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);
907 setShowProductsEnabled();
911 private IProgressIndicator progressBar;
916 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
919 public void setProgressBar(String message, long id)
921 progressBar.setProgressBar(message, id);
925 public void registerHandler(final long id,
926 final IProgressIndicatorHandler handler)
928 progressBar.registerHandler(id, handler);
933 * @return true if any progress bars are still active
936 public boolean operationInProgress()
938 return progressBar.operationInProgress();
942 public void setStatus(String text)
944 statusBar.setText(text);
948 * Added so Castor Mapping file can obtain Jalview Version
950 public String getVersion()
952 return jalview.bin.Cache.getProperty("VERSION");
955 public FeatureRenderer getFeatureRenderer()
957 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
961 public void fetchSequence_actionPerformed(ActionEvent e)
963 new SequenceFetcher(this);
967 public void addFromFile_actionPerformed(ActionEvent e)
969 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
973 public void reload_actionPerformed(ActionEvent e)
975 if (fileName != null)
977 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
978 // originating file's format
979 // TODO: work out how to recover feature settings for correct view(s) when
981 if (currentFileFormat.equals("Jalview"))
983 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
984 for (int i = 0; i < frames.length; i++)
986 if (frames[i] instanceof AlignFrame && frames[i] != this
987 && ((AlignFrame) frames[i]).fileName != null
988 && ((AlignFrame) frames[i]).fileName.equals(fileName))
992 frames[i].setSelected(true);
993 Desktop.instance.closeAssociatedWindows();
994 } catch (java.beans.PropertyVetoException ex)
1000 Desktop.instance.closeAssociatedWindows();
1002 FileLoader loader = new FileLoader();
1003 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1004 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1008 Rectangle bounds = this.getBounds();
1010 FileLoader loader = new FileLoader();
1011 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1012 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1013 protocol, currentFileFormat);
1015 newframe.setBounds(bounds);
1016 if (featureSettings != null && featureSettings.isShowing())
1018 final Rectangle fspos = featureSettings.frame.getBounds();
1019 // TODO: need a 'show feature settings' function that takes bounds -
1020 // need to refactor Desktop.addFrame
1021 newframe.featureSettings_actionPerformed(null);
1022 final FeatureSettings nfs = newframe.featureSettings;
1023 SwingUtilities.invokeLater(new Runnable()
1028 nfs.frame.setBounds(fspos);
1031 this.featureSettings.close();
1032 this.featureSettings = null;
1034 this.closeMenuItem_actionPerformed(true);
1040 public void addFromText_actionPerformed(ActionEvent e)
1042 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1047 public void addFromURL_actionPerformed(ActionEvent e)
1049 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1053 public void save_actionPerformed(ActionEvent e)
1055 if (fileName == null
1056 || (currentFileFormat == null || !jalview.io.FormatAdapter
1057 .isValidIOFormat(currentFileFormat, true))
1058 || fileName.startsWith("http"))
1060 saveAs_actionPerformed(null);
1064 saveAlignment(fileName, currentFileFormat);
1075 public void saveAs_actionPerformed(ActionEvent e)
1077 JalviewFileChooser chooser = new JalviewFileChooser(
1078 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1079 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1080 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1081 currentFileFormat, false);
1083 chooser.setFileView(new JalviewFileView());
1084 chooser.setDialogTitle(MessageManager
1085 .getString("label.save_alignment_to_file"));
1086 chooser.setToolTipText(MessageManager.getString("action.save"));
1088 int value = chooser.showSaveDialog(this);
1090 if (value == JalviewFileChooser.APPROVE_OPTION)
1092 currentFileFormat = chooser.getSelectedFormat();
1093 while (currentFileFormat == null)
1096 .showInternalMessageDialog(
1099 .getString("label.select_file_format_before_saving"),
1101 .getString("label.file_format_not_specified"),
1102 JOptionPane.WARNING_MESSAGE);
1103 currentFileFormat = chooser.getSelectedFormat();
1104 value = chooser.showSaveDialog(this);
1105 if (value != JalviewFileChooser.APPROVE_OPTION)
1111 fileName = chooser.getSelectedFile().getPath();
1113 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1116 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1117 if (currentFileFormat.indexOf(" ") > -1)
1119 currentFileFormat = currentFileFormat.substring(0,
1120 currentFileFormat.indexOf(" "));
1122 saveAlignment(fileName, currentFileFormat);
1126 public boolean saveAlignment(String file, String format)
1128 boolean success = true;
1130 if (format.equalsIgnoreCase("Jalview"))
1132 String shortName = title;
1134 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1136 shortName = shortName.substring(shortName
1137 .lastIndexOf(java.io.File.separatorChar) + 1);
1140 success = new Jalview2XML().saveAlignment(this, file, shortName);
1142 statusBar.setText(MessageManager.formatMessage(
1143 "label.successfully_saved_to_file_in_format", new Object[] {
1144 fileName, format }));
1149 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1151 warningMessage("Cannot save file " + fileName + " using format "
1152 + format, "Alignment output format not supported");
1153 if (!Jalview.isHeadlessMode())
1155 saveAs_actionPerformed(null);
1160 AlignmentExportData exportData = getAlignmentForExport(format,
1162 if (exportData.getSettings().isCancelled())
1166 FormatAdapter f = new FormatAdapter(alignPanel,
1167 exportData.getSettings());
1168 String output = f.formatSequences(
1170 exportData.getAlignment(), // class cast exceptions will
1171 // occur in the distant future
1172 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1173 f.getCacheSuffixDefault(format),
1174 viewport.getColumnSelection());
1184 java.io.PrintWriter out = new java.io.PrintWriter(
1185 new java.io.FileWriter(file));
1189 this.setTitle(file);
1190 statusBar.setText(MessageManager.formatMessage(
1191 "label.successfully_saved_to_file_in_format",
1192 new Object[] { fileName, format }));
1193 } catch (Exception ex)
1196 ex.printStackTrace();
1203 JOptionPane.showInternalMessageDialog(this, MessageManager
1204 .formatMessage("label.couldnt_save_file",
1205 new Object[] { fileName }), MessageManager
1206 .getString("label.error_saving_file"),
1207 JOptionPane.WARNING_MESSAGE);
1213 private void warningMessage(String warning, String title)
1215 if (new jalview.util.Platform().isHeadless())
1217 System.err.println("Warning: " + title + "\nWarning: " + warning);
1222 JOptionPane.showInternalMessageDialog(this, warning, title,
1223 JOptionPane.WARNING_MESSAGE);
1235 protected void outputText_actionPerformed(ActionEvent e)
1238 AlignmentExportData exportData = getAlignmentForExport(
1239 e.getActionCommand(), viewport, null);
1240 if (exportData.getSettings().isCancelled())
1244 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1245 cap.setForInput(null);
1248 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1249 .formatSequences(e.getActionCommand(),
1250 exportData.getAlignment(),
1251 exportData.getOmitHidden(),
1252 exportData.getStartEndPostions(),
1253 viewport.getColumnSelection()));
1254 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1255 "label.alignment_output_command",
1256 new Object[] { e.getActionCommand() }), 600, 500);
1257 } catch (OutOfMemoryError oom)
1259 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1265 public static AlignmentExportData getAlignmentForExport(
1266 String exportFormat, AlignViewportI viewport,
1267 AlignExportSettingI exportSettings)
1269 AlignmentI alignmentToExport = null;
1270 AlignExportSettingI settings = exportSettings;
1271 String[] omitHidden = null;
1272 int[] alignmentStartEnd = new int[2];
1274 HiddenSequences hiddenSeqs = viewport.getAlignment()
1275 .getHiddenSequences();
1277 alignmentToExport = viewport.getAlignment();
1278 alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
1280 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1281 if (settings == null)
1283 settings = new AlignExportSettings(hasHiddenSeqs,
1284 viewport.hasHiddenColumns(), exportFormat);
1286 // settings.isExportAnnotations();
1288 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1290 omitHidden = viewport.getViewAsString(false);
1293 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1295 alignmentToExport = hiddenSeqs.getFullAlignment();
1299 alignmentToExport = viewport.getAlignment();
1300 alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1301 .getColumnSelection().getHiddenColumns());
1303 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1304 omitHidden, alignmentStartEnd, settings);
1308 public static int[] getStartEnd(int[] aligmentStartEnd,
1309 List<int[]> hiddenCols)
1311 int startPos = aligmentStartEnd[0];
1312 int endPos = aligmentStartEnd[1];
1314 int[] lowestRange = new int[] { -1, -1 };
1315 int[] higestRange = new int[] { -1, -1 };
1317 for (int[] hiddenCol : hiddenCols)
1319 lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1320 higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1323 if (lowestRange[0] == -1 && lowestRange[1] == -1)
1325 startPos = aligmentStartEnd[0];
1329 startPos = lowestRange[1] + 1;
1332 if (higestRange[0] == -1 && higestRange[1] == -1)
1334 endPos = aligmentStartEnd[1];
1338 endPos = higestRange[0] - 1;
1341 // System.out.println("Export range : " + startPos + " - " + endPos);
1342 return new int[] { startPos, endPos };
1345 public static void main(String[] args)
1347 ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1348 hiddenCols.add(new int[] { 0, 0 });
1349 hiddenCols.add(new int[] { 6, 9 });
1350 hiddenCols.add(new int[] { 11, 12 });
1351 hiddenCols.add(new int[] { 33, 33 });
1352 hiddenCols.add(new int[] { 50, 50 });
1354 int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
1355 // System.out.println("Export range : " + x[0] + " - " + x[1]);
1365 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1367 new HtmlSvgOutput(null, alignPanel);
1371 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1373 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1374 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1377 public void createImageMap(File file, String image)
1379 alignPanel.makePNGImageMap(file, image);
1389 public void createPNG(File f)
1391 alignPanel.makePNG(f);
1401 public void createEPS(File f)
1403 alignPanel.makeEPS(f);
1407 public void createSVG(File f)
1409 alignPanel.makeSVG(f);
1413 public void pageSetup_actionPerformed(ActionEvent e)
1415 PrinterJob printJob = PrinterJob.getPrinterJob();
1416 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1426 public void printMenuItem_actionPerformed(ActionEvent e)
1428 // Putting in a thread avoids Swing painting problems
1429 PrintThread thread = new PrintThread(alignPanel);
1434 public void exportFeatures_actionPerformed(ActionEvent e)
1436 new AnnotationExporter().exportFeatures(alignPanel);
1440 public void exportAnnotations_actionPerformed(ActionEvent e)
1442 new AnnotationExporter().exportAnnotations(alignPanel);
1446 public void associatedData_actionPerformed(ActionEvent e)
1448 // Pick the tree file
1449 JalviewFileChooser chooser = new JalviewFileChooser(
1450 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1451 chooser.setFileView(new JalviewFileView());
1452 chooser.setDialogTitle(MessageManager
1453 .getString("label.load_jalview_annotations"));
1454 chooser.setToolTipText(MessageManager
1455 .getString("label.load_jalview_annotations"));
1457 int value = chooser.showOpenDialog(null);
1459 if (value == JalviewFileChooser.APPROVE_OPTION)
1461 String choice = chooser.getSelectedFile().getPath();
1462 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1463 loadJalviewDataFile(choice, null, null, null);
1469 * Close the current view or all views in the alignment frame. If the frame
1470 * only contains one view then the alignment will be removed from memory.
1472 * @param closeAllTabs
1475 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1477 if (alignPanels != null && alignPanels.size() < 2)
1479 closeAllTabs = true;
1484 if (alignPanels != null)
1488 if (this.isClosed())
1490 // really close all the windows - otherwise wait till
1491 // setClosed(true) is called
1492 for (int i = 0; i < alignPanels.size(); i++)
1494 AlignmentPanel ap = alignPanels.get(i);
1501 closeView(alignPanel);
1508 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1509 * be called recursively, with the frame now in 'closed' state
1511 this.setClosed(true);
1513 } catch (Exception ex)
1515 ex.printStackTrace();
1520 * Close the specified panel and close up tabs appropriately.
