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
1038 public void addFromURL_actionPerformed(ActionEvent e)
1040 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1044 public void save_actionPerformed(ActionEvent e)
1046 if (fileName == null
1047 || (currentFileFormat == null || !jalview.io.FormatAdapter
1048 .isValidIOFormat(currentFileFormat, true))
1049 || fileName.startsWith("http"))
1051 saveAs_actionPerformed(null);
1055 saveAlignment(fileName, currentFileFormat);
1066 public void saveAs_actionPerformed(ActionEvent e)
1068 JalviewFileChooser chooser = new JalviewFileChooser(
1069 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1070 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1071 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1072 currentFileFormat, false);
1074 chooser.setFileView(new JalviewFileView());
1075 chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1076 chooser.setToolTipText(MessageManager.getString("action.save"));
1078 int value = chooser.showSaveDialog(this);
1080 if (value == JalviewFileChooser.APPROVE_OPTION)
1082 currentFileFormat = chooser.getSelectedFormat();
1083 while (currentFileFormat == null)
1086 .showInternalMessageDialog(
1089 .getString("label.select_file_format_before_saving"),
1091 .getString("label.file_format_not_specified"),
1092 JOptionPane.WARNING_MESSAGE);
1093 currentFileFormat = chooser.getSelectedFormat();
1094 value = chooser.showSaveDialog(this);
1095 if (value != JalviewFileChooser.APPROVE_OPTION)
1101 fileName = chooser.getSelectedFile().getPath();
1103 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1106 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1107 if (currentFileFormat.indexOf(" ") > -1)
1109 currentFileFormat = currentFileFormat.substring(0,
1110 currentFileFormat.indexOf(" "));
1112 saveAlignment(fileName, currentFileFormat);
1116 public boolean saveAlignment(String file, String format)
1118 boolean success = true;
1120 if (format.equalsIgnoreCase("Jalview"))
1122 String shortName = title;
1124 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1126 shortName = shortName.substring(shortName
1127 .lastIndexOf(java.io.File.separatorChar) + 1);
1130 success = new Jalview2XML().saveAlignment(this, file, shortName);
1132 statusBar.setText(MessageManager.formatMessage(
1133 "label.successfully_saved_to_file_in_format", new Object[]
1134 { fileName, format }));
1139 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1141 warningMessage("Cannot save file " + fileName + " using format "
1142 + format, "Alignment output format not supported");
1143 if (!Jalview.isHeadlessMode())
1145 saveAs_actionPerformed(null);
1150 AlignmentExportData exportData = getAlignmentForExport(format, viewport);
1151 if (exportData.getSettings().isCancelled())
1155 FormatAdapter f = new FormatAdapter(alignPanel,
1156 exportData.getSettings());
1157 String output = f.formatSequences(format,
1158 exportData.getAlignment(), // class cast exceptions will
1159 // occur in the distant future
1160 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1161 f.getCacheSuffixDefault(format),
1162 viewport.getColumnSelection());
1172 java.io.PrintWriter out = new java.io.PrintWriter(
1173 new java.io.FileWriter(file));
1177 this.setTitle(file);
1178 statusBar.setText(MessageManager.formatMessage(
1179 "label.successfully_saved_to_file_in_format",
1181 { fileName, format }));
1182 } catch (Exception ex)
1185 ex.printStackTrace();
1192 JOptionPane.showInternalMessageDialog(this, MessageManager
1193 .formatMessage("label.couldnt_save_file", new Object[]
1194 { fileName }), MessageManager
1195 .getString("label.error_saving_file"),
1196 JOptionPane.WARNING_MESSAGE);
1203 private void warningMessage(String warning, String title)
1205 if (new jalview.util.Platform().isHeadless())
1207 System.err.println("Warning: " + title + "\nWarning: " + warning);
1212 JOptionPane.showInternalMessageDialog(this, warning, title,
1213 JOptionPane.WARNING_MESSAGE);
1225 protected void outputText_actionPerformed(ActionEvent e)
1228 AlignmentExportData exportData = getAlignmentForExport(
1229 e.getActionCommand(), viewport);
1230 if (exportData.getSettings().isCancelled())
1234 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1235 cap.setForInput(null);
1238 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1240 e.getActionCommand(),
1241 exportData.getAlignment(),
1242 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1243 viewport.getColumnSelection()));
1244 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1245 "label.alignment_output_command", new Object[]
1246 { e.getActionCommand() }), 600, 500);
1247 } catch (OutOfMemoryError oom)
1249 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1255 public static AlignmentExportData getAlignmentForExport(String exportFormat,
1256 AlignViewportI viewport)
1258 AlignmentI alignmentToExport = null;
1259 String[] omitHidden = null;
1260 int[] alignmentStartEnd = new int[2];
1262 HiddenSequences hiddenSeqs = viewport.getAlignment()
1263 .getHiddenSequences();
1266 alignmentToExport = viewport.getAlignment();
1267 alignmentStartEnd = new int[]
1268 { 0, alignmentToExport.getWidth() - 1 };
1270 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1271 AlignExportSettings settings = new AlignExportSettings(hasHiddenSeqs,
1272 viewport.hasHiddenColumns(), exportFormat);
1273 settings.isExportAnnotations();
1275 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1277 omitHidden = viewport.getViewAsString(false);
1280 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1282 alignmentToExport = hiddenSeqs.getFullAlignment();
1286 alignmentToExport = viewport.getAlignment();
1287 alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1288 .getColumnSelection().getHiddenColumns());
1290 AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd,
1295 public static int[] getStartEnd(int[] aligmentStartEnd,
1296 List<int[]> hiddenCols)
1298 int startPos = aligmentStartEnd[0];
1299 int endPos = aligmentStartEnd[1];
1301 int[] lowestRange = new int[2];
1302 int[] higestRange = new int[2];
1304 for (int[] hiddenCol : hiddenCols)
1306 // 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);
1502 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1503 * be called recursively, with the frame now in 'closed' state
1505 this.setClosed(true);
1507 } catch (Exception ex)
1509 ex.printStackTrace();
1514 * Close the specified panel and close up tabs appropriately.
1516 * @param panelToClose
1518 public void closeView(AlignmentPanel panelToClose)
1520 int index = tabbedPane.getSelectedIndex();
1521 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1522 alignPanels.remove(panelToClose);
1523 panelToClose.closePanel();
1524 panelToClose = null;
1526 tabbedPane.removeTabAt(closedindex);
1527 tabbedPane.validate();
1529 if (index > closedindex || index == tabbedPane.getTabCount())
1531 // modify currently selected tab index if necessary.
1535 this.tabSelectionChanged(index);
1541 void updateEditMenuBar()
1544 if (viewport.getHistoryList().size() > 0)
1546 undoMenuItem.setEnabled(true);
1547 CommandI command = viewport.getHistoryList().peek();
1548 undoMenuItem.setText(MessageManager.formatMessage(
1549 "label.undo_command", new Object[]
1550 { command.getDescription() }));
1554 undoMenuItem.setEnabled(false);
1555 undoMenuItem.setText(MessageManager.getString("action.undo"));
1558 if (viewport.getRedoList().size() > 0)
1560 redoMenuItem.setEnabled(true);
1562 CommandI command = viewport.getRedoList().peek();
1563 redoMenuItem.setText(MessageManager.formatMessage(
1564 "label.redo_command", new Object[]
1565 { command.getDescription() }));
1569 redoMenuItem.setEnabled(false);
1570 redoMenuItem.setText(MessageManager.getString("action.redo"));
1574 public void addHistoryItem(CommandI command)
1576 if (command.getSize() > 0)
1578 viewport.addToHistoryList(command);
1579 viewport.clearRedoList();
1580 updateEditMenuBar();
1581 viewport.updateHiddenColumns();
1582 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1583 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1584 // viewport.getColumnSelection()
1585 // .getHiddenColumns().size() > 0);
1591 * @return alignment objects for all views
1593 AlignmentI[] getViewAlignments()
1595 if (alignPanels != null)
1597 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1599 for (AlignmentPanel ap : alignPanels)
1601 als[i++] = ap.av.getAlignment();
1605 if (viewport != null)
1607 return new AlignmentI[]
1608 { viewport.getAlignment() };
1620 protected void undoMenuItem_actionPerformed(ActionEvent e)
1622 if (viewport.getHistoryList().isEmpty())
1626 CommandI command = viewport.getHistoryList().pop();
1627 viewport.addToRedoList(command);
1628 command.undoCommand(getViewAlignments());
1630 AlignmentViewport originalSource = getOriginatingSource(command);
1631 updateEditMenuBar();
1633 if (originalSource != null)
1635 if (originalSource != viewport)
1638 .warn("Implementation worry: mismatch of viewport origin for undo");
1640 originalSource.updateHiddenColumns();
1641 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1643 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1644 // viewport.getColumnSelection()
1645 // .getHiddenColumns().size() > 0);
1646 originalSource.firePropertyChange("alignment", null, originalSource
1647 .getAlignment().getSequences());
1658 protected void redoMenuItem_actionPerformed(ActionEvent e)
1660 if (viewport.getRedoList().size() < 1)
1665 CommandI command = viewport.getRedoList().pop();
1666 viewport.addToHistoryList(command);
1667 command.doCommand(getViewAlignments());
1669 AlignmentViewport originalSource = getOriginatingSource(command);
1670 updateEditMenuBar();
1672 if (originalSource != null)
1675 if (originalSource != viewport)
1678 .warn("Implementation worry: mismatch of viewport origin for redo");
1680 originalSource.updateHiddenColumns();
1681 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1683 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1684 // viewport.getColumnSelection()
1685 // .getHiddenColumns().size() > 0);
1686 originalSource.firePropertyChange("alignment", null, originalSource
1687 .getAlignment().getSequences());
1691 AlignmentViewport getOriginatingSource(CommandI command)
1693 AlignmentViewport originalSource = null;
1694 // For sequence removal and addition, we need to fire
1695 // the property change event FROM the viewport where the
1696 // original alignment was altered
1697 AlignmentI al = null;
1698 if (command instanceof EditCommand)
1700 EditCommand editCommand = (EditCommand) command;
1701 al = editCommand.getAlignment();
1702 List<Component> comps = PaintRefresher.components.get(viewport
1703 .getSequenceSetId());
1705 for (Component comp : comps)
1707 if (comp instanceof AlignmentPanel)
1709 if (al == ((AlignmentPanel) comp).av.getAlignment())
1711 originalSource = ((AlignmentPanel) comp).av;
1718 if (originalSource == null)
1720 // The original view is closed, we must validate
1721 // the current view against the closed view first
1724 PaintRefresher.validateSequences(al, viewport.getAlignment());
1727 originalSource = viewport;
1730 return originalSource;
1739 public void moveSelectedSequences(boolean up)
1741 SequenceGroup sg = viewport.getSelectionGroup();
1747 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1748 viewport.getHiddenRepSequences(), up);
1749 alignPanel.paintAlignment(true);
1752 synchronized void slideSequences(boolean right, int size)
1754 List<SequenceI> sg = new ArrayList<SequenceI>();
1755 if (viewport.cursorMode)
1757 sg.add(viewport.getAlignment().getSequenceAt(
1758 alignPanel.getSeqPanel().seqCanvas.cursorY));
1760 else if (viewport.getSelectionGroup() != null
1761 && viewport.getSelectionGroup().getSize() != viewport
1762 .getAlignment().getHeight())
1764 sg = viewport.getSelectionGroup().getSequences(
1765 viewport.getHiddenRepSequences());
1773 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1775 for (SequenceI seq : viewport.getAlignment().getSequences())
1777 if (!sg.contains(seq))
1779 invertGroup.add(seq);
1783 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1785 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1786 for (int i = 0; i < invertGroup.size(); i++)
1788 seqs2[i] = invertGroup.get(i);
1791 SlideSequencesCommand ssc;
1794 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1795 size, viewport.getGapCharacter());
1799 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1800 size, viewport.getGapCharacter());
1803 int groupAdjustment = 0;
1804 if (ssc.getGapsInsertedBegin() && right)
1806 if (viewport.cursorMode)
1808 alignPanel.getSeqPanel().moveCursor(size, 0);
1812 groupAdjustment = size;
1815 else if (!ssc.getGapsInsertedBegin() && !right)
1817 if (viewport.cursorMode)
1819 alignPanel.getSeqPanel().moveCursor(-size, 0);
1823 groupAdjustment = -size;
1827 if (groupAdjustment != 0)
1829 viewport.getSelectionGroup().setStartRes(
1830 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1831 viewport.getSelectionGroup().setEndRes(
1832 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1836 * just extend the last slide command if compatible; but not if in
1837 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1839 boolean appendHistoryItem = false;
1840 Deque<CommandI> historyList = viewport.getHistoryList();
1841 boolean inSplitFrame = getSplitViewContainer() != null;
1842 if (!inSplitFrame && historyList != null
1843 && historyList.size() > 0
1844 && historyList.peek() instanceof SlideSequencesCommand)
1846 appendHistoryItem = ssc
1847 .appendSlideCommand((SlideSequencesCommand) historyList
1851 if (!appendHistoryItem)
1853 addHistoryItem(ssc);
1866 protected void copy_actionPerformed(ActionEvent e)
1869 if (viewport.getSelectionGroup() == null)
1873 // TODO: preserve the ordering of displayed alignment annotation in any
1874 // internal paste (particularly sequence associated annotation)
1875 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1876 String[] omitHidden = null;
1878 if (viewport.hasHiddenColumns())
1880 omitHidden = viewport.getViewAsString(true);
1883 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1886 StringSelection ss = new StringSelection(output);
1890 jalview.gui.Desktop.internalCopy = true;
1891 // Its really worth setting the clipboard contents
1892 // to empty before setting the large StringSelection!!
