2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenColumns;
57 import jalview.datamodel.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FileParse;
74 import jalview.io.FormatAdapter;
75 import jalview.io.HtmlSvgOutput;
76 import jalview.io.IdentifyFile;
77 import jalview.io.JPredFile;
78 import jalview.io.JalviewFileChooser;
79 import jalview.io.JalviewFileView;
80 import jalview.io.JnetAnnotationMaker;
81 import jalview.io.NewickFile;
82 import jalview.io.ScoreMatrixFile;
83 import jalview.io.TCoffeeScoreFile;
84 import jalview.jbgui.GAlignFrame;
85 import jalview.schemes.ColourSchemeI;
86 import jalview.schemes.ColourSchemes;
87 import jalview.schemes.ResidueColourScheme;
88 import jalview.schemes.TCoffeeColourScheme;
89 import jalview.util.MessageManager;
90 import jalview.viewmodel.AlignmentViewport;
91 import jalview.viewmodel.ViewportRanges;
92 import jalview.ws.DBRefFetcher;
93 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
94 import jalview.ws.jws1.Discoverer;
95 import jalview.ws.jws2.Jws2Discoverer;
96 import jalview.ws.jws2.jabaws2.Jws2Instance;
97 import jalview.ws.seqfetcher.DbSourceProxy;
99 import java.awt.BorderLayout;
100 import java.awt.Component;
101 import java.awt.Rectangle;
102 import java.awt.Toolkit;
103 import java.awt.datatransfer.Clipboard;
104 import java.awt.datatransfer.DataFlavor;
105 import java.awt.datatransfer.StringSelection;
106 import java.awt.datatransfer.Transferable;
107 import java.awt.dnd.DnDConstants;
108 import java.awt.dnd.DropTargetDragEvent;
109 import java.awt.dnd.DropTargetDropEvent;
110 import java.awt.dnd.DropTargetEvent;
111 import java.awt.dnd.DropTargetListener;
112 import java.awt.event.ActionEvent;
113 import java.awt.event.ActionListener;
114 import java.awt.event.FocusAdapter;
115 import java.awt.event.FocusEvent;
116 import java.awt.event.ItemEvent;
117 import java.awt.event.ItemListener;
118 import java.awt.event.KeyAdapter;
119 import java.awt.event.KeyEvent;
120 import java.awt.event.MouseEvent;
121 import java.awt.print.PageFormat;
122 import java.awt.print.PrinterJob;
123 import java.beans.PropertyChangeEvent;
125 import java.io.FileWriter;
126 import java.io.PrintWriter;
128 import java.util.ArrayList;
129 import java.util.Arrays;
130 import java.util.Deque;
131 import java.util.Enumeration;
132 import java.util.Hashtable;
133 import java.util.List;
134 import java.util.Vector;
136 import javax.swing.JCheckBoxMenuItem;
137 import javax.swing.JEditorPane;
138 import javax.swing.JInternalFrame;
139 import javax.swing.JLayeredPane;
140 import javax.swing.JMenu;
141 import javax.swing.JMenuItem;
142 import javax.swing.JScrollPane;
143 import javax.swing.SwingUtilities;
149 * @version $Revision$
151 public class AlignFrame extends GAlignFrame implements DropTargetListener,
152 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
155 public static final int DEFAULT_WIDTH = 700;
157 public static final int DEFAULT_HEIGHT = 500;
160 * The currently displayed panel (selected tabbed view if more than one)
162 public AlignmentPanel alignPanel;
164 AlignViewport viewport;
166 ViewportRanges vpRanges;
168 public AlignViewControllerI avc;
170 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
173 * Last format used to load or save alignments in this window
175 FileFormatI currentFileFormat = null;
178 * Current filename for this alignment
180 String fileName = null;
183 * Creates a new AlignFrame object with specific width and height.
189 public AlignFrame(AlignmentI al, int width, int height)
191 this(al, null, width, height);
195 * Creates a new AlignFrame object with specific width, height and
201 * @param sequenceSetId
203 public AlignFrame(AlignmentI al, int width, int height,
204 String sequenceSetId)
206 this(al, null, width, height, sequenceSetId);
210 * Creates a new AlignFrame object with specific width, height and
216 * @param sequenceSetId
219 public AlignFrame(AlignmentI al, int width, int height,
220 String sequenceSetId, String viewId)
222 this(al, null, width, height, sequenceSetId, viewId);
226 * new alignment window with hidden columns
230 * @param hiddenColumns
231 * ColumnSelection or null
233 * Width of alignment frame
237 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
238 int width, int height)
240 this(al, hiddenColumns, width, height, null);
244 * Create alignment frame for al with hiddenColumns, a specific width and
245 * height, and specific sequenceId
248 * @param hiddenColumns
251 * @param sequenceSetId
254 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
255 int width, int height, String sequenceSetId)
257 this(al, hiddenColumns, width, height, sequenceSetId, null);
261 * Create alignment frame for al with hiddenColumns, a specific width and
262 * height, and specific sequenceId
265 * @param hiddenColumns
268 * @param sequenceSetId
273 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
274 int width, int height, String sequenceSetId, String viewId)
276 setSize(width, height);
278 if (al.getDataset() == null)
283 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
285 alignPanel = new AlignmentPanel(this, viewport);
287 addAlignmentPanel(alignPanel, true);
291 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
292 HiddenColumns hiddenColumns, int width, int height)
294 setSize(width, height);
296 if (al.getDataset() == null)
301 viewport = new AlignViewport(al, hiddenColumns);
303 if (hiddenSeqs != null && hiddenSeqs.length > 0)
305 viewport.hideSequence(hiddenSeqs);
307 alignPanel = new AlignmentPanel(this, viewport);
308 addAlignmentPanel(alignPanel, true);
313 * Make a new AlignFrame from existing alignmentPanels
320 public AlignFrame(AlignmentPanel ap)
324 addAlignmentPanel(ap, false);
329 * initalise the alignframe from the underlying viewport data and the
334 if (!Jalview.isHeadlessMode())
336 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
339 vpRanges = viewport.getRanges();
340 avc = new jalview.controller.AlignViewController(this, viewport,
342 if (viewport.getAlignmentConservationAnnotation() == null)
344 // BLOSUM62Colour.setEnabled(false);
345 conservationMenuItem.setEnabled(false);
346 modifyConservation.setEnabled(false);
347 // PIDColour.setEnabled(false);
348 // abovePIDThreshold.setEnabled(false);
349 // modifyPID.setEnabled(false);
352 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
355 if (sortby.equals("Id"))
357 sortIDMenuItem_actionPerformed(null);
359 else if (sortby.equals("Pairwise Identity"))
361 sortPairwiseMenuItem_actionPerformed(null);
365 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
367 setMenusFromViewport(viewport);
368 buildSortByAnnotationScoresMenu();
369 calculateTree.addActionListener(new ActionListener()
373 public void actionPerformed(ActionEvent e)
380 if (Desktop.desktop != null)
382 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
383 addServiceListeners();
387 if (viewport.getWrapAlignment())
389 wrapMenuItem_actionPerformed(null);
392 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
394 this.overviewMenuItem_actionPerformed(null);
399 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
400 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
401 final String menuLabel = MessageManager
402 .getString("label.copy_format_from");
403 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
404 new ViewSetProvider()
408 public AlignmentPanel[] getAllAlignmentPanels()
411 origview.add(alignPanel);
412 // make an array of all alignment panels except for this one
413 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
414 Arrays.asList(Desktop.getAlignmentPanels(null)));
415 aps.remove(AlignFrame.this.alignPanel);
416 return aps.toArray(new AlignmentPanel[aps.size()]);
418 }, selviews, new ItemListener()
422 public void itemStateChanged(ItemEvent e)
424 if (origview.size() > 0)
426 final AlignmentPanel ap = origview.get(0);
429 * Copy the ViewStyle of the selected panel to 'this one'.
430 * Don't change value of 'scaleProteinAsCdna' unless copying
433 ViewStyleI vs = selviews.get(0).getAlignViewport()
435 boolean fromSplitFrame = selviews.get(0)
436 .getAlignViewport().getCodingComplement() != null;
439 vs.setScaleProteinAsCdna(ap.getAlignViewport()
440 .getViewStyle().isScaleProteinAsCdna());
442 ap.getAlignViewport().setViewStyle(vs);
445 * Also rescale ViewStyle of SplitFrame complement if there is
446 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
447 * the whole ViewStyle (allow cDNA protein to have different
450 AlignViewportI complement = ap.getAlignViewport()
451 .getCodingComplement();
452 if (complement != null && vs.isScaleProteinAsCdna())
454 AlignFrame af = Desktop.getAlignFrameFor(complement);
455 ((SplitFrame) af.getSplitViewContainer())
457 af.setMenusForViewport();
461 ap.setSelected(true);
462 ap.alignFrame.setMenusForViewport();
467 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
468 .indexOf("devel") > -1
469 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
470 .indexOf("test") > -1)
472 formatMenu.add(vsel);
474 addFocusListener(new FocusAdapter()
477 public void focusGained(FocusEvent e)
479 Jalview.setCurrentAlignFrame(AlignFrame.this);
486 * Change the filename and format for the alignment, and enable the 'reload'
487 * button functionality.
494 public void setFileName(String file, FileFormatI format)
497 setFileFormat(format);
498 reload.setEnabled(true);
502 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
505 void addKeyListener()
507 addKeyListener(new KeyAdapter()
510 public void keyPressed(KeyEvent evt)
512 if (viewport.cursorMode
513 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
514 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
515 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
516 && Character.isDigit(evt.getKeyChar()))
518 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
521 switch (evt.getKeyCode())
524 case 27: // escape key
525 deselectAllSequenceMenuItem_actionPerformed(null);
529 case KeyEvent.VK_DOWN:
530 if (evt.isAltDown() || !viewport.cursorMode)
532 moveSelectedSequences(false);
534 if (viewport.cursorMode)
536 alignPanel.getSeqPanel().moveCursor(0, 1);
541 if (evt.isAltDown() || !viewport.cursorMode)
543 moveSelectedSequences(true);
545 if (viewport.cursorMode)
547 alignPanel.getSeqPanel().moveCursor(0, -1);
552 case KeyEvent.VK_LEFT:
553 if (evt.isAltDown() || !viewport.cursorMode)
555 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
559 alignPanel.getSeqPanel().moveCursor(-1, 0);
564 case KeyEvent.VK_RIGHT:
565 if (evt.isAltDown() || !viewport.cursorMode)
567 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
571 alignPanel.getSeqPanel().moveCursor(1, 0);
575 case KeyEvent.VK_SPACE:
576 if (viewport.cursorMode)
578 alignPanel.getSeqPanel().insertGapAtCursor(
579 evt.isControlDown() || evt.isShiftDown()
584 // case KeyEvent.VK_A:
585 // if (viewport.cursorMode)
587 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
588 // //System.out.println("A");
592 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
593 * System.out.println("closing bracket"); } break;
595 case KeyEvent.VK_DELETE:
596 case KeyEvent.VK_BACK_SPACE:
597 if (!viewport.cursorMode)
599 cut_actionPerformed(null);
603 alignPanel.getSeqPanel().deleteGapAtCursor(
604 evt.isControlDown() || evt.isShiftDown()
611 if (viewport.cursorMode)
613 alignPanel.getSeqPanel().setCursorRow();
617 if (viewport.cursorMode && !evt.isControlDown())
619 alignPanel.getSeqPanel().setCursorColumn();
623 if (viewport.cursorMode)
625 alignPanel.getSeqPanel().setCursorPosition();
629 case KeyEvent.VK_ENTER:
630 case KeyEvent.VK_COMMA:
631 if (viewport.cursorMode)
633 alignPanel.getSeqPanel().setCursorRowAndColumn();
638 if (viewport.cursorMode)
640 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
644 if (viewport.cursorMode)
646 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
651 viewport.cursorMode = !viewport.cursorMode;
652 statusBar.setText(MessageManager.formatMessage(
653 "label.keyboard_editing_mode",
654 new String[] { (viewport.cursorMode ? "on" : "off") }));
655 if (viewport.cursorMode)
657 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
659 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
662 alignPanel.getSeqPanel().seqCanvas.repaint();
668 Help.showHelpWindow();
669 } catch (Exception ex)
671 ex.printStackTrace();
676 boolean toggleSeqs = !evt.isControlDown();
677 boolean toggleCols = !evt.isShiftDown();
678 toggleHiddenRegions(toggleSeqs, toggleCols);
683 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
684 boolean modifyExisting = true; // always modify, don't clear
685 // evt.isShiftDown();
686 boolean invertHighlighted = evt.isAltDown();
687 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
691 case KeyEvent.VK_PAGE_UP:
692 if (viewport.getWrapAlignment())
694 vpRanges.scrollUp(true);
701 case KeyEvent.VK_PAGE_DOWN:
702 if (viewport.getWrapAlignment())
704 vpRanges.scrollUp(false);
715 public void keyReleased(KeyEvent evt)
717 switch (evt.getKeyCode())
719 case KeyEvent.VK_LEFT:
720 if (evt.isAltDown() || !viewport.cursorMode)
722 viewport.firePropertyChange("alignment", null, viewport
723 .getAlignment().getSequences());
727 case KeyEvent.VK_RIGHT:
728 if (evt.isAltDown() || !viewport.cursorMode)
730 viewport.firePropertyChange("alignment", null, viewport
731 .getAlignment().getSequences());
739 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
741 ap.alignFrame = this;
742 avc = new jalview.controller.AlignViewController(this, viewport,
747 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
749 int aSize = alignPanels.size();
751 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
753 if (aSize == 1 && ap.av.viewName == null)
755 this.getContentPane().add(ap, BorderLayout.CENTER);
761 setInitialTabVisible();
764 expandViews.setEnabled(true);
765 gatherViews.setEnabled(true);
766 tabbedPane.addTab(ap.av.viewName, ap);
768 ap.setVisible(false);
773 if (ap.av.isPadGaps())
775 ap.av.getAlignment().padGaps();
777 ap.av.updateConservation(ap);
778 ap.av.updateConsensus(ap);
779 ap.av.updateStrucConsensus(ap);
783 public void setInitialTabVisible()
785 expandViews.setEnabled(true);
786 gatherViews.setEnabled(true);
787 tabbedPane.setVisible(true);
788 AlignmentPanel first = alignPanels.get(0);
789 tabbedPane.addTab(first.av.viewName, first);
790 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
793 public AlignViewport getViewport()
798 /* Set up intrinsic listeners for dynamically generated GUI bits. */
799 private void addServiceListeners()
801 final java.beans.PropertyChangeListener thisListener;
802 Desktop.instance.addJalviewPropertyChangeListener("services",
803 thisListener = new java.beans.PropertyChangeListener()
806 public void propertyChange(PropertyChangeEvent evt)
808 // // System.out.println("Discoverer property change.");
809 // if (evt.getPropertyName().equals("services"))
811 SwingUtilities.invokeLater(new Runnable()
818 .println("Rebuild WS Menu for service change");
819 BuildWebServiceMenu();
826 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
829 public void internalFrameClosed(
830 javax.swing.event.InternalFrameEvent evt)
832 // System.out.println("deregistering discoverer listener");
833 Desktop.instance.removeJalviewPropertyChangeListener("services",
835 closeMenuItem_actionPerformed(true);
838 // Finally, build the menu once to get current service state
839 new Thread(new Runnable()
844 BuildWebServiceMenu();
850 * Configure menu items that vary according to whether the alignment is
851 * nucleotide or protein
853 public void setGUINucleotide()
855 AlignmentI al = getViewport().getAlignment();
856 boolean nucleotide = al.isNucleotide();
858 showTranslation.setVisible(nucleotide);
859 showReverse.setVisible(nucleotide);
860 showReverseComplement.setVisible(nucleotide);
861 conservationMenuItem.setEnabled(!nucleotide);
862 modifyConservation.setEnabled(!nucleotide
863 && conservationMenuItem.isSelected());
864 showGroupConservation.setEnabled(!nucleotide);
866 showComplementMenuItem.setText(nucleotide ? MessageManager
867 .getString("label.protein") : MessageManager
868 .getString("label.nucleotide"));
872 * set up menus for the current viewport. This may be called after any
873 * operation that affects the data in the current view (selection changed,
874 * etc) to update the menus to reflect the new state.
