2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 The Jalview Authors
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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 import jalview.analysis.AAFrequency;
22 import jalview.analysis.AlignmentSorter;
23 import jalview.analysis.Conservation;
24 import jalview.analysis.CrossRef;
25 import jalview.analysis.NJTree;
26 import jalview.analysis.ParseProperties;
27 import jalview.analysis.SequenceIdMatcher;
28 import jalview.api.AlignViewControllerGuiI;
29 import jalview.api.AlignViewControllerI;
30 import jalview.bin.Cache;
31 import jalview.commands.CommandI;
32 import jalview.commands.EditCommand;
33 import jalview.commands.OrderCommand;
34 import jalview.commands.RemoveGapColCommand;
35 import jalview.commands.RemoveGapsCommand;
36 import jalview.commands.SlideSequencesCommand;
37 import jalview.commands.TrimRegionCommand;
38 import jalview.datamodel.AlignedCodonFrame;
39 import jalview.datamodel.Alignment;
40 import jalview.datamodel.AlignmentAnnotation;
41 import jalview.datamodel.AlignmentI;
42 import jalview.datamodel.AlignmentOrder;
43 import jalview.datamodel.AlignmentView;
44 import jalview.datamodel.ColumnSelection;
45 import jalview.datamodel.PDBEntry;
46 import jalview.datamodel.SeqCigar;
47 import jalview.datamodel.Sequence;
48 import jalview.datamodel.SequenceGroup;
49 import jalview.datamodel.SequenceI;
50 import jalview.io.AlignmentProperties;
51 import jalview.io.AnnotationFile;
52 import jalview.io.FeaturesFile;
53 import jalview.io.FileLoader;
54 import jalview.io.FormatAdapter;
55 import jalview.io.HTMLOutput;
56 import jalview.io.IdentifyFile;
57 import jalview.io.JalviewFileChooser;
58 import jalview.io.JalviewFileView;
59 import jalview.io.JnetAnnotationMaker;
60 import jalview.io.NewickFile;
61 import jalview.io.TCoffeeScoreFile;
62 import jalview.jbgui.GAlignFrame;
63 import jalview.schemes.Blosum62ColourScheme;
64 import jalview.schemes.BuriedColourScheme;
65 import jalview.schemes.ClustalxColourScheme;
66 import jalview.schemes.ColourSchemeI;
67 import jalview.schemes.ColourSchemeProperty;
68 import jalview.schemes.HelixColourScheme;
69 import jalview.schemes.HydrophobicColourScheme;
70 import jalview.schemes.NucleotideColourScheme;
71 import jalview.schemes.PIDColourScheme;
72 import jalview.schemes.PurinePyrimidineColourScheme;
73 import jalview.schemes.RNAHelicesColourChooser;
74 import jalview.schemes.ResidueProperties;
75 import jalview.schemes.StrandColourScheme;
76 import jalview.schemes.TCoffeeColourScheme;
77 import jalview.schemes.TaylorColourScheme;
78 import jalview.schemes.TurnColourScheme;
79 import jalview.schemes.UserColourScheme;
80 import jalview.schemes.ZappoColourScheme;
81 import jalview.util.MessageManager;
82 import jalview.ws.jws1.Discoverer;
83 import jalview.ws.jws2.Jws2Discoverer;
84 import jalview.ws.jws2.jabaws2.Jws2Instance;
85 import jalview.ws.seqfetcher.DbSourceProxy;
87 import java.awt.BorderLayout;
88 import java.awt.Color;
89 import java.awt.Component;
90 import java.awt.GridLayout;
91 import java.awt.Rectangle;
92 import java.awt.Toolkit;
93 import java.awt.datatransfer.Clipboard;
94 import java.awt.datatransfer.DataFlavor;
95 import java.awt.datatransfer.StringSelection;
96 import java.awt.datatransfer.Transferable;
97 import java.awt.dnd.DnDConstants;
98 import java.awt.dnd.DropTargetDragEvent;
99 import java.awt.dnd.DropTargetDropEvent;
100 import java.awt.dnd.DropTargetEvent;
101 import java.awt.dnd.DropTargetListener;
102 import java.awt.event.ActionEvent;
103 import java.awt.event.ActionListener;
104 import java.awt.event.KeyAdapter;
105 import java.awt.event.KeyEvent;
106 import java.awt.event.MouseAdapter;
107 import java.awt.event.MouseEvent;
108 import java.awt.print.PageFormat;
109 import java.awt.print.PrinterJob;
110 import java.beans.PropertyChangeEvent;
113 import java.util.ArrayList;
114 import java.util.Enumeration;
115 import java.util.Hashtable;
116 import java.util.List;
117 import java.util.Vector;
119 import javax.swing.JButton;
120 import javax.swing.JEditorPane;
