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.SimilarityParamsI;
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.HiddenColumns;
57 import jalview.datamodel.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FileParse;
74 import jalview.io.FormatAdapter;
75 import jalview.io.HtmlSvgOutput;
76 import jalview.io.IdentifyFile;
77 import jalview.io.JPredFile;
78 import jalview.io.JalviewFileChooser;
79 import jalview.io.JalviewFileView;
80 import jalview.io.JnetAnnotationMaker;
81 import jalview.io.NewickFile;
82 import jalview.io.ScoreMatrixFile;
83 import jalview.io.TCoffeeScoreFile;
84 import jalview.jbgui.GAlignFrame;
85 import jalview.schemes.ColourSchemeI;
86 import jalview.schemes.ColourSchemes;
87 import jalview.schemes.ResidueColourScheme;
88 import jalview.schemes.TCoffeeColourScheme;
89 import jalview.util.MessageManager;
90 import jalview.viewmodel.AlignmentViewport;
91 import jalview.viewmodel.ViewportRanges;
92 import jalview.ws.DBRefFetcher;
93 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
94 import jalview.ws.jws1.Discoverer;
95 import jalview.ws.jws2.Jws2Discoverer;
96 import jalview.ws.jws2.jabaws2.Jws2Instance;
97 import jalview.ws.seqfetcher.DbSourceProxy;
99 import java.awt.BorderLayout;
100 import java.awt.Component;
101 import java.awt.Rectangle;
102 import java.awt.Toolkit;
103 import java.awt.datatransfer.Clipboard;
104 import java.awt.datatransfer.DataFlavor;
105 import java.awt.datatransfer.StringSelection;
106 import java.awt.datatransfer.Transferable;
107 import java.awt.dnd.DnDConstants;
108 import java.awt.dnd.DropTargetDragEvent;
109 import java.awt.dnd.DropTargetDropEvent;
110 import java.awt.dnd.DropTargetEvent;
111 import java.awt.dnd.DropTargetListener;
112 import java.awt.event.ActionEvent;
113 import java.awt.event.ActionListener;
114 import java.awt.event.FocusAdapter;
115 import java.awt.event.FocusEvent;
116 import java.awt.event.ItemEvent;
117 import java.awt.event.ItemListener;
118 import java.awt.event.KeyAdapter;
119 import java.awt.event.KeyEvent;
120 import java.awt.event.MouseEvent;
121 import java.awt.print.PageFormat;
122 import java.awt.print.PrinterJob;
123 import java.beans.PropertyChangeEvent;
125 import java.io.FileWriter;
126 import java.io.PrintWriter;
128 import java.util.ArrayList;
129 import java.util.Arrays;
130 import java.util.Deque;
131 import java.util.Enumeration;
132 import java.util.Hashtable;
133 import java.util.List;
134 import java.util.Vector;
136 import javax.swing.JCheckBoxMenuItem;
137 import javax.swing.JEditorPane;
138 import javax.swing.JInternalFrame;
139 import javax.swing.JLayeredPane;
140 import javax.swing.JMenu;
141 import javax.swing.JMenuItem;
142 import javax.swing.JScrollPane;
143 import javax.swing.SwingUtilities;
149 * @version $Revision$
151 public class AlignFrame extends GAlignFrame implements DropTargetListener,
152 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
155 public static final int DEFAULT_WIDTH = 700;
157 public static final int DEFAULT_HEIGHT = 500;
160 * The currently displayed panel (selected tabbed view if more than one)
162 public AlignmentPanel alignPanel;
164 AlignViewport viewport;
166 public AlignViewControllerI avc;
168 List<AlignmentPanel> alignPanels = new ArrayList<>();
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, HiddenColumns hiddenColumns, int width,
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, HiddenColumns hiddenColumns, int width,
253 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, HiddenColumns hiddenColumns, int width,
272 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 HiddenColumns 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 avc = new jalview.controller.AlignViewController(this, viewport,
339 if (viewport.getAlignmentConservationAnnotation() == null)
341 // BLOSUM62Colour.setEnabled(false);
342 conservationMenuItem.setEnabled(false);
343 modifyConservation.setEnabled(false);
344 // PIDColour.setEnabled(false);
345 // abovePIDThreshold.setEnabled(false);
346 // modifyPID.setEnabled(false);
349 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
352 if (sortby.equals("Id"))
354 sortIDMenuItem_actionPerformed(null);
356 else if (sortby.equals("Pairwise Identity"))
358 sortPairwiseMenuItem_actionPerformed(null);
362 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
364 setMenusFromViewport(viewport);
365 buildSortByAnnotationScoresMenu();
366 calculateTree.addActionListener(new ActionListener()
370 public void actionPerformed(ActionEvent e)
377 if (Desktop.desktop != null)
379 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
380 addServiceListeners();
384 if (viewport.getWrapAlignment())
386 wrapMenuItem_actionPerformed(null);
389 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
391 this.overviewMenuItem_actionPerformed(null);
396 final List<AlignmentPanel> selviews = new ArrayList<>();
397 final List<AlignmentPanel> origview = new ArrayList<>();
398 final String menuLabel = MessageManager
399 .getString("label.copy_format_from");
400 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
401 new ViewSetProvider()
405 public AlignmentPanel[] getAllAlignmentPanels()
408 origview.add(alignPanel);
409 // make an array of all alignment panels except for this one
410 List<AlignmentPanel> aps = new ArrayList<>(
411 Arrays.asList(Desktop.getAlignmentPanels(null)));
412 aps.remove(AlignFrame.this.alignPanel);
413 return aps.toArray(new AlignmentPanel[aps.size()]);
415 }, selviews, new ItemListener()
419 public void itemStateChanged(ItemEvent e)
421 if (origview.size() > 0)
423 final AlignmentPanel ap = origview.get(0);
426 * Copy the ViewStyle of the selected panel to 'this one'.
427 * Don't change value of 'scaleProteinAsCdna' unless copying
430 ViewStyleI vs = selviews.get(0).getAlignViewport()
432 boolean fromSplitFrame = selviews.get(0)
433 .getAlignViewport().getCodingComplement() != null;
436 vs.setScaleProteinAsCdna(ap.getAlignViewport()
437 .getViewStyle().isScaleProteinAsCdna());
439 ap.getAlignViewport().setViewStyle(vs);
442 * Also rescale ViewStyle of SplitFrame complement if there is
443 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
444 * the whole ViewStyle (allow cDNA protein to have different
447 AlignViewportI complement = ap.getAlignViewport()
448 .getCodingComplement();
449 if (complement != null && vs.isScaleProteinAsCdna())
451 AlignFrame af = Desktop.getAlignFrameFor(complement);
452 ((SplitFrame) af.getSplitViewContainer())
454 af.setMenusForViewport();
458 ap.setSelected(true);
459 ap.alignFrame.setMenusForViewport();
464 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
465 .indexOf("devel") > -1
466 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
467 .indexOf("test") > -1)
469 formatMenu.add(vsel);
471 addFocusListener(new FocusAdapter()
474 public void focusGained(FocusEvent e)
476 Jalview.setCurrentAlignFrame(AlignFrame.this);
483 * Change the filename and format for the alignment, and enable the 'reload'
484 * button functionality.
491 public void setFileName(String file, FileFormatI format)
494 setFileFormat(format);
495 reload.setEnabled(true);
499 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
502 void addKeyListener()
504 addKeyListener(new KeyAdapter()
507 public void keyPressed(KeyEvent evt)
509 if (viewport.cursorMode
510 && ((evt.getKeyCode() >= KeyEvent.VK_0
511 && evt.getKeyCode() <= KeyEvent.VK_9)
512 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
513 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
514 && Character.isDigit(evt.getKeyChar()))
516 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
519 switch (evt.getKeyCode())
522 case 27: // escape key
523 deselectAllSequenceMenuItem_actionPerformed(null);
527 case KeyEvent.VK_DOWN:
528 if (evt.isAltDown() || !viewport.cursorMode)
530 moveSelectedSequences(false);
532 if (viewport.cursorMode)
534 alignPanel.getSeqPanel().moveCursor(0, 1);
539 if (evt.isAltDown() || !viewport.cursorMode)
541 moveSelectedSequences(true);
543 if (viewport.cursorMode)
545 alignPanel.getSeqPanel().moveCursor(0, -1);
550 case KeyEvent.VK_LEFT:
551 if (evt.isAltDown() || !viewport.cursorMode)
553 slideSequences(false,
554 alignPanel.getSeqPanel().getKeyboardNo1());
558 alignPanel.getSeqPanel().moveCursor(-1, 0);
563 case KeyEvent.VK_RIGHT:
564 if (evt.isAltDown() || !viewport.cursorMode)
566 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
570 alignPanel.getSeqPanel().moveCursor(1, 0);
574 case KeyEvent.VK_SPACE:
575 if (viewport.cursorMode)
577 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
578 || evt.isShiftDown() || evt.isAltDown());
582 // case KeyEvent.VK_A:
583 // if (viewport.cursorMode)
585 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
586 // //System.out.println("A");
590 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
591 * System.out.println("closing bracket"); } break;
593 case KeyEvent.VK_DELETE:
594 case KeyEvent.VK_BACK_SPACE:
595 if (!viewport.cursorMode)
597 cut_actionPerformed(null);
601 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
602 || evt.isShiftDown() || evt.isAltDown());
608 if (viewport.cursorMode)
610 alignPanel.getSeqPanel().setCursorRow();
614 if (viewport.cursorMode && !evt.isControlDown())
616 alignPanel.getSeqPanel().setCursorColumn();
620 if (viewport.cursorMode)
622 alignPanel.getSeqPanel().setCursorPosition();
626 case KeyEvent.VK_ENTER:
627 case KeyEvent.VK_COMMA:
628 if (viewport.cursorMode)
630 alignPanel.getSeqPanel().setCursorRowAndColumn();
635 if (viewport.cursorMode)
637 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
641 if (viewport.cursorMode)
643 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
648 viewport.cursorMode = !viewport.cursorMode;
649 statusBar.setText(MessageManager
650 .formatMessage("label.keyboard_editing_mode", new String[]
651 { (viewport.cursorMode ? "on" : "off") }));
652 if (viewport.cursorMode)
654 ViewportRanges ranges = viewport.getRanges();
655 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
657 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
660 alignPanel.getSeqPanel().seqCanvas.repaint();
666 Help.showHelpWindow();
667 } catch (Exception ex)
669 ex.printStackTrace();
674 boolean toggleSeqs = !evt.isControlDown();
675 boolean toggleCols = !evt.isShiftDown();
676 toggleHiddenRegions(toggleSeqs, toggleCols);
681 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
682 boolean modifyExisting = true; // always modify, don't clear
683 // evt.isShiftDown();
684 boolean invertHighlighted = evt.isAltDown();
685 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
689 case KeyEvent.VK_PAGE_UP:
690 viewport.getRanges().pageUp();
692 case KeyEvent.VK_PAGE_DOWN:
693 viewport.getRanges().pageDown();
699 public void keyReleased(KeyEvent evt)
701 switch (evt.getKeyCode())
703 case KeyEvent.VK_LEFT:
704 if (evt.isAltDown() || !viewport.cursorMode)
706 viewport.firePropertyChange("alignment", null,
707 viewport.getAlignment().getSequences());
711 case KeyEvent.VK_RIGHT:
712 if (evt.isAltDown() || !viewport.cursorMode)
714 viewport.firePropertyChange("alignment", null,
715 viewport.getAlignment().getSequences());
723 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
725 ap.alignFrame = this;
726 avc = new jalview.controller.AlignViewController(this, viewport,
731 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
733 int aSize = alignPanels.size();
735 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
737 if (aSize == 1 && ap.av.viewName == null)
739 this.getContentPane().add(ap, BorderLayout.CENTER);
745 setInitialTabVisible();
748 expandViews.setEnabled(true);
749 gatherViews.setEnabled(true);
750 tabbedPane.addTab(ap.av.viewName, ap);
752 ap.setVisible(false);
757 if (ap.av.isPadGaps())
759 ap.av.getAlignment().padGaps();
761 ap.av.updateConservation(ap);
762 ap.av.updateConsensus(ap);
763 ap.av.updateStrucConsensus(ap);
767 public void setInitialTabVisible()
769 expandViews.setEnabled(true);
770 gatherViews.setEnabled(true);
771 tabbedPane.setVisible(true);
772 AlignmentPanel first = alignPanels.get(0);
773 tabbedPane.addTab(first.av.viewName, first);
774 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
777 public AlignViewport getViewport()
782 /* Set up intrinsic listeners for dynamically generated GUI bits. */
783 private void addServiceListeners()
785 final java.beans.PropertyChangeListener thisListener;
786 Desktop.instance.addJalviewPropertyChangeListener("services",
787 thisListener = new java.beans.PropertyChangeListener()
790 public void propertyChange(PropertyChangeEvent evt)
792 // // System.out.println("Discoverer property change.");
793 // if (evt.getPropertyName().equals("services"))
795 SwingUtilities.invokeLater(new Runnable()
802 "Rebuild WS Menu for service change");
803 BuildWebServiceMenu();
810 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
813 public void internalFrameClosed(
814 javax.swing.event.InternalFrameEvent evt)
816 // System.out.println("deregistering discoverer listener");
817 Desktop.instance.removeJalviewPropertyChangeListener("services",
819 closeMenuItem_actionPerformed(true);
822 // Finally, build the menu once to get current service state
823 new Thread(new Runnable()
828 BuildWebServiceMenu();
834 * Configure menu items that vary according to whether the alignment is
835 * nucleotide or protein
837 public void setGUINucleotide()
839 AlignmentI al = getViewport().getAlignment();
840 boolean nucleotide = al.isNucleotide();
842 showTranslation.setVisible(nucleotide);
843 showReverse.setVisible(nucleotide);
844 showReverseComplement.setVisible(nucleotide);
845 conservationMenuItem.setEnabled(!nucleotide);
847 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
848 showGroupConservation.setEnabled(!nucleotide);
850 showComplementMenuItem
851 .setText(nucleotide ? MessageManager.getString("label.protein")
852 : MessageManager.getString("label.nucleotide"));
856 * set up menus for the current viewport. This may be called after any
857 * operation that affects the data in the current view (selection changed,
858 * etc) to update the menus to reflect the new state.
