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.AnnotationSorter.SequenceAnnotationOrder;
26 import jalview.analysis.CrossRef;
27 import jalview.analysis.Dna;
28 import jalview.analysis.GeneticCodeI;
29 import jalview.analysis.ParseProperties;
30 import jalview.analysis.SequenceIdMatcher;
31 import jalview.api.AlignExportSettingI;
32 import jalview.api.AlignViewControllerGuiI;
33 import jalview.api.AlignViewControllerI;
34 import jalview.api.AlignViewportI;
35 import jalview.api.AlignmentViewPanel;
36 import jalview.api.FeatureSettingsControllerI;
37 import jalview.api.SplitContainerI;
38 import jalview.api.ViewStyleI;
39 import jalview.api.analysis.SimilarityParamsI;
40 import jalview.bin.Cache;
41 import jalview.bin.Jalview;
42 import jalview.commands.CommandI;
43 import jalview.commands.EditCommand;
44 import jalview.commands.EditCommand.Action;
45 import jalview.commands.OrderCommand;
46 import jalview.commands.RemoveGapColCommand;
47 import jalview.commands.RemoveGapsCommand;
48 import jalview.commands.SlideSequencesCommand;
49 import jalview.commands.TrimRegionCommand;
50 import jalview.datamodel.AlignedCodonFrame;
51 import jalview.datamodel.Alignment;
52 import jalview.datamodel.AlignmentAnnotation;
53 import jalview.datamodel.AlignmentExportData;
54 import jalview.datamodel.AlignmentI;
55 import jalview.datamodel.AlignmentOrder;
56 import jalview.datamodel.AlignmentView;
57 import jalview.datamodel.ColumnSelection;
58 import jalview.datamodel.HiddenColumns;
59 import jalview.datamodel.HiddenSequences;
60 import jalview.datamodel.PDBEntry;
61 import jalview.datamodel.SeqCigar;
62 import jalview.datamodel.Sequence;
63 import jalview.datamodel.SequenceGroup;
64 import jalview.datamodel.SequenceI;
65 import jalview.gui.ColourMenuHelper.ColourChangeListener;
66 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
67 import jalview.io.AlignmentProperties;
68 import jalview.io.AnnotationFile;
69 import jalview.io.BackupFiles;
70 import jalview.io.BioJsHTMLOutput;
71 import jalview.io.DataSourceType;
72 import jalview.io.FileFormat;
73 import jalview.io.FileFormatI;
74 import jalview.io.FileFormats;
75 import jalview.io.FileLoader;
76 import jalview.io.FileParse;
77 import jalview.io.FormatAdapter;
78 import jalview.io.HtmlSvgOutput;
79 import jalview.io.IdentifyFile;
80 import jalview.io.JPredFile;
81 import jalview.io.JalviewFileChooser;
82 import jalview.io.JalviewFileView;
83 import jalview.io.JnetAnnotationMaker;
84 import jalview.io.NewickFile;
85 import jalview.io.ScoreMatrixFile;
86 import jalview.io.TCoffeeScoreFile;
87 import jalview.io.vcf.VCFLoader;
88 import jalview.jbgui.GAlignFrame;
89 import jalview.schemes.ColourSchemeI;
90 import jalview.schemes.ColourSchemes;
91 import jalview.schemes.ResidueColourScheme;
92 import jalview.schemes.TCoffeeColourScheme;
93 import jalview.util.MessageManager;
94 import jalview.viewmodel.AlignmentViewport;
95 import jalview.viewmodel.ViewportRanges;
96 import jalview.ws.DBRefFetcher;
97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
98 import jalview.ws.jws1.Discoverer;
99 import jalview.ws.jws2.Jws2Discoverer;
100 import jalview.ws.jws2.jabaws2.Jws2Instance;
101 import jalview.ws.seqfetcher.DbSourceProxy;
103 import java.awt.BorderLayout;
104 import java.awt.Component;
105 import java.awt.Rectangle;
106 import java.awt.Toolkit;
107 import java.awt.datatransfer.Clipboard;
108 import java.awt.datatransfer.DataFlavor;
109 import java.awt.datatransfer.StringSelection;
110 import java.awt.datatransfer.Transferable;
111 import java.awt.dnd.DnDConstants;
112 import java.awt.dnd.DropTargetDragEvent;
113 import java.awt.dnd.DropTargetDropEvent;
114 import java.awt.dnd.DropTargetEvent;
115 import java.awt.dnd.DropTargetListener;
116 import java.awt.event.ActionEvent;
117 import java.awt.event.ActionListener;
118 import java.awt.event.FocusAdapter;
119 import java.awt.event.FocusEvent;
120 import java.awt.event.ItemEvent;
121 import java.awt.event.ItemListener;
122 import java.awt.event.KeyAdapter;
123 import java.awt.event.KeyEvent;
124 import java.awt.event.MouseEvent;
125 import java.awt.print.PageFormat;
126 import java.awt.print.PrinterJob;
127 import java.beans.PropertyChangeEvent;
129 import java.io.FileWriter;
130 import java.io.PrintWriter;
132 import java.util.ArrayList;
133 import java.util.Arrays;
134 import java.util.Deque;
135 import java.util.Enumeration;
136 import java.util.Hashtable;
137 import java.util.List;
138 import java.util.Vector;
140 import javax.swing.ButtonGroup;
141 import javax.swing.JCheckBoxMenuItem;
142 import javax.swing.JEditorPane;
143 import javax.swing.JInternalFrame;
144 import javax.swing.JLayeredPane;
145 import javax.swing.JMenu;
146 import javax.swing.JMenuItem;
147 import javax.swing.JScrollPane;
148 import javax.swing.SwingUtilities;
149 import javax.swing.event.MenuEvent;
150 import javax.swing.event.MenuListener;
156 * @version $Revision$
158 public class AlignFrame extends GAlignFrame implements DropTargetListener,
159 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
162 public static final int DEFAULT_WIDTH = 700;
164 public static final int DEFAULT_HEIGHT = 500;
167 * The currently displayed panel (selected tabbed view if more than one)
169 public AlignmentPanel alignPanel;
171 AlignViewport viewport;
173 public AlignViewControllerI avc;
175 List<AlignmentPanel> alignPanels = new ArrayList<>();
178 * Last format used to load or save alignments in this window
180 FileFormatI currentFileFormat = null;
183 * Current filename for this alignment
185 String fileName = null;
188 * Creates a new AlignFrame object with specific width and height.
194 public AlignFrame(AlignmentI al, int width, int height)
196 this(al, null, width, height);
200 * Creates a new AlignFrame object with specific width, height and
206 * @param sequenceSetId
208 public AlignFrame(AlignmentI al, int width, int height,
209 String sequenceSetId)
211 this(al, null, width, height, sequenceSetId);
215 * Creates a new AlignFrame object with specific width, height and
221 * @param sequenceSetId
224 public AlignFrame(AlignmentI al, int width, int height,
225 String sequenceSetId, String viewId)
227 this(al, null, width, height, sequenceSetId, viewId);
231 * new alignment window with hidden columns
235 * @param hiddenColumns
236 * ColumnSelection or null
238 * Width of alignment frame
242 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
245 this(al, hiddenColumns, width, height, null);
249 * Create alignment frame for al with hiddenColumns, a specific width and
250 * height, and specific sequenceId
253 * @param hiddenColumns
256 * @param sequenceSetId
259 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
260 int height, String sequenceSetId)
262 this(al, hiddenColumns, width, height, sequenceSetId, null);
266 * Create alignment frame for al with hiddenColumns, a specific width and
267 * height, and specific sequenceId
270 * @param hiddenColumns
273 * @param sequenceSetId
278 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
279 int height, String sequenceSetId, String viewId)
281 setSize(width, height);
283 if (al.getDataset() == null)
288 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
290 alignPanel = new AlignmentPanel(this, viewport);
292 addAlignmentPanel(alignPanel, true);
296 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
297 HiddenColumns hiddenColumns, int width, int height)
299 setSize(width, height);
301 if (al.getDataset() == null)
306 viewport = new AlignViewport(al, hiddenColumns);
308 if (hiddenSeqs != null && hiddenSeqs.length > 0)
310 viewport.hideSequence(hiddenSeqs);
312 alignPanel = new AlignmentPanel(this, viewport);
313 addAlignmentPanel(alignPanel, true);
318 * Make a new AlignFrame from existing alignmentPanels
325 public AlignFrame(AlignmentPanel ap)
329 addAlignmentPanel(ap, false);
334 * initalise the alignframe from the underlying viewport data and the
339 if (!Jalview.isHeadlessMode())
341 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
344 avc = new jalview.controller.AlignViewController(this, viewport,
346 if (viewport.getAlignmentConservationAnnotation() == null)
348 // BLOSUM62Colour.setEnabled(false);
349 conservationMenuItem.setEnabled(false);
350 modifyConservation.setEnabled(false);
351 // PIDColour.setEnabled(false);
352 // abovePIDThreshold.setEnabled(false);
353 // modifyPID.setEnabled(false);
356 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
359 if (sortby.equals("Id"))
361 sortIDMenuItem_actionPerformed(null);
363 else if (sortby.equals("Pairwise Identity"))
365 sortPairwiseMenuItem_actionPerformed(null);
368 setMenusFromViewport(viewport);
369 buildSortByAnnotationScoresMenu();
370 calculateTree.addActionListener(new ActionListener()
374 public void actionPerformed(ActionEvent e)
381 if (Desktop.desktop != null)
383 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
384 addServiceListeners();
388 if (viewport.getWrapAlignment())
390 wrapMenuItem_actionPerformed(null);
393 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
395 this.overviewMenuItem_actionPerformed(null);
400 final List<AlignmentPanel> selviews = new ArrayList<>();
401 final List<AlignmentPanel> origview = new ArrayList<>();
402 final String menuLabel = MessageManager
403 .getString("label.copy_format_from");
404 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
405 new ViewSetProvider()
409 public AlignmentPanel[] getAllAlignmentPanels()
412 origview.add(alignPanel);
413 // make an array of all alignment panels except for this one
414 List<AlignmentPanel> aps = new ArrayList<>(
415 Arrays.asList(Desktop.getAlignmentPanels(null)));
416 aps.remove(AlignFrame.this.alignPanel);
417 return aps.toArray(new AlignmentPanel[aps.size()]);
419 }, selviews, new ItemListener()
423 public void itemStateChanged(ItemEvent e)
425 if (origview.size() > 0)
427 final AlignmentPanel ap = origview.get(0);
430 * Copy the ViewStyle of the selected panel to 'this one'.
431 * Don't change value of 'scaleProteinAsCdna' unless copying
434 ViewStyleI vs = selviews.get(0).getAlignViewport()
436 boolean fromSplitFrame = selviews.get(0)
437 .getAlignViewport().getCodingComplement() != null;
440 vs.setScaleProteinAsCdna(ap.getAlignViewport()
441 .getViewStyle().isScaleProteinAsCdna());
443 ap.getAlignViewport().setViewStyle(vs);
446 * Also rescale ViewStyle of SplitFrame complement if there is
447 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
448 * the whole ViewStyle (allow cDNA protein to have different
451 AlignViewportI complement = ap.getAlignViewport()
452 .getCodingComplement();
453 if (complement != null && vs.isScaleProteinAsCdna())
455 AlignFrame af = Desktop.getAlignFrameFor(complement);
456 ((SplitFrame) af.getSplitViewContainer())
458 af.setMenusForViewport();
462 ap.setSelected(true);
463 ap.alignFrame.setMenusForViewport();
468 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
469 .indexOf("devel") > -1
470 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
471 .indexOf("test") > -1)
473 formatMenu.add(vsel);
475 addFocusListener(new FocusAdapter()
478 public void focusGained(FocusEvent e)
480 Jalview.setCurrentAlignFrame(AlignFrame.this);
485 * ensure By Label/Sequence are not selected if annotations
486 * have been reordered manually to CUSTOM order
488 annotationsMenu.addMenuListener(new MenuListener()
491 public void menuSelected(MenuEvent e)
493 SequenceAnnotationOrder sortAnnotationsBy = viewport
494 .getSortAnnotationsBy();
495 sortAnnByLabel.setSelected(
496 sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
497 sortAnnBySequence.setSelected(
498 sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
502 public void menuDeselected(MenuEvent e)
507 public void menuCanceled(MenuEvent e)
514 * Change the filename and format for the alignment, and enable the 'reload'
515 * button functionality.
