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);
1079 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1081 statusBar.setText(MessageManager.formatMessage(
1082 "label.successfully_saved_to_file_in_format", new String[]
1083 { fileName, format }));
1088 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1090 warningMessage("Cannot save file " + fileName + " using format "
1091 + format, "Alignment output format not supported");
1092 saveAs_actionPerformed(null);
1093 // JBPNote need to have a raise_gui flag here
1097 String[] omitHidden = null;
1099 if (viewport.hasHiddenColumns())
1101 int reply = JOptionPane
1102 .showInternalConfirmDialog(
1105 .getString("label.alignment_contains_hidden_columns"),
1107 .getString("action.save_omit_hidden_columns"),
1108 JOptionPane.YES_NO_OPTION,
1109 JOptionPane.QUESTION_MESSAGE);
1111 if (reply == JOptionPane.YES_OPTION)
1113 omitHidden = viewport.getViewAsString(false);
1116 FormatAdapter f = new FormatAdapter();
1117 String output = f.formatSequences(format,
1118 viewport.getAlignment(), // class cast exceptions will
1119 // occur in the distant future
1120 omitHidden, f.getCacheSuffixDefault(format),
1121 viewport.getColumnSelection());
1131 java.io.PrintWriter out = new java.io.PrintWriter(
1132 new java.io.FileWriter(file));
1136 this.setTitle(file);
1137 statusBar.setText(MessageManager.formatMessage(
1138 "label.successfully_saved_to_file_in_format",
1140 { fileName, format }));
1141 } catch (Exception ex)
1144 ex.printStackTrace();
1151 JOptionPane.showInternalMessageDialog(this, MessageManager
1152 .formatMessage("label.couldnt_save_file", new String[]
1153 { fileName }), MessageManager
1154 .getString("label.error_saving_file"),
1155 JOptionPane.WARNING_MESSAGE);
1161 private void warningMessage(String warning, String title)
1163 if (new jalview.util.Platform().isHeadless())
1165 System.err.println("Warning: " + title + "\nWarning: " + warning);
1170 JOptionPane.showInternalMessageDialog(this, warning, title,
1171 JOptionPane.WARNING_MESSAGE);
1183 protected void outputText_actionPerformed(ActionEvent e)
1185 String[] omitHidden = null;
1187 if (viewport.hasHiddenColumns())
1189 int reply = JOptionPane
1190 .showInternalConfirmDialog(
1193 .getString("label.alignment_contains_hidden_columns"),
1195 .getString("action.save_omit_hidden_columns"),
1196 JOptionPane.YES_NO_OPTION,
1197 JOptionPane.QUESTION_MESSAGE);
1199 if (reply == JOptionPane.YES_OPTION)
1201 omitHidden = viewport.getViewAsString(false);
1205 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1206 cap.setForInput(null);
1210 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1211 viewport.getAlignment(), omitHidden,
1212 viewport.getColumnSelection()));
1213 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1214 "label.alignment_output_command", new String[]
1215 { e.getActionCommand() }), 600, 500);
1216 } catch (OutOfMemoryError oom)
1218 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1231 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1233 // new HTMLOutput(alignPanel,
1234 // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
1235 // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
1236 new HtmlSvgOutput(null, alignPanel);
1240 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1242 new BioJsHTMLOutput(alignPanel,
1243 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
1245 public void createImageMap(File file, String image)
1247 alignPanel.makePNGImageMap(file, image);
1257 public void createPNG(File f)
1259 alignPanel.makePNG(f);
1269 public void createEPS(File f)
1271 alignPanel.makeEPS(f);
1274 public void createSVG(File f)
1276 alignPanel.makeSVG(f);
1279 public void pageSetup_actionPerformed(ActionEvent e)
1281 PrinterJob printJob = PrinterJob.getPrinterJob();
1282 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1292 public void printMenuItem_actionPerformed(ActionEvent e)
1294 // Putting in a thread avoids Swing painting problems
1295 PrintThread thread = new PrintThread(alignPanel);
1300 public void exportFeatures_actionPerformed(ActionEvent e)
1302 new AnnotationExporter().exportFeatures(alignPanel);
1306 public void exportAnnotations_actionPerformed(ActionEvent e)
1308 new AnnotationExporter().exportAnnotations(alignPanel,
1309 viewport.isShowAnnotation() ? viewport.getAlignment()
1310 .getAlignmentAnnotation() : null, viewport
1311 .getAlignment().getGroups(), ((Alignment) viewport
1312 .getAlignment()).alignmentProperties);
1316 public void associatedData_actionPerformed(ActionEvent e)
1318 // Pick the tree file
1319 JalviewFileChooser chooser = new JalviewFileChooser(
1320 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1321 chooser.setFileView(new JalviewFileView());
1322 chooser.setDialogTitle(MessageManager
1323 .getString("label.load_jalview_annotations"));
1324 chooser.setToolTipText(MessageManager
1325 .getString("label.load_jalview_annotations"));
1327 int value = chooser.showOpenDialog(null);
1329 if (value == JalviewFileChooser.APPROVE_OPTION)
1331 String choice = chooser.getSelectedFile().getPath();
1332 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1333 loadJalviewDataFile(choice, null, null, null);
1339 * Close the current view or all views in the alignment frame. If the frame
1340 * only contains one view then the alignment will be removed from memory.
1342 * @param closeAllTabs
1345 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1347 if (alignPanels != null && alignPanels.size() < 2)
1349 closeAllTabs = true;
1354 if (alignPanels != null)
1358 if (this.isClosed())
1360 // really close all the windows - otherwise wait till
1361 // setClosed(true) is called
1362 for (int i = 0; i < alignPanels.size(); i++)
1364 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1371 closeView(alignPanel);
1377 this.setClosed(true);
1379 } catch (Exception ex)
1381 ex.printStackTrace();
1386 * close alignPanel2 and shuffle tabs appropriately.
1388 * @param alignPanel2
1390 public void closeView(AlignmentPanel alignPanel2)
1392 int index = tabbedPane.getSelectedIndex();
1393 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1394 alignPanels.removeElement(alignPanel2);
1396 // if (viewport == alignPanel2.av)
1400 alignPanel2.closePanel();
1403 tabbedPane.removeTabAt(closedindex);
1404 tabbedPane.validate();
1406 if (index > closedindex || index == tabbedPane.getTabCount())
1408 // modify currently selected tab index if necessary.
1412 this.tabSelectionChanged(index);
1418 void updateEditMenuBar()
1421 if (viewport.historyList.size() > 0)
1423 undoMenuItem.setEnabled(true);
1424 CommandI command = viewport.historyList.peek();
1425 undoMenuItem.setText(MessageManager.formatMessage(
1426 "label.undo_command", new String[]
1427 { command.getDescription() }));
1431 undoMenuItem.setEnabled(false);
1432 undoMenuItem.setText(MessageManager.getString("action.undo"));
1435 if (viewport.redoList.size() > 0)
1437 redoMenuItem.setEnabled(true);
1439 CommandI command = viewport.redoList.peek();
1440 redoMenuItem.setText(MessageManager.formatMessage(
1441 "label.redo_command", new String[]
1442 { command.getDescription() }));
1446 redoMenuItem.setEnabled(false);
1447 redoMenuItem.setText(MessageManager.getString("action.redo"));
1451 public void addHistoryItem(CommandI command)
1453 if (command.getSize() > 0)
1455 viewport.historyList.push(command);
1456 viewport.redoList.clear();
1457 updateEditMenuBar();
1458 viewport.updateHiddenColumns();
1459 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1460 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1461 // viewport.getColumnSelection()
1462 // .getHiddenColumns().size() > 0);
1468 * @return alignment objects for all views
1470 AlignmentI[] getViewAlignments()
1472 if (alignPanels != null)
1474 Enumeration e = alignPanels.elements();
1475 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1476 for (int i = 0; e.hasMoreElements(); i++)
1478 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1482 if (viewport != null)
1484 return new AlignmentI[]
1485 { viewport.getAlignment() };
1497 protected void undoMenuItem_actionPerformed(ActionEvent e)
1499 if (viewport.historyList.empty())
1503 CommandI command = viewport.historyList.pop();
1504 viewport.redoList.push(command);
1505 command.undoCommand(getViewAlignments());
1507 AlignViewport originalSource = getOriginatingSource(command);
1508 updateEditMenuBar();
1510 if (originalSource != null)
1512 if (originalSource != viewport)
1515 .warn("Implementation worry: mismatch of viewport origin for undo");
1517 originalSource.updateHiddenColumns();
1518 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1520 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1521 // viewport.getColumnSelection()
1522 // .getHiddenColumns().size() > 0);
1523 originalSource.firePropertyChange("alignment", null, originalSource
1524 .getAlignment().getSequences());
1535 protected void redoMenuItem_actionPerformed(ActionEvent e)
1537 if (viewport.redoList.size() < 1)
1542 CommandI command = viewport.redoList.pop();
1543 viewport.historyList.push(command);
1544 command.doCommand(getViewAlignments());
1546 AlignViewport originalSource = getOriginatingSource(command);
1547 updateEditMenuBar();
1549 if (originalSource != null)
1552 if (originalSource != viewport)
1555 .warn("Implementation worry: mismatch of viewport origin for redo");
1557 originalSource.updateHiddenColumns();
1558 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1560 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1561 // viewport.getColumnSelection()
1562 // .getHiddenColumns().size() > 0);
1563 originalSource.firePropertyChange("alignment", null, originalSource
1564 .getAlignment().getSequences());
1568 AlignViewport getOriginatingSource(CommandI command)
1570 AlignViewport originalSource = null;
1571 // For sequence removal and addition, we need to fire
1572 // the property change event FROM the viewport where the
1573 // original alignment was altered
1574 AlignmentI al = null;
1575 if (command instanceof EditCommand)
1577 EditCommand editCommand = (EditCommand) command;
1578 al = editCommand.getAlignment();
1579 Vector comps = (Vector) PaintRefresher.components.get(viewport
1580 .getSequenceSetId());
1582 for (int i = 0; i < comps.size(); i++)
1584 if (comps.elementAt(i) instanceof AlignmentPanel)
1586 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1588 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1595 if (originalSource == null)
1597 // The original view is closed, we must validate
1598 // the current view against the closed view first
1601 PaintRefresher.validateSequences(al, viewport.getAlignment());
1604 originalSource = viewport;
1607 return originalSource;
1616 public void moveSelectedSequences(boolean up)
1618 SequenceGroup sg = viewport.getSelectionGroup();
1624 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1625 viewport.getHiddenRepSequences(), up);
1626 alignPanel.paintAlignment(true);
1629 synchronized void slideSequences(boolean right, int size)
1631 List<SequenceI> sg = new Vector();
1632 if (viewport.cursorMode)
1634 sg.add(viewport.getAlignment().getSequenceAt(
1635 alignPanel.getSeqPanel().seqCanvas.cursorY));
1637 else if (viewport.getSelectionGroup() != null
1638 && viewport.getSelectionGroup().getSize() != viewport
1639 .getAlignment().getHeight())
1641 sg = viewport.getSelectionGroup().getSequences(
1642 viewport.getHiddenRepSequences());
1650 Vector invertGroup = new Vector();
1652 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1654 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1656 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1660 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1662 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1663 for (int i = 0; i < invertGroup.size(); i++)
1665 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1668 SlideSequencesCommand ssc;
1671 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1672 size, viewport.getGapCharacter());
1676 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1677 size, viewport.getGapCharacter());
1680 int groupAdjustment = 0;
1681 if (ssc.getGapsInsertedBegin() && right)
1683 if (viewport.cursorMode)
1685 alignPanel.getSeqPanel().moveCursor(size, 0);
1689 groupAdjustment = size;
1692 else if (!ssc.getGapsInsertedBegin() && !right)
1694 if (viewport.cursorMode)
1696 alignPanel.getSeqPanel().moveCursor(-size, 0);
1700 groupAdjustment = -size;
1704 if (groupAdjustment != 0)
1706 viewport.getSelectionGroup().setStartRes(
1707 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1708 viewport.getSelectionGroup().setEndRes(
1709 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1712 boolean appendHistoryItem = false;
1713 if (viewport.historyList != null && viewport.historyList.size() > 0
1714 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1716 appendHistoryItem = ssc
1717 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1721 if (!appendHistoryItem)
1723 addHistoryItem(ssc);
1736 protected void copy_actionPerformed(ActionEvent e)
1739 if (viewport.getSelectionGroup() == null)
1743 // TODO: preserve the ordering of displayed alignment annotation in any
1744 // internal paste (particularly sequence associated annotation)
1745 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1746 String[] omitHidden = null;
1748 if (viewport.hasHiddenColumns())
1750 omitHidden = viewport.getViewAsString(true);
1753 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1756 StringSelection ss = new StringSelection(output);
1760 jalview.gui.Desktop.internalCopy = true;
1761 // Its really worth setting the clipboard contents
1762 // to empty before setting the large StringSelection!!