861 public void setMenusForViewport()
863 setMenusFromViewport(viewport);
867 * Need to call this method when tabs are selected for multiple views, or when
868 * loading from Jalview2XML.java
873 void setMenusFromViewport(AlignViewport av)
875 padGapsMenuitem.setSelected(av.isPadGaps());
876 colourTextMenuItem.setSelected(av.isShowColourText());
877 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
878 modifyPID.setEnabled(abovePIDThreshold.isSelected());
879 conservationMenuItem.setSelected(av.getConservationSelected());
880 modifyConservation.setEnabled(conservationMenuItem.isSelected());
881 seqLimits.setSelected(av.getShowJVSuffix());
882 idRightAlign.setSelected(av.isRightAlignIds());
883 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
884 renderGapsMenuItem.setSelected(av.isRenderGaps());
885 wrapMenuItem.setSelected(av.getWrapAlignment());
886 scaleAbove.setVisible(av.getWrapAlignment());
887 scaleLeft.setVisible(av.getWrapAlignment());
888 scaleRight.setVisible(av.getWrapAlignment());
889 annotationPanelMenuItem.setState(av.isShowAnnotation());
891 * Show/hide annotations only enabled if annotation panel is shown
893 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
894 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
895 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
896 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
897 viewBoxesMenuItem.setSelected(av.getShowBoxes());
898 viewTextMenuItem.setSelected(av.getShowText());
899 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
900 showGroupConsensus.setSelected(av.isShowGroupConsensus());
901 showGroupConservation.setSelected(av.isShowGroupConservation());
902 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
903 showSequenceLogo.setSelected(av.isShowSequenceLogo());
904 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
906 ColourMenuHelper.setColourSelected(colourMenu,
907 av.getGlobalColourScheme());
909 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
910 hiddenMarkers.setState(av.getShowHiddenMarkers());
911 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
912 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
913 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
914 autoCalculate.setSelected(av.autoCalculateConsensus);
915 sortByTree.setSelected(av.sortByTree);
916 listenToViewSelections.setSelected(av.followSelection);
918 showProducts.setEnabled(canShowProducts());
919 setGroovyEnabled(Desktop.getGroovyConsole() != null);
925 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
929 public void setGroovyEnabled(boolean b)
931 runGroovy.setEnabled(b);
934 private IProgressIndicator progressBar;
939 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
942 public void setProgressBar(String message, long id)
944 progressBar.setProgressBar(message, id);
948 public void registerHandler(final long id,
949 final IProgressIndicatorHandler handler)
951 progressBar.registerHandler(id, handler);
956 * @return true if any progress bars are still active
959 public boolean operationInProgress()
961 return progressBar.operationInProgress();
965 public void setStatus(String text)
967 statusBar.setText(text);
971 * Added so Castor Mapping file can obtain Jalview Version
973 public String getVersion()
975 return jalview.bin.Cache.getProperty("VERSION");
978 public FeatureRenderer getFeatureRenderer()
980 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
984 public void fetchSequence_actionPerformed(ActionEvent e)
986 new jalview.gui.SequenceFetcher(this);
990 public void addFromFile_actionPerformed(ActionEvent e)
992 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
996 public void reload_actionPerformed(ActionEvent e)
998 if (fileName != null)
1000 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1001 // originating file's format
1002 // TODO: work out how to recover feature settings for correct view(s) when
1003 // file is reloaded.
1004 if (FileFormat.Jalview.equals(currentFileFormat))
1006 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1007 for (int i = 0; i < frames.length; i++)
1009 if (frames[i] instanceof AlignFrame && frames[i] != this
1010 && ((AlignFrame) frames[i]).fileName != null
1011 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1015 frames[i].setSelected(true);
1016 Desktop.instance.closeAssociatedWindows();
1017 } catch (java.beans.PropertyVetoException ex)
1023 Desktop.instance.closeAssociatedWindows();
1025 FileLoader loader = new FileLoader();
1026 DataSourceType protocol = fileName.startsWith("http:")
1027 ? DataSourceType.URL
1028 : DataSourceType.FILE;
1029 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1033 Rectangle bounds = this.getBounds();
1035 FileLoader loader = new FileLoader();
1036 DataSourceType protocol = fileName.startsWith("http:")
1037 ? DataSourceType.URL
1038 : DataSourceType.FILE;
1039 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1040 protocol, currentFileFormat);
1042 newframe.setBounds(bounds);
1043 if (featureSettings != null && featureSettings.isShowing())
1045 final Rectangle fspos = featureSettings.frame.getBounds();
1046 // TODO: need a 'show feature settings' function that takes bounds -
1047 // need to refactor Desktop.addFrame
1048 newframe.featureSettings_actionPerformed(null);
1049 final FeatureSettings nfs = newframe.featureSettings;
1050 SwingUtilities.invokeLater(new Runnable()
1055 nfs.frame.setBounds(fspos);
1058 this.featureSettings.close();
1059 this.featureSettings = null;
1061 this.closeMenuItem_actionPerformed(true);
1067 public void addFromText_actionPerformed(ActionEvent e)
1070 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1074 public void addFromURL_actionPerformed(ActionEvent e)
1076 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1080 public void save_actionPerformed(ActionEvent e)
1082 if (fileName == null || (currentFileFormat == null)
1083 || fileName.startsWith("http"))
1085 saveAs_actionPerformed(null);
1089 saveAlignment(fileName, currentFileFormat);
1100 public void saveAs_actionPerformed(ActionEvent e)
1102 String format = currentFileFormat == null ? null
1103 : currentFileFormat.getName();
1104 JalviewFileChooser chooser = JalviewFileChooser
1105 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1107 chooser.setFileView(new JalviewFileView());
1108 chooser.setDialogTitle(
1109 MessageManager.getString("label.save_alignment_to_file"));
1110 chooser.setToolTipText(MessageManager.getString("action.save"));
1112 int value = chooser.showSaveDialog(this);
1114 if (value == JalviewFileChooser.APPROVE_OPTION)
1116 currentFileFormat = chooser.getSelectedFormat();
1117 while (currentFileFormat == null)
1119 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1120 MessageManager.getString(
1121 "label.select_file_format_before_saving"),
1122 MessageManager.getString("label.file_format_not_specified"),
1123 JvOptionPane.WARNING_MESSAGE);
1124 currentFileFormat = chooser.getSelectedFormat();
1125 value = chooser.showSaveDialog(this);
1126 if (value != JalviewFileChooser.APPROVE_OPTION)
1132 fileName = chooser.getSelectedFile().getPath();
1134 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1136 Cache.setProperty("LAST_DIRECTORY", fileName);
1137 saveAlignment(fileName, currentFileFormat);
1141 public boolean saveAlignment(String file, FileFormatI format)
1143 boolean success = true;
1145 if (FileFormat.Jalview.equals(format))
1147 String shortName = title;
1149 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1151 shortName = shortName.substring(
1152 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1155 success = new Jalview2XML().saveAlignment(this, file, shortName);
1157 statusBar.setText(MessageManager.formatMessage(
1158 "label.successfully_saved_to_file_in_format", new Object[]
1159 { fileName, format }));
1164 AlignmentExportData exportData = getAlignmentForExport(format,
1166 if (exportData.getSettings().isCancelled())
1170 FormatAdapter f = new FormatAdapter(alignPanel,
1171 exportData.getSettings());
1172 String output = f.formatSequences(format, exportData.getAlignment(), // class
1176 // occur in the distant future
1177 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1178 f.getCacheSuffixDefault(format),
1179 viewport.getAlignment().getHiddenColumns());
1189 PrintWriter out = new PrintWriter(new FileWriter(file));
1193 this.setTitle(file);
1194 statusBar.setText(MessageManager.formatMessage(
1195 "label.successfully_saved_to_file_in_format", new Object[]
1196 { fileName, format.getName() }));
1197 } catch (Exception ex)
1200 ex.printStackTrace();
1207 JvOptionPane.showInternalMessageDialog(this, MessageManager
1208 .formatMessage("label.couldnt_save_file", new Object[]
1210 MessageManager.getString("label.error_saving_file"),
1211 JvOptionPane.WARNING_MESSAGE);
1217 private void warningMessage(String warning, String title)
1219 if (new jalview.util.Platform().isHeadless())
1221 System.err.println("Warning: " + title + "\nWarning: " + warning);
1226 JvOptionPane.showInternalMessageDialog(this, warning, title,
1227 JvOptionPane.WARNING_MESSAGE);
1239 protected void outputText_actionPerformed(ActionEvent e)
1241 FileFormatI fileFormat = FileFormats.getInstance()
1242 .forName(e.getActionCommand());
1243 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1245 if (exportData.getSettings().isCancelled())
1249 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1250 cap.setForInput(null);
1253 FileFormatI format = fileFormat;
1254 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1255 .formatSequences(format, exportData.getAlignment(),
1256 exportData.getOmitHidden(),
1257 exportData.getStartEndPostions(),
1258 viewport.getAlignment().getHiddenColumns()));
1259 Desktop.addInternalFrame(cap, MessageManager
1260 .formatMessage("label.alignment_output_command", new Object[]
1261 { e.getActionCommand() }), 600, 500);
1262 } catch (OutOfMemoryError oom)
1264 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1271 public static AlignmentExportData getAlignmentForExport(
1272 FileFormatI format, AlignViewportI viewport,
1273 AlignExportSettingI exportSettings)
1275 AlignmentI alignmentToExport = null;
1276 AlignExportSettingI settings = exportSettings;
1277 String[] omitHidden = null;
1279 HiddenSequences hiddenSeqs = viewport.getAlignment()
1280 .getHiddenSequences();
1282 alignmentToExport = viewport.getAlignment();
1284 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1285 if (settings == null)
1287 settings = new AlignExportSettings(hasHiddenSeqs,
1288 viewport.hasHiddenColumns(), format);
1290 // settings.isExportAnnotations();
1292 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1294 omitHidden = viewport.getViewAsString(false,
1295 settings.isExportHiddenSequences());
1298 int[] alignmentStartEnd = new int[2];
1299 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1301 alignmentToExport = hiddenSeqs.getFullAlignment();
1305 alignmentToExport = viewport.getAlignment();
1307 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1308 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1309 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1310 omitHidden, alignmentStartEnd, settings);
1321 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1323 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1324 htmlSVG.exportHTML(null);
1328 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1330 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1331 bjs.exportHTML(null);
1334 public void createImageMap(File file, String image)
1336 alignPanel.makePNGImageMap(file, image);
1346 public void createPNG(File f)
1348 alignPanel.makePNG(f);
1358 public void createEPS(File f)
1360 alignPanel.makeEPS(f);
1364 public void createSVG(File f)
1366 alignPanel.makeSVG(f);
1370 public void pageSetup_actionPerformed(ActionEvent e)
1372 PrinterJob printJob = PrinterJob.getPrinterJob();
1373 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1383 public void printMenuItem_actionPerformed(ActionEvent e)
1385 // Putting in a thread avoids Swing painting problems
1386 PrintThread thread = new PrintThread(alignPanel);
1391 public void exportFeatures_actionPerformed(ActionEvent e)
1393 new AnnotationExporter().exportFeatures(alignPanel);
1397 public void exportAnnotations_actionPerformed(ActionEvent e)
1399 new AnnotationExporter().exportAnnotations(alignPanel);
1403 public void associatedData_actionPerformed(ActionEvent e)
1405 // Pick the tree file
1406 JalviewFileChooser chooser = new JalviewFileChooser(
1407 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1408 chooser.setFileView(new JalviewFileView());
1409 chooser.setDialogTitle(
1410 MessageManager.getString("label.load_jalview_annotations"));
1411 chooser.setToolTipText(
1412 MessageManager.getString("label.load_jalview_annotations"));
1414 int value = chooser.showOpenDialog(null);
1416 if (value == JalviewFileChooser.APPROVE_OPTION)
1418 String choice = chooser.getSelectedFile().getPath();
1419 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1420 loadJalviewDataFile(choice, null, null, null);
1426 * Close the current view or all views in the alignment frame. If the frame
1427 * only contains one view then the alignment will be removed from memory.
1429 * @param closeAllTabs
1432 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1434 if (alignPanels != null && alignPanels.size() < 2)
1436 closeAllTabs = true;
1441 if (alignPanels != null)
1445 if (this.isClosed())
1447 // really close all the windows - otherwise wait till
1448 // setClosed(true) is called
1449 for (int i = 0; i < alignPanels.size(); i++)
1451 AlignmentPanel ap = alignPanels.get(i);
1458 closeView(alignPanel);
1465 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1466 * be called recursively, with the frame now in 'closed' state
1468 this.setClosed(true);
1470 } catch (Exception ex)
1472 ex.printStackTrace();
1477 * Close the specified panel and close up tabs appropriately.