522 public void setFileName(String file, FileFormatI format)
525 setFileFormat(format);
526 reload.setEnabled(true);
530 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
533 void addKeyListener()
535 addKeyListener(new KeyAdapter()
538 public void keyPressed(KeyEvent evt)
540 if (viewport.cursorMode
541 && ((evt.getKeyCode() >= KeyEvent.VK_0
542 && evt.getKeyCode() <= KeyEvent.VK_9)
543 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
544 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
545 && Character.isDigit(evt.getKeyChar()))
547 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
550 switch (evt.getKeyCode())
553 case 27: // escape key
554 deselectAllSequenceMenuItem_actionPerformed(null);
558 case KeyEvent.VK_DOWN:
559 if (evt.isAltDown() || !viewport.cursorMode)
561 moveSelectedSequences(false);
563 if (viewport.cursorMode)
565 alignPanel.getSeqPanel().moveCursor(0, 1);
570 if (evt.isAltDown() || !viewport.cursorMode)
572 moveSelectedSequences(true);
574 if (viewport.cursorMode)
576 alignPanel.getSeqPanel().moveCursor(0, -1);
581 case KeyEvent.VK_LEFT:
582 if (evt.isAltDown() || !viewport.cursorMode)
584 slideSequences(false,
585 alignPanel.getSeqPanel().getKeyboardNo1());
589 alignPanel.getSeqPanel().moveCursor(-1, 0);
594 case KeyEvent.VK_RIGHT:
595 if (evt.isAltDown() || !viewport.cursorMode)
597 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
601 alignPanel.getSeqPanel().moveCursor(1, 0);
605 case KeyEvent.VK_SPACE:
606 if (viewport.cursorMode)
608 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
609 || evt.isShiftDown() || evt.isAltDown());
613 // case KeyEvent.VK_A:
614 // if (viewport.cursorMode)
616 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
617 // //System.out.println("A");
621 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
622 * System.out.println("closing bracket"); } break;
624 case KeyEvent.VK_DELETE:
625 case KeyEvent.VK_BACK_SPACE:
626 if (!viewport.cursorMode)
628 cut_actionPerformed(null);
632 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
633 || evt.isShiftDown() || evt.isAltDown());
639 if (viewport.cursorMode)
641 alignPanel.getSeqPanel().setCursorRow();
645 if (viewport.cursorMode && !evt.isControlDown())
647 alignPanel.getSeqPanel().setCursorColumn();
651 if (viewport.cursorMode)
653 alignPanel.getSeqPanel().setCursorPosition();
657 case KeyEvent.VK_ENTER:
658 case KeyEvent.VK_COMMA:
659 if (viewport.cursorMode)
661 alignPanel.getSeqPanel().setCursorRowAndColumn();
666 if (viewport.cursorMode)
668 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
672 if (viewport.cursorMode)
674 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
679 viewport.cursorMode = !viewport.cursorMode;
680 statusBar.setText(MessageManager
681 .formatMessage("label.keyboard_editing_mode", new String[]
682 { (viewport.cursorMode ? "on" : "off") }));
683 if (viewport.cursorMode)
685 ViewportRanges ranges = viewport.getRanges();
686 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
688 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
691 alignPanel.getSeqPanel().seqCanvas.repaint();
697 Help.showHelpWindow();
698 } catch (Exception ex)
700 ex.printStackTrace();
705 boolean toggleSeqs = !evt.isControlDown();
706 boolean toggleCols = !evt.isShiftDown();
707 toggleHiddenRegions(toggleSeqs, toggleCols);
712 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
713 boolean modifyExisting = true; // always modify, don't clear
714 // evt.isShiftDown();
715 boolean invertHighlighted = evt.isAltDown();
716 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
720 case KeyEvent.VK_PAGE_UP:
721 viewport.getRanges().pageUp();
723 case KeyEvent.VK_PAGE_DOWN:
724 viewport.getRanges().pageDown();
730 public void keyReleased(KeyEvent evt)
732 switch (evt.getKeyCode())
734 case KeyEvent.VK_LEFT:
735 if (evt.isAltDown() || !viewport.cursorMode)
737 viewport.firePropertyChange("alignment", null,
738 viewport.getAlignment().getSequences());
742 case KeyEvent.VK_RIGHT:
743 if (evt.isAltDown() || !viewport.cursorMode)
745 viewport.firePropertyChange("alignment", null,
746 viewport.getAlignment().getSequences());
754 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
756 ap.alignFrame = this;
757 avc = new jalview.controller.AlignViewController(this, viewport,
762 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
764 int aSize = alignPanels.size();
766 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
768 if (aSize == 1 && ap.av.getViewName() == null)
770 this.getContentPane().add(ap, BorderLayout.CENTER);
776 setInitialTabVisible();
779 expandViews.setEnabled(true);
780 gatherViews.setEnabled(true);
781 tabbedPane.addTab(ap.av.getViewName(), ap);
783 ap.setVisible(false);
788 if (ap.av.isPadGaps())
790 ap.av.getAlignment().padGaps();
792 ap.av.updateConservation(ap);
793 ap.av.updateConsensus(ap);
794 ap.av.updateStrucConsensus(ap);
798 public void setInitialTabVisible()
800 expandViews.setEnabled(true);
801 gatherViews.setEnabled(true);
802 tabbedPane.setVisible(true);
803 AlignmentPanel first = alignPanels.get(0);
804 tabbedPane.addTab(first.av.getViewName(), first);
805 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
808 public AlignViewport getViewport()
813 /* Set up intrinsic listeners for dynamically generated GUI bits. */
814 private void addServiceListeners()
816 final java.beans.PropertyChangeListener thisListener;
817 Desktop.instance.addJalviewPropertyChangeListener("services",
818 thisListener = new java.beans.PropertyChangeListener()
821 public void propertyChange(PropertyChangeEvent evt)
823 // // System.out.println("Discoverer property change.");
824 // if (evt.getPropertyName().equals("services"))
826 SwingUtilities.invokeLater(new Runnable()
833 "Rebuild WS Menu for service change");
834 BuildWebServiceMenu();
841 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
844 public void internalFrameClosed(
845 javax.swing.event.InternalFrameEvent evt)
847 // System.out.println("deregistering discoverer listener");
848 Desktop.instance.removeJalviewPropertyChangeListener("services",
850 closeMenuItem_actionPerformed(true);
853 // Finally, build the menu once to get current service state
854 new Thread(new Runnable()
859 BuildWebServiceMenu();
865 * Configure menu items that vary according to whether the alignment is
866 * nucleotide or protein
868 public void setGUINucleotide()
870 AlignmentI al = getViewport().getAlignment();
871 boolean nucleotide = al.isNucleotide();
873 loadVcf.setVisible(nucleotide);
874 showTranslation.setVisible(nucleotide);
875 showReverse.setVisible(nucleotide);
876 showReverseComplement.setVisible(nucleotide);
877 conservationMenuItem.setEnabled(!nucleotide);
879 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
880 showGroupConservation.setEnabled(!nucleotide);
882 showComplementMenuItem
883 .setText(nucleotide ? MessageManager.getString("label.protein")
884 : MessageManager.getString("label.nucleotide"));
888 * set up menus for the current viewport. This may be called after any
889 * operation that affects the data in the current view (selection changed,
890 * etc) to update the menus to reflect the new state.
893 public void setMenusForViewport()
895 setMenusFromViewport(viewport);
899 * Need to call this method when tabs are selected for multiple views, or when
900 * loading from Jalview2XML.java
905 public void setMenusFromViewport(AlignViewport av)
907 padGapsMenuitem.setSelected(av.isPadGaps());
908 colourTextMenuItem.setSelected(av.isShowColourText());
909 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
910 modifyPID.setEnabled(abovePIDThreshold.isSelected());
911 conservationMenuItem.setSelected(av.getConservationSelected());
912 modifyConservation.setEnabled(conservationMenuItem.isSelected());
913 seqLimits.setSelected(av.getShowJVSuffix());
914 idRightAlign.setSelected(av.isRightAlignIds());
915 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
916 renderGapsMenuItem.setSelected(av.isRenderGaps());
917 wrapMenuItem.setSelected(av.getWrapAlignment());
918 scaleAbove.setVisible(av.getWrapAlignment());
919 scaleLeft.setVisible(av.getWrapAlignment());
920 scaleRight.setVisible(av.getWrapAlignment());
921 annotationPanelMenuItem.setState(av.isShowAnnotation());
923 * Show/hide annotations only enabled if annotation panel is shown
925 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
926 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
927 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
928 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
929 viewBoxesMenuItem.setSelected(av.getShowBoxes());
930 viewTextMenuItem.setSelected(av.getShowText());
931 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
932 showGroupConsensus.setSelected(av.isShowGroupConsensus());
933 showGroupConservation.setSelected(av.isShowGroupConservation());
934 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
935 showSequenceLogo.setSelected(av.isShowSequenceLogo());
936 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
938 ColourMenuHelper.setColourSelected(colourMenu,
939 av.getGlobalColourScheme());
941 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
942 hiddenMarkers.setState(av.getShowHiddenMarkers());
943 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
944 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
945 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
946 autoCalculate.setSelected(av.autoCalculateConsensus);
947 sortByTree.setSelected(av.sortByTree);
948 listenToViewSelections.setSelected(av.followSelection);
950 showProducts.setEnabled(canShowProducts());
951 setGroovyEnabled(Desktop.getGroovyConsole() != null);
957 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
961 public void setGroovyEnabled(boolean b)
963 runGroovy.setEnabled(b);
966 private IProgressIndicator progressBar;
971 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
974 public void setProgressBar(String message, long id)
976 progressBar.setProgressBar(message, id);
980 public void registerHandler(final long id,
981 final IProgressIndicatorHandler handler)
983 progressBar.registerHandler(id, handler);
988 * @return true if any progress bars are still active
991 public boolean operationInProgress()
993 return progressBar.operationInProgress();
997 * Sets the text of the status bar. Note that setting a null or empty value
998 * will cause the status bar to be hidden, with possibly undesirable flicker
999 * of the screen layout.
1002 public void setStatus(String text)
1004 statusBar.setText(text == null || text.isEmpty() ? " " : text);
1008 * Added so Castor Mapping file can obtain Jalview Version
1010 public String getVersion()
1012 return jalview.bin.Cache.getProperty("VERSION");
1015 public FeatureRenderer getFeatureRenderer()
1017 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1021 public void fetchSequence_actionPerformed(ActionEvent e)
1023 new jalview.gui.SequenceFetcher(this);
1027 public void addFromFile_actionPerformed(ActionEvent e)
1029 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1033 public void reload_actionPerformed(ActionEvent e)
1035 if (fileName != null)
1037 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1038 // originating file's format
1039 // TODO: work out how to recover feature settings for correct view(s) when
1040 // file is reloaded.
1041 if (FileFormat.Jalview.equals(currentFileFormat))
1043 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1044 for (int i = 0; i < frames.length; i++)
1046 if (frames[i] instanceof AlignFrame && frames[i] != this
1047 && ((AlignFrame) frames[i]).fileName != null
1048 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1052 frames[i].setSelected(true);
1053 Desktop.instance.closeAssociatedWindows();
1054 } catch (java.beans.PropertyVetoException ex)
1060 Desktop.instance.closeAssociatedWindows();
1062 FileLoader loader = new FileLoader();
1063 DataSourceType protocol = fileName.startsWith("http:")
1064 ? DataSourceType.URL
1065 : DataSourceType.FILE;
1066 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1070 Rectangle bounds = this.getBounds();
1072 FileLoader loader = new FileLoader();
1073 DataSourceType protocol = fileName.startsWith("http:")
1074 ? DataSourceType.URL
1075 : DataSourceType.FILE;
1076 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1077 protocol, currentFileFormat);
1079 newframe.setBounds(bounds);
1080 if (featureSettings != null && featureSettings.isShowing())
1082 final Rectangle fspos = featureSettings.frame.getBounds();
1083 // TODO: need a 'show feature settings' function that takes bounds -
1084 // need to refactor Desktop.addFrame
1085 newframe.featureSettings_actionPerformed(null);
1086 final FeatureSettings nfs = newframe.featureSettings;
1087 SwingUtilities.invokeLater(new Runnable()
1092 nfs.frame.setBounds(fspos);
1095 this.featureSettings.close();
1096 this.featureSettings = null;
1098 this.closeMenuItem_actionPerformed(true);
1104 public void addFromText_actionPerformed(ActionEvent e)
1107 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1111 public void addFromURL_actionPerformed(ActionEvent e)
1113 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1117 public void save_actionPerformed(ActionEvent e)
1119 if (fileName == null || (currentFileFormat == null)
1120 || fileName.startsWith("http"))
1122 saveAs_actionPerformed(null);
1126 saveAlignment(fileName, currentFileFormat);
1137 public void saveAs_actionPerformed(ActionEvent e)
1139 String format = currentFileFormat == null ? null
1140 : currentFileFormat.getName();
1141 JalviewFileChooser chooser = JalviewFileChooser
1142 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1144 chooser.setFileView(new JalviewFileView());
1145 chooser.setDialogTitle(
1146 MessageManager.getString("label.save_alignment_to_file"));
1147 chooser.setToolTipText(MessageManager.getString("action.save"));
1149 int value = chooser.showSaveDialog(this);
1151 if (value == JalviewFileChooser.APPROVE_OPTION)
1153 currentFileFormat = chooser.getSelectedFormat();
1154 while (currentFileFormat == null)
1156 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1157 MessageManager.getString(
1158 "label.select_file_format_before_saving"),
1159 MessageManager.getString("label.file_format_not_specified"),
1160 JvOptionPane.WARNING_MESSAGE);
1161 currentFileFormat = chooser.getSelectedFormat();
1162 value = chooser.showSaveDialog(this);
1163 if (value != JalviewFileChooser.APPROVE_OPTION)
1169 fileName = chooser.getSelectedFile().getPath();
1171 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1173 Cache.setProperty("LAST_DIRECTORY", fileName);
1174 saveAlignment(fileName, currentFileFormat);
1178 public boolean saveAlignment(String file, FileFormatI format)
1180 boolean success = true;
1182 if (FileFormat.Jalview.equals(format))
1184 String shortName = title;
1186 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1188 shortName = shortName.substring(
1189 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1192 success = new jalview.project.Jalview2XML().saveAlignment(this, file,
1195 statusBar.setText(MessageManager.formatMessage(
1196 "label.successfully_saved_to_file_in_format", new Object[]
1197 { fileName, format }));
1202 AlignmentExportData exportData = getAlignmentForExport(format,
1204 if (exportData.getSettings().isCancelled())
1208 FormatAdapter f = new FormatAdapter(alignPanel,
1209 exportData.getSettings());
1210 String output = f.formatSequences(format, exportData.getAlignment(), // class
1214 // occur in the distant future
1215 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1216 f.getCacheSuffixDefault(format),
1217 viewport.getAlignment().getHiddenColumns());
1225 // create backupfiles object and get new temp filename destination
1226 BackupFiles backupfiles = new BackupFiles(file);
1230 PrintWriter out = new PrintWriter(
1231 new FileWriter(backupfiles.getTempFilePath()));
1235 this.setTitle(file);
1236 statusBar.setText(MessageManager.formatMessage(
1237 "label.successfully_saved_to_file_in_format", new Object[]
1238 { fileName, format.getName() }));
1239 } catch (Exception ex)
1242 ex.printStackTrace();
1245 backupfiles.setWriteSuccess(success);
1246 // do the backup file roll and rename the temp file to actual file
1247 success = backupfiles.rollBackupsAndRenameTempFile();
1254 JvOptionPane.showInternalMessageDialog(this, MessageManager
1255 .formatMessage("label.couldnt_save_file", new Object[]
1257 MessageManager.getString("label.error_saving_file"),
1258 JvOptionPane.WARNING_MESSAGE);
1264 private void warningMessage(String warning, String title)
1266 if (new jalview.util.Platform().isHeadless())
1268 System.err.println("Warning: " + title + "\nWarning: " + warning);
1273 JvOptionPane.showInternalMessageDialog(this, warning, title,
1274 JvOptionPane.WARNING_MESSAGE);
1286 protected void outputText_actionPerformed(ActionEvent e)
1288 FileFormatI fileFormat = FileFormats.getInstance()
1289 .forName(e.getActionCommand());
1290 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1292 if (exportData.getSettings().isCancelled())
1296 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1297 cap.setForInput(null);
1300 FileFormatI format = fileFormat;
1301 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1302 .formatSequences(format, exportData.getAlignment(),
1303 exportData.getOmitHidden(),
1304 exportData.getStartEndPostions(),
1305 viewport.getAlignment().getHiddenColumns()));
1306 Desktop.addInternalFrame(cap, MessageManager
1307 .formatMessage("label.alignment_output_command", new Object[]
1308 { e.getActionCommand() }), 600, 500);
1309 } catch (OutOfMemoryError oom)
1311 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1318 public static AlignmentExportData getAlignmentForExport(
1319 FileFormatI format, AlignViewportI viewport,
1320 AlignExportSettingI exportSettings)
1322 AlignmentI alignmentToExport = null;
1323 AlignExportSettingI settings = exportSettings;
1324 String[] omitHidden = null;
1326 HiddenSequences hiddenSeqs = viewport.getAlignment()
1327 .getHiddenSequences();
1329 alignmentToExport = viewport.getAlignment();
1331 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1332 if (settings == null)
1334 settings = new AlignExportSettings(hasHiddenSeqs,
1335 viewport.hasHiddenColumns(), format);
1337 // settings.isExportAnnotations();
1339 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1341 omitHidden = viewport.getViewAsString(false,
1342 settings.isExportHiddenSequences());
1345 int[] alignmentStartEnd = new int[2];
1346 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1348 alignmentToExport = hiddenSeqs.getFullAlignment();
1352 alignmentToExport = viewport.getAlignment();
1354 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1355 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1356 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1357 omitHidden, alignmentStartEnd, settings);
1368 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1370 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1371 htmlSVG.exportHTML(null);
1375 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1377 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1378 bjs.exportHTML(null);
1381 public void createImageMap(File file, String image)
1383 alignPanel.makePNGImageMap(file, image);
1393 public void createPNG(File f)
1395 alignPanel.makePNG(f);
1405 public void createEPS(File f)
1407 alignPanel.makeEPS(f);
1411 public void createSVG(File f)
1413 alignPanel.makeSVG(f);
1417 public void pageSetup_actionPerformed(ActionEvent e)
1419 PrinterJob printJob = PrinterJob.getPrinterJob();
1420 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1430 public void printMenuItem_actionPerformed(ActionEvent e)
1432 // Putting in a thread avoids Swing painting problems
1433 PrintThread thread = new PrintThread(alignPanel);
1438 public void exportFeatures_actionPerformed(ActionEvent e)
1440 new AnnotationExporter(alignPanel).exportFeatures();
1444 public void exportAnnotations_actionPerformed(ActionEvent e)
1446 new AnnotationExporter(alignPanel).exportAnnotations();
1450 public void associatedData_actionPerformed(ActionEvent e)
1452 // Pick the tree file
1453 JalviewFileChooser chooser = new JalviewFileChooser(
1454 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1455 chooser.setFileView(new JalviewFileView());
1456 chooser.setDialogTitle(
1457 MessageManager.getString("label.load_jalview_annotations"));
1458 chooser.setToolTipText(
1459 MessageManager.getString("label.load_jalview_annotations"));
1461 int value = chooser.showOpenDialog(null);
1463 if (value == JalviewFileChooser.APPROVE_OPTION)
1465 String choice = chooser.getSelectedFile().getPath();
1466 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1467 loadJalviewDataFile(choice, null, null, null);
1473 * Close the current view or all views in the alignment frame. If the frame
1474 * only contains one view then the alignment will be removed from memory.
