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.analysis.ScoreModelI;
34 import jalview.bin.Cache;
35 import jalview.commands.CommandI;
36 import jalview.commands.EditCommand;
37 import jalview.commands.EditCommand.Action;
38 import jalview.commands.OrderCommand;
39 import jalview.commands.RemoveGapColCommand;
40 import jalview.commands.RemoveGapsCommand;
41 import jalview.commands.SlideSequencesCommand;
42 import jalview.commands.TrimRegionCommand;
43 import jalview.datamodel.AlignedCodonFrame;
44 import jalview.datamodel.Alignment;
45 import jalview.datamodel.AlignmentAnnotation;
46 import jalview.datamodel.AlignmentI;
47 import jalview.datamodel.AlignmentOrder;
48 import jalview.datamodel.AlignmentView;
49 import jalview.datamodel.ColumnSelection;
50 import jalview.datamodel.PDBEntry;
51 import jalview.datamodel.SeqCigar;
52 import jalview.datamodel.Sequence;
53 import jalview.datamodel.SequenceGroup;
54 import jalview.datamodel.SequenceI;
55 import jalview.io.AlignmentProperties;
56 import jalview.io.AnnotationFile;
57 import jalview.io.BioJsHTMLOutput;
58 import jalview.io.FeaturesFile;
59 import jalview.io.FileLoader;
60 import jalview.io.FormatAdapter;
61 import jalview.io.HTMLOutput;
62 import jalview.io.IdentifyFile;
63 import jalview.io.JalviewFileChooser;
64 import jalview.io.JalviewFileView;
65 import jalview.io.JnetAnnotationMaker;
66 import jalview.io.NewickFile;
67 import jalview.io.TCoffeeScoreFile;
68 import jalview.jbgui.GAlignFrame;
69 import jalview.schemes.Blosum62ColourScheme;
70 import jalview.schemes.BuriedColourScheme;
71 import jalview.schemes.ClustalxColourScheme;
72 import jalview.schemes.ColourSchemeI;
73 import jalview.schemes.ColourSchemeProperty;
74 import jalview.schemes.HelixColourScheme;
75 import jalview.schemes.HydrophobicColourScheme;
76 import jalview.schemes.NucleotideColourScheme;
77 import jalview.schemes.PIDColourScheme;
78 import jalview.schemes.PurinePyrimidineColourScheme;
79 import jalview.schemes.RNAHelicesColourChooser;
80 import jalview.schemes.ResidueProperties;
81 import jalview.schemes.StrandColourScheme;
82 import jalview.schemes.TCoffeeColourScheme;
83 import jalview.schemes.TaylorColourScheme;
84 import jalview.schemes.TurnColourScheme;
85 import jalview.schemes.UserColourScheme;
86 import jalview.schemes.ZappoColourScheme;
87 import jalview.util.MessageManager;
88 import jalview.ws.jws1.Discoverer;
89 import jalview.ws.jws2.Jws2Discoverer;
90 import jalview.ws.jws2.jabaws2.Jws2Instance;
91 import jalview.ws.seqfetcher.DbSourceProxy;
93 import java.awt.BorderLayout;
94 import java.awt.Component;
95 import java.awt.GridLayout;
96 import java.awt.Rectangle;
97 import java.awt.Toolkit;
98 import java.awt.datatransfer.Clipboard;
99 import java.awt.datatransfer.DataFlavor;
100 import java.awt.datatransfer.StringSelection;
101 import java.awt.datatransfer.Transferable;
102 import java.awt.dnd.DnDConstants;
103 import java.awt.dnd.DropTargetDragEvent;
104 import java.awt.dnd.DropTargetDropEvent;
105 import java.awt.dnd.DropTargetEvent;
106 import java.awt.dnd.DropTargetListener;
107 import java.awt.event.ActionEvent;
108 import java.awt.event.ActionListener;
109 import java.awt.event.KeyAdapter;
110 import java.awt.event.KeyEvent;
111 import java.awt.event.MouseAdapter;
112 import java.awt.event.MouseEvent;
113 import java.awt.print.PageFormat;
114 import java.awt.print.PrinterJob;
115 import java.beans.PropertyChangeEvent;
118 import java.util.ArrayList;
119 import java.util.Enumeration;
120 import java.util.Hashtable;
121 import java.util.List;
122 import java.util.Vector;
124 import javax.swing.JButton;
125 import javax.swing.JCheckBoxMenuItem;
126 import javax.swing.JEditorPane;
127 import javax.swing.JInternalFrame;
128 import javax.swing.JLabel;
129 import javax.swing.JLayeredPane;
130 import javax.swing.JMenu;
131 import javax.swing.JMenuItem;
132 import javax.swing.JOptionPane;
133 import javax.swing.JPanel;
134 import javax.swing.JProgressBar;
135 import javax.swing.JRadioButtonMenuItem;
136 import javax.swing.JScrollPane;
137 import javax.swing.SwingUtilities;
143 * @version $Revision$
145 public class AlignFrame extends GAlignFrame implements DropTargetListener,
146 IProgressIndicator, AlignViewControllerGuiI
150 public static final int DEFAULT_WIDTH = 700;
153 public static final int DEFAULT_HEIGHT = 500;
155 public AlignmentPanel alignPanel;
157 AlignViewport viewport;
159 public AlignViewControllerI avc;
161 Vector alignPanels = new Vector();
164 * Last format used to load or save alignments in this window
166 String currentFileFormat = null;
169 * Current filename for this alignment
171 String fileName = null;
174 * Creates a new AlignFrame object with specific width and height.
180 public AlignFrame(AlignmentI al, int width, int height)
182 this(al, null, width, height);
186 * Creates a new AlignFrame object with specific width, height and
192 * @param sequenceSetId
194 public AlignFrame(AlignmentI al, int width, int height,
195 String sequenceSetId)
197 this(al, null, width, height, sequenceSetId);
201 * Creates a new AlignFrame object with specific width, height and
207 * @param sequenceSetId
210 public AlignFrame(AlignmentI al, int width, int height,
211 String sequenceSetId, String viewId)
213 this(al, null, width, height, sequenceSetId, viewId);
217 * new alignment window with hidden columns
221 * @param hiddenColumns
222 * ColumnSelection or null
224 * Width of alignment frame
228 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
229 int width, int height)
231 this(al, hiddenColumns, width, height, null);
235 * Create alignment frame for al with hiddenColumns, a specific width and
236 * height, and specific sequenceId
239 * @param hiddenColumns
242 * @param sequenceSetId
245 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
246 int width, int height, String sequenceSetId)
248 this(al, hiddenColumns, width, height, sequenceSetId, null);
252 * Create alignment frame for al with hiddenColumns, a specific width and
253 * height, and specific sequenceId
256 * @param hiddenColumns
259 * @param sequenceSetId
264 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
265 int width, int height, String sequenceSetId, String viewId)
267 setSize(width, height);
269 if (al.getDataset() == null)
274 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
276 alignPanel = new AlignmentPanel(this, viewport);
279 addAlignmentPanel(alignPanel, true);
284 * Make a new AlignFrame from existing alignmentPanels
291 public AlignFrame(AlignmentPanel ap)
295 addAlignmentPanel(ap, false);
300 * initalise the alignframe from the underlying viewport data and the
305 avc = new jalview.controller.AlignViewController(this, viewport,
307 if (viewport.getAlignmentConservationAnnotation() == null)
309 BLOSUM62Colour.setEnabled(false);
310 conservationMenuItem.setEnabled(false);
311 modifyConservation.setEnabled(false);
312 // PIDColour.setEnabled(false);
313 // abovePIDThreshold.setEnabled(false);
314 // modifyPID.setEnabled(false);
317 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
320 if (sortby.equals("Id"))
322 sortIDMenuItem_actionPerformed(null);
324 else if (sortby.equals("Pairwise Identity"))
326 sortPairwiseMenuItem_actionPerformed(null);
329 if (Desktop.desktop != null)
331 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
332 addServiceListeners();
333 setGUINucleotide(viewport.getAlignment().isNucleotide());
336 setMenusFromViewport(viewport);
337 buildSortByAnnotationScoresMenu();
340 if (viewport.wrapAlignment)
342 wrapMenuItem_actionPerformed(null);
345 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
347 this.overviewMenuItem_actionPerformed(null);
355 * Change the filename and format for the alignment, and enable the 'reload'
356 * button functionality.
363 public void setFileName(String file, String format)
366 currentFileFormat = format;
367 reload.setEnabled(true);
370 void addKeyListener()
372 addKeyListener(new KeyAdapter()
375 public void keyPressed(KeyEvent evt)
377 if (viewport.cursorMode
378 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
379 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
380 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
381 && Character.isDigit(evt.getKeyChar()))
383 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
386 switch (evt.getKeyCode())
389 case 27: // escape key
390 deselectAllSequenceMenuItem_actionPerformed(null);
394 case KeyEvent.VK_DOWN:
395 if (evt.isAltDown() || !viewport.cursorMode)
397 moveSelectedSequences(false);
399 if (viewport.cursorMode)
401 alignPanel.seqPanel.moveCursor(0, 1);
406 if (evt.isAltDown() || !viewport.cursorMode)
408 moveSelectedSequences(true);
410 if (viewport.cursorMode)
412 alignPanel.seqPanel.moveCursor(0, -1);
417 case KeyEvent.VK_LEFT:
418 if (evt.isAltDown() || !viewport.cursorMode)
420 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
424 alignPanel.seqPanel.moveCursor(-1, 0);
429 case KeyEvent.VK_RIGHT:
430 if (evt.isAltDown() || !viewport.cursorMode)
432 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
436 alignPanel.seqPanel.moveCursor(1, 0);
440 case KeyEvent.VK_SPACE:
441 if (viewport.cursorMode)
443 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
444 || evt.isShiftDown() || evt.isAltDown());
448 // case KeyEvent.VK_A:
449 // if (viewport.cursorMode)
451 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
452 // //System.out.println("A");
456 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
457 * System.out.println("closing bracket"); } break;
459 case KeyEvent.VK_DELETE:
460 case KeyEvent.VK_BACK_SPACE:
461 if (!viewport.cursorMode)
463 cut_actionPerformed(null);
467 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
468 || evt.isShiftDown() || evt.isAltDown());
474 if (viewport.cursorMode)
476 alignPanel.seqPanel.setCursorRow();
480 if (viewport.cursorMode && !evt.isControlDown())
482 alignPanel.seqPanel.setCursorColumn();
486 if (viewport.cursorMode)
488 alignPanel.seqPanel.setCursorPosition();
492 case KeyEvent.VK_ENTER:
493 case KeyEvent.VK_COMMA:
494 if (viewport.cursorMode)
496 alignPanel.seqPanel.setCursorRowAndColumn();
501 if (viewport.cursorMode)
503 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
507 if (viewport.cursorMode)
509 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
514 viewport.cursorMode = !viewport.cursorMode;
515 statusBar.setText(MessageManager.formatMessage(
516 "label.keyboard_editing_mode", new String[]
517 { (viewport.cursorMode ? "on" : "off") }));
518 if (viewport.cursorMode)
520 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
521 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
523 alignPanel.seqPanel.seqCanvas.repaint();
529 Help.showHelpWindow();
530 } catch (Exception ex)
532 ex.printStackTrace();
537 boolean toggleSeqs = !evt.isControlDown();
538 boolean toggleCols = !evt.isShiftDown();
539 toggleHiddenRegions(toggleSeqs, toggleCols);
542 case KeyEvent.VK_PAGE_UP:
543 if (viewport.wrapAlignment)
545 alignPanel.scrollUp(true);
549 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
550 - viewport.endSeq + viewport.startSeq);
553 case KeyEvent.VK_PAGE_DOWN:
554 if (viewport.wrapAlignment)
556 alignPanel.scrollUp(false);
560 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
561 + viewport.endSeq - viewport.startSeq);
568 public void keyReleased(KeyEvent evt)
570 switch (evt.getKeyCode())
572 case KeyEvent.VK_LEFT:
573 if (evt.isAltDown() || !viewport.cursorMode)
575 viewport.firePropertyChange("alignment", null, viewport
576 .getAlignment().getSequences());
580 case KeyEvent.VK_RIGHT:
581 if (evt.isAltDown() || !viewport.cursorMode)
583 viewport.firePropertyChange("alignment", null, viewport
584 .getAlignment().getSequences());
592 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
594 ap.alignFrame = this;
595 avc = new jalview.controller.AlignViewController(this, viewport,
598 alignPanels.addElement(ap);
600 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
602 int aSize = alignPanels.size();
604 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
606 if (aSize == 1 && ap.av.viewName == null)
608 this.getContentPane().add(ap, BorderLayout.CENTER);
614 setInitialTabVisible();
617 expandViews.setEnabled(true);
618 gatherViews.setEnabled(true);
619 tabbedPane.addTab(ap.av.viewName, ap);
621 ap.setVisible(false);
626 if (ap.av.isPadGaps())
628 ap.av.getAlignment().padGaps();
630 ap.av.updateConservation(ap);
631 ap.av.updateConsensus(ap);
632 ap.av.updateStrucConsensus(ap);
636 public void setInitialTabVisible()
638 expandViews.setEnabled(true);
639 gatherViews.setEnabled(true);
640 tabbedPane.setVisible(true);
641 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
642 tabbedPane.addTab(first.av.viewName, first);
643 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
646 public AlignViewport getViewport()
651 /* Set up intrinsic listeners for dynamically generated GUI bits. */
652 private void addServiceListeners()
654 final java.beans.PropertyChangeListener thisListener;
655 Desktop.instance.addJalviewPropertyChangeListener("services",
656 thisListener = new java.beans.PropertyChangeListener()
659 public void propertyChange(PropertyChangeEvent evt)
661 // // System.out.println("Discoverer property change.");
662 // if (evt.getPropertyName().equals("services"))
664 SwingUtilities.invokeLater(new Runnable()
671 .println("Rebuild WS Menu for service change");
672 BuildWebServiceMenu();
679 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
682 public void internalFrameClosed(
683 javax.swing.event.InternalFrameEvent evt)
685 System.out.println("deregistering discoverer listener");
686 Desktop.instance.removeJalviewPropertyChangeListener("services",
688 closeMenuItem_actionPerformed(true);
691 // Finally, build the menu once to get current service state
692 new Thread(new Runnable()
697 BuildWebServiceMenu();
702 public void setGUINucleotide(boolean nucleotide)
704 showTranslation.setVisible(nucleotide);
705 conservationMenuItem.setEnabled(!nucleotide);
706 modifyConservation.setEnabled(!nucleotide);
707 showGroupConservation.setEnabled(!nucleotide);
708 rnahelicesColour.setEnabled(nucleotide);
709 purinePyrimidineColour.setEnabled(nucleotide);
710 // Remember AlignFrame always starts as protein
714 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
719 * set up menus for the currently viewport. This may be called after any
720 * operation that affects the data in the current view (selection changed,
721 * etc) to update the menus to reflect the new state.