877 public void setMenusForViewport()
879 setMenusFromViewport(viewport);
883 * Need to call this method when tabs are selected for multiple views, or when
884 * loading from Jalview2XML.java
889 void setMenusFromViewport(AlignViewport av)
891 padGapsMenuitem.setSelected(av.isPadGaps());
892 colourTextMenuItem.setSelected(av.isShowColourText());
893 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
894 modifyPID.setEnabled(abovePIDThreshold.isSelected());
895 conservationMenuItem.setSelected(av.getConservationSelected());
896 modifyConservation.setEnabled(conservationMenuItem.isSelected());
897 seqLimits.setSelected(av.getShowJVSuffix());
898 idRightAlign.setSelected(av.isRightAlignIds());
899 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
900 renderGapsMenuItem.setSelected(av.isRenderGaps());
901 wrapMenuItem.setSelected(av.getWrapAlignment());
902 scaleAbove.setVisible(av.getWrapAlignment());
903 scaleLeft.setVisible(av.getWrapAlignment());
904 scaleRight.setVisible(av.getWrapAlignment());
905 annotationPanelMenuItem.setState(av.isShowAnnotation());
907 * Show/hide annotations only enabled if annotation panel is shown
909 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
910 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
911 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
912 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
913 viewBoxesMenuItem.setSelected(av.getShowBoxes());
914 viewTextMenuItem.setSelected(av.getShowText());
915 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
916 showGroupConsensus.setSelected(av.isShowGroupConsensus());
917 showGroupConservation.setSelected(av.isShowGroupConservation());
918 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
919 showSequenceLogo.setSelected(av.isShowSequenceLogo());
920 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
922 ColourMenuHelper.setColourSelected(colourMenu,
923 av.getGlobalColourScheme());
925 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
926 hiddenMarkers.setState(av.getShowHiddenMarkers());
927 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
928 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
929 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
930 autoCalculate.setSelected(av.autoCalculateConsensus);
931 sortByTree.setSelected(av.sortByTree);
932 listenToViewSelections.setSelected(av.followSelection);
934 showProducts.setEnabled(canShowProducts());
935 setGroovyEnabled(Desktop.getGroovyConsole() != null);
941 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
945 public void setGroovyEnabled(boolean b)
947 runGroovy.setEnabled(b);
950 private IProgressIndicator progressBar;
955 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
958 public void setProgressBar(String message, long id)
960 progressBar.setProgressBar(message, id);
964 public void registerHandler(final long id,
965 final IProgressIndicatorHandler handler)
967 progressBar.registerHandler(id, handler);
972 * @return true if any progress bars are still active
975 public boolean operationInProgress()
977 return progressBar.operationInProgress();
981 public void setStatus(String text)
983 statusBar.setText(text);
987 * Added so Castor Mapping file can obtain Jalview Version
989 public String getVersion()
991 return jalview.bin.Cache.getProperty("VERSION");
994 public FeatureRenderer getFeatureRenderer()
996 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1000 public void fetchSequence_actionPerformed(ActionEvent e)
1002 new jalview.gui.SequenceFetcher(this);
1006 public void addFromFile_actionPerformed(ActionEvent e)
1008 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1012 public void reload_actionPerformed(ActionEvent e)
1014 if (fileName != null)
1016 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1017 // originating file's format
1018 // TODO: work out how to recover feature settings for correct view(s) when
1019 // file is reloaded.
1020 if (FileFormat.Jalview.equals(currentFileFormat))
1022 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1023 for (int i = 0; i < frames.length; i++)
1025 if (frames[i] instanceof AlignFrame && frames[i] != this
1026 && ((AlignFrame) frames[i]).fileName != null
1027 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1031 frames[i].setSelected(true);
1032 Desktop.instance.closeAssociatedWindows();
1033 } catch (java.beans.PropertyVetoException ex)
1039 Desktop.instance.closeAssociatedWindows();
1041 FileLoader loader = new FileLoader();
1042 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1043 : DataSourceType.FILE;
1044 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1048 Rectangle bounds = this.getBounds();
1050 FileLoader loader = new FileLoader();
1051 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1052 : DataSourceType.FILE;
1053 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1054 protocol, currentFileFormat);
1056 newframe.setBounds(bounds);
1057 if (featureSettings != null && featureSettings.isShowing())
1059 final Rectangle fspos = featureSettings.frame.getBounds();
1060 // TODO: need a 'show feature settings' function that takes bounds -
1061 // need to refactor Desktop.addFrame
1062 newframe.featureSettings_actionPerformed(null);
1063 final FeatureSettings nfs = newframe.featureSettings;
1064 SwingUtilities.invokeLater(new Runnable()
1069 nfs.frame.setBounds(fspos);
1072 this.featureSettings.close();
1073 this.featureSettings = null;
1075 this.closeMenuItem_actionPerformed(true);
1081 public void addFromText_actionPerformed(ActionEvent e)
1083 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1088 public void addFromURL_actionPerformed(ActionEvent e)
1090 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1094 public void save_actionPerformed(ActionEvent e)
1096 if (fileName == null || (currentFileFormat == null)
1097 || fileName.startsWith("http"))
1099 saveAs_actionPerformed(null);
1103 saveAlignment(fileName, currentFileFormat);
1114 public void saveAs_actionPerformed(ActionEvent e)
1116 String format = currentFileFormat == null ? null : currentFileFormat
1118 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1119 Cache.getProperty("LAST_DIRECTORY"), format);
1121 chooser.setFileView(new JalviewFileView());
1122 chooser.setDialogTitle(MessageManager
1123 .getString("label.save_alignment_to_file"));
1124 chooser.setToolTipText(MessageManager.getString("action.save"));
1126 int value = chooser.showSaveDialog(this);
1128 if (value == JalviewFileChooser.APPROVE_OPTION)
1130 currentFileFormat = chooser.getSelectedFormat();
1131 while (currentFileFormat == null)
1134 .showInternalMessageDialog(
1137 .getString("label.select_file_format_before_saving"),
1139 .getString("label.file_format_not_specified"),
1140 JvOptionPane.WARNING_MESSAGE);
1141 currentFileFormat = chooser.getSelectedFormat();
1142 value = chooser.showSaveDialog(this);
1143 if (value != JalviewFileChooser.APPROVE_OPTION)
1149 fileName = chooser.getSelectedFile().getPath();
1151 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1153 Cache.setProperty("LAST_DIRECTORY", fileName);
1154 saveAlignment(fileName, currentFileFormat);
1158 public boolean saveAlignment(String file, FileFormatI format)
1160 boolean success = true;
1162 if (FileFormat.Jalview.equals(format))
1164 String shortName = title;
1166 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1168 shortName = shortName.substring(shortName
1169 .lastIndexOf(java.io.File.separatorChar) + 1);
1172 success = new Jalview2XML().saveAlignment(this, file, shortName);
1174 statusBar.setText(MessageManager.formatMessage(
1175 "label.successfully_saved_to_file_in_format", new Object[] {
1176 fileName, format }));
1181 AlignmentExportData exportData = getAlignmentForExport(format,
1183 if (exportData.getSettings().isCancelled())
1187 FormatAdapter f = new FormatAdapter(alignPanel,
1188 exportData.getSettings());
1189 String output = f.formatSequences(
1191 exportData.getAlignment(), // class cast exceptions will
1192 // occur in the distant future
1193 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1194 f.getCacheSuffixDefault(format), viewport.getAlignment()
1195 .getHiddenColumns());
1205 PrintWriter out = new PrintWriter(new FileWriter(file));
1209 this.setTitle(file);
1210 statusBar.setText(MessageManager.formatMessage(
1211 "label.successfully_saved_to_file_in_format",
1212 new Object[] { fileName, format.getName() }));
1213 } catch (Exception ex)
1216 ex.printStackTrace();
1223 JvOptionPane.showInternalMessageDialog(this, MessageManager
1224 .formatMessage("label.couldnt_save_file",
1225 new Object[] { fileName }), MessageManager
1226 .getString("label.error_saving_file"),
1227 JvOptionPane.WARNING_MESSAGE);
1233 private void warningMessage(String warning, String title)
1235 if (new jalview.util.Platform().isHeadless())
1237 System.err.println("Warning: " + title + "\nWarning: " + warning);
1242 JvOptionPane.showInternalMessageDialog(this, warning, title,
1243 JvOptionPane.WARNING_MESSAGE);
1255 protected void outputText_actionPerformed(ActionEvent e)
1257 FileFormatI fileFormat = FileFormats.getInstance().forName(
1258 e.getActionCommand());
1259 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1261 if (exportData.getSettings().isCancelled())
1265 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1266 cap.setForInput(null);
1269 FileFormatI format = fileFormat;
1270 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1271 .formatSequences(format, exportData.getAlignment(),
1272 exportData.getOmitHidden(),
1274 .getStartEndPostions(), viewport
1275 .getAlignment().getHiddenColumns()));
1276 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1277 "label.alignment_output_command",
1278 new Object[] { e.getActionCommand() }), 600, 500);
1279 } catch (OutOfMemoryError oom)
1281 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1287 public static AlignmentExportData getAlignmentForExport(
1288 FileFormatI format, AlignViewportI viewport,
1289 AlignExportSettingI exportSettings)
1291 AlignmentI alignmentToExport = null;
1292 AlignExportSettingI settings = exportSettings;
1293 String[] omitHidden = null;
1295 HiddenSequences hiddenSeqs = viewport.getAlignment()
1296 .getHiddenSequences();
1298 alignmentToExport = viewport.getAlignment();
1300 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1301 if (settings == null)
1303 settings = new AlignExportSettings(hasHiddenSeqs,
1304 viewport.hasHiddenColumns(), format);
1306 // settings.isExportAnnotations();
1308 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1310 omitHidden = viewport.getViewAsString(false,
1311 settings.isExportHiddenSequences());
1314 int[] alignmentStartEnd = new int[2];
1315 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1317 alignmentToExport = hiddenSeqs.getFullAlignment();
1321 alignmentToExport = viewport.getAlignment();
1323 alignmentStartEnd = alignmentToExport
1324 .getVisibleStartAndEndIndex(viewport.getAlignment()
1326 .getHiddenRegions());
1327 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1328 omitHidden, alignmentStartEnd, settings);
1339 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1341 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1342 htmlSVG.exportHTML(null);
1346 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1348 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1349 bjs.exportHTML(null);
1352 public void createImageMap(File file, String image)
1354 alignPanel.makePNGImageMap(file, image);
1364 public void createPNG(File f)
1366 alignPanel.makePNG(f);
1376 public void createEPS(File f)
1378 alignPanel.makeEPS(f);
1382 public void createSVG(File f)
1384 alignPanel.makeSVG(f);
1388 public void pageSetup_actionPerformed(ActionEvent e)
1390 PrinterJob printJob = PrinterJob.getPrinterJob();
1391 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1401 public void printMenuItem_actionPerformed(ActionEvent e)
1403 // Putting in a thread avoids Swing painting problems
1404 PrintThread thread = new PrintThread(alignPanel);
1409 public void exportFeatures_actionPerformed(ActionEvent e)
1411 new AnnotationExporter().exportFeatures(alignPanel);
1415 public void exportAnnotations_actionPerformed(ActionEvent e)
1417 new AnnotationExporter().exportAnnotations(alignPanel);
1421 public void associatedData_actionPerformed(ActionEvent e)
1423 // Pick the tree file
1424 JalviewFileChooser chooser = new JalviewFileChooser(
1425 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1426 chooser.setFileView(new JalviewFileView());
1427 chooser.setDialogTitle(MessageManager
1428 .getString("label.load_jalview_annotations"));
1429 chooser.setToolTipText(MessageManager
1430 .getString("label.load_jalview_annotations"));
1432 int value = chooser.showOpenDialog(null);
1434 if (value == JalviewFileChooser.APPROVE_OPTION)
1436 String choice = chooser.getSelectedFile().getPath();
1437 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1438 loadJalviewDataFile(choice, null, null, null);
1444 * Close the current view or all views in the alignment frame. If the frame
1445 * only contains one view then the alignment will be removed from memory.