1479 * @param panelToClose
1481 public void closeView(AlignmentPanel panelToClose)
1483 int index = tabbedPane.getSelectedIndex();
1484 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1485 alignPanels.remove(panelToClose);
1486 panelToClose.closePanel();
1487 panelToClose = null;
1489 tabbedPane.removeTabAt(closedindex);
1490 tabbedPane.validate();
1492 if (index > closedindex || index == tabbedPane.getTabCount())
1494 // modify currently selected tab index if necessary.
1498 this.tabSelectionChanged(index);
1504 void updateEditMenuBar()
1507 if (viewport.getHistoryList().size() > 0)
1509 undoMenuItem.setEnabled(true);
1510 CommandI command = viewport.getHistoryList().peek();
1511 undoMenuItem.setText(MessageManager
1512 .formatMessage("label.undo_command", new Object[]
1513 { command.getDescription() }));
1517 undoMenuItem.setEnabled(false);
1518 undoMenuItem.setText(MessageManager.getString("action.undo"));
1521 if (viewport.getRedoList().size() > 0)
1523 redoMenuItem.setEnabled(true);
1525 CommandI command = viewport.getRedoList().peek();
1526 redoMenuItem.setText(MessageManager
1527 .formatMessage("label.redo_command", new Object[]
1528 { command.getDescription() }));
1532 redoMenuItem.setEnabled(false);
1533 redoMenuItem.setText(MessageManager.getString("action.redo"));
1538 public void addHistoryItem(CommandI command)
1540 if (command.getSize() > 0)
1542 viewport.addToHistoryList(command);
1543 viewport.clearRedoList();
1544 updateEditMenuBar();
1545 viewport.updateHiddenColumns();
1546 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1547 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1548 // viewport.getColumnSelection()
1549 // .getHiddenColumns().size() > 0);
1555 * @return alignment objects for all views
1557 AlignmentI[] getViewAlignments()
1559 if (alignPanels != null)
1561 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1563 for (AlignmentPanel ap : alignPanels)
1565 als[i++] = ap.av.getAlignment();
1569 if (viewport != null)
1571 return new AlignmentI[] { viewport.getAlignment() };
1583 protected void undoMenuItem_actionPerformed(ActionEvent e)
1585 if (viewport.getHistoryList().isEmpty())
1589 CommandI command = viewport.getHistoryList().pop();
1590 viewport.addToRedoList(command);
1591 command.undoCommand(getViewAlignments());
1593 AlignmentViewport originalSource = getOriginatingSource(command);
1594 updateEditMenuBar();
1596 if (originalSource != null)
1598 if (originalSource != viewport)
1601 "Implementation worry: mismatch of viewport origin for undo");
1603 originalSource.updateHiddenColumns();
1604 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1606 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1607 // viewport.getColumnSelection()
1608 // .getHiddenColumns().size() > 0);
1609 originalSource.firePropertyChange("alignment", null,
1610 originalSource.getAlignment().getSequences());
1621 protected void redoMenuItem_actionPerformed(ActionEvent e)
1623 if (viewport.getRedoList().size() < 1)
1628 CommandI command = viewport.getRedoList().pop();
1629 viewport.addToHistoryList(command);
1630 command.doCommand(getViewAlignments());
1632 AlignmentViewport originalSource = getOriginatingSource(command);
1633 updateEditMenuBar();
1635 if (originalSource != null)
1638 if (originalSource != viewport)
1641 "Implementation worry: mismatch of viewport origin for redo");
1643 originalSource.updateHiddenColumns();
1644 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1646 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1647 // viewport.getColumnSelection()
1648 // .getHiddenColumns().size() > 0);
1649 originalSource.firePropertyChange("alignment", null,
1650 originalSource.getAlignment().getSequences());
1654 AlignmentViewport getOriginatingSource(CommandI command)
1656 AlignmentViewport originalSource = null;
1657 // For sequence removal and addition, we need to fire
1658 // the property change event FROM the viewport where the
1659 // original alignment was altered
1660 AlignmentI al = null;
1661 if (command instanceof EditCommand)
1663 EditCommand editCommand = (EditCommand) command;
1664 al = editCommand.getAlignment();
1665 List<Component> comps = PaintRefresher.components
1666 .get(viewport.getSequenceSetId());
1668 for (Component comp : comps)
1670 if (comp instanceof AlignmentPanel)
1672 if (al == ((AlignmentPanel) comp).av.getAlignment())
1674 originalSource = ((AlignmentPanel) comp).av;
1681 if (originalSource == null)
1683 // The original view is closed, we must validate
1684 // the current view against the closed view first
1687 PaintRefresher.validateSequences(al, viewport.getAlignment());
1690 originalSource = viewport;
1693 return originalSource;
1702 public void moveSelectedSequences(boolean up)
1704 SequenceGroup sg = viewport.getSelectionGroup();
1710 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1711 viewport.getHiddenRepSequences(), up);
1712 alignPanel.paintAlignment(true, false);
1715 synchronized void slideSequences(boolean right, int size)
1717 List<SequenceI> sg = new ArrayList<>();
1718 if (viewport.cursorMode)
1720 sg.add(viewport.getAlignment()
1721 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1723 else if (viewport.getSelectionGroup() != null
1724 && viewport.getSelectionGroup().getSize() != viewport
1725 .getAlignment().getHeight())
1727 sg = viewport.getSelectionGroup()
1728 .getSequences(viewport.getHiddenRepSequences());
1736 List<SequenceI> invertGroup = new ArrayList<>();
1738 for (SequenceI seq : viewport.getAlignment().getSequences())
1740 if (!sg.contains(seq))
1742 invertGroup.add(seq);
1746 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1748 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1749 for (int i = 0; i < invertGroup.size(); i++)
1751 seqs2[i] = invertGroup.get(i);
1754 SlideSequencesCommand ssc;
1757 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1758 viewport.getGapCharacter());
1762 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1763 viewport.getGapCharacter());
1766 int groupAdjustment = 0;
1767 if (ssc.getGapsInsertedBegin() && right)
1769 if (viewport.cursorMode)
1771 alignPanel.getSeqPanel().moveCursor(size, 0);
1775 groupAdjustment = size;
1778 else if (!ssc.getGapsInsertedBegin() && !right)
1780 if (viewport.cursorMode)
1782 alignPanel.getSeqPanel().moveCursor(-size, 0);
1786 groupAdjustment = -size;
1790 if (groupAdjustment != 0)
1792 viewport.getSelectionGroup().setStartRes(
1793 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1794 viewport.getSelectionGroup().setEndRes(
1795 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1799 * just extend the last slide command if compatible; but not if in
1800 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1802 boolean appendHistoryItem = false;
1803 Deque<CommandI> historyList = viewport.getHistoryList();
1804 boolean inSplitFrame = getSplitViewContainer() != null;
1805 if (!inSplitFrame && historyList != null && historyList.size() > 0
1806 && historyList.peek() instanceof SlideSequencesCommand)
1808 appendHistoryItem = ssc.appendSlideCommand(
1809 (SlideSequencesCommand) historyList.peek());
1812 if (!appendHistoryItem)
1814 addHistoryItem(ssc);
1827 protected void copy_actionPerformed(ActionEvent e)
1830 if (viewport.getSelectionGroup() == null)
1834 // TODO: preserve the ordering of displayed alignment annotation in any
1835 // internal paste (particularly sequence associated annotation)
1836 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1837 String[] omitHidden = null;
1839 if (viewport.hasHiddenColumns())
1841 omitHidden = viewport.getViewAsString(true);
1844 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1845 seqs, omitHidden, null);
1847 StringSelection ss = new StringSelection(output);
1851 jalview.gui.Desktop.internalCopy = true;
1852 // Its really worth setting the clipboard contents
1853 // to empty before setting the large StringSelection!!
1854 Toolkit.getDefaultToolkit().getSystemClipboard()
1855 .setContents(new StringSelection(""), null);
1857 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1859 } catch (OutOfMemoryError er)
1861 new OOMWarning("copying region", er);
1865 ArrayList<int[]> hiddenColumns = null;
1866 if (viewport.hasHiddenColumns())
1868 hiddenColumns = new ArrayList<>();
1869 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1870 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1871 ArrayList<int[]> hiddenRegions = viewport.getAlignment()
1872 .getHiddenColumns().getHiddenColumnsCopy();
1873 for (int[] region : hiddenRegions)
1875 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1879 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1884 Desktop.jalviewClipboard = new Object[] { seqs,
1885 viewport.getAlignment().getDataset(), hiddenColumns };
1886 statusBar.setText(MessageManager.formatMessage(
1887 "label.copied_sequences_to_clipboard", new Object[]
1888 { Integer.valueOf(seqs.length).toString() }));
1898 protected void pasteNew_actionPerformed(ActionEvent e)
1910 protected void pasteThis_actionPerformed(ActionEvent e)
1916 * Paste contents of Jalview clipboard
1918 * @param newAlignment
1919 * true to paste to a new alignment, otherwise add to this.
1921 void paste(boolean newAlignment)
1923 boolean externalPaste = true;
1926 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1927 Transferable contents = c.getContents(this);
1929 if (contents == null)
1938 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1939 if (str.length() < 1)
1944 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1946 } catch (OutOfMemoryError er)
1948 new OOMWarning("Out of memory pasting sequences!!", er);
1952 SequenceI[] sequences;
1953 boolean annotationAdded = false;
1954 AlignmentI alignment = null;
1956 if (Desktop.jalviewClipboard != null)
1958 // The clipboard was filled from within Jalview, we must use the
1960 // And dataset from the copied alignment
1961 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1962 // be doubly sure that we create *new* sequence objects.
1963 sequences = new SequenceI[newseq.length];
1964 for (int i = 0; i < newseq.length; i++)
1966 sequences[i] = new Sequence(newseq[i]);
1968 alignment = new Alignment(sequences);
1969 externalPaste = false;
1973 // parse the clipboard as an alignment.
1974 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1976 sequences = alignment.getSequencesArray();
1980 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1986 if (Desktop.jalviewClipboard != null)
1988 // dataset is inherited
1989 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1993 // new dataset is constructed
1994 alignment.setDataset(null);
1996 alwidth = alignment.getWidth() + 1;
2000 AlignmentI pastedal = alignment; // preserve pasted alignment object
2001 // Add pasted sequences and dataset into existing alignment.
2002 alignment = viewport.getAlignment();
2003 alwidth = alignment.getWidth() + 1;
2004 // decide if we need to import sequences from an existing dataset
2005 boolean importDs = Desktop.jalviewClipboard != null
2006 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2007 // importDs==true instructs us to copy over new dataset sequences from
2008 // an existing alignment
2009 Vector newDs = (importDs) ? new Vector() : null; // used to create
2010 // minimum dataset set
2012 for (int i = 0; i < sequences.length; i++)
2016 newDs.addElement(null);
2018 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2020 if (importDs && ds != null)
2022 if (!newDs.contains(ds))
2024 newDs.setElementAt(ds, i);
2025 ds = new Sequence(ds);
2026 // update with new dataset sequence
2027 sequences[i].setDatasetSequence(ds);
2031 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2036 // copy and derive new dataset sequence
2037 sequences[i] = sequences[i].deriveSequence();
2038 alignment.getDataset()
2039 .addSequence(sequences[i].getDatasetSequence());
2040 // TODO: avoid creation of duplicate dataset sequences with a
2041 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2043 alignment.addSequence(sequences[i]); // merges dataset
2047 newDs.clear(); // tidy up
2049 if (alignment.getAlignmentAnnotation() != null)
2051 for (AlignmentAnnotation alan : alignment
2052 .getAlignmentAnnotation())
2054 if (alan.graphGroup > fgroup)
2056 fgroup = alan.graphGroup;
2060 if (pastedal.getAlignmentAnnotation() != null)
2062 // Add any annotation attached to alignment.
2063 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2064 for (int i = 0; i < alann.length; i++)
2066 annotationAdded = true;
2067 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2069 AlignmentAnnotation newann = new AlignmentAnnotation(
2071 if (newann.graphGroup > -1)
2073 if (newGraphGroups.size() <= newann.graphGroup
2074 || newGraphGroups.get(newann.graphGroup) == null)
2076 for (int q = newGraphGroups
2077 .size(); q <= newann.graphGroup; q++)
2079 newGraphGroups.add(q, null);
2081 newGraphGroups.set(newann.graphGroup,
2082 new Integer(++fgroup));
2084 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2088 newann.padAnnotation(alwidth);
2089 alignment.addAnnotation(newann);
2099 addHistoryItem(new EditCommand(
2100 MessageManager.getString("label.add_sequences"),
2101 Action.PASTE, sequences, 0, alignment.getWidth(),
2104 // Add any annotations attached to sequences
2105 for (int i = 0; i < sequences.length; i++)
2107 if (sequences[i].getAnnotation() != null)
2109 AlignmentAnnotation newann;
2110 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2112 annotationAdded = true;
2113 newann = sequences[i].getAnnotation()[a];
2114 newann.adjustForAlignment();
2115 newann.padAnnotation(alwidth);
2116 if (newann.graphGroup > -1)
2118 if (newann.graphGroup > -1)
2120 if (newGraphGroups.size() <= newann.graphGroup
2121 || newGraphGroups.get(newann.graphGroup) == null)
2123 for (int q = newGraphGroups
2124 .size(); q <= newann.graphGroup; q++)
2126 newGraphGroups.add(q, null);
2128 newGraphGroups.set(newann.graphGroup,
2129 new Integer(++fgroup));
2131 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2135 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2139 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2147 // propagate alignment changed.
