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.ScoreModelI;
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.HiddenSequences;
57 import jalview.datamodel.PDBEntry;
58 import jalview.datamodel.SeqCigar;
59 import jalview.datamodel.Sequence;
60 import jalview.datamodel.SequenceGroup;
61 import jalview.datamodel.SequenceI;
62 import jalview.gui.ColourMenuHelper.ColourChangeListener;
63 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
64 import jalview.io.AlignmentProperties;
65 import jalview.io.AnnotationFile;
66 import jalview.io.BioJsHTMLOutput;
67 import jalview.io.DataSourceType;
68 import jalview.io.FileFormat;
69 import jalview.io.FileFormatI;
70 import jalview.io.FileFormats;
71 import jalview.io.FileLoader;
72 import jalview.io.FormatAdapter;
73 import jalview.io.HtmlSvgOutput;
74 import jalview.io.IdentifyFile;
75 import jalview.io.JPredFile;
76 import jalview.io.JalviewFileChooser;
77 import jalview.io.JalviewFileView;
78 import jalview.io.JnetAnnotationMaker;
79 import jalview.io.NewickFile;
80 import jalview.io.TCoffeeScoreFile;
81 import jalview.jbgui.GAlignFrame;
82 import jalview.schemes.ColourSchemeI;
83 import jalview.schemes.ColourSchemes;
84 import jalview.schemes.ResidueColourScheme;
85 import jalview.schemes.ResidueProperties;
86 import jalview.schemes.TCoffeeColourScheme;
87 import jalview.util.MessageManager;
88 import jalview.viewmodel.AlignmentViewport;
89 import jalview.ws.DBRefFetcher;
90 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
91 import jalview.ws.jws1.Discoverer;
92 import jalview.ws.jws2.Jws2Discoverer;
93 import jalview.ws.jws2.jabaws2.Jws2Instance;
94 import jalview.ws.seqfetcher.DbSourceProxy;
96 import java.awt.BorderLayout;
97 import java.awt.Component;
98 import java.awt.Rectangle;
99 import java.awt.Toolkit;
100 import java.awt.datatransfer.Clipboard;
101 import java.awt.datatransfer.DataFlavor;
102 import java.awt.datatransfer.StringSelection;
103 import java.awt.datatransfer.Transferable;
104 import java.awt.dnd.DnDConstants;
105 import java.awt.dnd.DropTargetDragEvent;
106 import java.awt.dnd.DropTargetDropEvent;
107 import java.awt.dnd.DropTargetEvent;
108 import java.awt.dnd.DropTargetListener;
109 import java.awt.event.ActionEvent;
110 import java.awt.event.ActionListener;
111 import java.awt.event.FocusAdapter;
112 import java.awt.event.FocusEvent;
113 import java.awt.event.ItemEvent;
114 import java.awt.event.ItemListener;
115 import java.awt.event.KeyAdapter;
116 import java.awt.event.KeyEvent;
117 import java.awt.event.MouseEvent;
118 import java.awt.print.PageFormat;
119 import java.awt.print.PrinterJob;
120 import java.beans.PropertyChangeEvent;
122 import java.io.FileWriter;
123 import java.io.PrintWriter;
125 import java.util.ArrayList;
126 import java.util.Arrays;
127 import java.util.Deque;
128 import java.util.Enumeration;
129 import java.util.Hashtable;
130 import java.util.List;
131 import java.util.Vector;
133 import javax.swing.JCheckBoxMenuItem;
134 import javax.swing.JEditorPane;
135 import javax.swing.JInternalFrame;
136 import javax.swing.JLayeredPane;
137 import javax.swing.JMenu;
138 import javax.swing.JMenuItem;
139 import javax.swing.JScrollPane;
140 import javax.swing.SwingUtilities;
146 * @version $Revision$
148 public class AlignFrame extends GAlignFrame implements DropTargetListener,
149 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
152 public static final int DEFAULT_WIDTH = 700;
154 public static final int DEFAULT_HEIGHT = 500;
157 * The currently displayed panel (selected tabbed view if more than one)
159 public AlignmentPanel alignPanel;
161 AlignViewport viewport;
163 public AlignViewControllerI avc;
165 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
168 * Last format used to load or save alignments in this window
170 FileFormatI currentFileFormat = null;
173 * Current filename for this alignment
175 String fileName = null;
178 * Creates a new AlignFrame object with specific width and height.
184 public AlignFrame(AlignmentI al, int width, int height)
186 this(al, null, width, height);
190 * Creates a new AlignFrame object with specific width, height and
196 * @param sequenceSetId
198 public AlignFrame(AlignmentI al, int width, int height,
199 String sequenceSetId)
201 this(al, null, width, height, sequenceSetId);
205 * Creates a new AlignFrame object with specific width, height and
211 * @param sequenceSetId
214 public AlignFrame(AlignmentI al, int width, int height,
215 String sequenceSetId, String viewId)
217 this(al, null, width, height, sequenceSetId, viewId);
221 * new alignment window with hidden columns
225 * @param hiddenColumns
226 * ColumnSelection or null
228 * Width of alignment frame
232 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
233 int width, int height)
235 this(al, hiddenColumns, width, height, null);
239 * Create alignment frame for al with hiddenColumns, a specific width and
240 * height, and specific sequenceId
243 * @param hiddenColumns
246 * @param sequenceSetId
249 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
250 int width, int height, String sequenceSetId)
252 this(al, hiddenColumns, width, height, sequenceSetId, null);
256 * Create alignment frame for al with hiddenColumns, a specific width and
257 * height, and specific sequenceId
260 * @param hiddenColumns
263 * @param sequenceSetId
268 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
269 int width, int height, String sequenceSetId, String viewId)
271 setSize(width, height);
273 if (al.getDataset() == null)
278 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
280 alignPanel = new AlignmentPanel(this, viewport);
282 addAlignmentPanel(alignPanel, true);
286 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
287 ColumnSelection hiddenColumns, int width, int height)
289 setSize(width, height);
291 if (al.getDataset() == null)
296 viewport = new AlignViewport(al, hiddenColumns);
298 if (hiddenSeqs != null && hiddenSeqs.length > 0)
300 viewport.hideSequence(hiddenSeqs);
302 alignPanel = new AlignmentPanel(this, viewport);
303 addAlignmentPanel(alignPanel, true);
308 * Make a new AlignFrame from existing alignmentPanels
315 public AlignFrame(AlignmentPanel ap)
319 addAlignmentPanel(ap, false);
324 * initalise the alignframe from the underlying viewport data and the
329 if (!Jalview.isHeadlessMode())
331 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
334 avc = new jalview.controller.AlignViewController(this, viewport,
336 if (viewport.getAlignmentConservationAnnotation() == null)
338 // BLOSUM62Colour.setEnabled(false);
339 conservationMenuItem.setEnabled(false);
340 modifyConservation.setEnabled(false);
341 // PIDColour.setEnabled(false);
342 // abovePIDThreshold.setEnabled(false);
343 // modifyPID.setEnabled(false);
346 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
349 if (sortby.equals("Id"))
351 sortIDMenuItem_actionPerformed(null);
353 else if (sortby.equals("Pairwise Identity"))
355 sortPairwiseMenuItem_actionPerformed(null);
359 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
361 setMenusFromViewport(viewport);
362 buildSortByAnnotationScoresMenu();
366 if (Desktop.desktop != null)
368 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
369 addServiceListeners();
373 if (viewport.getWrapAlignment())
375 wrapMenuItem_actionPerformed(null);
378 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
380 this.overviewMenuItem_actionPerformed(null);
385 final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
386 final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
387 final String menuLabel = MessageManager
388 .getString("label.copy_format_from");
389 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
390 new ViewSetProvider()
394 public AlignmentPanel[] getAllAlignmentPanels()
397 origview.add(alignPanel);
398 // make an array of all alignment panels except for this one
399 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
400 Arrays.asList(Desktop.getAlignmentPanels(null)));
401 aps.remove(AlignFrame.this.alignPanel);
402 return aps.toArray(new AlignmentPanel[aps.size()]);
404 }, selviews, new ItemListener()
408 public void itemStateChanged(ItemEvent e)
410 if (origview.size() > 0)
412 final AlignmentPanel ap = origview.get(0);
415 * Copy the ViewStyle of the selected panel to 'this one'.
416 * Don't change value of 'scaleProteinAsCdna' unless copying
419 ViewStyleI vs = selviews.get(0).getAlignViewport()
421 boolean fromSplitFrame = selviews.get(0)
422 .getAlignViewport().getCodingComplement() != null;
425 vs.setScaleProteinAsCdna(ap.getAlignViewport()
426 .getViewStyle().isScaleProteinAsCdna());
428 ap.getAlignViewport().setViewStyle(vs);
431 * Also rescale ViewStyle of SplitFrame complement if there is
432 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
433 * the whole ViewStyle (allow cDNA protein to have different
436 AlignViewportI complement = ap.getAlignViewport()
437 .getCodingComplement();
438 if (complement != null && vs.isScaleProteinAsCdna())
440 AlignFrame af = Desktop.getAlignFrameFor(complement);
441 ((SplitFrame) af.getSplitViewContainer())
443 af.setMenusForViewport();
447 ap.setSelected(true);
448 ap.alignFrame.setMenusForViewport();
453 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
454 .indexOf("devel") > -1
455 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
456 .indexOf("test") > -1)
458 formatMenu.add(vsel);
460 addFocusListener(new FocusAdapter()
463 public void focusGained(FocusEvent e)
465 Jalview.setCurrentAlignFrame(AlignFrame.this);
472 * Change the filename and format for the alignment, and enable the 'reload'
473 * button functionality.
480 public void setFileName(String file, FileFormatI format)
483 setFileFormat(format);
484 reload.setEnabled(true);
488 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
491 void addKeyListener()
493 addKeyListener(new KeyAdapter()
496 public void keyPressed(KeyEvent evt)
498 if (viewport.cursorMode
499 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
500 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
501 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
502 && Character.isDigit(evt.getKeyChar()))
504 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
507 switch (evt.getKeyCode())
510 case 27: // escape key
511 deselectAllSequenceMenuItem_actionPerformed(null);
515 case KeyEvent.VK_DOWN:
516 if (evt.isAltDown() || !viewport.cursorMode)
518 moveSelectedSequences(false);
520 if (viewport.cursorMode)
522 alignPanel.getSeqPanel().moveCursor(0, 1);
527 if (evt.isAltDown() || !viewport.cursorMode)
529 moveSelectedSequences(true);
531 if (viewport.cursorMode)
533 alignPanel.getSeqPanel().moveCursor(0, -1);
538 case KeyEvent.VK_LEFT:
539 if (evt.isAltDown() || !viewport.cursorMode)
541 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
545 alignPanel.getSeqPanel().moveCursor(-1, 0);
550 case KeyEvent.VK_RIGHT:
551 if (evt.isAltDown() || !viewport.cursorMode)
553 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
557 alignPanel.getSeqPanel().moveCursor(1, 0);
561 case KeyEvent.VK_SPACE:
562 if (viewport.cursorMode)
564 alignPanel.getSeqPanel().insertGapAtCursor(
565 evt.isControlDown() || evt.isShiftDown()
570 // case KeyEvent.VK_A:
571 // if (viewport.cursorMode)
573 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
574 // //System.out.println("A");
578 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
579 * System.out.println("closing bracket"); } break;
581 case KeyEvent.VK_DELETE:
582 case KeyEvent.VK_BACK_SPACE:
583 if (!viewport.cursorMode)
585 cut_actionPerformed(null);
589 alignPanel.getSeqPanel().deleteGapAtCursor(
590 evt.isControlDown() || evt.isShiftDown()
597 if (viewport.cursorMode)
599 alignPanel.getSeqPanel().setCursorRow();
603 if (viewport.cursorMode && !evt.isControlDown())
605 alignPanel.getSeqPanel().setCursorColumn();
609 if (viewport.cursorMode)
611 alignPanel.getSeqPanel().setCursorPosition();
615 case KeyEvent.VK_ENTER:
616 case KeyEvent.VK_COMMA:
617 if (viewport.cursorMode)
619 alignPanel.getSeqPanel().setCursorRowAndColumn();
624 if (viewport.cursorMode)
626 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
630 if (viewport.cursorMode)
632 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
637 viewport.cursorMode = !viewport.cursorMode;
638 statusBar.setText(MessageManager.formatMessage(
639 "label.keyboard_editing_mode",
640 new String[] { (viewport.cursorMode ? "on" : "off") }));
641 if (viewport.cursorMode)
643 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport
645 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport
648 alignPanel.getSeqPanel().seqCanvas.repaint();
654 Help.showHelpWindow();
655 } catch (Exception ex)
657 ex.printStackTrace();
662 boolean toggleSeqs = !evt.isControlDown();
663 boolean toggleCols = !evt.isShiftDown();
664 toggleHiddenRegions(toggleSeqs, toggleCols);
669 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
670 boolean modifyExisting = true; // always modify, don't clear
671 // evt.isShiftDown();
672 boolean invertHighlighted = evt.isAltDown();
673 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
677 case KeyEvent.VK_PAGE_UP:
678 if (viewport.getWrapAlignment())
680 alignPanel.scrollUp(true);
684 alignPanel.setScrollValues(viewport.getStartRes(),
685 2 * viewport.getStartSeq() - viewport.getEndSeq());
688 case KeyEvent.VK_PAGE_DOWN:
689 if (viewport.getWrapAlignment())
691 alignPanel.scrollUp(false);
695 alignPanel.setScrollValues(viewport.getStartRes(),
696 viewport.getEndSeq());
703 public void keyReleased(KeyEvent evt)
705 switch (evt.getKeyCode())
707 case KeyEvent.VK_LEFT:
708 if (evt.isAltDown() || !viewport.cursorMode)
710 viewport.firePropertyChange("alignment", null, viewport
711 .getAlignment().getSequences());
715 case KeyEvent.VK_RIGHT:
716 if (evt.isAltDown() || !viewport.cursorMode)
718 viewport.firePropertyChange("alignment", null, viewport
719 .getAlignment().getSequences());
727 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
729 ap.alignFrame = this;
730 avc = new jalview.controller.AlignViewController(this, viewport,
735 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
737 int aSize = alignPanels.size();
739 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
741 if (aSize == 1 && ap.av.viewName == null)
743 this.getContentPane().add(ap, BorderLayout.CENTER);
749 setInitialTabVisible();
752 expandViews.setEnabled(true);
753 gatherViews.setEnabled(true);
754 tabbedPane.addTab(ap.av.viewName, ap);
756 ap.setVisible(false);
761 if (ap.av.isPadGaps())
763 ap.av.getAlignment().padGaps();
765 ap.av.updateConservation(ap);
766 ap.av.updateConsensus(ap);
767 ap.av.updateStrucConsensus(ap);
771 public void setInitialTabVisible()
773 expandViews.setEnabled(true);
774 gatherViews.setEnabled(true);
775 tabbedPane.setVisible(true);
776 AlignmentPanel first = alignPanels.get(0);
777 tabbedPane.addTab(first.av.viewName, first);
778 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
781 public AlignViewport getViewport()
786 /* Set up intrinsic listeners for dynamically generated GUI bits. */
787 private void addServiceListeners()
789 final java.beans.PropertyChangeListener thisListener;
790 Desktop.instance.addJalviewPropertyChangeListener("services",
791 thisListener = new java.beans.PropertyChangeListener()
794 public void propertyChange(PropertyChangeEvent evt)
796 // // System.out.println("Discoverer property change.");
797 // if (evt.getPropertyName().equals("services"))
799 SwingUtilities.invokeLater(new Runnable()
806 .println("Rebuild WS Menu for service change");
807 BuildWebServiceMenu();
814 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
817 public void internalFrameClosed(
818 javax.swing.event.InternalFrameEvent evt)
820 // System.out.println("deregistering discoverer listener");
821 Desktop.instance.removeJalviewPropertyChangeListener("services",
823 closeMenuItem_actionPerformed(true);
826 // Finally, build the menu once to get current service state
827 new Thread(new Runnable()
832 BuildWebServiceMenu();
838 * Configure menu items that vary according to whether the alignment is
839 * nucleotide or protein
841 public void setGUINucleotide()
843 AlignmentI al = getViewport().getAlignment();
844 boolean nucleotide = al.isNucleotide();
846 showTranslation.setVisible(nucleotide);
847 showReverse.setVisible(nucleotide);
848 showReverseComplement.setVisible(nucleotide);
849 conservationMenuItem.setEnabled(!nucleotide);
850 modifyConservation.setEnabled(!nucleotide
851 && conservationMenuItem.isSelected());
852 showGroupConservation.setEnabled(!nucleotide);
854 showComplementMenuItem.setText(nucleotide ? MessageManager
855 .getString("label.protein") : MessageManager
856 .getString("label.nucleotide"));
860 * set up menus for the current viewport. This may be called after any
861 * operation that affects the data in the current view (selection changed,
862 * etc) to update the menus to reflect the new state.
