2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 import jalview.analysis.AAFrequency;
21 import jalview.analysis.AlignmentSorter;
22 import jalview.analysis.Conservation;
23 import jalview.analysis.CrossRef;
24 import jalview.analysis.NJTree;
25 import jalview.analysis.ParseProperties;
26 import jalview.analysis.SequenceIdMatcher;
27 import jalview.bin.Cache;
28 import jalview.commands.CommandI;
29 import jalview.commands.EditCommand;
30 import jalview.commands.OrderCommand;
31 import jalview.commands.RemoveGapColCommand;
32 import jalview.commands.RemoveGapsCommand;
33 import jalview.commands.SlideSequencesCommand;
34 import jalview.commands.TrimRegionCommand;
35 import jalview.datamodel.AlignedCodonFrame;
36 import jalview.datamodel.Alignment;
37 import jalview.datamodel.AlignmentAnnotation;
38 import jalview.datamodel.AlignmentI;
39 import jalview.datamodel.AlignmentOrder;
40 import jalview.datamodel.AlignmentView;
41 import jalview.datamodel.ColumnSelection;
42 import jalview.datamodel.PDBEntry;
43 import jalview.datamodel.SeqCigar;
44 import jalview.datamodel.Sequence;
45 import jalview.datamodel.SequenceGroup;
46 import jalview.datamodel.SequenceI;
47 import jalview.io.AlignmentProperties;
48 import jalview.io.AnnotationFile;
49 import jalview.io.FeaturesFile;
50 import jalview.io.FileLoader;
51 import jalview.io.FormatAdapter;
52 import jalview.io.HTMLOutput;
53 import jalview.io.IdentifyFile;
54 import jalview.io.JalviewFileChooser;
55 import jalview.io.JalviewFileView;
56 import jalview.io.JnetAnnotationMaker;
57 import jalview.io.NewickFile;
58 import jalview.io.TCoffeeScoreFile;
59 import jalview.jbgui.GAlignFrame;
60 import jalview.schemes.Blosum62ColourScheme;
61 import jalview.schemes.BuriedColourScheme;
62 import jalview.schemes.ClustalxColourScheme;
63 import jalview.schemes.ColourSchemeI;
64 import jalview.schemes.ColourSchemeProperty;
65 import jalview.schemes.HelixColourScheme;
66 import jalview.schemes.HydrophobicColourScheme;
67 import jalview.schemes.NucleotideColourScheme;
68 import jalview.schemes.PIDColourScheme;
69 import jalview.schemes.ResidueProperties;
70 import jalview.schemes.StrandColourScheme;
71 import jalview.schemes.TCoffeeColourScheme;
72 import jalview.schemes.TaylorColourScheme;
73 import jalview.schemes.TurnColourScheme;
74 import jalview.schemes.UserColourScheme;
75 import jalview.schemes.ZappoColourScheme;
76 import jalview.ws.jws1.Discoverer;
77 import jalview.ws.jws2.Jws2Discoverer;
79 import java.awt.BorderLayout;
80 import java.awt.Color;
81 import java.awt.Component;
82 import java.awt.GridLayout;
83 import java.awt.Rectangle;
84 import java.awt.Toolkit;
85 import java.awt.datatransfer.Clipboard;
86 import java.awt.datatransfer.DataFlavor;
87 import java.awt.datatransfer.StringSelection;
88 import java.awt.datatransfer.Transferable;
89 import java.awt.dnd.DnDConstants;
90 import java.awt.dnd.DropTargetDragEvent;
91 import java.awt.dnd.DropTargetDropEvent;
92 import java.awt.dnd.DropTargetEvent;
93 import java.awt.dnd.DropTargetListener;
94 import java.awt.event.ActionEvent;
95 import java.awt.event.ActionListener;
96 import java.awt.event.KeyAdapter;
97 import java.awt.event.KeyEvent;
98 import java.awt.event.MouseAdapter;
99 import java.awt.event.MouseEvent;
100 import java.awt.print.PageFormat;
101 import java.awt.print.PrinterJob;
102 import java.beans.PropertyChangeEvent;
105 import java.util.ArrayList;
106 import java.util.Enumeration;
107 import java.util.Hashtable;
108 import java.util.Vector;
110 import javax.swing.JButton;
111 import javax.swing.JEditorPane;
112 import javax.swing.JInternalFrame;
113 import javax.swing.JLabel;
114 import javax.swing.JLayeredPane;
115 import javax.swing.JMenu;
116 import javax.swing.JMenuItem;
117 import javax.swing.JOptionPane;
118 import javax.swing.JPanel;
119 import javax.swing.JProgressBar;
120 import javax.swing.JRadioButtonMenuItem;
121 import javax.swing.JScrollPane;
122 import javax.swing.SwingUtilities;
128 * @version $Revision$
130 public class AlignFrame extends GAlignFrame implements DropTargetListener,
135 public static final int DEFAULT_WIDTH = 700;
138 public static final int DEFAULT_HEIGHT = 500;
140 public AlignmentPanel alignPanel;
142 AlignViewport viewport;
144 Vector alignPanels = new Vector();
146 TCoffeeScoreFile tcoffeeScoreFile;
149 * Last format used to load or save alignments in this window
151 String currentFileFormat = null;
154 * Current filename for this alignment
156 String fileName = null;
159 * Creates a new AlignFrame object with specific width and height.
165 public AlignFrame(AlignmentI al, int width, int height)
167 this(al, null, width, height);
171 * Creates a new AlignFrame object with specific width, height and
177 * @param sequenceSetId
179 public AlignFrame(AlignmentI al, int width, int height,
180 String sequenceSetId)
182 this(al, null, width, height, sequenceSetId);
186 * Creates a new AlignFrame object with specific width, height and
192 * @param sequenceSetId
195 public AlignFrame(AlignmentI al, int width, int height,
196 String sequenceSetId, String viewId)
198 this(al, null, width, height, sequenceSetId, viewId);
202 * new alignment window with hidden columns
206 * @param hiddenColumns
207 * ColumnSelection or null
209 * Width of alignment frame
213 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
214 int width, int height)
216 this(al, hiddenColumns, width, height, null);
220 * Create alignment frame for al with hiddenColumns, a specific width and
221 * height, and specific sequenceId
224 * @param hiddenColumns
227 * @param sequenceSetId
230 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
231 int width, int height, String sequenceSetId)
233 this(al, hiddenColumns, width, height, sequenceSetId, null);
237 * Create alignment frame for al with hiddenColumns, a specific width and
238 * height, and specific sequenceId
241 * @param hiddenColumns
244 * @param sequenceSetId
249 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
250 int width, int height, String sequenceSetId, String viewId)
252 setSize(width, height);
253 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
255 alignPanel = new AlignmentPanel(this, viewport);
257 if (al.getDataset() == null)
262 addAlignmentPanel(alignPanel, true);
267 * Make a new AlignFrame from exisiting alignmentPanels
274 public AlignFrame(AlignmentPanel ap)
278 addAlignmentPanel(ap, false);
283 * initalise the alignframe from the underlying viewport data and the
288 if (viewport.conservation == null)
290 BLOSUM62Colour.setEnabled(false);
291 conservationMenuItem.setEnabled(false);
292 modifyConservation.setEnabled(false);
293 // PIDColour.setEnabled(false);
294 // abovePIDThreshold.setEnabled(false);
295 // modifyPID.setEnabled(false);
298 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
301 if (sortby.equals("Id"))
303 sortIDMenuItem_actionPerformed(null);
305 else if (sortby.equals("Pairwise Identity"))
307 sortPairwiseMenuItem_actionPerformed(null);
310 if (Desktop.desktop != null)
312 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
313 addServiceListeners();
314 setGUINucleotide(viewport.alignment.isNucleotide());
317 setMenusFromViewport(viewport);
318 buildSortByAnnotationScoresMenu();
319 if (viewport.wrapAlignment)
321 wrapMenuItem_actionPerformed(null);
324 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
326 this.overviewMenuItem_actionPerformed(null);
334 * Change the filename and format for the alignment, and enable the 'reload'
335 * button functionality.
342 public void setFileName(String file, String format)
345 currentFileFormat = format;
346 reload.setEnabled(true);
349 void addKeyListener()
351 addKeyListener(new KeyAdapter()
353 public void keyPressed(KeyEvent evt)
355 if (viewport.cursorMode
356 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
357 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
358 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
359 && Character.isDigit(evt.getKeyChar()))
360 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
362 switch (evt.getKeyCode())
365 case 27: // escape key
366 deselectAllSequenceMenuItem_actionPerformed(null);
370 case KeyEvent.VK_DOWN:
371 if (evt.isAltDown() || !viewport.cursorMode)
372 moveSelectedSequences(false);
373 if (viewport.cursorMode)
374 alignPanel.seqPanel.moveCursor(0, 1);
378 if (evt.isAltDown() || !viewport.cursorMode)
379 moveSelectedSequences(true);
380 if (viewport.cursorMode)
381 alignPanel.seqPanel.moveCursor(0, -1);
385 case KeyEvent.VK_LEFT:
386 if (evt.isAltDown() || !viewport.cursorMode)
387 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
389 alignPanel.seqPanel.moveCursor(-1, 0);
393 case KeyEvent.VK_RIGHT:
394 if (evt.isAltDown() || !viewport.cursorMode)
395 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
397 alignPanel.seqPanel.moveCursor(1, 0);
400 case KeyEvent.VK_SPACE:
401 if (viewport.cursorMode)
403 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
404 || evt.isShiftDown() || evt.isAltDown());
408 case KeyEvent.VK_DELETE:
409 case KeyEvent.VK_BACK_SPACE:
410 if (!viewport.cursorMode)
412 cut_actionPerformed(null);
416 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
417 || evt.isShiftDown() || evt.isAltDown());
423 if (viewport.cursorMode)
425 alignPanel.seqPanel.setCursorRow();
429 if (viewport.cursorMode && !evt.isControlDown())
431 alignPanel.seqPanel.setCursorColumn();
435 if (viewport.cursorMode)
437 alignPanel.seqPanel.setCursorPosition();
441 case KeyEvent.VK_ENTER:
442 case KeyEvent.VK_COMMA:
443 if (viewport.cursorMode)
445 alignPanel.seqPanel.setCursorRowAndColumn();
450 if (viewport.cursorMode)
452 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
456 if (viewport.cursorMode)
458 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
463 viewport.cursorMode = !viewport.cursorMode;
464 statusBar.setText("Keyboard editing mode is "
465 + (viewport.cursorMode ? "on" : "off"));
466 if (viewport.cursorMode)
468 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
469 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
471 alignPanel.seqPanel.seqCanvas.repaint();
477 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
478 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
480 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
482 javax.help.HelpBroker hb = hs.createHelpBroker();
483 hb.setCurrentID("home");
484 hb.setDisplayed(true);
485 } catch (Exception ex)
487 ex.printStackTrace();
492 boolean toggleSeqs = !evt.isControlDown();
493 boolean toggleCols = !evt.isShiftDown();
494 toggleHiddenRegions(toggleSeqs, toggleCols);
497 case KeyEvent.VK_PAGE_UP:
498 if (viewport.wrapAlignment)
500 alignPanel.scrollUp(true);
504 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
505 - viewport.endSeq + viewport.startSeq);
508 case KeyEvent.VK_PAGE_DOWN:
509 if (viewport.wrapAlignment)
511 alignPanel.scrollUp(false);
515 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
516 + viewport.endSeq - viewport.startSeq);
522 public void keyReleased(KeyEvent evt)
524 switch (evt.getKeyCode())
526 case KeyEvent.VK_LEFT:
527 if (evt.isAltDown() || !viewport.cursorMode)
528 viewport.firePropertyChange("alignment", null, viewport
529 .getAlignment().getSequences());
532 case KeyEvent.VK_RIGHT:
533 if (evt.isAltDown() || !viewport.cursorMode)
534 viewport.firePropertyChange("alignment", null, viewport
535 .getAlignment().getSequences());
542 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
544 ap.alignFrame = this;
546 alignPanels.addElement(ap);
548 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
550 int aSize = alignPanels.size();
552 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
554 if (aSize == 1 && ap.av.viewName == null)
556 this.getContentPane().add(ap, BorderLayout.CENTER);
562 setInitialTabVisible();
565 expandViews.setEnabled(true);
566 gatherViews.setEnabled(true);
567 tabbedPane.addTab(ap.av.viewName, ap);
569 ap.setVisible(false);
576 ap.av.alignment.padGaps();
578 ap.av.updateConservation(ap);
579 ap.av.updateConsensus(ap);
583 public void setInitialTabVisible()
585 expandViews.setEnabled(true);
586 gatherViews.setEnabled(true);
587 tabbedPane.setVisible(true);
588 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
589 tabbedPane.addTab(first.av.viewName, first);
590 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
593 public AlignViewport getViewport()
598 /* Set up intrinsic listeners for dynamically generated GUI bits. */
599 private void addServiceListeners()
601 final java.beans.PropertyChangeListener thisListener;
602 Desktop.instance.addJalviewPropertyChangeListener("services",
603 thisListener = new java.beans.PropertyChangeListener()
605 public void propertyChange(PropertyChangeEvent evt)
607 // // System.out.println("Discoverer property change.");
608 // if (evt.getPropertyName().equals("services"))
610 SwingUtilities.invokeLater(new Runnable()
616 .println("Rebuild WS Menu for service change");
617 BuildWebServiceMenu();
624 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
626 public void internalFrameClosed(
627 javax.swing.event.InternalFrameEvent evt)
629 System.out.println("deregistering discoverer listener");
630 Desktop.instance.removeJalviewPropertyChangeListener("services",
632 closeMenuItem_actionPerformed(true);
635 // Finally, build the menu once to get current service state
636 new Thread(new Runnable()
640 BuildWebServiceMenu();
645 public void setGUINucleotide(boolean nucleotide)
647 showTranslation.setVisible(nucleotide);
648 conservationMenuItem.setEnabled(!nucleotide);
649 modifyConservation.setEnabled(!nucleotide);
650 showGroupConservation.setEnabled(!nucleotide);
651 // Remember AlignFrame always starts as protein
654 calculateMenu.remove(calculateMenu.getItemCount() - 2);
659 * set up menus for the currently viewport. This may be called after any
660 * operation that affects the data in the current view (selection changed,
661 * etc) to update the menus to reflect the new state.