121 import javax.swing.JInternalFrame;
122 import javax.swing.JLabel;
123 import javax.swing.JLayeredPane;
124 import javax.swing.JMenu;
125 import javax.swing.JMenuItem;
126 import javax.swing.JOptionPane;
127 import javax.swing.JPanel;
128 import javax.swing.JProgressBar;
129 import javax.swing.JRadioButtonMenuItem;
130 import javax.swing.JScrollPane;
131 import javax.swing.SwingUtilities;
137 * @version $Revision$
139 public class AlignFrame extends GAlignFrame implements DropTargetListener,
140 IProgressIndicator, AlignViewControllerGuiI
144 public static final int DEFAULT_WIDTH = 700;
147 public static final int DEFAULT_HEIGHT = 500;
149 public AlignmentPanel alignPanel;
151 AlignViewport viewport;
153 public AlignViewControllerI avc;
156 Vector alignPanels = new Vector();
159 * Last format used to load or save alignments in this window
161 String currentFileFormat = null;
164 * Current filename for this alignment
166 String fileName = null;
169 * Creates a new AlignFrame object with specific width and height.
175 public AlignFrame(AlignmentI al, int width, int height)
177 this(al, null, width, height);
181 * Creates a new AlignFrame object with specific width, height and
187 * @param sequenceSetId
189 public AlignFrame(AlignmentI al, int width, int height,
190 String sequenceSetId)
192 this(al, null, width, height, sequenceSetId);
196 * Creates a new AlignFrame object with specific width, height and
202 * @param sequenceSetId
205 public AlignFrame(AlignmentI al, int width, int height,
206 String sequenceSetId, String viewId)
208 this(al, null, width, height, sequenceSetId, viewId);
212 * new alignment window with hidden columns
216 * @param hiddenColumns
217 * ColumnSelection or null
219 * Width of alignment frame
223 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
224 int width, int height)
226 this(al, hiddenColumns, width, height, null);
230 * Create alignment frame for al with hiddenColumns, a specific width and
231 * height, and specific sequenceId
234 * @param hiddenColumns
237 * @param sequenceSetId
240 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
241 int width, int height, String sequenceSetId)
243 this(al, hiddenColumns, width, height, sequenceSetId, null);
247 * Create alignment frame for al with hiddenColumns, a specific width and
248 * height, and specific sequenceId
251 * @param hiddenColumns
254 * @param sequenceSetId
259 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
260 int width, int height, String sequenceSetId, String viewId)
262 setSize(width, height);
263 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
265 alignPanel = new AlignmentPanel(this, viewport);
267 if (al.getDataset() == null)
272 addAlignmentPanel(alignPanel, true);
277 * Make a new AlignFrame from exisiting alignmentPanels
284 public AlignFrame(AlignmentPanel ap)
288 addAlignmentPanel(ap, false);
293 * initalise the alignframe from the underlying viewport data and the
298 avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
299 if (viewport.getAlignmentConservationAnnotation() == null)
301 BLOSUM62Colour.setEnabled(false);
302 conservationMenuItem.setEnabled(false);
303 modifyConservation.setEnabled(false);
304 // PIDColour.setEnabled(false);
305 // abovePIDThreshold.setEnabled(false);
306 // modifyPID.setEnabled(false);
309 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
312 if (sortby.equals("Id"))
314 sortIDMenuItem_actionPerformed(null);
316 else if (sortby.equals("Pairwise Identity"))
318 sortPairwiseMenuItem_actionPerformed(null);
321 if (Desktop.desktop != null)
323 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
324 addServiceListeners();
325 setGUINucleotide(viewport.getAlignment().isNucleotide());
328 setMenusFromViewport(viewport);
329 buildSortByAnnotationScoresMenu();
330 if (viewport.wrapAlignment)
332 wrapMenuItem_actionPerformed(null);
335 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
337 this.overviewMenuItem_actionPerformed(null);
345 * Change the filename and format for the alignment, and enable the 'reload'
346 * button functionality.