865 public void setMenusForViewport()
867 setMenusFromViewport(viewport);
871 * Need to call this method when tabs are selected for multiple views, or when
872 * loading from Jalview2XML.java
877 void setMenusFromViewport(AlignViewport av)
879 padGapsMenuitem.setSelected(av.isPadGaps());
880 colourTextMenuItem.setSelected(av.isShowColourText());
881 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
882 modifyPID.setEnabled(abovePIDThreshold.isSelected());
883 conservationMenuItem.setSelected(av.getConservationSelected());
884 modifyConservation.setEnabled(conservationMenuItem.isSelected());
885 seqLimits.setSelected(av.getShowJVSuffix());
886 idRightAlign.setSelected(av.isRightAlignIds());
887 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
888 renderGapsMenuItem.setSelected(av.isRenderGaps());
889 wrapMenuItem.setSelected(av.getWrapAlignment());
890 scaleAbove.setVisible(av.getWrapAlignment());
891 scaleLeft.setVisible(av.getWrapAlignment());
892 scaleRight.setVisible(av.getWrapAlignment());
893 annotationPanelMenuItem.setState(av.isShowAnnotation());
895 * Show/hide annotations only enabled if annotation panel is shown
897 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
898 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
899 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
900 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
901 viewBoxesMenuItem.setSelected(av.getShowBoxes());
902 viewTextMenuItem.setSelected(av.getShowText());
903 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
904 showGroupConsensus.setSelected(av.isShowGroupConsensus());
905 showGroupConservation.setSelected(av.isShowGroupConservation());
906 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
907 showSequenceLogo.setSelected(av.isShowSequenceLogo());
908 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
910 ColourMenuHelper.setColourSelected(colourMenu,
911 av.getGlobalColourScheme());
913 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
914 hiddenMarkers.setState(av.getShowHiddenMarkers());
915 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
916 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
917 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
918 autoCalculate.setSelected(av.autoCalculateConsensus);
919 sortByTree.setSelected(av.sortByTree);
920 listenToViewSelections.setSelected(av.followSelection);
922 showProducts.setEnabled(canShowProducts());
923 setGroovyEnabled(Desktop.getGroovyConsole() != null);
929 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
933 public void setGroovyEnabled(boolean b)
935 runGroovy.setEnabled(b);
938 private IProgressIndicator progressBar;
943 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
946 public void setProgressBar(String message, long id)
948 progressBar.setProgressBar(message, id);
952 public void registerHandler(final long id,
953 final IProgressIndicatorHandler handler)
955 progressBar.registerHandler(id, handler);
960 * @return true if any progress bars are still active
963 public boolean operationInProgress()
965 return progressBar.operationInProgress();
969 public void setStatus(String text)
971 statusBar.setText(text);
975 * Added so Castor Mapping file can obtain Jalview Version
977 public String getVersion()
979 return jalview.bin.Cache.getProperty("VERSION");
982 public FeatureRenderer getFeatureRenderer()
984 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
988 public void fetchSequence_actionPerformed(ActionEvent e)
990 new jalview.gui.SequenceFetcher(this);
994 public void addFromFile_actionPerformed(ActionEvent e)
996 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1000 public void reload_actionPerformed(ActionEvent e)
1002 if (fileName != null)
1004 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1005 // originating file's format
1006 // TODO: work out how to recover feature settings for correct view(s) when
1007 // file is reloaded.
1008 if (FileFormat.Jalview.equals(currentFileFormat))
1010 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1011 for (int i = 0; i < frames.length; i++)
1013 if (frames[i] instanceof AlignFrame && frames[i] != this
1014 && ((AlignFrame) frames[i]).fileName != null
1015 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1019 frames[i].setSelected(true);
1020 Desktop.instance.closeAssociatedWindows();
1021 } catch (java.beans.PropertyVetoException ex)
1027 Desktop.instance.closeAssociatedWindows();
1029 FileLoader loader = new FileLoader();
1030 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1031 : DataSourceType.FILE;
1032 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1036 Rectangle bounds = this.getBounds();
1038 FileLoader loader = new FileLoader();
1039 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1040 : DataSourceType.FILE;
1041 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1042 protocol, currentFileFormat);
1044 newframe.setBounds(bounds);
1045 if (featureSettings != null && featureSettings.isShowing())
1047 final Rectangle fspos = featureSettings.frame.getBounds();
1048 // TODO: need a 'show feature settings' function that takes bounds -
1049 // need to refactor Desktop.addFrame
1050 newframe.featureSettings_actionPerformed(null);
1051 final FeatureSettings nfs = newframe.featureSettings;
1052 SwingUtilities.invokeLater(new Runnable()
1057 nfs.frame.setBounds(fspos);
1060 this.featureSettings.close();
1061 this.featureSettings = null;
1063 this.closeMenuItem_actionPerformed(true);
1069 public void addFromText_actionPerformed(ActionEvent e)
1071 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1076 public void addFromURL_actionPerformed(ActionEvent e)
1078 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1082 public void save_actionPerformed(ActionEvent e)
1084 if (fileName == null || (currentFileFormat == null)
1085 || fileName.startsWith("http"))
1087 saveAs_actionPerformed(null);
1091 saveAlignment(fileName, currentFileFormat);
1102 public void saveAs_actionPerformed(ActionEvent e)
1104 String format = currentFileFormat == null ? null : currentFileFormat
1106 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1107 Cache.getProperty("LAST_DIRECTORY"), format);
1109 chooser.setFileView(new JalviewFileView());
1110 chooser.setDialogTitle(MessageManager
1111 .getString("label.save_alignment_to_file"));
1112 chooser.setToolTipText(MessageManager.getString("action.save"));
1114 int value = chooser.showSaveDialog(this);
1116 if (value == JalviewFileChooser.APPROVE_OPTION)
1118 currentFileFormat = chooser.getSelectedFormat();
1119 while (currentFileFormat == null)
1122 .showInternalMessageDialog(
1125 .getString("label.select_file_format_before_saving"),
1127 .getString("label.file_format_not_specified"),
1128 JvOptionPane.WARNING_MESSAGE);
1129 currentFileFormat = chooser.getSelectedFormat();
1130 value = chooser.showSaveDialog(this);
1131 if (value != JalviewFileChooser.APPROVE_OPTION)
1137 fileName = chooser.getSelectedFile().getPath();
1139 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1141 Cache.setProperty("LAST_DIRECTORY", fileName);
1142 saveAlignment(fileName, currentFileFormat);
1146 public boolean saveAlignment(String file, FileFormatI format)
1148 boolean success = true;
1150 if (FileFormat.Jalview.equals(format))
1152 String shortName = title;
1154 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1156 shortName = shortName.substring(shortName
1157 .lastIndexOf(java.io.File.separatorChar) + 1);
1160 success = new Jalview2XML().saveAlignment(this, file, shortName);
1162 statusBar.setText(MessageManager.formatMessage(
1163 "label.successfully_saved_to_file_in_format", new Object[] {
1164 fileName, format }));
1169 AlignmentExportData exportData = getAlignmentForExport(format,
1171 if (exportData.getSettings().isCancelled())
1175 FormatAdapter f = new FormatAdapter(alignPanel,
1176 exportData.getSettings());
1177 String output = f.formatSequences(
1179 exportData.getAlignment(), // class cast exceptions will
1180 // occur in the distant future
1181 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1182 f.getCacheSuffixDefault(format),
1183 viewport.getColumnSelection());
1193 PrintWriter out = new PrintWriter(new FileWriter(file));
1197 this.setTitle(file);
1198 statusBar.setText(MessageManager.formatMessage(
1199 "label.successfully_saved_to_file_in_format",
1200 new Object[] { fileName, format.getName() }));
1201 } catch (Exception ex)
1204 ex.printStackTrace();
1211 JvOptionPane.showInternalMessageDialog(this, MessageManager
1212 .formatMessage("label.couldnt_save_file",
1213 new Object[] { fileName }), MessageManager
1214 .getString("label.error_saving_file"),
1215 JvOptionPane.WARNING_MESSAGE);
1221 private void warningMessage(String warning, String title)
1223 if (new jalview.util.Platform().isHeadless())
1225 System.err.println("Warning: " + title + "\nWarning: " + warning);
1230 JvOptionPane.showInternalMessageDialog(this, warning, title,
1231 JvOptionPane.WARNING_MESSAGE);
1243 protected void outputText_actionPerformed(ActionEvent e)
1245 FileFormatI fileFormat = FileFormats.getInstance().forName(
1246 e.getActionCommand());
1247 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1249 if (exportData.getSettings().isCancelled())
1253 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1254 cap.setForInput(null);
1257 FileFormatI format = fileFormat;
1258 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1259 .formatSequences(format, exportData.getAlignment(),
1260 exportData.getOmitHidden(),
1261 exportData.getStartEndPostions(),
1262 viewport.getColumnSelection()));
1263 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1264 "label.alignment_output_command",
1265 new Object[] { e.getActionCommand() }), 600, 500);
1266 } catch (OutOfMemoryError oom)
1268 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1274 public static AlignmentExportData getAlignmentForExport(
1275 FileFormatI format, AlignViewportI viewport,
1276 AlignExportSettingI exportSettings)
1278 AlignmentI alignmentToExport = null;
1279 AlignExportSettingI settings = exportSettings;
1280 String[] omitHidden = null;
1282 HiddenSequences hiddenSeqs = viewport.getAlignment()
1283 .getHiddenSequences();
1285 alignmentToExport = viewport.getAlignment();
1287 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1288 if (settings == null)
1290 settings = new AlignExportSettings(hasHiddenSeqs,
1291 viewport.hasHiddenColumns(), format);
1293 // settings.isExportAnnotations();
1295 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1297 omitHidden = viewport.getViewAsString(false,
1298 settings.isExportHiddenSequences());
1301 int[] alignmentStartEnd = new int[2];
1302 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1304 alignmentToExport = hiddenSeqs.getFullAlignment();
1308 alignmentToExport = viewport.getAlignment();
1310 alignmentStartEnd = alignmentToExport
1311 .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1312 .getHiddenColumns());
1313 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1314 omitHidden, alignmentStartEnd, settings);
1325 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1327 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1328 htmlSVG.exportHTML(null);
1332 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1334 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1335 bjs.exportHTML(null);
1338 public void createImageMap(File file, String image)
1340 alignPanel.makePNGImageMap(file, image);
1350 public void createPNG(File f)
1352 alignPanel.makePNG(f);
1362 public void createEPS(File f)
1364 alignPanel.makeEPS(f);
1368 public void createSVG(File f)
1370 alignPanel.makeSVG(f);
1374 public void pageSetup_actionPerformed(ActionEvent e)
1376 PrinterJob printJob = PrinterJob.getPrinterJob();
1377 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1387 public void printMenuItem_actionPerformed(ActionEvent e)
1389 // Putting in a thread avoids Swing painting problems
1390 PrintThread thread = new PrintThread(alignPanel);
1395 public void exportFeatures_actionPerformed(ActionEvent e)
1397 new AnnotationExporter().exportFeatures(alignPanel);
1401 public void exportAnnotations_actionPerformed(ActionEvent e)
1403 new AnnotationExporter().exportAnnotations(alignPanel);
1407 public void associatedData_actionPerformed(ActionEvent e)
1409 // Pick the tree file
1410 JalviewFileChooser chooser = new JalviewFileChooser(
1411 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1412 chooser.setFileView(new JalviewFileView());
1413 chooser.setDialogTitle(MessageManager
1414 .getString("label.load_jalview_annotations"));
1415 chooser.setToolTipText(MessageManager
1416 .getString("label.load_jalview_annotations"));
1418 int value = chooser.showOpenDialog(null);
1420 if (value == JalviewFileChooser.APPROVE_OPTION)
1422 String choice = chooser.getSelectedFile().getPath();
1423 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1424 loadJalviewDataFile(choice, null, null, null);
1430 * Close the current view or all views in the alignment frame. If the frame
1431 * only contains one view then the alignment will be removed from memory.
