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();
147 * Last format used to load or save alignments in this window
149 String currentFileFormat = null;
152 * Current filename for this alignment
154 String fileName = null;
157 * Creates a new AlignFrame object with specific width and height.
163 public AlignFrame(AlignmentI al, int width, int height)
165 this(al, null, width, height);
169 * Creates a new AlignFrame object with specific width, height and
175 * @param sequenceSetId
177 public AlignFrame(AlignmentI al, int width, int height,
178 String sequenceSetId)
180 this(al, null, width, height, sequenceSetId);
184 * Creates a new AlignFrame object with specific width, height and
190 * @param sequenceSetId
193 public AlignFrame(AlignmentI al, int width, int height,
194 String sequenceSetId, String viewId)
196 this(al, null, width, height, sequenceSetId, viewId);
200 * new alignment window with hidden columns
204 * @param hiddenColumns
205 * ColumnSelection or null
207 * Width of alignment frame
211 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
212 int width, int height)
214 this(al, hiddenColumns, width, height, null);
218 * Create alignment frame for al with hiddenColumns, a specific width and
219 * height, and specific sequenceId
222 * @param hiddenColumns
225 * @param sequenceSetId
228 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
229 int width, int height, String sequenceSetId)
231 this(al, hiddenColumns, width, height, sequenceSetId, null);
235 * Create alignment frame for al with hiddenColumns, a specific width and
236 * height, and specific sequenceId
239 * @param hiddenColumns
242 * @param sequenceSetId
247 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
248 int width, int height, String sequenceSetId, String viewId)
250 setSize(width, height);
251 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
253 alignPanel = new AlignmentPanel(this, viewport);
255 if (al.getDataset() == null)
260 addAlignmentPanel(alignPanel, true);
265 * Make a new AlignFrame from exisiting alignmentPanels
272 public AlignFrame(AlignmentPanel ap)
276 addAlignmentPanel(ap, false);
281 * initalise the alignframe from the underlying viewport data and the
286 if (viewport.conservation == null)
288 BLOSUM62Colour.setEnabled(false);
289 conservationMenuItem.setEnabled(false);
290 modifyConservation.setEnabled(false);
291 // PIDColour.setEnabled(false);
292 // abovePIDThreshold.setEnabled(false);
293 // modifyPID.setEnabled(false);
296 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
299 if (sortby.equals("Id"))
301 sortIDMenuItem_actionPerformed(null);
303 else if (sortby.equals("Pairwise Identity"))
305 sortPairwiseMenuItem_actionPerformed(null);
308 if (Desktop.desktop != null)
310 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
311 addServiceListeners();
312 setGUINucleotide(viewport.alignment.isNucleotide());
315 setMenusFromViewport(viewport);
316 buildSortByAnnotationScoresMenu();
317 if (viewport.wrapAlignment)
319 wrapMenuItem_actionPerformed(null);
322 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
324 this.overviewMenuItem_actionPerformed(null);
332 * Change the filename and format for the alignment, and enable the 'reload'
333 * button functionality.
340 public void setFileName(String file, String format)
343 currentFileFormat = format;
344 reload.setEnabled(true);
347 void addKeyListener()
349 addKeyListener(new KeyAdapter()
351 public void keyPressed(KeyEvent evt)
353 if (viewport.cursorMode
354 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
355 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
356 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
357 && Character.isDigit(evt.getKeyChar()))
358 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
360 switch (evt.getKeyCode())
363 case 27: // escape key
364 deselectAllSequenceMenuItem_actionPerformed(null);
368 case KeyEvent.VK_DOWN:
369 if (evt.isAltDown() || !viewport.cursorMode)
370 moveSelectedSequences(false);
371 if (viewport.cursorMode)
372 alignPanel.seqPanel.moveCursor(0, 1);
376 if (evt.isAltDown() || !viewport.cursorMode)
377 moveSelectedSequences(true);
378 if (viewport.cursorMode)
379 alignPanel.seqPanel.moveCursor(0, -1);
383 case KeyEvent.VK_LEFT:
384 if (evt.isAltDown() || !viewport.cursorMode)
385 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
387 alignPanel.seqPanel.moveCursor(-1, 0);
391 case KeyEvent.VK_RIGHT:
392 if (evt.isAltDown() || !viewport.cursorMode)
393 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
395 alignPanel.seqPanel.moveCursor(1, 0);
398 case KeyEvent.VK_SPACE:
399 if (viewport.cursorMode)
401 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
402 || evt.isShiftDown() || evt.isAltDown());
406 case KeyEvent.VK_DELETE:
407 case KeyEvent.VK_BACK_SPACE:
408 if (!viewport.cursorMode)
410 cut_actionPerformed(null);
414 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
415 || evt.isShiftDown() || evt.isAltDown());
421 if (viewport.cursorMode)
423 alignPanel.seqPanel.setCursorRow();
427 if (viewport.cursorMode && !evt.isControlDown())
429 alignPanel.seqPanel.setCursorColumn();
433 if (viewport.cursorMode)
435 alignPanel.seqPanel.setCursorPosition();
439 case KeyEvent.VK_ENTER:
440 case KeyEvent.VK_COMMA:
441 if (viewport.cursorMode)
443 alignPanel.seqPanel.setCursorRowAndColumn();
448 if (viewport.cursorMode)
450 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
454 if (viewport.cursorMode)
456 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
461 viewport.cursorMode = !viewport.cursorMode;
462 statusBar.setText("Keyboard editing mode is "
463 + (viewport.cursorMode ? "on" : "off"));
464 if (viewport.cursorMode)
466 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
467 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
469 alignPanel.seqPanel.seqCanvas.repaint();
475 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
476 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
478 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
480 javax.help.HelpBroker hb = hs.createHelpBroker();
481 hb.setCurrentID("home");
482 hb.setDisplayed(true);
483 } catch (Exception ex)
485 ex.printStackTrace();
490 boolean toggleSeqs = !evt.isControlDown();
491 boolean toggleCols = !evt.isShiftDown();
492 toggleHiddenRegions(toggleSeqs, toggleCols);
495 case KeyEvent.VK_PAGE_UP:
496 if (viewport.wrapAlignment)
498 alignPanel.scrollUp(true);
502 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
503 - viewport.endSeq + viewport.startSeq);
506 case KeyEvent.VK_PAGE_DOWN:
507 if (viewport.wrapAlignment)
509 alignPanel.scrollUp(false);
513 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
514 + viewport.endSeq - viewport.startSeq);
520 public void keyReleased(KeyEvent evt)
522 switch (evt.getKeyCode())
524 case KeyEvent.VK_LEFT:
525 if (evt.isAltDown() || !viewport.cursorMode)
526 viewport.firePropertyChange("alignment", null, viewport
527 .getAlignment().getSequences());
530 case KeyEvent.VK_RIGHT:
531 if (evt.isAltDown() || !viewport.cursorMode)
532 viewport.firePropertyChange("alignment", null, viewport
533 .getAlignment().getSequences());
540 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
542 ap.alignFrame = this;
544 alignPanels.addElement(ap);
546 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
548 int aSize = alignPanels.size();
550 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
552 if (aSize == 1 && ap.av.viewName == null)
554 this.getContentPane().add(ap, BorderLayout.CENTER);
560 setInitialTabVisible();
563 expandViews.setEnabled(true);
564 gatherViews.setEnabled(true);
565 tabbedPane.addTab(ap.av.viewName, ap);
567 ap.setVisible(false);
574 ap.av.alignment.padGaps();
576 ap.av.updateConservation(ap);
577 ap.av.updateConsensus(ap);
581 public void setInitialTabVisible()
583 expandViews.setEnabled(true);
584 gatherViews.setEnabled(true);
585 tabbedPane.setVisible(true);
586 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
587 tabbedPane.addTab(first.av.viewName, first);
588 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
591 public AlignViewport getViewport()
596 /* Set up intrinsic listeners for dynamically generated GUI bits. */
597 private void addServiceListeners()
599 final java.beans.PropertyChangeListener thisListener;
600 Desktop.instance.addJalviewPropertyChangeListener("services",
601 thisListener = new java.beans.PropertyChangeListener()
603 public void propertyChange(PropertyChangeEvent evt)
605 // // System.out.println("Discoverer property change.");
606 // if (evt.getPropertyName().equals("services"))
608 SwingUtilities.invokeLater(new Runnable()
614 .println("Rebuild WS Menu for service change");
615 BuildWebServiceMenu();
622 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
624 public void internalFrameClosed(
625 javax.swing.event.InternalFrameEvent evt)
627 System.out.println("deregistering discoverer listener");
628 Desktop.instance.removeJalviewPropertyChangeListener("services",
630 closeMenuItem_actionPerformed(true);
633 // Finally, build the menu once to get current service state
634 new Thread(new Runnable()
638 BuildWebServiceMenu();
643 public void setGUINucleotide(boolean nucleotide)
645 showTranslation.setVisible(nucleotide);
646 conservationMenuItem.setEnabled(!nucleotide);
647 modifyConservation.setEnabled(!nucleotide);
648 showGroupConservation.setEnabled(!nucleotide);
649 // Remember AlignFrame always starts as protein
652 calculateMenu.remove(calculateMenu.getItemCount() - 2);
657 * set up menus for the currently viewport. This may be called after any
658 * operation that affects the data in the current view (selection changed,
659 * etc) to update the menus to reflect the new state.
