2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.api.AlignViewControllerI;
28 import jalview.bin.Cache;
29 import jalview.commands.CommandI;
30 import jalview.commands.EditCommand;
31 import jalview.commands.OrderCommand;
32 import jalview.commands.RemoveGapColCommand;
33 import jalview.commands.RemoveGapsCommand;
34 import jalview.commands.SlideSequencesCommand;
35 import jalview.commands.TrimRegionCommand;
36 import jalview.datamodel.AlignedCodonFrame;
37 import jalview.datamodel.Alignment;
38 import jalview.datamodel.AlignmentAnnotation;
39 import jalview.datamodel.AlignmentI;
40 import jalview.datamodel.AlignmentOrder;
41 import jalview.datamodel.AlignmentView;
42 import jalview.datamodel.ColumnSelection;
43 import jalview.datamodel.PDBEntry;
44 import jalview.datamodel.SeqCigar;
45 import jalview.datamodel.Sequence;
46 import jalview.datamodel.SequenceGroup;
47 import jalview.datamodel.SequenceI;
48 import jalview.io.AlignmentProperties;
49 import jalview.io.AnnotationFile;
50 import jalview.io.FeaturesFile;
51 import jalview.io.FileLoader;
52 import jalview.io.FormatAdapter;
53 import jalview.io.HTMLOutput;
54 import jalview.io.IdentifyFile;
55 import jalview.io.JalviewFileChooser;
56 import jalview.io.JalviewFileView;
57 import jalview.io.JnetAnnotationMaker;
58 import jalview.io.NewickFile;
59 import jalview.io.TCoffeeScoreFile;
60 import jalview.jbgui.GAlignFrame;
61 import jalview.schemes.Blosum62ColourScheme;
62 import jalview.schemes.BuriedColourScheme;
63 import jalview.schemes.ClustalxColourScheme;
64 import jalview.schemes.ColourSchemeI;
65 import jalview.schemes.ColourSchemeProperty;
66 import jalview.schemes.HelixColourScheme;
67 import jalview.schemes.HydrophobicColourScheme;
68 import jalview.schemes.NucleotideColourScheme;
69 import jalview.schemes.PIDColourScheme;
70 import jalview.schemes.PurinePyrimidineColourScheme;
71 import jalview.schemes.RNAHelicesColourChooser;
72 import jalview.schemes.ResidueProperties;
73 import jalview.schemes.StrandColourScheme;
74 import jalview.schemes.TCoffeeColourScheme;
75 import jalview.schemes.TaylorColourScheme;
76 import jalview.schemes.TurnColourScheme;
77 import jalview.schemes.UserColourScheme;
78 import jalview.schemes.ZappoColourScheme;
79 import jalview.util.MessageManager;
80 import jalview.ws.jws1.Discoverer;
81 import jalview.ws.jws2.Jws2Discoverer;
82 import jalview.ws.jws2.jabaws2.Jws2Instance;
83 import jalview.ws.seqfetcher.DbSourceProxy;
85 import java.awt.BorderLayout;
86 import java.awt.Color;
87 import java.awt.Component;
88 import java.awt.GridLayout;
89 import java.awt.Rectangle;
90 import java.awt.Toolkit;
91 import java.awt.datatransfer.Clipboard;
92 import java.awt.datatransfer.DataFlavor;
93 import java.awt.datatransfer.StringSelection;
94 import java.awt.datatransfer.Transferable;
95 import java.awt.dnd.DnDConstants;
96 import java.awt.dnd.DropTargetDragEvent;
97 import java.awt.dnd.DropTargetDropEvent;
98 import java.awt.dnd.DropTargetEvent;
99 import java.awt.dnd.DropTargetListener;
100 import java.awt.event.ActionEvent;
101 import java.awt.event.ActionListener;
102 import java.awt.event.KeyAdapter;
103 import java.awt.event.KeyEvent;
104 import java.awt.event.MouseAdapter;
105 import java.awt.event.MouseEvent;
106 import java.awt.print.PageFormat;
107 import java.awt.print.PrinterJob;
108 import java.beans.PropertyChangeEvent;
111 import java.util.ArrayList;
112 import java.util.Enumeration;
113 import java.util.Hashtable;
114 import java.util.List;
115 import java.util.Vector;
117 import javax.swing.JButton;
118 import javax.swing.JEditorPane;
119 import javax.swing.JInternalFrame;
120 import javax.swing.JLabel;
121 import javax.swing.JLayeredPane;
122 import javax.swing.JMenu;
123 import javax.swing.JMenuItem;
124 import javax.swing.JOptionPane;
125 import javax.swing.JPanel;
126 import javax.swing.JProgressBar;
127 import javax.swing.JRadioButtonMenuItem;
128 import javax.swing.JScrollPane;
129 import javax.swing.SwingUtilities;
135 * @version $Revision$
137 public class AlignFrame extends GAlignFrame implements DropTargetListener,
142 public static final int DEFAULT_WIDTH = 700;
145 public static final int DEFAULT_HEIGHT = 500;
147 public AlignmentPanel alignPanel;
149 AlignViewport viewport;
151 public AlignViewControllerI avc;
154 Vector alignPanels = new Vector();
157 * Last format used to load or save alignments in this window
159 String currentFileFormat = null;
162 * Current filename for this alignment
164 String fileName = null;
167 * Creates a new AlignFrame object with specific width and height.
173 public AlignFrame(AlignmentI al, int width, int height)
175 this(al, null, width, height);
179 * Creates a new AlignFrame object with specific width, height and
185 * @param sequenceSetId
187 public AlignFrame(AlignmentI al, int width, int height,
188 String sequenceSetId)
190 this(al, null, width, height, sequenceSetId);
194 * Creates a new AlignFrame object with specific width, height and
200 * @param sequenceSetId
203 public AlignFrame(AlignmentI al, int width, int height,
204 String sequenceSetId, String viewId)
206 this(al, null, width, height, sequenceSetId, viewId);
210 * new alignment window with hidden columns
214 * @param hiddenColumns
215 * ColumnSelection or null
217 * Width of alignment frame
221 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
222 int width, int height)
224 this(al, hiddenColumns, width, height, null);
228 * Create alignment frame for al with hiddenColumns, a specific width and
229 * height, and specific sequenceId
232 * @param hiddenColumns
235 * @param sequenceSetId
238 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
239 int width, int height, String sequenceSetId)
241 this(al, hiddenColumns, width, height, sequenceSetId, null);
245 * Create alignment frame for al with hiddenColumns, a specific width and
246 * height, and specific sequenceId
249 * @param hiddenColumns
252 * @param sequenceSetId
257 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
258 int width, int height, String sequenceSetId, String viewId)
260 setSize(width, height);
261 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
263 alignPanel = new AlignmentPanel(this, viewport);
265 if (al.getDataset() == null)
270 addAlignmentPanel(alignPanel, true);
275 * Make a new AlignFrame from exisiting alignmentPanels
282 public AlignFrame(AlignmentPanel ap)
286 addAlignmentPanel(ap, false);
291 * initalise the alignframe from the underlying viewport data and the
296 avc = new jalview.controller.AlignViewController(viewport, alignPanel);
297 if (viewport.getAlignmentConservationAnnotation() == null)
299 BLOSUM62Colour.setEnabled(false);
300 conservationMenuItem.setEnabled(false);
301 modifyConservation.setEnabled(false);
302 // PIDColour.setEnabled(false);
303 // abovePIDThreshold.setEnabled(false);
304 // modifyPID.setEnabled(false);
307 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
310 if (sortby.equals("Id"))
312 sortIDMenuItem_actionPerformed(null);
314 else if (sortby.equals("Pairwise Identity"))
316 sortPairwiseMenuItem_actionPerformed(null);
319 if (Desktop.desktop != null)
321 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
322 addServiceListeners();
323 setGUINucleotide(viewport.getAlignment().isNucleotide());
326 setMenusFromViewport(viewport);
327 buildSortByAnnotationScoresMenu();
328 if (viewport.wrapAlignment)
330 wrapMenuItem_actionPerformed(null);
333 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
335 this.overviewMenuItem_actionPerformed(null);
343 * Change the filename and format for the alignment, and enable the 'reload'
344 * button functionality.
351 public void setFileName(String file, String format)
354 currentFileFormat = format;
355 reload.setEnabled(true);
358 void addKeyListener()
360 addKeyListener(new KeyAdapter()
363 public void keyPressed(KeyEvent evt)
365 if (viewport.cursorMode
366 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
367 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
368 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
369 && Character.isDigit(evt.getKeyChar()))
370 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
372 switch (evt.getKeyCode())
375 case 27: // escape key
376 deselectAllSequenceMenuItem_actionPerformed(null);
380 case KeyEvent.VK_DOWN:
381 if (evt.isAltDown() || !viewport.cursorMode)
382 moveSelectedSequences(false);
383 if (viewport.cursorMode)
384 alignPanel.seqPanel.moveCursor(0, 1);
388 if (evt.isAltDown() || !viewport.cursorMode)
389 moveSelectedSequences(true);
390 if (viewport.cursorMode)
391 alignPanel.seqPanel.moveCursor(0, -1);
395 case KeyEvent.VK_LEFT:
396 if (evt.isAltDown() || !viewport.cursorMode)
397 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
399 alignPanel.seqPanel.moveCursor(-1, 0);
403 case KeyEvent.VK_RIGHT:
404 if (evt.isAltDown() || !viewport.cursorMode)
405 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
407 alignPanel.seqPanel.moveCursor(1, 0);
410 case KeyEvent.VK_SPACE:
411 if (viewport.cursorMode)
413 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
414 || evt.isShiftDown() || evt.isAltDown());
418 // case KeyEvent.VK_A:
419 // if (viewport.cursorMode)
421 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
422 // //System.out.println("A");
426 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
427 * System.out.println("closing bracket"); } break;
429 case KeyEvent.VK_DELETE:
430 case KeyEvent.VK_BACK_SPACE:
431 if (!viewport.cursorMode)
433 cut_actionPerformed(null);
437 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
438 || evt.isShiftDown() || evt.isAltDown());
444 if (viewport.cursorMode)
446 alignPanel.seqPanel.setCursorRow();
450 if (viewport.cursorMode && !evt.isControlDown())
452 alignPanel.seqPanel.setCursorColumn();
456 if (viewport.cursorMode)
458 alignPanel.seqPanel.setCursorPosition();
462 case KeyEvent.VK_ENTER:
463 case KeyEvent.VK_COMMA:
464 if (viewport.cursorMode)
466 alignPanel.seqPanel.setCursorRowAndColumn();
471 if (viewport.cursorMode)
473 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
477 if (viewport.cursorMode)
479 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
484 viewport.cursorMode = !viewport.cursorMode;
485 statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
486 if (viewport.cursorMode)
488 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
489 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
491 alignPanel.seqPanel.seqCanvas.repaint();
497 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
498 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
500 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
502 javax.help.HelpBroker hb = hs.createHelpBroker();
503 hb.setCurrentID("home");
504 hb.setDisplayed(true);
505 } catch (Exception ex)
507 ex.printStackTrace();
512 boolean toggleSeqs = !evt.isControlDown();
513 boolean toggleCols = !evt.isShiftDown();
514 toggleHiddenRegions(toggleSeqs, toggleCols);
517 case KeyEvent.VK_PAGE_UP:
518 if (viewport.wrapAlignment)
520 alignPanel.scrollUp(true);
524 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
525 - viewport.endSeq + viewport.startSeq);
528 case KeyEvent.VK_PAGE_DOWN:
529 if (viewport.wrapAlignment)
531 alignPanel.scrollUp(false);
535 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
536 + viewport.endSeq - viewport.startSeq);
543 public void keyReleased(KeyEvent evt)
545 switch (evt.getKeyCode())
547 case KeyEvent.VK_LEFT:
548 if (evt.isAltDown() || !viewport.cursorMode)
549 viewport.firePropertyChange("alignment", null, viewport
550 .getAlignment().getSequences());
553 case KeyEvent.VK_RIGHT:
554 if (evt.isAltDown() || !viewport.cursorMode)
555 viewport.firePropertyChange("alignment", null, viewport
556 .getAlignment().getSequences());
563 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
565 ap.alignFrame = this;
566 avc = new jalview.controller.AlignViewController(viewport, alignPanel);
568 alignPanels.addElement(ap);
570 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
572 int aSize = alignPanels.size();
574 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
576 if (aSize == 1 && ap.av.viewName == null)
578 this.getContentPane().add(ap, BorderLayout.CENTER);
584 setInitialTabVisible();
587 expandViews.setEnabled(true);
588 gatherViews.setEnabled(true);
589 tabbedPane.addTab(ap.av.viewName, ap);
591 ap.setVisible(false);
596 if (ap.av.isPadGaps())
598 ap.av.getAlignment().padGaps();
600 ap.av.updateConservation(ap);
601 ap.av.updateConsensus(ap);
602 ap.av.updateStrucConsensus(ap);
606 public void setInitialTabVisible()
608 expandViews.setEnabled(true);
609 gatherViews.setEnabled(true);
610 tabbedPane.setVisible(true);
611 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
612 tabbedPane.addTab(first.av.viewName, first);
613 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
616 public AlignViewport getViewport()
621 /* Set up intrinsic listeners for dynamically generated GUI bits. */
622 private void addServiceListeners()
624 final java.beans.PropertyChangeListener thisListener;
625 Desktop.instance.addJalviewPropertyChangeListener("services",
626 thisListener = new java.beans.PropertyChangeListener()
629 public void propertyChange(PropertyChangeEvent evt)
631 // // System.out.println("Discoverer property change.");
632 // if (evt.getPropertyName().equals("services"))
634 SwingUtilities.invokeLater(new Runnable()
641 .println("Rebuild WS Menu for service change");
642 BuildWebServiceMenu();
649 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
652 public void internalFrameClosed(
653 javax.swing.event.InternalFrameEvent evt)
655 System.out.println("deregistering discoverer listener");
656 Desktop.instance.removeJalviewPropertyChangeListener("services",
658 closeMenuItem_actionPerformed(true);
661 // Finally, build the menu once to get current service state
662 new Thread(new Runnable()
667 BuildWebServiceMenu();
672 public void setGUINucleotide(boolean nucleotide)
674 showTranslation.setVisible(nucleotide);
675 conservationMenuItem.setEnabled(!nucleotide);
676 modifyConservation.setEnabled(!nucleotide);
677 showGroupConservation.setEnabled(!nucleotide);
678 rnahelicesColour.setEnabled(nucleotide);
679 purinePyrimidineColour.setEnabled(nucleotide);
680 // Remember AlignFrame always starts as protein
684 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
689 * set up menus for the currently viewport. This may be called after any
690 * operation that affects the data in the current view (selection changed,
691 * etc) to update the menus to reflect the new state.