1763 Toolkit.getDefaultToolkit().getSystemClipboard()
1764 .setContents(new StringSelection(""), null);
1766 Toolkit.getDefaultToolkit().getSystemClipboard()
1767 .setContents(ss, Desktop.instance);
1768 } catch (OutOfMemoryError er)
1770 new OOMWarning("copying region", er);
1774 Vector hiddenColumns = null;
1775 if (viewport.hasHiddenColumns())
1777 hiddenColumns = new Vector();
1778 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1779 .getSelectionGroup().getEndRes();
1780 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1783 int[] region = (int[]) viewport.getColumnSelection()
1784 .getHiddenColumns().elementAt(i);
1785 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1787 hiddenColumns.addElement(new int[]
1788 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1793 Desktop.jalviewClipboard = new Object[]
1794 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1795 statusBar.setText(MessageManager.formatMessage(
1796 "label.copied_sequences_to_clipboard", new String[]
1797 { Integer.valueOf(seqs.length).toString() }));
1807 protected void pasteNew_actionPerformed(ActionEvent e)
1819 protected void pasteThis_actionPerformed(ActionEvent e)
1825 * Paste contents of Jalview clipboard
1827 * @param newAlignment
1828 * true to paste to a new alignment, otherwise add to this.
1830 void paste(boolean newAlignment)
1832 boolean externalPaste = true;
1835 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1836 Transferable contents = c.getContents(this);
1838 if (contents == null)
1846 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1847 if (str.length() < 1)
1852 format = new IdentifyFile().Identify(str, "Paste");
1854 } catch (OutOfMemoryError er)
1856 new OOMWarning("Out of memory pasting sequences!!", er);
1860 SequenceI[] sequences;
1861 boolean annotationAdded = false;
1862 AlignmentI alignment = null;
1864 if (Desktop.jalviewClipboard != null)
1866 // The clipboard was filled from within Jalview, we must use the
1868 // And dataset from the copied alignment
1869 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1870 // be doubly sure that we create *new* sequence objects.
1871 sequences = new SequenceI[newseq.length];
1872 for (int i = 0; i < newseq.length; i++)
1874 sequences[i] = new Sequence(newseq[i]);
1876 alignment = new Alignment(sequences);
1877 externalPaste = false;
1881 // parse the clipboard as an alignment.
1882 alignment = new FormatAdapter().readFile(str, "Paste", format);
1883 sequences = alignment.getSequencesArray();
1887 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1893 if (Desktop.jalviewClipboard != null)
1895 // dataset is inherited
1896 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1900 // new dataset is constructed
1901 alignment.setDataset(null);
1903 alwidth = alignment.getWidth() + 1;
1907 AlignmentI pastedal = alignment; // preserve pasted alignment object
1908 // Add pasted sequences and dataset into existing alignment.
1909 alignment = viewport.getAlignment();
1910 alwidth = alignment.getWidth() + 1;
1911 // decide if we need to import sequences from an existing dataset
1912 boolean importDs = Desktop.jalviewClipboard != null
1913 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1914 // importDs==true instructs us to copy over new dataset sequences from
1915 // an existing alignment
1916 Vector newDs = (importDs) ? new Vector() : null; // used to create
1917 // minimum dataset set
1919 for (int i = 0; i < sequences.length; i++)
1923 newDs.addElement(null);
1925 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1927 if (importDs && ds != null)
1929 if (!newDs.contains(ds))
1931 newDs.setElementAt(ds, i);
1932 ds = new Sequence(ds);
1933 // update with new dataset sequence
1934 sequences[i].setDatasetSequence(ds);
1938 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1943 // copy and derive new dataset sequence
1944 sequences[i] = sequences[i].deriveSequence();
1945 alignment.getDataset().addSequence(
1946 sequences[i].getDatasetSequence());
1947 // TODO: avoid creation of duplicate dataset sequences with a
1948 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1950 alignment.addSequence(sequences[i]); // merges dataset
1954 newDs.clear(); // tidy up
1956 if (alignment.getAlignmentAnnotation() != null)
1958 for (AlignmentAnnotation alan : alignment
1959 .getAlignmentAnnotation())
1961 if (alan.graphGroup > fgroup)
1963 fgroup = alan.graphGroup;
1967 if (pastedal.getAlignmentAnnotation() != null)
1969 // Add any annotation attached to alignment.
1970 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1971 for (int i = 0; i < alann.length; i++)
1973 annotationAdded = true;
1974 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1976 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1977 if (newann.graphGroup > -1)
1979 if (newGraphGroups.size() <= newann.graphGroup
1980 || newGraphGroups.get(newann.graphGroup) == null)
1982 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1984 newGraphGroups.add(q, null);
1986 newGraphGroups.set(newann.graphGroup, new Integer(
1989 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1993 newann.padAnnotation(alwidth);
1994 alignment.addAnnotation(newann);
2004 addHistoryItem(new EditCommand(
2005 MessageManager.getString("label.add_sequences"),
2007 sequences, 0, alignment.getWidth(), alignment));
2009 // Add any annotations attached to sequences
2010 for (int i = 0; i < sequences.length; i++)
2012 if (sequences[i].getAnnotation() != null)
2014 AlignmentAnnotation newann;
2015 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2017 annotationAdded = true;
2018 newann = sequences[i].getAnnotation()[a];
2019 newann.adjustForAlignment();
2020 newann.padAnnotation(alwidth);
2021 if (newann.graphGroup > -1)
2023 if (newann.graphGroup > -1)
2025 if (newGraphGroups.size() <= newann.graphGroup
2026 || newGraphGroups.get(newann.graphGroup) == null)
2028 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2030 newGraphGroups.add(q, null);
2032 newGraphGroups.set(newann.graphGroup, new Integer(
2035 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2039 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2044 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2051 // propagate alignment changed.
2052 viewport.setEndSeq(alignment.getHeight());
2053 if (annotationAdded)
2055 // Duplicate sequence annotation in all views.
2056 AlignmentI[] alview = this.getViewAlignments();
2057 for (int i = 0; i < sequences.length; i++)
2059 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2064 for (int avnum = 0; avnum < alview.length; avnum++)
2066 if (alview[avnum] != alignment)
2068 // duplicate in a view other than the one with input focus
2069 int avwidth = alview[avnum].getWidth() + 1;
2070 // this relies on sann being preserved after we
2071 // modify the sequence's annotation array for each duplication
2072 for (int a = 0; a < sann.length; a++)
2074 AlignmentAnnotation newann = new AlignmentAnnotation(
2076 sequences[i].addAlignmentAnnotation(newann);
2077 newann.padAnnotation(avwidth);
2078 alview[avnum].addAnnotation(newann); // annotation was
2079 // duplicated earlier
2080 // TODO JAL-1145 graphGroups are not updated for sequence
2081 // annotation added to several views. This may cause
2083 alview[avnum].setAnnotationIndex(newann, a);
2088 buildSortByAnnotationScoresMenu();
2090 viewport.firePropertyChange("alignment", null,
2091 alignment.getSequences());
2092 if (alignPanels != null)
2094 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2096 ap.validateAnnotationDimensions(false);
2101 alignPanel.validateAnnotationDimensions(false);
2107 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2109 String newtitle = new String("Copied sequences");
2111 if (Desktop.jalviewClipboard != null
2112 && Desktop.jalviewClipboard[2] != null)
2114 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2115 for (int i = 0; i < hc.size(); i++)
2117 int[] region = (int[]) hc.elementAt(i);
2118 af.viewport.hideColumns(region[0], region[1]);
2122 // >>>This is a fix for the moment, until a better solution is
2124 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2126 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2128 // TODO: maintain provenance of an alignment, rather than just make the
2129 // title a concatenation of operations.
2132 if (title.startsWith("Copied sequences"))
2138 newtitle = newtitle.concat("- from " + title);
2143 newtitle = new String("Pasted sequences");
2146 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2151 } catch (Exception ex)
2153 ex.printStackTrace();
2154 System.out.println("Exception whilst pasting: " + ex);
2155 // could be anything being pasted in here
2161 protected void expand_newalign(ActionEvent e)
2165 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2166 .getAlignment(), -1);
2167 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2169 String newtitle = new String("Flanking alignment");
2171 if (Desktop.jalviewClipboard != null
2172 && Desktop.jalviewClipboard[2] != null)
2174 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2175 for (int i = 0; i < hc.size(); i++)
2177 int[] region = (int[]) hc.elementAt(i);
2178 af.viewport.hideColumns(region[0], region[1]);
2182 // >>>This is a fix for the moment, until a better solution is
2184 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2186 alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
2188 // TODO: maintain provenance of an alignment, rather than just make the
2189 // title a concatenation of operations.