661 public void setMenusForViewport()
663 setMenusFromViewport(viewport);
667 * Need to call this method when tabs are selected for multiple views, or when
668 * loading from Jalview2XML.java
673 void setMenusFromViewport(AlignViewport av)
675 padGapsMenuitem.setSelected(av.padGaps);
676 colourTextMenuItem.setSelected(av.showColourText);
677 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
678 conservationMenuItem.setSelected(av.getConservationSelected());
679 seqLimits.setSelected(av.getShowJVSuffix());
680 idRightAlign.setSelected(av.rightAlignIds);
681 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
682 renderGapsMenuItem.setSelected(av.renderGaps);
683 wrapMenuItem.setSelected(av.wrapAlignment);
684 scaleAbove.setVisible(av.wrapAlignment);
685 scaleLeft.setVisible(av.wrapAlignment);
686 scaleRight.setVisible(av.wrapAlignment);
687 annotationPanelMenuItem.setState(av.showAnnotation);
688 viewBoxesMenuItem.setSelected(av.showBoxes);
689 viewTextMenuItem.setSelected(av.showText);
690 showNonconservedMenuItem.setSelected(av.showUnconserved);
691 showGroupConsensus.setSelected(av.showGroupConsensus);
692 showGroupConservation.setSelected(av.showGroupConservation);
693 showConsensusHistogram.setSelected(av.showConsensusHistogram);
694 showSequenceLogo.setSelected(av.showSequenceLogo);
695 setColourSelected(ColourSchemeProperty.getColourName(av
696 .getGlobalColourScheme()));
698 showSeqFeatures.setSelected(av.showSequenceFeatures);
699 hiddenMarkers.setState(av.showHiddenMarkers);
700 applyToAllGroups.setState(av.colourAppliesToAllGroups);
701 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
702 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
703 autoCalculate.setSelected(av.autoCalculateConsensus);
704 sortByTree.setSelected(av.sortByTree);
705 listenToViewSelections.setSelected(av.followSelection);
707 setShowProductsEnabled();
712 Hashtable progressBars, progressBarHandlers;
717 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
719 public void setProgressBar(String message, long id)
721 if (progressBars == null)
723 progressBars = new Hashtable();
724 progressBarHandlers = new Hashtable();
727 JPanel progressPanel;
728 Long lId = new Long(id);
729 GridLayout layout = (GridLayout) statusPanel.getLayout();
730 if (progressBars.get(lId) != null)
732 progressPanel = (JPanel) progressBars.get(new Long(id));
733 statusPanel.remove(progressPanel);
734 progressBars.remove(lId);
735 progressPanel = null;
738 statusBar.setText(message);
740 if (progressBarHandlers.contains(lId))
742 progressBarHandlers.remove(lId);
744 layout.setRows(layout.getRows() - 1);
748 progressPanel = new JPanel(new BorderLayout(10, 5));
750 JProgressBar progressBar = new JProgressBar();
751 progressBar.setIndeterminate(true);
753 progressPanel.add(new JLabel(message), BorderLayout.WEST);
754 progressPanel.add(progressBar, BorderLayout.CENTER);
756 layout.setRows(layout.getRows() + 1);
757 statusPanel.add(progressPanel);
759 progressBars.put(lId, progressPanel);
762 // setMenusForViewport();
766 public void registerHandler(final long id,
767 final IProgressIndicatorHandler handler)
769 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
772 "call setProgressBar before registering the progress bar's handler.");
774 progressBarHandlers.put(new Long(id), handler);
775 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
776 if (handler.canCancel())
778 JButton cancel = new JButton("Cancel");
779 final IProgressIndicator us = this;
780 cancel.addActionListener(new ActionListener()
783 public void actionPerformed(ActionEvent e)
785 handler.cancelActivity(id);
788 + ((JLabel) progressPanel.getComponent(0))
792 progressPanel.add(cancel, BorderLayout.EAST);
798 * @return true if any progress bars are still active
800 public boolean operationInProgress()
802 if (progressBars != null && progressBars.size() > 0)
810 * Added so Castor Mapping file can obtain Jalview Version
812 public String getVersion()
814 return jalview.bin.Cache.getProperty("VERSION");
817 public FeatureRenderer getFeatureRenderer()
819 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
822 public void fetchSequence_actionPerformed(ActionEvent e)
824 new SequenceFetcher(this);
827 public void addFromFile_actionPerformed(ActionEvent e)
829 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
832 public void reload_actionPerformed(ActionEvent e)
834 if (fileName != null)
836 // TODO: work out how to recover feature settings for correct view(s) when
838 if (currentFileFormat.equals("Jalview"))
840 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
841 for (int i = 0; i < frames.length; i++)
843 if (frames[i] instanceof AlignFrame && frames[i] != this
844 && ((AlignFrame) frames[i]).fileName.equals(fileName))
848 frames[i].setSelected(true);
849 Desktop.instance.closeAssociatedWindows();
850 } catch (java.beans.PropertyVetoException ex)
856 Desktop.instance.closeAssociatedWindows();
858 FileLoader loader = new FileLoader();
859 String protocol = fileName.startsWith("http:") ? "URL" : "File";
860 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
864 Rectangle bounds = this.getBounds();
866 FileLoader loader = new FileLoader();
867 String protocol = fileName.startsWith("http:") ? "URL" : "File";
868 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
869 protocol, currentFileFormat);
871 newframe.setBounds(bounds);
872 if (featureSettings != null && featureSettings.isShowing())
874 final Rectangle fspos = featureSettings.frame.getBounds();
875 // TODO: need a 'show feature settings' function that takes bounds -
876 // need to refactor Desktop.addFrame
877 newframe.featureSettings_actionPerformed(null);
878 final FeatureSettings nfs = newframe.featureSettings;
879 SwingUtilities.invokeLater(new Runnable()
883 nfs.frame.setBounds(fspos);
886 this.featureSettings.close();
887 this.featureSettings = null;
889 this.closeMenuItem_actionPerformed(true);
894 public void addFromText_actionPerformed(ActionEvent e)
896 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
899 public void addFromURL_actionPerformed(ActionEvent e)
901 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
904 public void save_actionPerformed(ActionEvent e)
907 || (currentFileFormat == null || !jalview.io.FormatAdapter
908 .isValidIOFormat(currentFileFormat, true))
909 || fileName.startsWith("http"))
911 saveAs_actionPerformed(null);
915 saveAlignment(fileName, currentFileFormat);
925 public void saveAs_actionPerformed(ActionEvent e)
927 JalviewFileChooser chooser = new JalviewFileChooser(
928 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
929 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
930 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
931 currentFileFormat, false);
933 chooser.setFileView(new JalviewFileView());
934 chooser.setDialogTitle("Save Alignment to file");
935 chooser.setToolTipText("Save");
937 int value = chooser.showSaveDialog(this);
939 if (value == JalviewFileChooser.APPROVE_OPTION)
941 currentFileFormat = chooser.getSelectedFormat();
942 if (currentFileFormat == null)
944 JOptionPane.showInternalMessageDialog(Desktop.desktop,
945 "You must select a file format before saving!",
946 "File format not specified", JOptionPane.WARNING_MESSAGE);
947 value = chooser.showSaveDialog(this);
951 fileName = chooser.getSelectedFile().getPath();
953 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
956 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
957 if (currentFileFormat.indexOf(" ") > -1)
959 currentFileFormat = currentFileFormat.substring(0,
960 currentFileFormat.indexOf(" "));
962 saveAlignment(fileName, currentFileFormat);
966 public boolean saveAlignment(String file, String format)
968 boolean success = true;
970 if (format.equalsIgnoreCase("Jalview"))
972 String shortName = title;
974 if (shortName.indexOf(java.io.File.separatorChar) > -1)
976 shortName = shortName.substring(shortName
977 .lastIndexOf(java.io.File.separatorChar) + 1);
980 success = new Jalview2XML().SaveAlignment(this, file, shortName);
982 statusBar.setText("Successfully saved to file: " + fileName + " in "
983 + format + " format.");
988 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
990 warningMessage("Cannot save file " + fileName + " using format "
991 + format, "Alignment output format not supported");
992 saveAs_actionPerformed(null);
993 // JBPNote need to have a raise_gui flag here
997 String[] omitHidden = null;
999 if (viewport.hasHiddenColumns)
1001 int reply = JOptionPane
1002 .showInternalConfirmDialog(
1004 "The Alignment contains hidden columns."
1005 + "\nDo you want to save only the visible alignment?",
1006 "Save / Omit Hidden Columns",
1007 JOptionPane.YES_NO_OPTION,
1008 JOptionPane.QUESTION_MESSAGE);
1010 if (reply == JOptionPane.YES_OPTION)
1012 omitHidden = viewport.getViewAsString(false);
1015 FormatAdapter f = new FormatAdapter();
1016 String output = f.formatSequences(format,
1017 viewport.alignment, // class cast exceptions will
1018 // occur in the distant future
1019 omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
1029 java.io.PrintWriter out = new java.io.PrintWriter(
1030 new java.io.FileWriter(file));
1034 this.setTitle(file);
1035 statusBar.setText("Successfully saved to file: " + fileName
1036 + " in " + format + " format.");
1037 } catch (Exception ex)
1040 ex.printStackTrace();
1047 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
1048 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
1054 private void warningMessage(String warning, String title)
1056 if (new jalview.util.Platform().isHeadless())
1058 System.err.println("Warning: " + title + "\nWarning: " + warning);
1063 JOptionPane.showInternalMessageDialog(this, warning, title,
1064 JOptionPane.WARNING_MESSAGE);
1075 protected void outputText_actionPerformed(ActionEvent e)
1077 String[] omitHidden = null;
1079 if (viewport.hasHiddenColumns)
1081 int reply = JOptionPane
1082 .showInternalConfirmDialog(
1084 "The Alignment contains hidden columns."
1085 + "\nDo you want to output only the visible alignment?",
1086 "Save / Omit Hidden Columns",
1087 JOptionPane.YES_NO_OPTION,
1088 JOptionPane.QUESTION_MESSAGE);
1090 if (reply == JOptionPane.YES_OPTION)
1092 omitHidden = viewport.getViewAsString(false);
1096 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1097 cap.setForInput(null);
1101 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1102 viewport.alignment, omitHidden, viewport.colSel));
1103 Desktop.addInternalFrame(cap,
1104 "Alignment output - " + e.getActionCommand(), 600, 500);
1105 } catch (OutOfMemoryError oom)
1107 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1119 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1121 new HTMLOutput(alignPanel,
1122 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1123 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1126 public void createImageMap(File file, String image)
1128 alignPanel.makePNGImageMap(file, image);
1137 public void createPNG(File f)
1139 alignPanel.makePNG(f);
1148 public void createEPS(File f)
1150 alignPanel.makeEPS(f);
1153 public void pageSetup_actionPerformed(ActionEvent e)
1155 PrinterJob printJob = PrinterJob.getPrinterJob();
1156 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1165 public void printMenuItem_actionPerformed(ActionEvent e)
1167 // Putting in a thread avoids Swing painting problems
1168 PrintThread thread = new PrintThread(alignPanel);
1172 public void exportFeatures_actionPerformed(ActionEvent e)
1174 new AnnotationExporter().exportFeatures(alignPanel);
1177 public void exportAnnotations_actionPerformed(ActionEvent e)
1179 new AnnotationExporter().exportAnnotations(
1181 viewport.showAnnotation ? viewport.alignment
1182 .getAlignmentAnnotation() : null, viewport.alignment
1184 ((Alignment) viewport.alignment).alignmentProperties);
1187 public void associatedData_actionPerformed(ActionEvent e)
1189 // Pick the tree file
1190 JalviewFileChooser chooser = new JalviewFileChooser(
1191 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1192 chooser.setFileView(new JalviewFileView());
1193 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1194 chooser.setToolTipText("Load Jalview Annotations / Features file");
1196 int value = chooser.showOpenDialog(null);
1198 if (value == JalviewFileChooser.APPROVE_OPTION)
1200 String choice = chooser.getSelectedFile().getPath();
1201 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1202 loadJalviewDataFile(choice, null, null, null);
1208 * Close the current view or all views in the alignment frame. If the frame
1209 * only contains one view then the alignment will be removed from memory.
1211 * @param closeAllTabs
1213 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1215 if (alignPanels != null && alignPanels.size() < 2)
1217 closeAllTabs = true;
1222 if (alignPanels != null)
1226 if (this.isClosed())
1228 // really close all the windows - otherwise wait till
1229 // setClosed(true) is called
1230 for (int i = 0; i < alignPanels.size(); i++)
1232 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1239 closeView(alignPanel);
1245 this.setClosed(true);
1247 } catch (Exception ex)
1249 ex.printStackTrace();
1254 * close alignPanel2 and shuffle tabs appropriately.
1256 * @param alignPanel2
1258 public void closeView(AlignmentPanel alignPanel2)
1260 int index = tabbedPane.getSelectedIndex();
1261 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1262 alignPanels.removeElement(alignPanel2);
1264 // if (viewport == alignPanel2.av)
1268 alignPanel2.closePanel();
1271 tabbedPane.removeTabAt(closedindex);
1272 tabbedPane.validate();
1274 if (index > closedindex || index == tabbedPane.getTabCount())
1276 // modify currently selected tab index if necessary.
