2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenColumns;
57 import jalview.datamodel.HiddenMarkovModel;
58 import jalview.datamodel.HiddenSequences;
59 import jalview.datamodel.PDBEntry;
60 import jalview.datamodel.SeqCigar;
61 import jalview.datamodel.Sequence;
62 import jalview.datamodel.SequenceGroup;
63 import jalview.datamodel.SequenceI;
64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
66 import jalview.hmmer.HMMAlignThread;
67 import jalview.hmmer.HMMBuildThread;
68 import jalview.hmmer.HMMERParamStore;
69 import jalview.hmmer.HMMERPreset;
70 import jalview.hmmer.HMMSearchThread;
71 import jalview.io.AlignmentProperties;
72 import jalview.io.AnnotationFile;
73 import jalview.io.BioJsHTMLOutput;
74 import jalview.io.DataSourceType;
75 import jalview.io.FileFormat;
76 import jalview.io.FileFormatI;
77 import jalview.io.FileFormats;
78 import jalview.io.FileLoader;
79 import jalview.io.FileParse;
80 import jalview.io.FormatAdapter;
81 import jalview.io.HtmlSvgOutput;
82 import jalview.io.IdentifyFile;
83 import jalview.io.JPredFile;
84 import jalview.io.JalviewFileChooser;
85 import jalview.io.JalviewFileView;
86 import jalview.io.JnetAnnotationMaker;
87 import jalview.io.NewickFile;
88 import jalview.io.ScoreMatrixFile;
89 import jalview.io.TCoffeeScoreFile;
90 import jalview.jbgui.GAlignFrame;
91 import jalview.schemes.ColourSchemeI;
92 import jalview.schemes.ColourSchemes;
93 import jalview.schemes.ResidueColourScheme;
94 import jalview.schemes.TCoffeeColourScheme;
95 import jalview.util.MessageManager;
96 import jalview.util.StringUtils;
97 import jalview.viewmodel.AlignmentViewport;
98 import jalview.viewmodel.ViewportRanges;
99 import jalview.ws.DBRefFetcher;
100 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
101 import jalview.ws.jws1.Discoverer;
102 import jalview.ws.jws2.Jws2Discoverer;
103 import jalview.ws.jws2.jabaws2.Jws2Instance;
104 import jalview.ws.params.ArgumentI;
105 import jalview.ws.params.ParamDatastoreI;
106 import jalview.ws.params.WsParamSetI;
107 import jalview.ws.seqfetcher.DbSourceProxy;
109 import java.awt.BorderLayout;
110 import java.awt.Component;
111 import java.awt.Rectangle;
112 import java.awt.Toolkit;
113 import java.awt.datatransfer.Clipboard;
114 import java.awt.datatransfer.DataFlavor;
115 import java.awt.datatransfer.StringSelection;
116 import java.awt.datatransfer.Transferable;
117 import java.awt.dnd.DnDConstants;
118 import java.awt.dnd.DropTargetDragEvent;
119 import java.awt.dnd.DropTargetDropEvent;
120 import java.awt.dnd.DropTargetEvent;
121 import java.awt.dnd.DropTargetListener;
122 import java.awt.event.ActionEvent;
123 import java.awt.event.ActionListener;
124 import java.awt.event.FocusAdapter;
125 import java.awt.event.FocusEvent;
126 import java.awt.event.ItemEvent;
127 import java.awt.event.ItemListener;
128 import java.awt.event.KeyAdapter;
129 import java.awt.event.KeyEvent;
130 import java.awt.event.MouseEvent;
131 import java.awt.print.PageFormat;
132 import java.awt.print.PrinterJob;
133 import java.beans.PropertyChangeEvent;
135 import java.io.FileWriter;
136 import java.io.IOException;
137 import java.io.PrintWriter;
139 import java.util.ArrayList;
140 import java.util.Arrays;
141 import java.util.Deque;
142 import java.util.Enumeration;
143 import java.util.HashMap;
144 import java.util.Hashtable;
145 import java.util.List;
146 import java.util.Map;
147 import java.util.Scanner;
148 import java.util.Vector;
150 import javax.swing.JCheckBoxMenuItem;
151 import javax.swing.JEditorPane;
152 import javax.swing.JFileChooser;
153 import javax.swing.JFrame;
154 import javax.swing.JInternalFrame;
155 import javax.swing.JLayeredPane;
156 import javax.swing.JMenu;
157 import javax.swing.JMenuItem;
158 import javax.swing.JOptionPane;
159 import javax.swing.JScrollPane;
160 import javax.swing.SwingUtilities;
166 * @version $Revision$
168 public class AlignFrame extends GAlignFrame implements DropTargetListener,
169 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
172 Map<String, Float> distribution = new HashMap<>(); // temporary
174 public static final int DEFAULT_WIDTH = 700;
176 public static final int DEFAULT_HEIGHT = 500;
179 * The currently displayed panel (selected tabbed view if more than one)
181 public AlignmentPanel alignPanel;
183 AlignViewport viewport;
185 ViewportRanges vpRanges;
187 public AlignViewControllerI avc;
189 * The selected HMM for this align frame
191 SequenceI selectedHMMSequence;
193 List<AlignmentPanel> alignPanels = new ArrayList<>();
196 * Last format used to load or save alignments in this window
198 FileFormatI currentFileFormat = null;
201 * Current filename for this alignment
203 String fileName = null;
207 * Creates a new AlignFrame object with specific width and height.
213 public AlignFrame(AlignmentI al, int width, int height)
215 this(al, null, width, height);
219 * Creates a new AlignFrame object with specific width, height and
225 * @param sequenceSetId
227 public AlignFrame(AlignmentI al, int width, int height,
228 String sequenceSetId)
230 this(al, null, width, height, sequenceSetId);
234 * Creates a new AlignFrame object with specific width, height and
240 * @param sequenceSetId
243 public AlignFrame(AlignmentI al, int width, int height,
244 String sequenceSetId, String viewId)
246 this(al, null, width, height, sequenceSetId, viewId);
250 * new alignment window with hidden columns
254 * @param hiddenColumns
255 * ColumnSelection or null
257 * Width of alignment frame
261 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
264 this(al, hiddenColumns, width, height, null);
268 * Create alignment frame for al with hiddenColumns, a specific width and
269 * height, and specific sequenceId
272 * @param hiddenColumns
275 * @param sequenceSetId
278 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
279 int height, String sequenceSetId)
281 this(al, hiddenColumns, width, height, sequenceSetId, null);
285 * Create alignment frame for al with hiddenColumns, a specific width and
286 * height, and specific sequenceId
289 * @param hiddenColumns
292 * @param sequenceSetId
297 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
298 int height, String sequenceSetId, String viewId)
300 setSize(width, height);
302 if (al.getDataset() == null)
307 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
309 alignPanel = new AlignmentPanel(this, viewport);
311 addAlignmentPanel(alignPanel, true);
315 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
316 HiddenColumns hiddenColumns, int width, int height)
318 setSize(width, height);
320 if (al.getDataset() == null)
325 viewport = new AlignViewport(al, hiddenColumns);
327 if (hiddenSeqs != null && hiddenSeqs.length > 0)
329 viewport.hideSequence(hiddenSeqs);
331 alignPanel = new AlignmentPanel(this, viewport);
332 addAlignmentPanel(alignPanel, true);
337 * Make a new AlignFrame from existing alignmentPanels
344 public AlignFrame(AlignmentPanel ap)
348 addAlignmentPanel(ap, false);
353 * initalise the alignframe from the underlying viewport data and the
358 if (!Jalview.isHeadlessMode())
360 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
363 vpRanges = viewport.getRanges();
364 avc = new jalview.controller.AlignViewController(this, viewport,
366 if (viewport.getAlignmentConservationAnnotation() == null)
368 // BLOSUM62Colour.setEnabled(false);
369 conservationMenuItem.setEnabled(false);
370 modifyConservation.setEnabled(false);
371 // PIDColour.setEnabled(false);
372 // abovePIDThreshold.setEnabled(false);
373 // modifyPID.setEnabled(false);
376 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
379 if (sortby.equals("Id"))
381 sortIDMenuItem_actionPerformed(null);
383 else if (sortby.equals("Pairwise Identity"))
385 sortPairwiseMenuItem_actionPerformed(null);
389 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
391 setMenusFromViewport(viewport);
392 buildSortByAnnotationScoresMenu();
393 calculateTree.addActionListener(new ActionListener()
397 public void actionPerformed(ActionEvent e)
405 if (Desktop.desktop != null)
407 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
408 addServiceListeners();
412 if (viewport.getWrapAlignment())
414 wrapMenuItem_actionPerformed(null);
417 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
419 this.overviewMenuItem_actionPerformed(null);
424 final List<AlignmentPanel> selviews = new ArrayList<>();
425 final List<AlignmentPanel> origview = new ArrayList<>();
426 final String menuLabel = MessageManager
427 .getString("label.copy_format_from");
428 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
429 new ViewSetProvider()
433 public AlignmentPanel[] getAllAlignmentPanels()
436 origview.add(alignPanel);
437 // make an array of all alignment panels except for this one
438 List<AlignmentPanel> aps = new ArrayList<>(
439 Arrays.asList(Desktop.getAlignmentPanels(null)));
440 aps.remove(AlignFrame.this.alignPanel);
441 return aps.toArray(new AlignmentPanel[aps.size()]);
443 }, selviews, new ItemListener()
447 public void itemStateChanged(ItemEvent e)
449 if (origview.size() > 0)
451 final AlignmentPanel ap = origview.get(0);
454 * Copy the ViewStyle of the selected panel to 'this one'.
455 * Don't change value of 'scaleProteinAsCdna' unless copying
458 ViewStyleI vs = selviews.get(0).getAlignViewport()
460 boolean fromSplitFrame = selviews.get(0)
461 .getAlignViewport().getCodingComplement() != null;
464 vs.setScaleProteinAsCdna(ap.getAlignViewport()
465 .getViewStyle().isScaleProteinAsCdna());
467 ap.getAlignViewport().setViewStyle(vs);
470 * Also rescale ViewStyle of SplitFrame complement if there is
471 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
472 * the whole ViewStyle (allow cDNA protein to have different
475 AlignViewportI complement = ap.getAlignViewport()
476 .getCodingComplement();
477 if (complement != null && vs.isScaleProteinAsCdna())
479 AlignFrame af = Desktop.getAlignFrameFor(complement);
480 ((SplitFrame) af.getSplitViewContainer())
482 af.setMenusForViewport();
486 ap.setSelected(true);
487 ap.alignFrame.setMenusForViewport();
492 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
493 .indexOf("devel") > -1
494 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
495 .indexOf("test") > -1)
497 formatMenu.add(vsel);
499 addFocusListener(new FocusAdapter()
502 public void focusGained(FocusEvent e)
504 Jalview.setCurrentAlignFrame(AlignFrame.this);
511 * Adds all menu items to the HMMER menu
513 private void buildHMMERMenu()
515 hmmerMenu.removeAll();
517 hmmerMenu.add(hmmAlign);
518 hmmerMenu.add(hmmBuild);
519 hmmerMenu.add(hmmSearch);
523 * Change the filename and format for the alignment, and enable the 'reload'
524 * button functionality.
531 public void setFileName(String file, FileFormatI format)
534 setFileFormat(format);
535 reload.setEnabled(true);
539 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
542 void addKeyListener()
544 addKeyListener(new KeyAdapter()
547 public void keyPressed(KeyEvent evt)
549 if (viewport.cursorMode
550 && ((evt.getKeyCode() >= KeyEvent.VK_0
551 && evt.getKeyCode() <= KeyEvent.VK_9)
552 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
553 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
554 && Character.isDigit(evt.getKeyChar()))
556 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
559 switch (evt.getKeyCode())
562 case 27: // escape key
563 deselectAllSequenceMenuItem_actionPerformed(null);
567 case KeyEvent.VK_DOWN:
568 if (evt.isAltDown() || !viewport.cursorMode)
570 moveSelectedSequences(false);
572 if (viewport.cursorMode)
574 alignPanel.getSeqPanel().moveCursor(0, 1);
579 if (evt.isAltDown() || !viewport.cursorMode)
581 moveSelectedSequences(true);
583 if (viewport.cursorMode)
585 alignPanel.getSeqPanel().moveCursor(0, -1);
590 case KeyEvent.VK_LEFT:
591 if (evt.isAltDown() || !viewport.cursorMode)
593 slideSequences(false,
594 alignPanel.getSeqPanel().getKeyboardNo1());
598 alignPanel.getSeqPanel().moveCursor(-1, 0);
603 case KeyEvent.VK_RIGHT:
604 if (evt.isAltDown() || !viewport.cursorMode)
606 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
610 alignPanel.getSeqPanel().moveCursor(1, 0);
614 case KeyEvent.VK_SPACE:
615 if (viewport.cursorMode)
617 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
618 || evt.isShiftDown() || evt.isAltDown());
622 // case KeyEvent.VK_A:
623 // if (viewport.cursorMode)
625 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
626 // //System.out.println("A");
630 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
631 * System.out.println("closing bracket"); } break;
633 case KeyEvent.VK_DELETE:
634 case KeyEvent.VK_BACK_SPACE:
635 if (!viewport.cursorMode)
637 cut_actionPerformed(null);
641 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
642 || evt.isShiftDown() || evt.isAltDown());
648 if (viewport.cursorMode)
650 alignPanel.getSeqPanel().setCursorRow();
654 if (viewport.cursorMode && !evt.isControlDown())
656 alignPanel.getSeqPanel().setCursorColumn();
660 if (viewport.cursorMode)
662 alignPanel.getSeqPanel().setCursorPosition();
666 case KeyEvent.VK_ENTER:
667 case KeyEvent.VK_COMMA:
668 if (viewport.cursorMode)
670 alignPanel.getSeqPanel().setCursorRowAndColumn();
675 if (viewport.cursorMode)
677 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
681 if (viewport.cursorMode)
683 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
688 viewport.cursorMode = !viewport.cursorMode;
689 statusBar.setText(MessageManager
690 .formatMessage("label.keyboard_editing_mode", new String[]
691 { (viewport.cursorMode ? "on" : "off") }));
692 if (viewport.cursorMode)
694 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
696 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
699 alignPanel.getSeqPanel().seqCanvas.repaint();
705 Help.showHelpWindow();
706 } catch (Exception ex)
708 ex.printStackTrace();
713 boolean toggleSeqs = !evt.isControlDown();
714 boolean toggleCols = !evt.isShiftDown();
715 toggleHiddenRegions(toggleSeqs, toggleCols);
720 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
721 boolean modifyExisting = true; // always modify, don't clear
722 // evt.isShiftDown();
723 boolean invertHighlighted = evt.isAltDown();
724 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
728 case KeyEvent.VK_PAGE_UP:
731 case KeyEvent.VK_PAGE_DOWN:
738 public void keyReleased(KeyEvent evt)
740 switch (evt.getKeyCode())
742 case KeyEvent.VK_LEFT:
743 if (evt.isAltDown() || !viewport.cursorMode)
745 viewport.firePropertyChange("alignment", null,
746 viewport.getAlignment().getSequences());
750 case KeyEvent.VK_RIGHT:
751 if (evt.isAltDown() || !viewport.cursorMode)
753 viewport.firePropertyChange("alignment", null,
754 viewport.getAlignment().getSequences());
762 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
764 ap.alignFrame = this;
765 avc = new jalview.controller.AlignViewController(this, viewport,
770 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
772 int aSize = alignPanels.size();
774 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
776 if (aSize == 1 && ap.av.viewName == null)
778 this.getContentPane().add(ap, BorderLayout.CENTER);
784 setInitialTabVisible();
787 expandViews.setEnabled(true);
788 gatherViews.setEnabled(true);
789 tabbedPane.addTab(ap.av.viewName, ap);
791 ap.setVisible(false);
796 if (ap.av.isPadGaps())
798 ap.av.getAlignment().padGaps();
800 ap.av.updateConservation(ap);
801 ap.av.updateConsensus(ap);
802 ap.av.updateStrucConsensus(ap);
803 ap.av.updateInformation(ap);
807 public void setInitialTabVisible()
809 expandViews.setEnabled(true);
810 gatherViews.setEnabled(true);
811 tabbedPane.setVisible(true);
812 AlignmentPanel first = alignPanels.get(0);
813 tabbedPane.addTab(first.av.viewName, first);
814 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
817 public AlignViewport getViewport()
822 /* Set up intrinsic listeners for dynamically generated GUI bits. */
823 private void addServiceListeners()
825 final java.beans.PropertyChangeListener thisListener;
826 Desktop.instance.addJalviewPropertyChangeListener("services",
827 thisListener = new java.beans.PropertyChangeListener()
830 public void propertyChange(PropertyChangeEvent evt)
832 // // System.out.println("Discoverer property change.");
833 // if (evt.getPropertyName().equals("services"))
835 SwingUtilities.invokeLater(new Runnable()
842 "Rebuild WS Menu for service change");
843 BuildWebServiceMenu();
850 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
853 public void internalFrameClosed(
854 javax.swing.event.InternalFrameEvent evt)
856 // System.out.println("deregistering discoverer listener");
857 Desktop.instance.removeJalviewPropertyChangeListener("services",
859 closeMenuItem_actionPerformed(true);
862 // Finally, build the menu once to get current service state
863 new Thread(new Runnable()
868 BuildWebServiceMenu();
874 * Configure menu items that vary according to whether the alignment is
875 * nucleotide or protein
877 public void setGUINucleotide()
879 AlignmentI al = getViewport().getAlignment();
880 boolean nucleotide = al.isNucleotide();
882 showTranslation.setVisible(nucleotide);
883 showReverse.setVisible(nucleotide);
884 showReverseComplement.setVisible(nucleotide);
885 conservationMenuItem.setEnabled(!nucleotide);
887 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
888 showGroupConservation.setEnabled(!nucleotide);
890 showComplementMenuItem
891 .setText(nucleotide ? MessageManager.getString("label.protein")
892 : MessageManager.getString("label.nucleotide"));
896 * set up menus for the current viewport. This may be called after any
897 * operation that affects the data in the current view (selection changed,
898 * etc) to update the menus to reflect the new state.
