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: work out how to recover feature settings for correct view(s) when
861 if (currentFileFormat.equals("Jalview"))
863 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
864 for (int i = 0; i < frames.length; i++)
866 if (frames[i] instanceof AlignFrame && frames[i] != this
867 && ((AlignFrame) frames[i]).fileName.equals(fileName))
871 frames[i].setSelected(true);
872 Desktop.instance.closeAssociatedWindows();
873 } catch (java.beans.PropertyVetoException ex)
879 Desktop.instance.closeAssociatedWindows();
881 FileLoader loader = new FileLoader();
882 String protocol = fileName.startsWith("http:") ? "URL" : "File";
883 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
887 Rectangle bounds = this.getBounds();
889 FileLoader loader = new FileLoader();
890 String protocol = fileName.startsWith("http:") ? "URL" : "File";
891 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
892 protocol, currentFileFormat);
894 newframe.setBounds(bounds);
895 if (featureSettings != null && featureSettings.isShowing())
897 final Rectangle fspos = featureSettings.frame.getBounds();
898 // TODO: need a 'show feature settings' function that takes bounds -
899 // need to refactor Desktop.addFrame
900 newframe.featureSettings_actionPerformed(null);
901 final FeatureSettings nfs = newframe.featureSettings;
902 SwingUtilities.invokeLater(new Runnable()
906 nfs.frame.setBounds(fspos);
909 this.featureSettings.close();
910 this.featureSettings = null;
912 this.closeMenuItem_actionPerformed(true);
917 public void addFromText_actionPerformed(ActionEvent e)
919 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
922 public void addFromURL_actionPerformed(ActionEvent e)
924 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
927 public void save_actionPerformed(ActionEvent e)
930 || (currentFileFormat == null || !jalview.io.FormatAdapter
931 .isValidIOFormat(currentFileFormat, true))
932 || fileName.startsWith("http"))
934 saveAs_actionPerformed(null);
938 saveAlignment(fileName, currentFileFormat);
948 public void saveAs_actionPerformed(ActionEvent e)
950 JalviewFileChooser chooser = new JalviewFileChooser(
951 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
952 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
953 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
954 currentFileFormat, false);
956 chooser.setFileView(new JalviewFileView());
957 chooser.setDialogTitle("Save Alignment to file");
958 chooser.setToolTipText("Save");
960 int value = chooser.showSaveDialog(this);
962 if (value == JalviewFileChooser.APPROVE_OPTION)
964 currentFileFormat = chooser.getSelectedFormat();
965 if (currentFileFormat == null)
967 JOptionPane.showInternalMessageDialog(Desktop.desktop,
968 "You must select a file format before saving!",
969 "File format not specified", JOptionPane.WARNING_MESSAGE);
970 value = chooser.showSaveDialog(this);
974 fileName = chooser.getSelectedFile().getPath();
976 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
979 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
980 if (currentFileFormat.indexOf(" ") > -1)
982 currentFileFormat = currentFileFormat.substring(0,
983 currentFileFormat.indexOf(" "));
985 saveAlignment(fileName, currentFileFormat);
989 public boolean saveAlignment(String file, String format)
991 boolean success = true;
993 if (format.equalsIgnoreCase("Jalview"))
995 String shortName = title;
997 if (shortName.indexOf(java.io.File.separatorChar) > -1)
999 shortName = shortName.substring(shortName
1000 .lastIndexOf(java.io.File.separatorChar) + 1);
1003 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1005 statusBar.setText("Successfully saved to file: " + fileName + " in "
1006 + format + " format.");
1011 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1013 warningMessage("Cannot save file " + fileName + " using format "
1014 + format, "Alignment output format not supported");
1015 saveAs_actionPerformed(null);
1016 // JBPNote need to have a raise_gui flag here
1020 String[] omitHidden = null;
1022 if (viewport.hasHiddenColumns())
1024 int reply = JOptionPane
1025 .showInternalConfirmDialog(
1027 "The Alignment contains hidden columns."
1028 + "\nDo you want to save only the visible alignment?",
1029 "Save / Omit Hidden Columns",
1030 JOptionPane.YES_NO_OPTION,
1031 JOptionPane.QUESTION_MESSAGE);
1033 if (reply == JOptionPane.YES_OPTION)
1035 omitHidden = viewport.getViewAsString(false);
1038 FormatAdapter f = new FormatAdapter();
1039 String output = f.formatSequences(
1041 (Alignment) viewport.getAlignment(), // class cast exceptions will
1042 // occur in the distant future
1043 omitHidden, f.getCacheSuffixDefault(format),
1044 viewport.getColumnSelection());
1054 java.io.PrintWriter out = new java.io.PrintWriter(
1055 new java.io.FileWriter(file));
1059 this.setTitle(file);
1060 statusBar.setText("Successfully saved to file: " + fileName
1061 + " in " + format + " format.");
1062 } catch (Exception ex)
1065 ex.printStackTrace();
1072 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
1073 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
1079 private void warningMessage(String warning, String title)
1081 if (new jalview.util.Platform().isHeadless())
1083 System.err.println("Warning: " + title + "\nWarning: " + warning);
1088 JOptionPane.showInternalMessageDialog(this, warning, title,
1089 JOptionPane.WARNING_MESSAGE);
1100 protected void outputText_actionPerformed(ActionEvent e)
1102 String[] omitHidden = null;
1104 if (viewport.hasHiddenColumns())
1106 int reply = JOptionPane
1107 .showInternalConfirmDialog(
1109 "The Alignment contains hidden columns."
1110 + "\nDo you want to output only the visible alignment?",
1111 "Save / Omit Hidden Columns",
1112 JOptionPane.YES_NO_OPTION,
1113 JOptionPane.QUESTION_MESSAGE);
1115 if (reply == JOptionPane.YES_OPTION)
1117 omitHidden = viewport.getViewAsString(false);
1121 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1122 cap.setForInput(null);
1126 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1127 viewport.getAlignment(), omitHidden,
1128 viewport.getColumnSelection()));
1129 Desktop.addInternalFrame(cap,
1130 "Alignment output - " + e.getActionCommand(), 600, 500);
1131 } catch (OutOfMemoryError oom)
1133 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1145 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1147 new HTMLOutput(alignPanel,
1148 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1149 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1152 public void createImageMap(File file, String image)
1154 alignPanel.makePNGImageMap(file, image);
1163 public void createPNG(File f)
1165 alignPanel.makePNG(f);
1174 public void createEPS(File f)
1176 alignPanel.makeEPS(f);
1179 public void pageSetup_actionPerformed(ActionEvent e)
1181 PrinterJob printJob = PrinterJob.getPrinterJob();
1182 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1191 public void printMenuItem_actionPerformed(ActionEvent e)
1193 // Putting in a thread avoids Swing painting problems
1194 PrintThread thread = new PrintThread(alignPanel);
1198 public void exportFeatures_actionPerformed(ActionEvent e)
1200 new AnnotationExporter().exportFeatures(alignPanel);
1203 public void exportAnnotations_actionPerformed(ActionEvent e)
1205 new AnnotationExporter().exportAnnotations(alignPanel,
1206 viewport.showAnnotation ? viewport.getAlignment()
1207 .getAlignmentAnnotation() : null, viewport
1208 .getAlignment().getGroups(), ((Alignment) viewport
1209 .getAlignment()).alignmentProperties);
1212 public void associatedData_actionPerformed(ActionEvent e)
1214 // Pick the tree file
1215 JalviewFileChooser chooser = new JalviewFileChooser(
1216 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1217 chooser.setFileView(new JalviewFileView());
1218 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1219 chooser.setToolTipText("Load Jalview Annotations / Features file");
1221 int value = chooser.showOpenDialog(null);
1223 if (value == JalviewFileChooser.APPROVE_OPTION)
1225 String choice = chooser.getSelectedFile().getPath();
1226 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1227 loadJalviewDataFile(choice, null, null, null);
1233 * Close the current view or all views in the alignment frame. If the frame
1234 * only contains one view then the alignment will be removed from memory.
1236 * @param closeAllTabs
1238 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1240 if (alignPanels != null && alignPanels.size() < 2)
1242 closeAllTabs = true;
1247 if (alignPanels != null)
1251 if (this.isClosed())
1253 // really close all the windows - otherwise wait till
1254 // setClosed(true) is called
1255 for (int i = 0; i < alignPanels.size(); i++)
1257 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1264 closeView(alignPanel);
1270 this.setClosed(true);
1272 } catch (Exception ex)
1274 ex.printStackTrace();
1279 * close alignPanel2 and shuffle tabs appropriately.
1281 * @param alignPanel2
1283 public void closeView(AlignmentPanel alignPanel2)
1285 int index = tabbedPane.getSelectedIndex();
1286 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1287 alignPanels.removeElement(alignPanel2);
1289 // if (viewport == alignPanel2.av)
1293 alignPanel2.closePanel();
1296 tabbedPane.removeTabAt(closedindex);
1297 tabbedPane.validate();
1299 if (index > closedindex || index == tabbedPane.getTabCount())
1301 // modify currently selected tab index if necessary.
