2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenColumns;
57 import jalview.datamodel.HiddenMarkovModel;
58 import jalview.datamodel.HiddenSequences;
59 import jalview.datamodel.PDBEntry;
60 import jalview.datamodel.SeqCigar;
61 import jalview.datamodel.Sequence;
62 import jalview.datamodel.SequenceGroup;
63 import jalview.datamodel.SequenceI;
64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
66 import jalview.io.AlignmentProperties;
67 import jalview.io.AnnotationFile;
68 import jalview.io.BioJsHTMLOutput;
69 import jalview.io.DataSourceType;
70 import jalview.io.FileFormat;
71 import jalview.io.FileFormatI;
72 import jalview.io.FileFormats;
73 import jalview.io.FileLoader;
74 import jalview.io.FileParse;
75 import jalview.io.FormatAdapter;
76 import jalview.io.HMMFile;
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.ResidueProperties;
91 import jalview.schemes.TCoffeeColourScheme;
92 import jalview.util.Comparison;
93 import jalview.util.MessageManager;
94 import jalview.viewmodel.AlignmentViewport;
95 import jalview.viewmodel.ViewportRanges;
96 import jalview.ws.DBRefFetcher;
97 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
98 import jalview.ws.jws1.Discoverer;
99 import jalview.ws.jws2.Jws2Discoverer;
100 import jalview.ws.jws2.jabaws2.Jws2Instance;
101 import jalview.ws.seqfetcher.DbSourceProxy;
103 import java.awt.BorderLayout;
104 import java.awt.Component;
105 import java.awt.Rectangle;
106 import java.awt.Toolkit;
107 import java.awt.datatransfer.Clipboard;
108 import java.awt.datatransfer.DataFlavor;
109 import java.awt.datatransfer.StringSelection;
110 import java.awt.datatransfer.Transferable;
111 import java.awt.dnd.DnDConstants;
112 import java.awt.dnd.DropTargetDragEvent;
113 import java.awt.dnd.DropTargetDropEvent;
114 import java.awt.dnd.DropTargetEvent;
115 import java.awt.dnd.DropTargetListener;
116 import java.awt.event.ActionEvent;
117 import java.awt.event.ActionListener;
118 import java.awt.event.FocusAdapter;
119 import java.awt.event.FocusEvent;
120 import java.awt.event.ItemEvent;
121 import java.awt.event.ItemListener;
122 import java.awt.event.KeyAdapter;
123 import java.awt.event.KeyEvent;
124 import java.awt.event.MouseEvent;
125 import java.awt.print.PageFormat;
126 import java.awt.print.PrinterJob;
127 import java.beans.PropertyChangeEvent;
128 import java.io.BufferedReader;
130 import java.io.FileReader;
131 import java.io.FileWriter;
132 import java.io.PrintWriter;
134 import java.util.ArrayList;
135 import java.util.Arrays;
136 import java.util.Deque;
137 import java.util.Enumeration;
138 import java.util.HashMap;
139 import java.util.Hashtable;
140 import java.util.List;
141 import java.util.Map;
142 import java.util.Scanner;
143 import java.util.Vector;
145 import javax.swing.JCheckBoxMenuItem;
146 import javax.swing.JEditorPane;
147 import javax.swing.JInternalFrame;
148 import javax.swing.JLayeredPane;
149 import javax.swing.JMenu;
150 import javax.swing.JMenuItem;
151 import javax.swing.JScrollPane;
152 import javax.swing.SwingUtilities;
158 * @version $Revision$
160 public class AlignFrame extends GAlignFrame implements DropTargetListener,
161 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
164 Map<String, Float> distribution = new HashMap<>(); // temporary
166 public static final int DEFAULT_WIDTH = 700;
168 public static final int DEFAULT_HEIGHT = 500;
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)
392 if (Desktop.desktop != null)
394 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
395 addServiceListeners();
399 if (viewport.getWrapAlignment())
401 wrapMenuItem_actionPerformed(null);
404 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
406 this.overviewMenuItem_actionPerformed(null);
411 final List<AlignmentPanel> selviews = new ArrayList<>();
412 final List<AlignmentPanel> origview = new ArrayList<>();
413 final String menuLabel = MessageManager
414 .getString("label.copy_format_from");
415 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
416 new ViewSetProvider()
420 public AlignmentPanel[] getAllAlignmentPanels()
423 origview.add(alignPanel);
424 // make an array of all alignment panels except for this one
425 List<AlignmentPanel> aps = new ArrayList<>(
426 Arrays.asList(Desktop.getAlignmentPanels(null)));
427 aps.remove(AlignFrame.this.alignPanel);
428 return aps.toArray(new AlignmentPanel[aps.size()]);
430 }, selviews, new ItemListener()
434 public void itemStateChanged(ItemEvent e)
436 if (origview.size() > 0)
438 final AlignmentPanel ap = origview.get(0);
441 * Copy the ViewStyle of the selected panel to 'this one'.
442 * Don't change value of 'scaleProteinAsCdna' unless copying
445 ViewStyleI vs = selviews.get(0).getAlignViewport()
447 boolean fromSplitFrame = selviews.get(0)
448 .getAlignViewport().getCodingComplement() != null;
451 vs.setScaleProteinAsCdna(ap.getAlignViewport()
452 .getViewStyle().isScaleProteinAsCdna());
454 ap.getAlignViewport().setViewStyle(vs);
457 * Also rescale ViewStyle of SplitFrame complement if there is
458 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
459 * the whole ViewStyle (allow cDNA protein to have different
462 AlignViewportI complement = ap.getAlignViewport()
463 .getCodingComplement();
464 if (complement != null && vs.isScaleProteinAsCdna())
466 AlignFrame af = Desktop.getAlignFrameFor(complement);
467 ((SplitFrame) af.getSplitViewContainer())
469 af.setMenusForViewport();
473 ap.setSelected(true);
474 ap.alignFrame.setMenusForViewport();
479 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
480 .indexOf("devel") > -1
481 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
482 .indexOf("test") > -1)
484 formatMenu.add(vsel);
486 addFocusListener(new FocusAdapter()
489 public void focusGained(FocusEvent e)
491 Jalview.setCurrentAlignFrame(AlignFrame.this);
498 * Change the filename and format for the alignment, and enable the 'reload'
499 * button functionality.
506 public void setFileName(String file, FileFormatI format)
509 setFileFormat(format);
510 reload.setEnabled(true);
514 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
517 void addKeyListener()
519 addKeyListener(new KeyAdapter()
522 public void keyPressed(KeyEvent evt)
524 if (viewport.cursorMode
525 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
526 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
527 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
528 && Character.isDigit(evt.getKeyChar()))
530 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
533 switch (evt.getKeyCode())
536 case 27: // escape key
537 deselectAllSequenceMenuItem_actionPerformed(null);
541 case KeyEvent.VK_DOWN:
542 if (evt.isAltDown() || !viewport.cursorMode)
544 moveSelectedSequences(false);
546 if (viewport.cursorMode)
548 alignPanel.getSeqPanel().moveCursor(0, 1);
553 if (evt.isAltDown() || !viewport.cursorMode)
555 moveSelectedSequences(true);
557 if (viewport.cursorMode)
559 alignPanel.getSeqPanel().moveCursor(0, -1);
564 case KeyEvent.VK_LEFT:
565 if (evt.isAltDown() || !viewport.cursorMode)
567 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
571 alignPanel.getSeqPanel().moveCursor(-1, 0);
576 case KeyEvent.VK_RIGHT:
577 if (evt.isAltDown() || !viewport.cursorMode)
579 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
583 alignPanel.getSeqPanel().moveCursor(1, 0);
587 case KeyEvent.VK_SPACE:
588 if (viewport.cursorMode)
590 alignPanel.getSeqPanel().insertGapAtCursor(
591 evt.isControlDown() || evt.isShiftDown()
596 // case KeyEvent.VK_A:
597 // if (viewport.cursorMode)
599 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
600 // //System.out.println("A");
604 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
605 * System.out.println("closing bracket"); } break;
607 case KeyEvent.VK_DELETE:
608 case KeyEvent.VK_BACK_SPACE:
609 if (!viewport.cursorMode)
611 cut_actionPerformed(null);
615 alignPanel.getSeqPanel().deleteGapAtCursor(
616 evt.isControlDown() || evt.isShiftDown()
623 if (viewport.cursorMode)
625 alignPanel.getSeqPanel().setCursorRow();
629 if (viewport.cursorMode && !evt.isControlDown())
631 alignPanel.getSeqPanel().setCursorColumn();
635 if (viewport.cursorMode)
637 alignPanel.getSeqPanel().setCursorPosition();
641 case KeyEvent.VK_ENTER:
642 case KeyEvent.VK_COMMA:
643 if (viewport.cursorMode)
645 alignPanel.getSeqPanel().setCursorRowAndColumn();
650 if (viewport.cursorMode)
652 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
656 if (viewport.cursorMode)
658 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
663 viewport.cursorMode = !viewport.cursorMode;
664 statusBar.setText(MessageManager.formatMessage(
665 "label.keyboard_editing_mode",
666 new String[] { (viewport.cursorMode ? "on" : "off") }));
667 if (viewport.cursorMode)
669 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
671 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
674 alignPanel.getSeqPanel().seqCanvas.repaint();
680 Help.showHelpWindow();
681 } catch (Exception ex)
683 ex.printStackTrace();
688 boolean toggleSeqs = !evt.isControlDown();
689 boolean toggleCols = !evt.isShiftDown();
690 toggleHiddenRegions(toggleSeqs, toggleCols);
695 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
696 boolean modifyExisting = true; // always modify, don't clear
697 // evt.isShiftDown();
698 boolean invertHighlighted = evt.isAltDown();
699 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
703 case KeyEvent.VK_PAGE_UP:
704 if (viewport.getWrapAlignment())
706 vpRanges.scrollUp(true);
713 case KeyEvent.VK_PAGE_DOWN:
714 if (viewport.getWrapAlignment())
716 vpRanges.scrollUp(false);
727 public void keyReleased(KeyEvent evt)
729 switch (evt.getKeyCode())
731 case KeyEvent.VK_LEFT:
732 if (evt.isAltDown() || !viewport.cursorMode)
734 viewport.firePropertyChange("alignment", null, viewport
735 .getAlignment().getSequences());
739 case KeyEvent.VK_RIGHT:
740 if (evt.isAltDown() || !viewport.cursorMode)
742 viewport.firePropertyChange("alignment", null, viewport
743 .getAlignment().getSequences());
751 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
753 ap.alignFrame = this;
754 avc = new jalview.controller.AlignViewController(this, viewport,
759 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
761 int aSize = alignPanels.size();
763 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
765 if (aSize == 1 && ap.av.viewName == null)
767 this.getContentPane().add(ap, BorderLayout.CENTER);
773 setInitialTabVisible();
776 expandViews.setEnabled(true);
777 gatherViews.setEnabled(true);
778 tabbedPane.addTab(ap.av.viewName, ap);
780 ap.setVisible(false);
785 if (ap.av.isPadGaps())
787 ap.av.getAlignment().padGaps();
789 ap.av.updateConservation(ap);
790 ap.av.updateConsensus(ap);
791 ap.av.updateStrucConsensus(ap);
795 public void setInitialTabVisible()
797 expandViews.setEnabled(true);
798 gatherViews.setEnabled(true);
799 tabbedPane.setVisible(true);
800 AlignmentPanel first = alignPanels.get(0);
801 tabbedPane.addTab(first.av.viewName, first);
802 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
805 public AlignViewport getViewport()
810 /* Set up intrinsic listeners for dynamically generated GUI bits. */
811 private void addServiceListeners()
813 final java.beans.PropertyChangeListener thisListener;
814 Desktop.instance.addJalviewPropertyChangeListener("services",
815 thisListener = new java.beans.PropertyChangeListener()
818 public void propertyChange(PropertyChangeEvent evt)
820 // // System.out.println("Discoverer property change.");
821 // if (evt.getPropertyName().equals("services"))
823 SwingUtilities.invokeLater(new Runnable()
830 .println("Rebuild WS Menu for service change");
831 BuildWebServiceMenu();
838 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
841 public void internalFrameClosed(
842 javax.swing.event.InternalFrameEvent evt)
844 // System.out.println("deregistering discoverer listener");
845 Desktop.instance.removeJalviewPropertyChangeListener("services",
847 closeMenuItem_actionPerformed(true);
850 // Finally, build the menu once to get current service state
851 new Thread(new Runnable()
856 BuildWebServiceMenu();
862 * Configure menu items that vary according to whether the alignment is
863 * nucleotide or protein
865 public void setGUINucleotide()
867 AlignmentI al = getViewport().getAlignment();
868 boolean nucleotide = al.isNucleotide();
870 showTranslation.setVisible(nucleotide);
871 showReverse.setVisible(nucleotide);
872 showReverseComplement.setVisible(nucleotide);
873 conservationMenuItem.setEnabled(!nucleotide);
874 modifyConservation.setEnabled(!nucleotide
875 && conservationMenuItem.isSelected());
876 showGroupConservation.setEnabled(!nucleotide);
878 showComplementMenuItem.setText(nucleotide ? MessageManager
879 .getString("label.protein") : MessageManager
880 .getString("label.nucleotide"));
884 * set up menus for the current viewport. This may be called after any
885 * operation that affects the data in the current view (selection changed,
886 * etc) to update the menus to reflect the new state.
