2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 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.jbgui.GAlignFrame;
59 import jalview.schemes.Blosum62ColourScheme;
60 import jalview.schemes.BuriedColourScheme;
61 import jalview.schemes.ClustalxColourScheme;
62 import jalview.schemes.ColourSchemeI;
63 import jalview.schemes.ColourSchemeProperty;
64 import jalview.schemes.HelixColourScheme;
65 import jalview.schemes.HydrophobicColourScheme;
66 import jalview.schemes.NucleotideColourScheme;
67 import jalview.schemes.PIDColourScheme;
68 import jalview.schemes.ResidueProperties;
69 import jalview.schemes.StrandColourScheme;
70 import jalview.schemes.TaylorColourScheme;
71 import jalview.schemes.TurnColourScheme;
72 import jalview.schemes.UserColourScheme;
73 import jalview.schemes.ZappoColourScheme;
74 import jalview.ws.WSMenuEntryProviderI;
75 import jalview.ws.jws1.Discoverer;
76 import jalview.ws.jws2.Jws2Discoverer;
78 import java.awt.BorderLayout;
79 import java.awt.Color;
80 import java.awt.Component;
81 import java.awt.GridLayout;
82 import java.awt.Rectangle;
83 import java.awt.Toolkit;
84 import java.awt.datatransfer.Clipboard;
85 import java.awt.datatransfer.DataFlavor;
86 import java.awt.datatransfer.StringSelection;
87 import java.awt.datatransfer.Transferable;
88 import java.awt.dnd.DnDConstants;
89 import java.awt.dnd.DropTargetDragEvent;
90 import java.awt.dnd.DropTargetDropEvent;
91 import java.awt.dnd.DropTargetEvent;
92 import java.awt.dnd.DropTargetListener;
93 import java.awt.event.ActionEvent;
94 import java.awt.event.ActionListener;
95 import java.awt.event.KeyAdapter;
96 import java.awt.event.KeyEvent;
97 import java.awt.event.MouseAdapter;
98 import java.awt.event.MouseEvent;
99 import java.awt.print.PageFormat;
100 import java.awt.print.PrinterJob;
101 import java.beans.PropertyChangeEvent;
104 import java.util.ArrayList;
105 import java.util.Enumeration;
106 import java.util.Hashtable;
107 import java.util.Vector;
109 import javax.swing.JButton;
110 import javax.swing.JEditorPane;
111 import javax.swing.JInternalFrame;
112 import javax.swing.JLabel;
113 import javax.swing.JLayeredPane;
114 import javax.swing.JMenu;
115 import javax.swing.JMenuItem;
116 import javax.swing.JOptionPane;
117 import javax.swing.JPanel;
118 import javax.swing.JProgressBar;
119 import javax.swing.JRadioButtonMenuItem;
120 import javax.swing.JScrollPane;
121 import javax.swing.SwingUtilities;
127 * @version $Revision$
129 public class AlignFrame extends GAlignFrame implements DropTargetListener,
134 public static final int DEFAULT_WIDTH = 700;
137 public static final int DEFAULT_HEIGHT = 500;
139 public AlignmentPanel alignPanel;
141 AlignViewport viewport;
143 Vector alignPanels = new Vector();
146 * Last format used to load or save alignments in this window
148 String currentFileFormat = null;
151 * Current filename for this alignment
153 String fileName = null;
156 * Creates a new AlignFrame object with specific width and height.
162 public AlignFrame(AlignmentI al, int width, int height)
164 this(al, null, width, height);
168 * Creates a new AlignFrame object with specific width, height and
174 * @param sequenceSetId
176 public AlignFrame(AlignmentI al, int width, int height,
177 String sequenceSetId)
179 this(al, null, width, height, sequenceSetId);
183 * Creates a new AlignFrame object with specific width, height and
189 * @param sequenceSetId
192 public AlignFrame(AlignmentI al, int width, int height,
193 String sequenceSetId, String viewId)
195 this(al, null, width, height, sequenceSetId, viewId);
199 * new alignment window with hidden columns
203 * @param hiddenColumns
204 * ColumnSelection or null
206 * Width of alignment frame
210 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
211 int width, int height)
213 this(al, hiddenColumns, width, height, null);
217 * Create alignment frame for al with hiddenColumns, a specific width and
218 * height, and specific sequenceId
221 * @param hiddenColumns
224 * @param sequenceSetId
227 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
228 int width, int height, String sequenceSetId)
230 this(al, hiddenColumns, width, height, sequenceSetId, null);
234 * Create alignment frame for al with hiddenColumns, a specific width and
235 * height, and specific sequenceId
238 * @param hiddenColumns
241 * @param sequenceSetId
246 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
247 int width, int height, String sequenceSetId, String viewId)
249 setSize(width, height);
250 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
252 alignPanel = new AlignmentPanel(this, viewport);
254 if (al.getDataset() == null)
259 addAlignmentPanel(alignPanel, true);
264 * Make a new AlignFrame from exisiting alignmentPanels
271 public AlignFrame(AlignmentPanel ap)
275 addAlignmentPanel(ap, false);
280 * initalise the alignframe from the underlying viewport data and the
285 if (viewport.conservation == null)
287 BLOSUM62Colour.setEnabled(false);
288 conservationMenuItem.setEnabled(false);
289 modifyConservation.setEnabled(false);
290 // PIDColour.setEnabled(false);
291 // abovePIDThreshold.setEnabled(false);
292 // modifyPID.setEnabled(false);
295 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
298 if (sortby.equals("Id"))
300 sortIDMenuItem_actionPerformed(null);
302 else if (sortby.equals("Pairwise Identity"))
304 sortPairwiseMenuItem_actionPerformed(null);
307 if (Desktop.desktop != null)
309 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
310 addServiceListeners();
311 setGUINucleotide(viewport.alignment.isNucleotide());
314 setMenusFromViewport(viewport);
315 buildSortByAnnotationScoresMenu();
316 if (viewport.wrapAlignment)
318 wrapMenuItem_actionPerformed(null);
321 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
323 this.overviewMenuItem_actionPerformed(null);
331 * Change the filename and format for the alignment, and enable the 'reload'
332 * button functionality.
339 public void setFileName(String file, String format)
342 currentFileFormat = format;
343 reload.setEnabled(true);
346 void addKeyListener()
348 addKeyListener(new KeyAdapter()
350 public void keyPressed(KeyEvent evt)
352 if (viewport.cursorMode
353 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
354 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
355 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
356 && Character.isDigit(evt.getKeyChar()))
357 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
359 switch (evt.getKeyCode())
362 case 27: // escape key
363 deselectAllSequenceMenuItem_actionPerformed(null);
367 case KeyEvent.VK_DOWN:
368 if (evt.isAltDown() || !viewport.cursorMode)
369 moveSelectedSequences(false);
370 if (viewport.cursorMode)
371 alignPanel.seqPanel.moveCursor(0, 1);
375 if (evt.isAltDown() || !viewport.cursorMode)
376 moveSelectedSequences(true);
377 if (viewport.cursorMode)
378 alignPanel.seqPanel.moveCursor(0, -1);
382 case KeyEvent.VK_LEFT:
383 if (evt.isAltDown() || !viewport.cursorMode)
384 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
386 alignPanel.seqPanel.moveCursor(-1, 0);
390 case KeyEvent.VK_RIGHT:
391 if (evt.isAltDown() || !viewport.cursorMode)
392 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
394 alignPanel.seqPanel.moveCursor(1, 0);
397 case KeyEvent.VK_SPACE:
398 if (viewport.cursorMode)
400 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
401 || evt.isShiftDown() || evt.isAltDown());
405 case KeyEvent.VK_DELETE:
406 case KeyEvent.VK_BACK_SPACE:
407 if (!viewport.cursorMode)
409 cut_actionPerformed(null);
413 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
414 || evt.isShiftDown() || evt.isAltDown());
420 if (viewport.cursorMode)
422 alignPanel.seqPanel.setCursorRow();
426 if (viewport.cursorMode && !evt.isControlDown())
428 alignPanel.seqPanel.setCursorColumn();
432 if (viewport.cursorMode)
434 alignPanel.seqPanel.setCursorPosition();
438 case KeyEvent.VK_ENTER:
439 case KeyEvent.VK_COMMA:
440 if (viewport.cursorMode)
442 alignPanel.seqPanel.setCursorRowAndColumn();
447 if (viewport.cursorMode)
449 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
453 if (viewport.cursorMode)
455 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
460 viewport.cursorMode = !viewport.cursorMode;
461 statusBar.setText("Keyboard editing mode is "
462 + (viewport.cursorMode ? "on" : "off"));
463 if (viewport.cursorMode)
465 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
466 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
468 alignPanel.seqPanel.seqCanvas.repaint();
474 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
475 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
477 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
479 javax.help.HelpBroker hb = hs.createHelpBroker();
480 hb.setCurrentID("home");
481 hb.setDisplayed(true);
482 } catch (Exception ex)
484 ex.printStackTrace();
489 boolean toggleSeqs = !evt.isControlDown();
490 boolean toggleCols = !evt.isShiftDown();
491 toggleHiddenRegions(toggleSeqs, toggleCols);
494 case KeyEvent.VK_PAGE_UP:
495 if (viewport.wrapAlignment)
497 alignPanel.scrollUp(true);
501 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
502 - viewport.endSeq + viewport.startSeq);
505 case KeyEvent.VK_PAGE_DOWN:
506 if (viewport.wrapAlignment)
508 alignPanel.scrollUp(false);
512 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
513 + viewport.endSeq - viewport.startSeq);
519 public void keyReleased(KeyEvent evt)
521 switch (evt.getKeyCode())
523 case KeyEvent.VK_LEFT:
524 if (evt.isAltDown() || !viewport.cursorMode)
525 viewport.firePropertyChange("alignment", null, viewport
526 .getAlignment().getSequences());
529 case KeyEvent.VK_RIGHT:
530 if (evt.isAltDown() || !viewport.cursorMode)
531 viewport.firePropertyChange("alignment", null, viewport
532 .getAlignment().getSequences());
539 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
541 ap.alignFrame = this;
543 alignPanels.addElement(ap);
545 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
547 int aSize = alignPanels.size();
549 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
551 if (aSize == 1 && ap.av.viewName == null)
553 this.getContentPane().add(ap, BorderLayout.CENTER);
559 setInitialTabVisible();
562 expandViews.setEnabled(true);
563 gatherViews.setEnabled(true);
564 tabbedPane.addTab(ap.av.viewName, ap);
566 ap.setVisible(false);
573 ap.av.alignment.padGaps();
575 ap.av.updateConservation(ap);
576 ap.av.updateConsensus(ap);
580 public void setInitialTabVisible()
582 expandViews.setEnabled(true);
583 gatherViews.setEnabled(true);
584 tabbedPane.setVisible(true);
585 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
586 tabbedPane.addTab(first.av.viewName, first);
587 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
590 public AlignViewport getViewport()
595 /* Set up intrinsic listeners for dynamically generated GUI bits. */
596 private void addServiceListeners()
598 final java.beans.PropertyChangeListener thisListener;
599 Desktop.instance.addJalviewPropertyChangeListener("services",
600 thisListener = new java.beans.PropertyChangeListener()
602 public void propertyChange(PropertyChangeEvent evt)
604 // // System.out.println("Discoverer property change.");
605 // if (evt.getPropertyName().equals("services"))
607 SwingUtilities.invokeLater(new Runnable()
613 .println("Rebuild WS Menu for service change");
614 BuildWebServiceMenu();
621 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
623 public void internalFrameClosed(
624 javax.swing.event.InternalFrameEvent evt)
626 System.out.println("deregistering discoverer listener");
627 Desktop.instance.removeJalviewPropertyChangeListener("services",
629 closeMenuItem_actionPerformed(true);
632 // Finally, build the menu once to get current service state
633 new Thread(new Runnable()
637 BuildWebServiceMenu();
642 public void setGUINucleotide(boolean nucleotide)
644 showTranslation.setVisible(nucleotide);
645 conservationMenuItem.setEnabled(!nucleotide);
646 modifyConservation.setEnabled(!nucleotide);
647 showGroupConservation.setEnabled(!nucleotide);
648 // Remember AlignFrame always starts as protein
651 calculateMenu.remove(calculateMenu.getItemCount() - 2);
656 * set up menus for the currently viewport. This may be called after any
657 * operation that affects the data in the current view (selection changed,
658 * etc) to update the menus to reflect the new state.
