2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenColumns;
57 import jalview.datamodel.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.hmmer.HMMAlignThread;
66 import jalview.hmmer.HMMBuildThread;
67 import jalview.io.AlignmentProperties;
68 import jalview.io.AnnotationFile;
69 import jalview.io.BioJsHTMLOutput;
70 import jalview.io.DataSourceType;
71 import jalview.io.FileFormat;
72 import jalview.io.FileFormatI;
73 import jalview.io.FileFormats;
74 import jalview.io.FileLoader;
75 import jalview.io.FileParse;
76 import jalview.io.FormatAdapter;
77 import jalview.io.HtmlSvgOutput;
78 import jalview.io.IdentifyFile;
79 import jalview.io.JPredFile;
80 import jalview.io.JalviewFileChooser;
81 import jalview.io.JalviewFileView;
82 import jalview.io.JnetAnnotationMaker;
83 import jalview.io.NewickFile;
84 import jalview.io.ScoreMatrixFile;
85 import jalview.io.TCoffeeScoreFile;
86 import jalview.jbgui.GAlignFrame;
87 import jalview.schemes.ColourSchemeI;
88 import jalview.schemes.ColourSchemes;
89 import jalview.schemes.ResidueColourScheme;
90 import jalview.schemes.TCoffeeColourScheme;
91 import jalview.util.MessageManager;
92 import jalview.viewmodel.AlignmentViewport;
93 import jalview.viewmodel.ViewportRanges;
94 import jalview.ws.DBRefFetcher;
95 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
96 import jalview.ws.jws1.Discoverer;
97 import jalview.ws.jws2.Jws2Discoverer;
98 import jalview.ws.jws2.jabaws2.Jws2Instance;
99 import jalview.ws.seqfetcher.DbSourceProxy;
101 import java.awt.BorderLayout;
102 import java.awt.Component;
103 import java.awt.Rectangle;
104 import java.awt.Toolkit;
105 import java.awt.datatransfer.Clipboard;
106 import java.awt.datatransfer.DataFlavor;
107 import java.awt.datatransfer.StringSelection;
108 import java.awt.datatransfer.Transferable;
109 import java.awt.dnd.DnDConstants;
110 import java.awt.dnd.DropTargetDragEvent;
111 import java.awt.dnd.DropTargetDropEvent;
112 import java.awt.dnd.DropTargetEvent;
113 import java.awt.dnd.DropTargetListener;
114 import java.awt.event.ActionEvent;
115 import java.awt.event.ActionListener;
116 import java.awt.event.FocusAdapter;
117 import java.awt.event.FocusEvent;
118 import java.awt.event.ItemEvent;
119 import java.awt.event.ItemListener;
120 import java.awt.event.KeyAdapter;
121 import java.awt.event.KeyEvent;
122 import java.awt.event.MouseEvent;
123 import java.awt.print.PageFormat;
124 import java.awt.print.PrinterJob;
125 import java.beans.PropertyChangeEvent;
127 import java.io.FileWriter;
128 import java.io.IOException;
129 import java.io.PrintWriter;
131 import java.util.ArrayList;
132 import java.util.Arrays;
133 import java.util.Deque;
134 import java.util.Enumeration;
135 import java.util.HashMap;
136 import java.util.Hashtable;
137 import java.util.List;
138 import java.util.Map;
139 import java.util.Vector;
141 import javax.swing.JCheckBoxMenuItem;
142 import javax.swing.JEditorPane;
143 import javax.swing.JInternalFrame;
144 import javax.swing.JLayeredPane;
145 import javax.swing.JMenu;
146 import javax.swing.JMenuItem;
147 import javax.swing.JOptionPane;
148 import javax.swing.JScrollPane;
149 import javax.swing.SwingUtilities;
155 * @version $Revision$
157 public class AlignFrame extends GAlignFrame implements DropTargetListener,
158 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
161 Map<String, Float> distribution = new HashMap<>(); // temporary
163 public static final int DEFAULT_WIDTH = 700;
165 public static final int DEFAULT_HEIGHT = 500;
167 boolean autoAlignNewSequences;
171 * The currently displayed panel (selected tabbed view if more than one)
173 public AlignmentPanel alignPanel;
175 AlignViewport viewport;
177 ViewportRanges vpRanges;
179 public AlignViewControllerI avc;
181 List<AlignmentPanel> alignPanels = new ArrayList<>();
184 * Last format used to load or save alignments in this window
186 FileFormatI currentFileFormat = null;
189 * Current filename for this alignment
191 String fileName = null;
195 * Creates a new AlignFrame object with specific width and height.
201 public AlignFrame(AlignmentI al, int width, int height)
203 this(al, null, width, height);
207 * Creates a new AlignFrame object with specific width, height and
213 * @param sequenceSetId
215 public AlignFrame(AlignmentI al, int width, int height,
216 String sequenceSetId)
218 this(al, null, width, height, sequenceSetId);
222 * Creates a new AlignFrame object with specific width, height and
228 * @param sequenceSetId
231 public AlignFrame(AlignmentI al, int width, int height,
232 String sequenceSetId, String viewId)
234 this(al, null, width, height, sequenceSetId, viewId);
238 * new alignment window with hidden columns
242 * @param hiddenColumns
243 * ColumnSelection or null
245 * Width of alignment frame
249 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
250 int width, int height)
252 this(al, hiddenColumns, width, height, null);
256 * Create alignment frame for al with hiddenColumns, a specific width and
257 * height, and specific sequenceId
260 * @param hiddenColumns
263 * @param sequenceSetId
266 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
267 int width, int height, String sequenceSetId)
269 this(al, hiddenColumns, width, height, sequenceSetId, null);
273 * Create alignment frame for al with hiddenColumns, a specific width and
274 * height, and specific sequenceId
277 * @param hiddenColumns
280 * @param sequenceSetId
285 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
286 int width, int height, String sequenceSetId, String viewId)
288 setSize(width, height);
290 if (al.getDataset() == null)
295 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
297 alignPanel = new AlignmentPanel(this, viewport);
299 addAlignmentPanel(alignPanel, true);
303 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
304 HiddenColumns hiddenColumns, int width, int height)
306 setSize(width, height);
308 if (al.getDataset() == null)
313 viewport = new AlignViewport(al, hiddenColumns);
315 if (hiddenSeqs != null && hiddenSeqs.length > 0)
317 viewport.hideSequence(hiddenSeqs);
319 alignPanel = new AlignmentPanel(this, viewport);
320 addAlignmentPanel(alignPanel, true);
325 * Make a new AlignFrame from existing alignmentPanels
332 public AlignFrame(AlignmentPanel ap)
336 addAlignmentPanel(ap, false);
341 * initalise the alignframe from the underlying viewport data and the
346 if (!Jalview.isHeadlessMode())
348 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
351 vpRanges = viewport.getRanges();
352 avc = new jalview.controller.AlignViewController(this, viewport,
354 if (viewport.getAlignmentConservationAnnotation() == null)
356 // BLOSUM62Colour.setEnabled(false);
357 conservationMenuItem.setEnabled(false);
358 modifyConservation.setEnabled(false);
359 // PIDColour.setEnabled(false);
360 // abovePIDThreshold.setEnabled(false);
361 // modifyPID.setEnabled(false);
364 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
367 if (sortby.equals("Id"))
369 sortIDMenuItem_actionPerformed(null);
371 else if (sortby.equals("Pairwise Identity"))
373 sortPairwiseMenuItem_actionPerformed(null);
377 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
379 setMenusFromViewport(viewport);
380 buildSortByAnnotationScoresMenu();
381 calculateTree.addActionListener(new ActionListener()
385 public void actionPerformed(ActionEvent e)
393 if (Desktop.desktop != null)
395 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
396 addServiceListeners();
400 if (viewport.getWrapAlignment())
402 wrapMenuItem_actionPerformed(null);
405 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
407 this.overviewMenuItem_actionPerformed(null);
412 final List<AlignmentPanel> selviews = new ArrayList<>();
413 final List<AlignmentPanel> origview = new ArrayList<>();
414 final String menuLabel = MessageManager
415 .getString("label.copy_format_from");
416 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
417 new ViewSetProvider()
421 public AlignmentPanel[] getAllAlignmentPanels()
424 origview.add(alignPanel);
425 // make an array of all alignment panels except for this one
426 List<AlignmentPanel> aps = new ArrayList<>(
427 Arrays.asList(Desktop.getAlignmentPanels(null)));
428 aps.remove(AlignFrame.this.alignPanel);
429 return aps.toArray(new AlignmentPanel[aps.size()]);
431 }, selviews, new ItemListener()
435 public void itemStateChanged(ItemEvent e)
437 if (origview.size() > 0)
439 final AlignmentPanel ap = origview.get(0);
442 * Copy the ViewStyle of the selected panel to 'this one'.
443 * Don't change value of 'scaleProteinAsCdna' unless copying
446 ViewStyleI vs = selviews.get(0).getAlignViewport()
448 boolean fromSplitFrame = selviews.get(0)
449 .getAlignViewport().getCodingComplement() != null;
452 vs.setScaleProteinAsCdna(ap.getAlignViewport()
453 .getViewStyle().isScaleProteinAsCdna());
455 ap.getAlignViewport().setViewStyle(vs);
458 * Also rescale ViewStyle of SplitFrame complement if there is
459 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
460 * the whole ViewStyle (allow cDNA protein to have different
463 AlignViewportI complement = ap.getAlignViewport()
464 .getCodingComplement();
465 if (complement != null && vs.isScaleProteinAsCdna())
467 AlignFrame af = Desktop.getAlignFrameFor(complement);
468 ((SplitFrame) af.getSplitViewContainer())
470 af.setMenusForViewport();
474 ap.setSelected(true);
475 ap.alignFrame.setMenusForViewport();
480 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
481 .indexOf("devel") > -1
482 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
483 .indexOf("test") > -1)
485 formatMenu.add(vsel);
487 addFocusListener(new FocusAdapter()
490 public void focusGained(FocusEvent e)
492 Jalview.setCurrentAlignFrame(AlignFrame.this);
498 private void buildHMMERMenu()
500 hmmerMenu.removeAll();
502 hmmerMenu.add(changeHMMERLocation);
503 hmmerMenu.addSeparator();
505 hmmerMenu.add(autoAlignSeqs);
506 hmmerMenu.addSeparator();
508 hmmerMenu.add(hmmAlign);
509 hmmerMenu.add(hmmBuild);
510 hmmerMenu.add(hmmSearch);
515 * Change the filename and format for the alignment, and enable the 'reload'
516 * button functionality.