889 public void setMenusForViewport()
891 setMenusFromViewport(viewport);
895 * Need to call this method when tabs are selected for multiple views, or when
896 * loading from Jalview2XML.java
901 void setMenusFromViewport(AlignViewport av)
903 padGapsMenuitem.setSelected(av.isPadGaps());
904 colourTextMenuItem.setSelected(av.isShowColourText());
905 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
906 modifyPID.setEnabled(abovePIDThreshold.isSelected());
907 conservationMenuItem.setSelected(av.getConservationSelected());
908 modifyConservation.setEnabled(conservationMenuItem.isSelected());
909 seqLimits.setSelected(av.getShowJVSuffix());
910 idRightAlign.setSelected(av.isRightAlignIds());
911 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
912 renderGapsMenuItem.setSelected(av.isRenderGaps());
913 wrapMenuItem.setSelected(av.getWrapAlignment());
914 scaleAbove.setVisible(av.getWrapAlignment());
915 scaleLeft.setVisible(av.getWrapAlignment());
916 scaleRight.setVisible(av.getWrapAlignment());
917 annotationPanelMenuItem.setState(av.isShowAnnotation());
919 * Show/hide annotations only enabled if annotation panel is shown
921 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
922 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
923 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
924 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
925 viewBoxesMenuItem.setSelected(av.getShowBoxes());
926 viewTextMenuItem.setSelected(av.getShowText());
927 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
928 showGroupConsensus.setSelected(av.isShowGroupConsensus());
929 showGroupConservation.setSelected(av.isShowGroupConservation());
930 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
931 showSequenceLogo.setSelected(av.isShowSequenceLogo());
932 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
933 showInformationHistogram.setSelected(av.isShowInformationHistogram());
934 showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
935 normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
937 ColourMenuHelper.setColourSelected(colourMenu,
938 av.getGlobalColourScheme());
940 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
941 hiddenMarkers.setState(av.getShowHiddenMarkers());
942 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
943 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
944 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
945 autoCalculate.setSelected(av.autoCalculateConsensus);
946 sortByTree.setSelected(av.sortByTree);
947 listenToViewSelections.setSelected(av.followSelection);
949 showProducts.setEnabled(canShowProducts());
950 setGroovyEnabled(Desktop.getGroovyConsole() != null);
956 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
960 public void setGroovyEnabled(boolean b)
962 runGroovy.setEnabled(b);
965 private IProgressIndicator progressBar;
970 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
973 public void setProgressBar(String message, long id)
975 progressBar.setProgressBar(message, id);
979 public void registerHandler(final long id,
980 final IProgressIndicatorHandler handler)
982 progressBar.registerHandler(id, handler);
987 * @return true if any progress bars are still active
990 public boolean operationInProgress()
992 return progressBar.operationInProgress();
996 public void setStatus(String text)
998 statusBar.setText(text);
1002 * Added so Castor Mapping file can obtain Jalview Version
1004 public String getVersion()
1006 return jalview.bin.Cache.getProperty("VERSION");
1009 public FeatureRenderer getFeatureRenderer()
1011 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1015 public void fetchSequence_actionPerformed(ActionEvent e)
1017 new jalview.gui.SequenceFetcher(this);
1021 public void addFromFile_actionPerformed(ActionEvent e)
1023 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1027 public void reload_actionPerformed(ActionEvent e)
1029 if (fileName != null)
1031 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1032 // originating file's format
1033 // TODO: work out how to recover feature settings for correct view(s) when
1034 // file is reloaded.
1035 if (FileFormat.Jalview.equals(currentFileFormat))
1037 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1038 for (int i = 0; i < frames.length; i++)
1040 if (frames[i] instanceof AlignFrame && frames[i] != this
1041 && ((AlignFrame) frames[i]).fileName != null
1042 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1046 frames[i].setSelected(true);
1047 Desktop.instance.closeAssociatedWindows();
1048 } catch (java.beans.PropertyVetoException ex)
1054 Desktop.instance.closeAssociatedWindows();
1056 FileLoader loader = new FileLoader();
1057 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1058 : DataSourceType.FILE;
1059 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1063 Rectangle bounds = this.getBounds();
1065 FileLoader loader = new FileLoader();
1066 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1067 : DataSourceType.FILE;
1068 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1069 protocol, currentFileFormat);
1071 newframe.setBounds(bounds);
1072 if (featureSettings != null && featureSettings.isShowing())
1074 final Rectangle fspos = featureSettings.frame.getBounds();
1075 // TODO: need a 'show feature settings' function that takes bounds -
1076 // need to refactor Desktop.addFrame
1077 newframe.featureSettings_actionPerformed(null);
1078 final FeatureSettings nfs = newframe.featureSettings;
1079 SwingUtilities.invokeLater(new Runnable()
1084 nfs.frame.setBounds(fspos);
1087 this.featureSettings.close();
1088 this.featureSettings = null;
1090 this.closeMenuItem_actionPerformed(true);
1096 public void addFromText_actionPerformed(ActionEvent e)
1098 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1103 public void addFromURL_actionPerformed(ActionEvent e)
1105 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1109 public void save_actionPerformed(ActionEvent e)
1111 if (fileName == null || (currentFileFormat == null)
1112 || fileName.startsWith("http"))
1114 saveAs_actionPerformed(null);
1118 saveAlignment(fileName, currentFileFormat);
1129 public void saveAs_actionPerformed(ActionEvent e)
1131 String format = currentFileFormat == null ? null : currentFileFormat
1133 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1134 Cache.getProperty("LAST_DIRECTORY"), format);
1136 chooser.setFileView(new JalviewFileView());
1137 chooser.setDialogTitle(MessageManager
1138 .getString("label.save_alignment_to_file"));
1139 chooser.setToolTipText(MessageManager.getString("action.save"));
1141 int value = chooser.showSaveDialog(this);
1143 if (value == JalviewFileChooser.APPROVE_OPTION)
1145 currentFileFormat = chooser.getSelectedFormat();
1146 while (currentFileFormat == null)
1149 .showInternalMessageDialog(
1152 .getString("label.select_file_format_before_saving"),
1154 .getString("label.file_format_not_specified"),
1155 JvOptionPane.WARNING_MESSAGE);
1156 currentFileFormat = chooser.getSelectedFormat();
1157 value = chooser.showSaveDialog(this);
1158 if (value != JalviewFileChooser.APPROVE_OPTION)
1164 fileName = chooser.getSelectedFile().getPath();
1166 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1168 Cache.setProperty("LAST_DIRECTORY", fileName);
1169 saveAlignment(fileName, currentFileFormat);
1173 public boolean saveAlignment(String file, FileFormatI format)
1175 boolean success = true;
1177 if (FileFormat.Jalview.equals(format))
1179 String shortName = title;
1181 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1183 shortName = shortName.substring(shortName
1184 .lastIndexOf(java.io.File.separatorChar) + 1);
1187 success = new Jalview2XML().saveAlignment(this, file, shortName);
1189 statusBar.setText(MessageManager.formatMessage(
1190 "label.successfully_saved_to_file_in_format", new Object[] {
1191 fileName, format }));
1196 AlignmentExportData exportData = getAlignmentForExport(format,
1198 if (exportData.getSettings().isCancelled())
1202 FormatAdapter f = new FormatAdapter(alignPanel,
1203 exportData.getSettings());
1204 String output = f.formatSequences(
1206 exportData.getAlignment(), // class cast exceptions will
1207 // occur in the distant future
1208 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1209 f.getCacheSuffixDefault(format), viewport.getAlignment()
1210 .getHiddenColumns());
1220 PrintWriter out = new PrintWriter(new FileWriter(file));
1224 this.setTitle(file);
1225 statusBar.setText(MessageManager.formatMessage(
1226 "label.successfully_saved_to_file_in_format",
1227 new Object[] { fileName, format.getName() }));
1228 } catch (Exception ex)
1231 ex.printStackTrace();
1238 JvOptionPane.showInternalMessageDialog(this, MessageManager
1239 .formatMessage("label.couldnt_save_file",
1240 new Object[] { fileName }), MessageManager
1241 .getString("label.error_saving_file"),
1242 JvOptionPane.WARNING_MESSAGE);
1248 private void warningMessage(String warning, String title)
1250 if (new jalview.util.Platform().isHeadless())
1252 System.err.println("Warning: " + title + "\nWarning: " + warning);
1257 JvOptionPane.showInternalMessageDialog(this, warning, title,
1258 JvOptionPane.WARNING_MESSAGE);
1270 protected void outputText_actionPerformed(ActionEvent e)
1272 FileFormatI fileFormat = FileFormats.getInstance().forName(
1273 e.getActionCommand());
1274 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1276 if (exportData.getSettings().isCancelled())
1280 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1281 cap.setForInput(null);
1284 FileFormatI format = fileFormat;
1285 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1286 .formatSequences(format, exportData.getAlignment(),
1287 exportData.getOmitHidden(),
1289 .getStartEndPostions(), viewport
1290 .getAlignment().getHiddenColumns()));
1291 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1292 "label.alignment_output_command",
1293 new Object[] { e.getActionCommand() }), 600, 500);
1294 } catch (OutOfMemoryError oom)
1296 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1302 public static AlignmentExportData getAlignmentForExport(
1303 FileFormatI format, AlignViewportI viewport,
1304 AlignExportSettingI exportSettings)
1306 AlignmentI alignmentToExport = null;
1307 AlignExportSettingI settings = exportSettings;
1308 String[] omitHidden = null;
1310 HiddenSequences hiddenSeqs = viewport.getAlignment()
1311 .getHiddenSequences();
1313 alignmentToExport = viewport.getAlignment();
1315 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1316 if (settings == null)
1318 settings = new AlignExportSettings(hasHiddenSeqs,
1319 viewport.hasHiddenColumns(), format);
1321 // settings.isExportAnnotations();
1323 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1325 omitHidden = viewport.getViewAsString(false,
1326 settings.isExportHiddenSequences());
1329 int[] alignmentStartEnd = new int[2];
1330 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1332 alignmentToExport = hiddenSeqs.getFullAlignment();
1336 alignmentToExport = viewport.getAlignment();
1338 alignmentStartEnd = alignmentToExport
1339 .getVisibleStartAndEndIndex(viewport.getAlignment()
1341 .getHiddenRegions());
1342 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1343 omitHidden, alignmentStartEnd, settings);
1354 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1356 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1357 htmlSVG.exportHTML(null);
1361 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1363 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1364 bjs.exportHTML(null);
1367 public void createImageMap(File file, String image)
1369 alignPanel.makePNGImageMap(file, image);
1379 public void createPNG(File f)
1381 alignPanel.makePNG(f);
1391 public void createEPS(File f)
1393 alignPanel.makeEPS(f);
1397 public void createSVG(File f)
1399 alignPanel.makeSVG(f);
1403 public void pageSetup_actionPerformed(ActionEvent e)
1405 PrinterJob printJob = PrinterJob.getPrinterJob();
1406 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1416 public void printMenuItem_actionPerformed(ActionEvent e)
1418 // Putting in a thread avoids Swing painting problems
1419 PrintThread thread = new PrintThread(alignPanel);
1424 public void exportFeatures_actionPerformed(ActionEvent e)
1426 new AnnotationExporter().exportFeatures(alignPanel);
1430 public void exportAnnotations_actionPerformed(ActionEvent e)
1432 new AnnotationExporter().exportAnnotations(alignPanel);
1436 public void associatedData_actionPerformed(ActionEvent e)
1438 // Pick the tree file
1439 JalviewFileChooser chooser = new JalviewFileChooser(
1440 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1441 chooser.setFileView(new JalviewFileView());
1442 chooser.setDialogTitle(MessageManager
1443 .getString("label.load_jalview_annotations"));
1444 chooser.setToolTipText(MessageManager
1445 .getString("label.load_jalview_annotations"));
1447 int value = chooser.showOpenDialog(null);
1449 if (value == JalviewFileChooser.APPROVE_OPTION)
1451 String choice = chooser.getSelectedFile().getPath();
1452 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1453 loadJalviewDataFile(choice, null, null, null);
1459 * Close the current view or all views in the alignment frame. If the frame
1460 * only contains one view then the alignment will be removed from memory.
1462 * @param closeAllTabs
1465 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1467 if (alignPanels != null && alignPanels.size() < 2)
1469 closeAllTabs = true;
1474 if (alignPanels != null)
1478 if (this.isClosed())
1480 // really close all the windows - otherwise wait till
1481 // setClosed(true) is called
1482 for (int i = 0; i < alignPanels.size(); i++)
1484 AlignmentPanel ap = alignPanels.get(i);
1491 closeView(alignPanel);
1498 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1499 * be called recursively, with the frame now in 'closed' state
1501 this.setClosed(true);
1503 } catch (Exception ex)
1505 ex.printStackTrace();
1510 * Close the specified panel and close up tabs appropriately.
1512 * @param panelToClose
1514 public void closeView(AlignmentPanel panelToClose)
1516 int index = tabbedPane.getSelectedIndex();
1517 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1518 alignPanels.remove(panelToClose);
1519 panelToClose.closePanel();
1520 panelToClose = null;
1522 tabbedPane.removeTabAt(closedindex);
1523 tabbedPane.validate();
1525 if (index > closedindex || index == tabbedPane.getTabCount())
1527 // modify currently selected tab index if necessary.