1305 this.tabSelectionChanged(index);
1311 void updateEditMenuBar()
1314 if (viewport.historyList.size() > 0)
1316 undoMenuItem.setEnabled(true);
1317 CommandI command = (CommandI) viewport.historyList.peek();
1318 undoMenuItem.setText("Undo " + command.getDescription());
1322 undoMenuItem.setEnabled(false);
1323 undoMenuItem.setText("Undo");
1326 if (viewport.redoList.size() > 0)
1328 redoMenuItem.setEnabled(true);
1330 CommandI command = (CommandI) viewport.redoList.peek();
1331 redoMenuItem.setText("Redo " + command.getDescription());
1335 redoMenuItem.setEnabled(false);
1336 redoMenuItem.setText("Redo");
1340 public void addHistoryItem(CommandI command)
1342 if (command.getSize() > 0)
1344 viewport.historyList.push(command);
1345 viewport.redoList.clear();
1346 updateEditMenuBar();
1347 viewport.updateHiddenColumns();
1348 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1349 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1350 // viewport.getColumnSelection()
1351 // .getHiddenColumns().size() > 0);
1357 * @return alignment objects for all views
1359 AlignmentI[] getViewAlignments()
1361 if (alignPanels != null)
1363 Enumeration e = alignPanels.elements();
1364 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1365 for (int i = 0; e.hasMoreElements(); i++)
1367 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1371 if (viewport != null)
1373 return new AlignmentI[]
1374 { viewport.getAlignment() };
1385 protected void undoMenuItem_actionPerformed(ActionEvent e)
1387 if (viewport.historyList.empty())
1389 CommandI command = (CommandI) viewport.historyList.pop();
1390 viewport.redoList.push(command);
1391 command.undoCommand(getViewAlignments());
1393 AlignViewport originalSource = getOriginatingSource(command);
1394 updateEditMenuBar();
1396 if (originalSource != null)
1398 if (originalSource != viewport)
1401 .warn("Implementation worry: mismatch of viewport origin for undo");
1403 originalSource.updateHiddenColumns();
1404 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1406 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1407 // viewport.getColumnSelection()
1408 // .getHiddenColumns().size() > 0);
1409 originalSource.firePropertyChange("alignment", null, originalSource
1410 .getAlignment().getSequences());
1420 protected void redoMenuItem_actionPerformed(ActionEvent e)
1422 if (viewport.redoList.size() < 1)
1427 CommandI command = (CommandI) viewport.redoList.pop();
1428 viewport.historyList.push(command);
1429 command.doCommand(getViewAlignments());
1431 AlignViewport originalSource = getOriginatingSource(command);
1432 updateEditMenuBar();
1434 if (originalSource != null)
1437 if (originalSource != viewport)
1440 .warn("Implementation worry: mismatch of viewport origin for redo");
1442 originalSource.updateHiddenColumns();
1443 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1445 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1446 // viewport.getColumnSelection()
1447 // .getHiddenColumns().size() > 0);
1448 originalSource.firePropertyChange("alignment", null, originalSource
1449 .getAlignment().getSequences());
1453 AlignViewport getOriginatingSource(CommandI command)
1455 AlignViewport originalSource = null;
1456 // For sequence removal and addition, we need to fire
1457 // the property change event FROM the viewport where the
1458 // original alignment was altered
1459 AlignmentI al = null;
1460 if (command instanceof EditCommand)
1462 EditCommand editCommand = (EditCommand) command;
1463 al = editCommand.getAlignment();
1464 Vector comps = (Vector) PaintRefresher.components.get(viewport
1465 .getSequenceSetId());
1467 for (int i = 0; i < comps.size(); i++)
1469 if (comps.elementAt(i) instanceof AlignmentPanel)
1471 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1473 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1480 if (originalSource == null)
1482 // The original view is closed, we must validate
1483 // the current view against the closed view first
1486 PaintRefresher.validateSequences(al, viewport.getAlignment());
1489 originalSource = viewport;
1492 return originalSource;
1501 public void moveSelectedSequences(boolean up)
1503 SequenceGroup sg = viewport.getSelectionGroup();
1512 for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
1514 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
1516 if (!sg.getSequences(null).contains(seq))
1521 SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
1523 if (sg.getSequences(null).contains(temp))
1528 viewport.getAlignment().getSequences().setElementAt(temp, i);
1529 viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
1534 for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
1536 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
1538 if (!sg.getSequences(null).contains(seq))
1543 SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
1545 if (sg.getSequences(null).contains(temp))
1550 viewport.getAlignment().getSequences().setElementAt(temp, i);
1551 viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
1555 alignPanel.paintAlignment(true);
1558 synchronized void slideSequences(boolean right, int size)
1560 Vector sg = new Vector();
1561 if (viewport.cursorMode)
1563 sg.addElement(viewport.getAlignment().getSequenceAt(
1564 alignPanel.seqPanel.seqCanvas.cursorY));
1566 else if (viewport.getSelectionGroup() != null
1567 && viewport.getSelectionGroup().getSize() != viewport
1568 .getAlignment().getHeight())
1570 sg = viewport.getSelectionGroup().getSequences(
1571 viewport.getHiddenRepSequences());
1579 Vector invertGroup = new Vector();
1581 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1583 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1584 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1587 SequenceI[] seqs1 = new SequenceI[sg.size()];
1588 for (int i = 0; i < sg.size(); i++)
1589 seqs1[i] = (SequenceI) sg.elementAt(i);
1591 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1592 for (int i = 0; i < invertGroup.size(); i++)
1593 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1595 SlideSequencesCommand ssc;
1597 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1598 size, viewport.getGapCharacter());
1600 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1601 size, viewport.getGapCharacter());
1603 int groupAdjustment = 0;
1604 if (ssc.getGapsInsertedBegin() && right)
1606 if (viewport.cursorMode)
1607 alignPanel.seqPanel.moveCursor(size, 0);
1609 groupAdjustment = size;
1611 else if (!ssc.getGapsInsertedBegin() && !right)
1613 if (viewport.cursorMode)
1614 alignPanel.seqPanel.moveCursor(-size, 0);
1616 groupAdjustment = -size;
1619 if (groupAdjustment != 0)
1621 viewport.getSelectionGroup().setStartRes(
1622 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1623 viewport.getSelectionGroup().setEndRes(
1624 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1627 boolean appendHistoryItem = false;
1628 if (viewport.historyList != null && viewport.historyList.size() > 0
1629 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1631 appendHistoryItem = ssc
1632 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1636 if (!appendHistoryItem)
1637 addHistoryItem(ssc);
1648 protected void copy_actionPerformed(ActionEvent e)
1651 if (viewport.getSelectionGroup() == null)
1655 // TODO: preserve the ordering of displayed alignment annotation in any
1656 // internal paste (particularly sequence associated annotation)
1657 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1658 String[] omitHidden = null;
1660 if (viewport.hasHiddenColumns())
1662 omitHidden = viewport.getViewAsString(true);
1665 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1668 StringSelection ss = new StringSelection(output);
1672 jalview.gui.Desktop.internalCopy = true;
1673 // Its really worth setting the clipboard contents
1674 // to empty before setting the large StringSelection!!
1675 Toolkit.getDefaultToolkit().getSystemClipboard()
1676 .setContents(new StringSelection(""), null);
1678 Toolkit.getDefaultToolkit().getSystemClipboard()
1679 .setContents(ss, Desktop.instance);
1680 } catch (OutOfMemoryError er)
1682 new OOMWarning("copying region", er);
1686 Vector hiddenColumns = null;
1687 if (viewport.hasHiddenColumns())
1689 hiddenColumns = new Vector();
1690 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1691 .getSelectionGroup().getEndRes();
1692 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1695 int[] region = (int[]) viewport.getColumnSelection()
1696 .getHiddenColumns().elementAt(i);
1697 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1699 hiddenColumns.addElement(new int[]
1700 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1705 Desktop.jalviewClipboard = new Object[]
1706 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1707 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1716 protected void pasteNew_actionPerformed(ActionEvent e)
1727 protected void pasteThis_actionPerformed(ActionEvent e)
1733 * Paste contents of Jalview clipboard
1735 * @param newAlignment
1736 * true to paste to a new alignment, otherwise add to this.
1738 void paste(boolean newAlignment)
1740 boolean externalPaste = true;
1743 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1744 Transferable contents = c.getContents(this);
1746 if (contents == null)
1754 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1755 if (str.length() < 1)
1760 format = new IdentifyFile().Identify(str, "Paste");
1762 } catch (OutOfMemoryError er)
1764 new OOMWarning("Out of memory pasting sequences!!", er);
1768 SequenceI[] sequences;
1769 boolean annotationAdded = false;
1770 AlignmentI alignment = null;
1772 if (Desktop.jalviewClipboard != null)
1774 // The clipboard was filled from within Jalview, we must use the
1776 // And dataset from the copied alignment
1777 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1778 // be doubly sure that we create *new* sequence objects.
1779 sequences = new SequenceI[newseq.length];
1780 for (int i = 0; i < newseq.length; i++)
1782 sequences[i] = new Sequence(newseq[i]);
1784 alignment = new Alignment(sequences);
1785 externalPaste = false;
1789 // parse the clipboard as an alignment.
1790 alignment = new FormatAdapter().readFile(str, "Paste", format);
1791 sequences = alignment.getSequencesArray();
1799 if (Desktop.jalviewClipboard != null)
1801 // dataset is inherited
1802 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1806 // new dataset is constructed
1807 alignment.setDataset(null);
1809 alwidth = alignment.getWidth() + 1;
1813 AlignmentI pastedal = alignment; // preserve pasted alignment object
1814 // Add pasted sequences and dataset into existing alignment.
1815 alignment = viewport.getAlignment();
1816 alwidth = alignment.getWidth() + 1;
1817 // decide if we need to import sequences from an existing dataset
1818 boolean importDs = Desktop.jalviewClipboard != null
1819 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1820 // importDs==true instructs us to copy over new dataset sequences from
1821 // an existing alignment
1822 Vector newDs = (importDs) ? new Vector() : null; // used to create
1823 // minimum dataset set
1825 for (int i = 0; i < sequences.length; i++)
1829 newDs.addElement(null);
1831 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1833 if (importDs && ds != null)
1835 if (!newDs.contains(ds))
1837 newDs.setElementAt(ds, i);
1838 ds = new Sequence(ds);
1839 // update with new dataset sequence
1840 sequences[i].setDatasetSequence(ds);
1844 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1849 // copy and derive new dataset sequence
1850 sequences[i] = sequences[i].deriveSequence();
1851 alignment.getDataset().addSequence(
1852 sequences[i].getDatasetSequence());
1853 // TODO: avoid creation of duplicate dataset sequences with a
1854 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1856 alignment.addSequence(sequences[i]); // merges dataset
1860 newDs.clear(); // tidy up
1862 if (pastedal.getAlignmentAnnotation() != null)
1864 // Add any annotation attached to alignment.
1865 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1866 for (int i = 0; i < alann.length; i++)
1868 annotationAdded = true;
1869 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1871 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1872 newann.padAnnotation(alwidth);
1873 alignment.addAnnotation(newann);
1883 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1884 sequences, 0, alignment.getWidth(), alignment));
1886 // Add any annotations attached to sequences
1887 for (int i = 0; i < sequences.length; i++)
1889 if (sequences[i].getAnnotation() != null)
1891 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1893 annotationAdded = true;
1894 sequences[i].getAnnotation()[a].adjustForAlignment();
1895 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1896 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1901 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1908 // propagate alignment changed.
1909 viewport.setEndSeq(alignment.getHeight());
1910 if (annotationAdded)
1912 // Duplicate sequence annotation in all views.
