2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.AAFrequency;
24 import jalview.analysis.AlignmentSorter;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.analysis.CrossRef;
28 import jalview.analysis.NJTree;
29 import jalview.analysis.ParseProperties;
30 import jalview.analysis.SequenceIdMatcher;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.AlignmentViewPanel;
34 import jalview.api.analysis.ScoreModelI;
35 import jalview.bin.Cache;
36 import jalview.commands.CommandI;
37 import jalview.commands.EditCommand;
38 import jalview.commands.EditCommand.Action;
39 import jalview.commands.OrderCommand;
40 import jalview.commands.RemoveGapColCommand;
41 import jalview.commands.RemoveGapsCommand;
42 import jalview.commands.SlideSequencesCommand;
43 import jalview.commands.TrimRegionCommand;
44 import jalview.datamodel.AlignedCodonFrame;
45 import jalview.datamodel.Alignment;
46 import jalview.datamodel.AlignmentAnnotation;
47 import jalview.datamodel.AlignmentI;
48 import jalview.datamodel.AlignmentOrder;
49 import jalview.datamodel.AlignmentView;
50 import jalview.datamodel.ColumnSelection;
51 import jalview.datamodel.PDBEntry;
52 import jalview.datamodel.SeqCigar;
53 import jalview.datamodel.Sequence;
54 import jalview.datamodel.SequenceGroup;
55 import jalview.datamodel.SequenceI;
56 import jalview.io.AlignmentProperties;
57 import jalview.io.AnnotationFile;
58 import jalview.io.BioJsHTMLOutput;
59 import jalview.io.FeaturesFile;
60 import jalview.io.FileLoader;
61 import jalview.io.FormatAdapter;
62 import jalview.io.HtmlSvgOutput;
63 import jalview.io.IdentifyFile;
64 import jalview.io.JalviewFileChooser;
65 import jalview.io.JalviewFileView;
66 import jalview.io.JnetAnnotationMaker;
67 import jalview.io.NewickFile;
68 import jalview.io.TCoffeeScoreFile;
69 import jalview.jbgui.GAlignFrame;
70 import jalview.schemes.Blosum62ColourScheme;
71 import jalview.schemes.BuriedColourScheme;
72 import jalview.schemes.ClustalxColourScheme;
73 import jalview.schemes.ColourSchemeI;
74 import jalview.schemes.ColourSchemeProperty;
75 import jalview.schemes.HelixColourScheme;
76 import jalview.schemes.HydrophobicColourScheme;
77 import jalview.schemes.NucleotideColourScheme;
78 import jalview.schemes.PIDColourScheme;
79 import jalview.schemes.PurinePyrimidineColourScheme;
80 import jalview.schemes.RNAHelicesColourChooser;
81 import jalview.schemes.ResidueProperties;
82 import jalview.schemes.StrandColourScheme;
83 import jalview.schemes.TCoffeeColourScheme;
84 import jalview.schemes.TaylorColourScheme;
85 import jalview.schemes.TurnColourScheme;
86 import jalview.schemes.UserColourScheme;
87 import jalview.schemes.ZappoColourScheme;
88 import jalview.util.MessageManager;
89 import jalview.ws.jws1.Discoverer;
90 import jalview.ws.jws2.Jws2Discoverer;
91 import jalview.ws.jws2.jabaws2.Jws2Instance;
92 import jalview.ws.seqfetcher.DbSourceProxy;
94 import java.awt.BorderLayout;
95 import java.awt.Component;
96 import java.awt.GridLayout;
97 import java.awt.Rectangle;
98 import java.awt.Toolkit;
99 import java.awt.datatransfer.Clipboard;
100 import java.awt.datatransfer.DataFlavor;
101 import java.awt.datatransfer.StringSelection;
102 import java.awt.datatransfer.Transferable;
103 import java.awt.dnd.DnDConstants;
104 import java.awt.dnd.DropTargetDragEvent;
105 import java.awt.dnd.DropTargetDropEvent;
106 import java.awt.dnd.DropTargetEvent;
107 import java.awt.dnd.DropTargetListener;
108 import java.awt.event.ActionEvent;
109 import java.awt.event.ActionListener;
110 import java.awt.event.KeyAdapter;
111 import java.awt.event.KeyEvent;
112 import java.awt.event.MouseAdapter;
113 import java.awt.event.MouseEvent;
114 import java.awt.print.PageFormat;
115 import java.awt.print.PrinterJob;
116 import java.beans.PropertyChangeEvent;
119 import java.util.ArrayList;
120 import java.util.Arrays;
121 import java.util.Enumeration;
122 import java.util.Hashtable;
123 import java.util.List;
124 import java.util.Vector;
126 import javax.swing.JButton;
127 import javax.swing.JCheckBoxMenuItem;
128 import javax.swing.JEditorPane;
129 import javax.swing.JInternalFrame;
130 import javax.swing.JLabel;
131 import javax.swing.JLayeredPane;
132 import javax.swing.JMenu;
133 import javax.swing.JMenuItem;
134 import javax.swing.JOptionPane;
135 import javax.swing.JPanel;
136 import javax.swing.JProgressBar;
137 import javax.swing.JRadioButtonMenuItem;
138 import javax.swing.JScrollPane;
139 import javax.swing.SwingUtilities;
145 * @version $Revision$
147 public class AlignFrame extends GAlignFrame implements DropTargetListener,
148 IProgressIndicator, AlignViewControllerGuiI
152 public static final int DEFAULT_WIDTH = 700;
155 public static final int DEFAULT_HEIGHT = 500;
157 public AlignmentPanel alignPanel;
159 AlignViewport viewport;
161 public AlignViewControllerI avc;
163 Vector alignPanels = new Vector();
166 * Last format used to load or save alignments in this window
168 String currentFileFormat = null;
171 * Current filename for this alignment
173 String fileName = null;
176 * Creates a new AlignFrame object with specific width and height.
182 public AlignFrame(AlignmentI al, int width, int height)
184 this(al, null, width, height);
188 * Creates a new AlignFrame object with specific width, height and
194 * @param sequenceSetId
196 public AlignFrame(AlignmentI al, int width, int height,
197 String sequenceSetId)
199 this(al, null, width, height, sequenceSetId);
203 * Creates a new AlignFrame object with specific width, height and
209 * @param sequenceSetId
212 public AlignFrame(AlignmentI al, int width, int height,
213 String sequenceSetId, String viewId)
215 this(al, null, width, height, sequenceSetId, viewId);
219 * new alignment window with hidden columns
223 * @param hiddenColumns
224 * ColumnSelection or null
226 * Width of alignment frame
230 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
231 int width, int height)
233 this(al, hiddenColumns, width, height, null);
237 * Create alignment frame for al with hiddenColumns, a specific width and
238 * height, and specific sequenceId
241 * @param hiddenColumns
244 * @param sequenceSetId
247 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
248 int width, int height, String sequenceSetId)
250 this(al, hiddenColumns, width, height, sequenceSetId, null);
254 * Create alignment frame for al with hiddenColumns, a specific width and
255 * height, and specific sequenceId
258 * @param hiddenColumns
261 * @param sequenceSetId
266 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
267 int width, int height, String sequenceSetId, String viewId)
269 setSize(width, height);
271 if (al.getDataset() == null)
276 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
278 alignPanel = new AlignmentPanel(this, viewport);
281 addAlignmentPanel(alignPanel, true);
286 * Make a new AlignFrame from existing alignmentPanels
293 public AlignFrame(AlignmentPanel ap)
297 addAlignmentPanel(ap, false);
302 * initalise the alignframe from the underlying viewport data and the
307 avc = new jalview.controller.AlignViewController(this, viewport,
309 if (viewport.getAlignmentConservationAnnotation() == null)
311 BLOSUM62Colour.setEnabled(false);
312 conservationMenuItem.setEnabled(false);
313 modifyConservation.setEnabled(false);
314 // PIDColour.setEnabled(false);
315 // abovePIDThreshold.setEnabled(false);
316 // modifyPID.setEnabled(false);
319 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
322 if (sortby.equals("Id"))
324 sortIDMenuItem_actionPerformed(null);
326 else if (sortby.equals("Pairwise Identity"))
328 sortPairwiseMenuItem_actionPerformed(null);
331 if (Desktop.desktop != null)
333 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
334 addServiceListeners();
335 setGUINucleotide(viewport.getAlignment().isNucleotide());
338 setMenusFromViewport(viewport);
339 buildSortByAnnotationScoresMenu();
342 if (viewport.wrapAlignment)
344 wrapMenuItem_actionPerformed(null);
347 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
349 this.overviewMenuItem_actionPerformed(null);
357 * Change the filename and format for the alignment, and enable the 'reload'
358 * button functionality.
365 public void setFileName(String file, String format)
368 currentFileFormat = format;
369 reload.setEnabled(true);
372 void addKeyListener()
374 addKeyListener(new KeyAdapter()
377 public void keyPressed(KeyEvent evt)
379 if (viewport.cursorMode
380 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
381 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
382 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
383 && Character.isDigit(evt.getKeyChar()))
385 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
388 switch (evt.getKeyCode())
391 case 27: // escape key
392 deselectAllSequenceMenuItem_actionPerformed(null);
396 case KeyEvent.VK_DOWN:
397 if (evt.isAltDown() || !viewport.cursorMode)
399 moveSelectedSequences(false);
401 if (viewport.cursorMode)
403 alignPanel.getSeqPanel().moveCursor(0, 1);
408 if (evt.isAltDown() || !viewport.cursorMode)
410 moveSelectedSequences(true);
412 if (viewport.cursorMode)
414 alignPanel.getSeqPanel().moveCursor(0, -1);
419 case KeyEvent.VK_LEFT:
420 if (evt.isAltDown() || !viewport.cursorMode)
422 slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
426 alignPanel.getSeqPanel().moveCursor(-1, 0);
431 case KeyEvent.VK_RIGHT:
432 if (evt.isAltDown() || !viewport.cursorMode)
434 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
438 alignPanel.getSeqPanel().moveCursor(1, 0);
442 case KeyEvent.VK_SPACE:
443 if (viewport.cursorMode)
445 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
446 || evt.isShiftDown() || evt.isAltDown());
450 // case KeyEvent.VK_A:
451 // if (viewport.cursorMode)
453 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
454 // //System.out.println("A");
458 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
459 * System.out.println("closing bracket"); } break;
461 case KeyEvent.VK_DELETE:
462 case KeyEvent.VK_BACK_SPACE:
463 if (!viewport.cursorMode)
465 cut_actionPerformed(null);
469 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
470 || evt.isShiftDown() || evt.isAltDown());
476 if (viewport.cursorMode)
478 alignPanel.getSeqPanel().setCursorRow();
482 if (viewport.cursorMode && !evt.isControlDown())
484 alignPanel.getSeqPanel().setCursorColumn();
488 if (viewport.cursorMode)
490 alignPanel.getSeqPanel().setCursorPosition();
494 case KeyEvent.VK_ENTER:
495 case KeyEvent.VK_COMMA:
496 if (viewport.cursorMode)
498 alignPanel.getSeqPanel().setCursorRowAndColumn();
503 if (viewport.cursorMode)
505 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
509 if (viewport.cursorMode)
511 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
516 viewport.cursorMode = !viewport.cursorMode;
517 statusBar.setText(MessageManager.formatMessage(
518 "label.keyboard_editing_mode", new String[]
519 { (viewport.cursorMode ? "on" : "off") }));
520 if (viewport.cursorMode)
522 alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
523 alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
525 alignPanel.getSeqPanel().seqCanvas.repaint();
531 Help.showHelpWindow();
532 } catch (Exception ex)
534 ex.printStackTrace();
539 boolean toggleSeqs = !evt.isControlDown();
540 boolean toggleCols = !evt.isShiftDown();
541 toggleHiddenRegions(toggleSeqs, toggleCols);
544 case KeyEvent.VK_PAGE_UP:
545 if (viewport.wrapAlignment)
547 alignPanel.scrollUp(true);
551 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
552 - viewport.endSeq + viewport.startSeq);
555 case KeyEvent.VK_PAGE_DOWN:
556 if (viewport.wrapAlignment)
558 alignPanel.scrollUp(false);
562 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
563 + viewport.endSeq - viewport.startSeq);
570 public void keyReleased(KeyEvent evt)
572 switch (evt.getKeyCode())
574 case KeyEvent.VK_LEFT:
575 if (evt.isAltDown() || !viewport.cursorMode)
577 viewport.firePropertyChange("alignment", null, viewport
578 .getAlignment().getSequences());
582 case KeyEvent.VK_RIGHT:
583 if (evt.isAltDown() || !viewport.cursorMode)
585 viewport.firePropertyChange("alignment", null, viewport
586 .getAlignment().getSequences());
594 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
596 ap.alignFrame = this;
597 avc = new jalview.controller.AlignViewController(this, viewport,
600 alignPanels.addElement(ap);
602 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
604 int aSize = alignPanels.size();
606 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
608 if (aSize == 1 && ap.av.viewName == null)
610 this.getContentPane().add(ap, BorderLayout.CENTER);
616 setInitialTabVisible();
619 expandViews.setEnabled(true);
620 gatherViews.setEnabled(true);
621 tabbedPane.addTab(ap.av.viewName, ap);
623 ap.setVisible(false);
628 if (ap.av.isPadGaps())
630 ap.av.getAlignment().padGaps();
632 ap.av.updateConservation(ap);
633 ap.av.updateConsensus(ap);
634 ap.av.updateStrucConsensus(ap);
638 public void setInitialTabVisible()
640 expandViews.setEnabled(true);
641 gatherViews.setEnabled(true);
642 tabbedPane.setVisible(true);
643 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
644 tabbedPane.addTab(first.av.viewName, first);
645 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
648 public AlignViewport getViewport()
653 /* Set up intrinsic listeners for dynamically generated GUI bits. */
654 private void addServiceListeners()
656 final java.beans.PropertyChangeListener thisListener;
657 Desktop.instance.addJalviewPropertyChangeListener("services",
658 thisListener = new java.beans.PropertyChangeListener()
661 public void propertyChange(PropertyChangeEvent evt)
663 // // System.out.println("Discoverer property change.");
664 // if (evt.getPropertyName().equals("services"))
666 SwingUtilities.invokeLater(new Runnable()
673 .println("Rebuild WS Menu for service change");
674 BuildWebServiceMenu();
681 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
684 public void internalFrameClosed(
685 javax.swing.event.InternalFrameEvent evt)
687 System.out.println("deregistering discoverer listener");
688 Desktop.instance.removeJalviewPropertyChangeListener("services",
690 closeMenuItem_actionPerformed(true);
693 // Finally, build the menu once to get current service state
694 new Thread(new Runnable()
699 BuildWebServiceMenu();
704 public void setGUINucleotide(boolean nucleotide)
706 showTranslation.setVisible(nucleotide);
707 conservationMenuItem.setEnabled(!nucleotide);
708 modifyConservation.setEnabled(!nucleotide);
709 showGroupConservation.setEnabled(!nucleotide);
710 rnahelicesColour.setEnabled(nucleotide);
711 purinePyrimidineColour.setEnabled(nucleotide);
712 // Remember AlignFrame always starts as protein
716 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
721 * set up menus for the currently viewport. This may be called after any
722 * operation that affects the data in the current view (selection changed,
723 * etc) to update the menus to reflect the new state.
