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 private 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]);
1307 lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1308 higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1310 // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
1311 // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
1313 if (lowestRange[0] == 0 && lowestRange[1] == 0)
1315 startPos = aligmentStartEnd[0];
1319 startPos = lowestRange[1] + 1;
1322 if (higestRange[0] == 0 && higestRange[1] == 0)
1324 endPos = aligmentStartEnd[1];
1328 endPos = higestRange[0];
1331 // System.out.println("Export range : " + minPos + " - " + maxPos);
1333 { startPos, endPos };
1336 public static void main(String[] args)
1338 ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1339 hiddenCols.add(new int[]
1341 hiddenCols.add(new int[]
1343 hiddenCols.add(new int[]
1345 hiddenCols.add(new int[]
1347 hiddenCols.add(new int[]
1350 int[] x = getStartEnd(new int[]
1351 { 0, 50 }, hiddenCols);
1352 // System.out.println("Export range : " + x[0] + " - " + x[1]);
1362 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1364 new HtmlSvgOutput(null, alignPanel);
1368 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1370 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1371 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1373 public void createImageMap(File file, String image)
1375 alignPanel.makePNGImageMap(file, image);
1385 public void createPNG(File f)
1387 alignPanel.makePNG(f);
1397 public void createEPS(File f)
1399 alignPanel.makeEPS(f);
1402 public void createSVG(File f)
1404 alignPanel.makeSVG(f);
1407 public void pageSetup_actionPerformed(ActionEvent e)
1409 PrinterJob printJob = PrinterJob.getPrinterJob();
1410 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1420 public void printMenuItem_actionPerformed(ActionEvent e)
1422 // Putting in a thread avoids Swing painting problems
1423 PrintThread thread = new PrintThread(alignPanel);
1428 public void exportFeatures_actionPerformed(ActionEvent e)
1430 new AnnotationExporter().exportFeatures(alignPanel);
1434 public void exportAnnotations_actionPerformed(ActionEvent e)
1436 new AnnotationExporter().exportAnnotations(alignPanel);
1440 public void associatedData_actionPerformed(ActionEvent e)
1442 // Pick the tree file
1443 JalviewFileChooser chooser = new JalviewFileChooser(
1444 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1445 chooser.setFileView(new JalviewFileView());
1446 chooser.setDialogTitle(MessageManager
1447 .getString("label.load_jalview_annotations"));
1448 chooser.setToolTipText(MessageManager
1449 .getString("label.load_jalview_annotations"));
1451 int value = chooser.showOpenDialog(null);
1453 if (value == JalviewFileChooser.APPROVE_OPTION)
1455 String choice = chooser.getSelectedFile().getPath();
1456 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1457 loadJalviewDataFile(choice, null, null, null);
1463 * Close the current view or all views in the alignment frame. If the frame
1464 * only contains one view then the alignment will be removed from memory.
1466 * @param closeAllTabs
1469 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1471 if (alignPanels != null && alignPanels.size() < 2)
1473 closeAllTabs = true;
1478 if (alignPanels != null)
1482 if (this.isClosed())
1484 // really close all the windows - otherwise wait till
1485 // setClosed(true) is called
1486 for (int i = 0; i < alignPanels.size(); i++)
1488 AlignmentPanel ap = alignPanels.get(i);
1495 closeView(alignPanel);
1501 this.setClosed(true);
1503 } catch (Exception ex)
1505 ex.printStackTrace();
1510 * Close the specified panel and close up tabs appropriately.
1512 * @param panelToClose
1514 public void closeView(AlignmentPanel panelToClose)
1516 int index = tabbedPane.getSelectedIndex();
1517 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1518 alignPanels.remove(panelToClose);
1519 panelToClose.closePanel();
1520 panelToClose = null;
1522 tabbedPane.removeTabAt(closedindex);
1523 tabbedPane.validate();
1525 if (index > closedindex || index == tabbedPane.getTabCount())
1527 // modify currently selected tab index if necessary.
1531 this.tabSelectionChanged(index);
1537 void updateEditMenuBar()
1540 if (viewport.getHistoryList().size() > 0)
1542 undoMenuItem.setEnabled(true);
1543 CommandI command = viewport.getHistoryList().peek();
1544 undoMenuItem.setText(MessageManager.formatMessage(
1545 "label.undo_command", new Object[]
1546 { command.getDescription() }));
1550 undoMenuItem.setEnabled(false);
1551 undoMenuItem.setText(MessageManager.getString("action.undo"));
1554 if (viewport.getRedoList().size() > 0)
1556 redoMenuItem.setEnabled(true);
1558 CommandI command = viewport.getRedoList().peek();
1559 redoMenuItem.setText(MessageManager.formatMessage(
1560 "label.redo_command", new Object[]
1561 { command.getDescription() }));
1565 redoMenuItem.setEnabled(false);
1566 redoMenuItem.setText(MessageManager.getString("action.redo"));
1570 public void addHistoryItem(CommandI command)
1572 if (command.getSize() > 0)
1574 viewport.addToHistoryList(command);
1575 viewport.clearRedoList();
1576 updateEditMenuBar();
1577 viewport.updateHiddenColumns();
1578 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1579 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1580 // viewport.getColumnSelection()
1581 // .getHiddenColumns().size() > 0);
1587 * @return alignment objects for all views
1589 AlignmentI[] getViewAlignments()
1591 if (alignPanels != null)
1593 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1595 for (AlignmentPanel ap : alignPanels)
1597 als[i++] = ap.av.getAlignment();
1601 if (viewport != null)
1603 return new AlignmentI[]
1604 { viewport.getAlignment() };
1616 protected void undoMenuItem_actionPerformed(ActionEvent e)
1618 if (viewport.getHistoryList().isEmpty())
1622 CommandI command = viewport.getHistoryList().pop();
1623 viewport.addToRedoList(command);
1624 command.undoCommand(getViewAlignments());
1626 AlignmentViewport originalSource = getOriginatingSource(command);
1627 updateEditMenuBar();
1629 if (originalSource != null)
1631 if (originalSource != viewport)
1634 .warn("Implementation worry: mismatch of viewport origin for undo");
1636 originalSource.updateHiddenColumns();
1637 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1639 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1640 // viewport.getColumnSelection()
1641 // .getHiddenColumns().size() > 0);
1642 originalSource.firePropertyChange("alignment", null, originalSource
1643 .getAlignment().getSequences());
1654 protected void redoMenuItem_actionPerformed(ActionEvent e)
1656 if (viewport.getRedoList().size() < 1)
1661 CommandI command = viewport.getRedoList().pop();
1662 viewport.addToHistoryList(command);
1663 command.doCommand(getViewAlignments());
1665 AlignmentViewport originalSource = getOriginatingSource(command);
1666 updateEditMenuBar();
1668 if (originalSource != null)
1671 if (originalSource != viewport)
1674 .warn("Implementation worry: mismatch of viewport origin for redo");
1676 originalSource.updateHiddenColumns();
1677 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1679 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1680 // viewport.getColumnSelection()
1681 // .getHiddenColumns().size() > 0);
1682 originalSource.firePropertyChange("alignment", null, originalSource
1683 .getAlignment().getSequences());
1687 AlignmentViewport getOriginatingSource(CommandI command)
1689 AlignmentViewport originalSource = null;
1690 // For sequence removal and addition, we need to fire
1691 // the property change event FROM the viewport where the
1692 // original alignment was altered
1693 AlignmentI al = null;
1694 if (command instanceof EditCommand)
1696 EditCommand editCommand = (EditCommand) command;
1697 al = editCommand.getAlignment();
1698 List<Component> comps = PaintRefresher.components.get(viewport
1699 .getSequenceSetId());
1701 for (Component comp : comps)
1703 if (comp instanceof AlignmentPanel)
1705 if (al == ((AlignmentPanel) comp).av.getAlignment())
1707 originalSource = ((AlignmentPanel) comp).av;
1714 if (originalSource == null)
1716 // The original view is closed, we must validate
1717 // the current view against the closed view first
1720 PaintRefresher.validateSequences(al, viewport.getAlignment());
1723 originalSource = viewport;
1726 return originalSource;
1735 public void moveSelectedSequences(boolean up)
1737 SequenceGroup sg = viewport.getSelectionGroup();
1743 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1744 viewport.getHiddenRepSequences(), up);
1745 alignPanel.paintAlignment(true);
1748 synchronized void slideSequences(boolean right, int size)
1750 List<SequenceI> sg = new ArrayList<SequenceI>();
1751 if (viewport.cursorMode)
1753 sg.add(viewport.getAlignment().getSequenceAt(
1754 alignPanel.getSeqPanel().seqCanvas.cursorY));
1756 else if (viewport.getSelectionGroup() != null
1757 && viewport.getSelectionGroup().getSize() != viewport
1758 .getAlignment().getHeight())
1760 sg = viewport.getSelectionGroup().getSequences(
1761 viewport.getHiddenRepSequences());
1769 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1771 for (SequenceI seq : viewport.getAlignment().getSequences())
1773 if (!sg.contains(seq))
1775 invertGroup.add(seq);
1779 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1781 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1782 for (int i = 0; i < invertGroup.size(); i++)
1784 seqs2[i] = invertGroup.get(i);
1787 SlideSequencesCommand ssc;
1790 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1791 size, viewport.getGapCharacter());
1795 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1796 size, viewport.getGapCharacter());
1799 int groupAdjustment = 0;
1800 if (ssc.getGapsInsertedBegin() && right)
1802 if (viewport.cursorMode)
1804 alignPanel.getSeqPanel().moveCursor(size, 0);
1808 groupAdjustment = size;
1811 else if (!ssc.getGapsInsertedBegin() && !right)
1813 if (viewport.cursorMode)
1815 alignPanel.getSeqPanel().moveCursor(-size, 0);
1819 groupAdjustment = -size;
1823 if (groupAdjustment != 0)
1825 viewport.getSelectionGroup().setStartRes(
1826 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1827 viewport.getSelectionGroup().setEndRes(
1828 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1832 * just extend the last slide command if compatible; but not if in
1833 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1835 boolean appendHistoryItem = false;
1836 Deque<CommandI> historyList = viewport.getHistoryList();
1837 boolean inSplitFrame = getSplitViewContainer() != null;
1838 if (!inSplitFrame && historyList != null
1839 && historyList.size() > 0
1840 && historyList.peek() instanceof SlideSequencesCommand)
1842 appendHistoryItem = ssc
1843 .appendSlideCommand((SlideSequencesCommand) historyList
1847 if (!appendHistoryItem)
1849 addHistoryItem(ssc);
1862 protected void copy_actionPerformed(ActionEvent e)
1865 if (viewport.getSelectionGroup() == null)
1869 // TODO: preserve the ordering of displayed alignment annotation in any
1870 // internal paste (particularly sequence associated annotation)
1871 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1872 String[] omitHidden = null;
1874 if (viewport.hasHiddenColumns())
1876 omitHidden = viewport.getViewAsString(true);
1879 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1882 StringSelection ss = new StringSelection(output);
1886 jalview.gui.Desktop.internalCopy = true;
1887 // Its really worth setting the clipboard contents
1888 // to empty before setting the large StringSelection!!
