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.ext.archaeopteryx.AptxInit;
64 import jalview.ext.forester.io.SupportedTreeFileFilter;
65 import jalview.ext.forester.io.TreeParser;
66 import jalview.gui.ColourMenuHelper.ColourChangeListener;
67 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
68 import jalview.io.AlignmentProperties;
69 import jalview.io.AnnotationFile;
70 import jalview.io.BioJsHTMLOutput;
71 import jalview.io.DataSourceType;
72 import jalview.io.FileFormat;
73 import jalview.io.FileFormatI;
74 import jalview.io.FileFormats;
75 import jalview.io.FileLoader;
76 import jalview.io.FileParse;
77 import jalview.io.FormatAdapter;
78 import jalview.io.HtmlSvgOutput;
79 import jalview.io.IdentifyFile;
80 import jalview.io.JPredFile;
81 import jalview.io.JalviewFileChooser;
82 import jalview.io.JalviewFileView;
83 import jalview.io.JnetAnnotationMaker;
84 import jalview.io.NewickFile;
85 import jalview.io.ScoreMatrixFile;
86 import jalview.io.TCoffeeScoreFile;
87 import jalview.jbgui.GAlignFrame;
88 import jalview.schemes.ColourSchemeI;
89 import jalview.schemes.ColourSchemes;
90 import jalview.schemes.ResidueColourScheme;
91 import jalview.schemes.TCoffeeColourScheme;
92 import jalview.util.MessageManager;
93 import jalview.viewmodel.AlignmentViewport;
94 import jalview.viewmodel.ViewportRanges;
95 import jalview.ws.DBRefFetcher;
96 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
97 import jalview.ws.jws1.Discoverer;
98 import jalview.ws.jws2.Jws2Discoverer;
99 import jalview.ws.jws2.jabaws2.Jws2Instance;
100 import jalview.ws.seqfetcher.DbSourceProxy;
102 import java.awt.BorderLayout;
103 import java.awt.Component;
104 import java.awt.Rectangle;
105 import java.awt.Toolkit;
106 import java.awt.datatransfer.Clipboard;
107 import java.awt.datatransfer.DataFlavor;
108 import java.awt.datatransfer.StringSelection;
109 import java.awt.datatransfer.Transferable;
110 import java.awt.dnd.DnDConstants;
111 import java.awt.dnd.DropTargetDragEvent;
112 import java.awt.dnd.DropTargetDropEvent;
113 import java.awt.dnd.DropTargetEvent;
114 import java.awt.dnd.DropTargetListener;
115 import java.awt.event.ActionEvent;
116 import java.awt.event.ActionListener;
117 import java.awt.event.FocusAdapter;
118 import java.awt.event.FocusEvent;
119 import java.awt.event.ItemEvent;
120 import java.awt.event.ItemListener;
121 import java.awt.event.KeyAdapter;
122 import java.awt.event.KeyEvent;
123 import java.awt.event.MouseEvent;
124 import java.awt.print.PageFormat;
125 import java.awt.print.PrinterJob;
126 import java.beans.PropertyChangeEvent;
128 import java.io.FileWriter;
129 import java.io.PrintWriter;
130 import java.net.MalformedURLException;
132 import java.util.ArrayList;
133 import java.util.Arrays;
134 import java.util.Deque;
135 import java.util.Enumeration;
136 import java.util.Hashtable;
137 import java.util.List;
138 import java.util.Vector;
140 import javax.swing.JCheckBoxMenuItem;
141 import javax.swing.JEditorPane;
142 import javax.swing.JInternalFrame;
143 import javax.swing.JLayeredPane;
144 import javax.swing.JMenu;
145 import javax.swing.JMenuItem;
146 import javax.swing.JScrollPane;
147 import javax.swing.SwingUtilities;
153 * @version $Revision$
155 public class AlignFrame extends GAlignFrame implements DropTargetListener,
156 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
159 public static final int DEFAULT_WIDTH = 700;
161 public static final int DEFAULT_HEIGHT = 500;
164 * The currently displayed panel (selected tabbed view if more than one)
166 public AlignmentPanel alignPanel;
168 AlignViewport viewport;
170 public AlignViewControllerI avc;
172 List<AlignmentPanel> alignPanels = new ArrayList<>();
175 * Last format used to load or save alignments in this window
177 FileFormatI currentFileFormat = null;
180 * Current filename for this alignment
182 String fileName = null;
185 * Creates a new AlignFrame object with specific width and height.
191 public AlignFrame(AlignmentI al, int width, int height)
193 this(al, null, width, height);
197 * Creates a new AlignFrame object with specific width, height and
203 * @param sequenceSetId
205 public AlignFrame(AlignmentI al, int width, int height,
206 String sequenceSetId)
208 this(al, null, width, height, sequenceSetId);
212 * Creates a new AlignFrame object with specific width, height and
218 * @param sequenceSetId
221 public AlignFrame(AlignmentI al, int width, int height,
222 String sequenceSetId, String viewId)
224 this(al, null, width, height, sequenceSetId, viewId);
228 * new alignment window with hidden columns
232 * @param hiddenColumns
233 * ColumnSelection or null
235 * Width of alignment frame
239 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
242 this(al, hiddenColumns, width, height, null);
246 * Create alignment frame for al with hiddenColumns, a specific width and
247 * height, and specific sequenceId
250 * @param hiddenColumns
253 * @param sequenceSetId
256 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
257 int height, String sequenceSetId)
259 this(al, hiddenColumns, width, height, sequenceSetId, null);
263 * Create alignment frame for al with hiddenColumns, a specific width and
264 * height, and specific sequenceId
267 * @param hiddenColumns
270 * @param sequenceSetId
275 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
276 int height, String sequenceSetId, String viewId)
278 setSize(width, height);
280 if (al.getDataset() == null)
285 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
287 alignPanel = new AlignmentPanel(this, viewport);
289 addAlignmentPanel(alignPanel, true);
293 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
294 HiddenColumns hiddenColumns, int width, int height)
296 setSize(width, height);
298 if (al.getDataset() == null)
303 viewport = new AlignViewport(al, hiddenColumns);
305 if (hiddenSeqs != null && hiddenSeqs.length > 0)
307 viewport.hideSequence(hiddenSeqs);
309 alignPanel = new AlignmentPanel(this, viewport);
310 addAlignmentPanel(alignPanel, true);
315 * Make a new AlignFrame from existing alignmentPanels
322 public AlignFrame(AlignmentPanel ap)
326 addAlignmentPanel(ap, false);
331 * initalise the alignframe from the underlying viewport data and the
336 if (!Jalview.isHeadlessMode())
338 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
341 avc = new jalview.controller.AlignViewController(this, viewport,
343 if (viewport.getAlignmentConservationAnnotation() == null)
345 // BLOSUM62Colour.setEnabled(false);
346 conservationMenuItem.setEnabled(false);
347 modifyConservation.setEnabled(false);
348 // PIDColour.setEnabled(false);
349 // abovePIDThreshold.setEnabled(false);
350 // modifyPID.setEnabled(false);
353 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
356 if (sortby.equals("Id"))
358 sortIDMenuItem_actionPerformed(null);
360 else if (sortby.equals("Pairwise Identity"))
362 sortPairwiseMenuItem_actionPerformed(null);
366 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
368 setMenusFromViewport(viewport);
369 buildSortByAnnotationScoresMenu();
370 calculateTree.addActionListener(new ActionListener()
374 public void actionPerformed(ActionEvent e)
381 if (Desktop.desktop != null)
383 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
384 addServiceListeners();
388 if (viewport.getWrapAlignment())
390 wrapMenuItem_actionPerformed(null);
393 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
395 this.overviewMenuItem_actionPerformed(null);
400 final List<AlignmentPanel> selviews = new ArrayList<>();
401 final List<AlignmentPanel> origview = new ArrayList<>();
402 final String menuLabel = MessageManager
403 .getString("label.copy_format_from");
404 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
405 new ViewSetProvider()
409 public AlignmentPanel[] getAllAlignmentPanels()
412 origview.add(alignPanel);
413 // make an array of all alignment panels except for this one
414 List<AlignmentPanel> aps = new ArrayList<>(
415 Arrays.asList(Desktop.getAlignmentPanels(null)));
416 aps.remove(AlignFrame.this.alignPanel);
417 return aps.toArray(new AlignmentPanel[aps.size()]);
419 }, selviews, new ItemListener()
423 public void itemStateChanged(ItemEvent e)
425 if (origview.size() > 0)
427 final AlignmentPanel ap = origview.get(0);
430 * Copy the ViewStyle of the selected panel to 'this one'.
431 * Don't change value of 'scaleProteinAsCdna' unless copying
434 ViewStyleI vs = selviews.get(0).getAlignViewport()
436 boolean fromSplitFrame = selviews.get(0)
437 .getAlignViewport().getCodingComplement() != null;
440 vs.setScaleProteinAsCdna(ap.getAlignViewport()
441 .getViewStyle().isScaleProteinAsCdna());
443 ap.getAlignViewport().setViewStyle(vs);
446 * Also rescale ViewStyle of SplitFrame complement if there is
447 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
448 * the whole ViewStyle (allow cDNA protein to have different
451 AlignViewportI complement = ap.getAlignViewport()
452 .getCodingComplement();
453 if (complement != null && vs.isScaleProteinAsCdna())
455 AlignFrame af = Desktop.getAlignFrameFor(complement);
456 ((SplitFrame) af.getSplitViewContainer())
458 af.setMenusForViewport();
462 ap.setSelected(true);
463 ap.alignFrame.setMenusForViewport();
468 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
469 .indexOf("devel") > -1
470 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
471 .indexOf("test") > -1)
473 formatMenu.add(vsel);
475 addFocusListener(new FocusAdapter()
478 public void focusGained(FocusEvent e)
480 Jalview.setCurrentAlignFrame(AlignFrame.this);
487 * Change the filename and format for the alignment, and enable the 'reload'
488 * button functionality.
495 public void setFileName(String file, FileFormatI format)
498 setFileFormat(format);
499 reload.setEnabled(true);
503 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
506 void addKeyListener()
508 addKeyListener(new KeyAdapter()
511 public void keyPressed(KeyEvent evt)
513 if (viewport.cursorMode
514 && ((evt.getKeyCode() >= KeyEvent.VK_0
515 && evt.getKeyCode() <= KeyEvent.VK_9)
516 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
517 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
518 && Character.isDigit(evt.getKeyChar()))
520 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
523 switch (evt.getKeyCode())
526 case 27: // escape key
527 deselectAllSequenceMenuItem_actionPerformed(null);
531 case KeyEvent.VK_DOWN:
532 if (evt.isAltDown() || !viewport.cursorMode)
534 moveSelectedSequences(false);
536 if (viewport.cursorMode)
538 alignPanel.getSeqPanel().moveCursor(0, 1);
543 if (evt.isAltDown() || !viewport.cursorMode)
545 moveSelectedSequences(true);
547 if (viewport.cursorMode)
549 alignPanel.getSeqPanel().moveCursor(0, -1);
554 case KeyEvent.VK_LEFT:
555 if (evt.isAltDown() || !viewport.cursorMode)
557 slideSequences(false,
558 alignPanel.getSeqPanel().getKeyboardNo1());
562 alignPanel.getSeqPanel().moveCursor(-1, 0);
567 case KeyEvent.VK_RIGHT:
568 if (evt.isAltDown() || !viewport.cursorMode)
570 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
574 alignPanel.getSeqPanel().moveCursor(1, 0);
578 case KeyEvent.VK_SPACE:
579 if (viewport.cursorMode)
581 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
582 || evt.isShiftDown() || evt.isAltDown());
586 // case KeyEvent.VK_A:
587 // if (viewport.cursorMode)
589 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
590 // //System.out.println("A");
594 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
595 * System.out.println("closing bracket"); } break;
597 case KeyEvent.VK_DELETE:
598 case KeyEvent.VK_BACK_SPACE:
599 if (!viewport.cursorMode)
601 cut_actionPerformed(null);
605 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
606 || evt.isShiftDown() || evt.isAltDown());
612 if (viewport.cursorMode)
614 alignPanel.getSeqPanel().setCursorRow();
618 if (viewport.cursorMode && !evt.isControlDown())
620 alignPanel.getSeqPanel().setCursorColumn();
624 if (viewport.cursorMode)
626 alignPanel.getSeqPanel().setCursorPosition();
630 case KeyEvent.VK_ENTER:
631 case KeyEvent.VK_COMMA:
632 if (viewport.cursorMode)
634 alignPanel.getSeqPanel().setCursorRowAndColumn();
639 if (viewport.cursorMode)
641 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
645 if (viewport.cursorMode)
647 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
652 viewport.cursorMode = !viewport.cursorMode;
653 statusBar.setText(MessageManager
654 .formatMessage("label.keyboard_editing_mode", new String[]
655 { (viewport.cursorMode ? "on" : "off") }));
656 if (viewport.cursorMode)
658 ViewportRanges ranges = viewport.getRanges();
659 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
661 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
664 alignPanel.getSeqPanel().seqCanvas.repaint();
670 Help.showHelpWindow();
671 } catch (Exception ex)
673 ex.printStackTrace();
678 boolean toggleSeqs = !evt.isControlDown();
679 boolean toggleCols = !evt.isShiftDown();
680 toggleHiddenRegions(toggleSeqs, toggleCols);
685 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
686 boolean modifyExisting = true; // always modify, don't clear
687 // evt.isShiftDown();
688 boolean invertHighlighted = evt.isAltDown();
689 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
693 case KeyEvent.VK_PAGE_UP:
694 viewport.getRanges().pageUp();
696 case KeyEvent.VK_PAGE_DOWN:
697 viewport.getRanges().pageDown();
703 public void keyReleased(KeyEvent evt)
705 switch (evt.getKeyCode())
707 case KeyEvent.VK_LEFT:
708 if (evt.isAltDown() || !viewport.cursorMode)
710 viewport.firePropertyChange("alignment", null,
711 viewport.getAlignment().getSequences());
715 case KeyEvent.VK_RIGHT:
716 if (evt.isAltDown() || !viewport.cursorMode)
718 viewport.firePropertyChange("alignment", null,
719 viewport.getAlignment().getSequences());
727 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
729 ap.alignFrame = this;
730 avc = new jalview.controller.AlignViewController(this, viewport,
735 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
737 int aSize = alignPanels.size();
739 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
741 if (aSize == 1 && ap.av.viewName == null)
743 this.getContentPane().add(ap, BorderLayout.CENTER);
749 setInitialTabVisible();
752 expandViews.setEnabled(true);
753 gatherViews.setEnabled(true);
754 tabbedPane.addTab(ap.av.viewName, ap);
756 ap.setVisible(false);
761 if (ap.av.isPadGaps())
763 ap.av.getAlignment().padGaps();
765 ap.av.updateConservation(ap);
766 ap.av.updateConsensus(ap);
767 ap.av.updateStrucConsensus(ap);
771 public void setInitialTabVisible()
773 expandViews.setEnabled(true);
774 gatherViews.setEnabled(true);
775 tabbedPane.setVisible(true);
776 AlignmentPanel first = alignPanels.get(0);
777 tabbedPane.addTab(first.av.viewName, first);
778 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
781 public AlignViewport getViewport()
786 /* Set up intrinsic listeners for dynamically generated GUI bits. */
787 private void addServiceListeners()
789 final java.beans.PropertyChangeListener thisListener;
790 Desktop.instance.addJalviewPropertyChangeListener("services",
791 thisListener = new java.beans.PropertyChangeListener()
794 public void propertyChange(PropertyChangeEvent evt)
796 // // System.out.println("Discoverer property change.");
797 // if (evt.getPropertyName().equals("services"))
799 SwingUtilities.invokeLater(new Runnable()
806 "Rebuild WS Menu for service change");
807 BuildWebServiceMenu();
814 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
817 public void internalFrameClosed(
818 javax.swing.event.InternalFrameEvent evt)
820 // System.out.println("deregistering discoverer listener");
821 Desktop.instance.removeJalviewPropertyChangeListener("services",
823 closeMenuItem_actionPerformed(true);
826 // Finally, build the menu once to get current service state
827 new Thread(new Runnable()
832 BuildWebServiceMenu();
838 * Configure menu items that vary according to whether the alignment is
839 * nucleotide or protein
841 public void setGUINucleotide()
843 AlignmentI al = getViewport().getAlignment();
844 boolean nucleotide = al.isNucleotide();
846 showTranslation.setVisible(nucleotide);
847 showReverse.setVisible(nucleotide);
848 showReverseComplement.setVisible(nucleotide);
849 conservationMenuItem.setEnabled(!nucleotide);
851 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
852 showGroupConservation.setEnabled(!nucleotide);
854 showComplementMenuItem
855 .setText(nucleotide ? MessageManager.getString("label.protein")
856 : MessageManager.getString("label.nucleotide"));
860 * set up menus for the current viewport. This may be called after any
861 * operation that affects the data in the current view (selection changed,
862 * etc) to update the menus to reflect the new state.
