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, this);
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.isEmpty())
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", true, seqs,
2577 column, viewport.getAlignment());
2578 viewport.setStartRes(0);
2582 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2583 column, viewport.getAlignment());
2586 statusBar.setText(MessageManager.formatMessage(
2587 "label.removed_columns",
2588 new String[] { Integer.valueOf(trimRegion.getSize())
2591 addHistoryItem(trimRegion);
2593 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2595 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2596 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2598 viewport.getAlignment().deleteGroup(sg);
2602 viewport.firePropertyChange("alignment", null, viewport
2603 .getAlignment().getSequences());
2614 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2616 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2619 if (viewport.getSelectionGroup() != null)
2621 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2622 viewport.getHiddenRepSequences());
2623 start = viewport.getSelectionGroup().getStartRes();
2624 end = viewport.getSelectionGroup().getEndRes();
2628 seqs = viewport.getAlignment().getSequencesArray();
2631 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2632 "Remove Gapped Columns", seqs, start, end,
2633 viewport.getAlignment());
2635 addHistoryItem(removeGapCols);
2637 statusBar.setText(MessageManager.formatMessage(
2638 "label.removed_empty_columns",
2639 new Object[] { Integer.valueOf(removeGapCols.getSize())
2642 // This is to maintain viewport position on first residue
2643 // of first sequence
2644 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2645 int startRes = seq.findPosition(viewport.startRes);
2646 // ShiftList shifts;
2647 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2648 // edit.alColumnChanges=shifts.getInverse();
2649 // if (viewport.hasHiddenColumns)
2650 // viewport.getColumnSelection().compensateForEdits(shifts);
2651 viewport.setStartRes(seq.findIndex(startRes) - 1);
2652 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2664 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2666 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2669 if (viewport.getSelectionGroup() != null)
2671 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2672 viewport.getHiddenRepSequences());
2673 start = viewport.getSelectionGroup().getStartRes();
2674 end = viewport.getSelectionGroup().getEndRes();
2678 seqs = viewport.getAlignment().getSequencesArray();
2681 // This is to maintain viewport position on first residue
2682 // of first sequence
2683 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2684 int startRes = seq.findPosition(viewport.startRes);
2686 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2687 viewport.getAlignment()));
2689 viewport.setStartRes(seq.findIndex(startRes) - 1);
2691 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2703 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2705 viewport.setPadGaps(padGapsMenuitem.isSelected());
2706 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2717 public void findMenuItem_actionPerformed(ActionEvent e)
2723 * Create a new view of the current alignment.
2726 public void newView_actionPerformed(ActionEvent e)
2728 newView(null, true);
2732 * Creates and shows a new view of the current alignment.
2735 * title of newly created view; if null, one will be generated
2736 * @param copyAnnotation
2737 * if true then duplicate all annnotation, groups and settings
2738 * @return new alignment panel, already displayed.
2740 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2743 * Create a new AlignmentPanel (with its own, new Viewport)
2745 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2747 if (!copyAnnotation)
2750 * remove all groups and annotation except for the automatic stuff
2752 newap.av.getAlignment().deleteAllGroups();
2753 newap.av.getAlignment().deleteAllAnnotations(false);
2756 newap.av.setGatherViewsHere(false);
2758 if (viewport.viewName == null)
2760 viewport.viewName = MessageManager
2761 .getString("label.view_name_original");
2765 * Views share the same edits undo and redo stacks
2767 newap.av.setHistoryList(viewport.getHistoryList());
2768 newap.av.setRedoList(viewport.getRedoList());
2771 * Views share the same mappings; need to deregister any new mappings
2772 * created by copyAlignPanel, and register the new reference to the shared
2775 newap.av.replaceMappings(viewport.getAlignment());
2777 newap.av.viewName = getNewViewName(viewTitle);
2779 addAlignmentPanel(newap, true);
2780 newap.alignmentChanged();
2782 if (alignPanels.size() == 2)
2784 viewport.setGatherViewsHere(true);
2786 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2791 * Make a new name for the view, ensuring it is unique within the current
2792 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2793 * these now use viewId. Unique view names are still desirable for usability.)
2798 protected String getNewViewName(String viewTitle)
2800 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2801 boolean addFirstIndex = false;
2802 if (viewTitle == null || viewTitle.trim().length() == 0)
2804 viewTitle = MessageManager.getString("action.view");
2805 addFirstIndex = true;
2809 index = 1;// we count from 1 if given a specific name
2811 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2813 List<Component> comps = PaintRefresher.components.get(viewport
2814 .getSequenceSetId());
2816 List<String> existingNames = getExistingViewNames(comps);
2818 while (existingNames.contains(newViewName))
2820 newViewName = viewTitle + " " + (++index);
2826 * Returns a list of distinct view names found in the given list of
2827 * components. View names are held on the viewport of an AlignmentPanel.
2832 protected List<String> getExistingViewNames(List<Component> comps)
2834 List<String> existingNames = new ArrayList<String>();
2835 for (Component comp : comps)
2837 if (comp instanceof AlignmentPanel)
2839 AlignmentPanel ap = (AlignmentPanel) comp;
2840 if (!existingNames.contains(ap.av.viewName))
2842 existingNames.add(ap.av.viewName);
2846 return existingNames;
2850 * Explode tabbed views into separate windows.
2853 public void expandViews_actionPerformed(ActionEvent e)
2855 Desktop.instance.explodeViews(this);
2859 * Gather views in separate windows back into a tabbed presentation.
2862 public void gatherViews_actionPerformed(ActionEvent e)
2864 Desktop.instance.gatherViews(this);
2874 public void font_actionPerformed(ActionEvent e)
2876 new FontChooser(alignPanel);
2886 protected void seqLimit_actionPerformed(ActionEvent e)
2888 viewport.setShowJVSuffix(seqLimits.isSelected());
2890 alignPanel.getIdPanel().getIdCanvas()
2891 .setPreferredSize(alignPanel.calculateIdWidth());
2892 alignPanel.paintAlignment(true);
2896 public void idRightAlign_actionPerformed(ActionEvent e)
2898 viewport.setRightAlignIds(idRightAlign.isSelected());
2899 alignPanel.paintAlignment(true);
2903 public void centreColumnLabels_actionPerformed(ActionEvent e)
2905 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2906 alignPanel.paintAlignment(true);
2912 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2915 protected void followHighlight_actionPerformed()
2918 * Set the 'follow' flag on the Viewport (and scroll to position if now
2921 final boolean state = this.followHighlightMenuItem.getState();
2922 viewport.setFollowHighlight(state);
2925 alignPanel.scrollToPosition(
2926 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2937 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2939 viewport.setColourText(colourTextMenuItem.isSelected());
2940 alignPanel.paintAlignment(true);
2950 public void wrapMenuItem_actionPerformed(ActionEvent e)
2952 scaleAbove.setVisible(wrapMenuItem.isSelected());
2953 scaleLeft.setVisible(wrapMenuItem.isSelected());
2954 scaleRight.setVisible(wrapMenuItem.isSelected());
2955 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2956 alignPanel.updateLayout();
2960 public void showAllSeqs_actionPerformed(ActionEvent e)
2962 viewport.showAllHiddenSeqs();
2966 public void showAllColumns_actionPerformed(ActionEvent e)
2968 viewport.showAllHiddenColumns();
2970 viewport.sendSelection();
2974 public void hideSelSequences_actionPerformed(ActionEvent e)
2976 viewport.hideAllSelectedSeqs();
2977 // alignPanel.paintAlignment(true);
2981 * called by key handler and the hide all/show all menu items
2986 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2989 boolean hide = false;
2990 SequenceGroup sg = viewport.getSelectionGroup();
2991 if (!toggleSeqs && !toggleCols)
2993 // Hide everything by the current selection - this is a hack - we do the
2994 // invert and then hide
2995 // first check that there will be visible columns after the invert.
2996 if ((viewport.getColumnSelection() != null
2997 && viewport.getColumnSelection().getSelected() != null && viewport
2998 .getColumnSelection().getSelected().size() > 0)
2999 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3002 // now invert the sequence set, if required - empty selection implies
3003 // that no hiding is required.
