2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.ParseProperties;
28 import jalview.analysis.SequenceIdMatcher;
29 import jalview.api.AlignExportSettingI;
30 import jalview.api.AlignViewControllerGuiI;
31 import jalview.api.AlignViewControllerI;
32 import jalview.api.AlignViewportI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.FeatureSettingsControllerI;
35 import jalview.api.SplitContainerI;
36 import jalview.api.ViewStyleI;
37 import jalview.api.analysis.SimilarityParamsI;
38 import jalview.bin.Cache;
39 import jalview.bin.Jalview;
40 import jalview.commands.CommandI;
41 import jalview.commands.EditCommand;
42 import jalview.commands.EditCommand.Action;
43 import jalview.commands.OrderCommand;
44 import jalview.commands.RemoveGapColCommand;
45 import jalview.commands.RemoveGapsCommand;
46 import jalview.commands.SlideSequencesCommand;
47 import jalview.commands.TrimRegionCommand;
48 import jalview.datamodel.AlignedCodonFrame;
49 import jalview.datamodel.Alignment;
50 import jalview.datamodel.AlignmentAnnotation;
51 import jalview.datamodel.AlignmentExportData;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.AlignmentOrder;
54 import jalview.datamodel.AlignmentView;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.HiddenColumns;
57 import jalview.datamodel.HiddenSequences;
58 import jalview.datamodel.PDBEntry;
59 import jalview.datamodel.SeqCigar;
60 import jalview.datamodel.Sequence;
61 import jalview.datamodel.SequenceGroup;
62 import jalview.datamodel.SequenceI;
63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
65 import jalview.io.AlignmentProperties;
66 import jalview.io.AnnotationFile;
67 import jalview.io.BioJsHTMLOutput;
68 import jalview.io.DataSourceType;
69 import jalview.io.FileFormat;
70 import jalview.io.FileFormatI;
71 import jalview.io.FileFormats;
72 import jalview.io.FileLoader;
73 import jalview.io.FileParse;
74 import jalview.io.FormatAdapter;
75 import jalview.io.HtmlSvgOutput;
76 import jalview.io.IdentifyFile;
77 import jalview.io.JPredFile;
78 import jalview.io.JalviewFileChooser;
79 import jalview.io.JalviewFileView;
80 import jalview.io.JnetAnnotationMaker;
81 import jalview.io.NewickFile;
82 import jalview.io.ScoreMatrixFile;
83 import jalview.io.TCoffeeScoreFile;
84 import jalview.jbgui.GAlignFrame;
85 import jalview.schemes.ColourSchemeI;
86 import jalview.schemes.ColourSchemes;
87 import jalview.schemes.ResidueColourScheme;
88 import jalview.schemes.TCoffeeColourScheme;
89 import jalview.util.MessageManager;
90 import jalview.viewmodel.AlignmentViewport;
91 import jalview.viewmodel.ViewportRanges;
92 import jalview.ws.DBRefFetcher;
93 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
94 import jalview.ws.jws1.Discoverer;
95 import jalview.ws.jws2.Jws2Discoverer;
96 import jalview.ws.jws2.jabaws2.Jws2Instance;
97 import jalview.ws.seqfetcher.DbSourceProxy;
99 import java.awt.BorderLayout;
100 import java.awt.Component;
101 import java.awt.Rectangle;
102 import java.awt.Toolkit;
103 import java.awt.datatransfer.Clipboard;
104 import java.awt.datatransfer.DataFlavor;
105 import java.awt.datatransfer.StringSelection;
106 import java.awt.datatransfer.Transferable;
107 import java.awt.dnd.DnDConstants;
108 import java.awt.dnd.DropTargetDragEvent;
109 import java.awt.dnd.DropTargetDropEvent;
110 import java.awt.dnd.DropTargetEvent;
111 import java.awt.dnd.DropTargetListener;
112 import java.awt.event.ActionEvent;
113 import java.awt.event.ActionListener;
114 import java.awt.event.FocusAdapter;
115 import java.awt.event.FocusEvent;
116 import java.awt.event.ItemEvent;
117 import java.awt.event.ItemListener;
118 import java.awt.event.KeyAdapter;
119 import java.awt.event.KeyEvent;
120 import java.awt.event.MouseEvent;
121 import java.awt.print.PageFormat;
122 import java.awt.print.PrinterJob;
123 import java.beans.PropertyChangeEvent;
125 import java.io.FileWriter;
126 import java.io.PrintWriter;
128 import java.util.ArrayList;
129 import java.util.Arrays;
130 import java.util.Deque;
131 import java.util.Enumeration;
132 import java.util.Hashtable;
133 import java.util.List;
134 import java.util.Vector;
136 import javax.swing.JCheckBoxMenuItem;
137 import javax.swing.JEditorPane;
138 import javax.swing.JInternalFrame;
139 import javax.swing.JLayeredPane;
140 import javax.swing.JMenu;
141 import javax.swing.JMenuItem;
142 import javax.swing.JScrollPane;
143 import javax.swing.SwingUtilities;
149 * @version $Revision$
151 public class AlignFrame extends GAlignFrame implements DropTargetListener,
152 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
155 public static final int DEFAULT_WIDTH = 700;
157 public static final int DEFAULT_HEIGHT = 500;
160 * The currently displayed panel (selected tabbed view if more than one)
162 public AlignmentPanel alignPanel;
164 AlignViewport viewport;
166 ViewportRanges vpRanges;
168 public AlignViewControllerI avc;
170 List<AlignmentPanel> alignPanels = new ArrayList<>();
173 * Last format used to load or save alignments in this window
175 FileFormatI currentFileFormat = null;
178 * Current filename for this alignment
180 String fileName = null;
183 * Creates a new AlignFrame object with specific width and height.
189 public AlignFrame(AlignmentI al, int width, int height)
191 this(al, null, width, height);
195 * Creates a new AlignFrame object with specific width, height and
201 * @param sequenceSetId
203 public AlignFrame(AlignmentI al, int width, int height,
204 String sequenceSetId)
206 this(al, null, width, height, sequenceSetId);
210 * Creates a new AlignFrame object with specific width, height and
216 * @param sequenceSetId
219 public AlignFrame(AlignmentI al, int width, int height,
220 String sequenceSetId, String viewId)
222 this(al, null, width, height, sequenceSetId, viewId);
226 * new alignment window with hidden columns
230 * @param hiddenColumns
231 * ColumnSelection or null
233 * Width of alignment frame
237 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
238 int width, int height)
240 this(al, hiddenColumns, width, height, null);
244 * Create alignment frame for al with hiddenColumns, a specific width and
245 * height, and specific sequenceId
248 * @param hiddenColumns
251 * @param sequenceSetId
254 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
255 int width, int height, String sequenceSetId)
257 this(al, hiddenColumns, width, height, sequenceSetId, null);
261 * Create alignment frame for al with hiddenColumns, a specific width and
262 * height, and specific sequenceId
265 * @param hiddenColumns
268 * @param sequenceSetId
273 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
274 int width, int height, String sequenceSetId, String viewId)
276 setSize(width, height);
278 if (al.getDataset() == null)
283 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
285 alignPanel = new AlignmentPanel(this, viewport);
287 addAlignmentPanel(alignPanel, true);
291 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
292 HiddenColumns hiddenColumns, int width, int height)
294 setSize(width, height);
296 if (al.getDataset() == null)
301 viewport = new AlignViewport(al, hiddenColumns);
303 if (hiddenSeqs != null && hiddenSeqs.length > 0)
305 viewport.hideSequence(hiddenSeqs);
307 alignPanel = new AlignmentPanel(this, viewport);
308 addAlignmentPanel(alignPanel, true);
313 * Make a new AlignFrame from existing alignmentPanels
320 public AlignFrame(AlignmentPanel ap)
324 addAlignmentPanel(ap, false);
329 * initalise the alignframe from the underlying viewport data and the
334 if (!Jalview.isHeadlessMode())
336 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
339 vpRanges = viewport.getRanges();
340 avc = new jalview.controller.AlignViewController(this, viewport,
342 if (viewport.getAlignmentConservationAnnotation() == null)
344 // BLOSUM62Colour.setEnabled(false);
345 conservationMenuItem.setEnabled(false);
346 modifyConservation.setEnabled(false);
347 // PIDColour.setEnabled(false);
348 // abovePIDThreshold.setEnabled(false);
349 // modifyPID.setEnabled(false);
352 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
355 if (sortby.equals("Id"))
357 sortIDMenuItem_actionPerformed(null);
359 else if (sortby.equals("Pairwise Identity"))
361 sortPairwiseMenuItem_actionPerformed(null);
365 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
367 setMenusFromViewport(viewport);
368 buildSortByAnnotationScoresMenu();
369 calculateTree.addActionListener(new ActionListener()
373 public void actionPerformed(ActionEvent e)
380 if (Desktop.desktop != null)
382 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
383 addServiceListeners();
387 if (viewport.getWrapAlignment())
389 wrapMenuItem_actionPerformed(null);
392 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
394 this.overviewMenuItem_actionPerformed(null);
399 final List<AlignmentPanel> selviews = new ArrayList<>();
400 final List<AlignmentPanel> origview = new ArrayList<>();
401 final String menuLabel = MessageManager
402 .getString("label.copy_format_from");
403 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
404 new ViewSetProvider()
408 public AlignmentPanel[] getAllAlignmentPanels()
411 origview.add(alignPanel);
412 // make an array of all alignment panels except for this one
413 List<AlignmentPanel> aps = new ArrayList<>(
414 Arrays.asList(Desktop.getAlignmentPanels(null)));
415 aps.remove(AlignFrame.this.alignPanel);
416 return aps.toArray(new AlignmentPanel[aps.size()]);
418 }, selviews, new ItemListener()
422 public void itemStateChanged(ItemEvent e)
424 if (origview.size() > 0)
426 final AlignmentPanel ap = origview.get(0);
429 * Copy the ViewStyle of the selected panel to 'this one'.
430 * Don't change value of 'scaleProteinAsCdna' unless copying
433 ViewStyleI vs = selviews.get(0).getAlignViewport()
435 boolean fromSplitFrame = selviews.get(0)
436 .getAlignViewport().getCodingComplement() != null;
439 vs.setScaleProteinAsCdna(ap.getAlignViewport()
440 .getViewStyle().isScaleProteinAsCdna());
442 ap.getAlignViewport().setViewStyle(vs);
445 * Also rescale ViewStyle of SplitFrame complement if there is
446 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
447 * the whole ViewStyle (allow cDNA protein to have different
450 AlignViewportI complement = ap.getAlignViewport()
451 .getCodingComplement();
452 if (complement != null && vs.isScaleProteinAsCdna())
454 AlignFrame af = Desktop.getAlignFrameFor(complement);
455 ((SplitFrame) af.getSplitViewContainer())
457 af.setMenusForViewport();
461 ap.setSelected(true);
462 ap.alignFrame.setMenusForViewport();
467 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
468 .indexOf("devel") > -1
469 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
470 .indexOf("test") > -1)
472 formatMenu.add(vsel);
474 addFocusListener(new FocusAdapter()
477 public void focusGained(FocusEvent e)
479 Jalview.setCurrentAlignFrame(AlignFrame.this);
486 * Change the filename and format for the alignment, and enable the 'reload'
487 * button functionality.
