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.HiddenMarkovModel;
58 import jalview.datamodel.HiddenSequences;
59 import jalview.datamodel.PDBEntry;
60 import jalview.datamodel.SeqCigar;
61 import jalview.datamodel.Sequence;
62 import jalview.datamodel.SequenceGroup;
63 import jalview.datamodel.SequenceI;
64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
66 import jalview.hmmer.HMMAlignThread;
67 import jalview.hmmer.HMMBuildThread;
68 import jalview.hmmer.HMMERParamStore;
69 import jalview.hmmer.HMMERPreset;
70 import jalview.hmmer.HMMSearchThread;
71 import jalview.io.AlignmentProperties;
72 import jalview.io.AnnotationFile;
73 import jalview.io.BioJsHTMLOutput;
74 import jalview.io.DataSourceType;
75 import jalview.io.FileFormat;
76 import jalview.io.FileFormatI;
77 import jalview.io.FileFormats;
78 import jalview.io.FileLoader;
79 import jalview.io.FileParse;
80 import jalview.io.FormatAdapter;
81 import jalview.io.HtmlSvgOutput;
82 import jalview.io.IdentifyFile;
83 import jalview.io.JPredFile;
84 import jalview.io.JalviewFileChooser;
85 import jalview.io.JalviewFileView;
86 import jalview.io.JnetAnnotationMaker;
87 import jalview.io.NewickFile;
88 import jalview.io.ScoreMatrixFile;
89 import jalview.io.TCoffeeScoreFile;
90 import jalview.jbgui.GAlignFrame;
91 import jalview.schemes.ColourSchemeI;
92 import jalview.schemes.ColourSchemes;
93 import jalview.schemes.ResidueColourScheme;
94 import jalview.schemes.TCoffeeColourScheme;
95 import jalview.util.MessageManager;
96 import jalview.util.StringUtils;
97 import jalview.viewmodel.AlignmentViewport;
98 import jalview.viewmodel.ViewportRanges;
99 import jalview.ws.DBRefFetcher;
100 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
101 import jalview.ws.jws1.Discoverer;
102 import jalview.ws.jws2.Jws2Discoverer;
103 import jalview.ws.jws2.jabaws2.Jws2Instance;
104 import jalview.ws.params.ArgumentI;
105 import jalview.ws.params.ParamDatastoreI;
106 import jalview.ws.params.WsParamSetI;
107 import jalview.ws.seqfetcher.DbSourceProxy;
109 import java.awt.BorderLayout;
110 import java.awt.Component;
111 import java.awt.Rectangle;
112 import java.awt.Toolkit;
113 import java.awt.datatransfer.Clipboard;
114 import java.awt.datatransfer.DataFlavor;
115 import java.awt.datatransfer.StringSelection;
116 import java.awt.datatransfer.Transferable;
117 import java.awt.dnd.DnDConstants;
118 import java.awt.dnd.DropTargetDragEvent;
119 import java.awt.dnd.DropTargetDropEvent;
120 import java.awt.dnd.DropTargetEvent;
121 import java.awt.dnd.DropTargetListener;
122 import java.awt.event.ActionEvent;
123 import java.awt.event.ActionListener;
124 import java.awt.event.FocusAdapter;
125 import java.awt.event.FocusEvent;
126 import java.awt.event.ItemEvent;
127 import java.awt.event.ItemListener;
128 import java.awt.event.KeyAdapter;
129 import java.awt.event.KeyEvent;
130 import java.awt.event.MouseEvent;
131 import java.awt.print.PageFormat;
132 import java.awt.print.PrinterJob;
133 import java.beans.PropertyChangeEvent;
135 import java.io.FileWriter;
136 import java.io.IOException;
137 import java.io.PrintWriter;
139 import java.util.ArrayList;
140 import java.util.Arrays;
141 import java.util.Deque;
142 import java.util.Enumeration;
143 import java.util.HashMap;
144 import java.util.Hashtable;
145 import java.util.List;
146 import java.util.Map;
147 import java.util.Scanner;
148 import java.util.Vector;
150 import javax.swing.JCheckBoxMenuItem;
151 import javax.swing.JEditorPane;
152 import javax.swing.JFileChooser;
153 import javax.swing.JFrame;
154 import javax.swing.JInternalFrame;
155 import javax.swing.JLayeredPane;
156 import javax.swing.JMenu;
157 import javax.swing.JMenuItem;
158 import javax.swing.JOptionPane;
159 import javax.swing.JScrollPane;
160 import javax.swing.SwingUtilities;
166 * @version $Revision$
168 public class AlignFrame extends GAlignFrame implements DropTargetListener,
169 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
172 Map<String, Float> distribution = new HashMap<>(); // temporary
174 public static final int DEFAULT_WIDTH = 700;
176 public static final int DEFAULT_HEIGHT = 500;
179 * The currently displayed panel (selected tabbed view if more than one)
181 public AlignmentPanel alignPanel;
183 AlignViewport viewport;
185 ViewportRanges vpRanges;
187 public AlignViewControllerI avc;
189 * The selected HMM for this align frame
191 SequenceI selectedHMMSequence;
193 List<AlignmentPanel> alignPanels = new ArrayList<>();
196 * Last format used to load or save alignments in this window
198 FileFormatI currentFileFormat = null;
201 * Current filename for this alignment
203 String fileName = null;
207 * Creates a new AlignFrame object with specific width and height.
213 public AlignFrame(AlignmentI al, int width, int height)
215 this(al, null, width, height);
219 * Creates a new AlignFrame object with specific width, height and
225 * @param sequenceSetId
227 public AlignFrame(AlignmentI al, int width, int height,
228 String sequenceSetId)
230 this(al, null, width, height, sequenceSetId);
234 * Creates a new AlignFrame object with specific width, height and
240 * @param sequenceSetId
243 public AlignFrame(AlignmentI al, int width, int height,
244 String sequenceSetId, String viewId)
246 this(al, null, width, height, sequenceSetId, viewId);
250 * new alignment window with hidden columns
254 * @param hiddenColumns
255 * ColumnSelection or null
257 * Width of alignment frame
261 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
264 this(al, hiddenColumns, width, height, null);
268 * Create alignment frame for al with hiddenColumns, a specific width and
269 * height, and specific sequenceId
272 * @param hiddenColumns
275 * @param sequenceSetId
278 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
279 int height, String sequenceSetId)
281 this(al, hiddenColumns, width, height, sequenceSetId, null);
285 * Create alignment frame for al with hiddenColumns, a specific width and
286 * height, and specific sequenceId
289 * @param hiddenColumns
292 * @param sequenceSetId
297 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
298 int height, String sequenceSetId, String viewId)
300 setSize(width, height);
302 if (al.getDataset() == null)
307 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
309 alignPanel = new AlignmentPanel(this, viewport);
311 addAlignmentPanel(alignPanel, true);
315 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
316 HiddenColumns hiddenColumns, int width, int height)
318 setSize(width, height);
320 if (al.getDataset() == null)
325 viewport = new AlignViewport(al, hiddenColumns);
327 if (hiddenSeqs != null && hiddenSeqs.length > 0)
329 viewport.hideSequence(hiddenSeqs);
331 alignPanel = new AlignmentPanel(this, viewport);
332 addAlignmentPanel(alignPanel, true);
337 * Make a new AlignFrame from existing alignmentPanels
344 public AlignFrame(AlignmentPanel ap)
348 addAlignmentPanel(ap, false);
353 * initalise the alignframe from the underlying viewport data and the
358 if (!Jalview.isHeadlessMode())
360 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
363 vpRanges = viewport.getRanges();
364 avc = new jalview.controller.AlignViewController(this, viewport,
366 if (viewport.getAlignmentConservationAnnotation() == null)
368 // BLOSUM62Colour.setEnabled(false);
369 conservationMenuItem.setEnabled(false);
370 modifyConservation.setEnabled(false);
371 // PIDColour.setEnabled(false);
372 // abovePIDThreshold.setEnabled(false);
373 // modifyPID.setEnabled(false);
376 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
379 if (sortby.equals("Id"))
381 sortIDMenuItem_actionPerformed(null);
383 else if (sortby.equals("Pairwise Identity"))
385 sortPairwiseMenuItem_actionPerformed(null);
389 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
391 setMenusFromViewport(viewport);
392 buildSortByAnnotationScoresMenu();
393 calculateTree.addActionListener(new ActionListener()
397 public void actionPerformed(ActionEvent e)
405 if (Desktop.desktop != null)
407 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
408 addServiceListeners();
412 if (viewport.getWrapAlignment())
414 wrapMenuItem_actionPerformed(null);
417 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
419 this.overviewMenuItem_actionPerformed(null);
424 final List<AlignmentPanel> selviews = new ArrayList<>();
425 final List<AlignmentPanel> origview = new ArrayList<>();
426 final String menuLabel = MessageManager
427 .getString("label.copy_format_from");
428 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
429 new ViewSetProvider()
433 public AlignmentPanel[] getAllAlignmentPanels()
436 origview.add(alignPanel);
437 // make an array of all alignment panels except for this one
438 List<AlignmentPanel> aps = new ArrayList<>(
439 Arrays.asList(Desktop.getAlignmentPanels(null)));
440 aps.remove(AlignFrame.this.alignPanel);
441 return aps.toArray(new AlignmentPanel[aps.size()]);
443 }, selviews, new ItemListener()
447 public void itemStateChanged(ItemEvent e)
449 if (origview.size() > 0)
451 final AlignmentPanel ap = origview.get(0);
454 * Copy the ViewStyle of the selected panel to 'this one'.
455 * Don't change value of 'scaleProteinAsCdna' unless copying
458 ViewStyleI vs = selviews.get(0).getAlignViewport()
460 boolean fromSplitFrame = selviews.get(0)
461 .getAlignViewport().getCodingComplement() != null;
464 vs.setScaleProteinAsCdna(ap.getAlignViewport()
465 .getViewStyle().isScaleProteinAsCdna());
467 ap.getAlignViewport().setViewStyle(vs);
470 * Also rescale ViewStyle of SplitFrame complement if there is
471 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
472 * the whole ViewStyle (allow cDNA protein to have different
475 AlignViewportI complement = ap.getAlignViewport()
476 .getCodingComplement();
477 if (complement != null && vs.isScaleProteinAsCdna())
479 AlignFrame af = Desktop.getAlignFrameFor(complement);
480 ((SplitFrame) af.getSplitViewContainer())
482 af.setMenusForViewport();
486 ap.setSelected(true);
487 ap.alignFrame.setMenusForViewport();
492 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
493 .indexOf("devel") > -1
494 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
495 .indexOf("test") > -1)
497 formatMenu.add(vsel);
499 addFocusListener(new FocusAdapter()
502 public void focusGained(FocusEvent e)
504 Jalview.setCurrentAlignFrame(AlignFrame.this);
511 * Adds all menu items to the HMMER menu
513 private void buildHMMERMenu()
515 hmmerMenu.removeAll();
517 hmmerMenu.add(hmmAlign);
518 hmmerMenu.add(hmmBuild);
519 hmmerMenu.add(hmmSearch);
523 * Change the filename and format for the alignment, and enable the 'reload'
524 * button functionality.
531 public void setFileName(String file, FileFormatI format)
534 setFileFormat(format);
535 reload.setEnabled(true);
539 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
542 void addKeyListener()
544 addKeyListener(new KeyAdapter()
547 public void keyPressed(KeyEvent evt)
549 if (viewport.cursorMode
550 && ((evt.getKeyCode() >= KeyEvent.VK_0
551 && evt.getKeyCode() <= KeyEvent.VK_9)
552 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
553 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
554 && Character.isDigit(evt.getKeyChar()))
556 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
559 switch (evt.getKeyCode())
562 case 27: // escape key
563 deselectAllSequenceMenuItem_actionPerformed(null);
567 case KeyEvent.VK_DOWN:
568 if (evt.isAltDown() || !viewport.cursorMode)
570 moveSelectedSequences(false);
572 if (viewport.cursorMode)
574 alignPanel.getSeqPanel().moveCursor(0, 1);
579 if (evt.isAltDown() || !viewport.cursorMode)
581 moveSelectedSequences(true);
583 if (viewport.cursorMode)
585 alignPanel.getSeqPanel().moveCursor(0, -1);
590 case KeyEvent.VK_LEFT:
591 if (evt.isAltDown() || !viewport.cursorMode)
593 slideSequences(false,
594 alignPanel.getSeqPanel().getKeyboardNo1());
598 alignPanel.getSeqPanel().moveCursor(-1, 0);
603 case KeyEvent.VK_RIGHT:
604 if (evt.isAltDown() || !viewport.cursorMode)
606 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
610 alignPanel.getSeqPanel().moveCursor(1, 0);
614 case KeyEvent.VK_SPACE:
615 if (viewport.cursorMode)
617 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
618 || evt.isShiftDown() || evt.isAltDown());
622 // case KeyEvent.VK_A:
623 // if (viewport.cursorMode)
625 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
626 // //System.out.println("A");
630 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
631 * System.out.println("closing bracket"); } break;
633 case KeyEvent.VK_DELETE:
634 case KeyEvent.VK_BACK_SPACE:
635 if (!viewport.cursorMode)
637 cut_actionPerformed(null);
641 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
642 || evt.isShiftDown() || evt.isAltDown());
648 if (viewport.cursorMode)
650 alignPanel.getSeqPanel().setCursorRow();
654 if (viewport.cursorMode && !evt.isControlDown())
656 alignPanel.getSeqPanel().setCursorColumn();
660 if (viewport.cursorMode)
662 alignPanel.getSeqPanel().setCursorPosition();
666 case KeyEvent.VK_ENTER:
667 case KeyEvent.VK_COMMA:
668 if (viewport.cursorMode)
670 alignPanel.getSeqPanel().setCursorRowAndColumn();
675 if (viewport.cursorMode)
677 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
681 if (viewport.cursorMode)
683 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
688 viewport.cursorMode = !viewport.cursorMode;
689 statusBar.setText(MessageManager
690 .formatMessage("label.keyboard_editing_mode", new String[]
691 { (viewport.cursorMode ? "on" : "off") }));
692 if (viewport.cursorMode)
694 alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
696 alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
699 alignPanel.getSeqPanel().seqCanvas.repaint();
705 Help.showHelpWindow();
706 } catch (Exception ex)
708 ex.printStackTrace();
713 boolean toggleSeqs = !evt.isControlDown();
714 boolean toggleCols = !evt.isShiftDown();
715 toggleHiddenRegions(toggleSeqs, toggleCols);
720 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
721 boolean modifyExisting = true; // always modify, don't clear
722 // evt.isShiftDown();
723 boolean invertHighlighted = evt.isAltDown();
724 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
728 case KeyEvent.VK_PAGE_UP:
731 case KeyEvent.VK_PAGE_DOWN:
738 public void keyReleased(KeyEvent evt)
740 switch (evt.getKeyCode())
742 case KeyEvent.VK_LEFT:
743 if (evt.isAltDown() || !viewport.cursorMode)
745 viewport.firePropertyChange("alignment", null,
746 viewport.getAlignment().getSequences());
750 case KeyEvent.VK_RIGHT:
751 if (evt.isAltDown() || !viewport.cursorMode)
753 viewport.firePropertyChange("alignment", null,
754 viewport.getAlignment().getSequences());
762 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
764 ap.alignFrame = this;
765 avc = new jalview.controller.AlignViewController(this, viewport,
770 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
772 int aSize = alignPanels.size();
774 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
776 if (aSize == 1 && ap.av.viewName == null)
778 this.getContentPane().add(ap, BorderLayout.CENTER);
784 setInitialTabVisible();
787 expandViews.setEnabled(true);
788 gatherViews.setEnabled(true);
789 tabbedPane.addTab(ap.av.viewName, ap);
791 ap.setVisible(false);
796 if (ap.av.isPadGaps())
798 ap.av.getAlignment().padGaps();
800 ap.av.updateConservation(ap);
801 ap.av.updateConsensus(ap);
802 ap.av.updateStrucConsensus(ap);
803 ap.av.updateInformation(ap);
807 public void setInitialTabVisible()
809 expandViews.setEnabled(true);
810 gatherViews.setEnabled(true);
811 tabbedPane.setVisible(true);
812 AlignmentPanel first = alignPanels.get(0);
813 tabbedPane.addTab(first.av.viewName, first);
814 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
817 public AlignViewport getViewport()
822 /* Set up intrinsic listeners for dynamically generated GUI bits. */
823 private void addServiceListeners()
825 final java.beans.PropertyChangeListener thisListener;
826 Desktop.instance.addJalviewPropertyChangeListener("services",
827 thisListener = new java.beans.PropertyChangeListener()
830 public void propertyChange(PropertyChangeEvent evt)
832 // // System.out.println("Discoverer property change.");
833 // if (evt.getPropertyName().equals("services"))
835 SwingUtilities.invokeLater(new Runnable()
842 "Rebuild WS Menu for service change");
843 BuildWebServiceMenu();
850 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
853 public void internalFrameClosed(
854 javax.swing.event.InternalFrameEvent evt)
856 // System.out.println("deregistering discoverer listener");
857 Desktop.instance.removeJalviewPropertyChangeListener("services",
859 closeMenuItem_actionPerformed(true);
862 // Finally, build the menu once to get current service state
863 new Thread(new Runnable()
868 BuildWebServiceMenu();
874 * Configure menu items that vary according to whether the alignment is
875 * nucleotide or protein
877 public void setGUINucleotide()
879 AlignmentI al = getViewport().getAlignment();
880 boolean nucleotide = al.isNucleotide();
882 showTranslation.setVisible(nucleotide);
883 showReverse.setVisible(nucleotide);
884 showReverseComplement.setVisible(nucleotide);
885 conservationMenuItem.setEnabled(!nucleotide);
887 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
888 showGroupConservation.setEnabled(!nucleotide);
890 showComplementMenuItem
891 .setText(nucleotide ? MessageManager.getString("label.protein")
892 : MessageManager.getString("label.nucleotide"));
896 * set up menus for the current viewport. This may be called after any
897 * operation that affects the data in the current view (selection changed,
898 * etc) to update the menus to reflect the new state.
