2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 import jalview.analysis.AAFrequency;
21 import jalview.analysis.AlignmentSorter;
22 import jalview.analysis.Conservation;
23 import jalview.analysis.CrossRef;
24 import jalview.analysis.NJTree;
25 import jalview.analysis.ParseProperties;
26 import jalview.analysis.SequenceIdMatcher;
27 import jalview.bin.Cache;
28 import jalview.commands.CommandI;
29 import jalview.commands.EditCommand;
30 import jalview.commands.OrderCommand;
31 import jalview.commands.RemoveGapColCommand;
32 import jalview.commands.RemoveGapsCommand;
33 import jalview.commands.SlideSequencesCommand;
34 import jalview.commands.TrimRegionCommand;
35 import jalview.datamodel.AlignedCodonFrame;
36 import jalview.datamodel.Alignment;
37 import jalview.datamodel.AlignmentAnnotation;
38 import jalview.datamodel.AlignmentI;
39 import jalview.datamodel.AlignmentOrder;
40 import jalview.datamodel.AlignmentView;
41 import jalview.datamodel.ColumnSelection;
42 import jalview.datamodel.PDBEntry;
43 import jalview.datamodel.SeqCigar;
44 import jalview.datamodel.Sequence;
45 import jalview.datamodel.SequenceGroup;
46 import jalview.datamodel.SequenceI;
47 import jalview.io.AlignmentProperties;
48 import jalview.io.AnnotationFile;
49 import jalview.io.FeaturesFile;
50 import jalview.io.FileLoader;
51 import jalview.io.FormatAdapter;
52 import jalview.io.HTMLOutput;
53 import jalview.io.IdentifyFile;
54 import jalview.io.JalviewFileChooser;
55 import jalview.io.JalviewFileView;
56 import jalview.io.JnetAnnotationMaker;
57 import jalview.io.NewickFile;
58 import jalview.io.TCoffeeScoreFile;
59 import jalview.jbgui.GAlignFrame;
60 import jalview.schemes.Blosum62ColourScheme;
61 import jalview.schemes.BuriedColourScheme;
62 import jalview.schemes.ClustalxColourScheme;
63 import jalview.schemes.ColourSchemeI;
64 import jalview.schemes.ColourSchemeProperty;
65 import jalview.schemes.HelixColourScheme;
66 import jalview.schemes.HydrophobicColourScheme;
67 import jalview.schemes.NucleotideColourScheme;
68 import jalview.schemes.PIDColourScheme;
69 import jalview.schemes.PurinePyrimidineColourScheme;
70 import jalview.schemes.RNAHelicesColourChooser;
71 import jalview.schemes.ResidueProperties;
72 import jalview.schemes.StrandColourScheme;
73 import jalview.schemes.TCoffeeColourScheme;
74 import jalview.schemes.TaylorColourScheme;
75 import jalview.schemes.TurnColourScheme;
76 import jalview.schemes.UserColourScheme;
77 import jalview.schemes.ZappoColourScheme;
78 import jalview.ws.jws1.Discoverer;
79 import jalview.ws.jws2.Jws2Discoverer;
80 import jalview.ws.seqfetcher.DbSourceProxy;
82 import java.awt.BorderLayout;
83 import java.awt.Color;
84 import java.awt.Component;
85 import java.awt.GridLayout;
86 import java.awt.Rectangle;
87 import java.awt.Toolkit;
88 import java.awt.datatransfer.Clipboard;
89 import java.awt.datatransfer.DataFlavor;
90 import java.awt.datatransfer.StringSelection;
91 import java.awt.datatransfer.Transferable;
92 import java.awt.dnd.DnDConstants;
93 import java.awt.dnd.DropTargetDragEvent;
94 import java.awt.dnd.DropTargetDropEvent;
95 import java.awt.dnd.DropTargetEvent;
96 import java.awt.dnd.DropTargetListener;
97 import java.awt.event.ActionEvent;
98 import java.awt.event.ActionListener;
99 import java.awt.event.KeyAdapter;
100 import java.awt.event.KeyEvent;
101 import java.awt.event.MouseAdapter;
102 import java.awt.event.MouseEvent;
103 import java.awt.print.PageFormat;
104 import java.awt.print.PrinterJob;
105 import java.beans.PropertyChangeEvent;
108 import java.util.ArrayList;
109 import java.util.Enumeration;
110 import java.util.Hashtable;
111 import java.util.List;
112 import java.util.Vector;
114 import javax.swing.JButton;
115 import javax.swing.JEditorPane;
116 import javax.swing.JInternalFrame;
117 import javax.swing.JLabel;
118 import javax.swing.JLayeredPane;
119 import javax.swing.JMenu;
120 import javax.swing.JMenuItem;
121 import javax.swing.JOptionPane;
122 import javax.swing.JPanel;
123 import javax.swing.JProgressBar;
124 import javax.swing.JRadioButtonMenuItem;
125 import javax.swing.JScrollPane;
126 import javax.swing.SwingUtilities;
132 * @version $Revision$
134 public class AlignFrame extends GAlignFrame implements DropTargetListener,
139 public static final int DEFAULT_WIDTH = 700;
142 public static final int DEFAULT_HEIGHT = 500;
144 public AlignmentPanel alignPanel;
146 AlignViewport viewport;
148 Vector alignPanels = new Vector();
151 * Last format used to load or save alignments in this window
153 String currentFileFormat = null;
156 * Current filename for this alignment
158 String fileName = null;
161 * Creates a new AlignFrame object with specific width and height.
167 public AlignFrame(AlignmentI al, int width, int height)
169 this(al, null, width, height);
173 * Creates a new AlignFrame object with specific width, height and
179 * @param sequenceSetId
181 public AlignFrame(AlignmentI al, int width, int height,
182 String sequenceSetId)
184 this(al, null, width, height, sequenceSetId);
188 * Creates a new AlignFrame object with specific width, height and
194 * @param sequenceSetId
197 public AlignFrame(AlignmentI al, int width, int height,
198 String sequenceSetId, String viewId)
200 this(al, null, width, height, sequenceSetId, viewId);
204 * new alignment window with hidden columns
208 * @param hiddenColumns
209 * ColumnSelection or null
211 * Width of alignment frame
215 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
216 int width, int height)
218 this(al, hiddenColumns, width, height, null);
222 * Create alignment frame for al with hiddenColumns, a specific width and
223 * height, and specific sequenceId
226 * @param hiddenColumns
229 * @param sequenceSetId
232 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
233 int width, int height, String sequenceSetId)
235 this(al, hiddenColumns, width, height, sequenceSetId, null);
239 * Create alignment frame for al with hiddenColumns, a specific width and
240 * height, and specific sequenceId
243 * @param hiddenColumns
246 * @param sequenceSetId
251 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
252 int width, int height, String sequenceSetId, String viewId)
254 setSize(width, height);
255 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
257 alignPanel = new AlignmentPanel(this, viewport);
259 if (al.getDataset() == null)
264 addAlignmentPanel(alignPanel, true);
269 * Make a new AlignFrame from exisiting alignmentPanels
276 public AlignFrame(AlignmentPanel ap)
280 addAlignmentPanel(ap, false);
285 * initalise the alignframe from the underlying viewport data and the
290 if (viewport.getAlignmentConservationAnnotation() == null)
292 BLOSUM62Colour.setEnabled(false);
293 conservationMenuItem.setEnabled(false);
294 modifyConservation.setEnabled(false);
295 // PIDColour.setEnabled(false);
296 // abovePIDThreshold.setEnabled(false);
297 // modifyPID.setEnabled(false);
300 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
303 if (sortby.equals("Id"))
305 sortIDMenuItem_actionPerformed(null);
307 else if (sortby.equals("Pairwise Identity"))
309 sortPairwiseMenuItem_actionPerformed(null);
312 if (Desktop.desktop != null)
314 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
315 addServiceListeners();
316 setGUINucleotide(viewport.getAlignment().isNucleotide());
319 setMenusFromViewport(viewport);
320 buildSortByAnnotationScoresMenu();
321 if (viewport.wrapAlignment)
323 wrapMenuItem_actionPerformed(null);
326 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
328 this.overviewMenuItem_actionPerformed(null);
336 * Change the filename and format for the alignment, and enable the 'reload'
337 * button functionality.
344 public void setFileName(String file, String format)
347 currentFileFormat = format;
348 reload.setEnabled(true);
351 void addKeyListener()
353 addKeyListener(new KeyAdapter()
356 public void keyPressed(KeyEvent evt)
358 if (viewport.cursorMode
359 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
360 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
361 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
362 && Character.isDigit(evt.getKeyChar()))
363 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
365 switch (evt.getKeyCode())
368 case 27: // escape key
369 deselectAllSequenceMenuItem_actionPerformed(null);
373 case KeyEvent.VK_DOWN:
374 if (evt.isAltDown() || !viewport.cursorMode)
375 moveSelectedSequences(false);
376 if (viewport.cursorMode)
377 alignPanel.seqPanel.moveCursor(0, 1);
381 if (evt.isAltDown() || !viewport.cursorMode)
382 moveSelectedSequences(true);
383 if (viewport.cursorMode)
384 alignPanel.seqPanel.moveCursor(0, -1);
388 case KeyEvent.VK_LEFT:
389 if (evt.isAltDown() || !viewport.cursorMode)
390 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
392 alignPanel.seqPanel.moveCursor(-1, 0);
396 case KeyEvent.VK_RIGHT:
397 if (evt.isAltDown() || !viewport.cursorMode)
398 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
400 alignPanel.seqPanel.moveCursor(1, 0);
403 case KeyEvent.VK_SPACE:
404 if (viewport.cursorMode)
406 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
407 || evt.isShiftDown() || evt.isAltDown());
411 // case KeyEvent.VK_A:
412 // if (viewport.cursorMode)
414 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
415 // //System.out.println("A");
419 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
420 * System.out.println("closing bracket"); } break;
422 case KeyEvent.VK_DELETE:
423 case KeyEvent.VK_BACK_SPACE:
424 if (!viewport.cursorMode)
426 cut_actionPerformed(null);
430 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
431 || evt.isShiftDown() || evt.isAltDown());
437 if (viewport.cursorMode)
439 alignPanel.seqPanel.setCursorRow();
443 if (viewport.cursorMode && !evt.isControlDown())
445 alignPanel.seqPanel.setCursorColumn();
449 if (viewport.cursorMode)
451 alignPanel.seqPanel.setCursorPosition();
455 case KeyEvent.VK_ENTER:
456 case KeyEvent.VK_COMMA:
457 if (viewport.cursorMode)
459 alignPanel.seqPanel.setCursorRowAndColumn();
464 if (viewport.cursorMode)
466 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
470 if (viewport.cursorMode)
472 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
477 viewport.cursorMode = !viewport.cursorMode;
478 statusBar.setText("Keyboard editing mode is "
479 + (viewport.cursorMode ? "on" : "off"));
480 if (viewport.cursorMode)
482 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
483 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
485 alignPanel.seqPanel.seqCanvas.repaint();
491 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
492 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
494 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
496 javax.help.HelpBroker hb = hs.createHelpBroker();
497 hb.setCurrentID("home");
498 hb.setDisplayed(true);
499 } catch (Exception ex)
501 ex.printStackTrace();
506 boolean toggleSeqs = !evt.isControlDown();
507 boolean toggleCols = !evt.isShiftDown();
508 toggleHiddenRegions(toggleSeqs, toggleCols);
511 case KeyEvent.VK_PAGE_UP:
512 if (viewport.wrapAlignment)
514 alignPanel.scrollUp(true);
518 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
519 - viewport.endSeq + viewport.startSeq);
522 case KeyEvent.VK_PAGE_DOWN:
523 if (viewport.wrapAlignment)
525 alignPanel.scrollUp(false);
529 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
530 + viewport.endSeq - viewport.startSeq);
537 public void keyReleased(KeyEvent evt)
539 switch (evt.getKeyCode())
541 case KeyEvent.VK_LEFT:
542 if (evt.isAltDown() || !viewport.cursorMode)
543 viewport.firePropertyChange("alignment", null, viewport
544 .getAlignment().getSequences());
547 case KeyEvent.VK_RIGHT:
548 if (evt.isAltDown() || !viewport.cursorMode)
549 viewport.firePropertyChange("alignment", null, viewport
550 .getAlignment().getSequences());
557 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
559 ap.alignFrame = this;
561 alignPanels.addElement(ap);
563 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
565 int aSize = alignPanels.size();
567 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
569 if (aSize == 1 && ap.av.viewName == null)
571 this.getContentPane().add(ap, BorderLayout.CENTER);
577 setInitialTabVisible();
580 expandViews.setEnabled(true);
581 gatherViews.setEnabled(true);
582 tabbedPane.addTab(ap.av.viewName, ap);
584 ap.setVisible(false);
589 if (ap.av.isPadGaps())
591 ap.av.getAlignment().padGaps();
593 ap.av.updateConservation(ap);
594 ap.av.updateConsensus(ap);
595 ap.av.updateStrucConsensus(ap);
599 public void setInitialTabVisible()
601 expandViews.setEnabled(true);
602 gatherViews.setEnabled(true);
603 tabbedPane.setVisible(true);
604 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
605 tabbedPane.addTab(first.av.viewName, first);
606 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
609 public AlignViewport getViewport()
614 /* Set up intrinsic listeners for dynamically generated GUI bits. */
615 private void addServiceListeners()
617 final java.beans.PropertyChangeListener thisListener;
618 Desktop.instance.addJalviewPropertyChangeListener("services",
619 thisListener = new java.beans.PropertyChangeListener()
622 public void propertyChange(PropertyChangeEvent evt)
624 // // System.out.println("Discoverer property change.");
625 // if (evt.getPropertyName().equals("services"))
627 SwingUtilities.invokeLater(new Runnable()
634 .println("Rebuild WS Menu for service change");
635 BuildWebServiceMenu();
642 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
645 public void internalFrameClosed(
646 javax.swing.event.InternalFrameEvent evt)
648 System.out.println("deregistering discoverer listener");
649 Desktop.instance.removeJalviewPropertyChangeListener("services",
651 closeMenuItem_actionPerformed(true);
654 // Finally, build the menu once to get current service state
655 new Thread(new Runnable()
660 BuildWebServiceMenu();
665 public void setGUINucleotide(boolean nucleotide)
667 showTranslation.setVisible(nucleotide);
668 conservationMenuItem.setEnabled(!nucleotide);
669 modifyConservation.setEnabled(!nucleotide);
670 showGroupConservation.setEnabled(!nucleotide);
671 rnahelicesColour.setEnabled(nucleotide);
672 purinePyrimidineColour.setEnabled(nucleotide);
673 // Remember AlignFrame always starts as protein
677 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
682 * set up menus for the currently viewport. This may be called after any
683 * operation that affects the data in the current view (selection changed,
684 * etc) to update the menus to reflect the new state.