523 public void setFileName(String file, FileFormatI format)
526 setFileFormat(format);
527 reload.setEnabled(true);
531 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
534 void addKeyListener()
536 addKeyListener(new KeyAdapter()
539 public void keyPressed(KeyEvent evt)
541 if (viewport.cursorMode
542 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
543 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
544 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
545 && Character.isDigit(evt.getKeyChar()))
547 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
550 switch (evt.getKeyCode())
553 case 27: // escape key
554 deselectAllSequenceMenuItem_actionPerformed(null);
558 case KeyEvent.VK_DOWN:
559 if (evt.isAltDown() || !viewport.cursorMode)
561 moveSelectedSequences(false);
563 if (viewport.cursorMode)
565 alignPanel.getSeqPanel().moveCursor(0, 1);
570 if (evt.isAltDown() || !viewport.cursorMode)
572 moveSelectedSequences(true);
574 if (viewport.cursorMode)
576 alignPanel.getSeqPanel().moveCursor(0, -1);
581 case KeyEvent.VK_LEFT:
582 if (evt.isAltDown() || !viewport.cursorMode)
584 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
588 alignPanel.getSeqPanel().moveCursor(-1, 0);
593 case KeyEvent.VK_RIGHT:
594 if (evt.isAltDown() || !viewport.cursorMode)
596 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
600 alignPanel.getSeqPanel().moveCursor(1, 0);
604 case KeyEvent.VK_SPACE:
605 if (viewport.cursorMode)
607 alignPanel.getSeqPanel().insertGapAtCursor(
608 evt.isControlDown() || evt.isShiftDown()
613 // case KeyEvent.VK_A:
614 // if (viewport.cursorMode)
616 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
617 // //System.out.println("A");
621 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
622 * System.out.println("closing bracket"); } break;
624 case KeyEvent.VK_DELETE:
625 case KeyEvent.VK_BACK_SPACE:
626 if (!viewport.cursorMode)
628 cut_actionPerformed(null);
632 alignPanel.getSeqPanel().deleteGapAtCursor(
633 evt.isControlDown() || evt.isShiftDown()
640 if (viewport.cursorMode)
642 alignPanel.getSeqPanel().setCursorRow();
646 if (viewport.cursorMode && !evt.isControlDown())
648 alignPanel.getSeqPanel().setCursorColumn();
652 if (viewport.cursorMode)
654 alignPanel.getSeqPanel().setCursorPosition();
658 case KeyEvent.VK_ENTER:
659 case KeyEvent.VK_COMMA:
660 if (viewport.cursorMode)
662 alignPanel.getSeqPanel().setCursorRowAndColumn();
667 if (viewport.cursorMode)
669 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
673 if (viewport.cursorMode)
675 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
680 viewport.cursorMode = !viewport.cursorMode;
681 statusBar.setText(MessageManager.formatMessage(
682 "label.keyboard_editing_mode",
683 new String[] { (viewport.cursorMode ? "on" : "off") }));
684 if (viewport.cursorMode)
686 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
688 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
691 alignPanel.getSeqPanel().seqCanvas.repaint();
697 Help.showHelpWindow();
698 } catch (Exception ex)
700 ex.printStackTrace();
705 boolean toggleSeqs = !evt.isControlDown();
706 boolean toggleCols = !evt.isShiftDown();
707 toggleHiddenRegions(toggleSeqs, toggleCols);
712 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
713 boolean modifyExisting = true; // always modify, don't clear
714 // evt.isShiftDown();
715 boolean invertHighlighted = evt.isAltDown();
716 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
720 case KeyEvent.VK_PAGE_UP:
721 if (viewport.getWrapAlignment())
723 vpRanges.scrollUp(true);
730 case KeyEvent.VK_PAGE_DOWN:
731 if (viewport.getWrapAlignment())
733 vpRanges.scrollUp(false);
744 public void keyReleased(KeyEvent evt)
746 switch (evt.getKeyCode())
748 case KeyEvent.VK_LEFT:
749 if (evt.isAltDown() || !viewport.cursorMode)
751 viewport.firePropertyChange("alignment", null, viewport
752 .getAlignment().getSequences());
756 case KeyEvent.VK_RIGHT:
757 if (evt.isAltDown() || !viewport.cursorMode)
759 viewport.firePropertyChange("alignment", null, viewport
760 .getAlignment().getSequences());
768 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
770 ap.alignFrame = this;
771 avc = new jalview.controller.AlignViewController(this, viewport,
776 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
778 int aSize = alignPanels.size();
780 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
782 if (aSize == 1 && ap.av.viewName == null)
784 this.getContentPane().add(ap, BorderLayout.CENTER);
790 setInitialTabVisible();
793 expandViews.setEnabled(true);
794 gatherViews.setEnabled(true);
795 tabbedPane.addTab(ap.av.viewName, ap);
797 ap.setVisible(false);
802 if (ap.av.isPadGaps())
804 ap.av.getAlignment().padGaps();
806 ap.av.updateConservation(ap);
807 ap.av.updateConsensus(ap);
808 ap.av.updateStrucConsensus(ap);
809 ap.av.updateInformation(ap);
813 public void setInitialTabVisible()
815 expandViews.setEnabled(true);
816 gatherViews.setEnabled(true);
817 tabbedPane.setVisible(true);
818 AlignmentPanel first = alignPanels.get(0);
819 tabbedPane.addTab(first.av.viewName, first);
820 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
823 public AlignViewport getViewport()
828 /* Set up intrinsic listeners for dynamically generated GUI bits. */
829 private void addServiceListeners()
831 final java.beans.PropertyChangeListener thisListener;
832 Desktop.instance.addJalviewPropertyChangeListener("services",
833 thisListener = new java.beans.PropertyChangeListener()
836 public void propertyChange(PropertyChangeEvent evt)
838 // // System.out.println("Discoverer property change.");
839 // if (evt.getPropertyName().equals("services"))
841 SwingUtilities.invokeLater(new Runnable()
848 .println("Rebuild WS Menu for service change");
849 BuildWebServiceMenu();
856 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
859 public void internalFrameClosed(
860 javax.swing.event.InternalFrameEvent evt)
862 // System.out.println("deregistering discoverer listener");
863 Desktop.instance.removeJalviewPropertyChangeListener("services",
865 closeMenuItem_actionPerformed(true);
868 // Finally, build the menu once to get current service state
869 new Thread(new Runnable()
874 BuildWebServiceMenu();
880 * Configure menu items that vary according to whether the alignment is
881 * nucleotide or protein
883 public void setGUINucleotide()
885 AlignmentI al = getViewport().getAlignment();
886 boolean nucleotide = al.isNucleotide();
888 showTranslation.setVisible(nucleotide);
889 showReverse.setVisible(nucleotide);
890 showReverseComplement.setVisible(nucleotide);
891 conservationMenuItem.setEnabled(!nucleotide);
892 modifyConservation.setEnabled(!nucleotide
893 && conservationMenuItem.isSelected());
894 showGroupConservation.setEnabled(!nucleotide);
896 showComplementMenuItem.setText(nucleotide ? MessageManager
897 .getString("label.protein") : MessageManager
898 .getString("label.nucleotide"));
902 * set up menus for the current viewport. This may be called after any
903 * operation that affects the data in the current view (selection changed,
904 * etc) to update the menus to reflect the new state.
907 public void setMenusForViewport()
909 setMenusFromViewport(viewport);
913 * Need to call this method when tabs are selected for multiple views, or when
914 * loading from Jalview2XML.java
919 void setMenusFromViewport(AlignViewport av)
921 padGapsMenuitem.setSelected(av.isPadGaps());
922 colourTextMenuItem.setSelected(av.isShowColourText());
923 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
924 modifyPID.setEnabled(abovePIDThreshold.isSelected());
925 conservationMenuItem.setSelected(av.getConservationSelected());
926 modifyConservation.setEnabled(conservationMenuItem.isSelected());
927 seqLimits.setSelected(av.getShowJVSuffix());
928 idRightAlign.setSelected(av.isRightAlignIds());
929 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
930 renderGapsMenuItem.setSelected(av.isRenderGaps());
931 wrapMenuItem.setSelected(av.getWrapAlignment());
932 scaleAbove.setVisible(av.getWrapAlignment());
933 scaleLeft.setVisible(av.getWrapAlignment());
934 scaleRight.setVisible(av.getWrapAlignment());
935 annotationPanelMenuItem.setState(av.isShowAnnotation());
937 * Show/hide annotations only enabled if annotation panel is shown
939 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
940 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
941 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
942 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
943 viewBoxesMenuItem.setSelected(av.getShowBoxes());
944 viewTextMenuItem.setSelected(av.getShowText());
945 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
946 showGroupConsensus.setSelected(av.isShowGroupConsensus());
947 showGroupConservation.setSelected(av.isShowGroupConservation());
948 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
949 showSequenceLogo.setSelected(av.isShowSequenceLogo());
950 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
951 showInformationHistogram.setSelected(av.isShowInformationHistogram());
952 showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
953 normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
955 ColourMenuHelper.setColourSelected(colourMenu,
956 av.getGlobalColourScheme());
958 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
959 hiddenMarkers.setState(av.getShowHiddenMarkers());
960 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
961 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
962 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
963 autoCalculate.setSelected(av.autoCalculateConsensus);
964 sortByTree.setSelected(av.sortByTree);
965 listenToViewSelections.setSelected(av.followSelection);
967 showProducts.setEnabled(canShowProducts());
968 setGroovyEnabled(Desktop.getGroovyConsole() != null);
974 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
978 public void setGroovyEnabled(boolean b)
980 runGroovy.setEnabled(b);
983 private IProgressIndicator progressBar;
988 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
991 public void setProgressBar(String message, long id)
993 progressBar.setProgressBar(message, id);
997 public void registerHandler(final long id,
998 final IProgressIndicatorHandler handler)
1000 progressBar.registerHandler(id, handler);
1005 * @return true if any progress bars are still active
1008 public boolean operationInProgress()
1010 return progressBar.operationInProgress();
1014 public void setStatus(String text)
1016 statusBar.setText(text);
1020 * Added so Castor Mapping file can obtain Jalview Version
1022 public String getVersion()
1024 return jalview.bin.Cache.getProperty("VERSION");
1027 public FeatureRenderer getFeatureRenderer()
1029 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1033 public void fetchSequence_actionPerformed(ActionEvent e)
1035 new jalview.gui.SequenceFetcher(this);
1039 public void addFromFile_actionPerformed(ActionEvent e)
1041 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1045 public void hmmBuild_actionPerformed(ActionEvent e)
1046 throws IOException, InterruptedException
1048 new Thread(new HMMBuildThread(this)).start();
1049 alignPanel.repaint();
1054 public void hmmAlign_actionPerformed(ActionEvent e)
1055 throws IOException, InterruptedException
1057 new Thread(new HMMAlignThread(this, true)).start();
1058 alignPanel.repaint();
1062 public void changeHMMERLocation_actionPerformed(ActionEvent e)
1064 String location = JOptionPane.showInputDialog(
1065 MessageManager.getString("label.enter_location"));
1066 Cache.setProperty(Preferences.HMMER_PATH, location);
1070 public void autoAlignSeqs_actionPerformed(boolean autoAlignSeqs)
1072 autoAlignNewSequences = autoAlignSeqs;
1073 alignPanel.repaint();
1077 public void hmmSearch_actionPerformed(ActionEvent e)
1079 alignPanel.repaint();
1083 public void reload_actionPerformed(ActionEvent e)
1085 if (fileName != null)
1087 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1088 // originating file's format
1089 // TODO: work out how to recover feature settings for correct view(s) when
1090 // file is reloaded.
1091 if (FileFormat.Jalview.equals(currentFileFormat))
1093 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1094 for (int i = 0; i < frames.length; i++)
1096 if (frames[i] instanceof AlignFrame && frames[i] != this
1097 && ((AlignFrame) frames[i]).fileName != null
1098 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1102 frames[i].setSelected(true);
1103 Desktop.instance.closeAssociatedWindows();
1104 } catch (java.beans.PropertyVetoException ex)
1110 Desktop.instance.closeAssociatedWindows();
1112 FileLoader loader = new FileLoader();
1113 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1114 : DataSourceType.FILE;
1115 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1119 Rectangle bounds = this.getBounds();
1121 FileLoader loader = new FileLoader();
1122 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1123 : DataSourceType.FILE;
1124 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1125 protocol, currentFileFormat);
1127 newframe.setBounds(bounds);
1128 if (featureSettings != null && featureSettings.isShowing())
1130 final Rectangle fspos = featureSettings.frame.getBounds();
1131 // TODO: need a 'show feature settings' function that takes bounds -
1132 // need to refactor Desktop.addFrame
1133 newframe.featureSettings_actionPerformed(null);
1134 final FeatureSettings nfs = newframe.featureSettings;
1135 SwingUtilities.invokeLater(new Runnable()
1140 nfs.frame.setBounds(fspos);
1143 this.featureSettings.close();
1144 this.featureSettings = null;
1146 this.closeMenuItem_actionPerformed(true);
1152 public void addFromText_actionPerformed(ActionEvent e)
1154 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1159 public void addFromURL_actionPerformed(ActionEvent e)
1161 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1165 public void save_actionPerformed(ActionEvent e)
1167 if (fileName == null || (currentFileFormat == null)
1168 || fileName.startsWith("http"))
1170 saveAs_actionPerformed(null);
1174 saveAlignment(fileName, currentFileFormat);
1185 public void saveAs_actionPerformed(ActionEvent e)
1187 String format = currentFileFormat == null ? null : currentFileFormat
1189 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1190 Cache.getProperty("LAST_DIRECTORY"), format);
1192 chooser.setFileView(new JalviewFileView());
1193 chooser.setDialogTitle(MessageManager
1194 .getString("label.save_alignment_to_file"));
1195 chooser.setToolTipText(MessageManager.getString("action.save"));
1197 int value = chooser.showSaveDialog(this);
1199 if (value == JalviewFileChooser.APPROVE_OPTION)
1201 currentFileFormat = chooser.getSelectedFormat();
1202 while (currentFileFormat == null)
1205 .showInternalMessageDialog(
1208 .getString("label.select_file_format_before_saving"),
1210 .getString("label.file_format_not_specified"),
1211 JvOptionPane.WARNING_MESSAGE);
1212 currentFileFormat = chooser.getSelectedFormat();
1213 value = chooser.showSaveDialog(this);
1214 if (value != JalviewFileChooser.APPROVE_OPTION)
1220 fileName = chooser.getSelectedFile().getPath();
1222 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1224 Cache.setProperty("LAST_DIRECTORY", fileName);
1225 saveAlignment(fileName, currentFileFormat);
1229 public boolean saveAlignment(String file, FileFormatI format)
1231 boolean success = true;
1233 if (FileFormat.Jalview.equals(format))
1235 String shortName = title;
1237 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1239 shortName = shortName.substring(shortName
1240 .lastIndexOf(java.io.File.separatorChar) + 1);
1243 success = new Jalview2XML().saveAlignment(this, file, shortName);
1245 statusBar.setText(MessageManager.formatMessage(
1246 "label.successfully_saved_to_file_in_format", new Object[] {
1247 fileName, format }));
1252 AlignmentExportData exportData = getAlignmentForExport(format,
1254 if (exportData.getSettings().isCancelled())
1258 FormatAdapter f = new FormatAdapter(alignPanel,
1259 exportData.getSettings());
1260 String output = f.formatSequences(
1262 exportData.getAlignment(), // class cast exceptions will
1263 // occur in the distant future
1264 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1265 f.getCacheSuffixDefault(format), viewport.getAlignment()
1266 .getHiddenColumns());
1276 PrintWriter out = new PrintWriter(new FileWriter(file));
1280 this.setTitle(file);
1281 statusBar.setText(MessageManager.formatMessage(
1282 "label.successfully_saved_to_file_in_format",
1283 new Object[] { fileName, format.getName() }));
1284 } catch (Exception ex)
1287 ex.printStackTrace();
1294 JvOptionPane.showInternalMessageDialog(this, MessageManager
1295 .formatMessage("label.couldnt_save_file",
1296 new Object[] { fileName }), MessageManager
1297 .getString("label.error_saving_file"),
1298 JvOptionPane.WARNING_MESSAGE);
1304 private void warningMessage(String warning, String title)
1306 if (new jalview.util.Platform().isHeadless())
1308 System.err.println("Warning: " + title + "\nWarning: " + warning);
1313 JvOptionPane.showInternalMessageDialog(this, warning, title,
1314 JvOptionPane.WARNING_MESSAGE);
1326 protected void outputText_actionPerformed(ActionEvent e)
1328 FileFormatI fileFormat = FileFormats.getInstance().forName(
1329 e.getActionCommand());
1330 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1332 if (exportData.getSettings().isCancelled())
1336 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1337 cap.setForInput(null);
1340 FileFormatI format = fileFormat;
1341 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1342 .formatSequences(format, exportData.getAlignment(),
1343 exportData.getOmitHidden(),
1345 .getStartEndPostions(), viewport
1346 .getAlignment().getHiddenColumns()));
1347 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1348 "label.alignment_output_command",
1349 new Object[] { e.getActionCommand() }), 600, 500);
1350 } catch (OutOfMemoryError oom)
1352 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1358 public static AlignmentExportData getAlignmentForExport(
1359 FileFormatI format, AlignViewportI viewport,
1360 AlignExportSettingI exportSettings)
1362 AlignmentI alignmentToExport = null;
1363 AlignExportSettingI settings = exportSettings;
1364 String[] omitHidden = null;
1366 HiddenSequences hiddenSeqs = viewport.getAlignment()
1367 .getHiddenSequences();
1369 alignmentToExport = viewport.getAlignment();
1371 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1372 if (settings == null)
1374 settings = new AlignExportSettings(hasHiddenSeqs,
1375 viewport.hasHiddenColumns(), format);
1377 // settings.isExportAnnotations();
1379 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1381 omitHidden = viewport.getViewAsString(false,
1382 settings.isExportHiddenSequences());
1385 int[] alignmentStartEnd = new int[2];
1386 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1388 alignmentToExport = hiddenSeqs.getFullAlignment();
1392 alignmentToExport = viewport.getAlignment();
1394 alignmentStartEnd = alignmentToExport
1395 .getVisibleStartAndEndIndex(viewport.getAlignment()
1397 .getHiddenRegions());
1398 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1399 omitHidden, alignmentStartEnd, settings);
1410 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1412 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1413 htmlSVG.exportHTML(null);
1417 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1419 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1420 bjs.exportHTML(null);
1423 public void createImageMap(File file, String image)
1425 alignPanel.makePNGImageMap(file, image);
1435 public void createPNG(File f)
1437 alignPanel.makePNG(f);
1447 public void createEPS(File f)
1449 alignPanel.makeEPS(f);
1453 public void createSVG(File f)
1455 alignPanel.makeSVG(f);
1459 public void pageSetup_actionPerformed(ActionEvent e)
1461 PrinterJob printJob = PrinterJob.getPrinterJob();
1462 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1472 public void printMenuItem_actionPerformed(ActionEvent e)
1474 // Putting in a thread avoids Swing painting problems
1475 PrintThread thread = new PrintThread(alignPanel);
1480 public void exportFeatures_actionPerformed(ActionEvent e)
1482 new AnnotationExporter().exportFeatures(alignPanel);
1486 public void exportAnnotations_actionPerformed(ActionEvent e)
1488 new AnnotationExporter().exportAnnotations(alignPanel);
1492 public void associatedData_actionPerformed(ActionEvent e)
1493 throws IOException, InterruptedException
1495 // Pick the tree file
1496 JalviewFileChooser chooser = new JalviewFileChooser(
1497 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1498 chooser.setFileView(new JalviewFileView());
1499 chooser.setDialogTitle(MessageManager
1500 .getString("label.load_jalview_annotations"));
1501 chooser.setToolTipText(MessageManager
1502 .getString("label.load_jalview_annotations"));
1504 int value = chooser.showOpenDialog(null);
1506 if (value == JalviewFileChooser.APPROVE_OPTION)
1508 String choice = chooser.getSelectedFile().getPath();
1509 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1510 loadJalviewDataFile(choice, null, null, null);
1516 * Close the current view or all views in the alignment frame. If the frame
1517 * only contains one view then the alignment will be removed from memory.