1531 this.tabSelectionChanged(index);
1537 void updateEditMenuBar()
1540 if (viewport.getHistoryList().size() > 0)
1542 undoMenuItem.setEnabled(true);
1543 CommandI command = viewport.getHistoryList().peek();
1544 undoMenuItem.setText(MessageManager.formatMessage(
1545 "label.undo_command",
1546 new Object[] { command.getDescription() }));
1550 undoMenuItem.setEnabled(false);
1551 undoMenuItem.setText(MessageManager.getString("action.undo"));
1554 if (viewport.getRedoList().size() > 0)
1556 redoMenuItem.setEnabled(true);
1558 CommandI command = viewport.getRedoList().peek();
1559 redoMenuItem.setText(MessageManager.formatMessage(
1560 "label.redo_command",
1561 new Object[] { command.getDescription() }));
1565 redoMenuItem.setEnabled(false);
1566 redoMenuItem.setText(MessageManager.getString("action.redo"));
1571 public void addHistoryItem(CommandI command)
1573 if (command.getSize() > 0)
1575 viewport.addToHistoryList(command);
1576 viewport.clearRedoList();
1577 updateEditMenuBar();
1578 viewport.updateHiddenColumns();
1579 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1580 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1581 // viewport.getColumnSelection()
1582 // .getHiddenColumns().size() > 0);
1588 * @return alignment objects for all views
1590 AlignmentI[] getViewAlignments()
1592 if (alignPanels != null)
1594 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1596 for (AlignmentPanel ap : alignPanels)
1598 als[i++] = ap.av.getAlignment();
1602 if (viewport != null)
1604 return new AlignmentI[] { viewport.getAlignment() };
1616 protected void undoMenuItem_actionPerformed(ActionEvent e)
1618 if (viewport.getHistoryList().isEmpty())
1622 CommandI command = viewport.getHistoryList().pop();
1623 viewport.addToRedoList(command);
1624 command.undoCommand(getViewAlignments());
1626 AlignmentViewport originalSource = getOriginatingSource(command);
1627 updateEditMenuBar();
1629 if (originalSource != null)
1631 if (originalSource != viewport)
1634 .warn("Implementation worry: mismatch of viewport origin for undo");
1636 originalSource.updateHiddenColumns();
1637 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1639 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1640 // viewport.getColumnSelection()
1641 // .getHiddenColumns().size() > 0);
1642 originalSource.firePropertyChange("alignment", null, originalSource
1643 .getAlignment().getSequences());
1654 protected void redoMenuItem_actionPerformed(ActionEvent e)
1656 if (viewport.getRedoList().size() < 1)
1661 CommandI command = viewport.getRedoList().pop();
1662 viewport.addToHistoryList(command);
1663 command.doCommand(getViewAlignments());
1665 AlignmentViewport originalSource = getOriginatingSource(command);
1666 updateEditMenuBar();
1668 if (originalSource != null)
1671 if (originalSource != viewport)
1674 .warn("Implementation worry: mismatch of viewport origin for redo");
1676 originalSource.updateHiddenColumns();
1677 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1679 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1680 // viewport.getColumnSelection()
1681 // .getHiddenColumns().size() > 0);
1682 originalSource.firePropertyChange("alignment", null, originalSource
1683 .getAlignment().getSequences());
1687 AlignmentViewport getOriginatingSource(CommandI command)
1689 AlignmentViewport originalSource = null;
1690 // For sequence removal and addition, we need to fire
1691 // the property change event FROM the viewport where the
1692 // original alignment was altered
1693 AlignmentI al = null;
1694 if (command instanceof EditCommand)
1696 EditCommand editCommand = (EditCommand) command;
1697 al = editCommand.getAlignment();
1698 List<Component> comps = PaintRefresher.components.get(viewport
1699 .getSequenceSetId());
1701 for (Component comp : comps)
1703 if (comp instanceof AlignmentPanel)
1705 if (al == ((AlignmentPanel) comp).av.getAlignment())
1707 originalSource = ((AlignmentPanel) comp).av;
1714 if (originalSource == null)
1716 // The original view is closed, we must validate
1717 // the current view against the closed view first
1720 PaintRefresher.validateSequences(al, viewport.getAlignment());
1723 originalSource = viewport;
1726 return originalSource;
1735 public void moveSelectedSequences(boolean up)
1737 SequenceGroup sg = viewport.getSelectionGroup();
1743 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1744 viewport.getHiddenRepSequences(), up);
1745 alignPanel.paintAlignment(true);
1748 synchronized void slideSequences(boolean right, int size)
1750 List<SequenceI> sg = new ArrayList<>();
1751 if (viewport.cursorMode)
1753 sg.add(viewport.getAlignment().getSequenceAt(
1754 alignPanel.getSeqPanel().seqCanvas.cursorY));
1756 else if (viewport.getSelectionGroup() != null
1757 && viewport.getSelectionGroup().getSize() != viewport
1758 .getAlignment().getHeight())
1760 sg = viewport.getSelectionGroup().getSequences(
1761 viewport.getHiddenRepSequences());
1769 List<SequenceI> invertGroup = new ArrayList<>();
1771 for (SequenceI seq : viewport.getAlignment().getSequences())
1773 if (!sg.contains(seq))
1775 invertGroup.add(seq);
1779 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1781 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1782 for (int i = 0; i < invertGroup.size(); i++)
1784 seqs2[i] = invertGroup.get(i);
1787 SlideSequencesCommand ssc;
1790 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1791 size, viewport.getGapCharacter());
1795 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1796 size, viewport.getGapCharacter());
1799 int groupAdjustment = 0;
1800 if (ssc.getGapsInsertedBegin() && right)
1802 if (viewport.cursorMode)
1804 alignPanel.getSeqPanel().moveCursor(size, 0);
1808 groupAdjustment = size;
1811 else if (!ssc.getGapsInsertedBegin() && !right)
1813 if (viewport.cursorMode)
1815 alignPanel.getSeqPanel().moveCursor(-size, 0);
1819 groupAdjustment = -size;
1823 if (groupAdjustment != 0)
1825 viewport.getSelectionGroup().setStartRes(
1826 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1827 viewport.getSelectionGroup().setEndRes(
1828 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1832 * just extend the last slide command if compatible; but not if in
1833 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1835 boolean appendHistoryItem = false;
1836 Deque<CommandI> historyList = viewport.getHistoryList();
1837 boolean inSplitFrame = getSplitViewContainer() != null;
1838 if (!inSplitFrame && historyList != null && historyList.size() > 0
1839 && historyList.peek() instanceof SlideSequencesCommand)
1841 appendHistoryItem = ssc
1842 .appendSlideCommand((SlideSequencesCommand) historyList
1846 if (!appendHistoryItem)
1848 addHistoryItem(ssc);
1861 protected void copy_actionPerformed(ActionEvent e)
1864 if (viewport.getSelectionGroup() == null)
1868 // TODO: preserve the ordering of displayed alignment annotation in any
1869 // internal paste (particularly sequence associated annotation)
1870 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1871 String[] omitHidden = null;
1873 if (viewport.hasHiddenColumns())
1875 omitHidden = viewport.getViewAsString(true);
1878 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1879 seqs, omitHidden, null);
1881 StringSelection ss = new StringSelection(output);
1885 jalview.gui.Desktop.internalCopy = true;
1886 // Its really worth setting the clipboard contents
1887 // to empty before setting the large StringSelection!!
1888 Toolkit.getDefaultToolkit().getSystemClipboard()
1889 .setContents(new StringSelection(""), null);
1891 Toolkit.getDefaultToolkit().getSystemClipboard()
1892 .setContents(ss, Desktop.instance);
1893 } catch (OutOfMemoryError er)
1895 new OOMWarning("copying region", er);
1899 ArrayList<int[]> hiddenColumns = null;
1900 if (viewport.hasHiddenColumns())
1902 hiddenColumns = new ArrayList<>();
1903 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1904 .getSelectionGroup().getEndRes();
1905 for (int[] region : viewport.getAlignment().getHiddenColumns()
1906 .getHiddenRegions())
1908 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1910 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1911 region[1] - hiddenOffset });
1916 Desktop.jalviewClipboard = new Object[] { seqs,
1917 viewport.getAlignment().getDataset(), hiddenColumns };
1918 statusBar.setText(MessageManager.formatMessage(
1919 "label.copied_sequences_to_clipboard", new Object[] { Integer
1920 .valueOf(seqs.length).toString() }));
1930 protected void pasteNew_actionPerformed(ActionEvent e)
1942 protected void pasteThis_actionPerformed(ActionEvent e)
1948 * Paste contents of Jalview clipboard
1950 * @param newAlignment
1951 * true to paste to a new alignment, otherwise add to this.
1953 void paste(boolean newAlignment)
1955 boolean externalPaste = true;
1958 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1959 Transferable contents = c.getContents(this);
1961 if (contents == null)
1970 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1971 if (str.length() < 1)
1976 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1978 } catch (OutOfMemoryError er)
1980 new OOMWarning("Out of memory pasting sequences!!", er);
1984 SequenceI[] sequences;
1985 boolean annotationAdded = false;
1986 AlignmentI alignment = null;
1988 if (Desktop.jalviewClipboard != null)
1990 // The clipboard was filled from within Jalview, we must use the
1992 // And dataset from the copied alignment
1993 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1994 // be doubly sure that we create *new* sequence objects.
1995 sequences = new SequenceI[newseq.length];
1996 for (int i = 0; i < newseq.length; i++)
1998 sequences[i] = new Sequence(newseq[i]);
2000 alignment = new Alignment(sequences);
2001 externalPaste = false;
2005 // parse the clipboard as an alignment.
2006 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2008 sequences = alignment.getSequencesArray();
2012 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2018 if (Desktop.jalviewClipboard != null)
2020 // dataset is inherited
2021 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2025 // new dataset is constructed
2026 alignment.setDataset(null);
2028 alwidth = alignment.getWidth() + 1;
2032 AlignmentI pastedal = alignment; // preserve pasted alignment object
2033 // Add pasted sequences and dataset into existing alignment.
2034 alignment = viewport.getAlignment();
2035 alwidth = alignment.getWidth() + 1;
2036 // decide if we need to import sequences from an existing dataset
2037 boolean importDs = Desktop.jalviewClipboard != null
2038 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2039 // importDs==true instructs us to copy over new dataset sequences from
2040 // an existing alignment
2041 Vector newDs = (importDs) ? new Vector() : null; // used to create
2042 // minimum dataset set
2044 for (int i = 0; i < sequences.length; i++)
2048 newDs.addElement(null);
2050 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2052 if (importDs && ds != null)
2054 if (!newDs.contains(ds))
2056 newDs.setElementAt(ds, i);
2057 ds = new Sequence(ds);
2058 // update with new dataset sequence
2059 sequences[i].setDatasetSequence(ds);
2063 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2068 // copy and derive new dataset sequence
2069 sequences[i] = sequences[i].deriveSequence();
2070 alignment.getDataset().addSequence(
2071 sequences[i].getDatasetSequence());
2072 // TODO: avoid creation of duplicate dataset sequences with a
2073 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2075 alignment.addSequence(sequences[i]); // merges dataset
2079 newDs.clear(); // tidy up
2081 if (alignment.getAlignmentAnnotation() != null)
2083 for (AlignmentAnnotation alan : alignment
2084 .getAlignmentAnnotation())
2086 if (alan.graphGroup > fgroup)
2088 fgroup = alan.graphGroup;
2092 if (pastedal.getAlignmentAnnotation() != null)
2094 // Add any annotation attached to alignment.
2095 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2096 for (int i = 0; i < alann.length; i++)
2098 annotationAdded = true;
2099 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2101 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2102 if (newann.graphGroup > -1)
2104 if (newGraphGroups.size() <= newann.graphGroup
2105 || newGraphGroups.get(newann.graphGroup) == null)
2107 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2109 newGraphGroups.add(q, null);
2111 newGraphGroups.set(newann.graphGroup, new Integer(
2114 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2118 newann.padAnnotation(alwidth);
2119 alignment.addAnnotation(newann);
2129 addHistoryItem(new EditCommand(
2130 MessageManager.getString("label.add_sequences"),
2131 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2133 // Add any annotations attached to sequences
2134 for (int i = 0; i < sequences.length; i++)
2136 if (sequences[i].getAnnotation() != null)
2138 AlignmentAnnotation newann;
2139 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2141 annotationAdded = true;
2142 newann = sequences[i].getAnnotation()[a];
2143 newann.adjustForAlignment();
2144 newann.padAnnotation(alwidth);
2145 if (newann.graphGroup > -1)
2147 if (newann.graphGroup > -1)
2149 if (newGraphGroups.size() <= newann.graphGroup
2150 || newGraphGroups.get(newann.graphGroup) == null)
2152 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2154 newGraphGroups.add(q, null);
2156 newGraphGroups.set(newann.graphGroup, new Integer(
2159 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2163 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2168 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2175 // propagate alignment changed.
2176 vpRanges.setEndSeq(alignment.getHeight());
2177 if (annotationAdded)
2179 // Duplicate sequence annotation in all views.
2180 AlignmentI[] alview = this.getViewAlignments();
2181 for (int i = 0; i < sequences.length; i++)
2183 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2188 for (int avnum = 0; avnum < alview.length; avnum++)
2190 if (alview[avnum] != alignment)
2192 // duplicate in a view other than the one with input focus
2193 int avwidth = alview[avnum].getWidth() + 1;
2194 // this relies on sann being preserved after we
2195 // modify the sequence's annotation array for each duplication
2196 for (int a = 0; a < sann.length; a++)
2198 AlignmentAnnotation newann = new AlignmentAnnotation(
2200 sequences[i].addAlignmentAnnotation(newann);
2201 newann.padAnnotation(avwidth);
2202 alview[avnum].addAnnotation(newann); // annotation was
2203 // duplicated earlier
2204 // TODO JAL-1145 graphGroups are not updated for sequence
2205 // annotation added to several views. This may cause
2207 alview[avnum].setAnnotationIndex(newann, a);
2212 buildSortByAnnotationScoresMenu();
2214 viewport.firePropertyChange("alignment", null,
2215 alignment.getSequences());
2216 if (alignPanels != null)
2218 for (AlignmentPanel ap : alignPanels)
2220 ap.validateAnnotationDimensions(false);
2225 alignPanel.validateAnnotationDimensions(false);
2231 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2233 String newtitle = new String("Copied sequences");
2235 if (Desktop.jalviewClipboard != null
2236 && Desktop.jalviewClipboard[2] != null)
2238 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2239 for (int[] region : hc)
2241 af.viewport.hideColumns(region[0], region[1]);
2245 // >>>This is a fix for the moment, until a better solution is
2247 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2249 alignPanel.getSeqPanel().seqCanvas
2250 .getFeatureRenderer());
2252 // TODO: maintain provenance of an alignment, rather than just make the
2253 // title a concatenation of operations.