1889 Toolkit.getDefaultToolkit().getSystemClipboard()
1890 .setContents(new StringSelection(""), null);
1892 Toolkit.getDefaultToolkit().getSystemClipboard()
1893 .setContents(ss, Desktop.instance);
1894 } catch (OutOfMemoryError er)
1896 new OOMWarning("copying region", er);
1900 ArrayList<int[]> hiddenColumns = null;
1901 if (viewport.hasHiddenColumns())
1903 hiddenColumns = new ArrayList<int[]>();
1904 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1905 .getSelectionGroup().getEndRes();
1906 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1908 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1910 hiddenColumns.add(new int[]
1911 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1916 Desktop.jalviewClipboard = new Object[]
1917 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1918 statusBar.setText(MessageManager.formatMessage(
1919 "label.copied_sequences_to_clipboard", new Object[]
1920 { Integer.valueOf(seqs.length).toString() }));
1930 protected void pasteNew_actionPerformed(ActionEvent e)
1942 protected void pasteThis_actionPerformed(ActionEvent e)
1948 * Paste contents of Jalview clipboard
1950 * @param newAlignment
1951 * true to paste to a new alignment, otherwise add to this.
1953 void paste(boolean newAlignment)
1955 boolean externalPaste = true;
1958 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1959 Transferable contents = c.getContents(this);
1961 if (contents == null)
1969 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1970 if (str.length() < 1)
1975 format = new IdentifyFile().Identify(str, "Paste");
1977 } catch (OutOfMemoryError er)
1979 new OOMWarning("Out of memory pasting sequences!!", er);
1983 SequenceI[] sequences;
1984 boolean annotationAdded = false;
1985 AlignmentI alignment = null;
1987 if (Desktop.jalviewClipboard != null)
1989 // The clipboard was filled from within Jalview, we must use the
1991 // And dataset from the copied alignment
1992 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1993 // be doubly sure that we create *new* sequence objects.
1994 sequences = new SequenceI[newseq.length];
1995 for (int i = 0; i < newseq.length; i++)
1997 sequences[i] = new Sequence(newseq[i]);
1999 alignment = new Alignment(sequences);
2000 externalPaste = false;
2004 // parse the clipboard as an alignment.
2005 alignment = new FormatAdapter().readFile(str, "Paste", format);
2006 sequences = alignment.getSequencesArray();
2010 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2016 if (Desktop.jalviewClipboard != null)
2018 // dataset is inherited
2019 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2023 // new dataset is constructed
2024 alignment.setDataset(null);
2026 alwidth = alignment.getWidth() + 1;
2030 AlignmentI pastedal = alignment; // preserve pasted alignment object
2031 // Add pasted sequences and dataset into existing alignment.
2032 alignment = viewport.getAlignment();
2033 alwidth = alignment.getWidth() + 1;
2034 // decide if we need to import sequences from an existing dataset
2035 boolean importDs = Desktop.jalviewClipboard != null
2036 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2037 // importDs==true instructs us to copy over new dataset sequences from
2038 // an existing alignment
2039 Vector newDs = (importDs) ? new Vector() : null; // used to create
2040 // minimum dataset set
2042 for (int i = 0; i < sequences.length; i++)
2046 newDs.addElement(null);
2048 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2050 if (importDs && ds != null)
2052 if (!newDs.contains(ds))
2054 newDs.setElementAt(ds, i);
2055 ds = new Sequence(ds);
2056 // update with new dataset sequence
2057 sequences[i].setDatasetSequence(ds);
2061 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2066 // copy and derive new dataset sequence
2067 sequences[i] = sequences[i].deriveSequence();
2068 alignment.getDataset().addSequence(
2069 sequences[i].getDatasetSequence());
2070 // TODO: avoid creation of duplicate dataset sequences with a
2071 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2073 alignment.addSequence(sequences[i]); // merges dataset
2077 newDs.clear(); // tidy up
2079 if (alignment.getAlignmentAnnotation() != null)
2081 for (AlignmentAnnotation alan : alignment
2082 .getAlignmentAnnotation())
2084 if (alan.graphGroup > fgroup)
2086 fgroup = alan.graphGroup;
2090 if (pastedal.getAlignmentAnnotation() != null)
2092 // Add any annotation attached to alignment.
2093 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2094 for (int i = 0; i < alann.length; i++)
2096 annotationAdded = true;
2097 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2099 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2100 if (newann.graphGroup > -1)
2102 if (newGraphGroups.size() <= newann.graphGroup
2103 || newGraphGroups.get(newann.graphGroup) == null)
2105 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2107 newGraphGroups.add(q, null);
2109 newGraphGroups.set(newann.graphGroup, new Integer(
2112 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2116 newann.padAnnotation(alwidth);
2117 alignment.addAnnotation(newann);
2127 addHistoryItem(new EditCommand(
2128 MessageManager.getString("label.add_sequences"),
2130 sequences, 0, alignment.getWidth(), alignment));
2132 // Add any annotations attached to sequences
2133 for (int i = 0; i < sequences.length; i++)
2135 if (sequences[i].getAnnotation() != null)
2137 AlignmentAnnotation newann;
2138 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2140 annotationAdded = true;
2141 newann = sequences[i].getAnnotation()[a];
2142 newann.adjustForAlignment();
2143 newann.padAnnotation(alwidth);
2144 if (newann.graphGroup > -1)
2146 if (newann.graphGroup > -1)
2148 if (newGraphGroups.size() <= newann.graphGroup
2149 || newGraphGroups.get(newann.graphGroup) == null)
2151 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2153 newGraphGroups.add(q, null);
2155 newGraphGroups.set(newann.graphGroup, new Integer(
2158 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2162 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2167 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2174 // propagate alignment changed.
2175 viewport.setEndSeq(alignment.getHeight());
2176 if (annotationAdded)
2178 // Duplicate sequence annotation in all views.
2179 AlignmentI[] alview = this.getViewAlignments();
2180 for (int i = 0; i < sequences.length; i++)
2182 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2187 for (int avnum = 0; avnum < alview.length; avnum++)
2189 if (alview[avnum] != alignment)
2191 // duplicate in a view other than the one with input focus
2192 int avwidth = alview[avnum].getWidth() + 1;
2193 // this relies on sann being preserved after we
2194 // modify the sequence's annotation array for each duplication
2195 for (int a = 0; a < sann.length; a++)
2197 AlignmentAnnotation newann = new AlignmentAnnotation(
2199 sequences[i].addAlignmentAnnotation(newann);
2200 newann.padAnnotation(avwidth);
2201 alview[avnum].addAnnotation(newann); // annotation was
2202 // duplicated earlier
2203 // TODO JAL-1145 graphGroups are not updated for sequence
2204 // annotation added to several views. This may cause
2206 alview[avnum].setAnnotationIndex(newann, a);
2211 buildSortByAnnotationScoresMenu();
2213 viewport.firePropertyChange("alignment", null,
2214 alignment.getSequences());
2215 if (alignPanels != null)
2217 for (AlignmentPanel ap : alignPanels)
2219 ap.validateAnnotationDimensions(false);
2224 alignPanel.validateAnnotationDimensions(false);
2230 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2232 String newtitle = new String("Copied sequences");
2234 if (Desktop.jalviewClipboard != null
2235 && Desktop.jalviewClipboard[2] != null)
2237 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2238 for (int[] region : hc)
2240 af.viewport.hideColumns(region[0], region[1]);
2244 // >>>This is a fix for the moment, until a better solution is
2246 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2248 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2250 // TODO: maintain provenance of an alignment, rather than just make the
2251 // title a concatenation of operations.
2254 if (title.startsWith("Copied sequences"))
2260 newtitle = newtitle.concat("- from " + title);
2265 newtitle = new String("Pasted sequences");
2268 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2273 } catch (Exception ex)
2275 ex.printStackTrace();
2276 System.out.println("Exception whilst pasting: " + ex);
2277 // could be anything being pasted in here
2283 protected void expand_newalign(ActionEvent e)
2287 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2288 .getAlignment(), -1);
2289 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2291 String newtitle = new String("Flanking alignment");
2293 if (Desktop.jalviewClipboard != null
2294 && Desktop.jalviewClipboard[2] != null)
2296 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2297 for (int region[] : hc)
2299 af.viewport.hideColumns(region[0], region[1]);
2303 // >>>This is a fix for the moment, until a better solution is
2305 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2307 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2309 // TODO: maintain provenance of an alignment, rather than just make the
2310 // title a concatenation of operations.
