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.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();
1788 if (Desktop.jalviewClipboard != null)
1790 // dataset is inherited
1791 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1795 // new dataset is constructed
1796 alignment.setDataset(null);
1798 alwidth = alignment.getWidth() + 1;
1802 AlignmentI pastedal = alignment; // preserve pasted alignment object
1803 // Add pasted sequences and dataset into existing alignment.
1804 alignment = viewport.getAlignment();
1805 alwidth = alignment.getWidth() + 1;
1806 // decide if we need to import sequences from an existing dataset
1807 boolean importDs = Desktop.jalviewClipboard != null
1808 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1809 // importDs==true instructs us to copy over new dataset sequences from
1810 // an existing alignment
1811 Vector newDs = (importDs) ? new Vector() : null; // used to create
1812 // minimum dataset set
1814 for (int i = 0; i < sequences.length; i++)
1818 newDs.addElement(null);
1820 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1822 if (importDs && ds != null)
1824 if (!newDs.contains(ds))
1826 newDs.setElementAt(ds, i);
1827 ds = new Sequence(ds);
1828 // update with new dataset sequence
1829 sequences[i].setDatasetSequence(ds);
1833 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1838 // copy and derive new dataset sequence
1839 sequences[i] = sequences[i].deriveSequence();
1840 alignment.getDataset().addSequence(
1841 sequences[i].getDatasetSequence());
1842 // TODO: avoid creation of duplicate dataset sequences with a
1843 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1845 alignment.addSequence(sequences[i]); // merges dataset
1849 newDs.clear(); // tidy up
1851 if (pastedal.getAlignmentAnnotation() != null)
1853 // Add any annotation attached to alignment.
1854 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1855 for (int i = 0; i < alann.length; i++)
1857 annotationAdded = true;
1858 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1860 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1861 newann.padAnnotation(alwidth);
1862 alignment.addAnnotation(newann);
1872 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1873 sequences, 0, alignment.getWidth(), alignment));
1875 // Add any annotations attached to sequences
1876 for (int i = 0; i < sequences.length; i++)
1878 if (sequences[i].getAnnotation() != null)
1880 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1882 annotationAdded = true;
1883 sequences[i].getAnnotation()[a].adjustForAlignment();
1884 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1885 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1890 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1897 // propagate alignment changed.
1898 viewport.setEndSeq(alignment.getHeight());
1899 if (annotationAdded)
1901 // Duplicate sequence annotation in all views.
1902 AlignmentI[] alview = this.getViewAlignments();
1903 for (int i = 0; i < sequences.length; i++)
1905 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1908 for (int avnum = 0; avnum < alview.length; avnum++)
1910 if (alview[avnum] != alignment)
1912 // duplicate in a view other than the one with input focus
1913 int avwidth = alview[avnum].getWidth() + 1;
1914 // this relies on sann being preserved after we
1915 // modify the sequence's annotation array for each duplication
1916 for (int a = 0; a < sann.length; a++)
1918 AlignmentAnnotation newann = new AlignmentAnnotation(
1920 sequences[i].addAlignmentAnnotation(newann);
1921 newann.padAnnotation(avwidth);
1922 alview[avnum].addAnnotation(newann); // annotation was
1923 // duplicated earlier
1924 alview[avnum].setAnnotationIndex(newann, a);
1929 buildSortByAnnotationScoresMenu();
1931 viewport.firePropertyChange("alignment", null,
1932 alignment.getSequences());
1933 if (alignPanels!=null ) {for (AlignmentPanel ap:((Vector<AlignmentPanel>)alignPanels))
1935 ap.validateAnnotationDimensions(false);
1936 }} else { alignPanel.validateAnnotationDimensions(false);}
1941 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1943 String newtitle = new String("Copied sequences");
1945 if (Desktop.jalviewClipboard != null
1946 && Desktop.jalviewClipboard[2] != null)
1948 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1949 for (int i = 0; i < hc.size(); i++)
1951 int[] region = (int[]) hc.elementAt(i);
1952 af.viewport.hideColumns(region[0], region[1]);
1956 // >>>This is a fix for the moment, until a better solution is
1958 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1960 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1962 // TODO: maintain provenance of an alignment, rather than just make the
1963 // title a concatenation of operations.
1966 if (title.startsWith("Copied sequences"))
1972 newtitle = newtitle.concat("- from " + title);
1977 newtitle = new String("Pasted sequences");
1980 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1985 } catch (Exception ex)
1987 ex.printStackTrace();
1988 System.out.println("Exception whilst pasting: " + ex);
1989 // could be anything being pasted in here
2001 protected void cut_actionPerformed(ActionEvent e)
2003 copy_actionPerformed(null);
2004 delete_actionPerformed(null);
2014 protected void delete_actionPerformed(ActionEvent evt)
2017 SequenceGroup sg = viewport.getSelectionGroup();
2023 Vector seqs = new Vector();
2025 for (int i = 0; i < sg.getSize(); i++)
2027 seq = sg.getSequenceAt(i);
2028 seqs.addElement(seq);
2031 // If the cut affects all sequences, remove highlighted columns
2032 if (sg.getSize() == viewport.getAlignment().getHeight())
2034 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2035 sg.getEndRes() + 1);
2038 SequenceI[] cut = new SequenceI[seqs.size()];
2039 for (int i = 0; i < seqs.size(); i++)
2041 cut[i] = (SequenceI) seqs.elementAt(i);
2045 * //ADD HISTORY ITEM
2047 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2048 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2049 viewport.getAlignment()));
2051 viewport.setSelectionGroup(null);
2052 viewport.sendSelection();
2053 viewport.getAlignment().deleteGroup(sg);
2055 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2057 if (viewport.getAlignment().getHeight() < 1)
2061 this.setClosed(true);
2062 } catch (Exception ex)
2075 protected void deleteGroups_actionPerformed(ActionEvent e)
2077 viewport.getAlignment().deleteAllGroups();
2078 viewport.sequenceColours = null;
2079 viewport.setSelectionGroup(null);
2080 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2081 alignPanel.updateAnnotation();
2082 alignPanel.paintAlignment(true);
2092 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2094 SequenceGroup sg = new SequenceGroup();
2096 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2098 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2101 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2102 viewport.setSelectionGroup(sg);
2103 viewport.sendSelection();
2104 alignPanel.paintAlignment(true);
2105 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2115 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2117 if (viewport.cursorMode)
2119 alignPanel.seqPanel.keyboardNo1 = null;
2120 alignPanel.seqPanel.keyboardNo2 = null;
2122 viewport.setSelectionGroup(null);
2123 viewport.getColumnSelection().clear();
2124 viewport.setSelectionGroup(null);
2125 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2126 alignPanel.idPanel.idCanvas.searchResults = null;
2127 alignPanel.paintAlignment(true);
2128 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2129 viewport.sendSelection();
2139 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2141 SequenceGroup sg = viewport.getSelectionGroup();
2145 selectAllSequenceMenuItem_actionPerformed(null);
2150 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2152 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2155 alignPanel.paintAlignment(true);
2156 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2157 viewport.sendSelection();
2161 public void invertColSel_actionPerformed(ActionEvent e)
2163 viewport.invertColumnSelection();
2164 alignPanel.paintAlignment(true);
2165 viewport.sendSelection();
2175 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2177 trimAlignment(true);
2187 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2189 trimAlignment(false);
2192 void trimAlignment(boolean trimLeft)
2194 ColumnSelection colSel = viewport.getColumnSelection();
2197 if (colSel.size() > 0)
2201 column = colSel.getMin();
2205 column = colSel.getMax();
2209 if (viewport.getSelectionGroup() != null)