723 public void setMenusForViewport()
725 setMenusFromViewport(viewport);
729 * Need to call this method when tabs are selected for multiple views, or when
730 * loading from Jalview2XML.java
735 void setMenusFromViewport(AlignViewport av)
737 padGapsMenuitem.setSelected(av.isPadGaps());
738 colourTextMenuItem.setSelected(av.showColourText);
739 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
740 conservationMenuItem.setSelected(av.getConservationSelected());
741 seqLimits.setSelected(av.getShowJVSuffix());
742 idRightAlign.setSelected(av.rightAlignIds);
743 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
744 renderGapsMenuItem.setSelected(av.renderGaps);
745 wrapMenuItem.setSelected(av.wrapAlignment);
746 scaleAbove.setVisible(av.wrapAlignment);
747 scaleLeft.setVisible(av.wrapAlignment);
748 scaleRight.setVisible(av.wrapAlignment);
749 annotationPanelMenuItem.setState(av.showAnnotation);
751 * Show/hide annotations only enabled if annotation panel is shown
753 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
754 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
755 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
756 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
757 viewBoxesMenuItem.setSelected(av.showBoxes);
758 viewTextMenuItem.setSelected(av.showText);
759 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
760 showGroupConsensus.setSelected(av.isShowGroupConsensus());
761 showGroupConservation.setSelected(av.isShowGroupConservation());
762 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
763 showSequenceLogo.setSelected(av.isShowSequenceLogo());
764 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
766 setColourSelected(ColourSchemeProperty.getColourName(av
767 .getGlobalColourScheme()));
769 showSeqFeatures.setSelected(av.showSequenceFeatures);
770 hiddenMarkers.setState(av.showHiddenMarkers);
771 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
772 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
773 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
774 autoCalculate.setSelected(av.autoCalculateConsensus);
775 sortByTree.setSelected(av.sortByTree);
776 listenToViewSelections.setSelected(av.followSelection);
777 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
779 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
780 setShowProductsEnabled();
784 // methods for implementing IProgressIndicator
785 // need to refactor to a reusable stub class
786 Hashtable progressBars, progressBarHandlers;
791 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
794 public void setProgressBar(String message, long id)
796 if (progressBars == null)
798 progressBars = new Hashtable();
799 progressBarHandlers = new Hashtable();
802 JPanel progressPanel;
803 Long lId = new Long(id);
804 GridLayout layout = (GridLayout) statusPanel.getLayout();
805 if (progressBars.get(lId) != null)
807 progressPanel = (JPanel) progressBars.get(new Long(id));
808 statusPanel.remove(progressPanel);
809 progressBars.remove(lId);
810 progressPanel = null;
813 statusBar.setText(message);
815 if (progressBarHandlers.contains(lId))
817 progressBarHandlers.remove(lId);
819 layout.setRows(layout.getRows() - 1);
823 progressPanel = new JPanel(new BorderLayout(10, 5));
825 JProgressBar progressBar = new JProgressBar();
826 progressBar.setIndeterminate(true);
828 progressPanel.add(new JLabel(message), BorderLayout.WEST);
829 progressPanel.add(progressBar, BorderLayout.CENTER);
831 layout.setRows(layout.getRows() + 1);
832 statusPanel.add(progressPanel);
834 progressBars.put(lId, progressPanel);
837 // setMenusForViewport();
842 public void registerHandler(final long id,
843 final IProgressIndicatorHandler handler)
845 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
847 throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
849 progressBarHandlers.put(new Long(id), handler);
850 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
851 if (handler.canCancel())
853 JButton cancel = new JButton(
854 MessageManager.getString("action.cancel"));
855 final IProgressIndicator us = this;
856 cancel.addActionListener(new ActionListener()
860 public void actionPerformed(ActionEvent e)
862 handler.cancelActivity(id);
863 us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
866 progressPanel.add(cancel, BorderLayout.EAST);
872 * @return true if any progress bars are still active
875 public boolean operationInProgress()
877 if (progressBars != null && progressBars.size() > 0)
885 public void setStatus(String text)
887 statusBar.setText(text);
891 * Added so Castor Mapping file can obtain Jalview Version
893 public String getVersion()
895 return jalview.bin.Cache.getProperty("VERSION");
898 public FeatureRenderer getFeatureRenderer()
900 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
904 public void fetchSequence_actionPerformed(ActionEvent e)
906 new SequenceFetcher(this);
910 public void addFromFile_actionPerformed(ActionEvent e)
912 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
916 public void reload_actionPerformed(ActionEvent e)
918 if (fileName != null)
920 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
921 // originating file's format
922 // TODO: work out how to recover feature settings for correct view(s) when
924 if (currentFileFormat.equals("Jalview"))
926 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
927 for (int i = 0; i < frames.length; i++)
929 if (frames[i] instanceof AlignFrame && frames[i] != this
930 && ((AlignFrame) frames[i]).fileName != null
931 && ((AlignFrame) frames[i]).fileName.equals(fileName))
935 frames[i].setSelected(true);
936 Desktop.instance.closeAssociatedWindows();
937 } catch (java.beans.PropertyVetoException ex)
943 Desktop.instance.closeAssociatedWindows();
945 FileLoader loader = new FileLoader();
946 String protocol = fileName.startsWith("http:") ? "URL" : "File";
947 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
951 Rectangle bounds = this.getBounds();
953 FileLoader loader = new FileLoader();
954 String protocol = fileName.startsWith("http:") ? "URL" : "File";
955 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
956 protocol, currentFileFormat);
958 newframe.setBounds(bounds);
959 if (featureSettings != null && featureSettings.isShowing())
961 final Rectangle fspos = featureSettings.frame.getBounds();
962 // TODO: need a 'show feature settings' function that takes bounds -
963 // need to refactor Desktop.addFrame
964 newframe.featureSettings_actionPerformed(null);
965 final FeatureSettings nfs = newframe.featureSettings;
966 SwingUtilities.invokeLater(new Runnable()
971 nfs.frame.setBounds(fspos);
974 this.featureSettings.close();
975 this.featureSettings = null;
977 this.closeMenuItem_actionPerformed(true);
983 public void addFromText_actionPerformed(ActionEvent e)
985 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
989 public void addFromURL_actionPerformed(ActionEvent e)
991 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
995 public void save_actionPerformed(ActionEvent e)
998 || (currentFileFormat == null || !jalview.io.FormatAdapter
999 .isValidIOFormat(currentFileFormat, true))
1000 || fileName.startsWith("http"))
1002 saveAs_actionPerformed(null);
1006 saveAlignment(fileName, currentFileFormat);
1017 public void saveAs_actionPerformed(ActionEvent e)
1019 JalviewFileChooser chooser = new JalviewFileChooser(
1020 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1021 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1022 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1023 currentFileFormat, false);
1025 chooser.setFileView(new JalviewFileView());
1026 chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1027 chooser.setToolTipText(MessageManager.getString("action.save"));
1029 int value = chooser.showSaveDialog(this);
1031 if (value == JalviewFileChooser.APPROVE_OPTION)
1033 currentFileFormat = chooser.getSelectedFormat();
1034 if (currentFileFormat == null)
1037 .showInternalMessageDialog(
1040 .getString("label.select_file_format_before_saving"),
1042 .getString("label.file_format_not_specified"),
1043 JOptionPane.WARNING_MESSAGE);
1044 value = chooser.showSaveDialog(this);
1048 fileName = chooser.getSelectedFile().getPath();
1050 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1053 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1054 if (currentFileFormat.indexOf(" ") > -1)
1056 currentFileFormat = currentFileFormat.substring(0,
1057 currentFileFormat.indexOf(" "));
1059 saveAlignment(fileName, currentFileFormat);
1063 public boolean saveAlignment(String file, String format)
1065 boolean success = true;
1067 if (format.equalsIgnoreCase("Jalview"))
1069 String shortName = title;
1071 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1073 shortName = shortName.substring(shortName
1074 .lastIndexOf(java.io.File.separatorChar) + 1);
1077 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1079 statusBar.setText(MessageManager.formatMessage(
1080 "label.successfully_saved_to_file_in_format", new String[]
1081 { fileName, format }));
1086 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1088 warningMessage("Cannot save file " + fileName + " using format "
1089 + format, "Alignment output format not supported");
1090 saveAs_actionPerformed(null);
1091 // JBPNote need to have a raise_gui flag here
1095 String[] omitHidden = null;
1097 if (viewport.hasHiddenColumns())
1099 int reply = JOptionPane
1100 .showInternalConfirmDialog(
1103 .getString("label.alignment_contains_hidden_columns"),
1105 .getString("action.save_omit_hidden_columns"),
1106 JOptionPane.YES_NO_OPTION,
1107 JOptionPane.QUESTION_MESSAGE);
1109 if (reply == JOptionPane.YES_OPTION)
1111 omitHidden = viewport.getViewAsString(false);
1114 FormatAdapter f = new FormatAdapter();
1115 String output = f.formatSequences(format,
1116 viewport.getAlignment(), // class cast exceptions will
1117 // occur in the distant future
1118 omitHidden, f.getCacheSuffixDefault(format),
1119 viewport.getColumnSelection());
1129 java.io.PrintWriter out = new java.io.PrintWriter(
1130 new java.io.FileWriter(file));
1134 this.setTitle(file);
1135 statusBar.setText(MessageManager.formatMessage(
1136 "label.successfully_saved_to_file_in_format",
1138 { fileName, format }));
1139 } catch (Exception ex)
1142 ex.printStackTrace();
1149 JOptionPane.showInternalMessageDialog(this, MessageManager
1150 .formatMessage("label.couldnt_save_file", new String[]
1151 { fileName }), MessageManager
1152 .getString("label.error_saving_file"),
1153 JOptionPane.WARNING_MESSAGE);
1159 private void warningMessage(String warning, String title)
1161 if (new jalview.util.Platform().isHeadless())
1163 System.err.println("Warning: " + title + "\nWarning: " + warning);
1168 JOptionPane.showInternalMessageDialog(this, warning, title,
1169 JOptionPane.WARNING_MESSAGE);
1181 protected void outputText_actionPerformed(ActionEvent e)
1183 String[] omitHidden = null;
1185 if (viewport.hasHiddenColumns())
1187 int reply = JOptionPane
1188 .showInternalConfirmDialog(
1191 .getString("label.alignment_contains_hidden_columns"),
1193 .getString("action.save_omit_hidden_columns"),
1194 JOptionPane.YES_NO_OPTION,
1195 JOptionPane.QUESTION_MESSAGE);
1197 if (reply == JOptionPane.YES_OPTION)
1199 omitHidden = viewport.getViewAsString(false);
1203 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1204 cap.setForInput(null);
1208 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1209 viewport.getAlignment(), omitHidden,
1210 viewport.getColumnSelection()));
1211 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1212 "label.alignment_output_command", new String[]
1213 { e.getActionCommand() }), 600, 500);
1214 } catch (OutOfMemoryError oom)
1216 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1229 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1231 new HTMLOutput(alignPanel,
1232 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1233 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1237 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1239 new BioJsHTMLOutput(alignPanel,
1240 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1242 public void createImageMap(File file, String image)
1244 alignPanel.makePNGImageMap(file, image);
1254 public void createPNG(File f)
1256 alignPanel.makePNG(f);
1266 public void createEPS(File f)
1268 alignPanel.makeEPS(f);
1271 public void createSVG(File f)
1273 alignPanel.makeSVG(f);
1276 public void pageSetup_actionPerformed(ActionEvent e)
1278 PrinterJob printJob = PrinterJob.getPrinterJob();
1279 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1289 public void printMenuItem_actionPerformed(ActionEvent e)
1291 // Putting in a thread avoids Swing painting problems
1292 PrintThread thread = new PrintThread(alignPanel);
1297 public void exportFeatures_actionPerformed(ActionEvent e)
1299 new AnnotationExporter().exportFeatures(alignPanel);
1303 public void exportAnnotations_actionPerformed(ActionEvent e)
1305 new AnnotationExporter().exportAnnotations(alignPanel,
1306 viewport.showAnnotation ? viewport.getAlignment()
1307 .getAlignmentAnnotation() : null, viewport
1308 .getAlignment().getGroups(), ((Alignment) viewport
1309 .getAlignment()).alignmentProperties);
1313 public void associatedData_actionPerformed(ActionEvent e)
1315 // Pick the tree file
1316 JalviewFileChooser chooser = new JalviewFileChooser(
1317 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1318 chooser.setFileView(new JalviewFileView());
1319 chooser.setDialogTitle(MessageManager
1320 .getString("label.load_jalview_annotations"));
1321 chooser.setToolTipText(MessageManager
1322 .getString("label.load_jalview_annotations"));
1324 int value = chooser.showOpenDialog(null);
1326 if (value == JalviewFileChooser.APPROVE_OPTION)
1328 String choice = chooser.getSelectedFile().getPath();
1329 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1330 loadJalviewDataFile(choice, null, null, null);
1336 * Close the current view or all views in the alignment frame. If the frame
1337 * only contains one view then the alignment will be removed from memory.