901 public void setMenusForViewport()
903 setMenusFromViewport(viewport);
907 * Need to call this method when tabs are selected for multiple views, or when
908 * loading from Jalview2XML.java
913 void setMenusFromViewport(AlignViewport av)
915 padGapsMenuitem.setSelected(av.isPadGaps());
916 colourTextMenuItem.setSelected(av.isShowColourText());
917 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
918 modifyPID.setEnabled(abovePIDThreshold.isSelected());
919 conservationMenuItem.setSelected(av.getConservationSelected());
920 modifyConservation.setEnabled(conservationMenuItem.isSelected());
921 seqLimits.setSelected(av.getShowJVSuffix());
922 idRightAlign.setSelected(av.isRightAlignIds());
923 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
924 renderGapsMenuItem.setSelected(av.isRenderGaps());
925 wrapMenuItem.setSelected(av.getWrapAlignment());
926 scaleAbove.setVisible(av.getWrapAlignment());
927 scaleLeft.setVisible(av.getWrapAlignment());
928 scaleRight.setVisible(av.getWrapAlignment());
929 annotationPanelMenuItem.setState(av.isShowAnnotation());
931 * Show/hide annotations only enabled if annotation panel is shown
933 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
934 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
935 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
936 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
937 viewBoxesMenuItem.setSelected(av.getShowBoxes());
938 viewTextMenuItem.setSelected(av.getShowText());
939 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
940 showGroupConsensus.setSelected(av.isShowGroupConsensus());
941 showGroupConservation.setSelected(av.isShowGroupConservation());
942 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
943 showSequenceLogo.setSelected(av.isShowSequenceLogo());
944 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
945 showInformationHistogram.setSelected(av.isShowInformationHistogram());
946 showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
947 normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
949 ColourMenuHelper.setColourSelected(colourMenu,
950 av.getGlobalColourScheme());
952 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
953 hiddenMarkers.setState(av.getShowHiddenMarkers());
954 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
955 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
956 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
957 autoCalculate.setSelected(av.autoCalculateConsensus);
958 sortByTree.setSelected(av.sortByTree);
959 listenToViewSelections.setSelected(av.followSelection);
961 showProducts.setEnabled(canShowProducts());
962 setGroovyEnabled(Desktop.getGroovyConsole() != null);
968 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
972 public void setGroovyEnabled(boolean b)
974 runGroovy.setEnabled(b);
977 private IProgressIndicator progressBar;
982 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
985 public void setProgressBar(String message, long id)
987 progressBar.setProgressBar(message, id);
991 public void registerHandler(final long id,
992 final IProgressIndicatorHandler handler)
994 progressBar.registerHandler(id, handler);
999 * @return true if any progress bars are still active
1002 public boolean operationInProgress()
1004 return progressBar.operationInProgress();
1008 public void setStatus(String text)
1010 statusBar.setText(text);
1014 * Added so Castor Mapping file can obtain Jalview Version
1016 public String getVersion()
1018 return jalview.bin.Cache.getProperty("VERSION");
1021 public FeatureRenderer getFeatureRenderer()
1023 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1027 public void fetchSequence_actionPerformed(ActionEvent e)
1029 new jalview.gui.SequenceFetcher(this);
1033 public void addFromFile_actionPerformed(ActionEvent e)
1035 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1039 public void hmmBuildSettings_actionPerformed(ActionEvent e)
1040 throws IOException, InterruptedException
1042 if (!(alignmentIsSufficient(1)))
1046 WsParamSetI set = new HMMERPreset();
1047 List<ArgumentI> args = new ArrayList<>();
1048 ParamDatastoreI store = new HMMERParamStore("hmmbuild");
1049 WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1051 if (params.showRunDialog())
1053 new Thread(new HMMBuildThread(this, params.getJobParams())).start();
1055 alignPanel.repaint();
1060 public void hmmAlignSettings_actionPerformed(ActionEvent e)
1061 throws IOException, InterruptedException
1063 if (!(checkForHMM() && alignmentIsSufficient(2)))
1067 WsParamSetI set = new HMMERPreset();
1068 List<ArgumentI> args = new ArrayList<>();
1069 ParamDatastoreI store = new HMMERParamStore("hmmalign");
1070 WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1072 if (params.showRunDialog())
1074 new Thread(new HMMAlignThread(this, true, params.getJobParams()))
1077 alignPanel.repaint();
1081 public void hmmSearchSettings_actionPerformed(ActionEvent e)
1087 WsParamSetI set = new HMMERPreset();
1088 List<ArgumentI> args = new ArrayList<>();
1089 ParamDatastoreI store = new HMMERParamStore("hmmsearch");
1090 WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1092 if (params.showRunDialog())
1094 new Thread(new HMMSearchThread(this, true, params.getJobParams()))
1097 alignPanel.repaint();
1101 public void hmmBuildRun_actionPerformed(ActionEvent e)
1102 throws IOException, InterruptedException
1104 if (!alignmentIsSufficient(1))
1108 new Thread(new HMMBuildThread(this, null))
1110 alignPanel.repaint();
1115 public void hmmAlignRun_actionPerformed(ActionEvent e)
1116 throws IOException, InterruptedException
1118 if (!(checkForHMM() && alignmentIsSufficient(2)))
1122 new Thread(new HMMAlignThread(this, true, null))
1124 alignPanel.repaint();
1128 public void hmmSearchRun_actionPerformed(ActionEvent e)
1134 new Thread(new HMMSearchThread(this, true, null))
1136 alignPanel.repaint();
1140 * Checks if the frame has a selected hidden Markov model
1144 private boolean checkForHMM()
1146 if (getSelectedHMM() == null)
1148 JOptionPane.showMessageDialog(this,
1149 MessageManager.getString("warn.no_selected_hmm"));
1156 * Checks if the alignment contains the required number of sequences.
1161 public boolean alignmentIsSufficient(int required)
1163 if (getViewport().getAlignment().getSequences().size() < required)
1165 JOptionPane.showMessageDialog(this,
1166 MessageManager.getString("warn.not_enough_sequences"));
1173 public void addDatabase_actionPerformed(ActionEvent e) throws IOException
1175 if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
1177 Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
1178 Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
1181 String path = openFileChooser(false);
1182 if (new File(path).exists())
1184 IdentifyFile identifier = new IdentifyFile();
1185 FileFormatI format = identifier.identify(path, DataSourceType.FILE);
1186 if (format == FileFormat.Fasta || format == FileFormat.Stockholm
1187 || format == FileFormat.Pfam)
1189 String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS);
1190 String currentDbPaths = Cache
1191 .getProperty(Preferences.HMMSEARCH_DB_PATHS);
1192 currentDbPaths += " " + path;
1194 String fileName = StringUtils.getLastToken(path, new String("/"));
1195 Scanner scanner = new Scanner(fileName).useDelimiter(".");
1196 String name = scanner.next();
1198 currentDbs += " " + path; // TODO remove path from file name
1201 Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths);
1202 Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
1206 JOptionPane.showMessageDialog(this,
1207 MessageManager.getString("warn.invalid_format"));
1212 JOptionPane.showMessageDialog(this,
1213 MessageManager.getString("warn.not_enough_sequences"));
1218 * Opens a file chooser
1223 protected String openFileChooser(boolean forFolder)
1225 String choice = null;
1226 JFileChooser chooser = new JFileChooser();
1229 chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
1231 chooser.setDialogTitle(
1232 MessageManager.getString("label.open_local_file"));
1233 chooser.setToolTipText(MessageManager.getString("action.open"));
1235 int value = chooser.showOpenDialog(this);
1237 if (value == JFileChooser.APPROVE_OPTION)
1239 choice = chooser.getSelectedFile().getPath();
1245 public void reload_actionPerformed(ActionEvent e)
1247 if (fileName != null)
1249 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1250 // originating file's format
1251 // TODO: work out how to recover feature settings for correct view(s) when
1252 // file is reloaded.
