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.AAFrequency;
24 import jalview.analysis.AlignmentSorter;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.analysis.CrossRef;
28 import jalview.analysis.Dna;
29 import jalview.analysis.ParseProperties;
30 import jalview.analysis.SequenceIdMatcher;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.AlignViewportI;
34 import jalview.api.AlignmentViewPanel;
35 import jalview.api.FeatureSettingsControllerI;
36 import jalview.api.SplitContainerI;
37 import jalview.api.ViewStyleI;
38 import jalview.api.analysis.ScoreModelI;
39 import jalview.bin.Cache;
40 import jalview.bin.Jalview;
41 import jalview.commands.CommandI;
42 import jalview.commands.EditCommand;
43 import jalview.commands.EditCommand.Action;
44 import jalview.commands.OrderCommand;
45 import jalview.commands.RemoveGapColCommand;
46 import jalview.commands.RemoveGapsCommand;
47 import jalview.commands.SlideSequencesCommand;
48 import jalview.commands.TrimRegionCommand;
49 import jalview.datamodel.AlignedCodonFrame;
50 import jalview.datamodel.Alignment;
51 import jalview.datamodel.AlignmentAnnotation;
52 import jalview.datamodel.AlignmentExportData;
53 import jalview.datamodel.AlignmentI;
54 import jalview.datamodel.AlignmentOrder;
55 import jalview.datamodel.AlignmentView;
56 import jalview.datamodel.ColumnSelection;
57 import jalview.datamodel.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
64 import jalview.io.AlignmentProperties;
65 import jalview.io.AnnotationFile;
66 import jalview.io.BioJsHTMLOutput;
67 import jalview.io.FileLoader;
68 import jalview.io.FormatAdapter;
69 import jalview.io.HtmlSvgOutput;
70 import jalview.io.IdentifyFile;
71 import jalview.io.JalviewFileChooser;
72 import jalview.io.JalviewFileView;
73 import jalview.io.JnetAnnotationMaker;
74 import jalview.io.NewickFile;
75 import jalview.io.TCoffeeScoreFile;
76 import jalview.jbgui.GAlignFrame;
77 import jalview.schemes.Blosum62ColourScheme;
78 import jalview.schemes.BuriedColourScheme;
79 import jalview.schemes.ClustalxColourScheme;
80 import jalview.schemes.ColourSchemeI;
81 import jalview.schemes.ColourSchemeProperty;
82 import jalview.schemes.HelixColourScheme;
83 import jalview.schemes.HydrophobicColourScheme;
84 import jalview.schemes.NucleotideColourScheme;
85 import jalview.schemes.PIDColourScheme;
86 import jalview.schemes.PurinePyrimidineColourScheme;
87 import jalview.schemes.RNAHelicesColourChooser;
88 import jalview.schemes.ResidueProperties;
89 import jalview.schemes.StrandColourScheme;
90 import jalview.schemes.TCoffeeColourScheme;
91 import jalview.schemes.TaylorColourScheme;
92 import jalview.schemes.TurnColourScheme;
93 import jalview.schemes.UserColourScheme;
94 import jalview.schemes.ZappoColourScheme;
95 import jalview.structure.StructureSelectionManager;
96 import jalview.util.MessageManager;
97 import jalview.viewmodel.AlignmentViewport;
98 import jalview.ws.jws1.Discoverer;
99 import jalview.ws.jws2.Jws2Discoverer;
100 import jalview.ws.jws2.jabaws2.Jws2Instance;
101 import jalview.ws.seqfetcher.DbSourceProxy;
103 import java.awt.BorderLayout;
104 import java.awt.Component;
105 import java.awt.Rectangle;
106 import java.awt.Toolkit;
107 import java.awt.datatransfer.Clipboard;
108 import java.awt.datatransfer.DataFlavor;
109 import java.awt.datatransfer.StringSelection;
110 import java.awt.datatransfer.Transferable;
111 import java.awt.dnd.DnDConstants;
112 import java.awt.dnd.DropTargetDragEvent;
113 import java.awt.dnd.DropTargetDropEvent;
114 import java.awt.dnd.DropTargetEvent;
115 import java.awt.dnd.DropTargetListener;
116 import java.awt.event.ActionEvent;
117 import java.awt.event.ActionListener;
118 import java.awt.event.ItemEvent;
119 import java.awt.event.ItemListener;
120 import java.awt.event.KeyAdapter;
121 import java.awt.event.KeyEvent;
122 import java.awt.event.MouseAdapter;
123 import java.awt.event.MouseEvent;
124 import java.awt.print.PageFormat;
125 import java.awt.print.PrinterJob;
126 import java.beans.PropertyChangeEvent;
129 import java.util.ArrayList;
130 import java.util.Arrays;
131 import java.util.Deque;
132 import java.util.Enumeration;
133 import java.util.Hashtable;
134 import java.util.List;
135 import java.util.Set;
136 import java.util.Vector;
138 import javax.swing.JCheckBoxMenuItem;
139 import javax.swing.JEditorPane;
140 import javax.swing.JInternalFrame;
141 import javax.swing.JLayeredPane;
142 import javax.swing.JMenu;
143 import javax.swing.JMenuItem;
144 import javax.swing.JOptionPane;
145 import javax.swing.JRadioButtonMenuItem;
146 import javax.swing.JScrollPane;
147 import javax.swing.SwingUtilities;
153 * @version $Revision$
155 public class AlignFrame extends GAlignFrame implements DropTargetListener,
156 IProgressIndicator, AlignViewControllerGuiI
159 public static final int DEFAULT_WIDTH = 700;
161 public static final int DEFAULT_HEIGHT = 500;
164 * The currently displayed panel (selected tabbed view if more than one)
166 public AlignmentPanel alignPanel;
168 AlignViewport viewport;
170 public AlignViewControllerI avc;
172 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
175 * Last format used to load or save alignments in this window
177 String currentFileFormat = null;
180 * Current filename for this alignment
182 String fileName = null;
185 * Creates a new AlignFrame object with specific width and height.
191 public AlignFrame(AlignmentI al, int width, int height)
193 this(al, null, width, height);
197 * Creates a new AlignFrame object with specific width, height and
203 * @param sequenceSetId
205 public AlignFrame(AlignmentI al, int width, int height,
206 String sequenceSetId)
208 this(al, null, width, height, sequenceSetId);
212 * Creates a new AlignFrame object with specific width, height and
218 * @param sequenceSetId
221 public AlignFrame(AlignmentI al, int width, int height,
222 String sequenceSetId, String viewId)
224 this(al, null, width, height, sequenceSetId, viewId);
228 * new alignment window with hidden columns
232 * @param hiddenColumns
233 * ColumnSelection or null
235 * Width of alignment frame
239 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
240 int width, int height)
242 this(al, hiddenColumns, width, height, null);
247 * Create alignment frame for al with hiddenColumns, a specific width and
248 * height, and specific sequenceId
251 * @param hiddenColumns
254 * @param sequenceSetId
257 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
258 int width, int height, String sequenceSetId)
260 this(al, hiddenColumns, width, height, sequenceSetId, null);
264 * Create alignment frame for al with hiddenColumns, a specific width and
265 * height, and specific sequenceId
268 * @param hiddenColumns
271 * @param sequenceSetId
276 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
277 int width, int height, String sequenceSetId, String viewId)
279 setSize(width, height);
281 if (al.getDataset() == null)
286 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
288 alignPanel = new AlignmentPanel(this, viewport);
291 addAlignmentPanel(alignPanel, true);
295 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
296 ColumnSelection hiddenColumns, int width, int height)
298 setSize(width, height);
300 if (al.getDataset() == null)
305 viewport = new AlignViewport(al, hiddenColumns);
307 if (hiddenSeqs != null && hiddenSeqs.length > 0)
309 viewport.hideSequence(hiddenSeqs);
311 alignPanel = new AlignmentPanel(this, viewport);
312 addAlignmentPanel(alignPanel, true);
318 * Make a new AlignFrame from existing alignmentPanels
325 public AlignFrame(AlignmentPanel ap)
329 addAlignmentPanel(ap, false);
334 * initalise the alignframe from the underlying viewport data and the
339 if (!Jalview.isHeadlessMode())
341 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
344 avc = new jalview.controller.AlignViewController(this, viewport,
346 if (viewport.getAlignmentConservationAnnotation() == null)
348 BLOSUM62Colour.setEnabled(false);
349 conservationMenuItem.setEnabled(false);
350 modifyConservation.setEnabled(false);
351 // PIDColour.setEnabled(false);
352 // abovePIDThreshold.setEnabled(false);
353 // modifyPID.setEnabled(false);
356 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
359 if (sortby.equals("Id"))
361 sortIDMenuItem_actionPerformed(null);
363 else if (sortby.equals("Pairwise Identity"))
365 sortPairwiseMenuItem_actionPerformed(null);
368 if (Desktop.desktop != null)
370 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
371 addServiceListeners();
372 setGUINucleotide(viewport.getAlignment().isNucleotide());
375 setMenusFromViewport(viewport);
376 buildSortByAnnotationScoresMenu();
379 if (viewport.getWrapAlignment())
381 wrapMenuItem_actionPerformed(null);
384 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
386 this.overviewMenuItem_actionPerformed(null);
391 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
392 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
393 final String menuLabel = MessageManager
394 .getString("label.copy_format_from");
395 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
396 new ViewSetProvider()
400 public AlignmentPanel[] getAllAlignmentPanels()
403 origview.add(alignPanel);
404 // make an array of all alignment panels except for this one
405 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
406 Arrays.asList(Desktop.getAlignmentPanels(null)));
407 aps.remove(AlignFrame.this.alignPanel);
408 return aps.toArray(new AlignmentPanel[aps.size()]);
410 }, selviews, new ItemListener()
414 public void itemStateChanged(ItemEvent e)
416 if (origview.size() > 0)
418 final AlignmentPanel ap = origview.get(0);
421 * Copy the ViewStyle of the selected panel to 'this one'.
422 * Don't change value of 'scaleProteinAsCdna' unless copying
425 ViewStyleI vs = selviews.get(0).getAlignViewport()
427 boolean fromSplitFrame = selviews.get(0)
428 .getAlignViewport().getCodingComplement() != null;
431 vs.setScaleProteinAsCdna(ap.getAlignViewport()
432 .getViewStyle().isScaleProteinAsCdna());
434 ap.getAlignViewport().setViewStyle(vs);
437 * Also rescale ViewStyle of SplitFrame complement if there is
438 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
439 * the whole ViewStyle (allow cDNA protein to have different
442 AlignViewportI complement = ap.getAlignViewport()
443 .getCodingComplement();
444 if (complement != null && vs.isScaleProteinAsCdna())
446 AlignFrame af = Desktop.getAlignFrameFor(complement);
447 ((SplitFrame) af.getSplitViewContainer())
449 af.setMenusForViewport();
453 ap.setSelected(true);
454 ap.alignFrame.setMenusForViewport();
459 formatMenu.add(vsel);
464 * Change the filename and format for the alignment, and enable the 'reload'
465 * button functionality.
472 public void setFileName(String file, String format)
475 setFileFormat(format);
476 reload.setEnabled(true);
480 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
483 void addKeyListener()
485 addKeyListener(new KeyAdapter()
488 public void keyPressed(KeyEvent evt)
490 if (viewport.cursorMode
491 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
492 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
493 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
494 && Character.isDigit(evt.getKeyChar()))
496 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
499 switch (evt.getKeyCode())
502 case 27: // escape key
503 deselectAllSequenceMenuItem_actionPerformed(null);
507 case KeyEvent.VK_DOWN:
508 if (evt.isAltDown() || !viewport.cursorMode)
510 moveSelectedSequences(false);
512 if (viewport.cursorMode)
514 alignPanel.getSeqPanel().moveCursor(0, 1);
519 if (evt.isAltDown() || !viewport.cursorMode)
521 moveSelectedSequences(true);
523 if (viewport.cursorMode)
525 alignPanel.getSeqPanel().moveCursor(0, -1);
530 case KeyEvent.VK_LEFT:
531 if (evt.isAltDown() || !viewport.cursorMode)
533 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
537 alignPanel.getSeqPanel().moveCursor(-1, 0);
542 case KeyEvent.VK_RIGHT:
543 if (evt.isAltDown() || !viewport.cursorMode)
545 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
549 alignPanel.getSeqPanel().moveCursor(1, 0);
553 case KeyEvent.VK_SPACE:
554 if (viewport.cursorMode)
556 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
557 || evt.isShiftDown() || evt.isAltDown());
561 // case KeyEvent.VK_A:
562 // if (viewport.cursorMode)
564 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
565 // //System.out.println("A");
569 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
570 * System.out.println("closing bracket"); } break;
572 case KeyEvent.VK_DELETE:
573 case KeyEvent.VK_BACK_SPACE:
574 if (!viewport.cursorMode)
576 cut_actionPerformed(null);
580 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
581 || evt.isShiftDown() || evt.isAltDown());
587 if (viewport.cursorMode)
589 alignPanel.getSeqPanel().setCursorRow();
593 if (viewport.cursorMode && !evt.isControlDown())
595 alignPanel.getSeqPanel().setCursorColumn();
599 if (viewport.cursorMode)
601 alignPanel.getSeqPanel().setCursorPosition();
605 case KeyEvent.VK_ENTER:
606 case KeyEvent.VK_COMMA:
607 if (viewport.cursorMode)
609 alignPanel.getSeqPanel().setCursorRowAndColumn();
614 if (viewport.cursorMode)
616 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
620 if (viewport.cursorMode)
622 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
627 viewport.cursorMode = !viewport.cursorMode;
628 statusBar.setText(MessageManager.formatMessage(
629 "label.keyboard_editing_mode", new String[]
630 { (viewport.cursorMode ? "on" : "off") }));
631 if (viewport.cursorMode)
633 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
634 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
636 alignPanel.getSeqPanel().seqCanvas.repaint();
642 Help.showHelpWindow();
643 } catch (Exception ex)
645 ex.printStackTrace();
650 boolean toggleSeqs = !evt.isControlDown();
651 boolean toggleCols = !evt.isShiftDown();
652 toggleHiddenRegions(toggleSeqs, toggleCols);
655 case KeyEvent.VK_PAGE_UP:
656 if (viewport.getWrapAlignment())
658 alignPanel.scrollUp(true);
662 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
663 - viewport.endSeq + viewport.startSeq);
666 case KeyEvent.VK_PAGE_DOWN:
667 if (viewport.getWrapAlignment())
669 alignPanel.scrollUp(false);
673 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
674 + viewport.endSeq - viewport.startSeq);
681 public void keyReleased(KeyEvent evt)
683 switch (evt.getKeyCode())
685 case KeyEvent.VK_LEFT:
686 if (evt.isAltDown() || !viewport.cursorMode)
688 viewport.firePropertyChange("alignment", null, viewport
689 .getAlignment().getSequences());
693 case KeyEvent.VK_RIGHT:
694 if (evt.isAltDown() || !viewport.cursorMode)
696 viewport.firePropertyChange("alignment", null, viewport
697 .getAlignment().getSequences());
705 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
707 ap.alignFrame = this;
708 avc = new jalview.controller.AlignViewController(this, viewport,
713 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
715 int aSize = alignPanels.size();
717 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
719 if (aSize == 1 && ap.av.viewName == null)
721 this.getContentPane().add(ap, BorderLayout.CENTER);
727 setInitialTabVisible();
730 expandViews.setEnabled(true);
731 gatherViews.setEnabled(true);
732 tabbedPane.addTab(ap.av.viewName, ap);
734 ap.setVisible(false);
739 if (ap.av.isPadGaps())
741 ap.av.getAlignment().padGaps();
743 ap.av.updateConservation(ap);
744 ap.av.updateConsensus(ap);
745 ap.av.updateStrucConsensus(ap);
749 public void setInitialTabVisible()
751 expandViews.setEnabled(true);
752 gatherViews.setEnabled(true);
753 tabbedPane.setVisible(true);
754 AlignmentPanel first = alignPanels.get(0);
755 tabbedPane.addTab(first.av.viewName, first);
756 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
759 public AlignViewport getViewport()
764 /* Set up intrinsic listeners for dynamically generated GUI bits. */
765 private void addServiceListeners()
767 final java.beans.PropertyChangeListener thisListener;
768 Desktop.instance.addJalviewPropertyChangeListener("services",
769 thisListener = new java.beans.PropertyChangeListener()
772 public void propertyChange(PropertyChangeEvent evt)
774 // // System.out.println("Discoverer property change.");
775 // if (evt.getPropertyName().equals("services"))
777 SwingUtilities.invokeLater(new Runnable()
784 .println("Rebuild WS Menu for service change");
785 BuildWebServiceMenu();
792 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
795 public void internalFrameClosed(
796 javax.swing.event.InternalFrameEvent evt)
798 System.out.println("deregistering discoverer listener");
799 Desktop.instance.removeJalviewPropertyChangeListener("services",
801 closeMenuItem_actionPerformed(true);
804 // Finally, build the menu once to get current service state
805 new Thread(new Runnable()
810 BuildWebServiceMenu();
816 * Configure menu items that vary according to whether the alignment is
817 * nucleotide or protein
821 public void setGUINucleotide(boolean nucleotide)
823 showTranslation.setVisible(nucleotide);
824 conservationMenuItem.setEnabled(!nucleotide);
825 modifyConservation.setEnabled(!nucleotide);
826 showGroupConservation.setEnabled(!nucleotide);
827 rnahelicesColour.setEnabled(nucleotide);
828 purinePyrimidineColour.setEnabled(nucleotide);
829 showComplementMenuItem.setText(MessageManager
830 .getString(nucleotide ? "label.protein" : "label.nucleotide"));
831 setColourSelected(jalview.bin.Cache.getDefault(
832 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
833 : Preferences.DEFAULT_COLOUR_PROT, "None"));
837 * set up menus for the current viewport. This may be called after any
838 * operation that affects the data in the current view (selection changed,
839 * etc) to update the menus to reflect the new state.