1519 * @param closeAllTabs
1522 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1524 if (alignPanels != null && alignPanels.size() < 2)
1526 closeAllTabs = true;
1531 if (alignPanels != null)
1535 if (this.isClosed())
1537 // really close all the windows - otherwise wait till
1538 // setClosed(true) is called
1539 for (int i = 0; i < alignPanels.size(); i++)
1541 AlignmentPanel ap = alignPanels.get(i);
1548 closeView(alignPanel);
1555 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1556 * be called recursively, with the frame now in 'closed' state
1558 this.setClosed(true);
1560 } catch (Exception ex)
1562 ex.printStackTrace();
1567 * Close the specified panel and close up tabs appropriately.
1569 * @param panelToClose
1571 public void closeView(AlignmentPanel panelToClose)
1573 int index = tabbedPane.getSelectedIndex();
1574 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1575 alignPanels.remove(panelToClose);
1576 panelToClose.closePanel();
1577 panelToClose = null;
1579 tabbedPane.removeTabAt(closedindex);
1580 tabbedPane.validate();
1582 if (index > closedindex || index == tabbedPane.getTabCount())
1584 // modify currently selected tab index if necessary.
1588 this.tabSelectionChanged(index);
1594 void updateEditMenuBar()
1597 if (viewport.getHistoryList().size() > 0)
1599 undoMenuItem.setEnabled(true);
1600 CommandI command = viewport.getHistoryList().peek();
1601 undoMenuItem.setText(MessageManager.formatMessage(
1602 "label.undo_command",
1603 new Object[] { command.getDescription() }));
1607 undoMenuItem.setEnabled(false);
1608 undoMenuItem.setText(MessageManager.getString("action.undo"));
1611 if (viewport.getRedoList().size() > 0)
1613 redoMenuItem.setEnabled(true);
1615 CommandI command = viewport.getRedoList().peek();
1616 redoMenuItem.setText(MessageManager.formatMessage(
1617 "label.redo_command",
1618 new Object[] { command.getDescription() }));
1622 redoMenuItem.setEnabled(false);
1623 redoMenuItem.setText(MessageManager.getString("action.redo"));
1628 public void addHistoryItem(CommandI command)
1630 if (command.getSize() > 0)
1632 viewport.addToHistoryList(command);
1633 viewport.clearRedoList();
1634 updateEditMenuBar();
1635 viewport.updateHiddenColumns();
1636 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1637 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1638 // viewport.getColumnSelection()
1639 // .getHiddenColumns().size() > 0);
1645 * @return alignment objects for all views
1647 AlignmentI[] getViewAlignments()
1649 if (alignPanels != null)
1651 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1653 for (AlignmentPanel ap : alignPanels)
1655 als[i++] = ap.av.getAlignment();
1659 if (viewport != null)
1661 return new AlignmentI[] { viewport.getAlignment() };
1673 protected void undoMenuItem_actionPerformed(ActionEvent e)
1675 if (viewport.getHistoryList().isEmpty())
1679 CommandI command = viewport.getHistoryList().pop();
1680 viewport.addToRedoList(command);
1681 command.undoCommand(getViewAlignments());
1683 AlignmentViewport originalSource = getOriginatingSource(command);
1684 updateEditMenuBar();
1686 if (originalSource != null)
1688 if (originalSource != viewport)
1691 .warn("Implementation worry: mismatch of viewport origin for undo");
1693 originalSource.updateHiddenColumns();
1694 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1696 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1697 // viewport.getColumnSelection()
1698 // .getHiddenColumns().size() > 0);
1699 originalSource.firePropertyChange("alignment", null, originalSource
1700 .getAlignment().getSequences());
1711 protected void redoMenuItem_actionPerformed(ActionEvent e)
1713 if (viewport.getRedoList().size() < 1)
1718 CommandI command = viewport.getRedoList().pop();
1719 viewport.addToHistoryList(command);
1720 command.doCommand(getViewAlignments());
1722 AlignmentViewport originalSource = getOriginatingSource(command);
1723 updateEditMenuBar();
1725 if (originalSource != null)
1728 if (originalSource != viewport)
1731 .warn("Implementation worry: mismatch of viewport origin for redo");
1733 originalSource.updateHiddenColumns();
1734 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1736 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1737 // viewport.getColumnSelection()
1738 // .getHiddenColumns().size() > 0);
1739 originalSource.firePropertyChange("alignment", null, originalSource
1740 .getAlignment().getSequences());
1744 AlignmentViewport getOriginatingSource(CommandI command)
1746 AlignmentViewport originalSource = null;
1747 // For sequence removal and addition, we need to fire
1748 // the property change event FROM the viewport where the
1749 // original alignment was altered
1750 AlignmentI al = null;
1751 if (command instanceof EditCommand)
1753 EditCommand editCommand = (EditCommand) command;
1754 al = editCommand.getAlignment();
1755 List<Component> comps = PaintRefresher.components.get(viewport
1756 .getSequenceSetId());
1758 for (Component comp : comps)
1760 if (comp instanceof AlignmentPanel)
1762 if (al == ((AlignmentPanel) comp).av.getAlignment())
1764 originalSource = ((AlignmentPanel) comp).av;
1771 if (originalSource == null)
1773 // The original view is closed, we must validate
1774 // the current view against the closed view first
1777 PaintRefresher.validateSequences(al, viewport.getAlignment());
1780 originalSource = viewport;
1783 return originalSource;
1792 public void moveSelectedSequences(boolean up)
1794 SequenceGroup sg = viewport.getSelectionGroup();
1800 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1801 viewport.getHiddenRepSequences(), up);
1802 alignPanel.paintAlignment(true);
1805 synchronized void slideSequences(boolean right, int size)
1807 List<SequenceI> sg = new ArrayList<>();
1808 if (viewport.cursorMode)
1810 sg.add(viewport.getAlignment().getSequenceAt(
1811 alignPanel.getSeqPanel().seqCanvas.cursorY));
1813 else if (viewport.getSelectionGroup() != null
1814 && viewport.getSelectionGroup().getSize() != viewport
1815 .getAlignment().getHeight())
1817 sg = viewport.getSelectionGroup().getSequences(
1818 viewport.getHiddenRepSequences());
1826 List<SequenceI> invertGroup = new ArrayList<>();
1828 for (SequenceI seq : viewport.getAlignment().getSequences())
1830 if (!sg.contains(seq))
1832 invertGroup.add(seq);
1836 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1838 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1839 for (int i = 0; i < invertGroup.size(); i++)
1841 seqs2[i] = invertGroup.get(i);
1844 SlideSequencesCommand ssc;
1847 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1848 size, viewport.getGapCharacter());
1852 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1853 size, viewport.getGapCharacter());
1856 int groupAdjustment = 0;
1857 if (ssc.getGapsInsertedBegin() && right)
1859 if (viewport.cursorMode)
1861 alignPanel.getSeqPanel().moveCursor(size, 0);
1865 groupAdjustment = size;
1868 else if (!ssc.getGapsInsertedBegin() && !right)
1870 if (viewport.cursorMode)
1872 alignPanel.getSeqPanel().moveCursor(-size, 0);
1876 groupAdjustment = -size;
1880 if (groupAdjustment != 0)
1882 viewport.getSelectionGroup().setStartRes(
1883 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1884 viewport.getSelectionGroup().setEndRes(
1885 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1889 * just extend the last slide command if compatible; but not if in
1890 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1892 boolean appendHistoryItem = false;
1893 Deque<CommandI> historyList = viewport.getHistoryList();
1894 boolean inSplitFrame = getSplitViewContainer() != null;
1895 if (!inSplitFrame && historyList != null && historyList.size() > 0
1896 && historyList.peek() instanceof SlideSequencesCommand)
1898 appendHistoryItem = ssc
1899 .appendSlideCommand((SlideSequencesCommand) historyList
1903 if (!appendHistoryItem)
1905 addHistoryItem(ssc);
1918 protected void copy_actionPerformed(ActionEvent e)
1921 if (viewport.getSelectionGroup() == null)
1925 // TODO: preserve the ordering of displayed alignment annotation in any
1926 // internal paste (particularly sequence associated annotation)
1927 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1928 String[] omitHidden = null;
1930 if (viewport.hasHiddenColumns())
1932 omitHidden = viewport.getViewAsString(true);
1935 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1936 seqs, omitHidden, null);
1938 StringSelection ss = new StringSelection(output);
1942 jalview.gui.Desktop.internalCopy = true;
1943 // Its really worth setting the clipboard contents
1944 // to empty before setting the large StringSelection!!
1945 Toolkit.getDefaultToolkit().getSystemClipboard()
1946 .setContents(new StringSelection(""), null);
1948 Toolkit.getDefaultToolkit().getSystemClipboard()
1949 .setContents(ss, Desktop.instance);
1950 } catch (OutOfMemoryError er)
1952 new OOMWarning("copying region", er);
1956 ArrayList<int[]> hiddenColumns = null;
1957 if (viewport.hasHiddenColumns())
1959 hiddenColumns = new ArrayList<>();
1960 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1961 .getSelectionGroup().getEndRes();
1962 for (int[] region : viewport.getAlignment().getHiddenColumns()
1963 .getHiddenRegions())
1965 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1967 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1968 region[1] - hiddenOffset });
1973 Desktop.jalviewClipboard = new Object[] { seqs,
1974 viewport.getAlignment().getDataset(), hiddenColumns };
1975 statusBar.setText(MessageManager.formatMessage(
1976 "label.copied_sequences_to_clipboard", new Object[] { Integer
1977 .valueOf(seqs.length).toString() }));
1985 * @throws InterruptedException
1986 * @throws IOException
1989 protected void pasteNew_actionPerformed(ActionEvent e)
1990 throws IOException, InterruptedException
2000 * @throws InterruptedException
2001 * @throws IOException
2004 protected void pasteThis_actionPerformed(ActionEvent e)
2005 throws IOException, InterruptedException
2011 * Paste contents of Jalview clipboard
2013 * @param newAlignment
2014 * true to paste to a new alignment, otherwise add to this.
2015 * @throws InterruptedException
2016 * @throws IOException
2018 void paste(boolean newAlignment) throws IOException, InterruptedException
2020 boolean externalPaste = true;
2023 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2024 Transferable contents = c.getContents(this);
2026 if (contents == null)
2035 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2036 if (str.length() < 1)
2041 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2043 } catch (OutOfMemoryError er)
2045 new OOMWarning("Out of memory pasting sequences!!", er);
2049 SequenceI[] sequences;
2050 boolean annotationAdded = false;
2051 AlignmentI alignment = null;
2053 if (Desktop.jalviewClipboard != null)
2055 // The clipboard was filled from within Jalview, we must use the
2057 // And dataset from the copied alignment
2058 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2059 // be doubly sure that we create *new* sequence objects.