1893 Toolkit.getDefaultToolkit().getSystemClipboard()
1894 .setContents(new StringSelection(""), null);
1896 Toolkit.getDefaultToolkit().getSystemClipboard()
1897 .setContents(ss, Desktop.instance);
1898 } catch (OutOfMemoryError er)
1900 new OOMWarning("copying region", er);
1904 ArrayList<int[]> hiddenColumns = null;
1905 if (viewport.hasHiddenColumns())
1907 hiddenColumns = new ArrayList<int[]>();
1908 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1909 .getSelectionGroup().getEndRes();
1910 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1912 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1914 hiddenColumns.add(new int[]
1915 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1920 Desktop.jalviewClipboard = new Object[]
1921 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1922 statusBar.setText(MessageManager.formatMessage(
1923 "label.copied_sequences_to_clipboard", new Object[]
1924 { Integer.valueOf(seqs.length).toString() }));
1934 protected void pasteNew_actionPerformed(ActionEvent e)
1946 protected void pasteThis_actionPerformed(ActionEvent e)
1952 * Paste contents of Jalview clipboard
1954 * @param newAlignment
1955 * true to paste to a new alignment, otherwise add to this.
1957 void paste(boolean newAlignment)
1959 boolean externalPaste = true;
1962 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1963 Transferable contents = c.getContents(this);
1965 if (contents == null)
1973 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1974 if (str.length() < 1)
1979 format = new IdentifyFile().Identify(str, "Paste");
1981 } catch (OutOfMemoryError er)
1983 new OOMWarning("Out of memory pasting sequences!!", er);
1987 SequenceI[] sequences;
1988 boolean annotationAdded = false;
1989 AlignmentI alignment = null;
1991 if (Desktop.jalviewClipboard != null)
1993 // The clipboard was filled from within Jalview, we must use the
1995 // And dataset from the copied alignment
1996 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1997 // be doubly sure that we create *new* sequence objects.
1998 sequences = new SequenceI[newseq.length];
1999 for (int i = 0; i < newseq.length; i++)
2001 sequences[i] = new Sequence(newseq[i]);
2003 alignment = new Alignment(sequences);
2004 externalPaste = false;
2008 // parse the clipboard as an alignment.
2009 alignment = new FormatAdapter().readFile(str, "Paste", format);
2010 sequences = alignment.getSequencesArray();
2014 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2020 if (Desktop.jalviewClipboard != null)
2022 // dataset is inherited
2023 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2027 // new dataset is constructed
2028 alignment.setDataset(null);
2030 alwidth = alignment.getWidth() + 1;
2034 AlignmentI pastedal = alignment; // preserve pasted alignment object
2035 // Add pasted sequences and dataset into existing alignment.
2036 alignment = viewport.getAlignment();
2037 alwidth = alignment.getWidth() + 1;
2038 // decide if we need to import sequences from an existing dataset
2039 boolean importDs = Desktop.jalviewClipboard != null
2040 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2041 // importDs==true instructs us to copy over new dataset sequences from
2042 // an existing alignment
2043 Vector newDs = (importDs) ? new Vector() : null; // used to create
2044 // minimum dataset set
2046 for (int i = 0; i < sequences.length; i++)
2050 newDs.addElement(null);
2052 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2054 if (importDs && ds != null)
2056 if (!newDs.contains(ds))
2058 newDs.setElementAt(ds, i);
2059 ds = new Sequence(ds);
2060 // update with new dataset sequence
2061 sequences[i].setDatasetSequence(ds);
2065 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2070 // copy and derive new dataset sequence
2071 sequences[i] = sequences[i].deriveSequence();
2072 alignment.getDataset().addSequence(
2073 sequences[i].getDatasetSequence());
2074 // TODO: avoid creation of duplicate dataset sequences with a
2075 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2077 alignment.addSequence(sequences[i]); // merges dataset
2081 newDs.clear(); // tidy up
2083 if (alignment.getAlignmentAnnotation() != null)
2085 for (AlignmentAnnotation alan : alignment
2086 .getAlignmentAnnotation())
2088 if (alan.graphGroup > fgroup)
2090 fgroup = alan.graphGroup;
2094 if (pastedal.getAlignmentAnnotation() != null)
2096 // Add any annotation attached to alignment.
2097 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2098 for (int i = 0; i < alann.length; i++)
2100 annotationAdded = true;
2101 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2103 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2104 if (newann.graphGroup > -1)
2106 if (newGraphGroups.size() <= newann.graphGroup
2107 || newGraphGroups.get(newann.graphGroup) == null)
2109 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2111 newGraphGroups.add(q, null);
2113 newGraphGroups.set(newann.graphGroup, new Integer(
2116 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2120 newann.padAnnotation(alwidth);
2121 alignment.addAnnotation(newann);
2131 addHistoryItem(new EditCommand(
2132 MessageManager.getString("label.add_sequences"),
2134 sequences, 0, alignment.getWidth(), alignment));
2136 // Add any annotations attached to sequences
2137 for (int i = 0; i < sequences.length; i++)
2139 if (sequences[i].getAnnotation() != null)
2141 AlignmentAnnotation newann;
2142 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2144 annotationAdded = true;
2145 newann = sequences[i].getAnnotation()[a];
2146 newann.adjustForAlignment();
2147 newann.padAnnotation(alwidth);
2148 if (newann.graphGroup > -1)
2150 if (newann.graphGroup > -1)
2152 if (newGraphGroups.size() <= newann.graphGroup
2153 || newGraphGroups.get(newann.graphGroup) == null)
2155 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2157 newGraphGroups.add(q, null);
2159 newGraphGroups.set(newann.graphGroup, new Integer(
2162 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2166 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2171 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2178 // propagate alignment changed.
2179 viewport.setEndSeq(alignment.getHeight());
2180 if (annotationAdded)
2182 // Duplicate sequence annotation in all views.
2183 AlignmentI[] alview = this.getViewAlignments();
2184 for (int i = 0; i < sequences.length; i++)
2186 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2191 for (int avnum = 0; avnum < alview.length; avnum++)
2193 if (alview[avnum] != alignment)
2195 // duplicate in a view other than the one with input focus
2196 int avwidth = alview[avnum].getWidth() + 1;
2197 // this relies on sann being preserved after we
2198 // modify the sequence's annotation array for each duplication
2199 for (int a = 0; a < sann.length; a++)
2201 AlignmentAnnotation newann = new AlignmentAnnotation(
2203 sequences[i].addAlignmentAnnotation(newann);
2204 newann.padAnnotation(avwidth);
2205 alview[avnum].addAnnotation(newann); // annotation was
2206 // duplicated earlier
2207 // TODO JAL-1145 graphGroups are not updated for sequence
2208 // annotation added to several views. This may cause
2210 alview[avnum].setAnnotationIndex(newann, a);
2215 buildSortByAnnotationScoresMenu();
2217 viewport.firePropertyChange("alignment", null,
2218 alignment.getSequences());
2219 if (alignPanels != null)
2221 for (AlignmentPanel ap : alignPanels)
2223 ap.validateAnnotationDimensions(false);
2228 alignPanel.validateAnnotationDimensions(false);
2234 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2236 String newtitle = new String("Copied sequences");
2238 if (Desktop.jalviewClipboard != null
2239 && Desktop.jalviewClipboard[2] != null)
2241 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2242 for (int[] region : hc)
2244 af.viewport.hideColumns(region[0], region[1]);
2248 // >>>This is a fix for the moment, until a better solution is
2250 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2252 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2254 // TODO: maintain provenance of an alignment, rather than just make the
2255 // title a concatenation of operations.
2258 if (title.startsWith("Copied sequences"))
2264 newtitle = newtitle.concat("- from " + title);
2269 newtitle = new String("Pasted sequences");
2272 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2277 } catch (Exception ex)
2279 ex.printStackTrace();
2280 System.out.println("Exception whilst pasting: " + ex);
2281 // could be anything being pasted in here
2287 protected void expand_newalign(ActionEvent e)
2291 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2292 .getAlignment(), -1);
2293 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2295 String newtitle = new String("Flanking alignment");
2297 if (Desktop.jalviewClipboard != null
2298 && Desktop.jalviewClipboard[2] != null)
2300 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2301 for (int region[] : hc)
2303 af.viewport.hideColumns(region[0], region[1]);
2307 // >>>This is a fix for the moment, until a better solution is
2309 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2311 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2313 // TODO: maintain provenance of an alignment, rather than just make the
2314 // title a concatenation of operations.