2191 if (title.startsWith("Copied sequences"))
2197 newtitle = newtitle.concat("- from " + title);
2201 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2203 } catch (Exception ex)
2205 ex.printStackTrace();
2206 System.out.println("Exception whilst pasting: " + ex);
2207 // could be anything being pasted in here
2208 } catch (OutOfMemoryError oom)
2210 new OOMWarning("Viewing flanking region of alignment", oom);
2221 protected void cut_actionPerformed(ActionEvent e)
2223 copy_actionPerformed(null);
2224 delete_actionPerformed(null);
2234 protected void delete_actionPerformed(ActionEvent evt)
2237 SequenceGroup sg = viewport.getSelectionGroup();
2243 List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
2245 for (int i = 0; i < sg.getSize(); i++)
2247 seq = sg.getSequenceAt(i);
2251 // If the cut affects all sequences, warn, remove highlighted columns
2252 if (sg.getSize() == viewport.getAlignment().getHeight())
2254 int confirm = JOptionPane.showConfirmDialog(this,
2255 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2256 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2257 JOptionPane.OK_CANCEL_OPTION);
2259 if (confirm == JOptionPane.CANCEL_OPTION
2260 || confirm == JOptionPane.CLOSED_OPTION)
2264 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2265 sg.getEndRes() + 1);
2268 SequenceI[] cut = new SequenceI[seqs.size()];
2269 for (int i = 0; i < seqs.size(); i++)
2271 cut[i] = seqs.get(i);
2275 * //ADD HISTORY ITEM
2277 addHistoryItem(new EditCommand(
2278 MessageManager.getString("label.cut_sequences"), Action.CUT,
2279 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2280 viewport.getAlignment()));
2282 viewport.setSelectionGroup(null);
2283 viewport.sendSelection();
2284 viewport.getAlignment().deleteGroup(sg);
2286 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2288 if (viewport.getAlignment().getHeight() < 1)
2292 this.setClosed(true);
2293 } catch (Exception ex)
2306 protected void deleteGroups_actionPerformed(ActionEvent e)
2308 if (avc.deleteGroups())
2310 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2311 alignPanel.updateAnnotation();
2312 alignPanel.paintAlignment(true);
2323 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2325 SequenceGroup sg = new SequenceGroup();
2327 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2329 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2332 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2333 viewport.setSelectionGroup(sg);
2334 viewport.sendSelection();
2335 alignPanel.paintAlignment(true);
2336 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2346 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2348 if (viewport.cursorMode)
2350 alignPanel.getSeqPanel().keyboardNo1 = null;
2351 alignPanel.getSeqPanel().keyboardNo2 = null;
2353 viewport.setSelectionGroup(null);
2354 viewport.getColumnSelection().clear();
2355 viewport.setSelectionGroup(null);
2356 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2357 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2358 alignPanel.paintAlignment(true);
2359 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2360 viewport.sendSelection();
2370 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2372 SequenceGroup sg = viewport.getSelectionGroup();
2376 selectAllSequenceMenuItem_actionPerformed(null);
2381 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2383 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2386 alignPanel.paintAlignment(true);
2387 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2388 viewport.sendSelection();
2392 public void invertColSel_actionPerformed(ActionEvent e)
2394 viewport.invertColumnSelection();
2395 alignPanel.paintAlignment(true);
2396 viewport.sendSelection();
2406 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2408 trimAlignment(true);
2418 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2420 trimAlignment(false);
2423 void trimAlignment(boolean trimLeft)
2425 ColumnSelection colSel = viewport.getColumnSelection();
2428 if (colSel.size() > 0)
2432 column = colSel.getMin();
2436 column = colSel.getMax();
2440 if (viewport.getSelectionGroup() != null)
2442 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2443 viewport.getHiddenRepSequences());
2447 seqs = viewport.getAlignment().getSequencesArray();
2450 TrimRegionCommand trimRegion;
2453 trimRegion = new TrimRegionCommand("Remove Left",
2454 TrimRegionCommand.TRIM_LEFT, seqs, column,
2455 viewport.getAlignment(), viewport.getColumnSelection(),
2456 viewport.getSelectionGroup());
2457 viewport.setStartRes(0);
2461 trimRegion = new TrimRegionCommand("Remove Right",
2462 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2463 viewport.getAlignment(), viewport.getColumnSelection(),
2464 viewport.getSelectionGroup());
2467 statusBar.setText(MessageManager.formatMessage(
2468 "label.removed_columns", new String[]
2469 { Integer.valueOf(trimRegion.getSize()).toString() }));
2471 addHistoryItem(trimRegion);
2473 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2475 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2476 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2478 viewport.getAlignment().deleteGroup(sg);
2482 viewport.firePropertyChange("alignment", null, viewport
2483 .getAlignment().getSequences());
2494 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2496 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2499 if (viewport.getSelectionGroup() != null)
2501 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2502 viewport.getHiddenRepSequences());
2503 start = viewport.getSelectionGroup().getStartRes();
2504 end = viewport.getSelectionGroup().getEndRes();
2508 seqs = viewport.getAlignment().getSequencesArray();
2511 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2512 "Remove Gapped Columns", seqs, start, end,
2513 viewport.getAlignment());
2515 addHistoryItem(removeGapCols);
2517 statusBar.setText(MessageManager.formatMessage(
2518 "label.removed_empty_columns", new String[]
2519 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2521 // This is to maintain viewport position on first residue
2522 // of first sequence
2523 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2524 int startRes = seq.findPosition(viewport.startRes);
2525 // ShiftList shifts;
2526 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2527 // edit.alColumnChanges=shifts.getInverse();
2528 // if (viewport.hasHiddenColumns)
2529 // viewport.getColumnSelection().compensateForEdits(shifts);
2530 viewport.setStartRes(seq.findIndex(startRes) - 1);
2531 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2543 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2545 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2548 if (viewport.getSelectionGroup() != null)
2550 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2551 viewport.getHiddenRepSequences());
2552 start = viewport.getSelectionGroup().getStartRes();
2553 end = viewport.getSelectionGroup().getEndRes();
2557 seqs = viewport.getAlignment().getSequencesArray();
2560 // This is to maintain viewport position on first residue
2561 // of first sequence
2562 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2563 int startRes = seq.findPosition(viewport.startRes);
2565 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2566 viewport.getAlignment()));
2568 viewport.setStartRes(seq.findIndex(startRes) - 1);
2570 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2582 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2584 viewport.setPadGaps(padGapsMenuitem.isSelected());
2585 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2591 // if (justifySeqs>0)
2593 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2606 public void findMenuItem_actionPerformed(ActionEvent e)
2612 public void newView_actionPerformed(ActionEvent e)
2619 * @param copyAnnotation
2620 * if true then duplicate all annnotation, groups and settings
2621 * @return new alignment panel, already displayed.
2623 public AlignmentPanel newView(boolean copyAnnotation)
2625 return newView(null, copyAnnotation);
2631 * title of newly created view
2632 * @return new alignment panel, already displayed.
2634 public AlignmentPanel newView(String viewTitle)
2636 return newView(viewTitle, true);
2642 * title of newly created view
2643 * @param copyAnnotation
2644 * if true then duplicate all annnotation, groups and settings
2645 * @return new alignment panel, already displayed.
2647 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2649 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2651 if (!copyAnnotation)
2653 // just remove all the current annotation except for the automatic stuff
2654 newap.av.getAlignment().deleteAllGroups();
2655 for (AlignmentAnnotation alan : newap.av.getAlignment()
2656 .getAlignmentAnnotation())
2658 if (!alan.autoCalculated)
2660 newap.av.getAlignment().deleteAnnotation(alan);
2666 newap.av.gatherViewsHere = false;
2668 if (viewport.viewName == null)
2670 viewport.viewName = "Original";
2673 newap.av.historyList = viewport.historyList;
2674 newap.av.redoList = viewport.redoList;
2676 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2677 // make sure the new view has a unique name - this is essential for Jalview
2679 boolean addFirstIndex = false;
2680 if (viewTitle == null || viewTitle.trim().length() == 0)
2682 viewTitle = MessageManager.getString("action.view");
2683 addFirstIndex = true;
2687 index = 1;// we count from 1 if given a specific name
2689 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2690 Vector comps = (Vector) PaintRefresher.components.get(viewport
2691 .getSequenceSetId());
2692 Vector existingNames = new Vector();
2693 for (int i = 0; i < comps.size(); i++)
2695 if (comps.elementAt(i) instanceof AlignmentPanel)
2697 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2698 if (!existingNames.contains(ap.av.viewName))
2700 existingNames.addElement(ap.av.viewName);
2705 while (existingNames.contains(newViewName))
2707 newViewName = viewTitle + " " + (++index);
2710 newap.av.viewName = newViewName;
2712 addAlignmentPanel(newap, true);
2713 newap.alignmentChanged();
2715 if (alignPanels.size() == 2)
2717 viewport.gatherViewsHere = true;
2719 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2724 public void expandViews_actionPerformed(ActionEvent e)
2726 Desktop.instance.explodeViews(this);
2730 public void gatherViews_actionPerformed(ActionEvent e)
2732 Desktop.instance.gatherViews(this);
2742 public void font_actionPerformed(ActionEvent e)
2744 new FontChooser(alignPanel);
2754 protected void seqLimit_actionPerformed(ActionEvent e)
2756 viewport.setShowJVSuffix(seqLimits.isSelected());
2758 alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
2759 .calculateIdWidth());
2760 alignPanel.paintAlignment(true);
2764 public void idRightAlign_actionPerformed(ActionEvent e)
2766 viewport.setRightAlignIds(idRightAlign.isSelected());
2767 alignPanel.paintAlignment(true);
2771 public void centreColumnLabels_actionPerformed(ActionEvent e)
2773 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2774 alignPanel.paintAlignment(true);
2780 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2783 protected void followHighlight_actionPerformed()
2785 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2787 alignPanel.scrollToPosition(
2788 alignPanel.getSeqPanel().seqCanvas.searchResults, false);
2799 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2801 viewport.setColourText(colourTextMenuItem.isSelected());
2802 alignPanel.paintAlignment(true);
2812 public void wrapMenuItem_actionPerformed(ActionEvent e)
2814 scaleAbove.setVisible(wrapMenuItem.isSelected());
2815 scaleLeft.setVisible(wrapMenuItem.isSelected());
2816 scaleRight.setVisible(wrapMenuItem.isSelected());
2817 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2818 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2822 public void showAllSeqs_actionPerformed(ActionEvent e)
2824 viewport.showAllHiddenSeqs();
2828 public void showAllColumns_actionPerformed(ActionEvent e)
2830 viewport.showAllHiddenColumns();
2835 public void hideSelSequences_actionPerformed(ActionEvent e)
2837 viewport.hideAllSelectedSeqs();
2838 alignPanel.paintAlignment(true);
2842 * called by key handler and the hide all/show all menu items
2847 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2850 boolean hide = false;
2851 SequenceGroup sg = viewport.getSelectionGroup();
2852 if (!toggleSeqs && !toggleCols)
2854 // Hide everything by the current selection - this is a hack - we do the
2855 // invert and then hide
2856 // first check that there will be visible columns after the invert.