663 public void setMenusForViewport()
665 setMenusFromViewport(viewport);
669 * Need to call this method when tabs are selected for multiple views, or when
670 * loading from Jalview2XML.java
675 void setMenusFromViewport(AlignViewport av)
677 padGapsMenuitem.setSelected(av.padGaps);
678 colourTextMenuItem.setSelected(av.showColourText);
679 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
680 conservationMenuItem.setSelected(av.getConservationSelected());
681 seqLimits.setSelected(av.getShowJVSuffix());
682 idRightAlign.setSelected(av.rightAlignIds);
683 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
684 renderGapsMenuItem.setSelected(av.renderGaps);
685 wrapMenuItem.setSelected(av.wrapAlignment);
686 scaleAbove.setVisible(av.wrapAlignment);
687 scaleLeft.setVisible(av.wrapAlignment);
688 scaleRight.setVisible(av.wrapAlignment);
689 annotationPanelMenuItem.setState(av.showAnnotation);
690 viewBoxesMenuItem.setSelected(av.showBoxes);
691 viewTextMenuItem.setSelected(av.showText);
692 showNonconservedMenuItem.setSelected(av.showUnconserved);
693 showGroupConsensus.setSelected(av.showGroupConsensus);
694 showGroupConservation.setSelected(av.showGroupConservation);
695 showConsensusHistogram.setSelected(av.showConsensusHistogram);
696 showSequenceLogo.setSelected(av.showSequenceLogo);
697 setColourSelected(ColourSchemeProperty.getColourName(av
698 .getGlobalColourScheme()));
700 showSeqFeatures.setSelected(av.showSequenceFeatures);
701 hiddenMarkers.setState(av.showHiddenMarkers);
702 applyToAllGroups.setState(av.colourAppliesToAllGroups);
703 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
704 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
705 autoCalculate.setSelected(av.autoCalculateConsensus);
706 sortByTree.setSelected(av.sortByTree);
707 listenToViewSelections.setSelected(av.followSelection);
709 setShowProductsEnabled();
714 Hashtable progressBars, progressBarHandlers;
719 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
721 public void setProgressBar(String message, long id)
723 if (progressBars == null)
725 progressBars = new Hashtable();
726 progressBarHandlers = new Hashtable();
729 JPanel progressPanel;
730 Long lId = new Long(id);
731 GridLayout layout = (GridLayout) statusPanel.getLayout();
732 if (progressBars.get(lId) != null)
734 progressPanel = (JPanel) progressBars.get(new Long(id));
735 statusPanel.remove(progressPanel);
736 progressBars.remove(lId);
737 progressPanel = null;
740 statusBar.setText(message);
742 if (progressBarHandlers.contains(lId))
744 progressBarHandlers.remove(lId);
746 layout.setRows(layout.getRows() - 1);
750 progressPanel = new JPanel(new BorderLayout(10, 5));
752 JProgressBar progressBar = new JProgressBar();
753 progressBar.setIndeterminate(true);
755 progressPanel.add(new JLabel(message), BorderLayout.WEST);
756 progressPanel.add(progressBar, BorderLayout.CENTER);
758 layout.setRows(layout.getRows() + 1);
759 statusPanel.add(progressPanel);
761 progressBars.put(lId, progressPanel);
764 // setMenusForViewport();
768 public void registerHandler(final long id,
769 final IProgressIndicatorHandler handler)
771 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
774 "call setProgressBar before registering the progress bar's handler.");
776 progressBarHandlers.put(new Long(id), handler);
777 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
778 if (handler.canCancel())
780 JButton cancel = new JButton("Cancel");
781 final IProgressIndicator us = this;
782 cancel.addActionListener(new ActionListener()
785 public void actionPerformed(ActionEvent e)
787 handler.cancelActivity(id);
790 + ((JLabel) progressPanel.getComponent(0))
794 progressPanel.add(cancel, BorderLayout.EAST);
800 * @return true if any progress bars are still active
802 public boolean operationInProgress()
804 if (progressBars != null && progressBars.size() > 0)
812 * Added so Castor Mapping file can obtain Jalview Version
814 public String getVersion()
816 return jalview.bin.Cache.getProperty("VERSION");
819 public FeatureRenderer getFeatureRenderer()
821 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
824 public void fetchSequence_actionPerformed(ActionEvent e)
826 new SequenceFetcher(this);
829 public void addFromFile_actionPerformed(ActionEvent e)
831 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
834 public void reload_actionPerformed(ActionEvent e)
836 if (fileName != null)
838 // TODO: work out how to recover feature settings for correct view(s) when
840 if (currentFileFormat.equals("Jalview"))
842 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
843 for (int i = 0; i < frames.length; i++)
845 if (frames[i] instanceof AlignFrame && frames[i] != this
846 && ((AlignFrame) frames[i]).fileName.equals(fileName))
850 frames[i].setSelected(true);
851 Desktop.instance.closeAssociatedWindows();
852 } catch (java.beans.PropertyVetoException ex)
858 Desktop.instance.closeAssociatedWindows();
860 FileLoader loader = new FileLoader();
861 String protocol = fileName.startsWith("http:") ? "URL" : "File";
862 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
866 Rectangle bounds = this.getBounds();
868 FileLoader loader = new FileLoader();
869 String protocol = fileName.startsWith("http:") ? "URL" : "File";
870 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
871 protocol, currentFileFormat);
873 newframe.setBounds(bounds);
874 if (featureSettings != null && featureSettings.isShowing())
876 final Rectangle fspos = featureSettings.frame.getBounds();
877 // TODO: need a 'show feature settings' function that takes bounds -
878 // need to refactor Desktop.addFrame
879 newframe.featureSettings_actionPerformed(null);
880 final FeatureSettings nfs = newframe.featureSettings;
881 SwingUtilities.invokeLater(new Runnable()
885 nfs.frame.setBounds(fspos);
888 this.featureSettings.close();
889 this.featureSettings = null;
891 this.closeMenuItem_actionPerformed(true);
896 public void addFromText_actionPerformed(ActionEvent e)
898 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
901 public void addFromURL_actionPerformed(ActionEvent e)
903 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
906 public void save_actionPerformed(ActionEvent e)
909 || (currentFileFormat == null || !jalview.io.FormatAdapter
910 .isValidIOFormat(currentFileFormat, true))
911 || fileName.startsWith("http"))
913 saveAs_actionPerformed(null);
917 saveAlignment(fileName, currentFileFormat);
927 public void saveAs_actionPerformed(ActionEvent e)
929 JalviewFileChooser chooser = new JalviewFileChooser(
930 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
931 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
932 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
933 currentFileFormat, false);
935 chooser.setFileView(new JalviewFileView());
936 chooser.setDialogTitle("Save Alignment to file");
937 chooser.setToolTipText("Save");
939 int value = chooser.showSaveDialog(this);
941 if (value == JalviewFileChooser.APPROVE_OPTION)
943 currentFileFormat = chooser.getSelectedFormat();
944 if (currentFileFormat == null)
946 JOptionPane.showInternalMessageDialog(Desktop.desktop,
947 "You must select a file format before saving!",
948 "File format not specified", JOptionPane.WARNING_MESSAGE);
949 value = chooser.showSaveDialog(this);
953 fileName = chooser.getSelectedFile().getPath();
955 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
958 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
959 if (currentFileFormat.indexOf(" ") > -1)
961 currentFileFormat = currentFileFormat.substring(0,
962 currentFileFormat.indexOf(" "));
964 saveAlignment(fileName, currentFileFormat);
968 public boolean saveAlignment(String file, String format)
970 boolean success = true;
972 if (format.equalsIgnoreCase("Jalview"))
974 String shortName = title;
976 if (shortName.indexOf(java.io.File.separatorChar) > -1)
978 shortName = shortName.substring(shortName
979 .lastIndexOf(java.io.File.separatorChar) + 1);
982 success = new Jalview2XML().SaveAlignment(this, file, shortName);
984 statusBar.setText("Successfully saved to file: " + fileName + " in "
985 + format + " format.");
990 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
992 warningMessage("Cannot save file " + fileName + " using format "
993 + format, "Alignment output format not supported");
994 saveAs_actionPerformed(null);
995 // JBPNote need to have a raise_gui flag here
999 String[] omitHidden = null;
1001 if (viewport.hasHiddenColumns)
1003 int reply = JOptionPane
1004 .showInternalConfirmDialog(
1006 "The Alignment contains hidden columns."
1007 + "\nDo you want to save only the visible alignment?",
1008 "Save / Omit Hidden Columns",
1009 JOptionPane.YES_NO_OPTION,
1010 JOptionPane.QUESTION_MESSAGE);
1012 if (reply == JOptionPane.YES_OPTION)
1014 omitHidden = viewport.getViewAsString(false);
1017 FormatAdapter f = new FormatAdapter();
1018 String output = f.formatSequences(format,
1019 (Alignment) viewport.alignment, // class cast exceptions will
1020 // occur in the distant future
1021 omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
1031 java.io.PrintWriter out = new java.io.PrintWriter(
1032 new java.io.FileWriter(file));
1036 this.setTitle(file);
1037 statusBar.setText("Successfully saved to file: " + fileName
1038 + " in " + format + " format.");
1039 } catch (Exception ex)
1042 ex.printStackTrace();
1049 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
1050 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
1056 private void warningMessage(String warning, String title)
1058 if (new jalview.util.Platform().isHeadless())
1060 System.err.println("Warning: " + title + "\nWarning: " + warning);
1065 JOptionPane.showInternalMessageDialog(this, warning, title,
1066 JOptionPane.WARNING_MESSAGE);
1077 protected void outputText_actionPerformed(ActionEvent e)
1079 String[] omitHidden = null;
1081 if (viewport.hasHiddenColumns)
1083 int reply = JOptionPane
1084 .showInternalConfirmDialog(
1086 "The Alignment contains hidden columns."