353 public void setFileName(String file, String format)
356 currentFileFormat = format;
357 reload.setEnabled(true);
360 void addKeyListener()
362 addKeyListener(new KeyAdapter()
365 public void keyPressed(KeyEvent evt)
367 if (viewport.cursorMode
368 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
369 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
370 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
371 && Character.isDigit(evt.getKeyChar()))
372 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
374 switch (evt.getKeyCode())
377 case 27: // escape key
378 deselectAllSequenceMenuItem_actionPerformed(null);
382 case KeyEvent.VK_DOWN:
383 if (evt.isAltDown() || !viewport.cursorMode)
384 moveSelectedSequences(false);
385 if (viewport.cursorMode)
386 alignPanel.seqPanel.moveCursor(0, 1);
390 if (evt.isAltDown() || !viewport.cursorMode)
391 moveSelectedSequences(true);
392 if (viewport.cursorMode)
393 alignPanel.seqPanel.moveCursor(0, -1);
397 case KeyEvent.VK_LEFT:
398 if (evt.isAltDown() || !viewport.cursorMode)
399 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
401 alignPanel.seqPanel.moveCursor(-1, 0);
405 case KeyEvent.VK_RIGHT:
406 if (evt.isAltDown() || !viewport.cursorMode)
407 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
409 alignPanel.seqPanel.moveCursor(1, 0);
412 case KeyEvent.VK_SPACE:
413 if (viewport.cursorMode)
415 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
416 || evt.isShiftDown() || evt.isAltDown());
420 // case KeyEvent.VK_A:
421 // if (viewport.cursorMode)
423 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
424 // //System.out.println("A");
428 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
429 * System.out.println("closing bracket"); } break;
431 case KeyEvent.VK_DELETE:
432 case KeyEvent.VK_BACK_SPACE:
433 if (!viewport.cursorMode)
435 cut_actionPerformed(null);
439 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
440 || evt.isShiftDown() || evt.isAltDown());
446 if (viewport.cursorMode)
448 alignPanel.seqPanel.setCursorRow();
452 if (viewport.cursorMode && !evt.isControlDown())
454 alignPanel.seqPanel.setCursorColumn();
458 if (viewport.cursorMode)
460 alignPanel.seqPanel.setCursorPosition();
464 case KeyEvent.VK_ENTER:
465 case KeyEvent.VK_COMMA:
466 if (viewport.cursorMode)
468 alignPanel.seqPanel.setCursorRowAndColumn();
473 if (viewport.cursorMode)
475 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
479 if (viewport.cursorMode)
481 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
486 viewport.cursorMode = !viewport.cursorMode;
487 statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
488 if (viewport.cursorMode)
490 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
491 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
493 alignPanel.seqPanel.seqCanvas.repaint();
499 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
500 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
502 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
504 javax.help.HelpBroker hb = hs.createHelpBroker();
505 hb.setCurrentID("home");
506 hb.setDisplayed(true);
507 } catch (Exception ex)
509 ex.printStackTrace();
514 boolean toggleSeqs = !evt.isControlDown();
515 boolean toggleCols = !evt.isShiftDown();
516 toggleHiddenRegions(toggleSeqs, toggleCols);
519 case KeyEvent.VK_PAGE_UP:
520 if (viewport.wrapAlignment)
522 alignPanel.scrollUp(true);
526 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
527 - viewport.endSeq + viewport.startSeq);
530 case KeyEvent.VK_PAGE_DOWN:
531 if (viewport.wrapAlignment)
533 alignPanel.scrollUp(false);
537 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
538 + viewport.endSeq - viewport.startSeq);
545 public void keyReleased(KeyEvent evt)
547 switch (evt.getKeyCode())
549 case KeyEvent.VK_LEFT:
550 if (evt.isAltDown() || !viewport.cursorMode)
551 viewport.firePropertyChange("alignment", null, viewport
552 .getAlignment().getSequences());
555 case KeyEvent.VK_RIGHT:
556 if (evt.isAltDown() || !viewport.cursorMode)
557 viewport.firePropertyChange("alignment", null, viewport
558 .getAlignment().getSequences());
565 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
567 ap.alignFrame = this;
568 avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
570 alignPanels.addElement(ap);
572 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
574 int aSize = alignPanels.size();
576 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
578 if (aSize == 1 && ap.av.viewName == null)
580 this.getContentPane().add(ap, BorderLayout.CENTER);
586 setInitialTabVisible();
589 expandViews.setEnabled(true);
590 gatherViews.setEnabled(true);
591 tabbedPane.addTab(ap.av.viewName, ap);
593 ap.setVisible(false);