1433 * @param closeAllTabs
1436 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1438 if (alignPanels != null && alignPanels.size() < 2)
1440 closeAllTabs = true;
1445 if (alignPanels != null)
1449 if (this.isClosed())
1451 // really close all the windows - otherwise wait till
1452 // setClosed(true) is called
1453 for (int i = 0; i < alignPanels.size(); i++)
1455 AlignmentPanel ap = alignPanels.get(i);
1462 closeView(alignPanel);
1469 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1470 * be called recursively, with the frame now in 'closed' state
1472 this.setClosed(true);
1474 } catch (Exception ex)
1476 ex.printStackTrace();
1481 * Close the specified panel and close up tabs appropriately.
1483 * @param panelToClose
1485 public void closeView(AlignmentPanel panelToClose)
1487 int index = tabbedPane.getSelectedIndex();
1488 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1489 alignPanels.remove(panelToClose);
1490 panelToClose.closePanel();
1491 panelToClose = null;
1493 tabbedPane.removeTabAt(closedindex);
1494 tabbedPane.validate();
1496 if (index > closedindex || index == tabbedPane.getTabCount())
1498 // modify currently selected tab index if necessary.
1502 this.tabSelectionChanged(index);
1508 void updateEditMenuBar()
1511 if (viewport.getHistoryList().size() > 0)
1513 undoMenuItem.setEnabled(true);
1514 CommandI command = viewport.getHistoryList().peek();
1515 undoMenuItem.setText(MessageManager.formatMessage(
1516 "label.undo_command",
1517 new Object[] { command.getDescription() }));
1521 undoMenuItem.setEnabled(false);
1522 undoMenuItem.setText(MessageManager.getString("action.undo"));
1525 if (viewport.getRedoList().size() > 0)
1527 redoMenuItem.setEnabled(true);
1529 CommandI command = viewport.getRedoList().peek();
1530 redoMenuItem.setText(MessageManager.formatMessage(
1531 "label.redo_command",
1532 new Object[] { command.getDescription() }));
1536 redoMenuItem.setEnabled(false);
1537 redoMenuItem.setText(MessageManager.getString("action.redo"));
1542 public void addHistoryItem(CommandI command)
1544 if (command.getSize() > 0)
1546 viewport.addToHistoryList(command);
1547 viewport.clearRedoList();
1548 updateEditMenuBar();
1549 viewport.updateHiddenColumns();
1550 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1551 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1552 // viewport.getColumnSelection()
1553 // .getHiddenColumns().size() > 0);
1559 * @return alignment objects for all views
1561 AlignmentI[] getViewAlignments()
1563 if (alignPanels != null)
1565 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1567 for (AlignmentPanel ap : alignPanels)
1569 als[i++] = ap.av.getAlignment();
1573 if (viewport != null)
1575 return new AlignmentI[] { viewport.getAlignment() };
1587 protected void undoMenuItem_actionPerformed(ActionEvent e)
1589 if (viewport.getHistoryList().isEmpty())
1593 CommandI command = viewport.getHistoryList().pop();
1594 viewport.addToRedoList(command);
1595 command.undoCommand(getViewAlignments());
1597 AlignmentViewport originalSource = getOriginatingSource(command);
1598 updateEditMenuBar();
1600 if (originalSource != null)
1602 if (originalSource != viewport)
1605 .warn("Implementation worry: mismatch of viewport origin for undo");
1607 originalSource.updateHiddenColumns();
1608 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1610 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1611 // viewport.getColumnSelection()
1612 // .getHiddenColumns().size() > 0);
1613 originalSource.firePropertyChange("alignment", null, originalSource
1614 .getAlignment().getSequences());
1625 protected void redoMenuItem_actionPerformed(ActionEvent e)
1627 if (viewport.getRedoList().size() < 1)
1632 CommandI command = viewport.getRedoList().pop();
1633 viewport.addToHistoryList(command);
1634 command.doCommand(getViewAlignments());
1636 AlignmentViewport originalSource = getOriginatingSource(command);
1637 updateEditMenuBar();
1639 if (originalSource != null)
1642 if (originalSource != viewport)
1645 .warn("Implementation worry: mismatch of viewport origin for redo");
1647 originalSource.updateHiddenColumns();
1648 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1650 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1651 // viewport.getColumnSelection()
1652 // .getHiddenColumns().size() > 0);
1653 originalSource.firePropertyChange("alignment", null, originalSource
1654 .getAlignment().getSequences());
1658 AlignmentViewport getOriginatingSource(CommandI command)
1660 AlignmentViewport originalSource = null;
1661 // For sequence removal and addition, we need to fire
1662 // the property change event FROM the viewport where the
1663 // original alignment was altered
1664 AlignmentI al = null;
1665 if (command instanceof EditCommand)
1667 EditCommand editCommand = (EditCommand) command;
1668 al = editCommand.getAlignment();
1669 List<Component> comps = PaintRefresher.components.get(viewport
1670 .getSequenceSetId());
1672 for (Component comp : comps)
1674 if (comp instanceof AlignmentPanel)
1676 if (al == ((AlignmentPanel) comp).av.getAlignment())
1678 originalSource = ((AlignmentPanel) comp).av;
1685 if (originalSource == null)
1687 // The original view is closed, we must validate
1688 // the current view against the closed view first
1691 PaintRefresher.validateSequences(al, viewport.getAlignment());
1694 originalSource = viewport;
1697 return originalSource;
1706 public void moveSelectedSequences(boolean up)
1708 SequenceGroup sg = viewport.getSelectionGroup();
1714 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1715 viewport.getHiddenRepSequences(), up);
1716 alignPanel.paintAlignment(true);
1719 synchronized void slideSequences(boolean right, int size)
1721 List<SequenceI> sg = new ArrayList<SequenceI>();
1722 if (viewport.cursorMode)
1724 sg.add(viewport.getAlignment().getSequenceAt(
1725 alignPanel.getSeqPanel().seqCanvas.cursorY));
1727 else if (viewport.getSelectionGroup() != null
1728 && viewport.getSelectionGroup().getSize() != viewport
1729 .getAlignment().getHeight())
1731 sg = viewport.getSelectionGroup().getSequences(
1732 viewport.getHiddenRepSequences());
1740 List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1742 for (SequenceI seq : viewport.getAlignment().getSequences())
1744 if (!sg.contains(seq))
1746 invertGroup.add(seq);
1750 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1752 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1753 for (int i = 0; i < invertGroup.size(); i++)
1755 seqs2[i] = invertGroup.get(i);
1758 SlideSequencesCommand ssc;
1761 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1762 size, viewport.getGapCharacter());
1766 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1767 size, viewport.getGapCharacter());
1770 int groupAdjustment = 0;
1771 if (ssc.getGapsInsertedBegin() && right)
1773 if (viewport.cursorMode)
1775 alignPanel.getSeqPanel().moveCursor(size, 0);
1779 groupAdjustment = size;
1782 else if (!ssc.getGapsInsertedBegin() && !right)
1784 if (viewport.cursorMode)
1786 alignPanel.getSeqPanel().moveCursor(-size, 0);
1790 groupAdjustment = -size;
1794 if (groupAdjustment != 0)
1796 viewport.getSelectionGroup().setStartRes(
1797 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1798 viewport.getSelectionGroup().setEndRes(
1799 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1803 * just extend the last slide command if compatible; but not if in
1804 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1806 boolean appendHistoryItem = false;
1807 Deque<CommandI> historyList = viewport.getHistoryList();
1808 boolean inSplitFrame = getSplitViewContainer() != null;
1809 if (!inSplitFrame && historyList != null && historyList.size() > 0
1810 && historyList.peek() instanceof SlideSequencesCommand)
1812 appendHistoryItem = ssc
1813 .appendSlideCommand((SlideSequencesCommand) historyList
1817 if (!appendHistoryItem)
1819 addHistoryItem(ssc);
1832 protected void copy_actionPerformed(ActionEvent e)
1835 if (viewport.getSelectionGroup() == null)
1839 // TODO: preserve the ordering of displayed alignment annotation in any
1840 // internal paste (particularly sequence associated annotation)
1841 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1842 String[] omitHidden = null;
1844 if (viewport.hasHiddenColumns())
1846 omitHidden = viewport.getViewAsString(true);
1849 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1850 seqs, omitHidden, null);
1852 StringSelection ss = new StringSelection(output);
1856 jalview.gui.Desktop.internalCopy = true;
1857 // Its really worth setting the clipboard contents
1858 // to empty before setting the large StringSelection!!
1859 Toolkit.getDefaultToolkit().getSystemClipboard()
1860 .setContents(new StringSelection(""), null);
1862 Toolkit.getDefaultToolkit().getSystemClipboard()
1863 .setContents(ss, Desktop.instance);
1864 } catch (OutOfMemoryError er)
1866 new OOMWarning("copying region", er);
1870 ArrayList<int[]> hiddenColumns = null;
1871 if (viewport.hasHiddenColumns())
1873 hiddenColumns = new ArrayList<int[]>();
1874 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1875 .getSelectionGroup().getEndRes();
1876 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1878 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1880 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1881 region[1] - hiddenOffset });
1886 Desktop.jalviewClipboard = new Object[] { seqs,
1887 viewport.getAlignment().getDataset(), hiddenColumns };
1888 statusBar.setText(MessageManager.formatMessage(
1889 "label.copied_sequences_to_clipboard", new Object[] { Integer
1890 .valueOf(seqs.length).toString() }));
1900 protected void pasteNew_actionPerformed(ActionEvent e)
1912 protected void pasteThis_actionPerformed(ActionEvent e)
1918 * Paste contents of Jalview clipboard
1920 * @param newAlignment
1921 * true to paste to a new alignment, otherwise add to this.
1923 void paste(boolean newAlignment)
1925 boolean externalPaste = true;
1928 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1929 Transferable contents = c.getContents(this);
1931 if (contents == null)
1940 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1941 if (str.length() < 1)
1946 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1948 } catch (OutOfMemoryError er)
1950 new OOMWarning("Out of memory pasting sequences!!", er);
1954 SequenceI[] sequences;
1955 boolean annotationAdded = false;
1956 AlignmentI alignment = null;
1958 if (Desktop.jalviewClipboard != null)
1960 // The clipboard was filled from within Jalview, we must use the
1962 // And dataset from the copied alignment
1963 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1964 // be doubly sure that we create *new* sequence objects.
1965 sequences = new SequenceI[newseq.length];
1966 for (int i = 0; i < newseq.length; i++)
1968 sequences[i] = new Sequence(newseq[i]);
1970 alignment = new Alignment(sequences);
1971 externalPaste = false;
1975 // parse the clipboard as an alignment.
1976 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1978 sequences = alignment.getSequencesArray();
1982 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1988 if (Desktop.jalviewClipboard != null)
1990 // dataset is inherited
1991 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1995 // new dataset is constructed
1996 alignment.setDataset(null);
1998 alwidth = alignment.getWidth() + 1;
2002 AlignmentI pastedal = alignment; // preserve pasted alignment object
2003 // Add pasted sequences and dataset into existing alignment.
2004 alignment = viewport.getAlignment();
2005 alwidth = alignment.getWidth() + 1;
2006 // decide if we need to import sequences from an existing dataset
2007 boolean importDs = Desktop.jalviewClipboard != null
2008 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2009 // importDs==true instructs us to copy over new dataset sequences from
2010 // an existing alignment
2011 Vector newDs = (importDs) ? new Vector() : null; // used to create
2012 // minimum dataset set
2014 for (int i = 0; i < sequences.length; i++)
2018 newDs.addElement(null);
2020 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2022 if (importDs && ds != null)
2024 if (!newDs.contains(ds))
2026 newDs.setElementAt(ds, i);
2027 ds = new Sequence(ds);
2028 // update with new dataset sequence
2029 sequences[i].setDatasetSequence(ds);
2033 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2038 // copy and derive new dataset sequence
2039 sequences[i] = sequences[i].deriveSequence();
2040 alignment.getDataset().addSequence(
2041 sequences[i].getDatasetSequence());
2042 // TODO: avoid creation of duplicate dataset sequences with a
2043 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2045 alignment.addSequence(sequences[i]); // merges dataset
2049 newDs.clear(); // tidy up
2051 if (alignment.getAlignmentAnnotation() != null)
2053 for (AlignmentAnnotation alan : alignment
2054 .getAlignmentAnnotation())
2056 if (alan.graphGroup > fgroup)
2058 fgroup = alan.graphGroup;
2062 if (pastedal.getAlignmentAnnotation() != null)
2064 // Add any annotation attached to alignment.