686 public void setMenusForViewport()
688 setMenusFromViewport(viewport);
692 * Need to call this method when tabs are selected for multiple views, or when
693 * loading from Jalview2XML.java
698 void setMenusFromViewport(AlignViewport av)
700 padGapsMenuitem.setSelected(av.isPadGaps());
701 colourTextMenuItem.setSelected(av.showColourText);
702 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
703 conservationMenuItem.setSelected(av.getConservationSelected());
704 seqLimits.setSelected(av.getShowJVSuffix());
705 idRightAlign.setSelected(av.rightAlignIds);
706 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
707 renderGapsMenuItem.setSelected(av.renderGaps);
708 wrapMenuItem.setSelected(av.wrapAlignment);
709 scaleAbove.setVisible(av.wrapAlignment);
710 scaleLeft.setVisible(av.wrapAlignment);
711 scaleRight.setVisible(av.wrapAlignment);
712 annotationPanelMenuItem.setState(av.showAnnotation);
713 viewBoxesMenuItem.setSelected(av.showBoxes);
714 viewTextMenuItem.setSelected(av.showText);
715 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
716 showGroupConsensus.setSelected(av.isShowGroupConsensus());
717 showGroupConservation.setSelected(av.isShowGroupConservation());
718 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
719 showSequenceLogo.setSelected(av.isShowSequenceLogo());
720 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
722 setColourSelected(ColourSchemeProperty.getColourName(av
723 .getGlobalColourScheme()));
725 showSeqFeatures.setSelected(av.showSequenceFeatures);
726 hiddenMarkers.setState(av.showHiddenMarkers);
727 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
728 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
729 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
730 autoCalculate.setSelected(av.autoCalculateConsensus);
731 sortByTree.setSelected(av.sortByTree);
732 listenToViewSelections.setSelected(av.followSelection);
733 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
735 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
736 setShowProductsEnabled();
740 // methods for implementing IProgressIndicator
741 // need to refactor to a reusable stub class
742 Hashtable progressBars, progressBarHandlers;
747 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
750 public void setProgressBar(String message, long id)
752 if (progressBars == null)
754 progressBars = new Hashtable();
755 progressBarHandlers = new Hashtable();
758 JPanel progressPanel;
759 Long lId = new Long(id);
760 GridLayout layout = (GridLayout) statusPanel.getLayout();
761 if (progressBars.get(lId) != null)
763 progressPanel = (JPanel) progressBars.get(new Long(id));
764 statusPanel.remove(progressPanel);
765 progressBars.remove(lId);
766 progressPanel = null;
769 statusBar.setText(message);
771 if (progressBarHandlers.contains(lId))
773 progressBarHandlers.remove(lId);
775 layout.setRows(layout.getRows() - 1);
779 progressPanel = new JPanel(new BorderLayout(10, 5));
781 JProgressBar progressBar = new JProgressBar();
782 progressBar.setIndeterminate(true);
784 progressPanel.add(new JLabel(message), BorderLayout.WEST);
785 progressPanel.add(progressBar, BorderLayout.CENTER);
787 layout.setRows(layout.getRows() + 1);
788 statusPanel.add(progressPanel);
790 progressBars.put(lId, progressPanel);
793 // setMenusForViewport();
798 public void registerHandler(final long id,
799 final IProgressIndicatorHandler handler)
801 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
804 "call setProgressBar before registering the progress bar's handler.");
806 progressBarHandlers.put(new Long(id), handler);
807 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
808 if (handler.canCancel())
810 JButton cancel = new JButton("Cancel");
811 final IProgressIndicator us = this;
812 cancel.addActionListener(new ActionListener()
816 public void actionPerformed(ActionEvent e)
818 handler.cancelActivity(id);
821 + ((JLabel) progressPanel.getComponent(0))
825 progressPanel.add(cancel, BorderLayout.EAST);
831 * @return true if any progress bars are still active
834 public boolean operationInProgress()
836 if (progressBars != null && progressBars.size() > 0)
844 * Added so Castor Mapping file can obtain Jalview Version
846 public String getVersion()
848 return jalview.bin.Cache.getProperty("VERSION");
851 public FeatureRenderer getFeatureRenderer()
853 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
857 public void fetchSequence_actionPerformed(ActionEvent e)
859 new SequenceFetcher(this);
863 public void addFromFile_actionPerformed(ActionEvent e)
865 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
869 public void reload_actionPerformed(ActionEvent e)
871 if (fileName != null)
873 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
874 // originating file's format
875 // TODO: work out how to recover feature settings for correct view(s) when
877 if (currentFileFormat.equals("Jalview"))
879 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
880 for (int i = 0; i < frames.length; i++)
882 if (frames[i] instanceof AlignFrame && frames[i] != this
883 && ((AlignFrame) frames[i]).fileName!=null && ((AlignFrame) frames[i]).fileName.equals(fileName))
887 frames[i].setSelected(true);
888 Desktop.instance.closeAssociatedWindows();
889 } catch (java.beans.PropertyVetoException ex)
895 Desktop.instance.closeAssociatedWindows();
897 FileLoader loader = new FileLoader();
898 String protocol = fileName.startsWith("http:") ? "URL" : "File";
899 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
903 Rectangle bounds = this.getBounds();
905 FileLoader loader = new FileLoader();
906 String protocol = fileName.startsWith("http:") ? "URL" : "File";
907 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
908 protocol, currentFileFormat);
910 newframe.setBounds(bounds);
911 if (featureSettings != null && featureSettings.isShowing())
913 final Rectangle fspos = featureSettings.frame.getBounds();
914 // TODO: need a 'show feature settings' function that takes bounds -
915 // need to refactor Desktop.addFrame
916 newframe.featureSettings_actionPerformed(null);
917 final FeatureSettings nfs = newframe.featureSettings;
918 SwingUtilities.invokeLater(new Runnable()
923 nfs.frame.setBounds(fspos);
926 this.featureSettings.close();
927 this.featureSettings = null;
929 this.closeMenuItem_actionPerformed(true);
935 public void addFromText_actionPerformed(ActionEvent e)
937 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
941 public void addFromURL_actionPerformed(ActionEvent e)
943 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
947 public void save_actionPerformed(ActionEvent e)
950 || (currentFileFormat == null || !jalview.io.FormatAdapter
951 .isValidIOFormat(currentFileFormat, true))
952 || fileName.startsWith("http"))
954 saveAs_actionPerformed(null);
958 saveAlignment(fileName, currentFileFormat);
969 public void saveAs_actionPerformed(ActionEvent e)
971 JalviewFileChooser chooser = new JalviewFileChooser(
972 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
973 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
974 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
975 currentFileFormat, false);
977 chooser.setFileView(new JalviewFileView());
978 chooser.setDialogTitle("Save Alignment to file");
979 chooser.setToolTipText("Save");
981 int value = chooser.showSaveDialog(this);
983 if (value == JalviewFileChooser.APPROVE_OPTION)
985 currentFileFormat = chooser.getSelectedFormat();
986 if (currentFileFormat == null)
988 JOptionPane.showInternalMessageDialog(Desktop.desktop,
989 "You must select a file format before saving!",
990 "File format not specified", JOptionPane.WARNING_MESSAGE);
991 value = chooser.showSaveDialog(this);
995 fileName = chooser.getSelectedFile().getPath();
997 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1000 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1001 if (currentFileFormat.indexOf(" ") > -1)
1003 currentFileFormat = currentFileFormat.substring(0,
1004 currentFileFormat.indexOf(" "));
1006 saveAlignment(fileName, currentFileFormat);
1010 public boolean saveAlignment(String file, String format)
1012 boolean success = true;
1014 if (format.equalsIgnoreCase("Jalview"))
1016 String shortName = title;
1018 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1020 shortName = shortName.substring(shortName
1021 .lastIndexOf(java.io.File.separatorChar) + 1);
1024 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1026 statusBar.setText("Successfully saved to file: " + fileName + " in "
1027 + format + " format.");
1032 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1034 warningMessage("Cannot save file " + fileName + " using format "
1035 + format, "Alignment output format not supported");
1036 saveAs_actionPerformed(null);
1037 // JBPNote need to have a raise_gui flag here
1041 String[] omitHidden = null;
1043 if (viewport.hasHiddenColumns())
1045 int reply = JOptionPane
1046 .showInternalConfirmDialog(
1048 "The Alignment contains hidden columns."
1049 + "\nDo you want to save only the visible alignment?",
1050 "Save / Omit Hidden Columns",
1051 JOptionPane.YES_NO_OPTION,
1052 JOptionPane.QUESTION_MESSAGE);
1054 if (reply == JOptionPane.YES_OPTION)
1056 omitHidden = viewport.getViewAsString(false);
1059 FormatAdapter f = new FormatAdapter();
1060 String output = f.formatSequences(
1062 viewport.getAlignment(), // class cast exceptions will
1063 // occur in the distant future
1064 omitHidden, f.getCacheSuffixDefault(format),
1065 viewport.getColumnSelection());
1075 java.io.PrintWriter out = new java.io.PrintWriter(
1076 new java.io.FileWriter(file));
1080 this.setTitle(file);
1081 statusBar.setText("Successfully saved to file: " + fileName
1082 + " in " + format + " format.");
1083 } catch (Exception ex)
1086 ex.printStackTrace();
1093 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
1094 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
1100 private void warningMessage(String warning, String title)
1102 if (new jalview.util.Platform().isHeadless())
1104 System.err.println("Warning: " + title + "\nWarning: " + warning);
1109 JOptionPane.showInternalMessageDialog(this, warning, title,
1110 JOptionPane.WARNING_MESSAGE);
1122 protected void outputText_actionPerformed(ActionEvent e)
1124 String[] omitHidden = null;
1126 if (viewport.hasHiddenColumns())
1128 int reply = JOptionPane
1129 .showInternalConfirmDialog(
1131 "The Alignment contains hidden columns."