865 public void setMenusForViewport()
867 setMenusFromViewport(viewport);
871 * Need to call this method when tabs are selected for multiple views, or when
872 * loading from Jalview2XML.java
877 void setMenusFromViewport(AlignViewport av)
879 padGapsMenuitem.setSelected(av.isPadGaps());
880 colourTextMenuItem.setSelected(av.isShowColourText());
881 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
882 modifyPID.setEnabled(abovePIDThreshold.isSelected());
883 conservationMenuItem.setSelected(av.getConservationSelected());
884 modifyConservation.setEnabled(conservationMenuItem.isSelected());
885 seqLimits.setSelected(av.getShowJVSuffix());
886 idRightAlign.setSelected(av.isRightAlignIds());
887 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
888 renderGapsMenuItem.setSelected(av.isRenderGaps());
889 wrapMenuItem.setSelected(av.getWrapAlignment());
890 scaleAbove.setVisible(av.getWrapAlignment());
891 scaleLeft.setVisible(av.getWrapAlignment());
892 scaleRight.setVisible(av.getWrapAlignment());
893 annotationPanelMenuItem.setState(av.isShowAnnotation());
895 * Show/hide annotations only enabled if annotation panel is shown
897 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
898 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
899 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
900 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
901 viewBoxesMenuItem.setSelected(av.getShowBoxes());
902 viewTextMenuItem.setSelected(av.getShowText());
903 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
904 showGroupConsensus.setSelected(av.isShowGroupConsensus());
905 showGroupConservation.setSelected(av.isShowGroupConservation());
906 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
907 showSequenceLogo.setSelected(av.isShowSequenceLogo());
908 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
910 ColourMenuHelper.setColourSelected(colourMenu,
911 av.getGlobalColourScheme());
913 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
914 hiddenMarkers.setState(av.getShowHiddenMarkers());
915 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
916 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
917 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
918 autoCalculate.setSelected(av.autoCalculateConsensus);
919 sortByTree.setSelected(av.sortByTree);
920 listenToViewSelections.setSelected(av.followSelection);
922 showProducts.setEnabled(canShowProducts());
923 setGroovyEnabled(Desktop.getGroovyConsole() != null);
929 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
933 public void setGroovyEnabled(boolean b)
935 runGroovy.setEnabled(b);
938 private IProgressIndicator progressBar;
943 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
946 public void setProgressBar(String message, long id)
948 progressBar.setProgressBar(message, id);
952 public void registerHandler(final long id,
953 final IProgressIndicatorHandler handler)
955 progressBar.registerHandler(id, handler);
960 * @return true if any progress bars are still active
963 public boolean operationInProgress()
965 return progressBar.operationInProgress();
969 public void setStatus(String text)
971 statusBar.setText(text);
975 * Added so Castor Mapping file can obtain Jalview Version
977 public String getVersion()
979 return jalview.bin.Cache.getProperty("VERSION");
982 public FeatureRenderer getFeatureRenderer()
984 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
988 public void fetchSequence_actionPerformed(ActionEvent e)
990 new jalview.gui.SequenceFetcher(this);
994 public void addFromFile_actionPerformed(ActionEvent e)
996 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1000 public void reload_actionPerformed(ActionEvent e)
1002 if (fileName != null)
1004 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1005 // originating file's format
1006 // TODO: work out how to recover feature settings for correct view(s) when
1007 // file is reloaded.
1008 if (FileFormat.Jalview.equals(currentFileFormat))
1010 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1011 for (int i = 0; i < frames.length; i++)
1013 if (frames[i] instanceof AlignFrame && frames[i] != this
1014 && ((AlignFrame) frames[i]).fileName != null
1015 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1019 frames[i].setSelected(true);
1020 Desktop.instance.closeAssociatedWindows();
1021 } catch (java.beans.PropertyVetoException ex)
1027 Desktop.instance.closeAssociatedWindows();
1029 FileLoader loader = new FileLoader();
1030 DataSourceType protocol = fileName.startsWith("http:")
1031 ? DataSourceType.URL
1032 : DataSourceType.FILE;
1033 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1037 Rectangle bounds = this.getBounds();
1039 FileLoader loader = new FileLoader();
1040 DataSourceType protocol = fileName.startsWith("http:")
1041 ? DataSourceType.URL
1042 : DataSourceType.FILE;
1043 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1044 protocol, currentFileFormat);
1046 newframe.setBounds(bounds);
1047 if (featureSettings != null && featureSettings.isShowing())
1049 final Rectangle fspos = featureSettings.frame.getBounds();
1050 // TODO: need a 'show feature settings' function that takes bounds -
1051 // need to refactor Desktop.addFrame
1052 newframe.featureSettings_actionPerformed(null);
1053 final FeatureSettings nfs = newframe.featureSettings;
1054 SwingUtilities.invokeLater(new Runnable()
1059 nfs.frame.setBounds(fspos);
1062 this.featureSettings.close();
1063 this.featureSettings = null;
1065 this.closeMenuItem_actionPerformed(true);
1071 public void addFromText_actionPerformed(ActionEvent e)
1074 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1078 public void addFromURL_actionPerformed(ActionEvent e)
1080 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1084 public void save_actionPerformed(ActionEvent e)
1086 if (fileName == null || (currentFileFormat == null)
1087 || fileName.startsWith("http"))
1089 saveAs_actionPerformed(null);
1093 saveAlignment(fileName, currentFileFormat);
1104 public void saveAs_actionPerformed(ActionEvent e)
1106 String format = currentFileFormat == null ? null
1107 : currentFileFormat.getName();
1108 JalviewFileChooser chooser = JalviewFileChooser
1109 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1111 chooser.setFileView(new JalviewFileView());
1112 chooser.setDialogTitle(
1113 MessageManager.getString("label.save_alignment_to_file"));
1114 chooser.setToolTipText(MessageManager.getString("action.save"));
1116 int value = chooser.showSaveDialog(this);
1118 if (value == JalviewFileChooser.APPROVE_OPTION)
1120 currentFileFormat = chooser.getSelectedFormat();
1121 while (currentFileFormat == null)
1123 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1124 MessageManager.getString(
1125 "label.select_file_format_before_saving"),
1126 MessageManager.getString("label.file_format_not_specified"),
1127 JvOptionPane.WARNING_MESSAGE);
1128 currentFileFormat = chooser.getSelectedFormat();
1129 value = chooser.showSaveDialog(this);
1130 if (value != JalviewFileChooser.APPROVE_OPTION)
1136 fileName = chooser.getSelectedFile().getPath();
1138 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1140 Cache.setProperty("LAST_DIRECTORY", fileName);
1141 saveAlignment(fileName, currentFileFormat);
1145 public boolean saveAlignment(String file, FileFormatI format)
1147 boolean success = true;
1149 if (FileFormat.Jalview.equals(format))
1151 String shortName = title;
1153 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1155 shortName = shortName.substring(
1156 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1159 success = new Jalview2XML().saveAlignment(this, file, shortName);
1161 statusBar.setText(MessageManager.formatMessage(
1162 "label.successfully_saved_to_file_in_format", new Object[]
1163 { fileName, format }));
1168 AlignmentExportData exportData = getAlignmentForExport(format,
1170 if (exportData.getSettings().isCancelled())
1174 FormatAdapter f = new FormatAdapter(alignPanel,
1175 exportData.getSettings());
1176 String output = f.formatSequences(format, exportData.getAlignment(), // class
1180 // occur in the distant future
1181 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1182 f.getCacheSuffixDefault(format),
1183 viewport.getAlignment().getHiddenColumns());
1193 PrintWriter out = new PrintWriter(new FileWriter(file));
1197 this.setTitle(file);
1198 statusBar.setText(MessageManager.formatMessage(
1199 "label.successfully_saved_to_file_in_format", new Object[]
1200 { fileName, format.getName() }));
1201 } catch (Exception ex)
1204 ex.printStackTrace();
1211 JvOptionPane.showInternalMessageDialog(this, MessageManager
1212 .formatMessage("label.couldnt_save_file", new Object[]
1214 MessageManager.getString("label.error_saving_file"),
1215 JvOptionPane.WARNING_MESSAGE);
1221 private void warningMessage(String warning, String title)
1223 if (new jalview.util.Platform().isHeadless())
1225 System.err.println("Warning: " + title + "\nWarning: " + warning);
1230 JvOptionPane.showInternalMessageDialog(this, warning, title,
1231 JvOptionPane.WARNING_MESSAGE);
1243 protected void outputText_actionPerformed(ActionEvent e)
1245 FileFormatI fileFormat = FileFormats.getInstance()
1246 .forName(e.getActionCommand());
1247 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1249 if (exportData.getSettings().isCancelled())
1253 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1254 cap.setForInput(null);
1257 FileFormatI format = fileFormat;
1258 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1259 .formatSequences(format, exportData.getAlignment(),
1260 exportData.getOmitHidden(),
1261 exportData.getStartEndPostions(),
1262 viewport.getAlignment().getHiddenColumns()));
1263 Desktop.addInternalFrame(cap, MessageManager
1264 .formatMessage("label.alignment_output_command", new Object[]
1265 { e.getActionCommand() }), 600, 500);
1266 } catch (OutOfMemoryError oom)
1268 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1275 public static AlignmentExportData getAlignmentForExport(
1276 FileFormatI format, AlignViewportI viewport,
1277 AlignExportSettingI exportSettings)
1279 AlignmentI alignmentToExport = null;
1280 AlignExportSettingI settings = exportSettings;
1281 String[] omitHidden = null;
1283 HiddenSequences hiddenSeqs = viewport.getAlignment()
1284 .getHiddenSequences();
1286 alignmentToExport = viewport.getAlignment();
1288 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1289 if (settings == null)
1291 settings = new AlignExportSettings(hasHiddenSeqs,
1292 viewport.hasHiddenColumns(), format);
1294 // settings.isExportAnnotations();
1296 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1298 omitHidden = viewport.getViewAsString(false,
1299 settings.isExportHiddenSequences());
1302 int[] alignmentStartEnd = new int[2];
1303 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1305 alignmentToExport = hiddenSeqs.getFullAlignment();
1309 alignmentToExport = viewport.getAlignment();
1311 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1312 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1313 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1314 omitHidden, alignmentStartEnd, settings);
1325 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1327 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1328 htmlSVG.exportHTML(null);
1332 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1334 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1335 bjs.exportHTML(null);
1338 public void createImageMap(File file, String image)
1340 alignPanel.makePNGImageMap(file, image);
1350 public void createPNG(File f)
1352 alignPanel.makePNG(f);
1362 public void createEPS(File f)
1364 alignPanel.makeEPS(f);
1368 public void createSVG(File f)
1370 alignPanel.makeSVG(f);
1374 public void pageSetup_actionPerformed(ActionEvent e)
1376 PrinterJob printJob = PrinterJob.getPrinterJob();
1377 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1387 public void printMenuItem_actionPerformed(ActionEvent e)
1389 // Putting in a thread avoids Swing painting problems
1390 PrintThread thread = new PrintThread(alignPanel);
1395 public void exportFeatures_actionPerformed(ActionEvent e)
1397 new AnnotationExporter().exportFeatures(alignPanel);
1401 public void exportAnnotations_actionPerformed(ActionEvent e)
1403 new AnnotationExporter().exportAnnotations(alignPanel);
1407 public void associatedData_actionPerformed(ActionEvent e)
1409 // Pick the tree file
1410 JalviewFileChooser chooser = new JalviewFileChooser(
1411 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1412 chooser.setFileView(new JalviewFileView());
1413 chooser.setDialogTitle(
1414 MessageManager.getString("label.load_jalview_annotations"));
1415 chooser.setToolTipText(
1416 MessageManager.getString("label.load_jalview_annotations"));
1418 int value = chooser.showOpenDialog(null);
1420 if (value == JalviewFileChooser.APPROVE_OPTION)
1422 String choice = chooser.getSelectedFile().getPath();
1423 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1424 loadJalviewDataFile(choice, null, null, null);
1430 * Close the current view or all views in the alignment frame. If the frame
1431 * only contains one view then the alignment will be removed from memory.