2060 sequences = new SequenceI[newseq.length];
2061 for (int i = 0; i < newseq.length; i++)
2063 sequences[i] = new Sequence(newseq[i]);
2065 alignment = new Alignment(sequences);
2066 externalPaste = false;
2070 // parse the clipboard as an alignment.
2071 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2073 sequences = alignment.getSequencesArray();
2077 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2083 if (Desktop.jalviewClipboard != null)
2085 // dataset is inherited
2086 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2090 // new dataset is constructed
2091 alignment.setDataset(null);
2093 alwidth = alignment.getWidth() + 1;
2097 AlignmentI pastedal = alignment; // preserve pasted alignment object
2098 // Add pasted sequences and dataset into existing alignment.
2099 alignment = viewport.getAlignment();
2100 alwidth = alignment.getWidth() + 1;
2101 // decide if we need to import sequences from an existing dataset
2102 boolean importDs = Desktop.jalviewClipboard != null
2103 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2104 // importDs==true instructs us to copy over new dataset sequences from
2105 // an existing alignment
2106 Vector newDs = (importDs) ? new Vector() : null; // used to create
2107 // minimum dataset set
2109 for (int i = 0; i < sequences.length; i++)
2113 newDs.addElement(null);
2115 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2117 if (importDs && ds != null)
2119 if (!newDs.contains(ds))
2121 newDs.setElementAt(ds, i);
2122 ds = new Sequence(ds);
2123 // update with new dataset sequence
2124 sequences[i].setDatasetSequence(ds);
2128 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2133 // copy and derive new dataset sequence
2134 sequences[i] = sequences[i].deriveSequence();
2135 alignment.getDataset().addSequence(
2136 sequences[i].getDatasetSequence());
2137 // TODO: avoid creation of duplicate dataset sequences with a
2138 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2140 alignment.addSequence(sequences[i]); // merges dataset
2144 newDs.clear(); // tidy up
2146 if (alignment.getAlignmentAnnotation() != null)
2148 for (AlignmentAnnotation alan : alignment
2149 .getAlignmentAnnotation())
2151 if (alan.graphGroup > fgroup)
2153 fgroup = alan.graphGroup;
2157 if (pastedal.getAlignmentAnnotation() != null)
2159 // Add any annotation attached to alignment.
2160 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2161 for (int i = 0; i < alann.length; i++)
2163 annotationAdded = true;
2164 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2166 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2167 if (newann.graphGroup > -1)
2169 if (newGraphGroups.size() <= newann.graphGroup
2170 || newGraphGroups.get(newann.graphGroup) == null)
2172 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2174 newGraphGroups.add(q, null);
2176 newGraphGroups.set(newann.graphGroup, new Integer(
2179 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2183 newann.padAnnotation(alwidth);
2184 alignment.addAnnotation(newann);
2194 addHistoryItem(new EditCommand(
2195 MessageManager.getString("label.add_sequences"),
2196 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2198 // Add any annotations attached to sequences
2199 for (int i = 0; i < sequences.length; i++)
2201 if (sequences[i].getAnnotation() != null)
2203 AlignmentAnnotation newann;
2204 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2206 annotationAdded = true;
2207 newann = sequences[i].getAnnotation()[a];
2208 newann.adjustForAlignment();
2209 newann.padAnnotation(alwidth);
2210 if (newann.graphGroup > -1)
2212 if (newann.graphGroup > -1)
2214 if (newGraphGroups.size() <= newann.graphGroup
2215 || newGraphGroups.get(newann.graphGroup) == null)
2217 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2219 newGraphGroups.add(q, null);
2221 newGraphGroups.set(newann.graphGroup, new Integer(
2224 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2228 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2233 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2240 // propagate alignment changed.
2241 vpRanges.setEndSeq(alignment.getHeight());
2242 if (annotationAdded)
2244 // Duplicate sequence annotation in all views.
2245 AlignmentI[] alview = this.getViewAlignments();
2246 for (int i = 0; i < sequences.length; i++)
2248 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2253 for (int avnum = 0; avnum < alview.length; avnum++)
2255 if (alview[avnum] != alignment)
2257 // duplicate in a view other than the one with input focus
2258 int avwidth = alview[avnum].getWidth() + 1;
2259 // this relies on sann being preserved after we
2260 // modify the sequence's annotation array for each duplication
2261 for (int a = 0; a < sann.length; a++)
2263 AlignmentAnnotation newann = new AlignmentAnnotation(
2265 sequences[i].addAlignmentAnnotation(newann);
2266 newann.padAnnotation(avwidth);
2267 alview[avnum].addAnnotation(newann); // annotation was
2268 // duplicated earlier
2269 // TODO JAL-1145 graphGroups are not updated for sequence
2270 // annotation added to several views. This may cause
2272 alview[avnum].setAnnotationIndex(newann, a);
2277 buildSortByAnnotationScoresMenu();
2279 viewport.firePropertyChange("alignment", null,
2280 alignment.getSequences());
2281 if (alignPanels != null)
2283 for (AlignmentPanel ap : alignPanels)
2285 ap.validateAnnotationDimensions(false);
2290 alignPanel.validateAnnotationDimensions(false);
2296 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2298 String newtitle = new String("Copied sequences");
2300 if (Desktop.jalviewClipboard != null
2301 && Desktop.jalviewClipboard[2] != null)
2303 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2304 for (int[] region : hc)
2306 af.viewport.hideColumns(region[0], region[1]);
2310 // >>>This is a fix for the moment, until a better solution is
2312 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2314 alignPanel.getSeqPanel().seqCanvas
2315 .getFeatureRenderer());
2317 // TODO: maintain provenance of an alignment, rather than just make the
2318 // title a concatenation of operations.
2321 if (title.startsWith("Copied sequences"))
2327 newtitle = newtitle.concat("- from " + title);
2332 newtitle = new String("Pasted sequences");
2335 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2340 } catch (Exception ex)
2342 ex.printStackTrace();
2343 System.out.println("Exception whilst pasting: " + ex);
2344 // could be anything being pasted in here
2349 protected void expand_newalign(ActionEvent e)
2353 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2354 .getAlignment(), -1);
2355 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2357 String newtitle = new String("Flanking alignment");
2359 if (Desktop.jalviewClipboard != null
2360 && Desktop.jalviewClipboard[2] != null)
2362 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2363 for (int region[] : hc)
2365 af.viewport.hideColumns(region[0], region[1]);
2369 // >>>This is a fix for the moment, until a better solution is
2371 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2373 alignPanel.getSeqPanel().seqCanvas
2374 .getFeatureRenderer());
2376 // TODO: maintain provenance of an alignment, rather than just make the
2377 // title a concatenation of operations.
2379 if (title.startsWith("Copied sequences"))
2385 newtitle = newtitle.concat("- from " + title);
2389 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2391 } catch (Exception ex)
2393 ex.printStackTrace();
2394 System.out.println("Exception whilst pasting: " + ex);
2395 // could be anything being pasted in here
2396 } catch (OutOfMemoryError oom)
2398 new OOMWarning("Viewing flanking region of alignment", oom);
2409 protected void cut_actionPerformed(ActionEvent e)
2411 copy_actionPerformed(null);
2412 delete_actionPerformed(null);
2422 protected void delete_actionPerformed(ActionEvent evt)
2425 SequenceGroup sg = viewport.getSelectionGroup();
2432 * If the cut affects all sequences, warn, remove highlighted columns
2434 if (sg.getSize() == viewport.getAlignment().getHeight())
2436 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2437 .getAlignment().getWidth()) ? true : false;
2438 if (isEntireAlignWidth)
2440 int confirm = JvOptionPane.showConfirmDialog(this,
2441 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2442 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2443 JvOptionPane.OK_CANCEL_OPTION);
2445 if (confirm == JvOptionPane.CANCEL_OPTION
2446 || confirm == JvOptionPane.CLOSED_OPTION)
2451 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2452 sg.getEndRes() + 1);
2454 SequenceI[] cut = sg.getSequences()
2455 .toArray(new SequenceI[sg.getSize()]);
2457 addHistoryItem(new EditCommand(
2458 MessageManager.getString("label.cut_sequences"), Action.CUT,
2459 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2460 viewport.getAlignment()));
2462 viewport.setSelectionGroup(null);
2463 viewport.sendSelection();
2464 viewport.getAlignment().deleteGroup(sg);
2466 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2468 if (viewport.getAlignment().getHeight() < 1)
2472 this.setClosed(true);
2473 } catch (Exception ex)
2486 protected void deleteGroups_actionPerformed(ActionEvent e)
2488 if (avc.deleteGroups())
2490 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2491 alignPanel.updateAnnotation();
2492 alignPanel.paintAlignment(true);
2503 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2505 SequenceGroup sg = new SequenceGroup();
2507 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2509 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2512 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2513 viewport.setSelectionGroup(sg);
2514 viewport.sendSelection();
2515 // JAL-2034 - should delegate to
2516 // alignPanel to decide if overview needs
2518 alignPanel.paintAlignment(false);
2519 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2529 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2531 if (viewport.cursorMode)
2533 alignPanel.getSeqPanel().keyboardNo1 = null;
2534 alignPanel.getSeqPanel().keyboardNo2 = null;
2536 viewport.setSelectionGroup(null);
2537 viewport.getColumnSelection().clear();
2538 viewport.setSelectionGroup(null);
2539 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2540 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2541 // JAL-2034 - should delegate to
2542 // alignPanel to decide if overview needs
2544 alignPanel.paintAlignment(false);
2545 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2546 viewport.sendSelection();
2556 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2558 SequenceGroup sg = viewport.getSelectionGroup();
2562 selectAllSequenceMenuItem_actionPerformed(null);
2567 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2569 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2571 // JAL-2034 - should delegate to
2572 // alignPanel to decide if overview needs
2575 alignPanel.paintAlignment(true);
2576 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2577 viewport.sendSelection();
2581 public void invertColSel_actionPerformed(ActionEvent e)
2583 viewport.invertColumnSelection();
2584 alignPanel.paintAlignment(true);
2585 viewport.sendSelection();
2595 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2597 trimAlignment(true);
2607 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2609 trimAlignment(false);
2612 void trimAlignment(boolean trimLeft)
2614 ColumnSelection colSel = viewport.getColumnSelection();
2617 if (!colSel.isEmpty())
2621 column = colSel.getMin();
2625 column = colSel.getMax();
2629 if (viewport.getSelectionGroup() != null)
2631 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2632 viewport.getHiddenRepSequences());
2636 seqs = viewport.getAlignment().getSequencesArray();
2639 TrimRegionCommand trimRegion;
2642 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2643 column, viewport.getAlignment());
2644 vpRanges.setStartRes(0);
2648 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2649 column, viewport.getAlignment());
2652 statusBar.setText(MessageManager.formatMessage(
2653 "label.removed_columns",
2654 new String[] { Integer.valueOf(trimRegion.getSize())
2657 addHistoryItem(trimRegion);
2659 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2661 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2662 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2664 viewport.getAlignment().deleteGroup(sg);
2668 viewport.firePropertyChange("alignment", null, viewport
2669 .getAlignment().getSequences());
2680 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2682 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2685 if (viewport.getSelectionGroup() != null)
2687 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2688 viewport.getHiddenRepSequences());
2689 start = viewport.getSelectionGroup().getStartRes();
2690 end = viewport.getSelectionGroup().getEndRes();
2694 seqs = viewport.getAlignment().getSequencesArray();
2697 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2698 "Remove Gapped Columns", seqs, start, end,
2699 viewport.getAlignment());
2701 addHistoryItem(removeGapCols);
2703 statusBar.setText(MessageManager.formatMessage(
2704 "label.removed_empty_columns",
2705 new Object[] { Integer.valueOf(removeGapCols.getSize())
2708 // This is to maintain viewport position on first residue
2709 // of first sequence
2710 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2711 int startRes = seq.findPosition(vpRanges.getStartRes());
2712 // ShiftList shifts;
2713 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2714 // edit.alColumnChanges=shifts.getInverse();
2715 // if (viewport.hasHiddenColumns)
2716 // viewport.getColumnSelection().compensateForEdits(shifts);
2717 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2718 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2730 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2732 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2735 if (viewport.getSelectionGroup() != null)
2737 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2738 viewport.getHiddenRepSequences());
2739 start = viewport.getSelectionGroup().getStartRes();
2740 end = viewport.getSelectionGroup().getEndRes();
2744 seqs = viewport.getAlignment().getSequencesArray();
2747 // This is to maintain viewport position on first residue
2748 // of first sequence
2749 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2750 int startRes = seq.findPosition(vpRanges.getStartRes());
2752 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2753 viewport.getAlignment()));
2755 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2757 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2769 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2771 viewport.setPadGaps(padGapsMenuitem.isSelected());
2772 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2783 public void findMenuItem_actionPerformed(ActionEvent e)
2789 * Create a new view of the current alignment.
2792 public void newView_actionPerformed(ActionEvent e)
2794 newView(null, true);
2798 * Creates and shows a new view of the current alignment.
2801 * title of newly created view; if null, one will be generated
2802 * @param copyAnnotation
2803 * if true then duplicate all annnotation, groups and settings
2804 * @return new alignment panel, already displayed.
2806 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2809 * Create a new AlignmentPanel (with its own, new Viewport)
2811 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2813 if (!copyAnnotation)
2816 * remove all groups and annotation except for the automatic stuff
2818 newap.av.getAlignment().deleteAllGroups();
2819 newap.av.getAlignment().deleteAllAnnotations(false);
2822 newap.av.setGatherViewsHere(false);
2824 if (viewport.viewName == null)
2826 viewport.viewName = MessageManager
2827 .getString("label.view_name_original");
2831 * Views share the same edits undo and redo stacks
2833 newap.av.setHistoryList(viewport.getHistoryList());
2834 newap.av.setRedoList(viewport.getRedoList());
2837 * Views share the same mappings; need to deregister any new mappings
2838 * created by copyAlignPanel, and register the new reference to the shared
2841 newap.av.replaceMappings(viewport.getAlignment());
2844 * start up cDNA consensus (if applicable) now mappings are in place
2846 if (newap.av.initComplementConsensus())
2848 newap.refresh(true); // adjust layout of annotations
2851 newap.av.viewName = getNewViewName(viewTitle);
2853 addAlignmentPanel(newap, true);
2854 newap.alignmentChanged();
2856 if (alignPanels.size() == 2)
2858 viewport.setGatherViewsHere(true);
2860 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2865 * Make a new name for the view, ensuring it is unique within the current
2866 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2867 * these now use viewId. Unique view names are still desirable for usability.)