725 public void setMenusForViewport()
727 setMenusFromViewport(viewport);
731 * Need to call this method when tabs are selected for multiple views, or when
732 * loading from Jalview2XML.java
737 void setMenusFromViewport(AlignViewport av)
739 padGapsMenuitem.setSelected(av.isPadGaps());
740 colourTextMenuItem.setSelected(av.showColourText);
741 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
742 conservationMenuItem.setSelected(av.getConservationSelected());
743 seqLimits.setSelected(av.getShowJVSuffix());
744 idRightAlign.setSelected(av.isRightAlignIds());
745 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
746 renderGapsMenuItem.setSelected(av.renderGaps);
747 wrapMenuItem.setSelected(av.wrapAlignment);
748 scaleAbove.setVisible(av.wrapAlignment);
749 scaleLeft.setVisible(av.wrapAlignment);
750 scaleRight.setVisible(av.wrapAlignment);
751 annotationPanelMenuItem.setState(av.isShowAnnotation());
753 * Show/hide annotations only enabled if annotation panel is shown
755 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
756 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
757 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
758 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
759 viewBoxesMenuItem.setSelected(av.showBoxes);
760 viewTextMenuItem.setSelected(av.showText);
761 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
762 showGroupConsensus.setSelected(av.isShowGroupConsensus());
763 showGroupConservation.setSelected(av.isShowGroupConservation());
764 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
765 showSequenceLogo.setSelected(av.isShowSequenceLogo());
766 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
768 setColourSelected(ColourSchemeProperty.getColourName(av
769 .getGlobalColourScheme()));
771 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
772 hiddenMarkers.setState(av.showHiddenMarkers);
773 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
774 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
775 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
776 autoCalculate.setSelected(av.autoCalculateConsensus);
777 sortByTree.setSelected(av.sortByTree);
778 listenToViewSelections.setSelected(av.followSelection);
779 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
781 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
782 setShowProductsEnabled();
786 // methods for implementing IProgressIndicator
787 // need to refactor to a reusable stub class
788 Hashtable progressBars, progressBarHandlers;
793 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
796 public void setProgressBar(String message, long id)
798 if (progressBars == null)
800 progressBars = new Hashtable();
801 progressBarHandlers = new Hashtable();
804 JPanel progressPanel;
805 Long lId = new Long(id);
806 GridLayout layout = (GridLayout) statusPanel.getLayout();
807 if (progressBars.get(lId) != null)
809 progressPanel = (JPanel) progressBars.get(new Long(id));
810 statusPanel.remove(progressPanel);
811 progressBars.remove(lId);
812 progressPanel = null;
815 statusBar.setText(message);
817 if (progressBarHandlers.contains(lId))
819 progressBarHandlers.remove(lId);
821 layout.setRows(layout.getRows() - 1);
825 progressPanel = new JPanel(new BorderLayout(10, 5));
827 JProgressBar progressBar = new JProgressBar();
828 progressBar.setIndeterminate(true);
830 progressPanel.add(new JLabel(message), BorderLayout.WEST);
831 progressPanel.add(progressBar, BorderLayout.CENTER);
833 layout.setRows(layout.getRows() + 1);
834 statusPanel.add(progressPanel);
836 progressBars.put(lId, progressPanel);
839 // setMenusForViewport();
844 public void registerHandler(final long id,
845 final IProgressIndicatorHandler handler)
847 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
849 throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
851 progressBarHandlers.put(new Long(id), handler);
852 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
853 if (handler.canCancel())
855 JButton cancel = new JButton(
856 MessageManager.getString("action.cancel"));
857 final IProgressIndicator us = this;
858 cancel.addActionListener(new ActionListener()
862 public void actionPerformed(ActionEvent e)
864 handler.cancelActivity(id);
865 us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
868 progressPanel.add(cancel, BorderLayout.EAST);
874 * @return true if any progress bars are still active
877 public boolean operationInProgress()
879 if (progressBars != null && progressBars.size() > 0)
887 public void setStatus(String text)
889 statusBar.setText(text);
893 * Added so Castor Mapping file can obtain Jalview Version
895 public String getVersion()
897 return jalview.bin.Cache.getProperty("VERSION");
900 public FeatureRenderer getFeatureRenderer()
902 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
906 public void fetchSequence_actionPerformed(ActionEvent e)
908 new SequenceFetcher(this);
912 public void addFromFile_actionPerformed(ActionEvent e)
914 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
918 public void reload_actionPerformed(ActionEvent e)
920 if (fileName != null)
922 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
923 // originating file's format
924 // TODO: work out how to recover feature settings for correct view(s) when
926 if (currentFileFormat.equals("Jalview"))
928 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
929 for (int i = 0; i < frames.length; i++)
931 if (frames[i] instanceof AlignFrame && frames[i] != this
932 && ((AlignFrame) frames[i]).fileName != null
933 && ((AlignFrame) frames[i]).fileName.equals(fileName))
937 frames[i].setSelected(true);
938 Desktop.instance.closeAssociatedWindows();
939 } catch (java.beans.PropertyVetoException ex)
945 Desktop.instance.closeAssociatedWindows();
947 FileLoader loader = new FileLoader();
948 String protocol = fileName.startsWith("http:") ? "URL" : "File";
949 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
953 Rectangle bounds = this.getBounds();
955 FileLoader loader = new FileLoader();
956 String protocol = fileName.startsWith("http:") ? "URL" : "File";
957 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
958 protocol, currentFileFormat);
960 newframe.setBounds(bounds);
961 if (featureSettings != null && featureSettings.isShowing())
963 final Rectangle fspos = featureSettings.frame.getBounds();
964 // TODO: need a 'show feature settings' function that takes bounds -
965 // need to refactor Desktop.addFrame
966 newframe.featureSettings_actionPerformed(null);
967 final FeatureSettings nfs = newframe.featureSettings;
968 SwingUtilities.invokeLater(new Runnable()
973 nfs.frame.setBounds(fspos);
976 this.featureSettings.close();
977 this.featureSettings = null;
979 this.closeMenuItem_actionPerformed(true);
985 public void addFromText_actionPerformed(ActionEvent e)
987 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
991 public void addFromURL_actionPerformed(ActionEvent e)
993 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
997 public void save_actionPerformed(ActionEvent e)
1000 || (currentFileFormat == null || !jalview.io.FormatAdapter
1001 .isValidIOFormat(currentFileFormat, true))
1002 || fileName.startsWith("http"))
1004 saveAs_actionPerformed(null);
1008 saveAlignment(fileName, currentFileFormat);
1019 public void saveAs_actionPerformed(ActionEvent e)
1021 JalviewFileChooser chooser = new JalviewFileChooser(
1022 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1023 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1024 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1025 currentFileFormat, false);
1027 chooser.setFileView(new JalviewFileView());
1028 chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1029 chooser.setToolTipText(MessageManager.getString("action.save"));
1031 int value = chooser.showSaveDialog(this);
1033 if (value == JalviewFileChooser.APPROVE_OPTION)
1035 currentFileFormat = chooser.getSelectedFormat();
1036 if (currentFileFormat == null)
1039 .showInternalMessageDialog(
1042 .getString("label.select_file_format_before_saving"),
1044 .getString("label.file_format_not_specified"),
1045 JOptionPane.WARNING_MESSAGE);
1046 value = chooser.showSaveDialog(this);
1050 fileName = chooser.getSelectedFile().getPath();
1052 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1055 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1056 if (currentFileFormat.indexOf(" ") > -1)
1058 currentFileFormat = currentFileFormat.substring(0,
1059 currentFileFormat.indexOf(" "));
1061 saveAlignment(fileName, currentFileFormat);
1065 public boolean saveAlignment(String file, String format)
1067 boolean success = true;
1069 if (format.equalsIgnoreCase("Jalview"))
1071 String shortName = title;
1073 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1075 shortName = shortName.substring(shortName
1076 .lastIndexOf(java.io.File.separatorChar) + 1);
1080 * First save any linked Chimera session.
1082 Desktop.instance.saveChimeraSessions(file);
1084 success = new Jalview2XML().saveAlignment(this, file, shortName);
1086 statusBar.setText(MessageManager.formatMessage(
1087 "label.successfully_saved_to_file_in_format", new Object[]
1088 { fileName, format }));
1093 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1095 warningMessage("Cannot save file " + fileName + " using format "
1096 + format, "Alignment output format not supported");
1097 saveAs_actionPerformed(null);
1098 // JBPNote need to have a raise_gui flag here
1102 String[] omitHidden = null;
1104 if (viewport.hasHiddenColumns())
1106 int reply = JOptionPane
1107 .showInternalConfirmDialog(
1110 .getString("label.alignment_contains_hidden_columns"),
1112 .getString("action.save_omit_hidden_columns"),
1113 JOptionPane.YES_NO_OPTION,
1114 JOptionPane.QUESTION_MESSAGE);
1116 if (reply == JOptionPane.YES_OPTION)
1118 omitHidden = viewport.getViewAsString(false);
1121 FormatAdapter f = new FormatAdapter();
1122 String output = f.formatSequences(format,
1123 viewport.getAlignment(), // class cast exceptions will
1124 // occur in the distant future
1125 omitHidden, f.getCacheSuffixDefault(format),
1126 viewport.getColumnSelection());
1136 java.io.PrintWriter out = new java.io.PrintWriter(
1137 new java.io.FileWriter(file));
1141 this.setTitle(file);
1142 statusBar.setText(MessageManager.formatMessage(
1143 "label.successfully_saved_to_file_in_format",
1145 { fileName, format }));
1146 } catch (Exception ex)
1149 ex.printStackTrace();
1156 JOptionPane.showInternalMessageDialog(this, MessageManager
1157 .formatMessage("label.couldnt_save_file", new String[]
1158 { fileName }), MessageManager
1159 .getString("label.error_saving_file"),
1160 JOptionPane.WARNING_MESSAGE);
1166 private void warningMessage(String warning, String title)
1168 if (new jalview.util.Platform().isHeadless())
1170 System.err.println("Warning: " + title + "\nWarning: " + warning);
1175 JOptionPane.showInternalMessageDialog(this, warning, title,
1176 JOptionPane.WARNING_MESSAGE);
1188 protected void outputText_actionPerformed(ActionEvent e)
1190 String[] omitHidden = null;
1192 if (viewport.hasHiddenColumns())
1194 int reply = JOptionPane
1195 .showInternalConfirmDialog(
1198 .getString("label.alignment_contains_hidden_columns"),
1200 .getString("action.save_omit_hidden_columns"),
1201 JOptionPane.YES_NO_OPTION,
1202 JOptionPane.QUESTION_MESSAGE);
1204 if (reply == JOptionPane.YES_OPTION)
1206 omitHidden = viewport.getViewAsString(false);
1210 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1211 cap.setForInput(null);
1215 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1216 viewport.getAlignment(), omitHidden,
1217 viewport.getColumnSelection()));
1218 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1219 "label.alignment_output_command", new String[]
1220 { e.getActionCommand() }), 600, 500);
1221 } catch (OutOfMemoryError oom)
1223 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1236 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1238 // new HTMLOutput(alignPanel,
1239 // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
1240 // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
1241 new HtmlSvgOutput(null, alignPanel);
1245 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1247 new BioJsHTMLOutput(alignPanel,
1248 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
1250 public void createImageMap(File file, String image)
1252 alignPanel.makePNGImageMap(file, image);
1262 public void createPNG(File f)
1264 alignPanel.makePNG(f);
1274 public void createEPS(File f)
1276 alignPanel.makeEPS(f);
1279 public void createSVG(File f)
1281 alignPanel.makeSVG(f);
1284 public void pageSetup_actionPerformed(ActionEvent e)
1286 PrinterJob printJob = PrinterJob.getPrinterJob();
1287 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1297 public void printMenuItem_actionPerformed(ActionEvent e)
1299 // Putting in a thread avoids Swing painting problems
1300 PrintThread thread = new PrintThread(alignPanel);
1305 public void exportFeatures_actionPerformed(ActionEvent e)
1307 new AnnotationExporter().exportFeatures(alignPanel);
1311 public void exportAnnotations_actionPerformed(ActionEvent e)
1313 new AnnotationExporter().exportAnnotations(alignPanel);
1317 public void associatedData_actionPerformed(ActionEvent e)
1319 // Pick the tree file
1320 JalviewFileChooser chooser = new JalviewFileChooser(
1321 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1322 chooser.setFileView(new JalviewFileView());
1323 chooser.setDialogTitle(MessageManager
1324 .getString("label.load_jalview_annotations"));
1325 chooser.setToolTipText(MessageManager
1326 .getString("label.load_jalview_annotations"));
1328 int value = chooser.showOpenDialog(null);
1330 if (value == JalviewFileChooser.APPROVE_OPTION)
1332 String choice = chooser.getSelectedFile().getPath();
1333 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1334 loadJalviewDataFile(choice, null, null, null);
1340 * Close the current view or all views in the alignment frame. If the frame
1341 * only contains one view then the alignment will be removed from memory.
