2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 import jalview.analysis.AAFrequency;
21 import jalview.analysis.AlignmentSorter;
22 import jalview.analysis.Conservation;
23 import jalview.analysis.CrossRef;
24 import jalview.analysis.NJTree;
25 import jalview.analysis.ParseProperties;
26 import jalview.analysis.SequenceIdMatcher;
27 import jalview.bin.Cache;
28 import jalview.commands.CommandI;
29 import jalview.commands.EditCommand;
30 import jalview.commands.OrderCommand;
31 import jalview.commands.RemoveGapColCommand;
32 import jalview.commands.RemoveGapsCommand;
33 import jalview.commands.SlideSequencesCommand;
34 import jalview.commands.TrimRegionCommand;
35 import jalview.datamodel.AlignedCodonFrame;
36 import jalview.datamodel.Alignment;
37 import jalview.datamodel.AlignmentAnnotation;
38 import jalview.datamodel.AlignmentI;
39 import jalview.datamodel.AlignmentOrder;
40 import jalview.datamodel.AlignmentView;
41 import jalview.datamodel.ColumnSelection;
42 import jalview.datamodel.PDBEntry;
43 import jalview.datamodel.SeqCigar;
44 import jalview.datamodel.Sequence;
45 import jalview.datamodel.SequenceGroup;
46 import jalview.datamodel.SequenceI;
47 import jalview.io.AlignmentProperties;
48 import jalview.io.AnnotationFile;
49 import jalview.io.FeaturesFile;
50 import jalview.io.FileLoader;
51 import jalview.io.FormatAdapter;
52 import jalview.io.HTMLOutput;
53 import jalview.io.IdentifyFile;
54 import jalview.io.JalviewFileChooser;
55 import jalview.io.JalviewFileView;
56 import jalview.io.JnetAnnotationMaker;
57 import jalview.io.NewickFile;
58 import jalview.io.TCoffeeScoreFile;
59 import jalview.jbgui.GAlignFrame;
60 import jalview.schemes.Blosum62ColourScheme;
61 import jalview.schemes.BuriedColourScheme;
62 import jalview.schemes.ClustalxColourScheme;
63 import jalview.schemes.ColourSchemeI;
64 import jalview.schemes.ColourSchemeProperty;
65 import jalview.schemes.HelixColourScheme;
66 import jalview.schemes.HydrophobicColourScheme;
67 import jalview.schemes.NucleotideColourScheme;
68 import jalview.schemes.PIDColourScheme;
69 import jalview.schemes.PurinePyrimidineColourScheme;
70 import jalview.schemes.RNAHelicesColourChooser;
71 import jalview.schemes.ResidueProperties;
72 import jalview.schemes.StrandColourScheme;
73 import jalview.schemes.TCoffeeColourScheme;
74 import jalview.schemes.TaylorColourScheme;
75 import jalview.schemes.TurnColourScheme;
76 import jalview.schemes.UserColourScheme;
77 import jalview.schemes.ZappoColourScheme;
78 import jalview.ws.jws1.Discoverer;
79 import jalview.ws.jws2.Jws2Discoverer;
80 import jalview.ws.seqfetcher.DbSourceProxy;
82 import java.awt.BorderLayout;
83 import java.awt.Color;
84 import java.awt.Component;
85 import java.awt.GridLayout;
86 import java.awt.Rectangle;
87 import java.awt.Toolkit;
88 import java.awt.datatransfer.Clipboard;
89 import java.awt.datatransfer.DataFlavor;
90 import java.awt.datatransfer.StringSelection;
91 import java.awt.datatransfer.Transferable;
92 import java.awt.dnd.DnDConstants;
93 import java.awt.dnd.DropTargetDragEvent;
94 import java.awt.dnd.DropTargetDropEvent;
95 import java.awt.dnd.DropTargetEvent;
96 import java.awt.dnd.DropTargetListener;
97 import java.awt.event.ActionEvent;
98 import java.awt.event.ActionListener;
99 import java.awt.event.KeyAdapter;
100 import java.awt.event.KeyEvent;
101 import java.awt.event.MouseAdapter;
102 import java.awt.event.MouseEvent;
103 import java.awt.print.PageFormat;
104 import java.awt.print.PrinterJob;
105 import java.beans.PropertyChangeEvent;
108 import java.util.ArrayList;
109 import java.util.Enumeration;
110 import java.util.Hashtable;
111 import java.util.List;
112 import java.util.Vector;
114 import javax.swing.JButton;
115 import javax.swing.JEditorPane;
116 import javax.swing.JInternalFrame;
117 import javax.swing.JLabel;
118 import javax.swing.JLayeredPane;
119 import javax.swing.JMenu;
120 import javax.swing.JMenuItem;
121 import javax.swing.JOptionPane;
122 import javax.swing.JPanel;
123 import javax.swing.JProgressBar;
124 import javax.swing.JRadioButtonMenuItem;
125 import javax.swing.JScrollPane;
126 import javax.swing.SwingUtilities;
132 * @version $Revision$
134 public class AlignFrame extends GAlignFrame implements DropTargetListener,
139 public static final int DEFAULT_WIDTH = 700;
142 public static final int DEFAULT_HEIGHT = 500;
144 public AlignmentPanel alignPanel;
146 AlignViewport viewport;
148 Vector alignPanels = new Vector();
151 * Last format used to load or save alignments in this window
153 String currentFileFormat = null;
156 * Current filename for this alignment
158 String fileName = null;
161 * Creates a new AlignFrame object with specific width and height.
167 public AlignFrame(AlignmentI al, int width, int height)
169 this(al, null, width, height);
173 * Creates a new AlignFrame object with specific width, height and
179 * @param sequenceSetId
181 public AlignFrame(AlignmentI al, int width, int height,
182 String sequenceSetId)
184 this(al, null, width, height, sequenceSetId);
188 * Creates a new AlignFrame object with specific width, height and
194 * @param sequenceSetId
197 public AlignFrame(AlignmentI al, int width, int height,
198 String sequenceSetId, String viewId)
200 this(al, null, width, height, sequenceSetId, viewId);
204 * new alignment window with hidden columns
208 * @param hiddenColumns
209 * ColumnSelection or null
211 * Width of alignment frame
215 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
216 int width, int height)
218 this(al, hiddenColumns, width, height, null);
222 * Create alignment frame for al with hiddenColumns, a specific width and
223 * height, and specific sequenceId
226 * @param hiddenColumns
229 * @param sequenceSetId
232 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
233 int width, int height, String sequenceSetId)
235 this(al, hiddenColumns, width, height, sequenceSetId, null);
239 * Create alignment frame for al with hiddenColumns, a specific width and
240 * height, and specific sequenceId
243 * @param hiddenColumns
246 * @param sequenceSetId
251 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
252 int width, int height, String sequenceSetId, String viewId)
254 setSize(width, height);
255 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
257 alignPanel = new AlignmentPanel(this, viewport);
259 if (al.getDataset() == null)
264 addAlignmentPanel(alignPanel, true);
269 * Make a new AlignFrame from exisiting alignmentPanels
276 public AlignFrame(AlignmentPanel ap)
280 addAlignmentPanel(ap, false);
285 * initalise the alignframe from the underlying viewport data and the
290 if (viewport.getAlignmentConservationAnnotation() == null)
292 BLOSUM62Colour.setEnabled(false);
293 conservationMenuItem.setEnabled(false);
294 modifyConservation.setEnabled(false);
295 // PIDColour.setEnabled(false);
296 // abovePIDThreshold.setEnabled(false);
297 // modifyPID.setEnabled(false);
300 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
303 if (sortby.equals("Id"))
305 sortIDMenuItem_actionPerformed(null);
307 else if (sortby.equals("Pairwise Identity"))
309 sortPairwiseMenuItem_actionPerformed(null);
312 if (Desktop.desktop != null)
314 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
315 addServiceListeners();
316 setGUINucleotide(viewport.getAlignment().isNucleotide());
319 setMenusFromViewport(viewport);
320 buildSortByAnnotationScoresMenu();
321 if (viewport.wrapAlignment)
323 wrapMenuItem_actionPerformed(null);
326 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
328 this.overviewMenuItem_actionPerformed(null);
336 * Change the filename and format for the alignment, and enable the 'reload'
337 * button functionality.
344 public void setFileName(String file, String format)
347 currentFileFormat = format;
348 reload.setEnabled(true);
351 void addKeyListener()
353 addKeyListener(new KeyAdapter()
355 public void keyPressed(KeyEvent evt)
357 if (viewport.cursorMode
358 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
359 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
360 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
361 && Character.isDigit(evt.getKeyChar()))
362 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
364 switch (evt.getKeyCode())
367 case 27: // escape key
368 deselectAllSequenceMenuItem_actionPerformed(null);
372 case KeyEvent.VK_DOWN:
373 if (evt.isAltDown() || !viewport.cursorMode)
374 moveSelectedSequences(false);
375 if (viewport.cursorMode)
376 alignPanel.seqPanel.moveCursor(0, 1);
380 if (evt.isAltDown() || !viewport.cursorMode)
381 moveSelectedSequences(true);
382 if (viewport.cursorMode)
383 alignPanel.seqPanel.moveCursor(0, -1);
387 case KeyEvent.VK_LEFT:
388 if (evt.isAltDown() || !viewport.cursorMode)
389 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
391 alignPanel.seqPanel.moveCursor(-1, 0);
395 case KeyEvent.VK_RIGHT:
396 if (evt.isAltDown() || !viewport.cursorMode)
397 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
399 alignPanel.seqPanel.moveCursor(1, 0);
402 case KeyEvent.VK_SPACE:
403 if (viewport.cursorMode)
405 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
406 || evt.isShiftDown() || evt.isAltDown());
410 // case KeyEvent.VK_A:
411 // if (viewport.cursorMode)
413 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
414 // //System.out.println("A");
418 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
419 * System.out.println("closing bracket"); } break;
421 case KeyEvent.VK_DELETE:
422 case KeyEvent.VK_BACK_SPACE:
423 if (!viewport.cursorMode)
425 cut_actionPerformed(null);
429 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
430 || evt.isShiftDown() || evt.isAltDown());
436 if (viewport.cursorMode)
438 alignPanel.seqPanel.setCursorRow();
442 if (viewport.cursorMode && !evt.isControlDown())
444 alignPanel.seqPanel.setCursorColumn();
448 if (viewport.cursorMode)
450 alignPanel.seqPanel.setCursorPosition();
454 case KeyEvent.VK_ENTER:
455 case KeyEvent.VK_COMMA:
456 if (viewport.cursorMode)
458 alignPanel.seqPanel.setCursorRowAndColumn();
463 if (viewport.cursorMode)
465 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
469 if (viewport.cursorMode)
471 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
476 viewport.cursorMode = !viewport.cursorMode;
477 statusBar.setText("Keyboard editing mode is "
478 + (viewport.cursorMode ? "on" : "off"));
479 if (viewport.cursorMode)
481 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
482 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
484 alignPanel.seqPanel.seqCanvas.repaint();
490 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
491 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
493 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
495 javax.help.HelpBroker hb = hs.createHelpBroker();
496 hb.setCurrentID("home");
497 hb.setDisplayed(true);
498 } catch (Exception ex)
500 ex.printStackTrace();
505 boolean toggleSeqs = !evt.isControlDown();
506 boolean toggleCols = !evt.isShiftDown();
507 toggleHiddenRegions(toggleSeqs, toggleCols);
510 case KeyEvent.VK_PAGE_UP:
511 if (viewport.wrapAlignment)
513 alignPanel.scrollUp(true);
517 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
518 - viewport.endSeq + viewport.startSeq);
521 case KeyEvent.VK_PAGE_DOWN:
522 if (viewport.wrapAlignment)
524 alignPanel.scrollUp(false);
528 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
529 + viewport.endSeq - viewport.startSeq);
535 public void keyReleased(KeyEvent evt)
537 switch (evt.getKeyCode())
539 case KeyEvent.VK_LEFT:
540 if (evt.isAltDown() || !viewport.cursorMode)
541 viewport.firePropertyChange("alignment", null, viewport
542 .getAlignment().getSequences());
545 case KeyEvent.VK_RIGHT:
546 if (evt.isAltDown() || !viewport.cursorMode)
547 viewport.firePropertyChange("alignment", null, viewport
548 .getAlignment().getSequences());
555 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
557 ap.alignFrame = this;
559 alignPanels.addElement(ap);
561 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
563 int aSize = alignPanels.size();
565 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
567 if (aSize == 1 && ap.av.viewName == null)
569 this.getContentPane().add(ap, BorderLayout.CENTER);
575 setInitialTabVisible();
578 expandViews.setEnabled(true);
579 gatherViews.setEnabled(true);
580 tabbedPane.addTab(ap.av.viewName, ap);
582 ap.setVisible(false);
587 if (ap.av.isPadGaps())
589 ap.av.getAlignment().padGaps();
591 ap.av.updateConservation(ap);
592 ap.av.updateConsensus(ap);
593 ap.av.updateStrucConsensus(ap);
597 public void setInitialTabVisible()
599 expandViews.setEnabled(true);
600 gatherViews.setEnabled(true);
601 tabbedPane.setVisible(true);
602 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
603 tabbedPane.addTab(first.av.viewName, first);
604 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
607 public AlignViewport getViewport()
612 /* Set up intrinsic listeners for dynamically generated GUI bits. */
613 private void addServiceListeners()
615 final java.beans.PropertyChangeListener thisListener;
616 Desktop.instance.addJalviewPropertyChangeListener("services",
617 thisListener = new java.beans.PropertyChangeListener()
619 public void propertyChange(PropertyChangeEvent evt)
621 // // System.out.println("Discoverer property change.");
622 // if (evt.getPropertyName().equals("services"))
624 SwingUtilities.invokeLater(new Runnable()
630 .println("Rebuild WS Menu for service change");
631 BuildWebServiceMenu();
638 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
640 public void internalFrameClosed(
641 javax.swing.event.InternalFrameEvent evt)
643 System.out.println("deregistering discoverer listener");
644 Desktop.instance.removeJalviewPropertyChangeListener("services",
646 closeMenuItem_actionPerformed(true);
649 // Finally, build the menu once to get current service state
650 new Thread(new Runnable()
654 BuildWebServiceMenu();
659 public void setGUINucleotide(boolean nucleotide)
661 showTranslation.setVisible(nucleotide);
662 conservationMenuItem.setEnabled(!nucleotide);
663 modifyConservation.setEnabled(!nucleotide);
664 showGroupConservation.setEnabled(!nucleotide);
665 rnahelicesColour.setEnabled(nucleotide);
666 purinePyrimidineColour.setEnabled(nucleotide);
667 // Remember AlignFrame always starts as protein
671 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
676 * set up menus for the currently viewport. This may be called after any
677 * operation that affects the data in the current view (selection changed,
678 * etc) to update the menus to reflect the new state.
