2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenColumns;
57 import jalview.datamodel.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FileParse;
74 import jalview.io.FormatAdapter;
75 import jalview.io.HtmlSvgOutput;
76 import jalview.io.IdentifyFile;
77 import jalview.io.JPredFile;
78 import jalview.io.JalviewFileChooser;
79 import jalview.io.JalviewFileView;
80 import jalview.io.JnetAnnotationMaker;
81 import jalview.io.NewickFile;
82 import jalview.io.ScoreMatrixFile;
83 import jalview.io.TCoffeeScoreFile;
84 import jalview.jbgui.GAlignFrame;
85 import jalview.schemes.ColourSchemeI;
86 import jalview.schemes.ColourSchemes;
87 import jalview.schemes.ResidueColourScheme;
88 import jalview.schemes.TCoffeeColourScheme;
89 import jalview.util.MessageManager;
90 import jalview.viewmodel.AlignmentViewport;
91 import jalview.viewmodel.ViewportRanges;
92 import jalview.ws.DBRefFetcher;
93 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
94 import jalview.ws.jws1.Discoverer;
95 import jalview.ws.jws2.Jws2Discoverer;
96 import jalview.ws.jws2.jabaws2.Jws2Instance;
97 import jalview.ws.seqfetcher.DbSourceProxy;
99 import java.awt.BorderLayout;
100 import java.awt.Component;
101 import java.awt.Rectangle;
102 import java.awt.Toolkit;
103 import java.awt.datatransfer.Clipboard;
104 import java.awt.datatransfer.DataFlavor;
105 import java.awt.datatransfer.StringSelection;
106 import java.awt.datatransfer.Transferable;
107 import java.awt.dnd.DnDConstants;
108 import java.awt.dnd.DropTargetDragEvent;
109 import java.awt.dnd.DropTargetDropEvent;
110 import java.awt.dnd.DropTargetEvent;
111 import java.awt.dnd.DropTargetListener;
112 import java.awt.event.ActionEvent;
113 import java.awt.event.ActionListener;
114 import java.awt.event.FocusAdapter;
115 import java.awt.event.FocusEvent;
116 import java.awt.event.ItemEvent;
117 import java.awt.event.ItemListener;
118 import java.awt.event.KeyAdapter;
119 import java.awt.event.KeyEvent;
120 import java.awt.event.MouseEvent;
121 import java.awt.print.PageFormat;
122 import java.awt.print.PrinterJob;
123 import java.beans.PropertyChangeEvent;
125 import java.io.FileWriter;
126 import java.io.PrintWriter;
128 import java.util.ArrayList;
129 import java.util.Arrays;
130 import java.util.Deque;
131 import java.util.Enumeration;
132 import java.util.Hashtable;
133 import java.util.List;
134 import java.util.Vector;
136 import javax.swing.JCheckBoxMenuItem;
137 import javax.swing.JEditorPane;
138 import javax.swing.JInternalFrame;
139 import javax.swing.JLayeredPane;
140 import javax.swing.JMenu;
141 import javax.swing.JMenuItem;
142 import javax.swing.JScrollPane;
143 import javax.swing.SwingUtilities;
149 * @version $Revision$
151 public class AlignFrame extends GAlignFrame implements DropTargetListener,
152 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
155 public static final int DEFAULT_WIDTH = 700;
157 public static final int DEFAULT_HEIGHT = 500;
160 * The currently displayed panel (selected tabbed view if more than one)
162 public AlignmentPanel alignPanel;
164 AlignViewport viewport;
166 public AlignViewControllerI avc;
168 List<AlignmentPanel> alignPanels = new ArrayList<>();
171 * Last format used to load or save alignments in this window
173 FileFormatI currentFileFormat = null;
176 * Current filename for this alignment
178 String fileName = null;
181 * Creates a new AlignFrame object with specific width and height.
187 public AlignFrame(AlignmentI al, int width, int height)
189 this(al, null, width, height);
193 * Creates a new AlignFrame object with specific width, height and
199 * @param sequenceSetId
201 public AlignFrame(AlignmentI al, int width, int height,
202 String sequenceSetId)
204 this(al, null, width, height, sequenceSetId);
208 * Creates a new AlignFrame object with specific width, height and
214 * @param sequenceSetId
217 public AlignFrame(AlignmentI al, int width, int height,
218 String sequenceSetId, String viewId)
220 this(al, null, width, height, sequenceSetId, viewId);
224 * new alignment window with hidden columns
228 * @param hiddenColumns
229 * ColumnSelection or null
231 * Width of alignment frame
235 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
238 this(al, hiddenColumns, width, height, null);
242 * Create alignment frame for al with hiddenColumns, a specific width and
243 * height, and specific sequenceId
246 * @param hiddenColumns
249 * @param sequenceSetId
252 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
253 int height, String sequenceSetId)
255 this(al, hiddenColumns, width, height, sequenceSetId, null);
259 * Create alignment frame for al with hiddenColumns, a specific width and
260 * height, and specific sequenceId
263 * @param hiddenColumns
266 * @param sequenceSetId
271 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
272 int height, String sequenceSetId, String viewId)
274 setSize(width, height);
276 if (al.getDataset() == null)
281 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
283 alignPanel = new AlignmentPanel(this, viewport);
285 addAlignmentPanel(alignPanel, true);
289 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
290 HiddenColumns hiddenColumns, int width, int height)
292 setSize(width, height);
294 if (al.getDataset() == null)
299 viewport = new AlignViewport(al, hiddenColumns);
301 if (hiddenSeqs != null && hiddenSeqs.length > 0)
303 viewport.hideSequence(hiddenSeqs);
305 alignPanel = new AlignmentPanel(this, viewport);
306 addAlignmentPanel(alignPanel, true);
311 * Make a new AlignFrame from existing alignmentPanels
318 public AlignFrame(AlignmentPanel ap)
322 addAlignmentPanel(ap, false);
327 * initalise the alignframe from the underlying viewport data and the
332 if (!Jalview.isHeadlessMode())
334 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
337 avc = new jalview.controller.AlignViewController(this, viewport,
339 if (viewport.getAlignmentConservationAnnotation() == null)
341 // BLOSUM62Colour.setEnabled(false);
342 conservationMenuItem.setEnabled(false);
343 modifyConservation.setEnabled(false);
344 // PIDColour.setEnabled(false);
345 // abovePIDThreshold.setEnabled(false);
346 // modifyPID.setEnabled(false);
349 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
352 if (sortby.equals("Id"))
354 sortIDMenuItem_actionPerformed(null);
356 else if (sortby.equals("Pairwise Identity"))
358 sortPairwiseMenuItem_actionPerformed(null);
362 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
364 setMenusFromViewport(viewport);
365 buildSortByAnnotationScoresMenu();
366 calculateTree.addActionListener(new ActionListener()
370 public void actionPerformed(ActionEvent e)
377 if (Desktop.desktop != null)
379 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
380 addServiceListeners();
384 if (viewport.getWrapAlignment())
386 wrapMenuItem_actionPerformed(null);
389 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
391 this.overviewMenuItem_actionPerformed(null);
396 final List<AlignmentPanel> selviews = new ArrayList<>();
397 final List<AlignmentPanel> origview = new ArrayList<>();
398 final String menuLabel = MessageManager
399 .getString("label.copy_format_from");
400 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
401 new ViewSetProvider()
405 public AlignmentPanel[] getAllAlignmentPanels()
408 origview.add(alignPanel);
409 // make an array of all alignment panels except for this one
410 List<AlignmentPanel> aps = new ArrayList<>(
411 Arrays.asList(Desktop.getAlignmentPanels(null)));
412 aps.remove(AlignFrame.this.alignPanel);
413 return aps.toArray(new AlignmentPanel[aps.size()]);
415 }, selviews, new ItemListener()
419 public void itemStateChanged(ItemEvent e)
421 if (origview.size() > 0)
423 final AlignmentPanel ap = origview.get(0);
426 * Copy the ViewStyle of the selected panel to 'this one'.
427 * Don't change value of 'scaleProteinAsCdna' unless copying
430 ViewStyleI vs = selviews.get(0).getAlignViewport()
432 boolean fromSplitFrame = selviews.get(0)
433 .getAlignViewport().getCodingComplement() != null;
436 vs.setScaleProteinAsCdna(ap.getAlignViewport()
437 .getViewStyle().isScaleProteinAsCdna());
439 ap.getAlignViewport().setViewStyle(vs);
442 * Also rescale ViewStyle of SplitFrame complement if there is
443 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
444 * the whole ViewStyle (allow cDNA protein to have different
447 AlignViewportI complement = ap.getAlignViewport()
448 .getCodingComplement();
449 if (complement != null && vs.isScaleProteinAsCdna())
451 AlignFrame af = Desktop.getAlignFrameFor(complement);
452 ((SplitFrame) af.getSplitViewContainer())
454 af.setMenusForViewport();
458 ap.setSelected(true);
459 ap.alignFrame.setMenusForViewport();
464 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
465 .indexOf("devel") > -1
466 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
467 .indexOf("test") > -1)
469 formatMenu.add(vsel);
471 addFocusListener(new FocusAdapter()
474 public void focusGained(FocusEvent e)
476 Jalview.setCurrentAlignFrame(AlignFrame.this);
483 * Change the filename and format for the alignment, and enable the 'reload'
484 * button functionality.
491 public void setFileName(String file, FileFormatI format)
494 setFileFormat(format);
495 reload.setEnabled(true);
499 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
502 void addKeyListener()
504 addKeyListener(new KeyAdapter()
507 public void keyPressed(KeyEvent evt)
509 if (viewport.cursorMode
510 && ((evt.getKeyCode() >= KeyEvent.VK_0
511 && evt.getKeyCode() <= KeyEvent.VK_9)
512 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
513 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
514 && Character.isDigit(evt.getKeyChar()))
516 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
519 switch (evt.getKeyCode())
522 case 27: // escape key
523 deselectAllSequenceMenuItem_actionPerformed(null);
527 case KeyEvent.VK_DOWN:
528 if (evt.isAltDown() || !viewport.cursorMode)
530 moveSelectedSequences(false);
532 if (viewport.cursorMode)
534 alignPanel.getSeqPanel().moveCursor(0, 1);
539 if (evt.isAltDown() || !viewport.cursorMode)
541 moveSelectedSequences(true);
543 if (viewport.cursorMode)
545 alignPanel.getSeqPanel().moveCursor(0, -1);
550 case KeyEvent.VK_LEFT:
551 if (evt.isAltDown() || !viewport.cursorMode)
553 slideSequences(false,
554 alignPanel.getSeqPanel().getKeyboardNo1());
558 alignPanel.getSeqPanel().moveCursor(-1, 0);
563 case KeyEvent.VK_RIGHT:
564 if (evt.isAltDown() || !viewport.cursorMode)
566 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
570 alignPanel.getSeqPanel().moveCursor(1, 0);
574 case KeyEvent.VK_SPACE:
575 if (viewport.cursorMode)
577 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
578 || evt.isShiftDown() || evt.isAltDown());
582 // case KeyEvent.VK_A:
583 // if (viewport.cursorMode)
585 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
586 // //System.out.println("A");
590 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
591 * System.out.println("closing bracket"); } break;
593 case KeyEvent.VK_DELETE:
594 case KeyEvent.VK_BACK_SPACE:
595 if (!viewport.cursorMode)
597 cut_actionPerformed(null);
601 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
602 || evt.isShiftDown() || evt.isAltDown());
608 if (viewport.cursorMode)
610 alignPanel.getSeqPanel().setCursorRow();
614 if (viewport.cursorMode && !evt.isControlDown())
616 alignPanel.getSeqPanel().setCursorColumn();
620 if (viewport.cursorMode)
622 alignPanel.getSeqPanel().setCursorPosition();
626 case KeyEvent.VK_ENTER:
627 case KeyEvent.VK_COMMA:
628 if (viewport.cursorMode)
630 alignPanel.getSeqPanel().setCursorRowAndColumn();
635 if (viewport.cursorMode)
637 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
641 if (viewport.cursorMode)
643 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
648 viewport.cursorMode = !viewport.cursorMode;
649 statusBar.setText(MessageManager
650 .formatMessage("label.keyboard_editing_mode", new String[]
651 { (viewport.cursorMode ? "on" : "off") }));
652 if (viewport.cursorMode)
654 ViewportRanges ranges = viewport.getRanges();
655 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
657 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
660 alignPanel.getSeqPanel().seqCanvas.repaint();
666 Help.showHelpWindow();
667 } catch (Exception ex)
669 ex.printStackTrace();
674 boolean toggleSeqs = !evt.isControlDown();
675 boolean toggleCols = !evt.isShiftDown();
676 toggleHiddenRegions(toggleSeqs, toggleCols);
681 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
682 boolean modifyExisting = true; // always modify, don't clear
683 // evt.isShiftDown();
684 boolean invertHighlighted = evt.isAltDown();
685 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
689 case KeyEvent.VK_PAGE_UP:
690 viewport.getRanges().pageUp();
692 case KeyEvent.VK_PAGE_DOWN:
693 viewport.getRanges().pageDown();
699 public void keyReleased(KeyEvent evt)
701 switch (evt.getKeyCode())
703 case KeyEvent.VK_LEFT:
704 if (evt.isAltDown() || !viewport.cursorMode)
706 viewport.firePropertyChange("alignment", null,
707 viewport.getAlignment().getSequences());
711 case KeyEvent.VK_RIGHT:
712 if (evt.isAltDown() || !viewport.cursorMode)
714 viewport.firePropertyChange("alignment", null,
715 viewport.getAlignment().getSequences());
723 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
725 ap.alignFrame = this;
726 avc = new jalview.controller.AlignViewController(this, viewport,
731 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
733 int aSize = alignPanels.size();
735 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
737 if (aSize == 1 && ap.av.viewName == null)
739 this.getContentPane().add(ap, BorderLayout.CENTER);
745 setInitialTabVisible();
748 expandViews.setEnabled(true);
749 gatherViews.setEnabled(true);
750 tabbedPane.addTab(ap.av.viewName, ap);
752 ap.setVisible(false);
757 if (ap.av.isPadGaps())
759 ap.av.getAlignment().padGaps();
761 ap.av.updateConservation(ap);
762 ap.av.updateConsensus(ap);
763 ap.av.updateStrucConsensus(ap);
767 public void setInitialTabVisible()
769 expandViews.setEnabled(true);
770 gatherViews.setEnabled(true);
771 tabbedPane.setVisible(true);
772 AlignmentPanel first = alignPanels.get(0);
773 tabbedPane.addTab(first.av.viewName, first);
774 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
777 public AlignViewport getViewport()
782 /* Set up intrinsic listeners for dynamically generated GUI bits. */
783 private void addServiceListeners()
785 final java.beans.PropertyChangeListener thisListener;
786 Desktop.instance.addJalviewPropertyChangeListener("services",
787 thisListener = new java.beans.PropertyChangeListener()
790 public void propertyChange(PropertyChangeEvent evt)
792 // // System.out.println("Discoverer property change.");
793 // if (evt.getPropertyName().equals("services"))
795 SwingUtilities.invokeLater(new Runnable()
802 "Rebuild WS Menu for service change");
803 BuildWebServiceMenu();
810 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
813 public void internalFrameClosed(
814 javax.swing.event.InternalFrameEvent evt)
816 // System.out.println("deregistering discoverer listener");
817 Desktop.instance.removeJalviewPropertyChangeListener("services",
819 closeMenuItem_actionPerformed(true);
822 // Finally, build the menu once to get current service state
823 new Thread(new Runnable()
828 BuildWebServiceMenu();
834 * Configure menu items that vary according to whether the alignment is
835 * nucleotide or protein
837 public void setGUINucleotide()
839 AlignmentI al = getViewport().getAlignment();
840 boolean nucleotide = al.isNucleotide();
842 showTranslation.setVisible(nucleotide);
843 showReverse.setVisible(nucleotide);
844 showReverseComplement.setVisible(nucleotide);
845 conservationMenuItem.setEnabled(!nucleotide);
847 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
848 showGroupConservation.setEnabled(!nucleotide);
850 showComplementMenuItem
851 .setText(nucleotide ? MessageManager.getString("label.protein")
852 : MessageManager.getString("label.nucleotide"));
856 * set up menus for the current viewport. This may be called after any
857 * operation that affects the data in the current view (selection changed,
858 * etc) to update the menus to reflect the new state.