1343 * @param closeAllTabs
1346 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1348 if (alignPanels != null && alignPanels.size() < 2)
1350 closeAllTabs = true;
1355 if (alignPanels != null)
1359 if (this.isClosed())
1361 // really close all the windows - otherwise wait till
1362 // setClosed(true) is called
1363 for (int i = 0; i < alignPanels.size(); i++)
1365 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1372 closeView(alignPanel);
1378 this.setClosed(true);
1380 } catch (Exception ex)
1382 ex.printStackTrace();
1387 * close alignPanel2 and shuffle tabs appropriately.
1389 * @param alignPanel2
1391 public void closeView(AlignmentPanel alignPanel2)
1393 int index = tabbedPane.getSelectedIndex();
1394 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1395 alignPanels.removeElement(alignPanel2);
1397 // if (viewport == alignPanel2.av)
1401 alignPanel2.closePanel();
1404 tabbedPane.removeTabAt(closedindex);
1405 tabbedPane.validate();
1407 if (index > closedindex || index == tabbedPane.getTabCount())
1409 // modify currently selected tab index if necessary.
1413 this.tabSelectionChanged(index);
1419 void updateEditMenuBar()
1422 if (viewport.historyList.size() > 0)
1424 undoMenuItem.setEnabled(true);
1425 CommandI command = viewport.historyList.peek();
1426 undoMenuItem.setText(MessageManager.formatMessage(
1427 "label.undo_command", new String[]
1428 { command.getDescription() }));
1432 undoMenuItem.setEnabled(false);
1433 undoMenuItem.setText(MessageManager.getString("action.undo"));
1436 if (viewport.redoList.size() > 0)
1438 redoMenuItem.setEnabled(true);
1440 CommandI command = viewport.redoList.peek();
1441 redoMenuItem.setText(MessageManager.formatMessage(
1442 "label.redo_command", new String[]
1443 { command.getDescription() }));
1447 redoMenuItem.setEnabled(false);
1448 redoMenuItem.setText(MessageManager.getString("action.redo"));
1452 public void addHistoryItem(CommandI command)
1454 if (command.getSize() > 0)
1456 viewport.historyList.push(command);
1457 viewport.redoList.clear();
1458 updateEditMenuBar();
1459 viewport.updateHiddenColumns();
1460 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1461 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1462 // viewport.getColumnSelection()
1463 // .getHiddenColumns().size() > 0);
1469 * @return alignment objects for all views
1471 AlignmentI[] getViewAlignments()
1473 if (alignPanels != null)
1475 Enumeration e = alignPanels.elements();
1476 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1477 for (int i = 0; e.hasMoreElements(); i++)
1479 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1483 if (viewport != null)
1485 return new AlignmentI[]
1486 { viewport.getAlignment() };
1498 protected void undoMenuItem_actionPerformed(ActionEvent e)
1500 if (viewport.historyList.empty())
1504 CommandI command = viewport.historyList.pop();
1505 viewport.redoList.push(command);
1506 command.undoCommand(getViewAlignments());
1508 AlignViewport originalSource = getOriginatingSource(command);
1509 updateEditMenuBar();
1511 if (originalSource != null)
1513 if (originalSource != viewport)
1516 .warn("Implementation worry: mismatch of viewport origin for undo");
1518 originalSource.updateHiddenColumns();
1519 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1521 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1522 // viewport.getColumnSelection()
1523 // .getHiddenColumns().size() > 0);
1524 originalSource.firePropertyChange("alignment", null, originalSource
1525 .getAlignment().getSequences());
1536 protected void redoMenuItem_actionPerformed(ActionEvent e)
1538 if (viewport.redoList.size() < 1)
1543 CommandI command = viewport.redoList.pop();
1544 viewport.historyList.push(command);
1545 command.doCommand(getViewAlignments());
1547 AlignViewport originalSource = getOriginatingSource(command);
1548 updateEditMenuBar();
1550 if (originalSource != null)
1553 if (originalSource != viewport)
1556 .warn("Implementation worry: mismatch of viewport origin for redo");
1558 originalSource.updateHiddenColumns();
1559 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1561 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1562 // viewport.getColumnSelection()
1563 // .getHiddenColumns().size() > 0);
1564 originalSource.firePropertyChange("alignment", null, originalSource
1565 .getAlignment().getSequences());
1569 AlignViewport getOriginatingSource(CommandI command)
1571 AlignViewport originalSource = null;
1572 // For sequence removal and addition, we need to fire
1573 // the property change event FROM the viewport where the
1574 // original alignment was altered
1575 AlignmentI al = null;
1576 if (command instanceof EditCommand)
1578 EditCommand editCommand = (EditCommand) command;
1579 al = editCommand.getAlignment();
1580 Vector comps = (Vector) PaintRefresher.components.get(viewport
1581 .getSequenceSetId());
1583 for (int i = 0; i < comps.size(); i++)
1585 if (comps.elementAt(i) instanceof AlignmentPanel)
1587 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1589 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1596 if (originalSource == null)
1598 // The original view is closed, we must validate
1599 // the current view against the closed view first
1602 PaintRefresher.validateSequences(al, viewport.getAlignment());
1605 originalSource = viewport;
1608 return originalSource;
1617 public void moveSelectedSequences(boolean up)
1619 SequenceGroup sg = viewport.getSelectionGroup();
1625 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1626 viewport.getHiddenRepSequences(), up);
1627 alignPanel.paintAlignment(true);
1630 synchronized void slideSequences(boolean right, int size)
1632 List<SequenceI> sg = new Vector();
1633 if (viewport.cursorMode)
1635 sg.add(viewport.getAlignment().getSequenceAt(
1636 alignPanel.getSeqPanel().seqCanvas.cursorY));
1638 else if (viewport.getSelectionGroup() != null
1639 && viewport.getSelectionGroup().getSize() != viewport
1640 .getAlignment().getHeight())
1642 sg = viewport.getSelectionGroup().getSequences(
1643 viewport.getHiddenRepSequences());
1651 Vector invertGroup = new Vector();
1653 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1655 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1657 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1661 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1663 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1664 for (int i = 0; i < invertGroup.size(); i++)
1666 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1669 SlideSequencesCommand ssc;
1672 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1673 size, viewport.getGapCharacter());
1677 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1678 size, viewport.getGapCharacter());
1681 int groupAdjustment = 0;
1682 if (ssc.getGapsInsertedBegin() && right)
1684 if (viewport.cursorMode)
1686 alignPanel.getSeqPanel().moveCursor(size, 0);
1690 groupAdjustment = size;
1693 else if (!ssc.getGapsInsertedBegin() && !right)
1695 if (viewport.cursorMode)
1697 alignPanel.getSeqPanel().moveCursor(-size, 0);
1701 groupAdjustment = -size;
1705 if (groupAdjustment != 0)
1707 viewport.getSelectionGroup().setStartRes(
1708 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1709 viewport.getSelectionGroup().setEndRes(
1710 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1713 boolean appendHistoryItem = false;
1714 if (viewport.historyList != null && viewport.historyList.size() > 0
1715 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1717 appendHistoryItem = ssc
1718 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1722 if (!appendHistoryItem)
1724 addHistoryItem(ssc);
1737 protected void copy_actionPerformed(ActionEvent e)
1740 if (viewport.getSelectionGroup() == null)
1744 // TODO: preserve the ordering of displayed alignment annotation in any
1745 // internal paste (particularly sequence associated annotation)
1746 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1747 String[] omitHidden = null;
1749 if (viewport.hasHiddenColumns())
1751 omitHidden = viewport.getViewAsString(true);
1754 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1757 StringSelection ss = new StringSelection(output);
1761 jalview.gui.Desktop.internalCopy = true;
1762 // Its really worth setting the clipboard contents
1763 // to empty before setting the large StringSelection!!
1764 Toolkit.getDefaultToolkit().getSystemClipboard()
1765 .setContents(new StringSelection(""), null);
1767 Toolkit.getDefaultToolkit().getSystemClipboard()
1768 .setContents(ss, Desktop.instance);
1769 } catch (OutOfMemoryError er)
1771 new OOMWarning("copying region", er);
1775 ArrayList<int[]> hiddenColumns = null;
1776 if (viewport.hasHiddenColumns())
1778 hiddenColumns = new ArrayList<int[]>();
1779 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1780 .getSelectionGroup().getEndRes();
1781 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1783 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1785 hiddenColumns.add(new int[]
1786 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1791 Desktop.jalviewClipboard = new Object[]
1792 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1793 statusBar.setText(MessageManager.formatMessage(
1794 "label.copied_sequences_to_clipboard", new String[]
1795 { Integer.valueOf(seqs.length).toString() }));
1805 protected void pasteNew_actionPerformed(ActionEvent e)
1817 protected void pasteThis_actionPerformed(ActionEvent e)
1823 * Paste contents of Jalview clipboard
1825 * @param newAlignment
1826 * true to paste to a new alignment, otherwise add to this.
1828 void paste(boolean newAlignment)
1830 boolean externalPaste = true;
1833 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1834 Transferable contents = c.getContents(this);
1836 if (contents == null)
1844 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1845 if (str.length() < 1)
1850 format = new IdentifyFile().Identify(str, "Paste");
1852 } catch (OutOfMemoryError er)
1854 new OOMWarning("Out of memory pasting sequences!!", er);
1858 SequenceI[] sequences;
1859 boolean annotationAdded = false;
1860 AlignmentI alignment = null;
1862 if (Desktop.jalviewClipboard != null)
1864 // The clipboard was filled from within Jalview, we must use the
1866 // And dataset from the copied alignment
1867 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1868 // be doubly sure that we create *new* sequence objects.
1869 sequences = new SequenceI[newseq.length];
1870 for (int i = 0; i < newseq.length; i++)
1872 sequences[i] = new Sequence(newseq[i]);
1874 alignment = new Alignment(sequences);
1875 externalPaste = false;
1879 // parse the clipboard as an alignment.
1880 alignment = new FormatAdapter().readFile(str, "Paste", format);
1881 sequences = alignment.getSequencesArray();
1885 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1891 if (Desktop.jalviewClipboard != null)
1893 // dataset is inherited
1894 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1898 // new dataset is constructed
1899 alignment.setDataset(null);
1901 alwidth = alignment.getWidth() + 1;
1905 AlignmentI pastedal = alignment; // preserve pasted alignment object
1906 // Add pasted sequences and dataset into existing alignment.
1907 alignment = viewport.getAlignment();
1908 alwidth = alignment.getWidth() + 1;
1909 // decide if we need to import sequences from an existing dataset
1910 boolean importDs = Desktop.jalviewClipboard != null
1911 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1912 // importDs==true instructs us to copy over new dataset sequences from
1913 // an existing alignment
1914 Vector newDs = (importDs) ? new Vector() : null; // used to create
1915 // minimum dataset set
1917 for (int i = 0; i < sequences.length; i++)
1921 newDs.addElement(null);
1923 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1925 if (importDs && ds != null)
1927 if (!newDs.contains(ds))
1929 newDs.setElementAt(ds, i);
1930 ds = new Sequence(ds);
1931 // update with new dataset sequence
1932 sequences[i].setDatasetSequence(ds);
1936 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1941 // copy and derive new dataset sequence
1942 sequences[i] = sequences[i].deriveSequence();
1943 alignment.getDataset().addSequence(
1944 sequences[i].getDatasetSequence());
1945 // TODO: avoid creation of duplicate dataset sequences with a
1946 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1948 alignment.addSequence(sequences[i]); // merges dataset
1952 newDs.clear(); // tidy up
1954 if (alignment.getAlignmentAnnotation() != null)
1956 for (AlignmentAnnotation alan : alignment
1957 .getAlignmentAnnotation())
1959 if (alan.graphGroup > fgroup)
1961 fgroup = alan.graphGroup;
1965 if (pastedal.getAlignmentAnnotation() != null)
1967 // Add any annotation attached to alignment.