1476 * @param closeAllTabs
1479 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1481 if (alignPanels != null && alignPanels.size() < 2)
1483 closeAllTabs = true;
1488 if (alignPanels != null)
1492 if (this.isClosed())
1494 // really close all the windows - otherwise wait till
1495 // setClosed(true) is called
1496 for (int i = 0; i < alignPanels.size(); i++)
1498 AlignmentPanel ap = alignPanels.get(i);
1505 closeView(alignPanel);
1512 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1513 * be called recursively, with the frame now in 'closed' state
1515 this.setClosed(true);
1517 } catch (Exception ex)
1519 ex.printStackTrace();
1524 * Close the specified panel and close up tabs appropriately.
1526 * @param panelToClose
1528 public void closeView(AlignmentPanel panelToClose)
1530 int index = tabbedPane.getSelectedIndex();
1531 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1532 alignPanels.remove(panelToClose);
1533 panelToClose.closePanel();
1534 panelToClose = null;
1536 tabbedPane.removeTabAt(closedindex);
1537 tabbedPane.validate();
1539 if (index > closedindex || index == tabbedPane.getTabCount())
1541 // modify currently selected tab index if necessary.
1545 this.tabSelectionChanged(index);
1551 void updateEditMenuBar()
1554 if (viewport.getHistoryList().size() > 0)
1556 undoMenuItem.setEnabled(true);
1557 CommandI command = viewport.getHistoryList().peek();
1558 undoMenuItem.setText(MessageManager
1559 .formatMessage("label.undo_command", new Object[]
1560 { command.getDescription() }));
1564 undoMenuItem.setEnabled(false);
1565 undoMenuItem.setText(MessageManager.getString("action.undo"));
1568 if (viewport.getRedoList().size() > 0)
1570 redoMenuItem.setEnabled(true);
1572 CommandI command = viewport.getRedoList().peek();
1573 redoMenuItem.setText(MessageManager
1574 .formatMessage("label.redo_command", new Object[]
1575 { command.getDescription() }));
1579 redoMenuItem.setEnabled(false);
1580 redoMenuItem.setText(MessageManager.getString("action.redo"));
1585 public void addHistoryItem(CommandI command)
1587 if (command.getSize() > 0)
1589 viewport.addToHistoryList(command);
1590 viewport.clearRedoList();
1591 updateEditMenuBar();
1592 viewport.updateHiddenColumns();
1593 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1594 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1595 // viewport.getColumnSelection()
1596 // .getHiddenColumns().size() > 0);
1602 * @return alignment objects for all views
1604 AlignmentI[] getViewAlignments()
1606 if (alignPanels != null)
1608 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1610 for (AlignmentPanel ap : alignPanels)
1612 als[i++] = ap.av.getAlignment();
1616 if (viewport != null)
1618 return new AlignmentI[] { viewport.getAlignment() };
1630 protected void undoMenuItem_actionPerformed(ActionEvent e)
1632 if (viewport.getHistoryList().isEmpty())
1636 CommandI command = viewport.getHistoryList().pop();
1637 viewport.addToRedoList(command);
1638 command.undoCommand(getViewAlignments());
1640 AlignmentViewport originalSource = getOriginatingSource(command);
1641 updateEditMenuBar();
1643 if (originalSource != null)
1645 if (originalSource != viewport)
1648 "Implementation worry: mismatch of viewport origin for undo");
1650 originalSource.updateHiddenColumns();
1651 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1653 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1654 // viewport.getColumnSelection()
1655 // .getHiddenColumns().size() > 0);
1656 originalSource.firePropertyChange("alignment", null,
1657 originalSource.getAlignment().getSequences());
1668 protected void redoMenuItem_actionPerformed(ActionEvent e)
1670 if (viewport.getRedoList().size() < 1)
1675 CommandI command = viewport.getRedoList().pop();
1676 viewport.addToHistoryList(command);
1677 command.doCommand(getViewAlignments());
1679 AlignmentViewport originalSource = getOriginatingSource(command);
1680 updateEditMenuBar();
1682 if (originalSource != null)
1685 if (originalSource != viewport)
1688 "Implementation worry: mismatch of viewport origin for redo");
1690 originalSource.updateHiddenColumns();
1691 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1693 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1694 // viewport.getColumnSelection()
1695 // .getHiddenColumns().size() > 0);
1696 originalSource.firePropertyChange("alignment", null,
1697 originalSource.getAlignment().getSequences());
1701 AlignmentViewport getOriginatingSource(CommandI command)
1703 AlignmentViewport originalSource = null;
1704 // For sequence removal and addition, we need to fire
1705 // the property change event FROM the viewport where the
1706 // original alignment was altered
1707 AlignmentI al = null;
1708 if (command instanceof EditCommand)
1710 EditCommand editCommand = (EditCommand) command;
1711 al = editCommand.getAlignment();
1712 List<Component> comps = PaintRefresher.components
1713 .get(viewport.getSequenceSetId());
1715 for (Component comp : comps)
1717 if (comp instanceof AlignmentPanel)
1719 if (al == ((AlignmentPanel) comp).av.getAlignment())
1721 originalSource = ((AlignmentPanel) comp).av;
1728 if (originalSource == null)
1730 // The original view is closed, we must validate
1731 // the current view against the closed view first
1734 PaintRefresher.validateSequences(al, viewport.getAlignment());
1737 originalSource = viewport;
1740 return originalSource;
1749 public void moveSelectedSequences(boolean up)
1751 SequenceGroup sg = viewport.getSelectionGroup();
1757 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1758 viewport.getHiddenRepSequences(), up);
1759 alignPanel.paintAlignment(true, false);
1762 synchronized void slideSequences(boolean right, int size)
1764 List<SequenceI> sg = new ArrayList<>();
1765 if (viewport.cursorMode)
1767 sg.add(viewport.getAlignment()
1768 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1770 else if (viewport.getSelectionGroup() != null
1771 && viewport.getSelectionGroup().getSize() != viewport
1772 .getAlignment().getHeight())
1774 sg = viewport.getSelectionGroup()
1775 .getSequences(viewport.getHiddenRepSequences());
1783 List<SequenceI> invertGroup = new ArrayList<>();
1785 for (SequenceI seq : viewport.getAlignment().getSequences())
1787 if (!sg.contains(seq))
1789 invertGroup.add(seq);
1793 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1795 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1796 for (int i = 0; i < invertGroup.size(); i++)
1798 seqs2[i] = invertGroup.get(i);
1801 SlideSequencesCommand ssc;
1804 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1805 viewport.getGapCharacter());
1809 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1810 viewport.getGapCharacter());
1813 int groupAdjustment = 0;
1814 if (ssc.getGapsInsertedBegin() && right)
1816 if (viewport.cursorMode)
1818 alignPanel.getSeqPanel().moveCursor(size, 0);
1822 groupAdjustment = size;
1825 else if (!ssc.getGapsInsertedBegin() && !right)
1827 if (viewport.cursorMode)
1829 alignPanel.getSeqPanel().moveCursor(-size, 0);
1833 groupAdjustment = -size;
1837 if (groupAdjustment != 0)
1839 viewport.getSelectionGroup().setStartRes(
1840 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1841 viewport.getSelectionGroup().setEndRes(
1842 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1846 * just extend the last slide command if compatible; but not if in
1847 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1849 boolean appendHistoryItem = false;
1850 Deque<CommandI> historyList = viewport.getHistoryList();
1851 boolean inSplitFrame = getSplitViewContainer() != null;
1852 if (!inSplitFrame && historyList != null && historyList.size() > 0
1853 && historyList.peek() instanceof SlideSequencesCommand)
1855 appendHistoryItem = ssc.appendSlideCommand(
1856 (SlideSequencesCommand) historyList.peek());
1859 if (!appendHistoryItem)
1861 addHistoryItem(ssc);
1874 protected void copy_actionPerformed(ActionEvent e)
1876 if (viewport.getSelectionGroup() == null)
1880 // TODO: preserve the ordering of displayed alignment annotation in any
1881 // internal paste (particularly sequence associated annotation)
1882 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1883 String[] omitHidden = null;
1885 if (viewport.hasHiddenColumns())
1887 omitHidden = viewport.getViewAsString(true);
1890 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1891 seqs, omitHidden, null);
1893 StringSelection ss = new StringSelection(output);
1897 jalview.gui.Desktop.internalCopy = true;
1898 // Its really worth setting the clipboard contents
1899 // to empty before setting the large StringSelection!!
1900 Toolkit.getDefaultToolkit().getSystemClipboard()
1901 .setContents(new StringSelection(""), null);
1903 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1905 } catch (OutOfMemoryError er)
1907 new OOMWarning("copying region", er);
1911 HiddenColumns hiddenColumns = null;
1912 if (viewport.hasHiddenColumns())
1914 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1915 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1917 // create new HiddenColumns object with copy of hidden regions
1918 // between startRes and endRes, offset by startRes
1919 hiddenColumns = new HiddenColumns(
1920 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1921 hiddenCutoff, hiddenOffset);
1924 Desktop.jalviewClipboard = new Object[] { seqs,
1925 viewport.getAlignment().getDataset(), hiddenColumns };
1926 statusBar.setText(MessageManager.formatMessage(
1927 "label.copied_sequences_to_clipboard", new Object[]
1928 { Integer.valueOf(seqs.length).toString() }));
1938 protected void pasteNew_actionPerformed(ActionEvent e)
1950 protected void pasteThis_actionPerformed(ActionEvent e)
1956 * Paste contents of Jalview clipboard
1958 * @param newAlignment
1959 * true to paste to a new alignment, otherwise add to this.
1961 void paste(boolean newAlignment)
1963 boolean externalPaste = true;
1966 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1967 Transferable contents = c.getContents(this);
1969 if (contents == null)
1978 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1979 if (str.length() < 1)
1984 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1986 } catch (OutOfMemoryError er)
1988 new OOMWarning("Out of memory pasting sequences!!", er);
1992 SequenceI[] sequences;
1993 boolean annotationAdded = false;
1994 AlignmentI alignment = null;
1996 if (Desktop.jalviewClipboard != null)
1998 // The clipboard was filled from within Jalview, we must use the
2000 // And dataset from the copied alignment
2001 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2002 // be doubly sure that we create *new* sequence objects.
2003 sequences = new SequenceI[newseq.length];
2004 for (int i = 0; i < newseq.length; i++)
2006 sequences[i] = new Sequence(newseq[i]);
2008 alignment = new Alignment(sequences);
2009 externalPaste = false;
2013 // parse the clipboard as an alignment.
2014 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2016 sequences = alignment.getSequencesArray();
2020 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2026 if (Desktop.jalviewClipboard != null)
2028 // dataset is inherited
2029 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2033 // new dataset is constructed
2034 alignment.setDataset(null);
2036 alwidth = alignment.getWidth() + 1;
2040 AlignmentI pastedal = alignment; // preserve pasted alignment object
2041 // Add pasted sequences and dataset into existing alignment.