861 public void setMenusForViewport()
863 setMenusFromViewport(viewport);
867 * Need to call this method when tabs are selected for multiple views, or when
868 * loading from Jalview2XML.java
873 void setMenusFromViewport(AlignViewport av)
875 padGapsMenuitem.setSelected(av.isPadGaps());
876 colourTextMenuItem.setSelected(av.isShowColourText());
877 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
878 modifyPID.setEnabled(abovePIDThreshold.isSelected());
879 conservationMenuItem.setSelected(av.getConservationSelected());
880 modifyConservation.setEnabled(conservationMenuItem.isSelected());
881 seqLimits.setSelected(av.getShowJVSuffix());
882 idRightAlign.setSelected(av.isRightAlignIds());
883 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
884 renderGapsMenuItem.setSelected(av.isRenderGaps());
885 wrapMenuItem.setSelected(av.getWrapAlignment());
886 scaleAbove.setVisible(av.getWrapAlignment());
887 scaleLeft.setVisible(av.getWrapAlignment());
888 scaleRight.setVisible(av.getWrapAlignment());
889 annotationPanelMenuItem.setState(av.isShowAnnotation());
891 * Show/hide annotations only enabled if annotation panel is shown
893 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
894 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
895 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
896 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
897 viewBoxesMenuItem.setSelected(av.getShowBoxes());
898 viewTextMenuItem.setSelected(av.getShowText());
899 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
900 showGroupConsensus.setSelected(av.isShowGroupConsensus());
901 showGroupConservation.setSelected(av.isShowGroupConservation());
902 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
903 showSequenceLogo.setSelected(av.isShowSequenceLogo());
904 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
906 ColourMenuHelper.setColourSelected(colourMenu,
907 av.getGlobalColourScheme());
909 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
910 hiddenMarkers.setState(av.getShowHiddenMarkers());
911 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
912 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
913 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
914 autoCalculate.setSelected(av.autoCalculateConsensus);
915 sortByTree.setSelected(av.sortByTree);
916 listenToViewSelections.setSelected(av.followSelection);
918 showProducts.setEnabled(canShowProducts());
919 setGroovyEnabled(Desktop.getGroovyConsole() != null);
925 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
929 public void setGroovyEnabled(boolean b)
931 runGroovy.setEnabled(b);
934 private IProgressIndicator progressBar;
939 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
942 public void setProgressBar(String message, long id)
944 progressBar.setProgressBar(message, id);
948 public void registerHandler(final long id,
949 final IProgressIndicatorHandler handler)
951 progressBar.registerHandler(id, handler);
956 * @return true if any progress bars are still active
959 public boolean operationInProgress()
961 return progressBar.operationInProgress();
965 public void setStatus(String text)
967 statusBar.setText(text);
971 * Added so Castor Mapping file can obtain Jalview Version
973 public String getVersion()
975 return jalview.bin.Cache.getProperty("VERSION");
978 public FeatureRenderer getFeatureRenderer()
980 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
984 public void fetchSequence_actionPerformed(ActionEvent e)
986 new jalview.gui.SequenceFetcher(this);
990 public void addFromFile_actionPerformed(ActionEvent e)
992 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
996 public void reload_actionPerformed(ActionEvent e)
998 if (fileName != null)
1000 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1001 // originating file's format
1002 // TODO: work out how to recover feature settings for correct view(s) when
1003 // file is reloaded.
1004 if (FileFormat.Jalview.equals(currentFileFormat))
1006 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1007 for (int i = 0; i < frames.length; i++)
1009 if (frames[i] instanceof AlignFrame && frames[i] != this
1010 && ((AlignFrame) frames[i]).fileName != null
1011 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1015 frames[i].setSelected(true);
1016 Desktop.instance.closeAssociatedWindows();
1017 } catch (java.beans.PropertyVetoException ex)
1023 Desktop.instance.closeAssociatedWindows();
1025 FileLoader loader = new FileLoader();
1026 DataSourceType protocol = fileName.startsWith("http:")
1027 ? DataSourceType.URL
1028 : DataSourceType.FILE;
1029 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1033 Rectangle bounds = this.getBounds();
1035 FileLoader loader = new FileLoader();
1036 DataSourceType protocol = fileName.startsWith("http:")
1037 ? DataSourceType.URL
1038 : DataSourceType.FILE;
1039 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1040 protocol, currentFileFormat);
1042 newframe.setBounds(bounds);
1043 if (featureSettings != null && featureSettings.isShowing())
1045 final Rectangle fspos = featureSettings.frame.getBounds();
1046 // TODO: need a 'show feature settings' function that takes bounds -
1047 // need to refactor Desktop.addFrame
1048 newframe.featureSettings_actionPerformed(null);
1049 final FeatureSettings nfs = newframe.featureSettings;
1050 SwingUtilities.invokeLater(new Runnable()
1055 nfs.frame.setBounds(fspos);
1058 this.featureSettings.close();
1059 this.featureSettings = null;
1061 this.closeMenuItem_actionPerformed(true);
1067 public void addFromText_actionPerformed(ActionEvent e)
1070 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1074 public void addFromURL_actionPerformed(ActionEvent e)
1076 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1080 public void save_actionPerformed(ActionEvent e)
1082 if (fileName == null || (currentFileFormat == null)
1083 || fileName.startsWith("http"))
1085 saveAs_actionPerformed(null);
1089 saveAlignment(fileName, currentFileFormat);
1100 public void saveAs_actionPerformed(ActionEvent e)
1102 String format = currentFileFormat == null ? null
1103 : currentFileFormat.getName();
1104 JalviewFileChooser chooser = JalviewFileChooser
1105 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1107 chooser.setFileView(new JalviewFileView());
1108 chooser.setDialogTitle(
1109 MessageManager.getString("label.save_alignment_to_file"));
1110 chooser.setToolTipText(MessageManager.getString("action.save"));
1112 int value = chooser.showSaveDialog(this);
1114 if (value == JalviewFileChooser.APPROVE_OPTION)
1116 currentFileFormat = chooser.getSelectedFormat();
1117 while (currentFileFormat == null)
1119 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1120 MessageManager.getString(
1121 "label.select_file_format_before_saving"),
1122 MessageManager.getString("label.file_format_not_specified"),
1123 JvOptionPane.WARNING_MESSAGE);
1124 currentFileFormat = chooser.getSelectedFormat();
1125 value = chooser.showSaveDialog(this);
1126 if (value != JalviewFileChooser.APPROVE_OPTION)
1132 fileName = chooser.getSelectedFile().getPath();
1134 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1136 Cache.setProperty("LAST_DIRECTORY", fileName);
1137 saveAlignment(fileName, currentFileFormat);
1141 public boolean saveAlignment(String file, FileFormatI format)
1143 boolean success = true;
1145 if (FileFormat.Jalview.equals(format))
1147 String shortName = title;
1149 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1151 shortName = shortName.substring(
1152 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1155 success = new Jalview2XML().saveAlignment(this, file, shortName);
1157 statusBar.setText(MessageManager.formatMessage(
1158 "label.successfully_saved_to_file_in_format", new Object[]
1159 { fileName, format }));
1164 AlignmentExportData exportData = getAlignmentForExport(format,
1166 if (exportData.getSettings().isCancelled())
1170 FormatAdapter f = new FormatAdapter(alignPanel,
1171 exportData.getSettings());
1172 String output = f.formatSequences(format, exportData.getAlignment(), // class
1176 // occur in the distant future
1177 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1178 f.getCacheSuffixDefault(format),
1179 viewport.getAlignment().getHiddenColumns());
1189 PrintWriter out = new PrintWriter(new FileWriter(file));
1193 this.setTitle(file);
1194 statusBar.setText(MessageManager.formatMessage(
1195 "label.successfully_saved_to_file_in_format", new Object[]
1196 { fileName, format.getName() }));
1197 } catch (Exception ex)
1200 ex.printStackTrace();
1207 JvOptionPane.showInternalMessageDialog(this, MessageManager
1208 .formatMessage("label.couldnt_save_file", new Object[]
1210 MessageManager.getString("label.error_saving_file"),
1211 JvOptionPane.WARNING_MESSAGE);
1217 private void warningMessage(String warning, String title)
1219 if (new jalview.util.Platform().isHeadless())
1221 System.err.println("Warning: " + title + "\nWarning: " + warning);
1226 JvOptionPane.showInternalMessageDialog(this, warning, title,
1227 JvOptionPane.WARNING_MESSAGE);
1239 protected void outputText_actionPerformed(ActionEvent e)
1241 FileFormatI fileFormat = FileFormats.getInstance()
1242 .forName(e.getActionCommand());
1243 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1245 if (exportData.getSettings().isCancelled())
1249 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1250 cap.setForInput(null);
1253 FileFormatI format = fileFormat;
1254 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1255 .formatSequences(format, exportData.getAlignment(),
1256 exportData.getOmitHidden(),
1257 exportData.getStartEndPostions(),
1258 viewport.getAlignment().getHiddenColumns()));
1259 Desktop.addInternalFrame(cap, MessageManager
1260 .formatMessage("label.alignment_output_command", new Object[]
1261 { e.getActionCommand() }), 600, 500);
1262 } catch (OutOfMemoryError oom)
1264 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1271 public static AlignmentExportData getAlignmentForExport(
1272 FileFormatI format, AlignViewportI viewport,
1273 AlignExportSettingI exportSettings)
1275 AlignmentI alignmentToExport = null;
1276 AlignExportSettingI settings = exportSettings;
1277 String[] omitHidden = null;
1279 HiddenSequences hiddenSeqs = viewport.getAlignment()
1280 .getHiddenSequences();
1282 alignmentToExport = viewport.getAlignment();
1284 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1285 if (settings == null)
1287 settings = new AlignExportSettings(hasHiddenSeqs,
1288 viewport.hasHiddenColumns(), format);
1290 // settings.isExportAnnotations();
1292 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1294 omitHidden = viewport.getViewAsString(false,
1295 settings.isExportHiddenSequences());
1298 int[] alignmentStartEnd = new int[2];
1299 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1301 alignmentToExport = hiddenSeqs.getFullAlignment();
1305 alignmentToExport = viewport.getAlignment();
1307 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1308 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1309 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1310 omitHidden, alignmentStartEnd, settings);
1321 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1323 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1324 htmlSVG.exportHTML(null);
1328 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1330 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1331 bjs.exportHTML(null);
1334 public void createImageMap(File file, String image)
1336 alignPanel.makePNGImageMap(file, image);
1346 public void createPNG(File f)
1348 alignPanel.makePNG(f);
1358 public void createEPS(File f)
1360 alignPanel.makeEPS(f);
1364 public void createSVG(File f)
1366 alignPanel.makeSVG(f);
1370 public void pageSetup_actionPerformed(ActionEvent e)
1372 PrinterJob printJob = PrinterJob.getPrinterJob();
1373 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1383 public void printMenuItem_actionPerformed(ActionEvent e)
1385 // Putting in a thread avoids Swing painting problems
1386 PrintThread thread = new PrintThread(alignPanel);
1391 public void exportFeatures_actionPerformed(ActionEvent e)
1393 new AnnotationExporter().exportFeatures(alignPanel);
1397 public void exportAnnotations_actionPerformed(ActionEvent e)
1399 new AnnotationExporter().exportAnnotations(alignPanel);
1403 public void associatedData_actionPerformed(ActionEvent e)
1405 // Pick the tree file
1406 JalviewFileChooser chooser = new JalviewFileChooser(
1407 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1408 chooser.setFileView(new JalviewFileView());
1409 chooser.setDialogTitle(
1410 MessageManager.getString("label.load_jalview_annotations"));
1411 chooser.setToolTipText(
1412 MessageManager.getString("label.load_jalview_annotations"));
1414 int value = chooser.showOpenDialog(null);
1416 if (value == JalviewFileChooser.APPROVE_OPTION)
1418 String choice = chooser.getSelectedFile().getPath();
1419 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1420 loadJalviewDataFile(choice, null, null, null);
1426 * Close the current view or all views in the alignment frame. If the frame
1427 * only contains one view then the alignment will be removed from memory.