2148 viewport.getRanges().setEndSeq(alignment.getHeight());
2149 if (annotationAdded)
2151 // Duplicate sequence annotation in all views.
2152 AlignmentI[] alview = this.getViewAlignments();
2153 for (int i = 0; i < sequences.length; i++)
2155 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2160 for (int avnum = 0; avnum < alview.length; avnum++)
2162 if (alview[avnum] != alignment)
2164 // duplicate in a view other than the one with input focus
2165 int avwidth = alview[avnum].getWidth() + 1;
2166 // this relies on sann being preserved after we
2167 // modify the sequence's annotation array for each duplication
2168 for (int a = 0; a < sann.length; a++)
2170 AlignmentAnnotation newann = new AlignmentAnnotation(
2172 sequences[i].addAlignmentAnnotation(newann);
2173 newann.padAnnotation(avwidth);
2174 alview[avnum].addAnnotation(newann); // annotation was
2175 // duplicated earlier
2176 // TODO JAL-1145 graphGroups are not updated for sequence
2177 // annotation added to several views. This may cause
2179 alview[avnum].setAnnotationIndex(newann, a);
2184 buildSortByAnnotationScoresMenu();
2186 viewport.firePropertyChange("alignment", null,
2187 alignment.getSequences());
2188 if (alignPanels != null)
2190 for (AlignmentPanel ap : alignPanels)
2192 ap.validateAnnotationDimensions(false);
2197 alignPanel.validateAnnotationDimensions(false);
2203 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2205 String newtitle = new String("Copied sequences");
2207 if (Desktop.jalviewClipboard != null
2208 && Desktop.jalviewClipboard[2] != null)
2210 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2211 for (int[] region : hc)
2213 af.viewport.hideColumns(region[0], region[1]);
2217 // >>>This is a fix for the moment, until a better solution is
2219 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2220 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2221 .getFeatureRenderer());
2223 // TODO: maintain provenance of an alignment, rather than just make the
2224 // title a concatenation of operations.
2227 if (title.startsWith("Copied sequences"))
2233 newtitle = newtitle.concat("- from " + title);
2238 newtitle = new String("Pasted sequences");
2241 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2246 } catch (Exception ex)
2248 ex.printStackTrace();
2249 System.out.println("Exception whilst pasting: " + ex);
2250 // could be anything being pasted in here
2256 protected void expand_newalign(ActionEvent e)
2260 AlignmentI alignment = AlignmentUtils
2261 .expandContext(getViewport().getAlignment(), -1);
2262 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2264 String newtitle = new String("Flanking alignment");
2266 if (Desktop.jalviewClipboard != null
2267 && Desktop.jalviewClipboard[2] != null)
2269 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2270 for (int region[] : hc)
2272 af.viewport.hideColumns(region[0], region[1]);
2276 // >>>This is a fix for the moment, until a better solution is
2278 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2279 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2280 .getFeatureRenderer());
2282 // TODO: maintain provenance of an alignment, rather than just make the
2283 // title a concatenation of operations.
2285 if (title.startsWith("Copied sequences"))
2291 newtitle = newtitle.concat("- from " + title);
2295 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2297 } catch (Exception ex)
2299 ex.printStackTrace();
2300 System.out.println("Exception whilst pasting: " + ex);
2301 // could be anything being pasted in here
2302 } catch (OutOfMemoryError oom)
2304 new OOMWarning("Viewing flanking region of alignment", oom);
2315 protected void cut_actionPerformed(ActionEvent e)
2317 copy_actionPerformed(null);
2318 delete_actionPerformed(null);
2328 protected void delete_actionPerformed(ActionEvent evt)
2331 SequenceGroup sg = viewport.getSelectionGroup();
2338 * If the cut affects all sequences, warn, remove highlighted columns
2340 if (sg.getSize() == viewport.getAlignment().getHeight())
2342 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2343 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2344 if (isEntireAlignWidth)
2346 int confirm = JvOptionPane.showConfirmDialog(this,
2347 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2348 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2349 JvOptionPane.OK_CANCEL_OPTION);
2351 if (confirm == JvOptionPane.CANCEL_OPTION
2352 || confirm == JvOptionPane.CLOSED_OPTION)
2357 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2358 sg.getEndRes() + 1);
2360 SequenceI[] cut = sg.getSequences()
2361 .toArray(new SequenceI[sg.getSize()]);
2363 addHistoryItem(new EditCommand(
2364 MessageManager.getString("label.cut_sequences"), Action.CUT,
2365 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2366 viewport.getAlignment()));
2368 viewport.setSelectionGroup(null);
2369 viewport.sendSelection();
2370 viewport.getAlignment().deleteGroup(sg);
2372 viewport.firePropertyChange("alignment", null,
2373 viewport.getAlignment().getSequences());
2374 if (viewport.getAlignment().getHeight() < 1)
2378 this.setClosed(true);
2379 } catch (Exception ex)
2392 protected void deleteGroups_actionPerformed(ActionEvent e)
2394 if (avc.deleteGroups())
2396 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2397 alignPanel.updateAnnotation();
2398 alignPanel.paintAlignment(true, true);
2409 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2411 SequenceGroup sg = new SequenceGroup();
2413 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2415 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2418 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2419 viewport.setSelectionGroup(sg);
2420 viewport.sendSelection();
2421 // JAL-2034 - should delegate to
2422 // alignPanel to decide if overview needs
2424 alignPanel.paintAlignment(false, false);
2425 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2435 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2437 if (viewport.cursorMode)
2439 alignPanel.getSeqPanel().keyboardNo1 = null;
2440 alignPanel.getSeqPanel().keyboardNo2 = null;
2442 viewport.setSelectionGroup(null);
2443 viewport.getColumnSelection().clear();
2444 viewport.setSelectionGroup(null);
2445 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2446 // JAL-2034 - should delegate to
2447 // alignPanel to decide if overview needs
2449 alignPanel.paintAlignment(false, false);
2450 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2451 viewport.sendSelection();
2461 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2463 SequenceGroup sg = viewport.getSelectionGroup();
2467 selectAllSequenceMenuItem_actionPerformed(null);
2472 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2474 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2476 // JAL-2034 - should delegate to
2477 // alignPanel to decide if overview needs
2480 alignPanel.paintAlignment(true, false);
2481 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2482 viewport.sendSelection();
2486 public void invertColSel_actionPerformed(ActionEvent e)
2488 viewport.invertColumnSelection();
2489 alignPanel.paintAlignment(true, false);
2490 viewport.sendSelection();
2500 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2502 trimAlignment(true);
2512 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2514 trimAlignment(false);
2517 void trimAlignment(boolean trimLeft)
2519 ColumnSelection colSel = viewport.getColumnSelection();
2522 if (!colSel.isEmpty())
2526 column = colSel.getMin();
2530 column = colSel.getMax();
2534 if (viewport.getSelectionGroup() != null)
2536 seqs = viewport.getSelectionGroup()
2537 .getSequencesAsArray(viewport.getHiddenRepSequences());
2541 seqs = viewport.getAlignment().getSequencesArray();
2544 TrimRegionCommand trimRegion;
2547 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2548 column, viewport.getAlignment());
2549 viewport.getRanges().setStartRes(0);
2553 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2554 column, viewport.getAlignment());
2557 statusBar.setText(MessageManager
2558 .formatMessage("label.removed_columns", new String[]
2559 { Integer.valueOf(trimRegion.getSize()).toString() }));
2561 addHistoryItem(trimRegion);
2563 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2565 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2566 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2568 viewport.getAlignment().deleteGroup(sg);
2572 viewport.firePropertyChange("alignment", null,
2573 viewport.getAlignment().getSequences());
2584 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2586 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2589 if (viewport.getSelectionGroup() != null)
2591 seqs = viewport.getSelectionGroup()
2592 .getSequencesAsArray(viewport.getHiddenRepSequences());
2593 start = viewport.getSelectionGroup().getStartRes();
2594 end = viewport.getSelectionGroup().getEndRes();
2598 seqs = viewport.getAlignment().getSequencesArray();
2601 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2602 "Remove Gapped Columns", seqs, start, end,
2603 viewport.getAlignment());
2605 addHistoryItem(removeGapCols);
2607 statusBar.setText(MessageManager
2608 .formatMessage("label.removed_empty_columns", new Object[]
2609 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2611 // This is to maintain viewport position on first residue
2612 // of first sequence
2613 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2614 ViewportRanges ranges = viewport.getRanges();
2615 int startRes = seq.findPosition(ranges.getStartRes());
2616 // ShiftList shifts;
2617 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2618 // edit.alColumnChanges=shifts.getInverse();
2619 // if (viewport.hasHiddenColumns)
2620 // viewport.getColumnSelection().compensateForEdits(shifts);
2621 ranges.setStartRes(seq.findIndex(startRes) - 1);
2622 viewport.firePropertyChange("alignment", null,
2623 viewport.getAlignment().getSequences());
2634 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2636 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2639 if (viewport.getSelectionGroup() != null)
2641 seqs = viewport.getSelectionGroup()
2642 .getSequencesAsArray(viewport.getHiddenRepSequences());
2643 start = viewport.getSelectionGroup().getStartRes();
2644 end = viewport.getSelectionGroup().getEndRes();
2648 seqs = viewport.getAlignment().getSequencesArray();
2651 // This is to maintain viewport position on first residue
2652 // of first sequence
2653 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2654 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2656 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2657 viewport.getAlignment()));
2659 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2661 viewport.firePropertyChange("alignment", null,
2662 viewport.getAlignment().getSequences());
2673 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2675 viewport.setPadGaps(padGapsMenuitem.isSelected());
2676 viewport.firePropertyChange("alignment", null,
2677 viewport.getAlignment().getSequences());
2687 public void findMenuItem_actionPerformed(ActionEvent e)
2693 * Create a new view of the current alignment.
2696 public void newView_actionPerformed(ActionEvent e)
2698 newView(null, true);
2702 * Creates and shows a new view of the current alignment.
2705 * title of newly created view; if null, one will be generated
2706 * @param copyAnnotation
2707 * if true then duplicate all annnotation, groups and settings
2708 * @return new alignment panel, already displayed.
2710 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2713 * Create a new AlignmentPanel (with its own, new Viewport)
2715 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2716 if (!copyAnnotation)
2719 * remove all groups and annotation except for the automatic stuff
2721 newap.av.getAlignment().deleteAllGroups();
2722 newap.av.getAlignment().deleteAllAnnotations(false);
2725 newap.av.setGatherViewsHere(false);
2727 if (viewport.viewName == null)
2729 viewport.viewName = MessageManager
2730 .getString("label.view_name_original");
2734 * Views share the same edits undo and redo stacks
2736 newap.av.setHistoryList(viewport.getHistoryList());
2737 newap.av.setRedoList(viewport.getRedoList());
2740 * Views share the same mappings; need to deregister any new mappings
2741 * created by copyAlignPanel, and register the new reference to the shared
2744 newap.av.replaceMappings(viewport.getAlignment());
2747 * start up cDNA consensus (if applicable) now mappings are in place
2749 if (newap.av.initComplementConsensus())
2751 newap.refresh(true); // adjust layout of annotations
2754 newap.av.viewName = getNewViewName(viewTitle);
2756 addAlignmentPanel(newap, true);
2757 newap.alignmentChanged();
2759 if (alignPanels.size() == 2)
2761 viewport.setGatherViewsHere(true);
2763 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2768 * Make a new name for the view, ensuring it is unique within the current
2769 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2770 * these now use viewId. Unique view names are still desirable for usability.)
2775 protected String getNewViewName(String viewTitle)
2777 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2778 boolean addFirstIndex = false;
2779 if (viewTitle == null || viewTitle.trim().length() == 0)
2781 viewTitle = MessageManager.getString("action.view");
2782 addFirstIndex = true;
2786 index = 1;// we count from 1 if given a specific name
2788 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2790 List<Component> comps = PaintRefresher.components
2791 .get(viewport.getSequenceSetId());
2793 List<String> existingNames = getExistingViewNames(comps);
2795 while (existingNames.contains(newViewName))
2797 newViewName = viewTitle + " " + (++index);
2803 * Returns a list of distinct view names found in the given list of
2804 * components. View names are held on the viewport of an AlignmentPanel.
2809 protected List<String> getExistingViewNames(List<Component> comps)
2811 List<String> existingNames = new ArrayList<>();
2812 for (Component comp : comps)
2814 if (comp instanceof AlignmentPanel)
2816 AlignmentPanel ap = (AlignmentPanel) comp;
2817 if (!existingNames.contains(ap.av.viewName))
2819 existingNames.add(ap.av.viewName);
2823 return existingNames;
2827 * Explode tabbed views into separate windows.
2830 public void expandViews_actionPerformed(ActionEvent e)
2832 Desktop.explodeViews(this);
2836 * Gather views in separate windows back into a tabbed presentation.