2857 if ((viewport.getColumnSelection() != null
2858 && viewport.getColumnSelection().getSelected() != null && viewport
2859 .getColumnSelection().getSelected().size() > 0)
2860 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2863 // now invert the sequence set, if required - empty selection implies
2864 // that no hiding is required.
2867 invertSequenceMenuItem_actionPerformed(null);
2868 sg = viewport.getSelectionGroup();
2872 viewport.expandColSelection(sg, true);
2873 // finally invert the column selection and get the new sequence
2875 invertColSel_actionPerformed(null);
2882 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2884 hideSelSequences_actionPerformed(null);
2887 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2890 showAllSeqs_actionPerformed(null);
2896 if (viewport.getColumnSelection().getSelected().size() > 0)
2898 hideSelColumns_actionPerformed(null);
2901 viewport.setSelectionGroup(sg);
2906 showAllColumns_actionPerformed(null);
2915 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2916 * event.ActionEvent)
2919 public void hideAllButSelection_actionPerformed(ActionEvent e)
2921 toggleHiddenRegions(false, false);
2928 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2932 public void hideAllSelection_actionPerformed(ActionEvent e)
2934 SequenceGroup sg = viewport.getSelectionGroup();
2935 viewport.expandColSelection(sg, false);
2936 viewport.hideAllSelectedSeqs();
2937 viewport.hideSelectedColumns();
2938 alignPanel.paintAlignment(true);
2945 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2949 public void showAllhidden_actionPerformed(ActionEvent e)
2951 viewport.showAllHiddenColumns();
2952 viewport.showAllHiddenSeqs();
2953 alignPanel.paintAlignment(true);
2957 public void hideSelColumns_actionPerformed(ActionEvent e)
2959 viewport.hideSelectedColumns();
2960 alignPanel.paintAlignment(true);
2964 public void hiddenMarkers_actionPerformed(ActionEvent e)
2966 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2977 protected void scaleAbove_actionPerformed(ActionEvent e)
2979 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2980 alignPanel.paintAlignment(true);
2990 protected void scaleLeft_actionPerformed(ActionEvent e)
2992 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2993 alignPanel.paintAlignment(true);
3003 protected void scaleRight_actionPerformed(ActionEvent e)
3005 viewport.setScaleRightWrapped(scaleRight.isSelected());
3006 alignPanel.paintAlignment(true);
3016 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3018 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3019 alignPanel.paintAlignment(true);
3029 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3031 viewport.setShowText(viewTextMenuItem.isSelected());
3032 alignPanel.paintAlignment(true);
3042 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3044 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3045 alignPanel.paintAlignment(true);
3048 public FeatureSettings featureSettings;
3051 public void featureSettings_actionPerformed(ActionEvent e)
3053 if (featureSettings != null)
3055 featureSettings.close();
3056 featureSettings = null;
3058 if (!showSeqFeatures.isSelected())
3060 // make sure features are actually displayed
3061 showSeqFeatures.setSelected(true);
3062 showSeqFeatures_actionPerformed(null);
3064 featureSettings = new FeatureSettings(this);
3068 * Set or clear 'Show Sequence Features'
3074 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3076 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3077 alignPanel.paintAlignment(true);
3078 if (alignPanel.getOverviewPanel() != null)
3080 alignPanel.getOverviewPanel().updateOverviewImage();
3085 * Set or clear 'Show Sequence Features'
3091 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3093 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3095 if (viewport.isShowSequenceFeaturesHeight())
3097 // ensure we're actually displaying features
3098 viewport.setShowSequenceFeatures(true);
3099 showSeqFeatures.setSelected(true);
3101 alignPanel.paintAlignment(true);
3102 if (alignPanel.getOverviewPanel() != null)
3104 alignPanel.getOverviewPanel().updateOverviewImage();
3109 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3110 * the annotations panel as a whole.
3112 * The options to show/hide all annotations should be enabled when the panel
3113 * is shown, and disabled when the panel is hidden.
3118 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3120 final boolean setVisible = annotationPanelMenuItem.isSelected();
3121 viewport.setShowAnnotation(setVisible);
3122 alignPanel.setAnnotationVisible(setVisible);
3123 this.showAllSeqAnnotations.setEnabled(setVisible);
3124 this.hideAllSeqAnnotations.setEnabled(setVisible);
3125 this.showAllAlAnnotations.setEnabled(setVisible);
3126 this.hideAllAlAnnotations.setEnabled(setVisible);
3130 public void alignmentProperties()
3132 JEditorPane editPane = new JEditorPane("text/html", "");
3133 editPane.setEditable(false);
3134 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3136 editPane.setText(MessageManager.formatMessage("label.html_content",
3138 { contents.toString() }));
3139 JInternalFrame frame = new JInternalFrame();
3140 frame.getContentPane().add(new JScrollPane(editPane));
3142 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3143 "label.alignment_properties", new String[]
3144 { getTitle() }), 500, 400);
3154 public void overviewMenuItem_actionPerformed(ActionEvent e)
3156 if (alignPanel.overviewPanel != null)
3161 JInternalFrame frame = new JInternalFrame();
3162 OverviewPanel overview = new OverviewPanel(alignPanel);
3163 frame.setContentPane(overview);
3164 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3165 "label.overview_params", new String[]
3166 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3168 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3169 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3172 public void internalFrameClosed(
3173 javax.swing.event.InternalFrameEvent evt)
3175 alignPanel.setOverviewPanel(null);
3179 alignPanel.setOverviewPanel(overview);
3183 public void textColour_actionPerformed(ActionEvent e)
3185 new TextColourChooser().chooseColour(alignPanel, null);
3195 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3207 public void clustalColour_actionPerformed(ActionEvent e)
3209 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3210 viewport.getHiddenRepSequences()));
3220 public void zappoColour_actionPerformed(ActionEvent e)
3222 changeColour(new ZappoColourScheme());
3232 public void taylorColour_actionPerformed(ActionEvent e)
3234 changeColour(new TaylorColourScheme());
3244 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3246 changeColour(new HydrophobicColourScheme());
3256 public void helixColour_actionPerformed(ActionEvent e)
3258 changeColour(new HelixColourScheme());
3268 public void strandColour_actionPerformed(ActionEvent e)
3270 changeColour(new StrandColourScheme());
3280 public void turnColour_actionPerformed(ActionEvent e)
3282 changeColour(new TurnColourScheme());
3292 public void buriedColour_actionPerformed(ActionEvent e)
3294 changeColour(new BuriedColourScheme());
3304 public void nucleotideColour_actionPerformed(ActionEvent e)
3306 changeColour(new NucleotideColourScheme());
3310 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3312 changeColour(new PurinePyrimidineColourScheme());
3316 * public void covariationColour_actionPerformed(ActionEvent e) {
3318 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3322 public void annotationColour_actionPerformed(ActionEvent e)
3324 new AnnotationColourChooser(viewport, alignPanel);
3328 public void annotationColumn_actionPerformed(ActionEvent e)
3330 new AnnotationColumnChooser(viewport, alignPanel);
3334 public void rnahelicesColour_actionPerformed(ActionEvent e)
3336 new RNAHelicesColourChooser(viewport, alignPanel);
3346 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3348 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3357 public void changeColour(ColourSchemeI cs)
3359 // TODO: compare with applet and pull up to model method
3364 if (viewport.getAbovePIDThreshold())
3366 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3368 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3372 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3375 if (viewport.getConservationSelected())
3378 Alignment al = (Alignment) viewport.getAlignment();
3379 Conservation c = new Conservation("All",
3380 ResidueProperties.propHash, 3, al.getSequences(), 0,
3384 c.verdict(false, viewport.getConsPercGaps());
3386 cs.setConservation(c);
3388 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3393 cs.setConservation(null);
3396 cs.setConsensus(viewport.getSequenceConsensusHash());
3399 viewport.setGlobalColourScheme(cs);
3401 if (viewport.getColourAppliesToAllGroups())
3404 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3412 if (cs instanceof ClustalxColourScheme)
3414 sg.cs = new ClustalxColourScheme(sg,
3415 viewport.getHiddenRepSequences());
3417 else if (cs instanceof UserColourScheme)
3419 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3425 sg.cs = cs.getClass().newInstance();
3426 } catch (Exception ex)
3431 if (viewport.getAbovePIDThreshold()
3432 || cs instanceof PIDColourScheme
3433 || cs instanceof Blosum62ColourScheme)
3435 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3437 sg.cs.setConsensus(AAFrequency.calculate(
3438 sg.getSequences(viewport.getHiddenRepSequences()),
3439 sg.getStartRes(), sg.getEndRes() + 1));
3443 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3446 if (viewport.getConservationSelected())
3448 Conservation c = new Conservation("Group",
3449 ResidueProperties.propHash, 3, sg.getSequences(viewport
3450 .getHiddenRepSequences()), sg.getStartRes(),
3451 sg.getEndRes() + 1);
3453 c.verdict(false, viewport.getConsPercGaps());
3454 sg.cs.setConservation(c);
3458 sg.cs.setConservation(null);
3463 if (alignPanel.getOverviewPanel() != null)
3465 alignPanel.getOverviewPanel().updateOverviewImage();
3468 alignPanel.paintAlignment(true);
3478 protected void modifyPID_actionPerformed(ActionEvent e)
3480 if (viewport.getAbovePIDThreshold()
3481 && viewport.getGlobalColourScheme() != null)
3483 SliderPanel.setPIDSliderSource(alignPanel,
3484 viewport.getGlobalColourScheme(), "Background");
3485 SliderPanel.showPIDSlider();
3496 protected void modifyConservation_actionPerformed(ActionEvent e)
3498 if (viewport.getConservationSelected()
3499 && viewport.getGlobalColourScheme() != null)
3501 SliderPanel.setConservationSlider(alignPanel,
3502 viewport.getGlobalColourScheme(), "Background");
3503 SliderPanel.showConservationSlider();
3514 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3516 viewport.setConservationSelected(conservationMenuItem.isSelected());
3518 viewport.setAbovePIDThreshold(false);
3519 abovePIDThreshold.setSelected(false);
3521 changeColour(viewport.getGlobalColourScheme());
3523 modifyConservation_actionPerformed(null);
3533 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3535 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3537 conservationMenuItem.setSelected(false);
3538 viewport.setConservationSelected(false);
3540 changeColour(viewport.getGlobalColourScheme());
3542 modifyPID_actionPerformed(null);
3552 public void userDefinedColour_actionPerformed(ActionEvent e)
3554 if (e.getActionCommand().equals(
3555 MessageManager.getString("action.user_defined")))
3557 new UserDefinedColours(alignPanel, null);
3561 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3562 .getUserColourSchemes().get(e.getActionCommand());
3568 public void updateUserColourMenu()
3571 Component[] menuItems = colourMenu.getMenuComponents();
3572 int i, iSize = menuItems.length;