1253 if (FileFormat.Jalview.equals(currentFileFormat))
1255 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1256 for (int i = 0; i < frames.length; i++)
1258 if (frames[i] instanceof AlignFrame && frames[i] != this
1259 && ((AlignFrame) frames[i]).fileName != null
1260 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1264 frames[i].setSelected(true);
1265 Desktop.instance.closeAssociatedWindows();
1266 } catch (java.beans.PropertyVetoException ex)
1272 Desktop.instance.closeAssociatedWindows();
1274 FileLoader loader = new FileLoader();
1275 DataSourceType protocol = fileName.startsWith("http:")
1276 ? DataSourceType.URL
1277 : DataSourceType.FILE;
1278 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1282 Rectangle bounds = this.getBounds();
1284 FileLoader loader = new FileLoader();
1285 DataSourceType protocol = fileName.startsWith("http:")
1286 ? DataSourceType.URL
1287 : DataSourceType.FILE;
1288 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1289 protocol, currentFileFormat);
1291 newframe.setBounds(bounds);
1292 if (featureSettings != null && featureSettings.isShowing())
1294 final Rectangle fspos = featureSettings.frame.getBounds();
1295 // TODO: need a 'show feature settings' function that takes bounds -
1296 // need to refactor Desktop.addFrame
1297 newframe.featureSettings_actionPerformed(null);
1298 final FeatureSettings nfs = newframe.featureSettings;
1299 SwingUtilities.invokeLater(new Runnable()
1304 nfs.frame.setBounds(fspos);
1307 this.featureSettings.close();
1308 this.featureSettings = null;
1310 this.closeMenuItem_actionPerformed(true);
1316 public void addFromText_actionPerformed(ActionEvent e)
1319 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1323 public void addFromURL_actionPerformed(ActionEvent e)
1325 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1329 public void save_actionPerformed(ActionEvent e)
1331 if (fileName == null || (currentFileFormat == null)
1332 || fileName.startsWith("http"))
1334 saveAs_actionPerformed(null);
1338 saveAlignment(fileName, currentFileFormat);
1349 public void saveAs_actionPerformed(ActionEvent e)
1351 String format = currentFileFormat == null ? null
1352 : currentFileFormat.getName();
1353 JalviewFileChooser chooser = JalviewFileChooser
1354 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1356 chooser.setFileView(new JalviewFileView());
1357 chooser.setDialogTitle(
1358 MessageManager.getString("label.save_alignment_to_file"));
1359 chooser.setToolTipText(MessageManager.getString("action.save"));
1361 int value = chooser.showSaveDialog(this);
1363 if (value == JalviewFileChooser.APPROVE_OPTION)
1365 currentFileFormat = chooser.getSelectedFormat();
1366 while (currentFileFormat == null)
1368 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1369 MessageManager.getString(
1370 "label.select_file_format_before_saving"),
1371 MessageManager.getString("label.file_format_not_specified"),
1372 JvOptionPane.WARNING_MESSAGE);
1373 currentFileFormat = chooser.getSelectedFormat();
1374 value = chooser.showSaveDialog(this);
1375 if (value != JalviewFileChooser.APPROVE_OPTION)
1381 fileName = chooser.getSelectedFile().getPath();
1383 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1385 Cache.setProperty("LAST_DIRECTORY", fileName);
1386 saveAlignment(fileName, currentFileFormat);
1390 public boolean saveAlignment(String file, FileFormatI format)
1392 boolean success = true;
1394 if (FileFormat.Jalview.equals(format))
1396 String shortName = title;
1398 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1400 shortName = shortName.substring(
1401 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1404 success = new Jalview2XML().saveAlignment(this, file, shortName);
1406 statusBar.setText(MessageManager.formatMessage(
1407 "label.successfully_saved_to_file_in_format", new Object[]
1408 { fileName, format }));
1413 AlignmentExportData exportData = getAlignmentForExport(format,
1415 if (exportData.getSettings().isCancelled())
1419 FormatAdapter f = new FormatAdapter(alignPanel,
1420 exportData.getSettings());
1421 String output = f.formatSequences(format, exportData.getAlignment(), // class
1425 // occur in the distant future
1426 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1427 f.getCacheSuffixDefault(format),
1428 viewport.getAlignment().getHiddenColumns());
1438 PrintWriter out = new PrintWriter(new FileWriter(file));
1442 this.setTitle(file);
1443 statusBar.setText(MessageManager.formatMessage(
1444 "label.successfully_saved_to_file_in_format", new Object[]
1445 { fileName, format.getName() }));
1446 } catch (Exception ex)
1449 ex.printStackTrace();
1456 JvOptionPane.showInternalMessageDialog(this, MessageManager
1457 .formatMessage("label.couldnt_save_file", new Object[]
1459 MessageManager.getString("label.error_saving_file"),
1460 JvOptionPane.WARNING_MESSAGE);
1466 private void warningMessage(String warning, String title)
1468 if (new jalview.util.Platform().isHeadless())
1470 System.err.println("Warning: " + title + "\nWarning: " + warning);
1475 JvOptionPane.showInternalMessageDialog(this, warning, title,
1476 JvOptionPane.WARNING_MESSAGE);
1488 protected void outputText_actionPerformed(ActionEvent e)
1490 FileFormatI fileFormat = FileFormats.getInstance()
1491 .forName(e.getActionCommand());
1492 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1494 if (exportData.getSettings().isCancelled())
1498 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1499 cap.setForInput(null);
1502 FileFormatI format = fileFormat;
1503 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1504 .formatSequences(format, exportData.getAlignment(),
1505 exportData.getOmitHidden(),
1506 exportData.getStartEndPostions(),
1507 viewport.getAlignment().getHiddenColumns()));
1508 Desktop.addInternalFrame(cap, MessageManager
1509 .formatMessage("label.alignment_output_command", new Object[]
1510 { e.getActionCommand() }), 600, 500);
1511 } catch (OutOfMemoryError oom)
1513 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1520 public static AlignmentExportData getAlignmentForExport(
1521 FileFormatI format, AlignViewportI viewport,
1522 AlignExportSettingI exportSettings)
1524 AlignmentI alignmentToExport = null;
1525 AlignExportSettingI settings = exportSettings;
1526 String[] omitHidden = null;
1528 HiddenSequences hiddenSeqs = viewport.getAlignment()
1529 .getHiddenSequences();
1531 alignmentToExport = viewport.getAlignment();
1533 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1534 if (settings == null)
1536 settings = new AlignExportSettings(hasHiddenSeqs,
1537 viewport.hasHiddenColumns(), format);
1539 // settings.isExportAnnotations();
1541 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1543 omitHidden = viewport.getViewAsString(false,
1544 settings.isExportHiddenSequences());
1547 int[] alignmentStartEnd = new int[2];
1548 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1550 alignmentToExport = hiddenSeqs.getFullAlignment();
1554 alignmentToExport = viewport.getAlignment();
1556 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1557 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1558 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1559 omitHidden, alignmentStartEnd, settings);
1570 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1572 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1573 htmlSVG.exportHTML(null);
1577 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1579 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1580 bjs.exportHTML(null);
1583 public void createImageMap(File file, String image)
1585 alignPanel.makePNGImageMap(file, image);
1595 public void createPNG(File f)
1597 alignPanel.makePNG(f);
1607 public void createEPS(File f)
1609 alignPanel.makeEPS(f);
1613 public void createSVG(File f)
1615 alignPanel.makeSVG(f);
1619 public void pageSetup_actionPerformed(ActionEvent e)
1621 PrinterJob printJob = PrinterJob.getPrinterJob();
1622 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1632 public void printMenuItem_actionPerformed(ActionEvent e)
1634 // Putting in a thread avoids Swing painting problems
1635 PrintThread thread = new PrintThread(alignPanel);
1640 public void exportFeatures_actionPerformed(ActionEvent e)
1642 new AnnotationExporter().exportFeatures(alignPanel);
1646 public void exportAnnotations_actionPerformed(ActionEvent e)
1648 new AnnotationExporter().exportAnnotations(alignPanel);
1652 public void associatedData_actionPerformed(ActionEvent e)
1653 throws IOException, InterruptedException
1655 // Pick the tree file
1656 JalviewFileChooser chooser = new JalviewFileChooser(
1657 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1658 chooser.setFileView(new JalviewFileView());
1659 chooser.setDialogTitle(
1660 MessageManager.getString("label.load_jalview_annotations"));
1661 chooser.setToolTipText(
1662 MessageManager.getString("label.load_jalview_annotations"));
1664 int value = chooser.showOpenDialog(null);
1666 if (value == JalviewFileChooser.APPROVE_OPTION)
1668 String choice = chooser.getSelectedFile().getPath();
1669 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1670 loadJalviewDataFile(choice, null, null, null);
1676 * Close the current view or all views in the alignment frame. If the frame
1677 * only contains one view then the alignment will be removed from memory.
1679 * @param closeAllTabs
1682 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1684 if (alignPanels != null && alignPanels.size() < 2)
1686 closeAllTabs = true;
1691 if (alignPanels != null)
1695 if (this.isClosed())
1697 // really close all the windows - otherwise wait till
1698 // setClosed(true) is called
1699 for (int i = 0; i < alignPanels.size(); i++)
1701 AlignmentPanel ap = alignPanels.get(i);
1708 closeView(alignPanel);
1715 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1716 * be called recursively, with the frame now in 'closed' state
1718 this.setClosed(true);
1720 } catch (Exception ex)
1722 ex.printStackTrace();
1727 * Close the specified panel and close up tabs appropriately.
1729 * @param panelToClose
1731 public void closeView(AlignmentPanel panelToClose)
1733 int index = tabbedPane.getSelectedIndex();
1734 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1735 alignPanels.remove(panelToClose);
1736 panelToClose.closePanel();
1737 panelToClose = null;
1739 tabbedPane.removeTabAt(closedindex);
1740 tabbedPane.validate();
1742 if (index > closedindex || index == tabbedPane.getTabCount())
1744 // modify currently selected tab index if necessary.
1748 this.tabSelectionChanged(index);
1754 void updateEditMenuBar()
1757 if (viewport.getHistoryList().size() > 0)
1759 undoMenuItem.setEnabled(true);
1760 CommandI command = viewport.getHistoryList().peek();
1761 undoMenuItem.setText(MessageManager
1762 .formatMessage("label.undo_command", new Object[]
1763 { command.getDescription() }));
1767 undoMenuItem.setEnabled(false);
1768 undoMenuItem.setText(MessageManager.getString("action.undo"));
1771 if (viewport.getRedoList().size() > 0)
1773 redoMenuItem.setEnabled(true);
1775 CommandI command = viewport.getRedoList().peek();
1776 redoMenuItem.setText(MessageManager
1777 .formatMessage("label.redo_command", new Object[]
1778 { command.getDescription() }));
1782 redoMenuItem.setEnabled(false);
1783 redoMenuItem.setText(MessageManager.getString("action.redo"));
1788 public void addHistoryItem(CommandI command)
1790 if (command.getSize() > 0)
1792 viewport.addToHistoryList(command);
1793 viewport.clearRedoList();
1794 updateEditMenuBar();
1795 viewport.updateHiddenColumns();
1796 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1797 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1798 // viewport.getColumnSelection()
1799 // .getHiddenColumns().size() > 0);
1805 * @return alignment objects for all views
1807 AlignmentI[] getViewAlignments()
1809 if (alignPanels != null)
1811 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1813 for (AlignmentPanel ap : alignPanels)
1815 als[i++] = ap.av.getAlignment();
1819 if (viewport != null)
1821 return new AlignmentI[] { viewport.getAlignment() };
1833 protected void undoMenuItem_actionPerformed(ActionEvent e)
1835 if (viewport.getHistoryList().isEmpty())
1839 CommandI command = viewport.getHistoryList().pop();
1840 viewport.addToRedoList(command);
1841 command.undoCommand(getViewAlignments());
1843 AlignmentViewport originalSource = getOriginatingSource(command);
1844 updateEditMenuBar();
1846 if (originalSource != null)
1848 if (originalSource != viewport)
1851 "Implementation worry: mismatch of viewport origin for undo");
1853 originalSource.updateHiddenColumns();
1854 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1856 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1857 // viewport.getColumnSelection()
1858 // .getHiddenColumns().size() > 0);
1859 originalSource.firePropertyChange("alignment", null,
1860 originalSource.getAlignment().getSequences());
1871 protected void redoMenuItem_actionPerformed(ActionEvent e)
1873 if (viewport.getRedoList().size() < 1)
1878 CommandI command = viewport.getRedoList().pop();
1879 viewport.addToHistoryList(command);
1880 command.doCommand(getViewAlignments());
1882 AlignmentViewport originalSource = getOriginatingSource(command);
1883 updateEditMenuBar();
1885 if (originalSource != null)
1888 if (originalSource != viewport)
1891 "Implementation worry: mismatch of viewport origin for redo");
1893 originalSource.updateHiddenColumns();
1894 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1896 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1897 // viewport.getColumnSelection()
1898 // .getHiddenColumns().size() > 0);
1899 originalSource.firePropertyChange("alignment", null,
1900 originalSource.getAlignment().getSequences());
1904 AlignmentViewport getOriginatingSource(CommandI command)
1906 AlignmentViewport originalSource = null;
1907 // For sequence removal and addition, we need to fire
1908 // the property change event FROM the viewport where the
1909 // original alignment was altered
1910 AlignmentI al = null;
1911 if (command instanceof EditCommand)
1913 EditCommand editCommand = (EditCommand) command;
1914 al = editCommand.getAlignment();
1915 List<Component> comps = PaintRefresher.components
1916 .get(viewport.getSequenceSetId());
1918 for (Component comp : comps)
1920 if (comp instanceof AlignmentPanel)
1922 if (al == ((AlignmentPanel) comp).av.getAlignment())
1924 originalSource = ((AlignmentPanel) comp).av;
1931 if (originalSource == null)
1933 // The original view is closed, we must validate
1934 // the current view against the closed view first
1937 PaintRefresher.validateSequences(al, viewport.getAlignment());
1940 originalSource = viewport;
1943 return originalSource;
1952 public void moveSelectedSequences(boolean up)
1954 SequenceGroup sg = viewport.getSelectionGroup();
1960 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1961 viewport.getHiddenRepSequences(), up);
1962 alignPanel.paintAlignment(true);
1965 synchronized void slideSequences(boolean right, int size)
1967 List<SequenceI> sg = new ArrayList<>();
1968 if (viewport.cursorMode)
1970 sg.add(viewport.getAlignment()
1971 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1973 else if (viewport.getSelectionGroup() != null
1974 && viewport.getSelectionGroup().getSize() != viewport
1975 .getAlignment().getHeight())
1977 sg = viewport.getSelectionGroup()
1978 .getSequences(viewport.getHiddenRepSequences());
1986 List<SequenceI> invertGroup = new ArrayList<>();
1988 for (SequenceI seq : viewport.getAlignment().getSequences())
1990 if (!sg.contains(seq))
1992 invertGroup.add(seq);
1996 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1998 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1999 for (int i = 0; i < invertGroup.size(); i++)
2001 seqs2[i] = invertGroup.get(i);
2004 SlideSequencesCommand ssc;
2007 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
2008 viewport.getGapCharacter());
2012 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
2013 viewport.getGapCharacter());
2016 int groupAdjustment = 0;
2017 if (ssc.getGapsInsertedBegin() && right)
2019 if (viewport.cursorMode)
2021 alignPanel.getSeqPanel().moveCursor(size, 0);
2025 groupAdjustment = size;
2028 else if (!ssc.getGapsInsertedBegin() && !right)
2030 if (viewport.cursorMode)
2032 alignPanel.getSeqPanel().moveCursor(-size, 0);
2036 groupAdjustment = -size;
2040 if (groupAdjustment != 0)
2042 viewport.getSelectionGroup().setStartRes(
2043 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2044 viewport.getSelectionGroup().setEndRes(
2045 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2049 * just extend the last slide command if compatible; but not if in
2050 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2052 boolean appendHistoryItem = false;
2053 Deque<CommandI> historyList = viewport.getHistoryList();
2054 boolean inSplitFrame = getSplitViewContainer() != null;
2055 if (!inSplitFrame && historyList != null && historyList.size() > 0
2056 && historyList.peek() instanceof SlideSequencesCommand)
2058 appendHistoryItem = ssc.appendSlideCommand(
2059 (SlideSequencesCommand) historyList.peek());
2062 if (!appendHistoryItem)
2064 addHistoryItem(ssc);
2077 protected void copy_actionPerformed(ActionEvent e)
2080 if (viewport.getSelectionGroup() == null)
2084 // TODO: preserve the ordering of displayed alignment annotation in any
2085 // internal paste (particularly sequence associated annotation)
2086 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2087 String[] omitHidden = null;
2089 if (viewport.hasHiddenColumns())
2091 omitHidden = viewport.getViewAsString(true);
2094 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2095 seqs, omitHidden, null);
2097 StringSelection ss = new StringSelection(output);
2101 jalview.gui.Desktop.internalCopy = true;
2102 // Its really worth setting the clipboard contents
2103 // to empty before setting the large StringSelection!!
2104 Toolkit.getDefaultToolkit().getSystemClipboard()
2105 .setContents(new StringSelection(""), null);
2107 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2109 } catch (OutOfMemoryError er)
2111 new OOMWarning("copying region", er);
2115 ArrayList<int[]> hiddenColumns = null;
2116 if (viewport.hasHiddenColumns())
2118 hiddenColumns = new ArrayList<>();
2120 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2121 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2122 ArrayList<int[]> hiddenRegions = viewport.getAlignment()
2123 .getHiddenColumns().getHiddenColumnsCopy();
2124 for (int[] region : hiddenRegions)
2127 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
2131 { region[0] - hiddenOffset, region[1] - hiddenOffset });
2136 Desktop.jalviewClipboard = new Object[] { seqs,
2137 viewport.getAlignment().getDataset(), hiddenColumns };
2138 statusBar.setText(MessageManager.formatMessage(
2139 "label.copied_sequences_to_clipboard", new Object[]
2140 { Integer.valueOf(seqs.length).toString() }));
2148 * @throws InterruptedException
2149 * @throws IOException
2152 protected void pasteNew_actionPerformed(ActionEvent e)
2153 throws IOException, InterruptedException
2163 * @throws InterruptedException
2164 * @throws IOException
2167 protected void pasteThis_actionPerformed(ActionEvent e)
2168 throws IOException, InterruptedException
2174 * Paste contents of Jalview clipboard
2176 * @param newAlignment
2177 * true to paste to a new alignment, otherwise add to this.