1913 AlignmentI[] alview = this.getViewAlignments();
1914 for (int i = 0; i < sequences.length; i++)
1916 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1919 for (int avnum = 0; avnum < alview.length; avnum++)
1921 if (alview[avnum] != alignment)
1923 // duplicate in a view other than the one with input focus
1924 int avwidth = alview[avnum].getWidth() + 1;
1925 // this relies on sann being preserved after we
1926 // modify the sequence's annotation array for each duplication
1927 for (int a = 0; a < sann.length; a++)
1929 AlignmentAnnotation newann = new AlignmentAnnotation(
1931 sequences[i].addAlignmentAnnotation(newann);
1932 newann.padAnnotation(avwidth);
1933 alview[avnum].addAnnotation(newann); // annotation was
1934 // duplicated earlier
1935 alview[avnum].setAnnotationIndex(newann, a);
1940 buildSortByAnnotationScoresMenu();
1942 viewport.firePropertyChange("alignment", null,
1943 alignment.getSequences());
1948 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1950 String newtitle = new String("Copied sequences");
1952 if (Desktop.jalviewClipboard != null
1953 && Desktop.jalviewClipboard[2] != null)
1955 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1956 for (int i = 0; i < hc.size(); i++)
1958 int[] region = (int[]) hc.elementAt(i);
1959 af.viewport.hideColumns(region[0], region[1]);
1963 // >>>This is a fix for the moment, until a better solution is
1965 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1967 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1969 // TODO: maintain provenance of an alignment, rather than just make the
1970 // title a concatenation of operations.
1973 if (title.startsWith("Copied sequences"))
1979 newtitle = newtitle.concat("- from " + title);
1984 newtitle = new String("Pasted sequences");
1987 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1992 } catch (Exception ex)
1994 ex.printStackTrace();
1995 System.out.println("Exception whilst pasting: " + ex);
1996 // could be anything being pasted in here
2007 protected void cut_actionPerformed(ActionEvent e)
2009 copy_actionPerformed(null);
2010 delete_actionPerformed(null);
2019 protected void delete_actionPerformed(ActionEvent evt)
2022 SequenceGroup sg = viewport.getSelectionGroup();
2028 Vector seqs = new Vector();
2030 for (int i = 0; i < sg.getSize(); i++)
2032 seq = sg.getSequenceAt(i);
2033 seqs.addElement(seq);
2036 // If the cut affects all sequences, remove highlighted columns
2037 if (sg.getSize() == viewport.getAlignment().getHeight())
2039 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2040 sg.getEndRes() + 1);
2043 SequenceI[] cut = new SequenceI[seqs.size()];
2044 for (int i = 0; i < seqs.size(); i++)
2046 cut[i] = (SequenceI) seqs.elementAt(i);
2050 * //ADD HISTORY ITEM
2052 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2053 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2054 viewport.getAlignment()));
2056 viewport.setSelectionGroup(null);
2057 viewport.sendSelection();
2058 viewport.getAlignment().deleteGroup(sg);
2060 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2062 if (viewport.getAlignment().getHeight() < 1)
2066 this.setClosed(true);
2067 } catch (Exception ex)
2079 protected void deleteGroups_actionPerformed(ActionEvent e)
2081 viewport.getAlignment().deleteAllGroups();
2082 viewport.sequenceColours = null;
2083 viewport.setSelectionGroup(null);
2084 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2085 alignPanel.updateAnnotation();
2086 alignPanel.paintAlignment(true);
2095 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2097 SequenceGroup sg = new SequenceGroup();
2099 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2101 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2104 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2105 viewport.setSelectionGroup(sg);
2106 viewport.sendSelection();
2107 alignPanel.paintAlignment(true);
2108 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2117 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2119 if (viewport.cursorMode)
2121 alignPanel.seqPanel.keyboardNo1 = null;
2122 alignPanel.seqPanel.keyboardNo2 = null;
2124 viewport.setSelectionGroup(null);
2125 viewport.getColumnSelection().clear();
2126 viewport.setSelectionGroup(null);
2127 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2128 alignPanel.idPanel.idCanvas.searchResults = null;
2129 alignPanel.paintAlignment(true);
2130 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2131 viewport.sendSelection();
2140 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2142 SequenceGroup sg = viewport.getSelectionGroup();
2146 selectAllSequenceMenuItem_actionPerformed(null);
2151 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2153 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2156 alignPanel.paintAlignment(true);
2157 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2158 viewport.sendSelection();
2161 public void invertColSel_actionPerformed(ActionEvent e)
2163 viewport.invertColumnSelection();
2164 alignPanel.paintAlignment(true);
2165 viewport.sendSelection();
2174 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2176 trimAlignment(true);
2185 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2187 trimAlignment(false);
2190 void trimAlignment(boolean trimLeft)
2192 ColumnSelection colSel = viewport.getColumnSelection();
2195 if (colSel.size() > 0)
2199 column = colSel.getMin();
2203 column = colSel.getMax();
2207 if (viewport.getSelectionGroup() != null)
2209 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2210 viewport.getHiddenRepSequences());
2214 seqs = viewport.getAlignment().getSequencesArray();
2217 TrimRegionCommand trimRegion;
2220 trimRegion = new TrimRegionCommand("Remove Left",
2221 TrimRegionCommand.TRIM_LEFT, seqs, column,
2222 viewport.getAlignment(), viewport.getColumnSelection(),
2223 viewport.getSelectionGroup());
2224 viewport.setStartRes(0);
2228 trimRegion = new TrimRegionCommand("Remove Right",
2229 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2230 viewport.getAlignment(), viewport.getColumnSelection(),
2231 viewport.getSelectionGroup());
2234 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2236 addHistoryItem(trimRegion);
2238 Vector groups = viewport.getAlignment().getGroups();
2240 for (int i = 0; i < groups.size(); i++)
2242 SequenceGroup sg = (SequenceGroup) groups.get(i);
2244 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2245 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2247 viewport.getAlignment().deleteGroup(sg);
2251 viewport.firePropertyChange("alignment", null, viewport
2252 .getAlignment().getSequences());
2262 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2264 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2267 if (viewport.getSelectionGroup() != null)
2269 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2270 viewport.getHiddenRepSequences());
2271 start = viewport.getSelectionGroup().getStartRes();
2272 end = viewport.getSelectionGroup().getEndRes();
2276 seqs = viewport.getAlignment().getSequencesArray();
2279 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2280 "Remove Gapped Columns", seqs, start, end,
2281 viewport.getAlignment());
2283 addHistoryItem(removeGapCols);
2285 statusBar.setText("Removed " + removeGapCols.getSize()
2286 + " empty columns.");
2288 // This is to maintain viewport position on first residue
2289 // of first sequence
2290 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2291 int startRes = seq.findPosition(viewport.startRes);
2292 // ShiftList shifts;
2293 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2294 // edit.alColumnChanges=shifts.getInverse();
2295 // if (viewport.hasHiddenColumns)
2296 // viewport.getColumnSelection().compensateForEdits(shifts);
2297 viewport.setStartRes(seq.findIndex(startRes) - 1);
2298 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2309 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2311 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2314 if (viewport.getSelectionGroup() != null)
2316 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2317 viewport.getHiddenRepSequences());
2318 start = viewport.getSelectionGroup().getStartRes();
2319 end = viewport.getSelectionGroup().getEndRes();
2323 seqs = viewport.getAlignment().getSequencesArray();
2326 // This is to maintain viewport position on first residue
2327 // of first sequence
2328 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2329 int startRes = seq.findPosition(viewport.startRes);
2331 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2332 viewport.getAlignment()));
2334 viewport.setStartRes(seq.findIndex(startRes) - 1);
2336 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2347 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2349 viewport.setPadGaps(padGapsMenuitem.isSelected());
2350 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2356 // if (justifySeqs>0)
2358 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2370 public void findMenuItem_actionPerformed(ActionEvent e)
2375 public void newView_actionPerformed(ActionEvent e)
2382 * @param copyAnnotation
2383 * if true then duplicate all annnotation, groups and settings
2384 * @return new alignment panel, already displayed.
2386 public AlignmentPanel newView(boolean copyAnnotation)
2388 return newView(null, copyAnnotation);
2394 * title of newly created view
2395 * @return new alignment panel, already displayed.
2397 public AlignmentPanel newView(String viewTitle)
2399 return newView(viewTitle, true);
2405 * title of newly created view
2406 * @param copyAnnotation
2407 * if true then duplicate all annnotation, groups and settings
2408 * @return new alignment panel, already displayed.
2410 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2412 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2414 if (!copyAnnotation)
2416 // just remove all the current annotation except for the automatic stuff
2417 newap.av.getAlignment().deleteAllGroups();
2418 for (AlignmentAnnotation alan : newap.av.getAlignment()
2419 .getAlignmentAnnotation())
2421 if (!alan.autoCalculated)
2423 newap.av.getAlignment().deleteAnnotation(alan);
2429 newap.av.gatherViewsHere = false;
2431 if (viewport.viewName == null)
2433 viewport.viewName = "Original";
2436 newap.av.historyList = viewport.historyList;
2437 newap.av.redoList = viewport.redoList;
2439 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2440 // make sure the new view has a unique name - this is essential for Jalview
2442 boolean addFirstIndex = false;
2443 if (viewTitle == null || viewTitle.trim().length() == 0)
2446 addFirstIndex = true;
2450 index = 1;// we count from 1 if given a specific name
2452 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2453 Vector comps = (Vector) PaintRefresher.components.get(viewport
2454 .getSequenceSetId());
2455 Vector existingNames = new Vector();
2456 for (int i = 0; i < comps.size(); i++)
2458 if (comps.elementAt(i) instanceof AlignmentPanel)
2460 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2461 if (!existingNames.contains(ap.av.viewName))
2463 existingNames.addElement(ap.av.viewName);
2468 while (existingNames.contains(newViewName))
2470 newViewName = viewTitle + " " + (++index);
2473 newap.av.viewName = newViewName;
2475 addAlignmentPanel(newap, true);
2477 if (alignPanels.size() == 2)
2479 viewport.gatherViewsHere = true;
2481 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2485 public void expandViews_actionPerformed(ActionEvent e)
2487 Desktop.instance.explodeViews(this);
2490 public void gatherViews_actionPerformed(ActionEvent e)
2492 Desktop.instance.gatherViews(this);
2501 public void font_actionPerformed(ActionEvent e)
2503 new FontChooser(alignPanel);
2512 protected void seqLimit_actionPerformed(ActionEvent e)
2514 viewport.setShowJVSuffix(seqLimits.isSelected());
2516 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2517 .calculateIdWidth());
2518 alignPanel.paintAlignment(true);
2521 public void idRightAlign_actionPerformed(ActionEvent e)
2523 viewport.rightAlignIds = idRightAlign.isSelected();
2524 alignPanel.paintAlignment(true);
2527 public void centreColumnLabels_actionPerformed(ActionEvent e)
2529 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2530 alignPanel.paintAlignment(true);
2536 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2538 protected void followHighlight_actionPerformed()
2540 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2542 alignPanel.scrollToPosition(
2543 alignPanel.seqPanel.seqCanvas.searchResults, false);
2553 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2555 viewport.setColourText(colourTextMenuItem.isSelected());
2556 alignPanel.paintAlignment(true);
2565 public void wrapMenuItem_actionPerformed(ActionEvent e)
2567 scaleAbove.setVisible(wrapMenuItem.isSelected());
2568 scaleLeft.setVisible(wrapMenuItem.isSelected());
2569 scaleRight.setVisible(wrapMenuItem.isSelected());
2570 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2571 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2574 public void showAllSeqs_actionPerformed(ActionEvent e)
2576 viewport.showAllHiddenSeqs();
2579 public void showAllColumns_actionPerformed(ActionEvent e)
2581 viewport.showAllHiddenColumns();
2585 public void hideSelSequences_actionPerformed(ActionEvent e)
2587 viewport.hideAllSelectedSeqs();
2588 alignPanel.paintAlignment(true);
2592 * called by key handler and the hide all/show all menu items
2597 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2600 boolean hide = false;
2601 SequenceGroup sg = viewport.getSelectionGroup();
2602 if (!toggleSeqs && !toggleCols)
2604 // Hide everything by the current selection - this is a hack - we do the
2605 // invert and then hide
2606 // first check that there will be visible columns after the invert.
