2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.ScoreModelI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenSequences;
57 import jalview.datamodel.PDBEntry;
58 import jalview.datamodel.SeqCigar;
59 import jalview.datamodel.Sequence;
60 import jalview.datamodel.SequenceGroup;
61 import jalview.datamodel.SequenceI;
62 import jalview.gui.ColourMenuHelper.ColourChangeListener;
63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
64 import jalview.io.AlignmentProperties;
65 import jalview.io.AnnotationFile;
66 import jalview.io.BioJsHTMLOutput;
67 import jalview.io.DataSourceType;
68 import jalview.io.FileFormat;
69 import jalview.io.FileFormatI;
70 import jalview.io.FileFormats;
71 import jalview.io.FileLoader;
72 import jalview.io.FormatAdapter;
73 import jalview.io.HtmlSvgOutput;
74 import jalview.io.IdentifyFile;
75 import jalview.io.JPredFile;
76 import jalview.io.JalviewFileChooser;
77 import jalview.io.JalviewFileView;
78 import jalview.io.JnetAnnotationMaker;
79 import jalview.io.NewickFile;
80 import jalview.io.TCoffeeScoreFile;
81 import jalview.jbgui.GAlignFrame;
82 import jalview.schemes.ColourSchemeI;
83 import jalview.schemes.ColourSchemes;
84 import jalview.schemes.ResidueColourScheme;
85 import jalview.schemes.ResidueProperties;
86 import jalview.schemes.TCoffeeColourScheme;
87 import jalview.util.MessageManager;
88 import jalview.viewmodel.AlignmentViewport;
89 import jalview.viewmodel.ViewportRanges;
90 import jalview.ws.DBRefFetcher;
91 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
92 import jalview.ws.jws1.Discoverer;
93 import jalview.ws.jws2.Jws2Discoverer;
94 import jalview.ws.jws2.jabaws2.Jws2Instance;
95 import jalview.ws.seqfetcher.DbSourceProxy;
97 import java.awt.BorderLayout;
98 import java.awt.Component;
99 import java.awt.Rectangle;
100 import java.awt.Toolkit;
101 import java.awt.datatransfer.Clipboard;
102 import java.awt.datatransfer.DataFlavor;
103 import java.awt.datatransfer.StringSelection;
104 import java.awt.datatransfer.Transferable;
105 import java.awt.dnd.DnDConstants;
106 import java.awt.dnd.DropTargetDragEvent;
107 import java.awt.dnd.DropTargetDropEvent;
108 import java.awt.dnd.DropTargetEvent;
109 import java.awt.dnd.DropTargetListener;
110 import java.awt.event.ActionEvent;
111 import java.awt.event.ActionListener;
112 import java.awt.event.FocusAdapter;
113 import java.awt.event.FocusEvent;
114 import java.awt.event.ItemEvent;
115 import java.awt.event.ItemListener;
116 import java.awt.event.KeyAdapter;
117 import java.awt.event.KeyEvent;
118 import java.awt.event.MouseEvent;
119 import java.awt.print.PageFormat;
120 import java.awt.print.PrinterJob;
121 import java.beans.PropertyChangeEvent;
123 import java.io.FileWriter;
124 import java.io.PrintWriter;
126 import java.util.ArrayList;
127 import java.util.Arrays;
128 import java.util.Deque;
129 import java.util.Enumeration;
130 import java.util.Hashtable;
131 import java.util.List;
132 import java.util.Vector;
134 import javax.swing.JCheckBoxMenuItem;
135 import javax.swing.JEditorPane;
136 import javax.swing.JInternalFrame;
137 import javax.swing.JLayeredPane;
138 import javax.swing.JMenu;
139 import javax.swing.JMenuItem;
140 import javax.swing.JScrollPane;
141 import javax.swing.SwingUtilities;
147 * @version $Revision$
149 public class AlignFrame extends GAlignFrame implements DropTargetListener,
150 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
153 public static final int DEFAULT_WIDTH = 700;
155 public static final int DEFAULT_HEIGHT = 500;
158 * The currently displayed panel (selected tabbed view if more than one)
160 public AlignmentPanel alignPanel;
162 AlignViewport viewport;
164 ViewportRanges vpRanges;
166 public AlignViewControllerI avc;
168 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
171 * Last format used to load or save alignments in this window
173 FileFormatI currentFileFormat = null;
176 * Current filename for this alignment
178 String fileName = null;
181 * Creates a new AlignFrame object with specific width and height.
187 public AlignFrame(AlignmentI al, int width, int height)
189 this(al, null, width, height);
193 * Creates a new AlignFrame object with specific width, height and
199 * @param sequenceSetId
201 public AlignFrame(AlignmentI al, int width, int height,
202 String sequenceSetId)
204 this(al, null, width, height, sequenceSetId);
208 * Creates a new AlignFrame object with specific width, height and
214 * @param sequenceSetId
217 public AlignFrame(AlignmentI al, int width, int height,
218 String sequenceSetId, String viewId)
220 this(al, null, width, height, sequenceSetId, viewId);
224 * new alignment window with hidden columns
228 * @param hiddenColumns
229 * ColumnSelection or null
231 * Width of alignment frame
235 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
236 int width, int height)
238 this(al, hiddenColumns, width, height, null);
242 * Create alignment frame for al with hiddenColumns, a specific width and
243 * height, and specific sequenceId
246 * @param hiddenColumns
249 * @param sequenceSetId
252 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
253 int width, int height, String sequenceSetId)
255 this(al, hiddenColumns, width, height, sequenceSetId, null);
259 * Create alignment frame for al with hiddenColumns, a specific width and
260 * height, and specific sequenceId
263 * @param hiddenColumns
266 * @param sequenceSetId
271 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
272 int width, int height, String sequenceSetId, String viewId)
274 setSize(width, height);
276 if (al.getDataset() == null)
281 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
283 alignPanel = new AlignmentPanel(this, viewport);
285 addAlignmentPanel(alignPanel, true);
289 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
290 ColumnSelection hiddenColumns, int width, int height)
292 setSize(width, height);
294 if (al.getDataset() == null)
299 viewport = new AlignViewport(al, hiddenColumns);
301 if (hiddenSeqs != null && hiddenSeqs.length > 0)
303 viewport.hideSequence(hiddenSeqs);
305 alignPanel = new AlignmentPanel(this, viewport);
306 addAlignmentPanel(alignPanel, true);
311 * Make a new AlignFrame from existing alignmentPanels
318 public AlignFrame(AlignmentPanel ap)
322 addAlignmentPanel(ap, false);
327 * initalise the alignframe from the underlying viewport data and the
332 if (!Jalview.isHeadlessMode())
334 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
337 vpRanges = viewport.getRanges();
338 avc = new jalview.controller.AlignViewController(this, viewport,
340 if (viewport.getAlignmentConservationAnnotation() == null)
342 // BLOSUM62Colour.setEnabled(false);
343 conservationMenuItem.setEnabled(false);
344 modifyConservation.setEnabled(false);
345 // PIDColour.setEnabled(false);
346 // abovePIDThreshold.setEnabled(false);
347 // modifyPID.setEnabled(false);
350 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
353 if (sortby.equals("Id"))
355 sortIDMenuItem_actionPerformed(null);
357 else if (sortby.equals("Pairwise Identity"))
359 sortPairwiseMenuItem_actionPerformed(null);
363 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
365 setMenusFromViewport(viewport);
366 buildSortByAnnotationScoresMenu();
370 if (Desktop.desktop != null)
372 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
373 addServiceListeners();
377 if (viewport.getWrapAlignment())
379 wrapMenuItem_actionPerformed(null);
382 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
384 this.overviewMenuItem_actionPerformed(null);
389 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
390 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
391 final String menuLabel = MessageManager
392 .getString("label.copy_format_from");
393 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
394 new ViewSetProvider()
398 public AlignmentPanel[] getAllAlignmentPanels()
401 origview.add(alignPanel);
402 // make an array of all alignment panels except for this one
403 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
404 Arrays.asList(Desktop.getAlignmentPanels(null)));
405 aps.remove(AlignFrame.this.alignPanel);
406 return aps.toArray(new AlignmentPanel[aps.size()]);
408 }, selviews, new ItemListener()
412 public void itemStateChanged(ItemEvent e)
414 if (origview.size() > 0)
416 final AlignmentPanel ap = origview.get(0);
419 * Copy the ViewStyle of the selected panel to 'this one'.
420 * Don't change value of 'scaleProteinAsCdna' unless copying
423 ViewStyleI vs = selviews.get(0).getAlignViewport()
425 boolean fromSplitFrame = selviews.get(0)
426 .getAlignViewport().getCodingComplement() != null;
429 vs.setScaleProteinAsCdna(ap.getAlignViewport()
430 .getViewStyle().isScaleProteinAsCdna());
432 ap.getAlignViewport().setViewStyle(vs);
435 * Also rescale ViewStyle of SplitFrame complement if there is
436 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
437 * the whole ViewStyle (allow cDNA protein to have different
440 AlignViewportI complement = ap.getAlignViewport()
441 .getCodingComplement();
442 if (complement != null && vs.isScaleProteinAsCdna())
444 AlignFrame af = Desktop.getAlignFrameFor(complement);
445 ((SplitFrame) af.getSplitViewContainer())
447 af.setMenusForViewport();
451 ap.setSelected(true);
452 ap.alignFrame.setMenusForViewport();
457 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
458 .indexOf("devel") > -1
459 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
460 .indexOf("test") > -1)
462 formatMenu.add(vsel);
464 addFocusListener(new FocusAdapter()
467 public void focusGained(FocusEvent e)
469 Jalview.setCurrentAlignFrame(AlignFrame.this);
476 * Change the filename and format for the alignment, and enable the 'reload'
477 * button functionality.
484 public void setFileName(String file, FileFormatI format)
487 setFileFormat(format);
488 reload.setEnabled(true);
492 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
495 void addKeyListener()
497 addKeyListener(new KeyAdapter()
500 public void keyPressed(KeyEvent evt)
502 if (viewport.cursorMode
503 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
504 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
505 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
506 && Character.isDigit(evt.getKeyChar()))
508 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
511 switch (evt.getKeyCode())
514 case 27: // escape key
515 deselectAllSequenceMenuItem_actionPerformed(null);
519 case KeyEvent.VK_DOWN:
520 if (evt.isAltDown() || !viewport.cursorMode)
522 moveSelectedSequences(false);
524 if (viewport.cursorMode)
526 alignPanel.getSeqPanel().moveCursor(0, 1);
531 if (evt.isAltDown() || !viewport.cursorMode)
533 moveSelectedSequences(true);
535 if (viewport.cursorMode)
537 alignPanel.getSeqPanel().moveCursor(0, -1);
542 case KeyEvent.VK_LEFT:
543 if (evt.isAltDown() || !viewport.cursorMode)
545 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
549 alignPanel.getSeqPanel().moveCursor(-1, 0);
554 case KeyEvent.VK_RIGHT:
555 if (evt.isAltDown() || !viewport.cursorMode)
557 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
561 alignPanel.getSeqPanel().moveCursor(1, 0);
565 case KeyEvent.VK_SPACE:
566 if (viewport.cursorMode)
568 alignPanel.getSeqPanel().insertGapAtCursor(
569 evt.isControlDown() || evt.isShiftDown()
574 // case KeyEvent.VK_A:
575 // if (viewport.cursorMode)
577 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
578 // //System.out.println("A");
582 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
583 * System.out.println("closing bracket"); } break;
585 case KeyEvent.VK_DELETE:
586 case KeyEvent.VK_BACK_SPACE:
587 if (!viewport.cursorMode)
589 cut_actionPerformed(null);
593 alignPanel.getSeqPanel().deleteGapAtCursor(
594 evt.isControlDown() || evt.isShiftDown()
601 if (viewport.cursorMode)
603 alignPanel.getSeqPanel().setCursorRow();
607 if (viewport.cursorMode && !evt.isControlDown())
609 alignPanel.getSeqPanel().setCursorColumn();
613 if (viewport.cursorMode)
615 alignPanel.getSeqPanel().setCursorPosition();
619 case KeyEvent.VK_ENTER:
620 case KeyEvent.VK_COMMA:
621 if (viewport.cursorMode)
623 alignPanel.getSeqPanel().setCursorRowAndColumn();
628 if (viewport.cursorMode)
630 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
634 if (viewport.cursorMode)
636 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
641 viewport.cursorMode = !viewport.cursorMode;
642 statusBar.setText(MessageManager.formatMessage(
643 "label.keyboard_editing_mode",
644 new String[] { (viewport.cursorMode ? "on" : "off") }));
645 if (viewport.cursorMode)
647 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
649 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
652 alignPanel.getSeqPanel().seqCanvas.repaint();
658 Help.showHelpWindow();
659 } catch (Exception ex)
661 ex.printStackTrace();
666 boolean toggleSeqs = !evt.isControlDown();
667 boolean toggleCols = !evt.isShiftDown();
668 toggleHiddenRegions(toggleSeqs, toggleCols);
673 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
674 boolean modifyExisting = true; // always modify, don't clear
675 // evt.isShiftDown();
676 boolean invertHighlighted = evt.isAltDown();
677 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
681 case KeyEvent.VK_PAGE_UP:
682 if (viewport.getWrapAlignment())
684 alignPanel.scrollUp(true);
688 alignPanel.setScrollValues(vpRanges.getStartRes(),
689 2 * vpRanges.getStartSeq() - vpRanges.getEndSeq());
692 case KeyEvent.VK_PAGE_DOWN:
693 if (viewport.getWrapAlignment())
695 alignPanel.scrollUp(false);
699 alignPanel.setScrollValues(vpRanges.getStartRes(),
700 vpRanges.getEndSeq());
707 public void keyReleased(KeyEvent evt)
709 switch (evt.getKeyCode())
711 case KeyEvent.VK_LEFT:
712 if (evt.isAltDown() || !viewport.cursorMode)
714 viewport.firePropertyChange("alignment", null, viewport
715 .getAlignment().getSequences());
719 case KeyEvent.VK_RIGHT:
720 if (evt.isAltDown() || !viewport.cursorMode)
722 viewport.firePropertyChange("alignment", null, viewport
723 .getAlignment().getSequences());
731 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
733 ap.alignFrame = this;
734 avc = new jalview.controller.AlignViewController(this, viewport,
739 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
741 int aSize = alignPanels.size();
743 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
745 if (aSize == 1 && ap.av.viewName == null)
747 this.getContentPane().add(ap, BorderLayout.CENTER);
753 setInitialTabVisible();
756 expandViews.setEnabled(true);
757 gatherViews.setEnabled(true);
758 tabbedPane.addTab(ap.av.viewName, ap);
760 ap.setVisible(false);
765 if (ap.av.isPadGaps())
767 ap.av.getAlignment().padGaps();
769 ap.av.updateConservation(ap);
770 ap.av.updateConsensus(ap);
771 ap.av.updateStrucConsensus(ap);
775 public void setInitialTabVisible()
777 expandViews.setEnabled(true);
778 gatherViews.setEnabled(true);
779 tabbedPane.setVisible(true);
780 AlignmentPanel first = alignPanels.get(0);
781 tabbedPane.addTab(first.av.viewName, first);
782 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
785 public AlignViewport getViewport()
790 /* Set up intrinsic listeners for dynamically generated GUI bits. */
791 private void addServiceListeners()
793 final java.beans.PropertyChangeListener thisListener;
794 Desktop.instance.addJalviewPropertyChangeListener("services",
795 thisListener = new java.beans.PropertyChangeListener()
798 public void propertyChange(PropertyChangeEvent evt)
800 // // System.out.println("Discoverer property change.");
801 // if (evt.getPropertyName().equals("services"))
803 SwingUtilities.invokeLater(new Runnable()
810 .println("Rebuild WS Menu for service change");
811 BuildWebServiceMenu();
818 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
821 public void internalFrameClosed(
822 javax.swing.event.InternalFrameEvent evt)
824 // System.out.println("deregistering discoverer listener");
825 Desktop.instance.removeJalviewPropertyChangeListener("services",
827 closeMenuItem_actionPerformed(true);
830 // Finally, build the menu once to get current service state
831 new Thread(new Runnable()
836 BuildWebServiceMenu();
842 * Configure menu items that vary according to whether the alignment is
843 * nucleotide or protein
845 public void setGUINucleotide()
847 AlignmentI al = getViewport().getAlignment();
848 boolean nucleotide = al.isNucleotide();
850 showTranslation.setVisible(nucleotide);
851 showReverse.setVisible(nucleotide);
852 showReverseComplement.setVisible(nucleotide);
853 conservationMenuItem.setEnabled(!nucleotide);
854 modifyConservation.setEnabled(!nucleotide
855 && conservationMenuItem.isSelected());
856 showGroupConservation.setEnabled(!nucleotide);
858 showComplementMenuItem.setText(nucleotide ? MessageManager
859 .getString("label.protein") : MessageManager
860 .getString("label.nucleotide"));
864 * set up menus for the current viewport. This may be called after any
865 * operation that affects the data in the current view (selection changed,
866 * etc) to update the menus to reflect the new state.