3006 invertSequenceMenuItem_actionPerformed(null);
3007 sg = viewport.getSelectionGroup();
3011 viewport.expandColSelection(sg, true);
3012 // finally invert the column selection and get the new sequence
3014 invertColSel_actionPerformed(null);
3021 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3023 hideSelSequences_actionPerformed(null);
3026 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3029 showAllSeqs_actionPerformed(null);
3035 if (viewport.getColumnSelection().getSelected().size() > 0)
3037 hideSelColumns_actionPerformed(null);
3040 viewport.setSelectionGroup(sg);
3045 showAllColumns_actionPerformed(null);
3054 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3055 * event.ActionEvent)
3058 public void hideAllButSelection_actionPerformed(ActionEvent e)
3060 toggleHiddenRegions(false, false);
3061 viewport.sendSelection();
3068 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3072 public void hideAllSelection_actionPerformed(ActionEvent e)
3074 SequenceGroup sg = viewport.getSelectionGroup();
3075 viewport.expandColSelection(sg, false);
3076 viewport.hideAllSelectedSeqs();
3077 viewport.hideSelectedColumns();
3078 alignPanel.paintAlignment(true);
3079 viewport.sendSelection();
3086 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3090 public void showAllhidden_actionPerformed(ActionEvent e)
3092 viewport.showAllHiddenColumns();
3093 viewport.showAllHiddenSeqs();
3094 alignPanel.paintAlignment(true);
3095 viewport.sendSelection();
3099 public void hideSelColumns_actionPerformed(ActionEvent e)
3101 viewport.hideSelectedColumns();
3102 alignPanel.paintAlignment(true);
3103 viewport.sendSelection();
3107 public void hiddenMarkers_actionPerformed(ActionEvent e)
3109 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3120 protected void scaleAbove_actionPerformed(ActionEvent e)
3122 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3123 alignPanel.paintAlignment(true);
3133 protected void scaleLeft_actionPerformed(ActionEvent e)
3135 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3136 alignPanel.paintAlignment(true);
3146 protected void scaleRight_actionPerformed(ActionEvent e)
3148 viewport.setScaleRightWrapped(scaleRight.isSelected());
3149 alignPanel.paintAlignment(true);
3159 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3161 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3162 alignPanel.paintAlignment(true);
3172 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3174 viewport.setShowText(viewTextMenuItem.isSelected());
3175 alignPanel.paintAlignment(true);
3185 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3187 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3188 alignPanel.paintAlignment(true);
3191 public FeatureSettings featureSettings;
3194 public FeatureSettingsControllerI getFeatureSettingsUI()
3196 return featureSettings;
3200 public void featureSettings_actionPerformed(ActionEvent e)
3202 if (featureSettings != null)
3204 featureSettings.close();
3205 featureSettings = null;
3207 if (!showSeqFeatures.isSelected())
3209 // make sure features are actually displayed
3210 showSeqFeatures.setSelected(true);
3211 showSeqFeatures_actionPerformed(null);
3213 featureSettings = new FeatureSettings(this);
3217 * Set or clear 'Show Sequence Features'
3223 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3225 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3226 alignPanel.paintAlignment(true);
3227 if (alignPanel.getOverviewPanel() != null)
3229 alignPanel.getOverviewPanel().updateOverviewImage();
3234 * Set or clear 'Show Sequence Features'
3240 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3242 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3244 if (viewport.isShowSequenceFeaturesHeight())
3246 // ensure we're actually displaying features
3247 viewport.setShowSequenceFeatures(true);
3248 showSeqFeatures.setSelected(true);
3250 alignPanel.paintAlignment(true);
3251 if (alignPanel.getOverviewPanel() != null)
3253 alignPanel.getOverviewPanel().updateOverviewImage();
3258 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3259 * the annotations panel as a whole.
3261 * The options to show/hide all annotations should be enabled when the panel
3262 * is shown, and disabled when the panel is hidden.
3267 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3269 final boolean setVisible = annotationPanelMenuItem.isSelected();
3270 viewport.setShowAnnotation(setVisible);
3271 this.showAllSeqAnnotations.setEnabled(setVisible);
3272 this.hideAllSeqAnnotations.setEnabled(setVisible);
3273 this.showAllAlAnnotations.setEnabled(setVisible);
3274 this.hideAllAlAnnotations.setEnabled(setVisible);
3275 alignPanel.updateLayout();
3279 public void alignmentProperties()
3281 JEditorPane editPane = new JEditorPane("text/html", "");
3282 editPane.setEditable(false);
3283 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3285 editPane.setText(MessageManager.formatMessage("label.html_content",
3286 new Object[] { contents.toString() }));
3287 JInternalFrame frame = new JInternalFrame();
3288 frame.getContentPane().add(new JScrollPane(editPane));
3290 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3291 "label.alignment_properties", new Object[] { getTitle() }),
3302 public void overviewMenuItem_actionPerformed(ActionEvent e)
3304 if (alignPanel.overviewPanel != null)
3309 JInternalFrame frame = new JInternalFrame();
3310 OverviewPanel overview = new OverviewPanel(alignPanel);
3311 frame.setContentPane(overview);
3312 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3313 "label.overview_params", new Object[] { this.getTitle() }),
3314 frame.getWidth(), frame.getHeight());
3316 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3317 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3320 public void internalFrameClosed(
3321 javax.swing.event.InternalFrameEvent evt)
3323 alignPanel.setOverviewPanel(null);
3327 alignPanel.setOverviewPanel(overview);
3331 public void textColour_actionPerformed(ActionEvent e)
3333 new TextColourChooser().chooseColour(alignPanel, null);
3343 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3355 public void clustalColour_actionPerformed(ActionEvent e)
3357 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3358 viewport.getHiddenRepSequences()));
3368 public void zappoColour_actionPerformed(ActionEvent e)
3370 changeColour(new ZappoColourScheme());
3380 public void taylorColour_actionPerformed(ActionEvent e)
3382 changeColour(new TaylorColourScheme());
3392 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3394 changeColour(new HydrophobicColourScheme());
3404 public void helixColour_actionPerformed(ActionEvent e)
3406 changeColour(new HelixColourScheme());
3416 public void strandColour_actionPerformed(ActionEvent e)
3418 changeColour(new StrandColourScheme());
3428 public void turnColour_actionPerformed(ActionEvent e)
3430 changeColour(new TurnColourScheme());
3440 public void buriedColour_actionPerformed(ActionEvent e)
3442 changeColour(new BuriedColourScheme());
3452 public void nucleotideColour_actionPerformed(ActionEvent e)
3454 changeColour(new NucleotideColourScheme());
3458 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3460 changeColour(new PurinePyrimidineColourScheme());
3464 * public void covariationColour_actionPerformed(ActionEvent e) {
3466 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3470 public void annotationColour_actionPerformed(ActionEvent e)
3472 new AnnotationColourChooser(viewport, alignPanel);
3476 public void annotationColumn_actionPerformed(ActionEvent e)
3478 new AnnotationColumnChooser(viewport, alignPanel);
3482 public void rnahelicesColour_actionPerformed(ActionEvent e)
3484 new RNAHelicesColourChooser(viewport, alignPanel);
3494 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3496 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3506 public void changeColour(ColourSchemeI cs)
3508 // TODO: pull up to controller method
3512 // Make sure viewport is up to date w.r.t. any sliders
3513 if (viewport.getAbovePIDThreshold())
3515 int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3517 viewport.setThreshold(threshold);
3520 if (viewport.getConservationSelected())
3522 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3525 if (cs instanceof TCoffeeColourScheme)
3527 tcoffeeColour.setEnabled(true);
3528 tcoffeeColour.setSelected(true);
3532 viewport.setGlobalColourScheme(cs);
3534 alignPanel.paintAlignment(true);
3544 protected void modifyPID_actionPerformed(ActionEvent e)
3546 if (viewport.getAbovePIDThreshold()
3547 && viewport.getGlobalColourScheme() != null)
3549 SliderPanel.setPIDSliderSource(alignPanel,
3550 viewport.getGlobalColourScheme(), "Background");
3551 SliderPanel.showPIDSlider();
3562 protected void modifyConservation_actionPerformed(ActionEvent e)
3564 if (viewport.getConservationSelected()
3565 && viewport.getGlobalColourScheme() != null)
3567 SliderPanel.setConservationSlider(alignPanel,
3568 viewport.getGlobalColourScheme(), "Background");
3569 SliderPanel.showConservationSlider();