494 public void setFileName(String file, FileFormatI format)
497 setFileFormat(format);
498 reload.setEnabled(true);
502 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
505 void addKeyListener()
507 addKeyListener(new KeyAdapter()
510 public void keyPressed(KeyEvent evt)
512 if (viewport.cursorMode
513 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
514 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
515 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
516 && Character.isDigit(evt.getKeyChar()))
518 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
521 switch (evt.getKeyCode())
524 case 27: // escape key
525 deselectAllSequenceMenuItem_actionPerformed(null);
529 case KeyEvent.VK_DOWN:
530 if (evt.isAltDown() || !viewport.cursorMode)
532 moveSelectedSequences(false);
534 if (viewport.cursorMode)
536 alignPanel.getSeqPanel().moveCursor(0, 1);
541 if (evt.isAltDown() || !viewport.cursorMode)
543 moveSelectedSequences(true);
545 if (viewport.cursorMode)
547 alignPanel.getSeqPanel().moveCursor(0, -1);
552 case KeyEvent.VK_LEFT:
553 if (evt.isAltDown() || !viewport.cursorMode)
555 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
559 alignPanel.getSeqPanel().moveCursor(-1, 0);
564 case KeyEvent.VK_RIGHT:
565 if (evt.isAltDown() || !viewport.cursorMode)
567 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
571 alignPanel.getSeqPanel().moveCursor(1, 0);
575 case KeyEvent.VK_SPACE:
576 if (viewport.cursorMode)
578 alignPanel.getSeqPanel().insertGapAtCursor(
579 evt.isControlDown() || evt.isShiftDown()
584 // case KeyEvent.VK_A:
585 // if (viewport.cursorMode)
587 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
588 // //System.out.println("A");
592 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
593 * System.out.println("closing bracket"); } break;
595 case KeyEvent.VK_DELETE:
596 case KeyEvent.VK_BACK_SPACE:
597 if (!viewport.cursorMode)
599 cut_actionPerformed(null);
603 alignPanel.getSeqPanel().deleteGapAtCursor(
604 evt.isControlDown() || evt.isShiftDown()
611 if (viewport.cursorMode)
613 alignPanel.getSeqPanel().setCursorRow();
617 if (viewport.cursorMode && !evt.isControlDown())
619 alignPanel.getSeqPanel().setCursorColumn();
623 if (viewport.cursorMode)
625 alignPanel.getSeqPanel().setCursorPosition();
629 case KeyEvent.VK_ENTER:
630 case KeyEvent.VK_COMMA:
631 if (viewport.cursorMode)
633 alignPanel.getSeqPanel().setCursorRowAndColumn();
638 if (viewport.cursorMode)
640 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
644 if (viewport.cursorMode)
646 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
651 viewport.cursorMode = !viewport.cursorMode;
652 statusBar.setText(MessageManager.formatMessage(
653 "label.keyboard_editing_mode",
654 new String[] { (viewport.cursorMode ? "on" : "off") }));
655 if (viewport.cursorMode)
657 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
659 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
662 alignPanel.getSeqPanel().seqCanvas.repaint();
668 Help.showHelpWindow();
669 } catch (Exception ex)
671 ex.printStackTrace();
676 boolean toggleSeqs = !evt.isControlDown();
677 boolean toggleCols = !evt.isShiftDown();
678 toggleHiddenRegions(toggleSeqs, toggleCols);
683 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
684 boolean modifyExisting = true; // always modify, don't clear
685 // evt.isShiftDown();
686 boolean invertHighlighted = evt.isAltDown();
687 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
691 case KeyEvent.VK_PAGE_UP:
692 if (viewport.getWrapAlignment())
694 vpRanges.scrollUp(true);
701 case KeyEvent.VK_PAGE_DOWN:
702 if (viewport.getWrapAlignment())
704 vpRanges.scrollUp(false);
715 public void keyReleased(KeyEvent evt)
717 switch (evt.getKeyCode())
719 case KeyEvent.VK_LEFT:
720 if (evt.isAltDown() || !viewport.cursorMode)
722 viewport.firePropertyChange("alignment", null, viewport
723 .getAlignment().getSequences());
727 case KeyEvent.VK_RIGHT:
728 if (evt.isAltDown() || !viewport.cursorMode)
730 viewport.firePropertyChange("alignment", null, viewport
731 .getAlignment().getSequences());
739 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
741 ap.alignFrame = this;
742 avc = new jalview.controller.AlignViewController(this, viewport,
747 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
749 int aSize = alignPanels.size();
751 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
753 if (aSize == 1 && ap.av.viewName == null)
755 this.getContentPane().add(ap, BorderLayout.CENTER);
761 setInitialTabVisible();
764 expandViews.setEnabled(true);
765 gatherViews.setEnabled(true);
766 tabbedPane.addTab(ap.av.viewName, ap);
768 ap.setVisible(false);
773 if (ap.av.isPadGaps())
775 ap.av.getAlignment().padGaps();
777 ap.av.updateConservation(ap);
778 ap.av.updateConsensus(ap);
779 ap.av.updateStrucConsensus(ap);
783 public void setInitialTabVisible()
785 expandViews.setEnabled(true);
786 gatherViews.setEnabled(true);
787 tabbedPane.setVisible(true);
788 AlignmentPanel first = alignPanels.get(0);
789 tabbedPane.addTab(first.av.viewName, first);
790 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
793 public AlignViewport getViewport()
798 /* Set up intrinsic listeners for dynamically generated GUI bits. */
799 private void addServiceListeners()
801 final java.beans.PropertyChangeListener thisListener;
802 Desktop.instance.addJalviewPropertyChangeListener("services",
803 thisListener = new java.beans.PropertyChangeListener()
806 public void propertyChange(PropertyChangeEvent evt)
808 // // System.out.println("Discoverer property change.");
809 // if (evt.getPropertyName().equals("services"))
811 SwingUtilities.invokeLater(new Runnable()
818 .println("Rebuild WS Menu for service change");
819 BuildWebServiceMenu();
826 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
829 public void internalFrameClosed(
830 javax.swing.event.InternalFrameEvent evt)
832 // System.out.println("deregistering discoverer listener");
833 Desktop.instance.removeJalviewPropertyChangeListener("services",
835 closeMenuItem_actionPerformed(true);
838 // Finally, build the menu once to get current service state
839 new Thread(new Runnable()
844 BuildWebServiceMenu();
850 * Configure menu items that vary according to whether the alignment is
851 * nucleotide or protein
853 public void setGUINucleotide()
855 AlignmentI al = getViewport().getAlignment();
856 boolean nucleotide = al.isNucleotide();
858 showTranslation.setVisible(nucleotide);
859 showReverse.setVisible(nucleotide);
860 showReverseComplement.setVisible(nucleotide);
861 conservationMenuItem.setEnabled(!nucleotide);
862 modifyConservation.setEnabled(!nucleotide
863 && conservationMenuItem.isSelected());
864 showGroupConservation.setEnabled(!nucleotide);
866 showComplementMenuItem.setText(nucleotide ? MessageManager
867 .getString("label.protein") : MessageManager
868 .getString("label.nucleotide"));
872 * set up menus for the current viewport. This may be called after any
873 * operation that affects the data in the current view (selection changed,
874 * etc) to update the menus to reflect the new state.
877 public void setMenusForViewport()
879 setMenusFromViewport(viewport);
883 * Need to call this method when tabs are selected for multiple views, or when
884 * loading from Jalview2XML.java
889 void setMenusFromViewport(AlignViewport av)
891 padGapsMenuitem.setSelected(av.isPadGaps());
892 colourTextMenuItem.setSelected(av.isShowColourText());
893 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
894 modifyPID.setEnabled(abovePIDThreshold.isSelected());
895 conservationMenuItem.setSelected(av.getConservationSelected());
896 modifyConservation.setEnabled(conservationMenuItem.isSelected());
897 seqLimits.setSelected(av.getShowJVSuffix());
898 idRightAlign.setSelected(av.isRightAlignIds());
899 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
900 renderGapsMenuItem.setSelected(av.isRenderGaps());
901 wrapMenuItem.setSelected(av.getWrapAlignment());
902 scaleAbove.setVisible(av.getWrapAlignment());
903 scaleLeft.setVisible(av.getWrapAlignment());
904 scaleRight.setVisible(av.getWrapAlignment());
905 annotationPanelMenuItem.setState(av.isShowAnnotation());
907 * Show/hide annotations only enabled if annotation panel is shown
909 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
910 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
911 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
912 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
913 viewBoxesMenuItem.setSelected(av.getShowBoxes());
914 viewTextMenuItem.setSelected(av.getShowText());
915 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
916 showGroupConsensus.setSelected(av.isShowGroupConsensus());
917 showGroupConservation.setSelected(av.isShowGroupConservation());
918 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
919 showSequenceLogo.setSelected(av.isShowSequenceLogo());
920 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
922 ColourMenuHelper.setColourSelected(colourMenu,
923 av.getGlobalColourScheme());
925 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
926 hiddenMarkers.setState(av.getShowHiddenMarkers());
927 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
928 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
929 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
930 autoCalculate.setSelected(av.autoCalculateConsensus);
931 sortByTree.setSelected(av.sortByTree);
932 listenToViewSelections.setSelected(av.followSelection);
934 showProducts.setEnabled(canShowProducts());
935 setGroovyEnabled(Desktop.getGroovyConsole() != null);
941 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
945 public void setGroovyEnabled(boolean b)
947 runGroovy.setEnabled(b);
950 private IProgressIndicator progressBar;
955 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
958 public void setProgressBar(String message, long id)
960 progressBar.setProgressBar(message, id);
964 public void registerHandler(final long id,
965 final IProgressIndicatorHandler handler)
967 progressBar.registerHandler(id, handler);
972 * @return true if any progress bars are still active
975 public boolean operationInProgress()
977 return progressBar.operationInProgress();
981 public void setStatus(String text)
983 statusBar.setText(text);
987 * Added so Castor Mapping file can obtain Jalview Version
989 public String getVersion()
991 return jalview.bin.Cache.getProperty("VERSION");
994 public FeatureRenderer getFeatureRenderer()
996 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1000 public void fetchSequence_actionPerformed(ActionEvent e)
1002 new jalview.gui.SequenceFetcher(this);
1006 public void addFromFile_actionPerformed(ActionEvent e)
1008 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1012 public void reload_actionPerformed(ActionEvent e)
1014 if (fileName != null)
1016 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1017 // originating file's format
1018 // TODO: work out how to recover feature settings for correct view(s) when
1019 // file is reloaded.
1020 if (FileFormat.Jalview.equals(currentFileFormat))
1022 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1023 for (int i = 0; i < frames.length; i++)
1025 if (frames[i] instanceof AlignFrame && frames[i] != this
1026 && ((AlignFrame) frames[i]).fileName != null
1027 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1031 frames[i].setSelected(true);
1032 Desktop.instance.closeAssociatedWindows();
1033 } catch (java.beans.PropertyVetoException ex)
1039 Desktop.instance.closeAssociatedWindows();
1041 FileLoader loader = new FileLoader();
1042 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1043 : DataSourceType.FILE;
1044 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1048 Rectangle bounds = this.getBounds();
1050 FileLoader loader = new FileLoader();
1051 DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1052 : DataSourceType.FILE;
1053 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1054 protocol, currentFileFormat);
1056 newframe.setBounds(bounds);
1057 if (featureSettings != null && featureSettings.isShowing())
1059 final Rectangle fspos = featureSettings.frame.getBounds();
1060 // TODO: need a 'show feature settings' function that takes bounds -
1061 // need to refactor Desktop.addFrame
1062 newframe.featureSettings_actionPerformed(null);
1063 final FeatureSettings nfs = newframe.featureSettings;
1064 SwingUtilities.invokeLater(new Runnable()
1069 nfs.frame.setBounds(fspos);
1072 this.featureSettings.close();
1073 this.featureSettings = null;
1075 this.closeMenuItem_actionPerformed(true);
1081 public void addFromText_actionPerformed(ActionEvent e)
1083 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1088 public void addFromURL_actionPerformed(ActionEvent e)
1090 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1094 public void save_actionPerformed(ActionEvent e)
1096 if (fileName == null || (currentFileFormat == null)
1097 || fileName.startsWith("http"))
1099 saveAs_actionPerformed(null);
1103 saveAlignment(fileName, currentFileFormat);
1114 public void saveAs_actionPerformed(ActionEvent e)
1116 String format = currentFileFormat == null ? null : currentFileFormat
1118 JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1119 Cache.getProperty("LAST_DIRECTORY"), format);
1121 chooser.setFileView(new JalviewFileView());
1122 chooser.setDialogTitle(MessageManager
1123 .getString("label.save_alignment_to_file"));
1124 chooser.setToolTipText(MessageManager.getString("action.save"));
1126 int value = chooser.showSaveDialog(this);
1128 if (value == JalviewFileChooser.APPROVE_OPTION)
1130 currentFileFormat = chooser.getSelectedFormat();
1131 while (currentFileFormat == null)
1134 .showInternalMessageDialog(
1137 .getString("label.select_file_format_before_saving"),
1139 .getString("label.file_format_not_specified"),
1140 JvOptionPane.WARNING_MESSAGE);
1141 currentFileFormat = chooser.getSelectedFormat();
1142 value = chooser.showSaveDialog(this);
1143 if (value != JalviewFileChooser.APPROVE_OPTION)
1149 fileName = chooser.getSelectedFile().getPath();
1151 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1153 Cache.setProperty("LAST_DIRECTORY", fileName);
1154 saveAlignment(fileName, currentFileFormat);
1158 public boolean saveAlignment(String file, FileFormatI format)
1160 boolean success = true;
1162 if (FileFormat.Jalview.equals(format))
1164 String shortName = title;
1166 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1168 shortName = shortName.substring(shortName
1169 .lastIndexOf(java.io.File.separatorChar) + 1);
1172 success = new Jalview2XML().saveAlignment(this, file, shortName);
1174 statusBar.setText(MessageManager.formatMessage(
1175 "label.successfully_saved_to_file_in_format", new Object[] {
1176 fileName, format }));
1181 AlignmentExportData exportData = getAlignmentForExport(format,
1183 if (exportData.getSettings().isCancelled())
1187 FormatAdapter f = new FormatAdapter(alignPanel,
1188 exportData.getSettings());
1189 String output = f.formatSequences(
1191 exportData.getAlignment(), // class cast exceptions will
1192 // occur in the distant future
1193 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1194 f.getCacheSuffixDefault(format), viewport.getAlignment()
1195 .getHiddenColumns());
1205 PrintWriter out = new PrintWriter(new FileWriter(file));
1209 this.setTitle(file);
1210 statusBar.setText(MessageManager.formatMessage(
1211 "label.successfully_saved_to_file_in_format",
1212 new Object[] { fileName, format.getName() }));
1213 } catch (Exception ex)
1216 ex.printStackTrace();
1223 JvOptionPane.showInternalMessageDialog(this, MessageManager
1224 .formatMessage("label.couldnt_save_file",
1225 new Object[] { fileName }), MessageManager
1226 .getString("label.error_saving_file"),
1227 JvOptionPane.WARNING_MESSAGE);
1233 private void warningMessage(String warning, String title)
1235 if (new jalview.util.Platform().isHeadless())
1237 System.err.println("Warning: " + title + "\nWarning: " + warning);
1242 JvOptionPane.showInternalMessageDialog(this, warning, title,
1243 JvOptionPane.WARNING_MESSAGE);
1255 protected void outputText_actionPerformed(ActionEvent e)
1257 FileFormatI fileFormat = FileFormats.getInstance().forName(
1258 e.getActionCommand());
1259 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1261 if (exportData.getSettings().isCancelled())
1265 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1266 cap.setForInput(null);
1269 FileFormatI format = fileFormat;
1270 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1271 .formatSequences(format, exportData.getAlignment(),
1272 exportData.getOmitHidden(),
1274 .getStartEndPostions(), viewport
1275 .getAlignment().getHiddenColumns()));
1276 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1277 "label.alignment_output_command",
1278 new Object[] { e.getActionCommand() }), 600, 500);
1279 } catch (OutOfMemoryError oom)
1281 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1287 public static AlignmentExportData getAlignmentForExport(
1288 FileFormatI format, AlignViewportI viewport,
1289 AlignExportSettingI exportSettings)
1291 AlignmentI alignmentToExport = null;
1292 AlignExportSettingI settings = exportSettings;
1293 String[] omitHidden = null;
1295 HiddenSequences hiddenSeqs = viewport.getAlignment()
1296 .getHiddenSequences();
1298 alignmentToExport = viewport.getAlignment();
1300 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1301 if (settings == null)
1303 settings = new AlignExportSettings(hasHiddenSeqs,
1304 viewport.hasHiddenColumns(), format);
1306 // settings.isExportAnnotations();
1308 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1310 omitHidden = viewport.getViewAsString(false,
1311 settings.isExportHiddenSequences());
1314 int[] alignmentStartEnd = new int[2];
1315 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1317 alignmentToExport = hiddenSeqs.getFullAlignment();
1321 alignmentToExport = viewport.getAlignment();
1323 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1324 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1325 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1326 omitHidden, alignmentStartEnd, settings);
1337 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1339 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1340 htmlSVG.exportHTML(null);
1344 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1346 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1347 bjs.exportHTML(null);
1350 public void createImageMap(File file, String image)
1352 alignPanel.makePNGImageMap(file, image);
1362 public void createPNG(File f)
1364 alignPanel.makePNG(f);
1374 public void createEPS(File f)
1376 alignPanel.makeEPS(f);
1380 public void createSVG(File f)
1382 alignPanel.makeSVG(f);
1386 public void pageSetup_actionPerformed(ActionEvent e)
1388 PrinterJob printJob = PrinterJob.getPrinterJob();
1389 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1399 public void printMenuItem_actionPerformed(ActionEvent e)
1401 // Putting in a thread avoids Swing painting problems
1402 PrintThread thread = new PrintThread(alignPanel);
1407 public void exportFeatures_actionPerformed(ActionEvent e)
1409 new AnnotationExporter().exportFeatures(alignPanel);
1413 public void exportAnnotations_actionPerformed(ActionEvent e)
1415 new AnnotationExporter().exportAnnotations(alignPanel);
1419 public void associatedData_actionPerformed(ActionEvent e)
1421 // Pick the tree file
1422 JalviewFileChooser chooser = new JalviewFileChooser(
1423 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1424 chooser.setFileView(new JalviewFileView());
1425 chooser.setDialogTitle(MessageManager
1426 .getString("label.load_jalview_annotations"));
1427 chooser.setToolTipText(MessageManager
1428 .getString("label.load_jalview_annotations"));
1430 int value = chooser.showOpenDialog(null);
1432 if (value == JalviewFileChooser.APPROVE_OPTION)
1434 String choice = chooser.getSelectedFile().getPath();
1435 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1436 loadJalviewDataFile(choice, null, null, null);
1442 * Close the current view or all views in the alignment frame. If the frame
1443 * only contains one view then the alignment will be removed from memory.