1433 * @param closeAllTabs
1436 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1438 if (alignPanels != null && alignPanels.size() < 2)
1440 closeAllTabs = true;
1445 if (alignPanels != null)
1449 if (this.isClosed())
1451 // really close all the windows - otherwise wait till
1452 // setClosed(true) is called
1453 for (int i = 0; i < alignPanels.size(); i++)
1455 AlignmentPanel ap = alignPanels.get(i);
1462 closeView(alignPanel);
1469 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1470 * be called recursively, with the frame now in 'closed' state
1472 this.setClosed(true);
1474 } catch (Exception ex)
1476 ex.printStackTrace();
1481 * Close the specified panel and close up tabs appropriately.
1483 * @param panelToClose
1485 public void closeView(AlignmentPanel panelToClose)
1487 int index = tabbedPane.getSelectedIndex();
1488 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1489 alignPanels.remove(panelToClose);
1490 panelToClose.closePanel();
1491 panelToClose = null;
1493 tabbedPane.removeTabAt(closedindex);
1494 tabbedPane.validate();
1496 if (index > closedindex || index == tabbedPane.getTabCount())
1498 // modify currently selected tab index if necessary.
1502 this.tabSelectionChanged(index);
1508 void updateEditMenuBar()
1511 if (viewport.getHistoryList().size() > 0)
1513 undoMenuItem.setEnabled(true);
1514 CommandI command = viewport.getHistoryList().peek();
1515 undoMenuItem.setText(MessageManager
1516 .formatMessage("label.undo_command", new Object[]
1517 { command.getDescription() }));
1521 undoMenuItem.setEnabled(false);
1522 undoMenuItem.setText(MessageManager.getString("action.undo"));
1525 if (viewport.getRedoList().size() > 0)
1527 redoMenuItem.setEnabled(true);
1529 CommandI command = viewport.getRedoList().peek();
1530 redoMenuItem.setText(MessageManager
1531 .formatMessage("label.redo_command", new Object[]
1532 { command.getDescription() }));
1536 redoMenuItem.setEnabled(false);
1537 redoMenuItem.setText(MessageManager.getString("action.redo"));
1542 public void addHistoryItem(CommandI command)
1544 if (command.getSize() > 0)
1546 viewport.addToHistoryList(command);
1547 viewport.clearRedoList();
1548 updateEditMenuBar();
1549 viewport.updateHiddenColumns();
1550 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1551 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1552 // viewport.getColumnSelection()
1553 // .getHiddenColumns().size() > 0);
1559 * @return alignment objects for all views
1561 AlignmentI[] getViewAlignments()
1563 if (alignPanels != null)
1565 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1567 for (AlignmentPanel ap : alignPanels)
1569 als[i++] = ap.av.getAlignment();
1573 if (viewport != null)
1575 return new AlignmentI[] { viewport.getAlignment() };
1587 protected void undoMenuItem_actionPerformed(ActionEvent e)
1589 if (viewport.getHistoryList().isEmpty())
1593 CommandI command = viewport.getHistoryList().pop();
1594 viewport.addToRedoList(command);
1595 command.undoCommand(getViewAlignments());
1597 AlignmentViewport originalSource = getOriginatingSource(command);
1598 updateEditMenuBar();
1600 if (originalSource != null)
1602 if (originalSource != viewport)
1605 "Implementation worry: mismatch of viewport origin for undo");
1607 originalSource.updateHiddenColumns();
1608 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1610 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1611 // viewport.getColumnSelection()
1612 // .getHiddenColumns().size() > 0);
1613 originalSource.firePropertyChange("alignment", null,
1614 originalSource.getAlignment().getSequences());
1625 protected void redoMenuItem_actionPerformed(ActionEvent e)
1627 if (viewport.getRedoList().size() < 1)
1632 CommandI command = viewport.getRedoList().pop();
1633 viewport.addToHistoryList(command);
1634 command.doCommand(getViewAlignments());
1636 AlignmentViewport originalSource = getOriginatingSource(command);
1637 updateEditMenuBar();
1639 if (originalSource != null)
1642 if (originalSource != viewport)
1645 "Implementation worry: mismatch of viewport origin for redo");
1647 originalSource.updateHiddenColumns();
1648 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1650 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1651 // viewport.getColumnSelection()
1652 // .getHiddenColumns().size() > 0);
1653 originalSource.firePropertyChange("alignment", null,
1654 originalSource.getAlignment().getSequences());
1658 AlignmentViewport getOriginatingSource(CommandI command)
1660 AlignmentViewport originalSource = null;
1661 // For sequence removal and addition, we need to fire
1662 // the property change event FROM the viewport where the
1663 // original alignment was altered
1664 AlignmentI al = null;
1665 if (command instanceof EditCommand)
1667 EditCommand editCommand = (EditCommand) command;
1668 al = editCommand.getAlignment();
1669 List<Component> comps = PaintRefresher.components
1670 .get(viewport.getSequenceSetId());
1672 for (Component comp : comps)
1674 if (comp instanceof AlignmentPanel)
1676 if (al == ((AlignmentPanel) comp).av.getAlignment())
1678 originalSource = ((AlignmentPanel) comp).av;
1685 if (originalSource == null)
1687 // The original view is closed, we must validate
1688 // the current view against the closed view first
1691 PaintRefresher.validateSequences(al, viewport.getAlignment());
1694 originalSource = viewport;
1697 return originalSource;
1706 public void moveSelectedSequences(boolean up)
1708 SequenceGroup sg = viewport.getSelectionGroup();
1714 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1715 viewport.getHiddenRepSequences(), up);
1716 alignPanel.paintAlignment(true, false);
1719 synchronized void slideSequences(boolean right, int size)
1721 List<SequenceI> sg = new ArrayList<>();
1722 if (viewport.cursorMode)
1724 sg.add(viewport.getAlignment()
1725 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1727 else if (viewport.getSelectionGroup() != null
1728 && viewport.getSelectionGroup().getSize() != viewport
1729 .getAlignment().getHeight())
1731 sg = viewport.getSelectionGroup()
1732 .getSequences(viewport.getHiddenRepSequences());
1740 List<SequenceI> invertGroup = new ArrayList<>();
1742 for (SequenceI seq : viewport.getAlignment().getSequences())
1744 if (!sg.contains(seq))
1746 invertGroup.add(seq);
1750 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1752 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1753 for (int i = 0; i < invertGroup.size(); i++)
1755 seqs2[i] = invertGroup.get(i);
1758 SlideSequencesCommand ssc;
1761 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1762 viewport.getGapCharacter());
1766 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1767 viewport.getGapCharacter());
1770 int groupAdjustment = 0;
1771 if (ssc.getGapsInsertedBegin() && right)
1773 if (viewport.cursorMode)
1775 alignPanel.getSeqPanel().moveCursor(size, 0);
1779 groupAdjustment = size;
1782 else if (!ssc.getGapsInsertedBegin() && !right)
1784 if (viewport.cursorMode)
1786 alignPanel.getSeqPanel().moveCursor(-size, 0);
1790 groupAdjustment = -size;
1794 if (groupAdjustment != 0)
1796 viewport.getSelectionGroup().setStartRes(
1797 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1798 viewport.getSelectionGroup().setEndRes(
1799 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1803 * just extend the last slide command if compatible; but not if in
1804 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1806 boolean appendHistoryItem = false;
1807 Deque<CommandI> historyList = viewport.getHistoryList();
1808 boolean inSplitFrame = getSplitViewContainer() != null;
1809 if (!inSplitFrame && historyList != null && historyList.size() > 0
1810 && historyList.peek() instanceof SlideSequencesCommand)
1812 appendHistoryItem = ssc.appendSlideCommand(
1813 (SlideSequencesCommand) historyList.peek());
1816 if (!appendHistoryItem)
1818 addHistoryItem(ssc);
1831 protected void copy_actionPerformed(ActionEvent e)
1834 if (viewport.getSelectionGroup() == null)
1838 // TODO: preserve the ordering of displayed alignment annotation in any
1839 // internal paste (particularly sequence associated annotation)
1840 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1841 String[] omitHidden = null;
1843 if (viewport.hasHiddenColumns())
1845 omitHidden = viewport.getViewAsString(true);
1848 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1849 seqs, omitHidden, null);
1851 StringSelection ss = new StringSelection(output);
1855 jalview.gui.Desktop.internalCopy = true;
1856 // Its really worth setting the clipboard contents
1857 // to empty before setting the large StringSelection!!
1858 Toolkit.getDefaultToolkit().getSystemClipboard()
1859 .setContents(new StringSelection(""), null);
1861 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1863 } catch (OutOfMemoryError er)
1865 new OOMWarning("copying region", er);
1869 ArrayList<int[]> hiddenColumns = null;
1870 if (viewport.hasHiddenColumns())
1872 hiddenColumns = new ArrayList<>();
1873 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1874 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1875 ArrayList<int[]> hiddenRegions = viewport.getAlignment()
1876 .getHiddenColumns().getHiddenColumnsCopy();
1877 for (int[] region : hiddenRegions)
1879 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1883 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1888 Desktop.jalviewClipboard = new Object[] { seqs,
1889 viewport.getAlignment().getDataset(), hiddenColumns };
1890 statusBar.setText(MessageManager.formatMessage(
1891 "label.copied_sequences_to_clipboard", new Object[]
1892 { Integer.valueOf(seqs.length).toString() }));
1902 protected void pasteNew_actionPerformed(ActionEvent e)
1914 protected void pasteThis_actionPerformed(ActionEvent e)
1920 * Paste contents of Jalview clipboard
1922 * @param newAlignment
1923 * true to paste to a new alignment, otherwise add to this.
1925 void paste(boolean newAlignment)
1927 boolean externalPaste = true;
1930 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1931 Transferable contents = c.getContents(this);
1933 if (contents == null)
1942 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1943 if (str.length() < 1)
1948 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1950 } catch (OutOfMemoryError er)
1952 new OOMWarning("Out of memory pasting sequences!!", er);
1956 SequenceI[] sequences;
1957 boolean annotationAdded = false;
1958 AlignmentI alignment = null;
1960 if (Desktop.jalviewClipboard != null)
1962 // The clipboard was filled from within Jalview, we must use the
1964 // And dataset from the copied alignment
1965 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1966 // be doubly sure that we create *new* sequence objects.
1967 sequences = new SequenceI[newseq.length];
1968 for (int i = 0; i < newseq.length; i++)
1970 sequences[i] = new Sequence(newseq[i]);
1972 alignment = new Alignment(sequences);
1973 externalPaste = false;
1977 // parse the clipboard as an alignment.
1978 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1980 sequences = alignment.getSequencesArray();
1984 ArrayList<Integer> newGraphGroups = new ArrayList<>();
1990 if (Desktop.jalviewClipboard != null)
1992 // dataset is inherited
1993 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1997 // new dataset is constructed
1998 alignment.setDataset(null);
2000 alwidth = alignment.getWidth() + 1;
2004 AlignmentI pastedal = alignment; // preserve pasted alignment object
2005 // Add pasted sequences and dataset into existing alignment.
2006 alignment = viewport.getAlignment();
2007 alwidth = alignment.getWidth() + 1;
2008 // decide if we need to import sequences from an existing dataset
2009 boolean importDs = Desktop.jalviewClipboard != null
2010 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2011 // importDs==true instructs us to copy over new dataset sequences from
2012 // an existing alignment
2013 Vector newDs = (importDs) ? new Vector() : null; // used to create
2014 // minimum dataset set
2016 for (int i = 0; i < sequences.length; i++)
2020 newDs.addElement(null);
2022 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2024 if (importDs && ds != null)
2026 if (!newDs.contains(ds))
2028 newDs.setElementAt(ds, i);
2029 ds = new Sequence(ds);
2030 // update with new dataset sequence
2031 sequences[i].setDatasetSequence(ds);
2035 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2040 // copy and derive new dataset sequence
2041 sequences[i] = sequences[i].deriveSequence();
2042 alignment.getDataset()
2043 .addSequence(sequences[i].getDatasetSequence());
2044 // TODO: avoid creation of duplicate dataset sequences with a
2045 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2047 alignment.addSequence(sequences[i]); // merges dataset
2051 newDs.clear(); // tidy up
2053 if (alignment.getAlignmentAnnotation() != null)
2055 for (AlignmentAnnotation alan : alignment
2056 .getAlignmentAnnotation())
2058 if (alan.graphGroup > fgroup)
2060 fgroup = alan.graphGroup;
2064 if (pastedal.getAlignmentAnnotation() != null)
2066 // Add any annotation attached to alignment.