1429 * @param closeAllTabs
1432 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1434 if (alignPanels != null && alignPanels.size() < 2)
1436 closeAllTabs = true;
1441 if (alignPanels != null)
1445 if (this.isClosed())
1447 // really close all the windows - otherwise wait till
1448 // setClosed(true) is called
1449 for (int i = 0; i < alignPanels.size(); i++)
1451 AlignmentPanel ap = alignPanels.get(i);
1458 closeView(alignPanel);
1465 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1466 * be called recursively, with the frame now in 'closed' state
1468 this.setClosed(true);
1470 } catch (Exception ex)
1472 ex.printStackTrace();
1477 * Close the specified panel and close up tabs appropriately.
1479 * @param panelToClose
1481 public void closeView(AlignmentPanel panelToClose)
1483 int index = tabbedPane.getSelectedIndex();
1484 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1485 alignPanels.remove(panelToClose);
1486 panelToClose.closePanel();
1487 panelToClose = null;
1489 tabbedPane.removeTabAt(closedindex);
1490 tabbedPane.validate();
1492 if (index > closedindex || index == tabbedPane.getTabCount())
1494 // modify currently selected tab index if necessary.
1498 this.tabSelectionChanged(index);
1504 void updateEditMenuBar()
1507 if (viewport.getHistoryList().size() > 0)
1509 undoMenuItem.setEnabled(true);
1510 CommandI command = viewport.getHistoryList().peek();
1511 undoMenuItem.setText(MessageManager
1512 .formatMessage("label.undo_command", new Object[]
1513 { command.getDescription() }));
1517 undoMenuItem.setEnabled(false);
1518 undoMenuItem.setText(MessageManager.getString("action.undo"));
1521 if (viewport.getRedoList().size() > 0)
1523 redoMenuItem.setEnabled(true);
1525 CommandI command = viewport.getRedoList().peek();
1526 redoMenuItem.setText(MessageManager
1527 .formatMessage("label.redo_command", new Object[]
1528 { command.getDescription() }));
1532 redoMenuItem.setEnabled(false);
1533 redoMenuItem.setText(MessageManager.getString("action.redo"));
1538 public void addHistoryItem(CommandI command)
1540 if (command.getSize() > 0)
1542 viewport.addToHistoryList(command);
1543 viewport.clearRedoList();
1544 updateEditMenuBar();
1545 viewport.updateHiddenColumns();
1546 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1547 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1548 // viewport.getColumnSelection()
1549 // .getHiddenColumns().size() > 0);
1555 * @return alignment objects for all views
1557 AlignmentI[] getViewAlignments()
1559 if (alignPanels != null)
1561 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1563 for (AlignmentPanel ap : alignPanels)
1565 als[i++] = ap.av.getAlignment();
1569 if (viewport != null)
1571 return new AlignmentI[] { viewport.getAlignment() };
1583 protected void undoMenuItem_actionPerformed(ActionEvent e)
1585 if (viewport.getHistoryList().isEmpty())
1589 CommandI command = viewport.getHistoryList().pop();
1590 viewport.addToRedoList(command);
1591 command.undoCommand(getViewAlignments());
1593 AlignmentViewport originalSource = getOriginatingSource(command);
1594 updateEditMenuBar();
1596 if (originalSource != null)
1598 if (originalSource != viewport)
1601 "Implementation worry: mismatch of viewport origin for undo");
1603 originalSource.updateHiddenColumns();
1604 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1606 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1607 // viewport.getColumnSelection()
1608 // .getHiddenColumns().size() > 0);
1609 originalSource.firePropertyChange("alignment", null,
1610 originalSource.getAlignment().getSequences());
1621 protected void redoMenuItem_actionPerformed(ActionEvent e)
1623 if (viewport.getRedoList().size() < 1)
1628 CommandI command = viewport.getRedoList().pop();
1629 viewport.addToHistoryList(command);
1630 command.doCommand(getViewAlignments());
1632 AlignmentViewport originalSource = getOriginatingSource(command);
1633 updateEditMenuBar();
1635 if (originalSource != null)
1638 if (originalSource != viewport)
1641 "Implementation worry: mismatch of viewport origin for redo");
1643 originalSource.updateHiddenColumns();
1644 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1646 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1647 // viewport.getColumnSelection()
1648 // .getHiddenColumns().size() > 0);
1649 originalSource.firePropertyChange("alignment", null,
1650 originalSource.getAlignment().getSequences());
1654 AlignmentViewport getOriginatingSource(CommandI command)
1656 AlignmentViewport originalSource = null;
1657 // For sequence removal and addition, we need to fire
1658 // the property change event FROM the viewport where the
1659 // original alignment was altered
1660 AlignmentI al = null;
1661 if (command instanceof EditCommand)
1663 EditCommand editCommand = (EditCommand) command;
1664 al = editCommand.getAlignment();
1665 List<Component> comps = PaintRefresher.components
1666 .get(viewport.getSequenceSetId());
1668 for (Component comp : comps)
1670 if (comp instanceof AlignmentPanel)
1672 if (al == ((AlignmentPanel) comp).av.getAlignment())
1674 originalSource = ((AlignmentPanel) comp).av;
1681 if (originalSource == null)
1683 // The original view is closed, we must validate
1684 // the current view against the closed view first
1687 PaintRefresher.validateSequences(al, viewport.getAlignment());
1690 originalSource = viewport;
1693 return originalSource;
1702 public void moveSelectedSequences(boolean up)
1704 SequenceGroup sg = viewport.getSelectionGroup();
1710 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1711 viewport.getHiddenRepSequences(), up);
1712 alignPanel.paintAlignment(true, false);
1715 synchronized void slideSequences(boolean right, int size)
1717 List<SequenceI> sg = new ArrayList<>();
1718 if (viewport.cursorMode)
1720 sg.add(viewport.getAlignment()
1721 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1723 else if (viewport.getSelectionGroup() != null
1724 && viewport.getSelectionGroup().getSize() != viewport
1725 .getAlignment().getHeight())
1727 sg = viewport.getSelectionGroup()
1728 .getSequences(viewport.getHiddenRepSequences());
1736 List<SequenceI> invertGroup = new ArrayList<>();
1738 for (SequenceI seq : viewport.getAlignment().getSequences())
1740 if (!sg.contains(seq))
1742 invertGroup.add(seq);
1746 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1748 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1749 for (int i = 0; i < invertGroup.size(); i++)
1751 seqs2[i] = invertGroup.get(i);
1754 SlideSequencesCommand ssc;
1757 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1758 viewport.getGapCharacter());
1762 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1763 viewport.getGapCharacter());
1766 int groupAdjustment = 0;
1767 if (ssc.getGapsInsertedBegin() && right)
1769 if (viewport.cursorMode)
1771 alignPanel.getSeqPanel().moveCursor(size, 0);
1775 groupAdjustment = size;
1778 else if (!ssc.getGapsInsertedBegin() && !right)
1780 if (viewport.cursorMode)
1782 alignPanel.getSeqPanel().moveCursor(-size, 0);
1786 groupAdjustment = -size;
1790 if (groupAdjustment != 0)
1792 viewport.getSelectionGroup().setStartRes(
1793 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1794 viewport.getSelectionGroup().setEndRes(
1795 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1799 * just extend the last slide command if compatible; but not if in
1800 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1802 boolean appendHistoryItem = false;
1803 Deque<CommandI> historyList = viewport.getHistoryList();
1804 boolean inSplitFrame = getSplitViewContainer() != null;
1805 if (!inSplitFrame && historyList != null && historyList.size() > 0
1806 && historyList.peek() instanceof SlideSequencesCommand)
1808 appendHistoryItem = ssc.appendSlideCommand(
1809 (SlideSequencesCommand) historyList.peek());
1812 if (!appendHistoryItem)
1814 addHistoryItem(ssc);
1827 protected void copy_actionPerformed(ActionEvent e)
1830 if (viewport.getSelectionGroup() == null)
1834 // TODO: preserve the ordering of displayed alignment annotation in any
1835 // internal paste (particularly sequence associated annotation)
1836 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1837 String[] omitHidden = null;
1839 if (viewport.hasHiddenColumns())
1841 omitHidden = viewport.getViewAsString(true);
1844 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1845 seqs, omitHidden, null);
1847 StringSelection ss = new StringSelection(output);
1851 jalview.gui.Desktop.internalCopy = true;
1852 // Its really worth setting the clipboard contents
1853 // to empty before setting the large StringSelection!!
1854 Toolkit.getDefaultToolkit().getSystemClipboard()
1855 .setContents(new StringSelection(""), null);
1857 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1859 } catch (OutOfMemoryError er)
1861 new OOMWarning("copying region", er);
1865 HiddenColumns hiddenColumns = null;
1866 if (viewport.hasHiddenColumns())
1868 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1869 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1871 // create new HiddenColumns object with copy of hidden regions
1872 // between startRes and endRes, offset by startRes
1873 hiddenColumns = new HiddenColumns(
1874 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1875 hiddenCutoff, hiddenOffset);
1878 Desktop.jalviewClipboard = new Object[] { seqs,
1879 viewport.getAlignment().getDataset(), hiddenColumns };
1880 statusBar.setText(MessageManager.formatMessage(
1881 "label.copied_sequences_to_clipboard", new Object[]
1882 { Integer.valueOf(seqs.length).toString() }));
1892 protected void pasteNew_actionPerformed(ActionEvent e)
1904 protected void pasteThis_actionPerformed(ActionEvent e)
1910 * Paste contents of Jalview clipboard
1912 * @param newAlignment
1913 * true to paste to a new alignment, otherwise add to this.
1915 void paste(boolean newAlignment)
1917 boolean externalPaste = true;
1920 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1921 Transferable contents = c.getContents(this);
1923 if (contents == null)
1932 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1933 if (str.length() < 1)
1938 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1940 } catch (OutOfMemoryError er)
1942 new OOMWarning("Out of memory pasting sequences!!", er);
1946 SequenceI[] sequences;
1947 boolean annotationAdded = false;
1948 AlignmentI alignment = null;
1950 if (Desktop.jalviewClipboard != null)
1952 // The clipboard was filled from within Jalview, we must use the
1954 // And dataset from the copied alignment
1955 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1956 // be doubly sure that we create *new* sequence objects.
1957 sequences = new SequenceI[newseq.length];
1958 for (int i = 0; i < newseq.length; i++)
1960 sequences[i] = new Sequence(newseq[i]);
1962 alignment = new Alignment(sequences);
1963 externalPaste = false;
1967 // parse the clipboard as an alignment.
1968 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1970 sequences = alignment.getSequencesArray();
1974 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1980 if (Desktop.jalviewClipboard != null)
1982 // dataset is inherited
1983 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1987 // new dataset is constructed
1988 alignment.setDataset(null);
1990 alwidth = alignment.getWidth() + 1;
1994 AlignmentI pastedal = alignment; // preserve pasted alignment object
1995 // Add pasted sequences and dataset into existing alignment.
1996 alignment = viewport.getAlignment();
1997 alwidth = alignment.getWidth() + 1;
1998 // decide if we need to import sequences from an existing dataset
1999 boolean importDs = Desktop.jalviewClipboard != null
2000 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2001 // importDs==true instructs us to copy over new dataset sequences from
2002 // an existing alignment
2003 Vector newDs = (importDs) ? new Vector() : null; // used to create
2004 // minimum dataset set
2006 for (int i = 0; i < sequences.length; i++)
2010 newDs.addElement(null);
2012 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2014 if (importDs && ds != null)
2016 if (!newDs.contains(ds))
2018 newDs.setElementAt(ds, i);
2019 ds = new Sequence(ds);
2020 // update with new dataset sequence
2021 sequences[i].setDatasetSequence(ds);
2025 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2030 // copy and derive new dataset sequence
2031 sequences[i] = sequences[i].deriveSequence();
2032 alignment.getDataset()
2033 .addSequence(sequences[i].getDatasetSequence());
2034 // TODO: avoid creation of duplicate dataset sequences with a
2035 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2037 alignment.addSequence(sequences[i]); // merges dataset
2041 newDs.clear(); // tidy up
2043 if (alignment.getAlignmentAnnotation() != null)
2045 for (AlignmentAnnotation alan : alignment
2046 .getAlignmentAnnotation())
2048 if (alan.graphGroup > fgroup)
2050 fgroup = alan.graphGroup;
2054 if (pastedal.getAlignmentAnnotation() != null)
2056 // Add any annotation attached to alignment.