2042 alignment = viewport.getAlignment();
2043 alwidth = alignment.getWidth() + 1;
2044 // decide if we need to import sequences from an existing dataset
2045 boolean importDs = Desktop.jalviewClipboard != null
2046 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2047 // importDs==true instructs us to copy over new dataset sequences from
2048 // an existing alignment
2049 Vector newDs = (importDs) ? new Vector() : null; // used to create
2050 // minimum dataset set
2052 for (int i = 0; i < sequences.length; i++)
2056 newDs.addElement(null);
2058 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2060 if (importDs && ds != null)
2062 if (!newDs.contains(ds))
2064 newDs.setElementAt(ds, i);
2065 ds = new Sequence(ds);
2066 // update with new dataset sequence
2067 sequences[i].setDatasetSequence(ds);
2071 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2076 // copy and derive new dataset sequence
2077 sequences[i] = sequences[i].deriveSequence();
2078 alignment.getDataset()
2079 .addSequence(sequences[i].getDatasetSequence());
2080 // TODO: avoid creation of duplicate dataset sequences with a
2081 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2083 alignment.addSequence(sequences[i]); // merges dataset
2087 newDs.clear(); // tidy up
2089 if (alignment.getAlignmentAnnotation() != null)
2091 for (AlignmentAnnotation alan : alignment
2092 .getAlignmentAnnotation())
2094 if (alan.graphGroup > fgroup)
2096 fgroup = alan.graphGroup;
2100 if (pastedal.getAlignmentAnnotation() != null)
2102 // Add any annotation attached to alignment.
2103 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2104 for (int i = 0; i < alann.length; i++)
2106 annotationAdded = true;
2107 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2109 AlignmentAnnotation newann = new AlignmentAnnotation(
2111 if (newann.graphGroup > -1)
2113 if (newGraphGroups.size() <= newann.graphGroup
2114 || newGraphGroups.get(newann.graphGroup) == null)
2116 for (int q = newGraphGroups
2117 .size(); q <= newann.graphGroup; q++)
2119 newGraphGroups.add(q, null);
2121 newGraphGroups.set(newann.graphGroup,
2122 new Integer(++fgroup));
2124 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2128 newann.padAnnotation(alwidth);
2129 alignment.addAnnotation(newann);
2139 addHistoryItem(new EditCommand(
2140 MessageManager.getString("label.add_sequences"),
2141 Action.PASTE, sequences, 0, alignment.getWidth(),
2144 // Add any annotations attached to sequences
2145 for (int i = 0; i < sequences.length; i++)
2147 if (sequences[i].getAnnotation() != null)
2149 AlignmentAnnotation newann;
2150 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2152 annotationAdded = true;
2153 newann = sequences[i].getAnnotation()[a];
2154 newann.adjustForAlignment();
2155 newann.padAnnotation(alwidth);
2156 if (newann.graphGroup > -1)
2158 if (newann.graphGroup > -1)
2160 if (newGraphGroups.size() <= newann.graphGroup
2161 || newGraphGroups.get(newann.graphGroup) == null)
2163 for (int q = newGraphGroups
2164 .size(); q <= newann.graphGroup; q++)
2166 newGraphGroups.add(q, null);
2168 newGraphGroups.set(newann.graphGroup,
2169 new Integer(++fgroup));
2171 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2175 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2179 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2187 // propagate alignment changed.
2188 viewport.getRanges().setEndSeq(alignment.getHeight());
2189 if (annotationAdded)
2191 // Duplicate sequence annotation in all views.
2192 AlignmentI[] alview = this.getViewAlignments();
2193 for (int i = 0; i < sequences.length; i++)
2195 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2200 for (int avnum = 0; avnum < alview.length; avnum++)
2202 if (alview[avnum] != alignment)
2204 // duplicate in a view other than the one with input focus
2205 int avwidth = alview[avnum].getWidth() + 1;
2206 // this relies on sann being preserved after we
2207 // modify the sequence's annotation array for each duplication
2208 for (int a = 0; a < sann.length; a++)
2210 AlignmentAnnotation newann = new AlignmentAnnotation(
2212 sequences[i].addAlignmentAnnotation(newann);
2213 newann.padAnnotation(avwidth);
2214 alview[avnum].addAnnotation(newann); // annotation was
2215 // duplicated earlier
2216 // TODO JAL-1145 graphGroups are not updated for sequence
2217 // annotation added to several views. This may cause
2219 alview[avnum].setAnnotationIndex(newann, a);
2224 buildSortByAnnotationScoresMenu();
2226 viewport.firePropertyChange("alignment", null,
2227 alignment.getSequences());
2228 if (alignPanels != null)
2230 for (AlignmentPanel ap : alignPanels)
2232 ap.validateAnnotationDimensions(false);
2237 alignPanel.validateAnnotationDimensions(false);
2243 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2245 String newtitle = new String("Copied sequences");
2247 if (Desktop.jalviewClipboard != null
2248 && Desktop.jalviewClipboard[2] != null)
2250 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2251 af.viewport.setHiddenColumns(hc);
2254 // >>>This is a fix for the moment, until a better solution is
2256 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2257 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2258 .getFeatureRenderer());
2260 // TODO: maintain provenance of an alignment, rather than just make the
2261 // title a concatenation of operations.
2264 if (title.startsWith("Copied sequences"))
2270 newtitle = newtitle.concat("- from " + title);
2275 newtitle = new String("Pasted sequences");
2278 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2283 } catch (Exception ex)
2285 ex.printStackTrace();
2286 System.out.println("Exception whilst pasting: " + ex);
2287 // could be anything being pasted in here
2293 protected void expand_newalign(ActionEvent e)
2297 AlignmentI alignment = AlignmentUtils
2298 .expandContext(getViewport().getAlignment(), -1);
2299 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2301 String newtitle = new String("Flanking alignment");
2303 if (Desktop.jalviewClipboard != null
2304 && Desktop.jalviewClipboard[2] != null)
2306 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2307 af.viewport.setHiddenColumns(hc);
2310 // >>>This is a fix for the moment, until a better solution is
2312 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2313 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2314 .getFeatureRenderer());
2316 // TODO: maintain provenance of an alignment, rather than just make the
2317 // title a concatenation of operations.
2319 if (title.startsWith("Copied sequences"))
2325 newtitle = newtitle.concat("- from " + title);
2329 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2331 } catch (Exception ex)
2333 ex.printStackTrace();
2334 System.out.println("Exception whilst pasting: " + ex);
2335 // could be anything being pasted in here
2336 } catch (OutOfMemoryError oom)
2338 new OOMWarning("Viewing flanking region of alignment", oom);
2349 protected void cut_actionPerformed(ActionEvent e)
2351 copy_actionPerformed(null);
2352 delete_actionPerformed(null);
2362 protected void delete_actionPerformed(ActionEvent evt)
2365 SequenceGroup sg = viewport.getSelectionGroup();
2372 * If the cut affects all sequences, warn, remove highlighted columns
2374 if (sg.getSize() == viewport.getAlignment().getHeight())
2376 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2377 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2378 if (isEntireAlignWidth)
2380 int confirm = JvOptionPane.showConfirmDialog(this,
2381 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2382 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2383 JvOptionPane.OK_CANCEL_OPTION);
2385 if (confirm == JvOptionPane.CANCEL_OPTION
2386 || confirm == JvOptionPane.CLOSED_OPTION)
2391 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2392 sg.getEndRes() + 1);
2394 SequenceI[] cut = sg.getSequences()
2395 .toArray(new SequenceI[sg.getSize()]);
2397 addHistoryItem(new EditCommand(
2398 MessageManager.getString("label.cut_sequences"), Action.CUT,
2399 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2400 viewport.getAlignment()));
2402 viewport.setSelectionGroup(null);
2403 viewport.sendSelection();
2404 viewport.getAlignment().deleteGroup(sg);
2406 viewport.firePropertyChange("alignment", null,
2407 viewport.getAlignment().getSequences());
2408 if (viewport.getAlignment().getHeight() < 1)
2412 this.setClosed(true);
2413 } catch (Exception ex)
2426 protected void deleteGroups_actionPerformed(ActionEvent e)
2428 if (avc.deleteGroups())
2430 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2431 alignPanel.updateAnnotation();
2432 alignPanel.paintAlignment(true, true);
2443 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2445 SequenceGroup sg = new SequenceGroup(
2446 viewport.getAlignment().getSequences());
2448 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2449 viewport.setSelectionGroup(sg);
2450 viewport.isSelectionGroupChanged(true);
2451 viewport.sendSelection();
2452 // JAL-2034 - should delegate to
2453 // alignPanel to decide if overview needs
2455 alignPanel.paintAlignment(false, false);
2456 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2466 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2468 if (viewport.cursorMode)
2470 alignPanel.getSeqPanel().keyboardNo1 = null;
2471 alignPanel.getSeqPanel().keyboardNo2 = null;
2473 viewport.setSelectionGroup(null);
2474 viewport.getColumnSelection().clear();
2475 viewport.setSelectionGroup(null);
2476 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2477 // JAL-2034 - should delegate to
2478 // alignPanel to decide if overview needs
2480 alignPanel.paintAlignment(false, false);
2481 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2482 viewport.sendSelection();
2492 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2494 SequenceGroup sg = viewport.getSelectionGroup();
2498 selectAllSequenceMenuItem_actionPerformed(null);
2503 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2505 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2507 // JAL-2034 - should delegate to
2508 // alignPanel to decide if overview needs
2511 alignPanel.paintAlignment(true, false);
2512 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2513 viewport.sendSelection();
2517 public void invertColSel_actionPerformed(ActionEvent e)
2519 viewport.invertColumnSelection();
2520 alignPanel.paintAlignment(true, false);
2521 viewport.sendSelection();
2531 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2533 trimAlignment(true);
2543 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2545 trimAlignment(false);
2548 void trimAlignment(boolean trimLeft)
2550 ColumnSelection colSel = viewport.getColumnSelection();
2553 if (!colSel.isEmpty())
2557 column = colSel.getMin();
2561 column = colSel.getMax();
2565 if (viewport.getSelectionGroup() != null)
2567 seqs = viewport.getSelectionGroup()
2568 .getSequencesAsArray(viewport.getHiddenRepSequences());
2572 seqs = viewport.getAlignment().getSequencesArray();
2575 TrimRegionCommand trimRegion;
2578 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2579 column, viewport.getAlignment());
2580 viewport.getRanges().setStartRes(0);
2584 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2585 column, viewport.getAlignment());
2588 statusBar.setText(MessageManager
2589 .formatMessage("label.removed_columns", new String[]
2590 { Integer.valueOf(trimRegion.getSize()).toString() }));
2592 addHistoryItem(trimRegion);
2594 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2596 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2597 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2599 viewport.getAlignment().deleteGroup(sg);
2603 viewport.firePropertyChange("alignment", null,
2604 viewport.getAlignment().getSequences());
2615 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2617 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2620 if (viewport.getSelectionGroup() != null)
2622 seqs = viewport.getSelectionGroup()
2623 .getSequencesAsArray(viewport.getHiddenRepSequences());
2624 start = viewport.getSelectionGroup().getStartRes();
2625 end = viewport.getSelectionGroup().getEndRes();
2629 seqs = viewport.getAlignment().getSequencesArray();
2632 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2633 "Remove Gapped Columns", seqs, start, end,
2634 viewport.getAlignment());
2636 addHistoryItem(removeGapCols);
2638 statusBar.setText(MessageManager
2639 .formatMessage("label.removed_empty_columns", new Object[]
2640 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2642 // This is to maintain viewport position on first residue
2643 // of first sequence
2644 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2645 ViewportRanges ranges = viewport.getRanges();
2646 int startRes = seq.findPosition(ranges.getStartRes());
2647 // ShiftList shifts;
2648 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2649 // edit.alColumnChanges=shifts.getInverse();
2650 // if (viewport.hasHiddenColumns)
2651 // viewport.getColumnSelection().compensateForEdits(shifts);
2652 ranges.setStartRes(seq.findIndex(startRes) - 1);
2653 viewport.firePropertyChange("alignment", null,
2654 viewport.getAlignment().getSequences());
2665 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2667 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2670 if (viewport.getSelectionGroup() != null)
2672 seqs = viewport.getSelectionGroup()
2673 .getSequencesAsArray(viewport.getHiddenRepSequences());
2674 start = viewport.getSelectionGroup().getStartRes();
2675 end = viewport.getSelectionGroup().getEndRes();
2679 seqs = viewport.getAlignment().getSequencesArray();
2682 // This is to maintain viewport position on first residue
2683 // of first sequence
2684 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2685 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2687 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2688 viewport.getAlignment()));
2690 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2692 viewport.firePropertyChange("alignment", null,
2693 viewport.getAlignment().getSequences());
2704 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2706 viewport.setPadGaps(padGapsMenuitem.isSelected());
2707 viewport.firePropertyChange("alignment", null,
2708 viewport.getAlignment().getSequences());
2718 public void findMenuItem_actionPerformed(ActionEvent e)
2724 * Create a new view of the current alignment.
2727 public void newView_actionPerformed(ActionEvent e)
2729 newView(null, true);
2733 * Creates and shows a new view of the current alignment.
2736 * title of newly created view; if null, one will be generated
2737 * @param copyAnnotation
2738 * if true then duplicate all annnotation, groups and settings
2739 * @return new alignment panel, already displayed.
2741 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2744 * Create a new AlignmentPanel (with its own, new Viewport)
2746 AlignmentPanel newap = new jalview.project.Jalview2XML()
2747 .copyAlignPanel(alignPanel);
2748 if (!copyAnnotation)
2751 * remove all groups and annotation except for the automatic stuff
2753 newap.av.getAlignment().deleteAllGroups();
2754 newap.av.getAlignment().deleteAllAnnotations(false);
2757 newap.av.setGatherViewsHere(false);
2759 if (viewport.getViewName() == null)
2761 viewport.setViewName(MessageManager
2762 .getString("label.view_name_original"));
2766 * Views share the same edits undo and redo stacks
2768 newap.av.setHistoryList(viewport.getHistoryList());
2769 newap.av.setRedoList(viewport.getRedoList());
2772 * copy any visualisation settings that are not saved in the project
2774 newap.av.setColourAppliesToAllGroups(
2775 viewport.getColourAppliesToAllGroups());
2778 * Views share the same mappings; need to deregister any new mappings
2779 * created by copyAlignPanel, and register the new reference to the shared
2782 newap.av.replaceMappings(viewport.getAlignment());
2785 * start up cDNA consensus (if applicable) now mappings are in place
2787 if (newap.av.initComplementConsensus())
2789 newap.refresh(true); // adjust layout of annotations
2792 newap.av.setViewName(getNewViewName(viewTitle));
2794 addAlignmentPanel(newap, true);
2795 newap.alignmentChanged();
2797 if (alignPanels.size() == 2)
2799 viewport.setGatherViewsHere(true);
2801 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2806 * Make a new name for the view, ensuring it is unique within the current
2807 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2808 * these now use viewId. Unique view names are still desirable for usability.)