2607 if ((viewport.getColumnSelection() != null
2608 && viewport.getColumnSelection().getSelected() != null && viewport
2609 .getColumnSelection().getSelected().size() > 0)
2610 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2613 // now invert the sequence set, if required - empty selection implies
2614 // that no hiding is required.
2617 invertSequenceMenuItem_actionPerformed(null);
2618 sg = viewport.getSelectionGroup();
2622 viewport.expandColSelection(sg, true);
2623 // finally invert the column selection and get the new sequence
2625 invertColSel_actionPerformed(null);
2632 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2634 hideSelSequences_actionPerformed(null);
2637 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2640 showAllSeqs_actionPerformed(null);
2646 if (viewport.getColumnSelection().getSelected().size() > 0)
2648 hideSelColumns_actionPerformed(null);
2651 viewport.setSelectionGroup(sg);
2656 showAllColumns_actionPerformed(null);
2665 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2666 * event.ActionEvent)
2668 public void hideAllButSelection_actionPerformed(ActionEvent e)
2670 toggleHiddenRegions(false, false);
2677 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2680 public void hideAllSelection_actionPerformed(ActionEvent e)
2682 SequenceGroup sg = viewport.getSelectionGroup();
2683 viewport.expandColSelection(sg, false);
2684 viewport.hideAllSelectedSeqs();
2685 viewport.hideSelectedColumns();
2686 alignPanel.paintAlignment(true);
2693 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2696 public void showAllhidden_actionPerformed(ActionEvent e)
2698 viewport.showAllHiddenColumns();
2699 viewport.showAllHiddenSeqs();
2700 alignPanel.paintAlignment(true);
2703 public void hideSelColumns_actionPerformed(ActionEvent e)
2705 viewport.hideSelectedColumns();
2706 alignPanel.paintAlignment(true);
2709 public void hiddenMarkers_actionPerformed(ActionEvent e)
2711 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2721 protected void scaleAbove_actionPerformed(ActionEvent e)
2723 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2724 alignPanel.paintAlignment(true);
2733 protected void scaleLeft_actionPerformed(ActionEvent e)
2735 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2736 alignPanel.paintAlignment(true);
2745 protected void scaleRight_actionPerformed(ActionEvent e)
2747 viewport.setScaleRightWrapped(scaleRight.isSelected());
2748 alignPanel.paintAlignment(true);
2757 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2759 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2760 alignPanel.paintAlignment(true);
2769 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2771 viewport.setShowText(viewTextMenuItem.isSelected());
2772 alignPanel.paintAlignment(true);
2781 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2783 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2784 alignPanel.paintAlignment(true);
2787 public FeatureSettings featureSettings;
2789 public void featureSettings_actionPerformed(ActionEvent e)
2791 if (featureSettings != null)
2793 featureSettings.close();
2794 featureSettings = null;
2796 if (!showSeqFeatures.isSelected())
2798 // make sure features are actually displayed
2799 showSeqFeatures.setSelected(true);
2800 showSeqFeatures_actionPerformed(null);
2802 featureSettings = new FeatureSettings(this);
2806 * Set or clear 'Show Sequence Features'
2811 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2813 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2814 alignPanel.paintAlignment(true);
2815 if (alignPanel.getOverviewPanel() != null)
2817 alignPanel.getOverviewPanel().updateOverviewImage();
2822 * Set or clear 'Show Sequence Features'
2827 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2829 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2831 if (viewport.getShowSequenceFeaturesHeight())
2833 // ensure we're actually displaying features
2834 viewport.setShowSequenceFeatures(true);
2835 showSeqFeatures.setSelected(true);
2837 alignPanel.paintAlignment(true);
2838 if (alignPanel.getOverviewPanel() != null)
2840 alignPanel.getOverviewPanel().updateOverviewImage();
2850 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2852 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2853 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2856 public void alignmentProperties()
2858 JEditorPane editPane = new JEditorPane("text/html", "");
2859 editPane.setEditable(false);
2860 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
2862 editPane.setText("<html>" + contents.toString() + "</html>");
2863 JInternalFrame frame = new JInternalFrame();
2864 frame.getContentPane().add(new JScrollPane(editPane));
2866 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2867 + getTitle(), 500, 400);
2876 public void overviewMenuItem_actionPerformed(ActionEvent e)
2878 if (alignPanel.overviewPanel != null)
2883 JInternalFrame frame = new JInternalFrame();
2884 OverviewPanel overview = new OverviewPanel(alignPanel);
2885 frame.setContentPane(overview);
2886 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2887 frame.getWidth(), frame.getHeight());
2889 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2890 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2892 public void internalFrameClosed(
2893 javax.swing.event.InternalFrameEvent evt)
2895 alignPanel.setOverviewPanel(null);
2899 alignPanel.setOverviewPanel(overview);
2902 public void textColour_actionPerformed(ActionEvent e)
2904 new TextColourChooser().chooseColour(alignPanel, null);
2913 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2924 public void clustalColour_actionPerformed(ActionEvent e)
2926 changeColour(new ClustalxColourScheme(viewport.getAlignment()
2927 .getSequences(), viewport.getAlignment().getWidth()));
2936 public void zappoColour_actionPerformed(ActionEvent e)
2938 changeColour(new ZappoColourScheme());
2947 public void taylorColour_actionPerformed(ActionEvent e)
2949 changeColour(new TaylorColourScheme());
2958 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2960 changeColour(new HydrophobicColourScheme());
2969 public void helixColour_actionPerformed(ActionEvent e)
2971 changeColour(new HelixColourScheme());
2980 public void strandColour_actionPerformed(ActionEvent e)
2982 changeColour(new StrandColourScheme());
2991 public void turnColour_actionPerformed(ActionEvent e)
2993 changeColour(new TurnColourScheme());
3002 public void buriedColour_actionPerformed(ActionEvent e)
3004 changeColour(new BuriedColourScheme());
3013 public void nucleotideColour_actionPerformed(ActionEvent e)
3015 changeColour(new NucleotideColourScheme());
3018 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3020 changeColour(new PurinePyrimidineColourScheme());
3024 * public void covariationColour_actionPerformed(ActionEvent e) {
3026 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3029 public void annotationColour_actionPerformed(ActionEvent e)
3031 new AnnotationColourChooser(viewport, alignPanel);
3034 public void rnahelicesColour_actionPerformed(ActionEvent e)
3036 new RNAHelicesColourChooser(viewport, alignPanel);
3045 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3047 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3056 public void changeColour(ColourSchemeI cs)
3058 // TODO: compare with applet and pull up to model method
3063 if (viewport.getAbovePIDThreshold())
3065 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3068 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3070 viewport.setGlobalColourScheme(cs);
3074 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3077 if (viewport.getConservationSelected())
3080 Alignment al = (Alignment) viewport.getAlignment();
3081 Conservation c = new Conservation("All",
3082 ResidueProperties.propHash, 3, al.getSequences(), 0,
3086 c.verdict(false, viewport.getConsPercGaps());
3088 cs.setConservation(c);
3090 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3095 cs.setConservation(null);
3098 cs.setConsensus(viewport.getSequenceConsensusHash());
3101 viewport.setGlobalColourScheme(cs);
3103 if (viewport.getColourAppliesToAllGroups())
3105 Vector groups = viewport.getAlignment().getGroups();
3107 for (int i = 0; i < groups.size(); i++)
3109 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
3117 if (cs instanceof ClustalxColourScheme)
3119 sg.cs = new ClustalxColourScheme(sg.getSequences(viewport
3120 .getHiddenRepSequences()), sg.getWidth());
3122 else if (cs instanceof UserColourScheme)
3124 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3130 sg.cs = cs.getClass().newInstance();
3131 } catch (Exception ex)
3136 if (viewport.getAbovePIDThreshold()
3137 || cs instanceof PIDColourScheme
3138 || cs instanceof Blosum62ColourScheme)
3140 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3142 sg.cs.setConsensus(AAFrequency.calculate(
3143 sg.getSequences(viewport.getHiddenRepSequences()),
3144 sg.getStartRes(), sg.getEndRes() + 1));
3148 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3151 if (viewport.getConservationSelected())
3153 Conservation c = new Conservation("Group",
3154 ResidueProperties.propHash, 3, sg.getSequences(viewport
3155 .getHiddenRepSequences()), sg.getStartRes(),
3156 sg.getEndRes() + 1);
3158 c.verdict(false, viewport.getConsPercGaps());
3159 sg.cs.setConservation(c);
3163 sg.cs.setConservation(null);
3168 if (alignPanel.getOverviewPanel() != null)
3170 alignPanel.getOverviewPanel().updateOverviewImage();
3173 alignPanel.paintAlignment(true);
3182 protected void modifyPID_actionPerformed(ActionEvent e)
3184 if (viewport.getAbovePIDThreshold()
3185 && viewport.getGlobalColourScheme() != null)
3187 SliderPanel.setPIDSliderSource(alignPanel,
3188 viewport.getGlobalColourScheme(), "Background");
3189 SliderPanel.showPIDSlider();
3199 protected void modifyConservation_actionPerformed(ActionEvent e)
3201 if (viewport.getConservationSelected()
3202 && viewport.getGlobalColourScheme() != null)
3204 SliderPanel.setConservationSlider(alignPanel,
3205 viewport.getGlobalColourScheme(), "Background");
3206 SliderPanel.showConservationSlider();
3216 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3218 viewport.setConservationSelected(conservationMenuItem.isSelected());
3220 viewport.setAbovePIDThreshold(false);
3221 abovePIDThreshold.setSelected(false);
3223 changeColour(viewport.getGlobalColourScheme());
3225 modifyConservation_actionPerformed(null);
3234 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3236 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3238 conservationMenuItem.setSelected(false);
3239 viewport.setConservationSelected(false);
3241 changeColour(viewport.getGlobalColourScheme());
3243 modifyPID_actionPerformed(null);
3252 public void userDefinedColour_actionPerformed(ActionEvent e)
3254 if (e.getActionCommand().equals("User Defined..."))