2316 if (title.startsWith("Copied sequences"))
2322 newtitle = newtitle.concat("- from " + title);
2326 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2328 } catch (Exception ex)
2330 ex.printStackTrace();
2331 System.out.println("Exception whilst pasting: " + ex);
2332 // could be anything being pasted in here
2333 } catch (OutOfMemoryError oom)
2335 new OOMWarning("Viewing flanking region of alignment", oom);
2346 protected void cut_actionPerformed(ActionEvent e)
2348 copy_actionPerformed(null);
2349 delete_actionPerformed(null);
2359 protected void delete_actionPerformed(ActionEvent evt)
2362 SequenceGroup sg = viewport.getSelectionGroup();
2369 * If the cut affects all sequences, warn, remove highlighted columns
2371 if (sg.getSize() == viewport.getAlignment().getHeight())
2373 int confirm = JOptionPane.showConfirmDialog(this,
2374 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2375 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2376 JOptionPane.OK_CANCEL_OPTION);
2378 if (confirm == JOptionPane.CANCEL_OPTION
2379 || confirm == JOptionPane.CLOSED_OPTION)
2383 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2384 sg.getEndRes() + 1);
2387 SequenceI[] cut = sg.getSequences()
2388 .toArray(new SequenceI[sg.getSize()]);
2390 addHistoryItem(new EditCommand(
2391 MessageManager.getString("label.cut_sequences"), Action.CUT,
2392 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2393 viewport.getAlignment()));
2395 viewport.setSelectionGroup(null);
2396 viewport.sendSelection();
2397 viewport.getAlignment().deleteGroup(sg);
2399 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2401 if (viewport.getAlignment().getHeight() < 1)
2405 this.setClosed(true);
2406 } catch (Exception ex)
2419 protected void deleteGroups_actionPerformed(ActionEvent e)
2421 if (avc.deleteGroups())
2423 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2424 alignPanel.updateAnnotation();
2425 alignPanel.paintAlignment(true);
2436 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2438 SequenceGroup sg = new SequenceGroup();
2440 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2442 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2445 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2446 viewport.setSelectionGroup(sg);
2447 viewport.sendSelection();
2448 alignPanel.paintAlignment(true);
2449 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2459 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2461 if (viewport.cursorMode)
2463 alignPanel.getSeqPanel().keyboardNo1 = null;
2464 alignPanel.getSeqPanel().keyboardNo2 = null;
2466 viewport.setSelectionGroup(null);
2467 viewport.getColumnSelection().clear();
2468 viewport.setSelectionGroup(null);
2469 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2470 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2471 alignPanel.paintAlignment(true);
2472 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2473 viewport.sendSelection();
2483 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2485 SequenceGroup sg = viewport.getSelectionGroup();
2489 selectAllSequenceMenuItem_actionPerformed(null);
2494 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2496 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2499 alignPanel.paintAlignment(true);
2500 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2501 viewport.sendSelection();
2505 public void invertColSel_actionPerformed(ActionEvent e)
2507 viewport.invertColumnSelection();
2508 alignPanel.paintAlignment(true);
2509 viewport.sendSelection();
2519 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2521 trimAlignment(true);
2531 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2533 trimAlignment(false);
2536 void trimAlignment(boolean trimLeft)
2538 ColumnSelection colSel = viewport.getColumnSelection();
2541 if (colSel.size() > 0)
2545 column = colSel.getMin();
2549 column = colSel.getMax();
2553 if (viewport.getSelectionGroup() != null)
2555 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2556 viewport.getHiddenRepSequences());
2560 seqs = viewport.getAlignment().getSequencesArray();
2563 TrimRegionCommand trimRegion;
2566 trimRegion = new TrimRegionCommand("Remove Left",
2567 TrimRegionCommand.TRIM_LEFT, seqs, column,
2568 viewport.getAlignment(), viewport.getColumnSelection(),
2569 viewport.getSelectionGroup());
2570 viewport.setStartRes(0);
2574 trimRegion = new TrimRegionCommand("Remove Right",
2575 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2576 viewport.getAlignment(), viewport.getColumnSelection(),
2577 viewport.getSelectionGroup());
2580 statusBar.setText(MessageManager.formatMessage(
2581 "label.removed_columns", new String[]
2582 { Integer.valueOf(trimRegion.getSize()).toString() }));
2584 addHistoryItem(trimRegion);
2586 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2588 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2589 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2591 viewport.getAlignment().deleteGroup(sg);
2595 viewport.firePropertyChange("alignment", null, viewport
2596 .getAlignment().getSequences());
2607 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2609 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2612 if (viewport.getSelectionGroup() != null)
2614 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2615 viewport.getHiddenRepSequences());
2616 start = viewport.getSelectionGroup().getStartRes();
2617 end = viewport.getSelectionGroup().getEndRes();
2621 seqs = viewport.getAlignment().getSequencesArray();
2624 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2625 "Remove Gapped Columns", seqs, start, end,
2626 viewport.getAlignment());
2628 addHistoryItem(removeGapCols);
2630 statusBar.setText(MessageManager.formatMessage(
2631 "label.removed_empty_columns", new Object[]
2632 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2634 // This is to maintain viewport position on first residue
2635 // of first sequence
2636 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2637 int startRes = seq.findPosition(viewport.startRes);
2638 // ShiftList shifts;
2639 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2640 // edit.alColumnChanges=shifts.getInverse();
2641 // if (viewport.hasHiddenColumns)
2642 // viewport.getColumnSelection().compensateForEdits(shifts);
2643 viewport.setStartRes(seq.findIndex(startRes) - 1);
2644 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2656 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2658 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2661 if (viewport.getSelectionGroup() != null)
2663 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2664 viewport.getHiddenRepSequences());
2665 start = viewport.getSelectionGroup().getStartRes();
2666 end = viewport.getSelectionGroup().getEndRes();
2670 seqs = viewport.getAlignment().getSequencesArray();
2673 // This is to maintain viewport position on first residue
2674 // of first sequence
2675 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2676 int startRes = seq.findPosition(viewport.startRes);
2678 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2679 viewport.getAlignment()));
2681 viewport.setStartRes(seq.findIndex(startRes) - 1);
2683 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2695 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2697 viewport.setPadGaps(padGapsMenuitem.isSelected());
2698 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2709 public void findMenuItem_actionPerformed(ActionEvent e)
2715 * Create a new view of the current alignment.
2718 public void newView_actionPerformed(ActionEvent e)
2720 newView(null, true);
2724 * Creates and shows a new view of the current alignment.
2727 * title of newly created view; if null, one will be generated
2728 * @param copyAnnotation
2729 * if true then duplicate all annnotation, groups and settings
2730 * @return new alignment panel, already displayed.
2732 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2735 * Create a new AlignmentPanel (with its own, new Viewport)
2737 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2739 if (!copyAnnotation)
2742 * remove all groups and annotation except for the automatic stuff
2744 newap.av.getAlignment().deleteAllGroups();
2745 newap.av.getAlignment().deleteAllAnnotations(false);
2748 newap.av.setGatherViewsHere(false);
2750 if (viewport.viewName == null)
2752 viewport.viewName = MessageManager
2753 .getString("label.view_name_original");
2757 * Views share the same edits undo and redo stacks
2759 newap.av.setHistoryList(viewport.getHistoryList());
2760 newap.av.setRedoList(viewport.getRedoList());
2763 * Views share the same mappings; need to deregister any new mappings
2764 * created by copyAlignPanel, and register the new reference to the shared
2767 newap.av.replaceMappings(viewport.getAlignment());
2769 newap.av.viewName = getNewViewName(viewTitle);
2771 addAlignmentPanel(newap, true);
2772 newap.alignmentChanged();
2774 if (alignPanels.size() == 2)
2776 viewport.setGatherViewsHere(true);
2778 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2783 * Make a new name for the view, ensuring it is unique within the current
2784 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2785 * these now use viewId. Unique view names are still desirable for usability.)
2790 protected String getNewViewName(String viewTitle)
2792 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2793 boolean addFirstIndex = false;
2794 if (viewTitle == null || viewTitle.trim().length() == 0)
2796 viewTitle = MessageManager.getString("action.view");
2797 addFirstIndex = true;
2801 index = 1;// we count from 1 if given a specific name
2803 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2805 List<Component> comps = PaintRefresher.components.get(viewport
2806 .getSequenceSetId());
2808 List<String> existingNames = getExistingViewNames(comps);
2810 while (existingNames.contains(newViewName))
2812 newViewName = viewTitle + " " + (++index);
2818 * Returns a list of distinct view names found in the given list of
2819 * components. View names are held on the viewport of an AlignmentPanel.
2824 protected List<String> getExistingViewNames(List<Component> comps)
2826 List<String> existingNames = new ArrayList<String>();
2827 for (Component comp : comps)
2829 if (comp instanceof AlignmentPanel)
2831 AlignmentPanel ap = (AlignmentPanel) comp;
2832 if (!existingNames.contains(ap.av.viewName))
2834 existingNames.add(ap.av.viewName);
2838 return existingNames;
2842 * Explode tabbed views into separate windows.
2845 public void expandViews_actionPerformed(ActionEvent e)
2847 Desktop.instance.explodeViews(this);
2851 * Gather views in separate windows back into a tabbed presentation.
2854 public void gatherViews_actionPerformed(ActionEvent e)
2856 Desktop.instance.gatherViews(this);
2866 public void font_actionPerformed(ActionEvent e)
2868 new FontChooser(alignPanel);
2878 protected void seqLimit_actionPerformed(ActionEvent e)
2880 viewport.setShowJVSuffix(seqLimits.isSelected());
2882 alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
2883 .calculateIdWidth());
2884 alignPanel.paintAlignment(true);
2888 public void idRightAlign_actionPerformed(ActionEvent e)
2890 viewport.setRightAlignIds(idRightAlign.isSelected());
2891 alignPanel.paintAlignment(true);
2895 public void centreColumnLabels_actionPerformed(ActionEvent e)
2897 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2898 alignPanel.paintAlignment(true);
2904 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2907 protected void followHighlight_actionPerformed()
2910 * Set the 'follow' flag on the Viewport (and scroll to position if now
2913 final boolean state = this.followHighlightMenuItem.getState();
2914 viewport.setFollowHighlight(state);
2917 alignPanel.scrollToPosition(
2918 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2929 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2931 viewport.setColourText(colourTextMenuItem.isSelected());
2932 alignPanel.paintAlignment(true);
2942 public void wrapMenuItem_actionPerformed(ActionEvent e)
2944 scaleAbove.setVisible(wrapMenuItem.isSelected());
2945 scaleLeft.setVisible(wrapMenuItem.isSelected());
2946 scaleRight.setVisible(wrapMenuItem.isSelected());
2947 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2948 alignPanel.updateLayout();
2952 public void showAllSeqs_actionPerformed(ActionEvent e)
2954 viewport.showAllHiddenSeqs();
2958 public void showAllColumns_actionPerformed(ActionEvent e)
2960 viewport.showAllHiddenColumns();
2965 public void hideSelSequences_actionPerformed(ActionEvent e)
2967 viewport.hideAllSelectedSeqs();
2968 // alignPanel.paintAlignment(true);
2972 * called by key handler and the hide all/show all menu items
2977 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2980 boolean hide = false;
2981 SequenceGroup sg = viewport.getSelectionGroup();
2982 if (!toggleSeqs && !toggleCols)
2984 // Hide everything by the current selection - this is a hack - we do the
2985 // invert and then hide
2986 // first check that there will be visible columns after the invert.
2987 if ((viewport.getColumnSelection() != null
2988 && viewport.getColumnSelection().getSelected() != null && viewport
2989 .getColumnSelection().getSelected().size() > 0)
2990 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2993 // now invert the sequence set, if required - empty selection implies
2994 // that no hiding is required.
