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 ArrayList<int[]> hiddenRegions = viewport.getAlignment()
1889 .getHiddenColumns().getHiddenColumnsCopy();
1890 for (int[] region : hiddenRegions)
1892 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1894 hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1895 region[1] - hiddenOffset });
1900 Desktop.jalviewClipboard = new Object[] { seqs,
1901 viewport.getAlignment().getDataset(), hiddenColumns };
1902 statusBar.setText(MessageManager.formatMessage(
1903 "label.copied_sequences_to_clipboard", new Object[] { Integer
1904 .valueOf(seqs.length).toString() }));
1914 protected void pasteNew_actionPerformed(ActionEvent e)
1926 protected void pasteThis_actionPerformed(ActionEvent e)
1932 * Paste contents of Jalview clipboard
1934 * @param newAlignment
1935 * true to paste to a new alignment, otherwise add to this.
1937 void paste(boolean newAlignment)
1939 boolean externalPaste = true;
1942 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1943 Transferable contents = c.getContents(this);
1945 if (contents == null)
1954 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1955 if (str.length() < 1)
1960 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1962 } catch (OutOfMemoryError er)
1964 new OOMWarning("Out of memory pasting sequences!!", er);
1968 SequenceI[] sequences;
1969 boolean annotationAdded = false;
1970 AlignmentI alignment = null;
1972 if (Desktop.jalviewClipboard != null)
1974 // The clipboard was filled from within Jalview, we must use the
1976 // And dataset from the copied alignment
1977 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1978 // be doubly sure that we create *new* sequence objects.
1979 sequences = new SequenceI[newseq.length];
1980 for (int i = 0; i < newseq.length; i++)
1982 sequences[i] = new Sequence(newseq[i]);
1984 alignment = new Alignment(sequences);
1985 externalPaste = false;
1989 // parse the clipboard as an alignment.
1990 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1992 sequences = alignment.getSequencesArray();
1996 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2002 if (Desktop.jalviewClipboard != null)
2004 // dataset is inherited
2005 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2009 // new dataset is constructed
2010 alignment.setDataset(null);
2012 alwidth = alignment.getWidth() + 1;
2016 AlignmentI pastedal = alignment; // preserve pasted alignment object
2017 // Add pasted sequences and dataset into existing alignment.
2018 alignment = viewport.getAlignment();
2019 alwidth = alignment.getWidth() + 1;
2020 // decide if we need to import sequences from an existing dataset
2021 boolean importDs = Desktop.jalviewClipboard != null
2022 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2023 // importDs==true instructs us to copy over new dataset sequences from
2024 // an existing alignment
2025 Vector newDs = (importDs) ? new Vector() : null; // used to create
2026 // minimum dataset set
2028 for (int i = 0; i < sequences.length; i++)
2032 newDs.addElement(null);
2034 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2036 if (importDs && ds != null)
2038 if (!newDs.contains(ds))
2040 newDs.setElementAt(ds, i);
2041 ds = new Sequence(ds);
2042 // update with new dataset sequence
2043 sequences[i].setDatasetSequence(ds);
2047 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2052 // copy and derive new dataset sequence
2053 sequences[i] = sequences[i].deriveSequence();
2054 alignment.getDataset().addSequence(
2055 sequences[i].getDatasetSequence());
2056 // TODO: avoid creation of duplicate dataset sequences with a
2057 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2059 alignment.addSequence(sequences[i]); // merges dataset
2063 newDs.clear(); // tidy up
2065 if (alignment.getAlignmentAnnotation() != null)
2067 for (AlignmentAnnotation alan : alignment
2068 .getAlignmentAnnotation())
2070 if (alan.graphGroup > fgroup)
2072 fgroup = alan.graphGroup;
2076 if (pastedal.getAlignmentAnnotation() != null)
2078 // Add any annotation attached to alignment.
2079 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2080 for (int i = 0; i < alann.length; i++)
2082 annotationAdded = true;
2083 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2085 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2086 if (newann.graphGroup > -1)
2088 if (newGraphGroups.size() <= newann.graphGroup
2089 || newGraphGroups.get(newann.graphGroup) == null)
2091 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2093 newGraphGroups.add(q, null);
2095 newGraphGroups.set(newann.graphGroup, new Integer(
2098 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2102 newann.padAnnotation(alwidth);
2103 alignment.addAnnotation(newann);
2113 addHistoryItem(new EditCommand(
2114 MessageManager.getString("label.add_sequences"),
2115 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2117 // Add any annotations attached to sequences
2118 for (int i = 0; i < sequences.length; i++)
2120 if (sequences[i].getAnnotation() != null)
2122 AlignmentAnnotation newann;
2123 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2125 annotationAdded = true;
2126 newann = sequences[i].getAnnotation()[a];
2127 newann.adjustForAlignment();
2128 newann.padAnnotation(alwidth);
2129 if (newann.graphGroup > -1)
2131 if (newann.graphGroup > -1)
2133 if (newGraphGroups.size() <= newann.graphGroup
2134 || newGraphGroups.get(newann.graphGroup) == null)
2136 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2138 newGraphGroups.add(q, null);
2140 newGraphGroups.set(newann.graphGroup, new Integer(
2143 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2147 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2152 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2159 // propagate alignment changed.
2160 vpRanges.setEndSeq(alignment.getHeight());
2161 if (annotationAdded)
2163 // Duplicate sequence annotation in all views.
2164 AlignmentI[] alview = this.getViewAlignments();
2165 for (int i = 0; i < sequences.length; i++)
2167 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2172 for (int avnum = 0; avnum < alview.length; avnum++)
2174 if (alview[avnum] != alignment)
2176 // duplicate in a view other than the one with input focus
2177 int avwidth = alview[avnum].getWidth() + 1;
2178 // this relies on sann being preserved after we
2179 // modify the sequence's annotation array for each duplication
2180 for (int a = 0; a < sann.length; a++)
2182 AlignmentAnnotation newann = new AlignmentAnnotation(
2184 sequences[i].addAlignmentAnnotation(newann);
2185 newann.padAnnotation(avwidth);
2186 alview[avnum].addAnnotation(newann); // annotation was
2187 // duplicated earlier
2188 // TODO JAL-1145 graphGroups are not updated for sequence
2189 // annotation added to several views. This may cause
2191 alview[avnum].setAnnotationIndex(newann, a);
2196 buildSortByAnnotationScoresMenu();
2198 viewport.firePropertyChange("alignment", null,
2199 alignment.getSequences());
2200 if (alignPanels != null)
2202 for (AlignmentPanel ap : alignPanels)
2204 ap.validateAnnotationDimensions(false);
2209 alignPanel.validateAnnotationDimensions(false);
2215 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2217 String newtitle = new String("Copied sequences");
2219 if (Desktop.jalviewClipboard != null
2220 && Desktop.jalviewClipboard[2] != null)
2222 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2223 for (int[] region : hc)
2225 af.viewport.hideColumns(region[0], region[1]);
2229 // >>>This is a fix for the moment, until a better solution is
2231 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2233 alignPanel.getSeqPanel().seqCanvas
2234 .getFeatureRenderer());
2236 // TODO: maintain provenance of an alignment, rather than just make the
2237 // title a concatenation of operations.
2240 if (title.startsWith("Copied sequences"))
2246 newtitle = newtitle.concat("- from " + title);
2251 newtitle = new String("Pasted sequences");
2254 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2259 } catch (Exception ex)
2261 ex.printStackTrace();
2262 System.out.println("Exception whilst pasting: " + ex);
2263 // could be anything being pasted in here
2269 protected void expand_newalign(ActionEvent e)
2273 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2274 .getAlignment(), -1);
2275 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2277 String newtitle = new String("Flanking alignment");
2279 if (Desktop.jalviewClipboard != null
2280 && Desktop.jalviewClipboard[2] != null)
2282 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2283 for (int region[] : hc)
2285 af.viewport.hideColumns(region[0], region[1]);
2289 // >>>This is a fix for the moment, until a better solution is
2291 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2293 alignPanel.getSeqPanel().seqCanvas
2294 .getFeatureRenderer());
2296 // TODO: maintain provenance of an alignment, rather than just make the
2297 // title a concatenation of operations.