2256 if (title.startsWith("Copied sequences"))
2262 newtitle = newtitle.concat("- from " + title);
2267 newtitle = new String("Pasted sequences");
2270 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2275 } catch (Exception ex)
2277 ex.printStackTrace();
2278 System.out.println("Exception whilst pasting: " + ex);
2279 // could be anything being pasted in here
2285 protected void expand_newalign(ActionEvent e)
2289 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2290 .getAlignment(), -1);
2291 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2293 String newtitle = new String("Flanking alignment");
2295 if (Desktop.jalviewClipboard != null
2296 && Desktop.jalviewClipboard[2] != null)
2298 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2299 for (int region[] : hc)
2301 af.viewport.hideColumns(region[0], region[1]);
2305 // >>>This is a fix for the moment, until a better solution is
2307 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2309 alignPanel.getSeqPanel().seqCanvas
2310 .getFeatureRenderer());
2312 // TODO: maintain provenance of an alignment, rather than just make the
2313 // title a concatenation of operations.
2315 if (title.startsWith("Copied sequences"))
2321 newtitle = newtitle.concat("- from " + title);
2325 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2327 } catch (Exception ex)
2329 ex.printStackTrace();
2330 System.out.println("Exception whilst pasting: " + ex);
2331 // could be anything being pasted in here
2332 } catch (OutOfMemoryError oom)
2334 new OOMWarning("Viewing flanking region of alignment", oom);
2345 protected void cut_actionPerformed(ActionEvent e)
2347 copy_actionPerformed(null);
2348 delete_actionPerformed(null);
2358 protected void delete_actionPerformed(ActionEvent evt)
2361 SequenceGroup sg = viewport.getSelectionGroup();
2368 * If the cut affects all sequences, warn, remove highlighted columns
2370 if (sg.getSize() == viewport.getAlignment().getHeight())
2372 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2373 .getAlignment().getWidth()) ? true : false;
2374 if (isEntireAlignWidth)
2376 int confirm = JvOptionPane.showConfirmDialog(this,
2377 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2378 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2379 JvOptionPane.OK_CANCEL_OPTION);
2381 if (confirm == JvOptionPane.CANCEL_OPTION
2382 || confirm == JvOptionPane.CLOSED_OPTION)
2387 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2388 sg.getEndRes() + 1);
2390 SequenceI[] cut = sg.getSequences()
2391 .toArray(new SequenceI[sg.getSize()]);
2393 addHistoryItem(new EditCommand(
2394 MessageManager.getString("label.cut_sequences"), Action.CUT,
2395 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2396 viewport.getAlignment()));
2398 viewport.setSelectionGroup(null);
2399 viewport.sendSelection();
2400 viewport.getAlignment().deleteGroup(sg);
2402 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2404 if (viewport.getAlignment().getHeight() < 1)
2408 this.setClosed(true);
2409 } catch (Exception ex)
2422 protected void deleteGroups_actionPerformed(ActionEvent e)
2424 if (avc.deleteGroups())
2426 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2427 alignPanel.updateAnnotation();
2428 alignPanel.paintAlignment(true);
2439 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2441 SequenceGroup sg = new SequenceGroup();
2443 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2445 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2448 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2449 viewport.setSelectionGroup(sg);
2450 viewport.sendSelection();
2451 // JAL-2034 - should delegate to
2452 // alignPanel to decide if overview needs
2454 alignPanel.paintAlignment(false);
2455 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2465 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2467 if (viewport.cursorMode)
2469 alignPanel.getSeqPanel().keyboardNo1 = null;
2470 alignPanel.getSeqPanel().keyboardNo2 = null;
2472 viewport.setSelectionGroup(null);
2473 viewport.getColumnSelection().clear();
2474 viewport.setSelectionGroup(null);
2475 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2476 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2477 // JAL-2034 - should delegate to
2478 // alignPanel to decide if overview needs
2480 alignPanel.paintAlignment(false);
2481 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2482 viewport.sendSelection();
2492 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2494 SequenceGroup sg = viewport.getSelectionGroup();
2498 selectAllSequenceMenuItem_actionPerformed(null);
2503 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2505 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2507 // JAL-2034 - should delegate to
2508 // alignPanel to decide if overview needs
2511 alignPanel.paintAlignment(true);
2512 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2513 viewport.sendSelection();
2517 public void invertColSel_actionPerformed(ActionEvent e)
2519 viewport.invertColumnSelection();
2520 alignPanel.paintAlignment(true);
2521 viewport.sendSelection();
2531 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2533 trimAlignment(true);
2543 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2545 trimAlignment(false);
2548 void trimAlignment(boolean trimLeft)
2550 ColumnSelection colSel = viewport.getColumnSelection();
2553 if (!colSel.isEmpty())
2557 column = colSel.getMin();
2561 column = colSel.getMax();
2565 if (viewport.getSelectionGroup() != null)
2567 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2568 viewport.getHiddenRepSequences());
2572 seqs = viewport.getAlignment().getSequencesArray();
2575 TrimRegionCommand trimRegion;
2578 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2579 column, viewport.getAlignment());
2580 vpRanges.setStartRes(0);
2584 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2585 column, viewport.getAlignment());
2588 statusBar.setText(MessageManager.formatMessage(
2589 "label.removed_columns",
2590 new String[] { Integer.valueOf(trimRegion.getSize())
2593 addHistoryItem(trimRegion);
2595 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2597 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2598 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2600 viewport.getAlignment().deleteGroup(sg);
2604 viewport.firePropertyChange("alignment", null, viewport
2605 .getAlignment().getSequences());
2616 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2618 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2621 if (viewport.getSelectionGroup() != null)
2623 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2624 viewport.getHiddenRepSequences());
2625 start = viewport.getSelectionGroup().getStartRes();
2626 end = viewport.getSelectionGroup().getEndRes();
2630 seqs = viewport.getAlignment().getSequencesArray();
2633 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2634 "Remove Gapped Columns", seqs, start, end,
2635 viewport.getAlignment());
2637 addHistoryItem(removeGapCols);
2639 statusBar.setText(MessageManager.formatMessage(
2640 "label.removed_empty_columns",
2641 new Object[] { Integer.valueOf(removeGapCols.getSize())
2644 // This is to maintain viewport position on first residue
2645 // of first sequence
2646 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2647 int startRes = seq.findPosition(vpRanges.getStartRes());
2648 // ShiftList shifts;
2649 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2650 // edit.alColumnChanges=shifts.getInverse();
2651 // if (viewport.hasHiddenColumns)
2652 // viewport.getColumnSelection().compensateForEdits(shifts);
2653 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2654 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2666 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2668 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2671 if (viewport.getSelectionGroup() != null)
2673 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2674 viewport.getHiddenRepSequences());
2675 start = viewport.getSelectionGroup().getStartRes();
2676 end = viewport.getSelectionGroup().getEndRes();
2680 seqs = viewport.getAlignment().getSequencesArray();
2683 // This is to maintain viewport position on first residue
2684 // of first sequence
2685 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2686 int startRes = seq.findPosition(vpRanges.getStartRes());
2688 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2689 viewport.getAlignment()));
2691 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2693 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2705 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2707 viewport.setPadGaps(padGapsMenuitem.isSelected());
2708 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2719 public void findMenuItem_actionPerformed(ActionEvent e)
2725 * Create a new view of the current alignment.
2728 public void newView_actionPerformed(ActionEvent e)
2730 newView(null, true);
2734 * Creates and shows a new view of the current alignment.
2737 * title of newly created view; if null, one will be generated
2738 * @param copyAnnotation
2739 * if true then duplicate all annnotation, groups and settings
2740 * @return new alignment panel, already displayed.
2742 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2745 * Create a new AlignmentPanel (with its own, new Viewport)
2747 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2749 if (!copyAnnotation)
2752 * remove all groups and annotation except for the automatic stuff
2754 newap.av.getAlignment().deleteAllGroups();
2755 newap.av.getAlignment().deleteAllAnnotations(false);
2758 newap.av.setGatherViewsHere(false);
2760 if (viewport.viewName == null)
2762 viewport.viewName = MessageManager
2763 .getString("label.view_name_original");
2767 * Views share the same edits undo and redo stacks
2769 newap.av.setHistoryList(viewport.getHistoryList());
2770 newap.av.setRedoList(viewport.getRedoList());
2773 * Views share the same mappings; need to deregister any new mappings
2774 * created by copyAlignPanel, and register the new reference to the shared
2777 newap.av.replaceMappings(viewport.getAlignment());
2780 * start up cDNA consensus (if applicable) now mappings are in place
2782 if (newap.av.initComplementConsensus())
2784 newap.refresh(true); // adjust layout of annotations
2787 newap.av.viewName = getNewViewName(viewTitle);
2789 addAlignmentPanel(newap, true);
2790 newap.alignmentChanged();
2792 if (alignPanels.size() == 2)
2794 viewport.setGatherViewsHere(true);
2796 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2801 * Make a new name for the view, ensuring it is unique within the current
2802 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2803 * these now use viewId. Unique view names are still desirable for usability.)
2808 protected String getNewViewName(String viewTitle)
2810 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2811 boolean addFirstIndex = false;
2812 if (viewTitle == null || viewTitle.trim().length() == 0)
2814 viewTitle = MessageManager.getString("action.view");
2815 addFirstIndex = true;
2819 index = 1;// we count from 1 if given a specific name
2821 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2823 List<Component> comps = PaintRefresher.components.get(viewport
2824 .getSequenceSetId());
2826 List<String> existingNames = getExistingViewNames(comps);
2828 while (existingNames.contains(newViewName))
2830 newViewName = viewTitle + " " + (++index);
2836 * Returns a list of distinct view names found in the given list of
2837 * components. View names are held on the viewport of an AlignmentPanel.
2842 protected List<String> getExistingViewNames(List<Component> comps)
2844 List<String> existingNames = new ArrayList<>();
2845 for (Component comp : comps)
2847 if (comp instanceof AlignmentPanel)
2849 AlignmentPanel ap = (AlignmentPanel) comp;
2850 if (!existingNames.contains(ap.av.viewName))
2852 existingNames.add(ap.av.viewName);
2856 return existingNames;
2860 * Explode tabbed views into separate windows.
2863 public void expandViews_actionPerformed(ActionEvent e)
2865 Desktop.explodeViews(this);
2869 * Gather views in separate windows back into a tabbed presentation.
2872 public void gatherViews_actionPerformed(ActionEvent e)
2874 Desktop.instance.gatherViews(this);
2884 public void font_actionPerformed(ActionEvent e)
2886 new FontChooser(alignPanel);
2896 protected void seqLimit_actionPerformed(ActionEvent e)
2898 viewport.setShowJVSuffix(seqLimits.isSelected());
2900 alignPanel.getIdPanel().getIdCanvas()
2901 .setPreferredSize(alignPanel.calculateIdWidth());
2902 alignPanel.paintAlignment(true);
2906 public void idRightAlign_actionPerformed(ActionEvent e)
2908 viewport.setRightAlignIds(idRightAlign.isSelected());
2909 alignPanel.paintAlignment(true);
2913 public void centreColumnLabels_actionPerformed(ActionEvent e)
2915 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2916 alignPanel.paintAlignment(true);
2922 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2925 protected void followHighlight_actionPerformed()
2928 * Set the 'follow' flag on the Viewport (and scroll to position if now
2931 final boolean state = this.followHighlightMenuItem.getState();
2932 viewport.setFollowHighlight(state);
2935 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2946 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2948 viewport.setColourText(colourTextMenuItem.isSelected());
2949 alignPanel.paintAlignment(true);
2959 public void wrapMenuItem_actionPerformed(ActionEvent e)
2961 scaleAbove.setVisible(wrapMenuItem.isSelected());
2962 scaleLeft.setVisible(wrapMenuItem.isSelected());
2963 scaleRight.setVisible(wrapMenuItem.isSelected());
2964 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2965 alignPanel.updateLayout();
2969 public void showAllSeqs_actionPerformed(ActionEvent e)
2971 viewport.showAllHiddenSeqs();
2975 public void showAllColumns_actionPerformed(ActionEvent e)
2977 viewport.showAllHiddenColumns();
2979 viewport.sendSelection();
2983 public void hideSelSequences_actionPerformed(ActionEvent e)
2985 viewport.hideAllSelectedSeqs();
2986 // alignPanel.paintAlignment(true);
2990 * called by key handler and the hide all/show all menu items
2995 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2998 boolean hide = false;
2999 SequenceGroup sg = viewport.getSelectionGroup();
3000 if (!toggleSeqs && !toggleCols)
3002 // Hide everything by the current selection - this is a hack - we do the
3003 // invert and then hide
3004 // first check that there will be visible columns after the invert.
3005 if (viewport.hasSelectedColumns()
3006 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
3009 // now invert the sequence set, if required - empty selection implies
3010 // that no hiding is required.