1447 * @param closeAllTabs
1450 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1452 if (alignPanels != null && alignPanels.size() < 2)
1454 closeAllTabs = true;
1459 if (alignPanels != null)
1463 if (this.isClosed())
1465 // really close all the windows - otherwise wait till
1466 // setClosed(true) is called
1467 for (int i = 0; i < alignPanels.size(); i++)
1469 AlignmentPanel ap = alignPanels.get(i);
1476 closeView(alignPanel);
1483 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1484 * be called recursively, with the frame now in 'closed' state
1486 this.setClosed(true);
1488 } catch (Exception ex)
1490 ex.printStackTrace();
1495 * Close the specified panel and close up tabs appropriately.
1497 * @param panelToClose
1499 public void closeView(AlignmentPanel panelToClose)
1501 int index = tabbedPane.getSelectedIndex();
1502 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1503 alignPanels.remove(panelToClose);
1504 panelToClose.closePanel();
1505 panelToClose = null;
1507 tabbedPane.removeTabAt(closedindex);
1508 tabbedPane.validate();
1510 if (index > closedindex || index == tabbedPane.getTabCount())
1512 // modify currently selected tab index if necessary.
1516 this.tabSelectionChanged(index);
1522 void updateEditMenuBar()
1525 if (viewport.getHistoryList().size() > 0)
1527 undoMenuItem.setEnabled(true);
1528 CommandI command = viewport.getHistoryList().peek();
1529 undoMenuItem.setText(MessageManager.formatMessage(
1530 "label.undo_command",
1531 new Object[] { command.getDescription() }));
1535 undoMenuItem.setEnabled(false);
1536 undoMenuItem.setText(MessageManager.getString("action.undo"));
1539 if (viewport.getRedoList().size() > 0)
1541 redoMenuItem.setEnabled(true);
1543 CommandI command = viewport.getRedoList().peek();
1544 redoMenuItem.setText(MessageManager.formatMessage(
1545 "label.redo_command",
1546 new Object[] { command.getDescription() }));
1550 redoMenuItem.setEnabled(false);
1551 redoMenuItem.setText(MessageManager.getString("action.redo"));
1556 public void addHistoryItem(CommandI command)
1558 if (command.getSize() > 0)
1560 viewport.addToHistoryList(command);
1561 viewport.clearRedoList();
1562 updateEditMenuBar();
1563 viewport.updateHiddenColumns();
1564 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1565 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1566 // viewport.getColumnSelection()
1567 // .getHiddenColumns().size() > 0);
1573 * @return alignment objects for all views
1575 AlignmentI[] getViewAlignments()
1577 if (alignPanels != null)
1579 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1581 for (AlignmentPanel ap : alignPanels)
1583 als[i++] = ap.av.getAlignment();
1587 if (viewport != null)
1589 return new AlignmentI[] { viewport.getAlignment() };
1601 protected void undoMenuItem_actionPerformed(ActionEvent e)
1603 if (viewport.getHistoryList().isEmpty())
1607 CommandI command = viewport.getHistoryList().pop();
1608 viewport.addToRedoList(command);
1609 command.undoCommand(getViewAlignments());
1611 AlignmentViewport originalSource = getOriginatingSource(command);
1612 updateEditMenuBar();
1614 if (originalSource != null)
1616 if (originalSource != viewport)
1619 .warn("Implementation worry: mismatch of viewport origin for undo");
1621 originalSource.updateHiddenColumns();
1622 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1624 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1625 // viewport.getColumnSelection()
1626 // .getHiddenColumns().size() > 0);
1627 originalSource.firePropertyChange("alignment", null, originalSource
1628 .getAlignment().getSequences());
1639 protected void redoMenuItem_actionPerformed(ActionEvent e)
1641 if (viewport.getRedoList().size() < 1)
1646 CommandI command = viewport.getRedoList().pop();
1647 viewport.addToHistoryList(command);
1648 command.doCommand(getViewAlignments());
1650 AlignmentViewport originalSource = getOriginatingSource(command);
1651 updateEditMenuBar();
1653 if (originalSource != null)
1656 if (originalSource != viewport)
1659 .warn("Implementation worry: mismatch of viewport origin for redo");
1661 originalSource.updateHiddenColumns();
1662 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1664 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1665 // viewport.getColumnSelection()
1666 // .getHiddenColumns().size() > 0);
1667 originalSource.firePropertyChange("alignment", null, originalSource
1668 .getAlignment().getSequences());
1672 AlignmentViewport getOriginatingSource(CommandI command)
1674 AlignmentViewport originalSource = null;
1675 // For sequence removal and addition, we need to fire
1676 // the property change event FROM the viewport where the
1677 // original alignment was altered
1678 AlignmentI al = null;
1679 if (command instanceof EditCommand)
1681 EditCommand editCommand = (EditCommand) command;
1682 al = editCommand.getAlignment();
1683 List<Component> comps = PaintRefresher.components.get(viewport
1684 .getSequenceSetId());
1686 for (Component comp : comps)
1688 if (comp instanceof AlignmentPanel)
1690 if (al == ((AlignmentPanel) comp).av.getAlignment())
1692 originalSource = ((AlignmentPanel) comp).av;
1699 if (originalSource == null)
1701 // The original view is closed, we must validate
1702 // the current view against the closed view first
1705 PaintRefresher.validateSequences(al, viewport.getAlignment());
1708 originalSource = viewport;
1711 return originalSource;
1720 public void moveSelectedSequences(boolean up)
1722 SequenceGroup sg = viewport.getSelectionGroup();
1728 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1729 viewport.getHiddenRepSequences(), up);
1730 alignPanel.paintAlignment(true);
1733 synchronized void slideSequences(boolean right, int size)
1735 List<SequenceI> sg = new ArrayList<SequenceI>();
1736 if (viewport.cursorMode)
1738 sg.add(viewport.getAlignment().getSequenceAt(
1739 alignPanel.getSeqPanel().seqCanvas.cursorY));
1741 else if (viewport.getSelectionGroup() != null
1742 && viewport.getSelectionGroup().getSize() != viewport
1743 .getAlignment().getHeight())
1745 sg = viewport.getSelectionGroup().getSequences(
1746 viewport.getHiddenRepSequences());
1754 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1756 for (SequenceI seq : viewport.getAlignment().getSequences())
1758 if (!sg.contains(seq))
1760 invertGroup.add(seq);
1764 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1766 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1767 for (int i = 0; i < invertGroup.size(); i++)
1769 seqs2[i] = invertGroup.get(i);
1772 SlideSequencesCommand ssc;
1775 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1776 size, viewport.getGapCharacter());
1780 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1781 size, viewport.getGapCharacter());
1784 int groupAdjustment = 0;
1785 if (ssc.getGapsInsertedBegin() && right)
1787 if (viewport.cursorMode)
1789 alignPanel.getSeqPanel().moveCursor(size, 0);
1793 groupAdjustment = size;
1796 else if (!ssc.getGapsInsertedBegin() && !right)
1798 if (viewport.cursorMode)
1800 alignPanel.getSeqPanel().moveCursor(-size, 0);
1804 groupAdjustment = -size;
1808 if (groupAdjustment != 0)
1810 viewport.getSelectionGroup().setStartRes(
1811 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1812 viewport.getSelectionGroup().setEndRes(
1813 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1817 * just extend the last slide command if compatible; but not if in
1818 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1820 boolean appendHistoryItem = false;
1821 Deque<CommandI> historyList = viewport.getHistoryList();
1822 boolean inSplitFrame = getSplitViewContainer() != null;
1823 if (!inSplitFrame && historyList != null && historyList.size() > 0
1824 && historyList.peek() instanceof SlideSequencesCommand)
1826 appendHistoryItem = ssc
1827 .appendSlideCommand((SlideSequencesCommand) historyList
1831 if (!appendHistoryItem)
1833 addHistoryItem(ssc);
1846 protected void copy_actionPerformed(ActionEvent e)
1849 if (viewport.getSelectionGroup() == null)
1853 // TODO: preserve the ordering of displayed alignment annotation in any
1854 // internal paste (particularly sequence associated annotation)
1855 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1856 String[] omitHidden = null;
1858 if (viewport.hasHiddenColumns())
1860 omitHidden = viewport.getViewAsString(true);
1863 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1864 seqs, omitHidden, null);
1866 StringSelection ss = new StringSelection(output);
1870 jalview.gui.Desktop.internalCopy = true;
1871 // Its really worth setting the clipboard contents
1872 // to empty before setting the large StringSelection!!
1873 Toolkit.getDefaultToolkit().getSystemClipboard()
1874 .setContents(new StringSelection(""), null);
1876 Toolkit.getDefaultToolkit().getSystemClipboard()
1877 .setContents(ss, Desktop.instance);
1878 } catch (OutOfMemoryError er)
1880 new OOMWarning("copying region", er);
1884 ArrayList<int[]> hiddenColumns = null;
1885 if (viewport.hasHiddenColumns())
1887 hiddenColumns = new ArrayList<int[]>();
1888 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1889 .getSelectionGroup().getEndRes();
1890 for (int[] region : viewport.getAlignment().getHiddenColumns()
1891 .getHiddenRegions())
1893 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1895 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1896 region[1] - hiddenOffset });
1901 Desktop.jalviewClipboard = new Object[] { seqs,
1902 viewport.getAlignment().getDataset(), hiddenColumns };
1903 statusBar.setText(MessageManager.formatMessage(
1904 "label.copied_sequences_to_clipboard", new Object[] { Integer
1905 .valueOf(seqs.length).toString() }));
1915 protected void pasteNew_actionPerformed(ActionEvent e)
1927 protected void pasteThis_actionPerformed(ActionEvent e)
1933 * Paste contents of Jalview clipboard
1935 * @param newAlignment
1936 * true to paste to a new alignment, otherwise add to this.
1938 void paste(boolean newAlignment)
1940 boolean externalPaste = true;
1943 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1944 Transferable contents = c.getContents(this);
1946 if (contents == null)
1955 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1956 if (str.length() < 1)
1961 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1963 } catch (OutOfMemoryError er)
1965 new OOMWarning("Out of memory pasting sequences!!", er);
1969 SequenceI[] sequences;
1970 boolean annotationAdded = false;
1971 AlignmentI alignment = null;
1973 if (Desktop.jalviewClipboard != null)
1975 // The clipboard was filled from within Jalview, we must use the
1977 // And dataset from the copied alignment
1978 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1979 // be doubly sure that we create *new* sequence objects.
1980 sequences = new SequenceI[newseq.length];
1981 for (int i = 0; i < newseq.length; i++)
1983 sequences[i] = new Sequence(newseq[i]);
1985 alignment = new Alignment(sequences);
1986 externalPaste = false;
1990 // parse the clipboard as an alignment.
1991 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1993 sequences = alignment.getSequencesArray();
1997 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2003 if (Desktop.jalviewClipboard != null)
2005 // dataset is inherited
2006 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2010 // new dataset is constructed
2011 alignment.setDataset(null);
2013 alwidth = alignment.getWidth() + 1;
2017 AlignmentI pastedal = alignment; // preserve pasted alignment object
2018 // Add pasted sequences and dataset into existing alignment.
2019 alignment = viewport.getAlignment();
2020 alwidth = alignment.getWidth() + 1;
2021 // decide if we need to import sequences from an existing dataset
2022 boolean importDs = Desktop.jalviewClipboard != null
2023 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2024 // importDs==true instructs us to copy over new dataset sequences from
2025 // an existing alignment
2026 Vector newDs = (importDs) ? new Vector() : null; // used to create
2027 // minimum dataset set
2029 for (int i = 0; i < sequences.length; i++)
2033 newDs.addElement(null);
2035 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2037 if (importDs && ds != null)
2039 if (!newDs.contains(ds))
2041 newDs.setElementAt(ds, i);
2042 ds = new Sequence(ds);
2043 // update with new dataset sequence
2044 sequences[i].setDatasetSequence(ds);
2048 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2053 // copy and derive new dataset sequence
2054 sequences[i] = sequences[i].deriveSequence();
2055 alignment.getDataset().addSequence(
2056 sequences[i].getDatasetSequence());
2057 // TODO: avoid creation of duplicate dataset sequences with a
2058 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2060 alignment.addSequence(sequences[i]); // merges dataset
2064 newDs.clear(); // tidy up
2066 if (alignment.getAlignmentAnnotation() != null)
2068 for (AlignmentAnnotation alan : alignment
2069 .getAlignmentAnnotation())
2071 if (alan.graphGroup > fgroup)
2073 fgroup = alan.graphGroup;
2077 if (pastedal.getAlignmentAnnotation() != null)
2079 // Add any annotation attached to alignment.