2178 * @throws InterruptedException
2179 * @throws IOException
2181 void paste(boolean newAlignment) throws IOException, InterruptedException
2183 boolean externalPaste = true;
2186 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2187 Transferable contents = c.getContents(this);
2189 if (contents == null)
2198 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2199 if (str.length() < 1)
2204 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2206 } catch (OutOfMemoryError er)
2208 new OOMWarning("Out of memory pasting sequences!!", er);
2212 SequenceI[] sequences;
2213 boolean annotationAdded = false;
2214 AlignmentI alignment = null;
2216 if (Desktop.jalviewClipboard != null)
2218 // The clipboard was filled from within Jalview, we must use the
2220 // And dataset from the copied alignment
2221 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2222 // be doubly sure that we create *new* sequence objects.
2223 sequences = new SequenceI[newseq.length];
2224 for (int i = 0; i < newseq.length; i++)
2226 sequences[i] = new Sequence(newseq[i]);
2228 alignment = new Alignment(sequences);
2229 externalPaste = false;
2233 // parse the clipboard as an alignment.
2234 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2236 sequences = alignment.getSequencesArray();
2240 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2246 if (Desktop.jalviewClipboard != null)
2248 // dataset is inherited
2249 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2253 // new dataset is constructed
2254 alignment.setDataset(null);
2256 alwidth = alignment.getWidth() + 1;
2260 AlignmentI pastedal = alignment; // preserve pasted alignment object
2261 // Add pasted sequences and dataset into existing alignment.
2262 alignment = viewport.getAlignment();
2263 alwidth = alignment.getWidth() + 1;
2264 // decide if we need to import sequences from an existing dataset
2265 boolean importDs = Desktop.jalviewClipboard != null
2266 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2267 // importDs==true instructs us to copy over new dataset sequences from
2268 // an existing alignment
2269 Vector newDs = (importDs) ? new Vector() : null; // used to create
2270 // minimum dataset set
2272 for (int i = 0; i < sequences.length; i++)
2276 newDs.addElement(null);
2278 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2280 if (importDs && ds != null)
2282 if (!newDs.contains(ds))
2284 newDs.setElementAt(ds, i);
2285 ds = new Sequence(ds);
2286 // update with new dataset sequence
2287 sequences[i].setDatasetSequence(ds);
2291 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2296 // copy and derive new dataset sequence
2297 sequences[i] = sequences[i].deriveSequence();
2298 alignment.getDataset()
2299 .addSequence(sequences[i].getDatasetSequence());
2300 // TODO: avoid creation of duplicate dataset sequences with a
2301 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2303 alignment.addSequence(sequences[i]); // merges dataset
2307 newDs.clear(); // tidy up
2309 if (alignment.getAlignmentAnnotation() != null)
2311 for (AlignmentAnnotation alan : alignment
2312 .getAlignmentAnnotation())
2314 if (alan.graphGroup > fgroup)
2316 fgroup = alan.graphGroup;
2320 if (pastedal.getAlignmentAnnotation() != null)
2322 // Add any annotation attached to alignment.
2323 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2324 for (int i = 0; i < alann.length; i++)
2326 annotationAdded = true;
2327 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2329 AlignmentAnnotation newann = new AlignmentAnnotation(
2331 if (newann.graphGroup > -1)
2333 if (newGraphGroups.size() <= newann.graphGroup
2334 || newGraphGroups.get(newann.graphGroup) == null)
2336 for (int q = newGraphGroups
2337 .size(); q <= newann.graphGroup; q++)
2339 newGraphGroups.add(q, null);
2341 newGraphGroups.set(newann.graphGroup,
2342 new Integer(++fgroup));
2344 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2348 newann.padAnnotation(alwidth);
2349 alignment.addAnnotation(newann);
2359 addHistoryItem(new EditCommand(
2360 MessageManager.getString("label.add_sequences"),
2361 Action.PASTE, sequences, 0, alignment.getWidth(),
2364 // Add any annotations attached to sequences
2365 for (int i = 0; i < sequences.length; i++)
2367 if (sequences[i].getAnnotation() != null)
2369 AlignmentAnnotation newann;
2370 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2372 annotationAdded = true;
2373 newann = sequences[i].getAnnotation()[a];
2374 newann.adjustForAlignment();
2375 newann.padAnnotation(alwidth);
2376 if (newann.graphGroup > -1)
2378 if (newann.graphGroup > -1)
2380 if (newGraphGroups.size() <= newann.graphGroup
2381 || newGraphGroups.get(newann.graphGroup) == null)
2383 for (int q = newGraphGroups
2384 .size(); q <= newann.graphGroup; q++)
2386 newGraphGroups.add(q, null);
2388 newGraphGroups.set(newann.graphGroup,
2389 new Integer(++fgroup));
2391 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2395 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2399 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2407 // propagate alignment changed.
2408 vpRanges.setEndSeq(alignment.getHeight());
2409 if (annotationAdded)
2411 // Duplicate sequence annotation in all views.
2412 AlignmentI[] alview = this.getViewAlignments();
2413 for (int i = 0; i < sequences.length; i++)
2415 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2420 for (int avnum = 0; avnum < alview.length; avnum++)
2422 if (alview[avnum] != alignment)
2424 // duplicate in a view other than the one with input focus
2425 int avwidth = alview[avnum].getWidth() + 1;
2426 // this relies on sann being preserved after we
2427 // modify the sequence's annotation array for each duplication
2428 for (int a = 0; a < sann.length; a++)
2430 AlignmentAnnotation newann = new AlignmentAnnotation(
2432 sequences[i].addAlignmentAnnotation(newann);
2433 newann.padAnnotation(avwidth);
2434 alview[avnum].addAnnotation(newann); // annotation was
2435 // duplicated earlier
2436 // TODO JAL-1145 graphGroups are not updated for sequence
2437 // annotation added to several views. This may cause
2439 alview[avnum].setAnnotationIndex(newann, a);
2444 buildSortByAnnotationScoresMenu();
2446 viewport.firePropertyChange("alignment", null,
2447 alignment.getSequences());
2448 if (alignPanels != null)
2450 for (AlignmentPanel ap : alignPanels)
2452 ap.validateAnnotationDimensions(false);
2457 alignPanel.validateAnnotationDimensions(false);
2463 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2465 String newtitle = new String("Copied sequences");
2467 if (Desktop.jalviewClipboard != null
2468 && Desktop.jalviewClipboard[2] != null)
2470 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2471 for (int[] region : hc)
2473 af.viewport.hideColumns(region[0], region[1]);
2477 // >>>This is a fix for the moment, until a better solution is
2479 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2480 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2481 .getFeatureRenderer());
2483 // TODO: maintain provenance of an alignment, rather than just make the
2484 // title a concatenation of operations.
2487 if (title.startsWith("Copied sequences"))
2493 newtitle = newtitle.concat("- from " + title);
2498 newtitle = new String("Pasted sequences");
2501 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2506 } catch (Exception ex)
2508 ex.printStackTrace();
2509 System.out.println("Exception whilst pasting: " + ex);
2510 // could be anything being pasted in here
2515 protected void expand_newalign(ActionEvent e)
2519 AlignmentI alignment = AlignmentUtils
2520 .expandContext(getViewport().getAlignment(), -1);
2521 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2523 String newtitle = new String("Flanking alignment");
2525 if (Desktop.jalviewClipboard != null
2526 && Desktop.jalviewClipboard[2] != null)
2528 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2529 for (int region[] : hc)
2531 af.viewport.hideColumns(region[0], region[1]);
2535 // >>>This is a fix for the moment, until a better solution is
2537 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2538 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2539 .getFeatureRenderer());
2541 // TODO: maintain provenance of an alignment, rather than just make the
2542 // title a concatenation of operations.
2544 if (title.startsWith("Copied sequences"))
2550 newtitle = newtitle.concat("- from " + title);
2554 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2556 } catch (Exception ex)
2558 ex.printStackTrace();
2559 System.out.println("Exception whilst pasting: " + ex);
2560 // could be anything being pasted in here
2561 } catch (OutOfMemoryError oom)
2563 new OOMWarning("Viewing flanking region of alignment", oom);
2574 protected void cut_actionPerformed(ActionEvent e)
2576 copy_actionPerformed(null);
2577 delete_actionPerformed(null);
2587 protected void delete_actionPerformed(ActionEvent evt)
2590 SequenceGroup sg = viewport.getSelectionGroup();
2597 * If the cut affects all sequences, warn, remove highlighted columns
2599 if (sg.getSize() == viewport.getAlignment().getHeight())
2601 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2602 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2603 if (isEntireAlignWidth)
2605 int confirm = JvOptionPane.showConfirmDialog(this,
2606 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2607 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2608 JvOptionPane.OK_CANCEL_OPTION);
2610 if (confirm == JvOptionPane.CANCEL_OPTION
2611 || confirm == JvOptionPane.CLOSED_OPTION)
2616 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2617 sg.getEndRes() + 1);
2619 SequenceI[] cut = sg.getSequences()
2620 .toArray(new SequenceI[sg.getSize()]);
2622 addHistoryItem(new EditCommand(
2623 MessageManager.getString("label.cut_sequences"), Action.CUT,
2624 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2625 viewport.getAlignment()));
2627 viewport.setSelectionGroup(null);
2628 viewport.sendSelection();
2629 viewport.getAlignment().deleteGroup(sg);
2631 viewport.firePropertyChange("alignment", null,
2632 viewport.getAlignment().getSequences());
2633 if (viewport.getAlignment().getHeight() < 1)
2637 this.setClosed(true);
2638 } catch (Exception ex)
2651 protected void deleteGroups_actionPerformed(ActionEvent e)
2653 if (avc.deleteGroups())
2655 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2656 alignPanel.updateAnnotation();
2657 alignPanel.paintAlignment(true);
2668 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2670 SequenceGroup sg = new SequenceGroup();
2672 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2674 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2677 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2678 viewport.setSelectionGroup(sg);
2679 viewport.sendSelection();
2680 // JAL-2034 - should delegate to
2681 // alignPanel to decide if overview needs
2683 alignPanel.paintAlignment(false);
2684 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2694 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2696 if (viewport.cursorMode)
2698 alignPanel.getSeqPanel().keyboardNo1 = null;
2699 alignPanel.getSeqPanel().keyboardNo2 = null;
2701 viewport.setSelectionGroup(null);
2702 viewport.getColumnSelection().clear();
2703 viewport.setSelectionGroup(null);
2704 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2705 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2706 // JAL-2034 - should delegate to
2707 // alignPanel to decide if overview needs
2709 alignPanel.paintAlignment(false);
2710 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2711 viewport.sendSelection();
2721 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2723 SequenceGroup sg = viewport.getSelectionGroup();
2727 selectAllSequenceMenuItem_actionPerformed(null);
2732 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2734 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2736 // JAL-2034 - should delegate to
2737 // alignPanel to decide if overview needs
2740 alignPanel.paintAlignment(true);
2741 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2742 viewport.sendSelection();
2746 public void invertColSel_actionPerformed(ActionEvent e)
2748 viewport.invertColumnSelection();
2749 alignPanel.paintAlignment(true);
2750 viewport.sendSelection();
2760 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2762 trimAlignment(true);
2772 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2774 trimAlignment(false);
2777 void trimAlignment(boolean trimLeft)
2779 ColumnSelection colSel = viewport.getColumnSelection();
2782 if (!colSel.isEmpty())
2786 column = colSel.getMin();
2790 column = colSel.getMax();
2794 if (viewport.getSelectionGroup() != null)
2796 seqs = viewport.getSelectionGroup()
2797 .getSequencesAsArray(viewport.getHiddenRepSequences());
2801 seqs = viewport.getAlignment().getSequencesArray();
2804 TrimRegionCommand trimRegion;
2807 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2808 column, viewport.getAlignment());
2809 vpRanges.setStartRes(0);
2813 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2814 column, viewport.getAlignment());
2817 statusBar.setText(MessageManager
2818 .formatMessage("label.removed_columns", new String[]
2819 { Integer.valueOf(trimRegion.getSize()).toString() }));
2821 addHistoryItem(trimRegion);
2823 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2825 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2826 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2828 viewport.getAlignment().deleteGroup(sg);
2832 viewport.firePropertyChange("alignment", null,
2833 viewport.getAlignment().getSequences());
2844 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2846 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2849 if (viewport.getSelectionGroup() != null)
2851 seqs = viewport.getSelectionGroup()
2852 .getSequencesAsArray(viewport.getHiddenRepSequences());
2853 start = viewport.getSelectionGroup().getStartRes();
2854 end = viewport.getSelectionGroup().getEndRes();
2858 seqs = viewport.getAlignment().getSequencesArray();
2861 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2862 "Remove Gapped Columns", seqs, start, end,
2863 viewport.getAlignment());
2865 addHistoryItem(removeGapCols);
2867 statusBar.setText(MessageManager
2868 .formatMessage("label.removed_empty_columns", new Object[]
2869 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2871 // This is to maintain viewport position on first residue
2872 // of first sequence
2873 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2874 int startRes = seq.findPosition(vpRanges.getStartRes());
2875 // ShiftList shifts;
2876 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2877 // edit.alColumnChanges=shifts.getInverse();
2878 // if (viewport.hasHiddenColumns)
2879 // viewport.getColumnSelection().compensateForEdits(shifts);
2880 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2881 viewport.firePropertyChange("alignment", null,
2882 viewport.getAlignment().getSequences());
2893 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2895 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2898 if (viewport.getSelectionGroup() != null)
2900 seqs = viewport.getSelectionGroup()
2901 .getSequencesAsArray(viewport.getHiddenRepSequences());
2902 start = viewport.getSelectionGroup().getStartRes();
2903 end = viewport.getSelectionGroup().getEndRes();
2907 seqs = viewport.getAlignment().getSequencesArray();
2910 // This is to maintain viewport position on first residue
2911 // of first sequence
2912 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2913 int startRes = seq.findPosition(vpRanges.getStartRes());
2915 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2916 viewport.getAlignment()));
2918 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2920 viewport.firePropertyChange("alignment", null,
2921 viewport.getAlignment().getSequences());
2932 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2934 viewport.setPadGaps(padGapsMenuitem.isSelected());
2935 viewport.firePropertyChange("alignment", null,
2936 viewport.getAlignment().getSequences());
2946 public void findMenuItem_actionPerformed(ActionEvent e)
2952 * Create a new view of the current alignment.