660 public void setMenusForViewport()
662 setMenusFromViewport(viewport);
666 * Need to call this method when tabs are selected for multiple views, or when
667 * loading from Jalview2XML.java
672 void setMenusFromViewport(AlignViewport av)
674 padGapsMenuitem.setSelected(av.padGaps);
675 colourTextMenuItem.setSelected(av.showColourText);
676 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
677 conservationMenuItem.setSelected(av.getConservationSelected());
678 seqLimits.setSelected(av.getShowJVSuffix());
679 idRightAlign.setSelected(av.rightAlignIds);
680 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
681 renderGapsMenuItem.setSelected(av.renderGaps);
682 wrapMenuItem.setSelected(av.wrapAlignment);
683 scaleAbove.setVisible(av.wrapAlignment);
684 scaleLeft.setVisible(av.wrapAlignment);
685 scaleRight.setVisible(av.wrapAlignment);
686 annotationPanelMenuItem.setState(av.showAnnotation);
687 viewBoxesMenuItem.setSelected(av.showBoxes);
688 viewTextMenuItem.setSelected(av.showText);
689 showNonconservedMenuItem.setSelected(av.showUnconserved);
690 showGroupConsensus.setSelected(av.showGroupConsensus);
691 showGroupConservation.setSelected(av.showGroupConservation);
692 showConsensusHistogram.setSelected(av.showConsensusHistogram);
693 showSequenceLogo.setSelected(av.showSequenceLogo);
694 setColourSelected(ColourSchemeProperty.getColourName(av
695 .getGlobalColourScheme()));
697 showSeqFeatures.setSelected(av.showSequenceFeatures);
698 hiddenMarkers.setState(av.showHiddenMarkers);
699 applyToAllGroups.setState(av.colourAppliesToAllGroups);
700 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
701 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
703 setShowProductsEnabled();
708 Hashtable progressBars, progressBarHandlers;
713 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
715 public void setProgressBar(String message, long id)
717 if (progressBars == null)
719 progressBars = new Hashtable();
720 progressBarHandlers = new Hashtable();
723 JPanel progressPanel;
724 Long lId = new Long(id);
725 GridLayout layout = (GridLayout) statusPanel.getLayout();
726 if (progressBars.get(lId) != null)
728 progressPanel = (JPanel) progressBars.get(new Long(id));
729 statusPanel.remove(progressPanel);
730 progressBars.remove(lId);
731 progressPanel = null;
734 statusBar.setText(message);
736 if (progressBarHandlers.contains(lId))
738 progressBarHandlers.remove(lId);
740 layout.setRows(layout.getRows() - 1);
744 progressPanel = new JPanel(new BorderLayout(10, 5));
746 JProgressBar progressBar = new JProgressBar();
747 progressBar.setIndeterminate(true);
749 progressPanel.add(new JLabel(message), BorderLayout.WEST);
750 progressPanel.add(progressBar, BorderLayout.CENTER);
752 layout.setRows(layout.getRows() + 1);
753 statusPanel.add(progressPanel);
755 progressBars.put(lId, progressPanel);
758 // setMenusForViewport();
762 public void registerHandler(final long id,
763 final IProgressIndicatorHandler handler)
765 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
768 "call setProgressBar before registering the progress bar's handler.");
770 progressBarHandlers.put(new Long(id), handler);
771 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
772 if (handler.canCancel())
774 JButton cancel = new JButton("Cancel");
775 final IProgressIndicator us = this;
776 cancel.addActionListener(new ActionListener()
779 public void actionPerformed(ActionEvent e)
781 handler.cancelActivity(id);
784 + ((JLabel) progressPanel.getComponent(0))
788 progressPanel.add(cancel, BorderLayout.EAST);
794 * @return true if any progress bars are still active
796 public boolean operationInProgress()
798 if (progressBars != null && progressBars.size() > 0)
806 * Added so Castor Mapping file can obtain Jalview Version
808 public String getVersion()
810 return jalview.bin.Cache.getProperty("VERSION");
813 public FeatureRenderer getFeatureRenderer()
815 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
818 public void fetchSequence_actionPerformed(ActionEvent e)
820 new SequenceFetcher(this);
823 public void addFromFile_actionPerformed(ActionEvent e)
825 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
828 public void reload_actionPerformed(ActionEvent e)
830 if (fileName != null)
832 // TODO: work out how to recover feature settings for correct view(s) when
834 if (currentFileFormat.equals("Jalview"))
836 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
837 for (int i = 0; i < frames.length; i++)
839 if (frames[i] instanceof AlignFrame && frames[i] != this
840 && ((AlignFrame) frames[i]).fileName.equals(fileName))
844 frames[i].setSelected(true);
845 Desktop.instance.closeAssociatedWindows();
846 } catch (java.beans.PropertyVetoException ex)
852 Desktop.instance.closeAssociatedWindows();
854 FileLoader loader = new FileLoader();
855 String protocol = fileName.startsWith("http:") ? "URL" : "File";
856 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
860 Rectangle bounds = this.getBounds();
862 FileLoader loader = new FileLoader();
863 String protocol = fileName.startsWith("http:") ? "URL" : "File";
864 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
865 protocol, currentFileFormat);
867 newframe.setBounds(bounds);
868 if (featureSettings != null && featureSettings.isShowing())
870 final Rectangle fspos = featureSettings.frame.getBounds();
871 // TODO: need a 'show feature settings' function that takes bounds -
872 // need to refactor Desktop.addFrame
873 newframe.featureSettings_actionPerformed(null);
874 final FeatureSettings nfs = newframe.featureSettings;
875 SwingUtilities.invokeLater(new Runnable()
879 nfs.frame.setBounds(fspos);
882 this.featureSettings.close();
883 this.featureSettings = null;
885 this.closeMenuItem_actionPerformed(true);
890 public void addFromText_actionPerformed(ActionEvent e)
892 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
895 public void addFromURL_actionPerformed(ActionEvent e)
897 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
900 public void save_actionPerformed(ActionEvent e)
903 || (currentFileFormat == null || !jalview.io.FormatAdapter
904 .isValidIOFormat(currentFileFormat, true))
905 || fileName.startsWith("http"))
907 saveAs_actionPerformed(null);
911 saveAlignment(fileName, currentFileFormat);
921 public void saveAs_actionPerformed(ActionEvent e)
923 JalviewFileChooser chooser = new JalviewFileChooser(
924 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
925 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
926 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
927 currentFileFormat, false);
929 chooser.setFileView(new JalviewFileView());
930 chooser.setDialogTitle("Save Alignment to file");
931 chooser.setToolTipText("Save");
933 int value = chooser.showSaveDialog(this);
935 if (value == JalviewFileChooser.APPROVE_OPTION)
937 currentFileFormat = chooser.getSelectedFormat();
938 if (currentFileFormat == null)
940 JOptionPane.showInternalMessageDialog(Desktop.desktop,
941 "You must select a file format before saving!",
942 "File format not specified", JOptionPane.WARNING_MESSAGE);
943 value = chooser.showSaveDialog(this);
947 fileName = chooser.getSelectedFile().getPath();
949 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
952 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
953 if (currentFileFormat.indexOf(" ") > -1)
955 currentFileFormat = currentFileFormat.substring(0,
956 currentFileFormat.indexOf(" "));
958 saveAlignment(fileName, currentFileFormat);
962 public boolean saveAlignment(String file, String format)
964 boolean success = true;
966 if (format.equalsIgnoreCase("Jalview"))
968 String shortName = title;
970 if (shortName.indexOf(java.io.File.separatorChar) > -1)
972 shortName = shortName.substring(shortName
973 .lastIndexOf(java.io.File.separatorChar) + 1);
976 success = new Jalview2XML().SaveAlignment(this, file, shortName);
978 statusBar.setText("Successfully saved to file: " + fileName + " in "
979 + format + " format.");
984 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
986 warningMessage("Cannot save file " + fileName + " using format "
987 + format, "Alignment output format not supported");
988 saveAs_actionPerformed(null);
989 // JBPNote need to have a raise_gui flag here
993 String[] omitHidden = null;
995 if (viewport.hasHiddenColumns)
997 int reply = JOptionPane
998 .showInternalConfirmDialog(
1000 "The Alignment contains hidden columns."
1001 + "\nDo you want to save only the visible alignment?",
1002 "Save / Omit Hidden Columns",
1003 JOptionPane.YES_NO_OPTION,
1004 JOptionPane.QUESTION_MESSAGE);
1006 if (reply == JOptionPane.YES_OPTION)
1008 omitHidden = viewport.getViewAsString(false);
1011 FormatAdapter f = new FormatAdapter();
1012 String output = f.formatSequences(format,
1013 (Alignment) viewport.alignment, // class cast exceptions will
1014 // occur in the distant future
1015 omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
1025 java.io.PrintWriter out = new java.io.PrintWriter(
1026 new java.io.FileWriter(file));
1030 this.setTitle(file);
1031 statusBar.setText("Successfully saved to file: " + fileName
1032 + " in " + format + " format.");
1033 } catch (Exception ex)
1036 ex.printStackTrace();
1043 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
1044 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
1050 private void warningMessage(String warning, String title)
1052 if (new jalview.util.Platform().isHeadless())
1054 System.err.println("Warning: " + title + "\nWarning: " + warning);
1059 JOptionPane.showInternalMessageDialog(this, warning, title,
1060 JOptionPane.WARNING_MESSAGE);
1071 protected void outputText_actionPerformed(ActionEvent e)
1073 String[] omitHidden = null;
1075 if (viewport.hasHiddenColumns)
1077 int reply = JOptionPane
1078 .showInternalConfirmDialog(
1080 "The Alignment contains hidden columns."
1081 + "\nDo you want to output only the visible alignment?",
1082 "Save / Omit Hidden Columns",
1083 JOptionPane.YES_NO_OPTION,
1084 JOptionPane.QUESTION_MESSAGE);
1086 if (reply == JOptionPane.YES_OPTION)
1088 omitHidden = viewport.getViewAsString(false);
1092 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1093 cap.setForInput(null);
1097 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1098 viewport.alignment, omitHidden, viewport.colSel));
1099 Desktop.addInternalFrame(cap,
1100 "Alignment output - " + e.getActionCommand(), 600, 500);
1101 } catch (OutOfMemoryError oom)
1103 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1115 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1117 new HTMLOutput(alignPanel,
1118 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1119 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1122 public void createImageMap(File file, String image)
1124 alignPanel.makePNGImageMap(file, image);
1133 public void createPNG(File f)
1135 alignPanel.makePNG(f);
1144 public void createEPS(File f)
1146 alignPanel.makeEPS(f);
1149 public void pageSetup_actionPerformed(ActionEvent e)
1151 PrinterJob printJob = PrinterJob.getPrinterJob();
1152 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1161 public void printMenuItem_actionPerformed(ActionEvent e)
1163 // Putting in a thread avoids Swing painting problems
1164 PrintThread thread = new PrintThread(alignPanel);
1168 public void exportFeatures_actionPerformed(ActionEvent e)
1170 new AnnotationExporter().exportFeatures(alignPanel);
1173 public void exportAnnotations_actionPerformed(ActionEvent e)
1175 new AnnotationExporter().exportAnnotations(
1177 viewport.showAnnotation ? viewport.alignment
1178 .getAlignmentAnnotation() : null, viewport.alignment
1180 ((Alignment) viewport.alignment).alignmentProperties);
1183 public void associatedData_actionPerformed(ActionEvent e)
1185 // Pick the tree file
1186 JalviewFileChooser chooser = new JalviewFileChooser(
1187 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1188 chooser.setFileView(new JalviewFileView());
1189 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1190 chooser.setToolTipText("Load Jalview Annotations / Features file");
1192 int value = chooser.showOpenDialog(null);
1194 if (value == JalviewFileChooser.APPROVE_OPTION)
1196 String choice = chooser.getSelectedFile().getPath();
1197 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1198 loadJalviewDataFile(choice, null, null, null);
1204 * Close the current view or all views in the alignment frame. If the frame
1205 * only contains one view then the alignment will be removed from memory.