2080 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2081 for (int i = 0; i < alann.length; i++)
2083 annotationAdded = true;
2084 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2086 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2087 if (newann.graphGroup > -1)
2089 if (newGraphGroups.size() <= newann.graphGroup
2090 || newGraphGroups.get(newann.graphGroup) == null)
2092 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2094 newGraphGroups.add(q, null);
2096 newGraphGroups.set(newann.graphGroup, new Integer(
2099 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2103 newann.padAnnotation(alwidth);
2104 alignment.addAnnotation(newann);
2114 addHistoryItem(new EditCommand(
2115 MessageManager.getString("label.add_sequences"),
2116 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2118 // Add any annotations attached to sequences
2119 for (int i = 0; i < sequences.length; i++)
2121 if (sequences[i].getAnnotation() != null)
2123 AlignmentAnnotation newann;
2124 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2126 annotationAdded = true;
2127 newann = sequences[i].getAnnotation()[a];
2128 newann.adjustForAlignment();
2129 newann.padAnnotation(alwidth);
2130 if (newann.graphGroup > -1)
2132 if (newann.graphGroup > -1)
2134 if (newGraphGroups.size() <= newann.graphGroup
2135 || newGraphGroups.get(newann.graphGroup) == null)
2137 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2139 newGraphGroups.add(q, null);
2141 newGraphGroups.set(newann.graphGroup, new Integer(
2144 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2148 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2153 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2160 // propagate alignment changed.
2161 vpRanges.setEndSeq(alignment.getHeight());
2162 if (annotationAdded)
2164 // Duplicate sequence annotation in all views.
2165 AlignmentI[] alview = this.getViewAlignments();
2166 for (int i = 0; i < sequences.length; i++)
2168 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2173 for (int avnum = 0; avnum < alview.length; avnum++)
2175 if (alview[avnum] != alignment)
2177 // duplicate in a view other than the one with input focus
2178 int avwidth = alview[avnum].getWidth() + 1;
2179 // this relies on sann being preserved after we
2180 // modify the sequence's annotation array for each duplication
2181 for (int a = 0; a < sann.length; a++)
2183 AlignmentAnnotation newann = new AlignmentAnnotation(
2185 sequences[i].addAlignmentAnnotation(newann);
2186 newann.padAnnotation(avwidth);
2187 alview[avnum].addAnnotation(newann); // annotation was
2188 // duplicated earlier
2189 // TODO JAL-1145 graphGroups are not updated for sequence
2190 // annotation added to several views. This may cause
2192 alview[avnum].setAnnotationIndex(newann, a);
2197 buildSortByAnnotationScoresMenu();
2199 viewport.firePropertyChange("alignment", null,
2200 alignment.getSequences());
2201 if (alignPanels != null)
2203 for (AlignmentPanel ap : alignPanels)
2205 ap.validateAnnotationDimensions(false);
2210 alignPanel.validateAnnotationDimensions(false);
2216 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2218 String newtitle = new String("Copied sequences");
2220 if (Desktop.jalviewClipboard != null
2221 && Desktop.jalviewClipboard[2] != null)
2223 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2224 for (int[] region : hc)
2226 af.viewport.hideColumns(region[0], region[1]);
2230 // >>>This is a fix for the moment, until a better solution is
2232 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2234 alignPanel.getSeqPanel().seqCanvas
2235 .getFeatureRenderer());
2237 // TODO: maintain provenance of an alignment, rather than just make the
2238 // title a concatenation of operations.
2241 if (title.startsWith("Copied sequences"))
2247 newtitle = newtitle.concat("- from " + title);
2252 newtitle = new String("Pasted sequences");
2255 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2260 } catch (Exception ex)
2262 ex.printStackTrace();
2263 System.out.println("Exception whilst pasting: " + ex);
2264 // could be anything being pasted in here
2270 protected void expand_newalign(ActionEvent e)
2274 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2275 .getAlignment(), -1);
2276 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2278 String newtitle = new String("Flanking alignment");
2280 if (Desktop.jalviewClipboard != null
2281 && Desktop.jalviewClipboard[2] != null)
2283 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2284 for (int region[] : hc)
2286 af.viewport.hideColumns(region[0], region[1]);
2290 // >>>This is a fix for the moment, until a better solution is
2292 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2294 alignPanel.getSeqPanel().seqCanvas
2295 .getFeatureRenderer());
2297 // TODO: maintain provenance of an alignment, rather than just make the
2298 // title a concatenation of operations.
2300 if (title.startsWith("Copied sequences"))
2306 newtitle = newtitle.concat("- from " + title);
2310 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2312 } catch (Exception ex)
2314 ex.printStackTrace();
2315 System.out.println("Exception whilst pasting: " + ex);
2316 // could be anything being pasted in here
2317 } catch (OutOfMemoryError oom)
2319 new OOMWarning("Viewing flanking region of alignment", oom);
2330 protected void cut_actionPerformed(ActionEvent e)
2332 copy_actionPerformed(null);
2333 delete_actionPerformed(null);
2343 protected void delete_actionPerformed(ActionEvent evt)
2346 SequenceGroup sg = viewport.getSelectionGroup();
2353 * If the cut affects all sequences, warn, remove highlighted columns
2355 if (sg.getSize() == viewport.getAlignment().getHeight())
2357 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2358 .getAlignment().getWidth()) ? true : false;
2359 if (isEntireAlignWidth)
2361 int confirm = JvOptionPane.showConfirmDialog(this,
2362 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2363 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2364 JvOptionPane.OK_CANCEL_OPTION);
2366 if (confirm == JvOptionPane.CANCEL_OPTION
2367 || confirm == JvOptionPane.CLOSED_OPTION)
2372 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2373 sg.getEndRes() + 1);
2375 SequenceI[] cut = sg.getSequences()
2376 .toArray(new SequenceI[sg.getSize()]);
2378 addHistoryItem(new EditCommand(
2379 MessageManager.getString("label.cut_sequences"), Action.CUT,
2380 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2381 viewport.getAlignment()));
2383 viewport.setSelectionGroup(null);
2384 viewport.sendSelection();
2385 viewport.getAlignment().deleteGroup(sg);
2387 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2389 if (viewport.getAlignment().getHeight() < 1)
2393 this.setClosed(true);
2394 } catch (Exception ex)
2407 protected void deleteGroups_actionPerformed(ActionEvent e)
2409 if (avc.deleteGroups())
2411 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2412 alignPanel.updateAnnotation();
2413 alignPanel.paintAlignment(true);
2424 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2426 SequenceGroup sg = new SequenceGroup();
2428 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2430 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2433 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2434 viewport.setSelectionGroup(sg);
2435 viewport.sendSelection();
2436 // JAL-2034 - should delegate to
2437 // alignPanel to decide if overview needs
2439 alignPanel.paintAlignment(false);
2440 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2450 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2452 if (viewport.cursorMode)
2454 alignPanel.getSeqPanel().keyboardNo1 = null;
2455 alignPanel.getSeqPanel().keyboardNo2 = null;
2457 viewport.setSelectionGroup(null);
2458 viewport.getColumnSelection().clear();
2459 viewport.setSelectionGroup(null);
2460 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2461 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2462 // JAL-2034 - should delegate to
2463 // alignPanel to decide if overview needs
2465 alignPanel.paintAlignment(false);
2466 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2467 viewport.sendSelection();
2477 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2479 SequenceGroup sg = viewport.getSelectionGroup();
2483 selectAllSequenceMenuItem_actionPerformed(null);
2488 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2490 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2492 // JAL-2034 - should delegate to
2493 // alignPanel to decide if overview needs
2496 alignPanel.paintAlignment(true);
2497 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2498 viewport.sendSelection();
2502 public void invertColSel_actionPerformed(ActionEvent e)
2504 viewport.invertColumnSelection();
2505 alignPanel.paintAlignment(true);
2506 viewport.sendSelection();
2516 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2518 trimAlignment(true);
2528 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2530 trimAlignment(false);
2533 void trimAlignment(boolean trimLeft)
2535 ColumnSelection colSel = viewport.getColumnSelection();
2538 if (!colSel.isEmpty())
2542 column = colSel.getMin();
2546 column = colSel.getMax();
2550 if (viewport.getSelectionGroup() != null)
2552 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2553 viewport.getHiddenRepSequences());
2557 seqs = viewport.getAlignment().getSequencesArray();
2560 TrimRegionCommand trimRegion;
2563 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2564 column, viewport.getAlignment());
2565 vpRanges.setStartRes(0);
2569 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2570 column, viewport.getAlignment());
2573 statusBar.setText(MessageManager.formatMessage(
2574 "label.removed_columns",
2575 new String[] { Integer.valueOf(trimRegion.getSize())
2578 addHistoryItem(trimRegion);
2580 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2582 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2583 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2585 viewport.getAlignment().deleteGroup(sg);
2589 viewport.firePropertyChange("alignment", null, viewport
2590 .getAlignment().getSequences());
2601 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2603 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2606 if (viewport.getSelectionGroup() != null)
2608 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2609 viewport.getHiddenRepSequences());
2610 start = viewport.getSelectionGroup().getStartRes();
2611 end = viewport.getSelectionGroup().getEndRes();
2615 seqs = viewport.getAlignment().getSequencesArray();
2618 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2619 "Remove Gapped Columns", seqs, start, end,
2620 viewport.getAlignment());
2622 addHistoryItem(removeGapCols);
2624 statusBar.setText(MessageManager.formatMessage(
2625 "label.removed_empty_columns",
2626 new Object[] { Integer.valueOf(removeGapCols.getSize())
2629 // This is to maintain viewport position on first residue
2630 // of first sequence
2631 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2632 int startRes = seq.findPosition(vpRanges.getStartRes());
2633 // ShiftList shifts;
2634 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2635 // edit.alColumnChanges=shifts.getInverse();
2636 // if (viewport.hasHiddenColumns)
2637 // viewport.getColumnSelection().compensateForEdits(shifts);
2638 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2639 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2651 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2653 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2656 if (viewport.getSelectionGroup() != null)
2658 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2659 viewport.getHiddenRepSequences());
2660 start = viewport.getSelectionGroup().getStartRes();
2661 end = viewport.getSelectionGroup().getEndRes();
2665 seqs = viewport.getAlignment().getSequencesArray();
2668 // This is to maintain viewport position on first residue
2669 // of first sequence
2670 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2671 int startRes = seq.findPosition(vpRanges.getStartRes());
2673 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2674 viewport.getAlignment()));
2676 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2678 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2690 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2692 viewport.setPadGaps(padGapsMenuitem.isSelected());
2693 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2704 public void findMenuItem_actionPerformed(ActionEvent e)
2710 * Create a new view of the current alignment.
2713 public void newView_actionPerformed(ActionEvent e)
2715 newView(null, true);
2719 * Creates and shows a new view of the current alignment.
2722 * title of newly created view; if null, one will be generated
2723 * @param copyAnnotation
2724 * if true then duplicate all annnotation, groups and settings
2725 * @return new alignment panel, already displayed.
2727 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2730 * Create a new AlignmentPanel (with its own, new Viewport)
2732 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2734 if (!copyAnnotation)
2737 * remove all groups and annotation except for the automatic stuff
2739 newap.av.getAlignment().deleteAllGroups();
2740 newap.av.getAlignment().deleteAllAnnotations(false);
2743 newap.av.setGatherViewsHere(false);
2745 if (viewport.viewName == null)
2747 viewport.viewName = MessageManager
2748 .getString("label.view_name_original");
2752 * Views share the same edits undo and redo stacks
2754 newap.av.setHistoryList(viewport.getHistoryList());
2755 newap.av.setRedoList(viewport.getRedoList());
2758 * Views share the same mappings; need to deregister any new mappings
2759 * created by copyAlignPanel, and register the new reference to the shared
2762 newap.av.replaceMappings(viewport.getAlignment());
2765 * start up cDNA consensus (if applicable) now mappings are in place
2767 if (newap.av.initComplementConsensus())
2769 newap.refresh(true); // adjust layout of annotations
2772 newap.av.viewName = getNewViewName(viewTitle);
2774 addAlignmentPanel(newap, true);
2775 newap.alignmentChanged();
2777 if (alignPanels.size() == 2)
2779 viewport.setGatherViewsHere(true);
2781 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2786 * Make a new name for the view, ensuring it is unique within the current
2787 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2788 * these now use viewId. Unique view names are still desirable for usability.)
2793 protected String getNewViewName(String viewTitle)
2795 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2796 boolean addFirstIndex = false;
2797 if (viewTitle == null || viewTitle.trim().length() == 0)
2799 viewTitle = MessageManager.getString("action.view");
2800 addFirstIndex = true;
2804 index = 1;// we count from 1 if given a specific name
2806 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2808 List<Component> comps = PaintRefresher.components.get(viewport
2809 .getSequenceSetId());
2811 List<String> existingNames = getExistingViewNames(comps);
2813 while (existingNames.contains(newViewName))
2815 newViewName = viewTitle + " " + (++index);
2821 * Returns a list of distinct view names found in the given list of
2822 * components. View names are held on the viewport of an AlignmentPanel.
