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.analysis.TreeModel;
30 import jalview.api.AlignExportSettingI;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.AlignViewportI;
34 import jalview.api.AlignmentViewPanel;
35 import jalview.api.FeatureSettingsControllerI;
36 import jalview.api.SplitContainerI;
37 import jalview.api.ViewStyleI;
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 ArrayList<int[]> hiddenColumns = null;
1866 if (viewport.hasHiddenColumns())
1868 hiddenColumns = new ArrayList<>();
1869 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1870 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1871 ArrayList<int[]> hiddenRegions = viewport.getAlignment()
1872 .getHiddenColumns().getHiddenColumnsCopy();
1873 for (int[] region : hiddenRegions)
1875 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1879 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1884 Desktop.jalviewClipboard = new Object[] { seqs,
1885 viewport.getAlignment().getDataset(), hiddenColumns };
1886 statusBar.setText(MessageManager.formatMessage(
1887 "label.copied_sequences_to_clipboard", new Object[]
1888 { Integer.valueOf(seqs.length).toString() }));
1898 protected void pasteNew_actionPerformed(ActionEvent e)
1910 protected void pasteThis_actionPerformed(ActionEvent e)
1916 * Paste contents of Jalview clipboard
1918 * @param newAlignment
1919 * true to paste to a new alignment, otherwise add to this.
1921 void paste(boolean newAlignment)
1923 boolean externalPaste = true;
1926 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1927 Transferable contents = c.getContents(this);
1929 if (contents == null)
1938 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1939 if (str.length() < 1)
1944 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1946 } catch (OutOfMemoryError er)
1948 new OOMWarning("Out of memory pasting sequences!!", er);
1952 SequenceI[] sequences;
1953 boolean annotationAdded = false;
1954 AlignmentI alignment = null;
1956 if (Desktop.jalviewClipboard != null)
1958 // The clipboard was filled from within Jalview, we must use the
1960 // And dataset from the copied alignment
1961 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1962 // be doubly sure that we create *new* sequence objects.
1963 sequences = new SequenceI[newseq.length];
1964 for (int i = 0; i < newseq.length; i++)
1966 sequences[i] = new Sequence(newseq[i]);
1968 alignment = new Alignment(sequences);
1969 externalPaste = false;
1973 // parse the clipboard as an alignment.
1974 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1976 sequences = alignment.getSequencesArray();
1980 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1986 if (Desktop.jalviewClipboard != null)
1988 // dataset is inherited
1989 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1993 // new dataset is constructed
1994 alignment.setDataset(null);
1996 alwidth = alignment.getWidth() + 1;
2000 AlignmentI pastedal = alignment; // preserve pasted alignment object
2001 // Add pasted sequences and dataset into existing alignment.
2002 alignment = viewport.getAlignment();
2003 alwidth = alignment.getWidth() + 1;
2004 // decide if we need to import sequences from an existing dataset
2005 boolean importDs = Desktop.jalviewClipboard != null
2006 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2007 // importDs==true instructs us to copy over new dataset sequences from
2008 // an existing alignment
2009 Vector newDs = (importDs) ? new Vector() : null; // used to create
2010 // minimum dataset set
2012 for (int i = 0; i < sequences.length; i++)
2016 newDs.addElement(null);
2018 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2020 if (importDs && ds != null)
2022 if (!newDs.contains(ds))
2024 newDs.setElementAt(ds, i);
2025 ds = new Sequence(ds);
2026 // update with new dataset sequence
2027 sequences[i].setDatasetSequence(ds);
2031 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2036 // copy and derive new dataset sequence
2037 sequences[i] = sequences[i].deriveSequence();
2038 alignment.getDataset()
2039 .addSequence(sequences[i].getDatasetSequence());
2040 // TODO: avoid creation of duplicate dataset sequences with a
2041 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2043 alignment.addSequence(sequences[i]); // merges dataset
2047 newDs.clear(); // tidy up
2049 if (alignment.getAlignmentAnnotation() != null)
2051 for (AlignmentAnnotation alan : alignment
2052 .getAlignmentAnnotation())
2054 if (alan.graphGroup > fgroup)
2056 fgroup = alan.graphGroup;
2060 if (pastedal.getAlignmentAnnotation() != null)
2062 // Add any annotation attached to alignment.
2063 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2064 for (int i = 0; i < alann.length; i++)
2066 annotationAdded = true;
2067 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2069 AlignmentAnnotation newann = new AlignmentAnnotation(
2071 if (newann.graphGroup > -1)
2073 if (newGraphGroups.size() <= newann.graphGroup
2074 || newGraphGroups.get(newann.graphGroup) == null)
2076 for (int q = newGraphGroups
2077 .size(); q <= newann.graphGroup; q++)
2079 newGraphGroups.add(q, null);
2081 newGraphGroups.set(newann.graphGroup,
2082 new Integer(++fgroup));
2084 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2088 newann.padAnnotation(alwidth);
2089 alignment.addAnnotation(newann);
2099 addHistoryItem(new EditCommand(
2100 MessageManager.getString("label.add_sequences"),
2101 Action.PASTE, sequences, 0, alignment.getWidth(),
2104 // Add any annotations attached to sequences
2105 for (int i = 0; i < sequences.length; i++)
2107 if (sequences[i].getAnnotation() != null)
2109 AlignmentAnnotation newann;
2110 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2112 annotationAdded = true;
2113 newann = sequences[i].getAnnotation()[a];
2114 newann.adjustForAlignment();
2115 newann.padAnnotation(alwidth);
2116 if (newann.graphGroup > -1)
2118 if (newann.graphGroup > -1)
2120 if (newGraphGroups.size() <= newann.graphGroup
2121 || newGraphGroups.get(newann.graphGroup) == null)
2123 for (int q = newGraphGroups
2124 .size(); q <= newann.graphGroup; q++)
2126 newGraphGroups.add(q, null);
2128 newGraphGroups.set(newann.graphGroup,
2129 new Integer(++fgroup));
2131 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2135 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2139 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2147 // propagate alignment changed.
2148 viewport.getRanges().setEndSeq(alignment.getHeight());
2149 if (annotationAdded)
2151 // Duplicate sequence annotation in all views.
2152 AlignmentI[] alview = this.getViewAlignments();
2153 for (int i = 0; i < sequences.length; i++)
2155 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2160 for (int avnum = 0; avnum < alview.length; avnum++)
2162 if (alview[avnum] != alignment)
2164 // duplicate in a view other than the one with input focus
2165 int avwidth = alview[avnum].getWidth() + 1;
2166 // this relies on sann being preserved after we
2167 // modify the sequence's annotation array for each duplication
2168 for (int a = 0; a < sann.length; a++)
2170 AlignmentAnnotation newann = new AlignmentAnnotation(
2172 sequences[i].addAlignmentAnnotation(newann);
2173 newann.padAnnotation(avwidth);
2174 alview[avnum].addAnnotation(newann); // annotation was
2175 // duplicated earlier
2176 // TODO JAL-1145 graphGroups are not updated for sequence
2177 // annotation added to several views. This may cause
2179 alview[avnum].setAnnotationIndex(newann, a);
2184 buildSortByAnnotationScoresMenu();
2186 viewport.firePropertyChange("alignment", null,
2187 alignment.getSequences());
2188 if (alignPanels != null)
2190 for (AlignmentPanel ap : alignPanels)
2192 ap.validateAnnotationDimensions(false);
2197 alignPanel.validateAnnotationDimensions(false);
2203 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2205 String newtitle = new String("Copied sequences");
2207 if (Desktop.jalviewClipboard != null
2208 && Desktop.jalviewClipboard[2] != null)
2210 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2211 for (int[] region : hc)
2213 af.viewport.hideColumns(region[0], region[1]);
2217 // >>>This is a fix for the moment, until a better solution is
2219 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2220 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2221 .getFeatureRenderer());
2223 // TODO: maintain provenance of an alignment, rather than just make the
2224 // title a concatenation of operations.
2227 if (title.startsWith("Copied sequences"))
2233 newtitle = newtitle.concat("- from " + title);
2238 newtitle = new String("Pasted sequences");
2241 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2246 } catch (Exception ex)
2248 ex.printStackTrace();
2249 System.out.println("Exception whilst pasting: " + ex);
2250 // could be anything being pasted in here
2256 protected void expand_newalign(ActionEvent e)
2260 AlignmentI alignment = AlignmentUtils
2261 .expandContext(getViewport().getAlignment(), -1);
2262 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2264 String newtitle = new String("Flanking alignment");
2266 if (Desktop.jalviewClipboard != null
2267 && Desktop.jalviewClipboard[2] != null)
2269 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2270 for (int region[] : hc)
2272 af.viewport.hideColumns(region[0], region[1]);
2276 // >>>This is a fix for the moment, until a better solution is
2278 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2279 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2280 .getFeatureRenderer());
2282 // TODO: maintain provenance of an alignment, rather than just make the
2283 // title a concatenation of operations.