2065 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2066 for (int i = 0; i < alann.length; i++)
2068 annotationAdded = true;
2069 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2071 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2072 if (newann.graphGroup > -1)
2074 if (newGraphGroups.size() <= newann.graphGroup
2075 || newGraphGroups.get(newann.graphGroup) == null)
2077 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2079 newGraphGroups.add(q, null);
2081 newGraphGroups.set(newann.graphGroup, new Integer(
2084 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2088 newann.padAnnotation(alwidth);
2089 alignment.addAnnotation(newann);
2099 addHistoryItem(new EditCommand(
2100 MessageManager.getString("label.add_sequences"),
2101 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2103 // Add any annotations attached to sequences
2104 for (int i = 0; i < sequences.length; i++)
2106 if (sequences[i].getAnnotation() != null)
2108 AlignmentAnnotation newann;
2109 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2111 annotationAdded = true;
2112 newann = sequences[i].getAnnotation()[a];
2113 newann.adjustForAlignment();
2114 newann.padAnnotation(alwidth);
2115 if (newann.graphGroup > -1)
2117 if (newann.graphGroup > -1)
2119 if (newGraphGroups.size() <= newann.graphGroup
2120 || newGraphGroups.get(newann.graphGroup) == null)
2122 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2124 newGraphGroups.add(q, null);
2126 newGraphGroups.set(newann.graphGroup, new Integer(
2129 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2133 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2138 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2145 // propagate alignment changed.
2146 viewport.setEndSeq(alignment.getHeight());
2147 if (annotationAdded)
2149 // Duplicate sequence annotation in all views.
2150 AlignmentI[] alview = this.getViewAlignments();
2151 for (int i = 0; i < sequences.length; i++)
2153 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2158 for (int avnum = 0; avnum < alview.length; avnum++)
2160 if (alview[avnum] != alignment)
2162 // duplicate in a view other than the one with input focus
2163 int avwidth = alview[avnum].getWidth() + 1;
2164 // this relies on sann being preserved after we
2165 // modify the sequence's annotation array for each duplication
2166 for (int a = 0; a < sann.length; a++)
2168 AlignmentAnnotation newann = new AlignmentAnnotation(
2170 sequences[i].addAlignmentAnnotation(newann);
2171 newann.padAnnotation(avwidth);
2172 alview[avnum].addAnnotation(newann); // annotation was
2173 // duplicated earlier
2174 // TODO JAL-1145 graphGroups are not updated for sequence
2175 // annotation added to several views. This may cause
2177 alview[avnum].setAnnotationIndex(newann, a);
2182 buildSortByAnnotationScoresMenu();
2184 viewport.firePropertyChange("alignment", null,
2185 alignment.getSequences());
2186 if (alignPanels != null)
2188 for (AlignmentPanel ap : alignPanels)
2190 ap.validateAnnotationDimensions(false);
2195 alignPanel.validateAnnotationDimensions(false);
2201 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2203 String newtitle = new String("Copied sequences");
2205 if (Desktop.jalviewClipboard != null
2206 && Desktop.jalviewClipboard[2] != null)
2208 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2209 for (int[] region : hc)
2211 af.viewport.hideColumns(region[0], region[1]);
2215 // >>>This is a fix for the moment, until a better solution is
2217 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2219 alignPanel.getSeqPanel().seqCanvas
2220 .getFeatureRenderer());
2222 // TODO: maintain provenance of an alignment, rather than just make the
2223 // title a concatenation of operations.
2226 if (title.startsWith("Copied sequences"))
2232 newtitle = newtitle.concat("- from " + title);
2237 newtitle = new String("Pasted sequences");
2240 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2245 } catch (Exception ex)
2247 ex.printStackTrace();
2248 System.out.println("Exception whilst pasting: " + ex);
2249 // could be anything being pasted in here
2255 protected void expand_newalign(ActionEvent e)
2259 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2260 .getAlignment(), -1);
2261 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2263 String newtitle = new String("Flanking alignment");
2265 if (Desktop.jalviewClipboard != null
2266 && Desktop.jalviewClipboard[2] != null)
2268 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2269 for (int region[] : hc)
2271 af.viewport.hideColumns(region[0], region[1]);
2275 // >>>This is a fix for the moment, until a better solution is
2277 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2279 alignPanel.getSeqPanel().seqCanvas
2280 .getFeatureRenderer());
2282 // TODO: maintain provenance of an alignment, rather than just make the
2283 // title a concatenation of operations.
2285 if (title.startsWith("Copied sequences"))
2291 newtitle = newtitle.concat("- from " + title);
2295 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2297 } catch (Exception ex)
2299 ex.printStackTrace();
2300 System.out.println("Exception whilst pasting: " + ex);
2301 // could be anything being pasted in here
2302 } catch (OutOfMemoryError oom)
2304 new OOMWarning("Viewing flanking region of alignment", oom);
2315 protected void cut_actionPerformed(ActionEvent e)
2317 copy_actionPerformed(null);
2318 delete_actionPerformed(null);
2328 protected void delete_actionPerformed(ActionEvent evt)
2331 SequenceGroup sg = viewport.getSelectionGroup();
2338 * If the cut affects all sequences, warn, remove highlighted columns
2340 if (sg.getSize() == viewport.getAlignment().getHeight())
2342 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2343 .getAlignment().getWidth()) ? true : false;
2344 if (isEntireAlignWidth)
2346 int confirm = JvOptionPane.showConfirmDialog(this,
2347 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2348 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2349 JvOptionPane.OK_CANCEL_OPTION);
2351 if (confirm == JvOptionPane.CANCEL_OPTION
2352 || confirm == JvOptionPane.CLOSED_OPTION)
2357 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2358 sg.getEndRes() + 1);
2360 SequenceI[] cut = sg.getSequences()
2361 .toArray(new SequenceI[sg.getSize()]);
2363 addHistoryItem(new EditCommand(
2364 MessageManager.getString("label.cut_sequences"), Action.CUT,
2365 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2366 viewport.getAlignment()));
2368 viewport.setSelectionGroup(null);
2369 viewport.sendSelection();
2370 viewport.getAlignment().deleteGroup(sg);
2372 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2374 if (viewport.getAlignment().getHeight() < 1)
2378 this.setClosed(true);
2379 } catch (Exception ex)
2392 protected void deleteGroups_actionPerformed(ActionEvent e)
2394 if (avc.deleteGroups())
2396 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2397 alignPanel.updateAnnotation();
2398 alignPanel.paintAlignment(true);
2409 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2411 SequenceGroup sg = new SequenceGroup();
2413 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2415 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2418 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2419 viewport.setSelectionGroup(sg);
2420 viewport.sendSelection();
2421 // JAL-2034 - should delegate to
2422 // alignPanel to decide if overview needs
2424 alignPanel.paintAlignment(false);
2425 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2435 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2437 if (viewport.cursorMode)
2439 alignPanel.getSeqPanel().keyboardNo1 = null;
2440 alignPanel.getSeqPanel().keyboardNo2 = null;
2442 viewport.setSelectionGroup(null);
2443 viewport.getColumnSelection().clear();
2444 viewport.setSelectionGroup(null);
2445 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2446 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2447 // JAL-2034 - should delegate to
2448 // alignPanel to decide if overview needs
2450 alignPanel.paintAlignment(false);
2451 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2452 viewport.sendSelection();
2462 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2464 SequenceGroup sg = viewport.getSelectionGroup();
2468 selectAllSequenceMenuItem_actionPerformed(null);
2473 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2475 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2477 // JAL-2034 - should delegate to
2478 // alignPanel to decide if overview needs
2481 alignPanel.paintAlignment(true);
2482 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2483 viewport.sendSelection();
2487 public void invertColSel_actionPerformed(ActionEvent e)
2489 viewport.invertColumnSelection();
2490 alignPanel.paintAlignment(true);
2491 viewport.sendSelection();
2501 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2503 trimAlignment(true);
2513 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2515 trimAlignment(false);
2518 void trimAlignment(boolean trimLeft)
2520 ColumnSelection colSel = viewport.getColumnSelection();
2523 if (!colSel.isEmpty())
2527 column = colSel.getMin();
2531 column = colSel.getMax();
2535 if (viewport.getSelectionGroup() != null)
2537 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2538 viewport.getHiddenRepSequences());
2542 seqs = viewport.getAlignment().getSequencesArray();
2545 TrimRegionCommand trimRegion;
2548 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2549 column, viewport.getAlignment());
2550 viewport.setStartRes(0);
2554 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2555 column, viewport.getAlignment());
2558 statusBar.setText(MessageManager.formatMessage(
2559 "label.removed_columns",
2560 new String[] { Integer.valueOf(trimRegion.getSize())
2563 addHistoryItem(trimRegion);
2565 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2567 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2568 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2570 viewport.getAlignment().deleteGroup(sg);
2574 viewport.firePropertyChange("alignment", null, viewport
2575 .getAlignment().getSequences());
2586 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2588 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2591 if (viewport.getSelectionGroup() != null)
2593 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2594 viewport.getHiddenRepSequences());
2595 start = viewport.getSelectionGroup().getStartRes();
2596 end = viewport.getSelectionGroup().getEndRes();
2600 seqs = viewport.getAlignment().getSequencesArray();
2603 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2604 "Remove Gapped Columns", seqs, start, end,
2605 viewport.getAlignment());
2607 addHistoryItem(removeGapCols);
2609 statusBar.setText(MessageManager.formatMessage(
2610 "label.removed_empty_columns",
2611 new Object[] { Integer.valueOf(removeGapCols.getSize())
2614 // This is to maintain viewport position on first residue
2615 // of first sequence
2616 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2617 int startRes = seq.findPosition(viewport.getStartRes());
2618 // ShiftList shifts;
2619 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2620 // edit.alColumnChanges=shifts.getInverse();
2621 // if (viewport.hasHiddenColumns)
2622 // viewport.getColumnSelection().compensateForEdits(shifts);
2623 viewport.setStartRes(seq.findIndex(startRes) - 1);
2624 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2636 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2638 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2641 if (viewport.getSelectionGroup() != null)
2643 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2644 viewport.getHiddenRepSequences());
2645 start = viewport.getSelectionGroup().getStartRes();
2646 end = viewport.getSelectionGroup().getEndRes();
2650 seqs = viewport.getAlignment().getSequencesArray();
2653 // This is to maintain viewport position on first residue
2654 // of first sequence
2655 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2656 int startRes = seq.findPosition(viewport.getStartRes());
2658 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2659 viewport.getAlignment()));
2661 viewport.setStartRes(seq.findIndex(startRes) - 1);
2663 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2675 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2677 viewport.setPadGaps(padGapsMenuitem.isSelected());
2678 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2689 public void findMenuItem_actionPerformed(ActionEvent e)
2695 * Create a new view of the current alignment.
2698 public void newView_actionPerformed(ActionEvent e)
2700 newView(null, true);
2704 * Creates and shows a new view of the current alignment.
2707 * title of newly created view; if null, one will be generated
2708 * @param copyAnnotation
2709 * if true then duplicate all annnotation, groups and settings
2710 * @return new alignment panel, already displayed.
2712 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2715 * Create a new AlignmentPanel (with its own, new Viewport)
2717 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2719 if (!copyAnnotation)
2722 * remove all groups and annotation except for the automatic stuff
2724 newap.av.getAlignment().deleteAllGroups();
2725 newap.av.getAlignment().deleteAllAnnotations(false);
2728 newap.av.setGatherViewsHere(false);
2730 if (viewport.viewName == null)
2732 viewport.viewName = MessageManager
2733 .getString("label.view_name_original");
2737 * Views share the same edits undo and redo stacks
2739 newap.av.setHistoryList(viewport.getHistoryList());
2740 newap.av.setRedoList(viewport.getRedoList());
2743 * Views share the same mappings; need to deregister any new mappings
2744 * created by copyAlignPanel, and register the new reference to the shared
2747 newap.av.replaceMappings(viewport.getAlignment());
2749 newap.av.viewName = getNewViewName(viewTitle);
2751 addAlignmentPanel(newap, true);
2752 newap.alignmentChanged();
2754 if (alignPanels.size() == 2)
2756 viewport.setGatherViewsHere(true);
2758 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2763 * Make a new name for the view, ensuring it is unique within the current
2764 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2765 * these now use viewId. Unique view names are still desirable for usability.)
2770 protected String getNewViewName(String viewTitle)
2772 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2773 boolean addFirstIndex = false;
2774 if (viewTitle == null || viewTitle.trim().length() == 0)
2776 viewTitle = MessageManager.getString("action.view");
2777 addFirstIndex = true;
2781 index = 1;// we count from 1 if given a specific name
2783 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2785 List<Component> comps = PaintRefresher.components.get(viewport
2786 .getSequenceSetId());
2788 List<String> existingNames = getExistingViewNames(comps);
2790 while (existingNames.contains(newViewName))
2792 newViewName = viewTitle + " " + (++index);
2798 * Returns a list of distinct view names found in the given list of
2799 * components. View names are held on the viewport of an AlignmentPanel.
2804 protected List<String> getExistingViewNames(List<Component> comps)
2806 List<String> existingNames = new ArrayList<String>();
2807 for (Component comp : comps)
2809 if (comp instanceof AlignmentPanel)
2811 AlignmentPanel ap = (AlignmentPanel) comp;
2812 if (!existingNames.contains(ap.av.viewName))
2814 existingNames.add(ap.av.viewName);
2818 return existingNames;
2822 * Explode tabbed views into separate windows.
