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 java.awt.BorderLayout;
24 import java.awt.Component;
25 import java.awt.Rectangle;
26 import java.awt.Toolkit;
27 import java.awt.datatransfer.Clipboard;
28 import java.awt.datatransfer.DataFlavor;
29 import java.awt.datatransfer.StringSelection;
30 import java.awt.datatransfer.Transferable;
31 import java.awt.dnd.DnDConstants;
32 import java.awt.dnd.DropTargetDragEvent;
33 import java.awt.dnd.DropTargetDropEvent;
34 import java.awt.dnd.DropTargetEvent;
35 import java.awt.dnd.DropTargetListener;
36 import java.awt.event.ActionEvent;
37 import java.awt.event.ActionListener;
38 import java.awt.event.ItemEvent;
39 import java.awt.event.ItemListener;
40 import java.awt.event.KeyAdapter;
41 import java.awt.event.KeyEvent;
42 import java.awt.event.MouseAdapter;
43 import java.awt.event.MouseEvent;
44 import java.awt.print.PageFormat;
45 import java.awt.print.PrinterJob;
46 import java.beans.PropertyChangeEvent;
49 import java.util.ArrayList;
50 import java.util.Arrays;
51 import java.util.Deque;
52 import java.util.Enumeration;
53 import java.util.Hashtable;
54 import java.util.List;
56 import java.util.Vector;
58 import javax.swing.JCheckBoxMenuItem;
59 import javax.swing.JEditorPane;
60 import javax.swing.JInternalFrame;
61 import javax.swing.JLayeredPane;
62 import javax.swing.JMenu;
63 import javax.swing.JMenuItem;
64 import javax.swing.JOptionPane;
65 import javax.swing.JRadioButtonMenuItem;
66 import javax.swing.JScrollPane;
67 import javax.swing.SwingUtilities;
69 import jalview.analysis.AAFrequency;
70 import jalview.analysis.AlignmentSorter;
71 import jalview.analysis.AlignmentUtils;
72 import jalview.analysis.Conservation;
73 import jalview.analysis.CrossRef;
74 import jalview.analysis.Dna;
75 import jalview.analysis.ParseProperties;
76 import jalview.analysis.SequenceIdMatcher;
77 import jalview.api.AlignViewControllerGuiI;
78 import jalview.api.AlignViewControllerI;
79 import jalview.api.AlignViewportI;
80 import jalview.api.AlignmentViewPanel;
81 import jalview.api.SplitContainerI;
82 import jalview.api.ViewStyleI;
83 import jalview.api.analysis.ScoreModelI;
84 import jalview.bin.Cache;
85 import jalview.commands.CommandI;
86 import jalview.commands.EditCommand;
87 import jalview.commands.EditCommand.Action;
88 import jalview.commands.OrderCommand;
89 import jalview.commands.RemoveGapColCommand;
90 import jalview.commands.RemoveGapsCommand;
91 import jalview.commands.SlideSequencesCommand;
92 import jalview.commands.TrimRegionCommand;
93 import jalview.datamodel.AlignedCodonFrame;
94 import jalview.datamodel.Alignment;
95 import jalview.datamodel.AlignmentAnnotation;
96 import jalview.datamodel.AlignmentI;
97 import jalview.datamodel.AlignmentOrder;
98 import jalview.datamodel.AlignmentView;
99 import jalview.datamodel.ColumnSelection;
100 import jalview.datamodel.HiddenSequences;
101 import jalview.datamodel.PDBEntry;
102 import jalview.datamodel.SeqCigar;
103 import jalview.datamodel.Sequence;
104 import jalview.datamodel.SequenceGroup;
105 import jalview.datamodel.SequenceI;
106 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
107 import jalview.io.AlignmentProperties;
108 import jalview.io.AnnotationFile;
109 import jalview.io.BioJsHTMLOutput;
110 import jalview.io.FeaturesFile;
111 import jalview.io.FileLoader;
112 import jalview.io.FormatAdapter;
113 import jalview.io.HtmlSvgOutput;
114 import jalview.io.IdentifyFile;
115 import jalview.io.JalviewFileChooser;
116 import jalview.io.JalviewFileView;
117 import jalview.io.JnetAnnotationMaker;
118 import jalview.io.NewickFile;
119 import jalview.io.TCoffeeScoreFile;
120 import jalview.jbgui.GAlignFrame;
121 import jalview.schemes.Blosum62ColourScheme;
122 import jalview.schemes.BuriedColourScheme;
123 import jalview.schemes.ClustalxColourScheme;
124 import jalview.schemes.ColourSchemeI;
125 import jalview.schemes.ColourSchemeProperty;
126 import jalview.schemes.HelixColourScheme;
127 import jalview.schemes.HydrophobicColourScheme;
128 import jalview.schemes.NucleotideColourScheme;
129 import jalview.schemes.PIDColourScheme;
130 import jalview.schemes.PurinePyrimidineColourScheme;
131 import jalview.schemes.RNAHelicesColourChooser;
132 import jalview.schemes.ResidueProperties;
133 import jalview.schemes.StrandColourScheme;
134 import jalview.schemes.TCoffeeColourScheme;
135 import jalview.schemes.TaylorColourScheme;
136 import jalview.schemes.TurnColourScheme;
137 import jalview.schemes.UserColourScheme;
138 import jalview.schemes.ZappoColourScheme;
139 import jalview.structure.StructureSelectionManager;
140 import jalview.util.MessageManager;
141 import jalview.viewmodel.AlignmentViewport;
142 import jalview.ws.jws1.Discoverer;
143 import jalview.ws.jws2.Jws2Discoverer;
144 import jalview.ws.jws2.jabaws2.Jws2Instance;
145 import jalview.ws.seqfetcher.DbSourceProxy;
151 * @version $Revision$
153 public class AlignFrame extends GAlignFrame implements DropTargetListener,
154 IProgressIndicator, AlignViewControllerGuiI
157 public static final int DEFAULT_WIDTH = 700;
159 public static final int DEFAULT_HEIGHT = 500;
162 * The currently displayed panel (selected tabbed view if more than one)
164 public AlignmentPanel alignPanel;
166 AlignViewport viewport;
168 public AlignViewControllerI avc;
170 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
173 * Last format used to load or save alignments in this window
175 String currentFileFormat = null;
178 * Current filename for this alignment
180 String fileName = null;
183 * Creates a new AlignFrame object with specific width and height.
189 public AlignFrame(AlignmentI al, int width, int height)
191 this(al, null, width, height);
195 * Creates a new AlignFrame object with specific width, height and
201 * @param sequenceSetId
203 public AlignFrame(AlignmentI al, int width, int height,
204 String sequenceSetId)
206 this(al, null, width, height, sequenceSetId);
210 * Creates a new AlignFrame object with specific width, height and
216 * @param sequenceSetId
219 public AlignFrame(AlignmentI al, int width, int height,
220 String sequenceSetId, String viewId)
222 this(al, null, width, height, sequenceSetId, viewId);
226 * new alignment window with hidden columns
230 * @param hiddenColumns
231 * ColumnSelection or null
233 * Width of alignment frame
237 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
238 int width, int height)
240 this(al, hiddenColumns, width, height, null);
244 * Create alignment frame for al with hiddenColumns, a specific width and
245 * height, and specific sequenceId
248 * @param hiddenColumns
251 * @param sequenceSetId
254 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
255 int width, int height, String sequenceSetId)
257 this(al, hiddenColumns, width, height, sequenceSetId, null);
261 * Create alignment frame for al with hiddenColumns, a specific width and
262 * height, and specific sequenceId
265 * @param hiddenColumns
268 * @param sequenceSetId
273 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
274 int width, int height, String sequenceSetId, String viewId)
276 setSize(width, height);
278 if (al.getDataset() == null)
283 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
285 alignPanel = new AlignmentPanel(this, viewport);
288 addAlignmentPanel(alignPanel, true);
293 * Make a new AlignFrame from existing alignmentPanels
300 public AlignFrame(AlignmentPanel ap)
304 addAlignmentPanel(ap, false);
309 * initalise the alignframe from the underlying viewport data and the
314 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
316 avc = new jalview.controller.AlignViewController(this, viewport,
318 if (viewport.getAlignmentConservationAnnotation() == null)
320 BLOSUM62Colour.setEnabled(false);
321 conservationMenuItem.setEnabled(false);
322 modifyConservation.setEnabled(false);
323 // PIDColour.setEnabled(false);
324 // abovePIDThreshold.setEnabled(false);
325 // modifyPID.setEnabled(false);
328 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
331 if (sortby.equals("Id"))
333 sortIDMenuItem_actionPerformed(null);
335 else if (sortby.equals("Pairwise Identity"))
337 sortPairwiseMenuItem_actionPerformed(null);
340 if (Desktop.desktop != null)
342 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
343 addServiceListeners();
344 setGUINucleotide(viewport.getAlignment().isNucleotide());
347 setMenusFromViewport(viewport);
348 buildSortByAnnotationScoresMenu();
351 if (viewport.getWrapAlignment())
353 wrapMenuItem_actionPerformed(null);
356 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
358 this.overviewMenuItem_actionPerformed(null);
363 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
364 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
365 final String menuLabel = MessageManager
366 .getString("label.copy_format_from");
367 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
368 new ViewSetProvider()
372 public AlignmentPanel[] getAllAlignmentPanels()
375 origview.add(alignPanel);
376 // make an array of all alignment panels except for this one
377 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
378 Arrays.asList(Desktop.getAlignmentPanels(null)));
379 aps.remove(AlignFrame.this.alignPanel);
380 return aps.toArray(new AlignmentPanel[aps.size()]);
382 }, selviews, new ItemListener()
386 public void itemStateChanged(ItemEvent e)
388 if (origview.size() > 0)
390 final AlignmentPanel ap = origview.get(0);
393 * Copy the ViewStyle of the selected panel to 'this one'.
394 * Don't change value of 'scaleProteinAsCdna' unless copying
397 ViewStyleI vs = selviews.get(0).getAlignViewport()
399 boolean fromSplitFrame = selviews.get(0)
400 .getAlignViewport().getCodingComplement() != null;
403 vs.setScaleProteinAsCdna(ap.getAlignViewport()
404 .getViewStyle().isScaleProteinAsCdna());
406 ap.getAlignViewport().setViewStyle(vs);
409 * Also rescale ViewStyle of SplitFrame complement if there is
410 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
411 * the whole ViewStyle (allow cDNA protein to have different
414 AlignViewportI complement = ap.getAlignViewport()
415 .getCodingComplement();
416 if (complement != null && vs.isScaleProteinAsCdna())
418 AlignFrame af = Desktop.getAlignFrameFor(complement);
419 ((SplitFrame) af.getSplitViewContainer())
421 af.setMenusForViewport();
425 ap.setSelected(true);
426 ap.alignFrame.setMenusForViewport();
431 formatMenu.add(vsel);
436 * Change the filename and format for the alignment, and enable the 'reload'
437 * button functionality.
444 public void setFileName(String file, String format)
447 setFileFormat(format);
448 reload.setEnabled(true);
452 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
455 void addKeyListener()
457 addKeyListener(new KeyAdapter()
460 public void keyPressed(KeyEvent evt)
462 if (viewport.cursorMode
463 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
464 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
465 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
466 && Character.isDigit(evt.getKeyChar()))
468 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
471 switch (evt.getKeyCode())
474 case 27: // escape key
475 deselectAllSequenceMenuItem_actionPerformed(null);
479 case KeyEvent.VK_DOWN:
480 if (evt.isAltDown() || !viewport.cursorMode)
482 moveSelectedSequences(false);
484 if (viewport.cursorMode)
486 alignPanel.getSeqPanel().moveCursor(0, 1);
491 if (evt.isAltDown() || !viewport.cursorMode)
493 moveSelectedSequences(true);
495 if (viewport.cursorMode)
497 alignPanel.getSeqPanel().moveCursor(0, -1);
502 case KeyEvent.VK_LEFT:
503 if (evt.isAltDown() || !viewport.cursorMode)
505 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
509 alignPanel.getSeqPanel().moveCursor(-1, 0);
514 case KeyEvent.VK_RIGHT:
515 if (evt.isAltDown() || !viewport.cursorMode)
517 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
521 alignPanel.getSeqPanel().moveCursor(1, 0);
525 case KeyEvent.VK_SPACE:
526 if (viewport.cursorMode)
528 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
529 || evt.isShiftDown() || evt.isAltDown());
533 // case KeyEvent.VK_A:
534 // if (viewport.cursorMode)
536 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
537 // //System.out.println("A");
541 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
542 * System.out.println("closing bracket"); } break;
544 case KeyEvent.VK_DELETE:
545 case KeyEvent.VK_BACK_SPACE:
546 if (!viewport.cursorMode)
548 cut_actionPerformed(null);
552 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
553 || evt.isShiftDown() || evt.isAltDown());
559 if (viewport.cursorMode)
561 alignPanel.getSeqPanel().setCursorRow();
565 if (viewport.cursorMode && !evt.isControlDown())
567 alignPanel.getSeqPanel().setCursorColumn();
571 if (viewport.cursorMode)
573 alignPanel.getSeqPanel().setCursorPosition();
577 case KeyEvent.VK_ENTER:
578 case KeyEvent.VK_COMMA:
579 if (viewport.cursorMode)
581 alignPanel.getSeqPanel().setCursorRowAndColumn();
586 if (viewport.cursorMode)
588 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
592 if (viewport.cursorMode)
594 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
599 viewport.cursorMode = !viewport.cursorMode;
600 statusBar.setText(MessageManager.formatMessage(
601 "label.keyboard_editing_mode", new String[]
602 { (viewport.cursorMode ? "on" : "off") }));
603 if (viewport.cursorMode)
605 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
606 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
608 alignPanel.getSeqPanel().seqCanvas.repaint();
614 Help.showHelpWindow();
615 } catch (Exception ex)
617 ex.printStackTrace();
622 boolean toggleSeqs = !evt.isControlDown();
623 boolean toggleCols = !evt.isShiftDown();
624 toggleHiddenRegions(toggleSeqs, toggleCols);
627 case KeyEvent.VK_PAGE_UP:
628 if (viewport.getWrapAlignment())
630 alignPanel.scrollUp(true);
634 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
635 - viewport.endSeq + viewport.startSeq);
638 case KeyEvent.VK_PAGE_DOWN:
639 if (viewport.getWrapAlignment())
641 alignPanel.scrollUp(false);
645 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
646 + viewport.endSeq - viewport.startSeq);
653 public void keyReleased(KeyEvent evt)
655 switch (evt.getKeyCode())
657 case KeyEvent.VK_LEFT:
658 if (evt.isAltDown() || !viewport.cursorMode)
660 viewport.firePropertyChange("alignment", null, viewport
661 .getAlignment().getSequences());
665 case KeyEvent.VK_RIGHT:
666 if (evt.isAltDown() || !viewport.cursorMode)
668 viewport.firePropertyChange("alignment", null, viewport
669 .getAlignment().getSequences());
677 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
679 ap.alignFrame = this;
680 avc = new jalview.controller.AlignViewController(this, viewport,
685 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
687 int aSize = alignPanels.size();
689 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
691 if (aSize == 1 && ap.av.viewName == null)
693 this.getContentPane().add(ap, BorderLayout.CENTER);
699 setInitialTabVisible();
702 expandViews.setEnabled(true);
703 gatherViews.setEnabled(true);
704 tabbedPane.addTab(ap.av.viewName, ap);
706 ap.setVisible(false);
711 if (ap.av.isPadGaps())
713 ap.av.getAlignment().padGaps();
715 ap.av.updateConservation(ap);
716 ap.av.updateConsensus(ap);
717 ap.av.updateStrucConsensus(ap);
721 public void setInitialTabVisible()
723 expandViews.setEnabled(true);
724 gatherViews.setEnabled(true);
725 tabbedPane.setVisible(true);
726 AlignmentPanel first = alignPanels.get(0);
727 tabbedPane.addTab(first.av.viewName, first);
728 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
731 public AlignViewport getViewport()
736 /* Set up intrinsic listeners for dynamically generated GUI bits. */
737 private void addServiceListeners()
739 final java.beans.PropertyChangeListener thisListener;
740 Desktop.instance.addJalviewPropertyChangeListener("services",
741 thisListener = new java.beans.PropertyChangeListener()
744 public void propertyChange(PropertyChangeEvent evt)
746 // // System.out.println("Discoverer property change.");
747 // if (evt.getPropertyName().equals("services"))
749 SwingUtilities.invokeLater(new Runnable()
756 .println("Rebuild WS Menu for service change");
757 BuildWebServiceMenu();
764 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
767 public void internalFrameClosed(
768 javax.swing.event.InternalFrameEvent evt)
770 System.out.println("deregistering discoverer listener");
771 Desktop.instance.removeJalviewPropertyChangeListener("services",
773 closeMenuItem_actionPerformed(true);
776 // Finally, build the menu once to get current service state
777 new Thread(new Runnable()
782 BuildWebServiceMenu();
788 * Configure menu items that vary according to whether the alignment is
789 * nucleotide or protein
793 public void setGUINucleotide(boolean nucleotide)
795 showTranslation.setVisible(nucleotide);
796 conservationMenuItem.setEnabled(!nucleotide);
797 modifyConservation.setEnabled(!nucleotide);
798 showGroupConservation.setEnabled(!nucleotide);
799 rnahelicesColour.setEnabled(nucleotide);
800 purinePyrimidineColour.setEnabled(nucleotide);
801 showComplementMenuItem.setText(MessageManager
802 .getString(nucleotide ? "label.protein" : "label.nucleotide"));
803 setColourSelected(jalview.bin.Cache.getDefault(
804 nucleotide ? Preferences.DEFAULT_COLOUR_NUC
805 : Preferences.DEFAULT_COLOUR_PROT, "None"));
809 * set up menus for the current viewport. This may be called after any
810 * operation that affects the data in the current view (selection changed,
811 * etc) to update the menus to reflect the new state.
