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.jbgui.GAlignFrame;
59 import jalview.schemes.Blosum62ColourScheme;
60 import jalview.schemes.BuriedColourScheme;
61 import jalview.schemes.ClustalxColourScheme;
62 import jalview.schemes.ColourSchemeI;
63 import jalview.schemes.ColourSchemeProperty;
64 import jalview.schemes.HelixColourScheme;
65 import jalview.schemes.HydrophobicColourScheme;
66 import jalview.schemes.NucleotideColourScheme;
67 import jalview.schemes.PIDColourScheme;
68 import jalview.schemes.PurinePyrimidineColourScheme;
69 import jalview.schemes.ResidueProperties;
70 import jalview.schemes.StrandColourScheme;
71 import jalview.schemes.TaylorColourScheme;
72 import jalview.schemes.TurnColourScheme;
73 import jalview.schemes.UserColourScheme;
74 import jalview.schemes.ZappoColourScheme;
75 import jalview.ws.WSMenuEntryProviderI;
76 import jalview.ws.jws1.Discoverer;
77 import jalview.ws.jws2.Jws2Discoverer;
79 import java.awt.BorderLayout;
80 import java.awt.Color;
81 import java.awt.Component;
82 import java.awt.GridLayout;
83 import java.awt.Rectangle;
84 import java.awt.Toolkit;
85 import java.awt.datatransfer.Clipboard;
86 import java.awt.datatransfer.DataFlavor;
87 import java.awt.datatransfer.StringSelection;
88 import java.awt.datatransfer.Transferable;
89 import java.awt.dnd.DnDConstants;
90 import java.awt.dnd.DropTargetDragEvent;
91 import java.awt.dnd.DropTargetDropEvent;
92 import java.awt.dnd.DropTargetEvent;
93 import java.awt.dnd.DropTargetListener;
94 import java.awt.event.ActionEvent;
95 import java.awt.event.ActionListener;
96 import java.awt.event.KeyAdapter;
97 import java.awt.event.KeyEvent;
98 import java.awt.event.MouseAdapter;
99 import java.awt.event.MouseEvent;
100 import java.awt.print.PageFormat;
101 import java.awt.print.PrinterJob;
102 import java.beans.PropertyChangeEvent;
105 import java.util.ArrayList;
106 import java.util.Enumeration;
107 import java.util.Hashtable;
108 import java.util.Vector;
110 import javax.swing.JButton;
111 import javax.swing.JEditorPane;
112 import javax.swing.JInternalFrame;
113 import javax.swing.JLabel;
114 import javax.swing.JLayeredPane;
115 import javax.swing.JMenu;
116 import javax.swing.JMenuItem;
117 import javax.swing.JOptionPane;
118 import javax.swing.JPanel;
119 import javax.swing.JProgressBar;
120 import javax.swing.JRadioButtonMenuItem;
121 import javax.swing.JScrollPane;
122 import javax.swing.SwingUtilities;
128 * @version $Revision$
130 public class AlignFrame extends GAlignFrame implements DropTargetListener,
135 public static final int DEFAULT_WIDTH = 700;
138 public static final int DEFAULT_HEIGHT = 500;
140 public AlignmentPanel alignPanel;
142 AlignViewport viewport;
144 Vector alignPanels = new Vector();
147 * Last format used to load or save alignments in this window
149 String currentFileFormat = null;
152 * Current filename for this alignment
154 String fileName = null;
157 * Creates a new AlignFrame object with specific width and height.
163 public AlignFrame(AlignmentI al, int width, int height)
165 this(al, null, width, height);
169 * Creates a new AlignFrame object with specific width, height and
175 * @param sequenceSetId
177 public AlignFrame(AlignmentI al, int width, int height,
178 String sequenceSetId)
180 this(al, null, width, height, sequenceSetId);
184 * Creates a new AlignFrame object with specific width, height and
190 * @param sequenceSetId
193 public AlignFrame(AlignmentI al, int width, int height,
194 String sequenceSetId, String viewId)
196 this(al, null, width, height, sequenceSetId, viewId);
200 * new alignment window with hidden columns
204 * @param hiddenColumns
205 * ColumnSelection or null
207 * Width of alignment frame
211 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
212 int width, int height)
214 this(al, hiddenColumns, width, height, null);
218 * Create alignment frame for al with hiddenColumns, a specific width and
219 * height, and specific sequenceId
222 * @param hiddenColumns
225 * @param sequenceSetId
228 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
229 int width, int height, String sequenceSetId)
231 this(al, hiddenColumns, width, height, sequenceSetId, null);
235 * Create alignment frame for al with hiddenColumns, a specific width and
236 * height, and specific sequenceId
239 * @param hiddenColumns
242 * @param sequenceSetId
247 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
248 int width, int height, String sequenceSetId, String viewId)
250 setSize(width, height);
251 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
253 alignPanel = new AlignmentPanel(this, viewport);
255 if (al.getDataset() == null)
260 addAlignmentPanel(alignPanel, true);
265 * Make a new AlignFrame from exisiting alignmentPanels
272 public AlignFrame(AlignmentPanel ap)
276 addAlignmentPanel(ap, false);
281 * initalise the alignframe from the underlying viewport data and the
286 if (viewport.getAlignmentConservationAnnotation()== null)
288 BLOSUM62Colour.setEnabled(false);
289 conservationMenuItem.setEnabled(false);
290 modifyConservation.setEnabled(false);
291 // PIDColour.setEnabled(false);
292 // abovePIDThreshold.setEnabled(false);
293 // modifyPID.setEnabled(false);
296 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
299 if (sortby.equals("Id"))
301 sortIDMenuItem_actionPerformed(null);
303 else if (sortby.equals("Pairwise Identity"))
305 sortPairwiseMenuItem_actionPerformed(null);
308 if (Desktop.desktop != null)
310 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
311 addServiceListeners();
312 setGUINucleotide(viewport.getAlignment().isNucleotide());
315 setMenusFromViewport(viewport);
316 buildSortByAnnotationScoresMenu();
317 if (viewport.wrapAlignment)
319 wrapMenuItem_actionPerformed(null);
322 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
324 this.overviewMenuItem_actionPerformed(null);
332 * Change the filename and format for the alignment, and enable the 'reload'
333 * button functionality.
340 public void setFileName(String file, String format)
343 currentFileFormat = format;
344 reload.setEnabled(true);
347 void addKeyListener()
349 addKeyListener(new KeyAdapter()
351 public void keyPressed(KeyEvent evt)
353 if (viewport.cursorMode
354 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
355 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
356 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
357 && Character.isDigit(evt.getKeyChar()))
358 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
360 switch (evt.getKeyCode())
363 case 27: // escape key
364 deselectAllSequenceMenuItem_actionPerformed(null);
368 case KeyEvent.VK_DOWN:
369 if (evt.isAltDown() || !viewport.cursorMode)
370 moveSelectedSequences(false);
371 if (viewport.cursorMode)
372 alignPanel.seqPanel.moveCursor(0, 1);
376 if (evt.isAltDown() || !viewport.cursorMode)
377 moveSelectedSequences(true);
378 if (viewport.cursorMode)
379 alignPanel.seqPanel.moveCursor(0, -1);
383 case KeyEvent.VK_LEFT:
384 if (evt.isAltDown() || !viewport.cursorMode)
385 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
387 alignPanel.seqPanel.moveCursor(-1, 0);
391 case KeyEvent.VK_RIGHT:
392 if (evt.isAltDown() || !viewport.cursorMode)
393 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
395 alignPanel.seqPanel.moveCursor(1, 0);
398 case KeyEvent.VK_SPACE:
399 if (viewport.cursorMode)
401 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
402 || evt.isShiftDown() || evt.isAltDown());
406 //case KeyEvent.VK_A:
407 // if (viewport.cursorMode)
409 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
410 // //System.out.println("A");
414 case KeyEvent.VK_CLOSE_BRACKET:
415 if (viewport.cursorMode)
417 System.out.println("closing bracket");
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());
728 rnahelicesColour.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
729 setShowProductsEnabled();
734 Hashtable progressBars, progressBarHandlers;
739 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
741 public void setProgressBar(String message, long id)
743 if (progressBars == null)
745 progressBars = new Hashtable();
746 progressBarHandlers = new Hashtable();
749 JPanel progressPanel;
750 Long lId = new Long(id);
751 GridLayout layout = (GridLayout) statusPanel.getLayout();
752 if (progressBars.get(lId) != null)
754 progressPanel = (JPanel) progressBars.get(new Long(id));
755 statusPanel.remove(progressPanel);
756 progressBars.remove(lId);
757 progressPanel = null;
760 statusBar.setText(message);
762 if (progressBarHandlers.contains(lId))
764 progressBarHandlers.remove(lId);
766 layout.setRows(layout.getRows() - 1);
770 progressPanel = new JPanel(new BorderLayout(10, 5));
772 JProgressBar progressBar = new JProgressBar();
773 progressBar.setIndeterminate(true);
775 progressPanel.add(new JLabel(message), BorderLayout.WEST);
776 progressPanel.add(progressBar, BorderLayout.CENTER);
778 layout.setRows(layout.getRows() + 1);
779 statusPanel.add(progressPanel);
781 progressBars.put(lId, progressPanel);
784 // setMenusForViewport();
788 public void registerHandler(final long id,
789 final IProgressIndicatorHandler handler)
791 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
794 "call setProgressBar before registering the progress bar's handler.");
796 progressBarHandlers.put(new Long(id), handler);
797 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
798 if (handler.canCancel())
800 JButton cancel = new JButton("Cancel");
801 final IProgressIndicator us = this;
802 cancel.addActionListener(new ActionListener()
805 public void actionPerformed(ActionEvent e)
807 handler.cancelActivity(id);
810 + ((JLabel) progressPanel.getComponent(0))
814 progressPanel.add(cancel, BorderLayout.EAST);
820 * @return true if any progress bars are still active
822 public boolean operationInProgress()
824 if (progressBars != null && progressBars.size() > 0)
832 * Added so Castor Mapping file can obtain Jalview Version
834 public String getVersion()
836 return jalview.bin.Cache.getProperty("VERSION");
839 public FeatureRenderer getFeatureRenderer()
841 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
844 public void fetchSequence_actionPerformed(ActionEvent e)
846 new SequenceFetcher(this);
849 public void addFromFile_actionPerformed(ActionEvent e)
851 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
854 public void reload_actionPerformed(ActionEvent e)
856 if (fileName != null)
858 // TODO: work out how to recover feature settings for correct view(s) when
860 if (currentFileFormat.equals("Jalview"))
862 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
863 for (int i = 0; i < frames.length; i++)
865 if (frames[i] instanceof AlignFrame && frames[i] != this
866 && ((AlignFrame) frames[i]).fileName.equals(fileName))
870 frames[i].setSelected(true);
871 Desktop.instance.closeAssociatedWindows();
872 } catch (java.beans.PropertyVetoException ex)
878 Desktop.instance.closeAssociatedWindows();
880 FileLoader loader = new FileLoader();
881 String protocol = fileName.startsWith("http:") ? "URL" : "File";
882 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
886 Rectangle bounds = this.getBounds();
888 FileLoader loader = new FileLoader();
889 String protocol = fileName.startsWith("http:") ? "URL" : "File";
890 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
891 protocol, currentFileFormat);
893 newframe.setBounds(bounds);
894 if (featureSettings != null && featureSettings.isShowing())
896 final Rectangle fspos = featureSettings.frame.getBounds();
897 // TODO: need a 'show feature settings' function that takes bounds -
898 // need to refactor Desktop.addFrame
899 newframe.featureSettings_actionPerformed(null);
900 final FeatureSettings nfs = newframe.featureSettings;
901 SwingUtilities.invokeLater(new Runnable()
905 nfs.frame.setBounds(fspos);
908 this.featureSettings.close();
909 this.featureSettings = null;
911 this.closeMenuItem_actionPerformed(true);
916 public void addFromText_actionPerformed(ActionEvent e)
918 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
921 public void addFromURL_actionPerformed(ActionEvent e)
923 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
926 public void save_actionPerformed(ActionEvent e)
929 || (currentFileFormat == null || !jalview.io.FormatAdapter
930 .isValidIOFormat(currentFileFormat, true))
931 || fileName.startsWith("http"))
933 saveAs_actionPerformed(null);
937 saveAlignment(fileName, currentFileFormat);
947 public void saveAs_actionPerformed(ActionEvent e)
949 JalviewFileChooser chooser = new JalviewFileChooser(
950 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
951 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
952 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
953 currentFileFormat, false);
955 chooser.setFileView(new JalviewFileView());
956 chooser.setDialogTitle("Save Alignment to file");
957 chooser.setToolTipText("Save");
959 int value = chooser.showSaveDialog(this);
961 if (value == JalviewFileChooser.APPROVE_OPTION)
963 currentFileFormat = chooser.getSelectedFormat();
964 if (currentFileFormat == null)
966 JOptionPane.showInternalMessageDialog(Desktop.desktop,
967 "You must select a file format before saving!",
968 "File format not specified", JOptionPane.WARNING_MESSAGE);
969 value = chooser.showSaveDialog(this);
973 fileName = chooser.getSelectedFile().getPath();
975 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
978 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
979 if (currentFileFormat.indexOf(" ") > -1)
981 currentFileFormat = currentFileFormat.substring(0,
982 currentFileFormat.indexOf(" "));
984 saveAlignment(fileName, currentFileFormat);
988 public boolean saveAlignment(String file, String format)
990 boolean success = true;
992 if (format.equalsIgnoreCase("Jalview"))
994 String shortName = title;
996 if (shortName.indexOf(java.io.File.separatorChar) > -1)
998 shortName = shortName.substring(shortName
999 .lastIndexOf(java.io.File.separatorChar) + 1);
1002 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1004 statusBar.setText("Successfully saved to file: " + fileName + " in "
1005 + format + " format.");
1010 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1012 warningMessage("Cannot save file " + fileName + " using format "
1013 + format, "Alignment output format not supported");
1014 saveAs_actionPerformed(null);
1015 // JBPNote need to have a raise_gui flag here
1019 String[] omitHidden = null;
1021 if (viewport.hasHiddenColumns())
1023 int reply = JOptionPane
1024 .showInternalConfirmDialog(
1026 "The Alignment contains hidden columns."