680 public void setMenusForViewport()
682 setMenusFromViewport(viewport);
686 * Need to call this method when tabs are selected for multiple views, or when
687 * loading from Jalview2XML.java
692 void setMenusFromViewport(AlignViewport av)
694 padGapsMenuitem.setSelected(av.isPadGaps());
695 colourTextMenuItem.setSelected(av.showColourText);
696 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
697 conservationMenuItem.setSelected(av.getConservationSelected());
698 seqLimits.setSelected(av.getShowJVSuffix());
699 idRightAlign.setSelected(av.rightAlignIds);
700 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
701 renderGapsMenuItem.setSelected(av.renderGaps);
702 wrapMenuItem.setSelected(av.wrapAlignment);
703 scaleAbove.setVisible(av.wrapAlignment);
704 scaleLeft.setVisible(av.wrapAlignment);
705 scaleRight.setVisible(av.wrapAlignment);
706 annotationPanelMenuItem.setState(av.showAnnotation);
707 viewBoxesMenuItem.setSelected(av.showBoxes);
708 viewTextMenuItem.setSelected(av.showText);
709 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
710 showGroupConsensus.setSelected(av.isShowGroupConsensus());
711 showGroupConservation.setSelected(av.isShowGroupConservation());
712 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
713 showSequenceLogo.setSelected(av.isShowSequenceLogo());
714 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
716 setColourSelected(ColourSchemeProperty.getColourName(av
717 .getGlobalColourScheme()));
719 showSeqFeatures.setSelected(av.showSequenceFeatures);
720 hiddenMarkers.setState(av.showHiddenMarkers);
721 applyToAllGroups.setState(av.colourAppliesToAllGroups);
722 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
723 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
724 autoCalculate.setSelected(av.autoCalculateConsensus);
725 sortByTree.setSelected(av.sortByTree);
726 listenToViewSelections.setSelected(av.followSelection);
727 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
729 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
730 setShowProductsEnabled();
735 Hashtable progressBars, progressBarHandlers;
740 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
742 public void setProgressBar(String message, long id)
744 if (progressBars == null)
746 progressBars = new Hashtable();
747 progressBarHandlers = new Hashtable();
750 JPanel progressPanel;
751 Long lId = new Long(id);
752 GridLayout layout = (GridLayout) statusPanel.getLayout();
753 if (progressBars.get(lId) != null)
755 progressPanel = (JPanel) progressBars.get(new Long(id));
756 statusPanel.remove(progressPanel);
757 progressBars.remove(lId);
758 progressPanel = null;
761 statusBar.setText(message);
763 if (progressBarHandlers.contains(lId))
765 progressBarHandlers.remove(lId);
767 layout.setRows(layout.getRows() - 1);
771 progressPanel = new JPanel(new BorderLayout(10, 5));
773 JProgressBar progressBar = new JProgressBar();
774 progressBar.setIndeterminate(true);
776 progressPanel.add(new JLabel(message), BorderLayout.WEST);
777 progressPanel.add(progressBar, BorderLayout.CENTER);
779 layout.setRows(layout.getRows() + 1);
780 statusPanel.add(progressPanel);
782 progressBars.put(lId, progressPanel);
785 // setMenusForViewport();
789 public void registerHandler(final long id,
790 final IProgressIndicatorHandler handler)
792 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
795 "call setProgressBar before registering the progress bar's handler.");
797 progressBarHandlers.put(new Long(id), handler);
798 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
799 if (handler.canCancel())
801 JButton cancel = new JButton("Cancel");
802 final IProgressIndicator us = this;
803 cancel.addActionListener(new ActionListener()
806 public void actionPerformed(ActionEvent e)
808 handler.cancelActivity(id);
811 + ((JLabel) progressPanel.getComponent(0))
815 progressPanel.add(cancel, BorderLayout.EAST);
821 * @return true if any progress bars are still active
823 public boolean operationInProgress()
825 if (progressBars != null && progressBars.size() > 0)
833 * Added so Castor Mapping file can obtain Jalview Version
835 public String getVersion()
837 return jalview.bin.Cache.getProperty("VERSION");
840 public FeatureRenderer getFeatureRenderer()
842 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
845 public void fetchSequence_actionPerformed(ActionEvent e)
847 new SequenceFetcher(this);
850 public void addFromFile_actionPerformed(ActionEvent e)
852 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
855 public void reload_actionPerformed(ActionEvent e)
857 if (fileName != null)
859 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
860 // originating file's format
861 // TODO: work out how to recover feature settings for correct view(s) when
863 if (currentFileFormat.equals("Jalview"))
865 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
866 for (int i = 0; i < frames.length; i++)
868 if (frames[i] instanceof AlignFrame && frames[i] != this
869 && ((AlignFrame) frames[i]).fileName.equals(fileName))
873 frames[i].setSelected(true);
874 Desktop.instance.closeAssociatedWindows();
875 } catch (java.beans.PropertyVetoException ex)
881 Desktop.instance.closeAssociatedWindows();
883 FileLoader loader = new FileLoader();
884 String protocol = fileName.startsWith("http:") ? "URL" : "File";
885 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
889 Rectangle bounds = this.getBounds();
891 FileLoader loader = new FileLoader();
892 String protocol = fileName.startsWith("http:") ? "URL" : "File";
893 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
894 protocol, currentFileFormat);
896 newframe.setBounds(bounds);
897 if (featureSettings != null && featureSettings.isShowing())
899 final Rectangle fspos = featureSettings.frame.getBounds();
900 // TODO: need a 'show feature settings' function that takes bounds -
901 // need to refactor Desktop.addFrame
902 newframe.featureSettings_actionPerformed(null);
903 final FeatureSettings nfs = newframe.featureSettings;
904 SwingUtilities.invokeLater(new Runnable()
908 nfs.frame.setBounds(fspos);
911 this.featureSettings.close();
912 this.featureSettings = null;
914 this.closeMenuItem_actionPerformed(true);
919 public void addFromText_actionPerformed(ActionEvent e)
921 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
924 public void addFromURL_actionPerformed(ActionEvent e)
926 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
929 public void save_actionPerformed(ActionEvent e)
932 || (currentFileFormat == null || !jalview.io.FormatAdapter
933 .isValidIOFormat(currentFileFormat, true))
934 || fileName.startsWith("http"))
936 saveAs_actionPerformed(null);
940 saveAlignment(fileName, currentFileFormat);
950 public void saveAs_actionPerformed(ActionEvent e)
952 JalviewFileChooser chooser = new JalviewFileChooser(
953 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
954 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
955 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
956 currentFileFormat, false);
958 chooser.setFileView(new JalviewFileView());
959 chooser.setDialogTitle("Save Alignment to file");
960 chooser.setToolTipText("Save");
962 int value = chooser.showSaveDialog(this);
964 if (value == JalviewFileChooser.APPROVE_OPTION)
966 currentFileFormat = chooser.getSelectedFormat();
967 if (currentFileFormat == null)
969 JOptionPane.showInternalMessageDialog(Desktop.desktop,
970 "You must select a file format before saving!",
971 "File format not specified", JOptionPane.WARNING_MESSAGE);
972 value = chooser.showSaveDialog(this);
976 fileName = chooser.getSelectedFile().getPath();
978 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
981 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
982 if (currentFileFormat.indexOf(" ") > -1)
984 currentFileFormat = currentFileFormat.substring(0,
985 currentFileFormat.indexOf(" "));
987 saveAlignment(fileName, currentFileFormat);
991 public boolean saveAlignment(String file, String format)
993 boolean success = true;
995 if (format.equalsIgnoreCase("Jalview"))
997 String shortName = title;
999 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1001 shortName = shortName.substring(shortName
1002 .lastIndexOf(java.io.File.separatorChar) + 1);
1005 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1007 statusBar.setText("Successfully saved to file: " + fileName + " in "
1008 + format + " format.");
1013 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1015 warningMessage("Cannot save file " + fileName + " using format "
1016 + format, "Alignment output format not supported");
1017 saveAs_actionPerformed(null);
1018 // JBPNote need to have a raise_gui flag here
1022 String[] omitHidden = null;
1024 if (viewport.hasHiddenColumns())
1026 int reply = JOptionPane
1027 .showInternalConfirmDialog(
1029 "The Alignment contains hidden columns."
1030 + "\nDo you want to save only the visible alignment?",
1031 "Save / Omit Hidden Columns",
1032 JOptionPane.YES_NO_OPTION,
1033 JOptionPane.QUESTION_MESSAGE);
1035 if (reply == JOptionPane.YES_OPTION)
1037 omitHidden = viewport.getViewAsString(false);
1040 FormatAdapter f = new FormatAdapter();
1041 String output = f.formatSequences(
1043 (Alignment) viewport.getAlignment(), // class cast exceptions will
1044 // occur in the distant future
1045 omitHidden, f.getCacheSuffixDefault(format),
1046 viewport.getColumnSelection());
1056 java.io.PrintWriter out = new java.io.PrintWriter(
1057 new java.io.FileWriter(file));
1061 this.setTitle(file);
1062 statusBar.setText("Successfully saved to file: " + fileName
1063 + " in " + format + " format.");
1064 } catch (Exception ex)
1067 ex.printStackTrace();
1074 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
1075 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
1081 private void warningMessage(String warning, String title)
1083 if (new jalview.util.Platform().isHeadless())
1085 System.err.println("Warning: " + title + "\nWarning: " + warning);
1090 JOptionPane.showInternalMessageDialog(this, warning, title,
1091 JOptionPane.WARNING_MESSAGE);
1102 protected void outputText_actionPerformed(ActionEvent e)
1104 String[] omitHidden = null;
1106 if (viewport.hasHiddenColumns())
1108 int reply = JOptionPane
1109 .showInternalConfirmDialog(
1111 "The Alignment contains hidden columns."