598 if (ap.av.isPadGaps())
600 ap.av.getAlignment().padGaps();
602 ap.av.updateConservation(ap);
603 ap.av.updateConsensus(ap);
604 ap.av.updateStrucConsensus(ap);
608 public void setInitialTabVisible()
610 expandViews.setEnabled(true);
611 gatherViews.setEnabled(true);
612 tabbedPane.setVisible(true);
613 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
614 tabbedPane.addTab(first.av.viewName, first);
615 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
618 public AlignViewport getViewport()
623 /* Set up intrinsic listeners for dynamically generated GUI bits. */
624 private void addServiceListeners()
626 final java.beans.PropertyChangeListener thisListener;
627 Desktop.instance.addJalviewPropertyChangeListener("services",
628 thisListener = new java.beans.PropertyChangeListener()
631 public void propertyChange(PropertyChangeEvent evt)
633 // // System.out.println("Discoverer property change.");
634 // if (evt.getPropertyName().equals("services"))
636 SwingUtilities.invokeLater(new Runnable()
643 .println("Rebuild WS Menu for service change");
644 BuildWebServiceMenu();
651 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
654 public void internalFrameClosed(
655 javax.swing.event.InternalFrameEvent evt)
657 System.out.println("deregistering discoverer listener");
658 Desktop.instance.removeJalviewPropertyChangeListener("services",
660 closeMenuItem_actionPerformed(true);
663 // Finally, build the menu once to get current service state
664 new Thread(new Runnable()
669 BuildWebServiceMenu();
674 public void setGUINucleotide(boolean nucleotide)
676 showTranslation.setVisible(nucleotide);
677 conservationMenuItem.setEnabled(!nucleotide);
678 modifyConservation.setEnabled(!nucleotide);
679 showGroupConservation.setEnabled(!nucleotide);
680 rnahelicesColour.setEnabled(nucleotide);
681 purinePyrimidineColour.setEnabled(nucleotide);
682 // Remember AlignFrame always starts as protein
686 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
691 * set up menus for the currently viewport. This may be called after any
692 * operation that affects the data in the current view (selection changed,
693 * etc) to update the menus to reflect the new state.
695 public void setMenusForViewport()
697 setMenusFromViewport(viewport);
701 * Need to call this method when tabs are selected for multiple views, or when
702 * loading from Jalview2XML.java
707 void setMenusFromViewport(AlignViewport av)
709 padGapsMenuitem.setSelected(av.isPadGaps());
710 colourTextMenuItem.setSelected(av.showColourText);
711 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
712 conservationMenuItem.setSelected(av.getConservationSelected());
713 seqLimits.setSelected(av.getShowJVSuffix());
714 idRightAlign.setSelected(av.rightAlignIds);
715 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
716 renderGapsMenuItem.setSelected(av.renderGaps);
717 wrapMenuItem.setSelected(av.wrapAlignment);
718 scaleAbove.setVisible(av.wrapAlignment);
719 scaleLeft.setVisible(av.wrapAlignment);
720 scaleRight.setVisible(av.wrapAlignment);
721 annotationPanelMenuItem.setState(av.showAnnotation);
722 viewBoxesMenuItem.setSelected(av.showBoxes);
723 viewTextMenuItem.setSelected(av.showText);
724 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
725 showGroupConsensus.setSelected(av.isShowGroupConsensus());
726 showGroupConservation.setSelected(av.isShowGroupConservation());
727 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
728 showSequenceLogo.setSelected(av.isShowSequenceLogo());
729 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
731 setColourSelected(ColourSchemeProperty.getColourName(av
732 .getGlobalColourScheme()));
734 showSeqFeatures.setSelected(av.showSequenceFeatures);
735 hiddenMarkers.setState(av.showHiddenMarkers);
736 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
737 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
738 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
739 autoCalculate.setSelected(av.autoCalculateConsensus);
740 sortByTree.setSelected(av.sortByTree);
741 listenToViewSelections.setSelected(av.followSelection);
742 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
744 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
745 setShowProductsEnabled();
749 // methods for implementing IProgressIndicator
750 // need to refactor to a reusable stub class
751 Hashtable progressBars, progressBarHandlers;
756 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
759 public void setProgressBar(String message, long id)
761 if (progressBars == null)
763 progressBars = new Hashtable();
764 progressBarHandlers = new Hashtable();
767 JPanel progressPanel;
768 Long lId = new Long(id);
769 GridLayout layout = (GridLayout) statusPanel.getLayout();