2955 public void newView_actionPerformed(ActionEvent e)
2957 newView(null, true);
2961 * Creates and shows a new view of the current alignment.
2964 * title of newly created view; if null, one will be generated
2965 * @param copyAnnotation
2966 * if true then duplicate all annnotation, groups and settings
2967 * @return new alignment panel, already displayed.
2969 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2972 * Create a new AlignmentPanel (with its own, new Viewport)
2974 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2976 if (!copyAnnotation)
2979 * remove all groups and annotation except for the automatic stuff
2981 newap.av.getAlignment().deleteAllGroups();
2982 newap.av.getAlignment().deleteAllAnnotations(false);
2985 newap.av.setGatherViewsHere(false);
2987 if (viewport.viewName == null)
2989 viewport.viewName = MessageManager
2990 .getString("label.view_name_original");
2994 * Views share the same edits undo and redo stacks
2996 newap.av.setHistoryList(viewport.getHistoryList());
2997 newap.av.setRedoList(viewport.getRedoList());
3000 * Views share the same mappings; need to deregister any new mappings
3001 * created by copyAlignPanel, and register the new reference to the shared
3004 newap.av.replaceMappings(viewport.getAlignment());
3007 * start up cDNA consensus (if applicable) now mappings are in place
3009 if (newap.av.initComplementConsensus())
3011 newap.refresh(true); // adjust layout of annotations
3014 newap.av.viewName = getNewViewName(viewTitle);
3016 addAlignmentPanel(newap, true);
3017 newap.alignmentChanged();
3019 if (alignPanels.size() == 2)
3021 viewport.setGatherViewsHere(true);
3023 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
3028 * Make a new name for the view, ensuring it is unique within the current
3029 * sequenceSetId. (This used to be essential for Jalview Project archives, but
3030 * these now use viewId. Unique view names are still desirable for usability.)
3035 protected String getNewViewName(String viewTitle)
3037 int index = Desktop.getViewCount(viewport.getSequenceSetId());
3038 boolean addFirstIndex = false;
3039 if (viewTitle == null || viewTitle.trim().length() == 0)
3041 viewTitle = MessageManager.getString("action.view");
3042 addFirstIndex = true;
3046 index = 1;// we count from 1 if given a specific name
3048 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3050 List<Component> comps = PaintRefresher.components
3051 .get(viewport.getSequenceSetId());
3053 List<String> existingNames = getExistingViewNames(comps);
3055 while (existingNames.contains(newViewName))
3057 newViewName = viewTitle + " " + (++index);
3063 * Returns a list of distinct view names found in the given list of
3064 * components. View names are held on the viewport of an AlignmentPanel.
3069 protected List<String> getExistingViewNames(List<Component> comps)
3071 List<String> existingNames = new ArrayList<>();
3072 for (Component comp : comps)
3074 if (comp instanceof AlignmentPanel)
3076 AlignmentPanel ap = (AlignmentPanel) comp;
3077 if (!existingNames.contains(ap.av.viewName))
3079 existingNames.add(ap.av.viewName);
3083 return existingNames;
3087 * Explode tabbed views into separate windows.
3090 public void expandViews_actionPerformed(ActionEvent e)
3092 Desktop.explodeViews(this);
3096 * Gather views in separate windows back into a tabbed presentation.
3099 public void gatherViews_actionPerformed(ActionEvent e)
3101 Desktop.instance.gatherViews(this);
3111 public void font_actionPerformed(ActionEvent e)
3113 new FontChooser(alignPanel);
3123 protected void seqLimit_actionPerformed(ActionEvent e)
3125 viewport.setShowJVSuffix(seqLimits.isSelected());
3127 alignPanel.getIdPanel().getIdCanvas()
3128 .setPreferredSize(alignPanel.calculateIdWidth());
3129 alignPanel.paintAlignment(true);
3133 public void idRightAlign_actionPerformed(ActionEvent e)
3135 viewport.setRightAlignIds(idRightAlign.isSelected());
3136 alignPanel.paintAlignment(true);
3140 public void centreColumnLabels_actionPerformed(ActionEvent e)
3142 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3143 alignPanel.paintAlignment(true);
3149 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3152 protected void followHighlight_actionPerformed()
3155 * Set the 'follow' flag on the Viewport (and scroll to position if now
3158 final boolean state = this.followHighlightMenuItem.getState();
3159 viewport.setFollowHighlight(state);
3162 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
3173 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3175 viewport.setColourText(colourTextMenuItem.isSelected());
3176 alignPanel.paintAlignment(true);
3186 public void wrapMenuItem_actionPerformed(ActionEvent e)
3188 scaleAbove.setVisible(wrapMenuItem.isSelected());
3189 scaleLeft.setVisible(wrapMenuItem.isSelected());
3190 scaleRight.setVisible(wrapMenuItem.isSelected());
3191 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3192 alignPanel.updateLayout();
3196 public void showAllSeqs_actionPerformed(ActionEvent e)
3198 viewport.showAllHiddenSeqs();
3202 public void showAllColumns_actionPerformed(ActionEvent e)
3204 viewport.showAllHiddenColumns();
3205 alignPanel.paintAlignment(true);
3206 viewport.sendSelection();
3210 public void hideSelSequences_actionPerformed(ActionEvent e)
3212 viewport.hideAllSelectedSeqs();
3216 * called by key handler and the hide all/show all menu items
3221 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3224 boolean hide = false;
3225 SequenceGroup sg = viewport.getSelectionGroup();
3226 if (!toggleSeqs && !toggleCols)
3228 // Hide everything by the current selection - this is a hack - we do the
3229 // invert and then hide
3230 // first check that there will be visible columns after the invert.
3231 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3232 && sg.getStartRes() <= sg.getEndRes()))
3234 // now invert the sequence set, if required - empty selection implies
3235 // that no hiding is required.
3238 invertSequenceMenuItem_actionPerformed(null);
3239 sg = viewport.getSelectionGroup();
3243 viewport.expandColSelection(sg, true);
3244 // finally invert the column selection and get the new sequence
3246 invertColSel_actionPerformed(null);
3253 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3255 hideSelSequences_actionPerformed(null);
3258 else if (!(toggleCols && viewport.hasSelectedColumns()))
3260 showAllSeqs_actionPerformed(null);
3266 if (viewport.hasSelectedColumns())
3268 hideSelColumns_actionPerformed(null);
3271 viewport.setSelectionGroup(sg);
3276 showAllColumns_actionPerformed(null);
3285 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3286 * event.ActionEvent)
3289 public void hideAllButSelection_actionPerformed(ActionEvent e)
3291 toggleHiddenRegions(false, false);
3292 viewport.sendSelection();
3299 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3303 public void hideAllSelection_actionPerformed(ActionEvent e)
3305 SequenceGroup sg = viewport.getSelectionGroup();
3306 viewport.expandColSelection(sg, false);
3307 viewport.hideAllSelectedSeqs();
3308 viewport.hideSelectedColumns();
3309 alignPanel.paintAlignment(true);
3310 viewport.sendSelection();
3317 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3321 public void showAllhidden_actionPerformed(ActionEvent e)
3323 viewport.showAllHiddenColumns();
3324 viewport.showAllHiddenSeqs();
3325 alignPanel.paintAlignment(true);
3326 viewport.sendSelection();
3330 public void hideSelColumns_actionPerformed(ActionEvent e)
3332 viewport.hideSelectedColumns();
3333 alignPanel.paintAlignment(true);
3334 viewport.sendSelection();
3338 public void hiddenMarkers_actionPerformed(ActionEvent e)
3340 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3351 protected void scaleAbove_actionPerformed(ActionEvent e)
3353 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3354 alignPanel.paintAlignment(true);
3364 protected void scaleLeft_actionPerformed(ActionEvent e)
3366 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3367 alignPanel.paintAlignment(true);
3377 protected void scaleRight_actionPerformed(ActionEvent e)
3379 viewport.setScaleRightWrapped(scaleRight.isSelected());
3380 alignPanel.paintAlignment(true);
3390 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3392 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3393 alignPanel.paintAlignment(true);
3403 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3405 viewport.setShowText(viewTextMenuItem.isSelected());
3406 alignPanel.paintAlignment(true);
3416 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3418 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3419 alignPanel.paintAlignment(true);
3422 public FeatureSettings featureSettings;
3425 public FeatureSettingsControllerI getFeatureSettingsUI()
3427 return featureSettings;
3431 public void featureSettings_actionPerformed(ActionEvent e)
3433 if (featureSettings != null)
3435 featureSettings.close();
3436 featureSettings = null;
3438 if (!showSeqFeatures.isSelected())
3440 // make sure features are actually displayed
3441 showSeqFeatures.setSelected(true);
3442 showSeqFeatures_actionPerformed(null);
3444 featureSettings = new FeatureSettings(this);
3448 * Set or clear 'Show Sequence Features'
3454 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3456 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3457 alignPanel.paintAlignment(true);
3461 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3462 * the annotations panel as a whole.
3464 * The options to show/hide all annotations should be enabled when the panel
3465 * is shown, and disabled when the panel is hidden.
3470 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3472 final boolean setVisible = annotationPanelMenuItem.isSelected();
3473 viewport.setShowAnnotation(setVisible);
3474 this.showAllSeqAnnotations.setEnabled(setVisible);
3475 this.hideAllSeqAnnotations.setEnabled(setVisible);
3476 this.showAllAlAnnotations.setEnabled(setVisible);
3477 this.hideAllAlAnnotations.setEnabled(setVisible);
3478 alignPanel.updateLayout();
3482 public void alignmentProperties()
3484 JEditorPane editPane = new JEditorPane("text/html", "");
3485 editPane.setEditable(false);
3486 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3489 MessageManager.formatMessage("label.html_content", new Object[]
3490 { contents.toString() }));
3491 JInternalFrame frame = new JInternalFrame();
3492 frame.getContentPane().add(new JScrollPane(editPane));
3494 Desktop.addInternalFrame(frame, MessageManager
3495 .formatMessage("label.alignment_properties", new Object[]
3496 { getTitle() }), 500, 400);
3506 public void overviewMenuItem_actionPerformed(ActionEvent e)
3508 if (alignPanel.overviewPanel != null)
3513 JInternalFrame frame = new JInternalFrame();
3514 final OverviewPanel overview = new OverviewPanel(alignPanel);
3515 frame.setContentPane(overview);
3516 Desktop.addInternalFrame(frame, MessageManager
3517 .formatMessage("label.overview_params", new Object[]
3518 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3521 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3522 frame.addInternalFrameListener(
3523 new javax.swing.event.InternalFrameAdapter()
3526 public void internalFrameClosed(
3527 javax.swing.event.InternalFrameEvent evt)
3530 alignPanel.setOverviewPanel(null);
3534 alignPanel.setOverviewPanel(overview);
3538 public void textColour_actionPerformed()
3540 new TextColourChooser().chooseColour(alignPanel, null);
3544 * public void covariationColour_actionPerformed() {
3546 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3550 public void annotationColour_actionPerformed()
3552 new AnnotationColourChooser(viewport, alignPanel);
3556 public void annotationColumn_actionPerformed(ActionEvent e)
3558 new AnnotationColumnChooser(viewport, alignPanel);
3562 * Action on the user checking or unchecking the option to apply the selected
3563 * colour scheme to all groups. If unchecked, groups may have their own
3564 * independent colour schemes.