2312 if (title.startsWith("Copied sequences"))
2318 newtitle = newtitle.concat("- from " + title);
2322 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2324 } catch (Exception ex)
2326 ex.printStackTrace();
2327 System.out.println("Exception whilst pasting: " + ex);
2328 // could be anything being pasted in here
2329 } catch (OutOfMemoryError oom)
2331 new OOMWarning("Viewing flanking region of alignment", oom);
2342 protected void cut_actionPerformed(ActionEvent e)
2344 copy_actionPerformed(null);
2345 delete_actionPerformed(null);
2355 protected void delete_actionPerformed(ActionEvent evt)
2358 SequenceGroup sg = viewport.getSelectionGroup();
2365 * If the cut affects all sequences, warn, remove highlighted columns
2367 if (sg.getSize() == viewport.getAlignment().getHeight())
2369 int confirm = JOptionPane.showConfirmDialog(this,
2370 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2371 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2372 JOptionPane.OK_CANCEL_OPTION);
2374 if (confirm == JOptionPane.CANCEL_OPTION
2375 || confirm == JOptionPane.CLOSED_OPTION)
2379 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2380 sg.getEndRes() + 1);
2383 SequenceI[] cut = sg.getSequences()
2384 .toArray(new SequenceI[sg.getSize()]);
2386 addHistoryItem(new EditCommand(
2387 MessageManager.getString("label.cut_sequences"), Action.CUT,
2388 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2389 viewport.getAlignment()));
2391 viewport.setSelectionGroup(null);
2392 viewport.sendSelection();
2393 viewport.getAlignment().deleteGroup(sg);
2395 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2397 if (viewport.getAlignment().getHeight() < 1)
2401 this.setClosed(true);
2402 } catch (Exception ex)
2415 protected void deleteGroups_actionPerformed(ActionEvent e)
2417 if (avc.deleteGroups())
2419 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2420 alignPanel.updateAnnotation();
2421 alignPanel.paintAlignment(true);
2432 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2434 SequenceGroup sg = new SequenceGroup();
2436 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2438 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2441 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2442 viewport.setSelectionGroup(sg);
2443 viewport.sendSelection();
2444 alignPanel.paintAlignment(true);
2445 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2455 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2457 if (viewport.cursorMode)
2459 alignPanel.getSeqPanel().keyboardNo1 = null;
2460 alignPanel.getSeqPanel().keyboardNo2 = null;
2462 viewport.setSelectionGroup(null);
2463 viewport.getColumnSelection().clear();
2464 viewport.setSelectionGroup(null);
2465 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2466 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2467 alignPanel.paintAlignment(true);
2468 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2469 viewport.sendSelection();
2479 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2481 SequenceGroup sg = viewport.getSelectionGroup();
2485 selectAllSequenceMenuItem_actionPerformed(null);
2490 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2492 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2495 alignPanel.paintAlignment(true);
2496 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2497 viewport.sendSelection();
2501 public void invertColSel_actionPerformed(ActionEvent e)
2503 viewport.invertColumnSelection();
2504 alignPanel.paintAlignment(true);
2505 viewport.sendSelection();
2515 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2517 trimAlignment(true);
2527 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2529 trimAlignment(false);
2532 void trimAlignment(boolean trimLeft)
2534 ColumnSelection colSel = viewport.getColumnSelection();
2537 if (colSel.size() > 0)
2541 column = colSel.getMin();
2545 column = colSel.getMax();
2549 if (viewport.getSelectionGroup() != null)
2551 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2552 viewport.getHiddenRepSequences());
2556 seqs = viewport.getAlignment().getSequencesArray();
2559 TrimRegionCommand trimRegion;
2562 trimRegion = new TrimRegionCommand("Remove Left",
2563 TrimRegionCommand.TRIM_LEFT, seqs, column,
2564 viewport.getAlignment(), viewport.getColumnSelection(),
2565 viewport.getSelectionGroup());
2566 viewport.setStartRes(0);
2570 trimRegion = new TrimRegionCommand("Remove Right",
2571 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2572 viewport.getAlignment(), viewport.getColumnSelection(),
2573 viewport.getSelectionGroup());
2576 statusBar.setText(MessageManager.formatMessage(
2577 "label.removed_columns", new String[]
2578 { Integer.valueOf(trimRegion.getSize()).toString() }));
2580 addHistoryItem(trimRegion);
2582 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2584 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2585 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2587 viewport.getAlignment().deleteGroup(sg);
2591 viewport.firePropertyChange("alignment", null, viewport
2592 .getAlignment().getSequences());
2603 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2605 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2608 if (viewport.getSelectionGroup() != null)
2610 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2611 viewport.getHiddenRepSequences());
2612 start = viewport.getSelectionGroup().getStartRes();
2613 end = viewport.getSelectionGroup().getEndRes();
2617 seqs = viewport.getAlignment().getSequencesArray();
2620 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2621 "Remove Gapped Columns", seqs, start, end,
2622 viewport.getAlignment());
2624 addHistoryItem(removeGapCols);
2626 statusBar.setText(MessageManager.formatMessage(
2627 "label.removed_empty_columns", new Object[]
2628 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2630 // This is to maintain viewport position on first residue
2631 // of first sequence
2632 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2633 int startRes = seq.findPosition(viewport.startRes);
2634 // ShiftList shifts;
2635 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2636 // edit.alColumnChanges=shifts.getInverse();
2637 // if (viewport.hasHiddenColumns)
2638 // viewport.getColumnSelection().compensateForEdits(shifts);
2639 viewport.setStartRes(seq.findIndex(startRes) - 1);
2640 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2652 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2654 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2657 if (viewport.getSelectionGroup() != null)
2659 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2660 viewport.getHiddenRepSequences());
2661 start = viewport.getSelectionGroup().getStartRes();
2662 end = viewport.getSelectionGroup().getEndRes();
2666 seqs = viewport.getAlignment().getSequencesArray();
2669 // This is to maintain viewport position on first residue
2670 // of first sequence
2671 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2672 int startRes = seq.findPosition(viewport.startRes);
2674 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2675 viewport.getAlignment()));
2677 viewport.setStartRes(seq.findIndex(startRes) - 1);
2679 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2691 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2693 viewport.setPadGaps(padGapsMenuitem.isSelected());
2694 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2705 public void findMenuItem_actionPerformed(ActionEvent e)
2711 * Create a new view of the current alignment.
2714 public void newView_actionPerformed(ActionEvent e)
2716 newView(null, true);
2720 * Creates and shows a new view of the current alignment.
2723 * title of newly created view; if null, one will be generated
2724 * @param copyAnnotation
2725 * if true then duplicate all annnotation, groups and settings
2726 * @return new alignment panel, already displayed.
2728 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2731 * Create a new AlignmentPanel (with its own, new Viewport)
2733 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2735 if (!copyAnnotation)
2738 * remove all groups and annotation except for the automatic stuff
2740 newap.av.getAlignment().deleteAllGroups();
2741 newap.av.getAlignment().deleteAllAnnotations(false);
2744 newap.av.setGatherViewsHere(false);
2746 if (viewport.viewName == null)
2748 viewport.viewName = MessageManager
2749 .getString("label.view_name_original");
2753 * Views share the same edits, undo and redo stacks, mappings.
2755 newap.av.setHistoryList(viewport.getHistoryList());
2756 newap.av.setRedoList(viewport.getRedoList());
2757 newap.av.getAlignment().setCodonFrames(
2758 viewport.getAlignment().getCodonFrames());
2760 newap.av.viewName = getNewViewName(viewTitle);
2762 addAlignmentPanel(newap, true);
2763 newap.alignmentChanged();
2765 if (alignPanels.size() == 2)
2767 viewport.setGatherViewsHere(true);
2769 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2774 * Make a new name for the view, ensuring it is unique within the current
2775 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2776 * these now use viewId. Unique view names are still desirable for usability.)
2781 protected String getNewViewName(String viewTitle)
2783 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2784 boolean addFirstIndex = false;
2785 if (viewTitle == null || viewTitle.trim().length() == 0)
2787 viewTitle = MessageManager.getString("action.view");
2788 addFirstIndex = true;
2792 index = 1;// we count from 1 if given a specific name
2794 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2796 List<Component> comps = PaintRefresher.components.get(viewport
2797 .getSequenceSetId());
2799 List<String> existingNames = getExistingViewNames(comps);
2801 while (existingNames.contains(newViewName))
2803 newViewName = viewTitle + " " + (++index);
2809 * Returns a list of distinct view names found in the given list of
2810 * components. View names are held on the viewport of an AlignmentPanel.
2815 protected List<String> getExistingViewNames(List<Component> comps)
2817 List<String> existingNames = new ArrayList<String>();
2818 for (Component comp : comps)
2820 if (comp instanceof AlignmentPanel)
2822 AlignmentPanel ap = (AlignmentPanel) comp;
2823 if (!existingNames.contains(ap.av.viewName))
2825 existingNames.add(ap.av.viewName);
2829 return existingNames;
2833 * Explode tabbed views into separate windows.
2836 public void expandViews_actionPerformed(ActionEvent e)
2838 Desktop.instance.explodeViews(this);
2842 * Gather views in separate windows back into a tabbed presentation.
2845 public void gatherViews_actionPerformed(ActionEvent e)
2847 Desktop.instance.gatherViews(this);
2857 public void font_actionPerformed(ActionEvent e)
2859 new FontChooser(alignPanel);
2869 protected void seqLimit_actionPerformed(ActionEvent e)
2871 viewport.setShowJVSuffix(seqLimits.isSelected());
2873 alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
2874 .calculateIdWidth());
2875 alignPanel.paintAlignment(true);
2879 public void idRightAlign_actionPerformed(ActionEvent e)
2881 viewport.setRightAlignIds(idRightAlign.isSelected());
2882 alignPanel.paintAlignment(true);
2886 public void centreColumnLabels_actionPerformed(ActionEvent e)
2888 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2889 alignPanel.paintAlignment(true);
2895 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2898 protected void followHighlight_actionPerformed()
2901 * Set the 'follow' flag on the Viewport (and scroll to position if now
2904 final boolean state = this.followHighlightMenuItem.getState();
2905 viewport.setFollowHighlight(state);
2908 alignPanel.scrollToPosition(
2909 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2920 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2922 viewport.setColourText(colourTextMenuItem.isSelected());
2923 alignPanel.paintAlignment(true);
2933 public void wrapMenuItem_actionPerformed(ActionEvent e)
2935 scaleAbove.setVisible(wrapMenuItem.isSelected());
2936 scaleLeft.setVisible(wrapMenuItem.isSelected());
2937 scaleRight.setVisible(wrapMenuItem.isSelected());
2938 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2939 alignPanel.updateLayout();
2943 public void showAllSeqs_actionPerformed(ActionEvent e)
2945 viewport.showAllHiddenSeqs();
2949 public void showAllColumns_actionPerformed(ActionEvent e)
2951 viewport.showAllHiddenColumns();
2956 public void hideSelSequences_actionPerformed(ActionEvent e)
2958 viewport.hideAllSelectedSeqs();
2959 // alignPanel.paintAlignment(true);
2963 * called by key handler and the hide all/show all menu items
2968 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2971 boolean hide = false;
2972 SequenceGroup sg = viewport.getSelectionGroup();
2973 if (!toggleSeqs && !toggleCols)
2975 // Hide everything by the current selection - this is a hack - we do the
2976 // invert and then hide
2977 // first check that there will be visible columns after the invert.
2978 if ((viewport.getColumnSelection() != null
2979 && viewport.getColumnSelection().getSelected() != null && viewport
2980 .getColumnSelection().getSelected().size() > 0)
2981 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2984 // now invert the sequence set, if required - empty selection implies
2985 // that no hiding is required.
2988 invertSequenceMenuItem_actionPerformed(null);
2989 sg = viewport.getSelectionGroup();
2993 viewport.expandColSelection(sg, true);
2994 // finally invert the column selection and get the new sequence
2996 invertColSel_actionPerformed(null);
3003 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3005 hideSelSequences_actionPerformed(null);
3008 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3011 showAllSeqs_actionPerformed(null);
3017 if (viewport.getColumnSelection().getSelected().size() > 0)
3019 hideSelColumns_actionPerformed(null);
3022 viewport.setSelectionGroup(sg);
3027 showAllColumns_actionPerformed(null);
3036 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3037 * event.ActionEvent)
3040 public void hideAllButSelection_actionPerformed(ActionEvent e)
3042 toggleHiddenRegions(false, false);
3049 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3053 public void hideAllSelection_actionPerformed(ActionEvent e)
3055 SequenceGroup sg = viewport.getSelectionGroup();
3056 viewport.expandColSelection(sg, false);
3057 viewport.hideAllSelectedSeqs();
3058 viewport.hideSelectedColumns();
3059 alignPanel.paintAlignment(true);
3066 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3070 public void showAllhidden_actionPerformed(ActionEvent e)
3072 viewport.showAllHiddenColumns();
3073 viewport.showAllHiddenSeqs();
3074 alignPanel.paintAlignment(true);
3078 public void hideSelColumns_actionPerformed(ActionEvent e)
3080 viewport.hideSelectedColumns();
3081 alignPanel.paintAlignment(true);
3085 public void hiddenMarkers_actionPerformed(ActionEvent e)
3087 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3098 protected void scaleAbove_actionPerformed(ActionEvent e)
3100 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3101 alignPanel.paintAlignment(true);
3111 protected void scaleLeft_actionPerformed(ActionEvent e)
3113 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3114 alignPanel.paintAlignment(true);
3124 protected void scaleRight_actionPerformed(ActionEvent e)
3126 viewport.setScaleRightWrapped(scaleRight.isSelected());
3127 alignPanel.paintAlignment(true);
3137 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3139 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3140 alignPanel.paintAlignment(true);
3150 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3152 viewport.setShowText(viewTextMenuItem.isSelected());
3153 alignPanel.paintAlignment(true);
3163 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3165 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3166 alignPanel.paintAlignment(true);
3169 public FeatureSettings featureSettings;
3172 public FeatureSettingsControllerI getFeatureSettingsUI()
3174 return featureSettings;
3178 public void featureSettings_actionPerformed(ActionEvent e)
3180 if (featureSettings != null)
3182 featureSettings.close();
3183 featureSettings = null;
3185 if (!showSeqFeatures.isSelected())
3187 // make sure features are actually displayed
3188 showSeqFeatures.setSelected(true);
3189 showSeqFeatures_actionPerformed(null);
3191 featureSettings = new FeatureSettings(this);
3195 * Set or clear 'Show Sequence Features'
3201 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3203 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3204 alignPanel.paintAlignment(true);
3205 if (alignPanel.getOverviewPanel() != null)
3207 alignPanel.getOverviewPanel().updateOverviewImage();
3212 * Set or clear 'Show Sequence Features'
3218 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3220 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3222 if (viewport.isShowSequenceFeaturesHeight())
3224 // ensure we're actually displaying features
3225 viewport.setShowSequenceFeatures(true);
3226 showSeqFeatures.setSelected(true);
3228 alignPanel.paintAlignment(true);
3229 if (alignPanel.getOverviewPanel() != null)
3231 alignPanel.getOverviewPanel().updateOverviewImage();
3236 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3237 * the annotations panel as a whole.