1112 + "\nDo you want to output only the visible alignment?",
1113 "Save / Omit Hidden Columns",
1114 JOptionPane.YES_NO_OPTION,
1115 JOptionPane.QUESTION_MESSAGE);
1117 if (reply == JOptionPane.YES_OPTION)
1119 omitHidden = viewport.getViewAsString(false);
1123 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1124 cap.setForInput(null);
1128 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1129 viewport.getAlignment(), omitHidden,
1130 viewport.getColumnSelection()));
1131 Desktop.addInternalFrame(cap,
1132 "Alignment output - " + e.getActionCommand(), 600, 500);
1133 } catch (OutOfMemoryError oom)
1135 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1147 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1149 new HTMLOutput(alignPanel,
1150 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1151 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1154 public void createImageMap(File file, String image)
1156 alignPanel.makePNGImageMap(file, image);
1165 public void createPNG(File f)
1167 alignPanel.makePNG(f);
1176 public void createEPS(File f)
1178 alignPanel.makeEPS(f);
1181 public void pageSetup_actionPerformed(ActionEvent e)
1183 PrinterJob printJob = PrinterJob.getPrinterJob();
1184 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1193 public void printMenuItem_actionPerformed(ActionEvent e)
1195 // Putting in a thread avoids Swing painting problems
1196 PrintThread thread = new PrintThread(alignPanel);
1200 public void exportFeatures_actionPerformed(ActionEvent e)
1202 new AnnotationExporter().exportFeatures(alignPanel);
1205 public void exportAnnotations_actionPerformed(ActionEvent e)
1207 new AnnotationExporter().exportAnnotations(alignPanel,
1208 viewport.showAnnotation ? viewport.getAlignment()
1209 .getAlignmentAnnotation() : null, viewport
1210 .getAlignment().getGroups(), ((Alignment) viewport
1211 .getAlignment()).alignmentProperties);
1214 public void associatedData_actionPerformed(ActionEvent e)
1216 // Pick the tree file
1217 JalviewFileChooser chooser = new JalviewFileChooser(
1218 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1219 chooser.setFileView(new JalviewFileView());
1220 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1221 chooser.setToolTipText("Load Jalview Annotations / Features file");
1223 int value = chooser.showOpenDialog(null);
1225 if (value == JalviewFileChooser.APPROVE_OPTION)
1227 String choice = chooser.getSelectedFile().getPath();
1228 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1229 loadJalviewDataFile(choice, null, null, null);
1235 * Close the current view or all views in the alignment frame. If the frame
1236 * only contains one view then the alignment will be removed from memory.
1238 * @param closeAllTabs
1240 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1242 if (alignPanels != null && alignPanels.size() < 2)
1244 closeAllTabs = true;
1249 if (alignPanels != null)
1253 if (this.isClosed())
1255 // really close all the windows - otherwise wait till
1256 // setClosed(true) is called
1257 for (int i = 0; i < alignPanels.size(); i++)
1259 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1266 closeView(alignPanel);
1272 this.setClosed(true);
1274 } catch (Exception ex)
1276 ex.printStackTrace();
1281 * close alignPanel2 and shuffle tabs appropriately.
1283 * @param alignPanel2
1285 public void closeView(AlignmentPanel alignPanel2)
1287 int index = tabbedPane.getSelectedIndex();
1288 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1289 alignPanels.removeElement(alignPanel2);
1291 // if (viewport == alignPanel2.av)
1295 alignPanel2.closePanel();
1298 tabbedPane.removeTabAt(closedindex);
1299 tabbedPane.validate();
1301 if (index > closedindex || index == tabbedPane.getTabCount())
1303 // modify currently selected tab index if necessary.
1307 this.tabSelectionChanged(index);
1313 void updateEditMenuBar()
1316 if (viewport.historyList.size() > 0)
1318 undoMenuItem.setEnabled(true);
1319 CommandI command = (CommandI) viewport.historyList.peek();
1320 undoMenuItem.setText("Undo " + command.getDescription());
1324 undoMenuItem.setEnabled(false);
1325 undoMenuItem.setText("Undo");
1328 if (viewport.redoList.size() > 0)
1330 redoMenuItem.setEnabled(true);
1332 CommandI command = (CommandI) viewport.redoList.peek();
1333 redoMenuItem.setText("Redo " + command.getDescription());
1337 redoMenuItem.setEnabled(false);
1338 redoMenuItem.setText("Redo");
1342 public void addHistoryItem(CommandI command)
1344 if (command.getSize() > 0)
1346 viewport.historyList.push(command);
1347 viewport.redoList.clear();
1348 updateEditMenuBar();
1349 viewport.updateHiddenColumns();
1350 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1351 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1352 // viewport.getColumnSelection()
1353 // .getHiddenColumns().size() > 0);
1359 * @return alignment objects for all views
1361 AlignmentI[] getViewAlignments()
1363 if (alignPanels != null)
1365 Enumeration e = alignPanels.elements();
1366 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1367 for (int i = 0; e.hasMoreElements(); i++)
1369 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1373 if (viewport != null)
1375 return new AlignmentI[]
1376 { viewport.getAlignment() };
1387 protected void undoMenuItem_actionPerformed(ActionEvent e)
1389 if (viewport.historyList.empty())
1391 CommandI command = (CommandI) viewport.historyList.pop();
1392 viewport.redoList.push(command);
1393 command.undoCommand(getViewAlignments());
1395 AlignViewport originalSource = getOriginatingSource(command);
1396 updateEditMenuBar();
1398 if (originalSource != null)
1400 if (originalSource != viewport)
1403 .warn("Implementation worry: mismatch of viewport origin for undo");
1405 originalSource.updateHiddenColumns();
1406 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1408 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1409 // viewport.getColumnSelection()
1410 // .getHiddenColumns().size() > 0);
1411 originalSource.firePropertyChange("alignment", null, originalSource
1412 .getAlignment().getSequences());
1422 protected void redoMenuItem_actionPerformed(ActionEvent e)
1424 if (viewport.redoList.size() < 1)
1429 CommandI command = (CommandI) viewport.redoList.pop();
1430 viewport.historyList.push(command);
1431 command.doCommand(getViewAlignments());
1433 AlignViewport originalSource = getOriginatingSource(command);
1434 updateEditMenuBar();
1436 if (originalSource != null)
1439 if (originalSource != viewport)
1442 .warn("Implementation worry: mismatch of viewport origin for redo");
1444 originalSource.updateHiddenColumns();
1445 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1447 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1448 // viewport.getColumnSelection()
1449 // .getHiddenColumns().size() > 0);
1450 originalSource.firePropertyChange("alignment", null, originalSource
1451 .getAlignment().getSequences());
1455 AlignViewport getOriginatingSource(CommandI command)
1457 AlignViewport originalSource = null;
1458 // For sequence removal and addition, we need to fire
1459 // the property change event FROM the viewport where the
1460 // original alignment was altered
1461 AlignmentI al = null;
1462 if (command instanceof EditCommand)
1464 EditCommand editCommand = (EditCommand) command;
1465 al = editCommand.getAlignment();
1466 Vector comps = (Vector) PaintRefresher.components.get(viewport
1467 .getSequenceSetId());
1469 for (int i = 0; i < comps.size(); i++)
1471 if (comps.elementAt(i) instanceof AlignmentPanel)
1473 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1475 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1482 if (originalSource == null)
1484 // The original view is closed, we must validate
1485 // the current view against the closed view first
1488 PaintRefresher.validateSequences(al, viewport.getAlignment());
1491 originalSource = viewport;
1494 return originalSource;
1503 public void moveSelectedSequences(boolean up)
1505 SequenceGroup sg = viewport.getSelectionGroup();
1514 for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
1516 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
1518 if (!sg.getSequences(null).contains(seq))
1523 SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
1525 if (sg.getSequences(null).contains(temp))
1530 viewport.getAlignment().getSequences().setElementAt(temp, i);
1531 viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
1536 for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
1538 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
1540 if (!sg.getSequences(null).contains(seq))
1545 SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
1547 if (sg.getSequences(null).contains(temp))
1552 viewport.getAlignment().getSequences().setElementAt(temp, i);
1553 viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
1557 alignPanel.paintAlignment(true);
1560 synchronized void slideSequences(boolean right, int size)
1562 Vector sg = new Vector();
1563 if (viewport.cursorMode)
1565 sg.addElement(viewport.getAlignment().getSequenceAt(
1566 alignPanel.seqPanel.seqCanvas.cursorY));
1568 else if (viewport.getSelectionGroup() != null
1569 && viewport.getSelectionGroup().getSize() != viewport
1570 .getAlignment().getHeight())
1572 sg = viewport.getSelectionGroup().getSequences(
1573 viewport.getHiddenRepSequences());
1581 Vector invertGroup = new Vector();
1583 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1585 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1586 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1589 SequenceI[] seqs1 = new SequenceI[sg.size()];
1590 for (int i = 0; i < sg.size(); i++)
1591 seqs1[i] = (SequenceI) sg.elementAt(i);
1593 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1594 for (int i = 0; i < invertGroup.size(); i++)
1595 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1597 SlideSequencesCommand ssc;
1599 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1600 size, viewport.getGapCharacter());
1602 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1603 size, viewport.getGapCharacter());
1605 int groupAdjustment = 0;
1606 if (ssc.getGapsInsertedBegin() && right)
1608 if (viewport.cursorMode)
1609 alignPanel.seqPanel.moveCursor(size, 0);
1611 groupAdjustment = size;
1613 else if (!ssc.getGapsInsertedBegin() && !right)
1615 if (viewport.cursorMode)
1616 alignPanel.seqPanel.moveCursor(-size, 0);
1618 groupAdjustment = -size;
1621 if (groupAdjustment != 0)
1623 viewport.getSelectionGroup().setStartRes(
1624 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1625 viewport.getSelectionGroup().setEndRes(
1626 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1629 boolean appendHistoryItem = false;
1630 if (viewport.historyList != null && viewport.historyList.size() > 0
1631 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1633 appendHistoryItem = ssc
1634 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1638 if (!appendHistoryItem)
1639 addHistoryItem(ssc);
1650 protected void copy_actionPerformed(ActionEvent e)
1653 if (viewport.getSelectionGroup() == null)
1657 // TODO: preserve the ordering of displayed alignment annotation in any
1658 // internal paste (particularly sequence associated annotation)
1659 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1660 String[] omitHidden = null;
1662 if (viewport.hasHiddenColumns())
1664 omitHidden = viewport.getViewAsString(true);
1667 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1670 StringSelection ss = new StringSelection(output);
1674 jalview.gui.Desktop.internalCopy = true;
1675 // Its really worth setting the clipboard contents
1676 // to empty before setting the large StringSelection!!
1677 Toolkit.getDefaultToolkit().getSystemClipboard()
1678 .setContents(new StringSelection(""), null);
1680 Toolkit.getDefaultToolkit().getSystemClipboard()
1681 .setContents(ss, Desktop.instance);
1682 } catch (OutOfMemoryError er)
1684 new OOMWarning("copying region", er);
1688 Vector hiddenColumns = null;
1689 if (viewport.hasHiddenColumns())
1691 hiddenColumns = new Vector();
1692 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1693 .getSelectionGroup().getEndRes();
1694 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1697 int[] region = (int[]) viewport.getColumnSelection()
1698 .getHiddenColumns().elementAt(i);
1699 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1701 hiddenColumns.addElement(new int[]
1702 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1707 Desktop.jalviewClipboard = new Object[]
1708 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1709 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1718 protected void pasteNew_actionPerformed(ActionEvent e)
1729 protected void pasteThis_actionPerformed(ActionEvent e)
1735 * Paste contents of Jalview clipboard
1737 * @param newAlignment
1738 * true to paste to a new alignment, otherwise add to this.
1740 void paste(boolean newAlignment)
1742 boolean externalPaste = true;
1745 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1746 Transferable contents = c.getContents(this);
1748 if (contents == null)
1756 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1757 if (str.length() < 1)
1762 format = new IdentifyFile().Identify(str, "Paste");
1764 } catch (OutOfMemoryError er)
1766 new OOMWarning("Out of memory pasting sequences!!", er);
1770 SequenceI[] sequences;
1771 boolean annotationAdded = false;
1772 AlignmentI alignment = null;
1774 if (Desktop.jalviewClipboard != null)
1776 // The clipboard was filled from within Jalview, we must use the
1778 // And dataset from the copied alignment
1779 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1780 // be doubly sure that we create *new* sequence objects.
1781 sequences = new SequenceI[newseq.length];
1782 for (int i = 0; i < newseq.length; i++)
1784 sequences[i] = new Sequence(newseq[i]);
1786 alignment = new Alignment(sequences);
1787 externalPaste = false;
1791 // parse the clipboard as an alignment.
1792 alignment = new FormatAdapter().readFile(str, "Paste", format);
1793 sequences = alignment.getSequencesArray();
1801 if (Desktop.jalviewClipboard != null)
1803 // dataset is inherited
1804 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1808 // new dataset is constructed
1809 alignment.setDataset(null);
1811 alwidth = alignment.getWidth() + 1;
1815 AlignmentI pastedal = alignment; // preserve pasted alignment object
1816 // Add pasted sequences and dataset into existing alignment.