3580 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3582 viewport.setConservationSelected(conservationMenuItem.isSelected());
3584 viewport.setAbovePIDThreshold(false);
3585 abovePIDThreshold.setSelected(false);
3587 changeColour(viewport.getGlobalColourScheme());
3589 modifyConservation_actionPerformed(null);
3599 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3601 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3603 conservationMenuItem.setSelected(false);
3604 viewport.setConservationSelected(false);
3606 changeColour(viewport.getGlobalColourScheme());
3608 modifyPID_actionPerformed(null);
3618 public void userDefinedColour_actionPerformed(ActionEvent e)
3620 if (e.getActionCommand().equals(
3621 MessageManager.getString("action.user_defined")))
3623 new UserDefinedColours(alignPanel, null);
3627 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3628 .getUserColourSchemes().get(e.getActionCommand());
3634 public void updateUserColourMenu()
3637 Component[] menuItems = colourMenu.getMenuComponents();
3638 int iSize = menuItems.length;
3639 for (int i = 0; i < iSize; i++)
3641 if (menuItems[i].getName() != null
3642 && menuItems[i].getName().equals("USER_DEFINED"))
3644 colourMenu.remove(menuItems[i]);
3648 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3650 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3651 .getUserColourSchemes().keys();
3653 while (userColours.hasMoreElements())
3655 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3656 userColours.nextElement().toString());
3657 radioItem.setName("USER_DEFINED");
3658 radioItem.addMouseListener(new MouseAdapter()
3661 public void mousePressed(MouseEvent evt)
3663 if (evt.isControlDown()
3664 || SwingUtilities.isRightMouseButton(evt))
3666 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3668 int option = JOptionPane.showInternalConfirmDialog(
3669 jalview.gui.Desktop.desktop,
3671 .getString("label.remove_from_default_list"),
3673 .getString("label.remove_user_defined_colour"),
3674 JOptionPane.YES_NO_OPTION);
3675 if (option == JOptionPane.YES_OPTION)
3677 jalview.gui.UserDefinedColours
3678 .removeColourFromDefaults(radioItem.getText());
3679 colourMenu.remove(radioItem);
3683 radioItem.addActionListener(new ActionListener()
3686 public void actionPerformed(ActionEvent evt)
3688 userDefinedColour_actionPerformed(evt);
3695 radioItem.addActionListener(new ActionListener()
3698 public void actionPerformed(ActionEvent evt)
3700 userDefinedColour_actionPerformed(evt);
3704 colourMenu.insert(radioItem, 15);
3705 colours.add(radioItem);
3717 public void PIDColour_actionPerformed(ActionEvent e)
3719 changeColour(new PIDColourScheme());
3729 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3731 changeColour(new Blosum62ColourScheme());
3741 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3743 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3744 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3745 .getAlignment().getSequenceAt(0), null);
3746 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3747 viewport.getAlignment()));
3748 alignPanel.paintAlignment(true);
3758 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3760 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3761 AlignmentSorter.sortByID(viewport.getAlignment());
3762 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3763 viewport.getAlignment()));
3764 alignPanel.paintAlignment(true);
3774 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3776 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3777 AlignmentSorter.sortByLength(viewport.getAlignment());
3778 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3779 viewport.getAlignment()));
3780 alignPanel.paintAlignment(true);
3790 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3792 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3793 AlignmentSorter.sortByGroup(viewport.getAlignment());
3794 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3795 viewport.getAlignment()));
3797 alignPanel.paintAlignment(true);
3807 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3809 new RedundancyPanel(alignPanel, this);
3819 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3821 if ((viewport.getSelectionGroup() == null)
3822 || (viewport.getSelectionGroup().getSize() < 2))
3824 JOptionPane.showInternalMessageDialog(this, MessageManager
3825 .getString("label.you_must_select_least_two_sequences"),
3826 MessageManager.getString("label.invalid_selection"),
3827 JOptionPane.WARNING_MESSAGE);
3831 JInternalFrame frame = new JInternalFrame();
3832 frame.setContentPane(new PairwiseAlignPanel(viewport));
3833 Desktop.addInternalFrame(frame,
3834 MessageManager.getString("action.pairwise_alignment"), 600,
3846 public void PCAMenuItem_actionPerformed(ActionEvent e)
3848 if (((viewport.getSelectionGroup() != null)
3849 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3850 .getSelectionGroup().getSize() > 0))
3851 || (viewport.getAlignment().getHeight() < 4))
3854 .showInternalMessageDialog(
3857 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3859 .getString("label.sequence_selection_insufficient"),
3860 JOptionPane.WARNING_MESSAGE);
3865 new PCAPanel(alignPanel);
3869 public void autoCalculate_actionPerformed(ActionEvent e)
3871 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3872 if (viewport.autoCalculateConsensus)
3874 viewport.firePropertyChange("alignment", null, viewport
3875 .getAlignment().getSequences());
3880 public void sortByTreeOption_actionPerformed(ActionEvent e)
3882 viewport.sortByTree = sortByTree.isSelected();
3886 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3888 viewport.followSelection = listenToViewSelections.isSelected();
3898 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3900 newTreePanel("AV", "PID", "Average distance tree using PID");
3910 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3912 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3922 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3924 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3934 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3936 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3949 void newTreePanel(String type, String pwType, String title)
3953 if (viewport.getSelectionGroup() != null
3954 && viewport.getSelectionGroup().getSize() > 0)
3956 if (viewport.getSelectionGroup().getSize() < 3)
3962 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3964 .getString("label.not_enough_sequences"),
3965 JOptionPane.WARNING_MESSAGE);
3969 SequenceGroup sg = viewport.getSelectionGroup();
3971 /* Decide if the selection is a column region */
3972 for (SequenceI _s : sg.getSequences())
3974 if (_s.getLength() < sg.getEndRes())
3980 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3982 .getString("label.sequences_selection_not_aligned"),
3983 JOptionPane.WARNING_MESSAGE);
3989 title = title + " on region";
3990 tp = new TreePanel(alignPanel, type, pwType);
3994 // are the visible sequences aligned?
3995 if (!viewport.getAlignment().isAligned(false))
4001 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4003 .getString("label.sequences_not_aligned"),
4004 JOptionPane.WARNING_MESSAGE);
4009 if (viewport.getAlignment().getHeight() < 2)
4014 tp = new TreePanel(alignPanel, type, pwType);
4019 if (viewport.viewName != null)
4021 title += viewport.viewName + " of ";
4024 title += this.title;
4026 Desktop.addInternalFrame(tp, title, 600, 500);
4037 public void addSortByOrderMenuItem(String title,
4038 final AlignmentOrder order)
4040 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4041 "action.by_title_param", new Object[] { title }));
4043 item.addActionListener(new java.awt.event.ActionListener()
4046 public void actionPerformed(ActionEvent e)
4048 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4050 // TODO: JBPNote - have to map order entries to curent SequenceI
4052 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4054 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4057 alignPanel.paintAlignment(true);
4063 * Add a new sort by annotation score menu item
4066 * the menu to add the option to
4068 * the label used to retrieve scores for each sequence on the
4071 public void addSortByAnnotScoreMenuItem(JMenu sort,
4072 final String scoreLabel)
4074 final JMenuItem item = new JMenuItem(scoreLabel);
4076 item.addActionListener(new java.awt.event.ActionListener()
4079 public void actionPerformed(ActionEvent e)
4081 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4082 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4083 viewport.getAlignment());// ,viewport.getSelectionGroup());
4084 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4085 viewport.getAlignment()));
4086 alignPanel.paintAlignment(true);
4092 * last hash for alignment's annotation array - used to minimise cost of
4095 protected int _annotationScoreVectorHash;
4098 * search the alignment and rebuild the sort by annotation score submenu the
4099 * last alignment annotation vector hash is stored to minimize cost of
4100 * rebuilding in subsequence calls.