3239 * The options to show/hide all annotations should be enabled when the panel
3240 * is shown, and disabled when the panel is hidden.
3245 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3247 final boolean setVisible = annotationPanelMenuItem.isSelected();
3248 viewport.setShowAnnotation(setVisible);
3249 this.showAllSeqAnnotations.setEnabled(setVisible);
3250 this.hideAllSeqAnnotations.setEnabled(setVisible);
3251 this.showAllAlAnnotations.setEnabled(setVisible);
3252 this.hideAllAlAnnotations.setEnabled(setVisible);
3253 alignPanel.updateLayout();
3257 public void alignmentProperties()
3259 JEditorPane editPane = new JEditorPane("text/html", "");
3260 editPane.setEditable(false);
3261 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3263 editPane.setText(MessageManager.formatMessage("label.html_content",
3265 { contents.toString() }));
3266 JInternalFrame frame = new JInternalFrame();
3267 frame.getContentPane().add(new JScrollPane(editPane));
3269 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3270 "label.alignment_properties", new Object[]
3271 { getTitle() }), 500, 400);
3281 public void overviewMenuItem_actionPerformed(ActionEvent e)
3283 if (alignPanel.overviewPanel != null)
3288 JInternalFrame frame = new JInternalFrame();
3289 OverviewPanel overview = new OverviewPanel(alignPanel);
3290 frame.setContentPane(overview);
3291 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3292 "label.overview_params", new Object[]
3293 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3295 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3296 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3299 public void internalFrameClosed(
3300 javax.swing.event.InternalFrameEvent evt)
3302 alignPanel.setOverviewPanel(null);
3306 alignPanel.setOverviewPanel(overview);
3310 public void textColour_actionPerformed(ActionEvent e)
3312 new TextColourChooser().chooseColour(alignPanel, null);
3322 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3334 public void clustalColour_actionPerformed(ActionEvent e)
3336 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3337 viewport.getHiddenRepSequences()));
3347 public void zappoColour_actionPerformed(ActionEvent e)
3349 changeColour(new ZappoColourScheme());
3359 public void taylorColour_actionPerformed(ActionEvent e)
3361 changeColour(new TaylorColourScheme());
3371 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3373 changeColour(new HydrophobicColourScheme());
3383 public void helixColour_actionPerformed(ActionEvent e)
3385 changeColour(new HelixColourScheme());
3395 public void strandColour_actionPerformed(ActionEvent e)
3397 changeColour(new StrandColourScheme());
3407 public void turnColour_actionPerformed(ActionEvent e)
3409 changeColour(new TurnColourScheme());
3419 public void buriedColour_actionPerformed(ActionEvent e)
3421 changeColour(new BuriedColourScheme());
3431 public void nucleotideColour_actionPerformed(ActionEvent e)
3433 changeColour(new NucleotideColourScheme());
3437 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3439 changeColour(new PurinePyrimidineColourScheme());
3443 * public void covariationColour_actionPerformed(ActionEvent e) {
3445 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3449 public void annotationColour_actionPerformed(ActionEvent e)
3451 new AnnotationColourChooser(viewport, alignPanel);
3455 public void annotationColumn_actionPerformed(ActionEvent e)
3457 new AnnotationColumnChooser(viewport, alignPanel);
3461 public void rnahelicesColour_actionPerformed(ActionEvent e)
3463 new RNAHelicesColourChooser(viewport, alignPanel);
3473 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3475 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3484 public void changeColour(ColourSchemeI cs)
3486 // TODO: compare with applet and pull up to model method
3491 if (viewport.getAbovePIDThreshold())
3493 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3495 cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
3499 cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
3502 if (viewport.getConservationSelected())
3505 Alignment al = (Alignment) viewport.getAlignment();
3506 Conservation c = new Conservation("All",
3507 ResidueProperties.propHash, 3, al.getSequences(), 0,
3511 c.verdict(false, viewport.getConsPercGaps());
3513 cs.setConservation(c);
3515 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3520 cs.setConservation(null);
3523 cs.setConsensus(viewport.getSequenceConsensusHash());
3526 viewport.setGlobalColourScheme(cs);
3528 if (viewport.getColourAppliesToAllGroups())
3531 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3539 if (cs instanceof ClustalxColourScheme)
3541 sg.cs = new ClustalxColourScheme(sg,
3542 viewport.getHiddenRepSequences());
3544 else if (cs instanceof UserColourScheme)
3546 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3552 sg.cs = cs.getClass().newInstance();
3553 } catch (Exception ex)
3558 if (viewport.getAbovePIDThreshold()
3559 || cs instanceof PIDColourScheme
3560 || cs instanceof Blosum62ColourScheme)
3562 sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
3564 sg.cs.setConsensus(AAFrequency.calculate(
3565 sg.getSequences(viewport.getHiddenRepSequences()),
3566 sg.getStartRes(), sg.getEndRes() + 1));
3570 sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
3573 if (viewport.getConservationSelected())
3575 Conservation c = new Conservation("Group",
3576 ResidueProperties.propHash, 3, sg.getSequences(viewport
3577 .getHiddenRepSequences()), sg.getStartRes(),
3578 sg.getEndRes() + 1);
3580 c.verdict(false, viewport.getConsPercGaps());
3581 sg.cs.setConservation(c);
3585 sg.cs.setConservation(null);
3590 if (alignPanel.getOverviewPanel() != null)
3592 alignPanel.getOverviewPanel().updateOverviewImage();
3595 alignPanel.paintAlignment(true);
3605 protected void modifyPID_actionPerformed(ActionEvent e)
3607 if (viewport.getAbovePIDThreshold()
3608 && viewport.getGlobalColourScheme() != null)
3610 SliderPanel.setPIDSliderSource(alignPanel,
3611 viewport.getGlobalColourScheme(), "Background");
3612 SliderPanel.showPIDSlider();
3623 protected void modifyConservation_actionPerformed(ActionEvent e)
3625 if (viewport.getConservationSelected()
3626 && viewport.getGlobalColourScheme() != null)
3628 SliderPanel.setConservationSlider(alignPanel,
3629 viewport.getGlobalColourScheme(), "Background");
3630 SliderPanel.showConservationSlider();
3641 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3643 viewport.setConservationSelected(conservationMenuItem.isSelected());
3645 viewport.setAbovePIDThreshold(false);
3646 abovePIDThreshold.setSelected(false);
3648 changeColour(viewport.getGlobalColourScheme());
3650 modifyConservation_actionPerformed(null);
3660 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3662 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3664 conservationMenuItem.setSelected(false);
3665 viewport.setConservationSelected(false);
3667 changeColour(viewport.getGlobalColourScheme());
3669 modifyPID_actionPerformed(null);
3679 public void userDefinedColour_actionPerformed(ActionEvent e)
3681 if (e.getActionCommand().equals(
3682 MessageManager.getString("action.user_defined")))
3684 new UserDefinedColours(alignPanel, null);
3688 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3689 .getUserColourSchemes().get(e.getActionCommand());
3695 public void updateUserColourMenu()
3698 Component[] menuItems = colourMenu.getMenuComponents();
3699 int iSize = menuItems.length;
3700 for (int i = 0; i < iSize; i++)
3702 if (menuItems[i].getName() != null
3703 && menuItems[i].getName().equals("USER_DEFINED"))
3705 colourMenu.remove(menuItems[i]);
3709 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3711 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3712 .getUserColourSchemes().keys();
3714 while (userColours.hasMoreElements())
3716 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3717 userColours.nextElement().toString());
3718 radioItem.setName("USER_DEFINED");
3719 radioItem.addMouseListener(new MouseAdapter()
3722 public void mousePressed(MouseEvent evt)
3724 if (evt.isControlDown()
3725 || SwingUtilities.isRightMouseButton(evt))
3727 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3729 int option = JOptionPane.showInternalConfirmDialog(
3730 jalview.gui.Desktop.desktop,
3732 .getString("label.remove_from_default_list"),
3734 .getString("label.remove_user_defined_colour"),
3735 JOptionPane.YES_NO_OPTION);
3736 if (option == JOptionPane.YES_OPTION)
3738 jalview.gui.UserDefinedColours
3739 .removeColourFromDefaults(radioItem.getText());
3740 colourMenu.remove(radioItem);
3744 radioItem.addActionListener(new ActionListener()
3747 public void actionPerformed(ActionEvent evt)
3749 userDefinedColour_actionPerformed(evt);
3756 radioItem.addActionListener(new ActionListener()
3759 public void actionPerformed(ActionEvent evt)
3761 userDefinedColour_actionPerformed(evt);
3765 colourMenu.insert(radioItem, 15);
3766 colours.add(radioItem);
3778 public void PIDColour_actionPerformed(ActionEvent e)
3780 changeColour(new PIDColourScheme());
3790 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3792 changeColour(new Blosum62ColourScheme());
3802 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3804 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3805 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3806 .getAlignment().getSequenceAt(0), null);
3807 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3808 viewport.getAlignment()));
3809 alignPanel.paintAlignment(true);
3819 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3821 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3822 AlignmentSorter.sortByID(viewport.getAlignment());
3823 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3824 viewport.getAlignment()));
3825 alignPanel.paintAlignment(true);
3835 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3837 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3838 AlignmentSorter.sortByLength(viewport.getAlignment());
3839 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3840 viewport.getAlignment()));
3841 alignPanel.paintAlignment(true);
3851 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3853 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3854 AlignmentSorter.sortByGroup(viewport.getAlignment());
3855 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3856 viewport.getAlignment()));
3858 alignPanel.paintAlignment(true);
3868 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3870 new RedundancyPanel(alignPanel, this);
3880 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3882 if ((viewport.getSelectionGroup() == null)
3883 || (viewport.getSelectionGroup().getSize() < 2))
3885 JOptionPane.showInternalMessageDialog(this, MessageManager
3886 .getString("label.you_must_select_least_two_sequences"),
3887 MessageManager.getString("label.invalid_selection"),
3888 JOptionPane.WARNING_MESSAGE);
3892 JInternalFrame frame = new JInternalFrame();
3893 frame.setContentPane(new PairwiseAlignPanel(viewport));
3894 Desktop.addInternalFrame(frame,
3895 MessageManager.getString("action.pairwise_alignment"), 600,
3907 public void PCAMenuItem_actionPerformed(ActionEvent e)
3909 if (((viewport.getSelectionGroup() != null)
3910 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3911 .getSelectionGroup().getSize() > 0))
3912 || (viewport.getAlignment().getHeight() < 4))
3915 .showInternalMessageDialog(
3918 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3920 .getString("label.sequence_selection_insufficient"),
3921 JOptionPane.WARNING_MESSAGE);
3926 new PCAPanel(alignPanel);
3930 public void autoCalculate_actionPerformed(ActionEvent e)
3932 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3933 if (viewport.autoCalculateConsensus)
3935 viewport.firePropertyChange("alignment", null, viewport
3936 .getAlignment().getSequences());
3941 public void sortByTreeOption_actionPerformed(ActionEvent e)
3943 viewport.sortByTree = sortByTree.isSelected();
3947 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3949 viewport.followSelection = listenToViewSelections.isSelected();
3959 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3961 newTreePanel("AV", "PID", "Average distance tree using PID");
3971 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3973 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3983 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3985 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3995 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3997 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
4010 void newTreePanel(String type, String pwType, String title)
4014 if (viewport.getSelectionGroup() != null
4015 && viewport.getSelectionGroup().getSize() > 0)
4017 if (viewport.getSelectionGroup().getSize() < 3)
4023 .getString("label.you_need_more_two_sequences_selected_build_tree"),
4025 .getString("label.not_enough_sequences"),
4026 JOptionPane.WARNING_MESSAGE);
4030 SequenceGroup sg = viewport.getSelectionGroup();
4032 /* Decide if the selection is a column region */
4033 for (SequenceI _s : sg.getSequences())
4035 if (_s.getLength() < sg.getEndRes())
4041 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
4043 .getString("label.sequences_selection_not_aligned"),
4044 JOptionPane.WARNING_MESSAGE);
4050 title = title + " on region";
4051 tp = new TreePanel(alignPanel, type, pwType);
4055 // are the visible sequences aligned?