1087 + "\nDo you want to output only the visible alignment?",
1088 "Save / Omit Hidden Columns",
1089 JOptionPane.YES_NO_OPTION,
1090 JOptionPane.QUESTION_MESSAGE);
1092 if (reply == JOptionPane.YES_OPTION)
1094 omitHidden = viewport.getViewAsString(false);
1098 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1099 cap.setForInput(null);
1103 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1104 viewport.alignment, omitHidden, viewport.colSel));
1105 Desktop.addInternalFrame(cap,
1106 "Alignment output - " + e.getActionCommand(), 600, 500);
1107 } catch (OutOfMemoryError oom)
1109 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1121 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1123 new HTMLOutput(alignPanel,
1124 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1125 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1128 public void createImageMap(File file, String image)
1130 alignPanel.makePNGImageMap(file, image);
1139 public void createPNG(File f)
1141 alignPanel.makePNG(f);
1150 public void createEPS(File f)
1152 alignPanel.makeEPS(f);
1155 public void pageSetup_actionPerformed(ActionEvent e)
1157 PrinterJob printJob = PrinterJob.getPrinterJob();
1158 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1167 public void printMenuItem_actionPerformed(ActionEvent e)
1169 // Putting in a thread avoids Swing painting problems
1170 PrintThread thread = new PrintThread(alignPanel);
1174 public void exportFeatures_actionPerformed(ActionEvent e)
1176 new AnnotationExporter().exportFeatures(alignPanel);
1179 public void exportAnnotations_actionPerformed(ActionEvent e)
1181 new AnnotationExporter().exportAnnotations(
1183 viewport.showAnnotation ? viewport.alignment
1184 .getAlignmentAnnotation() : null, viewport.alignment
1186 ((Alignment) viewport.alignment).alignmentProperties);
1189 public void associatedData_actionPerformed(ActionEvent e)
1191 // Pick the tree file
1192 JalviewFileChooser chooser = new JalviewFileChooser(
1193 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1194 chooser.setFileView(new JalviewFileView());
1195 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1196 chooser.setToolTipText("Load Jalview Annotations / Features file");
1198 int value = chooser.showOpenDialog(null);
1200 if (value == JalviewFileChooser.APPROVE_OPTION)
1202 String choice = chooser.getSelectedFile().getPath();
1203 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1204 loadJalviewDataFile(choice, null, null, null);
1210 * Close the current view or all views in the alignment frame. If the frame
1211 * only contains one view then the alignment will be removed from memory.
1213 * @param closeAllTabs
1215 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1217 if (alignPanels != null && alignPanels.size() < 2)
1219 closeAllTabs = true;
1224 if (alignPanels != null)
1228 if (this.isClosed())
1230 // really close all the windows - otherwise wait till
1231 // setClosed(true) is called
1232 for (int i = 0; i < alignPanels.size(); i++)
1234 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1241 closeView(alignPanel);
1247 this.setClosed(true);
1249 } catch (Exception ex)
1251 ex.printStackTrace();
1256 * close alignPanel2 and shuffle tabs appropriately.
1258 * @param alignPanel2
1260 public void closeView(AlignmentPanel alignPanel2)
1262 int index = tabbedPane.getSelectedIndex();
1263 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1264 alignPanels.removeElement(alignPanel2);
1266 // if (viewport == alignPanel2.av)
1270 alignPanel2.closePanel();
1273 tabbedPane.removeTabAt(closedindex);
1274 tabbedPane.validate();
1276 if (index > closedindex || index == tabbedPane.getTabCount())
1278 // modify currently selected tab index if necessary.
1282 this.tabSelectionChanged(index);
1288 void updateEditMenuBar()
1291 if (viewport.historyList.size() > 0)
1293 undoMenuItem.setEnabled(true);
1294 CommandI command = (CommandI) viewport.historyList.peek();
1295 undoMenuItem.setText("Undo " + command.getDescription());
1299 undoMenuItem.setEnabled(false);
1300 undoMenuItem.setText("Undo");
1303 if (viewport.redoList.size() > 0)
1305 redoMenuItem.setEnabled(true);
1307 CommandI command = (CommandI) viewport.redoList.peek();
1308 redoMenuItem.setText("Redo " + command.getDescription());
1312 redoMenuItem.setEnabled(false);
1313 redoMenuItem.setText("Redo");
1317 public void addHistoryItem(CommandI command)
1319 if (command.getSize() > 0)
1321 viewport.historyList.push(command);
1322 viewport.redoList.clear();
1323 updateEditMenuBar();
1324 viewport.hasHiddenColumns = (viewport.colSel != null
1325 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1326 .getHiddenColumns().size() > 0);
1332 * @return alignment objects for all views
1334 AlignmentI[] getViewAlignments()
1336 if (alignPanels != null)
1338 Enumeration e = alignPanels.elements();
1339 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1340 for (int i = 0; e.hasMoreElements(); i++)
1342 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1346 if (viewport != null)
1348 return new AlignmentI[]
1349 { viewport.alignment };
1360 protected void undoMenuItem_actionPerformed(ActionEvent e)
1362 if (viewport.historyList.empty())
1364 CommandI command = (CommandI) viewport.historyList.pop();
1365 viewport.redoList.push(command);
1366 command.undoCommand(getViewAlignments());
1368 AlignViewport originalSource = getOriginatingSource(command);
1369 updateEditMenuBar();
1371 if (originalSource != null)
1373 originalSource.hasHiddenColumns = (viewport.colSel != null
1374 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1375 .getHiddenColumns().size() > 0);
1376 originalSource.firePropertyChange("alignment", null,
1377 originalSource.alignment.getSequences());
1387 protected void redoMenuItem_actionPerformed(ActionEvent e)
1389 if (viewport.redoList.size() < 1)
1394 CommandI command = (CommandI) viewport.redoList.pop();
1395 viewport.historyList.push(command);
1396 command.doCommand(getViewAlignments());
1398 AlignViewport originalSource = getOriginatingSource(command);
1399 updateEditMenuBar();
1401 if (originalSource != null)
1403 originalSource.hasHiddenColumns = (viewport.colSel != null
1404 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1405 .getHiddenColumns().size() > 0);
1406 originalSource.firePropertyChange("alignment", null,
1407 originalSource.alignment.getSequences());
1411 AlignViewport getOriginatingSource(CommandI command)
1413 AlignViewport originalSource = null;
1414 // For sequence removal and addition, we need to fire
1415 // the property change event FROM the viewport where the
1416 // original alignment was altered
1417 AlignmentI al = null;
1418 if (command instanceof EditCommand)
1420 EditCommand editCommand = (EditCommand) command;
1421 al = editCommand.getAlignment();
1422 Vector comps = (Vector) PaintRefresher.components.get(viewport
1423 .getSequenceSetId());
1425 for (int i = 0; i < comps.size(); i++)
1427 if (comps.elementAt(i) instanceof AlignmentPanel)
1429 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1431 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1438 if (originalSource == null)
1440 // The original view is closed, we must validate
1441 // the current view against the closed view first
1444 PaintRefresher.validateSequences(al, viewport.alignment);
1447 originalSource = viewport;
1450 return originalSource;
1459 public void moveSelectedSequences(boolean up)
1461 SequenceGroup sg = viewport.getSelectionGroup();
1470 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1472 SequenceI seq = viewport.alignment.getSequenceAt(i);
1474 if (!sg.getSequences(null).contains(seq))
1479 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1481 if (sg.getSequences(null).contains(temp))
1486 viewport.alignment.getSequences().setElementAt(temp, i);
1487 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1492 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1494 SequenceI seq = viewport.alignment.getSequenceAt(i);
1496 if (!sg.getSequences(null).contains(seq))
1501 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1503 if (sg.getSequences(null).contains(temp))
1508 viewport.alignment.getSequences().setElementAt(temp, i);
1509 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1513 alignPanel.paintAlignment(true);
1516 synchronized void slideSequences(boolean right, int size)
1518 Vector sg = new Vector();
1519 if (viewport.cursorMode)
1521 sg.addElement(viewport.alignment
1522 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1524 else if (viewport.getSelectionGroup() != null
1525 && viewport.getSelectionGroup().getSize() != viewport.alignment
1528 sg = viewport.getSelectionGroup().getSequences(
1529 viewport.hiddenRepSequences);
1537 Vector invertGroup = new Vector();
1539 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1541 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1542 invertGroup.add(viewport.alignment.getSequenceAt(i));
1545 SequenceI[] seqs1 = new SequenceI[sg.size()];
1546 for (int i = 0; i < sg.size(); i++)
1547 seqs1[i] = (SequenceI) sg.elementAt(i);
1549 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1550 for (int i = 0; i < invertGroup.size(); i++)
1551 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1553 SlideSequencesCommand ssc;
1555 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1556 size, viewport.getGapCharacter());
1558 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1559 size, viewport.getGapCharacter());
1561 int groupAdjustment = 0;
1562 if (ssc.getGapsInsertedBegin() && right)
1564 if (viewport.cursorMode)
1565 alignPanel.seqPanel.moveCursor(size, 0);
1567 groupAdjustment = size;
1569 else if (!ssc.getGapsInsertedBegin() && !right)
1571 if (viewport.cursorMode)
1572 alignPanel.seqPanel.moveCursor(-size, 0);
1574 groupAdjustment = -size;
1577 if (groupAdjustment != 0)
1579 viewport.getSelectionGroup().setStartRes(
1580 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1581 viewport.getSelectionGroup().setEndRes(
1582 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1585 boolean appendHistoryItem = false;
1586 if (viewport.historyList != null && viewport.historyList.size() > 0
1587 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1589 appendHistoryItem = ssc
1590 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1594 if (!appendHistoryItem)
1595 addHistoryItem(ssc);
1606 protected void copy_actionPerformed(ActionEvent e)
1609 if (viewport.getSelectionGroup() == null)
1613 // TODO: preserve the ordering of displayed alignment annotation in any
1614 // internal paste (particularly sequence associated annotation)
1615 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1616 String[] omitHidden = null;
1618 if (viewport.hasHiddenColumns)
1620 omitHidden = viewport.getViewAsString(true);
1623 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1626 StringSelection ss = new StringSelection(output);
1630 jalview.gui.Desktop.internalCopy = true;
1631 // Its really worth setting the clipboard contents
1632 // to empty before setting the large StringSelection!!
1633 Toolkit.getDefaultToolkit().getSystemClipboard()
1634 .setContents(new StringSelection(""), null);
1636 Toolkit.getDefaultToolkit().getSystemClipboard()
1637 .setContents(ss, Desktop.instance);
1638 } catch (OutOfMemoryError er)
1640 new OOMWarning("copying region", er);
1644 Vector hiddenColumns = null;
1645 if (viewport.hasHiddenColumns)
1647 hiddenColumns = new Vector();
1648 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1649 .getSelectionGroup().getEndRes();
1650 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1653 int[] region = (int[]) viewport.getColumnSelection()
1654 .getHiddenColumns().elementAt(i);
1655 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1657 hiddenColumns.addElement(new int[]
1658 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1663 Desktop.jalviewClipboard = new Object[]
1664 { seqs, viewport.alignment.getDataset(), hiddenColumns };
1665 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1674 protected void pasteNew_actionPerformed(ActionEvent e)
1685 protected void pasteThis_actionPerformed(ActionEvent e)
1691 * Paste contents of Jalview clipboard
1693 * @param newAlignment
1694 * true to paste to a new alignment, otherwise add to this.
1696 void paste(boolean newAlignment)
1698 boolean externalPaste = true;
1701 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1702 Transferable contents = c.getContents(this);
1704 if (contents == null)
1712 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1713 if (str.length() < 1)
1718 format = new IdentifyFile().Identify(str, "Paste");
1720 } catch (OutOfMemoryError er)
1722 new OOMWarning("Out of memory pasting sequences!!", er);
1726 SequenceI[] sequences;
1727 boolean annotationAdded = false;
1728 AlignmentI alignment = null;
1730 if (Desktop.jalviewClipboard != null)
1732 // The clipboard was filled from within Jalview, we must use the
1734 // And dataset from the copied alignment
1735 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1736 // be doubly sure that we create *new* sequence objects.
1737 sequences = new SequenceI[newseq.length];
1738 for (int i = 0; i < newseq.length; i++)
1740 sequences[i] = new Sequence(newseq[i]);
1742 alignment = new Alignment(sequences);
1743 externalPaste = false;
1747 // parse the clipboard as an alignment.
1748 alignment = new FormatAdapter().readFile(str, "Paste", format);
1749 sequences = alignment.getSequencesArray();
1757 if (Desktop.jalviewClipboard != null)
1759 // dataset is inherited
1760 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1764 // new dataset is constructed
1765 alignment.setDataset(null);
1767 alwidth = alignment.getWidth() + 1;
1771 AlignmentI pastedal = alignment; // preserve pasted alignment object
1772 // Add pasted sequences and dataset into existing alignment.