2285 if (title.startsWith("Copied sequences"))
2291 newtitle = newtitle.concat("- from " + title);
2295 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2297 } catch (Exception ex)
2299 ex.printStackTrace();
2300 System.out.println("Exception whilst pasting: " + ex);
2301 // could be anything being pasted in here
2302 } catch (OutOfMemoryError oom)
2304 new OOMWarning("Viewing flanking region of alignment", oom);
2315 protected void cut_actionPerformed(ActionEvent e)
2317 copy_actionPerformed(null);
2318 delete_actionPerformed(null);
2328 protected void delete_actionPerformed(ActionEvent evt)
2331 SequenceGroup sg = viewport.getSelectionGroup();
2338 * If the cut affects all sequences, warn, remove highlighted columns
2340 if (sg.getSize() == viewport.getAlignment().getHeight())
2342 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2343 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2344 if (isEntireAlignWidth)
2346 int confirm = JvOptionPane.showConfirmDialog(this,
2347 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2348 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2349 JvOptionPane.OK_CANCEL_OPTION);
2351 if (confirm == JvOptionPane.CANCEL_OPTION
2352 || confirm == JvOptionPane.CLOSED_OPTION)
2357 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2358 sg.getEndRes() + 1);
2360 SequenceI[] cut = sg.getSequences()
2361 .toArray(new SequenceI[sg.getSize()]);
2363 addHistoryItem(new EditCommand(
2364 MessageManager.getString("label.cut_sequences"), Action.CUT,
2365 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2366 viewport.getAlignment()));
2368 viewport.setSelectionGroup(null);
2369 viewport.sendSelection();
2370 viewport.getAlignment().deleteGroup(sg);
2372 viewport.firePropertyChange("alignment", null,
2373 viewport.getAlignment().getSequences());
2374 if (viewport.getAlignment().getHeight() < 1)
2378 this.setClosed(true);
2379 } catch (Exception ex)
2392 protected void deleteGroups_actionPerformed(ActionEvent e)
2394 if (avc.deleteGroups())
2396 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2397 alignPanel.updateAnnotation();
2398 alignPanel.paintAlignment(true, true);
2409 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2411 SequenceGroup sg = new SequenceGroup();
2413 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2415 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2418 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2419 viewport.setSelectionGroup(sg);
2420 viewport.sendSelection();
2421 // JAL-2034 - should delegate to
2422 // alignPanel to decide if overview needs
2424 alignPanel.paintAlignment(false, false);
2425 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2435 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2437 if (viewport.cursorMode)
2439 alignPanel.getSeqPanel().keyboardNo1 = null;
2440 alignPanel.getSeqPanel().keyboardNo2 = null;
2442 viewport.setSelectionGroup(null);
2443 viewport.getColumnSelection().clear();
2444 viewport.setSelectionGroup(null);
2445 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2446 // JAL-2034 - should delegate to
2447 // alignPanel to decide if overview needs
2449 alignPanel.paintAlignment(false, false);
2450 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2451 viewport.sendSelection();
2461 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2463 SequenceGroup sg = viewport.getSelectionGroup();
2467 selectAllSequenceMenuItem_actionPerformed(null);
2472 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2474 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2476 // JAL-2034 - should delegate to
2477 // alignPanel to decide if overview needs
2480 alignPanel.paintAlignment(true, false);
2481 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2482 viewport.sendSelection();
2486 public void invertColSel_actionPerformed(ActionEvent e)
2488 viewport.invertColumnSelection();
2489 alignPanel.paintAlignment(true, false);
2490 viewport.sendSelection();
2500 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2502 trimAlignment(true);
2512 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2514 trimAlignment(false);
2517 void trimAlignment(boolean trimLeft)
2519 ColumnSelection colSel = viewport.getColumnSelection();
2522 if (!colSel.isEmpty())
2526 column = colSel.getMin();
2530 column = colSel.getMax();
2534 if (viewport.getSelectionGroup() != null)
2536 seqs = viewport.getSelectionGroup()
2537 .getSequencesAsArray(viewport.getHiddenRepSequences());
2541 seqs = viewport.getAlignment().getSequencesArray();
2544 TrimRegionCommand trimRegion;
2547 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2548 column, viewport.getAlignment());
2549 viewport.getRanges().setStartRes(0);
2553 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2554 column, viewport.getAlignment());
2557 statusBar.setText(MessageManager
2558 .formatMessage("label.removed_columns", new String[]
2559 { Integer.valueOf(trimRegion.getSize()).toString() }));
2561 addHistoryItem(trimRegion);
2563 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2565 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2566 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2568 viewport.getAlignment().deleteGroup(sg);
2572 viewport.firePropertyChange("alignment", null,
2573 viewport.getAlignment().getSequences());
2584 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2586 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2589 if (viewport.getSelectionGroup() != null)
2591 seqs = viewport.getSelectionGroup()
2592 .getSequencesAsArray(viewport.getHiddenRepSequences());
2593 start = viewport.getSelectionGroup().getStartRes();
2594 end = viewport.getSelectionGroup().getEndRes();
2598 seqs = viewport.getAlignment().getSequencesArray();
2601 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2602 "Remove Gapped Columns", seqs, start, end,
2603 viewport.getAlignment());
2605 addHistoryItem(removeGapCols);
2607 statusBar.setText(MessageManager
2608 .formatMessage("label.removed_empty_columns", new Object[]
2609 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2611 // This is to maintain viewport position on first residue
2612 // of first sequence
2613 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2614 ViewportRanges ranges = viewport.getRanges();
2615 int startRes = seq.findPosition(ranges.getStartRes());
2616 // ShiftList shifts;
2617 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2618 // edit.alColumnChanges=shifts.getInverse();
2619 // if (viewport.hasHiddenColumns)
2620 // viewport.getColumnSelection().compensateForEdits(shifts);
2621 ranges.setStartRes(seq.findIndex(startRes) - 1);
2622 viewport.firePropertyChange("alignment", null,
2623 viewport.getAlignment().getSequences());
2634 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2636 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2639 if (viewport.getSelectionGroup() != null)
2641 seqs = viewport.getSelectionGroup()
2642 .getSequencesAsArray(viewport.getHiddenRepSequences());
2643 start = viewport.getSelectionGroup().getStartRes();
2644 end = viewport.getSelectionGroup().getEndRes();
2648 seqs = viewport.getAlignment().getSequencesArray();
2651 // This is to maintain viewport position on first residue
2652 // of first sequence
2653 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2654 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2656 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2657 viewport.getAlignment()));
2659 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2661 viewport.firePropertyChange("alignment", null,
2662 viewport.getAlignment().getSequences());
2673 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2675 viewport.setPadGaps(padGapsMenuitem.isSelected());
2676 viewport.firePropertyChange("alignment", null,
2677 viewport.getAlignment().getSequences());
2687 public void findMenuItem_actionPerformed(ActionEvent e)
2693 * Create a new view of the current alignment.
2696 public void newView_actionPerformed(ActionEvent e)
2698 newView(null, true);
2702 * Creates and shows a new view of the current alignment.
2705 * title of newly created view; if null, one will be generated
2706 * @param copyAnnotation
2707 * if true then duplicate all annnotation, groups and settings
2708 * @return new alignment panel, already displayed.
2710 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2713 * Create a new AlignmentPanel (with its own, new Viewport)
2715 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2717 if (!copyAnnotation)
2720 * remove all groups and annotation except for the automatic stuff
2722 newap.av.getAlignment().deleteAllGroups();
2723 newap.av.getAlignment().deleteAllAnnotations(false);
2726 newap.av.setGatherViewsHere(false);
2728 if (viewport.viewName == null)
2730 viewport.viewName = MessageManager
2731 .getString("label.view_name_original");
2735 * Views share the same edits undo and redo stacks
2737 newap.av.setHistoryList(viewport.getHistoryList());
2738 newap.av.setRedoList(viewport.getRedoList());
2741 * Views share the same mappings; need to deregister any new mappings
2742 * created by copyAlignPanel, and register the new reference to the shared
2745 newap.av.replaceMappings(viewport.getAlignment());
2748 * start up cDNA consensus (if applicable) now mappings are in place
2750 if (newap.av.initComplementConsensus())
2752 newap.refresh(true); // adjust layout of annotations
2755 newap.av.viewName = getNewViewName(viewTitle);
2757 addAlignmentPanel(newap, true);
2758 newap.alignmentChanged();
2760 if (alignPanels.size() == 2)
2762 viewport.setGatherViewsHere(true);
2764 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2769 * Make a new name for the view, ensuring it is unique within the current
2770 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2771 * these now use viewId. Unique view names are still desirable for usability.)
2776 protected String getNewViewName(String viewTitle)
2778 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2779 boolean addFirstIndex = false;
2780 if (viewTitle == null || viewTitle.trim().length() == 0)
2782 viewTitle = MessageManager.getString("action.view");
2783 addFirstIndex = true;
2787 index = 1;// we count from 1 if given a specific name
2789 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2791 List<Component> comps = PaintRefresher.components
2792 .get(viewport.getSequenceSetId());
2794 List<String> existingNames = getExistingViewNames(comps);
2796 while (existingNames.contains(newViewName))
2798 newViewName = viewTitle + " " + (++index);
2804 * Returns a list of distinct view names found in the given list of
2805 * components. View names are held on the viewport of an AlignmentPanel.
2810 protected List<String> getExistingViewNames(List<Component> comps)
2812 List<String> existingNames = new ArrayList<>();
2813 for (Component comp : comps)
2815 if (comp instanceof AlignmentPanel)
2817 AlignmentPanel ap = (AlignmentPanel) comp;
2818 if (!existingNames.contains(ap.av.viewName))
2820 existingNames.add(ap.av.viewName);
2824 return existingNames;
2828 * Explode tabbed views into separate windows.
