2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingsI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignExportSettingsAdapter;
49 import jalview.datamodel.AlignedCodonFrame;
50 import jalview.datamodel.Alignment;
51 import jalview.datamodel.AlignmentAnnotation;
52 import jalview.datamodel.AlignmentExportData;
53 import jalview.datamodel.AlignmentI;
54 import jalview.datamodel.AlignmentOrder;
55 import jalview.datamodel.AlignmentView;
56 import jalview.datamodel.ColumnSelection;
57 import jalview.datamodel.HiddenColumns;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FileParse;
74 import jalview.io.FormatAdapter;
75 import jalview.io.HtmlSvgOutput;
76 import jalview.io.IdentifyFile;
77 import jalview.io.JPredFile;
78 import jalview.io.JalviewFileChooser;
79 import jalview.io.JalviewFileView;
80 import jalview.io.JnetAnnotationMaker;
81 import jalview.io.NewickFile;
82 import jalview.io.ScoreMatrixFile;
83 import jalview.io.TCoffeeScoreFile;
84 import jalview.io.vcf.VCFLoader;
85 import jalview.jbgui.GAlignFrame;
86 import jalview.schemes.ColourSchemeI;
87 import jalview.schemes.ColourSchemes;
88 import jalview.schemes.ResidueColourScheme;
89 import jalview.schemes.TCoffeeColourScheme;
90 import jalview.util.ImageMaker.TYPE;
91 import jalview.util.MessageManager;
92 import jalview.util.dialogrunner.RunResponse;
93 import jalview.viewmodel.AlignmentViewport;
94 import jalview.viewmodel.ViewportRanges;
95 import jalview.ws.DBRefFetcher;
96 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
97 import jalview.ws.jws1.Discoverer;
98 import jalview.ws.jws2.Jws2Discoverer;
99 import jalview.ws.jws2.jabaws2.Jws2Instance;
100 import jalview.ws.seqfetcher.DbSourceProxy;
102 import java.awt.BorderLayout;
103 import java.awt.Color;
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.JCheckBoxMenuItem;
141 import javax.swing.JComponent;
142 import javax.swing.JEditorPane;
143 import javax.swing.JInternalFrame;
144 import javax.swing.JLabel;
145 import javax.swing.JLayeredPane;
146 import javax.swing.JMenu;
147 import javax.swing.JMenuItem;
148 import javax.swing.JPanel;
149 import javax.swing.JScrollPane;
150 import javax.swing.SwingUtilities;
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;
190 * Creates a new AlignFrame object with specific width and height.
196 public AlignFrame(AlignmentI al, int width, int height)
198 this(al, null, width, height);
202 * Creates a new AlignFrame object with specific width, height and
208 * @param sequenceSetId
210 public AlignFrame(AlignmentI al, int width, int height,
211 String sequenceSetId)
213 this(al, null, width, height, sequenceSetId);
217 * Creates a new AlignFrame object with specific width, height and
223 * @param sequenceSetId
226 public AlignFrame(AlignmentI al, int width, int height,
227 String sequenceSetId, String viewId)
229 this(al, null, width, height, sequenceSetId, viewId);
233 * new alignment window with hidden columns
237 * @param hiddenColumns
238 * ColumnSelection or null
240 * Width of alignment frame
244 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
247 this(al, hiddenColumns, width, height, null);
251 * Create alignment frame for al with hiddenColumns, a specific width and
252 * height, and specific sequenceId
255 * @param hiddenColumns
258 * @param sequenceSetId
261 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
262 int height, String sequenceSetId)
264 this(al, hiddenColumns, width, height, sequenceSetId, null);
268 * Create alignment frame for al with hiddenColumns, a specific width and
269 * height, and specific sequenceId
272 * @param hiddenColumns
275 * @param sequenceSetId
280 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
281 int height, String sequenceSetId, String viewId)
283 setSize(width, height);
285 if (al.getDataset() == null)
290 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
292 alignPanel = new AlignmentPanel(this, viewport);
294 addAlignmentPanel(alignPanel, true);
298 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
299 HiddenColumns hiddenColumns, int width, int height)
301 setSize(width, height);
303 if (al.getDataset() == null)
308 viewport = new AlignViewport(al, hiddenColumns);
310 if (hiddenSeqs != null && hiddenSeqs.length > 0)
312 viewport.hideSequence(hiddenSeqs);
314 alignPanel = new AlignmentPanel(this, viewport);
315 addAlignmentPanel(alignPanel, true);
320 * Make a new AlignFrame from existing alignmentPanels
327 public AlignFrame(AlignmentPanel ap)
331 addAlignmentPanel(ap, false);
336 * initalise the alignframe from the underlying viewport data and the
341 if (!Jalview.isHeadlessMode())
343 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
346 avc = new jalview.controller.AlignViewController(this, viewport,
348 if (viewport.getAlignmentConservationAnnotation() == null)
350 // BLOSUM62Colour.setEnabled(false);
351 conservationMenuItem.setEnabled(false);
352 modifyConservation.setEnabled(false);
353 // PIDColour.setEnabled(false);
354 // abovePIDThreshold.setEnabled(false);
355 // modifyPID.setEnabled(false);
358 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
361 if (sortby.equals("Id"))
363 sortIDMenuItem_actionPerformed(null);
365 else if (sortby.equals("Pairwise Identity"))
367 sortPairwiseMenuItem_actionPerformed(null);
371 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
373 setMenusFromViewport(viewport);
374 buildSortByAnnotationScoresMenu();
375 calculateTree.addActionListener(new ActionListener()
379 public void actionPerformed(ActionEvent e)
386 if (Desktop.desktop != null)
388 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
390 * BH 2018 ignore service listeners
396 addServiceListeners();
401 if (viewport.getWrapAlignment())
403 wrapMenuItem_actionPerformed(null);
406 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
408 this.overviewMenuItem_actionPerformed(null);
413 final List<AlignmentPanel> selviews = new ArrayList<>();
414 final List<AlignmentPanel> origview = new ArrayList<>();
415 final String menuLabel = MessageManager
416 .getString("label.copy_format_from");
417 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
418 new ViewSetProvider()
422 public AlignmentPanel[] getAllAlignmentPanels()
425 origview.add(alignPanel);
426 // make an array of all alignment panels except for this one
427 List<AlignmentPanel> aps = new ArrayList<>(
428 Arrays.asList(Desktop.getAlignmentPanels(null)));
429 aps.remove(AlignFrame.this.alignPanel);
430 return aps.toArray(new AlignmentPanel[aps.size()]);
432 }, selviews, new ItemListener()
436 public void itemStateChanged(ItemEvent e)
438 if (origview.size() > 0)
440 final AlignmentPanel ap = origview.get(0);
443 * Copy the ViewStyle of the selected panel to 'this one'.
444 * Don't change value of 'scaleProteinAsCdna' unless copying
447 ViewStyleI vs = selviews.get(0).getAlignViewport()
449 boolean fromSplitFrame = selviews.get(0)
450 .getAlignViewport().getCodingComplement() != null;
453 vs.setScaleProteinAsCdna(ap.getAlignViewport()
454 .getViewStyle().isScaleProteinAsCdna());
456 ap.getAlignViewport().setViewStyle(vs);
459 * Also rescale ViewStyle of SplitFrame complement if there is
460 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
461 * the whole ViewStyle (allow cDNA protein to have different
464 AlignViewportI complement = ap.getAlignViewport()
465 .getCodingComplement();
466 if (complement != null && vs.isScaleProteinAsCdna())
468 AlignFrame af = Desktop.getAlignFrameFor(complement);
469 ((SplitFrame) af.getSplitViewContainer())
471 af.setMenusForViewport();
475 ap.setSelected(true);
476 ap.alignFrame.setMenusForViewport();
481 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
482 .indexOf("devel") > -1
483 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
484 .indexOf("test") > -1)
486 formatMenu.add(vsel);
488 addFocusListener(new FocusAdapter()
491 public void focusGained(FocusEvent e)
493 Jalview.setCurrentAlignFrame(AlignFrame.this);
500 * Change the filename and format for the alignment, and enable the 'reload'
501 * button functionality.
508 public void setFileName(String file, FileFormatI format)
511 setFileFormat(format);
512 reload.setEnabled(true);
516 * JavaScript will have this, maybe others. More dependable than a file name
517 * and maintains a reference to the actual bytes loaded.
521 public void setFileObject(File file)
523 this.fileObject = file;
527 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
530 void addKeyListener()
532 addKeyListener(new KeyAdapter()
535 public void keyPressed(KeyEvent evt)
537 if (viewport.cursorMode
538 && ((evt.getKeyCode() >= KeyEvent.VK_0
539 && evt.getKeyCode() <= KeyEvent.VK_9)
540 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
541 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
542 && Character.isDigit(evt.getKeyChar()))
544 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
547 switch (evt.getKeyCode())
550 case 27: // escape key
551 deselectAllSequenceMenuItem_actionPerformed(null);
555 case KeyEvent.VK_DOWN:
556 if (evt.isAltDown() || !viewport.cursorMode)
558 moveSelectedSequences(false);
560 if (viewport.cursorMode)
562 alignPanel.getSeqPanel().moveCursor(0, 1);
567 if (evt.isAltDown() || !viewport.cursorMode)
569 moveSelectedSequences(true);
571 if (viewport.cursorMode)
573 alignPanel.getSeqPanel().moveCursor(0, -1);
578 case KeyEvent.VK_LEFT:
579 if (evt.isAltDown() || !viewport.cursorMode)
581 slideSequences(false,
582 alignPanel.getSeqPanel().getKeyboardNo1());
586 alignPanel.getSeqPanel().moveCursor(-1, 0);
591 case KeyEvent.VK_RIGHT:
592 if (evt.isAltDown() || !viewport.cursorMode)
594 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
598 alignPanel.getSeqPanel().moveCursor(1, 0);
602 case KeyEvent.VK_SPACE:
603 if (viewport.cursorMode)
605 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
606 || evt.isShiftDown() || evt.isAltDown());
610 // case KeyEvent.VK_A:
611 // if (viewport.cursorMode)
613 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
614 // //System.out.println("A");
618 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
619 * System.out.println("closing bracket"); } break;
621 case KeyEvent.VK_DELETE:
622 case KeyEvent.VK_BACK_SPACE:
623 if (!viewport.cursorMode)
625 cut_actionPerformed(null);
629 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
630 || evt.isShiftDown() || evt.isAltDown());
636 if (viewport.cursorMode)
638 alignPanel.getSeqPanel().setCursorRow();
642 if (viewport.cursorMode && !evt.isControlDown())
644 alignPanel.getSeqPanel().setCursorColumn();
648 if (viewport.cursorMode)
650 alignPanel.getSeqPanel().setCursorPosition();
654 case KeyEvent.VK_ENTER:
655 case KeyEvent.VK_COMMA:
656 if (viewport.cursorMode)
658 alignPanel.getSeqPanel().setCursorRowAndColumn();
663 if (viewport.cursorMode)
665 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
669 if (viewport.cursorMode)
671 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
676 viewport.cursorMode = !viewport.cursorMode;
677 setStatus(MessageManager
678 .formatMessage("label.keyboard_editing_mode", new String[]
679 { (viewport.cursorMode ? "on" : "off") }));
680 if (viewport.cursorMode)
682 ViewportRanges ranges = viewport.getRanges();
683 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
685 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
688 alignPanel.getSeqPanel().seqCanvas.repaint();
694 Help.showHelpWindow();
695 } catch (Exception ex)
697 ex.printStackTrace();
702 boolean toggleSeqs = !evt.isControlDown();
703 boolean toggleCols = !evt.isShiftDown();
704 toggleHiddenRegions(toggleSeqs, toggleCols);
709 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
710 boolean modifyExisting = true; // always modify, don't clear
711 // evt.isShiftDown();
712 boolean invertHighlighted = evt.isAltDown();
713 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
717 case KeyEvent.VK_PAGE_UP:
718 viewport.getRanges().pageUp();
720 case KeyEvent.VK_PAGE_DOWN:
721 viewport.getRanges().pageDown();
727 public void keyReleased(KeyEvent evt)
729 switch (evt.getKeyCode())
731 case KeyEvent.VK_LEFT:
732 if (evt.isAltDown() || !viewport.cursorMode)
734 viewport.firePropertyChange("alignment", null,
735 viewport.getAlignment().getSequences());
739 case KeyEvent.VK_RIGHT:
740 if (evt.isAltDown() || !viewport.cursorMode)
742 viewport.firePropertyChange("alignment", null,
743 viewport.getAlignment().getSequences());
751 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
753 ap.alignFrame = this;
754 avc = new jalview.controller.AlignViewController(this, viewport,
759 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
761 int aSize = alignPanels.size();
763 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
765 if (aSize == 1 && ap.av.getViewName() == null)
767 this.getContentPane().add(ap, BorderLayout.CENTER);
773 setInitialTabVisible();
776 expandViews.setEnabled(true);
777 gatherViews.setEnabled(true);
778 tabbedPane.addTab(ap.av.getViewName(), ap);
780 ap.setVisible(false);
785 if (ap.av.isPadGaps())
787 ap.av.getAlignment().padGaps();
789 ap.av.updateConservation(ap);
790 ap.av.updateConsensus(ap);
791 ap.av.updateStrucConsensus(ap);
795 public void setInitialTabVisible()
797 expandViews.setEnabled(true);
798 gatherViews.setEnabled(true);
799 tabbedPane.setVisible(true);
800 AlignmentPanel first = alignPanels.get(0);
801 tabbedPane.addTab(first.av.getViewName(), first);
802 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
805 public AlignViewport getViewport()
810 /* Set up intrinsic listeners for dynamically generated GUI bits. */
811 private void addServiceListeners()
813 final java.beans.PropertyChangeListener thisListener;
814 Desktop.instance.addJalviewPropertyChangeListener("services",
815 thisListener = new java.beans.PropertyChangeListener()
818 public void propertyChange(PropertyChangeEvent evt)
820 // // System.out.println("Discoverer property change.");
821 // if (evt.getPropertyName().equals("services"))
823 SwingUtilities.invokeLater(new Runnable()
830 "Rebuild WS Menu for service change");
831 BuildWebServiceMenu();
838 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
841 public void internalFrameClosed(
842 javax.swing.event.InternalFrameEvent evt)
844 // System.out.println("deregistering discoverer listener");
845 Desktop.instance.removeJalviewPropertyChangeListener("services",
847 closeMenuItem_actionPerformed(true);
850 // Finally, build the menu once to get current service state
851 new Thread(new Runnable()
856 BuildWebServiceMenu();
862 * Configure menu items that vary according to whether the alignment is
863 * nucleotide or protein
865 public void setGUINucleotide()
867 AlignmentI al = getViewport().getAlignment();
868 boolean nucleotide = al.isNucleotide();
870 loadVcf.setVisible(nucleotide);
871 showTranslation.setVisible(nucleotide);
872 showReverse.setVisible(nucleotide);
873 showReverseComplement.setVisible(nucleotide);
874 conservationMenuItem.setEnabled(!nucleotide);
876 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
877 showGroupConservation.setEnabled(!nucleotide);
879 showComplementMenuItem
880 .setText(nucleotide ? MessageManager.getString("label.protein")
881 : MessageManager.getString("label.nucleotide"));
885 * set up menus for the current viewport. This may be called after any
886 * operation that affects the data in the current view (selection changed,
887 * etc) to update the menus to reflect the new state.