3573 for (i = 0; i < iSize; i++)
3575 if (menuItems[i].getName() != null
3576 && menuItems[i].getName().equals("USER_DEFINED"))
3578 colourMenu.remove(menuItems[i]);
3582 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3584 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3585 .getUserColourSchemes().keys();
3587 while (userColours.hasMoreElements())
3589 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3590 userColours.nextElement().toString());
3591 radioItem.setName("USER_DEFINED");
3592 radioItem.addMouseListener(new MouseAdapter()
3595 public void mousePressed(MouseEvent evt)
3597 if (evt.isControlDown()
3598 || SwingUtilities.isRightMouseButton(evt))
3600 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3602 int option = JOptionPane.showInternalConfirmDialog(
3603 jalview.gui.Desktop.desktop,
3605 .getString("label.remove_from_default_list"),
3607 .getString("label.remove_user_defined_colour"),
3608 JOptionPane.YES_NO_OPTION);
3609 if (option == JOptionPane.YES_OPTION)
3611 jalview.gui.UserDefinedColours
3612 .removeColourFromDefaults(radioItem.getText());
3613 colourMenu.remove(radioItem);
3617 radioItem.addActionListener(new ActionListener()
3620 public void actionPerformed(ActionEvent evt)
3622 userDefinedColour_actionPerformed(evt);
3629 radioItem.addActionListener(new ActionListener()
3632 public void actionPerformed(ActionEvent evt)
3634 userDefinedColour_actionPerformed(evt);
3638 colourMenu.insert(radioItem, 15);
3639 colours.add(radioItem);
3651 public void PIDColour_actionPerformed(ActionEvent e)
3653 changeColour(new PIDColourScheme());
3663 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3665 changeColour(new Blosum62ColourScheme());
3675 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3677 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3678 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3679 .getAlignment().getSequenceAt(0), null);
3680 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3681 viewport.getAlignment()));
3682 alignPanel.paintAlignment(true);
3692 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3694 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3695 AlignmentSorter.sortByID(viewport.getAlignment());
3696 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3697 viewport.getAlignment()));
3698 alignPanel.paintAlignment(true);
3708 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3710 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3711 AlignmentSorter.sortByLength(viewport.getAlignment());
3712 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3713 viewport.getAlignment()));
3714 alignPanel.paintAlignment(true);
3724 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3726 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3727 AlignmentSorter.sortByGroup(viewport.getAlignment());
3728 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3729 viewport.getAlignment()));
3731 alignPanel.paintAlignment(true);
3741 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3743 new RedundancyPanel(alignPanel, this);
3753 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3755 if ((viewport.getSelectionGroup() == null)
3756 || (viewport.getSelectionGroup().getSize() < 2))
3758 JOptionPane.showInternalMessageDialog(this, MessageManager
3759 .getString("label.you_must_select_least_two_sequences"),
3760 MessageManager.getString("label.invalid_selection"),
3761 JOptionPane.WARNING_MESSAGE);
3765 JInternalFrame frame = new JInternalFrame();
3766 frame.setContentPane(new PairwiseAlignPanel(viewport));
3767 Desktop.addInternalFrame(frame,
3768 MessageManager.getString("action.pairwise_alignment"), 600,
3780 public void PCAMenuItem_actionPerformed(ActionEvent e)
3782 if (((viewport.getSelectionGroup() != null)
3783 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3784 .getSelectionGroup().getSize() > 0))
3785 || (viewport.getAlignment().getHeight() < 4))
3788 .showInternalMessageDialog(
3791 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3793 .getString("label.sequence_selection_insufficient"),
3794 JOptionPane.WARNING_MESSAGE);
3799 new PCAPanel(alignPanel);
3803 public void autoCalculate_actionPerformed(ActionEvent e)
3805 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3806 if (viewport.autoCalculateConsensus)
3808 viewport.firePropertyChange("alignment", null, viewport
3809 .getAlignment().getSequences());
3814 public void sortByTreeOption_actionPerformed(ActionEvent e)
3816 viewport.sortByTree = sortByTree.isSelected();
3820 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3822 viewport.followSelection = listenToViewSelections.isSelected();
3832 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3834 NewTreePanel("AV", "PID", "Average distance tree using PID");
3844 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3846 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3856 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3858 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3868 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3870 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3883 void NewTreePanel(String type, String pwType, String title)
3887 if (viewport.getSelectionGroup() != null
3888 && viewport.getSelectionGroup().getSize() > 0)
3890 if (viewport.getSelectionGroup().getSize() < 3)
3896 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3898 .getString("label.not_enough_sequences"),
3899 JOptionPane.WARNING_MESSAGE);
3903 SequenceGroup sg = viewport.getSelectionGroup();
3905 /* Decide if the selection is a column region */
3906 for (SequenceI _s : sg.getSequences())
3908 if (_s.getLength() < sg.getEndRes())
3914 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3916 .getString("label.sequences_selection_not_aligned"),
3917 JOptionPane.WARNING_MESSAGE);
3923 title = title + " on region";
3924 tp = new TreePanel(alignPanel, type, pwType);
3928 // are the visible sequences aligned?
3929 if (!viewport.getAlignment().isAligned(false))
3935 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3937 .getString("label.sequences_not_aligned"),
3938 JOptionPane.WARNING_MESSAGE);
3943 if (viewport.getAlignment().getHeight() < 2)
3948 tp = new TreePanel(alignPanel, type, pwType);
3953 if (viewport.viewName != null)
3955 title += viewport.viewName + " of ";
3958 title += this.title;
3960 Desktop.addInternalFrame(tp, title, 600, 500);
3971 public void addSortByOrderMenuItem(String title,
3972 final AlignmentOrder order)
3974 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
3976 item.addActionListener(new java.awt.event.ActionListener()
3979 public void actionPerformed(ActionEvent e)
3981 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3983 // TODO: JBPNote - have to map order entries to curent SequenceI
3985 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3987 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3990 alignPanel.paintAlignment(true);
3996 * Add a new sort by annotation score menu item
3999 * the menu to add the option to
4001 * the label used to retrieve scores for each sequence on the
4004 public void addSortByAnnotScoreMenuItem(JMenu sort,
4005 final String scoreLabel)
4007 final JMenuItem item = new JMenuItem(scoreLabel);
4009 item.addActionListener(new java.awt.event.ActionListener()
4012 public void actionPerformed(ActionEvent e)
4014 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4015 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4016 viewport.getAlignment());// ,viewport.getSelectionGroup());
4017 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4018 viewport.getAlignment()));
4019 alignPanel.paintAlignment(true);
4025 * last hash for alignment's annotation array - used to minimise cost of
4028 protected int _annotationScoreVectorHash;
4031 * search the alignment and rebuild the sort by annotation score submenu the
4032 * last alignment annotation vector hash is stored to minimize cost of
4033 * rebuilding in subsequence calls.
4037 public void buildSortByAnnotationScoresMenu()
4039 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4044 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4046 sortByAnnotScore.removeAll();
4047 // almost certainly a quicker way to do this - but we keep it simple
4048 Hashtable scoreSorts = new Hashtable();
4049 AlignmentAnnotation aann[];
4050 for (SequenceI sqa : viewport.getAlignment().getSequences())
4052 aann = sqa.getAnnotation();
4053 for (int i = 0; aann != null && i < aann.length; i++)
4055 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4057 scoreSorts.put(aann[i].label, aann[i].label);
4061 Enumeration labels = scoreSorts.keys();
4062 while (labels.hasMoreElements())
4064 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4065 (String) labels.nextElement());
4067 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4070 _annotationScoreVectorHash = viewport.getAlignment()
4071 .getAlignmentAnnotation().hashCode();
4076 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4077 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4078 * call. Listeners are added to remove the menu item when the treePanel is
4079 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4083 * Displayed tree window.
4085 * SortBy menu item title.
4088 public void buildTreeMenu()
4090 calculateTree.removeAll();
4091 // build the calculate menu
4093 for (final String type : new String[]
4096 String treecalcnm = MessageManager.getString("label.tree_calc_"
4097 + type.toLowerCase());
4098 for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4100 JMenuItem tm = new JMenuItem();
4101 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4102 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4104 String smn = MessageManager.getStringOrReturn(
4105 "label.score_model_", sm.getName());
4106 final String title = MessageManager.formatMessage(
4107 "label.treecalc_title", treecalcnm, smn);
4108 tm.setText(title);//
4109 tm.addActionListener(new java.awt.event.ActionListener()
4112 public void actionPerformed(ActionEvent e)
4114 NewTreePanel(type, (String) pwtype, title);
4117 calculateTree.add(tm);
4122 sortByTreeMenu.removeAll();
4124 Vector comps = (Vector) PaintRefresher.components.get(viewport
4125 .getSequenceSetId());
4126 Vector treePanels = new Vector();
4127 int i, iSize = comps.size();
4128 for (i = 0; i < iSize; i++)
4130 if (comps.elementAt(i) instanceof TreePanel)
4132 treePanels.add(comps.elementAt(i));
4136 iSize = treePanels.size();
4140 sortByTreeMenu.setVisible(false);
4144 sortByTreeMenu.setVisible(true);
4146 for (i = 0; i < treePanels.size(); i++)
4148 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4149 final JMenuItem item = new JMenuItem(tp.getTitle());
4150 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4151 item.addActionListener(new java.awt.event.ActionListener()
4154 public void actionPerformed(ActionEvent e)
4156 tp.sortByTree_actionPerformed(null);
4157 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4162 sortByTreeMenu.add(item);
4166 public boolean sortBy(AlignmentOrder alorder, String undoname)
4168 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4169 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4170 if (undoname != null)
4172 addHistoryItem(new OrderCommand(undoname, oldOrder,
4173 viewport.getAlignment()));
4175 alignPanel.paintAlignment(true);
4180 * Work out whether the whole set of sequences or just the selected set will
4181 * be submitted for multiple alignment.
4184 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4186 // Now, check we have enough sequences
4187 AlignmentView msa = null;
4189 if ((viewport.getSelectionGroup() != null)
4190 && (viewport.getSelectionGroup().getSize() > 1))
4192 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4193 // some common interface!