1522 * @param panelToClose
1524 public void closeView(AlignmentPanel panelToClose)
1526 int index = tabbedPane.getSelectedIndex();
1527 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1528 alignPanels.remove(panelToClose);
1529 panelToClose.closePanel();
1530 panelToClose = null;
1532 tabbedPane.removeTabAt(closedindex);
1533 tabbedPane.validate();
1535 if (index > closedindex || index == tabbedPane.getTabCount())
1537 // modify currently selected tab index if necessary.
1541 this.tabSelectionChanged(index);
1547 void updateEditMenuBar()
1550 if (viewport.getHistoryList().size() > 0)
1552 undoMenuItem.setEnabled(true);
1553 CommandI command = viewport.getHistoryList().peek();
1554 undoMenuItem.setText(MessageManager.formatMessage(
1555 "label.undo_command",
1556 new Object[] { command.getDescription() }));
1560 undoMenuItem.setEnabled(false);
1561 undoMenuItem.setText(MessageManager.getString("action.undo"));
1564 if (viewport.getRedoList().size() > 0)
1566 redoMenuItem.setEnabled(true);
1568 CommandI command = viewport.getRedoList().peek();
1569 redoMenuItem.setText(MessageManager.formatMessage(
1570 "label.redo_command",
1571 new Object[] { command.getDescription() }));
1575 redoMenuItem.setEnabled(false);
1576 redoMenuItem.setText(MessageManager.getString("action.redo"));
1581 public void addHistoryItem(CommandI command)
1583 if (command.getSize() > 0)
1585 viewport.addToHistoryList(command);
1586 viewport.clearRedoList();
1587 updateEditMenuBar();
1588 viewport.updateHiddenColumns();
1589 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1590 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1591 // viewport.getColumnSelection()
1592 // .getHiddenColumns().size() > 0);
1598 * @return alignment objects for all views
1600 AlignmentI[] getViewAlignments()
1602 if (alignPanels != null)
1604 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1606 for (AlignmentPanel ap : alignPanels)
1608 als[i++] = ap.av.getAlignment();
1612 if (viewport != null)
1614 return new AlignmentI[] { viewport.getAlignment() };
1626 protected void undoMenuItem_actionPerformed(ActionEvent e)
1628 if (viewport.getHistoryList().isEmpty())
1632 CommandI command = viewport.getHistoryList().pop();
1633 viewport.addToRedoList(command);
1634 command.undoCommand(getViewAlignments());
1636 AlignmentViewport originalSource = getOriginatingSource(command);
1637 updateEditMenuBar();
1639 if (originalSource != null)
1641 if (originalSource != viewport)
1644 .warn("Implementation worry: mismatch of viewport origin for undo");
1646 originalSource.updateHiddenColumns();
1647 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1649 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1650 // viewport.getColumnSelection()
1651 // .getHiddenColumns().size() > 0);
1652 originalSource.firePropertyChange("alignment", null, originalSource
1653 .getAlignment().getSequences());
1664 protected void redoMenuItem_actionPerformed(ActionEvent e)
1666 if (viewport.getRedoList().size() < 1)
1671 CommandI command = viewport.getRedoList().pop();
1672 viewport.addToHistoryList(command);
1673 command.doCommand(getViewAlignments());
1675 AlignmentViewport originalSource = getOriginatingSource(command);
1676 updateEditMenuBar();
1678 if (originalSource != null)
1681 if (originalSource != viewport)
1684 .warn("Implementation worry: mismatch of viewport origin for redo");
1686 originalSource.updateHiddenColumns();
1687 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1689 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1690 // viewport.getColumnSelection()
1691 // .getHiddenColumns().size() > 0);
1692 originalSource.firePropertyChange("alignment", null, originalSource
1693 .getAlignment().getSequences());
1697 AlignmentViewport getOriginatingSource(CommandI command)
1699 AlignmentViewport originalSource = null;
1700 // For sequence removal and addition, we need to fire
1701 // the property change event FROM the viewport where the
1702 // original alignment was altered
1703 AlignmentI al = null;
1704 if (command instanceof EditCommand)
1706 EditCommand editCommand = (EditCommand) command;
1707 al = editCommand.getAlignment();
1708 List<Component> comps = PaintRefresher.components.get(viewport
1709 .getSequenceSetId());
1711 for (Component comp : comps)
1713 if (comp instanceof AlignmentPanel)
1715 if (al == ((AlignmentPanel) comp).av.getAlignment())
1717 originalSource = ((AlignmentPanel) comp).av;
1724 if (originalSource == null)
1726 // The original view is closed, we must validate
1727 // the current view against the closed view first
1730 PaintRefresher.validateSequences(al, viewport.getAlignment());
1733 originalSource = viewport;
1736 return originalSource;
1745 public void moveSelectedSequences(boolean up)
1747 SequenceGroup sg = viewport.getSelectionGroup();
1753 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1754 viewport.getHiddenRepSequences(), up);
1755 alignPanel.paintAlignment(true);
1758 synchronized void slideSequences(boolean right, int size)
1760 List<SequenceI> sg = new ArrayList<SequenceI>();
1761 if (viewport.cursorMode)
1763 sg.add(viewport.getAlignment().getSequenceAt(
1764 alignPanel.getSeqPanel().seqCanvas.cursorY));
1766 else if (viewport.getSelectionGroup() != null
1767 && viewport.getSelectionGroup().getSize() != viewport
1768 .getAlignment().getHeight())
1770 sg = viewport.getSelectionGroup().getSequences(
1771 viewport.getHiddenRepSequences());
1779 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1781 for (SequenceI seq : viewport.getAlignment().getSequences())
1783 if (!sg.contains(seq))
1785 invertGroup.add(seq);
1789 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1791 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1792 for (int i = 0; i < invertGroup.size(); i++)
1794 seqs2[i] = invertGroup.get(i);
1797 SlideSequencesCommand ssc;
1800 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1801 size, viewport.getGapCharacter());
1805 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1806 size, viewport.getGapCharacter());
1809 int groupAdjustment = 0;
1810 if (ssc.getGapsInsertedBegin() && right)
1812 if (viewport.cursorMode)
1814 alignPanel.getSeqPanel().moveCursor(size, 0);
1818 groupAdjustment = size;
1821 else if (!ssc.getGapsInsertedBegin() && !right)
1823 if (viewport.cursorMode)
1825 alignPanel.getSeqPanel().moveCursor(-size, 0);
1829 groupAdjustment = -size;
1833 if (groupAdjustment != 0)
1835 viewport.getSelectionGroup().setStartRes(
1836 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1837 viewport.getSelectionGroup().setEndRes(
1838 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1842 * just extend the last slide command if compatible; but not if in
1843 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1845 boolean appendHistoryItem = false;
1846 Deque<CommandI> historyList = viewport.getHistoryList();
1847 boolean inSplitFrame = getSplitViewContainer() != null;
1848 if (!inSplitFrame && historyList != null && historyList.size() > 0
1849 && historyList.peek() instanceof SlideSequencesCommand)
1851 appendHistoryItem = ssc
1852 .appendSlideCommand((SlideSequencesCommand) historyList
1856 if (!appendHistoryItem)
1858 addHistoryItem(ssc);
1871 protected void copy_actionPerformed(ActionEvent e)
1874 if (viewport.getSelectionGroup() == null)
1878 // TODO: preserve the ordering of displayed alignment annotation in any
1879 // internal paste (particularly sequence associated annotation)
1880 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1881 String[] omitHidden = null;
1883 if (viewport.hasHiddenColumns())
1885 omitHidden = viewport.getViewAsString(true);
1888 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1891 StringSelection ss = new StringSelection(output);
1895 jalview.gui.Desktop.internalCopy = true;
1896 // Its really worth setting the clipboard contents
1897 // to empty before setting the large StringSelection!!
1898 Toolkit.getDefaultToolkit().getSystemClipboard()
1899 .setContents(new StringSelection(""), null);
1901 Toolkit.getDefaultToolkit().getSystemClipboard()
1902 .setContents(ss, Desktop.instance);
1903 } catch (OutOfMemoryError er)
1905 new OOMWarning("copying region", er);
1909 ArrayList<int[]> hiddenColumns = null;
1910 if (viewport.hasHiddenColumns())
1912 hiddenColumns = new ArrayList<int[]>();
1913 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1914 .getSelectionGroup().getEndRes();
1915 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1917 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1919 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1920 region[1] - hiddenOffset });
1925 Desktop.jalviewClipboard = new Object[] { seqs,
1926 viewport.getAlignment().getDataset(), hiddenColumns };
1927 statusBar.setText(MessageManager.formatMessage(
1928 "label.copied_sequences_to_clipboard", new Object[] { Integer
1929 .valueOf(seqs.length).toString() }));
1939 protected void pasteNew_actionPerformed(ActionEvent e)
1951 protected void pasteThis_actionPerformed(ActionEvent e)
1957 * Paste contents of Jalview clipboard
1959 * @param newAlignment
1960 * true to paste to a new alignment, otherwise add to this.
1962 void paste(boolean newAlignment)
1964 boolean externalPaste = true;
1967 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1968 Transferable contents = c.getContents(this);
1970 if (contents == null)
1978 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1979 if (str.length() < 1)
1984 format = new IdentifyFile().identify(str, "Paste");
1986 } catch (OutOfMemoryError er)
1988 new OOMWarning("Out of memory pasting sequences!!", er);
1992 SequenceI[] sequences;
1993 boolean annotationAdded = false;
1994 AlignmentI alignment = null;
1996 if (Desktop.jalviewClipboard != null)
1998 // The clipboard was filled from within Jalview, we must use the
2000 // And dataset from the copied alignment
2001 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2002 // be doubly sure that we create *new* sequence objects.
2003 sequences = new SequenceI[newseq.length];
2004 for (int i = 0; i < newseq.length; i++)
2006 sequences[i] = new Sequence(newseq[i]);
2008 alignment = new Alignment(sequences);
2009 externalPaste = false;
2013 // parse the clipboard as an alignment.
2014 alignment = new FormatAdapter().readFile(str, "Paste", format);
2015 sequences = alignment.getSequencesArray();
2019 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2025 if (Desktop.jalviewClipboard != null)
2027 // dataset is inherited
2028 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2032 // new dataset is constructed
2033 alignment.setDataset(null);
2035 alwidth = alignment.getWidth() + 1;
2039 AlignmentI pastedal = alignment; // preserve pasted alignment object
2040 // Add pasted sequences and dataset into existing alignment.
2041 alignment = viewport.getAlignment();
2042 alwidth = alignment.getWidth() + 1;
2043 // decide if we need to import sequences from an existing dataset
2044 boolean importDs = Desktop.jalviewClipboard != null
2045 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2046 // importDs==true instructs us to copy over new dataset sequences from
2047 // an existing alignment
2048 Vector newDs = (importDs) ? new Vector() : null; // used to create
2049 // minimum dataset set
2051 for (int i = 0; i < sequences.length; i++)
2055 newDs.addElement(null);
2057 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2059 if (importDs && ds != null)
2061 if (!newDs.contains(ds))
2063 newDs.setElementAt(ds, i);
2064 ds = new Sequence(ds);
2065 // update with new dataset sequence
2066 sequences[i].setDatasetSequence(ds);
2070 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2075 // copy and derive new dataset sequence
2076 sequences[i] = sequences[i].deriveSequence();
2077 alignment.getDataset().addSequence(
2078 sequences[i].getDatasetSequence());
2079 // TODO: avoid creation of duplicate dataset sequences with a
2080 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2082 alignment.addSequence(sequences[i]); // merges dataset
2086 newDs.clear(); // tidy up
2088 if (alignment.getAlignmentAnnotation() != null)
2090 for (AlignmentAnnotation alan : alignment
2091 .getAlignmentAnnotation())
2093 if (alan.graphGroup > fgroup)
2095 fgroup = alan.graphGroup;
2099 if (pastedal.getAlignmentAnnotation() != null)
2101 // Add any annotation attached to alignment.