2825 public void expandViews_actionPerformed(ActionEvent e)
2827 Desktop.explodeViews(this);
2831 * Gather views in separate windows back into a tabbed presentation.
2834 public void gatherViews_actionPerformed(ActionEvent e)
2836 Desktop.instance.gatherViews(this);
2846 public void font_actionPerformed(ActionEvent e)
2848 new FontChooser(alignPanel);
2858 protected void seqLimit_actionPerformed(ActionEvent e)
2860 viewport.setShowJVSuffix(seqLimits.isSelected());
2862 alignPanel.getIdPanel().getIdCanvas()
2863 .setPreferredSize(alignPanel.calculateIdWidth());
2864 alignPanel.paintAlignment(true);
2868 public void idRightAlign_actionPerformed(ActionEvent e)
2870 viewport.setRightAlignIds(idRightAlign.isSelected());
2871 alignPanel.paintAlignment(true);
2875 public void centreColumnLabels_actionPerformed(ActionEvent e)
2877 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2878 alignPanel.paintAlignment(true);
2884 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2887 protected void followHighlight_actionPerformed()
2890 * Set the 'follow' flag on the Viewport (and scroll to position if now
2893 final boolean state = this.followHighlightMenuItem.getState();
2894 viewport.setFollowHighlight(state);
2897 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2908 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2910 viewport.setColourText(colourTextMenuItem.isSelected());
2911 alignPanel.paintAlignment(true);
2921 public void wrapMenuItem_actionPerformed(ActionEvent e)
2923 scaleAbove.setVisible(wrapMenuItem.isSelected());
2924 scaleLeft.setVisible(wrapMenuItem.isSelected());
2925 scaleRight.setVisible(wrapMenuItem.isSelected());
2926 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2927 alignPanel.updateLayout();
2931 public void showAllSeqs_actionPerformed(ActionEvent e)
2933 viewport.showAllHiddenSeqs();
2937 public void showAllColumns_actionPerformed(ActionEvent e)
2939 viewport.showAllHiddenColumns();
2941 viewport.sendSelection();
2945 public void hideSelSequences_actionPerformed(ActionEvent e)
2947 viewport.hideAllSelectedSeqs();
2948 // alignPanel.paintAlignment(true);
2952 * called by key handler and the hide all/show all menu items
2957 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2960 boolean hide = false;
2961 SequenceGroup sg = viewport.getSelectionGroup();
2962 if (!toggleSeqs && !toggleCols)
2964 // Hide everything by the current selection - this is a hack - we do the
2965 // invert and then hide
2966 // first check that there will be visible columns after the invert.
2967 if (viewport.hasSelectedColumns()
2968 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2971 // now invert the sequence set, if required - empty selection implies
2972 // that no hiding is required.
2975 invertSequenceMenuItem_actionPerformed(null);
2976 sg = viewport.getSelectionGroup();
2980 viewport.expandColSelection(sg, true);
2981 // finally invert the column selection and get the new sequence
2983 invertColSel_actionPerformed(null);
2990 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2992 hideSelSequences_actionPerformed(null);
2995 else if (!(toggleCols && viewport.hasSelectedColumns()))
2997 showAllSeqs_actionPerformed(null);
3003 if (viewport.hasSelectedColumns())
3005 hideSelColumns_actionPerformed(null);
3008 viewport.setSelectionGroup(sg);
3013 showAllColumns_actionPerformed(null);
3022 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3023 * event.ActionEvent)
3026 public void hideAllButSelection_actionPerformed(ActionEvent e)
3028 toggleHiddenRegions(false, false);
3029 viewport.sendSelection();
3036 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3040 public void hideAllSelection_actionPerformed(ActionEvent e)
3042 SequenceGroup sg = viewport.getSelectionGroup();
3043 viewport.expandColSelection(sg, false);
3044 viewport.hideAllSelectedSeqs();
3045 viewport.hideSelectedColumns();
3046 alignPanel.paintAlignment(true);
3047 viewport.sendSelection();
3054 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3058 public void showAllhidden_actionPerformed(ActionEvent e)
3060 viewport.showAllHiddenColumns();
3061 viewport.showAllHiddenSeqs();
3062 alignPanel.paintAlignment(true);
3063 viewport.sendSelection();
3067 public void hideSelColumns_actionPerformed(ActionEvent e)
3069 viewport.hideSelectedColumns();
3070 alignPanel.paintAlignment(true);
3071 viewport.sendSelection();
3075 public void hiddenMarkers_actionPerformed(ActionEvent e)
3077 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3088 protected void scaleAbove_actionPerformed(ActionEvent e)
3090 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3091 alignPanel.paintAlignment(true);
3101 protected void scaleLeft_actionPerformed(ActionEvent e)
3103 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3104 alignPanel.paintAlignment(true);
3114 protected void scaleRight_actionPerformed(ActionEvent e)
3116 viewport.setScaleRightWrapped(scaleRight.isSelected());
3117 alignPanel.paintAlignment(true);
3127 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3129 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3130 alignPanel.paintAlignment(true);
3140 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3142 viewport.setShowText(viewTextMenuItem.isSelected());
3143 alignPanel.paintAlignment(true);
3153 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3155 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3156 alignPanel.paintAlignment(true);
3159 public FeatureSettings featureSettings;
3162 public FeatureSettingsControllerI getFeatureSettingsUI()
3164 return featureSettings;
3168 public void featureSettings_actionPerformed(ActionEvent e)
3170 if (featureSettings != null)
3172 featureSettings.close();
3173 featureSettings = null;
3175 if (!showSeqFeatures.isSelected())
3177 // make sure features are actually displayed
3178 showSeqFeatures.setSelected(true);
3179 showSeqFeatures_actionPerformed(null);
3181 featureSettings = new FeatureSettings(this);
3185 * Set or clear 'Show Sequence Features'
3191 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3193 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3194 alignPanel.paintAlignment(true);
3195 if (alignPanel.getOverviewPanel() != null)
3197 alignPanel.getOverviewPanel().updateOverviewImage();
3202 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3203 * the annotations panel as a whole.
3205 * The options to show/hide all annotations should be enabled when the panel
3206 * is shown, and disabled when the panel is hidden.
3211 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3213 final boolean setVisible = annotationPanelMenuItem.isSelected();
3214 viewport.setShowAnnotation(setVisible);
3215 this.showAllSeqAnnotations.setEnabled(setVisible);
3216 this.hideAllSeqAnnotations.setEnabled(setVisible);
3217 this.showAllAlAnnotations.setEnabled(setVisible);
3218 this.hideAllAlAnnotations.setEnabled(setVisible);
3219 alignPanel.updateLayout();
3223 public void alignmentProperties()
3225 JEditorPane editPane = new JEditorPane("text/html", "");
3226 editPane.setEditable(false);
3227 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3229 editPane.setText(MessageManager.formatMessage("label.html_content",
3230 new Object[] { contents.toString() }));
3231 JInternalFrame frame = new JInternalFrame();
3232 frame.getContentPane().add(new JScrollPane(editPane));
3234 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3235 "label.alignment_properties", new Object[] { getTitle() }),
3246 public void overviewMenuItem_actionPerformed(ActionEvent e)
3248 if (alignPanel.overviewPanel != null)
3253 JInternalFrame frame = new JInternalFrame();
3254 OverviewPanel overview = new OverviewPanel(alignPanel);
3255 frame.setContentPane(overview);
3256 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3257 "label.overview_params", new Object[] { this.getTitle() }),
3258 frame.getWidth(), frame.getHeight());
3260 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3261 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3264 public void internalFrameClosed(
3265 javax.swing.event.InternalFrameEvent evt)
3267 alignPanel.setOverviewPanel(null);
3271 alignPanel.setOverviewPanel(overview);
3275 public void textColour_actionPerformed()
3277 new TextColourChooser().chooseColour(alignPanel, null);
3281 * public void covariationColour_actionPerformed() {
3283 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3287 public void annotationColour_actionPerformed()
3289 new AnnotationColourChooser(viewport, alignPanel);
3293 public void annotationColumn_actionPerformed(ActionEvent e)
3295 new AnnotationColumnChooser(viewport, alignPanel);
3299 * Action on the user checking or unchecking the option to apply the selected
3300 * colour scheme to all groups. If unchecked, groups may have their own
3301 * independent colour schemes.
3306 public void applyToAllGroups_actionPerformed(boolean selected)
3308 viewport.setColourAppliesToAllGroups(selected);
3312 * Action on user selecting a colour from the colour menu
3315 * the name (not the menu item label!) of the colour scheme
3318 public void changeColour_actionPerformed(String name)
3321 * 'User Defined' opens a panel to configure or load a
3322 * user-defined colour scheme
3324 if (ResidueColourScheme.USER_DEFINED.equals(name))
3326 new UserDefinedColours(alignPanel, null);
3331 * otherwise set the chosen colour scheme (or null for 'None')
3333 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3334 viewport.getAlignment(), viewport.getHiddenRepSequences());
3339 * Actions on setting or changing the alignment colour scheme
3344 public void changeColour(ColourSchemeI cs)
3346 // TODO: pull up to controller method
3349 ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
3352 viewport.setGlobalColourScheme(cs);
3354 alignPanel.paintAlignment(true);
3358 * Show the PID threshold slider panel
3361 protected void modifyPID_actionPerformed()
3363 SliderPanel.setPIDSliderSource(alignPanel,
3364 viewport.getResidueShading(), alignPanel.getViewName());
3365 SliderPanel.showPIDSlider();
3369 * Show the Conservation slider panel
3372 protected void modifyConservation_actionPerformed()
3374 SliderPanel.setConservationSlider(alignPanel,
3375 viewport.getResidueShading(), alignPanel.getViewName());
3376 SliderPanel.showConservationSlider();
3380 * Action on selecting or deselecting (Colour) By Conservation
3383 public void conservationMenuItem_actionPerformed(boolean selected)
3385 modifyConservation.setEnabled(selected);
3386 viewport.setConservationSelected(selected);
3387 viewport.getResidueShading().setConservationApplied(selected);
3389 changeColour(viewport.getGlobalColourScheme());
3392 modifyConservation_actionPerformed();
3396 SliderPanel.hideConservationSlider();
3401 * Action on selecting or deselecting (Colour) Above PID Threshold
3404 public void abovePIDThreshold_actionPerformed(boolean selected)
3406 modifyPID.setEnabled(selected);
3407 viewport.setAbovePIDThreshold(selected);
3410 viewport.getResidueShading().setThreshold(0,
3411 viewport.isIgnoreGapsConsensus());
3414 changeColour(viewport.getGlobalColourScheme());
3417 modifyPID_actionPerformed();
3421 SliderPanel.hidePIDSlider();
3432 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3434 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3435 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3436 .getAlignment().getSequenceAt(0), null);
3437 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3438 viewport.getAlignment()));
3439 alignPanel.paintAlignment(true);
3449 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3451 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3452 AlignmentSorter.sortByID(viewport.getAlignment());
3453 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3454 viewport.getAlignment()));
3455 alignPanel.paintAlignment(true);
3465 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3467 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3468 AlignmentSorter.sortByLength(viewport.getAlignment());
3469 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3470 viewport.getAlignment()));
3471 alignPanel.paintAlignment(true);
3481 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3483 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3484 AlignmentSorter.sortByGroup(viewport.getAlignment());
3485 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3486 viewport.getAlignment()));
3488 alignPanel.paintAlignment(true);
3498 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3500 new RedundancyPanel(alignPanel, this);
3510 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3512 if ((viewport.getSelectionGroup() == null)
3513 || (viewport.getSelectionGroup().getSize() < 2))
3515 JvOptionPane.showInternalMessageDialog(this, MessageManager
3516 .getString("label.you_must_select_least_two_sequences"),
3517 MessageManager.getString("label.invalid_selection"),
3518 JvOptionPane.WARNING_MESSAGE);
3522 JInternalFrame frame = new JInternalFrame();
3523 frame.setContentPane(new PairwiseAlignPanel(viewport));
3524 Desktop.addInternalFrame(frame,
3525 MessageManager.getString("action.pairwise_alignment"), 600,
3537 public void PCAMenuItem_actionPerformed(ActionEvent e)
3539 if (((viewport.getSelectionGroup() != null)
3540 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3541 .getSelectionGroup().getSize() > 0))
3542 || (viewport.getAlignment().getHeight() < 4))
3545 .showInternalMessageDialog(
3548 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3550 .getString("label.sequence_selection_insufficient"),
3551 JvOptionPane.WARNING_MESSAGE);
3556 new PCAPanel(alignPanel);
3560 public void autoCalculate_actionPerformed(ActionEvent e)
3562 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3563 if (viewport.autoCalculateConsensus)
3565 viewport.firePropertyChange("alignment", null, viewport
3566 .getAlignment().getSequences());
3571 public void sortByTreeOption_actionPerformed(ActionEvent e)
3573 viewport.sortByTree = sortByTree.isSelected();
3577 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3579 viewport.followSelection = listenToViewSelections.isSelected();
3589 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3591 newTreePanel("AV", "PID", "Average distance tree using PID");
3601 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3603 newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3613 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3615 newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3625 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3627 newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3640 void newTreePanel(String type, String pwType, String title)
3644 if (viewport.getSelectionGroup() != null
3645 && viewport.getSelectionGroup().getSize() > 0)
3647 if (viewport.getSelectionGroup().getSize() < 3)
3653 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3655 .getString("label.not_enough_sequences"),
3656 JvOptionPane.WARNING_MESSAGE);
3660 SequenceGroup sg = viewport.getSelectionGroup();
3662 /* Decide if the selection is a column region */
3663 for (SequenceI _s : sg.getSequences())
3665 if (_s.getLength() < sg.getEndRes())
3671 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3673 .getString("label.sequences_selection_not_aligned"),
3674 JvOptionPane.WARNING_MESSAGE);
3680 title = title + " on region";
3681 tp = new TreePanel(alignPanel, type, pwType);
3685 // are the visible sequences aligned?