4195 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4196 * SequenceI[sz = seqs.getSize(false)];
4198 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4199 * seqs.getSequenceAt(i); }
4201 msa = viewport.getAlignmentView(true);
4203 else if (viewport.getSelectionGroup() != null
4204 && viewport.getSelectionGroup().getSize() == 1)
4206 int option = JOptionPane.showConfirmDialog(this,
4207 MessageManager.getString("warn.oneseq_msainput_selection"),
4208 MessageManager.getString("label.invalid_selection"),
4209 JOptionPane.OK_CANCEL_OPTION);
4210 if (option == JOptionPane.OK_OPTION)
4212 msa = viewport.getAlignmentView(false);
4217 msa = viewport.getAlignmentView(false);
4223 * Decides what is submitted to a secondary structure prediction service: the
4224 * first sequence in the alignment, or in the current selection, or, if the
4225 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4226 * region or the whole alignment. (where the first sequence in the set is the
4227 * one that the prediction will be for).
4229 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4231 AlignmentView seqs = null;
4233 if ((viewport.getSelectionGroup() != null)
4234 && (viewport.getSelectionGroup().getSize() > 0))
4236 seqs = viewport.getAlignmentView(true);
4240 seqs = viewport.getAlignmentView(false);
4242 // limit sequences - JBPNote in future - could spawn multiple prediction
4244 // TODO: viewport.getAlignment().isAligned is a global state - the local
4245 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4246 if (!viewport.getAlignment().isAligned(false))
4248 seqs.setSequences(new SeqCigar[]
4249 { seqs.getSequences()[0] });
4250 // TODO: if seqs.getSequences().length>1 then should really have warned
4264 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4266 // Pick the tree file
4267 JalviewFileChooser chooser = new JalviewFileChooser(
4268 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4269 chooser.setFileView(new JalviewFileView());
4270 chooser.setDialogTitle(MessageManager
4271 .getString("label.select_newick_like_tree_file"));
4272 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4274 int value = chooser.showOpenDialog(null);
4276 if (value == JalviewFileChooser.APPROVE_OPTION)
4278 String choice = chooser.getSelectedFile().getPath();
4279 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4280 jalview.io.NewickFile fin = null;
4283 fin = new jalview.io.NewickFile(choice, "File");
4284 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4285 } catch (Exception ex)
4292 .getString("label.problem_reading_tree_file"),
4293 JOptionPane.WARNING_MESSAGE);
4294 ex.printStackTrace();
4296 if (fin != null && fin.hasWarningMessage())
4298 JOptionPane.showMessageDialog(Desktop.desktop, fin
4299 .getWarningMessage(), MessageManager
4300 .getString("label.possible_problem_with_tree_file"),
4301 JOptionPane.WARNING_MESSAGE);
4307 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4309 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4312 public TreePanel ShowNewickTree(NewickFile nf, String title)
4314 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4317 public TreePanel ShowNewickTree(NewickFile nf, String title,
4318 AlignmentView input)
4320 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4323 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4324 int h, int x, int y)
4326 return ShowNewickTree(nf, title, null, w, h, x, y);
4330 * Add a treeviewer for the tree extracted from a newick file object to the
4331 * current alignment view
4338 * Associated alignment input data (or null)
4347 * @return TreePanel handle
4349 public TreePanel ShowNewickTree(NewickFile nf, String title,
4350 AlignmentView input, int w, int h, int x, int y)
4352 TreePanel tp = null;
4358 if (nf.getTree() != null)
4360 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4366 tp.setLocation(x, y);
4369 Desktop.addInternalFrame(tp, title, w, h);
4371 } catch (Exception ex)
4373 ex.printStackTrace();
4379 private boolean buildingMenu = false;
4382 * Generates menu items and listener event actions for web service clients
4385 public void BuildWebServiceMenu()
4387 while (buildingMenu)
4391 System.err.println("Waiting for building menu to finish.");
4393 } catch (Exception e)
4398 final AlignFrame me = this;
4399 buildingMenu = true;
4400 new Thread(new Runnable()
4405 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4408 System.err.println("Building ws menu again "
4409 + Thread.currentThread());
4410 // TODO: add support for context dependent disabling of services based
4412 // alignment and current selection
4413 // TODO: add additional serviceHandle parameter to specify abstract
4415 // class independently of AbstractName
4416 // TODO: add in rediscovery GUI function to restart discoverer
4417 // TODO: group services by location as well as function and/or
4419 // object broker mechanism.
4420 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4421 final IProgressIndicator af = me;
4422 final JMenu msawsmenu = new JMenu("Alignment");
4423 final JMenu secstrmenu = new JMenu(
4424 "Secondary Structure Prediction");
4425 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4426 final JMenu analymenu = new JMenu("Analysis");
4427 final JMenu dismenu = new JMenu("Protein Disorder");
4428 // final JMenu msawsmenu = new
4429 // JMenu(MessageManager.getString("label.alignment"));
4430 // final JMenu secstrmenu = new
4431 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4432 // final JMenu seqsrchmenu = new
4433 // JMenu(MessageManager.getString("label.sequence_database_search"));
4434 // final JMenu analymenu = new
4435 // JMenu(MessageManager.getString("label.analysis"));
4436 // final JMenu dismenu = new
4437 // JMenu(MessageManager.getString("label.protein_disorder"));
4438 // JAL-940 - only show secondary structure prediction services from
4439 // the legacy server
4440 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4442 Discoverer.services != null && (Discoverer.services.size() > 0))
4444 // TODO: refactor to allow list of AbstractName/Handler bindings to
4446 // stored or retrieved from elsewhere
4447 // No MSAWS used any more:
4448 // Vector msaws = null; // (Vector)
4449 // Discoverer.services.get("MsaWS");
4450 Vector secstrpr = (Vector) Discoverer.services
4452 if (secstrpr != null)
4454 // Add any secondary structure prediction services
4455 for (int i = 0, j = secstrpr.size(); i < j; i++)
4457 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4459 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4460 .getServiceClient(sh);
4461 int p = secstrmenu.getItemCount();
4462 impl.attachWSMenuEntry(secstrmenu, me);
4463 int q = secstrmenu.getItemCount();
4464 for (int litm = p; litm < q; litm++)
4466 legacyItems.add(secstrmenu.getItem(litm));
4472 // Add all submenus in the order they should appear on the web
4474 wsmenu.add(msawsmenu);
4475 wsmenu.add(secstrmenu);
4476 wsmenu.add(dismenu);
4477 wsmenu.add(analymenu);
4478 // No search services yet
4479 // wsmenu.add(seqsrchmenu);
4481 javax.swing.SwingUtilities.invokeLater(new Runnable()
4488 webService.removeAll();
4489 // first, add discovered services onto the webservices menu
4490 if (wsmenu.size() > 0)
4492 for (int i = 0, j = wsmenu.size(); i < j; i++)
4494 webService.add(wsmenu.get(i));
4499 webService.add(me.webServiceNoServices);
4501 // TODO: move into separate menu builder class.
4502 boolean new_sspred = false;
4503 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4505 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4506 if (jws2servs != null)
4508 if (jws2servs.hasServices())
4510 jws2servs.attachWSMenuEntry(webService, me);
4511 for (Jws2Instance sv : jws2servs.getServices())
4513 if (sv.description.toLowerCase().contains("jpred"))
4515 for (JMenuItem jmi : legacyItems)
4517 jmi.setVisible(false);
4523 if (jws2servs.isRunning())
4525 JMenuItem tm = new JMenuItem(
4526 "Still discovering JABA Services");
4527 tm.setEnabled(false);
4532 build_urlServiceMenu(me.webService);
4533 build_fetchdbmenu(webService);
4534 for (JMenu item : wsmenu)
4536 if (item.getItemCount() == 0)
4538 item.setEnabled(false);
4542 item.setEnabled(true);
4545 } catch (Exception e)
4548 .debug("Exception during web service menu building process.",
4554 } catch (Exception e)
4559 buildingMenu = false;
4566 * construct any groupURL type service menu entries.
4570 private void build_urlServiceMenu(JMenu webService)
4572 // TODO: remove this code when 2.7 is released
4573 // DEBUG - alignmentView
4575 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4576 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4578 * @Override public void actionPerformed(ActionEvent e) {
4579 * jalview.datamodel.AlignmentView
4580 * .testSelectionViews(af.viewport.getAlignment(),
4581 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4583 * }); webService.add(testAlView);
4585 // TODO: refactor to RestClient discoverer and merge menu entries for
4586 // rest-style services with other types of analysis/calculation service
4587 // SHmmr test client - still being implemented.
4588 // DEBUG - alignmentView
4590 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4593 client.attachWSMenuEntry(
4594 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4600 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4601 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4602 * getProperty("LAST_DIRECTORY"));
4604 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4605 * to Vamsas file"); chooser.setToolTipText("Export");
4607 * int value = chooser.showSaveDialog(this);
4609 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4610 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4611 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4612 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4615 * prototype of an automatically enabled/disabled analysis function
4618 protected void setShowProductsEnabled()
4620 SequenceI[] selection = viewport.getSequenceSelection();
4621 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4622 viewport.getAlignment().getDataset()))
4624 showProducts.setEnabled(true);
4629 showProducts.setEnabled(false);
4634 * search selection for sequence xRef products and build the show products
4639 * @return true if showProducts menu should be enabled.
