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.io.AlignmentProperties;
69 import jalview.io.AnnotationFile;
70 import jalview.io.BioJsHTMLOutput;
71 import jalview.io.DataSourceType;
72 import jalview.io.FileFormat;
73 import jalview.io.FileFormatI;
74 import jalview.io.FileFormats;
75 import jalview.io.FileLoader;
76 import jalview.io.FileParse;
77 import jalview.io.FormatAdapter;
78 import jalview.io.HtmlSvgOutput;
79 import jalview.io.IdentifyFile;
80 import jalview.io.JPredFile;
81 import jalview.io.JalviewFileChooser;
82 import jalview.io.JalviewFileView;
83 import jalview.io.JnetAnnotationMaker;
84 import jalview.io.NewickFile;
85 import jalview.io.ScoreMatrixFile;
86 import jalview.io.TCoffeeScoreFile;
87 import jalview.jbgui.GAlignFrame;
88 import jalview.schemes.ColourSchemeI;
89 import jalview.schemes.ColourSchemes;
90 import jalview.schemes.ResidueColourScheme;
91 import jalview.schemes.TCoffeeColourScheme;
92 import jalview.util.MessageManager;
93 import jalview.viewmodel.AlignmentViewport;
94 import jalview.viewmodel.ViewportRanges;
95 import jalview.ws.DBRefFetcher;
96 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
97 import jalview.ws.jws1.Discoverer;
98 import jalview.ws.jws2.Jws2Discoverer;
99 import jalview.ws.jws2.jabaws2.Jws2Instance;
100 import jalview.ws.seqfetcher.DbSourceProxy;
102 import java.awt.BorderLayout;
103 import java.awt.Component;
104 import java.awt.Rectangle;
105 import java.awt.Toolkit;
106 import java.awt.datatransfer.Clipboard;
107 import java.awt.datatransfer.DataFlavor;
108 import java.awt.datatransfer.StringSelection;
109 import java.awt.datatransfer.Transferable;
110 import java.awt.dnd.DnDConstants;
111 import java.awt.dnd.DropTargetDragEvent;
112 import java.awt.dnd.DropTargetDropEvent;
113 import java.awt.dnd.DropTargetEvent;
114 import java.awt.dnd.DropTargetListener;
115 import java.awt.event.ActionEvent;
116 import java.awt.event.ActionListener;
117 import java.awt.event.FocusAdapter;
118 import java.awt.event.FocusEvent;
119 import java.awt.event.ItemEvent;
120 import java.awt.event.ItemListener;
121 import java.awt.event.KeyAdapter;
122 import java.awt.event.KeyEvent;
123 import java.awt.event.MouseEvent;
124 import java.awt.print.PageFormat;
125 import java.awt.print.PrinterJob;
126 import java.beans.PropertyChangeEvent;
128 import java.io.FileWriter;
129 import java.io.IOException;
130 import java.io.PrintWriter;
132 import java.util.ArrayList;
133 import java.util.Arrays;
134 import java.util.Deque;
135 import java.util.Enumeration;
136 import java.util.HashMap;
137 import java.util.Hashtable;
138 import java.util.List;
139 import java.util.Map;
140 import java.util.Vector;
142 import javax.swing.JCheckBoxMenuItem;
143 import javax.swing.JEditorPane;
144 import javax.swing.JInternalFrame;
145 import javax.swing.JLayeredPane;
146 import javax.swing.JMenu;
147 import javax.swing.JMenuItem;
148 import javax.swing.JOptionPane;
149 import javax.swing.JScrollPane;
150 import javax.swing.SwingUtilities;
156 * @version $Revision$
158 public class AlignFrame extends GAlignFrame implements DropTargetListener,
159 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
162 Map<String, Float> distribution = new HashMap<>(); // temporary
164 public static final int DEFAULT_WIDTH = 700;
166 public static final int DEFAULT_HEIGHT = 500;
168 boolean autoAlignNewSequences;
172 * The currently displayed panel (selected tabbed view if more than one)
174 public AlignmentPanel alignPanel;
176 AlignViewport viewport;
178 ViewportRanges vpRanges;
180 public AlignViewControllerI avc;
182 HiddenMarkovModel selectedHMM = null;
184 List<AlignmentPanel> alignPanels = new ArrayList<>();
187 * Last format used to load or save alignments in this window
189 FileFormatI currentFileFormat = null;
192 * Current filename for this alignment
194 String fileName = null;
198 * Creates a new AlignFrame object with specific width and height.
204 public AlignFrame(AlignmentI al, int width, int height)
206 this(al, null, width, height);
210 * Creates a new AlignFrame object with specific width, height and
216 * @param sequenceSetId
218 public AlignFrame(AlignmentI al, int width, int height,
219 String sequenceSetId)
221 this(al, null, width, height, sequenceSetId);
225 * Creates a new AlignFrame object with specific width, height and
231 * @param sequenceSetId
234 public AlignFrame(AlignmentI al, int width, int height,
235 String sequenceSetId, String viewId)
237 this(al, null, width, height, sequenceSetId, viewId);
241 * new alignment window with hidden columns
245 * @param hiddenColumns
246 * ColumnSelection or null
248 * Width of alignment frame
252 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
253 int width, int height)
255 this(al, hiddenColumns, width, height, null);
259 * Create alignment frame for al with hiddenColumns, a specific width and
260 * height, and specific sequenceId
263 * @param hiddenColumns
266 * @param sequenceSetId
269 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
270 int width, int height, String sequenceSetId)
272 this(al, hiddenColumns, width, height, sequenceSetId, null);
276 * Create alignment frame for al with hiddenColumns, a specific width and
277 * height, and specific sequenceId
280 * @param hiddenColumns
283 * @param sequenceSetId
288 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
289 int width, int height, String sequenceSetId, String viewId)
291 setSize(width, height);
293 if (al.getDataset() == null)
298 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
300 alignPanel = new AlignmentPanel(this, viewport);
302 addAlignmentPanel(alignPanel, true);
306 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
307 HiddenColumns hiddenColumns, int width, int height)
309 setSize(width, height);
311 if (al.getDataset() == null)
316 viewport = new AlignViewport(al, hiddenColumns);
318 if (hiddenSeqs != null && hiddenSeqs.length > 0)
320 viewport.hideSequence(hiddenSeqs);
322 alignPanel = new AlignmentPanel(this, viewport);
323 addAlignmentPanel(alignPanel, true);
328 * Make a new AlignFrame from existing alignmentPanels
335 public AlignFrame(AlignmentPanel ap)
339 addAlignmentPanel(ap, false);
344 * initalise the alignframe from the underlying viewport data and the
349 if (!Jalview.isHeadlessMode())
351 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
354 vpRanges = viewport.getRanges();
355 avc = new jalview.controller.AlignViewController(this, viewport,
357 if (viewport.getAlignmentConservationAnnotation() == null)
359 // BLOSUM62Colour.setEnabled(false);
360 conservationMenuItem.setEnabled(false);
361 modifyConservation.setEnabled(false);
362 // PIDColour.setEnabled(false);
363 // abovePIDThreshold.setEnabled(false);
364 // modifyPID.setEnabled(false);
367 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
370 if (sortby.equals("Id"))
372 sortIDMenuItem_actionPerformed(null);
374 else if (sortby.equals("Pairwise Identity"))
376 sortPairwiseMenuItem_actionPerformed(null);
380 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
382 setMenusFromViewport(viewport);
383 buildSortByAnnotationScoresMenu();
384 calculateTree.addActionListener(new ActionListener()
388 public void actionPerformed(ActionEvent e)
396 if (Desktop.desktop != null)
398 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
399 addServiceListeners();
403 if (viewport.getWrapAlignment())
405 wrapMenuItem_actionPerformed(null);
408 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
410 this.overviewMenuItem_actionPerformed(null);
415 final List<AlignmentPanel> selviews = new ArrayList<>();
416 final List<AlignmentPanel> origview = new ArrayList<>();
417 final String menuLabel = MessageManager
418 .getString("label.copy_format_from");
419 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
420 new ViewSetProvider()
424 public AlignmentPanel[] getAllAlignmentPanels()
427 origview.add(alignPanel);
428 // make an array of all alignment panels except for this one
429 List<AlignmentPanel> aps = new ArrayList<>(
430 Arrays.asList(Desktop.getAlignmentPanels(null)));
431 aps.remove(AlignFrame.this.alignPanel);
432 return aps.toArray(new AlignmentPanel[aps.size()]);
434 }, selviews, new ItemListener()
438 public void itemStateChanged(ItemEvent e)
440 if (origview.size() > 0)
442 final AlignmentPanel ap = origview.get(0);
445 * Copy the ViewStyle of the selected panel to 'this one'.
446 * Don't change value of 'scaleProteinAsCdna' unless copying
449 ViewStyleI vs = selviews.get(0).getAlignViewport()
451 boolean fromSplitFrame = selviews.get(0)
452 .getAlignViewport().getCodingComplement() != null;
455 vs.setScaleProteinAsCdna(ap.getAlignViewport()
456 .getViewStyle().isScaleProteinAsCdna());
458 ap.getAlignViewport().setViewStyle(vs);
461 * Also rescale ViewStyle of SplitFrame complement if there is
462 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
463 * the whole ViewStyle (allow cDNA protein to have different
466 AlignViewportI complement = ap.getAlignViewport()
467 .getCodingComplement();
468 if (complement != null && vs.isScaleProteinAsCdna())
470 AlignFrame af = Desktop.getAlignFrameFor(complement);
471 ((SplitFrame) af.getSplitViewContainer())
473 af.setMenusForViewport();
477 ap.setSelected(true);
478 ap.alignFrame.setMenusForViewport();
483 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
484 .indexOf("devel") > -1
485 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
486 .indexOf("test") > -1)
488 formatMenu.add(vsel);
490 addFocusListener(new FocusAdapter()
493 public void focusGained(FocusEvent e)
495 Jalview.setCurrentAlignFrame(AlignFrame.this);
501 private void buildHMMERMenu()
503 hmmerMenu.removeAll();
505 hmmerMenu.add(hmmAlign);
506 hmmerMenu.add(hmmBuild);
507 hmmerMenu.add(hmmSearch);
511 * Change the filename and format for the alignment, and enable the 'reload'
512 * button functionality.
519 public void setFileName(String file, FileFormatI format)
522 setFileFormat(format);
523 reload.setEnabled(true);
527 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
530 void addKeyListener()
532 addKeyListener(new KeyAdapter()
535 public void keyPressed(KeyEvent evt)
537 if (viewport.cursorMode
538 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
539 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
540 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
541 && Character.isDigit(evt.getKeyChar()))
543 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
546 switch (evt.getKeyCode())
549 case 27: // escape key
550 deselectAllSequenceMenuItem_actionPerformed(null);
554 case KeyEvent.VK_DOWN:
555 if (evt.isAltDown() || !viewport.cursorMode)
557 moveSelectedSequences(false);
559 if (viewport.cursorMode)
561 alignPanel.getSeqPanel().moveCursor(0, 1);
566 if (evt.isAltDown() || !viewport.cursorMode)
568 moveSelectedSequences(true);
570 if (viewport.cursorMode)
572 alignPanel.getSeqPanel().moveCursor(0, -1);
577 case KeyEvent.VK_LEFT:
578 if (evt.isAltDown() || !viewport.cursorMode)
580 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
584 alignPanel.getSeqPanel().moveCursor(-1, 0);
589 case KeyEvent.VK_RIGHT:
590 if (evt.isAltDown() || !viewport.cursorMode)
592 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
596 alignPanel.getSeqPanel().moveCursor(1, 0);
600 case KeyEvent.VK_SPACE:
601 if (viewport.cursorMode)
603 alignPanel.getSeqPanel().insertGapAtCursor(
604 evt.isControlDown() || evt.isShiftDown()
609 // case KeyEvent.VK_A:
610 // if (viewport.cursorMode)
612 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
613 // //System.out.println("A");
617 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
618 * System.out.println("closing bracket"); } break;
620 case KeyEvent.VK_DELETE:
621 case KeyEvent.VK_BACK_SPACE:
622 if (!viewport.cursorMode)
624 cut_actionPerformed(null);
628 alignPanel.getSeqPanel().deleteGapAtCursor(
629 evt.isControlDown() || evt.isShiftDown()
636 if (viewport.cursorMode)
638 alignPanel.getSeqPanel().setCursorRow();
642 if (viewport.cursorMode && !evt.isControlDown())
644 alignPanel.getSeqPanel().setCursorColumn();
648 if (viewport.cursorMode)
650 alignPanel.getSeqPanel().setCursorPosition();
654 case KeyEvent.VK_ENTER:
655 case KeyEvent.VK_COMMA:
656 if (viewport.cursorMode)
658 alignPanel.getSeqPanel().setCursorRowAndColumn();
663 if (viewport.cursorMode)
665 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
669 if (viewport.cursorMode)
671 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
676 viewport.cursorMode = !viewport.cursorMode;
677 statusBar.setText(MessageManager.formatMessage(
678 "label.keyboard_editing_mode",
679 new String[] { (viewport.cursorMode ? "on" : "off") }));
680 if (viewport.cursorMode)
682 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
684 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
687 alignPanel.getSeqPanel().seqCanvas.repaint();
693 Help.showHelpWindow();
694 } catch (Exception ex)
696 ex.printStackTrace();
701 boolean toggleSeqs = !evt.isControlDown();
702 boolean toggleCols = !evt.isShiftDown();
703 toggleHiddenRegions(toggleSeqs, toggleCols);
708 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
709 boolean modifyExisting = true; // always modify, don't clear
710 // evt.isShiftDown();
711 boolean invertHighlighted = evt.isAltDown();
712 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
716 case KeyEvent.VK_PAGE_UP:
717 if (viewport.getWrapAlignment())
719 vpRanges.scrollUp(true);
726 case KeyEvent.VK_PAGE_DOWN:
727 if (viewport.getWrapAlignment())
729 vpRanges.scrollUp(false);
740 public void keyReleased(KeyEvent evt)
742 switch (evt.getKeyCode())
744 case KeyEvent.VK_LEFT:
745 if (evt.isAltDown() || !viewport.cursorMode)
747 viewport.firePropertyChange("alignment", null, viewport
748 .getAlignment().getSequences());
752 case KeyEvent.VK_RIGHT:
753 if (evt.isAltDown() || !viewport.cursorMode)
755 viewport.firePropertyChange("alignment", null, viewport
756 .getAlignment().getSequences());
764 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
766 ap.alignFrame = this;
767 avc = new jalview.controller.AlignViewController(this, viewport,
772 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
774 int aSize = alignPanels.size();
776 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
778 if (aSize == 1 && ap.av.viewName == null)
780 this.getContentPane().add(ap, BorderLayout.CENTER);
786 setInitialTabVisible();
789 expandViews.setEnabled(true);
790 gatherViews.setEnabled(true);
791 tabbedPane.addTab(ap.av.viewName, ap);
793 ap.setVisible(false);
798 if (ap.av.isPadGaps())
800 ap.av.getAlignment().padGaps();
802 ap.av.updateConservation(ap);
803 ap.av.updateConsensus(ap);
804 ap.av.updateStrucConsensus(ap);
805 ap.av.updateInformation(ap);
809 public void setInitialTabVisible()
811 expandViews.setEnabled(true);
812 gatherViews.setEnabled(true);
813 tabbedPane.setVisible(true);
814 AlignmentPanel first = alignPanels.get(0);
815 tabbedPane.addTab(first.av.viewName, first);
816 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
819 public AlignViewport getViewport()
824 /* Set up intrinsic listeners for dynamically generated GUI bits. */
825 private void addServiceListeners()
827 final java.beans.PropertyChangeListener thisListener;
828 Desktop.instance.addJalviewPropertyChangeListener("services",
829 thisListener = new java.beans.PropertyChangeListener()
832 public void propertyChange(PropertyChangeEvent evt)
834 // // System.out.println("Discoverer property change.");
835 // if (evt.getPropertyName().equals("services"))
837 SwingUtilities.invokeLater(new Runnable()
844 .println("Rebuild WS Menu for service change");
845 BuildWebServiceMenu();
852 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
855 public void internalFrameClosed(
856 javax.swing.event.InternalFrameEvent evt)
858 // System.out.println("deregistering discoverer listener");
859 Desktop.instance.removeJalviewPropertyChangeListener("services",
861 closeMenuItem_actionPerformed(true);
864 // Finally, build the menu once to get current service state
865 new Thread(new Runnable()
870 BuildWebServiceMenu();
876 * Configure menu items that vary according to whether the alignment is
877 * nucleotide or protein
879 public void setGUINucleotide()
881 AlignmentI al = getViewport().getAlignment();
882 boolean nucleotide = al.isNucleotide();
884 showTranslation.setVisible(nucleotide);
885 showReverse.setVisible(nucleotide);
886 showReverseComplement.setVisible(nucleotide);
887 conservationMenuItem.setEnabled(!nucleotide);
888 modifyConservation.setEnabled(!nucleotide
889 && conservationMenuItem.isSelected());
890 showGroupConservation.setEnabled(!nucleotide);
892 showComplementMenuItem.setText(nucleotide ? MessageManager
893 .getString("label.protein") : MessageManager
894 .getString("label.nucleotide"));
898 * set up menus for the current viewport. This may be called after any
899 * operation that affects the data in the current view (selection changed,
900 * etc) to update the menus to reflect the new state.