2067 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2068 for (int i = 0; i < alann.length; i++)
2070 annotationAdded = true;
2071 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2073 AlignmentAnnotation newann = new AlignmentAnnotation(
2075 if (newann.graphGroup > -1)
2077 if (newGraphGroups.size() <= newann.graphGroup
2078 || newGraphGroups.get(newann.graphGroup) == null)
2080 for (int q = newGraphGroups
2081 .size(); q <= newann.graphGroup; q++)
2083 newGraphGroups.add(q, null);
2085 newGraphGroups.set(newann.graphGroup,
2086 new Integer(++fgroup));
2088 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2092 newann.padAnnotation(alwidth);
2093 alignment.addAnnotation(newann);
2103 addHistoryItem(new EditCommand(
2104 MessageManager.getString("label.add_sequences"),
2105 Action.PASTE, sequences, 0, alignment.getWidth(),
2108 // Add any annotations attached to sequences
2109 for (int i = 0; i < sequences.length; i++)
2111 if (sequences[i].getAnnotation() != null)
2113 AlignmentAnnotation newann;
2114 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2116 annotationAdded = true;
2117 newann = sequences[i].getAnnotation()[a];
2118 newann.adjustForAlignment();
2119 newann.padAnnotation(alwidth);
2120 if (newann.graphGroup > -1)
2122 if (newann.graphGroup > -1)
2124 if (newGraphGroups.size() <= newann.graphGroup
2125 || newGraphGroups.get(newann.graphGroup) == null)
2127 for (int q = newGraphGroups
2128 .size(); q <= newann.graphGroup; q++)
2130 newGraphGroups.add(q, null);
2132 newGraphGroups.set(newann.graphGroup,
2133 new Integer(++fgroup));
2135 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2139 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2143 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2151 // propagate alignment changed.
2152 viewport.getRanges().setEndSeq(alignment.getHeight());
2153 if (annotationAdded)
2155 // Duplicate sequence annotation in all views.
2156 AlignmentI[] alview = this.getViewAlignments();
2157 for (int i = 0; i < sequences.length; i++)
2159 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2164 for (int avnum = 0; avnum < alview.length; avnum++)
2166 if (alview[avnum] != alignment)
2168 // duplicate in a view other than the one with input focus
2169 int avwidth = alview[avnum].getWidth() + 1;
2170 // this relies on sann being preserved after we
2171 // modify the sequence's annotation array for each duplication
2172 for (int a = 0; a < sann.length; a++)
2174 AlignmentAnnotation newann = new AlignmentAnnotation(
2176 sequences[i].addAlignmentAnnotation(newann);
2177 newann.padAnnotation(avwidth);
2178 alview[avnum].addAnnotation(newann); // annotation was
2179 // duplicated earlier
2180 // TODO JAL-1145 graphGroups are not updated for sequence
2181 // annotation added to several views. This may cause
2183 alview[avnum].setAnnotationIndex(newann, a);
2188 buildSortByAnnotationScoresMenu();
2190 viewport.firePropertyChange("alignment", null,
2191 alignment.getSequences());
2192 if (alignPanels != null)
2194 for (AlignmentPanel ap : alignPanels)
2196 ap.validateAnnotationDimensions(false);
2201 alignPanel.validateAnnotationDimensions(false);
2207 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2209 String newtitle = new String("Copied sequences");
2211 if (Desktop.jalviewClipboard != null
2212 && Desktop.jalviewClipboard[2] != null)
2214 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2215 for (int[] region : hc)
2217 af.viewport.hideColumns(region[0], region[1]);
2221 // >>>This is a fix for the moment, until a better solution is
2223 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2224 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2225 .getFeatureRenderer());
2227 // TODO: maintain provenance of an alignment, rather than just make the
2228 // title a concatenation of operations.
2231 if (title.startsWith("Copied sequences"))
2237 newtitle = newtitle.concat("- from " + title);
2242 newtitle = new String("Pasted sequences");
2245 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2250 } catch (Exception ex)
2252 ex.printStackTrace();
2253 System.out.println("Exception whilst pasting: " + ex);
2254 // could be anything being pasted in here
2260 protected void expand_newalign(ActionEvent e)
2264 AlignmentI alignment = AlignmentUtils
2265 .expandContext(getViewport().getAlignment(), -1);
2266 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2268 String newtitle = new String("Flanking alignment");
2270 if (Desktop.jalviewClipboard != null
2271 && Desktop.jalviewClipboard[2] != null)
2273 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2274 for (int region[] : hc)
2276 af.viewport.hideColumns(region[0], region[1]);
2280 // >>>This is a fix for the moment, until a better solution is
2282 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2283 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2284 .getFeatureRenderer());
2286 // TODO: maintain provenance of an alignment, rather than just make the
2287 // title a concatenation of operations.
2289 if (title.startsWith("Copied sequences"))
2295 newtitle = newtitle.concat("- from " + title);
2299 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2301 } catch (Exception ex)
2303 ex.printStackTrace();
2304 System.out.println("Exception whilst pasting: " + ex);
2305 // could be anything being pasted in here
2306 } catch (OutOfMemoryError oom)
2308 new OOMWarning("Viewing flanking region of alignment", oom);
2319 protected void cut_actionPerformed(ActionEvent e)
2321 copy_actionPerformed(null);
2322 delete_actionPerformed(null);
2332 protected void delete_actionPerformed(ActionEvent evt)
2335 SequenceGroup sg = viewport.getSelectionGroup();
2342 * If the cut affects all sequences, warn, remove highlighted columns
2344 if (sg.getSize() == viewport.getAlignment().getHeight())
2346 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2347 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2348 if (isEntireAlignWidth)
2350 int confirm = JvOptionPane.showConfirmDialog(this,
2351 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2352 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2353 JvOptionPane.OK_CANCEL_OPTION);
2355 if (confirm == JvOptionPane.CANCEL_OPTION
2356 || confirm == JvOptionPane.CLOSED_OPTION)
2361 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2362 sg.getEndRes() + 1);
2364 SequenceI[] cut = sg.getSequences()
2365 .toArray(new SequenceI[sg.getSize()]);
2367 addHistoryItem(new EditCommand(
2368 MessageManager.getString("label.cut_sequences"), Action.CUT,
2369 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2370 viewport.getAlignment()));
2372 viewport.setSelectionGroup(null);
2373 viewport.sendSelection();
2374 viewport.getAlignment().deleteGroup(sg);
2376 viewport.firePropertyChange("alignment", null,
2377 viewport.getAlignment().getSequences());
2378 if (viewport.getAlignment().getHeight() < 1)
2382 this.setClosed(true);
2383 } catch (Exception ex)
2396 protected void deleteGroups_actionPerformed(ActionEvent e)
2398 if (avc.deleteGroups())
2400 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2401 alignPanel.updateAnnotation();
2402 alignPanel.paintAlignment(true, true);
2413 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2415 SequenceGroup sg = new SequenceGroup();
2417 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2419 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2422 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2423 viewport.setSelectionGroup(sg);
2424 viewport.sendSelection();
2425 // JAL-2034 - should delegate to
2426 // alignPanel to decide if overview needs
2428 alignPanel.paintAlignment(false, false);
2429 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2439 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2441 if (viewport.cursorMode)
2443 alignPanel.getSeqPanel().keyboardNo1 = null;
2444 alignPanel.getSeqPanel().keyboardNo2 = null;
2446 viewport.setSelectionGroup(null);
2447 viewport.getColumnSelection().clear();
2448 viewport.setSelectionGroup(null);
2449 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2450 // JAL-2034 - should delegate to
2451 // alignPanel to decide if overview needs
2453 alignPanel.paintAlignment(false, false);
2454 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2455 viewport.sendSelection();
2465 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2467 SequenceGroup sg = viewport.getSelectionGroup();
2471 selectAllSequenceMenuItem_actionPerformed(null);
2476 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2478 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2480 // JAL-2034 - should delegate to
2481 // alignPanel to decide if overview needs
2484 alignPanel.paintAlignment(true, false);
2485 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2486 viewport.sendSelection();
2490 public void invertColSel_actionPerformed(ActionEvent e)
2492 viewport.invertColumnSelection();
2493 alignPanel.paintAlignment(true, false);
2494 viewport.sendSelection();
2504 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2506 trimAlignment(true);
2516 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2518 trimAlignment(false);
2521 void trimAlignment(boolean trimLeft)
2523 ColumnSelection colSel = viewport.getColumnSelection();
2526 if (!colSel.isEmpty())
2530 column = colSel.getMin();
2534 column = colSel.getMax();
2538 if (viewport.getSelectionGroup() != null)
2540 seqs = viewport.getSelectionGroup()
2541 .getSequencesAsArray(viewport.getHiddenRepSequences());
2545 seqs = viewport.getAlignment().getSequencesArray();
2548 TrimRegionCommand trimRegion;
2551 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2552 column, viewport.getAlignment());
2553 viewport.getRanges().setStartRes(0);
2557 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2558 column, viewport.getAlignment());
2561 statusBar.setText(MessageManager
2562 .formatMessage("label.removed_columns", new String[]
2563 { Integer.valueOf(trimRegion.getSize()).toString() }));
2565 addHistoryItem(trimRegion);
2567 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2569 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2570 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2572 viewport.getAlignment().deleteGroup(sg);
2576 viewport.firePropertyChange("alignment", null,
2577 viewport.getAlignment().getSequences());
2588 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2590 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2593 if (viewport.getSelectionGroup() != null)
2595 seqs = viewport.getSelectionGroup()
2596 .getSequencesAsArray(viewport.getHiddenRepSequences());
2597 start = viewport.getSelectionGroup().getStartRes();
2598 end = viewport.getSelectionGroup().getEndRes();
2602 seqs = viewport.getAlignment().getSequencesArray();
2605 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2606 "Remove Gapped Columns", seqs, start, end,
2607 viewport.getAlignment());
2609 addHistoryItem(removeGapCols);
2611 statusBar.setText(MessageManager
2612 .formatMessage("label.removed_empty_columns", new Object[]
2613 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2615 // This is to maintain viewport position on first residue
2616 // of first sequence
2617 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2618 ViewportRanges ranges = viewport.getRanges();
2619 int startRes = seq.findPosition(ranges.getStartRes());
2620 // ShiftList shifts;
2621 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2622 // edit.alColumnChanges=shifts.getInverse();
2623 // if (viewport.hasHiddenColumns)
2624 // viewport.getColumnSelection().compensateForEdits(shifts);
2625 ranges.setStartRes(seq.findIndex(startRes) - 1);
2626 viewport.firePropertyChange("alignment", null,
2627 viewport.getAlignment().getSequences());
2638 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2640 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2643 if (viewport.getSelectionGroup() != null)
2645 seqs = viewport.getSelectionGroup()
2646 .getSequencesAsArray(viewport.getHiddenRepSequences());
2647 start = viewport.getSelectionGroup().getStartRes();
2648 end = viewport.getSelectionGroup().getEndRes();
2652 seqs = viewport.getAlignment().getSequencesArray();
2655 // This is to maintain viewport position on first residue
2656 // of first sequence
2657 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2658 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2660 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2661 viewport.getAlignment()));
2663 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2665 viewport.firePropertyChange("alignment", null,
2666 viewport.getAlignment().getSequences());
2677 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2679 viewport.setPadGaps(padGapsMenuitem.isSelected());
2680 viewport.firePropertyChange("alignment", null,
2681 viewport.getAlignment().getSequences());
2691 public void findMenuItem_actionPerformed(ActionEvent e)
2697 * Create a new view of the current alignment.
2700 public void newView_actionPerformed(ActionEvent e)
2702 newView(null, true);
2706 * Creates and shows a new view of the current alignment.
2709 * title of newly created view; if null, one will be generated
2710 * @param copyAnnotation
2711 * if true then duplicate all annnotation, groups and settings
2712 * @return new alignment panel, already displayed.
2714 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2717 * Create a new AlignmentPanel (with its own, new Viewport)
2719 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2720 if (!copyAnnotation)
2723 * remove all groups and annotation except for the automatic stuff
2725 newap.av.getAlignment().deleteAllGroups();
2726 newap.av.getAlignment().deleteAllAnnotations(false);
2729 newap.av.setGatherViewsHere(false);
2731 if (viewport.viewName == null)
2733 viewport.viewName = MessageManager
2734 .getString("label.view_name_original");
2738 * Views share the same edits undo and redo stacks
2740 newap.av.setHistoryList(viewport.getHistoryList());
2741 newap.av.setRedoList(viewport.getRedoList());
2744 * Views share the same mappings; need to deregister any new mappings
2745 * created by copyAlignPanel, and register the new reference to the shared
2748 newap.av.replaceMappings(viewport.getAlignment());
2751 * start up cDNA consensus (if applicable) now mappings are in place
2753 if (newap.av.initComplementConsensus())
2755 newap.refresh(true); // adjust layout of annotations
2758 newap.av.viewName = getNewViewName(viewTitle);
2760 addAlignmentPanel(newap, true);
2761 newap.alignmentChanged();
2763 if (alignPanels.size() == 2)
2765 viewport.setGatherViewsHere(true);
2767 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2772 * Make a new name for the view, ensuring it is unique within the current
2773 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2774 * these now use viewId. Unique view names are still desirable for usability.)
2779 protected String getNewViewName(String viewTitle)
2781 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2782 boolean addFirstIndex = false;
2783 if (viewTitle == null || viewTitle.trim().length() == 0)
2785 viewTitle = MessageManager.getString("action.view");
2786 addFirstIndex = true;
2790 index = 1;// we count from 1 if given a specific name
2792 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2794 List<Component> comps = PaintRefresher.components
2795 .get(viewport.getSequenceSetId());
2797 List<String> existingNames = getExistingViewNames(comps);
2799 while (existingNames.contains(newViewName))
2801 newViewName = viewTitle + " " + (++index);
2807 * Returns a list of distinct view names found in the given list of
2808 * components. View names are held on the viewport of an AlignmentPanel.
2813 protected List<String> getExistingViewNames(List<Component> comps)
2815 List<String> existingNames = new ArrayList<>();
2816 for (Component comp : comps)
2818 if (comp instanceof AlignmentPanel)
2820 AlignmentPanel ap = (AlignmentPanel) comp;
2821 if (!existingNames.contains(ap.av.viewName))
2823 existingNames.add(ap.av.viewName);
2827 return existingNames;
2831 * Explode tabbed views into separate windows.