890 public void setMenusForViewport()
892 setMenusFromViewport(viewport);
896 * Need to call this method when tabs are selected for multiple views, or when
897 * loading from Jalview2XML.java
902 public void setMenusFromViewport(AlignViewport av)
904 padGapsMenuitem.setSelected(av.isPadGaps());
905 colourTextMenuItem.setSelected(av.isShowColourText());
906 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
907 modifyPID.setEnabled(abovePIDThreshold.isSelected());
908 conservationMenuItem.setSelected(av.getConservationSelected());
909 modifyConservation.setEnabled(conservationMenuItem.isSelected());
910 seqLimits.setSelected(av.getShowJVSuffix());
911 idRightAlign.setSelected(av.isRightAlignIds());
912 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
913 renderGapsMenuItem.setSelected(av.isRenderGaps());
914 wrapMenuItem.setSelected(av.getWrapAlignment());
915 scaleAbove.setVisible(av.getWrapAlignment());
916 scaleLeft.setVisible(av.getWrapAlignment());
917 scaleRight.setVisible(av.getWrapAlignment());
918 annotationPanelMenuItem.setState(av.isShowAnnotation());
920 * Show/hide annotations only enabled if annotation panel is shown
922 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
923 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
924 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
925 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
926 viewBoxesMenuItem.setSelected(av.getShowBoxes());
927 viewTextMenuItem.setSelected(av.getShowText());
928 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
929 showGroupConsensus.setSelected(av.isShowGroupConsensus());
930 showGroupConservation.setSelected(av.isShowGroupConservation());
931 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
932 showSequenceLogo.setSelected(av.isShowSequenceLogo());
933 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
935 ColourMenuHelper.setColourSelected(colourMenu,
936 av.getGlobalColourScheme());
938 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
939 hiddenMarkers.setState(av.getShowHiddenMarkers());
940 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
941 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
942 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
943 autoCalculate.setSelected(av.autoCalculateConsensus);
944 sortByTree.setSelected(av.sortByTree);
945 listenToViewSelections.setSelected(av.followSelection);
947 showProducts.setEnabled(canShowProducts());
948 setGroovyEnabled(Desktop.getGroovyConsole() != null);
954 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
958 public void setGroovyEnabled(boolean b)
960 runGroovy.setEnabled(b);
963 private IProgressIndicator progressBar;
968 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
971 public void setProgressBar(String message, long id)
973 progressBar.setProgressBar(message, id);
977 public void registerHandler(final long id,
978 final IProgressIndicatorHandler handler)
980 progressBar.registerHandler(id, handler);
985 * @return true if any progress bars are still active
988 public boolean operationInProgress()
990 return progressBar.operationInProgress();
994 public void setStatus(String text)
996 statusBar.setText(text);
1000 * Added so Castor Mapping file can obtain Jalview Version
1002 public String getVersion()
1004 return jalview.bin.Cache.getProperty("VERSION");
1007 public FeatureRenderer getFeatureRenderer()
1009 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1013 public void fetchSequence_actionPerformed()
1015 new SequenceFetcher(this);
1019 public void addFromFile_actionPerformed(ActionEvent e)
1021 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1025 public void reload_actionPerformed(ActionEvent e)
1027 if (fileName != null)
1029 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1030 // originating file's format
1031 // TODO: work out how to recover feature settings for correct view(s) when
1032 // file is reloaded.
1033 if (FileFormat.Jalview.equals(currentFileFormat))
1035 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1036 for (int i = 0; i < frames.length; i++)
1038 if (frames[i] instanceof AlignFrame && frames[i] != this
1039 && ((AlignFrame) frames[i]).fileName != null
1040 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1044 frames[i].setSelected(true);
1045 Desktop.instance.closeAssociatedWindows();
1046 } catch (java.beans.PropertyVetoException ex)
1052 Desktop.instance.closeAssociatedWindows();
1054 FileLoader loader = new FileLoader();
1055 DataSourceType protocol = fileName.startsWith("http:")
1056 ? DataSourceType.URL
1057 : DataSourceType.FILE;
1058 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1062 Rectangle bounds = this.getBounds();
1064 FileLoader loader = new FileLoader();
1066 AlignFrame newframe = null;
1068 if (fileObject == null)
1071 DataSourceType protocol = (fileName.startsWith("http:")
1072 ? DataSourceType.URL
1073 : DataSourceType.FILE);
1074 newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1079 newframe = loader.LoadFileWaitTillLoaded(fileObject,
1080 DataSourceType.FILE, currentFileFormat);
1083 newframe.setBounds(bounds);
1084 if (featureSettings != null && featureSettings.isShowing())
1086 final Rectangle fspos = featureSettings.frame.getBounds();
1087 // TODO: need a 'show feature settings' function that takes bounds -
1088 // need to refactor Desktop.addFrame
1089 newframe.featureSettings_actionPerformed(null);
1090 final FeatureSettings nfs = newframe.featureSettings;
1091 SwingUtilities.invokeLater(new Runnable()
1096 nfs.frame.setBounds(fspos);
1099 this.featureSettings.close();
1100 this.featureSettings = null;
1102 this.closeMenuItem_actionPerformed(true);
1108 public void addFromText_actionPerformed(ActionEvent e)
1111 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1115 public void addFromURL_actionPerformed(ActionEvent e)
1117 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1121 public void save_actionPerformed(ActionEvent e)
1123 if (fileName == null || (currentFileFormat == null)
1124 || fileName.startsWith("http"))
1126 saveAs_actionPerformed();
1130 saveAlignment(fileName, currentFileFormat);
1135 * Saves the alignment to a file with a name chosen by the user, if necessary
1136 * warning if a file would be overwritten
1139 public void saveAs_actionPerformed()
1141 String format = currentFileFormat == null ? null
1142 : currentFileFormat.getName();
1143 JalviewFileChooser chooser = JalviewFileChooser
1144 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1146 chooser.setFileView(new JalviewFileView());
1147 chooser.setDialogTitle(
1148 MessageManager.getString("label.save_alignment_to_file"));
1149 chooser.setToolTipText(MessageManager.getString("action.save"));
1151 int value = chooser.showSaveDialog(this);
1153 if (value != JalviewFileChooser.APPROVE_OPTION)
1157 currentFileFormat = chooser.getSelectedFormat();
1158 // todo is this (2005) test now obsolete - value is never null?
1159 while (currentFileFormat == null)
1161 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1163 .getString("label.select_file_format_before_saving"),
1164 MessageManager.getString("label.file_format_not_specified"),
1165 JvOptionPane.WARNING_MESSAGE);
1166 currentFileFormat = chooser.getSelectedFormat();
1167 value = chooser.showSaveDialog(this);
1168 if (value != JalviewFileChooser.APPROVE_OPTION)
1174 fileName = chooser.getSelectedFile().getPath();
1176 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1177 Cache.setProperty("LAST_DIRECTORY", fileName);
1178 saveAlignment(fileName, currentFileFormat);
1181 boolean lastSaveSuccessful = false;
1183 FileFormatI lastFormatSaved;
1185 String lastFilenameSaved;
1188 * Raise a dialog or status message for the last call to saveAlignment.
1190 * @return true if last call to saveAlignment(file, format) was successful.
1192 public boolean isSaveAlignmentSuccessful()
1195 if (!lastSaveSuccessful)
1197 JvOptionPane.showInternalMessageDialog(this, MessageManager
1198 .formatMessage("label.couldnt_save_file", new Object[]
1199 { lastFilenameSaved }),
1200 MessageManager.getString("label.error_saving_file"),
1201 JvOptionPane.WARNING_MESSAGE);
1206 setStatus(MessageManager.formatMessage(
1207 "label.successfully_saved_to_file_in_format", new Object[]
1208 { lastFilenameSaved, lastFormatSaved }));
1211 return lastSaveSuccessful;
1215 * Saves the alignment to the specified file path, in the specified format,
1216 * which may be an alignment format, or Jalview project format. If the
1217 * alignment has hidden regions, or the format is one capable of including
1218 * non-sequence data (features, annotations, groups), then the user may be
1219 * prompted to specify what to include in the output.
1224 public void saveAlignment(String file, FileFormatI format)
1226 lastSaveSuccessful = false;
1227 lastFilenameSaved = file;
1228 lastFormatSaved = format;
1230 if (FileFormat.Jalview.equals(format))
1232 String shortName = title;
1233 if (shortName.indexOf(File.separatorChar) > -1)
1235 shortName = shortName.substring(
1236 shortName.lastIndexOf(File.separatorChar) + 1);
1238 lastSaveSuccessful = new jalview.project.Jalview2XML().saveAlignment(this, file,
1241 statusBar.setText(MessageManager.formatMessage(
1242 "label.successfully_saved_to_file_in_format", new Object[]
1243 { fileName, format }));
1248 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1249 RunResponse cancelAction = new RunResponse(JvOptionPane.CANCEL_OPTION)
1254 lastSaveSuccessful = false;
1257 RunResponse outputAction = new RunResponse(JvOptionPane.OK_OPTION)
1262 // todo defer this to inside formatSequences (or later)
1263 AlignmentExportData exportData = viewport
1264 .getAlignExportData(options);
1265 String output = new FormatAdapter(alignPanel, options)
1266 .formatSequences(format, exportData.getAlignment(),
1267 exportData.getOmitHidden(),
1268 exportData.getStartEndPostions(),
1269 viewport.getAlignment().getHiddenColumns());
1272 lastSaveSuccessful = false;
1278 PrintWriter out = new PrintWriter(new FileWriter(file));
1281 AlignFrame.this.setTitle(file);
1282 setStatus(MessageManager.formatMessage(
1283 "label.successfully_saved_to_file_in_format",
1285 { fileName, format.getName() }));
1286 } catch (Exception ex)
1288 lastSaveSuccessful = false;
1289 ex.printStackTrace();
1296 * show dialog with export options if applicable; else just do it
1298 if (AlignExportOptions.isNeeded(viewport, format))
1300 AlignExportOptions choices = new AlignExportOptions(
1301 alignPanel.getAlignViewport(), format, options);
1302 choices.setResponseAction(0, outputAction);
1303 choices.setResponseAction(1, cancelAction);
1304 choices.showDialog();
1313 * Outputs the alignment to textbox in the requested format, if necessary
1314 * first prompting the user for whether to include hidden regions or
1317 * @param fileFormatName
1320 protected void outputText_actionPerformed(String fileFormatName)
1322 FileFormatI fileFormat = FileFormats.getInstance()
1323 .forName(fileFormatName);
1324 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1325 RunResponse outputAction = new RunResponse(JvOptionPane.OK_OPTION)
1330 // todo defer this to inside formatSequences (or later)
1331 AlignmentExportData exportData = viewport
1332 .getAlignExportData(options);
1333 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1334 cap.setForInput(null);
1337 FileFormatI format = fileFormat;
1338 cap.setText(new FormatAdapter(alignPanel, options)
1339 .formatSequences(format, exportData.getAlignment(),
1340 exportData.getOmitHidden(),
1341 exportData.getStartEndPostions(),
1342 viewport.getAlignment().getHiddenColumns()));
1343 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1344 "label.alignment_output_command", new Object[]
1345 { fileFormat.getName() }), 600, 500);
1346 } catch (OutOfMemoryError oom)
1348 new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1356 * show dialog with export options if applicable; else just do it
1358 if (AlignExportOptions.isNeeded(viewport, fileFormat))
1360 AlignExportOptions choices = new AlignExportOptions(
1361 alignPanel.getAlignViewport(), fileFormat, options);
1362 choices.setResponseAction(0, outputAction);
1363 choices.showDialog();
1378 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1380 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1381 htmlSVG.exportHTML(null);
1385 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1387 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1388 bjs.exportHTML(null);
1391 public void createImageMap(File file, String image)
1393 alignPanel.makePNGImageMap(file, image);
1397 * Creates a PNG image of the alignment and writes it to the given file. If
1398 * the file is null, the user is prompted to choose a file.
1403 public void createPNG(File f)
1405 alignPanel.makeAlignmentImage(TYPE.PNG, f);
1409 * Creates an EPS image of the alignment and writes it to the given file. If
1410 * the file is null, the user is prompted to choose a file.
1415 public void createEPS(File f)
1417 alignPanel.makeAlignmentImage(TYPE.EPS, f);
1421 * Creates an SVG image of the alignment and writes it to the given file. If
1422 * the file is null, the user is prompted to choose a file.