813 public void setMenusForViewport()
815 setMenusFromViewport(viewport);
819 * Need to call this method when tabs are selected for multiple views, or when
820 * loading from Jalview2XML.java
825 void setMenusFromViewport(AlignViewport av)
827 padGapsMenuitem.setSelected(av.isPadGaps());
828 colourTextMenuItem.setSelected(av.isShowColourText());
829 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
830 conservationMenuItem.setSelected(av.getConservationSelected());
831 seqLimits.setSelected(av.getShowJVSuffix());
832 idRightAlign.setSelected(av.isRightAlignIds());
833 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
834 renderGapsMenuItem.setSelected(av.isRenderGaps());
835 wrapMenuItem.setSelected(av.getWrapAlignment());
836 scaleAbove.setVisible(av.getWrapAlignment());
837 scaleLeft.setVisible(av.getWrapAlignment());
838 scaleRight.setVisible(av.getWrapAlignment());
839 annotationPanelMenuItem.setState(av.isShowAnnotation());
841 * Show/hide annotations only enabled if annotation panel is shown
843 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
844 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
845 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
846 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
847 viewBoxesMenuItem.setSelected(av.getShowBoxes());
848 viewTextMenuItem.setSelected(av.getShowText());
849 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
850 showGroupConsensus.setSelected(av.isShowGroupConsensus());
851 showGroupConservation.setSelected(av.isShowGroupConservation());
852 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
853 showSequenceLogo.setSelected(av.isShowSequenceLogo());
854 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
856 setColourSelected(ColourSchemeProperty.getColourName(av
857 .getGlobalColourScheme()));
859 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
860 hiddenMarkers.setState(av.getShowHiddenMarkers());
861 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
862 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
863 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
864 autoCalculate.setSelected(av.autoCalculateConsensus);
865 sortByTree.setSelected(av.sortByTree);
866 listenToViewSelections.setSelected(av.followSelection);
867 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
869 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
870 setShowProductsEnabled();
874 private IProgressIndicator progressBar;
879 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
882 public void setProgressBar(String message, long id)
884 progressBar.setProgressBar(message, id);
888 public void registerHandler(final long id,
889 final IProgressIndicatorHandler handler)
891 progressBar.registerHandler(id, handler);
896 * @return true if any progress bars are still active
899 public boolean operationInProgress()
901 return progressBar.operationInProgress();
905 public void setStatus(String text)
907 statusBar.setText(text);
911 * Added so Castor Mapping file can obtain Jalview Version
913 public String getVersion()
915 return jalview.bin.Cache.getProperty("VERSION");
918 public FeatureRenderer getFeatureRenderer()
920 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
924 public void fetchSequence_actionPerformed(ActionEvent e)
926 new SequenceFetcher(this);
930 public void addFromFile_actionPerformed(ActionEvent e)
932 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
936 public void reload_actionPerformed(ActionEvent e)
938 if (fileName != null)
940 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
941 // originating file's format
942 // TODO: work out how to recover feature settings for correct view(s) when
944 if (currentFileFormat.equals("Jalview"))
946 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
947 for (int i = 0; i < frames.length; i++)
949 if (frames[i] instanceof AlignFrame && frames[i] != this
950 && ((AlignFrame) frames[i]).fileName != null
951 && ((AlignFrame) frames[i]).fileName.equals(fileName))
955 frames[i].setSelected(true);
956 Desktop.instance.closeAssociatedWindows();
957 } catch (java.beans.PropertyVetoException ex)
963 Desktop.instance.closeAssociatedWindows();
965 FileLoader loader = new FileLoader();
966 String protocol = fileName.startsWith("http:") ? "URL" : "File";
967 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
971 Rectangle bounds = this.getBounds();
973 FileLoader loader = new FileLoader();
974 String protocol = fileName.startsWith("http:") ? "URL" : "File";
975 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
976 protocol, currentFileFormat);
978 newframe.setBounds(bounds);
979 if (featureSettings != null && featureSettings.isShowing())
981 final Rectangle fspos = featureSettings.frame.getBounds();
982 // TODO: need a 'show feature settings' function that takes bounds -
983 // need to refactor Desktop.addFrame
984 newframe.featureSettings_actionPerformed(null);
985 final FeatureSettings nfs = newframe.featureSettings;
986 SwingUtilities.invokeLater(new Runnable()
991 nfs.frame.setBounds(fspos);
994 this.featureSettings.close();
995 this.featureSettings = null;
997 this.closeMenuItem_actionPerformed(true);
1003 public void addFromText_actionPerformed(ActionEvent e)
1005 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
1009 public void addFromURL_actionPerformed(ActionEvent e)
1011 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1015 public void save_actionPerformed(ActionEvent e)
1017 if (fileName == null
1018 || (currentFileFormat == null || !jalview.io.FormatAdapter
1019 .isValidIOFormat(currentFileFormat, true))
1020 || fileName.startsWith("http"))
1022 saveAs_actionPerformed(null);
1026 saveAlignment(fileName, currentFileFormat);
1037 public void saveAs_actionPerformed(ActionEvent e)
1039 JalviewFileChooser chooser = new JalviewFileChooser(
1040 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1041 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1042 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1043 currentFileFormat, false);
1045 chooser.setFileView(new JalviewFileView());
1046 chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1047 chooser.setToolTipText(MessageManager.getString("action.save"));
1049 int value = chooser.showSaveDialog(this);
1051 if (value == JalviewFileChooser.APPROVE_OPTION)
1053 currentFileFormat = chooser.getSelectedFormat();
1054 while (currentFileFormat == null)
1057 .showInternalMessageDialog(
1060 .getString("label.select_file_format_before_saving"),
1062 .getString("label.file_format_not_specified"),
1063 JOptionPane.WARNING_MESSAGE);
1064 currentFileFormat = chooser.getSelectedFormat();
1065 value = chooser.showSaveDialog(this);
1066 if (value != JalviewFileChooser.APPROVE_OPTION)
1072 fileName = chooser.getSelectedFile().getPath();
1074 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1077 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1078 if (currentFileFormat.indexOf(" ") > -1)
1080 currentFileFormat = currentFileFormat.substring(0,
1081 currentFileFormat.indexOf(" "));
1083 saveAlignment(fileName, currentFileFormat);
1087 public boolean saveAlignment(String file, String format)
1089 boolean success = true;
1091 if (format.equalsIgnoreCase("Jalview"))
1093 String shortName = title;
1095 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1097 shortName = shortName.substring(shortName
1098 .lastIndexOf(java.io.File.separatorChar) + 1);
1102 * First save any linked Chimera session.
1104 Desktop.instance.saveChimeraSessions(file);
1106 success = new Jalview2XML().saveAlignment(this, file, shortName);
1108 statusBar.setText(MessageManager.formatMessage(
1109 "label.successfully_saved_to_file_in_format", new Object[]
1110 { fileName, format }));
1115 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1117 warningMessage("Cannot save file " + fileName + " using format "
1118 + format, "Alignment output format not supported");
1119 saveAs_actionPerformed(null);
1120 // JBPNote need to have a raise_gui flag here
1124 ExportData exportData = getAlignmentForExport();
1125 FormatAdapter f = new FormatAdapter(viewport);
1126 String output = f.formatSequences(format,
1127 exportData.getAlignment(), // class cast exceptions will
1128 // occur in the distant future
1129 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1130 f.getCacheSuffixDefault(format),
1131 viewport.getColumnSelection());
1141 java.io.PrintWriter out = new java.io.PrintWriter(
1142 new java.io.FileWriter(file));
1146 this.setTitle(file);
1147 statusBar.setText(MessageManager.formatMessage(
1148 "label.successfully_saved_to_file_in_format",
1150 { fileName, format }));
1151 } catch (Exception ex)
1154 ex.printStackTrace();
1161 JOptionPane.showInternalMessageDialog(this, MessageManager
1162 .formatMessage("label.couldnt_save_file", new Object[]
1163 { fileName }), MessageManager
1164 .getString("label.error_saving_file"),
1165 JOptionPane.WARNING_MESSAGE);
1172 private void warningMessage(String warning, String title)
1174 if (new jalview.util.Platform().isHeadless())
1176 System.err.println("Warning: " + title + "\nWarning: " + warning);
1181 JOptionPane.showInternalMessageDialog(this, warning, title,
1182 JOptionPane.WARNING_MESSAGE);
1194 protected void outputText_actionPerformed(ActionEvent e)
1197 ExportData exportData = getAlignmentForExport();
1198 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1199 cap.setForInput(null);
1203 cap.setText(new FormatAdapter(viewport).formatSequences(
1204 e.getActionCommand(),
1205 exportData.getAlignment(),
1206 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1207 viewport.getColumnSelection()));
1208 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1209 "label.alignment_output_command", new Object[]
1210 { e.getActionCommand() }), 600, 500);
1211 } catch (OutOfMemoryError oom)
1213 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1219 public ExportData getAlignmentForExport()
1221 AlignmentI alignmentToExport = null;
1222 String[] omitHidden = null;
1223 int[] alignmentStartEnd = new int[2];
1224 FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
1225 viewport.setFeatureRenderer(fr);
1226 HiddenSequences hiddenSeqs = viewport.getAlignment()
1227 .getHiddenSequences();
1230 alignmentToExport = viewport.getAlignment();
1231 alignmentStartEnd = new int[]
1232 { 0, alignmentToExport.getWidth() - 1 };
1234 if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0)
1236 int reply = JOptionPane
1237 .showInternalConfirmDialog(
1240 .getString("label.alignment_contains_hidden_columns"),
1242 .getString("action.save_omit_hidden_columns"),
1243 JOptionPane.YES_NO_OPTION,
1244 JOptionPane.QUESTION_MESSAGE);
1246 if (reply == JOptionPane.YES_OPTION)
1248 // export only visible region
1249 omitHidden = viewport.getViewAsString(false);
1250 alignmentToExport = viewport.getAlignment();
1251 alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
1252 .getColumnSelection().getHiddenColumns());
1253 viewport.setIncludeHiddenRegion(false);
1257 // export all region including visible
1258 alignmentToExport = hiddenSeqs.getFullAlignment();
1259 viewport.setIncludeHiddenRegion(true);
1263 return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd);
1266 private static int[] getStartEnd(int[] aligmentStartEnd,
1267 List<int[]> hiddenCols)
1269 int startPos = aligmentStartEnd[0];
1270 int endPos = aligmentStartEnd[1];
1272 int[] lowestRange = new int[2];
1273 int[] higestRange = new int[2];
1275 for (int[] hiddenCol : hiddenCols)
1277 // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
1279 lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1280 higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1282 // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
1283 // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
1285 if (lowestRange[0] == 0 && lowestRange[1] == 0)
1287 startPos = aligmentStartEnd[0];
1291 startPos = lowestRange[1] + 1;
1294 if (higestRange[0] == 0 && higestRange[1] == 0)
1296 endPos = aligmentStartEnd[1];
1300 endPos = higestRange[0];
1303 // System.out.println("Export range : " + minPos + " - " + maxPos);
1305 { startPos, endPos };
1308 public static void main(String[] args)
1310 ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
1311 hiddenCols.add(new int[]
1313 hiddenCols.add(new int[]
1315 hiddenCols.add(new int[]
1317 hiddenCols.add(new int[]
1319 hiddenCols.add(new int[]
1322 int[] x = getStartEnd(new int[]
1323 { 0, 50 }, hiddenCols);
1324 // System.out.println("Export range : " + x[0] + " - " + x[1]);
1334 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1336 // new HTMLOutput(alignPanel,
1337 // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
1338 // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
1339 new HtmlSvgOutput(null, alignPanel);
1343 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1345 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel,
1346 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
1347 bjs.exportJalviewAlignmentAsBioJsHtmlFile();
1349 public void createImageMap(File file, String image)
1351 alignPanel.makePNGImageMap(file, image);
1361 public void createPNG(File f)
1363 alignPanel.makePNG(f);
1373 public void createEPS(File f)
1375 alignPanel.makeEPS(f);
1378 public void createSVG(File f)
1380 alignPanel.makeSVG(f);
1383 public void pageSetup_actionPerformed(ActionEvent e)
1385 PrinterJob printJob = PrinterJob.getPrinterJob();
1386 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1396 public void printMenuItem_actionPerformed(ActionEvent e)
1398 // Putting in a thread avoids Swing painting problems
1399 PrintThread thread = new PrintThread(alignPanel);
1404 public void exportFeatures_actionPerformed(ActionEvent e)
1406 new AnnotationExporter().exportFeatures(alignPanel);
1410 public void exportAnnotations_actionPerformed(ActionEvent e)
1412 new AnnotationExporter().exportAnnotations(alignPanel);
1416 public void associatedData_actionPerformed(ActionEvent e)
1418 // Pick the tree file
1419 JalviewFileChooser chooser = new JalviewFileChooser(
1420 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1421 chooser.setFileView(new JalviewFileView());
1422 chooser.setDialogTitle(MessageManager
1423 .getString("label.load_jalview_annotations"));
1424 chooser.setToolTipText(MessageManager
1425 .getString("label.load_jalview_annotations"));
1427 int value = chooser.showOpenDialog(null);
1429 if (value == JalviewFileChooser.APPROVE_OPTION)
1431 String choice = chooser.getSelectedFile().getPath();
1432 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1433 loadJalviewDataFile(choice, null, null, null);
1439 * Close the current view or all views in the alignment frame. If the frame
1440 * only contains one view then the alignment will be removed from memory.