1207 * @param closeAllTabs
1209 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1211 if (alignPanels != null && alignPanels.size() < 2)
1213 closeAllTabs = true;
1218 if (alignPanels != null)
1222 if (this.isClosed())
1224 // really close all the windows - otherwise wait till
1225 // setClosed(true) is called
1226 for (int i = 0; i < alignPanels.size(); i++)
1228 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1235 closeView(alignPanel);
1241 this.setClosed(true);
1243 } catch (Exception ex)
1245 ex.printStackTrace();
1250 * close alignPanel2 and shuffle tabs appropriately.
1252 * @param alignPanel2
1254 public void closeView(AlignmentPanel alignPanel2)
1256 int index = tabbedPane.getSelectedIndex();
1257 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1258 alignPanels.removeElement(alignPanel2);
1260 // if (viewport == alignPanel2.av)
1264 alignPanel2.closePanel();
1267 tabbedPane.removeTabAt(closedindex);
1268 tabbedPane.validate();
1270 if (index > closedindex || index == tabbedPane.getTabCount())
1272 // modify currently selected tab index if necessary.
1276 this.tabSelectionChanged(index);
1282 void updateEditMenuBar()
1285 if (viewport.historyList.size() > 0)
1287 undoMenuItem.setEnabled(true);
1288 CommandI command = (CommandI) viewport.historyList.peek();
1289 undoMenuItem.setText("Undo " + command.getDescription());
1293 undoMenuItem.setEnabled(false);
1294 undoMenuItem.setText("Undo");
1297 if (viewport.redoList.size() > 0)
1299 redoMenuItem.setEnabled(true);
1301 CommandI command = (CommandI) viewport.redoList.peek();
1302 redoMenuItem.setText("Redo " + command.getDescription());
1306 redoMenuItem.setEnabled(false);
1307 redoMenuItem.setText("Redo");
1311 public void addHistoryItem(CommandI command)
1313 if (command.getSize() > 0)
1315 viewport.historyList.push(command);
1316 viewport.redoList.clear();
1317 updateEditMenuBar();
1318 viewport.hasHiddenColumns = (viewport.colSel != null
1319 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1320 .getHiddenColumns().size() > 0);
1326 * @return alignment objects for all views
1328 AlignmentI[] getViewAlignments()
1330 if (alignPanels != null)
1332 Enumeration e = alignPanels.elements();
1333 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1334 for (int i = 0; e.hasMoreElements(); i++)
1336 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1340 if (viewport != null)
1342 return new AlignmentI[]
1343 { viewport.alignment };
1354 protected void undoMenuItem_actionPerformed(ActionEvent e)
1356 if (viewport.historyList.empty())
1358 CommandI command = (CommandI) viewport.historyList.pop();
1359 viewport.redoList.push(command);
1360 command.undoCommand(getViewAlignments());
1362 AlignViewport originalSource = getOriginatingSource(command);
1363 updateEditMenuBar();
1365 if (originalSource != null)
1367 originalSource.hasHiddenColumns = (viewport.colSel != null
1368 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1369 .getHiddenColumns().size() > 0);
1370 originalSource.firePropertyChange("alignment", null,
1371 originalSource.alignment.getSequences());
1381 protected void redoMenuItem_actionPerformed(ActionEvent e)
1383 if (viewport.redoList.size() < 1)
1388 CommandI command = (CommandI) viewport.redoList.pop();
1389 viewport.historyList.push(command);
1390 command.doCommand(getViewAlignments());
1392 AlignViewport originalSource = getOriginatingSource(command);
1393 updateEditMenuBar();
1395 if (originalSource != null)
1397 originalSource.hasHiddenColumns = (viewport.colSel != null
1398 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1399 .getHiddenColumns().size() > 0);
1400 originalSource.firePropertyChange("alignment", null,
1401 originalSource.alignment.getSequences());
1405 AlignViewport getOriginatingSource(CommandI command)
1407 AlignViewport originalSource = null;
1408 // For sequence removal and addition, we need to fire
1409 // the property change event FROM the viewport where the
1410 // original alignment was altered
1411 AlignmentI al = null;
1412 if (command instanceof EditCommand)
1414 EditCommand editCommand = (EditCommand) command;
1415 al = editCommand.getAlignment();
1416 Vector comps = (Vector) PaintRefresher.components.get(viewport
1417 .getSequenceSetId());
1419 for (int i = 0; i < comps.size(); i++)
1421 if (comps.elementAt(i) instanceof AlignmentPanel)
1423 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1425 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1432 if (originalSource == null)
1434 // The original view is closed, we must validate
1435 // the current view against the closed view first
1438 PaintRefresher.validateSequences(al, viewport.alignment);
1441 originalSource = viewport;
1444 return originalSource;
1453 public void moveSelectedSequences(boolean up)
1455 SequenceGroup sg = viewport.getSelectionGroup();
1464 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1466 SequenceI seq = viewport.alignment.getSequenceAt(i);
1468 if (!sg.getSequences(null).contains(seq))
1473 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1475 if (sg.getSequences(null).contains(temp))
1480 viewport.alignment.getSequences().setElementAt(temp, i);
1481 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1486 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1488 SequenceI seq = viewport.alignment.getSequenceAt(i);
1490 if (!sg.getSequences(null).contains(seq))
1495 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1497 if (sg.getSequences(null).contains(temp))
1502 viewport.alignment.getSequences().setElementAt(temp, i);
1503 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1507 alignPanel.paintAlignment(true);
1510 synchronized void slideSequences(boolean right, int size)
1512 Vector sg = new Vector();
1513 if (viewport.cursorMode)
1515 sg.addElement(viewport.alignment
1516 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1518 else if (viewport.getSelectionGroup() != null
1519 && viewport.getSelectionGroup().getSize() != viewport.alignment
1522 sg = viewport.getSelectionGroup().getSequences(
1523 viewport.hiddenRepSequences);
1531 Vector invertGroup = new Vector();
1533 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1535 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1536 invertGroup.add(viewport.alignment.getSequenceAt(i));
1539 SequenceI[] seqs1 = new SequenceI[sg.size()];
1540 for (int i = 0; i < sg.size(); i++)
1541 seqs1[i] = (SequenceI) sg.elementAt(i);
1543 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1544 for (int i = 0; i < invertGroup.size(); i++)
1545 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1547 SlideSequencesCommand ssc;
1549 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1550 size, viewport.getGapCharacter());
1552 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1553 size, viewport.getGapCharacter());
1555 int groupAdjustment = 0;
1556 if (ssc.getGapsInsertedBegin() && right)
1558 if (viewport.cursorMode)
1559 alignPanel.seqPanel.moveCursor(size, 0);
1561 groupAdjustment = size;
1563 else if (!ssc.getGapsInsertedBegin() && !right)
1565 if (viewport.cursorMode)
1566 alignPanel.seqPanel.moveCursor(-size, 0);
1568 groupAdjustment = -size;
1571 if (groupAdjustment != 0)
1573 viewport.getSelectionGroup().setStartRes(
1574 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1575 viewport.getSelectionGroup().setEndRes(
1576 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1579 boolean appendHistoryItem = false;
1580 if (viewport.historyList != null && viewport.historyList.size() > 0
1581 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1583 appendHistoryItem = ssc
1584 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1588 if (!appendHistoryItem)
1589 addHistoryItem(ssc);
1600 protected void copy_actionPerformed(ActionEvent e)
1603 if (viewport.getSelectionGroup() == null)
1607 // TODO: preserve the ordering of displayed alignment annotation in any
1608 // internal paste (particularly sequence associated annotation)
1609 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1610 String[] omitHidden = null;
1612 if (viewport.hasHiddenColumns)
1614 omitHidden = viewport.getViewAsString(true);
1617 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1620 StringSelection ss = new StringSelection(output);
1624 jalview.gui.Desktop.internalCopy = true;
1625 // Its really worth setting the clipboard contents
1626 // to empty before setting the large StringSelection!!
1627 Toolkit.getDefaultToolkit().getSystemClipboard()
1628 .setContents(new StringSelection(""), null);
1630 Toolkit.getDefaultToolkit().getSystemClipboard()
1631 .setContents(ss, Desktop.instance);
1632 } catch (OutOfMemoryError er)
1634 new OOMWarning("copying region", er);
1638 Vector hiddenColumns = null;
1639 if (viewport.hasHiddenColumns)
1641 hiddenColumns = new Vector();
1642 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1643 .getSelectionGroup().getEndRes();
1644 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1647 int[] region = (int[]) viewport.getColumnSelection()
1648 .getHiddenColumns().elementAt(i);
1649 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1651 hiddenColumns.addElement(new int[]
1652 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1657 Desktop.jalviewClipboard = new Object[]
1658 { seqs, viewport.alignment.getDataset(), hiddenColumns };
1659 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1668 protected void pasteNew_actionPerformed(ActionEvent e)
1679 protected void pasteThis_actionPerformed(ActionEvent e)
1685 * Paste contents of Jalview clipboard
1687 * @param newAlignment
1688 * true to paste to a new alignment, otherwise add to this.
1690 void paste(boolean newAlignment)
1692 boolean externalPaste = true;
1695 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1696 Transferable contents = c.getContents(this);
1698 if (contents == null)
1706 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1707 if (str.length() < 1)
1712 format = new IdentifyFile().Identify(str, "Paste");
1714 } catch (OutOfMemoryError er)
1716 new OOMWarning("Out of memory pasting sequences!!", er);
1720 SequenceI[] sequences;
1721 boolean annotationAdded = false;
1722 AlignmentI alignment = null;
1724 if (Desktop.jalviewClipboard != null)
1726 // The clipboard was filled from within Jalview, we must use the
1728 // And dataset from the copied alignment
1729 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1730 // be doubly sure that we create *new* sequence objects.
1731 sequences = new SequenceI[newseq.length];
1732 for (int i = 0; i < newseq.length; i++)
1734 sequences[i] = new Sequence(newseq[i]);
1736 alignment = new Alignment(sequences);
1737 externalPaste = false;
1741 // parse the clipboard as an alignment.
1742 alignment = new FormatAdapter().readFile(str, "Paste", format);
1743 sequences = alignment.getSequencesArray();
1751 if (Desktop.jalviewClipboard != null)
1753 // dataset is inherited
1754 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1758 // new dataset is constructed
1759 alignment.setDataset(null);
1761 alwidth = alignment.getWidth() + 1;
1765 AlignmentI pastedal = alignment; // preserve pasted alignment object
1766 // Add pasted sequences and dataset into existing alignment.
1767 alignment = viewport.getAlignment();
1768 alwidth = alignment.getWidth() + 1;
1769 // decide if we need to import sequences from an existing dataset
1770 boolean importDs = Desktop.jalviewClipboard != null
1771 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1772 // importDs==true instructs us to copy over new dataset sequences from
1773 // an existing alignment
1774 Vector newDs = (importDs) ? new Vector() : null; // used to create
1775 // minimum dataset set
1777 for (int i = 0; i < sequences.length; i++)
1781 newDs.addElement(null);
1783 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1785 if (importDs && ds != null)
1787 if (!newDs.contains(ds))
1789 newDs.setElementAt(ds, i);
1790 ds = new Sequence(ds);
1791 // update with new dataset sequence
1792 sequences[i].setDatasetSequence(ds);
1796 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1801 // copy and derive new dataset sequence
1802 sequences[i] = sequences[i].deriveSequence();
1803 alignment.getDataset().addSequence(
1804 sequences[i].getDatasetSequence());
1805 // TODO: avoid creation of duplicate dataset sequences with a
1806 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1808 alignment.addSequence(sequences[i]); // merges dataset
1812 newDs.clear(); // tidy up
1814 if (pastedal.getAlignmentAnnotation() != null)
1816 // Add any annotation attached to alignment.