841 public void setMenusForViewport()
843 setMenusFromViewport(viewport);
847 * Need to call this method when tabs are selected for multiple views, or when
848 * loading from Jalview2XML.java
853 void setMenusFromViewport(AlignViewport av)
855 padGapsMenuitem.setSelected(av.isPadGaps());
856 colourTextMenuItem.setSelected(av.isShowColourText());
857 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
858 conservationMenuItem.setSelected(av.getConservationSelected());
859 seqLimits.setSelected(av.getShowJVSuffix());
860 idRightAlign.setSelected(av.isRightAlignIds());
861 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
862 renderGapsMenuItem.setSelected(av.isRenderGaps());
863 wrapMenuItem.setSelected(av.getWrapAlignment());
864 scaleAbove.setVisible(av.getWrapAlignment());
865 scaleLeft.setVisible(av.getWrapAlignment());
866 scaleRight.setVisible(av.getWrapAlignment());
867 annotationPanelMenuItem.setState(av.isShowAnnotation());
869 * Show/hide annotations only enabled if annotation panel is shown
871 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
872 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
873 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
874 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
875 viewBoxesMenuItem.setSelected(av.getShowBoxes());
876 viewTextMenuItem.setSelected(av.getShowText());
877 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
878 showGroupConsensus.setSelected(av.isShowGroupConsensus());
879 showGroupConservation.setSelected(av.isShowGroupConservation());
880 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
881 showSequenceLogo.setSelected(av.isShowSequenceLogo());
882 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
884 setColourSelected(ColourSchemeProperty.getColourName(av
885 .getGlobalColourScheme()));
887 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
888 hiddenMarkers.setState(av.getShowHiddenMarkers());
889 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
890 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
891 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
892 autoCalculate.setSelected(av.autoCalculateConsensus);
893 sortByTree.setSelected(av.sortByTree);
894 listenToViewSelections.setSelected(av.followSelection);
895 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
897 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
898 setShowProductsEnabled();
902 private IProgressIndicator progressBar;
907 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
910 public void setProgressBar(String message, long id)
912 progressBar.setProgressBar(message, id);
916 public void registerHandler(final long id,
917 final IProgressIndicatorHandler handler)
919 progressBar.registerHandler(id, handler);
924 * @return true if any progress bars are still active
927 public boolean operationInProgress()
929 return progressBar.operationInProgress();
933 public void setStatus(String text)
935 statusBar.setText(text);
939 * Added so Castor Mapping file can obtain Jalview Version
941 public String getVersion()
943 return jalview.bin.Cache.getProperty("VERSION");
946 public FeatureRenderer getFeatureRenderer()
948 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
952 public void fetchSequence_actionPerformed(ActionEvent e)
954 new SequenceFetcher(this);
958 public void addFromFile_actionPerformed(ActionEvent e)
960 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
964 public void reload_actionPerformed(ActionEvent e)
966 if (fileName != null)
968 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
969 // originating file's format
970 // TODO: work out how to recover feature settings for correct view(s) when
972 if (currentFileFormat.equals("Jalview"))
974 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
975 for (int i = 0; i < frames.length; i++)
977 if (frames[i] instanceof AlignFrame && frames[i] != this
978 && ((AlignFrame) frames[i]).fileName != null
979 && ((AlignFrame) frames[i]).fileName.equals(fileName))
983 frames[i].setSelected(true);
984 Desktop.instance.closeAssociatedWindows();
985 } catch (java.beans.PropertyVetoException ex)
991 Desktop.instance.closeAssociatedWindows();
993 FileLoader loader = new FileLoader();
994 String protocol = fileName.startsWith("http:") ? "URL" : "File";
995 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
999 Rectangle bounds = this.getBounds();
1001 FileLoader loader = new FileLoader();
1002 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1003 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1004 protocol, currentFileFormat);
1006 newframe.setBounds(bounds);
1007 if (featureSettings != null && featureSettings.isShowing())
1009 final Rectangle fspos = featureSettings.frame.getBounds();
1010 // TODO: need a 'show feature settings' function that takes bounds -
1011 // need to refactor Desktop.addFrame
1012 newframe.featureSettings_actionPerformed(null);
1013 final FeatureSettings nfs = newframe.featureSettings;
1014 SwingUtilities.invokeLater(new Runnable()
1019 nfs.frame.setBounds(fspos);
1022 this.featureSettings.close();
1023 this.featureSettings = null;
1025 this.closeMenuItem_actionPerformed(true);
1031 public void addFromText_actionPerformed(ActionEvent e)
1033 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
1037 public void addFromURL_actionPerformed(ActionEvent e)
1039 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1043 public void save_actionPerformed(ActionEvent e)
1045 if (fileName == null
1046 || (currentFileFormat == null || !jalview.io.FormatAdapter
1047 .isValidIOFormat(currentFileFormat, true))
1048 || fileName.startsWith("http"))
1050 saveAs_actionPerformed(null);
1054 saveAlignment(fileName, currentFileFormat);
1065 public void saveAs_actionPerformed(ActionEvent e)
1067 JalviewFileChooser chooser = new JalviewFileChooser(
1068 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1069 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1070 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1071 currentFileFormat, false);
1073 chooser.setFileView(new JalviewFileView());
1074 chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1075 chooser.setToolTipText(MessageManager.getString("action.save"));
1077 int value = chooser.showSaveDialog(this);
1079 if (value == JalviewFileChooser.APPROVE_OPTION)
1081 currentFileFormat = chooser.getSelectedFormat();
1082 while (currentFileFormat == null)
1085 .showInternalMessageDialog(
1088 .getString("label.select_file_format_before_saving"),
1090 .getString("label.file_format_not_specified"),
1091 JOptionPane.WARNING_MESSAGE);
1092 currentFileFormat = chooser.getSelectedFormat();
1093 value = chooser.showSaveDialog(this);
1094 if (value != JalviewFileChooser.APPROVE_OPTION)
1100 fileName = chooser.getSelectedFile().getPath();
1102 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1105 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1106 if (currentFileFormat.indexOf(" ") > -1)
1108 currentFileFormat = currentFileFormat.substring(0,
1109 currentFileFormat.indexOf(" "));
1111 saveAlignment(fileName, currentFileFormat);
1115 public boolean saveAlignment(String file, String format)
1117 boolean success = true;
1119 if (format.equalsIgnoreCase("Jalview"))
1121 String shortName = title;
1123 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1125 shortName = shortName.substring(shortName
1126 .lastIndexOf(java.io.File.separatorChar) + 1);
1129 success = new Jalview2XML().saveAlignment(this, file, shortName);
1131 statusBar.setText(MessageManager.formatMessage(
1132 "label.successfully_saved_to_file_in_format", new Object[]
1133 { fileName, format }));
1138 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1140 warningMessage("Cannot save file " + fileName + " using format "
1141 + format, "Alignment output format not supported");
1142 if (!Jalview.isHeadlessMode())
1144 saveAs_actionPerformed(null);
1149 AlignmentExportData exportData = getAlignmentForExport(format, viewport);
1150 if (exportData.getSettings().isCancelled())
1154 FormatAdapter f = new FormatAdapter(alignPanel,
1155 exportData.getSettings());
1156 String output = f.formatSequences(format,
1157 exportData.getAlignment(), // class cast exceptions will
1158 // occur in the distant future
1159 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1160 f.getCacheSuffixDefault(format),
1161 viewport.getColumnSelection());
1171 java.io.PrintWriter out = new java.io.PrintWriter(
1172 new java.io.FileWriter(file));
1176 this.setTitle(file);
1177 statusBar.setText(MessageManager.formatMessage(
1178 "label.successfully_saved_to_file_in_format",
1180 { fileName, format }));
1181 } catch (Exception ex)
1184 ex.printStackTrace();
1191 JOptionPane.showInternalMessageDialog(this, MessageManager
1192 .formatMessage("label.couldnt_save_file", new Object[]
1193 { fileName }), MessageManager
1194 .getString("label.error_saving_file"),
1195 JOptionPane.WARNING_MESSAGE);
1202 private void warningMessage(String warning, String title)
1204 if (new jalview.util.Platform().isHeadless())
1206 System.err.println("Warning: " + title + "\nWarning: " + warning);
1211 JOptionPane.showInternalMessageDialog(this, warning, title,
1212 JOptionPane.WARNING_MESSAGE);
1224 protected void outputText_actionPerformed(ActionEvent e)
1227 AlignmentExportData exportData = getAlignmentForExport(
1228 e.getActionCommand(), viewport);
1229 if (exportData.getSettings().isCancelled())
1233 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1234 cap.setForInput(null);
1237 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1239 e.getActionCommand(),
1240 exportData.getAlignment(),
1241 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1242 viewport.getColumnSelection()));
1243 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1244 "label.alignment_output_command", new Object[]
1245 { e.getActionCommand() }), 600, 500);
1246 } catch (OutOfMemoryError oom)
1248 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1254 public static AlignmentExportData getAlignmentForExport(String exportFomat,
1255 AlignViewportI viewport)
1257 AlignmentI alignmentToExport = null;
1258 String[] omitHidden = null;
1259 int[] alignmentStartEnd = new int[2];
1261 HiddenSequences hiddenSeqs = viewport.getAlignment()
1262 .getHiddenSequences();
1265 alignmentToExport = viewport.getAlignment();
1266 alignmentStartEnd = new int[]
1267 { 0, alignmentToExport.getWidth() - 1 };
1269 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1270 AlignExportSettings settings = new AlignExportSettings(hasHiddenSeqs,
1271 viewport.hasHiddenColumns(), exportFomat);
1272 settings.isExportAnnotations();
1274 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1276 omitHidden = viewport.getViewAsString(false);
1279 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1281 alignmentToExport = hiddenSeqs.getFullAlignment();
1285 alignmentToExport = viewport.getAlignment();
1286 alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1287 .getColumnSelection().getHiddenColumns());
1289 AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd,
1294 public static int[] getStartEnd(int[] aligmentStartEnd,
1295 List<int[]> hiddenCols)
1297 int startPos = aligmentStartEnd[0];
1298 int endPos = aligmentStartEnd[1];
1300 int[] lowestRange = new int[2];
1301 int[] higestRange = new int[2];
1303 for (int[] hiddenCol : hiddenCols)
1305 // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
1306 lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1307 higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1309 // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
1310 // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
1312 if (lowestRange[0] == 0 && lowestRange[1] == 0)
1314 startPos = aligmentStartEnd[0];
1318 startPos = lowestRange[1] + 1;
1321 if (higestRange[0] == 0 && higestRange[1] == 0)
1323 endPos = aligmentStartEnd[1];
1327 endPos = higestRange[0];
1330 // System.out.println("Export range : " + minPos + " - " + maxPos);
1332 { startPos, endPos };
1335 public static void main(String[] args)
1337 ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1338 hiddenCols.add(new int[]
1340 hiddenCols.add(new int[]
1342 hiddenCols.add(new int[]
1344 hiddenCols.add(new int[]
1346 hiddenCols.add(new int[]
1349 int[] x = getStartEnd(new int[]
1350 { 0, 50 }, hiddenCols);
1351 // System.out.println("Export range : " + x[0] + " - " + x[1]);
1361 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1363 new HtmlSvgOutput(null, alignPanel);
1367 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1369 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1370 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1372 public void createImageMap(File file, String image)
1374 alignPanel.makePNGImageMap(file, image);
1384 public void createPNG(File f)
1386 alignPanel.makePNG(f);
1396 public void createEPS(File f)
1398 alignPanel.makeEPS(f);
1401 public void createSVG(File f)
1403 alignPanel.makeSVG(f);
1406 public void pageSetup_actionPerformed(ActionEvent e)
1408 PrinterJob printJob = PrinterJob.getPrinterJob();
1409 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1419 public void printMenuItem_actionPerformed(ActionEvent e)
1421 // Putting in a thread avoids Swing painting problems
1422 PrintThread thread = new PrintThread(alignPanel);
1427 public void exportFeatures_actionPerformed(ActionEvent e)
1429 new AnnotationExporter().exportFeatures(alignPanel);
1433 public void exportAnnotations_actionPerformed(ActionEvent e)
1435 new AnnotationExporter().exportAnnotations(alignPanel);
1439 public void associatedData_actionPerformed(ActionEvent e)
1441 // Pick the tree file
1442 JalviewFileChooser chooser = new JalviewFileChooser(
1443 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1444 chooser.setFileView(new JalviewFileView());
1445 chooser.setDialogTitle(MessageManager
1446 .getString("label.load_jalview_annotations"));
1447 chooser.setToolTipText(MessageManager
1448 .getString("label.load_jalview_annotations"));
1450 int value = chooser.showOpenDialog(null);
1452 if (value == JalviewFileChooser.APPROVE_OPTION)
1454 String choice = chooser.getSelectedFile().getPath();
1455 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1456 loadJalviewDataFile(choice, null, null, null);
1462 * Close the current view or all views in the alignment frame. If the frame
1463 * only contains one view then the alignment will be removed from memory.