3256 new UserDefinedColours(alignPanel, null);
3260 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3261 .getUserColourSchemes().get(e.getActionCommand());
3267 public void updateUserColourMenu()
3270 Component[] menuItems = colourMenu.getMenuComponents();
3271 int i, iSize = menuItems.length;
3272 for (i = 0; i < iSize; i++)
3274 if (menuItems[i].getName() != null
3275 && menuItems[i].getName().equals("USER_DEFINED"))
3277 colourMenu.remove(menuItems[i]);
3281 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3283 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3284 .getUserColourSchemes().keys();
3286 while (userColours.hasMoreElements())
3288 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3289 userColours.nextElement().toString());
3290 radioItem.setName("USER_DEFINED");
3291 radioItem.addMouseListener(new MouseAdapter()
3293 public void mousePressed(MouseEvent evt)
3295 if (evt.isControlDown()
3296 || SwingUtilities.isRightMouseButton(evt))
3298 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3300 int option = JOptionPane.showInternalConfirmDialog(
3301 jalview.gui.Desktop.desktop,
3302 "Remove from default list?",
3303 "Remove user defined colour",
3304 JOptionPane.YES_NO_OPTION);
3305 if (option == JOptionPane.YES_OPTION)
3307 jalview.gui.UserDefinedColours
3308 .removeColourFromDefaults(radioItem.getText());
3309 colourMenu.remove(radioItem);
3313 radioItem.addActionListener(new ActionListener()
3315 public void actionPerformed(ActionEvent evt)
3317 userDefinedColour_actionPerformed(evt);
3324 radioItem.addActionListener(new ActionListener()
3326 public void actionPerformed(ActionEvent evt)
3328 userDefinedColour_actionPerformed(evt);
3332 colourMenu.insert(radioItem, 15);
3333 colours.add(radioItem);
3344 public void PIDColour_actionPerformed(ActionEvent e)
3346 changeColour(new PIDColourScheme());
3355 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3357 changeColour(new Blosum62ColourScheme());
3366 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3368 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3369 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3370 .getAlignment().getSequenceAt(0), null);
3371 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3372 viewport.getAlignment()));
3373 alignPanel.paintAlignment(true);
3382 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3384 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3385 AlignmentSorter.sortByID(viewport.getAlignment());
3386 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3387 viewport.getAlignment()));
3388 alignPanel.paintAlignment(true);
3397 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3399 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3400 AlignmentSorter.sortByLength(viewport.getAlignment());
3401 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3402 viewport.getAlignment()));
3403 alignPanel.paintAlignment(true);
3412 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3414 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3415 AlignmentSorter.sortByGroup(viewport.getAlignment());
3416 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3417 viewport.getAlignment()));
3419 alignPanel.paintAlignment(true);
3428 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3430 new RedundancyPanel(alignPanel, this);
3439 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3441 if ((viewport.getSelectionGroup() == null)
3442 || (viewport.getSelectionGroup().getSize() < 2))
3444 JOptionPane.showInternalMessageDialog(this,
3445 "You must select at least 2 sequences.", "Invalid Selection",
3446 JOptionPane.WARNING_MESSAGE);
3450 JInternalFrame frame = new JInternalFrame();
3451 frame.setContentPane(new PairwiseAlignPanel(viewport));
3452 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3462 public void PCAMenuItem_actionPerformed(ActionEvent e)
3464 if (((viewport.getSelectionGroup() != null)
3465 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3466 .getSelectionGroup().getSize() > 0))
3467 || (viewport.getAlignment().getHeight() < 4))
3469 JOptionPane.showInternalMessageDialog(this,
3470 "Principal component analysis must take\n"
3471 + "at least 4 input sequences.",
3472 "Sequence selection insufficient",
3473 JOptionPane.WARNING_MESSAGE);
3478 new PCAPanel(alignPanel);
3481 public void autoCalculate_actionPerformed(ActionEvent e)
3483 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3484 if (viewport.autoCalculateConsensus)
3486 viewport.firePropertyChange("alignment", null, viewport
3487 .getAlignment().getSequences());
3491 public void sortByTreeOption_actionPerformed(ActionEvent e)
3493 viewport.sortByTree = sortByTree.isSelected();
3497 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3499 viewport.followSelection = listenToViewSelections.isSelected();
3508 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3510 NewTreePanel("AV", "PID", "Average distance tree using PID");
3519 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3521 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3530 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3532 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3541 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3543 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3556 void NewTreePanel(String type, String pwType, String title)
3560 if (viewport.getSelectionGroup() != null)
3562 if (viewport.getSelectionGroup().getSize() < 3)
3567 "You need to have more than two sequences selected to build a tree!",
3568 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3573 SequenceGroup sg = viewport.getSelectionGroup();
3575 /* Decide if the selection is a column region */
3576 while (s < sg.getSize())
3578 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3584 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3585 + "Try using the Pad function in the edit menu,\n"
3586 + "or one of the multiple sequence alignment web services.",
3587 "Sequences in selection are not aligned",
3588 JOptionPane.WARNING_MESSAGE);
3594 title = title + " on region";
3595 tp = new TreePanel(alignPanel, type, pwType);
3599 // are the visible sequences aligned?
3600 if (!viewport.getAlignment().isAligned(false))
3605 "The sequences must be aligned before creating a tree.\n"
3606 + "Try using the Pad function in the edit menu,\n"
3607 + "or one of the multiple sequence alignment web services.",
3608 "Sequences not aligned",
3609 JOptionPane.WARNING_MESSAGE);
3614 if (viewport.getAlignment().getHeight() < 2)
3619 tp = new TreePanel(alignPanel, type, pwType);
3624 if (viewport.viewName != null)
3626 title += viewport.viewName + " of ";
3629 title += this.title;
3631 Desktop.addInternalFrame(tp, title, 600, 500);
3642 public void addSortByOrderMenuItem(String title,
3643 final AlignmentOrder order)
3645 final JMenuItem item = new JMenuItem("by " + title);
3647 item.addActionListener(new java.awt.event.ActionListener()
3649 public void actionPerformed(ActionEvent e)
3651 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3653 // TODO: JBPNote - have to map order entries to curent SequenceI
3655 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3657 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3660 alignPanel.paintAlignment(true);
3666 * Add a new sort by annotation score menu item
3669 * the menu to add the option to
3671 * the label used to retrieve scores for each sequence on the
3674 public void addSortByAnnotScoreMenuItem(JMenu sort,
3675 final String scoreLabel)
3677 final JMenuItem item = new JMenuItem(scoreLabel);
3679 item.addActionListener(new java.awt.event.ActionListener()
3681 public void actionPerformed(ActionEvent e)
3683 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3684 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3685 viewport.getAlignment());// ,viewport.getSelectionGroup());
3686 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3687 viewport.getAlignment()));
3688 alignPanel.paintAlignment(true);
3694 * last hash for alignment's annotation array - used to minimise cost of
3697 protected int _annotationScoreVectorHash;
3700 * search the alignment and rebuild the sort by annotation score submenu the
3701 * last alignment annotation vector hash is stored to minimize cost of
3702 * rebuilding in subsequence calls.
3705 public void buildSortByAnnotationScoresMenu()
3707 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3712 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3714 sortByAnnotScore.removeAll();
3715 // almost certainly a quicker way to do this - but we keep it simple
3716 Hashtable scoreSorts = new Hashtable();
3717 AlignmentAnnotation aann[];
3718 Enumeration sq = viewport.getAlignment().getSequences().elements();
3719 while (sq.hasMoreElements())
3721 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3722 for (int i = 0; aann != null && i < aann.length; i++)
3724 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3726 scoreSorts.put(aann[i].label, aann[i].label);
3730 Enumeration labels = scoreSorts.keys();
3731 while (labels.hasMoreElements())
3733 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3734 (String) labels.nextElement());
3736 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3739 _annotationScoreVectorHash = viewport.getAlignment()
3740 .getAlignmentAnnotation().hashCode();
3745 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3746 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3747 * call. Listeners are added to remove the menu item when the treePanel is
3748 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3752 * Displayed tree window.
3754 * SortBy menu item title.
3756 public void buildTreeMenu()
3758 sortByTreeMenu.removeAll();
3760 Vector comps = (Vector) PaintRefresher.components.get(viewport
3761 .getSequenceSetId());
3762 Vector treePanels = new Vector();
3763 int i, iSize = comps.size();
3764 for (i = 0; i < iSize; i++)
3766 if (comps.elementAt(i) instanceof TreePanel)
3768 treePanels.add(comps.elementAt(i));
3772 iSize = treePanels.size();
3776 sortByTreeMenu.setVisible(false);
3780 sortByTreeMenu.setVisible(true);
3782 for (i = 0; i < treePanels.size(); i++)
3784 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3785 final JMenuItem item = new JMenuItem(tp.getTitle());
3786 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3787 item.addActionListener(new java.awt.event.ActionListener()
3789 public void actionPerformed(ActionEvent e)
3791 tp.sortByTree_actionPerformed(null);
3792 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3797 sortByTreeMenu.add(item);
3801 public boolean sortBy(AlignmentOrder alorder, String undoname)
3803 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3804 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3805 if (undoname != null)
3807 addHistoryItem(new OrderCommand(undoname, oldOrder,
3808 viewport.getAlignment()));
3810 alignPanel.paintAlignment(true);
3815 * Work out whether the whole set of sequences or just the selected set will
3816 * be submitted for multiple alignment.
3819 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3821 // Now, check we have enough sequences
3822 AlignmentView msa = null;
3824 if ((viewport.getSelectionGroup() != null)
3825 && (viewport.getSelectionGroup().getSize() > 1))
3827 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3828 // some common interface!