2872 protected String getNewViewName(String viewTitle)
2874 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2875 boolean addFirstIndex = false;
2876 if (viewTitle == null || viewTitle.trim().length() == 0)
2878 viewTitle = MessageManager.getString("action.view");
2879 addFirstIndex = true;
2883 index = 1;// we count from 1 if given a specific name
2885 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2887 List<Component> comps = PaintRefresher.components.get(viewport
2888 .getSequenceSetId());
2890 List<String> existingNames = getExistingViewNames(comps);
2892 while (existingNames.contains(newViewName))
2894 newViewName = viewTitle + " " + (++index);
2900 * Returns a list of distinct view names found in the given list of
2901 * components. View names are held on the viewport of an AlignmentPanel.
2906 protected List<String> getExistingViewNames(List<Component> comps)
2908 List<String> existingNames = new ArrayList<>();
2909 for (Component comp : comps)
2911 if (comp instanceof AlignmentPanel)
2913 AlignmentPanel ap = (AlignmentPanel) comp;
2914 if (!existingNames.contains(ap.av.viewName))
2916 existingNames.add(ap.av.viewName);
2920 return existingNames;
2924 * Explode tabbed views into separate windows.
2927 public void expandViews_actionPerformed(ActionEvent e)
2929 Desktop.explodeViews(this);
2933 * Gather views in separate windows back into a tabbed presentation.
2936 public void gatherViews_actionPerformed(ActionEvent e)
2938 Desktop.instance.gatherViews(this);
2948 public void font_actionPerformed(ActionEvent e)
2950 new FontChooser(alignPanel);
2960 protected void seqLimit_actionPerformed(ActionEvent e)
2962 viewport.setShowJVSuffix(seqLimits.isSelected());
2964 alignPanel.getIdPanel().getIdCanvas()
2965 .setPreferredSize(alignPanel.calculateIdWidth());
2966 alignPanel.paintAlignment(true);
2970 public void idRightAlign_actionPerformed(ActionEvent e)
2972 viewport.setRightAlignIds(idRightAlign.isSelected());
2973 alignPanel.paintAlignment(true);
2977 public void centreColumnLabels_actionPerformed(ActionEvent e)
2979 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2980 alignPanel.paintAlignment(true);
2986 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2989 protected void followHighlight_actionPerformed()
2992 * Set the 'follow' flag on the Viewport (and scroll to position if now
2995 final boolean state = this.followHighlightMenuItem.getState();
2996 viewport.setFollowHighlight(state);
2999 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
3010 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3012 viewport.setColourText(colourTextMenuItem.isSelected());
3013 alignPanel.paintAlignment(true);
3023 public void wrapMenuItem_actionPerformed(ActionEvent e)
3025 scaleAbove.setVisible(wrapMenuItem.isSelected());
3026 scaleLeft.setVisible(wrapMenuItem.isSelected());
3027 scaleRight.setVisible(wrapMenuItem.isSelected());
3028 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3029 alignPanel.updateLayout();
3033 public void showAllSeqs_actionPerformed(ActionEvent e)
3035 viewport.showAllHiddenSeqs();
3039 public void showAllColumns_actionPerformed(ActionEvent e)
3041 viewport.showAllHiddenColumns();
3043 viewport.sendSelection();
3047 public void hideSelSequences_actionPerformed(ActionEvent e)
3049 viewport.hideAllSelectedSeqs();
3050 // alignPanel.paintAlignment(true);
3054 * called by key handler and the hide all/show all menu items
3059 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3062 boolean hide = false;
3063 SequenceGroup sg = viewport.getSelectionGroup();
3064 if (!toggleSeqs && !toggleCols)
3066 // Hide everything by the current selection - this is a hack - we do the
3067 // invert and then hide
3068 // first check that there will be visible columns after the invert.
3069 if (viewport.hasSelectedColumns()
3070 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3073 // now invert the sequence set, if required - empty selection implies
3074 // that no hiding is required.
3077 invertSequenceMenuItem_actionPerformed(null);
3078 sg = viewport.getSelectionGroup();
3082 viewport.expandColSelection(sg, true);
3083 // finally invert the column selection and get the new sequence
3085 invertColSel_actionPerformed(null);
3092 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3094 hideSelSequences_actionPerformed(null);
3097 else if (!(toggleCols && viewport.hasSelectedColumns()))
3099 showAllSeqs_actionPerformed(null);
3105 if (viewport.hasSelectedColumns())
3107 hideSelColumns_actionPerformed(null);
3110 viewport.setSelectionGroup(sg);
3115 showAllColumns_actionPerformed(null);
3124 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3125 * event.ActionEvent)
3128 public void hideAllButSelection_actionPerformed(ActionEvent e)
3130 toggleHiddenRegions(false, false);
3131 viewport.sendSelection();
3138 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3142 public void hideAllSelection_actionPerformed(ActionEvent e)
3144 SequenceGroup sg = viewport.getSelectionGroup();
3145 viewport.expandColSelection(sg, false);
3146 viewport.hideAllSelectedSeqs();
3147 viewport.hideSelectedColumns();
3148 alignPanel.paintAlignment(true);
3149 viewport.sendSelection();
3156 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3160 public void showAllhidden_actionPerformed(ActionEvent e)
3162 viewport.showAllHiddenColumns();
3163 viewport.showAllHiddenSeqs();
3164 alignPanel.paintAlignment(true);
3165 viewport.sendSelection();
3169 public void hideSelColumns_actionPerformed(ActionEvent e)
3171 viewport.hideSelectedColumns();
3172 alignPanel.paintAlignment(true);
3173 viewport.sendSelection();
3177 public void hiddenMarkers_actionPerformed(ActionEvent e)
3179 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3190 protected void scaleAbove_actionPerformed(ActionEvent e)
3192 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3193 alignPanel.paintAlignment(true);
3203 protected void scaleLeft_actionPerformed(ActionEvent e)
3205 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3206 alignPanel.paintAlignment(true);
3216 protected void scaleRight_actionPerformed(ActionEvent e)
3218 viewport.setScaleRightWrapped(scaleRight.isSelected());
3219 alignPanel.paintAlignment(true);
3229 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3231 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3232 alignPanel.paintAlignment(true);
3242 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3244 viewport.setShowText(viewTextMenuItem.isSelected());
3245 alignPanel.paintAlignment(true);
3255 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3257 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3258 alignPanel.paintAlignment(true);
3261 public FeatureSettings featureSettings;
3264 public FeatureSettingsControllerI getFeatureSettingsUI()
3266 return featureSettings;
3270 public void featureSettings_actionPerformed(ActionEvent e)
3272 if (featureSettings != null)
3274 featureSettings.close();
3275 featureSettings = null;
3277 if (!showSeqFeatures.isSelected())
3279 // make sure features are actually displayed
3280 showSeqFeatures.setSelected(true);
3281 showSeqFeatures_actionPerformed(null);
3283 featureSettings = new FeatureSettings(this);
3287 * Set or clear 'Show Sequence Features'
3293 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3295 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3296 alignPanel.paintAlignment(true);
3297 if (alignPanel.getOverviewPanel() != null)
3299 alignPanel.getOverviewPanel().updateOverviewImage();
3304 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3305 * the annotations panel as a whole.
3307 * The options to show/hide all annotations should be enabled when the panel
3308 * is shown, and disabled when the panel is hidden.
3313 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3315 final boolean setVisible = annotationPanelMenuItem.isSelected();
3316 viewport.setShowAnnotation(setVisible);
3317 this.showAllSeqAnnotations.setEnabled(setVisible);
3318 this.hideAllSeqAnnotations.setEnabled(setVisible);
3319 this.showAllAlAnnotations.setEnabled(setVisible);
3320 this.hideAllAlAnnotations.setEnabled(setVisible);
3321 alignPanel.updateLayout();
3325 public void alignmentProperties()
3327 JEditorPane editPane = new JEditorPane("text/html", "");
3328 editPane.setEditable(false);
3329 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3331 editPane.setText(MessageManager.formatMessage("label.html_content",
3332 new Object[] { contents.toString() }));
3333 JInternalFrame frame = new JInternalFrame();
3334 frame.getContentPane().add(new JScrollPane(editPane));
3336 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3337 "label.alignment_properties", new Object[] { getTitle() }),
3348 public void overviewMenuItem_actionPerformed(ActionEvent e)
3350 if (alignPanel.overviewPanel != null)
3355 JInternalFrame frame = new JInternalFrame();
3356 OverviewPanel overview = new OverviewPanel(alignPanel);
3357 frame.setContentPane(overview);
3358 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3359 "label.overview_params", new Object[] { this.getTitle() }),
3360 true, frame.getWidth(), frame.getHeight(), true, true);
3362 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3363 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3366 public void internalFrameClosed(
3367 javax.swing.event.InternalFrameEvent evt)
3369 alignPanel.setOverviewPanel(null);
3373 alignPanel.setOverviewPanel(overview);
3377 public void textColour_actionPerformed()
3379 new TextColourChooser().chooseColour(alignPanel, null);
3383 * public void covariationColour_actionPerformed() {
3385 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3389 public void annotationColour_actionPerformed()
3391 new AnnotationColourChooser(viewport, alignPanel);
3395 public void annotationColumn_actionPerformed(ActionEvent e)
3397 new AnnotationColumnChooser(viewport, alignPanel);
3401 * Action on the user checking or unchecking the option to apply the selected
3402 * colour scheme to all groups. If unchecked, groups may have their own
3403 * independent colour schemes.
3408 public void applyToAllGroups_actionPerformed(boolean selected)
3410 viewport.setColourAppliesToAllGroups(selected);
3414 * Action on user selecting a colour from the colour menu
3417 * the name (not the menu item label!) of the colour scheme
3420 public void changeColour_actionPerformed(String name)
3423 * 'User Defined' opens a panel to configure or load a
3424 * user-defined colour scheme
3426 if (ResidueColourScheme.USER_DEFINED.equals(name))
3428 new UserDefinedColours(alignPanel);
3433 * otherwise set the chosen colour scheme (or null for 'None')
3435 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3436 viewport.getAlignment(), viewport.getHiddenRepSequences());
3441 * Actions on setting or changing the alignment colour scheme
3446 public void changeColour(ColourSchemeI cs)
3448 // TODO: pull up to controller method
3449 ColourMenuHelper.setColourSelected(colourMenu, cs);
3451 viewport.setGlobalColourScheme(cs);
3453 alignPanel.paintAlignment(true);
3457 * Show the PID threshold slider panel
3460 protected void modifyPID_actionPerformed()
3462 SliderPanel.setPIDSliderSource(alignPanel,
3463 viewport.getResidueShading(), alignPanel.getViewName());
3464 SliderPanel.showPIDSlider();
3468 * Show the Conservation slider panel
3471 protected void modifyConservation_actionPerformed()
3473 SliderPanel.setConservationSlider(alignPanel,
3474 viewport.getResidueShading(), alignPanel.getViewName());
3475 SliderPanel.showConservationSlider();
3479 * Action on selecting or deselecting (Colour) By Conservation
3482 public void conservationMenuItem_actionPerformed(boolean selected)
3484 modifyConservation.setEnabled(selected);
3485 viewport.setConservationSelected(selected);
3486 viewport.getResidueShading().setConservationApplied(selected);
3488 changeColour(viewport.getGlobalColourScheme());
3491 modifyConservation_actionPerformed();
3495 SliderPanel.hideConservationSlider();
3500 * Action on selecting or deselecting (Colour) Above PID Threshold
3503 public void abovePIDThreshold_actionPerformed(boolean selected)
3505 modifyPID.setEnabled(selected);
3506 viewport.setAbovePIDThreshold(selected);
3509 viewport.getResidueShading().setThreshold(0,
3510 viewport.isIgnoreGapsConsensus());
3513 changeColour(viewport.getGlobalColourScheme());
3516 modifyPID_actionPerformed();
3520 SliderPanel.hidePIDSlider();
3531 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3533 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3534 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3535 .getAlignment().getSequenceAt(0));
3536 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3537 viewport.getAlignment()));
3538 alignPanel.paintAlignment(true);
3548 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3550 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3551 AlignmentSorter.sortByID(viewport.getAlignment());
3552 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3553 viewport.getAlignment()));
3554 alignPanel.paintAlignment(true);
3564 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3566 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3567 AlignmentSorter.sortByLength(viewport.getAlignment());
3568 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3569 viewport.getAlignment()));
3570 alignPanel.paintAlignment(true);
3580 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3582 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3583 AlignmentSorter.sortByGroup(viewport.getAlignment());
3584 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3585 viewport.getAlignment()));
3587 alignPanel.paintAlignment(true);
3597 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3599 new RedundancyPanel(alignPanel, this);
3609 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3611 if ((viewport.getSelectionGroup() == null)
3612 || (viewport.getSelectionGroup().getSize() < 2))
3614 JvOptionPane.showInternalMessageDialog(this, MessageManager
3615 .getString("label.you_must_select_least_two_sequences"),
3616 MessageManager.getString("label.invalid_selection"),
3617 JvOptionPane.WARNING_MESSAGE);
3621 JInternalFrame frame = new JInternalFrame();
3622 frame.setContentPane(new PairwiseAlignPanel(viewport));
3623 Desktop.addInternalFrame(frame,
3624 MessageManager.getString("action.pairwise_alignment"), 600,
3630 public void autoCalculate_actionPerformed(ActionEvent e)
3632 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3633 if (viewport.autoCalculateConsensus)
3635 viewport.firePropertyChange("alignment", null, viewport
3636 .getAlignment().getSequences());
3641 public void sortByTreeOption_actionPerformed(ActionEvent e)
3643 viewport.sortByTree = sortByTree.isSelected();
3647 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3649 viewport.followSelection = listenToViewSelections.isSelected();
3653 * Constructs a tree panel and adds it to the desktop
3656 * tree type (NJ or AV)
3658 * name of score model used to compute the tree
3660 * parameters for the distance or similarity calculation
3662 void newTreePanel(String type, String modelName, SimilarityParamsI options)
3664 String frameTitle = "";
3667 boolean onSelection = false;
3668 if (viewport.getSelectionGroup() != null
3669 && viewport.getSelectionGroup().getSize() > 0)
3671 SequenceGroup sg = viewport.getSelectionGroup();
3673 /* Decide if the selection is a column region */
3674 for (SequenceI _s : sg.getSequences())
3676 if (_s.getLength() < sg.getEndRes())
3682 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3684 .getString("label.sequences_selection_not_aligned"),
3685 JvOptionPane.WARNING_MESSAGE);
3694 if (viewport.getAlignment().getHeight() < 2)
3700 tp = new TreePanel(alignPanel, type, modelName, options);
3701 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3703 frameTitle += " from ";
3705 if (viewport.viewName != null)
3707 frameTitle += viewport.viewName + " of ";
3710 frameTitle += this.title;
3712 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3723 public void addSortByOrderMenuItem(String title,
3724 final AlignmentOrder order)
3726 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3727 "action.by_title_param", new Object[] { title }));
3729 item.addActionListener(new java.awt.event.ActionListener()
3732 public void actionPerformed(ActionEvent e)
3734 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3736 // TODO: JBPNote - have to map order entries to curent SequenceI
3738 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3740 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3743 alignPanel.paintAlignment(true);
3749 * Add a new sort by annotation score menu item
3752 * the menu to add the option to
3754 * the label used to retrieve scores for each sequence on the
3757 public void addSortByAnnotScoreMenuItem(JMenu sort,
3758 final String scoreLabel)
3760 final JMenuItem item = new JMenuItem(scoreLabel);
3762 item.addActionListener(new java.awt.event.ActionListener()
3765 public void actionPerformed(ActionEvent e)
3767 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3768 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3769 viewport.getAlignment());// ,viewport.getSelectionGroup());
3770 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3771 viewport.getAlignment()));
3772 alignPanel.paintAlignment(true);
3778 * last hash for alignment's annotation array - used to minimise cost of
3781 protected int _annotationScoreVectorHash;
3784 * search the alignment and rebuild the sort by annotation score submenu the
3785 * last alignment annotation vector hash is stored to minimize cost of
3786 * rebuilding in subsequence calls.