1442 * @param closeAllTabs
1445 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1447 if (alignPanels != null && alignPanels.size() < 2)
1449 closeAllTabs = true;
1454 if (alignPanels != null)
1458 if (this.isClosed())
1460 // really close all the windows - otherwise wait till
1461 // setClosed(true) is called
1462 for (int i = 0; i < alignPanels.size(); i++)
1464 AlignmentPanel ap = alignPanels.get(i);
1471 closeView(alignPanel);
1477 this.setClosed(true);
1479 } catch (Exception ex)
1481 ex.printStackTrace();
1486 * Close the specified panel and close up tabs appropriately.
1488 * @param panelToClose
1490 public void closeView(AlignmentPanel panelToClose)
1492 int index = tabbedPane.getSelectedIndex();
1493 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1494 alignPanels.remove(panelToClose);
1495 panelToClose.closePanel();
1496 panelToClose = null;
1498 tabbedPane.removeTabAt(closedindex);
1499 tabbedPane.validate();
1501 if (index > closedindex || index == tabbedPane.getTabCount())
1503 // modify currently selected tab index if necessary.
1507 this.tabSelectionChanged(index);
1513 void updateEditMenuBar()
1516 if (viewport.getHistoryList().size() > 0)
1518 undoMenuItem.setEnabled(true);
1519 CommandI command = viewport.getHistoryList().peek();
1520 undoMenuItem.setText(MessageManager.formatMessage(
1521 "label.undo_command", new Object[]
1522 { command.getDescription() }));
1526 undoMenuItem.setEnabled(false);
1527 undoMenuItem.setText(MessageManager.getString("action.undo"));
1530 if (viewport.getRedoList().size() > 0)
1532 redoMenuItem.setEnabled(true);
1534 CommandI command = viewport.getRedoList().peek();
1535 redoMenuItem.setText(MessageManager.formatMessage(
1536 "label.redo_command", new Object[]
1537 { command.getDescription() }));
1541 redoMenuItem.setEnabled(false);
1542 redoMenuItem.setText(MessageManager.getString("action.redo"));
1546 public void addHistoryItem(CommandI command)
1548 if (command.getSize() > 0)
1550 viewport.addToHistoryList(command);
1551 viewport.clearRedoList();
1552 updateEditMenuBar();
1553 viewport.updateHiddenColumns();
1554 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1555 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1556 // viewport.getColumnSelection()
1557 // .getHiddenColumns().size() > 0);
1563 * @return alignment objects for all views
1565 AlignmentI[] getViewAlignments()
1567 if (alignPanels != null)
1569 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1571 for (AlignmentPanel ap : alignPanels)
1573 als[i++] = ap.av.getAlignment();
1577 if (viewport != null)
1579 return new AlignmentI[]
1580 { viewport.getAlignment() };
1592 protected void undoMenuItem_actionPerformed(ActionEvent e)
1594 if (viewport.getHistoryList().isEmpty())
1598 CommandI command = viewport.getHistoryList().pop();
1599 viewport.addToRedoList(command);
1600 command.undoCommand(getViewAlignments());
1602 AlignmentViewport originalSource = getOriginatingSource(command);
1603 updateEditMenuBar();
1605 if (originalSource != null)
1607 if (originalSource != viewport)
1610 .warn("Implementation worry: mismatch of viewport origin for undo");
1612 originalSource.updateHiddenColumns();
1613 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1615 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1616 // viewport.getColumnSelection()
1617 // .getHiddenColumns().size() > 0);
1618 originalSource.firePropertyChange("alignment", null, originalSource
1619 .getAlignment().getSequences());
1630 protected void redoMenuItem_actionPerformed(ActionEvent e)
1632 if (viewport.getRedoList().size() < 1)
1637 CommandI command = viewport.getRedoList().pop();
1638 viewport.addToHistoryList(command);
1639 command.doCommand(getViewAlignments());
1641 AlignmentViewport originalSource = getOriginatingSource(command);
1642 updateEditMenuBar();
1644 if (originalSource != null)
1647 if (originalSource != viewport)
1650 .warn("Implementation worry: mismatch of viewport origin for redo");
1652 originalSource.updateHiddenColumns();
1653 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1655 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1656 // viewport.getColumnSelection()
1657 // .getHiddenColumns().size() > 0);
1658 originalSource.firePropertyChange("alignment", null, originalSource
1659 .getAlignment().getSequences());
1663 AlignmentViewport getOriginatingSource(CommandI command)
1665 AlignmentViewport originalSource = null;
1666 // For sequence removal and addition, we need to fire
1667 // the property change event FROM the viewport where the
1668 // original alignment was altered
1669 AlignmentI al = null;
1670 if (command instanceof EditCommand)
1672 EditCommand editCommand = (EditCommand) command;
1673 al = editCommand.getAlignment();
1674 List<Component> comps = PaintRefresher.components.get(viewport
1675 .getSequenceSetId());
1677 for (Component comp : comps)
1679 if (comp instanceof AlignmentPanel)
1681 if (al == ((AlignmentPanel) comp).av.getAlignment())
1683 originalSource = ((AlignmentPanel) comp).av;
1690 if (originalSource == null)
1692 // The original view is closed, we must validate
1693 // the current view against the closed view first
1696 PaintRefresher.validateSequences(al, viewport.getAlignment());
1699 originalSource = viewport;
1702 return originalSource;
1711 public void moveSelectedSequences(boolean up)
1713 SequenceGroup sg = viewport.getSelectionGroup();
1719 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1720 viewport.getHiddenRepSequences(), up);
1721 alignPanel.paintAlignment(true);
1724 synchronized void slideSequences(boolean right, int size)
1726 List<SequenceI> sg = new ArrayList<SequenceI>();
1727 if (viewport.cursorMode)
1729 sg.add(viewport.getAlignment().getSequenceAt(
1730 alignPanel.getSeqPanel().seqCanvas.cursorY));
1732 else if (viewport.getSelectionGroup() != null
1733 && viewport.getSelectionGroup().getSize() != viewport
1734 .getAlignment().getHeight())
1736 sg = viewport.getSelectionGroup().getSequences(
1737 viewport.getHiddenRepSequences());
1745 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1747 for (SequenceI seq : viewport.getAlignment().getSequences())
1749 if (!sg.contains(seq))
1751 invertGroup.add(seq);
1755 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1757 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1758 for (int i = 0; i < invertGroup.size(); i++)
1760 seqs2[i] = invertGroup.get(i);
1763 SlideSequencesCommand ssc;
1766 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1767 size, viewport.getGapCharacter());
1771 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1772 size, viewport.getGapCharacter());
1775 int groupAdjustment = 0;
1776 if (ssc.getGapsInsertedBegin() && right)
1778 if (viewport.cursorMode)
1780 alignPanel.getSeqPanel().moveCursor(size, 0);
1784 groupAdjustment = size;
1787 else if (!ssc.getGapsInsertedBegin() && !right)
1789 if (viewport.cursorMode)
1791 alignPanel.getSeqPanel().moveCursor(-size, 0);
1795 groupAdjustment = -size;
1799 if (groupAdjustment != 0)
1801 viewport.getSelectionGroup().setStartRes(
1802 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1803 viewport.getSelectionGroup().setEndRes(
1804 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1807 boolean appendHistoryItem = false;
1808 Deque<CommandI> historyList = viewport.getHistoryList();
1809 if (historyList != null
1810 && historyList.size() > 0
1811 && historyList.peek() instanceof SlideSequencesCommand)
1813 appendHistoryItem = ssc
1814 .appendSlideCommand((SlideSequencesCommand) historyList
1818 if (!appendHistoryItem)
1820 addHistoryItem(ssc);
1833 protected void copy_actionPerformed(ActionEvent e)
1836 if (viewport.getSelectionGroup() == null)
1840 // TODO: preserve the ordering of displayed alignment annotation in any
1841 // internal paste (particularly sequence associated annotation)
1842 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1843 String[] omitHidden = null;
1845 if (viewport.hasHiddenColumns())
1847 omitHidden = viewport.getViewAsString(true);
1850 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1853 StringSelection ss = new StringSelection(output);
1857 jalview.gui.Desktop.internalCopy = true;
1858 // Its really worth setting the clipboard contents
1859 // to empty before setting the large StringSelection!!
1860 Toolkit.getDefaultToolkit().getSystemClipboard()
1861 .setContents(new StringSelection(""), null);
1863 Toolkit.getDefaultToolkit().getSystemClipboard()
1864 .setContents(ss, Desktop.instance);
1865 } catch (OutOfMemoryError er)
1867 new OOMWarning("copying region", er);
1871 ArrayList<int[]> hiddenColumns = null;
1872 if (viewport.hasHiddenColumns())
1874 hiddenColumns = new ArrayList<int[]>();
1875 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1876 .getSelectionGroup().getEndRes();
1877 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1879 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1881 hiddenColumns.add(new int[]
1882 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1887 Desktop.jalviewClipboard = new Object[]
1888 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1889 statusBar.setText(MessageManager.formatMessage(
1890 "label.copied_sequences_to_clipboard", new Object[]
1891 { Integer.valueOf(seqs.length).toString() }));
1901 protected void pasteNew_actionPerformed(ActionEvent e)
1913 protected void pasteThis_actionPerformed(ActionEvent e)
1919 * Paste contents of Jalview clipboard
1921 * @param newAlignment
1922 * true to paste to a new alignment, otherwise add to this.
1924 void paste(boolean newAlignment)
1926 boolean externalPaste = true;
1929 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1930 Transferable contents = c.getContents(this);
1932 if (contents == null)
1940 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1941 if (str.length() < 1)
1946 format = new IdentifyFile().Identify(str, "Paste");
1948 } catch (OutOfMemoryError er)
1950 new OOMWarning("Out of memory pasting sequences!!", er);
1954 SequenceI[] sequences;
1955 boolean annotationAdded = false;
1956 AlignmentI alignment = null;
1958 if (Desktop.jalviewClipboard != null)
1960 // The clipboard was filled from within Jalview, we must use the
1962 // And dataset from the copied alignment
1963 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1964 // be doubly sure that we create *new* sequence objects.
1965 sequences = new SequenceI[newseq.length];
1966 for (int i = 0; i < newseq.length; i++)
1968 sequences[i] = new Sequence(newseq[i]);
1970 alignment = new Alignment(sequences);
1971 externalPaste = false;
1975 // parse the clipboard as an alignment.
1976 alignment = new FormatAdapter().readFile(str, "Paste", format);
1977 sequences = alignment.getSequencesArray();
1981 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1987 if (Desktop.jalviewClipboard != null)
1989 // dataset is inherited
1990 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1994 // new dataset is constructed
1995 alignment.setDataset(null);
1997 alwidth = alignment.getWidth() + 1;
2001 AlignmentI pastedal = alignment; // preserve pasted alignment object
2002 // Add pasted sequences and dataset into existing alignment.
2003 alignment = viewport.getAlignment();
2004 alwidth = alignment.getWidth() + 1;
2005 // decide if we need to import sequences from an existing dataset
2006 boolean importDs = Desktop.jalviewClipboard != null
2007 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2008 // importDs==true instructs us to copy over new dataset sequences from
2009 // an existing alignment
2010 Vector newDs = (importDs) ? new Vector() : null; // used to create
2011 // minimum dataset set
2013 for (int i = 0; i < sequences.length; i++)
2017 newDs.addElement(null);
2019 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2021 if (importDs && ds != null)
2023 if (!newDs.contains(ds))
2025 newDs.setElementAt(ds, i);
2026 ds = new Sequence(ds);
2027 // update with new dataset sequence
2028 sequences[i].setDatasetSequence(ds);
2032 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2037 // copy and derive new dataset sequence
2038 sequences[i] = sequences[i].deriveSequence();
2039 alignment.getDataset().addSequence(
2040 sequences[i].getDatasetSequence());
2041 // TODO: avoid creation of duplicate dataset sequences with a
2042 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2044 alignment.addSequence(sequences[i]); // merges dataset
2048 newDs.clear(); // tidy up
2050 if (alignment.getAlignmentAnnotation() != null)
2052 for (AlignmentAnnotation alan : alignment
2053 .getAlignmentAnnotation())
2055 if (alan.graphGroup > fgroup)
2057 fgroup = alan.graphGroup;
2061 if (pastedal.getAlignmentAnnotation() != null)
2063 // Add any annotation attached to alignment.