1132 + "\nDo you want to output only the visible alignment?",
1133 "Save / Omit Hidden Columns",
1134 JOptionPane.YES_NO_OPTION,
1135 JOptionPane.QUESTION_MESSAGE);
1137 if (reply == JOptionPane.YES_OPTION)
1139 omitHidden = viewport.getViewAsString(false);
1143 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1144 cap.setForInput(null);
1148 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1149 viewport.getAlignment(), omitHidden,
1150 viewport.getColumnSelection()));
1151 Desktop.addInternalFrame(cap,
1152 "Alignment output - " + e.getActionCommand(), 600, 500);
1153 } catch (OutOfMemoryError oom)
1155 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1168 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1170 new HTMLOutput(alignPanel,
1171 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1172 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1175 public void createImageMap(File file, String image)
1177 alignPanel.makePNGImageMap(file, image);
1187 public void createPNG(File f)
1189 alignPanel.makePNG(f);
1199 public void createEPS(File f)
1201 alignPanel.makeEPS(f);
1205 public void pageSetup_actionPerformed(ActionEvent e)
1207 PrinterJob printJob = PrinterJob.getPrinterJob();
1208 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1218 public void printMenuItem_actionPerformed(ActionEvent e)
1220 // Putting in a thread avoids Swing painting problems
1221 PrintThread thread = new PrintThread(alignPanel);
1226 public void exportFeatures_actionPerformed(ActionEvent e)
1228 new AnnotationExporter().exportFeatures(alignPanel);
1232 public void exportAnnotations_actionPerformed(ActionEvent e)
1234 new AnnotationExporter().exportAnnotations(alignPanel,
1235 viewport.showAnnotation ? viewport.getAlignment()
1236 .getAlignmentAnnotation() : null, viewport
1237 .getAlignment().getGroups(), ((Alignment) viewport
1238 .getAlignment()).alignmentProperties);
1242 public void associatedData_actionPerformed(ActionEvent e)
1244 // Pick the tree file
1245 JalviewFileChooser chooser = new JalviewFileChooser(
1246 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1247 chooser.setFileView(new JalviewFileView());
1248 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1249 chooser.setToolTipText("Load Jalview Annotations / Features file");
1251 int value = chooser.showOpenDialog(null);
1253 if (value == JalviewFileChooser.APPROVE_OPTION)
1255 String choice = chooser.getSelectedFile().getPath();
1256 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1257 loadJalviewDataFile(choice, null, null, null);
1263 * Close the current view or all views in the alignment frame. If the frame
1264 * only contains one view then the alignment will be removed from memory.
1266 * @param closeAllTabs
1269 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1271 if (alignPanels != null && alignPanels.size() < 2)
1273 closeAllTabs = true;
1278 if (alignPanels != null)
1282 if (this.isClosed())
1284 // really close all the windows - otherwise wait till
1285 // setClosed(true) is called
1286 for (int i = 0; i < alignPanels.size(); i++)
1288 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1295 closeView(alignPanel);
1301 this.setClosed(true);
1303 } catch (Exception ex)
1305 ex.printStackTrace();
1310 * close alignPanel2 and shuffle tabs appropriately.
1312 * @param alignPanel2
1314 public void closeView(AlignmentPanel alignPanel2)
1316 int index = tabbedPane.getSelectedIndex();
1317 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1318 alignPanels.removeElement(alignPanel2);
1320 // if (viewport == alignPanel2.av)
1324 alignPanel2.closePanel();
1327 tabbedPane.removeTabAt(closedindex);
1328 tabbedPane.validate();
1330 if (index > closedindex || index == tabbedPane.getTabCount())
1332 // modify currently selected tab index if necessary.
1336 this.tabSelectionChanged(index);
1342 void updateEditMenuBar()
1345 if (viewport.historyList.size() > 0)
1347 undoMenuItem.setEnabled(true);
1348 CommandI command = (CommandI) viewport.historyList.peek();
1349 undoMenuItem.setText("Undo " + command.getDescription());
1353 undoMenuItem.setEnabled(false);
1354 undoMenuItem.setText("Undo");
1357 if (viewport.redoList.size() > 0)
1359 redoMenuItem.setEnabled(true);
1361 CommandI command = (CommandI) viewport.redoList.peek();
1362 redoMenuItem.setText("Redo " + command.getDescription());
1366 redoMenuItem.setEnabled(false);
1367 redoMenuItem.setText("Redo");
1371 public void addHistoryItem(CommandI command)
1373 if (command.getSize() > 0)
1375 viewport.historyList.push(command);
1376 viewport.redoList.clear();
1377 updateEditMenuBar();
1378 viewport.updateHiddenColumns();
1379 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1380 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1381 // viewport.getColumnSelection()
1382 // .getHiddenColumns().size() > 0);
1388 * @return alignment objects for all views
1390 AlignmentI[] getViewAlignments()
1392 if (alignPanels != null)
1394 Enumeration e = alignPanels.elements();
1395 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1396 for (int i = 0; e.hasMoreElements(); i++)
1398 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1402 if (viewport != null)
1404 return new AlignmentI[]
1405 { viewport.getAlignment() };
1417 protected void undoMenuItem_actionPerformed(ActionEvent e)
1419 if (viewport.historyList.empty())
1421 CommandI command = (CommandI) viewport.historyList.pop();
1422 viewport.redoList.push(command);
1423 command.undoCommand(getViewAlignments());
1425 AlignViewport originalSource = getOriginatingSource(command);
1426 updateEditMenuBar();
1428 if (originalSource != null)
1430 if (originalSource != viewport)
1433 .warn("Implementation worry: mismatch of viewport origin for undo");
1435 originalSource.updateHiddenColumns();
1436 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1438 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1439 // viewport.getColumnSelection()
1440 // .getHiddenColumns().size() > 0);
1441 originalSource.firePropertyChange("alignment", null, originalSource
1442 .getAlignment().getSequences());
1453 protected void redoMenuItem_actionPerformed(ActionEvent e)
1455 if (viewport.redoList.size() < 1)
1460 CommandI command = (CommandI) viewport.redoList.pop();
1461 viewport.historyList.push(command);
1462 command.doCommand(getViewAlignments());
1464 AlignViewport originalSource = getOriginatingSource(command);
1465 updateEditMenuBar();
1467 if (originalSource != null)
1470 if (originalSource != viewport)
1473 .warn("Implementation worry: mismatch of viewport origin for redo");
1475 originalSource.updateHiddenColumns();
1476 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1478 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1479 // viewport.getColumnSelection()
1480 // .getHiddenColumns().size() > 0);
1481 originalSource.firePropertyChange("alignment", null, originalSource
1482 .getAlignment().getSequences());
1486 AlignViewport getOriginatingSource(CommandI command)
1488 AlignViewport originalSource = null;
1489 // For sequence removal and addition, we need to fire
1490 // the property change event FROM the viewport where the
1491 // original alignment was altered
1492 AlignmentI al = null;
1493 if (command instanceof EditCommand)
1495 EditCommand editCommand = (EditCommand) command;
1496 al = editCommand.getAlignment();
1497 Vector comps = (Vector) PaintRefresher.components.get(viewport
1498 .getSequenceSetId());
1500 for (int i = 0; i < comps.size(); i++)
1502 if (comps.elementAt(i) instanceof AlignmentPanel)
1504 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1506 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1513 if (originalSource == null)
1515 // The original view is closed, we must validate
1516 // the current view against the closed view first
1519 PaintRefresher.validateSequences(al, viewport.getAlignment());
1522 originalSource = viewport;
1525 return originalSource;
1534 public void moveSelectedSequences(boolean up)
1536 SequenceGroup sg = viewport.getSelectionGroup();
1542 viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up);
1543 alignPanel.paintAlignment(true);
1546 synchronized void slideSequences(boolean right, int size)
1548 List<SequenceI> sg = new Vector();
1549 if (viewport.cursorMode)
1551 sg.add(viewport.getAlignment().getSequenceAt(
1552 alignPanel.seqPanel.seqCanvas.cursorY));
1554 else if (viewport.getSelectionGroup() != null
1555 && viewport.getSelectionGroup().getSize() != viewport
1556 .getAlignment().getHeight())
1558 sg = viewport.getSelectionGroup().getSequences(
1559 viewport.getHiddenRepSequences());
1567 Vector invertGroup = new Vector();
1569 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1571 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1572 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1575 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1577 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1578 for (int i = 0; i < invertGroup.size(); i++)
1579 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1581 SlideSequencesCommand ssc;
1583 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1584 size, viewport.getGapCharacter());
1586 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1587 size, viewport.getGapCharacter());
1589 int groupAdjustment = 0;
1590 if (ssc.getGapsInsertedBegin() && right)
1592 if (viewport.cursorMode)
1593 alignPanel.seqPanel.moveCursor(size, 0);
1595 groupAdjustment = size;
1597 else if (!ssc.getGapsInsertedBegin() && !right)
1599 if (viewport.cursorMode)
1600 alignPanel.seqPanel.moveCursor(-size, 0);
1602 groupAdjustment = -size;
1605 if (groupAdjustment != 0)
1607 viewport.getSelectionGroup().setStartRes(
1608 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1609 viewport.getSelectionGroup().setEndRes(
1610 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1613 boolean appendHistoryItem = false;
1614 if (viewport.historyList != null && viewport.historyList.size() > 0
1615 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1617 appendHistoryItem = ssc
1618 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1622 if (!appendHistoryItem)
1623 addHistoryItem(ssc);
1635 protected void copy_actionPerformed(ActionEvent e)
1638 if (viewport.getSelectionGroup() == null)
1642 // TODO: preserve the ordering of displayed alignment annotation in any
1643 // internal paste (particularly sequence associated annotation)
1644 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1645 String[] omitHidden = null;
1647 if (viewport.hasHiddenColumns())
1649 omitHidden = viewport.getViewAsString(true);
1652 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1655 StringSelection ss = new StringSelection(output);
1659 jalview.gui.Desktop.internalCopy = true;
1660 // Its really worth setting the clipboard contents
1661 // to empty before setting the large StringSelection!!
1662 Toolkit.getDefaultToolkit().getSystemClipboard()
1663 .setContents(new StringSelection(""), null);
1665 Toolkit.getDefaultToolkit().getSystemClipboard()
1666 .setContents(ss, Desktop.instance);
1667 } catch (OutOfMemoryError er)
1669 new OOMWarning("copying region", er);
1673 Vector hiddenColumns = null;
1674 if (viewport.hasHiddenColumns())
1676 hiddenColumns = new Vector();
1677 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1678 .getSelectionGroup().getEndRes();
1679 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1682 int[] region = (int[]) viewport.getColumnSelection()
1683 .getHiddenColumns().elementAt(i);
1684 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1686 hiddenColumns.addElement(new int[]
1687 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1692 Desktop.jalviewClipboard = new Object[]
1693 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1694 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1704 protected void pasteNew_actionPerformed(ActionEvent e)
1716 protected void pasteThis_actionPerformed(ActionEvent e)
1722 * Paste contents of Jalview clipboard
1724 * @param newAlignment
1725 * true to paste to a new alignment, otherwise add to this.
1727 void paste(boolean newAlignment)
1729 boolean externalPaste = true;
1732 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1733 Transferable contents = c.getContents(this);
1735 if (contents == null)
1743 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1744 if (str.length() < 1)
1749 format = new IdentifyFile().Identify(str, "Paste");
1751 } catch (OutOfMemoryError er)
1753 new OOMWarning("Out of memory pasting sequences!!", er);
1757 SequenceI[] sequences;
1758 boolean annotationAdded = false;
1759 AlignmentI alignment = null;
1761 if (Desktop.jalviewClipboard != null)
1763 // The clipboard was filled from within Jalview, we must use the
1765 // And dataset from the copied alignment
1766 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1767 // be doubly sure that we create *new* sequence objects.
1768 sequences = new SequenceI[newseq.length];
1769 for (int i = 0; i < newseq.length; i++)
1771 sequences[i] = new Sequence(newseq[i]);
1773 alignment = new Alignment(sequences);
1774 externalPaste = false;
1778 // parse the clipboard as an alignment.
1779 alignment = new FormatAdapter().readFile(str, "Paste", format);
1780 sequences = alignment.getSequencesArray();
1784 ArrayList<Integer> newGraphGroups=new ArrayList<Integer>();
1790 if (Desktop.jalviewClipboard != null)
1792 // dataset is inherited
1793 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1797 // new dataset is constructed
1798 alignment.setDataset(null);
1800 alwidth = alignment.getWidth() + 1;
1804 AlignmentI pastedal = alignment; // preserve pasted alignment object
1805 // Add pasted sequences and dataset into existing alignment.
1806 alignment = viewport.getAlignment();
1807 alwidth = alignment.getWidth() + 1;
1808 // decide if we need to import sequences from an existing dataset
1809 boolean importDs = Desktop.jalviewClipboard != null
1810 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1811 // importDs==true instructs us to copy over new dataset sequences from
1812 // an existing alignment
1813 Vector newDs = (importDs) ? new Vector() : null; // used to create
1814 // minimum dataset set
1816 for (int i = 0; i < sequences.length; i++)
1820 newDs.addElement(null);
1822 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1824 if (importDs && ds != null)
1826 if (!newDs.contains(ds))
1828 newDs.setElementAt(ds, i);
1829 ds = new Sequence(ds);
1830 // update with new dataset sequence
1831 sequences[i].setDatasetSequence(ds);
1835 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1840 // copy and derive new dataset sequence
1841 sequences[i] = sequences[i].deriveSequence();
1842 alignment.getDataset().addSequence(
1843 sequences[i].getDatasetSequence());
1844 // TODO: avoid creation of duplicate dataset sequences with a
1845 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1847 alignment.addSequence(sequences[i]); // merges dataset
1851 newDs.clear(); // tidy up
1853 if (alignment.getAlignmentAnnotation()!=null)
1855 for (AlignmentAnnotation alan:alignment.getAlignmentAnnotation())
1857 if (alan.graphGroup>fgroup)
1859 fgroup=alan.graphGroup;
1863 if (pastedal.getAlignmentAnnotation() != null)
1865 // Add any annotation attached to alignment.