2834 public void expandViews_actionPerformed(ActionEvent e)
2836 Desktop.explodeViews(this);
2840 * Gather views in separate windows back into a tabbed presentation.
2843 public void gatherViews_actionPerformed(ActionEvent e)
2845 Desktop.instance.gatherViews(this);
2855 public void font_actionPerformed(ActionEvent e)
2857 new FontChooser(alignPanel);
2867 protected void seqLimit_actionPerformed(ActionEvent e)
2869 viewport.setShowJVSuffix(seqLimits.isSelected());
2871 alignPanel.getIdPanel().getIdCanvas()
2872 .setPreferredSize(alignPanel.calculateIdWidth());
2873 alignPanel.paintAlignment(true, false);
2877 public void idRightAlign_actionPerformed(ActionEvent e)
2879 viewport.setRightAlignIds(idRightAlign.isSelected());
2880 alignPanel.paintAlignment(false, false);
2884 public void centreColumnLabels_actionPerformed(ActionEvent e)
2886 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2887 alignPanel.paintAlignment(false, false);
2893 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2896 protected void followHighlight_actionPerformed()
2899 * Set the 'follow' flag on the Viewport (and scroll to position if now
2902 final boolean state = this.followHighlightMenuItem.getState();
2903 viewport.setFollowHighlight(state);
2906 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2917 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2919 viewport.setColourText(colourTextMenuItem.isSelected());
2920 alignPanel.paintAlignment(false, false);
2930 public void wrapMenuItem_actionPerformed(ActionEvent e)
2932 scaleAbove.setVisible(wrapMenuItem.isSelected());
2933 scaleLeft.setVisible(wrapMenuItem.isSelected());
2934 scaleRight.setVisible(wrapMenuItem.isSelected());
2935 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2936 alignPanel.updateLayout();
2940 public void showAllSeqs_actionPerformed(ActionEvent e)
2942 viewport.showAllHiddenSeqs();
2946 public void showAllColumns_actionPerformed(ActionEvent e)
2948 viewport.showAllHiddenColumns();
2949 alignPanel.paintAlignment(true, true);
2950 viewport.sendSelection();
2954 public void hideSelSequences_actionPerformed(ActionEvent e)
2956 viewport.hideAllSelectedSeqs();
2960 * called by key handler and the hide all/show all menu items
2965 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2968 boolean hide = false;
2969 SequenceGroup sg = viewport.getSelectionGroup();
2970 if (!toggleSeqs && !toggleCols)
2972 // Hide everything by the current selection - this is a hack - we do the
2973 // invert and then hide
2974 // first check that there will be visible columns after the invert.
2975 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2976 && sg.getStartRes() <= sg.getEndRes()))
2978 // now invert the sequence set, if required - empty selection implies
2979 // that no hiding is required.
2982 invertSequenceMenuItem_actionPerformed(null);
2983 sg = viewport.getSelectionGroup();
2987 viewport.expandColSelection(sg, true);
2988 // finally invert the column selection and get the new sequence
2990 invertColSel_actionPerformed(null);
2997 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2999 hideSelSequences_actionPerformed(null);
3002 else if (!(toggleCols && viewport.hasSelectedColumns()))
3004 showAllSeqs_actionPerformed(null);
3010 if (viewport.hasSelectedColumns())
3012 hideSelColumns_actionPerformed(null);
3015 viewport.setSelectionGroup(sg);
3020 showAllColumns_actionPerformed(null);
3029 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3030 * event.ActionEvent)
3033 public void hideAllButSelection_actionPerformed(ActionEvent e)
3035 toggleHiddenRegions(false, false);
3036 viewport.sendSelection();
3043 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3047 public void hideAllSelection_actionPerformed(ActionEvent e)
3049 SequenceGroup sg = viewport.getSelectionGroup();
3050 viewport.expandColSelection(sg, false);
3051 viewport.hideAllSelectedSeqs();
3052 viewport.hideSelectedColumns();
3053 alignPanel.paintAlignment(true, true);
3054 viewport.sendSelection();
3061 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3065 public void showAllhidden_actionPerformed(ActionEvent e)
3067 viewport.showAllHiddenColumns();
3068 viewport.showAllHiddenSeqs();
3069 alignPanel.paintAlignment(true, true);
3070 viewport.sendSelection();
3074 public void hideSelColumns_actionPerformed(ActionEvent e)
3076 viewport.hideSelectedColumns();
3077 alignPanel.paintAlignment(true, true);
3078 viewport.sendSelection();
3082 public void hiddenMarkers_actionPerformed(ActionEvent e)
3084 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3095 protected void scaleAbove_actionPerformed(ActionEvent e)
3097 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3098 // TODO: do we actually need to update overview for scale above change ?
3099 alignPanel.paintAlignment(true, false);
3109 protected void scaleLeft_actionPerformed(ActionEvent e)
3111 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3112 alignPanel.paintAlignment(true, false);
3122 protected void scaleRight_actionPerformed(ActionEvent e)
3124 viewport.setScaleRightWrapped(scaleRight.isSelected());
3125 alignPanel.paintAlignment(true, false);
3135 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3137 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3138 alignPanel.paintAlignment(false, false);
3148 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3150 viewport.setShowText(viewTextMenuItem.isSelected());
3151 alignPanel.paintAlignment(false, false);
3161 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3163 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3164 alignPanel.paintAlignment(false, false);
3167 public FeatureSettings featureSettings;
3170 public FeatureSettingsControllerI getFeatureSettingsUI()
3172 return featureSettings;
3176 public void featureSettings_actionPerformed(ActionEvent e)
3178 if (featureSettings != null)
3180 featureSettings.close();
3181 featureSettings = null;
3183 if (!showSeqFeatures.isSelected())
3185 // make sure features are actually displayed
3186 showSeqFeatures.setSelected(true);
3187 showSeqFeatures_actionPerformed(null);
3189 featureSettings = new FeatureSettings(this);
3193 * Set or clear 'Show Sequence Features'
3199 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3201 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3202 alignPanel.paintAlignment(true, true);
3206 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3207 * the annotations panel as a whole.
3209 * The options to show/hide all annotations should be enabled when the panel
3210 * is shown, and disabled when the panel is hidden.
3215 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3217 final boolean setVisible = annotationPanelMenuItem.isSelected();
3218 viewport.setShowAnnotation(setVisible);
3219 this.showAllSeqAnnotations.setEnabled(setVisible);
3220 this.hideAllSeqAnnotations.setEnabled(setVisible);
3221 this.showAllAlAnnotations.setEnabled(setVisible);
3222 this.hideAllAlAnnotations.setEnabled(setVisible);
3223 alignPanel.updateLayout();
3227 public void alignmentProperties()
3229 JEditorPane editPane = new JEditorPane("text/html", "");
3230 editPane.setEditable(false);
3231 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3234 MessageManager.formatMessage("label.html_content", new Object[]
3235 { contents.toString() }));
3236 JInternalFrame frame = new JInternalFrame();
3237 frame.getContentPane().add(new JScrollPane(editPane));
3239 Desktop.addInternalFrame(frame, MessageManager
3240 .formatMessage("label.alignment_properties", new Object[]
3241 { getTitle() }), 500, 400);
3251 public void overviewMenuItem_actionPerformed(ActionEvent e)
3253 if (alignPanel.overviewPanel != null)
3258 JInternalFrame frame = new JInternalFrame();
3259 final OverviewPanel overview = new OverviewPanel(alignPanel);
3260 frame.setContentPane(overview);
3261 Desktop.addInternalFrame(frame, MessageManager
3262 .formatMessage("label.overview_params", new Object[]
3263 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3266 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3267 frame.addInternalFrameListener(
3268 new javax.swing.event.InternalFrameAdapter()
3271 public void internalFrameClosed(
3272 javax.swing.event.InternalFrameEvent evt)
3275 alignPanel.setOverviewPanel(null);
3279 alignPanel.setOverviewPanel(overview);
3283 public void textColour_actionPerformed()
3285 new TextColourChooser().chooseColour(alignPanel, null);
3289 * public void covariationColour_actionPerformed() {
3291 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3295 public void annotationColour_actionPerformed()
3297 new AnnotationColourChooser(viewport, alignPanel);
3301 public void annotationColumn_actionPerformed(ActionEvent e)
3303 new AnnotationColumnChooser(viewport, alignPanel);
3307 * Action on the user checking or unchecking the option to apply the selected
3308 * colour scheme to all groups. If unchecked, groups may have their own
3309 * independent colour schemes.
3314 public void applyToAllGroups_actionPerformed(boolean selected)
3316 viewport.setColourAppliesToAllGroups(selected);
3320 * Action on user selecting a colour from the colour menu
3323 * the name (not the menu item label!) of the colour scheme
3326 public void changeColour_actionPerformed(String name)
3329 * 'User Defined' opens a panel to configure or load a
3330 * user-defined colour scheme
3332 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3334 new UserDefinedColours(alignPanel);
3339 * otherwise set the chosen colour scheme (or null for 'None')
3341 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3342 viewport.getAlignment(), viewport.getHiddenRepSequences());
3347 * Actions on setting or changing the alignment colour scheme
3352 public void changeColour(ColourSchemeI cs)
3354 // TODO: pull up to controller method
3355 ColourMenuHelper.setColourSelected(colourMenu, cs);
3357 viewport.setGlobalColourScheme(cs);
3359 alignPanel.paintAlignment(true, true);
3363 * Show the PID threshold slider panel
3366 protected void modifyPID_actionPerformed()
3368 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3369 alignPanel.getViewName());
3370 SliderPanel.showPIDSlider();
3374 * Show the Conservation slider panel
3377 protected void modifyConservation_actionPerformed()
3379 SliderPanel.setConservationSlider(alignPanel,
3380 viewport.getResidueShading(), alignPanel.getViewName());
3381 SliderPanel.showConservationSlider();
3385 * Action on selecting or deselecting (Colour) By Conservation
3388 public void conservationMenuItem_actionPerformed(boolean selected)
3390 modifyConservation.setEnabled(selected);
3391 viewport.setConservationSelected(selected);
3392 viewport.getResidueShading().setConservationApplied(selected);
3394 changeColour(viewport.getGlobalColourScheme());
3397 modifyConservation_actionPerformed();
3401 SliderPanel.hideConservationSlider();
3406 * Action on selecting or deselecting (Colour) Above PID Threshold
3409 public void abovePIDThreshold_actionPerformed(boolean selected)
3411 modifyPID.setEnabled(selected);
3412 viewport.setAbovePIDThreshold(selected);
3415 viewport.getResidueShading().setThreshold(0,
3416 viewport.isIgnoreGapsConsensus());
3419 changeColour(viewport.getGlobalColourScheme());
3422 modifyPID_actionPerformed();
3426 SliderPanel.hidePIDSlider();
3437 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3439 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3440 AlignmentSorter.sortByPID(viewport.getAlignment(),
3441 viewport.getAlignment().getSequenceAt(0));
3442 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3443 viewport.getAlignment()));
3444 alignPanel.paintAlignment(true, false);
3454 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3456 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3457 AlignmentSorter.sortByID(viewport.getAlignment());
3459 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3460 alignPanel.paintAlignment(true, false);
3470 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3472 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3473 AlignmentSorter.sortByLength(viewport.getAlignment());
3474 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3475 viewport.getAlignment()));
3476 alignPanel.paintAlignment(true, false);
3486 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3488 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3489 AlignmentSorter.sortByGroup(viewport.getAlignment());
3490 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3491 viewport.getAlignment()));
3493 alignPanel.paintAlignment(true, false);
3503 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3505 new RedundancyPanel(alignPanel, this);
3515 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3517 if ((viewport.getSelectionGroup() == null)
3518 || (viewport.getSelectionGroup().getSize() < 2))
3520 JvOptionPane.showInternalMessageDialog(this,
3521 MessageManager.getString(
3522 "label.you_must_select_least_two_sequences"),
3523 MessageManager.getString("label.invalid_selection"),
3524 JvOptionPane.WARNING_MESSAGE);
3528 JInternalFrame frame = new JInternalFrame();
3529 frame.setContentPane(new PairwiseAlignPanel(viewport));
3530 Desktop.addInternalFrame(frame,
3531 MessageManager.getString("action.pairwise_alignment"), 600,
3537 public void autoCalculate_actionPerformed(ActionEvent e)
3539 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3540 if (viewport.autoCalculateConsensus)
3542 viewport.firePropertyChange("alignment", null,
3543 viewport.getAlignment().getSequences());
3548 public void sortByTreeOption_actionPerformed(ActionEvent e)
3550 viewport.sortByTree = sortByTree.isSelected();
3554 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3556 viewport.followSelection = listenToViewSelections.isSelected();
3560 * Constructs a tree panel and adds it to the desktop
3569 void newTreePanel(TreeModel tree, String treeAlgo,
3570 String substitutionMatrix)
3572 String frameTitle = "";
3575 boolean onSelection = false;
3576 if (viewport.getSelectionGroup() != null
3577 && viewport.getSelectionGroup().getSize() > 0)
3579 SequenceGroup sg = viewport.getSelectionGroup();
3581 /* Decide if the selection is a column region */
3582 for (SequenceI _s : sg.getSequences()) // port this to Archaeopteryx?