2057 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2058 for (int i = 0; i < alann.length; i++)
2060 annotationAdded = true;
2061 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2063 AlignmentAnnotation newann = new AlignmentAnnotation(
2065 if (newann.graphGroup > -1)
2067 if (newGraphGroups.size() <= newann.graphGroup
2068 || newGraphGroups.get(newann.graphGroup) == null)
2070 for (int q = newGraphGroups
2071 .size(); q <= newann.graphGroup; q++)
2073 newGraphGroups.add(q, null);
2075 newGraphGroups.set(newann.graphGroup,
2076 new Integer(++fgroup));
2078 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2082 newann.padAnnotation(alwidth);
2083 alignment.addAnnotation(newann);
2093 addHistoryItem(new EditCommand(
2094 MessageManager.getString("label.add_sequences"),
2095 Action.PASTE, sequences, 0, alignment.getWidth(),
2098 // Add any annotations attached to sequences
2099 for (int i = 0; i < sequences.length; i++)
2101 if (sequences[i].getAnnotation() != null)
2103 AlignmentAnnotation newann;
2104 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2106 annotationAdded = true;
2107 newann = sequences[i].getAnnotation()[a];
2108 newann.adjustForAlignment();
2109 newann.padAnnotation(alwidth);
2110 if (newann.graphGroup > -1)
2112 if (newann.graphGroup > -1)
2114 if (newGraphGroups.size() <= newann.graphGroup
2115 || newGraphGroups.get(newann.graphGroup) == null)
2117 for (int q = newGraphGroups
2118 .size(); q <= newann.graphGroup; q++)
2120 newGraphGroups.add(q, null);
2122 newGraphGroups.set(newann.graphGroup,
2123 new Integer(++fgroup));
2125 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2129 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2133 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2141 // propagate alignment changed.
2142 viewport.getRanges().setEndSeq(alignment.getHeight());
2143 if (annotationAdded)
2145 // Duplicate sequence annotation in all views.
2146 AlignmentI[] alview = this.getViewAlignments();
2147 for (int i = 0; i < sequences.length; i++)
2149 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2154 for (int avnum = 0; avnum < alview.length; avnum++)
2156 if (alview[avnum] != alignment)
2158 // duplicate in a view other than the one with input focus
2159 int avwidth = alview[avnum].getWidth() + 1;
2160 // this relies on sann being preserved after we
2161 // modify the sequence's annotation array for each duplication
2162 for (int a = 0; a < sann.length; a++)
2164 AlignmentAnnotation newann = new AlignmentAnnotation(
2166 sequences[i].addAlignmentAnnotation(newann);
2167 newann.padAnnotation(avwidth);
2168 alview[avnum].addAnnotation(newann); // annotation was
2169 // duplicated earlier
2170 // TODO JAL-1145 graphGroups are not updated for sequence
2171 // annotation added to several views. This may cause
2173 alview[avnum].setAnnotationIndex(newann, a);
2178 buildSortByAnnotationScoresMenu();
2180 viewport.firePropertyChange("alignment", null,
2181 alignment.getSequences());
2182 if (alignPanels != null)
2184 for (AlignmentPanel ap : alignPanels)
2186 ap.validateAnnotationDimensions(false);
2191 alignPanel.validateAnnotationDimensions(false);
2197 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2199 String newtitle = new String("Copied sequences");
2201 if (Desktop.jalviewClipboard != null
2202 && Desktop.jalviewClipboard[2] != null)
2204 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2205 af.viewport.setHiddenColumns(hc);
2208 // >>>This is a fix for the moment, until a better solution is
2210 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2211 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2212 .getFeatureRenderer());
2214 // TODO: maintain provenance of an alignment, rather than just make the
2215 // title a concatenation of operations.
2218 if (title.startsWith("Copied sequences"))
2224 newtitle = newtitle.concat("- from " + title);
2229 newtitle = new String("Pasted sequences");
2232 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2237 } catch (Exception ex)
2239 ex.printStackTrace();
2240 System.out.println("Exception whilst pasting: " + ex);
2241 // could be anything being pasted in here
2247 protected void expand_newalign(ActionEvent e)
2251 AlignmentI alignment = AlignmentUtils
2252 .expandContext(getViewport().getAlignment(), -1);
2253 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2255 String newtitle = new String("Flanking alignment");
2257 if (Desktop.jalviewClipboard != null
2258 && Desktop.jalviewClipboard[2] != null)
2260 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2261 af.viewport.setHiddenColumns(hc);
2264 // >>>This is a fix for the moment, until a better solution is
2266 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2267 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2268 .getFeatureRenderer());
2270 // TODO: maintain provenance of an alignment, rather than just make the
2271 // title a concatenation of operations.
2273 if (title.startsWith("Copied sequences"))
2279 newtitle = newtitle.concat("- from " + title);
2283 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2285 } catch (Exception ex)
2287 ex.printStackTrace();
2288 System.out.println("Exception whilst pasting: " + ex);
2289 // could be anything being pasted in here
2290 } catch (OutOfMemoryError oom)
2292 new OOMWarning("Viewing flanking region of alignment", oom);
2303 protected void cut_actionPerformed(ActionEvent e)
2305 copy_actionPerformed(null);
2306 delete_actionPerformed(null);
2316 protected void delete_actionPerformed(ActionEvent evt)
2319 SequenceGroup sg = viewport.getSelectionGroup();
2326 * If the cut affects all sequences, warn, remove highlighted columns
2328 if (sg.getSize() == viewport.getAlignment().getHeight())
2330 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2331 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2332 if (isEntireAlignWidth)
2334 int confirm = JvOptionPane.showConfirmDialog(this,
2335 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2336 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2337 JvOptionPane.OK_CANCEL_OPTION);
2339 if (confirm == JvOptionPane.CANCEL_OPTION
2340 || confirm == JvOptionPane.CLOSED_OPTION)
2345 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2346 sg.getEndRes() + 1);
2348 SequenceI[] cut = sg.getSequences()
2349 .toArray(new SequenceI[sg.getSize()]);
2351 addHistoryItem(new EditCommand(
2352 MessageManager.getString("label.cut_sequences"), Action.CUT,
2353 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2354 viewport.getAlignment()));
2356 viewport.setSelectionGroup(null);
2357 viewport.sendSelection();
2358 viewport.getAlignment().deleteGroup(sg);
2360 viewport.firePropertyChange("alignment", null,
2361 viewport.getAlignment().getSequences());
2362 if (viewport.getAlignment().getHeight() < 1)
2366 this.setClosed(true);
2367 } catch (Exception ex)
2380 protected void deleteGroups_actionPerformed(ActionEvent e)
2382 if (avc.deleteGroups())
2384 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2385 alignPanel.updateAnnotation();
2386 alignPanel.paintAlignment(true, true);
2397 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2399 SequenceGroup sg = new SequenceGroup();
2401 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2403 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2406 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2407 viewport.setSelectionGroup(sg);
2408 viewport.sendSelection();
2409 // JAL-2034 - should delegate to
2410 // alignPanel to decide if overview needs
2412 alignPanel.paintAlignment(false, false);
2413 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2423 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2425 if (viewport.cursorMode)
2427 alignPanel.getSeqPanel().keyboardNo1 = null;
2428 alignPanel.getSeqPanel().keyboardNo2 = null;
2430 viewport.setSelectionGroup(null);
2431 viewport.getColumnSelection().clear();
2432 viewport.setSelectionGroup(null);
2433 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2434 // JAL-2034 - should delegate to
2435 // alignPanel to decide if overview needs
2437 alignPanel.paintAlignment(false, false);
2438 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2439 viewport.sendSelection();
2449 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2451 SequenceGroup sg = viewport.getSelectionGroup();
2455 selectAllSequenceMenuItem_actionPerformed(null);
2460 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2462 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2464 // JAL-2034 - should delegate to
2465 // alignPanel to decide if overview needs
2468 alignPanel.paintAlignment(true, false);
2469 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2470 viewport.sendSelection();
2474 public void invertColSel_actionPerformed(ActionEvent e)
2476 viewport.invertColumnSelection();
2477 alignPanel.paintAlignment(true, false);
2478 viewport.sendSelection();
2488 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2490 trimAlignment(true);
2500 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2502 trimAlignment(false);
2505 void trimAlignment(boolean trimLeft)
2507 ColumnSelection colSel = viewport.getColumnSelection();
2510 if (!colSel.isEmpty())
2514 column = colSel.getMin();
2518 column = colSel.getMax();
2522 if (viewport.getSelectionGroup() != null)
2524 seqs = viewport.getSelectionGroup()
2525 .getSequencesAsArray(viewport.getHiddenRepSequences());
2529 seqs = viewport.getAlignment().getSequencesArray();
2532 TrimRegionCommand trimRegion;
2535 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2536 column, viewport.getAlignment());
2537 viewport.getRanges().setStartRes(0);
2541 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2542 column, viewport.getAlignment());
2545 statusBar.setText(MessageManager
2546 .formatMessage("label.removed_columns", new String[]
2547 { Integer.valueOf(trimRegion.getSize()).toString() }));
2549 addHistoryItem(trimRegion);
2551 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2553 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2554 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2556 viewport.getAlignment().deleteGroup(sg);
2560 viewport.firePropertyChange("alignment", null,
2561 viewport.getAlignment().getSequences());
2572 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2574 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2577 if (viewport.getSelectionGroup() != null)
2579 seqs = viewport.getSelectionGroup()
2580 .getSequencesAsArray(viewport.getHiddenRepSequences());
2581 start = viewport.getSelectionGroup().getStartRes();
2582 end = viewport.getSelectionGroup().getEndRes();
2586 seqs = viewport.getAlignment().getSequencesArray();
2589 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2590 "Remove Gapped Columns", seqs, start, end,
2591 viewport.getAlignment());
2593 addHistoryItem(removeGapCols);
2595 statusBar.setText(MessageManager
2596 .formatMessage("label.removed_empty_columns", new Object[]
2597 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2599 // This is to maintain viewport position on first residue
2600 // of first sequence
2601 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2602 ViewportRanges ranges = viewport.getRanges();
2603 int startRes = seq.findPosition(ranges.getStartRes());
2604 // ShiftList shifts;
2605 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2606 // edit.alColumnChanges=shifts.getInverse();
2607 // if (viewport.hasHiddenColumns)
2608 // viewport.getColumnSelection().compensateForEdits(shifts);
2609 ranges.setStartRes(seq.findIndex(startRes) - 1);
2610 viewport.firePropertyChange("alignment", null,
2611 viewport.getAlignment().getSequences());
2622 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2624 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2627 if (viewport.getSelectionGroup() != null)
2629 seqs = viewport.getSelectionGroup()
2630 .getSequencesAsArray(viewport.getHiddenRepSequences());
2631 start = viewport.getSelectionGroup().getStartRes();
2632 end = viewport.getSelectionGroup().getEndRes();
2636 seqs = viewport.getAlignment().getSequencesArray();
2639 // This is to maintain viewport position on first residue
2640 // of first sequence
2641 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2642 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2644 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2645 viewport.getAlignment()));
2647 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2649 viewport.firePropertyChange("alignment", null,
2650 viewport.getAlignment().getSequences());
2661 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2663 viewport.setPadGaps(padGapsMenuitem.isSelected());
2664 viewport.firePropertyChange("alignment", null,
2665 viewport.getAlignment().getSequences());
2675 public void findMenuItem_actionPerformed(ActionEvent e)
2681 * Create a new view of the current alignment.
2684 public void newView_actionPerformed(ActionEvent e)
2686 newView(null, true);
2690 * Creates and shows a new view of the current alignment.
2693 * title of newly created view; if null, one will be generated
2694 * @param copyAnnotation
2695 * if true then duplicate all annnotation, groups and settings
2696 * @return new alignment panel, already displayed.
2698 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2701 * Create a new AlignmentPanel (with its own, new Viewport)
2703 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2704 if (!copyAnnotation)
2707 * remove all groups and annotation except for the automatic stuff
2709 newap.av.getAlignment().deleteAllGroups();
2710 newap.av.getAlignment().deleteAllAnnotations(false);
2713 newap.av.setGatherViewsHere(false);
2715 if (viewport.viewName == null)
2717 viewport.viewName = MessageManager
2718 .getString("label.view_name_original");
2722 * Views share the same edits undo and redo stacks
2724 newap.av.setHistoryList(viewport.getHistoryList());
2725 newap.av.setRedoList(viewport.getRedoList());
2728 * Views share the same mappings; need to deregister any new mappings
2729 * created by copyAlignPanel, and register the new reference to the shared
2732 newap.av.replaceMappings(viewport.getAlignment());
2735 * start up cDNA consensus (if applicable) now mappings are in place
2737 if (newap.av.initComplementConsensus())
2739 newap.refresh(true); // adjust layout of annotations
2742 newap.av.viewName = getNewViewName(viewTitle);
2744 addAlignmentPanel(newap, true);
2745 newap.alignmentChanged();
2747 if (alignPanels.size() == 2)
2749 viewport.setGatherViewsHere(true);
2751 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2756 * Make a new name for the view, ensuring it is unique within the current
2757 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2758 * these now use viewId. Unique view names are still desirable for usability.)
2763 protected String getNewViewName(String viewTitle)
2765 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2766 boolean addFirstIndex = false;
2767 if (viewTitle == null || viewTitle.trim().length() == 0)
2769 viewTitle = MessageManager.getString("action.view");
2770 addFirstIndex = true;
2774 index = 1;// we count from 1 if given a specific name
2776 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2778 List<Component> comps = PaintRefresher.components
2779 .get(viewport.getSequenceSetId());
2781 List<String> existingNames = getExistingViewNames(comps);
2783 while (existingNames.contains(newViewName))
2785 newViewName = viewTitle + " " + (++index);
2791 * Returns a list of distinct view names found in the given list of
2792 * components. View names are held on the viewport of an AlignmentPanel.