1465 * @param closeAllTabs
1468 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1470 if (alignPanels != null && alignPanels.size() < 2)
1472 closeAllTabs = true;
1477 if (alignPanels != null)
1481 if (this.isClosed())
1483 // really close all the windows - otherwise wait till
1484 // setClosed(true) is called
1485 for (int i = 0; i < alignPanels.size(); i++)
1487 AlignmentPanel ap = alignPanels.get(i);
1494 closeView(alignPanel);
1500 this.setClosed(true);
1502 } catch (Exception ex)
1504 ex.printStackTrace();
1509 * Close the specified panel and close up tabs appropriately.
1511 * @param panelToClose
1513 public void closeView(AlignmentPanel panelToClose)
1515 int index = tabbedPane.getSelectedIndex();
1516 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1517 alignPanels.remove(panelToClose);
1518 panelToClose.closePanel();
1519 panelToClose = null;
1521 tabbedPane.removeTabAt(closedindex);
1522 tabbedPane.validate();
1524 if (index > closedindex || index == tabbedPane.getTabCount())
1526 // modify currently selected tab index if necessary.
1530 this.tabSelectionChanged(index);
1536 void updateEditMenuBar()
1539 if (viewport.getHistoryList().size() > 0)
1541 undoMenuItem.setEnabled(true);
1542 CommandI command = viewport.getHistoryList().peek();
1543 undoMenuItem.setText(MessageManager.formatMessage(
1544 "label.undo_command", new Object[]
1545 { command.getDescription() }));
1549 undoMenuItem.setEnabled(false);
1550 undoMenuItem.setText(MessageManager.getString("action.undo"));
1553 if (viewport.getRedoList().size() > 0)
1555 redoMenuItem.setEnabled(true);
1557 CommandI command = viewport.getRedoList().peek();
1558 redoMenuItem.setText(MessageManager.formatMessage(
1559 "label.redo_command", new Object[]
1560 { command.getDescription() }));
1564 redoMenuItem.setEnabled(false);
1565 redoMenuItem.setText(MessageManager.getString("action.redo"));
1569 public void addHistoryItem(CommandI command)
1571 if (command.getSize() > 0)
1573 viewport.addToHistoryList(command);
1574 viewport.clearRedoList();
1575 updateEditMenuBar();
1576 viewport.updateHiddenColumns();
1577 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1578 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1579 // viewport.getColumnSelection()
1580 // .getHiddenColumns().size() > 0);
1586 * @return alignment objects for all views
1588 AlignmentI[] getViewAlignments()
1590 if (alignPanels != null)
1592 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1594 for (AlignmentPanel ap : alignPanels)
1596 als[i++] = ap.av.getAlignment();
1600 if (viewport != null)
1602 return new AlignmentI[]
1603 { viewport.getAlignment() };
1615 protected void undoMenuItem_actionPerformed(ActionEvent e)
1617 if (viewport.getHistoryList().isEmpty())
1621 CommandI command = viewport.getHistoryList().pop();
1622 viewport.addToRedoList(command);
1623 command.undoCommand(getViewAlignments());
1625 AlignmentViewport originalSource = getOriginatingSource(command);
1626 updateEditMenuBar();
1628 if (originalSource != null)
1630 if (originalSource != viewport)
1633 .warn("Implementation worry: mismatch of viewport origin for undo");
1635 originalSource.updateHiddenColumns();
1636 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1638 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1639 // viewport.getColumnSelection()
1640 // .getHiddenColumns().size() > 0);
1641 originalSource.firePropertyChange("alignment", null, originalSource
1642 .getAlignment().getSequences());
1653 protected void redoMenuItem_actionPerformed(ActionEvent e)
1655 if (viewport.getRedoList().size() < 1)
1660 CommandI command = viewport.getRedoList().pop();
1661 viewport.addToHistoryList(command);
1662 command.doCommand(getViewAlignments());
1664 AlignmentViewport originalSource = getOriginatingSource(command);
1665 updateEditMenuBar();
1667 if (originalSource != null)
1670 if (originalSource != viewport)
1673 .warn("Implementation worry: mismatch of viewport origin for redo");
1675 originalSource.updateHiddenColumns();
1676 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1678 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1679 // viewport.getColumnSelection()
1680 // .getHiddenColumns().size() > 0);
1681 originalSource.firePropertyChange("alignment", null, originalSource
1682 .getAlignment().getSequences());
1686 AlignmentViewport getOriginatingSource(CommandI command)
1688 AlignmentViewport originalSource = null;
1689 // For sequence removal and addition, we need to fire
1690 // the property change event FROM the viewport where the
1691 // original alignment was altered
1692 AlignmentI al = null;
1693 if (command instanceof EditCommand)
1695 EditCommand editCommand = (EditCommand) command;
1696 al = editCommand.getAlignment();
1697 List<Component> comps = PaintRefresher.components.get(viewport
1698 .getSequenceSetId());
1700 for (Component comp : comps)
1702 if (comp instanceof AlignmentPanel)
1704 if (al == ((AlignmentPanel) comp).av.getAlignment())
1706 originalSource = ((AlignmentPanel) comp).av;
1713 if (originalSource == null)
1715 // The original view is closed, we must validate
1716 // the current view against the closed view first
1719 PaintRefresher.validateSequences(al, viewport.getAlignment());
1722 originalSource = viewport;
1725 return originalSource;
1734 public void moveSelectedSequences(boolean up)
1736 SequenceGroup sg = viewport.getSelectionGroup();
1742 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1743 viewport.getHiddenRepSequences(), up);
1744 alignPanel.paintAlignment(true);
1747 synchronized void slideSequences(boolean right, int size)
1749 List<SequenceI> sg = new ArrayList<SequenceI>();
1750 if (viewport.cursorMode)
1752 sg.add(viewport.getAlignment().getSequenceAt(
1753 alignPanel.getSeqPanel().seqCanvas.cursorY));
1755 else if (viewport.getSelectionGroup() != null
1756 && viewport.getSelectionGroup().getSize() != viewport
1757 .getAlignment().getHeight())
1759 sg = viewport.getSelectionGroup().getSequences(
1760 viewport.getHiddenRepSequences());
1768 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1770 for (SequenceI seq : viewport.getAlignment().getSequences())
1772 if (!sg.contains(seq))
1774 invertGroup.add(seq);
1778 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1780 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1781 for (int i = 0; i < invertGroup.size(); i++)
1783 seqs2[i] = invertGroup.get(i);
1786 SlideSequencesCommand ssc;
1789 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1790 size, viewport.getGapCharacter());
1794 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1795 size, viewport.getGapCharacter());
1798 int groupAdjustment = 0;
1799 if (ssc.getGapsInsertedBegin() && right)
1801 if (viewport.cursorMode)
1803 alignPanel.getSeqPanel().moveCursor(size, 0);
1807 groupAdjustment = size;
1810 else if (!ssc.getGapsInsertedBegin() && !right)
1812 if (viewport.cursorMode)
1814 alignPanel.getSeqPanel().moveCursor(-size, 0);
1818 groupAdjustment = -size;
1822 if (groupAdjustment != 0)
1824 viewport.getSelectionGroup().setStartRes(
1825 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1826 viewport.getSelectionGroup().setEndRes(
1827 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1831 * just extend the last slide command if compatible; but not if in
1832 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1834 boolean appendHistoryItem = false;
1835 Deque<CommandI> historyList = viewport.getHistoryList();
1836 boolean inSplitFrame = getSplitViewContainer() != null;
1837 if (!inSplitFrame && historyList != null
1838 && historyList.size() > 0
1839 && historyList.peek() instanceof SlideSequencesCommand)
1841 appendHistoryItem = ssc
1842 .appendSlideCommand((SlideSequencesCommand) historyList
1846 if (!appendHistoryItem)
1848 addHistoryItem(ssc);
1861 protected void copy_actionPerformed(ActionEvent e)
1864 if (viewport.getSelectionGroup() == null)
1868 // TODO: preserve the ordering of displayed alignment annotation in any
1869 // internal paste (particularly sequence associated annotation)
1870 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1871 String[] omitHidden = null;
1873 if (viewport.hasHiddenColumns())
1875 omitHidden = viewport.getViewAsString(true);
1878 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1881 StringSelection ss = new StringSelection(output);
1885 jalview.gui.Desktop.internalCopy = true;
1886 // Its really worth setting the clipboard contents
1887 // to empty before setting the large StringSelection!!
1888 Toolkit.getDefaultToolkit().getSystemClipboard()
1889 .setContents(new StringSelection(""), null);
1891 Toolkit.getDefaultToolkit().getSystemClipboard()
1892 .setContents(ss, Desktop.instance);
1893 } catch (OutOfMemoryError er)
1895 new OOMWarning("copying region", er);
1899 ArrayList<int[]> hiddenColumns = null;
1900 if (viewport.hasHiddenColumns())
1902 hiddenColumns = new ArrayList<int[]>();
1903 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1904 .getSelectionGroup().getEndRes();
1905 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1907 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1909 hiddenColumns.add(new int[]
1910 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1915 Desktop.jalviewClipboard = new Object[]
1916 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1917 statusBar.setText(MessageManager.formatMessage(
1918 "label.copied_sequences_to_clipboard", new Object[]
1919 { Integer.valueOf(seqs.length).toString() }));
1929 protected void pasteNew_actionPerformed(ActionEvent e)
1941 protected void pasteThis_actionPerformed(ActionEvent e)
1947 * Paste contents of Jalview clipboard
1949 * @param newAlignment
1950 * true to paste to a new alignment, otherwise add to this.
1952 void paste(boolean newAlignment)
1954 boolean externalPaste = true;
1957 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1958 Transferable contents = c.getContents(this);
1960 if (contents == null)
1968 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1969 if (str.length() < 1)
1974 format = new IdentifyFile().Identify(str, "Paste");
1976 } catch (OutOfMemoryError er)
1978 new OOMWarning("Out of memory pasting sequences!!", er);
1982 SequenceI[] sequences;
1983 boolean annotationAdded = false;
1984 AlignmentI alignment = null;
1986 if (Desktop.jalviewClipboard != null)
1988 // The clipboard was filled from within Jalview, we must use the
1990 // And dataset from the copied alignment
1991 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1992 // be doubly sure that we create *new* sequence objects.
1993 sequences = new SequenceI[newseq.length];
1994 for (int i = 0; i < newseq.length; i++)
1996 sequences[i] = new Sequence(newseq[i]);
1998 alignment = new Alignment(sequences);
1999 externalPaste = false;
2003 // parse the clipboard as an alignment.
2004 alignment = new FormatAdapter().readFile(str, "Paste", format);
2005 sequences = alignment.getSequencesArray();
2009 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2015 if (Desktop.jalviewClipboard != null)
2017 // dataset is inherited
2018 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2022 // new dataset is constructed
2023 alignment.setDataset(null);
2025 alwidth = alignment.getWidth() + 1;
2029 AlignmentI pastedal = alignment; // preserve pasted alignment object
2030 // Add pasted sequences and dataset into existing alignment.
2031 alignment = viewport.getAlignment();
2032 alwidth = alignment.getWidth() + 1;
2033 // decide if we need to import sequences from an existing dataset
2034 boolean importDs = Desktop.jalviewClipboard != null
2035 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2036 // importDs==true instructs us to copy over new dataset sequences from
2037 // an existing alignment
2038 Vector newDs = (importDs) ? new Vector() : null; // used to create
2039 // minimum dataset set
2041 for (int i = 0; i < sequences.length; i++)
2045 newDs.addElement(null);
2047 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2049 if (importDs && ds != null)
2051 if (!newDs.contains(ds))
2053 newDs.setElementAt(ds, i);
2054 ds = new Sequence(ds);
2055 // update with new dataset sequence
2056 sequences[i].setDatasetSequence(ds);
2060 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2065 // copy and derive new dataset sequence
2066 sequences[i] = sequences[i].deriveSequence();
2067 alignment.getDataset().addSequence(
2068 sequences[i].getDatasetSequence());
2069 // TODO: avoid creation of duplicate dataset sequences with a
2070 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2072 alignment.addSequence(sequences[i]); // merges dataset
2076 newDs.clear(); // tidy up
2078 if (alignment.getAlignmentAnnotation() != null)
2080 for (AlignmentAnnotation alan : alignment
2081 .getAlignmentAnnotation())
2083 if (alan.graphGroup > fgroup)
2085 fgroup = alan.graphGroup;
2089 if (pastedal.getAlignmentAnnotation() != null)
2091 // Add any annotation attached to alignment.