2831 public void expandViews_actionPerformed(ActionEvent e)
2833 Desktop.explodeViews(this);
2837 * Gather views in separate windows back into a tabbed presentation.
2840 public void gatherViews_actionPerformed(ActionEvent e)
2842 Desktop.instance.gatherViews(this);
2852 public void font_actionPerformed(ActionEvent e)
2854 new FontChooser(alignPanel);
2864 protected void seqLimit_actionPerformed(ActionEvent e)
2866 viewport.setShowJVSuffix(seqLimits.isSelected());
2868 alignPanel.getIdPanel().getIdCanvas()
2869 .setPreferredSize(alignPanel.calculateIdWidth());
2870 alignPanel.paintAlignment(true, false);
2874 public void idRightAlign_actionPerformed(ActionEvent e)
2876 viewport.setRightAlignIds(idRightAlign.isSelected());
2877 alignPanel.paintAlignment(false, false);
2881 public void centreColumnLabels_actionPerformed(ActionEvent e)
2883 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2884 alignPanel.paintAlignment(false, false);
2890 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2893 protected void followHighlight_actionPerformed()
2896 * Set the 'follow' flag on the Viewport (and scroll to position if now
2899 final boolean state = this.followHighlightMenuItem.getState();
2900 viewport.setFollowHighlight(state);
2903 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2914 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2916 viewport.setColourText(colourTextMenuItem.isSelected());
2917 alignPanel.paintAlignment(false, false);
2927 public void wrapMenuItem_actionPerformed(ActionEvent e)
2929 scaleAbove.setVisible(wrapMenuItem.isSelected());
2930 scaleLeft.setVisible(wrapMenuItem.isSelected());
2931 scaleRight.setVisible(wrapMenuItem.isSelected());
2932 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2933 alignPanel.updateLayout();
2937 public void showAllSeqs_actionPerformed(ActionEvent e)
2939 viewport.showAllHiddenSeqs();
2943 public void showAllColumns_actionPerformed(ActionEvent e)
2945 viewport.showAllHiddenColumns();
2946 alignPanel.paintAlignment(true, true);
2947 viewport.sendSelection();
2951 public void hideSelSequences_actionPerformed(ActionEvent e)
2953 viewport.hideAllSelectedSeqs();
2957 * called by key handler and the hide all/show all menu items
2962 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2965 boolean hide = false;
2966 SequenceGroup sg = viewport.getSelectionGroup();
2967 if (!toggleSeqs && !toggleCols)
2969 // Hide everything by the current selection - this is a hack - we do the
2970 // invert and then hide
2971 // first check that there will be visible columns after the invert.
2972 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2973 && sg.getStartRes() <= sg.getEndRes()))
2975 // now invert the sequence set, if required - empty selection implies
2976 // that no hiding is required.
2979 invertSequenceMenuItem_actionPerformed(null);
2980 sg = viewport.getSelectionGroup();
2984 viewport.expandColSelection(sg, true);
2985 // finally invert the column selection and get the new sequence
2987 invertColSel_actionPerformed(null);
2994 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2996 hideSelSequences_actionPerformed(null);
2999 else if (!(toggleCols && viewport.hasSelectedColumns()))
3001 showAllSeqs_actionPerformed(null);
3007 if (viewport.hasSelectedColumns())
3009 hideSelColumns_actionPerformed(null);
3012 viewport.setSelectionGroup(sg);
3017 showAllColumns_actionPerformed(null);
3026 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3027 * event.ActionEvent)
3030 public void hideAllButSelection_actionPerformed(ActionEvent e)
3032 toggleHiddenRegions(false, false);
3033 viewport.sendSelection();
3040 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3044 public void hideAllSelection_actionPerformed(ActionEvent e)
3046 SequenceGroup sg = viewport.getSelectionGroup();
3047 viewport.expandColSelection(sg, false);
3048 viewport.hideAllSelectedSeqs();
3049 viewport.hideSelectedColumns();
3050 alignPanel.paintAlignment(true, true);
3051 viewport.sendSelection();
3058 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3062 public void showAllhidden_actionPerformed(ActionEvent e)
3064 viewport.showAllHiddenColumns();
3065 viewport.showAllHiddenSeqs();
3066 alignPanel.paintAlignment(true, true);
3067 viewport.sendSelection();
3071 public void hideSelColumns_actionPerformed(ActionEvent e)
3073 viewport.hideSelectedColumns();
3074 alignPanel.paintAlignment(true, true);
3075 viewport.sendSelection();
3079 public void hiddenMarkers_actionPerformed(ActionEvent e)
3081 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3092 protected void scaleAbove_actionPerformed(ActionEvent e)
3094 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3095 // TODO: do we actually need to update overview for scale above change ?
3096 alignPanel.paintAlignment(true, false);
3106 protected void scaleLeft_actionPerformed(ActionEvent e)
3108 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3109 alignPanel.paintAlignment(true, false);
3119 protected void scaleRight_actionPerformed(ActionEvent e)
3121 viewport.setScaleRightWrapped(scaleRight.isSelected());
3122 alignPanel.paintAlignment(true, false);
3132 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3134 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3135 alignPanel.paintAlignment(false, false);
3145 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3147 viewport.setShowText(viewTextMenuItem.isSelected());
3148 alignPanel.paintAlignment(false, false);
3158 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3160 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3161 alignPanel.paintAlignment(false, false);
3164 public FeatureSettings featureSettings;
3167 public FeatureSettingsControllerI getFeatureSettingsUI()
3169 return featureSettings;
3173 public void featureSettings_actionPerformed(ActionEvent e)
3175 if (featureSettings != null)
3177 featureSettings.close();
3178 featureSettings = null;
3180 if (!showSeqFeatures.isSelected())
3182 // make sure features are actually displayed
3183 showSeqFeatures.setSelected(true);
3184 showSeqFeatures_actionPerformed(null);
3186 featureSettings = new FeatureSettings(this);
3190 * Set or clear 'Show Sequence Features'
3196 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3198 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3199 alignPanel.paintAlignment(true, true);
3203 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3204 * the annotations panel as a whole.
3206 * The options to show/hide all annotations should be enabled when the panel
3207 * is shown, and disabled when the panel is hidden.
3212 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3214 final boolean setVisible = annotationPanelMenuItem.isSelected();
3215 viewport.setShowAnnotation(setVisible);
3216 this.showAllSeqAnnotations.setEnabled(setVisible);
3217 this.hideAllSeqAnnotations.setEnabled(setVisible);
3218 this.showAllAlAnnotations.setEnabled(setVisible);
3219 this.hideAllAlAnnotations.setEnabled(setVisible);
3220 alignPanel.updateLayout();
3224 public void alignmentProperties()
3226 JEditorPane editPane = new JEditorPane("text/html", "");
3227 editPane.setEditable(false);
3228 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3231 MessageManager.formatMessage("label.html_content", new Object[]
3232 { contents.toString() }));
3233 JInternalFrame frame = new JInternalFrame();
3234 frame.getContentPane().add(new JScrollPane(editPane));
3236 Desktop.addInternalFrame(frame, MessageManager
3237 .formatMessage("label.alignment_properties", new Object[]
3238 { getTitle() }), 500, 400);
3248 public void overviewMenuItem_actionPerformed(ActionEvent e)
3250 if (alignPanel.overviewPanel != null)
3255 JInternalFrame frame = new JInternalFrame();
3256 final OverviewPanel overview = new OverviewPanel(alignPanel);
3257 frame.setContentPane(overview);
3258 Desktop.addInternalFrame(frame, MessageManager
3259 .formatMessage("label.overview_params", new Object[]
3260 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3263 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3264 frame.addInternalFrameListener(
3265 new javax.swing.event.InternalFrameAdapter()
3268 public void internalFrameClosed(
3269 javax.swing.event.InternalFrameEvent evt)
3272 alignPanel.setOverviewPanel(null);
3276 alignPanel.setOverviewPanel(overview);
3280 public void textColour_actionPerformed()
3282 new TextColourChooser().chooseColour(alignPanel, null);
3286 * public void covariationColour_actionPerformed() {
3288 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3292 public void annotationColour_actionPerformed()
3294 new AnnotationColourChooser(viewport, alignPanel);
3298 public void annotationColumn_actionPerformed(ActionEvent e)
3300 new AnnotationColumnChooser(viewport, alignPanel);
3304 * Action on the user checking or unchecking the option to apply the selected
3305 * colour scheme to all groups. If unchecked, groups may have their own
3306 * independent colour schemes.