2827 protected List<String> getExistingViewNames(List<Component> comps)
2829 List<String> existingNames = new ArrayList<String>();
2830 for (Component comp : comps)
2832 if (comp instanceof AlignmentPanel)
2834 AlignmentPanel ap = (AlignmentPanel) comp;
2835 if (!existingNames.contains(ap.av.viewName))
2837 existingNames.add(ap.av.viewName);
2841 return existingNames;
2845 * Explode tabbed views into separate windows.
2848 public void expandViews_actionPerformed(ActionEvent e)
2850 Desktop.explodeViews(this);
2854 * Gather views in separate windows back into a tabbed presentation.
2857 public void gatherViews_actionPerformed(ActionEvent e)
2859 Desktop.instance.gatherViews(this);
2869 public void font_actionPerformed(ActionEvent e)
2871 new FontChooser(alignPanel);
2881 protected void seqLimit_actionPerformed(ActionEvent e)
2883 viewport.setShowJVSuffix(seqLimits.isSelected());
2885 alignPanel.getIdPanel().getIdCanvas()
2886 .setPreferredSize(alignPanel.calculateIdWidth());
2887 alignPanel.paintAlignment(true);
2891 public void idRightAlign_actionPerformed(ActionEvent e)
2893 viewport.setRightAlignIds(idRightAlign.isSelected());
2894 alignPanel.paintAlignment(true);
2898 public void centreColumnLabels_actionPerformed(ActionEvent e)
2900 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2901 alignPanel.paintAlignment(true);
2907 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2910 protected void followHighlight_actionPerformed()
2913 * Set the 'follow' flag on the Viewport (and scroll to position if now
2916 final boolean state = this.followHighlightMenuItem.getState();
2917 viewport.setFollowHighlight(state);
2920 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2931 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2933 viewport.setColourText(colourTextMenuItem.isSelected());
2934 alignPanel.paintAlignment(true);
2944 public void wrapMenuItem_actionPerformed(ActionEvent e)
2946 scaleAbove.setVisible(wrapMenuItem.isSelected());
2947 scaleLeft.setVisible(wrapMenuItem.isSelected());
2948 scaleRight.setVisible(wrapMenuItem.isSelected());
2949 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2950 alignPanel.updateLayout();
2954 public void showAllSeqs_actionPerformed(ActionEvent e)
2956 viewport.showAllHiddenSeqs();
2960 public void showAllColumns_actionPerformed(ActionEvent e)
2962 viewport.showAllHiddenColumns();
2964 viewport.sendSelection();
2968 public void hideSelSequences_actionPerformed(ActionEvent e)
2970 viewport.hideAllSelectedSeqs();
2971 // alignPanel.paintAlignment(true);
2975 * called by key handler and the hide all/show all menu items
2980 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2983 boolean hide = false;
2984 SequenceGroup sg = viewport.getSelectionGroup();
2985 if (!toggleSeqs && !toggleCols)
2987 // Hide everything by the current selection - this is a hack - we do the
2988 // invert and then hide
2989 // first check that there will be visible columns after the invert.
2990 if (viewport.hasSelectedColumns()
2991 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2994 // now invert the sequence set, if required - empty selection implies
2995 // that no hiding is required.
2998 invertSequenceMenuItem_actionPerformed(null);
2999 sg = viewport.getSelectionGroup();
3003 viewport.expandColSelection(sg, true);
3004 // finally invert the column selection and get the new sequence
3006 invertColSel_actionPerformed(null);
3013 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3015 hideSelSequences_actionPerformed(null);
3018 else if (!(toggleCols && viewport.hasSelectedColumns()))
3020 showAllSeqs_actionPerformed(null);
3026 if (viewport.hasSelectedColumns())
3028 hideSelColumns_actionPerformed(null);
3031 viewport.setSelectionGroup(sg);
3036 showAllColumns_actionPerformed(null);
3045 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3046 * event.ActionEvent)
3049 public void hideAllButSelection_actionPerformed(ActionEvent e)
3051 toggleHiddenRegions(false, false);
3052 viewport.sendSelection();
3059 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3063 public void hideAllSelection_actionPerformed(ActionEvent e)
3065 SequenceGroup sg = viewport.getSelectionGroup();
3066 viewport.expandColSelection(sg, false);
3067 viewport.hideAllSelectedSeqs();
3068 viewport.hideSelectedColumns();
3069 alignPanel.paintAlignment(true);
3070 viewport.sendSelection();
3077 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3081 public void showAllhidden_actionPerformed(ActionEvent e)
3083 viewport.showAllHiddenColumns();
3084 viewport.showAllHiddenSeqs();
3085 alignPanel.paintAlignment(true);
3086 viewport.sendSelection();
3090 public void hideSelColumns_actionPerformed(ActionEvent e)
3092 viewport.hideSelectedColumns();
3093 alignPanel.paintAlignment(true);
3094 viewport.sendSelection();
3098 public void hiddenMarkers_actionPerformed(ActionEvent e)
3100 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3111 protected void scaleAbove_actionPerformed(ActionEvent e)
3113 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3114 alignPanel.paintAlignment(true);
3124 protected void scaleLeft_actionPerformed(ActionEvent e)
3126 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3127 alignPanel.paintAlignment(true);
3137 protected void scaleRight_actionPerformed(ActionEvent e)
3139 viewport.setScaleRightWrapped(scaleRight.isSelected());
3140 alignPanel.paintAlignment(true);
3150 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3152 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3153 alignPanel.paintAlignment(true);
3163 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3165 viewport.setShowText(viewTextMenuItem.isSelected());
3166 alignPanel.paintAlignment(true);
3176 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3178 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3179 alignPanel.paintAlignment(true);
3182 public FeatureSettings featureSettings;
3185 public FeatureSettingsControllerI getFeatureSettingsUI()
3187 return featureSettings;
3191 public void featureSettings_actionPerformed(ActionEvent e)
3193 if (featureSettings != null)
3195 featureSettings.close();
3196 featureSettings = null;
3198 if (!showSeqFeatures.isSelected())
3200 // make sure features are actually displayed
3201 showSeqFeatures.setSelected(true);
3202 showSeqFeatures_actionPerformed(null);
3204 featureSettings = new FeatureSettings(this);
3208 * Set or clear 'Show Sequence Features'
3214 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3216 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3217 alignPanel.paintAlignment(true);
3218 if (alignPanel.getOverviewPanel() != null)
3220 alignPanel.getOverviewPanel().updateOverviewImage();
3225 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3226 * the annotations panel as a whole.
3228 * The options to show/hide all annotations should be enabled when the panel
3229 * is shown, and disabled when the panel is hidden.
3234 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3236 final boolean setVisible = annotationPanelMenuItem.isSelected();
3237 viewport.setShowAnnotation(setVisible);
3238 this.showAllSeqAnnotations.setEnabled(setVisible);
3239 this.hideAllSeqAnnotations.setEnabled(setVisible);
3240 this.showAllAlAnnotations.setEnabled(setVisible);
3241 this.hideAllAlAnnotations.setEnabled(setVisible);
3242 alignPanel.updateLayout();
3246 public void alignmentProperties()
3248 JEditorPane editPane = new JEditorPane("text/html", "");
3249 editPane.setEditable(false);
3250 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3252 editPane.setText(MessageManager.formatMessage("label.html_content",
3253 new Object[] { contents.toString() }));
3254 JInternalFrame frame = new JInternalFrame();
3255 frame.getContentPane().add(new JScrollPane(editPane));
3257 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3258 "label.alignment_properties", new Object[] { getTitle() }),
3269 public void overviewMenuItem_actionPerformed(ActionEvent e)
3271 if (alignPanel.overviewPanel != null)
3276 JInternalFrame frame = new JInternalFrame();
3277 OverviewPanel overview = new OverviewPanel(alignPanel);
3278 frame.setContentPane(overview);
3279 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3280 "label.overview_params", new Object[] { this.getTitle() }),
3281 true, frame.getWidth(), frame.getHeight(), true, true);
3283 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3284 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3287 public void internalFrameClosed(
3288 javax.swing.event.InternalFrameEvent evt)
3290 alignPanel.setOverviewPanel(null);
3294 alignPanel.setOverviewPanel(overview);
3298 public void textColour_actionPerformed()
3300 new TextColourChooser().chooseColour(alignPanel, null);
3304 * public void covariationColour_actionPerformed() {
3306 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3310 public void annotationColour_actionPerformed()
3312 new AnnotationColourChooser(viewport, alignPanel);
3316 public void annotationColumn_actionPerformed(ActionEvent e)
3318 new AnnotationColumnChooser(viewport, alignPanel);
3322 * Action on the user checking or unchecking the option to apply the selected
3323 * colour scheme to all groups. If unchecked, groups may have their own
3324 * independent colour schemes.
3329 public void applyToAllGroups_actionPerformed(boolean selected)
3331 viewport.setColourAppliesToAllGroups(selected);
3335 * Action on user selecting a colour from the colour menu
3338 * the name (not the menu item label!) of the colour scheme
3341 public void changeColour_actionPerformed(String name)
3344 * 'User Defined' opens a panel to configure or load a
3345 * user-defined colour scheme
3347 if (ResidueColourScheme.USER_DEFINED.equals(name))
3349 new UserDefinedColours(alignPanel);
3354 * otherwise set the chosen colour scheme (or null for 'None')
3356 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3357 viewport.getAlignment(), viewport.getHiddenRepSequences());
3362 * Actions on setting or changing the alignment colour scheme
3367 public void changeColour(ColourSchemeI cs)
3369 // TODO: pull up to controller method
3370 ColourMenuHelper.setColourSelected(colourMenu, cs);
3372 viewport.setGlobalColourScheme(cs);
3374 alignPanel.paintAlignment(true);
3378 * Show the PID threshold slider panel
3381 protected void modifyPID_actionPerformed()
3383 SliderPanel.setPIDSliderSource(alignPanel,
3384 viewport.getResidueShading(), alignPanel.getViewName());
3385 SliderPanel.showPIDSlider();
3389 * Show the Conservation slider panel
3392 protected void modifyConservation_actionPerformed()
3394 SliderPanel.setConservationSlider(alignPanel,
3395 viewport.getResidueShading(), alignPanel.getViewName());
3396 SliderPanel.showConservationSlider();
3400 * Action on selecting or deselecting (Colour) By Conservation
3403 public void conservationMenuItem_actionPerformed(boolean selected)
3405 modifyConservation.setEnabled(selected);
3406 viewport.setConservationSelected(selected);
3407 viewport.getResidueShading().setConservationApplied(selected);
3409 changeColour(viewport.getGlobalColourScheme());
3412 modifyConservation_actionPerformed();
3416 SliderPanel.hideConservationSlider();
3421 * Action on selecting or deselecting (Colour) Above PID Threshold
3424 public void abovePIDThreshold_actionPerformed(boolean selected)
3426 modifyPID.setEnabled(selected);
3427 viewport.setAbovePIDThreshold(selected);
3430 viewport.getResidueShading().setThreshold(0,
3431 viewport.isIgnoreGapsConsensus());
3434 changeColour(viewport.getGlobalColourScheme());
3437 modifyPID_actionPerformed();
3441 SliderPanel.hidePIDSlider();
3452 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3454 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3455 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3456 .getAlignment().getSequenceAt(0));
3457 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3458 viewport.getAlignment()));
3459 alignPanel.paintAlignment(true);
3469 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3471 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3472 AlignmentSorter.sortByID(viewport.getAlignment());
3473 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3474 viewport.getAlignment()));
3475 alignPanel.paintAlignment(true);
3485 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3487 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3488 AlignmentSorter.sortByLength(viewport.getAlignment());
3489 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3490 viewport.getAlignment()));
3491 alignPanel.paintAlignment(true);
3501 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3503 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3504 AlignmentSorter.sortByGroup(viewport.getAlignment());
3505 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3506 viewport.getAlignment()));
3508 alignPanel.paintAlignment(true);
3518 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3520 new RedundancyPanel(alignPanel, this);
3530 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3532 if ((viewport.getSelectionGroup() == null)
3533 || (viewport.getSelectionGroup().getSize() < 2))
3535 JvOptionPane.showInternalMessageDialog(this, MessageManager
3536 .getString("label.you_must_select_least_two_sequences"),
3537 MessageManager.getString("label.invalid_selection"),
3538 JvOptionPane.WARNING_MESSAGE);
3542 JInternalFrame frame = new JInternalFrame();
3543 frame.setContentPane(new PairwiseAlignPanel(viewport));
3544 Desktop.addInternalFrame(frame,
3545 MessageManager.getString("action.pairwise_alignment"), 600,
3551 public void autoCalculate_actionPerformed(ActionEvent e)
3553 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3554 if (viewport.autoCalculateConsensus)
3556 viewport.firePropertyChange("alignment", null, viewport
3557 .getAlignment().getSequences());
3562 public void sortByTreeOption_actionPerformed(ActionEvent e)
3564 viewport.sortByTree = sortByTree.isSelected();
3568 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3570 viewport.followSelection = listenToViewSelections.isSelected();
3574 * Constructs a tree panel and adds it to the desktop
3577 * tree type (NJ or AV)
3579 * name of score model used to compute the tree
3581 * parameters for the distance or similarity calculation
3583 void newTreePanel(String type, String modelName, SimilarityParamsI options)
3585 String frameTitle = "";
3588 boolean onSelection = false;
3589 if (viewport.getSelectionGroup() != null
3590 && viewport.getSelectionGroup().getSize() > 0)
3592 SequenceGroup sg = viewport.getSelectionGroup();
3594 /* Decide if the selection is a column region */
3595 for (SequenceI _s : sg.getSequences())
3597 if (_s.getLength() < sg.getEndRes())
3603 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3605 .getString("label.sequences_selection_not_aligned"),
3606 JvOptionPane.WARNING_MESSAGE);
3615 if (viewport.getAlignment().getHeight() < 2)
3621 tp = new TreePanel(alignPanel, type, modelName, options);
3622 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3624 frameTitle += " from ";
3626 if (viewport.viewName != null)
3628 frameTitle += viewport.viewName + " of ";
3631 frameTitle += this.title;
3633 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3644 public void addSortByOrderMenuItem(String title,
3645 final AlignmentOrder order)
3647 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3648 "action.by_title_param", new Object[] { title }));
3650 item.addActionListener(new java.awt.event.ActionListener()
3653 public void actionPerformed(ActionEvent e)
3655 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3657 // TODO: JBPNote - have to map order entries to curent SequenceI
3659 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3661 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3664 alignPanel.paintAlignment(true);
3670 * Add a new sort by annotation score menu item
3673 * the menu to add the option to
3675 * the label used to retrieve scores for each sequence on the
3678 public void addSortByAnnotScoreMenuItem(JMenu sort,
3679 final String scoreLabel)
3681 final JMenuItem item = new JMenuItem(scoreLabel);
3683 item.addActionListener(new java.awt.event.ActionListener()
3686 public void actionPerformed(ActionEvent e)
3688 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3689 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3690 viewport.getAlignment());// ,viewport.getSelectionGroup());
3691 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3692 viewport.getAlignment()));
3693 alignPanel.paintAlignment(true);
3699 * last hash for alignment's annotation array - used to minimise cost of
3702 protected int _annotationScoreVectorHash;
3705 * search the alignment and rebuild the sort by annotation score submenu the
3706 * last alignment annotation vector hash is stored to minimize cost of
3707 * rebuilding in subsequence calls.