2813 protected String getNewViewName(String viewTitle)
2815 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2816 boolean addFirstIndex = false;
2817 if (viewTitle == null || viewTitle.trim().length() == 0)
2819 viewTitle = MessageManager.getString("action.view");
2820 addFirstIndex = true;
2824 index = 1;// we count from 1 if given a specific name
2826 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2828 List<Component> comps = PaintRefresher.components
2829 .get(viewport.getSequenceSetId());
2831 List<String> existingNames = getExistingViewNames(comps);
2833 while (existingNames.contains(newViewName))
2835 newViewName = viewTitle + " " + (++index);
2841 * Returns a list of distinct view names found in the given list of
2842 * components. View names are held on the viewport of an AlignmentPanel.
2847 protected List<String> getExistingViewNames(List<Component> comps)
2849 List<String> existingNames = new ArrayList<>();
2850 for (Component comp : comps)
2852 if (comp instanceof AlignmentPanel)
2854 AlignmentPanel ap = (AlignmentPanel) comp;
2855 if (!existingNames.contains(ap.av.getViewName()))
2857 existingNames.add(ap.av.getViewName());
2861 return existingNames;
2865 * Explode tabbed views into separate windows.
2868 public void expandViews_actionPerformed(ActionEvent e)
2870 Desktop.explodeViews(this);
2874 * Gather views in separate windows back into a tabbed presentation.
2877 public void gatherViews_actionPerformed(ActionEvent e)
2879 Desktop.instance.gatherViews(this);
2889 public void font_actionPerformed(ActionEvent e)
2891 new FontChooser(alignPanel);
2901 protected void seqLimit_actionPerformed(ActionEvent e)
2903 viewport.setShowJVSuffix(seqLimits.isSelected());
2905 alignPanel.getIdPanel().getIdCanvas()
2906 .setPreferredSize(alignPanel.calculateIdWidth());
2907 alignPanel.paintAlignment(true, false);
2911 public void idRightAlign_actionPerformed(ActionEvent e)
2913 viewport.setRightAlignIds(idRightAlign.isSelected());
2914 alignPanel.paintAlignment(false, false);
2918 public void centreColumnLabels_actionPerformed(ActionEvent e)
2920 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2921 alignPanel.paintAlignment(false, false);
2927 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2930 protected void followHighlight_actionPerformed()
2933 * Set the 'follow' flag on the Viewport (and scroll to position if now
2936 final boolean state = this.followHighlightMenuItem.getState();
2937 viewport.setFollowHighlight(state);
2940 alignPanel.scrollToPosition(viewport.getSearchResults());
2951 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2953 viewport.setColourText(colourTextMenuItem.isSelected());
2954 alignPanel.paintAlignment(false, false);
2964 public void wrapMenuItem_actionPerformed(ActionEvent e)
2966 scaleAbove.setVisible(wrapMenuItem.isSelected());
2967 scaleLeft.setVisible(wrapMenuItem.isSelected());
2968 scaleRight.setVisible(wrapMenuItem.isSelected());
2969 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2970 alignPanel.updateLayout();
2974 public void showAllSeqs_actionPerformed(ActionEvent e)
2976 viewport.showAllHiddenSeqs();
2980 public void showAllColumns_actionPerformed(ActionEvent e)
2982 viewport.showAllHiddenColumns();
2983 alignPanel.paintAlignment(true, true);
2984 viewport.sendSelection();
2988 public void hideSelSequences_actionPerformed(ActionEvent e)
2990 viewport.hideAllSelectedSeqs();
2994 * called by key handler and the hide all/show all menu items
2999 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3002 boolean hide = false;
3003 SequenceGroup sg = viewport.getSelectionGroup();
3004 if (!toggleSeqs && !toggleCols)
3006 // Hide everything by the current selection - this is a hack - we do the
3007 // invert and then hide
3008 // first check that there will be visible columns after the invert.
3009 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3010 && sg.getStartRes() <= sg.getEndRes()))
3012 // now invert the sequence set, if required - empty selection implies
3013 // that no hiding is required.
3016 invertSequenceMenuItem_actionPerformed(null);
3017 sg = viewport.getSelectionGroup();
3021 viewport.expandColSelection(sg, true);
3022 // finally invert the column selection and get the new sequence
3024 invertColSel_actionPerformed(null);
3031 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3033 hideSelSequences_actionPerformed(null);
3036 else if (!(toggleCols && viewport.hasSelectedColumns()))
3038 showAllSeqs_actionPerformed(null);
3044 if (viewport.hasSelectedColumns())
3046 hideSelColumns_actionPerformed(null);
3049 viewport.setSelectionGroup(sg);
3054 showAllColumns_actionPerformed(null);
3063 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3064 * event.ActionEvent)
3067 public void hideAllButSelection_actionPerformed(ActionEvent e)
3069 toggleHiddenRegions(false, false);
3070 viewport.sendSelection();
3077 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3081 public void hideAllSelection_actionPerformed(ActionEvent e)
3083 SequenceGroup sg = viewport.getSelectionGroup();
3084 viewport.expandColSelection(sg, false);
3085 viewport.hideAllSelectedSeqs();
3086 viewport.hideSelectedColumns();
3087 alignPanel.updateLayout();
3088 alignPanel.paintAlignment(true, true);
3089 viewport.sendSelection();
3096 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3100 public void showAllhidden_actionPerformed(ActionEvent e)
3102 viewport.showAllHiddenColumns();
3103 viewport.showAllHiddenSeqs();
3104 alignPanel.paintAlignment(true, true);
3105 viewport.sendSelection();
3109 public void hideSelColumns_actionPerformed(ActionEvent e)
3111 viewport.hideSelectedColumns();
3112 alignPanel.updateLayout();
3113 alignPanel.paintAlignment(true, true);
3114 viewport.sendSelection();
3118 public void hiddenMarkers_actionPerformed(ActionEvent e)
3120 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3131 protected void scaleAbove_actionPerformed(ActionEvent e)
3133 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3134 alignPanel.updateLayout();
3135 alignPanel.paintAlignment(true, false);
3145 protected void scaleLeft_actionPerformed(ActionEvent e)
3147 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3148 alignPanel.updateLayout();
3149 alignPanel.paintAlignment(true, false);
3159 protected void scaleRight_actionPerformed(ActionEvent e)
3161 viewport.setScaleRightWrapped(scaleRight.isSelected());
3162 alignPanel.updateLayout();
3163 alignPanel.paintAlignment(true, false);
3173 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3175 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3176 alignPanel.paintAlignment(false, false);
3186 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3188 viewport.setShowText(viewTextMenuItem.isSelected());
3189 alignPanel.paintAlignment(false, false);
3199 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3201 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3202 alignPanel.paintAlignment(false, false);
3205 public FeatureSettings featureSettings;
3208 public FeatureSettingsControllerI getFeatureSettingsUI()
3210 return featureSettings;
3214 public void featureSettings_actionPerformed(ActionEvent e)
3216 if (featureSettings != null)
3218 featureSettings.close();
3219 featureSettings = null;
3221 if (!showSeqFeatures.isSelected())
3223 // make sure features are actually displayed
3224 showSeqFeatures.setSelected(true);
3225 showSeqFeatures_actionPerformed(null);
3227 featureSettings = new FeatureSettings(this);
3231 * Set or clear 'Show Sequence Features'
3237 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3239 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3240 alignPanel.paintAlignment(true, true);
3244 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3245 * the annotations panel as a whole.
3247 * The options to show/hide all annotations should be enabled when the panel
3248 * is shown, and disabled when the panel is hidden.
3253 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3255 final boolean setVisible = annotationPanelMenuItem.isSelected();
3256 viewport.setShowAnnotation(setVisible);
3257 this.showAllSeqAnnotations.setEnabled(setVisible);
3258 this.hideAllSeqAnnotations.setEnabled(setVisible);
3259 this.showAllAlAnnotations.setEnabled(setVisible);
3260 this.hideAllAlAnnotations.setEnabled(setVisible);
3261 alignPanel.updateLayout();
3265 public void alignmentProperties()
3267 JEditorPane editPane = new JEditorPane("text/html", "");
3268 editPane.setEditable(false);
3269 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3272 MessageManager.formatMessage("label.html_content", new Object[]
3273 { contents.toString() }));
3274 JInternalFrame frame = new JInternalFrame();
3275 frame.getContentPane().add(new JScrollPane(editPane));
3277 Desktop.addInternalFrame(frame, MessageManager
3278 .formatMessage("label.alignment_properties", new Object[]
3279 { getTitle() }), 500, 400);
3289 public void overviewMenuItem_actionPerformed(ActionEvent e)
3291 if (alignPanel.overviewPanel != null)
3296 JInternalFrame frame = new JInternalFrame();
3297 final OverviewPanel overview = new OverviewPanel(alignPanel);
3298 frame.setContentPane(overview);
3299 Desktop.addInternalFrame(frame, MessageManager
3300 .formatMessage("label.overview_params", new Object[]
3301 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3304 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3305 frame.addInternalFrameListener(
3306 new javax.swing.event.InternalFrameAdapter()
3309 public void internalFrameClosed(
3310 javax.swing.event.InternalFrameEvent evt)
3313 alignPanel.setOverviewPanel(null);
3316 if (getKeyListeners().length > 0)
3318 frame.addKeyListener(getKeyListeners()[0]);
3321 alignPanel.setOverviewPanel(overview);
3325 public void textColour_actionPerformed()
3327 new TextColourChooser().chooseColour(alignPanel, null);
3331 * public void covariationColour_actionPerformed() {
3333 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3337 public void annotationColour_actionPerformed()
3339 new AnnotationColourChooser(viewport, alignPanel);
3343 public void annotationColumn_actionPerformed(ActionEvent e)
3345 new AnnotationColumnChooser(viewport, alignPanel);
3349 * Action on the user checking or unchecking the option to apply the selected
3350 * colour scheme to all groups. If unchecked, groups may have their own
3351 * independent colour schemes.
3356 public void applyToAllGroups_actionPerformed(boolean selected)
3358 viewport.setColourAppliesToAllGroups(selected);
3362 * Action on user selecting a colour from the colour menu
3365 * the name (not the menu item label!) of the colour scheme
3368 public void changeColour_actionPerformed(String name)
3371 * 'User Defined' opens a panel to configure or load a
3372 * user-defined colour scheme
3374 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3376 new UserDefinedColours(alignPanel);
3381 * otherwise set the chosen colour scheme (or null for 'None')
3383 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3385 viewport.getAlignment(), viewport.getHiddenRepSequences());
3390 * Actions on setting or changing the alignment colour scheme
3395 public void changeColour(ColourSchemeI cs)
3397 // TODO: pull up to controller method
3398 ColourMenuHelper.setColourSelected(colourMenu, cs);
3400 viewport.setGlobalColourScheme(cs);
3402 alignPanel.paintAlignment(true, true);
3406 * Show the PID threshold slider panel
3409 protected void modifyPID_actionPerformed()
3411 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3412 alignPanel.getViewName());
3413 SliderPanel.showPIDSlider();
3417 * Show the Conservation slider panel
3420 protected void modifyConservation_actionPerformed()
3422 SliderPanel.setConservationSlider(alignPanel,
3423 viewport.getResidueShading(), alignPanel.getViewName());
3424 SliderPanel.showConservationSlider();
3428 * Action on selecting or deselecting (Colour) By Conservation
3431 public void conservationMenuItem_actionPerformed(boolean selected)
3433 modifyConservation.setEnabled(selected);
3434 viewport.setConservationSelected(selected);
3435 viewport.getResidueShading().setConservationApplied(selected);
3437 changeColour(viewport.getGlobalColourScheme());
3440 modifyConservation_actionPerformed();
3444 SliderPanel.hideConservationSlider();
3449 * Action on selecting or deselecting (Colour) Above PID Threshold
3452 public void abovePIDThreshold_actionPerformed(boolean selected)
3454 modifyPID.setEnabled(selected);
3455 viewport.setAbovePIDThreshold(selected);
3458 viewport.getResidueShading().setThreshold(0,
3459 viewport.isIgnoreGapsConsensus());
3462 changeColour(viewport.getGlobalColourScheme());
3465 modifyPID_actionPerformed();
3469 SliderPanel.hidePIDSlider();
3480 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3482 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3483 AlignmentSorter.sortByPID(viewport.getAlignment(),
3484 viewport.getAlignment().getSequenceAt(0));
3485 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3486 viewport.getAlignment()));
3487 alignPanel.paintAlignment(true, false);
3497 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3499 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3500 AlignmentSorter.sortByID(viewport.getAlignment());
3502 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3503 alignPanel.paintAlignment(true, false);
3513 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3515 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3516 AlignmentSorter.sortByLength(viewport.getAlignment());
3517 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3518 viewport.getAlignment()));
3519 alignPanel.paintAlignment(true, false);
3529 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3531 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3532 AlignmentSorter.sortByGroup(viewport.getAlignment());
3533 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3534 viewport.getAlignment()));
3536 alignPanel.paintAlignment(true, false);
3546 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3548 new RedundancyPanel(alignPanel, this);
3558 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3560 if ((viewport.getSelectionGroup() == null)
3561 || (viewport.getSelectionGroup().getSize() < 2))
3563 JvOptionPane.showInternalMessageDialog(this,
3564 MessageManager.getString(
3565 "label.you_must_select_least_two_sequences"),
3566 MessageManager.getString("label.invalid_selection"),
3567 JvOptionPane.WARNING_MESSAGE);
3571 JInternalFrame frame = new JInternalFrame();
3572 frame.setContentPane(new PairwiseAlignPanel(viewport));
3573 Desktop.addInternalFrame(frame,
3574 MessageManager.getString("action.pairwise_alignment"), 600,
3580 public void autoCalculate_actionPerformed(ActionEvent e)
3582 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3583 if (viewport.autoCalculateConsensus)
3585 viewport.firePropertyChange("alignment", null,
3586 viewport.getAlignment().getSequences());
3591 public void sortByTreeOption_actionPerformed(ActionEvent e)
3593 viewport.sortByTree = sortByTree.isSelected();
3597 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3599 viewport.followSelection = listenToViewSelections.isSelected();
3603 * Constructs a tree panel and adds it to the desktop
3606 * tree type (NJ or AV)
3608 * name of score model used to compute the tree
3610 * parameters for the distance or similarity calculation
3612 void newTreePanel(String type, String modelName,
3613 SimilarityParamsI options)
3615 String frameTitle = "";
3618 boolean onSelection = false;
3619 if (viewport.getSelectionGroup() != null
3620 && viewport.getSelectionGroup().getSize() > 0)
3622 SequenceGroup sg = viewport.getSelectionGroup();
3624 /* Decide if the selection is a column region */
3625 for (SequenceI _s : sg.getSequences())
3627 if (_s.getLength() < sg.getEndRes())
3629 JvOptionPane.showMessageDialog(Desktop.desktop,
3630 MessageManager.getString(
3631 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3632 MessageManager.getString(
3633 "label.sequences_selection_not_aligned"),
3634 JvOptionPane.WARNING_MESSAGE);
3643 if (viewport.getAlignment().getHeight() < 2)
3649 tp = new TreePanel(alignPanel, type, modelName, options);
3650 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3652 frameTitle += " from ";
3654 if (viewport.getViewName() != null)
3656 frameTitle += viewport.getViewName() + " of ";
3659 frameTitle += this.title;
3661 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3672 public void addSortByOrderMenuItem(String title,
3673 final AlignmentOrder order)
3675 final JMenuItem item = new JMenuItem(MessageManager
3676 .formatMessage("action.by_title_param", new Object[]
3679 item.addActionListener(new java.awt.event.ActionListener()
3682 public void actionPerformed(ActionEvent e)
3684 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3686 // TODO: JBPNote - have to map order entries to curent SequenceI
3688 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3690 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3691 viewport.getAlignment()));
3693 alignPanel.paintAlignment(true, false);
3699 * Add a new sort by annotation score menu item
3702 * the menu to add the option to
3704 * the label used to retrieve scores for each sequence on the
3707 public void addSortByAnnotScoreMenuItem(JMenu sort,
3708 final String scoreLabel)
3710 final JMenuItem item = new JMenuItem(scoreLabel);
3712 item.addActionListener(new java.awt.event.ActionListener()
3715 public void actionPerformed(ActionEvent e)
3717 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3718 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3719 viewport.getAlignment());// ,viewport.getSelectionGroup());
3720 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3721 viewport.getAlignment()));
3722 alignPanel.paintAlignment(true, false);
3728 * last hash for alignment's annotation array - used to minimise cost of
3731 protected int _annotationScoreVectorHash;
3734 * search the alignment and rebuild the sort by annotation score submenu the
3735 * last alignment annotation vector hash is stored to minimize cost of
3736 * rebuilding in subsequence calls.