869 public void setMenusForViewport()
871 setMenusFromViewport(viewport);
875 * Need to call this method when tabs are selected for multiple views, or when
876 * loading from Jalview2XML.java
881 void setMenusFromViewport(AlignViewport av)
883 padGapsMenuitem.setSelected(av.isPadGaps());
884 colourTextMenuItem.setSelected(av.isShowColourText());
885 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
886 modifyPID.setEnabled(abovePIDThreshold.isSelected());
887 conservationMenuItem.setSelected(av.getConservationSelected());
888 modifyConservation.setEnabled(conservationMenuItem.isSelected());
889 seqLimits.setSelected(av.getShowJVSuffix());
890 idRightAlign.setSelected(av.isRightAlignIds());
891 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
892 renderGapsMenuItem.setSelected(av.isRenderGaps());
893 wrapMenuItem.setSelected(av.getWrapAlignment());
894 scaleAbove.setVisible(av.getWrapAlignment());
895 scaleLeft.setVisible(av.getWrapAlignment());
896 scaleRight.setVisible(av.getWrapAlignment());
897 annotationPanelMenuItem.setState(av.isShowAnnotation());
899 * Show/hide annotations only enabled if annotation panel is shown
901 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
902 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
903 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
904 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
905 viewBoxesMenuItem.setSelected(av.getShowBoxes());
906 viewTextMenuItem.setSelected(av.getShowText());
907 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
908 showGroupConsensus.setSelected(av.isShowGroupConsensus());
909 showGroupConservation.setSelected(av.isShowGroupConservation());
910 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
911 showSequenceLogo.setSelected(av.isShowSequenceLogo());
912 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
914 ColourMenuHelper.setColourSelected(colourMenu,
915 av.getGlobalColourScheme());
917 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
918 hiddenMarkers.setState(av.getShowHiddenMarkers());
919 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
920 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
921 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
922 autoCalculate.setSelected(av.autoCalculateConsensus);
923 sortByTree.setSelected(av.sortByTree);
924 listenToViewSelections.setSelected(av.followSelection);
926 showProducts.setEnabled(canShowProducts());
927 setGroovyEnabled(Desktop.getGroovyConsole() != null);
933 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
937 public void setGroovyEnabled(boolean b)
939 runGroovy.setEnabled(b);
942 private IProgressIndicator progressBar;
947 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
950 public void setProgressBar(String message, long id)
952 progressBar.setProgressBar(message, id);
956 public void registerHandler(final long id,
957 final IProgressIndicatorHandler handler)
959 progressBar.registerHandler(id, handler);
964 * @return true if any progress bars are still active
967 public boolean operationInProgress()
969 return progressBar.operationInProgress();
973 public void setStatus(String text)
975 statusBar.setText(text);
979 * Added so Castor Mapping file can obtain Jalview Version
981 public String getVersion()
983 return jalview.bin.Cache.getProperty("VERSION");
986 public FeatureRenderer getFeatureRenderer()
988 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
992 public void fetchSequence_actionPerformed(ActionEvent e)
994 new jalview.gui.SequenceFetcher(this);
998 public void addFromFile_actionPerformed(ActionEvent e)
1000 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1004 public void reload_actionPerformed(ActionEvent e)
1006 if (fileName != null)
1008 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1009 // originating file's format
1010 // TODO: work out how to recover feature settings for correct view(s) when
1011 // file is reloaded.
1012 if (FileFormat.Jalview.equals(currentFileFormat))
1014 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1015 for (int i = 0; i < frames.length; i++)
1017 if (frames[i] instanceof AlignFrame && frames[i] != this
1018 && ((AlignFrame) frames[i]).fileName != null
1019 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1023 frames[i].setSelected(true);
1024 Desktop.instance.closeAssociatedWindows();
1025 } catch (java.beans.PropertyVetoException ex)
1031 Desktop.instance.closeAssociatedWindows();
1033 FileLoader loader = new FileLoader();
1034 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1035 : DataSourceType.FILE;
1036 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1040 Rectangle bounds = this.getBounds();
1042 FileLoader loader = new FileLoader();
1043 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1044 : DataSourceType.FILE;
1045 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1046 protocol, currentFileFormat);
1048 newframe.setBounds(bounds);
1049 if (featureSettings != null && featureSettings.isShowing())
1051 final Rectangle fspos = featureSettings.frame.getBounds();
1052 // TODO: need a 'show feature settings' function that takes bounds -
1053 // need to refactor Desktop.addFrame
1054 newframe.featureSettings_actionPerformed(null);
1055 final FeatureSettings nfs = newframe.featureSettings;
1056 SwingUtilities.invokeLater(new Runnable()
1061 nfs.frame.setBounds(fspos);
1064 this.featureSettings.close();
1065 this.featureSettings = null;
1067 this.closeMenuItem_actionPerformed(true);
1073 public void addFromText_actionPerformed(ActionEvent e)
1075 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1080 public void addFromURL_actionPerformed(ActionEvent e)
1082 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1086 public void save_actionPerformed(ActionEvent e)
1088 if (fileName == null || (currentFileFormat == null)
1089 || fileName.startsWith("http"))
1091 saveAs_actionPerformed(null);
1095 saveAlignment(fileName, currentFileFormat);
1106 public void saveAs_actionPerformed(ActionEvent e)
1108 String format = currentFileFormat == null ? null : currentFileFormat
1110 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1111 Cache.getProperty("LAST_DIRECTORY"), format);
1113 chooser.setFileView(new JalviewFileView());
1114 chooser.setDialogTitle(MessageManager
1115 .getString("label.save_alignment_to_file"));
1116 chooser.setToolTipText(MessageManager.getString("action.save"));
1118 int value = chooser.showSaveDialog(this);
1120 if (value == JalviewFileChooser.APPROVE_OPTION)
1122 currentFileFormat = chooser.getSelectedFormat();
1123 while (currentFileFormat == null)
1126 .showInternalMessageDialog(
1129 .getString("label.select_file_format_before_saving"),
1131 .getString("label.file_format_not_specified"),
1132 JvOptionPane.WARNING_MESSAGE);
1133 currentFileFormat = chooser.getSelectedFormat();
1134 value = chooser.showSaveDialog(this);
1135 if (value != JalviewFileChooser.APPROVE_OPTION)
1141 fileName = chooser.getSelectedFile().getPath();
1143 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1145 Cache.setProperty("LAST_DIRECTORY", fileName);
1146 saveAlignment(fileName, currentFileFormat);
1150 public boolean saveAlignment(String file, FileFormatI format)
1152 boolean success = true;
1154 if (FileFormat.Jalview.equals(format))
1156 String shortName = title;
1158 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1160 shortName = shortName.substring(shortName
1161 .lastIndexOf(java.io.File.separatorChar) + 1);
1164 success = new Jalview2XML().saveAlignment(this, file, shortName);
1166 statusBar.setText(MessageManager.formatMessage(
1167 "label.successfully_saved_to_file_in_format", new Object[] {
1168 fileName, format }));
1173 AlignmentExportData exportData = getAlignmentForExport(format,
1175 if (exportData.getSettings().isCancelled())
1179 FormatAdapter f = new FormatAdapter(alignPanel,
1180 exportData.getSettings());
1181 String output = f.formatSequences(
1183 exportData.getAlignment(), // class cast exceptions will
1184 // occur in the distant future
1185 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1186 f.getCacheSuffixDefault(format),
1187 viewport.getColumnSelection());
1197 PrintWriter out = new PrintWriter(new FileWriter(file));
1201 this.setTitle(file);
1202 statusBar.setText(MessageManager.formatMessage(
1203 "label.successfully_saved_to_file_in_format",
1204 new Object[] { fileName, format.getName() }));
1205 } catch (Exception ex)
1208 ex.printStackTrace();
1215 JvOptionPane.showInternalMessageDialog(this, MessageManager
1216 .formatMessage("label.couldnt_save_file",
1217 new Object[] { fileName }), MessageManager
1218 .getString("label.error_saving_file"),
1219 JvOptionPane.WARNING_MESSAGE);
1225 private void warningMessage(String warning, String title)
1227 if (new jalview.util.Platform().isHeadless())
1229 System.err.println("Warning: " + title + "\nWarning: " + warning);
1234 JvOptionPane.showInternalMessageDialog(this, warning, title,
1235 JvOptionPane.WARNING_MESSAGE);
1247 protected void outputText_actionPerformed(ActionEvent e)
1249 FileFormatI fileFormat = FileFormats.getInstance().forName(
1250 e.getActionCommand());
1251 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1253 if (exportData.getSettings().isCancelled())
1257 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1258 cap.setForInput(null);
1261 FileFormatI format = fileFormat;
1262 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1263 .formatSequences(format, exportData.getAlignment(),
1264 exportData.getOmitHidden(),
1265 exportData.getStartEndPostions(),
1266 viewport.getColumnSelection()));
1267 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1268 "label.alignment_output_command",
1269 new Object[] { e.getActionCommand() }), 600, 500);
1270 } catch (OutOfMemoryError oom)
1272 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1278 public static AlignmentExportData getAlignmentForExport(
1279 FileFormatI format, AlignViewportI viewport,
1280 AlignExportSettingI exportSettings)
1282 AlignmentI alignmentToExport = null;
1283 AlignExportSettingI settings = exportSettings;
1284 String[] omitHidden = null;
1286 HiddenSequences hiddenSeqs = viewport.getAlignment()
1287 .getHiddenSequences();
1289 alignmentToExport = viewport.getAlignment();
1291 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1292 if (settings == null)
1294 settings = new AlignExportSettings(hasHiddenSeqs,
1295 viewport.hasHiddenColumns(), format);
1297 // settings.isExportAnnotations();
1299 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1301 omitHidden = viewport.getViewAsString(false,
1302 settings.isExportHiddenSequences());
1305 int[] alignmentStartEnd = new int[2];
1306 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1308 alignmentToExport = hiddenSeqs.getFullAlignment();
1312 alignmentToExport = viewport.getAlignment();
1314 alignmentStartEnd = alignmentToExport
1315 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1316 .getHiddenColumns());
1317 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1318 omitHidden, alignmentStartEnd, settings);
1329 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1331 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1332 htmlSVG.exportHTML(null);
1336 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1338 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1339 bjs.exportHTML(null);
1342 public void createImageMap(File file, String image)
1344 alignPanel.makePNGImageMap(file, image);
1354 public void createPNG(File f)
1356 alignPanel.makePNG(f);
1366 public void createEPS(File f)
1368 alignPanel.makeEPS(f);
1372 public void createSVG(File f)
1374 alignPanel.makeSVG(f);
1378 public void pageSetup_actionPerformed(ActionEvent e)
1380 PrinterJob printJob = PrinterJob.getPrinterJob();
1381 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1391 public void printMenuItem_actionPerformed(ActionEvent e)
1393 // Putting in a thread avoids Swing painting problems
1394 PrintThread thread = new PrintThread(alignPanel);
1399 public void exportFeatures_actionPerformed(ActionEvent e)
1401 new AnnotationExporter().exportFeatures(alignPanel);
1405 public void exportAnnotations_actionPerformed(ActionEvent e)
1407 new AnnotationExporter().exportAnnotations(alignPanel);
1411 public void associatedData_actionPerformed(ActionEvent e)
1413 // Pick the tree file
1414 JalviewFileChooser chooser = new JalviewFileChooser(
1415 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1416 chooser.setFileView(new JalviewFileView());
1417 chooser.setDialogTitle(MessageManager
1418 .getString("label.load_jalview_annotations"));
1419 chooser.setToolTipText(MessageManager
1420 .getString("label.load_jalview_annotations"));
1422 int value = chooser.showOpenDialog(null);
1424 if (value == JalviewFileChooser.APPROVE_OPTION)
1426 String choice = chooser.getSelectedFile().getPath();
1427 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1428 loadJalviewDataFile(choice, null, null, null);
1434 * Close the current view or all views in the alignment frame. If the frame
1435 * only contains one view then the alignment will be removed from memory.