3711 public void buildSortByAnnotationScoresMenu()
3713 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3718 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3720 sortByAnnotScore.removeAll();
3721 // almost certainly a quicker way to do this - but we keep it simple
3722 Hashtable scoreSorts = new Hashtable();
3723 AlignmentAnnotation aann[];
3724 for (SequenceI sqa : viewport.getAlignment().getSequences())
3726 aann = sqa.getAnnotation();
3727 for (int i = 0; aann != null && i < aann.length; i++)
3729 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3731 scoreSorts.put(aann[i].label, aann[i].label);
3735 Enumeration labels = scoreSorts.keys();
3736 while (labels.hasMoreElements())
3738 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3739 (String) labels.nextElement());
3741 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3744 _annotationScoreVectorHash = viewport.getAlignment()
3745 .getAlignmentAnnotation().hashCode();
3750 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3751 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3752 * call. Listeners are added to remove the menu item when the treePanel is
3753 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3757 public void buildTreeSortMenu()
3759 sortByTreeMenu.removeAll();
3761 List<Component> comps = PaintRefresher.components.get(viewport
3762 .getSequenceSetId());
3763 List<TreePanel> treePanels = new ArrayList<TreePanel>();
3764 for (Component comp : comps)
3766 if (comp instanceof TreePanel)
3768 treePanels.add((TreePanel) comp);
3772 if (treePanels.size() < 1)
3774 sortByTreeMenu.setVisible(false);
3778 sortByTreeMenu.setVisible(true);
3780 for (final TreePanel tp : treePanels)
3782 final JMenuItem item = new JMenuItem(tp.getTitle());
3783 item.addActionListener(new java.awt.event.ActionListener()
3786 public void actionPerformed(ActionEvent e)
3788 tp.sortByTree_actionPerformed();
3789 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3794 sortByTreeMenu.add(item);
3798 public boolean sortBy(AlignmentOrder alorder, String undoname)
3800 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3801 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3802 if (undoname != null)
3804 addHistoryItem(new OrderCommand(undoname, oldOrder,
3805 viewport.getAlignment()));
3807 alignPanel.paintAlignment(true);
3812 * Work out whether the whole set of sequences or just the selected set will
3813 * be submitted for multiple alignment.
3816 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3818 // Now, check we have enough sequences
3819 AlignmentView msa = null;
3821 if ((viewport.getSelectionGroup() != null)
3822 && (viewport.getSelectionGroup().getSize() > 1))
3824 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3825 // some common interface!
3827 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3828 * SequenceI[sz = seqs.getSize(false)];
3830 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3831 * seqs.getSequenceAt(i); }
3833 msa = viewport.getAlignmentView(true);
3835 else if (viewport.getSelectionGroup() != null
3836 && viewport.getSelectionGroup().getSize() == 1)
3838 int option = JvOptionPane.showConfirmDialog(this,
3839 MessageManager.getString("warn.oneseq_msainput_selection"),
3840 MessageManager.getString("label.invalid_selection"),
3841 JvOptionPane.OK_CANCEL_OPTION);
3842 if (option == JvOptionPane.OK_OPTION)
3844 msa = viewport.getAlignmentView(false);
3849 msa = viewport.getAlignmentView(false);
3855 * Decides what is submitted to a secondary structure prediction service: the
3856 * first sequence in the alignment, or in the current selection, or, if the
3857 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3858 * region or the whole alignment. (where the first sequence in the set is the
3859 * one that the prediction will be for).
3861 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3863 AlignmentView seqs = null;
3865 if ((viewport.getSelectionGroup() != null)
3866 && (viewport.getSelectionGroup().getSize() > 0))
3868 seqs = viewport.getAlignmentView(true);
3872 seqs = viewport.getAlignmentView(false);
3874 // limit sequences - JBPNote in future - could spawn multiple prediction
3876 // TODO: viewport.getAlignment().isAligned is a global state - the local
3877 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3878 if (!viewport.getAlignment().isAligned(false))
3880 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3881 // TODO: if seqs.getSequences().length>1 then should really have warned
3895 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3897 // Pick the tree file
3898 JalviewFileChooser chooser = new JalviewFileChooser(
3899 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3900 chooser.setFileView(new JalviewFileView());
3901 chooser.setDialogTitle(MessageManager
3902 .getString("label.select_newick_like_tree_file"));
3903 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3905 int value = chooser.showOpenDialog(null);
3907 if (value == JalviewFileChooser.APPROVE_OPTION)
3909 String filePath = chooser.getSelectedFile().getPath();
3910 Cache.setProperty("LAST_DIRECTORY", filePath);
3911 NewickFile fin = null;
3914 fin = new NewickFile(filePath, DataSourceType.FILE);
3915 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3916 } catch (Exception ex)
3923 .getString("label.problem_reading_tree_file"),
3924 JvOptionPane.WARNING_MESSAGE);
3925 ex.printStackTrace();
3927 if (fin != null && fin.hasWarningMessage())
3929 JvOptionPane.showMessageDialog(Desktop.desktop, fin
3930 .getWarningMessage(), MessageManager
3931 .getString("label.possible_problem_with_tree_file"),
3932 JvOptionPane.WARNING_MESSAGE);
3937 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3939 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3942 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3943 int h, int x, int y)
3945 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3949 * Add a treeviewer for the tree extracted from a Newick file object to the
3950 * current alignment view
3957 * Associated alignment input data (or null)
3966 * @return TreePanel handle
3968 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3969 AlignmentView input, int w, int h, int x, int y)
3971 TreePanel tp = null;
3977 if (nf.getTree() != null)
3979 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3985 tp.setLocation(x, y);
3988 Desktop.addInternalFrame(tp, treeTitle, w, h);
3990 } catch (Exception ex)
3992 ex.printStackTrace();
3998 private boolean buildingMenu = false;
4001 * Generates menu items and listener event actions for web service clients
4004 public void BuildWebServiceMenu()
4006 while (buildingMenu)
4010 System.err.println("Waiting for building menu to finish.");
4012 } catch (Exception e)
4016 final AlignFrame me = this;
4017 buildingMenu = true;
4018 new Thread(new Runnable()
4023 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4026 // System.err.println("Building ws menu again "
4027 // + Thread.currentThread());
4028 // TODO: add support for context dependent disabling of services based
4030 // alignment and current selection
4031 // TODO: add additional serviceHandle parameter to specify abstract
4033 // class independently of AbstractName
4034 // TODO: add in rediscovery GUI function to restart discoverer
4035 // TODO: group services by location as well as function and/or
4037 // object broker mechanism.
4038 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4039 final IProgressIndicator af = me;
4042 * do not i18n these strings - they are hard-coded in class
4043 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4044 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4046 final JMenu msawsmenu = new JMenu("Alignment");
4047 final JMenu secstrmenu = new JMenu(
4048 "Secondary Structure Prediction");
4049 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4050 final JMenu analymenu = new JMenu("Analysis");
4051 final JMenu dismenu = new JMenu("Protein Disorder");
4052 // JAL-940 - only show secondary structure prediction services from
4053 // the legacy server
4054 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4056 Discoverer.services != null && (Discoverer.services.size() > 0))
4058 // TODO: refactor to allow list of AbstractName/Handler bindings to
4060 // stored or retrieved from elsewhere
4061 // No MSAWS used any more:
4062 // Vector msaws = null; // (Vector)
4063 // Discoverer.services.get("MsaWS");
4064 Vector secstrpr = (Vector) Discoverer.services
4066 if (secstrpr != null)
4068 // Add any secondary structure prediction services
4069 for (int i = 0, j = secstrpr.size(); i < j; i++)
4071 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4073 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4074 .getServiceClient(sh);
4075 int p = secstrmenu.getItemCount();
4076 impl.attachWSMenuEntry(secstrmenu, me);
4077 int q = secstrmenu.getItemCount();
4078 for (int litm = p; litm < q; litm++)
4080 legacyItems.add(secstrmenu.getItem(litm));
4086 // Add all submenus in the order they should appear on the web
4088 wsmenu.add(msawsmenu);
4089 wsmenu.add(secstrmenu);
4090 wsmenu.add(dismenu);
4091 wsmenu.add(analymenu);
4092 // No search services yet
4093 // wsmenu.add(seqsrchmenu);
4095 javax.swing.SwingUtilities.invokeLater(new Runnable()
4102 webService.removeAll();
4103 // first, add discovered services onto the webservices menu
4104 if (wsmenu.size() > 0)
4106 for (int i = 0, j = wsmenu.size(); i < j; i++)
4108 webService.add(wsmenu.get(i));
4113 webService.add(me.webServiceNoServices);
4115 // TODO: move into separate menu builder class.
4116 boolean new_sspred = false;
4117 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4119 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4120 if (jws2servs != null)
4122 if (jws2servs.hasServices())
4124 jws2servs.attachWSMenuEntry(webService, me);
4125 for (Jws2Instance sv : jws2servs.getServices())
4127 if (sv.description.toLowerCase().contains("jpred"))
4129 for (JMenuItem jmi : legacyItems)
4131 jmi.setVisible(false);
4137 if (jws2servs.isRunning())
4139 JMenuItem tm = new JMenuItem(
4140 "Still discovering JABA Services");
4141 tm.setEnabled(false);
4146 build_urlServiceMenu(me.webService);
4147 build_fetchdbmenu(webService);
4148 for (JMenu item : wsmenu)
4150 if (item.getItemCount() == 0)
4152 item.setEnabled(false);
4156 item.setEnabled(true);
4159 } catch (Exception e)
4162 .debug("Exception during web service menu building process.",
4167 } catch (Exception e)
4170 buildingMenu = false;
4177 * construct any groupURL type service menu entries.
4181 private void build_urlServiceMenu(JMenu webService)
4183 // TODO: remove this code when 2.7 is released
4184 // DEBUG - alignmentView
4186 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4187 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4189 * @Override public void actionPerformed(ActionEvent e) {
4190 * jalview.datamodel.AlignmentView
4191 * .testSelectionViews(af.viewport.getAlignment(),
4192 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4194 * }); webService.add(testAlView);
4196 // TODO: refactor to RestClient discoverer and merge menu entries for
4197 // rest-style services with other types of analysis/calculation service
4198 // SHmmr test client - still being implemented.
4199 // DEBUG - alignmentView
4201 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4204 client.attachWSMenuEntry(
4205 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4211 * Searches the alignment sequences for xRefs and builds the Show
4212 * Cross-References menu (formerly called Show Products), with database
4213 * sources for which cross-references are found (protein sources for a
4214 * nucleotide alignment and vice versa)
4216 * @return true if Show Cross-references menu should be enabled
4218 public boolean canShowProducts()
4220 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4221 AlignmentI dataset = viewport.getAlignment().getDataset();
4223 showProducts.removeAll();
4224 final boolean dna = viewport.getAlignment().isNucleotide();
4226 if (seqs == null || seqs.length == 0)
4228 // nothing to see here.
