(ActionEvent e)
5914 alignPanel.alignmentChanged();
5919 * make the given alignmentPanel the currently selected tab
5921 * @param alignmentPanel
5923 public void setDisplayedView(AlignmentPanel alignmentPanel)
5925 if (!viewport.getSequenceSetId().equals(
5926 alignmentPanel.av.getSequenceSetId()))
5930 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5932 if (tabbedPane != null
5933 && tabbedPane.getTabCount() > 0
5934 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5935 .getSelectedIndex())
5937 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5942 * Action on selection of menu options to Show or Hide annotations.
5945 * @param forSequences
5946 * update sequence-related annotations
5947 * @param forAlignment
5948 * update non-sequence-related annotations
5951 protected void setAnnotationsVisibility(boolean visible,
5952 boolean forSequences, boolean forAlignment)
5954 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5955 .getAlignmentAnnotation())
5958 * don't display non-positional annotations on an alignment
5960 if (aa.annotations == null)
5964 boolean apply = (aa.sequenceRef == null && forAlignment)
5965 || (aa.sequenceRef != null && forSequences);
5968 aa.visible = visible;
5971 alignPanel.validateAnnotationDimensions(true);
5972 alignPanel.alignmentChanged();
5976 * Store selected annotation sort order for the view and repaint.
5979 protected void sortAnnotations_actionPerformed()
5981 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5983 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5984 alignPanel.paintAlignment(true);
5989 * @return alignment panels in this alignment frame
5991 public List<? extends AlignmentViewPanel> getAlignPanels()
5993 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5997 * Open a new alignment window, with the cDNA associated with this (protein)
5998 * alignment, aligned as is the protein.
6000 protected void viewAsCdna_actionPerformed()
6002 // TODO no longer a menu action - refactor as required
6003 final AlignmentI alignment = getViewport().getAlignment();
6004 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6005 if (mappings == null)
6009 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6010 for (SequenceI aaSeq : alignment.getSequences())
6012 for (AlignedCodonFrame acf : mappings)
6014 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6018 * There is a cDNA mapping for this protein sequence - add to new
6019 * alignment. It will share the same dataset sequence as other mapped
6020 * cDNA (no new mappings need to be created).
6022 final Sequence newSeq = new Sequence(dnaSeq);
6023 newSeq.setDatasetSequence(dnaSeq);
6024 cdnaSeqs.add(newSeq);
6028 if (cdnaSeqs.size() == 0)
6030 // show a warning dialog no mapped cDNA
6033 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6035 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6036 AlignFrame.DEFAULT_HEIGHT);
6037 cdna.alignAs(alignment);
6038 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6040 Desktop.addInternalFrame(alignFrame, newtitle,
6041 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6045 * Set visibility of dna/protein complement view (available when shown in a
6051 protected void showComplement_actionPerformed(boolean show)
6053 SplitContainerI sf = getSplitViewContainer();
6056 sf.setComplementVisible(this, show);
6061 * Generate the reverse (optionally complemented) of the selected sequences,
6062 * and add them to the alignment
6065 protected void showReverse_actionPerformed(boolean complement)
6067 AlignmentI al = null;
6070 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6072 al = dna.reverseCdna(complement);
6073 viewport.addAlignment(al, "");
6074 } catch (Exception ex)
6076 System.err.println(ex.getMessage());
6082 class PrintThread extends Thread
6086 public PrintThread(AlignmentPanel ap)
6091 static PageFormat pf;
6096 PrinterJob printJob = PrinterJob.getPrinterJob();
6100 printJob.setPrintable(ap, pf);
6104 printJob.setPrintable(ap);
6107 if (printJob.printDialog())
6112 } catch (Exception PrintException)
6114 PrintException.printStackTrace();