4104 public void buildSortByAnnotationScoresMenu()
4106 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4111 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4113 sortByAnnotScore.removeAll();
4114 // almost certainly a quicker way to do this - but we keep it simple
4115 Hashtable scoreSorts = new Hashtable();
4116 AlignmentAnnotation aann[];
4117 for (SequenceI sqa : viewport.getAlignment().getSequences())
4119 aann = sqa.getAnnotation();
4120 for (int i = 0; aann != null && i < aann.length; i++)
4122 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4124 scoreSorts.put(aann[i].label, aann[i].label);
4128 Enumeration labels = scoreSorts.keys();
4129 while (labels.hasMoreElements())
4131 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4132 (String) labels.nextElement());
4134 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4137 _annotationScoreVectorHash = viewport.getAlignment()
4138 .getAlignmentAnnotation().hashCode();
4143 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4144 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4145 * call. Listeners are added to remove the menu item when the treePanel is
4146 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4150 * Displayed tree window.
4152 * SortBy menu item title.
4155 public void buildTreeMenu()
4157 calculateTree.removeAll();
4158 // build the calculate menu
4160 for (final String type : new String[] { "NJ", "AV" })
4162 String treecalcnm = MessageManager.getString("label.tree_calc_"
4163 + type.toLowerCase());
4164 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4166 JMenuItem tm = new JMenuItem();
4167 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4168 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4170 String smn = MessageManager.getStringOrReturn(
4171 "label.score_model_", sm.getName());
4172 final String title = MessageManager.formatMessage(
4173 "label.treecalc_title", treecalcnm, smn);
4174 tm.setText(title);//
4175 tm.addActionListener(new java.awt.event.ActionListener()
4178 public void actionPerformed(ActionEvent e)
4180 newTreePanel(type, pwtype, title);
4183 calculateTree.add(tm);
4188 sortByTreeMenu.removeAll();
4190 List<Component> comps = PaintRefresher.components.get(viewport
4191 .getSequenceSetId());
4192 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4193 for (Component comp : comps)
4195 if (comp instanceof TreePanel)
4197 treePanels.add((TreePanel) comp);
4201 if (treePanels.size() < 1)
4203 sortByTreeMenu.setVisible(false);
4207 sortByTreeMenu.setVisible(true);
4209 for (final TreePanel tp : treePanels)
4211 final JMenuItem item = new JMenuItem(tp.getTitle());
4212 item.addActionListener(new java.awt.event.ActionListener()
4215 public void actionPerformed(ActionEvent e)
4217 tp.sortByTree_actionPerformed();
4218 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4223 sortByTreeMenu.add(item);
4227 public boolean sortBy(AlignmentOrder alorder, String undoname)
4229 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4230 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4231 if (undoname != null)
4233 addHistoryItem(new OrderCommand(undoname, oldOrder,
4234 viewport.getAlignment()));
4236 alignPanel.paintAlignment(true);
4241 * Work out whether the whole set of sequences or just the selected set will
4242 * be submitted for multiple alignment.
4245 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4247 // Now, check we have enough sequences
4248 AlignmentView msa = null;
4250 if ((viewport.getSelectionGroup() != null)
4251 && (viewport.getSelectionGroup().getSize() > 1))
4253 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4254 // some common interface!
4256 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4257 * SequenceI[sz = seqs.getSize(false)];
4259 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4260 * seqs.getSequenceAt(i); }
4262 msa = viewport.getAlignmentView(true);
4264 else if (viewport.getSelectionGroup() != null
4265 && viewport.getSelectionGroup().getSize() == 1)
4267 int option = JOptionPane.showConfirmDialog(this,
4268 MessageManager.getString("warn.oneseq_msainput_selection"),
4269 MessageManager.getString("label.invalid_selection"),
4270 JOptionPane.OK_CANCEL_OPTION);
4271 if (option == JOptionPane.OK_OPTION)
4273 msa = viewport.getAlignmentView(false);
4278 msa = viewport.getAlignmentView(false);
4284 * Decides what is submitted to a secondary structure prediction service: the
4285 * first sequence in the alignment, or in the current selection, or, if the
4286 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4287 * region or the whole alignment. (where the first sequence in the set is the
4288 * one that the prediction will be for).
4290 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4292 AlignmentView seqs = null;
4294 if ((viewport.getSelectionGroup() != null)
4295 && (viewport.getSelectionGroup().getSize() > 0))
4297 seqs = viewport.getAlignmentView(true);
4301 seqs = viewport.getAlignmentView(false);
4303 // limit sequences - JBPNote in future - could spawn multiple prediction
4305 // TODO: viewport.getAlignment().isAligned is a global state - the local
4306 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4307 if (!viewport.getAlignment().isAligned(false))
4309 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4310 // TODO: if seqs.getSequences().length>1 then should really have warned
4324 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4326 // Pick the tree file
4327 JalviewFileChooser chooser = new JalviewFileChooser(
4328 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4329 chooser.setFileView(new JalviewFileView());
4330 chooser.setDialogTitle(MessageManager
4331 .getString("label.select_newick_like_tree_file"));
4332 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4334 int value = chooser.showOpenDialog(null);
4336 if (value == JalviewFileChooser.APPROVE_OPTION)
4338 String choice = chooser.getSelectedFile().getPath();
4339 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4340 jalview.io.NewickFile fin = null;
4343 fin = new jalview.io.NewickFile(choice, "File");
4344 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4345 } catch (Exception ex)
4352 .getString("label.problem_reading_tree_file"),
4353 JOptionPane.WARNING_MESSAGE);
4354 ex.printStackTrace();
4356 if (fin != null && fin.hasWarningMessage())
4358 JOptionPane.showMessageDialog(Desktop.desktop, fin
4359 .getWarningMessage(), MessageManager
4360 .getString("label.possible_problem_with_tree_file"),
4361 JOptionPane.WARNING_MESSAGE);
4367 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4369 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4372 public TreePanel ShowNewickTree(NewickFile nf, String title)
4374 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4377 public TreePanel ShowNewickTree(NewickFile nf, String title,
4378 AlignmentView input)
4380 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4383 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4384 int h, int x, int y)
4386 return ShowNewickTree(nf, title, null, w, h, x, y);
4390 * Add a treeviewer for the tree extracted from a newick file object to the
4391 * current alignment view
4398 * Associated alignment input data (or null)
4407 * @return TreePanel handle
4409 public TreePanel ShowNewickTree(NewickFile nf, String title,
4410 AlignmentView input, int w, int h, int x, int y)
4412 TreePanel tp = null;
4418 if (nf.getTree() != null)
4420 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4426 tp.setLocation(x, y);
4429 Desktop.addInternalFrame(tp, title, w, h);
4431 } catch (Exception ex)
4433 ex.printStackTrace();
4439 private boolean buildingMenu = false;
4442 * Generates menu items and listener event actions for web service clients
4445 public void BuildWebServiceMenu()
4447 while (buildingMenu)
4451 System.err.println("Waiting for building menu to finish.");
4453 } catch (Exception e)
4457 final AlignFrame me = this;
4458 buildingMenu = true;
4459 new Thread(new Runnable()
4464 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4467 // System.err.println("Building ws menu again "
4468 // + Thread.currentThread());
4469 // TODO: add support for context dependent disabling of services based
4471 // alignment and current selection
4472 // TODO: add additional serviceHandle parameter to specify abstract
4474 // class independently of AbstractName
4475 // TODO: add in rediscovery GUI function to restart discoverer
4476 // TODO: group services by location as well as function and/or
4478 // object broker mechanism.