770 if (progressBars.get(lId) != null)
772 progressPanel = (JPanel) progressBars.get(new Long(id));
773 statusPanel.remove(progressPanel);
774 progressBars.remove(lId);
775 progressPanel = null;
778 statusBar.setText(message);
780 if (progressBarHandlers.contains(lId))
782 progressBarHandlers.remove(lId);
784 layout.setRows(layout.getRows() - 1);
788 progressPanel = new JPanel(new BorderLayout(10, 5));
790 JProgressBar progressBar = new JProgressBar();
791 progressBar.setIndeterminate(true);
793 progressPanel.add(new JLabel(message), BorderLayout.WEST);
794 progressPanel.add(progressBar, BorderLayout.CENTER);
796 layout.setRows(layout.getRows() + 1);
797 statusPanel.add(progressPanel);
799 progressBars.put(lId, progressPanel);
802 // setMenusForViewport();
807 public void registerHandler(final long id,
808 final IProgressIndicatorHandler handler)
810 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
813 "call setProgressBar before registering the progress bar's handler.");
815 progressBarHandlers.put(new Long(id), handler);
816 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
817 if (handler.canCancel())
819 JButton cancel = new JButton(MessageManager.getString("action.cancel"));
820 final IProgressIndicator us = this;
821 cancel.addActionListener(new ActionListener()
825 public void actionPerformed(ActionEvent e)
827 handler.cancelActivity(id);
830 + ((JLabel) progressPanel.getComponent(0))
834 progressPanel.add(cancel, BorderLayout.EAST);
840 * @return true if any progress bars are still active
843 public boolean operationInProgress()
845 if (progressBars != null && progressBars.size() > 0)
853 public void setStatus(String text) {
854 statusBar.setText(text);
857 * Added so Castor Mapping file can obtain Jalview Version
859 public String getVersion()
861 return jalview.bin.Cache.getProperty("VERSION");
864 public FeatureRenderer getFeatureRenderer()
866 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
870 public void fetchSequence_actionPerformed(ActionEvent e)
872 new SequenceFetcher(this);
876 public void addFromFile_actionPerformed(ActionEvent e)
878 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
882 public void reload_actionPerformed(ActionEvent e)
884 if (fileName != null)
886 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
887 // originating file's format
888 // TODO: work out how to recover feature settings for correct view(s) when
890 if (currentFileFormat.equals("Jalview"))
892 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
893 for (int i = 0; i < frames.length; i++)
895 if (frames[i] instanceof AlignFrame && frames[i] != this
896 && ((AlignFrame) frames[i]).fileName != null
897 && ((AlignFrame) frames[i]).fileName.equals(fileName))
901 frames[i].setSelected(true);
902 Desktop.instance.closeAssociatedWindows();
903 } catch (java.beans.PropertyVetoException ex)
909 Desktop.instance.closeAssociatedWindows();
911 FileLoader loader = new FileLoader();
912 String protocol = fileName.startsWith("http:") ? "URL" : "File";
913 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
917 Rectangle bounds = this.getBounds();
919 FileLoader loader = new FileLoader();
920 String protocol = fileName.startsWith("http:") ? "URL" : "File";
921 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
922 protocol, currentFileFormat);
924 newframe.setBounds(bounds);
925 if (featureSettings != null && featureSettings.isShowing())
927 final Rectangle fspos = featureSettings.frame.getBounds();
928 // TODO: need a 'show feature settings' function that takes bounds -
929 // need to refactor Desktop.addFrame
930 newframe.featureSettings_actionPerformed(null);
931 final FeatureSettings nfs = newframe.featureSettings;
932 SwingUtilities.invokeLater(new Runnable()
937 nfs.frame.setBounds(fspos);
940 this.featureSettings.close();
941 this.featureSettings = null;
943 this.closeMenuItem_actionPerformed(true);
949 public void addFromText_actionPerformed(ActionEvent e)
951 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
955 public void addFromURL_actionPerformed(ActionEvent e)
957 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
961 public void save_actionPerformed(ActionEvent e)
964 || (currentFileFormat == null || !jalview.io.FormatAdapter
965 .isValidIOFormat(currentFileFormat, true))
966 || fileName.startsWith("http"))
968 saveAs_actionPerformed(null);
972 saveAlignment(fileName, currentFileFormat);
983 public void saveAs_actionPerformed(ActionEvent e)
985 JalviewFileChooser chooser = new JalviewFileChooser(
986 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
987 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
988 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