2102 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2103 for (int i = 0; i < alann.length; i++)
2105 annotationAdded = true;
2106 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2108 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2109 if (newann.graphGroup > -1)
2111 if (newGraphGroups.size() <= newann.graphGroup
2112 || newGraphGroups.get(newann.graphGroup) == null)
2114 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2116 newGraphGroups.add(q, null);
2118 newGraphGroups.set(newann.graphGroup, new Integer(
2121 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2125 newann.padAnnotation(alwidth);
2126 alignment.addAnnotation(newann);
2136 addHistoryItem(new EditCommand(
2137 MessageManager.getString("label.add_sequences"),
2138 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2140 // Add any annotations attached to sequences
2141 for (int i = 0; i < sequences.length; i++)
2143 if (sequences[i].getAnnotation() != null)
2145 AlignmentAnnotation newann;
2146 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2148 annotationAdded = true;
2149 newann = sequences[i].getAnnotation()[a];
2150 newann.adjustForAlignment();
2151 newann.padAnnotation(alwidth);
2152 if (newann.graphGroup > -1)
2154 if (newann.graphGroup > -1)
2156 if (newGraphGroups.size() <= newann.graphGroup
2157 || newGraphGroups.get(newann.graphGroup) == null)
2159 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2161 newGraphGroups.add(q, null);
2163 newGraphGroups.set(newann.graphGroup, new Integer(
2166 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2170 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2175 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2182 // propagate alignment changed.
2183 viewport.setEndSeq(alignment.getHeight());
2184 if (annotationAdded)
2186 // Duplicate sequence annotation in all views.
2187 AlignmentI[] alview = this.getViewAlignments();
2188 for (int i = 0; i < sequences.length; i++)
2190 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2195 for (int avnum = 0; avnum < alview.length; avnum++)
2197 if (alview[avnum] != alignment)
2199 // duplicate in a view other than the one with input focus
2200 int avwidth = alview[avnum].getWidth() + 1;
2201 // this relies on sann being preserved after we
2202 // modify the sequence's annotation array for each duplication
2203 for (int a = 0; a < sann.length; a++)
2205 AlignmentAnnotation newann = new AlignmentAnnotation(
2207 sequences[i].addAlignmentAnnotation(newann);
2208 newann.padAnnotation(avwidth);
2209 alview[avnum].addAnnotation(newann); // annotation was
2210 // duplicated earlier
2211 // TODO JAL-1145 graphGroups are not updated for sequence
2212 // annotation added to several views. This may cause
2214 alview[avnum].setAnnotationIndex(newann, a);
2219 buildSortByAnnotationScoresMenu();
2221 viewport.firePropertyChange("alignment", null,
2222 alignment.getSequences());
2223 if (alignPanels != null)
2225 for (AlignmentPanel ap : alignPanels)
2227 ap.validateAnnotationDimensions(false);
2232 alignPanel.validateAnnotationDimensions(false);
2238 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2240 String newtitle = new String("Copied sequences");
2242 if (Desktop.jalviewClipboard != null
2243 && Desktop.jalviewClipboard[2] != null)
2245 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2246 for (int[] region : hc)
2248 af.viewport.hideColumns(region[0], region[1]);
2252 // >>>This is a fix for the moment, until a better solution is
2254 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2256 alignPanel.getSeqPanel().seqCanvas
2257 .getFeatureRenderer());
2259 // TODO: maintain provenance of an alignment, rather than just make the
2260 // title a concatenation of operations.
2263 if (title.startsWith("Copied sequences"))
2269 newtitle = newtitle.concat("- from " + title);
2274 newtitle = new String("Pasted sequences");
2277 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2282 } catch (Exception ex)
2284 ex.printStackTrace();
2285 System.out.println("Exception whilst pasting: " + ex);
2286 // could be anything being pasted in here
2292 protected void expand_newalign(ActionEvent e)
2296 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2297 .getAlignment(), -1);
2298 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2300 String newtitle = new String("Flanking alignment");
2302 if (Desktop.jalviewClipboard != null
2303 && Desktop.jalviewClipboard[2] != null)
2305 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2306 for (int region[] : hc)
2308 af.viewport.hideColumns(region[0], region[1]);
2312 // >>>This is a fix for the moment, until a better solution is
2314 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2316 alignPanel.getSeqPanel().seqCanvas
2317 .getFeatureRenderer());
2319 // TODO: maintain provenance of an alignment, rather than just make the
2320 // title a concatenation of operations.
2322 if (title.startsWith("Copied sequences"))
2328 newtitle = newtitle.concat("- from " + title);
2332 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2334 } catch (Exception ex)
2336 ex.printStackTrace();
2337 System.out.println("Exception whilst pasting: " + ex);
2338 // could be anything being pasted in here
2339 } catch (OutOfMemoryError oom)
2341 new OOMWarning("Viewing flanking region of alignment", oom);
2352 protected void cut_actionPerformed(ActionEvent e)
2354 copy_actionPerformed(null);
2355 delete_actionPerformed(null);
2365 protected void delete_actionPerformed(ActionEvent evt)
2368 SequenceGroup sg = viewport.getSelectionGroup();
2375 * If the cut affects all sequences, warn, remove highlighted columns
2377 if (sg.getSize() == viewport.getAlignment().getHeight())
2379 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2380 .getAlignment().getWidth()) ? true : false;
2381 if (isEntireAlignWidth)
2383 int confirm = JOptionPane.showConfirmDialog(this,
2384 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2385 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2386 JOptionPane.OK_CANCEL_OPTION);
2388 if (confirm == JOptionPane.CANCEL_OPTION
2389 || confirm == JOptionPane.CLOSED_OPTION)
2394 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2395 sg.getEndRes() + 1);
2397 SequenceI[] cut = sg.getSequences()
2398 .toArray(new SequenceI[sg.getSize()]);
2400 addHistoryItem(new EditCommand(
2401 MessageManager.getString("label.cut_sequences"), Action.CUT,
2402 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2403 viewport.getAlignment()));
2405 viewport.setSelectionGroup(null);
2406 viewport.sendSelection();
2407 viewport.getAlignment().deleteGroup(sg);
2409 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2411 if (viewport.getAlignment().getHeight() < 1)
2415 this.setClosed(true);
2416 } catch (Exception ex)
2429 protected void deleteGroups_actionPerformed(ActionEvent e)
2431 if (avc.deleteGroups())
2433 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2434 alignPanel.updateAnnotation();
2435 alignPanel.paintAlignment(true);
2446 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2448 SequenceGroup sg = new SequenceGroup();
2450 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2452 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2455 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2456 viewport.setSelectionGroup(sg);
2457 viewport.sendSelection();
2458 alignPanel.paintAlignment(true);
2459 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2469 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2471 if (viewport.cursorMode)
2473 alignPanel.getSeqPanel().keyboardNo1 = null;
2474 alignPanel.getSeqPanel().keyboardNo2 = null;
2476 viewport.setSelectionGroup(null);
2477 viewport.getColumnSelection().clear();
2478 viewport.setSelectionGroup(null);
2479 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2480 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2481 alignPanel.paintAlignment(true);
2482 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2483 viewport.sendSelection();
2493 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2495 SequenceGroup sg = viewport.getSelectionGroup();
2499 selectAllSequenceMenuItem_actionPerformed(null);
2504 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2506 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2509 alignPanel.paintAlignment(true);
2510 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2511 viewport.sendSelection();
2515 public void invertColSel_actionPerformed(ActionEvent e)
2517 viewport.invertColumnSelection();
2518 alignPanel.paintAlignment(true);
2519 viewport.sendSelection();
2529 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2531 trimAlignment(true);
2541 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2543 trimAlignment(false);
2546 void trimAlignment(boolean trimLeft)
2548 ColumnSelection colSel = viewport.getColumnSelection();
2551 if (colSel.size() > 0)
2555 column = colSel.getMin();
2559 column = colSel.getMax();
2563 if (viewport.getSelectionGroup() != null)
2565 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2566 viewport.getHiddenRepSequences());
2570 seqs = viewport.getAlignment().getSequencesArray();
2573 TrimRegionCommand trimRegion;
2576 trimRegion = new TrimRegionCommand("Remove Left",
2577 TrimRegionCommand.TRIM_LEFT, seqs, column,
2578 viewport.getAlignment(), viewport.getColumnSelection(),
2579 viewport.getSelectionGroup());
2580 viewport.setStartRes(0);
2584 trimRegion = new TrimRegionCommand("Remove Right",
2585 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2586 viewport.getAlignment(), viewport.getColumnSelection(),
2587 viewport.getSelectionGroup());
2590 statusBar.setText(MessageManager.formatMessage(
2591 "label.removed_columns",
2592 new String[] { Integer.valueOf(trimRegion.getSize())
2595 addHistoryItem(trimRegion);
2597 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2599 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2600 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2602 viewport.getAlignment().deleteGroup(sg);
2606 viewport.firePropertyChange("alignment", null, viewport
2607 .getAlignment().getSequences());
2618 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2620 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2623 if (viewport.getSelectionGroup() != null)
2625 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2626 viewport.getHiddenRepSequences());
2627 start = viewport.getSelectionGroup().getStartRes();
2628 end = viewport.getSelectionGroup().getEndRes();
2632 seqs = viewport.getAlignment().getSequencesArray();
2635 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2636 "Remove Gapped Columns", seqs, start, end,
2637 viewport.getAlignment());
2639 addHistoryItem(removeGapCols);
2641 statusBar.setText(MessageManager.formatMessage(
2642 "label.removed_empty_columns",
2643 new Object[] { Integer.valueOf(removeGapCols.getSize())
2646 // This is to maintain viewport position on first residue
2647 // of first sequence
2648 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2649 int startRes = seq.findPosition(viewport.startRes);
2650 // ShiftList shifts;
2651 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2652 // edit.alColumnChanges=shifts.getInverse();
2653 // if (viewport.hasHiddenColumns)
2654 // viewport.getColumnSelection().compensateForEdits(shifts);
2655 viewport.setStartRes(seq.findIndex(startRes) - 1);
2656 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2668 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2670 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2673 if (viewport.getSelectionGroup() != null)
2675 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2676 viewport.getHiddenRepSequences());
2677 start = viewport.getSelectionGroup().getStartRes();
2678 end = viewport.getSelectionGroup().getEndRes();
2682 seqs = viewport.getAlignment().getSequencesArray();
2685 // This is to maintain viewport position on first residue
2686 // of first sequence
2687 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2688 int startRes = seq.findPosition(viewport.startRes);
2690 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2691 viewport.getAlignment()));
2693 viewport.setStartRes(seq.findIndex(startRes) - 1);
2695 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2707 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2709 viewport.setPadGaps(padGapsMenuitem.isSelected());
2710 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2721 public void findMenuItem_actionPerformed(ActionEvent e)
2727 * Create a new view of the current alignment.
2730 public void newView_actionPerformed(ActionEvent e)
2732 newView(null, true);
2736 * Creates and shows a new view of the current alignment.
2739 * title of newly created view; if null, one will be generated
2740 * @param copyAnnotation
2741 * if true then duplicate all annnotation, groups and settings
2742 * @return new alignment panel, already displayed.
2744 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2747 * Create a new AlignmentPanel (with its own, new Viewport)
2749 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2751 if (!copyAnnotation)
2754 * remove all groups and annotation except for the automatic stuff
2756 newap.av.getAlignment().deleteAllGroups();
2757 newap.av.getAlignment().deleteAllAnnotations(false);
2760 newap.av.setGatherViewsHere(false);
2762 if (viewport.viewName == null)
2764 viewport.viewName = MessageManager
2765 .getString("label.view_name_original");
2769 * Views share the same edits undo and redo stacks
2771 newap.av.setHistoryList(viewport.getHistoryList());
2772 newap.av.setRedoList(viewport.getRedoList());
2775 * Views share the same mappings; need to deregister any new mappings
2776 * created by copyAlignPanel, and register the new reference to the shared
2779 newap.av.replaceMappings(viewport.getAlignment());
2781 newap.av.viewName = getNewViewName(viewTitle);
2783 addAlignmentPanel(newap, true);
2784 newap.alignmentChanged();
2786 if (alignPanels.size() == 2)
2788 viewport.setGatherViewsHere(true);
2790 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2795 * Make a new name for the view, ensuring it is unique within the current
2796 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2797 * these now use viewId. Unique view names are still desirable for usability.)