2797 protected List<String> getExistingViewNames(List<Component> comps)
2799 List<String> existingNames = new ArrayList<>();
2800 for (Component comp : comps)
2802 if (comp instanceof AlignmentPanel)
2804 AlignmentPanel ap = (AlignmentPanel) comp;
2805 if (!existingNames.contains(ap.av.viewName))
2807 existingNames.add(ap.av.viewName);
2811 return existingNames;
2815 * Explode tabbed views into separate windows.
2818 public void expandViews_actionPerformed(ActionEvent e)
2820 Desktop.explodeViews(this);
2824 * Gather views in separate windows back into a tabbed presentation.
2827 public void gatherViews_actionPerformed(ActionEvent e)
2829 Desktop.instance.gatherViews(this);
2839 public void font_actionPerformed(ActionEvent e)
2841 new FontChooser(alignPanel);
2851 protected void seqLimit_actionPerformed(ActionEvent e)
2853 viewport.setShowJVSuffix(seqLimits.isSelected());
2855 alignPanel.getIdPanel().getIdCanvas()
2856 .setPreferredSize(alignPanel.calculateIdWidth());
2857 alignPanel.paintAlignment(true, false);
2861 public void idRightAlign_actionPerformed(ActionEvent e)
2863 viewport.setRightAlignIds(idRightAlign.isSelected());
2864 alignPanel.paintAlignment(false, false);
2868 public void centreColumnLabels_actionPerformed(ActionEvent e)
2870 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2871 alignPanel.paintAlignment(false, false);
2877 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2880 protected void followHighlight_actionPerformed()
2883 * Set the 'follow' flag on the Viewport (and scroll to position if now
2886 final boolean state = this.followHighlightMenuItem.getState();
2887 viewport.setFollowHighlight(state);
2890 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2901 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2903 viewport.setColourText(colourTextMenuItem.isSelected());
2904 alignPanel.paintAlignment(false, false);
2914 public void wrapMenuItem_actionPerformed(ActionEvent e)
2916 scaleAbove.setVisible(wrapMenuItem.isSelected());
2917 scaleLeft.setVisible(wrapMenuItem.isSelected());
2918 scaleRight.setVisible(wrapMenuItem.isSelected());
2919 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2920 alignPanel.updateLayout();
2924 public void showAllSeqs_actionPerformed(ActionEvent e)
2926 viewport.showAllHiddenSeqs();
2930 public void showAllColumns_actionPerformed(ActionEvent e)
2932 viewport.showAllHiddenColumns();
2933 alignPanel.paintAlignment(true, true);
2934 viewport.sendSelection();
2938 public void hideSelSequences_actionPerformed(ActionEvent e)
2940 viewport.hideAllSelectedSeqs();
2944 * called by key handler and the hide all/show all menu items
2949 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2952 boolean hide = false;
2953 SequenceGroup sg = viewport.getSelectionGroup();
2954 if (!toggleSeqs && !toggleCols)
2956 // Hide everything by the current selection - this is a hack - we do the
2957 // invert and then hide
2958 // first check that there will be visible columns after the invert.
2959 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2960 && sg.getStartRes() <= sg.getEndRes()))
2962 // now invert the sequence set, if required - empty selection implies
2963 // that no hiding is required.
2966 invertSequenceMenuItem_actionPerformed(null);
2967 sg = viewport.getSelectionGroup();
2971 viewport.expandColSelection(sg, true);
2972 // finally invert the column selection and get the new sequence
2974 invertColSel_actionPerformed(null);
2981 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2983 hideSelSequences_actionPerformed(null);
2986 else if (!(toggleCols && viewport.hasSelectedColumns()))
2988 showAllSeqs_actionPerformed(null);
2994 if (viewport.hasSelectedColumns())
2996 hideSelColumns_actionPerformed(null);
2999 viewport.setSelectionGroup(sg);
3004 showAllColumns_actionPerformed(null);
3013 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3014 * event.ActionEvent)
3017 public void hideAllButSelection_actionPerformed(ActionEvent e)
3019 toggleHiddenRegions(false, false);
3020 viewport.sendSelection();
3027 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3031 public void hideAllSelection_actionPerformed(ActionEvent e)
3033 SequenceGroup sg = viewport.getSelectionGroup();
3034 viewport.expandColSelection(sg, false);
3035 viewport.hideAllSelectedSeqs();
3036 viewport.hideSelectedColumns();
3037 alignPanel.paintAlignment(true, true);
3038 viewport.sendSelection();
3045 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3049 public void showAllhidden_actionPerformed(ActionEvent e)
3051 viewport.showAllHiddenColumns();
3052 viewport.showAllHiddenSeqs();
3053 alignPanel.paintAlignment(true, true);
3054 viewport.sendSelection();
3058 public void hideSelColumns_actionPerformed(ActionEvent e)
3060 viewport.hideSelectedColumns();
3061 alignPanel.paintAlignment(true, true);
3062 viewport.sendSelection();
3066 public void hiddenMarkers_actionPerformed(ActionEvent e)
3068 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3079 protected void scaleAbove_actionPerformed(ActionEvent e)
3081 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3082 // TODO: do we actually need to update overview for scale above change ?
3083 alignPanel.paintAlignment(true, false);
3093 protected void scaleLeft_actionPerformed(ActionEvent e)
3095 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3096 alignPanel.paintAlignment(true, false);
3106 protected void scaleRight_actionPerformed(ActionEvent e)
3108 viewport.setScaleRightWrapped(scaleRight.isSelected());
3109 alignPanel.paintAlignment(true, false);
3119 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3121 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3122 alignPanel.paintAlignment(false, false);
3132 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3134 viewport.setShowText(viewTextMenuItem.isSelected());
3135 alignPanel.paintAlignment(false, false);
3145 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3147 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3148 alignPanel.paintAlignment(false, false);
3151 public FeatureSettings featureSettings;
3154 public FeatureSettingsControllerI getFeatureSettingsUI()
3156 return featureSettings;
3160 public void featureSettings_actionPerformed(ActionEvent e)
3162 if (featureSettings != null)
3164 featureSettings.close();
3165 featureSettings = null;
3167 if (!showSeqFeatures.isSelected())
3169 // make sure features are actually displayed
3170 showSeqFeatures.setSelected(true);
3171 showSeqFeatures_actionPerformed(null);
3173 featureSettings = new FeatureSettings(this);
3177 * Set or clear 'Show Sequence Features'
3183 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3185 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3186 alignPanel.paintAlignment(true, true);
3190 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3191 * the annotations panel as a whole.
3193 * The options to show/hide all annotations should be enabled when the panel
3194 * is shown, and disabled when the panel is hidden.
3199 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3201 final boolean setVisible = annotationPanelMenuItem.isSelected();
3202 viewport.setShowAnnotation(setVisible);
3203 this.showAllSeqAnnotations.setEnabled(setVisible);
3204 this.hideAllSeqAnnotations.setEnabled(setVisible);
3205 this.showAllAlAnnotations.setEnabled(setVisible);
3206 this.hideAllAlAnnotations.setEnabled(setVisible);
3207 alignPanel.updateLayout();
3211 public void alignmentProperties()
3213 JEditorPane editPane = new JEditorPane("text/html", "");
3214 editPane.setEditable(false);
3215 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3218 MessageManager.formatMessage("label.html_content", new Object[]
3219 { contents.toString() }));
3220 JInternalFrame frame = new JInternalFrame();
3221 frame.getContentPane().add(new JScrollPane(editPane));
3223 Desktop.addInternalFrame(frame, MessageManager
3224 .formatMessage("label.alignment_properties", new Object[]
3225 { getTitle() }), 500, 400);
3235 public void overviewMenuItem_actionPerformed(ActionEvent e)
3237 if (alignPanel.overviewPanel != null)
3242 JInternalFrame frame = new JInternalFrame();
3243 final OverviewPanel overview = new OverviewPanel(alignPanel);
3244 frame.setContentPane(overview);
3245 Desktop.addInternalFrame(frame, MessageManager
3246 .formatMessage("label.overview_params", new Object[]
3247 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3250 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3251 frame.addInternalFrameListener(
3252 new javax.swing.event.InternalFrameAdapter()
3255 public void internalFrameClosed(
3256 javax.swing.event.InternalFrameEvent evt)
3259 alignPanel.setOverviewPanel(null);
3263 alignPanel.setOverviewPanel(overview);
3267 public void textColour_actionPerformed()
3269 new TextColourChooser().chooseColour(alignPanel, null);
3273 * public void covariationColour_actionPerformed() {
3275 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3279 public void annotationColour_actionPerformed()
3281 new AnnotationColourChooser(viewport, alignPanel);
3285 public void annotationColumn_actionPerformed(ActionEvent e)
3287 new AnnotationColumnChooser(viewport, alignPanel);
3291 * Action on the user checking or unchecking the option to apply the selected
3292 * colour scheme to all groups. If unchecked, groups may have their own
3293 * independent colour schemes.
3298 public void applyToAllGroups_actionPerformed(boolean selected)
3300 viewport.setColourAppliesToAllGroups(selected);
3304 * Action on user selecting a colour from the colour menu
3307 * the name (not the menu item label!) of the colour scheme
3310 public void changeColour_actionPerformed(String name)
3313 * 'User Defined' opens a panel to configure or load a
3314 * user-defined colour scheme
3316 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3318 new UserDefinedColours(alignPanel);
3323 * otherwise set the chosen colour scheme (or null for 'None')
3325 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3326 viewport.getAlignment(), viewport.getHiddenRepSequences());
3331 * Actions on setting or changing the alignment colour scheme
3336 public void changeColour(ColourSchemeI cs)
3338 // TODO: pull up to controller method
3339 ColourMenuHelper.setColourSelected(colourMenu, cs);
3341 viewport.setGlobalColourScheme(cs);
3343 alignPanel.paintAlignment(true, true);
3347 * Show the PID threshold slider panel
3350 protected void modifyPID_actionPerformed()
3352 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3353 alignPanel.getViewName());
3354 SliderPanel.showPIDSlider();
3358 * Show the Conservation slider panel
3361 protected void modifyConservation_actionPerformed()
3363 SliderPanel.setConservationSlider(alignPanel,
3364 viewport.getResidueShading(), alignPanel.getViewName());
3365 SliderPanel.showConservationSlider();
3369 * Action on selecting or deselecting (Colour) By Conservation
3372 public void conservationMenuItem_actionPerformed(boolean selected)
3374 modifyConservation.setEnabled(selected);
3375 viewport.setConservationSelected(selected);
3376 viewport.getResidueShading().setConservationApplied(selected);
3378 changeColour(viewport.getGlobalColourScheme());
3381 modifyConservation_actionPerformed();
3385 SliderPanel.hideConservationSlider();
3390 * Action on selecting or deselecting (Colour) Above PID Threshold
3393 public void abovePIDThreshold_actionPerformed(boolean selected)
3395 modifyPID.setEnabled(selected);
3396 viewport.setAbovePIDThreshold(selected);
3399 viewport.getResidueShading().setThreshold(0,
3400 viewport.isIgnoreGapsConsensus());
3403 changeColour(viewport.getGlobalColourScheme());
3406 modifyPID_actionPerformed();
3410 SliderPanel.hidePIDSlider();
3421 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3423 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3424 AlignmentSorter.sortByPID(viewport.getAlignment(),
3425 viewport.getAlignment().getSequenceAt(0));
3426 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3427 viewport.getAlignment()));
3428 alignPanel.paintAlignment(true, false);
3438 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3440 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3441 AlignmentSorter.sortByID(viewport.getAlignment());
3443 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3444 alignPanel.paintAlignment(true, false);
3454 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3456 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3457 AlignmentSorter.sortByLength(viewport.getAlignment());
3458 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3459 viewport.getAlignment()));
3460 alignPanel.paintAlignment(true, false);
3470 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3472 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3473 AlignmentSorter.sortByGroup(viewport.getAlignment());
3474 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3475 viewport.getAlignment()));
3477 alignPanel.paintAlignment(true, false);
3487 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3489 new RedundancyPanel(alignPanel, this);
3499 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3501 if ((viewport.getSelectionGroup() == null)
3502 || (viewport.getSelectionGroup().getSize() < 2))
3504 JvOptionPane.showInternalMessageDialog(this,
3505 MessageManager.getString(
3506 "label.you_must_select_least_two_sequences"),
3507 MessageManager.getString("label.invalid_selection"),
3508 JvOptionPane.WARNING_MESSAGE);
3512 JInternalFrame frame = new JInternalFrame();
3513 frame.setContentPane(new PairwiseAlignPanel(viewport));
3514 Desktop.addInternalFrame(frame,
3515 MessageManager.getString("action.pairwise_alignment"), 600,
3521 public void autoCalculate_actionPerformed(ActionEvent e)
3523 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3524 if (viewport.autoCalculateConsensus)
3526 viewport.firePropertyChange("alignment", null,
3527 viewport.getAlignment().getSequences());
3532 public void sortByTreeOption_actionPerformed(ActionEvent e)
3534 viewport.sortByTree = sortByTree.isSelected();
3538 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3540 viewport.followSelection = listenToViewSelections.isSelected();
3544 * Constructs a tree panel and adds it to the desktop
3547 * tree type (NJ or AV)
3549 * name of score model used to compute the tree
3551 * parameters for the distance or similarity calculation
3553 void newTreePanel(String type, String modelName,
3554 SimilarityParamsI options)
3556 String frameTitle = "";
3559 boolean onSelection = false;
3560 if (viewport.getSelectionGroup() != null
3561 && viewport.getSelectionGroup().getSize() > 0)
3563 SequenceGroup sg = viewport.getSelectionGroup();
3565 /* Decide if the selection is a column region */
3566 for (SequenceI _s : sg.getSequences())
3568 if (_s.getLength() < sg.getEndRes())
3570 JvOptionPane.showMessageDialog(Desktop.desktop,
3571 MessageManager.getString(
3572 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3573 MessageManager.getString(
3574 "label.sequences_selection_not_aligned"),
3575 JvOptionPane.WARNING_MESSAGE);
3584 if (viewport.getAlignment().getHeight() < 2)
3590 tp = new TreePanel(alignPanel, type, modelName, options);
3591 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3593 frameTitle += " from ";
3595 if (viewport.viewName != null)
3597 frameTitle += viewport.viewName + " of ";
3600 frameTitle += this.title;
3602 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3613 public void addSortByOrderMenuItem(String title,
3614 final AlignmentOrder order)
3616 final JMenuItem item = new JMenuItem(MessageManager
3617 .formatMessage("action.by_title_param", new Object[]
3620 item.addActionListener(new java.awt.event.ActionListener()
3623 public void actionPerformed(ActionEvent e)
3625 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3627 // TODO: JBPNote - have to map order entries to curent SequenceI
3629 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3631 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3632 viewport.getAlignment()));
3634 alignPanel.paintAlignment(true, false);
3640 * Add a new sort by annotation score menu item
3643 * the menu to add the option to
3645 * the label used to retrieve scores for each sequence on the
3648 public void addSortByAnnotScoreMenuItem(JMenu sort,
3649 final String scoreLabel)
3651 final JMenuItem item = new JMenuItem(scoreLabel);
3653 item.addActionListener(new java.awt.event.ActionListener()
3656 public void actionPerformed(ActionEvent e)
3658 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3659 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3660 viewport.getAlignment());// ,viewport.getSelectionGroup());
3661 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3662 viewport.getAlignment()));
3663 alignPanel.paintAlignment(true, false);
3669 * last hash for alignment's annotation array - used to minimise cost of
3672 protected int _annotationScoreVectorHash;
3675 * search the alignment and rebuild the sort by annotation score submenu the
3676 * last alignment annotation vector hash is stored to minimize cost of
3677 * rebuilding in subsequence calls.