2092 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2093 for (int i = 0; i < alann.length; i++)
2095 annotationAdded = true;
2096 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2098 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2099 if (newann.graphGroup > -1)
2101 if (newGraphGroups.size() <= newann.graphGroup
2102 || newGraphGroups.get(newann.graphGroup) == null)
2104 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2106 newGraphGroups.add(q, null);
2108 newGraphGroups.set(newann.graphGroup, new Integer(
2111 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2115 newann.padAnnotation(alwidth);
2116 alignment.addAnnotation(newann);
2126 addHistoryItem(new EditCommand(
2127 MessageManager.getString("label.add_sequences"),
2129 sequences, 0, alignment.getWidth(), alignment));
2131 // Add any annotations attached to sequences
2132 for (int i = 0; i < sequences.length; i++)
2134 if (sequences[i].getAnnotation() != null)
2136 AlignmentAnnotation newann;
2137 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2139 annotationAdded = true;
2140 newann = sequences[i].getAnnotation()[a];
2141 newann.adjustForAlignment();
2142 newann.padAnnotation(alwidth);
2143 if (newann.graphGroup > -1)
2145 if (newann.graphGroup > -1)
2147 if (newGraphGroups.size() <= newann.graphGroup
2148 || newGraphGroups.get(newann.graphGroup) == null)
2150 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2152 newGraphGroups.add(q, null);
2154 newGraphGroups.set(newann.graphGroup, new Integer(
2157 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2161 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2166 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2173 // propagate alignment changed.
2174 viewport.setEndSeq(alignment.getHeight());
2175 if (annotationAdded)
2177 // Duplicate sequence annotation in all views.
2178 AlignmentI[] alview = this.getViewAlignments();
2179 for (int i = 0; i < sequences.length; i++)
2181 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2186 for (int avnum = 0; avnum < alview.length; avnum++)
2188 if (alview[avnum] != alignment)
2190 // duplicate in a view other than the one with input focus
2191 int avwidth = alview[avnum].getWidth() + 1;
2192 // this relies on sann being preserved after we
2193 // modify the sequence's annotation array for each duplication
2194 for (int a = 0; a < sann.length; a++)
2196 AlignmentAnnotation newann = new AlignmentAnnotation(
2198 sequences[i].addAlignmentAnnotation(newann);
2199 newann.padAnnotation(avwidth);
2200 alview[avnum].addAnnotation(newann); // annotation was
2201 // duplicated earlier
2202 // TODO JAL-1145 graphGroups are not updated for sequence
2203 // annotation added to several views. This may cause
2205 alview[avnum].setAnnotationIndex(newann, a);
2210 buildSortByAnnotationScoresMenu();
2212 viewport.firePropertyChange("alignment", null,
2213 alignment.getSequences());
2214 if (alignPanels != null)
2216 for (AlignmentPanel ap : alignPanels)
2218 ap.validateAnnotationDimensions(false);
2223 alignPanel.validateAnnotationDimensions(false);
2229 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2231 String newtitle = new String("Copied sequences");
2233 if (Desktop.jalviewClipboard != null
2234 && Desktop.jalviewClipboard[2] != null)
2236 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2237 for (int[] region : hc)
2239 af.viewport.hideColumns(region[0], region[1]);
2243 // >>>This is a fix for the moment, until a better solution is
2245 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2247 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2249 // TODO: maintain provenance of an alignment, rather than just make the
2250 // title a concatenation of operations.
2253 if (title.startsWith("Copied sequences"))
2259 newtitle = newtitle.concat("- from " + title);
2264 newtitle = new String("Pasted sequences");
2267 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2272 } catch (Exception ex)
2274 ex.printStackTrace();
2275 System.out.println("Exception whilst pasting: " + ex);
2276 // could be anything being pasted in here
2282 protected void expand_newalign(ActionEvent e)
2286 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2287 .getAlignment(), -1);
2288 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2290 String newtitle = new String("Flanking alignment");
2292 if (Desktop.jalviewClipboard != null
2293 && Desktop.jalviewClipboard[2] != null)
2295 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2296 for (int region[] : hc)
2298 af.viewport.hideColumns(region[0], region[1]);
2302 // >>>This is a fix for the moment, until a better solution is
2304 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2306 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2308 // TODO: maintain provenance of an alignment, rather than just make the
2309 // title a concatenation of operations.
2311 if (title.startsWith("Copied sequences"))
2317 newtitle = newtitle.concat("- from " + title);
2321 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2323 } catch (Exception ex)
2325 ex.printStackTrace();
2326 System.out.println("Exception whilst pasting: " + ex);
2327 // could be anything being pasted in here
2328 } catch (OutOfMemoryError oom)
2330 new OOMWarning("Viewing flanking region of alignment", oom);
2341 protected void cut_actionPerformed(ActionEvent e)
2343 copy_actionPerformed(null);
2344 delete_actionPerformed(null);
2354 protected void delete_actionPerformed(ActionEvent evt)
2357 SequenceGroup sg = viewport.getSelectionGroup();
2364 * If the cut affects all sequences, warn, remove highlighted columns
2366 if (sg.getSize() == viewport.getAlignment().getHeight())
2368 int confirm = JOptionPane.showConfirmDialog(this,
2369 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2370 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2371 JOptionPane.OK_CANCEL_OPTION);
2373 if (confirm == JOptionPane.CANCEL_OPTION
2374 || confirm == JOptionPane.CLOSED_OPTION)
2378 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2379 sg.getEndRes() + 1);
2382 SequenceI[] cut = sg.getSequences()
2383 .toArray(new SequenceI[sg.getSize()]);
2385 addHistoryItem(new EditCommand(
2386 MessageManager.getString("label.cut_sequences"), Action.CUT,
2387 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2388 viewport.getAlignment()));
2390 viewport.setSelectionGroup(null);
2391 viewport.sendSelection();
2392 viewport.getAlignment().deleteGroup(sg);
2394 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2396 if (viewport.getAlignment().getHeight() < 1)
2400 this.setClosed(true);
2401 } catch (Exception ex)
2414 protected void deleteGroups_actionPerformed(ActionEvent e)
2416 if (avc.deleteGroups())
2418 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2419 alignPanel.updateAnnotation();
2420 alignPanel.paintAlignment(true);
2431 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2433 SequenceGroup sg = new SequenceGroup();
2435 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2437 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2440 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2441 viewport.setSelectionGroup(sg);
2442 viewport.sendSelection();
2443 alignPanel.paintAlignment(true);
2444 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2454 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2456 if (viewport.cursorMode)
2458 alignPanel.getSeqPanel().keyboardNo1 = null;
2459 alignPanel.getSeqPanel().keyboardNo2 = null;
2461 viewport.setSelectionGroup(null);
2462 viewport.getColumnSelection().clear();
2463 viewport.setSelectionGroup(null);
2464 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2465 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2466 alignPanel.paintAlignment(true);
2467 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2468 viewport.sendSelection();
2478 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2480 SequenceGroup sg = viewport.getSelectionGroup();
2484 selectAllSequenceMenuItem_actionPerformed(null);
2489 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2491 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2494 alignPanel.paintAlignment(true);
2495 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2496 viewport.sendSelection();
2500 public void invertColSel_actionPerformed(ActionEvent e)
2502 viewport.invertColumnSelection();
2503 alignPanel.paintAlignment(true);
2504 viewport.sendSelection();
2514 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2516 trimAlignment(true);
2526 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2528 trimAlignment(false);
2531 void trimAlignment(boolean trimLeft)
2533 ColumnSelection colSel = viewport.getColumnSelection();
2536 if (colSel.size() > 0)
2540 column = colSel.getMin();
2544 column = colSel.getMax();
2548 if (viewport.getSelectionGroup() != null)
2550 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2551 viewport.getHiddenRepSequences());
2555 seqs = viewport.getAlignment().getSequencesArray();
2558 TrimRegionCommand trimRegion;
2561 trimRegion = new TrimRegionCommand("Remove Left",
2562 TrimRegionCommand.TRIM_LEFT, seqs, column,
2563 viewport.getAlignment(), viewport.getColumnSelection(),
2564 viewport.getSelectionGroup());
2565 viewport.setStartRes(0);
2569 trimRegion = new TrimRegionCommand("Remove Right",
2570 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2571 viewport.getAlignment(), viewport.getColumnSelection(),
2572 viewport.getSelectionGroup());
2575 statusBar.setText(MessageManager.formatMessage(
2576 "label.removed_columns", new String[]
2577 { Integer.valueOf(trimRegion.getSize()).toString() }));
2579 addHistoryItem(trimRegion);
2581 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2583 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2584 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2586 viewport.getAlignment().deleteGroup(sg);
2590 viewport.firePropertyChange("alignment", null, viewport
2591 .getAlignment().getSequences());
2602 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2604 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2607 if (viewport.getSelectionGroup() != null)
2609 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2610 viewport.getHiddenRepSequences());
2611 start = viewport.getSelectionGroup().getStartRes();
2612 end = viewport.getSelectionGroup().getEndRes();
2616 seqs = viewport.getAlignment().getSequencesArray();
2619 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2620 "Remove Gapped Columns", seqs, start, end,
2621 viewport.getAlignment());
2623 addHistoryItem(removeGapCols);
2625 statusBar.setText(MessageManager.formatMessage(
2626 "label.removed_empty_columns", new Object[]
2627 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2629 // This is to maintain viewport position on first residue
2630 // of first sequence
2631 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2632 int startRes = seq.findPosition(viewport.startRes);
2633 // ShiftList shifts;
2634 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2635 // edit.alColumnChanges=shifts.getInverse();
2636 // if (viewport.hasHiddenColumns)
2637 // viewport.getColumnSelection().compensateForEdits(shifts);
2638 viewport.setStartRes(seq.findIndex(startRes) - 1);
2639 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2651 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2653 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2656 if (viewport.getSelectionGroup() != null)
2658 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2659 viewport.getHiddenRepSequences());
2660 start = viewport.getSelectionGroup().getStartRes();
2661 end = viewport.getSelectionGroup().getEndRes();
2665 seqs = viewport.getAlignment().getSequencesArray();
2668 // This is to maintain viewport position on first residue
2669 // of first sequence
2670 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2671 int startRes = seq.findPosition(viewport.startRes);
2673 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2674 viewport.getAlignment()));
2676 viewport.setStartRes(seq.findIndex(startRes) - 1);
2678 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2690 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2692 viewport.setPadGaps(padGapsMenuitem.isSelected());
2693 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2704 public void findMenuItem_actionPerformed(ActionEvent e)
2710 * Create a new view of the current alignment.
2713 public void newView_actionPerformed(ActionEvent e)
2715 newView(null, true);
2719 * Creates and shows a new view of the current alignment.
2722 * title of newly created view; if null, one will be generated
2723 * @param copyAnnotation
2724 * if true then duplicate all annnotation, groups and settings
2725 * @return new alignment panel, already displayed.
2727 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2730 * Create a new AlignmentPanel (with its own, new Viewport)
2732 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2734 if (!copyAnnotation)
2737 * remove all groups and annotation except for the automatic stuff
2739 newap.av.getAlignment().deleteAllGroups();
2740 newap.av.getAlignment().deleteAllAnnotations(false);
2743 newap.av.setGatherViewsHere(false);
2745 if (viewport.viewName == null)
2747 viewport.viewName = MessageManager
2748 .getString("label.view_name_original");
2752 * Views share the same edits, undo and redo stacks, mappings.
2754 newap.av.setHistoryList(viewport.getHistoryList());
2755 newap.av.setRedoList(viewport.getRedoList());
2756 newap.av.getAlignment().setCodonFrames(
2757 viewport.getAlignment().getCodonFrames());
2759 newap.av.viewName = getNewViewName(viewTitle);
2761 addAlignmentPanel(newap, true);
2762 newap.alignmentChanged();
2764 if (alignPanels.size() == 2)
2766 viewport.setGatherViewsHere(true);
2768 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2773 * Make a new name for the view, ensuring it is unique within the current
2774 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2775 * these now use viewId. Unique view names are still desirable for usability.)
2780 protected String getNewViewName(String viewTitle)
2782 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2783 boolean addFirstIndex = false;
2784 if (viewTitle == null || viewTitle.trim().length() == 0)
2786 viewTitle = MessageManager.getString("action.view");
2787 addFirstIndex = true;
2791 index = 1;// we count from 1 if given a specific name
2793 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2795 List<Component> comps = PaintRefresher.components.get(viewport
2796 .getSequenceSetId());
2798 List<String> existingNames = getExistingViewNames(comps);
2800 while (existingNames.contains(newViewName))
2802 newViewName = viewTitle + " " + (++index);
2808 * Returns a list of distinct view names found in the given list of
2809 * components. View names are held on the viewport of an AlignmentPanel.
2814 protected List<String> getExistingViewNames(List<Component> comps)
2816 List<String> existingNames = new ArrayList<String>();
2817 for (Component comp : comps)
2819 if (comp instanceof AlignmentPanel)
2821 AlignmentPanel ap = (AlignmentPanel) comp;
2822 if (!existingNames.contains(ap.av.viewName))
2824 existingNames.add(ap.av.viewName);
2828 return existingNames;
2832 * Explode tabbed views into separate windows.
2835 public void expandViews_actionPerformed(ActionEvent e)
2837 Desktop.instance.explodeViews(this);
2841 * Gather views in separate windows back into a tabbed presentation.
2844 public void gatherViews_actionPerformed(ActionEvent e)
2846 Desktop.instance.gatherViews(this);
2856 public void font_actionPerformed(ActionEvent e)
2858 new FontChooser(alignPanel);
2868 protected void seqLimit_actionPerformed(ActionEvent e)
2870 viewport.setShowJVSuffix(seqLimits.isSelected());
2872 alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
2873 .calculateIdWidth());
2874 alignPanel.paintAlignment(true);
2878 public void idRightAlign_actionPerformed(ActionEvent e)
2880 viewport.setRightAlignIds(idRightAlign.isSelected());
2881 alignPanel.paintAlignment(true);
2885 public void centreColumnLabels_actionPerformed(ActionEvent e)
2887 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2888 alignPanel.paintAlignment(true);
2894 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2897 protected void followHighlight_actionPerformed()
2900 * Set the 'follow' flag on the Viewport (and scroll to position if now
2903 final boolean state = this.followHighlightMenuItem.getState();
2904 viewport.setFollowHighlight(state);
2907 alignPanel.scrollToPosition(
2908 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2919 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2921 viewport.setColourText(colourTextMenuItem.isSelected());
2922 alignPanel.paintAlignment(true);
2932 public void wrapMenuItem_actionPerformed(ActionEvent e)
2934 scaleAbove.setVisible(wrapMenuItem.isSelected());
2935 scaleLeft.setVisible(wrapMenuItem.isSelected());
2936 scaleRight.setVisible(wrapMenuItem.isSelected());
2937 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2938 alignPanel.updateLayout();
2942 public void showAllSeqs_actionPerformed(ActionEvent e)
2944 viewport.showAllHiddenSeqs();
2948 public void showAllColumns_actionPerformed(ActionEvent e)
2950 viewport.showAllHiddenColumns();
2955 public void hideSelSequences_actionPerformed(ActionEvent e)
2957 viewport.hideAllSelectedSeqs();
2958 // alignPanel.paintAlignment(true);
2962 * called by key handler and the hide all/show all menu items
2967 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2970 boolean hide = false;
2971 SequenceGroup sg = viewport.getSelectionGroup();
2972 if (!toggleSeqs && !toggleCols)
2974 // Hide everything by the current selection - this is a hack - we do the
2975 // invert and then hide
2976 // first check that there will be visible columns after the invert.