2211 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2212 viewport.getHiddenRepSequences());
2216 seqs = viewport.getAlignment().getSequencesArray();
2219 TrimRegionCommand trimRegion;
2222 trimRegion = new TrimRegionCommand("Remove Left",
2223 TrimRegionCommand.TRIM_LEFT, seqs, column,
2224 viewport.getAlignment(), viewport.getColumnSelection(),
2225 viewport.getSelectionGroup());
2226 viewport.setStartRes(0);
2230 trimRegion = new TrimRegionCommand("Remove Right",
2231 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2232 viewport.getAlignment(), viewport.getColumnSelection(),
2233 viewport.getSelectionGroup());
2236 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2238 addHistoryItem(trimRegion);
2240 for (SequenceGroup sg :viewport.getAlignment().getGroups())
2242 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2243 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2245 viewport.getAlignment().deleteGroup(sg);
2249 viewport.firePropertyChange("alignment", null, viewport
2250 .getAlignment().getSequences());
2261 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2263 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2266 if (viewport.getSelectionGroup() != null)
2268 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2269 viewport.getHiddenRepSequences());
2270 start = viewport.getSelectionGroup().getStartRes();
2271 end = viewport.getSelectionGroup().getEndRes();
2275 seqs = viewport.getAlignment().getSequencesArray();
2278 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2279 "Remove Gapped Columns", seqs, start, end,
2280 viewport.getAlignment());
2282 addHistoryItem(removeGapCols);
2284 statusBar.setText("Removed " + removeGapCols.getSize()
2285 + " empty columns.");
2287 // This is to maintain viewport position on first residue
2288 // of first sequence
2289 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2290 int startRes = seq.findPosition(viewport.startRes);
2291 // ShiftList shifts;
2292 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2293 // edit.alColumnChanges=shifts.getInverse();
2294 // if (viewport.hasHiddenColumns)
2295 // viewport.getColumnSelection().compensateForEdits(shifts);
2296 viewport.setStartRes(seq.findIndex(startRes) - 1);
2297 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2309 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2311 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2314 if (viewport.getSelectionGroup() != null)
2316 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2317 viewport.getHiddenRepSequences());
2318 start = viewport.getSelectionGroup().getStartRes();
2319 end = viewport.getSelectionGroup().getEndRes();
2323 seqs = viewport.getAlignment().getSequencesArray();
2326 // This is to maintain viewport position on first residue
2327 // of first sequence
2328 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2329 int startRes = seq.findPosition(viewport.startRes);
2331 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2332 viewport.getAlignment()));
2334 viewport.setStartRes(seq.findIndex(startRes) - 1);
2336 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2348 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2350 viewport.setPadGaps(padGapsMenuitem.isSelected());
2351 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2357 // if (justifySeqs>0)
2359 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2372 public void findMenuItem_actionPerformed(ActionEvent e)
2378 public void newView_actionPerformed(ActionEvent e)
2385 * @param copyAnnotation
2386 * if true then duplicate all annnotation, groups and settings
2387 * @return new alignment panel, already displayed.
2389 public AlignmentPanel newView(boolean copyAnnotation)
2391 return newView(null, copyAnnotation);
2397 * title of newly created view
2398 * @return new alignment panel, already displayed.
2400 public AlignmentPanel newView(String viewTitle)
2402 return newView(viewTitle, true);
2408 * title of newly created view
2409 * @param copyAnnotation
2410 * if true then duplicate all annnotation, groups and settings
2411 * @return new alignment panel, already displayed.
2413 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2415 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2417 if (!copyAnnotation)
2419 // just remove all the current annotation except for the automatic stuff
2420 newap.av.getAlignment().deleteAllGroups();
2421 for (AlignmentAnnotation alan : newap.av.getAlignment()
2422 .getAlignmentAnnotation())
2424 if (!alan.autoCalculated)
2426 newap.av.getAlignment().deleteAnnotation(alan);
2432 newap.av.gatherViewsHere = false;
2434 if (viewport.viewName == null)
2436 viewport.viewName = "Original";
2439 newap.av.historyList = viewport.historyList;
2440 newap.av.redoList = viewport.redoList;
2442 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2443 // make sure the new view has a unique name - this is essential for Jalview
2445 boolean addFirstIndex = false;
2446 if (viewTitle == null || viewTitle.trim().length() == 0)
2449 addFirstIndex = true;
2453 index = 1;// we count from 1 if given a specific name
2455 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2456 Vector comps = (Vector) PaintRefresher.components.get(viewport
2457 .getSequenceSetId());
2458 Vector existingNames = new Vector();
2459 for (int i = 0; i < comps.size(); i++)
2461 if (comps.elementAt(i) instanceof AlignmentPanel)
2463 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2464 if (!existingNames.contains(ap.av.viewName))
2466 existingNames.addElement(ap.av.viewName);
2471 while (existingNames.contains(newViewName))
2473 newViewName = viewTitle + " " + (++index);
2476 newap.av.viewName = newViewName;
2478 addAlignmentPanel(newap, true);
2480 if (alignPanels.size() == 2)
2482 viewport.gatherViewsHere = true;
2484 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2489 public void expandViews_actionPerformed(ActionEvent e)
2491 Desktop.instance.explodeViews(this);
2495 public void gatherViews_actionPerformed(ActionEvent e)
2497 Desktop.instance.gatherViews(this);
2507 public void font_actionPerformed(ActionEvent e)
2509 new FontChooser(alignPanel);
2519 protected void seqLimit_actionPerformed(ActionEvent e)
2521 viewport.setShowJVSuffix(seqLimits.isSelected());
2523 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2524 .calculateIdWidth());
2525 alignPanel.paintAlignment(true);
2529 public void idRightAlign_actionPerformed(ActionEvent e)
2531 viewport.rightAlignIds = idRightAlign.isSelected();
2532 alignPanel.paintAlignment(true);
2536 public void centreColumnLabels_actionPerformed(ActionEvent e)
2538 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2539 alignPanel.paintAlignment(true);
2545 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2548 protected void followHighlight_actionPerformed()
2550 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2552 alignPanel.scrollToPosition(
2553 alignPanel.seqPanel.seqCanvas.searchResults, false);
2564 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2566 viewport.setColourText(colourTextMenuItem.isSelected());
2567 alignPanel.paintAlignment(true);
2577 public void wrapMenuItem_actionPerformed(ActionEvent e)
2579 scaleAbove.setVisible(wrapMenuItem.isSelected());
2580 scaleLeft.setVisible(wrapMenuItem.isSelected());
2581 scaleRight.setVisible(wrapMenuItem.isSelected());
2582 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2583 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2587 public void showAllSeqs_actionPerformed(ActionEvent e)
2589 viewport.showAllHiddenSeqs();
2593 public void showAllColumns_actionPerformed(ActionEvent e)
2595 viewport.showAllHiddenColumns();
2600 public void hideSelSequences_actionPerformed(ActionEvent e)
2602 viewport.hideAllSelectedSeqs();
2603 alignPanel.paintAlignment(true);
2607 * called by key handler and the hide all/show all menu items
2612 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2615 boolean hide = false;
2616 SequenceGroup sg = viewport.getSelectionGroup();
2617 if (!toggleSeqs && !toggleCols)
2619 // Hide everything by the current selection - this is a hack - we do the
2620 // invert and then hide
2621 // first check that there will be visible columns after the invert.
2622 if ((viewport.getColumnSelection() != null
2623 && viewport.getColumnSelection().getSelected() != null && viewport
2624 .getColumnSelection().getSelected().size() > 0)
2625 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2628 // now invert the sequence set, if required - empty selection implies
2629 // that no hiding is required.