2299 if (title.startsWith("Copied sequences"))
2305 newtitle = newtitle.concat("- from " + title);
2309 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2311 } catch (Exception ex)
2313 ex.printStackTrace();
2314 System.out.println("Exception whilst pasting: " + ex);
2315 // could be anything being pasted in here
2316 } catch (OutOfMemoryError oom)
2318 new OOMWarning("Viewing flanking region of alignment", oom);
2329 protected void cut_actionPerformed(ActionEvent e)
2331 copy_actionPerformed(null);
2332 delete_actionPerformed(null);
2342 protected void delete_actionPerformed(ActionEvent evt)
2345 SequenceGroup sg = viewport.getSelectionGroup();
2352 * If the cut affects all sequences, warn, remove highlighted columns
2354 if (sg.getSize() == viewport.getAlignment().getHeight())
2356 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2357 .getAlignment().getWidth()) ? true : false;
2358 if (isEntireAlignWidth)
2360 int confirm = JvOptionPane.showConfirmDialog(this,
2361 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2362 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2363 JvOptionPane.OK_CANCEL_OPTION);
2365 if (confirm == JvOptionPane.CANCEL_OPTION
2366 || confirm == JvOptionPane.CLOSED_OPTION)
2371 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2372 sg.getEndRes() + 1);
2374 SequenceI[] cut = sg.getSequences()
2375 .toArray(new SequenceI[sg.getSize()]);
2377 addHistoryItem(new EditCommand(
2378 MessageManager.getString("label.cut_sequences"), Action.CUT,
2379 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2380 viewport.getAlignment()));
2382 viewport.setSelectionGroup(null);
2383 viewport.sendSelection();
2384 viewport.getAlignment().deleteGroup(sg);
2386 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2388 if (viewport.getAlignment().getHeight() < 1)
2392 this.setClosed(true);
2393 } catch (Exception ex)
2406 protected void deleteGroups_actionPerformed(ActionEvent e)
2408 if (avc.deleteGroups())
2410 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2411 alignPanel.updateAnnotation();
2412 alignPanel.paintAlignment(true);
2423 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2425 SequenceGroup sg = new SequenceGroup();
2427 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2429 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2432 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2433 viewport.setSelectionGroup(sg);
2434 viewport.sendSelection();
2435 // JAL-2034 - should delegate to
2436 // alignPanel to decide if overview needs
2438 alignPanel.paintAlignment(false);
2439 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2449 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2451 if (viewport.cursorMode)
2453 alignPanel.getSeqPanel().keyboardNo1 = null;
2454 alignPanel.getSeqPanel().keyboardNo2 = null;
2456 viewport.setSelectionGroup(null);
2457 viewport.getColumnSelection().clear();
2458 viewport.setSelectionGroup(null);
2459 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2460 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2461 // JAL-2034 - should delegate to
2462 // alignPanel to decide if overview needs
2464 alignPanel.paintAlignment(false);
2465 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2466 viewport.sendSelection();
2476 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2478 SequenceGroup sg = viewport.getSelectionGroup();
2482 selectAllSequenceMenuItem_actionPerformed(null);
2487 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2489 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2491 // JAL-2034 - should delegate to
2492 // alignPanel to decide if overview needs
2495 alignPanel.paintAlignment(true);
2496 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2497 viewport.sendSelection();
2501 public void invertColSel_actionPerformed(ActionEvent e)
2503 viewport.invertColumnSelection();
2504 alignPanel.paintAlignment(true);
2505 viewport.sendSelection();
2515 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2517 trimAlignment(true);
2527 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2529 trimAlignment(false);
2532 void trimAlignment(boolean trimLeft)
2534 ColumnSelection colSel = viewport.getColumnSelection();
2537 if (!colSel.isEmpty())
2541 column = colSel.getMin();
2545 column = colSel.getMax();
2549 if (viewport.getSelectionGroup() != null)
2551 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2552 viewport.getHiddenRepSequences());
2556 seqs = viewport.getAlignment().getSequencesArray();
2559 TrimRegionCommand trimRegion;
2562 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2563 column, viewport.getAlignment());
2564 vpRanges.setStartRes(0);
2568 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2569 column, viewport.getAlignment());
2572 statusBar.setText(MessageManager.formatMessage(
2573 "label.removed_columns",
2574 new String[] { Integer.valueOf(trimRegion.getSize())
2577 addHistoryItem(trimRegion);
2579 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2581 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2582 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2584 viewport.getAlignment().deleteGroup(sg);
2588 viewport.firePropertyChange("alignment", null, viewport
2589 .getAlignment().getSequences());
2600 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2602 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2605 if (viewport.getSelectionGroup() != null)
2607 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2608 viewport.getHiddenRepSequences());
2609 start = viewport.getSelectionGroup().getStartRes();
2610 end = viewport.getSelectionGroup().getEndRes();
2614 seqs = viewport.getAlignment().getSequencesArray();
2617 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2618 "Remove Gapped Columns", seqs, start, end,
2619 viewport.getAlignment());
2621 addHistoryItem(removeGapCols);
2623 statusBar.setText(MessageManager.formatMessage(
2624 "label.removed_empty_columns",
2625 new Object[] { Integer.valueOf(removeGapCols.getSize())
2628 // This is to maintain viewport position on first residue
2629 // of first sequence
2630 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2631 int startRes = seq.findPosition(vpRanges.getStartRes());
2632 // ShiftList shifts;
2633 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2634 // edit.alColumnChanges=shifts.getInverse();
2635 // if (viewport.hasHiddenColumns)
2636 // viewport.getColumnSelection().compensateForEdits(shifts);
2637 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2638 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2650 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2652 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2655 if (viewport.getSelectionGroup() != null)
2657 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2658 viewport.getHiddenRepSequences());
2659 start = viewport.getSelectionGroup().getStartRes();
2660 end = viewport.getSelectionGroup().getEndRes();
2664 seqs = viewport.getAlignment().getSequencesArray();
2667 // This is to maintain viewport position on first residue
2668 // of first sequence
2669 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2670 int startRes = seq.findPosition(vpRanges.getStartRes());
2672 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2673 viewport.getAlignment()));
2675 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2677 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2689 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2691 viewport.setPadGaps(padGapsMenuitem.isSelected());
2692 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2703 public void findMenuItem_actionPerformed(ActionEvent e)
2709 * Create a new view of the current alignment.
2712 public void newView_actionPerformed(ActionEvent e)
2714 newView(null, true);
2718 * Creates and shows a new view of the current alignment.
2721 * title of newly created view; if null, one will be generated
2722 * @param copyAnnotation
2723 * if true then duplicate all annnotation, groups and settings
2724 * @return new alignment panel, already displayed.
2726 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2729 * Create a new AlignmentPanel (with its own, new Viewport)
2731 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2733 if (!copyAnnotation)
2736 * remove all groups and annotation except for the automatic stuff
2738 newap.av.getAlignment().deleteAllGroups();
2739 newap.av.getAlignment().deleteAllAnnotations(false);
2742 newap.av.setGatherViewsHere(false);
2744 if (viewport.viewName == null)
2746 viewport.viewName = MessageManager
2747 .getString("label.view_name_original");
2751 * Views share the same edits undo and redo stacks
2753 newap.av.setHistoryList(viewport.getHistoryList());
2754 newap.av.setRedoList(viewport.getRedoList());
2757 * Views share the same mappings; need to deregister any new mappings
2758 * created by copyAlignPanel, and register the new reference to the shared
2761 newap.av.replaceMappings(viewport.getAlignment());
2764 * start up cDNA consensus (if applicable) now mappings are in place
2766 if (newap.av.initComplementConsensus())
2768 newap.refresh(true); // adjust layout of annotations
2771 newap.av.viewName = getNewViewName(viewTitle);
2773 addAlignmentPanel(newap, true);
2774 newap.alignmentChanged();
2776 if (alignPanels.size() == 2)
2778 viewport.setGatherViewsHere(true);
2780 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2785 * Make a new name for the view, ensuring it is unique within the current
2786 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2787 * these now use viewId. Unique view names are still desirable for usability.)
2792 protected String getNewViewName(String viewTitle)
2794 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2795 boolean addFirstIndex = false;
2796 if (viewTitle == null || viewTitle.trim().length() == 0)
2798 viewTitle = MessageManager.getString("action.view");
2799 addFirstIndex = true;
2803 index = 1;// we count from 1 if given a specific name
2805 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2807 List<Component> comps = PaintRefresher.components.get(viewport
2808 .getSequenceSetId());
2810 List<String> existingNames = getExistingViewNames(comps);
2812 while (existingNames.contains(newViewName))
2814 newViewName = viewTitle + " " + (++index);
2820 * Returns a list of distinct view names found in the given list of
2821 * components. View names are held on the viewport of an AlignmentPanel.
2826 protected List<String> getExistingViewNames(List<Component> comps)
2828 List<String> existingNames = new ArrayList<>();
2829 for (Component comp : comps)
2831 if (comp instanceof AlignmentPanel)
2833 AlignmentPanel ap = (AlignmentPanel) comp;
2834 if (!existingNames.contains(ap.av.viewName))
2836 existingNames.add(ap.av.viewName);
2840 return existingNames;
2844 * Explode tabbed views into separate windows.
2847 public void expandViews_actionPerformed(ActionEvent e)
2849 Desktop.explodeViews(this);
2853 * Gather views in separate windows back into a tabbed presentation.