3584 if (_s.getLength() < sg.getEndRes())
3586 JvOptionPane.showMessageDialog(Desktop.desktop,
3587 MessageManager.getString(
3588 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3589 MessageManager.getString(
3590 "label.sequences_selection_not_aligned"),
3591 JvOptionPane.WARNING_MESSAGE);
3600 if (viewport.getAlignment().getHeight() < 2)
3606 tp = new TreePanel(alignPanel, tree, treeAlgo, substitutionMatrix);
3607 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3609 frameTitle += " from ";
3611 if (viewport.viewName != null)
3613 frameTitle += viewport.viewName + " of ";
3616 frameTitle += this.title;
3618 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3629 public void addSortByOrderMenuItem(String title,
3630 final AlignmentOrder order)
3632 final JMenuItem item = new JMenuItem(MessageManager
3633 .formatMessage("action.by_title_param", new Object[]
3636 item.addActionListener(new java.awt.event.ActionListener()
3639 public void actionPerformed(ActionEvent e)
3641 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3643 // TODO: JBPNote - have to map order entries to curent SequenceI
3645 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3647 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3648 viewport.getAlignment()));
3650 alignPanel.paintAlignment(true, false);
3656 * Add a new sort by annotation score menu item
3659 * the menu to add the option to
3661 * the label used to retrieve scores for each sequence on the
3664 public void addSortByAnnotScoreMenuItem(JMenu sort,
3665 final String scoreLabel)
3667 final JMenuItem item = new JMenuItem(scoreLabel);
3669 item.addActionListener(new java.awt.event.ActionListener()
3672 public void actionPerformed(ActionEvent e)
3674 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3675 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3676 viewport.getAlignment());// ,viewport.getSelectionGroup());
3677 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3678 viewport.getAlignment()));
3679 alignPanel.paintAlignment(true, false);
3685 * last hash for alignment's annotation array - used to minimise cost of
3688 protected int _annotationScoreVectorHash;
3691 * search the alignment and rebuild the sort by annotation score submenu the
3692 * last alignment annotation vector hash is stored to minimize cost of
3693 * rebuilding in subsequence calls.
3697 public void buildSortByAnnotationScoresMenu()
3699 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3704 if (viewport.getAlignment().getAlignmentAnnotation()
3705 .hashCode() != _annotationScoreVectorHash)
3707 sortByAnnotScore.removeAll();
3708 // almost certainly a quicker way to do this - but we keep it simple
3709 Hashtable scoreSorts = new Hashtable();
3710 AlignmentAnnotation aann[];
3711 for (SequenceI sqa : viewport.getAlignment().getSequences())
3713 aann = sqa.getAnnotation();
3714 for (int i = 0; aann != null && i < aann.length; i++)
3716 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3718 scoreSorts.put(aann[i].label, aann[i].label);
3722 Enumeration labels = scoreSorts.keys();
3723 while (labels.hasMoreElements())
3725 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3726 (String) labels.nextElement());
3728 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3731 _annotationScoreVectorHash = viewport.getAlignment()
3732 .getAlignmentAnnotation().hashCode();
3737 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3738 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3739 * call. Listeners are added to remove the menu item when the treePanel is
3740 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3744 public void buildTreeSortMenu()
3746 sortByTreeMenu.removeAll();
3748 List<Component> comps = PaintRefresher.components
3749 .get(viewport.getSequenceSetId());
3750 List<TreePanel> treePanels = new ArrayList<>();
3751 for (Component comp : comps)
3753 if (comp instanceof TreePanel)
3755 treePanels.add((TreePanel) comp);
3759 if (treePanels.size() < 1)
3761 sortByTreeMenu.setVisible(false);
3765 sortByTreeMenu.setVisible(true);
3767 for (final TreePanel tp : treePanels)
3769 final JMenuItem item = new JMenuItem(tp.getTitle());
3770 item.addActionListener(new java.awt.event.ActionListener()
3773 public void actionPerformed(ActionEvent e)
3776 tp.sortByTree_actionPerformed();
3777 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3782 sortByTreeMenu.add(item);
3786 public boolean sortBy(AlignmentOrder alorder, String undoname)
3788 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3789 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3790 if (undoname != null)
3792 addHistoryItem(new OrderCommand(undoname, oldOrder,
3793 viewport.getAlignment()));
3795 alignPanel.paintAlignment(true, false);
3800 * Work out whether the whole set of sequences or just the selected set will
3801 * be submitted for multiple alignment.
3804 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3806 // Now, check we have enough sequences
3807 AlignmentView msa = null;
3809 if ((viewport.getSelectionGroup() != null)
3810 && (viewport.getSelectionGroup().getSize() > 1))
3812 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3813 // some common interface!
3815 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3816 * SequenceI[sz = seqs.getSize(false)];
3818 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3819 * seqs.getSequenceAt(i); }
3821 msa = viewport.getAlignmentView(true);
3823 else if (viewport.getSelectionGroup() != null
3824 && viewport.getSelectionGroup().getSize() == 1)
3826 int option = JvOptionPane.showConfirmDialog(this,
3827 MessageManager.getString("warn.oneseq_msainput_selection"),
3828 MessageManager.getString("label.invalid_selection"),
3829 JvOptionPane.OK_CANCEL_OPTION);
3830 if (option == JvOptionPane.OK_OPTION)
3832 msa = viewport.getAlignmentView(false);
3837 msa = viewport.getAlignmentView(false);
3843 * Decides what is submitted to a secondary structure prediction service: the
3844 * first sequence in the alignment, or in the current selection, or, if the
3845 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3846 * region or the whole alignment. (where the first sequence in the set is the
3847 * one that the prediction will be for).
3849 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3851 AlignmentView seqs = null;
3853 if ((viewport.getSelectionGroup() != null)
3854 && (viewport.getSelectionGroup().getSize() > 0))
3856 seqs = viewport.getAlignmentView(true);
3860 seqs = viewport.getAlignmentView(false);
3862 // limit sequences - JBPNote in future - could spawn multiple prediction
3864 // TODO: viewport.getAlignment().isAligned is a global state - the local
3865 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3866 if (!viewport.getAlignment().isAligned(false))
3868 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3869 // TODO: if seqs.getSequences().length>1 then should really have warned
3875 public void chooseTreeFile() {
3876 // Pick the tree file
3877 JalviewFileChooser chooser = new JalviewFileChooser(
3878 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3879 chooser.setFileView(new JalviewFileView());
3880 chooser.setDialogTitle(
3881 MessageManager.getString("label.select_newick_like_tree_file")); // modify
3882 chooser.setToolTipText(
3883 MessageManager.getString("label.load_tree_for_sequence_set"));
3884 for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter
3887 chooser.setFileFilter(treeFormat.getTreeFilter());
3890 int value = chooser.showOpenDialog(null);
3892 if (value == JalviewFileChooser.APPROVE_OPTION)
3894 String filePath = chooser.getSelectedFile().getPath();
3895 Cache.setProperty("LAST_DIRECTORY", filePath);
3897 TreeParser treeParser = new TreeParser(filePath);
3898 treeParser.loadTree(viewport);
3903 public void chooseTreeUrl()
3907 String urlString = JvOptionPane.showInputDialog(this,
3908 MessageManager.getString("label.tree_url_example"),
3909 MessageManager.getString("label.load_tree_url"),
3910 JvOptionPane.QUESTION_MESSAGE);
3911 if ((urlString != null) && (!urlString.isEmpty()))
3915 treeUrl = new URL(urlString);
3916 AptxInit.createInstanceFromUrl(treeUrl);
3918 } catch (MalformedURLException e)
3920 JvOptionPane.showMessageDialog(this,
3921 MessageManager.formatMessage(
3922 "exception.failed_to_read_data_from_source",
3925 MessageManager.getString("label.url_not_found")
3926 , JvOptionPane.ERROR_MESSAGE);
3932 // final String url_string = JOptionPane
3933 // .showInputDialog( this,
3935 // "Use URL/webservice to obtain a phylogeny",
3936 // JOptionPane.QUESTION_MESSAGE );
3937 // boolean nhx_or_nexus = false;
3938 // if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
3940 // url = new URL( url_string );
3950 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3956 protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
3962 protected void loadTreeDbItem_actionPerformed(ActionEvent e)
3967 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3969 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3972 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3973 int h, int x, int y)
3975 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3979 * Add a treeviewer for the tree extracted from a Newick file object to the
3980 * current alignment view
3987 * Associated alignment input data (or null)
3996 * @return TreePanel handle
3998 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3999 AlignmentView input, int w, int h, int x, int y)
4001 TreePanel tp = null;
4007 if (nf.getTree() != null)
4009 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4015 tp.setLocation(x, y);
4018 Desktop.addInternalFrame(tp, treeTitle, w, h);
4020 } catch (Exception ex)
4022 ex.printStackTrace();
4028 private boolean buildingMenu = false;
4031 * Generates menu items and listener event actions for web service clients
4034 public void BuildWebServiceMenu()
4036 while (buildingMenu)
4040 System.err.println("Waiting for building menu to finish.");
4042 } catch (Exception e)
4046 final AlignFrame me = this;
4047 buildingMenu = true;
4048 new Thread(new Runnable()
4053 final List<JMenuItem> legacyItems = new ArrayList<>();
4056 // System.err.println("Building ws menu again "
4057 // + Thread.currentThread());
4058 // TODO: add support for context dependent disabling of services based
4060 // alignment and current selection
4061 // TODO: add additional serviceHandle parameter to specify abstract
4063 // class independently of AbstractName
4064 // TODO: add in rediscovery GUI function to restart discoverer
4065 // TODO: group services by location as well as function and/or
4067 // object broker mechanism.
4068 final Vector<JMenu> wsmenu = new Vector<>();
4069 final IProgressIndicator af = me;
4072 * do not i18n these strings - they are hard-coded in class
4073 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4074 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4076 final JMenu msawsmenu = new JMenu("Alignment");
4077 final JMenu secstrmenu = new JMenu(
4078 "Secondary Structure Prediction");
4079 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4080 final JMenu analymenu = new JMenu("Analysis");
4081 final JMenu dismenu = new JMenu("Protein Disorder");
4082 final JMenu phylogenmenu = new JMenu("Phylogenetic inference");
4084 // JAL-940 - only show secondary structure prediction services from
4085 // the legacy server
4086 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4088 Discoverer.services != null && (Discoverer.services.size() > 0))
4090 // TODO: refactor to allow list of AbstractName/Handler bindings to
4092 // stored or retrieved from elsewhere
4093 // No MSAWS used any more:
4094 // Vector msaws = null; // (Vector)
4095 // Discoverer.services.get("MsaWS");
4096 Vector secstrpr = (Vector) Discoverer.services
4098 if (secstrpr != null)
4100 // Add any secondary structure prediction services
4101 for (int i = 0, j = secstrpr.size(); i < j; i++)
4103 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4105 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4106 .getServiceClient(sh);
4107 int p = secstrmenu.getItemCount();
4108 impl.attachWSMenuEntry(secstrmenu, me);
4109 int q = secstrmenu.getItemCount();
4110 for (int litm = p; litm < q; litm++)
4112 legacyItems.add(secstrmenu.getItem(litm));
4118 // Add all submenus in the order they should appear on the web
4120 wsmenu.add(msawsmenu);
4121 wsmenu.add(secstrmenu);
4122 wsmenu.add(dismenu);
4123 wsmenu.add(analymenu);
4124 wsmenu.add(phylogenmenu);
4125 // No search services yet
4126 // wsmenu.add(seqsrchmenu);
4128 javax.swing.SwingUtilities.invokeLater(new Runnable()
4135 webService.removeAll();
4136 // first, add discovered services onto the webservices menu
4137 if (wsmenu.size() > 0)
4139 for (int i = 0, j = wsmenu.size(); i < j; i++)
4141 webService.add(wsmenu.get(i));
4146 webService.add(me.webServiceNoServices);
4148 // TODO: move into separate menu builder class.
4149 boolean new_sspred = false;
4150 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4152 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4153 if (jws2servs != null)
4155 if (jws2servs.hasServices())
4157 jws2servs.attachWSMenuEntry(webService, me);
4158 for (Jws2Instance sv : jws2servs.getServices())
4160 if (sv.description.toLowerCase().contains("jpred"))
4162 for (JMenuItem jmi : legacyItems)
4164 jmi.setVisible(false);
4170 if (jws2servs.isRunning())
4172 JMenuItem tm = new JMenuItem(
4173 "Still discovering JABA Services");
4174 tm.setEnabled(false);
4179 build_urlServiceMenu(me.webService);
4180 build_fetchdbmenu(webService);
4181 for (JMenu item : wsmenu)
4183 if (item.getItemCount() == 0)
4185 item.setEnabled(false);
4189 item.setEnabled(true);
4192 } catch (Exception e)
4195 "Exception during web service menu building process.",
4200 } catch (Exception e)
4203 buildingMenu = false;
4205 }, "BuildWebServiceThread").start();
4210 * construct any groupURL type service menu entries.
4214 private void build_urlServiceMenu(JMenu webService)
4216 // TODO: remove this code when 2.7 is released
4217 // DEBUG - alignmentView
4219 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4220 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4222 * @Override public void actionPerformed(ActionEvent e) {
4223 * jalview.datamodel.AlignmentView
4224 * .testSelectionViews(af.viewport.getAlignment(),
4225 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4227 * }); webService.add(testAlView);
4229 // TODO: refactor to RestClient discoverer and merge menu entries for
4230 // rest-style services with other types of analysis/calculation service
4231 // SHmmr test client - still being implemented.
4232 // DEBUG - alignmentView
4234 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4237 client.attachWSMenuEntry(
4238 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4244 * Searches the alignment sequences for xRefs and builds the Show
4245 * Cross-References menu (formerly called Show Products), with database
4246 * sources for which cross-references are found (protein sources for a
4247 * nucleotide alignment and vice versa)
4249 * @return true if Show Cross-references menu should be enabled
4251 public boolean canShowProducts()
4253 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4254 AlignmentI dataset = viewport.getAlignment().getDataset();
4256 showProducts.removeAll();
4257 final boolean dna = viewport.getAlignment().isNucleotide();
4259 if (seqs == null || seqs.length == 0)
4261 // nothing to see here.
4265 boolean showp = false;
4268 List<String> ptypes = new CrossRef(seqs, dataset)
4269 .findXrefSourcesForSequences(dna);
4271 for (final String source : ptypes)
4274 final AlignFrame af = this;
4275 JMenuItem xtype = new JMenuItem(source);
4276 xtype.addActionListener(new ActionListener()
4279 public void actionPerformed(ActionEvent e)
4281 showProductsFor(af.viewport.getSequenceSelection(), dna,
4285 showProducts.add(xtype);
4287 showProducts.setVisible(showp);
4288 showProducts.setEnabled(showp);
4289 } catch (Exception e)
4292 "canShowProducts threw an exception - please report to help@jalview.org",
4300 * Finds and displays cross-references for the selected sequences (protein
4301 * products for nucleotide sequences, dna coding sequences for peptides).