3686 if (!viewport.getAlignment().isAligned(false))
3692 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3694 .getString("label.sequences_not_aligned"),
3695 JvOptionPane.WARNING_MESSAGE);
3700 if (viewport.getAlignment().getHeight() < 2)
3705 tp = new TreePanel(alignPanel, type, pwType);
3710 if (viewport.viewName != null)
3712 title += viewport.viewName + " of ";
3715 title += this.title;
3717 Desktop.addInternalFrame(tp, title, 600, 500);
3728 public void addSortByOrderMenuItem(String title,
3729 final AlignmentOrder order)
3731 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3732 "action.by_title_param", new Object[] { title }));
3734 item.addActionListener(new java.awt.event.ActionListener()
3737 public void actionPerformed(ActionEvent e)
3739 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3741 // TODO: JBPNote - have to map order entries to curent SequenceI
3743 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3745 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3748 alignPanel.paintAlignment(true);
3754 * Add a new sort by annotation score menu item
3757 * the menu to add the option to
3759 * the label used to retrieve scores for each sequence on the
3762 public void addSortByAnnotScoreMenuItem(JMenu sort,
3763 final String scoreLabel)
3765 final JMenuItem item = new JMenuItem(scoreLabel);
3767 item.addActionListener(new java.awt.event.ActionListener()
3770 public void actionPerformed(ActionEvent e)
3772 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3773 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3774 viewport.getAlignment());// ,viewport.getSelectionGroup());
3775 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3776 viewport.getAlignment()));
3777 alignPanel.paintAlignment(true);
3783 * last hash for alignment's annotation array - used to minimise cost of
3786 protected int _annotationScoreVectorHash;
3789 * search the alignment and rebuild the sort by annotation score submenu the
3790 * last alignment annotation vector hash is stored to minimize cost of
3791 * rebuilding in subsequence calls.
3795 public void buildSortByAnnotationScoresMenu()
3797 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3802 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3804 sortByAnnotScore.removeAll();
3805 // almost certainly a quicker way to do this - but we keep it simple
3806 Hashtable scoreSorts = new Hashtable();
3807 AlignmentAnnotation aann[];
3808 for (SequenceI sqa : viewport.getAlignment().getSequences())
3810 aann = sqa.getAnnotation();
3811 for (int i = 0; aann != null && i < aann.length; i++)
3813 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3815 scoreSorts.put(aann[i].label, aann[i].label);
3819 Enumeration labels = scoreSorts.keys();
3820 while (labels.hasMoreElements())
3822 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3823 (String) labels.nextElement());
3825 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3828 _annotationScoreVectorHash = viewport.getAlignment()
3829 .getAlignmentAnnotation().hashCode();
3834 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3835 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3836 * call. Listeners are added to remove the menu item when the treePanel is
3837 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3841 * Displayed tree window.
3843 * SortBy menu item title.
3846 public void buildTreeMenu()
3848 calculateTree.removeAll();
3849 // build the calculate menu
3851 for (final String type : new String[] { "NJ", "AV" })
3853 String treecalcnm = MessageManager.getString("label.tree_calc_"
3854 + type.toLowerCase());
3855 for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
3857 JMenuItem tm = new JMenuItem();
3858 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
3859 if (sm.isDNA() == viewport.getAlignment().isNucleotide()
3860 || sm.isProtein() == !viewport.getAlignment()
3863 String smn = MessageManager.getStringOrReturn(
3864 "label.score_model_", sm.getName());
3865 final String title = MessageManager.formatMessage(
3866 "label.treecalc_title", treecalcnm, smn);
3867 tm.setText(title);//
3868 tm.addActionListener(new java.awt.event.ActionListener()
3871 public void actionPerformed(ActionEvent e)
3873 newTreePanel(type, pwtype, title);
3876 calculateTree.add(tm);
3881 sortByTreeMenu.removeAll();
3883 List<Component> comps = PaintRefresher.components.get(viewport
3884 .getSequenceSetId());
3885 List<TreePanel> treePanels = new ArrayList<TreePanel>();
3886 for (Component comp : comps)
3888 if (comp instanceof TreePanel)
3890 treePanels.add((TreePanel) comp);
3894 if (treePanels.size() < 1)
3896 sortByTreeMenu.setVisible(false);
3900 sortByTreeMenu.setVisible(true);
3902 for (final TreePanel tp : treePanels)
3904 final JMenuItem item = new JMenuItem(tp.getTitle());
3905 item.addActionListener(new java.awt.event.ActionListener()
3908 public void actionPerformed(ActionEvent e)
3910 tp.sortByTree_actionPerformed();
3911 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3916 sortByTreeMenu.add(item);
3920 public boolean sortBy(AlignmentOrder alorder, String undoname)
3922 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3923 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3924 if (undoname != null)
3926 addHistoryItem(new OrderCommand(undoname, oldOrder,
3927 viewport.getAlignment()));
3929 alignPanel.paintAlignment(true);
3934 * Work out whether the whole set of sequences or just the selected set will
3935 * be submitted for multiple alignment.
3938 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3940 // Now, check we have enough sequences
3941 AlignmentView msa = null;
3943 if ((viewport.getSelectionGroup() != null)
3944 && (viewport.getSelectionGroup().getSize() > 1))
3946 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3947 // some common interface!
3949 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3950 * SequenceI[sz = seqs.getSize(false)];
3952 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3953 * seqs.getSequenceAt(i); }
3955 msa = viewport.getAlignmentView(true);
3957 else if (viewport.getSelectionGroup() != null
3958 && viewport.getSelectionGroup().getSize() == 1)
3960 int option = JvOptionPane.showConfirmDialog(this,
3961 MessageManager.getString("warn.oneseq_msainput_selection"),
3962 MessageManager.getString("label.invalid_selection"),
3963 JvOptionPane.OK_CANCEL_OPTION);
3964 if (option == JvOptionPane.OK_OPTION)
3966 msa = viewport.getAlignmentView(false);
3971 msa = viewport.getAlignmentView(false);
3977 * Decides what is submitted to a secondary structure prediction service: the
3978 * first sequence in the alignment, or in the current selection, or, if the
3979 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3980 * region or the whole alignment. (where the first sequence in the set is the
3981 * one that the prediction will be for).
3983 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3985 AlignmentView seqs = null;
3987 if ((viewport.getSelectionGroup() != null)
3988 && (viewport.getSelectionGroup().getSize() > 0))
3990 seqs = viewport.getAlignmentView(true);
3994 seqs = viewport.getAlignmentView(false);
3996 // limit sequences - JBPNote in future - could spawn multiple prediction
3998 // TODO: viewport.getAlignment().isAligned is a global state - the local
3999 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4000 if (!viewport.getAlignment().isAligned(false))
4002 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4003 // TODO: if seqs.getSequences().length>1 then should really have warned
4017 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4019 // Pick the tree file
4020 JalviewFileChooser chooser = new JalviewFileChooser(
4021 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4022 chooser.setFileView(new JalviewFileView());
4023 chooser.setDialogTitle(MessageManager
4024 .getString("label.select_newick_like_tree_file"));
4025 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4027 int value = chooser.showOpenDialog(null);
4029 if (value == JalviewFileChooser.APPROVE_OPTION)
4031 String choice = chooser.getSelectedFile().getPath();
4032 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4033 jalview.io.NewickFile fin = null;
4036 fin = new NewickFile(choice, DataSourceType.FILE);
4037 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4038 } catch (Exception ex)
4045 .getString("label.problem_reading_tree_file"),
4046 JvOptionPane.WARNING_MESSAGE);
4047 ex.printStackTrace();
4049 if (fin != null && fin.hasWarningMessage())
4051 JvOptionPane.showMessageDialog(Desktop.desktop, fin
4052 .getWarningMessage(), MessageManager
4053 .getString("label.possible_problem_with_tree_file"),
4054 JvOptionPane.WARNING_MESSAGE);
4059 public TreePanel ShowNewickTree(NewickFile nf, String title)
4061 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4064 public TreePanel ShowNewickTree(NewickFile nf, String title,
4065 AlignmentView input)
4067 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4070 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4071 int h, int x, int y)
4073 return ShowNewickTree(nf, title, null, w, h, x, y);
4077 * Add a treeviewer for the tree extracted from a newick file object to the
4078 * current alignment view
4085 * Associated alignment input data (or null)
4094 * @return TreePanel handle
4096 public TreePanel ShowNewickTree(NewickFile nf, String title,
4097 AlignmentView input, int w, int h, int x, int y)
4099 TreePanel tp = null;
4105 if (nf.getTree() != null)
4107 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4113 tp.setLocation(x, y);
4116 Desktop.addInternalFrame(tp, title, w, h);
4118 } catch (Exception ex)
4120 ex.printStackTrace();
4126 private boolean buildingMenu = false;
4129 * Generates menu items and listener event actions for web service clients
4132 public void BuildWebServiceMenu()
4134 while (buildingMenu)
4138 System.err.println("Waiting for building menu to finish.");
4140 } catch (Exception e)
4144 final AlignFrame me = this;
4145 buildingMenu = true;
4146 new Thread(new Runnable()
4151 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4154 // System.err.println("Building ws menu again "
4155 // + Thread.currentThread());
4156 // TODO: add support for context dependent disabling of services based
4158 // alignment and current selection
4159 // TODO: add additional serviceHandle parameter to specify abstract
4161 // class independently of AbstractName
4162 // TODO: add in rediscovery GUI function to restart discoverer
4163 // TODO: group services by location as well as function and/or
4165 // object broker mechanism.
4166 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4167 final IProgressIndicator af = me;
4170 * do not i18n these strings - they are hard-coded in class
4171 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4172 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4174 final JMenu msawsmenu = new JMenu("Alignment");
4175 final JMenu secstrmenu = new JMenu(
4176 "Secondary Structure Prediction");
4177 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4178 final JMenu analymenu = new JMenu("Analysis");
4179 final JMenu dismenu = new JMenu("Protein Disorder");
4180 // JAL-940 - only show secondary structure prediction services from
4181 // the legacy server
4182 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4184 Discoverer.services != null && (Discoverer.services.size() > 0))
4186 // TODO: refactor to allow list of AbstractName/Handler bindings to
4188 // stored or retrieved from elsewhere
4189 // No MSAWS used any more:
4190 // Vector msaws = null; // (Vector)
4191 // Discoverer.services.get("MsaWS");
4192 Vector secstrpr = (Vector) Discoverer.services
4194 if (secstrpr != null)
4196 // Add any secondary structure prediction services
4197 for (int i = 0, j = secstrpr.size(); i < j; i++)
4199 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4201 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4202 .getServiceClient(sh);
4203 int p = secstrmenu.getItemCount();
4204 impl.attachWSMenuEntry(secstrmenu, me);
4205 int q = secstrmenu.getItemCount();
4206 for (int litm = p; litm < q; litm++)
4208 legacyItems.add(secstrmenu.getItem(litm));
4214 // Add all submenus in the order they should appear on the web
4216 wsmenu.add(msawsmenu);
4217 wsmenu.add(secstrmenu);
4218 wsmenu.add(dismenu);
4219 wsmenu.add(analymenu);
4220 // No search services yet
4221 // wsmenu.add(seqsrchmenu);
4223 javax.swing.SwingUtilities.invokeLater(new Runnable()
4230 webService.removeAll();
4231 // first, add discovered services onto the webservices menu
4232 if (wsmenu.size() > 0)
4234 for (int i = 0, j = wsmenu.size(); i < j; i++)
4236 webService.add(wsmenu.get(i));
4241 webService.add(me.webServiceNoServices);
4243 // TODO: move into separate menu builder class.
4244 boolean new_sspred = false;
4245 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4247 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4248 if (jws2servs != null)
4250 if (jws2servs.hasServices())
4252 jws2servs.attachWSMenuEntry(webService, me);
4253 for (Jws2Instance sv : jws2servs.getServices())
4255 if (sv.description.toLowerCase().contains("jpred"))
4257 for (JMenuItem jmi : legacyItems)
4259 jmi.setVisible(false);
4265 if (jws2servs.isRunning())
4267 JMenuItem tm = new JMenuItem(
4268 "Still discovering JABA Services");
4269 tm.setEnabled(false);
4274 build_urlServiceMenu(me.webService);
4275 build_fetchdbmenu(webService);
4276 for (JMenu item : wsmenu)
4278 if (item.getItemCount() == 0)
4280 item.setEnabled(false);
4284 item.setEnabled(true);
4287 } catch (Exception e)
4290 .debug("Exception during web service menu building process.",
4295 } catch (Exception e)
4298 buildingMenu = false;
4305 * construct any groupURL type service menu entries.
4309 private void build_urlServiceMenu(JMenu webService)
4311 // TODO: remove this code when 2.7 is released
4312 // DEBUG - alignmentView
4314 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4315 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4317 * @Override public void actionPerformed(ActionEvent e) {
4318 * jalview.datamodel.AlignmentView
4319 * .testSelectionViews(af.viewport.getAlignment(),
4320 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4322 * }); webService.add(testAlView);
4324 // TODO: refactor to RestClient discoverer and merge menu entries for
4325 // rest-style services with other types of analysis/calculation service
4326 // SHmmr test client - still being implemented.