2856 public void gatherViews_actionPerformed(ActionEvent e)
2858 Desktop.instance.gatherViews(this);
2868 public void font_actionPerformed(ActionEvent e)
2870 new FontChooser(alignPanel);
2880 protected void seqLimit_actionPerformed(ActionEvent e)
2882 viewport.setShowJVSuffix(seqLimits.isSelected());
2884 alignPanel.getIdPanel().getIdCanvas()
2885 .setPreferredSize(alignPanel.calculateIdWidth());
2886 alignPanel.paintAlignment(true);
2890 public void idRightAlign_actionPerformed(ActionEvent e)
2892 viewport.setRightAlignIds(idRightAlign.isSelected());
2893 alignPanel.paintAlignment(true);
2897 public void centreColumnLabels_actionPerformed(ActionEvent e)
2899 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2900 alignPanel.paintAlignment(true);
2906 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2909 protected void followHighlight_actionPerformed()
2912 * Set the 'follow' flag on the Viewport (and scroll to position if now
2915 final boolean state = this.followHighlightMenuItem.getState();
2916 viewport.setFollowHighlight(state);
2919 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2930 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2932 viewport.setColourText(colourTextMenuItem.isSelected());
2933 alignPanel.paintAlignment(true);
2943 public void wrapMenuItem_actionPerformed(ActionEvent e)
2945 scaleAbove.setVisible(wrapMenuItem.isSelected());
2946 scaleLeft.setVisible(wrapMenuItem.isSelected());
2947 scaleRight.setVisible(wrapMenuItem.isSelected());
2948 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2949 alignPanel.updateLayout();
2953 public void showAllSeqs_actionPerformed(ActionEvent e)
2955 viewport.showAllHiddenSeqs();
2959 public void showAllColumns_actionPerformed(ActionEvent e)
2961 viewport.showAllHiddenColumns();
2963 viewport.sendSelection();
2967 public void hideSelSequences_actionPerformed(ActionEvent e)
2969 viewport.hideAllSelectedSeqs();
2970 // alignPanel.paintAlignment(true);
2974 * called by key handler and the hide all/show all menu items
2979 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2982 boolean hide = false;
2983 SequenceGroup sg = viewport.getSelectionGroup();
2984 if (!toggleSeqs && !toggleCols)
2986 // Hide everything by the current selection - this is a hack - we do the
2987 // invert and then hide
2988 // first check that there will be visible columns after the invert.
2989 if (viewport.hasSelectedColumns()
2990 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2993 // now invert the sequence set, if required - empty selection implies
2994 // that no hiding is required.
2997 invertSequenceMenuItem_actionPerformed(null);
2998 sg = viewport.getSelectionGroup();
3002 viewport.expandColSelection(sg, true);
3003 // finally invert the column selection and get the new sequence
3005 invertColSel_actionPerformed(null);
3012 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3014 hideSelSequences_actionPerformed(null);
3017 else if (!(toggleCols && viewport.hasSelectedColumns()))
3019 showAllSeqs_actionPerformed(null);
3025 if (viewport.hasSelectedColumns())
3027 hideSelColumns_actionPerformed(null);
3030 viewport.setSelectionGroup(sg);
3035 showAllColumns_actionPerformed(null);
3044 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3045 * event.ActionEvent)
3048 public void hideAllButSelection_actionPerformed(ActionEvent e)
3050 toggleHiddenRegions(false, false);
3051 viewport.sendSelection();
3058 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3062 public void hideAllSelection_actionPerformed(ActionEvent e)
3064 SequenceGroup sg = viewport.getSelectionGroup();
3065 viewport.expandColSelection(sg, false);
3066 viewport.hideAllSelectedSeqs();
3067 viewport.hideSelectedColumns();
3068 alignPanel.paintAlignment(true);
3069 viewport.sendSelection();
3076 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3080 public void showAllhidden_actionPerformed(ActionEvent e)
3082 viewport.showAllHiddenColumns();
3083 viewport.showAllHiddenSeqs();
3084 alignPanel.paintAlignment(true);
3085 viewport.sendSelection();
3089 public void hideSelColumns_actionPerformed(ActionEvent e)
3091 viewport.hideSelectedColumns();
3092 alignPanel.paintAlignment(true);
3093 viewport.sendSelection();
3097 public void hiddenMarkers_actionPerformed(ActionEvent e)
3099 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3110 protected void scaleAbove_actionPerformed(ActionEvent e)
3112 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3113 alignPanel.paintAlignment(true);
3123 protected void scaleLeft_actionPerformed(ActionEvent e)
3125 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3126 alignPanel.paintAlignment(true);
3136 protected void scaleRight_actionPerformed(ActionEvent e)
3138 viewport.setScaleRightWrapped(scaleRight.isSelected());
3139 alignPanel.paintAlignment(true);
3149 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3151 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3152 alignPanel.paintAlignment(true);
3162 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3164 viewport.setShowText(viewTextMenuItem.isSelected());
3165 alignPanel.paintAlignment(true);
3175 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3177 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3178 alignPanel.paintAlignment(true);
3181 public FeatureSettings featureSettings;
3184 public FeatureSettingsControllerI getFeatureSettingsUI()
3186 return featureSettings;
3190 public void featureSettings_actionPerformed(ActionEvent e)
3192 if (featureSettings != null)
3194 featureSettings.close();
3195 featureSettings = null;
3197 if (!showSeqFeatures.isSelected())
3199 // make sure features are actually displayed
3200 showSeqFeatures.setSelected(true);
3201 showSeqFeatures_actionPerformed(null);
3203 featureSettings = new FeatureSettings(this);
3207 * Set or clear 'Show Sequence Features'
3213 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3215 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3216 alignPanel.paintAlignment(true);
3217 if (alignPanel.getOverviewPanel() != null)
3219 alignPanel.getOverviewPanel().updateOverviewImage();
3224 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3225 * the annotations panel as a whole.
3227 * The options to show/hide all annotations should be enabled when the panel
3228 * is shown, and disabled when the panel is hidden.
3233 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3235 final boolean setVisible = annotationPanelMenuItem.isSelected();
3236 viewport.setShowAnnotation(setVisible);
3237 this.showAllSeqAnnotations.setEnabled(setVisible);
3238 this.hideAllSeqAnnotations.setEnabled(setVisible);
3239 this.showAllAlAnnotations.setEnabled(setVisible);
3240 this.hideAllAlAnnotations.setEnabled(setVisible);
3241 alignPanel.updateLayout();
3245 public void alignmentProperties()
3247 JEditorPane editPane = new JEditorPane("text/html", "");
3248 editPane.setEditable(false);
3249 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3251 editPane.setText(MessageManager.formatMessage("label.html_content",
3252 new Object[] { contents.toString() }));
3253 JInternalFrame frame = new JInternalFrame();
3254 frame.getContentPane().add(new JScrollPane(editPane));
3256 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3257 "label.alignment_properties", new Object[] { getTitle() }),
3268 public void overviewMenuItem_actionPerformed(ActionEvent e)
3270 if (alignPanel.overviewPanel != null)
3275 JInternalFrame frame = new JInternalFrame();
3276 OverviewPanel overview = new OverviewPanel(alignPanel);
3277 frame.setContentPane(overview);
3278 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3279 "label.overview_params", new Object[] { this.getTitle() }),
3280 true, frame.getWidth(), frame.getHeight(), true, true);
3282 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3283 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3286 public void internalFrameClosed(
3287 javax.swing.event.InternalFrameEvent evt)
3289 alignPanel.setOverviewPanel(null);
3293 alignPanel.setOverviewPanel(overview);
3297 public void textColour_actionPerformed()
3299 new TextColourChooser().chooseColour(alignPanel, null);
3303 * public void covariationColour_actionPerformed() {
3305 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3309 public void annotationColour_actionPerformed()
3311 new AnnotationColourChooser(viewport, alignPanel);
3315 public void annotationColumn_actionPerformed(ActionEvent e)
3317 new AnnotationColumnChooser(viewport, alignPanel);
3321 * Action on the user checking or unchecking the option to apply the selected
3322 * colour scheme to all groups. If unchecked, groups may have their own
3323 * independent colour schemes.