1817 alignment = viewport.getAlignment();
1818 alwidth = alignment.getWidth() + 1;
1819 // decide if we need to import sequences from an existing dataset
1820 boolean importDs = Desktop.jalviewClipboard != null
1821 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1822 // importDs==true instructs us to copy over new dataset sequences from
1823 // an existing alignment
1824 Vector newDs = (importDs) ? new Vector() : null; // used to create
1825 // minimum dataset set
1827 for (int i = 0; i < sequences.length; i++)
1831 newDs.addElement(null);
1833 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1835 if (importDs && ds != null)
1837 if (!newDs.contains(ds))
1839 newDs.setElementAt(ds, i);
1840 ds = new Sequence(ds);
1841 // update with new dataset sequence
1842 sequences[i].setDatasetSequence(ds);
1846 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1851 // copy and derive new dataset sequence
1852 sequences[i] = sequences[i].deriveSequence();
1853 alignment.getDataset().addSequence(
1854 sequences[i].getDatasetSequence());
1855 // TODO: avoid creation of duplicate dataset sequences with a
1856 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1858 alignment.addSequence(sequences[i]); // merges dataset
1862 newDs.clear(); // tidy up
1864 if (pastedal.getAlignmentAnnotation() != null)
1866 // Add any annotation attached to alignment.
1867 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1868 for (int i = 0; i < alann.length; i++)
1870 annotationAdded = true;
1871 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1873 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1874 newann.padAnnotation(alwidth);
1875 alignment.addAnnotation(newann);
1885 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1886 sequences, 0, alignment.getWidth(), alignment));
1888 // Add any annotations attached to sequences
1889 for (int i = 0; i < sequences.length; i++)
1891 if (sequences[i].getAnnotation() != null)
1893 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1895 annotationAdded = true;
1896 sequences[i].getAnnotation()[a].adjustForAlignment();
1897 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1898 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1903 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1910 // propagate alignment changed.
1911 viewport.setEndSeq(alignment.getHeight());
1912 if (annotationAdded)
1914 // Duplicate sequence annotation in all views.
1915 AlignmentI[] alview = this.getViewAlignments();
1916 for (int i = 0; i < sequences.length; i++)
1918 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1921 for (int avnum = 0; avnum < alview.length; avnum++)
1923 if (alview[avnum] != alignment)
1925 // duplicate in a view other than the one with input focus
1926 int avwidth = alview[avnum].getWidth() + 1;
1927 // this relies on sann being preserved after we
1928 // modify the sequence's annotation array for each duplication
1929 for (int a = 0; a < sann.length; a++)
1931 AlignmentAnnotation newann = new AlignmentAnnotation(
1933 sequences[i].addAlignmentAnnotation(newann);
1934 newann.padAnnotation(avwidth);
1935 alview[avnum].addAnnotation(newann); // annotation was
1936 // duplicated earlier
1937 alview[avnum].setAnnotationIndex(newann, a);
1942 buildSortByAnnotationScoresMenu();
1944 viewport.firePropertyChange("alignment", null,
1945 alignment.getSequences());
1950 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1952 String newtitle = new String("Copied sequences");
1954 if (Desktop.jalviewClipboard != null
1955 && Desktop.jalviewClipboard[2] != null)
1957 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1958 for (int i = 0; i < hc.size(); i++)
1960 int[] region = (int[]) hc.elementAt(i);
1961 af.viewport.hideColumns(region[0], region[1]);
1965 // >>>This is a fix for the moment, until a better solution is
1967 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1969 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1971 // TODO: maintain provenance of an alignment, rather than just make the
1972 // title a concatenation of operations.
1975 if (title.startsWith("Copied sequences"))
1981 newtitle = newtitle.concat("- from " + title);
1986 newtitle = new String("Pasted sequences");
1989 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1994 } catch (Exception ex)
1996 ex.printStackTrace();
1997 System.out.println("Exception whilst pasting: " + ex);
1998 // could be anything being pasted in here
2009 protected void cut_actionPerformed(ActionEvent e)
2011 copy_actionPerformed(null);
2012 delete_actionPerformed(null);
2021 protected void delete_actionPerformed(ActionEvent evt)
2024 SequenceGroup sg = viewport.getSelectionGroup();
2030 Vector seqs = new Vector();
2032 for (int i = 0; i < sg.getSize(); i++)
2034 seq = sg.getSequenceAt(i);
2035 seqs.addElement(seq);
2038 // If the cut affects all sequences, remove highlighted columns
2039 if (sg.getSize() == viewport.getAlignment().getHeight())
2041 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2042 sg.getEndRes() + 1);
2045 SequenceI[] cut = new SequenceI[seqs.size()];
2046 for (int i = 0; i < seqs.size(); i++)
2048 cut[i] = (SequenceI) seqs.elementAt(i);
2052 * //ADD HISTORY ITEM
2054 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2055 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2056 viewport.getAlignment()));
2058 viewport.setSelectionGroup(null);
2059 viewport.sendSelection();
2060 viewport.getAlignment().deleteGroup(sg);
2062 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2064 if (viewport.getAlignment().getHeight() < 1)
2068 this.setClosed(true);
2069 } catch (Exception ex)
2081 protected void deleteGroups_actionPerformed(ActionEvent e)
2083 viewport.getAlignment().deleteAllGroups();
2084 viewport.sequenceColours = null;
2085 viewport.setSelectionGroup(null);
2086 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2087 alignPanel.updateAnnotation();
2088 alignPanel.paintAlignment(true);
2097 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2099 SequenceGroup sg = new SequenceGroup();
2101 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2103 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2106 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2107 viewport.setSelectionGroup(sg);
2108 viewport.sendSelection();
2109 alignPanel.paintAlignment(true);
2110 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2119 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2121 if (viewport.cursorMode)
2123 alignPanel.seqPanel.keyboardNo1 = null;
2124 alignPanel.seqPanel.keyboardNo2 = null;
2126 viewport.setSelectionGroup(null);
2127 viewport.getColumnSelection().clear();
2128 viewport.setSelectionGroup(null);
2129 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2130 alignPanel.idPanel.idCanvas.searchResults = null;
2131 alignPanel.paintAlignment(true);
2132 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2133 viewport.sendSelection();
2142 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2144 SequenceGroup sg = viewport.getSelectionGroup();
2148 selectAllSequenceMenuItem_actionPerformed(null);
2153 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2155 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2158 alignPanel.paintAlignment(true);
2159 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2160 viewport.sendSelection();
2163 public void invertColSel_actionPerformed(ActionEvent e)
2165 viewport.invertColumnSelection();
2166 alignPanel.paintAlignment(true);
2167 viewport.sendSelection();
2176 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2178 trimAlignment(true);
2187 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2189 trimAlignment(false);
2192 void trimAlignment(boolean trimLeft)
2194 ColumnSelection colSel = viewport.getColumnSelection();
2197 if (colSel.size() > 0)
2201 column = colSel.getMin();
2205 column = colSel.getMax();
2209 if (viewport.getSelectionGroup() != null)
2211 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2212 viewport.getHiddenRepSequences());
2216 seqs = viewport.getAlignment().getSequencesArray();
2219 TrimRegionCommand trimRegion;
2222 trimRegion = new TrimRegionCommand("Remove Left",
2223 TrimRegionCommand.TRIM_LEFT, seqs, column,
2224 viewport.getAlignment(), viewport.getColumnSelection(),
2225 viewport.getSelectionGroup());
2226 viewport.setStartRes(0);
2230 trimRegion = new TrimRegionCommand("Remove Right",
2231 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2232 viewport.getAlignment(), viewport.getColumnSelection(),
2233 viewport.getSelectionGroup());
2236 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2238 addHistoryItem(trimRegion);
2240 Vector groups = viewport.getAlignment().getGroups();
2242 for (int i = 0; i < groups.size(); i++)
2244 SequenceGroup sg = (SequenceGroup) groups.get(i);
2246 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2247 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2249 viewport.getAlignment().deleteGroup(sg);
2253 viewport.firePropertyChange("alignment", null, viewport
2254 .getAlignment().getSequences());
2264 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2266 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2269 if (viewport.getSelectionGroup() != null)
2271 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2272 viewport.getHiddenRepSequences());
2273 start = viewport.getSelectionGroup().getStartRes();
2274 end = viewport.getSelectionGroup().getEndRes();
2278 seqs = viewport.getAlignment().getSequencesArray();
2281 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2282 "Remove Gapped Columns", seqs, start, end,
2283 viewport.getAlignment());
2285 addHistoryItem(removeGapCols);
2287 statusBar.setText("Removed " + removeGapCols.getSize()
2288 + " empty columns.");
2290 // This is to maintain viewport position on first residue
2291 // of first sequence
2292 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2293 int startRes = seq.findPosition(viewport.startRes);
2294 // ShiftList shifts;
2295 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2296 // edit.alColumnChanges=shifts.getInverse();
2297 // if (viewport.hasHiddenColumns)
2298 // viewport.getColumnSelection().compensateForEdits(shifts);
2299 viewport.setStartRes(seq.findIndex(startRes) - 1);
2300 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2311 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2313 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2316 if (viewport.getSelectionGroup() != null)
2318 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2319 viewport.getHiddenRepSequences());
2320 start = viewport.getSelectionGroup().getStartRes();
2321 end = viewport.getSelectionGroup().getEndRes();
2325 seqs = viewport.getAlignment().getSequencesArray();
2328 // This is to maintain viewport position on first residue
2329 // of first sequence
2330 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2331 int startRes = seq.findPosition(viewport.startRes);
2333 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2334 viewport.getAlignment()));
2336 viewport.setStartRes(seq.findIndex(startRes) - 1);
2338 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2349 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2351 viewport.setPadGaps(padGapsMenuitem.isSelected());
2352 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2358 // if (justifySeqs>0)
2360 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2372 public void findMenuItem_actionPerformed(ActionEvent e)
2377 public void newView_actionPerformed(ActionEvent e)
2384 * @param copyAnnotation
2385 * if true then duplicate all annnotation, groups and settings
2386 * @return new alignment panel, already displayed.
2388 public AlignmentPanel newView(boolean copyAnnotation)
2390 return newView(null, copyAnnotation);
2396 * title of newly created view
2397 * @return new alignment panel, already displayed.
2399 public AlignmentPanel newView(String viewTitle)
2401 return newView(viewTitle, true);
2407 * title of newly created view
2408 * @param copyAnnotation
2409 * if true then duplicate all annnotation, groups and settings
2410 * @return new alignment panel, already displayed.
2412 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2414 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2416 if (!copyAnnotation)
2418 // just remove all the current annotation except for the automatic stuff
2419 newap.av.getAlignment().deleteAllGroups();
2420 for (AlignmentAnnotation alan : newap.av.getAlignment()
2421 .getAlignmentAnnotation())
2423 if (!alan.autoCalculated)
2425 newap.av.getAlignment().deleteAnnotation(alan);
2431 newap.av.gatherViewsHere = false;
2433 if (viewport.viewName == null)
2435 viewport.viewName = "Original";
2438 newap.av.historyList = viewport.historyList;
2439 newap.av.redoList = viewport.redoList;
2441 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2442 // make sure the new view has a unique name - this is essential for Jalview
2444 boolean addFirstIndex = false;
2445 if (viewTitle == null || viewTitle.trim().length() == 0)
2448 addFirstIndex = true;
2452 index = 1;// we count from 1 if given a specific name
2454 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2455 Vector comps = (Vector) PaintRefresher.components.get(viewport
2456 .getSequenceSetId());
2457 Vector existingNames = new Vector();
2458 for (int i = 0; i < comps.size(); i++)
2460 if (comps.elementAt(i) instanceof AlignmentPanel)
2462 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2463 if (!existingNames.contains(ap.av.viewName))
2465 existingNames.addElement(ap.av.viewName);
2470 while (existingNames.contains(newViewName))
2472 newViewName = viewTitle + " " + (++index);
2475 newap.av.viewName = newViewName;
2477 addAlignmentPanel(newap, true);
2479 if (alignPanels.size() == 2)
2481 viewport.gatherViewsHere = true;
2483 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2487 public void expandViews_actionPerformed(ActionEvent e)
2489 Desktop.instance.explodeViews(this);
2492 public void gatherViews_actionPerformed(ActionEvent e)
2494 Desktop.instance.gatherViews(this);
2503 public void font_actionPerformed(ActionEvent e)
2505 new FontChooser(alignPanel);
2514 protected void seqLimit_actionPerformed(ActionEvent e)
2516 viewport.setShowJVSuffix(seqLimits.isSelected());
2518 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2519 .calculateIdWidth());
2520 alignPanel.paintAlignment(true);
2523 public void idRightAlign_actionPerformed(ActionEvent e)
2525 viewport.rightAlignIds = idRightAlign.isSelected();
2526 alignPanel.paintAlignment(true);
2529 public void centreColumnLabels_actionPerformed(ActionEvent e)
2531 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2532 alignPanel.paintAlignment(true);
2538 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2540 protected void followHighlight_actionPerformed()
2542 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2544 alignPanel.scrollToPosition(
2545 alignPanel.seqPanel.seqCanvas.searchResults, false);
2555 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2557 viewport.setColourText(colourTextMenuItem.isSelected());
2558 alignPanel.paintAlignment(true);
2567 public void wrapMenuItem_actionPerformed(ActionEvent e)
2569 scaleAbove.setVisible(wrapMenuItem.isSelected());
2570 scaleLeft.setVisible(wrapMenuItem.isSelected());
2571 scaleRight.setVisible(wrapMenuItem.isSelected());
2572 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2573 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2576 public void showAllSeqs_actionPerformed(ActionEvent e)
2578 viewport.showAllHiddenSeqs();
2581 public void showAllColumns_actionPerformed(ActionEvent e)
2583 viewport.showAllHiddenColumns();
2587 public void hideSelSequences_actionPerformed(ActionEvent e)
2589 viewport.hideAllSelectedSeqs();
2590 alignPanel.paintAlignment(true);
2594 * called by key handler and the hide all/show all menu items
2599 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2602 boolean hide = false;
2603 SequenceGroup sg = viewport.getSelectionGroup();
2604 if (!toggleSeqs && !toggleCols)
2606 // Hide everything by the current selection - this is a hack - we do the
2607 // invert and then hide
2608 // first check that there will be visible columns after the invert.