1773 alignment = viewport.getAlignment();
1774 alwidth = alignment.getWidth() + 1;
1775 // decide if we need to import sequences from an existing dataset
1776 boolean importDs = Desktop.jalviewClipboard != null
1777 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1778 // importDs==true instructs us to copy over new dataset sequences from
1779 // an existing alignment
1780 Vector newDs = (importDs) ? new Vector() : null; // used to create
1781 // minimum dataset set
1783 for (int i = 0; i < sequences.length; i++)
1787 newDs.addElement(null);
1789 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1791 if (importDs && ds != null)
1793 if (!newDs.contains(ds))
1795 newDs.setElementAt(ds, i);
1796 ds = new Sequence(ds);
1797 // update with new dataset sequence
1798 sequences[i].setDatasetSequence(ds);
1802 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1807 // copy and derive new dataset sequence
1808 sequences[i] = sequences[i].deriveSequence();
1809 alignment.getDataset().addSequence(
1810 sequences[i].getDatasetSequence());
1811 // TODO: avoid creation of duplicate dataset sequences with a
1812 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1814 alignment.addSequence(sequences[i]); // merges dataset
1818 newDs.clear(); // tidy up
1820 if (pastedal.getAlignmentAnnotation() != null)
1822 // Add any annotation attached to alignment.
1823 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1824 for (int i = 0; i < alann.length; i++)
1826 annotationAdded = true;
1827 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1829 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1830 newann.padAnnotation(alwidth);
1831 alignment.addAnnotation(newann);
1841 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1842 sequences, 0, alignment.getWidth(), alignment));
1844 // Add any annotations attached to sequences
1845 for (int i = 0; i < sequences.length; i++)
1847 if (sequences[i].getAnnotation() != null)
1849 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1851 annotationAdded = true;
1852 sequences[i].getAnnotation()[a].adjustForAlignment();
1853 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1854 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1859 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1866 // propagate alignment changed.
1867 viewport.setEndSeq(alignment.getHeight());
1868 if (annotationAdded)
1870 // Duplicate sequence annotation in all views.
1871 AlignmentI[] alview = this.getViewAlignments();
1872 for (int i = 0; i < sequences.length; i++)
1874 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1877 for (int avnum = 0; avnum < alview.length; avnum++)
1879 if (alview[avnum] != alignment)
1881 // duplicate in a view other than the one with input focus
1882 int avwidth = alview[avnum].getWidth() + 1;
1883 // this relies on sann being preserved after we
1884 // modify the sequence's annotation array for each duplication
1885 for (int a = 0; a < sann.length; a++)
1887 AlignmentAnnotation newann = new AlignmentAnnotation(
1889 sequences[i].addAlignmentAnnotation(newann);
1890 newann.padAnnotation(avwidth);
1891 alview[avnum].addAnnotation(newann); // annotation was
1892 // duplicated earlier
1893 alview[avnum].setAnnotationIndex(newann, a);
1898 buildSortByAnnotationScoresMenu();
1900 viewport.firePropertyChange("alignment", null,
1901 alignment.getSequences());
1906 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1908 String newtitle = new String("Copied sequences");
1910 if (Desktop.jalviewClipboard != null
1911 && Desktop.jalviewClipboard[2] != null)
1913 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1914 for (int i = 0; i < hc.size(); i++)
1916 int[] region = (int[]) hc.elementAt(i);
1917 af.viewport.hideColumns(region[0], region[1]);
1921 // >>>This is a fix for the moment, until a better solution is
1923 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1925 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1927 // TODO: maintain provenance of an alignment, rather than just make the
1928 // title a concatenation of operations.
1931 if (title.startsWith("Copied sequences"))
1937 newtitle = newtitle.concat("- from " + title);
1942 newtitle = new String("Pasted sequences");
1945 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1950 } catch (Exception ex)
1952 ex.printStackTrace();
1953 System.out.println("Exception whilst pasting: " + ex);
1954 // could be anything being pasted in here
1965 protected void cut_actionPerformed(ActionEvent e)
1967 copy_actionPerformed(null);
1968 delete_actionPerformed(null);
1977 protected void delete_actionPerformed(ActionEvent evt)
1980 SequenceGroup sg = viewport.getSelectionGroup();
1986 Vector seqs = new Vector();
1988 for (int i = 0; i < sg.getSize(); i++)
1990 seq = sg.getSequenceAt(i);
1991 seqs.addElement(seq);
1994 // If the cut affects all sequences, remove highlighted columns
1995 if (sg.getSize() == viewport.alignment.getHeight())
1997 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1998 sg.getEndRes() + 1);
2001 SequenceI[] cut = new SequenceI[seqs.size()];
2002 for (int i = 0; i < seqs.size(); i++)
2004 cut[i] = (SequenceI) seqs.elementAt(i);
2008 * //ADD HISTORY ITEM
2010 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2011 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2012 viewport.alignment));
2014 viewport.setSelectionGroup(null);
2015 viewport.sendSelection();
2016 viewport.alignment.deleteGroup(sg);
2018 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2020 if (viewport.getAlignment().getHeight() < 1)
2024 this.setClosed(true);
2025 } catch (Exception ex)
2037 protected void deleteGroups_actionPerformed(ActionEvent e)
2039 viewport.alignment.deleteAllGroups();
2040 viewport.sequenceColours = null;
2041 viewport.setSelectionGroup(null);
2042 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2043 alignPanel.updateAnnotation();
2044 alignPanel.paintAlignment(true);
2053 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2055 SequenceGroup sg = new SequenceGroup();
2057 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2059 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2062 sg.setEndRes(viewport.alignment.getWidth() - 1);
2063 viewport.setSelectionGroup(sg);
2064 viewport.sendSelection();
2065 alignPanel.paintAlignment(true);
2066 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2075 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2077 if (viewport.cursorMode)
2079 alignPanel.seqPanel.keyboardNo1 = null;
2080 alignPanel.seqPanel.keyboardNo2 = null;
2082 viewport.setSelectionGroup(null);
2083 viewport.getColumnSelection().clear();
2084 viewport.setSelectionGroup(null);
2085 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2086 alignPanel.idPanel.idCanvas.searchResults = null;
2087 alignPanel.paintAlignment(true);
2088 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2089 viewport.sendSelection();
2098 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2100 SequenceGroup sg = viewport.getSelectionGroup();
2104 selectAllSequenceMenuItem_actionPerformed(null);
2109 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2111 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2114 alignPanel.paintAlignment(true);
2115 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2116 viewport.sendSelection();
2119 public void invertColSel_actionPerformed(ActionEvent e)
2121 viewport.invertColumnSelection();
2122 alignPanel.paintAlignment(true);
2123 viewport.sendSelection();
2132 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2134 trimAlignment(true);
2143 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2145 trimAlignment(false);
2148 void trimAlignment(boolean trimLeft)
2150 ColumnSelection colSel = viewport.getColumnSelection();
2153 if (colSel.size() > 0)
2157 column = colSel.getMin();
2161 column = colSel.getMax();
2165 if (viewport.getSelectionGroup() != null)
2167 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2168 viewport.hiddenRepSequences);
2172 seqs = viewport.alignment.getSequencesArray();
2175 TrimRegionCommand trimRegion;
2178 trimRegion = new TrimRegionCommand("Remove Left",
2179 TrimRegionCommand.TRIM_LEFT, seqs, column,
2180 viewport.alignment, viewport.colSel,
2181 viewport.selectionGroup);
2182 viewport.setStartRes(0);
2186 trimRegion = new TrimRegionCommand("Remove Right",
2187 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2188 viewport.alignment, viewport.colSel,
2189 viewport.selectionGroup);
2192 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2194 addHistoryItem(trimRegion);
2196 Vector groups = viewport.alignment.getGroups();
2198 for (int i = 0; i < groups.size(); i++)
2200 SequenceGroup sg = (SequenceGroup) groups.get(i);
2202 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2203 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2205 viewport.alignment.deleteGroup(sg);
2209 viewport.firePropertyChange("alignment", null, viewport
2210 .getAlignment().getSequences());
2220 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2222 int start = 0, end = viewport.alignment.getWidth() - 1;
2225 if (viewport.getSelectionGroup() != null)
2227 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2228 viewport.hiddenRepSequences);
2229 start = viewport.getSelectionGroup().getStartRes();
2230 end = viewport.getSelectionGroup().getEndRes();
2234 seqs = viewport.alignment.getSequencesArray();
2237 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2238 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2240 addHistoryItem(removeGapCols);
2242 statusBar.setText("Removed " + removeGapCols.getSize()
2243 + " empty columns.");
2245 // This is to maintain viewport position on first residue
2246 // of first sequence
2247 SequenceI seq = viewport.alignment.getSequenceAt(0);
2248 int startRes = seq.findPosition(viewport.startRes);
2249 // ShiftList shifts;
2250 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2251 // edit.alColumnChanges=shifts.getInverse();
2252 // if (viewport.hasHiddenColumns)
2253 // viewport.getColumnSelection().compensateForEdits(shifts);
2254 viewport.setStartRes(seq.findIndex(startRes) - 1);
2255 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2266 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2268 int start = 0, end = viewport.alignment.getWidth() - 1;
2271 if (viewport.getSelectionGroup() != null)
2273 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2274 viewport.hiddenRepSequences);
2275 start = viewport.getSelectionGroup().getStartRes();
2276 end = viewport.getSelectionGroup().getEndRes();
2280 seqs = viewport.alignment.getSequencesArray();
2283 // This is to maintain viewport position on first residue
2284 // of first sequence
2285 SequenceI seq = viewport.alignment.getSequenceAt(0);
2286 int startRes = seq.findPosition(viewport.startRes);
2288 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2289 viewport.alignment));
2291 viewport.setStartRes(seq.findIndex(startRes) - 1);
2293 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2304 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2306 viewport.padGaps = padGapsMenuitem.isSelected();
2307 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2313 // if (justifySeqs>0)
2315 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2327 public void findMenuItem_actionPerformed(ActionEvent e)
2332 public void newView_actionPerformed(ActionEvent e)
2339 * @param copyAnnotation
2340 * if true then duplicate all annnotation, groups and settings
2341 * @return new alignment panel, already displayed.
2343 public AlignmentPanel newView(boolean copyAnnotation)
2345 return newView(null, copyAnnotation);
2351 * title of newly created view
2352 * @return new alignment panel, already displayed.
2354 public AlignmentPanel newView(String viewTitle)
2356 return newView(viewTitle, true);
2362 * title of newly created view
2363 * @param copyAnnotation
2364 * if true then duplicate all annnotation, groups and settings
2365 * @return new alignment panel, already displayed.