989 currentFileFormat, false);
991 chooser.setFileView(new JalviewFileView());
992 chooser.setDialogTitle("Save Alignment to file");
993 chooser.setToolTipText(MessageManager.getString("action.save"));
\r
995 int value = chooser.showSaveDialog(this);
997 if (value == JalviewFileChooser.APPROVE_OPTION)
999 currentFileFormat = chooser.getSelectedFormat();
1000 if (currentFileFormat == null)
1002 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1003 MessageManager.getString("label.select_file_format_before_saving"),
1004 MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE);
1005 value = chooser.showSaveDialog(this);
1009 fileName = chooser.getSelectedFile().getPath();
1011 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1014 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1015 if (currentFileFormat.indexOf(" ") > -1)
1017 currentFileFormat = currentFileFormat.substring(0,
1018 currentFileFormat.indexOf(" "));
1020 saveAlignment(fileName, currentFileFormat);
1024 public boolean saveAlignment(String file, String format)
1026 boolean success = true;
1028 if (format.equalsIgnoreCase("Jalview"))
1030 String shortName = title;
1032 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1034 shortName = shortName.substring(shortName
1035 .lastIndexOf(java.io.File.separatorChar) + 1);
1038 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1040 statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
1046 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1048 warningMessage("Cannot save file " + fileName + " using format "
1049 + format, "Alignment output format not supported");
1050 saveAs_actionPerformed(null);
1051 // JBPNote need to have a raise_gui flag here
1055 String[] omitHidden = null;
1057 if (viewport.hasHiddenColumns())
1059 int reply = JOptionPane
1060 .showInternalConfirmDialog(
1062 MessageManager.getString("label.alignment_contains_hidden_columns"),
1063 MessageManager.getString("action.save_omit_hidden_columns"),
1064 JOptionPane.YES_NO_OPTION,
1065 JOptionPane.QUESTION_MESSAGE);
1067 if (reply == JOptionPane.YES_OPTION)
1069 omitHidden = viewport.getViewAsString(false);
1072 FormatAdapter f = new FormatAdapter();
1073 String output = f.formatSequences(format,
1074 viewport.getAlignment(), // class cast exceptions will
1075 // occur in the distant future
1076 omitHidden, f.getCacheSuffixDefault(format),
1077 viewport.getColumnSelection());
1087 java.io.PrintWriter out = new java.io.PrintWriter(
1088 new java.io.FileWriter(file));
1092 this.setTitle(file);
1093 statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
1094 } catch (Exception ex)
1097 ex.printStackTrace();
1104 JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}),
1105 MessageManager.getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE);
1111 private void warningMessage(String warning, String title)
1113 if (new jalview.util.Platform().isHeadless())
1115 System.err.println("Warning: " + title + "\nWarning: " + warning);
1120 JOptionPane.showInternalMessageDialog(this, warning, title,
1121 JOptionPane.WARNING_MESSAGE);
1133 protected void outputText_actionPerformed(ActionEvent e)
1135 String[] omitHidden = null;
1137 if (viewport.hasHiddenColumns())
1139 int reply = JOptionPane
1140 .showInternalConfirmDialog(
1142 MessageManager.getString("label.alignment_contains_hidden_columns"),
1143 MessageManager.getString("action.save_omit_hidden_columns"),
1144 JOptionPane.YES_NO_OPTION,
1145 JOptionPane.QUESTION_MESSAGE);
1147 if (reply == JOptionPane.YES_OPTION)
1149 omitHidden = viewport.getViewAsString(false);
1153 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1154 cap.setForInput(null);
1158 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1159 viewport.getAlignment(), omitHidden,
1160 viewport.getColumnSelection()));
1161 Desktop.addInternalFrame(cap,
1162 MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);
\r
1163 } catch (OutOfMemoryError oom)
1165 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1178 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1180 new HTMLOutput(alignPanel,
1181 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1182 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1185 public void createImageMap(File file, String image)
1187 alignPanel.makePNGImageMap(file, image);
1197 public void createPNG(File f)
1199 alignPanel.makePNG(f);
1209 public void createEPS(File f)
1211 alignPanel.makeEPS(f);
1215 public void pageSetup_actionPerformed(ActionEvent e)
1217 PrinterJob printJob = PrinterJob.getPrinterJob();
1218 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1228 public void printMenuItem_actionPerformed(ActionEvent e)
1230 // Putting in a thread avoids Swing painting problems