1027 + "\nDo you want to save only the visible alignment?",
1028 "Save / Omit Hidden Columns",
1029 JOptionPane.YES_NO_OPTION,
1030 JOptionPane.QUESTION_MESSAGE);
1032 if (reply == JOptionPane.YES_OPTION)
1034 omitHidden = viewport.getViewAsString(false);
1037 FormatAdapter f = new FormatAdapter();
1038 String output = f.formatSequences(format,
1039 (Alignment) viewport.getAlignment(), // class cast exceptions will
1040 // occur in the distant future
1041 omitHidden, f.getCacheSuffixDefault(format), viewport.getColumnSelection());
1051 java.io.PrintWriter out = new java.io.PrintWriter(
1052 new java.io.FileWriter(file));
1056 this.setTitle(file);
1057 statusBar.setText("Successfully saved to file: " + fileName
1058 + " in " + format + " format.");
1059 } catch (Exception ex)
1062 ex.printStackTrace();
1069 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
1070 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
1076 private void warningMessage(String warning, String title)
1078 if (new jalview.util.Platform().isHeadless())
1080 System.err.println("Warning: " + title + "\nWarning: " + warning);
1085 JOptionPane.showInternalMessageDialog(this, warning, title,
1086 JOptionPane.WARNING_MESSAGE);
1097 protected void outputText_actionPerformed(ActionEvent e)
1099 String[] omitHidden = null;
1101 if (viewport.hasHiddenColumns())
1103 int reply = JOptionPane
1104 .showInternalConfirmDialog(
1106 "The Alignment contains hidden columns."
1107 + "\nDo you want to output only the visible alignment?",
1108 "Save / Omit Hidden Columns",
1109 JOptionPane.YES_NO_OPTION,
1110 JOptionPane.QUESTION_MESSAGE);
1112 if (reply == JOptionPane.YES_OPTION)
1114 omitHidden = viewport.getViewAsString(false);
1118 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1119 cap.setForInput(null);
1123 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1124 viewport.getAlignment(), omitHidden, viewport.getColumnSelection()));
1125 Desktop.addInternalFrame(cap,
1126 "Alignment output - " + e.getActionCommand(), 600, 500);
1127 } catch (OutOfMemoryError oom)
1129 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1141 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1143 new HTMLOutput(alignPanel,
1144 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1145 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1148 public void createImageMap(File file, String image)
1150 alignPanel.makePNGImageMap(file, image);
1159 public void createPNG(File f)
1161 alignPanel.makePNG(f);
1170 public void createEPS(File f)
1172 alignPanel.makeEPS(f);
1175 public void pageSetup_actionPerformed(ActionEvent e)
1177 PrinterJob printJob = PrinterJob.getPrinterJob();
1178 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1187 public void printMenuItem_actionPerformed(ActionEvent e)
1189 // Putting in a thread avoids Swing painting problems
1190 PrintThread thread = new PrintThread(alignPanel);
1194 public void exportFeatures_actionPerformed(ActionEvent e)
1196 new AnnotationExporter().exportFeatures(alignPanel);
1199 public void exportAnnotations_actionPerformed(ActionEvent e)
1201 new AnnotationExporter().exportAnnotations(
1203 viewport.showAnnotation ? viewport.getAlignment()
1204 .getAlignmentAnnotation() : null, viewport.getAlignment()
1206 ((Alignment) viewport.getAlignment()).alignmentProperties);
1209 public void associatedData_actionPerformed(ActionEvent e)
1211 // Pick the tree file
1212 JalviewFileChooser chooser = new JalviewFileChooser(
1213 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1214 chooser.setFileView(new JalviewFileView());
1215 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1216 chooser.setToolTipText("Load Jalview Annotations / Features file");
1218 int value = chooser.showOpenDialog(null);
1220 if (value == JalviewFileChooser.APPROVE_OPTION)
1222 String choice = chooser.getSelectedFile().getPath();
1223 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1224 loadJalviewDataFile(choice, null, null, null);
1230 * Close the current view or all views in the alignment frame. If the frame
1231 * only contains one view then the alignment will be removed from memory.
1233 * @param closeAllTabs
1235 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1237 if (alignPanels != null && alignPanels.size() < 2)
1239 closeAllTabs = true;
1244 if (alignPanels != null)
1248 if (this.isClosed())
1250 // really close all the windows - otherwise wait till
1251 // setClosed(true) is called
1252 for (int i = 0; i < alignPanels.size(); i++)
1254 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1261 closeView(alignPanel);
1267 this.setClosed(true);
1269 } catch (Exception ex)
1271 ex.printStackTrace();
1276 * close alignPanel2 and shuffle tabs appropriately.
1278 * @param alignPanel2
1280 public void closeView(AlignmentPanel alignPanel2)
1282 int index = tabbedPane.getSelectedIndex();
1283 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1284 alignPanels.removeElement(alignPanel2);
1286 // if (viewport == alignPanel2.av)
1290 alignPanel2.closePanel();
1293 tabbedPane.removeTabAt(closedindex);
1294 tabbedPane.validate();
1296 if (index > closedindex || index == tabbedPane.getTabCount())
1298 // modify currently selected tab index if necessary.