3790 public void buildSortByAnnotationScoresMenu()
3792 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3797 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3799 sortByAnnotScore.removeAll();
3800 // almost certainly a quicker way to do this - but we keep it simple
3801 Hashtable scoreSorts = new Hashtable();
3802 AlignmentAnnotation aann[];
3803 for (SequenceI sqa : viewport.getAlignment().getSequences())
3805 aann = sqa.getAnnotation();
3806 for (int i = 0; aann != null && i < aann.length; i++)
3808 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3810 scoreSorts.put(aann[i].label, aann[i].label);
3814 Enumeration labels = scoreSorts.keys();
3815 while (labels.hasMoreElements())
3817 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3818 (String) labels.nextElement());
3820 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3823 _annotationScoreVectorHash = viewport.getAlignment()
3824 .getAlignmentAnnotation().hashCode();
3829 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3830 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3831 * call. Listeners are added to remove the menu item when the treePanel is
3832 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3836 public void buildTreeSortMenu()
3838 sortByTreeMenu.removeAll();
3840 List<Component> comps = PaintRefresher.components.get(viewport
3841 .getSequenceSetId());
3842 List<TreePanel> treePanels = new ArrayList<>();
3843 for (Component comp : comps)
3845 if (comp instanceof TreePanel)
3847 treePanels.add((TreePanel) comp);
3851 if (treePanels.size() < 1)
3853 sortByTreeMenu.setVisible(false);
3857 sortByTreeMenu.setVisible(true);
3859 for (final TreePanel tp : treePanels)
3861 final JMenuItem item = new JMenuItem(tp.getTitle());
3862 item.addActionListener(new java.awt.event.ActionListener()
3865 public void actionPerformed(ActionEvent e)
3867 tp.sortByTree_actionPerformed();
3868 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3873 sortByTreeMenu.add(item);
3877 public boolean sortBy(AlignmentOrder alorder, String undoname)
3879 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3880 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3881 if (undoname != null)
3883 addHistoryItem(new OrderCommand(undoname, oldOrder,
3884 viewport.getAlignment()));
3886 alignPanel.paintAlignment(true);
3891 * Work out whether the whole set of sequences or just the selected set will
3892 * be submitted for multiple alignment.
3895 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3897 // Now, check we have enough sequences
3898 AlignmentView msa = null;
3900 if ((viewport.getSelectionGroup() != null)
3901 && (viewport.getSelectionGroup().getSize() > 1))
3903 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3904 // some common interface!
3906 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3907 * SequenceI[sz = seqs.getSize(false)];
3909 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3910 * seqs.getSequenceAt(i); }
3912 msa = viewport.getAlignmentView(true);
3914 else if (viewport.getSelectionGroup() != null
3915 && viewport.getSelectionGroup().getSize() == 1)
3917 int option = JvOptionPane.showConfirmDialog(this,
3918 MessageManager.getString("warn.oneseq_msainput_selection"),
3919 MessageManager.getString("label.invalid_selection"),
3920 JvOptionPane.OK_CANCEL_OPTION);
3921 if (option == JvOptionPane.OK_OPTION)
3923 msa = viewport.getAlignmentView(false);
3928 msa = viewport.getAlignmentView(false);
3934 * Decides what is submitted to a secondary structure prediction service: the
3935 * first sequence in the alignment, or in the current selection, or, if the
3936 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3937 * region or the whole alignment. (where the first sequence in the set is the
3938 * one that the prediction will be for).
3940 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3942 AlignmentView seqs = null;
3944 if ((viewport.getSelectionGroup() != null)
3945 && (viewport.getSelectionGroup().getSize() > 0))
3947 seqs = viewport.getAlignmentView(true);
3951 seqs = viewport.getAlignmentView(false);
3953 // limit sequences - JBPNote in future - could spawn multiple prediction
3955 // TODO: viewport.getAlignment().isAligned is a global state - the local
3956 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3957 if (!viewport.getAlignment().isAligned(false))
3959 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3960 // TODO: if seqs.getSequences().length>1 then should really have warned
3974 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3976 // Pick the tree file
3977 JalviewFileChooser chooser = new JalviewFileChooser(
3978 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3979 chooser.setFileView(new JalviewFileView());
3980 chooser.setDialogTitle(MessageManager
3981 .getString("label.select_newick_like_tree_file"));
3982 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3984 int value = chooser.showOpenDialog(null);
3986 if (value == JalviewFileChooser.APPROVE_OPTION)
3988 String filePath = chooser.getSelectedFile().getPath();
3989 Cache.setProperty("LAST_DIRECTORY", filePath);
3990 NewickFile fin = null;
3993 fin = new NewickFile(filePath, DataSourceType.FILE);
3994 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3995 } catch (Exception ex)
4002 .getString("label.problem_reading_tree_file"),
4003 JvOptionPane.WARNING_MESSAGE);
4004 ex.printStackTrace();
4006 if (fin != null && fin.hasWarningMessage())
4008 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4009 .getWarningMessage(), MessageManager
4010 .getString("label.possible_problem_with_tree_file"),
4011 JvOptionPane.WARNING_MESSAGE);
4016 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4018 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4021 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4022 int h, int x, int y)
4024 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4028 * Add a treeviewer for the tree extracted from a Newick file object to the
4029 * current alignment view
4036 * Associated alignment input data (or null)
4045 * @return TreePanel handle
4047 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4048 AlignmentView input, int w, int h, int x, int y)
4050 TreePanel tp = null;
4056 if (nf.getTree() != null)
4058 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4064 tp.setLocation(x, y);
4067 Desktop.addInternalFrame(tp, treeTitle, w, h);
4069 } catch (Exception ex)
4071 ex.printStackTrace();
4077 private boolean buildingMenu = false;
4080 * Generates menu items and listener event actions for web service clients
4083 public void BuildWebServiceMenu()
4085 while (buildingMenu)
4089 System.err.println("Waiting for building menu to finish.");
4091 } catch (Exception e)
4095 final AlignFrame me = this;
4096 buildingMenu = true;
4097 new Thread(new Runnable()
4102 final List<JMenuItem> legacyItems = new ArrayList<>();
4105 // System.err.println("Building ws menu again "
4106 // + Thread.currentThread());
4107 // TODO: add support for context dependent disabling of services based
4109 // alignment and current selection
4110 // TODO: add additional serviceHandle parameter to specify abstract
4112 // class independently of AbstractName
4113 // TODO: add in rediscovery GUI function to restart discoverer
4114 // TODO: group services by location as well as function and/or
4116 // object broker mechanism.
4117 final Vector<JMenu> wsmenu = new Vector<>();
4118 final IProgressIndicator af = me;
4121 * do not i18n these strings - they are hard-coded in class
4122 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4123 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4125 final JMenu msawsmenu = new JMenu("Alignment");
4126 final JMenu secstrmenu = new JMenu(
4127 "Secondary Structure Prediction");
4128 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4129 final JMenu analymenu = new JMenu("Analysis");
4130 final JMenu dismenu = new JMenu("Protein Disorder");
4131 // JAL-940 - only show secondary structure prediction services from
4132 // the legacy server
4133 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4135 Discoverer.services != null && (Discoverer.services.size() > 0))
4137 // TODO: refactor to allow list of AbstractName/Handler bindings to
4139 // stored or retrieved from elsewhere
4140 // No MSAWS used any more:
4141 // Vector msaws = null; // (Vector)
4142 // Discoverer.services.get("MsaWS");
4143 Vector secstrpr = (Vector) Discoverer.services
4145 if (secstrpr != null)
4147 // Add any secondary structure prediction services
4148 for (int i = 0, j = secstrpr.size(); i < j; i++)
4150 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4152 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4153 .getServiceClient(sh);
4154 int p = secstrmenu.getItemCount();
4155 impl.attachWSMenuEntry(secstrmenu, me);
4156 int q = secstrmenu.getItemCount();
4157 for (int litm = p; litm < q; litm++)
4159 legacyItems.add(secstrmenu.getItem(litm));
4165 // Add all submenus in the order they should appear on the web
4167 wsmenu.add(msawsmenu);
4168 wsmenu.add(secstrmenu);
4169 wsmenu.add(dismenu);
4170 wsmenu.add(analymenu);
4171 // No search services yet
4172 // wsmenu.add(seqsrchmenu);
4174 javax.swing.SwingUtilities.invokeLater(new Runnable()
4181 webService.removeAll();
4182 // first, add discovered services onto the webservices menu
4183 if (wsmenu.size() > 0)
4185 for (int i = 0, j = wsmenu.size(); i < j; i++)
4187 webService.add(wsmenu.get(i));
4192 webService.add(me.webServiceNoServices);
4194 // TODO: move into separate menu builder class.
4195 boolean new_sspred = false;
4196 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4198 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4199 if (jws2servs != null)
4201 if (jws2servs.hasServices())
4203 jws2servs.attachWSMenuEntry(webService, me);
4204 for (Jws2Instance sv : jws2servs.getServices())
4206 if (sv.description.toLowerCase().contains("jpred"))
4208 for (JMenuItem jmi : legacyItems)
4210 jmi.setVisible(false);
4216 if (jws2servs.isRunning())
4218 JMenuItem tm = new JMenuItem(
4219 "Still discovering JABA Services");
4220 tm.setEnabled(false);
4225 build_urlServiceMenu(me.webService);
4226 build_fetchdbmenu(webService);
4227 for (JMenu item : wsmenu)
4229 if (item.getItemCount() == 0)
4231 item.setEnabled(false);
4235 item.setEnabled(true);
4238 } catch (Exception e)
4241 .debug("Exception during web service menu building process.",
4246 } catch (Exception e)
4249 buildingMenu = false;
4256 * construct any groupURL type service menu entries.
4260 private void build_urlServiceMenu(JMenu webService)
4262 // TODO: remove this code when 2.7 is released
4263 // DEBUG - alignmentView
4265 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4266 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4268 * @Override public void actionPerformed(ActionEvent e) {
4269 * jalview.datamodel.AlignmentView
4270 * .testSelectionViews(af.viewport.getAlignment(),
4271 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4273 * }); webService.add(testAlView);
4275 // TODO: refactor to RestClient discoverer and merge menu entries for
4276 // rest-style services with other types of analysis/calculation service
4277 // SHmmr test client - still being implemented.
4278 // DEBUG - alignmentView
4280 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4283 client.attachWSMenuEntry(
4284 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4290 * Searches the alignment sequences for xRefs and builds the Show
4291 * Cross-References menu (formerly called Show Products), with database
4292 * sources for which cross-references are found (protein sources for a
4293 * nucleotide alignment and vice versa)
4295 * @return true if Show Cross-references menu should be enabled
4297 public boolean canShowProducts()
4299 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4300 AlignmentI dataset = viewport.getAlignment().getDataset();
4302 showProducts.removeAll();
4303 final boolean dna = viewport.getAlignment().isNucleotide();
4305 if (seqs == null || seqs.length == 0)
4307 // nothing to see here.