1968 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1969 for (int i = 0; i < alann.length; i++)
1971 annotationAdded = true;
1972 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1974 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1975 if (newann.graphGroup > -1)
1977 if (newGraphGroups.size() <= newann.graphGroup
1978 || newGraphGroups.get(newann.graphGroup) == null)
1980 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1982 newGraphGroups.add(q, null);
1984 newGraphGroups.set(newann.graphGroup, new Integer(
1987 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1991 newann.padAnnotation(alwidth);
1992 alignment.addAnnotation(newann);
2002 addHistoryItem(new EditCommand(
2003 MessageManager.getString("label.add_sequences"),
2005 sequences, 0, alignment.getWidth(), alignment));
2007 // Add any annotations attached to sequences
2008 for (int i = 0; i < sequences.length; i++)
2010 if (sequences[i].getAnnotation() != null)
2012 AlignmentAnnotation newann;
2013 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2015 annotationAdded = true;
2016 newann = sequences[i].getAnnotation()[a];
2017 newann.adjustForAlignment();
2018 newann.padAnnotation(alwidth);
2019 if (newann.graphGroup > -1)
2021 if (newann.graphGroup > -1)
2023 if (newGraphGroups.size() <= newann.graphGroup
2024 || newGraphGroups.get(newann.graphGroup) == null)
2026 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2028 newGraphGroups.add(q, null);
2030 newGraphGroups.set(newann.graphGroup, new Integer(
2033 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2037 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2042 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2049 // propagate alignment changed.
2050 viewport.setEndSeq(alignment.getHeight());
2051 if (annotationAdded)
2053 // Duplicate sequence annotation in all views.
2054 AlignmentI[] alview = this.getViewAlignments();
2055 for (int i = 0; i < sequences.length; i++)
2057 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2062 for (int avnum = 0; avnum < alview.length; avnum++)
2064 if (alview[avnum] != alignment)
2066 // duplicate in a view other than the one with input focus
2067 int avwidth = alview[avnum].getWidth() + 1;
2068 // this relies on sann being preserved after we
2069 // modify the sequence's annotation array for each duplication
2070 for (int a = 0; a < sann.length; a++)
2072 AlignmentAnnotation newann = new AlignmentAnnotation(
2074 sequences[i].addAlignmentAnnotation(newann);
2075 newann.padAnnotation(avwidth);
2076 alview[avnum].addAnnotation(newann); // annotation was
2077 // duplicated earlier
2078 // TODO JAL-1145 graphGroups are not updated for sequence
2079 // annotation added to several views. This may cause
2081 alview[avnum].setAnnotationIndex(newann, a);
2086 buildSortByAnnotationScoresMenu();
2088 viewport.firePropertyChange("alignment", null,
2089 alignment.getSequences());
2090 if (alignPanels != null)
2092 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2094 ap.validateAnnotationDimensions(false);
2099 alignPanel.validateAnnotationDimensions(false);
2105 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2107 String newtitle = new String("Copied sequences");
2109 if (Desktop.jalviewClipboard != null
2110 && Desktop.jalviewClipboard[2] != null)
2112 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2113 for (int[] region : hc)
2115 af.viewport.hideColumns(region[0], region[1]);
2119 // >>>This is a fix for the moment, until a better solution is
2121 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2123 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2125 // TODO: maintain provenance of an alignment, rather than just make the
2126 // title a concatenation of operations.
2129 if (title.startsWith("Copied sequences"))
2135 newtitle = newtitle.concat("- from " + title);
2140 newtitle = new String("Pasted sequences");
2143 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2148 } catch (Exception ex)
2150 ex.printStackTrace();
2151 System.out.println("Exception whilst pasting: " + ex);
2152 // could be anything being pasted in here
2158 protected void expand_newalign(ActionEvent e)
2162 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2163 .getAlignment(), -1);
2164 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2166 String newtitle = new String("Flanking alignment");
2168 if (Desktop.jalviewClipboard != null
2169 && Desktop.jalviewClipboard[2] != null)
2171 List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2172 for (int region[] : hc)
2174 af.viewport.hideColumns(region[0], region[1]);
2178 // >>>This is a fix for the moment, until a better solution is
2180 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2182 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2184 // TODO: maintain provenance of an alignment, rather than just make the
2185 // title a concatenation of operations.
2187 if (title.startsWith("Copied sequences"))
2193 newtitle = newtitle.concat("- from " + title);
2197 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2199 } catch (Exception ex)
2201 ex.printStackTrace();
2202 System.out.println("Exception whilst pasting: " + ex);
2203 // could be anything being pasted in here
2204 } catch (OutOfMemoryError oom)
2206 new OOMWarning("Viewing flanking region of alignment", oom);
2217 protected void cut_actionPerformed(ActionEvent e)
2219 copy_actionPerformed(null);
2220 delete_actionPerformed(null);
2230 protected void delete_actionPerformed(ActionEvent evt)
2233 SequenceGroup sg = viewport.getSelectionGroup();
2239 List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
2241 for (int i = 0; i < sg.getSize(); i++)
2243 seq = sg.getSequenceAt(i);
2247 // If the cut affects all sequences, warn, remove highlighted columns
2248 if (sg.getSize() == viewport.getAlignment().getHeight())
2250 int confirm = JOptionPane.showConfirmDialog(this,
2251 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2252 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2253 JOptionPane.OK_CANCEL_OPTION);
2255 if (confirm == JOptionPane.CANCEL_OPTION
2256 || confirm == JOptionPane.CLOSED_OPTION)
2260 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2261 sg.getEndRes() + 1);
2264 SequenceI[] cut = new SequenceI[seqs.size()];
2265 for (int i = 0; i < seqs.size(); i++)
2267 cut[i] = seqs.get(i);
2271 * //ADD HISTORY ITEM
2273 addHistoryItem(new EditCommand(
2274 MessageManager.getString("label.cut_sequences"), Action.CUT,
2275 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2276 viewport.getAlignment()));
2278 viewport.setSelectionGroup(null);
2279 viewport.sendSelection();
2280 viewport.getAlignment().deleteGroup(sg);
2282 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2284 if (viewport.getAlignment().getHeight() < 1)
2288 this.setClosed(true);
2289 } catch (Exception ex)
2302 protected void deleteGroups_actionPerformed(ActionEvent e)
2304 if (avc.deleteGroups())
2306 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2307 alignPanel.updateAnnotation();
2308 alignPanel.paintAlignment(true);
2319 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2321 SequenceGroup sg = new SequenceGroup();
2323 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2325 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2328 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2329 viewport.setSelectionGroup(sg);
2330 viewport.sendSelection();
2331 alignPanel.paintAlignment(true);
2332 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2342 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2344 if (viewport.cursorMode)
2346 alignPanel.getSeqPanel().keyboardNo1 = null;
2347 alignPanel.getSeqPanel().keyboardNo2 = null;
2349 viewport.setSelectionGroup(null);
2350 viewport.getColumnSelection().clear();
2351 viewport.setSelectionGroup(null);
2352 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2353 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2354 alignPanel.paintAlignment(true);
2355 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2356 viewport.sendSelection();
2366 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2368 SequenceGroup sg = viewport.getSelectionGroup();
2372 selectAllSequenceMenuItem_actionPerformed(null);
2377 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2379 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2382 alignPanel.paintAlignment(true);
2383 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2384 viewport.sendSelection();
2388 public void invertColSel_actionPerformed(ActionEvent e)
2390 viewport.invertColumnSelection();
2391 alignPanel.paintAlignment(true);
2392 viewport.sendSelection();
2402 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2404 trimAlignment(true);
2414 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2416 trimAlignment(false);
2419 void trimAlignment(boolean trimLeft)
2421 ColumnSelection colSel = viewport.getColumnSelection();
2424 if (colSel.size() > 0)
2428 column = colSel.getMin();
2432 column = colSel.getMax();
2436 if (viewport.getSelectionGroup() != null)
2438 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2439 viewport.getHiddenRepSequences());
2443 seqs = viewport.getAlignment().getSequencesArray();
2446 TrimRegionCommand trimRegion;
2449 trimRegion = new TrimRegionCommand("Remove Left",
2450 TrimRegionCommand.TRIM_LEFT, seqs, column,
2451 viewport.getAlignment(), viewport.getColumnSelection(),
2452 viewport.getSelectionGroup());
2453 viewport.setStartRes(0);
2457 trimRegion = new TrimRegionCommand("Remove Right",
2458 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2459 viewport.getAlignment(), viewport.getColumnSelection(),
2460 viewport.getSelectionGroup());
2463 statusBar.setText(MessageManager.formatMessage(
2464 "label.removed_columns", new String[]
2465 { Integer.valueOf(trimRegion.getSize()).toString() }));
2467 addHistoryItem(trimRegion);
2469 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2471 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2472 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2474 viewport.getAlignment().deleteGroup(sg);
2478 viewport.firePropertyChange("alignment", null, viewport
2479 .getAlignment().getSequences());
2490 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2492 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2495 if (viewport.getSelectionGroup() != null)
2497 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2498 viewport.getHiddenRepSequences());
2499 start = viewport.getSelectionGroup().getStartRes();
2500 end = viewport.getSelectionGroup().getEndRes();
2504 seqs = viewport.getAlignment().getSequencesArray();
2507 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2508 "Remove Gapped Columns", seqs, start, end,
2509 viewport.getAlignment());
2511 addHistoryItem(removeGapCols);
2513 statusBar.setText(MessageManager.formatMessage(
2514 "label.removed_empty_columns", new String[]
2515 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2517 // This is to maintain viewport position on first residue
2518 // of first sequence
2519 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2520 int startRes = seq.findPosition(viewport.startRes);
2521 // ShiftList shifts;
2522 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2523 // edit.alColumnChanges=shifts.getInverse();
2524 // if (viewport.hasHiddenColumns)
2525 // viewport.getColumnSelection().compensateForEdits(shifts);
2526 viewport.setStartRes(seq.findIndex(startRes) - 1);
2527 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2539 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2541 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2544 if (viewport.getSelectionGroup() != null)
2546 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2547 viewport.getHiddenRepSequences());
2548 start = viewport.getSelectionGroup().getStartRes();
2549 end = viewport.getSelectionGroup().getEndRes();
2553 seqs = viewport.getAlignment().getSequencesArray();
2556 // This is to maintain viewport position on first residue
2557 // of first sequence
2558 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2559 int startRes = seq.findPosition(viewport.startRes);
2561 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2562 viewport.getAlignment()));
2564 viewport.setStartRes(seq.findIndex(startRes) - 1);
2566 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2578 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2580 viewport.setPadGaps(padGapsMenuitem.isSelected());
2581 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2587 // if (justifySeqs>0)
2589 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2602 public void findMenuItem_actionPerformed(ActionEvent e)
2608 public void newView_actionPerformed(ActionEvent e)
2615 * @param copyAnnotation
2616 * if true then duplicate all annnotation, groups and settings
2617 * @return new alignment panel, already displayed.
2619 public AlignmentPanel newView(boolean copyAnnotation)
2621 return newView(null, copyAnnotation);
2627 * title of newly created view
2628 * @return new alignment panel, already displayed.
2630 public AlignmentPanel newView(String viewTitle)
2632 return newView(viewTitle, true);
2638 * title of newly created view
2639 * @param copyAnnotation
2640 * if true then duplicate all annnotation, groups and settings
2641 * @return new alignment panel, already displayed.
2643 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2645 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2647 if (!copyAnnotation)
2649 // just remove all the current annotation except for the automatic stuff
2650 newap.av.getAlignment().deleteAllGroups();
2651 for (AlignmentAnnotation alan : newap.av.getAlignment()
2652 .getAlignmentAnnotation())
2654 if (!alan.autoCalculated)
2656 newap.av.getAlignment().deleteAnnotation(alan);
2662 newap.av.gatherViewsHere = false;
2664 if (viewport.viewName == null)
2666 viewport.viewName = "Original";
2669 newap.av.historyList = viewport.historyList;
2670 newap.av.redoList = viewport.redoList;
2672 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2673 // make sure the new view has a unique name - this is essential for Jalview
2675 boolean addFirstIndex = false;
2676 if (viewTitle == null || viewTitle.trim().length() == 0)
2678 viewTitle = MessageManager.getString("action.view");
2679 addFirstIndex = true;
2683 index = 1;// we count from 1 if given a specific name
2685 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2686 Vector comps = (Vector) PaintRefresher.components.get(viewport
2687 .getSequenceSetId());
2688 Vector existingNames = new Vector();
2689 for (int i = 0; i < comps.size(); i++)
2691 if (comps.elementAt(i) instanceof AlignmentPanel)
2693 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2694 if (!existingNames.contains(ap.av.viewName))
2696 existingNames.addElement(ap.av.viewName);
2701 while (existingNames.contains(newViewName))
2703 newViewName = viewTitle + " " + (++index);
2706 newap.av.viewName = newViewName;
2708 addAlignmentPanel(newap, true);
2709 newap.alignmentChanged();
2711 if (alignPanels.size() == 2)
2713 viewport.gatherViewsHere = true;
2715 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2720 public void expandViews_actionPerformed(ActionEvent e)
2722 Desktop.instance.explodeViews(this);
2726 public void gatherViews_actionPerformed(ActionEvent e)
2728 Desktop.instance.gatherViews(this);
2738 public void font_actionPerformed(ActionEvent e)
2740 new FontChooser(alignPanel);
2750 protected void seqLimit_actionPerformed(ActionEvent e)
2752 viewport.setShowJVSuffix(seqLimits.isSelected());
2754 alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
2755 .calculateIdWidth());
2756 alignPanel.paintAlignment(true);
2760 public void idRightAlign_actionPerformed(ActionEvent e)
2762 viewport.setRightAlignIds(idRightAlign.isSelected());
2763 alignPanel.paintAlignment(true);
2767 public void centreColumnLabels_actionPerformed(ActionEvent e)
2769 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2770 alignPanel.paintAlignment(true);
2776 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2779 protected void followHighlight_actionPerformed()
2781 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2783 alignPanel.scrollToPosition(
2784 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2795 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2797 viewport.setColourText(colourTextMenuItem.isSelected());
2798 alignPanel.paintAlignment(true);
2808 public void wrapMenuItem_actionPerformed(ActionEvent e)
2810 scaleAbove.setVisible(wrapMenuItem.isSelected());
2811 scaleLeft.setVisible(wrapMenuItem.isSelected());
2812 scaleRight.setVisible(wrapMenuItem.isSelected());
2813 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2814 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2818 public void showAllSeqs_actionPerformed(ActionEvent e)
2820 viewport.showAllHiddenSeqs();
2824 public void showAllColumns_actionPerformed(ActionEvent e)
2826 viewport.showAllHiddenColumns();
2831 public void hideSelSequences_actionPerformed(ActionEvent e)
2833 viewport.hideAllSelectedSeqs();
2834 alignPanel.paintAlignment(true);
2838 * called by key handler and the hide all/show all menu items
2843 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2846 boolean hide = false;
2847 SequenceGroup sg = viewport.getSelectionGroup();
2848 if (!toggleSeqs && !toggleCols)
2850 // Hide everything by the current selection - this is a hack - we do the
2851 // invert and then hide
2852 // first check that there will be visible columns after the invert.