1280 this.tabSelectionChanged(index);
1286 void updateEditMenuBar()
1289 if (viewport.historyList.size() > 0)
1291 undoMenuItem.setEnabled(true);
1292 CommandI command = (CommandI) viewport.historyList.peek();
1293 undoMenuItem.setText("Undo " + command.getDescription());
1297 undoMenuItem.setEnabled(false);
1298 undoMenuItem.setText("Undo");
1301 if (viewport.redoList.size() > 0)
1303 redoMenuItem.setEnabled(true);
1305 CommandI command = (CommandI) viewport.redoList.peek();
1306 redoMenuItem.setText("Redo " + command.getDescription());
1310 redoMenuItem.setEnabled(false);
1311 redoMenuItem.setText("Redo");
1315 public void addHistoryItem(CommandI command)
1317 if (command.getSize() > 0)
1319 viewport.historyList.push(command);
1320 viewport.redoList.clear();
1321 updateEditMenuBar();
1322 viewport.hasHiddenColumns = (viewport.colSel != null
1323 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1324 .getHiddenColumns().size() > 0);
1330 * @return alignment objects for all views
1332 AlignmentI[] getViewAlignments()
1334 if (alignPanels != null)
1336 Enumeration e = alignPanels.elements();
1337 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1338 for (int i = 0; e.hasMoreElements(); i++)
1340 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1344 if (viewport != null)
1346 return new AlignmentI[]
1347 { viewport.alignment };
1358 protected void undoMenuItem_actionPerformed(ActionEvent e)
1360 if (viewport.historyList.empty())
1362 CommandI command = (CommandI) viewport.historyList.pop();
1363 viewport.redoList.push(command);
1364 command.undoCommand(getViewAlignments());
1366 AlignViewport originalSource = getOriginatingSource(command);
1367 updateEditMenuBar();
1369 if (originalSource != null)
1371 originalSource.hasHiddenColumns = (viewport.colSel != null
1372 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1373 .getHiddenColumns().size() > 0);
1374 originalSource.firePropertyChange("alignment", null,
1375 originalSource.alignment.getSequences());
1385 protected void redoMenuItem_actionPerformed(ActionEvent e)
1387 if (viewport.redoList.size() < 1)
1392 CommandI command = (CommandI) viewport.redoList.pop();
1393 viewport.historyList.push(command);
1394 command.doCommand(getViewAlignments());
1396 AlignViewport originalSource = getOriginatingSource(command);
1397 updateEditMenuBar();
1399 if (originalSource != null)
1401 originalSource.hasHiddenColumns = (viewport.colSel != null
1402 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1403 .getHiddenColumns().size() > 0);
1404 originalSource.firePropertyChange("alignment", null,
1405 originalSource.alignment.getSequences());
1409 AlignViewport getOriginatingSource(CommandI command)
1411 AlignViewport originalSource = null;
1412 // For sequence removal and addition, we need to fire
1413 // the property change event FROM the viewport where the
1414 // original alignment was altered
1415 AlignmentI al = null;
1416 if (command instanceof EditCommand)
1418 EditCommand editCommand = (EditCommand) command;
1419 al = editCommand.getAlignment();
1420 Vector comps = (Vector) PaintRefresher.components.get(viewport
1421 .getSequenceSetId());
1423 for (int i = 0; i < comps.size(); i++)
1425 if (comps.elementAt(i) instanceof AlignmentPanel)
1427 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1429 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1436 if (originalSource == null)
1438 // The original view is closed, we must validate
1439 // the current view against the closed view first
1442 PaintRefresher.validateSequences(al, viewport.alignment);
1445 originalSource = viewport;
1448 return originalSource;
1457 public void moveSelectedSequences(boolean up)
1459 SequenceGroup sg = viewport.getSelectionGroup();
1468 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1470 SequenceI seq = viewport.alignment.getSequenceAt(i);
1472 if (!sg.getSequences(null).contains(seq))
1477 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1479 if (sg.getSequences(null).contains(temp))
1484 viewport.alignment.getSequences().setElementAt(temp, i);
1485 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1490 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1492 SequenceI seq = viewport.alignment.getSequenceAt(i);
1494 if (!sg.getSequences(null).contains(seq))
1499 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1501 if (sg.getSequences(null).contains(temp))
1506 viewport.alignment.getSequences().setElementAt(temp, i);
1507 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1511 alignPanel.paintAlignment(true);
1514 synchronized void slideSequences(boolean right, int size)
1516 Vector sg = new Vector();
1517 if (viewport.cursorMode)
1519 sg.addElement(viewport.alignment
1520 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1522 else if (viewport.getSelectionGroup() != null
1523 && viewport.getSelectionGroup().getSize() != viewport.alignment
1526 sg = viewport.getSelectionGroup().getSequences(
1527 viewport.hiddenRepSequences);
1535 Vector invertGroup = new Vector();
1537 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1539 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1540 invertGroup.add(viewport.alignment.getSequenceAt(i));
1543 SequenceI[] seqs1 = new SequenceI[sg.size()];
1544 for (int i = 0; i < sg.size(); i++)
1545 seqs1[i] = (SequenceI) sg.elementAt(i);
1547 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1548 for (int i = 0; i < invertGroup.size(); i++)
1549 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1551 SlideSequencesCommand ssc;
1553 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1554 size, viewport.getGapCharacter());
1556 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1557 size, viewport.getGapCharacter());
1559 int groupAdjustment = 0;
1560 if (ssc.getGapsInsertedBegin() && right)
1562 if (viewport.cursorMode)
1563 alignPanel.seqPanel.moveCursor(size, 0);
1565 groupAdjustment = size;
1567 else if (!ssc.getGapsInsertedBegin() && !right)
1569 if (viewport.cursorMode)
1570 alignPanel.seqPanel.moveCursor(-size, 0);
1572 groupAdjustment = -size;
1575 if (groupAdjustment != 0)
1577 viewport.getSelectionGroup().setStartRes(
1578 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1579 viewport.getSelectionGroup().setEndRes(
1580 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1583 boolean appendHistoryItem = false;
1584 if (viewport.historyList != null && viewport.historyList.size() > 0
1585 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1587 appendHistoryItem = ssc
1588 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1592 if (!appendHistoryItem)
1593 addHistoryItem(ssc);
1604 protected void copy_actionPerformed(ActionEvent e)
1607 if (viewport.getSelectionGroup() == null)
1611 // TODO: preserve the ordering of displayed alignment annotation in any
1612 // internal paste (particularly sequence associated annotation)
1613 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1614 String[] omitHidden = null;
1616 if (viewport.hasHiddenColumns)
1618 omitHidden = viewport.getViewAsString(true);
1621 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1624 StringSelection ss = new StringSelection(output);
1628 jalview.gui.Desktop.internalCopy = true;
1629 // Its really worth setting the clipboard contents
1630 // to empty before setting the large StringSelection!!
1631 Toolkit.getDefaultToolkit().getSystemClipboard()
1632 .setContents(new StringSelection(""), null);
1634 Toolkit.getDefaultToolkit().getSystemClipboard()
1635 .setContents(ss, Desktop.instance);
1636 } catch (OutOfMemoryError er)
1638 new OOMWarning("copying region", er);
1642 Vector hiddenColumns = null;
1643 if (viewport.hasHiddenColumns)
1645 hiddenColumns = new Vector();
1646 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1647 .getSelectionGroup().getEndRes();
1648 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1651 int[] region = (int[]) viewport.getColumnSelection()
1652 .getHiddenColumns().elementAt(i);
1653 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1655 hiddenColumns.addElement(new int[]
1656 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1661 Desktop.jalviewClipboard = new Object[]
1662 { seqs, viewport.alignment.getDataset(), hiddenColumns };
1663 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1672 protected void pasteNew_actionPerformed(ActionEvent e)
1683 protected void pasteThis_actionPerformed(ActionEvent e)
1689 * Paste contents of Jalview clipboard
1691 * @param newAlignment
1692 * true to paste to a new alignment, otherwise add to this.
1694 void paste(boolean newAlignment)
1696 boolean externalPaste = true;
1699 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1700 Transferable contents = c.getContents(this);
1702 if (contents == null)
1710 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1711 if (str.length() < 1)
1716 format = new IdentifyFile().Identify(str, "Paste");
1718 } catch (OutOfMemoryError er)
1720 new OOMWarning("Out of memory pasting sequences!!", er);
1724 SequenceI[] sequences;
1725 boolean annotationAdded = false;
1726 AlignmentI alignment = null;
1728 if (Desktop.jalviewClipboard != null)
1730 // The clipboard was filled from within Jalview, we must use the
1732 // And dataset from the copied alignment
1733 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1734 // be doubly sure that we create *new* sequence objects.
1735 sequences = new SequenceI[newseq.length];
1736 for (int i = 0; i < newseq.length; i++)
1738 sequences[i] = new Sequence(newseq[i]);
1740 alignment = new Alignment(sequences);
1741 externalPaste = false;
1745 // parse the clipboard as an alignment.
1746 alignment = new FormatAdapter().readFile(str, "Paste", format);
1747 sequences = alignment.getSequencesArray();
1755 if (Desktop.jalviewClipboard != null)
1757 // dataset is inherited
1758 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1762 // new dataset is constructed
1763 alignment.setDataset(null);
1765 alwidth = alignment.getWidth() + 1;
1769 AlignmentI pastedal = alignment; // preserve pasted alignment object
1770 // Add pasted sequences and dataset into existing alignment.
1771 alignment = viewport.getAlignment();
1772 alwidth = alignment.getWidth() + 1;
1773 // decide if we need to import sequences from an existing dataset
1774 boolean importDs = Desktop.jalviewClipboard != null
1775 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1776 // importDs==true instructs us to copy over new dataset sequences from
1777 // an existing alignment
1778 Vector newDs = (importDs) ? new Vector() : null; // used to create
1779 // minimum dataset set
1781 for (int i = 0; i < sequences.length; i++)
1785 newDs.addElement(null);
1787 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1789 if (importDs && ds != null)
1791 if (!newDs.contains(ds))
1793 newDs.setElementAt(ds, i);
1794 ds = new Sequence(ds);
1795 // update with new dataset sequence
1796 sequences[i].setDatasetSequence(ds);
1800 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1805 // copy and derive new dataset sequence
1806 sequences[i] = sequences[i].deriveSequence();
1807 alignment.getDataset().addSequence(
1808 sequences[i].getDatasetSequence());
1809 // TODO: avoid creation of duplicate dataset sequences with a
1810 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1812 alignment.addSequence(sequences[i]); // merges dataset
1816 newDs.clear(); // tidy up
1818 if (pastedal.getAlignmentAnnotation() != null)
1820 // Add any annotation attached to alignment.
1821 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1822 for (int i = 0; i < alann.length; i++)
1824 annotationAdded = true;
1825 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1827 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1828 newann.padAnnotation(alwidth);
1829 alignment.addAnnotation(newann);
1839 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1840 sequences, 0, alignment.getWidth(), alignment));
1842 // Add any annotations attached to sequences
1843 for (int i = 0; i < sequences.length; i++)
1845 if (sequences[i].getAnnotation() != null)
1847 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1849 annotationAdded = true;
1850 sequences[i].getAnnotation()[a].adjustForAlignment();
1851 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1852 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1857 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1864 // propagate alignment changed.
1865 viewport.setEndSeq(alignment.getHeight());
1866 if (annotationAdded)
1868 // Duplicate sequence annotation in all views.
1869 AlignmentI[] alview = this.getViewAlignments();
1870 for (int i = 0; i < sequences.length; i++)
1872 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1875 for (int avnum = 0; avnum < alview.length; avnum++)
1877 if (alview[avnum] != alignment)
1879 // duplicate in a view other than the one with input focus
1880 int avwidth = alview[avnum].getWidth() + 1;
1881 // this relies on sann being preserved after we
1882 // modify the sequence's annotation array for each duplication
1883 for (int a = 0; a < sann.length; a++)
1885 AlignmentAnnotation newann = new AlignmentAnnotation(
1887 sequences[i].addAlignmentAnnotation(newann);
1888 newann.padAnnotation(avwidth);
1889 alview[avnum].addAnnotation(newann); // annotation was
1890 // duplicated earlier
1891 alview[avnum].setAnnotationIndex(newann, a);
1896 buildSortByAnnotationScoresMenu();
1898 viewport.firePropertyChange("alignment", null,
1899 alignment.getSequences());
1904 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1906 String newtitle = new String("Copied sequences");
1908 if (Desktop.jalviewClipboard != null
1909 && Desktop.jalviewClipboard[2] != null)
1911 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1912 for (int i = 0; i < hc.size(); i++)
1914 int[] region = (int[]) hc.elementAt(i);
1915 af.viewport.hideColumns(region[0], region[1]);
1919 // >>>This is a fix for the moment, until a better solution is
1921 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1923 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1925 // TODO: maintain provenance of an alignment, rather than just make the
1926 // title a concatenation of operations.