903 public void setMenusForViewport()
905 setMenusFromViewport(viewport);
909 * Need to call this method when tabs are selected for multiple views, or when
910 * loading from Jalview2XML.java
915 void setMenusFromViewport(AlignViewport av)
917 padGapsMenuitem.setSelected(av.isPadGaps());
918 colourTextMenuItem.setSelected(av.isShowColourText());
919 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
920 modifyPID.setEnabled(abovePIDThreshold.isSelected());
921 conservationMenuItem.setSelected(av.getConservationSelected());
922 modifyConservation.setEnabled(conservationMenuItem.isSelected());
923 seqLimits.setSelected(av.getShowJVSuffix());
924 idRightAlign.setSelected(av.isRightAlignIds());
925 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
926 renderGapsMenuItem.setSelected(av.isRenderGaps());
927 wrapMenuItem.setSelected(av.getWrapAlignment());
928 scaleAbove.setVisible(av.getWrapAlignment());
929 scaleLeft.setVisible(av.getWrapAlignment());
930 scaleRight.setVisible(av.getWrapAlignment());
931 annotationPanelMenuItem.setState(av.isShowAnnotation());
933 * Show/hide annotations only enabled if annotation panel is shown
935 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
936 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
937 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
938 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
939 viewBoxesMenuItem.setSelected(av.getShowBoxes());
940 viewTextMenuItem.setSelected(av.getShowText());
941 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
942 showGroupConsensus.setSelected(av.isShowGroupConsensus());
943 showGroupConservation.setSelected(av.isShowGroupConservation());
944 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
945 showSequenceLogo.setSelected(av.isShowSequenceLogo());
946 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
947 showInformationHistogram.setSelected(av.isShowInformationHistogram());
948 showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
949 normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
951 ColourMenuHelper.setColourSelected(colourMenu,
952 av.getGlobalColourScheme());
954 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
955 hiddenMarkers.setState(av.getShowHiddenMarkers());
956 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
957 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
958 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
959 autoCalculate.setSelected(av.autoCalculateConsensus);
960 sortByTree.setSelected(av.sortByTree);
961 listenToViewSelections.setSelected(av.followSelection);
963 showProducts.setEnabled(canShowProducts());
964 setGroovyEnabled(Desktop.getGroovyConsole() != null);
970 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
974 public void setGroovyEnabled(boolean b)
976 runGroovy.setEnabled(b);
979 private IProgressIndicator progressBar;
984 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
987 public void setProgressBar(String message, long id)
989 progressBar.setProgressBar(message, id);
993 public void registerHandler(final long id,
994 final IProgressIndicatorHandler handler)
996 progressBar.registerHandler(id, handler);
1001 * @return true if any progress bars are still active
1004 public boolean operationInProgress()
1006 return progressBar.operationInProgress();
1010 public void setStatus(String text)
1012 statusBar.setText(text);
1016 * Added so Castor Mapping file can obtain Jalview Version
1018 public String getVersion()
1020 return jalview.bin.Cache.getProperty("VERSION");
1023 public FeatureRenderer getFeatureRenderer()
1025 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1029 public void fetchSequence_actionPerformed(ActionEvent e)
1031 new jalview.gui.SequenceFetcher(this);
1035 public void addFromFile_actionPerformed(ActionEvent e)
1037 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1041 public void hmmBuild_actionPerformed(ActionEvent e)
1042 throws IOException, InterruptedException
1044 new Thread(new HMMBuildThread(this)).start();
1045 alignPanel.repaint();
1050 public void hmmAlign_actionPerformed(ActionEvent e)
1051 throws IOException, InterruptedException
1053 new Thread(new HMMAlignThread(this, true)).start();
1054 alignPanel.repaint();
1058 public void changeHMMERLocation_actionPerformed(ActionEvent e)
1060 String location = JOptionPane.showInputDialog(
1061 MessageManager.getString("label.enter_location"));
1062 Cache.setProperty(Preferences.HMMER_PATH, location);
1066 public void autoAlignSeqs_actionPerformed(boolean autoAlignSeqs)
1068 autoAlignNewSequences = autoAlignSeqs;
1069 alignPanel.repaint();
1073 public void hmmSearch_actionPerformed(ActionEvent e)
1075 alignPanel.repaint();
1079 public void reload_actionPerformed(ActionEvent e)
1081 if (fileName != null)
1083 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1084 // originating file's format
1085 // TODO: work out how to recover feature settings for correct view(s) when
1086 // file is reloaded.
1087 if (FileFormat.Jalview.equals(currentFileFormat))
1089 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1090 for (int i = 0; i < frames.length; i++)
1092 if (frames[i] instanceof AlignFrame && frames[i] != this
1093 && ((AlignFrame) frames[i]).fileName != null
1094 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1098 frames[i].setSelected(true);
1099 Desktop.instance.closeAssociatedWindows();
1100 } catch (java.beans.PropertyVetoException ex)
1106 Desktop.instance.closeAssociatedWindows();
1108 FileLoader loader = new FileLoader();
1109 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1110 : DataSourceType.FILE;
1111 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1115 Rectangle bounds = this.getBounds();
1117 FileLoader loader = new FileLoader();
1118 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1119 : DataSourceType.FILE;
1120 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1121 protocol, currentFileFormat);
1123 newframe.setBounds(bounds);
1124 if (featureSettings != null && featureSettings.isShowing())
1126 final Rectangle fspos = featureSettings.frame.getBounds();
1127 // TODO: need a 'show feature settings' function that takes bounds -
1128 // need to refactor Desktop.addFrame
1129 newframe.featureSettings_actionPerformed(null);
1130 final FeatureSettings nfs = newframe.featureSettings;
1131 SwingUtilities.invokeLater(new Runnable()
1136 nfs.frame.setBounds(fspos);
1139 this.featureSettings.close();
1140 this.featureSettings = null;
1142 this.closeMenuItem_actionPerformed(true);
1148 public void addFromText_actionPerformed(ActionEvent e)
1150 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1155 public void addFromURL_actionPerformed(ActionEvent e)
1157 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1161 public void save_actionPerformed(ActionEvent e)
1163 if (fileName == null || (currentFileFormat == null)
1164 || fileName.startsWith("http"))
1166 saveAs_actionPerformed(null);
1170 saveAlignment(fileName, currentFileFormat);
1181 public void saveAs_actionPerformed(ActionEvent e)
1183 String format = currentFileFormat == null ? null : currentFileFormat
1185 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1186 Cache.getProperty("LAST_DIRECTORY"), format);
1188 chooser.setFileView(new JalviewFileView());
1189 chooser.setDialogTitle(MessageManager
1190 .getString("label.save_alignment_to_file"));
1191 chooser.setToolTipText(MessageManager.getString("action.save"));
1193 int value = chooser.showSaveDialog(this);
1195 if (value == JalviewFileChooser.APPROVE_OPTION)
1197 currentFileFormat = chooser.getSelectedFormat();
1198 while (currentFileFormat == null)
1201 .showInternalMessageDialog(
1204 .getString("label.select_file_format_before_saving"),
1206 .getString("label.file_format_not_specified"),
1207 JvOptionPane.WARNING_MESSAGE);
1208 currentFileFormat = chooser.getSelectedFormat();
1209 value = chooser.showSaveDialog(this);
1210 if (value != JalviewFileChooser.APPROVE_OPTION)
1216 fileName = chooser.getSelectedFile().getPath();
1218 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1220 Cache.setProperty("LAST_DIRECTORY", fileName);
1221 saveAlignment(fileName, currentFileFormat);
1225 public boolean saveAlignment(String file, FileFormatI format)
1227 boolean success = true;
1229 if (FileFormat.Jalview.equals(format))
1231 String shortName = title;
1233 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1235 shortName = shortName.substring(shortName
1236 .lastIndexOf(java.io.File.separatorChar) + 1);
1239 success = new Jalview2XML().saveAlignment(this, file, shortName);
1241 statusBar.setText(MessageManager.formatMessage(
1242 "label.successfully_saved_to_file_in_format", new Object[] {
1243 fileName, format }));
1248 AlignmentExportData exportData = getAlignmentForExport(format,
1250 if (exportData.getSettings().isCancelled())
1254 FormatAdapter f = new FormatAdapter(alignPanel,
1255 exportData.getSettings());
1256 String output = f.formatSequences(
1258 exportData.getAlignment(), // class cast exceptions will
1259 // occur in the distant future
1260 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1261 f.getCacheSuffixDefault(format), viewport.getAlignment()
1262 .getHiddenColumns());
1272 PrintWriter out = new PrintWriter(new FileWriter(file));
1276 this.setTitle(file);
1277 statusBar.setText(MessageManager.formatMessage(
1278 "label.successfully_saved_to_file_in_format",
1279 new Object[] { fileName, format.getName() }));
1280 } catch (Exception ex)
1283 ex.printStackTrace();
1290 JvOptionPane.showInternalMessageDialog(this, MessageManager
1291 .formatMessage("label.couldnt_save_file",
1292 new Object[] { fileName }), MessageManager
1293 .getString("label.error_saving_file"),
1294 JvOptionPane.WARNING_MESSAGE);
1300 private void warningMessage(String warning, String title)
1302 if (new jalview.util.Platform().isHeadless())
1304 System.err.println("Warning: " + title + "\nWarning: " + warning);
1309 JvOptionPane.showInternalMessageDialog(this, warning, title,
1310 JvOptionPane.WARNING_MESSAGE);
1322 protected void outputText_actionPerformed(ActionEvent e)
1324 FileFormatI fileFormat = FileFormats.getInstance().forName(
1325 e.getActionCommand());
1326 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1328 if (exportData.getSettings().isCancelled())
1332 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1333 cap.setForInput(null);
1336 FileFormatI format = fileFormat;
1337 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1338 .formatSequences(format, exportData.getAlignment(),
1339 exportData.getOmitHidden(),
1341 .getStartEndPostions(), viewport
1342 .getAlignment().getHiddenColumns()));
1343 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1344 "label.alignment_output_command",
1345 new Object[] { e.getActionCommand() }), 600, 500);
1346 } catch (OutOfMemoryError oom)
1348 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1354 public static AlignmentExportData getAlignmentForExport(
1355 FileFormatI format, AlignViewportI viewport,
1356 AlignExportSettingI exportSettings)
1358 AlignmentI alignmentToExport = null;
1359 AlignExportSettingI settings = exportSettings;
1360 String[] omitHidden = null;
1362 HiddenSequences hiddenSeqs = viewport.getAlignment()
1363 .getHiddenSequences();
1365 alignmentToExport = viewport.getAlignment();
1367 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1368 if (settings == null)
1370 settings = new AlignExportSettings(hasHiddenSeqs,
1371 viewport.hasHiddenColumns(), format);
1373 // settings.isExportAnnotations();
1375 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1377 omitHidden = viewport.getViewAsString(false,
1378 settings.isExportHiddenSequences());
1381 int[] alignmentStartEnd = new int[2];
1382 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1384 alignmentToExport = hiddenSeqs.getFullAlignment();
1388 alignmentToExport = viewport.getAlignment();
1390 alignmentStartEnd = alignmentToExport
1391 .getVisibleStartAndEndIndex(viewport.getAlignment()
1393 .getHiddenRegions());
1394 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1395 omitHidden, alignmentStartEnd, settings);
1406 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1408 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1409 htmlSVG.exportHTML(null);
1413 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1415 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1416 bjs.exportHTML(null);
1419 public void createImageMap(File file, String image)
1421 alignPanel.makePNGImageMap(file, image);
1431 public void createPNG(File f)
1433 alignPanel.makePNG(f);
1443 public void createEPS(File f)
1445 alignPanel.makeEPS(f);
1449 public void createSVG(File f)
1451 alignPanel.makeSVG(f);
1455 public void pageSetup_actionPerformed(ActionEvent e)
1457 PrinterJob printJob = PrinterJob.getPrinterJob();
1458 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1468 public void printMenuItem_actionPerformed(ActionEvent e)
1470 // Putting in a thread avoids Swing painting problems
1471 PrintThread thread = new PrintThread(alignPanel);
1476 public void exportFeatures_actionPerformed(ActionEvent e)
1478 new AnnotationExporter().exportFeatures(alignPanel);
1482 public void exportAnnotations_actionPerformed(ActionEvent e)
1484 new AnnotationExporter().exportAnnotations(alignPanel);
1488 public void associatedData_actionPerformed(ActionEvent e)
1489 throws IOException, InterruptedException
1491 // Pick the tree file
1492 JalviewFileChooser chooser = new JalviewFileChooser(
1493 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1494 chooser.setFileView(new JalviewFileView());
1495 chooser.setDialogTitle(MessageManager
1496 .getString("label.load_jalview_annotations"));
1497 chooser.setToolTipText(MessageManager
1498 .getString("label.load_jalview_annotations"));
1500 int value = chooser.showOpenDialog(null);
1502 if (value == JalviewFileChooser.APPROVE_OPTION)
1504 String choice = chooser.getSelectedFile().getPath();
1505 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1506 loadJalviewDataFile(choice, null, null, null);
1512 * Close the current view or all views in the alignment frame. If the frame
1513 * only contains one view then the alignment will be removed from memory.