3328 public void applyToAllGroups_actionPerformed(boolean selected)
3330 viewport.setColourAppliesToAllGroups(selected);
3334 * Action on user selecting a colour from the colour menu
3337 * the name (not the menu item label!) of the colour scheme
3340 public void changeColour_actionPerformed(String name)
3343 * 'User Defined' opens a panel to configure or load a
3344 * user-defined colour scheme
3346 if (ResidueColourScheme.USER_DEFINED.equals(name))
3348 new UserDefinedColours(alignPanel);
3353 * otherwise set the chosen colour scheme (or null for 'None')
3355 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3356 viewport.getAlignment(), viewport.getHiddenRepSequences());
3361 * Actions on setting or changing the alignment colour scheme
3366 public void changeColour(ColourSchemeI cs)
3368 // TODO: pull up to controller method
3369 ColourMenuHelper.setColourSelected(colourMenu, cs);
3371 viewport.setGlobalColourScheme(cs);
3373 alignPanel.paintAlignment(true);
3377 * Show the PID threshold slider panel
3380 protected void modifyPID_actionPerformed()
3382 SliderPanel.setPIDSliderSource(alignPanel,
3383 viewport.getResidueShading(), alignPanel.getViewName());
3384 SliderPanel.showPIDSlider();
3388 * Show the Conservation slider panel
3391 protected void modifyConservation_actionPerformed()
3393 SliderPanel.setConservationSlider(alignPanel,
3394 viewport.getResidueShading(), alignPanel.getViewName());
3395 SliderPanel.showConservationSlider();
3399 * Action on selecting or deselecting (Colour) By Conservation
3402 public void conservationMenuItem_actionPerformed(boolean selected)
3404 modifyConservation.setEnabled(selected);
3405 viewport.setConservationSelected(selected);
3406 viewport.getResidueShading().setConservationApplied(selected);
3408 changeColour(viewport.getGlobalColourScheme());
3411 modifyConservation_actionPerformed();
3415 SliderPanel.hideConservationSlider();
3420 * Action on selecting or deselecting (Colour) Above PID Threshold
3423 public void abovePIDThreshold_actionPerformed(boolean selected)
3425 modifyPID.setEnabled(selected);
3426 viewport.setAbovePIDThreshold(selected);
3429 viewport.getResidueShading().setThreshold(0,
3430 viewport.isIgnoreGapsConsensus());
3433 changeColour(viewport.getGlobalColourScheme());
3436 modifyPID_actionPerformed();
3440 SliderPanel.hidePIDSlider();
3451 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3453 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3454 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3455 .getAlignment().getSequenceAt(0));
3456 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3457 viewport.getAlignment()));
3458 alignPanel.paintAlignment(true);
3468 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3470 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3471 AlignmentSorter.sortByID(viewport.getAlignment());
3472 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3473 viewport.getAlignment()));
3474 alignPanel.paintAlignment(true);
3484 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3486 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3487 AlignmentSorter.sortByLength(viewport.getAlignment());
3488 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3489 viewport.getAlignment()));
3490 alignPanel.paintAlignment(true);
3500 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3502 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3503 AlignmentSorter.sortByGroup(viewport.getAlignment());
3504 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3505 viewport.getAlignment()));
3507 alignPanel.paintAlignment(true);
3517 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3519 new RedundancyPanel(alignPanel, this);
3529 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3531 if ((viewport.getSelectionGroup() == null)
3532 || (viewport.getSelectionGroup().getSize() < 2))
3534 JvOptionPane.showInternalMessageDialog(this, MessageManager
3535 .getString("label.you_must_select_least_two_sequences"),
3536 MessageManager.getString("label.invalid_selection"),
3537 JvOptionPane.WARNING_MESSAGE);
3541 JInternalFrame frame = new JInternalFrame();
3542 frame.setContentPane(new PairwiseAlignPanel(viewport));
3543 Desktop.addInternalFrame(frame,
3544 MessageManager.getString("action.pairwise_alignment"), 600,
3550 public void autoCalculate_actionPerformed(ActionEvent e)
3552 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3553 if (viewport.autoCalculateConsensus)
3555 viewport.firePropertyChange("alignment", null, viewport
3556 .getAlignment().getSequences());
3561 public void sortByTreeOption_actionPerformed(ActionEvent e)
3563 viewport.sortByTree = sortByTree.isSelected();
3567 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3569 viewport.followSelection = listenToViewSelections.isSelected();
3573 * Constructs a tree panel and adds it to the desktop
3576 * tree type (NJ or AV)
3578 * name of score model used to compute the tree
3580 * parameters for the distance or similarity calculation
3582 void newTreePanel(String type, String modelName, SimilarityParamsI options)
3584 String frameTitle = "";
3587 boolean onSelection = false;
3588 if (viewport.getSelectionGroup() != null
3589 && viewport.getSelectionGroup().getSize() > 0)
3591 SequenceGroup sg = viewport.getSelectionGroup();
3593 /* Decide if the selection is a column region */
3594 for (SequenceI _s : sg.getSequences())
3596 if (_s.getLength() < sg.getEndRes())
3602 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3604 .getString("label.sequences_selection_not_aligned"),
3605 JvOptionPane.WARNING_MESSAGE);
3614 if (viewport.getAlignment().getHeight() < 2)
3620 tp = new TreePanel(alignPanel, type, modelName, options);
3621 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3623 frameTitle += " from ";
3625 if (viewport.viewName != null)
3627 frameTitle += viewport.viewName + " of ";
3630 frameTitle += this.title;
3632 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3643 public void addSortByOrderMenuItem(String title,
3644 final AlignmentOrder order)
3646 final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
3647 "action.by_title_param", new Object[] { title }));
3649 item.addActionListener(new java.awt.event.ActionListener()
3652 public void actionPerformed(ActionEvent e)
3654 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3656 // TODO: JBPNote - have to map order entries to curent SequenceI
3658 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3660 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3663 alignPanel.paintAlignment(true);
3669 * Add a new sort by annotation score menu item
3672 * the menu to add the option to
3674 * the label used to retrieve scores for each sequence on the
3677 public void addSortByAnnotScoreMenuItem(JMenu sort,
3678 final String scoreLabel)
3680 final JMenuItem item = new JMenuItem(scoreLabel);
3682 item.addActionListener(new java.awt.event.ActionListener()
3685 public void actionPerformed(ActionEvent e)
3687 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3688 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3689 viewport.getAlignment());// ,viewport.getSelectionGroup());
3690 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3691 viewport.getAlignment()));
3692 alignPanel.paintAlignment(true);
3698 * last hash for alignment's annotation array - used to minimise cost of
3701 protected int _annotationScoreVectorHash;
3704 * search the alignment and rebuild the sort by annotation score submenu the
3705 * last alignment annotation vector hash is stored to minimize cost of
3706 * rebuilding in subsequence calls.
3710 public void buildSortByAnnotationScoresMenu()
3712 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3717 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3719 sortByAnnotScore.removeAll();
3720 // almost certainly a quicker way to do this - but we keep it simple
3721 Hashtable scoreSorts = new Hashtable();
3722 AlignmentAnnotation aann[];
3723 for (SequenceI sqa : viewport.getAlignment().getSequences())
3725 aann = sqa.getAnnotation();
3726 for (int i = 0; aann != null && i < aann.length; i++)
3728 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3730 scoreSorts.put(aann[i].label, aann[i].label);
3734 Enumeration labels = scoreSorts.keys();
3735 while (labels.hasMoreElements())
3737 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3738 (String) labels.nextElement());
3740 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3743 _annotationScoreVectorHash = viewport.getAlignment()
3744 .getAlignmentAnnotation().hashCode();
3749 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3750 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3751 * call. Listeners are added to remove the menu item when the treePanel is
3752 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3756 public void buildTreeSortMenu()
3758 sortByTreeMenu.removeAll();
3760 List<Component> comps = PaintRefresher.components.get(viewport
3761 .getSequenceSetId());
3762 List<TreePanel> treePanels = new ArrayList<>();
3763 for (Component comp : comps)
3765 if (comp instanceof TreePanel)
3767 treePanels.add((TreePanel) comp);
3771 if (treePanels.size() < 1)
3773 sortByTreeMenu.setVisible(false);
3777 sortByTreeMenu.setVisible(true);
3779 for (final TreePanel tp : treePanels)
3781 final JMenuItem item = new JMenuItem(tp.getTitle());
3782 item.addActionListener(new java.awt.event.ActionListener()
3785 public void actionPerformed(ActionEvent e)
3787 tp.sortByTree_actionPerformed();
3788 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3793 sortByTreeMenu.add(item);
3797 public boolean sortBy(AlignmentOrder alorder, String undoname)
3799 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3800 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3801 if (undoname != null)
3803 addHistoryItem(new OrderCommand(undoname, oldOrder,
3804 viewport.getAlignment()));
3806 alignPanel.paintAlignment(true);
3811 * Work out whether the whole set of sequences or just the selected set will
3812 * be submitted for multiple alignment.
3815 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3817 // Now, check we have enough sequences
3818 AlignmentView msa = null;
3820 if ((viewport.getSelectionGroup() != null)
3821 && (viewport.getSelectionGroup().getSize() > 1))
3823 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3824 // some common interface!
3826 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3827 * SequenceI[sz = seqs.getSize(false)];
3829 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3830 * seqs.getSequenceAt(i); }
3832 msa = viewport.getAlignmentView(true);
3834 else if (viewport.getSelectionGroup() != null
3835 && viewport.getSelectionGroup().getSize() == 1)
3837 int option = JvOptionPane.showConfirmDialog(this,
3838 MessageManager.getString("warn.oneseq_msainput_selection"),
3839 MessageManager.getString("label.invalid_selection"),
3840 JvOptionPane.OK_CANCEL_OPTION);
3841 if (option == JvOptionPane.OK_OPTION)
3843 msa = viewport.getAlignmentView(false);
3848 msa = viewport.getAlignmentView(false);
3854 * Decides what is submitted to a secondary structure prediction service: the
3855 * first sequence in the alignment, or in the current selection, or, if the
3856 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3857 * region or the whole alignment. (where the first sequence in the set is the
3858 * one that the prediction will be for).