2367 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2369 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2371 if (!copyAnnotation)
2373 // just remove all the current annotation except for the automatic stuff
2374 newap.av.alignment.deleteAllGroups();
2375 for (AlignmentAnnotation alan : newap.av.alignment
2376 .getAlignmentAnnotation())
2378 if (!alan.autoCalculated)
2380 newap.av.alignment.deleteAnnotation(alan);
2386 newap.av.gatherViewsHere = false;
2388 if (viewport.viewName == null)
2390 viewport.viewName = "Original";
2393 newap.av.historyList = viewport.historyList;
2394 newap.av.redoList = viewport.redoList;
2396 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2397 // make sure the new view has a unique name - this is essential for Jalview
2399 boolean addFirstIndex = false;
2400 if (viewTitle == null || viewTitle.trim().length() == 0)
2403 addFirstIndex = true;
2407 index = 1;// we count from 1 if given a specific name
2409 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2410 Vector comps = (Vector) PaintRefresher.components.get(viewport
2411 .getSequenceSetId());
2412 Vector existingNames = new Vector();
2413 for (int i = 0; i < comps.size(); i++)
2415 if (comps.elementAt(i) instanceof AlignmentPanel)
2417 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2418 if (!existingNames.contains(ap.av.viewName))
2420 existingNames.addElement(ap.av.viewName);
2425 while (existingNames.contains(newViewName))
2427 newViewName = viewTitle + " " + (++index);
2430 newap.av.viewName = newViewName;
2432 addAlignmentPanel(newap, true);
2434 if (alignPanels.size() == 2)
2436 viewport.gatherViewsHere = true;
2438 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2442 public void expandViews_actionPerformed(ActionEvent e)
2444 Desktop.instance.explodeViews(this);
2447 public void gatherViews_actionPerformed(ActionEvent e)
2449 Desktop.instance.gatherViews(this);
2458 public void font_actionPerformed(ActionEvent e)
2460 new FontChooser(alignPanel);
2469 protected void seqLimit_actionPerformed(ActionEvent e)
2471 viewport.setShowJVSuffix(seqLimits.isSelected());
2473 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2474 .calculateIdWidth());
2475 alignPanel.paintAlignment(true);
2478 public void idRightAlign_actionPerformed(ActionEvent e)
2480 viewport.rightAlignIds = idRightAlign.isSelected();
2481 alignPanel.paintAlignment(true);
2484 public void centreColumnLabels_actionPerformed(ActionEvent e)
2486 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2487 alignPanel.paintAlignment(true);
2493 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2495 protected void followHighlight_actionPerformed()
2497 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2499 alignPanel.scrollToPosition(
2500 alignPanel.seqPanel.seqCanvas.searchResults, false);
2510 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2512 viewport.setColourText(colourTextMenuItem.isSelected());
2513 alignPanel.paintAlignment(true);
2522 public void wrapMenuItem_actionPerformed(ActionEvent e)
2524 scaleAbove.setVisible(wrapMenuItem.isSelected());
2525 scaleLeft.setVisible(wrapMenuItem.isSelected());
2526 scaleRight.setVisible(wrapMenuItem.isSelected());
2527 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2528 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2531 public void showAllSeqs_actionPerformed(ActionEvent e)
2533 viewport.showAllHiddenSeqs();
2536 public void showAllColumns_actionPerformed(ActionEvent e)
2538 viewport.showAllHiddenColumns();
2542 public void hideSelSequences_actionPerformed(ActionEvent e)
2544 viewport.hideAllSelectedSeqs();
2545 alignPanel.paintAlignment(true);
2549 * called by key handler and the hide all/show all menu items
2554 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2557 boolean hide = false;
2558 SequenceGroup sg = viewport.getSelectionGroup();
2559 if (!toggleSeqs && !toggleCols)
2561 // Hide everything by the current selection - this is a hack - we do the
2562 // invert and then hide
2563 // first check that there will be visible columns after the invert.
2564 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
2565 .getSelected().size() > 0)
2566 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2569 // now invert the sequence set, if required - empty selection implies
2570 // that no hiding is required.
2573 invertSequenceMenuItem_actionPerformed(null);
2574 sg = viewport.getSelectionGroup();
2578 viewport.expandColSelection(sg, true);
2579 // finally invert the column selection and get the new sequence
2581 invertColSel_actionPerformed(null);
2588 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
2590 hideSelSequences_actionPerformed(null);
2593 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
2595 showAllSeqs_actionPerformed(null);
2601 if (viewport.colSel.getSelected().size() > 0)
2603 hideSelColumns_actionPerformed(null);
2606 viewport.selectionGroup = sg;
2611 showAllColumns_actionPerformed(null);
2620 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2621 * event.ActionEvent)
2623 public void hideAllButSelection_actionPerformed(ActionEvent e)
2625 toggleHiddenRegions(false, false);
2632 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2635 public void hideAllSelection_actionPerformed(ActionEvent e)
2637 SequenceGroup sg = viewport.getSelectionGroup();
2638 viewport.expandColSelection(sg, false);
2639 viewport.hideAllSelectedSeqs();
2640 viewport.hideSelectedColumns();
2641 alignPanel.paintAlignment(true);
2648 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2651 public void showAllhidden_actionPerformed(ActionEvent e)
2653 viewport.showAllHiddenColumns();
2654 viewport.showAllHiddenSeqs();
2655 alignPanel.paintAlignment(true);
2658 public void hideSelColumns_actionPerformed(ActionEvent e)
2660 viewport.hideSelectedColumns();
2661 alignPanel.paintAlignment(true);
2664 public void hiddenMarkers_actionPerformed(ActionEvent e)
2666 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2676 protected void scaleAbove_actionPerformed(ActionEvent e)
2678 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2679 alignPanel.paintAlignment(true);
2688 protected void scaleLeft_actionPerformed(ActionEvent e)
2690 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2691 alignPanel.paintAlignment(true);
2700 protected void scaleRight_actionPerformed(ActionEvent e)
2702 viewport.setScaleRightWrapped(scaleRight.isSelected());
2703 alignPanel.paintAlignment(true);
2712 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2714 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2715 alignPanel.paintAlignment(true);
2724 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2726 viewport.setShowText(viewTextMenuItem.isSelected());
2727 alignPanel.paintAlignment(true);
2736 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2738 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2739 alignPanel.paintAlignment(true);
2742 public FeatureSettings featureSettings;
2744 public void featureSettings_actionPerformed(ActionEvent e)
2746 if (featureSettings != null)
2748 featureSettings.close();
2749 featureSettings = null;
2751 if (!showSeqFeatures.isSelected())
2753 // make sure features are actually displayed
2754 showSeqFeatures.setSelected(true);
2755 showSeqFeatures_actionPerformed(null);
2757 featureSettings = new FeatureSettings(this);
2761 * Set or clear 'Show Sequence Features'
2766 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2768 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2769 alignPanel.paintAlignment(true);
2770 if (alignPanel.getOverviewPanel() != null)
2772 alignPanel.getOverviewPanel().updateOverviewImage();
2777 * Set or clear 'Show Sequence Features'
2782 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2784 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2786 if (viewport.getShowSequenceFeaturesHeight())
2788 // ensure we're actually displaying features
2789 viewport.setShowSequenceFeatures(true);
2790 showSeqFeatures.setSelected(true);
2792 alignPanel.paintAlignment(true);
2793 if (alignPanel.getOverviewPanel() != null)
2795 alignPanel.getOverviewPanel().updateOverviewImage();
2805 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2807 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2808 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2811 public void alignmentProperties()
2813 JEditorPane editPane = new JEditorPane("text/html", "");
2814 editPane.setEditable(false);
2815 StringBuffer contents = new AlignmentProperties(viewport.alignment)
2817 editPane.setText("<html>" + contents.toString() + "</html>");
2818 JInternalFrame frame = new JInternalFrame();
2819 frame.getContentPane().add(new JScrollPane(editPane));
2821 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2822 + getTitle(), 500, 400);
2831 public void overviewMenuItem_actionPerformed(ActionEvent e)
2833 if (alignPanel.overviewPanel != null)
2838 JInternalFrame frame = new JInternalFrame();
2839 OverviewPanel overview = new OverviewPanel(alignPanel);
2840 frame.setContentPane(overview);
2841 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2842 frame.getWidth(), frame.getHeight());
2844 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2845 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2847 public void internalFrameClosed(
2848 javax.swing.event.InternalFrameEvent evt)
2850 alignPanel.setOverviewPanel(null);
2854 alignPanel.setOverviewPanel(overview);
2857 public void textColour_actionPerformed(ActionEvent e)
2859 new TextColourChooser().chooseColour(alignPanel, null);
2868 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2879 public void clustalColour_actionPerformed(ActionEvent e)
2881 changeColour(new ClustalxColourScheme(
2882 viewport.alignment.getSequences(),
2883 viewport.alignment.getWidth()));
2892 public void zappoColour_actionPerformed(ActionEvent e)
2894 changeColour(new ZappoColourScheme());
2903 public void taylorColour_actionPerformed(ActionEvent e)
2905 changeColour(new TaylorColourScheme());
2914 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2916 changeColour(new HydrophobicColourScheme());
2925 public void helixColour_actionPerformed(ActionEvent e)
2927 changeColour(new HelixColourScheme());
2936 public void strandColour_actionPerformed(ActionEvent e)
2938 changeColour(new StrandColourScheme());
2947 public void turnColour_actionPerformed(ActionEvent e)
2949 changeColour(new TurnColourScheme());
2958 public void buriedColour_actionPerformed(ActionEvent e)
2960 changeColour(new BuriedColourScheme());
2969 public void nucleotideColour_actionPerformed(ActionEvent e)
2971 changeColour(new NucleotideColourScheme());
2974 public void annotationColour_actionPerformed(ActionEvent e)
2976 new AnnotationColourChooser(viewport, alignPanel);
2985 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2987 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2996 public void changeColour(ColourSchemeI cs)
3002 if (viewport.getAbovePIDThreshold())
3004 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3007 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3009 viewport.setGlobalColourScheme(cs);
3013 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3016 if (viewport.getConservationSelected())
3019 Alignment al = (Alignment) viewport.alignment;
3020 Conservation c = new Conservation("All",
3021 ResidueProperties.propHash, 3, al.getSequences(), 0,
3025 c.verdict(false, viewport.ConsPercGaps);
3027 cs.setConservation(c);
3029 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3034 cs.setConservation(null);
3037 cs.setConsensus(viewport.hconsensus);
3040 viewport.setGlobalColourScheme(cs);
3042 if (viewport.getColourAppliesToAllGroups())
3044 Vector groups = viewport.alignment.getGroups();
3046 for (int i = 0; i < groups.size(); i++)
3048 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
3056 if (cs instanceof ClustalxColourScheme)
3058 sg.cs = new ClustalxColourScheme(
3059 sg.getSequences(viewport.hiddenRepSequences),
3062 else if (cs instanceof UserColourScheme)
3064 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3070 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
3071 } catch (Exception ex)
3076 if (viewport.getAbovePIDThreshold()
3077 || cs instanceof PIDColourScheme
3078 || cs instanceof Blosum62ColourScheme)
3080 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3082 sg.cs.setConsensus(AAFrequency.calculate(
3083 sg.getSequences(viewport.hiddenRepSequences),
3084 sg.getStartRes(), sg.getEndRes() + 1));
3088 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3091 if (viewport.getConservationSelected())
3093 Conservation c = new Conservation("Group",
3094 ResidueProperties.propHash, 3,
3095 sg.getSequences(viewport.hiddenRepSequences),
3096 sg.getStartRes(), sg.getEndRes() + 1);
3098 c.verdict(false, viewport.ConsPercGaps);
3099 sg.cs.setConservation(c);
3103 sg.cs.setConservation(null);
3108 if (alignPanel.getOverviewPanel() != null)
3110 alignPanel.getOverviewPanel().updateOverviewImage();
3113 alignPanel.paintAlignment(true);
3122 protected void modifyPID_actionPerformed(ActionEvent e)
3124 if (viewport.getAbovePIDThreshold()
3125 && viewport.globalColourScheme != null)
3127 SliderPanel.setPIDSliderSource(alignPanel,
3128 viewport.getGlobalColourScheme(), "Background");
3129 SliderPanel.showPIDSlider();
3139 protected void modifyConservation_actionPerformed(ActionEvent e)
3141 if (viewport.getConservationSelected()
3142 && viewport.globalColourScheme != null)
3144 SliderPanel.setConservationSlider(alignPanel,
3145 viewport.globalColourScheme, "Background");
3146 SliderPanel.showConservationSlider();
3156 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3158 viewport.setConservationSelected(conservationMenuItem.isSelected());
3160 viewport.setAbovePIDThreshold(false);
3161 abovePIDThreshold.setSelected(false);
3163 changeColour(viewport.getGlobalColourScheme());
3165 modifyConservation_actionPerformed(null);
3174 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3176 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3178 conservationMenuItem.setSelected(false);
3179 viewport.setConservationSelected(false);
3181 changeColour(viewport.getGlobalColourScheme());
3183 modifyPID_actionPerformed(null);
3192 public void userDefinedColour_actionPerformed(ActionEvent e)
3194 if (e.getActionCommand().equals("User Defined..."))