2609 if ((viewport.getColumnSelection() != null
2610 && viewport.getColumnSelection().getSelected() != null && viewport
2611 .getColumnSelection().getSelected().size() > 0)
2612 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2615 // now invert the sequence set, if required - empty selection implies
2616 // that no hiding is required.
2619 invertSequenceMenuItem_actionPerformed(null);
2620 sg = viewport.getSelectionGroup();
2624 viewport.expandColSelection(sg, true);
2625 // finally invert the column selection and get the new sequence
2627 invertColSel_actionPerformed(null);
2634 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2636 hideSelSequences_actionPerformed(null);
2639 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2642 showAllSeqs_actionPerformed(null);
2648 if (viewport.getColumnSelection().getSelected().size() > 0)
2650 hideSelColumns_actionPerformed(null);
2653 viewport.setSelectionGroup(sg);
2658 showAllColumns_actionPerformed(null);
2667 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2668 * event.ActionEvent)
2670 public void hideAllButSelection_actionPerformed(ActionEvent e)
2672 toggleHiddenRegions(false, false);
2679 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2682 public void hideAllSelection_actionPerformed(ActionEvent e)
2684 SequenceGroup sg = viewport.getSelectionGroup();
2685 viewport.expandColSelection(sg, false);
2686 viewport.hideAllSelectedSeqs();
2687 viewport.hideSelectedColumns();
2688 alignPanel.paintAlignment(true);
2695 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2698 public void showAllhidden_actionPerformed(ActionEvent e)
2700 viewport.showAllHiddenColumns();
2701 viewport.showAllHiddenSeqs();
2702 alignPanel.paintAlignment(true);
2705 public void hideSelColumns_actionPerformed(ActionEvent e)
2707 viewport.hideSelectedColumns();
2708 alignPanel.paintAlignment(true);
2711 public void hiddenMarkers_actionPerformed(ActionEvent e)
2713 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2723 protected void scaleAbove_actionPerformed(ActionEvent e)
2725 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2726 alignPanel.paintAlignment(true);
2735 protected void scaleLeft_actionPerformed(ActionEvent e)
2737 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2738 alignPanel.paintAlignment(true);
2747 protected void scaleRight_actionPerformed(ActionEvent e)
2749 viewport.setScaleRightWrapped(scaleRight.isSelected());
2750 alignPanel.paintAlignment(true);
2759 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2761 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2762 alignPanel.paintAlignment(true);
2771 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2773 viewport.setShowText(viewTextMenuItem.isSelected());
2774 alignPanel.paintAlignment(true);
2783 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2785 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2786 alignPanel.paintAlignment(true);
2789 public FeatureSettings featureSettings;
2791 public void featureSettings_actionPerformed(ActionEvent e)
2793 if (featureSettings != null)
2795 featureSettings.close();
2796 featureSettings = null;
2798 if (!showSeqFeatures.isSelected())
2800 // make sure features are actually displayed
2801 showSeqFeatures.setSelected(true);
2802 showSeqFeatures_actionPerformed(null);
2804 featureSettings = new FeatureSettings(this);
2808 * Set or clear 'Show Sequence Features'
2813 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2815 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2816 alignPanel.paintAlignment(true);
2817 if (alignPanel.getOverviewPanel() != null)
2819 alignPanel.getOverviewPanel().updateOverviewImage();
2824 * Set or clear 'Show Sequence Features'
2829 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2831 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2833 if (viewport.getShowSequenceFeaturesHeight())
2835 // ensure we're actually displaying features
2836 viewport.setShowSequenceFeatures(true);
2837 showSeqFeatures.setSelected(true);
2839 alignPanel.paintAlignment(true);
2840 if (alignPanel.getOverviewPanel() != null)
2842 alignPanel.getOverviewPanel().updateOverviewImage();
2852 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2854 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2855 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2858 public void alignmentProperties()
2860 JEditorPane editPane = new JEditorPane("text/html", "");
2861 editPane.setEditable(false);
2862 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
2864 editPane.setText("<html>" + contents.toString() + "</html>");
2865 JInternalFrame frame = new JInternalFrame();
2866 frame.getContentPane().add(new JScrollPane(editPane));
2868 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2869 + getTitle(), 500, 400);
2878 public void overviewMenuItem_actionPerformed(ActionEvent e)
2880 if (alignPanel.overviewPanel != null)
2885 JInternalFrame frame = new JInternalFrame();
2886 OverviewPanel overview = new OverviewPanel(alignPanel);
2887 frame.setContentPane(overview);
2888 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2889 frame.getWidth(), frame.getHeight());
2891 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2892 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2894 public void internalFrameClosed(
2895 javax.swing.event.InternalFrameEvent evt)
2897 alignPanel.setOverviewPanel(null);
2901 alignPanel.setOverviewPanel(overview);
2904 public void textColour_actionPerformed(ActionEvent e)
2906 new TextColourChooser().chooseColour(alignPanel, null);
2915 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2926 public void clustalColour_actionPerformed(ActionEvent e)
2928 changeColour(new ClustalxColourScheme(viewport.getAlignment()
2929 .getSequences(), viewport.getAlignment().getWidth()));
2938 public void zappoColour_actionPerformed(ActionEvent e)
2940 changeColour(new ZappoColourScheme());
2949 public void taylorColour_actionPerformed(ActionEvent e)
2951 changeColour(new TaylorColourScheme());
2960 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2962 changeColour(new HydrophobicColourScheme());
2971 public void helixColour_actionPerformed(ActionEvent e)
2973 changeColour(new HelixColourScheme());
2982 public void strandColour_actionPerformed(ActionEvent e)
2984 changeColour(new StrandColourScheme());
2993 public void turnColour_actionPerformed(ActionEvent e)
2995 changeColour(new TurnColourScheme());
3004 public void buriedColour_actionPerformed(ActionEvent e)
3006 changeColour(new BuriedColourScheme());
3015 public void nucleotideColour_actionPerformed(ActionEvent e)
3017 changeColour(new NucleotideColourScheme());
3020 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3022 changeColour(new PurinePyrimidineColourScheme());
3026 * public void covariationColour_actionPerformed(ActionEvent e) {
3028 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3031 public void annotationColour_actionPerformed(ActionEvent e)
3033 new AnnotationColourChooser(viewport, alignPanel);
3036 public void rnahelicesColour_actionPerformed(ActionEvent e)
3038 new RNAHelicesColourChooser(viewport, alignPanel);
3047 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3049 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3058 public void changeColour(ColourSchemeI cs)
3060 // TODO: compare with applet and pull up to model method
3065 if (viewport.getAbovePIDThreshold())
3067 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3070 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3072 viewport.setGlobalColourScheme(cs);
3076 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3079 if (viewport.getConservationSelected())
3082 Alignment al = (Alignment) viewport.getAlignment();
3083 Conservation c = new Conservation("All",
3084 ResidueProperties.propHash, 3, al.getSequences(), 0,
3088 c.verdict(false, viewport.getConsPercGaps());
3090 cs.setConservation(c);
3092 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3097 cs.setConservation(null);
3100 cs.setConsensus(viewport.getSequenceConsensusHash());
3103 viewport.setGlobalColourScheme(cs);
3105 if (viewport.getColourAppliesToAllGroups())
3107 Vector groups = viewport.getAlignment().getGroups();
3109 for (int i = 0; i < groups.size(); i++)
3111 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
3119 if (cs instanceof ClustalxColourScheme)
3121 sg.cs = new ClustalxColourScheme(sg.getSequences(viewport
3122 .getHiddenRepSequences()), sg.getWidth());
3124 else if (cs instanceof UserColourScheme)
3126 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3132 sg.cs = cs.getClass().newInstance();
3133 } catch (Exception ex)
3138 if (viewport.getAbovePIDThreshold()
3139 || cs instanceof PIDColourScheme
3140 || cs instanceof Blosum62ColourScheme)
3142 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3144 sg.cs.setConsensus(AAFrequency.calculate(
3145 sg.getSequences(viewport.getHiddenRepSequences()),
3146 sg.getStartRes(), sg.getEndRes() + 1));
3150 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3153 if (viewport.getConservationSelected())
3155 Conservation c = new Conservation("Group",
3156 ResidueProperties.propHash, 3, sg.getSequences(viewport
3157 .getHiddenRepSequences()), sg.getStartRes(),
3158 sg.getEndRes() + 1);
3160 c.verdict(false, viewport.getConsPercGaps());
3161 sg.cs.setConservation(c);
3165 sg.cs.setConservation(null);
3170 if (alignPanel.getOverviewPanel() != null)
3172 alignPanel.getOverviewPanel().updateOverviewImage();
3175 alignPanel.paintAlignment(true);
3184 protected void modifyPID_actionPerformed(ActionEvent e)
3186 if (viewport.getAbovePIDThreshold()
3187 && viewport.getGlobalColourScheme() != null)
3189 SliderPanel.setPIDSliderSource(alignPanel,
3190 viewport.getGlobalColourScheme(), "Background");
3191 SliderPanel.showPIDSlider();
3201 protected void modifyConservation_actionPerformed(ActionEvent e)
3203 if (viewport.getConservationSelected()
3204 && viewport.getGlobalColourScheme() != null)
3206 SliderPanel.setConservationSlider(alignPanel,
3207 viewport.getGlobalColourScheme(), "Background");
3208 SliderPanel.showConservationSlider();
3218 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3220 viewport.setConservationSelected(conservationMenuItem.isSelected());
3222 viewport.setAbovePIDThreshold(false);
3223 abovePIDThreshold.setSelected(false);
3225 changeColour(viewport.getGlobalColourScheme());
3227 modifyConservation_actionPerformed(null);
3236 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3238 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3240 conservationMenuItem.setSelected(false);
3241 viewport.setConservationSelected(false);
3243 changeColour(viewport.getGlobalColourScheme());
3245 modifyPID_actionPerformed(null);
3254 public void userDefinedColour_actionPerformed(ActionEvent e)
3256 if (e.getActionCommand().equals("User Defined..."))