2802 protected String getNewViewName(String viewTitle)
2804 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2805 boolean addFirstIndex = false;
2806 if (viewTitle == null || viewTitle.trim().length() == 0)
2808 viewTitle = MessageManager.getString("action.view");
2809 addFirstIndex = true;
2813 index = 1;// we count from 1 if given a specific name
2815 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2817 List<Component> comps = PaintRefresher.components.get(viewport
2818 .getSequenceSetId());
2820 List<String> existingNames = getExistingViewNames(comps);
2822 while (existingNames.contains(newViewName))
2824 newViewName = viewTitle + " " + (++index);
2830 * Returns a list of distinct view names found in the given list of
2831 * components. View names are held on the viewport of an AlignmentPanel.
2836 protected List<String> getExistingViewNames(List<Component> comps)
2838 List<String> existingNames = new ArrayList<String>();
2839 for (Component comp : comps)
2841 if (comp instanceof AlignmentPanel)
2843 AlignmentPanel ap = (AlignmentPanel) comp;
2844 if (!existingNames.contains(ap.av.viewName))
2846 existingNames.add(ap.av.viewName);
2850 return existingNames;
2854 * Explode tabbed views into separate windows.
2857 public void expandViews_actionPerformed(ActionEvent e)
2859 Desktop.instance.explodeViews(this);
2863 * Gather views in separate windows back into a tabbed presentation.
2866 public void gatherViews_actionPerformed(ActionEvent e)
2868 Desktop.instance.gatherViews(this);
2878 public void font_actionPerformed(ActionEvent e)
2880 new FontChooser(alignPanel);
2890 protected void seqLimit_actionPerformed(ActionEvent e)
2892 viewport.setShowJVSuffix(seqLimits.isSelected());
2894 alignPanel.getIdPanel().getIdCanvas()
2895 .setPreferredSize(alignPanel.calculateIdWidth());
2896 alignPanel.paintAlignment(true);
2900 public void idRightAlign_actionPerformed(ActionEvent e)
2902 viewport.setRightAlignIds(idRightAlign.isSelected());
2903 alignPanel.paintAlignment(true);
2907 public void centreColumnLabels_actionPerformed(ActionEvent e)
2909 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2910 alignPanel.paintAlignment(true);
2916 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2919 protected void followHighlight_actionPerformed()
2922 * Set the 'follow' flag on the Viewport (and scroll to position if now
2925 final boolean state = this.followHighlightMenuItem.getState();
2926 viewport.setFollowHighlight(state);
2929 alignPanel.scrollToPosition(
2930 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2941 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2943 viewport.setColourText(colourTextMenuItem.isSelected());
2944 alignPanel.paintAlignment(true);
2954 public void wrapMenuItem_actionPerformed(ActionEvent e)
2956 scaleAbove.setVisible(wrapMenuItem.isSelected());
2957 scaleLeft.setVisible(wrapMenuItem.isSelected());
2958 scaleRight.setVisible(wrapMenuItem.isSelected());
2959 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2960 alignPanel.updateLayout();
2964 public void showAllSeqs_actionPerformed(ActionEvent e)
2966 viewport.showAllHiddenSeqs();
2970 public void showAllColumns_actionPerformed(ActionEvent e)
2972 viewport.showAllHiddenColumns();
2977 public void hideSelSequences_actionPerformed(ActionEvent e)
2979 viewport.hideAllSelectedSeqs();
2980 // alignPanel.paintAlignment(true);
2984 * called by key handler and the hide all/show all menu items
2989 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2992 boolean hide = false;
2993 SequenceGroup sg = viewport.getSelectionGroup();
2994 if (!toggleSeqs && !toggleCols)
2996 // Hide everything by the current selection - this is a hack - we do the
2997 // invert and then hide
2998 // first check that there will be visible columns after the invert.
2999 if ((viewport.getColumnSelection() != null
3000 && viewport.getColumnSelection().getSelected() != null && viewport
3001 .getColumnSelection().getSelected().size() > 0)
3002 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3005 // now invert the sequence set, if required - empty selection implies
3006 // that no hiding is required.
3009 invertSequenceMenuItem_actionPerformed(null);
3010 sg = viewport.getSelectionGroup();
3014 viewport.expandColSelection(sg, true);
3015 // finally invert the column selection and get the new sequence
3017 invertColSel_actionPerformed(null);
3024 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3026 hideSelSequences_actionPerformed(null);
3029 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3032 showAllSeqs_actionPerformed(null);
3038 if (viewport.getColumnSelection().getSelected().size() > 0)
3040 hideSelColumns_actionPerformed(null);
3043 viewport.setSelectionGroup(sg);
3048 showAllColumns_actionPerformed(null);
3057 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3058 * event.ActionEvent)
3061 public void hideAllButSelection_actionPerformed(ActionEvent e)
3063 toggleHiddenRegions(false, false);
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);
3087 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3091 public void showAllhidden_actionPerformed(ActionEvent e)
3093 viewport.showAllHiddenColumns();
3094 viewport.showAllHiddenSeqs();
3095 alignPanel.paintAlignment(true);
3099 public void hideSelColumns_actionPerformed(ActionEvent e)
3101 viewport.hideSelectedColumns();
3102 alignPanel.paintAlignment(true);
3106 public void hiddenMarkers_actionPerformed(ActionEvent e)
3108 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3119 protected void scaleAbove_actionPerformed(ActionEvent e)
3121 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3122 alignPanel.paintAlignment(true);
3132 protected void scaleLeft_actionPerformed(ActionEvent e)
3134 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3135 alignPanel.paintAlignment(true);
3145 protected void scaleRight_actionPerformed(ActionEvent e)
3147 viewport.setScaleRightWrapped(scaleRight.isSelected());
3148 alignPanel.paintAlignment(true);
3158 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3160 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3161 alignPanel.paintAlignment(true);
3171 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3173 viewport.setShowText(viewTextMenuItem.isSelected());
3174 alignPanel.paintAlignment(true);
3184 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3186 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3187 alignPanel.paintAlignment(true);
3190 public FeatureSettings featureSettings;
3193 public FeatureSettingsControllerI getFeatureSettingsUI()
3195 return featureSettings;
3199 public void featureSettings_actionPerformed(ActionEvent e)
3201 if (featureSettings != null)
3203 featureSettings.close();
3204 featureSettings = null;
3206 if (!showSeqFeatures.isSelected())
3208 // make sure features are actually displayed
3209 showSeqFeatures.setSelected(true);
3210 showSeqFeatures_actionPerformed(null);
3212 featureSettings = new FeatureSettings(this);
3216 * Set or clear 'Show Sequence Features'
3222 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3224 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3225 alignPanel.paintAlignment(true);
3226 if (alignPanel.getOverviewPanel() != null)
3228 alignPanel.getOverviewPanel().updateOverviewImage();
3233 * Set or clear 'Show Sequence Features'
3239 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3241 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3243 if (viewport.isShowSequenceFeaturesHeight())
3245 // ensure we're actually displaying features
3246 viewport.setShowSequenceFeatures(true);
3247 showSeqFeatures.setSelected(true);
3249 alignPanel.paintAlignment(true);
3250 if (alignPanel.getOverviewPanel() != null)
3252 alignPanel.getOverviewPanel().updateOverviewImage();
3257 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3258 * the annotations panel as a whole.
3260 * The options to show/hide all annotations should be enabled when the panel
3261 * is shown, and disabled when the panel is hidden.
3266 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3268 final boolean setVisible = annotationPanelMenuItem.isSelected();
3269 viewport.setShowAnnotation(setVisible);
3270 this.showAllSeqAnnotations.setEnabled(setVisible);
3271 this.hideAllSeqAnnotations.setEnabled(setVisible);
3272 this.showAllAlAnnotations.setEnabled(setVisible);
3273 this.hideAllAlAnnotations.setEnabled(setVisible);
3274 alignPanel.updateLayout();
3278 public void alignmentProperties()
3280 JEditorPane editPane = new JEditorPane("text/html", "");
3281 editPane.setEditable(false);
3282 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3284 editPane.setText(MessageManager.formatMessage("label.html_content",
3285 new Object[] { contents.toString() }));
3286 JInternalFrame frame = new JInternalFrame();
3287 frame.getContentPane().add(new JScrollPane(editPane));
3289 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3290 "label.alignment_properties", new Object[] { getTitle() }),
3301 public void overviewMenuItem_actionPerformed(ActionEvent e)
3303 if (alignPanel.overviewPanel != null)
3308 JInternalFrame frame = new JInternalFrame();
3309 OverviewPanel overview = new OverviewPanel(alignPanel);
3310 frame.setContentPane(overview);
3311 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3312 "label.overview_params", new Object[] { this.getTitle() }),
3313 frame.getWidth(), frame.getHeight());
3315 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3316 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3319 public void internalFrameClosed(
3320 javax.swing.event.InternalFrameEvent evt)
3322 alignPanel.setOverviewPanel(null);
3326 alignPanel.setOverviewPanel(overview);
3330 public void textColour_actionPerformed(ActionEvent e)
3332 new TextColourChooser().chooseColour(alignPanel, null);
3342 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3354 public void clustalColour_actionPerformed(ActionEvent e)
3356 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3357 viewport.getHiddenRepSequences()));
3367 public void zappoColour_actionPerformed(ActionEvent e)
3369 changeColour(new ZappoColourScheme());
3379 public void taylorColour_actionPerformed(ActionEvent e)
3381 changeColour(new TaylorColourScheme());
3391 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3393 changeColour(new HydrophobicColourScheme());
3403 public void helixColour_actionPerformed(ActionEvent e)
3405 changeColour(new HelixColourScheme());
3415 public void strandColour_actionPerformed(ActionEvent e)
3417 changeColour(new StrandColourScheme());
3427 public void turnColour_actionPerformed(ActionEvent e)
3429 changeColour(new TurnColourScheme());
3439 public void buriedColour_actionPerformed(ActionEvent e)
3441 changeColour(new BuriedColourScheme());
3451 public void nucleotideColour_actionPerformed(ActionEvent e)
3453 changeColour(new NucleotideColourScheme());
3457 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3459 changeColour(new PurinePyrimidineColourScheme());
3463 * public void covariationColour_actionPerformed(ActionEvent e) {
3465 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3469 public void annotationColour_actionPerformed(ActionEvent e)
3471 new AnnotationColourChooser(viewport, alignPanel);
3475 public void annotationColumn_actionPerformed(ActionEvent e)
3477 new AnnotationColumnChooser(viewport, alignPanel);
3481 public void rnahelicesColour_actionPerformed(ActionEvent e)
3483 new RNAHelicesColourChooser(viewport, alignPanel);
3493 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3495 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3505 public void changeColour(ColourSchemeI cs)
3507 // TODO: pull up to controller method
3511 // Make sure viewport is up to date w.r.t. any sliders
3512 if (viewport.getAbovePIDThreshold())
3514 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3516 viewport.setThreshold(threshold);
3519 if (viewport.getConservationSelected())
3521 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3524 if (cs instanceof TCoffeeColourScheme)
3526 tcoffeeColour.setEnabled(true);
3527 tcoffeeColour.setSelected(true);
3531 viewport.setGlobalColourScheme(cs);
3533 alignPanel.paintAlignment(true);
3543 protected void modifyPID_actionPerformed(ActionEvent e)
3545 if (viewport.getAbovePIDThreshold()
3546 && viewport.getGlobalColourScheme() != null)
3548 SliderPanel.setPIDSliderSource(alignPanel,
3549 viewport.getGlobalColourScheme(), "Background");
3550 SliderPanel.showPIDSlider();
3561 protected void modifyConservation_actionPerformed(ActionEvent e)
3563 if (viewport.getConservationSelected()
3564 && viewport.getGlobalColourScheme() != null)
3566 SliderPanel.setConservationSlider(alignPanel,
3567 viewport.getGlobalColourScheme(), "Background");
3568 SliderPanel.showConservationSlider();
3579 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3581 viewport.setConservationSelected(conservationMenuItem.isSelected());
3583 viewport.setAbovePIDThreshold(false);
3584 abovePIDThreshold.setSelected(false);
3586 changeColour(viewport.getGlobalColourScheme());
3588 modifyConservation_actionPerformed(null);
3598 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3600 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3602 conservationMenuItem.setSelected(false);
3603 viewport.setConservationSelected(false);