4479 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4480 final IProgressIndicator af = me;
4481 final JMenu msawsmenu = new JMenu("Alignment");
4482 final JMenu secstrmenu = new JMenu(
4483 "Secondary Structure Prediction");
4484 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4485 final JMenu analymenu = new JMenu("Analysis");
4486 final JMenu dismenu = new JMenu("Protein Disorder");
4487 // final JMenu msawsmenu = new
4488 // JMenu(MessageManager.getString("label.alignment"));
4489 // final JMenu secstrmenu = new
4490 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4491 // final JMenu seqsrchmenu = new
4492 // JMenu(MessageManager.getString("label.sequence_database_search"));
4493 // final JMenu analymenu = new
4494 // JMenu(MessageManager.getString("label.analysis"));
4495 // final JMenu dismenu = new
4496 // JMenu(MessageManager.getString("label.protein_disorder"));
4497 // JAL-940 - only show secondary structure prediction services from
4498 // the legacy server
4499 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4501 Discoverer.services != null && (Discoverer.services.size() > 0))
4503 // TODO: refactor to allow list of AbstractName/Handler bindings to
4505 // stored or retrieved from elsewhere
4506 // No MSAWS used any more:
4507 // Vector msaws = null; // (Vector)
4508 // Discoverer.services.get("MsaWS");
4509 Vector secstrpr = (Vector) Discoverer.services
4511 if (secstrpr != null)
4513 // Add any secondary structure prediction services
4514 for (int i = 0, j = secstrpr.size(); i < j; i++)
4516 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4518 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4519 .getServiceClient(sh);
4520 int p = secstrmenu.getItemCount();
4521 impl.attachWSMenuEntry(secstrmenu, me);
4522 int q = secstrmenu.getItemCount();
4523 for (int litm = p; litm < q; litm++)
4525 legacyItems.add(secstrmenu.getItem(litm));
4531 // Add all submenus in the order they should appear on the web
4533 wsmenu.add(msawsmenu);
4534 wsmenu.add(secstrmenu);
4535 wsmenu.add(dismenu);
4536 wsmenu.add(analymenu);
4537 // No search services yet
4538 // wsmenu.add(seqsrchmenu);
4540 javax.swing.SwingUtilities.invokeLater(new Runnable()
4547 webService.removeAll();
4548 // first, add discovered services onto the webservices menu
4549 if (wsmenu.size() > 0)
4551 for (int i = 0, j = wsmenu.size(); i < j; i++)
4553 webService.add(wsmenu.get(i));
4558 webService.add(me.webServiceNoServices);
4560 // TODO: move into separate menu builder class.
4561 boolean new_sspred = false;
4562 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4564 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4565 if (jws2servs != null)
4567 if (jws2servs.hasServices())
4569 jws2servs.attachWSMenuEntry(webService, me);
4570 for (Jws2Instance sv : jws2servs.getServices())
4572 if (sv.description.toLowerCase().contains("jpred"))
4574 for (JMenuItem jmi : legacyItems)
4576 jmi.setVisible(false);
4582 if (jws2servs.isRunning())
4584 JMenuItem tm = new JMenuItem(
4585 "Still discovering JABA Services");
4586 tm.setEnabled(false);
4591 build_urlServiceMenu(me.webService);
4592 build_fetchdbmenu(webService);
4593 for (JMenu item : wsmenu)
4595 if (item.getItemCount() == 0)
4597 item.setEnabled(false);
4601 item.setEnabled(true);
4604 } catch (Exception e)
4607 .debug("Exception during web service menu building process.",
4612 } catch (Exception e)
4615 buildingMenu = false;
4622 * construct any groupURL type service menu entries.
4626 private void build_urlServiceMenu(JMenu webService)
4628 // TODO: remove this code when 2.7 is released
4629 // DEBUG - alignmentView
4631 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4632 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4634 * @Override public void actionPerformed(ActionEvent e) {
4635 * jalview.datamodel.AlignmentView
4636 * .testSelectionViews(af.viewport.getAlignment(),
4637 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4639 * }); webService.add(testAlView);
4641 // TODO: refactor to RestClient discoverer and merge menu entries for
4642 // rest-style services with other types of analysis/calculation service
4643 // SHmmr test client - still being implemented.
4644 // DEBUG - alignmentView
4646 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4649 client.attachWSMenuEntry(
4650 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4656 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4657 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4658 * getProperty("LAST_DIRECTORY"));
4660 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4661 * to Vamsas file"); chooser.setToolTipText("Export");
4663 * int value = chooser.showSaveDialog(this);
4665 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4666 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4667 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4668 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4671 * prototype of an automatically enabled/disabled analysis function
4674 protected void setShowProductsEnabled()
4676 SequenceI[] selection = viewport.getSequenceSelection();
4677 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4678 viewport.getAlignment().getDataset()))
4680 showProducts.setEnabled(true);
4685 showProducts.setEnabled(false);
4690 * search selection for sequence xRef products and build the show products
4695 * @return true if showProducts menu should be enabled.
4697 public boolean canShowProducts(SequenceI[] selection,
4698 boolean isRegionSelection, Alignment dataset)
4700 boolean showp = false;
4703 showProducts.removeAll();
4704 final boolean dna = viewport.getAlignment().isNucleotide();
4705 final Alignment ds = dataset;
4706 String[] ptypes = (selection == null || selection.length == 0) ? null
4707 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4709 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4710 // selection, dataset, true);
4711 final SequenceI[] sel = selection;
4712 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4715 final boolean isRegSel = isRegionSelection;
4716 final AlignFrame af = this;
4717 final String source = ptypes[t];
4718 JMenuItem xtype = new JMenuItem(ptypes[t]);
4719 xtype.addActionListener(new ActionListener()
4723 public void actionPerformed(ActionEvent e)
4725 // TODO: new thread for this call with vis-delay
4726 af.showProductsFor(af.viewport.getSequenceSelection(),
4727 isRegSel, dna, source);
4731 showProducts.add(xtype);
4733 showProducts.setVisible(showp);
4734 showProducts.setEnabled(showp);
4735 } catch (Exception e)
4737 jalview.bin.Cache.log
4738 .warn("canTranslate threw an exception - please report to help@jalview.org",
4745 protected void showProductsFor(final SequenceI[] sel,
4746 final boolean isRegSel, final boolean dna, final String source)
4748 Runnable foo = new Runnable()
4754 final long sttime = System.currentTimeMillis();
4755 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4756 "status.searching_for_sequences_from",
4757 new Object[] { source }), sttime);
4760 // update our local dataset reference
4761 Alignment ds = AlignFrame.this.getViewport().getAlignment()
4763 Alignment prods = CrossRef
4764 .findXrefSequences(sel, dna, source, ds);
4767 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4768 for (int s = 0; s < sprods.length; s++)
4770 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4771 if (ds.getSequences() == null
4772 || !ds.getSequences().contains(
4773 sprods[s].getDatasetSequence()))
4775 ds.addSequence(sprods[s].getDatasetSequence());
4777 sprods[s].updatePDBIds();
4779 Alignment al = new Alignment(sprods);
4783 * Copy dna-to-protein mappings to new alignment
4785 // TODO 1: no mappings are set up for EMBL product
4786 // TODO 2: if they were, should add them to protein alignment, not
4788 List<AlignedCodonFrame> cf = prods.getCodonFrames();
4789 for (AlignedCodonFrame acf : cf)
4791 al.addCodonFrame(acf);
4793 AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
4795 String newtitle = "" + (dna ? "Proteins" : "Nucleotides")
4796 + " for " + (isRegSel ? "selected region of " : "")
4798 newFrame.setTitle(newtitle);
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.makeCdsAlignment(
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 boolean showSequenceFeatures = viewport
4831 .isShowSequenceFeatures();
4832 newFrame.setShowSeqFeatures(showSequenceFeatures);
4833 copyThis.setShowSeqFeatures(showSequenceFeatures);
4834 FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
4835 .getFeatureRenderer();
4837 * copy feature rendering settings to split frame
4839 newFrame.alignPanel.getSeqPanel().seqCanvas
4840 .getFeatureRenderer().transferSettings(
4842 copyThis.alignPanel.getSeqPanel().seqCanvas
4843 .getFeatureRenderer().transferSettings(
4845 SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
4846 dna ? newFrame : copyThis);
4847 newFrame.setVisible(true);
4848 copyThis.setVisible(true);
4849 String linkedTitle = MessageManager
4850 .getString("label.linked_view_title");
4851 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4855 Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
4861 System.err.println("No Sequences generated for xRef type "
4864 } catch (Exception e)
4866 jalview.bin.Cache.log.error(
4867 "Exception when finding crossreferences", e);
4868 } catch (OutOfMemoryError e)
4870 new OOMWarning("whilst fetching crossreferences", e);
4873 jalview.bin.Cache.log.error("Error when finding crossreferences",
4876 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4877 "status.finished_searching_for_sequences_from",
4878 new Object[] { source }), sttime);
4882 Thread frunner = new Thread(foo);
4886 public boolean canShowTranslationProducts(SequenceI[] selection,
4887 AlignmentI alignment)
4892 return (jalview.analysis.Dna.canTranslate(selection,
4893 viewport.getViewAsVisibleContigs(true)));
4894 } catch (Exception e)
4896 jalview.bin.Cache.log
4897 .warn("canTranslate threw an exception - please report to help@jalview.org",
4904 * Construct and display a new frame containing the translation of this
4905 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4908 public void showTranslation_actionPerformed(ActionEvent e)
4910 AlignmentI al = null;
4913 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4915 al = dna.translateCdna();
4916 } catch (Exception ex)
4918 jalview.bin.Cache.log.error(
4919 "Exception during translation. Please report this !", ex);
4920 final String msg = MessageManager
4921 .getString("label.error_when_translating_sequences_submit_bug_report");
4922 final String errorTitle = MessageManager
4923 .getString("label.implementation_error")
4924 + MessageManager.getString("translation_failed");
4925 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4926 JOptionPane.ERROR_MESSAGE);
4929 if (al == null || al.getHeight() == 0)
4931 final String msg = MessageManager
4932 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4933 final String errorTitle = MessageManager
4934 .getString("label.translation_failed");
4935 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4936 JOptionPane.WARNING_MESSAGE);
4940 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4941 af.setFileFormat(this.currentFileFormat);
4942 final String newTitle = MessageManager.formatMessage(
4943 "label.translation_of_params",
4944 new Object[] { this.getTitle() });
4945 af.setTitle(newTitle);
4946 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4948 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4949 viewport.openSplitFrame(af, new Alignment(seqs));
4953 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4960 * Set the file format
4964 public void setFileFormat(String fileFormat)
4966 this.currentFileFormat = fileFormat;
4970 * Try to load a features file onto the alignment.