4056 if (!viewport.getAlignment().isAligned(false))
4062 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4064 .getString("label.sequences_not_aligned"),
4065 JOptionPane.WARNING_MESSAGE);
4070 if (viewport.getAlignment().getHeight() < 2)
4075 tp = new TreePanel(alignPanel, type, pwType);
4080 if (viewport.viewName != null)
4082 title += viewport.viewName + " of ";
4085 title += this.title;
4087 Desktop.addInternalFrame(tp, title, 600, 500);
4098 public void addSortByOrderMenuItem(String title,
4099 final AlignmentOrder order)
4101 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title}));
4103 item.addActionListener(new java.awt.event.ActionListener()
4106 public void actionPerformed(ActionEvent e)
4108 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4110 // TODO: JBPNote - have to map order entries to curent SequenceI
4112 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4114 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4117 alignPanel.paintAlignment(true);
4123 * Add a new sort by annotation score menu item
4126 * the menu to add the option to
4128 * the label used to retrieve scores for each sequence on the
4131 public void addSortByAnnotScoreMenuItem(JMenu sort,
4132 final String scoreLabel)
4134 final JMenuItem item = new JMenuItem(scoreLabel);
4136 item.addActionListener(new java.awt.event.ActionListener()
4139 public void actionPerformed(ActionEvent e)
4141 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4142 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4143 viewport.getAlignment());// ,viewport.getSelectionGroup());
4144 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4145 viewport.getAlignment()));
4146 alignPanel.paintAlignment(true);
4152 * last hash for alignment's annotation array - used to minimise cost of
4155 protected int _annotationScoreVectorHash;
4158 * search the alignment and rebuild the sort by annotation score submenu the
4159 * last alignment annotation vector hash is stored to minimize cost of
4160 * rebuilding in subsequence calls.
4164 public void buildSortByAnnotationScoresMenu()
4166 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4171 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4173 sortByAnnotScore.removeAll();
4174 // almost certainly a quicker way to do this - but we keep it simple
4175 Hashtable scoreSorts = new Hashtable();
4176 AlignmentAnnotation aann[];
4177 for (SequenceI sqa : viewport.getAlignment().getSequences())
4179 aann = sqa.getAnnotation();
4180 for (int i = 0; aann != null && i < aann.length; i++)
4182 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4184 scoreSorts.put(aann[i].label, aann[i].label);
4188 Enumeration labels = scoreSorts.keys();
4189 while (labels.hasMoreElements())
4191 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4192 (String) labels.nextElement());
4194 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4197 _annotationScoreVectorHash = viewport.getAlignment()
4198 .getAlignmentAnnotation().hashCode();
4203 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4204 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4205 * call. Listeners are added to remove the menu item when the treePanel is
4206 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4210 * Displayed tree window.
4212 * SortBy menu item title.
4215 public void buildTreeMenu()
4217 calculateTree.removeAll();
4218 // build the calculate menu
4220 for (final String type : new String[]
4223 String treecalcnm = MessageManager.getString("label.tree_calc_"
4224 + type.toLowerCase());
4225 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4227 JMenuItem tm = new JMenuItem();
4228 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4229 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4231 String smn = MessageManager.getStringOrReturn(
4232 "label.score_model_", sm.getName());
4233 final String title = MessageManager.formatMessage(
4234 "label.treecalc_title", treecalcnm, smn);
4235 tm.setText(title);//
4236 tm.addActionListener(new java.awt.event.ActionListener()
4239 public void actionPerformed(ActionEvent e)
4241 newTreePanel(type, pwtype, title);
4244 calculateTree.add(tm);
4249 sortByTreeMenu.removeAll();
4251 List<Component> comps = PaintRefresher.components.get(viewport
4252 .getSequenceSetId());
4253 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4254 for (Component comp : comps)
4256 if (comp instanceof TreePanel)
4258 treePanels.add((TreePanel) comp);
4262 if (treePanels.size() < 1)
4264 sortByTreeMenu.setVisible(false);
4268 sortByTreeMenu.setVisible(true);
4270 for (final TreePanel tp : treePanels)
4272 final JMenuItem item = new JMenuItem(tp.getTitle());
4273 item.addActionListener(new java.awt.event.ActionListener()
4276 public void actionPerformed(ActionEvent e)
4278 tp.sortByTree_actionPerformed();
4279 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4284 sortByTreeMenu.add(item);
4288 public boolean sortBy(AlignmentOrder alorder, String undoname)
4290 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4291 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4292 if (undoname != null)
4294 addHistoryItem(new OrderCommand(undoname, oldOrder,
4295 viewport.getAlignment()));
4297 alignPanel.paintAlignment(true);
4302 * Work out whether the whole set of sequences or just the selected set will
4303 * be submitted for multiple alignment.
4306 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4308 // Now, check we have enough sequences
4309 AlignmentView msa = null;
4311 if ((viewport.getSelectionGroup() != null)
4312 && (viewport.getSelectionGroup().getSize() > 1))
4314 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4315 // some common interface!
4317 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4318 * SequenceI[sz = seqs.getSize(false)];
4320 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4321 * seqs.getSequenceAt(i); }
4323 msa = viewport.getAlignmentView(true);
4325 else if (viewport.getSelectionGroup() != null
4326 && viewport.getSelectionGroup().getSize() == 1)
4328 int option = JOptionPane.showConfirmDialog(this,
4329 MessageManager.getString("warn.oneseq_msainput_selection"),
4330 MessageManager.getString("label.invalid_selection"),
4331 JOptionPane.OK_CANCEL_OPTION);
4332 if (option == JOptionPane.OK_OPTION)
4334 msa = viewport.getAlignmentView(false);
4339 msa = viewport.getAlignmentView(false);
4345 * Decides what is submitted to a secondary structure prediction service: the
4346 * first sequence in the alignment, or in the current selection, or, if the
4347 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4348 * region or the whole alignment. (where the first sequence in the set is the
4349 * one that the prediction will be for).
4351 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4353 AlignmentView seqs = null;
4355 if ((viewport.getSelectionGroup() != null)
4356 && (viewport.getSelectionGroup().getSize() > 0))
4358 seqs = viewport.getAlignmentView(true);
4362 seqs = viewport.getAlignmentView(false);
4364 // limit sequences - JBPNote in future - could spawn multiple prediction
4366 // TODO: viewport.getAlignment().isAligned is a global state - the local
4367 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4368 if (!viewport.getAlignment().isAligned(false))
4370 seqs.setSequences(new SeqCigar[]
4371 { seqs.getSequences()[0] });
4372 // TODO: if seqs.getSequences().length>1 then should really have warned
4386 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4388 // Pick the tree file
4389 JalviewFileChooser chooser = new JalviewFileChooser(
4390 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4391 chooser.setFileView(new JalviewFileView());
4392 chooser.setDialogTitle(MessageManager
4393 .getString("label.select_newick_like_tree_file"));
4394 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4396 int value = chooser.showOpenDialog(null);
4398 if (value == JalviewFileChooser.APPROVE_OPTION)
4400 String choice = chooser.getSelectedFile().getPath();
4401 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4402 jalview.io.NewickFile fin = null;
4405 fin = new jalview.io.NewickFile(choice, "File");
4406 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4407 } catch (Exception ex)
4414 .getString("label.problem_reading_tree_file"),
4415 JOptionPane.WARNING_MESSAGE);
4416 ex.printStackTrace();
4418 if (fin != null && fin.hasWarningMessage())
4420 JOptionPane.showMessageDialog(Desktop.desktop, fin
4421 .getWarningMessage(), MessageManager
4422 .getString("label.possible_problem_with_tree_file"),
4423 JOptionPane.WARNING_MESSAGE);
4429 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4431 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4434 public TreePanel ShowNewickTree(NewickFile nf, String title)
4436 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4439 public TreePanel ShowNewickTree(NewickFile nf, String title,
4440 AlignmentView input)
4442 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4445 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4446 int h, int x, int y)
4448 return ShowNewickTree(nf, title, null, w, h, x, y);
4452 * Add a treeviewer for the tree extracted from a newick file object to the
4453 * current alignment view
4460 * Associated alignment input data (or null)
4469 * @return TreePanel handle
4471 public TreePanel ShowNewickTree(NewickFile nf, String title,
4472 AlignmentView input, int w, int h, int x, int y)
4474 TreePanel tp = null;
4480 if (nf.getTree() != null)
4482 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4488 tp.setLocation(x, y);
4491 Desktop.addInternalFrame(tp, title, w, h);
4493 } catch (Exception ex)
4495 ex.printStackTrace();
4501 private boolean buildingMenu = false;
4504 * Generates menu items and listener event actions for web service clients
4507 public void BuildWebServiceMenu()
4509 while (buildingMenu)
4513 System.err.println("Waiting for building menu to finish.");
4515 } catch (Exception e)
4519 final AlignFrame me = this;
4520 buildingMenu = true;
4521 new Thread(new Runnable()
4526 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4529 System.err.println("Building ws menu again "
4530 + Thread.currentThread());
4531 // TODO: add support for context dependent disabling of services based
4533 // alignment and current selection
4534 // TODO: add additional serviceHandle parameter to specify abstract
4536 // class independently of AbstractName
4537 // TODO: add in rediscovery GUI function to restart discoverer
4538 // TODO: group services by location as well as function and/or
4540 // object broker mechanism.