3258 new UserDefinedColours(alignPanel, null);
3262 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3263 .getUserColourSchemes().get(e.getActionCommand());
3269 public void updateUserColourMenu()
3272 Component[] menuItems = colourMenu.getMenuComponents();
3273 int i, iSize = menuItems.length;
3274 for (i = 0; i < iSize; i++)
3276 if (menuItems[i].getName() != null
3277 && menuItems[i].getName().equals("USER_DEFINED"))
3279 colourMenu.remove(menuItems[i]);
3283 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3285 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3286 .getUserColourSchemes().keys();
3288 while (userColours.hasMoreElements())
3290 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3291 userColours.nextElement().toString());
3292 radioItem.setName("USER_DEFINED");
3293 radioItem.addMouseListener(new MouseAdapter()
3295 public void mousePressed(MouseEvent evt)
3297 if (evt.isControlDown()
3298 || SwingUtilities.isRightMouseButton(evt))
3300 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3302 int option = JOptionPane.showInternalConfirmDialog(
3303 jalview.gui.Desktop.desktop,
3304 "Remove from default list?",
3305 "Remove user defined colour",
3306 JOptionPane.YES_NO_OPTION);
3307 if (option == JOptionPane.YES_OPTION)
3309 jalview.gui.UserDefinedColours
3310 .removeColourFromDefaults(radioItem.getText());
3311 colourMenu.remove(radioItem);
3315 radioItem.addActionListener(new ActionListener()
3317 public void actionPerformed(ActionEvent evt)
3319 userDefinedColour_actionPerformed(evt);
3326 radioItem.addActionListener(new ActionListener()
3328 public void actionPerformed(ActionEvent evt)
3330 userDefinedColour_actionPerformed(evt);
3334 colourMenu.insert(radioItem, 15);
3335 colours.add(radioItem);
3346 public void PIDColour_actionPerformed(ActionEvent e)
3348 changeColour(new PIDColourScheme());
3357 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3359 changeColour(new Blosum62ColourScheme());
3368 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3370 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3371 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3372 .getAlignment().getSequenceAt(0), null);
3373 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3374 viewport.getAlignment()));
3375 alignPanel.paintAlignment(true);
3384 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3386 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3387 AlignmentSorter.sortByID(viewport.getAlignment());
3388 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3389 viewport.getAlignment()));
3390 alignPanel.paintAlignment(true);
3399 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3401 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3402 AlignmentSorter.sortByLength(viewport.getAlignment());
3403 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3404 viewport.getAlignment()));
3405 alignPanel.paintAlignment(true);
3414 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3416 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3417 AlignmentSorter.sortByGroup(viewport.getAlignment());
3418 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3419 viewport.getAlignment()));
3421 alignPanel.paintAlignment(true);
3430 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3432 new RedundancyPanel(alignPanel, this);
3441 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3443 if ((viewport.getSelectionGroup() == null)
3444 || (viewport.getSelectionGroup().getSize() < 2))
3446 JOptionPane.showInternalMessageDialog(this,
3447 "You must select at least 2 sequences.", "Invalid Selection",
3448 JOptionPane.WARNING_MESSAGE);
3452 JInternalFrame frame = new JInternalFrame();
3453 frame.setContentPane(new PairwiseAlignPanel(viewport));
3454 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3464 public void PCAMenuItem_actionPerformed(ActionEvent e)
3466 if (((viewport.getSelectionGroup() != null)
3467 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3468 .getSelectionGroup().getSize() > 0))
3469 || (viewport.getAlignment().getHeight() < 4))
3471 JOptionPane.showInternalMessageDialog(this,
3472 "Principal component analysis must take\n"
3473 + "at least 4 input sequences.",
3474 "Sequence selection insufficient",
3475 JOptionPane.WARNING_MESSAGE);
3480 new PCAPanel(alignPanel);
3483 public void autoCalculate_actionPerformed(ActionEvent e)
3485 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3486 if (viewport.autoCalculateConsensus)
3488 viewport.firePropertyChange("alignment", null, viewport
3489 .getAlignment().getSequences());
3493 public void sortByTreeOption_actionPerformed(ActionEvent e)
3495 viewport.sortByTree = sortByTree.isSelected();
3499 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3501 viewport.followSelection = listenToViewSelections.isSelected();
3510 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3512 NewTreePanel("AV", "PID", "Average distance tree using PID");
3521 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3523 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3532 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3534 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3543 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3545 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3558 void NewTreePanel(String type, String pwType, String title)
3562 if (viewport.getSelectionGroup() != null)
3564 if (viewport.getSelectionGroup().getSize() < 3)
3569 "You need to have more than two sequences selected to build a tree!",
3570 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3575 SequenceGroup sg = viewport.getSelectionGroup();
3577 /* Decide if the selection is a column region */
3578 while (s < sg.getSize())
3580 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3586 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3587 + "Try using the Pad function in the edit menu,\n"
3588 + "or one of the multiple sequence alignment web services.",
3589 "Sequences in selection are not aligned",
3590 JOptionPane.WARNING_MESSAGE);
3596 title = title + " on region";
3597 tp = new TreePanel(alignPanel, type, pwType);
3601 // are the visible sequences aligned?
3602 if (!viewport.getAlignment().isAligned(false))
3607 "The sequences must be aligned before creating a tree.\n"
3608 + "Try using the Pad function in the edit menu,\n"
3609 + "or one of the multiple sequence alignment web services.",
3610 "Sequences not aligned",
3611 JOptionPane.WARNING_MESSAGE);
3616 if (viewport.getAlignment().getHeight() < 2)
3621 tp = new TreePanel(alignPanel, type, pwType);
3626 if (viewport.viewName != null)
3628 title += viewport.viewName + " of ";
3631 title += this.title;
3633 Desktop.addInternalFrame(tp, title, 600, 500);
3644 public void addSortByOrderMenuItem(String title,
3645 final AlignmentOrder order)
3647 final JMenuItem item = new JMenuItem("by " + title);
3649 item.addActionListener(new java.awt.event.ActionListener()
3651 public void actionPerformed(ActionEvent e)
3653 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3655 // TODO: JBPNote - have to map order entries to curent SequenceI
3657 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3659 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3662 alignPanel.paintAlignment(true);
3668 * Add a new sort by annotation score menu item
3671 * the menu to add the option to
3673 * the label used to retrieve scores for each sequence on the
3676 public void addSortByAnnotScoreMenuItem(JMenu sort,
3677 final String scoreLabel)
3679 final JMenuItem item = new JMenuItem(scoreLabel);
3681 item.addActionListener(new java.awt.event.ActionListener()
3683 public void actionPerformed(ActionEvent e)
3685 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3686 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3687 viewport.getAlignment());// ,viewport.getSelectionGroup());
3688 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3689 viewport.getAlignment()));
3690 alignPanel.paintAlignment(true);
3696 * last hash for alignment's annotation array - used to minimise cost of
3699 protected int _annotationScoreVectorHash;
3702 * search the alignment and rebuild the sort by annotation score submenu the
3703 * last alignment annotation vector hash is stored to minimize cost of
3704 * rebuilding in subsequence calls.
3707 public void buildSortByAnnotationScoresMenu()
3709 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3714 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3716 sortByAnnotScore.removeAll();
3717 // almost certainly a quicker way to do this - but we keep it simple
3718 Hashtable scoreSorts = new Hashtable();
3719 AlignmentAnnotation aann[];
3720 Enumeration sq = viewport.getAlignment().getSequences().elements();
3721 while (sq.hasMoreElements())
3723 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3724 for (int i = 0; aann != null && i < aann.length; i++)
3726 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3728 scoreSorts.put(aann[i].label, aann[i].label);
3732 Enumeration labels = scoreSorts.keys();
3733 while (labels.hasMoreElements())
3735 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3736 (String) labels.nextElement());
3738 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3741 _annotationScoreVectorHash = viewport.getAlignment()
3742 .getAlignmentAnnotation().hashCode();
3747 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3748 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3749 * call. Listeners are added to remove the menu item when the treePanel is
3750 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3754 * Displayed tree window.
3756 * SortBy menu item title.
3758 public void buildTreeMenu()
3760 sortByTreeMenu.removeAll();
3762 Vector comps = (Vector) PaintRefresher.components.get(viewport
3763 .getSequenceSetId());
3764 Vector treePanels = new Vector();
3765 int i, iSize = comps.size();
3766 for (i = 0; i < iSize; i++)
3768 if (comps.elementAt(i) instanceof TreePanel)
3770 treePanels.add(comps.elementAt(i));
3774 iSize = treePanels.size();
3778 sortByTreeMenu.setVisible(false);
3782 sortByTreeMenu.setVisible(true);
3784 for (i = 0; i < treePanels.size(); i++)
3786 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3787 final JMenuItem item = new JMenuItem(tp.getTitle());
3788 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3789 item.addActionListener(new java.awt.event.ActionListener()
3791 public void actionPerformed(ActionEvent e)
3793 tp.sortByTree_actionPerformed(null);
3794 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3799 sortByTreeMenu.add(item);
3803 public boolean sortBy(AlignmentOrder alorder, String undoname)
3805 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3806 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3807 if (undoname != null)
3809 addHistoryItem(new OrderCommand(undoname, oldOrder,
3810 viewport.getAlignment()));
3812 alignPanel.paintAlignment(true);
3817 * Work out whether the whole set of sequences or just the selected set will
3818 * be submitted for multiple alignment.
3821 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3823 // Now, check we have enough sequences
3824 AlignmentView msa = null;
3826 if ((viewport.getSelectionGroup() != null)
3827 && (viewport.getSelectionGroup().getSize() > 1))
3829 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3830 // some common interface!
3832 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3833 * SequenceI[sz = seqs.getSize(false)];
3835 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3836 * seqs.getSequenceAt(i); }
3838 msa = viewport.getAlignmentView(true);
3843 * Vector seqs = viewport.getAlignment().getSequences();
3845 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3847 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3848 * seqs.elementAt(i); } }
3850 msa = viewport.getAlignmentView(false);
3856 * Decides what is submitted to a secondary structure prediction service: the
3857 * first sequence in the alignment, or in the current selection, or, if the
3858 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3859 * region or the whole alignment. (where the first sequence in the set is the
3860 * one that the prediction will be for).
3862 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3864 AlignmentView seqs = null;
3866 if ((viewport.getSelectionGroup() != null)
3867 && (viewport.getSelectionGroup().getSize() > 0))
3869 seqs = viewport.getAlignmentView(true);
3873 seqs = viewport.getAlignmentView(false);
3875 // limit sequences - JBPNote in future - could spawn multiple prediction
3877 // TODO: viewport.getAlignment().isAligned is a global state - the local
3878 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3879 if (!viewport.getAlignment().isAligned(false))
3881 seqs.setSequences(new SeqCigar[]
3882 { seqs.getSequences()[0] });
3883 // TODO: if seqs.getSequences().length>1 then should really have warned
3896 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3898 // Pick the tree file
3899 JalviewFileChooser chooser = new JalviewFileChooser(
3900 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3901 chooser.setFileView(new JalviewFileView());
3902 chooser.setDialogTitle("Select a newick-like tree file");
3903 chooser.setToolTipText("Load a tree file");
3905 int value = chooser.showOpenDialog(null);
3907 if (value == JalviewFileChooser.APPROVE_OPTION)
3909 String choice = chooser.getSelectedFile().getPath();
3910 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3911 jalview.io.NewickFile fin = null;
3914 fin = new jalview.io.NewickFile(choice, "File");
3915 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3916 } catch (Exception ex)
3918 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3919 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3920 ex.printStackTrace();
3922 if (fin != null && fin.hasWarningMessage())
3924 JOptionPane.showMessageDialog(Desktop.desktop,
3925 fin.getWarningMessage(), "Possible problem with tree file",
3926 JOptionPane.WARNING_MESSAGE);
3932 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
3934 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3937 public TreePanel ShowNewickTree(NewickFile nf, String title)
3939 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3942 public TreePanel ShowNewickTree(NewickFile nf, String title,
3943 AlignmentView input)
3945 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3948 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3949 int h, int x, int y)
3951 return ShowNewickTree(nf, title, null, w, h, x, y);
3955 * Add a treeviewer for the tree extracted from a newick file object to the
3956 * current alignment view
3963 * Associated alignment input data (or null)
3972 * @return TreePanel handle
3974 public TreePanel ShowNewickTree(NewickFile nf, String title,
3975 AlignmentView input, int w, int h, int x, int y)
3977 TreePanel tp = null;
3983 if (nf.getTree() != null)
3985 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3991 tp.setLocation(x, y);
3994 Desktop.addInternalFrame(tp, title, w, h);
3996 } catch (Exception ex)
3998 ex.printStackTrace();
4004 private boolean buildingMenu = false;
4007 * Generates menu items and listener event actions for web service clients
4010 public void BuildWebServiceMenu()
4012 while (buildingMenu)
4016 System.err.println("Waiting for building menu to finish.");
4018 } catch (Exception e)
4023 final AlignFrame me = this;
4024 buildingMenu = true;
4025 new Thread(new Runnable()
4031 System.err.println("Building ws menu again "
4032 + Thread.currentThread());
4033 // TODO: add support for context dependent disabling of services based
4035 // alignment and current selection
4036 // TODO: add additional serviceHandle parameter to specify abstract
4038 // class independently of AbstractName
4039 // TODO: add in rediscovery GUI function to restart discoverer
4040 // TODO: group services by location as well as function and/or
4042 // object broker mechanism.