2997 invertSequenceMenuItem_actionPerformed(null);
2998 sg = viewport.getSelectionGroup();
3002 viewport.expandColSelection(sg, true);
3003 // finally invert the column selection and get the new sequence
3005 invertColSel_actionPerformed(null);
3012 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3014 hideSelSequences_actionPerformed(null);
3017 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
3020 showAllSeqs_actionPerformed(null);
3026 if (viewport.getColumnSelection().getSelected().size() > 0)
3028 hideSelColumns_actionPerformed(null);
3031 viewport.setSelectionGroup(sg);
3036 showAllColumns_actionPerformed(null);
3045 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3046 * event.ActionEvent)
3049 public void hideAllButSelection_actionPerformed(ActionEvent e)
3051 toggleHiddenRegions(false, false);
3058 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3062 public void hideAllSelection_actionPerformed(ActionEvent e)
3064 SequenceGroup sg = viewport.getSelectionGroup();
3065 viewport.expandColSelection(sg, false);
3066 viewport.hideAllSelectedSeqs();
3067 viewport.hideSelectedColumns();
3068 alignPanel.paintAlignment(true);
3075 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3079 public void showAllhidden_actionPerformed(ActionEvent e)
3081 viewport.showAllHiddenColumns();
3082 viewport.showAllHiddenSeqs();
3083 alignPanel.paintAlignment(true);
3087 public void hideSelColumns_actionPerformed(ActionEvent e)
3089 viewport.hideSelectedColumns();
3090 alignPanel.paintAlignment(true);
3094 public void hiddenMarkers_actionPerformed(ActionEvent e)
3096 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3107 protected void scaleAbove_actionPerformed(ActionEvent e)
3109 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3110 alignPanel.paintAlignment(true);
3120 protected void scaleLeft_actionPerformed(ActionEvent e)
3122 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3123 alignPanel.paintAlignment(true);
3133 protected void scaleRight_actionPerformed(ActionEvent e)
3135 viewport.setScaleRightWrapped(scaleRight.isSelected());
3136 alignPanel.paintAlignment(true);
3146 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3148 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3149 alignPanel.paintAlignment(true);
3159 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3161 viewport.setShowText(viewTextMenuItem.isSelected());
3162 alignPanel.paintAlignment(true);
3172 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3174 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3175 alignPanel.paintAlignment(true);
3178 public FeatureSettings featureSettings;
3181 public FeatureSettingsControllerI getFeatureSettingsUI()
3183 return featureSettings;
3187 public void featureSettings_actionPerformed(ActionEvent e)
3189 if (featureSettings != null)
3191 featureSettings.close();
3192 featureSettings = null;
3194 if (!showSeqFeatures.isSelected())
3196 // make sure features are actually displayed
3197 showSeqFeatures.setSelected(true);
3198 showSeqFeatures_actionPerformed(null);
3200 featureSettings = new FeatureSettings(this);
3204 * Set or clear 'Show Sequence Features'
3210 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3212 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3213 alignPanel.paintAlignment(true);
3214 if (alignPanel.getOverviewPanel() != null)
3216 alignPanel.getOverviewPanel().updateOverviewImage();
3221 * Set or clear 'Show Sequence Features'
3227 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3229 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3231 if (viewport.isShowSequenceFeaturesHeight())
3233 // ensure we're actually displaying features
3234 viewport.setShowSequenceFeatures(true);
3235 showSeqFeatures.setSelected(true);
3237 alignPanel.paintAlignment(true);
3238 if (alignPanel.getOverviewPanel() != null)
3240 alignPanel.getOverviewPanel().updateOverviewImage();
3245 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3246 * the annotations panel as a whole.
3248 * The options to show/hide all annotations should be enabled when the panel
3249 * is shown, and disabled when the panel is hidden.
3254 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3256 final boolean setVisible = annotationPanelMenuItem.isSelected();
3257 viewport.setShowAnnotation(setVisible);
3258 this.showAllSeqAnnotations.setEnabled(setVisible);
3259 this.hideAllSeqAnnotations.setEnabled(setVisible);
3260 this.showAllAlAnnotations.setEnabled(setVisible);
3261 this.hideAllAlAnnotations.setEnabled(setVisible);
3262 alignPanel.updateLayout();
3266 public void alignmentProperties()
3268 JEditorPane editPane = new JEditorPane("text/html", "");
3269 editPane.setEditable(false);
3270 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3272 editPane.setText(MessageManager.formatMessage("label.html_content",
3274 { contents.toString() }));
3275 JInternalFrame frame = new JInternalFrame();
3276 frame.getContentPane().add(new JScrollPane(editPane));
3278 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3279 "label.alignment_properties", new Object[]
3280 { getTitle() }), 500, 400);
3290 public void overviewMenuItem_actionPerformed(ActionEvent e)
3292 if (alignPanel.overviewPanel != null)
3297 JInternalFrame frame = new JInternalFrame();
3298 OverviewPanel overview = new OverviewPanel(alignPanel);
3299 frame.setContentPane(overview);
3300 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3301 "label.overview_params", new Object[]
3302 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3304 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3305 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3308 public void internalFrameClosed(
3309 javax.swing.event.InternalFrameEvent evt)
3311 alignPanel.setOverviewPanel(null);
3315 alignPanel.setOverviewPanel(overview);
3319 public void textColour_actionPerformed(ActionEvent e)
3321 new TextColourChooser().chooseColour(alignPanel, null);
3331 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3343 public void clustalColour_actionPerformed(ActionEvent e)
3345 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3346 viewport.getHiddenRepSequences()));
3356 public void zappoColour_actionPerformed(ActionEvent e)
3358 changeColour(new ZappoColourScheme());
3368 public void taylorColour_actionPerformed(ActionEvent e)
3370 changeColour(new TaylorColourScheme());
3380 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3382 changeColour(new HydrophobicColourScheme());
3392 public void helixColour_actionPerformed(ActionEvent e)
3394 changeColour(new HelixColourScheme());
3404 public void strandColour_actionPerformed(ActionEvent e)
3406 changeColour(new StrandColourScheme());
3416 public void turnColour_actionPerformed(ActionEvent e)
3418 changeColour(new TurnColourScheme());
3428 public void buriedColour_actionPerformed(ActionEvent e)
3430 changeColour(new BuriedColourScheme());
3440 public void nucleotideColour_actionPerformed(ActionEvent e)
3442 changeColour(new NucleotideColourScheme());
3446 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3448 changeColour(new PurinePyrimidineColourScheme());
3452 * public void covariationColour_actionPerformed(ActionEvent e) {
3454 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3458 public void annotationColour_actionPerformed(ActionEvent e)
3460 new AnnotationColourChooser(viewport, alignPanel);
3464 public void annotationColumn_actionPerformed(ActionEvent e)
3466 new AnnotationColumnChooser(viewport, alignPanel);
3470 public void rnahelicesColour_actionPerformed(ActionEvent e)
3472 new RNAHelicesColourChooser(viewport, alignPanel);
3482 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3484 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3493 public void changeColour(ColourSchemeI cs)
3495 // TODO: compare with applet and pull up to model method
3500 if (viewport.getAbovePIDThreshold())
3502 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3504 cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
3508 cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
3511 if (viewport.getConservationSelected())
3514 Alignment al = (Alignment) viewport.getAlignment();
3515 Conservation c = new Conservation("All",
3516 ResidueProperties.propHash, 3, al.getSequences(), 0,
3520 c.verdict(false, viewport.getConsPercGaps());
3522 cs.setConservation(c);
3524 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3529 cs.setConservation(null);
3532 cs.setConsensus(viewport.getSequenceConsensusHash());
3535 viewport.setGlobalColourScheme(cs);
3537 if (viewport.getColourAppliesToAllGroups())
3540 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3548 if (cs instanceof ClustalxColourScheme)
3550 sg.cs = new ClustalxColourScheme(sg,
3551 viewport.getHiddenRepSequences());
3553 else if (cs instanceof UserColourScheme)
3555 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3561 sg.cs = cs.getClass().newInstance();
3562 } catch (Exception ex)
3567 if (viewport.getAbovePIDThreshold()
3568 || cs instanceof PIDColourScheme
3569 || cs instanceof Blosum62ColourScheme)
3571 sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
3573 sg.cs.setConsensus(AAFrequency.calculate(
3574 sg.getSequences(viewport.getHiddenRepSequences()),
3575 sg.getStartRes(), sg.getEndRes() + 1));
3579 sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
3582 if (viewport.getConservationSelected())
3584 Conservation c = new Conservation("Group",
3585 ResidueProperties.propHash, 3, sg.getSequences(viewport
3586 .getHiddenRepSequences()), sg.getStartRes(),
3587 sg.getEndRes() + 1);
3589 c.verdict(false, viewport.getConsPercGaps());
3590 sg.cs.setConservation(c);
3594 sg.cs.setConservation(null);
3599 if (alignPanel.getOverviewPanel() != null)
3601 alignPanel.getOverviewPanel().updateOverviewImage();
3604 alignPanel.paintAlignment(true);
3614 protected void modifyPID_actionPerformed(ActionEvent e)
3616 if (viewport.getAbovePIDThreshold()
3617 && viewport.getGlobalColourScheme() != null)
3619 SliderPanel.setPIDSliderSource(alignPanel,
3620 viewport.getGlobalColourScheme(), "Background");
3621 SliderPanel.showPIDSlider();
3632 protected void modifyConservation_actionPerformed(ActionEvent e)
3634 if (viewport.getConservationSelected()
3635 && viewport.getGlobalColourScheme() != null)
3637 SliderPanel.setConservationSlider(alignPanel,
3638 viewport.getGlobalColourScheme(), "Background");
3639 SliderPanel.showConservationSlider();
3650 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3652 viewport.setConservationSelected(conservationMenuItem.isSelected());
3654 viewport.setAbovePIDThreshold(false);
3655 abovePIDThreshold.setSelected(false);
3657 changeColour(viewport.getGlobalColourScheme());
3659 modifyConservation_actionPerformed(null);
3669 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3671 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3673 conservationMenuItem.setSelected(false);
3674 viewport.setConservationSelected(false);
3676 changeColour(viewport.getGlobalColourScheme());
3678 modifyPID_actionPerformed(null);
3688 public void userDefinedColour_actionPerformed(ActionEvent e)
3690 if (e.getActionCommand().equals(
3691 MessageManager.getString("action.user_defined")))
3693 new UserDefinedColours(alignPanel, null);
3697 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3698 .getUserColourSchemes().get(e.getActionCommand());
3704 public void updateUserColourMenu()
3707 Component[] menuItems = colourMenu.getMenuComponents();
3708 int iSize = menuItems.length;
3709 for (int i = 0; i < iSize; i++)
3711 if (menuItems[i].getName() != null
3712 && menuItems[i].getName().equals("USER_DEFINED"))
3714 colourMenu.remove(menuItems[i]);
3718 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3720 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3721 .getUserColourSchemes().keys();
3723 while (userColours.hasMoreElements())
3725 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3726 userColours.nextElement().toString());
3727 radioItem.setName("USER_DEFINED");
3728 radioItem.addMouseListener(new MouseAdapter()
3731 public void mousePressed(MouseEvent evt)