3196 new UserDefinedColours(alignPanel, null);
3200 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3201 .getUserColourSchemes().get(e.getActionCommand());
3207 public void updateUserColourMenu()
3210 Component[] menuItems = colourMenu.getMenuComponents();
3211 int i, iSize = menuItems.length;
3212 for (i = 0; i < iSize; i++)
3214 if (menuItems[i].getName() != null
3215 && menuItems[i].getName().equals("USER_DEFINED"))
3217 colourMenu.remove(menuItems[i]);
3221 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3223 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3224 .getUserColourSchemes().keys();
3226 while (userColours.hasMoreElements())
3228 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3229 userColours.nextElement().toString());
3230 radioItem.setName("USER_DEFINED");
3231 radioItem.addMouseListener(new MouseAdapter()
3233 public void mousePressed(MouseEvent evt)
3235 if (evt.isControlDown()
3236 || SwingUtilities.isRightMouseButton(evt))
3238 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3240 int option = JOptionPane.showInternalConfirmDialog(
3241 jalview.gui.Desktop.desktop,
3242 "Remove from default list?",
3243 "Remove user defined colour",
3244 JOptionPane.YES_NO_OPTION);
3245 if (option == JOptionPane.YES_OPTION)
3247 jalview.gui.UserDefinedColours
3248 .removeColourFromDefaults(radioItem.getText());
3249 colourMenu.remove(radioItem);
3253 radioItem.addActionListener(new ActionListener()
3255 public void actionPerformed(ActionEvent evt)
3257 userDefinedColour_actionPerformed(evt);
3264 radioItem.addActionListener(new ActionListener()
3266 public void actionPerformed(ActionEvent evt)
3268 userDefinedColour_actionPerformed(evt);
3272 colourMenu.insert(radioItem, 15);
3273 colours.add(radioItem);
3284 public void PIDColour_actionPerformed(ActionEvent e)
3286 changeColour(new PIDColourScheme());
3295 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3297 changeColour(new Blosum62ColourScheme());
3306 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3308 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3309 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3310 .getAlignment().getSequenceAt(0), null);
3311 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3312 viewport.alignment));
3313 alignPanel.paintAlignment(true);
3322 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3324 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3325 AlignmentSorter.sortByID(viewport.getAlignment());
3326 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3327 alignPanel.paintAlignment(true);
3336 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3338 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3339 AlignmentSorter.sortByLength(viewport.getAlignment());
3340 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3341 viewport.alignment));
3342 alignPanel.paintAlignment(true);
3351 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3353 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3354 AlignmentSorter.sortByGroup(viewport.getAlignment());
3355 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3356 viewport.alignment));
3358 alignPanel.paintAlignment(true);
3367 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3369 new RedundancyPanel(alignPanel, this);
3378 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3380 if ((viewport.getSelectionGroup() == null)
3381 || (viewport.getSelectionGroup().getSize() < 2))
3383 JOptionPane.showInternalMessageDialog(this,
3384 "You must select at least 2 sequences.", "Invalid Selection",
3385 JOptionPane.WARNING_MESSAGE);
3389 JInternalFrame frame = new JInternalFrame();
3390 frame.setContentPane(new PairwiseAlignPanel(viewport));
3391 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3401 public void PCAMenuItem_actionPerformed(ActionEvent e)
3403 if (((viewport.getSelectionGroup() != null)
3404 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3405 .getSelectionGroup().getSize() > 0))
3406 || (viewport.getAlignment().getHeight() < 4))
3408 JOptionPane.showInternalMessageDialog(this,
3409 "Principal component analysis must take\n"
3410 + "at least 4 input sequences.",
3411 "Sequence selection insufficient",
3412 JOptionPane.WARNING_MESSAGE);
3417 new PCAPanel(alignPanel);
3420 public void autoCalculate_actionPerformed(ActionEvent e)
3422 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3423 if (viewport.autoCalculateConsensus)
3425 viewport.firePropertyChange("alignment", null, viewport
3426 .getAlignment().getSequences());
3429 public void sortByTreeOption_actionPerformed(ActionEvent e)
3431 viewport.sortByTree = sortByTree.isSelected();
3435 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3437 viewport.followSelection = listenToViewSelections.isSelected();
3445 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3447 NewTreePanel("AV", "PID", "Average distance tree using PID");
3456 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3458 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3467 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3469 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3478 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3480 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3493 void NewTreePanel(String type, String pwType, String title)
3497 if (viewport.getSelectionGroup() != null)
3499 if (viewport.getSelectionGroup().getSize() < 3)
3504 "You need to have more than two sequences selected to build a tree!",
3505 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3510 SequenceGroup sg = viewport.getSelectionGroup();
3512 /* Decide if the selection is a column region */
3513 while (s < sg.getSize())
3515 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3521 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3522 + "Try using the Pad function in the edit menu,\n"
3523 + "or one of the multiple sequence alignment web services.",
3524 "Sequences in selection are not aligned",
3525 JOptionPane.WARNING_MESSAGE);
3531 title = title + " on region";
3532 tp = new TreePanel(alignPanel, type, pwType);
3536 // are the visible sequences aligned?
3537 if (!viewport.alignment.isAligned(false))
3542 "The sequences must be aligned before creating a tree.\n"
3543 + "Try using the Pad function in the edit menu,\n"
3544 + "or one of the multiple sequence alignment web services.",
3545 "Sequences not aligned",
3546 JOptionPane.WARNING_MESSAGE);
3551 if (viewport.alignment.getHeight() < 2)
3556 tp = new TreePanel(alignPanel, type, pwType);
3561 if (viewport.viewName != null)
3563 title += viewport.viewName + " of ";
3566 title += this.title;
3568 Desktop.addInternalFrame(tp, title, 600, 500);
3579 public void addSortByOrderMenuItem(String title,
3580 final AlignmentOrder order)
3582 final JMenuItem item = new JMenuItem("by " + title);
3584 item.addActionListener(new java.awt.event.ActionListener()
3586 public void actionPerformed(ActionEvent e)
3588 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3590 // TODO: JBPNote - have to map order entries to curent SequenceI
3592 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3594 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3595 viewport.alignment));
3597 alignPanel.paintAlignment(true);
3603 * Add a new sort by annotation score menu item
3606 * the menu to add the option to
3608 * the label used to retrieve scores for each sequence on the
3611 public void addSortByAnnotScoreMenuItem(JMenu sort,
3612 final String scoreLabel)
3614 final JMenuItem item = new JMenuItem(scoreLabel);
3616 item.addActionListener(new java.awt.event.ActionListener()
3618 public void actionPerformed(ActionEvent e)
3620 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3621 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3622 viewport.getAlignment());// ,viewport.getSelectionGroup());
3623 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3624 viewport.alignment));
3625 alignPanel.paintAlignment(true);
3631 * last hash for alignment's annotation array - used to minimise cost of
3634 protected int _annotationScoreVectorHash;
3637 * search the alignment and rebuild the sort by annotation score submenu the
3638 * last alignment annotation vector hash is stored to minimize cost of
3639 * rebuilding in subsequence calls.
3642 public void buildSortByAnnotationScoresMenu()
3644 if (viewport.alignment.getAlignmentAnnotation() == null)
3649 if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3651 sortByAnnotScore.removeAll();
3652 // almost certainly a quicker way to do this - but we keep it simple
3653 Hashtable scoreSorts = new Hashtable();
3654 AlignmentAnnotation aann[];
3655 Enumeration sq = viewport.alignment.getSequences().elements();
3656 while (sq.hasMoreElements())
3658 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3659 for (int i = 0; aann != null && i < aann.length; i++)
3661 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3663 scoreSorts.put(aann[i].label, aann[i].label);
3667 Enumeration labels = scoreSorts.keys();
3668 while (labels.hasMoreElements())
3670 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3671 (String) labels.nextElement());
3673 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3676 _annotationScoreVectorHash = viewport.alignment
3677 .getAlignmentAnnotation().hashCode();
3682 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3683 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3684 * call. Listeners are added to remove the menu item when the treePanel is
3685 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3689 * Displayed tree window.
3691 * SortBy menu item title.
3693 public void buildTreeMenu()
3695 sortByTreeMenu.removeAll();
3697 Vector comps = (Vector) PaintRefresher.components.get(viewport
3698 .getSequenceSetId());
3699 Vector treePanels = new Vector();
3700 int i, iSize = comps.size();
3701 for (i = 0; i < iSize; i++)
3703 if (comps.elementAt(i) instanceof TreePanel)
3705 treePanels.add(comps.elementAt(i));
3709 iSize = treePanels.size();
3713 sortByTreeMenu.setVisible(false);
3717 sortByTreeMenu.setVisible(true);
3719 for (i = 0; i < treePanels.size(); i++)
3721 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3722 final JMenuItem item = new JMenuItem(tp.getTitle());
3723 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3724 item.addActionListener(new java.awt.event.ActionListener()
3726 public void actionPerformed(ActionEvent e)
3728 tp.sortByTree_actionPerformed(null);
3729 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3734 sortByTreeMenu.add(item);
3738 public boolean sortBy(AlignmentOrder alorder, String undoname)
3740 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3741 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3742 if (undoname != null)
3744 addHistoryItem(new OrderCommand(undoname, oldOrder,
3745 viewport.alignment));
3747 alignPanel.paintAlignment(true);
3752 * Work out whether the whole set of sequences or just the selected set will
3753 * be submitted for multiple alignment.
3756 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3758 // Now, check we have enough sequences
3759 AlignmentView msa = null;
3761 if ((viewport.getSelectionGroup() != null)
3762 && (viewport.getSelectionGroup().getSize() > 1))
3764 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3765 // some common interface!
3767 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3768 * SequenceI[sz = seqs.getSize(false)];
3770 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3771 * seqs.getSequenceAt(i); }
3773 msa = viewport.getAlignmentView(true);
3778 * Vector seqs = viewport.getAlignment().getSequences();
3780 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3782 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3783 * seqs.elementAt(i); } }
3785 msa = viewport.getAlignmentView(false);
3791 * Decides what is submitted to a secondary structure prediction service: the
3792 * first sequence in the alignment, or in the current selection, or, if the
3793 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3794 * region or the whole alignment. (where the first sequence in the set is the
3795 * one that the prediction will be for).
3797 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3799 AlignmentView seqs = null;
3801 if ((viewport.getSelectionGroup() != null)
3802 && (viewport.getSelectionGroup().getSize() > 0))
3804 seqs = viewport.getAlignmentView(true);
3808 seqs = viewport.getAlignmentView(false);
3810 // limit sequences - JBPNote in future - could spawn multiple prediction
3812 // TODO: viewport.alignment.isAligned is a global state - the local
3813 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3814 if (!viewport.alignment.isAligned(false))
3816 seqs.setSequences(new SeqCigar[]
3817 { seqs.getSequences()[0] });
3818 // TODO: if seqs.getSequences().length>1 then should really have warned
3831 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3833 // Pick the tree file
3834 JalviewFileChooser chooser = new JalviewFileChooser(
3835 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3836 chooser.setFileView(new JalviewFileView());
3837 chooser.setDialogTitle("Select a newick-like tree file");
3838 chooser.setToolTipText("Load a tree file");
3840 int value = chooser.showOpenDialog(null);
3842 if (value == JalviewFileChooser.APPROVE_OPTION)
3844 String choice = chooser.getSelectedFile().getPath();
3845 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3846 jalview.io.NewickFile fin = null;
3849 fin = new jalview.io.NewickFile(choice, "File");
3850 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3851 } catch (Exception ex)
3853 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3854 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3855 ex.printStackTrace();
3857 if (fin != null && fin.hasWarningMessage())
3859 JOptionPane.showMessageDialog(Desktop.desktop,
3860 fin.getWarningMessage(), "Possible problem with tree file",
3861 JOptionPane.WARNING_MESSAGE);
3867 public void loadScores_actionPerformed(ActionEvent e)
3869 // Pick the tree file
3870 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3871 chooser.setFileView(new JalviewFileView());
3872 chooser.setDialogTitle("Select a T-Coffee scores ascii file");
3873 chooser.setToolTipText("Load a score file");
3875 int value = chooser.showOpenDialog(null);
3877 if (value == JalviewFileChooser.APPROVE_OPTION)
3879 String sFilePath = chooser.getSelectedFile().getPath();
3880 jalview.bin.Cache.setProperty("LAST_DIRECTORY", sFilePath);
3885 TCoffeeScoreFile result = TCoffeeScoreFile.load(new File(sFilePath));
3886 if( result == null ) { throw new RuntimeException("The file provided does not match the T-Coffee scores file format"); }
3888 // TODO check that the loaded scores matches the current MSA 'dimension'
3889 changeColour( new TCoffeeColourScheme(result) );
3890 tcoffeeScoreFile = result;
3891 tcoffeeColour.setEnabled(true);
3892 tcoffeeColour.setSelected(true);
3895 catch (Exception ex) {
3896 JOptionPane.showMessageDialog(
3899 "Problem reading tree file",
3900 JOptionPane.WARNING_MESSAGE);
3902 ex.printStackTrace();
3910 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) {
3911 if( tcoffeeScoreFile != null ) {
3912 changeColour( new TCoffeeColourScheme(tcoffeeScoreFile) );
3917 // * Load the (T-Coffee) score file from the specified url
3919 // * @param url The absolute path from where download and read the score file
3920 // * @throws IOException
3922 // public void loadScoreFile(URL url ) throws IOException {
3924 // TCoffeeScoreFile result = new TCoffeeScoreFile();
3925 // result.parse( new InputStreamReader( url.openStream() ) );
3926 // tcoffeeScoreFile = result;
3929 public TreePanel ShowNewickTree(NewickFile nf, String title)
3931 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3934 public TreePanel ShowNewickTree(NewickFile nf, String title,
3935 AlignmentView input)
3937 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3940 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3941 int h, int x, int y)
3943 return ShowNewickTree(nf, title, null, w, h, x, y);
3947 * Add a treeviewer for the tree extracted from a newick file object to the
3948 * current alignment view
3955 * Associated alignment input data (or null)
3964 * @return TreePanel handle
3966 public TreePanel ShowNewickTree(NewickFile nf, String title,
3967 AlignmentView input, int w, int h, int x, int y)
3969 TreePanel tp = null;
3975 if (nf.getTree() != null)
3977 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3983 tp.setLocation(x, y);
3986 Desktop.addInternalFrame(tp, title, w, h);
3988 } catch (Exception ex)
3990 ex.printStackTrace();
3996 private boolean buildingMenu = false;
3999 * Generates menu items and listener event actions for web service clients
4002 public void BuildWebServiceMenu()
4004 while (buildingMenu)
4008 System.err.println("Waiting for building menu to finish.");
4010 } catch (Exception e)
4015 final AlignFrame me = this;
4016 buildingMenu = true;
4017 new Thread(new Runnable()
4023 System.err.println("Building ws menu again "
4024 + Thread.currentThread());
4025 // TODO: add support for context dependent disabling of services based
4027 // alignment and current selection
4028 // TODO: add additional serviceHandle parameter to specify abstract
4030 // class independently of AbstractName
4031 // TODO: add in rediscovery GUI function to restart discoverer
4032 // TODO: group services by location as well as function and/or
4034 // object broker mechanism.