2632 invertSequenceMenuItem_actionPerformed(null);
2633 sg = viewport.getSelectionGroup();
2637 viewport.expandColSelection(sg, true);
2638 // finally invert the column selection and get the new sequence
2640 invertColSel_actionPerformed(null);
2647 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2649 hideSelSequences_actionPerformed(null);
2652 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2655 showAllSeqs_actionPerformed(null);
2661 if (viewport.getColumnSelection().getSelected().size() > 0)
2663 hideSelColumns_actionPerformed(null);
2666 viewport.setSelectionGroup(sg);
2671 showAllColumns_actionPerformed(null);
2680 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2681 * event.ActionEvent)
2684 public void hideAllButSelection_actionPerformed(ActionEvent e)
2686 toggleHiddenRegions(false, false);
2693 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2697 public void hideAllSelection_actionPerformed(ActionEvent e)
2699 SequenceGroup sg = viewport.getSelectionGroup();
2700 viewport.expandColSelection(sg, false);
2701 viewport.hideAllSelectedSeqs();
2702 viewport.hideSelectedColumns();
2703 alignPanel.paintAlignment(true);
2710 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2714 public void showAllhidden_actionPerformed(ActionEvent e)
2716 viewport.showAllHiddenColumns();
2717 viewport.showAllHiddenSeqs();
2718 alignPanel.paintAlignment(true);
2722 public void hideSelColumns_actionPerformed(ActionEvent e)
2724 viewport.hideSelectedColumns();
2725 alignPanel.paintAlignment(true);
2729 public void hiddenMarkers_actionPerformed(ActionEvent e)
2731 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2742 protected void scaleAbove_actionPerformed(ActionEvent e)
2744 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2745 alignPanel.paintAlignment(true);
2755 protected void scaleLeft_actionPerformed(ActionEvent e)
2757 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2758 alignPanel.paintAlignment(true);
2768 protected void scaleRight_actionPerformed(ActionEvent e)
2770 viewport.setScaleRightWrapped(scaleRight.isSelected());
2771 alignPanel.paintAlignment(true);
2781 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2783 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2784 alignPanel.paintAlignment(true);
2794 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2796 viewport.setShowText(viewTextMenuItem.isSelected());
2797 alignPanel.paintAlignment(true);
2807 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2809 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2810 alignPanel.paintAlignment(true);
2813 public FeatureSettings featureSettings;
2816 public void featureSettings_actionPerformed(ActionEvent e)
2818 if (featureSettings != null)
2820 featureSettings.close();
2821 featureSettings = null;
2823 if (!showSeqFeatures.isSelected())
2825 // make sure features are actually displayed
2826 showSeqFeatures.setSelected(true);
2827 showSeqFeatures_actionPerformed(null);
2829 featureSettings = new FeatureSettings(this);
2833 * Set or clear 'Show Sequence Features'
2839 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2841 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2842 alignPanel.paintAlignment(true);
2843 if (alignPanel.getOverviewPanel() != null)
2845 alignPanel.getOverviewPanel().updateOverviewImage();
2850 * Set or clear 'Show Sequence Features'
2856 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2858 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2860 if (viewport.getShowSequenceFeaturesHeight())
2862 // ensure we're actually displaying features
2863 viewport.setShowSequenceFeatures(true);
2864 showSeqFeatures.setSelected(true);
2866 alignPanel.paintAlignment(true);
2867 if (alignPanel.getOverviewPanel() != null)
2869 alignPanel.getOverviewPanel().updateOverviewImage();
2880 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2882 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2883 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2887 public void alignmentProperties()
2889 JEditorPane editPane = new JEditorPane("text/html", "");
2890 editPane.setEditable(false);
2891 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
2893 editPane.setText("<html>" + contents.toString() + "</html>");
2894 JInternalFrame frame = new JInternalFrame();
2895 frame.getContentPane().add(new JScrollPane(editPane));
2897 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2898 + getTitle(), 500, 400);
2908 public void overviewMenuItem_actionPerformed(ActionEvent e)
2910 if (alignPanel.overviewPanel != null)
2915 JInternalFrame frame = new JInternalFrame();
2916 OverviewPanel overview = new OverviewPanel(alignPanel);
2917 frame.setContentPane(overview);
2918 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2919 frame.getWidth(), frame.getHeight());
2921 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2922 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2925 public void internalFrameClosed(
2926 javax.swing.event.InternalFrameEvent evt)
2928 alignPanel.setOverviewPanel(null);
2932 alignPanel.setOverviewPanel(overview);
2936 public void textColour_actionPerformed(ActionEvent e)
2938 new TextColourChooser().chooseColour(alignPanel, null);
2948 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2960 public void clustalColour_actionPerformed(ActionEvent e)
2962 changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences()));
2972 public void zappoColour_actionPerformed(ActionEvent e)
2974 changeColour(new ZappoColourScheme());
2984 public void taylorColour_actionPerformed(ActionEvent e)
2986 changeColour(new TaylorColourScheme());
2996 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2998 changeColour(new HydrophobicColourScheme());
3008 public void helixColour_actionPerformed(ActionEvent e)
3010 changeColour(new HelixColourScheme());
3020 public void strandColour_actionPerformed(ActionEvent e)
3022 changeColour(new StrandColourScheme());
3032 public void turnColour_actionPerformed(ActionEvent e)
3034 changeColour(new TurnColourScheme());
3044 public void buriedColour_actionPerformed(ActionEvent e)
3046 changeColour(new BuriedColourScheme());
3056 public void nucleotideColour_actionPerformed(ActionEvent e)
3058 changeColour(new NucleotideColourScheme());
3062 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3064 changeColour(new PurinePyrimidineColourScheme());
3068 * public void covariationColour_actionPerformed(ActionEvent e) {
3070 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3074 public void annotationColour_actionPerformed(ActionEvent e)
3076 new AnnotationColourChooser(viewport, alignPanel);
3080 public void rnahelicesColour_actionPerformed(ActionEvent e)
3082 new RNAHelicesColourChooser(viewport, alignPanel);
3092 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3094 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3103 public void changeColour(ColourSchemeI cs)
3105 // TODO: compare with applet and pull up to model method
3110 if (viewport.getAbovePIDThreshold())
3112 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3115 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3117 viewport.setGlobalColourScheme(cs);
3121 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3124 if (viewport.getConservationSelected())
3127 Alignment al = (Alignment) viewport.getAlignment();
3128 Conservation c = new Conservation("All",
3129 ResidueProperties.propHash, 3, al.getSequences(), 0,
3133 c.verdict(false, viewport.getConsPercGaps());
3135 cs.setConservation(c);
3137 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3142 cs.setConservation(null);
3145 cs.setConsensus(viewport.getSequenceConsensusHash());
3148 viewport.setGlobalColourScheme(cs);
3150 if (viewport.getColourAppliesToAllGroups())
3154 for (SequenceGroup sg:viewport.getAlignment().getGroups())
3162 if (cs instanceof ClustalxColourScheme)
3164 sg.cs = new ClustalxColourScheme(sg, viewport
3165 .getHiddenRepSequences());
3167 else if (cs instanceof UserColourScheme)
3169 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3175 sg.cs = cs.getClass().newInstance();
3176 } catch (Exception ex)
3181 if (viewport.getAbovePIDThreshold()
3182 || cs instanceof PIDColourScheme
3183 || cs instanceof Blosum62ColourScheme)
3185 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3187 sg.cs.setConsensus(AAFrequency.calculate(
3188 sg.getSequences(viewport.getHiddenRepSequences()),
3189 sg.getStartRes(), sg.getEndRes() + 1));
3193 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3196 if (viewport.getConservationSelected())
3198 Conservation c = new Conservation("Group",
3199 ResidueProperties.propHash, 3, sg.getSequences(viewport
3200 .getHiddenRepSequences()), sg.getStartRes(),
3201 sg.getEndRes() + 1);
3203 c.verdict(false, viewport.getConsPercGaps());
3204 sg.cs.setConservation(c);
3208 sg.cs.setConservation(null);
3213 if (alignPanel.getOverviewPanel() != null)
3215 alignPanel.getOverviewPanel().updateOverviewImage();
3218 alignPanel.paintAlignment(true);
3228 protected void modifyPID_actionPerformed(ActionEvent e)
3230 if (viewport.getAbovePIDThreshold()
3231 && viewport.getGlobalColourScheme() != null)
3233 SliderPanel.setPIDSliderSource(alignPanel,
3234 viewport.getGlobalColourScheme(), "Background");
3235 SliderPanel.showPIDSlider();
3246 protected void modifyConservation_actionPerformed(ActionEvent e)
3248 if (viewport.getConservationSelected()
3249 && viewport.getGlobalColourScheme() != null)
3251 SliderPanel.setConservationSlider(alignPanel,
3252 viewport.getGlobalColourScheme(), "Background");
3253 SliderPanel.showConservationSlider();
3264 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3266 viewport.setConservationSelected(conservationMenuItem.isSelected());
3268 viewport.setAbovePIDThreshold(false);
3269 abovePIDThreshold.setSelected(false);
3271 changeColour(viewport.getGlobalColourScheme());
3273 modifyConservation_actionPerformed(null);
3283 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3285 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3287 conservationMenuItem.setSelected(false);
3288 viewport.setConservationSelected(false);
3290 changeColour(viewport.getGlobalColourScheme());
3292 modifyPID_actionPerformed(null);
3302 public void userDefinedColour_actionPerformed(ActionEvent e)
3304 if (e.getActionCommand().equals("User Defined..."))