4541 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4542 final IProgressIndicator af = me;
4543 final JMenu msawsmenu = new JMenu("Alignment");
4544 final JMenu secstrmenu = new JMenu(
4545 "Secondary Structure Prediction");
4546 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4547 final JMenu analymenu = new JMenu("Analysis");
4548 final JMenu dismenu = new JMenu("Protein Disorder");
4549 // final JMenu msawsmenu = new
4550 // JMenu(MessageManager.getString("label.alignment"));
4551 // final JMenu secstrmenu = new
4552 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4553 // final JMenu seqsrchmenu = new
4554 // JMenu(MessageManager.getString("label.sequence_database_search"));
4555 // final JMenu analymenu = new
4556 // JMenu(MessageManager.getString("label.analysis"));
4557 // final JMenu dismenu = new
4558 // JMenu(MessageManager.getString("label.protein_disorder"));
4559 // JAL-940 - only show secondary structure prediction services from
4560 // the legacy server
4561 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4563 Discoverer.services != null && (Discoverer.services.size() > 0))
4565 // TODO: refactor to allow list of AbstractName/Handler bindings to
4567 // stored or retrieved from elsewhere
4568 // No MSAWS used any more:
4569 // Vector msaws = null; // (Vector)
4570 // Discoverer.services.get("MsaWS");
4571 Vector secstrpr = (Vector) Discoverer.services
4573 if (secstrpr != null)
4575 // Add any secondary structure prediction services
4576 for (int i = 0, j = secstrpr.size(); i < j; i++)
4578 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4580 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4581 .getServiceClient(sh);
4582 int p = secstrmenu.getItemCount();
4583 impl.attachWSMenuEntry(secstrmenu, me);
4584 int q = secstrmenu.getItemCount();
4585 for (int litm = p; litm < q; litm++)
4587 legacyItems.add(secstrmenu.getItem(litm));
4593 // Add all submenus in the order they should appear on the web
4595 wsmenu.add(msawsmenu);
4596 wsmenu.add(secstrmenu);
4597 wsmenu.add(dismenu);
4598 wsmenu.add(analymenu);
4599 // No search services yet
4600 // wsmenu.add(seqsrchmenu);
4602 javax.swing.SwingUtilities.invokeLater(new Runnable()
4609 webService.removeAll();
4610 // first, add discovered services onto the webservices menu
4611 if (wsmenu.size() > 0)
4613 for (int i = 0, j = wsmenu.size(); i < j; i++)
4615 webService.add(wsmenu.get(i));
4620 webService.add(me.webServiceNoServices);
4622 // TODO: move into separate menu builder class.
4623 boolean new_sspred = false;
4624 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4626 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4627 if (jws2servs != null)
4629 if (jws2servs.hasServices())
4631 jws2servs.attachWSMenuEntry(webService, me);
4632 for (Jws2Instance sv : jws2servs.getServices())
4634 if (sv.description.toLowerCase().contains("jpred"))
4636 for (JMenuItem jmi : legacyItems)
4638 jmi.setVisible(false);
4644 if (jws2servs.isRunning())
4646 JMenuItem tm = new JMenuItem(
4647 "Still discovering JABA Services");
4648 tm.setEnabled(false);
4653 build_urlServiceMenu(me.webService);
4654 build_fetchdbmenu(webService);
4655 for (JMenu item : wsmenu)
4657 if (item.getItemCount() == 0)
4659 item.setEnabled(false);
4663 item.setEnabled(true);
4666 } catch (Exception e)
4669 .debug("Exception during web service menu building process.",
4674 } catch (Exception e)
4677 buildingMenu = false;
4684 * construct any groupURL type service menu entries.
4688 private void build_urlServiceMenu(JMenu webService)
4690 // TODO: remove this code when 2.7 is released
4691 // DEBUG - alignmentView
4693 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4694 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4696 * @Override public void actionPerformed(ActionEvent e) {
4697 * jalview.datamodel.AlignmentView
4698 * .testSelectionViews(af.viewport.getAlignment(),
4699 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4701 * }); webService.add(testAlView);
4703 // TODO: refactor to RestClient discoverer and merge menu entries for
4704 // rest-style services with other types of analysis/calculation service
4705 // SHmmr test client - still being implemented.
4706 // DEBUG - alignmentView
4708 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4711 client.attachWSMenuEntry(
4712 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4718 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4719 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4720 * getProperty("LAST_DIRECTORY"));
4722 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4723 * to Vamsas file"); chooser.setToolTipText("Export");
4725 * int value = chooser.showSaveDialog(this);
4727 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4728 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4729 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4730 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4733 * prototype of an automatically enabled/disabled analysis function
4736 protected void setShowProductsEnabled()
4738 SequenceI[] selection = viewport.getSequenceSelection();
4739 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4740 viewport.getAlignment().getDataset()))
4742 showProducts.setEnabled(true);
4747 showProducts.setEnabled(false);
4752 * search selection for sequence xRef products and build the show products
4757 * @return true if showProducts menu should be enabled.
4759 public boolean canShowProducts(SequenceI[] selection,
4760 boolean isRegionSelection, Alignment dataset)
4762 boolean showp = false;
4765 showProducts.removeAll();
4766 final boolean dna = viewport.getAlignment().isNucleotide();
4767 final Alignment ds = dataset;
4768 String[] ptypes = (selection == null || selection.length == 0) ? null
4769 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4771 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4772 // selection, dataset, true);
4773 final SequenceI[] sel = selection;
4774 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4777 final boolean isRegSel = isRegionSelection;
4778 final AlignFrame af = this;
4779 final String source = ptypes[t];
4780 JMenuItem xtype = new JMenuItem(ptypes[t]);
4781 xtype.addActionListener(new ActionListener()
4785 public void actionPerformed(ActionEvent e)
4787 // TODO: new thread for this call with vis-delay
4788 af.showProductsFor(af.viewport.getSequenceSelection(),
4789 isRegSel, dna, source);
4793 showProducts.add(xtype);
4795 showProducts.setVisible(showp);
4796 showProducts.setEnabled(showp);
4797 } catch (Exception e)
4799 jalview.bin.Cache.log
4800 .warn("canTranslate threw an exception - please report to help@jalview.org",
4807 protected void showProductsFor(final SequenceI[] sel,
4808 final boolean isRegSel, final boolean dna, final String source)
4810 Runnable foo = new Runnable()
4816 final long sttime = System.currentTimeMillis();
4817 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4818 "status.searching_for_sequences_from", new Object[]
4819 { source }), sttime);
4822 // update our local dataset reference
4823 Alignment ds = AlignFrame.this.getViewport().getAlignment()
4825 Alignment prods = CrossRef
4826 .findXrefSequences(sel, dna, source, ds);
4829 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4830 for (int s = 0; s < sprods.length; s++)
4832 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4833 if (ds.getSequences() == null
4834 || !ds.getSequences().contains(
4835 sprods[s].getDatasetSequence()))
4837 ds.addSequence(sprods[s].getDatasetSequence());
4839 sprods[s].updatePDBIds();
4841 Alignment al = new Alignment(sprods);
4845 * Copy dna-to-protein mappings to new alignment
4847 // TODO 1: no mappings are set up for EMBL product
4848 // TODO 2: if they were, should add them to protein alignment, not
4850 Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4851 for (AlignedCodonFrame acf : cf)
4853 al.addCodonFrame(acf);
4855 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4857 String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4858 + " for " + ((isRegSel) ? "selected region of " : "")
4860 naf.setTitle(newtitle);
4862 // temporary flag until SplitFrame is released
4863 boolean asSplitFrame = Cache.getDefault(
4864 Preferences.ENABLE_SPLIT_FRAME, false);
4868 * Make a copy of this alignment (sharing the same dataset
4869 * sequences). If we are DNA, drop introns and update mappings
4871 AlignmentI copyAlignment = null;
4872 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4873 .getSequenceSelection();
4876 copyAlignment = AlignmentUtils.makeExonAlignment(
4877 sequenceSelection, cf);
4878 al.getCodonFrames().clear();
4879 al.getCodonFrames().addAll(cf);
4880 final StructureSelectionManager ssm = StructureSelectionManager
4881 .getStructureSelectionManager(Desktop.instance);
4882 ssm.addMappings(cf);
4886 copyAlignment = new Alignment(new Alignment(
4887 sequenceSelection));
4889 AlignFrame copyThis = new AlignFrame(copyAlignment,
4890 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4891 copyThis.setTitle(AlignFrame.this.getTitle());
4892 // SplitFrame with dna above, protein below
4893 SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4894 dna ? naf : copyThis);
4895 naf.setVisible(true);
4896 copyThis.setVisible(true);
4897 String linkedTitle = MessageManager
4898 .getString("label.linked_view_title");
4899 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4903 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4909 System.err.println("No Sequences generated for xRef type "
4912 } catch (Exception e)
4914 jalview.bin.Cache.log.error(
4915 "Exception when finding crossreferences", e);
4916 } catch (OutOfMemoryError e)
4918 new OOMWarning("whilst fetching crossreferences", e);
4921 jalview.bin.Cache.log.error("Error when finding crossreferences",
4924 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4925 "status.finished_searching_for_sequences_from",
4932 Thread frunner = new Thread(foo);
4936 public boolean canShowTranslationProducts(SequenceI[] selection,
4937 AlignmentI alignment)
4942 return (jalview.analysis.Dna.canTranslate(selection,
4943 viewport.getViewAsVisibleContigs(true)));
4944 } catch (Exception e)
4946 jalview.bin.Cache.log
4947 .warn("canTranslate threw an exception - please report to help@jalview.org",
4954 * Construct and display a new frame containing the translation of this
4955 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4958 public void showTranslation_actionPerformed(ActionEvent e)
4960 AlignmentI al = null;
4963 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4965 al = dna.translateCdna();
4966 } catch (Exception ex)
4968 jalview.bin.Cache.log.error(
4969 "Exception during translation. Please report this !", ex);
4970 final String msg = MessageManager
4971 .getString("label.error_when_translating_sequences_submit_bug_report");
4972 final String title = MessageManager
4973 .getString("label.implementation_error")
4974 + MessageManager.getString("translation_failed");
4975 JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
4976 JOptionPane.ERROR_MESSAGE);
4979 if (al == null || al.getHeight() == 0)
4981 final String msg = MessageManager
4982 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4983 final String title = MessageManager
4984 .getString("label.translation_failed");
4985 JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
4986 JOptionPane.WARNING_MESSAGE);
4990 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4991 af.setFileFormat(this.currentFileFormat);
4992 final String newTitle = MessageManager.formatMessage(
4993 "label.translation_of_params", new Object[]
4994 { this.getTitle() });
4995 af.setTitle(newTitle);
4996 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
4998 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4999 viewport.openSplitFrame(af, new Alignment(seqs),
5000 al.getCodonFrames());
5004 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
5011 * Set the file format
5015 public void setFileFormat(String fileFormat)
5017 this.currentFileFormat = fileFormat;
5021 * Try to load a features file onto the alignment.