2977 if ((viewport.getColumnSelection() != null
2978 && viewport.getColumnSelection().getSelected() != null && viewport
2979 .getColumnSelection().getSelected().size() > 0)
2980 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2983 // now invert the sequence set, if required - empty selection implies
2984 // that no hiding is required.
2987 invertSequenceMenuItem_actionPerformed(null);
2988 sg = viewport.getSelectionGroup();
2992 viewport.expandColSelection(sg, true);
2993 // finally invert the column selection and get the new sequence
2995 invertColSel_actionPerformed(null);
3002 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3004 hideSelSequences_actionPerformed(null);
3007 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3010 showAllSeqs_actionPerformed(null);
3016 if (viewport.getColumnSelection().getSelected().size() > 0)
3018 hideSelColumns_actionPerformed(null);
3021 viewport.setSelectionGroup(sg);
3026 showAllColumns_actionPerformed(null);
3035 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3036 * event.ActionEvent)
3039 public void hideAllButSelection_actionPerformed(ActionEvent e)
3041 toggleHiddenRegions(false, false);
3048 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3052 public void hideAllSelection_actionPerformed(ActionEvent e)
3054 SequenceGroup sg = viewport.getSelectionGroup();
3055 viewport.expandColSelection(sg, false);
3056 viewport.hideAllSelectedSeqs();
3057 viewport.hideSelectedColumns();
3058 alignPanel.paintAlignment(true);
3065 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3069 public void showAllhidden_actionPerformed(ActionEvent e)
3071 viewport.showAllHiddenColumns();
3072 viewport.showAllHiddenSeqs();
3073 alignPanel.paintAlignment(true);
3077 public void hideSelColumns_actionPerformed(ActionEvent e)
3079 viewport.hideSelectedColumns();
3080 alignPanel.paintAlignment(true);
3084 public void hiddenMarkers_actionPerformed(ActionEvent e)
3086 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3097 protected void scaleAbove_actionPerformed(ActionEvent e)
3099 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3100 alignPanel.paintAlignment(true);
3110 protected void scaleLeft_actionPerformed(ActionEvent e)
3112 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3113 alignPanel.paintAlignment(true);
3123 protected void scaleRight_actionPerformed(ActionEvent e)
3125 viewport.setScaleRightWrapped(scaleRight.isSelected());
3126 alignPanel.paintAlignment(true);
3136 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3138 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3139 alignPanel.paintAlignment(true);
3149 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3151 viewport.setShowText(viewTextMenuItem.isSelected());
3152 alignPanel.paintAlignment(true);
3162 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3164 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3165 alignPanel.paintAlignment(true);
3168 public FeatureSettings featureSettings;
3171 public FeatureSettingsControllerI getFeatureSettingsUI()
3173 return featureSettings;
3177 public void featureSettings_actionPerformed(ActionEvent e)
3179 if (featureSettings != null)
3181 featureSettings.close();
3182 featureSettings = null;
3184 if (!showSeqFeatures.isSelected())
3186 // make sure features are actually displayed
3187 showSeqFeatures.setSelected(true);
3188 showSeqFeatures_actionPerformed(null);
3190 featureSettings = new FeatureSettings(this);
3194 * Set or clear 'Show Sequence Features'
3200 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3202 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3203 alignPanel.paintAlignment(true);
3204 if (alignPanel.getOverviewPanel() != null)
3206 alignPanel.getOverviewPanel().updateOverviewImage();
3211 * Set or clear 'Show Sequence Features'
3217 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3219 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3221 if (viewport.isShowSequenceFeaturesHeight())
3223 // ensure we're actually displaying features
3224 viewport.setShowSequenceFeatures(true);
3225 showSeqFeatures.setSelected(true);
3227 alignPanel.paintAlignment(true);
3228 if (alignPanel.getOverviewPanel() != null)
3230 alignPanel.getOverviewPanel().updateOverviewImage();
3235 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3236 * the annotations panel as a whole.
3238 * The options to show/hide all annotations should be enabled when the panel
3239 * is shown, and disabled when the panel is hidden.
3244 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3246 final boolean setVisible = annotationPanelMenuItem.isSelected();
3247 viewport.setShowAnnotation(setVisible);
3248 this.showAllSeqAnnotations.setEnabled(setVisible);
3249 this.hideAllSeqAnnotations.setEnabled(setVisible);
3250 this.showAllAlAnnotations.setEnabled(setVisible);
3251 this.hideAllAlAnnotations.setEnabled(setVisible);
3252 alignPanel.updateLayout();
3256 public void alignmentProperties()
3258 JEditorPane editPane = new JEditorPane("text/html", "");
3259 editPane.setEditable(false);
3260 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3262 editPane.setText(MessageManager.formatMessage("label.html_content",
3264 { contents.toString() }));
3265 JInternalFrame frame = new JInternalFrame();
3266 frame.getContentPane().add(new JScrollPane(editPane));
3268 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3269 "label.alignment_properties", new Object[]
3270 { getTitle() }), 500, 400);
3280 public void overviewMenuItem_actionPerformed(ActionEvent e)
3282 if (alignPanel.overviewPanel != null)
3287 JInternalFrame frame = new JInternalFrame();
3288 OverviewPanel overview = new OverviewPanel(alignPanel);
3289 frame.setContentPane(overview);
3290 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3291 "label.overview_params", new Object[]
3292 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3294 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3295 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3298 public void internalFrameClosed(
3299 javax.swing.event.InternalFrameEvent evt)
3301 alignPanel.setOverviewPanel(null);
3305 alignPanel.setOverviewPanel(overview);
3309 public void textColour_actionPerformed(ActionEvent e)
3311 new TextColourChooser().chooseColour(alignPanel, null);
3321 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3333 public void clustalColour_actionPerformed(ActionEvent e)
3335 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3336 viewport.getHiddenRepSequences()));
3346 public void zappoColour_actionPerformed(ActionEvent e)
3348 changeColour(new ZappoColourScheme());
3358 public void taylorColour_actionPerformed(ActionEvent e)
3360 changeColour(new TaylorColourScheme());
3370 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3372 changeColour(new HydrophobicColourScheme());
3382 public void helixColour_actionPerformed(ActionEvent e)
3384 changeColour(new HelixColourScheme());
3394 public void strandColour_actionPerformed(ActionEvent e)
3396 changeColour(new StrandColourScheme());
3406 public void turnColour_actionPerformed(ActionEvent e)
3408 changeColour(new TurnColourScheme());
3418 public void buriedColour_actionPerformed(ActionEvent e)
3420 changeColour(new BuriedColourScheme());
3430 public void nucleotideColour_actionPerformed(ActionEvent e)
3432 changeColour(new NucleotideColourScheme());
3436 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3438 changeColour(new PurinePyrimidineColourScheme());
3442 * public void covariationColour_actionPerformed(ActionEvent e) {
3444 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3448 public void annotationColour_actionPerformed(ActionEvent e)
3450 new AnnotationColourChooser(viewport, alignPanel);
3454 public void annotationColumn_actionPerformed(ActionEvent e)
3456 new AnnotationColumnChooser(viewport, alignPanel);
3460 public void rnahelicesColour_actionPerformed(ActionEvent e)
3462 new RNAHelicesColourChooser(viewport, alignPanel);
3472 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3474 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3483 public void changeColour(ColourSchemeI cs)
3485 // TODO: compare with applet and pull up to model method
3490 if (viewport.getAbovePIDThreshold())
3492 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3494 cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
3498 cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
3501 if (viewport.getConservationSelected())
3504 Alignment al = (Alignment) viewport.getAlignment();
3505 Conservation c = new Conservation("All",
3506 ResidueProperties.propHash, 3, al.getSequences(), 0,
3510 c.verdict(false, viewport.getConsPercGaps());
3512 cs.setConservation(c);
3514 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3519 cs.setConservation(null);
3522 cs.setConsensus(viewport.getSequenceConsensusHash());
3525 viewport.setGlobalColourScheme(cs);
3527 if (viewport.getColourAppliesToAllGroups())
3530 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3538 if (cs instanceof ClustalxColourScheme)
3540 sg.cs = new ClustalxColourScheme(sg,
3541 viewport.getHiddenRepSequences());
3543 else if (cs instanceof UserColourScheme)
3545 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3551 sg.cs = cs.getClass().newInstance();
3552 } catch (Exception ex)
3557 if (viewport.getAbovePIDThreshold()
3558 || cs instanceof PIDColourScheme
3559 || cs instanceof Blosum62ColourScheme)
3561 sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
3563 sg.cs.setConsensus(AAFrequency.calculate(
3564 sg.getSequences(viewport.getHiddenRepSequences()),
3565 sg.getStartRes(), sg.getEndRes() + 1));
3569 sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
3572 if (viewport.getConservationSelected())
3574 Conservation c = new Conservation("Group",
3575 ResidueProperties.propHash, 3, sg.getSequences(viewport
3576 .getHiddenRepSequences()), sg.getStartRes(),
3577 sg.getEndRes() + 1);
3579 c.verdict(false, viewport.getConsPercGaps());
3580 sg.cs.setConservation(c);
3584 sg.cs.setConservation(null);
3589 if (alignPanel.getOverviewPanel() != null)
3591 alignPanel.getOverviewPanel().updateOverviewImage();
3594 alignPanel.paintAlignment(true);
3604 protected void modifyPID_actionPerformed(ActionEvent e)
3606 if (viewport.getAbovePIDThreshold()
3607 && viewport.getGlobalColourScheme() != null)
3609 SliderPanel.setPIDSliderSource(alignPanel,
3610 viewport.getGlobalColourScheme(), "Background");
3611 SliderPanel.showPIDSlider();
3622 protected void modifyConservation_actionPerformed(ActionEvent e)
3624 if (viewport.getConservationSelected()
3625 && viewport.getGlobalColourScheme() != null)
3627 SliderPanel.setConservationSlider(alignPanel,
3628 viewport.getGlobalColourScheme(), "Background");
3629 SliderPanel.showConservationSlider();
3640 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3642 viewport.setConservationSelected(conservationMenuItem.isSelected());
3644 viewport.setAbovePIDThreshold(false);
3645 abovePIDThreshold.setSelected(false);
3647 changeColour(viewport.getGlobalColourScheme());
3649 modifyConservation_actionPerformed(null);
3659 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3661 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3663 conservationMenuItem.setSelected(false);
3664 viewport.setConservationSelected(false);
3666 changeColour(viewport.getGlobalColourScheme());
3668 modifyPID_actionPerformed(null);
3678 public void userDefinedColour_actionPerformed(ActionEvent e)
3680 if (e.getActionCommand().equals(
3681 MessageManager.getString("action.user_defined")))
3683 new UserDefinedColours(alignPanel, null);
3687 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3688 .getUserColourSchemes().get(e.getActionCommand());
3694 public void updateUserColourMenu()
3697 Component[] menuItems = colourMenu.getMenuComponents();
3698 int iSize = menuItems.length;
3699 for (int i = 0; i < iSize; i++)
3701 if (menuItems[i].getName() != null
3702 && menuItems[i].getName().equals("USER_DEFINED"))
3704 colourMenu.remove(menuItems[i]);
3708 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3710 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3711 .getUserColourSchemes().keys();
3713 while (userColours.hasMoreElements())
3715 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3716 userColours.nextElement().toString());
3717 radioItem.setName("USER_DEFINED");
3718 radioItem.addMouseListener(new MouseAdapter()
3721 public void mousePressed(MouseEvent evt)
3723 if (evt.isControlDown()
3724 || SwingUtilities.isRightMouseButton(evt))
3726 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3728 int option = JOptionPane.showInternalConfirmDialog(
3729 jalview.gui.Desktop.desktop,
3731 .getString("label.remove_from_default_list"),
3733 .getString("label.remove_user_defined_colour"),
3734 JOptionPane.YES_NO_OPTION);
3735 if (option == JOptionPane.YES_OPTION)
3737 jalview.gui.UserDefinedColours
3738 .removeColourFromDefaults(radioItem.getText());
3739 colourMenu.remove(radioItem);
3743 radioItem.addActionListener(new ActionListener()
3746 public void actionPerformed(ActionEvent evt)
3748 userDefinedColour_actionPerformed(evt);
3755 radioItem.addActionListener(new ActionListener()
3758 public void actionPerformed(ActionEvent evt)
3760 userDefinedColour_actionPerformed(evt);
3764 colourMenu.insert(radioItem, 15);
3765 colours.add(radioItem);
3777 public void PIDColour_actionPerformed(ActionEvent e)
3779 changeColour(new PIDColourScheme());
3789 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3791 changeColour(new Blosum62ColourScheme());
3801 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3803 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3804 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3805 .getAlignment().getSequenceAt(0), null);
3806 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3807 viewport.getAlignment()));
3808 alignPanel.paintAlignment(true);
3818 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3820 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3821 AlignmentSorter.sortByID(viewport.getAlignment());
3822 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3823 viewport.getAlignment()));
3824 alignPanel.paintAlignment(true);
3834 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3836 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3837 AlignmentSorter.sortByLength(viewport.getAlignment());
3838 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3839 viewport.getAlignment()));
3840 alignPanel.paintAlignment(true);
3850 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3852 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3853 AlignmentSorter.sortByGroup(viewport.getAlignment());
3854 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3855 viewport.getAlignment()));
3857 alignPanel.paintAlignment(true);
3867 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3869 new RedundancyPanel(alignPanel, this);
3879 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3881 if ((viewport.getSelectionGroup() == null)
3882 || (viewport.getSelectionGroup().getSize() < 2))
3884 JOptionPane.showInternalMessageDialog(this, MessageManager
3885 .getString("label.you_must_select_least_two_sequences"),
3886 MessageManager.getString("label.invalid_selection"),
3887 JOptionPane.WARNING_MESSAGE);
3891 JInternalFrame frame = new JInternalFrame();
3892 frame.setContentPane(new PairwiseAlignPanel(viewport));
3893 Desktop.addInternalFrame(frame,
3894 MessageManager.getString("action.pairwise_alignment"), 600,
3906 public void PCAMenuItem_actionPerformed(ActionEvent e)
3908 if (((viewport.getSelectionGroup() != null)
3909 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3910 .getSelectionGroup().getSize() > 0))
3911 || (viewport.getAlignment().getHeight() < 4))
3914 .showInternalMessageDialog(
3917 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3919 .getString("label.sequence_selection_insufficient"),
3920 JOptionPane.WARNING_MESSAGE);
3925 new PCAPanel(alignPanel);
3929 public void autoCalculate_actionPerformed(ActionEvent e)
3931 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3932 if (viewport.autoCalculateConsensus)
3934 viewport.firePropertyChange("alignment", null, viewport
3935 .getAlignment().getSequences());
3940 public void sortByTreeOption_actionPerformed(ActionEvent e)
3942 viewport.sortByTree = sortByTree.isSelected();
3946 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3948 viewport.followSelection = listenToViewSelections.isSelected();
3958 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3960 newTreePanel("AV", "PID", "Average distance tree using PID");
3970 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3972 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3982 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3984 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3994 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3996 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
4009 void newTreePanel(String type, String pwType, String title)
4013 if (viewport.getSelectionGroup() != null
4014 && viewport.getSelectionGroup().getSize() > 0)
4016 if (viewport.getSelectionGroup().getSize() < 3)
4022 .getString("label.you_need_more_two_sequences_selected_build_tree"),
4024 .getString("label.not_enough_sequences"),
4025 JOptionPane.WARNING_MESSAGE);
4029 SequenceGroup sg = viewport.getSelectionGroup();
4031 /* Decide if the selection is a column region */
4032 for (SequenceI _s : sg.getSequences())
4034 if (_s.getLength() < sg.getEndRes())
4040 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
4042 .getString("label.sequences_selection_not_aligned"),
4043 JOptionPane.WARNING_MESSAGE);
4049 title = title + " on region";
4050 tp = new TreePanel(alignPanel, type, pwType);
4054 // are the visible sequences aligned?