1302 this.tabSelectionChanged(index);
1308 void updateEditMenuBar()
1311 if (viewport.historyList.size() > 0)
1313 undoMenuItem.setEnabled(true);
1314 CommandI command = (CommandI) viewport.historyList.peek();
1315 undoMenuItem.setText("Undo " + command.getDescription());
1319 undoMenuItem.setEnabled(false);
1320 undoMenuItem.setText("Undo");
1323 if (viewport.redoList.size() > 0)
1325 redoMenuItem.setEnabled(true);
1327 CommandI command = (CommandI) viewport.redoList.peek();
1328 redoMenuItem.setText("Redo " + command.getDescription());
1332 redoMenuItem.setEnabled(false);
1333 redoMenuItem.setText("Redo");
1337 public void addHistoryItem(CommandI command)
1339 if (command.getSize() > 0)
1341 viewport.historyList.push(command);
1342 viewport.redoList.clear();
1343 updateEditMenuBar();
1344 viewport.updateHiddenColumns();
1345 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1346 // && viewport.getColumnSelection().getHiddenColumns() != null && viewport.getColumnSelection()
1347 // .getHiddenColumns().size() > 0);
1353 * @return alignment objects for all views
1355 AlignmentI[] getViewAlignments()
1357 if (alignPanels != null)
1359 Enumeration e = alignPanels.elements();
1360 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1361 for (int i = 0; e.hasMoreElements(); i++)
1363 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1367 if (viewport != null)
1369 return new AlignmentI[]
1370 { viewport.getAlignment() };
1381 protected void undoMenuItem_actionPerformed(ActionEvent e)
1383 if (viewport.historyList.empty())
1385 CommandI command = (CommandI) viewport.historyList.pop();
1386 viewport.redoList.push(command);
1387 command.undoCommand(getViewAlignments());
1389 AlignViewport originalSource = getOriginatingSource(command);
1390 updateEditMenuBar();
1392 if (originalSource != null)
1394 if (originalSource!=viewport)
1396 Cache.log.warn("Implementation worry: mismatch of viewport origin for undo");
1398 originalSource.updateHiddenColumns();
1399 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != null
1400 // && viewport.getColumnSelection().getHiddenColumns() != null && viewport.getColumnSelection()
1401 // .getHiddenColumns().size() > 0);
1402 originalSource.firePropertyChange("alignment", null,
1403 originalSource.getAlignment().getSequences());
1413 protected void redoMenuItem_actionPerformed(ActionEvent e)
1415 if (viewport.redoList.size() < 1)
1420 CommandI command = (CommandI) viewport.redoList.pop();
1421 viewport.historyList.push(command);
1422 command.doCommand(getViewAlignments());
1424 AlignViewport originalSource = getOriginatingSource(command);
1425 updateEditMenuBar();
1427 if (originalSource != null)
1430 if (originalSource!=viewport)
1432 Cache.log.warn("Implementation worry: mismatch of viewport origin for redo");
1434 originalSource.updateHiddenColumns();
1435 //originalSource.hasHiddenColumns = (viewport.getColumnSelection() != null
1436 // && viewport.getColumnSelection().getHiddenColumns() != null && viewport.getColumnSelection()
1437 // .getHiddenColumns().size() > 0);
1438 originalSource.firePropertyChange("alignment", null,
1439 originalSource.getAlignment().getSequences());
1443 AlignViewport getOriginatingSource(CommandI command)
1445 AlignViewport originalSource = null;
1446 // For sequence removal and addition, we need to fire
1447 // the property change event FROM the viewport where the
1448 // original alignment was altered
1449 AlignmentI al = null;
1450 if (command instanceof EditCommand)
1452 EditCommand editCommand = (EditCommand) command;
1453 al = editCommand.getAlignment();
1454 Vector comps = (Vector) PaintRefresher.components.get(viewport
1455 .getSequenceSetId());
1457 for (int i = 0; i < comps.size(); i++)
1459 if (comps.elementAt(i) instanceof AlignmentPanel)
1461 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1463 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1470 if (originalSource == null)
1472 // The original view is closed, we must validate
1473 // the current view against the closed view first
1476 PaintRefresher.validateSequences(al, viewport.getAlignment());
1479 originalSource = viewport;
1482 return originalSource;
1491 public void moveSelectedSequences(boolean up)
1493 SequenceGroup sg = viewport.getSelectionGroup();
1502 for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
1504 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
1506 if (!sg.getSequences(null).contains(seq))
1511 SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
1513 if (sg.getSequences(null).contains(temp))
1518 viewport.getAlignment().getSequences().setElementAt(temp, i);
1519 viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
1524 for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
1526 SequenceI seq = viewport.getAlignment().getSequenceAt(i);
1528 if (!sg.getSequences(null).contains(seq))
1533 SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
1535 if (sg.getSequences(null).contains(temp))
1540 viewport.getAlignment().getSequences().setElementAt(temp, i);
1541 viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
1545 alignPanel.paintAlignment(true);
1548 synchronized void slideSequences(boolean right, int size)
1550 Vector sg = new Vector();
1551 if (viewport.cursorMode)
1553 sg.addElement(viewport.getAlignment()
1554 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1556 else if (viewport.getSelectionGroup() != null
1557 && viewport.getSelectionGroup().getSize() != viewport.getAlignment()
1560 sg = viewport.getSelectionGroup().getSequences(
1561 viewport.getHiddenRepSequences());
1569 Vector invertGroup = new Vector();
1571 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1573 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1574 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1577 SequenceI[] seqs1 = new SequenceI[sg.size()];
1578 for (int i = 0; i < sg.size(); i++)
1579 seqs1[i] = (SequenceI) sg.elementAt(i);
1581 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1582 for (int i = 0; i < invertGroup.size(); i++)
1583 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1585 SlideSequencesCommand ssc;
1587 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1588 size, viewport.getGapCharacter());
1590 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1591 size, viewport.getGapCharacter());
1593 int groupAdjustment = 0;
1594 if (ssc.getGapsInsertedBegin() && right)
1596 if (viewport.cursorMode)
1597 alignPanel.seqPanel.moveCursor(size, 0);
1599 groupAdjustment = size;
1601 else if (!ssc.getGapsInsertedBegin() && !right)
1603 if (viewport.cursorMode)
1604 alignPanel.seqPanel.moveCursor(-size, 0);
1606 groupAdjustment = -size;
1609 if (groupAdjustment != 0)
1611 viewport.getSelectionGroup().setStartRes(
1612 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1613 viewport.getSelectionGroup().setEndRes(
1614 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1617 boolean appendHistoryItem = false;
1618 if (viewport.historyList != null && viewport.historyList.size() > 0
1619 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1621 appendHistoryItem = ssc
1622 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1626 if (!appendHistoryItem)
1627 addHistoryItem(ssc);
1638 protected void copy_actionPerformed(ActionEvent e)
1641 if (viewport.getSelectionGroup() == null)
1645 // TODO: preserve the ordering of displayed alignment annotation in any
1646 // internal paste (particularly sequence associated annotation)
1647 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1648 String[] omitHidden = null;
1650 if (viewport.hasHiddenColumns())
1652 omitHidden = viewport.getViewAsString(true);
1655 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1658 StringSelection ss = new StringSelection(output);
1662 jalview.gui.Desktop.internalCopy = true;
1663 // Its really worth setting the clipboard contents
1664 // to empty before setting the large StringSelection!!
1665 Toolkit.getDefaultToolkit().getSystemClipboard()
1666 .setContents(new StringSelection(""), null);
1668 Toolkit.getDefaultToolkit().getSystemClipboard()
1669 .setContents(ss, Desktop.instance);
1670 } catch (OutOfMemoryError er)
1672 new OOMWarning("copying region", er);
1676 Vector hiddenColumns = null;
1677 if (viewport.hasHiddenColumns())
1679 hiddenColumns = new Vector();
1680 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1681 .getSelectionGroup().getEndRes();
1682 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1685 int[] region = (int[]) viewport.getColumnSelection()
1686 .getHiddenColumns().elementAt(i);
1687 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1689 hiddenColumns.addElement(new int[]
1690 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1695 Desktop.jalviewClipboard = new Object[]
1696 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1697 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1706 protected void pasteNew_actionPerformed(ActionEvent e)
1717 protected void pasteThis_actionPerformed(ActionEvent e)
1723 * Paste contents of Jalview clipboard
1725 * @param newAlignment
1726 * true to paste to a new alignment, otherwise add to this.
1728 void paste(boolean newAlignment)
1730 boolean externalPaste = true;
1733 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1734 Transferable contents = c.getContents(this);
1736 if (contents == null)
1744 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1745 if (str.length() < 1)
1750 format = new IdentifyFile().Identify(str, "Paste");
1752 } catch (OutOfMemoryError er)
1754 new OOMWarning("Out of memory pasting sequences!!", er);
1758 SequenceI[] sequences;
1759 boolean annotationAdded = false;
1760 AlignmentI alignment = null;
1762 if (Desktop.jalviewClipboard != null)
1764 // The clipboard was filled from within Jalview, we must use the
1766 // And dataset from the copied alignment
1767 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1768 // be doubly sure that we create *new* sequence objects.
1769 sequences = new SequenceI[newseq.length];
1770 for (int i = 0; i < newseq.length; i++)
1772 sequences[i] = new Sequence(newseq[i]);
1774 alignment = new Alignment(sequences);
1775 externalPaste = false;
1779 // parse the clipboard as an alignment.
1780 alignment = new FormatAdapter().readFile(str, "Paste", format);
1781 sequences = alignment.getSequencesArray();
1789 if (Desktop.jalviewClipboard != null)
1791 // dataset is inherited
1792 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1796 // new dataset is constructed
1797 alignment.setDataset(null);
1799 alwidth = alignment.getWidth() + 1;
1803 AlignmentI pastedal = alignment; // preserve pasted alignment object
1804 // Add pasted sequences and dataset into existing alignment.
1805 alignment = viewport.getAlignment();
1806 alwidth = alignment.getWidth() + 1;
1807 // decide if we need to import sequences from an existing dataset
1808 boolean importDs = Desktop.jalviewClipboard != null
1809 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1810 // importDs==true instructs us to copy over new dataset sequences from
1811 // an existing alignment
1812 Vector newDs = (importDs) ? new Vector() : null; // used to create
1813 // minimum dataset set
1815 for (int i = 0; i < sequences.length; i++)
1819 newDs.addElement(null);
1821 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1823 if (importDs && ds != null)
1825 if (!newDs.contains(ds))
1827 newDs.setElementAt(ds, i);
1828 ds = new Sequence(ds);
1829 // update with new dataset sequence
1830 sequences[i].setDatasetSequence(ds);
1834 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1839 // copy and derive new dataset sequence
1840 sequences[i] = sequences[i].deriveSequence();
1841 alignment.getDataset().addSequence(
1842 sequences[i].getDatasetSequence());
1843 // TODO: avoid creation of duplicate dataset sequences with a
1844 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1846 alignment.addSequence(sequences[i]); // merges dataset
1850 newDs.clear(); // tidy up
1852 if (pastedal.getAlignmentAnnotation() != null)
1854 // Add any annotation attached to alignment.
1855 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1856 for (int i = 0; i < alann.length; i++)
1858 annotationAdded = true;
1859 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1861 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1862 newann.padAnnotation(alwidth);
1863 alignment.addAnnotation(newann);
1873 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1874 sequences, 0, alignment.getWidth(), alignment));
1876 // Add any annotations attached to sequences
1877 for (int i = 0; i < sequences.length; i++)
1879 if (sequences[i].getAnnotation() != null)
1881 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1883 annotationAdded = true;
1884 sequences[i].getAnnotation()[a].adjustForAlignment();
1885 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1886 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1891 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1898 // propagate alignment changed.
1899 viewport.setEndSeq(alignment.getHeight());
1900 if (annotationAdded)
1902 // Duplicate sequence annotation in all views.
1903 AlignmentI[] alview = this.getViewAlignments();
1904 for (int i = 0; i < sequences.length; i++)
1906 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1909 for (int avnum = 0; avnum < alview.length; avnum++)
1911 if (alview[avnum] != alignment)
1913 // duplicate in a view other than the one with input focus
1914 int avwidth = alview[avnum].getWidth() + 1;
1915 // this relies on sann being preserved after we
1916 // modify the sequence's annotation array for each duplication
1917 for (int a = 0; a < sann.length; a++)
1919 AlignmentAnnotation newann = new AlignmentAnnotation(
1921 sequences[i].addAlignmentAnnotation(newann);
1922 newann.padAnnotation(avwidth);
1923 alview[avnum].addAnnotation(newann); // annotation was
1924 // duplicated earlier
1925 alview[avnum].setAnnotationIndex(newann, a);
1930 buildSortByAnnotationScoresMenu();
1932 viewport.firePropertyChange("alignment", null,
1933 alignment.getSequences());
1938 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1940 String newtitle = new String("Copied sequences");
1942 if (Desktop.jalviewClipboard != null
1943 && Desktop.jalviewClipboard[2] != null)
1945 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1946 for (int i = 0; i < hc.size(); i++)
1948 int[] region = (int[]) hc.elementAt(i);
1949 af.viewport.hideColumns(region[0], region[1]);
1953 // >>>This is a fix for the moment, until a better solution is
1955 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1957 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1959 // TODO: maintain provenance of an alignment, rather than just make the
1960 // title a concatenation of operations.