1339 * @param closeAllTabs
1342 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1344 if (alignPanels != null && alignPanels.size() < 2)
1346 closeAllTabs = true;
1351 if (alignPanels != null)
1355 if (this.isClosed())
1357 // really close all the windows - otherwise wait till
1358 // setClosed(true) is called
1359 for (int i = 0; i < alignPanels.size(); i++)
1361 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1368 closeView(alignPanel);
1374 this.setClosed(true);
1376 } catch (Exception ex)
1378 ex.printStackTrace();
1383 * close alignPanel2 and shuffle tabs appropriately.
1385 * @param alignPanel2
1387 public void closeView(AlignmentPanel alignPanel2)
1389 int index = tabbedPane.getSelectedIndex();
1390 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1391 alignPanels.removeElement(alignPanel2);
1393 // if (viewport == alignPanel2.av)
1397 alignPanel2.closePanel();
1400 tabbedPane.removeTabAt(closedindex);
1401 tabbedPane.validate();
1403 if (index > closedindex || index == tabbedPane.getTabCount())
1405 // modify currently selected tab index if necessary.
1409 this.tabSelectionChanged(index);
1415 void updateEditMenuBar()
1418 if (viewport.historyList.size() > 0)
1420 undoMenuItem.setEnabled(true);
1421 CommandI command = viewport.historyList.peek();
1422 undoMenuItem.setText(MessageManager.formatMessage(
1423 "label.undo_command", new String[]
1424 { command.getDescription() }));
1428 undoMenuItem.setEnabled(false);
1429 undoMenuItem.setText(MessageManager.getString("action.undo"));
1432 if (viewport.redoList.size() > 0)
1434 redoMenuItem.setEnabled(true);
1436 CommandI command = viewport.redoList.peek();
1437 redoMenuItem.setText(MessageManager.formatMessage(
1438 "label.redo_command", new String[]
1439 { command.getDescription() }));
1443 redoMenuItem.setEnabled(false);
1444 redoMenuItem.setText(MessageManager.getString("action.redo"));
1448 public void addHistoryItem(CommandI command)
1450 if (command.getSize() > 0)
1452 viewport.historyList.push(command);
1453 viewport.redoList.clear();
1454 updateEditMenuBar();
1455 viewport.updateHiddenColumns();
1456 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1457 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1458 // viewport.getColumnSelection()
1459 // .getHiddenColumns().size() > 0);
1465 * @return alignment objects for all views
1467 AlignmentI[] getViewAlignments()
1469 if (alignPanels != null)
1471 Enumeration e = alignPanels.elements();
1472 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1473 for (int i = 0; e.hasMoreElements(); i++)
1475 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1479 if (viewport != null)
1481 return new AlignmentI[]
1482 { viewport.getAlignment() };
1494 protected void undoMenuItem_actionPerformed(ActionEvent e)
1496 if (viewport.historyList.empty())
1500 CommandI command = viewport.historyList.pop();
1501 viewport.redoList.push(command);
1502 command.undoCommand(getViewAlignments());
1504 AlignViewport originalSource = getOriginatingSource(command);
1505 updateEditMenuBar();
1507 if (originalSource != null)
1509 if (originalSource != viewport)
1512 .warn("Implementation worry: mismatch of viewport origin for undo");
1514 originalSource.updateHiddenColumns();
1515 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1517 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1518 // viewport.getColumnSelection()
1519 // .getHiddenColumns().size() > 0);
1520 originalSource.firePropertyChange("alignment", null, originalSource
1521 .getAlignment().getSequences());
1532 protected void redoMenuItem_actionPerformed(ActionEvent e)
1534 if (viewport.redoList.size() < 1)
1539 CommandI command = viewport.redoList.pop();
1540 viewport.historyList.push(command);
1541 command.doCommand(getViewAlignments());
1543 AlignViewport originalSource = getOriginatingSource(command);
1544 updateEditMenuBar();
1546 if (originalSource != null)
1549 if (originalSource != viewport)
1552 .warn("Implementation worry: mismatch of viewport origin for redo");
1554 originalSource.updateHiddenColumns();
1555 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1557 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1558 // viewport.getColumnSelection()
1559 // .getHiddenColumns().size() > 0);
1560 originalSource.firePropertyChange("alignment", null, originalSource
1561 .getAlignment().getSequences());
1565 AlignViewport getOriginatingSource(CommandI command)
1567 AlignViewport originalSource = null;
1568 // For sequence removal and addition, we need to fire
1569 // the property change event FROM the viewport where the
1570 // original alignment was altered
1571 AlignmentI al = null;
1572 if (command instanceof EditCommand)
1574 EditCommand editCommand = (EditCommand) command;
1575 al = editCommand.getAlignment();
1576 Vector comps = (Vector) PaintRefresher.components.get(viewport
1577 .getSequenceSetId());
1579 for (int i = 0; i < comps.size(); i++)
1581 if (comps.elementAt(i) instanceof AlignmentPanel)
1583 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1585 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1592 if (originalSource == null)
1594 // The original view is closed, we must validate
1595 // the current view against the closed view first
1598 PaintRefresher.validateSequences(al, viewport.getAlignment());
1601 originalSource = viewport;
1604 return originalSource;
1613 public void moveSelectedSequences(boolean up)
1615 SequenceGroup sg = viewport.getSelectionGroup();
1621 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1622 viewport.getHiddenRepSequences(), up);
1623 alignPanel.paintAlignment(true);
1626 synchronized void slideSequences(boolean right, int size)
1628 List<SequenceI> sg = new Vector();
1629 if (viewport.cursorMode)
1631 sg.add(viewport.getAlignment().getSequenceAt(
1632 alignPanel.seqPanel.seqCanvas.cursorY));
1634 else if (viewport.getSelectionGroup() != null
1635 && viewport.getSelectionGroup().getSize() != viewport
1636 .getAlignment().getHeight())
1638 sg = viewport.getSelectionGroup().getSequences(
1639 viewport.getHiddenRepSequences());
1647 Vector invertGroup = new Vector();
1649 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1651 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1653 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1657 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1659 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1660 for (int i = 0; i < invertGroup.size(); i++)
1662 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1665 SlideSequencesCommand ssc;
1668 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1669 size, viewport.getGapCharacter());
1673 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1674 size, viewport.getGapCharacter());
1677 int groupAdjustment = 0;
1678 if (ssc.getGapsInsertedBegin() && right)
1680 if (viewport.cursorMode)
1682 alignPanel.seqPanel.moveCursor(size, 0);
1686 groupAdjustment = size;
1689 else if (!ssc.getGapsInsertedBegin() && !right)
1691 if (viewport.cursorMode)
1693 alignPanel.seqPanel.moveCursor(-size, 0);
1697 groupAdjustment = -size;
1701 if (groupAdjustment != 0)
1703 viewport.getSelectionGroup().setStartRes(
1704 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1705 viewport.getSelectionGroup().setEndRes(
1706 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1709 boolean appendHistoryItem = false;
1710 if (viewport.historyList != null && viewport.historyList.size() > 0
1711 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1713 appendHistoryItem = ssc
1714 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1718 if (!appendHistoryItem)
1720 addHistoryItem(ssc);
1733 protected void copy_actionPerformed(ActionEvent e)
1736 if (viewport.getSelectionGroup() == null)
1740 // TODO: preserve the ordering of displayed alignment annotation in any
1741 // internal paste (particularly sequence associated annotation)
1742 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1743 String[] omitHidden = null;
1745 if (viewport.hasHiddenColumns())
1747 omitHidden = viewport.getViewAsString(true);
1750 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1753 StringSelection ss = new StringSelection(output);
1757 jalview.gui.Desktop.internalCopy = true;
1758 // Its really worth setting the clipboard contents
1759 // to empty before setting the large StringSelection!!
1760 Toolkit.getDefaultToolkit().getSystemClipboard()
1761 .setContents(new StringSelection(""), null);
1763 Toolkit.getDefaultToolkit().getSystemClipboard()
1764 .setContents(ss, Desktop.instance);
1765 } catch (OutOfMemoryError er)
1767 new OOMWarning("copying region", er);
1771 Vector hiddenColumns = null;
1772 if (viewport.hasHiddenColumns())
1774 hiddenColumns = new Vector();
1775 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1776 .getSelectionGroup().getEndRes();
1777 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1780 int[] region = (int[]) viewport.getColumnSelection()
1781 .getHiddenColumns().elementAt(i);
1782 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1784 hiddenColumns.addElement(new int[]
1785 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1790 Desktop.jalviewClipboard = new Object[]
1791 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1792 statusBar.setText(MessageManager.formatMessage(
1793 "label.copied_sequences_to_clipboard", new String[]
1794 { Integer.valueOf(seqs.length).toString() }));
1804 protected void pasteNew_actionPerformed(ActionEvent e)
1816 protected void pasteThis_actionPerformed(ActionEvent e)
1822 * Paste contents of Jalview clipboard
1824 * @param newAlignment
1825 * true to paste to a new alignment, otherwise add to this.
1827 void paste(boolean newAlignment)
1829 boolean externalPaste = true;
1832 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1833 Transferable contents = c.getContents(this);
1835 if (contents == null)
1843 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1844 if (str.length() < 1)
1849 format = new IdentifyFile().Identify(str, "Paste");
1851 } catch (OutOfMemoryError er)
1853 new OOMWarning("Out of memory pasting sequences!!", er);
1857 SequenceI[] sequences;
1858 boolean annotationAdded = false;
1859 AlignmentI alignment = null;
1861 if (Desktop.jalviewClipboard != null)
1863 // The clipboard was filled from within Jalview, we must use the
1865 // And dataset from the copied alignment
1866 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1867 // be doubly sure that we create *new* sequence objects.
1868 sequences = new SequenceI[newseq.length];
1869 for (int i = 0; i < newseq.length; i++)
1871 sequences[i] = new Sequence(newseq[i]);
1873 alignment = new Alignment(sequences);
1874 externalPaste = false;
1878 // parse the clipboard as an alignment.
1879 alignment = new FormatAdapter().readFile(str, "Paste", format);
1880 sequences = alignment.getSequencesArray();
1884 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1890 if (Desktop.jalviewClipboard != null)
1892 // dataset is inherited
1893 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1897 // new dataset is constructed
1898 alignment.setDataset(null);
1900 alwidth = alignment.getWidth() + 1;
1904 AlignmentI pastedal = alignment; // preserve pasted alignment object
1905 // Add pasted sequences and dataset into existing alignment.
1906 alignment = viewport.getAlignment();
1907 alwidth = alignment.getWidth() + 1;
1908 // decide if we need to import sequences from an existing dataset
1909 boolean importDs = Desktop.jalviewClipboard != null
1910 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1911 // importDs==true instructs us to copy over new dataset sequences from
1912 // an existing alignment
1913 Vector newDs = (importDs) ? new Vector() : null; // used to create
1914 // minimum dataset set
1916 for (int i = 0; i < sequences.length; i++)
1920 newDs.addElement(null);
1922 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1924 if (importDs && ds != null)
1926 if (!newDs.contains(ds))
1928 newDs.setElementAt(ds, i);
1929 ds = new Sequence(ds);
1930 // update with new dataset sequence
1931 sequences[i].setDatasetSequence(ds);
1935 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1940 // copy and derive new dataset sequence
1941 sequences[i] = sequences[i].deriveSequence();
1942 alignment.getDataset().addSequence(
1943 sequences[i].getDatasetSequence());
1944 // TODO: avoid creation of duplicate dataset sequences with a
1945 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1947 alignment.addSequence(sequences[i]); // merges dataset
1951 newDs.clear(); // tidy up
1953 if (alignment.getAlignmentAnnotation() != null)
1955 for (AlignmentAnnotation alan : alignment
1956 .getAlignmentAnnotation())
1958 if (alan.graphGroup > fgroup)
1960 fgroup = alan.graphGroup;
1964 if (pastedal.getAlignmentAnnotation() != null)
1966 // Add any annotation attached to alignment.