1437 * @param closeAllTabs
1440 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1442 if (alignPanels != null && alignPanels.size() < 2)
1444 closeAllTabs = true;
1449 if (alignPanels != null)
1453 if (this.isClosed())
1455 // really close all the windows - otherwise wait till
1456 // setClosed(true) is called
1457 for (int i = 0; i < alignPanels.size(); i++)
1459 AlignmentPanel ap = alignPanels.get(i);
1466 closeView(alignPanel);
1473 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1474 * be called recursively, with the frame now in 'closed' state
1476 this.setClosed(true);
1478 } catch (Exception ex)
1480 ex.printStackTrace();
1485 * Close the specified panel and close up tabs appropriately.
1487 * @param panelToClose
1489 public void closeView(AlignmentPanel panelToClose)
1491 int index = tabbedPane.getSelectedIndex();
1492 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1493 alignPanels.remove(panelToClose);
1494 panelToClose.closePanel();
1495 panelToClose = null;
1497 tabbedPane.removeTabAt(closedindex);
1498 tabbedPane.validate();
1500 if (index > closedindex || index == tabbedPane.getTabCount())
1502 // modify currently selected tab index if necessary.
1506 this.tabSelectionChanged(index);
1512 void updateEditMenuBar()
1515 if (viewport.getHistoryList().size() > 0)
1517 undoMenuItem.setEnabled(true);
1518 CommandI command = viewport.getHistoryList().peek();
1519 undoMenuItem.setText(MessageManager.formatMessage(
1520 "label.undo_command",
1521 new Object[] { command.getDescription() }));
1525 undoMenuItem.setEnabled(false);
1526 undoMenuItem.setText(MessageManager.getString("action.undo"));
1529 if (viewport.getRedoList().size() > 0)
1531 redoMenuItem.setEnabled(true);
1533 CommandI command = viewport.getRedoList().peek();
1534 redoMenuItem.setText(MessageManager.formatMessage(
1535 "label.redo_command",
1536 new Object[] { command.getDescription() }));
1540 redoMenuItem.setEnabled(false);
1541 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[] { viewport.getAlignment() };
1591 protected void undoMenuItem_actionPerformed(ActionEvent e)
1593 if (viewport.getHistoryList().isEmpty())
1597 CommandI command = viewport.getHistoryList().pop();
1598 viewport.addToRedoList(command);
1599 command.undoCommand(getViewAlignments());
1601 AlignmentViewport originalSource = getOriginatingSource(command);
1602 updateEditMenuBar();
1604 if (originalSource != null)
1606 if (originalSource != viewport)
1609 .warn("Implementation worry: mismatch of viewport origin for undo");
1611 originalSource.updateHiddenColumns();
1612 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1614 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1615 // viewport.getColumnSelection()
1616 // .getHiddenColumns().size() > 0);
1617 originalSource.firePropertyChange("alignment", null, originalSource
1618 .getAlignment().getSequences());
1629 protected void redoMenuItem_actionPerformed(ActionEvent e)
1631 if (viewport.getRedoList().size() < 1)
1636 CommandI command = viewport.getRedoList().pop();
1637 viewport.addToHistoryList(command);
1638 command.doCommand(getViewAlignments());
1640 AlignmentViewport originalSource = getOriginatingSource(command);
1641 updateEditMenuBar();
1643 if (originalSource != null)
1646 if (originalSource != viewport)
1649 .warn("Implementation worry: mismatch of viewport origin for redo");
1651 originalSource.updateHiddenColumns();
1652 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1654 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1655 // viewport.getColumnSelection()
1656 // .getHiddenColumns().size() > 0);
1657 originalSource.firePropertyChange("alignment", null, originalSource
1658 .getAlignment().getSequences());
1662 AlignmentViewport getOriginatingSource(CommandI command)
1664 AlignmentViewport originalSource = null;
1665 // For sequence removal and addition, we need to fire
1666 // the property change event FROM the viewport where the
1667 // original alignment was altered
1668 AlignmentI al = null;
1669 if (command instanceof EditCommand)
1671 EditCommand editCommand = (EditCommand) command;
1672 al = editCommand.getAlignment();
1673 List<Component> comps = PaintRefresher.components.get(viewport
1674 .getSequenceSetId());
1676 for (Component comp : comps)
1678 if (comp instanceof AlignmentPanel)
1680 if (al == ((AlignmentPanel) comp).av.getAlignment())
1682 originalSource = ((AlignmentPanel) comp).av;
1689 if (originalSource == null)
1691 // The original view is closed, we must validate
1692 // the current view against the closed view first
1695 PaintRefresher.validateSequences(al, viewport.getAlignment());
1698 originalSource = viewport;
1701 return originalSource;
1710 public void moveSelectedSequences(boolean up)
1712 SequenceGroup sg = viewport.getSelectionGroup();
1718 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1719 viewport.getHiddenRepSequences(), up);
1720 alignPanel.paintAlignment(true);
1723 synchronized void slideSequences(boolean right, int size)
1725 List<SequenceI> sg = new ArrayList<SequenceI>();
1726 if (viewport.cursorMode)
1728 sg.add(viewport.getAlignment().getSequenceAt(
1729 alignPanel.getSeqPanel().seqCanvas.cursorY));
1731 else if (viewport.getSelectionGroup() != null
1732 && viewport.getSelectionGroup().getSize() != viewport
1733 .getAlignment().getHeight())
1735 sg = viewport.getSelectionGroup().getSequences(
1736 viewport.getHiddenRepSequences());
1744 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1746 for (SequenceI seq : viewport.getAlignment().getSequences())
1748 if (!sg.contains(seq))
1750 invertGroup.add(seq);
1754 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1756 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1757 for (int i = 0; i < invertGroup.size(); i++)
1759 seqs2[i] = invertGroup.get(i);
1762 SlideSequencesCommand ssc;
1765 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1766 size, viewport.getGapCharacter());
1770 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1771 size, viewport.getGapCharacter());
1774 int groupAdjustment = 0;
1775 if (ssc.getGapsInsertedBegin() && right)
1777 if (viewport.cursorMode)
1779 alignPanel.getSeqPanel().moveCursor(size, 0);
1783 groupAdjustment = size;
1786 else if (!ssc.getGapsInsertedBegin() && !right)
1788 if (viewport.cursorMode)
1790 alignPanel.getSeqPanel().moveCursor(-size, 0);
1794 groupAdjustment = -size;
1798 if (groupAdjustment != 0)
1800 viewport.getSelectionGroup().setStartRes(
1801 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1802 viewport.getSelectionGroup().setEndRes(
1803 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1807 * just extend the last slide command if compatible; but not if in
1808 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1810 boolean appendHistoryItem = false;
1811 Deque<CommandI> historyList = viewport.getHistoryList();
1812 boolean inSplitFrame = getSplitViewContainer() != null;
1813 if (!inSplitFrame && historyList != null && historyList.size() > 0
1814 && historyList.peek() instanceof SlideSequencesCommand)
1816 appendHistoryItem = ssc
1817 .appendSlideCommand((SlideSequencesCommand) historyList
1821 if (!appendHistoryItem)
1823 addHistoryItem(ssc);
1836 protected void copy_actionPerformed(ActionEvent e)
1839 if (viewport.getSelectionGroup() == null)
1843 // TODO: preserve the ordering of displayed alignment annotation in any
1844 // internal paste (particularly sequence associated annotation)
1845 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1846 String[] omitHidden = null;
1848 if (viewport.hasHiddenColumns())
1850 omitHidden = viewport.getViewAsString(true);
1853 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1854 seqs, omitHidden, null);
1856 StringSelection ss = new StringSelection(output);
1860 jalview.gui.Desktop.internalCopy = true;
1861 // Its really worth setting the clipboard contents
1862 // to empty before setting the large StringSelection!!
1863 Toolkit.getDefaultToolkit().getSystemClipboard()
1864 .setContents(new StringSelection(""), null);
1866 Toolkit.getDefaultToolkit().getSystemClipboard()
1867 .setContents(ss, Desktop.instance);
1868 } catch (OutOfMemoryError er)
1870 new OOMWarning("copying region", er);
1874 ArrayList<int[]> hiddenColumns = null;
1875 if (viewport.hasHiddenColumns())
1877 hiddenColumns = new ArrayList<int[]>();
1878 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1879 .getSelectionGroup().getEndRes();
1880 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1882 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1884 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1885 region[1] - hiddenOffset });
1890 Desktop.jalviewClipboard = new Object[] { seqs,
1891 viewport.getAlignment().getDataset(), hiddenColumns };
1892 statusBar.setText(MessageManager.formatMessage(
1893 "label.copied_sequences_to_clipboard", new Object[] { Integer
1894 .valueOf(seqs.length).toString() }));
1904 protected void pasteNew_actionPerformed(ActionEvent e)
1916 protected void pasteThis_actionPerformed(ActionEvent e)
1922 * Paste contents of Jalview clipboard
1924 * @param newAlignment
1925 * true to paste to a new alignment, otherwise add to this.
1927 void paste(boolean newAlignment)
1929 boolean externalPaste = true;
1932 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1933 Transferable contents = c.getContents(this);
1935 if (contents == null)
1944 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1945 if (str.length() < 1)
1950 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1952 } catch (OutOfMemoryError er)
1954 new OOMWarning("Out of memory pasting sequences!!", er);
1958 SequenceI[] sequences;
1959 boolean annotationAdded = false;
1960 AlignmentI alignment = null;
1962 if (Desktop.jalviewClipboard != null)
1964 // The clipboard was filled from within Jalview, we must use the
1966 // And dataset from the copied alignment
1967 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1968 // be doubly sure that we create *new* sequence objects.
1969 sequences = new SequenceI[newseq.length];
1970 for (int i = 0; i < newseq.length; i++)
1972 sequences[i] = new Sequence(newseq[i]);
1974 alignment = new Alignment(sequences);
1975 externalPaste = false;
1979 // parse the clipboard as an alignment.
1980 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1982 sequences = alignment.getSequencesArray();
1986 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1992 if (Desktop.jalviewClipboard != null)
1994 // dataset is inherited
1995 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1999 // new dataset is constructed
2000 alignment.setDataset(null);
2002 alwidth = alignment.getWidth() + 1;
2006 AlignmentI pastedal = alignment; // preserve pasted alignment object
2007 // Add pasted sequences and dataset into existing alignment.
2008 alignment = viewport.getAlignment();
2009 alwidth = alignment.getWidth() + 1;
2010 // decide if we need to import sequences from an existing dataset
2011 boolean importDs = Desktop.jalviewClipboard != null
2012 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2013 // importDs==true instructs us to copy over new dataset sequences from
2014 // an existing alignment
2015 Vector newDs = (importDs) ? new Vector() : null; // used to create
2016 // minimum dataset set
2018 for (int i = 0; i < sequences.length; i++)
2022 newDs.addElement(null);
2024 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2026 if (importDs && ds != null)
2028 if (!newDs.contains(ds))
2030 newDs.setElementAt(ds, i);
2031 ds = new Sequence(ds);
2032 // update with new dataset sequence
2033 sequences[i].setDatasetSequence(ds);
2037 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2042 // copy and derive new dataset sequence
2043 sequences[i] = sequences[i].deriveSequence();
2044 alignment.getDataset().addSequence(
2045 sequences[i].getDatasetSequence());
2046 // TODO: avoid creation of duplicate dataset sequences with a
2047 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2049 alignment.addSequence(sequences[i]); // merges dataset
2053 newDs.clear(); // tidy up
2055 if (alignment.getAlignmentAnnotation() != null)
2057 for (AlignmentAnnotation alan : alignment
2058 .getAlignmentAnnotation())
2060 if (alan.graphGroup > fgroup)
2062 fgroup = alan.graphGroup;
2066 if (pastedal.getAlignmentAnnotation() != null)
2068 // Add any annotation attached to alignment.