4973 * contents or path to retrieve file
4975 * access mode of file (see jalview.io.AlignFile)
4976 * @return true if features file was parsed correctly.
4978 public boolean parseFeaturesFile(String file, String type)
4980 return avc.parseFeaturesFile(file, type,
4981 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4986 public void refreshFeatureUI(boolean enableIfNecessary)
4988 // note - currently this is only still here rather than in the controller
4989 // because of the featureSettings hard reference that is yet to be
4991 if (enableIfNecessary)
4993 viewport.setShowSequenceFeatures(true);
4994 showSeqFeatures.setSelected(true);
5000 public void dragEnter(DropTargetDragEvent evt)
5005 public void dragExit(DropTargetEvent evt)
5010 public void dragOver(DropTargetDragEvent evt)
5015 public void dropActionChanged(DropTargetDragEvent evt)
5020 public void drop(DropTargetDropEvent evt)
5022 Transferable t = evt.getTransferable();
5023 java.util.List files = null;
5027 DataFlavor uriListFlavor = new DataFlavor(
5028 "text/uri-list;class=java.lang.String");
5029 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5031 // Works on Windows and MacOSX
5032 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5033 files = (java.util.List) t
5034 .getTransferData(DataFlavor.javaFileListFlavor);
5036 else if (t.isDataFlavorSupported(uriListFlavor))
5038 // This is used by Unix drag system
5039 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5040 String data = (String) t.getTransferData(uriListFlavor);
5041 files = new java.util.ArrayList(1);
5042 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5043 data, "\r\n"); st.hasMoreTokens();)
5045 String s = st.nextToken();
5046 if (s.startsWith("#"))
5048 // the line is a comment (as per the RFC 2483)
5052 java.net.URI uri = new java.net.URI(s);
5053 // check to see if we can handle this kind of URI
5054 if (uri.getScheme().toLowerCase().startsWith("http"))
5056 files.add(uri.toString());
5060 // otherwise preserve old behaviour: catch all for file objects
5061 java.io.File file = new java.io.File(uri);
5062 files.add(file.toString());
5066 } catch (Exception e)
5068 e.printStackTrace();
5074 // check to see if any of these files have names matching sequences in
5076 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5077 .getAlignment().getSequencesArray());
5079 * Object[] { String,SequenceI}
5081 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5082 ArrayList<String> filesnotmatched = new ArrayList<String>();
5083 for (int i = 0; i < files.size(); i++)
5085 String file = files.get(i).toString();
5087 String protocol = FormatAdapter.checkProtocol(file);
5088 if (protocol == jalview.io.FormatAdapter.FILE)
5090 File fl = new File(file);
5091 pdbfn = fl.getName();
5093 else if (protocol == jalview.io.FormatAdapter.URL)
5095 URL url = new URL(file);
5096 pdbfn = url.getFile();
5098 if (pdbfn.length() > 0)
5100 // attempt to find a match in the alignment
5101 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5102 int l = 0, c = pdbfn.indexOf(".");
5103 while (mtch == null && c != -1)
5108 } while ((c = pdbfn.indexOf(".", l)) > l);
5111 pdbfn = pdbfn.substring(0, l);
5113 mtch = idm.findAllIdMatches(pdbfn);
5120 type = new IdentifyFile().identify(file, protocol);
5121 } catch (Exception ex)
5127 if (type.equalsIgnoreCase("PDB"))
5129 filesmatched.add(new Object[] { file, protocol, mtch });
5134 // File wasn't named like one of the sequences or wasn't a PDB file.
5135 filesnotmatched.add(file);
5139 if (filesmatched.size() > 0)
5141 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5147 "label.automatically_associate_pdb_files_with_sequences_same_name",
5148 new Object[] { Integer
5154 .getString("label.automatically_associate_pdb_files_by_name"),
5155 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5158 for (Object[] fm : filesmatched)
5160 // try and associate
5161 // TODO: may want to set a standard ID naming formalism for
5162 // associating PDB files which have no IDs.
5163 for (SequenceI toassoc : (SequenceI[]) fm[2])
5165 PDBEntry pe = new AssociatePdbFileWithSeq()
5166 .associatePdbWithSeq((String) fm[0],
5167 (String) fm[1], toassoc, false,
5171 System.err.println("Associated file : "
5172 + ((String) fm[0]) + " with "
5173 + toassoc.getDisplayId(true));
5177 alignPanel.paintAlignment(true);
5181 if (filesnotmatched.size() > 0)
5184 && (Cache.getDefault(
5185 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5191 "label.ignore_unmatched_dropped_files_info",
5192 new Object[] { Integer
5199 .getString("label.ignore_unmatched_dropped_files"),
5200 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5204 for (String fn : filesnotmatched)
5206 loadJalviewDataFile(fn, null, null, null);
5210 } catch (Exception ex)
5212 ex.printStackTrace();
5218 * Attempt to load a "dropped" file or URL string: First by testing whether
5219 * it's an Annotation file, then a JNet file, and finally a features file. If
5220 * all are false then the user may have dropped an alignment file onto this
5224 * either a filename or a URL string.
5226 public void loadJalviewDataFile(String file, String protocol,
5227 String format, SequenceI assocSeq)
5231 if (protocol == null)
5233 protocol = FormatAdapter.checkProtocol(file);
5235 // if the file isn't identified, or not positively identified as some
5236 // other filetype (PFAM is default unidentified alignment file type) then
5237 // try to parse as annotation.