3311 public void applyToAllGroups_actionPerformed(boolean selected)
3313 viewport.setColourAppliesToAllGroups(selected);
3317 * Action on user selecting a colour from the colour menu
3320 * the name (not the menu item label!) of the colour scheme
3323 public void changeColour_actionPerformed(String name)
3326 * 'User Defined' opens a panel to configure or load a
3327 * user-defined colour scheme
3329 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3331 new UserDefinedColours(alignPanel);
3336 * otherwise set the chosen colour scheme (or null for 'None')
3338 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3339 viewport.getAlignment(), viewport.getHiddenRepSequences());
3344 * Actions on setting or changing the alignment colour scheme
3349 public void changeColour(ColourSchemeI cs)
3351 // TODO: pull up to controller method
3352 ColourMenuHelper.setColourSelected(colourMenu, cs);
3354 viewport.setGlobalColourScheme(cs);
3356 alignPanel.paintAlignment(true, true);
3360 * Show the PID threshold slider panel
3363 protected void modifyPID_actionPerformed()
3365 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3366 alignPanel.getViewName());
3367 SliderPanel.showPIDSlider();
3371 * Show the Conservation slider panel
3374 protected void modifyConservation_actionPerformed()
3376 SliderPanel.setConservationSlider(alignPanel,
3377 viewport.getResidueShading(), alignPanel.getViewName());
3378 SliderPanel.showConservationSlider();
3382 * Action on selecting or deselecting (Colour) By Conservation
3385 public void conservationMenuItem_actionPerformed(boolean selected)
3387 modifyConservation.setEnabled(selected);
3388 viewport.setConservationSelected(selected);
3389 viewport.getResidueShading().setConservationApplied(selected);
3391 changeColour(viewport.getGlobalColourScheme());
3394 modifyConservation_actionPerformed();
3398 SliderPanel.hideConservationSlider();
3403 * Action on selecting or deselecting (Colour) Above PID Threshold
3406 public void abovePIDThreshold_actionPerformed(boolean selected)
3408 modifyPID.setEnabled(selected);
3409 viewport.setAbovePIDThreshold(selected);
3412 viewport.getResidueShading().setThreshold(0,
3413 viewport.isIgnoreGapsConsensus());
3416 changeColour(viewport.getGlobalColourScheme());
3419 modifyPID_actionPerformed();
3423 SliderPanel.hidePIDSlider();
3434 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3436 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3437 AlignmentSorter.sortByPID(viewport.getAlignment(),
3438 viewport.getAlignment().getSequenceAt(0));
3439 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3440 viewport.getAlignment()));
3441 alignPanel.paintAlignment(true, false);
3451 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3453 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3454 AlignmentSorter.sortByID(viewport.getAlignment());
3456 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3457 alignPanel.paintAlignment(true, false);
3467 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3469 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3470 AlignmentSorter.sortByLength(viewport.getAlignment());
3471 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3472 viewport.getAlignment()));
3473 alignPanel.paintAlignment(true, false);
3483 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3485 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3486 AlignmentSorter.sortByGroup(viewport.getAlignment());
3487 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3488 viewport.getAlignment()));
3490 alignPanel.paintAlignment(true, false);
3500 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3502 new RedundancyPanel(alignPanel, this);
3512 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3514 if ((viewport.getSelectionGroup() == null)
3515 || (viewport.getSelectionGroup().getSize() < 2))
3517 JvOptionPane.showInternalMessageDialog(this,
3518 MessageManager.getString(
3519 "label.you_must_select_least_two_sequences"),
3520 MessageManager.getString("label.invalid_selection"),
3521 JvOptionPane.WARNING_MESSAGE);
3525 JInternalFrame frame = new JInternalFrame();
3526 frame.setContentPane(new PairwiseAlignPanel(viewport));
3527 Desktop.addInternalFrame(frame,
3528 MessageManager.getString("action.pairwise_alignment"), 600,
3534 public void autoCalculate_actionPerformed(ActionEvent e)
3536 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3537 if (viewport.autoCalculateConsensus)
3539 viewport.firePropertyChange("alignment", null,
3540 viewport.getAlignment().getSequences());
3545 public void sortByTreeOption_actionPerformed(ActionEvent e)
3547 viewport.sortByTree = sortByTree.isSelected();
3551 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3553 viewport.followSelection = listenToViewSelections.isSelected();
3557 * Constructs a tree panel and adds it to the desktop
3566 void newTreePanel(TreeModel tree, String treeAlgo,
3567 String substitutionMatrix)
3569 String frameTitle = "";
3572 boolean onSelection = false;
3573 if (viewport.getSelectionGroup() != null
3574 && viewport.getSelectionGroup().getSize() > 0)
3576 SequenceGroup sg = viewport.getSelectionGroup();
3578 /* Decide if the selection is a column region */
3579 for (SequenceI _s : sg.getSequences())
3581 if (_s.getLength() < sg.getEndRes())
3583 JvOptionPane.showMessageDialog(Desktop.desktop,
3584 MessageManager.getString(
3585 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3586 MessageManager.getString(
3587 "label.sequences_selection_not_aligned"),
3588 JvOptionPane.WARNING_MESSAGE);
3597 if (viewport.getAlignment().getHeight() < 2)
3603 tp = new TreePanel(alignPanel, tree, treeAlgo, substitutionMatrix);
3604 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3606 frameTitle += " from ";
3608 if (viewport.viewName != null)
3610 frameTitle += viewport.viewName + " of ";
3613 frameTitle += this.title;
3615 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3626 public void addSortByOrderMenuItem(String title,
3627 final AlignmentOrder order)
3629 final JMenuItem item = new JMenuItem(MessageManager
3630 .formatMessage("action.by_title_param", new Object[]
3633 item.addActionListener(new java.awt.event.ActionListener()
3636 public void actionPerformed(ActionEvent e)
3638 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3640 // TODO: JBPNote - have to map order entries to curent SequenceI
3642 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3644 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3645 viewport.getAlignment()));
3647 alignPanel.paintAlignment(true, false);
3653 * Add a new sort by annotation score menu item
3656 * the menu to add the option to
3658 * the label used to retrieve scores for each sequence on the
3661 public void addSortByAnnotScoreMenuItem(JMenu sort,
3662 final String scoreLabel)
3664 final JMenuItem item = new JMenuItem(scoreLabel);
3666 item.addActionListener(new java.awt.event.ActionListener()
3669 public void actionPerformed(ActionEvent e)
3671 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3672 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3673 viewport.getAlignment());// ,viewport.getSelectionGroup());
3674 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3675 viewport.getAlignment()));
3676 alignPanel.paintAlignment(true, false);
3682 * last hash for alignment's annotation array - used to minimise cost of
3685 protected int _annotationScoreVectorHash;
3688 * search the alignment and rebuild the sort by annotation score submenu the
3689 * last alignment annotation vector hash is stored to minimize cost of
3690 * rebuilding in subsequence calls.
3694 public void buildSortByAnnotationScoresMenu()
3696 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3701 if (viewport.getAlignment().getAlignmentAnnotation()
3702 .hashCode() != _annotationScoreVectorHash)
3704 sortByAnnotScore.removeAll();
3705 // almost certainly a quicker way to do this - but we keep it simple
3706 Hashtable scoreSorts = new Hashtable();
3707 AlignmentAnnotation aann[];
3708 for (SequenceI sqa : viewport.getAlignment().getSequences())
3710 aann = sqa.getAnnotation();
3711 for (int i = 0; aann != null && i < aann.length; i++)
3713 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3715 scoreSorts.put(aann[i].label, aann[i].label);
3719 Enumeration labels = scoreSorts.keys();
3720 while (labels.hasMoreElements())
3722 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3723 (String) labels.nextElement());
3725 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3728 _annotationScoreVectorHash = viewport.getAlignment()
3729 .getAlignmentAnnotation().hashCode();
3734 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3735 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3736 * call. Listeners are added to remove the menu item when the treePanel is
3737 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3741 public void buildTreeSortMenu()
3743 sortByTreeMenu.removeAll();
3745 List<Component> comps = PaintRefresher.components
3746 .get(viewport.getSequenceSetId());
3747 List<TreePanel> treePanels = new ArrayList<>();
3748 for (Component comp : comps)
3750 if (comp instanceof TreePanel)
3752 treePanels.add((TreePanel) comp);
3756 if (treePanels.size() < 1)
3758 sortByTreeMenu.setVisible(false);
3762 sortByTreeMenu.setVisible(true);
3764 for (final TreePanel tp : treePanels)
3766 final JMenuItem item = new JMenuItem(tp.getTitle());
3767 item.addActionListener(new java.awt.event.ActionListener()
3770 public void actionPerformed(ActionEvent e)
3772 tp.sortByTree_actionPerformed();
3773 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3778 sortByTreeMenu.add(item);
3782 public boolean sortBy(AlignmentOrder alorder, String undoname)
3784 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3785 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3786 if (undoname != null)
3788 addHistoryItem(new OrderCommand(undoname, oldOrder,
3789 viewport.getAlignment()));
3791 alignPanel.paintAlignment(true, false);
3796 * Work out whether the whole set of sequences or just the selected set will
3797 * be submitted for multiple alignment.
3800 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3802 // Now, check we have enough sequences
3803 AlignmentView msa = null;
3805 if ((viewport.getSelectionGroup() != null)
3806 && (viewport.getSelectionGroup().getSize() > 1))
3808 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3809 // some common interface!
3811 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3812 * SequenceI[sz = seqs.getSize(false)];
3814 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3815 * seqs.getSequenceAt(i); }
3817 msa = viewport.getAlignmentView(true);
3819 else if (viewport.getSelectionGroup() != null
3820 && viewport.getSelectionGroup().getSize() == 1)
3822 int option = JvOptionPane.showConfirmDialog(this,
3823 MessageManager.getString("warn.oneseq_msainput_selection"),
3824 MessageManager.getString("label.invalid_selection"),
3825 JvOptionPane.OK_CANCEL_OPTION);
3826 if (option == JvOptionPane.OK_OPTION)
3828 msa = viewport.getAlignmentView(false);
3833 msa = viewport.getAlignmentView(false);
3839 * Decides what is submitted to a secondary structure prediction service: the
3840 * first sequence in the alignment, or in the current selection, or, if the
3841 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3842 * region or the whole alignment. (where the first sequence in the set is the
3843 * one that the prediction will be for).