4327 // DEBUG - alignmentView
4329 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4332 client.attachWSMenuEntry(
4333 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4339 * Searches the alignment sequences for xRefs and builds the Show
4340 * Cross-References menu (formerly called Show Products), with database
4341 * sources for which cross-references are found (protein sources for a
4342 * nucleotide alignment and vice versa)
4344 * @return true if Show Cross-references menu should be enabled
4346 public boolean canShowProducts()
4348 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4349 AlignmentI dataset = viewport.getAlignment().getDataset();
4351 showProducts.removeAll();
4352 final boolean dna = viewport.getAlignment().isNucleotide();
4354 if (seqs == null || seqs.length == 0)
4356 // nothing to see here.
4360 boolean showp = false;
4363 List<String> ptypes = new CrossRef(seqs, dataset)
4364 .findXrefSourcesForSequences(dna);
4366 for (final String source : ptypes)
4369 final AlignFrame af = this;
4370 JMenuItem xtype = new JMenuItem(source);
4371 xtype.addActionListener(new ActionListener()
4374 public void actionPerformed(ActionEvent e)
4376 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4379 showProducts.add(xtype);
4381 showProducts.setVisible(showp);
4382 showProducts.setEnabled(showp);
4383 } catch (Exception e)
4386 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4394 * Finds and displays cross-references for the selected sequences (protein
4395 * products for nucleotide sequences, dna coding sequences for peptides).
4398 * the sequences to show cross-references for
4400 * true if from a nucleotide alignment (so showing proteins)
4402 * the database to show cross-references for
4404 protected void showProductsFor(final SequenceI[] sel,
4405 final boolean _odna, final String source)
4407 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4412 * Construct and display a new frame containing the translation of this
4413 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4416 public void showTranslation_actionPerformed(ActionEvent e)
4418 AlignmentI al = null;
4421 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4423 al = dna.translateCdna();
4424 } catch (Exception ex)
4426 jalview.bin.Cache.log.error(
4427 "Exception during translation. Please report this !", ex);
4428 final String msg = MessageManager
4429 .getString("label.error_when_translating_sequences_submit_bug_report");
4430 final String errorTitle = MessageManager
4431 .getString("label.implementation_error")
4432 + MessageManager.getString("label.translation_failed");
4433 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4434 JvOptionPane.ERROR_MESSAGE);
4437 if (al == null || al.getHeight() == 0)
4439 final String msg = MessageManager
4440 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4441 final String errorTitle = MessageManager
4442 .getString("label.translation_failed");
4443 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4444 JvOptionPane.WARNING_MESSAGE);
4448 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4449 af.setFileFormat(this.currentFileFormat);
4450 final String newTitle = MessageManager.formatMessage(
4451 "label.translation_of_params",
4452 new Object[] { this.getTitle() });
4453 af.setTitle(newTitle);
4454 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4456 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4457 viewport.openSplitFrame(af, new Alignment(seqs));
4461 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4468 * Set the file format
4472 public void setFileFormat(FileFormatI format)
4474 this.currentFileFormat = format;
4478 * Try to load a features file onto the alignment.
4481 * contents or path to retrieve file
4483 * access mode of file (see jalview.io.AlignFile)
4484 * @return true if features file was parsed correctly.
4486 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4488 return avc.parseFeaturesFile(file, sourceType,
4489 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4494 public void refreshFeatureUI(boolean enableIfNecessary)
4496 // note - currently this is only still here rather than in the controller
4497 // because of the featureSettings hard reference that is yet to be
4499 if (enableIfNecessary)
4501 viewport.setShowSequenceFeatures(true);
4502 showSeqFeatures.setSelected(true);
4508 public void dragEnter(DropTargetDragEvent evt)
4513 public void dragExit(DropTargetEvent evt)
4518 public void dragOver(DropTargetDragEvent evt)
4523 public void dropActionChanged(DropTargetDragEvent evt)
4528 public void drop(DropTargetDropEvent evt)
4530 // JAL-1552 - acceptDrop required before getTransferable call for
4531 // Java's Transferable for native dnd
4532 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4533 Transferable t = evt.getTransferable();
4534 List<String> files = new ArrayList<String>();
4535 List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4539 Desktop.transferFromDropTarget(files, protocols, evt, t);
4540 } catch (Exception e)
4542 e.printStackTrace();
4548 // check to see if any of these files have names matching sequences in
4550 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4551 .getAlignment().getSequencesArray());
4553 * Object[] { String,SequenceI}
4555 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4556 ArrayList<String> filesnotmatched = new ArrayList<String>();
4557 for (int i = 0; i < files.size(); i++)
4559 String file = files.get(i).toString();
4561 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4562 if (protocol == DataSourceType.FILE)
4564 File fl = new File(file);
4565 pdbfn = fl.getName();
4567 else if (protocol == DataSourceType.URL)
4569 URL url = new URL(file);
4570 pdbfn = url.getFile();
4572 if (pdbfn.length() > 0)
4574 // attempt to find a match in the alignment
4575 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4576 int l = 0, c = pdbfn.indexOf(".");
4577 while (mtch == null && c != -1)
4582 } while ((c = pdbfn.indexOf(".", l)) > l);
4585 pdbfn = pdbfn.substring(0, l);
4587 mtch = idm.findAllIdMatches(pdbfn);
4591 FileFormatI type = null;
4594 type = new IdentifyFile().identify(file, protocol);
4595 } catch (Exception ex)
4599 if (type != null && type.isStructureFile())
4601 filesmatched.add(new Object[] { file, protocol, mtch });
4605 // File wasn't named like one of the sequences or wasn't a PDB file.
4606 filesnotmatched.add(file);
4610 if (filesmatched.size() > 0)
4612 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4618 "label.automatically_associate_structure_files_with_sequences_same_name",
4619 new Object[] { Integer
4625 .getString("label.automatically_associate_structure_files_by_name"),
4626 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4629 for (Object[] fm : filesmatched)
4631 // try and associate
4632 // TODO: may want to set a standard ID naming formalism for
4633 // associating PDB files which have no IDs.
4634 for (SequenceI toassoc : (SequenceI[]) fm[2])
4636 PDBEntry pe = new AssociatePdbFileWithSeq()
4637 .associatePdbWithSeq((String) fm[0],
4638 (DataSourceType) fm[1], toassoc, false,
4642 System.err.println("Associated file : "
4643 + ((String) fm[0]) + " with "
4644 + toassoc.getDisplayId(true));
4648 alignPanel.paintAlignment(true);
4652 if (filesnotmatched.size() > 0)
4655 && (Cache.getDefault(
4656 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4662 "label.ignore_unmatched_dropped_files_info",
4663 new Object[] { Integer
4670 .getString("label.ignore_unmatched_dropped_files"),
4671 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4675 for (String fn : filesnotmatched)
4677 loadJalviewDataFile(fn, null, null, null);
4681 } catch (Exception ex)
4683 ex.printStackTrace();
4689 * Attempt to load a "dropped" file or URL string: First by testing whether
4690 * it's an Annotation file, then a JNet file, and finally a features file. If
4691 * all are false then the user may have dropped an alignment file onto this
4695 * either a filename or a URL string.
4697 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4698 FileFormatI format, SequenceI assocSeq)
4702 if (sourceType == null)
4704 sourceType = FormatAdapter.checkProtocol(file);
4706 // if the file isn't identified, or not positively identified as some
4707 // other filetype (PFAM is default unidentified alignment file type) then
4708 // try to parse as annotation.
4709 boolean isAnnotation = (format == null || FileFormat.Pfam
4710 .equals(format)) ? new AnnotationFile()
4711 .annotateAlignmentView(viewport, file, sourceType) : false;
4715 // first see if its a T-COFFEE score file
4716 TCoffeeScoreFile tcf = null;
4719 tcf = new TCoffeeScoreFile(file, sourceType);
4722 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4725 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4726 isAnnotation = true;
4728 .setText(MessageManager
4729 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4733 // some problem - if no warning its probable that the ID matching
4734 // process didn't work
4738 tcf.getWarningMessage() == null ? MessageManager
4739 .getString("label.check_file_matches_sequence_ids_alignment")
4740 : tcf.getWarningMessage(),
4742 .getString("label.problem_reading_tcoffee_score_file"),
4743 JvOptionPane.WARNING_MESSAGE);
4750 } catch (Exception x)
4753 .debug("Exception when processing data source as T-COFFEE score file",
4759 // try to see if its a JNet 'concise' style annotation file *before*
4761 // try to parse it as a features file
4764 format = new IdentifyFile().identify(file, sourceType);
4766 if (FileFormat.Jnet.equals(format))
4768 JPredFile predictions = new JPredFile(file, sourceType);
4769 new JnetAnnotationMaker();
4770 JnetAnnotationMaker.add_annotation(predictions,
4771 viewport.getAlignment(), 0, false);
4772 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4773 viewport.getAlignment().setSeqrep(repseq);
4774 ColumnSelection cs = new ColumnSelection();
4775 cs.hideInsertionsFor(repseq);
4776 viewport.setColumnSelection(cs);
4777 isAnnotation = true;
4779 // else if (IdentifyFile.FeaturesFile.equals(format))
4780 else if (FileFormat.Features.equals(format))
4782 if (parseFeaturesFile(file, sourceType))
4784 alignPanel.paintAlignment(true);
4789 new FileLoader().LoadFile(viewport, file, sourceType, format);
4796 alignPanel.adjustAnnotationHeight();
4797 viewport.updateSequenceIdColours();
4798 buildSortByAnnotationScoresMenu();
4799 alignPanel.paintAlignment(true);
4801 } catch (Exception ex)
4803 ex.printStackTrace();
4804 } catch (OutOfMemoryError oom)
4809 } catch (Exception x)
4814 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4815 : "using " + sourceType + " from " + file)
4817 + (format != null ? "(parsing as '" + format
4818 + "' file)" : ""), oom, Desktop.desktop);
4823 * Method invoked by the ChangeListener on the tabbed pane, in other words
4824 * when a different tabbed pane is selected by the user or programmatically.
4827 public void tabSelectionChanged(int index)
4831 alignPanel = alignPanels.get(index);
4832 viewport = alignPanel.av;
4833 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4834 setMenusFromViewport(viewport);
4838 * 'focus' any colour slider that is open to the selected viewport
4840 if (viewport.getConservationSelected())
4842 SliderPanel.setConservationSlider(alignPanel,
4843 viewport.getResidueShading(), alignPanel.getViewName());
4847 SliderPanel.hideConservationSlider();
4849 if (viewport.getAbovePIDThreshold())
4851 SliderPanel.setPIDSliderSource(alignPanel,
4852 viewport.getResidueShading(), alignPanel.getViewName());
4856 SliderPanel.hidePIDSlider();
4860 * If there is a frame linked to this one in a SplitPane, switch it to the
4861 * same view tab index. No infinite recursion of calls should happen, since
4862 * tabSelectionChanged() should not get invoked on setting the selected
4863 * index to an unchanged value. Guard against setting an invalid index
4864 * before the new view peer tab has been created.
4866 final AlignViewportI peer = viewport.getCodingComplement();
4869 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4870 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4872 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4878 * On right mouse click on view tab, prompt for and set new view name.
4881 public void tabbedPane_mousePressed(MouseEvent e)
4883 if (e.isPopupTrigger())
4885 String msg = MessageManager.getString("label.enter_view_name");
4886 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4887 JvOptionPane.QUESTION_MESSAGE);
4891 viewport.viewName = reply;
4892 // TODO warn if reply is in getExistingViewNames()?
4893 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4898 public AlignViewport getCurrentView()
4904 * Open the dialog for regex description parsing.
4907 protected void extractScores_actionPerformed(ActionEvent e)
4909 ParseProperties pp = new jalview.analysis.ParseProperties(
4910 viewport.getAlignment());
4911 // TODO: verify regex and introduce GUI dialog for version 2.5
4912 // if (pp.getScoresFromDescription("col", "score column ",
4913 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4915 if (pp.getScoresFromDescription("description column",
4916 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4918 buildSortByAnnotationScoresMenu();
4926 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4930 protected void showDbRefs_actionPerformed(ActionEvent e)
4932 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4938 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4942 protected void showNpFeats_actionPerformed(ActionEvent e)
4944 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4948 * find the viewport amongst the tabs in this alignment frame and close that
4953 public boolean closeView(AlignViewportI av)
4957 this.closeMenuItem_actionPerformed(false);
4960 Component[] comp = tabbedPane.getComponents();
4961 for (int i = 0; comp != null && i < comp.length; i++)
4963 if (comp[i] instanceof AlignmentPanel)
4965 if (((AlignmentPanel) comp[i]).av == av)
4968 closeView((AlignmentPanel) comp[i]);
4976 protected void build_fetchdbmenu(JMenu webService)
4978 // Temporary hack - DBRef Fetcher always top level ws entry.