901 public void setMenusForViewport()
903 setMenusFromViewport(viewport);
907 * Need to call this method when tabs are selected for multiple views, or when
908 * loading from Jalview2XML.java
913 void setMenusFromViewport(AlignViewport av)
915 padGapsMenuitem.setSelected(av.isPadGaps());
916 colourTextMenuItem.setSelected(av.isShowColourText());
917 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
918 modifyPID.setEnabled(abovePIDThreshold.isSelected());
919 conservationMenuItem.setSelected(av.getConservationSelected());
920 modifyConservation.setEnabled(conservationMenuItem.isSelected());
921 seqLimits.setSelected(av.getShowJVSuffix());
922 idRightAlign.setSelected(av.isRightAlignIds());
923 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
924 renderGapsMenuItem.setSelected(av.isRenderGaps());
925 wrapMenuItem.setSelected(av.getWrapAlignment());
926 scaleAbove.setVisible(av.getWrapAlignment());
927 scaleLeft.setVisible(av.getWrapAlignment());
928 scaleRight.setVisible(av.getWrapAlignment());
929 annotationPanelMenuItem.setState(av.isShowAnnotation());
931 * Show/hide annotations only enabled if annotation panel is shown
933 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
934 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
935 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
936 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
937 viewBoxesMenuItem.setSelected(av.getShowBoxes());
938 viewTextMenuItem.setSelected(av.getShowText());
939 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
940 showGroupConsensus.setSelected(av.isShowGroupConsensus());
941 showGroupConservation.setSelected(av.isShowGroupConservation());
942 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
943 showSequenceLogo.setSelected(av.isShowSequenceLogo());
944 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
945 showInformationHistogram.setSelected(av.isShowInformationHistogram());
946 showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
947 normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
949 ColourMenuHelper.setColourSelected(colourMenu,
950 av.getGlobalColourScheme());
952 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
953 hiddenMarkers.setState(av.getShowHiddenMarkers());
954 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
955 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
956 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
957 autoCalculate.setSelected(av.autoCalculateConsensus);
958 sortByTree.setSelected(av.sortByTree);
959 listenToViewSelections.setSelected(av.followSelection);
961 showProducts.setEnabled(canShowProducts());
962 setGroovyEnabled(Desktop.getGroovyConsole() != null);
968 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
972 public void setGroovyEnabled(boolean b)
974 runGroovy.setEnabled(b);
977 private IProgressIndicator progressBar;
982 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
985 public void setProgressBar(String message, long id)
987 progressBar.setProgressBar(message, id);
991 public void registerHandler(final long id,
992 final IProgressIndicatorHandler handler)
994 progressBar.registerHandler(id, handler);
999 * @return true if any progress bars are still active
1002 public boolean operationInProgress()
1004 return progressBar.operationInProgress();
1008 public void setStatus(String text)
1010 statusBar.setText(text);
1014 * Added so Castor Mapping file can obtain Jalview Version
1016 public String getVersion()
1018 return jalview.bin.Cache.getProperty("VERSION");
1021 public FeatureRenderer getFeatureRenderer()
1023 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1027 public void fetchSequence_actionPerformed(ActionEvent e)
1029 new jalview.gui.SequenceFetcher(this);
1033 public void addFromFile_actionPerformed(ActionEvent e)
1035 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1039 public void hmmBuildSettings_actionPerformed(ActionEvent e)
1040 throws IOException, InterruptedException
1042 if (!(alignmentIsSufficient(1)))
1046 WsParamSetI set = new HMMERPreset();
1047 List<ArgumentI> args = new ArrayList<>();
1048 ParamDatastoreI store = new HMMERParamStore("hmmalign");
1049 WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1051 if (params.showRunDialog())
1053 new Thread(new HMMBuildThread(this, params.getJobParams())).start();
1055 alignPanel.repaint();
1060 public void hmmAlignSettings_actionPerformed(ActionEvent e)
1061 throws IOException, InterruptedException
1063 if (!(checkForHMM() && alignmentIsSufficient(2)))
1067 WsParamSetI set = new HMMERPreset();
1068 List<ArgumentI> args = new ArrayList<>();
1069 ParamDatastoreI store = new HMMERParamStore("hmmalign");
1070 WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1072 if (params.showRunDialog())
1074 new Thread(new HMMAlignThread(this, true, params.getJobParams()))
1077 alignPanel.repaint();
1081 public void hmmSearchSettings_actionPerformed(ActionEvent e)
1087 WsParamSetI set = new HMMERPreset();
1088 List<ArgumentI> args = new ArrayList<>();
1089 ParamDatastoreI store = new HMMERParamStore("hmmsearch");
1090 WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
1092 if (params.showRunDialog())
1094 new Thread(new HMMSearchThread(this, true, params.getJobParams()))
1097 alignPanel.repaint();
1101 public void hmmBuildRun_actionPerformed(ActionEvent e)
1102 throws IOException, InterruptedException
1104 if (!alignmentIsSufficient(1))
1108 new Thread(new HMMBuildThread(this, null)).start();
1109 alignPanel.repaint();
1114 public void hmmAlignRun_actionPerformed(ActionEvent e)
1115 throws IOException, InterruptedException
1117 if (!(checkForHMM() && alignmentIsSufficient(2)))
1121 new Thread(new HMMAlignThread(this, true, null))
1123 alignPanel.repaint();
1127 public void hmmSearchRun_actionPerformed(ActionEvent e)
1133 new Thread(new HMMSearchThread(this, true, null))
1135 alignPanel.repaint();
1139 * Checks if the frame has a selected hidden Markov model
1143 private boolean checkForHMM()
1145 if (getSelectedHMM() == null)
1147 JOptionPane.showMessageDialog(this,
1148 MessageManager.getString("warn.no_selected_hmm"));
1155 * Checks if the alignment contains the required number of sequences.
1160 public boolean alignmentIsSufficient(int required)
1162 if (getViewport().getAlignment().getSequences().size() < required)
1164 JOptionPane.showMessageDialog(this,
1165 MessageManager.getString("warn.not_enough_sequences"));
1172 public void addDatabase_actionPerformed(ActionEvent e) throws IOException
1174 if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
1176 Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
1177 Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
1180 String path = openFileChooser(false);
1181 if (new File(path).exists())
1183 IdentifyFile identifier = new IdentifyFile();
1184 FileFormatI format = identifier.identify(path, DataSourceType.FILE);
1185 if (format == FileFormat.Fasta || format == FileFormat.Stockholm
1186 || format == FileFormat.Pfam)
1188 String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS);
1189 String currentDbPaths = Cache
1190 .getProperty(Preferences.HMMSEARCH_DB_PATHS);
1191 currentDbPaths += " " + path;
1193 String fileName = StringUtils.getLastToken(path, new String("/"));
1194 Scanner scanner = new Scanner(fileName).useDelimiter(".");
1195 String name = scanner.next();
1197 currentDbs += " " + path; // TODO remove path from file name
1200 Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths);
1201 Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
1205 JOptionPane.showMessageDialog(this,
1206 MessageManager.getString("warn.invalid_format"));
1211 JOptionPane.showMessageDialog(this,
1212 MessageManager.getString("warn.not_enough_sequences"));
1217 * Opens a file chooser
1222 protected String openFileChooser(boolean forFolder)
1224 String choice = null;
1225 JFileChooser chooser = new JFileChooser();
1228 chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
1230 chooser.setDialogTitle(
1231 MessageManager.getString("label.open_local_file"));
1232 chooser.setToolTipText(MessageManager.getString("action.open"));
1234 int value = chooser.showOpenDialog(this);
1236 if (value == JFileChooser.APPROVE_OPTION)
1238 choice = chooser.getSelectedFile().getPath();
1244 public void reload_actionPerformed(ActionEvent e)
1246 if (fileName != null)
1248 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1249 // originating file's format
1250 // TODO: work out how to recover feature settings for correct view(s) when
1251 // file is reloaded.