2064 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2065 for (int i = 0; i < alann.length; i++)
2067 annotationAdded = true;
2068 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2070 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2071 if (newann.graphGroup > -1)
2073 if (newGraphGroups.size() <= newann.graphGroup
2074 || newGraphGroups.get(newann.graphGroup) == null)
2076 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2078 newGraphGroups.add(q, null);
2080 newGraphGroups.set(newann.graphGroup, new Integer(
2083 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2087 newann.padAnnotation(alwidth);
2088 alignment.addAnnotation(newann);
2098 addHistoryItem(new EditCommand(
2099 MessageManager.getString("label.add_sequences"),
2101 sequences, 0, alignment.getWidth(), alignment));
2103 // Add any annotations attached to sequences
2104 for (int i = 0; i < sequences.length; i++)
2106 if (sequences[i].getAnnotation() != null)
2108 AlignmentAnnotation newann;
2109 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2111 annotationAdded = true;
2112 newann = sequences[i].getAnnotation()[a];
2113 newann.adjustForAlignment();
2114 newann.padAnnotation(alwidth);
2115 if (newann.graphGroup > -1)
2117 if (newann.graphGroup > -1)
2119 if (newGraphGroups.size() <= newann.graphGroup
2120 || newGraphGroups.get(newann.graphGroup) == null)
2122 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2124 newGraphGroups.add(q, null);
2126 newGraphGroups.set(newann.graphGroup, new Integer(
2129 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2133 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2138 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2145 // propagate alignment changed.
2146 viewport.setEndSeq(alignment.getHeight());
2147 if (annotationAdded)
2149 // Duplicate sequence annotation in all views.
2150 AlignmentI[] alview = this.getViewAlignments();
2151 for (int i = 0; i < sequences.length; i++)
2153 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2158 for (int avnum = 0; avnum < alview.length; avnum++)
2160 if (alview[avnum] != alignment)
2162 // duplicate in a view other than the one with input focus
2163 int avwidth = alview[avnum].getWidth() + 1;
2164 // this relies on sann being preserved after we
2165 // modify the sequence's annotation array for each duplication
2166 for (int a = 0; a < sann.length; a++)
2168 AlignmentAnnotation newann = new AlignmentAnnotation(
2170 sequences[i].addAlignmentAnnotation(newann);
2171 newann.padAnnotation(avwidth);
2172 alview[avnum].addAnnotation(newann); // annotation was
2173 // duplicated earlier
2174 // TODO JAL-1145 graphGroups are not updated for sequence
2175 // annotation added to several views. This may cause
2177 alview[avnum].setAnnotationIndex(newann, a);
2182 buildSortByAnnotationScoresMenu();
2184 viewport.firePropertyChange("alignment", null,
2185 alignment.getSequences());
2186 if (alignPanels != null)
2188 for (AlignmentPanel ap : alignPanels)
2190 ap.validateAnnotationDimensions(false);
2195 alignPanel.validateAnnotationDimensions(false);
2201 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2203 String newtitle = new String("Copied sequences");
2205 if (Desktop.jalviewClipboard != null
2206 && Desktop.jalviewClipboard[2] != null)
2208 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2209 for (int[] region : hc)
2211 af.viewport.hideColumns(region[0], region[1]);
2215 // >>>This is a fix for the moment, until a better solution is
2217 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2219 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2221 // TODO: maintain provenance of an alignment, rather than just make the
2222 // title a concatenation of operations.
2225 if (title.startsWith("Copied sequences"))
2231 newtitle = newtitle.concat("- from " + title);
2236 newtitle = new String("Pasted sequences");
2239 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2244 } catch (Exception ex)
2246 ex.printStackTrace();
2247 System.out.println("Exception whilst pasting: " + ex);
2248 // could be anything being pasted in here
2254 protected void expand_newalign(ActionEvent e)
2258 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2259 .getAlignment(), -1);
2260 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2262 String newtitle = new String("Flanking alignment");
2264 if (Desktop.jalviewClipboard != null
2265 && Desktop.jalviewClipboard[2] != null)
2267 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2268 for (int region[] : hc)
2270 af.viewport.hideColumns(region[0], region[1]);
2274 // >>>This is a fix for the moment, until a better solution is
2276 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2278 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2280 // TODO: maintain provenance of an alignment, rather than just make the
2281 // title a concatenation of operations.
2283 if (title.startsWith("Copied sequences"))
2289 newtitle = newtitle.concat("- from " + title);
2293 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2295 } catch (Exception ex)
2297 ex.printStackTrace();
2298 System.out.println("Exception whilst pasting: " + ex);
2299 // could be anything being pasted in here
2300 } catch (OutOfMemoryError oom)
2302 new OOMWarning("Viewing flanking region of alignment", oom);
2313 protected void cut_actionPerformed(ActionEvent e)
2315 copy_actionPerformed(null);
2316 delete_actionPerformed(null);
2326 protected void delete_actionPerformed(ActionEvent evt)
2329 SequenceGroup sg = viewport.getSelectionGroup();
2336 * If the cut affects all sequences, warn, remove highlighted columns
2338 if (sg.getSize() == viewport.getAlignment().getHeight())
2340 int confirm = JOptionPane.showConfirmDialog(this,
2341 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2342 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2343 JOptionPane.OK_CANCEL_OPTION);
2345 if (confirm == JOptionPane.CANCEL_OPTION
2346 || confirm == JOptionPane.CLOSED_OPTION)
2350 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2351 sg.getEndRes() + 1);
2354 SequenceI[] cut = sg.getSequences()
2355 .toArray(new SequenceI[sg.getSize()]);
2357 addHistoryItem(new EditCommand(
2358 MessageManager.getString("label.cut_sequences"), Action.CUT,
2359 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2360 viewport.getAlignment()));
2362 viewport.setSelectionGroup(null);
2363 viewport.sendSelection();
2364 viewport.getAlignment().deleteGroup(sg);
2366 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2368 if (viewport.getAlignment().getHeight() < 1)
2372 this.setClosed(true);
2373 } catch (Exception ex)
2386 protected void deleteGroups_actionPerformed(ActionEvent e)
2388 if (avc.deleteGroups())
2390 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2391 alignPanel.updateAnnotation();
2392 alignPanel.paintAlignment(true);
2403 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2405 SequenceGroup sg = new SequenceGroup();
2407 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2409 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2412 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2413 viewport.setSelectionGroup(sg);
2414 viewport.sendSelection();
2415 alignPanel.paintAlignment(true);
2416 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2426 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2428 if (viewport.cursorMode)
2430 alignPanel.getSeqPanel().keyboardNo1 = null;
2431 alignPanel.getSeqPanel().keyboardNo2 = null;
2433 viewport.setSelectionGroup(null);
2434 viewport.getColumnSelection().clear();
2435 viewport.setSelectionGroup(null);
2436 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2437 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2438 alignPanel.paintAlignment(true);
2439 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2440 viewport.sendSelection();
2450 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2452 SequenceGroup sg = viewport.getSelectionGroup();
2456 selectAllSequenceMenuItem_actionPerformed(null);
2461 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2463 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2466 alignPanel.paintAlignment(true);
2467 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2468 viewport.sendSelection();
2472 public void invertColSel_actionPerformed(ActionEvent e)
2474 viewport.invertColumnSelection();
2475 alignPanel.paintAlignment(true);
2476 viewport.sendSelection();
2486 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2488 trimAlignment(true);
2498 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2500 trimAlignment(false);
2503 void trimAlignment(boolean trimLeft)
2505 ColumnSelection colSel = viewport.getColumnSelection();
2508 if (colSel.size() > 0)
2512 column = colSel.getMin();
2516 column = colSel.getMax();
2520 if (viewport.getSelectionGroup() != null)
2522 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2523 viewport.getHiddenRepSequences());
2527 seqs = viewport.getAlignment().getSequencesArray();
2530 TrimRegionCommand trimRegion;
2533 trimRegion = new TrimRegionCommand("Remove Left",
2534 TrimRegionCommand.TRIM_LEFT, seqs, column,
2535 viewport.getAlignment(), viewport.getColumnSelection(),
2536 viewport.getSelectionGroup());
2537 viewport.setStartRes(0);
2541 trimRegion = new TrimRegionCommand("Remove Right",
2542 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2543 viewport.getAlignment(), viewport.getColumnSelection(),
2544 viewport.getSelectionGroup());
2547 statusBar.setText(MessageManager.formatMessage(
2548 "label.removed_columns", new String[]
2549 { Integer.valueOf(trimRegion.getSize()).toString() }));
2551 addHistoryItem(trimRegion);
2553 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2555 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2556 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2558 viewport.getAlignment().deleteGroup(sg);
2562 viewport.firePropertyChange("alignment", null, viewport
2563 .getAlignment().getSequences());
2574 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2576 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2579 if (viewport.getSelectionGroup() != null)
2581 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2582 viewport.getHiddenRepSequences());
2583 start = viewport.getSelectionGroup().getStartRes();
2584 end = viewport.getSelectionGroup().getEndRes();
2588 seqs = viewport.getAlignment().getSequencesArray();
2591 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2592 "Remove Gapped Columns", seqs, start, end,
2593 viewport.getAlignment());
2595 addHistoryItem(removeGapCols);
2597 statusBar.setText(MessageManager.formatMessage(
2598 "label.removed_empty_columns", new Object[]
2599 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2601 // This is to maintain viewport position on first residue
2602 // of first sequence
2603 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2604 int startRes = seq.findPosition(viewport.startRes);
2605 // ShiftList shifts;
2606 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2607 // edit.alColumnChanges=shifts.getInverse();
2608 // if (viewport.hasHiddenColumns)
2609 // viewport.getColumnSelection().compensateForEdits(shifts);
2610 viewport.setStartRes(seq.findIndex(startRes) - 1);
2611 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2623 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2625 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2628 if (viewport.getSelectionGroup() != null)
2630 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2631 viewport.getHiddenRepSequences());
2632 start = viewport.getSelectionGroup().getStartRes();
2633 end = viewport.getSelectionGroup().getEndRes();
2637 seqs = viewport.getAlignment().getSequencesArray();
2640 // This is to maintain viewport position on first residue
2641 // of first sequence
2642 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2643 int startRes = seq.findPosition(viewport.startRes);
2645 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2646 viewport.getAlignment()));
2648 viewport.setStartRes(seq.findIndex(startRes) - 1);
2650 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2662 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2664 viewport.setPadGaps(padGapsMenuitem.isSelected());
2665 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2676 public void findMenuItem_actionPerformed(ActionEvent e)
2682 * Create a new view of the current alignment.
2685 public void newView_actionPerformed(ActionEvent e)
2687 newView(null, true);
2691 * Creates and shows a new view of the current alignment.
2694 * title of newly created view; if null, one will be generated
2695 * @param copyAnnotation
2696 * if true then duplicate all annnotation, groups and settings
2697 * @return new alignment panel, already displayed.
2699 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2702 * Create a new AlignmentPanel (with its own, new Viewport)
2704 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2706 if (!copyAnnotation)
2709 * remove all groups and annotation except for the automatic stuff
2711 newap.av.getAlignment().deleteAllGroups();
2712 newap.av.getAlignment().deleteAllAnnotations(false);
2715 newap.av.setGatherViewsHere(false);
2717 if (viewport.viewName == null)
2719 viewport.viewName = MessageManager
2720 .getString("label.view_name_original");
2724 * Views share the same edits, undo and redo stacks, mappings.
2726 newap.av.setHistoryList(viewport.getHistoryList());
2727 newap.av.setRedoList(viewport.getRedoList());
2728 newap.av.getAlignment().setCodonFrames(
2729 viewport.getAlignment().getCodonFrames());
2731 newap.av.viewName = getNewViewName(viewTitle);
2733 addAlignmentPanel(newap, true);
2734 newap.alignmentChanged();
2736 if (alignPanels.size() == 2)
2738 viewport.setGatherViewsHere(true);
2740 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2745 * Make a new name for the view, ensuring it is unique within the current
2746 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2747 * these now use viewId. Unique view names are still desirable for usability.)
2752 protected String getNewViewName(String viewTitle)
2754 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2755 boolean addFirstIndex = false;
2756 if (viewTitle == null || viewTitle.trim().length() == 0)
2758 viewTitle = MessageManager.getString("action.view");
2759 addFirstIndex = true;
2763 index = 1;// we count from 1 if given a specific name
2765 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2767 List<Component> comps = PaintRefresher.components.get(viewport
2768 .getSequenceSetId());
2770 List<String> existingNames = getExistingViewNames(comps);
2772 while (existingNames.contains(newViewName))
2774 newViewName = viewTitle + " " + (++index);
2780 * Returns a list of distinct view names found in the given list of
2781 * components. View names are held on the viewport of an AlignmentPanel.
2786 protected List<String> getExistingViewNames(List<Component> comps)
2788 List<String> existingNames = new ArrayList<String>();
2789 for (Component comp : comps)
2791 if (comp instanceof AlignmentPanel)
2793 AlignmentPanel ap = (AlignmentPanel) comp;
2794 if (!existingNames.contains(ap.av.viewName))
2796 existingNames.add(ap.av.viewName);
2800 return existingNames;
2804 * Explode tabbed views into separate windows.
2807 public void expandViews_actionPerformed(ActionEvent e)
2809 Desktop.instance.explodeViews(this);
2813 * Gather views in separate windows back into a tabbed presentation.
2816 public void gatherViews_actionPerformed(ActionEvent e)
2818 Desktop.instance.gatherViews(this);
2828 public void font_actionPerformed(ActionEvent e)
2830 new FontChooser(alignPanel);
2840 protected void seqLimit_actionPerformed(ActionEvent e)
2842 viewport.setShowJVSuffix(seqLimits.isSelected());
2844 alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
2845 .calculateIdWidth());
2846 alignPanel.paintAlignment(true);
2850 public void idRightAlign_actionPerformed(ActionEvent e)
2852 viewport.setRightAlignIds(idRightAlign.isSelected());
2853 alignPanel.paintAlignment(true);
2857 public void centreColumnLabels_actionPerformed(ActionEvent e)
2859 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2860 alignPanel.paintAlignment(true);
2866 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2869 protected void followHighlight_actionPerformed()
2872 * Set the 'follow' flag on the Viewport (and scroll to position if now
2875 final boolean state = this.followHighlightMenuItem.getState();
2876 viewport.setFollowHighlight(state);
2879 alignPanel.scrollToPosition(
2880 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2891 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2893 viewport.setColourText(colourTextMenuItem.isSelected());
2894 alignPanel.paintAlignment(true);
2904 public void wrapMenuItem_actionPerformed(ActionEvent e)
2906 scaleAbove.setVisible(wrapMenuItem.isSelected());
2907 scaleLeft.setVisible(wrapMenuItem.isSelected());
2908 scaleRight.setVisible(wrapMenuItem.isSelected());
2909 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2910 alignPanel.updateLayout();
2914 public void showAllSeqs_actionPerformed(ActionEvent e)
2916 viewport.showAllHiddenSeqs();
2920 public void showAllColumns_actionPerformed(ActionEvent e)
2922 viewport.showAllHiddenColumns();
2927 public void hideSelSequences_actionPerformed(ActionEvent e)
2929 viewport.hideAllSelectedSeqs();
2930 // alignPanel.paintAlignment(true);
2934 * called by key handler and the hide all/show all menu items
2939 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2942 boolean hide = false;
2943 SequenceGroup sg = viewport.getSelectionGroup();
2944 if (!toggleSeqs && !toggleCols)
2946 // Hide everything by the current selection - this is a hack - we do the
2947 // invert and then hide
2948 // first check that there will be visible columns after the invert.