2839 public void gatherViews_actionPerformed(ActionEvent e)
2841 Desktop.instance.gatherViews(this);
2851 public void font_actionPerformed(ActionEvent e)
2853 new FontChooser(alignPanel);
2863 protected void seqLimit_actionPerformed(ActionEvent e)
2865 viewport.setShowJVSuffix(seqLimits.isSelected());
2867 alignPanel.getIdPanel().getIdCanvas()
2868 .setPreferredSize(alignPanel.calculateIdWidth());
2869 alignPanel.paintAlignment(true, false);
2873 public void idRightAlign_actionPerformed(ActionEvent e)
2875 viewport.setRightAlignIds(idRightAlign.isSelected());
2876 alignPanel.paintAlignment(false, false);
2880 public void centreColumnLabels_actionPerformed(ActionEvent e)
2882 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2883 alignPanel.paintAlignment(false, false);
2889 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2892 protected void followHighlight_actionPerformed()
2895 * Set the 'follow' flag on the Viewport (and scroll to position if now
2898 final boolean state = this.followHighlightMenuItem.getState();
2899 viewport.setFollowHighlight(state);
2902 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2913 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2915 viewport.setColourText(colourTextMenuItem.isSelected());
2916 alignPanel.paintAlignment(false, false);
2926 public void wrapMenuItem_actionPerformed(ActionEvent e)
2928 scaleAbove.setVisible(wrapMenuItem.isSelected());
2929 scaleLeft.setVisible(wrapMenuItem.isSelected());
2930 scaleRight.setVisible(wrapMenuItem.isSelected());
2931 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2932 alignPanel.updateLayout();
2936 public void showAllSeqs_actionPerformed(ActionEvent e)
2938 viewport.showAllHiddenSeqs();
2942 public void showAllColumns_actionPerformed(ActionEvent e)
2944 viewport.showAllHiddenColumns();
2945 alignPanel.paintAlignment(true, true);
2946 viewport.sendSelection();
2950 public void hideSelSequences_actionPerformed(ActionEvent e)
2952 viewport.hideAllSelectedSeqs();
2956 * called by key handler and the hide all/show all menu items
2961 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2964 boolean hide = false;
2965 SequenceGroup sg = viewport.getSelectionGroup();
2966 if (!toggleSeqs && !toggleCols)
2968 // Hide everything by the current selection - this is a hack - we do the
2969 // invert and then hide
2970 // first check that there will be visible columns after the invert.
2971 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2972 && sg.getStartRes() <= sg.getEndRes()))
2974 // now invert the sequence set, if required - empty selection implies
2975 // that no hiding is required.
2978 invertSequenceMenuItem_actionPerformed(null);
2979 sg = viewport.getSelectionGroup();
2983 viewport.expandColSelection(sg, true);
2984 // finally invert the column selection and get the new sequence
2986 invertColSel_actionPerformed(null);
2993 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2995 hideSelSequences_actionPerformed(null);
2998 else if (!(toggleCols && viewport.hasSelectedColumns()))
3000 showAllSeqs_actionPerformed(null);
3006 if (viewport.hasSelectedColumns())
3008 hideSelColumns_actionPerformed(null);
3011 viewport.setSelectionGroup(sg);
3016 showAllColumns_actionPerformed(null);
3025 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3026 * event.ActionEvent)
3029 public void hideAllButSelection_actionPerformed(ActionEvent e)
3031 toggleHiddenRegions(false, false);
3032 viewport.sendSelection();
3039 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3043 public void hideAllSelection_actionPerformed(ActionEvent e)
3045 SequenceGroup sg = viewport.getSelectionGroup();
3046 viewport.expandColSelection(sg, false);
3047 viewport.hideAllSelectedSeqs();
3048 viewport.hideSelectedColumns();
3049 alignPanel.paintAlignment(true, true);
3050 viewport.sendSelection();
3057 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3061 public void showAllhidden_actionPerformed(ActionEvent e)
3063 viewport.showAllHiddenColumns();
3064 viewport.showAllHiddenSeqs();
3065 alignPanel.paintAlignment(true, true);
3066 viewport.sendSelection();
3070 public void hideSelColumns_actionPerformed(ActionEvent e)
3072 viewport.hideSelectedColumns();
3073 alignPanel.paintAlignment(true, true);
3074 viewport.sendSelection();
3078 public void hiddenMarkers_actionPerformed(ActionEvent e)
3080 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3091 protected void scaleAbove_actionPerformed(ActionEvent e)
3093 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3094 // TODO: do we actually need to update overview for scale above change ?
3095 alignPanel.paintAlignment(true, false);
3105 protected void scaleLeft_actionPerformed(ActionEvent e)
3107 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3108 alignPanel.paintAlignment(true, false);
3118 protected void scaleRight_actionPerformed(ActionEvent e)
3120 viewport.setScaleRightWrapped(scaleRight.isSelected());
3121 alignPanel.paintAlignment(true, false);
3131 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3133 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3134 alignPanel.paintAlignment(false, false);
3144 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3146 viewport.setShowText(viewTextMenuItem.isSelected());
3147 alignPanel.paintAlignment(false, false);
3157 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3159 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3160 alignPanel.paintAlignment(false, false);
3163 public FeatureSettings featureSettings;
3166 public FeatureSettingsControllerI getFeatureSettingsUI()
3168 return featureSettings;
3172 public void featureSettings_actionPerformed(ActionEvent e)
3174 if (featureSettings != null)
3176 featureSettings.close();
3177 featureSettings = null;
3179 if (!showSeqFeatures.isSelected())
3181 // make sure features are actually displayed
3182 showSeqFeatures.setSelected(true);
3183 showSeqFeatures_actionPerformed(null);
3185 featureSettings = new FeatureSettings(this);
3189 * Set or clear 'Show Sequence Features'
3195 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3197 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3198 alignPanel.paintAlignment(true, true);
3202 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3203 * the annotations panel as a whole.
3205 * The options to show/hide all annotations should be enabled when the panel
3206 * is shown, and disabled when the panel is hidden.
3211 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3213 final boolean setVisible = annotationPanelMenuItem.isSelected();
3214 viewport.setShowAnnotation(setVisible);
3215 this.showAllSeqAnnotations.setEnabled(setVisible);
3216 this.hideAllSeqAnnotations.setEnabled(setVisible);
3217 this.showAllAlAnnotations.setEnabled(setVisible);
3218 this.hideAllAlAnnotations.setEnabled(setVisible);
3219 alignPanel.updateLayout();
3223 public void alignmentProperties()
3225 JEditorPane editPane = new JEditorPane("text/html", "");
3226 editPane.setEditable(false);
3227 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3230 MessageManager.formatMessage("label.html_content", new Object[]
3231 { contents.toString() }));
3232 JInternalFrame frame = new JInternalFrame();
3233 frame.getContentPane().add(new JScrollPane(editPane));
3235 Desktop.addInternalFrame(frame, MessageManager
3236 .formatMessage("label.alignment_properties", new Object[]
3237 { getTitle() }), 500, 400);
3247 public void overviewMenuItem_actionPerformed(ActionEvent e)
3249 if (alignPanel.overviewPanel != null)
3254 JInternalFrame frame = new JInternalFrame();
3255 final OverviewPanel overview = new OverviewPanel(alignPanel);
3256 frame.setContentPane(overview);
3257 Desktop.addInternalFrame(frame, MessageManager
3258 .formatMessage("label.overview_params", new Object[]
3259 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3262 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3263 frame.addInternalFrameListener(
3264 new javax.swing.event.InternalFrameAdapter()
3267 public void internalFrameClosed(
3268 javax.swing.event.InternalFrameEvent evt)
3271 alignPanel.setOverviewPanel(null);
3275 alignPanel.setOverviewPanel(overview);
3279 public void textColour_actionPerformed()
3281 new TextColourChooser().chooseColour(alignPanel, null);
3285 * public void covariationColour_actionPerformed() {
3287 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3291 public void annotationColour_actionPerformed()
3293 new AnnotationColourChooser(viewport, alignPanel);
3297 public void annotationColumn_actionPerformed(ActionEvent e)
3299 new AnnotationColumnChooser(viewport, alignPanel);
3303 * Action on the user checking or unchecking the option to apply the selected
3304 * colour scheme to all groups. If unchecked, groups may have their own
3305 * independent colour schemes.
3310 public void applyToAllGroups_actionPerformed(boolean selected)
3312 viewport.setColourAppliesToAllGroups(selected);
3316 * Action on user selecting a colour from the colour menu
3319 * the name (not the menu item label!) of the colour scheme
3322 public void changeColour_actionPerformed(String name)
3325 * 'User Defined' opens a panel to configure or load a
3326 * user-defined colour scheme
3328 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3330 new UserDefinedColours(alignPanel);
3335 * otherwise set the chosen colour scheme (or null for 'None')
3337 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3338 viewport.getAlignment(), viewport.getHiddenRepSequences());
3343 * Actions on setting or changing the alignment colour scheme
3348 public void changeColour(ColourSchemeI cs)
3350 // TODO: pull up to controller method
3351 ColourMenuHelper.setColourSelected(colourMenu, cs);
3353 viewport.setGlobalColourScheme(cs);
3355 alignPanel.paintAlignment(true, true);
3359 * Show the PID threshold slider panel
3362 protected void modifyPID_actionPerformed()
3364 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3365 alignPanel.getViewName());
3366 SliderPanel.showPIDSlider();
3370 * Show the Conservation slider panel
3373 protected void modifyConservation_actionPerformed()
3375 SliderPanel.setConservationSlider(alignPanel,
3376 viewport.getResidueShading(), alignPanel.getViewName());
3377 SliderPanel.showConservationSlider();
3381 * Action on selecting or deselecting (Colour) By Conservation
3384 public void conservationMenuItem_actionPerformed(boolean selected)
3386 modifyConservation.setEnabled(selected);
3387 viewport.setConservationSelected(selected);
3388 viewport.getResidueShading().setConservationApplied(selected);
3390 changeColour(viewport.getGlobalColourScheme());
3393 modifyConservation_actionPerformed();
3397 SliderPanel.hideConservationSlider();
3402 * Action on selecting or deselecting (Colour) Above PID Threshold
3405 public void abovePIDThreshold_actionPerformed(boolean selected)
3407 modifyPID.setEnabled(selected);
3408 viewport.setAbovePIDThreshold(selected);
3411 viewport.getResidueShading().setThreshold(0,
3412 viewport.isIgnoreGapsConsensus());
3415 changeColour(viewport.getGlobalColourScheme());
3418 modifyPID_actionPerformed();
3422 SliderPanel.hidePIDSlider();
3433 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3435 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3436 AlignmentSorter.sortByPID(viewport.getAlignment(),
3437 viewport.getAlignment().getSequenceAt(0));
3438 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3439 viewport.getAlignment()));
3440 alignPanel.paintAlignment(true, false);
3450 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3452 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3453 AlignmentSorter.sortByID(viewport.getAlignment());
3455 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3456 alignPanel.paintAlignment(true, false);
3466 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3468 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3469 AlignmentSorter.sortByLength(viewport.getAlignment());
3470 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3471 viewport.getAlignment()));
3472 alignPanel.paintAlignment(true, false);
3482 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3484 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3485 AlignmentSorter.sortByGroup(viewport.getAlignment());
3486 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3487 viewport.getAlignment()));
3489 alignPanel.paintAlignment(true, false);
3499 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3501 new RedundancyPanel(alignPanel, this);
3511 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3513 if ((viewport.getSelectionGroup() == null)
3514 || (viewport.getSelectionGroup().getSize() < 2))
3516 JvOptionPane.showInternalMessageDialog(this,
3517 MessageManager.getString(
3518 "label.you_must_select_least_two_sequences"),
3519 MessageManager.getString("label.invalid_selection"),
3520 JvOptionPane.WARNING_MESSAGE);
3524 JInternalFrame frame = new JInternalFrame();
3525 frame.setContentPane(new PairwiseAlignPanel(viewport));
3526 Desktop.addInternalFrame(frame,
3527 MessageManager.getString("action.pairwise_alignment"), 600,
3533 public void autoCalculate_actionPerformed(ActionEvent e)
3535 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3536 if (viewport.autoCalculateConsensus)
3538 viewport.firePropertyChange("alignment", null,
3539 viewport.getAlignment().getSequences());
3544 public void sortByTreeOption_actionPerformed(ActionEvent e)
3546 viewport.sortByTree = sortByTree.isSelected();
3550 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3552 viewport.followSelection = listenToViewSelections.isSelected();
3556 * Constructs a tree panel and adds it to the desktop
3559 * tree type (NJ or AV)
3561 * name of score model used to compute the tree
3563 * parameters for the distance or similarity calculation
3565 void newTreePanel(String type, String modelName,
3566 SimilarityParamsI options)
3568 String frameTitle = "";
3571 boolean onSelection = false;
3572 if (viewport.getSelectionGroup() != null
3573 && viewport.getSelectionGroup().getSize() > 0)
3575 SequenceGroup sg = viewport.getSelectionGroup();
3577 /* Decide if the selection is a column region */
3578 for (SequenceI _s : sg.getSequences())
3580 if (_s.getLength() < sg.getEndRes())
3582 JvOptionPane.showMessageDialog(Desktop.desktop,
3583 MessageManager.getString(
3584 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3585 MessageManager.getString(
3586 "label.sequences_selection_not_aligned"),
3587 JvOptionPane.WARNING_MESSAGE);
3596 if (viewport.getAlignment().getHeight() < 2)
3602 tp = new TreePanel(alignPanel, type, modelName, options);
3603 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3605 frameTitle += " from ";
3607 if (viewport.viewName != null)
3609 frameTitle += viewport.viewName + " of ";
3612 frameTitle += this.title;
3614 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3625 public void addSortByOrderMenuItem(String title,
3626 final AlignmentOrder order)
3628 final JMenuItem item = new JMenuItem(MessageManager
3629 .formatMessage("action.by_title_param", new Object[]
3632 item.addActionListener(new java.awt.event.ActionListener()
3635 public void actionPerformed(ActionEvent e)
3637 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3639 // TODO: JBPNote - have to map order entries to curent SequenceI
3641 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3643 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3644 viewport.getAlignment()));
3646 alignPanel.paintAlignment(true, false);
3652 * Add a new sort by annotation score menu item
3655 * the menu to add the option to
3657 * the label used to retrieve scores for each sequence on the
3660 public void addSortByAnnotScoreMenuItem(JMenu sort,
3661 final String scoreLabel)
3663 final JMenuItem item = new JMenuItem(scoreLabel);
3665 item.addActionListener(new java.awt.event.ActionListener()
3668 public void actionPerformed(ActionEvent e)
3670 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3671 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3672 viewport.getAlignment());// ,viewport.getSelectionGroup());
3673 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3674 viewport.getAlignment()));
3675 alignPanel.paintAlignment(true, false);
3681 * last hash for alignment's annotation array - used to minimise cost of
3684 protected int _annotationScoreVectorHash;
3687 * search the alignment and rebuild the sort by annotation score submenu the
3688 * last alignment annotation vector hash is stored to minimize cost of
3689 * rebuilding in subsequence calls.