2069 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2070 for (int i = 0; i < alann.length; i++)
2072 annotationAdded = true;
2073 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2075 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2076 if (newann.graphGroup > -1)
2078 if (newGraphGroups.size() <= newann.graphGroup
2079 || newGraphGroups.get(newann.graphGroup) == null)
2081 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2083 newGraphGroups.add(q, null);
2085 newGraphGroups.set(newann.graphGroup, new Integer(
2088 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2092 newann.padAnnotation(alwidth);
2093 alignment.addAnnotation(newann);
2103 addHistoryItem(new EditCommand(
2104 MessageManager.getString("label.add_sequences"),
2105 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2107 // Add any annotations attached to sequences
2108 for (int i = 0; i < sequences.length; i++)
2110 if (sequences[i].getAnnotation() != null)
2112 AlignmentAnnotation newann;
2113 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2115 annotationAdded = true;
2116 newann = sequences[i].getAnnotation()[a];
2117 newann.adjustForAlignment();
2118 newann.padAnnotation(alwidth);
2119 if (newann.graphGroup > -1)
2121 if (newann.graphGroup > -1)
2123 if (newGraphGroups.size() <= newann.graphGroup
2124 || newGraphGroups.get(newann.graphGroup) == null)
2126 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2128 newGraphGroups.add(q, null);
2130 newGraphGroups.set(newann.graphGroup, new Integer(
2133 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2137 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2142 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2149 // propagate alignment changed.
2150 vpRanges.setEndSeq(alignment.getHeight());
2151 if (annotationAdded)
2153 // Duplicate sequence annotation in all views.
2154 AlignmentI[] alview = this.getViewAlignments();
2155 for (int i = 0; i < sequences.length; i++)
2157 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2162 for (int avnum = 0; avnum < alview.length; avnum++)
2164 if (alview[avnum] != alignment)
2166 // duplicate in a view other than the one with input focus
2167 int avwidth = alview[avnum].getWidth() + 1;
2168 // this relies on sann being preserved after we
2169 // modify the sequence's annotation array for each duplication
2170 for (int a = 0; a < sann.length; a++)
2172 AlignmentAnnotation newann = new AlignmentAnnotation(
2174 sequences[i].addAlignmentAnnotation(newann);
2175 newann.padAnnotation(avwidth);
2176 alview[avnum].addAnnotation(newann); // annotation was
2177 // duplicated earlier
2178 // TODO JAL-1145 graphGroups are not updated for sequence
2179 // annotation added to several views. This may cause
2181 alview[avnum].setAnnotationIndex(newann, a);
2186 buildSortByAnnotationScoresMenu();
2188 viewport.firePropertyChange("alignment", null,
2189 alignment.getSequences());
2190 if (alignPanels != null)
2192 for (AlignmentPanel ap : alignPanels)
2194 ap.validateAnnotationDimensions(false);
2199 alignPanel.validateAnnotationDimensions(false);
2205 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2207 String newtitle = new String("Copied sequences");
2209 if (Desktop.jalviewClipboard != null
2210 && Desktop.jalviewClipboard[2] != null)
2212 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2213 for (int[] region : hc)
2215 af.viewport.hideColumns(region[0], region[1]);
2219 // >>>This is a fix for the moment, until a better solution is
2221 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2223 alignPanel.getSeqPanel().seqCanvas
2224 .getFeatureRenderer());
2226 // TODO: maintain provenance of an alignment, rather than just make the
2227 // title a concatenation of operations.
2230 if (title.startsWith("Copied sequences"))
2236 newtitle = newtitle.concat("- from " + title);
2241 newtitle = new String("Pasted sequences");
2244 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2249 } catch (Exception ex)
2251 ex.printStackTrace();
2252 System.out.println("Exception whilst pasting: " + ex);
2253 // could be anything being pasted in here
2259 protected void expand_newalign(ActionEvent e)
2263 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2264 .getAlignment(), -1);
2265 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2267 String newtitle = new String("Flanking alignment");
2269 if (Desktop.jalviewClipboard != null
2270 && Desktop.jalviewClipboard[2] != null)
2272 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2273 for (int region[] : hc)
2275 af.viewport.hideColumns(region[0], region[1]);
2279 // >>>This is a fix for the moment, until a better solution is
2281 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2283 alignPanel.getSeqPanel().seqCanvas
2284 .getFeatureRenderer());
2286 // TODO: maintain provenance of an alignment, rather than just make the
2287 // title a concatenation of operations.
2289 if (title.startsWith("Copied sequences"))
2295 newtitle = newtitle.concat("- from " + title);
2299 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2301 } catch (Exception ex)
2303 ex.printStackTrace();
2304 System.out.println("Exception whilst pasting: " + ex);
2305 // could be anything being pasted in here
2306 } catch (OutOfMemoryError oom)
2308 new OOMWarning("Viewing flanking region of alignment", oom);
2319 protected void cut_actionPerformed(ActionEvent e)
2321 copy_actionPerformed(null);
2322 delete_actionPerformed(null);
2332 protected void delete_actionPerformed(ActionEvent evt)
2335 SequenceGroup sg = viewport.getSelectionGroup();
2342 * If the cut affects all sequences, warn, remove highlighted columns
2344 if (sg.getSize() == viewport.getAlignment().getHeight())
2346 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2347 .getAlignment().getWidth()) ? true : false;
2348 if (isEntireAlignWidth)
2350 int confirm = JvOptionPane.showConfirmDialog(this,
2351 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2352 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2353 JvOptionPane.OK_CANCEL_OPTION);
2355 if (confirm == JvOptionPane.CANCEL_OPTION
2356 || confirm == JvOptionPane.CLOSED_OPTION)
2361 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2362 sg.getEndRes() + 1);
2364 SequenceI[] cut = sg.getSequences()
2365 .toArray(new SequenceI[sg.getSize()]);
2367 addHistoryItem(new EditCommand(
2368 MessageManager.getString("label.cut_sequences"), Action.CUT,
2369 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2370 viewport.getAlignment()));
2372 viewport.setSelectionGroup(null);
2373 viewport.sendSelection();
2374 viewport.getAlignment().deleteGroup(sg);
2376 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2378 if (viewport.getAlignment().getHeight() < 1)
2382 this.setClosed(true);
2383 } catch (Exception ex)
2396 protected void deleteGroups_actionPerformed(ActionEvent e)
2398 if (avc.deleteGroups())
2400 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2401 alignPanel.updateAnnotation();
2402 alignPanel.paintAlignment(true);
2413 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2415 SequenceGroup sg = new SequenceGroup();
2417 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2419 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2422 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2423 viewport.setSelectionGroup(sg);
2424 viewport.sendSelection();
2425 // JAL-2034 - should delegate to
2426 // alignPanel to decide if overview needs
2428 alignPanel.paintAlignment(false);
2429 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2439 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2441 if (viewport.cursorMode)
2443 alignPanel.getSeqPanel().keyboardNo1 = null;
2444 alignPanel.getSeqPanel().keyboardNo2 = null;
2446 viewport.setSelectionGroup(null);
2447 viewport.getColumnSelection().clear();
2448 viewport.setSelectionGroup(null);
2449 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2450 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2451 // JAL-2034 - should delegate to
2452 // alignPanel to decide if overview needs
2454 alignPanel.paintAlignment(false);
2455 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2456 viewport.sendSelection();
2466 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2468 SequenceGroup sg = viewport.getSelectionGroup();
2472 selectAllSequenceMenuItem_actionPerformed(null);
2477 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2479 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2481 // JAL-2034 - should delegate to
2482 // alignPanel to decide if overview needs
2485 alignPanel.paintAlignment(true);
2486 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2487 viewport.sendSelection();
2491 public void invertColSel_actionPerformed(ActionEvent e)
2493 viewport.invertColumnSelection();
2494 alignPanel.paintAlignment(true);
2495 viewport.sendSelection();
2505 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2507 trimAlignment(true);
2517 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2519 trimAlignment(false);
2522 void trimAlignment(boolean trimLeft)
2524 ColumnSelection colSel = viewport.getColumnSelection();
2527 if (!colSel.isEmpty())
2531 column = colSel.getMin();
2535 column = colSel.getMax();
2539 if (viewport.getSelectionGroup() != null)
2541 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2542 viewport.getHiddenRepSequences());
2546 seqs = viewport.getAlignment().getSequencesArray();
2549 TrimRegionCommand trimRegion;
2552 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2553 column, viewport.getAlignment());
2554 vpRanges.setStartRes(0);
2558 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2559 column, viewport.getAlignment());
2562 statusBar.setText(MessageManager.formatMessage(
2563 "label.removed_columns",
2564 new String[] { Integer.valueOf(trimRegion.getSize())
2567 addHistoryItem(trimRegion);
2569 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2571 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2572 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2574 viewport.getAlignment().deleteGroup(sg);
2578 viewport.firePropertyChange("alignment", null, viewport
2579 .getAlignment().getSequences());
2590 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2592 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2595 if (viewport.getSelectionGroup() != null)
2597 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2598 viewport.getHiddenRepSequences());
2599 start = viewport.getSelectionGroup().getStartRes();
2600 end = viewport.getSelectionGroup().getEndRes();
2604 seqs = viewport.getAlignment().getSequencesArray();
2607 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2608 "Remove Gapped Columns", seqs, start, end,
2609 viewport.getAlignment());
2611 addHistoryItem(removeGapCols);
2613 statusBar.setText(MessageManager.formatMessage(
2614 "label.removed_empty_columns",
2615 new Object[] { Integer.valueOf(removeGapCols.getSize())
2618 // This is to maintain viewport position on first residue
2619 // of first sequence
2620 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2621 int startRes = seq.findPosition(vpRanges.getStartRes());
2622 // ShiftList shifts;
2623 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2624 // edit.alColumnChanges=shifts.getInverse();
2625 // if (viewport.hasHiddenColumns)
2626 // viewport.getColumnSelection().compensateForEdits(shifts);
2627 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2628 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2640 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2642 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2645 if (viewport.getSelectionGroup() != null)
2647 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2648 viewport.getHiddenRepSequences());
2649 start = viewport.getSelectionGroup().getStartRes();
2650 end = viewport.getSelectionGroup().getEndRes();
2654 seqs = viewport.getAlignment().getSequencesArray();
2657 // This is to maintain viewport position on first residue
2658 // of first sequence
2659 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2660 int startRes = seq.findPosition(vpRanges.getStartRes());
2662 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2663 viewport.getAlignment()));
2665 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2667 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2679 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2681 viewport.setPadGaps(padGapsMenuitem.isSelected());
2682 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2693 public void findMenuItem_actionPerformed(ActionEvent e)
2699 * Create a new view of the current alignment.
2702 public void newView_actionPerformed(ActionEvent e)
2704 newView(null, true);
2708 * Creates and shows a new view of the current alignment.
2711 * title of newly created view; if null, one will be generated
2712 * @param copyAnnotation
2713 * if true then duplicate all annnotation, groups and settings
2714 * @return new alignment panel, already displayed.
2716 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2719 * Create a new AlignmentPanel (with its own, new Viewport)
2721 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2723 if (!copyAnnotation)
2726 * remove all groups and annotation except for the automatic stuff
2728 newap.av.getAlignment().deleteAllGroups();
2729 newap.av.getAlignment().deleteAllAnnotations(false);
2732 newap.av.setGatherViewsHere(false);
2734 if (viewport.viewName == null)
2736 viewport.viewName = MessageManager
2737 .getString("label.view_name_original");
2741 * Views share the same edits undo and redo stacks
2743 newap.av.setHistoryList(viewport.getHistoryList());
2744 newap.av.setRedoList(viewport.getRedoList());
2747 * Views share the same mappings; need to deregister any new mappings
2748 * created by copyAlignPanel, and register the new reference to the shared
2751 newap.av.replaceMappings(viewport.getAlignment());
2754 * start up cDNA consensus (if applicable) now mappings are in place
2756 if (newap.av.initComplementConsensus())
2758 newap.refresh(true); // adjust layout of annotations
2761 newap.av.viewName = getNewViewName(viewTitle);
2763 addAlignmentPanel(newap, true);
2764 newap.alignmentChanged();
2766 if (alignPanels.size() == 2)
2768 viewport.setGatherViewsHere(true);
2770 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2775 * Make a new name for the view, ensuring it is unique within the current
2776 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2777 * these now use viewId. Unique view names are still desirable for usability.)
2782 protected String getNewViewName(String viewTitle)
2784 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2785 boolean addFirstIndex = false;
2786 if (viewTitle == null || viewTitle.trim().length() == 0)
2788 viewTitle = MessageManager.getString("action.view");
2789 addFirstIndex = true;
2793 index = 1;// we count from 1 if given a specific name
2795 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2797 List<Component> comps = PaintRefresher.components.get(viewport
2798 .getSequenceSetId());
2800 List<String> existingNames = getExistingViewNames(comps);
2802 while (existingNames.contains(newViewName))
2804 newViewName = viewTitle + " " + (++index);
2810 * Returns a list of distinct view names found in the given list of
2811 * components. View names are held on the viewport of an AlignmentPanel.
2816 protected List<String> getExistingViewNames(List<Component> comps)
2818 List<String> existingNames = new ArrayList<String>();
2819 for (Component comp : comps)
2821 if (comp instanceof AlignmentPanel)
2823 AlignmentPanel ap = (AlignmentPanel) comp;
2824 if (!existingNames.contains(ap.av.viewName))
2826 existingNames.add(ap.av.viewName);
2830 return existingNames;
2834 * Explode tabbed views into separate windows.