1866 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1867 for (int i = 0; i < alann.length; i++)
1869 annotationAdded = true;
1870 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1872 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1873 if (newann.graphGroup>-1)
1875 if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
1877 for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
1879 newGraphGroups.add(q, null);
1881 newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
1883 newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
1886 newann.padAnnotation(alwidth);
1887 alignment.addAnnotation(newann);
1897 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1898 sequences, 0, alignment.getWidth(), alignment));
1900 // Add any annotations attached to sequences
1901 for (int i = 0; i < sequences.length; i++)
1903 if (sequences[i].getAnnotation() != null)
1905 AlignmentAnnotation newann;
1906 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1908 annotationAdded = true;
1909 newann=sequences[i].getAnnotation()[a];
1910 newann.adjustForAlignment();
1911 newann.padAnnotation(alwidth);
1912 if (newann.graphGroup>-1)
1914 if (newann.graphGroup>-1)
1916 if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
1918 for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
1920 newGraphGroups.add(q, null);
1922 newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
1924 newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
1927 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1932 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1939 // propagate alignment changed.
1940 viewport.setEndSeq(alignment.getHeight());
1941 if (annotationAdded)
1943 // Duplicate sequence annotation in all views.
1944 AlignmentI[] alview = this.getViewAlignments();
1945 for (int i = 0; i < sequences.length; i++)
1947 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1950 for (int avnum = 0; avnum < alview.length; avnum++)
1952 if (alview[avnum] != alignment)
1954 // duplicate in a view other than the one with input focus
1955 int avwidth = alview[avnum].getWidth() + 1;
1956 // this relies on sann being preserved after we
1957 // modify the sequence's annotation array for each duplication
1958 for (int a = 0; a < sann.length; a++)
1960 AlignmentAnnotation newann = new AlignmentAnnotation(
1962 sequences[i].addAlignmentAnnotation(newann);
1963 newann.padAnnotation(avwidth);
1964 alview[avnum].addAnnotation(newann); // annotation was
1965 // duplicated earlier
1966 // TODO JAL-1145 graphGroups are not updated for sequence annotation added to several views. This may cause strangeness
1967 alview[avnum].setAnnotationIndex(newann, a);
1972 buildSortByAnnotationScoresMenu();
1974 viewport.firePropertyChange("alignment", null,
1975 alignment.getSequences());
1976 if (alignPanels!=null ) {for (AlignmentPanel ap:((Vector<AlignmentPanel>)alignPanels))
1978 ap.validateAnnotationDimensions(false);
1979 }} else { alignPanel.validateAnnotationDimensions(false);}
1984 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1986 String newtitle = new String("Copied sequences");
1988 if (Desktop.jalviewClipboard != null
1989 && Desktop.jalviewClipboard[2] != null)
1991 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1992 for (int i = 0; i < hc.size(); i++)
1994 int[] region = (int[]) hc.elementAt(i);
1995 af.viewport.hideColumns(region[0], region[1]);
1999 // >>>This is a fix for the moment, until a better solution is
2001 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2003 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2005 // TODO: maintain provenance of an alignment, rather than just make the
2006 // title a concatenation of operations.
2009 if (title.startsWith("Copied sequences"))
2015 newtitle = newtitle.concat("- from " + title);
2020 newtitle = new String("Pasted sequences");
2023 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2028 } catch (Exception ex)
2030 ex.printStackTrace();
2031 System.out.println("Exception whilst pasting: " + ex);
2032 // could be anything being pasted in here
2044 protected void cut_actionPerformed(ActionEvent e)
2046 copy_actionPerformed(null);
2047 delete_actionPerformed(null);
2057 protected void delete_actionPerformed(ActionEvent evt)
2060 SequenceGroup sg = viewport.getSelectionGroup();
2066 Vector seqs = new Vector();
2068 for (int i = 0; i < sg.getSize(); i++)
2070 seq = sg.getSequenceAt(i);
2071 seqs.addElement(seq);
2074 // If the cut affects all sequences, remove highlighted columns
2075 if (sg.getSize() == viewport.getAlignment().getHeight())
2077 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2078 sg.getEndRes() + 1);
2081 SequenceI[] cut = new SequenceI[seqs.size()];
2082 for (int i = 0; i < seqs.size(); i++)
2084 cut[i] = (SequenceI) seqs.elementAt(i);
2088 * //ADD HISTORY ITEM
2090 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2091 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2092 viewport.getAlignment()));
2094 viewport.setSelectionGroup(null);
2095 viewport.sendSelection();
2096 viewport.getAlignment().deleteGroup(sg);
2098 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2100 if (viewport.getAlignment().getHeight() < 1)
2104 this.setClosed(true);
2105 } catch (Exception ex)
2118 protected void deleteGroups_actionPerformed(ActionEvent e)
2120 viewport.getAlignment().deleteAllGroups();
2121 viewport.sequenceColours = null;
2122 viewport.setSelectionGroup(null);
2123 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2124 alignPanel.updateAnnotation();
2125 alignPanel.paintAlignment(true);
2135 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2137 SequenceGroup sg = new SequenceGroup();
2139 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2141 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2144 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2145 viewport.setSelectionGroup(sg);
2146 viewport.sendSelection();
2147 alignPanel.paintAlignment(true);
2148 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2158 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2160 if (viewport.cursorMode)
2162 alignPanel.seqPanel.keyboardNo1 = null;
2163 alignPanel.seqPanel.keyboardNo2 = null;
2165 viewport.setSelectionGroup(null);
2166 viewport.getColumnSelection().clear();
2167 viewport.setSelectionGroup(null);
2168 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2169 alignPanel.idPanel.idCanvas.searchResults = null;
2170 alignPanel.paintAlignment(true);
2171 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2172 viewport.sendSelection();
2182 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2184 SequenceGroup sg = viewport.getSelectionGroup();
2188 selectAllSequenceMenuItem_actionPerformed(null);
2193 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2195 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2198 alignPanel.paintAlignment(true);
2199 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2200 viewport.sendSelection();
2204 public void invertColSel_actionPerformed(ActionEvent e)
2206 viewport.invertColumnSelection();
2207 alignPanel.paintAlignment(true);
2208 viewport.sendSelection();
2218 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2220 trimAlignment(true);
2230 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2232 trimAlignment(false);
2235 void trimAlignment(boolean trimLeft)
2237 ColumnSelection colSel = viewport.getColumnSelection();
2240 if (colSel.size() > 0)
2244 column = colSel.getMin();
2248 column = colSel.getMax();
2252 if (viewport.getSelectionGroup() != null)
2254 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2255 viewport.getHiddenRepSequences());
2259 seqs = viewport.getAlignment().getSequencesArray();
2262 TrimRegionCommand trimRegion;
2265 trimRegion = new TrimRegionCommand("Remove Left",
2266 TrimRegionCommand.TRIM_LEFT, seqs, column,
2267 viewport.getAlignment(), viewport.getColumnSelection(),
2268 viewport.getSelectionGroup());
2269 viewport.setStartRes(0);
2273 trimRegion = new TrimRegionCommand("Remove Right",
2274 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2275 viewport.getAlignment(), viewport.getColumnSelection(),
2276 viewport.getSelectionGroup());
2279 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2281 addHistoryItem(trimRegion);
2283 for (SequenceGroup sg :viewport.getAlignment().getGroups())
2285 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2286 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2288 viewport.getAlignment().deleteGroup(sg);
2292 viewport.firePropertyChange("alignment", null, viewport
2293 .getAlignment().getSequences());
2304 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2306 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2309 if (viewport.getSelectionGroup() != null)
2311 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2312 viewport.getHiddenRepSequences());
2313 start = viewport.getSelectionGroup().getStartRes();
2314 end = viewport.getSelectionGroup().getEndRes();
2318 seqs = viewport.getAlignment().getSequencesArray();
2321 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2322 "Remove Gapped Columns", seqs, start, end,
2323 viewport.getAlignment());
2325 addHistoryItem(removeGapCols);
2327 statusBar.setText("Removed " + removeGapCols.getSize()
2328 + " empty columns.");
2330 // This is to maintain viewport position on first residue
2331 // of first sequence
2332 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2333 int startRes = seq.findPosition(viewport.startRes);
2334 // ShiftList shifts;
2335 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2336 // edit.alColumnChanges=shifts.getInverse();
2337 // if (viewport.hasHiddenColumns)
2338 // viewport.getColumnSelection().compensateForEdits(shifts);
2339 viewport.setStartRes(seq.findIndex(startRes) - 1);
2340 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2352 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2354 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2357 if (viewport.getSelectionGroup() != null)
2359 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2360 viewport.getHiddenRepSequences());
2361 start = viewport.getSelectionGroup().getStartRes();
2362 end = viewport.getSelectionGroup().getEndRes();
2366 seqs = viewport.getAlignment().getSequencesArray();
2369 // This is to maintain viewport position on first residue
2370 // of first sequence
2371 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2372 int startRes = seq.findPosition(viewport.startRes);
2374 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2375 viewport.getAlignment()));
2377 viewport.setStartRes(seq.findIndex(startRes) - 1);
2379 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2391 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2393 viewport.setPadGaps(padGapsMenuitem.isSelected());
2394 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2400 // if (justifySeqs>0)
2402 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2415 public void findMenuItem_actionPerformed(ActionEvent e)
2421 public void newView_actionPerformed(ActionEvent e)
2428 * @param copyAnnotation
2429 * if true then duplicate all annnotation, groups and settings
2430 * @return new alignment panel, already displayed.
2432 public AlignmentPanel newView(boolean copyAnnotation)
2434 return newView(null, copyAnnotation);
2440 * title of newly created view
2441 * @return new alignment panel, already displayed.
2443 public AlignmentPanel newView(String viewTitle)
2445 return newView(viewTitle, true);
2451 * title of newly created view
2452 * @param copyAnnotation
2453 * if true then duplicate all annnotation, groups and settings
2454 * @return new alignment panel, already displayed.
2456 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2458 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2460 if (!copyAnnotation)
2462 // just remove all the current annotation except for the automatic stuff
2463 newap.av.getAlignment().deleteAllGroups();
2464 for (AlignmentAnnotation alan : newap.av.getAlignment()
2465 .getAlignmentAnnotation())
2467 if (!alan.autoCalculated)
2469 newap.av.getAlignment().deleteAnnotation(alan);
2475 newap.av.gatherViewsHere = false;
2477 if (viewport.viewName == null)
2479 viewport.viewName = "Original";
2482 newap.av.historyList = viewport.historyList;
2483 newap.av.redoList = viewport.redoList;
2485 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2486 // make sure the new view has a unique name - this is essential for Jalview
2488 boolean addFirstIndex = false;
2489 if (viewTitle == null || viewTitle.trim().length() == 0)
2492 addFirstIndex = true;
2496 index = 1;// we count from 1 if given a specific name
2498 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2499 Vector comps = (Vector) PaintRefresher.components.get(viewport
2500 .getSequenceSetId());
2501 Vector existingNames = new Vector();
2502 for (int i = 0; i < comps.size(); i++)
2504 if (comps.elementAt(i) instanceof AlignmentPanel)
2506 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2507 if (!existingNames.contains(ap.av.viewName))
2509 existingNames.addElement(ap.av.viewName);
2514 while (existingNames.contains(newViewName))
2516 newViewName = viewTitle + " " + (++index);
2519 newap.av.viewName = newViewName;
2521 addAlignmentPanel(newap, true);
2523 if (alignPanels.size() == 2)
2525 viewport.gatherViewsHere = true;
2527 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2532 public void expandViews_actionPerformed(ActionEvent e)
2534 Desktop.instance.explodeViews(this);
2538 public void gatherViews_actionPerformed(ActionEvent e)
2540 Desktop.instance.gatherViews(this);
2550 public void font_actionPerformed(ActionEvent e)
2552 new FontChooser(alignPanel);
2562 protected void seqLimit_actionPerformed(ActionEvent e)
2564 viewport.setShowJVSuffix(seqLimits.isSelected());
2566 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2567 .calculateIdWidth());
2568 alignPanel.paintAlignment(true);
2572 public void idRightAlign_actionPerformed(ActionEvent e)
2574 viewport.rightAlignIds = idRightAlign.isSelected();
2575 alignPanel.paintAlignment(true);
2579 public void centreColumnLabels_actionPerformed(ActionEvent e)
2581 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2582 alignPanel.paintAlignment(true);
2588 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2591 protected void followHighlight_actionPerformed()
2593 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2595 alignPanel.scrollToPosition(
2596 alignPanel.seqPanel.seqCanvas.searchResults, false);
2607 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2609 viewport.setColourText(colourTextMenuItem.isSelected());
2610 alignPanel.paintAlignment(true);
2620 public void wrapMenuItem_actionPerformed(ActionEvent e)
2622 scaleAbove.setVisible(wrapMenuItem.isSelected());
2623 scaleLeft.setVisible(wrapMenuItem.isSelected());
2624 scaleRight.setVisible(wrapMenuItem.isSelected());
2625 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2626 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2630 public void showAllSeqs_actionPerformed(ActionEvent e)
2632 viewport.showAllHiddenSeqs();
2636 public void showAllColumns_actionPerformed(ActionEvent e)
2638 viewport.showAllHiddenColumns();
2643 public void hideSelSequences_actionPerformed(ActionEvent e)
2645 viewport.hideAllSelectedSeqs();
2646 alignPanel.paintAlignment(true);
2650 * called by key handler and the hide all/show all menu items
2655 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2658 boolean hide = false;
2659 SequenceGroup sg = viewport.getSelectionGroup();
2660 if (!toggleSeqs && !toggleCols)
2662 // Hide everything by the current selection - this is a hack - we do the
2663 // invert and then hide
2664 // first check that there will be visible columns after the invert.