3681 public void buildSortByAnnotationScoresMenu()
3683 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3688 if (viewport.getAlignment().getAlignmentAnnotation()
3689 .hashCode() != _annotationScoreVectorHash)
3691 sortByAnnotScore.removeAll();
3692 // almost certainly a quicker way to do this - but we keep it simple
3693 Hashtable scoreSorts = new Hashtable();
3694 AlignmentAnnotation aann[];
3695 for (SequenceI sqa : viewport.getAlignment().getSequences())
3697 aann = sqa.getAnnotation();
3698 for (int i = 0; aann != null && i < aann.length; i++)
3700 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3702 scoreSorts.put(aann[i].label, aann[i].label);
3706 Enumeration labels = scoreSorts.keys();
3707 while (labels.hasMoreElements())
3709 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3710 (String) labels.nextElement());
3712 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3715 _annotationScoreVectorHash = viewport.getAlignment()
3716 .getAlignmentAnnotation().hashCode();
3721 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3722 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3723 * call. Listeners are added to remove the menu item when the treePanel is
3724 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3728 public void buildTreeSortMenu()
3730 sortByTreeMenu.removeAll();
3732 List<Component> comps = PaintRefresher.components
3733 .get(viewport.getSequenceSetId());
3734 List<TreePanel> treePanels = new ArrayList<>();
3735 for (Component comp : comps)
3737 if (comp instanceof TreePanel)
3739 treePanels.add((TreePanel) comp);
3743 if (treePanels.size() < 1)
3745 sortByTreeMenu.setVisible(false);
3749 sortByTreeMenu.setVisible(true);
3751 for (final TreePanel tp : treePanels)
3753 final JMenuItem item = new JMenuItem(tp.getTitle());
3754 item.addActionListener(new java.awt.event.ActionListener()
3757 public void actionPerformed(ActionEvent e)
3759 tp.sortByTree_actionPerformed();
3760 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3765 sortByTreeMenu.add(item);
3769 public boolean sortBy(AlignmentOrder alorder, String undoname)
3771 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3772 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3773 if (undoname != null)
3775 addHistoryItem(new OrderCommand(undoname, oldOrder,
3776 viewport.getAlignment()));
3778 alignPanel.paintAlignment(true, false);
3783 * Work out whether the whole set of sequences or just the selected set will
3784 * be submitted for multiple alignment.
3787 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3789 // Now, check we have enough sequences
3790 AlignmentView msa = null;
3792 if ((viewport.getSelectionGroup() != null)
3793 && (viewport.getSelectionGroup().getSize() > 1))
3795 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3796 // some common interface!
3798 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3799 * SequenceI[sz = seqs.getSize(false)];
3801 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3802 * seqs.getSequenceAt(i); }
3804 msa = viewport.getAlignmentView(true);
3806 else if (viewport.getSelectionGroup() != null
3807 && viewport.getSelectionGroup().getSize() == 1)
3809 int option = JvOptionPane.showConfirmDialog(this,
3810 MessageManager.getString("warn.oneseq_msainput_selection"),
3811 MessageManager.getString("label.invalid_selection"),
3812 JvOptionPane.OK_CANCEL_OPTION);
3813 if (option == JvOptionPane.OK_OPTION)
3815 msa = viewport.getAlignmentView(false);
3820 msa = viewport.getAlignmentView(false);
3826 * Decides what is submitted to a secondary structure prediction service: the
3827 * first sequence in the alignment, or in the current selection, or, if the
3828 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3829 * region or the whole alignment. (where the first sequence in the set is the
3830 * one that the prediction will be for).
3832 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3834 AlignmentView seqs = null;
3836 if ((viewport.getSelectionGroup() != null)
3837 && (viewport.getSelectionGroup().getSize() > 0))
3839 seqs = viewport.getAlignmentView(true);
3843 seqs = viewport.getAlignmentView(false);
3845 // limit sequences - JBPNote in future - could spawn multiple prediction
3847 // TODO: viewport.getAlignment().isAligned is a global state - the local
3848 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3849 if (!viewport.getAlignment().isAligned(false))
3851 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3852 // TODO: if seqs.getSequences().length>1 then should really have warned
3866 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3868 // Pick the tree file
3869 JalviewFileChooser chooser = new JalviewFileChooser(
3870 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3871 chooser.setFileView(new JalviewFileView());
3872 chooser.setDialogTitle(
3873 MessageManager.getString("label.select_newick_like_tree_file"));
3874 chooser.setToolTipText(
3875 MessageManager.getString("label.load_tree_file"));
3877 int value = chooser.showOpenDialog(null);
3879 if (value == JalviewFileChooser.APPROVE_OPTION)
3881 String filePath = chooser.getSelectedFile().getPath();
3882 Cache.setProperty("LAST_DIRECTORY", filePath);
3883 NewickFile fin = null;
3886 fin = new NewickFile(filePath, DataSourceType.FILE);
3887 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3888 } catch (Exception ex)
3890 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3891 MessageManager.getString("label.problem_reading_tree_file"),
3892 JvOptionPane.WARNING_MESSAGE);
3893 ex.printStackTrace();
3895 if (fin != null && fin.hasWarningMessage())
3897 JvOptionPane.showMessageDialog(Desktop.desktop,
3898 fin.getWarningMessage(),
3900 .getString("label.possible_problem_with_tree_file"),
3901 JvOptionPane.WARNING_MESSAGE);
3906 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3908 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3911 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3912 int h, int x, int y)
3914 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3918 * Add a treeviewer for the tree extracted from a Newick file object to the
3919 * current alignment view
3926 * Associated alignment input data (or null)
3935 * @return TreePanel handle
3937 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3938 AlignmentView input, int w, int h, int x, int y)
3940 TreePanel tp = null;
3946 if (nf.getTree() != null)
3948 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3954 tp.setLocation(x, y);
3957 Desktop.addInternalFrame(tp, treeTitle, w, h);
3959 } catch (Exception ex)
3961 ex.printStackTrace();
3967 private boolean buildingMenu = false;
3970 * Generates menu items and listener event actions for web service clients
3973 public void BuildWebServiceMenu()
3975 while (buildingMenu)
3979 System.err.println("Waiting for building menu to finish.");
3981 } catch (Exception e)
3985 final AlignFrame me = this;
3986 buildingMenu = true;
3987 new Thread(new Runnable()
3992 final List<JMenuItem> legacyItems = new ArrayList<>();
3995 // System.err.println("Building ws menu again "
3996 // + Thread.currentThread());
3997 // TODO: add support for context dependent disabling of services based
3999 // alignment and current selection
4000 // TODO: add additional serviceHandle parameter to specify abstract
4002 // class independently of AbstractName
4003 // TODO: add in rediscovery GUI function to restart discoverer
4004 // TODO: group services by location as well as function and/or
4006 // object broker mechanism.
4007 final Vector<JMenu> wsmenu = new Vector<>();
4008 final IProgressIndicator af = me;
4011 * do not i18n these strings - they are hard-coded in class
4012 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4013 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4015 final JMenu msawsmenu = new JMenu("Alignment");
4016 final JMenu secstrmenu = new JMenu(
4017 "Secondary Structure Prediction");
4018 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4019 final JMenu analymenu = new JMenu("Analysis");
4020 final JMenu dismenu = new JMenu("Protein Disorder");
4021 // JAL-940 - only show secondary structure prediction services from
4022 // the legacy server
4023 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4025 Discoverer.services != null && (Discoverer.services.size() > 0))
4027 // TODO: refactor to allow list of AbstractName/Handler bindings to
4029 // stored or retrieved from elsewhere
4030 // No MSAWS used any more:
4031 // Vector msaws = null; // (Vector)
4032 // Discoverer.services.get("MsaWS");
4033 Vector secstrpr = (Vector) Discoverer.services
4035 if (secstrpr != null)
4037 // Add any secondary structure prediction services
4038 for (int i = 0, j = secstrpr.size(); i < j; i++)
4040 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4042 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4043 .getServiceClient(sh);
4044 int p = secstrmenu.getItemCount();
4045 impl.attachWSMenuEntry(secstrmenu, me);
4046 int q = secstrmenu.getItemCount();
4047 for (int litm = p; litm < q; litm++)
4049 legacyItems.add(secstrmenu.getItem(litm));
4055 // Add all submenus in the order they should appear on the web
4057 wsmenu.add(msawsmenu);
4058 wsmenu.add(secstrmenu);
4059 wsmenu.add(dismenu);
4060 wsmenu.add(analymenu);
4061 // No search services yet
4062 // wsmenu.add(seqsrchmenu);
4064 javax.swing.SwingUtilities.invokeLater(new Runnable()
4071 webService.removeAll();
4072 // first, add discovered services onto the webservices menu
4073 if (wsmenu.size() > 0)
4075 for (int i = 0, j = wsmenu.size(); i < j; i++)
4077 webService.add(wsmenu.get(i));
4082 webService.add(me.webServiceNoServices);
4084 // TODO: move into separate menu builder class.
4085 boolean new_sspred = false;
4086 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4088 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4089 if (jws2servs != null)
4091 if (jws2servs.hasServices())
4093 jws2servs.attachWSMenuEntry(webService, me);
4094 for (Jws2Instance sv : jws2servs.getServices())
4096 if (sv.description.toLowerCase().contains("jpred"))
4098 for (JMenuItem jmi : legacyItems)
4100 jmi.setVisible(false);
4106 if (jws2servs.isRunning())
4108 JMenuItem tm = new JMenuItem(
4109 "Still discovering JABA Services");
4110 tm.setEnabled(false);
4115 build_urlServiceMenu(me.webService);
4116 build_fetchdbmenu(webService);
4117 for (JMenu item : wsmenu)
4119 if (item.getItemCount() == 0)
4121 item.setEnabled(false);
4125 item.setEnabled(true);
4128 } catch (Exception e)
4131 "Exception during web service menu building process.",
4136 } catch (Exception e)
4139 buildingMenu = false;
4146 * construct any groupURL type service menu entries.
4150 private void build_urlServiceMenu(JMenu webService)
4152 // TODO: remove this code when 2.7 is released
4153 // DEBUG - alignmentView
4155 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4156 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4158 * @Override public void actionPerformed(ActionEvent e) {
4159 * jalview.datamodel.AlignmentView
4160 * .testSelectionViews(af.viewport.getAlignment(),
4161 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4163 * }); webService.add(testAlView);
4165 // TODO: refactor to RestClient discoverer and merge menu entries for
4166 // rest-style services with other types of analysis/calculation service
4167 // SHmmr test client - still being implemented.
4168 // DEBUG - alignmentView
4170 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4173 client.attachWSMenuEntry(
4174 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4180 * Searches the alignment sequences for xRefs and builds the Show
4181 * Cross-References menu (formerly called Show Products), with database
4182 * sources for which cross-references are found (protein sources for a
4183 * nucleotide alignment and vice versa)
4185 * @return true if Show Cross-references menu should be enabled
4187 public boolean canShowProducts()
4189 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4190 AlignmentI dataset = viewport.getAlignment().getDataset();
4192 showProducts.removeAll();
4193 final boolean dna = viewport.getAlignment().isNucleotide();
4195 if (seqs == null || seqs.length == 0)
4197 // nothing to see here.
4201 boolean showp = false;
4204 List<String> ptypes = new CrossRef(seqs, dataset)
4205 .findXrefSourcesForSequences(dna);
4207 for (final String source : ptypes)
4210 final AlignFrame af = this;
4211 JMenuItem xtype = new JMenuItem(source);
4212 xtype.addActionListener(new ActionListener()
4215 public void actionPerformed(ActionEvent e)
4217 showProductsFor(af.viewport.getSequenceSelection(), dna,
4221 showProducts.add(xtype);
4223 showProducts.setVisible(showp);
4224 showProducts.setEnabled(showp);
4225 } catch (Exception e)
4228 "canShowProducts threw an exception - please report to help@jalview.org",
4236 * Finds and displays cross-references for the selected sequences (protein
4237 * products for nucleotide sequences, dna coding sequences for peptides).