3013 invertSequenceMenuItem_actionPerformed(null);
3014 sg = viewport.getSelectionGroup();
3018 viewport.expandColSelection(sg, true);
3019 // finally invert the column selection and get the new sequence
3021 invertColSel_actionPerformed(null);
3028 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3030 hideSelSequences_actionPerformed(null);
3033 else if (!(toggleCols && viewport.hasSelectedColumns()))
3035 showAllSeqs_actionPerformed(null);
3041 if (viewport.hasSelectedColumns())
3043 hideSelColumns_actionPerformed(null);
3046 viewport.setSelectionGroup(sg);
3051 showAllColumns_actionPerformed(null);
3060 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3061 * event.ActionEvent)
3064 public void hideAllButSelection_actionPerformed(ActionEvent e)
3066 toggleHiddenRegions(false, false);
3067 viewport.sendSelection();
3074 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3078 public void hideAllSelection_actionPerformed(ActionEvent e)
3080 SequenceGroup sg = viewport.getSelectionGroup();
3081 viewport.expandColSelection(sg, false);
3082 viewport.hideAllSelectedSeqs();
3083 viewport.hideSelectedColumns();
3084 alignPanel.paintAlignment(true);
3085 viewport.sendSelection();
3092 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3096 public void showAllhidden_actionPerformed(ActionEvent e)
3098 viewport.showAllHiddenColumns();
3099 viewport.showAllHiddenSeqs();
3100 alignPanel.paintAlignment(true);
3101 viewport.sendSelection();
3105 public void hideSelColumns_actionPerformed(ActionEvent e)
3107 viewport.hideSelectedColumns();
3108 alignPanel.paintAlignment(true);
3109 viewport.sendSelection();
3113 public void hiddenMarkers_actionPerformed(ActionEvent e)
3115 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3126 protected void scaleAbove_actionPerformed(ActionEvent e)
3128 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3129 alignPanel.paintAlignment(true);
3139 protected void scaleLeft_actionPerformed(ActionEvent e)
3141 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3142 alignPanel.paintAlignment(true);
3152 protected void scaleRight_actionPerformed(ActionEvent e)
3154 viewport.setScaleRightWrapped(scaleRight.isSelected());
3155 alignPanel.paintAlignment(true);
3165 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3167 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3168 alignPanel.paintAlignment(true);
3178 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3180 viewport.setShowText(viewTextMenuItem.isSelected());
3181 alignPanel.paintAlignment(true);
3191 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3193 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3194 alignPanel.paintAlignment(true);
3197 public FeatureSettings featureSettings;
3200 public FeatureSettingsControllerI getFeatureSettingsUI()
3202 return featureSettings;
3206 public void featureSettings_actionPerformed(ActionEvent e)
3208 if (featureSettings != null)
3210 featureSettings.close();
3211 featureSettings = null;
3213 if (!showSeqFeatures.isSelected())
3215 // make sure features are actually displayed
3216 showSeqFeatures.setSelected(true);
3217 showSeqFeatures_actionPerformed(null);
3219 featureSettings = new FeatureSettings(this);
3223 * Set or clear 'Show Sequence Features'
3229 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3231 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3232 alignPanel.paintAlignment(true);
3233 if (alignPanel.getOverviewPanel() != null)
3235 alignPanel.getOverviewPanel().updateOverviewImage();
3240 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3241 * the annotations panel as a whole.
3243 * The options to show/hide all annotations should be enabled when the panel
3244 * is shown, and disabled when the panel is hidden.
3249 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3251 final boolean setVisible = annotationPanelMenuItem.isSelected();
3252 viewport.setShowAnnotation(setVisible);
3253 this.showAllSeqAnnotations.setEnabled(setVisible);
3254 this.hideAllSeqAnnotations.setEnabled(setVisible);
3255 this.showAllAlAnnotations.setEnabled(setVisible);
3256 this.hideAllAlAnnotations.setEnabled(setVisible);
3257 alignPanel.updateLayout();
3261 public void alignmentProperties()
3263 JEditorPane editPane = new JEditorPane("text/html", "");
3264 editPane.setEditable(false);
3265 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3267 editPane.setText(MessageManager.formatMessage("label.html_content",
3268 new Object[] { contents.toString() }));
3269 JInternalFrame frame = new JInternalFrame();
3270 frame.getContentPane().add(new JScrollPane(editPane));
3272 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3273 "label.alignment_properties", new Object[] { getTitle() }),
3284 public void overviewMenuItem_actionPerformed(ActionEvent e)
3286 if (alignPanel.overviewPanel != null)
3291 JInternalFrame frame = new JInternalFrame();
3292 OverviewPanel overview = new OverviewPanel(alignPanel);
3293 frame.setContentPane(overview);
3294 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3295 "label.overview_params", new Object[] { this.getTitle() }),
3296 true, frame.getWidth(), frame.getHeight(), true, true);
3298 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3299 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3302 public void internalFrameClosed(
3303 javax.swing.event.InternalFrameEvent evt)
3305 alignPanel.setOverviewPanel(null);
3309 alignPanel.setOverviewPanel(overview);
3313 public void textColour_actionPerformed()
3315 new TextColourChooser().chooseColour(alignPanel, null);
3319 * public void covariationColour_actionPerformed() {
3321 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3325 public void annotationColour_actionPerformed()
3327 new AnnotationColourChooser(viewport, alignPanel);
3331 public void annotationColumn_actionPerformed(ActionEvent e)
3333 new AnnotationColumnChooser(viewport, alignPanel);
3337 * Action on the user checking or unchecking the option to apply the selected
3338 * colour scheme to all groups. If unchecked, groups may have their own
3339 * independent colour schemes.
3344 public void applyToAllGroups_actionPerformed(boolean selected)
3346 viewport.setColourAppliesToAllGroups(selected);
3350 * Action on user selecting a colour from the colour menu
3353 * the name (not the menu item label!) of the colour scheme
3356 public void changeColour_actionPerformed(String name)
3359 * 'User Defined' opens a panel to configure or load a
3360 * user-defined colour scheme
3362 if (ResidueColourScheme.USER_DEFINED.equals(name))
3364 new UserDefinedColours(alignPanel);
3369 * otherwise set the chosen colour scheme (or null for 'None')
3371 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3372 viewport.getAlignment(), viewport.getHiddenRepSequences());
3377 * Actions on setting or changing the alignment colour scheme
3382 public void changeColour(ColourSchemeI cs)
3384 // TODO: pull up to controller method
3385 ColourMenuHelper.setColourSelected(colourMenu, cs);
3387 viewport.setGlobalColourScheme(cs);
3389 alignPanel.paintAlignment(true);
3393 * Show the PID threshold slider panel
3396 protected void modifyPID_actionPerformed()
3398 SliderPanel.setPIDSliderSource(alignPanel,
3399 viewport.getResidueShading(), alignPanel.getViewName());
3400 SliderPanel.showPIDSlider();
3404 * Show the Conservation slider panel
3407 protected void modifyConservation_actionPerformed()
3409 SliderPanel.setConservationSlider(alignPanel,
3410 viewport.getResidueShading(), alignPanel.getViewName());
3411 SliderPanel.showConservationSlider();
3415 * Action on selecting or deselecting (Colour) By Conservation
3418 public void conservationMenuItem_actionPerformed(boolean selected)
3420 modifyConservation.setEnabled(selected);
3421 viewport.setConservationSelected(selected);
3422 viewport.getResidueShading().setConservationApplied(selected);
3424 changeColour(viewport.getGlobalColourScheme());
3427 modifyConservation_actionPerformed();
3431 SliderPanel.hideConservationSlider();
3436 * Action on selecting or deselecting (Colour) Above PID Threshold
3439 public void abovePIDThreshold_actionPerformed(boolean selected)
3441 modifyPID.setEnabled(selected);
3442 viewport.setAbovePIDThreshold(selected);
3445 viewport.getResidueShading().setThreshold(0,
3446 viewport.isIgnoreGapsConsensus());
3449 changeColour(viewport.getGlobalColourScheme());
3452 modifyPID_actionPerformed();
3456 SliderPanel.hidePIDSlider();
3467 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3469 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3470 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3471 .getAlignment().getSequenceAt(0));
3472 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3473 viewport.getAlignment()));
3474 alignPanel.paintAlignment(true);
3484 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3486 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3487 AlignmentSorter.sortByID(viewport.getAlignment());
3488 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3489 viewport.getAlignment()));
3490 alignPanel.paintAlignment(true);
3500 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3502 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3503 AlignmentSorter.sortByLength(viewport.getAlignment());
3504 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3505 viewport.getAlignment()));
3506 alignPanel.paintAlignment(true);
3516 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3518 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3519 AlignmentSorter.sortByGroup(viewport.getAlignment());
3520 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3521 viewport.getAlignment()));
3523 alignPanel.paintAlignment(true);
3533 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3535 new RedundancyPanel(alignPanel, this);
3545 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3547 if ((viewport.getSelectionGroup() == null)
3548 || (viewport.getSelectionGroup().getSize() < 2))
3550 JvOptionPane.showInternalMessageDialog(this, MessageManager
3551 .getString("label.you_must_select_least_two_sequences"),
3552 MessageManager.getString("label.invalid_selection"),
3553 JvOptionPane.WARNING_MESSAGE);
3557 JInternalFrame frame = new JInternalFrame();
3558 frame.setContentPane(new PairwiseAlignPanel(viewport));
3559 Desktop.addInternalFrame(frame,
3560 MessageManager.getString("action.pairwise_alignment"), 600,
3566 public void autoCalculate_actionPerformed(ActionEvent e)
3568 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3569 if (viewport.autoCalculateConsensus)
3571 viewport.firePropertyChange("alignment", null, viewport
3572 .getAlignment().getSequences());
3577 public void sortByTreeOption_actionPerformed(ActionEvent e)
3579 viewport.sortByTree = sortByTree.isSelected();
3583 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3585 viewport.followSelection = listenToViewSelections.isSelected();
3589 * Constructs a tree panel and adds it to the desktop
3592 * tree type (NJ or AV)
3594 * name of score model used to compute the tree
3596 * parameters for the distance or similarity calculation
3598 void newTreePanel(String type, String modelName, SimilarityParamsI options)
3600 String frameTitle = "";
3603 boolean onSelection = false;
3604 if (viewport.getSelectionGroup() != null
3605 && viewport.getSelectionGroup().getSize() > 0)
3607 SequenceGroup sg = viewport.getSelectionGroup();
3609 /* Decide if the selection is a column region */
3610 for (SequenceI _s : sg.getSequences())
3612 if (_s.getLength() < sg.getEndRes())
3618 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3620 .getString("label.sequences_selection_not_aligned"),
3621 JvOptionPane.WARNING_MESSAGE);
3630 if (viewport.getAlignment().getHeight() < 2)
3636 tp = new TreePanel(alignPanel, type, modelName, options);
3637 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3639 frameTitle += " from ";
3641 if (viewport.viewName != null)
3643 frameTitle += viewport.viewName + " of ";
3646 frameTitle += this.title;
3648 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3659 public void addSortByOrderMenuItem(String title,
3660 final AlignmentOrder order)
3662 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3663 "action.by_title_param", new Object[] { title }));
3665 item.addActionListener(new java.awt.event.ActionListener()
3668 public void actionPerformed(ActionEvent e)
3670 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3672 // TODO: JBPNote - have to map order entries to curent SequenceI
3674 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3676 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3679 alignPanel.paintAlignment(true);
3685 * Add a new sort by annotation score menu item
3688 * the menu to add the option to
3690 * the label used to retrieve scores for each sequence on the
3693 public void addSortByAnnotScoreMenuItem(JMenu sort,
3694 final String scoreLabel)
3696 final JMenuItem item = new JMenuItem(scoreLabel);
3698 item.addActionListener(new java.awt.event.ActionListener()
3701 public void actionPerformed(ActionEvent e)
3703 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3704 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3705 viewport.getAlignment());// ,viewport.getSelectionGroup());
3706 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3707 viewport.getAlignment()));
3708 alignPanel.paintAlignment(true);
3714 * last hash for alignment's annotation array - used to minimise cost of
3717 protected int _annotationScoreVectorHash;
3720 * search the alignment and rebuild the sort by annotation score submenu the
3721 * last alignment annotation vector hash is stored to minimize cost of
3722 * rebuilding in subsequence calls.
3726 public void buildSortByAnnotationScoresMenu()
3728 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3733 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3735 sortByAnnotScore.removeAll();
3736 // almost certainly a quicker way to do this - but we keep it simple
3737 Hashtable scoreSorts = new Hashtable();
3738 AlignmentAnnotation aann[];
3739 for (SequenceI sqa : viewport.getAlignment().getSequences())
3741 aann = sqa.getAnnotation();
3742 for (int i = 0; aann != null && i < aann.length; i++)
3744 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3746 scoreSorts.put(aann[i].label, aann[i].label);
3750 Enumeration labels = scoreSorts.keys();
3751 while (labels.hasMoreElements())
3753 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3754 (String) labels.nextElement());
3756 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3759 _annotationScoreVectorHash = viewport.getAlignment()
3760 .getAlignmentAnnotation().hashCode();
3765 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3766 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3767 * call. Listeners are added to remove the menu item when the treePanel is
3768 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3772 public void buildTreeSortMenu()
3774 sortByTreeMenu.removeAll();
3776 List<Component> comps = PaintRefresher.components.get(viewport
3777 .getSequenceSetId());
3778 List<TreePanel> treePanels = new ArrayList<>();
3779 for (Component comp : comps)
3781 if (comp instanceof TreePanel)
3783 treePanels.add((TreePanel) comp);
3787 if (treePanels.size() < 1)
3789 sortByTreeMenu.setVisible(false);
3793 sortByTreeMenu.setVisible(true);
3795 for (final TreePanel tp : treePanels)
3797 final JMenuItem item = new JMenuItem(tp.getTitle());
3798 item.addActionListener(new java.awt.event.ActionListener()
3801 public void actionPerformed(ActionEvent e)
3803 tp.sortByTree_actionPerformed();
3804 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3809 sortByTreeMenu.add(item);
3813 public boolean sortBy(AlignmentOrder alorder, String undoname)
3815 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3816 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3817 if (undoname != null)
3819 addHistoryItem(new OrderCommand(undoname, oldOrder,
3820 viewport.getAlignment()));
3822 alignPanel.paintAlignment(true);
3827 * Work out whether the whole set of sequences or just the selected set will
3828 * be submitted for multiple alignment.