3860 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3862 AlignmentView seqs = null;
3864 if ((viewport.getSelectionGroup() != null)
3865 && (viewport.getSelectionGroup().getSize() > 0))
3867 seqs = viewport.getAlignmentView(true);
3871 seqs = viewport.getAlignmentView(false);
3873 // limit sequences - JBPNote in future - could spawn multiple prediction
3875 // TODO: viewport.getAlignment().isAligned is a global state - the local
3876 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3877 if (!viewport.getAlignment().isAligned(false))
3879 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3880 // TODO: if seqs.getSequences().length>1 then should really have warned
3894 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3896 // Pick the tree file
3897 JalviewFileChooser chooser = new JalviewFileChooser(
3898 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3899 chooser.setFileView(new JalviewFileView());
3900 chooser.setDialogTitle(MessageManager
3901 .getString("label.select_newick_like_tree_file"));
3902 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
3904 int value = chooser.showOpenDialog(null);
3906 if (value == JalviewFileChooser.APPROVE_OPTION)
3908 String filePath = chooser.getSelectedFile().getPath();
3909 Cache.setProperty("LAST_DIRECTORY", filePath);
3910 NewickFile fin = null;
3913 fin = new NewickFile(filePath, DataSourceType.FILE);
3914 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3915 } catch (Exception ex)
3922 .getString("label.problem_reading_tree_file"),
3923 JvOptionPane.WARNING_MESSAGE);
3924 ex.printStackTrace();
3926 if (fin != null && fin.hasWarningMessage())
3928 JvOptionPane.showMessageDialog(Desktop.desktop, fin
3929 .getWarningMessage(), MessageManager
3930 .getString("label.possible_problem_with_tree_file"),
3931 JvOptionPane.WARNING_MESSAGE);
3936 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3938 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3941 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3942 int h, int x, int y)
3944 return showNewickTree(nf, treeTitle, null, w, h, x, y);
3948 * Add a treeviewer for the tree extracted from a Newick file object to the
3949 * current alignment view
3956 * Associated alignment input data (or null)
3965 * @return TreePanel handle
3967 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3968 AlignmentView input, int w, int h, int x, int y)
3970 TreePanel tp = null;
3976 if (nf.getTree() != null)
3978 tp = new TreePanel(alignPanel, nf, treeTitle, input);
3984 tp.setLocation(x, y);
3987 Desktop.addInternalFrame(tp, treeTitle, w, h);
3989 } catch (Exception ex)
3991 ex.printStackTrace();
3997 private boolean buildingMenu = false;
4000 * Generates menu items and listener event actions for web service clients
4003 public void BuildWebServiceMenu()
4005 while (buildingMenu)
4009 System.err.println("Waiting for building menu to finish.");
4011 } catch (Exception e)
4015 final AlignFrame me = this;
4016 buildingMenu = true;
4017 new Thread(new Runnable()
4022 final List<JMenuItem> legacyItems = new ArrayList<>();
4025 // System.err.println("Building ws menu again "
4026 // + Thread.currentThread());
4027 // TODO: add support for context dependent disabling of services based
4029 // alignment and current selection
4030 // TODO: add additional serviceHandle parameter to specify abstract
4032 // class independently of AbstractName
4033 // TODO: add in rediscovery GUI function to restart discoverer
4034 // TODO: group services by location as well as function and/or
4036 // object broker mechanism.
4037 final Vector<JMenu> wsmenu = new Vector<>();
4038 final IProgressIndicator af = me;
4041 * do not i18n these strings - they are hard-coded in class
4042 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4043 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4045 final JMenu msawsmenu = new JMenu("Alignment");
4046 final JMenu secstrmenu = new JMenu(
4047 "Secondary Structure Prediction");
4048 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4049 final JMenu analymenu = new JMenu("Analysis");
4050 final JMenu dismenu = new JMenu("Protein Disorder");
4051 // JAL-940 - only show secondary structure prediction services from
4052 // the legacy server
4053 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4055 Discoverer.services != null && (Discoverer.services.size() > 0))
4057 // TODO: refactor to allow list of AbstractName/Handler bindings to
4059 // stored or retrieved from elsewhere
4060 // No MSAWS used any more:
4061 // Vector msaws = null; // (Vector)
4062 // Discoverer.services.get("MsaWS");
4063 Vector secstrpr = (Vector) Discoverer.services
4065 if (secstrpr != null)
4067 // Add any secondary structure prediction services
4068 for (int i = 0, j = secstrpr.size(); i < j; i++)
4070 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4072 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4073 .getServiceClient(sh);
4074 int p = secstrmenu.getItemCount();
4075 impl.attachWSMenuEntry(secstrmenu, me);
4076 int q = secstrmenu.getItemCount();
4077 for (int litm = p; litm < q; litm++)
4079 legacyItems.add(secstrmenu.getItem(litm));
4085 // Add all submenus in the order they should appear on the web
4087 wsmenu.add(msawsmenu);
4088 wsmenu.add(secstrmenu);
4089 wsmenu.add(dismenu);
4090 wsmenu.add(analymenu);
4091 // No search services yet
4092 // wsmenu.add(seqsrchmenu);
4094 javax.swing.SwingUtilities.invokeLater(new Runnable()
4101 webService.removeAll();
4102 // first, add discovered services onto the webservices menu
4103 if (wsmenu.size() > 0)
4105 for (int i = 0, j = wsmenu.size(); i < j; i++)
4107 webService.add(wsmenu.get(i));
4112 webService.add(me.webServiceNoServices);
4114 // TODO: move into separate menu builder class.
4115 boolean new_sspred = false;
4116 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4118 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4119 if (jws2servs != null)
4121 if (jws2servs.hasServices())
4123 jws2servs.attachWSMenuEntry(webService, me);
4124 for (Jws2Instance sv : jws2servs.getServices())
4126 if (sv.description.toLowerCase().contains("jpred"))
4128 for (JMenuItem jmi : legacyItems)
4130 jmi.setVisible(false);
4136 if (jws2servs.isRunning())
4138 JMenuItem tm = new JMenuItem(
4139 "Still discovering JABA Services");
4140 tm.setEnabled(false);
4145 build_urlServiceMenu(me.webService);
4146 build_fetchdbmenu(webService);
4147 for (JMenu item : wsmenu)
4149 if (item.getItemCount() == 0)
4151 item.setEnabled(false);
4155 item.setEnabled(true);
4158 } catch (Exception e)
4161 .debug("Exception during web service menu building process.",
4166 } catch (Exception e)
4169 buildingMenu = false;
4176 * construct any groupURL type service menu entries.
4180 private void build_urlServiceMenu(JMenu webService)
4182 // TODO: remove this code when 2.7 is released
4183 // DEBUG - alignmentView
4185 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4186 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4188 * @Override public void actionPerformed(ActionEvent e) {
4189 * jalview.datamodel.AlignmentView
4190 * .testSelectionViews(af.viewport.getAlignment(),
4191 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4193 * }); webService.add(testAlView);
4195 // TODO: refactor to RestClient discoverer and merge menu entries for
4196 // rest-style services with other types of analysis/calculation service
4197 // SHmmr test client - still being implemented.
4198 // DEBUG - alignmentView
4200 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4203 client.attachWSMenuEntry(
4204 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4210 * Searches the alignment sequences for xRefs and builds the Show
4211 * Cross-References menu (formerly called Show Products), with database
4212 * sources for which cross-references are found (protein sources for a
4213 * nucleotide alignment and vice versa)
4215 * @return true if Show Cross-references menu should be enabled
4217 public boolean canShowProducts()
4219 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4220 AlignmentI dataset = viewport.getAlignment().getDataset();
4222 showProducts.removeAll();
4223 final boolean dna = viewport.getAlignment().isNucleotide();
4225 if (seqs == null || seqs.length == 0)
4227 // nothing to see here.
4231 boolean showp = false;
4234 List<String> ptypes = new CrossRef(seqs, dataset)
4235 .findXrefSourcesForSequences(dna);
4237 for (final String source : ptypes)
4240 final AlignFrame af = this;
4241 JMenuItem xtype = new JMenuItem(source);
4242 xtype.addActionListener(new ActionListener()
4245 public void actionPerformed(ActionEvent e)
4247 showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4250 showProducts.add(xtype);
4252 showProducts.setVisible(showp);
4253 showProducts.setEnabled(showp);
4254 } catch (Exception e)
4257 .warn("canShowProducts threw an exception - please report to help@jalview.org",
4265 * Finds and displays cross-references for the selected sequences (protein
4266 * products for nucleotide sequences, dna coding sequences for peptides).