1445 * @param closeAllTabs
1448 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1450 if (alignPanels != null && alignPanels.size() < 2)
1452 closeAllTabs = true;
1457 if (alignPanels != null)
1461 if (this.isClosed())
1463 // really close all the windows - otherwise wait till
1464 // setClosed(true) is called
1465 for (int i = 0; i < alignPanels.size(); i++)
1467 AlignmentPanel ap = alignPanels.get(i);
1474 closeView(alignPanel);
1481 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1482 * be called recursively, with the frame now in 'closed' state
1484 this.setClosed(true);
1486 } catch (Exception ex)
1488 ex.printStackTrace();
1493 * Close the specified panel and close up tabs appropriately.
1495 * @param panelToClose
1497 public void closeView(AlignmentPanel panelToClose)
1499 int index = tabbedPane.getSelectedIndex();
1500 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1501 alignPanels.remove(panelToClose);
1502 panelToClose.closePanel();
1503 panelToClose = null;
1505 tabbedPane.removeTabAt(closedindex);
1506 tabbedPane.validate();
1508 if (index > closedindex || index == tabbedPane.getTabCount())
1510 // modify currently selected tab index if necessary.
1514 this.tabSelectionChanged(index);
1520 void updateEditMenuBar()
1523 if (viewport.getHistoryList().size() > 0)
1525 undoMenuItem.setEnabled(true);
1526 CommandI command = viewport.getHistoryList().peek();
1527 undoMenuItem.setText(MessageManager.formatMessage(
1528 "label.undo_command",
1529 new Object[] { command.getDescription() }));
1533 undoMenuItem.setEnabled(false);
1534 undoMenuItem.setText(MessageManager.getString("action.undo"));
1537 if (viewport.getRedoList().size() > 0)
1539 redoMenuItem.setEnabled(true);
1541 CommandI command = viewport.getRedoList().peek();
1542 redoMenuItem.setText(MessageManager.formatMessage(
1543 "label.redo_command",
1544 new Object[] { command.getDescription() }));
1548 redoMenuItem.setEnabled(false);
1549 redoMenuItem.setText(MessageManager.getString("action.redo"));
1554 public void addHistoryItem(CommandI command)
1556 if (command.getSize() > 0)
1558 viewport.addToHistoryList(command);
1559 viewport.clearRedoList();
1560 updateEditMenuBar();
1561 viewport.updateHiddenColumns();
1562 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1563 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1564 // viewport.getColumnSelection()
1565 // .getHiddenColumns().size() > 0);
1571 * @return alignment objects for all views
1573 AlignmentI[] getViewAlignments()
1575 if (alignPanels != null)
1577 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1579 for (AlignmentPanel ap : alignPanels)
1581 als[i++] = ap.av.getAlignment();
1585 if (viewport != null)
1587 return new AlignmentI[] { viewport.getAlignment() };
1599 protected void undoMenuItem_actionPerformed(ActionEvent e)
1601 if (viewport.getHistoryList().isEmpty())
1605 CommandI command = viewport.getHistoryList().pop();
1606 viewport.addToRedoList(command);
1607 command.undoCommand(getViewAlignments());
1609 AlignmentViewport originalSource = getOriginatingSource(command);
1610 updateEditMenuBar();
1612 if (originalSource != null)
1614 if (originalSource != viewport)
1617 .warn("Implementation worry: mismatch of viewport origin for undo");
1619 originalSource.updateHiddenColumns();
1620 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1622 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1623 // viewport.getColumnSelection()
1624 // .getHiddenColumns().size() > 0);
1625 originalSource.firePropertyChange("alignment", null, originalSource
1626 .getAlignment().getSequences());
1637 protected void redoMenuItem_actionPerformed(ActionEvent e)
1639 if (viewport.getRedoList().size() < 1)
1644 CommandI command = viewport.getRedoList().pop();
1645 viewport.addToHistoryList(command);
1646 command.doCommand(getViewAlignments());
1648 AlignmentViewport originalSource = getOriginatingSource(command);
1649 updateEditMenuBar();
1651 if (originalSource != null)
1654 if (originalSource != viewport)
1657 .warn("Implementation worry: mismatch of viewport origin for redo");
1659 originalSource.updateHiddenColumns();
1660 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1662 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1663 // viewport.getColumnSelection()
1664 // .getHiddenColumns().size() > 0);
1665 originalSource.firePropertyChange("alignment", null, originalSource
1666 .getAlignment().getSequences());
1670 AlignmentViewport getOriginatingSource(CommandI command)
1672 AlignmentViewport originalSource = null;
1673 // For sequence removal and addition, we need to fire
1674 // the property change event FROM the viewport where the
1675 // original alignment was altered
1676 AlignmentI al = null;
1677 if (command instanceof EditCommand)
1679 EditCommand editCommand = (EditCommand) command;
1680 al = editCommand.getAlignment();
1681 List<Component> comps = PaintRefresher.components.get(viewport
1682 .getSequenceSetId());
1684 for (Component comp : comps)
1686 if (comp instanceof AlignmentPanel)
1688 if (al == ((AlignmentPanel) comp).av.getAlignment())
1690 originalSource = ((AlignmentPanel) comp).av;
1697 if (originalSource == null)
1699 // The original view is closed, we must validate
1700 // the current view against the closed view first
1703 PaintRefresher.validateSequences(al, viewport.getAlignment());
1706 originalSource = viewport;
1709 return originalSource;
1718 public void moveSelectedSequences(boolean up)
1720 SequenceGroup sg = viewport.getSelectionGroup();
1726 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1727 viewport.getHiddenRepSequences(), up);
1728 alignPanel.paintAlignment(true);
1731 synchronized void slideSequences(boolean right, int size)
1733 List<SequenceI> sg = new ArrayList<>();
1734 if (viewport.cursorMode)
1736 sg.add(viewport.getAlignment().getSequenceAt(
1737 alignPanel.getSeqPanel().seqCanvas.cursorY));
1739 else if (viewport.getSelectionGroup() != null
1740 && viewport.getSelectionGroup().getSize() != viewport
1741 .getAlignment().getHeight())
1743 sg = viewport.getSelectionGroup().getSequences(
1744 viewport.getHiddenRepSequences());
1752 List<SequenceI> invertGroup = new ArrayList<>();
1754 for (SequenceI seq : viewport.getAlignment().getSequences())
1756 if (!sg.contains(seq))
1758 invertGroup.add(seq);
1762 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1764 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1765 for (int i = 0; i < invertGroup.size(); i++)
1767 seqs2[i] = invertGroup.get(i);
1770 SlideSequencesCommand ssc;
1773 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1774 size, viewport.getGapCharacter());
1778 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1779 size, viewport.getGapCharacter());
1782 int groupAdjustment = 0;
1783 if (ssc.getGapsInsertedBegin() && right)
1785 if (viewport.cursorMode)
1787 alignPanel.getSeqPanel().moveCursor(size, 0);
1791 groupAdjustment = size;
1794 else if (!ssc.getGapsInsertedBegin() && !right)
1796 if (viewport.cursorMode)
1798 alignPanel.getSeqPanel().moveCursor(-size, 0);
1802 groupAdjustment = -size;
1806 if (groupAdjustment != 0)
1808 viewport.getSelectionGroup().setStartRes(
1809 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1810 viewport.getSelectionGroup().setEndRes(
1811 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1815 * just extend the last slide command if compatible; but not if in
1816 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1818 boolean appendHistoryItem = false;
1819 Deque<CommandI> historyList = viewport.getHistoryList();
1820 boolean inSplitFrame = getSplitViewContainer() != null;
1821 if (!inSplitFrame && historyList != null && historyList.size() > 0
1822 && historyList.peek() instanceof SlideSequencesCommand)
1824 appendHistoryItem = ssc
1825 .appendSlideCommand((SlideSequencesCommand) historyList
1829 if (!appendHistoryItem)
1831 addHistoryItem(ssc);
1844 protected void copy_actionPerformed(ActionEvent e)
1847 if (viewport.getSelectionGroup() == null)
1851 // TODO: preserve the ordering of displayed alignment annotation in any
1852 // internal paste (particularly sequence associated annotation)
1853 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1854 String[] omitHidden = null;
1856 if (viewport.hasHiddenColumns())
1858 omitHidden = viewport.getViewAsString(true);
1861 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1862 seqs, omitHidden, null);
1864 StringSelection ss = new StringSelection(output);
1868 jalview.gui.Desktop.internalCopy = true;
1869 // Its really worth setting the clipboard contents
1870 // to empty before setting the large StringSelection!!
1871 Toolkit.getDefaultToolkit().getSystemClipboard()
1872 .setContents(new StringSelection(""), null);
1874 Toolkit.getDefaultToolkit().getSystemClipboard()
1875 .setContents(ss, Desktop.instance);
1876 } catch (OutOfMemoryError er)
1878 new OOMWarning("copying region", er);
1882 ArrayList<int[]> hiddenColumns = null;
1883 if (viewport.hasHiddenColumns())
1885 hiddenColumns = new ArrayList<>();
1886 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1887 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1888 for (int[] region : viewport.getAlignment().getHiddenColumns())
1890 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1892 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1893 region[1] - hiddenOffset });
1898 Desktop.jalviewClipboard = new Object[] { seqs,
1899 viewport.getAlignment().getDataset(), hiddenColumns };
1900 statusBar.setText(MessageManager.formatMessage(
1901 "label.copied_sequences_to_clipboard", new Object[] { Integer
1902 .valueOf(seqs.length).toString() }));
1912 protected void pasteNew_actionPerformed(ActionEvent e)
1924 protected void pasteThis_actionPerformed(ActionEvent e)
1930 * Paste contents of Jalview clipboard
1932 * @param newAlignment
1933 * true to paste to a new alignment, otherwise add to this.
1935 void paste(boolean newAlignment)
1937 boolean externalPaste = true;
1940 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1941 Transferable contents = c.getContents(this);
1943 if (contents == null)
1952 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1953 if (str.length() < 1)
1958 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1960 } catch (OutOfMemoryError er)
1962 new OOMWarning("Out of memory pasting sequences!!", er);
1966 SequenceI[] sequences;
1967 boolean annotationAdded = false;
1968 AlignmentI alignment = null;
1970 if (Desktop.jalviewClipboard != null)
1972 // The clipboard was filled from within Jalview, we must use the
1974 // And dataset from the copied alignment
1975 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1976 // be doubly sure that we create *new* sequence objects.
1977 sequences = new SequenceI[newseq.length];
1978 for (int i = 0; i < newseq.length; i++)
1980 sequences[i] = new Sequence(newseq[i]);
1982 alignment = new Alignment(sequences);
1983 externalPaste = false;
1987 // parse the clipboard as an alignment.