3831 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3833 // Now, check we have enough sequences
3834 AlignmentView msa = null;
3836 if ((viewport.getSelectionGroup() != null)
3837 && (viewport.getSelectionGroup().getSize() > 1))
3839 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3840 // some common interface!
3842 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3843 * SequenceI[sz = seqs.getSize(false)];
3845 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3846 * seqs.getSequenceAt(i); }
3848 msa = viewport.getAlignmentView(true);
3850 else if (viewport.getSelectionGroup() != null
3851 && viewport.getSelectionGroup().getSize() == 1)
3853 int option = JvOptionPane.showConfirmDialog(this,
3854 MessageManager.getString("warn.oneseq_msainput_selection"),
3855 MessageManager.getString("label.invalid_selection"),
3856 JvOptionPane.OK_CANCEL_OPTION);
3857 if (option == JvOptionPane.OK_OPTION)
3859 msa = viewport.getAlignmentView(false);
3864 msa = viewport.getAlignmentView(false);
3870 * Decides what is submitted to a secondary structure prediction service: the
3871 * first sequence in the alignment, or in the current selection, or, if the
3872 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3873 * region or the whole alignment. (where the first sequence in the set is the
3874 * one that the prediction will be for).
3876 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3878 AlignmentView seqs = null;
3880 if ((viewport.getSelectionGroup() != null)
3881 && (viewport.getSelectionGroup().getSize() > 0))
3883 seqs = viewport.getAlignmentView(true);
3887 seqs = viewport.getAlignmentView(false);
3889 // limit sequences - JBPNote in future - could spawn multiple prediction
3891 // TODO: viewport.getAlignment().isAligned is a global state - the local
3892 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3893 if (!viewport.getAlignment().isAligned(false))
3895 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3896 // TODO: if seqs.getSequences().length>1 then should really have warned
3910 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3912 // Pick the tree file
3913 JalviewFileChooser chooser = new JalviewFileChooser(
3914 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3915 chooser.setFileView(new JalviewFileView());
3916 chooser.setDialogTitle(MessageManager
3917 .getString("label.select_newick_like_tree_file"));
3918 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3920 int value = chooser.showOpenDialog(null);
3922 if (value == JalviewFileChooser.APPROVE_OPTION)
3924 String filePath = chooser.getSelectedFile().getPath();
3925 Cache.setProperty("LAST_DIRECTORY", filePath);
3926 NewickFile fin = null;
3929 fin = new NewickFile(filePath, DataSourceType.FILE);
3930 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3931 } catch (Exception ex)
3938 .getString("label.problem_reading_tree_file"),
3939 JvOptionPane.WARNING_MESSAGE);
3940 ex.printStackTrace();
3942 if (fin != null && fin.hasWarningMessage())
3944 JvOptionPane.showMessageDialog(Desktop.desktop, fin
3945 .getWarningMessage(), MessageManager
3946 .getString("label.possible_problem_with_tree_file"),
3947 JvOptionPane.WARNING_MESSAGE);
3952 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3954 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3957 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3958 int h, int x, int y)
3960 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3964 * Add a treeviewer for the tree extracted from a Newick file object to the
3965 * current alignment view
3972 * Associated alignment input data (or null)
3981 * @return TreePanel handle
3983 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3984 AlignmentView input, int w, int h, int x, int y)
3986 TreePanel tp = null;
3992 if (nf.getTree() != null)
3994 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4000 tp.setLocation(x, y);
4003 Desktop.addInternalFrame(tp, treeTitle, w, h);
4005 } catch (Exception ex)
4007 ex.printStackTrace();
4013 private boolean buildingMenu = false;
4016 * Generates menu items and listener event actions for web service clients
4019 public void BuildWebServiceMenu()
4021 while (buildingMenu)
4025 System.err.println("Waiting for building menu to finish.");
4027 } catch (Exception e)
4031 final AlignFrame me = this;
4032 buildingMenu = true;
4033 new Thread(new Runnable()
4038 final List<JMenuItem> legacyItems = new ArrayList<>();
4041 // System.err.println("Building ws menu again "
4042 // + Thread.currentThread());
4043 // TODO: add support for context dependent disabling of services based
4045 // alignment and current selection
4046 // TODO: add additional serviceHandle parameter to specify abstract
4048 // class independently of AbstractName
4049 // TODO: add in rediscovery GUI function to restart discoverer
4050 // TODO: group services by location as well as function and/or
4052 // object broker mechanism.
4053 final Vector<JMenu> wsmenu = new Vector<>();
4054 final IProgressIndicator af = me;
4057 * do not i18n these strings - they are hard-coded in class
4058 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4059 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4061 final JMenu msawsmenu = new JMenu("Alignment");
4062 final JMenu secstrmenu = new JMenu(
4063 "Secondary Structure Prediction");
4064 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4065 final JMenu analymenu = new JMenu("Analysis");
4066 final JMenu dismenu = new JMenu("Protein Disorder");
4067 // JAL-940 - only show secondary structure prediction services from
4068 // the legacy server
4069 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4071 Discoverer.services != null && (Discoverer.services.size() > 0))
4073 // TODO: refactor to allow list of AbstractName/Handler bindings to
4075 // stored or retrieved from elsewhere
4076 // No MSAWS used any more:
4077 // Vector msaws = null; // (Vector)
4078 // Discoverer.services.get("MsaWS");
4079 Vector secstrpr = (Vector) Discoverer.services
4081 if (secstrpr != null)
4083 // Add any secondary structure prediction services
4084 for (int i = 0, j = secstrpr.size(); i < j; i++)
4086 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4088 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4089 .getServiceClient(sh);
4090 int p = secstrmenu.getItemCount();
4091 impl.attachWSMenuEntry(secstrmenu, me);
4092 int q = secstrmenu.getItemCount();
4093 for (int litm = p; litm < q; litm++)
4095 legacyItems.add(secstrmenu.getItem(litm));
4101 // Add all submenus in the order they should appear on the web
4103 wsmenu.add(msawsmenu);
4104 wsmenu.add(secstrmenu);
4105 wsmenu.add(dismenu);
4106 wsmenu.add(analymenu);
4107 // No search services yet
4108 // wsmenu.add(seqsrchmenu);
4110 javax.swing.SwingUtilities.invokeLater(new Runnable()
4117 webService.removeAll();
4118 // first, add discovered services onto the webservices menu
4119 if (wsmenu.size() > 0)
4121 for (int i = 0, j = wsmenu.size(); i < j; i++)
4123 webService.add(wsmenu.get(i));
4128 webService.add(me.webServiceNoServices);
4130 // TODO: move into separate menu builder class.
4131 boolean new_sspred = false;
4132 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4134 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4135 if (jws2servs != null)
4137 if (jws2servs.hasServices())
4139 jws2servs.attachWSMenuEntry(webService, me);
4140 for (Jws2Instance sv : jws2servs.getServices())
4142 if (sv.description.toLowerCase().contains("jpred"))
4144 for (JMenuItem jmi : legacyItems)
4146 jmi.setVisible(false);
4152 if (jws2servs.isRunning())
4154 JMenuItem tm = new JMenuItem(
4155 "Still discovering JABA Services");
4156 tm.setEnabled(false);
4161 build_urlServiceMenu(me.webService);
4162 build_fetchdbmenu(webService);
4163 for (JMenu item : wsmenu)
4165 if (item.getItemCount() == 0)
4167 item.setEnabled(false);
4171 item.setEnabled(true);
4174 } catch (Exception e)
4177 .debug("Exception during web service menu building process.",
4182 } catch (Exception e)
4185 buildingMenu = false;
4192 * construct any groupURL type service menu entries.
4196 private void build_urlServiceMenu(JMenu webService)
4198 // TODO: remove this code when 2.7 is released
4199 // DEBUG - alignmentView
4201 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4202 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4204 * @Override public void actionPerformed(ActionEvent e) {
4205 * jalview.datamodel.AlignmentView
4206 * .testSelectionViews(af.viewport.getAlignment(),
4207 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4209 * }); webService.add(testAlView);
4211 // TODO: refactor to RestClient discoverer and merge menu entries for
4212 // rest-style services with other types of analysis/calculation service
4213 // SHmmr test client - still being implemented.
4214 // DEBUG - alignmentView
4216 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4219 client.attachWSMenuEntry(
4220 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4226 * Searches the alignment sequences for xRefs and builds the Show
4227 * Cross-References menu (formerly called Show Products), with database
4228 * sources for which cross-references are found (protein sources for a
4229 * nucleotide alignment and vice versa)
4231 * @return true if Show Cross-references menu should be enabled
4233 public boolean canShowProducts()
4235 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4236 AlignmentI dataset = viewport.getAlignment().getDataset();
4238 showProducts.removeAll();
4239 final boolean dna = viewport.getAlignment().isNucleotide();
4241 if (seqs == null || seqs.length == 0)
4243 // nothing to see here.
4247 boolean showp = false;
4250 List<String> ptypes = new CrossRef(seqs, dataset)
4251 .findXrefSourcesForSequences(dna);
4253 for (final String source : ptypes)
4256 final AlignFrame af = this;
4257 JMenuItem xtype = new JMenuItem(source);
4258 xtype.addActionListener(new ActionListener()
4261 public void actionPerformed(ActionEvent e)
4263 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4266 showProducts.add(xtype);
4268 showProducts.setVisible(showp);
4269 showProducts.setEnabled(showp);
4270 } catch (Exception e)
4273 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4281 * Finds and displays cross-references for the selected sequences (protein
4282 * products for nucleotide sequences, dna coding sequences for peptides).
4285 * the sequences to show cross-references for
4287 * true if from a nucleotide alignment (so showing proteins)
4289 * the database to show cross-references for
4291 protected void showProductsFor(final SequenceI[] sel,
4292 final boolean _odna, final String source)
4294 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4299 * Construct and display a new frame containing the translation of this
4300 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4303 public void showTranslation_actionPerformed(ActionEvent e)
4305 AlignmentI al = null;
4308 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4310 al = dna.translateCdna();
4311 } catch (Exception ex)
4313 jalview.bin.Cache.log.error(
4314 "Exception during translation. Please report this !", ex);
4315 final String msg = MessageManager
4316 .getString("label.error_when_translating_sequences_submit_bug_report");
4317 final String errorTitle = MessageManager
4318 .getString("label.implementation_error")
4319 + MessageManager.getString("label.translation_failed");
4320 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4321 JvOptionPane.ERROR_MESSAGE);
4324 if (al == null || al.getHeight() == 0)
4326 final String msg = MessageManager
4327 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4328 final String errorTitle = MessageManager
4329 .getString("label.translation_failed");
4330 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4331 JvOptionPane.WARNING_MESSAGE);
4335 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4336 af.setFileFormat(this.currentFileFormat);
4337 final String newTitle = MessageManager.formatMessage(
4338 "label.translation_of_params",
4339 new Object[] { this.getTitle() });
4340 af.setTitle(newTitle);
4341 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4343 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4344 viewport.openSplitFrame(af, new Alignment(seqs));
4348 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4355 * Set the file format
4359 public void setFileFormat(FileFormatI format)
4361 this.currentFileFormat = format;
4365 * Try to load a features file onto the alignment.
4368 * contents or path to retrieve file
4370 * access mode of file (see jalview.io.AlignFile)
4371 * @return true if features file was parsed correctly.
4373 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4375 return avc.parseFeaturesFile(file, sourceType,
4376 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4381 public void refreshFeatureUI(boolean enableIfNecessary)
4383 // note - currently this is only still here rather than in the controller
4384 // because of the featureSettings hard reference that is yet to be
4386 if (enableIfNecessary)
4388 viewport.setShowSequenceFeatures(true);
4389 showSeqFeatures.setSelected(true);
4395 public void dragEnter(DropTargetDragEvent evt)
4400 public void dragExit(DropTargetEvent evt)
4405 public void dragOver(DropTargetDragEvent evt)
4410 public void dropActionChanged(DropTargetDragEvent evt)
4415 public void drop(DropTargetDropEvent evt)
4417 // JAL-1552 - acceptDrop required before getTransferable call for
4418 // Java's Transferable for native dnd
4419 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4420 Transferable t = evt.getTransferable();
4421 List<String> files = new ArrayList<>();
4422 List<DataSourceType> protocols = new ArrayList<>();
4426 Desktop.transferFromDropTarget(files, protocols, evt, t);
4427 } catch (Exception e)
4429 e.printStackTrace();
4435 // check to see if any of these files have names matching sequences in
4437 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4438 .getAlignment().getSequencesArray());
4440 * Object[] { String,SequenceI}
4442 ArrayList<Object[]> filesmatched = new ArrayList<>();
4443 ArrayList<String> filesnotmatched = new ArrayList<>();
4444 for (int i = 0; i < files.size(); i++)
4446 String file = files.get(i).toString();
4448 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4449 if (protocol == DataSourceType.FILE)
4451 File fl = new File(file);
4452 pdbfn = fl.getName();
4454 else if (protocol == DataSourceType.URL)
4456 URL url = new URL(file);
4457 pdbfn = url.getFile();
4459 if (pdbfn.length() > 0)
4461 // attempt to find a match in the alignment
4462 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4463 int l = 0, c = pdbfn.indexOf(".");
4464 while (mtch == null && c != -1)
4469 } while ((c = pdbfn.indexOf(".", l)) > l);
4472 pdbfn = pdbfn.substring(0, l);
4474 mtch = idm.findAllIdMatches(pdbfn);
4478 FileFormatI type = null;
4481 type = new IdentifyFile().identify(file, protocol);
4482 } catch (Exception ex)
4486 if (type != null && type.isStructureFile())
4488 filesmatched.add(new Object[] { file, protocol, mtch });
4492 // File wasn't named like one of the sequences or wasn't a PDB file.