693 public void setMenusForViewport()
695 setMenusFromViewport(viewport);
699 * Need to call this method when tabs are selected for multiple views, or when
700 * loading from Jalview2XML.java
705 void setMenusFromViewport(AlignViewport av)
707 padGapsMenuitem.setSelected(av.isPadGaps());
708 colourTextMenuItem.setSelected(av.showColourText);
709 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
710 conservationMenuItem.setSelected(av.getConservationSelected());
711 seqLimits.setSelected(av.getShowJVSuffix());
712 idRightAlign.setSelected(av.rightAlignIds);
713 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
714 renderGapsMenuItem.setSelected(av.renderGaps);
715 wrapMenuItem.setSelected(av.wrapAlignment);
716 scaleAbove.setVisible(av.wrapAlignment);
717 scaleLeft.setVisible(av.wrapAlignment);
718 scaleRight.setVisible(av.wrapAlignment);
719 annotationPanelMenuItem.setState(av.showAnnotation);
720 viewBoxesMenuItem.setSelected(av.showBoxes);
721 viewTextMenuItem.setSelected(av.showText);
722 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
723 showGroupConsensus.setSelected(av.isShowGroupConsensus());
724 showGroupConservation.setSelected(av.isShowGroupConservation());
725 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
726 showSequenceLogo.setSelected(av.isShowSequenceLogo());
727 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
729 setColourSelected(ColourSchemeProperty.getColourName(av
730 .getGlobalColourScheme()));
732 showSeqFeatures.setSelected(av.showSequenceFeatures);
733 hiddenMarkers.setState(av.showHiddenMarkers);
734 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
735 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
736 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
737 autoCalculate.setSelected(av.autoCalculateConsensus);
738 sortByTree.setSelected(av.sortByTree);
739 listenToViewSelections.setSelected(av.followSelection);
740 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
742 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
743 setShowProductsEnabled();
747 // methods for implementing IProgressIndicator
748 // need to refactor to a reusable stub class
749 Hashtable progressBars, progressBarHandlers;
754 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
757 public void setProgressBar(String message, long id)
759 if (progressBars == null)
761 progressBars = new Hashtable();
762 progressBarHandlers = new Hashtable();
765 JPanel progressPanel;
766 Long lId = new Long(id);
767 GridLayout layout = (GridLayout) statusPanel.getLayout();
768 if (progressBars.get(lId) != null)
770 progressPanel = (JPanel) progressBars.get(new Long(id));
771 statusPanel.remove(progressPanel);
772 progressBars.remove(lId);
773 progressPanel = null;
776 statusBar.setText(message);
778 if (progressBarHandlers.contains(lId))
780 progressBarHandlers.remove(lId);
782 layout.setRows(layout.getRows() - 1);
786 progressPanel = new JPanel(new BorderLayout(10, 5));
788 JProgressBar progressBar = new JProgressBar();
789 progressBar.setIndeterminate(true);
791 progressPanel.add(new JLabel(message), BorderLayout.WEST);
792 progressPanel.add(progressBar, BorderLayout.CENTER);
794 layout.setRows(layout.getRows() + 1);
795 statusPanel.add(progressPanel);
797 progressBars.put(lId, progressPanel);
800 // setMenusForViewport();
805 public void registerHandler(final long id,
806 final IProgressIndicatorHandler handler)
808 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
811 "call setProgressBar before registering the progress bar's handler.");
813 progressBarHandlers.put(new Long(id), handler);
814 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
815 if (handler.canCancel())
817 JButton cancel = new JButton(MessageManager.getString("action.cancel"));
818 final IProgressIndicator us = this;
819 cancel.addActionListener(new ActionListener()
823 public void actionPerformed(ActionEvent e)
825 handler.cancelActivity(id);
828 + ((JLabel) progressPanel.getComponent(0))
832 progressPanel.add(cancel, BorderLayout.EAST);
838 * @return true if any progress bars are still active
841 public boolean operationInProgress()
843 if (progressBars != null && progressBars.size() > 0)
851 * Added so Castor Mapping file can obtain Jalview Version
853 public String getVersion()
855 return jalview.bin.Cache.getProperty("VERSION");
858 public FeatureRenderer getFeatureRenderer()
860 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
864 public void fetchSequence_actionPerformed(ActionEvent e)
866 new SequenceFetcher(this);
870 public void addFromFile_actionPerformed(ActionEvent e)
872 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
876 public void reload_actionPerformed(ActionEvent e)
878 if (fileName != null)
880 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
881 // originating file's format
882 // TODO: work out how to recover feature settings for correct view(s) when
884 if (currentFileFormat.equals("Jalview"))
886 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
887 for (int i = 0; i < frames.length; i++)
889 if (frames[i] instanceof AlignFrame && frames[i] != this
890 && ((AlignFrame) frames[i]).fileName != null
891 && ((AlignFrame) frames[i]).fileName.equals(fileName))
895 frames[i].setSelected(true);
896 Desktop.instance.closeAssociatedWindows();
897 } catch (java.beans.PropertyVetoException ex)
903 Desktop.instance.closeAssociatedWindows();
905 FileLoader loader = new FileLoader();
906 String protocol = fileName.startsWith("http:") ? "URL" : "File";
907 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
911 Rectangle bounds = this.getBounds();
913 FileLoader loader = new FileLoader();
914 String protocol = fileName.startsWith("http:") ? "URL" : "File";
915 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
916 protocol, currentFileFormat);
918 newframe.setBounds(bounds);
919 if (featureSettings != null && featureSettings.isShowing())
921 final Rectangle fspos = featureSettings.frame.getBounds();
922 // TODO: need a 'show feature settings' function that takes bounds -
923 // need to refactor Desktop.addFrame
924 newframe.featureSettings_actionPerformed(null);
925 final FeatureSettings nfs = newframe.featureSettings;
926 SwingUtilities.invokeLater(new Runnable()
931 nfs.frame.setBounds(fspos);
934 this.featureSettings.close();
935 this.featureSettings = null;
937 this.closeMenuItem_actionPerformed(true);
943 public void addFromText_actionPerformed(ActionEvent e)
945 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
949 public void addFromURL_actionPerformed(ActionEvent e)
951 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
955 public void save_actionPerformed(ActionEvent e)
958 || (currentFileFormat == null || !jalview.io.FormatAdapter
959 .isValidIOFormat(currentFileFormat, true))
960 || fileName.startsWith("http"))
962 saveAs_actionPerformed(null);
966 saveAlignment(fileName, currentFileFormat);
977 public void saveAs_actionPerformed(ActionEvent e)
979 JalviewFileChooser chooser = new JalviewFileChooser(
980 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
981 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
982 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
983 currentFileFormat, false);
985 chooser.setFileView(new JalviewFileView());
986 chooser.setDialogTitle("Save Alignment to file");
987 chooser.setToolTipText("Save");
989 int value = chooser.showSaveDialog(this);
991 if (value == JalviewFileChooser.APPROVE_OPTION)
993 currentFileFormat = chooser.getSelectedFormat();
994 if (currentFileFormat == null)
996 JOptionPane.showInternalMessageDialog(Desktop.desktop,
997 MessageManager.getString("label.select_file_format_before_saving"),
998 MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE);
999 value = chooser.showSaveDialog(this);
1003 fileName = chooser.getSelectedFile().getPath();
1005 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1008 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1009 if (currentFileFormat.indexOf(" ") > -1)
1011 currentFileFormat = currentFileFormat.substring(0,
1012 currentFileFormat.indexOf(" "));
1014 saveAlignment(fileName, currentFileFormat);
1018 public boolean saveAlignment(String file, String format)
1020 boolean success = true;
1022 if (format.equalsIgnoreCase("Jalview"))
1024 String shortName = title;
1026 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1028 shortName = shortName.substring(shortName
1029 .lastIndexOf(java.io.File.separatorChar) + 1);
1032 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1034 statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
1040 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1042 warningMessage("Cannot save file " + fileName + " using format "
1043 + format, "Alignment output format not supported");
1044 saveAs_actionPerformed(null);
1045 // JBPNote need to have a raise_gui flag here
1049 String[] omitHidden = null;
1051 if (viewport.hasHiddenColumns())
1053 int reply = JOptionPane
1054 .showInternalConfirmDialog(
1056 MessageManager.getString("label.alignment_contains_hidden_columns"),
1057 MessageManager.getString("action.save_omit_hidden_columns"),
1058 JOptionPane.YES_NO_OPTION,
1059 JOptionPane.QUESTION_MESSAGE);
1061 if (reply == JOptionPane.YES_OPTION)
1063 omitHidden = viewport.getViewAsString(false);
1066 FormatAdapter f = new FormatAdapter();
1067 String output = f.formatSequences(format,
1068 viewport.getAlignment(), // class cast exceptions will
1069 // occur in the distant future
1070 omitHidden, f.getCacheSuffixDefault(format),
1071 viewport.getColumnSelection());
1081 java.io.PrintWriter out = new java.io.PrintWriter(
1082 new java.io.FileWriter(file));
1086 this.setTitle(file);
1087 statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
1088 } catch (Exception ex)
1091 ex.printStackTrace();
1098 JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}),
1099 MessageManager.getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE);
1105 private void warningMessage(String warning, String title)
1107 if (new jalview.util.Platform().isHeadless())
1109 System.err.println("Warning: " + title + "\nWarning: " + warning);
1114 JOptionPane.showInternalMessageDialog(this, warning, title,
1115 JOptionPane.WARNING_MESSAGE);
1127 protected void outputText_actionPerformed(ActionEvent e)
1129 String[] omitHidden = null;
1131 if (viewport.hasHiddenColumns())
1133 int reply = JOptionPane
1134 .showInternalConfirmDialog(
1136 MessageManager.getString("label.alignment_contains_hidden_columns"),
1137 MessageManager.getString("action.save_omit_hidden_columns"),
1138 JOptionPane.YES_NO_OPTION,
1139 JOptionPane.QUESTION_MESSAGE);
1141 if (reply == JOptionPane.YES_OPTION)
1143 omitHidden = viewport.getViewAsString(false);
1147 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1148 cap.setForInput(null);
1152 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1153 viewport.getAlignment(), omitHidden,
1154 viewport.getColumnSelection()));
1155 Desktop.addInternalFrame(cap,
1156 "Alignment output - " + e.getActionCommand(), 600, 500);
1157 } catch (OutOfMemoryError oom)
1159 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1172 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1174 new HTMLOutput(alignPanel,
1175 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1176 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1179 public void createImageMap(File file, String image)
1181 alignPanel.makePNGImageMap(file, image);
1191 public void createPNG(File f)
1193 alignPanel.makePNG(f);
1203 public void createEPS(File f)
1205 alignPanel.makeEPS(f);
1209 public void pageSetup_actionPerformed(ActionEvent e)
1211 PrinterJob printJob = PrinterJob.getPrinterJob();
1212 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1222 public void printMenuItem_actionPerformed(ActionEvent e)
1224 // Putting in a thread avoids Swing painting problems
1225 PrintThread thread = new PrintThread(alignPanel);
1230 public void exportFeatures_actionPerformed(ActionEvent e)
1232 new AnnotationExporter().exportFeatures(alignPanel);
1236 public void exportAnnotations_actionPerformed(ActionEvent e)
1238 new AnnotationExporter().exportAnnotations(alignPanel,
1239 viewport.showAnnotation ? viewport.getAlignment()
1240 .getAlignmentAnnotation() : null, viewport
1241 .getAlignment().getGroups(), ((Alignment) viewport
1242 .getAlignment()).alignmentProperties);
1246 public void associatedData_actionPerformed(ActionEvent e)
1248 // Pick the tree file
1249 JalviewFileChooser chooser = new JalviewFileChooser(
1250 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1251 chooser.setFileView(new JalviewFileView());
1252 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1253 chooser.setToolTipText("Load Jalview Annotations / Features file");
1255 int value = chooser.showOpenDialog(null);
1257 if (value == JalviewFileChooser.APPROVE_OPTION)
1259 String choice = chooser.getSelectedFile().getPath();
1260 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1261 loadJalviewDataFile(choice, null, null, null);
1267 * Close the current view or all views in the alignment frame. If the frame
1268 * only contains one view then the alignment will be removed from memory.