4304 * the sequences to show cross-references for
4306 * true if from a nucleotide alignment (so showing proteins)
4308 * the database to show cross-references for
4310 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4311 final String source)
4313 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this),
4314 "CrossReferencesThread")
4319 * Construct and display a new frame containing the translation of this
4320 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4323 public void showTranslation_actionPerformed(ActionEvent e)
4325 AlignmentI al = null;
4328 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4330 al = dna.translateCdna();
4331 } catch (Exception ex)
4333 jalview.bin.Cache.log.error(
4334 "Exception during translation. Please report this !", ex);
4335 final String msg = MessageManager.getString(
4336 "label.error_when_translating_sequences_submit_bug_report");
4337 final String errorTitle = MessageManager
4338 .getString("label.implementation_error")
4339 + MessageManager.getString("label.translation_failed");
4340 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4341 JvOptionPane.ERROR_MESSAGE);
4344 if (al == null || al.getHeight() == 0)
4346 final String msg = MessageManager.getString(
4347 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4348 final String errorTitle = MessageManager
4349 .getString("label.translation_failed");
4350 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4351 JvOptionPane.WARNING_MESSAGE);
4355 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4356 af.setFileFormat(this.currentFileFormat);
4357 final String newTitle = MessageManager
4358 .formatMessage("label.translation_of_params", new Object[]
4359 { this.getTitle() });
4360 af.setTitle(newTitle);
4361 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4363 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4364 viewport.openSplitFrame(af, new Alignment(seqs));
4368 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4375 * Set the file format
4379 public void setFileFormat(FileFormatI format)
4381 this.currentFileFormat = format;
4385 * Try to load a features file onto the alignment.
4388 * contents or path to retrieve file
4390 * access mode of file (see jalview.io.AlignFile)
4391 * @return true if features file was parsed correctly.
4393 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4395 return avc.parseFeaturesFile(file, sourceType,
4396 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4401 public void refreshFeatureUI(boolean enableIfNecessary)
4403 // note - currently this is only still here rather than in the controller
4404 // because of the featureSettings hard reference that is yet to be
4406 if (enableIfNecessary)
4408 viewport.setShowSequenceFeatures(true);
4409 showSeqFeatures.setSelected(true);
4415 public void dragEnter(DropTargetDragEvent evt)
4420 public void dragExit(DropTargetEvent evt)
4425 public void dragOver(DropTargetDragEvent evt)
4430 public void dropActionChanged(DropTargetDragEvent evt)
4435 public void drop(DropTargetDropEvent evt)
4437 // JAL-1552 - acceptDrop required before getTransferable call for
4438 // Java's Transferable for native dnd
4439 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4440 Transferable t = evt.getTransferable();
4441 final AlignFrame thisaf = this;
4442 final List<String> files = new ArrayList<>();
4443 List<DataSourceType> protocols = new ArrayList<>();
4447 Desktop.transferFromDropTarget(files, protocols, evt, t);
4448 } catch (Exception e)
4450 e.printStackTrace();
4454 new Thread(new Runnable()
4461 // check to see if any of these files have names matching sequences
4464 SequenceIdMatcher idm = new SequenceIdMatcher(
4465 viewport.getAlignment().getSequencesArray());
4467 * Object[] { String,SequenceI}
4469 ArrayList<Object[]> filesmatched = new ArrayList<>();
4470 ArrayList<String> filesnotmatched = new ArrayList<>();
4471 for (int i = 0; i < files.size(); i++)
4473 String file = files.get(i).toString();
4475 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4476 if (protocol == DataSourceType.FILE)
4478 File fl = new File(file);
4479 pdbfn = fl.getName();
4481 else if (protocol == DataSourceType.URL)
4483 URL url = new URL(file);
4484 pdbfn = url.getFile();
4486 if (pdbfn.length() > 0)
4488 // attempt to find a match in the alignment
4489 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4490 int l = 0, c = pdbfn.indexOf(".");
4491 while (mtch == null && c != -1)
4496 } while ((c = pdbfn.indexOf(".", l)) > l);
4499 pdbfn = pdbfn.substring(0, l);
4501 mtch = idm.findAllIdMatches(pdbfn);
4505 FileFormatI type = null;
4508 type = new IdentifyFile().identify(file, protocol);
4509 } catch (Exception ex)
4513 if (type != null && type.isStructureFile())
4515 filesmatched.add(new Object[] { file, protocol, mtch });
4519 // File wasn't named like one of the sequences or wasn't a PDB
4521 filesnotmatched.add(file);
4525 if (filesmatched.size() > 0)
4527 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4528 || JvOptionPane.showConfirmDialog(thisaf,
4529 MessageManager.formatMessage(
4530 "label.automatically_associate_structure_files_with_sequences_same_name",
4532 { Integer.valueOf(filesmatched.size())
4534 MessageManager.getString(
4535 "label.automatically_associate_structure_files_by_name"),
4536 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4539 for (Object[] fm : filesmatched)
4541 // try and associate
4542 // TODO: may want to set a standard ID naming formalism for
4543 // associating PDB files which have no IDs.
4544 for (SequenceI toassoc : (SequenceI[]) fm[2])
4546 PDBEntry pe = new AssociatePdbFileWithSeq()
4547 .associatePdbWithSeq((String) fm[0],
4548 (DataSourceType) fm[1], toassoc, false,
4552 System.err.println("Associated file : "
4553 + ((String) fm[0]) + " with "
4554 + toassoc.getDisplayId(true));
4558 // TODO: do we need to update overview ? only if features are
4560 alignPanel.paintAlignment(true, false);
4564 if (filesnotmatched.size() > 0)
4566 if (assocfiles > 0 && (Cache.getDefault(
4567 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4568 || JvOptionPane.showConfirmDialog(thisaf,
4569 "<html>" + MessageManager.formatMessage(
4570 "label.ignore_unmatched_dropped_files_info",
4573 filesnotmatched.size())
4576 MessageManager.getString(
4577 "label.ignore_unmatched_dropped_files"),
4578 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4582 for (String fn : filesnotmatched)
4584 loadJalviewDataFile(fn, null, null, null);
4588 } catch (Exception ex)
4590 ex.printStackTrace();
4593 }, "DropFileThread").start();
4598 * Attempt to load a "dropped" file or URL string, by testing in turn for
4600 * <li>an Annotation file</li>
4601 * <li>a JNet file</li>
4602 * <li>a features file</li>
4603 * <li>else try to interpret as an alignment file</li>
4607 * either a filename or a URL string.
4609 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4610 FileFormatI format, SequenceI assocSeq)
4614 if (sourceType == null)
4616 sourceType = FormatAdapter.checkProtocol(file);
4618 // if the file isn't identified, or not positively identified as some
4619 // other filetype (PFAM is default unidentified alignment file type) then
4620 // try to parse as annotation.
4621 boolean isAnnotation = (format == null
4622 || FileFormat.Pfam.equals(format))
4623 ? new AnnotationFile().annotateAlignmentView(viewport,
4629 // first see if its a T-COFFEE score file
4630 TCoffeeScoreFile tcf = null;
4633 tcf = new TCoffeeScoreFile(file, sourceType);
4636 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4640 new TCoffeeColourScheme(viewport.getAlignment()));
4641 isAnnotation = true;
4642 statusBar.setText(MessageManager.getString(
4643 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4647 // some problem - if no warning its probable that the ID matching
4648 // process didn't work
4649 JvOptionPane.showMessageDialog(Desktop.desktop,
4650 tcf.getWarningMessage() == null
4651 ? MessageManager.getString(
4652 "label.check_file_matches_sequence_ids_alignment")
4653 : tcf.getWarningMessage(),
4654 MessageManager.getString(
4655 "label.problem_reading_tcoffee_score_file"),
4656 JvOptionPane.WARNING_MESSAGE);
4663 } catch (Exception x)
4666 "Exception when processing data source as T-COFFEE score file",
4672 // try to see if its a JNet 'concise' style annotation file *before*
4674 // try to parse it as a features file
4677 format = new IdentifyFile().identify(file, sourceType);
4679 if (FileFormat.ScoreMatrix == format)
4681 ScoreMatrixFile sm = new ScoreMatrixFile(
4682 new FileParse(file, sourceType));
4684 // todo: i18n this message
4685 statusBar.setText(MessageManager.formatMessage(
4686 "label.successfully_loaded_matrix",
4687 sm.getMatrixName()));
4689 else if (FileFormat.Jnet.equals(format))
4691 JPredFile predictions = new JPredFile(file, sourceType);
4692 new JnetAnnotationMaker();
4693 JnetAnnotationMaker.add_annotation(predictions,
4694 viewport.getAlignment(), 0, false);
4695 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4696 viewport.getAlignment().setSeqrep(repseq);
4697 HiddenColumns cs = new HiddenColumns();
4698 cs.hideInsertionsFor(repseq);
4699 viewport.getAlignment().setHiddenColumns(cs);
4700 isAnnotation = true;
4702 // else if (IdentifyFile.FeaturesFile.equals(format))
4703 else if (FileFormat.Features.equals(format))
4705 if (parseFeaturesFile(file, sourceType))
4707 alignPanel.paintAlignment(true, true);
4712 new FileLoader().LoadFile(viewport, file, sourceType, format);
4719 alignPanel.adjustAnnotationHeight();
4720 viewport.updateSequenceIdColours();
4721 buildSortByAnnotationScoresMenu();
4722 alignPanel.paintAlignment(true, true);
4724 } catch (Exception ex)
4726 ex.printStackTrace();
4727 } catch (OutOfMemoryError oom)
4732 } catch (Exception x)
4737 + (sourceType != null
4738 ? (sourceType == DataSourceType.PASTE
4740 : "using " + sourceType + " from "
4744 ? "(parsing as '" + format + "' file)"
4746 oom, Desktop.desktop);
4751 * Method invoked by the ChangeListener on the tabbed pane, in other words
4752 * when a different tabbed pane is selected by the user or programmatically.
4755 public void tabSelectionChanged(int index)
4759 alignPanel = alignPanels.get(index);
4760 viewport = alignPanel.av;
4761 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4762 setMenusFromViewport(viewport);
4766 * 'focus' any colour slider that is open to the selected viewport
4768 if (viewport.getConservationSelected())
4770 SliderPanel.setConservationSlider(alignPanel,
4771 viewport.getResidueShading(), alignPanel.getViewName());
4775 SliderPanel.hideConservationSlider();
4777 if (viewport.getAbovePIDThreshold())
4779 SliderPanel.setPIDSliderSource(alignPanel,
4780 viewport.getResidueShading(), alignPanel.getViewName());
4784 SliderPanel.hidePIDSlider();
4788 * If there is a frame linked to this one in a SplitPane, switch it to the
4789 * same view tab index. No infinite recursion of calls should happen, since
4790 * tabSelectionChanged() should not get invoked on setting the selected
4791 * index to an unchanged value. Guard against setting an invalid index
4792 * before the new view peer tab has been created.
4794 final AlignViewportI peer = viewport.getCodingComplement();
4797 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4798 .getAlignPanel().alignFrame;
4799 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4801 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4807 * On right mouse click on view tab, prompt for and set new view name.
4810 public void tabbedPane_mousePressed(MouseEvent e)
4812 if (e.isPopupTrigger())
4814 String msg = MessageManager.getString("label.enter_view_name");
4815 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4816 JvOptionPane.QUESTION_MESSAGE);
4820 viewport.viewName = reply;
4821 // TODO warn if reply is in getExistingViewNames()?
4822 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4827 public AlignViewport getCurrentView()
4833 * Open the dialog for regex description parsing.
4836 protected void extractScores_actionPerformed(ActionEvent e)
4838 ParseProperties pp = new jalview.analysis.ParseProperties(
4839 viewport.getAlignment());
4840 // TODO: verify regex and introduce GUI dialog for version 2.5
4841 // if (pp.getScoresFromDescription("col", "score column ",
4842 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4844 if (pp.getScoresFromDescription("description column",
4845 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4847 buildSortByAnnotationScoresMenu();
4855 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4859 protected void showDbRefs_actionPerformed(ActionEvent e)
4861 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4867 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4871 protected void showNpFeats_actionPerformed(ActionEvent e)
4873 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4877 * find the viewport amongst the tabs in this alignment frame and close that
4882 public boolean closeView(AlignViewportI av)
4886 this.closeMenuItem_actionPerformed(false);
4889 Component[] comp = tabbedPane.getComponents();
4890 for (int i = 0; comp != null && i < comp.length; i++)
4892 if (comp[i] instanceof AlignmentPanel)
4894 if (((AlignmentPanel) comp[i]).av == av)
4897 closeView((AlignmentPanel) comp[i]);
4905 protected void build_fetchdbmenu(JMenu webService)
4907 // Temporary hack - DBRef Fetcher always top level ws entry.