4493 filesnotmatched.add(file);
4497 if (filesmatched.size() > 0)
4499 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4505 "label.automatically_associate_structure_files_with_sequences_same_name",
4506 new Object[] { Integer
4512 .getString("label.automatically_associate_structure_files_by_name"),
4513 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4516 for (Object[] fm : filesmatched)
4518 // try and associate
4519 // TODO: may want to set a standard ID naming formalism for
4520 // associating PDB files which have no IDs.
4521 for (SequenceI toassoc : (SequenceI[]) fm[2])
4523 PDBEntry pe = new AssociatePdbFileWithSeq()
4524 .associatePdbWithSeq((String) fm[0],
4525 (DataSourceType) fm[1], toassoc, false,
4529 System.err.println("Associated file : "
4530 + ((String) fm[0]) + " with "
4531 + toassoc.getDisplayId(true));
4535 alignPanel.paintAlignment(true);
4539 if (filesnotmatched.size() > 0)
4542 && (Cache.getDefault(
4543 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4549 "label.ignore_unmatched_dropped_files_info",
4550 new Object[] { Integer
4557 .getString("label.ignore_unmatched_dropped_files"),
4558 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4562 for (String fn : filesnotmatched)
4564 loadJalviewDataFile(fn, null, null, null);
4568 } catch (Exception ex)
4570 ex.printStackTrace();
4576 * Attempt to load a "dropped" file or URL string, by testing in turn for
4578 * <li>an Annotation file</li>
4579 * <li>a JNet file</li>
4580 * <li>a features file</li>
4581 * <li>else try to interpret as an alignment file</li>
4585 * either a filename or a URL string.
4587 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4588 FileFormatI format, SequenceI assocSeq)
4592 if (sourceType == null)
4594 sourceType = FormatAdapter.checkProtocol(file);
4596 // if the file isn't identified, or not positively identified as some
4597 // other filetype (PFAM is default unidentified alignment file type) then
4598 // try to parse as annotation.
4599 boolean isAnnotation = (format == null || FileFormat.Pfam
4600 .equals(format)) ? new AnnotationFile()
4601 .annotateAlignmentView(viewport, file, sourceType) : false;
4605 // first see if its a T-COFFEE score file
4606 TCoffeeScoreFile tcf = null;
4609 tcf = new TCoffeeScoreFile(file, sourceType);
4612 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4615 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4616 isAnnotation = true;
4618 .setText(MessageManager
4619 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4623 // some problem - if no warning its probable that the ID matching
4624 // process didn't work
4628 tcf.getWarningMessage() == null ? MessageManager
4629 .getString("label.check_file_matches_sequence_ids_alignment")
4630 : tcf.getWarningMessage(),
4632 .getString("label.problem_reading_tcoffee_score_file"),
4633 JvOptionPane.WARNING_MESSAGE);
4640 } catch (Exception x)
4643 .debug("Exception when processing data source as T-COFFEE score file",
4649 // try to see if its a JNet 'concise' style annotation file *before*
4651 // try to parse it as a features file
4654 format = new IdentifyFile().identify(file, sourceType);
4656 if (FileFormat.ScoreMatrix == format)
4658 ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4661 // todo: i18n this message
4663 .setText(MessageManager.formatMessage(
4664 "label.successfully_loaded_matrix",
4665 sm.getMatrixName()));
4667 else if (FileFormat.HMMER3.equals(format))
4669 HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType)); // TODO
4676 HiddenMarkovModel hmm = hmmFile.getHMM();
4677 AlignmentAnnotation annotation = hmm.createAnnotation(
4678 getViewport().getAlignment().getWidth());
4679 getViewport().getAlignment().addAnnotation(annotation);
4680 annotation.setHMM(hmm);
4681 isAnnotation = true;
4683 BufferedReader input = new BufferedReader(new FileReader(
4684 "H:/Desktop/Distributions/BadAlignment-8.csv"));
4685 String line = input.readLine();
4687 while (!("".equals(line)) && line != null)
4689 Scanner scanner = new Scanner(line);
4690 if (scanner.hasNext())
4692 scanner.useDelimiter(",");
4693 String value = scanner.next();
4695 distribution.put(value, scanner.nextFloat());
4696 line = input.readLine();
4701 AlignmentI alignment = getViewport().getAlignment();
4703 final int AMINO = 0;
4706 if ("amino".equals(hmm.getAlphabetType()))
4710 else if ("DNA".equals(hmm.getAlphabetType()))
4714 else if ("RNA".equals(hmm.getAlphabetType()))
4722 for (int l = 1; l < hmm.getLength() + 1; l++)
4724 for (int n = 0; n < alignment.getHeight(); n++)
4727 char character = alignment.getSequenceAt(n)
4728 .getCharAt(hmm.getNodeAlignmentColumn(l));
4729 character = Character.toUpperCase(character);
4735 containedD = ResidueProperties.dnaBackgroundFrequencies
4736 .containsKey(character);
4737 containedA = ResidueProperties.aminoBackgroundFrequencies
4738 .containsKey(character);
4739 containedR = ResidueProperties.rnaBackgroundFrequencies
4740 .containsKey(character);
4742 if (!Comparison.isGap(character)
4743 && ((alpha == DNA && containedD)
4744 || (alpha == AMINO && containedA)))
4752 for (int l = 1; l < hmm.getLength() + 1; l++)
4754 for (int n = 0; n < alignment.getHeight(); n++)
4758 character = alignment.getSequenceAt(n)
4759 .getCharAt(hmm.getNodeAlignmentColumn(l));
4760 character = Character.toUpperCase(character);
4765 containedN = ResidueProperties.dnaBackgroundFrequencies
4766 .containsKey(character);
4767 containedA = ResidueProperties.aminoBackgroundFrequencies
4768 .containsKey(character);
4769 containedR = ResidueProperties.rnaBackgroundFrequencies
4770 .containsKey(character);
4772 if (!Comparison.isGap(character)
4773 && ((alpha == DNA && containedN)
4774 || (alpha == AMINO && containedA)))
4776 prob = hmm.getMatchEmissionProbability(
4777 hmm.getNodeAlignmentColumn(l), character);
4780 System.out.println("?");
4786 freq = ResidueProperties.aminoBackgroundFrequencies
4791 freq = ResidueProperties.dnaBackgroundFrequencies
4796 freq = ResidueProperties.rnaBackgroundFrequencies
4799 Double doubleValue = Math.log(prob / freq);
4801 String value = String.format("%.1f", doubleValue);
4802 if ("-0.0".equals(value))
4806 if (distribution.containsKey(value))
4808 float prev = distribution.get(value);
4809 prev = prev + (10000f / size);
4810 distribution.put(value, prev);
4814 distribution.put(value, 10000f / size);
4823 PrintWriter writer = new PrintWriter(
4825 "H:/Desktop/Distributions/BadAlignment-8.csv"));
4826 for (Map.Entry<String, Float> entry : distribution
4829 writer.println(entry.getKey() + "," + entry.getValue());
4837 else if (FileFormat.Jnet.equals(format))
4839 JPredFile predictions = new JPredFile(file, sourceType);
4840 new JnetAnnotationMaker();
4841 JnetAnnotationMaker.add_annotation(predictions,
4842 viewport.getAlignment(), 0, false);
4843 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4844 viewport.getAlignment().setSeqrep(repseq);
4845 HiddenColumns cs = new HiddenColumns();
4846 cs.hideInsertionsFor(repseq);
4847 viewport.getAlignment().setHiddenColumns(cs);
4848 isAnnotation = true;
4850 // else if (IdentifyFile.FeaturesFile.equals(format))
4851 else if (FileFormat.Features.equals(format))
4853 if (parseFeaturesFile(file, sourceType))
4855 alignPanel.paintAlignment(true);
4860 new FileLoader().LoadFile(viewport, file, sourceType, format);
4867 alignPanel.adjustAnnotationHeight();
4868 viewport.updateSequenceIdColours();
4869 buildSortByAnnotationScoresMenu();
4870 alignPanel.paintAlignment(true);
4872 } catch (Exception ex)
4874 ex.printStackTrace();
4875 } catch (OutOfMemoryError oom)
4880 } catch (Exception x)
4885 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4886 : "using " + sourceType + " from " + file)
4888 + (format != null ? "(parsing as '" + format
4889 + "' file)" : ""), oom, Desktop.desktop);
4894 * Method invoked by the ChangeListener on the tabbed pane, in other words
4895 * when a different tabbed pane is selected by the user or programmatically.
4898 public void tabSelectionChanged(int index)
4902 alignPanel = alignPanels.get(index);
4903 viewport = alignPanel.av;
4904 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4905 setMenusFromViewport(viewport);
4909 * 'focus' any colour slider that is open to the selected viewport
4911 if (viewport.getConservationSelected())
4913 SliderPanel.setConservationSlider(alignPanel,
4914 viewport.getResidueShading(), alignPanel.getViewName());
4918 SliderPanel.hideConservationSlider();
4920 if (viewport.getAbovePIDThreshold())
4922 SliderPanel.setPIDSliderSource(alignPanel,
4923 viewport.getResidueShading(), alignPanel.getViewName());
4927 SliderPanel.hidePIDSlider();
4931 * If there is a frame linked to this one in a SplitPane, switch it to the
4932 * same view tab index. No infinite recursion of calls should happen, since
4933 * tabSelectionChanged() should not get invoked on setting the selected
4934 * index to an unchanged value. Guard against setting an invalid index
4935 * before the new view peer tab has been created.
4937 final AlignViewportI peer = viewport.getCodingComplement();
4940 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4941 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4943 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4949 * On right mouse click on view tab, prompt for and set new view name.
4952 public void tabbedPane_mousePressed(MouseEvent e)
4954 if (e.isPopupTrigger())
4956 String msg = MessageManager.getString("label.enter_view_name");
4957 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4958 JvOptionPane.QUESTION_MESSAGE);
4962 viewport.viewName = reply;
4963 // TODO warn if reply is in getExistingViewNames()?
4964 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4969 public AlignViewport getCurrentView()
4975 * Open the dialog for regex description parsing.
4978 protected void extractScores_actionPerformed(ActionEvent e)
4980 ParseProperties pp = new jalview.analysis.ParseProperties(
4981 viewport.getAlignment());
4982 // TODO: verify regex and introduce GUI dialog for version 2.5
4983 // if (pp.getScoresFromDescription("col", "score column ",
4984 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4986 if (pp.getScoresFromDescription("description column",
4987 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4989 buildSortByAnnotationScoresMenu();
4997 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5001 protected void showDbRefs_actionPerformed(ActionEvent e)
5003 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5009 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5013 protected void showNpFeats_actionPerformed(ActionEvent e)
5015 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5019 * find the viewport amongst the tabs in this alignment frame and close that
5024 public boolean closeView(AlignViewportI av)
5028 this.closeMenuItem_actionPerformed(false);
5031 Component[] comp = tabbedPane.getComponents();
5032 for (int i = 0; comp != null && i < comp.length; i++)
5034 if (comp[i] instanceof AlignmentPanel)
5036 if (((AlignmentPanel) comp[i]).av == av)
5039 closeView((AlignmentPanel) comp[i]);
5047 protected void build_fetchdbmenu(JMenu webService)
5049 // Temporary hack - DBRef Fetcher always top level ws entry.