1817 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1818 for (int i = 0; i < alann.length; i++)
1820 annotationAdded = true;
1821 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1823 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1824 newann.padAnnotation(alwidth);
1825 alignment.addAnnotation(newann);
1835 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1836 sequences, 0, alignment.getWidth(), alignment));
1838 // Add any annotations attached to sequences
1839 for (int i = 0; i < sequences.length; i++)
1841 if (sequences[i].getAnnotation() != null)
1843 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1845 annotationAdded = true;
1846 sequences[i].getAnnotation()[a].adjustForAlignment();
1847 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1848 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1853 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1860 // propagate alignment changed.
1861 viewport.setEndSeq(alignment.getHeight());
1862 if (annotationAdded)
1864 // Duplicate sequence annotation in all views.
1865 AlignmentI[] alview = this.getViewAlignments();
1866 for (int i = 0; i < sequences.length; i++)
1868 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1871 for (int avnum = 0; avnum < alview.length; avnum++)
1873 if (alview[avnum] != alignment)
1875 // duplicate in a view other than the one with input focus
1876 int avwidth = alview[avnum].getWidth() + 1;
1877 // this relies on sann being preserved after we
1878 // modify the sequence's annotation array for each duplication
1879 for (int a = 0; a < sann.length; a++)
1881 AlignmentAnnotation newann = new AlignmentAnnotation(
1883 sequences[i].addAlignmentAnnotation(newann);
1884 newann.padAnnotation(avwidth);
1885 alview[avnum].addAnnotation(newann); // annotation was
1886 // duplicated earlier
1887 alview[avnum].setAnnotationIndex(newann, a);
1892 buildSortByAnnotationScoresMenu();
1894 viewport.firePropertyChange("alignment", null,
1895 alignment.getSequences());
1900 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1902 String newtitle = new String("Copied sequences");
1904 if (Desktop.jalviewClipboard != null
1905 && Desktop.jalviewClipboard[2] != null)
1907 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1908 for (int i = 0; i < hc.size(); i++)
1910 int[] region = (int[]) hc.elementAt(i);
1911 af.viewport.hideColumns(region[0], region[1]);
1915 // >>>This is a fix for the moment, until a better solution is
1917 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1919 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1921 // TODO: maintain provenance of an alignment, rather than just make the
1922 // title a concatenation of operations.
1925 if (title.startsWith("Copied sequences"))
1931 newtitle = newtitle.concat("- from " + title);
1936 newtitle = new String("Pasted sequences");
1939 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1944 } catch (Exception ex)
1946 ex.printStackTrace();
1947 System.out.println("Exception whilst pasting: " + ex);
1948 // could be anything being pasted in here
1959 protected void cut_actionPerformed(ActionEvent e)
1961 copy_actionPerformed(null);
1962 delete_actionPerformed(null);
1971 protected void delete_actionPerformed(ActionEvent evt)
1974 SequenceGroup sg = viewport.getSelectionGroup();
1980 Vector seqs = new Vector();
1982 for (int i = 0; i < sg.getSize(); i++)
1984 seq = sg.getSequenceAt(i);
1985 seqs.addElement(seq);
1988 // If the cut affects all sequences, remove highlighted columns
1989 if (sg.getSize() == viewport.alignment.getHeight())
1991 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1992 sg.getEndRes() + 1);
1995 SequenceI[] cut = new SequenceI[seqs.size()];
1996 for (int i = 0; i < seqs.size(); i++)
1998 cut[i] = (SequenceI) seqs.elementAt(i);
2002 * //ADD HISTORY ITEM
2004 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2005 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2006 viewport.alignment));
2008 viewport.setSelectionGroup(null);
2009 viewport.sendSelection();
2010 viewport.alignment.deleteGroup(sg);
2012 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2014 if (viewport.getAlignment().getHeight() < 1)
2018 this.setClosed(true);
2019 } catch (Exception ex)
2031 protected void deleteGroups_actionPerformed(ActionEvent e)
2033 viewport.alignment.deleteAllGroups();
2034 viewport.sequenceColours = null;
2035 viewport.setSelectionGroup(null);
2036 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2037 alignPanel.updateAnnotation();
2038 alignPanel.paintAlignment(true);
2047 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2049 SequenceGroup sg = new SequenceGroup();
2051 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2053 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2056 sg.setEndRes(viewport.alignment.getWidth() - 1);
2057 viewport.setSelectionGroup(sg);
2058 viewport.sendSelection();
2059 alignPanel.paintAlignment(true);
2060 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2069 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2071 if (viewport.cursorMode)
2073 alignPanel.seqPanel.keyboardNo1 = null;
2074 alignPanel.seqPanel.keyboardNo2 = null;
2076 viewport.setSelectionGroup(null);
2077 viewport.getColumnSelection().clear();
2078 viewport.setSelectionGroup(null);
2079 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2080 alignPanel.idPanel.idCanvas.searchResults = null;
2081 alignPanel.paintAlignment(true);
2082 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2083 viewport.sendSelection();
2092 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2094 SequenceGroup sg = viewport.getSelectionGroup();
2098 selectAllSequenceMenuItem_actionPerformed(null);
2103 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2105 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2108 alignPanel.paintAlignment(true);
2109 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2110 viewport.sendSelection();
2113 public void invertColSel_actionPerformed(ActionEvent e)
2115 viewport.invertColumnSelection();
2116 alignPanel.paintAlignment(true);
2117 viewport.sendSelection();
2126 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2128 trimAlignment(true);
2137 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2139 trimAlignment(false);
2142 void trimAlignment(boolean trimLeft)
2144 ColumnSelection colSel = viewport.getColumnSelection();
2147 if (colSel.size() > 0)
2151 column = colSel.getMin();
2155 column = colSel.getMax();
2159 if (viewport.getSelectionGroup() != null)
2161 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2162 viewport.hiddenRepSequences);
2166 seqs = viewport.alignment.getSequencesArray();
2169 TrimRegionCommand trimRegion;
2172 trimRegion = new TrimRegionCommand("Remove Left",
2173 TrimRegionCommand.TRIM_LEFT, seqs, column,
2174 viewport.alignment, viewport.colSel,
2175 viewport.selectionGroup);
2176 viewport.setStartRes(0);
2180 trimRegion = new TrimRegionCommand("Remove Right",
2181 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2182 viewport.alignment, viewport.colSel,
2183 viewport.selectionGroup);
2186 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2188 addHistoryItem(trimRegion);
2190 Vector groups = viewport.alignment.getGroups();
2192 for (int i = 0; i < groups.size(); i++)
2194 SequenceGroup sg = (SequenceGroup) groups.get(i);
2196 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2197 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2199 viewport.alignment.deleteGroup(sg);
2203 viewport.firePropertyChange("alignment", null, viewport
2204 .getAlignment().getSequences());
2214 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2216 int start = 0, end = viewport.alignment.getWidth() - 1;
2219 if (viewport.getSelectionGroup() != null)
2221 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2222 viewport.hiddenRepSequences);
2223 start = viewport.getSelectionGroup().getStartRes();
2224 end = viewport.getSelectionGroup().getEndRes();
2228 seqs = viewport.alignment.getSequencesArray();
2231 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2232 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2234 addHistoryItem(removeGapCols);
2236 statusBar.setText("Removed " + removeGapCols.getSize()
2237 + " empty columns.");
2239 // This is to maintain viewport position on first residue
2240 // of first sequence
2241 SequenceI seq = viewport.alignment.getSequenceAt(0);
2242 int startRes = seq.findPosition(viewport.startRes);
2243 // ShiftList shifts;
2244 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2245 // edit.alColumnChanges=shifts.getInverse();
2246 // if (viewport.hasHiddenColumns)
2247 // viewport.getColumnSelection().compensateForEdits(shifts);
2248 viewport.setStartRes(seq.findIndex(startRes) - 1);
2249 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2260 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2262 int start = 0, end = viewport.alignment.getWidth() - 1;
2265 if (viewport.getSelectionGroup() != null)
2267 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2268 viewport.hiddenRepSequences);
2269 start = viewport.getSelectionGroup().getStartRes();
2270 end = viewport.getSelectionGroup().getEndRes();
2274 seqs = viewport.alignment.getSequencesArray();
2277 // This is to maintain viewport position on first residue
2278 // of first sequence
2279 SequenceI seq = viewport.alignment.getSequenceAt(0);
2280 int startRes = seq.findPosition(viewport.startRes);
2282 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2283 viewport.alignment));
2285 viewport.setStartRes(seq.findIndex(startRes) - 1);
2287 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2298 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2300 viewport.padGaps = padGapsMenuitem.isSelected();
2301 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2307 // if (justifySeqs>0)
2309 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2321 public void findMenuItem_actionPerformed(ActionEvent e)
2326 public void newView_actionPerformed(ActionEvent e)
2333 * @param copyAnnotation
2334 * if true then duplicate all annnotation, groups and settings
2335 * @return new alignment panel, already displayed.
2337 public AlignmentPanel newView(boolean copyAnnotation)
2339 return newView(null, copyAnnotation);
2345 * title of newly created view
2346 * @return new alignment panel, already displayed.
2348 public AlignmentPanel newView(String viewTitle)
2350 return newView(viewTitle, true);
2356 * title of newly created view
2357 * @param copyAnnotation
2358 * if true then duplicate all annnotation, groups and settings
2359 * @return new alignment panel, already displayed.
2361 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2363 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2365 if (!copyAnnotation)
2367 // just remove all the current annotation except for the automatic stuff
2368 newap.av.alignment.deleteAllGroups();
2369 for (AlignmentAnnotation alan : newap.av.alignment
2370 .getAlignmentAnnotation())
2372 if (!alan.autoCalculated)
2374 newap.av.alignment.deleteAnnotation(alan);
2380 newap.av.gatherViewsHere = false;
2382 if (viewport.viewName == null)
2384 viewport.viewName = "Original";
2387 newap.av.historyList = viewport.historyList;
2388 newap.av.redoList = viewport.redoList;
2390 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2391 // make sure the new view has a unique name - this is essential for Jalview
2393 boolean addFirstIndex = false;
2394 if (viewTitle == null || viewTitle.trim().length() == 0)
2397 addFirstIndex = true;
2401 index = 1;// we count from 1 if given a specific name
2403 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2404 Vector comps = (Vector) PaintRefresher.components.get(viewport
2405 .getSequenceSetId());
2406 Vector existingNames = new Vector();
2407 for (int i = 0; i < comps.size(); i++)
2409 if (comps.elementAt(i) instanceof AlignmentPanel)
2411 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2412 if (!existingNames.contains(ap.av.viewName))
2414 existingNames.addElement(ap.av.viewName);
2419 while (existingNames.contains(newViewName))
2421 newViewName = viewTitle + " " + (++index);
2424 newap.av.viewName = newViewName;
2426 addAlignmentPanel(newap, true);
2428 if (alignPanels.size() == 2)
2430 viewport.gatherViewsHere = true;
2432 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2436 public void expandViews_actionPerformed(ActionEvent e)
2438 Desktop.instance.explodeViews(this);
2441 public void gatherViews_actionPerformed(ActionEvent e)
2443 Desktop.instance.gatherViews(this);
2452 public void font_actionPerformed(ActionEvent e)
2454 new FontChooser(alignPanel);
2463 protected void seqLimit_actionPerformed(ActionEvent e)
2465 viewport.setShowJVSuffix(seqLimits.isSelected());
2467 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2468 .calculateIdWidth());
2469 alignPanel.paintAlignment(true);
2472 public void idRightAlign_actionPerformed(ActionEvent e)
2474 viewport.rightAlignIds = idRightAlign.isSelected();
2475 alignPanel.paintAlignment(true);
2478 public void centreColumnLabels_actionPerformed(ActionEvent e)
2480 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2481 alignPanel.paintAlignment(true);
2487 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2489 protected void followHighlight_actionPerformed()
2491 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2493 alignPanel.scrollToPosition(
2494 alignPanel.seqPanel.seqCanvas.searchResults, false);
2504 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2506 viewport.setColourText(colourTextMenuItem.isSelected());
2507 alignPanel.paintAlignment(true);
2516 public void wrapMenuItem_actionPerformed(ActionEvent e)
2518 scaleAbove.setVisible(wrapMenuItem.isSelected());
2519 scaleLeft.setVisible(wrapMenuItem.isSelected());
2520 scaleRight.setVisible(wrapMenuItem.isSelected());
2521 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2522 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2525 public void showAllSeqs_actionPerformed(ActionEvent e)
2527 viewport.showAllHiddenSeqs();
2530 public void showAllColumns_actionPerformed(ActionEvent e)
2532 viewport.showAllHiddenColumns();
2536 public void hideSelSequences_actionPerformed(ActionEvent e)
2538 viewport.hideAllSelectedSeqs();
2539 alignPanel.paintAlignment(true);
2543 * called by key handler and the hide all/show all menu items
2548 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2551 boolean hide = false;
2552 SequenceGroup sg = viewport.getSelectionGroup();
2553 if (!toggleSeqs && !toggleCols)
2555 // Hide everything by the current selection - this is a hack - we do the
2556 // invert and then hide
2557 // first check that there will be visible columns after the invert.