4055 if (!viewport.getAlignment().isAligned(false))
4061 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4063 .getString("label.sequences_not_aligned"),
4064 JOptionPane.WARNING_MESSAGE);
4069 if (viewport.getAlignment().getHeight() < 2)
4074 tp = new TreePanel(alignPanel, type, pwType);
4079 if (viewport.viewName != null)
4081 title += viewport.viewName + " of ";
4084 title += this.title;
4086 Desktop.addInternalFrame(tp, title, 600, 500);
4097 public void addSortByOrderMenuItem(String title,
4098 final AlignmentOrder order)
4100 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title}));
4102 item.addActionListener(new java.awt.event.ActionListener()
4105 public void actionPerformed(ActionEvent e)
4107 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4109 // TODO: JBPNote - have to map order entries to curent SequenceI
4111 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4113 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4116 alignPanel.paintAlignment(true);
4122 * Add a new sort by annotation score menu item
4125 * the menu to add the option to
4127 * the label used to retrieve scores for each sequence on the
4130 public void addSortByAnnotScoreMenuItem(JMenu sort,
4131 final String scoreLabel)
4133 final JMenuItem item = new JMenuItem(scoreLabel);
4135 item.addActionListener(new java.awt.event.ActionListener()
4138 public void actionPerformed(ActionEvent e)
4140 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4141 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4142 viewport.getAlignment());// ,viewport.getSelectionGroup());
4143 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4144 viewport.getAlignment()));
4145 alignPanel.paintAlignment(true);
4151 * last hash for alignment's annotation array - used to minimise cost of
4154 protected int _annotationScoreVectorHash;
4157 * search the alignment and rebuild the sort by annotation score submenu the
4158 * last alignment annotation vector hash is stored to minimize cost of
4159 * rebuilding in subsequence calls.
4163 public void buildSortByAnnotationScoresMenu()
4165 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4170 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4172 sortByAnnotScore.removeAll();
4173 // almost certainly a quicker way to do this - but we keep it simple
4174 Hashtable scoreSorts = new Hashtable();
4175 AlignmentAnnotation aann[];
4176 for (SequenceI sqa : viewport.getAlignment().getSequences())
4178 aann = sqa.getAnnotation();
4179 for (int i = 0; aann != null && i < aann.length; i++)
4181 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4183 scoreSorts.put(aann[i].label, aann[i].label);
4187 Enumeration labels = scoreSorts.keys();
4188 while (labels.hasMoreElements())
4190 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4191 (String) labels.nextElement());
4193 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4196 _annotationScoreVectorHash = viewport.getAlignment()
4197 .getAlignmentAnnotation().hashCode();
4202 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4203 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4204 * call. Listeners are added to remove the menu item when the treePanel is
4205 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4209 * Displayed tree window.
4211 * SortBy menu item title.
4214 public void buildTreeMenu()
4216 calculateTree.removeAll();
4217 // build the calculate menu
4219 for (final String type : new String[]
4222 String treecalcnm = MessageManager.getString("label.tree_calc_"
4223 + type.toLowerCase());
4224 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4226 JMenuItem tm = new JMenuItem();
4227 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4228 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4230 String smn = MessageManager.getStringOrReturn(
4231 "label.score_model_", sm.getName());
4232 final String title = MessageManager.formatMessage(
4233 "label.treecalc_title", treecalcnm, smn);
4234 tm.setText(title);//
4235 tm.addActionListener(new java.awt.event.ActionListener()
4238 public void actionPerformed(ActionEvent e)
4240 newTreePanel(type, pwtype, title);
4243 calculateTree.add(tm);
4248 sortByTreeMenu.removeAll();
4250 List<Component> comps = PaintRefresher.components.get(viewport
4251 .getSequenceSetId());
4252 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4253 for (Component comp : comps)
4255 if (comp instanceof TreePanel)
4257 treePanels.add((TreePanel) comp);
4261 if (treePanels.size() < 1)
4263 sortByTreeMenu.setVisible(false);
4267 sortByTreeMenu.setVisible(true);
4269 for (final TreePanel tp : treePanels)
4271 final JMenuItem item = new JMenuItem(tp.getTitle());
4272 item.addActionListener(new java.awt.event.ActionListener()
4275 public void actionPerformed(ActionEvent e)
4277 tp.sortByTree_actionPerformed();
4278 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4283 sortByTreeMenu.add(item);
4287 public boolean sortBy(AlignmentOrder alorder, String undoname)
4289 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4290 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4291 if (undoname != null)
4293 addHistoryItem(new OrderCommand(undoname, oldOrder,
4294 viewport.getAlignment()));
4296 alignPanel.paintAlignment(true);
4301 * Work out whether the whole set of sequences or just the selected set will
4302 * be submitted for multiple alignment.
4305 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4307 // Now, check we have enough sequences
4308 AlignmentView msa = null;
4310 if ((viewport.getSelectionGroup() != null)
4311 && (viewport.getSelectionGroup().getSize() > 1))
4313 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4314 // some common interface!
4316 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4317 * SequenceI[sz = seqs.getSize(false)];
4319 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4320 * seqs.getSequenceAt(i); }
4322 msa = viewport.getAlignmentView(true);
4324 else if (viewport.getSelectionGroup() != null
4325 && viewport.getSelectionGroup().getSize() == 1)
4327 int option = JOptionPane.showConfirmDialog(this,
4328 MessageManager.getString("warn.oneseq_msainput_selection"),
4329 MessageManager.getString("label.invalid_selection"),
4330 JOptionPane.OK_CANCEL_OPTION);
4331 if (option == JOptionPane.OK_OPTION)
4333 msa = viewport.getAlignmentView(false);
4338 msa = viewport.getAlignmentView(false);
4344 * Decides what is submitted to a secondary structure prediction service: the
4345 * first sequence in the alignment, or in the current selection, or, if the
4346 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4347 * region or the whole alignment. (where the first sequence in the set is the
4348 * one that the prediction will be for).
4350 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4352 AlignmentView seqs = null;
4354 if ((viewport.getSelectionGroup() != null)
4355 && (viewport.getSelectionGroup().getSize() > 0))
4357 seqs = viewport.getAlignmentView(true);
4361 seqs = viewport.getAlignmentView(false);
4363 // limit sequences - JBPNote in future - could spawn multiple prediction
4365 // TODO: viewport.getAlignment().isAligned is a global state - the local
4366 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4367 if (!viewport.getAlignment().isAligned(false))
4369 seqs.setSequences(new SeqCigar[]
4370 { seqs.getSequences()[0] });
4371 // TODO: if seqs.getSequences().length>1 then should really have warned
4385 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4387 // Pick the tree file
4388 JalviewFileChooser chooser = new JalviewFileChooser(
4389 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4390 chooser.setFileView(new JalviewFileView());
4391 chooser.setDialogTitle(MessageManager
4392 .getString("label.select_newick_like_tree_file"));
4393 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4395 int value = chooser.showOpenDialog(null);
4397 if (value == JalviewFileChooser.APPROVE_OPTION)
4399 String choice = chooser.getSelectedFile().getPath();
4400 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4401 jalview.io.NewickFile fin = null;
4404 fin = new jalview.io.NewickFile(choice, "File");
4405 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4406 } catch (Exception ex)
4413 .getString("label.problem_reading_tree_file"),
4414 JOptionPane.WARNING_MESSAGE);
4415 ex.printStackTrace();
4417 if (fin != null && fin.hasWarningMessage())
4419 JOptionPane.showMessageDialog(Desktop.desktop, fin
4420 .getWarningMessage(), MessageManager
4421 .getString("label.possible_problem_with_tree_file"),
4422 JOptionPane.WARNING_MESSAGE);
4428 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4430 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4433 public TreePanel ShowNewickTree(NewickFile nf, String title)
4435 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4438 public TreePanel ShowNewickTree(NewickFile nf, String title,
4439 AlignmentView input)
4441 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4444 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4445 int h, int x, int y)
4447 return ShowNewickTree(nf, title, null, w, h, x, y);
4451 * Add a treeviewer for the tree extracted from a newick file object to the
4452 * current alignment view
4459 * Associated alignment input data (or null)
4468 * @return TreePanel handle
4470 public TreePanel ShowNewickTree(NewickFile nf, String title,
4471 AlignmentView input, int w, int h, int x, int y)
4473 TreePanel tp = null;
4479 if (nf.getTree() != null)
4481 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4487 tp.setLocation(x, y);
4490 Desktop.addInternalFrame(tp, title, w, h);
4492 } catch (Exception ex)
4494 ex.printStackTrace();
4500 private boolean buildingMenu = false;
4503 * Generates menu items and listener event actions for web service clients
4506 public void BuildWebServiceMenu()
4508 while (buildingMenu)
4512 System.err.println("Waiting for building menu to finish.");
4514 } catch (Exception e)
4518 final AlignFrame me = this;
4519 buildingMenu = true;
4520 new Thread(new Runnable()
4525 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4528 System.err.println("Building ws menu again "
4529 + Thread.currentThread());
4530 // TODO: add support for context dependent disabling of services based
4532 // alignment and current selection
4533 // TODO: add additional serviceHandle parameter to specify abstract
4535 // class independently of AbstractName
4536 // TODO: add in rediscovery GUI function to restart discoverer
4537 // TODO: group services by location as well as function and/or
4539 // object broker mechanism.
4540 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4541 final IProgressIndicator af = me;
4542 final JMenu msawsmenu = new JMenu("Alignment");
4543 final JMenu secstrmenu = new JMenu(
4544 "Secondary Structure Prediction");
4545 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4546 final JMenu analymenu = new JMenu("Analysis");
4547 final JMenu dismenu = new JMenu("Protein Disorder");
4548 // final JMenu msawsmenu = new
4549 // JMenu(MessageManager.getString("label.alignment"));
4550 // final JMenu secstrmenu = new
4551 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4552 // final JMenu seqsrchmenu = new
4553 // JMenu(MessageManager.getString("label.sequence_database_search"));
4554 // final JMenu analymenu = new
4555 // JMenu(MessageManager.getString("label.analysis"));
4556 // final JMenu dismenu = new
4557 // JMenu(MessageManager.getString("label.protein_disorder"));
4558 // JAL-940 - only show secondary structure prediction services from
4559 // the legacy server
4560 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4562 Discoverer.services != null && (Discoverer.services.size() > 0))
4564 // TODO: refactor to allow list of AbstractName/Handler bindings to
4566 // stored or retrieved from elsewhere
4567 // No MSAWS used any more:
4568 // Vector msaws = null; // (Vector)
4569 // Discoverer.services.get("MsaWS");
4570 Vector secstrpr = (Vector) Discoverer.services
4572 if (secstrpr != null)
4574 // Add any secondary structure prediction services
4575 for (int i = 0, j = secstrpr.size(); i < j; i++)
4577 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4579 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4580 .getServiceClient(sh);
4581 int p = secstrmenu.getItemCount();
4582 impl.attachWSMenuEntry(secstrmenu, me);
4583 int q = secstrmenu.getItemCount();
4584 for (int litm = p; litm < q; litm++)
4586 legacyItems.add(secstrmenu.getItem(litm));
4592 // Add all submenus in the order they should appear on the web
4594 wsmenu.add(msawsmenu);
4595 wsmenu.add(secstrmenu);
4596 wsmenu.add(dismenu);
4597 wsmenu.add(analymenu);
4598 // No search services yet
4599 // wsmenu.add(seqsrchmenu);
4601 javax.swing.SwingUtilities.invokeLater(new Runnable()
4608 webService.removeAll();
4609 // first, add discovered services onto the webservices menu
4610 if (wsmenu.size() > 0)
4612 for (int i = 0, j = wsmenu.size(); i < j; i++)
4614 webService.add(wsmenu.get(i));
4619 webService.add(me.webServiceNoServices);
4621 // TODO: move into separate menu builder class.