1270 * @param closeAllTabs
1273 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1275 if (alignPanels != null && alignPanels.size() < 2)
1277 closeAllTabs = true;
1282 if (alignPanels != null)
1286 if (this.isClosed())
1288 // really close all the windows - otherwise wait till
1289 // setClosed(true) is called
1290 for (int i = 0; i < alignPanels.size(); i++)
1292 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1299 closeView(alignPanel);
1305 this.setClosed(true);
1307 } catch (Exception ex)
1309 ex.printStackTrace();
1314 * close alignPanel2 and shuffle tabs appropriately.
1316 * @param alignPanel2
1318 public void closeView(AlignmentPanel alignPanel2)
1320 int index = tabbedPane.getSelectedIndex();
1321 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1322 alignPanels.removeElement(alignPanel2);
1324 // if (viewport == alignPanel2.av)
1328 alignPanel2.closePanel();
1331 tabbedPane.removeTabAt(closedindex);
1332 tabbedPane.validate();
1334 if (index > closedindex || index == tabbedPane.getTabCount())
1336 // modify currently selected tab index if necessary.
1340 this.tabSelectionChanged(index);
1346 void updateEditMenuBar()
1349 if (viewport.historyList.size() > 0)
1351 undoMenuItem.setEnabled(true);
1352 CommandI command = (CommandI) viewport.historyList.peek();
1353 undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
1357 undoMenuItem.setEnabled(false);
1358 undoMenuItem.setText(MessageManager.getString("action.undo"));
1361 if (viewport.redoList.size() > 0)
1363 redoMenuItem.setEnabled(true);
1365 CommandI command = (CommandI) viewport.redoList.peek();
1366 redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
1370 redoMenuItem.setEnabled(false);
1371 redoMenuItem.setText(MessageManager.getString("action.redo"));
1375 public void addHistoryItem(CommandI command)
1377 if (command.getSize() > 0)
1379 viewport.historyList.push(command);
1380 viewport.redoList.clear();
1381 updateEditMenuBar();
1382 viewport.updateHiddenColumns();
1383 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1384 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1385 // viewport.getColumnSelection()
1386 // .getHiddenColumns().size() > 0);
1392 * @return alignment objects for all views
1394 AlignmentI[] getViewAlignments()
1396 if (alignPanels != null)
1398 Enumeration e = alignPanels.elements();
1399 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1400 for (int i = 0; e.hasMoreElements(); i++)
1402 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1406 if (viewport != null)
1408 return new AlignmentI[]
1409 { viewport.getAlignment() };
1421 protected void undoMenuItem_actionPerformed(ActionEvent e)
1423 if (viewport.historyList.empty())
1425 CommandI command = (CommandI) viewport.historyList.pop();
1426 viewport.redoList.push(command);
1427 command.undoCommand(getViewAlignments());
1429 AlignViewport originalSource = getOriginatingSource(command);
1430 updateEditMenuBar();
1432 if (originalSource != null)
1434 if (originalSource != viewport)
1437 .warn("Implementation worry: mismatch of viewport origin for undo");
1439 originalSource.updateHiddenColumns();
1440 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1442 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1443 // viewport.getColumnSelection()
1444 // .getHiddenColumns().size() > 0);
1445 originalSource.firePropertyChange("alignment", null, originalSource
1446 .getAlignment().getSequences());
1457 protected void redoMenuItem_actionPerformed(ActionEvent e)
1459 if (viewport.redoList.size() < 1)
1464 CommandI command = (CommandI) viewport.redoList.pop();
1465 viewport.historyList.push(command);
1466 command.doCommand(getViewAlignments());
1468 AlignViewport originalSource = getOriginatingSource(command);
1469 updateEditMenuBar();
1471 if (originalSource != null)
1474 if (originalSource != viewport)
1477 .warn("Implementation worry: mismatch of viewport origin for redo");
1479 originalSource.updateHiddenColumns();
1480 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1482 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1483 // viewport.getColumnSelection()
1484 // .getHiddenColumns().size() > 0);
1485 originalSource.firePropertyChange("alignment", null, originalSource
1486 .getAlignment().getSequences());
1490 AlignViewport getOriginatingSource(CommandI command)
1492 AlignViewport originalSource = null;
1493 // For sequence removal and addition, we need to fire
1494 // the property change event FROM the viewport where the
1495 // original alignment was altered
1496 AlignmentI al = null;
1497 if (command instanceof EditCommand)
1499 EditCommand editCommand = (EditCommand) command;
1500 al = editCommand.getAlignment();
1501 Vector comps = (Vector) PaintRefresher.components.get(viewport
1502 .getSequenceSetId());
1504 for (int i = 0; i < comps.size(); i++)
1506 if (comps.elementAt(i) instanceof AlignmentPanel)
1508 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1510 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1517 if (originalSource == null)
1519 // The original view is closed, we must validate
1520 // the current view against the closed view first
1523 PaintRefresher.validateSequences(al, viewport.getAlignment());
1526 originalSource = viewport;
1529 return originalSource;
1538 public void moveSelectedSequences(boolean up)
1540 SequenceGroup sg = viewport.getSelectionGroup();
1546 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1547 viewport.getHiddenRepSequences(), up);
1548 alignPanel.paintAlignment(true);
1551 synchronized void slideSequences(boolean right, int size)
1553 List<SequenceI> sg = new Vector();
1554 if (viewport.cursorMode)
1556 sg.add(viewport.getAlignment().getSequenceAt(
1557 alignPanel.seqPanel.seqCanvas.cursorY));
1559 else if (viewport.getSelectionGroup() != null
1560 && viewport.getSelectionGroup().getSize() != viewport
1561 .getAlignment().getHeight())
1563 sg = viewport.getSelectionGroup().getSequences(
1564 viewport.getHiddenRepSequences());
1572 Vector invertGroup = new Vector();
1574 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1576 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1577 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1580 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1582 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1583 for (int i = 0; i < invertGroup.size(); i++)
1584 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1586 SlideSequencesCommand ssc;
1588 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1589 size, viewport.getGapCharacter());
1591 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1592 size, viewport.getGapCharacter());
1594 int groupAdjustment = 0;
1595 if (ssc.getGapsInsertedBegin() && right)
1597 if (viewport.cursorMode)
1598 alignPanel.seqPanel.moveCursor(size, 0);
1600 groupAdjustment = size;
1602 else if (!ssc.getGapsInsertedBegin() && !right)
1604 if (viewport.cursorMode)
1605 alignPanel.seqPanel.moveCursor(-size, 0);
1607 groupAdjustment = -size;
1610 if (groupAdjustment != 0)
1612 viewport.getSelectionGroup().setStartRes(
1613 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1614 viewport.getSelectionGroup().setEndRes(
1615 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1618 boolean appendHistoryItem = false;
1619 if (viewport.historyList != null && viewport.historyList.size() > 0
1620 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1622 appendHistoryItem = ssc
1623 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1627 if (!appendHistoryItem)
1628 addHistoryItem(ssc);
1640 protected void copy_actionPerformed(ActionEvent e)
1643 if (viewport.getSelectionGroup() == null)
1647 // TODO: preserve the ordering of displayed alignment annotation in any
1648 // internal paste (particularly sequence associated annotation)
1649 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1650 String[] omitHidden = null;
1652 if (viewport.hasHiddenColumns())
1654 omitHidden = viewport.getViewAsString(true);
1657 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1660 StringSelection ss = new StringSelection(output);
1664 jalview.gui.Desktop.internalCopy = true;
1665 // Its really worth setting the clipboard contents
1666 // to empty before setting the large StringSelection!!
1667 Toolkit.getDefaultToolkit().getSystemClipboard()
1668 .setContents(new StringSelection(""), null);
1670 Toolkit.getDefaultToolkit().getSystemClipboard()
1671 .setContents(ss, Desktop.instance);
1672 } catch (OutOfMemoryError er)
1674 new OOMWarning("copying region", er);
1678 Vector hiddenColumns = null;
1679 if (viewport.hasHiddenColumns())
1681 hiddenColumns = new Vector();
1682 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1683 .getSelectionGroup().getEndRes();
1684 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1687 int[] region = (int[]) viewport.getColumnSelection()
1688 .getHiddenColumns().elementAt(i);
1689 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1691 hiddenColumns.addElement(new int[]
1692 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1697 Desktop.jalviewClipboard = new Object[]
1698 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1699 statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()}));
1709 protected void pasteNew_actionPerformed(ActionEvent e)
1721 protected void pasteThis_actionPerformed(ActionEvent e)
1727 * Paste contents of Jalview clipboard
1729 * @param newAlignment
1730 * true to paste to a new alignment, otherwise add to this.
1732 void paste(boolean newAlignment)
1734 boolean externalPaste = true;
1737 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1738 Transferable contents = c.getContents(this);
1740 if (contents == null)
1748 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1749 if (str.length() < 1)
1754 format = new IdentifyFile().Identify(str, "Paste");
1756 } catch (OutOfMemoryError er)
1758 new OOMWarning("Out of memory pasting sequences!!", er);
1762 SequenceI[] sequences;
1763 boolean annotationAdded = false;
1764 AlignmentI alignment = null;
1766 if (Desktop.jalviewClipboard != null)
1768 // The clipboard was filled from within Jalview, we must use the
1770 // And dataset from the copied alignment
1771 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1772 // be doubly sure that we create *new* sequence objects.
1773 sequences = new SequenceI[newseq.length];
1774 for (int i = 0; i < newseq.length; i++)
1776 sequences[i] = new Sequence(newseq[i]);
1778 alignment = new Alignment(sequences);
1779 externalPaste = false;
1783 // parse the clipboard as an alignment.
1784 alignment = new FormatAdapter().readFile(str, "Paste", format);
1785 sequences = alignment.getSequencesArray();
1789 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1795 if (Desktop.jalviewClipboard != null)
1797 // dataset is inherited
1798 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1802 // new dataset is constructed
1803 alignment.setDataset(null);
1805 alwidth = alignment.getWidth() + 1;
1809 AlignmentI pastedal = alignment; // preserve pasted alignment object
1810 // Add pasted sequences and dataset into existing alignment.
1811 alignment = viewport.getAlignment();
1812 alwidth = alignment.getWidth() + 1;
1813 // decide if we need to import sequences from an existing dataset
1814 boolean importDs = Desktop.jalviewClipboard != null
1815 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1816 // importDs==true instructs us to copy over new dataset sequences from
1817 // an existing alignment
1818 Vector newDs = (importDs) ? new Vector() : null; // used to create
1819 // minimum dataset set
1821 for (int i = 0; i < sequences.length; i++)
1825 newDs.addElement(null);
1827 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1829 if (importDs && ds != null)
1831 if (!newDs.contains(ds))
1833 newDs.setElementAt(ds, i);
1834 ds = new Sequence(ds);
1835 // update with new dataset sequence
1836 sequences[i].setDatasetSequence(ds);
1840 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1845 // copy and derive new dataset sequence
1846 sequences[i] = sequences[i].deriveSequence();
1847 alignment.getDataset().addSequence(
1848 sequences[i].getDatasetSequence());
1849 // TODO: avoid creation of duplicate dataset sequences with a
1850 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1852 alignment.addSequence(sequences[i]); // merges dataset
1856 newDs.clear(); // tidy up
1858 if (alignment.getAlignmentAnnotation() != null)
1860 for (AlignmentAnnotation alan : alignment
1861 .getAlignmentAnnotation())
1863 if (alan.graphGroup > fgroup)
1865 fgroup = alan.graphGroup;
1869 if (pastedal.getAlignmentAnnotation() != null)
1871 // Add any annotation attached to alignment.