1988 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1990 sequences = alignment.getSequencesArray();
1994 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2000 if (Desktop.jalviewClipboard != null)
2002 // dataset is inherited
2003 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2007 // new dataset is constructed
2008 alignment.setDataset(null);
2010 alwidth = alignment.getWidth() + 1;
2014 AlignmentI pastedal = alignment; // preserve pasted alignment object
2015 // Add pasted sequences and dataset into existing alignment.
2016 alignment = viewport.getAlignment();
2017 alwidth = alignment.getWidth() + 1;
2018 // decide if we need to import sequences from an existing dataset
2019 boolean importDs = Desktop.jalviewClipboard != null
2020 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2021 // importDs==true instructs us to copy over new dataset sequences from
2022 // an existing alignment
2023 Vector newDs = (importDs) ? new Vector() : null; // used to create
2024 // minimum dataset set
2026 for (int i = 0; i < sequences.length; i++)
2030 newDs.addElement(null);
2032 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2034 if (importDs && ds != null)
2036 if (!newDs.contains(ds))
2038 newDs.setElementAt(ds, i);
2039 ds = new Sequence(ds);
2040 // update with new dataset sequence
2041 sequences[i].setDatasetSequence(ds);
2045 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2050 // copy and derive new dataset sequence
2051 sequences[i] = sequences[i].deriveSequence();
2052 alignment.getDataset().addSequence(
2053 sequences[i].getDatasetSequence());
2054 // TODO: avoid creation of duplicate dataset sequences with a
2055 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2057 alignment.addSequence(sequences[i]); // merges dataset
2061 newDs.clear(); // tidy up
2063 if (alignment.getAlignmentAnnotation() != null)
2065 for (AlignmentAnnotation alan : alignment
2066 .getAlignmentAnnotation())
2068 if (alan.graphGroup > fgroup)
2070 fgroup = alan.graphGroup;
2074 if (pastedal.getAlignmentAnnotation() != null)
2076 // Add any annotation attached to alignment.
2077 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2078 for (int i = 0; i < alann.length; i++)
2080 annotationAdded = true;
2081 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2083 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2084 if (newann.graphGroup > -1)
2086 if (newGraphGroups.size() <= newann.graphGroup
2087 || newGraphGroups.get(newann.graphGroup) == null)
2089 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2091 newGraphGroups.add(q, null);
2093 newGraphGroups.set(newann.graphGroup, new Integer(
2096 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2100 newann.padAnnotation(alwidth);
2101 alignment.addAnnotation(newann);
2111 addHistoryItem(new EditCommand(
2112 MessageManager.getString("label.add_sequences"),
2113 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2115 // Add any annotations attached to sequences
2116 for (int i = 0; i < sequences.length; i++)
2118 if (sequences[i].getAnnotation() != null)
2120 AlignmentAnnotation newann;
2121 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2123 annotationAdded = true;
2124 newann = sequences[i].getAnnotation()[a];
2125 newann.adjustForAlignment();
2126 newann.padAnnotation(alwidth);
2127 if (newann.graphGroup > -1)
2129 if (newann.graphGroup > -1)
2131 if (newGraphGroups.size() <= newann.graphGroup
2132 || newGraphGroups.get(newann.graphGroup) == null)
2134 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2136 newGraphGroups.add(q, null);
2138 newGraphGroups.set(newann.graphGroup, new Integer(
2141 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2145 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2150 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2157 // propagate alignment changed.
2158 vpRanges.setEndSeq(alignment.getHeight());
2159 if (annotationAdded)
2161 // Duplicate sequence annotation in all views.
2162 AlignmentI[] alview = this.getViewAlignments();
2163 for (int i = 0; i < sequences.length; i++)
2165 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2170 for (int avnum = 0; avnum < alview.length; avnum++)
2172 if (alview[avnum] != alignment)
2174 // duplicate in a view other than the one with input focus
2175 int avwidth = alview[avnum].getWidth() + 1;
2176 // this relies on sann being preserved after we
2177 // modify the sequence's annotation array for each duplication
2178 for (int a = 0; a < sann.length; a++)
2180 AlignmentAnnotation newann = new AlignmentAnnotation(
2182 sequences[i].addAlignmentAnnotation(newann);
2183 newann.padAnnotation(avwidth);
2184 alview[avnum].addAnnotation(newann); // annotation was
2185 // duplicated earlier
2186 // TODO JAL-1145 graphGroups are not updated for sequence
2187 // annotation added to several views. This may cause
2189 alview[avnum].setAnnotationIndex(newann, a);
2194 buildSortByAnnotationScoresMenu();
2196 viewport.firePropertyChange("alignment", null,
2197 alignment.getSequences());
2198 if (alignPanels != null)
2200 for (AlignmentPanel ap : alignPanels)
2202 ap.validateAnnotationDimensions(false);
2207 alignPanel.validateAnnotationDimensions(false);
2213 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2215 String newtitle = new String("Copied sequences");
2217 if (Desktop.jalviewClipboard != null
2218 && Desktop.jalviewClipboard[2] != null)
2220 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2221 for (int[] region : hc)
2223 af.viewport.hideColumns(region[0], region[1]);
2227 // >>>This is a fix for the moment, until a better solution is
2229 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2231 alignPanel.getSeqPanel().seqCanvas
2232 .getFeatureRenderer());
2234 // TODO: maintain provenance of an alignment, rather than just make the
2235 // title a concatenation of operations.
2238 if (title.startsWith("Copied sequences"))
2244 newtitle = newtitle.concat("- from " + title);
2249 newtitle = new String("Pasted sequences");
2252 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2257 } catch (Exception ex)
2259 ex.printStackTrace();
2260 System.out.println("Exception whilst pasting: " + ex);
2261 // could be anything being pasted in here
2267 protected void expand_newalign(ActionEvent e)
2271 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2272 .getAlignment(), -1);
2273 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2275 String newtitle = new String("Flanking alignment");
2277 if (Desktop.jalviewClipboard != null
2278 && Desktop.jalviewClipboard[2] != null)
2280 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2281 for (int region[] : hc)
2283 af.viewport.hideColumns(region[0], region[1]);
2287 // >>>This is a fix for the moment, until a better solution is
2289 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2291 alignPanel.getSeqPanel().seqCanvas
2292 .getFeatureRenderer());
2294 // TODO: maintain provenance of an alignment, rather than just make the
2295 // title a concatenation of operations.
2297 if (title.startsWith("Copied sequences"))
2303 newtitle = newtitle.concat("- from " + title);
2307 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2309 } catch (Exception ex)
2311 ex.printStackTrace();
2312 System.out.println("Exception whilst pasting: " + ex);
2313 // could be anything being pasted in here
2314 } catch (OutOfMemoryError oom)
2316 new OOMWarning("Viewing flanking region of alignment", oom);
2327 protected void cut_actionPerformed(ActionEvent e)
2329 copy_actionPerformed(null);
2330 delete_actionPerformed(null);
2340 protected void delete_actionPerformed(ActionEvent evt)
2343 SequenceGroup sg = viewport.getSelectionGroup();
2350 * If the cut affects all sequences, warn, remove highlighted columns
2352 if (sg.getSize() == viewport.getAlignment().getHeight())
2354 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2355 .getAlignment().getWidth()) ? true : false;
2356 if (isEntireAlignWidth)
2358 int confirm = JvOptionPane.showConfirmDialog(this,
2359 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2360 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2361 JvOptionPane.OK_CANCEL_OPTION);
2363 if (confirm == JvOptionPane.CANCEL_OPTION
2364 || confirm == JvOptionPane.CLOSED_OPTION)
2369 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2370 sg.getEndRes() + 1);
2372 SequenceI[] cut = sg.getSequences()
2373 .toArray(new SequenceI[sg.getSize()]);
2375 addHistoryItem(new EditCommand(
2376 MessageManager.getString("label.cut_sequences"), Action.CUT,
2377 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2378 viewport.getAlignment()));
2380 viewport.setSelectionGroup(null);
2381 viewport.sendSelection();
2382 viewport.getAlignment().deleteGroup(sg);
2384 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2386 if (viewport.getAlignment().getHeight() < 1)
2390 this.setClosed(true);
2391 } catch (Exception ex)
2404 protected void deleteGroups_actionPerformed(ActionEvent e)
2406 if (avc.deleteGroups())
2408 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2409 alignPanel.updateAnnotation();
2410 alignPanel.paintAlignment(true);
2421 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2423 SequenceGroup sg = new SequenceGroup();
2425 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2427 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2430 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2431 viewport.setSelectionGroup(sg);
2432 viewport.sendSelection();
2433 // JAL-2034 - should delegate to
2434 // alignPanel to decide if overview needs
2436 alignPanel.paintAlignment(false);
2437 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2447 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2449 if (viewport.cursorMode)
2451 alignPanel.getSeqPanel().keyboardNo1 = null;
2452 alignPanel.getSeqPanel().keyboardNo2 = null;
2454 viewport.setSelectionGroup(null);
2455 viewport.getColumnSelection().clear();
2456 viewport.setSelectionGroup(null);
2457 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2458 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2459 // JAL-2034 - should delegate to
2460 // alignPanel to decide if overview needs
2462 alignPanel.paintAlignment(false);
2463 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2464 viewport.sendSelection();
2474 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2476 SequenceGroup sg = viewport.getSelectionGroup();
2480 selectAllSequenceMenuItem_actionPerformed(null);
2485 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2487 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2489 // JAL-2034 - should delegate to
2490 // alignPanel to decide if overview needs
2493 alignPanel.paintAlignment(true);
2494 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2495 viewport.sendSelection();
2499 public void invertColSel_actionPerformed(ActionEvent e)
2501 viewport.invertColumnSelection();
2502 alignPanel.paintAlignment(true);
2503 viewport.sendSelection();
2513 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2515 trimAlignment(true);
2525 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2527 trimAlignment(false);
2530 void trimAlignment(boolean trimLeft)
2532 ColumnSelection colSel = viewport.getColumnSelection();
2535 if (!colSel.isEmpty())
2539 column = colSel.getMin();
2543 column = colSel.getMax();
2547 if (viewport.getSelectionGroup() != null)
2549 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2550 viewport.getHiddenRepSequences());
2554 seqs = viewport.getAlignment().getSequencesArray();
2557 TrimRegionCommand trimRegion;
2560 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2561 column, viewport.getAlignment());
2562 vpRanges.setStartRes(0);
2566 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2567 column, viewport.getAlignment());
2570 statusBar.setText(MessageManager.formatMessage(
2571 "label.removed_columns",
2572 new String[] { Integer.valueOf(trimRegion.getSize())
2575 addHistoryItem(trimRegion);
2577 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2579 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2580 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2582 viewport.getAlignment().deleteGroup(sg);
2586 viewport.firePropertyChange("alignment", null, viewport
2587 .getAlignment().getSequences());
2598 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2600 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2603 if (viewport.getSelectionGroup() != null)
2605 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2606 viewport.getHiddenRepSequences());
2607 start = viewport.getSelectionGroup().getStartRes();
2608 end = viewport.getSelectionGroup().getEndRes();
2612 seqs = viewport.getAlignment().getSequencesArray();
2615 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2616 "Remove Gapped Columns", seqs, start, end,
2617 viewport.getAlignment());
2619 addHistoryItem(removeGapCols);
2621 statusBar.setText(MessageManager.formatMessage(
2622 "label.removed_empty_columns",
2623 new Object[] { Integer.valueOf(removeGapCols.getSize())
2626 // This is to maintain viewport position on first residue
2627 // of first sequence
2628 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2629 int startRes = seq.findPosition(vpRanges.getStartRes());
2630 // ShiftList shifts;
2631 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2632 // edit.alColumnChanges=shifts.getInverse();
2633 // if (viewport.hasHiddenColumns)
2634 // viewport.getColumnSelection().compensateForEdits(shifts);
2635 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2636 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2648 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2650 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2653 if (viewport.getSelectionGroup() != null)
2655 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2656 viewport.getHiddenRepSequences());
2657 start = viewport.getSelectionGroup().getStartRes();
2658 end = viewport.getSelectionGroup().getEndRes();
2662 seqs = viewport.getAlignment().getSequencesArray();
2665 // This is to maintain viewport position on first residue
2666 // of first sequence
2667 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2668 int startRes = seq.findPosition(vpRanges.getStartRes());
2670 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2671 viewport.getAlignment()));
2673 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2675 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2687 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2689 viewport.setPadGaps(padGapsMenuitem.isSelected());
2690 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2701 public void findMenuItem_actionPerformed(ActionEvent e)
2707 * Create a new view of the current alignment.
2710 public void newView_actionPerformed(ActionEvent e)
2712 newView(null, true);
2716 * Creates and shows a new view of the current alignment.
2719 * title of newly created view; if null, one will be generated
2720 * @param copyAnnotation
2721 * if true then duplicate all annnotation, groups and settings
2722 * @return new alignment panel, already displayed.
2724 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2727 * Create a new AlignmentPanel (with its own, new Viewport)
2729 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2731 if (!copyAnnotation)
2734 * remove all groups and annotation except for the automatic stuff
2736 newap.av.getAlignment().deleteAllGroups();
2737 newap.av.getAlignment().deleteAllAnnotations(false);
2740 newap.av.setGatherViewsHere(false);
2742 if (viewport.viewName == null)
2744 viewport.viewName = MessageManager
2745 .getString("label.view_name_original");
2749 * Views share the same edits undo and redo stacks
2751 newap.av.setHistoryList(viewport.getHistoryList());
2752 newap.av.setRedoList(viewport.getRedoList());
2755 * Views share the same mappings; need to deregister any new mappings
2756 * created by copyAlignPanel, and register the new reference to the shared
2759 newap.av.replaceMappings(viewport.getAlignment());
2762 * start up cDNA consensus (if applicable) now mappings are in place
2764 if (newap.av.initComplementConsensus())
2766 newap.refresh(true); // adjust layout of annotations
2769 newap.av.viewName = getNewViewName(viewTitle);
2771 addAlignmentPanel(newap, true);
2772 newap.alignmentChanged();
2774 if (alignPanels.size() == 2)
2776 viewport.setGatherViewsHere(true);
2778 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2783 * Make a new name for the view, ensuring it is unique within the current
2784 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2785 * these now use viewId. Unique view names are still desirable for usability.)