3733 if (evt.isControlDown()
3734 || SwingUtilities.isRightMouseButton(evt))
3736 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3738 int option = JOptionPane.showInternalConfirmDialog(
3739 jalview.gui.Desktop.desktop,
3741 .getString("label.remove_from_default_list"),
3743 .getString("label.remove_user_defined_colour"),
3744 JOptionPane.YES_NO_OPTION);
3745 if (option == JOptionPane.YES_OPTION)
3747 jalview.gui.UserDefinedColours
3748 .removeColourFromDefaults(radioItem.getText());
3749 colourMenu.remove(radioItem);
3753 radioItem.addActionListener(new ActionListener()
3756 public void actionPerformed(ActionEvent evt)
3758 userDefinedColour_actionPerformed(evt);
3765 radioItem.addActionListener(new ActionListener()
3768 public void actionPerformed(ActionEvent evt)
3770 userDefinedColour_actionPerformed(evt);
3774 colourMenu.insert(radioItem, 15);
3775 colours.add(radioItem);
3787 public void PIDColour_actionPerformed(ActionEvent e)
3789 changeColour(new PIDColourScheme());
3799 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3801 changeColour(new Blosum62ColourScheme());
3811 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3813 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3814 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3815 .getAlignment().getSequenceAt(0), null);
3816 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3817 viewport.getAlignment()));
3818 alignPanel.paintAlignment(true);
3828 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3830 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3831 AlignmentSorter.sortByID(viewport.getAlignment());
3832 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3833 viewport.getAlignment()));
3834 alignPanel.paintAlignment(true);
3844 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3846 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3847 AlignmentSorter.sortByLength(viewport.getAlignment());
3848 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3849 viewport.getAlignment()));
3850 alignPanel.paintAlignment(true);
3860 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3862 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3863 AlignmentSorter.sortByGroup(viewport.getAlignment());
3864 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3865 viewport.getAlignment()));
3867 alignPanel.paintAlignment(true);
3877 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3879 new RedundancyPanel(alignPanel, this);
3889 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3891 if ((viewport.getSelectionGroup() == null)
3892 || (viewport.getSelectionGroup().getSize() < 2))
3894 JOptionPane.showInternalMessageDialog(this, MessageManager
3895 .getString("label.you_must_select_least_two_sequences"),
3896 MessageManager.getString("label.invalid_selection"),
3897 JOptionPane.WARNING_MESSAGE);
3901 JInternalFrame frame = new JInternalFrame();
3902 frame.setContentPane(new PairwiseAlignPanel(viewport));
3903 Desktop.addInternalFrame(frame,
3904 MessageManager.getString("action.pairwise_alignment"), 600,
3916 public void PCAMenuItem_actionPerformed(ActionEvent e)
3918 if (((viewport.getSelectionGroup() != null)
3919 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3920 .getSelectionGroup().getSize() > 0))
3921 || (viewport.getAlignment().getHeight() < 4))
3924 .showInternalMessageDialog(
3927 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3929 .getString("label.sequence_selection_insufficient"),
3930 JOptionPane.WARNING_MESSAGE);
3935 new PCAPanel(alignPanel);
3939 public void autoCalculate_actionPerformed(ActionEvent e)
3941 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3942 if (viewport.autoCalculateConsensus)
3944 viewport.firePropertyChange("alignment", null, viewport
3945 .getAlignment().getSequences());
3950 public void sortByTreeOption_actionPerformed(ActionEvent e)
3952 viewport.sortByTree = sortByTree.isSelected();
3956 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3958 viewport.followSelection = listenToViewSelections.isSelected();
3968 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3970 newTreePanel("AV", "PID", "Average distance tree using PID");
3980 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3982 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3992 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3994 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
4004 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
4006 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
4019 void newTreePanel(String type, String pwType, String title)
4023 if (viewport.getSelectionGroup() != null
4024 && viewport.getSelectionGroup().getSize() > 0)
4026 if (viewport.getSelectionGroup().getSize() < 3)
4032 .getString("label.you_need_more_two_sequences_selected_build_tree"),
4034 .getString("label.not_enough_sequences"),
4035 JOptionPane.WARNING_MESSAGE);
4039 SequenceGroup sg = viewport.getSelectionGroup();
4041 /* Decide if the selection is a column region */
4042 for (SequenceI _s : sg.getSequences())
4044 if (_s.getLength() < sg.getEndRes())
4050 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
4052 .getString("label.sequences_selection_not_aligned"),
4053 JOptionPane.WARNING_MESSAGE);
4059 title = title + " on region";
4060 tp = new TreePanel(alignPanel, type, pwType);
4064 // are the visible sequences aligned?
4065 if (!viewport.getAlignment().isAligned(false))
4071 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4073 .getString("label.sequences_not_aligned"),
4074 JOptionPane.WARNING_MESSAGE);
4079 if (viewport.getAlignment().getHeight() < 2)
4084 tp = new TreePanel(alignPanel, type, pwType);
4089 if (viewport.viewName != null)
4091 title += viewport.viewName + " of ";
4094 title += this.title;
4096 Desktop.addInternalFrame(tp, title, 600, 500);
4107 public void addSortByOrderMenuItem(String title,
4108 final AlignmentOrder order)
4110 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title}));
4112 item.addActionListener(new java.awt.event.ActionListener()
4115 public void actionPerformed(ActionEvent e)
4117 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4119 // TODO: JBPNote - have to map order entries to curent SequenceI
4121 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4123 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4126 alignPanel.paintAlignment(true);
4132 * Add a new sort by annotation score menu item
4135 * the menu to add the option to
4137 * the label used to retrieve scores for each sequence on the
4140 public void addSortByAnnotScoreMenuItem(JMenu sort,
4141 final String scoreLabel)
4143 final JMenuItem item = new JMenuItem(scoreLabel);
4145 item.addActionListener(new java.awt.event.ActionListener()
4148 public void actionPerformed(ActionEvent e)
4150 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4151 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4152 viewport.getAlignment());// ,viewport.getSelectionGroup());
4153 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4154 viewport.getAlignment()));
4155 alignPanel.paintAlignment(true);
4161 * last hash for alignment's annotation array - used to minimise cost of
4164 protected int _annotationScoreVectorHash;
4167 * search the alignment and rebuild the sort by annotation score submenu the
4168 * last alignment annotation vector hash is stored to minimize cost of
4169 * rebuilding in subsequence calls.
4173 public void buildSortByAnnotationScoresMenu()
4175 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4180 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4182 sortByAnnotScore.removeAll();
4183 // almost certainly a quicker way to do this - but we keep it simple
4184 Hashtable scoreSorts = new Hashtable();
4185 AlignmentAnnotation aann[];
4186 for (SequenceI sqa : viewport.getAlignment().getSequences())
4188 aann = sqa.getAnnotation();
4189 for (int i = 0; aann != null && i < aann.length; i++)
4191 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4193 scoreSorts.put(aann[i].label, aann[i].label);
4197 Enumeration labels = scoreSorts.keys();
4198 while (labels.hasMoreElements())
4200 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4201 (String) labels.nextElement());
4203 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4206 _annotationScoreVectorHash = viewport.getAlignment()
4207 .getAlignmentAnnotation().hashCode();
4212 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4213 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4214 * call. Listeners are added to remove the menu item when the treePanel is
4215 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4219 * Displayed tree window.
4221 * SortBy menu item title.
4224 public void buildTreeMenu()
4226 calculateTree.removeAll();
4227 // build the calculate menu
4229 for (final String type : new String[]
4232 String treecalcnm = MessageManager.getString("label.tree_calc_"
4233 + type.toLowerCase());
4234 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4236 JMenuItem tm = new JMenuItem();
4237 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4238 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4240 String smn = MessageManager.getStringOrReturn(
4241 "label.score_model_", sm.getName());
4242 final String title = MessageManager.formatMessage(
4243 "label.treecalc_title", treecalcnm, smn);
4244 tm.setText(title);//
4245 tm.addActionListener(new java.awt.event.ActionListener()
4248 public void actionPerformed(ActionEvent e)
4250 newTreePanel(type, pwtype, title);
4253 calculateTree.add(tm);
4258 sortByTreeMenu.removeAll();
4260 List<Component> comps = PaintRefresher.components.get(viewport
4261 .getSequenceSetId());
4262 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4263 for (Component comp : comps)
4265 if (comp instanceof TreePanel)
4267 treePanels.add((TreePanel) comp);
4271 if (treePanels.size() < 1)
4273 sortByTreeMenu.setVisible(false);
4277 sortByTreeMenu.setVisible(true);
4279 for (final TreePanel tp : treePanels)
4281 final JMenuItem item = new JMenuItem(tp.getTitle());
4282 item.addActionListener(new java.awt.event.ActionListener()
4285 public void actionPerformed(ActionEvent e)
4287 tp.sortByTree_actionPerformed();
4288 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4293 sortByTreeMenu.add(item);
4297 public boolean sortBy(AlignmentOrder alorder, String undoname)
4299 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4300 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4301 if (undoname != null)
4303 addHistoryItem(new OrderCommand(undoname, oldOrder,
4304 viewport.getAlignment()));
4306 alignPanel.paintAlignment(true);
4311 * Work out whether the whole set of sequences or just the selected set will
4312 * be submitted for multiple alignment.
4315 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4317 // Now, check we have enough sequences
4318 AlignmentView msa = null;
4320 if ((viewport.getSelectionGroup() != null)
4321 && (viewport.getSelectionGroup().getSize() > 1))
4323 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4324 // some common interface!
4326 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4327 * SequenceI[sz = seqs.getSize(false)];
4329 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4330 * seqs.getSequenceAt(i); }
4332 msa = viewport.getAlignmentView(true);
4334 else if (viewport.getSelectionGroup() != null
4335 && viewport.getSelectionGroup().getSize() == 1)
4337 int option = JOptionPane.showConfirmDialog(this,
4338 MessageManager.getString("warn.oneseq_msainput_selection"),
4339 MessageManager.getString("label.invalid_selection"),
4340 JOptionPane.OK_CANCEL_OPTION);
4341 if (option == JOptionPane.OK_OPTION)
4343 msa = viewport.getAlignmentView(false);
4348 msa = viewport.getAlignmentView(false);
4354 * Decides what is submitted to a secondary structure prediction service: the
4355 * first sequence in the alignment, or in the current selection, or, if the
4356 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4357 * region or the whole alignment. (where the first sequence in the set is the
4358 * one that the prediction will be for).