1872 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1873 for (int i = 0; i < alann.length; i++)
1875 annotationAdded = true;
1876 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1878 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1879 if (newann.graphGroup > -1)
1881 if (newGraphGroups.size() <= newann.graphGroup
1882 || newGraphGroups.get(newann.graphGroup) == null)
1884 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1886 newGraphGroups.add(q, null);
1888 newGraphGroups.set(newann.graphGroup, new Integer(
1891 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1895 newann.padAnnotation(alwidth);
1896 alignment.addAnnotation(newann);
1906 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1907 sequences, 0, alignment.getWidth(), alignment));
1909 // Add any annotations attached to sequences
1910 for (int i = 0; i < sequences.length; i++)
1912 if (sequences[i].getAnnotation() != null)
1914 AlignmentAnnotation newann;
1915 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1917 annotationAdded = true;
1918 newann = sequences[i].getAnnotation()[a];
1919 newann.adjustForAlignment();
1920 newann.padAnnotation(alwidth);
1921 if (newann.graphGroup > -1)
1923 if (newann.graphGroup > -1)
1925 if (newGraphGroups.size() <= newann.graphGroup
1926 || newGraphGroups.get(newann.graphGroup) == null)
1928 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1930 newGraphGroups.add(q, null);
1932 newGraphGroups.set(newann.graphGroup, new Integer(
1935 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1939 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1944 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1951 // propagate alignment changed.
1952 viewport.setEndSeq(alignment.getHeight());
1953 if (annotationAdded)
1955 // Duplicate sequence annotation in all views.
1956 AlignmentI[] alview = this.getViewAlignments();
1957 for (int i = 0; i < sequences.length; i++)
1959 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1962 for (int avnum = 0; avnum < alview.length; avnum++)
1964 if (alview[avnum] != alignment)
1966 // duplicate in a view other than the one with input focus
1967 int avwidth = alview[avnum].getWidth() + 1;
1968 // this relies on sann being preserved after we
1969 // modify the sequence's annotation array for each duplication
1970 for (int a = 0; a < sann.length; a++)
1972 AlignmentAnnotation newann = new AlignmentAnnotation(
1974 sequences[i].addAlignmentAnnotation(newann);
1975 newann.padAnnotation(avwidth);
1976 alview[avnum].addAnnotation(newann); // annotation was
1977 // duplicated earlier
1978 // TODO JAL-1145 graphGroups are not updated for sequence
1979 // annotation added to several views. This may cause
1981 alview[avnum].setAnnotationIndex(newann, a);
1986 buildSortByAnnotationScoresMenu();
1988 viewport.firePropertyChange("alignment", null,
1989 alignment.getSequences());
1990 if (alignPanels != null)
1992 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
1994 ap.validateAnnotationDimensions(false);
1999 alignPanel.validateAnnotationDimensions(false);
2005 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2007 String newtitle = new String("Copied sequences");
2009 if (Desktop.jalviewClipboard != null
2010 && Desktop.jalviewClipboard[2] != null)
2012 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2013 for (int i = 0; i < hc.size(); i++)
2015 int[] region = (int[]) hc.elementAt(i);
2016 af.viewport.hideColumns(region[0], region[1]);
2020 // >>>This is a fix for the moment, until a better solution is
2022 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2024 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2026 // TODO: maintain provenance of an alignment, rather than just make the
2027 // title a concatenation of operations.
2030 if (title.startsWith("Copied sequences"))
2036 newtitle = newtitle.concat("- from " + title);
2041 newtitle = new String("Pasted sequences");
2044 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2049 } catch (Exception ex)
2051 ex.printStackTrace();
2052 System.out.println("Exception whilst pasting: " + ex);
2053 // could be anything being pasted in here
2065 protected void cut_actionPerformed(ActionEvent e)
2067 copy_actionPerformed(null);
2068 delete_actionPerformed(null);
2078 protected void delete_actionPerformed(ActionEvent evt)
2081 SequenceGroup sg = viewport.getSelectionGroup();
2087 Vector seqs = new Vector();
2089 for (int i = 0; i < sg.getSize(); i++)
2091 seq = sg.getSequenceAt(i);
2092 seqs.addElement(seq);
2095 // If the cut affects all sequences, remove highlighted columns
2096 if (sg.getSize() == viewport.getAlignment().getHeight())
2098 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2099 sg.getEndRes() + 1);
2102 SequenceI[] cut = new SequenceI[seqs.size()];
2103 for (int i = 0; i < seqs.size(); i++)
2105 cut[i] = (SequenceI) seqs.elementAt(i);
2109 * //ADD HISTORY ITEM
2111 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2112 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2113 viewport.getAlignment()));
2115 viewport.setSelectionGroup(null);
2116 viewport.sendSelection();
2117 viewport.getAlignment().deleteGroup(sg);
2119 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2121 if (viewport.getAlignment().getHeight() < 1)
2125 this.setClosed(true);
2126 } catch (Exception ex)
2139 protected void deleteGroups_actionPerformed(ActionEvent e)
2141 if (avc.deleteGroups()) {
2142 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2143 alignPanel.updateAnnotation();
2144 alignPanel.paintAlignment(true);
2155 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2157 SequenceGroup sg = new SequenceGroup();
2159 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2161 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2164 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2165 viewport.setSelectionGroup(sg);
2166 viewport.sendSelection();
2167 alignPanel.paintAlignment(true);
2168 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2178 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2180 if (viewport.cursorMode)
2182 alignPanel.seqPanel.keyboardNo1 = null;
2183 alignPanel.seqPanel.keyboardNo2 = null;
2185 viewport.setSelectionGroup(null);
2186 viewport.getColumnSelection().clear();
2187 viewport.setSelectionGroup(null);
2188 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2189 alignPanel.idPanel.idCanvas.searchResults = null;
2190 alignPanel.paintAlignment(true);
2191 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2192 viewport.sendSelection();
2202 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2204 SequenceGroup sg = viewport.getSelectionGroup();
2208 selectAllSequenceMenuItem_actionPerformed(null);
2213 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2215 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2218 alignPanel.paintAlignment(true);
2219 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2220 viewport.sendSelection();
2224 public void invertColSel_actionPerformed(ActionEvent e)
2226 viewport.invertColumnSelection();
2227 alignPanel.paintAlignment(true);
2228 viewport.sendSelection();
2238 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2240 trimAlignment(true);
2250 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2252 trimAlignment(false);
2255 void trimAlignment(boolean trimLeft)
2257 ColumnSelection colSel = viewport.getColumnSelection();
2260 if (colSel.size() > 0)
2264 column = colSel.getMin();
2268 column = colSel.getMax();
2272 if (viewport.getSelectionGroup() != null)
2274 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2275 viewport.getHiddenRepSequences());
2279 seqs = viewport.getAlignment().getSequencesArray();
2282 TrimRegionCommand trimRegion;
2285 trimRegion = new TrimRegionCommand("Remove Left",
2286 TrimRegionCommand.TRIM_LEFT, seqs, column,
2287 viewport.getAlignment(), viewport.getColumnSelection(),
2288 viewport.getSelectionGroup());
2289 viewport.setStartRes(0);
2293 trimRegion = new TrimRegionCommand("Remove Right",
2294 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2295 viewport.getAlignment(), viewport.getColumnSelection(),
2296 viewport.getSelectionGroup());
2299 statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
2301 addHistoryItem(trimRegion);
2303 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2305 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2306 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2308 viewport.getAlignment().deleteGroup(sg);
2312 viewport.firePropertyChange("alignment", null, viewport
2313 .getAlignment().getSequences());
2324 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2326 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2329 if (viewport.getSelectionGroup() != null)
2331 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2332 viewport.getHiddenRepSequences());
2333 start = viewport.getSelectionGroup().getStartRes();
2334 end = viewport.getSelectionGroup().getEndRes();
2338 seqs = viewport.getAlignment().getSequencesArray();
2341 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2342 "Remove Gapped Columns", seqs, start, end,
2343 viewport.getAlignment());
2345 addHistoryItem(removeGapCols);
2347 statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
2349 // This is to maintain viewport position on first residue
2350 // of first sequence
2351 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2352 int startRes = seq.findPosition(viewport.startRes);
2353 // ShiftList shifts;
2354 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2355 // edit.alColumnChanges=shifts.getInverse();
2356 // if (viewport.hasHiddenColumns)
2357 // viewport.getColumnSelection().compensateForEdits(shifts);
2358 viewport.setStartRes(seq.findIndex(startRes) - 1);
2359 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2371 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2373 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2376 if (viewport.getSelectionGroup() != null)
2378 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2379 viewport.getHiddenRepSequences());
2380 start = viewport.getSelectionGroup().getStartRes();
2381 end = viewport.getSelectionGroup().getEndRes();
2385 seqs = viewport.getAlignment().getSequencesArray();
2388 // This is to maintain viewport position on first residue
2389 // of first sequence
2390 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2391 int startRes = seq.findPosition(viewport.startRes);
2393 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2394 viewport.getAlignment()));
2396 viewport.setStartRes(seq.findIndex(startRes) - 1);
2398 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2410 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2412 viewport.setPadGaps(padGapsMenuitem.isSelected());
2413 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2419 // if (justifySeqs>0)
2421 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2434 public void findMenuItem_actionPerformed(ActionEvent e)
2440 public void newView_actionPerformed(ActionEvent e)
2447 * @param copyAnnotation
2448 * if true then duplicate all annnotation, groups and settings
2449 * @return new alignment panel, already displayed.
2451 public AlignmentPanel newView(boolean copyAnnotation)
2453 return newView(null, copyAnnotation);
2459 * title of newly created view
2460 * @return new alignment panel, already displayed.
2462 public AlignmentPanel newView(String viewTitle)
2464 return newView(viewTitle, true);
2470 * title of newly created view
2471 * @param copyAnnotation
2472 * if true then duplicate all annnotation, groups and settings
2473 * @return new alignment panel, already displayed.
2475 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2477 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2479 if (!copyAnnotation)
2481 // just remove all the current annotation except for the automatic stuff
2482 newap.av.getAlignment().deleteAllGroups();
2483 for (AlignmentAnnotation alan : newap.av.getAlignment()
2484 .getAlignmentAnnotation())
2486 if (!alan.autoCalculated)
2488 newap.av.getAlignment().deleteAnnotation(alan);
2494 newap.av.gatherViewsHere = false;
2496 if (viewport.viewName == null)
2498 viewport.viewName = "Original";
2501 newap.av.historyList = viewport.historyList;
2502 newap.av.redoList = viewport.redoList;
2504 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2505 // make sure the new view has a unique name - this is essential for Jalview
2507 boolean addFirstIndex = false;
2508 if (viewTitle == null || viewTitle.trim().length() == 0)
2511 addFirstIndex = true;
2515 index = 1;// we count from 1 if given a specific name
2517 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2518 Vector comps = (Vector) PaintRefresher.components.get(viewport
2519 .getSequenceSetId());
2520 Vector existingNames = new Vector();
2521 for (int i = 0; i < comps.size(); i++)
2523 if (comps.elementAt(i) instanceof AlignmentPanel)
2525 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2526 if (!existingNames.contains(ap.av.viewName))
2528 existingNames.addElement(ap.av.viewName);
2533 while (existingNames.contains(newViewName))
2535 newViewName = viewTitle + " " + (++index);
2538 newap.av.viewName = newViewName;
2540 addAlignmentPanel(newap, true);
2541 newap.alignmentChanged();
2543 if (alignPanels.size() == 2)
2545 viewport.gatherViewsHere = true;
2547 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2552 public void expandViews_actionPerformed(ActionEvent e)
2554 Desktop.instance.explodeViews(this);
2558 public void gatherViews_actionPerformed(ActionEvent e)
2560 Desktop.instance.gatherViews(this);
2570 public void font_actionPerformed(ActionEvent e)
2572 new FontChooser(alignPanel);
2582 protected void seqLimit_actionPerformed(ActionEvent e)
2584 viewport.setShowJVSuffix(seqLimits.isSelected());
2586 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2587 .calculateIdWidth());
2588 alignPanel.paintAlignment(true);
2592 public void idRightAlign_actionPerformed(ActionEvent e)
2594 viewport.rightAlignIds = idRightAlign.isSelected();
2595 alignPanel.paintAlignment(true);
2599 public void centreColumnLabels_actionPerformed(ActionEvent e)
2601 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2602 alignPanel.paintAlignment(true);
2608 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2611 protected void followHighlight_actionPerformed()
2613 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2615 alignPanel.scrollToPosition(
2616 alignPanel.seqPanel.seqCanvas.searchResults, false);
2627 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2629 viewport.setColourText(colourTextMenuItem.isSelected());
2630 alignPanel.paintAlignment(true);
2640 public void wrapMenuItem_actionPerformed(ActionEvent e)
2642 scaleAbove.setVisible(wrapMenuItem.isSelected());
2643 scaleLeft.setVisible(wrapMenuItem.isSelected());
2644 scaleRight.setVisible(wrapMenuItem.isSelected());
2645 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2646 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2650 public void showAllSeqs_actionPerformed(ActionEvent e)
2652 viewport.showAllHiddenSeqs();
2656 public void showAllColumns_actionPerformed(ActionEvent e)
2658 viewport.showAllHiddenColumns();
2663 public void hideSelSequences_actionPerformed(ActionEvent e)
2665 viewport.hideAllSelectedSeqs();
2666 alignPanel.paintAlignment(true);
2670 * called by key handler and the hide all/show all menu items
2675 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2678 boolean hide = false;
2679 SequenceGroup sg = viewport.getSelectionGroup();
2680 if (!toggleSeqs && !toggleCols)
2682 // Hide everything by the current selection - this is a hack - we do the
2683 // invert and then hide
2684 // first check that there will be visible columns after the invert.