2790 protected String getNewViewName(String viewTitle)
2792 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2793 boolean addFirstIndex = false;
2794 if (viewTitle == null || viewTitle.trim().length() == 0)
2796 viewTitle = MessageManager.getString("action.view");
2797 addFirstIndex = true;
2801 index = 1;// we count from 1 if given a specific name
2803 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2805 List<Component> comps = PaintRefresher.components.get(viewport
2806 .getSequenceSetId());
2808 List<String> existingNames = getExistingViewNames(comps);
2810 while (existingNames.contains(newViewName))
2812 newViewName = viewTitle + " " + (++index);
2818 * Returns a list of distinct view names found in the given list of
2819 * components. View names are held on the viewport of an AlignmentPanel.
2824 protected List<String> getExistingViewNames(List<Component> comps)
2826 List<String> existingNames = new ArrayList<>();
2827 for (Component comp : comps)
2829 if (comp instanceof AlignmentPanel)
2831 AlignmentPanel ap = (AlignmentPanel) comp;
2832 if (!existingNames.contains(ap.av.viewName))
2834 existingNames.add(ap.av.viewName);
2838 return existingNames;
2842 * Explode tabbed views into separate windows.
2845 public void expandViews_actionPerformed(ActionEvent e)
2847 Desktop.explodeViews(this);
2851 * Gather views in separate windows back into a tabbed presentation.
2854 public void gatherViews_actionPerformed(ActionEvent e)
2856 Desktop.instance.gatherViews(this);
2866 public void font_actionPerformed(ActionEvent e)
2868 new FontChooser(alignPanel);
2878 protected void seqLimit_actionPerformed(ActionEvent e)
2880 viewport.setShowJVSuffix(seqLimits.isSelected());
2882 alignPanel.getIdPanel().getIdCanvas()
2883 .setPreferredSize(alignPanel.calculateIdWidth());
2884 alignPanel.paintAlignment(true);
2888 public void idRightAlign_actionPerformed(ActionEvent e)
2890 viewport.setRightAlignIds(idRightAlign.isSelected());
2891 alignPanel.paintAlignment(true);
2895 public void centreColumnLabels_actionPerformed(ActionEvent e)
2897 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2898 alignPanel.paintAlignment(true);
2904 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2907 protected void followHighlight_actionPerformed()
2910 * Set the 'follow' flag on the Viewport (and scroll to position if now
2913 final boolean state = this.followHighlightMenuItem.getState();
2914 viewport.setFollowHighlight(state);
2917 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2928 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2930 viewport.setColourText(colourTextMenuItem.isSelected());
2931 alignPanel.paintAlignment(true);
2941 public void wrapMenuItem_actionPerformed(ActionEvent e)
2943 scaleAbove.setVisible(wrapMenuItem.isSelected());
2944 scaleLeft.setVisible(wrapMenuItem.isSelected());
2945 scaleRight.setVisible(wrapMenuItem.isSelected());
2946 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2947 alignPanel.updateLayout();
2951 public void showAllSeqs_actionPerformed(ActionEvent e)
2953 viewport.showAllHiddenSeqs();
2957 public void showAllColumns_actionPerformed(ActionEvent e)
2959 viewport.showAllHiddenColumns();
2961 viewport.sendSelection();
2965 public void hideSelSequences_actionPerformed(ActionEvent e)
2967 viewport.hideAllSelectedSeqs();
2968 // alignPanel.paintAlignment(true);
2972 * called by key handler and the hide all/show all menu items
2977 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2980 boolean hide = false;
2981 SequenceGroup sg = viewport.getSelectionGroup();
2982 if (!toggleSeqs && !toggleCols)
2984 // Hide everything by the current selection - this is a hack - we do the
2985 // invert and then hide
2986 // first check that there will be visible columns after the invert.
2987 if (viewport.hasSelectedColumns()
2988 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2991 // now invert the sequence set, if required - empty selection implies
2992 // that no hiding is required.
2995 invertSequenceMenuItem_actionPerformed(null);
2996 sg = viewport.getSelectionGroup();
3000 viewport.expandColSelection(sg, true);
3001 // finally invert the column selection and get the new sequence
3003 invertColSel_actionPerformed(null);
3010 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3012 hideSelSequences_actionPerformed(null);
3015 else if (!(toggleCols && viewport.hasSelectedColumns()))
3017 showAllSeqs_actionPerformed(null);
3023 if (viewport.hasSelectedColumns())
3025 hideSelColumns_actionPerformed(null);
3028 viewport.setSelectionGroup(sg);
3033 showAllColumns_actionPerformed(null);
3042 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3043 * event.ActionEvent)
3046 public void hideAllButSelection_actionPerformed(ActionEvent e)
3048 toggleHiddenRegions(false, false);
3049 viewport.sendSelection();
3056 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3060 public void hideAllSelection_actionPerformed(ActionEvent e)
3062 SequenceGroup sg = viewport.getSelectionGroup();
3063 viewport.expandColSelection(sg, false);
3064 viewport.hideAllSelectedSeqs();
3065 viewport.hideSelectedColumns();
3066 alignPanel.paintAlignment(true);
3067 viewport.sendSelection();
3074 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3078 public void showAllhidden_actionPerformed(ActionEvent e)
3080 viewport.showAllHiddenColumns();
3081 viewport.showAllHiddenSeqs();
3082 alignPanel.paintAlignment(true);
3083 viewport.sendSelection();
3087 public void hideSelColumns_actionPerformed(ActionEvent e)
3089 viewport.hideSelectedColumns();
3090 alignPanel.paintAlignment(true);
3091 viewport.sendSelection();
3095 public void hiddenMarkers_actionPerformed(ActionEvent e)
3097 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3108 protected void scaleAbove_actionPerformed(ActionEvent e)
3110 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3111 alignPanel.paintAlignment(true);
3121 protected void scaleLeft_actionPerformed(ActionEvent e)
3123 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3124 alignPanel.paintAlignment(true);
3134 protected void scaleRight_actionPerformed(ActionEvent e)
3136 viewport.setScaleRightWrapped(scaleRight.isSelected());
3137 alignPanel.paintAlignment(true);
3147 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3149 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3150 alignPanel.paintAlignment(true);
3160 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3162 viewport.setShowText(viewTextMenuItem.isSelected());
3163 alignPanel.paintAlignment(true);
3173 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3175 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3176 alignPanel.paintAlignment(true);
3179 public FeatureSettings featureSettings;
3182 public FeatureSettingsControllerI getFeatureSettingsUI()
3184 return featureSettings;
3188 public void featureSettings_actionPerformed(ActionEvent e)
3190 if (featureSettings != null)
3192 featureSettings.close();
3193 featureSettings = null;
3195 if (!showSeqFeatures.isSelected())
3197 // make sure features are actually displayed
3198 showSeqFeatures.setSelected(true);
3199 showSeqFeatures_actionPerformed(null);
3201 featureSettings = new FeatureSettings(this);
3205 * Set or clear 'Show Sequence Features'
3211 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3213 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3214 alignPanel.paintAlignment(true);
3215 if (alignPanel.getOverviewPanel() != null)
3217 alignPanel.getOverviewPanel().updateOverviewImage();
3222 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3223 * the annotations panel as a whole.
3225 * The options to show/hide all annotations should be enabled when the panel
3226 * is shown, and disabled when the panel is hidden.
3231 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3233 final boolean setVisible = annotationPanelMenuItem.isSelected();
3234 viewport.setShowAnnotation(setVisible);
3235 this.showAllSeqAnnotations.setEnabled(setVisible);
3236 this.hideAllSeqAnnotations.setEnabled(setVisible);
3237 this.showAllAlAnnotations.setEnabled(setVisible);
3238 this.hideAllAlAnnotations.setEnabled(setVisible);
3239 alignPanel.updateLayout();
3243 public void alignmentProperties()
3245 JEditorPane editPane = new JEditorPane("text/html", "");
3246 editPane.setEditable(false);
3247 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3249 editPane.setText(MessageManager.formatMessage("label.html_content",
3250 new Object[] { contents.toString() }));
3251 JInternalFrame frame = new JInternalFrame();
3252 frame.getContentPane().add(new JScrollPane(editPane));
3254 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3255 "label.alignment_properties", new Object[] { getTitle() }),
3266 public void overviewMenuItem_actionPerformed(ActionEvent e)
3268 if (alignPanel.overviewPanel != null)
3273 JInternalFrame frame = new JInternalFrame();
3274 OverviewPanel overview = new OverviewPanel(alignPanel);
3275 frame.setContentPane(overview);
3276 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3277 "label.overview_params", new Object[] { this.getTitle() }),
3278 true, frame.getWidth(), frame.getHeight(), true, true);
3280 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3281 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3284 public void internalFrameClosed(
3285 javax.swing.event.InternalFrameEvent evt)
3287 alignPanel.setOverviewPanel(null);
3291 alignPanel.setOverviewPanel(overview);
3295 public void textColour_actionPerformed()
3297 new TextColourChooser().chooseColour(alignPanel, null);
3301 * public void covariationColour_actionPerformed() {
3303 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3307 public void annotationColour_actionPerformed()
3309 new AnnotationColourChooser(viewport, alignPanel);
3313 public void annotationColumn_actionPerformed(ActionEvent e)
3315 new AnnotationColumnChooser(viewport, alignPanel);
3319 * Action on the user checking or unchecking the option to apply the selected
3320 * colour scheme to all groups. If unchecked, groups may have their own
3321 * independent colour schemes.
3326 public void applyToAllGroups_actionPerformed(boolean selected)
3328 viewport.setColourAppliesToAllGroups(selected);
3332 * Action on user selecting a colour from the colour menu
3335 * the name (not the menu item label!) of the colour scheme
3338 public void changeColour_actionPerformed(String name)
3341 * 'User Defined' opens a panel to configure or load a
3342 * user-defined colour scheme
3344 if (ResidueColourScheme.USER_DEFINED.equals(name))
3346 new UserDefinedColours(alignPanel);
3351 * otherwise set the chosen colour scheme (or null for 'None')
3353 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3354 viewport.getAlignment(), viewport.getHiddenRepSequences());
3359 * Actions on setting or changing the alignment colour scheme
3364 public void changeColour(ColourSchemeI cs)
3366 // TODO: pull up to controller method
3367 ColourMenuHelper.setColourSelected(colourMenu, cs);
3369 viewport.setGlobalColourScheme(cs);
3371 alignPanel.paintAlignment(true);
3375 * Show the PID threshold slider panel
3378 protected void modifyPID_actionPerformed()
3380 SliderPanel.setPIDSliderSource(alignPanel,
3381 viewport.getResidueShading(), alignPanel.getViewName());
3382 SliderPanel.showPIDSlider();
3386 * Show the Conservation slider panel
3389 protected void modifyConservation_actionPerformed()
3391 SliderPanel.setConservationSlider(alignPanel,
3392 viewport.getResidueShading(), alignPanel.getViewName());
3393 SliderPanel.showConservationSlider();
3397 * Action on selecting or deselecting (Colour) By Conservation
3400 public void conservationMenuItem_actionPerformed(boolean selected)
3402 modifyConservation.setEnabled(selected);
3403 viewport.setConservationSelected(selected);
3404 viewport.getResidueShading().setConservationApplied(selected);
3406 changeColour(viewport.getGlobalColourScheme());
3409 modifyConservation_actionPerformed();
3413 SliderPanel.hideConservationSlider();
3418 * Action on selecting or deselecting (Colour) Above PID Threshold
3421 public void abovePIDThreshold_actionPerformed(boolean selected)
3423 modifyPID.setEnabled(selected);
3424 viewport.setAbovePIDThreshold(selected);
3427 viewport.getResidueShading().setThreshold(0,
3428 viewport.isIgnoreGapsConsensus());
3431 changeColour(viewport.getGlobalColourScheme());
3434 modifyPID_actionPerformed();
3438 SliderPanel.hidePIDSlider();
3449 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3451 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3452 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3453 .getAlignment().getSequenceAt(0));
3454 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3455 viewport.getAlignment()));
3456 alignPanel.paintAlignment(true);
3466 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3468 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3469 AlignmentSorter.sortByID(viewport.getAlignment());
3470 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3471 viewport.getAlignment()));
3472 alignPanel.paintAlignment(true);
3482 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3484 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3485 AlignmentSorter.sortByLength(viewport.getAlignment());
3486 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3487 viewport.getAlignment()));
3488 alignPanel.paintAlignment(true);
3498 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3500 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3501 AlignmentSorter.sortByGroup(viewport.getAlignment());
3502 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3503 viewport.getAlignment()));
3505 alignPanel.paintAlignment(true);
3515 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3517 new RedundancyPanel(alignPanel, this);
3527 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3529 if ((viewport.getSelectionGroup() == null)
3530 || (viewport.getSelectionGroup().getSize() < 2))
3532 JvOptionPane.showInternalMessageDialog(this, MessageManager
3533 .getString("label.you_must_select_least_two_sequences"),
3534 MessageManager.getString("label.invalid_selection"),
3535 JvOptionPane.WARNING_MESSAGE);
3539 JInternalFrame frame = new JInternalFrame();
3540 frame.setContentPane(new PairwiseAlignPanel(viewport));
3541 Desktop.addInternalFrame(frame,
3542 MessageManager.getString("action.pairwise_alignment"), 600,
3548 public void autoCalculate_actionPerformed(ActionEvent e)
3550 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3551 if (viewport.autoCalculateConsensus)
3553 viewport.firePropertyChange("alignment", null, viewport
3554 .getAlignment().getSequences());
3559 public void sortByTreeOption_actionPerformed(ActionEvent e)
3561 viewport.sortByTree = sortByTree.isSelected();
3565 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3567 viewport.followSelection = listenToViewSelections.isSelected();
3571 * Constructs a tree panel and adds it to the desktop
3574 * tree type (NJ or AV)
3576 * name of score model used to compute the tree
3578 * parameters for the distance or similarity calculation
3580 void newTreePanel(String type, String modelName, SimilarityParamsI options)
3582 String frameTitle = "";
3585 boolean onSelection = false;
3586 if (viewport.getSelectionGroup() != null
3587 && viewport.getSelectionGroup().getSize() > 0)
3589 SequenceGroup sg = viewport.getSelectionGroup();
3591 /* Decide if the selection is a column region */
3592 for (SequenceI _s : sg.getSequences())
3594 if (_s.getLength() < sg.getEndRes())
3600 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3602 .getString("label.sequences_selection_not_aligned"),
3603 JvOptionPane.WARNING_MESSAGE);
3612 if (viewport.getAlignment().getHeight() < 2)
3618 tp = new TreePanel(alignPanel, type, modelName, options);
3619 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3621 frameTitle += " from ";
3623 if (viewport.viewName != null)
3625 frameTitle += viewport.viewName + " of ";
3628 frameTitle += this.title;
3630 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3641 public void addSortByOrderMenuItem(String title,
3642 final AlignmentOrder order)
3644 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3645 "action.by_title_param", new Object[] { title }));
3647 item.addActionListener(new java.awt.event.ActionListener()
3650 public void actionPerformed(ActionEvent e)
3652 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3654 // TODO: JBPNote - have to map order entries to curent SequenceI
3656 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3658 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3661 alignPanel.paintAlignment(true);
3667 * Add a new sort by annotation score menu item
3670 * the menu to add the option to
3672 * the label used to retrieve scores for each sequence on the
3675 public void addSortByAnnotScoreMenuItem(JMenu sort,
3676 final String scoreLabel)
3678 final JMenuItem item = new JMenuItem(scoreLabel);
3680 item.addActionListener(new java.awt.event.ActionListener()
3683 public void actionPerformed(ActionEvent e)
3685 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3686 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3687 viewport.getAlignment());// ,viewport.getSelectionGroup());
3688 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3689 viewport.getAlignment()));
3690 alignPanel.paintAlignment(true);
3696 * last hash for alignment's annotation array - used to minimise cost of
3699 protected int _annotationScoreVectorHash;
3702 * search the alignment and rebuild the sort by annotation score submenu the
3703 * last alignment annotation vector hash is stored to minimize cost of
3704 * rebuilding in subsequence calls.