1252 if (FileFormat.Jalview.equals(currentFileFormat))
1254 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1255 for (int i = 0; i < frames.length; i++)
1257 if (frames[i] instanceof AlignFrame && frames[i] != this
1258 && ((AlignFrame) frames[i]).fileName != null
1259 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1263 frames[i].setSelected(true);
1264 Desktop.instance.closeAssociatedWindows();
1265 } catch (java.beans.PropertyVetoException ex)
1271 Desktop.instance.closeAssociatedWindows();
1273 FileLoader loader = new FileLoader();
1274 DataSourceType protocol = fileName.startsWith("http:")
1275 ? DataSourceType.URL
1276 : DataSourceType.FILE;
1277 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1281 Rectangle bounds = this.getBounds();
1283 FileLoader loader = new FileLoader();
1284 DataSourceType protocol = fileName.startsWith("http:")
1285 ? DataSourceType.URL
1286 : DataSourceType.FILE;
1287 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1288 protocol, currentFileFormat);
1290 newframe.setBounds(bounds);
1291 if (featureSettings != null && featureSettings.isShowing())
1293 final Rectangle fspos = featureSettings.frame.getBounds();
1294 // TODO: need a 'show feature settings' function that takes bounds -
1295 // need to refactor Desktop.addFrame
1296 newframe.featureSettings_actionPerformed(null);
1297 final FeatureSettings nfs = newframe.featureSettings;
1298 SwingUtilities.invokeLater(new Runnable()
1303 nfs.frame.setBounds(fspos);
1306 this.featureSettings.close();
1307 this.featureSettings = null;
1309 this.closeMenuItem_actionPerformed(true);
1315 public void addFromText_actionPerformed(ActionEvent e)
1318 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1322 public void addFromURL_actionPerformed(ActionEvent e)
1324 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1328 public void save_actionPerformed(ActionEvent e)
1330 if (fileName == null || (currentFileFormat == null)
1331 || fileName.startsWith("http"))
1333 saveAs_actionPerformed(null);
1337 saveAlignment(fileName, currentFileFormat);
1348 public void saveAs_actionPerformed(ActionEvent e)
1350 String format = currentFileFormat == null ? null
1351 : currentFileFormat.getName();
1352 JalviewFileChooser chooser = JalviewFileChooser
1353 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1355 chooser.setFileView(new JalviewFileView());
1356 chooser.setDialogTitle(
1357 MessageManager.getString("label.save_alignment_to_file"));
1358 chooser.setToolTipText(MessageManager.getString("action.save"));
1360 int value = chooser.showSaveDialog(this);
1362 if (value == JalviewFileChooser.APPROVE_OPTION)
1364 currentFileFormat = chooser.getSelectedFormat();
1365 while (currentFileFormat == null)
1367 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1368 MessageManager.getString(
1369 "label.select_file_format_before_saving"),
1370 MessageManager.getString("label.file_format_not_specified"),
1371 JvOptionPane.WARNING_MESSAGE);
1372 currentFileFormat = chooser.getSelectedFormat();
1373 value = chooser.showSaveDialog(this);
1374 if (value != JalviewFileChooser.APPROVE_OPTION)
1380 fileName = chooser.getSelectedFile().getPath();
1382 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1384 Cache.setProperty("LAST_DIRECTORY", fileName);
1385 saveAlignment(fileName, currentFileFormat);
1389 public boolean saveAlignment(String file, FileFormatI format)
1391 boolean success = true;
1393 if (FileFormat.Jalview.equals(format))
1395 String shortName = title;
1397 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1399 shortName = shortName.substring(
1400 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1403 success = new Jalview2XML().saveAlignment(this, file, shortName);
1405 statusBar.setText(MessageManager.formatMessage(
1406 "label.successfully_saved_to_file_in_format", new Object[]
1407 { fileName, format }));
1412 AlignmentExportData exportData = getAlignmentForExport(format,
1414 if (exportData.getSettings().isCancelled())
1418 FormatAdapter f = new FormatAdapter(alignPanel,
1419 exportData.getSettings());
1420 String output = f.formatSequences(format, exportData.getAlignment(), // class
1424 // occur in the distant future
1425 exportData.getOmitHidden(), exportData.getStartEndPostions(),
1426 f.getCacheSuffixDefault(format),
1427 viewport.getAlignment().getHiddenColumns());
1437 PrintWriter out = new PrintWriter(new FileWriter(file));
1441 this.setTitle(file);
1442 statusBar.setText(MessageManager.formatMessage(
1443 "label.successfully_saved_to_file_in_format", new Object[]
1444 { fileName, format.getName() }));
1445 } catch (Exception ex)
1448 ex.printStackTrace();
1455 JvOptionPane.showInternalMessageDialog(this, MessageManager
1456 .formatMessage("label.couldnt_save_file", new Object[]
1458 MessageManager.getString("label.error_saving_file"),
1459 JvOptionPane.WARNING_MESSAGE);
1465 private void warningMessage(String warning, String title)
1467 if (new jalview.util.Platform().isHeadless())
1469 System.err.println("Warning: " + title + "\nWarning: " + warning);
1474 JvOptionPane.showInternalMessageDialog(this, warning, title,
1475 JvOptionPane.WARNING_MESSAGE);
1487 protected void outputText_actionPerformed(ActionEvent e)
1489 FileFormatI fileFormat = FileFormats.getInstance()
1490 .forName(e.getActionCommand());
1491 AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1493 if (exportData.getSettings().isCancelled())
1497 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1498 cap.setForInput(null);
1501 FileFormatI format = fileFormat;
1502 cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1503 .formatSequences(format, exportData.getAlignment(),
1504 exportData.getOmitHidden(),
1505 exportData.getStartEndPostions(),
1506 viewport.getAlignment().getHiddenColumns()));
1507 Desktop.addInternalFrame(cap, MessageManager
1508 .formatMessage("label.alignment_output_command", new Object[]
1509 { e.getActionCommand() }), 600, 500);
1510 } catch (OutOfMemoryError oom)
1512 new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1519 public static AlignmentExportData getAlignmentForExport(
1520 FileFormatI format, AlignViewportI viewport,
1521 AlignExportSettingI exportSettings)
1523 AlignmentI alignmentToExport = null;
1524 AlignExportSettingI settings = exportSettings;
1525 String[] omitHidden = null;
1527 HiddenSequences hiddenSeqs = viewport.getAlignment()
1528 .getHiddenSequences();
1530 alignmentToExport = viewport.getAlignment();
1532 boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1533 if (settings == null)
1535 settings = new AlignExportSettings(hasHiddenSeqs,
1536 viewport.hasHiddenColumns(), format);
1538 // settings.isExportAnnotations();
1540 if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1542 omitHidden = viewport.getViewAsString(false,
1543 settings.isExportHiddenSequences());
1546 int[] alignmentStartEnd = new int[2];
1547 if (hasHiddenSeqs && settings.isExportHiddenSequences())
1549 alignmentToExport = hiddenSeqs.getFullAlignment();
1553 alignmentToExport = viewport.getAlignment();
1555 alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1556 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1557 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1558 omitHidden, alignmentStartEnd, settings);
1569 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1571 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1572 htmlSVG.exportHTML(null);
1576 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1578 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1579 bjs.exportHTML(null);
1582 public void createImageMap(File file, String image)
1584 alignPanel.makePNGImageMap(file, image);
1594 public void createPNG(File f)
1596 alignPanel.makePNG(f);
1606 public void createEPS(File f)
1608 alignPanel.makeEPS(f);
1612 public void createSVG(File f)
1614 alignPanel.makeSVG(f);
1618 public void pageSetup_actionPerformed(ActionEvent e)
1620 PrinterJob printJob = PrinterJob.getPrinterJob();
1621 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1631 public void printMenuItem_actionPerformed(ActionEvent e)
1633 // Putting in a thread avoids Swing painting problems
1634 PrintThread thread = new PrintThread(alignPanel);
1639 public void exportFeatures_actionPerformed(ActionEvent e)
1641 new AnnotationExporter().exportFeatures(alignPanel);
1645 public void exportAnnotations_actionPerformed(ActionEvent e)
1647 new AnnotationExporter().exportAnnotations(alignPanel);
1651 public void associatedData_actionPerformed(ActionEvent e)
1652 throws IOException, InterruptedException
1654 // Pick the tree file
1655 JalviewFileChooser chooser = new JalviewFileChooser(
1656 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1657 chooser.setFileView(new JalviewFileView());
1658 chooser.setDialogTitle(
1659 MessageManager.getString("label.load_jalview_annotations"));
1660 chooser.setToolTipText(
1661 MessageManager.getString("label.load_jalview_annotations"));
1663 int value = chooser.showOpenDialog(null);
1665 if (value == JalviewFileChooser.APPROVE_OPTION)
1667 String choice = chooser.getSelectedFile().getPath();
1668 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1669 loadJalviewDataFile(choice, null, null, null);
1675 * Close the current view or all views in the alignment frame. If the frame
1676 * only contains one view then the alignment will be removed from memory.
1678 * @param closeAllTabs
1681 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1683 if (alignPanels != null && alignPanels.size() < 2)
1685 closeAllTabs = true;
1690 if (alignPanels != null)
1694 if (this.isClosed())
1696 // really close all the windows - otherwise wait till
1697 // setClosed(true) is called
1698 for (int i = 0; i < alignPanels.size(); i++)
1700 AlignmentPanel ap = alignPanels.get(i);
1707 closeView(alignPanel);
1714 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1715 * be called recursively, with the frame now in 'closed' state
1717 this.setClosed(true);
1719 } catch (Exception ex)
1721 ex.printStackTrace();
1726 * Close the specified panel and close up tabs appropriately.
1728 * @param panelToClose
1730 public void closeView(AlignmentPanel panelToClose)
1732 int index = tabbedPane.getSelectedIndex();
1733 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1734 alignPanels.remove(panelToClose);
1735 panelToClose.closePanel();
1736 panelToClose = null;
1738 tabbedPane.removeTabAt(closedindex);
1739 tabbedPane.validate();
1741 if (index > closedindex || index == tabbedPane.getTabCount())
1743 // modify currently selected tab index if necessary.
1747 this.tabSelectionChanged(index);
1753 void updateEditMenuBar()
1756 if (viewport.getHistoryList().size() > 0)
1758 undoMenuItem.setEnabled(true);
1759 CommandI command = viewport.getHistoryList().peek();
1760 undoMenuItem.setText(MessageManager
1761 .formatMessage("label.undo_command", new Object[]
1762 { command.getDescription() }));
1766 undoMenuItem.setEnabled(false);
1767 undoMenuItem.setText(MessageManager.getString("action.undo"));
1770 if (viewport.getRedoList().size() > 0)
1772 redoMenuItem.setEnabled(true);
1774 CommandI command = viewport.getRedoList().peek();
1775 redoMenuItem.setText(MessageManager
1776 .formatMessage("label.redo_command", new Object[]
1777 { command.getDescription() }));
1781 redoMenuItem.setEnabled(false);
1782 redoMenuItem.setText(MessageManager.getString("action.redo"));
1787 public void addHistoryItem(CommandI command)
1789 if (command.getSize() > 0)
1791 viewport.addToHistoryList(command);
1792 viewport.clearRedoList();
1793 updateEditMenuBar();
1794 viewport.updateHiddenColumns();
1795 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1796 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1797 // viewport.getColumnSelection()
1798 // .getHiddenColumns().size() > 0);
1804 * @return alignment objects for all views
1806 AlignmentI[] getViewAlignments()
1808 if (alignPanels != null)
1810 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1812 for (AlignmentPanel ap : alignPanels)
1814 als[i++] = ap.av.getAlignment();
1818 if (viewport != null)
1820 return new AlignmentI[] { viewport.getAlignment() };
1832 protected void undoMenuItem_actionPerformed(ActionEvent e)
1834 if (viewport.getHistoryList().isEmpty())
1838 CommandI command = viewport.getHistoryList().pop();
1839 viewport.addToRedoList(command);
1840 command.undoCommand(getViewAlignments());
1842 AlignmentViewport originalSource = getOriginatingSource(command);
1843 updateEditMenuBar();
1845 if (originalSource != null)
1847 if (originalSource != viewport)
1850 "Implementation worry: mismatch of viewport origin for undo");
1852 originalSource.updateHiddenColumns();
1853 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1855 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1856 // viewport.getColumnSelection()
1857 // .getHiddenColumns().size() > 0);
1858 originalSource.firePropertyChange("alignment", null,
1859 originalSource.getAlignment().getSequences());
1870 protected void redoMenuItem_actionPerformed(ActionEvent e)
1872 if (viewport.getRedoList().size() < 1)
1877 CommandI command = viewport.getRedoList().pop();
1878 viewport.addToHistoryList(command);
1879 command.doCommand(getViewAlignments());
1881 AlignmentViewport originalSource = getOriginatingSource(command);
1882 updateEditMenuBar();
1884 if (originalSource != null)
1887 if (originalSource != viewport)
1890 "Implementation worry: mismatch of viewport origin for redo");
1892 originalSource.updateHiddenColumns();
1893 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1895 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1896 // viewport.getColumnSelection()
1897 // .getHiddenColumns().size() > 0);
1898 originalSource.firePropertyChange("alignment", null,
1899 originalSource.getAlignment().getSequences());
1903 AlignmentViewport getOriginatingSource(CommandI command)
1905 AlignmentViewport originalSource = null;
1906 // For sequence removal and addition, we need to fire
1907 // the property change event FROM the viewport where the
1908 // original alignment was altered
1909 AlignmentI al = null;
1910 if (command instanceof EditCommand)
1912 EditCommand editCommand = (EditCommand) command;
1913 al = editCommand.getAlignment();
1914 List<Component> comps = PaintRefresher.components
1915 .get(viewport.getSequenceSetId());
1917 for (Component comp : comps)
1919 if (comp instanceof AlignmentPanel)
1921 if (al == ((AlignmentPanel) comp).av.getAlignment())
1923 originalSource = ((AlignmentPanel) comp).av;
1930 if (originalSource == null)
1932 // The original view is closed, we must validate
1933 // the current view against the closed view first
1936 PaintRefresher.validateSequences(al, viewport.getAlignment());
1939 originalSource = viewport;
1942 return originalSource;
1951 public void moveSelectedSequences(boolean up)
1953 SequenceGroup sg = viewport.getSelectionGroup();
1959 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1960 viewport.getHiddenRepSequences(), up);
1961 alignPanel.paintAlignment(true);
1964 synchronized void slideSequences(boolean right, int size)
1966 List<SequenceI> sg = new ArrayList<>();
1967 if (viewport.cursorMode)
1969 sg.add(viewport.getAlignment()
1970 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1972 else if (viewport.getSelectionGroup() != null
1973 && viewport.getSelectionGroup().getSize() != viewport
1974 .getAlignment().getHeight())
1976 sg = viewport.getSelectionGroup()
1977 .getSequences(viewport.getHiddenRepSequences());
1985 List<SequenceI> invertGroup = new ArrayList<>();
1987 for (SequenceI seq : viewport.getAlignment().getSequences())
1989 if (!sg.contains(seq))
1991 invertGroup.add(seq);
1995 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1997 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1998 for (int i = 0; i < invertGroup.size(); i++)
2000 seqs2[i] = invertGroup.get(i);
2003 SlideSequencesCommand ssc;
2006 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
2007 viewport.getGapCharacter());
2011 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
2012 viewport.getGapCharacter());
2015 int groupAdjustment = 0;
2016 if (ssc.getGapsInsertedBegin() && right)
2018 if (viewport.cursorMode)
2020 alignPanel.getSeqPanel().moveCursor(size, 0);
2024 groupAdjustment = size;
2027 else if (!ssc.getGapsInsertedBegin() && !right)
2029 if (viewport.cursorMode)
2031 alignPanel.getSeqPanel().moveCursor(-size, 0);
2035 groupAdjustment = -size;
2039 if (groupAdjustment != 0)
2041 viewport.getSelectionGroup().setStartRes(
2042 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
2043 viewport.getSelectionGroup().setEndRes(
2044 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
2048 * just extend the last slide command if compatible; but not if in
2049 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
2051 boolean appendHistoryItem = false;
2052 Deque<CommandI> historyList = viewport.getHistoryList();
2053 boolean inSplitFrame = getSplitViewContainer() != null;
2054 if (!inSplitFrame && historyList != null && historyList.size() > 0
2055 && historyList.peek() instanceof SlideSequencesCommand)
2057 appendHistoryItem = ssc.appendSlideCommand(
2058 (SlideSequencesCommand) historyList.peek());
2061 if (!appendHistoryItem)
2063 addHistoryItem(ssc);
2076 protected void copy_actionPerformed(ActionEvent e)
2079 if (viewport.getSelectionGroup() == null)
2083 // TODO: preserve the ordering of displayed alignment annotation in any
2084 // internal paste (particularly sequence associated annotation)
2085 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
2086 String[] omitHidden = null;
2088 if (viewport.hasHiddenColumns())
2090 omitHidden = viewport.getViewAsString(true);
2093 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
2094 seqs, omitHidden, null);
2096 StringSelection ss = new StringSelection(output);
2100 jalview.gui.Desktop.internalCopy = true;
2101 // Its really worth setting the clipboard contents
2102 // to empty before setting the large StringSelection!!
2103 Toolkit.getDefaultToolkit().getSystemClipboard()
2104 .setContents(new StringSelection(""), null);
2106 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2108 } catch (OutOfMemoryError er)
2110 new OOMWarning("copying region", er);
2114 ArrayList<int[]> hiddenColumns = null;
2115 if (viewport.hasHiddenColumns())
2117 hiddenColumns = new ArrayList<>();
2119 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2120 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2121 ArrayList<int[]> hiddenRegions = viewport.getAlignment()
2122 .getHiddenColumns().getHiddenColumnsCopy();
2123 for (int[] region : hiddenRegions)
2126 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
2130 { region[0] - hiddenOffset, region[1] - hiddenOffset });
2135 Desktop.jalviewClipboard = new Object[] { seqs,
2136 viewport.getAlignment().getDataset(), hiddenColumns };
2137 statusBar.setText(MessageManager.formatMessage(
2138 "label.copied_sequences_to_clipboard", new Object[]
2139 { Integer.valueOf(seqs.length).toString() }));
2147 * @throws InterruptedException
2148 * @throws IOException
2151 protected void pasteNew_actionPerformed(ActionEvent e)
2152 throws IOException, InterruptedException
2162 * @throws InterruptedException
2163 * @throws IOException
2166 protected void pasteThis_actionPerformed(ActionEvent e)
2167 throws IOException, InterruptedException
2173 * Paste contents of Jalview clipboard
2175 * @param newAlignment
2176 * true to paste to a new alignment, otherwise add to this.