2685 if ((viewport.getColumnSelection() != null
2686 && viewport.getColumnSelection().getSelected() != null && viewport
2687 .getColumnSelection().getSelected().size() > 0)
2688 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2691 // now invert the sequence set, if required - empty selection implies
2692 // that no hiding is required.
2695 invertSequenceMenuItem_actionPerformed(null);
2696 sg = viewport.getSelectionGroup();
2700 viewport.expandColSelection(sg, true);
2701 // finally invert the column selection and get the new sequence
2703 invertColSel_actionPerformed(null);
2710 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2712 hideSelSequences_actionPerformed(null);
2715 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2718 showAllSeqs_actionPerformed(null);
2724 if (viewport.getColumnSelection().getSelected().size() > 0)
2726 hideSelColumns_actionPerformed(null);
2729 viewport.setSelectionGroup(sg);
2734 showAllColumns_actionPerformed(null);
2743 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2744 * event.ActionEvent)
2747 public void hideAllButSelection_actionPerformed(ActionEvent e)
2749 toggleHiddenRegions(false, false);
2756 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2760 public void hideAllSelection_actionPerformed(ActionEvent e)
2762 SequenceGroup sg = viewport.getSelectionGroup();
2763 viewport.expandColSelection(sg, false);
2764 viewport.hideAllSelectedSeqs();
2765 viewport.hideSelectedColumns();
2766 alignPanel.paintAlignment(true);
2773 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2777 public void showAllhidden_actionPerformed(ActionEvent e)
2779 viewport.showAllHiddenColumns();
2780 viewport.showAllHiddenSeqs();
2781 alignPanel.paintAlignment(true);
2785 public void hideSelColumns_actionPerformed(ActionEvent e)
2787 viewport.hideSelectedColumns();
2788 alignPanel.paintAlignment(true);
2792 public void hiddenMarkers_actionPerformed(ActionEvent e)
2794 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2805 protected void scaleAbove_actionPerformed(ActionEvent e)
2807 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2808 alignPanel.paintAlignment(true);
2818 protected void scaleLeft_actionPerformed(ActionEvent e)
2820 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2821 alignPanel.paintAlignment(true);
2831 protected void scaleRight_actionPerformed(ActionEvent e)
2833 viewport.setScaleRightWrapped(scaleRight.isSelected());
2834 alignPanel.paintAlignment(true);
2844 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2846 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2847 alignPanel.paintAlignment(true);
2857 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2859 viewport.setShowText(viewTextMenuItem.isSelected());
2860 alignPanel.paintAlignment(true);
2870 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2872 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2873 alignPanel.paintAlignment(true);
2876 public FeatureSettings featureSettings;
2879 public void featureSettings_actionPerformed(ActionEvent e)
2881 if (featureSettings != null)
2883 featureSettings.close();
2884 featureSettings = null;
2886 if (!showSeqFeatures.isSelected())
2888 // make sure features are actually displayed
2889 showSeqFeatures.setSelected(true);
2890 showSeqFeatures_actionPerformed(null);
2892 featureSettings = new FeatureSettings(this);
2896 * Set or clear 'Show Sequence Features'
2902 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2904 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2905 alignPanel.paintAlignment(true);
2906 if (alignPanel.getOverviewPanel() != null)
2908 alignPanel.getOverviewPanel().updateOverviewImage();
2913 * Set or clear 'Show Sequence Features'
2919 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2921 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2923 if (viewport.getShowSequenceFeaturesHeight())
2925 // ensure we're actually displaying features
2926 viewport.setShowSequenceFeatures(true);
2927 showSeqFeatures.setSelected(true);
2929 alignPanel.paintAlignment(true);
2930 if (alignPanel.getOverviewPanel() != null)
2932 alignPanel.getOverviewPanel().updateOverviewImage();
2943 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2945 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2946 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2950 public void alignmentProperties()
2952 JEditorPane editPane = new JEditorPane("text/html", "");
2953 editPane.setEditable(false);
2954 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
2956 editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
2957 JInternalFrame frame = new JInternalFrame();
2958 frame.getContentPane().add(new JScrollPane(editPane));
2960 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2961 + getTitle(), 500, 400);
2971 public void overviewMenuItem_actionPerformed(ActionEvent e)
2973 if (alignPanel.overviewPanel != null)
2978 JInternalFrame frame = new JInternalFrame();
2979 OverviewPanel overview = new OverviewPanel(alignPanel);
2980 frame.setContentPane(overview);
2981 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2982 frame.getWidth(), frame.getHeight());
2984 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2985 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2988 public void internalFrameClosed(
2989 javax.swing.event.InternalFrameEvent evt)
2991 alignPanel.setOverviewPanel(null);
2995 alignPanel.setOverviewPanel(overview);
2999 public void textColour_actionPerformed(ActionEvent e)
3001 new TextColourChooser().chooseColour(alignPanel, null);
3011 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3023 public void clustalColour_actionPerformed(ActionEvent e)
3025 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3026 viewport.getHiddenRepSequences()));
3036 public void zappoColour_actionPerformed(ActionEvent e)
3038 changeColour(new ZappoColourScheme());
3048 public void taylorColour_actionPerformed(ActionEvent e)
3050 changeColour(new TaylorColourScheme());
3060 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3062 changeColour(new HydrophobicColourScheme());
3072 public void helixColour_actionPerformed(ActionEvent e)
3074 changeColour(new HelixColourScheme());
3084 public void strandColour_actionPerformed(ActionEvent e)
3086 changeColour(new StrandColourScheme());
3096 public void turnColour_actionPerformed(ActionEvent e)
3098 changeColour(new TurnColourScheme());
3108 public void buriedColour_actionPerformed(ActionEvent e)
3110 changeColour(new BuriedColourScheme());
3120 public void nucleotideColour_actionPerformed(ActionEvent e)
3122 changeColour(new NucleotideColourScheme());
3126 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3128 changeColour(new PurinePyrimidineColourScheme());
3132 * public void covariationColour_actionPerformed(ActionEvent e) {
3134 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3138 public void annotationColour_actionPerformed(ActionEvent e)
3140 new AnnotationColourChooser(viewport, alignPanel);
3144 public void rnahelicesColour_actionPerformed(ActionEvent e)
3146 new RNAHelicesColourChooser(viewport, alignPanel);
3156 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3158 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3167 public void changeColour(ColourSchemeI cs)
3169 // TODO: compare with applet and pull up to model method
3174 if (viewport.getAbovePIDThreshold())
3176 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3179 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3181 viewport.setGlobalColourScheme(cs);
3185 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3188 if (viewport.getConservationSelected())
3191 Alignment al = (Alignment) viewport.getAlignment();
3192 Conservation c = new Conservation("All",
3193 ResidueProperties.propHash, 3, al.getSequences(), 0,
3197 c.verdict(false, viewport.getConsPercGaps());
3199 cs.setConservation(c);
3201 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3206 cs.setConservation(null);
3209 cs.setConsensus(viewport.getSequenceConsensusHash());
3212 viewport.setGlobalColourScheme(cs);
3214 if (viewport.getColourAppliesToAllGroups())
3217 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3225 if (cs instanceof ClustalxColourScheme)
3227 sg.cs = new ClustalxColourScheme(sg,
3228 viewport.getHiddenRepSequences());
3230 else if (cs instanceof UserColourScheme)
3232 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3238 sg.cs = cs.getClass().newInstance();
3239 } catch (Exception ex)
3244 if (viewport.getAbovePIDThreshold()
3245 || cs instanceof PIDColourScheme
3246 || cs instanceof Blosum62ColourScheme)
3248 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3250 sg.cs.setConsensus(AAFrequency.calculate(
3251 sg.getSequences(viewport.getHiddenRepSequences()),
3252 sg.getStartRes(), sg.getEndRes() + 1));
3256 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3259 if (viewport.getConservationSelected())
3261 Conservation c = new Conservation("Group",
3262 ResidueProperties.propHash, 3, sg.getSequences(viewport
3263 .getHiddenRepSequences()), sg.getStartRes(),
3264 sg.getEndRes() + 1);
3266 c.verdict(false, viewport.getConsPercGaps());
3267 sg.cs.setConservation(c);
3271 sg.cs.setConservation(null);
3276 if (alignPanel.getOverviewPanel() != null)
3278 alignPanel.getOverviewPanel().updateOverviewImage();
3281 alignPanel.paintAlignment(true);
3291 protected void modifyPID_actionPerformed(ActionEvent e)
3293 if (viewport.getAbovePIDThreshold()
3294 && viewport.getGlobalColourScheme() != null)
3296 SliderPanel.setPIDSliderSource(alignPanel,
3297 viewport.getGlobalColourScheme(), "Background");
3298 SliderPanel.showPIDSlider();
3309 protected void modifyConservation_actionPerformed(ActionEvent e)
3311 if (viewport.getConservationSelected()
3312 && viewport.getGlobalColourScheme() != null)
3314 SliderPanel.setConservationSlider(alignPanel,
3315 viewport.getGlobalColourScheme(), "Background");
3316 SliderPanel.showConservationSlider();
3327 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3329 viewport.setConservationSelected(conservationMenuItem.isSelected());
3331 viewport.setAbovePIDThreshold(false);
3332 abovePIDThreshold.setSelected(false);
3334 changeColour(viewport.getGlobalColourScheme());
3336 modifyConservation_actionPerformed(null);
3346 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3348 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3350 conservationMenuItem.setSelected(false);
3351 viewport.setConservationSelected(false);
3353 changeColour(viewport.getGlobalColourScheme());
3355 modifyPID_actionPerformed(null);
3365 public void userDefinedColour_actionPerformed(ActionEvent e)
3367 if (e.getActionCommand().equals("User Defined..."))