4269 * the sequences to show cross-references for
4271 * true if from a nucleotide alignment (so showing proteins)
4273 * the database to show cross-references for
4275 protected void showProductsFor(final SequenceI[] sel,
4276 final boolean _odna, final String source)
4278 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4283 * Construct and display a new frame containing the translation of this
4284 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4287 public void showTranslation_actionPerformed(ActionEvent e)
4289 AlignmentI al = null;
4292 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4294 al = dna.translateCdna();
4295 } catch (Exception ex)
4297 jalview.bin.Cache.log.error(
4298 "Exception during translation. Please report this !", ex);
4299 final String msg = MessageManager
4300 .getString("label.error_when_translating_sequences_submit_bug_report");
4301 final String errorTitle = MessageManager
4302 .getString("label.implementation_error")
4303 + MessageManager.getString("label.translation_failed");
4304 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4305 JvOptionPane.ERROR_MESSAGE);
4308 if (al == null || al.getHeight() == 0)
4310 final String msg = MessageManager
4311 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4312 final String errorTitle = MessageManager
4313 .getString("label.translation_failed");
4314 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4315 JvOptionPane.WARNING_MESSAGE);
4319 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4320 af.setFileFormat(this.currentFileFormat);
4321 final String newTitle = MessageManager.formatMessage(
4322 "label.translation_of_params",
4323 new Object[] { this.getTitle() });
4324 af.setTitle(newTitle);
4325 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4327 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4328 viewport.openSplitFrame(af, new Alignment(seqs));
4332 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4339 * Set the file format
4343 public void setFileFormat(FileFormatI format)
4345 this.currentFileFormat = format;
4349 * Try to load a features file onto the alignment.
4352 * contents or path to retrieve file
4354 * access mode of file (see jalview.io.AlignFile)
4355 * @return true if features file was parsed correctly.
4357 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4359 return avc.parseFeaturesFile(file, sourceType,
4360 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4365 public void refreshFeatureUI(boolean enableIfNecessary)
4367 // note - currently this is only still here rather than in the controller
4368 // because of the featureSettings hard reference that is yet to be
4370 if (enableIfNecessary)
4372 viewport.setShowSequenceFeatures(true);
4373 showSeqFeatures.setSelected(true);
4379 public void dragEnter(DropTargetDragEvent evt)
4384 public void dragExit(DropTargetEvent evt)
4389 public void dragOver(DropTargetDragEvent evt)
4394 public void dropActionChanged(DropTargetDragEvent evt)
4399 public void drop(DropTargetDropEvent evt)
4401 // JAL-1552 - acceptDrop required before getTransferable call for
4402 // Java's Transferable for native dnd
4403 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4404 Transferable t = evt.getTransferable();
4405 List<String> files = new ArrayList<>();
4406 List<DataSourceType> protocols = new ArrayList<>();
4410 Desktop.transferFromDropTarget(files, protocols, evt, t);
4411 } catch (Exception e)
4413 e.printStackTrace();
4419 // check to see if any of these files have names matching sequences in
4421 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4422 .getAlignment().getSequencesArray());
4424 * Object[] { String,SequenceI}
4426 ArrayList<Object[]> filesmatched = new ArrayList<>();
4427 ArrayList<String> filesnotmatched = new ArrayList<>();
4428 for (int i = 0; i < files.size(); i++)
4430 String file = files.get(i).toString();
4432 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4433 if (protocol == DataSourceType.FILE)
4435 File fl = new File(file);
4436 pdbfn = fl.getName();
4438 else if (protocol == DataSourceType.URL)
4440 URL url = new URL(file);
4441 pdbfn = url.getFile();
4443 if (pdbfn.length() > 0)
4445 // attempt to find a match in the alignment
4446 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4447 int l = 0, c = pdbfn.indexOf(".");
4448 while (mtch == null && c != -1)
4453 } while ((c = pdbfn.indexOf(".", l)) > l);
4456 pdbfn = pdbfn.substring(0, l);
4458 mtch = idm.findAllIdMatches(pdbfn);
4462 FileFormatI type = null;
4465 type = new IdentifyFile().identify(file, protocol);
4466 } catch (Exception ex)
4470 if (type != null && type.isStructureFile())
4472 filesmatched.add(new Object[] { file, protocol, mtch });
4476 // File wasn't named like one of the sequences or wasn't a PDB file.
4477 filesnotmatched.add(file);
4481 if (filesmatched.size() > 0)
4483 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4489 "label.automatically_associate_structure_files_with_sequences_same_name",
4490 new Object[] { Integer
4496 .getString("label.automatically_associate_structure_files_by_name"),
4497 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4500 for (Object[] fm : filesmatched)
4502 // try and associate
4503 // TODO: may want to set a standard ID naming formalism for
4504 // associating PDB files which have no IDs.
4505 for (SequenceI toassoc : (SequenceI[]) fm[2])
4507 PDBEntry pe = new AssociatePdbFileWithSeq()
4508 .associatePdbWithSeq((String) fm[0],
4509 (DataSourceType) fm[1], toassoc, false,
4513 System.err.println("Associated file : "
4514 + ((String) fm[0]) + " with "
4515 + toassoc.getDisplayId(true));
4519 alignPanel.paintAlignment(true);
4523 if (filesnotmatched.size() > 0)
4526 && (Cache.getDefault(
4527 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4533 "label.ignore_unmatched_dropped_files_info",
4534 new Object[] { Integer
4541 .getString("label.ignore_unmatched_dropped_files"),
4542 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4546 for (String fn : filesnotmatched)
4548 loadJalviewDataFile(fn, null, null, null);
4552 } catch (Exception ex)
4554 ex.printStackTrace();
4560 * Attempt to load a "dropped" file or URL string, by testing in turn for
4562 * <li>an Annotation file</li>
4563 * <li>a JNet file</li>
4564 * <li>a features file</li>
4565 * <li>else try to interpret as an alignment file</li>
4569 * either a filename or a URL string.
4571 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4572 FileFormatI format, SequenceI assocSeq)
4576 if (sourceType == null)
4578 sourceType = FormatAdapter.checkProtocol(file);
4580 // if the file isn't identified, or not positively identified as some
4581 // other filetype (PFAM is default unidentified alignment file type) then
4582 // try to parse as annotation.
4583 boolean isAnnotation = (format == null || FileFormat.Pfam
4584 .equals(format)) ? new AnnotationFile()
4585 .annotateAlignmentView(viewport, file, sourceType) : false;
4589 // first see if its a T-COFFEE score file
4590 TCoffeeScoreFile tcf = null;
4593 tcf = new TCoffeeScoreFile(file, sourceType);
4596 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4599 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4600 isAnnotation = true;
4602 .setText(MessageManager
4603 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4607 // some problem - if no warning its probable that the ID matching
4608 // process didn't work
4612 tcf.getWarningMessage() == null ? MessageManager
4613 .getString("label.check_file_matches_sequence_ids_alignment")
4614 : tcf.getWarningMessage(),
4616 .getString("label.problem_reading_tcoffee_score_file"),
4617 JvOptionPane.WARNING_MESSAGE);
4624 } catch (Exception x)
4627 .debug("Exception when processing data source as T-COFFEE score file",
4633 // try to see if its a JNet 'concise' style annotation file *before*
4635 // try to parse it as a features file
4638 format = new IdentifyFile().identify(file, sourceType);
4640 if (FileFormat.ScoreMatrix == format)
4642 ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
4645 // todo: i18n this message
4647 .setText(MessageManager.formatMessage(
4648 "label.successfully_loaded_matrix",
4649 sm.getMatrixName()));
4651 else if (FileFormat.Jnet.equals(format))
4653 JPredFile predictions = new JPredFile(file, sourceType);
4654 new JnetAnnotationMaker();
4655 JnetAnnotationMaker.add_annotation(predictions,
4656 viewport.getAlignment(), 0, false);
4657 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4658 viewport.getAlignment().setSeqrep(repseq);
4659 HiddenColumns cs = new HiddenColumns();
4660 cs.hideInsertionsFor(repseq);
4661 viewport.getAlignment().setHiddenColumns(cs);
4662 isAnnotation = true;
4664 // else if (IdentifyFile.FeaturesFile.equals(format))
4665 else if (FileFormat.Features.equals(format))
4667 if (parseFeaturesFile(file, sourceType))
4669 alignPanel.paintAlignment(true);
4674 new FileLoader().LoadFile(viewport, file, sourceType, format);
4681 alignPanel.adjustAnnotationHeight();
4682 viewport.updateSequenceIdColours();
4683 buildSortByAnnotationScoresMenu();
4684 alignPanel.paintAlignment(true);
4686 } catch (Exception ex)
4688 ex.printStackTrace();
4689 } catch (OutOfMemoryError oom)
4694 } catch (Exception x)
4699 + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
4700 : "using " + sourceType + " from " + file)
4702 + (format != null ? "(parsing as '" + format
4703 + "' file)" : ""), oom, Desktop.desktop);
4708 * Method invoked by the ChangeListener on the tabbed pane, in other words
4709 * when a different tabbed pane is selected by the user or programmatically.