2853 if ((viewport.getColumnSelection() != null
2854 && viewport.getColumnSelection().getSelected() != null && viewport
2855 .getColumnSelection().getSelected().size() > 0)
2856 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2859 // now invert the sequence set, if required - empty selection implies
2860 // that no hiding is required.
2863 invertSequenceMenuItem_actionPerformed(null);
2864 sg = viewport.getSelectionGroup();
2868 viewport.expandColSelection(sg, true);
2869 // finally invert the column selection and get the new sequence
2871 invertColSel_actionPerformed(null);
2878 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2880 hideSelSequences_actionPerformed(null);
2883 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2886 showAllSeqs_actionPerformed(null);
2892 if (viewport.getColumnSelection().getSelected().size() > 0)
2894 hideSelColumns_actionPerformed(null);
2897 viewport.setSelectionGroup(sg);
2902 showAllColumns_actionPerformed(null);
2911 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2912 * event.ActionEvent)
2915 public void hideAllButSelection_actionPerformed(ActionEvent e)
2917 toggleHiddenRegions(false, false);
2924 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2928 public void hideAllSelection_actionPerformed(ActionEvent e)
2930 SequenceGroup sg = viewport.getSelectionGroup();
2931 viewport.expandColSelection(sg, false);
2932 viewport.hideAllSelectedSeqs();
2933 viewport.hideSelectedColumns();
2934 alignPanel.paintAlignment(true);
2941 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2945 public void showAllhidden_actionPerformed(ActionEvent e)
2947 viewport.showAllHiddenColumns();
2948 viewport.showAllHiddenSeqs();
2949 alignPanel.paintAlignment(true);
2953 public void hideSelColumns_actionPerformed(ActionEvent e)
2955 viewport.hideSelectedColumns();
2956 alignPanel.paintAlignment(true);
2960 public void hiddenMarkers_actionPerformed(ActionEvent e)
2962 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2973 protected void scaleAbove_actionPerformed(ActionEvent e)
2975 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2976 alignPanel.paintAlignment(true);
2986 protected void scaleLeft_actionPerformed(ActionEvent e)
2988 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2989 alignPanel.paintAlignment(true);
2999 protected void scaleRight_actionPerformed(ActionEvent e)
3001 viewport.setScaleRightWrapped(scaleRight.isSelected());
3002 alignPanel.paintAlignment(true);
3012 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3014 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3015 alignPanel.paintAlignment(true);
3025 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3027 viewport.setShowText(viewTextMenuItem.isSelected());
3028 alignPanel.paintAlignment(true);
3038 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3040 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3041 alignPanel.paintAlignment(true);
3044 public FeatureSettings featureSettings;
3047 public void featureSettings_actionPerformed(ActionEvent e)
3049 if (featureSettings != null)
3051 featureSettings.close();
3052 featureSettings = null;
3054 if (!showSeqFeatures.isSelected())
3056 // make sure features are actually displayed
3057 showSeqFeatures.setSelected(true);
3058 showSeqFeatures_actionPerformed(null);
3060 featureSettings = new FeatureSettings(this);
3064 * Set or clear 'Show Sequence Features'
3070 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3072 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3073 alignPanel.paintAlignment(true);
3074 if (alignPanel.getOverviewPanel() != null)
3076 alignPanel.getOverviewPanel().updateOverviewImage();
3081 * Set or clear 'Show Sequence Features'
3087 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3089 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3091 if (viewport.isShowSequenceFeaturesHeight())
3093 // ensure we're actually displaying features
3094 viewport.setShowSequenceFeatures(true);
3095 showSeqFeatures.setSelected(true);
3097 alignPanel.paintAlignment(true);
3098 if (alignPanel.getOverviewPanel() != null)
3100 alignPanel.getOverviewPanel().updateOverviewImage();
3105 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3106 * the annotations panel as a whole.
3108 * The options to show/hide all annotations should be enabled when the panel
3109 * is shown, and disabled when the panel is hidden.
3114 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3116 final boolean setVisible = annotationPanelMenuItem.isSelected();
3117 viewport.setShowAnnotation(setVisible);
3118 alignPanel.setAnnotationVisible(setVisible);
3119 this.showAllSeqAnnotations.setEnabled(setVisible);
3120 this.hideAllSeqAnnotations.setEnabled(setVisible);
3121 this.showAllAlAnnotations.setEnabled(setVisible);
3122 this.hideAllAlAnnotations.setEnabled(setVisible);
3126 public void alignmentProperties()
3128 JEditorPane editPane = new JEditorPane("text/html", "");
3129 editPane.setEditable(false);
3130 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3132 editPane.setText(MessageManager.formatMessage("label.html_content",
3134 { contents.toString() }));
3135 JInternalFrame frame = new JInternalFrame();
3136 frame.getContentPane().add(new JScrollPane(editPane));
3138 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3139 "label.alignment_properties", new String[]
3140 { getTitle() }), 500, 400);
3150 public void overviewMenuItem_actionPerformed(ActionEvent e)
3152 if (alignPanel.overviewPanel != null)
3157 JInternalFrame frame = new JInternalFrame();
3158 OverviewPanel overview = new OverviewPanel(alignPanel);
3159 frame.setContentPane(overview);
3160 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3161 "label.overview_params", new String[]
3162 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3164 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3165 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3168 public void internalFrameClosed(
3169 javax.swing.event.InternalFrameEvent evt)
3171 alignPanel.setOverviewPanel(null);
3175 alignPanel.setOverviewPanel(overview);
3179 public void textColour_actionPerformed(ActionEvent e)
3181 new TextColourChooser().chooseColour(alignPanel, null);
3191 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3203 public void clustalColour_actionPerformed(ActionEvent e)
3205 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3206 viewport.getHiddenRepSequences()));
3216 public void zappoColour_actionPerformed(ActionEvent e)
3218 changeColour(new ZappoColourScheme());
3228 public void taylorColour_actionPerformed(ActionEvent e)
3230 changeColour(new TaylorColourScheme());
3240 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3242 changeColour(new HydrophobicColourScheme());
3252 public void helixColour_actionPerformed(ActionEvent e)
3254 changeColour(new HelixColourScheme());
3264 public void strandColour_actionPerformed(ActionEvent e)
3266 changeColour(new StrandColourScheme());
3276 public void turnColour_actionPerformed(ActionEvent e)
3278 changeColour(new TurnColourScheme());
3288 public void buriedColour_actionPerformed(ActionEvent e)
3290 changeColour(new BuriedColourScheme());
3300 public void nucleotideColour_actionPerformed(ActionEvent e)
3302 changeColour(new NucleotideColourScheme());
3306 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3308 changeColour(new PurinePyrimidineColourScheme());
3312 * public void covariationColour_actionPerformed(ActionEvent e) {
3314 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3318 public void annotationColour_actionPerformed(ActionEvent e)
3320 new AnnotationColourChooser(viewport, alignPanel);
3324 public void annotationColumn_actionPerformed(ActionEvent e)
3326 new AnnotationColumnChooser(viewport, alignPanel);
3330 public void rnahelicesColour_actionPerformed(ActionEvent e)
3332 new RNAHelicesColourChooser(viewport, alignPanel);
3342 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3344 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3353 public void changeColour(ColourSchemeI cs)
3355 // TODO: compare with applet and pull up to model method
3360 if (viewport.getAbovePIDThreshold())
3362 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3364 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3368 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3371 if (viewport.getConservationSelected())
3374 Alignment al = (Alignment) viewport.getAlignment();
3375 Conservation c = new Conservation("All",
3376 ResidueProperties.propHash, 3, al.getSequences(), 0,
3380 c.verdict(false, viewport.getConsPercGaps());
3382 cs.setConservation(c);
3384 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3389 cs.setConservation(null);
3392 cs.setConsensus(viewport.getSequenceConsensusHash());
3395 viewport.setGlobalColourScheme(cs);
3397 if (viewport.getColourAppliesToAllGroups())
3400 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3408 if (cs instanceof ClustalxColourScheme)
3410 sg.cs = new ClustalxColourScheme(sg,
3411 viewport.getHiddenRepSequences());
3413 else if (cs instanceof UserColourScheme)
3415 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3421 sg.cs = cs.getClass().newInstance();
3422 } catch (Exception ex)
3427 if (viewport.getAbovePIDThreshold()
3428 || cs instanceof PIDColourScheme
3429 || cs instanceof Blosum62ColourScheme)
3431 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3433 sg.cs.setConsensus(AAFrequency.calculate(
3434 sg.getSequences(viewport.getHiddenRepSequences()),
3435 sg.getStartRes(), sg.getEndRes() + 1));
3439 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3442 if (viewport.getConservationSelected())
3444 Conservation c = new Conservation("Group",
3445 ResidueProperties.propHash, 3, sg.getSequences(viewport
3446 .getHiddenRepSequences()), sg.getStartRes(),
3447 sg.getEndRes() + 1);
3449 c.verdict(false, viewport.getConsPercGaps());
3450 sg.cs.setConservation(c);
3454 sg.cs.setConservation(null);
3459 if (alignPanel.getOverviewPanel() != null)
3461 alignPanel.getOverviewPanel().updateOverviewImage();
3464 alignPanel.paintAlignment(true);
3474 protected void modifyPID_actionPerformed(ActionEvent e)
3476 if (viewport.getAbovePIDThreshold()
3477 && viewport.getGlobalColourScheme() != null)
3479 SliderPanel.setPIDSliderSource(alignPanel,
3480 viewport.getGlobalColourScheme(), "Background");
3481 SliderPanel.showPIDSlider();
3492 protected void modifyConservation_actionPerformed(ActionEvent e)
3494 if (viewport.getConservationSelected()
3495 && viewport.getGlobalColourScheme() != null)
3497 SliderPanel.setConservationSlider(alignPanel,
3498 viewport.getGlobalColourScheme(), "Background");
3499 SliderPanel.showConservationSlider();
3510 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3512 viewport.setConservationSelected(conservationMenuItem.isSelected());
3514 viewport.setAbovePIDThreshold(false);
3515 abovePIDThreshold.setSelected(false);
3517 changeColour(viewport.getGlobalColourScheme());
3519 modifyConservation_actionPerformed(null);
3529 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3531 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3533 conservationMenuItem.setSelected(false);
3534 viewport.setConservationSelected(false);
3536 changeColour(viewport.getGlobalColourScheme());
3538 modifyPID_actionPerformed(null);
3548 public void userDefinedColour_actionPerformed(ActionEvent e)
3550 if (e.getActionCommand().equals(
3551 MessageManager.getString("action.user_defined")))
3553 new UserDefinedColours(alignPanel, null);
3557 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3558 .getUserColourSchemes().get(e.getActionCommand());
3564 public void updateUserColourMenu()
3567 Component[] menuItems = colourMenu.getMenuComponents();
3568 int i, iSize = menuItems.length;
3569 for (i = 0; i < iSize; i++)
3571 if (menuItems[i].getName() != null
3572 && menuItems[i].getName().equals("USER_DEFINED"))
3574 colourMenu.remove(menuItems[i]);
3578 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3580 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3581 .getUserColourSchemes().keys();
3583 while (userColours.hasMoreElements())
3585 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3586 userColours.nextElement().toString());
3587 radioItem.setName("USER_DEFINED");
3588 radioItem.addMouseListener(new MouseAdapter()
3591 public void mousePressed(MouseEvent evt)
3593 if (evt.isControlDown()
3594 || SwingUtilities.isRightMouseButton(evt))
3596 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3598 int option = JOptionPane.showInternalConfirmDialog(
3599 jalview.gui.Desktop.desktop,
3601 .getString("label.remove_from_default_list"),
3603 .getString("label.remove_user_defined_colour"),
3604 JOptionPane.YES_NO_OPTION);
3605 if (option == JOptionPane.YES_OPTION)
3607 jalview.gui.UserDefinedColours
3608 .removeColourFromDefaults(radioItem.getText());
3609 colourMenu.remove(radioItem);
3613 radioItem.addActionListener(new ActionListener()
3616 public void actionPerformed(ActionEvent evt)
3618 userDefinedColour_actionPerformed(evt);
3625 radioItem.addActionListener(new ActionListener()
3628 public void actionPerformed(ActionEvent evt)
3630 userDefinedColour_actionPerformed(evt);
3634 colourMenu.insert(radioItem, 15);
3635 colours.add(radioItem);
3647 public void PIDColour_actionPerformed(ActionEvent e)
3649 changeColour(new PIDColourScheme());
3659 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3661 changeColour(new Blosum62ColourScheme());
3671 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3673 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3674 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3675 .getAlignment().getSequenceAt(0), null);
3676 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3677 viewport.getAlignment()));
3678 alignPanel.paintAlignment(true);
3688 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3690 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3691 AlignmentSorter.sortByID(viewport.getAlignment());
3692 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3693 viewport.getAlignment()));
3694 alignPanel.paintAlignment(true);
3704 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3706 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3707 AlignmentSorter.sortByLength(viewport.getAlignment());
3708 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3709 viewport.getAlignment()));
3710 alignPanel.paintAlignment(true);
3720 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3722 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3723 AlignmentSorter.sortByGroup(viewport.getAlignment());
3724 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3725 viewport.getAlignment()));
3727 alignPanel.paintAlignment(true);
3737 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3739 new RedundancyPanel(alignPanel, this);
3749 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3751 if ((viewport.getSelectionGroup() == null)
3752 || (viewport.getSelectionGroup().getSize() < 2))
3754 JOptionPane.showInternalMessageDialog(this, MessageManager
3755 .getString("label.you_must_select_least_two_sequences"),
3756 MessageManager.getString("label.invalid_selection"),
3757 JOptionPane.WARNING_MESSAGE);
3761 JInternalFrame frame = new JInternalFrame();
3762 frame.setContentPane(new PairwiseAlignPanel(viewport));
3763 Desktop.addInternalFrame(frame,
3764 MessageManager.getString("action.pairwise_alignment"), 600,
3776 public void PCAMenuItem_actionPerformed(ActionEvent e)
3778 if (((viewport.getSelectionGroup() != null)
3779 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3780 .getSelectionGroup().getSize() > 0))
3781 || (viewport.getAlignment().getHeight() < 4))
3784 .showInternalMessageDialog(
3787 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3789 .getString("label.sequence_selection_insufficient"),
3790 JOptionPane.WARNING_MESSAGE);
3795 new PCAPanel(alignPanel);
3799 public void autoCalculate_actionPerformed(ActionEvent e)
3801 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3802 if (viewport.autoCalculateConsensus)
3804 viewport.firePropertyChange("alignment", null, viewport
3805 .getAlignment().getSequences());
3810 public void sortByTreeOption_actionPerformed(ActionEvent e)
3812 viewport.sortByTree = sortByTree.isSelected();
3816 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3818 viewport.followSelection = listenToViewSelections.isSelected();
3828 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3830 NewTreePanel("AV", "PID", "Average distance tree using PID");
3840 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3842 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3852 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3854 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3864 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3866 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3879 void NewTreePanel(String type, String pwType, String title)
3883 if (viewport.getSelectionGroup() != null
3884 && viewport.getSelectionGroup().getSize() > 0)
3886 if (viewport.getSelectionGroup().getSize() < 3)
3892 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3894 .getString("label.not_enough_sequences"),
3895 JOptionPane.WARNING_MESSAGE);
3899 SequenceGroup sg = viewport.getSelectionGroup();
3901 /* Decide if the selection is a column region */
3902 for (SequenceI _s : sg.getSequences())
3904 if (_s.getLength() < sg.getEndRes())
3910 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3912 .getString("label.sequences_selection_not_aligned"),
3913 JOptionPane.WARNING_MESSAGE);
3919 title = title + " on region";
3920 tp = new TreePanel(alignPanel, type, pwType);
3924 // are the visible sequences aligned?