1967 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1968 for (int i = 0; i < alann.length; i++)
1970 annotationAdded = true;
1971 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1973 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1974 if (newann.graphGroup > -1)
1976 if (newGraphGroups.size() <= newann.graphGroup
1977 || newGraphGroups.get(newann.graphGroup) == null)
1979 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1981 newGraphGroups.add(q, null);
1983 newGraphGroups.set(newann.graphGroup, new Integer(
1986 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1990 newann.padAnnotation(alwidth);
1991 alignment.addAnnotation(newann);
2001 addHistoryItem(new EditCommand(
2002 MessageManager.getString("label.add_sequences"),
2004 sequences, 0, alignment.getWidth(), alignment));
2006 // Add any annotations attached to sequences
2007 for (int i = 0; i < sequences.length; i++)
2009 if (sequences[i].getAnnotation() != null)
2011 AlignmentAnnotation newann;
2012 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2014 annotationAdded = true;
2015 newann = sequences[i].getAnnotation()[a];
2016 newann.adjustForAlignment();
2017 newann.padAnnotation(alwidth);
2018 if (newann.graphGroup > -1)
2020 if (newann.graphGroup > -1)
2022 if (newGraphGroups.size() <= newann.graphGroup
2023 || newGraphGroups.get(newann.graphGroup) == null)
2025 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2027 newGraphGroups.add(q, null);
2029 newGraphGroups.set(newann.graphGroup, new Integer(
2032 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2036 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2041 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2048 // propagate alignment changed.
2049 viewport.setEndSeq(alignment.getHeight());
2050 if (annotationAdded)
2052 // Duplicate sequence annotation in all views.
2053 AlignmentI[] alview = this.getViewAlignments();
2054 for (int i = 0; i < sequences.length; i++)
2056 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2061 for (int avnum = 0; avnum < alview.length; avnum++)
2063 if (alview[avnum] != alignment)
2065 // duplicate in a view other than the one with input focus
2066 int avwidth = alview[avnum].getWidth() + 1;
2067 // this relies on sann being preserved after we
2068 // modify the sequence's annotation array for each duplication
2069 for (int a = 0; a < sann.length; a++)
2071 AlignmentAnnotation newann = new AlignmentAnnotation(
2073 sequences[i].addAlignmentAnnotation(newann);
2074 newann.padAnnotation(avwidth);
2075 alview[avnum].addAnnotation(newann); // annotation was
2076 // duplicated earlier
2077 // TODO JAL-1145 graphGroups are not updated for sequence
2078 // annotation added to several views. This may cause
2080 alview[avnum].setAnnotationIndex(newann, a);
2085 buildSortByAnnotationScoresMenu();
2087 viewport.firePropertyChange("alignment", null,
2088 alignment.getSequences());
2089 if (alignPanels != null)
2091 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2093 ap.validateAnnotationDimensions(false);
2098 alignPanel.validateAnnotationDimensions(false);
2104 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2106 String newtitle = new String("Copied sequences");
2108 if (Desktop.jalviewClipboard != null
2109 && Desktop.jalviewClipboard[2] != null)
2111 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2112 for (int i = 0; i < hc.size(); i++)
2114 int[] region = (int[]) hc.elementAt(i);
2115 af.viewport.hideColumns(region[0], region[1]);
2119 // >>>This is a fix for the moment, until a better solution is
2121 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2123 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2125 // TODO: maintain provenance of an alignment, rather than just make the
2126 // title a concatenation of operations.
2129 if (title.startsWith("Copied sequences"))
2135 newtitle = newtitle.concat("- from " + title);
2140 newtitle = new String("Pasted sequences");
2143 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2148 } catch (Exception ex)
2150 ex.printStackTrace();
2151 System.out.println("Exception whilst pasting: " + ex);
2152 // could be anything being pasted in here
2158 protected void expand_newalign(ActionEvent e)
2162 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2163 .getAlignment(), -1);
2164 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2166 String newtitle = new String("Flanking alignment");
2168 if (Desktop.jalviewClipboard != null
2169 && Desktop.jalviewClipboard[2] != null)
2171 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2172 for (int i = 0; i < hc.size(); i++)
2174 int[] region = (int[]) hc.elementAt(i);
2175 af.viewport.hideColumns(region[0], region[1]);
2179 // >>>This is a fix for the moment, until a better solution is
2181 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2183 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2185 // TODO: maintain provenance of an alignment, rather than just make the
2186 // title a concatenation of operations.
2188 if (title.startsWith("Copied sequences"))
2194 newtitle = newtitle.concat("- from " + title);
2198 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2200 } catch (Exception ex)
2202 ex.printStackTrace();
2203 System.out.println("Exception whilst pasting: " + ex);
2204 // could be anything being pasted in here
2205 } catch (OutOfMemoryError oom)
2207 new OOMWarning("Viewing flanking region of alignment", oom);
2218 protected void cut_actionPerformed(ActionEvent e)
2220 copy_actionPerformed(null);
2221 delete_actionPerformed(null);
2231 protected void delete_actionPerformed(ActionEvent evt)
2234 SequenceGroup sg = viewport.getSelectionGroup();
2240 List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
2242 for (int i = 0; i < sg.getSize(); i++)
2244 seq = sg.getSequenceAt(i);
2248 // If the cut affects all sequences, warn, remove highlighted columns
2249 if (sg.getSize() == viewport.getAlignment().getHeight())
2251 int confirm = JOptionPane.showConfirmDialog(this,
2252 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2253 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2254 JOptionPane.OK_CANCEL_OPTION);
2256 if (confirm == JOptionPane.CANCEL_OPTION
2257 || confirm == JOptionPane.CLOSED_OPTION)
2261 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2262 sg.getEndRes() + 1);
2265 SequenceI[] cut = new SequenceI[seqs.size()];
2266 for (int i = 0; i < seqs.size(); i++)
2268 cut[i] = seqs.get(i);
2272 * //ADD HISTORY ITEM
2274 addHistoryItem(new EditCommand(
2275 MessageManager.getString("label.cut_sequences"), Action.CUT,
2276 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2277 viewport.getAlignment()));
2279 viewport.setSelectionGroup(null);
2280 viewport.sendSelection();
2281 viewport.getAlignment().deleteGroup(sg);
2283 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2285 if (viewport.getAlignment().getHeight() < 1)
2289 this.setClosed(true);
2290 } catch (Exception ex)
2303 protected void deleteGroups_actionPerformed(ActionEvent e)
2305 if (avc.deleteGroups())
2307 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2308 alignPanel.updateAnnotation();
2309 alignPanel.paintAlignment(true);
2320 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2322 SequenceGroup sg = new SequenceGroup();
2324 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2326 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2329 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2330 viewport.setSelectionGroup(sg);
2331 viewport.sendSelection();
2332 alignPanel.paintAlignment(true);
2333 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2343 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2345 if (viewport.cursorMode)
2347 alignPanel.seqPanel.keyboardNo1 = null;
2348 alignPanel.seqPanel.keyboardNo2 = null;
2350 viewport.setSelectionGroup(null);
2351 viewport.getColumnSelection().clear();
2352 viewport.setSelectionGroup(null);
2353 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2354 alignPanel.idPanel.idCanvas.searchResults = null;
2355 alignPanel.paintAlignment(true);
2356 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2357 viewport.sendSelection();
2367 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2369 SequenceGroup sg = viewport.getSelectionGroup();
2373 selectAllSequenceMenuItem_actionPerformed(null);
2378 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2380 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2383 alignPanel.paintAlignment(true);
2384 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2385 viewport.sendSelection();
2389 public void invertColSel_actionPerformed(ActionEvent e)
2391 viewport.invertColumnSelection();
2392 alignPanel.paintAlignment(true);
2393 viewport.sendSelection();
2403 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2405 trimAlignment(true);
2415 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2417 trimAlignment(false);
2420 void trimAlignment(boolean trimLeft)
2422 ColumnSelection colSel = viewport.getColumnSelection();
2425 if (colSel.size() > 0)
2429 column = colSel.getMin();
2433 column = colSel.getMax();
2437 if (viewport.getSelectionGroup() != null)
2439 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2440 viewport.getHiddenRepSequences());
2444 seqs = viewport.getAlignment().getSequencesArray();
2447 TrimRegionCommand trimRegion;
2450 trimRegion = new TrimRegionCommand("Remove Left",
2451 TrimRegionCommand.TRIM_LEFT, seqs, column,
2452 viewport.getAlignment(), viewport.getColumnSelection(),
2453 viewport.getSelectionGroup());
2454 viewport.setStartRes(0);
2458 trimRegion = new TrimRegionCommand("Remove Right",
2459 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2460 viewport.getAlignment(), viewport.getColumnSelection(),
2461 viewport.getSelectionGroup());
2464 statusBar.setText(MessageManager.formatMessage(
2465 "label.removed_columns", new String[]
2466 { Integer.valueOf(trimRegion.getSize()).toString() }));
2468 addHistoryItem(trimRegion);
2470 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2472 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2473 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2475 viewport.getAlignment().deleteGroup(sg);
2479 viewport.firePropertyChange("alignment", null, viewport
2480 .getAlignment().getSequences());
2491 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2493 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2496 if (viewport.getSelectionGroup() != null)
2498 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2499 viewport.getHiddenRepSequences());
2500 start = viewport.getSelectionGroup().getStartRes();
2501 end = viewport.getSelectionGroup().getEndRes();
2505 seqs = viewport.getAlignment().getSequencesArray();
2508 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2509 "Remove Gapped Columns", seqs, start, end,
2510 viewport.getAlignment());
2512 addHistoryItem(removeGapCols);
2514 statusBar.setText(MessageManager.formatMessage(
2515 "label.removed_empty_columns", new String[]
2516 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2518 // This is to maintain viewport position on first residue
2519 // of first sequence
2520 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2521 int startRes = seq.findPosition(viewport.startRes);
2522 // ShiftList shifts;
2523 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2524 // edit.alColumnChanges=shifts.getInverse();
2525 // if (viewport.hasHiddenColumns)
2526 // viewport.getColumnSelection().compensateForEdits(shifts);
2527 viewport.setStartRes(seq.findIndex(startRes) - 1);
2528 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2540 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2542 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2545 if (viewport.getSelectionGroup() != null)
2547 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2548 viewport.getHiddenRepSequences());
2549 start = viewport.getSelectionGroup().getStartRes();
2550 end = viewport.getSelectionGroup().getEndRes();
2554 seqs = viewport.getAlignment().getSequencesArray();
2557 // This is to maintain viewport position on first residue
2558 // of first sequence
2559 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2560 int startRes = seq.findPosition(viewport.startRes);
2562 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2563 viewport.getAlignment()));
2565 viewport.setStartRes(seq.findIndex(startRes) - 1);
2567 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2579 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2581 viewport.setPadGaps(padGapsMenuitem.isSelected());
2582 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2588 // if (justifySeqs>0)
2590 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2603 public void findMenuItem_actionPerformed(ActionEvent e)
2609 public void newView_actionPerformed(ActionEvent e)
2616 * @param copyAnnotation
2617 * if true then duplicate all annnotation, groups and settings
2618 * @return new alignment panel, already displayed.
2620 public AlignmentPanel newView(boolean copyAnnotation)
2622 return newView(null, copyAnnotation);
2628 * title of newly created view
2629 * @return new alignment panel, already displayed.
2631 public AlignmentPanel newView(String viewTitle)
2633 return newView(viewTitle, true);
2639 * title of newly created view
2640 * @param copyAnnotation
2641 * if true then duplicate all annnotation, groups and settings
2642 * @return new alignment panel, already displayed.
2644 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2646 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2648 if (!copyAnnotation)
2650 // just remove all the current annotation except for the automatic stuff
2651 newap.av.getAlignment().deleteAllGroups();
2652 for (AlignmentAnnotation alan : newap.av.getAlignment()
2653 .getAlignmentAnnotation())
2655 if (!alan.autoCalculated)
2657 newap.av.getAlignment().deleteAnnotation(alan);
2663 newap.av.gatherViewsHere = false;
2665 if (viewport.viewName == null)
2667 viewport.viewName = "Original";
2670 newap.av.historyList = viewport.historyList;
2671 newap.av.redoList = viewport.redoList;
2673 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2674 // make sure the new view has a unique name - this is essential for Jalview
2676 boolean addFirstIndex = false;
2677 if (viewTitle == null || viewTitle.trim().length() == 0)
2679 viewTitle = MessageManager.getString("action.view");
2680 addFirstIndex = true;
2684 index = 1;// we count from 1 if given a specific name
2686 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2687 Vector comps = (Vector) PaintRefresher.components.get(viewport
2688 .getSequenceSetId());
2689 Vector existingNames = new Vector();
2690 for (int i = 0; i < comps.size(); i++)
2692 if (comps.elementAt(i) instanceof AlignmentPanel)
2694 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2695 if (!existingNames.contains(ap.av.viewName))
2697 existingNames.addElement(ap.av.viewName);
2702 while (existingNames.contains(newViewName))
2704 newViewName = viewTitle + " " + (++index);
2707 newap.av.viewName = newViewName;
2709 addAlignmentPanel(newap, true);
2710 newap.alignmentChanged();
2712 if (alignPanels.size() == 2)
2714 viewport.gatherViewsHere = true;
2716 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2721 public void expandViews_actionPerformed(ActionEvent e)
2723 Desktop.instance.explodeViews(this);
2727 public void gatherViews_actionPerformed(ActionEvent e)
2729 Desktop.instance.gatherViews(this);
2739 public void font_actionPerformed(ActionEvent e)
2741 new FontChooser(alignPanel);
2751 protected void seqLimit_actionPerformed(ActionEvent e)
2753 viewport.setShowJVSuffix(seqLimits.isSelected());
2755 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2756 .calculateIdWidth());
2757 alignPanel.paintAlignment(true);
2761 public void idRightAlign_actionPerformed(ActionEvent e)
2763 viewport.rightAlignIds = idRightAlign.isSelected();
2764 alignPanel.paintAlignment(true);
2768 public void centreColumnLabels_actionPerformed(ActionEvent e)
2770 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2771 alignPanel.paintAlignment(true);
2777 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2780 protected void followHighlight_actionPerformed()
2782 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2784 alignPanel.scrollToPosition(
2785 alignPanel.seqPanel.seqCanvas.searchResults, false);
2796 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2798 viewport.setColourText(colourTextMenuItem.isSelected());
2799 alignPanel.paintAlignment(true);
2809 public void wrapMenuItem_actionPerformed(ActionEvent e)
2811 scaleAbove.setVisible(wrapMenuItem.isSelected());
2812 scaleLeft.setVisible(wrapMenuItem.isSelected());
2813 scaleRight.setVisible(wrapMenuItem.isSelected());
2814 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2815 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2819 public void showAllSeqs_actionPerformed(ActionEvent e)
2821 viewport.showAllHiddenSeqs();
2825 public void showAllColumns_actionPerformed(ActionEvent e)
2827 viewport.showAllHiddenColumns();
2832 public void hideSelSequences_actionPerformed(ActionEvent e)
2834 viewport.hideAllSelectedSeqs();
2835 alignPanel.paintAlignment(true);
2839 * called by key handler and the hide all/show all menu items
2844 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2847 boolean hide = false;
2848 SequenceGroup sg = viewport.getSelectionGroup();
2849 if (!toggleSeqs && !toggleCols)
2851 // Hide everything by the current selection - this is a hack - we do the
2852 // invert and then hide
2853 // first check that there will be visible columns after the invert.