1427 public void createSVG(File f)
1429 alignPanel.makeAlignmentImage(TYPE.SVG, f);
1433 public void pageSetup_actionPerformed(ActionEvent e)
1435 PrinterJob printJob = PrinterJob.getPrinterJob();
1436 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1446 public void printMenuItem_actionPerformed(ActionEvent e)
1448 // Putting in a thread avoids Swing painting problems
1449 PrintThread thread = new PrintThread(alignPanel);
1454 public void exportFeatures_actionPerformed(ActionEvent e)
1456 new AnnotationExporter(alignPanel).exportFeatures();
1460 public void exportAnnotations_actionPerformed(ActionEvent e)
1462 new AnnotationExporter(alignPanel).exportAnnotations();
1466 public void associatedData_actionPerformed(ActionEvent e)
1468 final JalviewFileChooser chooser = new JalviewFileChooser(
1469 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1470 chooser.setFileView(new JalviewFileView());
1471 chooser.setDialogTitle(
1472 MessageManager.getString("label.load_jalview_annotations"));
1473 chooser.setToolTipText(
1474 MessageManager.getString("label.load_jalview_annotations"));
1475 chooser.addResponse(0, new RunResponse(JalviewFileChooser.APPROVE_OPTION)
1480 String choice = chooser.getSelectedFile().getPath();
1481 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1482 loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1486 chooser.showOpenDialog(this);
1490 * Close the current view or all views in the alignment frame. If the frame
1491 * only contains one view then the alignment will be removed from memory.
1493 * @param closeAllTabs
1496 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1498 if (alignPanels != null && alignPanels.size() < 2)
1500 closeAllTabs = true;
1505 if (alignPanels != null)
1509 if (this.isClosed())
1511 // really close all the windows - otherwise wait till
1512 // setClosed(true) is called
1513 for (int i = 0; i < alignPanels.size(); i++)
1515 AlignmentPanel ap = alignPanels.get(i);
1522 closeView(alignPanel);
1529 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1530 * be called recursively, with the frame now in 'closed' state
1532 this.setClosed(true);
1534 } catch (Exception ex)
1536 ex.printStackTrace();
1541 * Close the specified panel and close up tabs appropriately.
1543 * @param panelToClose
1545 public void closeView(AlignmentPanel panelToClose)
1547 int index = tabbedPane.getSelectedIndex();
1548 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1549 alignPanels.remove(panelToClose);
1550 panelToClose.closePanel();
1551 panelToClose = null;
1553 tabbedPane.removeTabAt(closedindex);
1554 tabbedPane.validate();
1556 if (index > closedindex || index == tabbedPane.getTabCount())
1558 // modify currently selected tab index if necessary.
1562 this.tabSelectionChanged(index);
1568 void updateEditMenuBar()
1571 if (viewport.getHistoryList().size() > 0)
1573 undoMenuItem.setEnabled(true);
1574 CommandI command = viewport.getHistoryList().peek();
1575 undoMenuItem.setText(MessageManager
1576 .formatMessage("label.undo_command", new Object[]
1577 { command.getDescription() }));
1581 undoMenuItem.setEnabled(false);
1582 undoMenuItem.setText(MessageManager.getString("action.undo"));
1585 if (viewport.getRedoList().size() > 0)
1587 redoMenuItem.setEnabled(true);
1589 CommandI command = viewport.getRedoList().peek();
1590 redoMenuItem.setText(MessageManager
1591 .formatMessage("label.redo_command", new Object[]
1592 { command.getDescription() }));
1596 redoMenuItem.setEnabled(false);
1597 redoMenuItem.setText(MessageManager.getString("action.redo"));
1602 public void addHistoryItem(CommandI command)
1604 if (command.getSize() > 0)
1606 viewport.addToHistoryList(command);
1607 viewport.clearRedoList();
1608 updateEditMenuBar();
1609 viewport.updateHiddenColumns();
1610 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1611 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1612 // viewport.getColumnSelection()
1613 // .getHiddenColumns().size() > 0);
1619 * @return alignment objects for all views
1621 AlignmentI[] getViewAlignments()
1623 if (alignPanels != null)
1625 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1627 for (AlignmentPanel ap : alignPanels)
1629 als[i++] = ap.av.getAlignment();
1633 if (viewport != null)
1635 return new AlignmentI[] { viewport.getAlignment() };
1647 protected void undoMenuItem_actionPerformed(ActionEvent e)
1649 if (viewport.getHistoryList().isEmpty())
1653 CommandI command = viewport.getHistoryList().pop();
1654 viewport.addToRedoList(command);
1655 command.undoCommand(getViewAlignments());
1657 AlignmentViewport originalSource = getOriginatingSource(command);
1658 updateEditMenuBar();
1660 if (originalSource != null)
1662 if (originalSource != viewport)
1665 "Implementation worry: mismatch of viewport origin for undo");
1667 originalSource.updateHiddenColumns();
1668 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1670 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1671 // viewport.getColumnSelection()
1672 // .getHiddenColumns().size() > 0);
1673 originalSource.firePropertyChange("alignment", null,
1674 originalSource.getAlignment().getSequences());
1685 protected void redoMenuItem_actionPerformed(ActionEvent e)
1687 if (viewport.getRedoList().size() < 1)
1692 CommandI command = viewport.getRedoList().pop();
1693 viewport.addToHistoryList(command);
1694 command.doCommand(getViewAlignments());
1696 AlignmentViewport originalSource = getOriginatingSource(command);
1697 updateEditMenuBar();
1699 if (originalSource != null)
1702 if (originalSource != viewport)
1705 "Implementation worry: mismatch of viewport origin for redo");
1707 originalSource.updateHiddenColumns();
1708 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1710 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1711 // viewport.getColumnSelection()
1712 // .getHiddenColumns().size() > 0);
1713 originalSource.firePropertyChange("alignment", null,
1714 originalSource.getAlignment().getSequences());
1718 AlignmentViewport getOriginatingSource(CommandI command)
1720 AlignmentViewport originalSource = null;
1721 // For sequence removal and addition, we need to fire
1722 // the property change event FROM the viewport where the
1723 // original alignment was altered
1724 AlignmentI al = null;
1725 if (command instanceof EditCommand)
1727 EditCommand editCommand = (EditCommand) command;
1728 al = editCommand.getAlignment();
1729 List<Component> comps = PaintRefresher.components
1730 .get(viewport.getSequenceSetId());
1732 for (Component comp : comps)
1734 if (comp instanceof AlignmentPanel)
1736 if (al == ((AlignmentPanel) comp).av.getAlignment())
1738 originalSource = ((AlignmentPanel) comp).av;
1745 if (originalSource == null)
1747 // The original view is closed, we must validate
1748 // the current view against the closed view first
1751 PaintRefresher.validateSequences(al, viewport.getAlignment());
1754 originalSource = viewport;
1757 return originalSource;
1766 public void moveSelectedSequences(boolean up)
1768 SequenceGroup sg = viewport.getSelectionGroup();
1774 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1775 viewport.getHiddenRepSequences(), up);
1776 alignPanel.paintAlignment(true, false);
1779 synchronized void slideSequences(boolean right, int size)
1781 List<SequenceI> sg = new ArrayList<>();
1782 if (viewport.cursorMode)
1784 sg.add(viewport.getAlignment()
1785 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1787 else if (viewport.getSelectionGroup() != null
1788 && viewport.getSelectionGroup().getSize() != viewport
1789 .getAlignment().getHeight())
1791 sg = viewport.getSelectionGroup()
1792 .getSequences(viewport.getHiddenRepSequences());
1800 List<SequenceI> invertGroup = new ArrayList<>();
1802 for (SequenceI seq : viewport.getAlignment().getSequences())
1804 if (!sg.contains(seq))
1806 invertGroup.add(seq);
1810 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1812 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1813 for (int i = 0; i < invertGroup.size(); i++)
1815 seqs2[i] = invertGroup.get(i);
1818 SlideSequencesCommand ssc;
1821 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1822 viewport.getGapCharacter());
1826 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1827 viewport.getGapCharacter());
1830 int groupAdjustment = 0;
1831 if (ssc.getGapsInsertedBegin() && right)
1833 if (viewport.cursorMode)
1835 alignPanel.getSeqPanel().moveCursor(size, 0);
1839 groupAdjustment = size;
1842 else if (!ssc.getGapsInsertedBegin() && !right)
1844 if (viewport.cursorMode)
1846 alignPanel.getSeqPanel().moveCursor(-size, 0);
1850 groupAdjustment = -size;
1854 if (groupAdjustment != 0)
1856 viewport.getSelectionGroup().setStartRes(
1857 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1858 viewport.getSelectionGroup().setEndRes(
1859 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1863 * just extend the last slide command if compatible; but not if in
1864 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1866 boolean appendHistoryItem = false;
1867 Deque<CommandI> historyList = viewport.getHistoryList();
1868 boolean inSplitFrame = getSplitViewContainer() != null;
1869 if (!inSplitFrame && historyList != null && historyList.size() > 0
1870 && historyList.peek() instanceof SlideSequencesCommand)
1872 appendHistoryItem = ssc.appendSlideCommand(
1873 (SlideSequencesCommand) historyList.peek());
1876 if (!appendHistoryItem)
1878 addHistoryItem(ssc);
1891 protected void copy_actionPerformed(ActionEvent e)
1893 if (viewport.getSelectionGroup() == null)
1897 // TODO: preserve the ordering of displayed alignment annotation in any
1898 // internal paste (particularly sequence associated annotation)
1899 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1900 String[] omitHidden = null;
1902 if (viewport.hasHiddenColumns())
1904 omitHidden = viewport.getViewAsString(true);
1907 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1908 seqs, omitHidden, null);
1910 StringSelection ss = new StringSelection(output);
1914 jalview.gui.Desktop.internalCopy = true;
1915 // Its really worth setting the clipboard contents
1916 // to empty before setting the large StringSelection!!
1917 Toolkit.getDefaultToolkit().getSystemClipboard()
1918 .setContents(new StringSelection(""), null);
1920 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1922 } catch (OutOfMemoryError er)
1924 new OOMWarning("copying region", er);
1928 HiddenColumns hiddenColumns = null;
1929 if (viewport.hasHiddenColumns())
1931 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1932 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1934 // create new HiddenColumns object with copy of hidden regions
1935 // between startRes and endRes, offset by startRes
1936 hiddenColumns = new HiddenColumns(
1937 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1938 hiddenCutoff, hiddenOffset);
1941 Desktop.jalviewClipboard = new Object[] { seqs,
1942 viewport.getAlignment().getDataset(), hiddenColumns };
1943 setStatus(MessageManager.formatMessage(
1944 "label.copied_sequences_to_clipboard", new Object[]
1945 { Integer.valueOf(seqs.length).toString() }));
1955 protected void pasteNew_actionPerformed(ActionEvent e)
1967 protected void pasteThis_actionPerformed(ActionEvent e)
1973 * Paste contents of Jalview clipboard
1975 * @param newAlignment
1976 * true to paste to a new alignment, otherwise add to this.
1978 void paste(boolean newAlignment)
1980 boolean externalPaste = true;
1983 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1984 Transferable contents = c.getContents(this);
1986 if (contents == null)
1995 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1996 if (str.length() < 1)
2001 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2003 } catch (OutOfMemoryError er)
2005 new OOMWarning("Out of memory pasting sequences!!", er);
2009 SequenceI[] sequences;
2010 boolean annotationAdded = false;
2011 AlignmentI alignment = null;
2013 if (Desktop.jalviewClipboard != null)
2015 // The clipboard was filled from within Jalview, we must use the
2017 // And dataset from the copied alignment
2018 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2019 // be doubly sure that we create *new* sequence objects.
2020 sequences = new SequenceI[newseq.length];
2021 for (int i = 0; i < newseq.length; i++)
2023 sequences[i] = new Sequence(newseq[i]);
2025 alignment = new Alignment(sequences);
2026 externalPaste = false;
2030 // parse the clipboard as an alignment.
2031 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2033 sequences = alignment.getSequencesArray();
2037 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2043 if (Desktop.jalviewClipboard != null)
2045 // dataset is inherited
2046 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2050 // new dataset is constructed
2051 alignment.setDataset(null);
2053 alwidth = alignment.getWidth() + 1;
2057 AlignmentI pastedal = alignment; // preserve pasted alignment object
2058 // Add pasted sequences and dataset into existing alignment.
2059 alignment = viewport.getAlignment();
2060 alwidth = alignment.getWidth() + 1;
2061 // decide if we need to import sequences from an existing dataset
2062 boolean importDs = Desktop.jalviewClipboard != null
2063 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2064 // importDs==true instructs us to copy over new dataset sequences from
2065 // an existing alignment
2066 Vector newDs = (importDs) ? new Vector() : null; // used to create
2067 // minimum dataset set
2069 for (int i = 0; i < sequences.length; i++)
2073 newDs.addElement(null);
2075 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2077 if (importDs && ds != null)
2079 if (!newDs.contains(ds))
2081 newDs.setElementAt(ds, i);
2082 ds = new Sequence(ds);
2083 // update with new dataset sequence
2084 sequences[i].setDatasetSequence(ds);
2088 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2093 // copy and derive new dataset sequence
2094 sequences[i] = sequences[i].deriveSequence();
2095 alignment.getDataset()
2096 .addSequence(sequences[i].getDatasetSequence());
2097 // TODO: avoid creation of duplicate dataset sequences with a
2098 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2100 alignment.addSequence(sequences[i]); // merges dataset
2104 newDs.clear(); // tidy up
2106 if (alignment.getAlignmentAnnotation() != null)
2108 for (AlignmentAnnotation alan : alignment
2109 .getAlignmentAnnotation())
2111 if (alan.graphGroup > fgroup)
2113 fgroup = alan.graphGroup;
2117 if (pastedal.getAlignmentAnnotation() != null)
2119 // Add any annotation attached to alignment.