2837 public void expandViews_actionPerformed(ActionEvent e)
2839 Desktop.explodeViews(this);
2843 * Gather views in separate windows back into a tabbed presentation.
2846 public void gatherViews_actionPerformed(ActionEvent e)
2848 Desktop.instance.gatherViews(this);
2858 public void font_actionPerformed(ActionEvent e)
2860 new FontChooser(alignPanel);
2870 protected void seqLimit_actionPerformed(ActionEvent e)
2872 viewport.setShowJVSuffix(seqLimits.isSelected());
2874 alignPanel.getIdPanel().getIdCanvas()
2875 .setPreferredSize(alignPanel.calculateIdWidth());
2876 alignPanel.paintAlignment(true);
2880 public void idRightAlign_actionPerformed(ActionEvent e)
2882 viewport.setRightAlignIds(idRightAlign.isSelected());
2883 alignPanel.paintAlignment(true);
2887 public void centreColumnLabels_actionPerformed(ActionEvent e)
2889 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2890 alignPanel.paintAlignment(true);
2896 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2899 protected void followHighlight_actionPerformed()
2902 * Set the 'follow' flag on the Viewport (and scroll to position if now
2905 final boolean state = this.followHighlightMenuItem.getState();
2906 viewport.setFollowHighlight(state);
2909 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2920 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2922 viewport.setColourText(colourTextMenuItem.isSelected());
2923 alignPanel.paintAlignment(true);
2933 public void wrapMenuItem_actionPerformed(ActionEvent e)
2935 scaleAbove.setVisible(wrapMenuItem.isSelected());
2936 scaleLeft.setVisible(wrapMenuItem.isSelected());
2937 scaleRight.setVisible(wrapMenuItem.isSelected());
2938 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2939 alignPanel.updateLayout();
2943 public void showAllSeqs_actionPerformed(ActionEvent e)
2945 viewport.showAllHiddenSeqs();
2949 public void showAllColumns_actionPerformed(ActionEvent e)
2951 viewport.showAllHiddenColumns();
2953 viewport.sendSelection();
2957 public void hideSelSequences_actionPerformed(ActionEvent e)
2959 viewport.hideAllSelectedSeqs();
2960 // alignPanel.paintAlignment(true);
2964 * called by key handler and the hide all/show all menu items
2969 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2972 boolean hide = false;
2973 SequenceGroup sg = viewport.getSelectionGroup();
2974 if (!toggleSeqs && !toggleCols)
2976 // Hide everything by the current selection - this is a hack - we do the
2977 // invert and then hide
2978 // first check that there will be visible columns after the invert.
2979 if (viewport.hasSelectedColumns()
2980 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2983 // now invert the sequence set, if required - empty selection implies
2984 // that no hiding is required.
2987 invertSequenceMenuItem_actionPerformed(null);
2988 sg = viewport.getSelectionGroup();
2992 viewport.expandColSelection(sg, true);
2993 // finally invert the column selection and get the new sequence
2995 invertColSel_actionPerformed(null);
3002 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3004 hideSelSequences_actionPerformed(null);
3007 else if (!(toggleCols && viewport.hasSelectedColumns()))
3009 showAllSeqs_actionPerformed(null);
3015 if (viewport.hasSelectedColumns())
3017 hideSelColumns_actionPerformed(null);
3020 viewport.setSelectionGroup(sg);
3025 showAllColumns_actionPerformed(null);
3034 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3035 * event.ActionEvent)
3038 public void hideAllButSelection_actionPerformed(ActionEvent e)
3040 toggleHiddenRegions(false, false);
3041 viewport.sendSelection();
3048 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3052 public void hideAllSelection_actionPerformed(ActionEvent e)
3054 SequenceGroup sg = viewport.getSelectionGroup();
3055 viewport.expandColSelection(sg, false);
3056 viewport.hideAllSelectedSeqs();
3057 viewport.hideSelectedColumns();
3058 alignPanel.paintAlignment(true);
3059 viewport.sendSelection();
3066 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3070 public void showAllhidden_actionPerformed(ActionEvent e)
3072 viewport.showAllHiddenColumns();
3073 viewport.showAllHiddenSeqs();
3074 alignPanel.paintAlignment(true);
3075 viewport.sendSelection();
3079 public void hideSelColumns_actionPerformed(ActionEvent e)
3081 viewport.hideSelectedColumns();
3082 alignPanel.paintAlignment(true);
3083 viewport.sendSelection();
3087 public void hiddenMarkers_actionPerformed(ActionEvent e)
3089 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3100 protected void scaleAbove_actionPerformed(ActionEvent e)
3102 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3103 alignPanel.paintAlignment(true);
3113 protected void scaleLeft_actionPerformed(ActionEvent e)
3115 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3116 alignPanel.paintAlignment(true);
3126 protected void scaleRight_actionPerformed(ActionEvent e)
3128 viewport.setScaleRightWrapped(scaleRight.isSelected());
3129 alignPanel.paintAlignment(true);
3139 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3141 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3142 alignPanel.paintAlignment(true);
3152 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3154 viewport.setShowText(viewTextMenuItem.isSelected());
3155 alignPanel.paintAlignment(true);
3165 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3167 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3168 alignPanel.paintAlignment(true);
3171 public FeatureSettings featureSettings;
3174 public FeatureSettingsControllerI getFeatureSettingsUI()
3176 return featureSettings;
3180 public void featureSettings_actionPerformed(ActionEvent e)
3182 if (featureSettings != null)
3184 featureSettings.close();
3185 featureSettings = null;
3187 if (!showSeqFeatures.isSelected())
3189 // make sure features are actually displayed
3190 showSeqFeatures.setSelected(true);
3191 showSeqFeatures_actionPerformed(null);
3193 featureSettings = new FeatureSettings(this);
3197 * Set or clear 'Show Sequence Features'
3203 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3205 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3206 alignPanel.paintAlignment(true);
3207 if (alignPanel.getOverviewPanel() != null)
3209 alignPanel.getOverviewPanel().updateOverviewImage();
3214 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3215 * the annotations panel as a whole.
3217 * The options to show/hide all annotations should be enabled when the panel
3218 * is shown, and disabled when the panel is hidden.
3223 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3225 final boolean setVisible = annotationPanelMenuItem.isSelected();
3226 viewport.setShowAnnotation(setVisible);
3227 this.showAllSeqAnnotations.setEnabled(setVisible);
3228 this.hideAllSeqAnnotations.setEnabled(setVisible);
3229 this.showAllAlAnnotations.setEnabled(setVisible);
3230 this.hideAllAlAnnotations.setEnabled(setVisible);
3231 alignPanel.updateLayout();
3235 public void alignmentProperties()
3237 JEditorPane editPane = new JEditorPane("text/html", "");
3238 editPane.setEditable(false);
3239 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3241 editPane.setText(MessageManager.formatMessage("label.html_content",
3242 new Object[] { contents.toString() }));
3243 JInternalFrame frame = new JInternalFrame();
3244 frame.getContentPane().add(new JScrollPane(editPane));
3246 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3247 "label.alignment_properties", new Object[] { getTitle() }),
3258 public void overviewMenuItem_actionPerformed(ActionEvent e)
3260 if (alignPanel.overviewPanel != null)
3265 JInternalFrame frame = new JInternalFrame();
3266 OverviewPanel overview = new OverviewPanel(alignPanel);
3267 frame.setContentPane(overview);
3268 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3269 "label.overview_params", new Object[] { this.getTitle() }),
3270 frame.getWidth(), frame.getHeight());
3272 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3273 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3276 public void internalFrameClosed(
3277 javax.swing.event.InternalFrameEvent evt)
3279 alignPanel.setOverviewPanel(null);
3283 alignPanel.setOverviewPanel(overview);
3287 public void textColour_actionPerformed()
3289 new TextColourChooser().chooseColour(alignPanel, null);
3293 * public void covariationColour_actionPerformed() {
3295 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3299 public void annotationColour_actionPerformed()
3301 new AnnotationColourChooser(viewport, alignPanel);
3305 public void annotationColumn_actionPerformed(ActionEvent e)
3307 new AnnotationColumnChooser(viewport, alignPanel);
3311 * Action on the user checking or unchecking the option to apply the selected
3312 * colour scheme to all groups. If unchecked, groups may have their own
3313 * independent colour schemes.
3318 public void applyToAllGroups_actionPerformed(boolean selected)
3320 viewport.setColourAppliesToAllGroups(selected);
3324 * Action on user selecting a colour from the colour menu
3327 * the name (not the menu item label!) of the colour scheme
3330 public void changeColour_actionPerformed(String name)
3333 * 'User Defined' opens a panel to configure or load a
3334 * user-defined colour scheme
3336 if (ResidueColourScheme.USER_DEFINED.equals(name))
3338 new UserDefinedColours(alignPanel, null);
3343 * otherwise set the chosen colour scheme (or null for 'None')
3345 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3346 viewport.getAlignment(), viewport.getHiddenRepSequences());
3351 * Actions on setting or changing the alignment colour scheme
3356 public void changeColour(ColourSchemeI cs)
3358 // TODO: pull up to controller method
3361 ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3364 viewport.setGlobalColourScheme(cs);
3366 alignPanel.paintAlignment(true);
3370 * Show the PID threshold slider panel
3373 protected void modifyPID_actionPerformed()
3375 SliderPanel.setPIDSliderSource(alignPanel,
3376 viewport.getResidueShading(), alignPanel.getViewName());
3377 SliderPanel.showPIDSlider();
3381 * Show the Conservation slider panel
3384 protected void modifyConservation_actionPerformed()
3386 SliderPanel.setConservationSlider(alignPanel,
3387 viewport.getResidueShading(), alignPanel.getViewName());
3388 SliderPanel.showConservationSlider();
3392 * Action on selecting or deselecting (Colour) By Conservation
3395 public void conservationMenuItem_actionPerformed(boolean selected)
3397 modifyConservation.setEnabled(selected);
3398 viewport.setConservationSelected(selected);
3399 viewport.getResidueShading().setConservationApplied(selected);
3401 changeColour(viewport.getGlobalColourScheme());
3404 modifyConservation_actionPerformed();
3408 SliderPanel.hideConservationSlider();
3413 * Action on selecting or deselecting (Colour) Above PID Threshold
3416 public void abovePIDThreshold_actionPerformed(boolean selected)
3418 modifyPID.setEnabled(selected);
3419 viewport.setAbovePIDThreshold(selected);
3422 viewport.getResidueShading().setThreshold(0,
3423 viewport.isIgnoreGapsConsensus());
3426 changeColour(viewport.getGlobalColourScheme());
3429 modifyPID_actionPerformed();
3433 SliderPanel.hidePIDSlider();
3444 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3446 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3447 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3448 .getAlignment().getSequenceAt(0), null);
3449 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3450 viewport.getAlignment()));
3451 alignPanel.paintAlignment(true);
3461 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3463 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3464 AlignmentSorter.sortByID(viewport.getAlignment());
3465 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3466 viewport.getAlignment()));
3467 alignPanel.paintAlignment(true);
3477 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3479 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3480 AlignmentSorter.sortByLength(viewport.getAlignment());
3481 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3482 viewport.getAlignment()));
3483 alignPanel.paintAlignment(true);
3493 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3495 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3496 AlignmentSorter.sortByGroup(viewport.getAlignment());
3497 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3498 viewport.getAlignment()));
3500 alignPanel.paintAlignment(true);
3510 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3512 new RedundancyPanel(alignPanel, this);
3522 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3524 if ((viewport.getSelectionGroup() == null)
3525 || (viewport.getSelectionGroup().getSize() < 2))
3527 JvOptionPane.showInternalMessageDialog(this, MessageManager
3528 .getString("label.you_must_select_least_two_sequences"),
3529 MessageManager.getString("label.invalid_selection"),
3530 JvOptionPane.WARNING_MESSAGE);
3534 JInternalFrame frame = new JInternalFrame();
3535 frame.setContentPane(new PairwiseAlignPanel(viewport));
3536 Desktop.addInternalFrame(frame,
3537 MessageManager.getString("action.pairwise_alignment"), 600,
3549 public void PCAMenuItem_actionPerformed(ActionEvent e)
3551 if (((viewport.getSelectionGroup() != null)
3552 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3553 .getSelectionGroup().getSize() > 0))
3554 || (viewport.getAlignment().getHeight() < 4))
3557 .showInternalMessageDialog(
3560 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3562 .getString("label.sequence_selection_insufficient"),
3563 JvOptionPane.WARNING_MESSAGE);
3568 new PCAPanel(alignPanel);
3572 public void autoCalculate_actionPerformed(ActionEvent e)
3574 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3575 if (viewport.autoCalculateConsensus)
3577 viewport.firePropertyChange("alignment", null, viewport
3578 .getAlignment().getSequences());
3583 public void sortByTreeOption_actionPerformed(ActionEvent e)
3585 viewport.sortByTree = sortByTree.isSelected();
3589 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3591 viewport.followSelection = listenToViewSelections.isSelected();
3601 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3603 newTreePanel("AV", "PID", "Average distance tree using PID");
3613 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3615 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3625 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3627 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3637 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3639 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3652 void newTreePanel(String type, String pwType, String title)
3656 if (viewport.getSelectionGroup() != null
3657 && viewport.getSelectionGroup().getSize() > 0)
3659 if (viewport.getSelectionGroup().getSize() < 3)
3665 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3667 .getString("label.not_enough_sequences"),
3668 JvOptionPane.WARNING_MESSAGE);
3672 SequenceGroup sg = viewport.getSelectionGroup();
3674 /* Decide if the selection is a column region */
3675 for (SequenceI _s : sg.getSequences())
3677 if (_s.getLength() < sg.getEndRes())
3683 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3685 .getString("label.sequences_selection_not_aligned"),
3686 JvOptionPane.WARNING_MESSAGE);
3692 title = title + " on region";
3693 tp = new TreePanel(alignPanel, type, pwType);
3697 // are the visible sequences aligned?