2854 if ((viewport.getColumnSelection() != null
2855 && viewport.getColumnSelection().getSelected() != null && viewport
2856 .getColumnSelection().getSelected().size() > 0)
2857 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2860 // now invert the sequence set, if required - empty selection implies
2861 // that no hiding is required.
2864 invertSequenceMenuItem_actionPerformed(null);
2865 sg = viewport.getSelectionGroup();
2869 viewport.expandColSelection(sg, true);
2870 // finally invert the column selection and get the new sequence
2872 invertColSel_actionPerformed(null);
2879 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2881 hideSelSequences_actionPerformed(null);
2884 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2887 showAllSeqs_actionPerformed(null);
2893 if (viewport.getColumnSelection().getSelected().size() > 0)
2895 hideSelColumns_actionPerformed(null);
2898 viewport.setSelectionGroup(sg);
2903 showAllColumns_actionPerformed(null);
2912 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2913 * event.ActionEvent)
2916 public void hideAllButSelection_actionPerformed(ActionEvent e)
2918 toggleHiddenRegions(false, false);
2925 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2929 public void hideAllSelection_actionPerformed(ActionEvent e)
2931 SequenceGroup sg = viewport.getSelectionGroup();
2932 viewport.expandColSelection(sg, false);
2933 viewport.hideAllSelectedSeqs();
2934 viewport.hideSelectedColumns();
2935 alignPanel.paintAlignment(true);
2942 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2946 public void showAllhidden_actionPerformed(ActionEvent e)
2948 viewport.showAllHiddenColumns();
2949 viewport.showAllHiddenSeqs();
2950 alignPanel.paintAlignment(true);
2954 public void hideSelColumns_actionPerformed(ActionEvent e)
2956 viewport.hideSelectedColumns();
2957 alignPanel.paintAlignment(true);
2961 public void hiddenMarkers_actionPerformed(ActionEvent e)
2963 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2974 protected void scaleAbove_actionPerformed(ActionEvent e)
2976 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2977 alignPanel.paintAlignment(true);
2987 protected void scaleLeft_actionPerformed(ActionEvent e)
2989 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2990 alignPanel.paintAlignment(true);
3000 protected void scaleRight_actionPerformed(ActionEvent e)
3002 viewport.setScaleRightWrapped(scaleRight.isSelected());
3003 alignPanel.paintAlignment(true);
3013 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3015 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3016 alignPanel.paintAlignment(true);
3026 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3028 viewport.setShowText(viewTextMenuItem.isSelected());
3029 alignPanel.paintAlignment(true);
3039 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3041 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3042 alignPanel.paintAlignment(true);
3045 public FeatureSettings featureSettings;
3048 public void featureSettings_actionPerformed(ActionEvent e)
3050 if (featureSettings != null)
3052 featureSettings.close();
3053 featureSettings = null;
3055 if (!showSeqFeatures.isSelected())
3057 // make sure features are actually displayed
3058 showSeqFeatures.setSelected(true);
3059 showSeqFeatures_actionPerformed(null);
3061 featureSettings = new FeatureSettings(this);
3065 * Set or clear 'Show Sequence Features'
3071 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3073 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3074 alignPanel.paintAlignment(true);
3075 if (alignPanel.getOverviewPanel() != null)
3077 alignPanel.getOverviewPanel().updateOverviewImage();
3082 * Set or clear 'Show Sequence Features'
3088 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3090 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3092 if (viewport.getShowSequenceFeaturesHeight())
3094 // ensure we're actually displaying features
3095 viewport.setShowSequenceFeatures(true);
3096 showSeqFeatures.setSelected(true);
3098 alignPanel.paintAlignment(true);
3099 if (alignPanel.getOverviewPanel() != null)
3101 alignPanel.getOverviewPanel().updateOverviewImage();
3106 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3107 * the annotations panel as a whole.
3109 * The options to show/hide all annotations should be enabled when the panel
3110 * is shown, and disabled when the panel is hidden.
3115 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3117 final boolean setVisible = annotationPanelMenuItem.isSelected();
3118 viewport.setShowAnnotation(setVisible);
3119 alignPanel.setAnnotationVisible(setVisible);
3120 this.showAllSeqAnnotations.setEnabled(setVisible);
3121 this.hideAllSeqAnnotations.setEnabled(setVisible);
3122 this.showAllAlAnnotations.setEnabled(setVisible);
3123 this.hideAllAlAnnotations.setEnabled(setVisible);
3127 public void alignmentProperties()
3129 JEditorPane editPane = new JEditorPane("text/html", "");
3130 editPane.setEditable(false);
3131 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3133 editPane.setText(MessageManager.formatMessage("label.html_content",
3135 { contents.toString() }));
3136 JInternalFrame frame = new JInternalFrame();
3137 frame.getContentPane().add(new JScrollPane(editPane));
3139 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3140 "label.alignment_properties", new String[]
3141 { getTitle() }), 500, 400);
3151 public void overviewMenuItem_actionPerformed(ActionEvent e)
3153 if (alignPanel.overviewPanel != null)
3158 JInternalFrame frame = new JInternalFrame();
3159 OverviewPanel overview = new OverviewPanel(alignPanel);
3160 frame.setContentPane(overview);
3161 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3162 "label.overview_params", new String[]
3163 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3165 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3166 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3169 public void internalFrameClosed(
3170 javax.swing.event.InternalFrameEvent evt)
3172 alignPanel.setOverviewPanel(null);
3176 alignPanel.setOverviewPanel(overview);
3180 public void textColour_actionPerformed(ActionEvent e)
3182 new TextColourChooser().chooseColour(alignPanel, null);
3192 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3204 public void clustalColour_actionPerformed(ActionEvent e)
3206 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3207 viewport.getHiddenRepSequences()));
3217 public void zappoColour_actionPerformed(ActionEvent e)
3219 changeColour(new ZappoColourScheme());
3229 public void taylorColour_actionPerformed(ActionEvent e)
3231 changeColour(new TaylorColourScheme());
3241 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3243 changeColour(new HydrophobicColourScheme());
3253 public void helixColour_actionPerformed(ActionEvent e)
3255 changeColour(new HelixColourScheme());
3265 public void strandColour_actionPerformed(ActionEvent e)
3267 changeColour(new StrandColourScheme());
3277 public void turnColour_actionPerformed(ActionEvent e)
3279 changeColour(new TurnColourScheme());
3289 public void buriedColour_actionPerformed(ActionEvent e)
3291 changeColour(new BuriedColourScheme());
3301 public void nucleotideColour_actionPerformed(ActionEvent e)
3303 changeColour(new NucleotideColourScheme());
3307 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3309 changeColour(new PurinePyrimidineColourScheme());
3313 * public void covariationColour_actionPerformed(ActionEvent e) {
3315 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3319 public void annotationColour_actionPerformed(ActionEvent e)
3321 new AnnotationColourChooser(viewport, alignPanel);
3325 public void rnahelicesColour_actionPerformed(ActionEvent e)
3327 new RNAHelicesColourChooser(viewport, alignPanel);
3337 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3339 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3348 public void changeColour(ColourSchemeI cs)
3350 // TODO: compare with applet and pull up to model method
3355 if (viewport.getAbovePIDThreshold())
3357 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3359 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3363 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3366 if (viewport.getConservationSelected())
3369 Alignment al = (Alignment) viewport.getAlignment();
3370 Conservation c = new Conservation("All",
3371 ResidueProperties.propHash, 3, al.getSequences(), 0,
3375 c.verdict(false, viewport.getConsPercGaps());
3377 cs.setConservation(c);
3379 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3384 cs.setConservation(null);
3387 cs.setConsensus(viewport.getSequenceConsensusHash());
3390 viewport.setGlobalColourScheme(cs);
3392 if (viewport.getColourAppliesToAllGroups())
3395 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3403 if (cs instanceof ClustalxColourScheme)
3405 sg.cs = new ClustalxColourScheme(sg,
3406 viewport.getHiddenRepSequences());
3408 else if (cs instanceof UserColourScheme)
3410 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3416 sg.cs = cs.getClass().newInstance();
3417 } catch (Exception ex)
3422 if (viewport.getAbovePIDThreshold()
3423 || cs instanceof PIDColourScheme
3424 || cs instanceof Blosum62ColourScheme)
3426 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3428 sg.cs.setConsensus(AAFrequency.calculate(
3429 sg.getSequences(viewport.getHiddenRepSequences()),
3430 sg.getStartRes(), sg.getEndRes() + 1));
3434 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3437 if (viewport.getConservationSelected())
3439 Conservation c = new Conservation("Group",
3440 ResidueProperties.propHash, 3, sg.getSequences(viewport
3441 .getHiddenRepSequences()), sg.getStartRes(),
3442 sg.getEndRes() + 1);
3444 c.verdict(false, viewport.getConsPercGaps());
3445 sg.cs.setConservation(c);
3449 sg.cs.setConservation(null);
3454 if (alignPanel.getOverviewPanel() != null)
3456 alignPanel.getOverviewPanel().updateOverviewImage();
3459 alignPanel.paintAlignment(true);
3469 protected void modifyPID_actionPerformed(ActionEvent e)
3471 if (viewport.getAbovePIDThreshold()
3472 && viewport.getGlobalColourScheme() != null)
3474 SliderPanel.setPIDSliderSource(alignPanel,
3475 viewport.getGlobalColourScheme(), "Background");
3476 SliderPanel.showPIDSlider();
3487 protected void modifyConservation_actionPerformed(ActionEvent e)
3489 if (viewport.getConservationSelected()
3490 && viewport.getGlobalColourScheme() != null)
3492 SliderPanel.setConservationSlider(alignPanel,
3493 viewport.getGlobalColourScheme(), "Background");
3494 SliderPanel.showConservationSlider();
3505 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3507 viewport.setConservationSelected(conservationMenuItem.isSelected());
3509 viewport.setAbovePIDThreshold(false);
3510 abovePIDThreshold.setSelected(false);
3512 changeColour(viewport.getGlobalColourScheme());
3514 modifyConservation_actionPerformed(null);
3524 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3526 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3528 conservationMenuItem.setSelected(false);
3529 viewport.setConservationSelected(false);
3531 changeColour(viewport.getGlobalColourScheme());
3533 modifyPID_actionPerformed(null);
3543 public void userDefinedColour_actionPerformed(ActionEvent e)
3545 if (e.getActionCommand().equals(
3546 MessageManager.getString("action.user_defined")))
3548 new UserDefinedColours(alignPanel, null);
3552 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3553 .getUserColourSchemes().get(e.getActionCommand());
3559 public void updateUserColourMenu()
3562 Component[] menuItems = colourMenu.getMenuComponents();
3563 int i, iSize = menuItems.length;
3564 for (i = 0; i < iSize; i++)
3566 if (menuItems[i].getName() != null
3567 && menuItems[i].getName().equals("USER_DEFINED"))
3569 colourMenu.remove(menuItems[i]);
3573 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3575 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3576 .getUserColourSchemes().keys();
3578 while (userColours.hasMoreElements())
3580 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3581 userColours.nextElement().toString());
3582 radioItem.setName("USER_DEFINED");
3583 radioItem.addMouseListener(new MouseAdapter()
3586 public void mousePressed(MouseEvent evt)
3588 if (evt.isControlDown()
3589 || SwingUtilities.isRightMouseButton(evt))
3591 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3593 int option = JOptionPane.showInternalConfirmDialog(
3594 jalview.gui.Desktop.desktop,
3596 .getString("label.remove_from_default_list"),
3598 .getString("label.remove_user_defined_colour"),
3599 JOptionPane.YES_NO_OPTION);
3600 if (option == JOptionPane.YES_OPTION)
3602 jalview.gui.UserDefinedColours
3603 .removeColourFromDefaults(radioItem.getText());
3604 colourMenu.remove(radioItem);
3608 radioItem.addActionListener(new ActionListener()
3611 public void actionPerformed(ActionEvent evt)
3613 userDefinedColour_actionPerformed(evt);
3620 radioItem.addActionListener(new ActionListener()
3623 public void actionPerformed(ActionEvent evt)
3625 userDefinedColour_actionPerformed(evt);
3629 colourMenu.insert(radioItem, 15);
3630 colours.add(radioItem);
3642 public void PIDColour_actionPerformed(ActionEvent e)
3644 changeColour(new PIDColourScheme());
3654 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3656 changeColour(new Blosum62ColourScheme());
3666 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3668 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3669 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3670 .getAlignment().getSequenceAt(0), null);
3671 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3672 viewport.getAlignment()));
3673 alignPanel.paintAlignment(true);
3683 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3685 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3686 AlignmentSorter.sortByID(viewport.getAlignment());
3687 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3688 viewport.getAlignment()));
3689 alignPanel.paintAlignment(true);
3699 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3701 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3702 AlignmentSorter.sortByLength(viewport.getAlignment());
3703 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3704 viewport.getAlignment()));
3705 alignPanel.paintAlignment(true);
3715 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3717 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3718 AlignmentSorter.sortByGroup(viewport.getAlignment());
3719 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3720 viewport.getAlignment()));
3722 alignPanel.paintAlignment(true);
3732 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3734 new RedundancyPanel(alignPanel, this);
3744 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3746 if ((viewport.getSelectionGroup() == null)
3747 || (viewport.getSelectionGroup().getSize() < 2))
3749 JOptionPane.showInternalMessageDialog(this, MessageManager
3750 .getString("label.you_must_select_least_two_sequences"),
3751 MessageManager.getString("label.invalid_selection"),
3752 JOptionPane.WARNING_MESSAGE);
3756 JInternalFrame frame = new JInternalFrame();
3757 frame.setContentPane(new PairwiseAlignPanel(viewport));
3758 Desktop.addInternalFrame(frame,
3759 MessageManager.getString("action.pairwise_alignment"), 600,
3771 public void PCAMenuItem_actionPerformed(ActionEvent e)
3773 if (((viewport.getSelectionGroup() != null)
3774 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3775 .getSelectionGroup().getSize() > 0))
3776 || (viewport.getAlignment().getHeight() < 4))
3779 .showInternalMessageDialog(
3782 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3784 .getString("label.sequence_selection_insufficient"),
3785 JOptionPane.WARNING_MESSAGE);
3790 new PCAPanel(alignPanel);
3794 public void autoCalculate_actionPerformed(ActionEvent e)
3796 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3797 if (viewport.autoCalculateConsensus)
3799 viewport.firePropertyChange("alignment", null, viewport
3800 .getAlignment().getSequences());
3805 public void sortByTreeOption_actionPerformed(ActionEvent e)
3807 viewport.sortByTree = sortByTree.isSelected();
3811 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3813 viewport.followSelection = listenToViewSelections.isSelected();
3823 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3825 NewTreePanel("AV", "PID", "Average distance tree using PID");
3835 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3837 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3847 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3849 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3859 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3861 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3874 void NewTreePanel(String type, String pwType, String title)
3878 if (viewport.getSelectionGroup() != null
3879 && viewport.getSelectionGroup().getSize() > 0)
3881 if (viewport.getSelectionGroup().getSize() < 3)
3887 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3889 .getString("label.not_enough_sequences"),
3890 JOptionPane.WARNING_MESSAGE);
3894 SequenceGroup sg = viewport.getSelectionGroup();
3896 /* Decide if the selection is a column region */
3897 for (SequenceI _s : sg.getSequences())
3899 if (_s.getLength() < sg.getEndRes())
3905 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3907 .getString("label.sequences_selection_not_aligned"),
3908 JOptionPane.WARNING_MESSAGE);
3914 title = title + " on region";
3915 tp = new TreePanel(alignPanel, type, pwType);
3919 // are the visible sequences aligned?