2558 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
2559 .getSelected().size() > 0)
2560 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2563 // now invert the sequence set, if required - empty selection implies
2564 // that no hiding is required.
2567 invertSequenceMenuItem_actionPerformed(null);
2568 sg = viewport.getSelectionGroup();
2572 viewport.expandColSelection(sg, true);
2573 // finally invert the column selection and get the new sequence
2575 invertColSel_actionPerformed(null);
2582 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
2584 hideSelSequences_actionPerformed(null);
2587 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
2589 showAllSeqs_actionPerformed(null);
2595 if (viewport.colSel.getSelected().size() > 0)
2597 hideSelColumns_actionPerformed(null);
2600 viewport.selectionGroup = sg;
2605 showAllColumns_actionPerformed(null);
2614 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2615 * event.ActionEvent)
2617 public void hideAllButSelection_actionPerformed(ActionEvent e)
2619 toggleHiddenRegions(false, false);
2626 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2629 public void hideAllSelection_actionPerformed(ActionEvent e)
2631 SequenceGroup sg = viewport.getSelectionGroup();
2632 viewport.expandColSelection(sg, false);
2633 viewport.hideAllSelectedSeqs();
2634 viewport.hideSelectedColumns();
2635 alignPanel.paintAlignment(true);
2642 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2645 public void showAllhidden_actionPerformed(ActionEvent e)
2647 viewport.showAllHiddenColumns();
2648 viewport.showAllHiddenSeqs();
2649 alignPanel.paintAlignment(true);
2652 public void hideSelColumns_actionPerformed(ActionEvent e)
2654 viewport.hideSelectedColumns();
2655 alignPanel.paintAlignment(true);
2658 public void hiddenMarkers_actionPerformed(ActionEvent e)
2660 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2670 protected void scaleAbove_actionPerformed(ActionEvent e)
2672 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2673 alignPanel.paintAlignment(true);
2682 protected void scaleLeft_actionPerformed(ActionEvent e)
2684 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2685 alignPanel.paintAlignment(true);
2694 protected void scaleRight_actionPerformed(ActionEvent e)
2696 viewport.setScaleRightWrapped(scaleRight.isSelected());
2697 alignPanel.paintAlignment(true);
2706 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2708 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2709 alignPanel.paintAlignment(true);
2718 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2720 viewport.setShowText(viewTextMenuItem.isSelected());
2721 alignPanel.paintAlignment(true);
2730 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2732 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2733 alignPanel.paintAlignment(true);
2736 public FeatureSettings featureSettings;
2738 public void featureSettings_actionPerformed(ActionEvent e)
2740 if (featureSettings != null)
2742 featureSettings.close();
2743 featureSettings = null;
2745 if (!showSeqFeatures.isSelected())
2747 // make sure features are actually displayed
2748 showSeqFeatures.setSelected(true);
2749 showSeqFeatures_actionPerformed(null);
2751 featureSettings = new FeatureSettings(this);
2755 * Set or clear 'Show Sequence Features'
2760 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2762 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2763 alignPanel.paintAlignment(true);
2764 if (alignPanel.getOverviewPanel() != null)
2766 alignPanel.getOverviewPanel().updateOverviewImage();
2771 * Set or clear 'Show Sequence Features'
2776 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2778 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2780 if (viewport.getShowSequenceFeaturesHeight())
2782 // ensure we're actually displaying features
2783 viewport.setShowSequenceFeatures(true);
2784 showSeqFeatures.setSelected(true);
2786 alignPanel.paintAlignment(true);
2787 if (alignPanel.getOverviewPanel() != null)
2789 alignPanel.getOverviewPanel().updateOverviewImage();
2799 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2801 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2802 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2805 public void alignmentProperties()
2807 JEditorPane editPane = new JEditorPane("text/html", "");
2808 editPane.setEditable(false);
2809 StringBuffer contents = new AlignmentProperties(viewport.alignment)
2811 editPane.setText("<html>" + contents.toString() + "</html>");
2812 JInternalFrame frame = new JInternalFrame();
2813 frame.getContentPane().add(new JScrollPane(editPane));
2815 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2816 + getTitle(), 500, 400);
2825 public void overviewMenuItem_actionPerformed(ActionEvent e)
2827 if (alignPanel.overviewPanel != null)
2832 JInternalFrame frame = new JInternalFrame();
2833 OverviewPanel overview = new OverviewPanel(alignPanel);
2834 frame.setContentPane(overview);
2835 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2836 frame.getWidth(), frame.getHeight());
2838 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2839 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2841 public void internalFrameClosed(
2842 javax.swing.event.InternalFrameEvent evt)
2844 alignPanel.setOverviewPanel(null);
2848 alignPanel.setOverviewPanel(overview);
2851 public void textColour_actionPerformed(ActionEvent e)
2853 new TextColourChooser().chooseColour(alignPanel, null);
2862 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2873 public void clustalColour_actionPerformed(ActionEvent e)
2875 changeColour(new ClustalxColourScheme(
2876 viewport.alignment.getSequences(),
2877 viewport.alignment.getWidth()));
2886 public void zappoColour_actionPerformed(ActionEvent e)
2888 changeColour(new ZappoColourScheme());
2897 public void taylorColour_actionPerformed(ActionEvent e)
2899 changeColour(new TaylorColourScheme());
2908 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2910 changeColour(new HydrophobicColourScheme());
2919 public void helixColour_actionPerformed(ActionEvent e)
2921 changeColour(new HelixColourScheme());
2930 public void strandColour_actionPerformed(ActionEvent e)
2932 changeColour(new StrandColourScheme());
2941 public void turnColour_actionPerformed(ActionEvent e)
2943 changeColour(new TurnColourScheme());
2952 public void buriedColour_actionPerformed(ActionEvent e)
2954 changeColour(new BuriedColourScheme());
2963 public void nucleotideColour_actionPerformed(ActionEvent e)
2965 changeColour(new NucleotideColourScheme());
2968 public void annotationColour_actionPerformed(ActionEvent e)
2970 new AnnotationColourChooser(viewport, alignPanel);
2979 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2981 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2990 public void changeColour(ColourSchemeI cs)
2996 if (viewport.getAbovePIDThreshold())
2998 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3001 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3003 viewport.setGlobalColourScheme(cs);
3007 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3010 if (viewport.getConservationSelected())
3013 Alignment al = (Alignment) viewport.alignment;
3014 Conservation c = new Conservation("All",
3015 ResidueProperties.propHash, 3, al.getSequences(), 0,
3019 c.verdict(false, viewport.ConsPercGaps);
3021 cs.setConservation(c);
3023 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3028 cs.setConservation(null);
3031 cs.setConsensus(viewport.hconsensus);
3034 viewport.setGlobalColourScheme(cs);
3036 if (viewport.getColourAppliesToAllGroups())
3038 Vector groups = viewport.alignment.getGroups();
3040 for (int i = 0; i < groups.size(); i++)
3042 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
3050 if (cs instanceof ClustalxColourScheme)
3052 sg.cs = new ClustalxColourScheme(
3053 sg.getSequences(viewport.hiddenRepSequences),
3056 else if (cs instanceof UserColourScheme)
3058 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3064 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
3065 } catch (Exception ex)
3070 if (viewport.getAbovePIDThreshold()
3071 || cs instanceof PIDColourScheme
3072 || cs instanceof Blosum62ColourScheme)
3074 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3076 sg.cs.setConsensus(AAFrequency.calculate(
3077 sg.getSequences(viewport.hiddenRepSequences),
3078 sg.getStartRes(), sg.getEndRes() + 1));
3082 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3085 if (viewport.getConservationSelected())
3087 Conservation c = new Conservation("Group",
3088 ResidueProperties.propHash, 3,
3089 sg.getSequences(viewport.hiddenRepSequences),
3090 sg.getStartRes(), sg.getEndRes() + 1);
3092 c.verdict(false, viewport.ConsPercGaps);
3093 sg.cs.setConservation(c);
3097 sg.cs.setConservation(null);
3102 if (alignPanel.getOverviewPanel() != null)
3104 alignPanel.getOverviewPanel().updateOverviewImage();
3107 alignPanel.paintAlignment(true);
3116 protected void modifyPID_actionPerformed(ActionEvent e)
3118 if (viewport.getAbovePIDThreshold()
3119 && viewport.globalColourScheme != null)
3121 SliderPanel.setPIDSliderSource(alignPanel,
3122 viewport.getGlobalColourScheme(), "Background");
3123 SliderPanel.showPIDSlider();
3133 protected void modifyConservation_actionPerformed(ActionEvent e)
3135 if (viewport.getConservationSelected()
3136 && viewport.globalColourScheme != null)
3138 SliderPanel.setConservationSlider(alignPanel,
3139 viewport.globalColourScheme, "Background");
3140 SliderPanel.showConservationSlider();
3150 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3152 viewport.setConservationSelected(conservationMenuItem.isSelected());
3154 viewport.setAbovePIDThreshold(false);
3155 abovePIDThreshold.setSelected(false);
3157 changeColour(viewport.getGlobalColourScheme());
3159 modifyConservation_actionPerformed(null);
3168 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3170 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3172 conservationMenuItem.setSelected(false);
3173 viewport.setConservationSelected(false);
3175 changeColour(viewport.getGlobalColourScheme());
3177 modifyPID_actionPerformed(null);
3186 public void userDefinedColour_actionPerformed(ActionEvent e)
3188 if (e.getActionCommand().equals("User Defined..."))