2177 * @throws InterruptedException
2178 * @throws IOException
2180 void paste(boolean newAlignment) throws IOException, InterruptedException
2182 boolean externalPaste = true;
2185 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2186 Transferable contents = c.getContents(this);
2188 if (contents == null)
2197 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2198 if (str.length() < 1)
2203 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2205 } catch (OutOfMemoryError er)
2207 new OOMWarning("Out of memory pasting sequences!!", er);
2211 SequenceI[] sequences;
2212 boolean annotationAdded = false;
2213 AlignmentI alignment = null;
2215 if (Desktop.jalviewClipboard != null)
2217 // The clipboard was filled from within Jalview, we must use the
2219 // And dataset from the copied alignment
2220 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2221 // be doubly sure that we create *new* sequence objects.
2222 sequences = new SequenceI[newseq.length];
2223 for (int i = 0; i < newseq.length; i++)
2225 sequences[i] = new Sequence(newseq[i]);
2227 alignment = new Alignment(sequences);
2228 externalPaste = false;
2232 // parse the clipboard as an alignment.
2233 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2235 sequences = alignment.getSequencesArray();
2239 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2245 if (Desktop.jalviewClipboard != null)
2247 // dataset is inherited
2248 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2252 // new dataset is constructed
2253 alignment.setDataset(null);
2255 alwidth = alignment.getWidth() + 1;
2259 AlignmentI pastedal = alignment; // preserve pasted alignment object
2260 // Add pasted sequences and dataset into existing alignment.
2261 alignment = viewport.getAlignment();
2262 alwidth = alignment.getWidth() + 1;
2263 // decide if we need to import sequences from an existing dataset
2264 boolean importDs = Desktop.jalviewClipboard != null
2265 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2266 // importDs==true instructs us to copy over new dataset sequences from
2267 // an existing alignment
2268 Vector newDs = (importDs) ? new Vector() : null; // used to create
2269 // minimum dataset set
2271 for (int i = 0; i < sequences.length; i++)
2275 newDs.addElement(null);
2277 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2279 if (importDs && ds != null)
2281 if (!newDs.contains(ds))
2283 newDs.setElementAt(ds, i);
2284 ds = new Sequence(ds);
2285 // update with new dataset sequence
2286 sequences[i].setDatasetSequence(ds);
2290 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2295 // copy and derive new dataset sequence
2296 sequences[i] = sequences[i].deriveSequence();
2297 alignment.getDataset()
2298 .addSequence(sequences[i].getDatasetSequence());
2299 // TODO: avoid creation of duplicate dataset sequences with a
2300 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2302 alignment.addSequence(sequences[i]); // merges dataset
2306 newDs.clear(); // tidy up
2308 if (alignment.getAlignmentAnnotation() != null)
2310 for (AlignmentAnnotation alan : alignment
2311 .getAlignmentAnnotation())
2313 if (alan.graphGroup > fgroup)
2315 fgroup = alan.graphGroup;
2319 if (pastedal.getAlignmentAnnotation() != null)
2321 // Add any annotation attached to alignment.
2322 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2323 for (int i = 0; i < alann.length; i++)
2325 annotationAdded = true;
2326 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2328 AlignmentAnnotation newann = new AlignmentAnnotation(
2330 if (newann.graphGroup > -1)
2332 if (newGraphGroups.size() <= newann.graphGroup
2333 || newGraphGroups.get(newann.graphGroup) == null)
2335 for (int q = newGraphGroups
2336 .size(); q <= newann.graphGroup; q++)
2338 newGraphGroups.add(q, null);
2340 newGraphGroups.set(newann.graphGroup,
2341 new Integer(++fgroup));
2343 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2347 newann.padAnnotation(alwidth);
2348 alignment.addAnnotation(newann);
2358 addHistoryItem(new EditCommand(
2359 MessageManager.getString("label.add_sequences"),
2360 Action.PASTE, sequences, 0, alignment.getWidth(),
2363 // Add any annotations attached to sequences
2364 for (int i = 0; i < sequences.length; i++)
2366 if (sequences[i].getAnnotation() != null)
2368 AlignmentAnnotation newann;
2369 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2371 annotationAdded = true;
2372 newann = sequences[i].getAnnotation()[a];
2373 newann.adjustForAlignment();
2374 newann.padAnnotation(alwidth);
2375 if (newann.graphGroup > -1)
2377 if (newann.graphGroup > -1)
2379 if (newGraphGroups.size() <= newann.graphGroup
2380 || newGraphGroups.get(newann.graphGroup) == null)
2382 for (int q = newGraphGroups
2383 .size(); q <= newann.graphGroup; q++)
2385 newGraphGroups.add(q, null);
2387 newGraphGroups.set(newann.graphGroup,
2388 new Integer(++fgroup));
2390 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2394 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2398 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2406 // propagate alignment changed.
2407 vpRanges.setEndSeq(alignment.getHeight());
2408 if (annotationAdded)
2410 // Duplicate sequence annotation in all views.
2411 AlignmentI[] alview = this.getViewAlignments();
2412 for (int i = 0; i < sequences.length; i++)
2414 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2419 for (int avnum = 0; avnum < alview.length; avnum++)
2421 if (alview[avnum] != alignment)
2423 // duplicate in a view other than the one with input focus
2424 int avwidth = alview[avnum].getWidth() + 1;
2425 // this relies on sann being preserved after we
2426 // modify the sequence's annotation array for each duplication
2427 for (int a = 0; a < sann.length; a++)
2429 AlignmentAnnotation newann = new AlignmentAnnotation(
2431 sequences[i].addAlignmentAnnotation(newann);
2432 newann.padAnnotation(avwidth);
2433 alview[avnum].addAnnotation(newann); // annotation was
2434 // duplicated earlier
2435 // TODO JAL-1145 graphGroups are not updated for sequence
2436 // annotation added to several views. This may cause
2438 alview[avnum].setAnnotationIndex(newann, a);
2443 buildSortByAnnotationScoresMenu();
2445 viewport.firePropertyChange("alignment", null,
2446 alignment.getSequences());
2447 if (alignPanels != null)
2449 for (AlignmentPanel ap : alignPanels)
2451 ap.validateAnnotationDimensions(false);
2456 alignPanel.validateAnnotationDimensions(false);
2462 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2464 String newtitle = new String("Copied sequences");
2466 if (Desktop.jalviewClipboard != null
2467 && Desktop.jalviewClipboard[2] != null)
2469 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2470 for (int[] region : hc)
2472 af.viewport.hideColumns(region[0], region[1]);
2476 // >>>This is a fix for the moment, until a better solution is
2478 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2479 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2480 .getFeatureRenderer());
2482 // TODO: maintain provenance of an alignment, rather than just make the
2483 // title a concatenation of operations.
2486 if (title.startsWith("Copied sequences"))
2492 newtitle = newtitle.concat("- from " + title);
2497 newtitle = new String("Pasted sequences");
2500 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2505 } catch (Exception ex)
2507 ex.printStackTrace();
2508 System.out.println("Exception whilst pasting: " + ex);
2509 // could be anything being pasted in here
2514 protected void expand_newalign(ActionEvent e)
2518 AlignmentI alignment = AlignmentUtils
2519 .expandContext(getViewport().getAlignment(), -1);
2520 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2522 String newtitle = new String("Flanking alignment");
2524 if (Desktop.jalviewClipboard != null
2525 && Desktop.jalviewClipboard[2] != null)
2527 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2528 for (int region[] : hc)
2530 af.viewport.hideColumns(region[0], region[1]);
2534 // >>>This is a fix for the moment, until a better solution is
2536 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2537 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2538 .getFeatureRenderer());
2540 // TODO: maintain provenance of an alignment, rather than just make the
2541 // title a concatenation of operations.
2543 if (title.startsWith("Copied sequences"))
2549 newtitle = newtitle.concat("- from " + title);
2553 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2555 } catch (Exception ex)
2557 ex.printStackTrace();
2558 System.out.println("Exception whilst pasting: " + ex);
2559 // could be anything being pasted in here
2560 } catch (OutOfMemoryError oom)
2562 new OOMWarning("Viewing flanking region of alignment", oom);
2573 protected void cut_actionPerformed(ActionEvent e)
2575 copy_actionPerformed(null);
2576 delete_actionPerformed(null);
2586 protected void delete_actionPerformed(ActionEvent evt)
2589 SequenceGroup sg = viewport.getSelectionGroup();
2596 * If the cut affects all sequences, warn, remove highlighted columns
2598 if (sg.getSize() == viewport.getAlignment().getHeight())
2600 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2601 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2602 if (isEntireAlignWidth)
2604 int confirm = JvOptionPane.showConfirmDialog(this,
2605 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2606 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2607 JvOptionPane.OK_CANCEL_OPTION);
2609 if (confirm == JvOptionPane.CANCEL_OPTION
2610 || confirm == JvOptionPane.CLOSED_OPTION)
2615 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2616 sg.getEndRes() + 1);
2618 SequenceI[] cut = sg.getSequences()
2619 .toArray(new SequenceI[sg.getSize()]);
2621 addHistoryItem(new EditCommand(
2622 MessageManager.getString("label.cut_sequences"), Action.CUT,
2623 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2624 viewport.getAlignment()));
2626 viewport.setSelectionGroup(null);
2627 viewport.sendSelection();
2628 viewport.getAlignment().deleteGroup(sg);
2630 viewport.firePropertyChange("alignment", null,
2631 viewport.getAlignment().getSequences());
2632 if (viewport.getAlignment().getHeight() < 1)
2636 this.setClosed(true);
2637 } catch (Exception ex)
2650 protected void deleteGroups_actionPerformed(ActionEvent e)
2652 if (avc.deleteGroups())
2654 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2655 alignPanel.updateAnnotation();
2656 alignPanel.paintAlignment(true);
2667 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2669 SequenceGroup sg = new SequenceGroup();
2671 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2673 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2676 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2677 viewport.setSelectionGroup(sg);
2678 viewport.sendSelection();
2679 // JAL-2034 - should delegate to
2680 // alignPanel to decide if overview needs
2682 alignPanel.paintAlignment(false);
2683 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2693 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2695 if (viewport.cursorMode)
2697 alignPanel.getSeqPanel().keyboardNo1 = null;
2698 alignPanel.getSeqPanel().keyboardNo2 = null;
2700 viewport.setSelectionGroup(null);
2701 viewport.getColumnSelection().clear();
2702 viewport.setSelectionGroup(null);
2703 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2704 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2705 // JAL-2034 - should delegate to
2706 // alignPanel to decide if overview needs
2708 alignPanel.paintAlignment(false);
2709 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2710 viewport.sendSelection();
2720 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2722 SequenceGroup sg = viewport.getSelectionGroup();
2726 selectAllSequenceMenuItem_actionPerformed(null);
2731 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2733 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2735 // JAL-2034 - should delegate to
2736 // alignPanel to decide if overview needs
2739 alignPanel.paintAlignment(true);
2740 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2741 viewport.sendSelection();
2745 public void invertColSel_actionPerformed(ActionEvent e)
2747 viewport.invertColumnSelection();
2748 alignPanel.paintAlignment(true);
2749 viewport.sendSelection();
2759 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2761 trimAlignment(true);
2771 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2773 trimAlignment(false);
2776 void trimAlignment(boolean trimLeft)
2778 ColumnSelection colSel = viewport.getColumnSelection();
2781 if (!colSel.isEmpty())
2785 column = colSel.getMin();
2789 column = colSel.getMax();
2793 if (viewport.getSelectionGroup() != null)
2795 seqs = viewport.getSelectionGroup()
2796 .getSequencesAsArray(viewport.getHiddenRepSequences());
2800 seqs = viewport.getAlignment().getSequencesArray();
2803 TrimRegionCommand trimRegion;
2806 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2807 column, viewport.getAlignment());
2808 vpRanges.setStartRes(0);
2812 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2813 column, viewport.getAlignment());
2816 statusBar.setText(MessageManager
2817 .formatMessage("label.removed_columns", new String[]
2818 { Integer.valueOf(trimRegion.getSize()).toString() }));
2820 addHistoryItem(trimRegion);
2822 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2824 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2825 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2827 viewport.getAlignment().deleteGroup(sg);
2831 viewport.firePropertyChange("alignment", null,
2832 viewport.getAlignment().getSequences());
2843 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2845 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2848 if (viewport.getSelectionGroup() != null)
2850 seqs = viewport.getSelectionGroup()
2851 .getSequencesAsArray(viewport.getHiddenRepSequences());
2852 start = viewport.getSelectionGroup().getStartRes();
2853 end = viewport.getSelectionGroup().getEndRes();
2857 seqs = viewport.getAlignment().getSequencesArray();
2860 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2861 "Remove Gapped Columns", seqs, start, end,
2862 viewport.getAlignment());
2864 addHistoryItem(removeGapCols);
2866 statusBar.setText(MessageManager
2867 .formatMessage("label.removed_empty_columns", new Object[]
2868 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2870 // This is to maintain viewport position on first residue
2871 // of first sequence
2872 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2873 int startRes = seq.findPosition(vpRanges.getStartRes());
2874 // ShiftList shifts;
2875 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2876 // edit.alColumnChanges=shifts.getInverse();
2877 // if (viewport.hasHiddenColumns)
2878 // viewport.getColumnSelection().compensateForEdits(shifts);
2879 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2880 viewport.firePropertyChange("alignment", null,
2881 viewport.getAlignment().getSequences());
2892 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2894 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2897 if (viewport.getSelectionGroup() != null)
2899 seqs = viewport.getSelectionGroup()
2900 .getSequencesAsArray(viewport.getHiddenRepSequences());
2901 start = viewport.getSelectionGroup().getStartRes();
2902 end = viewport.getSelectionGroup().getEndRes();
2906 seqs = viewport.getAlignment().getSequencesArray();
2909 // This is to maintain viewport position on first residue
2910 // of first sequence
2911 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2912 int startRes = seq.findPosition(vpRanges.getStartRes());
2914 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2915 viewport.getAlignment()));
2917 vpRanges.setStartRes(seq.findIndex(startRes) - 1);
2919 viewport.firePropertyChange("alignment", null,
2920 viewport.getAlignment().getSequences());
2931 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2933 viewport.setPadGaps(padGapsMenuitem.isSelected());
2934 viewport.firePropertyChange("alignment", null,
2935 viewport.getAlignment().getSequences());
2945 public void findMenuItem_actionPerformed(ActionEvent e)
2951 * Create a new view of the current alignment.