4232 boolean showp = false;
4235 List<String> ptypes = new CrossRef(seqs, dataset)
4236 .findXrefSourcesForSequences(dna);
4238 for (final String source : ptypes)
4241 final AlignFrame af = this;
4242 JMenuItem xtype = new JMenuItem(source);
4243 xtype.addActionListener(new ActionListener()
4246 public void actionPerformed(ActionEvent e)
4248 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4251 showProducts.add(xtype);
4253 showProducts.setVisible(showp);
4254 showProducts.setEnabled(showp);
4255 } catch (Exception e)
4258 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4266 * Finds and displays cross-references for the selected sequences (protein
4267 * products for nucleotide sequences, dna coding sequences for peptides).
4270 * the sequences to show cross-references for
4272 * true if from a nucleotide alignment (so showing proteins)
4274 * the database to show cross-references for
4276 protected void showProductsFor(final SequenceI[] sel,
4277 final boolean _odna, final String source)
4279 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4284 * Construct and display a new frame containing the translation of this
4285 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4288 public void showTranslation_actionPerformed(ActionEvent e)
4290 AlignmentI al = null;
4293 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4295 al = dna.translateCdna();
4296 } catch (Exception ex)
4298 jalview.bin.Cache.log.error(
4299 "Exception during translation. Please report this !", ex);
4300 final String msg = MessageManager
4301 .getString("label.error_when_translating_sequences_submit_bug_report");
4302 final String errorTitle = MessageManager
4303 .getString("label.implementation_error")
4304 + MessageManager.getString("label.translation_failed");
4305 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4306 JvOptionPane.ERROR_MESSAGE);
4309 if (al == null || al.getHeight() == 0)
4311 final String msg = MessageManager
4312 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4313 final String errorTitle = MessageManager
4314 .getString("label.translation_failed");
4315 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4316 JvOptionPane.WARNING_MESSAGE);
4320 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4321 af.setFileFormat(this.currentFileFormat);
4322 final String newTitle = MessageManager.formatMessage(
4323 "label.translation_of_params",
4324 new Object[] { this.getTitle() });
4325 af.setTitle(newTitle);
4326 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4328 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4329 viewport.openSplitFrame(af, new Alignment(seqs));
4333 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4340 * Set the file format
4344 public void setFileFormat(FileFormatI format)
4346 this.currentFileFormat = format;
4350 * Try to load a features file onto the alignment.
4353 * contents or path to retrieve file
4355 * access mode of file (see jalview.io.AlignFile)
4356 * @return true if features file was parsed correctly.
4358 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4360 return avc.parseFeaturesFile(file, sourceType,
4361 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4366 public void refreshFeatureUI(boolean enableIfNecessary)
4368 // note - currently this is only still here rather than in the controller
4369 // because of the featureSettings hard reference that is yet to be
4371 if (enableIfNecessary)
4373 viewport.setShowSequenceFeatures(true);
4374 showSeqFeatures.setSelected(true);
4380 public void dragEnter(DropTargetDragEvent evt)
4385 public void dragExit(DropTargetEvent evt)
4390 public void dragOver(DropTargetDragEvent evt)
4395 public void dropActionChanged(DropTargetDragEvent evt)
4400 public void drop(DropTargetDropEvent evt)
4402 // JAL-1552 - acceptDrop required before getTransferable call for
4403 // Java's Transferable for native dnd
4404 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4405 Transferable t = evt.getTransferable();
4406 List<String> files = new ArrayList<String>();
4407 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4411 Desktop.transferFromDropTarget(files, protocols, evt, t);
4412 } catch (Exception e)
4414 e.printStackTrace();
4420 // check to see if any of these files have names matching sequences in
4422 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4423 .getAlignment().getSequencesArray());
4425 * Object[] { String,SequenceI}
4427 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4428 ArrayList<String> filesnotmatched = new ArrayList<String>();
4429 for (int i = 0; i < files.size(); i++)
4431 String file = files.get(i).toString();
4433 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4434 if (protocol == DataSourceType.FILE)
4436 File fl = new File(file);
4437 pdbfn = fl.getName();
4439 else if (protocol == DataSourceType.URL)
4441 URL url = new URL(file);
4442 pdbfn = url.getFile();
4444 if (pdbfn.length() > 0)
4446 // attempt to find a match in the alignment
4447 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4448 int l = 0, c = pdbfn.indexOf(".");
4449 while (mtch == null && c != -1)
4454 } while ((c = pdbfn.indexOf(".", l)) > l);
4457 pdbfn = pdbfn.substring(0, l);
4459 mtch = idm.findAllIdMatches(pdbfn);
4463 FileFormatI type = null;
4466 type = new IdentifyFile().identify(file, protocol);
4467 } catch (Exception ex)
4471 if (type != null && type.isStructureFile())
4473 filesmatched.add(new Object[] { file, protocol, mtch });
4477 // File wasn't named like one of the sequences or wasn't a PDB file.
4478 filesnotmatched.add(file);
4482 if (filesmatched.size() > 0)
4484 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4490 "label.automatically_associate_structure_files_with_sequences_same_name",
4491 new Object[] { Integer
4497 .getString("label.automatically_associate_structure_files_by_name"),
4498 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4501 for (Object[] fm : filesmatched)
4503 // try and associate
4504 // TODO: may want to set a standard ID naming formalism for
4505 // associating PDB files which have no IDs.
4506 for (SequenceI toassoc : (SequenceI[]) fm[2])
4508 PDBEntry pe = new AssociatePdbFileWithSeq()
4509 .associatePdbWithSeq((String) fm[0],
4510 (DataSourceType) fm[1], toassoc, false,
4514 System.err.println("Associated file : "
4515 + ((String) fm[0]) + " with "
4516 + toassoc.getDisplayId(true));
4520 alignPanel.paintAlignment(true);
4524 if (filesnotmatched.size() > 0)
4527 && (Cache.getDefault(
4528 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4534 "label.ignore_unmatched_dropped_files_info",
4535 new Object[] { Integer
4542 .getString("label.ignore_unmatched_dropped_files"),
4543 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4547 for (String fn : filesnotmatched)
4549 loadJalviewDataFile(fn, null, null, null);
4553 } catch (Exception ex)
4555 ex.printStackTrace();
4561 * Attempt to load a "dropped" file or URL string, by testing in turn for
4563 * <li>an Annotation file</li>
4564 * <li>a JNet file</li>
4565 * <li>a features file</li>
4566 * <li>else try to interpret as an alignment file</li>
4570 * either a filename or a URL string.
4572 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4573 FileFormatI format, SequenceI assocSeq)
4577 if (sourceType == null)
4579 sourceType = FormatAdapter.checkProtocol(file);
4581 // if the file isn't identified, or not positively identified as some
4582 // other filetype (PFAM is default unidentified alignment file type) then
4583 // try to parse as annotation.
4584 boolean isAnnotation = (format == null || FileFormat.Pfam
4585 .equals(format)) ? new AnnotationFile()
4586 .annotateAlignmentView(viewport, file, sourceType) : false;
4590 // first see if its a T-COFFEE score file
4591 TCoffeeScoreFile tcf = null;
4594 tcf = new TCoffeeScoreFile(file, sourceType);
4597 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4600 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4601 isAnnotation = true;
4603 .setText(MessageManager
4604 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4608 // some problem - if no warning its probable that the ID matching
4609 // process didn't work
4613 tcf.getWarningMessage() == null ? MessageManager
4614 .getString("label.check_file_matches_sequence_ids_alignment")
4615 : tcf.getWarningMessage(),
4617 .getString("label.problem_reading_tcoffee_score_file"),
4618 JvOptionPane.WARNING_MESSAGE);
4625 } catch (Exception x)
4628 .debug("Exception when processing data source as T-COFFEE score file",
4634 // try to see if its a JNet 'concise' style annotation file *before*
4636 // try to parse it as a features file
4639 format = new IdentifyFile().identify(file, sourceType);
4641 if (FileFormat.ScoreMatrix == format)
4643 ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4646 // todo: i18n this message
4648 .setText(MessageManager.formatMessage(
4649 "label.successfully_loaded_matrix",
4650 sm.getMatrixName()));
4652 else if (FileFormat.Jnet.equals(format))
4654 JPredFile predictions = new JPredFile(file, sourceType);
4655 new JnetAnnotationMaker();
4656 JnetAnnotationMaker.add_annotation(predictions,
4657 viewport.getAlignment(), 0, false);
4658 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4659 viewport.getAlignment().setSeqrep(repseq);
4660 HiddenColumns cs = new HiddenColumns();
4661 cs.hideInsertionsFor(repseq);
4662 viewport.getAlignment().setHiddenColumns(cs);
4663 isAnnotation = true;
4665 // else if (IdentifyFile.FeaturesFile.equals(format))
4666 else if (FileFormat.Features.equals(format))
4668 if (parseFeaturesFile(file, sourceType))
4670 alignPanel.paintAlignment(true);
4675 new FileLoader().LoadFile(viewport, file, sourceType, format);
4682 alignPanel.adjustAnnotationHeight();
4683 viewport.updateSequenceIdColours();
4684 buildSortByAnnotationScoresMenu();
4685 alignPanel.paintAlignment(true);
4687 } catch (Exception ex)
4689 ex.printStackTrace();
4690 } catch (OutOfMemoryError oom)
4695 } catch (Exception x)
4700 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4701 : "using " + sourceType + " from " + file)
4703 + (format != null ? "(parsing as '" + format
4704 + "' file)" : ""), oom, Desktop.desktop);
4709 * Method invoked by the ChangeListener on the tabbed pane, in other words
4710 * when a different tabbed pane is selected by the user or programmatically.
4713 public void tabSelectionChanged(int index)
4717 alignPanel = alignPanels.get(index);
4718 viewport = alignPanel.av;
4719 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4720 setMenusFromViewport(viewport);
4724 * 'focus' any colour slider that is open to the selected viewport
4726 if (viewport.getConservationSelected())
4728 SliderPanel.setConservationSlider(alignPanel,
4729 viewport.getResidueShading(), alignPanel.getViewName());
4733 SliderPanel.hideConservationSlider();
4735 if (viewport.getAbovePIDThreshold())
4737 SliderPanel.setPIDSliderSource(alignPanel,
4738 viewport.getResidueShading(), alignPanel.getViewName());
4742 SliderPanel.hidePIDSlider();
4746 * If there is a frame linked to this one in a SplitPane, switch it to the
4747 * same view tab index. No infinite recursion of calls should happen, since
4748 * tabSelectionChanged() should not get invoked on setting the selected
4749 * index to an unchanged value. Guard against setting an invalid index
4750 * before the new view peer tab has been created.
4752 final AlignViewportI peer = viewport.getCodingComplement();
4755 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4756 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4758 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4764 * On right mouse click on view tab, prompt for and set new view name.
4767 public void tabbedPane_mousePressed(MouseEvent e)
4769 if (e.isPopupTrigger())
4771 String msg = MessageManager.getString("label.enter_view_name");
4772 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4773 JvOptionPane.QUESTION_MESSAGE);
4777 viewport.viewName = reply;
4778 // TODO warn if reply is in getExistingViewNames()?
4779 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4784 public AlignViewport getCurrentView()
4790 * Open the dialog for regex description parsing.
4793 protected void extractScores_actionPerformed(ActionEvent e)
4795 ParseProperties pp = new jalview.analysis.ParseProperties(
4796 viewport.getAlignment());
4797 // TODO: verify regex and introduce GUI dialog for version 2.5
4798 // if (pp.getScoresFromDescription("col", "score column ",
4799 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4801 if (pp.getScoresFromDescription("description column",
4802 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4804 buildSortByAnnotationScoresMenu();
4812 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4816 protected void showDbRefs_actionPerformed(ActionEvent e)
4818 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4824 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4828 protected void showNpFeats_actionPerformed(ActionEvent e)
4830 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4834 * find the viewport amongst the tabs in this alignment frame and close that
4839 public boolean closeView(AlignViewportI av)
4843 this.closeMenuItem_actionPerformed(false);
4846 Component[] comp = tabbedPane.getComponents();
4847 for (int i = 0; comp != null && i < comp.length; i++)
4849 if (comp[i] instanceof AlignmentPanel)
4851 if (((AlignmentPanel) comp[i]).av == av)
4854 closeView((AlignmentPanel) comp[i]);
4862 protected void build_fetchdbmenu(JMenu webService)
4864 // Temporary hack - DBRef Fetcher always top level ws entry.