3605 changeColour(viewport.getGlobalColourScheme());
3607 modifyPID_actionPerformed(null);
3617 public void userDefinedColour_actionPerformed(ActionEvent e)
3619 if (e.getActionCommand().equals(
3620 MessageManager.getString("action.user_defined")))
3622 new UserDefinedColours(alignPanel, null);
3626 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3627 .getUserColourSchemes().get(e.getActionCommand());
3633 public void updateUserColourMenu()
3636 Component[] menuItems = colourMenu.getMenuComponents();
3637 int iSize = menuItems.length;
3638 for (int i = 0; i < iSize; i++)
3640 if (menuItems[i].getName() != null
3641 && menuItems[i].getName().equals("USER_DEFINED"))
3643 colourMenu.remove(menuItems[i]);
3647 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3649 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3650 .getUserColourSchemes().keys();
3652 while (userColours.hasMoreElements())
3654 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3655 userColours.nextElement().toString());
3656 radioItem.setName("USER_DEFINED");
3657 radioItem.addMouseListener(new MouseAdapter()
3660 public void mousePressed(MouseEvent evt)
3662 if (evt.isControlDown()
3663 || SwingUtilities.isRightMouseButton(evt))
3665 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3667 int option = JOptionPane.showInternalConfirmDialog(
3668 jalview.gui.Desktop.desktop,
3670 .getString("label.remove_from_default_list"),
3672 .getString("label.remove_user_defined_colour"),
3673 JOptionPane.YES_NO_OPTION);
3674 if (option == JOptionPane.YES_OPTION)
3676 jalview.gui.UserDefinedColours
3677 .removeColourFromDefaults(radioItem.getText());
3678 colourMenu.remove(radioItem);
3682 radioItem.addActionListener(new ActionListener()
3685 public void actionPerformed(ActionEvent evt)
3687 userDefinedColour_actionPerformed(evt);
3694 radioItem.addActionListener(new ActionListener()
3697 public void actionPerformed(ActionEvent evt)
3699 userDefinedColour_actionPerformed(evt);
3703 colourMenu.insert(radioItem, 15);
3704 colours.add(radioItem);
3716 public void PIDColour_actionPerformed(ActionEvent e)
3718 changeColour(new PIDColourScheme());
3728 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3730 changeColour(new Blosum62ColourScheme());
3740 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3742 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3743 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3744 .getAlignment().getSequenceAt(0), null);
3745 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3746 viewport.getAlignment()));
3747 alignPanel.paintAlignment(true);
3757 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3759 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3760 AlignmentSorter.sortByID(viewport.getAlignment());
3761 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3762 viewport.getAlignment()));
3763 alignPanel.paintAlignment(true);
3773 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3775 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3776 AlignmentSorter.sortByLength(viewport.getAlignment());
3777 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3778 viewport.getAlignment()));
3779 alignPanel.paintAlignment(true);
3789 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3791 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3792 AlignmentSorter.sortByGroup(viewport.getAlignment());
3793 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3794 viewport.getAlignment()));
3796 alignPanel.paintAlignment(true);
3806 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3808 new RedundancyPanel(alignPanel, this);
3818 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3820 if ((viewport.getSelectionGroup() == null)
3821 || (viewport.getSelectionGroup().getSize() < 2))
3823 JOptionPane.showInternalMessageDialog(this, MessageManager
3824 .getString("label.you_must_select_least_two_sequences"),
3825 MessageManager.getString("label.invalid_selection"),
3826 JOptionPane.WARNING_MESSAGE);
3830 JInternalFrame frame = new JInternalFrame();
3831 frame.setContentPane(new PairwiseAlignPanel(viewport));
3832 Desktop.addInternalFrame(frame,
3833 MessageManager.getString("action.pairwise_alignment"), 600,
3845 public void PCAMenuItem_actionPerformed(ActionEvent e)
3847 if (((viewport.getSelectionGroup() != null)
3848 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3849 .getSelectionGroup().getSize() > 0))
3850 || (viewport.getAlignment().getHeight() < 4))
3853 .showInternalMessageDialog(
3856 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3858 .getString("label.sequence_selection_insufficient"),
3859 JOptionPane.WARNING_MESSAGE);
3864 new PCAPanel(alignPanel);
3868 public void autoCalculate_actionPerformed(ActionEvent e)
3870 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3871 if (viewport.autoCalculateConsensus)
3873 viewport.firePropertyChange("alignment", null, viewport
3874 .getAlignment().getSequences());
3879 public void sortByTreeOption_actionPerformed(ActionEvent e)
3881 viewport.sortByTree = sortByTree.isSelected();
3885 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3887 viewport.followSelection = listenToViewSelections.isSelected();
3897 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3899 newTreePanel("AV", "PID", "Average distance tree using PID");
3909 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3911 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3921 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3923 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3933 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3935 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3948 void newTreePanel(String type, String pwType, String title)
3952 if (viewport.getSelectionGroup() != null
3953 && viewport.getSelectionGroup().getSize() > 0)
3955 if (viewport.getSelectionGroup().getSize() < 3)
3961 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3963 .getString("label.not_enough_sequences"),
3964 JOptionPane.WARNING_MESSAGE);
3968 SequenceGroup sg = viewport.getSelectionGroup();
3970 /* Decide if the selection is a column region */
3971 for (SequenceI _s : sg.getSequences())
3973 if (_s.getLength() < sg.getEndRes())
3979 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3981 .getString("label.sequences_selection_not_aligned"),
3982 JOptionPane.WARNING_MESSAGE);
3988 title = title + " on region";
3989 tp = new TreePanel(alignPanel, type, pwType);
3993 // are the visible sequences aligned?
3994 if (!viewport.getAlignment().isAligned(false))
4000 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4002 .getString("label.sequences_not_aligned"),
4003 JOptionPane.WARNING_MESSAGE);
4008 if (viewport.getAlignment().getHeight() < 2)
4013 tp = new TreePanel(alignPanel, type, pwType);
4018 if (viewport.viewName != null)
4020 title += viewport.viewName + " of ";
4023 title += this.title;
4025 Desktop.addInternalFrame(tp, title, 600, 500);
4036 public void addSortByOrderMenuItem(String title,
4037 final AlignmentOrder order)
4039 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4040 "action.by_title_param", new Object[] { title }));
4042 item.addActionListener(new java.awt.event.ActionListener()
4045 public void actionPerformed(ActionEvent e)
4047 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4049 // TODO: JBPNote - have to map order entries to curent SequenceI
4051 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4053 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4056 alignPanel.paintAlignment(true);
4062 * Add a new sort by annotation score menu item
4065 * the menu to add the option to
4067 * the label used to retrieve scores for each sequence on the
4070 public void addSortByAnnotScoreMenuItem(JMenu sort,
4071 final String scoreLabel)
4073 final JMenuItem item = new JMenuItem(scoreLabel);
4075 item.addActionListener(new java.awt.event.ActionListener()
4078 public void actionPerformed(ActionEvent e)
4080 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4081 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4082 viewport.getAlignment());// ,viewport.getSelectionGroup());
4083 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4084 viewport.getAlignment()));
4085 alignPanel.paintAlignment(true);
4091 * last hash for alignment's annotation array - used to minimise cost of
4094 protected int _annotationScoreVectorHash;
4097 * search the alignment and rebuild the sort by annotation score submenu the
4098 * last alignment annotation vector hash is stored to minimize cost of
4099 * rebuilding in subsequence calls.
4103 public void buildSortByAnnotationScoresMenu()
4105 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4110 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4112 sortByAnnotScore.removeAll();
4113 // almost certainly a quicker way to do this - but we keep it simple
4114 Hashtable scoreSorts = new Hashtable();
4115 AlignmentAnnotation aann[];
4116 for (SequenceI sqa : viewport.getAlignment().getSequences())
4118 aann = sqa.getAnnotation();
4119 for (int i = 0; aann != null && i < aann.length; i++)
4121 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4123 scoreSorts.put(aann[i].label, aann[i].label);
4127 Enumeration labels = scoreSorts.keys();
4128 while (labels.hasMoreElements())
4130 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4131 (String) labels.nextElement());
4133 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4136 _annotationScoreVectorHash = viewport.getAlignment()
4137 .getAlignmentAnnotation().hashCode();
4142 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4143 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4144 * call. Listeners are added to remove the menu item when the treePanel is
4145 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4149 * Displayed tree window.
4151 * SortBy menu item title.
4154 public void buildTreeMenu()
4156 calculateTree.removeAll();
4157 // build the calculate menu
4159 for (final String type : new String[] { "NJ", "AV" })
4161 String treecalcnm = MessageManager.getString("label.tree_calc_"
4162 + type.toLowerCase());
4163 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4165 JMenuItem tm = new JMenuItem();
4166 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4167 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4169 String smn = MessageManager.getStringOrReturn(
4170 "label.score_model_", sm.getName());
4171 final String title = MessageManager.formatMessage(
4172 "label.treecalc_title", treecalcnm, smn);
4173 tm.setText(title);//
4174 tm.addActionListener(new java.awt.event.ActionListener()
4177 public void actionPerformed(ActionEvent e)
4179 newTreePanel(type, pwtype, title);
4182 calculateTree.add(tm);
4187 sortByTreeMenu.removeAll();
4189 List<Component> comps = PaintRefresher.components.get(viewport
4190 .getSequenceSetId());
4191 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4192 for (Component comp : comps)
4194 if (comp instanceof TreePanel)
4196 treePanels.add((TreePanel) comp);
4200 if (treePanels.size() < 1)
4202 sortByTreeMenu.setVisible(false);
4206 sortByTreeMenu.setVisible(true);
4208 for (final TreePanel tp : treePanels)
4210 final JMenuItem item = new JMenuItem(tp.getTitle());
4211 item.addActionListener(new java.awt.event.ActionListener()
4214 public void actionPerformed(ActionEvent e)
4216 tp.sortByTree_actionPerformed();
4217 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4222 sortByTreeMenu.add(item);
4226 public boolean sortBy(AlignmentOrder alorder, String undoname)
4228 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4229 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4230 if (undoname != null)
4232 addHistoryItem(new OrderCommand(undoname, oldOrder,
4233 viewport.getAlignment()));
4235 alignPanel.paintAlignment(true);
4240 * Work out whether the whole set of sequences or just the selected set will
4241 * be submitted for multiple alignment.
4244 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4246 // Now, check we have enough sequences
4247 AlignmentView msa = null;
4249 if ((viewport.getSelectionGroup() != null)
4250 && (viewport.getSelectionGroup().getSize() > 1))
4252 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4253 // some common interface!
4255 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4256 * SequenceI[sz = seqs.getSize(false)];
4258 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4259 * seqs.getSequenceAt(i); }
4261 msa = viewport.getAlignmentView(true);
4263 else if (viewport.getSelectionGroup() != null
4264 && viewport.getSelectionGroup().getSize() == 1)
4266 int option = JOptionPane.showConfirmDialog(this,
4267 MessageManager.getString("warn.oneseq_msainput_selection"),
4268 MessageManager.getString("label.invalid_selection"),
4269 JOptionPane.OK_CANCEL_OPTION);
4270 if (option == JOptionPane.OK_OPTION)
4272 msa = viewport.getAlignmentView(false);
4277 msa = viewport.getAlignmentView(false);
4283 * Decides what is submitted to a secondary structure prediction service: the
4284 * first sequence in the alignment, or in the current selection, or, if the
4285 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4286 * region or the whole alignment. (where the first sequence in the set is the
4287 * one that the prediction will be for).