2954 public void newView_actionPerformed(ActionEvent e)
2956 newView(null, true);
2960 * Creates and shows a new view of the current alignment.
2963 * title of newly created view; if null, one will be generated
2964 * @param copyAnnotation
2965 * if true then duplicate all annnotation, groups and settings
2966 * @return new alignment panel, already displayed.
2968 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2971 * Create a new AlignmentPanel (with its own, new Viewport)
2973 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2975 if (!copyAnnotation)
2978 * remove all groups and annotation except for the automatic stuff
2980 newap.av.getAlignment().deleteAllGroups();
2981 newap.av.getAlignment().deleteAllAnnotations(false);
2984 newap.av.setGatherViewsHere(false);
2986 if (viewport.viewName == null)
2988 viewport.viewName = MessageManager
2989 .getString("label.view_name_original");
2993 * Views share the same edits undo and redo stacks
2995 newap.av.setHistoryList(viewport.getHistoryList());
2996 newap.av.setRedoList(viewport.getRedoList());
2999 * Views share the same mappings; need to deregister any new mappings
3000 * created by copyAlignPanel, and register the new reference to the shared
3003 newap.av.replaceMappings(viewport.getAlignment());
3006 * start up cDNA consensus (if applicable) now mappings are in place
3008 if (newap.av.initComplementConsensus())
3010 newap.refresh(true); // adjust layout of annotations
3013 newap.av.viewName = getNewViewName(viewTitle);
3015 addAlignmentPanel(newap, true);
3016 newap.alignmentChanged();
3018 if (alignPanels.size() == 2)
3020 viewport.setGatherViewsHere(true);
3022 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
3027 * Make a new name for the view, ensuring it is unique within the current
3028 * sequenceSetId. (This used to be essential for Jalview Project archives, but
3029 * these now use viewId. Unique view names are still desirable for usability.)
3034 protected String getNewViewName(String viewTitle)
3036 int index = Desktop.getViewCount(viewport.getSequenceSetId());
3037 boolean addFirstIndex = false;
3038 if (viewTitle == null || viewTitle.trim().length() == 0)
3040 viewTitle = MessageManager.getString("action.view");
3041 addFirstIndex = true;
3045 index = 1;// we count from 1 if given a specific name
3047 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
3049 List<Component> comps = PaintRefresher.components
3050 .get(viewport.getSequenceSetId());
3052 List<String> existingNames = getExistingViewNames(comps);
3054 while (existingNames.contains(newViewName))
3056 newViewName = viewTitle + " " + (++index);
3062 * Returns a list of distinct view names found in the given list of
3063 * components. View names are held on the viewport of an AlignmentPanel.
3068 protected List<String> getExistingViewNames(List<Component> comps)
3070 List<String> existingNames = new ArrayList<>();
3071 for (Component comp : comps)
3073 if (comp instanceof AlignmentPanel)
3075 AlignmentPanel ap = (AlignmentPanel) comp;
3076 if (!existingNames.contains(ap.av.viewName))
3078 existingNames.add(ap.av.viewName);
3082 return existingNames;
3086 * Explode tabbed views into separate windows.
3089 public void expandViews_actionPerformed(ActionEvent e)
3091 Desktop.explodeViews(this);
3095 * Gather views in separate windows back into a tabbed presentation.
3098 public void gatherViews_actionPerformed(ActionEvent e)
3100 Desktop.instance.gatherViews(this);
3110 public void font_actionPerformed(ActionEvent e)
3112 new FontChooser(alignPanel);
3122 protected void seqLimit_actionPerformed(ActionEvent e)
3124 viewport.setShowJVSuffix(seqLimits.isSelected());
3126 alignPanel.getIdPanel().getIdCanvas()
3127 .setPreferredSize(alignPanel.calculateIdWidth());
3128 alignPanel.paintAlignment(true);
3132 public void idRightAlign_actionPerformed(ActionEvent e)
3134 viewport.setRightAlignIds(idRightAlign.isSelected());
3135 alignPanel.paintAlignment(true);
3139 public void centreColumnLabels_actionPerformed(ActionEvent e)
3141 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3142 alignPanel.paintAlignment(true);
3148 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3151 protected void followHighlight_actionPerformed()
3154 * Set the 'follow' flag on the Viewport (and scroll to position if now
3157 final boolean state = this.followHighlightMenuItem.getState();
3158 viewport.setFollowHighlight(state);
3161 alignPanel.scrollToPosition(viewport.getSearchResults(), false);
3172 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3174 viewport.setColourText(colourTextMenuItem.isSelected());
3175 alignPanel.paintAlignment(true);
3185 public void wrapMenuItem_actionPerformed(ActionEvent e)
3187 scaleAbove.setVisible(wrapMenuItem.isSelected());
3188 scaleLeft.setVisible(wrapMenuItem.isSelected());
3189 scaleRight.setVisible(wrapMenuItem.isSelected());
3190 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3191 alignPanel.updateLayout();
3195 public void showAllSeqs_actionPerformed(ActionEvent e)
3197 viewport.showAllHiddenSeqs();
3201 public void showAllColumns_actionPerformed(ActionEvent e)
3203 viewport.showAllHiddenColumns();
3204 alignPanel.paintAlignment(true);
3205 viewport.sendSelection();
3209 public void hideSelSequences_actionPerformed(ActionEvent e)
3211 viewport.hideAllSelectedSeqs();
3215 * called by key handler and the hide all/show all menu items
3220 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3223 boolean hide = false;
3224 SequenceGroup sg = viewport.getSelectionGroup();
3225 if (!toggleSeqs && !toggleCols)
3227 // Hide everything by the current selection - this is a hack - we do the
3228 // invert and then hide
3229 // first check that there will be visible columns after the invert.
3230 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3231 && sg.getStartRes() <= sg.getEndRes()))
3233 // now invert the sequence set, if required - empty selection implies
3234 // that no hiding is required.
3237 invertSequenceMenuItem_actionPerformed(null);
3238 sg = viewport.getSelectionGroup();
3242 viewport.expandColSelection(sg, true);
3243 // finally invert the column selection and get the new sequence
3245 invertColSel_actionPerformed(null);
3252 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3254 hideSelSequences_actionPerformed(null);
3257 else if (!(toggleCols && viewport.hasSelectedColumns()))
3259 showAllSeqs_actionPerformed(null);
3265 if (viewport.hasSelectedColumns())
3267 hideSelColumns_actionPerformed(null);
3270 viewport.setSelectionGroup(sg);
3275 showAllColumns_actionPerformed(null);
3284 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3285 * event.ActionEvent)
3288 public void hideAllButSelection_actionPerformed(ActionEvent e)
3290 toggleHiddenRegions(false, false);
3291 viewport.sendSelection();
3298 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3302 public void hideAllSelection_actionPerformed(ActionEvent e)
3304 SequenceGroup sg = viewport.getSelectionGroup();
3305 viewport.expandColSelection(sg, false);
3306 viewport.hideAllSelectedSeqs();
3307 viewport.hideSelectedColumns();
3308 alignPanel.paintAlignment(true);
3309 viewport.sendSelection();
3316 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3320 public void showAllhidden_actionPerformed(ActionEvent e)
3322 viewport.showAllHiddenColumns();
3323 viewport.showAllHiddenSeqs();
3324 alignPanel.paintAlignment(true);
3325 viewport.sendSelection();
3329 public void hideSelColumns_actionPerformed(ActionEvent e)
3331 viewport.hideSelectedColumns();
3332 alignPanel.paintAlignment(true);
3333 viewport.sendSelection();
3337 public void hiddenMarkers_actionPerformed(ActionEvent e)
3339 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3350 protected void scaleAbove_actionPerformed(ActionEvent e)
3352 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3353 alignPanel.paintAlignment(true);
3363 protected void scaleLeft_actionPerformed(ActionEvent e)
3365 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3366 alignPanel.paintAlignment(true);
3376 protected void scaleRight_actionPerformed(ActionEvent e)
3378 viewport.setScaleRightWrapped(scaleRight.isSelected());
3379 alignPanel.paintAlignment(true);
3389 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3391 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3392 alignPanel.paintAlignment(true);
3402 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3404 viewport.setShowText(viewTextMenuItem.isSelected());
3405 alignPanel.paintAlignment(true);
3415 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3417 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3418 alignPanel.paintAlignment(true);
3421 public FeatureSettings featureSettings;
3424 public FeatureSettingsControllerI getFeatureSettingsUI()
3426 return featureSettings;
3430 public void featureSettings_actionPerformed(ActionEvent e)
3432 if (featureSettings != null)
3434 featureSettings.close();
3435 featureSettings = null;
3437 if (!showSeqFeatures.isSelected())
3439 // make sure features are actually displayed
3440 showSeqFeatures.setSelected(true);
3441 showSeqFeatures_actionPerformed(null);
3443 featureSettings = new FeatureSettings(this);
3447 * Set or clear 'Show Sequence Features'
3453 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3455 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3456 alignPanel.paintAlignment(true);
3460 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3461 * the annotations panel as a whole.
3463 * The options to show/hide all annotations should be enabled when the panel
3464 * is shown, and disabled when the panel is hidden.
3469 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3471 final boolean setVisible = annotationPanelMenuItem.isSelected();
3472 viewport.setShowAnnotation(setVisible);
3473 this.showAllSeqAnnotations.setEnabled(setVisible);
3474 this.hideAllSeqAnnotations.setEnabled(setVisible);
3475 this.showAllAlAnnotations.setEnabled(setVisible);
3476 this.hideAllAlAnnotations.setEnabled(setVisible);
3477 alignPanel.updateLayout();
3481 public void alignmentProperties()
3483 JEditorPane editPane = new JEditorPane("text/html", "");
3484 editPane.setEditable(false);
3485 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3488 MessageManager.formatMessage("label.html_content", new Object[]
3489 { contents.toString() }));
3490 JInternalFrame frame = new JInternalFrame();
3491 frame.getContentPane().add(new JScrollPane(editPane));
3493 Desktop.addInternalFrame(frame, MessageManager
3494 .formatMessage("label.alignment_properties", new Object[]
3495 { getTitle() }), 500, 400);
3505 public void overviewMenuItem_actionPerformed(ActionEvent e)
3507 if (alignPanel.overviewPanel != null)
3512 JInternalFrame frame = new JInternalFrame();
3513 final OverviewPanel overview = new OverviewPanel(alignPanel);
3514 frame.setContentPane(overview);
3515 Desktop.addInternalFrame(frame, MessageManager
3516 .formatMessage("label.overview_params", new Object[]
3517 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3520 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3521 frame.addInternalFrameListener(
3522 new javax.swing.event.InternalFrameAdapter()
3525 public void internalFrameClosed(
3526 javax.swing.event.InternalFrameEvent evt)
3529 alignPanel.setOverviewPanel(null);
3533 alignPanel.setOverviewPanel(overview);
3537 public void textColour_actionPerformed()
3539 new TextColourChooser().chooseColour(alignPanel, null);
3543 * public void covariationColour_actionPerformed() {
3545 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3549 public void annotationColour_actionPerformed()
3551 new AnnotationColourChooser(viewport, alignPanel);
3555 public void annotationColumn_actionPerformed(ActionEvent e)
3557 new AnnotationColumnChooser(viewport, alignPanel);
3561 * Action on the user checking or unchecking the option to apply the selected
3562 * colour scheme to all groups. If unchecked, groups may have their own
3563 * independent colour schemes.
3568 public void applyToAllGroups_actionPerformed(boolean selected)
3570 viewport.setColourAppliesToAllGroups(selected);
3574 * Action on user selecting a colour from the colour menu
3577 * the name (not the menu item label!) of the colour scheme
3580 public void changeColour_actionPerformed(String name)
3583 * 'User Defined' opens a panel to configure or load a
3584 * user-defined colour scheme
3586 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3588 new UserDefinedColours(alignPanel);
3593 * otherwise set the chosen colour scheme (or null for 'None')
3595 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3596 viewport.getAlignment(), viewport.getHiddenRepSequences());
3601 * Actions on setting or changing the alignment colour scheme
3606 public void changeColour(ColourSchemeI cs)
3608 // TODO: pull up to controller method
3609 ColourMenuHelper.setColourSelected(colourMenu, cs);
3611 viewport.setGlobalColourScheme(cs);
3613 alignPanel.paintAlignment(true);
3617 * Show the PID threshold slider panel
3620 protected void modifyPID_actionPerformed()
3622 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3623 alignPanel.getViewName());
3624 SliderPanel.showPIDSlider();
3628 * Show the Conservation slider panel
3631 protected void modifyConservation_actionPerformed()
3633 SliderPanel.setConservationSlider(alignPanel,
3634 viewport.getResidueShading(), alignPanel.getViewName());
3635 SliderPanel.showConservationSlider();
3639 * Action on selecting or deselecting (Colour) By Conservation
3642 public void conservationMenuItem_actionPerformed(boolean selected)
3644 modifyConservation.setEnabled(selected);
3645 viewport.setConservationSelected(selected);
3646 viewport.getResidueShading().setConservationApplied(selected);
3648 changeColour(viewport.getGlobalColourScheme());
3651 modifyConservation_actionPerformed();
3655 SliderPanel.hideConservationSlider();
3660 * Action on selecting or deselecting (Colour) Above PID Threshold
3663 public void abovePIDThreshold_actionPerformed(boolean selected)
3665 modifyPID.setEnabled(selected);
3666 viewport.setAbovePIDThreshold(selected);
3669 viewport.getResidueShading().setThreshold(0,
3670 viewport.isIgnoreGapsConsensus());
3673 changeColour(viewport.getGlobalColourScheme());
3676 modifyPID_actionPerformed();
3680 SliderPanel.hidePIDSlider();
3691 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3693 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3694 AlignmentSorter.sortByPID(viewport.getAlignment(),
3695 viewport.getAlignment().getSequenceAt(0));
3696 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3697 viewport.getAlignment()));
3698 alignPanel.paintAlignment(true);
3708 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3710 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3711 AlignmentSorter.sortByID(viewport.getAlignment());
3713 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3714 alignPanel.paintAlignment(true);
3724 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3726 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3727 AlignmentSorter.sortByLength(viewport.getAlignment());
3728 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3729 viewport.getAlignment()));
3730 alignPanel.paintAlignment(true);
3740 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3742 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3743 AlignmentSorter.sortByGroup(viewport.getAlignment());
3744 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3745 viewport.getAlignment()));
3747 alignPanel.paintAlignment(true);
3757 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3759 new RedundancyPanel(alignPanel, this);
3769 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3771 if ((viewport.getSelectionGroup() == null)
3772 || (viewport.getSelectionGroup().getSize() < 2))
3774 JvOptionPane.showInternalMessageDialog(this,
3775 MessageManager.getString(
3776 "label.you_must_select_least_two_sequences"),
3777 MessageManager.getString("label.invalid_selection"),
3778 JvOptionPane.WARNING_MESSAGE);
3782 JInternalFrame frame = new JInternalFrame();
3783 frame.setContentPane(new PairwiseAlignPanel(viewport));
3784 Desktop.addInternalFrame(frame,
3785 MessageManager.getString("action.pairwise_alignment"), 600,
3791 public void autoCalculate_actionPerformed(ActionEvent e)
3793 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3794 if (viewport.autoCalculateConsensus)
3796 viewport.firePropertyChange("alignment", null,
3797 viewport.getAlignment().getSequences());
3802 public void sortByTreeOption_actionPerformed(ActionEvent e)
3804 viewport.sortByTree = sortByTree.isSelected();
3808 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3810 viewport.followSelection = listenToViewSelections.isSelected();
3814 * Constructs a tree panel and adds it to the desktop
3817 * tree type (NJ or AV)
3819 * name of score model used to compute the tree
3821 * parameters for the distance or similarity calculation
3823 void newTreePanel(String type, String modelName,
3824 SimilarityParamsI options)
3826 String frameTitle = "";
3829 boolean onSelection = false;
3830 if (viewport.getSelectionGroup() != null
3831 && viewport.getSelectionGroup().getSize() > 0)
3833 SequenceGroup sg = viewport.getSelectionGroup();
3835 /* Decide if the selection is a column region */
3836 for (SequenceI _s : sg.getSequences())
3838 if (_s.getLength() < sg.getEndRes())
3840 JvOptionPane.showMessageDialog(Desktop.desktop,
3841 MessageManager.getString(
3842 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3843 MessageManager.getString(
3844 "label.sequences_selection_not_aligned"),
3845 JvOptionPane.WARNING_MESSAGE);
3854 if (viewport.getAlignment().getHeight() < 2)
3860 tp = new TreePanel(alignPanel, type, modelName, options);
3861 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3863 frameTitle += " from ";
3865 if (viewport.viewName != null)
3867 frameTitle += viewport.viewName + " of ";
3870 frameTitle += this.title;
3872 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3883 public void addSortByOrderMenuItem(String title,
3884 final AlignmentOrder order)
3886 final JMenuItem item = new JMenuItem(MessageManager
3887 .formatMessage("action.by_title_param", new Object[]
3890 item.addActionListener(new java.awt.event.ActionListener()
3893 public void actionPerformed(ActionEvent e)
3895 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3897 // TODO: JBPNote - have to map order entries to curent SequenceI
3899 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3901 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3902 viewport.getAlignment()));
3904 alignPanel.paintAlignment(true);
3910 * Add a new sort by annotation score menu item
3913 * the menu to add the option to
3915 * the label used to retrieve scores for each sequence on the
3918 public void addSortByAnnotScoreMenuItem(JMenu sort,
3919 final String scoreLabel)
3921 final JMenuItem item = new JMenuItem(scoreLabel);
3923 item.addActionListener(new java.awt.event.ActionListener()
3926 public void actionPerformed(ActionEvent e)
3928 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3929 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3930 viewport.getAlignment());// ,viewport.getSelectionGroup());
3931 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3932 viewport.getAlignment()));
3933 alignPanel.paintAlignment(true);
3939 * last hash for alignment's annotation array - used to minimise cost of
3942 protected int _annotationScoreVectorHash;
3945 * search the alignment and rebuild the sort by annotation score submenu the
3946 * last alignment annotation vector hash is stored to minimize cost of
3947 * rebuilding in subsequence calls.