3698 if (!viewport.getAlignment().isAligned(false))
3704 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3706 .getString("label.sequences_not_aligned"),
3707 JvOptionPane.WARNING_MESSAGE);
3712 if (viewport.getAlignment().getHeight() < 2)
3717 tp = new TreePanel(alignPanel, type, pwType);
3722 if (viewport.viewName != null)
3724 title += viewport.viewName + " of ";
3727 title += this.title;
3729 Desktop.addInternalFrame(tp, title, 600, 500);
3740 public void addSortByOrderMenuItem(String title,
3741 final AlignmentOrder order)
3743 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3744 "action.by_title_param", new Object[] { title }));
3746 item.addActionListener(new java.awt.event.ActionListener()
3749 public void actionPerformed(ActionEvent e)
3751 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3753 // TODO: JBPNote - have to map order entries to curent SequenceI
3755 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3757 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3760 alignPanel.paintAlignment(true);
3766 * Add a new sort by annotation score menu item
3769 * the menu to add the option to
3771 * the label used to retrieve scores for each sequence on the
3774 public void addSortByAnnotScoreMenuItem(JMenu sort,
3775 final String scoreLabel)
3777 final JMenuItem item = new JMenuItem(scoreLabel);
3779 item.addActionListener(new java.awt.event.ActionListener()
3782 public void actionPerformed(ActionEvent e)
3784 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3785 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3786 viewport.getAlignment());// ,viewport.getSelectionGroup());
3787 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3788 viewport.getAlignment()));
3789 alignPanel.paintAlignment(true);
3795 * last hash for alignment's annotation array - used to minimise cost of
3798 protected int _annotationScoreVectorHash;
3801 * search the alignment and rebuild the sort by annotation score submenu the
3802 * last alignment annotation vector hash is stored to minimize cost of
3803 * rebuilding in subsequence calls.
3807 public void buildSortByAnnotationScoresMenu()
3809 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3814 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3816 sortByAnnotScore.removeAll();
3817 // almost certainly a quicker way to do this - but we keep it simple
3818 Hashtable scoreSorts = new Hashtable();
3819 AlignmentAnnotation aann[];
3820 for (SequenceI sqa : viewport.getAlignment().getSequences())
3822 aann = sqa.getAnnotation();
3823 for (int i = 0; aann != null && i < aann.length; i++)
3825 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3827 scoreSorts.put(aann[i].label, aann[i].label);
3831 Enumeration labels = scoreSorts.keys();
3832 while (labels.hasMoreElements())
3834 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3835 (String) labels.nextElement());
3837 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3840 _annotationScoreVectorHash = viewport.getAlignment()
3841 .getAlignmentAnnotation().hashCode();
3846 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3847 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3848 * call. Listeners are added to remove the menu item when the treePanel is
3849 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3853 * Displayed tree window.
3855 * SortBy menu item title.
3858 public void buildTreeMenu()
3860 calculateTree.removeAll();
3861 // build the calculate menu
3863 for (final String type : new String[] { "NJ", "AV" })
3865 String treecalcnm = MessageManager.getString("label.tree_calc_"
3866 + type.toLowerCase());
3867 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3869 JMenuItem tm = new JMenuItem();
3870 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3871 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3872 || sm.isProtein() == !viewport.getAlignment()
3875 String smn = MessageManager.getStringOrReturn(
3876 "label.score_model_", sm.getName());
3877 final String title = MessageManager.formatMessage(
3878 "label.treecalc_title", treecalcnm, smn);
3879 tm.setText(title);//
3880 tm.addActionListener(new java.awt.event.ActionListener()
3883 public void actionPerformed(ActionEvent e)
3885 newTreePanel(type, pwtype, title);
3888 calculateTree.add(tm);
3893 sortByTreeMenu.removeAll();
3895 List<Component> comps = PaintRefresher.components.get(viewport
3896 .getSequenceSetId());
3897 List<TreePanel> treePanels = new ArrayList<TreePanel>();
3898 for (Component comp : comps)
3900 if (comp instanceof TreePanel)
3902 treePanels.add((TreePanel) comp);
3906 if (treePanels.size() < 1)
3908 sortByTreeMenu.setVisible(false);
3912 sortByTreeMenu.setVisible(true);
3914 for (final TreePanel tp : treePanels)
3916 final JMenuItem item = new JMenuItem(tp.getTitle());
3917 item.addActionListener(new java.awt.event.ActionListener()
3920 public void actionPerformed(ActionEvent e)
3922 tp.sortByTree_actionPerformed();
3923 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3928 sortByTreeMenu.add(item);
3932 public boolean sortBy(AlignmentOrder alorder, String undoname)
3934 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3935 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3936 if (undoname != null)
3938 addHistoryItem(new OrderCommand(undoname, oldOrder,
3939 viewport.getAlignment()));
3941 alignPanel.paintAlignment(true);
3946 * Work out whether the whole set of sequences or just the selected set will
3947 * be submitted for multiple alignment.
3950 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3952 // Now, check we have enough sequences
3953 AlignmentView msa = null;
3955 if ((viewport.getSelectionGroup() != null)
3956 && (viewport.getSelectionGroup().getSize() > 1))
3958 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3959 // some common interface!
3961 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3962 * SequenceI[sz = seqs.getSize(false)];
3964 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3965 * seqs.getSequenceAt(i); }
3967 msa = viewport.getAlignmentView(true);
3969 else if (viewport.getSelectionGroup() != null
3970 && viewport.getSelectionGroup().getSize() == 1)
3972 int option = JvOptionPane.showConfirmDialog(this,
3973 MessageManager.getString("warn.oneseq_msainput_selection"),
3974 MessageManager.getString("label.invalid_selection"),
3975 JvOptionPane.OK_CANCEL_OPTION);
3976 if (option == JvOptionPane.OK_OPTION)
3978 msa = viewport.getAlignmentView(false);
3983 msa = viewport.getAlignmentView(false);
3989 * Decides what is submitted to a secondary structure prediction service: the
3990 * first sequence in the alignment, or in the current selection, or, if the
3991 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3992 * region or the whole alignment. (where the first sequence in the set is the
3993 * one that the prediction will be for).
3995 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3997 AlignmentView seqs = null;
3999 if ((viewport.getSelectionGroup() != null)
4000 && (viewport.getSelectionGroup().getSize() > 0))
4002 seqs = viewport.getAlignmentView(true);
4006 seqs = viewport.getAlignmentView(false);
4008 // limit sequences - JBPNote in future - could spawn multiple prediction
4010 // TODO: viewport.getAlignment().isAligned is a global state - the local
4011 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4012 if (!viewport.getAlignment().isAligned(false))
4014 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4015 // TODO: if seqs.getSequences().length>1 then should really have warned
4029 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4031 // Pick the tree file
4032 JalviewFileChooser chooser = new JalviewFileChooser(
4033 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4034 chooser.setFileView(new JalviewFileView());
4035 chooser.setDialogTitle(MessageManager
4036 .getString("label.select_newick_like_tree_file"));
4037 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4039 int value = chooser.showOpenDialog(null);
4041 if (value == JalviewFileChooser.APPROVE_OPTION)
4043 String choice = chooser.getSelectedFile().getPath();
4044 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4045 jalview.io.NewickFile fin = null;
4048 fin = new NewickFile(choice, DataSourceType.FILE);
4049 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4050 } catch (Exception ex)
4057 .getString("label.problem_reading_tree_file"),
4058 JvOptionPane.WARNING_MESSAGE);
4059 ex.printStackTrace();
4061 if (fin != null && fin.hasWarningMessage())
4063 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4064 .getWarningMessage(), MessageManager
4065 .getString("label.possible_problem_with_tree_file"),
4066 JvOptionPane.WARNING_MESSAGE);
4071 public TreePanel ShowNewickTree(NewickFile nf, String title)
4073 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4076 public TreePanel ShowNewickTree(NewickFile nf, String title,
4077 AlignmentView input)
4079 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4082 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4083 int h, int x, int y)
4085 return ShowNewickTree(nf, title, null, w, h, x, y);
4089 * Add a treeviewer for the tree extracted from a newick file object to the
4090 * current alignment view
4097 * Associated alignment input data (or null)
4106 * @return TreePanel handle
4108 public TreePanel ShowNewickTree(NewickFile nf, String title,
4109 AlignmentView input, int w, int h, int x, int y)
4111 TreePanel tp = null;
4117 if (nf.getTree() != null)
4119 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4125 tp.setLocation(x, y);
4128 Desktop.addInternalFrame(tp, title, w, h);
4130 } catch (Exception ex)
4132 ex.printStackTrace();
4138 private boolean buildingMenu = false;
4141 * Generates menu items and listener event actions for web service clients
4144 public void BuildWebServiceMenu()
4146 while (buildingMenu)
4150 System.err.println("Waiting for building menu to finish.");
4152 } catch (Exception e)
4156 final AlignFrame me = this;
4157 buildingMenu = true;
4158 new Thread(new Runnable()
4163 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4166 // System.err.println("Building ws menu again "
4167 // + Thread.currentThread());
4168 // TODO: add support for context dependent disabling of services based
4170 // alignment and current selection
4171 // TODO: add additional serviceHandle parameter to specify abstract
4173 // class independently of AbstractName
4174 // TODO: add in rediscovery GUI function to restart discoverer
4175 // TODO: group services by location as well as function and/or
4177 // object broker mechanism.
4178 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4179 final IProgressIndicator af = me;
4182 * do not i18n these strings - they are hard-coded in class
4183 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4184 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4186 final JMenu msawsmenu = new JMenu("Alignment");
4187 final JMenu secstrmenu = new JMenu(
4188 "Secondary Structure Prediction");
4189 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4190 final JMenu analymenu = new JMenu("Analysis");
4191 final JMenu dismenu = new JMenu("Protein Disorder");
4192 // JAL-940 - only show secondary structure prediction services from
4193 // the legacy server
4194 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4196 Discoverer.services != null && (Discoverer.services.size() > 0))
4198 // TODO: refactor to allow list of AbstractName/Handler bindings to
4200 // stored or retrieved from elsewhere
4201 // No MSAWS used any more:
4202 // Vector msaws = null; // (Vector)
4203 // Discoverer.services.get("MsaWS");
4204 Vector secstrpr = (Vector) Discoverer.services
4206 if (secstrpr != null)
4208 // Add any secondary structure prediction services
4209 for (int i = 0, j = secstrpr.size(); i < j; i++)
4211 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4213 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4214 .getServiceClient(sh);
4215 int p = secstrmenu.getItemCount();
4216 impl.attachWSMenuEntry(secstrmenu, me);
4217 int q = secstrmenu.getItemCount();
4218 for (int litm = p; litm < q; litm++)
4220 legacyItems.add(secstrmenu.getItem(litm));
4226 // Add all submenus in the order they should appear on the web
4228 wsmenu.add(msawsmenu);
4229 wsmenu.add(secstrmenu);
4230 wsmenu.add(dismenu);
4231 wsmenu.add(analymenu);
4232 // No search services yet
4233 // wsmenu.add(seqsrchmenu);
4235 javax.swing.SwingUtilities.invokeLater(new Runnable()
4242 webService.removeAll();
4243 // first, add discovered services onto the webservices menu
4244 if (wsmenu.size() > 0)
4246 for (int i = 0, j = wsmenu.size(); i < j; i++)
4248 webService.add(wsmenu.get(i));
4253 webService.add(me.webServiceNoServices);
4255 // TODO: move into separate menu builder class.
4256 boolean new_sspred = false;
4257 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4259 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4260 if (jws2servs != null)
4262 if (jws2servs.hasServices())
4264 jws2servs.attachWSMenuEntry(webService, me);
4265 for (Jws2Instance sv : jws2servs.getServices())
4267 if (sv.description.toLowerCase().contains("jpred"))
4269 for (JMenuItem jmi : legacyItems)
4271 jmi.setVisible(false);
4277 if (jws2servs.isRunning())
4279 JMenuItem tm = new JMenuItem(
4280 "Still discovering JABA Services");
4281 tm.setEnabled(false);
4286 build_urlServiceMenu(me.webService);
4287 build_fetchdbmenu(webService);
4288 for (JMenu item : wsmenu)
4290 if (item.getItemCount() == 0)
4292 item.setEnabled(false);
4296 item.setEnabled(true);
4299 } catch (Exception e)
4302 .debug("Exception during web service menu building process.",
4307 } catch (Exception e)
4310 buildingMenu = false;
4317 * construct any groupURL type service menu entries.
4321 private void build_urlServiceMenu(JMenu webService)
4323 // TODO: remove this code when 2.7 is released
4324 // DEBUG - alignmentView
4326 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4327 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4329 * @Override public void actionPerformed(ActionEvent e) {
4330 * jalview.datamodel.AlignmentView
4331 * .testSelectionViews(af.viewport.getAlignment(),
4332 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4334 * }); webService.add(testAlView);
4336 // TODO: refactor to RestClient discoverer and merge menu entries for
4337 // rest-style services with other types of analysis/calculation service
4338 // SHmmr test client - still being implemented.