2665 if ((viewport.getColumnSelection() != null
2666 && viewport.getColumnSelection().getSelected() != null && viewport
2667 .getColumnSelection().getSelected().size() > 0)
2668 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2671 // now invert the sequence set, if required - empty selection implies
2672 // that no hiding is required.
2675 invertSequenceMenuItem_actionPerformed(null);
2676 sg = viewport.getSelectionGroup();
2680 viewport.expandColSelection(sg, true);
2681 // finally invert the column selection and get the new sequence
2683 invertColSel_actionPerformed(null);
2690 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2692 hideSelSequences_actionPerformed(null);
2695 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2698 showAllSeqs_actionPerformed(null);
2704 if (viewport.getColumnSelection().getSelected().size() > 0)
2706 hideSelColumns_actionPerformed(null);
2709 viewport.setSelectionGroup(sg);
2714 showAllColumns_actionPerformed(null);
2723 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2724 * event.ActionEvent)
2727 public void hideAllButSelection_actionPerformed(ActionEvent e)
2729 toggleHiddenRegions(false, false);
2736 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2740 public void hideAllSelection_actionPerformed(ActionEvent e)
2742 SequenceGroup sg = viewport.getSelectionGroup();
2743 viewport.expandColSelection(sg, false);
2744 viewport.hideAllSelectedSeqs();
2745 viewport.hideSelectedColumns();
2746 alignPanel.paintAlignment(true);
2753 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2757 public void showAllhidden_actionPerformed(ActionEvent e)
2759 viewport.showAllHiddenColumns();
2760 viewport.showAllHiddenSeqs();
2761 alignPanel.paintAlignment(true);
2765 public void hideSelColumns_actionPerformed(ActionEvent e)
2767 viewport.hideSelectedColumns();
2768 alignPanel.paintAlignment(true);
2772 public void hiddenMarkers_actionPerformed(ActionEvent e)
2774 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2785 protected void scaleAbove_actionPerformed(ActionEvent e)
2787 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2788 alignPanel.paintAlignment(true);
2798 protected void scaleLeft_actionPerformed(ActionEvent e)
2800 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2801 alignPanel.paintAlignment(true);
2811 protected void scaleRight_actionPerformed(ActionEvent e)
2813 viewport.setScaleRightWrapped(scaleRight.isSelected());
2814 alignPanel.paintAlignment(true);
2824 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2826 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2827 alignPanel.paintAlignment(true);
2837 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2839 viewport.setShowText(viewTextMenuItem.isSelected());
2840 alignPanel.paintAlignment(true);
2850 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2852 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2853 alignPanel.paintAlignment(true);
2856 public FeatureSettings featureSettings;
2859 public void featureSettings_actionPerformed(ActionEvent e)
2861 if (featureSettings != null)
2863 featureSettings.close();
2864 featureSettings = null;
2866 if (!showSeqFeatures.isSelected())
2868 // make sure features are actually displayed
2869 showSeqFeatures.setSelected(true);
2870 showSeqFeatures_actionPerformed(null);
2872 featureSettings = new FeatureSettings(this);
2876 * Set or clear 'Show Sequence Features'
2882 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2884 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2885 alignPanel.paintAlignment(true);
2886 if (alignPanel.getOverviewPanel() != null)
2888 alignPanel.getOverviewPanel().updateOverviewImage();
2893 * Set or clear 'Show Sequence Features'
2899 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2901 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2903 if (viewport.getShowSequenceFeaturesHeight())
2905 // ensure we're actually displaying features
2906 viewport.setShowSequenceFeatures(true);
2907 showSeqFeatures.setSelected(true);
2909 alignPanel.paintAlignment(true);
2910 if (alignPanel.getOverviewPanel() != null)
2912 alignPanel.getOverviewPanel().updateOverviewImage();
2923 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2925 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2926 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2930 public void alignmentProperties()
2932 JEditorPane editPane = new JEditorPane("text/html", "");
2933 editPane.setEditable(false);
2934 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
2936 editPane.setText("<html>" + contents.toString() + "</html>");
2937 JInternalFrame frame = new JInternalFrame();
2938 frame.getContentPane().add(new JScrollPane(editPane));
2940 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2941 + getTitle(), 500, 400);
2951 public void overviewMenuItem_actionPerformed(ActionEvent e)
2953 if (alignPanel.overviewPanel != null)
2958 JInternalFrame frame = new JInternalFrame();
2959 OverviewPanel overview = new OverviewPanel(alignPanel);
2960 frame.setContentPane(overview);
2961 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2962 frame.getWidth(), frame.getHeight());
2964 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2965 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2968 public void internalFrameClosed(
2969 javax.swing.event.InternalFrameEvent evt)
2971 alignPanel.setOverviewPanel(null);
2975 alignPanel.setOverviewPanel(overview);
2979 public void textColour_actionPerformed(ActionEvent e)
2981 new TextColourChooser().chooseColour(alignPanel, null);
2991 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3003 public void clustalColour_actionPerformed(ActionEvent e)
3005 changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences()));
3015 public void zappoColour_actionPerformed(ActionEvent e)
3017 changeColour(new ZappoColourScheme());
3027 public void taylorColour_actionPerformed(ActionEvent e)
3029 changeColour(new TaylorColourScheme());
3039 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3041 changeColour(new HydrophobicColourScheme());
3051 public void helixColour_actionPerformed(ActionEvent e)
3053 changeColour(new HelixColourScheme());
3063 public void strandColour_actionPerformed(ActionEvent e)
3065 changeColour(new StrandColourScheme());
3075 public void turnColour_actionPerformed(ActionEvent e)
3077 changeColour(new TurnColourScheme());
3087 public void buriedColour_actionPerformed(ActionEvent e)
3089 changeColour(new BuriedColourScheme());
3099 public void nucleotideColour_actionPerformed(ActionEvent e)
3101 changeColour(new NucleotideColourScheme());
3105 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3107 changeColour(new PurinePyrimidineColourScheme());
3111 * public void covariationColour_actionPerformed(ActionEvent e) {
3113 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3117 public void annotationColour_actionPerformed(ActionEvent e)
3119 new AnnotationColourChooser(viewport, alignPanel);
3123 public void rnahelicesColour_actionPerformed(ActionEvent e)
3125 new RNAHelicesColourChooser(viewport, alignPanel);
3135 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3137 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3146 public void changeColour(ColourSchemeI cs)
3148 // TODO: compare with applet and pull up to model method
3153 if (viewport.getAbovePIDThreshold())
3155 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3158 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3160 viewport.setGlobalColourScheme(cs);
3164 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3167 if (viewport.getConservationSelected())
3170 Alignment al = (Alignment) viewport.getAlignment();
3171 Conservation c = new Conservation("All",
3172 ResidueProperties.propHash, 3, al.getSequences(), 0,
3176 c.verdict(false, viewport.getConsPercGaps());
3178 cs.setConservation(c);
3180 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3185 cs.setConservation(null);
3188 cs.setConsensus(viewport.getSequenceConsensusHash());
3191 viewport.setGlobalColourScheme(cs);
3193 if (viewport.getColourAppliesToAllGroups())
3197 for (SequenceGroup sg:viewport.getAlignment().getGroups())
3205 if (cs instanceof ClustalxColourScheme)
3207 sg.cs = new ClustalxColourScheme(sg, viewport
3208 .getHiddenRepSequences());
3210 else if (cs instanceof UserColourScheme)
3212 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3218 sg.cs = cs.getClass().newInstance();
3219 } catch (Exception ex)
3224 if (viewport.getAbovePIDThreshold()
3225 || cs instanceof PIDColourScheme
3226 || cs instanceof Blosum62ColourScheme)
3228 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3230 sg.cs.setConsensus(AAFrequency.calculate(
3231 sg.getSequences(viewport.getHiddenRepSequences()),
3232 sg.getStartRes(), sg.getEndRes() + 1));
3236 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3239 if (viewport.getConservationSelected())
3241 Conservation c = new Conservation("Group",
3242 ResidueProperties.propHash, 3, sg.getSequences(viewport
3243 .getHiddenRepSequences()), sg.getStartRes(),
3244 sg.getEndRes() + 1);
3246 c.verdict(false, viewport.getConsPercGaps());
3247 sg.cs.setConservation(c);
3251 sg.cs.setConservation(null);
3256 if (alignPanel.getOverviewPanel() != null)
3258 alignPanel.getOverviewPanel().updateOverviewImage();
3261 alignPanel.paintAlignment(true);
3271 protected void modifyPID_actionPerformed(ActionEvent e)
3273 if (viewport.getAbovePIDThreshold()
3274 && viewport.getGlobalColourScheme() != null)
3276 SliderPanel.setPIDSliderSource(alignPanel,
3277 viewport.getGlobalColourScheme(), "Background");
3278 SliderPanel.showPIDSlider();
3289 protected void modifyConservation_actionPerformed(ActionEvent e)
3291 if (viewport.getConservationSelected()
3292 && viewport.getGlobalColourScheme() != null)
3294 SliderPanel.setConservationSlider(alignPanel,
3295 viewport.getGlobalColourScheme(), "Background");
3296 SliderPanel.showConservationSlider();
3307 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3309 viewport.setConservationSelected(conservationMenuItem.isSelected());
3311 viewport.setAbovePIDThreshold(false);
3312 abovePIDThreshold.setSelected(false);
3314 changeColour(viewport.getGlobalColourScheme());
3316 modifyConservation_actionPerformed(null);
3326 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3328 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3330 conservationMenuItem.setSelected(false);
3331 viewport.setConservationSelected(false);
3333 changeColour(viewport.getGlobalColourScheme());
3335 modifyPID_actionPerformed(null);
3345 public void userDefinedColour_actionPerformed(ActionEvent e)
3347 if (e.getActionCommand().equals("User Defined..."))