4712 public void tabSelectionChanged(int index)
4716 alignPanel = alignPanels.get(index);
4717 viewport = alignPanel.av;
4718 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4719 setMenusFromViewport(viewport);
4723 * 'focus' any colour slider that is open to the selected viewport
4725 if (viewport.getConservationSelected())
4727 SliderPanel.setConservationSlider(alignPanel,
4728 viewport.getResidueShading(), alignPanel.getViewName());
4732 SliderPanel.hideConservationSlider();
4734 if (viewport.getAbovePIDThreshold())
4736 SliderPanel.setPIDSliderSource(alignPanel,
4737 viewport.getResidueShading(), alignPanel.getViewName());
4741 SliderPanel.hidePIDSlider();
4745 * If there is a frame linked to this one in a SplitPane, switch it to the
4746 * same view tab index. No infinite recursion of calls should happen, since
4747 * tabSelectionChanged() should not get invoked on setting the selected
4748 * index to an unchanged value. Guard against setting an invalid index
4749 * before the new view peer tab has been created.
4751 final AlignViewportI peer = viewport.getCodingComplement();
4754 AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
4755 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4757 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4763 * On right mouse click on view tab, prompt for and set new view name.
4766 public void tabbedPane_mousePressed(MouseEvent e)
4768 if (e.isPopupTrigger())
4770 String msg = MessageManager.getString("label.enter_view_name");
4771 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4772 JvOptionPane.QUESTION_MESSAGE);
4776 viewport.viewName = reply;
4777 // TODO warn if reply is in getExistingViewNames()?
4778 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4783 public AlignViewport getCurrentView()
4789 * Open the dialog for regex description parsing.
4792 protected void extractScores_actionPerformed(ActionEvent e)
4794 ParseProperties pp = new jalview.analysis.ParseProperties(
4795 viewport.getAlignment());
4796 // TODO: verify regex and introduce GUI dialog for version 2.5
4797 // if (pp.getScoresFromDescription("col", "score column ",
4798 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4800 if (pp.getScoresFromDescription("description column",
4801 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4803 buildSortByAnnotationScoresMenu();
4811 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4815 protected void showDbRefs_actionPerformed(ActionEvent e)
4817 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4823 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4827 protected void showNpFeats_actionPerformed(ActionEvent e)
4829 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4833 * find the viewport amongst the tabs in this alignment frame and close that
4838 public boolean closeView(AlignViewportI av)
4842 this.closeMenuItem_actionPerformed(false);
4845 Component[] comp = tabbedPane.getComponents();
4846 for (int i = 0; comp != null && i < comp.length; i++)
4848 if (comp[i] instanceof AlignmentPanel)
4850 if (((AlignmentPanel) comp[i]).av == av)
4853 closeView((AlignmentPanel) comp[i]);
4861 protected void build_fetchdbmenu(JMenu webService)
4863 // Temporary hack - DBRef Fetcher always top level ws entry.
4864 // TODO We probably want to store a sequence database checklist in
4865 // preferences and have checkboxes.. rather than individual sources selected
4867 final JMenu rfetch = new JMenu(
4868 MessageManager.getString("action.fetch_db_references"));
4869 rfetch.setToolTipText(MessageManager
4870 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4871 webService.add(rfetch);
4873 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4874 MessageManager.getString("option.trim_retrieved_seqs"));
4875 trimrs.setToolTipText(MessageManager
4876 .getString("label.trim_retrieved_sequences"));
4877 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
4878 trimrs.addActionListener(new ActionListener()
4881 public void actionPerformed(ActionEvent e)
4883 trimrs.setSelected(trimrs.isSelected());
4884 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
4885 Boolean.valueOf(trimrs.isSelected()).toString());
4889 JMenuItem fetchr = new JMenuItem(
4890 MessageManager.getString("label.standard_databases"));
4891 fetchr.setToolTipText(MessageManager
4892 .getString("label.fetch_embl_uniprot"));
4893 fetchr.addActionListener(new ActionListener()
4897 public void actionPerformed(ActionEvent e)
4899 new Thread(new Runnable()
4904 boolean isNucleotide = alignPanel.alignFrame.getViewport()
4905 .getAlignment().isNucleotide();
4906 DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
4907 .getSequenceSelection(), alignPanel.alignFrame, null,
4908 alignPanel.alignFrame.featureSettings, isNucleotide);
4909 dbRefFetcher.addListener(new FetchFinishedListenerI()
4912 public void finished()
4914 AlignFrame.this.setMenusForViewport();
4917 dbRefFetcher.fetchDBRefs(false);
4925 final AlignFrame me = this;
4926 new Thread(new Runnable()
4931 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4932 .getSequenceFetcherSingleton(me);
4933 javax.swing.SwingUtilities.invokeLater(new Runnable()
4938 String[] dbclasses = sf.getOrderedSupportedSources();
4939 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4940 // jalview.util.QuickSort.sort(otherdb, otherdb);
4941 List<DbSourceProxy> otherdb;
4942 JMenu dfetch = new JMenu();
4943 JMenu ifetch = new JMenu();
4944 JMenuItem fetchr = null;
4945 int comp = 0, icomp = 0, mcomp = 15;
4946 String mname = null;
4948 for (String dbclass : dbclasses)
4950 otherdb = sf.getSourceProxy(dbclass);
4951 // add a single entry for this class, or submenu allowing 'fetch
4953 if (otherdb == null || otherdb.size() < 1)
4957 // List<DbSourceProxy> dbs=otherdb;
4958 // otherdb=new ArrayList<DbSourceProxy>();
4959 // for (DbSourceProxy db:dbs)
4961 // if (!db.isA(DBRefSource.ALIGNMENTDB)
4965 mname = "From " + dbclass;
4967 if (otherdb.size() == 1)
4969 final DbSourceProxy[] dassource = otherdb
4970 .toArray(new DbSourceProxy[0]);
4971 DbSourceProxy src = otherdb.get(0);
4972 fetchr = new JMenuItem(src.getDbSource());
4973 fetchr.addActionListener(new ActionListener()
4977 public void actionPerformed(ActionEvent e)
4979 new Thread(new Runnable()
4985 boolean isNucleotide = alignPanel.alignFrame
4986 .getViewport().getAlignment()
4988 DBRefFetcher dbRefFetcher = new DBRefFetcher(
4989 alignPanel.av.getSequenceSelection(),
4990 alignPanel.alignFrame, dassource,
4991 alignPanel.alignFrame.featureSettings,
4994 .addListener(new FetchFinishedListenerI()
4997 public void finished()
4999 AlignFrame.this.setMenusForViewport();
5002 dbRefFetcher.fetchDBRefs(false);
5008 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5009 MessageManager.formatMessage(
5010 "label.fetch_retrieve_from",
5011 new Object[] { src.getDbName() })));
5017 final DbSourceProxy[] dassource = otherdb
5018 .toArray(new DbSourceProxy[0]);
5020 DbSourceProxy src = otherdb.get(0);
5021 fetchr = new JMenuItem(MessageManager.formatMessage(
5022 "label.fetch_all_param",
5023 new Object[] { src.getDbSource() }));
5024 fetchr.addActionListener(new ActionListener()
5027 public void actionPerformed(ActionEvent e)
5029 new Thread(new Runnable()
5035 boolean isNucleotide = alignPanel.alignFrame
5036 .getViewport().getAlignment()
5038 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5039 alignPanel.av.getSequenceSelection(),
5040 alignPanel.alignFrame, dassource,
5041 alignPanel.alignFrame.featureSettings,
5044 .addListener(new FetchFinishedListenerI()
5047 public void finished()
5049 AlignFrame.this.setMenusForViewport();
5052 dbRefFetcher.fetchDBRefs(false);
5058 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5059 MessageManager.formatMessage(
5060 "label.fetch_retrieve_from_all_sources",
5062 Integer.valueOf(otherdb.size())
5063 .toString(), src.getDbSource(),
5064 src.getDbName() })));
5067 // and then build the rest of the individual menus
5068 ifetch = new JMenu(MessageManager.formatMessage(
5069 "label.source_from_db_source",
5070 new Object[] { src.getDbSource() }));
5072 String imname = null;
5074 for (DbSourceProxy sproxy : otherdb)
5076 String dbname = sproxy.getDbName();
5077 String sname = dbname.length() > 5 ? dbname.substring(0,
5078 5) + "..." : dbname;
5079 String msname = dbname.length() > 10 ? dbname.substring(
5080 0, 10) + "..." : dbname;
5083 imname = MessageManager.formatMessage(
5084 "label.from_msname", new Object[] { sname });
5086 fetchr = new JMenuItem(msname);
5087 final DbSourceProxy[] dassrc = { sproxy };
5088 fetchr.addActionListener(new ActionListener()
5092 public void actionPerformed(ActionEvent e)
5094 new Thread(new Runnable()
5100 boolean isNucleotide = alignPanel.alignFrame
5101 .getViewport().getAlignment()
5103 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5104 alignPanel.av.getSequenceSelection(),
5105 alignPanel.alignFrame, dassrc,
5106 alignPanel.alignFrame.featureSettings,
5109 .addListener(new FetchFinishedListenerI()
5112 public void finished()
5114 AlignFrame.this.setMenusForViewport();
5117 dbRefFetcher.fetchDBRefs(false);
5123 fetchr.setToolTipText("<html>"
5124 + MessageManager.formatMessage(
5125 "label.fetch_retrieve_from", new Object[]
5129 if (++icomp >= mcomp || i == (otherdb.size()))
5131 ifetch.setText(MessageManager.formatMessage(
5132 "label.source_to_target", imname, sname));
5134 ifetch = new JMenu();
5142 if (comp >= mcomp || dbi >= (dbclasses.length))
5144 dfetch.setText(MessageManager.formatMessage(
5145 "label.source_to_target", mname, dbclass));
5147 dfetch = new JMenu();
5160 * Left justify the whole alignment.