1963 if (title.startsWith("Copied sequences"))
1969 newtitle = newtitle.concat("- from " + title);
1974 newtitle = new String("Pasted sequences");
1977 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1982 } catch (Exception ex)
1984 ex.printStackTrace();
1985 System.out.println("Exception whilst pasting: " + ex);
1986 // could be anything being pasted in here
1997 protected void cut_actionPerformed(ActionEvent e)
1999 copy_actionPerformed(null);
2000 delete_actionPerformed(null);
2009 protected void delete_actionPerformed(ActionEvent evt)
2012 SequenceGroup sg = viewport.getSelectionGroup();
2018 Vector seqs = new Vector();
2020 for (int i = 0; i < sg.getSize(); i++)
2022 seq = sg.getSequenceAt(i);
2023 seqs.addElement(seq);
2026 // If the cut affects all sequences, remove highlighted columns
2027 if (sg.getSize() == viewport.getAlignment().getHeight())
2029 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2030 sg.getEndRes() + 1);
2033 SequenceI[] cut = new SequenceI[seqs.size()];
2034 for (int i = 0; i < seqs.size(); i++)
2036 cut[i] = (SequenceI) seqs.elementAt(i);
2040 * //ADD HISTORY ITEM
2042 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2043 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2044 viewport.getAlignment()));
2046 viewport.setSelectionGroup(null);
2047 viewport.sendSelection();
2048 viewport.getAlignment().deleteGroup(sg);
2050 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2052 if (viewport.getAlignment().getHeight() < 1)
2056 this.setClosed(true);
2057 } catch (Exception ex)
2069 protected void deleteGroups_actionPerformed(ActionEvent e)
2071 viewport.getAlignment().deleteAllGroups();
2072 viewport.sequenceColours = null;
2073 viewport.setSelectionGroup(null);
2074 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2075 alignPanel.updateAnnotation();
2076 alignPanel.paintAlignment(true);
2085 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2087 SequenceGroup sg = new SequenceGroup();
2089 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2091 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2094 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2095 viewport.setSelectionGroup(sg);
2096 viewport.sendSelection();
2097 alignPanel.paintAlignment(true);
2098 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2107 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2109 if (viewport.cursorMode)
2111 alignPanel.seqPanel.keyboardNo1 = null;
2112 alignPanel.seqPanel.keyboardNo2 = null;
2114 viewport.setSelectionGroup(null);
2115 viewport.getColumnSelection().clear();
2116 viewport.setSelectionGroup(null);
2117 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2118 alignPanel.idPanel.idCanvas.searchResults = null;
2119 alignPanel.paintAlignment(true);
2120 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2121 viewport.sendSelection();
2130 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2132 SequenceGroup sg = viewport.getSelectionGroup();
2136 selectAllSequenceMenuItem_actionPerformed(null);
2141 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2143 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2146 alignPanel.paintAlignment(true);
2147 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2148 viewport.sendSelection();
2151 public void invertColSel_actionPerformed(ActionEvent e)
2153 viewport.invertColumnSelection();
2154 alignPanel.paintAlignment(true);
2155 viewport.sendSelection();
2164 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2166 trimAlignment(true);
2175 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2177 trimAlignment(false);
2180 void trimAlignment(boolean trimLeft)
2182 ColumnSelection colSel = viewport.getColumnSelection();
2185 if (colSel.size() > 0)
2189 column = colSel.getMin();
2193 column = colSel.getMax();
2197 if (viewport.getSelectionGroup() != null)
2199 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2200 viewport.getHiddenRepSequences());
2204 seqs = viewport.getAlignment().getSequencesArray();
2207 TrimRegionCommand trimRegion;
2210 trimRegion = new TrimRegionCommand("Remove Left",
2211 TrimRegionCommand.TRIM_LEFT, seqs, column,
2212 viewport.getAlignment(), viewport.getColumnSelection(),
2213 viewport.getSelectionGroup());
2214 viewport.setStartRes(0);
2218 trimRegion = new TrimRegionCommand("Remove Right",
2219 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2220 viewport.getAlignment(), viewport.getColumnSelection(),
2221 viewport.getSelectionGroup());
2224 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2226 addHistoryItem(trimRegion);
2228 Vector groups = viewport.getAlignment().getGroups();
2230 for (int i = 0; i < groups.size(); i++)
2232 SequenceGroup sg = (SequenceGroup) groups.get(i);
2234 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2235 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2237 viewport.getAlignment().deleteGroup(sg);
2241 viewport.firePropertyChange("alignment", null, viewport
2242 .getAlignment().getSequences());
2252 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2254 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2257 if (viewport.getSelectionGroup() != null)
2259 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2260 viewport.getHiddenRepSequences());
2261 start = viewport.getSelectionGroup().getStartRes();
2262 end = viewport.getSelectionGroup().getEndRes();
2266 seqs = viewport.getAlignment().getSequencesArray();
2269 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2270 "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());
2272 addHistoryItem(removeGapCols);
2274 statusBar.setText("Removed " + removeGapCols.getSize()
2275 + " empty columns.");
2277 // This is to maintain viewport position on first residue
2278 // of first sequence
2279 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2280 int startRes = seq.findPosition(viewport.startRes);
2281 // ShiftList shifts;
2282 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2283 // edit.alColumnChanges=shifts.getInverse();
2284 // if (viewport.hasHiddenColumns)
2285 // viewport.getColumnSelection().compensateForEdits(shifts);
2286 viewport.setStartRes(seq.findIndex(startRes) - 1);
2287 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2298 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2300 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2303 if (viewport.getSelectionGroup() != null)
2305 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2306 viewport.getHiddenRepSequences());
2307 start = viewport.getSelectionGroup().getStartRes();
2308 end = viewport.getSelectionGroup().getEndRes();
2312 seqs = viewport.getAlignment().getSequencesArray();
2315 // This is to maintain viewport position on first residue
2316 // of first sequence
2317 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2318 int startRes = seq.findPosition(viewport.startRes);
2320 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2321 viewport.getAlignment()));
2323 viewport.setStartRes(seq.findIndex(startRes) - 1);
2325 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2336 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2338 viewport.setPadGaps(padGapsMenuitem.isSelected());
2339 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2345 // if (justifySeqs>0)
2347 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2359 public void findMenuItem_actionPerformed(ActionEvent e)
2364 public void newView_actionPerformed(ActionEvent e)
2371 * @param copyAnnotation
2372 * if true then duplicate all annnotation, groups and settings
2373 * @return new alignment panel, already displayed.
2375 public AlignmentPanel newView(boolean copyAnnotation)
2377 return newView(null, copyAnnotation);
2383 * title of newly created view
2384 * @return new alignment panel, already displayed.
2386 public AlignmentPanel newView(String viewTitle)
2388 return newView(viewTitle, true);
2394 * title of newly created view
2395 * @param copyAnnotation
2396 * if true then duplicate all annnotation, groups and settings
2397 * @return new alignment panel, already displayed.
2399 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2401 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2403 if (!copyAnnotation)
2405 // just remove all the current annotation except for the automatic stuff
2406 newap.av.getAlignment().deleteAllGroups();
2407 for (AlignmentAnnotation alan : newap.av.getAlignment()
2408 .getAlignmentAnnotation())
2410 if (!alan.autoCalculated)
2412 newap.av.getAlignment().deleteAnnotation(alan);
2418 newap.av.gatherViewsHere = false;
2420 if (viewport.viewName == null)
2422 viewport.viewName = "Original";
2425 newap.av.historyList = viewport.historyList;
2426 newap.av.redoList = viewport.redoList;
2428 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2429 // make sure the new view has a unique name - this is essential for Jalview
2431 boolean addFirstIndex = false;
2432 if (viewTitle == null || viewTitle.trim().length() == 0)
2435 addFirstIndex = true;
2439 index = 1;// we count from 1 if given a specific name
2441 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2442 Vector comps = (Vector) PaintRefresher.components.get(viewport
2443 .getSequenceSetId());
2444 Vector existingNames = new Vector();
2445 for (int i = 0; i < comps.size(); i++)
2447 if (comps.elementAt(i) instanceof AlignmentPanel)
2449 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2450 if (!existingNames.contains(ap.av.viewName))
2452 existingNames.addElement(ap.av.viewName);
2457 while (existingNames.contains(newViewName))
2459 newViewName = viewTitle + " " + (++index);
2462 newap.av.viewName = newViewName;
2464 addAlignmentPanel(newap, true);
2466 if (alignPanels.size() == 2)
2468 viewport.gatherViewsHere = true;
2470 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2474 public void expandViews_actionPerformed(ActionEvent e)
2476 Desktop.instance.explodeViews(this);
2479 public void gatherViews_actionPerformed(ActionEvent e)
2481 Desktop.instance.gatherViews(this);
2490 public void font_actionPerformed(ActionEvent e)
2492 new FontChooser(alignPanel);
2501 protected void seqLimit_actionPerformed(ActionEvent e)
2503 viewport.setShowJVSuffix(seqLimits.isSelected());
2505 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2506 .calculateIdWidth());
2507 alignPanel.paintAlignment(true);
2510 public void idRightAlign_actionPerformed(ActionEvent e)
2512 viewport.rightAlignIds = idRightAlign.isSelected();
2513 alignPanel.paintAlignment(true);
2516 public void centreColumnLabels_actionPerformed(ActionEvent e)
2518 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2519 alignPanel.paintAlignment(true);
2525 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2527 protected void followHighlight_actionPerformed()
2529 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2531 alignPanel.scrollToPosition(
2532 alignPanel.seqPanel.seqCanvas.searchResults, false);
2542 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2544 viewport.setColourText(colourTextMenuItem.isSelected());
2545 alignPanel.paintAlignment(true);
2554 public void wrapMenuItem_actionPerformed(ActionEvent e)
2556 scaleAbove.setVisible(wrapMenuItem.isSelected());
2557 scaleLeft.setVisible(wrapMenuItem.isSelected());
2558 scaleRight.setVisible(wrapMenuItem.isSelected());
2559 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2560 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2563 public void showAllSeqs_actionPerformed(ActionEvent e)
2565 viewport.showAllHiddenSeqs();
2568 public void showAllColumns_actionPerformed(ActionEvent e)
2570 viewport.showAllHiddenColumns();
2574 public void hideSelSequences_actionPerformed(ActionEvent e)
2576 viewport.hideAllSelectedSeqs();
2577 alignPanel.paintAlignment(true);
2581 * called by key handler and the hide all/show all menu items
2586 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2589 boolean hide = false;
2590 SequenceGroup sg = viewport.getSelectionGroup();
2591 if (!toggleSeqs && !toggleCols)
2593 // Hide everything by the current selection - this is a hack - we do the
2594 // invert and then hide
2595 // first check that there will be visible columns after the invert.
2596 if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()
2597 .getSelected().size() > 0)
2598 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2601 // now invert the sequence set, if required - empty selection implies
2602 // that no hiding is required.