1929 if (title.startsWith("Copied sequences"))
1935 newtitle = newtitle.concat("- from " + title);
1940 newtitle = new String("Pasted sequences");
1943 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1948 } catch (Exception ex)
1950 ex.printStackTrace();
1951 System.out.println("Exception whilst pasting: " + ex);
1952 // could be anything being pasted in here
1963 protected void cut_actionPerformed(ActionEvent e)
1965 copy_actionPerformed(null);
1966 delete_actionPerformed(null);
1975 protected void delete_actionPerformed(ActionEvent evt)
1978 SequenceGroup sg = viewport.getSelectionGroup();
1984 Vector seqs = new Vector();
1986 for (int i = 0; i < sg.getSize(); i++)
1988 seq = sg.getSequenceAt(i);
1989 seqs.addElement(seq);
1992 // If the cut affects all sequences, remove highlighted columns
1993 if (sg.getSize() == viewport.alignment.getHeight())
1995 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1996 sg.getEndRes() + 1);
1999 SequenceI[] cut = new SequenceI[seqs.size()];
2000 for (int i = 0; i < seqs.size(); i++)
2002 cut[i] = (SequenceI) seqs.elementAt(i);
2006 * //ADD HISTORY ITEM
2008 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2009 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2010 viewport.alignment));
2012 viewport.setSelectionGroup(null);
2013 viewport.sendSelection();
2014 viewport.alignment.deleteGroup(sg);
2016 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2018 if (viewport.getAlignment().getHeight() < 1)
2022 this.setClosed(true);
2023 } catch (Exception ex)
2035 protected void deleteGroups_actionPerformed(ActionEvent e)
2037 viewport.alignment.deleteAllGroups();
2038 viewport.sequenceColours = null;
2039 viewport.setSelectionGroup(null);
2040 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2041 alignPanel.updateAnnotation();
2042 alignPanel.paintAlignment(true);
2051 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2053 SequenceGroup sg = new SequenceGroup();
2055 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2057 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2060 sg.setEndRes(viewport.alignment.getWidth() - 1);
2061 viewport.setSelectionGroup(sg);
2062 viewport.sendSelection();
2063 alignPanel.paintAlignment(true);
2064 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2073 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2075 if (viewport.cursorMode)
2077 alignPanel.seqPanel.keyboardNo1 = null;
2078 alignPanel.seqPanel.keyboardNo2 = null;
2080 viewport.setSelectionGroup(null);
2081 viewport.getColumnSelection().clear();
2082 viewport.setSelectionGroup(null);
2083 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2084 alignPanel.idPanel.idCanvas.searchResults = null;
2085 alignPanel.paintAlignment(true);
2086 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2087 viewport.sendSelection();
2096 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2098 SequenceGroup sg = viewport.getSelectionGroup();
2102 selectAllSequenceMenuItem_actionPerformed(null);
2107 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2109 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2112 alignPanel.paintAlignment(true);
2113 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2114 viewport.sendSelection();
2117 public void invertColSel_actionPerformed(ActionEvent e)
2119 viewport.invertColumnSelection();
2120 alignPanel.paintAlignment(true);
2121 viewport.sendSelection();
2130 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2132 trimAlignment(true);
2141 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2143 trimAlignment(false);
2146 void trimAlignment(boolean trimLeft)
2148 ColumnSelection colSel = viewport.getColumnSelection();
2151 if (colSel.size() > 0)
2155 column = colSel.getMin();
2159 column = colSel.getMax();
2163 if (viewport.getSelectionGroup() != null)
2165 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2166 viewport.hiddenRepSequences);
2170 seqs = viewport.alignment.getSequencesArray();
2173 TrimRegionCommand trimRegion;
2176 trimRegion = new TrimRegionCommand("Remove Left",
2177 TrimRegionCommand.TRIM_LEFT, seqs, column,
2178 viewport.alignment, viewport.colSel,
2179 viewport.selectionGroup);
2180 viewport.setStartRes(0);
2184 trimRegion = new TrimRegionCommand("Remove Right",
2185 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2186 viewport.alignment, viewport.colSel,
2187 viewport.selectionGroup);
2190 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2192 addHistoryItem(trimRegion);
2194 Vector groups = viewport.alignment.getGroups();
2196 for (int i = 0; i < groups.size(); i++)
2198 SequenceGroup sg = (SequenceGroup) groups.get(i);
2200 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2201 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2203 viewport.alignment.deleteGroup(sg);
2207 viewport.firePropertyChange("alignment", null, viewport
2208 .getAlignment().getSequences());
2218 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2220 int start = 0, end = viewport.alignment.getWidth() - 1;
2223 if (viewport.getSelectionGroup() != null)
2225 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2226 viewport.hiddenRepSequences);
2227 start = viewport.getSelectionGroup().getStartRes();
2228 end = viewport.getSelectionGroup().getEndRes();
2232 seqs = viewport.alignment.getSequencesArray();
2235 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2236 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2238 addHistoryItem(removeGapCols);
2240 statusBar.setText("Removed " + removeGapCols.getSize()
2241 + " empty columns.");
2243 // This is to maintain viewport position on first residue
2244 // of first sequence
2245 SequenceI seq = viewport.alignment.getSequenceAt(0);
2246 int startRes = seq.findPosition(viewport.startRes);
2247 // ShiftList shifts;
2248 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2249 // edit.alColumnChanges=shifts.getInverse();
2250 // if (viewport.hasHiddenColumns)
2251 // viewport.getColumnSelection().compensateForEdits(shifts);
2252 viewport.setStartRes(seq.findIndex(startRes) - 1);
2253 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2264 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2266 int start = 0, end = viewport.alignment.getWidth() - 1;
2269 if (viewport.getSelectionGroup() != null)
2271 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2272 viewport.hiddenRepSequences);
2273 start = viewport.getSelectionGroup().getStartRes();
2274 end = viewport.getSelectionGroup().getEndRes();
2278 seqs = viewport.alignment.getSequencesArray();
2281 // This is to maintain viewport position on first residue
2282 // of first sequence
2283 SequenceI seq = viewport.alignment.getSequenceAt(0);
2284 int startRes = seq.findPosition(viewport.startRes);
2286 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2287 viewport.alignment));
2289 viewport.setStartRes(seq.findIndex(startRes) - 1);
2291 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2302 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2304 viewport.padGaps = padGapsMenuitem.isSelected();
2305 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2311 // if (justifySeqs>0)
2313 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2325 public void findMenuItem_actionPerformed(ActionEvent e)
2330 public void newView_actionPerformed(ActionEvent e)
2337 * @param copyAnnotation
2338 * if true then duplicate all annnotation, groups and settings
2339 * @return new alignment panel, already displayed.
2341 public AlignmentPanel newView(boolean copyAnnotation)
2343 return newView(null, copyAnnotation);
2349 * title of newly created view
2350 * @return new alignment panel, already displayed.
2352 public AlignmentPanel newView(String viewTitle)
2354 return newView(viewTitle, true);
2360 * title of newly created view
2361 * @param copyAnnotation
2362 * if true then duplicate all annnotation, groups and settings
2363 * @return new alignment panel, already displayed.
2365 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2367 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2369 if (!copyAnnotation)
2371 // just remove all the current annotation except for the automatic stuff
2372 newap.av.alignment.deleteAllGroups();
2373 for (AlignmentAnnotation alan : newap.av.alignment
2374 .getAlignmentAnnotation())
2376 if (!alan.autoCalculated)
2378 newap.av.alignment.deleteAnnotation(alan);
2384 newap.av.gatherViewsHere = false;
2386 if (viewport.viewName == null)
2388 viewport.viewName = "Original";
2391 newap.av.historyList = viewport.historyList;
2392 newap.av.redoList = viewport.redoList;
2394 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2395 // make sure the new view has a unique name - this is essential for Jalview
2397 boolean addFirstIndex = false;
2398 if (viewTitle == null || viewTitle.trim().length() == 0)
2401 addFirstIndex = true;
2405 index = 1;// we count from 1 if given a specific name
2407 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2408 Vector comps = (Vector) PaintRefresher.components.get(viewport
2409 .getSequenceSetId());
2410 Vector existingNames = new Vector();
2411 for (int i = 0; i < comps.size(); i++)
2413 if (comps.elementAt(i) instanceof AlignmentPanel)
2415 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2416 if (!existingNames.contains(ap.av.viewName))
2418 existingNames.addElement(ap.av.viewName);
2423 while (existingNames.contains(newViewName))
2425 newViewName = viewTitle + " " + (++index);
2428 newap.av.viewName = newViewName;
2430 addAlignmentPanel(newap, true);
2432 if (alignPanels.size() == 2)
2434 viewport.gatherViewsHere = true;
2436 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2440 public void expandViews_actionPerformed(ActionEvent e)
2442 Desktop.instance.explodeViews(this);
2445 public void gatherViews_actionPerformed(ActionEvent e)
2447 Desktop.instance.gatherViews(this);
2456 public void font_actionPerformed(ActionEvent e)
2458 new FontChooser(alignPanel);
2467 protected void seqLimit_actionPerformed(ActionEvent e)
2469 viewport.setShowJVSuffix(seqLimits.isSelected());
2471 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2472 .calculateIdWidth());
2473 alignPanel.paintAlignment(true);
2476 public void idRightAlign_actionPerformed(ActionEvent e)
2478 viewport.rightAlignIds = idRightAlign.isSelected();
2479 alignPanel.paintAlignment(true);
2482 public void centreColumnLabels_actionPerformed(ActionEvent e)
2484 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2485 alignPanel.paintAlignment(true);
2491 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2493 protected void followHighlight_actionPerformed()
2495 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2497 alignPanel.scrollToPosition(
2498 alignPanel.seqPanel.seqCanvas.searchResults, false);
2508 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2510 viewport.setColourText(colourTextMenuItem.isSelected());
2511 alignPanel.paintAlignment(true);
2520 public void wrapMenuItem_actionPerformed(ActionEvent e)
2522 scaleAbove.setVisible(wrapMenuItem.isSelected());
2523 scaleLeft.setVisible(wrapMenuItem.isSelected());
2524 scaleRight.setVisible(wrapMenuItem.isSelected());
2525 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2526 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2529 public void showAllSeqs_actionPerformed(ActionEvent e)
2531 viewport.showAllHiddenSeqs();
2534 public void showAllColumns_actionPerformed(ActionEvent e)
2536 viewport.showAllHiddenColumns();
2540 public void hideSelSequences_actionPerformed(ActionEvent e)
2542 viewport.hideAllSelectedSeqs();
2543 alignPanel.paintAlignment(true);
2547 * called by key handler and the hide all/show all menu items
2552 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2555 boolean hide = false;
2556 SequenceGroup sg = viewport.getSelectionGroup();
2557 if (!toggleSeqs && !toggleCols)
2559 // Hide everything by the current selection - this is a hack - we do the
2560 // invert and then hide
2561 // first check that there will be visible columns after the invert.
2562 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
2563 .getSelected().size() > 0)
2564 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2567 // now invert the sequence set, if required - empty selection implies
2568 // that no hiding is required.