4311 boolean showp = false;
4314 List<String> ptypes = new CrossRef(seqs, dataset)
4315 .findXrefSourcesForSequences(dna);
4317 for (final String source : ptypes)
4320 final AlignFrame af = this;
4321 JMenuItem xtype = new JMenuItem(source);
4322 xtype.addActionListener(new ActionListener()
4325 public void actionPerformed(ActionEvent e)
4327 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4330 showProducts.add(xtype);
4332 showProducts.setVisible(showp);
4333 showProducts.setEnabled(showp);
4334 } catch (Exception e)
4337 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4345 * Finds and displays cross-references for the selected sequences (protein
4346 * products for nucleotide sequences, dna coding sequences for peptides).
4349 * the sequences to show cross-references for
4351 * true if from a nucleotide alignment (so showing proteins)
4353 * the database to show cross-references for
4355 protected void showProductsFor(final SequenceI[] sel,
4356 final boolean _odna, final String source)
4358 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4363 * Construct and display a new frame containing the translation of this
4364 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4367 public void showTranslation_actionPerformed(ActionEvent e)
4369 AlignmentI al = null;
4372 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4374 al = dna.translateCdna();
4375 } catch (Exception ex)
4377 jalview.bin.Cache.log.error(
4378 "Exception during translation. Please report this !", ex);
4379 final String msg = MessageManager
4380 .getString("label.error_when_translating_sequences_submit_bug_report");
4381 final String errorTitle = MessageManager
4382 .getString("label.implementation_error")
4383 + MessageManager.getString("label.translation_failed");
4384 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4385 JvOptionPane.ERROR_MESSAGE);
4388 if (al == null || al.getHeight() == 0)
4390 final String msg = MessageManager
4391 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4392 final String errorTitle = MessageManager
4393 .getString("label.translation_failed");
4394 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4395 JvOptionPane.WARNING_MESSAGE);
4399 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4400 af.setFileFormat(this.currentFileFormat);
4401 final String newTitle = MessageManager.formatMessage(
4402 "label.translation_of_params",
4403 new Object[] { this.getTitle() });
4404 af.setTitle(newTitle);
4405 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4407 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4408 viewport.openSplitFrame(af, new Alignment(seqs));
4412 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4419 * Set the file format
4423 public void setFileFormat(FileFormatI format)
4425 this.currentFileFormat = format;
4429 * Try to load a features file onto the alignment.
4432 * contents or path to retrieve file
4434 * access mode of file (see jalview.io.AlignFile)
4435 * @return true if features file was parsed correctly.
4437 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4439 return avc.parseFeaturesFile(file, sourceType,
4440 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4445 public void refreshFeatureUI(boolean enableIfNecessary)
4447 // note - currently this is only still here rather than in the controller
4448 // because of the featureSettings hard reference that is yet to be
4450 if (enableIfNecessary)
4452 viewport.setShowSequenceFeatures(true);
4453 showSeqFeatures.setSelected(true);
4459 public void dragEnter(DropTargetDragEvent evt)
4464 public void dragExit(DropTargetEvent evt)
4469 public void dragOver(DropTargetDragEvent evt)
4474 public void dropActionChanged(DropTargetDragEvent evt)
4479 public void drop(DropTargetDropEvent evt)
4481 // JAL-1552 - acceptDrop required before getTransferable call for
4482 // Java's Transferable for native dnd
4483 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4484 Transferable t = evt.getTransferable();
4485 List<String> files = new ArrayList<>();
4486 List<DataSourceType> protocols = new ArrayList<>();
4490 Desktop.transferFromDropTarget(files, protocols, evt, t);
4491 } catch (Exception e)
4493 e.printStackTrace();
4499 // check to see if any of these files have names matching sequences in
4501 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4502 .getAlignment().getSequencesArray());
4504 * Object[] { String,SequenceI}
4506 ArrayList<Object[]> filesmatched = new ArrayList<>();
4507 ArrayList<String> filesnotmatched = new ArrayList<>();
4508 for (int i = 0; i < files.size(); i++)
4510 String file = files.get(i).toString();
4512 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4513 if (protocol == DataSourceType.FILE)
4515 File fl = new File(file);
4516 pdbfn = fl.getName();
4518 else if (protocol == DataSourceType.URL)
4520 URL url = new URL(file);
4521 pdbfn = url.getFile();
4523 if (pdbfn.length() > 0)
4525 // attempt to find a match in the alignment
4526 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4527 int l = 0, c = pdbfn.indexOf(".");
4528 while (mtch == null && c != -1)
4533 } while ((c = pdbfn.indexOf(".", l)) > l);
4536 pdbfn = pdbfn.substring(0, l);
4538 mtch = idm.findAllIdMatches(pdbfn);
4542 FileFormatI type = null;
4545 type = new IdentifyFile().identify(file, protocol);
4546 } catch (Exception ex)
4550 if (type != null && type.isStructureFile())
4552 filesmatched.add(new Object[] { file, protocol, mtch });
4556 // File wasn't named like one of the sequences or wasn't a PDB file.
4557 filesnotmatched.add(file);
4561 if (filesmatched.size() > 0)
4563 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4569 "label.automatically_associate_structure_files_with_sequences_same_name",
4570 new Object[] { Integer
4576 .getString("label.automatically_associate_structure_files_by_name"),
4577 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4580 for (Object[] fm : filesmatched)
4582 // try and associate
4583 // TODO: may want to set a standard ID naming formalism for
4584 // associating PDB files which have no IDs.
4585 for (SequenceI toassoc : (SequenceI[]) fm[2])
4587 PDBEntry pe = new AssociatePdbFileWithSeq()
4588 .associatePdbWithSeq((String) fm[0],
4589 (DataSourceType) fm[1], toassoc, false,
4593 System.err.println("Associated file : "
4594 + ((String) fm[0]) + " with "
4595 + toassoc.getDisplayId(true));
4599 alignPanel.paintAlignment(true);
4603 if (filesnotmatched.size() > 0)
4606 && (Cache.getDefault(
4607 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4613 "label.ignore_unmatched_dropped_files_info",
4614 new Object[] { Integer
4621 .getString("label.ignore_unmatched_dropped_files"),
4622 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4626 for (String fn : filesnotmatched)
4628 loadJalviewDataFile(fn, null, null, null);
4632 } catch (Exception ex)
4634 ex.printStackTrace();
4640 * Attempt to load a "dropped" file or URL string, by testing in turn for
4642 * <li>an Annotation file</li>
4643 * <li>a JNet file</li>
4644 * <li>a features file</li>
4645 * <li>else try to interpret as an alignment file</li>
4649 * either a filename or a URL string.
4650 * @throws InterruptedException
4651 * @throws IOException
4653 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4654 FileFormatI format, SequenceI assocSeq)
4658 if (sourceType == null)
4660 sourceType = FormatAdapter.checkProtocol(file);
4662 // if the file isn't identified, or not positively identified as some
4663 // other filetype (PFAM is default unidentified alignment file type) then
4664 // try to parse as annotation.
4665 boolean isAnnotation = (format == null || FileFormat.Pfam
4666 .equals(format)) ? new AnnotationFile()
4667 .annotateAlignmentView(viewport, file, sourceType) : false;
4671 // first see if its a T-COFFEE score file
4672 TCoffeeScoreFile tcf = null;
4675 tcf = new TCoffeeScoreFile(file, sourceType);
4678 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4681 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4682 isAnnotation = true;
4684 .setText(MessageManager
4685 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4689 // some problem - if no warning its probable that the ID matching
4690 // process didn't work
4694 tcf.getWarningMessage() == null ? MessageManager
4695 .getString("label.check_file_matches_sequence_ids_alignment")
4696 : tcf.getWarningMessage(),
4698 .getString("label.problem_reading_tcoffee_score_file"),
4699 JvOptionPane.WARNING_MESSAGE);
4706 } catch (Exception x)
4709 .debug("Exception when processing data source as T-COFFEE score file",
4715 // try to see if its a JNet 'concise' style annotation file *before*
4717 // try to parse it as a features file
4720 format = new IdentifyFile().identify(file, sourceType);
4722 if (FileFormat.ScoreMatrix == format)
4724 ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4727 // todo: i18n this message
4729 .setText(MessageManager.formatMessage(
4730 "label.successfully_loaded_matrix",
4731 sm.getMatrixName()));
4733 else if (FileFormat.Jnet.equals(format))
4735 JPredFile predictions = new JPredFile(file, sourceType);
4736 new JnetAnnotationMaker();
4737 JnetAnnotationMaker.add_annotation(predictions,
4738 viewport.getAlignment(), 0, false);
4739 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4740 viewport.getAlignment().setSeqrep(repseq);
4741 HiddenColumns cs = new HiddenColumns();
4742 cs.hideInsertionsFor(repseq);
4743 viewport.getAlignment().setHiddenColumns(cs);
4744 isAnnotation = true;
4746 // else if (IdentifyFile.FeaturesFile.equals(format))
4747 else if (FileFormat.Features.equals(format))
4749 if (parseFeaturesFile(file, sourceType))
4751 alignPanel.paintAlignment(true);
4756 new FileLoader().LoadFile(viewport, file, sourceType, format);
4762 alignPanel.adjustAnnotationHeight();
4763 viewport.updateSequenceIdColours();
4764 buildSortByAnnotationScoresMenu();
4765 alignPanel.paintAlignment(true);
4767 } catch (Exception ex)
4769 ex.printStackTrace();
4770 } catch (OutOfMemoryError oom)
4775 } catch (Exception x)
4780 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4781 : "using " + sourceType + " from " + file)
4783 + (format != null ? "(parsing as '" + format
4784 + "' file)" : ""), oom, Desktop.desktop);
4789 * Method invoked by the ChangeListener on the tabbed pane, in other words
4790 * when a different tabbed pane is selected by the user or programmatically.
4793 public void tabSelectionChanged(int index)
4797 alignPanel = alignPanels.get(index);
4798 viewport = alignPanel.av;
4799 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4800 setMenusFromViewport(viewport);
4804 * 'focus' any colour slider that is open to the selected viewport
4806 if (viewport.getConservationSelected())
4808 SliderPanel.setConservationSlider(alignPanel,
4809 viewport.getResidueShading(), alignPanel.getViewName());
4813 SliderPanel.hideConservationSlider();
4815 if (viewport.getAbovePIDThreshold())
4817 SliderPanel.setPIDSliderSource(alignPanel,
4818 viewport.getResidueShading(), alignPanel.getViewName());
4822 SliderPanel.hidePIDSlider();
4826 * If there is a frame linked to this one in a SplitPane, switch it to the
4827 * same view tab index. No infinite recursion of calls should happen, since
4828 * tabSelectionChanged() should not get invoked on setting the selected
4829 * index to an unchanged value. Guard against setting an invalid index
4830 * before the new view peer tab has been created.
4832 final AlignViewportI peer = viewport.getCodingComplement();
4835 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4836 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4838 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4844 * On right mouse click on view tab, prompt for and set new view name.
4847 public void tabbedPane_mousePressed(MouseEvent e)
4849 if (e.isPopupTrigger())
4851 String msg = MessageManager.getString("label.enter_view_name");
4852 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4853 JvOptionPane.QUESTION_MESSAGE);
4857 viewport.viewName = reply;
4858 // TODO warn if reply is in getExistingViewNames()?
4859 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4864 public AlignViewport getCurrentView()
4870 * Open the dialog for regex description parsing.
4873 protected void extractScores_actionPerformed(ActionEvent e)
4875 ParseProperties pp = new jalview.analysis.ParseProperties(
4876 viewport.getAlignment());
4877 // TODO: verify regex and introduce GUI dialog for version 2.5
4878 // if (pp.getScoresFromDescription("col", "score column ",
4879 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4881 if (pp.getScoresFromDescription("description column",
4882 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4884 buildSortByAnnotationScoresMenu();
4892 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4896 protected void showDbRefs_actionPerformed(ActionEvent e)
4898 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4904 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4908 protected void showNpFeats_actionPerformed(ActionEvent e)
4910 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4914 * find the viewport amongst the tabs in this alignment frame and close that
4919 public boolean closeView(AlignViewportI av)
4923 this.closeMenuItem_actionPerformed(false);
4926 Component[] comp = tabbedPane.getComponents();
4927 for (int i = 0; comp != null && i < comp.length; i++)
4929 if (comp[i] instanceof AlignmentPanel)
4931 if (((AlignmentPanel) comp[i]).av == av)
4934 closeView((AlignmentPanel) comp[i]);
4942 protected void build_fetchdbmenu(JMenu webService)
4944 // Temporary hack - DBRef Fetcher always top level ws entry.