2605 invertSequenceMenuItem_actionPerformed(null);
2606 sg = viewport.getSelectionGroup();
2610 viewport.expandColSelection(sg, true);
2611 // finally invert the column selection and get the new sequence
2613 invertColSel_actionPerformed(null);
2620 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2622 hideSelSequences_actionPerformed(null);
2625 else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))
2627 showAllSeqs_actionPerformed(null);
2633 if (viewport.getColumnSelection().getSelected().size() > 0)
2635 hideSelColumns_actionPerformed(null);
2638 viewport.setSelectionGroup(sg);
2643 showAllColumns_actionPerformed(null);
2652 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2653 * event.ActionEvent)
2655 public void hideAllButSelection_actionPerformed(ActionEvent e)
2657 toggleHiddenRegions(false, false);
2664 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2667 public void hideAllSelection_actionPerformed(ActionEvent e)
2669 SequenceGroup sg = viewport.getSelectionGroup();
2670 viewport.expandColSelection(sg, false);
2671 viewport.hideAllSelectedSeqs();
2672 viewport.hideSelectedColumns();
2673 alignPanel.paintAlignment(true);
2680 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2683 public void showAllhidden_actionPerformed(ActionEvent e)
2685 viewport.showAllHiddenColumns();
2686 viewport.showAllHiddenSeqs();
2687 alignPanel.paintAlignment(true);
2690 public void hideSelColumns_actionPerformed(ActionEvent e)
2692 viewport.hideSelectedColumns();
2693 alignPanel.paintAlignment(true);
2696 public void hiddenMarkers_actionPerformed(ActionEvent e)
2698 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2708 protected void scaleAbove_actionPerformed(ActionEvent e)
2710 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2711 alignPanel.paintAlignment(true);
2720 protected void scaleLeft_actionPerformed(ActionEvent e)
2722 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2723 alignPanel.paintAlignment(true);
2732 protected void scaleRight_actionPerformed(ActionEvent e)
2734 viewport.setScaleRightWrapped(scaleRight.isSelected());
2735 alignPanel.paintAlignment(true);
2744 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2746 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2747 alignPanel.paintAlignment(true);
2756 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2758 viewport.setShowText(viewTextMenuItem.isSelected());
2759 alignPanel.paintAlignment(true);
2768 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2770 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2771 alignPanel.paintAlignment(true);
2774 public FeatureSettings featureSettings;
2776 public void featureSettings_actionPerformed(ActionEvent e)
2778 if (featureSettings != null)
2780 featureSettings.close();
2781 featureSettings = null;
2783 if (!showSeqFeatures.isSelected())
2785 // make sure features are actually displayed
2786 showSeqFeatures.setSelected(true);
2787 showSeqFeatures_actionPerformed(null);
2789 featureSettings = new FeatureSettings(this);
2793 * Set or clear 'Show Sequence Features'
2798 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2800 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2801 alignPanel.paintAlignment(true);
2802 if (alignPanel.getOverviewPanel() != null)
2804 alignPanel.getOverviewPanel().updateOverviewImage();
2809 * Set or clear 'Show Sequence Features'
2814 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2816 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2818 if (viewport.getShowSequenceFeaturesHeight())
2820 // ensure we're actually displaying features
2821 viewport.setShowSequenceFeatures(true);
2822 showSeqFeatures.setSelected(true);
2824 alignPanel.paintAlignment(true);
2825 if (alignPanel.getOverviewPanel() != null)
2827 alignPanel.getOverviewPanel().updateOverviewImage();
2837 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2839 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2840 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2843 public void alignmentProperties()
2845 JEditorPane editPane = new JEditorPane("text/html", "");
2846 editPane.setEditable(false);
2847 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
2849 editPane.setText("<html>" + contents.toString() + "</html>");
2850 JInternalFrame frame = new JInternalFrame();
2851 frame.getContentPane().add(new JScrollPane(editPane));
2853 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2854 + getTitle(), 500, 400);
2863 public void overviewMenuItem_actionPerformed(ActionEvent e)
2865 if (alignPanel.overviewPanel != null)
2870 JInternalFrame frame = new JInternalFrame();
2871 OverviewPanel overview = new OverviewPanel(alignPanel);
2872 frame.setContentPane(overview);
2873 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2874 frame.getWidth(), frame.getHeight());
2876 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2877 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2879 public void internalFrameClosed(
2880 javax.swing.event.InternalFrameEvent evt)
2882 alignPanel.setOverviewPanel(null);
2886 alignPanel.setOverviewPanel(overview);
2889 public void textColour_actionPerformed(ActionEvent e)
2891 new TextColourChooser().chooseColour(alignPanel, null);
2900 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2911 public void clustalColour_actionPerformed(ActionEvent e)
2913 changeColour(new ClustalxColourScheme(
2914 viewport.getAlignment().getSequences(),
2915 viewport.getAlignment().getWidth()));
2924 public void zappoColour_actionPerformed(ActionEvent e)
2926 changeColour(new ZappoColourScheme());
2935 public void taylorColour_actionPerformed(ActionEvent e)
2937 changeColour(new TaylorColourScheme());
2946 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2948 changeColour(new HydrophobicColourScheme());
2957 public void helixColour_actionPerformed(ActionEvent e)
2959 changeColour(new HelixColourScheme());
2968 public void strandColour_actionPerformed(ActionEvent e)
2970 changeColour(new StrandColourScheme());
2979 public void turnColour_actionPerformed(ActionEvent e)
2981 changeColour(new TurnColourScheme());
2990 public void buriedColour_actionPerformed(ActionEvent e)
2992 changeColour(new BuriedColourScheme());
3001 public void nucleotideColour_actionPerformed(ActionEvent e)
3003 changeColour(new NucleotideColourScheme());
3006 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3008 changeColour(new PurinePyrimidineColourScheme());
3011 public void covariationColour_actionPerformed(ActionEvent e)
3013 changeColour(new CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation()[0]));
3016 public void annotationColour_actionPerformed(ActionEvent e)
3018 new AnnotationColourChooser(viewport, alignPanel);
3021 public void rnahelicesColour_actionPerformed(ActionEvent e)
3023 new RNAHelicesColourChooser(viewport, alignPanel);
3032 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3034 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3043 public void changeColour(ColourSchemeI cs)
3049 if (viewport.getAbovePIDThreshold())
3051 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3054 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3056 viewport.setGlobalColourScheme(cs);
3060 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3063 if (viewport.getConservationSelected())
3066 Alignment al = (Alignment) viewport.getAlignment();
3067 Conservation c = new Conservation("All",
3068 ResidueProperties.propHash, 3, al.getSequences(), 0,
3072 c.verdict(false, viewport.getConsPercGaps());
3074 cs.setConservation(c);
3076 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3081 cs.setConservation(null);
3084 cs.setConsensus(viewport.getSequenceConsensusHash());
3087 viewport.setGlobalColourScheme(cs);
3089 if (viewport.getColourAppliesToAllGroups())
3091 Vector groups = viewport.getAlignment().getGroups();
3093 for (int i = 0; i < groups.size(); i++)
3095 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
3103 if (cs instanceof ClustalxColourScheme)
3105 sg.cs = new ClustalxColourScheme(
3106 sg.getSequences(viewport.getHiddenRepSequences()),
3109 else if (cs instanceof UserColourScheme)
3111 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3117 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
3118 } catch (Exception ex)
3123 if (viewport.getAbovePIDThreshold()
3124 || cs instanceof PIDColourScheme
3125 || cs instanceof Blosum62ColourScheme)
3127 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3129 sg.cs.setConsensus(AAFrequency.calculate(
3130 sg.getSequences(viewport.getHiddenRepSequences()),
3131 sg.getStartRes(), sg.getEndRes() + 1));
3135 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3138 if (viewport.getConservationSelected())
3140 Conservation c = new Conservation("Group",
3141 ResidueProperties.propHash, 3,
3142 sg.getSequences(viewport.getHiddenRepSequences()),
3143 sg.getStartRes(), sg.getEndRes() + 1);
3145 c.verdict(false, viewport.getConsPercGaps());
3146 sg.cs.setConservation(c);
3150 sg.cs.setConservation(null);
3155 if (alignPanel.getOverviewPanel() != null)
3157 alignPanel.getOverviewPanel().updateOverviewImage();
3160 alignPanel.paintAlignment(true);
3169 protected void modifyPID_actionPerformed(ActionEvent e)
3171 if (viewport.getAbovePIDThreshold()
3172 && viewport.getGlobalColourScheme() != null)
3174 SliderPanel.setPIDSliderSource(alignPanel,
3175 viewport.getGlobalColourScheme(), "Background");
3176 SliderPanel.showPIDSlider();
3186 protected void modifyConservation_actionPerformed(ActionEvent e)
3188 if (viewport.getConservationSelected()
3189 && viewport.getGlobalColourScheme()!= null)
3191 SliderPanel.setConservationSlider(alignPanel,
3192 viewport.getGlobalColourScheme(), "Background");
3193 SliderPanel.showConservationSlider();
3203 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3205 viewport.setConservationSelected(conservationMenuItem.isSelected());
3207 viewport.setAbovePIDThreshold(false);
3208 abovePIDThreshold.setSelected(false);
3210 changeColour(viewport.getGlobalColourScheme());
3212 modifyConservation_actionPerformed(null);
3221 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3223 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3225 conservationMenuItem.setSelected(false);
3226 viewport.setConservationSelected(false);
3228 changeColour(viewport.getGlobalColourScheme());
3230 modifyPID_actionPerformed(null);
3239 public void userDefinedColour_actionPerformed(ActionEvent e)
3241 if (e.getActionCommand().equals("User Defined..."))
3243 new UserDefinedColours(alignPanel, null);
3247 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3248 .getUserColourSchemes().get(e.getActionCommand());
3254 public void updateUserColourMenu()
3257 Component[] menuItems = colourMenu.getMenuComponents();
3258 int i, iSize = menuItems.length;
3259 for (i = 0; i < iSize; i++)
3261 if (menuItems[i].getName() != null
3262 && menuItems[i].getName().equals("USER_DEFINED"))
3264 colourMenu.remove(menuItems[i]);
3268 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3270 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3271 .getUserColourSchemes().keys();
3273 while (userColours.hasMoreElements())
3275 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3276 userColours.nextElement().toString());
3277 radioItem.setName("USER_DEFINED");
3278 radioItem.addMouseListener(new MouseAdapter()
3280 public void mousePressed(MouseEvent evt)
3282 if (evt.isControlDown()
3283 || SwingUtilities.isRightMouseButton(evt))
3285 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3287 int option = JOptionPane.showInternalConfirmDialog(
3288 jalview.gui.Desktop.desktop,
3289 "Remove from default list?",
3290 "Remove user defined colour",
3291 JOptionPane.YES_NO_OPTION);
3292 if (option == JOptionPane.YES_OPTION)
3294 jalview.gui.UserDefinedColours
3295 .removeColourFromDefaults(radioItem.getText());
3296 colourMenu.remove(radioItem);
3300 radioItem.addActionListener(new ActionListener()
3302 public void actionPerformed(ActionEvent evt)
3304 userDefinedColour_actionPerformed(evt);
3311 radioItem.addActionListener(new ActionListener()
3313 public void actionPerformed(ActionEvent evt)
3315 userDefinedColour_actionPerformed(evt);
3319 colourMenu.insert(radioItem, 15);
3320 colours.add(radioItem);
3331 public void PIDColour_actionPerformed(ActionEvent e)
3333 changeColour(new PIDColourScheme());
3342 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3344 changeColour(new Blosum62ColourScheme());
3353 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3355 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3356 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3357 .getAlignment().getSequenceAt(0), null);
3358 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3359 viewport.getAlignment()));
3360 alignPanel.paintAlignment(true);
3369 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3371 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3372 AlignmentSorter.sortByID(viewport.getAlignment());
3373 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3374 alignPanel.paintAlignment(true);
3383 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3385 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3386 AlignmentSorter.sortByLength(viewport.getAlignment());
3387 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3388 viewport.getAlignment()));
3389 alignPanel.paintAlignment(true);
3398 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3400 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3401 AlignmentSorter.sortByGroup(viewport.getAlignment());
3402 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3403 viewport.getAlignment()));
3405 alignPanel.paintAlignment(true);
3414 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3416 new RedundancyPanel(alignPanel, this);
3425 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3427 if ((viewport.getSelectionGroup() == null)
3428 || (viewport.getSelectionGroup().getSize() < 2))
3430 JOptionPane.showInternalMessageDialog(this,
3431 "You must select at least 2 sequences.", "Invalid Selection",
3432 JOptionPane.WARNING_MESSAGE);
3436 JInternalFrame frame = new JInternalFrame();
3437 frame.setContentPane(new PairwiseAlignPanel(viewport));
3438 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3448 public void PCAMenuItem_actionPerformed(ActionEvent e)
3450 if (((viewport.getSelectionGroup() != null)
3451 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3452 .getSelectionGroup().getSize() > 0))
3453 || (viewport.getAlignment().getHeight() < 4))
3455 JOptionPane.showInternalMessageDialog(this,
3456 "Principal component analysis must take\n"
3457 + "at least 4 input sequences.",
3458 "Sequence selection insufficient",
3459 JOptionPane.WARNING_MESSAGE);
3464 new PCAPanel(alignPanel);
3467 public void autoCalculate_actionPerformed(ActionEvent e)
3469 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3470 if (viewport.autoCalculateConsensus)
3472 viewport.firePropertyChange("alignment", null, viewport
3473 .getAlignment().getSequences());
3476 public void sortByTreeOption_actionPerformed(ActionEvent e)
3478 viewport.sortByTree = sortByTree.isSelected();
3482 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3484 viewport.followSelection = listenToViewSelections.isSelected();
3492 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3494 NewTreePanel("AV", "PID", "Average distance tree using PID");
3503 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3505 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3514 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3516 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3525 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3527 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3540 void NewTreePanel(String type, String pwType, String title)
3544 if (viewport.getSelectionGroup() != null)
3546 if (viewport.getSelectionGroup().getSize() < 3)
3551 "You need to have more than two sequences selected to build a tree!",
3552 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3557 SequenceGroup sg = viewport.getSelectionGroup();
3559 /* Decide if the selection is a column region */
3560 while (s < sg.getSize())
3562 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3568 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3569 + "Try using the Pad function in the edit menu,\n"
3570 + "or one of the multiple sequence alignment web services.",
3571 "Sequences in selection are not aligned",
3572 JOptionPane.WARNING_MESSAGE);
3578 title = title + " on region";
3579 tp = new TreePanel(alignPanel, type, pwType);
3583 // are the visible sequences aligned?