3740 public void buildSortByAnnotationScoresMenu()
3742 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3747 if (viewport.getAlignment().getAlignmentAnnotation()
3748 .hashCode() != _annotationScoreVectorHash)
3750 sortByAnnotScore.removeAll();
3751 // almost certainly a quicker way to do this - but we keep it simple
3752 Hashtable scoreSorts = new Hashtable();
3753 AlignmentAnnotation aann[];
3754 for (SequenceI sqa : viewport.getAlignment().getSequences())
3756 aann = sqa.getAnnotation();
3757 for (int i = 0; aann != null && i < aann.length; i++)
3759 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3761 scoreSorts.put(aann[i].label, aann[i].label);
3765 Enumeration labels = scoreSorts.keys();
3766 while (labels.hasMoreElements())
3768 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3769 (String) labels.nextElement());
3771 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3774 _annotationScoreVectorHash = viewport.getAlignment()
3775 .getAlignmentAnnotation().hashCode();
3780 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3781 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3782 * call. Listeners are added to remove the menu item when the treePanel is
3783 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3787 public void buildTreeSortMenu()
3789 sortByTreeMenu.removeAll();
3791 List<Component> comps = PaintRefresher.components
3792 .get(viewport.getSequenceSetId());
3793 List<TreePanel> treePanels = new ArrayList<>();
3794 for (Component comp : comps)
3796 if (comp instanceof TreePanel)
3798 treePanels.add((TreePanel) comp);
3802 if (treePanels.size() < 1)
3804 sortByTreeMenu.setVisible(false);
3808 sortByTreeMenu.setVisible(true);
3810 for (final TreePanel tp : treePanels)
3812 final JMenuItem item = new JMenuItem(tp.getTitle());
3813 item.addActionListener(new java.awt.event.ActionListener()
3816 public void actionPerformed(ActionEvent e)
3818 tp.sortByTree_actionPerformed();
3819 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3824 sortByTreeMenu.add(item);
3828 public boolean sortBy(AlignmentOrder alorder, String undoname)
3830 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3831 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3832 if (undoname != null)
3834 addHistoryItem(new OrderCommand(undoname, oldOrder,
3835 viewport.getAlignment()));
3837 alignPanel.paintAlignment(true, false);
3842 * Work out whether the whole set of sequences or just the selected set will
3843 * be submitted for multiple alignment.
3846 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3848 // Now, check we have enough sequences
3849 AlignmentView msa = null;
3851 if ((viewport.getSelectionGroup() != null)
3852 && (viewport.getSelectionGroup().getSize() > 1))
3854 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3855 // some common interface!
3857 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3858 * SequenceI[sz = seqs.getSize(false)];
3860 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3861 * seqs.getSequenceAt(i); }
3863 msa = viewport.getAlignmentView(true);
3865 else if (viewport.getSelectionGroup() != null
3866 && viewport.getSelectionGroup().getSize() == 1)
3868 int option = JvOptionPane.showConfirmDialog(this,
3869 MessageManager.getString("warn.oneseq_msainput_selection"),
3870 MessageManager.getString("label.invalid_selection"),
3871 JvOptionPane.OK_CANCEL_OPTION);
3872 if (option == JvOptionPane.OK_OPTION)
3874 msa = viewport.getAlignmentView(false);
3879 msa = viewport.getAlignmentView(false);
3885 * Decides what is submitted to a secondary structure prediction service: the
3886 * first sequence in the alignment, or in the current selection, or, if the
3887 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3888 * region or the whole alignment. (where the first sequence in the set is the
3889 * one that the prediction will be for).
3891 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3893 AlignmentView seqs = null;
3895 if ((viewport.getSelectionGroup() != null)
3896 && (viewport.getSelectionGroup().getSize() > 0))
3898 seqs = viewport.getAlignmentView(true);
3902 seqs = viewport.getAlignmentView(false);
3904 // limit sequences - JBPNote in future - could spawn multiple prediction
3906 // TODO: viewport.getAlignment().isAligned is a global state - the local
3907 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3908 if (!viewport.getAlignment().isAligned(false))
3910 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3911 // TODO: if seqs.getSequences().length>1 then should really have warned
3925 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3927 // Pick the tree file
3928 JalviewFileChooser chooser = new JalviewFileChooser(
3929 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3930 chooser.setFileView(new JalviewFileView());
3931 chooser.setDialogTitle(
3932 MessageManager.getString("label.select_newick_like_tree_file"));
3933 chooser.setToolTipText(
3934 MessageManager.getString("label.load_tree_file"));
3936 int value = chooser.showOpenDialog(null);
3938 if (value == JalviewFileChooser.APPROVE_OPTION)
3940 String filePath = chooser.getSelectedFile().getPath();
3941 Cache.setProperty("LAST_DIRECTORY", filePath);
3942 NewickFile fin = null;
3945 fin = new NewickFile(filePath, DataSourceType.FILE);
3946 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3947 } catch (Exception ex)
3949 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3950 MessageManager.getString("label.problem_reading_tree_file"),
3951 JvOptionPane.WARNING_MESSAGE);
3952 ex.printStackTrace();
3954 if (fin != null && fin.hasWarningMessage())
3956 JvOptionPane.showMessageDialog(Desktop.desktop,
3957 fin.getWarningMessage(),
3959 .getString("label.possible_problem_with_tree_file"),
3960 JvOptionPane.WARNING_MESSAGE);
3965 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3967 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3970 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3971 int h, int x, int y)
3973 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3977 * Add a treeviewer for the tree extracted from a Newick file object to the
3978 * current alignment view
3985 * Associated alignment input data (or null)
3994 * @return TreePanel handle
3996 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3997 AlignmentView input, int w, int h, int x, int y)
3999 TreePanel tp = null;
4005 if (nf.getTree() != null)
4007 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4013 tp.setLocation(x, y);
4016 Desktop.addInternalFrame(tp, treeTitle, w, h);
4018 } catch (Exception ex)
4020 ex.printStackTrace();
4026 private boolean buildingMenu = false;
4029 * Generates menu items and listener event actions for web service clients
4032 public void BuildWebServiceMenu()
4034 while (buildingMenu)
4038 System.err.println("Waiting for building menu to finish.");
4040 } catch (Exception e)
4044 final AlignFrame me = this;
4045 buildingMenu = true;
4046 new Thread(new Runnable()
4051 final List<JMenuItem> legacyItems = new ArrayList<>();
4054 // System.err.println("Building ws menu again "
4055 // + Thread.currentThread());
4056 // TODO: add support for context dependent disabling of services based
4058 // alignment and current selection
4059 // TODO: add additional serviceHandle parameter to specify abstract
4061 // class independently of AbstractName
4062 // TODO: add in rediscovery GUI function to restart discoverer
4063 // TODO: group services by location as well as function and/or
4065 // object broker mechanism.
4066 final Vector<JMenu> wsmenu = new Vector<>();
4067 final IProgressIndicator af = me;
4070 * do not i18n these strings - they are hard-coded in class
4071 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4072 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4074 final JMenu msawsmenu = new JMenu("Alignment");
4075 final JMenu secstrmenu = new JMenu(
4076 "Secondary Structure Prediction");
4077 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4078 final JMenu analymenu = new JMenu("Analysis");
4079 final JMenu dismenu = new JMenu("Protein Disorder");
4080 // JAL-940 - only show secondary structure prediction services from
4081 // the legacy server
4082 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4084 Discoverer.services != null && (Discoverer.services.size() > 0))
4086 // TODO: refactor to allow list of AbstractName/Handler bindings to
4088 // stored or retrieved from elsewhere
4089 // No MSAWS used any more:
4090 // Vector msaws = null; // (Vector)
4091 // Discoverer.services.get("MsaWS");
4092 Vector secstrpr = (Vector) Discoverer.services
4094 if (secstrpr != null)
4096 // Add any secondary structure prediction services
4097 for (int i = 0, j = secstrpr.size(); i < j; i++)
4099 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4101 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4102 .getServiceClient(sh);
4103 int p = secstrmenu.getItemCount();
4104 impl.attachWSMenuEntry(secstrmenu, me);
4105 int q = secstrmenu.getItemCount();
4106 for (int litm = p; litm < q; litm++)
4108 legacyItems.add(secstrmenu.getItem(litm));
4114 // Add all submenus in the order they should appear on the web
4116 wsmenu.add(msawsmenu);
4117 wsmenu.add(secstrmenu);
4118 wsmenu.add(dismenu);
4119 wsmenu.add(analymenu);
4120 // No search services yet
4121 // wsmenu.add(seqsrchmenu);
4123 javax.swing.SwingUtilities.invokeLater(new Runnable()
4130 webService.removeAll();
4131 // first, add discovered services onto the webservices menu
4132 if (wsmenu.size() > 0)
4134 for (int i = 0, j = wsmenu.size(); i < j; i++)
4136 webService.add(wsmenu.get(i));
4141 webService.add(me.webServiceNoServices);
4143 // TODO: move into separate menu builder class.
4144 boolean new_sspred = false;
4145 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4147 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4148 if (jws2servs != null)
4150 if (jws2servs.hasServices())
4152 jws2servs.attachWSMenuEntry(webService, me);
4153 for (Jws2Instance sv : jws2servs.getServices())
4155 if (sv.description.toLowerCase().contains("jpred"))
4157 for (JMenuItem jmi : legacyItems)
4159 jmi.setVisible(false);
4165 if (jws2servs.isRunning())
4167 JMenuItem tm = new JMenuItem(
4168 "Still discovering JABA Services");
4169 tm.setEnabled(false);
4174 build_urlServiceMenu(me.webService);
4175 build_fetchdbmenu(webService);
4176 for (JMenu item : wsmenu)
4178 if (item.getItemCount() == 0)
4180 item.setEnabled(false);
4184 item.setEnabled(true);
4187 } catch (Exception e)
4190 "Exception during web service menu building process.",
4195 } catch (Exception e)
4198 buildingMenu = false;
4205 * construct any groupURL type service menu entries.
4209 private void build_urlServiceMenu(JMenu webService)
4211 // TODO: remove this code when 2.7 is released
4212 // DEBUG - alignmentView
4214 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4215 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4217 * @Override public void actionPerformed(ActionEvent e) {
4218 * jalview.datamodel.AlignmentView
4219 * .testSelectionViews(af.viewport.getAlignment(),
4220 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4222 * }); webService.add(testAlView);
4224 // TODO: refactor to RestClient discoverer and merge menu entries for
4225 // rest-style services with other types of analysis/calculation service
4226 // SHmmr test client - still being implemented.
4227 // DEBUG - alignmentView
4229 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4232 client.attachWSMenuEntry(
4233 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4239 * Searches the alignment sequences for xRefs and builds the Show
4240 * Cross-References menu (formerly called Show Products), with database
4241 * sources for which cross-references are found (protein sources for a
4242 * nucleotide alignment and vice versa)
4244 * @return true if Show Cross-references menu should be enabled
4246 public boolean canShowProducts()
4248 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4249 AlignmentI dataset = viewport.getAlignment().getDataset();
4251 showProducts.removeAll();
4252 final boolean dna = viewport.getAlignment().isNucleotide();
4254 if (seqs == null || seqs.length == 0)
4256 // nothing to see here.
4260 boolean showp = false;
4263 List<String> ptypes = new CrossRef(seqs, dataset)
4264 .findXrefSourcesForSequences(dna);
4266 for (final String source : ptypes)
4269 final AlignFrame af = this;
4270 JMenuItem xtype = new JMenuItem(source);
4271 xtype.addActionListener(new ActionListener()
4274 public void actionPerformed(ActionEvent e)
4276 showProductsFor(af.viewport.getSequenceSelection(), dna,
4280 showProducts.add(xtype);
4282 showProducts.setVisible(showp);
4283 showProducts.setEnabled(showp);
4284 } catch (Exception e)
4287 "canShowProducts threw an exception - please report to help@jalview.org",
4295 * Finds and displays cross-references for the selected sequences (protein
4296 * products for nucleotide sequences, dna coding sequences for peptides).