2120 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2121 for (int i = 0; i < alann.length; i++)
2123 annotationAdded = true;
2124 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2126 AlignmentAnnotation newann = new AlignmentAnnotation(
2128 if (newann.graphGroup > -1)
2130 if (newGraphGroups.size() <= newann.graphGroup
2131 || newGraphGroups.get(newann.graphGroup) == null)
2133 for (int q = newGraphGroups
2134 .size(); q <= newann.graphGroup; q++)
2136 newGraphGroups.add(q, null);
2138 newGraphGroups.set(newann.graphGroup,
2139 new Integer(++fgroup));
2141 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2145 newann.padAnnotation(alwidth);
2146 alignment.addAnnotation(newann);
2156 addHistoryItem(new EditCommand(
2157 MessageManager.getString("label.add_sequences"),
2158 Action.PASTE, sequences, 0, alignment.getWidth(),
2161 // Add any annotations attached to sequences
2162 for (int i = 0; i < sequences.length; i++)
2164 if (sequences[i].getAnnotation() != null)
2166 AlignmentAnnotation newann;
2167 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2169 annotationAdded = true;
2170 newann = sequences[i].getAnnotation()[a];
2171 newann.adjustForAlignment();
2172 newann.padAnnotation(alwidth);
2173 if (newann.graphGroup > -1)
2175 if (newann.graphGroup > -1)
2177 if (newGraphGroups.size() <= newann.graphGroup
2178 || newGraphGroups.get(newann.graphGroup) == null)
2180 for (int q = newGraphGroups
2181 .size(); q <= newann.graphGroup; q++)
2183 newGraphGroups.add(q, null);
2185 newGraphGroups.set(newann.graphGroup,
2186 new Integer(++fgroup));
2188 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2192 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2196 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2204 // propagate alignment changed.
2205 viewport.getRanges().setEndSeq(alignment.getHeight());
2206 if (annotationAdded)
2208 // Duplicate sequence annotation in all views.
2209 AlignmentI[] alview = this.getViewAlignments();
2210 for (int i = 0; i < sequences.length; i++)
2212 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2217 for (int avnum = 0; avnum < alview.length; avnum++)
2219 if (alview[avnum] != alignment)
2221 // duplicate in a view other than the one with input focus
2222 int avwidth = alview[avnum].getWidth() + 1;
2223 // this relies on sann being preserved after we
2224 // modify the sequence's annotation array for each duplication
2225 for (int a = 0; a < sann.length; a++)
2227 AlignmentAnnotation newann = new AlignmentAnnotation(
2229 sequences[i].addAlignmentAnnotation(newann);
2230 newann.padAnnotation(avwidth);
2231 alview[avnum].addAnnotation(newann); // annotation was
2232 // duplicated earlier
2233 // TODO JAL-1145 graphGroups are not updated for sequence
2234 // annotation added to several views. This may cause
2236 alview[avnum].setAnnotationIndex(newann, a);
2241 buildSortByAnnotationScoresMenu();
2243 viewport.firePropertyChange("alignment", null,
2244 alignment.getSequences());
2245 if (alignPanels != null)
2247 for (AlignmentPanel ap : alignPanels)
2249 ap.validateAnnotationDimensions(false);
2254 alignPanel.validateAnnotationDimensions(false);
2260 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2262 String newtitle = new String("Copied sequences");
2264 if (Desktop.jalviewClipboard != null
2265 && Desktop.jalviewClipboard[2] != null)
2267 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2268 af.viewport.setHiddenColumns(hc);
2271 // >>>This is a fix for the moment, until a better solution is
2273 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2274 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2275 .getFeatureRenderer());
2277 // TODO: maintain provenance of an alignment, rather than just make the
2278 // title a concatenation of operations.
2281 if (title.startsWith("Copied sequences"))
2287 newtitle = newtitle.concat("- from " + title);
2292 newtitle = new String("Pasted sequences");
2295 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2300 } catch (Exception ex)
2302 ex.printStackTrace();
2303 System.out.println("Exception whilst pasting: " + ex);
2304 // could be anything being pasted in here
2310 protected void expand_newalign(ActionEvent e)
2314 AlignmentI alignment = AlignmentUtils
2315 .expandContext(getViewport().getAlignment(), -1);
2316 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2318 String newtitle = new String("Flanking alignment");
2320 if (Desktop.jalviewClipboard != null
2321 && Desktop.jalviewClipboard[2] != null)
2323 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2324 af.viewport.setHiddenColumns(hc);
2327 // >>>This is a fix for the moment, until a better solution is
2329 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2330 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2331 .getFeatureRenderer());
2333 // TODO: maintain provenance of an alignment, rather than just make the
2334 // title a concatenation of operations.
2336 if (title.startsWith("Copied sequences"))
2342 newtitle = newtitle.concat("- from " + title);
2346 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2348 } catch (Exception ex)
2350 ex.printStackTrace();
2351 System.out.println("Exception whilst pasting: " + ex);
2352 // could be anything being pasted in here
2353 } catch (OutOfMemoryError oom)
2355 new OOMWarning("Viewing flanking region of alignment", oom);
2366 protected void cut_actionPerformed(ActionEvent e)
2368 copy_actionPerformed(null);
2369 delete_actionPerformed(null);
2379 protected void delete_actionPerformed(ActionEvent evt)
2382 SequenceGroup sg = viewport.getSelectionGroup();
2389 * If the cut affects all sequences, warn, remove highlighted columns
2391 if (sg.getSize() == viewport.getAlignment().getHeight())
2393 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2394 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2395 if (isEntireAlignWidth)
2397 int confirm = JvOptionPane.showConfirmDialog(this,
2398 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2399 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2400 JvOptionPane.OK_CANCEL_OPTION);
2402 if (confirm == JvOptionPane.CANCEL_OPTION
2403 || confirm == JvOptionPane.CLOSED_OPTION)
2408 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2409 sg.getEndRes() + 1);
2411 SequenceI[] cut = sg.getSequences()
2412 .toArray(new SequenceI[sg.getSize()]);
2414 addHistoryItem(new EditCommand(
2415 MessageManager.getString("label.cut_sequences"), Action.CUT,
2416 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2417 viewport.getAlignment()));
2419 viewport.setSelectionGroup(null);
2420 viewport.sendSelection();
2421 viewport.getAlignment().deleteGroup(sg);
2423 viewport.firePropertyChange("alignment", null,
2424 viewport.getAlignment().getSequences());
2425 if (viewport.getAlignment().getHeight() < 1)
2429 this.setClosed(true);
2430 } catch (Exception ex)
2443 protected void deleteGroups_actionPerformed(ActionEvent e)
2445 if (avc.deleteGroups())
2447 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2448 alignPanel.updateAnnotation();
2449 alignPanel.paintAlignment(true, true);
2460 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2462 SequenceGroup sg = new SequenceGroup();
2464 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2466 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2469 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2470 viewport.setSelectionGroup(sg);
2471 viewport.sendSelection();
2472 // JAL-2034 - should delegate to
2473 // alignPanel to decide if overview needs
2475 alignPanel.paintAlignment(false, false);
2476 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2486 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2488 if (viewport.cursorMode)
2490 alignPanel.getSeqPanel().keyboardNo1 = null;
2491 alignPanel.getSeqPanel().keyboardNo2 = null;
2493 viewport.setSelectionGroup(null);
2494 viewport.getColumnSelection().clear();
2495 viewport.setSelectionGroup(null);
2496 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2497 // JAL-2034 - should delegate to
2498 // alignPanel to decide if overview needs
2500 alignPanel.paintAlignment(false, false);
2501 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2502 viewport.sendSelection();
2512 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2514 SequenceGroup sg = viewport.getSelectionGroup();
2518 selectAllSequenceMenuItem_actionPerformed(null);
2523 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2525 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2527 // JAL-2034 - should delegate to
2528 // alignPanel to decide if overview needs
2531 alignPanel.paintAlignment(true, false);
2532 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2533 viewport.sendSelection();
2537 public void invertColSel_actionPerformed(ActionEvent e)
2539 viewport.invertColumnSelection();
2540 alignPanel.paintAlignment(true, false);
2541 viewport.sendSelection();
2551 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2553 trimAlignment(true);
2563 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2565 trimAlignment(false);
2568 void trimAlignment(boolean trimLeft)
2570 ColumnSelection colSel = viewport.getColumnSelection();
2573 if (!colSel.isEmpty())
2577 column = colSel.getMin();
2581 column = colSel.getMax();
2585 if (viewport.getSelectionGroup() != null)
2587 seqs = viewport.getSelectionGroup()
2588 .getSequencesAsArray(viewport.getHiddenRepSequences());
2592 seqs = viewport.getAlignment().getSequencesArray();
2595 TrimRegionCommand trimRegion;
2598 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2599 column, viewport.getAlignment());
2600 viewport.getRanges().setStartRes(0);
2604 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2605 column, viewport.getAlignment());
2608 setStatus(MessageManager
2609 .formatMessage("label.removed_columns", new String[]
2610 { Integer.valueOf(trimRegion.getSize()).toString() }));
2612 addHistoryItem(trimRegion);
2614 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2616 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2617 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2619 viewport.getAlignment().deleteGroup(sg);
2623 viewport.firePropertyChange("alignment", null,
2624 viewport.getAlignment().getSequences());
2635 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2637 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2640 if (viewport.getSelectionGroup() != null)
2642 seqs = viewport.getSelectionGroup()
2643 .getSequencesAsArray(viewport.getHiddenRepSequences());
2644 start = viewport.getSelectionGroup().getStartRes();
2645 end = viewport.getSelectionGroup().getEndRes();
2649 seqs = viewport.getAlignment().getSequencesArray();
2652 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2653 "Remove Gapped Columns", seqs, start, end,
2654 viewport.getAlignment());
2656 addHistoryItem(removeGapCols);
2658 setStatus(MessageManager
2659 .formatMessage("label.removed_empty_columns", new Object[]
2660 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2662 // This is to maintain viewport position on first residue
2663 // of first sequence
2664 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2665 ViewportRanges ranges = viewport.getRanges();
2666 int startRes = seq.findPosition(ranges.getStartRes());
2667 // ShiftList shifts;
2668 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2669 // edit.alColumnChanges=shifts.getInverse();
2670 // if (viewport.hasHiddenColumns)
2671 // viewport.getColumnSelection().compensateForEdits(shifts);
2672 ranges.setStartRes(seq.findIndex(startRes) - 1);
2673 viewport.firePropertyChange("alignment", null,
2674 viewport.getAlignment().getSequences());
2685 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2687 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2690 if (viewport.getSelectionGroup() != null)
2692 seqs = viewport.getSelectionGroup()
2693 .getSequencesAsArray(viewport.getHiddenRepSequences());
2694 start = viewport.getSelectionGroup().getStartRes();
2695 end = viewport.getSelectionGroup().getEndRes();
2699 seqs = viewport.getAlignment().getSequencesArray();
2702 // This is to maintain viewport position on first residue
2703 // of first sequence
2704 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2705 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2707 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2708 viewport.getAlignment()));
2710 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2712 viewport.firePropertyChange("alignment", null,
2713 viewport.getAlignment().getSequences());
2724 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2726 viewport.setPadGaps(padGapsMenuitem.isSelected());
2727 viewport.firePropertyChange("alignment", null,
2728 viewport.getAlignment().getSequences());
2738 public void findMenuItem_actionPerformed(ActionEvent e)
2744 * Create a new view of the current alignment.
2747 public void newView_actionPerformed(ActionEvent e)
2749 newView(null, true);
2753 * Creates and shows a new view of the current alignment.
2756 * title of newly created view; if null, one will be generated
2757 * @param copyAnnotation
2758 * if true then duplicate all annnotation, groups and settings
2759 * @return new alignment panel, already displayed.
2761 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2764 * Create a new AlignmentPanel (with its own, new Viewport)
2766 AlignmentPanel newap = new jalview.project.Jalview2XML()
2767 .copyAlignPanel(alignPanel);
2768 if (!copyAnnotation)
2771 * remove all groups and annotation except for the automatic stuff
2773 newap.av.getAlignment().deleteAllGroups();
2774 newap.av.getAlignment().deleteAllAnnotations(false);
2777 newap.av.setGatherViewsHere(false);
2779 if (viewport.getViewName() == null)
2781 viewport.setViewName(MessageManager
2782 .getString("label.view_name_original"));
2786 * Views share the same edits undo and redo stacks
2788 newap.av.setHistoryList(viewport.getHistoryList());
2789 newap.av.setRedoList(viewport.getRedoList());
2792 * Views share the same mappings; need to deregister any new mappings
2793 * created by copyAlignPanel, and register the new reference to the shared
2796 newap.av.replaceMappings(viewport.getAlignment());
2799 * start up cDNA consensus (if applicable) now mappings are in place
2801 if (newap.av.initComplementConsensus())
2803 newap.refresh(true); // adjust layout of annotations
2806 newap.av.setViewName(getNewViewName(viewTitle));
2808 addAlignmentPanel(newap, true);
2809 newap.alignmentChanged();
2811 if (alignPanels.size() == 2)
2813 viewport.setGatherViewsHere(true);
2815 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2820 * Make a new name for the view, ensuring it is unique within the current
2821 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2822 * these now use viewId. Unique view names are still desirable for usability.)
2827 protected String getNewViewName(String viewTitle)
2829 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2830 boolean addFirstIndex = false;
2831 if (viewTitle == null || viewTitle.trim().length() == 0)
2833 viewTitle = MessageManager.getString("action.view");
2834 addFirstIndex = true;
2838 index = 1;// we count from 1 if given a specific name
2840 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2842 List<Component> comps = PaintRefresher.components
2843 .get(viewport.getSequenceSetId());
2845 List<String> existingNames = getExistingViewNames(comps);
2847 while (existingNames.contains(newViewName))
2849 newViewName = viewTitle + " " + (++index);
2855 * Returns a list of distinct view names found in the given list of
2856 * components. View names are held on the viewport of an AlignmentPanel.
2861 protected List<String> getExistingViewNames(List<Component> comps)
2863 List<String> existingNames = new ArrayList<>();
2864 for (Component comp : comps)
2866 if (comp instanceof AlignmentPanel)
2868 AlignmentPanel ap = (AlignmentPanel) comp;
2869 if (!existingNames.contains(ap.av.getViewName()))
2871 existingNames.add(ap.av.getViewName());
2875 return existingNames;
2879 * Explode tabbed views into separate windows.