3830 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3831 * SequenceI[sz = seqs.getSize(false)];
3833 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3834 * seqs.getSequenceAt(i); }
3836 msa = viewport.getAlignmentView(true);
3841 * Vector seqs = viewport.getAlignment().getSequences();
3843 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3845 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3846 * seqs.elementAt(i); } }
3848 msa = viewport.getAlignmentView(false);
3854 * Decides what is submitted to a secondary structure prediction service: the
3855 * first sequence in the alignment, or in the current selection, or, if the
3856 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3857 * region or the whole alignment. (where the first sequence in the set is the
3858 * one that the prediction will be for).
3860 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3862 AlignmentView seqs = null;
3864 if ((viewport.getSelectionGroup() != null)
3865 && (viewport.getSelectionGroup().getSize() > 0))
3867 seqs = viewport.getAlignmentView(true);
3871 seqs = viewport.getAlignmentView(false);
3873 // limit sequences - JBPNote in future - could spawn multiple prediction
3875 // TODO: viewport.getAlignment().isAligned is a global state - the local
3876 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3877 if (!viewport.getAlignment().isAligned(false))
3879 seqs.setSequences(new SeqCigar[]
3880 { seqs.getSequences()[0] });
3881 // TODO: if seqs.getSequences().length>1 then should really have warned
3894 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3896 // Pick the tree file
3897 JalviewFileChooser chooser = new JalviewFileChooser(
3898 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3899 chooser.setFileView(new JalviewFileView());
3900 chooser.setDialogTitle("Select a newick-like tree file");
3901 chooser.setToolTipText("Load a tree file");
3903 int value = chooser.showOpenDialog(null);
3905 if (value == JalviewFileChooser.APPROVE_OPTION)
3907 String choice = chooser.getSelectedFile().getPath();
3908 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3909 jalview.io.NewickFile fin = null;
3912 fin = new jalview.io.NewickFile(choice, "File");
3913 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3914 } catch (Exception ex)
3916 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3917 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3918 ex.printStackTrace();
3920 if (fin != null && fin.hasWarningMessage())
3922 JOptionPane.showMessageDialog(Desktop.desktop,
3923 fin.getWarningMessage(), "Possible problem with tree file",
3924 JOptionPane.WARNING_MESSAGE);
3930 public void loadScores_actionPerformed(ActionEvent e)
3932 // Pick the tree file
3933 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3934 chooser.setFileView(new JalviewFileView());
3935 chooser.setDialogTitle("Select a T-Coffee scores ascii file");
3936 chooser.setToolTipText("Load a score file");
3938 int value = chooser.showOpenDialog(null);
3940 if (value == JalviewFileChooser.APPROVE_OPTION)
3942 String sFilePath = chooser.getSelectedFile().getPath();
3943 jalview.bin.Cache.setProperty("LAST_DIRECTORY", sFilePath);
3948 TCoffeeScoreFile result = new TCoffeeScoreFile(sFilePath, FormatAdapter.FILE);
3949 if (!result.isValid()) {
3950 JOptionPane.showMessageDialog(Desktop.desktop, result.getWarningMessage(),
3951 "Problem reading T-COFFEE score file", JOptionPane.WARNING_MESSAGE);
3956 * check that the score matrix matches the alignment dimensions
3959 if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != result.getHeight() || aln.getWidth() != result.getWidth()) ) {
3960 // TODO: raise a dialog box here rather than bomb out.
3961 throw new RuntimeException("The scores matrix does not match the alignment dimensions");
3963 if (result.annotateAlignment(alignPanel.getAlignment(), true))
3965 tcoffeeColour.setEnabled(true);
3966 tcoffeeColour.setSelected(true);
3967 // switch to this color
3968 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3970 tcoffeeColour.setEnabled(false);
3971 tcoffeeColour.setSelected(false);
3974 catch (Exception ex) {
3975 JOptionPane.showMessageDialog(
3978 "Problem reading tree file",
3979 JOptionPane.WARNING_MESSAGE);
3981 ex.printStackTrace();
3989 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) {
3990 changeColour( new TCoffeeColourScheme(alignPanel.getAlignment()) );
3994 // * Load the (T-Coffee) score file from the specified url
3996 // * @param url The absolute path from where download and read the score file
3997 // * @throws IOException
3999 // public void loadScoreFile(URL url ) throws IOException {
4001 // TCoffeeScoreFile result = new TCoffeeScoreFile();
4002 // result.parse( new InputStreamReader( url.openStream() ) );
4003 // tcoffeeScoreFile = result;
4006 public TreePanel ShowNewickTree(NewickFile nf, String title)
4008 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4011 public TreePanel ShowNewickTree(NewickFile nf, String title,
4012 AlignmentView input)
4014 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4017 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4018 int h, int x, int y)
4020 return ShowNewickTree(nf, title, null, w, h, x, y);
4024 * Add a treeviewer for the tree extracted from a newick file object to the
4025 * current alignment view
4032 * Associated alignment input data (or null)
4041 * @return TreePanel handle
4043 public TreePanel ShowNewickTree(NewickFile nf, String title,
4044 AlignmentView input, int w, int h, int x, int y)
4046 TreePanel tp = null;
4052 if (nf.getTree() != null)
4054 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4060 tp.setLocation(x, y);
4063 Desktop.addInternalFrame(tp, title, w, h);
4065 } catch (Exception ex)
4067 ex.printStackTrace();
4073 private boolean buildingMenu = false;
4076 * Generates menu items and listener event actions for web service clients
4079 public void BuildWebServiceMenu()
4081 while (buildingMenu)
4085 System.err.println("Waiting for building menu to finish.");
4087 } catch (Exception e)
4092 final AlignFrame me = this;
4093 buildingMenu = true;
4094 new Thread(new Runnable()
4100 System.err.println("Building ws menu again "
4101 + Thread.currentThread());
4102 // TODO: add support for context dependent disabling of services based
4104 // alignment and current selection
4105 // TODO: add additional serviceHandle parameter to specify abstract
4107 // class independently of AbstractName
4108 // TODO: add in rediscovery GUI function to restart discoverer
4109 // TODO: group services by location as well as function and/or
4111 // object broker mechanism.
4112 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4113 final IProgressIndicator af = me;
4114 final JMenu msawsmenu = new JMenu("Alignment");
4115 final JMenu secstrmenu = new JMenu(
4116 "Secondary Structure Prediction");
4117 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4118 final JMenu analymenu = new JMenu("Analysis");
4119 final JMenu dismenu = new JMenu("Disorder");
4120 // JAL-940 - only show secondary structure prediction services from
4121 // the legacy server
4122 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4124 Discoverer.services != null && (Discoverer.services.size() > 0))
4126 // TODO: refactor to allow list of AbstractName/Handler bindings to
4128 // stored or retrieved from elsewhere
4129 Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4130 Vector secstrpr = (Vector) Discoverer.services
4132 Vector seqsrch = null; // (Vector)
4133 // Discoverer.services.get("SeqSearch");
4134 // TODO: move GUI generation code onto service implementation - so a
4135 // client instance attaches itself to the GUI with method call like
4136 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
4140 // Add any Multiple Sequence Alignment Services
4141 for (int i = 0, j = msaws.size(); i < j; i++)
4143 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
4145 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4146 .getServiceClient(sh);
4147 impl.attachWSMenuEntry(msawsmenu, me);
4151 if (secstrpr != null)
4153 // Add any secondary structure prediction services
4154 for (int i = 0, j = secstrpr.size(); i < j; i++)
4156 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4158 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4159 .getServiceClient(sh);
4160 impl.attachWSMenuEntry(secstrmenu, me);
4163 if (seqsrch != null)
4165 // Add any sequence search services
4166 for (int i = 0, j = seqsrch.size(); i < j; i++)
4168 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
4170 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4171 .getServiceClient(sh);
4172 impl.attachWSMenuEntry(seqsrchmenu, me);
4177 // Add all submenus in the order they should appear on the web
4179 wsmenu.add(msawsmenu);
4180 wsmenu.add(secstrmenu);
4181 wsmenu.add(dismenu);
4182 wsmenu.add(analymenu);
4183 // final ArrayList<JMenu> submens=new ArrayList<JMenu>();
4184 // submens.add(msawsmenu);
4185 // submens.add(secstrmenu);
4186 // submens.add(dismenu);
4187 // submens.add(analymenu);
4189 // No search services yet
4190 // wsmenu.add(seqsrchmenu);
4192 javax.swing.SwingUtilities.invokeLater(new Runnable()
4198 webService.removeAll();
4199 // first, add discovered services onto the webservices menu
4200 if (wsmenu.size() > 0)
4202 for (int i = 0, j = wsmenu.size(); i < j; i++)
4204 webService.add((JMenu) wsmenu.get(i));
4209 webService.add(me.webServiceNoServices);
4211 // TODO: move into separate menu builder class.
4212 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4214 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4215 if (jws2servs != null)
4217 if (jws2servs.hasServices())
4219 jws2servs.attachWSMenuEntry(webService, me);
4221 if (jws2servs.isRunning())
4223 JMenuItem tm = new JMenuItem(
4224 "Still discovering JABA Services");
4225 tm.setEnabled(false);
4231 build_urlServiceMenu(me.webService);
4232 build_fetchdbmenu(webService);
4233 for (JMenu item : wsmenu)
4235 if (item.getItemCount() == 0)
4237 item.setEnabled(false);
4241 item.setEnabled(true);
4244 } catch (Exception e)
4250 } catch (Exception e)
4255 buildingMenu = false;
4262 * construct any groupURL type service menu entries.
4266 private void build_urlServiceMenu(JMenu webService)
4268 // TODO: remove this code when 2.7 is released
4269 // DEBUG - alignmentView
4271 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4272 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4274 * @Override public void actionPerformed(ActionEvent e) {
4275 * jalview.datamodel.AlignmentView
4276 * .testSelectionViews(af.viewport.getAlignment(),
4277 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4279 * }); webService.add(testAlView);
4281 // TODO: refactor to RestClient discoverer and merge menu entries for
4282 // rest-style services with other types of analysis/calculation service
4283 // SHmmr test client - still being implemented.
4284 // DEBUG - alignmentView
4286 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4289 client.attachWSMenuEntry(
4290 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4294 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4296 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4302 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4303 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4304 * getProperty("LAST_DIRECTORY"));
4306 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4307 * to Vamsas file"); chooser.setToolTipText("Export");
4309 * int value = chooser.showSaveDialog(this);
4311 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4312 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4313 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4314 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4317 * prototype of an automatically enabled/disabled analysis function
4320 protected void setShowProductsEnabled()
4322 SequenceI[] selection = viewport.getSequenceSelection();
4323 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4324 viewport.getAlignment().getDataset()))
4326 showProducts.setEnabled(true);
4331 showProducts.setEnabled(false);
4336 * search selection for sequence xRef products and build the show products
4341 * @return true if showProducts menu should be enabled.