3569 public void applyToAllGroups_actionPerformed(boolean selected)
3571 viewport.setColourAppliesToAllGroups(selected);
3575 * Action on user selecting a colour from the colour menu
3578 * the name (not the menu item label!) of the colour scheme
3581 public void changeColour_actionPerformed(String name)
3584 * 'User Defined' opens a panel to configure or load a
3585 * user-defined colour scheme
3587 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3589 new UserDefinedColours(alignPanel);
3594 * otherwise set the chosen colour scheme (or null for 'None')
3596 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3597 viewport.getAlignment(), viewport.getHiddenRepSequences());
3602 * Actions on setting or changing the alignment colour scheme
3607 public void changeColour(ColourSchemeI cs)
3609 // TODO: pull up to controller method
3610 ColourMenuHelper.setColourSelected(colourMenu, cs);
3612 viewport.setGlobalColourScheme(cs);
3614 alignPanel.paintAlignment(true);
3618 * Show the PID threshold slider panel
3621 protected void modifyPID_actionPerformed()
3623 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3624 alignPanel.getViewName());
3625 SliderPanel.showPIDSlider();
3629 * Show the Conservation slider panel
3632 protected void modifyConservation_actionPerformed()
3634 SliderPanel.setConservationSlider(alignPanel,
3635 viewport.getResidueShading(), alignPanel.getViewName());
3636 SliderPanel.showConservationSlider();
3640 * Action on selecting or deselecting (Colour) By Conservation
3643 public void conservationMenuItem_actionPerformed(boolean selected)
3645 modifyConservation.setEnabled(selected);
3646 viewport.setConservationSelected(selected);
3647 viewport.getResidueShading().setConservationApplied(selected);
3649 changeColour(viewport.getGlobalColourScheme());
3652 modifyConservation_actionPerformed();
3656 SliderPanel.hideConservationSlider();
3661 * Action on selecting or deselecting (Colour) Above PID Threshold
3664 public void abovePIDThreshold_actionPerformed(boolean selected)
3666 modifyPID.setEnabled(selected);
3667 viewport.setAbovePIDThreshold(selected);
3670 viewport.getResidueShading().setThreshold(0,
3671 viewport.isIgnoreGapsConsensus());
3674 changeColour(viewport.getGlobalColourScheme());
3677 modifyPID_actionPerformed();
3681 SliderPanel.hidePIDSlider();
3692 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3694 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3695 AlignmentSorter.sortByPID(viewport.getAlignment(),
3696 viewport.getAlignment().getSequenceAt(0));
3697 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3698 viewport.getAlignment()));
3699 alignPanel.paintAlignment(true);
3709 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3711 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3712 AlignmentSorter.sortByID(viewport.getAlignment());
3714 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3715 alignPanel.paintAlignment(true);
3725 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3727 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3728 AlignmentSorter.sortByLength(viewport.getAlignment());
3729 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3730 viewport.getAlignment()));
3731 alignPanel.paintAlignment(true);
3741 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3743 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3744 AlignmentSorter.sortByGroup(viewport.getAlignment());
3745 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3746 viewport.getAlignment()));
3748 alignPanel.paintAlignment(true);
3758 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3760 new RedundancyPanel(alignPanel, this);
3770 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3772 if ((viewport.getSelectionGroup() == null)
3773 || (viewport.getSelectionGroup().getSize() < 2))
3775 JvOptionPane.showInternalMessageDialog(this,
3776 MessageManager.getString(
3777 "label.you_must_select_least_two_sequences"),
3778 MessageManager.getString("label.invalid_selection"),
3779 JvOptionPane.WARNING_MESSAGE);
3783 JInternalFrame frame = new JInternalFrame();
3784 frame.setContentPane(new PairwiseAlignPanel(viewport));
3785 Desktop.addInternalFrame(frame,
3786 MessageManager.getString("action.pairwise_alignment"), 600,
3792 public void autoCalculate_actionPerformed(ActionEvent e)
3794 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3795 if (viewport.autoCalculateConsensus)
3797 viewport.firePropertyChange("alignment", null,
3798 viewport.getAlignment().getSequences());
3803 public void sortByTreeOption_actionPerformed(ActionEvent e)
3805 viewport.sortByTree = sortByTree.isSelected();
3809 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3811 viewport.followSelection = listenToViewSelections.isSelected();
3815 * Constructs a tree panel and adds it to the desktop
3818 * tree type (NJ or AV)
3820 * name of score model used to compute the tree
3822 * parameters for the distance or similarity calculation
3824 void newTreePanel(String type, String modelName,
3825 SimilarityParamsI options)
3827 String frameTitle = "";
3830 boolean onSelection = false;
3831 if (viewport.getSelectionGroup() != null
3832 && viewport.getSelectionGroup().getSize() > 0)
3834 SequenceGroup sg = viewport.getSelectionGroup();
3836 /* Decide if the selection is a column region */
3837 for (SequenceI _s : sg.getSequences())
3839 if (_s.getLength() < sg.getEndRes())
3841 JvOptionPane.showMessageDialog(Desktop.desktop,
3842 MessageManager.getString(
3843 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3844 MessageManager.getString(
3845 "label.sequences_selection_not_aligned"),
3846 JvOptionPane.WARNING_MESSAGE);
3855 if (viewport.getAlignment().getHeight() < 2)
3861 tp = new TreePanel(alignPanel, type, modelName, options);
3862 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3864 frameTitle += " from ";
3866 if (viewport.viewName != null)
3868 frameTitle += viewport.viewName + " of ";
3871 frameTitle += this.title;
3873 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3884 public void addSortByOrderMenuItem(String title,
3885 final AlignmentOrder order)
3887 final JMenuItem item = new JMenuItem(MessageManager
3888 .formatMessage("action.by_title_param", new Object[]
3891 item.addActionListener(new java.awt.event.ActionListener()
3894 public void actionPerformed(ActionEvent e)
3896 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3898 // TODO: JBPNote - have to map order entries to curent SequenceI
3900 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3902 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3903 viewport.getAlignment()));
3905 alignPanel.paintAlignment(true);
3911 * Add a new sort by annotation score menu item
3914 * the menu to add the option to
3916 * the label used to retrieve scores for each sequence on the
3919 public void addSortByAnnotScoreMenuItem(JMenu sort,
3920 final String scoreLabel)
3922 final JMenuItem item = new JMenuItem(scoreLabel);
3924 item.addActionListener(new java.awt.event.ActionListener()
3927 public void actionPerformed(ActionEvent e)
3929 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3930 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3931 viewport.getAlignment());// ,viewport.getSelectionGroup());
3932 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3933 viewport.getAlignment()));
3934 alignPanel.paintAlignment(true);
3940 * last hash for alignment's annotation array - used to minimise cost of
3943 protected int _annotationScoreVectorHash;
3946 * search the alignment and rebuild the sort by annotation score submenu the
3947 * last alignment annotation vector hash is stored to minimize cost of
3948 * rebuilding in subsequence calls.
3952 public void buildSortByAnnotationScoresMenu()
3954 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3959 if (viewport.getAlignment().getAlignmentAnnotation()
3960 .hashCode() != _annotationScoreVectorHash)
3962 sortByAnnotScore.removeAll();
3963 // almost certainly a quicker way to do this - but we keep it simple
3964 Hashtable scoreSorts = new Hashtable();
3965 AlignmentAnnotation aann[];
3966 for (SequenceI sqa : viewport.getAlignment().getSequences())
3968 aann = sqa.getAnnotation();
3969 for (int i = 0; aann != null && i < aann.length; i++)
3971 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3973 scoreSorts.put(aann[i].label, aann[i].label);
3977 Enumeration labels = scoreSorts.keys();
3978 while (labels.hasMoreElements())
3980 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3981 (String) labels.nextElement());
3983 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3986 _annotationScoreVectorHash = viewport.getAlignment()
3987 .getAlignmentAnnotation().hashCode();
3992 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3993 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3994 * call. Listeners are added to remove the menu item when the treePanel is
3995 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3999 public void buildTreeSortMenu()
4001 sortByTreeMenu.removeAll();
4003 List<Component> comps = PaintRefresher.components
4004 .get(viewport.getSequenceSetId());
4005 List<TreePanel> treePanels = new ArrayList<>();
4006 for (Component comp : comps)
4008 if (comp instanceof TreePanel)
4010 treePanels.add((TreePanel) comp);
4014 if (treePanels.size() < 1)
4016 sortByTreeMenu.setVisible(false);
4020 sortByTreeMenu.setVisible(true);
4022 for (final TreePanel tp : treePanels)
4024 final JMenuItem item = new JMenuItem(tp.getTitle());
4025 item.addActionListener(new java.awt.event.ActionListener()
4028 public void actionPerformed(ActionEvent e)
4030 tp.sortByTree_actionPerformed();
4031 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4036 sortByTreeMenu.add(item);
4040 public boolean sortBy(AlignmentOrder alorder, String undoname)
4042 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4043 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4044 if (undoname != null)
4046 addHistoryItem(new OrderCommand(undoname, oldOrder,
4047 viewport.getAlignment()));
4049 alignPanel.paintAlignment(true);
4054 * Work out whether the whole set of sequences or just the selected set will
4055 * be submitted for multiple alignment.
4058 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4060 // Now, check we have enough sequences
4061 AlignmentView msa = null;
4063 if ((viewport.getSelectionGroup() != null)
4064 && (viewport.getSelectionGroup().getSize() > 1))
4066 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4067 // some common interface!
4069 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4070 * SequenceI[sz = seqs.getSize(false)];
4072 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4073 * seqs.getSequenceAt(i); }
4075 msa = viewport.getAlignmentView(true);
4077 else if (viewport.getSelectionGroup() != null
4078 && viewport.getSelectionGroup().getSize() == 1)
4080 int option = JvOptionPane.showConfirmDialog(this,
4081 MessageManager.getString("warn.oneseq_msainput_selection"),
4082 MessageManager.getString("label.invalid_selection"),
4083 JvOptionPane.OK_CANCEL_OPTION);
4084 if (option == JvOptionPane.OK_OPTION)
4086 msa = viewport.getAlignmentView(false);
4091 msa = viewport.getAlignmentView(false);
4097 * Decides what is submitted to a secondary structure prediction service: the
4098 * first sequence in the alignment, or in the current selection, or, if the
4099 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4100 * region or the whole alignment. (where the first sequence in the set is the
4101 * one that the prediction will be for).
4103 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4105 AlignmentView seqs = null;
4107 if ((viewport.getSelectionGroup() != null)
4108 && (viewport.getSelectionGroup().getSize() > 0))
4110 seqs = viewport.getAlignmentView(true);
4114 seqs = viewport.getAlignmentView(false);
4116 // limit sequences - JBPNote in future - could spawn multiple prediction
4118 // TODO: viewport.getAlignment().isAligned is a global state - the local
4119 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4120 if (!viewport.getAlignment().isAligned(false))
4122 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4123 // TODO: if seqs.getSequences().length>1 then should really have warned
4137 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4139 // Pick the tree file
4140 JalviewFileChooser chooser = new JalviewFileChooser(
4141 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4142 chooser.setFileView(new JalviewFileView());
4143 chooser.setDialogTitle(
4144 MessageManager.getString("label.select_newick_like_tree_file"));
4145 chooser.setToolTipText(
4146 MessageManager.getString("label.load_tree_file"));
4148 int value = chooser.showOpenDialog(null);
4150 if (value == JalviewFileChooser.APPROVE_OPTION)
4152 String filePath = chooser.getSelectedFile().getPath();
4153 Cache.setProperty("LAST_DIRECTORY", filePath);
4154 NewickFile fin = null;
4157 fin = new NewickFile(filePath, DataSourceType.FILE);
4158 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4159 } catch (Exception ex)
4161 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4162 MessageManager.getString("label.problem_reading_tree_file"),
4163 JvOptionPane.WARNING_MESSAGE);
4164 ex.printStackTrace();
4166 if (fin != null && fin.hasWarningMessage())
4168 JvOptionPane.showMessageDialog(Desktop.desktop,
4169 fin.getWarningMessage(),
4171 .getString("label.possible_problem_with_tree_file"),
4172 JvOptionPane.WARNING_MESSAGE);
4177 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4179 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4182 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4183 int h, int x, int y)
4185 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4189 * Add a treeviewer for the tree extracted from a Newick file object to the
4190 * current alignment view
4197 * Associated alignment input data (or null)
4206 * @return TreePanel handle
4208 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4209 AlignmentView input, int w, int h, int x, int y)
4211 TreePanel tp = null;
4217 if (nf.getTree() != null)
4219 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4225 tp.setLocation(x, y);
4228 Desktop.addInternalFrame(tp, treeTitle, w, h);
4230 } catch (Exception ex)
4232 ex.printStackTrace();
4238 private boolean buildingMenu = false;
4241 * Generates menu items and listener event actions for web service clients
4244 public void BuildWebServiceMenu()
4246 while (buildingMenu)
4250 System.err.println("Waiting for building menu to finish.");
4252 } catch (Exception e)
4256 final AlignFrame me = this;
4257 buildingMenu = true;
4258 new Thread(new Runnable()
4263 final List<JMenuItem> legacyItems = new ArrayList<>();
4266 // System.err.println("Building ws menu again "
4267 // + Thread.currentThread());
4268 // TODO: add support for context dependent disabling of services based
4270 // alignment and current selection
4271 // TODO: add additional serviceHandle parameter to specify abstract
4273 // class independently of AbstractName
4274 // TODO: add in rediscovery GUI function to restart discoverer
4275 // TODO: group services by location as well as function and/or
4277 // object broker mechanism.
4278 final Vector<JMenu> wsmenu = new Vector<>();
4279 final IProgressIndicator af = me;
4282 * do not i18n these strings - they are hard-coded in class
4283 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4284 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4286 final JMenu msawsmenu = new JMenu("Alignment");
4287 final JMenu secstrmenu = new JMenu(
4288 "Secondary Structure Prediction");
4289 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4290 final JMenu analymenu = new JMenu("Analysis");
4291 final JMenu dismenu = new JMenu("Protein Disorder");
4292 // JAL-940 - only show secondary structure prediction services from
4293 // the legacy server
4294 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4296 Discoverer.services != null && (Discoverer.services.size() > 0))
4298 // TODO: refactor to allow list of AbstractName/Handler bindings to
4300 // stored or retrieved from elsewhere
4301 // No MSAWS used any more:
4302 // Vector msaws = null; // (Vector)
4303 // Discoverer.services.get("MsaWS");
4304 Vector secstrpr = (Vector) Discoverer.services
4306 if (secstrpr != null)
4308 // Add any secondary structure prediction services
4309 for (int i = 0, j = secstrpr.size(); i < j; i++)
4311 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4313 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4314 .getServiceClient(sh);
4315 int p = secstrmenu.getItemCount();
4316 impl.attachWSMenuEntry(secstrmenu, me);
4317 int q = secstrmenu.getItemCount();
4318 for (int litm = p; litm < q; litm++)
4320 legacyItems.add(secstrmenu.getItem(litm));
4326 // Add all submenus in the order they should appear on the web
4328 wsmenu.add(msawsmenu);
4329 wsmenu.add(secstrmenu);
4330 wsmenu.add(dismenu);
4331 wsmenu.add(analymenu);
4332 // No search services yet
4333 // wsmenu.add(seqsrchmenu);
4335 javax.swing.SwingUtilities.invokeLater(new Runnable()
4342 webService.removeAll();
4343 // first, add discovered services onto the webservices menu
4344 if (wsmenu.size() > 0)
4346 for (int i = 0, j = wsmenu.size(); i < j; i++)
4348 webService.add(wsmenu.get(i));
4353 webService.add(me.webServiceNoServices);
4355 // TODO: move into separate menu builder class.
4356 boolean new_sspred = false;
4357 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4359 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4360 if (jws2servs != null)
4362 if (jws2servs.hasServices())
4364 jws2servs.attachWSMenuEntry(webService, me);
4365 for (Jws2Instance sv : jws2servs.getServices())
4367 if (sv.description.toLowerCase().contains("jpred"))
4369 for (JMenuItem jmi : legacyItems)
4371 jmi.setVisible(false);
4377 if (jws2servs.isRunning())
4379 JMenuItem tm = new JMenuItem(
4380 "Still discovering JABA Services");
4381 tm.setEnabled(false);
4386 build_urlServiceMenu(me.webService);
4387 build_fetchdbmenu(webService);
4388 for (JMenu item : wsmenu)
4390 if (item.getItemCount() == 0)
4392 item.setEnabled(false);
4396 item.setEnabled(true);
4399 } catch (Exception e)
4402 "Exception during web service menu building process.",
4407 } catch (Exception e)
4410 buildingMenu = false;
4417 * construct any groupURL type service menu entries.
4421 private void build_urlServiceMenu(JMenu webService)
4423 // TODO: remove this code when 2.7 is released
4424 // DEBUG - alignmentView
4426 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4427 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4429 * @Override public void actionPerformed(ActionEvent e) {
4430 * jalview.datamodel.AlignmentView
4431 * .testSelectionViews(af.viewport.getAlignment(),
4432 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4434 * }); webService.add(testAlView);
4436 // TODO: refactor to RestClient discoverer and merge menu entries for
4437 // rest-style services with other types of analysis/calculation service
4438 // SHmmr test client - still being implemented.
4439 // DEBUG - alignmentView
4441 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4444 client.attachWSMenuEntry(
4445 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4451 * Searches the alignment sequences for xRefs and builds the Show
4452 * Cross-References menu (formerly called Show Products), with database
4453 * sources for which cross-references are found (protein sources for a
4454 * nucleotide alignment and vice versa)
4456 * @return true if Show Cross-references menu should be enabled
4458 public boolean canShowProducts()
4460 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4461 AlignmentI dataset = viewport.getAlignment().getDataset();
4463 showProducts.removeAll();
4464 final boolean dna = viewport.getAlignment().isNucleotide();
4466 if (seqs == null || seqs.length == 0)
4468 // nothing to see here.