3306 new UserDefinedColours(alignPanel, null);
3310 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3311 .getUserColourSchemes().get(e.getActionCommand());
3317 public void updateUserColourMenu()
3320 Component[] menuItems = colourMenu.getMenuComponents();
3321 int i, iSize = menuItems.length;
3322 for (i = 0; i < iSize; i++)
3324 if (menuItems[i].getName() != null
3325 && menuItems[i].getName().equals("USER_DEFINED"))
3327 colourMenu.remove(menuItems[i]);
3331 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3333 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3334 .getUserColourSchemes().keys();
3336 while (userColours.hasMoreElements())
3338 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3339 userColours.nextElement().toString());
3340 radioItem.setName("USER_DEFINED");
3341 radioItem.addMouseListener(new MouseAdapter()
3344 public void mousePressed(MouseEvent evt)
3346 if (evt.isControlDown()
3347 || SwingUtilities.isRightMouseButton(evt))
3349 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3351 int option = JOptionPane.showInternalConfirmDialog(
3352 jalview.gui.Desktop.desktop,
3353 "Remove from default list?",
3354 "Remove user defined colour",
3355 JOptionPane.YES_NO_OPTION);
3356 if (option == JOptionPane.YES_OPTION)
3358 jalview.gui.UserDefinedColours
3359 .removeColourFromDefaults(radioItem.getText());
3360 colourMenu.remove(radioItem);
3364 radioItem.addActionListener(new ActionListener()
3367 public void actionPerformed(ActionEvent evt)
3369 userDefinedColour_actionPerformed(evt);
3376 radioItem.addActionListener(new ActionListener()
3379 public void actionPerformed(ActionEvent evt)
3381 userDefinedColour_actionPerformed(evt);
3385 colourMenu.insert(radioItem, 15);
3386 colours.add(radioItem);
3398 public void PIDColour_actionPerformed(ActionEvent e)
3400 changeColour(new PIDColourScheme());
3410 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3412 changeColour(new Blosum62ColourScheme());
3422 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3424 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3425 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3426 .getAlignment().getSequenceAt(0), null);
3427 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3428 viewport.getAlignment()));
3429 alignPanel.paintAlignment(true);
3439 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3441 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3442 AlignmentSorter.sortByID(viewport.getAlignment());
3443 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3444 viewport.getAlignment()));
3445 alignPanel.paintAlignment(true);
3455 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3457 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3458 AlignmentSorter.sortByLength(viewport.getAlignment());
3459 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3460 viewport.getAlignment()));
3461 alignPanel.paintAlignment(true);
3471 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3473 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3474 AlignmentSorter.sortByGroup(viewport.getAlignment());
3475 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3476 viewport.getAlignment()));
3478 alignPanel.paintAlignment(true);
3488 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3490 new RedundancyPanel(alignPanel, this);
3500 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3502 if ((viewport.getSelectionGroup() == null)
3503 || (viewport.getSelectionGroup().getSize() < 2))
3505 JOptionPane.showInternalMessageDialog(this,
3506 "You must select at least 2 sequences.", "Invalid Selection",
3507 JOptionPane.WARNING_MESSAGE);
3511 JInternalFrame frame = new JInternalFrame();
3512 frame.setContentPane(new PairwiseAlignPanel(viewport));
3513 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3524 public void PCAMenuItem_actionPerformed(ActionEvent e)
3526 if (((viewport.getSelectionGroup() != null)
3527 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3528 .getSelectionGroup().getSize() > 0))
3529 || (viewport.getAlignment().getHeight() < 4))
3531 JOptionPane.showInternalMessageDialog(this,
3532 "Principal component analysis must take\n"
3533 + "at least 4 input sequences.",
3534 "Sequence selection insufficient",
3535 JOptionPane.WARNING_MESSAGE);
3540 new PCAPanel(alignPanel);
3544 public void autoCalculate_actionPerformed(ActionEvent e)
3546 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3547 if (viewport.autoCalculateConsensus)
3549 viewport.firePropertyChange("alignment", null, viewport
3550 .getAlignment().getSequences());
3555 public void sortByTreeOption_actionPerformed(ActionEvent e)
3557 viewport.sortByTree = sortByTree.isSelected();
3561 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3563 viewport.followSelection = listenToViewSelections.isSelected();
3573 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3575 NewTreePanel("AV", "PID", "Average distance tree using PID");
3585 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3587 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3597 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3599 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3609 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3611 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3624 void NewTreePanel(String type, String pwType, String title)
3628 if (viewport.getSelectionGroup() != null)
3630 if (viewport.getSelectionGroup().getSize() < 3)
3635 "You need to have more than two sequences selected to build a tree!",
3636 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3640 SequenceGroup sg = viewport.getSelectionGroup();
3642 /* Decide if the selection is a column region */
3643 for (SequenceI _s:sg.getSequences())
3645 if (_s.getLength() < sg
3651 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3652 + "Try using the Pad function in the edit menu,\n"
3653 + "or one of the multiple sequence alignment web services.",
3654 "Sequences in selection are not aligned",
3655 JOptionPane.WARNING_MESSAGE);
3661 title = title + " on region";
3662 tp = new TreePanel(alignPanel, type, pwType);
3666 // are the visible sequences aligned?
3667 if (!viewport.getAlignment().isAligned(false))
3672 "The sequences must be aligned before creating a tree.\n"
3673 + "Try using the Pad function in the edit menu,\n"
3674 + "or one of the multiple sequence alignment web services.",
3675 "Sequences not aligned",
3676 JOptionPane.WARNING_MESSAGE);
3681 if (viewport.getAlignment().getHeight() < 2)
3686 tp = new TreePanel(alignPanel, type, pwType);
3691 if (viewport.viewName != null)
3693 title += viewport.viewName + " of ";
3696 title += this.title;
3698 Desktop.addInternalFrame(tp, title, 600, 500);
3709 public void addSortByOrderMenuItem(String title,
3710 final AlignmentOrder order)
3712 final JMenuItem item = new JMenuItem("by " + title);
3714 item.addActionListener(new java.awt.event.ActionListener()
3717 public void actionPerformed(ActionEvent e)
3719 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3721 // TODO: JBPNote - have to map order entries to curent SequenceI
3723 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3725 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3728 alignPanel.paintAlignment(true);
3734 * Add a new sort by annotation score menu item
3737 * the menu to add the option to
3739 * the label used to retrieve scores for each sequence on the
3742 public void addSortByAnnotScoreMenuItem(JMenu sort,
3743 final String scoreLabel)
3745 final JMenuItem item = new JMenuItem(scoreLabel);
3747 item.addActionListener(new java.awt.event.ActionListener()
3750 public void actionPerformed(ActionEvent e)
3752 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3753 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3754 viewport.getAlignment());// ,viewport.getSelectionGroup());
3755 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3756 viewport.getAlignment()));
3757 alignPanel.paintAlignment(true);
3763 * last hash for alignment's annotation array - used to minimise cost of
3766 protected int _annotationScoreVectorHash;
3769 * search the alignment and rebuild the sort by annotation score submenu the
3770 * last alignment annotation vector hash is stored to minimize cost of
3771 * rebuilding in subsequence calls.
3775 public void buildSortByAnnotationScoresMenu()
3777 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3782 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3784 sortByAnnotScore.removeAll();
3785 // almost certainly a quicker way to do this - but we keep it simple
3786 Hashtable scoreSorts = new Hashtable();
3787 AlignmentAnnotation aann[];
3788 for (SequenceI sqa:viewport.getAlignment().getSequences())
3790 aann = sqa.getAnnotation();
3791 for (int i = 0; aann != null && i < aann.length; i++)
3793 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3795 scoreSorts.put(aann[i].label, aann[i].label);
3799 Enumeration labels = scoreSorts.keys();
3800 while (labels.hasMoreElements())
3802 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3803 (String) labels.nextElement());
3805 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3808 _annotationScoreVectorHash = viewport.getAlignment()
3809 .getAlignmentAnnotation().hashCode();
3814 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3815 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3816 * call. Listeners are added to remove the menu item when the treePanel is
3817 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3821 * Displayed tree window.