3369 new UserDefinedColours(alignPanel, null);
3373 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3374 .getUserColourSchemes().get(e.getActionCommand());
3380 public void updateUserColourMenu()
3383 Component[] menuItems = colourMenu.getMenuComponents();
3384 int i, iSize = menuItems.length;
3385 for (i = 0; i < iSize; i++)
3387 if (menuItems[i].getName() != null
3388 && menuItems[i].getName().equals("USER_DEFINED"))
3390 colourMenu.remove(menuItems[i]);
3394 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3396 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3397 .getUserColourSchemes().keys();
3399 while (userColours.hasMoreElements())
3401 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3402 userColours.nextElement().toString());
3403 radioItem.setName("USER_DEFINED");
3404 radioItem.addMouseListener(new MouseAdapter()
3407 public void mousePressed(MouseEvent evt)
3409 if (evt.isControlDown()
3410 || SwingUtilities.isRightMouseButton(evt))
3412 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3414 int option = JOptionPane.showInternalConfirmDialog(
3415 jalview.gui.Desktop.desktop,
3416 MessageManager.getString("label.remove_from_default_list"),
3417 MessageManager.getString("label.remove_user_defined_colour"),
3418 JOptionPane.YES_NO_OPTION);
3419 if (option == JOptionPane.YES_OPTION)
3421 jalview.gui.UserDefinedColours
3422 .removeColourFromDefaults(radioItem.getText());
3423 colourMenu.remove(radioItem);
3427 radioItem.addActionListener(new ActionListener()
3430 public void actionPerformed(ActionEvent evt)
3432 userDefinedColour_actionPerformed(evt);
3439 radioItem.addActionListener(new ActionListener()
3442 public void actionPerformed(ActionEvent evt)
3444 userDefinedColour_actionPerformed(evt);
3448 colourMenu.insert(radioItem, 15);
3449 colours.add(radioItem);
3461 public void PIDColour_actionPerformed(ActionEvent e)
3463 changeColour(new PIDColourScheme());
3473 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3475 changeColour(new Blosum62ColourScheme());
3485 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3487 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3488 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3489 .getAlignment().getSequenceAt(0), null);
3490 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3491 viewport.getAlignment()));
3492 alignPanel.paintAlignment(true);
3502 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3504 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3505 AlignmentSorter.sortByID(viewport.getAlignment());
3506 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3507 viewport.getAlignment()));
3508 alignPanel.paintAlignment(true);
3518 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3520 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3521 AlignmentSorter.sortByLength(viewport.getAlignment());
3522 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3523 viewport.getAlignment()));
3524 alignPanel.paintAlignment(true);
3534 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3536 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3537 AlignmentSorter.sortByGroup(viewport.getAlignment());
3538 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3539 viewport.getAlignment()));
3541 alignPanel.paintAlignment(true);
3551 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3553 new RedundancyPanel(alignPanel, this);
3563 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3565 if ((viewport.getSelectionGroup() == null)
3566 || (viewport.getSelectionGroup().getSize() < 2))
3568 JOptionPane.showInternalMessageDialog(this,
3569 MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"),
3570 JOptionPane.WARNING_MESSAGE);
3574 JInternalFrame frame = new JInternalFrame();
3575 frame.setContentPane(new PairwiseAlignPanel(viewport));
3576 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3587 public void PCAMenuItem_actionPerformed(ActionEvent e)
3589 if (((viewport.getSelectionGroup() != null)
3590 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3591 .getSelectionGroup().getSize() > 0))
3592 || (viewport.getAlignment().getHeight() < 4))
3594 JOptionPane.showInternalMessageDialog(this,
3595 MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3596 MessageManager.getString("label.sequence_selection_insufficient"),
3597 JOptionPane.WARNING_MESSAGE);
3602 new PCAPanel(alignPanel);
3606 public void autoCalculate_actionPerformed(ActionEvent e)
3608 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3609 if (viewport.autoCalculateConsensus)
3611 viewport.firePropertyChange("alignment", null, viewport
3612 .getAlignment().getSequences());
3617 public void sortByTreeOption_actionPerformed(ActionEvent e)
3619 viewport.sortByTree = sortByTree.isSelected();
3623 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3625 viewport.followSelection = listenToViewSelections.isSelected();
3635 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3637 NewTreePanel("AV", "PID", "Average distance tree using PID");
3647 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3649 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3659 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3661 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3671 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3673 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3686 void NewTreePanel(String type, String pwType, String title)
3690 if (viewport.getSelectionGroup() != null
3691 && viewport.getSelectionGroup().getSize() > 0)
3693 if (viewport.getSelectionGroup().getSize() < 3)
3698 MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"),
3699 MessageManager.getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE);
3703 SequenceGroup sg = viewport.getSelectionGroup();
3705 /* Decide if the selection is a column region */
3706 for (SequenceI _s : sg.getSequences())
3708 if (_s.getLength() < sg.getEndRes())
3713 MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3714 MessageManager.getString("label.sequences_selection_not_aligned"),
3715 JOptionPane.WARNING_MESSAGE);
3721 title = title + " on region";
3722 tp = new TreePanel(alignPanel, type, pwType);
3726 // are the visible sequences aligned?
3727 if (!viewport.getAlignment().isAligned(false))
3732 MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"),
3733 MessageManager.getString("label.sequences_not_aligned"),
3734 JOptionPane.WARNING_MESSAGE);
3739 if (viewport.getAlignment().getHeight() < 2)
3744 tp = new TreePanel(alignPanel, type, pwType);
3749 if (viewport.viewName != null)
3751 title += viewport.viewName + " of ";
3754 title += this.title;
3756 Desktop.addInternalFrame(tp, title, 600, 500);
3767 public void addSortByOrderMenuItem(String title,
3768 final AlignmentOrder order)
3770 final JMenuItem item = new JMenuItem("by " + title);
3772 item.addActionListener(new java.awt.event.ActionListener()
3775 public void actionPerformed(ActionEvent e)
3777 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3779 // TODO: JBPNote - have to map order entries to curent SequenceI
3781 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3783 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3786 alignPanel.paintAlignment(true);
3792 * Add a new sort by annotation score menu item
3795 * the menu to add the option to
3797 * the label used to retrieve scores for each sequence on the
3800 public void addSortByAnnotScoreMenuItem(JMenu sort,
3801 final String scoreLabel)
3803 final JMenuItem item = new JMenuItem(scoreLabel);
3805 item.addActionListener(new java.awt.event.ActionListener()
3808 public void actionPerformed(ActionEvent e)
3810 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3811 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3812 viewport.getAlignment());// ,viewport.getSelectionGroup());
3813 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3814 viewport.getAlignment()));
3815 alignPanel.paintAlignment(true);
3821 * last hash for alignment's annotation array - used to minimise cost of
3824 protected int _annotationScoreVectorHash;
3827 * search the alignment and rebuild the sort by annotation score submenu the
3828 * last alignment annotation vector hash is stored to minimize cost of
3829 * rebuilding in subsequence calls.
3833 public void buildSortByAnnotationScoresMenu()
3835 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3840 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3842 sortByAnnotScore.removeAll();
3843 // almost certainly a quicker way to do this - but we keep it simple
3844 Hashtable scoreSorts = new Hashtable();
3845 AlignmentAnnotation aann[];
3846 for (SequenceI sqa : viewport.getAlignment().getSequences())
3848 aann = sqa.getAnnotation();
3849 for (int i = 0; aann != null && i < aann.length; i++)
3851 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3853 scoreSorts.put(aann[i].label, aann[i].label);
3857 Enumeration labels = scoreSorts.keys();
3858 while (labels.hasMoreElements())
3860 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3861 (String) labels.nextElement());
3863 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3866 _annotationScoreVectorHash = viewport.getAlignment()
3867 .getAlignmentAnnotation().hashCode();
3872 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3873 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3874 * call. Listeners are added to remove the menu item when the treePanel is
3875 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3879 * Displayed tree window.
3881 * SortBy menu item title.
3884 public void buildTreeMenu()
3886 sortByTreeMenu.removeAll();
3888 Vector comps = (Vector) PaintRefresher.components.get(viewport
3889 .getSequenceSetId());
3890 Vector treePanels = new Vector();
3891 int i, iSize = comps.size();
3892 for (i = 0; i < iSize; i++)
3894 if (comps.elementAt(i) instanceof TreePanel)
3896 treePanels.add(comps.elementAt(i));
3900 iSize = treePanels.size();
3904 sortByTreeMenu.setVisible(false);
3908 sortByTreeMenu.setVisible(true);
3910 for (i = 0; i < treePanels.size(); i++)
3912 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3913 final JMenuItem item = new JMenuItem(tp.getTitle());
3914 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3915 item.addActionListener(new java.awt.event.ActionListener()
3918 public void actionPerformed(ActionEvent e)
3920 tp.sortByTree_actionPerformed(null);
3921 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3926 sortByTreeMenu.add(item);
3930 public boolean sortBy(AlignmentOrder alorder, String undoname)
3932 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3933 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3934 if (undoname != null)
3936 addHistoryItem(new OrderCommand(undoname, oldOrder,
3937 viewport.getAlignment()));
3939 alignPanel.paintAlignment(true);
3944 * Work out whether the whole set of sequences or just the selected set will
3945 * be submitted for multiple alignment.
3948 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3950 // Now, check we have enough sequences
3951 AlignmentView msa = null;
3953 if ((viewport.getSelectionGroup() != null)
3954 && (viewport.getSelectionGroup().getSize() > 1))
3956 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3957 // some common interface!
3959 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3960 * SequenceI[sz = seqs.getSize(false)];
3962 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3963 * seqs.getSequenceAt(i); }
3965 msa = viewport.getAlignmentView(true);
3970 * Vector seqs = viewport.getAlignment().getSequences();
3972 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3974 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3975 * seqs.elementAt(i); } }
3977 msa = viewport.getAlignmentView(false);
3983 * Decides what is submitted to a secondary structure prediction service: the
3984 * first sequence in the alignment, or in the current selection, or, if the
3985 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3986 * region or the whole alignment. (where the first sequence in the set is the
3987 * one that the prediction will be for).
3989 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3991 AlignmentView seqs = null;
3993 if ((viewport.getSelectionGroup() != null)
3994 && (viewport.getSelectionGroup().getSize() > 0))
3996 seqs = viewport.getAlignmentView(true);
4000 seqs = viewport.getAlignmentView(false);
4002 // limit sequences - JBPNote in future - could spawn multiple prediction
4004 // TODO: viewport.getAlignment().isAligned is a global state - the local
4005 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4006 if (!viewport.getAlignment().isAligned(false))
4008 seqs.setSequences(new SeqCigar[]
4009 { seqs.getSequences()[0] });
4010 // TODO: if seqs.getSequences().length>1 then should really have warned
4024 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4026 // Pick the tree file
4027 JalviewFileChooser chooser = new JalviewFileChooser(
4028 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4029 chooser.setFileView(new JalviewFileView());
4030 chooser.setDialogTitle("Select a newick-like tree file");
4031 chooser.setToolTipText("Load a tree file");
4033 int value = chooser.showOpenDialog(null);
4035 if (value == JalviewFileChooser.APPROVE_OPTION)
4037 String choice = chooser.getSelectedFile().getPath();
4038 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4039 jalview.io.NewickFile fin = null;
4042 fin = new jalview.io.NewickFile(choice, "File");
4043 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4044 } catch (Exception ex)
4046 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4047 MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE);
4048 ex.printStackTrace();
4050 if (fin != null && fin.hasWarningMessage())
4052 JOptionPane.showMessageDialog(Desktop.desktop,
4053 fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"),
4054 JOptionPane.WARNING_MESSAGE);
4060 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4062 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4065 public TreePanel ShowNewickTree(NewickFile nf, String title)
4067 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4070 public TreePanel ShowNewickTree(NewickFile nf, String title,
4071 AlignmentView input)
4073 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4076 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4077 int h, int x, int y)
4079 return ShowNewickTree(nf, title, null, w, h, x, y);
4083 * Add a treeviewer for the tree extracted from a newick file object to the
4084 * current alignment view
4091 * Associated alignment input data (or null)
4100 * @return TreePanel handle
4102 public TreePanel ShowNewickTree(NewickFile nf, String title,
4103 AlignmentView input, int w, int h, int x, int y)
4105 TreePanel tp = null;
4111 if (nf.getTree() != null)
4113 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4119 tp.setLocation(x, y);
4122 Desktop.addInternalFrame(tp, title, w, h);
4124 } catch (Exception ex)
4126 ex.printStackTrace();
4132 private boolean buildingMenu = false;
4135 * Generates menu items and listener event actions for web service clients
4138 public void BuildWebServiceMenu()
4140 while (buildingMenu)
4144 System.err.println("Waiting for building menu to finish.");
4146 } catch (Exception e)
4151 final AlignFrame me = this;
4152 buildingMenu = true;
4153 new Thread(new Runnable()
4158 final List<JMenuItem> legacyItems=new ArrayList<JMenuItem>();
4161 System.err.println("Building ws menu again "
4162 + Thread.currentThread());
4163 // TODO: add support for context dependent disabling of services based
4165 // alignment and current selection
4166 // TODO: add additional serviceHandle parameter to specify abstract
4168 // class independently of AbstractName
4169 // TODO: add in rediscovery GUI function to restart discoverer
4170 // TODO: group services by location as well as function and/or
4172 // object broker mechanism.