5024 * contents or path to retrieve file
5026 * access mode of file (see jalview.io.AlignFile)
5027 * @return true if features file was parsed correctly.
5029 public boolean parseFeaturesFile(String file, String type)
5031 return avc.parseFeaturesFile(file, type,
5032 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5037 public void refreshFeatureUI(boolean enableIfNecessary)
5039 // note - currently this is only still here rather than in the controller
5040 // because of the featureSettings hard reference that is yet to be
5042 if (enableIfNecessary)
5044 viewport.setShowSequenceFeatures(true);
5045 showSeqFeatures.setSelected(true);
5051 public void dragEnter(DropTargetDragEvent evt)
5056 public void dragExit(DropTargetEvent evt)
5061 public void dragOver(DropTargetDragEvent evt)
5066 public void dropActionChanged(DropTargetDragEvent evt)
5071 public void drop(DropTargetDropEvent evt)
5073 Transferable t = evt.getTransferable();
5074 java.util.List files = null;
5078 DataFlavor uriListFlavor = new DataFlavor(
5079 "text/uri-list;class=java.lang.String");
5080 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5082 // Works on Windows and MacOSX
5083 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5084 files = (java.util.List) t
5085 .getTransferData(DataFlavor.javaFileListFlavor);
5087 else if (t.isDataFlavorSupported(uriListFlavor))
5089 // This is used by Unix drag system
5090 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5091 String data = (String) t.getTransferData(uriListFlavor);
5092 files = new java.util.ArrayList(1);
5093 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5094 data, "\r\n"); st.hasMoreTokens();)
5096 String s = st.nextToken();
5097 if (s.startsWith("#"))
5099 // the line is a comment (as per the RFC 2483)
5103 java.net.URI uri = new java.net.URI(s);
5104 // check to see if we can handle this kind of URI
5105 if (uri.getScheme().toLowerCase().startsWith("http"))
5107 files.add(uri.toString());
5111 // otherwise preserve old behaviour: catch all for file objects
5112 java.io.File file = new java.io.File(uri);
5113 files.add(file.toString());
5117 } catch (Exception e)
5119 e.printStackTrace();
5125 // check to see if any of these files have names matching sequences in
5127 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5128 .getAlignment().getSequencesArray());
5130 * Object[] { String,SequenceI}
5132 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5133 ArrayList<String> filesnotmatched = new ArrayList<String>();
5134 for (int i = 0; i < files.size(); i++)
5136 String file = files.get(i).toString();
5138 String protocol = FormatAdapter.checkProtocol(file);
5139 if (protocol == jalview.io.FormatAdapter.FILE)
5141 File fl = new File(file);
5142 pdbfn = fl.getName();
5144 else if (protocol == jalview.io.FormatAdapter.URL)
5146 URL url = new URL(file);
5147 pdbfn = url.getFile();
5149 if (pdbfn.length() > 0)
5151 // attempt to find a match in the alignment
5152 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5153 int l = 0, c = pdbfn.indexOf(".");
5154 while (mtch == null && c != -1)
5159 } while ((c = pdbfn.indexOf(".", l)) > l);
5162 pdbfn = pdbfn.substring(0, l);
5164 mtch = idm.findAllIdMatches(pdbfn);
5171 type = new IdentifyFile().Identify(file, protocol);
5172 } catch (Exception ex)
5178 if (type.equalsIgnoreCase("PDB"))
5180 filesmatched.add(new Object[]
5181 { file, protocol, mtch });
5186 // File wasn't named like one of the sequences or wasn't a PDB file.
5187 filesnotmatched.add(file);
5191 if (filesmatched.size() > 0)
5193 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5199 "label.automatically_associate_pdb_files_with_sequences_same_name",
5206 .getString("label.automatically_associate_pdb_files_by_name"),
5207 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5210 for (Object[] fm : filesmatched)
5212 // try and associate
5213 // TODO: may want to set a standard ID naming formalism for
5214 // associating PDB files which have no IDs.
5215 for (SequenceI toassoc : (SequenceI[]) fm[2])
5217 PDBEntry pe = new AssociatePdbFileWithSeq()
5218 .associatePdbWithSeq((String) fm[0],
5219 (String) fm[1], toassoc, false,
5223 System.err.println("Associated file : "
5224 + ((String) fm[0]) + " with "
5225 + toassoc.getDisplayId(true));
5229 alignPanel.paintAlignment(true);
5233 if (filesnotmatched.size() > 0)
5236 && (Cache.getDefault(
5237 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5240 "<html>"+MessageManager
5242 "label.ignore_unmatched_dropped_files_info",
5247 .toString() })+"</html>",
5249 .getString("label.ignore_unmatched_dropped_files"),
5250 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5254 for (String fn : filesnotmatched)
5256 loadJalviewDataFile(fn, null, null, null);
5260 } catch (Exception ex)
5262 ex.printStackTrace();
5268 * Attempt to load a "dropped" file or URL string: First by testing whether
5269 * it's and Annotation file, then a JNet file, and finally a features file. If
5270 * all are false then the user may have dropped an alignment file onto this
5274 * either a filename or a URL string.
5276 public void loadJalviewDataFile(String file, String protocol,
5277 String format, SequenceI assocSeq)
5281 if (protocol == null)
5283 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5285 // if the file isn't identified, or not positively identified as some
5286 // other filetype (PFAM is default unidentified alignment file type) then
5287 // try to parse as annotation.
5288 boolean isAnnotation = (format == null || format
5289 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5290 .annotateAlignmentView(viewport, file, protocol)
5295 // first see if its a T-COFFEE score file
5296 TCoffeeScoreFile tcf = null;
5299 tcf = new TCoffeeScoreFile(file, protocol);
5302 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5304 tcoffeeColour.setEnabled(true);
5305 tcoffeeColour.setSelected(true);
5306 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5307 isAnnotation = true;
5309 .setText(MessageManager
5310 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5314 // some problem - if no warning its probable that the ID matching
5315 // process didn't work
5319 tcf.getWarningMessage() == null ? MessageManager
5320 .getString("label.check_file_matches_sequence_ids_alignment")
5321 : tcf.getWarningMessage(),
5323 .getString("label.problem_reading_tcoffee_score_file"),
5324 JOptionPane.WARNING_MESSAGE);
5331 } catch (Exception x)
5334 .debug("Exception when processing data source as T-COFFEE score file",
5340 // try to see if its a JNet 'concise' style annotation file *before*
5342 // try to parse it as a features file
5345 format = new IdentifyFile().Identify(file, protocol);
5347 if (format.equalsIgnoreCase("JnetFile"))
5349 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5351 new JnetAnnotationMaker();
5352 JnetAnnotationMaker.add_annotation(predictions,
5353 viewport.getAlignment(), 0, false);
5354 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5355 viewport.getAlignment().setSeqrep(repseq);
5356 ColumnSelection cs = new ColumnSelection();
5357 cs.hideInsertionsFor(repseq);
5358 viewport.setColumnSelection(cs);
5359 isAnnotation = true;
5364 * if (format.equalsIgnoreCase("PDB")) {
5366 * String pdbfn = ""; // try to match up filename with sequence id
5367 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5368 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5369 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5370 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5371 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5372 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5373 * // attempt to find a match in the alignment SequenceI mtch =
5374 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5375 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5376 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5377 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5378 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5379 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5380 * { System.err.println("Associated file : " + file + " with " +
5381 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5382 * TODO: maybe need to load as normal otherwise return; } }
5384 // try to parse it as a features file
5385 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5386 // if it wasn't a features file then we just treat it as a general
5387 // alignment file to load into the current view.
5390 new FileLoader().LoadFile(viewport, file, protocol, format);
5394 alignPanel.paintAlignment(true);
5402 alignPanel.adjustAnnotationHeight();
5403 viewport.updateSequenceIdColours();
5404 buildSortByAnnotationScoresMenu();
5405 alignPanel.paintAlignment(true);
5407 } catch (Exception ex)
5409 ex.printStackTrace();
5410 } catch (OutOfMemoryError oom)
5415 } catch (Exception x)
5421 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5422 : "using " + protocol + " from " + file)
5424 + (format != null ? "(parsing as '" + format
5425 + "' file)" : ""), oom, Desktop.desktop);
5430 * Method invoked by the ChangeListener on the tabbed pane, in other words
5431 * when a different tabbed pane is selected by the user or programmatically.
5434 public void tabSelectionChanged(int index)
5438 alignPanel = alignPanels.get(index);
5439 viewport = alignPanel.av;
5440 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5441 setMenusFromViewport(viewport);
5445 * If there is a frame linked to this one in a SplitPane, switch it to the
5446 * same view tab index. No infinite recursion of calls should happen, since
5447 * tabSelectionChanged() should not get invoked on setting the selected
5448 * index to an unchanged value. Guard against setting an invalid index
5449 * before the new view peer tab has been created.
5451 final AlignViewportI peer = viewport.getCodingComplement();
5454 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5455 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5457 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5463 * On right mouse click on view tab, prompt for and set new view name.
5466 public void tabbedPane_mousePressed(MouseEvent e)
5468 if (SwingUtilities.isRightMouseButton(e))
5470 String msg = MessageManager.getString("label.enter_view_name");
5471 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5472 JOptionPane.QUESTION_MESSAGE);
5476 viewport.viewName = reply;
5477 // TODO warn if reply is in getExistingViewNames()?
5478 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5483 public AlignViewport getCurrentView()
5489 * Open the dialog for regex description parsing.