4035 final Vector wsmenu = new Vector();
4036 final IProgressIndicator af = me;
4037 final JMenu msawsmenu = new JMenu("Alignment");
4038 final JMenu secstrmenu = new JMenu(
4039 "Secondary Structure Prediction");
4040 final JMenu seqsrchmenu = new JMenu(
4041 "Sequence Database Search");
4042 final JMenu analymenu = new JMenu(
4044 // JAL-940 - only show secondary structure prediction services from the legacy server
4045 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4047 Discoverer.services != null
4048 && (Discoverer.services.size() > 0))
4050 // TODO: refactor to allow list of AbstractName/Handler bindings to
4052 // stored or retrieved from elsewhere
4053 Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4054 Vector secstrpr = (Vector) Discoverer.services
4056 Vector seqsrch = null; // (Vector) Discoverer.services.get("SeqSearch");
4057 // TODO: move GUI generation code onto service implementation - so a
4058 // client instance attaches itself to the GUI with method call like
4059 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
4063 // Add any Multiple Sequence Alignment Services
4064 for (int i = 0, j = msaws.size(); i < j; i++)
4066 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
4068 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4069 .getServiceClient(sh);
4070 impl.attachWSMenuEntry(msawsmenu, me);
4074 if (secstrpr != null)
4076 // Add any secondary structure prediction services
4077 for (int i = 0, j = secstrpr.size(); i < j; i++)
4079 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4081 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4082 .getServiceClient(sh);
4083 impl.attachWSMenuEntry(secstrmenu, me);
4086 if (seqsrch != null)
4088 // Add any sequence search services
4089 for (int i = 0, j = seqsrch.size(); i < j; i++)
4091 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
4093 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4094 .getServiceClient(sh);
4095 impl.attachWSMenuEntry(seqsrchmenu, me);
4100 // TODO: move into separate menu builder class.
4101 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4103 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4104 if (jws2servs != null)
4106 if (jws2servs.hasServices())
4108 jws2servs.attachWSMenuEntry(msawsmenu, me);
4112 // Add all submenus in the order they should appear on the web services menu
4113 wsmenu.add(msawsmenu);
4114 wsmenu.add(secstrmenu);
4115 wsmenu.add(analymenu);
4116 // No search services yet
4117 // wsmenu.add(seqsrchmenu);
4119 javax.swing.SwingUtilities.invokeLater(new Runnable()
4125 webService.removeAll();
4126 // first, add discovered services onto the webservices menu
4127 if (wsmenu.size() > 0)
4129 for (int i = 0, j = wsmenu.size(); i < j; i++)
4131 webService.add((JMenu) wsmenu.get(i));
4136 webService.add(me.webServiceNoServices);
4138 build_urlServiceMenu(me.webService);
4139 build_fetchdbmenu(webService);
4140 } catch (Exception e)
4146 } catch (Exception e)
4151 buildingMenu = false;
4159 * construct any groupURL type service menu entries.
4163 private void build_urlServiceMenu(JMenu webService)
4165 // TODO: remove this code when 2.7 is released
4166 // DEBUG - alignmentView
4168 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4169 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4171 * @Override public void actionPerformed(ActionEvent e) {
4172 * jalview.datamodel.AlignmentView.testSelectionViews(af.viewport.alignment,
4173 * af.viewport.colSel, af.viewport.selectionGroup); }
4175 * }); webService.add(testAlView);
4177 // TODO: refactor to RestClient discoverer and merge menu entries for
4178 // rest-style services with other types of analysis/calculation service
4179 // SHmmr test client - still being implemented.
4180 // DEBUG - alignmentView
4182 for (jalview.ws.rest.RestClient client: jalview.ws.rest.RestClient.getRestClients()) {
4183 client.attachWSMenuEntry(JvSwingUtils.findOrCreateMenu(webService, client.getAction()), this);
4186 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4188 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4194 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4195 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4196 * getProperty("LAST_DIRECTORY"));
4198 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4199 * to Vamsas file"); chooser.setToolTipText("Export");
4201 * int value = chooser.showSaveDialog(this);
4203 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4204 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4205 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4206 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4209 * prototype of an automatically enabled/disabled analysis function
4212 protected void setShowProductsEnabled()
4214 SequenceI[] selection = viewport.getSequenceSelection();
4215 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4216 viewport.getAlignment().getDataset()))
4218 showProducts.setEnabled(true);
4223 showProducts.setEnabled(false);
4228 * search selection for sequence xRef products and build the show products
4233 * @return true if showProducts menu should be enabled.
4235 public boolean canShowProducts(SequenceI[] selection,
4236 boolean isRegionSelection, Alignment dataset)
4238 boolean showp = false;
4241 showProducts.removeAll();
4242 final boolean dna = viewport.getAlignment().isNucleotide();
4243 final Alignment ds = dataset;
4244 String[] ptypes = (selection == null || selection.length == 0) ? null
4245 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4247 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4248 // selection, dataset, true);
4249 final SequenceI[] sel = selection;
4250 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4253 final boolean isRegSel = isRegionSelection;
4254 final AlignFrame af = this;
4255 final String source = ptypes[t];
4256 JMenuItem xtype = new JMenuItem(ptypes[t]);
4257 xtype.addActionListener(new ActionListener()
4260 public void actionPerformed(ActionEvent e)
4262 // TODO: new thread for this call with vis-delay
4263 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4264 isRegSel, dna, source);
4268 showProducts.add(xtype);
4270 showProducts.setVisible(showp);
4271 showProducts.setEnabled(showp);
4272 } catch (Exception e)
4274 jalview.bin.Cache.log
4275 .warn("canTranslate threw an exception - please report to help@jalview.org",
4282 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4283 boolean isRegSel, boolean dna, String source)
4285 final boolean fisRegSel = isRegSel;
4286 final boolean fdna = dna;
4287 final String fsrc = source;
4288 final AlignFrame ths = this;
4289 final SequenceI[] fsel = sel;
4290 Runnable foo = new Runnable()
4295 final long sttime = System.currentTimeMillis();
4296 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4299 Alignment ds = ths.getViewport().alignment.getDataset(); // update
4303 Alignment prods = CrossRef
4304 .findXrefSequences(fsel, fdna, fsrc, ds);
4307 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4308 for (int s = 0; s < sprods.length; s++)
4310 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4311 if (ds.getSequences() == null
4312 || !ds.getSequences().contains(
4313 sprods[s].getDatasetSequence()))
4314 ds.addSequence(sprods[s].getDatasetSequence());
4315 sprods[s].updatePDBIds();
4317 Alignment al = new Alignment(sprods);
4318 AlignedCodonFrame[] cf = prods.getCodonFrames();
4320 for (int s = 0; cf != null && s < cf.length; s++)
4322 al.addCodonFrame(cf[s]);
4325 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4327 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4328 + " for " + ((fisRegSel) ? "selected region of " : "")
4330 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4335 System.err.println("No Sequences generated for xRef type "
4338 } catch (Exception e)
4340 jalview.bin.Cache.log.error(
4341 "Exception when finding crossreferences", e);
4342 } catch (OutOfMemoryError e)
4344 new OOMWarning("whilst fetching crossreferences", e);
4347 jalview.bin.Cache.log.error("Error when finding crossreferences",
4350 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4355 Thread frunner = new Thread(foo);
4359 public boolean canShowTranslationProducts(SequenceI[] selection,
4360 AlignmentI alignment)
4365 return (jalview.analysis.Dna.canTranslate(selection,
4366 viewport.getViewAsVisibleContigs(true)));
4367 } catch (Exception e)
4369 jalview.bin.Cache.log
4370 .warn("canTranslate threw an exception - please report to help@jalview.org",
4376 public void showProducts_actionPerformed(ActionEvent e)
4378 // /////////////////////////////
4379 // Collect Data to be translated/transferred
4381 SequenceI[] selection = viewport.getSequenceSelection();
4382 AlignmentI al = null;
4385 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4386 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4387 viewport.getAlignment().getDataset());
4388 } catch (Exception ex)
4391 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4398 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4399 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4403 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4404 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4405 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4409 public void showTranslation_actionPerformed(ActionEvent e)
4411 // /////////////////////////////
4412 // Collect Data to be translated/transferred
4414 SequenceI[] selection = viewport.getSequenceSelection();
4415 String[] seqstring = viewport.getViewAsString(true);
4416 AlignmentI al = null;
4419 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4420 viewport.getViewAsVisibleContigs(true), viewport
4421 .getGapCharacter(), viewport.alignment
4422 .getAlignmentAnnotation(), viewport.alignment
4423 .getWidth(), viewport.getAlignment().getDataset());
4424 } catch (Exception ex)
4427 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4434 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4435 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4439 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4440 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4441 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4446 * Try to load a features file onto the alignment.
4449 * contents or path to retrieve file
4451 * access mode of file (see jalview.io.AlignFile)
4452 * @return true if features file was parsed corectly.