4360 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4362 AlignmentView seqs = null;
4364 if ((viewport.getSelectionGroup() != null)
4365 && (viewport.getSelectionGroup().getSize() > 0))
4367 seqs = viewport.getAlignmentView(true);
4371 seqs = viewport.getAlignmentView(false);
4373 // limit sequences - JBPNote in future - could spawn multiple prediction
4375 // TODO: viewport.getAlignment().isAligned is a global state - the local
4376 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4377 if (!viewport.getAlignment().isAligned(false))
4379 seqs.setSequences(new SeqCigar[]
4380 { seqs.getSequences()[0] });
4381 // TODO: if seqs.getSequences().length>1 then should really have warned
4395 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4397 // Pick the tree file
4398 JalviewFileChooser chooser = new JalviewFileChooser(
4399 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4400 chooser.setFileView(new JalviewFileView());
4401 chooser.setDialogTitle(MessageManager
4402 .getString("label.select_newick_like_tree_file"));
4403 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4405 int value = chooser.showOpenDialog(null);
4407 if (value == JalviewFileChooser.APPROVE_OPTION)
4409 String choice = chooser.getSelectedFile().getPath();
4410 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4411 jalview.io.NewickFile fin = null;
4414 fin = new jalview.io.NewickFile(choice, "File");
4415 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4416 } catch (Exception ex)
4423 .getString("label.problem_reading_tree_file"),
4424 JOptionPane.WARNING_MESSAGE);
4425 ex.printStackTrace();
4427 if (fin != null && fin.hasWarningMessage())
4429 JOptionPane.showMessageDialog(Desktop.desktop, fin
4430 .getWarningMessage(), MessageManager
4431 .getString("label.possible_problem_with_tree_file"),
4432 JOptionPane.WARNING_MESSAGE);
4438 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4440 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4443 public TreePanel ShowNewickTree(NewickFile nf, String title)
4445 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4448 public TreePanel ShowNewickTree(NewickFile nf, String title,
4449 AlignmentView input)
4451 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4454 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4455 int h, int x, int y)
4457 return ShowNewickTree(nf, title, null, w, h, x, y);
4461 * Add a treeviewer for the tree extracted from a newick file object to the
4462 * current alignment view
4469 * Associated alignment input data (or null)
4478 * @return TreePanel handle
4480 public TreePanel ShowNewickTree(NewickFile nf, String title,
4481 AlignmentView input, int w, int h, int x, int y)
4483 TreePanel tp = null;
4489 if (nf.getTree() != null)
4491 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4497 tp.setLocation(x, y);
4500 Desktop.addInternalFrame(tp, title, w, h);
4502 } catch (Exception ex)
4504 ex.printStackTrace();
4510 private boolean buildingMenu = false;
4513 * Generates menu items and listener event actions for web service clients
4516 public void BuildWebServiceMenu()
4518 while (buildingMenu)
4522 System.err.println("Waiting for building menu to finish.");
4524 } catch (Exception e)
4528 final AlignFrame me = this;
4529 buildingMenu = true;
4530 new Thread(new Runnable()
4535 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4538 // System.err.println("Building ws menu again "
4539 // + Thread.currentThread());
4540 // TODO: add support for context dependent disabling of services based
4542 // alignment and current selection
4543 // TODO: add additional serviceHandle parameter to specify abstract
4545 // class independently of AbstractName
4546 // TODO: add in rediscovery GUI function to restart discoverer
4547 // TODO: group services by location as well as function and/or
4549 // object broker mechanism.
4550 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4551 final IProgressIndicator af = me;
4552 final JMenu msawsmenu = new JMenu("Alignment");
4553 final JMenu secstrmenu = new JMenu(
4554 "Secondary Structure Prediction");
4555 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4556 final JMenu analymenu = new JMenu("Analysis");
4557 final JMenu dismenu = new JMenu("Protein Disorder");
4558 // final JMenu msawsmenu = new
4559 // JMenu(MessageManager.getString("label.alignment"));
4560 // final JMenu secstrmenu = new
4561 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4562 // final JMenu seqsrchmenu = new
4563 // JMenu(MessageManager.getString("label.sequence_database_search"));
4564 // final JMenu analymenu = new
4565 // JMenu(MessageManager.getString("label.analysis"));
4566 // final JMenu dismenu = new
4567 // JMenu(MessageManager.getString("label.protein_disorder"));
4568 // JAL-940 - only show secondary structure prediction services from
4569 // the legacy server
4570 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4572 Discoverer.services != null && (Discoverer.services.size() > 0))
4574 // TODO: refactor to allow list of AbstractName/Handler bindings to
4576 // stored or retrieved from elsewhere
4577 // No MSAWS used any more:
4578 // Vector msaws = null; // (Vector)
4579 // Discoverer.services.get("MsaWS");
4580 Vector secstrpr = (Vector) Discoverer.services
4582 if (secstrpr != null)
4584 // Add any secondary structure prediction services
4585 for (int i = 0, j = secstrpr.size(); i < j; i++)
4587 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4589 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4590 .getServiceClient(sh);
4591 int p = secstrmenu.getItemCount();
4592 impl.attachWSMenuEntry(secstrmenu, me);
4593 int q = secstrmenu.getItemCount();
4594 for (int litm = p; litm < q; litm++)
4596 legacyItems.add(secstrmenu.getItem(litm));
4602 // Add all submenus in the order they should appear on the web
4604 wsmenu.add(msawsmenu);
4605 wsmenu.add(secstrmenu);
4606 wsmenu.add(dismenu);
4607 wsmenu.add(analymenu);
4608 // No search services yet
4609 // wsmenu.add(seqsrchmenu);
4611 javax.swing.SwingUtilities.invokeLater(new Runnable()
4618 webService.removeAll();
4619 // first, add discovered services onto the webservices menu
4620 if (wsmenu.size() > 0)
4622 for (int i = 0, j = wsmenu.size(); i < j; i++)
4624 webService.add(wsmenu.get(i));
4629 webService.add(me.webServiceNoServices);
4631 // TODO: move into separate menu builder class.
4632 boolean new_sspred = false;
4633 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4635 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4636 if (jws2servs != null)
4638 if (jws2servs.hasServices())
4640 jws2servs.attachWSMenuEntry(webService, me);
4641 for (Jws2Instance sv : jws2servs.getServices())
4643 if (sv.description.toLowerCase().contains("jpred"))
4645 for (JMenuItem jmi : legacyItems)
4647 jmi.setVisible(false);
4653 if (jws2servs.isRunning())
4655 JMenuItem tm = new JMenuItem(
4656 "Still discovering JABA Services");
4657 tm.setEnabled(false);
4662 build_urlServiceMenu(me.webService);
4663 build_fetchdbmenu(webService);
4664 for (JMenu item : wsmenu)
4666 if (item.getItemCount() == 0)
4668 item.setEnabled(false);
4672 item.setEnabled(true);
4675 } catch (Exception e)
4678 .debug("Exception during web service menu building process.",
4683 } catch (Exception e)
4686 buildingMenu = false;
4693 * construct any groupURL type service menu entries.
4697 private void build_urlServiceMenu(JMenu webService)
4699 // TODO: remove this code when 2.7 is released
4700 // DEBUG - alignmentView
4702 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4703 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4705 * @Override public void actionPerformed(ActionEvent e) {
4706 * jalview.datamodel.AlignmentView
4707 * .testSelectionViews(af.viewport.getAlignment(),
4708 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4710 * }); webService.add(testAlView);
4712 // TODO: refactor to RestClient discoverer and merge menu entries for
4713 // rest-style services with other types of analysis/calculation service
4714 // SHmmr test client - still being implemented.
4715 // DEBUG - alignmentView
4717 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4720 client.attachWSMenuEntry(
4721 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4727 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4728 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4729 * getProperty("LAST_DIRECTORY"));
4731 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4732 * to Vamsas file"); chooser.setToolTipText("Export");
4734 * int value = chooser.showSaveDialog(this);
4736 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4737 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4738 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4739 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4742 * prototype of an automatically enabled/disabled analysis function
4745 protected void setShowProductsEnabled()
4747 SequenceI[] selection = viewport.getSequenceSelection();
4748 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4749 viewport.getAlignment().getDataset()))
4751 showProducts.setEnabled(true);
4756 showProducts.setEnabled(false);
4761 * search selection for sequence xRef products and build the show products
4766 * @return true if showProducts menu should be enabled.
4768 public boolean canShowProducts(SequenceI[] selection,
4769 boolean isRegionSelection, Alignment dataset)
4771 boolean showp = false;
4774 showProducts.removeAll();
4775 final boolean dna = viewport.getAlignment().isNucleotide();
4776 final Alignment ds = dataset;
4777 String[] ptypes = (selection == null || selection.length == 0) ? null
4778 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4780 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4781 // selection, dataset, true);
4782 final SequenceI[] sel = selection;
4783 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4786 final boolean isRegSel = isRegionSelection;
4787 final AlignFrame af = this;
4788 final String source = ptypes[t];
4789 JMenuItem xtype = new JMenuItem(ptypes[t]);
4790 xtype.addActionListener(new ActionListener()
4794 public void actionPerformed(ActionEvent e)
4796 // TODO: new thread for this call with vis-delay
4797 af.showProductsFor(af.viewport.getSequenceSelection(),
4798 isRegSel, dna, source);
4802 showProducts.add(xtype);
4804 showProducts.setVisible(showp);
4805 showProducts.setEnabled(showp);
4806 } catch (Exception e)
4808 jalview.bin.Cache.log
4809 .warn("canTranslate threw an exception - please report to help@jalview.org",
4816 protected void showProductsFor(final SequenceI[] sel,
4817 final boolean isRegSel, final boolean dna, final String source)
4819 Runnable foo = new Runnable()
4825 final long sttime = System.currentTimeMillis();
4826 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4827 "status.searching_for_sequences_from", new Object[]
4828 { source }), sttime);
4831 // update our local dataset reference
4832 Alignment ds = AlignFrame.this.getViewport().getAlignment()
4834 Alignment prods = CrossRef
4835 .findXrefSequences(sel, dna, source, ds);
4838 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4839 for (int s = 0; s < sprods.length; s++)
4841 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4842 if (ds.getSequences() == null
4843 || !ds.getSequences().contains(
4844 sprods[s].getDatasetSequence()))
4846 ds.addSequence(sprods[s].getDatasetSequence());
4848 sprods[s].updatePDBIds();
4850 Alignment al = new Alignment(sprods);
4854 * Copy dna-to-protein mappings to new alignment
4856 // TODO 1: no mappings are set up for EMBL product
4857 // TODO 2: if they were, should add them to protein alignment, not
4859 Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4860 for (AlignedCodonFrame acf : cf)
4862 al.addCodonFrame(acf);
4864 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4866 String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4867 + " for " + ((isRegSel) ? "selected region of " : "")
4869 naf.setTitle(newtitle);
4871 // temporary flag until SplitFrame is released
4872 boolean asSplitFrame = Cache.getDefault(
4873 Preferences.ENABLE_SPLIT_FRAME, true);
4877 * Make a copy of this alignment (sharing the same dataset
4878 * sequences). If we are DNA, drop introns and update mappings
4880 AlignmentI copyAlignment = null;
4881 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4882 .getSequenceSelection();
4885 copyAlignment = AlignmentUtils.makeExonAlignment(
4886 sequenceSelection, cf);
4887 al.getCodonFrames().clear();
4888 al.getCodonFrames().addAll(cf);
4889 final StructureSelectionManager ssm = StructureSelectionManager
4890 .getStructureSelectionManager(Desktop.instance);
4891 ssm.registerMappings(cf);
4895 copyAlignment = new Alignment(new Alignment(
4896 sequenceSelection));
4898 AlignFrame copyThis = new AlignFrame(copyAlignment,
4899 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4900 copyThis.setTitle(AlignFrame.this.getTitle());
4901 // SplitFrame with dna above, protein below
4902 SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4903 dna ? naf : copyThis);
4904 naf.setVisible(true);
4905 copyThis.setVisible(true);
4906 String linkedTitle = MessageManager
4907 .getString("label.linked_view_title");
4908 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4912 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4918 System.err.println("No Sequences generated for xRef type "
4921 } catch (Exception e)
4923 jalview.bin.Cache.log.error(
4924 "Exception when finding crossreferences", e);
4925 } catch (OutOfMemoryError e)
4927 new OOMWarning("whilst fetching crossreferences", e);
4930 jalview.bin.Cache.log.error("Error when finding crossreferences",
4933 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4934 "status.finished_searching_for_sequences_from",
4941 Thread frunner = new Thread(foo);
4945 public boolean canShowTranslationProducts(SequenceI[] selection,
4946 AlignmentI alignment)
4951 return (jalview.analysis.Dna.canTranslate(selection,
4952 viewport.getViewAsVisibleContigs(true)));
4953 } catch (Exception e)
4955 jalview.bin.Cache.log
4956 .warn("canTranslate threw an exception - please report to help@jalview.org",
4963 * Construct and display a new frame containing the translation of this
4964 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4967 public void showTranslation_actionPerformed(ActionEvent e)
4969 AlignmentI al = null;
4972 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4974 al = dna.translateCdna();
4975 } catch (Exception ex)
4977 jalview.bin.Cache.log.error(
4978 "Exception during translation. Please report this !", ex);
4979 final String msg = MessageManager
4980 .getString("label.error_when_translating_sequences_submit_bug_report");
4981 final String errorTitle = MessageManager
4982 .getString("label.implementation_error")
4983 + MessageManager.getString("translation_failed");
4984 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4985 JOptionPane.ERROR_MESSAGE);
4988 if (al == null || al.getHeight() == 0)
4990 final String msg = MessageManager
4991 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4992 final String errorTitle = MessageManager
4993 .getString("label.translation_failed");
4994 JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4995 JOptionPane.WARNING_MESSAGE);
4999 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
5000 af.setFileFormat(this.currentFileFormat);
5001 final String newTitle = MessageManager.formatMessage(
5002 "label.translation_of_params", new Object[]
5003 { this.getTitle() });
5004 af.setTitle(newTitle);
5005 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
5007 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
5008 viewport.openSplitFrame(af, new Alignment(seqs));
5012 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
5019 * Set the file format
5023 public void setFileFormat(String fileFormat)
5025 this.currentFileFormat = fileFormat;
5029 * Try to load a features file onto the alignment.