3584 if (!viewport.getAlignment().isAligned(false))
3589 "The sequences must be aligned before creating a tree.\n"
3590 + "Try using the Pad function in the edit menu,\n"
3591 + "or one of the multiple sequence alignment web services.",
3592 "Sequences not aligned",
3593 JOptionPane.WARNING_MESSAGE);
3598 if (viewport.getAlignment().getHeight() < 2)
3603 tp = new TreePanel(alignPanel, type, pwType);
3608 if (viewport.viewName != null)
3610 title += viewport.viewName + " of ";
3613 title += this.title;
3615 Desktop.addInternalFrame(tp, title, 600, 500);
3626 public void addSortByOrderMenuItem(String title,
3627 final AlignmentOrder order)
3629 final JMenuItem item = new JMenuItem("by " + title);
3631 item.addActionListener(new java.awt.event.ActionListener()
3633 public void actionPerformed(ActionEvent e)
3635 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3637 // TODO: JBPNote - have to map order entries to curent SequenceI
3639 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3641 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3642 viewport.getAlignment()));
3644 alignPanel.paintAlignment(true);
3650 * Add a new sort by annotation score menu item
3653 * the menu to add the option to
3655 * the label used to retrieve scores for each sequence on the
3658 public void addSortByAnnotScoreMenuItem(JMenu sort,
3659 final String scoreLabel)
3661 final JMenuItem item = new JMenuItem(scoreLabel);
3663 item.addActionListener(new java.awt.event.ActionListener()
3665 public void actionPerformed(ActionEvent e)
3667 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3668 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3669 viewport.getAlignment());// ,viewport.getSelectionGroup());
3670 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3671 viewport.getAlignment()));
3672 alignPanel.paintAlignment(true);
3678 * last hash for alignment's annotation array - used to minimise cost of
3681 protected int _annotationScoreVectorHash;
3684 * search the alignment and rebuild the sort by annotation score submenu the
3685 * last alignment annotation vector hash is stored to minimize cost of
3686 * rebuilding in subsequence calls.
3689 public void buildSortByAnnotationScoresMenu()
3691 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3696 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3698 sortByAnnotScore.removeAll();
3699 // almost certainly a quicker way to do this - but we keep it simple
3700 Hashtable scoreSorts = new Hashtable();
3701 AlignmentAnnotation aann[];
3702 Enumeration sq = viewport.getAlignment().getSequences().elements();
3703 while (sq.hasMoreElements())
3705 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3706 for (int i = 0; aann != null && i < aann.length; i++)
3708 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3710 scoreSorts.put(aann[i].label, aann[i].label);
3714 Enumeration labels = scoreSorts.keys();
3715 while (labels.hasMoreElements())
3717 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3718 (String) labels.nextElement());
3720 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3723 _annotationScoreVectorHash = viewport.getAlignment()
3724 .getAlignmentAnnotation().hashCode();
3729 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3730 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3731 * call. Listeners are added to remove the menu item when the treePanel is
3732 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3736 * Displayed tree window.
3738 * SortBy menu item title.
3740 public void buildTreeMenu()
3742 sortByTreeMenu.removeAll();
3744 Vector comps = (Vector) PaintRefresher.components.get(viewport
3745 .getSequenceSetId());
3746 Vector treePanels = new Vector();
3747 int i, iSize = comps.size();
3748 for (i = 0; i < iSize; i++)
3750 if (comps.elementAt(i) instanceof TreePanel)
3752 treePanels.add(comps.elementAt(i));
3756 iSize = treePanels.size();
3760 sortByTreeMenu.setVisible(false);
3764 sortByTreeMenu.setVisible(true);
3766 for (i = 0; i < treePanels.size(); i++)
3768 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3769 final JMenuItem item = new JMenuItem(tp.getTitle());
3770 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3771 item.addActionListener(new java.awt.event.ActionListener()
3773 public void actionPerformed(ActionEvent e)
3775 tp.sortByTree_actionPerformed(null);
3776 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3781 sortByTreeMenu.add(item);
3785 public boolean sortBy(AlignmentOrder alorder, String undoname)
3787 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3788 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3789 if (undoname != null)
3791 addHistoryItem(new OrderCommand(undoname, oldOrder,
3792 viewport.getAlignment()));
3794 alignPanel.paintAlignment(true);
3799 * Work out whether the whole set of sequences or just the selected set will
3800 * be submitted for multiple alignment.
3803 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3805 // Now, check we have enough sequences
3806 AlignmentView msa = null;
3808 if ((viewport.getSelectionGroup() != null)
3809 && (viewport.getSelectionGroup().getSize() > 1))
3811 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3812 // some common interface!
3814 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3815 * SequenceI[sz = seqs.getSize(false)];
3817 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3818 * seqs.getSequenceAt(i); }
3820 msa = viewport.getAlignmentView(true);
3825 * Vector seqs = viewport.getAlignment().getSequences();
3827 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3829 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3830 * seqs.elementAt(i); } }
3832 msa = viewport.getAlignmentView(false);
3838 * Decides what is submitted to a secondary structure prediction service: the
3839 * first sequence in the alignment, or in the current selection, or, if the
3840 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3841 * region or the whole alignment. (where the first sequence in the set is the
3842 * one that the prediction will be for).
3844 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3846 AlignmentView seqs = null;
3848 if ((viewport.getSelectionGroup() != null)
3849 && (viewport.getSelectionGroup().getSize() > 0))
3851 seqs = viewport.getAlignmentView(true);
3855 seqs = viewport.getAlignmentView(false);
3857 // limit sequences - JBPNote in future - could spawn multiple prediction
3859 // TODO: viewport.getAlignment().isAligned is a global state - the local
3860 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3861 if (!viewport.getAlignment().isAligned(false))
3863 seqs.setSequences(new SeqCigar[]
3864 { seqs.getSequences()[0] });
3865 // TODO: if seqs.getSequences().length>1 then should really have warned
3878 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3880 // Pick the tree file
3881 JalviewFileChooser chooser = new JalviewFileChooser(
3882 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3883 chooser.setFileView(new JalviewFileView());
3884 chooser.setDialogTitle("Select a newick-like tree file");
3885 chooser.setToolTipText("Load a tree file");
3887 int value = chooser.showOpenDialog(null);
3889 if (value == JalviewFileChooser.APPROVE_OPTION)
3891 String choice = chooser.getSelectedFile().getPath();
3892 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3893 jalview.io.NewickFile fin = null;
3896 fin = new jalview.io.NewickFile(choice, "File");
3897 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3898 } catch (Exception ex)
3900 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3901 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3902 ex.printStackTrace();
3904 if (fin != null && fin.hasWarningMessage())
3906 JOptionPane.showMessageDialog(Desktop.desktop,
3907 fin.getWarningMessage(), "Possible problem with tree file",
3908 JOptionPane.WARNING_MESSAGE);
3913 public TreePanel ShowNewickTree(NewickFile nf, String title)
3915 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3918 public TreePanel ShowNewickTree(NewickFile nf, String title,
3919 AlignmentView input)
3921 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3924 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3925 int h, int x, int y)
3927 return ShowNewickTree(nf, title, null, w, h, x, y);
3931 * Add a treeviewer for the tree extracted from a newick file object to the
3932 * current alignment view
3939 * Associated alignment input data (or null)
3948 * @return TreePanel handle
3950 public TreePanel ShowNewickTree(NewickFile nf, String title,
3951 AlignmentView input, int w, int h, int x, int y)
3953 TreePanel tp = null;
3959 if (nf.getTree() != null)
3961 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3967 tp.setLocation(x, y);
3970 Desktop.addInternalFrame(tp, title, w, h);
3972 } catch (Exception ex)
3974 ex.printStackTrace();
3980 private boolean buildingMenu = false;
3983 * Generates menu items and listener event actions for web service clients
3986 public void BuildWebServiceMenu()
3988 while (buildingMenu)
3992 System.err.println("Waiting for building menu to finish.");
3994 } catch (Exception e)
3999 final AlignFrame me = this;
4000 buildingMenu = true;
4001 new Thread(new Runnable()
4007 System.err.println("Building ws menu again "
4008 + Thread.currentThread());
4009 // TODO: add support for context dependent disabling of services based
4011 // alignment and current selection
4012 // TODO: add additional serviceHandle parameter to specify abstract
4014 // class independently of AbstractName
4015 // TODO: add in rediscovery GUI function to restart discoverer
4016 // TODO: group services by location as well as function and/or
4018 // object broker mechanism.