3349 new UserDefinedColours(alignPanel, null);
3353 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3354 .getUserColourSchemes().get(e.getActionCommand());
3360 public void updateUserColourMenu()
3363 Component[] menuItems = colourMenu.getMenuComponents();
3364 int i, iSize = menuItems.length;
3365 for (i = 0; i < iSize; i++)
3367 if (menuItems[i].getName() != null
3368 && menuItems[i].getName().equals("USER_DEFINED"))
3370 colourMenu.remove(menuItems[i]);
3374 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3376 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3377 .getUserColourSchemes().keys();
3379 while (userColours.hasMoreElements())
3381 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3382 userColours.nextElement().toString());
3383 radioItem.setName("USER_DEFINED");
3384 radioItem.addMouseListener(new MouseAdapter()
3387 public void mousePressed(MouseEvent evt)
3389 if (evt.isControlDown()
3390 || SwingUtilities.isRightMouseButton(evt))
3392 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3394 int option = JOptionPane.showInternalConfirmDialog(
3395 jalview.gui.Desktop.desktop,
3396 "Remove from default list?",
3397 "Remove user defined colour",
3398 JOptionPane.YES_NO_OPTION);
3399 if (option == JOptionPane.YES_OPTION)
3401 jalview.gui.UserDefinedColours
3402 .removeColourFromDefaults(radioItem.getText());
3403 colourMenu.remove(radioItem);
3407 radioItem.addActionListener(new ActionListener()
3410 public void actionPerformed(ActionEvent evt)
3412 userDefinedColour_actionPerformed(evt);
3419 radioItem.addActionListener(new ActionListener()
3422 public void actionPerformed(ActionEvent evt)
3424 userDefinedColour_actionPerformed(evt);
3428 colourMenu.insert(radioItem, 15);
3429 colours.add(radioItem);
3441 public void PIDColour_actionPerformed(ActionEvent e)
3443 changeColour(new PIDColourScheme());
3453 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3455 changeColour(new Blosum62ColourScheme());
3465 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3467 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3468 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3469 .getAlignment().getSequenceAt(0), null);
3470 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3471 viewport.getAlignment()));
3472 alignPanel.paintAlignment(true);
3482 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3484 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3485 AlignmentSorter.sortByID(viewport.getAlignment());
3486 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3487 viewport.getAlignment()));
3488 alignPanel.paintAlignment(true);
3498 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3500 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3501 AlignmentSorter.sortByLength(viewport.getAlignment());
3502 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3503 viewport.getAlignment()));
3504 alignPanel.paintAlignment(true);
3514 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3516 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3517 AlignmentSorter.sortByGroup(viewport.getAlignment());
3518 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3519 viewport.getAlignment()));
3521 alignPanel.paintAlignment(true);
3531 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3533 new RedundancyPanel(alignPanel, this);
3543 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3545 if ((viewport.getSelectionGroup() == null)
3546 || (viewport.getSelectionGroup().getSize() < 2))
3548 JOptionPane.showInternalMessageDialog(this,
3549 "You must select at least 2 sequences.", "Invalid Selection",
3550 JOptionPane.WARNING_MESSAGE);
3554 JInternalFrame frame = new JInternalFrame();
3555 frame.setContentPane(new PairwiseAlignPanel(viewport));
3556 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3567 public void PCAMenuItem_actionPerformed(ActionEvent e)
3569 if (((viewport.getSelectionGroup() != null)
3570 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3571 .getSelectionGroup().getSize() > 0))
3572 || (viewport.getAlignment().getHeight() < 4))
3574 JOptionPane.showInternalMessageDialog(this,
3575 "Principal component analysis must take\n"
3576 + "at least 4 input sequences.",
3577 "Sequence selection insufficient",
3578 JOptionPane.WARNING_MESSAGE);
3583 new PCAPanel(alignPanel);
3587 public void autoCalculate_actionPerformed(ActionEvent e)
3589 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3590 if (viewport.autoCalculateConsensus)
3592 viewport.firePropertyChange("alignment", null, viewport
3593 .getAlignment().getSequences());
3598 public void sortByTreeOption_actionPerformed(ActionEvent e)
3600 viewport.sortByTree = sortByTree.isSelected();
3604 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3606 viewport.followSelection = listenToViewSelections.isSelected();
3616 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3618 NewTreePanel("AV", "PID", "Average distance tree using PID");
3628 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3630 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3640 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3642 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3652 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3654 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3667 void NewTreePanel(String type, String pwType, String title)
3671 if (viewport.getSelectionGroup() != null)
3673 if (viewport.getSelectionGroup().getSize() < 3)
3678 "You need to have more than two sequences selected to build a tree!",
3679 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3683 SequenceGroup sg = viewport.getSelectionGroup();
3685 /* Decide if the selection is a column region */
3686 for (SequenceI _s:sg.getSequences())
3688 if (_s.getLength() < sg
3694 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3695 + "Try using the Pad function in the edit menu,\n"
3696 + "or one of the multiple sequence alignment web services.",
3697 "Sequences in selection are not aligned",
3698 JOptionPane.WARNING_MESSAGE);
3704 title = title + " on region";
3705 tp = new TreePanel(alignPanel, type, pwType);
3709 // are the visible sequences aligned?
3710 if (!viewport.getAlignment().isAligned(false))
3715 "The sequences must be aligned before creating a tree.\n"
3716 + "Try using the Pad function in the edit menu,\n"
3717 + "or one of the multiple sequence alignment web services.",
3718 "Sequences not aligned",
3719 JOptionPane.WARNING_MESSAGE);
3724 if (viewport.getAlignment().getHeight() < 2)
3729 tp = new TreePanel(alignPanel, type, pwType);
3734 if (viewport.viewName != null)
3736 title += viewport.viewName + " of ";
3739 title += this.title;
3741 Desktop.addInternalFrame(tp, title, 600, 500);
3752 public void addSortByOrderMenuItem(String title,
3753 final AlignmentOrder order)
3755 final JMenuItem item = new JMenuItem("by " + title);
3757 item.addActionListener(new java.awt.event.ActionListener()
3760 public void actionPerformed(ActionEvent e)
3762 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3764 // TODO: JBPNote - have to map order entries to curent SequenceI
3766 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3768 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3771 alignPanel.paintAlignment(true);
3777 * Add a new sort by annotation score menu item
3780 * the menu to add the option to
3782 * the label used to retrieve scores for each sequence on the
3785 public void addSortByAnnotScoreMenuItem(JMenu sort,
3786 final String scoreLabel)
3788 final JMenuItem item = new JMenuItem(scoreLabel);
3790 item.addActionListener(new java.awt.event.ActionListener()
3793 public void actionPerformed(ActionEvent e)
3795 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3796 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3797 viewport.getAlignment());// ,viewport.getSelectionGroup());
3798 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3799 viewport.getAlignment()));
3800 alignPanel.paintAlignment(true);
3806 * last hash for alignment's annotation array - used to minimise cost of
3809 protected int _annotationScoreVectorHash;
3812 * search the alignment and rebuild the sort by annotation score submenu the
3813 * last alignment annotation vector hash is stored to minimize cost of
3814 * rebuilding in subsequence calls.
3818 public void buildSortByAnnotationScoresMenu()
3820 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3825 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3827 sortByAnnotScore.removeAll();
3828 // almost certainly a quicker way to do this - but we keep it simple
3829 Hashtable scoreSorts = new Hashtable();
3830 AlignmentAnnotation aann[];
3831 for (SequenceI sqa:viewport.getAlignment().getSequences())
3833 aann = sqa.getAnnotation();
3834 for (int i = 0; aann != null && i < aann.length; i++)
3836 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3838 scoreSorts.put(aann[i].label, aann[i].label);
3842 Enumeration labels = scoreSorts.keys();
3843 while (labels.hasMoreElements())
3845 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3846 (String) labels.nextElement());
3848 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3851 _annotationScoreVectorHash = viewport.getAlignment()
3852 .getAlignmentAnnotation().hashCode();
3857 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3858 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3859 * call. Listeners are added to remove the menu item when the treePanel is
3860 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3864 * Displayed tree window.
3866 * SortBy menu item title.
3869 public void buildTreeMenu()
3871 sortByTreeMenu.removeAll();
3873 Vector comps = (Vector) PaintRefresher.components.get(viewport
3874 .getSequenceSetId());
3875 Vector treePanels = new Vector();
3876 int i, iSize = comps.size();
3877 for (i = 0; i < iSize; i++)
3879 if (comps.elementAt(i) instanceof TreePanel)
3881 treePanels.add(comps.elementAt(i));
3885 iSize = treePanels.size();
3889 sortByTreeMenu.setVisible(false);
3893 sortByTreeMenu.setVisible(true);
3895 for (i = 0; i < treePanels.size(); i++)
3897 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3898 final JMenuItem item = new JMenuItem(tp.getTitle());
3899 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3900 item.addActionListener(new java.awt.event.ActionListener()
3903 public void actionPerformed(ActionEvent e)
3905 tp.sortByTree_actionPerformed(null);
3906 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3911 sortByTreeMenu.add(item);
3915 public boolean sortBy(AlignmentOrder alorder, String undoname)
3917 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3918 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3919 if (undoname != null)
3921 addHistoryItem(new OrderCommand(undoname, oldOrder,
3922 viewport.getAlignment()));
3924 alignPanel.paintAlignment(true);
3929 * Work out whether the whole set of sequences or just the selected set will
3930 * be submitted for multiple alignment.
3933 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3935 // Now, check we have enough sequences
3936 AlignmentView msa = null;
3938 if ((viewport.getSelectionGroup() != null)
3939 && (viewport.getSelectionGroup().getSize() > 1))
3941 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3942 // some common interface!
3944 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3945 * SequenceI[sz = seqs.getSize(false)];
3947 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3948 * seqs.getSequenceAt(i); }
3950 msa = viewport.getAlignmentView(true);
3955 * Vector seqs = viewport.getAlignment().getSequences();
3957 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3959 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3960 * seqs.elementAt(i); } }
3962 msa = viewport.getAlignmentView(false);
3968 * Decides what is submitted to a secondary structure prediction service: the
3969 * first sequence in the alignment, or in the current selection, or, if the
3970 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3971 * region or the whole alignment. (where the first sequence in the set is the
3972 * one that the prediction will be for).
3974 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3976 AlignmentView seqs = null;
3978 if ((viewport.getSelectionGroup() != null)
3979 && (viewport.getSelectionGroup().getSize() > 0))
3981 seqs = viewport.getAlignmentView(true);
3985 seqs = viewport.getAlignmentView(false);
3987 // limit sequences - JBPNote in future - could spawn multiple prediction
3989 // TODO: viewport.getAlignment().isAligned is a global state - the local
3990 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3991 if (!viewport.getAlignment().isAligned(false))
3993 seqs.setSequences(new SeqCigar[]
3994 { seqs.getSequences()[0] });
3995 // TODO: if seqs.getSequences().length>1 then should really have warned
4009 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4011 // Pick the tree file
4012 JalviewFileChooser chooser = new JalviewFileChooser(
4013 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4014 chooser.setFileView(new JalviewFileView());
4015 chooser.setDialogTitle("Select a newick-like tree file");
4016 chooser.setToolTipText("Load a tree file");
4018 int value = chooser.showOpenDialog(null);
4020 if (value == JalviewFileChooser.APPROVE_OPTION)
4022 String choice = chooser.getSelectedFile().getPath();
4023 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4024 jalview.io.NewickFile fin = null;
4027 fin = new jalview.io.NewickFile(choice, "File");
4028 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4029 } catch (Exception ex)
4031 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4032 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
4033 ex.printStackTrace();
4035 if (fin != null && fin.hasWarningMessage())
4037 JOptionPane.showMessageDialog(Desktop.desktop,
4038 fin.getWarningMessage(), "Possible problem with tree file",
4039 JOptionPane.WARNING_MESSAGE);
4045 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4047 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4050 public TreePanel ShowNewickTree(NewickFile nf, String title)
4052 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4055 public TreePanel ShowNewickTree(NewickFile nf, String title,
4056 AlignmentView input)
4058 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4061 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4062 int h, int x, int y)
4064 return ShowNewickTree(nf, title, null, w, h, x, y);
4068 * Add a treeviewer for the tree extracted from a newick file object to the
4069 * current alignment view
4076 * Associated alignment input data (or null)
4085 * @return TreePanel handle
4087 public TreePanel ShowNewickTree(NewickFile nf, String title,
4088 AlignmentView input, int w, int h, int x, int y)
4090 TreePanel tp = null;
4096 if (nf.getTree() != null)
4098 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4104 tp.setLocation(x, y);
4107 Desktop.addInternalFrame(tp, title, w, h);
4109 } catch (Exception ex)
4111 ex.printStackTrace();
4117 private boolean buildingMenu = false;
4120 * Generates menu items and listener event actions for web service clients
4123 public void BuildWebServiceMenu()
4125 while (buildingMenu)
4129 System.err.println("Waiting for building menu to finish.");
4131 } catch (Exception e)
4136 final AlignFrame me = this;
4137 buildingMenu = true;
4138 new Thread(new Runnable()
4145 System.err.println("Building ws menu again "
4146 + Thread.currentThread());
4147 // TODO: add support for context dependent disabling of services based
4149 // alignment and current selection
4150 // TODO: add additional serviceHandle parameter to specify abstract
4152 // class independently of AbstractName
4153 // TODO: add in rediscovery GUI function to restart discoverer
4154 // TODO: group services by location as well as function and/or
4156 // object broker mechanism.