5238 boolean isAnnotation = (format == null || format
5239 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5240 .annotateAlignmentView(viewport, file, protocol) : false;
5244 // first see if its a T-COFFEE score file
5245 TCoffeeScoreFile tcf = null;
5248 tcf = new TCoffeeScoreFile(file, protocol);
5251 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5253 tcoffeeColour.setEnabled(true);
5254 tcoffeeColour.setSelected(true);
5255 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5256 isAnnotation = true;
5258 .setText(MessageManager
5259 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5263 // some problem - if no warning its probable that the ID matching
5264 // process didn't work
5268 tcf.getWarningMessage() == null ? MessageManager
5269 .getString("label.check_file_matches_sequence_ids_alignment")
5270 : tcf.getWarningMessage(),
5272 .getString("label.problem_reading_tcoffee_score_file"),
5273 JOptionPane.WARNING_MESSAGE);
5280 } catch (Exception x)
5283 .debug("Exception when processing data source as T-COFFEE score file",
5289 // try to see if its a JNet 'concise' style annotation file *before*
5291 // try to parse it as a features file
5294 format = new IdentifyFile().identify(file, protocol);
5296 if (format.equalsIgnoreCase("JnetFile"))
5298 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5300 new JnetAnnotationMaker();
5301 JnetAnnotationMaker.add_annotation(predictions,
5302 viewport.getAlignment(), 0, false);
5303 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5304 viewport.getAlignment().setSeqrep(repseq);
5305 ColumnSelection cs = new ColumnSelection();
5306 cs.hideInsertionsFor(repseq);
5307 viewport.setColumnSelection(cs);
5308 isAnnotation = true;
5310 else if (IdentifyFile.FeaturesFile.equals(format))
5312 if (parseFeaturesFile(file, protocol))
5314 alignPanel.paintAlignment(true);
5319 new FileLoader().LoadFile(viewport, file, protocol, format);
5326 alignPanel.adjustAnnotationHeight();
5327 viewport.updateSequenceIdColours();
5328 buildSortByAnnotationScoresMenu();
5329 alignPanel.paintAlignment(true);
5331 } catch (Exception ex)
5333 ex.printStackTrace();
5334 } catch (OutOfMemoryError oom)
5339 } catch (Exception x)
5344 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5345 : "using " + protocol + " from " + file)
5347 + (format != null ? "(parsing as '" + format
5348 + "' file)" : ""), oom, Desktop.desktop);
5353 * Method invoked by the ChangeListener on the tabbed pane, in other words
5354 * when a different tabbed pane is selected by the user or programmatically.
5357 public void tabSelectionChanged(int index)
5361 alignPanel = alignPanels.get(index);
5362 viewport = alignPanel.av;
5363 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5364 setMenusFromViewport(viewport);
5368 * If there is a frame linked to this one in a SplitPane, switch it to the
5369 * same view tab index. No infinite recursion of calls should happen, since
5370 * tabSelectionChanged() should not get invoked on setting the selected
5371 * index to an unchanged value. Guard against setting an invalid index
5372 * before the new view peer tab has been created.
5374 final AlignViewportI peer = viewport.getCodingComplement();
5377 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5378 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5380 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5386 * On right mouse click on view tab, prompt for and set new view name.
5389 public void tabbedPane_mousePressed(MouseEvent e)
5391 if (SwingUtilities.isRightMouseButton(e))
5393 String msg = MessageManager.getString("label.enter_view_name");
5394 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5395 JOptionPane.QUESTION_MESSAGE);
5399 viewport.viewName = reply;
5400 // TODO warn if reply is in getExistingViewNames()?
5401 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5406 public AlignViewport getCurrentView()
5412 * Open the dialog for regex description parsing.
5415 protected void extractScores_actionPerformed(ActionEvent e)
5417 ParseProperties pp = new jalview.analysis.ParseProperties(
5418 viewport.getAlignment());
5419 // TODO: verify regex and introduce GUI dialog for version 2.5
5420 // if (pp.getScoresFromDescription("col", "score column ",
5421 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5423 if (pp.getScoresFromDescription("description column",
5424 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5426 buildSortByAnnotationScoresMenu();
5434 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5438 protected void showDbRefs_actionPerformed(ActionEvent e)
5440 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5446 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5450 protected void showNpFeats_actionPerformed(ActionEvent e)
5452 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5456 * find the viewport amongst the tabs in this alignment frame and close that
5461 public boolean closeView(AlignViewportI av)
5465 this.closeMenuItem_actionPerformed(false);
5468 Component[] comp = tabbedPane.getComponents();
5469 for (int i = 0; comp != null && i < comp.length; i++)
5471 if (comp[i] instanceof AlignmentPanel)
5473 if (((AlignmentPanel) comp[i]).av == av)
5476 closeView((AlignmentPanel) comp[i]);
5484 protected void build_fetchdbmenu(JMenu webService)
5486 // Temporary hack - DBRef Fetcher always top level ws entry.
5487 // TODO We probably want to store a sequence database checklist in
5488 // preferences and have checkboxes.. rather than individual sources selected
5490 final JMenu rfetch = new JMenu(
5491 MessageManager.getString("action.fetch_db_references"));
5492 rfetch.setToolTipText(MessageManager
5493 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5494 webService.add(rfetch);
5496 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5497 MessageManager.getString("option.trim_retrieved_seqs"));
5498 trimrs.setToolTipText(MessageManager
5499 .getString("label.trim_retrieved_sequences"));
5500 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5501 trimrs.addActionListener(new ActionListener()
5504 public void actionPerformed(ActionEvent e)
5506 trimrs.setSelected(trimrs.isSelected());
5507 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5508 Boolean.valueOf(trimrs.isSelected()).toString());
5512 JMenuItem fetchr = new JMenuItem(
5513 MessageManager.getString("label.standard_databases"));
5514 fetchr.setToolTipText(MessageManager
5515 .getString("label.fetch_embl_uniprot"));
5516 fetchr.addActionListener(new ActionListener()
5520 public void actionPerformed(ActionEvent e)
5522 new Thread(new Runnable()
5528 boolean isNuclueotide = alignPanel.alignFrame
5529 .getViewport().getAlignment()
5531 new jalview.ws.DBRefFetcher(alignPanel.av
5532 .getSequenceSelection(),
5533 alignPanel.alignFrame, null,
5534 alignPanel.alignFrame.featureSettings,
5536 .fetchDBRefs(false);
5544 final AlignFrame me = this;
5545 new Thread(new Runnable()
5550 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5551 .getSequenceFetcherSingleton(me);
5552 javax.swing.SwingUtilities.invokeLater(new Runnable()
5557 String[] dbclasses = sf.getOrderedSupportedSources();
5558 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5559 // jalview.util.QuickSort.sort(otherdb, otherdb);
5560 List<DbSourceProxy> otherdb;
5561 JMenu dfetch = new JMenu();
5562 JMenu ifetch = new JMenu();
5563 JMenuItem fetchr = null;
5564 int comp = 0, icomp = 0, mcomp = 15;
5565 String mname = null;
5567 for (String dbclass : dbclasses)
5569 otherdb = sf.getSourceProxy(dbclass);
5570 // add a single entry for this class, or submenu allowing 'fetch
5572 if (otherdb == null || otherdb.size() < 1)
5576 // List<DbSourceProxy> dbs=otherdb;
5577 // otherdb=new ArrayList<DbSourceProxy>();
5578 // for (DbSourceProxy db:dbs)
5580 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5584 mname = "From " + dbclass;
5586 if (otherdb.size() == 1)
5588 final DbSourceProxy[] dassource = otherdb
5589 .toArray(new DbSourceProxy[0]);
5590 DbSourceProxy src = otherdb.get(0);
5591 fetchr = new JMenuItem(src.getDbSource());
5592 fetchr.addActionListener(new ActionListener()
5596 public void actionPerformed(ActionEvent e)
5598 new Thread(new Runnable()
5604 boolean isNuclueotide = alignPanel.alignFrame
5605 .getViewport().getAlignment()
5607 new jalview.ws.DBRefFetcher(alignPanel.av
5608 .getSequenceSelection(),
5609 alignPanel.alignFrame, dassource,
5610 alignPanel.alignFrame.featureSettings,
5612 .fetchDBRefs(false);
5618 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5619 MessageManager.formatMessage(
5620 "label.fetch_retrieve_from",
5621 new Object[] { src.getDbName() })));
5627 final DbSourceProxy[] dassource = otherdb
5628 .toArray(new DbSourceProxy[0]);
5630 DbSourceProxy src = otherdb.get(0);
5631 fetchr = new JMenuItem(MessageManager.formatMessage(
5632 "label.fetch_all_param",
5633 new Object[] { src.getDbSource() }));
5634 fetchr.addActionListener(new ActionListener()
5637 public void actionPerformed(ActionEvent e)
5639 new Thread(new Runnable()
5645 boolean isNuclueotide = alignPanel.alignFrame