3708 public void buildSortByAnnotationScoresMenu()
3710 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3715 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3717 sortByAnnotScore.removeAll();
3718 // almost certainly a quicker way to do this - but we keep it simple
3719 Hashtable scoreSorts = new Hashtable();
3720 AlignmentAnnotation aann[];
3721 for (SequenceI sqa : viewport.getAlignment().getSequences())
3723 aann = sqa.getAnnotation();
3724 for (int i = 0; aann != null && i < aann.length; i++)
3726 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3728 scoreSorts.put(aann[i].label, aann[i].label);
3732 Enumeration labels = scoreSorts.keys();
3733 while (labels.hasMoreElements())
3735 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3736 (String) labels.nextElement());
3738 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3741 _annotationScoreVectorHash = viewport.getAlignment()
3742 .getAlignmentAnnotation().hashCode();
3747 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3748 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3749 * call. Listeners are added to remove the menu item when the treePanel is
3750 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3754 public void buildTreeSortMenu()
3756 sortByTreeMenu.removeAll();
3758 List<Component> comps = PaintRefresher.components.get(viewport
3759 .getSequenceSetId());
3760 List<TreePanel> treePanels = new ArrayList<>();
3761 for (Component comp : comps)
3763 if (comp instanceof TreePanel)
3765 treePanels.add((TreePanel) comp);
3769 if (treePanels.size() < 1)
3771 sortByTreeMenu.setVisible(false);
3775 sortByTreeMenu.setVisible(true);
3777 for (final TreePanel tp : treePanels)
3779 final JMenuItem item = new JMenuItem(tp.getTitle());
3780 item.addActionListener(new java.awt.event.ActionListener()
3783 public void actionPerformed(ActionEvent e)
3785 tp.sortByTree_actionPerformed();
3786 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3791 sortByTreeMenu.add(item);
3795 public boolean sortBy(AlignmentOrder alorder, String undoname)
3797 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3798 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3799 if (undoname != null)
3801 addHistoryItem(new OrderCommand(undoname, oldOrder,
3802 viewport.getAlignment()));
3804 alignPanel.paintAlignment(true);
3809 * Work out whether the whole set of sequences or just the selected set will
3810 * be submitted for multiple alignment.
3813 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3815 // Now, check we have enough sequences
3816 AlignmentView msa = null;
3818 if ((viewport.getSelectionGroup() != null)
3819 && (viewport.getSelectionGroup().getSize() > 1))
3821 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3822 // some common interface!
3824 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3825 * SequenceI[sz = seqs.getSize(false)];
3827 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3828 * seqs.getSequenceAt(i); }
3830 msa = viewport.getAlignmentView(true);
3832 else if (viewport.getSelectionGroup() != null
3833 && viewport.getSelectionGroup().getSize() == 1)
3835 int option = JvOptionPane.showConfirmDialog(this,
3836 MessageManager.getString("warn.oneseq_msainput_selection"),
3837 MessageManager.getString("label.invalid_selection"),
3838 JvOptionPane.OK_CANCEL_OPTION);
3839 if (option == JvOptionPane.OK_OPTION)
3841 msa = viewport.getAlignmentView(false);
3846 msa = viewport.getAlignmentView(false);
3852 * Decides what is submitted to a secondary structure prediction service: the
3853 * first sequence in the alignment, or in the current selection, or, if the
3854 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3855 * region or the whole alignment. (where the first sequence in the set is the
3856 * one that the prediction will be for).
3858 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3860 AlignmentView seqs = null;
3862 if ((viewport.getSelectionGroup() != null)
3863 && (viewport.getSelectionGroup().getSize() > 0))
3865 seqs = viewport.getAlignmentView(true);
3869 seqs = viewport.getAlignmentView(false);
3871 // limit sequences - JBPNote in future - could spawn multiple prediction
3873 // TODO: viewport.getAlignment().isAligned is a global state - the local
3874 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3875 if (!viewport.getAlignment().isAligned(false))
3877 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3878 // TODO: if seqs.getSequences().length>1 then should really have warned
3892 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3894 // Pick the tree file
3895 JalviewFileChooser chooser = new JalviewFileChooser(
3896 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3897 chooser.setFileView(new JalviewFileView());
3898 chooser.setDialogTitle(MessageManager
3899 .getString("label.select_newick_like_tree_file"));
3900 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3902 int value = chooser.showOpenDialog(null);
3904 if (value == JalviewFileChooser.APPROVE_OPTION)
3906 String filePath = chooser.getSelectedFile().getPath();
3907 Cache.setProperty("LAST_DIRECTORY", filePath);
3908 NewickFile fin = null;
3911 fin = new NewickFile(filePath, DataSourceType.FILE);
3912 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3913 } catch (Exception ex)
3920 .getString("label.problem_reading_tree_file"),
3921 JvOptionPane.WARNING_MESSAGE);
3922 ex.printStackTrace();
3924 if (fin != null && fin.hasWarningMessage())
3926 JvOptionPane.showMessageDialog(Desktop.desktop, fin
3927 .getWarningMessage(), MessageManager
3928 .getString("label.possible_problem_with_tree_file"),
3929 JvOptionPane.WARNING_MESSAGE);
3934 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3936 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3939 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3940 int h, int x, int y)
3942 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3946 * Add a treeviewer for the tree extracted from a Newick file object to the
3947 * current alignment view
3954 * Associated alignment input data (or null)
3963 * @return TreePanel handle
3965 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3966 AlignmentView input, int w, int h, int x, int y)
3968 TreePanel tp = null;
3974 if (nf.getTree() != null)
3976 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3982 tp.setLocation(x, y);
3985 Desktop.addInternalFrame(tp, treeTitle, w, h);
3987 } catch (Exception ex)
3989 ex.printStackTrace();
3995 private boolean buildingMenu = false;
3998 * Generates menu items and listener event actions for web service clients
4001 public void BuildWebServiceMenu()
4003 while (buildingMenu)
4007 System.err.println("Waiting for building menu to finish.");
4009 } catch (Exception e)
4013 final AlignFrame me = this;
4014 buildingMenu = true;
4015 new Thread(new Runnable()
4020 final List<JMenuItem> legacyItems = new ArrayList<>();
4023 // System.err.println("Building ws menu again "
4024 // + Thread.currentThread());
4025 // TODO: add support for context dependent disabling of services based
4027 // alignment and current selection
4028 // TODO: add additional serviceHandle parameter to specify abstract
4030 // class independently of AbstractName
4031 // TODO: add in rediscovery GUI function to restart discoverer
4032 // TODO: group services by location as well as function and/or
4034 // object broker mechanism.
4035 final Vector<JMenu> wsmenu = new Vector<>();
4036 final IProgressIndicator af = me;
4039 * do not i18n these strings - they are hard-coded in class
4040 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4041 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4043 final JMenu msawsmenu = new JMenu("Alignment");
4044 final JMenu secstrmenu = new JMenu(
4045 "Secondary Structure Prediction");
4046 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4047 final JMenu analymenu = new JMenu("Analysis");
4048 final JMenu dismenu = new JMenu("Protein Disorder");
4049 // JAL-940 - only show secondary structure prediction services from
4050 // the legacy server
4051 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4053 Discoverer.services != null && (Discoverer.services.size() > 0))
4055 // TODO: refactor to allow list of AbstractName/Handler bindings to
4057 // stored or retrieved from elsewhere
4058 // No MSAWS used any more:
4059 // Vector msaws = null; // (Vector)
4060 // Discoverer.services.get("MsaWS");
4061 Vector secstrpr = (Vector) Discoverer.services
4063 if (secstrpr != null)
4065 // Add any secondary structure prediction services
4066 for (int i = 0, j = secstrpr.size(); i < j; i++)
4068 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4070 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4071 .getServiceClient(sh);
4072 int p = secstrmenu.getItemCount();
4073 impl.attachWSMenuEntry(secstrmenu, me);
4074 int q = secstrmenu.getItemCount();
4075 for (int litm = p; litm < q; litm++)
4077 legacyItems.add(secstrmenu.getItem(litm));
4083 // Add all submenus in the order they should appear on the web
4085 wsmenu.add(msawsmenu);
4086 wsmenu.add(secstrmenu);
4087 wsmenu.add(dismenu);
4088 wsmenu.add(analymenu);
4089 // No search services yet
4090 // wsmenu.add(seqsrchmenu);
4092 javax.swing.SwingUtilities.invokeLater(new Runnable()
4099 webService.removeAll();
4100 // first, add discovered services onto the webservices menu
4101 if (wsmenu.size() > 0)
4103 for (int i = 0, j = wsmenu.size(); i < j; i++)
4105 webService.add(wsmenu.get(i));
4110 webService.add(me.webServiceNoServices);
4112 // TODO: move into separate menu builder class.
4113 boolean new_sspred = false;
4114 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4116 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4117 if (jws2servs != null)
4119 if (jws2servs.hasServices())
4121 jws2servs.attachWSMenuEntry(webService, me);
4122 for (Jws2Instance sv : jws2servs.getServices())
4124 if (sv.description.toLowerCase().contains("jpred"))
4126 for (JMenuItem jmi : legacyItems)
4128 jmi.setVisible(false);
4134 if (jws2servs.isRunning())
4136 JMenuItem tm = new JMenuItem(
4137 "Still discovering JABA Services");
4138 tm.setEnabled(false);
4143 build_urlServiceMenu(me.webService);
4144 build_fetchdbmenu(webService);
4145 for (JMenu item : wsmenu)
4147 if (item.getItemCount() == 0)
4149 item.setEnabled(false);
4153 item.setEnabled(true);
4156 } catch (Exception e)
4159 .debug("Exception during web service menu building process.",
4164 } catch (Exception e)
4167 buildingMenu = false;
4174 * construct any groupURL type service menu entries.
4178 private void build_urlServiceMenu(JMenu webService)
4180 // TODO: remove this code when 2.7 is released
4181 // DEBUG - alignmentView
4183 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4184 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4186 * @Override public void actionPerformed(ActionEvent e) {
4187 * jalview.datamodel.AlignmentView
4188 * .testSelectionViews(af.viewport.getAlignment(),
4189 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4191 * }); webService.add(testAlView);
4193 // TODO: refactor to RestClient discoverer and merge menu entries for
4194 // rest-style services with other types of analysis/calculation service
4195 // SHmmr test client - still being implemented.
4196 // DEBUG - alignmentView
4198 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4201 client.attachWSMenuEntry(
4202 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4208 * Searches the alignment sequences for xRefs and builds the Show
4209 * Cross-References menu (formerly called Show Products), with database
4210 * sources for which cross-references are found (protein sources for a
4211 * nucleotide alignment and vice versa)
4213 * @return true if Show Cross-references menu should be enabled
4215 public boolean canShowProducts()
4217 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4218 AlignmentI dataset = viewport.getAlignment().getDataset();
4220 showProducts.removeAll();
4221 final boolean dna = viewport.getAlignment().isNucleotide();
4223 if (seqs == null || seqs.length == 0)
4225 // nothing to see here.