5032 * contents or path to retrieve file
5034 * access mode of file (see jalview.io.AlignFile)
5035 * @return true if features file was parsed correctly.
5037 public boolean parseFeaturesFile(String file, String type)
5039 return avc.parseFeaturesFile(file, type,
5040 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5045 public void refreshFeatureUI(boolean enableIfNecessary)
5047 // note - currently this is only still here rather than in the controller
5048 // because of the featureSettings hard reference that is yet to be
5050 if (enableIfNecessary)
5052 viewport.setShowSequenceFeatures(true);
5053 showSeqFeatures.setSelected(true);
5059 public void dragEnter(DropTargetDragEvent evt)
5064 public void dragExit(DropTargetEvent evt)
5069 public void dragOver(DropTargetDragEvent evt)
5074 public void dropActionChanged(DropTargetDragEvent evt)
5079 public void drop(DropTargetDropEvent evt)
5081 Transferable t = evt.getTransferable();
5082 java.util.List files = null;
5086 DataFlavor uriListFlavor = new DataFlavor(
5087 "text/uri-list;class=java.lang.String");
5088 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5090 // Works on Windows and MacOSX
5091 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5092 files = (java.util.List) t
5093 .getTransferData(DataFlavor.javaFileListFlavor);
5095 else if (t.isDataFlavorSupported(uriListFlavor))
5097 // This is used by Unix drag system
5098 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5099 String data = (String) t.getTransferData(uriListFlavor);
5100 files = new java.util.ArrayList(1);
5101 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5102 data, "\r\n"); st.hasMoreTokens();)
5104 String s = st.nextToken();
5105 if (s.startsWith("#"))
5107 // the line is a comment (as per the RFC 2483)
5111 java.net.URI uri = new java.net.URI(s);
5112 // check to see if we can handle this kind of URI
5113 if (uri.getScheme().toLowerCase().startsWith("http"))
5115 files.add(uri.toString());
5119 // otherwise preserve old behaviour: catch all for file objects
5120 java.io.File file = new java.io.File(uri);
5121 files.add(file.toString());
5125 } catch (Exception e)
5127 e.printStackTrace();
5133 // check to see if any of these files have names matching sequences in
5135 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5136 .getAlignment().getSequencesArray());
5138 * Object[] { String,SequenceI}
5140 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5141 ArrayList<String> filesnotmatched = new ArrayList<String>();
5142 for (int i = 0; i < files.size(); i++)
5144 String file = files.get(i).toString();
5146 String protocol = FormatAdapter.checkProtocol(file);
5147 if (protocol == jalview.io.FormatAdapter.FILE)
5149 File fl = new File(file);
5150 pdbfn = fl.getName();
5152 else if (protocol == jalview.io.FormatAdapter.URL)
5154 URL url = new URL(file);
5155 pdbfn = url.getFile();
5157 if (pdbfn.length() > 0)
5159 // attempt to find a match in the alignment
5160 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5161 int l = 0, c = pdbfn.indexOf(".");
5162 while (mtch == null && c != -1)
5167 } while ((c = pdbfn.indexOf(".", l)) > l);
5170 pdbfn = pdbfn.substring(0, l);
5172 mtch = idm.findAllIdMatches(pdbfn);
5179 type = new IdentifyFile().Identify(file, protocol);
5180 } catch (Exception ex)
5186 if (type.equalsIgnoreCase("PDB"))
5188 filesmatched.add(new Object[]
5189 { file, protocol, mtch });
5194 // File wasn't named like one of the sequences or wasn't a PDB file.
5195 filesnotmatched.add(file);
5199 if (filesmatched.size() > 0)
5201 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5207 "label.automatically_associate_pdb_files_with_sequences_same_name",
5214 .getString("label.automatically_associate_pdb_files_by_name"),
5215 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5218 for (Object[] fm : filesmatched)
5220 // try and associate
5221 // TODO: may want to set a standard ID naming formalism for
5222 // associating PDB files which have no IDs.
5223 for (SequenceI toassoc : (SequenceI[]) fm[2])
5225 PDBEntry pe = new AssociatePdbFileWithSeq()
5226 .associatePdbWithSeq((String) fm[0],
5227 (String) fm[1], toassoc, false,
5231 System.err.println("Associated file : "
5232 + ((String) fm[0]) + " with "
5233 + toassoc.getDisplayId(true));
5237 alignPanel.paintAlignment(true);
5241 if (filesnotmatched.size() > 0)
5244 && (Cache.getDefault(
5245 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5248 "<html>"+MessageManager
5250 "label.ignore_unmatched_dropped_files_info",
5255 .toString() })+"</html>",
5257 .getString("label.ignore_unmatched_dropped_files"),
5258 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5262 for (String fn : filesnotmatched)
5264 loadJalviewDataFile(fn, null, null, null);
5268 } catch (Exception ex)
5270 ex.printStackTrace();
5276 * Attempt to load a "dropped" file or URL string: First by testing whether
5277 * it's and Annotation file, then a JNet file, and finally a features file. If
5278 * all are false then the user may have dropped an alignment file onto this
5282 * either a filename or a URL string.
5284 public void loadJalviewDataFile(String file, String protocol,
5285 String format, SequenceI assocSeq)
5289 if (protocol == null)
5291 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5293 // if the file isn't identified, or not positively identified as some
5294 // other filetype (PFAM is default unidentified alignment file type) then
5295 // try to parse as annotation.
5296 boolean isAnnotation = (format == null || format
5297 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5298 .annotateAlignmentView(viewport, file, protocol)
5303 // first see if its a T-COFFEE score file
5304 TCoffeeScoreFile tcf = null;
5307 tcf = new TCoffeeScoreFile(file, protocol);
5310 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5312 tcoffeeColour.setEnabled(true);
5313 tcoffeeColour.setSelected(true);
5314 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5315 isAnnotation = true;
5317 .setText(MessageManager
5318 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5322 // some problem - if no warning its probable that the ID matching
5323 // process didn't work
5327 tcf.getWarningMessage() == null ? MessageManager
5328 .getString("label.check_file_matches_sequence_ids_alignment")
5329 : tcf.getWarningMessage(),
5331 .getString("label.problem_reading_tcoffee_score_file"),
5332 JOptionPane.WARNING_MESSAGE);
5339 } catch (Exception x)
5342 .debug("Exception when processing data source as T-COFFEE score file",
5348 // try to see if its a JNet 'concise' style annotation file *before*
5350 // try to parse it as a features file
5353 format = new IdentifyFile().Identify(file, protocol);
5355 if (format.equalsIgnoreCase("JnetFile"))
5357 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5359 new JnetAnnotationMaker();
5360 JnetAnnotationMaker.add_annotation(predictions,
5361 viewport.getAlignment(), 0, false);
5362 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5363 viewport.getAlignment().setSeqrep(repseq);
5364 ColumnSelection cs = new ColumnSelection();
5365 cs.hideInsertionsFor(repseq);
5366 viewport.setColumnSelection(cs);
5367 isAnnotation = true;
5372 * if (format.equalsIgnoreCase("PDB")) {
5374 * String pdbfn = ""; // try to match up filename with sequence id
5375 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5376 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5377 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5378 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5379 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5380 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5381 * // attempt to find a match in the alignment SequenceI mtch =
5382 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5383 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5384 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5385 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5386 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5387 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5388 * { System.err.println("Associated file : " + file + " with " +
5389 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5390 * TODO: maybe need to load as normal otherwise return; } }
5392 // try to parse it as a features file
5393 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5394 // if it wasn't a features file then we just treat it as a general
5395 // alignment file to load into the current view.
5398 new FileLoader().LoadFile(viewport, file, protocol, format);
5402 alignPanel.paintAlignment(true);
5410 alignPanel.adjustAnnotationHeight();
5411 viewport.updateSequenceIdColours();
5412 buildSortByAnnotationScoresMenu();
5413 alignPanel.paintAlignment(true);
5415 } catch (Exception ex)
5417 ex.printStackTrace();
5418 } catch (OutOfMemoryError oom)
5423 } catch (Exception x)
5429 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5430 : "using " + protocol + " from " + file)
5432 + (format != null ? "(parsing as '" + format
5433 + "' file)" : ""), oom, Desktop.desktop);
5438 * Method invoked by the ChangeListener on the tabbed pane, in other words
5439 * when a different tabbed pane is selected by the user or programmatically.
5442 public void tabSelectionChanged(int index)
5446 alignPanel = alignPanels.get(index);
5447 viewport = alignPanel.av;
5448 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5449 setMenusFromViewport(viewport);
5453 * If there is a frame linked to this one in a SplitPane, switch it to the
5454 * same view tab index. No infinite recursion of calls should happen, since
5455 * tabSelectionChanged() should not get invoked on setting the selected
5456 * index to an unchanged value. Guard against setting an invalid index
5457 * before the new view peer tab has been created.
5459 final AlignViewportI peer = viewport.getCodingComplement();
5462 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5463 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5465 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5471 * On right mouse click on view tab, prompt for and set new view name.
5474 public void tabbedPane_mousePressed(MouseEvent e)
5476 if (SwingUtilities.isRightMouseButton(e))
5478 String msg = MessageManager.getString("label.enter_view_name");
5479 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5480 JOptionPane.QUESTION_MESSAGE);
5484 viewport.viewName = reply;
5485 // TODO warn if reply is in getExistingViewNames()?
5486 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5491 public AlignViewport getCurrentView()
5497 * Open the dialog for regex description parsing.