4472 boolean showp = false;
4475 List<String> ptypes = new CrossRef(seqs, dataset)
4476 .findXrefSourcesForSequences(dna);
4478 for (final String source : ptypes)
4481 final AlignFrame af = this;
4482 JMenuItem xtype = new JMenuItem(source);
4483 xtype.addActionListener(new ActionListener()
4486 public void actionPerformed(ActionEvent e)
4488 showProductsFor(af.viewport.getSequenceSelection(), dna,
4492 showProducts.add(xtype);
4494 showProducts.setVisible(showp);
4495 showProducts.setEnabled(showp);
4496 } catch (Exception e)
4499 "canShowProducts threw an exception - please report to help@jalview.org",
4507 * Finds and displays cross-references for the selected sequences (protein
4508 * products for nucleotide sequences, dna coding sequences for peptides).
4511 * the sequences to show cross-references for
4513 * true if from a nucleotide alignment (so showing proteins)
4515 * the database to show cross-references for
4517 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4518 final String source)
4520 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4525 * Construct and display a new frame containing the translation of this
4526 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4529 public void showTranslation_actionPerformed(ActionEvent e)
4531 AlignmentI al = null;
4534 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4536 al = dna.translateCdna();
4537 } catch (Exception ex)
4539 jalview.bin.Cache.log.error(
4540 "Exception during translation. Please report this !", ex);
4541 final String msg = MessageManager.getString(
4542 "label.error_when_translating_sequences_submit_bug_report");
4543 final String errorTitle = MessageManager
4544 .getString("label.implementation_error")
4545 + MessageManager.getString("label.translation_failed");
4546 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4547 JvOptionPane.ERROR_MESSAGE);
4550 if (al == null || al.getHeight() == 0)
4552 final String msg = MessageManager.getString(
4553 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4554 final String errorTitle = MessageManager
4555 .getString("label.translation_failed");
4556 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4557 JvOptionPane.WARNING_MESSAGE);
4561 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4562 af.setFileFormat(this.currentFileFormat);
4563 final String newTitle = MessageManager
4564 .formatMessage("label.translation_of_params", new Object[]
4565 { this.getTitle() });
4566 af.setTitle(newTitle);
4567 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4569 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4570 viewport.openSplitFrame(af, new Alignment(seqs));
4574 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4581 * Set the file format
4585 public void setFileFormat(FileFormatI format)
4587 this.currentFileFormat = format;
4591 * Try to load a features file onto the alignment.
4594 * contents or path to retrieve file
4596 * access mode of file (see jalview.io.AlignFile)
4597 * @return true if features file was parsed correctly.
4599 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4601 return avc.parseFeaturesFile(file, sourceType,
4602 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4607 public void refreshFeatureUI(boolean enableIfNecessary)
4609 // note - currently this is only still here rather than in the controller
4610 // because of the featureSettings hard reference that is yet to be
4612 if (enableIfNecessary)
4614 viewport.setShowSequenceFeatures(true);
4615 showSeqFeatures.setSelected(true);
4621 public void dragEnter(DropTargetDragEvent evt)
4626 public void dragExit(DropTargetEvent evt)
4631 public void dragOver(DropTargetDragEvent evt)
4636 public void dropActionChanged(DropTargetDragEvent evt)
4641 public void drop(DropTargetDropEvent evt)
4643 // JAL-1552 - acceptDrop required before getTransferable call for
4644 // Java's Transferable for native dnd
4645 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4646 Transferable t = evt.getTransferable();
4647 List<String> files = new ArrayList<>();
4648 List<DataSourceType> protocols = new ArrayList<>();
4652 Desktop.transferFromDropTarget(files, protocols, evt, t);
4653 } catch (Exception e)
4655 e.printStackTrace();
4661 // check to see if any of these files have names matching sequences in
4663 SequenceIdMatcher idm = new SequenceIdMatcher(
4664 viewport.getAlignment().getSequencesArray());
4666 * Object[] { String,SequenceI}
4668 ArrayList<Object[]> filesmatched = new ArrayList<>();
4669 ArrayList<String> filesnotmatched = new ArrayList<>();
4670 for (int i = 0; i < files.size(); i++)
4672 String file = files.get(i).toString();
4674 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4675 if (protocol == DataSourceType.FILE)
4677 File fl = new File(file);
4678 pdbfn = fl.getName();
4680 else if (protocol == DataSourceType.URL)
4682 URL url = new URL(file);
4683 pdbfn = url.getFile();
4685 if (pdbfn.length() > 0)
4687 // attempt to find a match in the alignment
4688 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4689 int l = 0, c = pdbfn.indexOf(".");
4690 while (mtch == null && c != -1)
4695 } while ((c = pdbfn.indexOf(".", l)) > l);
4698 pdbfn = pdbfn.substring(0, l);
4700 mtch = idm.findAllIdMatches(pdbfn);
4704 FileFormatI type = null;
4707 type = new IdentifyFile().identify(file, protocol);
4708 } catch (Exception ex)
4712 if (type != null && type.isStructureFile())
4714 filesmatched.add(new Object[] { file, protocol, mtch });
4718 // File wasn't named like one of the sequences or wasn't a PDB file.
4719 filesnotmatched.add(file);
4723 if (filesmatched.size() > 0)
4725 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4726 || JvOptionPane.showConfirmDialog(this,
4727 MessageManager.formatMessage(
4728 "label.automatically_associate_structure_files_with_sequences_same_name",
4730 { Integer.valueOf(filesmatched.size())
4732 MessageManager.getString(
4733 "label.automatically_associate_structure_files_by_name"),
4734 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4737 for (Object[] fm : filesmatched)
4739 // try and associate
4740 // TODO: may want to set a standard ID naming formalism for
4741 // associating PDB files which have no IDs.
4742 for (SequenceI toassoc : (SequenceI[]) fm[2])
4744 PDBEntry pe = new AssociatePdbFileWithSeq()
4745 .associatePdbWithSeq((String) fm[0],
4746 (DataSourceType) fm[1], toassoc, false,
4750 System.err.println("Associated file : " + ((String) fm[0])
4751 + " with " + toassoc.getDisplayId(true));
4755 alignPanel.paintAlignment(true);
4759 if (filesnotmatched.size() > 0)
4761 if (assocfiles > 0 && (Cache.getDefault(
4762 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4763 || JvOptionPane.showConfirmDialog(this,
4764 "<html>" + MessageManager.formatMessage(
4765 "label.ignore_unmatched_dropped_files_info",
4767 { Integer.valueOf(filesnotmatched.size())
4770 MessageManager.getString(
4771 "label.ignore_unmatched_dropped_files"),
4772 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4776 for (String fn : filesnotmatched)
4778 loadJalviewDataFile(fn, null, null, null);
4782 } catch (Exception ex)
4784 ex.printStackTrace();
4790 * Attempt to load a "dropped" file or URL string, by testing in turn for
4792 * <li>an Annotation file</li>
4793 * <li>a JNet file</li>
4794 * <li>a features file</li>
4795 * <li>else try to interpret as an alignment file</li>
4799 * either a filename or a URL string.
4800 * @throws InterruptedException
4801 * @throws IOException
4803 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4804 FileFormatI format, SequenceI assocSeq)
4808 if (sourceType == null)
4810 sourceType = FormatAdapter.checkProtocol(file);
4812 // if the file isn't identified, or not positively identified as some
4813 // other filetype (PFAM is default unidentified alignment file type) then
4814 // try to parse as annotation.
4815 boolean isAnnotation = (format == null
4816 || FileFormat.Pfam.equals(format))
4817 ? new AnnotationFile().annotateAlignmentView(viewport,
4823 // first see if its a T-COFFEE score file
4824 TCoffeeScoreFile tcf = null;
4827 tcf = new TCoffeeScoreFile(file, sourceType);
4830 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4834 new TCoffeeColourScheme(viewport.getAlignment()));
4835 isAnnotation = true;
4836 statusBar.setText(MessageManager.getString(
4837 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4841 // some problem - if no warning its probable that the ID matching
4842 // process didn't work
4843 JvOptionPane.showMessageDialog(Desktop.desktop,
4844 tcf.getWarningMessage() == null
4845 ? MessageManager.getString(
4846 "label.check_file_matches_sequence_ids_alignment")
4847 : tcf.getWarningMessage(),
4848 MessageManager.getString(
4849 "label.problem_reading_tcoffee_score_file"),
4850 JvOptionPane.WARNING_MESSAGE);
4857 } catch (Exception x)
4860 "Exception when processing data source as T-COFFEE score file",
4866 // try to see if its a JNet 'concise' style annotation file *before*
4868 // try to parse it as a features file
4871 format = new IdentifyFile().identify(file, sourceType);
4873 if (FileFormat.ScoreMatrix == format)
4875 ScoreMatrixFile sm = new ScoreMatrixFile(
4876 new FileParse(file, sourceType));
4878 // todo: i18n this message
4879 statusBar.setText(MessageManager.formatMessage(
4880 "label.successfully_loaded_matrix",
4881 sm.getMatrixName()));
4883 else if (FileFormat.Jnet.equals(format))
4885 JPredFile predictions = new JPredFile(file, sourceType);
4886 new JnetAnnotationMaker();
4887 JnetAnnotationMaker.add_annotation(predictions,
4888 viewport.getAlignment(), 0, false);
4889 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4890 viewport.getAlignment().setSeqrep(repseq);
4891 HiddenColumns cs = new HiddenColumns();
4892 cs.hideInsertionsFor(repseq);
4893 viewport.getAlignment().setHiddenColumns(cs);
4894 isAnnotation = true;
4896 // else if (IdentifyFile.FeaturesFile.equals(format))
4897 else if (FileFormat.Features.equals(format))
4899 if (parseFeaturesFile(file, sourceType))
4901 alignPanel.paintAlignment(true);
4906 new FileLoader().LoadFile(viewport, file, sourceType, format);
4912 alignPanel.adjustAnnotationHeight();
4913 viewport.updateSequenceIdColours();
4914 buildSortByAnnotationScoresMenu();
4915 alignPanel.paintAlignment(true);
4917 } catch (Exception ex)
4919 ex.printStackTrace();
4920 } catch (OutOfMemoryError oom)
4925 } catch (Exception x)
4930 + (sourceType != null
4931 ? (sourceType == DataSourceType.PASTE
4933 : "using " + sourceType + " from "
4937 ? "(parsing as '" + format + "' file)"
4939 oom, Desktop.desktop);
4944 * Method invoked by the ChangeListener on the tabbed pane, in other words
4945 * when a different tabbed pane is selected by the user or programmatically.
4948 public void tabSelectionChanged(int index)
4952 alignPanel = alignPanels.get(index);
4953 viewport = alignPanel.av;
4954 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4955 setMenusFromViewport(viewport);
4959 * 'focus' any colour slider that is open to the selected viewport
4961 if (viewport.getConservationSelected())
4963 SliderPanel.setConservationSlider(alignPanel,
4964 viewport.getResidueShading(), alignPanel.getViewName());
4968 SliderPanel.hideConservationSlider();
4970 if (viewport.getAbovePIDThreshold())
4972 SliderPanel.setPIDSliderSource(alignPanel,
4973 viewport.getResidueShading(), alignPanel.getViewName());
4977 SliderPanel.hidePIDSlider();
4981 * If there is a frame linked to this one in a SplitPane, switch it to the
4982 * same view tab index. No infinite recursion of calls should happen, since
4983 * tabSelectionChanged() should not get invoked on setting the selected
4984 * index to an unchanged value. Guard against setting an invalid index
4985 * before the new view peer tab has been created.
4987 final AlignViewportI peer = viewport.getCodingComplement();
4990 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4991 .getAlignPanel().alignFrame;
4992 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4994 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5000 * On right mouse click on view tab, prompt for and set new view name.
5003 public void tabbedPane_mousePressed(MouseEvent e)
5005 if (e.isPopupTrigger())
5007 String msg = MessageManager.getString("label.enter_view_name");
5008 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5009 JvOptionPane.QUESTION_MESSAGE);
5013 viewport.viewName = reply;
5014 // TODO warn if reply is in getExistingViewNames()?
5015 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5020 public AlignViewport getCurrentView()
5026 * Open the dialog for regex description parsing.
5029 protected void extractScores_actionPerformed(ActionEvent e)
5031 ParseProperties pp = new jalview.analysis.ParseProperties(
5032 viewport.getAlignment());
5033 // TODO: verify regex and introduce GUI dialog for version 2.5
5034 // if (pp.getScoresFromDescription("col", "score column ",
5035 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5037 if (pp.getScoresFromDescription("description column",
5038 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5040 buildSortByAnnotationScoresMenu();
5048 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5052 protected void showDbRefs_actionPerformed(ActionEvent e)
5054 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5060 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5064 protected void showNpFeats_actionPerformed(ActionEvent e)
5066 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5070 * find the viewport amongst the tabs in this alignment frame and close that
5075 public boolean closeView(AlignViewportI av)
5079 this.closeMenuItem_actionPerformed(false);
5082 Component[] comp = tabbedPane.getComponents();
5083 for (int i = 0; comp != null && i < comp.length; i++)
5085 if (comp[i] instanceof AlignmentPanel)
5087 if (((AlignmentPanel) comp[i]).av == av)
5090 closeView((AlignmentPanel) comp[i]);
5098 protected void build_fetchdbmenu(JMenu webService)
5100 // Temporary hack - DBRef Fetcher always top level ws entry.