4157 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4158 final IProgressIndicator af = me;
4159 final JMenu msawsmenu = new JMenu("Alignment");
4160 final JMenu secstrmenu = new JMenu(
4161 "Secondary Structure Prediction");
4162 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4163 final JMenu analymenu = new JMenu("Analysis");
4164 final JMenu dismenu = new JMenu("Protein Disorder");
4165 // JAL-940 - only show secondary structure prediction services from
4166 // the legacy server
4167 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4169 Discoverer.services != null && (Discoverer.services.size() > 0))
4171 // TODO: refactor to allow list of AbstractName/Handler bindings to
4173 // stored or retrieved from elsewhere
4174 Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4175 Vector secstrpr = (Vector) Discoverer.services
4177 Vector seqsrch = null; // (Vector)
4178 // Discoverer.services.get("SeqSearch");
4179 // TODO: move GUI generation code onto service implementation - so a
4180 // client instance attaches itself to the GUI with method call like
4181 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
4185 // Add any Multiple Sequence Alignment Services
4186 for (int i = 0, j = msaws.size(); i < j; i++)
4188 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
4190 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4191 .getServiceClient(sh);
4192 impl.attachWSMenuEntry(msawsmenu, me);
4196 if (secstrpr != null)
4198 // Add any secondary structure prediction services
4199 for (int i = 0, j = secstrpr.size(); i < j; i++)
4201 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4203 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4204 .getServiceClient(sh);
4205 impl.attachWSMenuEntry(secstrmenu, me);
4208 if (seqsrch != null)
4210 // Add any sequence search services
4211 for (int i = 0, j = seqsrch.size(); i < j; i++)
4213 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
4215 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4216 .getServiceClient(sh);
4217 impl.attachWSMenuEntry(seqsrchmenu, me);
4222 // Add all submenus in the order they should appear on the web
4224 wsmenu.add(msawsmenu);
4225 wsmenu.add(secstrmenu);
4226 wsmenu.add(dismenu);
4227 wsmenu.add(analymenu);
4228 // final ArrayList<JMenu> submens=new ArrayList<JMenu>();
4229 // submens.add(msawsmenu);
4230 // submens.add(secstrmenu);
4231 // submens.add(dismenu);
4232 // submens.add(analymenu);
4234 // No search services yet
4235 // wsmenu.add(seqsrchmenu);
4237 javax.swing.SwingUtilities.invokeLater(new Runnable()
4244 webService.removeAll();
4245 // first, add discovered services onto the webservices menu
4246 if (wsmenu.size() > 0)
4248 for (int i = 0, j = wsmenu.size(); i < j; i++)
4250 webService.add(wsmenu.get(i));
4255 webService.add(me.webServiceNoServices);
4257 // TODO: move into separate menu builder class.
4258 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4260 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4261 if (jws2servs != null)
4263 if (jws2servs.hasServices())
4265 jws2servs.attachWSMenuEntry(webService, me);
4267 if (jws2servs.isRunning())
4269 JMenuItem tm = new JMenuItem(
4270 "Still discovering JABA Services");
4271 tm.setEnabled(false);
4277 build_urlServiceMenu(me.webService);
4278 build_fetchdbmenu(webService);
4279 for (JMenu item : wsmenu)
4281 if (item.getItemCount() == 0)
4283 item.setEnabled(false);
4287 item.setEnabled(true);
4290 } catch (Exception e)
4292 Cache.log.debug("Exception during web service menu building process.",e);
4297 } catch (Exception e)
4302 buildingMenu = false;
4309 * construct any groupURL type service menu entries.
4313 private void build_urlServiceMenu(JMenu webService)
4315 // TODO: remove this code when 2.7 is released
4316 // DEBUG - alignmentView
4318 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4319 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4321 * @Override public void actionPerformed(ActionEvent e) {
4322 * jalview.datamodel.AlignmentView
4323 * .testSelectionViews(af.viewport.getAlignment(),
4324 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4326 * }); webService.add(testAlView);
4328 // TODO: refactor to RestClient discoverer and merge menu entries for
4329 // rest-style services with other types of analysis/calculation service
4330 // SHmmr test client - still being implemented.
4331 // DEBUG - alignmentView
4333 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4336 client.attachWSMenuEntry(
4337 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4341 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4343 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4349 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4350 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4351 * getProperty("LAST_DIRECTORY"));
4353 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4354 * to Vamsas file"); chooser.setToolTipText("Export");
4356 * int value = chooser.showSaveDialog(this);
4358 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4359 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4360 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4361 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4364 * prototype of an automatically enabled/disabled analysis function
4367 protected void setShowProductsEnabled()
4369 SequenceI[] selection = viewport.getSequenceSelection();
4370 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4371 viewport.getAlignment().getDataset()))
4373 showProducts.setEnabled(true);
4378 showProducts.setEnabled(false);
4383 * search selection for sequence xRef products and build the show products
4388 * @return true if showProducts menu should be enabled.
4390 public boolean canShowProducts(SequenceI[] selection,
4391 boolean isRegionSelection, Alignment dataset)
4393 boolean showp = false;
4396 showProducts.removeAll();
4397 final boolean dna = viewport.getAlignment().isNucleotide();
4398 final Alignment ds = dataset;
4399 String[] ptypes = (selection == null || selection.length == 0) ? null
4400 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4402 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4403 // selection, dataset, true);
4404 final SequenceI[] sel = selection;
4405 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4408 final boolean isRegSel = isRegionSelection;
4409 final AlignFrame af = this;
4410 final String source = ptypes[t];
4411 JMenuItem xtype = new JMenuItem(ptypes[t]);
4412 xtype.addActionListener(new ActionListener()
4416 public void actionPerformed(ActionEvent e)
4418 // TODO: new thread for this call with vis-delay
4419 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4420 isRegSel, dna, source);
4424 showProducts.add(xtype);
4426 showProducts.setVisible(showp);
4427 showProducts.setEnabled(showp);
4428 } catch (Exception e)
4430 jalview.bin.Cache.log
4431 .warn("canTranslate threw an exception - please report to help@jalview.org",
4438 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4439 boolean isRegSel, boolean dna, String source)
4441 final boolean fisRegSel = isRegSel;
4442 final boolean fdna = dna;
4443 final String fsrc = source;
4444 final AlignFrame ths = this;
4445 final SequenceI[] fsel = sel;
4446 Runnable foo = new Runnable()
4452 final long sttime = System.currentTimeMillis();
4453 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4456 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4460 Alignment prods = CrossRef
4461 .findXrefSequences(fsel, fdna, fsrc, ds);
4464 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4465 for (int s = 0; s < sprods.length; s++)
4467 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4468 if (ds.getSequences() == null
4469 || !ds.getSequences().contains(
4470 sprods[s].getDatasetSequence()))
4471 ds.addSequence(sprods[s].getDatasetSequence());
4472 sprods[s].updatePDBIds();
4474 Alignment al = new Alignment(sprods);
4475 AlignedCodonFrame[] cf = prods.getCodonFrames();
4477 for (int s = 0; cf != null && s < cf.length; s++)
4479 al.addCodonFrame(cf[s]);
4482 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4484 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4485 + " for " + ((fisRegSel) ? "selected region of " : "")
4487 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4492 System.err.println("No Sequences generated for xRef type "
4495 } catch (Exception e)
4497 jalview.bin.Cache.log.error(
4498 "Exception when finding crossreferences", e);
4499 } catch (OutOfMemoryError e)
4501 new OOMWarning("whilst fetching crossreferences", e);
4504 jalview.bin.Cache.log.error("Error when finding crossreferences",
4507 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4512 Thread frunner = new Thread(foo);
4516 public boolean canShowTranslationProducts(SequenceI[] selection,
4517 AlignmentI alignment)
4522 return (jalview.analysis.Dna.canTranslate(selection,
4523 viewport.getViewAsVisibleContigs(true)));
4524 } catch (Exception e)
4526 jalview.bin.Cache.log
4527 .warn("canTranslate threw an exception - please report to help@jalview.org",
4534 public void showProducts_actionPerformed(ActionEvent e)
4536 // /////////////////////////////
4537 // Collect Data to be translated/transferred
4539 SequenceI[] selection = viewport.getSequenceSelection();
4540 AlignmentI al = null;
4543 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4544 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4545 viewport.getAlignment().getDataset());
4546 } catch (Exception ex)
4549 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4556 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4557 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4561 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4562 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4563 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4568 public void showTranslation_actionPerformed(ActionEvent e)
4570 // /////////////////////////////
4571 // Collect Data to be translated/transferred
4573 SequenceI[] selection = viewport.getSequenceSelection();
4574 String[] seqstring = viewport.getViewAsString(true);
4575 AlignmentI al = null;
4578 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4579 viewport.getViewAsVisibleContigs(true), viewport
4580 .getGapCharacter(), viewport.getAlignment()
4581 .getAlignmentAnnotation(), viewport.getAlignment()
4582 .getWidth(), viewport.getAlignment().getDataset());
4583 } catch (Exception ex)
4586 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4593 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4594 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4598 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4599 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4600 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4605 * Try to load a features file onto the alignment.
4608 * contents or path to retrieve file
4610 * access mode of file (see jalview.io.AlignFile)
4611 * @return true if features file was parsed corectly.
4613 public boolean parseFeaturesFile(String file, String type)
4615 boolean featuresFile = false;
4618 featuresFile = new FeaturesFile(file, type).parse(viewport
4619 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4620 .getFeatureRenderer().featureColours, false,
4621 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4622 } catch (Exception ex)
4624 ex.printStackTrace();
4629 viewport.showSequenceFeatures = true;
4630 showSeqFeatures.setSelected(true);
4631 if (alignPanel.seqPanel.seqCanvas.fr != null)
4633 // update the min/max ranges where necessary
4634 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4636 if (featureSettings != null)
4638 featureSettings.setTableData();
4640 alignPanel.paintAlignment(true);
4643 return featuresFile;
4647 public void dragEnter(DropTargetDragEvent evt)
4652 public void dragExit(DropTargetEvent evt)
4657 public void dragOver(DropTargetDragEvent evt)
4662 public void dropActionChanged(DropTargetDragEvent evt)
4667 public void drop(DropTargetDropEvent evt)
4669 Transferable t = evt.getTransferable();
4670 java.util.List files = null;
4674 DataFlavor uriListFlavor = new DataFlavor(
4675 "text/uri-list;class=java.lang.String");
4676 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4678 // Works on Windows and MacOSX
4679 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4680 files = (java.util.List) t
4681 .getTransferData(DataFlavor.javaFileListFlavor);
4683 else if (t.isDataFlavorSupported(uriListFlavor))
4685 // This is used by Unix drag system
4686 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4687 String data = (String) t.getTransferData(uriListFlavor);
4688 files = new java.util.ArrayList(1);
4689 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4690 data, "\r\n"); st.hasMoreTokens();)
4692 String s = st.nextToken();
4693 if (s.startsWith("#"))
4695 // the line is a comment (as per the RFC 2483)
4699 java.net.URI uri = new java.net.URI(s);
4700 // check to see if we can handle this kind of URI
4701 if (uri.getScheme().toLowerCase().startsWith("http"))
4703 files.add(uri.toString());
4707 // otherwise preserve old behaviour: catch all for file objects
4708 java.io.File file = new java.io.File(uri);
4709 files.add(file.toString());
4713 } catch (Exception e)
4715 e.printStackTrace();
4721 // check to see if any of these files have names matching sequences in
4723 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4724 .getAlignment().getSequencesArray());
4726 * Object[] { String,SequenceI}
4728 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4729 ArrayList<String> filesnotmatched = new ArrayList<String>();
4730 for (int i = 0; i < files.size(); i++)
4732 String file = files.get(i).toString();
4734 String protocol = FormatAdapter.checkProtocol(file);
4735 if (protocol == jalview.io.FormatAdapter.FILE)
4737 File fl = new File(file);
4738 pdbfn = fl.getName();
4740 else if (protocol == jalview.io.FormatAdapter.URL)
4742 URL url = new URL(file);
4743 pdbfn = url.getFile();
4745 if (pdbfn.length() > 0)
4747 // attempt to find a match in the alignment
4748 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4749 int l = 0, c = pdbfn.indexOf(".");
4750 while (mtch == null && c != -1)
4755 } while ((c = pdbfn.indexOf(".", l)) > l);
4758 pdbfn = pdbfn.substring(0, l);
4760 mtch = idm.findAllIdMatches(pdbfn);
4767 type = new IdentifyFile().Identify(file, protocol);
4768 } catch (Exception ex)
4774 if (type.equalsIgnoreCase("PDB"))
4776 filesmatched.add(new Object[]
4777 { file, protocol, mtch });
4782 // File wasn't named like one of the sequences or wasn't a PDB file.
4783 filesnotmatched.add(file);
4787 if (filesmatched.size() > 0)
4789 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4793 "Do you want to automatically associate the "
4794 + filesmatched.size()
4795 + " PDB files with sequences in the alignment that have the same name ?",
4796 "Automatically Associate PDB files by name",
4797 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4800 for (Object[] fm : filesmatched)
4802 // try and associate
4803 // TODO: may want to set a standard ID naming formalism for
4804 // associating PDB files which have no IDs.