1515 * @param closeAllTabs
1518 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1520 if (alignPanels != null && alignPanels.size() < 2)
1522 closeAllTabs = true;
1527 if (alignPanels != null)
1531 if (this.isClosed())
1533 // really close all the windows - otherwise wait till
1534 // setClosed(true) is called
1535 for (int i = 0; i < alignPanels.size(); i++)
1537 AlignmentPanel ap = alignPanels.get(i);
1544 closeView(alignPanel);
1551 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1552 * be called recursively, with the frame now in 'closed' state
1554 this.setClosed(true);
1556 } catch (Exception ex)
1558 ex.printStackTrace();
1563 * Close the specified panel and close up tabs appropriately.
1565 * @param panelToClose
1567 public void closeView(AlignmentPanel panelToClose)
1569 int index = tabbedPane.getSelectedIndex();
1570 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1571 alignPanels.remove(panelToClose);
1572 panelToClose.closePanel();
1573 panelToClose = null;
1575 tabbedPane.removeTabAt(closedindex);
1576 tabbedPane.validate();
1578 if (index > closedindex || index == tabbedPane.getTabCount())
1580 // modify currently selected tab index if necessary.
1584 this.tabSelectionChanged(index);
1590 void updateEditMenuBar()
1593 if (viewport.getHistoryList().size() > 0)
1595 undoMenuItem.setEnabled(true);
1596 CommandI command = viewport.getHistoryList().peek();
1597 undoMenuItem.setText(MessageManager.formatMessage(
1598 "label.undo_command",
1599 new Object[] { command.getDescription() }));
1603 undoMenuItem.setEnabled(false);
1604 undoMenuItem.setText(MessageManager.getString("action.undo"));
1607 if (viewport.getRedoList().size() > 0)
1609 redoMenuItem.setEnabled(true);
1611 CommandI command = viewport.getRedoList().peek();
1612 redoMenuItem.setText(MessageManager.formatMessage(
1613 "label.redo_command",
1614 new Object[] { command.getDescription() }));
1618 redoMenuItem.setEnabled(false);
1619 redoMenuItem.setText(MessageManager.getString("action.redo"));
1624 public void addHistoryItem(CommandI command)
1626 if (command.getSize() > 0)
1628 viewport.addToHistoryList(command);
1629 viewport.clearRedoList();
1630 updateEditMenuBar();
1631 viewport.updateHiddenColumns();
1632 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1633 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1634 // viewport.getColumnSelection()
1635 // .getHiddenColumns().size() > 0);
1641 * @return alignment objects for all views
1643 AlignmentI[] getViewAlignments()
1645 if (alignPanels != null)
1647 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1649 for (AlignmentPanel ap : alignPanels)
1651 als[i++] = ap.av.getAlignment();
1655 if (viewport != null)
1657 return new AlignmentI[] { viewport.getAlignment() };
1669 protected void undoMenuItem_actionPerformed(ActionEvent e)
1671 if (viewport.getHistoryList().isEmpty())
1675 CommandI command = viewport.getHistoryList().pop();
1676 viewport.addToRedoList(command);
1677 command.undoCommand(getViewAlignments());
1679 AlignmentViewport originalSource = getOriginatingSource(command);
1680 updateEditMenuBar();
1682 if (originalSource != null)
1684 if (originalSource != viewport)
1687 .warn("Implementation worry: mismatch of viewport origin for undo");
1689 originalSource.updateHiddenColumns();
1690 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1692 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1693 // viewport.getColumnSelection()
1694 // .getHiddenColumns().size() > 0);
1695 originalSource.firePropertyChange("alignment", null, originalSource
1696 .getAlignment().getSequences());
1707 protected void redoMenuItem_actionPerformed(ActionEvent e)
1709 if (viewport.getRedoList().size() < 1)
1714 CommandI command = viewport.getRedoList().pop();
1715 viewport.addToHistoryList(command);
1716 command.doCommand(getViewAlignments());
1718 AlignmentViewport originalSource = getOriginatingSource(command);
1719 updateEditMenuBar();
1721 if (originalSource != null)
1724 if (originalSource != viewport)
1727 .warn("Implementation worry: mismatch of viewport origin for redo");
1729 originalSource.updateHiddenColumns();
1730 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1732 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1733 // viewport.getColumnSelection()
1734 // .getHiddenColumns().size() > 0);
1735 originalSource.firePropertyChange("alignment", null, originalSource
1736 .getAlignment().getSequences());
1740 AlignmentViewport getOriginatingSource(CommandI command)
1742 AlignmentViewport originalSource = null;
1743 // For sequence removal and addition, we need to fire
1744 // the property change event FROM the viewport where the
1745 // original alignment was altered
1746 AlignmentI al = null;
1747 if (command instanceof EditCommand)
1749 EditCommand editCommand = (EditCommand) command;
1750 al = editCommand.getAlignment();
1751 List<Component> comps = PaintRefresher.components.get(viewport
1752 .getSequenceSetId());
1754 for (Component comp : comps)
1756 if (comp instanceof AlignmentPanel)
1758 if (al == ((AlignmentPanel) comp).av.getAlignment())
1760 originalSource = ((AlignmentPanel) comp).av;
1767 if (originalSource == null)
1769 // The original view is closed, we must validate
1770 // the current view against the closed view first
1773 PaintRefresher.validateSequences(al, viewport.getAlignment());
1776 originalSource = viewport;
1779 return originalSource;
1788 public void moveSelectedSequences(boolean up)
1790 SequenceGroup sg = viewport.getSelectionGroup();
1796 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1797 viewport.getHiddenRepSequences(), up);
1798 alignPanel.paintAlignment(true);
1801 synchronized void slideSequences(boolean right, int size)
1803 List<SequenceI> sg = new ArrayList<>();
1804 if (viewport.cursorMode)
1806 sg.add(viewport.getAlignment().getSequenceAt(
1807 alignPanel.getSeqPanel().seqCanvas.cursorY));
1809 else if (viewport.getSelectionGroup() != null
1810 && viewport.getSelectionGroup().getSize() != viewport
1811 .getAlignment().getHeight())
1813 sg = viewport.getSelectionGroup().getSequences(
1814 viewport.getHiddenRepSequences());
1822 List<SequenceI> invertGroup = new ArrayList<>();
1824 for (SequenceI seq : viewport.getAlignment().getSequences())
1826 if (!sg.contains(seq))
1828 invertGroup.add(seq);
1832 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1834 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1835 for (int i = 0; i < invertGroup.size(); i++)
1837 seqs2[i] = invertGroup.get(i);
1840 SlideSequencesCommand ssc;
1843 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1844 size, viewport.getGapCharacter());
1848 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1849 size, viewport.getGapCharacter());
1852 int groupAdjustment = 0;
1853 if (ssc.getGapsInsertedBegin() && right)
1855 if (viewport.cursorMode)
1857 alignPanel.getSeqPanel().moveCursor(size, 0);
1861 groupAdjustment = size;
1864 else if (!ssc.getGapsInsertedBegin() && !right)
1866 if (viewport.cursorMode)
1868 alignPanel.getSeqPanel().moveCursor(-size, 0);
1872 groupAdjustment = -size;
1876 if (groupAdjustment != 0)
1878 viewport.getSelectionGroup().setStartRes(
1879 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1880 viewport.getSelectionGroup().setEndRes(
1881 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1885 * just extend the last slide command if compatible; but not if in
1886 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1888 boolean appendHistoryItem = false;
1889 Deque<CommandI> historyList = viewport.getHistoryList();
1890 boolean inSplitFrame = getSplitViewContainer() != null;
1891 if (!inSplitFrame && historyList != null && historyList.size() > 0
1892 && historyList.peek() instanceof SlideSequencesCommand)
1894 appendHistoryItem = ssc
1895 .appendSlideCommand((SlideSequencesCommand) historyList
1899 if (!appendHistoryItem)
1901 addHistoryItem(ssc);
1914 protected void copy_actionPerformed(ActionEvent e)
1917 if (viewport.getSelectionGroup() == null)
1921 // TODO: preserve the ordering of displayed alignment annotation in any
1922 // internal paste (particularly sequence associated annotation)
1923 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1924 String[] omitHidden = null;
1926 if (viewport.hasHiddenColumns())
1928 omitHidden = viewport.getViewAsString(true);
1931 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1932 seqs, omitHidden, null);
1934 StringSelection ss = new StringSelection(output);
1938 jalview.gui.Desktop.internalCopy = true;
1939 // Its really worth setting the clipboard contents
1940 // to empty before setting the large StringSelection!!
1941 Toolkit.getDefaultToolkit().getSystemClipboard()
1942 .setContents(new StringSelection(""), null);
1944 Toolkit.getDefaultToolkit().getSystemClipboard()
1945 .setContents(ss, Desktop.instance);
1946 } catch (OutOfMemoryError er)
1948 new OOMWarning("copying region", er);
1952 ArrayList<int[]> hiddenColumns = null;
1953 if (viewport.hasHiddenColumns())
1955 hiddenColumns = new ArrayList<>();
1956 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1957 .getSelectionGroup().getEndRes();
1958 for (int[] region : viewport.getAlignment().getHiddenColumns()
1959 .getHiddenRegions())
1961 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1963 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1964 region[1] - hiddenOffset });
1969 Desktop.jalviewClipboard = new Object[] { seqs,
1970 viewport.getAlignment().getDataset(), hiddenColumns };
1971 statusBar.setText(MessageManager.formatMessage(
1972 "label.copied_sequences_to_clipboard", new Object[] { Integer
1973 .valueOf(seqs.length).toString() }));
1981 * @throws InterruptedException
1982 * @throws IOException
1985 protected void pasteNew_actionPerformed(ActionEvent e)
1986 throws IOException, InterruptedException
1996 * @throws InterruptedException
1997 * @throws IOException
2000 protected void pasteThis_actionPerformed(ActionEvent e)
2001 throws IOException, InterruptedException
2007 * Paste contents of Jalview clipboard
2009 * @param newAlignment
2010 * true to paste to a new alignment, otherwise add to this.
2011 * @throws InterruptedException
2012 * @throws IOException
2014 void paste(boolean newAlignment) throws IOException, InterruptedException
2016 boolean externalPaste = true;
2019 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2020 Transferable contents = c.getContents(this);
2022 if (contents == null)
2031 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2032 if (str.length() < 1)
2037 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2039 } catch (OutOfMemoryError er)
2041 new OOMWarning("Out of memory pasting sequences!!", er);
2045 SequenceI[] sequences;
2046 boolean annotationAdded = false;
2047 AlignmentI alignment = null;
2049 if (Desktop.jalviewClipboard != null)
2051 // The clipboard was filled from within Jalview, we must use the
2053 // And dataset from the copied alignment
2054 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2055 // be doubly sure that we create *new* sequence objects.
2056 sequences = new SequenceI[newseq.length];
2057 for (int i = 0; i < newseq.length; i++)
2059 sequences[i] = new Sequence(newseq[i]);
2061 alignment = new Alignment(sequences);
2062 externalPaste = false;
2066 // parse the clipboard as an alignment.