3693 public void buildSortByAnnotationScoresMenu()
3695 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3700 if (viewport.getAlignment().getAlignmentAnnotation()
3701 .hashCode() != _annotationScoreVectorHash)
3703 sortByAnnotScore.removeAll();
3704 // almost certainly a quicker way to do this - but we keep it simple
3705 Hashtable scoreSorts = new Hashtable();
3706 AlignmentAnnotation aann[];
3707 for (SequenceI sqa : viewport.getAlignment().getSequences())
3709 aann = sqa.getAnnotation();
3710 for (int i = 0; aann != null && i < aann.length; i++)
3712 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3714 scoreSorts.put(aann[i].label, aann[i].label);
3718 Enumeration labels = scoreSorts.keys();
3719 while (labels.hasMoreElements())
3721 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3722 (String) labels.nextElement());
3724 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3727 _annotationScoreVectorHash = viewport.getAlignment()
3728 .getAlignmentAnnotation().hashCode();
3733 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3734 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3735 * call. Listeners are added to remove the menu item when the treePanel is
3736 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3740 public void buildTreeSortMenu()
3742 sortByTreeMenu.removeAll();
3744 List<Component> comps = PaintRefresher.components
3745 .get(viewport.getSequenceSetId());
3746 List<TreePanel> treePanels = new ArrayList<>();
3747 for (Component comp : comps)
3749 if (comp instanceof TreePanel)
3751 treePanels.add((TreePanel) comp);
3755 if (treePanels.size() < 1)
3757 sortByTreeMenu.setVisible(false);
3761 sortByTreeMenu.setVisible(true);
3763 for (final TreePanel tp : treePanels)
3765 final JMenuItem item = new JMenuItem(tp.getTitle());
3766 item.addActionListener(new java.awt.event.ActionListener()
3769 public void actionPerformed(ActionEvent e)
3771 tp.sortByTree_actionPerformed();
3772 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3777 sortByTreeMenu.add(item);
3781 public boolean sortBy(AlignmentOrder alorder, String undoname)
3783 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3784 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3785 if (undoname != null)
3787 addHistoryItem(new OrderCommand(undoname, oldOrder,
3788 viewport.getAlignment()));
3790 alignPanel.paintAlignment(true, false);
3795 * Work out whether the whole set of sequences or just the selected set will
3796 * be submitted for multiple alignment.
3799 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3801 // Now, check we have enough sequences
3802 AlignmentView msa = null;
3804 if ((viewport.getSelectionGroup() != null)
3805 && (viewport.getSelectionGroup().getSize() > 1))
3807 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3808 // some common interface!
3810 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3811 * SequenceI[sz = seqs.getSize(false)];
3813 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3814 * seqs.getSequenceAt(i); }
3816 msa = viewport.getAlignmentView(true);
3818 else if (viewport.getSelectionGroup() != null
3819 && viewport.getSelectionGroup().getSize() == 1)
3821 int option = JvOptionPane.showConfirmDialog(this,
3822 MessageManager.getString("warn.oneseq_msainput_selection"),
3823 MessageManager.getString("label.invalid_selection"),
3824 JvOptionPane.OK_CANCEL_OPTION);
3825 if (option == JvOptionPane.OK_OPTION)
3827 msa = viewport.getAlignmentView(false);
3832 msa = viewport.getAlignmentView(false);
3838 * Decides what is submitted to a secondary structure prediction service: the
3839 * first sequence in the alignment, or in the current selection, or, if the
3840 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3841 * region or the whole alignment. (where the first sequence in the set is the
3842 * one that the prediction will be for).
3844 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3846 AlignmentView seqs = null;
3848 if ((viewport.getSelectionGroup() != null)
3849 && (viewport.getSelectionGroup().getSize() > 0))
3851 seqs = viewport.getAlignmentView(true);
3855 seqs = viewport.getAlignmentView(false);
3857 // limit sequences - JBPNote in future - could spawn multiple prediction
3859 // TODO: viewport.getAlignment().isAligned is a global state - the local
3860 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3861 if (!viewport.getAlignment().isAligned(false))
3863 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3864 // TODO: if seqs.getSequences().length>1 then should really have warned
3878 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3880 // Pick the tree file
3881 JalviewFileChooser chooser = new JalviewFileChooser(
3882 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3883 chooser.setFileView(new JalviewFileView());
3884 chooser.setDialogTitle(
3885 MessageManager.getString("label.select_newick_like_tree_file"));
3886 chooser.setToolTipText(
3887 MessageManager.getString("label.load_tree_file"));
3889 int value = chooser.showOpenDialog(null);
3891 if (value == JalviewFileChooser.APPROVE_OPTION)
3893 String filePath = chooser.getSelectedFile().getPath();
3894 Cache.setProperty("LAST_DIRECTORY", filePath);
3895 NewickFile fin = null;
3898 fin = new NewickFile(filePath, DataSourceType.FILE);
3899 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3900 } catch (Exception ex)
3902 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3903 MessageManager.getString("label.problem_reading_tree_file"),
3904 JvOptionPane.WARNING_MESSAGE);
3905 ex.printStackTrace();
3907 if (fin != null && fin.hasWarningMessage())
3909 JvOptionPane.showMessageDialog(Desktop.desktop,
3910 fin.getWarningMessage(),
3912 .getString("label.possible_problem_with_tree_file"),
3913 JvOptionPane.WARNING_MESSAGE);
3918 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3920 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3923 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3924 int h, int x, int y)
3926 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3930 * Add a treeviewer for the tree extracted from a Newick file object to the
3931 * current alignment view
3938 * Associated alignment input data (or null)
3947 * @return TreePanel handle
3949 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3950 AlignmentView input, int w, int h, int x, int y)
3952 TreePanel tp = null;
3958 if (nf.getTree() != null)
3960 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3966 tp.setLocation(x, y);
3969 Desktop.addInternalFrame(tp, treeTitle, w, h);
3971 } catch (Exception ex)
3973 ex.printStackTrace();
3979 private boolean buildingMenu = false;
3982 * Generates menu items and listener event actions for web service clients
3985 public void BuildWebServiceMenu()
3987 while (buildingMenu)
3991 System.err.println("Waiting for building menu to finish.");
3993 } catch (Exception e)
3997 final AlignFrame me = this;
3998 buildingMenu = true;
3999 new Thread(new Runnable()
4004 final List<JMenuItem> legacyItems = new ArrayList<>();
4007 // System.err.println("Building ws menu again "
4008 // + Thread.currentThread());
4009 // TODO: add support for context dependent disabling of services based
4011 // alignment and current selection
4012 // TODO: add additional serviceHandle parameter to specify abstract
4014 // class independently of AbstractName
4015 // TODO: add in rediscovery GUI function to restart discoverer
4016 // TODO: group services by location as well as function and/or
4018 // object broker mechanism.
4019 final Vector<JMenu> wsmenu = new Vector<>();
4020 final IProgressIndicator af = me;
4023 * do not i18n these strings - they are hard-coded in class
4024 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4025 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4027 final JMenu msawsmenu = new JMenu("Alignment");
4028 final JMenu secstrmenu = new JMenu(
4029 "Secondary Structure Prediction");
4030 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4031 final JMenu analymenu = new JMenu("Analysis");
4032 final JMenu dismenu = new JMenu("Protein Disorder");
4033 // JAL-940 - only show secondary structure prediction services from
4034 // the legacy server
4035 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4037 Discoverer.services != null && (Discoverer.services.size() > 0))
4039 // TODO: refactor to allow list of AbstractName/Handler bindings to
4041 // stored or retrieved from elsewhere
4042 // No MSAWS used any more:
4043 // Vector msaws = null; // (Vector)
4044 // Discoverer.services.get("MsaWS");
4045 Vector secstrpr = (Vector) Discoverer.services
4047 if (secstrpr != null)
4049 // Add any secondary structure prediction services
4050 for (int i = 0, j = secstrpr.size(); i < j; i++)
4052 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4054 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4055 .getServiceClient(sh);
4056 int p = secstrmenu.getItemCount();
4057 impl.attachWSMenuEntry(secstrmenu, me);
4058 int q = secstrmenu.getItemCount();
4059 for (int litm = p; litm < q; litm++)
4061 legacyItems.add(secstrmenu.getItem(litm));
4067 // Add all submenus in the order they should appear on the web
4069 wsmenu.add(msawsmenu);
4070 wsmenu.add(secstrmenu);
4071 wsmenu.add(dismenu);
4072 wsmenu.add(analymenu);
4073 // No search services yet
4074 // wsmenu.add(seqsrchmenu);
4076 javax.swing.SwingUtilities.invokeLater(new Runnable()
4083 webService.removeAll();
4084 // first, add discovered services onto the webservices menu
4085 if (wsmenu.size() > 0)
4087 for (int i = 0, j = wsmenu.size(); i < j; i++)
4089 webService.add(wsmenu.get(i));
4094 webService.add(me.webServiceNoServices);
4096 // TODO: move into separate menu builder class.
4097 boolean new_sspred = false;
4098 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4100 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4101 if (jws2servs != null)
4103 if (jws2servs.hasServices())
4105 jws2servs.attachWSMenuEntry(webService, me);
4106 for (Jws2Instance sv : jws2servs.getServices())
4108 if (sv.description.toLowerCase().contains("jpred"))
4110 for (JMenuItem jmi : legacyItems)
4112 jmi.setVisible(false);
4118 if (jws2servs.isRunning())
4120 JMenuItem tm = new JMenuItem(
4121 "Still discovering JABA Services");
4122 tm.setEnabled(false);
4127 build_urlServiceMenu(me.webService);
4128 build_fetchdbmenu(webService);
4129 for (JMenu item : wsmenu)
4131 if (item.getItemCount() == 0)
4133 item.setEnabled(false);
4137 item.setEnabled(true);
4140 } catch (Exception e)
4143 "Exception during web service menu building process.",
4148 } catch (Exception e)
4151 buildingMenu = false;
4158 * construct any groupURL type service menu entries.
4162 private void build_urlServiceMenu(JMenu webService)
4164 // TODO: remove this code when 2.7 is released
4165 // DEBUG - alignmentView
4167 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4168 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4170 * @Override public void actionPerformed(ActionEvent e) {
4171 * jalview.datamodel.AlignmentView
4172 * .testSelectionViews(af.viewport.getAlignment(),
4173 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4175 * }); webService.add(testAlView);
4177 // TODO: refactor to RestClient discoverer and merge menu entries for
4178 // rest-style services with other types of analysis/calculation service
4179 // SHmmr test client - still being implemented.
4180 // DEBUG - alignmentView
4182 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4185 client.attachWSMenuEntry(
4186 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4192 * Searches the alignment sequences for xRefs and builds the Show
4193 * Cross-References menu (formerly called Show Products), with database
4194 * sources for which cross-references are found (protein sources for a
4195 * nucleotide alignment and vice versa)
4197 * @return true if Show Cross-references menu should be enabled
4199 public boolean canShowProducts()
4201 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4202 AlignmentI dataset = viewport.getAlignment().getDataset();
4204 showProducts.removeAll();
4205 final boolean dna = viewport.getAlignment().isNucleotide();
4207 if (seqs == null || seqs.length == 0)
4209 // nothing to see here.
4213 boolean showp = false;
4216 List<String> ptypes = new CrossRef(seqs, dataset)
4217 .findXrefSourcesForSequences(dna);
4219 for (final String source : ptypes)
4222 final AlignFrame af = this;
4223 JMenuItem xtype = new JMenuItem(source);
4224 xtype.addActionListener(new ActionListener()
4227 public void actionPerformed(ActionEvent e)
4229 showProductsFor(af.viewport.getSequenceSelection(), dna,
4233 showProducts.add(xtype);
4235 showProducts.setVisible(showp);
4236 showProducts.setEnabled(showp);
4237 } catch (Exception e)
4240 "canShowProducts threw an exception - please report to help@jalview.org",
4248 * Finds and displays cross-references for the selected sequences (protein
4249 * products for nucleotide sequences, dna coding sequences for peptides).