4043 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4044 final IProgressIndicator af = me;
4045 final JMenu msawsmenu = new JMenu("Alignment");
4046 final JMenu secstrmenu = new JMenu(
4047 "Secondary Structure Prediction");
4048 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4049 final JMenu analymenu = new JMenu("Analysis");
4050 final JMenu dismenu = new JMenu("Disorder");
4051 // JAL-940 - only show secondary structure prediction services from
4052 // the legacy server
4053 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4055 Discoverer.services != null && (Discoverer.services.size() > 0))
4057 // TODO: refactor to allow list of AbstractName/Handler bindings to
4059 // stored or retrieved from elsewhere
4060 Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4061 Vector secstrpr = (Vector) Discoverer.services
4063 Vector seqsrch = null; // (Vector)
4064 // Discoverer.services.get("SeqSearch");
4065 // TODO: move GUI generation code onto service implementation - so a
4066 // client instance attaches itself to the GUI with method call like
4067 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
4071 // Add any Multiple Sequence Alignment Services
4072 for (int i = 0, j = msaws.size(); i < j; i++)
4074 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
4076 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4077 .getServiceClient(sh);
4078 impl.attachWSMenuEntry(msawsmenu, me);
4082 if (secstrpr != null)
4084 // Add any secondary structure prediction services
4085 for (int i = 0, j = secstrpr.size(); i < j; i++)
4087 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4089 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4090 .getServiceClient(sh);
4091 impl.attachWSMenuEntry(secstrmenu, me);
4094 if (seqsrch != null)
4096 // Add any sequence search services
4097 for (int i = 0, j = seqsrch.size(); i < j; i++)
4099 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
4101 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4102 .getServiceClient(sh);
4103 impl.attachWSMenuEntry(seqsrchmenu, me);
4108 // Add all submenus in the order they should appear on the web
4110 wsmenu.add(msawsmenu);
4111 wsmenu.add(secstrmenu);
4112 wsmenu.add(dismenu);
4113 wsmenu.add(analymenu);
4114 // final ArrayList<JMenu> submens=new ArrayList<JMenu>();
4115 // submens.add(msawsmenu);
4116 // submens.add(secstrmenu);
4117 // submens.add(dismenu);
4118 // submens.add(analymenu);
4120 // No search services yet
4121 // wsmenu.add(seqsrchmenu);
4123 javax.swing.SwingUtilities.invokeLater(new Runnable()
4129 webService.removeAll();
4130 // first, add discovered services onto the webservices menu
4131 if (wsmenu.size() > 0)
4133 for (int i = 0, j = wsmenu.size(); i < j; i++)
4135 webService.add((JMenu) wsmenu.get(i));
4140 webService.add(me.webServiceNoServices);
4142 // TODO: move into separate menu builder class.
4143 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4145 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4146 if (jws2servs != null)
4148 if (jws2servs.hasServices())
4150 jws2servs.attachWSMenuEntry(webService, me);
4152 if (jws2servs.isRunning())
4154 JMenuItem tm = new JMenuItem(
4155 "Still discovering JABA Services");
4156 tm.setEnabled(false);
4162 build_urlServiceMenu(me.webService);
4163 build_fetchdbmenu(webService);
4164 for (JMenu item : wsmenu)
4166 if (item.getItemCount() == 0)
4168 item.setEnabled(false);
4172 item.setEnabled(true);
4175 } catch (Exception e)
4181 } catch (Exception e)
4186 buildingMenu = false;
4193 * construct any groupURL type service menu entries.
4197 private void build_urlServiceMenu(JMenu webService)
4199 // TODO: remove this code when 2.7 is released
4200 // DEBUG - alignmentView
4202 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4203 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4205 * @Override public void actionPerformed(ActionEvent e) {
4206 * jalview.datamodel.AlignmentView
4207 * .testSelectionViews(af.viewport.getAlignment(),
4208 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4210 * }); webService.add(testAlView);
4212 // TODO: refactor to RestClient discoverer and merge menu entries for
4213 // rest-style services with other types of analysis/calculation service
4214 // SHmmr test client - still being implemented.
4215 // DEBUG - alignmentView
4217 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4220 client.attachWSMenuEntry(
4221 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4225 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4227 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4233 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4234 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4235 * getProperty("LAST_DIRECTORY"));
4237 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4238 * to Vamsas file"); chooser.setToolTipText("Export");
4240 * int value = chooser.showSaveDialog(this);
4242 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4243 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4244 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4245 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4248 * prototype of an automatically enabled/disabled analysis function
4251 protected void setShowProductsEnabled()
4253 SequenceI[] selection = viewport.getSequenceSelection();
4254 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4255 viewport.getAlignment().getDataset()))
4257 showProducts.setEnabled(true);
4262 showProducts.setEnabled(false);
4267 * search selection for sequence xRef products and build the show products
4272 * @return true if showProducts menu should be enabled.
4274 public boolean canShowProducts(SequenceI[] selection,
4275 boolean isRegionSelection, Alignment dataset)
4277 boolean showp = false;
4280 showProducts.removeAll();
4281 final boolean dna = viewport.getAlignment().isNucleotide();
4282 final Alignment ds = dataset;
4283 String[] ptypes = (selection == null || selection.length == 0) ? null
4284 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4286 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4287 // selection, dataset, true);
4288 final SequenceI[] sel = selection;
4289 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4292 final boolean isRegSel = isRegionSelection;
4293 final AlignFrame af = this;
4294 final String source = ptypes[t];
4295 JMenuItem xtype = new JMenuItem(ptypes[t]);
4296 xtype.addActionListener(new ActionListener()
4299 public void actionPerformed(ActionEvent e)
4301 // TODO: new thread for this call with vis-delay
4302 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4303 isRegSel, dna, source);
4307 showProducts.add(xtype);
4309 showProducts.setVisible(showp);
4310 showProducts.setEnabled(showp);
4311 } catch (Exception e)
4313 jalview.bin.Cache.log
4314 .warn("canTranslate threw an exception - please report to help@jalview.org",
4321 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4322 boolean isRegSel, boolean dna, String source)
4324 final boolean fisRegSel = isRegSel;
4325 final boolean fdna = dna;
4326 final String fsrc = source;
4327 final AlignFrame ths = this;
4328 final SequenceI[] fsel = sel;
4329 Runnable foo = new Runnable()
4334 final long sttime = System.currentTimeMillis();
4335 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4338 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4342 Alignment prods = CrossRef
4343 .findXrefSequences(fsel, fdna, fsrc, ds);
4346 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4347 for (int s = 0; s < sprods.length; s++)
4349 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4350 if (ds.getSequences() == null
4351 || !ds.getSequences().contains(
4352 sprods[s].getDatasetSequence()))
4353 ds.addSequence(sprods[s].getDatasetSequence());
4354 sprods[s].updatePDBIds();
4356 Alignment al = new Alignment(sprods);
4357 AlignedCodonFrame[] cf = prods.getCodonFrames();
4359 for (int s = 0; cf != null && s < cf.length; s++)
4361 al.addCodonFrame(cf[s]);
4364 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4366 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4367 + " for " + ((fisRegSel) ? "selected region of " : "")
4369 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4374 System.err.println("No Sequences generated for xRef type "
4377 } catch (Exception e)
4379 jalview.bin.Cache.log.error(
4380 "Exception when finding crossreferences", e);
4381 } catch (OutOfMemoryError e)
4383 new OOMWarning("whilst fetching crossreferences", e);
4386 jalview.bin.Cache.log.error("Error when finding crossreferences",
4389 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4394 Thread frunner = new Thread(foo);
4398 public boolean canShowTranslationProducts(SequenceI[] selection,
4399 AlignmentI alignment)
4404 return (jalview.analysis.Dna.canTranslate(selection,
4405 viewport.getViewAsVisibleContigs(true)));
4406 } catch (Exception e)
4408 jalview.bin.Cache.log
4409 .warn("canTranslate threw an exception - please report to help@jalview.org",
4415 public void showProducts_actionPerformed(ActionEvent e)
4417 // /////////////////////////////
4418 // Collect Data to be translated/transferred
4420 SequenceI[] selection = viewport.getSequenceSelection();
4421 AlignmentI al = null;
4424 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4425 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4426 viewport.getAlignment().getDataset());
4427 } catch (Exception ex)
4430 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4437 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4438 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4442 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4443 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4444 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4448 public void showTranslation_actionPerformed(ActionEvent e)
4450 // /////////////////////////////
4451 // Collect Data to be translated/transferred
4453 SequenceI[] selection = viewport.getSequenceSelection();
4454 String[] seqstring = viewport.getViewAsString(true);
4455 AlignmentI al = null;
4458 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4459 viewport.getViewAsVisibleContigs(true), viewport
4460 .getGapCharacter(), viewport.getAlignment()
4461 .getAlignmentAnnotation(), viewport.getAlignment()
4462 .getWidth(), viewport.getAlignment().getDataset());
4463 } catch (Exception ex)
4466 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4473 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4474 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4478 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4479 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4480 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4485 * Try to load a features file onto the alignment.
4488 * contents or path to retrieve file
4490 * access mode of file (see jalview.io.AlignFile)
4491 * @return true if features file was parsed corectly.
4493 public boolean parseFeaturesFile(String file, String type)
4495 boolean featuresFile = false;
4498 featuresFile = new FeaturesFile(file, type).parse(viewport
4499 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4500 .getFeatureRenderer().featureColours, false,
4501 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4502 } catch (Exception ex)
4504 ex.printStackTrace();
4509 viewport.showSequenceFeatures = true;
4510 showSeqFeatures.setSelected(true);
4511 if (alignPanel.seqPanel.seqCanvas.fr != null)
4513 // update the min/max ranges where necessary
4514 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4516 if (featureSettings != null)
4518 featureSettings.setTableData();
4520 alignPanel.paintAlignment(true);
4523 return featuresFile;
4526 public void dragEnter(DropTargetDragEvent evt)
4530 public void dragExit(DropTargetEvent evt)
4534 public void dragOver(DropTargetDragEvent evt)
4538 public void dropActionChanged(DropTargetDragEvent evt)
4542 public void drop(DropTargetDropEvent evt)
4544 Transferable t = evt.getTransferable();
4545 java.util.List files = null;
4549 DataFlavor uriListFlavor = new DataFlavor(
4550 "text/uri-list;class=java.lang.String");
4551 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4553 // Works on Windows and MacOSX
4554 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4555 files = (java.util.List) t
4556 .getTransferData(DataFlavor.javaFileListFlavor);
4558 else if (t.isDataFlavorSupported(uriListFlavor))
4560 // This is used by Unix drag system
4561 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4562 String data = (String) t.getTransferData(uriListFlavor);
4563 files = new java.util.ArrayList(1);
4564 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4565 data, "\r\n"); st.hasMoreTokens();)
4567 String s = st.nextToken();
4568 if (s.startsWith("#"))
4570 // the line is a comment (as per the RFC 2483)
4574 java.net.URI uri = new java.net.URI(s);
4575 // check to see if we can handle this kind of URI
4576 if (uri.getScheme().toLowerCase().startsWith("http"))
4578 files.add(uri.toString());
4582 // otherwise preserve old behaviour: catch all for file objects
4583 java.io.File file = new java.io.File(uri);
4584 files.add(file.toString());
4588 } catch (Exception e)
4590 e.printStackTrace();
4596 // check to see if any of these files have names matching sequences in
4598 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4599 .getAlignment().getSequencesArray());
4601 * Object[] { String,SequenceI}
4603 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4604 ArrayList<String> filesnotmatched = new ArrayList<String>();
4605 for (int i = 0; i < files.size(); i++)
4607 String file = files.get(i).toString();
4609 String protocol = FormatAdapter.checkProtocol(file);
4610 if (protocol == jalview.io.FormatAdapter.FILE)
4612 File fl = new File(file);
4613 pdbfn = fl.getName();
4615 else if (protocol == jalview.io.FormatAdapter.URL)
4617 URL url = new URL(file);
4618 pdbfn = url.getFile();
4620 if (pdbfn.length() > 0)
4622 // attempt to find a match in the alignment
4623 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4624 int l = 0, c = pdbfn.indexOf(".");
4625 while (mtch == null && c != -1)
4630 } while ((c = pdbfn.indexOf(".", l)) > l);
4633 pdbfn = pdbfn.substring(0, l);
4635 mtch = idm.findAllIdMatches(pdbfn);
4642 type = new IdentifyFile().Identify(file, protocol);
4643 } catch (Exception ex)
4649 if (type.equalsIgnoreCase("PDB"))
4651 filesmatched.add(new Object[]
4652 { file, protocol, mtch });
4657 // File wasn't named like one of the sequences or wasn't a PDB file.
4658 filesnotmatched.add(file);
4662 if (filesmatched.size() > 0)
4664 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4668 "Do you want to automatically associate the "
4669 + filesmatched.size()
4670 + " PDB files with sequences in the alignment that have the same name ?",
4671 "Automatically Associate PDB files by name",
4672 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4675 for (Object[] fm : filesmatched)
4677 // try and associate
4678 // TODO: may want to set a standard ID naming formalism for
4679 // associating PDB files which have no IDs.