4173 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4174 final IProgressIndicator af = me;
4175 final JMenu msawsmenu = new JMenu("Alignment");
4176 final JMenu secstrmenu = new JMenu(
4177 "Secondary Structure Prediction");
4178 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4179 final JMenu analymenu = new JMenu("Analysis");
4180 final JMenu dismenu = new JMenu("Protein Disorder");
4181 // JAL-940 - only show secondary structure prediction services from
4182 // the legacy server
4183 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4185 Discoverer.services != null && (Discoverer.services.size() > 0))
4187 // TODO: refactor to allow list of AbstractName/Handler bindings to
4189 // stored or retrieved from elsewhere
4190 // No MSAWS used any more:
4191 // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4192 Vector secstrpr = (Vector) Discoverer.services
4194 if (secstrpr != null)
4196 // Add any secondary structure prediction services
4197 for (int i = 0, j = secstrpr.size(); i < j; i++)
4199 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4201 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4202 .getServiceClient(sh);
4203 int p=secstrmenu.getItemCount();
4204 impl.attachWSMenuEntry(secstrmenu, me);
4205 int q=secstrmenu.getItemCount();
4206 for (int litm=p;litm<q; litm++)
4208 legacyItems.add(secstrmenu.getItem(litm));
4214 // Add all submenus in the order they should appear on the web
4216 wsmenu.add(msawsmenu);
4217 wsmenu.add(secstrmenu);
4218 wsmenu.add(dismenu);
4219 wsmenu.add(analymenu);
4220 // No search services yet
4221 // wsmenu.add(seqsrchmenu);
4223 javax.swing.SwingUtilities.invokeLater(new Runnable()
4230 webService.removeAll();
4231 // first, add discovered services onto the webservices menu
4232 if (wsmenu.size() > 0)
4234 for (int i = 0, j = wsmenu.size(); i < j; i++)
4236 webService.add(wsmenu.get(i));
4241 webService.add(me.webServiceNoServices);
4243 // TODO: move into separate menu builder class.
4244 boolean new_sspred=false;
4245 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4247 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4248 if (jws2servs != null)
4250 if (jws2servs.hasServices())
4252 jws2servs.attachWSMenuEntry(webService, me);
4253 for (Jws2Instance sv:jws2servs.getServices()) {
4254 if (sv.description.toLowerCase().contains("jpred"))
4256 for (JMenuItem jmi:legacyItems)
4258 jmi.setVisible(false);
4264 if (jws2servs.isRunning())
4266 JMenuItem tm = new JMenuItem(
4267 "Still discovering JABA Services");
4268 tm.setEnabled(false);
4273 build_urlServiceMenu(me.webService);
4274 build_fetchdbmenu(webService);
4275 for (JMenu item : wsmenu)
4277 if (item.getItemCount() == 0)
4279 item.setEnabled(false);
4283 item.setEnabled(true);
4286 } catch (Exception e)
4289 .debug("Exception during web service menu building process.",
4295 } catch (Exception e)
4300 buildingMenu = false;
4307 * construct any groupURL type service menu entries.
4311 private void build_urlServiceMenu(JMenu webService)
4313 // TODO: remove this code when 2.7 is released
4314 // DEBUG - alignmentView
4316 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4317 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4319 * @Override public void actionPerformed(ActionEvent e) {
4320 * jalview.datamodel.AlignmentView
4321 * .testSelectionViews(af.viewport.getAlignment(),
4322 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4324 * }); webService.add(testAlView);
4326 // TODO: refactor to RestClient discoverer and merge menu entries for
4327 // rest-style services with other types of analysis/calculation service
4328 // SHmmr test client - still being implemented.
4329 // DEBUG - alignmentView
4331 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4334 client.attachWSMenuEntry(
4335 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4339 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4341 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4347 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4348 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4349 * getProperty("LAST_DIRECTORY"));
4351 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4352 * to Vamsas file"); chooser.setToolTipText("Export");
4354 * int value = chooser.showSaveDialog(this);
4356 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4357 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4358 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4359 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4362 * prototype of an automatically enabled/disabled analysis function
4365 protected void setShowProductsEnabled()
4367 SequenceI[] selection = viewport.getSequenceSelection();
4368 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4369 viewport.getAlignment().getDataset()))
4371 showProducts.setEnabled(true);
4376 showProducts.setEnabled(false);
4381 * search selection for sequence xRef products and build the show products
4386 * @return true if showProducts menu should be enabled.
4388 public boolean canShowProducts(SequenceI[] selection,
4389 boolean isRegionSelection, Alignment dataset)
4391 boolean showp = false;
4394 showProducts.removeAll();
4395 final boolean dna = viewport.getAlignment().isNucleotide();
4396 final Alignment ds = dataset;
4397 String[] ptypes = (selection == null || selection.length == 0) ? null
4398 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4400 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4401 // selection, dataset, true);
4402 final SequenceI[] sel = selection;
4403 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4406 final boolean isRegSel = isRegionSelection;
4407 final AlignFrame af = this;
4408 final String source = ptypes[t];
4409 JMenuItem xtype = new JMenuItem(ptypes[t]);
4410 xtype.addActionListener(new ActionListener()
4414 public void actionPerformed(ActionEvent e)
4416 // TODO: new thread for this call with vis-delay
4417 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4418 isRegSel, dna, source);
4422 showProducts.add(xtype);
4424 showProducts.setVisible(showp);
4425 showProducts.setEnabled(showp);
4426 } catch (Exception e)
4428 jalview.bin.Cache.log
4429 .warn("canTranslate threw an exception - please report to help@jalview.org",
4436 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4437 boolean isRegSel, boolean dna, String source)
4439 final boolean fisRegSel = isRegSel;
4440 final boolean fdna = dna;
4441 final String fsrc = source;
4442 final AlignFrame ths = this;
4443 final SequenceI[] fsel = sel;
4444 Runnable foo = new Runnable()
4450 final long sttime = System.currentTimeMillis();
4451 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4454 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4458 Alignment prods = CrossRef
4459 .findXrefSequences(fsel, fdna, fsrc, ds);
4462 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4463 for (int s = 0; s < sprods.length; s++)
4465 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4466 if (ds.getSequences() == null
4467 || !ds.getSequences().contains(
4468 sprods[s].getDatasetSequence()))
4469 ds.addSequence(sprods[s].getDatasetSequence());
4470 sprods[s].updatePDBIds();
4472 Alignment al = new Alignment(sprods);
4473 AlignedCodonFrame[] cf = prods.getCodonFrames();
4475 for (int s = 0; cf != null && s < cf.length; s++)
4477 al.addCodonFrame(cf[s]);
4480 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4482 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4483 + " for " + ((fisRegSel) ? "selected region of " : "")
4485 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4490 System.err.println("No Sequences generated for xRef type "
4493 } catch (Exception e)
4495 jalview.bin.Cache.log.error(
4496 "Exception when finding crossreferences", e);
4497 } catch (OutOfMemoryError e)
4499 new OOMWarning("whilst fetching crossreferences", e);
4502 jalview.bin.Cache.log.error("Error when finding crossreferences",
4505 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4510 Thread frunner = new Thread(foo);
4514 public boolean canShowTranslationProducts(SequenceI[] selection,
4515 AlignmentI alignment)
4520 return (jalview.analysis.Dna.canTranslate(selection,
4521 viewport.getViewAsVisibleContigs(true)));
4522 } catch (Exception e)
4524 jalview.bin.Cache.log
4525 .warn("canTranslate threw an exception - please report to help@jalview.org",
4532 public void showProducts_actionPerformed(ActionEvent e)
4534 // /////////////////////////////
4535 // Collect Data to be translated/transferred
4537 SequenceI[] selection = viewport.getSequenceSelection();
4538 AlignmentI al = null;
4541 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4542 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4543 viewport.getAlignment().getDataset());
4544 } catch (Exception ex)
4547 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4554 MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4555 MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
4559 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4560 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4561 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4566 public void showTranslation_actionPerformed(ActionEvent e)
4568 // /////////////////////////////
4569 // Collect Data to be translated/transferred
4571 SequenceI[] selection = viewport.getSequenceSelection();
4572 String[] seqstring = viewport.getViewAsString(true);
4573 AlignmentI al = null;
4576 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4577 viewport.getViewAsVisibleContigs(true), viewport
4578 .getGapCharacter(), viewport.getAlignment()
4579 .getAlignmentAnnotation(), viewport.getAlignment()
4580 .getWidth(), viewport.getAlignment().getDataset());
4581 } catch (Exception ex)
4584 jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex);
4588 MessageManager.getString("label.error_when_translating_sequences_submit_bug_report"),
4589 MessageManager.getString("label.implementation_error") + MessageManager.getString("translation_failed"), JOptionPane.ERROR_MESSAGE);
4597 MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4598 MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
4602 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4603 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4604 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4609 * Try to load a features file onto the alignment.
4612 * contents or path to retrieve file
4614 * access mode of file (see jalview.io.AlignFile)
4615 * @return true if features file was parsed corectly.
4617 public boolean parseFeaturesFile(String file, String type)
4619 boolean featuresFile = false;
4622 featuresFile = new FeaturesFile(file, type).parse(viewport
4623 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4624 .getFeatureRenderer().featureColours, false,
4625 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4626 } catch (Exception ex)
4628 ex.printStackTrace();
4633 viewport.showSequenceFeatures = true;
4634 showSeqFeatures.setSelected(true);
4635 if (alignPanel.seqPanel.seqCanvas.fr != null)
4637 // update the min/max ranges where necessary
4638 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4640 if (featureSettings != null)
4642 featureSettings.setTableData();
4644 alignPanel.paintAlignment(true);
4647 return featuresFile;
4651 public void dragEnter(DropTargetDragEvent evt)
4656 public void dragExit(DropTargetEvent evt)
4661 public void dragOver(DropTargetDragEvent evt)
4666 public void dropActionChanged(DropTargetDragEvent evt)
4671 public void drop(DropTargetDropEvent evt)
4673 Transferable t = evt.getTransferable();
4674 java.util.List files = null;
4678 DataFlavor uriListFlavor = new DataFlavor(
4679 "text/uri-list;class=java.lang.String");
4680 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4682 // Works on Windows and MacOSX
4683 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4684 files = (java.util.List) t
4685 .getTransferData(DataFlavor.javaFileListFlavor);
4687 else if (t.isDataFlavorSupported(uriListFlavor))
4689 // This is used by Unix drag system
4690 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4691 String data = (String) t.getTransferData(uriListFlavor);
4692 files = new java.util.ArrayList(1);
4693 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4694 data, "\r\n"); st.hasMoreTokens();)
4696 String s = st.nextToken();
4697 if (s.startsWith("#"))
4699 // the line is a comment (as per the RFC 2483)
4703 java.net.URI uri = new java.net.URI(s);
4704 // check to see if we can handle this kind of URI
4705 if (uri.getScheme().toLowerCase().startsWith("http"))
4707 files.add(uri.toString());
4711 // otherwise preserve old behaviour: catch all for file objects
4712 java.io.File file = new java.io.File(uri);
4713 files.add(file.toString());
4717 } catch (Exception e)
4719 e.printStackTrace();
4725 // check to see if any of these files have names matching sequences in
4727 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4728 .getAlignment().getSequencesArray());
4730 * Object[] { String,SequenceI}
4732 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4733 ArrayList<String> filesnotmatched = new ArrayList<String>();
4734 for (int i = 0; i < files.size(); i++)
4736 String file = files.get(i).toString();
4738 String protocol = FormatAdapter.checkProtocol(file);
4739 if (protocol == jalview.io.FormatAdapter.FILE)
4741 File fl = new File(file);
4742 pdbfn = fl.getName();
4744 else if (protocol == jalview.io.FormatAdapter.URL)
4746 URL url = new URL(file);
4747 pdbfn = url.getFile();
4749 if (pdbfn.length() > 0)
4751 // attempt to find a match in the alignment
4752 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4753 int l = 0, c = pdbfn.indexOf(".");
4754 while (mtch == null && c != -1)
4759 } while ((c = pdbfn.indexOf(".", l)) > l);
4762 pdbfn = pdbfn.substring(0, l);
4764 mtch = idm.findAllIdMatches(pdbfn);
4771 type = new IdentifyFile().Identify(file, protocol);
4772 } catch (Exception ex)
4778 if (type.equalsIgnoreCase("PDB"))
4780 filesmatched.add(new Object[]
4781 { file, protocol, mtch });
4786 // File wasn't named like one of the sequences or wasn't a PDB file.
4787 filesnotmatched.add(file);
4791 if (filesmatched.size() > 0)
4793 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4797 MessageManager.formatMessage("label.automatically_associate_pdb_files_with_sequences_same_name",
4798 new String[]{Integer.valueOf(filesmatched.size()).toString()}),
4799 MessageManager.getString("label.automatically_associate_pdb_files_by_name"),
4800 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4803 for (Object[] fm : filesmatched)
4805 // try and associate
4806 // TODO: may want to set a standard ID naming formalism for
4807 // associating PDB files which have no IDs.