2882 public void expandViews_actionPerformed(ActionEvent e)
2884 Desktop.explodeViews(this);
2888 * Gather views in separate windows back into a tabbed presentation.
2891 public void gatherViews_actionPerformed(ActionEvent e)
2893 Desktop.instance.gatherViews(this);
2903 public void font_actionPerformed(ActionEvent e)
2905 new FontChooser(alignPanel);
2915 protected void seqLimit_actionPerformed(ActionEvent e)
2917 viewport.setShowJVSuffix(seqLimits.isSelected());
2919 alignPanel.getIdPanel().getIdCanvas()
2920 .setPreferredSize(alignPanel.calculateIdWidth());
2921 alignPanel.paintAlignment(true, false);
2925 public void idRightAlign_actionPerformed(ActionEvent e)
2927 viewport.setRightAlignIds(idRightAlign.isSelected());
2928 alignPanel.paintAlignment(false, false);
2932 public void centreColumnLabels_actionPerformed(ActionEvent e)
2934 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2935 alignPanel.paintAlignment(false, false);
2941 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2944 protected void followHighlight_actionPerformed()
2947 * Set the 'follow' flag on the Viewport (and scroll to position if now
2950 final boolean state = this.followHighlightMenuItem.getState();
2951 viewport.setFollowHighlight(state);
2954 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2965 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2967 viewport.setColourText(colourTextMenuItem.isSelected());
2968 alignPanel.paintAlignment(false, false);
2978 public void wrapMenuItem_actionPerformed(ActionEvent e)
2980 scaleAbove.setVisible(wrapMenuItem.isSelected());
2981 scaleLeft.setVisible(wrapMenuItem.isSelected());
2982 scaleRight.setVisible(wrapMenuItem.isSelected());
2983 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2984 alignPanel.updateLayout();
2988 public void showAllSeqs_actionPerformed(ActionEvent e)
2990 viewport.showAllHiddenSeqs();
2994 public void showAllColumns_actionPerformed(ActionEvent e)
2996 viewport.showAllHiddenColumns();
2997 alignPanel.paintAlignment(true, true);
2998 viewport.sendSelection();
3002 public void hideSelSequences_actionPerformed(ActionEvent e)
3004 viewport.hideAllSelectedSeqs();
3008 * called by key handler and the hide all/show all menu items
3013 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3016 boolean hide = false;
3017 SequenceGroup sg = viewport.getSelectionGroup();
3018 if (!toggleSeqs && !toggleCols)
3020 // Hide everything by the current selection - this is a hack - we do the
3021 // invert and then hide
3022 // first check that there will be visible columns after the invert.
3023 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3024 && sg.getStartRes() <= sg.getEndRes()))
3026 // now invert the sequence set, if required - empty selection implies
3027 // that no hiding is required.
3030 invertSequenceMenuItem_actionPerformed(null);
3031 sg = viewport.getSelectionGroup();
3035 viewport.expandColSelection(sg, true);
3036 // finally invert the column selection and get the new sequence
3038 invertColSel_actionPerformed(null);
3045 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3047 hideSelSequences_actionPerformed(null);
3050 else if (!(toggleCols && viewport.hasSelectedColumns()))
3052 showAllSeqs_actionPerformed(null);
3058 if (viewport.hasSelectedColumns())
3060 hideSelColumns_actionPerformed(null);
3063 viewport.setSelectionGroup(sg);
3068 showAllColumns_actionPerformed(null);
3077 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3078 * event.ActionEvent)
3081 public void hideAllButSelection_actionPerformed(ActionEvent e)
3083 toggleHiddenRegions(false, false);
3084 viewport.sendSelection();
3091 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3095 public void hideAllSelection_actionPerformed(ActionEvent e)
3097 SequenceGroup sg = viewport.getSelectionGroup();
3098 viewport.expandColSelection(sg, false);
3099 viewport.hideAllSelectedSeqs();
3100 viewport.hideSelectedColumns();
3101 alignPanel.paintAlignment(true, true);
3102 viewport.sendSelection();
3109 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3113 public void showAllhidden_actionPerformed(ActionEvent e)
3115 viewport.showAllHiddenColumns();
3116 viewport.showAllHiddenSeqs();
3117 alignPanel.paintAlignment(true, true);
3118 viewport.sendSelection();
3122 public void hideSelColumns_actionPerformed(ActionEvent e)
3124 viewport.hideSelectedColumns();
3125 alignPanel.paintAlignment(true, true);
3126 viewport.sendSelection();
3130 public void hiddenMarkers_actionPerformed(ActionEvent e)
3132 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3143 protected void scaleAbove_actionPerformed(ActionEvent e)
3145 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3146 // TODO: do we actually need to update overview for scale above change ?
3147 alignPanel.paintAlignment(true, false);
3157 protected void scaleLeft_actionPerformed(ActionEvent e)
3159 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3160 alignPanel.paintAlignment(true, false);
3170 protected void scaleRight_actionPerformed(ActionEvent e)
3172 viewport.setScaleRightWrapped(scaleRight.isSelected());
3173 alignPanel.paintAlignment(true, false);
3183 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3185 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3186 alignPanel.paintAlignment(false, false);
3196 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3198 viewport.setShowText(viewTextMenuItem.isSelected());
3199 alignPanel.paintAlignment(false, false);
3209 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3211 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3212 alignPanel.paintAlignment(false, false);
3215 public FeatureSettings featureSettings;
3218 public FeatureSettingsControllerI getFeatureSettingsUI()
3220 return featureSettings;
3224 public void featureSettings_actionPerformed(ActionEvent e)
3226 if (featureSettings != null)
3228 featureSettings.close();
3229 featureSettings = null;
3231 if (!showSeqFeatures.isSelected())
3233 // make sure features are actually displayed
3234 showSeqFeatures.setSelected(true);
3235 showSeqFeatures_actionPerformed(null);
3237 featureSettings = new FeatureSettings(this);
3241 * Set or clear 'Show Sequence Features'
3247 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3249 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3250 alignPanel.paintAlignment(true, true);
3254 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3255 * the annotations panel as a whole.
3257 * The options to show/hide all annotations should be enabled when the panel
3258 * is shown, and disabled when the panel is hidden.
3263 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3265 final boolean setVisible = annotationPanelMenuItem.isSelected();
3266 viewport.setShowAnnotation(setVisible);
3267 this.showAllSeqAnnotations.setEnabled(setVisible);
3268 this.hideAllSeqAnnotations.setEnabled(setVisible);
3269 this.showAllAlAnnotations.setEnabled(setVisible);
3270 this.hideAllAlAnnotations.setEnabled(setVisible);
3271 alignPanel.updateLayout();
3275 public void alignmentProperties()
3278 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3281 String content = MessageManager.formatMessage("label.html_content",
3283 { contents.toString() });
3288 JLabel textLabel = new JLabel();
3289 textLabel.setText(content);
3290 textLabel.setBackground(Color.WHITE);
3292 pane = new JPanel(new BorderLayout());
3293 ((JPanel) pane).setOpaque(true);
3294 pane.setBackground(Color.WHITE);
3295 ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3299 JEditorPane editPane = new JEditorPane("text/html", "");
3300 editPane.setEditable(false);
3301 editPane.setText(content);
3305 JInternalFrame frame = new JInternalFrame();
3307 frame.getContentPane().add(new JScrollPane(pane));
3309 Desktop.addInternalFrame(frame, MessageManager
3310 .formatMessage("label.alignment_properties", new Object[]
3311 { getTitle() }), 500, 400);
3321 public void overviewMenuItem_actionPerformed(ActionEvent e)
3323 if (alignPanel.overviewPanel != null)
3328 JInternalFrame frame = new JInternalFrame();
3329 final OverviewPanel overview = new OverviewPanel(alignPanel);
3330 frame.setContentPane(overview);
3331 Desktop.addInternalFrame(frame, MessageManager
3332 .formatMessage("label.overview_params", new Object[]
3333 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3336 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3337 frame.addInternalFrameListener(
3338 new javax.swing.event.InternalFrameAdapter()
3341 public void internalFrameClosed(
3342 javax.swing.event.InternalFrameEvent evt)
3345 alignPanel.setOverviewPanel(null);
3348 if (getKeyListeners().length > 0)
3350 frame.addKeyListener(getKeyListeners()[0]);
3353 alignPanel.setOverviewPanel(overview);
3357 public void textColour_actionPerformed()
3359 new TextColourChooser().chooseColour(alignPanel, null);
3363 * public void covariationColour_actionPerformed() {
3365 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3369 public void annotationColour_actionPerformed()
3371 new AnnotationColourChooser(viewport, alignPanel);
3375 public void annotationColumn_actionPerformed(ActionEvent e)
3377 new AnnotationColumnChooser(viewport, alignPanel);
3381 * Action on the user checking or unchecking the option to apply the selected
3382 * colour scheme to all groups. If unchecked, groups may have their own
3383 * independent colour schemes.
3388 public void applyToAllGroups_actionPerformed(boolean selected)
3390 viewport.setColourAppliesToAllGroups(selected);
3394 * Action on user selecting a colour from the colour menu
3397 * the name (not the menu item label!) of the colour scheme
3400 public void changeColour_actionPerformed(String name)
3403 * 'User Defined' opens a panel to configure or load a
3404 * user-defined colour scheme
3406 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3408 new UserDefinedColours(alignPanel);
3413 * otherwise set the chosen colour scheme (or null for 'None')
3415 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3416 viewport.getAlignment(), viewport.getHiddenRepSequences());
3421 * Actions on setting or changing the alignment colour scheme
3426 public void changeColour(ColourSchemeI cs)
3428 // TODO: pull up to controller method
3429 ColourMenuHelper.setColourSelected(colourMenu, cs);
3431 viewport.setGlobalColourScheme(cs);
3433 alignPanel.paintAlignment(true, true);
3437 * Show the PID threshold slider panel
3440 protected void modifyPID_actionPerformed()
3442 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3443 alignPanel.getViewName());
3444 SliderPanel.showPIDSlider();
3448 * Show the Conservation slider panel
3451 protected void modifyConservation_actionPerformed()
3453 SliderPanel.setConservationSlider(alignPanel,
3454 viewport.getResidueShading(), alignPanel.getViewName());
3455 SliderPanel.showConservationSlider();
3459 * Action on selecting or deselecting (Colour) By Conservation
3462 public void conservationMenuItem_actionPerformed(boolean selected)
3464 modifyConservation.setEnabled(selected);
3465 viewport.setConservationSelected(selected);
3466 viewport.getResidueShading().setConservationApplied(selected);
3468 changeColour(viewport.getGlobalColourScheme());
3471 modifyConservation_actionPerformed();
3475 SliderPanel.hideConservationSlider();
3480 * Action on selecting or deselecting (Colour) Above PID Threshold
3483 public void abovePIDThreshold_actionPerformed(boolean selected)
3485 modifyPID.setEnabled(selected);
3486 viewport.setAbovePIDThreshold(selected);
3489 viewport.getResidueShading().setThreshold(0,
3490 viewport.isIgnoreGapsConsensus());
3493 changeColour(viewport.getGlobalColourScheme());
3496 modifyPID_actionPerformed();
3500 SliderPanel.hidePIDSlider();
3511 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3513 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3514 AlignmentSorter.sortByPID(viewport.getAlignment(),
3515 viewport.getAlignment().getSequenceAt(0));
3516 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3517 viewport.getAlignment()));
3518 alignPanel.paintAlignment(true, false);
3528 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3530 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3531 AlignmentSorter.sortByID(viewport.getAlignment());
3533 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3534 alignPanel.paintAlignment(true, false);
3544 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3546 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3547 AlignmentSorter.sortByLength(viewport.getAlignment());
3548 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3549 viewport.getAlignment()));
3550 alignPanel.paintAlignment(true, false);
3560 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3562 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3563 AlignmentSorter.sortByGroup(viewport.getAlignment());
3564 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3565 viewport.getAlignment()));
3567 alignPanel.paintAlignment(true, false);
3577 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3579 new RedundancyPanel(alignPanel, this);
3589 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3591 if ((viewport.getSelectionGroup() == null)
3592 || (viewport.getSelectionGroup().getSize() < 2))
3594 JvOptionPane.showInternalMessageDialog(this,
3595 MessageManager.getString(
3596 "label.you_must_select_least_two_sequences"),
3597 MessageManager.getString("label.invalid_selection"),
3598 JvOptionPane.WARNING_MESSAGE);
3602 JInternalFrame frame = new JInternalFrame();
3603 frame.setContentPane(new PairwiseAlignPanel(viewport));
3604 Desktop.addInternalFrame(frame,
3605 MessageManager.getString("action.pairwise_alignment"), 600,
3611 public void autoCalculate_actionPerformed(ActionEvent e)
3613 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3614 if (viewport.autoCalculateConsensus)
3616 viewport.firePropertyChange("alignment", null,
3617 viewport.getAlignment().getSequences());
3622 public void sortByTreeOption_actionPerformed(ActionEvent e)
3624 viewport.sortByTree = sortByTree.isSelected();
3628 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3630 viewport.followSelection = listenToViewSelections.isSelected();
3634 * Constructs a tree panel and adds it to the desktop
3637 * tree type (NJ or AV)
3639 * name of score model used to compute the tree
3641 * parameters for the distance or similarity calculation
3643 void newTreePanel(String type, String modelName,
3644 SimilarityParamsI options)
3646 String frameTitle = "";
3649 boolean onSelection = false;
3650 if (viewport.getSelectionGroup() != null
3651 && viewport.getSelectionGroup().getSize() > 0)
3653 SequenceGroup sg = viewport.getSelectionGroup();
3655 /* Decide if the selection is a column region */
3656 for (SequenceI _s : sg.getSequences())
3658 if (_s.getLength() < sg.getEndRes())
3660 JvOptionPane.showMessageDialog(Desktop.desktop,
3661 MessageManager.getString(
3662 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3663 MessageManager.getString(
3664 "label.sequences_selection_not_aligned"),
3665 JvOptionPane.WARNING_MESSAGE);
3674 if (viewport.getAlignment().getHeight() < 2)
3680 tp = new TreePanel(alignPanel, type, modelName, options);
3681 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3683 frameTitle += " from ";
3685 if (viewport.getViewName() != null)
3687 frameTitle += viewport.getViewName() + " of ";
3690 frameTitle += this.title;
3692 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3703 public void addSortByOrderMenuItem(String title,
3704 final AlignmentOrder order)
3706 final JMenuItem item = new JMenuItem(MessageManager
3707 .formatMessage("action.by_title_param", new Object[]
3710 item.addActionListener(new java.awt.event.ActionListener()
3713 public void actionPerformed(ActionEvent e)
3715 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3717 // TODO: JBPNote - have to map order entries to curent SequenceI
3719 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3721 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3722 viewport.getAlignment()));
3724 alignPanel.paintAlignment(true, false);
3730 * Add a new sort by annotation score menu item
3733 * the menu to add the option to
3735 * the label used to retrieve scores for each sequence on the
3738 public void addSortByAnnotScoreMenuItem(JMenu sort,
3739 final String scoreLabel)
3741 final JMenuItem item = new JMenuItem(scoreLabel);
3743 item.addActionListener(new java.awt.event.ActionListener()
3746 public void actionPerformed(ActionEvent e)
3748 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3749 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3750 viewport.getAlignment());// ,viewport.getSelectionGroup());
3751 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3752 viewport.getAlignment()));
3753 alignPanel.paintAlignment(true, false);
3759 * last hash for alignment's annotation array - used to minimise cost of
3762 protected int _annotationScoreVectorHash;
3765 * search the alignment and rebuild the sort by annotation score submenu the
3766 * last alignment annotation vector hash is stored to minimize cost of
3767 * rebuilding in subsequence calls.