4240 * the sequences to show cross-references for
4242 * true if from a nucleotide alignment (so showing proteins)
4244 * the database to show cross-references for
4246 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4247 final String source)
4249 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4254 * Construct and display a new frame containing the translation of this
4255 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4258 public void showTranslation_actionPerformed(ActionEvent e)
4260 AlignmentI al = null;
4263 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4265 al = dna.translateCdna();
4266 } catch (Exception ex)
4268 jalview.bin.Cache.log.error(
4269 "Exception during translation. Please report this !", ex);
4270 final String msg = MessageManager.getString(
4271 "label.error_when_translating_sequences_submit_bug_report");
4272 final String errorTitle = MessageManager
4273 .getString("label.implementation_error")
4274 + MessageManager.getString("label.translation_failed");
4275 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4276 JvOptionPane.ERROR_MESSAGE);
4279 if (al == null || al.getHeight() == 0)
4281 final String msg = MessageManager.getString(
4282 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4283 final String errorTitle = MessageManager
4284 .getString("label.translation_failed");
4285 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4286 JvOptionPane.WARNING_MESSAGE);
4290 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4291 af.setFileFormat(this.currentFileFormat);
4292 final String newTitle = MessageManager
4293 .formatMessage("label.translation_of_params", new Object[]
4294 { this.getTitle() });
4295 af.setTitle(newTitle);
4296 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4298 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4299 viewport.openSplitFrame(af, new Alignment(seqs));
4303 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4310 * Set the file format
4314 public void setFileFormat(FileFormatI format)
4316 this.currentFileFormat = format;
4320 * Try to load a features file onto the alignment.
4323 * contents or path to retrieve file
4325 * access mode of file (see jalview.io.AlignFile)
4326 * @return true if features file was parsed correctly.
4328 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4330 return avc.parseFeaturesFile(file, sourceType,
4331 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4336 public void refreshFeatureUI(boolean enableIfNecessary)
4338 // note - currently this is only still here rather than in the controller
4339 // because of the featureSettings hard reference that is yet to be
4341 if (enableIfNecessary)
4343 viewport.setShowSequenceFeatures(true);
4344 showSeqFeatures.setSelected(true);
4350 public void dragEnter(DropTargetDragEvent evt)
4355 public void dragExit(DropTargetEvent evt)
4360 public void dragOver(DropTargetDragEvent evt)
4365 public void dropActionChanged(DropTargetDragEvent evt)
4370 public void drop(DropTargetDropEvent evt)
4372 // JAL-1552 - acceptDrop required before getTransferable call for
4373 // Java's Transferable for native dnd
4374 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4375 Transferable t = evt.getTransferable();
4376 final AlignFrame thisaf = this;
4377 final List<String> files = new ArrayList<>();
4378 List<DataSourceType> protocols = new ArrayList<>();
4382 Desktop.transferFromDropTarget(files, protocols, evt, t);
4383 } catch (Exception e)
4385 e.printStackTrace();
4389 new Thread(new Runnable()
4396 // check to see if any of these files have names matching sequences
4399 SequenceIdMatcher idm = new SequenceIdMatcher(
4400 viewport.getAlignment().getSequencesArray());
4402 * Object[] { String,SequenceI}
4404 ArrayList<Object[]> filesmatched = new ArrayList<>();
4405 ArrayList<String> filesnotmatched = new ArrayList<>();
4406 for (int i = 0; i < files.size(); i++)
4408 String file = files.get(i).toString();
4410 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4411 if (protocol == DataSourceType.FILE)
4413 File fl = new File(file);
4414 pdbfn = fl.getName();
4416 else if (protocol == DataSourceType.URL)
4418 URL url = new URL(file);
4419 pdbfn = url.getFile();
4421 if (pdbfn.length() > 0)
4423 // attempt to find a match in the alignment
4424 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4425 int l = 0, c = pdbfn.indexOf(".");
4426 while (mtch == null && c != -1)
4431 } while ((c = pdbfn.indexOf(".", l)) > l);
4434 pdbfn = pdbfn.substring(0, l);
4436 mtch = idm.findAllIdMatches(pdbfn);
4440 FileFormatI type = null;
4443 type = new IdentifyFile().identify(file, protocol);
4444 } catch (Exception ex)
4448 if (type != null && type.isStructureFile())
4450 filesmatched.add(new Object[] { file, protocol, mtch });
4454 // File wasn't named like one of the sequences or wasn't a PDB
4456 filesnotmatched.add(file);
4460 if (filesmatched.size() > 0)
4462 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4463 || JvOptionPane.showConfirmDialog(thisaf,
4464 MessageManager.formatMessage(
4465 "label.automatically_associate_structure_files_with_sequences_same_name",
4467 { Integer.valueOf(filesmatched.size())
4469 MessageManager.getString(
4470 "label.automatically_associate_structure_files_by_name"),
4471 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4474 for (Object[] fm : filesmatched)
4476 // try and associate
4477 // TODO: may want to set a standard ID naming formalism for
4478 // associating PDB files which have no IDs.
4479 for (SequenceI toassoc : (SequenceI[]) fm[2])
4481 PDBEntry pe = new AssociatePdbFileWithSeq()
4482 .associatePdbWithSeq((String) fm[0],
4483 (DataSourceType) fm[1], toassoc, false,
4487 System.err.println("Associated file : "
4488 + ((String) fm[0]) + " with "
4489 + toassoc.getDisplayId(true));
4493 // TODO: do we need to update overview ? only if features are
4495 alignPanel.paintAlignment(true, false);
4499 if (filesnotmatched.size() > 0)
4501 if (assocfiles > 0 && (Cache.getDefault(
4502 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4503 || JvOptionPane.showConfirmDialog(thisaf,
4504 "<html>" + MessageManager.formatMessage(
4505 "label.ignore_unmatched_dropped_files_info",
4508 filesnotmatched.size())
4511 MessageManager.getString(
4512 "label.ignore_unmatched_dropped_files"),
4513 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4517 for (String fn : filesnotmatched)
4519 loadJalviewDataFile(fn, null, null, null);
4523 } catch (Exception ex)
4525 ex.printStackTrace();
4533 * Attempt to load a "dropped" file or URL string, by testing in turn for
4535 * <li>an Annotation file</li>
4536 * <li>a JNet file</li>
4537 * <li>a features file</li>
4538 * <li>else try to interpret as an alignment file</li>
4542 * either a filename or a URL string.
4544 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4545 FileFormatI format, SequenceI assocSeq)
4549 if (sourceType == null)
4551 sourceType = FormatAdapter.checkProtocol(file);
4553 // if the file isn't identified, or not positively identified as some
4554 // other filetype (PFAM is default unidentified alignment file type) then
4555 // try to parse as annotation.
4556 boolean isAnnotation = (format == null
4557 || FileFormat.Pfam.equals(format))
4558 ? new AnnotationFile().annotateAlignmentView(viewport,
4564 // first see if its a T-COFFEE score file
4565 TCoffeeScoreFile tcf = null;
4568 tcf = new TCoffeeScoreFile(file, sourceType);
4571 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4575 new TCoffeeColourScheme(viewport.getAlignment()));
4576 isAnnotation = true;
4577 statusBar.setText(MessageManager.getString(
4578 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4582 // some problem - if no warning its probable that the ID matching
4583 // process didn't work
4584 JvOptionPane.showMessageDialog(Desktop.desktop,
4585 tcf.getWarningMessage() == null
4586 ? MessageManager.getString(
4587 "label.check_file_matches_sequence_ids_alignment")
4588 : tcf.getWarningMessage(),
4589 MessageManager.getString(
4590 "label.problem_reading_tcoffee_score_file"),
4591 JvOptionPane.WARNING_MESSAGE);
4598 } catch (Exception x)
4601 "Exception when processing data source as T-COFFEE score file",
4607 // try to see if its a JNet 'concise' style annotation file *before*
4609 // try to parse it as a features file
4612 format = new IdentifyFile().identify(file, sourceType);
4614 if (FileFormat.ScoreMatrix == format)
4616 ScoreMatrixFile sm = new ScoreMatrixFile(
4617 new FileParse(file, sourceType));
4619 // todo: i18n this message
4620 statusBar.setText(MessageManager.formatMessage(
4621 "label.successfully_loaded_matrix",
4622 sm.getMatrixName()));
4624 else if (FileFormat.Jnet.equals(format))
4626 JPredFile predictions = new JPredFile(file, sourceType);
4627 new JnetAnnotationMaker();
4628 JnetAnnotationMaker.add_annotation(predictions,
4629 viewport.getAlignment(), 0, false);
4630 viewport.getAlignment().setupJPredAlignment();
4631 isAnnotation = true;
4633 // else if (IdentifyFile.FeaturesFile.equals(format))
4634 else if (FileFormat.Features.equals(format))
4636 if (parseFeaturesFile(file, sourceType))
4638 alignPanel.paintAlignment(true, true);
4643 new FileLoader().LoadFile(viewport, file, sourceType, format);
4650 alignPanel.adjustAnnotationHeight();
4651 viewport.updateSequenceIdColours();
4652 buildSortByAnnotationScoresMenu();
4653 alignPanel.paintAlignment(true, true);
4655 } catch (Exception ex)
4657 ex.printStackTrace();
4658 } catch (OutOfMemoryError oom)
4663 } catch (Exception x)
4668 + (sourceType != null
4669 ? (sourceType == DataSourceType.PASTE
4671 : "using " + sourceType + " from "
4675 ? "(parsing as '" + format + "' file)"
4677 oom, Desktop.desktop);
4682 * Method invoked by the ChangeListener on the tabbed pane, in other words
4683 * when a different tabbed pane is selected by the user or programmatically.
4686 public void tabSelectionChanged(int index)
4690 alignPanel = alignPanels.get(index);
4691 viewport = alignPanel.av;
4692 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4693 setMenusFromViewport(viewport);
4697 * 'focus' any colour slider that is open to the selected viewport
4699 if (viewport.getConservationSelected())
4701 SliderPanel.setConservationSlider(alignPanel,
4702 viewport.getResidueShading(), alignPanel.getViewName());
4706 SliderPanel.hideConservationSlider();
4708 if (viewport.getAbovePIDThreshold())
4710 SliderPanel.setPIDSliderSource(alignPanel,
4711 viewport.getResidueShading(), alignPanel.getViewName());
4715 SliderPanel.hidePIDSlider();
4719 * If there is a frame linked to this one in a SplitPane, switch it to the
4720 * same view tab index. No infinite recursion of calls should happen, since
4721 * tabSelectionChanged() should not get invoked on setting the selected
4722 * index to an unchanged value. Guard against setting an invalid index
4723 * before the new view peer tab has been created.
4725 final AlignViewportI peer = viewport.getCodingComplement();
4728 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4729 .getAlignPanel().alignFrame;
4730 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4732 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4738 * On right mouse click on view tab, prompt for and set new view name.
4741 public void tabbedPane_mousePressed(MouseEvent e)
4743 if (e.isPopupTrigger())
4745 String msg = MessageManager.getString("label.enter_view_name");
4746 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4747 JvOptionPane.QUESTION_MESSAGE);
4751 viewport.viewName = reply;
4752 // TODO warn if reply is in getExistingViewNames()?
4753 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4758 public AlignViewport getCurrentView()
4764 * Open the dialog for regex description parsing.
4767 protected void extractScores_actionPerformed(ActionEvent e)
4769 ParseProperties pp = new jalview.analysis.ParseProperties(
4770 viewport.getAlignment());
4771 // TODO: verify regex and introduce GUI dialog for version 2.5
4772 // if (pp.getScoresFromDescription("col", "score column ",
4773 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4775 if (pp.getScoresFromDescription("description column",
4776 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4778 buildSortByAnnotationScoresMenu();
4786 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4790 protected void showDbRefs_actionPerformed(ActionEvent e)
4792 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4798 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4802 protected void showNpFeats_actionPerformed(ActionEvent e)
4804 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4808 * find the viewport amongst the tabs in this alignment frame and close that
4813 public boolean closeView(AlignViewportI av)
4817 this.closeMenuItem_actionPerformed(false);
4820 Component[] comp = tabbedPane.getComponents();
4821 for (int i = 0; comp != null && i < comp.length; i++)
4823 if (comp[i] instanceof AlignmentPanel)
4825 if (((AlignmentPanel) comp[i]).av == av)
4828 closeView((AlignmentPanel) comp[i]);
4836 protected void build_fetchdbmenu(JMenu webService)
4838 // Temporary hack - DBRef Fetcher always top level ws entry.