4808 for (SequenceI toassoc : (SequenceI[]) fm[2])
4810 PDBEntry pe = new AssociatePdbFileWithSeq()
4811 .associatePdbWithSeq((String) fm[0],
4812 (String) fm[1], toassoc, false);
4815 System.err.println("Associated file : "
4816 + ((String) fm[0]) + " with "
4817 + toassoc.getDisplayId(true));
4821 alignPanel.paintAlignment(true);
4825 if (filesnotmatched.size() > 0)
4828 && (Cache.getDefault(
4829 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4832 MessageManager.formatMessage("label.ignore_unmatched_dropped_files_info", new String[]{Integer.valueOf(filesnotmatched.size()).toString()}),
4833 MessageManager.getString("label.ignore_unmatched_dropped_files"),
4834 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4838 for (String fn : filesnotmatched)
4840 loadJalviewDataFile(fn, null, null, null);
4844 } catch (Exception ex)
4846 ex.printStackTrace();
4852 * Attempt to load a "dropped" file or URL string: First by testing whether
4853 * it's and Annotation file, then a JNet file, and finally a features file. If
4854 * all are false then the user may have dropped an alignment file onto this
4858 * either a filename or a URL string.
4860 public void loadJalviewDataFile(String file, String protocol,
4861 String format, SequenceI assocSeq)
4865 if (protocol == null)
4867 protocol = jalview.io.FormatAdapter.checkProtocol(file);
4869 // if the file isn't identified, or not positively identified as some
4870 // other filetype (PFAM is default unidentified alignment file type) then
4871 // try to parse as annotation.
4872 boolean isAnnotation = (format == null || format
4873 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4874 .readAnnotationFile(viewport.getAlignment(), file, protocol)
4879 // first see if its a T-COFFEE score file
4880 TCoffeeScoreFile tcf = null;
4883 tcf = new TCoffeeScoreFile(file, protocol);
4886 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4888 tcoffeeColour.setEnabled(true);
4889 tcoffeeColour.setSelected(true);
4890 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4891 isAnnotation = true;
4892 statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4896 // some problem - if no warning its probable that the ID matching
4897 // process didn't work
4901 tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment")
4902 : tcf.getWarningMessage(),
4903 MessageManager.getString("label.problem_reading_tcoffee_score_file"),
4904 JOptionPane.WARNING_MESSAGE);
4911 } catch (Exception x)
4914 .debug("Exception when processing data source as T-COFFEE score file",
4920 // try to see if its a JNet 'concise' style annotation file *before*
4922 // try to parse it as a features file
4925 format = new IdentifyFile().Identify(file, protocol);
4927 if (format.equalsIgnoreCase("JnetFile"))
4929 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
4931 new JnetAnnotationMaker().add_annotation(predictions,
4932 viewport.getAlignment(), 0, false);
4933 isAnnotation = true;
4938 * if (format.equalsIgnoreCase("PDB")) {
4940 * String pdbfn = ""; // try to match up filename with sequence id
4941 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
4942 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
4943 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4944 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
4945 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4946 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
4947 * // attempt to find a match in the alignment SequenceI mtch =
4948 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4949 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
4950 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
4951 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
4952 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4953 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
4954 * { System.err.println("Associated file : " + file + " with " +
4955 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4956 * TODO: maybe need to load as normal otherwise return; } }
4958 // try to parse it as a features file
4959 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4960 // if it wasn't a features file then we just treat it as a general
4961 // alignment file to load into the current view.
4964 new FileLoader().LoadFile(viewport, file, protocol, format);
4968 alignPanel.paintAlignment(true);
4976 alignPanel.adjustAnnotationHeight();
4977 viewport.updateSequenceIdColours();
4978 buildSortByAnnotationScoresMenu();
4979 alignPanel.paintAlignment(true);
4981 } catch (Exception ex)
4983 ex.printStackTrace();
4984 } catch (OutOfMemoryError oom)
4989 } catch (Exception x)
4995 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
4996 : "using " + protocol + " from " + file)
4998 + (format != null ? "(parsing as '" + format
4999 + "' file)" : ""), oom, Desktop.desktop);
5004 public void tabSelectionChanged(int index)
5008 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5009 viewport = alignPanel.av;
5010 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5011 setMenusFromViewport(viewport);
5016 public void tabbedPane_mousePressed(MouseEvent e)
5018 if (SwingUtilities.isRightMouseButton(e))
5020 String reply = JOptionPane.showInternalInputDialog(this,
5021 MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name"),
5022 JOptionPane.QUESTION_MESSAGE);
5026 viewport.viewName = reply;
5027 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5032 public AlignViewport getCurrentView()
5038 * Open the dialog for regex description parsing.
5041 protected void extractScores_actionPerformed(ActionEvent e)
5043 ParseProperties pp = new jalview.analysis.ParseProperties(
5044 viewport.getAlignment());
5045 // TODO: verify regex and introduce GUI dialog for version 2.5
5046 // if (pp.getScoresFromDescription("col", "score column ",
5047 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5049 if (pp.getScoresFromDescription("description column",
5050 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5052 buildSortByAnnotationScoresMenu();
5060 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5064 protected void showDbRefs_actionPerformed(ActionEvent e)
5066 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5072 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5076 protected void showNpFeats_actionPerformed(ActionEvent e)
5078 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5082 * find the viewport amongst the tabs in this alignment frame and close that
5087 public boolean closeView(AlignViewport av)
5091 this.closeMenuItem_actionPerformed(false);
5094 Component[] comp = tabbedPane.getComponents();
5095 for (int i = 0; comp != null && i < comp.length; i++)
5097 if (comp[i] instanceof AlignmentPanel)
5099 if (((AlignmentPanel) comp[i]).av == av)
5102 closeView((AlignmentPanel) comp[i]);
5110 protected void build_fetchdbmenu(JMenu webService)
5112 // Temporary hack - DBRef Fetcher always top level ws entry.
5113 // TODO We probably want to store a sequence database checklist in
5114 // preferences and have checkboxes.. rather than individual sources selected
5116 final JMenu rfetch = new JMenu("Fetch DB References");
5117 rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
5118 webService.add(rfetch);
5120 JMenuItem fetchr = new JMenuItem("Standard Databases");
5121 fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
5122 fetchr.addActionListener(new ActionListener()
5126 public void actionPerformed(ActionEvent e)
5128 new Thread(new Runnable()
5134 new jalview.ws.DBRefFetcher(alignPanel.av
5135 .getSequenceSelection(), alignPanel.alignFrame)
5136 .fetchDBRefs(false);
5144 final AlignFrame me = this;
5145 new Thread(new Runnable()
5150 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5151 .getSequenceFetcherSingleton(me);
5152 javax.swing.SwingUtilities.invokeLater(new Runnable()
5157 String[] dbclasses = sf.getOrderedSupportedSources();
5158 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5159 // jalview.util.QuickSort.sort(otherdb, otherdb);
5160 List<DbSourceProxy> otherdb;
5161 JMenu dfetch = new JMenu();
5162 JMenu ifetch = new JMenu();
5163 JMenuItem fetchr = null;
5164 int comp = 0, icomp = 0, mcomp = 15;
5165 String mname = null;
5167 for (String dbclass : dbclasses)
5169 otherdb = sf.getSourceProxy(dbclass);
5170 // add a single entry for this class, or submenu allowing 'fetch
5172 if (otherdb == null || otherdb.size() < 1)
5176 // List<DbSourceProxy> dbs=otherdb;
5177 // otherdb=new ArrayList<DbSourceProxy>();
5178 // for (DbSourceProxy db:dbs)
5180 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5184 mname = "From " + dbclass;
5186 if (otherdb.size() == 1)
5188 final DbSourceProxy[] dassource = otherdb
5189 .toArray(new DbSourceProxy[0]);
5190 DbSourceProxy src = otherdb.get(0);
5191 fetchr = new JMenuItem(src.getDbSource());
5192 fetchr.addActionListener(new ActionListener()
5196 public void actionPerformed(ActionEvent e)
5198 new Thread(new Runnable()
5204 new jalview.ws.DBRefFetcher(alignPanel.av
5205 .getSequenceSelection(),
5206 alignPanel.alignFrame, dassource)
5207 .fetchDBRefs(false);
5213 fetchr.setToolTipText("<html>"
5214 + JvSwingUtils.wrapTooltip("Retrieve from "
5215 + src.getDbName()) + "<html>");
5221 final DbSourceProxy[] dassource = otherdb
5222 .toArray(new DbSourceProxy[0]);
5224 DbSourceProxy src = otherdb.get(0);
5225 fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
5227 fetchr.addActionListener(new ActionListener()
5230 public void actionPerformed(ActionEvent e)
5232 new Thread(new Runnable()
5238 new jalview.ws.DBRefFetcher(alignPanel.av
5239 .getSequenceSelection(),
5240 alignPanel.alignFrame, dassource)
5241 .fetchDBRefs(false);
5247 fetchr.setToolTipText("<html>"
5248 + JvSwingUtils.wrapTooltip("Retrieve from all "
5249 + otherdb.size() + " sources in "
5250 + src.getDbSource() + "<br>First is :"
5251 + src.getDbName()) + "<html>");
5254 // and then build the rest of the individual menus
5255 ifetch = new JMenu("Sources from " + src.getDbSource());
5257 String imname = null;
5259 for (DbSourceProxy sproxy : otherdb)
5261 String dbname = sproxy.getDbName();
5262 String sname = dbname.length() > 5 ? dbname.substring(0,
5263 5) + "..." : dbname;
5264 String msname = dbname.length() > 10 ? dbname.substring(
5265 0, 10) + "..." : dbname;
5268 imname = "from '" + sname + "'";
5270 fetchr = new JMenuItem(msname);
5271 final DbSourceProxy[] dassrc =
5273 fetchr.addActionListener(new ActionListener()
5277 public void actionPerformed(ActionEvent e)
5279 new Thread(new Runnable()
5285 new jalview.ws.DBRefFetcher(alignPanel.av
5286 .getSequenceSelection(),
5287 alignPanel.alignFrame, dassrc)
5288 .fetchDBRefs(false);
5294 fetchr.setToolTipText("<html>"
5295 + JvSwingUtils.wrapTooltip("Retrieve from "
5296 + dbname) + "</html>");
5299 if (++icomp >= mcomp || i == (otherdb.size()))
5301 ifetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{imname,sname}));
5303 ifetch = new JMenu();
5311 if (comp >= mcomp || dbi >= (dbclasses.length))
5313 dfetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{mname,dbclass}));
5315 dfetch = new JMenu();
5328 * Left justify the whole alignment.
5331 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5333 AlignmentI al = viewport.getAlignment();
5335 viewport.firePropertyChange("alignment", null, al);
5339 * Right justify the whole alignment.
5342 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5344 AlignmentI al = viewport.getAlignment();
5346 viewport.firePropertyChange("alignment", null, al);
5349 public void setShowSeqFeatures(boolean b)
5351 showSeqFeatures.setSelected(true);
5352 viewport.setShowSequenceFeatures(true);
5359 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5360 * awt.event.ActionEvent)
5363 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5365 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5366 alignPanel.paintAlignment(true);
5373 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5377 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5379 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5380 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5388 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5389 * .event.ActionEvent)
5392 protected void showGroupConservation_actionPerformed(ActionEvent e)
5394 viewport.setShowGroupConservation(showGroupConservation.getState());
5395 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5402 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5403 * .event.ActionEvent)
5406 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5408 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5409 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5416 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5417 * .event.ActionEvent)
5420 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5422 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5423 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5427 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5429 showSequenceLogo.setState(true);
5430 viewport.setShowSequenceLogo(true);
5431 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5432 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5436 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5438 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5445 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5446 * .event.ActionEvent)
5449 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5451 if (avc.makeGroupsFromSelection()) {
5452 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5453 alignPanel.updateAnnotation();
5454 alignPanel.paintAlignment(true);
5459 protected void createGroup_actionPerformed(ActionEvent e)
5461 if (avc.createGroup())
5463 alignPanel.alignmentChanged();
5468 protected void unGroup_actionPerformed(ActionEvent e)
5472 alignPanel.alignmentChanged();
5477 * make the given alignmentPanel the currently selected tab
5479 * @param alignmentPanel
5481 public void setDisplayedView(AlignmentPanel alignmentPanel)
5483 if (!viewport.getSequenceSetId().equals(
5484 alignmentPanel.av.getSequenceSetId()))
5487 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5489 if (tabbedPane != null
5490 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5491 .getSelectedIndex())
5493 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5498 class PrintThread extends Thread
5502 public PrintThread(AlignmentPanel ap)
5507 static PageFormat pf;
5512 PrinterJob printJob = PrinterJob.getPrinterJob();
5516 printJob.setPrintable(ap, pf);
5520 printJob.setPrintable(ap);
5523 if (printJob.printDialog())
5528 } catch (Exception PrintException)
5530 PrintException.printStackTrace();