3823 * SortBy menu item title.
3826 public void buildTreeMenu()
3828 sortByTreeMenu.removeAll();
3830 Vector comps = (Vector) PaintRefresher.components.get(viewport
3831 .getSequenceSetId());
3832 Vector treePanels = new Vector();
3833 int i, iSize = comps.size();
3834 for (i = 0; i < iSize; i++)
3836 if (comps.elementAt(i) instanceof TreePanel)
3838 treePanels.add(comps.elementAt(i));
3842 iSize = treePanels.size();
3846 sortByTreeMenu.setVisible(false);
3850 sortByTreeMenu.setVisible(true);
3852 for (i = 0; i < treePanels.size(); i++)
3854 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3855 final JMenuItem item = new JMenuItem(tp.getTitle());
3856 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3857 item.addActionListener(new java.awt.event.ActionListener()
3860 public void actionPerformed(ActionEvent e)
3862 tp.sortByTree_actionPerformed(null);
3863 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3868 sortByTreeMenu.add(item);
3872 public boolean sortBy(AlignmentOrder alorder, String undoname)
3874 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3875 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3876 if (undoname != null)
3878 addHistoryItem(new OrderCommand(undoname, oldOrder,
3879 viewport.getAlignment()));
3881 alignPanel.paintAlignment(true);
3886 * Work out whether the whole set of sequences or just the selected set will
3887 * be submitted for multiple alignment.
3890 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3892 // Now, check we have enough sequences
3893 AlignmentView msa = null;
3895 if ((viewport.getSelectionGroup() != null)
3896 && (viewport.getSelectionGroup().getSize() > 1))
3898 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3899 // some common interface!
3901 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3902 * SequenceI[sz = seqs.getSize(false)];
3904 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3905 * seqs.getSequenceAt(i); }
3907 msa = viewport.getAlignmentView(true);
3912 * Vector seqs = viewport.getAlignment().getSequences();
3914 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3916 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3917 * seqs.elementAt(i); } }
3919 msa = viewport.getAlignmentView(false);
3925 * Decides what is submitted to a secondary structure prediction service: the
3926 * first sequence in the alignment, or in the current selection, or, if the
3927 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3928 * region or the whole alignment. (where the first sequence in the set is the
3929 * one that the prediction will be for).
3931 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3933 AlignmentView seqs = null;
3935 if ((viewport.getSelectionGroup() != null)
3936 && (viewport.getSelectionGroup().getSize() > 0))
3938 seqs = viewport.getAlignmentView(true);
3942 seqs = viewport.getAlignmentView(false);
3944 // limit sequences - JBPNote in future - could spawn multiple prediction
3946 // TODO: viewport.getAlignment().isAligned is a global state - the local
3947 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3948 if (!viewport.getAlignment().isAligned(false))
3950 seqs.setSequences(new SeqCigar[]
3951 { seqs.getSequences()[0] });
3952 // TODO: if seqs.getSequences().length>1 then should really have warned
3966 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3968 // Pick the tree file
3969 JalviewFileChooser chooser = new JalviewFileChooser(
3970 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3971 chooser.setFileView(new JalviewFileView());
3972 chooser.setDialogTitle("Select a newick-like tree file");
3973 chooser.setToolTipText("Load a tree file");
3975 int value = chooser.showOpenDialog(null);
3977 if (value == JalviewFileChooser.APPROVE_OPTION)
3979 String choice = chooser.getSelectedFile().getPath();
3980 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3981 jalview.io.NewickFile fin = null;
3984 fin = new jalview.io.NewickFile(choice, "File");
3985 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3986 } catch (Exception ex)
3988 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3989 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3990 ex.printStackTrace();
3992 if (fin != null && fin.hasWarningMessage())
3994 JOptionPane.showMessageDialog(Desktop.desktop,
3995 fin.getWarningMessage(), "Possible problem with tree file",
3996 JOptionPane.WARNING_MESSAGE);
4002 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4004 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4007 public TreePanel ShowNewickTree(NewickFile nf, String title)
4009 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4012 public TreePanel ShowNewickTree(NewickFile nf, String title,
4013 AlignmentView input)
4015 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4018 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4019 int h, int x, int y)
4021 return ShowNewickTree(nf, title, null, w, h, x, y);
4025 * Add a treeviewer for the tree extracted from a newick file object to the
4026 * current alignment view
4033 * Associated alignment input data (or null)
4042 * @return TreePanel handle
4044 public TreePanel ShowNewickTree(NewickFile nf, String title,
4045 AlignmentView input, int w, int h, int x, int y)
4047 TreePanel tp = null;
4053 if (nf.getTree() != null)
4055 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4061 tp.setLocation(x, y);
4064 Desktop.addInternalFrame(tp, title, w, h);
4066 } catch (Exception ex)
4068 ex.printStackTrace();
4074 private boolean buildingMenu = false;
4077 * Generates menu items and listener event actions for web service clients
4080 public void BuildWebServiceMenu()
4082 while (buildingMenu)
4086 System.err.println("Waiting for building menu to finish.");
4088 } catch (Exception e)
4093 final AlignFrame me = this;
4094 buildingMenu = true;
4095 new Thread(new Runnable()
4102 System.err.println("Building ws menu again "
4103 + Thread.currentThread());
4104 // TODO: add support for context dependent disabling of services based
4106 // alignment and current selection
4107 // TODO: add additional serviceHandle parameter to specify abstract
4109 // class independently of AbstractName
4110 // TODO: add in rediscovery GUI function to restart discoverer
4111 // TODO: group services by location as well as function and/or
4113 // object broker mechanism.
4114 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4115 final IProgressIndicator af = me;
4116 final JMenu msawsmenu = new JMenu("Alignment");
4117 final JMenu secstrmenu = new JMenu(
4118 "Secondary Structure Prediction");
4119 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4120 final JMenu analymenu = new JMenu("Analysis");
4121 final JMenu dismenu = new JMenu("Protein Disorder");
4122 // JAL-940 - only show secondary structure prediction services from
4123 // the legacy server
4124 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4126 Discoverer.services != null && (Discoverer.services.size() > 0))
4128 // TODO: refactor to allow list of AbstractName/Handler bindings to
4130 // stored or retrieved from elsewhere
4131 Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4132 Vector secstrpr = (Vector) Discoverer.services
4134 Vector seqsrch = null; // (Vector)
4135 // Discoverer.services.get("SeqSearch");
4136 // TODO: move GUI generation code onto service implementation - so a
4137 // client instance attaches itself to the GUI with method call like
4138 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
4142 // Add any Multiple Sequence Alignment Services
4143 for (int i = 0, j = msaws.size(); i < j; i++)
4145 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
4147 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4148 .getServiceClient(sh);
4149 impl.attachWSMenuEntry(msawsmenu, me);
4153 if (secstrpr != null)
4155 // Add any secondary structure prediction services
4156 for (int i = 0, j = secstrpr.size(); i < j; i++)
4158 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4160 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4161 .getServiceClient(sh);
4162 impl.attachWSMenuEntry(secstrmenu, me);
4165 if (seqsrch != null)
4167 // Add any sequence search services
4168 for (int i = 0, j = seqsrch.size(); i < j; i++)
4170 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
4172 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4173 .getServiceClient(sh);
4174 impl.attachWSMenuEntry(seqsrchmenu, me);
4179 // Add all submenus in the order they should appear on the web
4181 wsmenu.add(msawsmenu);
4182 wsmenu.add(secstrmenu);
4183 wsmenu.add(dismenu);
4184 wsmenu.add(analymenu);
4185 // final ArrayList<JMenu> submens=new ArrayList<JMenu>();
4186 // submens.add(msawsmenu);
4187 // submens.add(secstrmenu);
4188 // submens.add(dismenu);
4189 // submens.add(analymenu);
4191 // No search services yet
4192 // wsmenu.add(seqsrchmenu);
4194 javax.swing.SwingUtilities.invokeLater(new Runnable()
4201 webService.removeAll();
4202 // first, add discovered services onto the webservices menu
4203 if (wsmenu.size() > 0)
4205 for (int i = 0, j = wsmenu.size(); i < j; i++)
4207 webService.add(wsmenu.get(i));
4212 webService.add(me.webServiceNoServices);
4214 // TODO: move into separate menu builder class.