3771 public void buildSortByAnnotationScoresMenu()
3773 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3778 if (viewport.getAlignment().getAlignmentAnnotation()
3779 .hashCode() != _annotationScoreVectorHash)
3781 sortByAnnotScore.removeAll();
3782 // almost certainly a quicker way to do this - but we keep it simple
3783 Hashtable scoreSorts = new Hashtable();
3784 AlignmentAnnotation aann[];
3785 for (SequenceI sqa : viewport.getAlignment().getSequences())
3787 aann = sqa.getAnnotation();
3788 for (int i = 0; aann != null && i < aann.length; i++)
3790 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3792 scoreSorts.put(aann[i].label, aann[i].label);
3796 Enumeration labels = scoreSorts.keys();
3797 while (labels.hasMoreElements())
3799 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3800 (String) labels.nextElement());
3802 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3805 _annotationScoreVectorHash = viewport.getAlignment()
3806 .getAlignmentAnnotation().hashCode();
3811 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3812 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3813 * call. Listeners are added to remove the menu item when the treePanel is
3814 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3818 public void buildTreeSortMenu()
3820 sortByTreeMenu.removeAll();
3822 List<Component> comps = PaintRefresher.components
3823 .get(viewport.getSequenceSetId());
3824 List<TreePanel> treePanels = new ArrayList<>();
3825 for (Component comp : comps)
3827 if (comp instanceof TreePanel)
3829 treePanels.add((TreePanel) comp);
3833 if (treePanels.size() < 1)
3835 sortByTreeMenu.setVisible(false);
3839 sortByTreeMenu.setVisible(true);
3841 for (final TreePanel tp : treePanels)
3843 final JMenuItem item = new JMenuItem(tp.getTitle());
3844 item.addActionListener(new java.awt.event.ActionListener()
3847 public void actionPerformed(ActionEvent e)
3849 tp.sortByTree_actionPerformed();
3850 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3855 sortByTreeMenu.add(item);
3859 public boolean sortBy(AlignmentOrder alorder, String undoname)
3861 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3862 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3863 if (undoname != null)
3865 addHistoryItem(new OrderCommand(undoname, oldOrder,
3866 viewport.getAlignment()));
3868 alignPanel.paintAlignment(true, false);
3873 * Work out whether the whole set of sequences or just the selected set will
3874 * be submitted for multiple alignment.
3877 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3879 // Now, check we have enough sequences
3880 AlignmentView msa = null;
3882 if ((viewport.getSelectionGroup() != null)
3883 && (viewport.getSelectionGroup().getSize() > 1))
3885 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3886 // some common interface!
3888 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3889 * SequenceI[sz = seqs.getSize(false)];
3891 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3892 * seqs.getSequenceAt(i); }
3894 msa = viewport.getAlignmentView(true);
3896 else if (viewport.getSelectionGroup() != null
3897 && viewport.getSelectionGroup().getSize() == 1)
3899 int option = JvOptionPane.showConfirmDialog(this,
3900 MessageManager.getString("warn.oneseq_msainput_selection"),
3901 MessageManager.getString("label.invalid_selection"),
3902 JvOptionPane.OK_CANCEL_OPTION);
3903 if (option == JvOptionPane.OK_OPTION)
3905 msa = viewport.getAlignmentView(false);
3910 msa = viewport.getAlignmentView(false);
3916 * Decides what is submitted to a secondary structure prediction service: the
3917 * first sequence in the alignment, or in the current selection, or, if the
3918 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3919 * region or the whole alignment. (where the first sequence in the set is the
3920 * one that the prediction will be for).
3922 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3924 AlignmentView seqs = null;
3926 if ((viewport.getSelectionGroup() != null)
3927 && (viewport.getSelectionGroup().getSize() > 0))
3929 seqs = viewport.getAlignmentView(true);
3933 seqs = viewport.getAlignmentView(false);
3935 // limit sequences - JBPNote in future - could spawn multiple prediction
3937 // TODO: viewport.getAlignment().isAligned is a global state - the local
3938 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3939 if (!viewport.getAlignment().isAligned(false))
3941 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3942 // TODO: if seqs.getSequences().length>1 then should really have warned
3956 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3958 // Pick the tree file
3959 JalviewFileChooser chooser = new JalviewFileChooser(
3960 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3961 chooser.setFileView(new JalviewFileView());
3962 chooser.setDialogTitle(
3963 MessageManager.getString("label.select_newick_like_tree_file"));
3964 chooser.setToolTipText(
3965 MessageManager.getString("label.load_tree_file"));
3967 chooser.addResponse(0,new RunResponse(JalviewFileChooser.APPROVE_OPTION)
3972 String filePath = chooser.getSelectedFile().getPath();
3973 Cache.setProperty("LAST_DIRECTORY", filePath);
3974 NewickFile fin = null;
3977 fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
3978 DataSourceType.FILE));
3979 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3980 } catch (Exception ex)
3982 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3984 .getString("label.problem_reading_tree_file"),
3985 JvOptionPane.WARNING_MESSAGE);
3986 ex.printStackTrace();
3988 if (fin != null && fin.hasWarningMessage())
3990 JvOptionPane.showMessageDialog(Desktop.desktop,
3991 fin.getWarningMessage(),
3992 MessageManager.getString(
3993 "label.possible_problem_with_tree_file"),
3994 JvOptionPane.WARNING_MESSAGE);
3998 chooser.showOpenDialog(this);
4001 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4003 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4006 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4007 int h, int x, int y)
4009 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4013 * Add a treeviewer for the tree extracted from a Newick file object to the
4014 * current alignment view
4021 * Associated alignment input data (or null)
4030 * @return TreePanel handle
4032 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4033 AlignmentView input, int w, int h, int x, int y)
4035 TreePanel tp = null;
4041 if (nf.getTree() != null)
4043 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4049 tp.setLocation(x, y);
4052 Desktop.addInternalFrame(tp, treeTitle, w, h);
4054 } catch (Exception ex)
4056 ex.printStackTrace();
4062 private boolean buildingMenu = false;
4065 * Generates menu items and listener event actions for web service clients
4068 public void BuildWebServiceMenu()
4070 while (buildingMenu)
4074 System.err.println("Waiting for building menu to finish.");
4076 } catch (Exception e)
4080 final AlignFrame me = this;
4081 buildingMenu = true;
4082 new Thread(new Runnable()
4087 final List<JMenuItem> legacyItems = new ArrayList<>();
4090 // System.err.println("Building ws menu again "
4091 // + Thread.currentThread());
4092 // TODO: add support for context dependent disabling of services based
4094 // alignment and current selection
4095 // TODO: add additional serviceHandle parameter to specify abstract
4097 // class independently of AbstractName
4098 // TODO: add in rediscovery GUI function to restart discoverer
4099 // TODO: group services by location as well as function and/or
4101 // object broker mechanism.
4102 final Vector<JMenu> wsmenu = new Vector<>();
4103 final IProgressIndicator af = me;
4106 * do not i18n these strings - they are hard-coded in class
4107 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4108 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4110 final JMenu msawsmenu = new JMenu("Alignment");
4111 final JMenu secstrmenu = new JMenu(
4112 "Secondary Structure Prediction");
4113 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4114 final JMenu analymenu = new JMenu("Analysis");
4115 final JMenu dismenu = new JMenu("Protein Disorder");
4116 // JAL-940 - only show secondary structure prediction services from
4117 // the legacy server
4118 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4120 Discoverer.services != null && (Discoverer.services.size() > 0))
4122 // TODO: refactor to allow list of AbstractName/Handler bindings to
4124 // stored or retrieved from elsewhere
4125 // No MSAWS used any more:
4126 // Vector msaws = null; // (Vector)
4127 // Discoverer.services.get("MsaWS");
4128 Vector secstrpr = (Vector) Discoverer.services
4130 if (secstrpr != null)
4132 // Add any secondary structure prediction services
4133 for (int i = 0, j = secstrpr.size(); i < j; i++)
4135 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4137 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4138 .getServiceClient(sh);
4139 int p = secstrmenu.getItemCount();
4140 impl.attachWSMenuEntry(secstrmenu, me);
4141 int q = secstrmenu.getItemCount();
4142 for (int litm = p; litm < q; litm++)
4144 legacyItems.add(secstrmenu.getItem(litm));
4150 // Add all submenus in the order they should appear on the web
4152 wsmenu.add(msawsmenu);
4153 wsmenu.add(secstrmenu);
4154 wsmenu.add(dismenu);
4155 wsmenu.add(analymenu);
4156 // No search services yet
4157 // wsmenu.add(seqsrchmenu);
4159 javax.swing.SwingUtilities.invokeLater(new Runnable()
4166 webService.removeAll();
4167 // first, add discovered services onto the webservices menu
4168 if (wsmenu.size() > 0)
4170 for (int i = 0, j = wsmenu.size(); i < j; i++)
4172 webService.add(wsmenu.get(i));
4177 webService.add(me.webServiceNoServices);
4179 // TODO: move into separate menu builder class.
4180 boolean new_sspred = false;
4181 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4183 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4184 if (jws2servs != null)
4186 if (jws2servs.hasServices())
4188 jws2servs.attachWSMenuEntry(webService, me);
4189 for (Jws2Instance sv : jws2servs.getServices())
4191 if (sv.description.toLowerCase().contains("jpred"))
4193 for (JMenuItem jmi : legacyItems)
4195 jmi.setVisible(false);
4201 if (jws2servs.isRunning())
4203 JMenuItem tm = new JMenuItem(
4204 "Still discovering JABA Services");
4205 tm.setEnabled(false);
4210 build_urlServiceMenu(me.webService);
4211 build_fetchdbmenu(webService);
4212 for (JMenu item : wsmenu)
4214 if (item.getItemCount() == 0)
4216 item.setEnabled(false);
4220 item.setEnabled(true);
4223 } catch (Exception e)
4226 "Exception during web service menu building process.",
4231 } catch (Exception e)
4234 buildingMenu = false;
4241 * construct any groupURL type service menu entries.
4245 private void build_urlServiceMenu(JMenu webService)
4247 // TODO: remove this code when 2.7 is released
4248 // DEBUG - alignmentView
4250 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4251 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4253 * @Override public void actionPerformed(ActionEvent e) {
4254 * jalview.datamodel.AlignmentView
4255 * .testSelectionViews(af.viewport.getAlignment(),
4256 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4258 * }); webService.add(testAlView);
4260 // TODO: refactor to RestClient discoverer and merge menu entries for
4261 // rest-style services with other types of analysis/calculation service
4262 // SHmmr test client - still being implemented.
4263 // DEBUG - alignmentView
4265 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4268 client.attachWSMenuEntry(
4269 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4275 * Searches the alignment sequences for xRefs and builds the Show
4276 * Cross-References menu (formerly called Show Products), with database
4277 * sources for which cross-references are found (protein sources for a
4278 * nucleotide alignment and vice versa)
4280 * @return true if Show Cross-references menu should be enabled
4282 public boolean canShowProducts()
4284 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4285 AlignmentI dataset = viewport.getAlignment().getDataset();
4287 showProducts.removeAll();
4288 final boolean dna = viewport.getAlignment().isNucleotide();
4290 if (seqs == null || seqs.length == 0)
4292 // nothing to see here.
4296 boolean showp = false;
4299 List<String> ptypes = new CrossRef(seqs, dataset)
4300 .findXrefSourcesForSequences(dna);
4302 for (final String source : ptypes)
4305 final AlignFrame af = this;
4306 JMenuItem xtype = new JMenuItem(source);
4307 xtype.addActionListener(new ActionListener()
4310 public void actionPerformed(ActionEvent e)
4312 showProductsFor(af.viewport.getSequenceSelection(), dna,
4316 showProducts.add(xtype);
4318 showProducts.setVisible(showp);
4319 showProducts.setEnabled(showp);
4320 } catch (Exception e)
4323 "canShowProducts threw an exception - please report to help@jalview.org",
4331 * Finds and displays cross-references for the selected sequences (protein
4332 * products for nucleotide sequences, dna coding sequences for peptides).