4908 // TODO We probably want to store a sequence database checklist in
4909 // preferences and have checkboxes.. rather than individual sources selected
4911 final JMenu rfetch = new JMenu(
4912 MessageManager.getString("action.fetch_db_references"));
4913 rfetch.setToolTipText(MessageManager.getString(
4914 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4915 webService.add(rfetch);
4917 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4918 MessageManager.getString("option.trim_retrieved_seqs"));
4919 trimrs.setToolTipText(
4920 MessageManager.getString("label.trim_retrieved_sequences"));
4921 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4922 trimrs.addActionListener(new ActionListener()
4925 public void actionPerformed(ActionEvent e)
4927 trimrs.setSelected(trimrs.isSelected());
4928 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4929 Boolean.valueOf(trimrs.isSelected()).toString());
4933 JMenuItem fetchr = new JMenuItem(
4934 MessageManager.getString("label.standard_databases"));
4935 fetchr.setToolTipText(
4936 MessageManager.getString("label.fetch_embl_uniprot"));
4937 fetchr.addActionListener(new ActionListener()
4941 public void actionPerformed(ActionEvent e)
4943 new Thread(new Runnable()
4948 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4949 .getAlignment().isNucleotide();
4950 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4951 alignPanel.av.getSequenceSelection(),
4952 alignPanel.alignFrame, null,
4953 alignPanel.alignFrame.featureSettings, isNucleotide);
4954 dbRefFetcher.addListener(new FetchFinishedListenerI()
4957 public void finished()
4959 AlignFrame.this.setMenusForViewport();
4962 dbRefFetcher.fetchDBRefs(false);
4964 }, "BuildFetchDBMenuThread").start();
4970 final AlignFrame me = this;
4971 new Thread(new Runnable()
4976 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4977 .getSequenceFetcherSingleton(me);
4978 javax.swing.SwingUtilities.invokeLater(new Runnable()
4983 String[] dbclasses = sf.getOrderedSupportedSources();
4984 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4985 // jalview.util.QuickSort.sort(otherdb, otherdb);
4986 List<DbSourceProxy> otherdb;
4987 JMenu dfetch = new JMenu();
4988 JMenu ifetch = new JMenu();
4989 JMenuItem fetchr = null;
4990 int comp = 0, icomp = 0, mcomp = 15;
4991 String mname = null;
4993 for (String dbclass : dbclasses)
4995 otherdb = sf.getSourceProxy(dbclass);
4996 // add a single entry for this class, or submenu allowing 'fetch
4998 if (otherdb == null || otherdb.size() < 1)
5002 // List<DbSourceProxy> dbs=otherdb;
5003 // otherdb=new ArrayList<DbSourceProxy>();
5004 // for (DbSourceProxy db:dbs)
5006 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5010 mname = "From " + dbclass;
5012 if (otherdb.size() == 1)
5014 final DbSourceProxy[] dassource = otherdb
5015 .toArray(new DbSourceProxy[0]);
5016 DbSourceProxy src = otherdb.get(0);
5017 fetchr = new JMenuItem(src.getDbSource());
5018 fetchr.addActionListener(new ActionListener()
5022 public void actionPerformed(ActionEvent e)
5024 new Thread(new Runnable()
5030 boolean isNucleotide = alignPanel.alignFrame
5031 .getViewport().getAlignment()
5033 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5034 alignPanel.av.getSequenceSelection(),
5035 alignPanel.alignFrame, dassource,
5036 alignPanel.alignFrame.featureSettings,
5039 .addListener(new FetchFinishedListenerI()
5042 public void finished()
5044 AlignFrame.this.setMenusForViewport();
5047 dbRefFetcher.fetchDBRefs(false);
5053 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5054 MessageManager.formatMessage(
5055 "label.fetch_retrieve_from", new Object[]
5056 { src.getDbName() })));
5062 final DbSourceProxy[] dassource = otherdb
5063 .toArray(new DbSourceProxy[0]);
5065 DbSourceProxy src = otherdb.get(0);
5066 fetchr = new JMenuItem(MessageManager
5067 .formatMessage("label.fetch_all_param", new Object[]
5068 { src.getDbSource() }));
5069 fetchr.addActionListener(new ActionListener()
5072 public void actionPerformed(ActionEvent e)
5074 new Thread(new Runnable()
5080 boolean isNucleotide = alignPanel.alignFrame
5081 .getViewport().getAlignment()
5083 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5084 alignPanel.av.getSequenceSelection(),
5085 alignPanel.alignFrame, dassource,
5086 alignPanel.alignFrame.featureSettings,
5089 .addListener(new FetchFinishedListenerI()
5092 public void finished()
5094 AlignFrame.this.setMenusForViewport();
5097 dbRefFetcher.fetchDBRefs(false);
5103 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5104 MessageManager.formatMessage(
5105 "label.fetch_retrieve_from_all_sources",
5107 { Integer.valueOf(otherdb.size())
5109 src.getDbSource(), src.getDbName() })));
5112 // and then build the rest of the individual menus
5113 ifetch = new JMenu(MessageManager.formatMessage(
5114 "label.source_from_db_source", new Object[]
5115 { src.getDbSource() }));
5117 String imname = null;
5119 for (DbSourceProxy sproxy : otherdb)
5121 String dbname = sproxy.getDbName();
5122 String sname = dbname.length() > 5
5123 ? dbname.substring(0, 5) + "..."
5125 String msname = dbname.length() > 10
5126 ? dbname.substring(0, 10) + "..."
5130 imname = MessageManager
5131 .formatMessage("label.from_msname", new Object[]
5134 fetchr = new JMenuItem(msname);
5135 final DbSourceProxy[] dassrc = { sproxy };
5136 fetchr.addActionListener(new ActionListener()
5140 public void actionPerformed(ActionEvent e)
5142 new Thread(new Runnable()
5148 boolean isNucleotide = alignPanel.alignFrame
5149 .getViewport().getAlignment()
5151 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5152 alignPanel.av.getSequenceSelection(),
5153 alignPanel.alignFrame, dassrc,
5154 alignPanel.alignFrame.featureSettings,
5157 .addListener(new FetchFinishedListenerI()
5160 public void finished()
5162 AlignFrame.this.setMenusForViewport();
5165 dbRefFetcher.fetchDBRefs(false);
5171 fetchr.setToolTipText(
5172 "<html>" + MessageManager.formatMessage(
5173 "label.fetch_retrieve_from", new Object[]
5177 if (++icomp >= mcomp || i == (otherdb.size()))
5179 ifetch.setText(MessageManager.formatMessage(
5180 "label.source_to_target", imname, sname));
5182 ifetch = new JMenu();
5190 if (comp >= mcomp || dbi >= (dbclasses.length))
5192 dfetch.setText(MessageManager.formatMessage(
5193 "label.source_to_target", mname, dbclass));
5195 dfetch = new JMenu();
5208 * Left justify the whole alignment.
5211 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5213 AlignmentI al = viewport.getAlignment();
5215 viewport.firePropertyChange("alignment", null, al);
5219 * Right justify the whole alignment.
5222 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5224 AlignmentI al = viewport.getAlignment();
5226 viewport.firePropertyChange("alignment", null, al);
5230 public void setShowSeqFeatures(boolean b)
5232 showSeqFeatures.setSelected(b);
5233 viewport.setShowSequenceFeatures(b);
5240 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5241 * awt.event.ActionEvent)
5244 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5246 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5247 alignPanel.paintAlignment(false, false);
5254 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5258 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5260 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5261 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5269 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5270 * .event.ActionEvent)
5273 protected void showGroupConservation_actionPerformed(ActionEvent e)
5275 viewport.setShowGroupConservation(showGroupConservation.getState());
5276 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5283 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5284 * .event.ActionEvent)
5287 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5289 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5290 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5297 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5298 * .event.ActionEvent)
5301 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5303 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5304 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5308 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5310 showSequenceLogo.setState(true);
5311 viewport.setShowSequenceLogo(true);
5312 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5313 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5317 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5319 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5326 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5327 * .event.ActionEvent)
5330 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5332 if (avc.makeGroupsFromSelection())
5334 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5335 alignPanel.updateAnnotation();
5336 alignPanel.paintAlignment(true, true);
5340 public void clearAlignmentSeqRep()
5342 // TODO refactor alignmentseqrep to controller
5343 if (viewport.getAlignment().hasSeqrep())
5345 viewport.getAlignment().setSeqrep(null);
5346 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5347 alignPanel.updateAnnotation();
5348 alignPanel.paintAlignment(true, true);
5353 protected void createGroup_actionPerformed(ActionEvent e)
5355 if (avc.createGroup())
5357 alignPanel.alignmentChanged();
5362 protected void unGroup_actionPerformed(ActionEvent e)
5366 alignPanel.alignmentChanged();
5371 * make the given alignmentPanel the currently selected tab
5373 * @param alignmentPanel
5375 public void setDisplayedView(AlignmentPanel alignmentPanel)
5377 if (!viewport.getSequenceSetId()
5378 .equals(alignmentPanel.av.getSequenceSetId()))
5380 throw new Error(MessageManager.getString(
5381 "error.implementation_error_cannot_show_view_alignment_frame"));
5383 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5384 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5386 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5391 * Action on selection of menu options to Show or Hide annotations.
5394 * @param forSequences
5395 * update sequence-related annotations
5396 * @param forAlignment
5397 * update non-sequence-related annotations
5400 protected void setAnnotationsVisibility(boolean visible,
5401 boolean forSequences, boolean forAlignment)
5403 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5404 .getAlignmentAnnotation();
5409 for (AlignmentAnnotation aa : anns)
5412 * don't display non-positional annotations on an alignment
5414 if (aa.annotations == null)
5418 boolean apply = (aa.sequenceRef == null && forAlignment)
5419 || (aa.sequenceRef != null && forSequences);
5422 aa.visible = visible;
5425 alignPanel.validateAnnotationDimensions(true);
5426 alignPanel.alignmentChanged();
5430 * Store selected annotation sort order for the view and repaint.
5433 protected void sortAnnotations_actionPerformed()
5435 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5437 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5438 alignPanel.paintAlignment(false, false);
5443 * @return alignment panels in this alignment frame
5445 public List<? extends AlignmentViewPanel> getAlignPanels()
5447 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5451 * Open a new alignment window, with the cDNA associated with this (protein)
5452 * alignment, aligned as is the protein.
5454 protected void viewAsCdna_actionPerformed()
5456 // TODO no longer a menu action - refactor as required
5457 final AlignmentI alignment = getViewport().getAlignment();
5458 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5459 if (mappings == null)
5463 List<SequenceI> cdnaSeqs = new ArrayList<>();
5464 for (SequenceI aaSeq : alignment.getSequences())
5466 for (AlignedCodonFrame acf : mappings)
5468 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5472 * There is a cDNA mapping for this protein sequence - add to new
5473 * alignment. It will share the same dataset sequence as other mapped
5474 * cDNA (no new mappings need to be created).
5476 final Sequence newSeq = new Sequence(dnaSeq);
5477 newSeq.setDatasetSequence(dnaSeq);
5478 cdnaSeqs.add(newSeq);
5482 if (cdnaSeqs.size() == 0)
5484 // show a warning dialog no mapped cDNA
5487 AlignmentI cdna = new Alignment(
5488 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5489 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5490 AlignFrame.DEFAULT_HEIGHT);
5491 cdna.alignAs(alignment);
5492 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5494 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5495 AlignFrame.DEFAULT_HEIGHT);
5499 * Set visibility of dna/protein complement view (available when shown in a
5505 protected void showComplement_actionPerformed(boolean show)
5507 SplitContainerI sf = getSplitViewContainer();
5510 sf.setComplementVisible(this, show);
5515 * Generate the reverse (optionally complemented) of the selected sequences,
5516 * and add them to the alignment
5519 protected void showReverse_actionPerformed(boolean complement)
5521 AlignmentI al = null;
5524 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5525 al = dna.reverseCdna(complement);
5526 viewport.addAlignment(al, "");
5527 addHistoryItem(new EditCommand(
5528 MessageManager.getString("label.add_sequences"), Action.PASTE,
5529 al.getSequencesArray(), 0, al.getWidth(),
5530 viewport.getAlignment()));
5531 } catch (Exception ex)
5533 System.err.println(ex.getMessage());
5539 * Try to run a script in the Groovy console, having first ensured that this
5540 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5541 * be targeted at this alignment.
5544 protected void runGroovy_actionPerformed()
5546 Jalview.setCurrentAlignFrame(this);
5547 groovy.ui.Console console = Desktop.getGroovyConsole();
5548 if (console != null)
5552 console.runScript();
5553 } catch (Exception ex)
5555 System.err.println((ex.toString()));
5556 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5557 MessageManager.getString("label.couldnt_run_groovy_script"),
5558 MessageManager.getString("label.groovy_support_failed"),
5559 JvOptionPane.ERROR_MESSAGE);
5564 System.err.println("Can't run Groovy script as console not found");
5569 * Hides columns containing (or not containing) a specified feature, provided
5570 * that would not leave all columns hidden
5572 * @param featureType
5573 * @param columnsContaining
5576 public boolean hideFeatureColumns(String featureType,
5577 boolean columnsContaining)
5579 boolean notForHiding = avc.markColumnsContainingFeatures(
5580 columnsContaining, false, false, featureType);
5583 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5584 false, featureType))
5586 getViewport().hideSelectedColumns();
5594 protected void selectHighlightedColumns_actionPerformed(
5595 ActionEvent actionEvent)
5597 // include key modifier check in case user selects from menu
5598 avc.markHighlightedColumns(
5599 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5600 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5601 | ActionEvent.CTRL_MASK)) != 0);
5605 * Rebuilds the Colour menu, including any user-defined colours which have
5606 * been loaded either on startup or during the session
5608 public void buildColourMenu()
5610 colourMenu.removeAll();
5612 colourMenu.add(applyToAllGroups);
5613 colourMenu.add(textColour);
5614 colourMenu.addSeparator();
5616 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5619 colourMenu.addSeparator();
5620 colourMenu.add(conservationMenuItem);
5621 colourMenu.add(modifyConservation);
5622 colourMenu.add(abovePIDThreshold);
5623 colourMenu.add(modifyPID);
5624 colourMenu.add(annotationColour);
5626 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5627 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5631 * Open a dialog (if not already open) that allows the user to select and
5632 * calculate PCA or Tree analysis
5634 protected void openTreePcaDialog()
5636 if (alignPanel.getCalculationDialog() == null)
5638 new CalculationChooser(AlignFrame.this);
5643 class PrintThread extends Thread
5647 public PrintThread(AlignmentPanel ap)
5652 static PageFormat pf;
5657 PrinterJob printJob = PrinterJob.getPrinterJob();
5661 printJob.setPrintable(ap, pf);
5665 printJob.setPrintable(ap);
5668 if (printJob.printDialog())
5673 } catch (Exception PrintException)
5675 PrintException.printStackTrace();