4229 boolean showp = false;
4232 List<String> ptypes = new CrossRef(seqs, dataset)
4233 .findXrefSourcesForSequences(dna);
4235 for (final String source : ptypes)
4238 final AlignFrame af = this;
4239 JMenuItem xtype = new JMenuItem(source);
4240 xtype.addActionListener(new ActionListener()
4243 public void actionPerformed(ActionEvent e)
4245 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4248 showProducts.add(xtype);
4250 showProducts.setVisible(showp);
4251 showProducts.setEnabled(showp);
4252 } catch (Exception e)
4255 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4263 * Finds and displays cross-references for the selected sequences (protein
4264 * products for nucleotide sequences, dna coding sequences for peptides).
4267 * the sequences to show cross-references for
4269 * true if from a nucleotide alignment (so showing proteins)
4271 * the database to show cross-references for
4273 protected void showProductsFor(final SequenceI[] sel,
4274 final boolean _odna, final String source)
4276 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4281 * Construct and display a new frame containing the translation of this
4282 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4285 public void showTranslation_actionPerformed(ActionEvent e)
4287 AlignmentI al = null;
4290 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4292 al = dna.translateCdna();
4293 } catch (Exception ex)
4295 jalview.bin.Cache.log.error(
4296 "Exception during translation. Please report this !", ex);
4297 final String msg = MessageManager
4298 .getString("label.error_when_translating_sequences_submit_bug_report");
4299 final String errorTitle = MessageManager
4300 .getString("label.implementation_error")
4301 + MessageManager.getString("label.translation_failed");
4302 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4303 JvOptionPane.ERROR_MESSAGE);
4306 if (al == null || al.getHeight() == 0)
4308 final String msg = MessageManager
4309 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4310 final String errorTitle = MessageManager
4311 .getString("label.translation_failed");
4312 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4313 JvOptionPane.WARNING_MESSAGE);
4317 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4318 af.setFileFormat(this.currentFileFormat);
4319 final String newTitle = MessageManager.formatMessage(
4320 "label.translation_of_params",
4321 new Object[] { this.getTitle() });
4322 af.setTitle(newTitle);
4323 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4325 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4326 viewport.openSplitFrame(af, new Alignment(seqs));
4330 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4337 * Set the file format
4341 public void setFileFormat(FileFormatI format)
4343 this.currentFileFormat = format;
4347 * Try to load a features file onto the alignment.
4350 * contents or path to retrieve file
4352 * access mode of file (see jalview.io.AlignFile)
4353 * @return true if features file was parsed correctly.
4355 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4357 return avc.parseFeaturesFile(file, sourceType,
4358 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4363 public void refreshFeatureUI(boolean enableIfNecessary)
4365 // note - currently this is only still here rather than in the controller
4366 // because of the featureSettings hard reference that is yet to be
4368 if (enableIfNecessary)
4370 viewport.setShowSequenceFeatures(true);
4371 showSeqFeatures.setSelected(true);
4377 public void dragEnter(DropTargetDragEvent evt)
4382 public void dragExit(DropTargetEvent evt)
4387 public void dragOver(DropTargetDragEvent evt)
4392 public void dropActionChanged(DropTargetDragEvent evt)
4397 public void drop(DropTargetDropEvent evt)
4399 // JAL-1552 - acceptDrop required before getTransferable call for
4400 // Java's Transferable for native dnd
4401 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4402 Transferable t = evt.getTransferable();
4403 List<String> files = new ArrayList<>();
4404 List<DataSourceType> protocols = new ArrayList<>();
4408 Desktop.transferFromDropTarget(files, protocols, evt, t);
4409 } catch (Exception e)
4411 e.printStackTrace();
4417 // check to see if any of these files have names matching sequences in
4419 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4420 .getAlignment().getSequencesArray());
4422 * Object[] { String,SequenceI}
4424 ArrayList<Object[]> filesmatched = new ArrayList<>();
4425 ArrayList<String> filesnotmatched = new ArrayList<>();
4426 for (int i = 0; i < files.size(); i++)
4428 String file = files.get(i).toString();
4430 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4431 if (protocol == DataSourceType.FILE)
4433 File fl = new File(file);
4434 pdbfn = fl.getName();
4436 else if (protocol == DataSourceType.URL)
4438 URL url = new URL(file);
4439 pdbfn = url.getFile();
4441 if (pdbfn.length() > 0)
4443 // attempt to find a match in the alignment
4444 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4445 int l = 0, c = pdbfn.indexOf(".");
4446 while (mtch == null && c != -1)
4451 } while ((c = pdbfn.indexOf(".", l)) > l);
4454 pdbfn = pdbfn.substring(0, l);
4456 mtch = idm.findAllIdMatches(pdbfn);
4460 FileFormatI type = null;
4463 type = new IdentifyFile().identify(file, protocol);
4464 } catch (Exception ex)
4468 if (type != null && type.isStructureFile())
4470 filesmatched.add(new Object[] { file, protocol, mtch });
4474 // File wasn't named like one of the sequences or wasn't a PDB file.
4475 filesnotmatched.add(file);
4479 if (filesmatched.size() > 0)
4481 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4487 "label.automatically_associate_structure_files_with_sequences_same_name",
4488 new Object[] { Integer
4494 .getString("label.automatically_associate_structure_files_by_name"),
4495 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4498 for (Object[] fm : filesmatched)
4500 // try and associate
4501 // TODO: may want to set a standard ID naming formalism for
4502 // associating PDB files which have no IDs.
4503 for (SequenceI toassoc : (SequenceI[]) fm[2])
4505 PDBEntry pe = new AssociatePdbFileWithSeq()
4506 .associatePdbWithSeq((String) fm[0],
4507 (DataSourceType) fm[1], toassoc, false,
4511 System.err.println("Associated file : "
4512 + ((String) fm[0]) + " with "
4513 + toassoc.getDisplayId(true));
4517 alignPanel.paintAlignment(true);
4521 if (filesnotmatched.size() > 0)
4524 && (Cache.getDefault(
4525 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4531 "label.ignore_unmatched_dropped_files_info",
4532 new Object[] { Integer
4539 .getString("label.ignore_unmatched_dropped_files"),
4540 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4544 for (String fn : filesnotmatched)
4546 loadJalviewDataFile(fn, null, null, null);
4550 } catch (Exception ex)
4552 ex.printStackTrace();
4558 * Attempt to load a "dropped" file or URL string, by testing in turn for
4560 * <li>an Annotation file</li>
4561 * <li>a JNet file</li>
4562 * <li>a features file</li>
4563 * <li>else try to interpret as an alignment file</li>
4567 * either a filename or a URL string.
4569 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4570 FileFormatI format, SequenceI assocSeq)
4574 if (sourceType == null)
4576 sourceType = FormatAdapter.checkProtocol(file);
4578 // if the file isn't identified, or not positively identified as some
4579 // other filetype (PFAM is default unidentified alignment file type) then
4580 // try to parse as annotation.
4581 boolean isAnnotation = (format == null || FileFormat.Pfam
4582 .equals(format)) ? new AnnotationFile()
4583 .annotateAlignmentView(viewport, file, sourceType) : false;
4587 // first see if its a T-COFFEE score file
4588 TCoffeeScoreFile tcf = null;
4591 tcf = new TCoffeeScoreFile(file, sourceType);
4594 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4597 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4598 isAnnotation = true;
4600 .setText(MessageManager
4601 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4605 // some problem - if no warning its probable that the ID matching
4606 // process didn't work
4610 tcf.getWarningMessage() == null ? MessageManager
4611 .getString("label.check_file_matches_sequence_ids_alignment")
4612 : tcf.getWarningMessage(),
4614 .getString("label.problem_reading_tcoffee_score_file"),
4615 JvOptionPane.WARNING_MESSAGE);
4622 } catch (Exception x)
4625 .debug("Exception when processing data source as T-COFFEE score file",
4631 // try to see if its a JNet 'concise' style annotation file *before*
4633 // try to parse it as a features file
4636 format = new IdentifyFile().identify(file, sourceType);
4638 if (FileFormat.ScoreMatrix == format)
4640 ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4643 // todo: i18n this message
4645 .setText(MessageManager.formatMessage(
4646 "label.successfully_loaded_matrix",
4647 sm.getMatrixName()));
4649 else if (FileFormat.Jnet.equals(format))
4651 JPredFile predictions = new JPredFile(file, sourceType);
4652 new JnetAnnotationMaker();
4653 JnetAnnotationMaker.add_annotation(predictions,
4654 viewport.getAlignment(), 0, false);
4655 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4656 viewport.getAlignment().setSeqrep(repseq);
4657 HiddenColumns cs = new HiddenColumns();
4658 cs.hideInsertionsFor(repseq);
4659 viewport.getAlignment().setHiddenColumns(cs);
4660 isAnnotation = true;
4662 // else if (IdentifyFile.FeaturesFile.equals(format))
4663 else if (FileFormat.Features.equals(format))
4665 if (parseFeaturesFile(file, sourceType))
4667 alignPanel.paintAlignment(true);
4672 new FileLoader().LoadFile(viewport, file, sourceType, format);
4679 alignPanel.adjustAnnotationHeight();
4680 viewport.updateSequenceIdColours();
4681 buildSortByAnnotationScoresMenu();
4682 alignPanel.paintAlignment(true);
4684 } catch (Exception ex)
4686 ex.printStackTrace();
4687 } catch (OutOfMemoryError oom)
4692 } catch (Exception x)
4697 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4698 : "using " + sourceType + " from " + file)
4700 + (format != null ? "(parsing as '" + format
4701 + "' file)" : ""), oom, Desktop.desktop);
4706 * Method invoked by the ChangeListener on the tabbed pane, in other words
4707 * when a different tabbed pane is selected by the user or programmatically.
4710 public void tabSelectionChanged(int index)
4714 alignPanel = alignPanels.get(index);
4715 viewport = alignPanel.av;
4716 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4717 setMenusFromViewport(viewport);
4721 * 'focus' any colour slider that is open to the selected viewport
4723 if (viewport.getConservationSelected())
4725 SliderPanel.setConservationSlider(alignPanel,
4726 viewport.getResidueShading(), alignPanel.getViewName());
4730 SliderPanel.hideConservationSlider();
4732 if (viewport.getAbovePIDThreshold())
4734 SliderPanel.setPIDSliderSource(alignPanel,
4735 viewport.getResidueShading(), alignPanel.getViewName());
4739 SliderPanel.hidePIDSlider();
4743 * If there is a frame linked to this one in a SplitPane, switch it to the
4744 * same view tab index. No infinite recursion of calls should happen, since
4745 * tabSelectionChanged() should not get invoked on setting the selected
4746 * index to an unchanged value. Guard against setting an invalid index
4747 * before the new view peer tab has been created.
4749 final AlignViewportI peer = viewport.getCodingComplement();
4752 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4753 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4755 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4761 * On right mouse click on view tab, prompt for and set new view name.
4764 public void tabbedPane_mousePressed(MouseEvent e)
4766 if (e.isPopupTrigger())
4768 String msg = MessageManager.getString("label.enter_view_name");
4769 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4770 JvOptionPane.QUESTION_MESSAGE);
4774 viewport.viewName = reply;
4775 // TODO warn if reply is in getExistingViewNames()?
4776 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4781 public AlignViewport getCurrentView()
4787 * Open the dialog for regex description parsing.
4790 protected void extractScores_actionPerformed(ActionEvent e)
4792 ParseProperties pp = new jalview.analysis.ParseProperties(
4793 viewport.getAlignment());
4794 // TODO: verify regex and introduce GUI dialog for version 2.5
4795 // if (pp.getScoresFromDescription("col", "score column ",
4796 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4798 if (pp.getScoresFromDescription("description column",
4799 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4801 buildSortByAnnotationScoresMenu();
4809 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4813 protected void showDbRefs_actionPerformed(ActionEvent e)
4815 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4821 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4825 protected void showNpFeats_actionPerformed(ActionEvent e)
4827 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4831 * find the viewport amongst the tabs in this alignment frame and close that
4836 public boolean closeView(AlignViewportI av)
4840 this.closeMenuItem_actionPerformed(false);
4843 Component[] comp = tabbedPane.getComponents();
4844 for (int i = 0; comp != null && i < comp.length; i++)
4846 if (comp[i] instanceof AlignmentPanel)
4848 if (((AlignmentPanel) comp[i]).av == av)
4851 closeView((AlignmentPanel) comp[i]);
4859 protected void build_fetchdbmenu(JMenu webService)
4861 // Temporary hack - DBRef Fetcher always top level ws entry.