2067 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2069 sequences = alignment.getSequencesArray();
2073 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2079 if (Desktop.jalviewClipboard != null)
2081 // dataset is inherited
2082 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2086 // new dataset is constructed
2087 alignment.setDataset(null);
2089 alwidth = alignment.getWidth() + 1;
2093 AlignmentI pastedal = alignment; // preserve pasted alignment object
2094 // Add pasted sequences and dataset into existing alignment.
2095 alignment = viewport.getAlignment();
2096 alwidth = alignment.getWidth() + 1;
2097 // decide if we need to import sequences from an existing dataset
2098 boolean importDs = Desktop.jalviewClipboard != null
2099 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2100 // importDs==true instructs us to copy over new dataset sequences from
2101 // an existing alignment
2102 Vector newDs = (importDs) ? new Vector() : null; // used to create
2103 // minimum dataset set
2105 for (int i = 0; i < sequences.length; i++)
2109 newDs.addElement(null);
2111 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2113 if (importDs && ds != null)
2115 if (!newDs.contains(ds))
2117 newDs.setElementAt(ds, i);
2118 ds = new Sequence(ds);
2119 // update with new dataset sequence
2120 sequences[i].setDatasetSequence(ds);
2124 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2129 // copy and derive new dataset sequence
2130 sequences[i] = sequences[i].deriveSequence();
2131 alignment.getDataset().addSequence(
2132 sequences[i].getDatasetSequence());
2133 // TODO: avoid creation of duplicate dataset sequences with a
2134 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2136 alignment.addSequence(sequences[i]); // merges dataset
2140 newDs.clear(); // tidy up
2142 if (alignment.getAlignmentAnnotation() != null)
2144 for (AlignmentAnnotation alan : alignment
2145 .getAlignmentAnnotation())
2147 if (alan.graphGroup > fgroup)
2149 fgroup = alan.graphGroup;
2153 if (pastedal.getAlignmentAnnotation() != null)
2155 // Add any annotation attached to alignment.
2156 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2157 for (int i = 0; i < alann.length; i++)
2159 annotationAdded = true;
2160 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2162 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2163 if (newann.graphGroup > -1)
2165 if (newGraphGroups.size() <= newann.graphGroup
2166 || newGraphGroups.get(newann.graphGroup) == null)
2168 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2170 newGraphGroups.add(q, null);
2172 newGraphGroups.set(newann.graphGroup, new Integer(
2175 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2179 newann.padAnnotation(alwidth);
2180 alignment.addAnnotation(newann);
2190 addHistoryItem(new EditCommand(
2191 MessageManager.getString("label.add_sequences"),
2192 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2194 // Add any annotations attached to sequences
2195 for (int i = 0; i < sequences.length; i++)
2197 if (sequences[i].getAnnotation() != null)
2199 AlignmentAnnotation newann;
2200 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2202 annotationAdded = true;
2203 newann = sequences[i].getAnnotation()[a];
2204 newann.adjustForAlignment();
2205 newann.padAnnotation(alwidth);
2206 if (newann.graphGroup > -1)
2208 if (newann.graphGroup > -1)
2210 if (newGraphGroups.size() <= newann.graphGroup
2211 || newGraphGroups.get(newann.graphGroup) == null)
2213 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2215 newGraphGroups.add(q, null);
2217 newGraphGroups.set(newann.graphGroup, new Integer(
2220 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2224 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2229 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2236 // propagate alignment changed.
2237 vpRanges.setEndSeq(alignment.getHeight());
2238 if (annotationAdded)
2240 // Duplicate sequence annotation in all views.
2241 AlignmentI[] alview = this.getViewAlignments();
2242 for (int i = 0; i < sequences.length; i++)
2244 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2249 for (int avnum = 0; avnum < alview.length; avnum++)
2251 if (alview[avnum] != alignment)
2253 // duplicate in a view other than the one with input focus
2254 int avwidth = alview[avnum].getWidth() + 1;
2255 // this relies on sann being preserved after we
2256 // modify the sequence's annotation array for each duplication
2257 for (int a = 0; a < sann.length; a++)
2259 AlignmentAnnotation newann = new AlignmentAnnotation(
2261 sequences[i].addAlignmentAnnotation(newann);
2262 newann.padAnnotation(avwidth);
2263 alview[avnum].addAnnotation(newann); // annotation was
2264 // duplicated earlier
2265 // TODO JAL-1145 graphGroups are not updated for sequence
2266 // annotation added to several views. This may cause
2268 alview[avnum].setAnnotationIndex(newann, a);
2273 buildSortByAnnotationScoresMenu();
2275 viewport.firePropertyChange("alignment", null,
2276 alignment.getSequences());
2277 if (alignPanels != null)
2279 for (AlignmentPanel ap : alignPanels)
2281 ap.validateAnnotationDimensions(false);
2286 alignPanel.validateAnnotationDimensions(false);
2292 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2294 String newtitle = new String("Copied sequences");
2296 if (Desktop.jalviewClipboard != null
2297 && Desktop.jalviewClipboard[2] != null)
2299 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2300 for (int[] region : hc)
2302 af.viewport.hideColumns(region[0], region[1]);
2306 // >>>This is a fix for the moment, until a better solution is
2308 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2310 alignPanel.getSeqPanel().seqCanvas
2311 .getFeatureRenderer());
2313 // TODO: maintain provenance of an alignment, rather than just make the
2314 // title a concatenation of operations.
2317 if (title.startsWith("Copied sequences"))
2323 newtitle = newtitle.concat("- from " + title);
2328 newtitle = new String("Pasted sequences");
2331 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2336 } catch (Exception ex)
2338 ex.printStackTrace();
2339 System.out.println("Exception whilst pasting: " + ex);
2340 // could be anything being pasted in here
2345 protected void expand_newalign(ActionEvent e)
2349 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2350 .getAlignment(), -1);
2351 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2353 String newtitle = new String("Flanking alignment");
2355 if (Desktop.jalviewClipboard != null
2356 && Desktop.jalviewClipboard[2] != null)
2358 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2359 for (int region[] : hc)
2361 af.viewport.hideColumns(region[0], region[1]);
2365 // >>>This is a fix for the moment, until a better solution is
2367 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2369 alignPanel.getSeqPanel().seqCanvas
2370 .getFeatureRenderer());
2372 // TODO: maintain provenance of an alignment, rather than just make the
2373 // title a concatenation of operations.
2375 if (title.startsWith("Copied sequences"))
2381 newtitle = newtitle.concat("- from " + title);
2385 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2387 } catch (Exception ex)
2389 ex.printStackTrace();
2390 System.out.println("Exception whilst pasting: " + ex);
2391 // could be anything being pasted in here
2392 } catch (OutOfMemoryError oom)
2394 new OOMWarning("Viewing flanking region of alignment", oom);
2405 protected void cut_actionPerformed(ActionEvent e)
2407 copy_actionPerformed(null);
2408 delete_actionPerformed(null);
2418 protected void delete_actionPerformed(ActionEvent evt)
2421 SequenceGroup sg = viewport.getSelectionGroup();
2428 * If the cut affects all sequences, warn, remove highlighted columns
2430 if (sg.getSize() == viewport.getAlignment().getHeight())
2432 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2433 .getAlignment().getWidth()) ? true : false;
2434 if (isEntireAlignWidth)
2436 int confirm = JvOptionPane.showConfirmDialog(this,
2437 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2438 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2439 JvOptionPane.OK_CANCEL_OPTION);
2441 if (confirm == JvOptionPane.CANCEL_OPTION
2442 || confirm == JvOptionPane.CLOSED_OPTION)
2447 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2448 sg.getEndRes() + 1);
2450 SequenceI[] cut = sg.getSequences()
2451 .toArray(new SequenceI[sg.getSize()]);
2453 addHistoryItem(new EditCommand(
2454 MessageManager.getString("label.cut_sequences"), Action.CUT,
2455 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2456 viewport.getAlignment()));
2458 viewport.setSelectionGroup(null);
2459 viewport.sendSelection();
2460 viewport.getAlignment().deleteGroup(sg);
2462 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2464 if (viewport.getAlignment().getHeight() < 1)
2468 this.setClosed(true);
2469 } catch (Exception ex)
2482 protected void deleteGroups_actionPerformed(ActionEvent e)
2484 if (avc.deleteGroups())
2486 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2487 alignPanel.updateAnnotation();
2488 alignPanel.paintAlignment(true);
2499 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2501 SequenceGroup sg = new SequenceGroup();
2503 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2505 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2508 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2509 viewport.setSelectionGroup(sg);
2510 viewport.sendSelection();
2511 // JAL-2034 - should delegate to
2512 // alignPanel to decide if overview needs
2514 alignPanel.paintAlignment(false);
2515 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2525 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2527 if (viewport.cursorMode)
2529 alignPanel.getSeqPanel().keyboardNo1 = null;
2530 alignPanel.getSeqPanel().keyboardNo2 = null;
2532 viewport.setSelectionGroup(null);
2533 viewport.getColumnSelection().clear();
2534 viewport.setSelectionGroup(null);
2535 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2536 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2537 // JAL-2034 - should delegate to
2538 // alignPanel to decide if overview needs
2540 alignPanel.paintAlignment(false);
2541 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2542 viewport.sendSelection();
2552 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2554 SequenceGroup sg = viewport.getSelectionGroup();
2558 selectAllSequenceMenuItem_actionPerformed(null);
2563 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2565 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2567 // JAL-2034 - should delegate to
2568 // alignPanel to decide if overview needs
2571 alignPanel.paintAlignment(true);
2572 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2573 viewport.sendSelection();
2577 public void invertColSel_actionPerformed(ActionEvent e)
2579 viewport.invertColumnSelection();
2580 alignPanel.paintAlignment(true);
2581 viewport.sendSelection();
2591 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2593 trimAlignment(true);
2603 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2605 trimAlignment(false);
2608 void trimAlignment(boolean trimLeft)
2610 ColumnSelection colSel = viewport.getColumnSelection();
2613 if (!colSel.isEmpty())
2617 column = colSel.getMin();
2621 column = colSel.getMax();
2625 if (viewport.getSelectionGroup() != null)
2627 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2628 viewport.getHiddenRepSequences());
2632 seqs = viewport.getAlignment().getSequencesArray();
2635 TrimRegionCommand trimRegion;
2638 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2639 column, viewport.getAlignment());
2640 vpRanges.setStartRes(0);
2644 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2645 column, viewport.getAlignment());
2648 statusBar.setText(MessageManager.formatMessage(
2649 "label.removed_columns",
2650 new String[] { Integer.valueOf(trimRegion.getSize())
2653 addHistoryItem(trimRegion);
2655 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2657 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2658 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2660 viewport.getAlignment().deleteGroup(sg);
2664 viewport.firePropertyChange("alignment", null, viewport
2665 .getAlignment().getSequences());
2676 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2678 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2681 if (viewport.getSelectionGroup() != null)
2683 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2684 viewport.getHiddenRepSequences());
2685 start = viewport.getSelectionGroup().getStartRes();
2686 end = viewport.getSelectionGroup().getEndRes();
2690 seqs = viewport.getAlignment().getSequencesArray();
2693 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2694 "Remove Gapped Columns", seqs, start, end,
2695 viewport.getAlignment());
2697 addHistoryItem(removeGapCols);
2699 statusBar.setText(MessageManager.formatMessage(
2700 "label.removed_empty_columns",
2701 new Object[] { Integer.valueOf(removeGapCols.getSize())
2704 // This is to maintain viewport position on first residue
2705 // of first sequence
2706 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2707 int startRes = seq.findPosition(vpRanges.getStartRes());
2708 // ShiftList shifts;
2709 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2710 // edit.alColumnChanges=shifts.getInverse();
2711 // if (viewport.hasHiddenColumns)
2712 // viewport.getColumnSelection().compensateForEdits(shifts);
2713 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2714 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2726 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2728 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2731 if (viewport.getSelectionGroup() != null)
2733 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2734 viewport.getHiddenRepSequences());
2735 start = viewport.getSelectionGroup().getStartRes();
2736 end = viewport.getSelectionGroup().getEndRes();
2740 seqs = viewport.getAlignment().getSequencesArray();
2743 // This is to maintain viewport position on first residue
2744 // of first sequence
2745 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2746 int startRes = seq.findPosition(vpRanges.getStartRes());
2748 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2749 viewport.getAlignment()));
2751 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2753 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2765 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2767 viewport.setPadGaps(padGapsMenuitem.isSelected());
2768 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2779 public void findMenuItem_actionPerformed(ActionEvent e)
2785 * Create a new view of the current alignment.
2788 public void newView_actionPerformed(ActionEvent e)
2790 newView(null, true);
2794 * Creates and shows a new view of the current alignment.
2797 * title of newly created view; if null, one will be generated
2798 * @param copyAnnotation
2799 * if true then duplicate all annnotation, groups and settings
2800 * @return new alignment panel, already displayed.
2802 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2805 * Create a new AlignmentPanel (with its own, new Viewport)
2807 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2809 if (!copyAnnotation)
2812 * remove all groups and annotation except for the automatic stuff
2814 newap.av.getAlignment().deleteAllGroups();
2815 newap.av.getAlignment().deleteAllAnnotations(false);
2818 newap.av.setGatherViewsHere(false);
2820 if (viewport.viewName == null)
2822 viewport.viewName = MessageManager
2823 .getString("label.view_name_original");
2827 * Views share the same edits undo and redo stacks
2829 newap.av.setHistoryList(viewport.getHistoryList());
2830 newap.av.setRedoList(viewport.getRedoList());
2833 * Views share the same mappings; need to deregister any new mappings
2834 * created by copyAlignPanel, and register the new reference to the shared
2837 newap.av.replaceMappings(viewport.getAlignment());
2840 * start up cDNA consensus (if applicable) now mappings are in place
2842 if (newap.av.initComplementConsensus())
2844 newap.refresh(true); // adjust layout of annotations
2847 newap.av.viewName = getNewViewName(viewTitle);
2849 addAlignmentPanel(newap, true);
2850 newap.alignmentChanged();
2852 if (alignPanels.size() == 2)
2854 viewport.setGatherViewsHere(true);
2856 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2861 * Make a new name for the view, ensuring it is unique within the current
2862 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2863 * these now use viewId. Unique view names are still desirable for usability.)