2571 invertSequenceMenuItem_actionPerformed(null);
2572 sg = viewport.getSelectionGroup();
2576 viewport.expandColSelection(sg, true);
2577 // finally invert the column selection and get the new sequence
2579 invertColSel_actionPerformed(null);
2586 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
2588 hideSelSequences_actionPerformed(null);
2591 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
2593 showAllSeqs_actionPerformed(null);
2599 if (viewport.colSel.getSelected().size() > 0)
2601 hideSelColumns_actionPerformed(null);
2604 viewport.selectionGroup = sg;
2609 showAllColumns_actionPerformed(null);
2618 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2619 * event.ActionEvent)
2621 public void hideAllButSelection_actionPerformed(ActionEvent e)
2623 toggleHiddenRegions(false, false);
2630 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2633 public void hideAllSelection_actionPerformed(ActionEvent e)
2635 SequenceGroup sg = viewport.getSelectionGroup();
2636 viewport.expandColSelection(sg, false);
2637 viewport.hideAllSelectedSeqs();
2638 viewport.hideSelectedColumns();
2639 alignPanel.paintAlignment(true);
2646 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2649 public void showAllhidden_actionPerformed(ActionEvent e)
2651 viewport.showAllHiddenColumns();
2652 viewport.showAllHiddenSeqs();
2653 alignPanel.paintAlignment(true);
2656 public void hideSelColumns_actionPerformed(ActionEvent e)
2658 viewport.hideSelectedColumns();
2659 alignPanel.paintAlignment(true);
2662 public void hiddenMarkers_actionPerformed(ActionEvent e)
2664 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2674 protected void scaleAbove_actionPerformed(ActionEvent e)
2676 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2677 alignPanel.paintAlignment(true);
2686 protected void scaleLeft_actionPerformed(ActionEvent e)
2688 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2689 alignPanel.paintAlignment(true);
2698 protected void scaleRight_actionPerformed(ActionEvent e)
2700 viewport.setScaleRightWrapped(scaleRight.isSelected());
2701 alignPanel.paintAlignment(true);
2710 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2712 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2713 alignPanel.paintAlignment(true);
2722 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2724 viewport.setShowText(viewTextMenuItem.isSelected());
2725 alignPanel.paintAlignment(true);
2734 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2736 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2737 alignPanel.paintAlignment(true);
2740 public FeatureSettings featureSettings;
2742 public void featureSettings_actionPerformed(ActionEvent e)
2744 if (featureSettings != null)
2746 featureSettings.close();
2747 featureSettings = null;
2749 if (!showSeqFeatures.isSelected())
2751 // make sure features are actually displayed
2752 showSeqFeatures.setSelected(true);
2753 showSeqFeatures_actionPerformed(null);
2755 featureSettings = new FeatureSettings(this);
2759 * Set or clear 'Show Sequence Features'
2764 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2766 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2767 alignPanel.paintAlignment(true);
2768 if (alignPanel.getOverviewPanel() != null)
2770 alignPanel.getOverviewPanel().updateOverviewImage();
2775 * Set or clear 'Show Sequence Features'
2780 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2782 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2784 if (viewport.getShowSequenceFeaturesHeight())
2786 // ensure we're actually displaying features
2787 viewport.setShowSequenceFeatures(true);
2788 showSeqFeatures.setSelected(true);
2790 alignPanel.paintAlignment(true);
2791 if (alignPanel.getOverviewPanel() != null)
2793 alignPanel.getOverviewPanel().updateOverviewImage();
2803 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2805 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2806 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2809 public void alignmentProperties()
2811 JEditorPane editPane = new JEditorPane("text/html", "");
2812 editPane.setEditable(false);
2813 StringBuffer contents = new AlignmentProperties(viewport.alignment)
2815 editPane.setText("<html>" + contents.toString() + "</html>");
2816 JInternalFrame frame = new JInternalFrame();
2817 frame.getContentPane().add(new JScrollPane(editPane));
2819 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2820 + getTitle(), 500, 400);
2829 public void overviewMenuItem_actionPerformed(ActionEvent e)
2831 if (alignPanel.overviewPanel != null)
2836 JInternalFrame frame = new JInternalFrame();
2837 OverviewPanel overview = new OverviewPanel(alignPanel);
2838 frame.setContentPane(overview);
2839 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2840 frame.getWidth(), frame.getHeight());
2842 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2843 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2845 public void internalFrameClosed(
2846 javax.swing.event.InternalFrameEvent evt)
2848 alignPanel.setOverviewPanel(null);
2852 alignPanel.setOverviewPanel(overview);
2855 public void textColour_actionPerformed(ActionEvent e)
2857 new TextColourChooser().chooseColour(alignPanel, null);
2866 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2877 public void clustalColour_actionPerformed(ActionEvent e)
2879 changeColour(new ClustalxColourScheme(
2880 viewport.alignment.getSequences(),
2881 viewport.alignment.getWidth()));
2890 public void zappoColour_actionPerformed(ActionEvent e)
2892 changeColour(new ZappoColourScheme());
2901 public void taylorColour_actionPerformed(ActionEvent e)
2903 changeColour(new TaylorColourScheme());
2912 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2914 changeColour(new HydrophobicColourScheme());
2923 public void helixColour_actionPerformed(ActionEvent e)
2925 changeColour(new HelixColourScheme());
2934 public void strandColour_actionPerformed(ActionEvent e)
2936 changeColour(new StrandColourScheme());
2945 public void turnColour_actionPerformed(ActionEvent e)
2947 changeColour(new TurnColourScheme());
2956 public void buriedColour_actionPerformed(ActionEvent e)
2958 changeColour(new BuriedColourScheme());
2967 public void nucleotideColour_actionPerformed(ActionEvent e)
2969 changeColour(new NucleotideColourScheme());
2972 public void annotationColour_actionPerformed(ActionEvent e)
2974 new AnnotationColourChooser(viewport, alignPanel);
2983 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2985 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2994 public void changeColour(ColourSchemeI cs)
3000 if (viewport.getAbovePIDThreshold())
3002 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3005 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3007 viewport.setGlobalColourScheme(cs);
3011 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3014 if (viewport.getConservationSelected())
3017 Alignment al = (Alignment) viewport.alignment;
3018 Conservation c = new Conservation("All",
3019 ResidueProperties.propHash, 3, al.getSequences(), 0,
3023 c.verdict(false, viewport.ConsPercGaps);
3025 cs.setConservation(c);
3027 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3032 cs.setConservation(null);
3035 cs.setConsensus(viewport.hconsensus);
3038 viewport.setGlobalColourScheme(cs);
3040 if (viewport.getColourAppliesToAllGroups())
3042 Vector groups = viewport.alignment.getGroups();
3044 for (int i = 0; i < groups.size(); i++)
3046 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
3054 if (cs instanceof ClustalxColourScheme)
3056 sg.cs = new ClustalxColourScheme(
3057 sg.getSequences(viewport.hiddenRepSequences),
3060 else if (cs instanceof UserColourScheme)
3062 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3068 sg.cs = cs.getClass().newInstance();
3069 } catch (Exception ex)
3074 if (viewport.getAbovePIDThreshold()
3075 || cs instanceof PIDColourScheme
3076 || cs instanceof Blosum62ColourScheme)
3078 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3080 sg.cs.setConsensus(AAFrequency.calculate(
3081 sg.getSequences(viewport.hiddenRepSequences),
3082 sg.getStartRes(), sg.getEndRes() + 1));
3086 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3089 if (viewport.getConservationSelected())
3091 Conservation c = new Conservation("Group",
3092 ResidueProperties.propHash, 3,
3093 sg.getSequences(viewport.hiddenRepSequences),
3094 sg.getStartRes(), sg.getEndRes() + 1);
3096 c.verdict(false, viewport.ConsPercGaps);
3097 sg.cs.setConservation(c);
3101 sg.cs.setConservation(null);
3106 if (alignPanel.getOverviewPanel() != null)
3108 alignPanel.getOverviewPanel().updateOverviewImage();
3111 alignPanel.paintAlignment(true);
3120 protected void modifyPID_actionPerformed(ActionEvent e)
3122 if (viewport.getAbovePIDThreshold()
3123 && viewport.globalColourScheme != null)
3125 SliderPanel.setPIDSliderSource(alignPanel,
3126 viewport.getGlobalColourScheme(), "Background");
3127 SliderPanel.showPIDSlider();
3137 protected void modifyConservation_actionPerformed(ActionEvent e)
3139 if (viewport.getConservationSelected()
3140 && viewport.globalColourScheme != null)
3142 SliderPanel.setConservationSlider(alignPanel,
3143 viewport.globalColourScheme, "Background");
3144 SliderPanel.showConservationSlider();
3154 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3156 viewport.setConservationSelected(conservationMenuItem.isSelected());
3158 viewport.setAbovePIDThreshold(false);
3159 abovePIDThreshold.setSelected(false);
3161 changeColour(viewport.getGlobalColourScheme());
3163 modifyConservation_actionPerformed(null);
3172 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3174 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3176 conservationMenuItem.setSelected(false);
3177 viewport.setConservationSelected(false);
3179 changeColour(viewport.getGlobalColourScheme());
3181 modifyPID_actionPerformed(null);
3190 public void userDefinedColour_actionPerformed(ActionEvent e)
3192 if (e.getActionCommand().equals("User Defined..."))
3194 new UserDefinedColours(alignPanel, null);
3198 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3199 .getUserColourSchemes().get(e.getActionCommand());
3205 public void updateUserColourMenu()
3208 Component[] menuItems = colourMenu.getMenuComponents();
3209 int i, iSize = menuItems.length;
3210 for (i = 0; i < iSize; i++)
3212 if (menuItems[i].getName() != null
3213 && menuItems[i].getName().equals("USER_DEFINED"))
3215 colourMenu.remove(menuItems[i]);
3219 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3221 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3222 .getUserColourSchemes().keys();
3224 while (userColours.hasMoreElements())
3226 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3227 userColours.nextElement().toString());
3228 radioItem.setName("USER_DEFINED");
3229 radioItem.addMouseListener(new MouseAdapter()
3231 public void mousePressed(MouseEvent evt)
3233 if (evt.isControlDown()
3234 || SwingUtilities.isRightMouseButton(evt))
3236 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3238 int option = JOptionPane.showInternalConfirmDialog(
3239 jalview.gui.Desktop.desktop,
3240 "Remove from default list?",
3241 "Remove user defined colour",
3242 JOptionPane.YES_NO_OPTION);
3243 if (option == JOptionPane.YES_OPTION)
3245 jalview.gui.UserDefinedColours
3246 .removeColourFromDefaults(radioItem.getText());
3247 colourMenu.remove(radioItem);
3251 radioItem.addActionListener(new ActionListener()
3253 public void actionPerformed(ActionEvent evt)
3255 userDefinedColour_actionPerformed(evt);
3262 radioItem.addActionListener(new ActionListener()
3264 public void actionPerformed(ActionEvent evt)
3266 userDefinedColour_actionPerformed(evt);
3270 colourMenu.insert(radioItem, 15);
3271 colours.add(radioItem);
3282 public void PIDColour_actionPerformed(ActionEvent e)
3284 changeColour(new PIDColourScheme());
3293 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3295 changeColour(new Blosum62ColourScheme());
3304 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3306 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3307 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3308 .getAlignment().getSequenceAt(0), null);
3309 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3310 viewport.alignment));
3311 alignPanel.paintAlignment(true);
3320 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3322 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3323 AlignmentSorter.sortByID(viewport.getAlignment());
3324 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3325 alignPanel.paintAlignment(true);
3334 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3336 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3337 AlignmentSorter.sortByLength(viewport.getAlignment());
3338 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3339 viewport.alignment));
3340 alignPanel.paintAlignment(true);
3349 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3351 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3352 AlignmentSorter.sortByGroup(viewport.getAlignment());
3353 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3354 viewport.alignment));
3356 alignPanel.paintAlignment(true);
3365 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3367 new RedundancyPanel(alignPanel, this);
3376 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3378 if ((viewport.getSelectionGroup() == null)
3379 || (viewport.getSelectionGroup().getSize() < 2))
3381 JOptionPane.showInternalMessageDialog(this,
3382 "You must select at least 2 sequences.", "Invalid Selection",
3383 JOptionPane.WARNING_MESSAGE);
3387 JInternalFrame frame = new JInternalFrame();
3388 frame.setContentPane(new PairwiseAlignPanel(viewport));
3389 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3399 public void PCAMenuItem_actionPerformed(ActionEvent e)
3401 if (((viewport.getSelectionGroup() != null)
3402 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3403 .getSelectionGroup().getSize() > 0))
3404 || (viewport.getAlignment().getHeight() < 4))
3406 JOptionPane.showInternalMessageDialog(this,
3407 "Principal component analysis must take\n"
3408 + "at least 4 input sequences.",
3409 "Sequence selection insufficient",
3410 JOptionPane.WARNING_MESSAGE);
3415 new PCAPanel(alignPanel);
3418 public void autoCalculate_actionPerformed(ActionEvent e)
3420 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3421 if (viewport.autoCalculateConsensus)
3423 viewport.firePropertyChange("alignment", null, viewport
3424 .getAlignment().getSequences());
3427 public void sortByTreeOption_actionPerformed(ActionEvent e)
3429 viewport.sortByTree = sortByTree.isSelected();
3433 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3435 viewport.followSelection = listenToViewSelections.isSelected();
3443 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3445 NewTreePanel("AV", "PID", "Average distance tree using PID");
3454 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3456 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3465 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3467 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3476 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3478 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3491 void NewTreePanel(String type, String pwType, String title)
3495 if (viewport.getSelectionGroup() != null)
3497 if (viewport.getSelectionGroup().getSize() < 3)
3502 "You need to have more than two sequences selected to build a tree!",
3503 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3508 SequenceGroup sg = viewport.getSelectionGroup();
3510 /* Decide if the selection is a column region */
3511 while (s < sg.getSize())
3513 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3519 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3520 + "Try using the Pad function in the edit menu,\n"
3521 + "or one of the multiple sequence alignment web services.",
3522 "Sequences in selection are not aligned",
3523 JOptionPane.WARNING_MESSAGE);
3529 title = title + " on region";
3530 tp = new TreePanel(alignPanel, type, pwType);
3534 // are the visible sequences aligned?