5646 .getViewport().getAlignment()
5648 new jalview.ws.DBRefFetcher(alignPanel.av
5649 .getSequenceSelection(),
5650 alignPanel.alignFrame, dassource,
5651 alignPanel.alignFrame.featureSettings,
5653 .fetchDBRefs(false);
5659 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5660 MessageManager.formatMessage(
5661 "label.fetch_retrieve_from_all_sources",
5663 Integer.valueOf(otherdb.size())
5664 .toString(), src.getDbSource(),
5665 src.getDbName() })));
5668 // and then build the rest of the individual menus
5669 ifetch = new JMenu(MessageManager.formatMessage(
5670 "label.source_from_db_source",
5671 new Object[] { src.getDbSource() }));
5673 String imname = null;
5675 for (DbSourceProxy sproxy : otherdb)
5677 String dbname = sproxy.getDbName();
5678 String sname = dbname.length() > 5 ? dbname.substring(0,
5679 5) + "..." : dbname;
5680 String msname = dbname.length() > 10 ? dbname.substring(
5681 0, 10) + "..." : dbname;
5684 imname = MessageManager.formatMessage(
5685 "label.from_msname", new Object[] { sname });
5687 fetchr = new JMenuItem(msname);
5688 final DbSourceProxy[] dassrc = { sproxy };
5689 fetchr.addActionListener(new ActionListener()
5693 public void actionPerformed(ActionEvent e)
5695 new Thread(new Runnable()
5701 boolean isNuclueotide = alignPanel.alignFrame
5702 .getViewport().getAlignment()
5704 new jalview.ws.DBRefFetcher(alignPanel.av
5705 .getSequenceSelection(),
5706 alignPanel.alignFrame, dassrc,
5707 alignPanel.alignFrame.featureSettings,
5709 .fetchDBRefs(false);
5715 fetchr.setToolTipText("<html>"
5716 + MessageManager.formatMessage(
5717 "label.fetch_retrieve_from", new Object[]
5721 if (++icomp >= mcomp || i == (otherdb.size()))
5723 ifetch.setText(MessageManager.formatMessage(
5724 "label.source_to_target", imname, sname));
5726 ifetch = new JMenu();
5734 if (comp >= mcomp || dbi >= (dbclasses.length))
5736 dfetch.setText(MessageManager.formatMessage(
5737 "label.source_to_target", mname, dbclass));
5739 dfetch = new JMenu();
5752 * Left justify the whole alignment.
5755 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5757 AlignmentI al = viewport.getAlignment();
5759 viewport.firePropertyChange("alignment", null, al);
5763 * Right justify the whole alignment.
5766 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5768 AlignmentI al = viewport.getAlignment();
5770 viewport.firePropertyChange("alignment", null, al);
5774 public void setShowSeqFeatures(boolean b)
5776 showSeqFeatures.setSelected(b);
5777 viewport.setShowSequenceFeatures(b);
5784 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5785 * awt.event.ActionEvent)
5788 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5790 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5791 alignPanel.paintAlignment(true);
5798 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5802 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5804 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5805 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5813 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5814 * .event.ActionEvent)
5817 protected void showGroupConservation_actionPerformed(ActionEvent e)
5819 viewport.setShowGroupConservation(showGroupConservation.getState());
5820 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5827 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5828 * .event.ActionEvent)
5831 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5833 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5834 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5841 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5842 * .event.ActionEvent)
5845 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5847 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5848 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5852 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5854 showSequenceLogo.setState(true);
5855 viewport.setShowSequenceLogo(true);
5856 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5857 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5861 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5863 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5870 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5871 * .event.ActionEvent)
5874 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5876 if (avc.makeGroupsFromSelection())
5878 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5879 alignPanel.updateAnnotation();
5880 alignPanel.paintAlignment(true);
5884 public void clearAlignmentSeqRep()
5886 // TODO refactor alignmentseqrep to controller
5887 if (viewport.getAlignment().hasSeqrep())
5889 viewport.getAlignment().setSeqrep(null);
5890 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5891 alignPanel.updateAnnotation();
5892 alignPanel.paintAlignment(true);
5897 protected void createGroup_actionPerformed(ActionEvent e)
5899 if (avc.createGroup())
5901 alignPanel.alignmentChanged();
5906 protected void unGroup_actionPerformed(ActionEvent e)
5910 alignPanel.alignmentChanged();
5915 * make the given alignmentPanel the currently selected tab
5917 * @param alignmentPanel
5919 public void setDisplayedView(AlignmentPanel alignmentPanel)
5921 if (!viewport.getSequenceSetId().equals(
5922 alignmentPanel.av.getSequenceSetId()))
5926 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5928 if (tabbedPane != null
5929 && tabbedPane.getTabCount() > 0
5930 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5931 .getSelectedIndex())
5933 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5938 * Action on selection of menu options to Show or Hide annotations.
5941 * @param forSequences
5942 * update sequence-related annotations
5943 * @param forAlignment
5944 * update non-sequence-related annotations
5947 protected void setAnnotationsVisibility(boolean visible,
5948 boolean forSequences, boolean forAlignment)
5950 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5951 .getAlignmentAnnotation())
5954 * don't display non-positional annotations on an alignment
5956 if (aa.annotations == null)
5960 boolean apply = (aa.sequenceRef == null && forAlignment)
5961 || (aa.sequenceRef != null && forSequences);
5964 aa.visible = visible;
5967 alignPanel.validateAnnotationDimensions(true);
5968 alignPanel.alignmentChanged();
5972 * Store selected annotation sort order for the view and repaint.
5975 protected void sortAnnotations_actionPerformed()
5977 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5979 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5980 alignPanel.paintAlignment(true);
5985 * @return alignment panels in this alignment frame
5987 public List<? extends AlignmentViewPanel> getAlignPanels()
5989 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5993 * Open a new alignment window, with the cDNA associated with this (protein)
5994 * alignment, aligned as is the protein.
5996 protected void viewAsCdna_actionPerformed()
5998 // TODO no longer a menu action - refactor as required
5999 final AlignmentI alignment = getViewport().getAlignment();
6000 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6001 if (mappings == null)
6005 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6006 for (SequenceI aaSeq : alignment.getSequences())
6008 for (AlignedCodonFrame acf : mappings)
6010 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6014 * There is a cDNA mapping for this protein sequence - add to new
6015 * alignment. It will share the same dataset sequence as other mapped
6016 * cDNA (no new mappings need to be created).
6018 final Sequence newSeq = new Sequence(dnaSeq);
6019 newSeq.setDatasetSequence(dnaSeq);
6020 cdnaSeqs.add(newSeq);
6024 if (cdnaSeqs.size() == 0)
6026 // show a warning dialog no mapped cDNA
6029 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6031 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6032 AlignFrame.DEFAULT_HEIGHT);
6033 cdna.alignAs(alignment);
6034 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6036 Desktop.addInternalFrame(alignFrame, newtitle,
6037 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
6041 * Set visibility of dna/protein complement view (available when shown in a
6047 protected void showComplement_actionPerformed(boolean show)
6049 SplitContainerI sf = getSplitViewContainer();
6052 sf.setComplementVisible(this, show);
6057 * Generate the reverse (optionally complemented) of the selected sequences,
6058 * and add them to the alignment
6061 protected void showReverse_actionPerformed(boolean complement)
6063 AlignmentI al = null;
6066 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
6068 al = dna.reverseCdna(complement);
6069 viewport.addAlignment(al, "");
6070 } catch (Exception ex)
6072 System.err.println(ex.getMessage());
6078 class PrintThread extends Thread
6082 public PrintThread(AlignmentPanel ap)
6087 static PageFormat pf;
6092 PrinterJob printJob = PrinterJob.getPrinterJob();
6096 printJob.setPrintable(ap, pf);
6100 printJob.setPrintable(ap);
6103 if (printJob.printDialog())
6108 } catch (Exception PrintException)
6110 PrintException.printStackTrace();