4335 * the sequences to show cross-references for
4337 * true if from a nucleotide alignment (so showing proteins)
4339 * the database to show cross-references for
4341 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4342 final String source)
4344 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4349 * Construct and display a new frame containing the translation of this
4350 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4353 public void showTranslation_actionPerformed(ActionEvent e)
4355 AlignmentI al = null;
4358 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4360 al = dna.translateCdna();
4361 } catch (Exception ex)
4363 jalview.bin.Cache.log.error(
4364 "Exception during translation. Please report this !", ex);
4365 final String msg = MessageManager.getString(
4366 "label.error_when_translating_sequences_submit_bug_report");
4367 final String errorTitle = MessageManager
4368 .getString("label.implementation_error")
4369 + MessageManager.getString("label.translation_failed");
4370 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4371 JvOptionPane.ERROR_MESSAGE);
4374 if (al == null || al.getHeight() == 0)
4376 final String msg = MessageManager.getString(
4377 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4378 final String errorTitle = MessageManager
4379 .getString("label.translation_failed");
4380 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4381 JvOptionPane.WARNING_MESSAGE);
4385 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4386 af.setFileFormat(this.currentFileFormat);
4387 final String newTitle = MessageManager
4388 .formatMessage("label.translation_of_params", new Object[]
4389 { this.getTitle() });
4390 af.setTitle(newTitle);
4391 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4393 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4394 viewport.openSplitFrame(af, new Alignment(seqs));
4398 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4405 * Set the file format
4409 public void setFileFormat(FileFormatI format)
4411 this.currentFileFormat = format;
4415 * Try to load a features file onto the alignment.
4418 * contents or path to retrieve file or a File object
4420 * access mode of file (see jalview.io.AlignFile)
4421 * @return true if features file was parsed correctly.
4423 public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4426 return avc.parseFeaturesFile(file, sourceType,
4427 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4432 public void refreshFeatureUI(boolean enableIfNecessary)
4434 // note - currently this is only still here rather than in the controller
4435 // because of the featureSettings hard reference that is yet to be
4437 if (enableIfNecessary)
4439 viewport.setShowSequenceFeatures(true);
4440 showSeqFeatures.setSelected(true);
4446 public void dragEnter(DropTargetDragEvent evt)
4451 public void dragExit(DropTargetEvent evt)
4456 public void dragOver(DropTargetDragEvent evt)
4461 public void dropActionChanged(DropTargetDragEvent evt)
4466 public void drop(DropTargetDropEvent evt)
4468 // JAL-1552 - acceptDrop required before getTransferable call for
4469 // Java's Transferable for native dnd
4470 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4471 Transferable t = evt.getTransferable();
4473 final AlignFrame thisaf = this;
4474 final List<Object> files = new ArrayList<>();
4475 List<DataSourceType> protocols = new ArrayList<>();
4479 Desktop.transferFromDropTarget(files, protocols, evt, t);
4480 } catch (Exception e)
4482 e.printStackTrace();
4486 new Thread(new Runnable()
4493 // check to see if any of these files have names matching sequences
4496 SequenceIdMatcher idm = new SequenceIdMatcher(
4497 viewport.getAlignment().getSequencesArray());
4499 * Object[] { String,SequenceI}
4501 ArrayList<Object[]> filesmatched = new ArrayList<>();
4502 ArrayList<Object> filesnotmatched = new ArrayList<>();
4503 for (int i = 0; i < files.size(); i++)
4506 Object file = files.get(i);
4507 String fileName = file.toString();
4509 DataSourceType protocol = (file instanceof File
4510 ? DataSourceType.FILE
4511 : FormatAdapter.checkProtocol(fileName));
4512 if (protocol == DataSourceType.FILE)
4514 File fl = (file instanceof File ? (File) file
4515 : new File(fileName));
4516 pdbfn = fl.getName();
4518 else if (protocol == DataSourceType.URL)
4520 URL url = new URL(fileName);
4521 pdbfn = url.getFile();
4523 if (pdbfn.length() > 0)
4525 // attempt to find a match in the alignment
4526 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4527 int l = 0, c = pdbfn.indexOf(".");
4528 while (mtch == null && c != -1)
4533 } while ((c = pdbfn.indexOf(".", l)) > l);
4536 pdbfn = pdbfn.substring(0, l);
4538 mtch = idm.findAllIdMatches(pdbfn);
4545 type = new IdentifyFile().identify(file, protocol);
4546 } catch (Exception ex)
4550 if (type != null && type.isStructureFile())
4552 filesmatched.add(new Object[] { file, protocol, mtch });
4556 // File wasn't named like one of the sequences or wasn't a PDB
4558 filesnotmatched.add(file);
4562 if (filesmatched.size() > 0)
4564 boolean autoAssociate = Cache
4565 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4568 String msg = MessageManager.formatMessage(
4569 "label.automatically_associate_structure_files_with_sequences_same_name",
4571 { Integer.valueOf(filesmatched.size())
4573 String ttl = MessageManager.getString(
4574 "label.automatically_associate_structure_files_by_name");
4575 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4576 ttl, JvOptionPane.YES_NO_OPTION);
4577 autoAssociate = choice == JvOptionPane.YES_OPTION;
4581 for (Object[] fm : filesmatched)
4583 // try and associate
4584 // TODO: may want to set a standard ID naming formalism for
4585 // associating PDB files which have no IDs.
4586 for (SequenceI toassoc : (SequenceI[]) fm[2])
4588 PDBEntry pe = new AssociatePdbFileWithSeq()
4589 .associatePdbWithSeq(fm[0].toString(),
4590 (DataSourceType) fm[1], toassoc, false,
4594 System.err.println("Associated file : "
4595 + (fm[0].toString()) + " with "
4596 + toassoc.getDisplayId(true));
4600 // TODO: do we need to update overview ? only if features are
4602 alignPanel.paintAlignment(true, false);
4608 * add declined structures as sequences
4610 for (Object[] o : filesmatched)
4612 filesnotmatched.add(o[0]);
4616 if (filesnotmatched.size() > 0)
4618 if (assocfiles > 0 && (Cache.getDefault(
4619 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4620 || JvOptionPane.showConfirmDialog(thisaf,
4621 "<html>" + MessageManager.formatMessage(
4622 "label.ignore_unmatched_dropped_files_info",
4625 filesnotmatched.size())
4628 MessageManager.getString(
4629 "label.ignore_unmatched_dropped_files"),
4630 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4634 for (Object fn : filesnotmatched)
4636 loadJalviewDataFile(fn, null, null, null);
4640 } catch (Exception ex)
4642 ex.printStackTrace();
4650 * Attempt to load a "dropped" file or URL string, by testing in turn for
4652 * <li>an Annotation file</li>
4653 * <li>a JNet file</li>
4654 * <li>a features file</li>
4655 * <li>else try to interpret as an alignment file</li>
4659 * either a filename or a URL string.
4661 public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4662 FileFormatI format, SequenceI assocSeq)
4664 // BH 2018 was String file
4667 if (sourceType == null)
4669 sourceType = FormatAdapter.checkProtocol(file);
4671 // if the file isn't identified, or not positively identified as some
4672 // other filetype (PFAM is default unidentified alignment file type) then
4673 // try to parse as annotation.
4674 boolean isAnnotation = (format == null
4675 || FileFormat.Pfam.equals(format))
4676 ? new AnnotationFile().annotateAlignmentView(viewport,
4682 // first see if its a T-COFFEE score file
4683 TCoffeeScoreFile tcf = null;
4686 tcf = new TCoffeeScoreFile(file, sourceType);
4689 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4693 new TCoffeeColourScheme(viewport.getAlignment()));
4694 isAnnotation = true;
4695 setStatus(MessageManager.getString(
4696 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4700 // some problem - if no warning its probable that the ID matching
4701 // process didn't work
4702 JvOptionPane.showMessageDialog(Desktop.desktop,
4703 tcf.getWarningMessage() == null
4704 ? MessageManager.getString(
4705 "label.check_file_matches_sequence_ids_alignment")
4706 : tcf.getWarningMessage(),
4707 MessageManager.getString(
4708 "label.problem_reading_tcoffee_score_file"),
4709 JvOptionPane.WARNING_MESSAGE);
4716 } catch (Exception x)
4719 "Exception when processing data source as T-COFFEE score file",
4725 // try to see if its a JNet 'concise' style annotation file *before*
4727 // try to parse it as a features file
4730 format = new IdentifyFile().identify(file, sourceType);
4732 if (FileFormat.ScoreMatrix == format)
4734 ScoreMatrixFile sm = new ScoreMatrixFile(
4735 new FileParse(file, sourceType));
4737 // todo: i18n this message
4738 setStatus(MessageManager.formatMessage(
4739 "label.successfully_loaded_matrix",
4740 sm.getMatrixName()));
4742 else if (FileFormat.Jnet.equals(format))
4744 JPredFile predictions = new JPredFile(file, sourceType);
4745 new JnetAnnotationMaker();
4746 JnetAnnotationMaker.add_annotation(predictions,
4747 viewport.getAlignment(), 0, false);
4748 viewport.getAlignment().setupJPredAlignment();
4749 isAnnotation = true;
4751 // else if (IdentifyFile.FeaturesFile.equals(format))
4752 else if (FileFormat.Features.equals(format))
4754 if (parseFeaturesFile(file, sourceType))
4756 alignPanel.paintAlignment(true, true);
4761 new FileLoader().LoadFile(viewport, file, sourceType, format);
4768 alignPanel.adjustAnnotationHeight();
4769 viewport.updateSequenceIdColours();
4770 buildSortByAnnotationScoresMenu();
4771 alignPanel.paintAlignment(true, true);
4773 } catch (Exception ex)
4775 ex.printStackTrace();
4776 } catch (OutOfMemoryError oom)
4781 } catch (Exception x)
4786 + (sourceType != null
4787 ? (sourceType == DataSourceType.PASTE
4789 : "using " + sourceType + " from "
4793 ? "(parsing as '" + format + "' file)"
4795 oom, Desktop.desktop);
4800 * Method invoked by the ChangeListener on the tabbed pane, in other words
4801 * when a different tabbed pane is selected by the user or programmatically.
4804 public void tabSelectionChanged(int index)
4808 alignPanel = alignPanels.get(index);
4809 viewport = alignPanel.av;
4810 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4811 setMenusFromViewport(viewport);
4815 * 'focus' any colour slider that is open to the selected viewport
4817 if (viewport.getConservationSelected())
4819 SliderPanel.setConservationSlider(alignPanel,
4820 viewport.getResidueShading(), alignPanel.getViewName());
4824 SliderPanel.hideConservationSlider();
4826 if (viewport.getAbovePIDThreshold())
4828 SliderPanel.setPIDSliderSource(alignPanel,
4829 viewport.getResidueShading(), alignPanel.getViewName());
4833 SliderPanel.hidePIDSlider();
4837 * If there is a frame linked to this one in a SplitPane, switch it to the
4838 * same view tab index. No infinite recursion of calls should happen, since
4839 * tabSelectionChanged() should not get invoked on setting the selected
4840 * index to an unchanged value. Guard against setting an invalid index
4841 * before the new view peer tab has been created.
4843 final AlignViewportI peer = viewport.getCodingComplement();
4846 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4847 .getAlignPanel().alignFrame;
4848 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4850 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4856 * On right mouse click on view tab, prompt for and set new view name.
4859 public void tabbedPane_mousePressed(MouseEvent e)
4861 if (e.isPopupTrigger())
4863 String msg = MessageManager.getString("label.enter_view_name");
4864 String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
4865 String reply = JvOptionPane.showInputDialog(msg, ttl);
4869 viewport.setViewName(reply);
4870 // TODO warn if reply is in getExistingViewNames()?
4871 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4876 public AlignViewport getCurrentView()
4882 * Open the dialog for regex description parsing.
4885 protected void extractScores_actionPerformed(ActionEvent e)
4887 ParseProperties pp = new jalview.analysis.ParseProperties(
4888 viewport.getAlignment());
4889 // TODO: verify regex and introduce GUI dialog for version 2.5
4890 // if (pp.getScoresFromDescription("col", "score column ",
4891 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4893 if (pp.getScoresFromDescription("description column",
4894 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4896 buildSortByAnnotationScoresMenu();
4904 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4908 protected void showDbRefs_actionPerformed(ActionEvent e)
4910 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4916 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4920 protected void showNpFeats_actionPerformed(ActionEvent e)
4922 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4926 * find the viewport amongst the tabs in this alignment frame and close that
4931 public boolean closeView(AlignViewportI av)
4935 this.closeMenuItem_actionPerformed(false);
4938 Component[] comp = tabbedPane.getComponents();
4939 for (int i = 0; comp != null && i < comp.length; i++)
4941 if (comp[i] instanceof AlignmentPanel)
4943 if (((AlignmentPanel) comp[i]).av == av)
4946 closeView((AlignmentPanel) comp[i]);
4954 protected void build_fetchdbmenu(JMenu webService)
4956 // Temporary hack - DBRef Fetcher always top level ws entry.