4289 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4291 AlignmentView seqs = null;
4293 if ((viewport.getSelectionGroup() != null)
4294 && (viewport.getSelectionGroup().getSize() > 0))
4296 seqs = viewport.getAlignmentView(true);
4300 seqs = viewport.getAlignmentView(false);
4302 // limit sequences - JBPNote in future - could spawn multiple prediction
4304 // TODO: viewport.getAlignment().isAligned is a global state - the local
4305 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4306 if (!viewport.getAlignment().isAligned(false))
4308 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4309 // TODO: if seqs.getSequences().length>1 then should really have warned
4323 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4325 // Pick the tree file
4326 JalviewFileChooser chooser = new JalviewFileChooser(
4327 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4328 chooser.setFileView(new JalviewFileView());
4329 chooser.setDialogTitle(MessageManager
4330 .getString("label.select_newick_like_tree_file"));
4331 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4333 int value = chooser.showOpenDialog(null);
4335 if (value == JalviewFileChooser.APPROVE_OPTION)
4337 String choice = chooser.getSelectedFile().getPath();
4338 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4339 jalview.io.NewickFile fin = null;
4342 fin = new jalview.io.NewickFile(choice, "File");
4343 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4344 } catch (Exception ex)
4351 .getString("label.problem_reading_tree_file"),
4352 JOptionPane.WARNING_MESSAGE);
4353 ex.printStackTrace();
4355 if (fin != null && fin.hasWarningMessage())
4357 JOptionPane.showMessageDialog(Desktop.desktop, fin
4358 .getWarningMessage(), MessageManager
4359 .getString("label.possible_problem_with_tree_file"),
4360 JOptionPane.WARNING_MESSAGE);
4366 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4368 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4371 public TreePanel ShowNewickTree(NewickFile nf, String title)
4373 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4376 public TreePanel ShowNewickTree(NewickFile nf, String title,
4377 AlignmentView input)
4379 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4382 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4383 int h, int x, int y)
4385 return ShowNewickTree(nf, title, null, w, h, x, y);
4389 * Add a treeviewer for the tree extracted from a newick file object to the
4390 * current alignment view
4397 * Associated alignment input data (or null)
4406 * @return TreePanel handle
4408 public TreePanel ShowNewickTree(NewickFile nf, String title,
4409 AlignmentView input, int w, int h, int x, int y)
4411 TreePanel tp = null;
4417 if (nf.getTree() != null)
4419 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4425 tp.setLocation(x, y);
4428 Desktop.addInternalFrame(tp, title, w, h);
4430 } catch (Exception ex)
4432 ex.printStackTrace();
4438 private boolean buildingMenu = false;
4441 * Generates menu items and listener event actions for web service clients
4444 public void BuildWebServiceMenu()
4446 while (buildingMenu)
4450 System.err.println("Waiting for building menu to finish.");
4452 } catch (Exception e)
4456 final AlignFrame me = this;
4457 buildingMenu = true;
4458 new Thread(new Runnable()
4463 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4466 // System.err.println("Building ws menu again "
4467 // + Thread.currentThread());
4468 // TODO: add support for context dependent disabling of services based
4470 // alignment and current selection
4471 // TODO: add additional serviceHandle parameter to specify abstract
4473 // class independently of AbstractName
4474 // TODO: add in rediscovery GUI function to restart discoverer
4475 // TODO: group services by location as well as function and/or
4477 // object broker mechanism.
4478 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4479 final IProgressIndicator af = me;
4480 final JMenu msawsmenu = new JMenu("Alignment");
4481 final JMenu secstrmenu = new JMenu(
4482 "Secondary Structure Prediction");
4483 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4484 final JMenu analymenu = new JMenu("Analysis");
4485 final JMenu dismenu = new JMenu("Protein Disorder");
4486 // final JMenu msawsmenu = new
4487 // JMenu(MessageManager.getString("label.alignment"));
4488 // final JMenu secstrmenu = new
4489 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4490 // final JMenu seqsrchmenu = new
4491 // JMenu(MessageManager.getString("label.sequence_database_search"));
4492 // final JMenu analymenu = new
4493 // JMenu(MessageManager.getString("label.analysis"));
4494 // final JMenu dismenu = new
4495 // JMenu(MessageManager.getString("label.protein_disorder"));
4496 // JAL-940 - only show secondary structure prediction services from
4497 // the legacy server
4498 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4500 Discoverer.services != null && (Discoverer.services.size() > 0))
4502 // TODO: refactor to allow list of AbstractName/Handler bindings to
4504 // stored or retrieved from elsewhere
4505 // No MSAWS used any more:
4506 // Vector msaws = null; // (Vector)
4507 // Discoverer.services.get("MsaWS");
4508 Vector secstrpr = (Vector) Discoverer.services
4510 if (secstrpr != null)
4512 // Add any secondary structure prediction services
4513 for (int i = 0, j = secstrpr.size(); i < j; i++)
4515 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4517 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4518 .getServiceClient(sh);
4519 int p = secstrmenu.getItemCount();
4520 impl.attachWSMenuEntry(secstrmenu, me);
4521 int q = secstrmenu.getItemCount();
4522 for (int litm = p; litm < q; litm++)
4524 legacyItems.add(secstrmenu.getItem(litm));
4530 // Add all submenus in the order they should appear on the web
4532 wsmenu.add(msawsmenu);
4533 wsmenu.add(secstrmenu);
4534 wsmenu.add(dismenu);
4535 wsmenu.add(analymenu);
4536 // No search services yet
4537 // wsmenu.add(seqsrchmenu);
4539 javax.swing.SwingUtilities.invokeLater(new Runnable()
4546 webService.removeAll();
4547 // first, add discovered services onto the webservices menu
4548 if (wsmenu.size() > 0)
4550 for (int i = 0, j = wsmenu.size(); i < j; i++)
4552 webService.add(wsmenu.get(i));
4557 webService.add(me.webServiceNoServices);
4559 // TODO: move into separate menu builder class.
4560 boolean new_sspred = false;
4561 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4563 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4564 if (jws2servs != null)
4566 if (jws2servs.hasServices())
4568 jws2servs.attachWSMenuEntry(webService, me);
4569 for (Jws2Instance sv : jws2servs.getServices())
4571 if (sv.description.toLowerCase().contains("jpred"))
4573 for (JMenuItem jmi : legacyItems)
4575 jmi.setVisible(false);
4581 if (jws2servs.isRunning())
4583 JMenuItem tm = new JMenuItem(
4584 "Still discovering JABA Services");
4585 tm.setEnabled(false);
4590 build_urlServiceMenu(me.webService);
4591 build_fetchdbmenu(webService);
4592 for (JMenu item : wsmenu)
4594 if (item.getItemCount() == 0)
4596 item.setEnabled(false);
4600 item.setEnabled(true);
4603 } catch (Exception e)
4606 .debug("Exception during web service menu building process.",
4611 } catch (Exception e)
4614 buildingMenu = false;
4621 * construct any groupURL type service menu entries.
4625 private void build_urlServiceMenu(JMenu webService)
4627 // TODO: remove this code when 2.7 is released
4628 // DEBUG - alignmentView
4630 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4631 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4633 * @Override public void actionPerformed(ActionEvent e) {
4634 * jalview.datamodel.AlignmentView
4635 * .testSelectionViews(af.viewport.getAlignment(),
4636 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4638 * }); webService.add(testAlView);
4640 // TODO: refactor to RestClient discoverer and merge menu entries for
4641 // rest-style services with other types of analysis/calculation service
4642 // SHmmr test client - still being implemented.
4643 // DEBUG - alignmentView
4645 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4648 client.attachWSMenuEntry(
4649 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4655 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4656 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4657 * getProperty("LAST_DIRECTORY"));
4659 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4660 * to Vamsas file"); chooser.setToolTipText("Export");
4662 * int value = chooser.showSaveDialog(this);
4664 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4665 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4666 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4667 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4670 * prototype of an automatically enabled/disabled analysis function
4673 protected void setShowProductsEnabled()
4675 SequenceI[] selection = viewport.getSequenceSelection();
4676 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4677 viewport.getAlignment().getDataset()))
4679 showProducts.setEnabled(true);
4684 showProducts.setEnabled(false);
4689 * search selection for sequence xRef products and build the show products
4694 * @return true if showProducts menu should be enabled.
4696 public boolean canShowProducts(SequenceI[] selection,
4697 boolean isRegionSelection, Alignment dataset)
4699 boolean showp = false;
4702 showProducts.removeAll();
4703 final boolean dna = viewport.getAlignment().isNucleotide();
4704 final Alignment ds = dataset;
4705 String[] ptypes = (selection == null || selection.length == 0) ? null
4706 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4708 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4709 // selection, dataset, true);
4710 final SequenceI[] sel = selection;
4711 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4714 final boolean isRegSel = isRegionSelection;
4715 final AlignFrame af = this;
4716 final String source = ptypes[t];
4717 JMenuItem xtype = new JMenuItem(ptypes[t]);
4718 xtype.addActionListener(new ActionListener()
4722 public void actionPerformed(ActionEvent e)
4724 // TODO: new thread for this call with vis-delay
4725 af.showProductsFor(af.viewport.getSequenceSelection(),
4726 isRegSel, dna, source);
4730 showProducts.add(xtype);
4732 showProducts.setVisible(showp);
4733 showProducts.setEnabled(showp);
4734 } catch (Exception e)
4736 jalview.bin.Cache.log
4737 .warn("canTranslate threw an exception - please report to help@jalview.org",
4744 protected void showProductsFor(final SequenceI[] sel,
4745 final boolean isRegSel, final boolean dna, final String source)
4747 Runnable foo = new Runnable()
4753 final long sttime = System.currentTimeMillis();
4754 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4755 "status.searching_for_sequences_from",
4756 new Object[] { source }), sttime);
4759 // update our local dataset reference
4760 Alignment ds = AlignFrame.this.getViewport().getAlignment()
4762 Alignment prods = CrossRef
4763 .findXrefSequences(sel, dna, source, ds);
4766 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4767 for (int s = 0; s < sprods.length; s++)
4769 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4770 if (ds.getSequences() == null
4771 || !ds.getSequences().contains(
4772 sprods[s].getDatasetSequence()))
4774 ds.addSequence(sprods[s].getDatasetSequence());
4776 sprods[s].updatePDBIds();
4778 Alignment al = new Alignment(sprods);
4782 * Copy dna-to-protein mappings to new alignment
4784 // TODO 1: no mappings are set up for EMBL product
4785 // TODO 2: if they were, should add them to protein alignment, not
4787 List<AlignedCodonFrame> cf = prods.getCodonFrames();
4788 for (AlignedCodonFrame acf : cf)
4790 al.addCodonFrame(acf);
4792 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4794 String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4795 + " for " + ((isRegSel) ? "selected region of " : "")
4797 naf.setTitle(newtitle);
4799 // temporary flag until SplitFrame is released
4800 boolean asSplitFrame = Cache.getDefault(
4801 Preferences.ENABLE_SPLIT_FRAME, true);
4805 * Make a copy of this alignment (sharing the same dataset
4806 * sequences). If we are DNA, drop introns and update mappings
4808 AlignmentI copyAlignment = null;
4809 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4810 .getSequenceSelection();
4813 copyAlignment = AlignmentUtils.makeExonAlignment(
4814 sequenceSelection, cf);
4815 al.getCodonFrames().clear();
4816 al.getCodonFrames().addAll(cf);
4817 final StructureSelectionManager ssm = StructureSelectionManager
4818 .getStructureSelectionManager(Desktop.instance);
4819 ssm.registerMappings(cf);
4823 copyAlignment = new Alignment(new Alignment(
4824 sequenceSelection));
4826 AlignFrame copyThis = new AlignFrame(copyAlignment,
4827 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4828 copyThis.setTitle(AlignFrame.this.getTitle());
4829 // SplitFrame with dna above, protein below
4830 SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4831 dna ? naf : copyThis);
4832 naf.setVisible(true);
4833 copyThis.setVisible(true);
4834 String linkedTitle = MessageManager
4835 .getString("label.linked_view_title");
4836 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4840 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4846 System.err.println("No Sequences generated for xRef type "
4849 } catch (Exception e)
4851 jalview.bin.Cache.log.error(
4852 "Exception when finding crossreferences", e);
4853 } catch (OutOfMemoryError e)
4855 new OOMWarning("whilst fetching crossreferences", e);
4858 jalview.bin.Cache.log.error("Error when finding crossreferences",
4861 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4862 "status.finished_searching_for_sequences_from",
4863 new Object[] { source }), sttime);
4867 Thread frunner = new Thread(foo);
4871 public boolean canShowTranslationProducts(SequenceI[] selection,
4872 AlignmentI alignment)
4877 return (jalview.analysis.Dna.canTranslate(selection,
4878 viewport.getViewAsVisibleContigs(true)));
4879 } catch (Exception e)
4881 jalview.bin.Cache.log
4882 .warn("canTranslate threw an exception - please report to help@jalview.org",
4889 * Construct and display a new frame containing the translation of this
4890 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4893 public void showTranslation_actionPerformed(ActionEvent e)
4895 AlignmentI al = null;
4898 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4900 al = dna.translateCdna();
4901 } catch (Exception ex)
4903 jalview.bin.Cache.log.error(
4904 "Exception during translation. Please report this !", ex);
4905 final String msg = MessageManager
4906 .getString("label.error_when_translating_sequences_submit_bug_report");
4907 final String errorTitle = MessageManager
4908 .getString("label.implementation_error")
4909 + MessageManager.getString("translation_failed");
4910 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4911 JOptionPane.ERROR_MESSAGE);
4914 if (al == null || al.getHeight() == 0)
4916 final String msg = MessageManager
4917 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4918 final String errorTitle = MessageManager
4919 .getString("label.translation_failed");
4920 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4921 JOptionPane.WARNING_MESSAGE);
4925 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4926 af.setFileFormat(this.currentFileFormat);
4927 final String newTitle = MessageManager.formatMessage(
4928 "label.translation_of_params",
4929 new Object[] { this.getTitle() });
4930 af.setTitle(newTitle);
4931 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4933 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4934 viewport.openSplitFrame(af, new Alignment(seqs));
4938 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4945 * Set the file format
4949 public void setFileFormat(String fileFormat)
4951 this.currentFileFormat = fileFormat;
4955 * Try to load a features file onto the alignment.