5492 protected void extractScores_actionPerformed(ActionEvent e)
5494 ParseProperties pp = new jalview.analysis.ParseProperties(
5495 viewport.getAlignment());
5496 // TODO: verify regex and introduce GUI dialog for version 2.5
5497 // if (pp.getScoresFromDescription("col", "score column ",
5498 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5500 if (pp.getScoresFromDescription("description column",
5501 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5503 buildSortByAnnotationScoresMenu();
5511 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5515 protected void showDbRefs_actionPerformed(ActionEvent e)
5517 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5523 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5527 protected void showNpFeats_actionPerformed(ActionEvent e)
5529 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5533 * find the viewport amongst the tabs in this alignment frame and close that
5538 public boolean closeView(AlignViewportI av)
5542 this.closeMenuItem_actionPerformed(false);
5545 Component[] comp = tabbedPane.getComponents();
5546 for (int i = 0; comp != null && i < comp.length; i++)
5548 if (comp[i] instanceof AlignmentPanel)
5550 if (((AlignmentPanel) comp[i]).av == av)
5553 closeView((AlignmentPanel) comp[i]);
5561 protected void build_fetchdbmenu(JMenu webService)
5563 // Temporary hack - DBRef Fetcher always top level ws entry.
5564 // TODO We probably want to store a sequence database checklist in
5565 // preferences and have checkboxes.. rather than individual sources selected
5567 final JMenu rfetch = new JMenu(
5568 MessageManager.getString("action.fetch_db_references"));
5569 rfetch.setToolTipText(MessageManager
5570 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5571 webService.add(rfetch);
5573 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5574 MessageManager.getString("option.trim_retrieved_seqs"));
5575 trimrs.setToolTipText(MessageManager
5576 .getString("label.trim_retrieved_sequences"));
5577 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5578 trimrs.addActionListener(new ActionListener()
5581 public void actionPerformed(ActionEvent e)
5583 trimrs.setSelected(trimrs.isSelected());
5584 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5585 Boolean.valueOf(trimrs.isSelected()).toString());
5589 JMenuItem fetchr = new JMenuItem(
5590 MessageManager.getString("label.standard_databases"));
5591 fetchr.setToolTipText(MessageManager
5592 .getString("label.fetch_embl_uniprot"));
5593 fetchr.addActionListener(new ActionListener()
5597 public void actionPerformed(ActionEvent e)
5599 new Thread(new Runnable()
5605 new jalview.ws.DBRefFetcher(alignPanel.av
5606 .getSequenceSelection(), alignPanel.alignFrame)
5607 .fetchDBRefs(false);
5615 final AlignFrame me = this;
5616 new Thread(new Runnable()
5621 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5622 .getSequenceFetcherSingleton(me);
5623 javax.swing.SwingUtilities.invokeLater(new Runnable()
5628 String[] dbclasses = sf.getOrderedSupportedSources();
5629 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5630 // jalview.util.QuickSort.sort(otherdb, otherdb);
5631 List<DbSourceProxy> otherdb;
5632 JMenu dfetch = new JMenu();
5633 JMenu ifetch = new JMenu();
5634 JMenuItem fetchr = null;
5635 int comp = 0, icomp = 0, mcomp = 15;
5636 String mname = null;
5638 for (String dbclass : dbclasses)
5640 otherdb = sf.getSourceProxy(dbclass);
5641 // add a single entry for this class, or submenu allowing 'fetch
5643 if (otherdb == null || otherdb.size() < 1)
5647 // List<DbSourceProxy> dbs=otherdb;
5648 // otherdb=new ArrayList<DbSourceProxy>();
5649 // for (DbSourceProxy db:dbs)
5651 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5655 mname = "From " + dbclass;
5657 if (otherdb.size() == 1)
5659 final DbSourceProxy[] dassource = otherdb
5660 .toArray(new DbSourceProxy[0]);
5661 DbSourceProxy src = otherdb.get(0);
5662 fetchr = new JMenuItem(src.getDbSource());
5663 fetchr.addActionListener(new ActionListener()
5667 public void actionPerformed(ActionEvent e)
5669 new Thread(new Runnable()
5675 new jalview.ws.DBRefFetcher(alignPanel.av
5676 .getSequenceSelection(),
5677 alignPanel.alignFrame, dassource)
5678 .fetchDBRefs(false);
5684 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()})));
5690 final DbSourceProxy[] dassource = otherdb
5691 .toArray(new DbSourceProxy[0]);
5693 DbSourceProxy src = otherdb.get(0);
5694 fetchr = new JMenuItem(MessageManager.formatMessage(
5695 "label.fetch_all_param", new Object[]
5696 { src.getDbSource() }));
5697 fetchr.addActionListener(new ActionListener()
5700 public void actionPerformed(ActionEvent e)
5702 new Thread(new Runnable()
5708 new jalview.ws.DBRefFetcher(alignPanel.av
5709 .getSequenceSelection(),
5710 alignPanel.alignFrame, dassource)
5711 .fetchDBRefs(false);
5717 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new Object[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5720 // and then build the rest of the individual menus
5721 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()}));
5723 String imname = null;
5725 for (DbSourceProxy sproxy : otherdb)
5727 String dbname = sproxy.getDbName();
5728 String sname = dbname.length() > 5 ? dbname.substring(0,
5729 5) + "..." : dbname;
5730 String msname = dbname.length() > 10 ? dbname.substring(
5731 0, 10) + "..." : dbname;
5734 imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname});
5736 fetchr = new JMenuItem(msname);
5737 final DbSourceProxy[] dassrc =
5739 fetchr.addActionListener(new ActionListener()
5743 public void actionPerformed(ActionEvent e)
5745 new Thread(new Runnable()
5751 new jalview.ws.DBRefFetcher(alignPanel.av
5752 .getSequenceSelection(),
5753 alignPanel.alignFrame, dassrc)
5754 .fetchDBRefs(false);
5760 fetchr.setToolTipText("<html>"
5761 + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname}));
5764 if (++icomp >= mcomp || i == (otherdb.size()))
5766 ifetch.setText(MessageManager.formatMessage(
5767 "label.source_to_target", imname, sname));
5769 ifetch = new JMenu();
5777 if (comp >= mcomp || dbi >= (dbclasses.length))
5779 dfetch.setText(MessageManager.formatMessage(
5780 "label.source_to_target", mname, dbclass));
5782 dfetch = new JMenu();
5795 * Left justify the whole alignment.
5798 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5800 AlignmentI al = viewport.getAlignment();
5802 viewport.firePropertyChange("alignment", null, al);
5806 * Right justify the whole alignment.
5809 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5811 AlignmentI al = viewport.getAlignment();
5813 viewport.firePropertyChange("alignment", null, al);
5816 public void setShowSeqFeatures(boolean b)
5818 showSeqFeatures.setSelected(b);
5819 viewport.setShowSequenceFeatures(b);
5826 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5827 * awt.event.ActionEvent)
5830 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5832 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5833 alignPanel.paintAlignment(true);
5840 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5844 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5846 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5847 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5855 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5856 * .event.ActionEvent)
5859 protected void showGroupConservation_actionPerformed(ActionEvent e)
5861 viewport.setShowGroupConservation(showGroupConservation.getState());
5862 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5869 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5870 * .event.ActionEvent)
5873 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5875 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5876 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5883 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5884 * .event.ActionEvent)
5887 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5889 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5890 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5894 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5896 showSequenceLogo.setState(true);
5897 viewport.setShowSequenceLogo(true);
5898 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5899 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5903 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5905 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5912 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5913 * .event.ActionEvent)
5916 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5918 if (avc.makeGroupsFromSelection())
5920 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5921 alignPanel.updateAnnotation();
5922 alignPanel.paintAlignment(true);
5925 public void clearAlignmentSeqRep()
5927 // TODO refactor alignmentseqrep to controller
5928 if (viewport.getAlignment().hasSeqrep()) {
5929 viewport.getAlignment().setSeqrep(null);
5930 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5931 alignPanel.updateAnnotation();
5932 alignPanel.paintAlignment(true);
5937 protected void createGroup_actionPerformed(ActionEvent e)
5939 if (avc.createGroup())
5941 alignPanel.alignmentChanged();
5946 protected void unGroup_actionPerformed(ActionEvent e)
5950 alignPanel.alignmentChanged();
5955 * make the given alignmentPanel the currently selected tab
5957 * @param alignmentPanel
5959 public void setDisplayedView(AlignmentPanel alignmentPanel)
5961 if (!viewport.getSequenceSetId().equals(
5962 alignmentPanel.av.getSequenceSetId()))
5964 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5966 if (tabbedPane != null
5967 && tabbedPane.getTabCount() > 0
5968 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5969 .getSelectedIndex())
5971 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5976 * Action on selection of menu options to Show or Hide annotations.
5979 * @param forSequences
5980 * update sequence-related annotations
5981 * @param forAlignment
5982 * update non-sequence-related annotations
5985 protected void setAnnotationsVisibility(boolean visible,
5986 boolean forSequences, boolean forAlignment)
5988 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5989 .getAlignmentAnnotation())
5992 * don't display non-positional annotations on an alignment
5994 if (aa.annotations == null)
5998 boolean apply = (aa.sequenceRef == null && forAlignment)
5999 || (aa.sequenceRef != null && forSequences);
6002 aa.visible = visible;
6005 alignPanel.validateAnnotationDimensions(true);
6006 alignPanel.alignmentChanged();
6010 * Store selected annotation sort order for the view and repaint.
6013 protected void sortAnnotations_actionPerformed()
6015 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6017 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6018 alignPanel.paintAlignment(true);
6023 * @return alignment panels in this alignment frame
6025 public List<? extends AlignmentViewPanel> getAlignPanels()
6027 return alignPanels == null ? Arrays.asList(alignPanel)
6032 * Open a new alignment window, with the cDNA associated with this (protein)
6033 * alignment, aligned as is the protein.
6035 protected void viewAsCdna_actionPerformed()
6037 // TODO no longer a menu action - refactor as required
6038 final AlignmentI alignment = getViewport().getAlignment();
6039 Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6040 if (mappings == null)
6044 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6045 for (SequenceI aaSeq : alignment.getSequences()) {
6046 for (AlignedCodonFrame acf : mappings) {
6047 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6051 * There is a cDNA mapping for this protein sequence - add to new
6052 * alignment. It will share the same dataset sequence as other mapped
6053 * cDNA (no new mappings need to be created).
6055 final Sequence newSeq = new Sequence(dnaSeq);
6056 newSeq.setDatasetSequence(dnaSeq);
6057 cdnaSeqs.add(newSeq);
6061 if (cdnaSeqs.size() == 0)
6063 // show a warning dialog no mapped cDNA
6066 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6068 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6069 AlignFrame.DEFAULT_HEIGHT);
6070 cdna.alignAs(alignment);
6071 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6073 Desktop.addInternalFrame(alignFrame, newtitle,
6074 AlignFrame.DEFAULT_WIDTH,
6075 AlignFrame.DEFAULT_HEIGHT);
6079 * Set visibility of dna/protein complement view (available when shown in a
6085 protected void showComplement_actionPerformed(boolean show)
6087 SplitContainerI sf = getSplitViewContainer();
6089 sf.setComplementVisible(this, show);
6095 class PrintThread extends Thread
6099 public PrintThread(AlignmentPanel ap)
6104 static PageFormat pf;
6109 PrinterJob printJob = PrinterJob.getPrinterJob();
6113 printJob.setPrintable(ap, pf);
6117 printJob.setPrintable(ap);
6120 if (printJob.printDialog())
6125 } catch (Exception PrintException)
6127 PrintException.printStackTrace();