3920 if (!viewport.getAlignment().isAligned(false))
3926 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3928 .getString("label.sequences_not_aligned"),
3929 JOptionPane.WARNING_MESSAGE);
3934 if (viewport.getAlignment().getHeight() < 2)
3939 tp = new TreePanel(alignPanel, type, pwType);
3944 if (viewport.viewName != null)
3946 title += viewport.viewName + " of ";
3949 title += this.title;
3951 Desktop.addInternalFrame(tp, title, 600, 500);
3962 public void addSortByOrderMenuItem(String title,
3963 final AlignmentOrder order)
3965 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
3967 item.addActionListener(new java.awt.event.ActionListener()
3970 public void actionPerformed(ActionEvent e)
3972 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3974 // TODO: JBPNote - have to map order entries to curent SequenceI
3976 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3978 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3981 alignPanel.paintAlignment(true);
3987 * Add a new sort by annotation score menu item
3990 * the menu to add the option to
3992 * the label used to retrieve scores for each sequence on the
3995 public void addSortByAnnotScoreMenuItem(JMenu sort,
3996 final String scoreLabel)
3998 final JMenuItem item = new JMenuItem(scoreLabel);
4000 item.addActionListener(new java.awt.event.ActionListener()
4003 public void actionPerformed(ActionEvent e)
4005 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4006 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4007 viewport.getAlignment());// ,viewport.getSelectionGroup());
4008 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4009 viewport.getAlignment()));
4010 alignPanel.paintAlignment(true);
4016 * last hash for alignment's annotation array - used to minimise cost of
4019 protected int _annotationScoreVectorHash;
4022 * search the alignment and rebuild the sort by annotation score submenu the
4023 * last alignment annotation vector hash is stored to minimize cost of
4024 * rebuilding in subsequence calls.
4028 public void buildSortByAnnotationScoresMenu()
4030 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4035 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4037 sortByAnnotScore.removeAll();
4038 // almost certainly a quicker way to do this - but we keep it simple
4039 Hashtable scoreSorts = new Hashtable();
4040 AlignmentAnnotation aann[];
4041 for (SequenceI sqa : viewport.getAlignment().getSequences())
4043 aann = sqa.getAnnotation();
4044 for (int i = 0; aann != null && i < aann.length; i++)
4046 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4048 scoreSorts.put(aann[i].label, aann[i].label);
4052 Enumeration labels = scoreSorts.keys();
4053 while (labels.hasMoreElements())
4055 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4056 (String) labels.nextElement());
4058 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4061 _annotationScoreVectorHash = viewport.getAlignment()
4062 .getAlignmentAnnotation().hashCode();
4067 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4068 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4069 * call. Listeners are added to remove the menu item when the treePanel is
4070 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4074 * Displayed tree window.
4076 * SortBy menu item title.
4079 public void buildTreeMenu()
4081 calculateTree.removeAll();
4082 // build the calculate menu
4084 for (final String type : new String[]
4087 String treecalcnm = MessageManager.getString("label.tree_calc_"
4088 + type.toLowerCase());
4089 for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4091 JMenuItem tm = new JMenuItem();
4092 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4093 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4095 String smn = MessageManager.getStringOrReturn(
4096 "label.score_model_", sm.getName());
4097 final String title = MessageManager.formatMessage(
4098 "label.treecalc_title", treecalcnm, smn);
4099 tm.setText(title);//
4100 tm.addActionListener(new java.awt.event.ActionListener()
4103 public void actionPerformed(ActionEvent e)
4105 NewTreePanel(type, (String) pwtype, title);
4108 calculateTree.add(tm);
4113 sortByTreeMenu.removeAll();
4115 Vector comps = (Vector) PaintRefresher.components.get(viewport
4116 .getSequenceSetId());
4117 Vector treePanels = new Vector();
4118 int i, iSize = comps.size();
4119 for (i = 0; i < iSize; i++)
4121 if (comps.elementAt(i) instanceof TreePanel)
4123 treePanels.add(comps.elementAt(i));
4127 iSize = treePanels.size();
4131 sortByTreeMenu.setVisible(false);
4135 sortByTreeMenu.setVisible(true);
4137 for (i = 0; i < treePanels.size(); i++)
4139 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4140 final JMenuItem item = new JMenuItem(tp.getTitle());
4141 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4142 item.addActionListener(new java.awt.event.ActionListener()
4145 public void actionPerformed(ActionEvent e)
4147 tp.sortByTree_actionPerformed(null);
4148 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4153 sortByTreeMenu.add(item);
4157 public boolean sortBy(AlignmentOrder alorder, String undoname)
4159 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4160 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4161 if (undoname != null)
4163 addHistoryItem(new OrderCommand(undoname, oldOrder,
4164 viewport.getAlignment()));
4166 alignPanel.paintAlignment(true);
4171 * Work out whether the whole set of sequences or just the selected set will
4172 * be submitted for multiple alignment.
4175 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4177 // Now, check we have enough sequences
4178 AlignmentView msa = null;
4180 if ((viewport.getSelectionGroup() != null)
4181 && (viewport.getSelectionGroup().getSize() > 1))
4183 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4184 // some common interface!
4186 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4187 * SequenceI[sz = seqs.getSize(false)];
4189 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4190 * seqs.getSequenceAt(i); }
4192 msa = viewport.getAlignmentView(true);
4197 * Vector seqs = viewport.getAlignment().getSequences();
4199 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
4201 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
4202 * seqs.elementAt(i); } }
4204 msa = viewport.getAlignmentView(false);
4210 * Decides what is submitted to a secondary structure prediction service: the
4211 * first sequence in the alignment, or in the current selection, or, if the
4212 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4213 * region or the whole alignment. (where the first sequence in the set is the
4214 * one that the prediction will be for).
4216 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4218 AlignmentView seqs = null;
4220 if ((viewport.getSelectionGroup() != null)
4221 && (viewport.getSelectionGroup().getSize() > 0))
4223 seqs = viewport.getAlignmentView(true);
4227 seqs = viewport.getAlignmentView(false);
4229 // limit sequences - JBPNote in future - could spawn multiple prediction
4231 // TODO: viewport.getAlignment().isAligned is a global state - the local
4232 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4233 if (!viewport.getAlignment().isAligned(false))
4235 seqs.setSequences(new SeqCigar[]
4236 { seqs.getSequences()[0] });
4237 // TODO: if seqs.getSequences().length>1 then should really have warned
4251 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4253 // Pick the tree file
4254 JalviewFileChooser chooser = new JalviewFileChooser(
4255 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4256 chooser.setFileView(new JalviewFileView());
4257 chooser.setDialogTitle(MessageManager
4258 .getString("label.select_newick_like_tree_file"));
4259 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4261 int value = chooser.showOpenDialog(null);
4263 if (value == JalviewFileChooser.APPROVE_OPTION)
4265 String choice = chooser.getSelectedFile().getPath();
4266 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4267 jalview.io.NewickFile fin = null;
4270 fin = new jalview.io.NewickFile(choice, "File");
4271 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4272 } catch (Exception ex)
4279 .getString("label.problem_reading_tree_file"),
4280 JOptionPane.WARNING_MESSAGE);
4281 ex.printStackTrace();
4283 if (fin != null && fin.hasWarningMessage())
4285 JOptionPane.showMessageDialog(Desktop.desktop, fin
4286 .getWarningMessage(), MessageManager
4287 .getString("label.possible_problem_with_tree_file"),
4288 JOptionPane.WARNING_MESSAGE);
4294 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4296 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4299 public TreePanel ShowNewickTree(NewickFile nf, String title)
4301 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4304 public TreePanel ShowNewickTree(NewickFile nf, String title,
4305 AlignmentView input)
4307 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4310 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4311 int h, int x, int y)
4313 return ShowNewickTree(nf, title, null, w, h, x, y);
4317 * Add a treeviewer for the tree extracted from a newick file object to the
4318 * current alignment view
4325 * Associated alignment input data (or null)
4334 * @return TreePanel handle
4336 public TreePanel ShowNewickTree(NewickFile nf, String title,
4337 AlignmentView input, int w, int h, int x, int y)
4339 TreePanel tp = null;
4345 if (nf.getTree() != null)
4347 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4353 tp.setLocation(x, y);
4356 Desktop.addInternalFrame(tp, title, w, h);
4358 } catch (Exception ex)
4360 ex.printStackTrace();
4366 private boolean buildingMenu = false;
4369 * Generates menu items and listener event actions for web service clients
4372 public void BuildWebServiceMenu()
4374 while (buildingMenu)
4378 System.err.println("Waiting for building menu to finish.");
4380 } catch (Exception e)
4385 final AlignFrame me = this;
4386 buildingMenu = true;
4387 new Thread(new Runnable()
4392 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4395 System.err.println("Building ws menu again "
4396 + Thread.currentThread());
4397 // TODO: add support for context dependent disabling of services based
4399 // alignment and current selection
4400 // TODO: add additional serviceHandle parameter to specify abstract
4402 // class independently of AbstractName
4403 // TODO: add in rediscovery GUI function to restart discoverer
4404 // TODO: group services by location as well as function and/or
4406 // object broker mechanism.