3535 if (!viewport.alignment.isAligned(false))
3540 "The sequences must be aligned before creating a tree.\n"
3541 + "Try using the Pad function in the edit menu,\n"
3542 + "or one of the multiple sequence alignment web services.",
3543 "Sequences not aligned",
3544 JOptionPane.WARNING_MESSAGE);
3549 if (viewport.alignment.getHeight() < 2)
3554 tp = new TreePanel(alignPanel, type, pwType);
3559 if (viewport.viewName != null)
3561 title += viewport.viewName + " of ";
3564 title += this.title;
3566 Desktop.addInternalFrame(tp, title, 600, 500);
3577 public void addSortByOrderMenuItem(String title,
3578 final AlignmentOrder order)
3580 final JMenuItem item = new JMenuItem("by " + title);
3582 item.addActionListener(new java.awt.event.ActionListener()
3584 public void actionPerformed(ActionEvent e)
3586 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3588 // TODO: JBPNote - have to map order entries to curent SequenceI
3590 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3592 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3593 viewport.alignment));
3595 alignPanel.paintAlignment(true);
3601 * Add a new sort by annotation score menu item
3604 * the menu to add the option to
3606 * the label used to retrieve scores for each sequence on the
3609 public void addSortByAnnotScoreMenuItem(JMenu sort,
3610 final String scoreLabel)
3612 final JMenuItem item = new JMenuItem(scoreLabel);
3614 item.addActionListener(new java.awt.event.ActionListener()
3616 public void actionPerformed(ActionEvent e)
3618 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3619 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3620 viewport.getAlignment());// ,viewport.getSelectionGroup());
3621 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3622 viewport.alignment));
3623 alignPanel.paintAlignment(true);
3629 * last hash for alignment's annotation array - used to minimise cost of
3632 protected int _annotationScoreVectorHash;
3635 * search the alignment and rebuild the sort by annotation score submenu the
3636 * last alignment annotation vector hash is stored to minimize cost of
3637 * rebuilding in subsequence calls.
3640 public void buildSortByAnnotationScoresMenu()
3642 if (viewport.alignment.getAlignmentAnnotation() == null)
3647 if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3649 sortByAnnotScore.removeAll();
3650 // almost certainly a quicker way to do this - but we keep it simple
3651 Hashtable scoreSorts = new Hashtable();
3652 AlignmentAnnotation aann[];
3653 Enumeration sq = viewport.alignment.getSequences().elements();
3654 while (sq.hasMoreElements())
3656 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3657 for (int i = 0; aann != null && i < aann.length; i++)
3659 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3661 scoreSorts.put(aann[i].label, aann[i].label);
3665 Enumeration labels = scoreSorts.keys();
3666 while (labels.hasMoreElements())
3668 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3669 (String) labels.nextElement());
3671 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3674 _annotationScoreVectorHash = viewport.alignment
3675 .getAlignmentAnnotation().hashCode();
3680 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3681 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3682 * call. Listeners are added to remove the menu item when the treePanel is
3683 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3687 * Displayed tree window.
3689 * SortBy menu item title.
3691 public void buildTreeMenu()
3693 sortByTreeMenu.removeAll();
3695 Vector comps = (Vector) PaintRefresher.components.get(viewport
3696 .getSequenceSetId());
3697 Vector treePanels = new Vector();
3698 int i, iSize = comps.size();
3699 for (i = 0; i < iSize; i++)
3701 if (comps.elementAt(i) instanceof TreePanel)
3703 treePanels.add(comps.elementAt(i));
3707 iSize = treePanels.size();
3711 sortByTreeMenu.setVisible(false);
3715 sortByTreeMenu.setVisible(true);
3717 for (i = 0; i < treePanels.size(); i++)
3719 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3720 final JMenuItem item = new JMenuItem(tp.getTitle());
3721 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3722 item.addActionListener(new java.awt.event.ActionListener()
3724 public void actionPerformed(ActionEvent e)
3726 tp.sortByTree_actionPerformed(null);
3727 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3732 sortByTreeMenu.add(item);
3736 public boolean sortBy(AlignmentOrder alorder, String undoname)
3738 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3739 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3740 if (undoname != null)
3742 addHistoryItem(new OrderCommand(undoname, oldOrder,
3743 viewport.alignment));
3745 alignPanel.paintAlignment(true);
3750 * Work out whether the whole set of sequences or just the selected set will
3751 * be submitted for multiple alignment.
3754 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3756 // Now, check we have enough sequences
3757 AlignmentView msa = null;
3759 if ((viewport.getSelectionGroup() != null)
3760 && (viewport.getSelectionGroup().getSize() > 1))
3762 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3763 // some common interface!
3765 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3766 * SequenceI[sz = seqs.getSize(false)];
3768 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3769 * seqs.getSequenceAt(i); }
3771 msa = viewport.getAlignmentView(true);
3776 * Vector seqs = viewport.getAlignment().getSequences();
3778 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3780 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3781 * seqs.elementAt(i); } }
3783 msa = viewport.getAlignmentView(false);
3789 * Decides what is submitted to a secondary structure prediction service: the
3790 * first sequence in the alignment, or in the current selection, or, if the
3791 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3792 * region or the whole alignment. (where the first sequence in the set is the
3793 * one that the prediction will be for).
3795 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3797 AlignmentView seqs = null;
3799 if ((viewport.getSelectionGroup() != null)
3800 && (viewport.getSelectionGroup().getSize() > 0))
3802 seqs = viewport.getAlignmentView(true);
3806 seqs = viewport.getAlignmentView(false);
3808 // limit sequences - JBPNote in future - could spawn multiple prediction
3810 // TODO: viewport.alignment.isAligned is a global state - the local
3811 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3812 if (!viewport.alignment.isAligned(false))
3814 seqs.setSequences(new SeqCigar[]
3815 { seqs.getSequences()[0] });
3816 // TODO: if seqs.getSequences().length>1 then should really have warned
3829 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3831 // Pick the tree file
3832 JalviewFileChooser chooser = new JalviewFileChooser(
3833 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3834 chooser.setFileView(new JalviewFileView());
3835 chooser.setDialogTitle("Select a newick-like tree file");
3836 chooser.setToolTipText("Load a tree file");
3838 int value = chooser.showOpenDialog(null);
3840 if (value == JalviewFileChooser.APPROVE_OPTION)
3842 String choice = chooser.getSelectedFile().getPath();
3843 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3844 jalview.io.NewickFile fin = null;
3847 fin = new jalview.io.NewickFile(choice, "File");
3848 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3849 } catch (Exception ex)
3851 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3852 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3853 ex.printStackTrace();
3855 if (fin != null && fin.hasWarningMessage())
3857 JOptionPane.showMessageDialog(Desktop.desktop,
3858 fin.getWarningMessage(), "Possible problem with tree file",
3859 JOptionPane.WARNING_MESSAGE);
3865 public void loadScores_actionPerformed(ActionEvent e)
3867 // Pick the tree file
3868 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3869 chooser.setFileView(new JalviewFileView());
3870 chooser.setDialogTitle("Select a T-Coffee scores ascii file");
3871 chooser.setToolTipText("Load a score file");
3873 int value = chooser.showOpenDialog(null);
3875 if (value == JalviewFileChooser.APPROVE_OPTION)
3877 String sFilePath = chooser.getSelectedFile().getPath();
3878 jalview.bin.Cache.setProperty("LAST_DIRECTORY", sFilePath);
3883 TCoffeeScoreFile result = TCoffeeScoreFile.load(new File(sFilePath));
3884 if( result == null ) {
3885 // TODO: raise a dialog box here rather than bomb out.
3887 throw new RuntimeException("The file provided does not match the T-Coffee scores file format");
3891 * check that the score matrix matches the alignment dimensions
3894 if( (aln=viewport.alignment) != null && (aln.getHeight() != result.getHeight() || aln.getWidth() != result.getWidth()) ) {
3895 // TODO: raise a dialog box here rather than bomb out.
3896 throw new RuntimeException("The scores matrix does not match the alignment dimensions");
3898 if (result.annotateAlignment(alignPanel.getAlignment(), true))
3900 tcoffeeColour.setEnabled(true);
3901 tcoffeeColour.setSelected(true);
3902 // switch to this color
3903 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3905 tcoffeeColour.setEnabled(false);
3906 tcoffeeColour.setSelected(false);
3909 catch (Exception ex) {
3910 JOptionPane.showMessageDialog(
3913 "Problem reading tree file",
3914 JOptionPane.WARNING_MESSAGE);
3916 ex.printStackTrace();
3924 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) {
3925 changeColour( new TCoffeeColourScheme(alignPanel.getAlignment()) );
3929 // * Load the (T-Coffee) score file from the specified url
3931 // * @param url The absolute path from where download and read the score file
3932 // * @throws IOException
3934 // public void loadScoreFile(URL url ) throws IOException {
3936 // TCoffeeScoreFile result = new TCoffeeScoreFile();
3937 // result.parse( new InputStreamReader( url.openStream() ) );
3938 // tcoffeeScoreFile = result;
3941 public TreePanel ShowNewickTree(NewickFile nf, String title)
3943 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3946 public TreePanel ShowNewickTree(NewickFile nf, String title,
3947 AlignmentView input)
3949 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3952 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3953 int h, int x, int y)
3955 return ShowNewickTree(nf, title, null, w, h, x, y);
3959 * Add a treeviewer for the tree extracted from a newick file object to the
3960 * current alignment view
3967 * Associated alignment input data (or null)
3976 * @return TreePanel handle
3978 public TreePanel ShowNewickTree(NewickFile nf, String title,
3979 AlignmentView input, int w, int h, int x, int y)
3981 TreePanel tp = null;
3987 if (nf.getTree() != null)
3989 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3995 tp.setLocation(x, y);
3998 Desktop.addInternalFrame(tp, title, w, h);
4000 } catch (Exception ex)
4002 ex.printStackTrace();
4008 private boolean buildingMenu = false;
4011 * Generates menu items and listener event actions for web service clients
4014 public void BuildWebServiceMenu()
4016 while (buildingMenu)
4020 System.err.println("Waiting for building menu to finish.");
4022 } catch (Exception e)
4027 final AlignFrame me = this;
4028 buildingMenu = true;
4029 new Thread(new Runnable()
4035 System.err.println("Building ws menu again "
4036 + Thread.currentThread());
4037 // TODO: add support for context dependent disabling of services based
4039 // alignment and current selection
4040 // TODO: add additional serviceHandle parameter to specify abstract
4042 // class independently of AbstractName
4043 // TODO: add in rediscovery GUI function to restart discoverer
4044 // TODO: group services by location as well as function and/or
4046 // object broker mechanism.