3845 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3847 AlignmentView seqs = null;
3849 if ((viewport.getSelectionGroup() != null)
3850 && (viewport.getSelectionGroup().getSize() > 0))
3852 seqs = viewport.getAlignmentView(true);
3856 seqs = viewport.getAlignmentView(false);
3858 // limit sequences - JBPNote in future - could spawn multiple prediction
3860 // TODO: viewport.getAlignment().isAligned is a global state - the local
3861 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3862 if (!viewport.getAlignment().isAligned(false))
3864 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3865 // TODO: if seqs.getSequences().length>1 then should really have warned
3879 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3881 // Pick the tree file
3882 JalviewFileChooser chooser = new JalviewFileChooser(
3883 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3884 chooser.setFileView(new JalviewFileView());
3885 chooser.setDialogTitle(
3886 MessageManager.getString("label.select_newick_like_tree_file"));
3887 chooser.setToolTipText(
3888 MessageManager.getString("label.load_tree_file"));
3890 int value = chooser.showOpenDialog(null);
3892 if (value == JalviewFileChooser.APPROVE_OPTION)
3894 String filePath = chooser.getSelectedFile().getPath();
3895 Cache.setProperty("LAST_DIRECTORY", filePath);
3896 NewickFile fin = null;
3899 fin = new NewickFile(filePath, DataSourceType.FILE);
3900 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3901 } catch (Exception ex)
3903 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3904 MessageManager.getString("label.problem_reading_tree_file"),
3905 JvOptionPane.WARNING_MESSAGE);
3906 ex.printStackTrace();
3908 if (fin != null && fin.hasWarningMessage())
3910 JvOptionPane.showMessageDialog(Desktop.desktop,
3911 fin.getWarningMessage(),
3913 .getString("label.possible_problem_with_tree_file"),
3914 JvOptionPane.WARNING_MESSAGE);
3919 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3921 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3924 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3925 int h, int x, int y)
3927 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3931 * Add a treeviewer for the tree extracted from a Newick file object to the
3932 * current alignment view
3939 * Associated alignment input data (or null)
3948 * @return TreePanel handle
3950 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3951 AlignmentView input, int w, int h, int x, int y)
3953 TreePanel tp = null;
3959 if (nf.getTree() != null)
3961 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3967 tp.setLocation(x, y);
3970 Desktop.addInternalFrame(tp, treeTitle, w, h);
3972 } catch (Exception ex)
3974 ex.printStackTrace();
3980 private boolean buildingMenu = false;
3983 * Generates menu items and listener event actions for web service clients
3986 public void BuildWebServiceMenu()
3988 while (buildingMenu)
3992 System.err.println("Waiting for building menu to finish.");
3994 } catch (Exception e)
3998 final AlignFrame me = this;
3999 buildingMenu = true;
4000 new Thread(new Runnable()
4005 final List<JMenuItem> legacyItems = new ArrayList<>();
4008 // System.err.println("Building ws menu again "
4009 // + Thread.currentThread());
4010 // TODO: add support for context dependent disabling of services based
4012 // alignment and current selection
4013 // TODO: add additional serviceHandle parameter to specify abstract
4015 // class independently of AbstractName
4016 // TODO: add in rediscovery GUI function to restart discoverer
4017 // TODO: group services by location as well as function and/or
4019 // object broker mechanism.
4020 final Vector<JMenu> wsmenu = new Vector<>();
4021 final IProgressIndicator af = me;
4024 * do not i18n these strings - they are hard-coded in class
4025 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4026 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4028 final JMenu msawsmenu = new JMenu("Alignment");
4029 final JMenu secstrmenu = new JMenu(
4030 "Secondary Structure Prediction");
4031 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4032 final JMenu analymenu = new JMenu("Analysis");
4033 final JMenu dismenu = new JMenu("Protein Disorder");
4034 final JMenu phylogenmenu = new JMenu("Phylogenetic inference");
4036 // JAL-940 - only show secondary structure prediction services from
4037 // the legacy server
4038 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4040 Discoverer.services != null && (Discoverer.services.size() > 0))
4042 // TODO: refactor to allow list of AbstractName/Handler bindings to
4044 // stored or retrieved from elsewhere
4045 // No MSAWS used any more:
4046 // Vector msaws = null; // (Vector)
4047 // Discoverer.services.get("MsaWS");
4048 Vector secstrpr = (Vector) Discoverer.services
4050 if (secstrpr != null)
4052 // Add any secondary structure prediction services
4053 for (int i = 0, j = secstrpr.size(); i < j; i++)
4055 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4057 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4058 .getServiceClient(sh);
4059 int p = secstrmenu.getItemCount();
4060 impl.attachWSMenuEntry(secstrmenu, me);
4061 int q = secstrmenu.getItemCount();
4062 for (int litm = p; litm < q; litm++)
4064 legacyItems.add(secstrmenu.getItem(litm));
4070 // Add all submenus in the order they should appear on the web
4072 wsmenu.add(msawsmenu);
4073 wsmenu.add(secstrmenu);
4074 wsmenu.add(dismenu);
4075 wsmenu.add(analymenu);
4076 wsmenu.add(phylogenmenu);
4077 // No search services yet
4078 // wsmenu.add(seqsrchmenu);
4080 javax.swing.SwingUtilities.invokeLater(new Runnable()
4087 webService.removeAll();
4088 // first, add discovered services onto the webservices menu
4089 if (wsmenu.size() > 0)
4091 for (int i = 0, j = wsmenu.size(); i < j; i++)
4093 webService.add(wsmenu.get(i));
4098 webService.add(me.webServiceNoServices);
4100 // TODO: move into separate menu builder class.
4101 boolean new_sspred = false;
4102 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4104 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4105 if (jws2servs != null)
4107 if (jws2servs.hasServices())
4109 jws2servs.attachWSMenuEntry(webService, me);
4110 for (Jws2Instance sv : jws2servs.getServices())
4112 if (sv.description.toLowerCase().contains("jpred"))
4114 for (JMenuItem jmi : legacyItems)
4116 jmi.setVisible(false);
4122 if (jws2servs.isRunning())
4124 JMenuItem tm = new JMenuItem(
4125 "Still discovering JABA Services");
4126 tm.setEnabled(false);
4131 build_urlServiceMenu(me.webService);
4132 build_fetchdbmenu(webService);
4133 for (JMenu item : wsmenu)
4135 if (item.getItemCount() == 0)
4137 item.setEnabled(false);
4141 item.setEnabled(true);
4144 } catch (Exception e)
4147 "Exception during web service menu building process.",
4152 } catch (Exception e)
4155 buildingMenu = false;
4157 }, "BuildWebServiceThread").start();
4162 * construct any groupURL type service menu entries.
4166 private void build_urlServiceMenu(JMenu webService)
4168 // TODO: remove this code when 2.7 is released
4169 // DEBUG - alignmentView
4171 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4172 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4174 * @Override public void actionPerformed(ActionEvent e) {
4175 * jalview.datamodel.AlignmentView
4176 * .testSelectionViews(af.viewport.getAlignment(),
4177 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4179 * }); webService.add(testAlView);
4181 // TODO: refactor to RestClient discoverer and merge menu entries for
4182 // rest-style services with other types of analysis/calculation service
4183 // SHmmr test client - still being implemented.
4184 // DEBUG - alignmentView
4186 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4189 client.attachWSMenuEntry(
4190 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4196 * Searches the alignment sequences for xRefs and builds the Show
4197 * Cross-References menu (formerly called Show Products), with database
4198 * sources for which cross-references are found (protein sources for a
4199 * nucleotide alignment and vice versa)
4201 * @return true if Show Cross-references menu should be enabled
4203 public boolean canShowProducts()
4205 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4206 AlignmentI dataset = viewport.getAlignment().getDataset();
4208 showProducts.removeAll();
4209 final boolean dna = viewport.getAlignment().isNucleotide();
4211 if (seqs == null || seqs.length == 0)
4213 // nothing to see here.
4217 boolean showp = false;
4220 List<String> ptypes = new CrossRef(seqs, dataset)
4221 .findXrefSourcesForSequences(dna);
4223 for (final String source : ptypes)
4226 final AlignFrame af = this;
4227 JMenuItem xtype = new JMenuItem(source);
4228 xtype.addActionListener(new ActionListener()
4231 public void actionPerformed(ActionEvent e)
4233 showProductsFor(af.viewport.getSequenceSelection(), dna,
4237 showProducts.add(xtype);
4239 showProducts.setVisible(showp);
4240 showProducts.setEnabled(showp);
4241 } catch (Exception e)
4244 "canShowProducts threw an exception - please report to help@jalview.org",
4252 * Finds and displays cross-references for the selected sequences (protein
4253 * products for nucleotide sequences, dna coding sequences for peptides).