3190 new UserDefinedColours(alignPanel, null);
3194 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3195 .getUserColourSchemes().get(e.getActionCommand());
3201 public void updateUserColourMenu()
3204 Component[] menuItems = colourMenu.getMenuComponents();
3205 int i, iSize = menuItems.length;
3206 for (i = 0; i < iSize; i++)
3208 if (menuItems[i].getName() != null
3209 && menuItems[i].getName().equals("USER_DEFINED"))
3211 colourMenu.remove(menuItems[i]);
3215 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3217 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3218 .getUserColourSchemes().keys();
3220 while (userColours.hasMoreElements())
3222 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3223 userColours.nextElement().toString());
3224 radioItem.setName("USER_DEFINED");
3225 radioItem.addMouseListener(new MouseAdapter()
3227 public void mousePressed(MouseEvent evt)
3229 if (evt.isControlDown()
3230 || SwingUtilities.isRightMouseButton(evt))
3232 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3234 int option = JOptionPane.showInternalConfirmDialog(
3235 jalview.gui.Desktop.desktop,
3236 "Remove from default list?",
3237 "Remove user defined colour",
3238 JOptionPane.YES_NO_OPTION);
3239 if (option == JOptionPane.YES_OPTION)
3241 jalview.gui.UserDefinedColours
3242 .removeColourFromDefaults(radioItem.getText());
3243 colourMenu.remove(radioItem);
3247 radioItem.addActionListener(new ActionListener()
3249 public void actionPerformed(ActionEvent evt)
3251 userDefinedColour_actionPerformed(evt);
3258 radioItem.addActionListener(new ActionListener()
3260 public void actionPerformed(ActionEvent evt)
3262 userDefinedColour_actionPerformed(evt);
3266 colourMenu.insert(radioItem, 15);
3267 colours.add(radioItem);
3278 public void PIDColour_actionPerformed(ActionEvent e)
3280 changeColour(new PIDColourScheme());
3289 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3291 changeColour(new Blosum62ColourScheme());
3300 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3302 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3303 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3304 .getAlignment().getSequenceAt(0), null);
3305 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3306 viewport.alignment));
3307 alignPanel.paintAlignment(true);
3316 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3318 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3319 AlignmentSorter.sortByID(viewport.getAlignment());
3320 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3321 alignPanel.paintAlignment(true);
3330 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3332 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3333 AlignmentSorter.sortByLength(viewport.getAlignment());
3334 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3335 viewport.alignment));
3336 alignPanel.paintAlignment(true);
3345 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3347 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3348 AlignmentSorter.sortByGroup(viewport.getAlignment());
3349 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3350 viewport.alignment));
3352 alignPanel.paintAlignment(true);
3361 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3363 new RedundancyPanel(alignPanel, this);
3372 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3374 if ((viewport.getSelectionGroup() == null)
3375 || (viewport.getSelectionGroup().getSize() < 2))
3377 JOptionPane.showInternalMessageDialog(this,
3378 "You must select at least 2 sequences.", "Invalid Selection",
3379 JOptionPane.WARNING_MESSAGE);
3383 JInternalFrame frame = new JInternalFrame();
3384 frame.setContentPane(new PairwiseAlignPanel(viewport));
3385 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3395 public void PCAMenuItem_actionPerformed(ActionEvent e)
3397 if (((viewport.getSelectionGroup() != null)
3398 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3399 .getSelectionGroup().getSize() > 0))
3400 || (viewport.getAlignment().getHeight() < 4))
3402 JOptionPane.showInternalMessageDialog(this,
3403 "Principal component analysis must take\n"
3404 + "at least 4 input sequences.",
3405 "Sequence selection insufficient",
3406 JOptionPane.WARNING_MESSAGE);
3411 new PCAPanel(alignPanel);
3414 public void autoCalculate_actionPerformed(ActionEvent e)
3416 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3417 if (viewport.autoCalculateConsensus)
3419 viewport.firePropertyChange("alignment", null, viewport
3420 .getAlignment().getSequences());
3430 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3432 NewTreePanel("AV", "PID", "Average distance tree using PID");
3441 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3443 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3452 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3454 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3463 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3465 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3478 void NewTreePanel(String type, String pwType, String title)
3482 if (viewport.getSelectionGroup() != null)
3484 if (viewport.getSelectionGroup().getSize() < 3)
3489 "You need to have more than two sequences selected to build a tree!",
3490 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3495 SequenceGroup sg = viewport.getSelectionGroup();
3497 /* Decide if the selection is a column region */
3498 while (s < sg.getSize())
3500 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3506 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3507 + "Try using the Pad function in the edit menu,\n"
3508 + "or one of the multiple sequence alignment web services.",
3509 "Sequences in selection are not aligned",
3510 JOptionPane.WARNING_MESSAGE);
3516 title = title + " on region";
3517 tp = new TreePanel(alignPanel, type, pwType);
3521 // are the visible sequences aligned?
3522 if (!viewport.alignment.isAligned(false))
3527 "The sequences must be aligned before creating a tree.\n"
3528 + "Try using the Pad function in the edit menu,\n"
3529 + "or one of the multiple sequence alignment web services.",
3530 "Sequences not aligned",
3531 JOptionPane.WARNING_MESSAGE);
3536 if (viewport.alignment.getHeight() < 2)
3541 tp = new TreePanel(alignPanel, type, pwType);
3546 if (viewport.viewName != null)
3548 title += viewport.viewName + " of ";
3551 title += this.title;
3553 Desktop.addInternalFrame(tp, title, 600, 500);
3564 public void addSortByOrderMenuItem(String title,
3565 final AlignmentOrder order)
3567 final JMenuItem item = new JMenuItem("by " + title);
3569 item.addActionListener(new java.awt.event.ActionListener()
3571 public void actionPerformed(ActionEvent e)
3573 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3575 // TODO: JBPNote - have to map order entries to curent SequenceI
3577 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3579 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3580 viewport.alignment));
3582 alignPanel.paintAlignment(true);
3588 * Add a new sort by annotation score menu item
3591 * the menu to add the option to
3593 * the label used to retrieve scores for each sequence on the
3596 public void addSortByAnnotScoreMenuItem(JMenu sort,
3597 final String scoreLabel)
3599 final JMenuItem item = new JMenuItem(scoreLabel);
3601 item.addActionListener(new java.awt.event.ActionListener()
3603 public void actionPerformed(ActionEvent e)
3605 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3606 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3607 viewport.getAlignment());// ,viewport.getSelectionGroup());
3608 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3609 viewport.alignment));
3610 alignPanel.paintAlignment(true);
3616 * last hash for alignment's annotation array - used to minimise cost of
3619 protected int _annotationScoreVectorHash;
3622 * search the alignment and rebuild the sort by annotation score submenu the
3623 * last alignment annotation vector hash is stored to minimize cost of
3624 * rebuilding in subsequence calls.
3627 public void buildSortByAnnotationScoresMenu()
3629 if (viewport.alignment.getAlignmentAnnotation() == null)
3634 if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3636 sortByAnnotScore.removeAll();
3637 // almost certainly a quicker way to do this - but we keep it simple
3638 Hashtable scoreSorts = new Hashtable();
3639 AlignmentAnnotation aann[];
3640 Enumeration sq = viewport.alignment.getSequences().elements();
3641 while (sq.hasMoreElements())
3643 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3644 for (int i = 0; aann != null && i < aann.length; i++)
3646 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3648 scoreSorts.put(aann[i].label, aann[i].label);
3652 Enumeration labels = scoreSorts.keys();
3653 while (labels.hasMoreElements())
3655 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3656 (String) labels.nextElement());
3658 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3661 _annotationScoreVectorHash = viewport.alignment
3662 .getAlignmentAnnotation().hashCode();
3667 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3668 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3669 * call. Listeners are added to remove the menu item when the treePanel is
3670 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3674 * Displayed tree window.
3676 * SortBy menu item title.
3678 public void buildTreeMenu()
3680 sortByTreeMenu.removeAll();
3682 Vector comps = (Vector) PaintRefresher.components.get(viewport
3683 .getSequenceSetId());
3684 Vector treePanels = new Vector();
3685 int i, iSize = comps.size();
3686 for (i = 0; i < iSize; i++)
3688 if (comps.elementAt(i) instanceof TreePanel)
3690 treePanels.add(comps.elementAt(i));
3694 iSize = treePanels.size();
3698 sortByTreeMenu.setVisible(false);
3702 sortByTreeMenu.setVisible(true);
3704 for (i = 0; i < treePanels.size(); i++)
3706 TreePanel tp = (TreePanel) treePanels.elementAt(i);
3707 final JMenuItem item = new JMenuItem(tp.getTitle());
3708 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3709 item.addActionListener(new java.awt.event.ActionListener()
3711 public void actionPerformed(ActionEvent e)
3713 SequenceI[] oldOrder = viewport.getAlignment()
3714 .getSequencesArray();
3715 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3717 addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
3718 viewport.alignment));
3720 alignPanel.paintAlignment(true);
3724 sortByTreeMenu.add(item);
3728 public boolean sortBy(AlignmentOrder alorder, String undoname)
3730 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3731 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3732 if (undoname != null)
3734 addHistoryItem(new OrderCommand(undoname, oldOrder,
3735 viewport.alignment));
3737 alignPanel.paintAlignment(true);
3742 * Work out whether the whole set of sequences or just the selected set will
3743 * be submitted for multiple alignment.
3746 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3748 // Now, check we have enough sequences
3749 AlignmentView msa = null;
3751 if ((viewport.getSelectionGroup() != null)
3752 && (viewport.getSelectionGroup().getSize() > 1))
3754 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3755 // some common interface!
3757 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3758 * SequenceI[sz = seqs.getSize(false)];
3760 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3761 * seqs.getSequenceAt(i); }
3763 msa = viewport.getAlignmentView(true);
3768 * Vector seqs = viewport.getAlignment().getSequences();
3770 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3772 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3773 * seqs.elementAt(i); } }
3775 msa = viewport.getAlignmentView(false);
3781 * Decides what is submitted to a secondary structure prediction service: the
3782 * first sequence in the alignment, or in the current selection, or, if the
3783 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3784 * region or the whole alignment. (where the first sequence in the set is the
3785 * one that the prediction will be for).
3787 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3789 AlignmentView seqs = null;
3791 if ((viewport.getSelectionGroup() != null)
3792 && (viewport.getSelectionGroup().getSize() > 0))
3794 seqs = viewport.getAlignmentView(true);
3798 seqs = viewport.getAlignmentView(false);
3800 // limit sequences - JBPNote in future - could spawn multiple prediction
3802 // TODO: viewport.alignment.isAligned is a global state - the local
3803 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3804 if (!viewport.alignment.isAligned(false))
3806 seqs.setSequences(new SeqCigar[]
3807 { seqs.getSequences()[0] });
3808 // TODO: if seqs.getSequences().length>1 then should really have warned
3821 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3823 // Pick the tree file
3824 JalviewFileChooser chooser = new JalviewFileChooser(
3825 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3826 chooser.setFileView(new JalviewFileView());
3827 chooser.setDialogTitle("Select a newick-like tree file");
3828 chooser.setToolTipText("Load a tree file");
3830 int value = chooser.showOpenDialog(null);
3832 if (value == JalviewFileChooser.APPROVE_OPTION)
3834 String choice = chooser.getSelectedFile().getPath();
3835 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3836 jalview.io.NewickFile fin = null;
3839 fin = new jalview.io.NewickFile(choice, "File");
3840 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3841 } catch (Exception ex)
3843 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3844 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3845 ex.printStackTrace();
3847 if (fin != null && fin.hasWarningMessage())
3849 JOptionPane.showMessageDialog(Desktop.desktop,
3850 fin.getWarningMessage(), "Possible problem with tree file",
3851 JOptionPane.WARNING_MESSAGE);
3856 public TreePanel ShowNewickTree(NewickFile nf, String title)
3858 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3861 public TreePanel ShowNewickTree(NewickFile nf, String title,
3862 AlignmentView input)
3864 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3867 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3868 int h, int x, int y)
3870 return ShowNewickTree(nf, title, null, w, h, x, y);
3874 * Add a treeviewer for the tree extracted from a newick file object to the
3875 * current alignment view
3882 * Associated alignment input data (or null)
3891 * @return TreePanel handle
3893 public TreePanel ShowNewickTree(NewickFile nf, String title,
3894 AlignmentView input, int w, int h, int x, int y)
3896 TreePanel tp = null;
3902 if (nf.getTree() != null)
3904 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3910 tp.setLocation(x, y);
3913 Desktop.addInternalFrame(tp, title, w, h);
3915 } catch (Exception ex)
3917 ex.printStackTrace();
3923 private boolean buildingMenu = false;
3926 * Generates menu items and listener event actions for web service clients
3929 public void BuildWebServiceMenu()
3931 while (buildingMenu)
3935 System.err.println("Waiting for building menu to finish.");
3937 } catch (Exception e)
3942 final AlignFrame me = this;
3943 buildingMenu = true;
3944 new Thread(new Runnable()
3950 System.err.println("Building ws menu again "
3951 + Thread.currentThread());
3952 // TODO: add support for context dependent disabling of services based
3954 // alignment and current selection
3955 // TODO: add additional serviceHandle parameter to specify abstract
3957 // class independently of AbstractName
3958 // TODO: add in rediscovery GUI function to restart discoverer
3959 // TODO: group services by location as well as function and/or
3961 // object broker mechanism.