2868 protected String getNewViewName(String viewTitle)
2870 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2871 boolean addFirstIndex = false;
2872 if (viewTitle == null || viewTitle.trim().length() == 0)
2874 viewTitle = MessageManager.getString("action.view");
2875 addFirstIndex = true;
2879 index = 1;// we count from 1 if given a specific name
2881 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2883 List<Component> comps = PaintRefresher.components.get(viewport
2884 .getSequenceSetId());
2886 List<String> existingNames = getExistingViewNames(comps);
2888 while (existingNames.contains(newViewName))
2890 newViewName = viewTitle + " " + (++index);
2896 * Returns a list of distinct view names found in the given list of
2897 * components. View names are held on the viewport of an AlignmentPanel.
2902 protected List<String> getExistingViewNames(List<Component> comps)
2904 List<String> existingNames = new ArrayList<>();
2905 for (Component comp : comps)
2907 if (comp instanceof AlignmentPanel)
2909 AlignmentPanel ap = (AlignmentPanel) comp;
2910 if (!existingNames.contains(ap.av.viewName))
2912 existingNames.add(ap.av.viewName);
2916 return existingNames;
2920 * Explode tabbed views into separate windows.
2923 public void expandViews_actionPerformed(ActionEvent e)
2925 Desktop.explodeViews(this);
2929 * Gather views in separate windows back into a tabbed presentation.
2932 public void gatherViews_actionPerformed(ActionEvent e)
2934 Desktop.instance.gatherViews(this);
2944 public void font_actionPerformed(ActionEvent e)
2946 new FontChooser(alignPanel);
2956 protected void seqLimit_actionPerformed(ActionEvent e)
2958 viewport.setShowJVSuffix(seqLimits.isSelected());
2960 alignPanel.getIdPanel().getIdCanvas()
2961 .setPreferredSize(alignPanel.calculateIdWidth());
2962 alignPanel.paintAlignment(true);
2966 public void idRightAlign_actionPerformed(ActionEvent e)
2968 viewport.setRightAlignIds(idRightAlign.isSelected());
2969 alignPanel.paintAlignment(true);
2973 public void centreColumnLabels_actionPerformed(ActionEvent e)
2975 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2976 alignPanel.paintAlignment(true);
2982 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2985 protected void followHighlight_actionPerformed()
2988 * Set the 'follow' flag on the Viewport (and scroll to position if now
2991 final boolean state = this.followHighlightMenuItem.getState();
2992 viewport.setFollowHighlight(state);
2995 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
3006 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3008 viewport.setColourText(colourTextMenuItem.isSelected());
3009 alignPanel.paintAlignment(true);
3019 public void wrapMenuItem_actionPerformed(ActionEvent e)
3021 scaleAbove.setVisible(wrapMenuItem.isSelected());
3022 scaleLeft.setVisible(wrapMenuItem.isSelected());
3023 scaleRight.setVisible(wrapMenuItem.isSelected());
3024 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3025 alignPanel.updateLayout();
3029 public void showAllSeqs_actionPerformed(ActionEvent e)
3031 viewport.showAllHiddenSeqs();
3035 public void showAllColumns_actionPerformed(ActionEvent e)
3037 viewport.showAllHiddenColumns();
3039 viewport.sendSelection();
3043 public void hideSelSequences_actionPerformed(ActionEvent e)
3045 viewport.hideAllSelectedSeqs();
3046 // alignPanel.paintAlignment(true);
3050 * called by key handler and the hide all/show all menu items
3055 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3058 boolean hide = false;
3059 SequenceGroup sg = viewport.getSelectionGroup();
3060 if (!toggleSeqs && !toggleCols)
3062 // Hide everything by the current selection - this is a hack - we do the
3063 // invert and then hide
3064 // first check that there will be visible columns after the invert.
3065 if (viewport.hasSelectedColumns()
3066 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3069 // now invert the sequence set, if required - empty selection implies
3070 // that no hiding is required.
3073 invertSequenceMenuItem_actionPerformed(null);
3074 sg = viewport.getSelectionGroup();
3078 viewport.expandColSelection(sg, true);
3079 // finally invert the column selection and get the new sequence
3081 invertColSel_actionPerformed(null);
3088 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3090 hideSelSequences_actionPerformed(null);
3093 else if (!(toggleCols && viewport.hasSelectedColumns()))
3095 showAllSeqs_actionPerformed(null);
3101 if (viewport.hasSelectedColumns())
3103 hideSelColumns_actionPerformed(null);
3106 viewport.setSelectionGroup(sg);
3111 showAllColumns_actionPerformed(null);
3120 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3121 * event.ActionEvent)
3124 public void hideAllButSelection_actionPerformed(ActionEvent e)
3126 toggleHiddenRegions(false, false);
3127 viewport.sendSelection();
3134 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3138 public void hideAllSelection_actionPerformed(ActionEvent e)
3140 SequenceGroup sg = viewport.getSelectionGroup();
3141 viewport.expandColSelection(sg, false);
3142 viewport.hideAllSelectedSeqs();
3143 viewport.hideSelectedColumns();
3144 alignPanel.paintAlignment(true);
3145 viewport.sendSelection();
3152 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3156 public void showAllhidden_actionPerformed(ActionEvent e)
3158 viewport.showAllHiddenColumns();
3159 viewport.showAllHiddenSeqs();
3160 alignPanel.paintAlignment(true);
3161 viewport.sendSelection();
3165 public void hideSelColumns_actionPerformed(ActionEvent e)
3167 viewport.hideSelectedColumns();
3168 alignPanel.paintAlignment(true);
3169 viewport.sendSelection();
3173 public void hiddenMarkers_actionPerformed(ActionEvent e)
3175 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3186 protected void scaleAbove_actionPerformed(ActionEvent e)
3188 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3189 alignPanel.paintAlignment(true);
3199 protected void scaleLeft_actionPerformed(ActionEvent e)
3201 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3202 alignPanel.paintAlignment(true);
3212 protected void scaleRight_actionPerformed(ActionEvent e)
3214 viewport.setScaleRightWrapped(scaleRight.isSelected());
3215 alignPanel.paintAlignment(true);
3225 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3227 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3228 alignPanel.paintAlignment(true);
3238 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3240 viewport.setShowText(viewTextMenuItem.isSelected());
3241 alignPanel.paintAlignment(true);
3251 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3253 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3254 alignPanel.paintAlignment(true);
3257 public FeatureSettings featureSettings;
3260 public FeatureSettingsControllerI getFeatureSettingsUI()
3262 return featureSettings;
3266 public void featureSettings_actionPerformed(ActionEvent e)
3268 if (featureSettings != null)
3270 featureSettings.close();
3271 featureSettings = null;
3273 if (!showSeqFeatures.isSelected())
3275 // make sure features are actually displayed
3276 showSeqFeatures.setSelected(true);
3277 showSeqFeatures_actionPerformed(null);
3279 featureSettings = new FeatureSettings(this);
3283 * Set or clear 'Show Sequence Features'
3289 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3291 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3292 alignPanel.paintAlignment(true);
3293 if (alignPanel.getOverviewPanel() != null)
3295 alignPanel.getOverviewPanel().updateOverviewImage();
3300 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3301 * the annotations panel as a whole.
3303 * The options to show/hide all annotations should be enabled when the panel
3304 * is shown, and disabled when the panel is hidden.
3309 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3311 final boolean setVisible = annotationPanelMenuItem.isSelected();
3312 viewport.setShowAnnotation(setVisible);
3313 this.showAllSeqAnnotations.setEnabled(setVisible);
3314 this.hideAllSeqAnnotations.setEnabled(setVisible);
3315 this.showAllAlAnnotations.setEnabled(setVisible);
3316 this.hideAllAlAnnotations.setEnabled(setVisible);
3317 alignPanel.updateLayout();
3321 public void alignmentProperties()
3323 JEditorPane editPane = new JEditorPane("text/html", "");
3324 editPane.setEditable(false);
3325 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3327 editPane.setText(MessageManager.formatMessage("label.html_content",
3328 new Object[] { contents.toString() }));
3329 JInternalFrame frame = new JInternalFrame();
3330 frame.getContentPane().add(new JScrollPane(editPane));
3332 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3333 "label.alignment_properties", new Object[] { getTitle() }),
3344 public void overviewMenuItem_actionPerformed(ActionEvent e)
3346 if (alignPanel.overviewPanel != null)
3351 JInternalFrame frame = new JInternalFrame();
3352 OverviewPanel overview = new OverviewPanel(alignPanel);
3353 frame.setContentPane(overview);
3354 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3355 "label.overview_params", new Object[] { this.getTitle() }),
3356 true, frame.getWidth(), frame.getHeight(), true, true);
3358 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3359 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3362 public void internalFrameClosed(
3363 javax.swing.event.InternalFrameEvent evt)
3365 alignPanel.setOverviewPanel(null);
3369 alignPanel.setOverviewPanel(overview);
3373 public void textColour_actionPerformed()
3375 new TextColourChooser().chooseColour(alignPanel, null);
3379 * public void covariationColour_actionPerformed() {
3381 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3385 public void annotationColour_actionPerformed()
3387 new AnnotationColourChooser(viewport, alignPanel);
3391 public void annotationColumn_actionPerformed(ActionEvent e)
3393 new AnnotationColumnChooser(viewport, alignPanel);
3397 * Action on the user checking or unchecking the option to apply the selected
3398 * colour scheme to all groups. If unchecked, groups may have their own
3399 * independent colour schemes.
3404 public void applyToAllGroups_actionPerformed(boolean selected)
3406 viewport.setColourAppliesToAllGroups(selected);
3410 * Action on user selecting a colour from the colour menu
3413 * the name (not the menu item label!) of the colour scheme
3416 public void changeColour_actionPerformed(String name)
3419 * 'User Defined' opens a panel to configure or load a
3420 * user-defined colour scheme
3422 if (ResidueColourScheme.USER_DEFINED.equals(name))
3424 new UserDefinedColours(alignPanel);
3429 * otherwise set the chosen colour scheme (or null for 'None')
3431 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3432 viewport.getAlignment(), viewport.getHiddenRepSequences());
3437 * Actions on setting or changing the alignment colour scheme
3442 public void changeColour(ColourSchemeI cs)
3444 // TODO: pull up to controller method
3445 ColourMenuHelper.setColourSelected(colourMenu, cs);
3447 viewport.setGlobalColourScheme(cs);
3449 alignPanel.paintAlignment(true);
3453 * Show the PID threshold slider panel
3456 protected void modifyPID_actionPerformed()
3458 SliderPanel.setPIDSliderSource(alignPanel,
3459 viewport.getResidueShading(), alignPanel.getViewName());
3460 SliderPanel.showPIDSlider();
3464 * Show the Conservation slider panel
3467 protected void modifyConservation_actionPerformed()
3469 SliderPanel.setConservationSlider(alignPanel,
3470 viewport.getResidueShading(), alignPanel.getViewName());
3471 SliderPanel.showConservationSlider();
3475 * Action on selecting or deselecting (Colour) By Conservation
3478 public void conservationMenuItem_actionPerformed(boolean selected)
3480 modifyConservation.setEnabled(selected);
3481 viewport.setConservationSelected(selected);
3482 viewport.getResidueShading().setConservationApplied(selected);
3484 changeColour(viewport.getGlobalColourScheme());
3487 modifyConservation_actionPerformed();
3491 SliderPanel.hideConservationSlider();
3496 * Action on selecting or deselecting (Colour) Above PID Threshold
3499 public void abovePIDThreshold_actionPerformed(boolean selected)
3501 modifyPID.setEnabled(selected);
3502 viewport.setAbovePIDThreshold(selected);
3505 viewport.getResidueShading().setThreshold(0,
3506 viewport.isIgnoreGapsConsensus());
3509 changeColour(viewport.getGlobalColourScheme());
3512 modifyPID_actionPerformed();
3516 SliderPanel.hidePIDSlider();
3527 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3529 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3530 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3531 .getAlignment().getSequenceAt(0));
3532 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3533 viewport.getAlignment()));
3534 alignPanel.paintAlignment(true);
3544 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3546 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3547 AlignmentSorter.sortByID(viewport.getAlignment());
3548 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3549 viewport.getAlignment()));
3550 alignPanel.paintAlignment(true);
3560 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3562 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3563 AlignmentSorter.sortByLength(viewport.getAlignment());
3564 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3565 viewport.getAlignment()));
3566 alignPanel.paintAlignment(true);
3576 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3578 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3579 AlignmentSorter.sortByGroup(viewport.getAlignment());
3580 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3581 viewport.getAlignment()));
3583 alignPanel.paintAlignment(true);
3593 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3595 new RedundancyPanel(alignPanel, this);
3605 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3607 if ((viewport.getSelectionGroup() == null)
3608 || (viewport.getSelectionGroup().getSize() < 2))
3610 JvOptionPane.showInternalMessageDialog(this, MessageManager
3611 .getString("label.you_must_select_least_two_sequences"),
3612 MessageManager.getString("label.invalid_selection"),
3613 JvOptionPane.WARNING_MESSAGE);
3617 JInternalFrame frame = new JInternalFrame();
3618 frame.setContentPane(new PairwiseAlignPanel(viewport));
3619 Desktop.addInternalFrame(frame,
3620 MessageManager.getString("action.pairwise_alignment"), 600,
3626 public void autoCalculate_actionPerformed(ActionEvent e)
3628 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3629 if (viewport.autoCalculateConsensus)
3631 viewport.firePropertyChange("alignment", null, viewport
3632 .getAlignment().getSequences());
3637 public void sortByTreeOption_actionPerformed(ActionEvent e)
3639 viewport.sortByTree = sortByTree.isSelected();
3643 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3645 viewport.followSelection = listenToViewSelections.isSelected();
3649 * Constructs a tree panel and adds it to the desktop
3652 * tree type (NJ or AV)
3654 * name of score model used to compute the tree
3656 * parameters for the distance or similarity calculation
3658 void newTreePanel(String type, String modelName, SimilarityParamsI options)
3660 String frameTitle = "";
3663 boolean onSelection = false;
3664 if (viewport.getSelectionGroup() != null
3665 && viewport.getSelectionGroup().getSize() > 0)
3667 SequenceGroup sg = viewport.getSelectionGroup();
3669 /* Decide if the selection is a column region */
3670 for (SequenceI _s : sg.getSequences())
3672 if (_s.getLength() < sg.getEndRes())
3678 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3680 .getString("label.sequences_selection_not_aligned"),
3681 JvOptionPane.WARNING_MESSAGE);
3690 if (viewport.getAlignment().getHeight() < 2)
3696 tp = new TreePanel(alignPanel, type, modelName, options);
3697 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3699 frameTitle += " from ";
3701 if (viewport.viewName != null)
3703 frameTitle += viewport.viewName + " of ";
3706 frameTitle += this.title;
3708 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3719 public void addSortByOrderMenuItem(String title,
3720 final AlignmentOrder order)
3722 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3723 "action.by_title_param", new Object[] { title }));
3725 item.addActionListener(new java.awt.event.ActionListener()
3728 public void actionPerformed(ActionEvent e)
3730 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3732 // TODO: JBPNote - have to map order entries to curent SequenceI
3734 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3736 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3739 alignPanel.paintAlignment(true);
3745 * Add a new sort by annotation score menu item
3748 * the menu to add the option to
3750 * the label used to retrieve scores for each sequence on the
3753 public void addSortByAnnotScoreMenuItem(JMenu sort,
3754 final String scoreLabel)
3756 final JMenuItem item = new JMenuItem(scoreLabel);
3758 item.addActionListener(new java.awt.event.ActionListener()
3761 public void actionPerformed(ActionEvent e)
3763 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3764 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3765 viewport.getAlignment());// ,viewport.getSelectionGroup());
3766 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3767 viewport.getAlignment()));
3768 alignPanel.paintAlignment(true);
3774 * last hash for alignment's annotation array - used to minimise cost of
3777 protected int _annotationScoreVectorHash;
3780 * search the alignment and rebuild the sort by annotation score submenu the
3781 * last alignment annotation vector hash is stored to minimize cost of
3782 * rebuilding in subsequence calls.