4047 final Vector wsmenu = new Vector();
4048 final IProgressIndicator af = me;
4049 final JMenu msawsmenu = new JMenu("Alignment");
4050 final JMenu secstrmenu = new JMenu(
4051 "Secondary Structure Prediction");
4052 final JMenu seqsrchmenu = new JMenu(
4053 "Sequence Database Search");
4054 final JMenu analymenu = new JMenu(
4056 // JAL-940 - only show secondary structure prediction services from the legacy server
4057 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4059 Discoverer.services != null
4060 && (Discoverer.services.size() > 0))
4062 // TODO: refactor to allow list of AbstractName/Handler bindings to
4064 // stored or retrieved from elsewhere
4065 Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4066 Vector secstrpr = (Vector) Discoverer.services
4068 Vector seqsrch = null; // (Vector) Discoverer.services.get("SeqSearch");
4069 // TODO: move GUI generation code onto service implementation - so a
4070 // client instance attaches itself to the GUI with method call like
4071 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
4075 // Add any Multiple Sequence Alignment Services
4076 for (int i = 0, j = msaws.size(); i < j; i++)
4078 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
4080 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4081 .getServiceClient(sh);
4082 impl.attachWSMenuEntry(msawsmenu, me);
4086 if (secstrpr != null)
4088 // Add any secondary structure prediction services
4089 for (int i = 0, j = secstrpr.size(); i < j; i++)
4091 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4093 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4094 .getServiceClient(sh);
4095 impl.attachWSMenuEntry(secstrmenu, me);
4098 if (seqsrch != null)
4100 // Add any sequence search services
4101 for (int i = 0, j = seqsrch.size(); i < j; i++)
4103 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
4105 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4106 .getServiceClient(sh);
4107 impl.attachWSMenuEntry(seqsrchmenu, me);
4112 // TODO: move into separate menu builder class.
4113 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4115 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4116 if (jws2servs != null)
4118 if (jws2servs.hasServices())
4120 jws2servs.attachWSMenuEntry(msawsmenu, me);
4124 // Add all submenus in the order they should appear on the web services menu
4125 wsmenu.add(msawsmenu);
4126 wsmenu.add(secstrmenu);
4127 wsmenu.add(analymenu);
4128 // No search services yet
4129 // wsmenu.add(seqsrchmenu);
4131 javax.swing.SwingUtilities.invokeLater(new Runnable()
4137 webService.removeAll();
4138 // first, add discovered services onto the webservices menu
4139 if (wsmenu.size() > 0)
4141 for (int i = 0, j = wsmenu.size(); i < j; i++)
4143 webService.add((JMenu) wsmenu.get(i));
4148 webService.add(me.webServiceNoServices);
4150 build_urlServiceMenu(me.webService);
4151 build_fetchdbmenu(webService);
4152 } catch (Exception e)
4158 } catch (Exception e)
4163 buildingMenu = false;
4171 * construct any groupURL type service menu entries.
4175 private void build_urlServiceMenu(JMenu webService)
4177 // TODO: remove this code when 2.7 is released
4178 // DEBUG - alignmentView
4180 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4181 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4183 * @Override public void actionPerformed(ActionEvent e) {
4184 * jalview.datamodel.AlignmentView.testSelectionViews(af.viewport.alignment,
4185 * af.viewport.colSel, af.viewport.selectionGroup); }
4187 * }); webService.add(testAlView);
4189 // TODO: refactor to RestClient discoverer and merge menu entries for
4190 // rest-style services with other types of analysis/calculation service
4191 // SHmmr test client - still being implemented.
4192 // DEBUG - alignmentView
4194 for (jalview.ws.rest.RestClient client: jalview.ws.rest.RestClient.getRestClients()) {
4195 client.attachWSMenuEntry(JvSwingUtils.findOrCreateMenu(webService, client.getAction()), this);
4198 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4200 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4206 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4207 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4208 * getProperty("LAST_DIRECTORY"));
4210 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4211 * to Vamsas file"); chooser.setToolTipText("Export");
4213 * int value = chooser.showSaveDialog(this);
4215 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4216 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4217 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4218 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4221 * prototype of an automatically enabled/disabled analysis function
4224 protected void setShowProductsEnabled()
4226 SequenceI[] selection = viewport.getSequenceSelection();
4227 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4228 viewport.getAlignment().getDataset()))
4230 showProducts.setEnabled(true);
4235 showProducts.setEnabled(false);
4240 * search selection for sequence xRef products and build the show products
4245 * @return true if showProducts menu should be enabled.
4247 public boolean canShowProducts(SequenceI[] selection,
4248 boolean isRegionSelection, Alignment dataset)
4250 boolean showp = false;
4253 showProducts.removeAll();
4254 final boolean dna = viewport.getAlignment().isNucleotide();
4255 final Alignment ds = dataset;
4256 String[] ptypes = (selection == null || selection.length == 0) ? null
4257 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4259 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4260 // selection, dataset, true);
4261 final SequenceI[] sel = selection;
4262 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4265 final boolean isRegSel = isRegionSelection;
4266 final AlignFrame af = this;
4267 final String source = ptypes[t];
4268 JMenuItem xtype = new JMenuItem(ptypes[t]);
4269 xtype.addActionListener(new ActionListener()
4272 public void actionPerformed(ActionEvent e)
4274 // TODO: new thread for this call with vis-delay
4275 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4276 isRegSel, dna, source);
4280 showProducts.add(xtype);
4282 showProducts.setVisible(showp);
4283 showProducts.setEnabled(showp);
4284 } catch (Exception e)
4286 jalview.bin.Cache.log
4287 .warn("canTranslate threw an exception - please report to help@jalview.org",
4294 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4295 boolean isRegSel, boolean dna, String source)
4297 final boolean fisRegSel = isRegSel;
4298 final boolean fdna = dna;
4299 final String fsrc = source;
4300 final AlignFrame ths = this;
4301 final SequenceI[] fsel = sel;
4302 Runnable foo = new Runnable()
4307 final long sttime = System.currentTimeMillis();
4308 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4311 Alignment ds = ths.getViewport().alignment.getDataset(); // update
4315 Alignment prods = CrossRef
4316 .findXrefSequences(fsel, fdna, fsrc, ds);
4319 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4320 for (int s = 0; s < sprods.length; s++)
4322 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4323 if (ds.getSequences() == null
4324 || !ds.getSequences().contains(
4325 sprods[s].getDatasetSequence()))
4326 ds.addSequence(sprods[s].getDatasetSequence());
4327 sprods[s].updatePDBIds();
4329 Alignment al = new Alignment(sprods);
4330 AlignedCodonFrame[] cf = prods.getCodonFrames();
4332 for (int s = 0; cf != null && s < cf.length; s++)
4334 al.addCodonFrame(cf[s]);
4337 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4339 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4340 + " for " + ((fisRegSel) ? "selected region of " : "")
4342 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4347 System.err.println("No Sequences generated for xRef type "
4350 } catch (Exception e)
4352 jalview.bin.Cache.log.error(
4353 "Exception when finding crossreferences", e);
4354 } catch (OutOfMemoryError e)
4356 new OOMWarning("whilst fetching crossreferences", e);
4359 jalview.bin.Cache.log.error("Error when finding crossreferences",
4362 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4367 Thread frunner = new Thread(foo);
4371 public boolean canShowTranslationProducts(SequenceI[] selection,
4372 AlignmentI alignment)
4377 return (jalview.analysis.Dna.canTranslate(selection,
4378 viewport.getViewAsVisibleContigs(true)));
4379 } catch (Exception e)
4381 jalview.bin.Cache.log
4382 .warn("canTranslate threw an exception - please report to help@jalview.org",
4388 public void showProducts_actionPerformed(ActionEvent e)
4390 // /////////////////////////////
4391 // Collect Data to be translated/transferred
4393 SequenceI[] selection = viewport.getSequenceSelection();
4394 AlignmentI al = null;
4397 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4398 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4399 viewport.getAlignment().getDataset());
4400 } catch (Exception ex)
4403 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4410 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4411 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4415 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4416 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4417 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4421 public void showTranslation_actionPerformed(ActionEvent e)
4423 // /////////////////////////////
4424 // Collect Data to be translated/transferred
4426 SequenceI[] selection = viewport.getSequenceSelection();
4427 String[] seqstring = viewport.getViewAsString(true);
4428 AlignmentI al = null;
4431 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4432 viewport.getViewAsVisibleContigs(true), viewport
4433 .getGapCharacter(), viewport.alignment
4434 .getAlignmentAnnotation(), viewport.alignment
4435 .getWidth(), viewport.getAlignment().getDataset());
4436 } catch (Exception ex)
4439 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4446 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4447 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4451 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4452 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4453 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4458 * Try to load a features file onto the alignment.
4461 * contents or path to retrieve file
4463 * access mode of file (see jalview.io.AlignFile)
4464 * @return true if features file was parsed corectly.
4466 public boolean parseFeaturesFile(String file, String type)
4468 boolean featuresFile = false;
4471 featuresFile = new FeaturesFile(file, type)
4472 .parse(viewport.alignment.getDataset(),
4473 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
4474 false, jalview.bin.Cache.getDefault(
4475 "RELAXEDSEQIDMATCHING", false));
4476 } catch (Exception ex)
4478 ex.printStackTrace();
4483 viewport.showSequenceFeatures = true;
4484 showSeqFeatures.setSelected(true);
4485 if (alignPanel.seqPanel.seqCanvas.fr != null)
4487 // update the min/max ranges where necessary
4488 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4490 if (featureSettings != null)
4492 featureSettings.setTableData();
4494 alignPanel.paintAlignment(true);
4497 return featuresFile;
4500 public void dragEnter(DropTargetDragEvent evt)
4504 public void dragExit(DropTargetEvent evt)
4508 public void dragOver(DropTargetDragEvent evt)
4512 public void dropActionChanged(DropTargetDragEvent evt)
4516 public void drop(DropTargetDropEvent evt)
4518 Transferable t = evt.getTransferable();
4519 java.util.List files = null;
4523 DataFlavor uriListFlavor = new DataFlavor(
4524 "text/uri-list;class=java.lang.String");
4525 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4527 // Works on Windows and MacOSX
4528 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4529 files = (java.util.List) t
4530 .getTransferData(DataFlavor.javaFileListFlavor);
4532 else if (t.isDataFlavorSupported(uriListFlavor))
4534 // This is used by Unix drag system
4535 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4536 String data = (String) t.getTransferData(uriListFlavor);
4537 files = new java.util.ArrayList(1);
4538 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4539 data, "\r\n"); st.hasMoreTokens();)
4541 String s = st.nextToken();
4542 if (s.startsWith("#"))
4544 // the line is a comment (as per the RFC 2483)
4548 java.net.URI uri = new java.net.URI(s);
4549 // check to see if we can handle this kind of URI
4550 if (uri.getScheme().toLowerCase().startsWith("http"))
4552 files.add(uri.toString());
4556 // otherwise preserve old behaviour: catch all for file objects
4557 java.io.File file = new java.io.File(uri);
4558 files.add(file.toString());
4562 } catch (Exception e)
4564 e.printStackTrace();
4570 // check to see if any of these files have names matching sequences in
4572 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4573 .getAlignment().getSequencesArray());
4575 * Object[] { String,SequenceI}
4577 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4578 ArrayList<String> filesnotmatched = new ArrayList<String>();
4579 for (int i = 0; i < files.size(); i++)
4581 String file = files.get(i).toString();
4583 String protocol = FormatAdapter.checkProtocol(file);
4584 if (protocol == jalview.io.FormatAdapter.FILE)
4586 File fl = new File(file);
4587 pdbfn = fl.getName();
4589 else if (protocol == jalview.io.FormatAdapter.URL)
4591 URL url = new URL(file);
4592 pdbfn = url.getFile();
4594 if (pdbfn.length() > 0)
4596 // attempt to find a match in the alignment
4597 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4598 int l = 0, c = pdbfn.indexOf(".");
4599 while (mtch == null && c != -1)
4604 } while ((c = pdbfn.indexOf(".", l)) > l);
4607 pdbfn = pdbfn.substring(0, l);
4609 mtch = idm.findAllIdMatches(pdbfn);
4616 type = new IdentifyFile().Identify(file, protocol);
4617 } catch (Exception ex)
4623 if (type.equalsIgnoreCase("PDB"))
4625 filesmatched.add(new Object[]
4626 { file, protocol, mtch });
4631 // File wasn't named like one of the sequences or wasn't a PDB file.