4215 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4217 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4218 if (jws2servs != null)
4220 if (jws2servs.hasServices())
4222 jws2servs.attachWSMenuEntry(webService, me);
4224 if (jws2servs.isRunning())
4226 JMenuItem tm = new JMenuItem(
4227 "Still discovering JABA Services");
4228 tm.setEnabled(false);
4234 build_urlServiceMenu(me.webService);
4235 build_fetchdbmenu(webService);
4236 for (JMenu item : wsmenu)
4238 if (item.getItemCount() == 0)
4240 item.setEnabled(false);
4244 item.setEnabled(true);
4247 } catch (Exception e)
4249 Cache.log.debug("Exception during web service menu building process.",e);
4254 } catch (Exception e)
4259 buildingMenu = false;
4266 * construct any groupURL type service menu entries.
4270 private void build_urlServiceMenu(JMenu webService)
4272 // TODO: remove this code when 2.7 is released
4273 // DEBUG - alignmentView
4275 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4276 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4278 * @Override public void actionPerformed(ActionEvent e) {
4279 * jalview.datamodel.AlignmentView
4280 * .testSelectionViews(af.viewport.getAlignment(),
4281 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4283 * }); webService.add(testAlView);
4285 // TODO: refactor to RestClient discoverer and merge menu entries for
4286 // rest-style services with other types of analysis/calculation service
4287 // SHmmr test client - still being implemented.
4288 // DEBUG - alignmentView
4290 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4293 client.attachWSMenuEntry(
4294 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4298 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4300 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4306 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4307 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4308 * getProperty("LAST_DIRECTORY"));
4310 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4311 * to Vamsas file"); chooser.setToolTipText("Export");
4313 * int value = chooser.showSaveDialog(this);
4315 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4316 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4317 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4318 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4321 * prototype of an automatically enabled/disabled analysis function
4324 protected void setShowProductsEnabled()
4326 SequenceI[] selection = viewport.getSequenceSelection();
4327 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4328 viewport.getAlignment().getDataset()))
4330 showProducts.setEnabled(true);
4335 showProducts.setEnabled(false);
4340 * search selection for sequence xRef products and build the show products
4345 * @return true if showProducts menu should be enabled.
4347 public boolean canShowProducts(SequenceI[] selection,
4348 boolean isRegionSelection, Alignment dataset)
4350 boolean showp = false;
4353 showProducts.removeAll();
4354 final boolean dna = viewport.getAlignment().isNucleotide();
4355 final Alignment ds = dataset;
4356 String[] ptypes = (selection == null || selection.length == 0) ? null
4357 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4359 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4360 // selection, dataset, true);
4361 final SequenceI[] sel = selection;
4362 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4365 final boolean isRegSel = isRegionSelection;
4366 final AlignFrame af = this;
4367 final String source = ptypes[t];
4368 JMenuItem xtype = new JMenuItem(ptypes[t]);
4369 xtype.addActionListener(new ActionListener()
4373 public void actionPerformed(ActionEvent e)
4375 // TODO: new thread for this call with vis-delay
4376 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4377 isRegSel, dna, source);
4381 showProducts.add(xtype);
4383 showProducts.setVisible(showp);
4384 showProducts.setEnabled(showp);
4385 } catch (Exception e)
4387 jalview.bin.Cache.log
4388 .warn("canTranslate threw an exception - please report to help@jalview.org",
4395 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4396 boolean isRegSel, boolean dna, String source)
4398 final boolean fisRegSel = isRegSel;
4399 final boolean fdna = dna;
4400 final String fsrc = source;
4401 final AlignFrame ths = this;
4402 final SequenceI[] fsel = sel;
4403 Runnable foo = new Runnable()
4409 final long sttime = System.currentTimeMillis();
4410 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4413 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4417 Alignment prods = CrossRef
4418 .findXrefSequences(fsel, fdna, fsrc, ds);
4421 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4422 for (int s = 0; s < sprods.length; s++)
4424 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4425 if (ds.getSequences() == null
4426 || !ds.getSequences().contains(
4427 sprods[s].getDatasetSequence()))
4428 ds.addSequence(sprods[s].getDatasetSequence());
4429 sprods[s].updatePDBIds();
4431 Alignment al = new Alignment(sprods);
4432 AlignedCodonFrame[] cf = prods.getCodonFrames();
4434 for (int s = 0; cf != null && s < cf.length; s++)
4436 al.addCodonFrame(cf[s]);
4439 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4441 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4442 + " for " + ((fisRegSel) ? "selected region of " : "")
4444 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4449 System.err.println("No Sequences generated for xRef type "
4452 } catch (Exception e)
4454 jalview.bin.Cache.log.error(
4455 "Exception when finding crossreferences", e);
4456 } catch (OutOfMemoryError e)
4458 new OOMWarning("whilst fetching crossreferences", e);
4461 jalview.bin.Cache.log.error("Error when finding crossreferences",
4464 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4469 Thread frunner = new Thread(foo);
4473 public boolean canShowTranslationProducts(SequenceI[] selection,
4474 AlignmentI alignment)
4479 return (jalview.analysis.Dna.canTranslate(selection,
4480 viewport.getViewAsVisibleContigs(true)));
4481 } catch (Exception e)
4483 jalview.bin.Cache.log
4484 .warn("canTranslate threw an exception - please report to help@jalview.org",
4491 public void showProducts_actionPerformed(ActionEvent e)
4493 // /////////////////////////////
4494 // Collect Data to be translated/transferred
4496 SequenceI[] selection = viewport.getSequenceSelection();
4497 AlignmentI al = null;
4500 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4501 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4502 viewport.getAlignment().getDataset());
4503 } catch (Exception ex)
4506 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4513 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4514 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4518 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4519 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4520 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4525 public void showTranslation_actionPerformed(ActionEvent e)
4527 // /////////////////////////////
4528 // Collect Data to be translated/transferred
4530 SequenceI[] selection = viewport.getSequenceSelection();
4531 String[] seqstring = viewport.getViewAsString(true);
4532 AlignmentI al = null;
4535 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4536 viewport.getViewAsVisibleContigs(true), viewport
4537 .getGapCharacter(), viewport.getAlignment()
4538 .getAlignmentAnnotation(), viewport.getAlignment()
4539 .getWidth(), viewport.getAlignment().getDataset());
4540 } catch (Exception ex)
4543 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4550 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4551 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4555 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4556 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4557 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4562 * Try to load a features file onto the alignment.
4565 * contents or path to retrieve file
4567 * access mode of file (see jalview.io.AlignFile)
4568 * @return true if features file was parsed corectly.