3786 public void buildSortByAnnotationScoresMenu()
3788 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3793 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3795 sortByAnnotScore.removeAll();
3796 // almost certainly a quicker way to do this - but we keep it simple
3797 Hashtable scoreSorts = new Hashtable();
3798 AlignmentAnnotation aann[];
3799 for (SequenceI sqa : viewport.getAlignment().getSequences())
3801 aann = sqa.getAnnotation();
3802 for (int i = 0; aann != null && i < aann.length; i++)
3804 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3806 scoreSorts.put(aann[i].label, aann[i].label);
3810 Enumeration labels = scoreSorts.keys();
3811 while (labels.hasMoreElements())
3813 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3814 (String) labels.nextElement());
3816 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3819 _annotationScoreVectorHash = viewport.getAlignment()
3820 .getAlignmentAnnotation().hashCode();
3825 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3826 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3827 * call. Listeners are added to remove the menu item when the treePanel is
3828 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3832 public void buildTreeSortMenu()
3834 sortByTreeMenu.removeAll();
3836 List<Component> comps = PaintRefresher.components.get(viewport
3837 .getSequenceSetId());
3838 List<TreePanel> treePanels = new ArrayList<>();
3839 for (Component comp : comps)
3841 if (comp instanceof TreePanel)
3843 treePanels.add((TreePanel) comp);
3847 if (treePanels.size() < 1)
3849 sortByTreeMenu.setVisible(false);
3853 sortByTreeMenu.setVisible(true);
3855 for (final TreePanel tp : treePanels)
3857 final JMenuItem item = new JMenuItem(tp.getTitle());
3858 item.addActionListener(new java.awt.event.ActionListener()
3861 public void actionPerformed(ActionEvent e)
3863 tp.sortByTree_actionPerformed();
3864 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3869 sortByTreeMenu.add(item);
3873 public boolean sortBy(AlignmentOrder alorder, String undoname)
3875 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3876 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3877 if (undoname != null)
3879 addHistoryItem(new OrderCommand(undoname, oldOrder,
3880 viewport.getAlignment()));
3882 alignPanel.paintAlignment(true);
3887 * Work out whether the whole set of sequences or just the selected set will
3888 * be submitted for multiple alignment.
3891 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3893 // Now, check we have enough sequences
3894 AlignmentView msa = null;
3896 if ((viewport.getSelectionGroup() != null)
3897 && (viewport.getSelectionGroup().getSize() > 1))
3899 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3900 // some common interface!
3902 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3903 * SequenceI[sz = seqs.getSize(false)];
3905 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3906 * seqs.getSequenceAt(i); }
3908 msa = viewport.getAlignmentView(true);
3910 else if (viewport.getSelectionGroup() != null
3911 && viewport.getSelectionGroup().getSize() == 1)
3913 int option = JvOptionPane.showConfirmDialog(this,
3914 MessageManager.getString("warn.oneseq_msainput_selection"),
3915 MessageManager.getString("label.invalid_selection"),
3916 JvOptionPane.OK_CANCEL_OPTION);
3917 if (option == JvOptionPane.OK_OPTION)
3919 msa = viewport.getAlignmentView(false);
3924 msa = viewport.getAlignmentView(false);
3930 * Decides what is submitted to a secondary structure prediction service: the
3931 * first sequence in the alignment, or in the current selection, or, if the
3932 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3933 * region or the whole alignment. (where the first sequence in the set is the
3934 * one that the prediction will be for).
3936 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3938 AlignmentView seqs = null;
3940 if ((viewport.getSelectionGroup() != null)
3941 && (viewport.getSelectionGroup().getSize() > 0))
3943 seqs = viewport.getAlignmentView(true);
3947 seqs = viewport.getAlignmentView(false);
3949 // limit sequences - JBPNote in future - could spawn multiple prediction
3951 // TODO: viewport.getAlignment().isAligned is a global state - the local
3952 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3953 if (!viewport.getAlignment().isAligned(false))
3955 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3956 // TODO: if seqs.getSequences().length>1 then should really have warned
3970 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3972 // Pick the tree file
3973 JalviewFileChooser chooser = new JalviewFileChooser(
3974 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3975 chooser.setFileView(new JalviewFileView());
3976 chooser.setDialogTitle(MessageManager
3977 .getString("label.select_newick_like_tree_file"));
3978 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3980 int value = chooser.showOpenDialog(null);
3982 if (value == JalviewFileChooser.APPROVE_OPTION)
3984 String filePath = chooser.getSelectedFile().getPath();
3985 Cache.setProperty("LAST_DIRECTORY", filePath);
3986 NewickFile fin = null;
3989 fin = new NewickFile(filePath, DataSourceType.FILE);
3990 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3991 } catch (Exception ex)
3998 .getString("label.problem_reading_tree_file"),
3999 JvOptionPane.WARNING_MESSAGE);
4000 ex.printStackTrace();
4002 if (fin != null && fin.hasWarningMessage())
4004 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4005 .getWarningMessage(), MessageManager
4006 .getString("label.possible_problem_with_tree_file"),
4007 JvOptionPane.WARNING_MESSAGE);
4012 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4014 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4017 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4018 int h, int x, int y)
4020 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4024 * Add a treeviewer for the tree extracted from a Newick file object to the
4025 * current alignment view
4032 * Associated alignment input data (or null)
4041 * @return TreePanel handle
4043 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4044 AlignmentView input, int w, int h, int x, int y)
4046 TreePanel tp = null;
4052 if (nf.getTree() != null)
4054 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4060 tp.setLocation(x, y);
4063 Desktop.addInternalFrame(tp, treeTitle, w, h);
4065 } catch (Exception ex)
4067 ex.printStackTrace();
4073 private boolean buildingMenu = false;
4076 * Generates menu items and listener event actions for web service clients
4079 public void BuildWebServiceMenu()
4081 while (buildingMenu)
4085 System.err.println("Waiting for building menu to finish.");
4087 } catch (Exception e)
4091 final AlignFrame me = this;
4092 buildingMenu = true;
4093 new Thread(new Runnable()
4098 final List<JMenuItem> legacyItems = new ArrayList<>();
4101 // System.err.println("Building ws menu again "
4102 // + Thread.currentThread());
4103 // TODO: add support for context dependent disabling of services based
4105 // alignment and current selection
4106 // TODO: add additional serviceHandle parameter to specify abstract
4108 // class independently of AbstractName
4109 // TODO: add in rediscovery GUI function to restart discoverer
4110 // TODO: group services by location as well as function and/or
4112 // object broker mechanism.
4113 final Vector<JMenu> wsmenu = new Vector<>();
4114 final IProgressIndicator af = me;
4117 * do not i18n these strings - they are hard-coded in class
4118 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4119 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4121 final JMenu msawsmenu = new JMenu("Alignment");
4122 final JMenu secstrmenu = new JMenu(
4123 "Secondary Structure Prediction");
4124 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4125 final JMenu analymenu = new JMenu("Analysis");
4126 final JMenu dismenu = new JMenu("Protein Disorder");
4127 // JAL-940 - only show secondary structure prediction services from
4128 // the legacy server
4129 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4131 Discoverer.services != null && (Discoverer.services.size() > 0))
4133 // TODO: refactor to allow list of AbstractName/Handler bindings to
4135 // stored or retrieved from elsewhere
4136 // No MSAWS used any more:
4137 // Vector msaws = null; // (Vector)
4138 // Discoverer.services.get("MsaWS");
4139 Vector secstrpr = (Vector) Discoverer.services
4141 if (secstrpr != null)
4143 // Add any secondary structure prediction services
4144 for (int i = 0, j = secstrpr.size(); i < j; i++)
4146 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4148 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4149 .getServiceClient(sh);
4150 int p = secstrmenu.getItemCount();
4151 impl.attachWSMenuEntry(secstrmenu, me);
4152 int q = secstrmenu.getItemCount();
4153 for (int litm = p; litm < q; litm++)
4155 legacyItems.add(secstrmenu.getItem(litm));
4161 // Add all submenus in the order they should appear on the web
4163 wsmenu.add(msawsmenu);
4164 wsmenu.add(secstrmenu);
4165 wsmenu.add(dismenu);
4166 wsmenu.add(analymenu);
4167 // No search services yet
4168 // wsmenu.add(seqsrchmenu);
4170 javax.swing.SwingUtilities.invokeLater(new Runnable()
4177 webService.removeAll();
4178 // first, add discovered services onto the webservices menu
4179 if (wsmenu.size() > 0)
4181 for (int i = 0, j = wsmenu.size(); i < j; i++)
4183 webService.add(wsmenu.get(i));
4188 webService.add(me.webServiceNoServices);
4190 // TODO: move into separate menu builder class.
4191 boolean new_sspred = false;
4192 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4194 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4195 if (jws2servs != null)
4197 if (jws2servs.hasServices())
4199 jws2servs.attachWSMenuEntry(webService, me);
4200 for (Jws2Instance sv : jws2servs.getServices())
4202 if (sv.description.toLowerCase().contains("jpred"))
4204 for (JMenuItem jmi : legacyItems)
4206 jmi.setVisible(false);
4212 if (jws2servs.isRunning())
4214 JMenuItem tm = new JMenuItem(
4215 "Still discovering JABA Services");
4216 tm.setEnabled(false);
4221 build_urlServiceMenu(me.webService);
4222 build_fetchdbmenu(webService);
4223 for (JMenu item : wsmenu)
4225 if (item.getItemCount() == 0)
4227 item.setEnabled(false);
4231 item.setEnabled(true);
4234 } catch (Exception e)
4237 .debug("Exception during web service menu building process.",
4242 } catch (Exception e)
4245 buildingMenu = false;
4252 * construct any groupURL type service menu entries.
4256 private void build_urlServiceMenu(JMenu webService)
4258 // TODO: remove this code when 2.7 is released
4259 // DEBUG - alignmentView
4261 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4262 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4264 * @Override public void actionPerformed(ActionEvent e) {
4265 * jalview.datamodel.AlignmentView
4266 * .testSelectionViews(af.viewport.getAlignment(),
4267 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4269 * }); webService.add(testAlView);
4271 // TODO: refactor to RestClient discoverer and merge menu entries for
4272 // rest-style services with other types of analysis/calculation service
4273 // SHmmr test client - still being implemented.
4274 // DEBUG - alignmentView
4276 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4279 client.attachWSMenuEntry(
4280 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4286 * Searches the alignment sequences for xRefs and builds the Show
4287 * Cross-References menu (formerly called Show Products), with database
4288 * sources for which cross-references are found (protein sources for a
4289 * nucleotide alignment and vice versa)
4291 * @return true if Show Cross-references menu should be enabled
4293 public boolean canShowProducts()
4295 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4296 AlignmentI dataset = viewport.getAlignment().getDataset();
4298 showProducts.removeAll();
4299 final boolean dna = viewport.getAlignment().isNucleotide();
4301 if (seqs == null || seqs.length == 0)
4303 // nothing to see here.
4307 boolean showp = false;
4310 List<String> ptypes = new CrossRef(seqs, dataset)
4311 .findXrefSourcesForSequences(dna);
4313 for (final String source : ptypes)
4316 final AlignFrame af = this;
4317 JMenuItem xtype = new JMenuItem(source);
4318 xtype.addActionListener(new ActionListener()
4321 public void actionPerformed(ActionEvent e)
4323 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4326 showProducts.add(xtype);
4328 showProducts.setVisible(showp);
4329 showProducts.setEnabled(showp);
4330 } catch (Exception e)
4333 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4341 * Finds and displays cross-references for the selected sequences (protein
4342 * products for nucleotide sequences, dna coding sequences for peptides).