2949 if ((viewport.getColumnSelection() != null
2950 && viewport.getColumnSelection().getSelected() != null && viewport
2951 .getColumnSelection().getSelected().size() > 0)
2952 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2955 // now invert the sequence set, if required - empty selection implies
2956 // that no hiding is required.
2959 invertSequenceMenuItem_actionPerformed(null);
2960 sg = viewport.getSelectionGroup();
2964 viewport.expandColSelection(sg, true);
2965 // finally invert the column selection and get the new sequence
2967 invertColSel_actionPerformed(null);
2974 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2976 hideSelSequences_actionPerformed(null);
2979 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2982 showAllSeqs_actionPerformed(null);
2988 if (viewport.getColumnSelection().getSelected().size() > 0)
2990 hideSelColumns_actionPerformed(null);
2993 viewport.setSelectionGroup(sg);
2998 showAllColumns_actionPerformed(null);
3007 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3008 * event.ActionEvent)
3011 public void hideAllButSelection_actionPerformed(ActionEvent e)
3013 toggleHiddenRegions(false, false);
3020 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3024 public void hideAllSelection_actionPerformed(ActionEvent e)
3026 SequenceGroup sg = viewport.getSelectionGroup();
3027 viewport.expandColSelection(sg, false);
3028 viewport.hideAllSelectedSeqs();
3029 viewport.hideSelectedColumns();
3030 alignPanel.paintAlignment(true);
3037 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3041 public void showAllhidden_actionPerformed(ActionEvent e)
3043 viewport.showAllHiddenColumns();
3044 viewport.showAllHiddenSeqs();
3045 alignPanel.paintAlignment(true);
3049 public void hideSelColumns_actionPerformed(ActionEvent e)
3051 viewport.hideSelectedColumns();
3052 alignPanel.paintAlignment(true);
3056 public void hiddenMarkers_actionPerformed(ActionEvent e)
3058 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3069 protected void scaleAbove_actionPerformed(ActionEvent e)
3071 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3072 alignPanel.paintAlignment(true);
3082 protected void scaleLeft_actionPerformed(ActionEvent e)
3084 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3085 alignPanel.paintAlignment(true);
3095 protected void scaleRight_actionPerformed(ActionEvent e)
3097 viewport.setScaleRightWrapped(scaleRight.isSelected());
3098 alignPanel.paintAlignment(true);
3108 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3110 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3111 alignPanel.paintAlignment(true);
3121 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3123 viewport.setShowText(viewTextMenuItem.isSelected());
3124 alignPanel.paintAlignment(true);
3134 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3136 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3137 alignPanel.paintAlignment(true);
3140 public FeatureSettings featureSettings;
3143 public void featureSettings_actionPerformed(ActionEvent e)
3145 if (featureSettings != null)
3147 featureSettings.close();
3148 featureSettings = null;
3150 if (!showSeqFeatures.isSelected())
3152 // make sure features are actually displayed
3153 showSeqFeatures.setSelected(true);
3154 showSeqFeatures_actionPerformed(null);
3156 featureSettings = new FeatureSettings(this);
3160 * Set or clear 'Show Sequence Features'
3166 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3168 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3169 alignPanel.paintAlignment(true);
3170 if (alignPanel.getOverviewPanel() != null)
3172 alignPanel.getOverviewPanel().updateOverviewImage();
3177 * Set or clear 'Show Sequence Features'
3183 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3185 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3187 if (viewport.isShowSequenceFeaturesHeight())
3189 // ensure we're actually displaying features
3190 viewport.setShowSequenceFeatures(true);
3191 showSeqFeatures.setSelected(true);
3193 alignPanel.paintAlignment(true);
3194 if (alignPanel.getOverviewPanel() != null)
3196 alignPanel.getOverviewPanel().updateOverviewImage();
3201 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3202 * the annotations panel as a whole.
3204 * The options to show/hide all annotations should be enabled when the panel
3205 * is shown, and disabled when the panel is hidden.
3210 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3212 final boolean setVisible = annotationPanelMenuItem.isSelected();
3213 viewport.setShowAnnotation(setVisible);
3214 this.showAllSeqAnnotations.setEnabled(setVisible);
3215 this.hideAllSeqAnnotations.setEnabled(setVisible);
3216 this.showAllAlAnnotations.setEnabled(setVisible);
3217 this.hideAllAlAnnotations.setEnabled(setVisible);
3218 alignPanel.updateLayout();
3222 public void alignmentProperties()
3224 JEditorPane editPane = new JEditorPane("text/html", "");
3225 editPane.setEditable(false);
3226 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3228 editPane.setText(MessageManager.formatMessage("label.html_content",
3230 { contents.toString() }));
3231 JInternalFrame frame = new JInternalFrame();
3232 frame.getContentPane().add(new JScrollPane(editPane));
3234 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3235 "label.alignment_properties", new Object[]
3236 { getTitle() }), 500, 400);
3246 public void overviewMenuItem_actionPerformed(ActionEvent e)
3248 if (alignPanel.overviewPanel != null)
3253 JInternalFrame frame = new JInternalFrame();
3254 OverviewPanel overview = new OverviewPanel(alignPanel);
3255 frame.setContentPane(overview);
3256 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3257 "label.overview_params", new Object[]
3258 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3260 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3261 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3264 public void internalFrameClosed(
3265 javax.swing.event.InternalFrameEvent evt)
3267 alignPanel.setOverviewPanel(null);
3271 alignPanel.setOverviewPanel(overview);
3275 public void textColour_actionPerformed(ActionEvent e)
3277 new TextColourChooser().chooseColour(alignPanel, null);
3287 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3299 public void clustalColour_actionPerformed(ActionEvent e)
3301 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3302 viewport.getHiddenRepSequences()));
3312 public void zappoColour_actionPerformed(ActionEvent e)
3314 changeColour(new ZappoColourScheme());
3324 public void taylorColour_actionPerformed(ActionEvent e)
3326 changeColour(new TaylorColourScheme());
3336 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3338 changeColour(new HydrophobicColourScheme());
3348 public void helixColour_actionPerformed(ActionEvent e)
3350 changeColour(new HelixColourScheme());
3360 public void strandColour_actionPerformed(ActionEvent e)
3362 changeColour(new StrandColourScheme());
3372 public void turnColour_actionPerformed(ActionEvent e)
3374 changeColour(new TurnColourScheme());
3384 public void buriedColour_actionPerformed(ActionEvent e)
3386 changeColour(new BuriedColourScheme());
3396 public void nucleotideColour_actionPerformed(ActionEvent e)
3398 changeColour(new NucleotideColourScheme());
3402 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3404 changeColour(new PurinePyrimidineColourScheme());
3408 * public void covariationColour_actionPerformed(ActionEvent e) {
3410 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3414 public void annotationColour_actionPerformed(ActionEvent e)
3416 new AnnotationColourChooser(viewport, alignPanel);
3420 public void annotationColumn_actionPerformed(ActionEvent e)
3422 new AnnotationColumnChooser(viewport, alignPanel);
3426 public void rnahelicesColour_actionPerformed(ActionEvent e)
3428 new RNAHelicesColourChooser(viewport, alignPanel);
3438 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3440 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3449 public void changeColour(ColourSchemeI cs)
3451 // TODO: compare with applet and pull up to model method
3456 if (viewport.getAbovePIDThreshold())
3458 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3460 cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
3464 cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
3467 if (viewport.getConservationSelected())
3470 Alignment al = (Alignment) viewport.getAlignment();
3471 Conservation c = new Conservation("All",
3472 ResidueProperties.propHash, 3, al.getSequences(), 0,
3476 c.verdict(false, viewport.getConsPercGaps());
3478 cs.setConservation(c);
3480 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3485 cs.setConservation(null);
3488 cs.setConsensus(viewport.getSequenceConsensusHash());
3491 viewport.setGlobalColourScheme(cs);
3493 if (viewport.getColourAppliesToAllGroups())
3496 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3504 if (cs instanceof ClustalxColourScheme)
3506 sg.cs = new ClustalxColourScheme(sg,
3507 viewport.getHiddenRepSequences());
3509 else if (cs instanceof UserColourScheme)
3511 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3517 sg.cs = cs.getClass().newInstance();
3518 } catch (Exception ex)
3523 if (viewport.getAbovePIDThreshold()
3524 || cs instanceof PIDColourScheme
3525 || cs instanceof Blosum62ColourScheme)
3527 sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
3529 sg.cs.setConsensus(AAFrequency.calculate(
3530 sg.getSequences(viewport.getHiddenRepSequences()),
3531 sg.getStartRes(), sg.getEndRes() + 1));
3535 sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
3538 if (viewport.getConservationSelected())
3540 Conservation c = new Conservation("Group",
3541 ResidueProperties.propHash, 3, sg.getSequences(viewport
3542 .getHiddenRepSequences()), sg.getStartRes(),
3543 sg.getEndRes() + 1);
3545 c.verdict(false, viewport.getConsPercGaps());
3546 sg.cs.setConservation(c);
3550 sg.cs.setConservation(null);
3555 if (alignPanel.getOverviewPanel() != null)
3557 alignPanel.getOverviewPanel().updateOverviewImage();
3560 alignPanel.paintAlignment(true);
3570 protected void modifyPID_actionPerformed(ActionEvent e)
3572 if (viewport.getAbovePIDThreshold()
3573 && viewport.getGlobalColourScheme() != null)
3575 SliderPanel.setPIDSliderSource(alignPanel,
3576 viewport.getGlobalColourScheme(), "Background");
3577 SliderPanel.showPIDSlider();
3588 protected void modifyConservation_actionPerformed(ActionEvent e)
3590 if (viewport.getConservationSelected()
3591 && viewport.getGlobalColourScheme() != null)
3593 SliderPanel.setConservationSlider(alignPanel,
3594 viewport.getGlobalColourScheme(), "Background");
3595 SliderPanel.showConservationSlider();
3606 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3608 viewport.setConservationSelected(conservationMenuItem.isSelected());
3610 viewport.setAbovePIDThreshold(false);
3611 abovePIDThreshold.setSelected(false);
3613 changeColour(viewport.getGlobalColourScheme());
3615 modifyConservation_actionPerformed(null);
3625 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3627 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3629 conservationMenuItem.setSelected(false);
3630 viewport.setConservationSelected(false);
3632 changeColour(viewport.getGlobalColourScheme());
3634 modifyPID_actionPerformed(null);
3644 public void userDefinedColour_actionPerformed(ActionEvent e)
3646 if (e.getActionCommand().equals(
3647 MessageManager.getString("action.user_defined")))
3649 new UserDefinedColours(alignPanel, null);
3653 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3654 .getUserColourSchemes().get(e.getActionCommand());
3660 public void updateUserColourMenu()
3663 Component[] menuItems = colourMenu.getMenuComponents();
3664 int iSize = menuItems.length;
3665 for (int i = 0; i < iSize; i++)
3667 if (menuItems[i].getName() != null
3668 && menuItems[i].getName().equals("USER_DEFINED"))
3670 colourMenu.remove(menuItems[i]);
3674 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3676 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3677 .getUserColourSchemes().keys();
3679 while (userColours.hasMoreElements())
3681 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3682 userColours.nextElement().toString());
3683 radioItem.setName("USER_DEFINED");
3684 radioItem.addMouseListener(new MouseAdapter()
3687 public void mousePressed(MouseEvent evt)
3689 if (evt.isControlDown()
3690 || SwingUtilities.isRightMouseButton(evt))
3692 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3694 int option = JOptionPane.showInternalConfirmDialog(
3695 jalview.gui.Desktop.desktop,
3697 .getString("label.remove_from_default_list"),
3699 .getString("label.remove_user_defined_colour"),
3700 JOptionPane.YES_NO_OPTION);
3701 if (option == JOptionPane.YES_OPTION)
3703 jalview.gui.UserDefinedColours
3704 .removeColourFromDefaults(radioItem.getText());
3705 colourMenu.remove(radioItem);
3709 radioItem.addActionListener(new ActionListener()
3712 public void actionPerformed(ActionEvent evt)
3714 userDefinedColour_actionPerformed(evt);
3721 radioItem.addActionListener(new ActionListener()
3724 public void actionPerformed(ActionEvent evt)
3726 userDefinedColour_actionPerformed(evt);
3730 colourMenu.insert(radioItem, 15);
3731 colours.add(radioItem);
3743 public void PIDColour_actionPerformed(ActionEvent e)
3745 changeColour(new PIDColourScheme());
3755 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3757 changeColour(new Blosum62ColourScheme());
3767 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3769 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3770 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3771 .getAlignment().getSequenceAt(0), null);
3772 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3773 viewport.getAlignment()));
3774 alignPanel.paintAlignment(true);
3784 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3786 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3787 AlignmentSorter.sortByID(viewport.getAlignment());
3788 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3789 viewport.getAlignment()));
3790 alignPanel.paintAlignment(true);
3800 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3802 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3803 AlignmentSorter.sortByLength(viewport.getAlignment());
3804 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3805 viewport.getAlignment()));
3806 alignPanel.paintAlignment(true);
3816 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3818 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3819 AlignmentSorter.sortByGroup(viewport.getAlignment());
3820 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3821 viewport.getAlignment()));
3823 alignPanel.paintAlignment(true);
3833 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3835 new RedundancyPanel(alignPanel, this);
3845 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3847 if ((viewport.getSelectionGroup() == null)
3848 || (viewport.getSelectionGroup().getSize() < 2))
3850 JOptionPane.showInternalMessageDialog(this, MessageManager
3851 .getString("label.you_must_select_least_two_sequences"),
3852 MessageManager.getString("label.invalid_selection"),
3853 JOptionPane.WARNING_MESSAGE);
3857 JInternalFrame frame = new JInternalFrame();
3858 frame.setContentPane(new PairwiseAlignPanel(viewport));
3859 Desktop.addInternalFrame(frame,
3860 MessageManager.getString("action.pairwise_alignment"), 600,
3872 public void PCAMenuItem_actionPerformed(ActionEvent e)
3874 if (((viewport.getSelectionGroup() != null)
3875 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3876 .getSelectionGroup().getSize() > 0))
3877 || (viewport.getAlignment().getHeight() < 4))
3880 .showInternalMessageDialog(
3883 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3885 .getString("label.sequence_selection_insufficient"),
3886 JOptionPane.WARNING_MESSAGE);
3891 new PCAPanel(alignPanel);
3895 public void autoCalculate_actionPerformed(ActionEvent e)
3897 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3898 if (viewport.autoCalculateConsensus)
3900 viewport.firePropertyChange("alignment", null, viewport
3901 .getAlignment().getSequences());
3906 public void sortByTreeOption_actionPerformed(ActionEvent e)
3908 viewport.sortByTree = sortByTree.isSelected();
3912 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3914 viewport.followSelection = listenToViewSelections.isSelected();
3924 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3926 newTreePanel("AV", "PID", "Average distance tree using PID");
3936 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3938 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3948 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3950 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3960 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3962 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3975 void newTreePanel(String type, String pwType, String title)
3979 if (viewport.getSelectionGroup() != null
3980 && viewport.getSelectionGroup().getSize() > 0)
3982 if (viewport.getSelectionGroup().getSize() < 3)
3988 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3990 .getString("label.not_enough_sequences"),
3991 JOptionPane.WARNING_MESSAGE);
3995 SequenceGroup sg = viewport.getSelectionGroup();
3997 /* Decide if the selection is a column region */
3998 for (SequenceI _s : sg.getSequences())
4000 if (_s.getLength() < sg.getEndRes())
4006 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
4008 .getString("label.sequences_selection_not_aligned"),
4009 JOptionPane.WARNING_MESSAGE);
4015 title = title + " on region";
4016 tp = new TreePanel(alignPanel, type, pwType);
4020 // are the visible sequences aligned?