4641 public boolean canShowProducts(SequenceI[] selection,
4642 boolean isRegionSelection, Alignment dataset)
4644 boolean showp = false;
4647 showProducts.removeAll();
4648 final boolean dna = viewport.getAlignment().isNucleotide();
4649 final Alignment ds = dataset;
4650 String[] ptypes = (selection == null || selection.length == 0) ? null
4651 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4653 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4654 // selection, dataset, true);
4655 final SequenceI[] sel = selection;
4656 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4659 final boolean isRegSel = isRegionSelection;
4660 final AlignFrame af = this;
4661 final String source = ptypes[t];
4662 JMenuItem xtype = new JMenuItem(ptypes[t]);
4663 xtype.addActionListener(new ActionListener()
4667 public void actionPerformed(ActionEvent e)
4669 // TODO: new thread for this call with vis-delay
4670 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4671 isRegSel, dna, source);
4675 showProducts.add(xtype);
4677 showProducts.setVisible(showp);
4678 showProducts.setEnabled(showp);
4679 } catch (Exception e)
4681 jalview.bin.Cache.log
4682 .warn("canTranslate threw an exception - please report to help@jalview.org",
4689 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4690 boolean isRegSel, boolean dna, String source)
4692 final boolean fisRegSel = isRegSel;
4693 final boolean fdna = dna;
4694 final String fsrc = source;
4695 final AlignFrame ths = this;
4696 final SequenceI[] fsel = sel;
4697 Runnable foo = new Runnable()
4703 final long sttime = System.currentTimeMillis();
4704 ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
4707 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4711 Alignment prods = CrossRef
4712 .findXrefSequences(fsel, fdna, fsrc, ds);
4715 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4716 for (int s = 0; s < sprods.length; s++)
4718 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4719 if (ds.getSequences() == null
4720 || !ds.getSequences().contains(
4721 sprods[s].getDatasetSequence()))
4723 ds.addSequence(sprods[s].getDatasetSequence());
4725 sprods[s].updatePDBIds();
4727 Alignment al = new Alignment(sprods);
4728 AlignedCodonFrame[] cf = prods.getCodonFrames();
4730 for (int s = 0; cf != null && s < cf.length; s++)
4732 al.addCodonFrame(cf[s]);
4735 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4737 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4738 + " for " + ((fisRegSel) ? "selected region of " : "")
4740 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4745 System.err.println("No Sequences generated for xRef type "
4748 } catch (Exception e)
4750 jalview.bin.Cache.log.error(
4751 "Exception when finding crossreferences", e);
4752 } catch (OutOfMemoryError e)
4754 new OOMWarning("whilst fetching crossreferences", e);
4757 jalview.bin.Cache.log.error("Error when finding crossreferences",
4760 ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
4765 Thread frunner = new Thread(foo);
4769 public boolean canShowTranslationProducts(SequenceI[] selection,
4770 AlignmentI alignment)
4775 return (jalview.analysis.Dna.canTranslate(selection,
4776 viewport.getViewAsVisibleContigs(true)));
4777 } catch (Exception e)
4779 jalview.bin.Cache.log
4780 .warn("canTranslate threw an exception - please report to help@jalview.org",
4787 public void showProducts_actionPerformed(ActionEvent e)
4789 // /////////////////////////////
4790 // Collect Data to be translated/transferred
4792 SequenceI[] selection = viewport.getSequenceSelection();
4793 AlignmentI al = null;
4796 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4797 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4798 viewport.getAlignment().getDataset());
4799 } catch (Exception ex)
4802 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4810 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4811 MessageManager.getString("label.translation_failed"),
4812 JOptionPane.WARNING_MESSAGE);
4816 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4817 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4818 "label.translation_of_params", new String[]
4819 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4824 public void showTranslation_actionPerformed(ActionEvent e)
4826 // /////////////////////////////
4827 // Collect Data to be translated/transferred
4829 SequenceI[] selection = viewport.getSequenceSelection();
4830 String[] seqstring = viewport.getViewAsString(true);
4831 AlignmentI al = null;
4834 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4835 viewport.getViewAsVisibleContigs(true), viewport
4836 .getGapCharacter(), viewport.getAlignment()
4837 .getAlignmentAnnotation(), viewport.getAlignment()
4838 .getWidth(), viewport.getAlignment().getDataset());
4839 } catch (Exception ex)
4842 jalview.bin.Cache.log.error(
4843 "Exception during translation. Please report this !", ex);
4848 .getString("label.error_when_translating_sequences_submit_bug_report"),
4850 .getString("label.implementation_error")
4852 .getString("translation_failed"),
4853 JOptionPane.ERROR_MESSAGE);
4862 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4863 MessageManager.getString("label.translation_failed"),
4864 JOptionPane.WARNING_MESSAGE);
4868 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4869 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4870 "label.translation_of_params", new String[]
4871 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4876 * Try to load a features file onto the alignment.
4879 * contents or path to retrieve file
4881 * access mode of file (see jalview.io.AlignFile)
4882 * @return true if features file was parsed corectly.
4884 public boolean parseFeaturesFile(String file, String type)
4886 boolean featuresFile = false;
4889 featuresFile = new FeaturesFile(file, type).parse(viewport
4890 .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
4891 .getFeatureRenderer().getFeatureColours(), false,
4892 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4893 } catch (Exception ex)
4895 ex.printStackTrace();
4900 viewport.setShowSequenceFeatures(true);
4901 showSeqFeatures.setSelected(true);
4902 if (alignPanel.getSeqPanel().seqCanvas.fr != null)
4904 // update the min/max ranges where necessary
4905 alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
4907 if (featureSettings != null)
4909 featureSettings.setTableData();
4911 alignPanel.paintAlignment(true);
4914 return featuresFile;
4918 public void dragEnter(DropTargetDragEvent evt)
4923 public void dragExit(DropTargetEvent evt)
4928 public void dragOver(DropTargetDragEvent evt)
4933 public void dropActionChanged(DropTargetDragEvent evt)
4938 public void drop(DropTargetDropEvent evt)
4940 Transferable t = evt.getTransferable();
4941 java.util.List files = null;
4945 DataFlavor uriListFlavor = new DataFlavor(
4946 "text/uri-list;class=java.lang.String");
4947 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4949 // Works on Windows and MacOSX
4950 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4951 files = (java.util.List) t
4952 .getTransferData(DataFlavor.javaFileListFlavor);
4954 else if (t.isDataFlavorSupported(uriListFlavor))
4956 // This is used by Unix drag system
4957 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4958 String data = (String) t.getTransferData(uriListFlavor);
4959 files = new java.util.ArrayList(1);
4960 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4961 data, "\r\n"); st.hasMoreTokens();)
4963 String s = st.nextToken();
4964 if (s.startsWith("#"))
4966 // the line is a comment (as per the RFC 2483)
4970 java.net.URI uri = new java.net.URI(s);
4971 // check to see if we can handle this kind of URI
4972 if (uri.getScheme().toLowerCase().startsWith("http"))
4974 files.add(uri.toString());
4978 // otherwise preserve old behaviour: catch all for file objects
4979 java.io.File file = new java.io.File(uri);
4980 files.add(file.toString());
4984 } catch (Exception e)
4986 e.printStackTrace();
4992 // check to see if any of these files have names matching sequences in
4994 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4995 .getAlignment().getSequencesArray());
4997 * Object[] { String,SequenceI}
4999 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5000 ArrayList<String> filesnotmatched = new ArrayList<String>();
5001 for (int i = 0; i < files.size(); i++)
5003 String file = files.get(i).toString();
5005 String protocol = FormatAdapter.checkProtocol(file);
5006 if (protocol == jalview.io.FormatAdapter.FILE)
5008 File fl = new File(file);
5009 pdbfn = fl.getName();
5011 else if (protocol == jalview.io.FormatAdapter.URL)
5013 URL url = new URL(file);
5014 pdbfn = url.getFile();
5016 if (pdbfn.length() > 0)
5018 // attempt to find a match in the alignment
5019 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5020 int l = 0, c = pdbfn.indexOf(".");
5021 while (mtch == null && c != -1)
5026 } while ((c = pdbfn.indexOf(".", l)) > l);
5029 pdbfn = pdbfn.substring(0, l);
5031 mtch = idm.findAllIdMatches(pdbfn);
5038 type = new IdentifyFile().Identify(file, protocol);
5039 } catch (Exception ex)
5045 if (type.equalsIgnoreCase("PDB"))
5047 filesmatched.add(new Object[]
5048 { file, protocol, mtch });
5053 // File wasn't named like one of the sequences or wasn't a PDB file.
5054 filesnotmatched.add(file);
5058 if (filesmatched.size() > 0)
5060 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5066 "label.automatically_associate_pdb_files_with_sequences_same_name",
5073 .getString("label.automatically_associate_pdb_files_by_name"),
5074 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5077 for (Object[] fm : filesmatched)
5079 // try and associate
5080 // TODO: may want to set a standard ID naming formalism for
5081 // associating PDB files which have no IDs.
5082 for (SequenceI toassoc : (SequenceI[]) fm[2])
5084 PDBEntry pe = new AssociatePdbFileWithSeq()
5085 .associatePdbWithSeq((String) fm[0],
5086 (String) fm[1], toassoc, false,
5090 System.err.println("Associated file : "
5091 + ((String) fm[0]) + " with "
5092 + toassoc.getDisplayId(true));
5096 alignPanel.paintAlignment(true);
5100 if (filesnotmatched.size() > 0)
5103 && (Cache.getDefault(
5104 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5107 "<html>"+MessageManager
5109 "label.ignore_unmatched_dropped_files_info",
5114 .toString() })+"</html>",
5116 .getString("label.ignore_unmatched_dropped_files"),
5117 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5121 for (String fn : filesnotmatched)
5123 loadJalviewDataFile(fn, null, null, null);
5127 } catch (Exception ex)
5129 ex.printStackTrace();
5135 * Attempt to load a "dropped" file or URL string: First by testing whether
5136 * it's and Annotation file, then a JNet file, and finally a features file. If
5137 * all are false then the user may have dropped an alignment file onto this
5141 * either a filename or a URL string.
5143 public void loadJalviewDataFile(String file, String protocol,
5144 String format, SequenceI assocSeq)
5148 if (protocol == null)
5150 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5152 // if the file isn't identified, or not positively identified as some
5153 // other filetype (PFAM is default unidentified alignment file type) then
5154 // try to parse as annotation.
5155 boolean isAnnotation = (format == null || format
5156 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5157 .readAnnotationFile(viewport.getAlignment(), file, protocol)
5162 // first see if its a T-COFFEE score file
5163 TCoffeeScoreFile tcf = null;
5166 tcf = new TCoffeeScoreFile(file, protocol);
5169 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5171 tcoffeeColour.setEnabled(true);
5172 tcoffeeColour.setSelected(true);
5173 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5174 isAnnotation = true;
5176 .setText(MessageManager
5177 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5181 // some problem - if no warning its probable that the ID matching
5182 // process didn't work
5186 tcf.getWarningMessage() == null ? MessageManager
5187 .getString("label.check_file_matches_sequence_ids_alignment")
5188 : tcf.getWarningMessage(),
5190 .getString("label.problem_reading_tcoffee_score_file"),
5191 JOptionPane.WARNING_MESSAGE);
5198 } catch (Exception x)
5201 .debug("Exception when processing data source as T-COFFEE score file",
5207 // try to see if its a JNet 'concise' style annotation file *before*
5209 // try to parse it as a features file
5212 format = new IdentifyFile().Identify(file, protocol);
5214 if (format.equalsIgnoreCase("JnetFile"))
5216 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5218 new JnetAnnotationMaker().add_annotation(predictions,
5219 viewport.getAlignment(), 0, false);
5220 isAnnotation = true;
5225 * if (format.equalsIgnoreCase("PDB")) {
5227 * String pdbfn = ""; // try to match up filename with sequence id
5228 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5229 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5230 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5231 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5232 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5233 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5234 * // attempt to find a match in the alignment SequenceI mtch =
5235 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5236 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5237 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5238 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5239 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5240 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5241 * { System.err.println("Associated file : " + file + " with " +
5242 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5243 * TODO: maybe need to load as normal otherwise return; } }
5245 // try to parse it as a features file
5246 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5247 // if it wasn't a features file then we just treat it as a general
5248 // alignment file to load into the current view.