4839 // TODO We probably want to store a sequence database checklist in
4840 // preferences and have checkboxes.. rather than individual sources selected
4842 final JMenu rfetch = new JMenu(
4843 MessageManager.getString("action.fetch_db_references"));
4844 rfetch.setToolTipText(MessageManager.getString(
4845 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4846 webService.add(rfetch);
4848 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4849 MessageManager.getString("option.trim_retrieved_seqs"));
4850 trimrs.setToolTipText(
4851 MessageManager.getString("label.trim_retrieved_sequences"));
4853 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4854 trimrs.addActionListener(new ActionListener()
4857 public void actionPerformed(ActionEvent e)
4859 trimrs.setSelected(trimrs.isSelected());
4860 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4861 Boolean.valueOf(trimrs.isSelected()).toString());
4865 JMenuItem fetchr = new JMenuItem(
4866 MessageManager.getString("label.standard_databases"));
4867 fetchr.setToolTipText(
4868 MessageManager.getString("label.fetch_embl_uniprot"));
4869 fetchr.addActionListener(new ActionListener()
4873 public void actionPerformed(ActionEvent e)
4875 new Thread(new Runnable()
4880 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4881 .getAlignment().isNucleotide();
4882 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4883 alignPanel.av.getSequenceSelection(),
4884 alignPanel.alignFrame, null,
4885 alignPanel.alignFrame.featureSettings, isNucleotide);
4886 dbRefFetcher.addListener(new FetchFinishedListenerI()
4889 public void finished()
4891 AlignFrame.this.setMenusForViewport();
4894 dbRefFetcher.fetchDBRefs(false);
4902 final AlignFrame me = this;
4903 new Thread(new Runnable()
4908 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4909 .getSequenceFetcherSingleton(me);
4910 javax.swing.SwingUtilities.invokeLater(new Runnable()
4915 String[] dbclasses = sf.getOrderedSupportedSources();
4916 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4917 // jalview.util.QuickSort.sort(otherdb, otherdb);
4918 List<DbSourceProxy> otherdb;
4919 JMenu dfetch = new JMenu();
4920 JMenu ifetch = new JMenu();
4921 JMenuItem fetchr = null;
4922 int comp = 0, icomp = 0, mcomp = 15;
4923 String mname = null;
4925 for (String dbclass : dbclasses)
4927 otherdb = sf.getSourceProxy(dbclass);
4928 // add a single entry for this class, or submenu allowing 'fetch
4930 if (otherdb == null || otherdb.size() < 1)
4934 // List<DbSourceProxy> dbs=otherdb;
4935 // otherdb=new ArrayList<DbSourceProxy>();
4936 // for (DbSourceProxy db:dbs)
4938 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4942 mname = "From " + dbclass;
4944 if (otherdb.size() == 1)
4946 final DbSourceProxy[] dassource = otherdb
4947 .toArray(new DbSourceProxy[0]);
4948 DbSourceProxy src = otherdb.get(0);
4949 fetchr = new JMenuItem(src.getDbSource());
4950 fetchr.addActionListener(new ActionListener()
4954 public void actionPerformed(ActionEvent e)
4956 new Thread(new Runnable()
4962 boolean isNucleotide = alignPanel.alignFrame
4963 .getViewport().getAlignment()
4965 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4966 alignPanel.av.getSequenceSelection(),
4967 alignPanel.alignFrame, dassource,
4968 alignPanel.alignFrame.featureSettings,
4971 .addListener(new FetchFinishedListenerI()
4974 public void finished()
4976 AlignFrame.this.setMenusForViewport();
4979 dbRefFetcher.fetchDBRefs(false);
4985 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
4986 MessageManager.formatMessage(
4987 "label.fetch_retrieve_from", new Object[]
4988 { src.getDbName() })));
4994 final DbSourceProxy[] dassource = otherdb
4995 .toArray(new DbSourceProxy[0]);
4997 DbSourceProxy src = otherdb.get(0);
4998 fetchr = new JMenuItem(MessageManager
4999 .formatMessage("label.fetch_all_param", new Object[]
5000 { src.getDbSource() }));
5001 fetchr.addActionListener(new ActionListener()
5004 public void actionPerformed(ActionEvent e)
5006 new Thread(new Runnable()
5012 boolean isNucleotide = alignPanel.alignFrame
5013 .getViewport().getAlignment()
5015 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5016 alignPanel.av.getSequenceSelection(),
5017 alignPanel.alignFrame, dassource,
5018 alignPanel.alignFrame.featureSettings,
5021 .addListener(new FetchFinishedListenerI()
5024 public void finished()
5026 AlignFrame.this.setMenusForViewport();
5029 dbRefFetcher.fetchDBRefs(false);
5035 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5036 MessageManager.formatMessage(
5037 "label.fetch_retrieve_from_all_sources",
5039 { Integer.valueOf(otherdb.size())
5041 src.getDbSource(), src.getDbName() })));
5044 // and then build the rest of the individual menus
5045 ifetch = new JMenu(MessageManager.formatMessage(
5046 "label.source_from_db_source", new Object[]
5047 { src.getDbSource() }));
5049 String imname = null;
5051 for (DbSourceProxy sproxy : otherdb)
5053 String dbname = sproxy.getDbName();
5054 String sname = dbname.length() > 5
5055 ? dbname.substring(0, 5) + "..."
5057 String msname = dbname.length() > 10
5058 ? dbname.substring(0, 10) + "..."
5062 imname = MessageManager
5063 .formatMessage("label.from_msname", new Object[]
5066 fetchr = new JMenuItem(msname);
5067 final DbSourceProxy[] dassrc = { sproxy };
5068 fetchr.addActionListener(new ActionListener()
5072 public void actionPerformed(ActionEvent e)
5074 new Thread(new Runnable()
5080 boolean isNucleotide = alignPanel.alignFrame
5081 .getViewport().getAlignment()
5083 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5084 alignPanel.av.getSequenceSelection(),
5085 alignPanel.alignFrame, dassrc,
5086 alignPanel.alignFrame.featureSettings,
5089 .addListener(new FetchFinishedListenerI()
5092 public void finished()
5094 AlignFrame.this.setMenusForViewport();
5097 dbRefFetcher.fetchDBRefs(false);
5103 fetchr.setToolTipText(
5104 "<html>" + MessageManager.formatMessage(
5105 "label.fetch_retrieve_from", new Object[]
5109 if (++icomp >= mcomp || i == (otherdb.size()))
5111 ifetch.setText(MessageManager.formatMessage(
5112 "label.source_to_target", imname, sname));
5114 ifetch = new JMenu();
5122 if (comp >= mcomp || dbi >= (dbclasses.length))
5124 dfetch.setText(MessageManager.formatMessage(
5125 "label.source_to_target", mname, dbclass));
5127 dfetch = new JMenu();
5140 * Left justify the whole alignment.
5143 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5145 AlignmentI al = viewport.getAlignment();
5147 viewport.firePropertyChange("alignment", null, al);
5151 * Right justify the whole alignment.
5154 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5156 AlignmentI al = viewport.getAlignment();
5158 viewport.firePropertyChange("alignment", null, al);
5162 public void setShowSeqFeatures(boolean b)
5164 showSeqFeatures.setSelected(b);
5165 viewport.setShowSequenceFeatures(b);
5172 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5173 * awt.event.ActionEvent)
5176 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5178 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5179 alignPanel.paintAlignment(false, false);
5186 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5190 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5192 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5193 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5201 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5202 * .event.ActionEvent)
5205 protected void showGroupConservation_actionPerformed(ActionEvent e)
5207 viewport.setShowGroupConservation(showGroupConservation.getState());
5208 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5215 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5216 * .event.ActionEvent)
5219 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5221 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5222 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5229 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5230 * .event.ActionEvent)
5233 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5235 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5236 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5240 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5242 showSequenceLogo.setState(true);
5243 viewport.setShowSequenceLogo(true);
5244 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5245 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5249 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5251 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5258 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5259 * .event.ActionEvent)
5262 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5264 if (avc.makeGroupsFromSelection())
5266 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5267 alignPanel.updateAnnotation();
5268 alignPanel.paintAlignment(true, true);
5272 public void clearAlignmentSeqRep()
5274 // TODO refactor alignmentseqrep to controller
5275 if (viewport.getAlignment().hasSeqrep())
5277 viewport.getAlignment().setSeqrep(null);
5278 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5279 alignPanel.updateAnnotation();
5280 alignPanel.paintAlignment(true, true);
5285 protected void createGroup_actionPerformed(ActionEvent e)
5287 if (avc.createGroup())
5289 alignPanel.alignmentChanged();
5294 protected void unGroup_actionPerformed(ActionEvent e)
5298 alignPanel.alignmentChanged();
5303 * make the given alignmentPanel the currently selected tab
5305 * @param alignmentPanel
5307 public void setDisplayedView(AlignmentPanel alignmentPanel)
5309 if (!viewport.getSequenceSetId()
5310 .equals(alignmentPanel.av.getSequenceSetId()))
5312 throw new Error(MessageManager.getString(
5313 "error.implementation_error_cannot_show_view_alignment_frame"));
5315 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5316 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5318 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5323 * Action on selection of menu options to Show or Hide annotations.
5326 * @param forSequences
5327 * update sequence-related annotations
5328 * @param forAlignment
5329 * update non-sequence-related annotations
5332 protected void setAnnotationsVisibility(boolean visible,
5333 boolean forSequences, boolean forAlignment)
5335 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5336 .getAlignmentAnnotation();
5341 for (AlignmentAnnotation aa : anns)
5344 * don't display non-positional annotations on an alignment
5346 if (aa.annotations == null)
5350 boolean apply = (aa.sequenceRef == null && forAlignment)
5351 || (aa.sequenceRef != null && forSequences);
5354 aa.visible = visible;
5357 alignPanel.validateAnnotationDimensions(true);
5358 alignPanel.alignmentChanged();
5362 * Store selected annotation sort order for the view and repaint.
5365 protected void sortAnnotations_actionPerformed()
5367 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5369 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5370 alignPanel.paintAlignment(false, false);
5375 * @return alignment panels in this alignment frame
5377 public List<? extends AlignmentViewPanel> getAlignPanels()
5379 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5383 * Open a new alignment window, with the cDNA associated with this (protein)
5384 * alignment, aligned as is the protein.
5386 protected void viewAsCdna_actionPerformed()
5388 // TODO no longer a menu action - refactor as required
5389 final AlignmentI alignment = getViewport().getAlignment();
5390 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5391 if (mappings == null)
5395 List<SequenceI> cdnaSeqs = new ArrayList<>();
5396 for (SequenceI aaSeq : alignment.getSequences())
5398 for (AlignedCodonFrame acf : mappings)
5400 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5404 * There is a cDNA mapping for this protein sequence - add to new
5405 * alignment. It will share the same dataset sequence as other mapped
5406 * cDNA (no new mappings need to be created).
5408 final Sequence newSeq = new Sequence(dnaSeq);
5409 newSeq.setDatasetSequence(dnaSeq);
5410 cdnaSeqs.add(newSeq);
5414 if (cdnaSeqs.size() == 0)
5416 // show a warning dialog no mapped cDNA
5419 AlignmentI cdna = new Alignment(
5420 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5421 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5422 AlignFrame.DEFAULT_HEIGHT);
5423 cdna.alignAs(alignment);
5424 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5426 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5427 AlignFrame.DEFAULT_HEIGHT);
5431 * Set visibility of dna/protein complement view (available when shown in a
5437 protected void showComplement_actionPerformed(boolean show)
5439 SplitContainerI sf = getSplitViewContainer();
5442 sf.setComplementVisible(this, show);
5447 * Generate the reverse (optionally complemented) of the selected sequences,
5448 * and add them to the alignment
5451 protected void showReverse_actionPerformed(boolean complement)
5453 AlignmentI al = null;
5456 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5457 al = dna.reverseCdna(complement);
5458 viewport.addAlignment(al, "");
5459 addHistoryItem(new EditCommand(
5460 MessageManager.getString("label.add_sequences"), Action.PASTE,
5461 al.getSequencesArray(), 0, al.getWidth(),
5462 viewport.getAlignment()));
5463 } catch (Exception ex)
5465 System.err.println(ex.getMessage());
5471 * Try to run a script in the Groovy console, having first ensured that this
5472 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5473 * be targeted at this alignment.
5476 protected void runGroovy_actionPerformed()
5478 Jalview.setCurrentAlignFrame(this);
5479 groovy.ui.Console console = Desktop.getGroovyConsole();
5480 if (console != null)
5484 console.runScript();
5485 } catch (Exception ex)
5487 System.err.println((ex.toString()));
5488 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5489 MessageManager.getString("label.couldnt_run_groovy_script"),
5490 MessageManager.getString("label.groovy_support_failed"),
5491 JvOptionPane.ERROR_MESSAGE);
5496 System.err.println("Can't run Groovy script as console not found");
5501 * Hides columns containing (or not containing) a specified feature, provided
5502 * that would not leave all columns hidden
5504 * @param featureType
5505 * @param columnsContaining
5508 public boolean hideFeatureColumns(String featureType,
5509 boolean columnsContaining)
5511 boolean notForHiding = avc.markColumnsContainingFeatures(
5512 columnsContaining, false, false, featureType);
5515 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5516 false, featureType))
5518 getViewport().hideSelectedColumns();
5526 protected void selectHighlightedColumns_actionPerformed(
5527 ActionEvent actionEvent)
5529 // include key modifier check in case user selects from menu
5530 avc.markHighlightedColumns(
5531 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5532 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5533 | ActionEvent.CTRL_MASK)) != 0);
5537 * Rebuilds the Colour menu, including any user-defined colours which have
5538 * been loaded either on startup or during the session
5540 public void buildColourMenu()
5542 colourMenu.removeAll();
5544 colourMenu.add(applyToAllGroups);
5545 colourMenu.add(textColour);
5546 colourMenu.addSeparator();
5548 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5551 colourMenu.addSeparator();
5552 colourMenu.add(conservationMenuItem);
5553 colourMenu.add(modifyConservation);
5554 colourMenu.add(abovePIDThreshold);
5555 colourMenu.add(modifyPID);
5556 colourMenu.add(annotationColour);
5558 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5559 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5563 * Open a dialog (if not already open) that allows the user to select and
5564 * calculate PCA or Tree analysis
5566 protected void openTreePcaDialog()
5568 if (alignPanel.getCalculationDialog() == null)
5570 new CalculationChooser(AlignFrame.this);
5575 class PrintThread extends Thread
5579 public PrintThread(AlignmentPanel ap)
5584 static PageFormat pf;
5589 PrinterJob printJob = PrinterJob.getPrinterJob();
5593 printJob.setPrintable(ap, pf);
5597 printJob.setPrintable(ap);
5600 if (printJob.printDialog())
5605 } catch (Exception PrintException)
5607 PrintException.printStackTrace();