3962 final Vector wsmenu = new Vector();
3963 final IProgressIndicator af = me;
3964 final JMenu msawsmenu = new JMenu("Alignment");
3965 final JMenu secstrmenu = new JMenu(
3966 "Secondary Structure Prediction");
3967 final JMenu seqsrchmenu = new JMenu(
3968 "Sequence Database Search");
3969 final JMenu analymenu = new JMenu(
3970 "Analyse Alignment");
3972 if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
3973 && Discoverer.services != null
3974 && (Discoverer.services.size() > 0))
3976 // TODO: refactor to allow list of AbstractName/Handler bindings to
3978 // stored or retrieved from elsewhere
3979 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3980 Vector secstrpr = (Vector) Discoverer.services
3982 Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
3983 // TODO: move GUI generation code onto service implementation - so a
3984 // client instance attaches itself to the GUI with method call like
3985 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
3989 // Add any Multiple Sequence Alignment Services
3990 for (int i = 0, j = msaws.size(); i < j; i++)
3992 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
3994 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3995 .getServiceClient(sh);
3996 impl.attachWSMenuEntry(msawsmenu, me);
4000 if (secstrpr != null)
4002 // Add any secondary structure prediction services
4003 for (int i = 0, j = secstrpr.size(); i < j; i++)
4005 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4007 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4008 .getServiceClient(sh);
4009 impl.attachWSMenuEntry(secstrmenu, me);
4012 if (seqsrch != null)
4014 // Add any sequence search services
4015 for (int i = 0, j = seqsrch.size(); i < j; i++)
4017 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
4019 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4020 .getServiceClient(sh);
4021 impl.attachWSMenuEntry(seqsrchmenu, me);
4026 // TODO: move into separate menu builder class.
4027 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4029 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4030 if (jws2servs != null)
4032 if (jws2servs.hasServices())
4034 JMenu jws2men = new JMenu("Jaba Web Services");
4035 jws2servs.attachWSMenuEntry(msawsmenu, me);
4036 // for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
4038 // msawsmenu.add(jws2men.getMenuComponent(i));
4043 if (msawsmenu.getMenuComponentCount()>0)
4044 wsmenu.add(msawsmenu);
4045 if (secstrmenu.getMenuComponentCount()>0)
4046 wsmenu.add(secstrmenu);
4047 if (analymenu.getMenuComponentCount()>0)
4048 wsmenu.add(analymenu);
4049 if (seqsrchmenu.getMenuComponentCount()>0)
4050 wsmenu.add(seqsrchmenu);
4052 javax.swing.SwingUtilities.invokeLater(new Runnable()
4059 resetWebServiceMenu();
4060 // finally, add the whole shebang onto the webservices menu
4061 if (wsmenu.size() > 0)
4063 for (int i = 0, j = wsmenu.size(); i < j; i++)
4065 webService.add((JMenu) wsmenu.get(i));
4070 me.webService.add(me.webServiceNoServices);
4072 } catch (Exception e)
4078 } catch (Exception e)
4083 buildingMenu = false;
4090 * empty the web service menu and add any ad-hoc functions not dynamically
4094 private void resetWebServiceMenu()
4096 webService.removeAll();
4097 build_fetchdbmenu(webService);
4098 build_urlServiceMenu(webService);
4102 * construct any groupURL type service menu entries.
4106 private void build_urlServiceMenu(JMenu webService)
4108 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4110 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4113 // TODO: remove this code when 2.7 is released
4114 // DEBUG - alignmentView
4116 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4117 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4119 * @Override public void actionPerformed(ActionEvent e) {
4120 * jalview.datamodel.AlignmentView.testSelectionViews(af.viewport.alignment,
4121 * af.viewport.colSel, af.viewport.selectionGroup); }
4123 * }); webService.add(testAlView);
4125 // TODO: refactor to RestClient discoverer and merge menu entries for
4126 // rest-style services with other types of analysis/calculation service
4127 // SHmmr test client - still being implemented.
4129 for (jalview.ws.rest.RestClient client: jalview.ws.rest.RestClient.getRestClients()) {
4130 client.attachWSMenuEntry(JvSwingUtils.findOrCreateMenu(webService, client.getAction()), this);
4132 // DEBUG - alignmentView
4136 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4137 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4138 * getProperty("LAST_DIRECTORY"));
4140 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4141 * to Vamsas file"); chooser.setToolTipText("Export");
4143 * int value = chooser.showSaveDialog(this);
4145 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4146 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4147 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4148 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4151 * prototype of an automatically enabled/disabled analysis function
4154 protected void setShowProductsEnabled()
4156 SequenceI[] selection = viewport.getSequenceSelection();
4157 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4158 viewport.getAlignment().getDataset()))
4160 showProducts.setEnabled(true);
4165 showProducts.setEnabled(false);
4170 * search selection for sequence xRef products and build the show products
4175 * @return true if showProducts menu should be enabled.
4177 public boolean canShowProducts(SequenceI[] selection,
4178 boolean isRegionSelection, Alignment dataset)
4180 boolean showp = false;
4183 showProducts.removeAll();
4184 final boolean dna = viewport.getAlignment().isNucleotide();
4185 final Alignment ds = dataset;
4186 String[] ptypes = (selection == null || selection.length == 0) ? null
4187 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4189 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4190 // selection, dataset, true);
4191 final SequenceI[] sel = selection;
4192 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4195 final boolean isRegSel = isRegionSelection;
4196 final AlignFrame af = this;
4197 final String source = ptypes[t];
4198 JMenuItem xtype = new JMenuItem(ptypes[t]);
4199 xtype.addActionListener(new ActionListener()
4202 public void actionPerformed(ActionEvent e)
4204 // TODO: new thread for this call with vis-delay
4205 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4206 isRegSel, dna, source);
4210 showProducts.add(xtype);
4212 showProducts.setVisible(showp);
4213 showProducts.setEnabled(showp);
4214 } catch (Exception e)
4216 jalview.bin.Cache.log
4217 .warn("canTranslate threw an exception - please report to help@jalview.org",
4224 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4225 boolean isRegSel, boolean dna, String source)
4227 final boolean fisRegSel = isRegSel;
4228 final boolean fdna = dna;
4229 final String fsrc = source;
4230 final AlignFrame ths = this;
4231 final SequenceI[] fsel = sel;
4232 Runnable foo = new Runnable()
4237 final long sttime = System.currentTimeMillis();
4238 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4241 Alignment ds = ths.getViewport().alignment.getDataset(); // update
4245 Alignment prods = CrossRef
4246 .findXrefSequences(fsel, fdna, fsrc, ds);
4249 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4250 for (int s = 0; s < sprods.length; s++)
4252 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4253 if (ds.getSequences() == null
4254 || !ds.getSequences().contains(
4255 sprods[s].getDatasetSequence()))
4256 ds.addSequence(sprods[s].getDatasetSequence());
4257 sprods[s].updatePDBIds();
4259 Alignment al = new Alignment(sprods);
4260 AlignedCodonFrame[] cf = prods.getCodonFrames();
4262 for (int s = 0; cf != null && s < cf.length; s++)
4264 al.addCodonFrame(cf[s]);
4267 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4269 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4270 + " for " + ((fisRegSel) ? "selected region of " : "")
4272 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4277 System.err.println("No Sequences generated for xRef type "
4280 } catch (Exception e)
4282 jalview.bin.Cache.log.error(
4283 "Exception when finding crossreferences", e);
4284 } catch (OutOfMemoryError e)
4286 new OOMWarning("whilst fetching crossreferences", e);
4289 jalview.bin.Cache.log.error("Error when finding crossreferences",
4292 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4297 Thread frunner = new Thread(foo);
4301 public boolean canShowTranslationProducts(SequenceI[] selection,
4302 AlignmentI alignment)
4307 return (jalview.analysis.Dna.canTranslate(selection,
4308 viewport.getViewAsVisibleContigs(true)));
4309 } catch (Exception e)
4311 jalview.bin.Cache.log
4312 .warn("canTranslate threw an exception - please report to help@jalview.org",
4318 public void showProducts_actionPerformed(ActionEvent e)
4320 // /////////////////////////////
4321 // Collect Data to be translated/transferred
4323 SequenceI[] selection = viewport.getSequenceSelection();
4324 AlignmentI al = null;
4327 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4328 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4329 viewport.getAlignment().getDataset());
4330 } catch (Exception ex)
4333 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4340 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4341 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4345 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4346 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4347 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4351 public void showTranslation_actionPerformed(ActionEvent e)
4353 // /////////////////////////////
4354 // Collect Data to be translated/transferred
4356 SequenceI[] selection = viewport.getSequenceSelection();
4357 String[] seqstring = viewport.getViewAsString(true);
4358 AlignmentI al = null;
4361 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4362 viewport.getViewAsVisibleContigs(true), viewport
4363 .getGapCharacter(), viewport.alignment
4364 .getAlignmentAnnotation(), viewport.alignment
4365 .getWidth(), viewport.getAlignment().getDataset());
4366 } catch (Exception ex)
4369 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4376 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4377 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4381 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4382 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4383 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4388 * Try to load a features file onto the alignment.
4391 * contents or path to retrieve file
4393 * access mode of file (see jalview.io.AlignFile)
4394 * @return true if features file was parsed corectly.
4396 public boolean parseFeaturesFile(String file, String type)
4398 boolean featuresFile = false;
4401 featuresFile = new FeaturesFile(file, type)
4402 .parse(viewport.alignment.getDataset(),
4403 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
4404 false, jalview.bin.Cache.getDefault(
4405 "RELAXEDSEQIDMATCHING", false));
4406 } catch (Exception ex)
4408 ex.printStackTrace();
4413 viewport.showSequenceFeatures = true;
4414 showSeqFeatures.setSelected(true);
4415 if (alignPanel.seqPanel.seqCanvas.fr != null)
4417 // update the min/max ranges where necessary
4418 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4420 if (featureSettings != null)
4422 featureSettings.setTableData();
4424 alignPanel.paintAlignment(true);
4427 return featuresFile;
4430 public void dragEnter(DropTargetDragEvent evt)
4434 public void dragExit(DropTargetEvent evt)
4438 public void dragOver(DropTargetDragEvent evt)
4442 public void dropActionChanged(DropTargetDragEvent evt)
4446 public void drop(DropTargetDropEvent evt)
4448 Transferable t = evt.getTransferable();
4449 java.util.List files = null;
4453 DataFlavor uriListFlavor = new DataFlavor(
4454 "text/uri-list;class=java.lang.String");
4455 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4457 // Works on Windows and MacOSX
4458 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4459 files = (java.util.List) t
4460 .getTransferData(DataFlavor.javaFileListFlavor);
4462 else if (t.isDataFlavorSupported(uriListFlavor))
4464 // This is used by Unix drag system
4465 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4466 String data = (String) t.getTransferData(uriListFlavor);
4467 files = new java.util.ArrayList(1);
4468 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4469 data, "\r\n"); st.hasMoreTokens();)
4471 String s = st.nextToken();
4472 if (s.startsWith("#"))
4474 // the line is a comment (as per the RFC 2483)
4478 java.net.URI uri = new java.net.URI(s);
4479 // check to see if we can handle this kind of URI
4480 if (uri.getScheme().toLowerCase().startsWith("http"))
4482 files.add(uri.toString());
4486 // otherwise preserve old behaviour: catch all for file objects
4487 java.io.File file = new java.io.File(uri);
4488 files.add(file.toString());
4492 } catch (Exception e)
4494 e.printStackTrace();
4500 // check to see if any of these files have names matching sequences in
4502 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4503 .getAlignment().getSequencesArray());
4505 * Object[] { String,SequenceI}
4507 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4508 ArrayList<String> filesnotmatched = new ArrayList<String>();
4509 for (int i = 0; i < files.size(); i++)
4511 String file = files.get(i).toString();
4513 String protocol = FormatAdapter.checkProtocol(file);
4514 if (protocol == jalview.io.FormatAdapter.FILE)
4516 File fl = new File(file);
4517 pdbfn = fl.getName();
4519 else if (protocol == jalview.io.FormatAdapter.URL)
4521 URL url = new URL(file);
4522 pdbfn = url.getFile();
4524 if (pdbfn.length() > 0)
4526 // attempt to find a match in the alignment
4527 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4528 int l = 0, c = pdbfn.indexOf(".");
4529 while (mtch == null && c != -1)
4534 } while ((c = pdbfn.indexOf(".", l)) > l);
4537 pdbfn = pdbfn.substring(0, l);
4539 mtch = idm.findAllIdMatches(pdbfn);
4546 type = new IdentifyFile().Identify(file, protocol);
4547 } catch (Exception ex)
4553 if (type.equalsIgnoreCase("PDB"))
4555 filesmatched.add(new Object[]
4556 { file, protocol, mtch });
4561 // File wasn't named like one of the sequences or wasn't a PDB file.