4021 if (!viewport.getAlignment().isAligned(false))
4027 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4029 .getString("label.sequences_not_aligned"),
4030 JOptionPane.WARNING_MESSAGE);
4035 if (viewport.getAlignment().getHeight() < 2)
4040 tp = new TreePanel(alignPanel, type, pwType);
4045 if (viewport.viewName != null)
4047 title += viewport.viewName + " of ";
4050 title += this.title;
4052 Desktop.addInternalFrame(tp, title, 600, 500);
4063 public void addSortByOrderMenuItem(String title,
4064 final AlignmentOrder order)
4066 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title}));
4068 item.addActionListener(new java.awt.event.ActionListener()
4071 public void actionPerformed(ActionEvent e)
4073 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4075 // TODO: JBPNote - have to map order entries to curent SequenceI
4077 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4079 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4082 alignPanel.paintAlignment(true);
4088 * Add a new sort by annotation score menu item
4091 * the menu to add the option to
4093 * the label used to retrieve scores for each sequence on the
4096 public void addSortByAnnotScoreMenuItem(JMenu sort,
4097 final String scoreLabel)
4099 final JMenuItem item = new JMenuItem(scoreLabel);
4101 item.addActionListener(new java.awt.event.ActionListener()
4104 public void actionPerformed(ActionEvent e)
4106 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4107 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4108 viewport.getAlignment());// ,viewport.getSelectionGroup());
4109 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4110 viewport.getAlignment()));
4111 alignPanel.paintAlignment(true);
4117 * last hash for alignment's annotation array - used to minimise cost of
4120 protected int _annotationScoreVectorHash;
4123 * search the alignment and rebuild the sort by annotation score submenu the
4124 * last alignment annotation vector hash is stored to minimize cost of
4125 * rebuilding in subsequence calls.
4129 public void buildSortByAnnotationScoresMenu()
4131 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4136 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4138 sortByAnnotScore.removeAll();
4139 // almost certainly a quicker way to do this - but we keep it simple
4140 Hashtable scoreSorts = new Hashtable();
4141 AlignmentAnnotation aann[];
4142 for (SequenceI sqa : viewport.getAlignment().getSequences())
4144 aann = sqa.getAnnotation();
4145 for (int i = 0; aann != null && i < aann.length; i++)
4147 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4149 scoreSorts.put(aann[i].label, aann[i].label);
4153 Enumeration labels = scoreSorts.keys();
4154 while (labels.hasMoreElements())
4156 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4157 (String) labels.nextElement());
4159 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4162 _annotationScoreVectorHash = viewport.getAlignment()
4163 .getAlignmentAnnotation().hashCode();
4168 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4169 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4170 * call. Listeners are added to remove the menu item when the treePanel is
4171 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4175 * Displayed tree window.
4177 * SortBy menu item title.
4180 public void buildTreeMenu()
4182 calculateTree.removeAll();
4183 // build the calculate menu
4185 for (final String type : new String[]
4188 String treecalcnm = MessageManager.getString("label.tree_calc_"
4189 + type.toLowerCase());
4190 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4192 JMenuItem tm = new JMenuItem();
4193 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4194 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4196 String smn = MessageManager.getStringOrReturn(
4197 "label.score_model_", sm.getName());
4198 final String title = MessageManager.formatMessage(
4199 "label.treecalc_title", treecalcnm, smn);
4200 tm.setText(title);//
4201 tm.addActionListener(new java.awt.event.ActionListener()
4204 public void actionPerformed(ActionEvent e)
4206 newTreePanel(type, pwtype, title);
4209 calculateTree.add(tm);
4214 sortByTreeMenu.removeAll();
4216 List<Component> comps = PaintRefresher.components.get(viewport
4217 .getSequenceSetId());
4218 List<TreePanel> treePanels = new ArrayList<TreePanel>();
4219 for (Component comp : comps)
4221 if (comp instanceof TreePanel)
4223 treePanels.add((TreePanel) comp);
4227 if (treePanels.size() < 1)
4229 sortByTreeMenu.setVisible(false);
4233 sortByTreeMenu.setVisible(true);
4235 for (final TreePanel tp : treePanels)
4237 final JMenuItem item = new JMenuItem(tp.getTitle());
4238 item.addActionListener(new java.awt.event.ActionListener()
4241 public void actionPerformed(ActionEvent e)
4243 tp.sortByTree_actionPerformed();
4244 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4249 sortByTreeMenu.add(item);
4253 public boolean sortBy(AlignmentOrder alorder, String undoname)
4255 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4256 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4257 if (undoname != null)
4259 addHistoryItem(new OrderCommand(undoname, oldOrder,
4260 viewport.getAlignment()));
4262 alignPanel.paintAlignment(true);
4267 * Work out whether the whole set of sequences or just the selected set will
4268 * be submitted for multiple alignment.
4271 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4273 // Now, check we have enough sequences
4274 AlignmentView msa = null;
4276 if ((viewport.getSelectionGroup() != null)
4277 && (viewport.getSelectionGroup().getSize() > 1))
4279 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4280 // some common interface!
4282 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4283 * SequenceI[sz = seqs.getSize(false)];
4285 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4286 * seqs.getSequenceAt(i); }
4288 msa = viewport.getAlignmentView(true);
4290 else if (viewport.getSelectionGroup() != null
4291 && viewport.getSelectionGroup().getSize() == 1)
4293 int option = JOptionPane.showConfirmDialog(this,
4294 MessageManager.getString("warn.oneseq_msainput_selection"),
4295 MessageManager.getString("label.invalid_selection"),
4296 JOptionPane.OK_CANCEL_OPTION);
4297 if (option == JOptionPane.OK_OPTION)
4299 msa = viewport.getAlignmentView(false);
4304 msa = viewport.getAlignmentView(false);
4310 * Decides what is submitted to a secondary structure prediction service: the
4311 * first sequence in the alignment, or in the current selection, or, if the
4312 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4313 * region or the whole alignment. (where the first sequence in the set is the
4314 * one that the prediction will be for).
4316 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4318 AlignmentView seqs = null;
4320 if ((viewport.getSelectionGroup() != null)
4321 && (viewport.getSelectionGroup().getSize() > 0))
4323 seqs = viewport.getAlignmentView(true);
4327 seqs = viewport.getAlignmentView(false);
4329 // limit sequences - JBPNote in future - could spawn multiple prediction
4331 // TODO: viewport.getAlignment().isAligned is a global state - the local
4332 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4333 if (!viewport.getAlignment().isAligned(false))
4335 seqs.setSequences(new SeqCigar[]
4336 { seqs.getSequences()[0] });
4337 // TODO: if seqs.getSequences().length>1 then should really have warned
4351 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4353 // Pick the tree file
4354 JalviewFileChooser chooser = new JalviewFileChooser(
4355 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4356 chooser.setFileView(new JalviewFileView());
4357 chooser.setDialogTitle(MessageManager
4358 .getString("label.select_newick_like_tree_file"));
4359 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4361 int value = chooser.showOpenDialog(null);
4363 if (value == JalviewFileChooser.APPROVE_OPTION)
4365 String choice = chooser.getSelectedFile().getPath();
4366 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4367 jalview.io.NewickFile fin = null;
4370 fin = new jalview.io.NewickFile(choice, "File");
4371 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4372 } catch (Exception ex)
4379 .getString("label.problem_reading_tree_file"),
4380 JOptionPane.WARNING_MESSAGE);
4381 ex.printStackTrace();
4383 if (fin != null && fin.hasWarningMessage())
4385 JOptionPane.showMessageDialog(Desktop.desktop, fin
4386 .getWarningMessage(), MessageManager
4387 .getString("label.possible_problem_with_tree_file"),
4388 JOptionPane.WARNING_MESSAGE);
4394 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4396 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4399 public TreePanel ShowNewickTree(NewickFile nf, String title)
4401 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4404 public TreePanel ShowNewickTree(NewickFile nf, String title,
4405 AlignmentView input)
4407 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4410 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4411 int h, int x, int y)
4413 return ShowNewickTree(nf, title, null, w, h, x, y);
4417 * Add a treeviewer for the tree extracted from a newick file object to the
4418 * current alignment view
4425 * Associated alignment input data (or null)
4434 * @return TreePanel handle
4436 public TreePanel ShowNewickTree(NewickFile nf, String title,
4437 AlignmentView input, int w, int h, int x, int y)
4439 TreePanel tp = null;
4445 if (nf.getTree() != null)
4447 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4453 tp.setLocation(x, y);
4456 Desktop.addInternalFrame(tp, title, w, h);
4458 } catch (Exception ex)
4460 ex.printStackTrace();
4466 private boolean buildingMenu = false;
4469 * Generates menu items and listener event actions for web service clients
4472 public void BuildWebServiceMenu()
4474 while (buildingMenu)
4478 System.err.println("Waiting for building menu to finish.");
4480 } catch (Exception e)
4484 final AlignFrame me = this;
4485 buildingMenu = true;
4486 new Thread(new Runnable()
4491 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4494 System.err.println("Building ws menu again "
4495 + Thread.currentThread());
4496 // TODO: add support for context dependent disabling of services based
4498 // alignment and current selection
4499 // TODO: add additional serviceHandle parameter to specify abstract
4501 // class independently of AbstractName
4502 // TODO: add in rediscovery GUI function to restart discoverer
4503 // TODO: group services by location as well as function and/or
4505 // object broker mechanism.
4506 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4507 final IProgressIndicator af = me;
4508 final JMenu msawsmenu = new JMenu("Alignment");
4509 final JMenu secstrmenu = new JMenu(
4510 "Secondary Structure Prediction");
4511 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4512 final JMenu analymenu = new JMenu("Analysis");
4513 final JMenu dismenu = new JMenu("Protein Disorder");
4514 // final JMenu msawsmenu = new
4515 // JMenu(MessageManager.getString("label.alignment"));
4516 // final JMenu secstrmenu = new
4517 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4518 // final JMenu seqsrchmenu = new
4519 // JMenu(MessageManager.getString("label.sequence_database_search"));
4520 // final JMenu analymenu = new
4521 // JMenu(MessageManager.getString("label.analysis"));
4522 // final JMenu dismenu = new
4523 // JMenu(MessageManager.getString("label.protein_disorder"));
4524 // JAL-940 - only show secondary structure prediction services from
4525 // the legacy server
4526 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4528 Discoverer.services != null && (Discoverer.services.size() > 0))
4530 // TODO: refactor to allow list of AbstractName/Handler bindings to
4532 // stored or retrieved from elsewhere
4533 // No MSAWS used any more:
4534 // Vector msaws = null; // (Vector)
4535 // Discoverer.services.get("MsaWS");
4536 Vector secstrpr = (Vector) Discoverer.services
4538 if (secstrpr != null)
4540 // Add any secondary structure prediction services
4541 for (int i = 0, j = secstrpr.size(); i < j; i++)
4543 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4545 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4546 .getServiceClient(sh);
4547 int p = secstrmenu.getItemCount();
4548 impl.attachWSMenuEntry(secstrmenu, me);
4549 int q = secstrmenu.getItemCount();
4550 for (int litm = p; litm < q; litm++)
4552 legacyItems.add(secstrmenu.getItem(litm));
4558 // Add all submenus in the order they should appear on the web
4560 wsmenu.add(msawsmenu);
4561 wsmenu.add(secstrmenu);
4562 wsmenu.add(dismenu);
4563 wsmenu.add(analymenu);
4564 // No search services yet
4565 // wsmenu.add(seqsrchmenu);
4567 javax.swing.SwingUtilities.invokeLater(new Runnable()
4574 webService.removeAll();
4575 // first, add discovered services onto the webservices menu
4576 if (wsmenu.size() > 0)
4578 for (int i = 0, j = wsmenu.size(); i < j; i++)
4580 webService.add(wsmenu.get(i));
4585 webService.add(me.webServiceNoServices);
4587 // TODO: move into separate menu builder class.
4588 boolean new_sspred = false;
4589 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4591 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4592 if (jws2servs != null)
4594 if (jws2servs.hasServices())
4596 jws2servs.attachWSMenuEntry(webService, me);
4597 for (Jws2Instance sv : jws2servs.getServices())
4599 if (sv.description.toLowerCase().contains("jpred"))
4601 for (JMenuItem jmi : legacyItems)
4603 jmi.setVisible(false);
4609 if (jws2servs.isRunning())
4611 JMenuItem tm = new JMenuItem(
4612 "Still discovering JABA Services");
4613 tm.setEnabled(false);
4618 build_urlServiceMenu(me.webService);
4619 build_fetchdbmenu(webService);
4620 for (JMenu item : wsmenu)
4622 if (item.getItemCount() == 0)
4624 item.setEnabled(false);
4628 item.setEnabled(true);
4631 } catch (Exception e)
4634 .debug("Exception during web service menu building process.",
4639 } catch (Exception e)
4642 buildingMenu = false;
4649 * construct any groupURL type service menu entries.
4653 private void build_urlServiceMenu(JMenu webService)
4655 // TODO: remove this code when 2.7 is released
4656 // DEBUG - alignmentView
4658 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4659 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4661 * @Override public void actionPerformed(ActionEvent e) {
4662 * jalview.datamodel.AlignmentView
4663 * .testSelectionViews(af.viewport.getAlignment(),
4664 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4666 * }); webService.add(testAlView);
4668 // TODO: refactor to RestClient discoverer and merge menu entries for
4669 // rest-style services with other types of analysis/calculation service
4670 // SHmmr test client - still being implemented.