4339 // DEBUG - alignmentView
4341 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4344 client.attachWSMenuEntry(
4345 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4351 * Searches the alignment sequences for xRefs and builds the Show
4352 * Cross-References menu (formerly called Show Products), with database
4353 * sources for which cross-references are found (protein sources for a
4354 * nucleotide alignment and vice versa)
4356 * @return true if Show Cross-references menu should be enabled
4358 public boolean canShowProducts()
4360 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4361 AlignmentI dataset = viewport.getAlignment().getDataset();
4363 showProducts.removeAll();
4364 final boolean dna = viewport.getAlignment().isNucleotide();
4366 if (seqs == null || seqs.length == 0)
4368 // nothing to see here.
4372 boolean showp = false;
4375 List<String> ptypes = new CrossRef(seqs, dataset)
4376 .findXrefSourcesForSequences(dna);
4378 for (final String source : ptypes)
4381 final AlignFrame af = this;
4382 JMenuItem xtype = new JMenuItem(source);
4383 xtype.addActionListener(new ActionListener()
4386 public void actionPerformed(ActionEvent e)
4388 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4391 showProducts.add(xtype);
4393 showProducts.setVisible(showp);
4394 showProducts.setEnabled(showp);
4395 } catch (Exception e)
4398 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4406 * Finds and displays cross-references for the selected sequences (protein
4407 * products for nucleotide sequences, dna coding sequences for peptides).
4410 * the sequences to show cross-references for
4412 * true if from a nucleotide alignment (so showing proteins)
4414 * the database to show cross-references for
4416 protected void showProductsFor(final SequenceI[] sel,
4417 final boolean _odna, final String source)
4419 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4424 * Construct and display a new frame containing the translation of this
4425 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4428 public void showTranslation_actionPerformed(ActionEvent e)
4430 AlignmentI al = null;
4433 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4435 al = dna.translateCdna();
4436 } catch (Exception ex)
4438 jalview.bin.Cache.log.error(
4439 "Exception during translation. Please report this !", ex);
4440 final String msg = MessageManager
4441 .getString("label.error_when_translating_sequences_submit_bug_report");
4442 final String errorTitle = MessageManager
4443 .getString("label.implementation_error")
4444 + MessageManager.getString("label.translation_failed");
4445 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4446 JvOptionPane.ERROR_MESSAGE);
4449 if (al == null || al.getHeight() == 0)
4451 final String msg = MessageManager
4452 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4453 final String errorTitle = MessageManager
4454 .getString("label.translation_failed");
4455 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4456 JvOptionPane.WARNING_MESSAGE);
4460 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4461 af.setFileFormat(this.currentFileFormat);
4462 final String newTitle = MessageManager.formatMessage(
4463 "label.translation_of_params",
4464 new Object[] { this.getTitle() });
4465 af.setTitle(newTitle);
4466 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4468 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4469 viewport.openSplitFrame(af, new Alignment(seqs));
4473 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4480 * Set the file format
4484 public void setFileFormat(FileFormatI format)
4486 this.currentFileFormat = format;
4490 * Try to load a features file onto the alignment.
4493 * contents or path to retrieve file
4495 * access mode of file (see jalview.io.AlignFile)
4496 * @return true if features file was parsed correctly.
4498 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4500 return avc.parseFeaturesFile(file, sourceType,
4501 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4506 public void refreshFeatureUI(boolean enableIfNecessary)
4508 // note - currently this is only still here rather than in the controller
4509 // because of the featureSettings hard reference that is yet to be
4511 if (enableIfNecessary)
4513 viewport.setShowSequenceFeatures(true);
4514 showSeqFeatures.setSelected(true);
4520 public void dragEnter(DropTargetDragEvent evt)
4525 public void dragExit(DropTargetEvent evt)
4530 public void dragOver(DropTargetDragEvent evt)
4535 public void dropActionChanged(DropTargetDragEvent evt)
4540 public void drop(DropTargetDropEvent evt)
4542 // JAL-1552 - acceptDrop required before getTransferable call for
4543 // Java's Transferable for native dnd
4544 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4545 Transferable t = evt.getTransferable();
4546 List<String> files = new ArrayList<String>();
4547 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4551 Desktop.transferFromDropTarget(files, protocols, evt, t);
4552 } catch (Exception e)
4554 e.printStackTrace();
4560 // check to see if any of these files have names matching sequences in
4562 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4563 .getAlignment().getSequencesArray());
4565 * Object[] { String,SequenceI}
4567 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4568 ArrayList<String> filesnotmatched = new ArrayList<String>();
4569 for (int i = 0; i < files.size(); i++)
4571 String file = files.get(i).toString();
4573 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4574 if (protocol == DataSourceType.FILE)
4576 File fl = new File(file);
4577 pdbfn = fl.getName();
4579 else if (protocol == DataSourceType.URL)
4581 URL url = new URL(file);
4582 pdbfn = url.getFile();
4584 if (pdbfn.length() > 0)
4586 // attempt to find a match in the alignment
4587 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4588 int l = 0, c = pdbfn.indexOf(".");
4589 while (mtch == null && c != -1)
4594 } while ((c = pdbfn.indexOf(".", l)) > l);
4597 pdbfn = pdbfn.substring(0, l);
4599 mtch = idm.findAllIdMatches(pdbfn);
4603 FileFormatI type = null;
4606 type = new IdentifyFile().identify(file, protocol);
4607 } catch (Exception ex)
4611 if (type != null && type.isStructureFile())
4613 filesmatched.add(new Object[] { file, protocol, mtch });
4617 // File wasn't named like one of the sequences or wasn't a PDB file.
4618 filesnotmatched.add(file);
4622 if (filesmatched.size() > 0)
4624 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4630 "label.automatically_associate_structure_files_with_sequences_same_name",
4631 new Object[] { Integer
4637 .getString("label.automatically_associate_structure_files_by_name"),
4638 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4641 for (Object[] fm : filesmatched)
4643 // try and associate
4644 // TODO: may want to set a standard ID naming formalism for
4645 // associating PDB files which have no IDs.
4646 for (SequenceI toassoc : (SequenceI[]) fm[2])
4648 PDBEntry pe = new AssociatePdbFileWithSeq()
4649 .associatePdbWithSeq((String) fm[0],
4650 (DataSourceType) fm[1], toassoc, false,
4654 System.err.println("Associated file : "
4655 + ((String) fm[0]) + " with "
4656 + toassoc.getDisplayId(true));
4660 alignPanel.paintAlignment(true);
4664 if (filesnotmatched.size() > 0)
4667 && (Cache.getDefault(
4668 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4674 "label.ignore_unmatched_dropped_files_info",
4675 new Object[] { Integer
4682 .getString("label.ignore_unmatched_dropped_files"),
4683 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4687 for (String fn : filesnotmatched)
4689 loadJalviewDataFile(fn, null, null, null);
4693 } catch (Exception ex)
4695 ex.printStackTrace();
4701 * Attempt to load a "dropped" file or URL string: First by testing whether
4702 * it's an Annotation file, then a JNet file, and finally a features file. If
4703 * all are false then the user may have dropped an alignment file onto this
4707 * either a filename or a URL string.
4709 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4710 FileFormatI format, SequenceI assocSeq)
4714 if (sourceType == null)
4716 sourceType = FormatAdapter.checkProtocol(file);
4718 // if the file isn't identified, or not positively identified as some
4719 // other filetype (PFAM is default unidentified alignment file type) then
4720 // try to parse as annotation.
4721 boolean isAnnotation = (format == null || FileFormat.Pfam
4722 .equals(format)) ? new AnnotationFile()
4723 .annotateAlignmentView(viewport, file, sourceType) : false;
4727 // first see if its a T-COFFEE score file
4728 TCoffeeScoreFile tcf = null;
4731 tcf = new TCoffeeScoreFile(file, sourceType);
4734 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4737 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4738 isAnnotation = true;
4740 .setText(MessageManager
4741 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4745 // some problem - if no warning its probable that the ID matching
4746 // process didn't work
4750 tcf.getWarningMessage() == null ? MessageManager
4751 .getString("label.check_file_matches_sequence_ids_alignment")
4752 : tcf.getWarningMessage(),
4754 .getString("label.problem_reading_tcoffee_score_file"),
4755 JvOptionPane.WARNING_MESSAGE);
4762 } catch (Exception x)
4765 .debug("Exception when processing data source as T-COFFEE score file",
4771 // try to see if its a JNet 'concise' style annotation file *before*
4773 // try to parse it as a features file
4776 format = new IdentifyFile().identify(file, sourceType);
4778 if (FileFormat.Jnet.equals(format))
4780 JPredFile predictions = new JPredFile(file, sourceType);
4781 new JnetAnnotationMaker();
4782 JnetAnnotationMaker.add_annotation(predictions,
4783 viewport.getAlignment(), 0, false);
4784 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4785 viewport.getAlignment().setSeqrep(repseq);
4786 ColumnSelection cs = new ColumnSelection();
4787 cs.hideInsertionsFor(repseq);
4788 viewport.setColumnSelection(cs);
4789 isAnnotation = true;
4791 // else if (IdentifyFile.FeaturesFile.equals(format))
4792 else if (FileFormat.Features.equals(format))
4794 if (parseFeaturesFile(file, sourceType))
4796 alignPanel.paintAlignment(true);
4801 new FileLoader().LoadFile(viewport, file, sourceType, format);
4808 alignPanel.adjustAnnotationHeight();
4809 viewport.updateSequenceIdColours();
4810 buildSortByAnnotationScoresMenu();
4811 alignPanel.paintAlignment(true);
4813 } catch (Exception ex)
4815 ex.printStackTrace();
4816 } catch (OutOfMemoryError oom)
4821 } catch (Exception x)
4826 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4827 : "using " + sourceType + " from " + file)
4829 + (format != null ? "(parsing as '" + format
4830 + "' file)" : ""), oom, Desktop.desktop);
4835 * Method invoked by the ChangeListener on the tabbed pane, in other words
4836 * when a different tabbed pane is selected by the user or programmatically.
4839 public void tabSelectionChanged(int index)
4843 alignPanel = alignPanels.get(index);
4844 viewport = alignPanel.av;
4845 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4846 setMenusFromViewport(viewport);
4850 * 'focus' any colour slider that is open to the selected viewport
4852 if (viewport.getConservationSelected())
4854 SliderPanel.setConservationSlider(alignPanel,
4855 viewport.getResidueShading(), alignPanel.getViewName());
4859 SliderPanel.hideConservationSlider();
4861 if (viewport.getAbovePIDThreshold())
4863 SliderPanel.setPIDSliderSource(alignPanel,
4864 viewport.getResidueShading(), alignPanel.getViewName());
4868 SliderPanel.hidePIDSlider();
4872 * If there is a frame linked to this one in a SplitPane, switch it to the
4873 * same view tab index. No infinite recursion of calls should happen, since
4874 * tabSelectionChanged() should not get invoked on setting the selected
4875 * index to an unchanged value. Guard against setting an invalid index
4876 * before the new view peer tab has been created.
4878 final AlignViewportI peer = viewport.getCodingComplement();
4881 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4882 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4884 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4890 * On right mouse click on view tab, prompt for and set new view name.
4893 public void tabbedPane_mousePressed(MouseEvent e)
4895 if (e.isPopupTrigger())
4897 String msg = MessageManager.getString("label.enter_view_name");
4898 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4899 JvOptionPane.QUESTION_MESSAGE);
4903 viewport.viewName = reply;
4904 // TODO warn if reply is in getExistingViewNames()?
4905 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4910 public AlignViewport getCurrentView()
4916 * Open the dialog for regex description parsing.
4919 protected void extractScores_actionPerformed(ActionEvent e)
4921 ParseProperties pp = new jalview.analysis.ParseProperties(
4922 viewport.getAlignment());
4923 // TODO: verify regex and introduce GUI dialog for version 2.5
4924 // if (pp.getScoresFromDescription("col", "score column ",
4925 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4927 if (pp.getScoresFromDescription("description column",
4928 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4930 buildSortByAnnotationScoresMenu();
4938 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4942 protected void showDbRefs_actionPerformed(ActionEvent e)
4944 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4950 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4954 protected void showNpFeats_actionPerformed(ActionEvent e)
4956 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4960 * find the viewport amongst the tabs in this alignment frame and close that
4965 public boolean closeView(AlignViewportI av)
4969 this.closeMenuItem_actionPerformed(false);
4972 Component[] comp = tabbedPane.getComponents();
4973 for (int i = 0; comp != null && i < comp.length; i++)
4975 if (comp[i] instanceof AlignmentPanel)
4977 if (((AlignmentPanel) comp[i]).av == av)
4980 closeView((AlignmentPanel) comp[i]);
4988 protected void build_fetchdbmenu(JMenu webService)
4990 // Temporary hack - DBRef Fetcher always top level ws entry.