4958 * contents or path to retrieve file
4960 * access mode of file (see jalview.io.AlignFile)
4961 * @return true if features file was parsed correctly.
4963 public boolean parseFeaturesFile(String file, String type)
4965 return avc.parseFeaturesFile(file, type,
4966 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4971 public void refreshFeatureUI(boolean enableIfNecessary)
4973 // note - currently this is only still here rather than in the controller
4974 // because of the featureSettings hard reference that is yet to be
4976 if (enableIfNecessary)
4978 viewport.setShowSequenceFeatures(true);
4979 showSeqFeatures.setSelected(true);
4985 public void dragEnter(DropTargetDragEvent evt)
4990 public void dragExit(DropTargetEvent evt)
4995 public void dragOver(DropTargetDragEvent evt)
5000 public void dropActionChanged(DropTargetDragEvent evt)
5005 public void drop(DropTargetDropEvent evt)
5007 Transferable t = evt.getTransferable();
5008 java.util.List files = null;
5012 DataFlavor uriListFlavor = new DataFlavor(
5013 "text/uri-list;class=java.lang.String");
5014 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5016 // Works on Windows and MacOSX
5017 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5018 files = (java.util.List) t
5019 .getTransferData(DataFlavor.javaFileListFlavor);
5021 else if (t.isDataFlavorSupported(uriListFlavor))
5023 // This is used by Unix drag system
5024 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5025 String data = (String) t.getTransferData(uriListFlavor);
5026 files = new java.util.ArrayList(1);
5027 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5028 data, "\r\n"); st.hasMoreTokens();)
5030 String s = st.nextToken();
5031 if (s.startsWith("#"))
5033 // the line is a comment (as per the RFC 2483)
5037 java.net.URI uri = new java.net.URI(s);
5038 // check to see if we can handle this kind of URI
5039 if (uri.getScheme().toLowerCase().startsWith("http"))
5041 files.add(uri.toString());
5045 // otherwise preserve old behaviour: catch all for file objects
5046 java.io.File file = new java.io.File(uri);
5047 files.add(file.toString());
5051 } catch (Exception e)
5053 e.printStackTrace();
5059 // check to see if any of these files have names matching sequences in
5061 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5062 .getAlignment().getSequencesArray());
5064 * Object[] { String,SequenceI}
5066 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5067 ArrayList<String> filesnotmatched = new ArrayList<String>();
5068 for (int i = 0; i < files.size(); i++)
5070 String file = files.get(i).toString();
5072 String protocol = FormatAdapter.checkProtocol(file);
5073 if (protocol == jalview.io.FormatAdapter.FILE)
5075 File fl = new File(file);
5076 pdbfn = fl.getName();
5078 else if (protocol == jalview.io.FormatAdapter.URL)
5080 URL url = new URL(file);
5081 pdbfn = url.getFile();
5083 if (pdbfn.length() > 0)
5085 // attempt to find a match in the alignment
5086 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5087 int l = 0, c = pdbfn.indexOf(".");
5088 while (mtch == null && c != -1)
5093 } while ((c = pdbfn.indexOf(".", l)) > l);
5096 pdbfn = pdbfn.substring(0, l);
5098 mtch = idm.findAllIdMatches(pdbfn);
5105 type = new IdentifyFile().identify(file, protocol);
5106 } catch (Exception ex)
5112 if (type.equalsIgnoreCase("PDB"))
5114 filesmatched.add(new Object[] { file, protocol, mtch });
5119 // File wasn't named like one of the sequences or wasn't a PDB file.
5120 filesnotmatched.add(file);
5124 if (filesmatched.size() > 0)
5126 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5132 "label.automatically_associate_pdb_files_with_sequences_same_name",
5133 new Object[] { Integer
5139 .getString("label.automatically_associate_pdb_files_by_name"),
5140 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5143 for (Object[] fm : filesmatched)
5145 // try and associate
5146 // TODO: may want to set a standard ID naming formalism for
5147 // associating PDB files which have no IDs.
5148 for (SequenceI toassoc : (SequenceI[]) fm[2])
5150 PDBEntry pe = new AssociatePdbFileWithSeq()
5151 .associatePdbWithSeq((String) fm[0],
5152 (String) fm[1], toassoc, false,
5156 System.err.println("Associated file : "
5157 + ((String) fm[0]) + " with "
5158 + toassoc.getDisplayId(true));
5162 alignPanel.paintAlignment(true);
5166 if (filesnotmatched.size() > 0)
5169 && (Cache.getDefault(
5170 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5176 "label.ignore_unmatched_dropped_files_info",
5177 new Object[] { Integer
5184 .getString("label.ignore_unmatched_dropped_files"),
5185 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5189 for (String fn : filesnotmatched)
5191 loadJalviewDataFile(fn, null, null, null);
5195 } catch (Exception ex)
5197 ex.printStackTrace();
5203 * Attempt to load a "dropped" file or URL string: First by testing whether
5204 * it's an Annotation file, then a JNet file, and finally a features file. If
5205 * all are false then the user may have dropped an alignment file onto this
5209 * either a filename or a URL string.
5211 public void loadJalviewDataFile(String file, String protocol,
5212 String format, SequenceI assocSeq)
5216 if (protocol == null)
5218 protocol = FormatAdapter.checkProtocol(file);
5220 // if the file isn't identified, or not positively identified as some
5221 // other filetype (PFAM is default unidentified alignment file type) then
5222 // try to parse as annotation.
5223 boolean isAnnotation = (format == null || format
5224 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5225 .annotateAlignmentView(viewport, file, protocol) : false;
5229 // first see if its a T-COFFEE score file
5230 TCoffeeScoreFile tcf = null;
5233 tcf = new TCoffeeScoreFile(file, protocol);
5236 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5238 tcoffeeColour.setEnabled(true);
5239 tcoffeeColour.setSelected(true);
5240 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5241 isAnnotation = true;
5243 .setText(MessageManager
5244 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5248 // some problem - if no warning its probable that the ID matching
5249 // process didn't work
5253 tcf.getWarningMessage() == null ? MessageManager
5254 .getString("label.check_file_matches_sequence_ids_alignment")
5255 : tcf.getWarningMessage(),
5257 .getString("label.problem_reading_tcoffee_score_file"),
5258 JOptionPane.WARNING_MESSAGE);
5265 } catch (Exception x)
5268 .debug("Exception when processing data source as T-COFFEE score file",
5274 // try to see if its a JNet 'concise' style annotation file *before*
5276 // try to parse it as a features file
5279 format = new IdentifyFile().identify(file, protocol);
5281 if (format.equalsIgnoreCase("JnetFile"))
5283 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5285 new JnetAnnotationMaker();
5286 JnetAnnotationMaker.add_annotation(predictions,
5287 viewport.getAlignment(), 0, false);
5288 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5289 viewport.getAlignment().setSeqrep(repseq);
5290 ColumnSelection cs = new ColumnSelection();
5291 cs.hideInsertionsFor(repseq);
5292 viewport.setColumnSelection(cs);
5293 isAnnotation = true;
5295 else if (IdentifyFile.FeaturesFile.equals(format))
5297 if (parseFeaturesFile(file, protocol))
5299 alignPanel.paintAlignment(true);
5304 new FileLoader().LoadFile(viewport, file, protocol, format);
5311 alignPanel.adjustAnnotationHeight();
5312 viewport.updateSequenceIdColours();
5313 buildSortByAnnotationScoresMenu();
5314 alignPanel.paintAlignment(true);
5316 } catch (Exception ex)
5318 ex.printStackTrace();
5319 } catch (OutOfMemoryError oom)
5324 } catch (Exception x)
5329 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5330 : "using " + protocol + " from " + file)
5332 + (format != null ? "(parsing as '" + format
5333 + "' file)" : ""), oom, Desktop.desktop);
5338 * Method invoked by the ChangeListener on the tabbed pane, in other words
5339 * when a different tabbed pane is selected by the user or programmatically.
5342 public void tabSelectionChanged(int index)
5346 alignPanel = alignPanels.get(index);
5347 viewport = alignPanel.av;
5348 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5349 setMenusFromViewport(viewport);
5353 * If there is a frame linked to this one in a SplitPane, switch it to the
5354 * same view tab index. No infinite recursion of calls should happen, since
5355 * tabSelectionChanged() should not get invoked on setting the selected
5356 * index to an unchanged value. Guard against setting an invalid index
5357 * before the new view peer tab has been created.
5359 final AlignViewportI peer = viewport.getCodingComplement();
5362 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5363 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5365 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5371 * On right mouse click on view tab, prompt for and set new view name.
5374 public void tabbedPane_mousePressed(MouseEvent e)
5376 if (SwingUtilities.isRightMouseButton(e))
5378 String msg = MessageManager.getString("label.enter_view_name");
5379 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5380 JOptionPane.QUESTION_MESSAGE);
5384 viewport.viewName = reply;
5385 // TODO warn if reply is in getExistingViewNames()?
5386 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5391 public AlignViewport getCurrentView()
5397 * Open the dialog for regex description parsing.