3925 if (!viewport.getAlignment().isAligned(false))
3931 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3933 .getString("label.sequences_not_aligned"),
3934 JOptionPane.WARNING_MESSAGE);
3939 if (viewport.getAlignment().getHeight() < 2)
3944 tp = new TreePanel(alignPanel, type, pwType);
3949 if (viewport.viewName != null)
3951 title += viewport.viewName + " of ";
3954 title += this.title;
3956 Desktop.addInternalFrame(tp, title, 600, 500);
3967 public void addSortByOrderMenuItem(String title,
3968 final AlignmentOrder order)
3970 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
3972 item.addActionListener(new java.awt.event.ActionListener()
3975 public void actionPerformed(ActionEvent e)
3977 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3979 // TODO: JBPNote - have to map order entries to curent SequenceI
3981 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3983 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3986 alignPanel.paintAlignment(true);
3992 * Add a new sort by annotation score menu item
3995 * the menu to add the option to
3997 * the label used to retrieve scores for each sequence on the
4000 public void addSortByAnnotScoreMenuItem(JMenu sort,
4001 final String scoreLabel)
4003 final JMenuItem item = new JMenuItem(scoreLabel);
4005 item.addActionListener(new java.awt.event.ActionListener()
4008 public void actionPerformed(ActionEvent e)
4010 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4011 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4012 viewport.getAlignment());// ,viewport.getSelectionGroup());
4013 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4014 viewport.getAlignment()));
4015 alignPanel.paintAlignment(true);
4021 * last hash for alignment's annotation array - used to minimise cost of
4024 protected int _annotationScoreVectorHash;
4027 * search the alignment and rebuild the sort by annotation score submenu the
4028 * last alignment annotation vector hash is stored to minimize cost of
4029 * rebuilding in subsequence calls.
4033 public void buildSortByAnnotationScoresMenu()
4035 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4040 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4042 sortByAnnotScore.removeAll();
4043 // almost certainly a quicker way to do this - but we keep it simple
4044 Hashtable scoreSorts = new Hashtable();
4045 AlignmentAnnotation aann[];
4046 for (SequenceI sqa : viewport.getAlignment().getSequences())
4048 aann = sqa.getAnnotation();
4049 for (int i = 0; aann != null && i < aann.length; i++)
4051 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4053 scoreSorts.put(aann[i].label, aann[i].label);
4057 Enumeration labels = scoreSorts.keys();
4058 while (labels.hasMoreElements())
4060 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4061 (String) labels.nextElement());
4063 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4066 _annotationScoreVectorHash = viewport.getAlignment()
4067 .getAlignmentAnnotation().hashCode();
4072 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4073 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4074 * call. Listeners are added to remove the menu item when the treePanel is
4075 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4079 * Displayed tree window.
4081 * SortBy menu item title.
4084 public void buildTreeMenu()
4086 calculateTree.removeAll();
4087 // build the calculate menu
4089 for (final String type : new String[]
4092 String treecalcnm = MessageManager.getString("label.tree_calc_"
4093 + type.toLowerCase());
4094 for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4096 JMenuItem tm = new JMenuItem();
4097 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4098 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4100 String smn = MessageManager.getStringOrReturn(
4101 "label.score_model_", sm.getName());
4102 final String title = MessageManager.formatMessage(
4103 "label.treecalc_title", treecalcnm, smn);
4104 tm.setText(title);//
4105 tm.addActionListener(new java.awt.event.ActionListener()
4108 public void actionPerformed(ActionEvent e)
4110 NewTreePanel(type, (String) pwtype, title);
4113 calculateTree.add(tm);
4118 sortByTreeMenu.removeAll();
4120 Vector comps = (Vector) PaintRefresher.components.get(viewport
4121 .getSequenceSetId());
4122 Vector treePanels = new Vector();
4123 int i, iSize = comps.size();
4124 for (i = 0; i < iSize; i++)
4126 if (comps.elementAt(i) instanceof TreePanel)
4128 treePanels.add(comps.elementAt(i));
4132 iSize = treePanels.size();
4136 sortByTreeMenu.setVisible(false);
4140 sortByTreeMenu.setVisible(true);
4142 for (i = 0; i < treePanels.size(); i++)
4144 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4145 final JMenuItem item = new JMenuItem(tp.getTitle());
4146 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4147 item.addActionListener(new java.awt.event.ActionListener()
4150 public void actionPerformed(ActionEvent e)
4152 tp.sortByTree_actionPerformed(null);
4153 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4158 sortByTreeMenu.add(item);
4162 public boolean sortBy(AlignmentOrder alorder, String undoname)
4164 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4165 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4166 if (undoname != null)
4168 addHistoryItem(new OrderCommand(undoname, oldOrder,
4169 viewport.getAlignment()));
4171 alignPanel.paintAlignment(true);
4176 * Work out whether the whole set of sequences or just the selected set will
4177 * be submitted for multiple alignment.
4180 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4182 // Now, check we have enough sequences
4183 AlignmentView msa = null;
4185 if ((viewport.getSelectionGroup() != null)
4186 && (viewport.getSelectionGroup().getSize() > 1))
4188 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4189 // some common interface!
4191 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4192 * SequenceI[sz = seqs.getSize(false)];
4194 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4195 * seqs.getSequenceAt(i); }
4197 msa = viewport.getAlignmentView(true);
4199 else if (viewport.getSelectionGroup() != null
4200 && viewport.getSelectionGroup().getSize() == 1)
4202 int option = JOptionPane.showConfirmDialog(this,
4203 MessageManager.getString("warn.oneseq_msainput_selection"),
4204 MessageManager.getString("label.invalid_selection"),
4205 JOptionPane.OK_CANCEL_OPTION);
4206 if (option == JOptionPane.OK_OPTION)
4208 msa = viewport.getAlignmentView(false);
4213 msa = viewport.getAlignmentView(false);
4219 * Decides what is submitted to a secondary structure prediction service: the
4220 * first sequence in the alignment, or in the current selection, or, if the
4221 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4222 * region or the whole alignment. (where the first sequence in the set is the
4223 * one that the prediction will be for).
4225 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4227 AlignmentView seqs = null;
4229 if ((viewport.getSelectionGroup() != null)
4230 && (viewport.getSelectionGroup().getSize() > 0))
4232 seqs = viewport.getAlignmentView(true);
4236 seqs = viewport.getAlignmentView(false);
4238 // limit sequences - JBPNote in future - could spawn multiple prediction
4240 // TODO: viewport.getAlignment().isAligned is a global state - the local
4241 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4242 if (!viewport.getAlignment().isAligned(false))
4244 seqs.setSequences(new SeqCigar[]
4245 { seqs.getSequences()[0] });
4246 // TODO: if seqs.getSequences().length>1 then should really have warned
4260 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4262 // Pick the tree file
4263 JalviewFileChooser chooser = new JalviewFileChooser(
4264 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4265 chooser.setFileView(new JalviewFileView());
4266 chooser.setDialogTitle(MessageManager
4267 .getString("label.select_newick_like_tree_file"));
4268 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4270 int value = chooser.showOpenDialog(null);
4272 if (value == JalviewFileChooser.APPROVE_OPTION)
4274 String choice = chooser.getSelectedFile().getPath();
4275 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4276 jalview.io.NewickFile fin = null;
4279 fin = new jalview.io.NewickFile(choice, "File");
4280 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4281 } catch (Exception ex)
4288 .getString("label.problem_reading_tree_file"),
4289 JOptionPane.WARNING_MESSAGE);
4290 ex.printStackTrace();
4292 if (fin != null && fin.hasWarningMessage())
4294 JOptionPane.showMessageDialog(Desktop.desktop, fin
4295 .getWarningMessage(), MessageManager
4296 .getString("label.possible_problem_with_tree_file"),
4297 JOptionPane.WARNING_MESSAGE);
4303 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4305 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4308 public TreePanel ShowNewickTree(NewickFile nf, String title)
4310 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4313 public TreePanel ShowNewickTree(NewickFile nf, String title,
4314 AlignmentView input)
4316 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4319 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4320 int h, int x, int y)
4322 return ShowNewickTree(nf, title, null, w, h, x, y);
4326 * Add a treeviewer for the tree extracted from a newick file object to the
4327 * current alignment view
4334 * Associated alignment input data (or null)
4343 * @return TreePanel handle
4345 public TreePanel ShowNewickTree(NewickFile nf, String title,
4346 AlignmentView input, int w, int h, int x, int y)
4348 TreePanel tp = null;
4354 if (nf.getTree() != null)
4356 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4362 tp.setLocation(x, y);
4365 Desktop.addInternalFrame(tp, title, w, h);
4367 } catch (Exception ex)
4369 ex.printStackTrace();
4375 private boolean buildingMenu = false;
4378 * Generates menu items and listener event actions for web service clients
4381 public void BuildWebServiceMenu()
4383 while (buildingMenu)
4387 System.err.println("Waiting for building menu to finish.");
4389 } catch (Exception e)
4394 final AlignFrame me = this;
4395 buildingMenu = true;
4396 new Thread(new Runnable()
4401 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4404 System.err.println("Building ws menu again "
4405 + Thread.currentThread());
4406 // TODO: add support for context dependent disabling of services based
4408 // alignment and current selection
4409 // TODO: add additional serviceHandle parameter to specify abstract
4411 // class independently of AbstractName
4412 // TODO: add in rediscovery GUI function to restart discoverer
4413 // TODO: group services by location as well as function and/or
4415 // object broker mechanism.