4979 // TODO We probably want to store a sequence database checklist in
4980 // preferences and have checkboxes.. rather than individual sources selected
4982 final JMenu rfetch = new JMenu(
4983 MessageManager.getString("action.fetch_db_references"));
4984 rfetch.setToolTipText(MessageManager
4985 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4986 webService.add(rfetch);
4988 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4989 MessageManager.getString("option.trim_retrieved_seqs"));
4990 trimrs.setToolTipText(MessageManager
4991 .getString("label.trim_retrieved_sequences"));
4992 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4993 trimrs.addActionListener(new ActionListener()
4996 public void actionPerformed(ActionEvent e)
4998 trimrs.setSelected(trimrs.isSelected());
4999 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5000 Boolean.valueOf(trimrs.isSelected()).toString());
5004 JMenuItem fetchr = new JMenuItem(
5005 MessageManager.getString("label.standard_databases"));
5006 fetchr.setToolTipText(MessageManager
5007 .getString("label.fetch_embl_uniprot"));
5008 fetchr.addActionListener(new ActionListener()
5012 public void actionPerformed(ActionEvent e)
5014 new Thread(new Runnable()
5019 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5020 .getAlignment().isNucleotide();
5021 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5022 .getSequenceSelection(), alignPanel.alignFrame, null,
5023 alignPanel.alignFrame.featureSettings, isNucleotide);
5024 dbRefFetcher.addListener(new FetchFinishedListenerI()
5027 public void finished()
5029 AlignFrame.this.setMenusForViewport();
5032 dbRefFetcher.fetchDBRefs(false);
5040 final AlignFrame me = this;
5041 new Thread(new Runnable()
5046 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5047 .getSequenceFetcherSingleton(me);
5048 javax.swing.SwingUtilities.invokeLater(new Runnable()
5053 String[] dbclasses = sf.getOrderedSupportedSources();
5054 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5055 // jalview.util.QuickSort.sort(otherdb, otherdb);
5056 List<DbSourceProxy> otherdb;
5057 JMenu dfetch = new JMenu();
5058 JMenu ifetch = new JMenu();
5059 JMenuItem fetchr = null;
5060 int comp = 0, icomp = 0, mcomp = 15;
5061 String mname = null;
5063 for (String dbclass : dbclasses)
5065 otherdb = sf.getSourceProxy(dbclass);
5066 // add a single entry for this class, or submenu allowing 'fetch
5068 if (otherdb == null || otherdb.size() < 1)
5072 // List<DbSourceProxy> dbs=otherdb;
5073 // otherdb=new ArrayList<DbSourceProxy>();
5074 // for (DbSourceProxy db:dbs)
5076 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5080 mname = "From " + dbclass;
5082 if (otherdb.size() == 1)
5084 final DbSourceProxy[] dassource = otherdb
5085 .toArray(new DbSourceProxy[0]);
5086 DbSourceProxy src = otherdb.get(0);
5087 fetchr = new JMenuItem(src.getDbSource());
5088 fetchr.addActionListener(new ActionListener()
5092 public void actionPerformed(ActionEvent e)
5094 new Thread(new Runnable()
5100 boolean isNucleotide = alignPanel.alignFrame
5101 .getViewport().getAlignment()
5103 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5104 alignPanel.av.getSequenceSelection(),
5105 alignPanel.alignFrame, dassource,
5106 alignPanel.alignFrame.featureSettings,
5109 .addListener(new FetchFinishedListenerI()
5112 public void finished()
5114 AlignFrame.this.setMenusForViewport();
5117 dbRefFetcher.fetchDBRefs(false);
5123 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5124 MessageManager.formatMessage(
5125 "label.fetch_retrieve_from",
5126 new Object[] { src.getDbName() })));
5132 final DbSourceProxy[] dassource = otherdb
5133 .toArray(new DbSourceProxy[0]);
5135 DbSourceProxy src = otherdb.get(0);
5136 fetchr = new JMenuItem(MessageManager.formatMessage(
5137 "label.fetch_all_param",
5138 new Object[] { src.getDbSource() }));
5139 fetchr.addActionListener(new ActionListener()
5142 public void actionPerformed(ActionEvent e)
5144 new Thread(new Runnable()
5150 boolean isNucleotide = alignPanel.alignFrame
5151 .getViewport().getAlignment()
5153 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5154 alignPanel.av.getSequenceSelection(),
5155 alignPanel.alignFrame, dassource,
5156 alignPanel.alignFrame.featureSettings,
5159 .addListener(new FetchFinishedListenerI()
5162 public void finished()
5164 AlignFrame.this.setMenusForViewport();
5167 dbRefFetcher.fetchDBRefs(false);
5173 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5174 MessageManager.formatMessage(
5175 "label.fetch_retrieve_from_all_sources",
5177 Integer.valueOf(otherdb.size())
5178 .toString(), src.getDbSource(),
5179 src.getDbName() })));
5182 // and then build the rest of the individual menus
5183 ifetch = new JMenu(MessageManager.formatMessage(
5184 "label.source_from_db_source",
5185 new Object[] { src.getDbSource() }));
5187 String imname = null;
5189 for (DbSourceProxy sproxy : otherdb)
5191 String dbname = sproxy.getDbName();
5192 String sname = dbname.length() > 5 ? dbname.substring(0,
5193 5) + "..." : dbname;
5194 String msname = dbname.length() > 10 ? dbname.substring(
5195 0, 10) + "..." : dbname;
5198 imname = MessageManager.formatMessage(
5199 "label.from_msname", new Object[] { sname });
5201 fetchr = new JMenuItem(msname);
5202 final DbSourceProxy[] dassrc = { sproxy };
5203 fetchr.addActionListener(new ActionListener()
5207 public void actionPerformed(ActionEvent e)
5209 new Thread(new Runnable()
5215 boolean isNucleotide = alignPanel.alignFrame
5216 .getViewport().getAlignment()
5218 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5219 alignPanel.av.getSequenceSelection(),
5220 alignPanel.alignFrame, dassrc,
5221 alignPanel.alignFrame.featureSettings,
5224 .addListener(new FetchFinishedListenerI()
5227 public void finished()
5229 AlignFrame.this.setMenusForViewport();
5232 dbRefFetcher.fetchDBRefs(false);
5238 fetchr.setToolTipText("<html>"
5239 + MessageManager.formatMessage(
5240 "label.fetch_retrieve_from", new Object[]
5244 if (++icomp >= mcomp || i == (otherdb.size()))
5246 ifetch.setText(MessageManager.formatMessage(
5247 "label.source_to_target", imname, sname));
5249 ifetch = new JMenu();
5257 if (comp >= mcomp || dbi >= (dbclasses.length))
5259 dfetch.setText(MessageManager.formatMessage(
5260 "label.source_to_target", mname, dbclass));
5262 dfetch = new JMenu();
5275 * Left justify the whole alignment.
5278 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5280 AlignmentI al = viewport.getAlignment();
5282 viewport.firePropertyChange("alignment", null, al);
5286 * Right justify the whole alignment.
5289 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5291 AlignmentI al = viewport.getAlignment();
5293 viewport.firePropertyChange("alignment", null, al);
5297 public void setShowSeqFeatures(boolean b)
5299 showSeqFeatures.setSelected(b);
5300 viewport.setShowSequenceFeatures(b);
5307 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5308 * awt.event.ActionEvent)
5311 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5313 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5314 alignPanel.paintAlignment(true);
5321 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5325 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5327 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5328 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5336 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5337 * .event.ActionEvent)
5340 protected void showGroupConservation_actionPerformed(ActionEvent e)
5342 viewport.setShowGroupConservation(showGroupConservation.getState());
5343 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5350 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5351 * .event.ActionEvent)
5354 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5356 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5357 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5364 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5365 * .event.ActionEvent)
5368 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5370 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5371 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5375 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5377 showSequenceLogo.setState(true);
5378 viewport.setShowSequenceLogo(true);
5379 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5380 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5384 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5386 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5393 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5394 * .event.ActionEvent)
5397 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5399 if (avc.makeGroupsFromSelection())
5401 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5402 alignPanel.updateAnnotation();
5403 alignPanel.paintAlignment(true);
5407 public void clearAlignmentSeqRep()
5409 // TODO refactor alignmentseqrep to controller
5410 if (viewport.getAlignment().hasSeqrep())
5412 viewport.getAlignment().setSeqrep(null);
5413 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5414 alignPanel.updateAnnotation();
5415 alignPanel.paintAlignment(true);
5420 protected void createGroup_actionPerformed(ActionEvent e)
5422 if (avc.createGroup())
5424 alignPanel.alignmentChanged();
5429 protected void unGroup_actionPerformed(ActionEvent e)
5433 alignPanel.alignmentChanged();
5438 * make the given alignmentPanel the currently selected tab
5440 * @param alignmentPanel
5442 public void setDisplayedView(AlignmentPanel alignmentPanel)
5444 if (!viewport.getSequenceSetId().equals(
5445 alignmentPanel.av.getSequenceSetId()))
5449 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5451 if (tabbedPane != null
5452 && tabbedPane.getTabCount() > 0
5453 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5454 .getSelectedIndex())
5456 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5461 * Action on selection of menu options to Show or Hide annotations.
5464 * @param forSequences
5465 * update sequence-related annotations
5466 * @param forAlignment
5467 * update non-sequence-related annotations
5470 protected void setAnnotationsVisibility(boolean visible,
5471 boolean forSequences, boolean forAlignment)
5473 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5474 .getAlignmentAnnotation();
5479 for (AlignmentAnnotation aa : anns)
5482 * don't display non-positional annotations on an alignment
5484 if (aa.annotations == null)
5488 boolean apply = (aa.sequenceRef == null && forAlignment)
5489 || (aa.sequenceRef != null && forSequences);
5492 aa.visible = visible;
5495 alignPanel.validateAnnotationDimensions(true);
5496 alignPanel.alignmentChanged();
5500 * Store selected annotation sort order for the view and repaint.
5503 protected void sortAnnotations_actionPerformed()
5505 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5507 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5508 alignPanel.paintAlignment(true);
5513 * @return alignment panels in this alignment frame
5515 public List<? extends AlignmentViewPanel> getAlignPanels()
5517 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5521 * Open a new alignment window, with the cDNA associated with this (protein)
5522 * alignment, aligned as is the protein.
5524 protected void viewAsCdna_actionPerformed()
5526 // TODO no longer a menu action - refactor as required
5527 final AlignmentI alignment = getViewport().getAlignment();
5528 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5529 if (mappings == null)
5533 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5534 for (SequenceI aaSeq : alignment.getSequences())
5536 for (AlignedCodonFrame acf : mappings)
5538 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5542 * There is a cDNA mapping for this protein sequence - add to new
5543 * alignment. It will share the same dataset sequence as other mapped
5544 * cDNA (no new mappings need to be created).
5546 final Sequence newSeq = new Sequence(dnaSeq);
5547 newSeq.setDatasetSequence(dnaSeq);
5548 cdnaSeqs.add(newSeq);
5552 if (cdnaSeqs.size() == 0)
5554 // show a warning dialog no mapped cDNA
5557 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5559 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5560 AlignFrame.DEFAULT_HEIGHT);
5561 cdna.alignAs(alignment);
5562 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5564 Desktop.addInternalFrame(alignFrame, newtitle,
5565 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5569 * Set visibility of dna/protein complement view (available when shown in a
5575 protected void showComplement_actionPerformed(boolean show)
5577 SplitContainerI sf = getSplitViewContainer();
5580 sf.setComplementVisible(this, show);
5585 * Generate the reverse (optionally complemented) of the selected sequences,
5586 * and add them to the alignment
5589 protected void showReverse_actionPerformed(boolean complement)
5591 AlignmentI al = null;
5594 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5595 al = dna.reverseCdna(complement);
5596 viewport.addAlignment(al, "");
5597 addHistoryItem(new EditCommand(
5598 MessageManager.getString("label.add_sequences"),
5599 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5600 viewport.getAlignment()));
5601 } catch (Exception ex)
5603 System.err.println(ex.getMessage());
5609 * Try to run a script in the Groovy console, having first ensured that this
5610 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5611 * be targeted at this alignment.
5614 protected void runGroovy_actionPerformed()
5616 Jalview.setCurrentAlignFrame(this);
5617 groovy.ui.Console console = Desktop.getGroovyConsole();
5618 if (console != null)
5622 console.runScript();
5623 } catch (Exception ex)
5625 System.err.println((ex.toString()));
5627 .showInternalMessageDialog(Desktop.desktop, MessageManager
5628 .getString("label.couldnt_run_groovy_script"),
5630 .getString("label.groovy_support_failed"),
5631 JvOptionPane.ERROR_MESSAGE);
5636 System.err.println("Can't run Groovy script as console not found");
5641 * Hides columns containing (or not containing) a specified feature, provided
5642 * that would not leave all columns hidden
5644 * @param featureType
5645 * @param columnsContaining
5648 public boolean hideFeatureColumns(String featureType,
5649 boolean columnsContaining)
5651 boolean notForHiding = avc.markColumnsContainingFeatures(
5652 columnsContaining, false, false, featureType);
5655 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5656 false, featureType))
5658 getViewport().hideSelectedColumns();
5666 protected void selectHighlightedColumns_actionPerformed(
5667 ActionEvent actionEvent)
5669 // include key modifier check in case user selects from menu
5670 avc.markHighlightedColumns(
5671 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5673 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5677 * Rebuilds the Colour menu, including any user-defined colours which have
5678 * been loaded either on startup or during the session
5680 public void buildColourMenu()
5682 colourMenu.removeAll();
5684 colourMenu.add(applyToAllGroups);
5685 colourMenu.add(textColour);
5686 colourMenu.addSeparator();
5688 ColourMenuHelper.addMenuItems(colourMenu, this,
5689 viewport.getAlignment(), false);
5691 colourMenu.addSeparator();
5692 colourMenu.add(conservationMenuItem);
5693 colourMenu.add(modifyConservation);
5694 colourMenu.add(abovePIDThreshold);
5695 colourMenu.add(modifyPID);
5696 colourMenu.add(annotationColour);
5698 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5699 String schemeName = colourScheme == null ? null : colourScheme
5702 ColourMenuHelper.setColourSelected(colourMenu, schemeName);
5706 class PrintThread extends Thread
5710 public PrintThread(AlignmentPanel ap)
5715 static PageFormat pf;
5720 PrinterJob printJob = PrinterJob.getPrinterJob();
5724 printJob.setPrintable(ap, pf);
5728 printJob.setPrintable(ap);
5731 if (printJob.printDialog())
5736 } catch (Exception PrintException)
5738 PrintException.printStackTrace();