4680 for (SequenceI toassoc : (SequenceI[]) fm[2])
4682 PDBEntry pe = new AssociatePdbFileWithSeq()
4683 .associatePdbWithSeq((String) fm[0],
4684 (String) fm[1], toassoc, false);
4687 System.err.println("Associated file : "
4688 + ((String) fm[0]) + " with "
4689 + toassoc.getDisplayId(true));
4693 alignPanel.paintAlignment(true);
4697 if (filesnotmatched.size() > 0)
4700 && (Cache.getDefault(
4701 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4704 "<html>Do you want to <em>ignore</em> the "
4705 + filesnotmatched.size()
4706 + " files whose names did not match any sequence IDs ?</html>",
4707 "Ignore unmatched dropped files ?",
4708 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4712 for (String fn : filesnotmatched)
4714 loadJalviewDataFile(fn, null, null, null);
4718 } catch (Exception ex)
4720 ex.printStackTrace();
4726 * Attempt to load a "dropped" file or URL string: First by testing whether
4727 * it's and Annotation file, then a JNet file, and finally a features file. If
4728 * all are false then the user may have dropped an alignment file onto this
4732 * either a filename or a URL string.
4734 public void loadJalviewDataFile(String file, String protocol,
4735 String format, SequenceI assocSeq)
4739 if (protocol == null)
4741 protocol = jalview.io.FormatAdapter.checkProtocol(file);
4743 // if the file isn't identified, or not positively identified as some
4744 // other filetype (PFAM is default unidentified alignment file type) then
4745 // try to parse as annotation.
4746 boolean isAnnotation = (format == null || format
4747 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4748 .readAnnotationFile(viewport.getAlignment(), file, protocol)
4753 // first see if its a T-COFFEE score file
4754 TCoffeeScoreFile tcf = null;
4757 tcf = new TCoffeeScoreFile(file, protocol);
4760 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4762 tcoffeeColour.setEnabled(true);
4763 tcoffeeColour.setSelected(true);
4764 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4765 isAnnotation = true;
4767 .setText("Successfully pasted T-Coffee scores to alignment.");
4771 // some problem - if no warning its probable that the ID matching process didn't work
4772 JOptionPane.showMessageDialog(Desktop.desktop,
4773 tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(),
4774 "Problem reading T-COFFEE score file",
4775 JOptionPane.WARNING_MESSAGE);
4782 } catch (Exception x)
4784 Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
4789 // try to see if its a JNet 'concise' style annotation file *before*
4791 // try to parse it as a features file
4794 format = new IdentifyFile().Identify(file, protocol);
4796 if (format.equalsIgnoreCase("JnetFile"))
4798 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
4800 new JnetAnnotationMaker().add_annotation(predictions,
4801 viewport.getAlignment(), 0, false);
4802 isAnnotation = true;
4807 * if (format.equalsIgnoreCase("PDB")) {
4809 * String pdbfn = ""; // try to match up filename with sequence id
4810 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
4811 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
4812 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4813 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
4814 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4815 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
4816 * // attempt to find a match in the alignment SequenceI mtch =
4817 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4818 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
4819 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
4820 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
4821 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4822 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
4823 * { System.err.println("Associated file : " + file + " with " +
4824 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4825 * TODO: maybe need to load as normal otherwise return; } }
4827 // try to parse it as a features file
4828 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4829 // if it wasn't a features file then we just treat it as a general
4830 // alignment file to load into the current view.
4833 new FileLoader().LoadFile(viewport, file, protocol, format);
4837 alignPanel.paintAlignment(true);
4845 alignPanel.adjustAnnotationHeight();
4846 viewport.updateSequenceIdColours();
4847 buildSortByAnnotationScoresMenu();
4848 alignPanel.paintAlignment(true);
4850 } catch (Exception ex)
4852 ex.printStackTrace();
4856 public void tabSelectionChanged(int index)
4860 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4861 viewport = alignPanel.av;
4862 setMenusFromViewport(viewport);
4866 public void tabbedPane_mousePressed(MouseEvent e)
4868 if (SwingUtilities.isRightMouseButton(e))
4870 String reply = JOptionPane.showInternalInputDialog(this,
4871 "Enter View Name", "Edit View Name",
4872 JOptionPane.QUESTION_MESSAGE);
4876 viewport.viewName = reply;
4877 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4882 public AlignViewport getCurrentView()
4888 * Open the dialog for regex description parsing.
4890 protected void extractScores_actionPerformed(ActionEvent e)
4892 ParseProperties pp = new jalview.analysis.ParseProperties(
4893 viewport.getAlignment());
4894 // TODO: verify regex and introduce GUI dialog for version 2.5
4895 // if (pp.getScoresFromDescription("col", "score column ",
4896 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4898 if (pp.getScoresFromDescription("description column",
4899 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4901 buildSortByAnnotationScoresMenu();
4909 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4912 protected void showDbRefs_actionPerformed(ActionEvent e)
4914 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4920 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4923 protected void showNpFeats_actionPerformed(ActionEvent e)
4925 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4929 * find the viewport amongst the tabs in this alignment frame and close that
4934 public boolean closeView(AlignViewport av)
4938 this.closeMenuItem_actionPerformed(false);
4941 Component[] comp = tabbedPane.getComponents();
4942 for (int i = 0; comp != null && i < comp.length; i++)
4944 if (comp[i] instanceof AlignmentPanel)
4946 if (((AlignmentPanel) comp[i]).av == av)
4949 closeView((AlignmentPanel) comp[i]);
4957 protected void build_fetchdbmenu(JMenu webService)
4959 // Temporary hack - DBRef Fetcher always top level ws entry.
4960 // TODO We probably want to store a sequence database checklist in
4961 // preferences and have checkboxes.. rather than individual sources selected
4963 final JMenu rfetch = new JMenu("Fetch DB References");
4964 rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4965 webService.add(rfetch);
4967 JMenuItem fetchr = new JMenuItem("Standard Databases");
4968 fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4969 fetchr.addActionListener(new ActionListener()
4972 public void actionPerformed(ActionEvent e)
4974 new Thread(new Runnable()
4979 new jalview.ws.DBRefFetcher(alignPanel.av
4980 .getSequenceSelection(), alignPanel.alignFrame)
4981 .fetchDBRefs(false);
4989 final AlignFrame me = this;
4990 new Thread(new Runnable()
4994 final jalview.ws.SequenceFetcher sf = SequenceFetcher
4995 .getSequenceFetcherSingleton(me);
4996 javax.swing.SwingUtilities.invokeLater(new Runnable()
5000 String[] dbclasses = sf.getOrderedSupportedSources();
5001 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5002 // jalview.util.QuickSort.sort(otherdb, otherdb);
5003 List<DbSourceProxy> otherdb;
5004 JMenu dfetch = new JMenu();
5005 JMenu ifetch = new JMenu();
5006 JMenuItem fetchr = null;
5007 int comp = 0, icomp = 0, mcomp = 15;
5008 String mname = null;
5010 for (String dbclass : dbclasses)
5012 otherdb = sf.getSourceProxy(dbclass);
5013 // add a single entry for this class, or submenu allowing 'fetch
5015 if (otherdb == null || otherdb.size() < 1)
5019 // List<DbSourceProxy> dbs=otherdb;
5020 // otherdb=new ArrayList<DbSourceProxy>();
5021 // for (DbSourceProxy db:dbs)
5023 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5027 mname = "From " + dbclass;
5029 if (otherdb.size() == 1)
5031 final DbSourceProxy[] dassource = otherdb
5032 .toArray(new DbSourceProxy[0]);
5033 DbSourceProxy src = otherdb.get(0);
5034 fetchr = new JMenuItem(src.getDbSource());
5035 fetchr.addActionListener(new ActionListener()
5038 public void actionPerformed(ActionEvent e)
5040 new Thread(new Runnable()
5045 new jalview.ws.DBRefFetcher(alignPanel.av
5046 .getSequenceSelection(),
5047 alignPanel.alignFrame, dassource)
5048 .fetchDBRefs(false);
5054 fetchr.setToolTipText("<html>"
5055 + JvSwingUtils.wrapTooltip("Retrieve from "
5056 + src.getDbName()) + "<html>");
5062 final DbSourceProxy[] dassource = otherdb
5063 .toArray(new DbSourceProxy[0]);
5065 DbSourceProxy src = otherdb.get(0);
5066 fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
5068 fetchr.addActionListener(new ActionListener()
5070 public void actionPerformed(ActionEvent e)
5072 new Thread(new Runnable()
5077 new jalview.ws.DBRefFetcher(alignPanel.av
5078 .getSequenceSelection(),
5079 alignPanel.alignFrame, dassource)
5080 .fetchDBRefs(false);
5086 fetchr.setToolTipText("<html>"
5087 + JvSwingUtils.wrapTooltip("Retrieve from all "
5088 + otherdb.size() + " sources in "
5089 + src.getDbSource() + "<br>First is :"
5090 + src.getDbName()) + "<html>");
5093 // and then build the rest of the individual menus
5094 ifetch = new JMenu("Sources from " + src.getDbSource());
5096 String imname = null;
5098 for (DbSourceProxy sproxy : otherdb)
5100 String dbname = sproxy.getDbName();
5101 String sname = dbname.length() > 5 ? dbname.substring(0,
5102 5) + "..." : dbname;
5103 String msname = dbname.length() > 10 ? dbname.substring(
5104 0, 10) + "..." : dbname;
5107 imname = "from '" + sname + "'";
5109 fetchr = new JMenuItem(msname);
5110 final DbSourceProxy[] dassrc =
5112 fetchr.addActionListener(new ActionListener()
5115 public void actionPerformed(ActionEvent e)
5117 new Thread(new Runnable()
5122 new jalview.ws.DBRefFetcher(alignPanel.av
5123 .getSequenceSelection(),
5124 alignPanel.alignFrame, dassrc)
5125 .fetchDBRefs(false);
5131 fetchr.setToolTipText("<html>"
5132 + JvSwingUtils.wrapTooltip("Retrieve from "
5133 + dbname) + "</html>");
5136 if (++icomp >= mcomp || i == (otherdb.size()))
5138 ifetch.setText(imname + " to '" + sname + "'");
5140 ifetch = new JMenu();
5148 if (comp >= mcomp || dbi >= (dbclasses.length))
5150 dfetch.setText(mname + " to '" + dbclass + "'");
5152 dfetch = new JMenu();
5165 * Left justify the whole alignment.
5167 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5169 AlignmentI al = viewport.getAlignment();
5171 viewport.firePropertyChange("alignment", null, al);
5175 * Right justify the whole alignment.
5177 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5179 AlignmentI al = viewport.getAlignment();
5181 viewport.firePropertyChange("alignment", null, al);
5184 public void setShowSeqFeatures(boolean b)
5186 showSeqFeatures.setSelected(true);
5187 viewport.setShowSequenceFeatures(true);
5194 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5195 * awt.event.ActionEvent)
5197 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5199 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5200 alignPanel.paintAlignment(true);
5207 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5210 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5212 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5213 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5221 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5222 * .event.ActionEvent)
5224 protected void showGroupConservation_actionPerformed(ActionEvent e)
5226 viewport.setShowGroupConservation(showGroupConservation.getState());
5227 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5234 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5235 * .event.ActionEvent)
5237 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5239 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5240 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5247 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5248 * .event.ActionEvent)
5250 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5252 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5253 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5256 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5258 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5259 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5262 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5264 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5271 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5272 * .event.ActionEvent)
5274 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5276 if (viewport.getSelectionGroup() != null)
5278 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
5279 viewport.getSequenceSelection(),
5280 viewport.getAlignmentView(true).getSequenceStrings(
5281 viewport.getGapCharacter()), viewport.getAlignment()
5283 viewport.getAlignment().deleteAllGroups();
5284 viewport.sequenceColours = null;
5285 viewport.setSelectionGroup(null);
5286 // set view properties for each group
5287 for (int g = 0; g < gps.length; g++)
5289 gps[g].setShowNonconserved(viewport.getShowUnconserved());
5290 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
5291 viewport.getAlignment().addGroup(gps[g]);
5292 Color col = new Color((int) (Math.random() * 255),
5293 (int) (Math.random() * 255), (int) (Math.random() * 255));
5294 col = col.brighter();
5295 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
5296 .hasMoreElements(); viewport.setSequenceColour(
5297 (SequenceI) sq.nextElement(), col))
5300 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5301 alignPanel.updateAnnotation();
5302 alignPanel.paintAlignment(true);
5307 * make the given alignmentPanel the currently selected tab
5309 * @param alignmentPanel
5311 public void setDisplayedView(AlignmentPanel alignmentPanel)
5313 if (!viewport.getSequenceSetId().equals(
5314 alignmentPanel.av.getSequenceSetId()))
5317 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5319 if (tabbedPane != null
5320 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5321 .getSelectedIndex())
5323 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5328 class PrintThread extends Thread
5332 public PrintThread(AlignmentPanel ap)
5337 static PageFormat pf;
5341 PrinterJob printJob = PrinterJob.getPrinterJob();
5345 printJob.setPrintable(ap, pf);
5349 printJob.setPrintable(ap);
5352 if (printJob.printDialog())
5357 } catch (Exception PrintException)
5359 PrintException.printStackTrace();