4416 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4417 final IProgressIndicator af = me;
4418 final JMenu msawsmenu = new JMenu("Alignment");
4419 final JMenu secstrmenu = new JMenu(
4420 "Secondary Structure Prediction");
4421 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4422 final JMenu analymenu = new JMenu("Analysis");
4423 final JMenu dismenu = new JMenu("Protein Disorder");
4424 // final JMenu msawsmenu = new
4425 // JMenu(MessageManager.getString("label.alignment"));
4426 // final JMenu secstrmenu = new
4427 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4428 // final JMenu seqsrchmenu = new
4429 // JMenu(MessageManager.getString("label.sequence_database_search"));
4430 // final JMenu analymenu = new
4431 // JMenu(MessageManager.getString("label.analysis"));
4432 // final JMenu dismenu = new
4433 // JMenu(MessageManager.getString("label.protein_disorder"));
4434 // JAL-940 - only show secondary structure prediction services from
4435 // the legacy server
4436 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4438 Discoverer.services != null && (Discoverer.services.size() > 0))
4440 // TODO: refactor to allow list of AbstractName/Handler bindings to
4442 // stored or retrieved from elsewhere
4443 // No MSAWS used any more:
4444 // Vector msaws = null; // (Vector)
4445 // Discoverer.services.get("MsaWS");
4446 Vector secstrpr = (Vector) Discoverer.services
4448 if (secstrpr != null)
4450 // Add any secondary structure prediction services
4451 for (int i = 0, j = secstrpr.size(); i < j; i++)
4453 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4455 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4456 .getServiceClient(sh);
4457 int p = secstrmenu.getItemCount();
4458 impl.attachWSMenuEntry(secstrmenu, me);
4459 int q = secstrmenu.getItemCount();
4460 for (int litm = p; litm < q; litm++)
4462 legacyItems.add(secstrmenu.getItem(litm));
4468 // Add all submenus in the order they should appear on the web
4470 wsmenu.add(msawsmenu);
4471 wsmenu.add(secstrmenu);
4472 wsmenu.add(dismenu);
4473 wsmenu.add(analymenu);
4474 // No search services yet
4475 // wsmenu.add(seqsrchmenu);
4477 javax.swing.SwingUtilities.invokeLater(new Runnable()
4484 webService.removeAll();
4485 // first, add discovered services onto the webservices menu
4486 if (wsmenu.size() > 0)
4488 for (int i = 0, j = wsmenu.size(); i < j; i++)
4490 webService.add(wsmenu.get(i));
4495 webService.add(me.webServiceNoServices);
4497 // TODO: move into separate menu builder class.
4498 boolean new_sspred = false;
4499 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4501 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4502 if (jws2servs != null)
4504 if (jws2servs.hasServices())
4506 jws2servs.attachWSMenuEntry(webService, me);
4507 for (Jws2Instance sv : jws2servs.getServices())
4509 if (sv.description.toLowerCase().contains("jpred"))
4511 for (JMenuItem jmi : legacyItems)
4513 jmi.setVisible(false);
4519 if (jws2servs.isRunning())
4521 JMenuItem tm = new JMenuItem(
4522 "Still discovering JABA Services");
4523 tm.setEnabled(false);
4528 build_urlServiceMenu(me.webService);
4529 build_fetchdbmenu(webService);
4530 for (JMenu item : wsmenu)
4532 if (item.getItemCount() == 0)
4534 item.setEnabled(false);
4538 item.setEnabled(true);
4541 } catch (Exception e)
4544 .debug("Exception during web service menu building process.",
4550 } catch (Exception e)
4555 buildingMenu = false;
4562 * construct any groupURL type service menu entries.
4566 private void build_urlServiceMenu(JMenu webService)
4568 // TODO: remove this code when 2.7 is released
4569 // DEBUG - alignmentView
4571 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4572 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4574 * @Override public void actionPerformed(ActionEvent e) {
4575 * jalview.datamodel.AlignmentView
4576 * .testSelectionViews(af.viewport.getAlignment(),
4577 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4579 * }); webService.add(testAlView);
4581 // TODO: refactor to RestClient discoverer and merge menu entries for
4582 // rest-style services with other types of analysis/calculation service
4583 // SHmmr test client - still being implemented.
4584 // DEBUG - alignmentView
4586 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4589 client.attachWSMenuEntry(
4590 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4596 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4597 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4598 * getProperty("LAST_DIRECTORY"));
4600 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4601 * to Vamsas file"); chooser.setToolTipText("Export");
4603 * int value = chooser.showSaveDialog(this);
4605 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4606 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4607 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4608 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4611 * prototype of an automatically enabled/disabled analysis function
4614 protected void setShowProductsEnabled()
4616 SequenceI[] selection = viewport.getSequenceSelection();
4617 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4618 viewport.getAlignment().getDataset()))
4620 showProducts.setEnabled(true);
4625 showProducts.setEnabled(false);
4630 * search selection for sequence xRef products and build the show products
4635 * @return true if showProducts menu should be enabled.
4637 public boolean canShowProducts(SequenceI[] selection,
4638 boolean isRegionSelection, Alignment dataset)
4640 boolean showp = false;
4643 showProducts.removeAll();
4644 final boolean dna = viewport.getAlignment().isNucleotide();
4645 final Alignment ds = dataset;
4646 String[] ptypes = (selection == null || selection.length == 0) ? null
4647 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4649 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4650 // selection, dataset, true);
4651 final SequenceI[] sel = selection;
4652 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4655 final boolean isRegSel = isRegionSelection;
4656 final AlignFrame af = this;
4657 final String source = ptypes[t];
4658 JMenuItem xtype = new JMenuItem(ptypes[t]);
4659 xtype.addActionListener(new ActionListener()
4663 public void actionPerformed(ActionEvent e)
4665 // TODO: new thread for this call with vis-delay
4666 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4667 isRegSel, dna, source);
4671 showProducts.add(xtype);
4673 showProducts.setVisible(showp);
4674 showProducts.setEnabled(showp);
4675 } catch (Exception e)
4677 jalview.bin.Cache.log
4678 .warn("canTranslate threw an exception - please report to help@jalview.org",
4685 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4686 boolean isRegSel, boolean dna, String source)
4688 final boolean fisRegSel = isRegSel;
4689 final boolean fdna = dna;
4690 final String fsrc = source;
4691 final AlignFrame ths = this;
4692 final SequenceI[] fsel = sel;
4693 Runnable foo = new Runnable()
4699 final long sttime = System.currentTimeMillis();
4700 ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
4703 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4707 Alignment prods = CrossRef
4708 .findXrefSequences(fsel, fdna, fsrc, ds);
4711 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4712 for (int s = 0; s < sprods.length; s++)
4714 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4715 if (ds.getSequences() == null
4716 || !ds.getSequences().contains(
4717 sprods[s].getDatasetSequence()))
4719 ds.addSequence(sprods[s].getDatasetSequence());
4721 sprods[s].updatePDBIds();
4723 Alignment al = new Alignment(sprods);
4724 AlignedCodonFrame[] cf = prods.getCodonFrames();
4726 for (int s = 0; cf != null && s < cf.length; s++)
4728 al.addCodonFrame(cf[s]);
4731 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4733 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4734 + " for " + ((fisRegSel) ? "selected region of " : "")
4736 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4741 System.err.println("No Sequences generated for xRef type "
4744 } catch (Exception e)
4746 jalview.bin.Cache.log.error(
4747 "Exception when finding crossreferences", e);
4748 } catch (OutOfMemoryError e)
4750 new OOMWarning("whilst fetching crossreferences", e);
4753 jalview.bin.Cache.log.error("Error when finding crossreferences",
4756 ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
4761 Thread frunner = new Thread(foo);
4765 public boolean canShowTranslationProducts(SequenceI[] selection,
4766 AlignmentI alignment)
4771 return (jalview.analysis.Dna.canTranslate(selection,
4772 viewport.getViewAsVisibleContigs(true)));
4773 } catch (Exception e)
4775 jalview.bin.Cache.log
4776 .warn("canTranslate threw an exception - please report to help@jalview.org",
4783 public void showProducts_actionPerformed(ActionEvent e)
4785 // /////////////////////////////
4786 // Collect Data to be translated/transferred
4788 SequenceI[] selection = viewport.getSequenceSelection();
4789 AlignmentI al = null;
4792 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4793 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4794 viewport.getAlignment().getDataset());
4795 } catch (Exception ex)
4798 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4806 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4807 MessageManager.getString("label.translation_failed"),
4808 JOptionPane.WARNING_MESSAGE);
4812 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4813 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4814 "label.translation_of_params", new String[]
4815 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4820 public void showTranslation_actionPerformed(ActionEvent e)
4822 // /////////////////////////////
4823 // Collect Data to be translated/transferred
4825 SequenceI[] selection = viewport.getSequenceSelection();
4826 String[] seqstring = viewport.getViewAsString(true);
4827 AlignmentI al = null;
4830 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4831 viewport.getViewAsVisibleContigs(true), viewport
4832 .getGapCharacter(), viewport.getAlignment()
4833 .getAlignmentAnnotation(), viewport.getAlignment()
4834 .getWidth(), viewport.getAlignment().getDataset());
4835 } catch (Exception ex)
4838 jalview.bin.Cache.log.error(
4839 "Exception during translation. Please report this !", ex);
4844 .getString("label.error_when_translating_sequences_submit_bug_report"),
4846 .getString("label.implementation_error")
4848 .getString("translation_failed"),
4849 JOptionPane.ERROR_MESSAGE);
4858 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4859 MessageManager.getString("label.translation_failed"),
4860 JOptionPane.WARNING_MESSAGE);
4864 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4865 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4866 "label.translation_of_params", new String[]
4867 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4872 * Try to load a features file onto the alignment.
4875 * contents or path to retrieve file
4877 * access mode of file (see jalview.io.AlignFile)
4878 * @return true if features file was parsed corectly.
4880 public boolean parseFeaturesFile(String file, String type)
4882 boolean featuresFile = false;
4885 featuresFile = new FeaturesFile(file, type).parse(viewport
4886 .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
4887 .getFeatureRenderer().getFeatureColours(), false,
4888 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4889 } catch (Exception ex)
4891 ex.printStackTrace();
4896 viewport.setShowSequenceFeatures(true);
4897 showSeqFeatures.setSelected(true);
4898 if (alignPanel.getSeqPanel().seqCanvas.fr != null)
4900 // update the min/max ranges where necessary
4901 alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
4903 if (featureSettings != null)
4905 featureSettings.setTableData();
4907 alignPanel.paintAlignment(true);
4910 return featuresFile;
4914 public void dragEnter(DropTargetDragEvent evt)
4919 public void dragExit(DropTargetEvent evt)
4924 public void dragOver(DropTargetDragEvent evt)
4929 public void dropActionChanged(DropTargetDragEvent evt)
4934 public void drop(DropTargetDropEvent evt)
4936 Transferable t = evt.getTransferable();
4937 java.util.List files = null;
4941 DataFlavor uriListFlavor = new DataFlavor(
4942 "text/uri-list;class=java.lang.String");
4943 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4945 // Works on Windows and MacOSX
4946 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4947 files = (java.util.List) t
4948 .getTransferData(DataFlavor.javaFileListFlavor);
4950 else if (t.isDataFlavorSupported(uriListFlavor))
4952 // This is used by Unix drag system
4953 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4954 String data = (String) t.getTransferData(uriListFlavor);
4955 files = new java.util.ArrayList(1);
4956 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4957 data, "\r\n"); st.hasMoreTokens();)
4959 String s = st.nextToken();
4960 if (s.startsWith("#"))
4962 // the line is a comment (as per the RFC 2483)
4966 java.net.URI uri = new java.net.URI(s);
4967 // check to see if we can handle this kind of URI
4968 if (uri.getScheme().toLowerCase().startsWith("http"))
4970 files.add(uri.toString());
4974 // otherwise preserve old behaviour: catch all for file objects
4975 java.io.File file = new java.io.File(uri);
4976 files.add(file.toString());
4980 } catch (Exception e)
4982 e.printStackTrace();
4988 // check to see if any of these files have names matching sequences in
4990 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4991 .getAlignment().getSequencesArray());
4993 * Object[] { String,SequenceI}
4995 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4996 ArrayList<String> filesnotmatched = new ArrayList<String>();
4997 for (int i = 0; i < files.size(); i++)
4999 String file = files.get(i).toString();
5001 String protocol = FormatAdapter.checkProtocol(file);
5002 if (protocol == jalview.io.FormatAdapter.FILE)
5004 File fl = new File(file);
5005 pdbfn = fl.getName();
5007 else if (protocol == jalview.io.FormatAdapter.URL)
5009 URL url = new URL(file);
5010 pdbfn = url.getFile();
5012 if (pdbfn.length() > 0)
5014 // attempt to find a match in the alignment
5015 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5016 int l = 0, c = pdbfn.indexOf(".");
5017 while (mtch == null && c != -1)
5022 } while ((c = pdbfn.indexOf(".", l)) > l);
5025 pdbfn = pdbfn.substring(0, l);
5027 mtch = idm.findAllIdMatches(pdbfn);
5034 type = new IdentifyFile().Identify(file, protocol);
5035 } catch (Exception ex)
5041 if (type.equalsIgnoreCase("PDB"))
5043 filesmatched.add(new Object[]
5044 { file, protocol, mtch });
5049 // File wasn't named like one of the sequences or wasn't a PDB file.
5050 filesnotmatched.add(file);
5054 if (filesmatched.size() > 0)
5056 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5062 "label.automatically_associate_pdb_files_with_sequences_same_name",
5069 .getString("label.automatically_associate_pdb_files_by_name"),
5070 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5073 for (Object[] fm : filesmatched)
5075 // try and associate
5076 // TODO: may want to set a standard ID naming formalism for
5077 // associating PDB files which have no IDs.
5078 for (SequenceI toassoc : (SequenceI[]) fm[2])
5080 PDBEntry pe = new AssociatePdbFileWithSeq()
5081 .associatePdbWithSeq((String) fm[0],
5082 (String) fm[1], toassoc, false,
5086 System.err.println("Associated file : "
5087 + ((String) fm[0]) + " with "
5088 + toassoc.getDisplayId(true));
5092 alignPanel.paintAlignment(true);
5096 if (filesnotmatched.size() > 0)
5099 && (Cache.getDefault(
5100 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5103 "<html>"+MessageManager
5105 "label.ignore_unmatched_dropped_files_info",
5110 .toString() })+"</html>",
5112 .getString("label.ignore_unmatched_dropped_files"),
5113 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5117 for (String fn : filesnotmatched)
5119 loadJalviewDataFile(fn, null, null, null);
5123 } catch (Exception ex)
5125 ex.printStackTrace();
5131 * Attempt to load a "dropped" file or URL string: First by testing whether
5132 * it's and Annotation file, then a JNet file, and finally a features file. If
5133 * all are false then the user may have dropped an alignment file onto this
5137 * either a filename or a URL string.