4957 // TODO We probably want to store a sequence database checklist in
4958 // preferences and have checkboxes.. rather than individual sources selected
4960 final JMenu rfetch = new JMenu(
4961 MessageManager.getString("action.fetch_db_references"));
4962 rfetch.setToolTipText(MessageManager.getString(
4963 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4964 webService.add(rfetch);
4966 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4967 MessageManager.getString("option.trim_retrieved_seqs"));
4968 trimrs.setToolTipText(
4969 MessageManager.getString("label.trim_retrieved_sequences"));
4971 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4972 trimrs.addActionListener(new ActionListener()
4975 public void actionPerformed(ActionEvent e)
4977 trimrs.setSelected(trimrs.isSelected());
4978 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4979 Boolean.valueOf(trimrs.isSelected()).toString());
4983 JMenuItem fetchr = new JMenuItem(
4984 MessageManager.getString("label.standard_databases"));
4985 fetchr.setToolTipText(
4986 MessageManager.getString("label.fetch_embl_uniprot"));
4987 fetchr.addActionListener(new ActionListener()
4991 public void actionPerformed(ActionEvent e)
4993 new Thread(new Runnable()
4998 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4999 .getAlignment().isNucleotide();
5000 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5001 alignPanel.av.getSequenceSelection(),
5002 alignPanel.alignFrame, null,
5003 alignPanel.alignFrame.featureSettings, isNucleotide);
5004 dbRefFetcher.addListener(new FetchFinishedListenerI()
5007 public void finished()
5009 AlignFrame.this.setMenusForViewport();
5012 dbRefFetcher.fetchDBRefs(false);
5020 new Thread(new Runnable()
5025 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5026 .getSequenceFetcherSingleton();
5027 javax.swing.SwingUtilities.invokeLater(new Runnable()
5032 String[] dbclasses = sf.getNonAlignmentSources();
5033 List<DbSourceProxy> otherdb;
5034 JMenu dfetch = new JMenu();
5035 JMenu ifetch = new JMenu();
5036 JMenuItem fetchr = null;
5037 int comp = 0, icomp = 0, mcomp = 15;
5038 String mname = null;
5040 for (String dbclass : dbclasses)
5042 otherdb = sf.getSourceProxy(dbclass);
5043 // add a single entry for this class, or submenu allowing 'fetch
5045 if (otherdb == null || otherdb.size() < 1)
5051 mname = "From " + dbclass;
5053 if (otherdb.size() == 1)
5055 final DbSourceProxy[] dassource = otherdb
5056 .toArray(new DbSourceProxy[0]);
5057 DbSourceProxy src = otherdb.get(0);
5058 fetchr = new JMenuItem(src.getDbSource());
5059 fetchr.addActionListener(new ActionListener()
5063 public void actionPerformed(ActionEvent e)
5065 new Thread(new Runnable()
5071 boolean isNucleotide = alignPanel.alignFrame
5072 .getViewport().getAlignment()
5074 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5075 alignPanel.av.getSequenceSelection(),
5076 alignPanel.alignFrame, dassource,
5077 alignPanel.alignFrame.featureSettings,
5080 .addListener(new FetchFinishedListenerI()
5083 public void finished()
5085 AlignFrame.this.setMenusForViewport();
5088 dbRefFetcher.fetchDBRefs(false);
5094 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5095 MessageManager.formatMessage(
5096 "label.fetch_retrieve_from", new Object[]
5097 { src.getDbName() })));
5103 final DbSourceProxy[] dassource = otherdb
5104 .toArray(new DbSourceProxy[0]);
5106 DbSourceProxy src = otherdb.get(0);
5107 fetchr = new JMenuItem(MessageManager
5108 .formatMessage("label.fetch_all_param", new Object[]
5109 { src.getDbSource() }));
5110 fetchr.addActionListener(new ActionListener()
5113 public void actionPerformed(ActionEvent e)
5115 new Thread(new Runnable()
5121 boolean isNucleotide = alignPanel.alignFrame
5122 .getViewport().getAlignment()
5124 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5125 alignPanel.av.getSequenceSelection(),
5126 alignPanel.alignFrame, dassource,
5127 alignPanel.alignFrame.featureSettings,
5130 .addListener(new FetchFinishedListenerI()
5133 public void finished()
5135 AlignFrame.this.setMenusForViewport();
5138 dbRefFetcher.fetchDBRefs(false);
5144 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5145 MessageManager.formatMessage(
5146 "label.fetch_retrieve_from_all_sources",
5148 { Integer.valueOf(otherdb.size())
5150 src.getDbSource(), src.getDbName() })));
5153 // and then build the rest of the individual menus
5154 ifetch = new JMenu(MessageManager.formatMessage(
5155 "label.source_from_db_source", new Object[]
5156 { src.getDbSource() }));
5158 String imname = null;
5160 for (DbSourceProxy sproxy : otherdb)
5162 String dbname = sproxy.getDbName();
5163 String sname = dbname.length() > 5
5164 ? dbname.substring(0, 5) + "..."
5166 String msname = dbname.length() > 10
5167 ? dbname.substring(0, 10) + "..."
5171 imname = MessageManager
5172 .formatMessage("label.from_msname", new Object[]
5175 fetchr = new JMenuItem(msname);
5176 final DbSourceProxy[] dassrc = { sproxy };
5177 fetchr.addActionListener(new ActionListener()
5181 public void actionPerformed(ActionEvent e)
5183 new Thread(new Runnable()
5189 boolean isNucleotide = alignPanel.alignFrame
5190 .getViewport().getAlignment()
5192 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5193 alignPanel.av.getSequenceSelection(),
5194 alignPanel.alignFrame, dassrc,
5195 alignPanel.alignFrame.featureSettings,
5198 .addListener(new FetchFinishedListenerI()
5201 public void finished()
5203 AlignFrame.this.setMenusForViewport();
5206 dbRefFetcher.fetchDBRefs(false);
5212 fetchr.setToolTipText(
5213 "<html>" + MessageManager.formatMessage(
5214 "label.fetch_retrieve_from", new Object[]
5218 if (++icomp >= mcomp || i == (otherdb.size()))
5220 ifetch.setText(MessageManager.formatMessage(
5221 "label.source_to_target", imname, sname));
5223 ifetch = new JMenu();
5231 if (comp >= mcomp || dbi >= (dbclasses.length))
5233 dfetch.setText(MessageManager.formatMessage(
5234 "label.source_to_target", mname, dbclass));
5236 dfetch = new JMenu();
5249 * Left justify the whole alignment.
5252 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5254 AlignmentI al = viewport.getAlignment();
5256 viewport.firePropertyChange("alignment", null, al);
5260 * Right justify the whole alignment.
5263 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5265 AlignmentI al = viewport.getAlignment();
5267 viewport.firePropertyChange("alignment", null, al);
5271 public void setShowSeqFeatures(boolean b)
5273 showSeqFeatures.setSelected(b);
5274 viewport.setShowSequenceFeatures(b);
5281 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5282 * awt.event.ActionEvent)
5285 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5287 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5288 alignPanel.paintAlignment(false, false);
5295 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5299 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5301 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5302 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5310 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5311 * .event.ActionEvent)
5314 protected void showGroupConservation_actionPerformed(ActionEvent e)
5316 viewport.setShowGroupConservation(showGroupConservation.getState());
5317 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5324 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5325 * .event.ActionEvent)
5328 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5330 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5331 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5338 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5339 * .event.ActionEvent)
5342 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5344 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5345 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5349 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5351 showSequenceLogo.setState(true);
5352 viewport.setShowSequenceLogo(true);
5353 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5354 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5358 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5360 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5367 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5368 * .event.ActionEvent)
5371 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5373 if (avc.makeGroupsFromSelection())
5375 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5376 alignPanel.updateAnnotation();
5377 alignPanel.paintAlignment(true, true);
5381 public void clearAlignmentSeqRep()
5383 // TODO refactor alignmentseqrep to controller
5384 if (viewport.getAlignment().hasSeqrep())
5386 viewport.getAlignment().setSeqrep(null);
5387 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5388 alignPanel.updateAnnotation();
5389 alignPanel.paintAlignment(true, true);
5394 protected void createGroup_actionPerformed(ActionEvent e)
5396 if (avc.createGroup())
5398 if (applyAutoAnnotationSettings.isSelected())
5400 alignPanel.updateAnnotation(true, false);
5402 alignPanel.alignmentChanged();
5407 protected void unGroup_actionPerformed(ActionEvent e)
5411 alignPanel.alignmentChanged();
5416 * make the given alignmentPanel the currently selected tab
5418 * @param alignmentPanel
5420 public void setDisplayedView(AlignmentPanel alignmentPanel)
5422 if (!viewport.getSequenceSetId()
5423 .equals(alignmentPanel.av.getSequenceSetId()))
5425 throw new Error(MessageManager.getString(
5426 "error.implementation_error_cannot_show_view_alignment_frame"));
5428 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5429 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5431 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5436 * Action on selection of menu options to Show or Hide annotations.
5439 * @param forSequences
5440 * update sequence-related annotations
5441 * @param forAlignment
5442 * update non-sequence-related annotations
5445 protected void setAnnotationsVisibility(boolean visible,
5446 boolean forSequences, boolean forAlignment)
5448 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5449 .getAlignmentAnnotation();
5454 for (AlignmentAnnotation aa : anns)
5457 * don't display non-positional annotations on an alignment
5459 if (aa.annotations == null)
5463 boolean apply = (aa.sequenceRef == null && forAlignment)
5464 || (aa.sequenceRef != null && forSequences);
5467 aa.visible = visible;
5470 alignPanel.validateAnnotationDimensions(true);
5471 alignPanel.alignmentChanged();
5475 * Store selected annotation sort order for the view and repaint.
5478 protected void sortAnnotations_actionPerformed()
5480 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5482 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5483 alignPanel.paintAlignment(false, false);
5488 * @return alignment panels in this alignment frame
5490 public List<? extends AlignmentViewPanel> getAlignPanels()
5492 // alignPanels is never null
5493 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5498 * Open a new alignment window, with the cDNA associated with this (protein)
5499 * alignment, aligned as is the protein.
5501 protected void viewAsCdna_actionPerformed()
5503 // TODO no longer a menu action - refactor as required
5504 final AlignmentI alignment = getViewport().getAlignment();
5505 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5506 if (mappings == null)
5510 List<SequenceI> cdnaSeqs = new ArrayList<>();
5511 for (SequenceI aaSeq : alignment.getSequences())
5513 for (AlignedCodonFrame acf : mappings)
5515 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5519 * There is a cDNA mapping for this protein sequence - add to new
5520 * alignment. It will share the same dataset sequence as other mapped
5521 * cDNA (no new mappings need to be created).
5523 final Sequence newSeq = new Sequence(dnaSeq);
5524 newSeq.setDatasetSequence(dnaSeq);
5525 cdnaSeqs.add(newSeq);
5529 if (cdnaSeqs.size() == 0)
5531 // show a warning dialog no mapped cDNA
5534 AlignmentI cdna = new Alignment(
5535 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5536 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5537 AlignFrame.DEFAULT_HEIGHT);
5538 cdna.alignAs(alignment);
5539 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5541 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5542 AlignFrame.DEFAULT_HEIGHT);
5546 * Set visibility of dna/protein complement view (available when shown in a
5552 protected void showComplement_actionPerformed(boolean show)
5554 SplitContainerI sf = getSplitViewContainer();
5557 sf.setComplementVisible(this, show);
5562 * Generate the reverse (optionally complemented) of the selected sequences,
5563 * and add them to the alignment
5566 protected void showReverse_actionPerformed(boolean complement)
5568 AlignmentI al = null;
5571 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5572 al = dna.reverseCdna(complement);
5573 viewport.addAlignment(al, "");
5574 addHistoryItem(new EditCommand(
5575 MessageManager.getString("label.add_sequences"), Action.PASTE,
5576 al.getSequencesArray(), 0, al.getWidth(),
5577 viewport.getAlignment()));
5578 } catch (Exception ex)
5580 System.err.println(ex.getMessage());
5586 * Try to run a script in the Groovy console, having first ensured that this
5587 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5588 * be targeted at this alignment.
5591 protected void runGroovy_actionPerformed()
5593 Jalview.setCurrentAlignFrame(this);
5594 groovy.ui.Console console = Desktop.getGroovyConsole();
5595 if (console != null)
5599 console.runScript();
5600 } catch (Exception ex)
5602 System.err.println((ex.toString()));
5603 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5604 MessageManager.getString("label.couldnt_run_groovy_script"),
5605 MessageManager.getString("label.groovy_support_failed"),
5606 JvOptionPane.ERROR_MESSAGE);
5611 System.err.println("Can't run Groovy script as console not found");
5616 * Hides columns containing (or not containing) a specified feature, provided
5617 * that would not leave all columns hidden
5619 * @param featureType
5620 * @param columnsContaining
5623 public boolean hideFeatureColumns(String featureType,
5624 boolean columnsContaining)
5626 boolean notForHiding = avc.markColumnsContainingFeatures(
5627 columnsContaining, false, false, featureType);
5630 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5631 false, featureType))
5633 getViewport().hideSelectedColumns();
5641 protected void selectHighlightedColumns_actionPerformed(
5642 ActionEvent actionEvent)
5644 // include key modifier check in case user selects from menu
5645 avc.markHighlightedColumns(
5646 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5647 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5648 | ActionEvent.CTRL_MASK)) != 0);
5652 * Rebuilds the Colour menu, including any user-defined colours which have
5653 * been loaded either on startup or during the session
5655 public void buildColourMenu()
5657 colourMenu.removeAll();
5659 colourMenu.add(applyToAllGroups);
5660 colourMenu.add(textColour);
5661 colourMenu.addSeparator();
5663 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5666 colourMenu.addSeparator();
5667 colourMenu.add(conservationMenuItem);
5668 colourMenu.add(modifyConservation);
5669 colourMenu.add(abovePIDThreshold);
5670 colourMenu.add(modifyPID);
5671 colourMenu.add(annotationColour);
5673 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5674 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5678 * Open a dialog (if not already open) that allows the user to select and
5679 * calculate PCA or Tree analysis
5681 protected void openTreePcaDialog()
5683 if (alignPanel.getCalculationDialog() == null)
5685 new CalculationChooser(AlignFrame.this);
5690 protected void loadVcf_actionPerformed()
5692 JalviewFileChooser chooser = new JalviewFileChooser(
5693 Cache.getProperty("LAST_DIRECTORY"));
5694 chooser.setFileView(new JalviewFileView());
5695 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5696 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5697 final AlignFrame us = this;
5698 chooser.addResponse(0, new RunResponse(JalviewFileChooser.APPROVE_OPTION)
5703 String choice = chooser.getSelectedFile().getPath();
5704 Cache.setProperty("LAST_DIRECTORY", choice);
5705 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5706 new VCFLoader(choice).loadVCF(seqs, us);
5709 chooser.showOpenDialog(null);
5715 class PrintThread extends Thread
5719 public PrintThread(AlignmentPanel ap)
5724 static PageFormat pf;
5729 PrinterJob printJob = PrinterJob.getPrinterJob();
5733 printJob.setPrintable(ap, pf);
5737 printJob.setPrintable(ap);
5740 if (printJob.printDialog())
5745 } catch (Exception PrintException)
5747 PrintException.printStackTrace();