4865 // TODO We probably want to store a sequence database checklist in
4866 // preferences and have checkboxes.. rather than individual sources selected
4868 final JMenu rfetch = new JMenu(
4869 MessageManager.getString("action.fetch_db_references"));
4870 rfetch.setToolTipText(MessageManager
4871 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4872 webService.add(rfetch);
4874 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4875 MessageManager.getString("option.trim_retrieved_seqs"));
4876 trimrs.setToolTipText(MessageManager
4877 .getString("label.trim_retrieved_sequences"));
4878 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4879 trimrs.addActionListener(new ActionListener()
4882 public void actionPerformed(ActionEvent e)
4884 trimrs.setSelected(trimrs.isSelected());
4885 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4886 Boolean.valueOf(trimrs.isSelected()).toString());
4890 JMenuItem fetchr = new JMenuItem(
4891 MessageManager.getString("label.standard_databases"));
4892 fetchr.setToolTipText(MessageManager
4893 .getString("label.fetch_embl_uniprot"));
4894 fetchr.addActionListener(new ActionListener()
4898 public void actionPerformed(ActionEvent e)
4900 new Thread(new Runnable()
4905 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4906 .getAlignment().isNucleotide();
4907 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4908 .getSequenceSelection(), alignPanel.alignFrame, null,
4909 alignPanel.alignFrame.featureSettings, isNucleotide);
4910 dbRefFetcher.addListener(new FetchFinishedListenerI()
4913 public void finished()
4915 AlignFrame.this.setMenusForViewport();
4918 dbRefFetcher.fetchDBRefs(false);
4926 final AlignFrame me = this;
4927 new Thread(new Runnable()
4932 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4933 .getSequenceFetcherSingleton(me);
4934 javax.swing.SwingUtilities.invokeLater(new Runnable()
4939 String[] dbclasses = sf.getOrderedSupportedSources();
4940 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4941 // jalview.util.QuickSort.sort(otherdb, otherdb);
4942 List<DbSourceProxy> otherdb;
4943 JMenu dfetch = new JMenu();
4944 JMenu ifetch = new JMenu();
4945 JMenuItem fetchr = null;
4946 int comp = 0, icomp = 0, mcomp = 15;
4947 String mname = null;
4949 for (String dbclass : dbclasses)
4951 otherdb = sf.getSourceProxy(dbclass);
4952 // add a single entry for this class, or submenu allowing 'fetch
4954 if (otherdb == null || otherdb.size() < 1)
4958 // List<DbSourceProxy> dbs=otherdb;
4959 // otherdb=new ArrayList<DbSourceProxy>();
4960 // for (DbSourceProxy db:dbs)
4962 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4966 mname = "From " + dbclass;
4968 if (otherdb.size() == 1)
4970 final DbSourceProxy[] dassource = otherdb
4971 .toArray(new DbSourceProxy[0]);
4972 DbSourceProxy src = otherdb.get(0);
4973 fetchr = new JMenuItem(src.getDbSource());
4974 fetchr.addActionListener(new ActionListener()
4978 public void actionPerformed(ActionEvent e)
4980 new Thread(new Runnable()
4986 boolean isNucleotide = alignPanel.alignFrame
4987 .getViewport().getAlignment()
4989 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4990 alignPanel.av.getSequenceSelection(),
4991 alignPanel.alignFrame, dassource,
4992 alignPanel.alignFrame.featureSettings,
4995 .addListener(new FetchFinishedListenerI()
4998 public void finished()
5000 AlignFrame.this.setMenusForViewport();
5003 dbRefFetcher.fetchDBRefs(false);
5009 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5010 MessageManager.formatMessage(
5011 "label.fetch_retrieve_from",
5012 new Object[] { src.getDbName() })));
5018 final DbSourceProxy[] dassource = otherdb
5019 .toArray(new DbSourceProxy[0]);
5021 DbSourceProxy src = otherdb.get(0);
5022 fetchr = new JMenuItem(MessageManager.formatMessage(
5023 "label.fetch_all_param",
5024 new Object[] { src.getDbSource() }));
5025 fetchr.addActionListener(new ActionListener()
5028 public void actionPerformed(ActionEvent e)
5030 new Thread(new Runnable()
5036 boolean isNucleotide = alignPanel.alignFrame
5037 .getViewport().getAlignment()
5039 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5040 alignPanel.av.getSequenceSelection(),
5041 alignPanel.alignFrame, dassource,
5042 alignPanel.alignFrame.featureSettings,
5045 .addListener(new FetchFinishedListenerI()
5048 public void finished()
5050 AlignFrame.this.setMenusForViewport();
5053 dbRefFetcher.fetchDBRefs(false);
5059 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5060 MessageManager.formatMessage(
5061 "label.fetch_retrieve_from_all_sources",
5063 Integer.valueOf(otherdb.size())
5064 .toString(), src.getDbSource(),
5065 src.getDbName() })));
5068 // and then build the rest of the individual menus
5069 ifetch = new JMenu(MessageManager.formatMessage(
5070 "label.source_from_db_source",
5071 new Object[] { src.getDbSource() }));
5073 String imname = null;
5075 for (DbSourceProxy sproxy : otherdb)
5077 String dbname = sproxy.getDbName();
5078 String sname = dbname.length() > 5 ? dbname.substring(0,
5079 5) + "..." : dbname;
5080 String msname = dbname.length() > 10 ? dbname.substring(
5081 0, 10) + "..." : dbname;
5084 imname = MessageManager.formatMessage(
5085 "label.from_msname", new Object[] { sname });
5087 fetchr = new JMenuItem(msname);
5088 final DbSourceProxy[] dassrc = { sproxy };
5089 fetchr.addActionListener(new ActionListener()
5093 public void actionPerformed(ActionEvent e)
5095 new Thread(new Runnable()
5101 boolean isNucleotide = alignPanel.alignFrame
5102 .getViewport().getAlignment()
5104 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5105 alignPanel.av.getSequenceSelection(),
5106 alignPanel.alignFrame, dassrc,
5107 alignPanel.alignFrame.featureSettings,
5110 .addListener(new FetchFinishedListenerI()
5113 public void finished()
5115 AlignFrame.this.setMenusForViewport();
5118 dbRefFetcher.fetchDBRefs(false);
5124 fetchr.setToolTipText("<html>"
5125 + MessageManager.formatMessage(
5126 "label.fetch_retrieve_from", new Object[]
5130 if (++icomp >= mcomp || i == (otherdb.size()))
5132 ifetch.setText(MessageManager.formatMessage(
5133 "label.source_to_target", imname, sname));
5135 ifetch = new JMenu();
5143 if (comp >= mcomp || dbi >= (dbclasses.length))
5145 dfetch.setText(MessageManager.formatMessage(
5146 "label.source_to_target", mname, dbclass));
5148 dfetch = new JMenu();
5161 * Left justify the whole alignment.
5164 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5166 AlignmentI al = viewport.getAlignment();
5168 viewport.firePropertyChange("alignment", null, al);
5172 * Right justify the whole alignment.
5175 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5177 AlignmentI al = viewport.getAlignment();
5179 viewport.firePropertyChange("alignment", null, al);
5183 public void setShowSeqFeatures(boolean b)
5185 showSeqFeatures.setSelected(b);
5186 viewport.setShowSequenceFeatures(b);
5193 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5194 * awt.event.ActionEvent)
5197 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5199 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5200 alignPanel.paintAlignment(true);
5207 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5211 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5213 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5214 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5222 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5223 * .event.ActionEvent)
5226 protected void showGroupConservation_actionPerformed(ActionEvent e)
5228 viewport.setShowGroupConservation(showGroupConservation.getState());
5229 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5236 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5237 * .event.ActionEvent)
5240 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5242 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5243 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5250 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5251 * .event.ActionEvent)
5254 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5256 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5257 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5261 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5263 showSequenceLogo.setState(true);
5264 viewport.setShowSequenceLogo(true);
5265 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5266 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5270 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5272 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5279 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5280 * .event.ActionEvent)
5283 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5285 if (avc.makeGroupsFromSelection())
5287 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5288 alignPanel.updateAnnotation();
5289 alignPanel.paintAlignment(true);
5293 public void clearAlignmentSeqRep()
5295 // TODO refactor alignmentseqrep to controller
5296 if (viewport.getAlignment().hasSeqrep())
5298 viewport.getAlignment().setSeqrep(null);
5299 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5300 alignPanel.updateAnnotation();
5301 alignPanel.paintAlignment(true);
5306 protected void createGroup_actionPerformed(ActionEvent e)
5308 if (avc.createGroup())
5310 alignPanel.alignmentChanged();
5315 protected void unGroup_actionPerformed(ActionEvent e)
5319 alignPanel.alignmentChanged();
5324 * make the given alignmentPanel the currently selected tab
5326 * @param alignmentPanel
5328 public void setDisplayedView(AlignmentPanel alignmentPanel)
5330 if (!viewport.getSequenceSetId().equals(
5331 alignmentPanel.av.getSequenceSetId()))
5335 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5337 if (tabbedPane != null
5338 && tabbedPane.getTabCount() > 0
5339 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5340 .getSelectedIndex())
5342 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5347 * Action on selection of menu options to Show or Hide annotations.
5350 * @param forSequences
5351 * update sequence-related annotations
5352 * @param forAlignment
5353 * update non-sequence-related annotations
5356 protected void setAnnotationsVisibility(boolean visible,
5357 boolean forSequences, boolean forAlignment)
5359 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5360 .getAlignmentAnnotation();
5365 for (AlignmentAnnotation aa : anns)
5368 * don't display non-positional annotations on an alignment
5370 if (aa.annotations == null)
5374 boolean apply = (aa.sequenceRef == null && forAlignment)
5375 || (aa.sequenceRef != null && forSequences);
5378 aa.visible = visible;
5381 alignPanel.validateAnnotationDimensions(true);
5382 alignPanel.alignmentChanged();
5386 * Store selected annotation sort order for the view and repaint.
5389 protected void sortAnnotations_actionPerformed()
5391 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5393 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5394 alignPanel.paintAlignment(true);
5399 * @return alignment panels in this alignment frame
5401 public List<? extends AlignmentViewPanel> getAlignPanels()
5403 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5407 * Open a new alignment window, with the cDNA associated with this (protein)
5408 * alignment, aligned as is the protein.
5410 protected void viewAsCdna_actionPerformed()
5412 // TODO no longer a menu action - refactor as required
5413 final AlignmentI alignment = getViewport().getAlignment();
5414 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5415 if (mappings == null)
5419 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5420 for (SequenceI aaSeq : alignment.getSequences())
5422 for (AlignedCodonFrame acf : mappings)
5424 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5428 * There is a cDNA mapping for this protein sequence - add to new
5429 * alignment. It will share the same dataset sequence as other mapped
5430 * cDNA (no new mappings need to be created).
5432 final Sequence newSeq = new Sequence(dnaSeq);
5433 newSeq.setDatasetSequence(dnaSeq);
5434 cdnaSeqs.add(newSeq);
5438 if (cdnaSeqs.size() == 0)
5440 // show a warning dialog no mapped cDNA
5443 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5445 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5446 AlignFrame.DEFAULT_HEIGHT);
5447 cdna.alignAs(alignment);
5448 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5450 Desktop.addInternalFrame(alignFrame, newtitle,
5451 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5455 * Set visibility of dna/protein complement view (available when shown in a
5461 protected void showComplement_actionPerformed(boolean show)
5463 SplitContainerI sf = getSplitViewContainer();
5466 sf.setComplementVisible(this, show);
5471 * Generate the reverse (optionally complemented) of the selected sequences,
5472 * and add them to the alignment
5475 protected void showReverse_actionPerformed(boolean complement)
5477 AlignmentI al = null;
5480 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5481 al = dna.reverseCdna(complement);
5482 viewport.addAlignment(al, "");
5483 addHistoryItem(new EditCommand(
5484 MessageManager.getString("label.add_sequences"),
5485 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5486 viewport.getAlignment()));
5487 } catch (Exception ex)
5489 System.err.println(ex.getMessage());
5495 * Try to run a script in the Groovy console, having first ensured that this
5496 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5497 * be targeted at this alignment.
5500 protected void runGroovy_actionPerformed()
5502 Jalview.setCurrentAlignFrame(this);
5503 groovy.ui.Console console = Desktop.getGroovyConsole();
5504 if (console != null)
5508 console.runScript();
5509 } catch (Exception ex)
5511 System.err.println((ex.toString()));
5513 .showInternalMessageDialog(Desktop.desktop, MessageManager
5514 .getString("label.couldnt_run_groovy_script"),
5516 .getString("label.groovy_support_failed"),
5517 JvOptionPane.ERROR_MESSAGE);
5522 System.err.println("Can't run Groovy script as console not found");
5527 * Hides columns containing (or not containing) a specified feature, provided
5528 * that would not leave all columns hidden
5530 * @param featureType
5531 * @param columnsContaining
5534 public boolean hideFeatureColumns(String featureType,
5535 boolean columnsContaining)
5537 boolean notForHiding = avc.markColumnsContainingFeatures(
5538 columnsContaining, false, false, featureType);
5541 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5542 false, featureType))
5544 getViewport().hideSelectedColumns();
5552 protected void selectHighlightedColumns_actionPerformed(
5553 ActionEvent actionEvent)
5555 // include key modifier check in case user selects from menu
5556 avc.markHighlightedColumns(
5557 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5559 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5563 * Rebuilds the Colour menu, including any user-defined colours which have
5564 * been loaded either on startup or during the session
5566 public void buildColourMenu()
5568 colourMenu.removeAll();
5570 colourMenu.add(applyToAllGroups);
5571 colourMenu.add(textColour);
5572 colourMenu.addSeparator();
5574 ColourMenuHelper.addMenuItems(colourMenu, this,
5575 viewport.getAlignment(), false);
5577 colourMenu.addSeparator();
5578 colourMenu.add(conservationMenuItem);
5579 colourMenu.add(modifyConservation);
5580 colourMenu.add(abovePIDThreshold);
5581 colourMenu.add(modifyPID);
5582 colourMenu.add(annotationColour);
5584 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5585 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5589 * Open a dialog (if not already open) that allows the user to select and
5590 * calculate PCA or Tree analysis
5592 protected void openTreePcaDialog()
5594 if (alignPanel.getCalculationDialog() == null)
5596 new CalculationChooser(AlignFrame.this);
5601 class PrintThread extends Thread
5605 public PrintThread(AlignmentPanel ap)
5610 static PageFormat pf;
5615 PrinterJob printJob = PrinterJob.getPrinterJob();
5619 printJob.setPrintable(ap, pf);
5623 printJob.setPrintable(ap);
5626 if (printJob.printDialog())
5631 } catch (Exception PrintException)
5633 PrintException.printStackTrace();