5139 public void loadJalviewDataFile(String file, String protocol,
5140 String format, SequenceI assocSeq)
5144 if (protocol == null)
5146 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5148 // if the file isn't identified, or not positively identified as some
5149 // other filetype (PFAM is default unidentified alignment file type) then
5150 // try to parse as annotation.
5151 boolean isAnnotation = (format == null || format
5152 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5153 .annotateAlignmentView(viewport, file, protocol)
5158 // first see if its a T-COFFEE score file
5159 TCoffeeScoreFile tcf = null;
5162 tcf = new TCoffeeScoreFile(file, protocol);
5165 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5167 tcoffeeColour.setEnabled(true);
5168 tcoffeeColour.setSelected(true);
5169 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5170 isAnnotation = true;
5172 .setText(MessageManager
5173 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5177 // some problem - if no warning its probable that the ID matching
5178 // process didn't work
5182 tcf.getWarningMessage() == null ? MessageManager
5183 .getString("label.check_file_matches_sequence_ids_alignment")
5184 : tcf.getWarningMessage(),
5186 .getString("label.problem_reading_tcoffee_score_file"),
5187 JOptionPane.WARNING_MESSAGE);
5194 } catch (Exception x)
5197 .debug("Exception when processing data source as T-COFFEE score file",
5203 // try to see if its a JNet 'concise' style annotation file *before*
5205 // try to parse it as a features file
5208 format = new IdentifyFile().Identify(file, protocol);
5210 if (format.equalsIgnoreCase("JnetFile"))
5212 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5214 new JnetAnnotationMaker().add_annotation(predictions,
5215 viewport.getAlignment(), 0, false);
5216 isAnnotation = true;
5221 * if (format.equalsIgnoreCase("PDB")) {
5223 * String pdbfn = ""; // try to match up filename with sequence id
5224 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5225 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5226 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5227 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5228 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5229 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5230 * // attempt to find a match in the alignment SequenceI mtch =
5231 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5232 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5233 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5234 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5235 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5236 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5237 * { System.err.println("Associated file : " + file + " with " +
5238 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5239 * TODO: maybe need to load as normal otherwise return; } }
5241 // try to parse it as a features file
5242 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5243 // if it wasn't a features file then we just treat it as a general
5244 // alignment file to load into the current view.
5247 new FileLoader().LoadFile(viewport, file, protocol, format);
5251 alignPanel.paintAlignment(true);
5259 alignPanel.adjustAnnotationHeight();
5260 viewport.updateSequenceIdColours();
5261 buildSortByAnnotationScoresMenu();
5262 alignPanel.paintAlignment(true);
5264 } catch (Exception ex)
5266 ex.printStackTrace();
5267 } catch (OutOfMemoryError oom)
5272 } catch (Exception x)
5278 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5279 : "using " + protocol + " from " + file)
5281 + (format != null ? "(parsing as '" + format
5282 + "' file)" : ""), oom, Desktop.desktop);
5287 public void tabSelectionChanged(int index)
5291 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5292 viewport = alignPanel.av;
5293 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5294 setMenusFromViewport(viewport);
5299 public void tabbedPane_mousePressed(MouseEvent e)
5301 if (SwingUtilities.isRightMouseButton(e))
5303 String reply = JOptionPane.showInternalInputDialog(this,
5304 MessageManager.getString("label.enter_view_name"),
5305 MessageManager.getString("label.enter_view_name"),
5306 JOptionPane.QUESTION_MESSAGE);
5310 viewport.viewName = reply;
5311 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5316 public AlignViewport getCurrentView()
5322 * Open the dialog for regex description parsing.
5325 protected void extractScores_actionPerformed(ActionEvent e)
5327 ParseProperties pp = new jalview.analysis.ParseProperties(
5328 viewport.getAlignment());
5329 // TODO: verify regex and introduce GUI dialog for version 2.5
5330 // if (pp.getScoresFromDescription("col", "score column ",
5331 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5333 if (pp.getScoresFromDescription("description column",
5334 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5336 buildSortByAnnotationScoresMenu();
5344 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5348 protected void showDbRefs_actionPerformed(ActionEvent e)
5350 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5356 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5360 protected void showNpFeats_actionPerformed(ActionEvent e)
5362 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5366 * find the viewport amongst the tabs in this alignment frame and close that
5371 public boolean closeView(AlignViewport av)
5375 this.closeMenuItem_actionPerformed(false);
5378 Component[] comp = tabbedPane.getComponents();
5379 for (int i = 0; comp != null && i < comp.length; i++)
5381 if (comp[i] instanceof AlignmentPanel)
5383 if (((AlignmentPanel) comp[i]).av == av)
5386 closeView((AlignmentPanel) comp[i]);
5394 protected void build_fetchdbmenu(JMenu webService)
5396 // Temporary hack - DBRef Fetcher always top level ws entry.
5397 // TODO We probably want to store a sequence database checklist in
5398 // preferences and have checkboxes.. rather than individual sources selected
5400 final JMenu rfetch = new JMenu(
5401 MessageManager.getString("action.fetch_db_references"));
5402 rfetch.setToolTipText(MessageManager
5403 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5404 webService.add(rfetch);
5406 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5407 MessageManager.getString("option.trim_retrieved_seqs"));
5408 trimrs.setToolTipText(MessageManager
5409 .getString("label.trim_retrieved_sequences"));
5410 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5411 trimrs.addActionListener(new ActionListener()
5414 public void actionPerformed(ActionEvent e)
5416 trimrs.setSelected(trimrs.isSelected());
5417 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5418 Boolean.valueOf(trimrs.isSelected()).toString());
5422 JMenuItem fetchr = new JMenuItem(
5423 MessageManager.getString("label.standard_databases"));
5424 fetchr.setToolTipText(MessageManager
5425 .getString("label.fetch_embl_uniprot"));
5426 fetchr.addActionListener(new ActionListener()
5430 public void actionPerformed(ActionEvent e)
5432 new Thread(new Runnable()
5438 new jalview.ws.DBRefFetcher(alignPanel.av
5439 .getSequenceSelection(), alignPanel.alignFrame)
5440 .fetchDBRefs(false);
5448 final AlignFrame me = this;
5449 new Thread(new Runnable()
5454 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5455 .getSequenceFetcherSingleton(me);
5456 javax.swing.SwingUtilities.invokeLater(new Runnable()
5461 String[] dbclasses = sf.getOrderedSupportedSources();
5462 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5463 // jalview.util.QuickSort.sort(otherdb, otherdb);
5464 List<DbSourceProxy> otherdb;
5465 JMenu dfetch = new JMenu();
5466 JMenu ifetch = new JMenu();
5467 JMenuItem fetchr = null;
5468 int comp = 0, icomp = 0, mcomp = 15;
5469 String mname = null;
5471 for (String dbclass : dbclasses)
5473 otherdb = sf.getSourceProxy(dbclass);
5474 // add a single entry for this class, or submenu allowing 'fetch
5476 if (otherdb == null || otherdb.size() < 1)
5480 // List<DbSourceProxy> dbs=otherdb;
5481 // otherdb=new ArrayList<DbSourceProxy>();
5482 // for (DbSourceProxy db:dbs)
5484 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5488 mname = "From " + dbclass;
5490 if (otherdb.size() == 1)
5492 final DbSourceProxy[] dassource = otherdb
5493 .toArray(new DbSourceProxy[0]);
5494 DbSourceProxy src = otherdb.get(0);
5495 fetchr = new JMenuItem(src.getDbSource());
5496 fetchr.addActionListener(new ActionListener()
5500 public void actionPerformed(ActionEvent e)
5502 new Thread(new Runnable()
5508 new jalview.ws.DBRefFetcher(alignPanel.av
5509 .getSequenceSelection(),
5510 alignPanel.alignFrame, dassource)
5511 .fetchDBRefs(false);
5517 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
5523 final DbSourceProxy[] dassource = otherdb
5524 .toArray(new DbSourceProxy[0]);
5526 DbSourceProxy src = otherdb.get(0);
5527 fetchr = new JMenuItem(MessageManager.formatMessage(
5528 "label.fetch_all_param", new String[]
5529 { src.getDbSource() }));
5530 fetchr.addActionListener(new ActionListener()
5533 public void actionPerformed(ActionEvent e)
5535 new Thread(new Runnable()
5541 new jalview.ws.DBRefFetcher(alignPanel.av
5542 .getSequenceSelection(),
5543 alignPanel.alignFrame, dassource)
5544 .fetchDBRefs(false);
5550 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5553 // and then build the rest of the individual menus
5554 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
5556 String imname = null;
5558 for (DbSourceProxy sproxy : otherdb)
5560 String dbname = sproxy.getDbName();
5561 String sname = dbname.length() > 5 ? dbname.substring(0,
5562 5) + "..." : dbname;
5563 String msname = dbname.length() > 10 ? dbname.substring(
5564 0, 10) + "..." : dbname;
5567 imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
5569 fetchr = new JMenuItem(msname);
5570 final DbSourceProxy[] dassrc =
5572 fetchr.addActionListener(new ActionListener()
5576 public void actionPerformed(ActionEvent e)
5578 new Thread(new Runnable()
5584 new jalview.ws.DBRefFetcher(alignPanel.av
5585 .getSequenceSelection(),
5586 alignPanel.alignFrame, dassrc)
5587 .fetchDBRefs(false);
5593 fetchr.setToolTipText("<html>"
5594 + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
5597 if (++icomp >= mcomp || i == (otherdb.size()))
5599 ifetch.setText(MessageManager.formatMessage(
5600 "label.source_to_target", imname, sname));
5602 ifetch = new JMenu();
5610 if (comp >= mcomp || dbi >= (dbclasses.length))
5612 dfetch.setText(MessageManager.formatMessage(
5613 "label.source_to_target", mname, dbclass));
5615 dfetch = new JMenu();
5628 * Left justify the whole alignment.
5631 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5633 AlignmentI al = viewport.getAlignment();
5635 viewport.firePropertyChange("alignment", null, al);
5639 * Right justify the whole alignment.
5642 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5644 AlignmentI al = viewport.getAlignment();
5646 viewport.firePropertyChange("alignment", null, al);
5649 public void setShowSeqFeatures(boolean b)
5651 showSeqFeatures.setSelected(true);
5652 viewport.setShowSequenceFeatures(true);
5659 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5660 * awt.event.ActionEvent)
5663 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5665 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5666 alignPanel.paintAlignment(true);
5673 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5677 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5679 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5680 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5688 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5689 * .event.ActionEvent)
5692 protected void showGroupConservation_actionPerformed(ActionEvent e)
5694 viewport.setShowGroupConservation(showGroupConservation.getState());
5695 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5702 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5703 * .event.ActionEvent)
5706 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5708 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5709 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5716 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5717 * .event.ActionEvent)
5720 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5722 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5723 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5727 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5729 showSequenceLogo.setState(true);
5730 viewport.setShowSequenceLogo(true);
5731 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5732 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5736 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5738 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5745 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5746 * .event.ActionEvent)
5749 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5751 if (avc.makeGroupsFromSelection())
5753 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5754 alignPanel.updateAnnotation();
5755 alignPanel.paintAlignment(true);
5758 public void clearAlignmentSeqRep()
5760 // TODO refactor alignmentseqrep to controller
5761 if (viewport.getAlignment().hasSeqrep()) {
5762 viewport.getAlignment().setSeqrep(null);
5763 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5764 alignPanel.updateAnnotation();
5765 alignPanel.paintAlignment(true);
5770 protected void createGroup_actionPerformed(ActionEvent e)
5772 if (avc.createGroup())
5774 alignPanel.alignmentChanged();
5779 protected void unGroup_actionPerformed(ActionEvent e)
5783 alignPanel.alignmentChanged();
5788 * make the given alignmentPanel the currently selected tab
5790 * @param alignmentPanel
5792 public void setDisplayedView(AlignmentPanel alignmentPanel)
5794 if (!viewport.getSequenceSetId().equals(
5795 alignmentPanel.av.getSequenceSetId()))
5797 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5799 if (tabbedPane != null
5800 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5801 .getSelectedIndex())
5803 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5808 * Action on selection of menu options to Show or Hide annotations.
5811 * @param forSequences
5812 * update sequence-related annotations
5813 * @param forAlignment
5814 * update non-sequence-related annotations
5817 protected void setAnnotationsVisibility(boolean visible,
5818 boolean forSequences, boolean forAlignment)
5820 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5821 .getAlignmentAnnotation())
5823 boolean apply = (aa.sequenceRef == null && forAlignment)
5824 || (aa.sequenceRef != null && forSequences);
5827 aa.visible = visible;
5830 alignPanel.validateAnnotationDimensions(false);
5831 alignPanel.alignmentChanged();
5835 * Store selected annotation sort order for the view and repaint.
5838 protected void sortAnnotations_actionPerformed()
5840 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5842 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5843 alignPanel.paintAlignment(true);
5848 * @return alignment panels in this alignemnt frame
5850 public List<AlignmentViewPanel> getAlignPanels()
5852 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5856 class PrintThread extends Thread
5860 public PrintThread(AlignmentPanel ap)
5865 static PageFormat pf;
5870 PrinterJob printJob = PrinterJob.getPrinterJob();
5874 printJob.setPrintable(ap, pf);
5878 printJob.setPrintable(ap);
5881 if (printJob.printDialog())
5886 } catch (Exception PrintException)
5888 PrintException.printStackTrace();