4256 * the sequences to show cross-references for
4258 * true if from a nucleotide alignment (so showing proteins)
4260 * the database to show cross-references for
4262 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4263 final String source)
4265 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this),
4266 "CrossReferencesThread")
4271 * Construct and display a new frame containing the translation of this
4272 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4275 public void showTranslation_actionPerformed(ActionEvent e)
4277 AlignmentI al = null;
4280 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4282 al = dna.translateCdna();
4283 } catch (Exception ex)
4285 jalview.bin.Cache.log.error(
4286 "Exception during translation. Please report this !", ex);
4287 final String msg = MessageManager.getString(
4288 "label.error_when_translating_sequences_submit_bug_report");
4289 final String errorTitle = MessageManager
4290 .getString("label.implementation_error")
4291 + MessageManager.getString("label.translation_failed");
4292 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4293 JvOptionPane.ERROR_MESSAGE);
4296 if (al == null || al.getHeight() == 0)
4298 final String msg = MessageManager.getString(
4299 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4300 final String errorTitle = MessageManager
4301 .getString("label.translation_failed");
4302 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4303 JvOptionPane.WARNING_MESSAGE);
4307 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4308 af.setFileFormat(this.currentFileFormat);
4309 final String newTitle = MessageManager
4310 .formatMessage("label.translation_of_params", new Object[]
4311 { this.getTitle() });
4312 af.setTitle(newTitle);
4313 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4315 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4316 viewport.openSplitFrame(af, new Alignment(seqs));
4320 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4327 * Set the file format
4331 public void setFileFormat(FileFormatI format)
4333 this.currentFileFormat = format;
4337 * Try to load a features file onto the alignment.
4340 * contents or path to retrieve file
4342 * access mode of file (see jalview.io.AlignFile)
4343 * @return true if features file was parsed correctly.
4345 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4347 return avc.parseFeaturesFile(file, sourceType,
4348 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4353 public void refreshFeatureUI(boolean enableIfNecessary)
4355 // note - currently this is only still here rather than in the controller
4356 // because of the featureSettings hard reference that is yet to be
4358 if (enableIfNecessary)
4360 viewport.setShowSequenceFeatures(true);
4361 showSeqFeatures.setSelected(true);
4367 public void dragEnter(DropTargetDragEvent evt)
4372 public void dragExit(DropTargetEvent evt)
4377 public void dragOver(DropTargetDragEvent evt)
4382 public void dropActionChanged(DropTargetDragEvent evt)
4387 public void drop(DropTargetDropEvent evt)
4389 // JAL-1552 - acceptDrop required before getTransferable call for
4390 // Java's Transferable for native dnd
4391 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4392 Transferable t = evt.getTransferable();
4393 final AlignFrame thisaf = this;
4394 final List<String> files = new ArrayList<>();
4395 List<DataSourceType> protocols = new ArrayList<>();
4399 Desktop.transferFromDropTarget(files, protocols, evt, t);
4400 } catch (Exception e)
4402 e.printStackTrace();
4406 new Thread(new Runnable()
4413 // check to see if any of these files have names matching sequences
4416 SequenceIdMatcher idm = new SequenceIdMatcher(
4417 viewport.getAlignment().getSequencesArray());
4419 * Object[] { String,SequenceI}
4421 ArrayList<Object[]> filesmatched = new ArrayList<>();
4422 ArrayList<String> filesnotmatched = new ArrayList<>();
4423 for (int i = 0; i < files.size(); i++)
4425 String file = files.get(i).toString();
4427 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4428 if (protocol == DataSourceType.FILE)
4430 File fl = new File(file);
4431 pdbfn = fl.getName();
4433 else if (protocol == DataSourceType.URL)
4435 URL url = new URL(file);
4436 pdbfn = url.getFile();
4438 if (pdbfn.length() > 0)
4440 // attempt to find a match in the alignment
4441 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4442 int l = 0, c = pdbfn.indexOf(".");
4443 while (mtch == null && c != -1)
4448 } while ((c = pdbfn.indexOf(".", l)) > l);
4451 pdbfn = pdbfn.substring(0, l);
4453 mtch = idm.findAllIdMatches(pdbfn);
4457 FileFormatI type = null;
4460 type = new IdentifyFile().identify(file, protocol);
4461 } catch (Exception ex)
4465 if (type != null && type.isStructureFile())
4467 filesmatched.add(new Object[] { file, protocol, mtch });
4471 // File wasn't named like one of the sequences or wasn't a PDB
4473 filesnotmatched.add(file);
4477 if (filesmatched.size() > 0)
4479 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4480 || JvOptionPane.showConfirmDialog(thisaf,
4481 MessageManager.formatMessage(
4482 "label.automatically_associate_structure_files_with_sequences_same_name",
4484 { Integer.valueOf(filesmatched.size())
4486 MessageManager.getString(
4487 "label.automatically_associate_structure_files_by_name"),
4488 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4491 for (Object[] fm : filesmatched)
4493 // try and associate
4494 // TODO: may want to set a standard ID naming formalism for
4495 // associating PDB files which have no IDs.
4496 for (SequenceI toassoc : (SequenceI[]) fm[2])
4498 PDBEntry pe = new AssociatePdbFileWithSeq()
4499 .associatePdbWithSeq((String) fm[0],
4500 (DataSourceType) fm[1], toassoc, false,
4504 System.err.println("Associated file : "
4505 + ((String) fm[0]) + " with "
4506 + toassoc.getDisplayId(true));
4510 // TODO: do we need to update overview ? only if features are
4512 alignPanel.paintAlignment(true, false);
4516 if (filesnotmatched.size() > 0)
4518 if (assocfiles > 0 && (Cache.getDefault(
4519 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4520 || JvOptionPane.showConfirmDialog(thisaf,
4521 "<html>" + MessageManager.formatMessage(
4522 "label.ignore_unmatched_dropped_files_info",
4525 filesnotmatched.size())
4528 MessageManager.getString(
4529 "label.ignore_unmatched_dropped_files"),
4530 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4534 for (String fn : filesnotmatched)
4536 loadJalviewDataFile(fn, null, null, null);
4540 } catch (Exception ex)
4542 ex.printStackTrace();
4545 }, "DropFileThread").start();
4550 * Attempt to load a "dropped" file or URL string, by testing in turn for
4552 * <li>an Annotation file</li>
4553 * <li>a JNet file</li>
4554 * <li>a features file</li>
4555 * <li>else try to interpret as an alignment file</li>
4559 * either a filename or a URL string.
4561 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4562 FileFormatI format, SequenceI assocSeq)
4566 if (sourceType == null)
4568 sourceType = FormatAdapter.checkProtocol(file);
4570 // if the file isn't identified, or not positively identified as some
4571 // other filetype (PFAM is default unidentified alignment file type) then
4572 // try to parse as annotation.
4573 boolean isAnnotation = (format == null
4574 || FileFormat.Pfam.equals(format))
4575 ? new AnnotationFile().annotateAlignmentView(viewport,
4581 // first see if its a T-COFFEE score file
4582 TCoffeeScoreFile tcf = null;
4585 tcf = new TCoffeeScoreFile(file, sourceType);
4588 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4592 new TCoffeeColourScheme(viewport.getAlignment()));
4593 isAnnotation = true;
4594 statusBar.setText(MessageManager.getString(
4595 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4599 // some problem - if no warning its probable that the ID matching
4600 // process didn't work
4601 JvOptionPane.showMessageDialog(Desktop.desktop,
4602 tcf.getWarningMessage() == null
4603 ? MessageManager.getString(
4604 "label.check_file_matches_sequence_ids_alignment")
4605 : tcf.getWarningMessage(),
4606 MessageManager.getString(
4607 "label.problem_reading_tcoffee_score_file"),
4608 JvOptionPane.WARNING_MESSAGE);
4615 } catch (Exception x)
4618 "Exception when processing data source as T-COFFEE score file",
4624 // try to see if its a JNet 'concise' style annotation file *before*
4626 // try to parse it as a features file
4629 format = new IdentifyFile().identify(file, sourceType);
4631 if (FileFormat.ScoreMatrix == format)
4633 ScoreMatrixFile sm = new ScoreMatrixFile(
4634 new FileParse(file, sourceType));
4636 // todo: i18n this message
4637 statusBar.setText(MessageManager.formatMessage(
4638 "label.successfully_loaded_matrix",
4639 sm.getMatrixName()));
4641 else if (FileFormat.Jnet.equals(format))
4643 JPredFile predictions = new JPredFile(file, sourceType);
4644 new JnetAnnotationMaker();
4645 JnetAnnotationMaker.add_annotation(predictions,
4646 viewport.getAlignment(), 0, false);
4647 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4648 viewport.getAlignment().setSeqrep(repseq);
4649 HiddenColumns cs = new HiddenColumns();
4650 cs.hideInsertionsFor(repseq);
4651 viewport.getAlignment().setHiddenColumns(cs);
4652 isAnnotation = true;
4654 // else if (IdentifyFile.FeaturesFile.equals(format))
4655 else if (FileFormat.Features.equals(format))
4657 if (parseFeaturesFile(file, sourceType))
4659 alignPanel.paintAlignment(true, true);
4664 new FileLoader().LoadFile(viewport, file, sourceType, format);
4671 alignPanel.adjustAnnotationHeight();
4672 viewport.updateSequenceIdColours();
4673 buildSortByAnnotationScoresMenu();
4674 alignPanel.paintAlignment(true, true);
4676 } catch (Exception ex)
4678 ex.printStackTrace();
4679 } catch (OutOfMemoryError oom)
4684 } catch (Exception x)
4689 + (sourceType != null
4690 ? (sourceType == DataSourceType.PASTE
4692 : "using " + sourceType + " from "
4696 ? "(parsing as '" + format + "' file)"
4698 oom, Desktop.desktop);
4703 * Method invoked by the ChangeListener on the tabbed pane, in other words
4704 * when a different tabbed pane is selected by the user or programmatically.