4345 * the sequences to show cross-references for
4347 * true if from a nucleotide alignment (so showing proteins)
4349 * the database to show cross-references for
4351 protected void showProductsFor(final SequenceI[] sel,
4352 final boolean _odna, final String source)
4354 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4359 * Construct and display a new frame containing the translation of this
4360 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4363 public void showTranslation_actionPerformed(ActionEvent e)
4365 AlignmentI al = null;
4368 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4370 al = dna.translateCdna();
4371 } catch (Exception ex)
4373 jalview.bin.Cache.log.error(
4374 "Exception during translation. Please report this !", ex);
4375 final String msg = MessageManager
4376 .getString("label.error_when_translating_sequences_submit_bug_report");
4377 final String errorTitle = MessageManager
4378 .getString("label.implementation_error")
4379 + MessageManager.getString("label.translation_failed");
4380 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4381 JvOptionPane.ERROR_MESSAGE);
4384 if (al == null || al.getHeight() == 0)
4386 final String msg = MessageManager
4387 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4388 final String errorTitle = MessageManager
4389 .getString("label.translation_failed");
4390 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4391 JvOptionPane.WARNING_MESSAGE);
4395 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4396 af.setFileFormat(this.currentFileFormat);
4397 final String newTitle = MessageManager.formatMessage(
4398 "label.translation_of_params",
4399 new Object[] { this.getTitle() });
4400 af.setTitle(newTitle);
4401 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4403 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4404 viewport.openSplitFrame(af, new Alignment(seqs));
4408 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4415 * Set the file format
4419 public void setFileFormat(FileFormatI format)
4421 this.currentFileFormat = format;
4425 * Try to load a features file onto the alignment.
4428 * contents or path to retrieve file
4430 * access mode of file (see jalview.io.AlignFile)
4431 * @return true if features file was parsed correctly.
4433 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4435 return avc.parseFeaturesFile(file, sourceType,
4436 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4441 public void refreshFeatureUI(boolean enableIfNecessary)
4443 // note - currently this is only still here rather than in the controller
4444 // because of the featureSettings hard reference that is yet to be
4446 if (enableIfNecessary)
4448 viewport.setShowSequenceFeatures(true);
4449 showSeqFeatures.setSelected(true);
4455 public void dragEnter(DropTargetDragEvent evt)
4460 public void dragExit(DropTargetEvent evt)
4465 public void dragOver(DropTargetDragEvent evt)
4470 public void dropActionChanged(DropTargetDragEvent evt)
4475 public void drop(DropTargetDropEvent evt)
4477 // JAL-1552 - acceptDrop required before getTransferable call for
4478 // Java's Transferable for native dnd
4479 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4480 Transferable t = evt.getTransferable();
4481 List<String> files = new ArrayList<>();
4482 List<DataSourceType> protocols = new ArrayList<>();
4486 Desktop.transferFromDropTarget(files, protocols, evt, t);
4487 } catch (Exception e)
4489 e.printStackTrace();
4495 // check to see if any of these files have names matching sequences in
4497 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4498 .getAlignment().getSequencesArray());
4500 * Object[] { String,SequenceI}
4502 ArrayList<Object[]> filesmatched = new ArrayList<>();
4503 ArrayList<String> filesnotmatched = new ArrayList<>();
4504 for (int i = 0; i < files.size(); i++)
4506 String file = files.get(i).toString();
4508 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4509 if (protocol == DataSourceType.FILE)
4511 File fl = new File(file);
4512 pdbfn = fl.getName();
4514 else if (protocol == DataSourceType.URL)
4516 URL url = new URL(file);
4517 pdbfn = url.getFile();
4519 if (pdbfn.length() > 0)
4521 // attempt to find a match in the alignment
4522 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4523 int l = 0, c = pdbfn.indexOf(".");
4524 while (mtch == null && c != -1)
4529 } while ((c = pdbfn.indexOf(".", l)) > l);
4532 pdbfn = pdbfn.substring(0, l);
4534 mtch = idm.findAllIdMatches(pdbfn);
4538 FileFormatI type = null;
4541 type = new IdentifyFile().identify(file, protocol);
4542 } catch (Exception ex)
4546 if (type != null && type.isStructureFile())
4548 filesmatched.add(new Object[] { file, protocol, mtch });
4552 // File wasn't named like one of the sequences or wasn't a PDB file.
4553 filesnotmatched.add(file);
4557 if (filesmatched.size() > 0)
4559 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4565 "label.automatically_associate_structure_files_with_sequences_same_name",
4566 new Object[] { Integer
4572 .getString("label.automatically_associate_structure_files_by_name"),
4573 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4576 for (Object[] fm : filesmatched)
4578 // try and associate
4579 // TODO: may want to set a standard ID naming formalism for
4580 // associating PDB files which have no IDs.
4581 for (SequenceI toassoc : (SequenceI[]) fm[2])
4583 PDBEntry pe = new AssociatePdbFileWithSeq()
4584 .associatePdbWithSeq((String) fm[0],
4585 (DataSourceType) fm[1], toassoc, false,
4589 System.err.println("Associated file : "
4590 + ((String) fm[0]) + " with "
4591 + toassoc.getDisplayId(true));
4595 alignPanel.paintAlignment(true);
4599 if (filesnotmatched.size() > 0)
4602 && (Cache.getDefault(
4603 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4609 "label.ignore_unmatched_dropped_files_info",
4610 new Object[] { Integer
4617 .getString("label.ignore_unmatched_dropped_files"),
4618 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4622 for (String fn : filesnotmatched)
4624 loadJalviewDataFile(fn, null, null, null);
4628 } catch (Exception ex)
4630 ex.printStackTrace();
4636 * Attempt to load a "dropped" file or URL string, by testing in turn for
4638 * <li>an Annotation file</li>
4639 * <li>a JNet file</li>
4640 * <li>a features file</li>
4641 * <li>else try to interpret as an alignment file</li>
4645 * either a filename or a URL string.
4646 * @throws InterruptedException
4647 * @throws IOException
4649 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4650 FileFormatI format, SequenceI assocSeq)
4654 if (sourceType == null)
4656 sourceType = FormatAdapter.checkProtocol(file);
4658 // if the file isn't identified, or not positively identified as some
4659 // other filetype (PFAM is default unidentified alignment file type) then
4660 // try to parse as annotation.
4661 boolean isAnnotation = (format == null || FileFormat.Pfam
4662 .equals(format)) ? new AnnotationFile()
4663 .annotateAlignmentView(viewport, file, sourceType) : false;
4667 // first see if its a T-COFFEE score file
4668 TCoffeeScoreFile tcf = null;
4671 tcf = new TCoffeeScoreFile(file, sourceType);
4674 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4677 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4678 isAnnotation = true;
4680 .setText(MessageManager
4681 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4685 // some problem - if no warning its probable that the ID matching
4686 // process didn't work
4690 tcf.getWarningMessage() == null ? MessageManager
4691 .getString("label.check_file_matches_sequence_ids_alignment")
4692 : tcf.getWarningMessage(),
4694 .getString("label.problem_reading_tcoffee_score_file"),
4695 JvOptionPane.WARNING_MESSAGE);
4702 } catch (Exception x)
4705 .debug("Exception when processing data source as T-COFFEE score file",
4711 // try to see if its a JNet 'concise' style annotation file *before*
4713 // try to parse it as a features file
4716 format = new IdentifyFile().identify(file, sourceType);
4718 if (FileFormat.ScoreMatrix == format)
4720 ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4723 // todo: i18n this message
4725 .setText(MessageManager.formatMessage(
4726 "label.successfully_loaded_matrix",
4727 sm.getMatrixName()));
4729 else if (FileFormat.Jnet.equals(format))
4731 JPredFile predictions = new JPredFile(file, sourceType);
4732 new JnetAnnotationMaker();
4733 JnetAnnotationMaker.add_annotation(predictions,
4734 viewport.getAlignment(), 0, false);
4735 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4736 viewport.getAlignment().setSeqrep(repseq);
4737 HiddenColumns cs = new HiddenColumns();
4738 cs.hideInsertionsFor(repseq);
4739 viewport.getAlignment().setHiddenColumns(cs);
4740 isAnnotation = true;
4742 // else if (IdentifyFile.FeaturesFile.equals(format))
4743 else if (FileFormat.Features.equals(format))
4745 if (parseFeaturesFile(file, sourceType))
4747 alignPanel.paintAlignment(true);
4752 new FileLoader().LoadFile(viewport, file, sourceType, format);
4758 alignPanel.adjustAnnotationHeight();
4759 viewport.updateSequenceIdColours();
4760 buildSortByAnnotationScoresMenu();
4761 alignPanel.paintAlignment(true);
4763 } catch (Exception ex)
4765 ex.printStackTrace();
4766 } catch (OutOfMemoryError oom)
4771 } catch (Exception x)
4776 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4777 : "using " + sourceType + " from " + file)
4779 + (format != null ? "(parsing as '" + format
4780 + "' file)" : ""), oom, Desktop.desktop);
4785 * Method invoked by the ChangeListener on the tabbed pane, in other words
4786 * when a different tabbed pane is selected by the user or programmatically.
4789 public void tabSelectionChanged(int index)
4793 alignPanel = alignPanels.get(index);
4794 viewport = alignPanel.av;
4795 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4796 setMenusFromViewport(viewport);
4800 * 'focus' any colour slider that is open to the selected viewport
4802 if (viewport.getConservationSelected())
4804 SliderPanel.setConservationSlider(alignPanel,
4805 viewport.getResidueShading(), alignPanel.getViewName());
4809 SliderPanel.hideConservationSlider();
4811 if (viewport.getAbovePIDThreshold())
4813 SliderPanel.setPIDSliderSource(alignPanel,
4814 viewport.getResidueShading(), alignPanel.getViewName());
4818 SliderPanel.hidePIDSlider();
4822 * If there is a frame linked to this one in a SplitPane, switch it to the
4823 * same view tab index. No infinite recursion of calls should happen, since
4824 * tabSelectionChanged() should not get invoked on setting the selected
4825 * index to an unchanged value. Guard against setting an invalid index
4826 * before the new view peer tab has been created.
4828 final AlignViewportI peer = viewport.getCodingComplement();
4831 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4832 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4834 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4840 * On right mouse click on view tab, prompt for and set new view name.
4843 public void tabbedPane_mousePressed(MouseEvent e)
4845 if (e.isPopupTrigger())
4847 String msg = MessageManager.getString("label.enter_view_name");
4848 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4849 JvOptionPane.QUESTION_MESSAGE);
4853 viewport.viewName = reply;
4854 // TODO warn if reply is in getExistingViewNames()?
4855 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4860 public AlignViewport getCurrentView()
4866 * Open the dialog for regex description parsing.
4869 protected void extractScores_actionPerformed(ActionEvent e)
4871 ParseProperties pp = new jalview.analysis.ParseProperties(
4872 viewport.getAlignment());
4873 // TODO: verify regex and introduce GUI dialog for version 2.5
4874 // if (pp.getScoresFromDescription("col", "score column ",
4875 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4877 if (pp.getScoresFromDescription("description column",
4878 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4880 buildSortByAnnotationScoresMenu();
4888 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4892 protected void showDbRefs_actionPerformed(ActionEvent e)
4894 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4900 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4904 protected void showNpFeats_actionPerformed(ActionEvent e)
4906 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4910 * find the viewport amongst the tabs in this alignment frame and close that
4915 public boolean closeView(AlignViewportI av)
4919 this.closeMenuItem_actionPerformed(false);
4922 Component[] comp = tabbedPane.getComponents();
4923 for (int i = 0; comp != null && i < comp.length; i++)
4925 if (comp[i] instanceof AlignmentPanel)
4927 if (((AlignmentPanel) comp[i]).av == av)
4930 closeView((AlignmentPanel) comp[i]);
4938 protected void build_fetchdbmenu(JMenu webService)
4940 // Temporary hack - DBRef Fetcher always top level ws entry.