4252 * the sequences to show cross-references for
4254 * true if from a nucleotide alignment (so showing proteins)
4256 * the database to show cross-references for
4258 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4259 final String source)
4261 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4266 * Construct and display a new frame containing the translation of this
4267 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4270 public void showTranslation_actionPerformed(ActionEvent e)
4272 AlignmentI al = null;
4275 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4277 al = dna.translateCdna();
4278 } catch (Exception ex)
4280 jalview.bin.Cache.log.error(
4281 "Exception during translation. Please report this !", ex);
4282 final String msg = MessageManager.getString(
4283 "label.error_when_translating_sequences_submit_bug_report");
4284 final String errorTitle = MessageManager
4285 .getString("label.implementation_error")
4286 + MessageManager.getString("label.translation_failed");
4287 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4288 JvOptionPane.ERROR_MESSAGE);
4291 if (al == null || al.getHeight() == 0)
4293 final String msg = MessageManager.getString(
4294 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4295 final String errorTitle = MessageManager
4296 .getString("label.translation_failed");
4297 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4298 JvOptionPane.WARNING_MESSAGE);
4302 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4303 af.setFileFormat(this.currentFileFormat);
4304 final String newTitle = MessageManager
4305 .formatMessage("label.translation_of_params", new Object[]
4306 { this.getTitle() });
4307 af.setTitle(newTitle);
4308 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4310 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4311 viewport.openSplitFrame(af, new Alignment(seqs));
4315 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4322 * Set the file format
4326 public void setFileFormat(FileFormatI format)
4328 this.currentFileFormat = format;
4332 * Try to load a features file onto the alignment.
4335 * contents or path to retrieve file
4337 * access mode of file (see jalview.io.AlignFile)
4338 * @return true if features file was parsed correctly.
4340 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4342 return avc.parseFeaturesFile(file, sourceType,
4343 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4348 public void refreshFeatureUI(boolean enableIfNecessary)
4350 // note - currently this is only still here rather than in the controller
4351 // because of the featureSettings hard reference that is yet to be
4353 if (enableIfNecessary)
4355 viewport.setShowSequenceFeatures(true);
4356 showSeqFeatures.setSelected(true);
4362 public void dragEnter(DropTargetDragEvent evt)
4367 public void dragExit(DropTargetEvent evt)
4372 public void dragOver(DropTargetDragEvent evt)
4377 public void dropActionChanged(DropTargetDragEvent evt)
4382 public void drop(DropTargetDropEvent evt)
4384 // JAL-1552 - acceptDrop required before getTransferable call for
4385 // Java's Transferable for native dnd
4386 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4387 Transferable t = evt.getTransferable();
4388 final AlignFrame thisaf = this;
4389 final List<String> files = new ArrayList<>();
4390 List<DataSourceType> protocols = new ArrayList<>();
4394 Desktop.transferFromDropTarget(files, protocols, evt, t);
4395 } catch (Exception e)
4397 e.printStackTrace();
4401 new Thread(new Runnable()
4408 // check to see if any of these files have names matching sequences
4411 SequenceIdMatcher idm = new SequenceIdMatcher(
4412 viewport.getAlignment().getSequencesArray());
4414 * Object[] { String,SequenceI}
4416 ArrayList<Object[]> filesmatched = new ArrayList<>();
4417 ArrayList<String> filesnotmatched = new ArrayList<>();
4418 for (int i = 0; i < files.size(); i++)
4420 String file = files.get(i).toString();
4422 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4423 if (protocol == DataSourceType.FILE)
4425 File fl = new File(file);
4426 pdbfn = fl.getName();
4428 else if (protocol == DataSourceType.URL)
4430 URL url = new URL(file);
4431 pdbfn = url.getFile();
4433 if (pdbfn.length() > 0)
4435 // attempt to find a match in the alignment
4436 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4437 int l = 0, c = pdbfn.indexOf(".");
4438 while (mtch == null && c != -1)
4443 } while ((c = pdbfn.indexOf(".", l)) > l);
4446 pdbfn = pdbfn.substring(0, l);
4448 mtch = idm.findAllIdMatches(pdbfn);
4452 FileFormatI type = null;
4455 type = new IdentifyFile().identify(file, protocol);
4456 } catch (Exception ex)
4460 if (type != null && type.isStructureFile())
4462 filesmatched.add(new Object[] { file, protocol, mtch });
4466 // File wasn't named like one of the sequences or wasn't a PDB
4468 filesnotmatched.add(file);
4472 if (filesmatched.size() > 0)
4474 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4475 || JvOptionPane.showConfirmDialog(thisaf,
4476 MessageManager.formatMessage(
4477 "label.automatically_associate_structure_files_with_sequences_same_name",
4479 { Integer.valueOf(filesmatched.size())
4481 MessageManager.getString(
4482 "label.automatically_associate_structure_files_by_name"),
4483 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4486 for (Object[] fm : filesmatched)
4488 // try and associate
4489 // TODO: may want to set a standard ID naming formalism for
4490 // associating PDB files which have no IDs.
4491 for (SequenceI toassoc : (SequenceI[]) fm[2])
4493 PDBEntry pe = new AssociatePdbFileWithSeq()
4494 .associatePdbWithSeq((String) fm[0],
4495 (DataSourceType) fm[1], toassoc, false,
4499 System.err.println("Associated file : "
4500 + ((String) fm[0]) + " with "
4501 + toassoc.getDisplayId(true));
4505 // TODO: do we need to update overview ? only if features are
4507 alignPanel.paintAlignment(true, false);
4511 if (filesnotmatched.size() > 0)
4513 if (assocfiles > 0 && (Cache.getDefault(
4514 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4515 || JvOptionPane.showConfirmDialog(thisaf,
4516 "<html>" + MessageManager.formatMessage(
4517 "label.ignore_unmatched_dropped_files_info",
4520 filesnotmatched.size())
4523 MessageManager.getString(
4524 "label.ignore_unmatched_dropped_files"),
4525 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4529 for (String fn : filesnotmatched)
4531 loadJalviewDataFile(fn, null, null, null);
4535 } catch (Exception ex)
4537 ex.printStackTrace();
4545 * Attempt to load a "dropped" file or URL string, by testing in turn for
4547 * <li>an Annotation file</li>
4548 * <li>a JNet file</li>
4549 * <li>a features file</li>
4550 * <li>else try to interpret as an alignment file</li>
4554 * either a filename or a URL string.
4556 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4557 FileFormatI format, SequenceI assocSeq)
4561 if (sourceType == null)
4563 sourceType = FormatAdapter.checkProtocol(file);
4565 // if the file isn't identified, or not positively identified as some
4566 // other filetype (PFAM is default unidentified alignment file type) then
4567 // try to parse as annotation.
4568 boolean isAnnotation = (format == null
4569 || FileFormat.Pfam.equals(format))
4570 ? new AnnotationFile().annotateAlignmentView(viewport,
4576 // first see if its a T-COFFEE score file
4577 TCoffeeScoreFile tcf = null;
4580 tcf = new TCoffeeScoreFile(file, sourceType);
4583 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4587 new TCoffeeColourScheme(viewport.getAlignment()));
4588 isAnnotation = true;
4589 statusBar.setText(MessageManager.getString(
4590 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4594 // some problem - if no warning its probable that the ID matching
4595 // process didn't work
4596 JvOptionPane.showMessageDialog(Desktop.desktop,
4597 tcf.getWarningMessage() == null
4598 ? MessageManager.getString(
4599 "label.check_file_matches_sequence_ids_alignment")
4600 : tcf.getWarningMessage(),
4601 MessageManager.getString(
4602 "label.problem_reading_tcoffee_score_file"),
4603 JvOptionPane.WARNING_MESSAGE);
4610 } catch (Exception x)
4613 "Exception when processing data source as T-COFFEE score file",
4619 // try to see if its a JNet 'concise' style annotation file *before*
4621 // try to parse it as a features file
4624 format = new IdentifyFile().identify(file, sourceType);
4626 if (FileFormat.ScoreMatrix == format)
4628 ScoreMatrixFile sm = new ScoreMatrixFile(
4629 new FileParse(file, sourceType));
4631 // todo: i18n this message
4632 statusBar.setText(MessageManager.formatMessage(
4633 "label.successfully_loaded_matrix",
4634 sm.getMatrixName()));
4636 else if (FileFormat.Jnet.equals(format))
4638 JPredFile predictions = new JPredFile(file, sourceType);
4639 new JnetAnnotationMaker();
4640 JnetAnnotationMaker.add_annotation(predictions,
4641 viewport.getAlignment(), 0, false);
4642 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4643 viewport.getAlignment().setSeqrep(repseq);
4644 HiddenColumns cs = new HiddenColumns();
4645 cs.hideInsertionsFor(repseq);
4646 viewport.getAlignment().setHiddenColumns(cs);
4647 isAnnotation = true;
4649 // else if (IdentifyFile.FeaturesFile.equals(format))
4650 else if (FileFormat.Features.equals(format))
4652 if (parseFeaturesFile(file, sourceType))
4654 alignPanel.paintAlignment(true, true);
4659 new FileLoader().LoadFile(viewport, file, sourceType, format);
4666 alignPanel.adjustAnnotationHeight();
4667 viewport.updateSequenceIdColours();
4668 buildSortByAnnotationScoresMenu();
4669 alignPanel.paintAlignment(true, true);
4671 } catch (Exception ex)
4673 ex.printStackTrace();
4674 } catch (OutOfMemoryError oom)
4679 } catch (Exception x)
4684 + (sourceType != null
4685 ? (sourceType == DataSourceType.PASTE
4687 : "using " + sourceType + " from "
4691 ? "(parsing as '" + format + "' file)"
4693 oom, Desktop.desktop);
4698 * Method invoked by the ChangeListener on the tabbed pane, in other words
4699 * when a different tabbed pane is selected by the user or programmatically.
4702 public void tabSelectionChanged(int index)
4706 alignPanel = alignPanels.get(index);
4707 viewport = alignPanel.av;
4708 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4709 setMenusFromViewport(viewport);
4713 * 'focus' any colour slider that is open to the selected viewport
4715 if (viewport.getConservationSelected())
4717 SliderPanel.setConservationSlider(alignPanel,
4718 viewport.getResidueShading(), alignPanel.getViewName());
4722 SliderPanel.hideConservationSlider();
4724 if (viewport.getAbovePIDThreshold())
4726 SliderPanel.setPIDSliderSource(alignPanel,
4727 viewport.getResidueShading(), alignPanel.getViewName());
4731 SliderPanel.hidePIDSlider();
4735 * If there is a frame linked to this one in a SplitPane, switch it to the
4736 * same view tab index. No infinite recursion of calls should happen, since
4737 * tabSelectionChanged() should not get invoked on setting the selected
4738 * index to an unchanged value. Guard against setting an invalid index
4739 * before the new view peer tab has been created.
4741 final AlignViewportI peer = viewport.getCodingComplement();
4744 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4745 .getAlignPanel().alignFrame;
4746 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4748 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4754 * On right mouse click on view tab, prompt for and set new view name.
4757 public void tabbedPane_mousePressed(MouseEvent e)
4759 if (e.isPopupTrigger())
4761 String msg = MessageManager.getString("label.enter_view_name");
4762 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4763 JvOptionPane.QUESTION_MESSAGE);
4767 viewport.viewName = reply;
4768 // TODO warn if reply is in getExistingViewNames()?
4769 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4774 public AlignViewport getCurrentView()
4780 * Open the dialog for regex description parsing.
4783 protected void extractScores_actionPerformed(ActionEvent e)
4785 ParseProperties pp = new jalview.analysis.ParseProperties(
4786 viewport.getAlignment());
4787 // TODO: verify regex and introduce GUI dialog for version 2.5
4788 // if (pp.getScoresFromDescription("col", "score column ",
4789 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4791 if (pp.getScoresFromDescription("description column",
4792 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4794 buildSortByAnnotationScoresMenu();
4802 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4806 protected void showDbRefs_actionPerformed(ActionEvent e)
4808 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4814 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4818 protected void showNpFeats_actionPerformed(ActionEvent e)
4820 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4824 * find the viewport amongst the tabs in this alignment frame and close that
4829 public boolean closeView(AlignViewportI av)
4833 this.closeMenuItem_actionPerformed(false);
4836 Component[] comp = tabbedPane.getComponents();
4837 for (int i = 0; comp != null && i < comp.length; i++)
4839 if (comp[i] instanceof AlignmentPanel)
4841 if (((AlignmentPanel) comp[i]).av == av)
4844 closeView((AlignmentPanel) comp[i]);
4852 protected void build_fetchdbmenu(JMenu webService)
4854 // Temporary hack - DBRef Fetcher always top level ws entry.