4622 boolean new_sspred = false;
4623 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4625 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4626 if (jws2servs != null)
4628 if (jws2servs.hasServices())
4630 jws2servs.attachWSMenuEntry(webService, me);
4631 for (Jws2Instance sv : jws2servs.getServices())
4633 if (sv.description.toLowerCase().contains("jpred"))
4635 for (JMenuItem jmi : legacyItems)
4637 jmi.setVisible(false);
4643 if (jws2servs.isRunning())
4645 JMenuItem tm = new JMenuItem(
4646 "Still discovering JABA Services");
4647 tm.setEnabled(false);
4652 build_urlServiceMenu(me.webService);
4653 build_fetchdbmenu(webService);
4654 for (JMenu item : wsmenu)
4656 if (item.getItemCount() == 0)
4658 item.setEnabled(false);
4662 item.setEnabled(true);
4665 } catch (Exception e)
4668 .debug("Exception during web service menu building process.",
4673 } catch (Exception e)
4676 buildingMenu = false;
4683 * construct any groupURL type service menu entries.
4687 private void build_urlServiceMenu(JMenu webService)
4689 // TODO: remove this code when 2.7 is released
4690 // DEBUG - alignmentView
4692 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4693 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4695 * @Override public void actionPerformed(ActionEvent e) {
4696 * jalview.datamodel.AlignmentView
4697 * .testSelectionViews(af.viewport.getAlignment(),
4698 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4700 * }); webService.add(testAlView);
4702 // TODO: refactor to RestClient discoverer and merge menu entries for
4703 // rest-style services with other types of analysis/calculation service
4704 // SHmmr test client - still being implemented.
4705 // DEBUG - alignmentView
4707 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4710 client.attachWSMenuEntry(
4711 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4717 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4718 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4719 * getProperty("LAST_DIRECTORY"));
4721 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4722 * to Vamsas file"); chooser.setToolTipText("Export");
4724 * int value = chooser.showSaveDialog(this);
4726 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4727 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4728 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4729 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4732 * prototype of an automatically enabled/disabled analysis function
4735 protected void setShowProductsEnabled()
4737 SequenceI[] selection = viewport.getSequenceSelection();
4738 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4739 viewport.getAlignment().getDataset()))
4741 showProducts.setEnabled(true);
4746 showProducts.setEnabled(false);
4751 * search selection for sequence xRef products and build the show products
4756 * @return true if showProducts menu should be enabled.
4758 public boolean canShowProducts(SequenceI[] selection,
4759 boolean isRegionSelection, Alignment dataset)
4761 boolean showp = false;
4764 showProducts.removeAll();
4765 final boolean dna = viewport.getAlignment().isNucleotide();
4766 final Alignment ds = dataset;
4767 String[] ptypes = (selection == null || selection.length == 0) ? null
4768 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4770 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4771 // selection, dataset, true);
4772 final SequenceI[] sel = selection;
4773 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4776 final boolean isRegSel = isRegionSelection;
4777 final AlignFrame af = this;
4778 final String source = ptypes[t];
4779 JMenuItem xtype = new JMenuItem(ptypes[t]);
4780 xtype.addActionListener(new ActionListener()
4784 public void actionPerformed(ActionEvent e)
4786 // TODO: new thread for this call with vis-delay
4787 af.showProductsFor(af.viewport.getSequenceSelection(),
4788 isRegSel, dna, source);
4792 showProducts.add(xtype);
4794 showProducts.setVisible(showp);
4795 showProducts.setEnabled(showp);
4796 } catch (Exception e)
4798 jalview.bin.Cache.log
4799 .warn("canTranslate threw an exception - please report to help@jalview.org",
4806 protected void showProductsFor(final SequenceI[] sel,
4807 final boolean isRegSel, final boolean dna, final String source)
4809 Runnable foo = new Runnable()
4815 final long sttime = System.currentTimeMillis();
4816 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4817 "status.searching_for_sequences_from", new Object[]
4818 { source }), sttime);
4821 // update our local dataset reference
4822 Alignment ds = AlignFrame.this.getViewport().getAlignment()
4824 Alignment prods = CrossRef
4825 .findXrefSequences(sel, dna, source, ds);
4828 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4829 for (int s = 0; s < sprods.length; s++)
4831 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4832 if (ds.getSequences() == null
4833 || !ds.getSequences().contains(
4834 sprods[s].getDatasetSequence()))
4836 ds.addSequence(sprods[s].getDatasetSequence());
4838 sprods[s].updatePDBIds();
4840 Alignment al = new Alignment(sprods);
4844 * Copy dna-to-protein mappings to new alignment
4846 // TODO 1: no mappings are set up for EMBL product
4847 // TODO 2: if they were, should add them to protein alignment, not
4849 Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4850 for (AlignedCodonFrame acf : cf)
4852 al.addCodonFrame(acf);
4854 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4856 String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4857 + " for " + ((isRegSel) ? "selected region of " : "")
4859 naf.setTitle(newtitle);
4861 // temporary flag until SplitFrame is released
4862 boolean asSplitFrame = Cache.getDefault(
4863 Preferences.ENABLE_SPLIT_FRAME, true);
4867 * Make a copy of this alignment (sharing the same dataset
4868 * sequences). If we are DNA, drop introns and update mappings
4870 AlignmentI copyAlignment = null;
4871 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4872 .getSequenceSelection();
4875 copyAlignment = AlignmentUtils.makeExonAlignment(
4876 sequenceSelection, cf);
4877 al.getCodonFrames().clear();
4878 al.getCodonFrames().addAll(cf);
4879 final StructureSelectionManager ssm = StructureSelectionManager
4880 .getStructureSelectionManager(Desktop.instance);
4881 ssm.addMappings(cf);
4885 copyAlignment = new Alignment(new Alignment(
4886 sequenceSelection));
4888 AlignFrame copyThis = new AlignFrame(copyAlignment,
4889 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4890 copyThis.setTitle(AlignFrame.this.getTitle());
4891 // SplitFrame with dna above, protein below
4892 SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4893 dna ? naf : copyThis);
4894 naf.setVisible(true);
4895 copyThis.setVisible(true);
4896 String linkedTitle = MessageManager
4897 .getString("label.linked_view_title");
4898 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4902 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4908 System.err.println("No Sequences generated for xRef type "
4911 } catch (Exception e)
4913 jalview.bin.Cache.log.error(
4914 "Exception when finding crossreferences", e);
4915 } catch (OutOfMemoryError e)
4917 new OOMWarning("whilst fetching crossreferences", e);
4920 jalview.bin.Cache.log.error("Error when finding crossreferences",
4923 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4924 "status.finished_searching_for_sequences_from",
4931 Thread frunner = new Thread(foo);
4935 public boolean canShowTranslationProducts(SequenceI[] selection,
4936 AlignmentI alignment)
4941 return (jalview.analysis.Dna.canTranslate(selection,
4942 viewport.getViewAsVisibleContigs(true)));
4943 } catch (Exception e)
4945 jalview.bin.Cache.log
4946 .warn("canTranslate threw an exception - please report to help@jalview.org",
4953 * Construct and display a new frame containing the translation of this
4954 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4957 public void showTranslation_actionPerformed(ActionEvent e)
4959 AlignmentI al = null;
4962 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4964 al = dna.translateCdna();
4965 } catch (Exception ex)
4967 jalview.bin.Cache.log.error(
4968 "Exception during translation. Please report this !", ex);
4969 final String msg = MessageManager
4970 .getString("label.error_when_translating_sequences_submit_bug_report");
4971 final String title = MessageManager
4972 .getString("label.implementation_error")
4973 + MessageManager.getString("translation_failed");
4974 JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
4975 JOptionPane.ERROR_MESSAGE);
4978 if (al == null || al.getHeight() == 0)
4980 final String msg = MessageManager
4981 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4982 final String title = MessageManager
4983 .getString("label.translation_failed");
4984 JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
4985 JOptionPane.WARNING_MESSAGE);
4989 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4990 af.setFileFormat(this.currentFileFormat);
4991 final String newTitle = MessageManager.formatMessage(
4992 "label.translation_of_params", new Object[]
4993 { this.getTitle() });
4994 af.setTitle(newTitle);
4995 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4997 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4998 viewport.openSplitFrame(af, new Alignment(seqs),
4999 al.getCodonFrames());
5003 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
5010 * Set the file format
5014 public void setFileFormat(String fileFormat)
5016 this.currentFileFormat = fileFormat;
5020 * Try to load a features file onto the alignment.
5023 * contents or path to retrieve file
5025 * access mode of file (see jalview.io.AlignFile)
5026 * @return true if features file was parsed correctly.
5028 public boolean parseFeaturesFile(String file, String type)
5030 return avc.parseFeaturesFile(file, type,
5031 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5036 public void refreshFeatureUI(boolean enableIfNecessary)
5038 // note - currently this is only still here rather than in the controller
5039 // because of the featureSettings hard reference that is yet to be
5041 if (enableIfNecessary)
5043 viewport.setShowSequenceFeatures(true);
5044 showSeqFeatures.setSelected(true);
5050 public void dragEnter(DropTargetDragEvent evt)
5055 public void dragExit(DropTargetEvent evt)
5060 public void dragOver(DropTargetDragEvent evt)
5065 public void dropActionChanged(DropTargetDragEvent evt)
5070 public void drop(DropTargetDropEvent evt)
5072 Transferable t = evt.getTransferable();
5073 java.util.List files = null;
5077 DataFlavor uriListFlavor = new DataFlavor(
5078 "text/uri-list;class=java.lang.String");
5079 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5081 // Works on Windows and MacOSX
5082 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5083 files = (java.util.List) t
5084 .getTransferData(DataFlavor.javaFileListFlavor);
5086 else if (t.isDataFlavorSupported(uriListFlavor))
5088 // This is used by Unix drag system
5089 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5090 String data = (String) t.getTransferData(uriListFlavor);
5091 files = new java.util.ArrayList(1);
5092 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5093 data, "\r\n"); st.hasMoreTokens();)
5095 String s = st.nextToken();
5096 if (s.startsWith("#"))
5098 // the line is a comment (as per the RFC 2483)
5102 java.net.URI uri = new java.net.URI(s);
5103 // check to see if we can handle this kind of URI
5104 if (uri.getScheme().toLowerCase().startsWith("http"))
5106 files.add(uri.toString());
5110 // otherwise preserve old behaviour: catch all for file objects
5111 java.io.File file = new java.io.File(uri);
5112 files.add(file.toString());
5116 } catch (Exception e)
5118 e.printStackTrace();
5124 // check to see if any of these files have names matching sequences in
5126 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5127 .getAlignment().getSequencesArray());
5129 * Object[] { String,SequenceI}
5131 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5132 ArrayList<String> filesnotmatched = new ArrayList<String>();
5133 for (int i = 0; i < files.size(); i++)
5135 String file = files.get(i).toString();
5137 String protocol = FormatAdapter.checkProtocol(file);
5138 if (protocol == jalview.io.FormatAdapter.FILE)
5140 File fl = new File(file);
5141 pdbfn = fl.getName();
5143 else if (protocol == jalview.io.FormatAdapter.URL)
5145 URL url = new URL(file);
5146 pdbfn = url.getFile();
5148 if (pdbfn.length() > 0)
5150 // attempt to find a match in the alignment
5151 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5152 int l = 0, c = pdbfn.indexOf(".");
5153 while (mtch == null && c != -1)
5158 } while ((c = pdbfn.indexOf(".", l)) > l);
5161 pdbfn = pdbfn.substring(0, l);
5163 mtch = idm.findAllIdMatches(pdbfn);
5170 type = new IdentifyFile().Identify(file, protocol);
5171 } catch (Exception ex)
5177 if (type.equalsIgnoreCase("PDB"))
5179 filesmatched.add(new Object[]
5180 { file, protocol, mtch });
5185 // File wasn't named like one of the sequences or wasn't a PDB file.
5186 filesnotmatched.add(file);
5190 if (filesmatched.size() > 0)
5192 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5198 "label.automatically_associate_pdb_files_with_sequences_same_name",
5205 .getString("label.automatically_associate_pdb_files_by_name"),
5206 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5209 for (Object[] fm : filesmatched)
5211 // try and associate
5212 // TODO: may want to set a standard ID naming formalism for
5213 // associating PDB files which have no IDs.
5214 for (SequenceI toassoc : (SequenceI[]) fm[2])
5216 PDBEntry pe = new AssociatePdbFileWithSeq()
5217 .associatePdbWithSeq((String) fm[0],
5218 (String) fm[1], toassoc, false,
5222 System.err.println("Associated file : "
5223 + ((String) fm[0]) + " with "
5224 + toassoc.getDisplayId(true));
5228 alignPanel.paintAlignment(true);
5232 if (filesnotmatched.size() > 0)
5235 && (Cache.getDefault(
5236 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5239 "<html>"+MessageManager
5241 "label.ignore_unmatched_dropped_files_info",
5246 .toString() })+"</html>",
5248 .getString("label.ignore_unmatched_dropped_files"),
5249 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5253 for (String fn : filesnotmatched)
5255 loadJalviewDataFile(fn, null, null, null);
5259 } catch (Exception ex)
5261 ex.printStackTrace();
5267 * Attempt to load a "dropped" file or URL string: First by testing whether
5268 * it's and Annotation file, then a JNet file, and finally a features file. If
5269 * all are false then the user may have dropped an alignment file onto this
5273 * either a filename or a URL string.
5275 public void loadJalviewDataFile(String file, String protocol,
5276 String format, SequenceI assocSeq)
5280 if (protocol == null)
5282 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5284 // if the file isn't identified, or not positively identified as some
5285 // other filetype (PFAM is default unidentified alignment file type) then
5286 // try to parse as annotation.
5287 boolean isAnnotation = (format == null || format
5288 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5289 .annotateAlignmentView(viewport, file, protocol)
5294 // first see if its a T-COFFEE score file
5295 TCoffeeScoreFile tcf = null;
5298 tcf = new TCoffeeScoreFile(file, protocol);
5301 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5303 tcoffeeColour.setEnabled(true);
5304 tcoffeeColour.setSelected(true);
5305 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5306 isAnnotation = true;
5308 .setText(MessageManager
5309 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5313 // some problem - if no warning its probable that the ID matching
5314 // process didn't work
5318 tcf.getWarningMessage() == null ? MessageManager
5319 .getString("label.check_file_matches_sequence_ids_alignment")
5320 : tcf.getWarningMessage(),
5322 .getString("label.problem_reading_tcoffee_score_file"),
5323 JOptionPane.WARNING_MESSAGE);
5330 } catch (Exception x)
5333 .debug("Exception when processing data source as T-COFFEE score file",
5339 // try to see if its a JNet 'concise' style annotation file *before*
5341 // try to parse it as a features file
5344 format = new IdentifyFile().Identify(file, protocol);
5346 if (format.equalsIgnoreCase("JnetFile"))
5348 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5350 new JnetAnnotationMaker();
5351 JnetAnnotationMaker.add_annotation(predictions,
5352 viewport.getAlignment(), 0, false);
5353 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5354 viewport.getAlignment().setSeqrep(repseq);
5355 ColumnSelection cs = new ColumnSelection();
5356 cs.hideInsertionsFor(repseq);
5357 viewport.setColumnSelection(cs);
5358 isAnnotation = true;
5363 * if (format.equalsIgnoreCase("PDB")) {
5365 * String pdbfn = ""; // try to match up filename with sequence id
5366 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5367 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5368 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5369 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5370 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5371 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5372 * // attempt to find a match in the alignment SequenceI mtch =
5373 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5374 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5375 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5376 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5377 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5378 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5379 * { System.err.println("Associated file : " + file + " with " +
5380 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5381 * TODO: maybe need to load as normal otherwise return; } }
5383 // try to parse it as a features file
5384 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5385 // if it wasn't a features file then we just treat it as a general
5386 // alignment file to load into the current view.