5050 // TODO We probably want to store a sequence database checklist in
5051 // preferences and have checkboxes.. rather than individual sources selected
5053 final JMenu rfetch = new JMenu(
5054 MessageManager.getString("action.fetch_db_references"));
5055 rfetch.setToolTipText(MessageManager
5056 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5057 webService.add(rfetch);
5059 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5060 MessageManager.getString("option.trim_retrieved_seqs"));
5061 trimrs.setToolTipText(MessageManager
5062 .getString("label.trim_retrieved_sequences"));
5063 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5064 trimrs.addActionListener(new ActionListener()
5067 public void actionPerformed(ActionEvent e)
5069 trimrs.setSelected(trimrs.isSelected());
5070 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5071 Boolean.valueOf(trimrs.isSelected()).toString());
5075 JMenuItem fetchr = new JMenuItem(
5076 MessageManager.getString("label.standard_databases"));
5077 fetchr.setToolTipText(MessageManager
5078 .getString("label.fetch_embl_uniprot"));
5079 fetchr.addActionListener(new ActionListener()
5083 public void actionPerformed(ActionEvent e)
5085 new Thread(new Runnable()
5090 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5091 .getAlignment().isNucleotide();
5092 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5093 .getSequenceSelection(), alignPanel.alignFrame, null,
5094 alignPanel.alignFrame.featureSettings, isNucleotide);
5095 dbRefFetcher.addListener(new FetchFinishedListenerI()
5098 public void finished()
5100 AlignFrame.this.setMenusForViewport();
5103 dbRefFetcher.fetchDBRefs(false);
5111 final AlignFrame me = this;
5112 new Thread(new Runnable()
5117 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5118 .getSequenceFetcherSingleton(me);
5119 javax.swing.SwingUtilities.invokeLater(new Runnable()
5124 String[] dbclasses = sf.getOrderedSupportedSources();
5125 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5126 // jalview.util.QuickSort.sort(otherdb, otherdb);
5127 List<DbSourceProxy> otherdb;
5128 JMenu dfetch = new JMenu();
5129 JMenu ifetch = new JMenu();
5130 JMenuItem fetchr = null;
5131 int comp = 0, icomp = 0, mcomp = 15;
5132 String mname = null;
5134 for (String dbclass : dbclasses)
5136 otherdb = sf.getSourceProxy(dbclass);
5137 // add a single entry for this class, or submenu allowing 'fetch
5139 if (otherdb == null || otherdb.size() < 1)
5143 // List<DbSourceProxy> dbs=otherdb;
5144 // otherdb=new ArrayList<DbSourceProxy>();
5145 // for (DbSourceProxy db:dbs)
5147 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5151 mname = "From " + dbclass;
5153 if (otherdb.size() == 1)
5155 final DbSourceProxy[] dassource = otherdb
5156 .toArray(new DbSourceProxy[0]);
5157 DbSourceProxy src = otherdb.get(0);
5158 fetchr = new JMenuItem(src.getDbSource());
5159 fetchr.addActionListener(new ActionListener()
5163 public void actionPerformed(ActionEvent e)
5165 new Thread(new Runnable()
5171 boolean isNucleotide = alignPanel.alignFrame
5172 .getViewport().getAlignment()
5174 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5175 alignPanel.av.getSequenceSelection(),
5176 alignPanel.alignFrame, dassource,
5177 alignPanel.alignFrame.featureSettings,
5180 .addListener(new FetchFinishedListenerI()
5183 public void finished()
5185 AlignFrame.this.setMenusForViewport();
5188 dbRefFetcher.fetchDBRefs(false);
5194 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5195 MessageManager.formatMessage(
5196 "label.fetch_retrieve_from",
5197 new Object[] { src.getDbName() })));
5203 final DbSourceProxy[] dassource = otherdb
5204 .toArray(new DbSourceProxy[0]);
5206 DbSourceProxy src = otherdb.get(0);
5207 fetchr = new JMenuItem(MessageManager.formatMessage(
5208 "label.fetch_all_param",
5209 new Object[] { src.getDbSource() }));
5210 fetchr.addActionListener(new ActionListener()
5213 public void actionPerformed(ActionEvent e)
5215 new Thread(new Runnable()
5221 boolean isNucleotide = alignPanel.alignFrame
5222 .getViewport().getAlignment()
5224 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5225 alignPanel.av.getSequenceSelection(),
5226 alignPanel.alignFrame, dassource,
5227 alignPanel.alignFrame.featureSettings,
5230 .addListener(new FetchFinishedListenerI()
5233 public void finished()
5235 AlignFrame.this.setMenusForViewport();
5238 dbRefFetcher.fetchDBRefs(false);
5244 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5245 MessageManager.formatMessage(
5246 "label.fetch_retrieve_from_all_sources",
5248 Integer.valueOf(otherdb.size())
5249 .toString(), src.getDbSource(),
5250 src.getDbName() })));
5253 // and then build the rest of the individual menus
5254 ifetch = new JMenu(MessageManager.formatMessage(
5255 "label.source_from_db_source",
5256 new Object[] { src.getDbSource() }));
5258 String imname = null;
5260 for (DbSourceProxy sproxy : otherdb)
5262 String dbname = sproxy.getDbName();
5263 String sname = dbname.length() > 5 ? dbname.substring(0,
5264 5) + "..." : dbname;
5265 String msname = dbname.length() > 10 ? dbname.substring(
5266 0, 10) + "..." : dbname;
5269 imname = MessageManager.formatMessage(
5270 "label.from_msname", new Object[] { sname });
5272 fetchr = new JMenuItem(msname);
5273 final DbSourceProxy[] dassrc = { sproxy };
5274 fetchr.addActionListener(new ActionListener()
5278 public void actionPerformed(ActionEvent e)
5280 new Thread(new Runnable()
5286 boolean isNucleotide = alignPanel.alignFrame
5287 .getViewport().getAlignment()
5289 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5290 alignPanel.av.getSequenceSelection(),
5291 alignPanel.alignFrame, dassrc,
5292 alignPanel.alignFrame.featureSettings,
5295 .addListener(new FetchFinishedListenerI()
5298 public void finished()
5300 AlignFrame.this.setMenusForViewport();
5303 dbRefFetcher.fetchDBRefs(false);
5309 fetchr.setToolTipText("<html>"
5310 + MessageManager.formatMessage(
5311 "label.fetch_retrieve_from", new Object[]
5315 if (++icomp >= mcomp || i == (otherdb.size()))
5317 ifetch.setText(MessageManager.formatMessage(
5318 "label.source_to_target", imname, sname));
5320 ifetch = new JMenu();
5328 if (comp >= mcomp || dbi >= (dbclasses.length))
5330 dfetch.setText(MessageManager.formatMessage(
5331 "label.source_to_target", mname, dbclass));
5333 dfetch = new JMenu();
5346 * Left justify the whole alignment.
5349 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5351 AlignmentI al = viewport.getAlignment();
5353 viewport.firePropertyChange("alignment", null, al);
5357 * Right justify the whole alignment.
5360 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5362 AlignmentI al = viewport.getAlignment();
5364 viewport.firePropertyChange("alignment", null, al);
5368 public void setShowSeqFeatures(boolean b)
5370 showSeqFeatures.setSelected(b);
5371 viewport.setShowSequenceFeatures(b);
5378 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5379 * awt.event.ActionEvent)
5382 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5384 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5385 alignPanel.paintAlignment(true);
5392 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5396 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5398 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5399 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5407 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5408 * .event.ActionEvent)
5411 protected void showGroupConservation_actionPerformed(ActionEvent e)
5413 viewport.setShowGroupConservation(showGroupConservation.getState());
5414 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5421 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5422 * .event.ActionEvent)
5425 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5427 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5428 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5435 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5436 * .event.ActionEvent)
5439 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5441 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5442 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5446 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5448 showSequenceLogo.setState(true);
5449 viewport.setShowSequenceLogo(true);
5450 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5451 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5455 protected void showInformationHistogram_actionPerformed(ActionEvent e)
5457 viewport.setShowInformationHistogram(
5458 showInformationHistogram.getState());
5459 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5463 protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5465 viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5466 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5470 protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5472 showHMMSequenceLogo.setState(true);
5473 viewport.setShowHMMSequenceLogo(true);
5474 viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5475 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5479 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5481 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5488 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5489 * .event.ActionEvent)
5492 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5494 if (avc.makeGroupsFromSelection())
5496 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5497 alignPanel.updateAnnotation();
5498 alignPanel.paintAlignment(true);
5502 public void clearAlignmentSeqRep()
5504 // TODO refactor alignmentseqrep to controller
5505 if (viewport.getAlignment().hasSeqrep())
5507 viewport.getAlignment().setSeqrep(null);
5508 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5509 alignPanel.updateAnnotation();
5510 alignPanel.paintAlignment(true);
5515 protected void createGroup_actionPerformed(ActionEvent e)
5517 if (avc.createGroup())
5519 alignPanel.alignmentChanged();
5524 protected void unGroup_actionPerformed(ActionEvent e)
5528 alignPanel.alignmentChanged();
5533 * make the given alignmentPanel the currently selected tab
5535 * @param alignmentPanel
5537 public void setDisplayedView(AlignmentPanel alignmentPanel)
5539 if (!viewport.getSequenceSetId().equals(
5540 alignmentPanel.av.getSequenceSetId()))
5544 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5546 if (tabbedPane != null
5547 && tabbedPane.getTabCount() > 0
5548 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5549 .getSelectedIndex())
5551 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5556 * Action on selection of menu options to Show or Hide annotations.
5559 * @param forSequences
5560 * update sequence-related annotations
5561 * @param forAlignment
5562 * update non-sequence-related annotations
5565 protected void setAnnotationsVisibility(boolean visible,
5566 boolean forSequences, boolean forAlignment)
5568 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5569 .getAlignmentAnnotation();
5574 for (AlignmentAnnotation aa : anns)
5577 * don't display non-positional annotations on an alignment
5579 if (aa.annotations == null)
5583 boolean apply = (aa.sequenceRef == null && forAlignment)
5584 || (aa.sequenceRef != null && forSequences);
5587 aa.visible = visible;
5590 alignPanel.validateAnnotationDimensions(true);
5591 alignPanel.alignmentChanged();
5595 * Store selected annotation sort order for the view and repaint.
5598 protected void sortAnnotations_actionPerformed()
5600 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5602 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5603 alignPanel.paintAlignment(true);
5608 * @return alignment panels in this alignment frame
5610 public List<? extends AlignmentViewPanel> getAlignPanels()
5612 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5616 * Open a new alignment window, with the cDNA associated with this (protein)
5617 * alignment, aligned as is the protein.
5619 protected void viewAsCdna_actionPerformed()
5621 // TODO no longer a menu action - refactor as required
5622 final AlignmentI alignment = getViewport().getAlignment();
5623 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5624 if (mappings == null)
5628 List<SequenceI> cdnaSeqs = new ArrayList<>();
5629 for (SequenceI aaSeq : alignment.getSequences())
5631 for (AlignedCodonFrame acf : mappings)
5633 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5637 * There is a cDNA mapping for this protein sequence - add to new
5638 * alignment. It will share the same dataset sequence as other mapped
5639 * cDNA (no new mappings need to be created).
5641 final Sequence newSeq = new Sequence(dnaSeq);
5642 newSeq.setDatasetSequence(dnaSeq);
5643 cdnaSeqs.add(newSeq);
5647 if (cdnaSeqs.size() == 0)
5649 // show a warning dialog no mapped cDNA
5652 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5654 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5655 AlignFrame.DEFAULT_HEIGHT);
5656 cdna.alignAs(alignment);
5657 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5659 Desktop.addInternalFrame(alignFrame, newtitle,
5660 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5664 * Set visibility of dna/protein complement view (available when shown in a
5670 protected void showComplement_actionPerformed(boolean show)
5672 SplitContainerI sf = getSplitViewContainer();
5675 sf.setComplementVisible(this, show);
5680 * Generate the reverse (optionally complemented) of the selected sequences,
5681 * and add them to the alignment
5684 protected void showReverse_actionPerformed(boolean complement)
5686 AlignmentI al = null;
5689 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5690 al = dna.reverseCdna(complement);
5691 viewport.addAlignment(al, "");
5692 addHistoryItem(new EditCommand(
5693 MessageManager.getString("label.add_sequences"),
5694 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5695 viewport.getAlignment()));
5696 } catch (Exception ex)
5698 System.err.println(ex.getMessage());
5704 * Try to run a script in the Groovy console, having first ensured that this
5705 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5706 * be targeted at this alignment.
5709 protected void runGroovy_actionPerformed()
5711 Jalview.setCurrentAlignFrame(this);
5712 groovy.ui.Console console = Desktop.getGroovyConsole();
5713 if (console != null)
5717 console.runScript();
5718 } catch (Exception ex)
5720 System.err.println((ex.toString()));
5722 .showInternalMessageDialog(Desktop.desktop, MessageManager
5723 .getString("label.couldnt_run_groovy_script"),
5725 .getString("label.groovy_support_failed"),
5726 JvOptionPane.ERROR_MESSAGE);
5731 System.err.println("Can't run Groovy script as console not found");
5736 * Hides columns containing (or not containing) a specified feature, provided
5737 * that would not leave all columns hidden
5739 * @param featureType
5740 * @param columnsContaining
5743 public boolean hideFeatureColumns(String featureType,
5744 boolean columnsContaining)
5746 boolean notForHiding = avc.markColumnsContainingFeatures(
5747 columnsContaining, false, false, featureType);
5750 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5751 false, featureType))
5753 getViewport().hideSelectedColumns();
5761 protected void selectHighlightedColumns_actionPerformed(
5762 ActionEvent actionEvent)
5764 // include key modifier check in case user selects from menu
5765 avc.markHighlightedColumns(
5766 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5768 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5772 * Rebuilds the Colour menu, including any user-defined colours which have
5773 * been loaded either on startup or during the session
5775 public void buildColourMenu()
5777 colourMenu.removeAll();
5779 colourMenu.add(applyToAllGroups);
5780 colourMenu.add(textColour);
5781 colourMenu.addSeparator();
5783 ColourMenuHelper.addMenuItems(colourMenu, this,
5784 viewport.getAlignment(), false);
5786 colourMenu.addSeparator();
5787 colourMenu.add(conservationMenuItem);
5788 colourMenu.add(modifyConservation);
5789 colourMenu.add(abovePIDThreshold);
5790 colourMenu.add(modifyPID);
5791 colourMenu.add(annotationColour);
5793 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5794 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5798 * Open a dialog (if not already open) that allows the user to select and
5799 * calculate PCA or Tree analysis
5801 protected void openTreePcaDialog()
5803 if (alignPanel.getCalculationDialog() == null)
5805 new CalculationChooser(AlignFrame.this);
5810 class PrintThread extends Thread
5814 public PrintThread(AlignmentPanel ap)
5819 static PageFormat pf;
5824 PrinterJob printJob = PrinterJob.getPrinterJob();
5828 printJob.setPrintable(ap, pf);
5832 printJob.setPrintable(ap);
5835 if (printJob.printDialog())
5840 } catch (Exception PrintException)
5842 PrintException.printStackTrace();