4454 public boolean parseFeaturesFile(String file, String type)
4456 boolean featuresFile = false;
4459 featuresFile = new FeaturesFile(file, type)
4460 .parse(viewport.alignment.getDataset(),
4461 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
4462 false, jalview.bin.Cache.getDefault(
4463 "RELAXEDSEQIDMATCHING", false));
4464 } catch (Exception ex)
4466 ex.printStackTrace();
4471 viewport.showSequenceFeatures = true;
4472 showSeqFeatures.setSelected(true);
4473 if (alignPanel.seqPanel.seqCanvas.fr != null)
4475 // update the min/max ranges where necessary
4476 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4478 if (featureSettings != null)
4480 featureSettings.setTableData();
4482 alignPanel.paintAlignment(true);
4485 return featuresFile;
4488 public void dragEnter(DropTargetDragEvent evt)
4492 public void dragExit(DropTargetEvent evt)
4496 public void dragOver(DropTargetDragEvent evt)
4500 public void dropActionChanged(DropTargetDragEvent evt)
4504 public void drop(DropTargetDropEvent evt)
4506 Transferable t = evt.getTransferable();
4507 java.util.List files = null;
4511 DataFlavor uriListFlavor = new DataFlavor(
4512 "text/uri-list;class=java.lang.String");
4513 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4515 // Works on Windows and MacOSX
4516 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4517 files = (java.util.List) t
4518 .getTransferData(DataFlavor.javaFileListFlavor);
4520 else if (t.isDataFlavorSupported(uriListFlavor))
4522 // This is used by Unix drag system
4523 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4524 String data = (String) t.getTransferData(uriListFlavor);
4525 files = new java.util.ArrayList(1);
4526 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4527 data, "\r\n"); st.hasMoreTokens();)
4529 String s = st.nextToken();
4530 if (s.startsWith("#"))
4532 // the line is a comment (as per the RFC 2483)
4536 java.net.URI uri = new java.net.URI(s);
4537 // check to see if we can handle this kind of URI
4538 if (uri.getScheme().toLowerCase().startsWith("http"))
4540 files.add(uri.toString());
4544 // otherwise preserve old behaviour: catch all for file objects
4545 java.io.File file = new java.io.File(uri);
4546 files.add(file.toString());
4550 } catch (Exception e)
4552 e.printStackTrace();
4558 // check to see if any of these files have names matching sequences in
4560 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4561 .getAlignment().getSequencesArray());
4563 * Object[] { String,SequenceI}
4565 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4566 ArrayList<String> filesnotmatched = new ArrayList<String>();
4567 for (int i = 0; i < files.size(); i++)
4569 String file = files.get(i).toString();
4571 String protocol = FormatAdapter.checkProtocol(file);
4572 if (protocol == jalview.io.FormatAdapter.FILE)
4574 File fl = new File(file);
4575 pdbfn = fl.getName();
4577 else if (protocol == jalview.io.FormatAdapter.URL)
4579 URL url = new URL(file);
4580 pdbfn = url.getFile();
4582 if (pdbfn.length() > 0)
4584 // attempt to find a match in the alignment
4585 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4586 int l = 0, c = pdbfn.indexOf(".");
4587 while (mtch == null && c != -1)
4592 } while ((c = pdbfn.indexOf(".", l)) > l);
4595 pdbfn = pdbfn.substring(0, l);
4597 mtch = idm.findAllIdMatches(pdbfn);
4604 type = new IdentifyFile().Identify(file, protocol);
4605 } catch (Exception ex)
4611 if (type.equalsIgnoreCase("PDB"))
4613 filesmatched.add(new Object[]
4614 { file, protocol, mtch });
4619 // File wasn't named like one of the sequences or wasn't a PDB file.
4620 filesnotmatched.add(file);
4624 if (filesmatched.size() > 0)
4626 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4630 "Do you want to automatically associate the "
4631 + filesmatched.size()
4632 + " PDB files with sequences in the alignment that have the same name ?",
4633 "Automatically Associate PDB files by name",
4634 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4637 for (Object[] fm : filesmatched)
4639 // try and associate
4640 // TODO: may want to set a standard ID naming formalism for
4641 // associating PDB files which have no IDs.
4642 for (SequenceI toassoc: (SequenceI[])fm[2]) {
4643 PDBEntry pe = new AssociatePdbFileWithSeq()
4644 .associatePdbWithSeq((String) fm[0], (String) fm[1],
4649 .println("Associated file : " + ((String) fm[0])
4651 + toassoc.getDisplayId(true));
4655 alignPanel.paintAlignment(true);
4659 if (filesnotmatched.size() > 0)
4662 && (Cache.getDefault(
4663 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4666 "<html>Do you want to <em>ignore</em> the "
4667 + filesnotmatched.size()
4668 + " files whose names did not match any sequence IDs ?</html>",
4669 "Ignore unmatched dropped files ?",
4670 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4674 for (String fn : filesnotmatched)
4676 loadJalviewDataFile(fn, null, null, null);
4680 } catch (Exception ex)
4682 ex.printStackTrace();
4688 * Attempt to load a "dropped" file or URL string: First by testing whether
4689 * it's and Annotation file, then a JNet file, and finally a features file. If
4690 * all are false then the user may have dropped an alignment file onto this
4694 * either a filename or a URL string.
4696 public void loadJalviewDataFile(String file, String protocol,
4697 String format, SequenceI assocSeq)
4701 if (protocol == null)
4703 protocol = jalview.io.FormatAdapter.checkProtocol(file);
4705 // if the file isn't identified, or not positively identified as some
4706 // other filetype (PFAM is default unidentified alignment file type) then
4707 // try to parse as annotation.
4708 boolean isAnnotation = (format == null || format
4709 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4710 .readAnnotationFile(viewport.alignment, file, protocol)
4715 // try to see if its a JNet 'concise' style annotation file *before* we
4716 // try to parse it as a features file
4719 format = new IdentifyFile().Identify(file, protocol);
4721 if (format.equalsIgnoreCase("JnetFile"))
4723 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4725 new JnetAnnotationMaker().add_annotation(predictions,
4726 viewport.getAlignment(), 0, false);
4727 isAnnotation = true;
4732 * if (format.equalsIgnoreCase("PDB")) {
4734 * String pdbfn = ""; // try to match up filename with sequence id try
4735 * { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = new
4736 * File(file); pdbfn = fl.getName(); } else if (protocol ==
4737 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4738 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == null)
4739 * { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4740 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { //
4741 * attempt to find a match in the alignment SequenceI mtch =
4742 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4743 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > l)
4744 * { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch =
4745 * idm.findIdMatch(pdbfn); } if (mtch != null) { // try and associate
4746 * // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4747 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) {
4748 * System.err.println("Associated file : " + file + " with " +
4749 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4750 * TODO: maybe need to load as normal otherwise return; } }
4752 // try to parse it as a features file
4753 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4754 // if it wasn't a features file then we just treat it as a general
4755 // alignment file to load into the current view.
4758 new FileLoader().LoadFile(viewport, file, protocol, format);
4762 alignPanel.paintAlignment(true);
4769 alignPanel.adjustAnnotationHeight();
4770 viewport.updateSequenceIdColours();
4771 buildSortByAnnotationScoresMenu();
4772 alignPanel.paintAlignment(true);
4774 } catch (Exception ex)
4776 ex.printStackTrace();
4780 public void tabSelectionChanged(int index)
4784 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4785 viewport = alignPanel.av;
4786 setMenusFromViewport(viewport);
4790 public void tabbedPane_mousePressed(MouseEvent e)
4792 if (SwingUtilities.isRightMouseButton(e))
4794 String reply = JOptionPane.showInternalInputDialog(this,
4795 "Enter View Name", "Edit View Name",
4796 JOptionPane.QUESTION_MESSAGE);
4800 viewport.viewName = reply;
4801 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4806 public AlignViewport getCurrentView()
4812 * Open the dialog for regex description parsing.
4814 protected void extractScores_actionPerformed(ActionEvent e)
4816 ParseProperties pp = new jalview.analysis.ParseProperties(
4817 viewport.alignment);
4818 // TODO: verify regex and introduce GUI dialog for version 2.5
4819 // if (pp.getScoresFromDescription("col", "score column ",
4820 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4822 if (pp.getScoresFromDescription("description column",
4823 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4825 buildSortByAnnotationScoresMenu();
4833 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4836 protected void showDbRefs_actionPerformed(ActionEvent e)
4838 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4844 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4847 protected void showNpFeats_actionPerformed(ActionEvent e)
4849 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4853 * find the viewport amongst the tabs in this alignment frame and close that
4858 public boolean closeView(AlignViewport av)
4862 this.closeMenuItem_actionPerformed(false);
4865 Component[] comp = tabbedPane.getComponents();
4866 for (int i = 0; comp != null && i < comp.length; i++)
4868 if (comp[i] instanceof AlignmentPanel)
4870 if (((AlignmentPanel) comp[i]).av == av)
4873 closeView((AlignmentPanel) comp[i]);
4881 protected void build_fetchdbmenu(JMenu webService)
4883 // Temporary hack - DBRef Fetcher always top level ws entry.
4884 // TODO We probably want to store a sequence database checklist in
4885 // preferences and have checkboxes.. rather than individual sources selected
4887 final JMenu rfetch = new JMenu("Fetch DB References");
4888 rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4889 webService.add(rfetch);
4891 JMenuItem fetchr = new JMenuItem("Standard Databases");
4892 fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4893 fetchr.addActionListener(new ActionListener()
4896 public void actionPerformed(ActionEvent e)
4898 new Thread(new Runnable()
4903 new jalview.ws.DBRefFetcher(alignPanel.av
4904 .getSequenceSelection(), alignPanel.alignFrame)
4905 .fetchDBRefs(false);
4913 final AlignFrame me = this;
4914 new Thread(new Runnable()
4918 final jalview.ws.SequenceFetcher sf = SequenceFetcher
4919 .getSequenceFetcherSingleton(me);
4920 final String[] otherdb = sf.getOrderedSupportedSources();
4921 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4922 // jalview.util.QuickSort.sort(otherdb, otherdb);
4923 javax.swing.SwingUtilities.invokeLater(new Runnable()
4928 JMenu dfetch = new JMenu();
4931 int comp = 0, mcomp = 15;
4932 String mname = null;
4933 if (otherdb != null && otherdb.length > 0)
4935 for (int i = 0; i < otherdb.length; i++)
4937 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4940 mname = "from '" + dbname + "'";
4942 fetchr = new JMenuItem(otherdb[i]);
4943 final String[] dassource = new String[]
4945 fetchr.addActionListener(new ActionListener()
4948 public void actionPerformed(ActionEvent e)
4950 new Thread(new Runnable()
4955 new jalview.ws.DBRefFetcher(alignPanel.av
4956 .getSequenceSelection(),
4957 alignPanel.alignFrame, dassource)
4958 .fetchDBRefs(false);
4964 fetchr.setToolTipText("Retrieve from " + dbname);
4966 if (comp++ == mcomp || i == (otherdb.length - 1))
4968 dfetch.setText(mname + " to '" + dbname + "'");
4970 dfetch = new JMenu();
4984 * Left justify the whole alignment.
4986 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4988 AlignmentI al = viewport.getAlignment();
4990 viewport.firePropertyChange("alignment", null, al);
4994 * Right justify the whole alignment.
4996 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4998 AlignmentI al = viewport.getAlignment();
5000 viewport.firePropertyChange("alignment", null, al);
5003 public void setShowSeqFeatures(boolean b)
5005 showSeqFeatures.setSelected(true);
5006 viewport.setShowSequenceFeatures(true);
5013 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5014 * awt.event.ActionEvent)
5016 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5018 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5019 alignPanel.paintAlignment(true);
5026 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5029 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5031 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5032 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5040 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5041 * .event.ActionEvent)
5043 protected void showGroupConservation_actionPerformed(ActionEvent e)
5045 viewport.setShowGroupConservation(showGroupConservation.getState());
5046 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5053 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5054 * .event.ActionEvent)
5056 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5058 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5059 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5066 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5067 * .event.ActionEvent)
5069 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5071 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5072 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5075 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5077 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5084 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5085 * .event.ActionEvent)
5087 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5089 if (viewport.getSelectionGroup() != null)
5091 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
5092 viewport.getSequenceSelection(),
5093 viewport.getAlignmentView(true).getSequenceStrings(
5094 viewport.getGapCharacter()),
5095 viewport.alignment.getGroups());
5096 viewport.alignment.deleteAllGroups();
5097 viewport.sequenceColours = null;
5098 viewport.setSelectionGroup(null);
5099 // set view properties for each group
5100 for (int g = 0; g < gps.length; g++)
5102 gps[g].setShowNonconserved(viewport.getShowUnconserved());
5103 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
5104 viewport.alignment.addGroup(gps[g]);
5105 Color col = new Color((int) (Math.random() * 255),
5106 (int) (Math.random() * 255), (int) (Math.random() * 255));
5107 col = col.brighter();
5108 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
5109 .hasMoreElements(); viewport.setSequenceColour(
5110 (SequenceI) sq.nextElement(), col))
5113 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5114 alignPanel.updateAnnotation();
5115 alignPanel.paintAlignment(true);
5120 * make the given alignmentPanel the currently selected tab
5122 * @param alignmentPanel
5124 public void setDisplayedView(AlignmentPanel alignmentPanel)
5126 if (!viewport.getSequenceSetId().equals(
5127 alignmentPanel.av.getSequenceSetId()))
5130 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5132 if (tabbedPane != null
5133 & alignPanels.indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5135 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5140 class PrintThread extends Thread
5144 public PrintThread(AlignmentPanel ap)
5149 static PageFormat pf;
5153 PrinterJob printJob = PrinterJob.getPrinterJob();
5157 printJob.setPrintable(ap, pf);
5161 printJob.setPrintable(ap);
5164 if (printJob.printDialog())
5169 } catch (Exception PrintException)
5171 PrintException.printStackTrace();