4862 // TODO We probably want to store a sequence database checklist in
4863 // preferences and have checkboxes.. rather than individual sources selected
4865 final JMenu rfetch = new JMenu(
4866 MessageManager.getString("action.fetch_db_references"));
4867 rfetch.setToolTipText(MessageManager
4868 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4869 webService.add(rfetch);
4871 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4872 MessageManager.getString("option.trim_retrieved_seqs"));
4873 trimrs.setToolTipText(MessageManager
4874 .getString("label.trim_retrieved_sequences"));
4875 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4876 trimrs.addActionListener(new ActionListener()
4879 public void actionPerformed(ActionEvent e)
4881 trimrs.setSelected(trimrs.isSelected());
4882 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4883 Boolean.valueOf(trimrs.isSelected()).toString());
4887 JMenuItem fetchr = new JMenuItem(
4888 MessageManager.getString("label.standard_databases"));
4889 fetchr.setToolTipText(MessageManager
4890 .getString("label.fetch_embl_uniprot"));
4891 fetchr.addActionListener(new ActionListener()
4895 public void actionPerformed(ActionEvent e)
4897 new Thread(new Runnable()
4902 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4903 .getAlignment().isNucleotide();
4904 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4905 .getSequenceSelection(), alignPanel.alignFrame, null,
4906 alignPanel.alignFrame.featureSettings, isNucleotide);
4907 dbRefFetcher.addListener(new FetchFinishedListenerI()
4910 public void finished()
4912 AlignFrame.this.setMenusForViewport();
4915 dbRefFetcher.fetchDBRefs(false);
4923 final AlignFrame me = this;
4924 new Thread(new Runnable()
4929 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4930 .getSequenceFetcherSingleton(me);
4931 javax.swing.SwingUtilities.invokeLater(new Runnable()
4936 String[] dbclasses = sf.getOrderedSupportedSources();
4937 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4938 // jalview.util.QuickSort.sort(otherdb, otherdb);
4939 List<DbSourceProxy> otherdb;
4940 JMenu dfetch = new JMenu();
4941 JMenu ifetch = new JMenu();
4942 JMenuItem fetchr = null;
4943 int comp = 0, icomp = 0, mcomp = 15;
4944 String mname = null;
4946 for (String dbclass : dbclasses)
4948 otherdb = sf.getSourceProxy(dbclass);
4949 // add a single entry for this class, or submenu allowing 'fetch
4951 if (otherdb == null || otherdb.size() < 1)
4955 // List<DbSourceProxy> dbs=otherdb;
4956 // otherdb=new ArrayList<DbSourceProxy>();
4957 // for (DbSourceProxy db:dbs)
4959 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4963 mname = "From " + dbclass;
4965 if (otherdb.size() == 1)
4967 final DbSourceProxy[] dassource = otherdb
4968 .toArray(new DbSourceProxy[0]);
4969 DbSourceProxy src = otherdb.get(0);
4970 fetchr = new JMenuItem(src.getDbSource());
4971 fetchr.addActionListener(new ActionListener()
4975 public void actionPerformed(ActionEvent e)
4977 new Thread(new Runnable()
4983 boolean isNucleotide = alignPanel.alignFrame
4984 .getViewport().getAlignment()
4986 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4987 alignPanel.av.getSequenceSelection(),
4988 alignPanel.alignFrame, dassource,
4989 alignPanel.alignFrame.featureSettings,
4992 .addListener(new FetchFinishedListenerI()
4995 public void finished()
4997 AlignFrame.this.setMenusForViewport();
5000 dbRefFetcher.fetchDBRefs(false);
5006 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5007 MessageManager.formatMessage(
5008 "label.fetch_retrieve_from",
5009 new Object[] { src.getDbName() })));
5015 final DbSourceProxy[] dassource = otherdb
5016 .toArray(new DbSourceProxy[0]);
5018 DbSourceProxy src = otherdb.get(0);
5019 fetchr = new JMenuItem(MessageManager.formatMessage(
5020 "label.fetch_all_param",
5021 new Object[] { src.getDbSource() }));
5022 fetchr.addActionListener(new ActionListener()
5025 public void actionPerformed(ActionEvent e)
5027 new Thread(new Runnable()
5033 boolean isNucleotide = alignPanel.alignFrame
5034 .getViewport().getAlignment()
5036 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5037 alignPanel.av.getSequenceSelection(),
5038 alignPanel.alignFrame, dassource,
5039 alignPanel.alignFrame.featureSettings,
5042 .addListener(new FetchFinishedListenerI()
5045 public void finished()
5047 AlignFrame.this.setMenusForViewport();
5050 dbRefFetcher.fetchDBRefs(false);
5056 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5057 MessageManager.formatMessage(
5058 "label.fetch_retrieve_from_all_sources",
5060 Integer.valueOf(otherdb.size())
5061 .toString(), src.getDbSource(),
5062 src.getDbName() })));
5065 // and then build the rest of the individual menus
5066 ifetch = new JMenu(MessageManager.formatMessage(
5067 "label.source_from_db_source",
5068 new Object[] { src.getDbSource() }));
5070 String imname = null;
5072 for (DbSourceProxy sproxy : otherdb)
5074 String dbname = sproxy.getDbName();
5075 String sname = dbname.length() > 5 ? dbname.substring(0,
5076 5) + "..." : dbname;
5077 String msname = dbname.length() > 10 ? dbname.substring(
5078 0, 10) + "..." : dbname;
5081 imname = MessageManager.formatMessage(
5082 "label.from_msname", new Object[] { sname });
5084 fetchr = new JMenuItem(msname);
5085 final DbSourceProxy[] dassrc = { sproxy };
5086 fetchr.addActionListener(new ActionListener()
5090 public void actionPerformed(ActionEvent e)
5092 new Thread(new Runnable()
5098 boolean isNucleotide = alignPanel.alignFrame
5099 .getViewport().getAlignment()
5101 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5102 alignPanel.av.getSequenceSelection(),
5103 alignPanel.alignFrame, dassrc,
5104 alignPanel.alignFrame.featureSettings,
5107 .addListener(new FetchFinishedListenerI()
5110 public void finished()
5112 AlignFrame.this.setMenusForViewport();
5115 dbRefFetcher.fetchDBRefs(false);
5121 fetchr.setToolTipText("<html>"
5122 + MessageManager.formatMessage(
5123 "label.fetch_retrieve_from", new Object[]
5127 if (++icomp >= mcomp || i == (otherdb.size()))
5129 ifetch.setText(MessageManager.formatMessage(
5130 "label.source_to_target", imname, sname));
5132 ifetch = new JMenu();
5140 if (comp >= mcomp || dbi >= (dbclasses.length))
5142 dfetch.setText(MessageManager.formatMessage(
5143 "label.source_to_target", mname, dbclass));
5145 dfetch = new JMenu();
5158 * Left justify the whole alignment.
5161 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5163 AlignmentI al = viewport.getAlignment();
5165 viewport.firePropertyChange("alignment", null, al);
5169 * Right justify the whole alignment.
5172 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5174 AlignmentI al = viewport.getAlignment();
5176 viewport.firePropertyChange("alignment", null, al);
5180 public void setShowSeqFeatures(boolean b)
5182 showSeqFeatures.setSelected(b);
5183 viewport.setShowSequenceFeatures(b);
5190 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5191 * awt.event.ActionEvent)
5194 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5196 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5197 alignPanel.paintAlignment(true);
5204 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5208 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5210 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5211 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5219 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5220 * .event.ActionEvent)
5223 protected void showGroupConservation_actionPerformed(ActionEvent e)
5225 viewport.setShowGroupConservation(showGroupConservation.getState());
5226 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5233 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5234 * .event.ActionEvent)
5237 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5239 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5240 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5247 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5248 * .event.ActionEvent)
5251 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5253 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5254 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5258 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5260 showSequenceLogo.setState(true);
5261 viewport.setShowSequenceLogo(true);
5262 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5263 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5267 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5269 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5276 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5277 * .event.ActionEvent)
5280 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5282 if (avc.makeGroupsFromSelection())
5284 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5285 alignPanel.updateAnnotation();
5286 alignPanel.paintAlignment(true);
5290 public void clearAlignmentSeqRep()
5292 // TODO refactor alignmentseqrep to controller
5293 if (viewport.getAlignment().hasSeqrep())
5295 viewport.getAlignment().setSeqrep(null);
5296 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5297 alignPanel.updateAnnotation();
5298 alignPanel.paintAlignment(true);
5303 protected void createGroup_actionPerformed(ActionEvent e)
5305 if (avc.createGroup())
5307 alignPanel.alignmentChanged();
5312 protected void unGroup_actionPerformed(ActionEvent e)
5316 alignPanel.alignmentChanged();
5321 * make the given alignmentPanel the currently selected tab
5323 * @param alignmentPanel
5325 public void setDisplayedView(AlignmentPanel alignmentPanel)
5327 if (!viewport.getSequenceSetId().equals(
5328 alignmentPanel.av.getSequenceSetId()))
5332 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5334 if (tabbedPane != null
5335 && tabbedPane.getTabCount() > 0
5336 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5337 .getSelectedIndex())
5339 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5344 * Action on selection of menu options to Show or Hide annotations.
5347 * @param forSequences
5348 * update sequence-related annotations
5349 * @param forAlignment
5350 * update non-sequence-related annotations
5353 protected void setAnnotationsVisibility(boolean visible,
5354 boolean forSequences, boolean forAlignment)
5356 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5357 .getAlignmentAnnotation();
5362 for (AlignmentAnnotation aa : anns)
5365 * don't display non-positional annotations on an alignment
5367 if (aa.annotations == null)
5371 boolean apply = (aa.sequenceRef == null && forAlignment)
5372 || (aa.sequenceRef != null && forSequences);
5375 aa.visible = visible;
5378 alignPanel.validateAnnotationDimensions(true);
5379 alignPanel.alignmentChanged();
5383 * Store selected annotation sort order for the view and repaint.
5386 protected void sortAnnotations_actionPerformed()
5388 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5390 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5391 alignPanel.paintAlignment(true);
5396 * @return alignment panels in this alignment frame
5398 public List<? extends AlignmentViewPanel> getAlignPanels()
5400 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5404 * Open a new alignment window, with the cDNA associated with this (protein)
5405 * alignment, aligned as is the protein.
5407 protected void viewAsCdna_actionPerformed()
5409 // TODO no longer a menu action - refactor as required
5410 final AlignmentI alignment = getViewport().getAlignment();
5411 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5412 if (mappings == null)
5416 List<SequenceI> cdnaSeqs = new ArrayList<>();
5417 for (SequenceI aaSeq : alignment.getSequences())
5419 for (AlignedCodonFrame acf : mappings)
5421 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5425 * There is a cDNA mapping for this protein sequence - add to new
5426 * alignment. It will share the same dataset sequence as other mapped
5427 * cDNA (no new mappings need to be created).
5429 final Sequence newSeq = new Sequence(dnaSeq);
5430 newSeq.setDatasetSequence(dnaSeq);
5431 cdnaSeqs.add(newSeq);
5435 if (cdnaSeqs.size() == 0)
5437 // show a warning dialog no mapped cDNA
5440 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5442 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5443 AlignFrame.DEFAULT_HEIGHT);
5444 cdna.alignAs(alignment);
5445 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5447 Desktop.addInternalFrame(alignFrame, newtitle,
5448 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5452 * Set visibility of dna/protein complement view (available when shown in a
5458 protected void showComplement_actionPerformed(boolean show)
5460 SplitContainerI sf = getSplitViewContainer();
5463 sf.setComplementVisible(this, show);
5468 * Generate the reverse (optionally complemented) of the selected sequences,
5469 * and add them to the alignment
5472 protected void showReverse_actionPerformed(boolean complement)
5474 AlignmentI al = null;
5477 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5478 al = dna.reverseCdna(complement);
5479 viewport.addAlignment(al, "");
5480 addHistoryItem(new EditCommand(
5481 MessageManager.getString("label.add_sequences"),
5482 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5483 viewport.getAlignment()));
5484 } catch (Exception ex)
5486 System.err.println(ex.getMessage());
5492 * Try to run a script in the Groovy console, having first ensured that this
5493 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5494 * be targeted at this alignment.
5497 protected void runGroovy_actionPerformed()
5499 Jalview.setCurrentAlignFrame(this);
5500 groovy.ui.Console console = Desktop.getGroovyConsole();
5501 if (console != null)
5505 console.runScript();
5506 } catch (Exception ex)
5508 System.err.println((ex.toString()));
5510 .showInternalMessageDialog(Desktop.desktop, MessageManager
5511 .getString("label.couldnt_run_groovy_script"),
5513 .getString("label.groovy_support_failed"),
5514 JvOptionPane.ERROR_MESSAGE);
5519 System.err.println("Can't run Groovy script as console not found");
5524 * Hides columns containing (or not containing) a specified feature, provided
5525 * that would not leave all columns hidden
5527 * @param featureType
5528 * @param columnsContaining
5531 public boolean hideFeatureColumns(String featureType,
5532 boolean columnsContaining)
5534 boolean notForHiding = avc.markColumnsContainingFeatures(
5535 columnsContaining, false, false, featureType);
5538 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5539 false, featureType))
5541 getViewport().hideSelectedColumns();
5549 protected void selectHighlightedColumns_actionPerformed(
5550 ActionEvent actionEvent)
5552 // include key modifier check in case user selects from menu
5553 avc.markHighlightedColumns(
5554 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5556 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5560 * Rebuilds the Colour menu, including any user-defined colours which have
5561 * been loaded either on startup or during the session
5563 public void buildColourMenu()
5565 colourMenu.removeAll();
5567 colourMenu.add(applyToAllGroups);
5568 colourMenu.add(textColour);
5569 colourMenu.addSeparator();
5571 ColourMenuHelper.addMenuItems(colourMenu, this,
5572 viewport.getAlignment(), false);
5574 colourMenu.addSeparator();
5575 colourMenu.add(conservationMenuItem);
5576 colourMenu.add(modifyConservation);
5577 colourMenu.add(abovePIDThreshold);
5578 colourMenu.add(modifyPID);
5579 colourMenu.add(annotationColour);
5581 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5582 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5586 * Open a dialog (if not already open) that allows the user to select and
5587 * calculate PCA or Tree analysis
5589 protected void openTreePcaDialog()
5591 if (alignPanel.getCalculationDialog() == null)
5593 new CalculationChooser(AlignFrame.this);
5598 class PrintThread extends Thread
5602 public PrintThread(AlignmentPanel ap)
5607 static PageFormat pf;
5612 PrinterJob printJob = PrinterJob.getPrinterJob();
5616 printJob.setPrintable(ap, pf);
5620 printJob.setPrintable(ap);
5623 if (printJob.printDialog())
5628 } catch (Exception PrintException)
5630 PrintException.printStackTrace();