4570 public boolean parseFeaturesFile(String file, String type)
4572 boolean featuresFile = false;
4575 featuresFile = new FeaturesFile(file, type).parse(viewport
4576 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4577 .getFeatureRenderer().featureColours, false,
4578 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4579 } catch (Exception ex)
4581 ex.printStackTrace();
4586 viewport.showSequenceFeatures = true;
4587 showSeqFeatures.setSelected(true);
4588 if (alignPanel.seqPanel.seqCanvas.fr != null)
4590 // update the min/max ranges where necessary
4591 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4593 if (featureSettings != null)
4595 featureSettings.setTableData();
4597 alignPanel.paintAlignment(true);
4600 return featuresFile;
4604 public void dragEnter(DropTargetDragEvent evt)
4609 public void dragExit(DropTargetEvent evt)
4614 public void dragOver(DropTargetDragEvent evt)
4619 public void dropActionChanged(DropTargetDragEvent evt)
4624 public void drop(DropTargetDropEvent evt)
4626 Transferable t = evt.getTransferable();
4627 java.util.List files = null;
4631 DataFlavor uriListFlavor = new DataFlavor(
4632 "text/uri-list;class=java.lang.String");
4633 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4635 // Works on Windows and MacOSX
4636 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4637 files = (java.util.List) t
4638 .getTransferData(DataFlavor.javaFileListFlavor);
4640 else if (t.isDataFlavorSupported(uriListFlavor))
4642 // This is used by Unix drag system
4643 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4644 String data = (String) t.getTransferData(uriListFlavor);
4645 files = new java.util.ArrayList(1);
4646 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4647 data, "\r\n"); st.hasMoreTokens();)
4649 String s = st.nextToken();
4650 if (s.startsWith("#"))
4652 // the line is a comment (as per the RFC 2483)
4656 java.net.URI uri = new java.net.URI(s);
4657 // check to see if we can handle this kind of URI
4658 if (uri.getScheme().toLowerCase().startsWith("http"))
4660 files.add(uri.toString());
4664 // otherwise preserve old behaviour: catch all for file objects
4665 java.io.File file = new java.io.File(uri);
4666 files.add(file.toString());
4670 } catch (Exception e)
4672 e.printStackTrace();
4678 // check to see if any of these files have names matching sequences in
4680 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4681 .getAlignment().getSequencesArray());
4683 * Object[] { String,SequenceI}
4685 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4686 ArrayList<String> filesnotmatched = new ArrayList<String>();
4687 for (int i = 0; i < files.size(); i++)
4689 String file = files.get(i).toString();
4691 String protocol = FormatAdapter.checkProtocol(file);
4692 if (protocol == jalview.io.FormatAdapter.FILE)
4694 File fl = new File(file);
4695 pdbfn = fl.getName();
4697 else if (protocol == jalview.io.FormatAdapter.URL)
4699 URL url = new URL(file);
4700 pdbfn = url.getFile();
4702 if (pdbfn.length() > 0)
4704 // attempt to find a match in the alignment
4705 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4706 int l = 0, c = pdbfn.indexOf(".");
4707 while (mtch == null && c != -1)
4712 } while ((c = pdbfn.indexOf(".", l)) > l);
4715 pdbfn = pdbfn.substring(0, l);
4717 mtch = idm.findAllIdMatches(pdbfn);
4724 type = new IdentifyFile().Identify(file, protocol);
4725 } catch (Exception ex)
4731 if (type.equalsIgnoreCase("PDB"))
4733 filesmatched.add(new Object[]
4734 { file, protocol, mtch });
4739 // File wasn't named like one of the sequences or wasn't a PDB file.
4740 filesnotmatched.add(file);
4744 if (filesmatched.size() > 0)
4746 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4750 "Do you want to automatically associate the "
4751 + filesmatched.size()
4752 + " PDB files with sequences in the alignment that have the same name ?",
4753 "Automatically Associate PDB files by name",
4754 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4757 for (Object[] fm : filesmatched)
4759 // try and associate
4760 // TODO: may want to set a standard ID naming formalism for
4761 // associating PDB files which have no IDs.
4762 for (SequenceI toassoc : (SequenceI[]) fm[2])
4764 PDBEntry pe = new AssociatePdbFileWithSeq()
4765 .associatePdbWithSeq((String) fm[0],
4766 (String) fm[1], toassoc, false);
4769 System.err.println("Associated file : "
4770 + ((String) fm[0]) + " with "
4771 + toassoc.getDisplayId(true));
4775 alignPanel.paintAlignment(true);
4779 if (filesnotmatched.size() > 0)
4782 && (Cache.getDefault(
4783 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4786 "<html>Do you want to <em>ignore</em> the "
4787 + filesnotmatched.size()
4788 + " files whose names did not match any sequence IDs ?</html>",
4789 "Ignore unmatched dropped files ?",
4790 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4794 for (String fn : filesnotmatched)
4796 loadJalviewDataFile(fn, null, null, null);
4800 } catch (Exception ex)
4802 ex.printStackTrace();
4808 * Attempt to load a "dropped" file or URL string: First by testing whether
4809 * it's and Annotation file, then a JNet file, and finally a features file. If
4810 * all are false then the user may have dropped an alignment file onto this
4814 * either a filename or a URL string.
4816 public void loadJalviewDataFile(String file, String protocol,
4817 String format, SequenceI assocSeq)
4821 if (protocol == null)
4823 protocol = jalview.io.FormatAdapter.checkProtocol(file);
4825 // if the file isn't identified, or not positively identified as some
4826 // other filetype (PFAM is default unidentified alignment file type) then
4827 // try to parse as annotation.
4828 boolean isAnnotation = (format == null || format
4829 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4830 .readAnnotationFile(viewport.getAlignment(), file, protocol)
4835 // first see if its a T-COFFEE score file
4836 TCoffeeScoreFile tcf = null;
4839 tcf = new TCoffeeScoreFile(file, protocol);
4842 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4844 tcoffeeColour.setEnabled(true);
4845 tcoffeeColour.setSelected(true);
4846 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4847 isAnnotation = true;
4849 .setText("Successfully pasted T-Coffee scores to alignment.");
4853 // some problem - if no warning its probable that the ID matching process didn't work
4854 JOptionPane.showMessageDialog(Desktop.desktop,
4855 tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(),
4856 "Problem reading T-COFFEE score file",
4857 JOptionPane.WARNING_MESSAGE);
4864 } catch (Exception x)
4866 Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
4871 // try to see if its a JNet 'concise' style annotation file *before*
4873 // try to parse it as a features file
4876 format = new IdentifyFile().Identify(file, protocol);
4878 if (format.equalsIgnoreCase("JnetFile"))
4880 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
4882 new JnetAnnotationMaker().add_annotation(predictions,
4883 viewport.getAlignment(), 0, false);
4884 isAnnotation = true;
4889 * if (format.equalsIgnoreCase("PDB")) {
4891 * String pdbfn = ""; // try to match up filename with sequence id
4892 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
4893 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
4894 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4895 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
4896 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4897 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
4898 * // attempt to find a match in the alignment SequenceI mtch =
4899 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4900 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
4901 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
4902 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
4903 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4904 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
4905 * { System.err.println("Associated file : " + file + " with " +
4906 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4907 * TODO: maybe need to load as normal otherwise return; } }
4909 // try to parse it as a features file
4910 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4911 // if it wasn't a features file then we just treat it as a general
4912 // alignment file to load into the current view.
4915 new FileLoader().LoadFile(viewport, file, protocol, format);
4919 alignPanel.paintAlignment(true);
4927 alignPanel.adjustAnnotationHeight();
4928 viewport.updateSequenceIdColours();
4929 buildSortByAnnotationScoresMenu();
4930 alignPanel.paintAlignment(true);
4932 } catch (Exception ex)
4934 ex.printStackTrace();
4939 public void tabSelectionChanged(int index)
4943 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4944 viewport = alignPanel.av;
4945 setMenusFromViewport(viewport);
4950 public void tabbedPane_mousePressed(MouseEvent e)
4952 if (SwingUtilities.isRightMouseButton(e))
4954 String reply = JOptionPane.showInternalInputDialog(this,
4955 "Enter View Name", "Edit View Name",
4956 JOptionPane.QUESTION_MESSAGE);
4960 viewport.viewName = reply;
4961 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4966 public AlignViewport getCurrentView()
4972 * Open the dialog for regex description parsing.
4975 protected void extractScores_actionPerformed(ActionEvent e)
4977 ParseProperties pp = new jalview.analysis.ParseProperties(
4978 viewport.getAlignment());
4979 // TODO: verify regex and introduce GUI dialog for version 2.5
4980 // if (pp.getScoresFromDescription("col", "score column ",
4981 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4983 if (pp.getScoresFromDescription("description column",
4984 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4986 buildSortByAnnotationScoresMenu();
4994 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4998 protected void showDbRefs_actionPerformed(ActionEvent e)
5000 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5006 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5010 protected void showNpFeats_actionPerformed(ActionEvent e)
5012 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5016 * find the viewport amongst the tabs in this alignment frame and close that
5021 public boolean closeView(AlignViewport av)
5025 this.closeMenuItem_actionPerformed(false);
5028 Component[] comp = tabbedPane.getComponents();
5029 for (int i = 0; comp != null && i < comp.length; i++)
5031 if (comp[i] instanceof AlignmentPanel)
5033 if (((AlignmentPanel) comp[i]).av == av)
5036 closeView((AlignmentPanel) comp[i]);
5044 protected void build_fetchdbmenu(JMenu webService)
5046 // Temporary hack - DBRef Fetcher always top level ws entry.