4671 // DEBUG - alignmentView
4673 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4676 client.attachWSMenuEntry(
4677 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4683 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4684 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4685 * getProperty("LAST_DIRECTORY"));
4687 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4688 * to Vamsas file"); chooser.setToolTipText("Export");
4690 * int value = chooser.showSaveDialog(this);
4692 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4693 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4694 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4695 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4698 * prototype of an automatically enabled/disabled analysis function
4701 protected void setShowProductsEnabled()
4703 SequenceI[] selection = viewport.getSequenceSelection();
4704 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4705 viewport.getAlignment().getDataset()))
4707 showProducts.setEnabled(true);
4712 showProducts.setEnabled(false);
4717 * search selection for sequence xRef products and build the show products
4722 * @return true if showProducts menu should be enabled.
4724 public boolean canShowProducts(SequenceI[] selection,
4725 boolean isRegionSelection, Alignment dataset)
4727 boolean showp = false;
4730 showProducts.removeAll();
4731 final boolean dna = viewport.getAlignment().isNucleotide();
4732 final Alignment ds = dataset;
4733 String[] ptypes = (selection == null || selection.length == 0) ? null
4734 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4736 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4737 // selection, dataset, true);
4738 final SequenceI[] sel = selection;
4739 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4742 final boolean isRegSel = isRegionSelection;
4743 final AlignFrame af = this;
4744 final String source = ptypes[t];
4745 JMenuItem xtype = new JMenuItem(ptypes[t]);
4746 xtype.addActionListener(new ActionListener()
4750 public void actionPerformed(ActionEvent e)
4752 // TODO: new thread for this call with vis-delay
4753 af.showProductsFor(af.viewport.getSequenceSelection(),
4754 isRegSel, dna, source);
4758 showProducts.add(xtype);
4760 showProducts.setVisible(showp);
4761 showProducts.setEnabled(showp);
4762 } catch (Exception e)
4764 jalview.bin.Cache.log
4765 .warn("canTranslate threw an exception - please report to help@jalview.org",
4772 protected void showProductsFor(final SequenceI[] sel,
4773 final boolean isRegSel, final boolean dna, final String source)
4775 Runnable foo = new Runnable()
4781 final long sttime = System.currentTimeMillis();
4782 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4783 "status.searching_for_sequences_from", new Object[]
4784 { source }), sttime);
4787 // update our local dataset reference
4788 Alignment ds = AlignFrame.this.getViewport().getAlignment()
4790 Alignment prods = CrossRef
4791 .findXrefSequences(sel, dna, source, ds);
4794 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4795 for (int s = 0; s < sprods.length; s++)
4797 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4798 if (ds.getSequences() == null
4799 || !ds.getSequences().contains(
4800 sprods[s].getDatasetSequence()))
4802 ds.addSequence(sprods[s].getDatasetSequence());
4804 sprods[s].updatePDBIds();
4806 Alignment al = new Alignment(sprods);
4810 * Copy dna-to-protein mappings to new alignment
4812 // TODO 1: no mappings are set up for EMBL product
4813 // TODO 2: if they were, should add them to protein alignment, not
4815 Set<AlignedCodonFrame> cf = prods.getCodonFrames();
4816 for (AlignedCodonFrame acf : cf)
4818 al.addCodonFrame(acf);
4820 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4822 String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
4823 + " for " + ((isRegSel) ? "selected region of " : "")
4825 naf.setTitle(newtitle);
4827 // temporary flag until SplitFrame is released
4828 boolean asSplitFrame = Cache.getDefault(
4829 Preferences.ENABLE_SPLIT_FRAME, false);
4833 * Make a copy of this alignment (sharing the same dataset
4834 * sequences). If we are DNA, drop introns and update mappings
4836 AlignmentI copyAlignment = null;
4837 final SequenceI[] sequenceSelection = AlignFrame.this.viewport
4838 .getSequenceSelection();
4841 copyAlignment = AlignmentUtils.makeExonAlignment(
4842 sequenceSelection, cf);
4843 al.getCodonFrames().clear();
4844 al.getCodonFrames().addAll(cf);
4845 final StructureSelectionManager ssm = StructureSelectionManager
4846 .getStructureSelectionManager(Desktop.instance);
4847 ssm.addMappings(cf);
4851 copyAlignment = new Alignment(new Alignment(
4852 sequenceSelection));
4854 AlignFrame copyThis = new AlignFrame(copyAlignment,
4855 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
4856 copyThis.setTitle(AlignFrame.this.getTitle());
4857 // SplitFrame with dna above, protein below
4858 SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
4859 dna ? naf : copyThis);
4860 naf.setVisible(true);
4861 copyThis.setVisible(true);
4862 String linkedTitle = MessageManager
4863 .getString("label.linked_view_title");
4864 Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
4868 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4874 System.err.println("No Sequences generated for xRef type "
4877 } catch (Exception e)
4879 jalview.bin.Cache.log.error(
4880 "Exception when finding crossreferences", e);
4881 } catch (OutOfMemoryError e)
4883 new OOMWarning("whilst fetching crossreferences", e);
4886 jalview.bin.Cache.log.error("Error when finding crossreferences",
4889 AlignFrame.this.setProgressBar(MessageManager.formatMessage(
4890 "status.finished_searching_for_sequences_from",
4897 Thread frunner = new Thread(foo);
4901 public boolean canShowTranslationProducts(SequenceI[] selection,
4902 AlignmentI alignment)
4907 return (jalview.analysis.Dna.canTranslate(selection,
4908 viewport.getViewAsVisibleContigs(true)));
4909 } catch (Exception e)
4911 jalview.bin.Cache.log
4912 .warn("canTranslate threw an exception - please report to help@jalview.org",
4919 * Construct and display a new frame containing the translation of this
4920 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4923 public void showTranslation_actionPerformed(ActionEvent e)
4925 AlignmentI al = null;
4928 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4930 al = dna.translateCdna();
4931 } catch (Exception ex)
4933 jalview.bin.Cache.log.error(
4934 "Exception during translation. Please report this !", ex);
4935 final String msg = MessageManager
4936 .getString("label.error_when_translating_sequences_submit_bug_report");
4937 final String title = MessageManager
4938 .getString("label.implementation_error")
4939 + MessageManager.getString("translation_failed");
4940 JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
4941 JOptionPane.ERROR_MESSAGE);
4944 if (al == null || al.getHeight() == 0)
4946 final String msg = MessageManager
4947 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4948 final String title = MessageManager
4949 .getString("label.translation_failed");
4950 JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
4951 JOptionPane.WARNING_MESSAGE);
4955 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4956 af.setFileFormat(this.currentFileFormat);
4957 final String newTitle = MessageManager.formatMessage(
4958 "label.translation_of_params", new Object[]
4959 { this.getTitle() });
4960 af.setTitle(newTitle);
4961 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
4963 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4964 viewport.openSplitFrame(af, new Alignment(seqs),
4965 al.getCodonFrames());
4969 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4976 * Set the file format
4980 public void setFileFormat(String fileFormat)
4982 this.currentFileFormat = fileFormat;
4986 * Try to load a features file onto the alignment.
4989 * contents or path to retrieve file
4991 * access mode of file (see jalview.io.AlignFile)
4992 * @return true if features file was parsed corectly.
4994 public boolean parseFeaturesFile(String file, String type)
4996 boolean featuresFile = false;
4999 featuresFile = new FeaturesFile(file, type).parse(viewport
5000 .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
5001 .getFeatureRenderer().getFeatureColours(), false,
5002 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
5003 } catch (Exception ex)
5005 ex.printStackTrace();
5010 viewport.setShowSequenceFeatures(true);
5011 showSeqFeatures.setSelected(true);
5012 if (alignPanel.getSeqPanel().seqCanvas.fr != null)
5014 // update the min/max ranges where necessary
5015 alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
5017 if (featureSettings != null)
5019 featureSettings.setTableData();
5021 alignPanel.paintAlignment(true);
5024 return featuresFile;
5028 public void dragEnter(DropTargetDragEvent evt)
5033 public void dragExit(DropTargetEvent evt)
5038 public void dragOver(DropTargetDragEvent evt)
5043 public void dropActionChanged(DropTargetDragEvent evt)
5048 public void drop(DropTargetDropEvent evt)
5050 Transferable t = evt.getTransferable();
5051 java.util.List files = null;
5055 DataFlavor uriListFlavor = new DataFlavor(
5056 "text/uri-list;class=java.lang.String");
5057 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5059 // Works on Windows and MacOSX
5060 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5061 files = (java.util.List) t
5062 .getTransferData(DataFlavor.javaFileListFlavor);
5064 else if (t.isDataFlavorSupported(uriListFlavor))
5066 // This is used by Unix drag system
5067 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5068 String data = (String) t.getTransferData(uriListFlavor);
5069 files = new java.util.ArrayList(1);
5070 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5071 data, "\r\n"); st.hasMoreTokens();)
5073 String s = st.nextToken();
5074 if (s.startsWith("#"))
5076 // the line is a comment (as per the RFC 2483)
5080 java.net.URI uri = new java.net.URI(s);
5081 // check to see if we can handle this kind of URI
5082 if (uri.getScheme().toLowerCase().startsWith("http"))
5084 files.add(uri.toString());
5088 // otherwise preserve old behaviour: catch all for file objects
5089 java.io.File file = new java.io.File(uri);
5090 files.add(file.toString());
5094 } catch (Exception e)
5096 e.printStackTrace();
5102 // check to see if any of these files have names matching sequences in
5104 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5105 .getAlignment().getSequencesArray());
5107 * Object[] { String,SequenceI}
5109 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5110 ArrayList<String> filesnotmatched = new ArrayList<String>();
5111 for (int i = 0; i < files.size(); i++)
5113 String file = files.get(i).toString();
5115 String protocol = FormatAdapter.checkProtocol(file);
5116 if (protocol == jalview.io.FormatAdapter.FILE)
5118 File fl = new File(file);
5119 pdbfn = fl.getName();
5121 else if (protocol == jalview.io.FormatAdapter.URL)
5123 URL url = new URL(file);
5124 pdbfn = url.getFile();
5126 if (pdbfn.length() > 0)
5128 // attempt to find a match in the alignment
5129 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5130 int l = 0, c = pdbfn.indexOf(".");
5131 while (mtch == null && c != -1)
5136 } while ((c = pdbfn.indexOf(".", l)) > l);
5139 pdbfn = pdbfn.substring(0, l);
5141 mtch = idm.findAllIdMatches(pdbfn);
5148 type = new IdentifyFile().Identify(file, protocol);
5149 } catch (Exception ex)
5155 if (type.equalsIgnoreCase("PDB"))
5157 filesmatched.add(new Object[]
5158 { file, protocol, mtch });
5163 // File wasn't named like one of the sequences or wasn't a PDB file.
5164 filesnotmatched.add(file);
5168 if (filesmatched.size() > 0)
5170 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5176 "label.automatically_associate_pdb_files_with_sequences_same_name",
5183 .getString("label.automatically_associate_pdb_files_by_name"),
5184 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5187 for (Object[] fm : filesmatched)
5189 // try and associate
5190 // TODO: may want to set a standard ID naming formalism for
5191 // associating PDB files which have no IDs.
5192 for (SequenceI toassoc : (SequenceI[]) fm[2])
5194 PDBEntry pe = new AssociatePdbFileWithSeq()
5195 .associatePdbWithSeq((String) fm[0],
5196 (String) fm[1], toassoc, false,
5200 System.err.println("Associated file : "
5201 + ((String) fm[0]) + " with "
5202 + toassoc.getDisplayId(true));
5206 alignPanel.paintAlignment(true);
5210 if (filesnotmatched.size() > 0)
5213 && (Cache.getDefault(
5214 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5217 "<html>"+MessageManager
5219 "label.ignore_unmatched_dropped_files_info",
5224 .toString() })+"</html>",
5226 .getString("label.ignore_unmatched_dropped_files"),
5227 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5231 for (String fn : filesnotmatched)
5233 loadJalviewDataFile(fn, null, null, null);
5237 } catch (Exception ex)
5239 ex.printStackTrace();
5245 * Attempt to load a "dropped" file or URL string: First by testing whether
5246 * it's and Annotation file, then a JNet file, and finally a features file. If
5247 * all are false then the user may have dropped an alignment file onto this
5251 * either a filename or a URL string.
5253 public void loadJalviewDataFile(String file, String protocol,
5254 String format, SequenceI assocSeq)
5258 if (protocol == null)
5260 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5262 // if the file isn't identified, or not positively identified as some
5263 // other filetype (PFAM is default unidentified alignment file type) then
5264 // try to parse as annotation.
5265 boolean isAnnotation = (format == null || format
5266 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5267 .annotateAlignmentView(viewport, file, protocol)
5272 // first see if its a T-COFFEE score file
5273 TCoffeeScoreFile tcf = null;
5276 tcf = new TCoffeeScoreFile(file, protocol);
5279 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5281 tcoffeeColour.setEnabled(true);
5282 tcoffeeColour.setSelected(true);
5283 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5284 isAnnotation = true;
5286 .setText(MessageManager
5287 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5291 // some problem - if no warning its probable that the ID matching
5292 // process didn't work
5296 tcf.getWarningMessage() == null ? MessageManager
5297 .getString("label.check_file_matches_sequence_ids_alignment")
5298 : tcf.getWarningMessage(),
5300 .getString("label.problem_reading_tcoffee_score_file"),
5301 JOptionPane.WARNING_MESSAGE);
5308 } catch (Exception x)
5311 .debug("Exception when processing data source as T-COFFEE score file",
5317 // try to see if its a JNet 'concise' style annotation file *before*
5319 // try to parse it as a features file
5322 format = new IdentifyFile().Identify(file, protocol);
5324 if (format.equalsIgnoreCase("JnetFile"))
5326 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5328 new JnetAnnotationMaker();
5329 JnetAnnotationMaker.add_annotation(predictions,
5330 viewport.getAlignment(), 0, false);
5331 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5332 viewport.getAlignment().setSeqrep(repseq);
5333 ColumnSelection cs = new ColumnSelection();
5334 cs.hideInsertionsFor(repseq);
5335 viewport.setColumnSelection(cs);
5336 isAnnotation = true;
5341 * if (format.equalsIgnoreCase("PDB")) {
5343 * String pdbfn = ""; // try to match up filename with sequence id
5344 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5345 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5346 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5347 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5348 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5349 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5350 * // attempt to find a match in the alignment SequenceI mtch =
5351 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5352 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5353 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5354 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5355 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5356 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5357 * { System.err.println("Associated file : " + file + " with " +
5358 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5359 * TODO: maybe need to load as normal otherwise return; } }
5361 // try to parse it as a features file
5362 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5363 // if it wasn't a features file then we just treat it as a general
5364 // alignment file to load into the current view.