4941 // TODO We probably want to store a sequence database checklist in
4942 // preferences and have checkboxes.. rather than individual sources selected
4944 final JMenu rfetch = new JMenu(
4945 MessageManager.getString("action.fetch_db_references"));
4946 rfetch.setToolTipText(MessageManager
4947 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4948 webService.add(rfetch);
4950 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4951 MessageManager.getString("option.trim_retrieved_seqs"));
4952 trimrs.setToolTipText(MessageManager
4953 .getString("label.trim_retrieved_sequences"));
4954 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4955 trimrs.addActionListener(new ActionListener()
4958 public void actionPerformed(ActionEvent e)
4960 trimrs.setSelected(trimrs.isSelected());
4961 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4962 Boolean.valueOf(trimrs.isSelected()).toString());
4966 JMenuItem fetchr = new JMenuItem(
4967 MessageManager.getString("label.standard_databases"));
4968 fetchr.setToolTipText(MessageManager
4969 .getString("label.fetch_embl_uniprot"));
4970 fetchr.addActionListener(new ActionListener()
4974 public void actionPerformed(ActionEvent e)
4976 new Thread(new Runnable()
4981 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4982 .getAlignment().isNucleotide();
4983 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4984 .getSequenceSelection(), alignPanel.alignFrame, null,
4985 alignPanel.alignFrame.featureSettings, isNucleotide);
4986 dbRefFetcher.addListener(new FetchFinishedListenerI()
4989 public void finished()
4991 AlignFrame.this.setMenusForViewport();
4994 dbRefFetcher.fetchDBRefs(false);
5002 final AlignFrame me = this;
5003 new Thread(new Runnable()
5008 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5009 .getSequenceFetcherSingleton(me);
5010 javax.swing.SwingUtilities.invokeLater(new Runnable()
5015 String[] dbclasses = sf.getOrderedSupportedSources();
5016 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5017 // jalview.util.QuickSort.sort(otherdb, otherdb);
5018 List<DbSourceProxy> otherdb;
5019 JMenu dfetch = new JMenu();
5020 JMenu ifetch = new JMenu();
5021 JMenuItem fetchr = null;
5022 int comp = 0, icomp = 0, mcomp = 15;
5023 String mname = null;
5025 for (String dbclass : dbclasses)
5027 otherdb = sf.getSourceProxy(dbclass);
5028 // add a single entry for this class, or submenu allowing 'fetch
5030 if (otherdb == null || otherdb.size() < 1)
5034 // List<DbSourceProxy> dbs=otherdb;
5035 // otherdb=new ArrayList<DbSourceProxy>();
5036 // for (DbSourceProxy db:dbs)
5038 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5042 mname = "From " + dbclass;
5044 if (otherdb.size() == 1)
5046 final DbSourceProxy[] dassource = otherdb
5047 .toArray(new DbSourceProxy[0]);
5048 DbSourceProxy src = otherdb.get(0);
5049 fetchr = new JMenuItem(src.getDbSource());
5050 fetchr.addActionListener(new ActionListener()
5054 public void actionPerformed(ActionEvent e)
5056 new Thread(new Runnable()
5062 boolean isNucleotide = alignPanel.alignFrame
5063 .getViewport().getAlignment()
5065 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5066 alignPanel.av.getSequenceSelection(),
5067 alignPanel.alignFrame, dassource,
5068 alignPanel.alignFrame.featureSettings,
5071 .addListener(new FetchFinishedListenerI()
5074 public void finished()
5076 AlignFrame.this.setMenusForViewport();
5079 dbRefFetcher.fetchDBRefs(false);
5085 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5086 MessageManager.formatMessage(
5087 "label.fetch_retrieve_from",
5088 new Object[] { src.getDbName() })));
5094 final DbSourceProxy[] dassource = otherdb
5095 .toArray(new DbSourceProxy[0]);
5097 DbSourceProxy src = otherdb.get(0);
5098 fetchr = new JMenuItem(MessageManager.formatMessage(
5099 "label.fetch_all_param",
5100 new Object[] { src.getDbSource() }));
5101 fetchr.addActionListener(new ActionListener()
5104 public void actionPerformed(ActionEvent e)
5106 new Thread(new Runnable()
5112 boolean isNucleotide = alignPanel.alignFrame
5113 .getViewport().getAlignment()
5115 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5116 alignPanel.av.getSequenceSelection(),
5117 alignPanel.alignFrame, dassource,
5118 alignPanel.alignFrame.featureSettings,
5121 .addListener(new FetchFinishedListenerI()
5124 public void finished()
5126 AlignFrame.this.setMenusForViewport();
5129 dbRefFetcher.fetchDBRefs(false);
5135 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5136 MessageManager.formatMessage(
5137 "label.fetch_retrieve_from_all_sources",
5139 Integer.valueOf(otherdb.size())
5140 .toString(), src.getDbSource(),
5141 src.getDbName() })));
5144 // and then build the rest of the individual menus
5145 ifetch = new JMenu(MessageManager.formatMessage(
5146 "label.source_from_db_source",
5147 new Object[] { src.getDbSource() }));
5149 String imname = null;
5151 for (DbSourceProxy sproxy : otherdb)
5153 String dbname = sproxy.getDbName();
5154 String sname = dbname.length() > 5 ? dbname.substring(0,
5155 5) + "..." : dbname;
5156 String msname = dbname.length() > 10 ? dbname.substring(
5157 0, 10) + "..." : dbname;
5160 imname = MessageManager.formatMessage(
5161 "label.from_msname", new Object[] { sname });
5163 fetchr = new JMenuItem(msname);
5164 final DbSourceProxy[] dassrc = { sproxy };
5165 fetchr.addActionListener(new ActionListener()
5169 public void actionPerformed(ActionEvent e)
5171 new Thread(new Runnable()
5177 boolean isNucleotide = alignPanel.alignFrame
5178 .getViewport().getAlignment()
5180 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5181 alignPanel.av.getSequenceSelection(),
5182 alignPanel.alignFrame, dassrc,
5183 alignPanel.alignFrame.featureSettings,
5186 .addListener(new FetchFinishedListenerI()
5189 public void finished()
5191 AlignFrame.this.setMenusForViewport();
5194 dbRefFetcher.fetchDBRefs(false);
5200 fetchr.setToolTipText("<html>"
5201 + MessageManager.formatMessage(
5202 "label.fetch_retrieve_from", new Object[]
5206 if (++icomp >= mcomp || i == (otherdb.size()))
5208 ifetch.setText(MessageManager.formatMessage(
5209 "label.source_to_target", imname, sname));
5211 ifetch = new JMenu();
5219 if (comp >= mcomp || dbi >= (dbclasses.length))
5221 dfetch.setText(MessageManager.formatMessage(
5222 "label.source_to_target", mname, dbclass));
5224 dfetch = new JMenu();
5237 * Left justify the whole alignment.
5240 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5242 AlignmentI al = viewport.getAlignment();
5244 viewport.firePropertyChange("alignment", null, al);
5248 * Right justify the whole alignment.
5251 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5253 AlignmentI al = viewport.getAlignment();
5255 viewport.firePropertyChange("alignment", null, al);
5259 public void setShowSeqFeatures(boolean b)
5261 showSeqFeatures.setSelected(b);
5262 viewport.setShowSequenceFeatures(b);
5269 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5270 * awt.event.ActionEvent)
5273 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5275 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5276 alignPanel.paintAlignment(true);
5283 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5287 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5289 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5290 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5298 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5299 * .event.ActionEvent)
5302 protected void showGroupConservation_actionPerformed(ActionEvent e)
5304 viewport.setShowGroupConservation(showGroupConservation.getState());
5305 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5312 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5313 * .event.ActionEvent)
5316 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5318 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5319 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5326 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5327 * .event.ActionEvent)
5330 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5332 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5333 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5337 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5339 showSequenceLogo.setState(true);
5340 viewport.setShowSequenceLogo(true);
5341 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5342 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5346 protected void showInformationHistogram_actionPerformed(ActionEvent e)
5348 viewport.setShowInformationHistogram(
5349 showInformationHistogram.getState());
5350 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5354 protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5356 viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5357 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5361 protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5363 showHMMSequenceLogo.setState(true);
5364 viewport.setShowHMMSequenceLogo(true);
5365 viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5366 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5370 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5372 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5379 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5380 * .event.ActionEvent)
5383 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5385 if (avc.makeGroupsFromSelection())
5387 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5388 alignPanel.updateAnnotation();
5389 alignPanel.paintAlignment(true);
5393 public void clearAlignmentSeqRep()
5395 // TODO refactor alignmentseqrep to controller
5396 if (viewport.getAlignment().hasSeqrep())
5398 viewport.getAlignment().setSeqrep(null);
5399 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5400 alignPanel.updateAnnotation();
5401 alignPanel.paintAlignment(true);
5406 protected void createGroup_actionPerformed(ActionEvent e)
5408 if (avc.createGroup())
5410 alignPanel.alignmentChanged();
5415 protected void unGroup_actionPerformed(ActionEvent e)
5419 alignPanel.alignmentChanged();
5424 * make the given alignmentPanel the currently selected tab
5426 * @param alignmentPanel
5428 public void setDisplayedView(AlignmentPanel alignmentPanel)
5430 if (!viewport.getSequenceSetId().equals(
5431 alignmentPanel.av.getSequenceSetId()))
5435 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5437 if (tabbedPane != null
5438 && tabbedPane.getTabCount() > 0
5439 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5440 .getSelectedIndex())
5442 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5447 * Action on selection of menu options to Show or Hide annotations.
5450 * @param forSequences
5451 * update sequence-related annotations
5452 * @param forAlignment
5453 * update non-sequence-related annotations
5456 protected void setAnnotationsVisibility(boolean visible,
5457 boolean forSequences, boolean forAlignment)
5459 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5460 .getAlignmentAnnotation();
5465 for (AlignmentAnnotation aa : anns)
5468 * don't display non-positional annotations on an alignment
5470 if (aa.annotations == null)
5474 boolean apply = (aa.sequenceRef == null && forAlignment)
5475 || (aa.sequenceRef != null && forSequences);
5478 aa.visible = visible;
5481 alignPanel.validateAnnotationDimensions(true);
5482 alignPanel.alignmentChanged();
5486 * Store selected annotation sort order for the view and repaint.
5489 protected void sortAnnotations_actionPerformed()
5491 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5493 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5494 alignPanel.paintAlignment(true);
5499 * @return alignment panels in this alignment frame
5501 public List<? extends AlignmentViewPanel> getAlignPanels()
5503 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5507 * Open a new alignment window, with the cDNA associated with this (protein)
5508 * alignment, aligned as is the protein.
5510 protected void viewAsCdna_actionPerformed()
5512 // TODO no longer a menu action - refactor as required
5513 final AlignmentI alignment = getViewport().getAlignment();
5514 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5515 if (mappings == null)
5519 List<SequenceI> cdnaSeqs = new ArrayList<>();
5520 for (SequenceI aaSeq : alignment.getSequences())
5522 for (AlignedCodonFrame acf : mappings)
5524 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5528 * There is a cDNA mapping for this protein sequence - add to new
5529 * alignment. It will share the same dataset sequence as other mapped
5530 * cDNA (no new mappings need to be created).
5532 final Sequence newSeq = new Sequence(dnaSeq);
5533 newSeq.setDatasetSequence(dnaSeq);
5534 cdnaSeqs.add(newSeq);
5538 if (cdnaSeqs.size() == 0)
5540 // show a warning dialog no mapped cDNA
5543 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5545 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5546 AlignFrame.DEFAULT_HEIGHT);
5547 cdna.alignAs(alignment);
5548 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5550 Desktop.addInternalFrame(alignFrame, newtitle,
5551 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5555 * Set visibility of dna/protein complement view (available when shown in a
5561 protected void showComplement_actionPerformed(boolean show)
5563 SplitContainerI sf = getSplitViewContainer();
5566 sf.setComplementVisible(this, show);
5571 * Generate the reverse (optionally complemented) of the selected sequences,
5572 * and add them to the alignment
5575 protected void showReverse_actionPerformed(boolean complement)
5577 AlignmentI al = null;
5580 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5581 al = dna.reverseCdna(complement);
5582 viewport.addAlignment(al, "");
5583 addHistoryItem(new EditCommand(
5584 MessageManager.getString("label.add_sequences"),
5585 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5586 viewport.getAlignment()));
5587 } catch (Exception ex)
5589 System.err.println(ex.getMessage());
5595 * Try to run a script in the Groovy console, having first ensured that this
5596 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5597 * be targeted at this alignment.
5600 protected void runGroovy_actionPerformed()
5602 Jalview.setCurrentAlignFrame(this);
5603 groovy.ui.Console console = Desktop.getGroovyConsole();
5604 if (console != null)
5608 console.runScript();
5609 } catch (Exception ex)
5611 System.err.println((ex.toString()));
5613 .showInternalMessageDialog(Desktop.desktop, MessageManager
5614 .getString("label.couldnt_run_groovy_script"),
5616 .getString("label.groovy_support_failed"),
5617 JvOptionPane.ERROR_MESSAGE);
5622 System.err.println("Can't run Groovy script as console not found");
5627 * Hides columns containing (or not containing) a specified feature, provided
5628 * that would not leave all columns hidden
5630 * @param featureType
5631 * @param columnsContaining
5634 public boolean hideFeatureColumns(String featureType,
5635 boolean columnsContaining)
5637 boolean notForHiding = avc.markColumnsContainingFeatures(
5638 columnsContaining, false, false, featureType);
5641 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5642 false, featureType))
5644 getViewport().hideSelectedColumns();
5652 protected void selectHighlightedColumns_actionPerformed(
5653 ActionEvent actionEvent)
5655 // include key modifier check in case user selects from menu
5656 avc.markHighlightedColumns(
5657 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5659 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5663 * Rebuilds the Colour menu, including any user-defined colours which have
5664 * been loaded either on startup or during the session
5666 public void buildColourMenu()
5668 colourMenu.removeAll();
5670 colourMenu.add(applyToAllGroups);
5671 colourMenu.add(textColour);
5672 colourMenu.addSeparator();
5674 ColourMenuHelper.addMenuItems(colourMenu, this,
5675 viewport.getAlignment(), false);
5677 colourMenu.addSeparator();
5678 colourMenu.add(conservationMenuItem);
5679 colourMenu.add(modifyConservation);
5680 colourMenu.add(abovePIDThreshold);
5681 colourMenu.add(modifyPID);
5682 colourMenu.add(annotationColour);
5684 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5685 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5689 * Open a dialog (if not already open) that allows the user to select and
5690 * calculate PCA or Tree analysis
5692 protected void openTreePcaDialog()
5694 if (alignPanel.getCalculationDialog() == null)
5696 new CalculationChooser(AlignFrame.this);
5700 public void updateHMMERStatus(boolean status)
5702 hmmerMenu.setEnabled(status);
5705 public HiddenMarkovModel getSelectedHMM()
5711 * Sets the selected hidden Markov model
5713 * @param selectedHMM
5715 public void setSelectedHMM(HiddenMarkovModel selectedHMM)
5717 this.selectedHMM = selectedHMM;
5718 hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
5719 + selectedHMM.getName() + "_HMM");
5720 hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
5721 + selectedHMM.getName() + "_HMM");
5725 public void hmmerMenu_actionPerformed(ActionEvent e)
5727 SequenceGroup grp = getViewport().getSelectionGroup();
5730 hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
5735 hmmBuild.setText(MessageManager.getString("label.hmmbuild")
5736 + " from Alignment");
5742 class PrintThread extends Thread
5746 public PrintThread(AlignmentPanel ap)
5751 static PageFormat pf;
5756 PrinterJob printJob = PrinterJob.getPrinterJob();
5760 printJob.setPrintable(ap, pf);
5764 printJob.setPrintable(ap);
5767 if (printJob.printDialog())
5772 } catch (Exception PrintException)
5774 PrintException.printStackTrace();