3951 public void buildSortByAnnotationScoresMenu()
3953 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3958 if (viewport.getAlignment().getAlignmentAnnotation()
3959 .hashCode() != _annotationScoreVectorHash)
3961 sortByAnnotScore.removeAll();
3962 // almost certainly a quicker way to do this - but we keep it simple
3963 Hashtable scoreSorts = new Hashtable();
3964 AlignmentAnnotation aann[];
3965 for (SequenceI sqa : viewport.getAlignment().getSequences())
3967 aann = sqa.getAnnotation();
3968 for (int i = 0; aann != null && i < aann.length; i++)
3970 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3972 scoreSorts.put(aann[i].label, aann[i].label);
3976 Enumeration labels = scoreSorts.keys();
3977 while (labels.hasMoreElements())
3979 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3980 (String) labels.nextElement());
3982 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3985 _annotationScoreVectorHash = viewport.getAlignment()
3986 .getAlignmentAnnotation().hashCode();
3991 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3992 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3993 * call. Listeners are added to remove the menu item when the treePanel is
3994 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3998 public void buildTreeSortMenu()
4000 sortByTreeMenu.removeAll();
4002 List<Component> comps = PaintRefresher.components
4003 .get(viewport.getSequenceSetId());
4004 List<TreePanel> treePanels = new ArrayList<>();
4005 for (Component comp : comps)
4007 if (comp instanceof TreePanel)
4009 treePanels.add((TreePanel) comp);
4013 if (treePanels.size() < 1)
4015 sortByTreeMenu.setVisible(false);
4019 sortByTreeMenu.setVisible(true);
4021 for (final TreePanel tp : treePanels)
4023 final JMenuItem item = new JMenuItem(tp.getTitle());
4024 item.addActionListener(new java.awt.event.ActionListener()
4027 public void actionPerformed(ActionEvent e)
4029 tp.sortByTree_actionPerformed();
4030 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4035 sortByTreeMenu.add(item);
4039 public boolean sortBy(AlignmentOrder alorder, String undoname)
4041 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4042 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4043 if (undoname != null)
4045 addHistoryItem(new OrderCommand(undoname, oldOrder,
4046 viewport.getAlignment()));
4048 alignPanel.paintAlignment(true);
4053 * Work out whether the whole set of sequences or just the selected set will
4054 * be submitted for multiple alignment.
4057 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4059 // Now, check we have enough sequences
4060 AlignmentView msa = null;
4062 if ((viewport.getSelectionGroup() != null)
4063 && (viewport.getSelectionGroup().getSize() > 1))
4065 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4066 // some common interface!
4068 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4069 * SequenceI[sz = seqs.getSize(false)];
4071 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4072 * seqs.getSequenceAt(i); }
4074 msa = viewport.getAlignmentView(true);
4076 else if (viewport.getSelectionGroup() != null
4077 && viewport.getSelectionGroup().getSize() == 1)
4079 int option = JvOptionPane.showConfirmDialog(this,
4080 MessageManager.getString("warn.oneseq_msainput_selection"),
4081 MessageManager.getString("label.invalid_selection"),
4082 JvOptionPane.OK_CANCEL_OPTION);
4083 if (option == JvOptionPane.OK_OPTION)
4085 msa = viewport.getAlignmentView(false);
4090 msa = viewport.getAlignmentView(false);
4096 * Decides what is submitted to a secondary structure prediction service: the
4097 * first sequence in the alignment, or in the current selection, or, if the
4098 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4099 * region or the whole alignment. (where the first sequence in the set is the
4100 * one that the prediction will be for).
4102 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4104 AlignmentView seqs = null;
4106 if ((viewport.getSelectionGroup() != null)
4107 && (viewport.getSelectionGroup().getSize() > 0))
4109 seqs = viewport.getAlignmentView(true);
4113 seqs = viewport.getAlignmentView(false);
4115 // limit sequences - JBPNote in future - could spawn multiple prediction
4117 // TODO: viewport.getAlignment().isAligned is a global state - the local
4118 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4119 if (!viewport.getAlignment().isAligned(false))
4121 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4122 // TODO: if seqs.getSequences().length>1 then should really have warned
4136 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4138 // Pick the tree file
4139 JalviewFileChooser chooser = new JalviewFileChooser(
4140 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4141 chooser.setFileView(new JalviewFileView());
4142 chooser.setDialogTitle(
4143 MessageManager.getString("label.select_newick_like_tree_file"));
4144 chooser.setToolTipText(
4145 MessageManager.getString("label.load_tree_file"));
4147 int value = chooser.showOpenDialog(null);
4149 if (value == JalviewFileChooser.APPROVE_OPTION)
4151 String filePath = chooser.getSelectedFile().getPath();
4152 Cache.setProperty("LAST_DIRECTORY", filePath);
4153 NewickFile fin = null;
4156 fin = new NewickFile(filePath, DataSourceType.FILE);
4157 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4158 } catch (Exception ex)
4160 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4161 MessageManager.getString("label.problem_reading_tree_file"),
4162 JvOptionPane.WARNING_MESSAGE);
4163 ex.printStackTrace();
4165 if (fin != null && fin.hasWarningMessage())
4167 JvOptionPane.showMessageDialog(Desktop.desktop,
4168 fin.getWarningMessage(),
4170 .getString("label.possible_problem_with_tree_file"),
4171 JvOptionPane.WARNING_MESSAGE);
4176 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4178 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4181 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4182 int h, int x, int y)
4184 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4188 * Add a treeviewer for the tree extracted from a Newick file object to the
4189 * current alignment view
4196 * Associated alignment input data (or null)
4205 * @return TreePanel handle
4207 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4208 AlignmentView input, int w, int h, int x, int y)
4210 TreePanel tp = null;
4216 if (nf.getTree() != null)
4218 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4224 tp.setLocation(x, y);
4227 Desktop.addInternalFrame(tp, treeTitle, w, h);
4229 } catch (Exception ex)
4231 ex.printStackTrace();
4237 private boolean buildingMenu = false;
4240 * Generates menu items and listener event actions for web service clients
4243 public void BuildWebServiceMenu()
4245 while (buildingMenu)
4249 System.err.println("Waiting for building menu to finish.");
4251 } catch (Exception e)
4255 final AlignFrame me = this;
4256 buildingMenu = true;
4257 new Thread(new Runnable()
4262 final List<JMenuItem> legacyItems = new ArrayList<>();
4265 // System.err.println("Building ws menu again "
4266 // + Thread.currentThread());
4267 // TODO: add support for context dependent disabling of services based
4269 // alignment and current selection
4270 // TODO: add additional serviceHandle parameter to specify abstract
4272 // class independently of AbstractName
4273 // TODO: add in rediscovery GUI function to restart discoverer
4274 // TODO: group services by location as well as function and/or
4276 // object broker mechanism.
4277 final Vector<JMenu> wsmenu = new Vector<>();
4278 final IProgressIndicator af = me;
4281 * do not i18n these strings - they are hard-coded in class
4282 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4283 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4285 final JMenu msawsmenu = new JMenu("Alignment");
4286 final JMenu secstrmenu = new JMenu(
4287 "Secondary Structure Prediction");
4288 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4289 final JMenu analymenu = new JMenu("Analysis");
4290 final JMenu dismenu = new JMenu("Protein Disorder");
4291 // JAL-940 - only show secondary structure prediction services from
4292 // the legacy server
4293 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4295 Discoverer.services != null && (Discoverer.services.size() > 0))
4297 // TODO: refactor to allow list of AbstractName/Handler bindings to
4299 // stored or retrieved from elsewhere
4300 // No MSAWS used any more:
4301 // Vector msaws = null; // (Vector)
4302 // Discoverer.services.get("MsaWS");
4303 Vector secstrpr = (Vector) Discoverer.services
4305 if (secstrpr != null)
4307 // Add any secondary structure prediction services
4308 for (int i = 0, j = secstrpr.size(); i < j; i++)
4310 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4312 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4313 .getServiceClient(sh);
4314 int p = secstrmenu.getItemCount();
4315 impl.attachWSMenuEntry(secstrmenu, me);
4316 int q = secstrmenu.getItemCount();
4317 for (int litm = p; litm < q; litm++)
4319 legacyItems.add(secstrmenu.getItem(litm));
4325 // Add all submenus in the order they should appear on the web
4327 wsmenu.add(msawsmenu);
4328 wsmenu.add(secstrmenu);
4329 wsmenu.add(dismenu);
4330 wsmenu.add(analymenu);
4331 // No search services yet
4332 // wsmenu.add(seqsrchmenu);
4334 javax.swing.SwingUtilities.invokeLater(new Runnable()
4341 webService.removeAll();
4342 // first, add discovered services onto the webservices menu
4343 if (wsmenu.size() > 0)
4345 for (int i = 0, j = wsmenu.size(); i < j; i++)
4347 webService.add(wsmenu.get(i));
4352 webService.add(me.webServiceNoServices);
4354 // TODO: move into separate menu builder class.
4355 boolean new_sspred = false;
4356 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4358 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4359 if (jws2servs != null)
4361 if (jws2servs.hasServices())
4363 jws2servs.attachWSMenuEntry(webService, me);
4364 for (Jws2Instance sv : jws2servs.getServices())
4366 if (sv.description.toLowerCase().contains("jpred"))
4368 for (JMenuItem jmi : legacyItems)
4370 jmi.setVisible(false);
4376 if (jws2servs.isRunning())
4378 JMenuItem tm = new JMenuItem(
4379 "Still discovering JABA Services");
4380 tm.setEnabled(false);
4385 build_urlServiceMenu(me.webService);
4386 build_fetchdbmenu(webService);
4387 for (JMenu item : wsmenu)
4389 if (item.getItemCount() == 0)
4391 item.setEnabled(false);
4395 item.setEnabled(true);
4398 } catch (Exception e)
4401 "Exception during web service menu building process.",
4406 } catch (Exception e)
4409 buildingMenu = false;
4416 * construct any groupURL type service menu entries.
4420 private void build_urlServiceMenu(JMenu webService)
4422 // TODO: remove this code when 2.7 is released
4423 // DEBUG - alignmentView
4425 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4426 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4428 * @Override public void actionPerformed(ActionEvent e) {
4429 * jalview.datamodel.AlignmentView
4430 * .testSelectionViews(af.viewport.getAlignment(),
4431 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4433 * }); webService.add(testAlView);
4435 // TODO: refactor to RestClient discoverer and merge menu entries for
4436 // rest-style services with other types of analysis/calculation service
4437 // SHmmr test client - still being implemented.
4438 // DEBUG - alignmentView
4440 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4443 client.attachWSMenuEntry(
4444 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4450 * Searches the alignment sequences for xRefs and builds the Show
4451 * Cross-References menu (formerly called Show Products), with database
4452 * sources for which cross-references are found (protein sources for a
4453 * nucleotide alignment and vice versa)
4455 * @return true if Show Cross-references menu should be enabled
4457 public boolean canShowProducts()
4459 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4460 AlignmentI dataset = viewport.getAlignment().getDataset();
4462 showProducts.removeAll();
4463 final boolean dna = viewport.getAlignment().isNucleotide();
4465 if (seqs == null || seqs.length == 0)
4467 // nothing to see here.