4707 public void tabSelectionChanged(int index)
4711 alignPanel = alignPanels.get(index);
4712 viewport = alignPanel.av;
4713 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4714 setMenusFromViewport(viewport);
4718 * 'focus' any colour slider that is open to the selected viewport
4720 if (viewport.getConservationSelected())
4722 SliderPanel.setConservationSlider(alignPanel,
4723 viewport.getResidueShading(), alignPanel.getViewName());
4727 SliderPanel.hideConservationSlider();
4729 if (viewport.getAbovePIDThreshold())
4731 SliderPanel.setPIDSliderSource(alignPanel,
4732 viewport.getResidueShading(), alignPanel.getViewName());
4736 SliderPanel.hidePIDSlider();
4740 * If there is a frame linked to this one in a SplitPane, switch it to the
4741 * same view tab index. No infinite recursion of calls should happen, since
4742 * tabSelectionChanged() should not get invoked on setting the selected
4743 * index to an unchanged value. Guard against setting an invalid index
4744 * before the new view peer tab has been created.
4746 final AlignViewportI peer = viewport.getCodingComplement();
4749 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4750 .getAlignPanel().alignFrame;
4751 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4753 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4759 * On right mouse click on view tab, prompt for and set new view name.
4762 public void tabbedPane_mousePressed(MouseEvent e)
4764 if (e.isPopupTrigger())
4766 String msg = MessageManager.getString("label.enter_view_name");
4767 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4768 JvOptionPane.QUESTION_MESSAGE);
4772 viewport.viewName = reply;
4773 // TODO warn if reply is in getExistingViewNames()?
4774 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4779 public AlignViewport getCurrentView()
4785 * Open the dialog for regex description parsing.
4788 protected void extractScores_actionPerformed(ActionEvent e)
4790 ParseProperties pp = new jalview.analysis.ParseProperties(
4791 viewport.getAlignment());
4792 // TODO: verify regex and introduce GUI dialog for version 2.5
4793 // if (pp.getScoresFromDescription("col", "score column ",
4794 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4796 if (pp.getScoresFromDescription("description column",
4797 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4799 buildSortByAnnotationScoresMenu();
4807 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4811 protected void showDbRefs_actionPerformed(ActionEvent e)
4813 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4819 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4823 protected void showNpFeats_actionPerformed(ActionEvent e)
4825 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4829 * find the viewport amongst the tabs in this alignment frame and close that
4834 public boolean closeView(AlignViewportI av)
4838 this.closeMenuItem_actionPerformed(false);
4841 Component[] comp = tabbedPane.getComponents();
4842 for (int i = 0; comp != null && i < comp.length; i++)
4844 if (comp[i] instanceof AlignmentPanel)
4846 if (((AlignmentPanel) comp[i]).av == av)
4849 closeView((AlignmentPanel) comp[i]);
4857 protected void build_fetchdbmenu(JMenu webService)
4859 // Temporary hack - DBRef Fetcher always top level ws entry.
4860 // TODO We probably want to store a sequence database checklist in
4861 // preferences and have checkboxes.. rather than individual sources selected
4863 final JMenu rfetch = new JMenu(
4864 MessageManager.getString("action.fetch_db_references"));
4865 rfetch.setToolTipText(MessageManager.getString(
4866 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4867 webService.add(rfetch);
4869 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4870 MessageManager.getString("option.trim_retrieved_seqs"));
4871 trimrs.setToolTipText(
4872 MessageManager.getString("label.trim_retrieved_sequences"));
4873 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4874 trimrs.addActionListener(new ActionListener()
4877 public void actionPerformed(ActionEvent e)
4879 trimrs.setSelected(trimrs.isSelected());
4880 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4881 Boolean.valueOf(trimrs.isSelected()).toString());
4885 JMenuItem fetchr = new JMenuItem(
4886 MessageManager.getString("label.standard_databases"));
4887 fetchr.setToolTipText(
4888 MessageManager.getString("label.fetch_embl_uniprot"));
4889 fetchr.addActionListener(new ActionListener()
4893 public void actionPerformed(ActionEvent e)
4895 new Thread(new Runnable()
4900 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4901 .getAlignment().isNucleotide();
4902 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4903 alignPanel.av.getSequenceSelection(),
4904 alignPanel.alignFrame, null,
4905 alignPanel.alignFrame.featureSettings, isNucleotide);
4906 dbRefFetcher.addListener(new FetchFinishedListenerI()
4909 public void finished()
4911 AlignFrame.this.setMenusForViewport();
4914 dbRefFetcher.fetchDBRefs(false);
4916 }, "BuildFetchDBMenuThread").start();
4922 final AlignFrame me = this;
4923 new Thread(new Runnable()
4928 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4929 .getSequenceFetcherSingleton(me);
4930 javax.swing.SwingUtilities.invokeLater(new Runnable()
4935 String[] dbclasses = sf.getOrderedSupportedSources();
4936 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4937 // jalview.util.QuickSort.sort(otherdb, otherdb);
4938 List<DbSourceProxy> otherdb;
4939 JMenu dfetch = new JMenu();
4940 JMenu ifetch = new JMenu();
4941 JMenuItem fetchr = null;
4942 int comp = 0, icomp = 0, mcomp = 15;
4943 String mname = null;
4945 for (String dbclass : dbclasses)
4947 otherdb = sf.getSourceProxy(dbclass);
4948 // add a single entry for this class, or submenu allowing 'fetch
4950 if (otherdb == null || otherdb.size() < 1)
4954 // List<DbSourceProxy> dbs=otherdb;
4955 // otherdb=new ArrayList<DbSourceProxy>();
4956 // for (DbSourceProxy db:dbs)
4958 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4962 mname = "From " + dbclass;
4964 if (otherdb.size() == 1)
4966 final DbSourceProxy[] dassource = otherdb
4967 .toArray(new DbSourceProxy[0]);
4968 DbSourceProxy src = otherdb.get(0);
4969 fetchr = new JMenuItem(src.getDbSource());
4970 fetchr.addActionListener(new ActionListener()
4974 public void actionPerformed(ActionEvent e)
4976 new Thread(new Runnable()
4982 boolean isNucleotide = alignPanel.alignFrame
4983 .getViewport().getAlignment()
4985 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4986 alignPanel.av.getSequenceSelection(),
4987 alignPanel.alignFrame, dassource,
4988 alignPanel.alignFrame.featureSettings,
4991 .addListener(new FetchFinishedListenerI()
4994 public void finished()
4996 AlignFrame.this.setMenusForViewport();
4999 dbRefFetcher.fetchDBRefs(false);
5005 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5006 MessageManager.formatMessage(
5007 "label.fetch_retrieve_from", new Object[]
5008 { src.getDbName() })));
5014 final DbSourceProxy[] dassource = otherdb
5015 .toArray(new DbSourceProxy[0]);
5017 DbSourceProxy src = otherdb.get(0);
5018 fetchr = new JMenuItem(MessageManager
5019 .formatMessage("label.fetch_all_param", new Object[]
5020 { src.getDbSource() }));
5021 fetchr.addActionListener(new ActionListener()
5024 public void actionPerformed(ActionEvent e)
5026 new Thread(new Runnable()
5032 boolean isNucleotide = alignPanel.alignFrame
5033 .getViewport().getAlignment()
5035 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5036 alignPanel.av.getSequenceSelection(),
5037 alignPanel.alignFrame, dassource,
5038 alignPanel.alignFrame.featureSettings,
5041 .addListener(new FetchFinishedListenerI()
5044 public void finished()
5046 AlignFrame.this.setMenusForViewport();
5049 dbRefFetcher.fetchDBRefs(false);
5055 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5056 MessageManager.formatMessage(
5057 "label.fetch_retrieve_from_all_sources",
5059 { Integer.valueOf(otherdb.size())
5061 src.getDbSource(), src.getDbName() })));
5064 // and then build the rest of the individual menus
5065 ifetch = new JMenu(MessageManager.formatMessage(
5066 "label.source_from_db_source", new Object[]
5067 { src.getDbSource() }));
5069 String imname = null;
5071 for (DbSourceProxy sproxy : otherdb)
5073 String dbname = sproxy.getDbName();
5074 String sname = dbname.length() > 5
5075 ? dbname.substring(0, 5) + "..."
5077 String msname = dbname.length() > 10
5078 ? dbname.substring(0, 10) + "..."