4562 filesnotmatched.add(file);
4566 if (filesmatched.size() > 0)
4568 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4572 "Do you want to automatically associate the "
4573 + filesmatched.size()
4574 + " PDB files with sequences in the alignment that have the same name ?",
4575 "Automatically Associate PDB files by name",
4576 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4579 for (Object[] fm : filesmatched)
4581 // try and associate
4582 // TODO: may want to set a standard ID naming formalism for
4583 // associating PDB files which have no IDs.
4584 for (SequenceI toassoc: (SequenceI[])fm[2]) {
4585 PDBEntry pe = new AssociatePdbFileWithSeq()
4586 .associatePdbWithSeq((String) fm[0], (String) fm[1],
4591 .println("Associated file : " + ((String) fm[0])
4593 + toassoc.getDisplayId(true));
4597 alignPanel.paintAlignment(true);
4601 if (filesnotmatched.size() > 0)
4604 && (Cache.getDefault(
4605 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4608 "<html>Do you want to <em>ignore</em> the "
4609 + filesnotmatched.size()
4610 + " files whose names did not match any sequence IDs ?</html>",
4611 "Ignore unmatched dropped files ?",
4612 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4616 for (String fn : filesnotmatched)
4618 loadJalviewDataFile(fn, null, null, null);
4622 } catch (Exception ex)
4624 ex.printStackTrace();
4630 * Attempt to load a "dropped" file or URL string: First by testing whether
4631 * it's and Annotation file, then a JNet file, and finally a features file. If
4632 * all are false then the user may have dropped an alignment file onto this
4636 * either a filename or a URL string.
4638 public void loadJalviewDataFile(String file, String protocol,
4639 String format, SequenceI assocSeq)
4643 if (protocol == null)
4645 protocol = jalview.io.FormatAdapter.checkProtocol(file);
4647 // if the file isn't identified, or not positively identified as some
4648 // other filetype (PFAM is default unidentified alignment file type) then
4649 // try to parse as annotation.
4650 boolean isAnnotation = (format == null || format
4651 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4652 .readAnnotationFile(viewport.alignment, file, protocol)
4657 // try to see if its a JNet 'concise' style annotation file *before* we
4658 // try to parse it as a features file
4661 format = new IdentifyFile().Identify(file, protocol);
4663 if (format.equalsIgnoreCase("JnetFile"))
4665 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4667 new JnetAnnotationMaker().add_annotation(predictions,
4668 viewport.getAlignment(), 0, false);
4669 isAnnotation = true;
4674 * if (format.equalsIgnoreCase("PDB")) {
4676 * String pdbfn = ""; // try to match up filename with sequence id try
4677 * { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = new
4678 * File(file); pdbfn = fl.getName(); } else if (protocol ==
4679 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4680 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == null)
4681 * { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4682 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { //
4683 * attempt to find a match in the alignment SequenceI mtch =
4684 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4685 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > l)
4686 * { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch =
4687 * idm.findIdMatch(pdbfn); } if (mtch != null) { // try and associate
4688 * // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4689 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) {
4690 * System.err.println("Associated file : " + file + " with " +
4691 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4692 * TODO: maybe need to load as normal otherwise return; } }
4694 // try to parse it as a features file
4695 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4696 // if it wasn't a features file then we just treat it as a general
4697 // alignment file to load into the current view.
4700 new FileLoader().LoadFile(viewport, file, protocol, format);
4704 alignPanel.paintAlignment(true);
4711 alignPanel.adjustAnnotationHeight();
4712 viewport.updateSequenceIdColours();
4713 buildSortByAnnotationScoresMenu();
4714 alignPanel.paintAlignment(true);
4716 } catch (Exception ex)
4718 ex.printStackTrace();
4722 public void tabSelectionChanged(int index)
4726 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4727 viewport = alignPanel.av;
4728 setMenusFromViewport(viewport);
4732 public void tabbedPane_mousePressed(MouseEvent e)
4734 if (SwingUtilities.isRightMouseButton(e))
4736 String reply = JOptionPane.showInternalInputDialog(this,
4737 "Enter View Name", "Edit View Name",
4738 JOptionPane.QUESTION_MESSAGE);
4742 viewport.viewName = reply;
4743 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4748 public AlignViewport getCurrentView()
4754 * Open the dialog for regex description parsing.
4756 protected void extractScores_actionPerformed(ActionEvent e)
4758 ParseProperties pp = new jalview.analysis.ParseProperties(
4759 viewport.alignment);
4760 // TODO: verify regex and introduce GUI dialog for version 2.5
4761 // if (pp.getScoresFromDescription("col", "score column ",
4762 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4764 if (pp.getScoresFromDescription("description column",
4765 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4767 buildSortByAnnotationScoresMenu();
4775 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4778 protected void showDbRefs_actionPerformed(ActionEvent e)
4780 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4786 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4789 protected void showNpFeats_actionPerformed(ActionEvent e)
4791 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4795 * find the viewport amongst the tabs in this alignment frame and close that
4800 public boolean closeView(AlignViewport av)
4804 this.closeMenuItem_actionPerformed(false);
4807 Component[] comp = tabbedPane.getComponents();
4808 for (int i = 0; comp != null && i < comp.length; i++)
4810 if (comp[i] instanceof AlignmentPanel)
4812 if (((AlignmentPanel) comp[i]).av == av)
4815 closeView((AlignmentPanel) comp[i]);
4823 protected void build_fetchdbmenu(JMenu webService)
4825 // Temporary hack - DBRef Fetcher always top level ws entry.
4826 // TODO We probably want to store a sequence database checklist in
4827 // preferences and have checkboxes.. rather than individual sources selected
4829 final JMenu rfetch = new JMenu("Fetch DB References");
4830 rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4831 webService.add(rfetch);
4833 JMenuItem fetchr = new JMenuItem("Standard Databases");
4834 fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4835 fetchr.addActionListener(new ActionListener()
4838 public void actionPerformed(ActionEvent e)
4840 new Thread(new Runnable()
4845 new jalview.ws.DBRefFetcher(alignPanel.av
4846 .getSequenceSelection(), alignPanel.alignFrame)
4847 .fetchDBRefs(false);
4855 final AlignFrame me = this;
4856 new Thread(new Runnable()
4860 final jalview.ws.SequenceFetcher sf = SequenceFetcher
4861 .getSequenceFetcherSingleton(me);
4862 final String[] otherdb = sf.getOrderedSupportedSources();
4863 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4864 // jalview.util.QuickSort.sort(otherdb, otherdb);
4865 javax.swing.SwingUtilities.invokeLater(new Runnable()
4870 JMenu dfetch = new JMenu();
4873 int comp = 0, mcomp = 15;
4874 String mname = null;
4875 if (otherdb != null && otherdb.length > 0)
4877 for (int i = 0; i < otherdb.length; i++)
4879 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4882 mname = "from '" + dbname + "'";
4884 fetchr = new JMenuItem(otherdb[i]);
4885 final String[] dassource = new String[]
4887 fetchr.addActionListener(new ActionListener()
4890 public void actionPerformed(ActionEvent e)
4892 new Thread(new Runnable()
4897 new jalview.ws.DBRefFetcher(alignPanel.av
4898 .getSequenceSelection(),
4899 alignPanel.alignFrame, dassource)
4900 .fetchDBRefs(false);
4906 fetchr.setToolTipText("Retrieve from " + dbname);
4908 if (comp++ == mcomp || i == (otherdb.length - 1))
4910 dfetch.setText(mname + " to '" + dbname + "'");
4912 dfetch = new JMenu();
4926 * Left justify the whole alignment.
4928 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4930 AlignmentI al = viewport.getAlignment();
4932 viewport.firePropertyChange("alignment", null, al);
4936 * Right justify the whole alignment.
4938 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4940 AlignmentI al = viewport.getAlignment();
4942 viewport.firePropertyChange("alignment", null, al);
4945 public void setShowSeqFeatures(boolean b)
4947 showSeqFeatures.setSelected(true);
4948 viewport.setShowSequenceFeatures(true);
4955 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4956 * awt.event.ActionEvent)
4958 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
4960 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
4961 alignPanel.paintAlignment(true);
4968 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
4971 protected void showGroupConsensus_actionPerformed(ActionEvent e)
4973 viewport.setShowGroupConsensus(showGroupConsensus.getState());
4974 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4982 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
4983 * .event.ActionEvent)
4985 protected void showGroupConservation_actionPerformed(ActionEvent e)
4987 viewport.setShowGroupConservation(showGroupConservation.getState());
4988 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4995 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
4996 * .event.ActionEvent)
4998 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5000 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5001 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5008 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5009 * .event.ActionEvent)
5011 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5013 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5014 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5017 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5019 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5026 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5027 * .event.ActionEvent)
5029 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5031 if (viewport.getSelectionGroup() != null)
5033 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
5034 viewport.getSequenceSelection(),
5035 viewport.getAlignmentView(true).getSequenceStrings(
5036 viewport.getGapCharacter()),
5037 viewport.alignment.getGroups());
5038 viewport.alignment.deleteAllGroups();
5039 viewport.sequenceColours = null;
5040 viewport.setSelectionGroup(null);
5041 // set view properties for each group
5042 for (int g = 0; g < gps.length; g++)
5044 gps[g].setShowNonconserved(viewport.getShowUnconserved());
5045 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
5046 viewport.alignment.addGroup(gps[g]);
5047 Color col = new Color((int) (Math.random() * 255),
5048 (int) (Math.random() * 255), (int) (Math.random() * 255));
5049 col = col.brighter();
5050 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
5051 .hasMoreElements(); viewport.setSequenceColour(
5052 (SequenceI) sq.nextElement(), col))
5055 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5056 alignPanel.updateAnnotation();
5057 alignPanel.paintAlignment(true);
5062 * make the given alignmentPanel the currently selected tab
5064 * @param alignmentPanel
5066 public void setDisplayedView(AlignmentPanel alignmentPanel)
5068 if (!viewport.getSequenceSetId().equals(
5069 alignmentPanel.av.getSequenceSetId()))
5072 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5074 if (tabbedPane != null
5075 & alignPanels.indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5077 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5082 class PrintThread extends Thread
5086 public PrintThread(AlignmentPanel ap)
5091 static PageFormat pf;
5095 PrinterJob printJob = PrinterJob.getPrinterJob();
5099 printJob.setPrintable(ap, pf);
5103 printJob.setPrintable(ap);
5106 if (printJob.printDialog())
5111 } catch (Exception PrintException)
5113 PrintException.printStackTrace();