5389 new FileLoader().LoadFile(viewport, file, protocol, format);
5393 alignPanel.paintAlignment(true);
5401 alignPanel.adjustAnnotationHeight();
5402 viewport.updateSequenceIdColours();
5403 buildSortByAnnotationScoresMenu();
5404 alignPanel.paintAlignment(true);
5406 } catch (Exception ex)
5408 ex.printStackTrace();
5409 } catch (OutOfMemoryError oom)
5414 } catch (Exception x)
5420 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5421 : "using " + protocol + " from " + file)
5423 + (format != null ? "(parsing as '" + format
5424 + "' file)" : ""), oom, Desktop.desktop);
5429 * Method invoked by the ChangeListener on the tabbed pane, in other words
5430 * when a different tabbed pane is selected by the user or programmatically.
5433 public void tabSelectionChanged(int index)
5437 alignPanel = alignPanels.get(index);
5438 viewport = alignPanel.av;
5439 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5440 setMenusFromViewport(viewport);
5444 * If there is a frame linked to this one in a SplitPane, switch it to the
5445 * same view tab index. No infinite recursion of calls should happen, since
5446 * tabSelectionChanged() should not get invoked on setting the selected
5447 * index to an unchanged value. Guard against setting an invalid index
5448 * before the new view peer tab has been created.
5450 final AlignViewportI peer = viewport.getCodingComplement();
5453 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5454 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5456 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5462 * On right mouse click on view tab, prompt for and set new view name.
5465 public void tabbedPane_mousePressed(MouseEvent e)
5467 if (SwingUtilities.isRightMouseButton(e))
5469 String msg = MessageManager.getString("label.enter_view_name");
5470 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5471 JOptionPane.QUESTION_MESSAGE);
5475 viewport.viewName = reply;
5476 // TODO warn if reply is in getExistingViewNames()?
5477 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5482 public AlignViewport getCurrentView()
5488 * Open the dialog for regex description parsing.
5491 protected void extractScores_actionPerformed(ActionEvent e)
5493 ParseProperties pp = new jalview.analysis.ParseProperties(
5494 viewport.getAlignment());
5495 // TODO: verify regex and introduce GUI dialog for version 2.5
5496 // if (pp.getScoresFromDescription("col", "score column ",
5497 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5499 if (pp.getScoresFromDescription("description column",
5500 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5502 buildSortByAnnotationScoresMenu();
5510 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5514 protected void showDbRefs_actionPerformed(ActionEvent e)
5516 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5522 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5526 protected void showNpFeats_actionPerformed(ActionEvent e)
5528 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5532 * find the viewport amongst the tabs in this alignment frame and close that
5537 public boolean closeView(AlignViewportI av)
5541 this.closeMenuItem_actionPerformed(false);
5544 Component[] comp = tabbedPane.getComponents();
5545 for (int i = 0; comp != null && i < comp.length; i++)
5547 if (comp[i] instanceof AlignmentPanel)
5549 if (((AlignmentPanel) comp[i]).av == av)
5552 closeView((AlignmentPanel) comp[i]);
5560 protected void build_fetchdbmenu(JMenu webService)
5562 // Temporary hack - DBRef Fetcher always top level ws entry.
5563 // TODO We probably want to store a sequence database checklist in
5564 // preferences and have checkboxes.. rather than individual sources selected
5566 final JMenu rfetch = new JMenu(
5567 MessageManager.getString("action.fetch_db_references"));
5568 rfetch.setToolTipText(MessageManager
5569 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5570 webService.add(rfetch);
5572 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5573 MessageManager.getString("option.trim_retrieved_seqs"));
5574 trimrs.setToolTipText(MessageManager
5575 .getString("label.trim_retrieved_sequences"));
5576 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5577 trimrs.addActionListener(new ActionListener()
5580 public void actionPerformed(ActionEvent e)
5582 trimrs.setSelected(trimrs.isSelected());
5583 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5584 Boolean.valueOf(trimrs.isSelected()).toString());
5588 JMenuItem fetchr = new JMenuItem(
5589 MessageManager.getString("label.standard_databases"));
5590 fetchr.setToolTipText(MessageManager
5591 .getString("label.fetch_embl_uniprot"));
5592 fetchr.addActionListener(new ActionListener()
5596 public void actionPerformed(ActionEvent e)
5598 new Thread(new Runnable()
5604 new jalview.ws.DBRefFetcher(alignPanel.av
5605 .getSequenceSelection(), alignPanel.alignFrame)
5606 .fetchDBRefs(false);
5614 final AlignFrame me = this;
5615 new Thread(new Runnable()
5620 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5621 .getSequenceFetcherSingleton(me);
5622 javax.swing.SwingUtilities.invokeLater(new Runnable()
5627 String[] dbclasses = sf.getOrderedSupportedSources();
5628 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5629 // jalview.util.QuickSort.sort(otherdb, otherdb);
5630 List<DbSourceProxy> otherdb;
5631 JMenu dfetch = new JMenu();
5632 JMenu ifetch = new JMenu();
5633 JMenuItem fetchr = null;
5634 int comp = 0, icomp = 0, mcomp = 15;
5635 String mname = null;
5637 for (String dbclass : dbclasses)
5639 otherdb = sf.getSourceProxy(dbclass);
5640 // add a single entry for this class, or submenu allowing 'fetch
5642 if (otherdb == null || otherdb.size() < 1)
5646 // List<DbSourceProxy> dbs=otherdb;
5647 // otherdb=new ArrayList<DbSourceProxy>();
5648 // for (DbSourceProxy db:dbs)
5650 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5654 mname = "From " + dbclass;
5656 if (otherdb.size() == 1)
5658 final DbSourceProxy[] dassource = otherdb
5659 .toArray(new DbSourceProxy[0]);
5660 DbSourceProxy src = otherdb.get(0);
5661 fetchr = new JMenuItem(src.getDbSource());
5662 fetchr.addActionListener(new ActionListener()
5666 public void actionPerformed(ActionEvent e)
5668 new Thread(new Runnable()
5674 new jalview.ws.DBRefFetcher(alignPanel.av
5675 .getSequenceSelection(),
5676 alignPanel.alignFrame, dassource)
5677 .fetchDBRefs(false);
5683 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()})));
5689 final DbSourceProxy[] dassource = otherdb
5690 .toArray(new DbSourceProxy[0]);
5692 DbSourceProxy src = otherdb.get(0);
5693 fetchr = new JMenuItem(MessageManager.formatMessage(
5694 "label.fetch_all_param", new Object[]
5695 { src.getDbSource() }));
5696 fetchr.addActionListener(new ActionListener()
5699 public void actionPerformed(ActionEvent e)
5701 new Thread(new Runnable()
5707 new jalview.ws.DBRefFetcher(alignPanel.av
5708 .getSequenceSelection(),
5709 alignPanel.alignFrame, dassource)
5710 .fetchDBRefs(false);
5716 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new Object[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5719 // and then build the rest of the individual menus
5720 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()}));
5722 String imname = null;
5724 for (DbSourceProxy sproxy : otherdb)
5726 String dbname = sproxy.getDbName();
5727 String sname = dbname.length() > 5 ? dbname.substring(0,
5728 5) + "..." : dbname;
5729 String msname = dbname.length() > 10 ? dbname.substring(
5730 0, 10) + "..." : dbname;
5733 imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname});
5735 fetchr = new JMenuItem(msname);
5736 final DbSourceProxy[] dassrc =
5738 fetchr.addActionListener(new ActionListener()
5742 public void actionPerformed(ActionEvent e)
5744 new Thread(new Runnable()
5750 new jalview.ws.DBRefFetcher(alignPanel.av
5751 .getSequenceSelection(),
5752 alignPanel.alignFrame, dassrc)
5753 .fetchDBRefs(false);
5759 fetchr.setToolTipText("<html>"
5760 + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname}));
5763 if (++icomp >= mcomp || i == (otherdb.size()))
5765 ifetch.setText(MessageManager.formatMessage(
5766 "label.source_to_target", imname, sname));
5768 ifetch = new JMenu();
5776 if (comp >= mcomp || dbi >= (dbclasses.length))
5778 dfetch.setText(MessageManager.formatMessage(
5779 "label.source_to_target", mname, dbclass));
5781 dfetch = new JMenu();
5794 * Left justify the whole alignment.
5797 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5799 AlignmentI al = viewport.getAlignment();
5801 viewport.firePropertyChange("alignment", null, al);
5805 * Right justify the whole alignment.
5808 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5810 AlignmentI al = viewport.getAlignment();
5812 viewport.firePropertyChange("alignment", null, al);
5815 public void setShowSeqFeatures(boolean b)
5817 showSeqFeatures.setSelected(b);
5818 viewport.setShowSequenceFeatures(b);
5825 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5826 * awt.event.ActionEvent)
5829 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5831 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5832 alignPanel.paintAlignment(true);
5839 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5843 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5845 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5846 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5854 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5855 * .event.ActionEvent)
5858 protected void showGroupConservation_actionPerformed(ActionEvent e)
5860 viewport.setShowGroupConservation(showGroupConservation.getState());
5861 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5868 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5869 * .event.ActionEvent)
5872 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5874 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5875 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5882 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5883 * .event.ActionEvent)
5886 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5888 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5889 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5893 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5895 showSequenceLogo.setState(true);
5896 viewport.setShowSequenceLogo(true);
5897 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5898 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5902 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5904 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5911 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5912 * .event.ActionEvent)
5915 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5917 if (avc.makeGroupsFromSelection())
5919 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5920 alignPanel.updateAnnotation();
5921 alignPanel.paintAlignment(true);
5924 public void clearAlignmentSeqRep()
5926 // TODO refactor alignmentseqrep to controller
5927 if (viewport.getAlignment().hasSeqrep()) {
5928 viewport.getAlignment().setSeqrep(null);
5929 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5930 alignPanel.updateAnnotation();
5931 alignPanel.paintAlignment(true);
5936 protected void createGroup_actionPerformed(ActionEvent e)
5938 if (avc.createGroup())
5940 alignPanel.alignmentChanged();
5945 protected void unGroup_actionPerformed(ActionEvent e)
5949 alignPanel.alignmentChanged();
5954 * make the given alignmentPanel the currently selected tab
5956 * @param alignmentPanel
5958 public void setDisplayedView(AlignmentPanel alignmentPanel)
5960 if (!viewport.getSequenceSetId().equals(
5961 alignmentPanel.av.getSequenceSetId()))
5963 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5965 if (tabbedPane != null
5966 && tabbedPane.getTabCount() > 0
5967 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5968 .getSelectedIndex())
5970 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5975 * Action on selection of menu options to Show or Hide annotations.
5978 * @param forSequences
5979 * update sequence-related annotations
5980 * @param forAlignment
5981 * update non-sequence-related annotations
5984 protected void setAnnotationsVisibility(boolean visible,
5985 boolean forSequences, boolean forAlignment)
5987 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5988 .getAlignmentAnnotation())
5991 * don't display non-positional annotations on an alignment
5993 if (aa.annotations == null)
5997 boolean apply = (aa.sequenceRef == null && forAlignment)
5998 || (aa.sequenceRef != null && forSequences);
6001 aa.visible = visible;
6004 alignPanel.validateAnnotationDimensions(true);
6005 alignPanel.alignmentChanged();
6009 * Store selected annotation sort order for the view and repaint.
6012 protected void sortAnnotations_actionPerformed()
6014 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6016 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6017 alignPanel.paintAlignment(true);
6022 * @return alignment panels in this alignment frame
6024 public List<? extends AlignmentViewPanel> getAlignPanels()
6026 return alignPanels == null ? Arrays.asList(alignPanel)
6031 * Open a new alignment window, with the cDNA associated with this (protein)
6032 * alignment, aligned as is the protein.
6034 protected void viewAsCdna_actionPerformed()
6036 // TODO no longer a menu action - refactor as required
6037 final AlignmentI alignment = getViewport().getAlignment();
6038 Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6039 if (mappings == null)
6043 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6044 for (SequenceI aaSeq : alignment.getSequences()) {
6045 for (AlignedCodonFrame acf : mappings) {
6046 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6050 * There is a cDNA mapping for this protein sequence - add to new
6051 * alignment. It will share the same dataset sequence as other mapped
6052 * cDNA (no new mappings need to be created).
6054 final Sequence newSeq = new Sequence(dnaSeq);
6055 newSeq.setDatasetSequence(dnaSeq);
6056 cdnaSeqs.add(newSeq);
6060 if (cdnaSeqs.size() == 0)
6062 // show a warning dialog no mapped cDNA
6065 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6067 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6068 AlignFrame.DEFAULT_HEIGHT);
6069 cdna.alignAs(alignment);
6070 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6072 Desktop.addInternalFrame(alignFrame, newtitle,
6073 AlignFrame.DEFAULT_WIDTH,
6074 AlignFrame.DEFAULT_HEIGHT);
6078 * Set visibility of dna/protein complement view (available when shown in a
6084 protected void showComplement_actionPerformed(boolean show)
6086 SplitContainerI sf = getSplitViewContainer();
6088 sf.setComplementVisible(this, show);
6094 class PrintThread extends Thread
6098 public PrintThread(AlignmentPanel ap)
6103 static PageFormat pf;
6108 PrinterJob printJob = PrinterJob.getPrinterJob();
6112 printJob.setPrintable(ap, pf);
6116 printJob.setPrintable(ap);
6119 if (printJob.printDialog())
6124 } catch (Exception PrintException)
6126 PrintException.printStackTrace();