5082 imname = MessageManager
5083 .formatMessage("label.from_msname", new Object[]
5086 fetchr = new JMenuItem(msname);
5087 final DbSourceProxy[] dassrc = { sproxy };
5088 fetchr.addActionListener(new ActionListener()
5092 public void actionPerformed(ActionEvent e)
5094 new Thread(new Runnable()
5100 boolean isNucleotide = alignPanel.alignFrame
5101 .getViewport().getAlignment()
5103 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5104 alignPanel.av.getSequenceSelection(),
5105 alignPanel.alignFrame, dassrc,
5106 alignPanel.alignFrame.featureSettings,
5109 .addListener(new FetchFinishedListenerI()
5112 public void finished()
5114 AlignFrame.this.setMenusForViewport();
5117 dbRefFetcher.fetchDBRefs(false);
5123 fetchr.setToolTipText(
5124 "<html>" + MessageManager.formatMessage(
5125 "label.fetch_retrieve_from", new Object[]
5129 if (++icomp >= mcomp || i == (otherdb.size()))
5131 ifetch.setText(MessageManager.formatMessage(
5132 "label.source_to_target", imname, sname));
5134 ifetch = new JMenu();
5142 if (comp >= mcomp || dbi >= (dbclasses.length))
5144 dfetch.setText(MessageManager.formatMessage(
5145 "label.source_to_target", mname, dbclass));
5147 dfetch = new JMenu();
5160 * Left justify the whole alignment.
5163 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5165 AlignmentI al = viewport.getAlignment();
5167 viewport.firePropertyChange("alignment", null, al);
5171 * Right justify the whole alignment.
5174 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5176 AlignmentI al = viewport.getAlignment();
5178 viewport.firePropertyChange("alignment", null, al);
5182 public void setShowSeqFeatures(boolean b)
5184 showSeqFeatures.setSelected(b);
5185 viewport.setShowSequenceFeatures(b);
5192 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5193 * awt.event.ActionEvent)
5196 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5198 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5199 alignPanel.paintAlignment(false, false);
5206 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5210 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5212 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5213 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5221 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5222 * .event.ActionEvent)
5225 protected void showGroupConservation_actionPerformed(ActionEvent e)
5227 viewport.setShowGroupConservation(showGroupConservation.getState());
5228 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5235 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5236 * .event.ActionEvent)
5239 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5241 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5242 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5249 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5250 * .event.ActionEvent)
5253 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5255 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5256 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5260 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5262 showSequenceLogo.setState(true);
5263 viewport.setShowSequenceLogo(true);
5264 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5265 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5269 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5271 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5278 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5279 * .event.ActionEvent)
5282 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5284 if (avc.makeGroupsFromSelection())
5286 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5287 alignPanel.updateAnnotation();
5288 alignPanel.paintAlignment(true, true);
5292 public void clearAlignmentSeqRep()
5294 // TODO refactor alignmentseqrep to controller
5295 if (viewport.getAlignment().hasSeqrep())
5297 viewport.getAlignment().setSeqrep(null);
5298 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5299 alignPanel.updateAnnotation();
5300 alignPanel.paintAlignment(true, true);
5305 protected void createGroup_actionPerformed(ActionEvent e)
5307 if (avc.createGroup())
5309 alignPanel.alignmentChanged();
5314 protected void unGroup_actionPerformed(ActionEvent e)
5318 alignPanel.alignmentChanged();
5323 * make the given alignmentPanel the currently selected tab
5325 * @param alignmentPanel
5327 public void setDisplayedView(AlignmentPanel alignmentPanel)
5329 if (!viewport.getSequenceSetId()
5330 .equals(alignmentPanel.av.getSequenceSetId()))
5332 throw new Error(MessageManager.getString(
5333 "error.implementation_error_cannot_show_view_alignment_frame"));
5335 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5336 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5338 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5343 * Action on selection of menu options to Show or Hide annotations.
5346 * @param forSequences
5347 * update sequence-related annotations
5348 * @param forAlignment
5349 * update non-sequence-related annotations
5352 protected void setAnnotationsVisibility(boolean visible,
5353 boolean forSequences, boolean forAlignment)
5355 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5356 .getAlignmentAnnotation();
5361 for (AlignmentAnnotation aa : anns)
5364 * don't display non-positional annotations on an alignment
5366 if (aa.annotations == null)
5370 boolean apply = (aa.sequenceRef == null && forAlignment)
5371 || (aa.sequenceRef != null && forSequences);
5374 aa.visible = visible;
5377 alignPanel.validateAnnotationDimensions(true);
5378 alignPanel.alignmentChanged();
5382 * Store selected annotation sort order for the view and repaint.
5385 protected void sortAnnotations_actionPerformed()
5387 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5389 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5390 alignPanel.paintAlignment(false, false);
5395 * @return alignment panels in this alignment frame
5397 public List<? extends AlignmentViewPanel> getAlignPanels()
5399 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5403 * Open a new alignment window, with the cDNA associated with this (protein)
5404 * alignment, aligned as is the protein.
5406 protected void viewAsCdna_actionPerformed()
5408 // TODO no longer a menu action - refactor as required
5409 final AlignmentI alignment = getViewport().getAlignment();
5410 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5411 if (mappings == null)
5415 List<SequenceI> cdnaSeqs = new ArrayList<>();
5416 for (SequenceI aaSeq : alignment.getSequences())
5418 for (AlignedCodonFrame acf : mappings)
5420 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5424 * There is a cDNA mapping for this protein sequence - add to new
5425 * alignment. It will share the same dataset sequence as other mapped
5426 * cDNA (no new mappings need to be created).
5428 final Sequence newSeq = new Sequence(dnaSeq);
5429 newSeq.setDatasetSequence(dnaSeq);
5430 cdnaSeqs.add(newSeq);
5434 if (cdnaSeqs.size() == 0)
5436 // show a warning dialog no mapped cDNA
5439 AlignmentI cdna = new Alignment(
5440 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5441 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5442 AlignFrame.DEFAULT_HEIGHT);
5443 cdna.alignAs(alignment);
5444 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5446 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5447 AlignFrame.DEFAULT_HEIGHT);
5451 * Set visibility of dna/protein complement view (available when shown in a
5457 protected void showComplement_actionPerformed(boolean show)
5459 SplitContainerI sf = getSplitViewContainer();
5462 sf.setComplementVisible(this, show);
5467 * Generate the reverse (optionally complemented) of the selected sequences,
5468 * and add them to the alignment
5471 protected void showReverse_actionPerformed(boolean complement)
5473 AlignmentI al = null;
5476 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5477 al = dna.reverseCdna(complement);
5478 viewport.addAlignment(al, "");
5479 addHistoryItem(new EditCommand(
5480 MessageManager.getString("label.add_sequences"), Action.PASTE,
5481 al.getSequencesArray(), 0, al.getWidth(),
5482 viewport.getAlignment()));
5483 } catch (Exception ex)
5485 System.err.println(ex.getMessage());
5491 * Try to run a script in the Groovy console, having first ensured that this
5492 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5493 * be targeted at this alignment.
5496 protected void runGroovy_actionPerformed()
5498 Jalview.setCurrentAlignFrame(this);
5499 groovy.ui.Console console = Desktop.getGroovyConsole();
5500 if (console != null)
5504 console.runScript();
5505 } catch (Exception ex)
5507 System.err.println((ex.toString()));
5508 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5509 MessageManager.getString("label.couldnt_run_groovy_script"),
5510 MessageManager.getString("label.groovy_support_failed"),
5511 JvOptionPane.ERROR_MESSAGE);
5516 System.err.println("Can't run Groovy script as console not found");
5521 * Hides columns containing (or not containing) a specified feature, provided
5522 * that would not leave all columns hidden
5524 * @param featureType
5525 * @param columnsContaining
5528 public boolean hideFeatureColumns(String featureType,
5529 boolean columnsContaining)
5531 boolean notForHiding = avc.markColumnsContainingFeatures(
5532 columnsContaining, false, false, featureType);
5535 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5536 false, featureType))
5538 getViewport().hideSelectedColumns();
5546 protected void selectHighlightedColumns_actionPerformed(
5547 ActionEvent actionEvent)
5549 // include key modifier check in case user selects from menu
5550 avc.markHighlightedColumns(
5551 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5552 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5553 | ActionEvent.CTRL_MASK)) != 0);
5557 * Rebuilds the Colour menu, including any user-defined colours which have
5558 * been loaded either on startup or during the session
5560 public void buildColourMenu()
5562 colourMenu.removeAll();
5564 colourMenu.add(applyToAllGroups);
5565 colourMenu.add(textColour);
5566 colourMenu.addSeparator();
5568 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5571 colourMenu.addSeparator();
5572 colourMenu.add(conservationMenuItem);
5573 colourMenu.add(modifyConservation);
5574 colourMenu.add(abovePIDThreshold);
5575 colourMenu.add(modifyPID);
5576 colourMenu.add(annotationColour);
5578 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5579 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5583 * Open a dialog (if not already open) that allows the user to select and
5584 * calculate PCA or Tree analysis
5586 protected void openTreePcaDialog()
5588 if (alignPanel.getCalculationDialog() == null)
5590 new CalculationChooser(AlignFrame.this);
5595 class PrintThread extends Thread
5599 public PrintThread(AlignmentPanel ap)
5604 static PageFormat pf;
5609 PrinterJob printJob = PrinterJob.getPrinterJob();
5613 printJob.setPrintable(ap, pf);
5617 printJob.setPrintable(ap);
5620 if (printJob.printDialog())
5625 } catch (Exception PrintException)
5627 PrintException.printStackTrace();