4805 for (SequenceI toassoc : (SequenceI[]) fm[2])
4807 PDBEntry pe = new AssociatePdbFileWithSeq()
4808 .associatePdbWithSeq((String) fm[0],
4809 (String) fm[1], toassoc, false);
4812 System.err.println("Associated file : "
4813 + ((String) fm[0]) + " with "
4814 + toassoc.getDisplayId(true));
4818 alignPanel.paintAlignment(true);
4822 if (filesnotmatched.size() > 0)
4825 && (Cache.getDefault(
4826 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4829 "<html>Do you want to <em>ignore</em> the "
4830 + filesnotmatched.size()
4831 + " files whose names did not match any sequence IDs ?</html>",
4832 "Ignore unmatched dropped files ?",
4833 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4837 for (String fn : filesnotmatched)
4839 loadJalviewDataFile(fn, null, null, null);
4843 } catch (Exception ex)
4845 ex.printStackTrace();
4851 * Attempt to load a "dropped" file or URL string: First by testing whether
4852 * it's and Annotation file, then a JNet file, and finally a features file. If
4853 * all are false then the user may have dropped an alignment file onto this
4857 * either a filename or a URL string.
4859 public void loadJalviewDataFile(String file, String protocol,
4860 String format, SequenceI assocSeq)
4864 if (protocol == null)
4866 protocol = jalview.io.FormatAdapter.checkProtocol(file);
4868 // if the file isn't identified, or not positively identified as some
4869 // other filetype (PFAM is default unidentified alignment file type) then
4870 // try to parse as annotation.
4871 boolean isAnnotation = (format == null || format
4872 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4873 .readAnnotationFile(viewport.getAlignment(), file, protocol)
4878 // first see if its a T-COFFEE score file
4879 TCoffeeScoreFile tcf = null;
4882 tcf = new TCoffeeScoreFile(file, protocol);
4885 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4887 tcoffeeColour.setEnabled(true);
4888 tcoffeeColour.setSelected(true);
4889 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4890 isAnnotation = true;
4892 .setText("Successfully pasted T-Coffee scores to alignment.");
4896 // some problem - if no warning its probable that the ID matching process didn't work
4897 JOptionPane.showMessageDialog(Desktop.desktop,
4898 tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(),
4899 "Problem reading T-COFFEE score file",
4900 JOptionPane.WARNING_MESSAGE);
4907 } catch (Exception x)
4909 Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
4914 // try to see if its a JNet 'concise' style annotation file *before*
4916 // try to parse it as a features file
4919 format = new IdentifyFile().Identify(file, protocol);
4921 if (format.equalsIgnoreCase("JnetFile"))
4923 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
4925 new JnetAnnotationMaker().add_annotation(predictions,
4926 viewport.getAlignment(), 0, false);
4927 isAnnotation = true;
4932 * if (format.equalsIgnoreCase("PDB")) {
4934 * String pdbfn = ""; // try to match up filename with sequence id
4935 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
4936 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
4937 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4938 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
4939 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4940 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
4941 * // attempt to find a match in the alignment SequenceI mtch =
4942 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4943 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
4944 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
4945 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
4946 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4947 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
4948 * { System.err.println("Associated file : " + file + " with " +
4949 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4950 * TODO: maybe need to load as normal otherwise return; } }
4952 // try to parse it as a features file
4953 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4954 // if it wasn't a features file then we just treat it as a general
4955 // alignment file to load into the current view.
4958 new FileLoader().LoadFile(viewport, file, protocol, format);
4962 alignPanel.paintAlignment(true);
4970 alignPanel.adjustAnnotationHeight();
4971 viewport.updateSequenceIdColours();
4972 buildSortByAnnotationScoresMenu();
4973 alignPanel.paintAlignment(true);
4975 } catch (Exception ex)
4977 ex.printStackTrace();
4982 public void tabSelectionChanged(int index)
4986 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4987 viewport = alignPanel.av;
4988 setMenusFromViewport(viewport);
4993 public void tabbedPane_mousePressed(MouseEvent e)
4995 if (SwingUtilities.isRightMouseButton(e))
4997 String reply = JOptionPane.showInternalInputDialog(this,
4998 "Enter View Name", "Edit View Name",
4999 JOptionPane.QUESTION_MESSAGE);
5003 viewport.viewName = reply;
5004 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5009 public AlignViewport getCurrentView()
5015 * Open the dialog for regex description parsing.
5018 protected void extractScores_actionPerformed(ActionEvent e)
5020 ParseProperties pp = new jalview.analysis.ParseProperties(
5021 viewport.getAlignment());
5022 // TODO: verify regex and introduce GUI dialog for version 2.5
5023 // if (pp.getScoresFromDescription("col", "score column ",
5024 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5026 if (pp.getScoresFromDescription("description column",
5027 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5029 buildSortByAnnotationScoresMenu();
5037 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5041 protected void showDbRefs_actionPerformed(ActionEvent e)
5043 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5049 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5053 protected void showNpFeats_actionPerformed(ActionEvent e)
5055 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5059 * find the viewport amongst the tabs in this alignment frame and close that
5064 public boolean closeView(AlignViewport av)
5068 this.closeMenuItem_actionPerformed(false);
5071 Component[] comp = tabbedPane.getComponents();
5072 for (int i = 0; comp != null && i < comp.length; i++)
5074 if (comp[i] instanceof AlignmentPanel)
5076 if (((AlignmentPanel) comp[i]).av == av)
5079 closeView((AlignmentPanel) comp[i]);
5087 protected void build_fetchdbmenu(JMenu webService)
5089 // Temporary hack - DBRef Fetcher always top level ws entry.
5090 // TODO We probably want to store a sequence database checklist in
5091 // preferences and have checkboxes.. rather than individual sources selected
5093 final JMenu rfetch = new JMenu("Fetch DB References");
5094 rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
5095 webService.add(rfetch);
5097 JMenuItem fetchr = new JMenuItem("Standard Databases");
5098 fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
5099 fetchr.addActionListener(new ActionListener()
5103 public void actionPerformed(ActionEvent e)
5105 new Thread(new Runnable()
5111 new jalview.ws.DBRefFetcher(alignPanel.av
5112 .getSequenceSelection(), alignPanel.alignFrame)
5113 .fetchDBRefs(false);
5121 final AlignFrame me = this;
5122 new Thread(new Runnable()
5127 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5128 .getSequenceFetcherSingleton(me);
5129 javax.swing.SwingUtilities.invokeLater(new Runnable()
5134 String[] dbclasses = sf.getOrderedSupportedSources();
5135 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5136 // jalview.util.QuickSort.sort(otherdb, otherdb);
5137 List<DbSourceProxy> otherdb;
5138 JMenu dfetch = new JMenu();
5139 JMenu ifetch = new JMenu();
5140 JMenuItem fetchr = null;
5141 int comp = 0, icomp = 0, mcomp = 15;
5142 String mname = null;
5144 for (String dbclass : dbclasses)
5146 otherdb = sf.getSourceProxy(dbclass);
5147 // add a single entry for this class, or submenu allowing 'fetch
5149 if (otherdb == null || otherdb.size() < 1)
5153 // List<DbSourceProxy> dbs=otherdb;
5154 // otherdb=new ArrayList<DbSourceProxy>();
5155 // for (DbSourceProxy db:dbs)
5157 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5161 mname = "From " + dbclass;
5163 if (otherdb.size() == 1)
5165 final DbSourceProxy[] dassource = otherdb
5166 .toArray(new DbSourceProxy[0]);
5167 DbSourceProxy src = otherdb.get(0);
5168 fetchr = new JMenuItem(src.getDbSource());
5169 fetchr.addActionListener(new ActionListener()
5173 public void actionPerformed(ActionEvent e)
5175 new Thread(new Runnable()
5181 new jalview.ws.DBRefFetcher(alignPanel.av
5182 .getSequenceSelection(),
5183 alignPanel.alignFrame, dassource)
5184 .fetchDBRefs(false);
5190 fetchr.setToolTipText("<html>"
5191 + JvSwingUtils.wrapTooltip("Retrieve from "
5192 + src.getDbName()) + "<html>");
5198 final DbSourceProxy[] dassource = otherdb
5199 .toArray(new DbSourceProxy[0]);
5201 DbSourceProxy src = otherdb.get(0);
5202 fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
5204 fetchr.addActionListener(new ActionListener()
5207 public void actionPerformed(ActionEvent e)
5209 new Thread(new Runnable()
5215 new jalview.ws.DBRefFetcher(alignPanel.av
5216 .getSequenceSelection(),
5217 alignPanel.alignFrame, dassource)
5218 .fetchDBRefs(false);
5224 fetchr.setToolTipText("<html>"
5225 + JvSwingUtils.wrapTooltip("Retrieve from all "
5226 + otherdb.size() + " sources in "
5227 + src.getDbSource() + "<br>First is :"
5228 + src.getDbName()) + "<html>");
5231 // and then build the rest of the individual menus
5232 ifetch = new JMenu("Sources from " + src.getDbSource());
5234 String imname = null;
5236 for (DbSourceProxy sproxy : otherdb)
5238 String dbname = sproxy.getDbName();
5239 String sname = dbname.length() > 5 ? dbname.substring(0,
5240 5) + "..." : dbname;
5241 String msname = dbname.length() > 10 ? dbname.substring(
5242 0, 10) + "..." : dbname;
5245 imname = "from '" + sname + "'";
5247 fetchr = new JMenuItem(msname);
5248 final DbSourceProxy[] dassrc =
5250 fetchr.addActionListener(new ActionListener()
5254 public void actionPerformed(ActionEvent e)
5256 new Thread(new Runnable()
5262 new jalview.ws.DBRefFetcher(alignPanel.av
5263 .getSequenceSelection(),
5264 alignPanel.alignFrame, dassrc)
5265 .fetchDBRefs(false);
5271 fetchr.setToolTipText("<html>"
5272 + JvSwingUtils.wrapTooltip("Retrieve from "
5273 + dbname) + "</html>");
5276 if (++icomp >= mcomp || i == (otherdb.size()))
5278 ifetch.setText(imname + " to '" + sname + "'");
5280 ifetch = new JMenu();
5288 if (comp >= mcomp || dbi >= (dbclasses.length))
5290 dfetch.setText(mname + " to '" + dbclass + "'");
5292 dfetch = new JMenu();
5305 * Left justify the whole alignment.
5308 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5310 AlignmentI al = viewport.getAlignment();
5312 viewport.firePropertyChange("alignment", null, al);
5316 * Right justify the whole alignment.
5319 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5321 AlignmentI al = viewport.getAlignment();
5323 viewport.firePropertyChange("alignment", null, al);
5326 public void setShowSeqFeatures(boolean b)
5328 showSeqFeatures.setSelected(true);
5329 viewport.setShowSequenceFeatures(true);
5336 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5337 * awt.event.ActionEvent)
5340 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5342 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5343 alignPanel.paintAlignment(true);
5350 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5354 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5356 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5357 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5365 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5366 * .event.ActionEvent)
5369 protected void showGroupConservation_actionPerformed(ActionEvent e)
5371 viewport.setShowGroupConservation(showGroupConservation.getState());
5372 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5379 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5380 * .event.ActionEvent)
5383 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5385 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5386 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5393 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5394 * .event.ActionEvent)
5397 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5399 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5400 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5404 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5406 showSequenceLogo.setState(true);
5407 viewport.setShowSequenceLogo(true);
5408 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5409 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5413 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5415 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5422 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5423 * .event.ActionEvent)
5426 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5428 if (viewport.getSelectionGroup() != null)
5430 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
5431 viewport.getSequenceSelection(),
5432 viewport.getAlignmentView(true).getSequenceStrings(
5433 viewport.getGapCharacter()), viewport.getAlignment()
5435 viewport.getAlignment().deleteAllGroups();
5436 viewport.sequenceColours = null;
5437 viewport.setSelectionGroup(null);
5438 // set view properties for each group
5439 for (int g = 0; g < gps.length; g++)
5441 gps[g].setShowNonconserved(viewport.getShowUnconserved());
5442 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
5443 viewport.getAlignment().addGroup(gps[g]);
5444 Color col = new Color((int) (Math.random() * 255),
5445 (int) (Math.random() * 255), (int) (Math.random() * 255));
5446 col = col.brighter();
5447 for (SequenceI s:gps[g].getSequences())
5448 viewport.setSequenceColour(
5452 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5453 alignPanel.updateAnnotation();
5454 alignPanel.paintAlignment(true);
5459 * make the given alignmentPanel the currently selected tab
5461 * @param alignmentPanel
5463 public void setDisplayedView(AlignmentPanel alignmentPanel)
5465 if (!viewport.getSequenceSetId().equals(
5466 alignmentPanel.av.getSequenceSetId()))
5469 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5471 if (tabbedPane != null
5472 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5473 .getSelectedIndex())
5475 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5480 class PrintThread extends Thread
5484 public PrintThread(AlignmentPanel ap)
5489 static PageFormat pf;
5494 PrinterJob printJob = PrinterJob.getPrinterJob();
5498 printJob.setPrintable(ap, pf);
5502 printJob.setPrintable(ap);
5505 if (printJob.printDialog())
5510 } catch (Exception PrintException)
5512 PrintException.printStackTrace();