4991 // TODO We probably want to store a sequence database checklist in
4992 // preferences and have checkboxes.. rather than individual sources selected
4994 final JMenu rfetch = new JMenu(
4995 MessageManager.getString("action.fetch_db_references"));
4996 rfetch.setToolTipText(MessageManager
4997 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4998 webService.add(rfetch);
5000 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5001 MessageManager.getString("option.trim_retrieved_seqs"));
5002 trimrs.setToolTipText(MessageManager
5003 .getString("label.trim_retrieved_sequences"));
5004 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5005 trimrs.addActionListener(new ActionListener()
5008 public void actionPerformed(ActionEvent e)
5010 trimrs.setSelected(trimrs.isSelected());
5011 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5012 Boolean.valueOf(trimrs.isSelected()).toString());
5016 JMenuItem fetchr = new JMenuItem(
5017 MessageManager.getString("label.standard_databases"));
5018 fetchr.setToolTipText(MessageManager
5019 .getString("label.fetch_embl_uniprot"));
5020 fetchr.addActionListener(new ActionListener()
5024 public void actionPerformed(ActionEvent e)
5026 new Thread(new Runnable()
5031 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5032 .getAlignment().isNucleotide();
5033 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5034 .getSequenceSelection(), alignPanel.alignFrame, null,
5035 alignPanel.alignFrame.featureSettings, isNucleotide);
5036 dbRefFetcher.addListener(new FetchFinishedListenerI()
5039 public void finished()
5041 AlignFrame.this.setMenusForViewport();
5044 dbRefFetcher.fetchDBRefs(false);
5052 final AlignFrame me = this;
5053 new Thread(new Runnable()
5058 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5059 .getSequenceFetcherSingleton(me);
5060 javax.swing.SwingUtilities.invokeLater(new Runnable()
5065 String[] dbclasses = sf.getOrderedSupportedSources();
5066 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5067 // jalview.util.QuickSort.sort(otherdb, otherdb);
5068 List<DbSourceProxy> otherdb;
5069 JMenu dfetch = new JMenu();
5070 JMenu ifetch = new JMenu();
5071 JMenuItem fetchr = null;
5072 int comp = 0, icomp = 0, mcomp = 15;
5073 String mname = null;
5075 for (String dbclass : dbclasses)
5077 otherdb = sf.getSourceProxy(dbclass);
5078 // add a single entry for this class, or submenu allowing 'fetch
5080 if (otherdb == null || otherdb.size() < 1)
5084 // List<DbSourceProxy> dbs=otherdb;
5085 // otherdb=new ArrayList<DbSourceProxy>();
5086 // for (DbSourceProxy db:dbs)
5088 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5092 mname = "From " + dbclass;
5094 if (otherdb.size() == 1)
5096 final DbSourceProxy[] dassource = otherdb
5097 .toArray(new DbSourceProxy[0]);
5098 DbSourceProxy src = otherdb.get(0);
5099 fetchr = new JMenuItem(src.getDbSource());
5100 fetchr.addActionListener(new ActionListener()
5104 public void actionPerformed(ActionEvent e)
5106 new Thread(new Runnable()
5112 boolean isNucleotide = alignPanel.alignFrame
5113 .getViewport().getAlignment()
5115 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5116 alignPanel.av.getSequenceSelection(),
5117 alignPanel.alignFrame, dassource,
5118 alignPanel.alignFrame.featureSettings,
5121 .addListener(new FetchFinishedListenerI()
5124 public void finished()
5126 AlignFrame.this.setMenusForViewport();
5129 dbRefFetcher.fetchDBRefs(false);
5135 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5136 MessageManager.formatMessage(
5137 "label.fetch_retrieve_from",
5138 new Object[] { src.getDbName() })));
5144 final DbSourceProxy[] dassource = otherdb
5145 .toArray(new DbSourceProxy[0]);
5147 DbSourceProxy src = otherdb.get(0);
5148 fetchr = new JMenuItem(MessageManager.formatMessage(
5149 "label.fetch_all_param",
5150 new Object[] { src.getDbSource() }));
5151 fetchr.addActionListener(new ActionListener()
5154 public void actionPerformed(ActionEvent e)
5156 new Thread(new Runnable()
5162 boolean isNucleotide = alignPanel.alignFrame
5163 .getViewport().getAlignment()
5165 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5166 alignPanel.av.getSequenceSelection(),
5167 alignPanel.alignFrame, dassource,
5168 alignPanel.alignFrame.featureSettings,
5171 .addListener(new FetchFinishedListenerI()
5174 public void finished()
5176 AlignFrame.this.setMenusForViewport();
5179 dbRefFetcher.fetchDBRefs(false);
5185 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5186 MessageManager.formatMessage(
5187 "label.fetch_retrieve_from_all_sources",
5189 Integer.valueOf(otherdb.size())
5190 .toString(), src.getDbSource(),
5191 src.getDbName() })));
5194 // and then build the rest of the individual menus
5195 ifetch = new JMenu(MessageManager.formatMessage(
5196 "label.source_from_db_source",
5197 new Object[] { src.getDbSource() }));
5199 String imname = null;
5201 for (DbSourceProxy sproxy : otherdb)
5203 String dbname = sproxy.getDbName();
5204 String sname = dbname.length() > 5 ? dbname.substring(0,
5205 5) + "..." : dbname;
5206 String msname = dbname.length() > 10 ? dbname.substring(
5207 0, 10) + "..." : dbname;
5210 imname = MessageManager.formatMessage(
5211 "label.from_msname", new Object[] { sname });
5213 fetchr = new JMenuItem(msname);
5214 final DbSourceProxy[] dassrc = { sproxy };
5215 fetchr.addActionListener(new ActionListener()
5219 public void actionPerformed(ActionEvent e)
5221 new Thread(new Runnable()
5227 boolean isNucleotide = alignPanel.alignFrame
5228 .getViewport().getAlignment()
5230 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5231 alignPanel.av.getSequenceSelection(),
5232 alignPanel.alignFrame, dassrc,
5233 alignPanel.alignFrame.featureSettings,
5236 .addListener(new FetchFinishedListenerI()
5239 public void finished()
5241 AlignFrame.this.setMenusForViewport();
5244 dbRefFetcher.fetchDBRefs(false);
5250 fetchr.setToolTipText("<html>"
5251 + MessageManager.formatMessage(
5252 "label.fetch_retrieve_from", new Object[]
5256 if (++icomp >= mcomp || i == (otherdb.size()))
5258 ifetch.setText(MessageManager.formatMessage(
5259 "label.source_to_target", imname, sname));
5261 ifetch = new JMenu();
5269 if (comp >= mcomp || dbi >= (dbclasses.length))
5271 dfetch.setText(MessageManager.formatMessage(
5272 "label.source_to_target", mname, dbclass));
5274 dfetch = new JMenu();
5287 * Left justify the whole alignment.
5290 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5292 AlignmentI al = viewport.getAlignment();
5294 viewport.firePropertyChange("alignment", null, al);
5298 * Right justify the whole alignment.
5301 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5303 AlignmentI al = viewport.getAlignment();
5305 viewport.firePropertyChange("alignment", null, al);
5309 public void setShowSeqFeatures(boolean b)
5311 showSeqFeatures.setSelected(b);
5312 viewport.setShowSequenceFeatures(b);
5319 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5320 * awt.event.ActionEvent)
5323 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5325 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5326 alignPanel.paintAlignment(true);
5333 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5337 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5339 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5340 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5348 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5349 * .event.ActionEvent)
5352 protected void showGroupConservation_actionPerformed(ActionEvent e)
5354 viewport.setShowGroupConservation(showGroupConservation.getState());
5355 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5362 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5363 * .event.ActionEvent)
5366 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5368 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5369 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5376 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5377 * .event.ActionEvent)
5380 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5382 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5383 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5387 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5389 showSequenceLogo.setState(true);
5390 viewport.setShowSequenceLogo(true);
5391 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5392 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5396 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5398 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5405 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5406 * .event.ActionEvent)
5409 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5411 if (avc.makeGroupsFromSelection())
5413 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5414 alignPanel.updateAnnotation();
5415 alignPanel.paintAlignment(true);
5419 public void clearAlignmentSeqRep()
5421 // TODO refactor alignmentseqrep to controller
5422 if (viewport.getAlignment().hasSeqrep())
5424 viewport.getAlignment().setSeqrep(null);
5425 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5426 alignPanel.updateAnnotation();
5427 alignPanel.paintAlignment(true);
5432 protected void createGroup_actionPerformed(ActionEvent e)
5434 if (avc.createGroup())
5436 alignPanel.alignmentChanged();
5441 protected void unGroup_actionPerformed(ActionEvent e)
5445 alignPanel.alignmentChanged();
5450 * make the given alignmentPanel the currently selected tab
5452 * @param alignmentPanel
5454 public void setDisplayedView(AlignmentPanel alignmentPanel)
5456 if (!viewport.getSequenceSetId().equals(
5457 alignmentPanel.av.getSequenceSetId()))
5461 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5463 if (tabbedPane != null
5464 && tabbedPane.getTabCount() > 0
5465 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5466 .getSelectedIndex())
5468 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5473 * Action on selection of menu options to Show or Hide annotations.
5476 * @param forSequences
5477 * update sequence-related annotations
5478 * @param forAlignment
5479 * update non-sequence-related annotations
5482 protected void setAnnotationsVisibility(boolean visible,
5483 boolean forSequences, boolean forAlignment)
5485 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5486 .getAlignmentAnnotation();
5491 for (AlignmentAnnotation aa : anns)
5494 * don't display non-positional annotations on an alignment
5496 if (aa.annotations == null)
5500 boolean apply = (aa.sequenceRef == null && forAlignment)
5501 || (aa.sequenceRef != null && forSequences);
5504 aa.visible = visible;
5507 alignPanel.validateAnnotationDimensions(true);
5508 alignPanel.alignmentChanged();
5512 * Store selected annotation sort order for the view and repaint.
5515 protected void sortAnnotations_actionPerformed()
5517 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5519 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5520 alignPanel.paintAlignment(true);
5525 * @return alignment panels in this alignment frame
5527 public List<? extends AlignmentViewPanel> getAlignPanels()
5529 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5533 * Open a new alignment window, with the cDNA associated with this (protein)
5534 * alignment, aligned as is the protein.
5536 protected void viewAsCdna_actionPerformed()
5538 // TODO no longer a menu action - refactor as required
5539 final AlignmentI alignment = getViewport().getAlignment();
5540 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5541 if (mappings == null)
5545 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5546 for (SequenceI aaSeq : alignment.getSequences())
5548 for (AlignedCodonFrame acf : mappings)
5550 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5554 * There is a cDNA mapping for this protein sequence - add to new
5555 * alignment. It will share the same dataset sequence as other mapped
5556 * cDNA (no new mappings need to be created).
5558 final Sequence newSeq = new Sequence(dnaSeq);
5559 newSeq.setDatasetSequence(dnaSeq);
5560 cdnaSeqs.add(newSeq);
5564 if (cdnaSeqs.size() == 0)
5566 // show a warning dialog no mapped cDNA
5569 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5571 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5572 AlignFrame.DEFAULT_HEIGHT);
5573 cdna.alignAs(alignment);
5574 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5576 Desktop.addInternalFrame(alignFrame, newtitle,
5577 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5581 * Set visibility of dna/protein complement view (available when shown in a
5587 protected void showComplement_actionPerformed(boolean show)
5589 SplitContainerI sf = getSplitViewContainer();
5592 sf.setComplementVisible(this, show);
5597 * Generate the reverse (optionally complemented) of the selected sequences,
5598 * and add them to the alignment
5601 protected void showReverse_actionPerformed(boolean complement)
5603 AlignmentI al = null;
5606 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5607 al = dna.reverseCdna(complement);
5608 viewport.addAlignment(al, "");
5609 addHistoryItem(new EditCommand(
5610 MessageManager.getString("label.add_sequences"),
5611 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5612 viewport.getAlignment()));
5613 } catch (Exception ex)
5615 System.err.println(ex.getMessage());
5621 * Try to run a script in the Groovy console, having first ensured that this
5622 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5623 * be targeted at this alignment.
5626 protected void runGroovy_actionPerformed()
5628 Jalview.setCurrentAlignFrame(this);
5629 groovy.ui.Console console = Desktop.getGroovyConsole();
5630 if (console != null)
5634 console.runScript();
5635 } catch (Exception ex)
5637 System.err.println((ex.toString()));
5639 .showInternalMessageDialog(Desktop.desktop, MessageManager
5640 .getString("label.couldnt_run_groovy_script"),
5642 .getString("label.groovy_support_failed"),
5643 JvOptionPane.ERROR_MESSAGE);
5648 System.err.println("Can't run Groovy script as console not found");
5653 * Hides columns containing (or not containing) a specified feature, provided
5654 * that would not leave all columns hidden
5656 * @param featureType
5657 * @param columnsContaining
5660 public boolean hideFeatureColumns(String featureType,
5661 boolean columnsContaining)
5663 boolean notForHiding = avc.markColumnsContainingFeatures(
5664 columnsContaining, false, false, featureType);
5667 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5668 false, featureType))
5670 getViewport().hideSelectedColumns();
5678 protected void selectHighlightedColumns_actionPerformed(
5679 ActionEvent actionEvent)
5681 // include key modifier check in case user selects from menu
5682 avc.markHighlightedColumns(
5683 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5685 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5689 * Rebuilds the Colour menu, including any user-defined colours which have
5690 * been loaded either on startup or during the session
5692 public void buildColourMenu()
5694 colourMenu.removeAll();
5696 colourMenu.add(applyToAllGroups);
5697 colourMenu.add(textColour);
5698 colourMenu.addSeparator();
5700 ColourMenuHelper.addMenuItems(colourMenu, this,
5701 viewport.getAlignment(), false);
5703 colourMenu.addSeparator();
5704 colourMenu.add(conservationMenuItem);
5705 colourMenu.add(modifyConservation);
5706 colourMenu.add(abovePIDThreshold);
5707 colourMenu.add(modifyPID);
5708 colourMenu.add(annotationColour);
5710 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5711 String schemeName = colourScheme == null ? null : colourScheme
5714 ColourMenuHelper.setColourSelected(colourMenu, schemeName);
5718 class PrintThread extends Thread
5722 public PrintThread(AlignmentPanel ap)
5727 static PageFormat pf;
5732 PrinterJob printJob = PrinterJob.getPrinterJob();
5736 printJob.setPrintable(ap, pf);
5740 printJob.setPrintable(ap);
5743 if (printJob.printDialog())
5748 } catch (Exception PrintException)
5750 PrintException.printStackTrace();