4019 final Vector wsmenu = new Vector();
4020 final IProgressIndicator af = me;
4021 final JMenu msawsmenu = new JMenu("Alignment");
4022 final JMenu secstrmenu = new JMenu(
4023 "Secondary Structure Prediction");
4024 final JMenu seqsrchmenu = new JMenu(
4025 "Sequence Database Search");
4026 final JMenu analymenu = new JMenu(
4028 // JAL-940 - only show secondary structure prediction services from the legacy server
4029 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4031 Discoverer.services != null
4032 && (Discoverer.services.size() > 0))
4034 // TODO: refactor to allow list of AbstractName/Handler bindings to
4036 // stored or retrieved from elsewhere
4037 Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4038 Vector secstrpr = (Vector) Discoverer.services
4040 Vector seqsrch = null; // (Vector) Discoverer.services.get("SeqSearch");
4041 // TODO: move GUI generation code onto service implementation - so a
4042 // client instance attaches itself to the GUI with method call like
4043 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
4047 // Add any Multiple Sequence Alignment Services
4048 for (int i = 0, j = msaws.size(); i < j; i++)
4050 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
4052 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4053 .getServiceClient(sh);
4054 impl.attachWSMenuEntry(msawsmenu, me);
4058 if (secstrpr != null)
4060 // Add any secondary structure prediction services
4061 for (int i = 0, j = secstrpr.size(); i < j; i++)
4063 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4065 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4066 .getServiceClient(sh);
4067 impl.attachWSMenuEntry(secstrmenu, me);
4070 if (seqsrch != null)
4072 // Add any sequence search services
4073 for (int i = 0, j = seqsrch.size(); i < j; i++)
4075 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
4077 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4078 .getServiceClient(sh);
4079 impl.attachWSMenuEntry(seqsrchmenu, me);
4084 // TODO: move into separate menu builder class.
4085 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4087 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4088 if (jws2servs != null)
4090 if (jws2servs.hasServices())
4092 jws2servs.attachWSMenuEntry(msawsmenu, me);
4096 // Add all submenus in the order they should appear on the web services menu
4097 wsmenu.add(msawsmenu);
4098 wsmenu.add(secstrmenu);
4099 wsmenu.add(analymenu);
4100 // No search services yet
4101 // wsmenu.add(seqsrchmenu);
4103 javax.swing.SwingUtilities.invokeLater(new Runnable()
4109 webService.removeAll();
4110 // first, add discovered services onto the webservices menu
4111 if (wsmenu.size() > 0)
4113 for (int i = 0, j = wsmenu.size(); i < j; i++)
4115 webService.add((JMenu) wsmenu.get(i));
4120 webService.add(me.webServiceNoServices);
4122 build_urlServiceMenu(me.webService);
4123 build_fetchdbmenu(webService);
4124 } catch (Exception e)
4130 } catch (Exception e)
4135 buildingMenu = false;
4143 * construct any groupURL type service menu entries.
4147 private void build_urlServiceMenu(JMenu webService)
4149 // TODO: remove this code when 2.7 is released
4150 // DEBUG - alignmentView
4152 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4153 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4155 * @Override public void actionPerformed(ActionEvent e) {
4156 * jalview.datamodel.AlignmentView.testSelectionViews(af.viewport.getAlignment(),
4157 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4159 * }); webService.add(testAlView);
4161 // TODO: refactor to RestClient discoverer and merge menu entries for
4162 // rest-style services with other types of analysis/calculation service
4163 // SHmmr test client - still being implemented.
4164 // DEBUG - alignmentView
4166 for (jalview.ws.rest.RestClient client: jalview.ws.rest.RestClient.getRestClients()) {
4167 client.attachWSMenuEntry(JvSwingUtils.findOrCreateMenu(webService, client.getAction()), this);
4170 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4172 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4178 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4179 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4180 * getProperty("LAST_DIRECTORY"));
4182 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4183 * to Vamsas file"); chooser.setToolTipText("Export");
4185 * int value = chooser.showSaveDialog(this);
4187 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4188 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4189 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4190 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4193 * prototype of an automatically enabled/disabled analysis function
4196 protected void setShowProductsEnabled()
4198 SequenceI[] selection = viewport.getSequenceSelection();
4199 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4200 viewport.getAlignment().getDataset()))
4202 showProducts.setEnabled(true);
4207 showProducts.setEnabled(false);
4212 * search selection for sequence xRef products and build the show products
4217 * @return true if showProducts menu should be enabled.
4219 public boolean canShowProducts(SequenceI[] selection,
4220 boolean isRegionSelection, Alignment dataset)
4222 boolean showp = false;
4225 showProducts.removeAll();
4226 final boolean dna = viewport.getAlignment().isNucleotide();
4227 final Alignment ds = dataset;
4228 String[] ptypes = (selection == null || selection.length == 0) ? null
4229 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4231 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4232 // selection, dataset, true);
4233 final SequenceI[] sel = selection;
4234 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4237 final boolean isRegSel = isRegionSelection;
4238 final AlignFrame af = this;
4239 final String source = ptypes[t];
4240 JMenuItem xtype = new JMenuItem(ptypes[t]);
4241 xtype.addActionListener(new ActionListener()
4244 public void actionPerformed(ActionEvent e)
4246 // TODO: new thread for this call with vis-delay
4247 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4248 isRegSel, dna, source);
4252 showProducts.add(xtype);
4254 showProducts.setVisible(showp);
4255 showProducts.setEnabled(showp);
4256 } catch (Exception e)
4258 jalview.bin.Cache.log
4259 .warn("canTranslate threw an exception - please report to help@jalview.org",
4266 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4267 boolean isRegSel, boolean dna, String source)
4269 final boolean fisRegSel = isRegSel;
4270 final boolean fdna = dna;
4271 final String fsrc = source;
4272 final AlignFrame ths = this;
4273 final SequenceI[] fsel = sel;
4274 Runnable foo = new Runnable()
4279 final long sttime = System.currentTimeMillis();
4280 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4283 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4287 Alignment prods = CrossRef
4288 .findXrefSequences(fsel, fdna, fsrc, ds);
4291 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4292 for (int s = 0; s < sprods.length; s++)
4294 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4295 if (ds.getSequences() == null
4296 || !ds.getSequences().contains(
4297 sprods[s].getDatasetSequence()))
4298 ds.addSequence(sprods[s].getDatasetSequence());
4299 sprods[s].updatePDBIds();
4301 Alignment al = new Alignment(sprods);
4302 AlignedCodonFrame[] cf = prods.getCodonFrames();
4304 for (int s = 0; cf != null && s < cf.length; s++)
4306 al.addCodonFrame(cf[s]);
4309 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4311 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4312 + " for " + ((fisRegSel) ? "selected region of " : "")
4314 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4319 System.err.println("No Sequences generated for xRef type "
4322 } catch (Exception e)
4324 jalview.bin.Cache.log.error(
4325 "Exception when finding crossreferences", e);
4326 } catch (OutOfMemoryError e)
4328 new OOMWarning("whilst fetching crossreferences", e);
4331 jalview.bin.Cache.log.error("Error when finding crossreferences",
4334 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4339 Thread frunner = new Thread(foo);
4343 public boolean canShowTranslationProducts(SequenceI[] selection,
4344 AlignmentI alignment)
4349 return (jalview.analysis.Dna.canTranslate(selection,
4350 viewport.getViewAsVisibleContigs(true)));
4351 } catch (Exception e)
4353 jalview.bin.Cache.log
4354 .warn("canTranslate threw an exception - please report to help@jalview.org",
4360 public void showProducts_actionPerformed(ActionEvent e)
4362 // /////////////////////////////
4363 // Collect Data to be translated/transferred
4365 SequenceI[] selection = viewport.getSequenceSelection();
4366 AlignmentI al = null;
4369 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4370 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4371 viewport.getAlignment().getDataset());
4372 } catch (Exception ex)
4375 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4382 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4383 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4387 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4388 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4389 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4393 public void showTranslation_actionPerformed(ActionEvent e)
4395 // /////////////////////////////
4396 // Collect Data to be translated/transferred
4398 SequenceI[] selection = viewport.getSequenceSelection();
4399 String[] seqstring = viewport.getViewAsString(true);
4400 AlignmentI al = null;
4403 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4404 viewport.getViewAsVisibleContigs(true), viewport
4405 .getGapCharacter(), viewport.getAlignment()
4406 .getAlignmentAnnotation(), viewport.getAlignment()
4407 .getWidth(), viewport.getAlignment().getDataset());
4408 } catch (Exception ex)
4411 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4418 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4419 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4423 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4424 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4425 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4430 * Try to load a features file onto the alignment.
4433 * contents or path to retrieve file
4435 * access mode of file (see jalview.io.AlignFile)
4436 * @return true if features file was parsed corectly.
4438 public boolean parseFeaturesFile(String file, String type)
4440 boolean featuresFile = false;
4443 featuresFile = new FeaturesFile(file, type)
4444 .parse(viewport.getAlignment().getDataset(),
4445 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
4446 false, jalview.bin.Cache.getDefault(
4447 "RELAXEDSEQIDMATCHING", false));
4448 } catch (Exception ex)
4450 ex.printStackTrace();
4455 viewport.showSequenceFeatures = true;
4456 showSeqFeatures.setSelected(true);
4457 if (alignPanel.seqPanel.seqCanvas.fr != null)
4459 // update the min/max ranges where necessary
4460 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4462 if (featureSettings != null)
4464 featureSettings.setTableData();
4466 alignPanel.paintAlignment(true);
4469 return featuresFile;
4472 public void dragEnter(DropTargetDragEvent evt)
4476 public void dragExit(DropTargetEvent evt)
4480 public void dragOver(DropTargetDragEvent evt)
4484 public void dropActionChanged(DropTargetDragEvent evt)
4488 public void drop(DropTargetDropEvent evt)
4490 Transferable t = evt.getTransferable();
4491 java.util.List files = null;
4495 DataFlavor uriListFlavor = new DataFlavor(
4496 "text/uri-list;class=java.lang.String");
4497 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4499 // Works on Windows and MacOSX
4500 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4501 files = (java.util.List) t
4502 .getTransferData(DataFlavor.javaFileListFlavor);
4504 else if (t.isDataFlavorSupported(uriListFlavor))
4506 // This is used by Unix drag system
4507 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4508 String data = (String) t.getTransferData(uriListFlavor);
4509 files = new java.util.ArrayList(1);
4510 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4511 data, "\r\n"); st.hasMoreTokens();)
4513 String s = st.nextToken();
4514 if (s.startsWith("#"))
4516 // the line is a comment (as per the RFC 2483)
4520 java.net.URI uri = new java.net.URI(s);
4521 // check to see if we can handle this kind of URI
4522 if (uri.getScheme().toLowerCase().startsWith("http"))
4524 files.add(uri.toString());
4528 // otherwise preserve old behaviour: catch all for file objects
4529 java.io.File file = new java.io.File(uri);
4530 files.add(file.toString());
4534 } catch (Exception e)
4536 e.printStackTrace();
4542 // check to see if any of these files have names matching sequences in
4544 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4545 .getAlignment().getSequencesArray());
4547 * Object[] { String,SequenceI}
4549 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4550 ArrayList<String> filesnotmatched = new ArrayList<String>();
4551 for (int i = 0; i < files.size(); i++)
4553 String file = files.get(i).toString();
4555 String protocol = FormatAdapter.checkProtocol(file);
4556 if (protocol == jalview.io.FormatAdapter.FILE)
4558 File fl = new File(file);
4559 pdbfn = fl.getName();
4561 else if (protocol == jalview.io.FormatAdapter.URL)
4563 URL url = new URL(file);
4564 pdbfn = url.getFile();
4566 if (pdbfn.length() > 0)
4568 // attempt to find a match in the alignment
4569 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4570 int l = 0, c = pdbfn.indexOf(".");
4571 while (mtch == null && c != -1)
4576 } while ((c = pdbfn.indexOf(".", l)) > l);
4579 pdbfn = pdbfn.substring(0, l);
4581 mtch = idm.findAllIdMatches(pdbfn);
4588 type = new IdentifyFile().Identify(file, protocol);
4589 } catch (Exception ex)
4595 if (type.equalsIgnoreCase("PDB"))
4597 filesmatched.add(new Object[]
4598 { file, protocol, mtch });
4603 // File wasn't named like one of the sequences or wasn't a PDB file.