4855 // TODO We probably want to store a sequence database checklist in
4856 // preferences and have checkboxes.. rather than individual sources selected
4858 final JMenu rfetch = new JMenu(
4859 MessageManager.getString("action.fetch_db_references"));
4860 rfetch.setToolTipText(MessageManager.getString(
4861 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4862 webService.add(rfetch);
4864 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4865 MessageManager.getString("option.trim_retrieved_seqs"));
4866 trimrs.setToolTipText(
4867 MessageManager.getString("label.trim_retrieved_sequences"));
4869 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4870 trimrs.addActionListener(new ActionListener()
4873 public void actionPerformed(ActionEvent e)
4875 trimrs.setSelected(trimrs.isSelected());
4876 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4877 Boolean.valueOf(trimrs.isSelected()).toString());
4881 JMenuItem fetchr = new JMenuItem(
4882 MessageManager.getString("label.standard_databases"));
4883 fetchr.setToolTipText(
4884 MessageManager.getString("label.fetch_embl_uniprot"));
4885 fetchr.addActionListener(new ActionListener()
4889 public void actionPerformed(ActionEvent e)
4891 new Thread(new Runnable()
4896 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4897 .getAlignment().isNucleotide();
4898 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4899 alignPanel.av.getSequenceSelection(),
4900 alignPanel.alignFrame, null,
4901 alignPanel.alignFrame.featureSettings, isNucleotide);
4902 dbRefFetcher.addListener(new FetchFinishedListenerI()
4905 public void finished()
4907 AlignFrame.this.setMenusForViewport();
4910 dbRefFetcher.fetchDBRefs(false);
4918 final AlignFrame me = this;
4919 new Thread(new Runnable()
4924 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4925 .getSequenceFetcherSingleton(me);
4926 javax.swing.SwingUtilities.invokeLater(new Runnable()
4931 String[] dbclasses = sf.getOrderedSupportedSources();
4932 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4933 // jalview.util.QuickSort.sort(otherdb, otherdb);
4934 List<DbSourceProxy> otherdb;
4935 JMenu dfetch = new JMenu();
4936 JMenu ifetch = new JMenu();
4937 JMenuItem fetchr = null;
4938 int comp = 0, icomp = 0, mcomp = 15;
4939 String mname = null;
4941 for (String dbclass : dbclasses)
4943 otherdb = sf.getSourceProxy(dbclass);
4944 // add a single entry for this class, or submenu allowing 'fetch
4946 if (otherdb == null || otherdb.size() < 1)
4950 // List<DbSourceProxy> dbs=otherdb;
4951 // otherdb=new ArrayList<DbSourceProxy>();
4952 // for (DbSourceProxy db:dbs)
4954 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4958 mname = "From " + dbclass;
4960 if (otherdb.size() == 1)
4962 final DbSourceProxy[] dassource = otherdb
4963 .toArray(new DbSourceProxy[0]);
4964 DbSourceProxy src = otherdb.get(0);
4965 fetchr = new JMenuItem(src.getDbSource());
4966 fetchr.addActionListener(new ActionListener()
4970 public void actionPerformed(ActionEvent e)
4972 new Thread(new Runnable()
4978 boolean isNucleotide = alignPanel.alignFrame
4979 .getViewport().getAlignment()
4981 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4982 alignPanel.av.getSequenceSelection(),
4983 alignPanel.alignFrame, dassource,
4984 alignPanel.alignFrame.featureSettings,
4987 .addListener(new FetchFinishedListenerI()
4990 public void finished()
4992 AlignFrame.this.setMenusForViewport();
4995 dbRefFetcher.fetchDBRefs(false);
5001 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5002 MessageManager.formatMessage(
5003 "label.fetch_retrieve_from", new Object[]
5004 { src.getDbName() })));
5010 final DbSourceProxy[] dassource = otherdb
5011 .toArray(new DbSourceProxy[0]);
5013 DbSourceProxy src = otherdb.get(0);
5014 fetchr = new JMenuItem(MessageManager
5015 .formatMessage("label.fetch_all_param", new Object[]
5016 { src.getDbSource() }));
5017 fetchr.addActionListener(new ActionListener()
5020 public void actionPerformed(ActionEvent e)
5022 new Thread(new Runnable()
5028 boolean isNucleotide = alignPanel.alignFrame
5029 .getViewport().getAlignment()
5031 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5032 alignPanel.av.getSequenceSelection(),
5033 alignPanel.alignFrame, dassource,
5034 alignPanel.alignFrame.featureSettings,
5037 .addListener(new FetchFinishedListenerI()
5040 public void finished()
5042 AlignFrame.this.setMenusForViewport();
5045 dbRefFetcher.fetchDBRefs(false);
5051 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5052 MessageManager.formatMessage(
5053 "label.fetch_retrieve_from_all_sources",
5055 { Integer.valueOf(otherdb.size())
5057 src.getDbSource(), src.getDbName() })));
5060 // and then build the rest of the individual menus
5061 ifetch = new JMenu(MessageManager.formatMessage(
5062 "label.source_from_db_source", new Object[]
5063 { src.getDbSource() }));
5065 String imname = null;
5067 for (DbSourceProxy sproxy : otherdb)
5069 String dbname = sproxy.getDbName();
5070 String sname = dbname.length() > 5
5071 ? dbname.substring(0, 5) + "..."
5073 String msname = dbname.length() > 10
5074 ? dbname.substring(0, 10) + "..."
5078 imname = MessageManager
5079 .formatMessage("label.from_msname", new Object[]
5082 fetchr = new JMenuItem(msname);
5083 final DbSourceProxy[] dassrc = { sproxy };
5084 fetchr.addActionListener(new ActionListener()
5088 public void actionPerformed(ActionEvent e)
5090 new Thread(new Runnable()
5096 boolean isNucleotide = alignPanel.alignFrame
5097 .getViewport().getAlignment()
5099 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5100 alignPanel.av.getSequenceSelection(),
5101 alignPanel.alignFrame, dassrc,
5102 alignPanel.alignFrame.featureSettings,
5105 .addListener(new FetchFinishedListenerI()
5108 public void finished()
5110 AlignFrame.this.setMenusForViewport();
5113 dbRefFetcher.fetchDBRefs(false);
5119 fetchr.setToolTipText(
5120 "<html>" + MessageManager.formatMessage(
5121 "label.fetch_retrieve_from", new Object[]
5125 if (++icomp >= mcomp || i == (otherdb.size()))
5127 ifetch.setText(MessageManager.formatMessage(
5128 "label.source_to_target", imname, sname));
5130 ifetch = new JMenu();
5138 if (comp >= mcomp || dbi >= (dbclasses.length))
5140 dfetch.setText(MessageManager.formatMessage(
5141 "label.source_to_target", mname, dbclass));
5143 dfetch = new JMenu();
5156 * Left justify the whole alignment.
5159 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5161 AlignmentI al = viewport.getAlignment();
5163 viewport.firePropertyChange("alignment", null, al);
5167 * Right justify the whole alignment.
5170 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5172 AlignmentI al = viewport.getAlignment();
5174 viewport.firePropertyChange("alignment", null, al);
5178 public void setShowSeqFeatures(boolean b)
5180 showSeqFeatures.setSelected(b);
5181 viewport.setShowSequenceFeatures(b);
5188 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5189 * awt.event.ActionEvent)
5192 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5194 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5195 alignPanel.paintAlignment(false, false);
5202 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5206 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5208 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5209 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5217 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5218 * .event.ActionEvent)
5221 protected void showGroupConservation_actionPerformed(ActionEvent e)
5223 viewport.setShowGroupConservation(showGroupConservation.getState());
5224 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5231 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5232 * .event.ActionEvent)
5235 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5237 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5238 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5245 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5246 * .event.ActionEvent)
5249 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5251 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5252 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5256 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5258 showSequenceLogo.setState(true);
5259 viewport.setShowSequenceLogo(true);
5260 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5261 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5265 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5267 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5274 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5275 * .event.ActionEvent)
5278 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5280 if (avc.makeGroupsFromSelection())
5282 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5283 alignPanel.updateAnnotation();
5284 alignPanel.paintAlignment(true, true);
5288 public void clearAlignmentSeqRep()
5290 // TODO refactor alignmentseqrep to controller
5291 if (viewport.getAlignment().hasSeqrep())
5293 viewport.getAlignment().setSeqrep(null);
5294 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5295 alignPanel.updateAnnotation();
5296 alignPanel.paintAlignment(true, true);
5301 protected void createGroup_actionPerformed(ActionEvent e)
5303 if (avc.createGroup())
5305 alignPanel.alignmentChanged();
5310 protected void unGroup_actionPerformed(ActionEvent e)
5314 alignPanel.alignmentChanged();
5319 * make the given alignmentPanel the currently selected tab
5321 * @param alignmentPanel
5323 public void setDisplayedView(AlignmentPanel alignmentPanel)
5325 if (!viewport.getSequenceSetId()
5326 .equals(alignmentPanel.av.getSequenceSetId()))
5328 throw new Error(MessageManager.getString(
5329 "error.implementation_error_cannot_show_view_alignment_frame"));
5331 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5332 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5334 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5339 * Action on selection of menu options to Show or Hide annotations.
5342 * @param forSequences
5343 * update sequence-related annotations
5344 * @param forAlignment
5345 * update non-sequence-related annotations
5348 protected void setAnnotationsVisibility(boolean visible,
5349 boolean forSequences, boolean forAlignment)
5351 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5352 .getAlignmentAnnotation();
5357 for (AlignmentAnnotation aa : anns)
5360 * don't display non-positional annotations on an alignment
5362 if (aa.annotations == null)
5366 boolean apply = (aa.sequenceRef == null && forAlignment)
5367 || (aa.sequenceRef != null && forSequences);
5370 aa.visible = visible;
5373 alignPanel.validateAnnotationDimensions(true);
5374 alignPanel.alignmentChanged();
5378 * Store selected annotation sort order for the view and repaint.
5381 protected void sortAnnotations_actionPerformed()
5383 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5385 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5386 alignPanel.paintAlignment(false, false);
5391 * @return alignment panels in this alignment frame
5393 public List<? extends AlignmentViewPanel> getAlignPanels()
5395 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5399 * Open a new alignment window, with the cDNA associated with this (protein)
5400 * alignment, aligned as is the protein.
5402 protected void viewAsCdna_actionPerformed()
5404 // TODO no longer a menu action - refactor as required
5405 final AlignmentI alignment = getViewport().getAlignment();
5406 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5407 if (mappings == null)
5411 List<SequenceI> cdnaSeqs = new ArrayList<>();
5412 for (SequenceI aaSeq : alignment.getSequences())
5414 for (AlignedCodonFrame acf : mappings)
5416 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5420 * There is a cDNA mapping for this protein sequence - add to new
5421 * alignment. It will share the same dataset sequence as other mapped
5422 * cDNA (no new mappings need to be created).
5424 final Sequence newSeq = new Sequence(dnaSeq);
5425 newSeq.setDatasetSequence(dnaSeq);
5426 cdnaSeqs.add(newSeq);
5430 if (cdnaSeqs.size() == 0)
5432 // show a warning dialog no mapped cDNA
5435 AlignmentI cdna = new Alignment(
5436 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5437 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5438 AlignFrame.DEFAULT_HEIGHT);
5439 cdna.alignAs(alignment);
5440 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5442 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5443 AlignFrame.DEFAULT_HEIGHT);
5447 * Set visibility of dna/protein complement view (available when shown in a
5453 protected void showComplement_actionPerformed(boolean show)
5455 SplitContainerI sf = getSplitViewContainer();
5458 sf.setComplementVisible(this, show);
5463 * Generate the reverse (optionally complemented) of the selected sequences,
5464 * and add them to the alignment
5467 protected void showReverse_actionPerformed(boolean complement)
5469 AlignmentI al = null;
5472 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5473 al = dna.reverseCdna(complement);
5474 viewport.addAlignment(al, "");
5475 addHistoryItem(new EditCommand(
5476 MessageManager.getString("label.add_sequences"), Action.PASTE,
5477 al.getSequencesArray(), 0, al.getWidth(),
5478 viewport.getAlignment()));
5479 } catch (Exception ex)
5481 System.err.println(ex.getMessage());
5487 * Try to run a script in the Groovy console, having first ensured that this
5488 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5489 * be targeted at this alignment.
5492 protected void runGroovy_actionPerformed()
5494 Jalview.setCurrentAlignFrame(this);
5495 groovy.ui.Console console = Desktop.getGroovyConsole();
5496 if (console != null)
5500 console.runScript();
5501 } catch (Exception ex)
5503 System.err.println((ex.toString()));
5504 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5505 MessageManager.getString("label.couldnt_run_groovy_script"),
5506 MessageManager.getString("label.groovy_support_failed"),
5507 JvOptionPane.ERROR_MESSAGE);
5512 System.err.println("Can't run Groovy script as console not found");
5517 * Hides columns containing (or not containing) a specified feature, provided
5518 * that would not leave all columns hidden
5520 * @param featureType
5521 * @param columnsContaining
5524 public boolean hideFeatureColumns(String featureType,
5525 boolean columnsContaining)
5527 boolean notForHiding = avc.markColumnsContainingFeatures(
5528 columnsContaining, false, false, featureType);
5531 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5532 false, featureType))
5534 getViewport().hideSelectedColumns();
5542 protected void selectHighlightedColumns_actionPerformed(
5543 ActionEvent actionEvent)
5545 // include key modifier check in case user selects from menu
5546 avc.markHighlightedColumns(
5547 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5548 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5549 | ActionEvent.CTRL_MASK)) != 0);
5553 * Rebuilds the Colour menu, including any user-defined colours which have
5554 * been loaded either on startup or during the session
5556 public void buildColourMenu()
5558 colourMenu.removeAll();
5560 colourMenu.add(applyToAllGroups);
5561 colourMenu.add(textColour);
5562 colourMenu.addSeparator();
5564 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5567 colourMenu.addSeparator();
5568 colourMenu.add(conservationMenuItem);
5569 colourMenu.add(modifyConservation);
5570 colourMenu.add(abovePIDThreshold);
5571 colourMenu.add(modifyPID);
5572 colourMenu.add(annotationColour);
5574 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5575 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5579 * Open a dialog (if not already open) that allows the user to select and
5580 * calculate PCA or Tree analysis
5582 protected void openTreePcaDialog()
5584 if (alignPanel.getCalculationDialog() == null)
5586 new CalculationChooser(AlignFrame.this);
5591 class PrintThread extends Thread
5595 public PrintThread(AlignmentPanel ap)
5600 static PageFormat pf;
5605 PrinterJob printJob = PrinterJob.getPrinterJob();
5609 printJob.setPrintable(ap, pf);
5613 printJob.setPrintable(ap);
5616 if (printJob.printDialog())
5621 } catch (Exception PrintException)
5623 PrintException.printStackTrace();