1231 PrintThread thread = new PrintThread(alignPanel);
1236 public void exportFeatures_actionPerformed(ActionEvent e)
1238 new AnnotationExporter().exportFeatures(alignPanel);
1242 public void exportAnnotations_actionPerformed(ActionEvent e)
1244 new AnnotationExporter().exportAnnotations(alignPanel,
1245 viewport.showAnnotation ? viewport.getAlignment()
1246 .getAlignmentAnnotation() : null, viewport
1247 .getAlignment().getGroups(), ((Alignment) viewport
1248 .getAlignment()).alignmentProperties);
1252 public void associatedData_actionPerformed(ActionEvent e)
1254 // Pick the tree file
1255 JalviewFileChooser chooser = new JalviewFileChooser(
1256 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1257 chooser.setFileView(new JalviewFileView());
1258 chooser.setDialogTitle(MessageManager.getString("label.load_jalview_annotations"));
\r
1259 chooser.setToolTipText(MessageManager.getString("label.load_jalview_annotations"));
\r
1261 int value = chooser.showOpenDialog(null);
1263 if (value == JalviewFileChooser.APPROVE_OPTION)
1265 String choice = chooser.getSelectedFile().getPath();
1266 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1267 loadJalviewDataFile(choice, null, null, null);
1273 * Close the current view or all views in the alignment frame. If the frame
1274 * only contains one view then the alignment will be removed from memory.
1276 * @param closeAllTabs
1279 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1281 if (alignPanels != null && alignPanels.size() < 2)
1283 closeAllTabs = true;
1288 if (alignPanels != null)
1292 if (this.isClosed())
1294 // really close all the windows - otherwise wait till
1295 // setClosed(true) is called
1296 for (int i = 0; i < alignPanels.size(); i++)
1298 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1305 closeView(alignPanel);
1311 this.setClosed(true);
1313 } catch (Exception ex)
1315 ex.printStackTrace();
1320 * close alignPanel2 and shuffle tabs appropriately.
1322 * @param alignPanel2
1324 public void closeView(AlignmentPanel alignPanel2)
1326 int index = tabbedPane.getSelectedIndex();
1327 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1328 alignPanels.removeElement(alignPanel2);
1330 // if (viewport == alignPanel2.av)
1334 alignPanel2.closePanel();
1337 tabbedPane.removeTabAt(closedindex);
1338 tabbedPane.validate();
1340 if (index > closedindex || index == tabbedPane.getTabCount())
1342 // modify currently selected tab index if necessary.
1346 this.tabSelectionChanged(index);
1352 void updateEditMenuBar()
1355 if (viewport.historyList.size() > 0)
1357 undoMenuItem.setEnabled(true);
1358 CommandI command = (CommandI) viewport.historyList.peek();
1359 undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
1363 undoMenuItem.setEnabled(false);
1364 undoMenuItem.setText(MessageManager.getString("action.undo"));
1367 if (viewport.redoList.size() > 0)
1369 redoMenuItem.setEnabled(true);
1371 CommandI command = (CommandI) viewport.redoList.peek();
1372 redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
1376 redoMenuItem.setEnabled(false);
1377 redoMenuItem.setText(MessageManager.getString("action.redo"));
1381 public void addHistoryItem(CommandI command)
1383 if (command.getSize() > 0)
1385 viewport.historyList.push(command);
1386 viewport.redoList.clear();
1387 updateEditMenuBar();
1388 viewport.updateHiddenColumns();
1389 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1390 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1391 // viewport.getColumnSelection()
1392 // .getHiddenColumns().size() > 0);
1398 * @return alignment objects for all views
1400 AlignmentI[] getViewAlignments()
1402 if (alignPanels != null)
1404 Enumeration e = alignPanels.elements();
1405 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1406 for (int i = 0; e.hasMoreElements(); i++)
1408 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1412 if (viewport != null)
1414 return new AlignmentI[]
1415 { viewport.getAlignment() };
1427 protected void undoMenuItem_actionPerformed(ActionEvent e)
1429 if (viewport.historyList.empty())
1431 CommandI command = (CommandI) viewport.historyList.pop();
1432 viewport.redoList.push(command);
1433 command.undoCommand(getViewAlignments());
1435 AlignViewport originalSource = getOriginatingSource(command);
1436 updateEditMenuBar();
1438 if (originalSource != null)
1440 if (originalSource != viewport)
1443 .warn("Implementation worry: mismatch of viewport origin for undo");
1445 originalSource.updateHiddenColumns();
1446 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1448 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1449 // viewport.getColumnSelection()
1450 // .getHiddenColumns().size() > 0);