4299 * the sequences to show cross-references for
4301 * true if from a nucleotide alignment (so showing proteins)
4303 * the database to show cross-references for
4305 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4306 final String source)
4308 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4313 * Construct and display a new frame containing the translation of this
4314 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4317 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4319 AlignmentI al = null;
4322 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4324 al = dna.translateCdna(codeTable);
4325 } catch (Exception ex)
4327 jalview.bin.Cache.log.error(
4328 "Exception during translation. Please report this !", ex);
4329 final String msg = MessageManager.getString(
4330 "label.error_when_translating_sequences_submit_bug_report");
4331 final String errorTitle = MessageManager
4332 .getString("label.implementation_error")
4333 + MessageManager.getString("label.translation_failed");
4334 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4335 JvOptionPane.ERROR_MESSAGE);
4338 if (al == null || al.getHeight() == 0)
4340 final String msg = MessageManager.getString(
4341 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4342 final String errorTitle = MessageManager
4343 .getString("label.translation_failed");
4344 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4345 JvOptionPane.WARNING_MESSAGE);
4349 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4350 af.setFileFormat(this.currentFileFormat);
4351 final String newTitle = MessageManager
4352 .formatMessage("label.translation_of_params", new Object[]
4353 { this.getTitle(), codeTable.getId() });
4354 af.setTitle(newTitle);
4355 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4357 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4358 viewport.openSplitFrame(af, new Alignment(seqs));
4362 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4369 * Set the file format
4373 public void setFileFormat(FileFormatI format)
4375 this.currentFileFormat = format;
4379 * Try to load a features file onto the alignment.
4382 * contents or path to retrieve file
4384 * access mode of file (see jalview.io.AlignFile)
4385 * @return true if features file was parsed correctly.
4387 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4389 return avc.parseFeaturesFile(file, sourceType,
4390 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4395 public void refreshFeatureUI(boolean enableIfNecessary)
4397 // note - currently this is only still here rather than in the controller
4398 // because of the featureSettings hard reference that is yet to be
4400 if (enableIfNecessary)
4402 viewport.setShowSequenceFeatures(true);
4403 showSeqFeatures.setSelected(true);
4409 public void dragEnter(DropTargetDragEvent evt)
4414 public void dragExit(DropTargetEvent evt)
4419 public void dragOver(DropTargetDragEvent evt)
4424 public void dropActionChanged(DropTargetDragEvent evt)
4429 public void drop(DropTargetDropEvent evt)
4431 // JAL-1552 - acceptDrop required before getTransferable call for
4432 // Java's Transferable for native dnd
4433 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4434 Transferable t = evt.getTransferable();
4435 final AlignFrame thisaf = this;
4436 final List<String> files = new ArrayList<>();
4437 List<DataSourceType> protocols = new ArrayList<>();
4441 Desktop.transferFromDropTarget(files, protocols, evt, t);
4442 } catch (Exception e)
4444 e.printStackTrace();
4448 new Thread(new Runnable()
4455 // check to see if any of these files have names matching sequences
4458 SequenceIdMatcher idm = new SequenceIdMatcher(
4459 viewport.getAlignment().getSequencesArray());
4461 * Object[] { String,SequenceI}
4463 ArrayList<Object[]> filesmatched = new ArrayList<>();
4464 ArrayList<String> filesnotmatched = new ArrayList<>();
4465 for (int i = 0; i < files.size(); i++)
4467 String file = files.get(i).toString();
4469 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4470 if (protocol == DataSourceType.FILE)
4472 File fl = new File(file);
4473 pdbfn = fl.getName();
4475 else if (protocol == DataSourceType.URL)
4477 URL url = new URL(file);
4478 pdbfn = url.getFile();
4480 if (pdbfn.length() > 0)
4482 // attempt to find a match in the alignment
4483 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4484 int l = 0, c = pdbfn.indexOf(".");
4485 while (mtch == null && c != -1)
4490 } while ((c = pdbfn.indexOf(".", l)) > l);
4493 pdbfn = pdbfn.substring(0, l);
4495 mtch = idm.findAllIdMatches(pdbfn);
4499 FileFormatI type = null;
4502 type = new IdentifyFile().identify(file, protocol);
4503 } catch (Exception ex)
4507 if (type != null && type.isStructureFile())
4509 filesmatched.add(new Object[] { file, protocol, mtch });
4513 // File wasn't named like one of the sequences or wasn't a PDB
4515 filesnotmatched.add(file);
4519 if (filesmatched.size() > 0)
4521 boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4524 String msg = MessageManager.formatMessage(
4525 "label.automatically_associate_structure_files_with_sequences_same_name",
4527 { Integer.valueOf(filesmatched.size())
4529 String ttl = MessageManager.getString(
4530 "label.automatically_associate_structure_files_by_name");
4531 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4532 ttl, JvOptionPane.YES_NO_OPTION);
4533 autoAssociate = choice == JvOptionPane.YES_OPTION;
4537 for (Object[] fm : filesmatched)
4539 // try and associate
4540 // TODO: may want to set a standard ID naming formalism for
4541 // associating PDB files which have no IDs.
4542 for (SequenceI toassoc : (SequenceI[]) fm[2])
4544 PDBEntry pe = new AssociatePdbFileWithSeq()
4545 .associatePdbWithSeq((String) fm[0],
4546 (DataSourceType) fm[1], toassoc, false,
4550 System.err.println("Associated file : "
4551 + ((String) fm[0]) + " with "
4552 + toassoc.getDisplayId(true));
4556 // TODO: do we need to update overview ? only if features are
4558 alignPanel.paintAlignment(true, false);
4564 * add declined structures as sequences
4566 for (Object[] o : filesmatched)
4568 filesnotmatched.add((String) o[0]);
4572 if (filesnotmatched.size() > 0)
4574 if (assocfiles > 0 && (Cache.getDefault(
4575 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4576 || JvOptionPane.showConfirmDialog(thisaf,
4577 "<html>" + MessageManager.formatMessage(
4578 "label.ignore_unmatched_dropped_files_info",
4581 filesnotmatched.size())
4584 MessageManager.getString(
4585 "label.ignore_unmatched_dropped_files"),
4586 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4590 for (String fn : filesnotmatched)
4592 loadJalviewDataFile(fn, null, null, null);
4596 } catch (Exception ex)
4598 ex.printStackTrace();
4606 * Attempt to load a "dropped" file or URL string, by testing in turn for
4608 * <li>an Annotation file</li>
4609 * <li>a JNet file</li>
4610 * <li>a features file</li>
4611 * <li>else try to interpret as an alignment file</li>
4615 * either a filename or a URL string.
4617 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4618 FileFormatI format, SequenceI assocSeq)
4622 if (sourceType == null)
4624 sourceType = FormatAdapter.checkProtocol(file);
4626 // if the file isn't identified, or not positively identified as some
4627 // other filetype (PFAM is default unidentified alignment file type) then
4628 // try to parse as annotation.
4629 boolean isAnnotation = (format == null
4630 || FileFormat.Pfam.equals(format))
4631 ? new AnnotationFile().annotateAlignmentView(viewport,
4637 // first see if its a T-COFFEE score file
4638 TCoffeeScoreFile tcf = null;
4641 tcf = new TCoffeeScoreFile(file, sourceType);
4644 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4648 new TCoffeeColourScheme(viewport.getAlignment()));
4649 isAnnotation = true;
4650 statusBar.setText(MessageManager.getString(
4651 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4655 // some problem - if no warning its probable that the ID matching
4656 // process didn't work
4657 JvOptionPane.showMessageDialog(Desktop.desktop,
4658 tcf.getWarningMessage() == null
4659 ? MessageManager.getString(
4660 "label.check_file_matches_sequence_ids_alignment")
4661 : tcf.getWarningMessage(),
4662 MessageManager.getString(
4663 "label.problem_reading_tcoffee_score_file"),
4664 JvOptionPane.WARNING_MESSAGE);
4671 } catch (Exception x)
4674 "Exception when processing data source as T-COFFEE score file",
4680 // try to see if its a JNet 'concise' style annotation file *before*
4682 // try to parse it as a features file
4685 format = new IdentifyFile().identify(file, sourceType);
4687 if (FileFormat.ScoreMatrix == format)
4689 ScoreMatrixFile sm = new ScoreMatrixFile(
4690 new FileParse(file, sourceType));
4692 // todo: i18n this message
4693 statusBar.setText(MessageManager.formatMessage(
4694 "label.successfully_loaded_matrix",
4695 sm.getMatrixName()));
4697 else if (FileFormat.Jnet.equals(format))
4699 JPredFile predictions = new JPredFile(file, sourceType);
4700 new JnetAnnotationMaker();
4701 JnetAnnotationMaker.add_annotation(predictions,
4702 viewport.getAlignment(), 0, false);
4703 viewport.getAlignment().setupJPredAlignment();
4704 isAnnotation = true;
4706 // else if (IdentifyFile.FeaturesFile.equals(format))
4707 else if (FileFormat.Features.equals(format))
4709 if (parseFeaturesFile(file, sourceType))
4711 alignPanel.paintAlignment(true, true);
4716 new FileLoader().LoadFile(viewport, file, sourceType, format);
4723 alignPanel.adjustAnnotationHeight();
4724 viewport.updateSequenceIdColours();
4725 buildSortByAnnotationScoresMenu();
4726 alignPanel.paintAlignment(true, true);
4728 } catch (Exception ex)
4730 ex.printStackTrace();
4731 } catch (OutOfMemoryError oom)
4736 } catch (Exception x)
4741 + (sourceType != null
4742 ? (sourceType == DataSourceType.PASTE
4744 : "using " + sourceType + " from "
4748 ? "(parsing as '" + format + "' file)"
4750 oom, Desktop.desktop);
4755 * Method invoked by the ChangeListener on the tabbed pane, in other words
4756 * when a different tabbed pane is selected by the user or programmatically.
4759 public void tabSelectionChanged(int index)
4763 alignPanel = alignPanels.get(index);
4764 viewport = alignPanel.av;
4765 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4766 setMenusFromViewport(viewport);
4770 * 'focus' any colour slider that is open to the selected viewport
4772 if (viewport.getConservationSelected())
4774 SliderPanel.setConservationSlider(alignPanel,
4775 viewport.getResidueShading(), alignPanel.getViewName());
4779 SliderPanel.hideConservationSlider();
4781 if (viewport.getAbovePIDThreshold())
4783 SliderPanel.setPIDSliderSource(alignPanel,
4784 viewport.getResidueShading(), alignPanel.getViewName());
4788 SliderPanel.hidePIDSlider();
4792 * If there is a frame linked to this one in a SplitPane, switch it to the
4793 * same view tab index. No infinite recursion of calls should happen, since
4794 * tabSelectionChanged() should not get invoked on setting the selected
4795 * index to an unchanged value. Guard against setting an invalid index
4796 * before the new view peer tab has been created.
4798 final AlignViewportI peer = viewport.getCodingComplement();
4801 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4802 .getAlignPanel().alignFrame;
4803 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4805 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4811 * On right mouse click on view tab, prompt for and set new view name.
4814 public void tabbedPane_mousePressed(MouseEvent e)
4816 if (e.isPopupTrigger())
4818 String msg = MessageManager.getString("label.enter_view_name");
4819 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4820 JvOptionPane.QUESTION_MESSAGE);
4824 viewport.setViewName(reply);
4825 // TODO warn if reply is in getExistingViewNames()?
4826 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4831 public AlignViewport getCurrentView()
4837 * Open the dialog for regex description parsing.
4840 protected void extractScores_actionPerformed(ActionEvent e)
4842 ParseProperties pp = new jalview.analysis.ParseProperties(
4843 viewport.getAlignment());
4844 // TODO: verify regex and introduce GUI dialog for version 2.5
4845 // if (pp.getScoresFromDescription("col", "score column ",
4846 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4848 if (pp.getScoresFromDescription("description column",
4849 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4851 buildSortByAnnotationScoresMenu();
4859 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4863 protected void showDbRefs_actionPerformed(ActionEvent e)
4865 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4871 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4875 protected void showNpFeats_actionPerformed(ActionEvent e)
4877 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4881 * find the viewport amongst the tabs in this alignment frame and close that
4886 public boolean closeView(AlignViewportI av)
4890 this.closeMenuItem_actionPerformed(false);
4893 Component[] comp = tabbedPane.getComponents();
4894 for (int i = 0; comp != null && i < comp.length; i++)
4896 if (comp[i] instanceof AlignmentPanel)
4898 if (((AlignmentPanel) comp[i]).av == av)
4901 closeView((AlignmentPanel) comp[i]);
4909 protected void build_fetchdbmenu(JMenu webService)
4911 // Temporary hack - DBRef Fetcher always top level ws entry.