5163 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5165 AlignmentI al = viewport.getAlignment();
5167 viewport.firePropertyChange("alignment", null, al);
5171 * Right justify the whole alignment.
5174 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5176 AlignmentI al = viewport.getAlignment();
5178 viewport.firePropertyChange("alignment", null, al);
5182 public void setShowSeqFeatures(boolean b)
5184 showSeqFeatures.setSelected(b);
5185 viewport.setShowSequenceFeatures(b);
5192 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5193 * awt.event.ActionEvent)
5196 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5198 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5199 alignPanel.paintAlignment(true);
5206 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5210 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5212 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5213 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5221 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5222 * .event.ActionEvent)
5225 protected void showGroupConservation_actionPerformed(ActionEvent e)
5227 viewport.setShowGroupConservation(showGroupConservation.getState());
5228 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5235 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5236 * .event.ActionEvent)
5239 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5241 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5242 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5249 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5250 * .event.ActionEvent)
5253 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5255 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5256 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5260 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5262 showSequenceLogo.setState(true);
5263 viewport.setShowSequenceLogo(true);
5264 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5265 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5269 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5271 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5278 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5279 * .event.ActionEvent)
5282 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5284 if (avc.makeGroupsFromSelection())
5286 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5287 alignPanel.updateAnnotation();
5288 alignPanel.paintAlignment(true);
5292 public void clearAlignmentSeqRep()
5294 // TODO refactor alignmentseqrep to controller
5295 if (viewport.getAlignment().hasSeqrep())
5297 viewport.getAlignment().setSeqrep(null);
5298 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5299 alignPanel.updateAnnotation();
5300 alignPanel.paintAlignment(true);
5305 protected void createGroup_actionPerformed(ActionEvent e)
5307 if (avc.createGroup())
5309 alignPanel.alignmentChanged();
5314 protected void unGroup_actionPerformed(ActionEvent e)
5318 alignPanel.alignmentChanged();
5323 * make the given alignmentPanel the currently selected tab
5325 * @param alignmentPanel
5327 public void setDisplayedView(AlignmentPanel alignmentPanel)
5329 if (!viewport.getSequenceSetId().equals(
5330 alignmentPanel.av.getSequenceSetId()))
5334 .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5336 if (tabbedPane != null
5337 && tabbedPane.getTabCount() > 0
5338 && alignPanels.indexOf(alignmentPanel) != tabbedPane
5339 .getSelectedIndex())
5341 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5346 * Action on selection of menu options to Show or Hide annotations.
5349 * @param forSequences
5350 * update sequence-related annotations
5351 * @param forAlignment
5352 * update non-sequence-related annotations
5355 protected void setAnnotationsVisibility(boolean visible,
5356 boolean forSequences, boolean forAlignment)
5358 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5359 .getAlignmentAnnotation();
5364 for (AlignmentAnnotation aa : anns)
5367 * don't display non-positional annotations on an alignment
5369 if (aa.annotations == null)
5373 boolean apply = (aa.sequenceRef == null && forAlignment)
5374 || (aa.sequenceRef != null && forSequences);
5377 aa.visible = visible;
5380 alignPanel.validateAnnotationDimensions(true);
5381 alignPanel.alignmentChanged();
5385 * Store selected annotation sort order for the view and repaint.
5388 protected void sortAnnotations_actionPerformed()
5390 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5392 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5393 alignPanel.paintAlignment(true);
5398 * @return alignment panels in this alignment frame
5400 public List<? extends AlignmentViewPanel> getAlignPanels()
5402 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5406 * Open a new alignment window, with the cDNA associated with this (protein)
5407 * alignment, aligned as is the protein.
5409 protected void viewAsCdna_actionPerformed()
5411 // TODO no longer a menu action - refactor as required
5412 final AlignmentI alignment = getViewport().getAlignment();
5413 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5414 if (mappings == null)
5418 List<SequenceI> cdnaSeqs = new ArrayList<>();
5419 for (SequenceI aaSeq : alignment.getSequences())
5421 for (AlignedCodonFrame acf : mappings)
5423 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5427 * There is a cDNA mapping for this protein sequence - add to new
5428 * alignment. It will share the same dataset sequence as other mapped
5429 * cDNA (no new mappings need to be created).
5431 final Sequence newSeq = new Sequence(dnaSeq);
5432 newSeq.setDatasetSequence(dnaSeq);
5433 cdnaSeqs.add(newSeq);
5437 if (cdnaSeqs.size() == 0)
5439 // show a warning dialog no mapped cDNA
5442 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5444 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5445 AlignFrame.DEFAULT_HEIGHT);
5446 cdna.alignAs(alignment);
5447 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5449 Desktop.addInternalFrame(alignFrame, newtitle,
5450 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5454 * Set visibility of dna/protein complement view (available when shown in a
5460 protected void showComplement_actionPerformed(boolean show)
5462 SplitContainerI sf = getSplitViewContainer();
5465 sf.setComplementVisible(this, show);
5470 * Generate the reverse (optionally complemented) of the selected sequences,
5471 * and add them to the alignment
5474 protected void showReverse_actionPerformed(boolean complement)
5476 AlignmentI al = null;
5479 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5480 al = dna.reverseCdna(complement);
5481 viewport.addAlignment(al, "");
5482 addHistoryItem(new EditCommand(
5483 MessageManager.getString("label.add_sequences"),
5484 Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5485 viewport.getAlignment()));
5486 } catch (Exception ex)
5488 System.err.println(ex.getMessage());
5494 * Try to run a script in the Groovy console, having first ensured that this
5495 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5496 * be targeted at this alignment.
5499 protected void runGroovy_actionPerformed()
5501 Jalview.setCurrentAlignFrame(this);
5502 groovy.ui.Console console = Desktop.getGroovyConsole();
5503 if (console != null)
5507 console.runScript();
5508 } catch (Exception ex)
5510 System.err.println((ex.toString()));
5512 .showInternalMessageDialog(Desktop.desktop, MessageManager
5513 .getString("label.couldnt_run_groovy_script"),
5515 .getString("label.groovy_support_failed"),
5516 JvOptionPane.ERROR_MESSAGE);
5521 System.err.println("Can't run Groovy script as console not found");
5526 * Hides columns containing (or not containing) a specified feature, provided
5527 * that would not leave all columns hidden
5529 * @param featureType
5530 * @param columnsContaining
5533 public boolean hideFeatureColumns(String featureType,
5534 boolean columnsContaining)
5536 boolean notForHiding = avc.markColumnsContainingFeatures(
5537 columnsContaining, false, false, featureType);
5540 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5541 false, featureType))
5543 getViewport().hideSelectedColumns();
5551 protected void selectHighlightedColumns_actionPerformed(
5552 ActionEvent actionEvent)
5554 // include key modifier check in case user selects from menu
5555 avc.markHighlightedColumns(
5556 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5558 (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5562 * Rebuilds the Colour menu, including any user-defined colours which have
5563 * been loaded either on startup or during the session
5565 public void buildColourMenu()
5567 colourMenu.removeAll();
5569 colourMenu.add(applyToAllGroups);
5570 colourMenu.add(textColour);
5571 colourMenu.addSeparator();
5573 ColourMenuHelper.addMenuItems(colourMenu, this,
5574 viewport.getAlignment(), false);
5576 colourMenu.addSeparator();
5577 colourMenu.add(conservationMenuItem);
5578 colourMenu.add(modifyConservation);
5579 colourMenu.add(abovePIDThreshold);
5580 colourMenu.add(modifyPID);
5581 colourMenu.add(annotationColour);
5583 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5584 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5588 * Open a dialog (if not already open) that allows the user to select and
5589 * calculate PCA or Tree analysis
5591 protected void openTreePcaDialog()
5593 if (alignPanel.getCalculationDialog() == null)
5595 new CalculationChooser(AlignFrame.this);
5600 class PrintThread extends Thread
5604 public PrintThread(AlignmentPanel ap)
5609 static PageFormat pf;
5614 PrinterJob printJob = PrinterJob.getPrinterJob();
5618 printJob.setPrintable(ap, pf);
5622 printJob.setPrintable(ap);
5625 if (printJob.printDialog())
5630 } catch (Exception PrintException)
5632 PrintException.printStackTrace();