4945 // TODO We probably want to store a sequence database checklist in
4946 // preferences and have checkboxes.. rather than individual sources selected
4948 final JMenu rfetch = new JMenu(
4949 MessageManager.getString("action.fetch_db_references"));
4950 rfetch.setToolTipText(MessageManager
4951 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4952 webService.add(rfetch);
4954 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4955 MessageManager.getString("option.trim_retrieved_seqs"));
4956 trimrs.setToolTipText(MessageManager
4957 .getString("label.trim_retrieved_sequences"));
4958 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4959 trimrs.addActionListener(new ActionListener()
4962 public void actionPerformed(ActionEvent e)
4964 trimrs.setSelected(trimrs.isSelected());
4965 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4966 Boolean.valueOf(trimrs.isSelected()).toString());
4970 JMenuItem fetchr = new JMenuItem(
4971 MessageManager.getString("label.standard_databases"));
4972 fetchr.setToolTipText(MessageManager
4973 .getString("label.fetch_embl_uniprot"));
4974 fetchr.addActionListener(new ActionListener()
4978 public void actionPerformed(ActionEvent e)
4980 new Thread(new Runnable()
4985 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4986 .getAlignment().isNucleotide();
4987 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4988 .getSequenceSelection(), alignPanel.alignFrame, null,
4989 alignPanel.alignFrame.featureSettings, isNucleotide);
4990 dbRefFetcher.addListener(new FetchFinishedListenerI()
4993 public void finished()
4995 AlignFrame.this.setMenusForViewport();
4998 dbRefFetcher.fetchDBRefs(false);
5006 final AlignFrame me = this;
5007 new Thread(new Runnable()
5012 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5013 .getSequenceFetcherSingleton(me);
5014 javax.swing.SwingUtilities.invokeLater(new Runnable()
5019 String[] dbclasses = sf.getOrderedSupportedSources();
5020 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5021 // jalview.util.QuickSort.sort(otherdb, otherdb);
5022 List<DbSourceProxy> otherdb;
5023 JMenu dfetch = new JMenu();
5024 JMenu ifetch = new JMenu();
5025 JMenuItem fetchr = null;
5026 int comp = 0, icomp = 0, mcomp = 15;
5027 String mname = null;
5029 for (String dbclass : dbclasses)
5031 otherdb = sf.getSourceProxy(dbclass);
5032 // add a single entry for this class, or submenu allowing 'fetch
5034 if (otherdb == null || otherdb.size() < 1)
5038 // List<DbSourceProxy> dbs=otherdb;
5039 // otherdb=new ArrayList<DbSourceProxy>();
5040 // for (DbSourceProxy db:dbs)
5042 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5046 mname = "From " + dbclass;
5048 if (otherdb.size() == 1)
5050 final DbSourceProxy[] dassource = otherdb
5051 .toArray(new DbSourceProxy[0]);
5052 DbSourceProxy src = otherdb.get(0);
5053 fetchr = new JMenuItem(src.getDbSource());
5054 fetchr.addActionListener(new ActionListener()
5058 public void actionPerformed(ActionEvent e)
5060 new Thread(new Runnable()
5066 boolean isNucleotide = alignPanel.alignFrame
5067 .getViewport().getAlignment()
5069 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5070 alignPanel.av.getSequenceSelection(),
5071 alignPanel.alignFrame, dassource,
5072 alignPanel.alignFrame.featureSettings,
5075 .addListener(new FetchFinishedListenerI()
5078 public void finished()
5080 AlignFrame.this.setMenusForViewport();
5083 dbRefFetcher.fetchDBRefs(false);
5089 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5090 MessageManager.formatMessage(
5091 "label.fetch_retrieve_from",
5092 new Object[] { src.getDbName() })));
5098 final DbSourceProxy[] dassource = otherdb
5099 .toArray(new DbSourceProxy[0]);
5101 DbSourceProxy src = otherdb.get(0);
5102 fetchr = new JMenuItem(MessageManager.formatMessage(
5103 "label.fetch_all_param",
5104 new Object[] { src.getDbSource() }));
5105 fetchr.addActionListener(new ActionListener()
5108 public void actionPerformed(ActionEvent e)
5110 new Thread(new Runnable()
5116 boolean isNucleotide = alignPanel.alignFrame
5117 .getViewport().getAlignment()
5119 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5120 alignPanel.av.getSequenceSelection(),
5121 alignPanel.alignFrame, dassource,
5122 alignPanel.alignFrame.featureSettings,
5125 .addListener(new FetchFinishedListenerI()
5128 public void finished()
5130 AlignFrame.this.setMenusForViewport();
5133 dbRefFetcher.fetchDBRefs(false);
5139 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5140 MessageManager.formatMessage(
5141 "label.fetch_retrieve_from_all_sources",
5143 Integer.valueOf(otherdb.size())
5144 .toString(), src.getDbSource(),
5145 src.getDbName() })));
5148 // and then build the rest of the individual menus
5149 ifetch = new JMenu(MessageManager.formatMessage(
5150 "label.source_from_db_source",
5151 new Object[] { src.getDbSource() }));
5153 String imname = null;
5155 for (DbSourceProxy sproxy : otherdb)
5157 String dbname = sproxy.getDbName();
5158 String sname = dbname.length() > 5 ? dbname.substring(0,
5159 5) + "..." : dbname;
5160 String msname = dbname.length() > 10 ? dbname.substring(
5161 0, 10) + "..." : dbname;
5164 imname = MessageManager.formatMessage(
5165 "label.from_msname", new Object[] { sname });
5167 fetchr = new JMenuItem(msname);
5168 final DbSourceProxy[] dassrc = { sproxy };
5169 fetchr.addActionListener(new ActionListener()
5173 public void actionPerformed(ActionEvent e)
5175 new Thread(new Runnable()
5181 boolean isNucleotide = alignPanel.alignFrame
5182 .getViewport().getAlignment()
5184 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5185 alignPanel.av.getSequenceSelection(),
5186 alignPanel.alignFrame, dassrc,
5187 alignPanel.alignFrame.featureSettings,
5190 .addListener(new FetchFinishedListenerI()
5193 public void finished()
5195 AlignFrame.this.setMenusForViewport();
5198 dbRefFetcher.fetchDBRefs(false);
5204 fetchr.setToolTipText("<html>"
5205 + MessageManager.formatMessage(
5206 "label.fetch_retrieve_from", new Object[]
5210 if (++icomp >= mcomp || i == (otherdb.size()))
5212 ifetch.setText(MessageManager.formatMessage(
5213 "label.source_to_target", imname, sname));
5215 ifetch = new JMenu();
5223 if (comp >= mcomp || dbi >= (dbclasses.length))
5225 dfetch.setText(MessageManager.formatMessage(
5226 "label.source_to_target", mname, dbclass));
5228 dfetch = new JMenu();
5241 * Left justify the whole alignment.
5244 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5246 AlignmentI al = viewport.getAlignment();
5248 viewport.firePropertyChange("alignment", null, al);
5252 * Right justify the whole alignment.
5255 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5257 AlignmentI al = viewport.getAlignment();
5259 viewport.firePropertyChange("alignment", null, al);
5263 public void setShowSeqFeatures(boolean b)
5265 showSeqFeatures.setSelected(b);
5266 viewport.setShowSequenceFeatures(b);
5273 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5274 * awt.event.ActionEvent)
5277 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5279 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5280 alignPanel.paintAlignment(true);
5287 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5291 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5293 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5294 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5302 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5303 * .event.ActionEvent)
5306 protected void showGroupConservation_actionPerformed(ActionEvent e)
5308 viewport.setShowGroupConservation(showGroupConservation.getState());
5309 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5316 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5317 * .event.ActionEvent)
5320 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5322 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5323 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5330 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5331 * .event.ActionEvent)
5334 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5336 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5337 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5341 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5343 showSequenceLogo.setState(true);
5344 viewport.setShowSequenceLogo(true);
5345 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5346 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5350 protected void showInformationHistogram_actionPerformed(ActionEvent e)
5352 viewport.setShowInformationHistogram(
5353 showInformationHistogram.getState());
5354 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5358 protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5360 viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5361 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5365 protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5367 showHMMSequenceLogo.setState(true);
5368 viewport.setShowHMMSequenceLogo(true);
5369 viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5370 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5374 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5376 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5383 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5384 * .event.ActionEvent)
5387 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5389 if (avc.makeGroupsFromSelection())
5391 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5392 alignPanel.updateAnnotation();
5393 alignPanel.paintAlignment(true);
5397 public void clearAlignmentSeqRep()
5399 // TODO refactor alignmentseqrep to controller
5400 if (viewport.getAlignment().hasSeqrep())
5402 viewport.getAlignment().setSeqrep(null);
5403 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5404 alignPanel.updateAnnotation();
5405 alignPanel.paintAlignment(true);
5410 protected void createGroup_actionPerformed(ActionEvent e)
5412 if (avc.createGroup())
5414 alignPanel.alignmentChanged();
5419 protected void unGroup_actionPerformed(ActionEvent e)
5423 alignPanel.alignmentChanged();
5428 * make the given alignmentPanel the currently selected tab
5430 * @param alignmentPanel
5432 public void setDisplayedView(AlignmentPanel alignmentPanel)
5434 if (!viewport.getSequenceSetId().equals(
5435 alignmentPanel.av.getSequenceSetId()))
5439 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5441 if (tabbedPane != null
5442 && tabbedPane.getTabCount() > 0
5443 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5444 .getSelectedIndex())
5446 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5451 * Action on selection of menu options to Show or Hide annotations.
5454 * @param forSequences
5455 * update sequence-related annotations
5456 * @param forAlignment
5457 * update non-sequence-related annotations
5460 protected void setAnnotationsVisibility(boolean visible,
5461 boolean forSequences, boolean forAlignment)
5463 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5464 .getAlignmentAnnotation();
5469 for (AlignmentAnnotation aa : anns)
5472 * don't display non-positional annotations on an alignment
5474 if (aa.annotations == null)
5478 boolean apply = (aa.sequenceRef == null && forAlignment)
5479 || (aa.sequenceRef != null && forSequences);
5482 aa.visible = visible;
5485 alignPanel.validateAnnotationDimensions(true);
5486 alignPanel.alignmentChanged();
5490 * Store selected annotation sort order for the view and repaint.
5493 protected void sortAnnotations_actionPerformed()
5495 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5497 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5498 alignPanel.paintAlignment(true);
5503 * @return alignment panels in this alignment frame
5505 public List<? extends AlignmentViewPanel> getAlignPanels()
5507 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5511 * Open a new alignment window, with the cDNA associated with this (protein)
5512 * alignment, aligned as is the protein.
5514 protected void viewAsCdna_actionPerformed()
5516 // TODO no longer a menu action - refactor as required
5517 final AlignmentI alignment = getViewport().getAlignment();
5518 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5519 if (mappings == null)
5523 List<SequenceI> cdnaSeqs = new ArrayList<>();
5524 for (SequenceI aaSeq : alignment.getSequences())
5526 for (AlignedCodonFrame acf : mappings)
5528 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5532 * There is a cDNA mapping for this protein sequence - add to new
5533 * alignment. It will share the same dataset sequence as other mapped
5534 * cDNA (no new mappings need to be created).
5536 final Sequence newSeq = new Sequence(dnaSeq);
5537 newSeq.setDatasetSequence(dnaSeq);
5538 cdnaSeqs.add(newSeq);
5542 if (cdnaSeqs.size() == 0)
5544 // show a warning dialog no mapped cDNA
5547 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5549 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5550 AlignFrame.DEFAULT_HEIGHT);
5551 cdna.alignAs(alignment);
5552 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5554 Desktop.addInternalFrame(alignFrame, newtitle,
5555 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5559 * Set visibility of dna/protein complement view (available when shown in a
5565 protected void showComplement_actionPerformed(boolean show)
5567 SplitContainerI sf = getSplitViewContainer();
5570 sf.setComplementVisible(this, show);
5575 * Generate the reverse (optionally complemented) of the selected sequences,
5576 * and add them to the alignment
5579 protected void showReverse_actionPerformed(boolean complement)
5581 AlignmentI al = null;
5584 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5585 al = dna.reverseCdna(complement);
5586 viewport.addAlignment(al, "");
5587 addHistoryItem(new EditCommand(
5588 MessageManager.getString("label.add_sequences"),
5589 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5590 viewport.getAlignment()));
5591 } catch (Exception ex)
5593 System.err.println(ex.getMessage());
5599 * Try to run a script in the Groovy console, having first ensured that this
5600 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5601 * be targeted at this alignment.
5604 protected void runGroovy_actionPerformed()
5606 Jalview.setCurrentAlignFrame(this);
5607 groovy.ui.Console console = Desktop.getGroovyConsole();
5608 if (console != null)
5612 console.runScript();
5613 } catch (Exception ex)
5615 System.err.println((ex.toString()));
5617 .showInternalMessageDialog(Desktop.desktop, MessageManager
5618 .getString("label.couldnt_run_groovy_script"),
5620 .getString("label.groovy_support_failed"),
5621 JvOptionPane.ERROR_MESSAGE);
5626 System.err.println("Can't run Groovy script as console not found");
5631 * Hides columns containing (or not containing) a specified feature, provided
5632 * that would not leave all columns hidden
5634 * @param featureType
5635 * @param columnsContaining
5638 public boolean hideFeatureColumns(String featureType,
5639 boolean columnsContaining)
5641 boolean notForHiding = avc.markColumnsContainingFeatures(
5642 columnsContaining, false, false, featureType);
5645 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5646 false, featureType))
5648 getViewport().hideSelectedColumns();
5656 protected void selectHighlightedColumns_actionPerformed(
5657 ActionEvent actionEvent)
5659 // include key modifier check in case user selects from menu
5660 avc.markHighlightedColumns(
5661 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5663 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5667 * Rebuilds the Colour menu, including any user-defined colours which have
5668 * been loaded either on startup or during the session
5670 public void buildColourMenu()
5672 colourMenu.removeAll();
5674 colourMenu.add(applyToAllGroups);
5675 colourMenu.add(textColour);
5676 colourMenu.addSeparator();
5678 ColourMenuHelper.addMenuItems(colourMenu, this,
5679 viewport.getAlignment(), false);
5681 colourMenu.addSeparator();
5682 colourMenu.add(conservationMenuItem);
5683 colourMenu.add(modifyConservation);
5684 colourMenu.add(abovePIDThreshold);
5685 colourMenu.add(modifyPID);
5686 colourMenu.add(annotationColour);
5688 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5689 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5693 * Open a dialog (if not already open) that allows the user to select and
5694 * calculate PCA or Tree analysis
5696 protected void openTreePcaDialog()
5698 if (alignPanel.getCalculationDialog() == null)
5700 new CalculationChooser(AlignFrame.this);
5705 class PrintThread extends Thread
5709 public PrintThread(AlignmentPanel ap)
5714 static PageFormat pf;
5719 PrinterJob printJob = PrinterJob.getPrinterJob();
5723 printJob.setPrintable(ap, pf);
5727 printJob.setPrintable(ap);
5730 if (printJob.printDialog())
5735 } catch (Exception PrintException)
5737 PrintException.printStackTrace();