4343 public boolean canShowProducts(SequenceI[] selection,
4344 boolean isRegionSelection, Alignment dataset)
4346 boolean showp = false;
4349 showProducts.removeAll();
4350 final boolean dna = viewport.getAlignment().isNucleotide();
4351 final Alignment ds = dataset;
4352 String[] ptypes = (selection == null || selection.length == 0) ? null
4353 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4355 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4356 // selection, dataset, true);
4357 final SequenceI[] sel = selection;
4358 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4361 final boolean isRegSel = isRegionSelection;
4362 final AlignFrame af = this;
4363 final String source = ptypes[t];
4364 JMenuItem xtype = new JMenuItem(ptypes[t]);
4365 xtype.addActionListener(new ActionListener()
4368 public void actionPerformed(ActionEvent e)
4370 // TODO: new thread for this call with vis-delay
4371 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4372 isRegSel, dna, source);
4376 showProducts.add(xtype);
4378 showProducts.setVisible(showp);
4379 showProducts.setEnabled(showp);
4380 } catch (Exception e)
4382 jalview.bin.Cache.log
4383 .warn("canTranslate threw an exception - please report to help@jalview.org",
4390 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4391 boolean isRegSel, boolean dna, String source)
4393 final boolean fisRegSel = isRegSel;
4394 final boolean fdna = dna;
4395 final String fsrc = source;
4396 final AlignFrame ths = this;
4397 final SequenceI[] fsel = sel;
4398 Runnable foo = new Runnable()
4403 final long sttime = System.currentTimeMillis();
4404 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4407 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4411 Alignment prods = CrossRef
4412 .findXrefSequences(fsel, fdna, fsrc, ds);
4415 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4416 for (int s = 0; s < sprods.length; s++)
4418 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4419 if (ds.getSequences() == null
4420 || !ds.getSequences().contains(
4421 sprods[s].getDatasetSequence()))
4422 ds.addSequence(sprods[s].getDatasetSequence());
4423 sprods[s].updatePDBIds();
4425 Alignment al = new Alignment(sprods);
4426 AlignedCodonFrame[] cf = prods.getCodonFrames();
4428 for (int s = 0; cf != null && s < cf.length; s++)
4430 al.addCodonFrame(cf[s]);
4433 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4435 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4436 + " for " + ((fisRegSel) ? "selected region of " : "")
4438 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4443 System.err.println("No Sequences generated for xRef type "
4446 } catch (Exception e)
4448 jalview.bin.Cache.log.error(
4449 "Exception when finding crossreferences", e);
4450 } catch (OutOfMemoryError e)
4452 new OOMWarning("whilst fetching crossreferences", e);
4455 jalview.bin.Cache.log.error("Error when finding crossreferences",
4458 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4463 Thread frunner = new Thread(foo);
4467 public boolean canShowTranslationProducts(SequenceI[] selection,
4468 AlignmentI alignment)
4473 return (jalview.analysis.Dna.canTranslate(selection,
4474 viewport.getViewAsVisibleContigs(true)));
4475 } catch (Exception e)
4477 jalview.bin.Cache.log
4478 .warn("canTranslate threw an exception - please report to help@jalview.org",
4484 public void showProducts_actionPerformed(ActionEvent e)
4486 // /////////////////////////////
4487 // Collect Data to be translated/transferred
4489 SequenceI[] selection = viewport.getSequenceSelection();
4490 AlignmentI al = null;
4493 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4494 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4495 viewport.getAlignment().getDataset());
4496 } catch (Exception ex)
4499 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4506 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4507 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4511 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4512 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4513 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4517 public void showTranslation_actionPerformed(ActionEvent e)
4519 // /////////////////////////////
4520 // Collect Data to be translated/transferred
4522 SequenceI[] selection = viewport.getSequenceSelection();
4523 String[] seqstring = viewport.getViewAsString(true);
4524 AlignmentI al = null;
4527 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4528 viewport.getViewAsVisibleContigs(true), viewport
4529 .getGapCharacter(), viewport.getAlignment()
4530 .getAlignmentAnnotation(), viewport.getAlignment()
4531 .getWidth(), viewport.getAlignment().getDataset());
4532 } catch (Exception ex)
4535 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4542 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4543 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4547 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4548 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4549 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4554 * Try to load a features file onto the alignment.
4557 * contents or path to retrieve file
4559 * access mode of file (see jalview.io.AlignFile)
4560 * @return true if features file was parsed corectly.
4562 public boolean parseFeaturesFile(String file, String type)
4564 boolean featuresFile = false;
4567 featuresFile = new FeaturesFile(file, type).parse(viewport
4568 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4569 .getFeatureRenderer().featureColours, false,
4570 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4571 } catch (Exception ex)
4573 ex.printStackTrace();
4578 viewport.showSequenceFeatures = true;
4579 showSeqFeatures.setSelected(true);
4580 if (alignPanel.seqPanel.seqCanvas.fr != null)
4582 // update the min/max ranges where necessary
4583 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4585 if (featureSettings != null)
4587 featureSettings.setTableData();
4589 alignPanel.paintAlignment(true);
4592 return featuresFile;
4595 public void dragEnter(DropTargetDragEvent evt)
4599 public void dragExit(DropTargetEvent evt)
4603 public void dragOver(DropTargetDragEvent evt)
4607 public void dropActionChanged(DropTargetDragEvent evt)
4611 public void drop(DropTargetDropEvent evt)
4613 Transferable t = evt.getTransferable();
4614 java.util.List files = null;
4618 DataFlavor uriListFlavor = new DataFlavor(
4619 "text/uri-list;class=java.lang.String");
4620 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4622 // Works on Windows and MacOSX
4623 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4624 files = (java.util.List) t
4625 .getTransferData(DataFlavor.javaFileListFlavor);
4627 else if (t.isDataFlavorSupported(uriListFlavor))
4629 // This is used by Unix drag system
4630 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4631 String data = (String) t.getTransferData(uriListFlavor);
4632 files = new java.util.ArrayList(1);
4633 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4634 data, "\r\n"); st.hasMoreTokens();)
4636 String s = st.nextToken();
4637 if (s.startsWith("#"))
4639 // the line is a comment (as per the RFC 2483)
4643 java.net.URI uri = new java.net.URI(s);
4644 // check to see if we can handle this kind of URI
4645 if (uri.getScheme().toLowerCase().startsWith("http"))
4647 files.add(uri.toString());
4651 // otherwise preserve old behaviour: catch all for file objects
4652 java.io.File file = new java.io.File(uri);
4653 files.add(file.toString());
4657 } catch (Exception e)
4659 e.printStackTrace();
4665 // check to see if any of these files have names matching sequences in
4667 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4668 .getAlignment().getSequencesArray());
4670 * Object[] { String,SequenceI}
4672 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4673 ArrayList<String> filesnotmatched = new ArrayList<String>();
4674 for (int i = 0; i < files.size(); i++)
4676 String file = files.get(i).toString();
4678 String protocol = FormatAdapter.checkProtocol(file);
4679 if (protocol == jalview.io.FormatAdapter.FILE)
4681 File fl = new File(file);
4682 pdbfn = fl.getName();
4684 else if (protocol == jalview.io.FormatAdapter.URL)
4686 URL url = new URL(file);
4687 pdbfn = url.getFile();
4689 if (pdbfn.length() > 0)
4691 // attempt to find a match in the alignment
4692 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4693 int l = 0, c = pdbfn.indexOf(".");
4694 while (mtch == null && c != -1)
4699 } while ((c = pdbfn.indexOf(".", l)) > l);
4702 pdbfn = pdbfn.substring(0, l);
4704 mtch = idm.findAllIdMatches(pdbfn);
4711 type = new IdentifyFile().Identify(file, protocol);
4712 } catch (Exception ex)
4718 if (type.equalsIgnoreCase("PDB"))
4720 filesmatched.add(new Object[]
4721 { file, protocol, mtch });
4726 // File wasn't named like one of the sequences or wasn't a PDB file.
4727 filesnotmatched.add(file);
4731 if (filesmatched.size() > 0)
4733 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4737 "Do you want to automatically associate the "
4738 + filesmatched.size()
4739 + " PDB files with sequences in the alignment that have the same name ?",
4740 "Automatically Associate PDB files by name",
4741 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4744 for (Object[] fm : filesmatched)
4746 // try and associate
4747 // TODO: may want to set a standard ID naming formalism for
4748 // associating PDB files which have no IDs.
4749 for (SequenceI toassoc : (SequenceI[]) fm[2])
4751 PDBEntry pe = new AssociatePdbFileWithSeq()
4752 .associatePdbWithSeq((String) fm[0],
4753 (String) fm[1], toassoc, false);
4756 System.err.println("Associated file : "
4757 + ((String) fm[0]) + " with "
4758 + toassoc.getDisplayId(true));
4762 alignPanel.paintAlignment(true);
4766 if (filesnotmatched.size() > 0)
4769 && (Cache.getDefault(
4770 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4773 "<html>Do you want to <em>ignore</em> the "
4774 + filesnotmatched.size()
4775 + " files whose names did not match any sequence IDs ?</html>",
4776 "Ignore unmatched dropped files ?",
4777 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4781 for (String fn : filesnotmatched)
4783 loadJalviewDataFile(fn, null, null, null);
4787 } catch (Exception ex)
4789 ex.printStackTrace();
4795 * Attempt to load a "dropped" file or URL string: First by testing whether
4796 * it's and Annotation file, then a JNet file, and finally a features file. If
4797 * all are false then the user may have dropped an alignment file onto this
4801 * either a filename or a URL string.
4803 public void loadJalviewDataFile(String file, String protocol,
4804 String format, SequenceI assocSeq)
4808 if (protocol == null)
4810 protocol = jalview.io.FormatAdapter.checkProtocol(file);
4812 // if the file isn't identified, or not positively identified as some
4813 // other filetype (PFAM is default unidentified alignment file type) then
4814 // try to parse as annotation.