4632 filesnotmatched.add(file);
4636 if (filesmatched.size() > 0)
4638 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4642 "Do you want to automatically associate the "
4643 + filesmatched.size()
4644 + " PDB files with sequences in the alignment that have the same name ?",
4645 "Automatically Associate PDB files by name",
4646 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4649 for (Object[] fm : filesmatched)
4651 // try and associate
4652 // TODO: may want to set a standard ID naming formalism for
4653 // associating PDB files which have no IDs.
4654 for (SequenceI toassoc: (SequenceI[])fm[2]) {
4655 PDBEntry pe = new AssociatePdbFileWithSeq()
4656 .associatePdbWithSeq((String) fm[0], (String) fm[1],
4661 .println("Associated file : " + ((String) fm[0])
4663 + toassoc.getDisplayId(true));
4667 alignPanel.paintAlignment(true);
4671 if (filesnotmatched.size() > 0)
4674 && (Cache.getDefault(
4675 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4678 "<html>Do you want to <em>ignore</em> the "
4679 + filesnotmatched.size()
4680 + " files whose names did not match any sequence IDs ?</html>",
4681 "Ignore unmatched dropped files ?",
4682 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4686 for (String fn : filesnotmatched)
4688 loadJalviewDataFile(fn, null, null, null);
4692 } catch (Exception ex)
4694 ex.printStackTrace();
4700 * Attempt to load a "dropped" file or URL string: First by testing whether
4701 * it's and Annotation file, then a JNet file, and finally a features file. If
4702 * all are false then the user may have dropped an alignment file onto this
4706 * either a filename or a URL string.
4708 public void loadJalviewDataFile(String file, String protocol,
4709 String format, SequenceI assocSeq)
4713 if (protocol == null)
4715 protocol = jalview.io.FormatAdapter.checkProtocol(file);
4717 // if the file isn't identified, or not positively identified as some
4718 // other filetype (PFAM is default unidentified alignment file type) then
4719 // try to parse as annotation.
4720 boolean isAnnotation = (format == null || format
4721 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4722 .readAnnotationFile(viewport.alignment, file, protocol)
4727 // try to see if its a JNet 'concise' style annotation file *before* we
4728 // try to parse it as a features file
4731 format = new IdentifyFile().Identify(file, protocol);
4733 if (format.equalsIgnoreCase("JnetFile"))
4735 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4737 new JnetAnnotationMaker().add_annotation(predictions,
4738 viewport.getAlignment(), 0, false);
4739 isAnnotation = true;
4744 * if (format.equalsIgnoreCase("PDB")) {
4746 * String pdbfn = ""; // try to match up filename with sequence id try
4747 * { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = new
4748 * File(file); pdbfn = fl.getName(); } else if (protocol ==
4749 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4750 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == null)
4751 * { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4752 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { //
4753 * attempt to find a match in the alignment SequenceI mtch =
4754 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4755 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > l)
4756 * { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch =
4757 * idm.findIdMatch(pdbfn); } if (mtch != null) { // try and associate
4758 * // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4759 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) {
4760 * System.err.println("Associated file : " + file + " with " +
4761 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4762 * TODO: maybe need to load as normal otherwise return; } }
4764 // try to parse it as a features file
4765 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4766 // if it wasn't a features file then we just treat it as a general
4767 // alignment file to load into the current view.
4770 new FileLoader().LoadFile(viewport, file, protocol, format);
4774 alignPanel.paintAlignment(true);
4781 alignPanel.adjustAnnotationHeight();
4782 viewport.updateSequenceIdColours();
4783 buildSortByAnnotationScoresMenu();
4784 alignPanel.paintAlignment(true);
4786 } catch (Exception ex)
4788 ex.printStackTrace();
4792 public void tabSelectionChanged(int index)
4796 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4797 viewport = alignPanel.av;
4798 setMenusFromViewport(viewport);
4802 public void tabbedPane_mousePressed(MouseEvent e)
4804 if (SwingUtilities.isRightMouseButton(e))
4806 String reply = JOptionPane.showInternalInputDialog(this,
4807 "Enter View Name", "Edit View Name",
4808 JOptionPane.QUESTION_MESSAGE);
4812 viewport.viewName = reply;
4813 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4818 public AlignViewport getCurrentView()
4824 * Open the dialog for regex description parsing.
4826 protected void extractScores_actionPerformed(ActionEvent e)
4828 ParseProperties pp = new jalview.analysis.ParseProperties(
4829 viewport.alignment);
4830 // TODO: verify regex and introduce GUI dialog for version 2.5
4831 // if (pp.getScoresFromDescription("col", "score column ",
4832 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4834 if (pp.getScoresFromDescription("description column",
4835 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4837 buildSortByAnnotationScoresMenu();
4845 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4848 protected void showDbRefs_actionPerformed(ActionEvent e)
4850 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4856 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4859 protected void showNpFeats_actionPerformed(ActionEvent e)
4861 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4865 * find the viewport amongst the tabs in this alignment frame and close that
4870 public boolean closeView(AlignViewport av)
4874 this.closeMenuItem_actionPerformed(false);
4877 Component[] comp = tabbedPane.getComponents();
4878 for (int i = 0; comp != null && i < comp.length; i++)
4880 if (comp[i] instanceof AlignmentPanel)
4882 if (((AlignmentPanel) comp[i]).av == av)
4885 closeView((AlignmentPanel) comp[i]);
4893 protected void build_fetchdbmenu(JMenu webService)
4895 // Temporary hack - DBRef Fetcher always top level ws entry.
4896 // TODO We probably want to store a sequence database checklist in
4897 // preferences and have checkboxes.. rather than individual sources selected
4899 final JMenu rfetch = new JMenu("Fetch DB References");
4900 rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4901 webService.add(rfetch);
4903 JMenuItem fetchr = new JMenuItem("Standard Databases");
4904 fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4905 fetchr.addActionListener(new ActionListener()
4908 public void actionPerformed(ActionEvent e)
4910 new Thread(new Runnable()
4915 new jalview.ws.DBRefFetcher(alignPanel.av
4916 .getSequenceSelection(), alignPanel.alignFrame)
4917 .fetchDBRefs(false);
4925 final AlignFrame me = this;
4926 new Thread(new Runnable()
4930 final jalview.ws.SequenceFetcher sf = SequenceFetcher
4931 .getSequenceFetcherSingleton(me);
4932 final String[] otherdb = sf.getOrderedSupportedSources();
4933 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4934 // jalview.util.QuickSort.sort(otherdb, otherdb);
4935 javax.swing.SwingUtilities.invokeLater(new Runnable()
4940 JMenu dfetch = new JMenu();
4943 int comp = 0, mcomp = 15;
4944 String mname = null;
4945 if (otherdb != null && otherdb.length > 0)
4947 for (int i = 0; i < otherdb.length; i++)
4949 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4952 mname = "from '" + dbname + "'";
4954 fetchr = new JMenuItem(otherdb[i]);
4955 final String[] dassource = new String[]
4957 fetchr.addActionListener(new ActionListener()
4960 public void actionPerformed(ActionEvent e)
4962 new Thread(new Runnable()
4967 new jalview.ws.DBRefFetcher(alignPanel.av
4968 .getSequenceSelection(),
4969 alignPanel.alignFrame, dassource)
4970 .fetchDBRefs(false);
4976 fetchr.setToolTipText("Retrieve from " + dbname);
4978 if (comp++ == mcomp || i == (otherdb.length - 1))
4980 dfetch.setText(mname + " to '" + dbname + "'");
4982 dfetch = new JMenu();
4996 * Left justify the whole alignment.
4998 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5000 AlignmentI al = viewport.getAlignment();
5002 viewport.firePropertyChange("alignment", null, al);
5006 * Right justify the whole alignment.
5008 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5010 AlignmentI al = viewport.getAlignment();
5012 viewport.firePropertyChange("alignment", null, al);
5015 public void setShowSeqFeatures(boolean b)
5017 showSeqFeatures.setSelected(true);
5018 viewport.setShowSequenceFeatures(true);
5025 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5026 * awt.event.ActionEvent)
5028 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5030 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5031 alignPanel.paintAlignment(true);
5038 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5041 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5043 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5044 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5052 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5053 * .event.ActionEvent)
5055 protected void showGroupConservation_actionPerformed(ActionEvent e)
5057 viewport.setShowGroupConservation(showGroupConservation.getState());
5058 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5065 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5066 * .event.ActionEvent)
5068 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5070 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5071 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5078 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5079 * .event.ActionEvent)
5081 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5083 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5084 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5087 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5089 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5096 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5097 * .event.ActionEvent)
5099 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5101 if (viewport.getSelectionGroup() != null)
5103 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
5104 viewport.getSequenceSelection(),
5105 viewport.getAlignmentView(true).getSequenceStrings(
5106 viewport.getGapCharacter()),
5107 viewport.alignment.getGroups());
5108 viewport.alignment.deleteAllGroups();
5109 viewport.sequenceColours = null;
5110 viewport.setSelectionGroup(null);
5111 // set view properties for each group
5112 for (int g = 0; g < gps.length; g++)
5114 gps[g].setShowNonconserved(viewport.getShowUnconserved());
5115 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
5116 viewport.alignment.addGroup(gps[g]);
5117 Color col = new Color((int) (Math.random() * 255),
5118 (int) (Math.random() * 255), (int) (Math.random() * 255));
5119 col = col.brighter();
5120 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
5121 .hasMoreElements(); viewport.setSequenceColour(
5122 (SequenceI) sq.nextElement(), col))
5125 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5126 alignPanel.updateAnnotation();
5127 alignPanel.paintAlignment(true);
5132 * make the given alignmentPanel the currently selected tab
5134 * @param alignmentPanel
5136 public void setDisplayedView(AlignmentPanel alignmentPanel)
5138 if (!viewport.getSequenceSetId().equals(
5139 alignmentPanel.av.getSequenceSetId()))
5142 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5144 if (tabbedPane != null
5145 & alignPanels.indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5147 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5152 class PrintThread extends Thread
5156 public PrintThread(AlignmentPanel ap)
5161 static PageFormat pf;
5165 PrinterJob printJob = PrinterJob.getPrinterJob();
5169 printJob.setPrintable(ap, pf);
5173 printJob.setPrintable(ap);
5176 if (printJob.printDialog())
5181 } catch (Exception PrintException)
5183 PrintException.printStackTrace();