5367 new FileLoader().LoadFile(viewport, file, protocol, format);
5371 alignPanel.paintAlignment(true);
5379 alignPanel.adjustAnnotationHeight();
5380 viewport.updateSequenceIdColours();
5381 buildSortByAnnotationScoresMenu();
5382 alignPanel.paintAlignment(true);
5384 } catch (Exception ex)
5386 ex.printStackTrace();
5387 } catch (OutOfMemoryError oom)
5392 } catch (Exception x)
5398 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5399 : "using " + protocol + " from " + file)
5401 + (format != null ? "(parsing as '" + format
5402 + "' file)" : ""), oom, Desktop.desktop);
5407 * Method invoked by the ChangeListener on the tabbed pane, in other words
5408 * when a different tabbed pane is selected by the user or programmatically.
5411 public void tabSelectionChanged(int index)
5415 alignPanel = alignPanels.get(index);
5416 viewport = alignPanel.av;
5417 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5418 setMenusFromViewport(viewport);
5422 * If there is a frame linked to this one in a SplitPane, switch it to the
5423 * same view tab index. No infinite recursion of calls should happen, since
5424 * tabSelectionChanged() should not get invoked on setting the selected
5425 * index to an unchanged value. Guard against setting an invalid index
5426 * before the new view peer tab has been created.
5428 final AlignViewportI peer = viewport.getCodingComplement();
5431 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5432 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5434 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5440 * On right mouse click on view tab, prompt for and set new view name.
5443 public void tabbedPane_mousePressed(MouseEvent e)
5445 if (SwingUtilities.isRightMouseButton(e))
5447 String msg = MessageManager.getString("label.enter_view_name");
5448 String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
5449 JOptionPane.QUESTION_MESSAGE);
5453 viewport.viewName = reply;
5454 // TODO warn if reply is in getExistingViewNames()?
5455 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5460 public AlignViewport getCurrentView()
5466 * Open the dialog for regex description parsing.
5469 protected void extractScores_actionPerformed(ActionEvent e)
5471 ParseProperties pp = new jalview.analysis.ParseProperties(
5472 viewport.getAlignment());
5473 // TODO: verify regex and introduce GUI dialog for version 2.5
5474 // if (pp.getScoresFromDescription("col", "score column ",
5475 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5477 if (pp.getScoresFromDescription("description column",
5478 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5480 buildSortByAnnotationScoresMenu();
5488 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5492 protected void showDbRefs_actionPerformed(ActionEvent e)
5494 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5500 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5504 protected void showNpFeats_actionPerformed(ActionEvent e)
5506 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5510 * find the viewport amongst the tabs in this alignment frame and close that
5515 public boolean closeView(AlignViewportI av)
5519 this.closeMenuItem_actionPerformed(false);
5522 Component[] comp = tabbedPane.getComponents();
5523 for (int i = 0; comp != null && i < comp.length; i++)
5525 if (comp[i] instanceof AlignmentPanel)
5527 if (((AlignmentPanel) comp[i]).av == av)
5530 closeView((AlignmentPanel) comp[i]);
5538 protected void build_fetchdbmenu(JMenu webService)
5540 // Temporary hack - DBRef Fetcher always top level ws entry.
5541 // TODO We probably want to store a sequence database checklist in
5542 // preferences and have checkboxes.. rather than individual sources selected
5544 final JMenu rfetch = new JMenu(
5545 MessageManager.getString("action.fetch_db_references"));
5546 rfetch.setToolTipText(MessageManager
5547 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5548 webService.add(rfetch);
5550 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5551 MessageManager.getString("option.trim_retrieved_seqs"));
5552 trimrs.setToolTipText(MessageManager
5553 .getString("label.trim_retrieved_sequences"));
5554 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5555 trimrs.addActionListener(new ActionListener()
5558 public void actionPerformed(ActionEvent e)
5560 trimrs.setSelected(trimrs.isSelected());
5561 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5562 Boolean.valueOf(trimrs.isSelected()).toString());
5566 JMenuItem fetchr = new JMenuItem(
5567 MessageManager.getString("label.standard_databases"));
5568 fetchr.setToolTipText(MessageManager
5569 .getString("label.fetch_embl_uniprot"));
5570 fetchr.addActionListener(new ActionListener()
5574 public void actionPerformed(ActionEvent e)
5576 new Thread(new Runnable()
5582 new jalview.ws.DBRefFetcher(alignPanel.av
5583 .getSequenceSelection(), alignPanel.alignFrame)
5584 .fetchDBRefs(false);
5592 final AlignFrame me = this;
5593 new Thread(new Runnable()
5598 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5599 .getSequenceFetcherSingleton(me);
5600 javax.swing.SwingUtilities.invokeLater(new Runnable()
5605 String[] dbclasses = sf.getOrderedSupportedSources();
5606 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5607 // jalview.util.QuickSort.sort(otherdb, otherdb);
5608 List<DbSourceProxy> otherdb;
5609 JMenu dfetch = new JMenu();
5610 JMenu ifetch = new JMenu();
5611 JMenuItem fetchr = null;
5612 int comp = 0, icomp = 0, mcomp = 15;
5613 String mname = null;
5615 for (String dbclass : dbclasses)
5617 otherdb = sf.getSourceProxy(dbclass);
5618 // add a single entry for this class, or submenu allowing 'fetch
5620 if (otherdb == null || otherdb.size() < 1)
5624 // List<DbSourceProxy> dbs=otherdb;
5625 // otherdb=new ArrayList<DbSourceProxy>();
5626 // for (DbSourceProxy db:dbs)
5628 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5632 mname = "From " + dbclass;
5634 if (otherdb.size() == 1)
5636 final DbSourceProxy[] dassource = otherdb
5637 .toArray(new DbSourceProxy[0]);
5638 DbSourceProxy src = otherdb.get(0);
5639 fetchr = new JMenuItem(src.getDbSource());
5640 fetchr.addActionListener(new ActionListener()
5644 public void actionPerformed(ActionEvent e)
5646 new Thread(new Runnable()
5652 new jalview.ws.DBRefFetcher(alignPanel.av
5653 .getSequenceSelection(),
5654 alignPanel.alignFrame, dassource)
5655 .fetchDBRefs(false);
5661 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()})));
5667 final DbSourceProxy[] dassource = otherdb
5668 .toArray(new DbSourceProxy[0]);
5670 DbSourceProxy src = otherdb.get(0);
5671 fetchr = new JMenuItem(MessageManager.formatMessage(
5672 "label.fetch_all_param", new Object[]
5673 { src.getDbSource() }));
5674 fetchr.addActionListener(new ActionListener()
5677 public void actionPerformed(ActionEvent e)
5679 new Thread(new Runnable()
5685 new jalview.ws.DBRefFetcher(alignPanel.av
5686 .getSequenceSelection(),
5687 alignPanel.alignFrame, dassource)
5688 .fetchDBRefs(false);
5694 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new Object[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5697 // and then build the rest of the individual menus
5698 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()}));
5700 String imname = null;
5702 for (DbSourceProxy sproxy : otherdb)
5704 String dbname = sproxy.getDbName();
5705 String sname = dbname.length() > 5 ? dbname.substring(0,
5706 5) + "..." : dbname;
5707 String msname = dbname.length() > 10 ? dbname.substring(
5708 0, 10) + "..." : dbname;
5711 imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname});
5713 fetchr = new JMenuItem(msname);
5714 final DbSourceProxy[] dassrc =
5716 fetchr.addActionListener(new ActionListener()
5720 public void actionPerformed(ActionEvent e)
5722 new Thread(new Runnable()
5728 new jalview.ws.DBRefFetcher(alignPanel.av
5729 .getSequenceSelection(),
5730 alignPanel.alignFrame, dassrc)
5731 .fetchDBRefs(false);
5737 fetchr.setToolTipText("<html>"
5738 + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname}));
5741 if (++icomp >= mcomp || i == (otherdb.size()))
5743 ifetch.setText(MessageManager.formatMessage(
5744 "label.source_to_target", imname, sname));
5746 ifetch = new JMenu();
5754 if (comp >= mcomp || dbi >= (dbclasses.length))
5756 dfetch.setText(MessageManager.formatMessage(
5757 "label.source_to_target", mname, dbclass));
5759 dfetch = new JMenu();
5772 * Left justify the whole alignment.
5775 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5777 AlignmentI al = viewport.getAlignment();
5779 viewport.firePropertyChange("alignment", null, al);
5783 * Right justify the whole alignment.
5786 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5788 AlignmentI al = viewport.getAlignment();
5790 viewport.firePropertyChange("alignment", null, al);
5793 public void setShowSeqFeatures(boolean b)
5795 showSeqFeatures.setSelected(b);
5796 viewport.setShowSequenceFeatures(b);
5803 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5804 * awt.event.ActionEvent)
5807 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5809 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5810 alignPanel.paintAlignment(true);
5817 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5821 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5823 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5824 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5832 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5833 * .event.ActionEvent)
5836 protected void showGroupConservation_actionPerformed(ActionEvent e)
5838 viewport.setShowGroupConservation(showGroupConservation.getState());
5839 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5846 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5847 * .event.ActionEvent)
5850 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5852 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5853 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5860 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5861 * .event.ActionEvent)
5864 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5866 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5867 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5871 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5873 showSequenceLogo.setState(true);
5874 viewport.setShowSequenceLogo(true);
5875 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5876 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5880 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5882 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5889 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5890 * .event.ActionEvent)
5893 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5895 if (avc.makeGroupsFromSelection())
5897 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5898 alignPanel.updateAnnotation();
5899 alignPanel.paintAlignment(true);
5902 public void clearAlignmentSeqRep()
5904 // TODO refactor alignmentseqrep to controller
5905 if (viewport.getAlignment().hasSeqrep()) {
5906 viewport.getAlignment().setSeqrep(null);
5907 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5908 alignPanel.updateAnnotation();
5909 alignPanel.paintAlignment(true);
5914 protected void createGroup_actionPerformed(ActionEvent e)
5916 if (avc.createGroup())
5918 alignPanel.alignmentChanged();
5923 protected void unGroup_actionPerformed(ActionEvent e)
5927 alignPanel.alignmentChanged();
5932 * make the given alignmentPanel the currently selected tab
5934 * @param alignmentPanel
5936 public void setDisplayedView(AlignmentPanel alignmentPanel)
5938 if (!viewport.getSequenceSetId().equals(
5939 alignmentPanel.av.getSequenceSetId()))
5941 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5943 if (tabbedPane != null
5944 && tabbedPane.getTabCount() > 0
5945 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5946 .getSelectedIndex())
5948 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5953 * Action on selection of menu options to Show or Hide annotations.
5956 * @param forSequences
5957 * update sequence-related annotations
5958 * @param forAlignment
5959 * update non-sequence-related annotations
5962 protected void setAnnotationsVisibility(boolean visible,
5963 boolean forSequences, boolean forAlignment)
5965 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5966 .getAlignmentAnnotation())
5969 * don't display non-positional annotations on an alignment
5971 if (aa.annotations == null)
5975 boolean apply = (aa.sequenceRef == null && forAlignment)
5976 || (aa.sequenceRef != null && forSequences);
5979 aa.visible = visible;
5982 alignPanel.validateAnnotationDimensions(false);
5983 alignPanel.alignmentChanged();
5987 * Store selected annotation sort order for the view and repaint.
5990 protected void sortAnnotations_actionPerformed()
5992 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5994 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5995 alignPanel.paintAlignment(true);
6000 * @return alignment panels in this alignment frame
6002 public List<? extends AlignmentViewPanel> getAlignPanels()
6004 return alignPanels == null ? Arrays.asList(alignPanel)
6009 * Open a new alignment window, with the cDNA associated with this (protein)
6010 * alignment, aligned as is the protein.
6012 protected void viewAsCdna_actionPerformed()
6014 // TODO no longer a menu action - refactor as required
6015 final AlignmentI alignment = getViewport().getAlignment();
6016 Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
6017 if (mappings == null)
6021 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
6022 for (SequenceI aaSeq : alignment.getSequences()) {
6023 for (AlignedCodonFrame acf : mappings) {
6024 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
6028 * There is a cDNA mapping for this protein sequence - add to new
6029 * alignment. It will share the same dataset sequence as other mapped
6030 * cDNA (no new mappings need to be created).
6032 final Sequence newSeq = new Sequence(dnaSeq);
6033 newSeq.setDatasetSequence(dnaSeq);
6034 cdnaSeqs.add(newSeq);
6038 if (cdnaSeqs.size() == 0)
6040 // show a warning dialog no mapped cDNA
6043 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
6045 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
6046 AlignFrame.DEFAULT_HEIGHT);
6047 cdna.alignAs(alignment);
6048 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
6050 Desktop.addInternalFrame(alignFrame, newtitle,
6051 AlignFrame.DEFAULT_WIDTH,
6052 AlignFrame.DEFAULT_HEIGHT);
6056 * Set visibility of dna/protein complement view (available when shown in a
6062 protected void showComplement_actionPerformed(boolean show)
6064 SplitContainerI sf = getSplitViewContainer();
6066 sf.setComplementVisible(this, show);
6070 public class ExportData
6072 private AlignmentI alignment;
6074 private String[] omitHidden;
6076 private int[] startEnd;
6078 public ExportData(AlignmentI align, String[] ommit, int[] startEnd)
6080 this.alignment = align;
6081 this.omitHidden = ommit;
6082 this.startEnd = startEnd;
6085 public AlignmentI getAlignment()
6090 public void setAlignment(AlignmentI alignment)
6092 this.alignment = alignment;
6095 public String[] getOmitHidden()
6100 public void setOmitHidden(String[] omitHidden)
6102 this.omitHidden = omitHidden;
6105 public int[] getStartEndPostions()
6110 public void setStartEndPostions(int[] startEnd)
6112 this.startEnd = startEnd;
6117 public void hideColumns(List<int[]> colsToHide)
6119 for (int[] colRange : colsToHide)
6121 viewport.hideColumns(colRange[0], colRange[1]);
6127 public void syncHiddenSequences()
6129 AlignmentI al = viewport.getAlignment();
6130 HiddenSequences hiddenSeqs = al.getHiddenSequences();
6131 boolean hasHiddenRows = false;
6132 for (SequenceI seq : al.getSequencesArray())
6136 hiddenSeqs.hideSequence(seq);
6137 hasHiddenRows = true;
6140 viewport.setHasHiddenRows(hasHiddenRows);
6141 firePropertyChange("alignment", null, al.getSequences());
6145 class PrintThread extends Thread
6149 public PrintThread(AlignmentPanel ap)
6154 static PageFormat pf;
6159 PrinterJob printJob = PrinterJob.getPrinterJob();
6163 printJob.setPrintable(ap, pf);
6167 printJob.setPrintable(ap);
6170 if (printJob.printDialog())
6175 } catch (Exception PrintException)
6177 PrintException.printStackTrace();