4815 boolean isAnnotation = (format == null || format
4816 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4817 .readAnnotationFile(viewport.getAlignment(), file, protocol)
4822 // try to see if its a JNet 'concise' style annotation file *before* we
4823 // try to parse it as a features file
4826 format = new IdentifyFile().Identify(file, protocol);
4828 if (format.equalsIgnoreCase("JnetFile"))
4830 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4832 new JnetAnnotationMaker().add_annotation(predictions,
4833 viewport.getAlignment(), 0, false);
4834 isAnnotation = true;
4839 * if (format.equalsIgnoreCase("PDB")) {
4841 * String pdbfn = ""; // try to match up filename with sequence id try
4842 * { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = new
4843 * File(file); pdbfn = fl.getName(); } else if (protocol ==
4844 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4845 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == null)
4846 * { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4847 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { //
4848 * attempt to find a match in the alignment SequenceI mtch =
4849 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4850 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > l)
4851 * { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch =
4852 * idm.findIdMatch(pdbfn); } if (mtch != null) { // try and associate
4853 * // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4854 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) {
4855 * System.err.println("Associated file : " + file + " with " +
4856 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4857 * TODO: maybe need to load as normal otherwise return; } }
4859 // try to parse it as a features file
4860 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4861 // if it wasn't a features file then we just treat it as a general
4862 // alignment file to load into the current view.
4865 new FileLoader().LoadFile(viewport, file, protocol, format);
4869 alignPanel.paintAlignment(true);
4876 alignPanel.adjustAnnotationHeight();
4877 viewport.updateSequenceIdColours();
4878 buildSortByAnnotationScoresMenu();
4879 alignPanel.paintAlignment(true);
4881 } catch (Exception ex)
4883 ex.printStackTrace();
4887 public void tabSelectionChanged(int index)
4891 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4892 viewport = alignPanel.av;
4893 setMenusFromViewport(viewport);
4897 public void tabbedPane_mousePressed(MouseEvent e)
4899 if (SwingUtilities.isRightMouseButton(e))
4901 String reply = JOptionPane.showInternalInputDialog(this,
4902 "Enter View Name", "Edit View Name",
4903 JOptionPane.QUESTION_MESSAGE);
4907 viewport.viewName = reply;
4908 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4913 public AlignViewport getCurrentView()
4919 * Open the dialog for regex description parsing.
4921 protected void extractScores_actionPerformed(ActionEvent e)
4923 ParseProperties pp = new jalview.analysis.ParseProperties(
4924 viewport.getAlignment());
4925 // TODO: verify regex and introduce GUI dialog for version 2.5
4926 // if (pp.getScoresFromDescription("col", "score column ",
4927 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4929 if (pp.getScoresFromDescription("description column",
4930 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4932 buildSortByAnnotationScoresMenu();
4940 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4943 protected void showDbRefs_actionPerformed(ActionEvent e)
4945 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4951 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4954 protected void showNpFeats_actionPerformed(ActionEvent e)
4956 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4960 * find the viewport amongst the tabs in this alignment frame and close that
4965 public boolean closeView(AlignViewport av)
4969 this.closeMenuItem_actionPerformed(false);
4972 Component[] comp = tabbedPane.getComponents();
4973 for (int i = 0; comp != null && i < comp.length; i++)
4975 if (comp[i] instanceof AlignmentPanel)
4977 if (((AlignmentPanel) comp[i]).av == av)
4980 closeView((AlignmentPanel) comp[i]);
4988 protected void build_fetchdbmenu(JMenu webService)
4990 // Temporary hack - DBRef Fetcher always top level ws entry.
4991 // TODO We probably want to store a sequence database checklist in
4992 // preferences and have checkboxes.. rather than individual sources selected
4994 final JMenu rfetch = new JMenu("Fetch DB References");
4995 rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4996 webService.add(rfetch);
4998 JMenuItem fetchr = new JMenuItem("Standard Databases");
4999 fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
5000 fetchr.addActionListener(new ActionListener()
5003 public void actionPerformed(ActionEvent e)
5005 new Thread(new Runnable()
5010 new jalview.ws.DBRefFetcher(alignPanel.av
5011 .getSequenceSelection(), alignPanel.alignFrame)
5012 .fetchDBRefs(false);
5020 final AlignFrame me = this;
5021 new Thread(new Runnable()
5025 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5026 .getSequenceFetcherSingleton(me);
5027 javax.swing.SwingUtilities.invokeLater(new Runnable()
5031 String[] dbclasses = sf.getOrderedSupportedSources();
5032 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5033 // jalview.util.QuickSort.sort(otherdb, otherdb);
5034 List<DbSourceProxy> otherdb;
5035 JMenu dfetch = new JMenu();
5036 JMenu ifetch = new JMenu();
5037 JMenuItem fetchr = null;
5038 int comp = 0, icomp = 0, mcomp = 15;
5039 String mname = null;
5041 for (String dbclass : dbclasses)
5043 otherdb = sf.getSourceProxy(dbclass);
5044 // add a single entry for this class, or submenu allowing 'fetch
5046 if (otherdb == null || otherdb.size() < 1)
5050 // List<DbSourceProxy> dbs=otherdb;
5051 // otherdb=new ArrayList<DbSourceProxy>();
5052 // for (DbSourceProxy db:dbs)
5054 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5058 mname = "From " + dbclass;
5060 if (otherdb.size() == 1)
5062 final DbSourceProxy[] dassource = otherdb
5063 .toArray(new DbSourceProxy[0]);
5064 DbSourceProxy src = otherdb.get(0);
5065 fetchr = new JMenuItem(src.getDbSource());
5066 fetchr.addActionListener(new ActionListener()
5069 public void actionPerformed(ActionEvent e)
5071 new Thread(new Runnable()
5076 new jalview.ws.DBRefFetcher(alignPanel.av
5077 .getSequenceSelection(),
5078 alignPanel.alignFrame, dassource)
5079 .fetchDBRefs(false);
5085 fetchr.setToolTipText("<html>"
5086 + JvSwingUtils.wrapTooltip("Retrieve from "
5087 + src.getDbName()) + "<html>");
5093 final DbSourceProxy[] dassource = otherdb
5094 .toArray(new DbSourceProxy[0]);
5096 DbSourceProxy src = otherdb.get(0);
5097 fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
5099 fetchr.addActionListener(new ActionListener()
5101 public void actionPerformed(ActionEvent e)
5103 new Thread(new Runnable()
5108 new jalview.ws.DBRefFetcher(alignPanel.av
5109 .getSequenceSelection(),
5110 alignPanel.alignFrame, dassource)
5111 .fetchDBRefs(false);
5117 fetchr.setToolTipText("<html>"
5118 + JvSwingUtils.wrapTooltip("Retrieve from all "
5119 + otherdb.size() + " sources in "
5120 + src.getDbSource() + "<br>First is :"
5121 + src.getDbName()) + "<html>");
5124 // and then build the rest of the individual menus
5125 ifetch = new JMenu("Sources from " + src.getDbSource());
5127 String imname = null;
5129 for (DbSourceProxy sproxy : otherdb)
5131 String dbname = sproxy.getDbName();
5132 String sname = dbname.length() > 5 ? dbname.substring(0,
5133 5) + "..." : dbname;
5134 String msname = dbname.length() > 10 ? dbname.substring(
5135 0, 10) + "..." : dbname;
5138 imname = "from '" + sname + "'";
5140 fetchr = new JMenuItem(msname);
5141 final DbSourceProxy[] dassrc =
5143 fetchr.addActionListener(new ActionListener()
5146 public void actionPerformed(ActionEvent e)
5148 new Thread(new Runnable()
5153 new jalview.ws.DBRefFetcher(alignPanel.av
5154 .getSequenceSelection(),
5155 alignPanel.alignFrame, dassrc)
5156 .fetchDBRefs(false);
5162 fetchr.setToolTipText("<html>"
5163 + JvSwingUtils.wrapTooltip("Retrieve from "
5164 + dbname) + "</html>");
5167 if (++icomp >= mcomp || i == (otherdb.size()))
5169 ifetch.setText(imname + " to '" + sname + "'");
5171 ifetch = new JMenu();
5179 if (comp >= mcomp || dbi >= (dbclasses.length))
5181 dfetch.setText(mname + " to '" + dbclass + "'");
5183 dfetch = new JMenu();
5196 * Left justify the whole alignment.
5198 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5200 AlignmentI al = viewport.getAlignment();
5202 viewport.firePropertyChange("alignment", null, al);
5206 * Right justify the whole alignment.
5208 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5210 AlignmentI al = viewport.getAlignment();
5212 viewport.firePropertyChange("alignment", null, al);
5215 public void setShowSeqFeatures(boolean b)
5217 showSeqFeatures.setSelected(true);
5218 viewport.setShowSequenceFeatures(true);
5225 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5226 * awt.event.ActionEvent)
5228 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5230 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5231 alignPanel.paintAlignment(true);
5238 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5241 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5243 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5244 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5252 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5253 * .event.ActionEvent)
5255 protected void showGroupConservation_actionPerformed(ActionEvent e)
5257 viewport.setShowGroupConservation(showGroupConservation.getState());
5258 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5265 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5266 * .event.ActionEvent)
5268 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5270 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5271 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5278 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5279 * .event.ActionEvent)
5281 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5283 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5284 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5287 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5289 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5290 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5293 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5295 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5302 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5303 * .event.ActionEvent)
5305 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5307 if (viewport.getSelectionGroup() != null)
5309 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
5310 viewport.getSequenceSelection(),
5311 viewport.getAlignmentView(true).getSequenceStrings(
5312 viewport.getGapCharacter()), viewport.getAlignment()
5314 viewport.getAlignment().deleteAllGroups();
5315 viewport.sequenceColours = null;
5316 viewport.setSelectionGroup(null);
5317 // set view properties for each group
5318 for (int g = 0; g < gps.length; g++)
5320 gps[g].setShowNonconserved(viewport.getShowUnconserved());
5321 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
5322 viewport.getAlignment().addGroup(gps[g]);
5323 Color col = new Color((int) (Math.random() * 255),
5324 (int) (Math.random() * 255), (int) (Math.random() * 255));
5325 col = col.brighter();
5326 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
5327 .hasMoreElements(); viewport.setSequenceColour(
5328 (SequenceI) sq.nextElement(), col))
5331 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5332 alignPanel.updateAnnotation();
5333 alignPanel.paintAlignment(true);
5338 * make the given alignmentPanel the currently selected tab
5340 * @param alignmentPanel
5342 public void setDisplayedView(AlignmentPanel alignmentPanel)
5344 if (!viewport.getSequenceSetId().equals(
5345 alignmentPanel.av.getSequenceSetId()))
5348 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5350 if (tabbedPane != null
5351 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5352 .getSelectedIndex())
5354 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5359 class PrintThread extends Thread
5363 public PrintThread(AlignmentPanel ap)
5368 static PageFormat pf;
5372 PrinterJob printJob = PrinterJob.getPrinterJob();
5376 printJob.setPrintable(ap, pf);
5380 printJob.setPrintable(ap);
5383 if (printJob.printDialog())
5388 } catch (Exception PrintException)
5390 PrintException.printStackTrace();