5047 // TODO We probably want to store a sequence database checklist in
5048 // preferences and have checkboxes.. rather than individual sources selected
5050 final JMenu rfetch = new JMenu("Fetch DB References");
5051 rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
5052 webService.add(rfetch);
5054 JMenuItem fetchr = new JMenuItem("Standard Databases");
5055 fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
5056 fetchr.addActionListener(new ActionListener()
5060 public void actionPerformed(ActionEvent e)
5062 new Thread(new Runnable()
5068 new jalview.ws.DBRefFetcher(alignPanel.av
5069 .getSequenceSelection(), alignPanel.alignFrame)
5070 .fetchDBRefs(false);
5078 final AlignFrame me = this;
5079 new Thread(new Runnable()
5084 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5085 .getSequenceFetcherSingleton(me);
5086 javax.swing.SwingUtilities.invokeLater(new Runnable()
5091 String[] dbclasses = sf.getOrderedSupportedSources();
5092 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5093 // jalview.util.QuickSort.sort(otherdb, otherdb);
5094 List<DbSourceProxy> otherdb;
5095 JMenu dfetch = new JMenu();
5096 JMenu ifetch = new JMenu();
5097 JMenuItem fetchr = null;
5098 int comp = 0, icomp = 0, mcomp = 15;
5099 String mname = null;
5101 for (String dbclass : dbclasses)
5103 otherdb = sf.getSourceProxy(dbclass);
5104 // add a single entry for this class, or submenu allowing 'fetch
5106 if (otherdb == null || otherdb.size() < 1)
5110 // List<DbSourceProxy> dbs=otherdb;
5111 // otherdb=new ArrayList<DbSourceProxy>();
5112 // for (DbSourceProxy db:dbs)
5114 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5118 mname = "From " + dbclass;
5120 if (otherdb.size() == 1)
5122 final DbSourceProxy[] dassource = otherdb
5123 .toArray(new DbSourceProxy[0]);
5124 DbSourceProxy src = otherdb.get(0);
5125 fetchr = new JMenuItem(src.getDbSource());
5126 fetchr.addActionListener(new ActionListener()
5130 public void actionPerformed(ActionEvent e)
5132 new Thread(new Runnable()
5138 new jalview.ws.DBRefFetcher(alignPanel.av
5139 .getSequenceSelection(),
5140 alignPanel.alignFrame, dassource)
5141 .fetchDBRefs(false);
5147 fetchr.setToolTipText("<html>"
5148 + JvSwingUtils.wrapTooltip("Retrieve from "
5149 + src.getDbName()) + "<html>");
5155 final DbSourceProxy[] dassource = otherdb
5156 .toArray(new DbSourceProxy[0]);
5158 DbSourceProxy src = otherdb.get(0);
5159 fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
5161 fetchr.addActionListener(new ActionListener()
5164 public void actionPerformed(ActionEvent e)
5166 new Thread(new Runnable()
5172 new jalview.ws.DBRefFetcher(alignPanel.av
5173 .getSequenceSelection(),
5174 alignPanel.alignFrame, dassource)
5175 .fetchDBRefs(false);
5181 fetchr.setToolTipText("<html>"
5182 + JvSwingUtils.wrapTooltip("Retrieve from all "
5183 + otherdb.size() + " sources in "
5184 + src.getDbSource() + "<br>First is :"
5185 + src.getDbName()) + "<html>");
5188 // and then build the rest of the individual menus
5189 ifetch = new JMenu("Sources from " + src.getDbSource());
5191 String imname = null;
5193 for (DbSourceProxy sproxy : otherdb)
5195 String dbname = sproxy.getDbName();
5196 String sname = dbname.length() > 5 ? dbname.substring(0,
5197 5) + "..." : dbname;
5198 String msname = dbname.length() > 10 ? dbname.substring(
5199 0, 10) + "..." : dbname;
5202 imname = "from '" + sname + "'";
5204 fetchr = new JMenuItem(msname);
5205 final DbSourceProxy[] dassrc =
5207 fetchr.addActionListener(new ActionListener()
5211 public void actionPerformed(ActionEvent e)
5213 new Thread(new Runnable()
5219 new jalview.ws.DBRefFetcher(alignPanel.av
5220 .getSequenceSelection(),
5221 alignPanel.alignFrame, dassrc)
5222 .fetchDBRefs(false);
5228 fetchr.setToolTipText("<html>"
5229 + JvSwingUtils.wrapTooltip("Retrieve from "
5230 + dbname) + "</html>");
5233 if (++icomp >= mcomp || i == (otherdb.size()))
5235 ifetch.setText(imname + " to '" + sname + "'");
5237 ifetch = new JMenu();
5245 if (comp >= mcomp || dbi >= (dbclasses.length))
5247 dfetch.setText(mname + " to '" + dbclass + "'");
5249 dfetch = new JMenu();
5262 * Left justify the whole alignment.
5265 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5267 AlignmentI al = viewport.getAlignment();
5269 viewport.firePropertyChange("alignment", null, al);
5273 * Right justify the whole alignment.
5276 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5278 AlignmentI al = viewport.getAlignment();
5280 viewport.firePropertyChange("alignment", null, al);
5283 public void setShowSeqFeatures(boolean b)
5285 showSeqFeatures.setSelected(true);
5286 viewport.setShowSequenceFeatures(true);
5293 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5294 * awt.event.ActionEvent)
5297 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5299 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5300 alignPanel.paintAlignment(true);
5307 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5311 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5313 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5314 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5322 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5323 * .event.ActionEvent)
5326 protected void showGroupConservation_actionPerformed(ActionEvent e)
5328 viewport.setShowGroupConservation(showGroupConservation.getState());
5329 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5336 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5337 * .event.ActionEvent)
5340 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5342 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5343 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5350 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5351 * .event.ActionEvent)
5354 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5356 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5357 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5361 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5363 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5364 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5368 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5370 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5377 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5378 * .event.ActionEvent)
5381 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5383 if (viewport.getSelectionGroup() != null)
5385 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
5386 viewport.getSequenceSelection(),
5387 viewport.getAlignmentView(true).getSequenceStrings(
5388 viewport.getGapCharacter()), viewport.getAlignment()
5390 viewport.getAlignment().deleteAllGroups();
5391 viewport.sequenceColours = null;
5392 viewport.setSelectionGroup(null);
5393 // set view properties for each group
5394 for (int g = 0; g < gps.length; g++)
5396 gps[g].setShowNonconserved(viewport.getShowUnconserved());
5397 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
5398 viewport.getAlignment().addGroup(gps[g]);
5399 Color col = new Color((int) (Math.random() * 255),
5400 (int) (Math.random() * 255), (int) (Math.random() * 255));
5401 col = col.brighter();
5402 for (SequenceI s:gps[g].getSequences())
5403 viewport.setSequenceColour(
5407 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5408 alignPanel.updateAnnotation();
5409 alignPanel.paintAlignment(true);
5414 * make the given alignmentPanel the currently selected tab
5416 * @param alignmentPanel
5418 public void setDisplayedView(AlignmentPanel alignmentPanel)
5420 if (!viewport.getSequenceSetId().equals(
5421 alignmentPanel.av.getSequenceSetId()))
5424 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5426 if (tabbedPane != null
5427 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5428 .getSelectedIndex())
5430 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5435 class PrintThread extends Thread
5439 public PrintThread(AlignmentPanel ap)
5444 static PageFormat pf;
5449 PrinterJob printJob = PrinterJob.getPrinterJob();
5453 printJob.setPrintable(ap, pf);
5457 printJob.setPrintable(ap);
5460 if (printJob.printDialog())
5465 } catch (Exception PrintException)
5467 PrintException.printStackTrace();