5500 protected void extractScores_actionPerformed(ActionEvent e)
5502 ParseProperties pp = new jalview.analysis.ParseProperties(
5503 viewport.getAlignment());
5504 // TODO: verify regex and introduce GUI dialog for version 2.5
5505 // if (pp.getScoresFromDescription("col", "score column ",
5506 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5508 if (pp.getScoresFromDescription("description column",
5509 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5511 buildSortByAnnotationScoresMenu();
5519 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5523 protected void showDbRefs_actionPerformed(ActionEvent e)
5525 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5531 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5535 protected void showNpFeats_actionPerformed(ActionEvent e)
5537 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5541 * find the viewport amongst the tabs in this alignment frame and close that
5546 public boolean closeView(AlignViewportI av)
5550 this.closeMenuItem_actionPerformed(false);
5553 Component[] comp = tabbedPane.getComponents();
5554 for (int i = 0; comp != null && i < comp.length; i++)
5556 if (comp[i] instanceof AlignmentPanel)
5558 if (((AlignmentPanel) comp[i]).av == av)
5561 closeView((AlignmentPanel) comp[i]);
5569 protected void build_fetchdbmenu(JMenu webService)
5571 // Temporary hack - DBRef Fetcher always top level ws entry.
5572 // TODO We probably want to store a sequence database checklist in
5573 // preferences and have checkboxes.. rather than individual sources selected
5575 final JMenu rfetch = new JMenu(
5576 MessageManager.getString("action.fetch_db_references"));
5577 rfetch.setToolTipText(MessageManager
5578 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5579 webService.add(rfetch);
5581 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5582 MessageManager.getString("option.trim_retrieved_seqs"));
5583 trimrs.setToolTipText(MessageManager
5584 .getString("label.trim_retrieved_sequences"));
5585 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5586 trimrs.addActionListener(new ActionListener()
5589 public void actionPerformed(ActionEvent e)
5591 trimrs.setSelected(trimrs.isSelected());
5592 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5593 Boolean.valueOf(trimrs.isSelected()).toString());
5597 JMenuItem fetchr = new JMenuItem(
5598 MessageManager.getString("label.standard_databases"));
5599 fetchr.setToolTipText(MessageManager
5600 .getString("label.fetch_embl_uniprot"));
5601 fetchr.addActionListener(new ActionListener()
5605 public void actionPerformed(ActionEvent e)
5607 new Thread(new Runnable()
5613 new jalview.ws.DBRefFetcher(alignPanel.av
5614 .getSequenceSelection(), alignPanel.alignFrame)
5615 .fetchDBRefs(false);
5623 final AlignFrame me = this;
5624 new Thread(new Runnable()
5629 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5630 .getSequenceFetcherSingleton(me);
5631 javax.swing.SwingUtilities.invokeLater(new Runnable()
5636 String[] dbclasses = sf.getOrderedSupportedSources();
5637 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5638 // jalview.util.QuickSort.sort(otherdb, otherdb);
5639 List<DbSourceProxy> otherdb;
5640 JMenu dfetch = new JMenu();
5641 JMenu ifetch = new JMenu();
5642 JMenuItem fetchr = null;
5643 int comp = 0, icomp = 0, mcomp = 15;
5644 String mname = null;
5646 for (String dbclass : dbclasses)
5648 otherdb = sf.getSourceProxy(dbclass);
5649 // add a single entry for this class, or submenu allowing 'fetch
5651 if (otherdb == null || otherdb.size() < 1)
5655 // List<DbSourceProxy> dbs=otherdb;
5656 // otherdb=new ArrayList<DbSourceProxy>();
5657 // for (DbSourceProxy db:dbs)
5659 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5663 mname = "From " + dbclass;
5665 if (otherdb.size() == 1)
5667 final DbSourceProxy[] dassource = otherdb
5668 .toArray(new DbSourceProxy[0]);
5669 DbSourceProxy src = otherdb.get(0);
5670 fetchr = new JMenuItem(src.getDbSource());
5671 fetchr.addActionListener(new ActionListener()
5675 public void actionPerformed(ActionEvent e)
5677 new Thread(new Runnable()
5683 new jalview.ws.DBRefFetcher(alignPanel.av
5684 .getSequenceSelection(),
5685 alignPanel.alignFrame, dassource)
5686 .fetchDBRefs(false);
5692 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()})));
5698 final DbSourceProxy[] dassource = otherdb
5699 .toArray(new DbSourceProxy[0]);
5701 DbSourceProxy src = otherdb.get(0);
5702 fetchr = new JMenuItem(MessageManager.formatMessage(
5703 "label.fetch_all_param", new Object[]
5704 { src.getDbSource() }));
5705 fetchr.addActionListener(new ActionListener()
5708 public void actionPerformed(ActionEvent e)
5710 new Thread(new Runnable()
5716 new jalview.ws.DBRefFetcher(alignPanel.av
5717 .getSequenceSelection(),
5718 alignPanel.alignFrame, dassource)
5719 .fetchDBRefs(false);
5725 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new Object[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5728 // and then build the rest of the individual menus
5729 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()}));
5731 String imname = null;
5733 for (DbSourceProxy sproxy : otherdb)
5735 String dbname = sproxy.getDbName();
5736 String sname = dbname.length() > 5 ? dbname.substring(0,
5737 5) + "..." : dbname;
5738 String msname = dbname.length() > 10 ? dbname.substring(
5739 0, 10) + "..." : dbname;
5742 imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname});
5744 fetchr = new JMenuItem(msname);
5745 final DbSourceProxy[] dassrc =
5747 fetchr.addActionListener(new ActionListener()
5751 public void actionPerformed(ActionEvent e)
5753 new Thread(new Runnable()
5759 new jalview.ws.DBRefFetcher(alignPanel.av
5760 .getSequenceSelection(),
5761 alignPanel.alignFrame, dassrc)
5762 .fetchDBRefs(false);
5768 fetchr.setToolTipText("<html>"
5769 + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname}));
5772 if (++icomp >= mcomp || i == (otherdb.size()))
5774 ifetch.setText(MessageManager.formatMessage(
5775 "label.source_to_target", imname, sname));
5777 ifetch = new JMenu();
5785 if (comp >= mcomp || dbi >= (dbclasses.length))
5787 dfetch.setText(MessageManager.formatMessage(
5788 "label.source_to_target", mname, dbclass));
5790 dfetch = new JMenu();
5803 * Left justify the whole alignment.
5806 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5808 AlignmentI al = viewport.getAlignment();
5810 viewport.firePropertyChange("alignment", null, al);
5814 * Right justify the whole alignment.
5817 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5819 AlignmentI al = viewport.getAlignment();
5821 viewport.firePropertyChange("alignment", null, al);
5824 public void setShowSeqFeatures(boolean b)
5826 showSeqFeatures.setSelected(b);
5827 viewport.setShowSequenceFeatures(b);
5834 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5835 * awt.event.ActionEvent)
5838 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5840 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5841 alignPanel.paintAlignment(true);
5848 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5852 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5854 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5855 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5863 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5864 * .event.ActionEvent)
5867 protected void showGroupConservation_actionPerformed(ActionEvent e)
5869 viewport.setShowGroupConservation(showGroupConservation.getState());
5870 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5877 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5878 * .event.ActionEvent)
5881 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5883 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5884 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5891 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5892 * .event.ActionEvent)
5895 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5897 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5898 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5902 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5904 showSequenceLogo.setState(true);
5905 viewport.setShowSequenceLogo(true);
5906 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5907 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5911 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5913 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5920 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5921 * .event.ActionEvent)
5924 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5926 if (avc.makeGroupsFromSelection())
5928 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5929 alignPanel.updateAnnotation();
5930 alignPanel.paintAlignment(true);
5933 public void clearAlignmentSeqRep()
5935 // TODO refactor alignmentseqrep to controller
5936 if (viewport.getAlignment().hasSeqrep()) {
5937 viewport.getAlignment().setSeqrep(null);
5938 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5939 alignPanel.updateAnnotation();
5940 alignPanel.paintAlignment(true);
5945 protected void createGroup_actionPerformed(ActionEvent e)
5947 if (avc.createGroup())
5949 alignPanel.alignmentChanged();
5954 protected void unGroup_actionPerformed(ActionEvent e)
5958 alignPanel.alignmentChanged();
5963 * make the given alignmentPanel the currently selected tab
5965 * @param alignmentPanel
5967 public void setDisplayedView(AlignmentPanel alignmentPanel)
5969 if (!viewport.getSequenceSetId().equals(
5970 alignmentPanel.av.getSequenceSetId()))
5972 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5974 if (tabbedPane != null
5975 && tabbedPane.getTabCount() > 0
5976 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5977 .getSelectedIndex())
5979 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5984 * Action on selection of menu options to Show or Hide annotations.
5987 * @param forSequences
5988 * update sequence-related annotations
5989 * @param forAlignment
5990 * update non-sequence-related annotations
5993 protected void setAnnotationsVisibility(boolean visible,
5994 boolean forSequences, boolean forAlignment)
5996 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5997 .getAlignmentAnnotation())
6000 * don't display non-positional annotations on an alignment
6002 if (aa.annotations == null)
6006 boolean apply = (aa.sequenceRef == null && forAlignment)
6007 || (aa.sequenceRef != null && forSequences);
6010 aa.visible = visible;
6013 alignPanel.validateAnnotationDimensions(true);
6014 alignPanel.alignmentChanged();
6018 * Store selected annotation sort order for the view and repaint.
6021 protected void sortAnnotations_actionPerformed()
6023 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
6025 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
6026 alignPanel.paintAlignment(true);
6031 * @return alignment panels in this alignment frame
6033 public List<? extends AlignmentViewPanel> getAlignPanels()
6035 return alignPanels == null ? Arrays.asList(alignPanel)
6040 * Open a new alignment window, with the cDNA associated with this (protein)
6041 * alignment, aligned as is the protein.
6043 protected void viewAsCdna_actionPerformed()
6045 // TODO no longer a menu action - refactor as required
6046 final AlignmentI alignment = getViewport().getAlignment();
6047 Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6048 if (mappings == null)
6052 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6053 for (SequenceI aaSeq : alignment.getSequences()) {
6054 for (AlignedCodonFrame acf : mappings) {
6055 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6059 * There is a cDNA mapping for this protein sequence - add to new
6060 * alignment. It will share the same dataset sequence as other mapped
6061 * cDNA (no new mappings need to be created).
6063 final Sequence newSeq = new Sequence(dnaSeq);
6064 newSeq.setDatasetSequence(dnaSeq);
6065 cdnaSeqs.add(newSeq);
6069 if (cdnaSeqs.size() == 0)
6071 // show a warning dialog no mapped cDNA
6074 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6076 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6077 AlignFrame.DEFAULT_HEIGHT);
6078 cdna.alignAs(alignment);
6079 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6081 Desktop.addInternalFrame(alignFrame, newtitle,
6082 AlignFrame.DEFAULT_WIDTH,
6083 AlignFrame.DEFAULT_HEIGHT);
6087 * Set visibility of dna/protein complement view (available when shown in a
6093 protected void showComplement_actionPerformed(boolean show)
6095 SplitContainerI sf = getSplitViewContainer();
6097 sf.setComplementVisible(this, show);
6102 class PrintThread extends Thread
6106 public PrintThread(AlignmentPanel ap)
6111 static PageFormat pf;
6116 PrinterJob printJob = PrinterJob.getPrinterJob();
6120 printJob.setPrintable(ap, pf);
6124 printJob.setPrintable(ap);
6127 if (printJob.printDialog())
6132 } catch (Exception PrintException)
6134 PrintException.printStackTrace();