5101 // TODO We probably want to store a sequence database checklist in
5102 // preferences and have checkboxes.. rather than individual sources selected
5104 final JMenu rfetch = new JMenu(
5105 MessageManager.getString("action.fetch_db_references"));
5106 rfetch.setToolTipText(MessageManager.getString(
5107 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5108 webService.add(rfetch);
5110 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5111 MessageManager.getString("option.trim_retrieved_seqs"));
5112 trimrs.setToolTipText(
5113 MessageManager.getString("label.trim_retrieved_sequences"));
5114 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5115 trimrs.addActionListener(new ActionListener()
5118 public void actionPerformed(ActionEvent e)
5120 trimrs.setSelected(trimrs.isSelected());
5121 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5122 Boolean.valueOf(trimrs.isSelected()).toString());
5126 JMenuItem fetchr = new JMenuItem(
5127 MessageManager.getString("label.standard_databases"));
5128 fetchr.setToolTipText(
5129 MessageManager.getString("label.fetch_embl_uniprot"));
5130 fetchr.addActionListener(new ActionListener()
5134 public void actionPerformed(ActionEvent e)
5136 new Thread(new Runnable()
5141 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5142 .getAlignment().isNucleotide();
5143 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5144 alignPanel.av.getSequenceSelection(),
5145 alignPanel.alignFrame, null,
5146 alignPanel.alignFrame.featureSettings, isNucleotide);
5147 dbRefFetcher.addListener(new FetchFinishedListenerI()
5150 public void finished()
5152 AlignFrame.this.setMenusForViewport();
5155 dbRefFetcher.fetchDBRefs(false);
5163 final AlignFrame me = this;
5164 new Thread(new Runnable()
5169 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5170 .getSequenceFetcherSingleton(me);
5171 javax.swing.SwingUtilities.invokeLater(new Runnable()
5176 String[] dbclasses = sf.getOrderedSupportedSources();
5177 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5178 // jalview.util.QuickSort.sort(otherdb, otherdb);
5179 List<DbSourceProxy> otherdb;
5180 JMenu dfetch = new JMenu();
5181 JMenu ifetch = new JMenu();
5182 JMenuItem fetchr = null;
5183 int comp = 0, icomp = 0, mcomp = 15;
5184 String mname = null;
5186 for (String dbclass : dbclasses)
5188 otherdb = sf.getSourceProxy(dbclass);
5189 // add a single entry for this class, or submenu allowing 'fetch
5191 if (otherdb == null || otherdb.size() < 1)
5195 // List<DbSourceProxy> dbs=otherdb;
5196 // otherdb=new ArrayList<DbSourceProxy>();
5197 // for (DbSourceProxy db:dbs)
5199 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5203 mname = "From " + dbclass;
5205 if (otherdb.size() == 1)
5207 final DbSourceProxy[] dassource = otherdb
5208 .toArray(new DbSourceProxy[0]);
5209 DbSourceProxy src = otherdb.get(0);
5210 fetchr = new JMenuItem(src.getDbSource());
5211 fetchr.addActionListener(new ActionListener()
5215 public void actionPerformed(ActionEvent e)
5217 new Thread(new Runnable()
5223 boolean isNucleotide = alignPanel.alignFrame
5224 .getViewport().getAlignment()
5226 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5227 alignPanel.av.getSequenceSelection(),
5228 alignPanel.alignFrame, dassource,
5229 alignPanel.alignFrame.featureSettings,
5232 .addListener(new FetchFinishedListenerI()
5235 public void finished()
5237 AlignFrame.this.setMenusForViewport();
5240 dbRefFetcher.fetchDBRefs(false);
5246 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5247 MessageManager.formatMessage(
5248 "label.fetch_retrieve_from", new Object[]
5249 { src.getDbName() })));
5255 final DbSourceProxy[] dassource = otherdb
5256 .toArray(new DbSourceProxy[0]);
5258 DbSourceProxy src = otherdb.get(0);
5259 fetchr = new JMenuItem(MessageManager
5260 .formatMessage("label.fetch_all_param", new Object[]
5261 { src.getDbSource() }));
5262 fetchr.addActionListener(new ActionListener()
5265 public void actionPerformed(ActionEvent e)
5267 new Thread(new Runnable()
5273 boolean isNucleotide = alignPanel.alignFrame
5274 .getViewport().getAlignment()
5276 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5277 alignPanel.av.getSequenceSelection(),
5278 alignPanel.alignFrame, dassource,
5279 alignPanel.alignFrame.featureSettings,
5282 .addListener(new FetchFinishedListenerI()
5285 public void finished()
5287 AlignFrame.this.setMenusForViewport();
5290 dbRefFetcher.fetchDBRefs(false);
5296 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5297 MessageManager.formatMessage(
5298 "label.fetch_retrieve_from_all_sources",
5300 { Integer.valueOf(otherdb.size())
5302 src.getDbSource(), src.getDbName() })));
5305 // and then build the rest of the individual menus
5306 ifetch = new JMenu(MessageManager.formatMessage(
5307 "label.source_from_db_source", new Object[]
5308 { src.getDbSource() }));
5310 String imname = null;
5312 for (DbSourceProxy sproxy : otherdb)
5314 String dbname = sproxy.getDbName();
5315 String sname = dbname.length() > 5
5316 ? dbname.substring(0, 5) + "..."
5318 String msname = dbname.length() > 10
5319 ? dbname.substring(0, 10) + "..."
5323 imname = MessageManager
5324 .formatMessage("label.from_msname", new Object[]
5327 fetchr = new JMenuItem(msname);
5328 final DbSourceProxy[] dassrc = { sproxy };
5329 fetchr.addActionListener(new ActionListener()
5333 public void actionPerformed(ActionEvent e)
5335 new Thread(new Runnable()
5341 boolean isNucleotide = alignPanel.alignFrame
5342 .getViewport().getAlignment()
5344 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5345 alignPanel.av.getSequenceSelection(),
5346 alignPanel.alignFrame, dassrc,
5347 alignPanel.alignFrame.featureSettings,
5350 .addListener(new FetchFinishedListenerI()
5353 public void finished()
5355 AlignFrame.this.setMenusForViewport();
5358 dbRefFetcher.fetchDBRefs(false);
5364 fetchr.setToolTipText(
5365 "<html>" + MessageManager.formatMessage(
5366 "label.fetch_retrieve_from", new Object[]
5370 if (++icomp >= mcomp || i == (otherdb.size()))
5372 ifetch.setText(MessageManager.formatMessage(
5373 "label.source_to_target", imname, sname));
5375 ifetch = new JMenu();
5383 if (comp >= mcomp || dbi >= (dbclasses.length))
5385 dfetch.setText(MessageManager.formatMessage(
5386 "label.source_to_target", mname, dbclass));
5388 dfetch = new JMenu();
5401 * Left justify the whole alignment.
5404 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5406 AlignmentI al = viewport.getAlignment();
5408 viewport.firePropertyChange("alignment", null, al);
5412 * Right justify the whole alignment.
5415 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5417 AlignmentI al = viewport.getAlignment();
5419 viewport.firePropertyChange("alignment", null, al);
5423 public void setShowSeqFeatures(boolean b)
5425 showSeqFeatures.setSelected(b);
5426 viewport.setShowSequenceFeatures(b);
5433 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5434 * awt.event.ActionEvent)
5437 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5439 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5440 alignPanel.paintAlignment(true);
5447 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5451 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5453 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5454 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5462 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5463 * .event.ActionEvent)
5466 protected void showGroupConservation_actionPerformed(ActionEvent e)
5468 viewport.setShowGroupConservation(showGroupConservation.getState());
5469 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5476 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5477 * .event.ActionEvent)
5480 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5482 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5483 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5490 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5491 * .event.ActionEvent)
5494 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5496 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5497 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5501 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5503 showSequenceLogo.setState(true);
5504 viewport.setShowSequenceLogo(true);
5505 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5506 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5510 protected void showInformationHistogram_actionPerformed(ActionEvent e)
5512 viewport.setShowInformationHistogram(
5513 showInformationHistogram.getState());
5514 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5518 protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5520 viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5521 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5525 protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5527 showHMMSequenceLogo.setState(true);
5528 viewport.setShowHMMSequenceLogo(true);
5529 viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5530 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5534 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5536 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5543 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5544 * .event.ActionEvent)
5547 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5549 if (avc.makeGroupsFromSelection())
5551 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5552 alignPanel.updateAnnotation();
5553 alignPanel.paintAlignment(true);
5557 public void clearAlignmentSeqRep()
5559 // TODO refactor alignmentseqrep to controller
5560 if (viewport.getAlignment().hasSeqrep())
5562 viewport.getAlignment().setSeqrep(null);
5563 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5564 alignPanel.updateAnnotation();
5565 alignPanel.paintAlignment(true);
5570 protected void createGroup_actionPerformed(ActionEvent e)
5572 if (avc.createGroup())
5574 alignPanel.alignmentChanged();
5579 protected void unGroup_actionPerformed(ActionEvent e)
5583 alignPanel.alignmentChanged();
5588 * make the given alignmentPanel the currently selected tab
5590 * @param alignmentPanel
5592 public void setDisplayedView(AlignmentPanel alignmentPanel)
5594 if (!viewport.getSequenceSetId()
5595 .equals(alignmentPanel.av.getSequenceSetId()))
5597 throw new Error(MessageManager.getString(
5598 "error.implementation_error_cannot_show_view_alignment_frame"));
5600 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5601 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5603 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5608 * Action on selection of menu options to Show or Hide annotations.
5611 * @param forSequences
5612 * update sequence-related annotations
5613 * @param forAlignment
5614 * update non-sequence-related annotations
5617 protected void setAnnotationsVisibility(boolean visible,
5618 boolean forSequences, boolean forAlignment)
5620 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5621 .getAlignmentAnnotation();
5626 for (AlignmentAnnotation aa : anns)
5629 * don't display non-positional annotations on an alignment
5631 if (aa.annotations == null)
5635 boolean apply = (aa.sequenceRef == null && forAlignment)
5636 || (aa.sequenceRef != null && forSequences);
5639 aa.visible = visible;
5642 alignPanel.validateAnnotationDimensions(true);
5643 alignPanel.alignmentChanged();
5647 * Store selected annotation sort order for the view and repaint.
5650 protected void sortAnnotations_actionPerformed()
5652 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5654 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5655 alignPanel.paintAlignment(true);
5660 * @return alignment panels in this alignment frame
5662 public List<? extends AlignmentViewPanel> getAlignPanels()
5664 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5668 * Open a new alignment window, with the cDNA associated with this (protein)
5669 * alignment, aligned as is the protein.
5671 protected void viewAsCdna_actionPerformed()
5673 // TODO no longer a menu action - refactor as required
5674 final AlignmentI alignment = getViewport().getAlignment();
5675 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5676 if (mappings == null)
5680 List<SequenceI> cdnaSeqs = new ArrayList<>();
5681 for (SequenceI aaSeq : alignment.getSequences())
5683 for (AlignedCodonFrame acf : mappings)
5685 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5689 * There is a cDNA mapping for this protein sequence - add to new
5690 * alignment. It will share the same dataset sequence as other mapped
5691 * cDNA (no new mappings need to be created).
5693 final Sequence newSeq = new Sequence(dnaSeq);
5694 newSeq.setDatasetSequence(dnaSeq);
5695 cdnaSeqs.add(newSeq);
5699 if (cdnaSeqs.size() == 0)
5701 // show a warning dialog no mapped cDNA
5704 AlignmentI cdna = new Alignment(
5705 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5706 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5707 AlignFrame.DEFAULT_HEIGHT);
5708 cdna.alignAs(alignment);
5709 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5711 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5712 AlignFrame.DEFAULT_HEIGHT);
5716 * Set visibility of dna/protein complement view (available when shown in a
5722 protected void showComplement_actionPerformed(boolean show)
5724 SplitContainerI sf = getSplitViewContainer();
5727 sf.setComplementVisible(this, show);
5732 * Generate the reverse (optionally complemented) of the selected sequences,
5733 * and add them to the alignment
5736 protected void showReverse_actionPerformed(boolean complement)
5738 AlignmentI al = null;
5741 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5742 al = dna.reverseCdna(complement);
5743 viewport.addAlignment(al, "");
5744 addHistoryItem(new EditCommand(
5745 MessageManager.getString("label.add_sequences"), Action.PASTE,
5746 al.getSequencesArray(), 0, al.getWidth(),
5747 viewport.getAlignment()));
5748 } catch (Exception ex)
5750 System.err.println(ex.getMessage());
5756 * Try to run a script in the Groovy console, having first ensured that this
5757 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5758 * be targeted at this alignment.
5761 protected void runGroovy_actionPerformed()
5763 Jalview.setCurrentAlignFrame(this);
5764 groovy.ui.Console console = Desktop.getGroovyConsole();
5765 if (console != null)
5769 console.runScript();
5770 } catch (Exception ex)
5772 System.err.println((ex.toString()));
5773 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5774 MessageManager.getString("label.couldnt_run_groovy_script"),
5775 MessageManager.getString("label.groovy_support_failed"),
5776 JvOptionPane.ERROR_MESSAGE);
5781 System.err.println("Can't run Groovy script as console not found");
5786 * Hides columns containing (or not containing) a specified feature, provided
5787 * that would not leave all columns hidden
5789 * @param featureType
5790 * @param columnsContaining
5793 public boolean hideFeatureColumns(String featureType,
5794 boolean columnsContaining)
5796 boolean notForHiding = avc.markColumnsContainingFeatures(
5797 columnsContaining, false, false, featureType);
5800 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5801 false, featureType))
5803 getViewport().hideSelectedColumns();
5811 protected void selectHighlightedColumns_actionPerformed(
5812 ActionEvent actionEvent)
5814 // include key modifier check in case user selects from menu
5815 avc.markHighlightedColumns(
5816 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5817 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5818 | ActionEvent.CTRL_MASK)) != 0);
5822 * Rebuilds the Colour menu, including any user-defined colours which have
5823 * been loaded either on startup or during the session
5825 public void buildColourMenu()
5827 colourMenu.removeAll();
5829 colourMenu.add(applyToAllGroups);
5830 colourMenu.add(textColour);
5831 colourMenu.addSeparator();
5833 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5836 colourMenu.addSeparator();
5837 colourMenu.add(conservationMenuItem);
5838 colourMenu.add(modifyConservation);
5839 colourMenu.add(abovePIDThreshold);
5840 colourMenu.add(modifyPID);
5841 colourMenu.add(annotationColour);
5843 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5844 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5848 * Open a dialog (if not already open) that allows the user to select and
5849 * calculate PCA or Tree analysis
5851 protected void openTreePcaDialog()
5853 if (alignPanel.getCalculationDialog() == null)
5855 new CalculationChooser(AlignFrame.this);
5860 * Sets the status of the HMMER menu
5864 public void updateHMMERStatus(boolean status)
5866 hmmerMenu.setEnabled(status);
5870 * Returns the selected hidden Markov model.
5874 public HiddenMarkovModel getSelectedHMM()
5876 if (selectedHMMSequence == null)
5880 return selectedHMMSequence.getHMM();
5884 * Returns the selected hidden Markov model.
5888 public SequenceI getSelectedHMMSequence()
5890 return selectedHMMSequence;
5894 * Sets the selected hidden Markov model
5896 * @param selectedHMM
5898 public void setSelectedHMMSequence(SequenceI selectedHMM)
5900 this.selectedHMMSequence = selectedHMM;
5901 hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
5902 + selectedHMM.getHMM().getName());
5903 hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
5904 + selectedHMM.getHMM().getName());
5908 public void hmmerMenu_actionPerformed(ActionEvent e)
5910 SequenceGroup grp = getViewport().getSelectionGroup();
5913 hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
5918 hmmBuild.setText(MessageManager.getString("label.hmmbuild")
5919 + " from Alignment");
5925 class PrintThread extends Thread
5929 public PrintThread(AlignmentPanel ap)
5934 static PageFormat pf;
5939 PrinterJob printJob = PrinterJob.getPrinterJob();
5943 printJob.setPrintable(ap, pf);
5947 printJob.setPrintable(ap);
5950 if (printJob.printDialog())
5955 } catch (Exception PrintException)
5957 PrintException.printStackTrace();