4471 boolean showp = false;
4474 List<String> ptypes = new CrossRef(seqs, dataset)
4475 .findXrefSourcesForSequences(dna);
4477 for (final String source : ptypes)
4480 final AlignFrame af = this;
4481 JMenuItem xtype = new JMenuItem(source);
4482 xtype.addActionListener(new ActionListener()
4485 public void actionPerformed(ActionEvent e)
4487 showProductsFor(af.viewport.getSequenceSelection(), dna,
4491 showProducts.add(xtype);
4493 showProducts.setVisible(showp);
4494 showProducts.setEnabled(showp);
4495 } catch (Exception e)
4498 "canShowProducts threw an exception - please report to help@jalview.org",
4506 * Finds and displays cross-references for the selected sequences (protein
4507 * products for nucleotide sequences, dna coding sequences for peptides).
4510 * the sequences to show cross-references for
4512 * true if from a nucleotide alignment (so showing proteins)
4514 * the database to show cross-references for
4516 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4517 final String source)
4519 new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4524 * Construct and display a new frame containing the translation of this
4525 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4528 public void showTranslation_actionPerformed(ActionEvent e)
4530 AlignmentI al = null;
4533 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4535 al = dna.translateCdna();
4536 } catch (Exception ex)
4538 jalview.bin.Cache.log.error(
4539 "Exception during translation. Please report this !", ex);
4540 final String msg = MessageManager.getString(
4541 "label.error_when_translating_sequences_submit_bug_report");
4542 final String errorTitle = MessageManager
4543 .getString("label.implementation_error")
4544 + MessageManager.getString("label.translation_failed");
4545 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4546 JvOptionPane.ERROR_MESSAGE);
4549 if (al == null || al.getHeight() == 0)
4551 final String msg = MessageManager.getString(
4552 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4553 final String errorTitle = MessageManager
4554 .getString("label.translation_failed");
4555 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4556 JvOptionPane.WARNING_MESSAGE);
4560 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4561 af.setFileFormat(this.currentFileFormat);
4562 final String newTitle = MessageManager
4563 .formatMessage("label.translation_of_params", new Object[]
4564 { this.getTitle() });
4565 af.setTitle(newTitle);
4566 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4568 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4569 viewport.openSplitFrame(af, new Alignment(seqs));
4573 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4580 * Set the file format
4584 public void setFileFormat(FileFormatI format)
4586 this.currentFileFormat = format;
4590 * Try to load a features file onto the alignment.
4593 * contents or path to retrieve file
4595 * access mode of file (see jalview.io.AlignFile)
4596 * @return true if features file was parsed correctly.
4598 public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4600 return avc.parseFeaturesFile(file, sourceType,
4601 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4606 public void refreshFeatureUI(boolean enableIfNecessary)
4608 // note - currently this is only still here rather than in the controller
4609 // because of the featureSettings hard reference that is yet to be
4611 if (enableIfNecessary)
4613 viewport.setShowSequenceFeatures(true);
4614 showSeqFeatures.setSelected(true);
4620 public void dragEnter(DropTargetDragEvent evt)
4625 public void dragExit(DropTargetEvent evt)
4630 public void dragOver(DropTargetDragEvent evt)
4635 public void dropActionChanged(DropTargetDragEvent evt)
4640 public void drop(DropTargetDropEvent evt)
4642 // JAL-1552 - acceptDrop required before getTransferable call for
4643 // Java's Transferable for native dnd
4644 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4645 Transferable t = evt.getTransferable();
4646 List<String> files = new ArrayList<>();
4647 List<DataSourceType> protocols = new ArrayList<>();
4651 Desktop.transferFromDropTarget(files, protocols, evt, t);
4652 } catch (Exception e)
4654 e.printStackTrace();
4660 // check to see if any of these files have names matching sequences in
4662 SequenceIdMatcher idm = new SequenceIdMatcher(
4663 viewport.getAlignment().getSequencesArray());
4665 * Object[] { String,SequenceI}
4667 ArrayList<Object[]> filesmatched = new ArrayList<>();
4668 ArrayList<String> filesnotmatched = new ArrayList<>();
4669 for (int i = 0; i < files.size(); i++)
4671 String file = files.get(i).toString();
4673 DataSourceType protocol = FormatAdapter.checkProtocol(file);
4674 if (protocol == DataSourceType.FILE)
4676 File fl = new File(file);
4677 pdbfn = fl.getName();
4679 else if (protocol == DataSourceType.URL)
4681 URL url = new URL(file);
4682 pdbfn = url.getFile();
4684 if (pdbfn.length() > 0)
4686 // attempt to find a match in the alignment
4687 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4688 int l = 0, c = pdbfn.indexOf(".");
4689 while (mtch == null && c != -1)
4694 } while ((c = pdbfn.indexOf(".", l)) > l);
4697 pdbfn = pdbfn.substring(0, l);
4699 mtch = idm.findAllIdMatches(pdbfn);
4703 FileFormatI type = null;
4706 type = new IdentifyFile().identify(file, protocol);
4707 } catch (Exception ex)
4711 if (type != null && type.isStructureFile())
4713 filesmatched.add(new Object[] { file, protocol, mtch });
4717 // File wasn't named like one of the sequences or wasn't a PDB file.
4718 filesnotmatched.add(file);
4722 if (filesmatched.size() > 0)
4724 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4725 || JvOptionPane.showConfirmDialog(this,
4726 MessageManager.formatMessage(
4727 "label.automatically_associate_structure_files_with_sequences_same_name",
4729 { Integer.valueOf(filesmatched.size())
4731 MessageManager.getString(
4732 "label.automatically_associate_structure_files_by_name"),
4733 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4736 for (Object[] fm : filesmatched)
4738 // try and associate
4739 // TODO: may want to set a standard ID naming formalism for
4740 // associating PDB files which have no IDs.
4741 for (SequenceI toassoc : (SequenceI[]) fm[2])
4743 PDBEntry pe = new AssociatePdbFileWithSeq()
4744 .associatePdbWithSeq((String) fm[0],
4745 (DataSourceType) fm[1], toassoc, false,
4749 System.err.println("Associated file : " + ((String) fm[0])
4750 + " with " + toassoc.getDisplayId(true));
4754 alignPanel.paintAlignment(true);
4758 if (filesnotmatched.size() > 0)
4760 if (assocfiles > 0 && (Cache.getDefault(
4761 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4762 || JvOptionPane.showConfirmDialog(this,
4763 "<html>" + MessageManager.formatMessage(
4764 "label.ignore_unmatched_dropped_files_info",
4766 { Integer.valueOf(filesnotmatched.size())
4769 MessageManager.getString(
4770 "label.ignore_unmatched_dropped_files"),
4771 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4775 for (String fn : filesnotmatched)
4777 loadJalviewDataFile(fn, null, null, null);
4781 } catch (Exception ex)
4783 ex.printStackTrace();
4789 * Attempt to load a "dropped" file or URL string, by testing in turn for
4791 * <li>an Annotation file</li>
4792 * <li>a JNet file</li>
4793 * <li>a features file</li>
4794 * <li>else try to interpret as an alignment file</li>
4798 * either a filename or a URL string.
4799 * @throws InterruptedException
4800 * @throws IOException
4802 public void loadJalviewDataFile(String file, DataSourceType sourceType,
4803 FileFormatI format, SequenceI assocSeq)
4807 if (sourceType == null)
4809 sourceType = FormatAdapter.checkProtocol(file);
4811 // if the file isn't identified, or not positively identified as some
4812 // other filetype (PFAM is default unidentified alignment file type) then
4813 // try to parse as annotation.
4814 boolean isAnnotation = (format == null
4815 || FileFormat.Pfam.equals(format))
4816 ? new AnnotationFile().annotateAlignmentView(viewport,
4822 // first see if its a T-COFFEE score file
4823 TCoffeeScoreFile tcf = null;
4826 tcf = new TCoffeeScoreFile(file, sourceType);
4829 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4833 new TCoffeeColourScheme(viewport.getAlignment()));
4834 isAnnotation = true;
4835 statusBar.setText(MessageManager.getString(
4836 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4840 // some problem - if no warning its probable that the ID matching
4841 // process didn't work
4842 JvOptionPane.showMessageDialog(Desktop.desktop,
4843 tcf.getWarningMessage() == null
4844 ? MessageManager.getString(
4845 "label.check_file_matches_sequence_ids_alignment")
4846 : tcf.getWarningMessage(),
4847 MessageManager.getString(
4848 "label.problem_reading_tcoffee_score_file"),
4849 JvOptionPane.WARNING_MESSAGE);
4856 } catch (Exception x)
4859 "Exception when processing data source as T-COFFEE score file",
4865 // try to see if its a JNet 'concise' style annotation file *before*
4867 // try to parse it as a features file
4870 format = new IdentifyFile().identify(file, sourceType);
4872 if (FileFormat.ScoreMatrix == format)
4874 ScoreMatrixFile sm = new ScoreMatrixFile(
4875 new FileParse(file, sourceType));
4877 // todo: i18n this message
4878 statusBar.setText(MessageManager.formatMessage(
4879 "label.successfully_loaded_matrix",
4880 sm.getMatrixName()));
4882 else if (FileFormat.Jnet.equals(format))
4884 JPredFile predictions = new JPredFile(file, sourceType);
4885 new JnetAnnotationMaker();
4886 JnetAnnotationMaker.add_annotation(predictions,
4887 viewport.getAlignment(), 0, false);
4888 SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
4889 viewport.getAlignment().setSeqrep(repseq);
4890 HiddenColumns cs = new HiddenColumns();
4891 cs.hideInsertionsFor(repseq);
4892 viewport.getAlignment().setHiddenColumns(cs);
4893 isAnnotation = true;
4895 // else if (IdentifyFile.FeaturesFile.equals(format))
4896 else if (FileFormat.Features.equals(format))
4898 if (parseFeaturesFile(file, sourceType))
4900 alignPanel.paintAlignment(true);
4905 new FileLoader().LoadFile(viewport, file, sourceType, format);
4911 alignPanel.adjustAnnotationHeight();
4912 viewport.updateSequenceIdColours();
4913 buildSortByAnnotationScoresMenu();
4914 alignPanel.paintAlignment(true);
4916 } catch (Exception ex)
4918 ex.printStackTrace();
4919 } catch (OutOfMemoryError oom)
4924 } catch (Exception x)
4929 + (sourceType != null
4930 ? (sourceType == DataSourceType.PASTE
4932 : "using " + sourceType + " from "
4936 ? "(parsing as '" + format + "' file)"
4938 oom, Desktop.desktop);
4943 * Method invoked by the ChangeListener on the tabbed pane, in other words
4944 * when a different tabbed pane is selected by the user or programmatically.
4947 public void tabSelectionChanged(int index)
4951 alignPanel = alignPanels.get(index);
4952 viewport = alignPanel.av;
4953 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4954 setMenusFromViewport(viewport);
4958 * 'focus' any colour slider that is open to the selected viewport
4960 if (viewport.getConservationSelected())
4962 SliderPanel.setConservationSlider(alignPanel,
4963 viewport.getResidueShading(), alignPanel.getViewName());
4967 SliderPanel.hideConservationSlider();
4969 if (viewport.getAbovePIDThreshold())
4971 SliderPanel.setPIDSliderSource(alignPanel,
4972 viewport.getResidueShading(), alignPanel.getViewName());
4976 SliderPanel.hidePIDSlider();
4980 * If there is a frame linked to this one in a SplitPane, switch it to the
4981 * same view tab index. No infinite recursion of calls should happen, since
4982 * tabSelectionChanged() should not get invoked on setting the selected
4983 * index to an unchanged value. Guard against setting an invalid index
4984 * before the new view peer tab has been created.
4986 final AlignViewportI peer = viewport.getCodingComplement();
4989 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4990 .getAlignPanel().alignFrame;
4991 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4993 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4999 * On right mouse click on view tab, prompt for and set new view name.
5002 public void tabbedPane_mousePressed(MouseEvent e)
5004 if (e.isPopupTrigger())
5006 String msg = MessageManager.getString("label.enter_view_name");
5007 String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5008 JvOptionPane.QUESTION_MESSAGE);
5012 viewport.viewName = reply;
5013 // TODO warn if reply is in getExistingViewNames()?
5014 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5019 public AlignViewport getCurrentView()
5025 * Open the dialog for regex description parsing.
5028 protected void extractScores_actionPerformed(ActionEvent e)
5030 ParseProperties pp = new jalview.analysis.ParseProperties(
5031 viewport.getAlignment());
5032 // TODO: verify regex and introduce GUI dialog for version 2.5
5033 // if (pp.getScoresFromDescription("col", "score column ",
5034 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5036 if (pp.getScoresFromDescription("description column",
5037 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5039 buildSortByAnnotationScoresMenu();
5047 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5051 protected void showDbRefs_actionPerformed(ActionEvent e)
5053 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5059 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5063 protected void showNpFeats_actionPerformed(ActionEvent e)
5065 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5069 * find the viewport amongst the tabs in this alignment frame and close that
5074 public boolean closeView(AlignViewportI av)
5078 this.closeMenuItem_actionPerformed(false);
5081 Component[] comp = tabbedPane.getComponents();
5082 for (int i = 0; comp != null && i < comp.length; i++)
5084 if (comp[i] instanceof AlignmentPanel)
5086 if (((AlignmentPanel) comp[i]).av == av)
5089 closeView((AlignmentPanel) comp[i]);
5097 protected void build_fetchdbmenu(JMenu webService)
5099 // Temporary hack - DBRef Fetcher always top level ws entry.