4912 // TODO We probably want to store a sequence database checklist in
4913 // preferences and have checkboxes.. rather than individual sources selected
4915 final JMenu rfetch = new JMenu(
4916 MessageManager.getString("action.fetch_db_references"));
4917 rfetch.setToolTipText(MessageManager.getString(
4918 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4919 webService.add(rfetch);
4921 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4922 MessageManager.getString("option.trim_retrieved_seqs"));
4923 trimrs.setToolTipText(
4924 MessageManager.getString("label.trim_retrieved_sequences"));
4926 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4927 trimrs.addActionListener(new ActionListener()
4930 public void actionPerformed(ActionEvent e)
4932 trimrs.setSelected(trimrs.isSelected());
4933 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4934 Boolean.valueOf(trimrs.isSelected()).toString());
4938 JMenuItem fetchr = new JMenuItem(
4939 MessageManager.getString("label.standard_databases"));
4940 fetchr.setToolTipText(
4941 MessageManager.getString("label.fetch_embl_uniprot"));
4942 fetchr.addActionListener(new ActionListener()
4946 public void actionPerformed(ActionEvent e)
4948 new Thread(new Runnable()
4953 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4954 .getAlignment().isNucleotide();
4955 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4956 alignPanel.av.getSequenceSelection(),
4957 alignPanel.alignFrame, null,
4958 alignPanel.alignFrame.featureSettings, isNucleotide);
4959 dbRefFetcher.addListener(new FetchFinishedListenerI()
4962 public void finished()
4964 AlignFrame.this.setMenusForViewport();
4967 dbRefFetcher.fetchDBRefs(false);
4975 final AlignFrame me = this;
4976 new Thread(new Runnable()
4981 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4982 .getSequenceFetcherSingleton(me);
4983 javax.swing.SwingUtilities.invokeLater(new Runnable()
4988 String[] dbclasses = sf.getOrderedSupportedSources();
4989 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4990 // jalview.util.QuickSort.sort(otherdb, otherdb);
4991 List<DbSourceProxy> otherdb;
4992 JMenu dfetch = new JMenu();
4993 JMenu ifetch = new JMenu();
4994 JMenuItem fetchr = null;
4995 int comp = 0, icomp = 0, mcomp = 15;
4996 String mname = null;
4998 for (String dbclass : dbclasses)
5000 otherdb = sf.getSourceProxy(dbclass);
5001 // add a single entry for this class, or submenu allowing 'fetch
5003 if (otherdb == null || otherdb.size() < 1)
5007 // List<DbSourceProxy> dbs=otherdb;
5008 // otherdb=new ArrayList<DbSourceProxy>();
5009 // for (DbSourceProxy db:dbs)
5011 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5015 mname = "From " + dbclass;
5017 if (otherdb.size() == 1)
5019 final DbSourceProxy[] dassource = otherdb
5020 .toArray(new DbSourceProxy[0]);
5021 DbSourceProxy src = otherdb.get(0);
5022 fetchr = new JMenuItem(src.getDbSource());
5023 fetchr.addActionListener(new ActionListener()
5027 public void actionPerformed(ActionEvent e)
5029 new Thread(new Runnable()
5035 boolean isNucleotide = alignPanel.alignFrame
5036 .getViewport().getAlignment()
5038 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5039 alignPanel.av.getSequenceSelection(),
5040 alignPanel.alignFrame, dassource,
5041 alignPanel.alignFrame.featureSettings,
5044 .addListener(new FetchFinishedListenerI()
5047 public void finished()
5049 AlignFrame.this.setMenusForViewport();
5052 dbRefFetcher.fetchDBRefs(false);
5058 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5059 MessageManager.formatMessage(
5060 "label.fetch_retrieve_from", new Object[]
5061 { src.getDbName() })));
5067 final DbSourceProxy[] dassource = otherdb
5068 .toArray(new DbSourceProxy[0]);
5070 DbSourceProxy src = otherdb.get(0);
5071 fetchr = new JMenuItem(MessageManager
5072 .formatMessage("label.fetch_all_param", new Object[]
5073 { src.getDbSource() }));
5074 fetchr.addActionListener(new ActionListener()
5077 public void actionPerformed(ActionEvent e)
5079 new Thread(new Runnable()
5085 boolean isNucleotide = alignPanel.alignFrame
5086 .getViewport().getAlignment()
5088 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5089 alignPanel.av.getSequenceSelection(),
5090 alignPanel.alignFrame, dassource,
5091 alignPanel.alignFrame.featureSettings,
5094 .addListener(new FetchFinishedListenerI()
5097 public void finished()
5099 AlignFrame.this.setMenusForViewport();
5102 dbRefFetcher.fetchDBRefs(false);
5108 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5109 MessageManager.formatMessage(
5110 "label.fetch_retrieve_from_all_sources",
5112 { Integer.valueOf(otherdb.size())
5114 src.getDbSource(), src.getDbName() })));
5117 // and then build the rest of the individual menus
5118 ifetch = new JMenu(MessageManager.formatMessage(
5119 "label.source_from_db_source", new Object[]
5120 { src.getDbSource() }));
5122 String imname = null;
5124 for (DbSourceProxy sproxy : otherdb)
5126 String dbname = sproxy.getDbName();
5127 String sname = dbname.length() > 5
5128 ? dbname.substring(0, 5) + "..."
5130 String msname = dbname.length() > 10
5131 ? dbname.substring(0, 10) + "..."
5135 imname = MessageManager
5136 .formatMessage("label.from_msname", new Object[]
5139 fetchr = new JMenuItem(msname);
5140 final DbSourceProxy[] dassrc = { sproxy };
5141 fetchr.addActionListener(new ActionListener()
5145 public void actionPerformed(ActionEvent e)
5147 new Thread(new Runnable()
5153 boolean isNucleotide = alignPanel.alignFrame
5154 .getViewport().getAlignment()
5156 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5157 alignPanel.av.getSequenceSelection(),
5158 alignPanel.alignFrame, dassrc,
5159 alignPanel.alignFrame.featureSettings,
5162 .addListener(new FetchFinishedListenerI()
5165 public void finished()
5167 AlignFrame.this.setMenusForViewport();
5170 dbRefFetcher.fetchDBRefs(false);
5176 fetchr.setToolTipText(
5177 "<html>" + MessageManager.formatMessage(
5178 "label.fetch_retrieve_from", new Object[]
5182 if (++icomp >= mcomp || i == (otherdb.size()))
5184 ifetch.setText(MessageManager.formatMessage(
5185 "label.source_to_target", imname, sname));
5187 ifetch = new JMenu();
5195 if (comp >= mcomp || dbi >= (dbclasses.length))
5197 dfetch.setText(MessageManager.formatMessage(
5198 "label.source_to_target", mname, dbclass));
5200 dfetch = new JMenu();
5213 * Left justify the whole alignment.
5216 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5218 AlignmentI al = viewport.getAlignment();
5220 viewport.firePropertyChange("alignment", null, al);
5224 * Right justify the whole alignment.
5227 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5229 AlignmentI al = viewport.getAlignment();
5231 viewport.firePropertyChange("alignment", null, al);
5235 public void setShowSeqFeatures(boolean b)
5237 showSeqFeatures.setSelected(b);
5238 viewport.setShowSequenceFeatures(b);
5245 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5246 * awt.event.ActionEvent)
5249 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5251 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5252 alignPanel.paintAlignment(false, false);
5259 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5263 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5265 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5266 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5274 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5275 * .event.ActionEvent)
5278 protected void showGroupConservation_actionPerformed(ActionEvent e)
5280 viewport.setShowGroupConservation(showGroupConservation.getState());
5281 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5288 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5289 * .event.ActionEvent)
5292 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5294 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5295 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5302 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5303 * .event.ActionEvent)
5306 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5308 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5309 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5313 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5315 showSequenceLogo.setState(true);
5316 viewport.setShowSequenceLogo(true);
5317 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5318 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5322 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5324 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5331 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5332 * .event.ActionEvent)
5335 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5337 if (avc.makeGroupsFromSelection())
5339 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5340 alignPanel.updateAnnotation();
5341 alignPanel.paintAlignment(true,
5342 viewport.needToUpdateStructureViews());
5346 public void clearAlignmentSeqRep()
5348 // TODO refactor alignmentseqrep to controller
5349 if (viewport.getAlignment().hasSeqrep())
5351 viewport.getAlignment().setSeqrep(null);
5352 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5353 alignPanel.updateAnnotation();
5354 alignPanel.paintAlignment(true, true);
5359 protected void createGroup_actionPerformed(ActionEvent e)
5361 if (avc.createGroup())
5363 if (applyAutoAnnotationSettings.isSelected())
5365 alignPanel.updateAnnotation(true, false);
5367 alignPanel.alignmentChanged();
5372 protected void unGroup_actionPerformed(ActionEvent e)
5376 alignPanel.alignmentChanged();
5381 * make the given alignmentPanel the currently selected tab
5383 * @param alignmentPanel
5385 public void setDisplayedView(AlignmentPanel alignmentPanel)
5387 if (!viewport.getSequenceSetId()
5388 .equals(alignmentPanel.av.getSequenceSetId()))
5390 throw new Error(MessageManager.getString(
5391 "error.implementation_error_cannot_show_view_alignment_frame"));
5393 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5394 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5396 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5401 * Action on selection of menu options to Show or Hide annotations.
5404 * @param forSequences
5405 * update sequence-related annotations
5406 * @param forAlignment
5407 * update non-sequence-related annotations
5410 protected void setAnnotationsVisibility(boolean visible,
5411 boolean forSequences, boolean forAlignment)
5413 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5414 .getAlignmentAnnotation();
5419 for (AlignmentAnnotation aa : anns)
5422 * don't display non-positional annotations on an alignment
5424 if (aa.annotations == null)
5428 boolean apply = (aa.sequenceRef == null && forAlignment)
5429 || (aa.sequenceRef != null && forSequences);
5432 aa.visible = visible;
5435 alignPanel.validateAnnotationDimensions(true);
5436 alignPanel.alignmentChanged();
5440 * Sorts annotations and repaints the alignment
5443 protected void sortAnnotations()
5445 alignPanel.sortAnnotations();
5446 alignPanel.paintAlignment(false, false);
5451 * @return alignment panels in this alignment frame
5453 public List<? extends AlignmentViewPanel> getAlignPanels()
5455 // alignPanels is never null
5456 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5461 * Open a new alignment window, with the cDNA associated with this (protein)
5462 * alignment, aligned as is the protein.
5464 protected void viewAsCdna_actionPerformed()
5466 // TODO no longer a menu action - refactor as required
5467 final AlignmentI alignment = getViewport().getAlignment();
5468 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5469 if (mappings == null)
5473 List<SequenceI> cdnaSeqs = new ArrayList<>();
5474 for (SequenceI aaSeq : alignment.getSequences())
5476 for (AlignedCodonFrame acf : mappings)
5478 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5482 * There is a cDNA mapping for this protein sequence - add to new
5483 * alignment. It will share the same dataset sequence as other mapped
5484 * cDNA (no new mappings need to be created).
5486 final Sequence newSeq = new Sequence(dnaSeq);
5487 newSeq.setDatasetSequence(dnaSeq);
5488 cdnaSeqs.add(newSeq);
5492 if (cdnaSeqs.size() == 0)
5494 // show a warning dialog no mapped cDNA
5497 AlignmentI cdna = new Alignment(
5498 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5499 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5500 AlignFrame.DEFAULT_HEIGHT);
5501 cdna.alignAs(alignment);
5502 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5504 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5505 AlignFrame.DEFAULT_HEIGHT);
5509 * Set visibility of dna/protein complement view (available when shown in a
5515 protected void showComplement_actionPerformed(boolean show)
5517 SplitContainerI sf = getSplitViewContainer();
5520 sf.setComplementVisible(this, show);
5525 * Generate the reverse (optionally complemented) of the selected sequences,
5526 * and add them to the alignment
5529 protected void showReverse_actionPerformed(boolean complement)
5531 AlignmentI al = null;
5534 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5535 al = dna.reverseCdna(complement);
5536 viewport.addAlignment(al, "");
5537 addHistoryItem(new EditCommand(
5538 MessageManager.getString("label.add_sequences"), Action.PASTE,
5539 al.getSequencesArray(), 0, al.getWidth(),
5540 viewport.getAlignment()));
5541 } catch (Exception ex)
5543 System.err.println(ex.getMessage());
5549 * Try to run a script in the Groovy console, having first ensured that this
5550 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5551 * be targeted at this alignment.
5554 protected void runGroovy_actionPerformed()
5556 Jalview.setCurrentAlignFrame(this);
5557 groovy.ui.Console console = Desktop.getGroovyConsole();
5558 if (console != null)
5562 console.runScript();
5563 } catch (Exception ex)
5565 System.err.println((ex.toString()));
5566 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5567 MessageManager.getString("label.couldnt_run_groovy_script"),
5568 MessageManager.getString("label.groovy_support_failed"),
5569 JvOptionPane.ERROR_MESSAGE);
5574 System.err.println("Can't run Groovy script as console not found");
5579 * Hides columns containing (or not containing) a specified feature, provided
5580 * that would not leave all columns hidden
5582 * @param featureType
5583 * @param columnsContaining
5586 public boolean hideFeatureColumns(String featureType,
5587 boolean columnsContaining)
5589 boolean notForHiding = avc.markColumnsContainingFeatures(
5590 columnsContaining, false, false, featureType);
5593 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5594 false, featureType))
5596 getViewport().hideSelectedColumns();
5604 protected void selectHighlightedColumns_actionPerformed(
5605 ActionEvent actionEvent)
5607 // include key modifier check in case user selects from menu
5608 avc.markHighlightedColumns(
5609 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5610 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5611 | ActionEvent.CTRL_MASK)) != 0);
5615 * Rebuilds the Colour menu, including any user-defined colours which have
5616 * been loaded either on startup or during the session
5618 public void buildColourMenu()
5620 colourMenu.removeAll();
5622 colourMenu.add(applyToAllGroups);
5623 colourMenu.add(textColour);
5624 colourMenu.addSeparator();
5626 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5627 viewport.getAlignment(), false);
5629 colourMenu.add(annotationColour);
5630 bg.add(annotationColour);
5631 colourMenu.addSeparator();
5632 colourMenu.add(conservationMenuItem);
5633 colourMenu.add(modifyConservation);
5634 colourMenu.add(abovePIDThreshold);
5635 colourMenu.add(modifyPID);
5637 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5638 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5642 * Open a dialog (if not already open) that allows the user to select and
5643 * calculate PCA or Tree analysis
5645 protected void openTreePcaDialog()
5647 if (alignPanel.getCalculationDialog() == null)
5649 new CalculationChooser(AlignFrame.this);
5654 protected void loadVcf_actionPerformed()
5656 JalviewFileChooser chooser = new JalviewFileChooser(
5657 Cache.getProperty("LAST_DIRECTORY"));
5658 chooser.setFileView(new JalviewFileView());
5659 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5660 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5662 int value = chooser.showOpenDialog(null);
5664 if (value == JalviewFileChooser.APPROVE_OPTION)
5666 String choice = chooser.getSelectedFile().getPath();
5667 Cache.setProperty("LAST_DIRECTORY", choice);
5668 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5669 new VCFLoader(choice).loadVCF(seqs, this);
5675 protected boolean setShowAutoCalculatedAbove(
5676 boolean showAutoCalculatedAbove)
5678 if (viewport.isShowAutocalculatedAbove() != showAutoCalculatedAbove)
5680 viewport.setShowAutocalculatedAbove(showAutoCalculatedAbove);
5683 * change CUSTOM annotation ordering to NONE
5684 * so that sorting actually does something
5686 if (viewport.getSortAnnotationsBy() == SequenceAnnotationOrder.CUSTOM)
5688 viewport.setSortAnnotationsBy(SequenceAnnotationOrder.NONE);
5696 public void setAnnotationSortOrder(
5697 SequenceAnnotationOrder annotationSortOrder)
5699 viewport.setSortAnnotationsBy(annotationSortOrder);
5703 class PrintThread extends Thread
5707 public PrintThread(AlignmentPanel ap)
5712 static PageFormat pf;
5717 PrinterJob printJob = PrinterJob.getPrinterJob();
5721 printJob.setPrintable(ap, pf);
5725 printJob.setPrintable(ap);
5728 if (printJob.printDialog())
5733 } catch (Exception PrintException)
5735 PrintException.printStackTrace();