4407 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4408 final IProgressIndicator af = me;
4409 final JMenu msawsmenu = new JMenu("Alignment");
4410 final JMenu secstrmenu = new JMenu(
4411 "Secondary Structure Prediction");
4412 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4413 final JMenu analymenu = new JMenu("Analysis");
4414 final JMenu dismenu = new JMenu("Protein Disorder");
4415 // final JMenu msawsmenu = new
4416 // JMenu(MessageManager.getString("label.alignment"));
4417 // final JMenu secstrmenu = new
4418 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4419 // final JMenu seqsrchmenu = new
4420 // JMenu(MessageManager.getString("label.sequence_database_search"));
4421 // final JMenu analymenu = new
4422 // JMenu(MessageManager.getString("label.analysis"));
4423 // final JMenu dismenu = new
4424 // JMenu(MessageManager.getString("label.protein_disorder"));
4425 // JAL-940 - only show secondary structure prediction services from
4426 // the legacy server
4427 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4429 Discoverer.services != null && (Discoverer.services.size() > 0))
4431 // TODO: refactor to allow list of AbstractName/Handler bindings to
4433 // stored or retrieved from elsewhere
4434 // No MSAWS used any more:
4435 // Vector msaws = null; // (Vector)
4436 // Discoverer.services.get("MsaWS");
4437 Vector secstrpr = (Vector) Discoverer.services
4439 if (secstrpr != null)
4441 // Add any secondary structure prediction services
4442 for (int i = 0, j = secstrpr.size(); i < j; i++)
4444 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4446 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4447 .getServiceClient(sh);
4448 int p = secstrmenu.getItemCount();
4449 impl.attachWSMenuEntry(secstrmenu, me);
4450 int q = secstrmenu.getItemCount();
4451 for (int litm = p; litm < q; litm++)
4453 legacyItems.add(secstrmenu.getItem(litm));
4459 // Add all submenus in the order they should appear on the web
4461 wsmenu.add(msawsmenu);
4462 wsmenu.add(secstrmenu);
4463 wsmenu.add(dismenu);
4464 wsmenu.add(analymenu);
4465 // No search services yet
4466 // wsmenu.add(seqsrchmenu);
4468 javax.swing.SwingUtilities.invokeLater(new Runnable()
4475 webService.removeAll();
4476 // first, add discovered services onto the webservices menu
4477 if (wsmenu.size() > 0)
4479 for (int i = 0, j = wsmenu.size(); i < j; i++)
4481 webService.add(wsmenu.get(i));
4486 webService.add(me.webServiceNoServices);
4488 // TODO: move into separate menu builder class.
4489 boolean new_sspred = false;
4490 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4492 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4493 if (jws2servs != null)
4495 if (jws2servs.hasServices())
4497 jws2servs.attachWSMenuEntry(webService, me);
4498 for (Jws2Instance sv : jws2servs.getServices())
4500 if (sv.description.toLowerCase().contains("jpred"))
4502 for (JMenuItem jmi : legacyItems)
4504 jmi.setVisible(false);
4510 if (jws2servs.isRunning())
4512 JMenuItem tm = new JMenuItem(
4513 "Still discovering JABA Services");
4514 tm.setEnabled(false);
4519 build_urlServiceMenu(me.webService);
4520 build_fetchdbmenu(webService);
4521 for (JMenu item : wsmenu)
4523 if (item.getItemCount() == 0)
4525 item.setEnabled(false);
4529 item.setEnabled(true);
4532 } catch (Exception e)
4535 .debug("Exception during web service menu building process.",
4541 } catch (Exception e)
4546 buildingMenu = false;
4553 * construct any groupURL type service menu entries.
4557 private void build_urlServiceMenu(JMenu webService)
4559 // TODO: remove this code when 2.7 is released
4560 // DEBUG - alignmentView
4562 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4563 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4565 * @Override public void actionPerformed(ActionEvent e) {
4566 * jalview.datamodel.AlignmentView
4567 * .testSelectionViews(af.viewport.getAlignment(),
4568 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4570 * }); webService.add(testAlView);
4572 // TODO: refactor to RestClient discoverer and merge menu entries for
4573 // rest-style services with other types of analysis/calculation service
4574 // SHmmr test client - still being implemented.
4575 // DEBUG - alignmentView
4577 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4580 client.attachWSMenuEntry(
4581 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4587 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4588 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4589 * getProperty("LAST_DIRECTORY"));
4591 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4592 * to Vamsas file"); chooser.setToolTipText("Export");
4594 * int value = chooser.showSaveDialog(this);
4596 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4597 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4598 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4599 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4602 * prototype of an automatically enabled/disabled analysis function
4605 protected void setShowProductsEnabled()
4607 SequenceI[] selection = viewport.getSequenceSelection();
4608 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4609 viewport.getAlignment().getDataset()))
4611 showProducts.setEnabled(true);
4616 showProducts.setEnabled(false);
4621 * search selection for sequence xRef products and build the show products
4626 * @return true if showProducts menu should be enabled.
4628 public boolean canShowProducts(SequenceI[] selection,
4629 boolean isRegionSelection, Alignment dataset)
4631 boolean showp = false;
4634 showProducts.removeAll();
4635 final boolean dna = viewport.getAlignment().isNucleotide();
4636 final Alignment ds = dataset;
4637 String[] ptypes = (selection == null || selection.length == 0) ? null
4638 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4640 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4641 // selection, dataset, true);
4642 final SequenceI[] sel = selection;
4643 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4646 final boolean isRegSel = isRegionSelection;
4647 final AlignFrame af = this;
4648 final String source = ptypes[t];
4649 JMenuItem xtype = new JMenuItem(ptypes[t]);
4650 xtype.addActionListener(new ActionListener()
4654 public void actionPerformed(ActionEvent e)
4656 // TODO: new thread for this call with vis-delay
4657 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4658 isRegSel, dna, source);
4662 showProducts.add(xtype);
4664 showProducts.setVisible(showp);
4665 showProducts.setEnabled(showp);
4666 } catch (Exception e)
4668 jalview.bin.Cache.log
4669 .warn("canTranslate threw an exception - please report to help@jalview.org",
4676 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4677 boolean isRegSel, boolean dna, String source)
4679 final boolean fisRegSel = isRegSel;
4680 final boolean fdna = dna;
4681 final String fsrc = source;
4682 final AlignFrame ths = this;
4683 final SequenceI[] fsel = sel;
4684 Runnable foo = new Runnable()
4690 final long sttime = System.currentTimeMillis();
4691 ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
4694 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4698 Alignment prods = CrossRef
4699 .findXrefSequences(fsel, fdna, fsrc, ds);
4702 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4703 for (int s = 0; s < sprods.length; s++)
4705 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4706 if (ds.getSequences() == null
4707 || !ds.getSequences().contains(
4708 sprods[s].getDatasetSequence()))
4710 ds.addSequence(sprods[s].getDatasetSequence());
4712 sprods[s].updatePDBIds();
4714 Alignment al = new Alignment(sprods);
4715 AlignedCodonFrame[] cf = prods.getCodonFrames();
4717 for (int s = 0; cf != null && s < cf.length; s++)
4719 al.addCodonFrame(cf[s]);
4722 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4724 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4725 + " for " + ((fisRegSel) ? "selected region of " : "")
4727 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4732 System.err.println("No Sequences generated for xRef type "
4735 } catch (Exception e)
4737 jalview.bin.Cache.log.error(
4738 "Exception when finding crossreferences", e);
4739 } catch (OutOfMemoryError e)
4741 new OOMWarning("whilst fetching crossreferences", e);
4744 jalview.bin.Cache.log.error("Error when finding crossreferences",
4747 ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
4752 Thread frunner = new Thread(foo);
4756 public boolean canShowTranslationProducts(SequenceI[] selection,
4757 AlignmentI alignment)
4762 return (jalview.analysis.Dna.canTranslate(selection,
4763 viewport.getViewAsVisibleContigs(true)));
4764 } catch (Exception e)
4766 jalview.bin.Cache.log
4767 .warn("canTranslate threw an exception - please report to help@jalview.org",
4774 public void showProducts_actionPerformed(ActionEvent e)
4776 // /////////////////////////////
4777 // Collect Data to be translated/transferred
4779 SequenceI[] selection = viewport.getSequenceSelection();
4780 AlignmentI al = null;
4783 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4784 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4785 viewport.getAlignment().getDataset());
4786 } catch (Exception ex)
4789 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4797 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4798 MessageManager.getString("label.translation_failed"),
4799 JOptionPane.WARNING_MESSAGE);
4803 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4804 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4805 "label.translation_of_params", new String[]
4806 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4811 public void showTranslation_actionPerformed(ActionEvent e)
4813 // /////////////////////////////
4814 // Collect Data to be translated/transferred
4816 SequenceI[] selection = viewport.getSequenceSelection();
4817 String[] seqstring = viewport.getViewAsString(true);
4818 AlignmentI al = null;
4821 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4822 viewport.getViewAsVisibleContigs(true), viewport
4823 .getGapCharacter(), viewport.getAlignment()
4824 .getAlignmentAnnotation(), viewport.getAlignment()
4825 .getWidth(), viewport.getAlignment().getDataset());
4826 } catch (Exception ex)
4829 jalview.bin.Cache.log.error(
4830 "Exception during translation. Please report this !", ex);
4835 .getString("label.error_when_translating_sequences_submit_bug_report"),
4837 .getString("label.implementation_error")
4839 .getString("translation_failed"),
4840 JOptionPane.ERROR_MESSAGE);
4849 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4850 MessageManager.getString("label.translation_failed"),
4851 JOptionPane.WARNING_MESSAGE);
4855 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4856 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4857 "label.translation_of_params", new String[]
4858 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4863 * Try to load a features file onto the alignment.
4866 * contents or path to retrieve file
4868 * access mode of file (see jalview.io.AlignFile)
4869 * @return true if features file was parsed corectly.
4871 public boolean parseFeaturesFile(String file, String type)
4873 boolean featuresFile = false;
4876 featuresFile = new FeaturesFile(file, type).parse(viewport
4877 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4878 .getFeatureRenderer().featureColours, false,
4879 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4880 } catch (Exception ex)
4882 ex.printStackTrace();
4887 viewport.showSequenceFeatures = true;
4888 showSeqFeatures.setSelected(true);
4889 if (alignPanel.seqPanel.seqCanvas.fr != null)
4891 // update the min/max ranges where necessary
4892 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4894 if (featureSettings != null)
4896 featureSettings.setTableData();
4898 alignPanel.paintAlignment(true);
4901 return featuresFile;
4905 public void dragEnter(DropTargetDragEvent evt)
4910 public void dragExit(DropTargetEvent evt)
4915 public void dragOver(DropTargetDragEvent evt)
4920 public void dropActionChanged(DropTargetDragEvent evt)
4925 public void drop(DropTargetDropEvent evt)
4927 Transferable t = evt.getTransferable();
4928 java.util.List files = null;
4932 DataFlavor uriListFlavor = new DataFlavor(
4933 "text/uri-list;class=java.lang.String");
4934 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4936 // Works on Windows and MacOSX
4937 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4938 files = (java.util.List) t
4939 .getTransferData(DataFlavor.javaFileListFlavor);
4941 else if (t.isDataFlavorSupported(uriListFlavor))
4943 // This is used by Unix drag system
4944 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4945 String data = (String) t.getTransferData(uriListFlavor);
4946 files = new java.util.ArrayList(1);
4947 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4948 data, "\r\n"); st.hasMoreTokens();)
4950 String s = st.nextToken();
4951 if (s.startsWith("#"))
4953 // the line is a comment (as per the RFC 2483)
4957 java.net.URI uri = new java.net.URI(s);
4958 // check to see if we can handle this kind of URI
4959 if (uri.getScheme().toLowerCase().startsWith("http"))
4961 files.add(uri.toString());
4965 // otherwise preserve old behaviour: catch all for file objects
4966 java.io.File file = new java.io.File(uri);
4967 files.add(file.toString());
4971 } catch (Exception e)
4973 e.printStackTrace();
4979 // check to see if any of these files have names matching sequences in
4981 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4982 .getAlignment().getSequencesArray());
4984 * Object[] { String,SequenceI}
4986 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4987 ArrayList<String> filesnotmatched = new ArrayList<String>();
4988 for (int i = 0; i < files.size(); i++)
4990 String file = files.get(i).toString();
4992 String protocol = FormatAdapter.checkProtocol(file);
4993 if (protocol == jalview.io.FormatAdapter.FILE)
4995 File fl = new File(file);
4996 pdbfn = fl.getName();
4998 else if (protocol == jalview.io.FormatAdapter.URL)
5000 URL url = new URL(file);
5001 pdbfn = url.getFile();
5003 if (pdbfn.length() > 0)
5005 // attempt to find a match in the alignment
5006 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5007 int l = 0, c = pdbfn.indexOf(".");
5008 while (mtch == null && c != -1)
5013 } while ((c = pdbfn.indexOf(".", l)) > l);
5016 pdbfn = pdbfn.substring(0, l);
5018 mtch = idm.findAllIdMatches(pdbfn);
5025 type = new IdentifyFile().Identify(file, protocol);
5026 } catch (Exception ex)
5032 if (type.equalsIgnoreCase("PDB"))
5034 filesmatched.add(new Object[]
5035 { file, protocol, mtch });
5040 // File wasn't named like one of the sequences or wasn't a PDB file.
5041 filesnotmatched.add(file);
5045 if (filesmatched.size() > 0)
5047 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5053 "label.automatically_associate_pdb_files_with_sequences_same_name",
5060 .getString("label.automatically_associate_pdb_files_by_name"),
5061 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5064 for (Object[] fm : filesmatched)
5066 // try and associate
5067 // TODO: may want to set a standard ID naming formalism for
5068 // associating PDB files which have no IDs.
5069 for (SequenceI toassoc : (SequenceI[]) fm[2])
5071 PDBEntry pe = new AssociatePdbFileWithSeq()
5072 .associatePdbWithSeq((String) fm[0],
5073 (String) fm[1], toassoc, false,
5077 System.err.println("Associated file : "
5078 + ((String) fm[0]) + " with "
5079 + toassoc.getDisplayId(true));
5083 alignPanel.paintAlignment(true);
5087 if (filesnotmatched.size() > 0)
5090 && (Cache.getDefault(
5091 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5094 "<html>"+MessageManager
5096 "label.ignore_unmatched_dropped_files_info",
5101 .toString() })+"</html>",
5103 .getString("label.ignore_unmatched_dropped_files"),
5104 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5108 for (String fn : filesnotmatched)
5110 loadJalviewDataFile(fn, null, null, null);
5114 } catch (Exception ex)
5116 ex.printStackTrace();
5122 * Attempt to load a "dropped" file or URL string: First by testing whether
5123 * it's and Annotation file, then a JNet file, and finally a features file. If
5124 * all are false then the user may have dropped an alignment file onto this
5128 * either a filename or a URL string.