5100 // TODO We probably want to store a sequence database checklist in
5101 // preferences and have checkboxes.. rather than individual sources selected
5103 final JMenu rfetch = new JMenu(
5104 MessageManager.getString("action.fetch_db_references"));
5105 rfetch.setToolTipText(MessageManager.getString(
5106 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5107 webService.add(rfetch);
5109 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5110 MessageManager.getString("option.trim_retrieved_seqs"));
5111 trimrs.setToolTipText(
5112 MessageManager.getString("label.trim_retrieved_sequences"));
5113 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5114 trimrs.addActionListener(new ActionListener()
5117 public void actionPerformed(ActionEvent e)
5119 trimrs.setSelected(trimrs.isSelected());
5120 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5121 Boolean.valueOf(trimrs.isSelected()).toString());
5125 JMenuItem fetchr = new JMenuItem(
5126 MessageManager.getString("label.standard_databases"));
5127 fetchr.setToolTipText(
5128 MessageManager.getString("label.fetch_embl_uniprot"));
5129 fetchr.addActionListener(new ActionListener()
5133 public void actionPerformed(ActionEvent e)
5135 new Thread(new Runnable()
5140 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5141 .getAlignment().isNucleotide();
5142 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5143 alignPanel.av.getSequenceSelection(),
5144 alignPanel.alignFrame, null,
5145 alignPanel.alignFrame.featureSettings, isNucleotide);
5146 dbRefFetcher.addListener(new FetchFinishedListenerI()
5149 public void finished()
5151 AlignFrame.this.setMenusForViewport();
5154 dbRefFetcher.fetchDBRefs(false);
5162 final AlignFrame me = this;
5163 new Thread(new Runnable()
5168 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5169 .getSequenceFetcherSingleton(me);
5170 javax.swing.SwingUtilities.invokeLater(new Runnable()
5175 String[] dbclasses = sf.getOrderedSupportedSources();
5176 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5177 // jalview.util.QuickSort.sort(otherdb, otherdb);
5178 List<DbSourceProxy> otherdb;
5179 JMenu dfetch = new JMenu();
5180 JMenu ifetch = new JMenu();
5181 JMenuItem fetchr = null;
5182 int comp = 0, icomp = 0, mcomp = 15;
5183 String mname = null;
5185 for (String dbclass : dbclasses)
5187 otherdb = sf.getSourceProxy(dbclass);
5188 // add a single entry for this class, or submenu allowing 'fetch
5190 if (otherdb == null || otherdb.size() < 1)
5194 // List<DbSourceProxy> dbs=otherdb;
5195 // otherdb=new ArrayList<DbSourceProxy>();
5196 // for (DbSourceProxy db:dbs)
5198 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5202 mname = "From " + dbclass;
5204 if (otherdb.size() == 1)
5206 final DbSourceProxy[] dassource = otherdb
5207 .toArray(new DbSourceProxy[0]);
5208 DbSourceProxy src = otherdb.get(0);
5209 fetchr = new JMenuItem(src.getDbSource());
5210 fetchr.addActionListener(new ActionListener()
5214 public void actionPerformed(ActionEvent e)
5216 new Thread(new Runnable()
5222 boolean isNucleotide = alignPanel.alignFrame
5223 .getViewport().getAlignment()
5225 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5226 alignPanel.av.getSequenceSelection(),
5227 alignPanel.alignFrame, dassource,
5228 alignPanel.alignFrame.featureSettings,
5231 .addListener(new FetchFinishedListenerI()
5234 public void finished()
5236 AlignFrame.this.setMenusForViewport();
5239 dbRefFetcher.fetchDBRefs(false);
5245 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5246 MessageManager.formatMessage(
5247 "label.fetch_retrieve_from", new Object[]
5248 { src.getDbName() })));
5254 final DbSourceProxy[] dassource = otherdb
5255 .toArray(new DbSourceProxy[0]);
5257 DbSourceProxy src = otherdb.get(0);
5258 fetchr = new JMenuItem(MessageManager
5259 .formatMessage("label.fetch_all_param", new Object[]
5260 { src.getDbSource() }));
5261 fetchr.addActionListener(new ActionListener()
5264 public void actionPerformed(ActionEvent e)
5266 new Thread(new Runnable()
5272 boolean isNucleotide = alignPanel.alignFrame
5273 .getViewport().getAlignment()
5275 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5276 alignPanel.av.getSequenceSelection(),
5277 alignPanel.alignFrame, dassource,
5278 alignPanel.alignFrame.featureSettings,
5281 .addListener(new FetchFinishedListenerI()
5284 public void finished()
5286 AlignFrame.this.setMenusForViewport();
5289 dbRefFetcher.fetchDBRefs(false);
5295 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5296 MessageManager.formatMessage(
5297 "label.fetch_retrieve_from_all_sources",
5299 { Integer.valueOf(otherdb.size())
5301 src.getDbSource(), src.getDbName() })));
5304 // and then build the rest of the individual menus
5305 ifetch = new JMenu(MessageManager.formatMessage(
5306 "label.source_from_db_source", new Object[]
5307 { src.getDbSource() }));
5309 String imname = null;
5311 for (DbSourceProxy sproxy : otherdb)
5313 String dbname = sproxy.getDbName();
5314 String sname = dbname.length() > 5
5315 ? dbname.substring(0, 5) + "..."
5317 String msname = dbname.length() > 10
5318 ? dbname.substring(0, 10) + "..."
5322 imname = MessageManager
5323 .formatMessage("label.from_msname", new Object[]
5326 fetchr = new JMenuItem(msname);
5327 final DbSourceProxy[] dassrc = { sproxy };
5328 fetchr.addActionListener(new ActionListener()
5332 public void actionPerformed(ActionEvent e)
5334 new Thread(new Runnable()
5340 boolean isNucleotide = alignPanel.alignFrame
5341 .getViewport().getAlignment()
5343 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5344 alignPanel.av.getSequenceSelection(),
5345 alignPanel.alignFrame, dassrc,
5346 alignPanel.alignFrame.featureSettings,
5349 .addListener(new FetchFinishedListenerI()
5352 public void finished()
5354 AlignFrame.this.setMenusForViewport();
5357 dbRefFetcher.fetchDBRefs(false);
5363 fetchr.setToolTipText(
5364 "<html>" + MessageManager.formatMessage(
5365 "label.fetch_retrieve_from", new Object[]
5369 if (++icomp >= mcomp || i == (otherdb.size()))
5371 ifetch.setText(MessageManager.formatMessage(
5372 "label.source_to_target", imname, sname));
5374 ifetch = new JMenu();
5382 if (comp >= mcomp || dbi >= (dbclasses.length))
5384 dfetch.setText(MessageManager.formatMessage(
5385 "label.source_to_target", mname, dbclass));
5387 dfetch = new JMenu();
5400 * Left justify the whole alignment.
5403 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5405 AlignmentI al = viewport.getAlignment();
5407 viewport.firePropertyChange("alignment", null, al);
5411 * Right justify the whole alignment.
5414 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5416 AlignmentI al = viewport.getAlignment();
5418 viewport.firePropertyChange("alignment", null, al);
5422 public void setShowSeqFeatures(boolean b)
5424 showSeqFeatures.setSelected(b);
5425 viewport.setShowSequenceFeatures(b);
5432 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5433 * awt.event.ActionEvent)
5436 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5438 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5439 alignPanel.paintAlignment(true);
5446 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5450 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5452 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5453 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5461 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5462 * .event.ActionEvent)
5465 protected void showGroupConservation_actionPerformed(ActionEvent e)
5467 viewport.setShowGroupConservation(showGroupConservation.getState());
5468 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5475 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5476 * .event.ActionEvent)
5479 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5481 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5482 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5489 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5490 * .event.ActionEvent)
5493 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5495 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5496 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5500 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5502 showSequenceLogo.setState(true);
5503 viewport.setShowSequenceLogo(true);
5504 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5505 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5509 protected void showInformationHistogram_actionPerformed(ActionEvent e)
5511 viewport.setShowInformationHistogram(
5512 showInformationHistogram.getState());
5513 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5517 protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
5519 viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
5520 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5524 protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
5526 showHMMSequenceLogo.setState(true);
5527 viewport.setShowHMMSequenceLogo(true);
5528 viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
5529 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5533 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5535 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5542 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5543 * .event.ActionEvent)
5546 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5548 if (avc.makeGroupsFromSelection())
5550 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5551 alignPanel.updateAnnotation();
5552 alignPanel.paintAlignment(true);
5556 public void clearAlignmentSeqRep()
5558 // TODO refactor alignmentseqrep to controller
5559 if (viewport.getAlignment().hasSeqrep())
5561 viewport.getAlignment().setSeqrep(null);
5562 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5563 alignPanel.updateAnnotation();
5564 alignPanel.paintAlignment(true);
5569 protected void createGroup_actionPerformed(ActionEvent e)
5571 if (avc.createGroup())
5573 alignPanel.alignmentChanged();
5578 protected void unGroup_actionPerformed(ActionEvent e)
5582 alignPanel.alignmentChanged();
5587 * make the given alignmentPanel the currently selected tab
5589 * @param alignmentPanel
5591 public void setDisplayedView(AlignmentPanel alignmentPanel)
5593 if (!viewport.getSequenceSetId()
5594 .equals(alignmentPanel.av.getSequenceSetId()))
5596 throw new Error(MessageManager.getString(
5597 "error.implementation_error_cannot_show_view_alignment_frame"));
5599 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5600 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5602 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5607 * Action on selection of menu options to Show or Hide annotations.
5610 * @param forSequences
5611 * update sequence-related annotations
5612 * @param forAlignment
5613 * update non-sequence-related annotations
5616 protected void setAnnotationsVisibility(boolean visible,
5617 boolean forSequences, boolean forAlignment)
5619 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5620 .getAlignmentAnnotation();
5625 for (AlignmentAnnotation aa : anns)
5628 * don't display non-positional annotations on an alignment
5630 if (aa.annotations == null)
5634 boolean apply = (aa.sequenceRef == null && forAlignment)
5635 || (aa.sequenceRef != null && forSequences);
5638 aa.visible = visible;
5641 alignPanel.validateAnnotationDimensions(true);
5642 alignPanel.alignmentChanged();
5646 * Store selected annotation sort order for the view and repaint.
5649 protected void sortAnnotations_actionPerformed()
5651 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5653 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5654 alignPanel.paintAlignment(true);
5659 * @return alignment panels in this alignment frame
5661 public List<? extends AlignmentViewPanel> getAlignPanels()
5663 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5667 * Open a new alignment window, with the cDNA associated with this (protein)
5668 * alignment, aligned as is the protein.
5670 protected void viewAsCdna_actionPerformed()
5672 // TODO no longer a menu action - refactor as required
5673 final AlignmentI alignment = getViewport().getAlignment();
5674 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5675 if (mappings == null)
5679 List<SequenceI> cdnaSeqs = new ArrayList<>();
5680 for (SequenceI aaSeq : alignment.getSequences())
5682 for (AlignedCodonFrame acf : mappings)
5684 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5688 * There is a cDNA mapping for this protein sequence - add to new
5689 * alignment. It will share the same dataset sequence as other mapped
5690 * cDNA (no new mappings need to be created).
5692 final Sequence newSeq = new Sequence(dnaSeq);
5693 newSeq.setDatasetSequence(dnaSeq);
5694 cdnaSeqs.add(newSeq);
5698 if (cdnaSeqs.size() == 0)
5700 // show a warning dialog no mapped cDNA
5703 AlignmentI cdna = new Alignment(
5704 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5705 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5706 AlignFrame.DEFAULT_HEIGHT);
5707 cdna.alignAs(alignment);
5708 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5710 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5711 AlignFrame.DEFAULT_HEIGHT);
5715 * Set visibility of dna/protein complement view (available when shown in a
5721 protected void showComplement_actionPerformed(boolean show)
5723 SplitContainerI sf = getSplitViewContainer();
5726 sf.setComplementVisible(this, show);
5731 * Generate the reverse (optionally complemented) of the selected sequences,
5732 * and add them to the alignment
5735 protected void showReverse_actionPerformed(boolean complement)
5737 AlignmentI al = null;
5740 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5741 al = dna.reverseCdna(complement);
5742 viewport.addAlignment(al, "");
5743 addHistoryItem(new EditCommand(
5744 MessageManager.getString("label.add_sequences"), Action.PASTE,
5745 al.getSequencesArray(), 0, al.getWidth(),
5746 viewport.getAlignment()));
5747 } catch (Exception ex)
5749 System.err.println(ex.getMessage());
5755 * Try to run a script in the Groovy console, having first ensured that this
5756 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5757 * be targeted at this alignment.
5760 protected void runGroovy_actionPerformed()
5762 Jalview.setCurrentAlignFrame(this);
5763 groovy.ui.Console console = Desktop.getGroovyConsole();
5764 if (console != null)
5768 console.runScript();
5769 } catch (Exception ex)
5771 System.err.println((ex.toString()));
5772 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5773 MessageManager.getString("label.couldnt_run_groovy_script"),
5774 MessageManager.getString("label.groovy_support_failed"),
5775 JvOptionPane.ERROR_MESSAGE);
5780 System.err.println("Can't run Groovy script as console not found");
5785 * Hides columns containing (or not containing) a specified feature, provided
5786 * that would not leave all columns hidden
5788 * @param featureType
5789 * @param columnsContaining
5792 public boolean hideFeatureColumns(String featureType,
5793 boolean columnsContaining)
5795 boolean notForHiding = avc.markColumnsContainingFeatures(
5796 columnsContaining, false, false, featureType);
5799 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5800 false, featureType))
5802 getViewport().hideSelectedColumns();
5810 protected void selectHighlightedColumns_actionPerformed(
5811 ActionEvent actionEvent)
5813 // include key modifier check in case user selects from menu
5814 avc.markHighlightedColumns(
5815 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5816 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5817 | ActionEvent.CTRL_MASK)) != 0);
5821 * Rebuilds the Colour menu, including any user-defined colours which have
5822 * been loaded either on startup or during the session
5824 public void buildColourMenu()
5826 colourMenu.removeAll();
5828 colourMenu.add(applyToAllGroups);
5829 colourMenu.add(textColour);
5830 colourMenu.addSeparator();
5832 ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5835 colourMenu.addSeparator();
5836 colourMenu.add(conservationMenuItem);
5837 colourMenu.add(modifyConservation);
5838 colourMenu.add(abovePIDThreshold);
5839 colourMenu.add(modifyPID);
5840 colourMenu.add(annotationColour);
5842 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5843 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5847 * Open a dialog (if not already open) that allows the user to select and
5848 * calculate PCA or Tree analysis
5850 protected void openTreePcaDialog()
5852 if (alignPanel.getCalculationDialog() == null)
5854 new CalculationChooser(AlignFrame.this);
5859 * Sets the status of the HMMER menu
5863 public void updateHMMERStatus(boolean status)
5865 hmmerMenu.setEnabled(status);
5869 * Returns the selected hidden Markov model.
5873 public HiddenMarkovModel getSelectedHMM()
5875 if (selectedHMMSequence == null)
5879 return selectedHMMSequence.getHMM();
5883 * Returns the selected hidden Markov model.
5887 public SequenceI getSelectedHMMSequence()
5889 return selectedHMMSequence;
5893 * Sets the selected hidden Markov model
5895 * @param selectedHMM
5897 public void setSelectedHMMSequence(SequenceI selectedHMM)
5899 this.selectedHMMSequence = selectedHMM;
5900 hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
5901 + selectedHMM.getHMM().getName() + "_HMM");
5902 hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
5903 + selectedHMM.getHMM().getName() + "_HMM");
5907 public void hmmerMenu_actionPerformed(ActionEvent e)
5909 SequenceGroup grp = getViewport().getSelectionGroup();
5912 hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
5917 hmmBuild.setText(MessageManager.getString("label.hmmbuild")
5918 + " from Alignment");
5924 class PrintThread extends Thread
5928 public PrintThread(AlignmentPanel ap)
5933 static PageFormat pf;
5938 PrinterJob printJob = PrinterJob.getPrinterJob();
5942 printJob.setPrintable(ap, pf);
5946 printJob.setPrintable(ap);
5949 if (printJob.printDialog())
5954 } catch (Exception PrintException)
5956 PrintException.printStackTrace();