5400 protected void extractScores_actionPerformed(ActionEvent e)
5402 ParseProperties pp = new jalview.analysis.ParseProperties(
5403 viewport.getAlignment());
5404 // TODO: verify regex and introduce GUI dialog for version 2.5
5405 // if (pp.getScoresFromDescription("col", "score column ",
5406 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5408 if (pp.getScoresFromDescription("description column",
5409 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5411 buildSortByAnnotationScoresMenu();
5419 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5423 protected void showDbRefs_actionPerformed(ActionEvent e)
5425 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5431 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5435 protected void showNpFeats_actionPerformed(ActionEvent e)
5437 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5441 * find the viewport amongst the tabs in this alignment frame and close that
5446 public boolean closeView(AlignViewportI av)
5450 this.closeMenuItem_actionPerformed(false);
5453 Component[] comp = tabbedPane.getComponents();
5454 for (int i = 0; comp != null && i < comp.length; i++)
5456 if (comp[i] instanceof AlignmentPanel)
5458 if (((AlignmentPanel) comp[i]).av == av)
5461 closeView((AlignmentPanel) comp[i]);
5469 protected void build_fetchdbmenu(JMenu webService)
5471 // Temporary hack - DBRef Fetcher always top level ws entry.
5472 // TODO We probably want to store a sequence database checklist in
5473 // preferences and have checkboxes.. rather than individual sources selected
5475 final JMenu rfetch = new JMenu(
5476 MessageManager.getString("action.fetch_db_references"));
5477 rfetch.setToolTipText(MessageManager
5478 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5479 webService.add(rfetch);
5481 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5482 MessageManager.getString("option.trim_retrieved_seqs"));
5483 trimrs.setToolTipText(MessageManager
5484 .getString("label.trim_retrieved_sequences"));
5485 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5486 trimrs.addActionListener(new ActionListener()
5489 public void actionPerformed(ActionEvent e)
5491 trimrs.setSelected(trimrs.isSelected());
5492 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5493 Boolean.valueOf(trimrs.isSelected()).toString());
5497 JMenuItem fetchr = new JMenuItem(
5498 MessageManager.getString("label.standard_databases"));
5499 fetchr.setToolTipText(MessageManager
5500 .getString("label.fetch_embl_uniprot"));
5501 fetchr.addActionListener(new ActionListener()
5505 public void actionPerformed(ActionEvent e)
5507 new Thread(new Runnable()
5513 new jalview.ws.DBRefFetcher(alignPanel.av
5514 .getSequenceSelection(), alignPanel.alignFrame)
5515 .fetchDBRefs(false);
5523 final AlignFrame me = this;
5524 new Thread(new Runnable()
5529 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5530 .getSequenceFetcherSingleton(me);
5531 javax.swing.SwingUtilities.invokeLater(new Runnable()
5536 String[] dbclasses = sf.getOrderedSupportedSources();
5537 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5538 // jalview.util.QuickSort.sort(otherdb, otherdb);
5539 List<DbSourceProxy> otherdb;
5540 JMenu dfetch = new JMenu();
5541 JMenu ifetch = new JMenu();
5542 JMenuItem fetchr = null;
5543 int comp = 0, icomp = 0, mcomp = 15;
5544 String mname = null;
5546 for (String dbclass : dbclasses)
5548 otherdb = sf.getSourceProxy(dbclass);
5549 // add a single entry for this class, or submenu allowing 'fetch
5551 if (otherdb == null || otherdb.size() < 1)
5555 // List<DbSourceProxy> dbs=otherdb;
5556 // otherdb=new ArrayList<DbSourceProxy>();
5557 // for (DbSourceProxy db:dbs)
5559 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5563 mname = "From " + dbclass;
5565 if (otherdb.size() == 1)
5567 final DbSourceProxy[] dassource = otherdb
5568 .toArray(new DbSourceProxy[0]);
5569 DbSourceProxy src = otherdb.get(0);
5570 fetchr = new JMenuItem(src.getDbSource());
5571 fetchr.addActionListener(new ActionListener()
5575 public void actionPerformed(ActionEvent e)
5577 new Thread(new Runnable()
5583 new jalview.ws.DBRefFetcher(alignPanel.av
5584 .getSequenceSelection(),
5585 alignPanel.alignFrame, dassource)
5586 .fetchDBRefs(false);
5592 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5593 MessageManager.formatMessage(
5594 "label.fetch_retrieve_from",
5595 new Object[] { src.getDbName() })));
5601 final DbSourceProxy[] dassource = otherdb
5602 .toArray(new DbSourceProxy[0]);
5604 DbSourceProxy src = otherdb.get(0);
5605 fetchr = new JMenuItem(MessageManager.formatMessage(
5606 "label.fetch_all_param",
5607 new Object[] { src.getDbSource() }));
5608 fetchr.addActionListener(new ActionListener()
5611 public void actionPerformed(ActionEvent e)
5613 new Thread(new Runnable()
5619 new jalview.ws.DBRefFetcher(alignPanel.av
5620 .getSequenceSelection(),
5621 alignPanel.alignFrame, dassource)
5622 .fetchDBRefs(false);
5628 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5629 MessageManager.formatMessage(
5630 "label.fetch_retrieve_from_all_sources",
5632 Integer.valueOf(otherdb.size())
5633 .toString(), src.getDbSource(),
5634 src.getDbName() })));
5637 // and then build the rest of the individual menus
5638 ifetch = new JMenu(MessageManager.formatMessage(
5639 "label.source_from_db_source",
5640 new Object[] { src.getDbSource() }));
5642 String imname = null;
5644 for (DbSourceProxy sproxy : otherdb)
5646 String dbname = sproxy.getDbName();
5647 String sname = dbname.length() > 5 ? dbname.substring(0,
5648 5) + "..." : dbname;
5649 String msname = dbname.length() > 10 ? dbname.substring(
5650 0, 10) + "..." : dbname;
5653 imname = MessageManager.formatMessage(
5654 "label.from_msname", new Object[] { sname });
5656 fetchr = new JMenuItem(msname);
5657 final DbSourceProxy[] dassrc = { sproxy };
5658 fetchr.addActionListener(new ActionListener()
5662 public void actionPerformed(ActionEvent e)
5664 new Thread(new Runnable()
5670 new jalview.ws.DBRefFetcher(alignPanel.av
5671 .getSequenceSelection(),
5672 alignPanel.alignFrame, dassrc)
5673 .fetchDBRefs(false);
5679 fetchr.setToolTipText("<html>"
5680 + MessageManager.formatMessage(
5681 "label.fetch_retrieve_from", new Object[]
5685 if (++icomp >= mcomp || i == (otherdb.size()))
5687 ifetch.setText(MessageManager.formatMessage(
5688 "label.source_to_target", imname, sname));
5690 ifetch = new JMenu();
5698 if (comp >= mcomp || dbi >= (dbclasses.length))
5700 dfetch.setText(MessageManager.formatMessage(
5701 "label.source_to_target", mname, dbclass));
5703 dfetch = new JMenu();
5716 * Left justify the whole alignment.
5719 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5721 AlignmentI al = viewport.getAlignment();
5723 viewport.firePropertyChange("alignment", null, al);
5727 * Right justify the whole alignment.
5730 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5732 AlignmentI al = viewport.getAlignment();
5734 viewport.firePropertyChange("alignment", null, al);
5738 public void setShowSeqFeatures(boolean b)
5740 showSeqFeatures.setSelected(b);
5741 viewport.setShowSequenceFeatures(b);
5748 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5749 * awt.event.ActionEvent)
5752 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5754 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5755 alignPanel.paintAlignment(true);
5762 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5766 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5768 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5769 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5777 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5778 * .event.ActionEvent)
5781 protected void showGroupConservation_actionPerformed(ActionEvent e)
5783 viewport.setShowGroupConservation(showGroupConservation.getState());
5784 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5791 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5792 * .event.ActionEvent)
5795 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5797 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5798 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5805 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5806 * .event.ActionEvent)
5809 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5811 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5812 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5816 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5818 showSequenceLogo.setState(true);
5819 viewport.setShowSequenceLogo(true);
5820 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5821 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5825 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5827 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5834 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5835 * .event.ActionEvent)
5838 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5840 if (avc.makeGroupsFromSelection())
5842 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5843 alignPanel.updateAnnotation();
5844 alignPanel.paintAlignment(true);
5848 public void clearAlignmentSeqRep()
5850 // TODO refactor alignmentseqrep to controller
5851 if (viewport.getAlignment().hasSeqrep())
5853 viewport.getAlignment().setSeqrep(null);
5854 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5855 alignPanel.updateAnnotation();
5856 alignPanel.paintAlignment(true);
5861 protected void createGroup_actionPerformed(ActionEvent e)
5863 if (avc.createGroup())
5865 alignPanel.alignmentChanged();
5870 protected void unGroup_actionPerformed(ActionEvent e)
5874 alignPanel.alignmentChanged();
5879 * make the given alignmentPanel the currently selected tab
5881 * @param alignmentPanel
5883 public void setDisplayedView(AlignmentPanel alignmentPanel)
5885 if (!viewport.getSequenceSetId().equals(
5886 alignmentPanel.av.getSequenceSetId()))
5890 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5892 if (tabbedPane != null
5893 && tabbedPane.getTabCount() > 0
5894 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5895 .getSelectedIndex())
5897 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5902 * Action on selection of menu options to Show or Hide annotations.
5905 * @param forSequences
5906 * update sequence-related annotations
5907 * @param forAlignment
5908 * update non-sequence-related annotations
5911 protected void setAnnotationsVisibility(boolean visible,
5912 boolean forSequences, boolean forAlignment)
5914 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5915 .getAlignmentAnnotation())
5918 * don't display non-positional annotations on an alignment
5920 if (aa.annotations == null)
5924 boolean apply = (aa.sequenceRef == null && forAlignment)
5925 || (aa.sequenceRef != null && forSequences);
5928 aa.visible = visible;
5931 alignPanel.validateAnnotationDimensions(true);
5932 alignPanel.alignmentChanged();
5936 * Store selected annotation sort order for the view and repaint.
5939 protected void sortAnnotations_actionPerformed()
5941 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5943 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5944 alignPanel.paintAlignment(true);
5949 * @return alignment panels in this alignment frame
5951 public List<? extends AlignmentViewPanel> getAlignPanels()
5953 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5957 * Open a new alignment window, with the cDNA associated with this (protein)
5958 * alignment, aligned as is the protein.
5960 protected void viewAsCdna_actionPerformed()
5962 // TODO no longer a menu action - refactor as required
5963 final AlignmentI alignment = getViewport().getAlignment();
5964 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5965 if (mappings == null)
5969 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5970 for (SequenceI aaSeq : alignment.getSequences())
5972 for (AlignedCodonFrame acf : mappings)
5974 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5978 * There is a cDNA mapping for this protein sequence - add to new
5979 * alignment. It will share the same dataset sequence as other mapped
5980 * cDNA (no new mappings need to be created).
5982 final Sequence newSeq = new Sequence(dnaSeq);
5983 newSeq.setDatasetSequence(dnaSeq);
5984 cdnaSeqs.add(newSeq);
5988 if (cdnaSeqs.size() == 0)
5990 // show a warning dialog no mapped cDNA
5993 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5995 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5996 AlignFrame.DEFAULT_HEIGHT);
5997 cdna.alignAs(alignment);
5998 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6000 Desktop.addInternalFrame(alignFrame, newtitle,
6001 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6005 * Set visibility of dna/protein complement view (available when shown in a
6011 protected void showComplement_actionPerformed(boolean show)
6013 SplitContainerI sf = getSplitViewContainer();
6016 sf.setComplementVisible(this, show);
6021 * Generate the reverse (optionally complemented) of the selected sequences,
6022 * and add them to the alignment
6025 protected void showReverse_actionPerformed(boolean complement)
6027 AlignmentI al = null;
6030 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6032 al = dna.reverseCdna(complement);
6033 viewport.addAlignment(al, "");
6034 } catch (Exception ex)
6036 System.err.println(ex.getMessage());
6042 class PrintThread extends Thread
6046 public PrintThread(AlignmentPanel ap)
6051 static PageFormat pf;
6056 PrinterJob printJob = PrinterJob.getPrinterJob();
6060 printJob.setPrintable(ap, pf);
6064 printJob.setPrintable(ap);
6067 if (printJob.printDialog())
6072 } catch (Exception PrintException)
6074 PrintException.printStackTrace();