5251 new FileLoader().LoadFile(viewport, file, protocol, format);
5255 alignPanel.paintAlignment(true);
5263 alignPanel.adjustAnnotationHeight();
5264 viewport.updateSequenceIdColours();
5265 buildSortByAnnotationScoresMenu();
5266 alignPanel.paintAlignment(true);
5268 } catch (Exception ex)
5270 ex.printStackTrace();
5271 } catch (OutOfMemoryError oom)
5276 } catch (Exception x)
5282 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5283 : "using " + protocol + " from " + file)
5285 + (format != null ? "(parsing as '" + format
5286 + "' file)" : ""), oom, Desktop.desktop);
5291 public void tabSelectionChanged(int index)
5295 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5296 viewport = alignPanel.av;
5297 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5298 setMenusFromViewport(viewport);
5303 public void tabbedPane_mousePressed(MouseEvent e)
5305 if (SwingUtilities.isRightMouseButton(e))
5307 String reply = JOptionPane.showInternalInputDialog(this,
5308 MessageManager.getString("label.enter_view_name"),
5309 MessageManager.getString("label.enter_view_name"),
5310 JOptionPane.QUESTION_MESSAGE);
5314 viewport.viewName = reply;
5315 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5320 public AlignViewport getCurrentView()
5326 * Open the dialog for regex description parsing.
5329 protected void extractScores_actionPerformed(ActionEvent e)
5331 ParseProperties pp = new jalview.analysis.ParseProperties(
5332 viewport.getAlignment());
5333 // TODO: verify regex and introduce GUI dialog for version 2.5
5334 // if (pp.getScoresFromDescription("col", "score column ",
5335 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5337 if (pp.getScoresFromDescription("description column",
5338 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5340 buildSortByAnnotationScoresMenu();
5348 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5352 protected void showDbRefs_actionPerformed(ActionEvent e)
5354 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5360 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5364 protected void showNpFeats_actionPerformed(ActionEvent e)
5366 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5370 * find the viewport amongst the tabs in this alignment frame and close that
5375 public boolean closeView(AlignViewport av)
5379 this.closeMenuItem_actionPerformed(false);
5382 Component[] comp = tabbedPane.getComponents();
5383 for (int i = 0; comp != null && i < comp.length; i++)
5385 if (comp[i] instanceof AlignmentPanel)
5387 if (((AlignmentPanel) comp[i]).av == av)
5390 closeView((AlignmentPanel) comp[i]);
5398 protected void build_fetchdbmenu(JMenu webService)
5400 // Temporary hack - DBRef Fetcher always top level ws entry.
5401 // TODO We probably want to store a sequence database checklist in
5402 // preferences and have checkboxes.. rather than individual sources selected
5404 final JMenu rfetch = new JMenu(
5405 MessageManager.getString("action.fetch_db_references"));
5406 rfetch.setToolTipText(MessageManager
5407 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5408 webService.add(rfetch);
5410 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5411 MessageManager.getString("option.trim_retrieved_seqs"));
5412 trimrs.setToolTipText(MessageManager
5413 .getString("label.trim_retrieved_sequences"));
5414 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5415 trimrs.addActionListener(new ActionListener()
5418 public void actionPerformed(ActionEvent e)
5420 trimrs.setSelected(trimrs.isSelected());
5421 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5422 Boolean.valueOf(trimrs.isSelected()).toString());
5426 JMenuItem fetchr = new JMenuItem(
5427 MessageManager.getString("label.standard_databases"));
5428 fetchr.setToolTipText(MessageManager
5429 .getString("label.fetch_embl_uniprot"));
5430 fetchr.addActionListener(new ActionListener()
5434 public void actionPerformed(ActionEvent e)
5436 new Thread(new Runnable()
5442 new jalview.ws.DBRefFetcher(alignPanel.av
5443 .getSequenceSelection(), alignPanel.alignFrame)
5444 .fetchDBRefs(false);
5452 final AlignFrame me = this;
5453 new Thread(new Runnable()
5458 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5459 .getSequenceFetcherSingleton(me);
5460 javax.swing.SwingUtilities.invokeLater(new Runnable()
5465 String[] dbclasses = sf.getOrderedSupportedSources();
5466 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5467 // jalview.util.QuickSort.sort(otherdb, otherdb);
5468 List<DbSourceProxy> otherdb;
5469 JMenu dfetch = new JMenu();
5470 JMenu ifetch = new JMenu();
5471 JMenuItem fetchr = null;
5472 int comp = 0, icomp = 0, mcomp = 15;
5473 String mname = null;
5475 for (String dbclass : dbclasses)
5477 otherdb = sf.getSourceProxy(dbclass);
5478 // add a single entry for this class, or submenu allowing 'fetch
5480 if (otherdb == null || otherdb.size() < 1)
5484 // List<DbSourceProxy> dbs=otherdb;
5485 // otherdb=new ArrayList<DbSourceProxy>();
5486 // for (DbSourceProxy db:dbs)
5488 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5492 mname = "From " + dbclass;
5494 if (otherdb.size() == 1)
5496 final DbSourceProxy[] dassource = otherdb
5497 .toArray(new DbSourceProxy[0]);
5498 DbSourceProxy src = otherdb.get(0);
5499 fetchr = new JMenuItem(src.getDbSource());
5500 fetchr.addActionListener(new ActionListener()
5504 public void actionPerformed(ActionEvent e)
5506 new Thread(new Runnable()
5512 new jalview.ws.DBRefFetcher(alignPanel.av
5513 .getSequenceSelection(),
5514 alignPanel.alignFrame, dassource)
5515 .fetchDBRefs(false);
5521 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
5527 final DbSourceProxy[] dassource = otherdb
5528 .toArray(new DbSourceProxy[0]);
5530 DbSourceProxy src = otherdb.get(0);
5531 fetchr = new JMenuItem(MessageManager.formatMessage(
5532 "label.fetch_all_param", new String[]
5533 { src.getDbSource() }));
5534 fetchr.addActionListener(new ActionListener()
5537 public void actionPerformed(ActionEvent e)
5539 new Thread(new Runnable()
5545 new jalview.ws.DBRefFetcher(alignPanel.av
5546 .getSequenceSelection(),
5547 alignPanel.alignFrame, dassource)
5548 .fetchDBRefs(false);
5554 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5557 // and then build the rest of the individual menus
5558 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
5560 String imname = null;
5562 for (DbSourceProxy sproxy : otherdb)
5564 String dbname = sproxy.getDbName();
5565 String sname = dbname.length() > 5 ? dbname.substring(0,
5566 5) + "..." : dbname;
5567 String msname = dbname.length() > 10 ? dbname.substring(
5568 0, 10) + "..." : dbname;
5571 imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
5573 fetchr = new JMenuItem(msname);
5574 final DbSourceProxy[] dassrc =
5576 fetchr.addActionListener(new ActionListener()
5580 public void actionPerformed(ActionEvent e)
5582 new Thread(new Runnable()
5588 new jalview.ws.DBRefFetcher(alignPanel.av
5589 .getSequenceSelection(),
5590 alignPanel.alignFrame, dassrc)
5591 .fetchDBRefs(false);
5597 fetchr.setToolTipText("<html>"
5598 + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
5601 if (++icomp >= mcomp || i == (otherdb.size()))
5603 ifetch.setText(MessageManager.formatMessage(
5604 "label.source_to_target", imname, sname));
5606 ifetch = new JMenu();
5614 if (comp >= mcomp || dbi >= (dbclasses.length))
5616 dfetch.setText(MessageManager.formatMessage(
5617 "label.source_to_target", mname, dbclass));
5619 dfetch = new JMenu();
5632 * Left justify the whole alignment.
5635 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5637 AlignmentI al = viewport.getAlignment();
5639 viewport.firePropertyChange("alignment", null, al);
5643 * Right justify the whole alignment.
5646 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5648 AlignmentI al = viewport.getAlignment();
5650 viewport.firePropertyChange("alignment", null, al);
5653 public void setShowSeqFeatures(boolean b)
5655 showSeqFeatures.setSelected(true);
5656 viewport.setShowSequenceFeatures(true);
5663 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5664 * awt.event.ActionEvent)
5667 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5669 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5670 alignPanel.paintAlignment(true);
5677 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5681 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5683 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5684 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5692 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5693 * .event.ActionEvent)
5696 protected void showGroupConservation_actionPerformed(ActionEvent e)
5698 viewport.setShowGroupConservation(showGroupConservation.getState());
5699 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5706 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5707 * .event.ActionEvent)
5710 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5712 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5713 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5720 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5721 * .event.ActionEvent)
5724 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5726 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5727 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5731 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5733 showSequenceLogo.setState(true);
5734 viewport.setShowSequenceLogo(true);
5735 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5736 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5740 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5742 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5749 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5750 * .event.ActionEvent)
5753 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5755 if (avc.makeGroupsFromSelection())
5757 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5758 alignPanel.updateAnnotation();
5759 alignPanel.paintAlignment(true);
5764 protected void createGroup_actionPerformed(ActionEvent e)
5766 if (avc.createGroup())
5768 alignPanel.alignmentChanged();
5773 protected void unGroup_actionPerformed(ActionEvent e)
5777 alignPanel.alignmentChanged();
5782 * make the given alignmentPanel the currently selected tab
5784 * @param alignmentPanel
5786 public void setDisplayedView(AlignmentPanel alignmentPanel)
5788 if (!viewport.getSequenceSetId().equals(
5789 alignmentPanel.av.getSequenceSetId()))
5791 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5793 if (tabbedPane != null
5794 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5795 .getSelectedIndex())
5797 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5802 * Action on selection of menu options to Show or Hide annotations.
5805 * @param forSequences
5806 * update sequence-related annotations
5807 * @param forAlignment
5808 * update non-sequence-related annotations
5811 protected void setAnnotationsVisibility(boolean visible,
5812 boolean forSequences, boolean forAlignment)
5814 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5815 .getAlignmentAnnotation())
5817 boolean apply = (aa.sequenceRef == null && forAlignment)
5818 || (aa.sequenceRef != null && forSequences);
5821 aa.visible = visible;
5824 alignPanel.validateAnnotationDimensions(false);
5825 alignPanel.alignmentChanged();
5829 * Store selected annotation sort order for the view and repaint.
5832 protected void sortAnnotations_actionPerformed()
5834 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5836 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5837 alignPanel.paintAlignment(true);
5842 * @return alignment panels in this alignemnt frame
5844 public List<AlignmentViewPanel> getAlignPanels()
5846 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5850 class PrintThread extends Thread
5854 public PrintThread(AlignmentPanel ap)
5859 static PageFormat pf;
5864 PrinterJob printJob = PrinterJob.getPrinterJob();
5868 printJob.setPrintable(ap, pf);
5872 printJob.setPrintable(ap);
5875 if (printJob.printDialog())
5880 } catch (Exception PrintException)
5882 PrintException.printStackTrace();