4604 filesnotmatched.add(file);
4608 if (filesmatched.size() > 0)
4610 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4614 "Do you want to automatically associate the "
4615 + filesmatched.size()
4616 + " PDB files with sequences in the alignment that have the same name ?",
4617 "Automatically Associate PDB files by name",
4618 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4621 for (Object[] fm : filesmatched)
4623 // try and associate
4624 // TODO: may want to set a standard ID naming formalism for
4625 // associating PDB files which have no IDs.
4626 for (SequenceI toassoc: (SequenceI[])fm[2]) {
4627 PDBEntry pe = new AssociatePdbFileWithSeq()
4628 .associatePdbWithSeq((String) fm[0], (String) fm[1],
4633 .println("Associated file : " + ((String) fm[0])
4635 + toassoc.getDisplayId(true));
4639 alignPanel.paintAlignment(true);
4643 if (filesnotmatched.size() > 0)
4646 && (Cache.getDefault(
4647 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4650 "<html>Do you want to <em>ignore</em> the "
4651 + filesnotmatched.size()
4652 + " files whose names did not match any sequence IDs ?</html>",
4653 "Ignore unmatched dropped files ?",
4654 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4658 for (String fn : filesnotmatched)
4660 loadJalviewDataFile(fn, null, null, null);
4664 } catch (Exception ex)
4666 ex.printStackTrace();
4672 * Attempt to load a "dropped" file or URL string: First by testing whether
4673 * it's and Annotation file, then a JNet file, and finally a features file. If
4674 * all are false then the user may have dropped an alignment file onto this
4678 * either a filename or a URL string.
4680 public void loadJalviewDataFile(String file, String protocol,
4681 String format, SequenceI assocSeq)
4685 if (protocol == null)
4687 protocol = jalview.io.FormatAdapter.checkProtocol(file);
4689 // if the file isn't identified, or not positively identified as some
4690 // other filetype (PFAM is default unidentified alignment file type) then
4691 // try to parse as annotation.
4692 boolean isAnnotation = (format == null || format
4693 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4694 .readAnnotationFile(viewport.getAlignment(), file, protocol)
4699 // try to see if its a JNet 'concise' style annotation file *before* we
4700 // try to parse it as a features file
4703 format = new IdentifyFile().Identify(file, protocol);
4705 if (format.equalsIgnoreCase("JnetFile"))
4707 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4709 new JnetAnnotationMaker().add_annotation(predictions,
4710 viewport.getAlignment(), 0, false);
4711 isAnnotation = true;
4716 * if (format.equalsIgnoreCase("PDB")) {
4718 * String pdbfn = ""; // try to match up filename with sequence id try
4719 * { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = new
4720 * File(file); pdbfn = fl.getName(); } else if (protocol ==
4721 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4722 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == null)
4723 * { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4724 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { //
4725 * attempt to find a match in the alignment SequenceI mtch =
4726 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4727 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > l)
4728 * { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch =
4729 * idm.findIdMatch(pdbfn); } if (mtch != null) { // try and associate
4730 * // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4731 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) {
4732 * System.err.println("Associated file : " + file + " with " +
4733 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4734 * TODO: maybe need to load as normal otherwise return; } }
4736 // try to parse it as a features file
4737 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4738 // if it wasn't a features file then we just treat it as a general
4739 // alignment file to load into the current view.
4742 new FileLoader().LoadFile(viewport, file, protocol, format);
4746 alignPanel.paintAlignment(true);
4753 alignPanel.adjustAnnotationHeight();
4754 viewport.updateSequenceIdColours();
4755 buildSortByAnnotationScoresMenu();
4756 alignPanel.paintAlignment(true);
4758 } catch (Exception ex)
4760 ex.printStackTrace();
4764 public void tabSelectionChanged(int index)
4768 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4769 viewport = alignPanel.av;
4770 setMenusFromViewport(viewport);
4774 public void tabbedPane_mousePressed(MouseEvent e)
4776 if (SwingUtilities.isRightMouseButton(e))
4778 String reply = JOptionPane.showInternalInputDialog(this,
4779 "Enter View Name", "Edit View Name",
4780 JOptionPane.QUESTION_MESSAGE);
4784 viewport.viewName = reply;
4785 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4790 public AlignViewport getCurrentView()
4796 * Open the dialog for regex description parsing.
4798 protected void extractScores_actionPerformed(ActionEvent e)
4800 ParseProperties pp = new jalview.analysis.ParseProperties(
4801 viewport.getAlignment());
4802 // TODO: verify regex and introduce GUI dialog for version 2.5
4803 // if (pp.getScoresFromDescription("col", "score column ",
4804 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4806 if (pp.getScoresFromDescription("description column",
4807 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4809 buildSortByAnnotationScoresMenu();
4817 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4820 protected void showDbRefs_actionPerformed(ActionEvent e)
4822 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4828 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4831 protected void showNpFeats_actionPerformed(ActionEvent e)
4833 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4837 * find the viewport amongst the tabs in this alignment frame and close that
4842 public boolean closeView(AlignViewport av)
4846 this.closeMenuItem_actionPerformed(false);
4849 Component[] comp = tabbedPane.getComponents();
4850 for (int i = 0; comp != null && i < comp.length; i++)
4852 if (comp[i] instanceof AlignmentPanel)
4854 if (((AlignmentPanel) comp[i]).av == av)
4857 closeView((AlignmentPanel) comp[i]);
4865 protected void build_fetchdbmenu(JMenu webService)
4867 // Temporary hack - DBRef Fetcher always top level ws entry.
4868 // TODO We probably want to store a sequence database checklist in
4869 // preferences and have checkboxes.. rather than individual sources selected
4871 final JMenu rfetch = new JMenu("Fetch DB References");
4872 rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4873 webService.add(rfetch);
4875 JMenuItem fetchr = new JMenuItem("Standard Databases");
4876 fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4877 fetchr.addActionListener(new ActionListener()
4880 public void actionPerformed(ActionEvent e)
4882 new Thread(new Runnable()
4887 new jalview.ws.DBRefFetcher(alignPanel.av
4888 .getSequenceSelection(), alignPanel.alignFrame)
4889 .fetchDBRefs(false);
4897 final AlignFrame me = this;
4898 new Thread(new Runnable()
4902 final jalview.ws.SequenceFetcher sf = SequenceFetcher
4903 .getSequenceFetcherSingleton(me);
4904 final String[] otherdb = sf.getOrderedSupportedSources();
4905 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4906 // jalview.util.QuickSort.sort(otherdb, otherdb);
4907 javax.swing.SwingUtilities.invokeLater(new Runnable()
4912 JMenu dfetch = new JMenu();
4915 int comp = 0, mcomp = 15;
4916 String mname = null;
4917 if (otherdb != null && otherdb.length > 0)
4919 for (int i = 0; i < otherdb.length; i++)
4921 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4924 mname = "from '" + dbname + "'";
4926 fetchr = new JMenuItem(otherdb[i]);
4927 final String[] dassource = new String[]
4929 fetchr.addActionListener(new ActionListener()
4932 public void actionPerformed(ActionEvent e)
4934 new Thread(new Runnable()
4939 new jalview.ws.DBRefFetcher(alignPanel.av
4940 .getSequenceSelection(),
4941 alignPanel.alignFrame, dassource)
4942 .fetchDBRefs(false);
4948 fetchr.setToolTipText("Retrieve from " + dbname);
4950 if (comp++ == mcomp || i == (otherdb.length - 1))
4952 dfetch.setText(mname + " to '" + dbname + "'");
4954 dfetch = new JMenu();
4968 * Left justify the whole alignment.
4970 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4972 AlignmentI al = viewport.getAlignment();
4974 viewport.firePropertyChange("alignment", null, al);
4978 * Right justify the whole alignment.
4980 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4982 AlignmentI al = viewport.getAlignment();
4984 viewport.firePropertyChange("alignment", null, al);
4987 public void setShowSeqFeatures(boolean b)
4989 showSeqFeatures.setSelected(true);
4990 viewport.setShowSequenceFeatures(true);
4997 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4998 * awt.event.ActionEvent)
5000 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5002 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5003 alignPanel.paintAlignment(true);
5010 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5013 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5015 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5016 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5024 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5025 * .event.ActionEvent)
5027 protected void showGroupConservation_actionPerformed(ActionEvent e)
5029 viewport.setShowGroupConservation(showGroupConservation.getState());
5030 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5037 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5038 * .event.ActionEvent)
5040 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5042 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5043 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5050 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5051 * .event.ActionEvent)
5053 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5055 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5056 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5058 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5060 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5061 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5063 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5065 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5072 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5073 * .event.ActionEvent)
5075 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5077 if (viewport.getSelectionGroup() != null)
5079 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
5080 viewport.getSequenceSelection(),
5081 viewport.getAlignmentView(true).getSequenceStrings(
5082 viewport.getGapCharacter()),
5083 viewport.getAlignment().getGroups());
5084 viewport.getAlignment().deleteAllGroups();
5085 viewport.sequenceColours = null;
5086 viewport.setSelectionGroup(null);
5087 // set view properties for each group
5088 for (int g = 0; g < gps.length; g++)
5090 gps[g].setShowNonconserved(viewport.getShowUnconserved());
5091 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
5092 viewport.getAlignment().addGroup(gps[g]);
5093 Color col = new Color((int) (Math.random() * 255),
5094 (int) (Math.random() * 255), (int) (Math.random() * 255));
5095 col = col.brighter();
5096 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
5097 .hasMoreElements(); viewport.setSequenceColour(
5098 (SequenceI) sq.nextElement(), col))
5101 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5102 alignPanel.updateAnnotation();
5103 alignPanel.paintAlignment(true);
5108 * make the given alignmentPanel the currently selected tab
5110 * @param alignmentPanel
5112 public void setDisplayedView(AlignmentPanel alignmentPanel)
5114 if (!viewport.getSequenceSetId().equals(
5115 alignmentPanel.av.getSequenceSetId()))
5118 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5120 if (tabbedPane != null
5121 & alignPanels.indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5123 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5128 class PrintThread extends Thread
5132 public PrintThread(AlignmentPanel ap)
5137 static PageFormat pf;
5141 PrinterJob printJob = PrinterJob.getPrinterJob();
5145 printJob.setPrintable(ap, pf);
5149 printJob.setPrintable(ap);
5152 if (printJob.printDialog())
5157 } catch (Exception PrintException)
5159 PrintException.printStackTrace();