5130 public void loadJalviewDataFile(String file, String protocol,
5131 String format, SequenceI assocSeq)
5135 if (protocol == null)
5137 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5139 // if the file isn't identified, or not positively identified as some
5140 // other filetype (PFAM is default unidentified alignment file type) then
5141 // try to parse as annotation.
5142 boolean isAnnotation = (format == null || format
5143 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5144 .readAnnotationFile(viewport.getAlignment(), file, protocol)
5149 // first see if its a T-COFFEE score file
5150 TCoffeeScoreFile tcf = null;
5153 tcf = new TCoffeeScoreFile(file, protocol);
5156 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5158 tcoffeeColour.setEnabled(true);
5159 tcoffeeColour.setSelected(true);
5160 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5161 isAnnotation = true;
5163 .setText(MessageManager
5164 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5168 // some problem - if no warning its probable that the ID matching
5169 // process didn't work
5173 tcf.getWarningMessage() == null ? MessageManager
5174 .getString("label.check_file_matches_sequence_ids_alignment")
5175 : tcf.getWarningMessage(),
5177 .getString("label.problem_reading_tcoffee_score_file"),
5178 JOptionPane.WARNING_MESSAGE);
5185 } catch (Exception x)
5188 .debug("Exception when processing data source as T-COFFEE score file",
5194 // try to see if its a JNet 'concise' style annotation file *before*
5196 // try to parse it as a features file
5199 format = new IdentifyFile().Identify(file, protocol);
5201 if (format.equalsIgnoreCase("JnetFile"))
5203 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5205 new JnetAnnotationMaker().add_annotation(predictions,
5206 viewport.getAlignment(), 0, false);
5207 isAnnotation = true;
5212 * if (format.equalsIgnoreCase("PDB")) {
5214 * String pdbfn = ""; // try to match up filename with sequence id
5215 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5216 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5217 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5218 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5219 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5220 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5221 * // attempt to find a match in the alignment SequenceI mtch =
5222 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5223 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5224 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5225 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5226 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5227 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5228 * { System.err.println("Associated file : " + file + " with " +
5229 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5230 * TODO: maybe need to load as normal otherwise return; } }
5232 // try to parse it as a features file
5233 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5234 // if it wasn't a features file then we just treat it as a general
5235 // alignment file to load into the current view.
5238 new FileLoader().LoadFile(viewport, file, protocol, format);
5242 alignPanel.paintAlignment(true);
5250 alignPanel.adjustAnnotationHeight();
5251 viewport.updateSequenceIdColours();
5252 buildSortByAnnotationScoresMenu();
5253 alignPanel.paintAlignment(true);
5255 } catch (Exception ex)
5257 ex.printStackTrace();
5258 } catch (OutOfMemoryError oom)
5263 } catch (Exception x)
5269 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5270 : "using " + protocol + " from " + file)
5272 + (format != null ? "(parsing as '" + format
5273 + "' file)" : ""), oom, Desktop.desktop);
5278 public void tabSelectionChanged(int index)
5282 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5283 viewport = alignPanel.av;
5284 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5285 setMenusFromViewport(viewport);
5290 public void tabbedPane_mousePressed(MouseEvent e)
5292 if (SwingUtilities.isRightMouseButton(e))
5294 String reply = JOptionPane.showInternalInputDialog(this,
5295 MessageManager.getString("label.enter_view_name"),
5296 MessageManager.getString("label.enter_view_name"),
5297 JOptionPane.QUESTION_MESSAGE);
5301 viewport.viewName = reply;
5302 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5307 public AlignViewport getCurrentView()
5313 * Open the dialog for regex description parsing.
5316 protected void extractScores_actionPerformed(ActionEvent e)
5318 ParseProperties pp = new jalview.analysis.ParseProperties(
5319 viewport.getAlignment());
5320 // TODO: verify regex and introduce GUI dialog for version 2.5
5321 // if (pp.getScoresFromDescription("col", "score column ",
5322 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5324 if (pp.getScoresFromDescription("description column",
5325 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5327 buildSortByAnnotationScoresMenu();
5335 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5339 protected void showDbRefs_actionPerformed(ActionEvent e)
5341 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5347 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5351 protected void showNpFeats_actionPerformed(ActionEvent e)
5353 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5357 * find the viewport amongst the tabs in this alignment frame and close that
5362 public boolean closeView(AlignViewport av)
5366 this.closeMenuItem_actionPerformed(false);
5369 Component[] comp = tabbedPane.getComponents();
5370 for (int i = 0; comp != null && i < comp.length; i++)
5372 if (comp[i] instanceof AlignmentPanel)
5374 if (((AlignmentPanel) comp[i]).av == av)
5377 closeView((AlignmentPanel) comp[i]);
5385 protected void build_fetchdbmenu(JMenu webService)
5387 // Temporary hack - DBRef Fetcher always top level ws entry.
5388 // TODO We probably want to store a sequence database checklist in
5389 // preferences and have checkboxes.. rather than individual sources selected
5391 final JMenu rfetch = new JMenu(
5392 MessageManager.getString("action.fetch_db_references"));
5393 rfetch.setToolTipText(MessageManager
5394 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5395 webService.add(rfetch);
5397 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5398 MessageManager.getString("option.trim_retrieved_seqs"));
5399 trimrs.setToolTipText(MessageManager
5400 .getString("label.trim_retrieved_sequences"));
5401 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5402 trimrs.addActionListener(new ActionListener()
5405 public void actionPerformed(ActionEvent e)
5407 trimrs.setSelected(trimrs.isSelected());
5408 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5409 Boolean.valueOf(trimrs.isSelected()).toString());
5413 JMenuItem fetchr = new JMenuItem(
5414 MessageManager.getString("label.standard_databases"));
5415 fetchr.setToolTipText(MessageManager
5416 .getString("label.fetch_embl_uniprot"));
5417 fetchr.addActionListener(new ActionListener()
5421 public void actionPerformed(ActionEvent e)
5423 new Thread(new Runnable()
5429 new jalview.ws.DBRefFetcher(alignPanel.av
5430 .getSequenceSelection(), alignPanel.alignFrame)
5431 .fetchDBRefs(false);
5439 final AlignFrame me = this;
5440 new Thread(new Runnable()
5445 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5446 .getSequenceFetcherSingleton(me);
5447 javax.swing.SwingUtilities.invokeLater(new Runnable()
5452 String[] dbclasses = sf.getOrderedSupportedSources();
5453 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5454 // jalview.util.QuickSort.sort(otherdb, otherdb);
5455 List<DbSourceProxy> otherdb;
5456 JMenu dfetch = new JMenu();
5457 JMenu ifetch = new JMenu();
5458 JMenuItem fetchr = null;
5459 int comp = 0, icomp = 0, mcomp = 15;
5460 String mname = null;
5462 for (String dbclass : dbclasses)
5464 otherdb = sf.getSourceProxy(dbclass);
5465 // add a single entry for this class, or submenu allowing 'fetch
5467 if (otherdb == null || otherdb.size() < 1)
5471 // List<DbSourceProxy> dbs=otherdb;
5472 // otherdb=new ArrayList<DbSourceProxy>();
5473 // for (DbSourceProxy db:dbs)
5475 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5479 mname = "From " + dbclass;
5481 if (otherdb.size() == 1)
5483 final DbSourceProxy[] dassource = otherdb
5484 .toArray(new DbSourceProxy[0]);
5485 DbSourceProxy src = otherdb.get(0);
5486 fetchr = new JMenuItem(src.getDbSource());
5487 fetchr.addActionListener(new ActionListener()
5491 public void actionPerformed(ActionEvent e)
5493 new Thread(new Runnable()
5499 new jalview.ws.DBRefFetcher(alignPanel.av
5500 .getSequenceSelection(),
5501 alignPanel.alignFrame, dassource)
5502 .fetchDBRefs(false);
5508 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
5514 final DbSourceProxy[] dassource = otherdb
5515 .toArray(new DbSourceProxy[0]);
5517 DbSourceProxy src = otherdb.get(0);
5518 fetchr = new JMenuItem(MessageManager.formatMessage(
5519 "label.fetch_all_param", new String[]
5520 { src.getDbSource() }));
5521 fetchr.addActionListener(new ActionListener()
5524 public void actionPerformed(ActionEvent e)
5526 new Thread(new Runnable()
5532 new jalview.ws.DBRefFetcher(alignPanel.av
5533 .getSequenceSelection(),
5534 alignPanel.alignFrame, dassource)
5535 .fetchDBRefs(false);
5541 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5544 // and then build the rest of the individual menus
5545 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
5547 String imname = null;
5549 for (DbSourceProxy sproxy : otherdb)
5551 String dbname = sproxy.getDbName();
5552 String sname = dbname.length() > 5 ? dbname.substring(0,
5553 5) + "..." : dbname;
5554 String msname = dbname.length() > 10 ? dbname.substring(
5555 0, 10) + "..." : dbname;
5558 imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
5560 fetchr = new JMenuItem(msname);
5561 final DbSourceProxy[] dassrc =
5563 fetchr.addActionListener(new ActionListener()
5567 public void actionPerformed(ActionEvent e)
5569 new Thread(new Runnable()
5575 new jalview.ws.DBRefFetcher(alignPanel.av
5576 .getSequenceSelection(),
5577 alignPanel.alignFrame, dassrc)
5578 .fetchDBRefs(false);
5584 fetchr.setToolTipText("<html>"
5585 + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
5588 if (++icomp >= mcomp || i == (otherdb.size()))
5590 ifetch.setText(MessageManager.formatMessage(
5591 "label.source_to_target", imname, sname));
5593 ifetch = new JMenu();
5601 if (comp >= mcomp || dbi >= (dbclasses.length))
5603 dfetch.setText(MessageManager.formatMessage(
5604 "label.source_to_target", mname, dbclass));
5606 dfetch = new JMenu();
5619 * Left justify the whole alignment.
5622 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5624 AlignmentI al = viewport.getAlignment();
5626 viewport.firePropertyChange("alignment", null, al);
5630 * Right justify the whole alignment.
5633 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5635 AlignmentI al = viewport.getAlignment();
5637 viewport.firePropertyChange("alignment", null, al);
5640 public void setShowSeqFeatures(boolean b)
5642 showSeqFeatures.setSelected(true);
5643 viewport.setShowSequenceFeatures(true);
5650 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5651 * awt.event.ActionEvent)
5654 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5656 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5657 alignPanel.paintAlignment(true);
5664 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5668 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5670 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5671 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5679 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5680 * .event.ActionEvent)
5683 protected void showGroupConservation_actionPerformed(ActionEvent e)
5685 viewport.setShowGroupConservation(showGroupConservation.getState());
5686 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5693 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5694 * .event.ActionEvent)
5697 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5699 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5700 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5707 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5708 * .event.ActionEvent)
5711 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5713 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5714 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5718 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5720 showSequenceLogo.setState(true);
5721 viewport.setShowSequenceLogo(true);
5722 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5723 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5727 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5729 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5736 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5737 * .event.ActionEvent)
5740 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5742 if (avc.makeGroupsFromSelection())
5744 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5745 alignPanel.updateAnnotation();
5746 alignPanel.paintAlignment(true);
5751 protected void createGroup_actionPerformed(ActionEvent e)
5753 if (avc.createGroup())
5755 alignPanel.alignmentChanged();
5760 protected void unGroup_actionPerformed(ActionEvent e)
5764 alignPanel.alignmentChanged();
5769 * make the given alignmentPanel the currently selected tab
5771 * @param alignmentPanel
5773 public void setDisplayedView(AlignmentPanel alignmentPanel)
5775 if (!viewport.getSequenceSetId().equals(
5776 alignmentPanel.av.getSequenceSetId()))
5778 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5780 if (tabbedPane != null
5781 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5782 .getSelectedIndex())
5784 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5789 * Action on selection of menu options to Show or Hide annotations.
5792 * @param forSequences
5793 * update sequence-related annotations
5794 * @param forAlignment
5795 * update non-sequence-related annotations
5798 protected void setAnnotationsVisibility(boolean visible,
5799 boolean forSequences, boolean forAlignment)
5801 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5802 .getAlignmentAnnotation())
5804 boolean apply = (aa.sequenceRef == null && forAlignment)
5805 || (aa.sequenceRef != null && forSequences);
5808 aa.visible = visible;
5811 alignPanel.validateAnnotationDimensions(false);
5812 alignPanel.alignmentChanged();
5816 * Store selected annotation sort order for the view and repaint.
5819 protected void sortAnnotations_actionPerformed()
5821 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5823 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5824 alignPanel.paintAlignment(true);
5828 class PrintThread extends Thread
5832 public PrintThread(AlignmentPanel ap)
5837 static PageFormat pf;
5842 PrinterJob printJob = PrinterJob.getPrinterJob();
5846 printJob.setPrintable(ap, pf);
5850 printJob.setPrintable(ap);
5853 if (printJob.printDialog())
5858 } catch (Exception PrintException)
5860 PrintException.printStackTrace();