1451 originalSource.firePropertyChange("alignment", null, originalSource
1452 .getAlignment().getSequences());
1463 protected void redoMenuItem_actionPerformed(ActionEvent e)
1465 if (viewport.redoList.size() < 1)
1470 CommandI command = (CommandI) viewport.redoList.pop();
1471 viewport.historyList.push(command);
1472 command.doCommand(getViewAlignments());
1474 AlignViewport originalSource = getOriginatingSource(command);
1475 updateEditMenuBar();
1477 if (originalSource != null)
1480 if (originalSource != viewport)
1483 .warn("Implementation worry: mismatch of viewport origin for redo");
1485 originalSource.updateHiddenColumns();
1486 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1488 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1489 // viewport.getColumnSelection()
1490 // .getHiddenColumns().size() > 0);
1491 originalSource.firePropertyChange("alignment", null, originalSource
1492 .getAlignment().getSequences());
1496 AlignViewport getOriginatingSource(CommandI command)
1498 AlignViewport originalSource = null;
1499 // For sequence removal and addition, we need to fire
1500 // the property change event FROM the viewport where the
1501 // original alignment was altered
1502 AlignmentI al = null;
1503 if (command instanceof EditCommand)
1505 EditCommand editCommand = (EditCommand) command;
1506 al = editCommand.getAlignment();
1507 Vector comps = (Vector) PaintRefresher.components.get(viewport
1508 .getSequenceSetId());
1510 for (int i = 0; i < comps.size(); i++)
1512 if (comps.elementAt(i) instanceof AlignmentPanel)
1514 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1516 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1523 if (originalSource == null)
1525 // The original view is closed, we must validate
1526 // the current view against the closed view first
1529 PaintRefresher.validateSequences(al, viewport.getAlignment());
1532 originalSource = viewport;
1535 return originalSource;
1544 public void moveSelectedSequences(boolean up)
1546 SequenceGroup sg = viewport.getSelectionGroup();
1552 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1553 viewport.getHiddenRepSequences(), up);
1554 alignPanel.paintAlignment(true);
1557 synchronized void slideSequences(boolean right, int size)
1559 List<SequenceI> sg = new Vector();
1560 if (viewport.cursorMode)
1562 sg.add(viewport.getAlignment().getSequenceAt(
1563 alignPanel.seqPanel.seqCanvas.cursorY));
1565 else if (viewport.getSelectionGroup() != null
1566 && viewport.getSelectionGroup().getSize() != viewport
1567 .getAlignment().getHeight())
1569 sg = viewport.getSelectionGroup().getSequences(
1570 viewport.getHiddenRepSequences());
1578 Vector invertGroup = new Vector();
1580 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1582 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1583 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1586 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1588 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1589 for (int i = 0; i < invertGroup.size(); i++)
1590 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1592 SlideSequencesCommand ssc;
1594 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1595 size, viewport.getGapCharacter());
1597 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1598 size, viewport.getGapCharacter());
1600 int groupAdjustment = 0;
1601 if (ssc.getGapsInsertedBegin() && right)
1603 if (viewport.cursorMode)
1604 alignPanel.seqPanel.moveCursor(size, 0);
1606 groupAdjustment = size;
1608 else if (!ssc.getGapsInsertedBegin() && !right)
1610 if (viewport.cursorMode)
1611 alignPanel.seqPanel.moveCursor(-size, 0);
1613 groupAdjustment = -size;
1616 if (groupAdjustment != 0)
1618 viewport.getSelectionGroup().setStartRes(
1619 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1620 viewport.getSelectionGroup().setEndRes(
1621 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1624 boolean appendHistoryItem = false;
1625 if (viewport.historyList != null && viewport.historyList.size() > 0
1626 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1628 appendHistoryItem = ssc
1629 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1633 if (!appendHistoryItem)
1634 addHistoryItem(ssc);
1646 protected void copy_actionPerformed(ActionEvent e)
1649 if (viewport.getSelectionGroup() == null)
1653 // TODO: preserve the ordering of displayed alignment annotation in any
1654 // internal paste (particularly sequence associated annotation)
1655 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1656 String[] omitHidden = null;
1658 if (viewport.hasHiddenColumns())
1660 omitHidden = viewport.getViewAsString(true);
1663 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1666 StringSelection ss = new StringSelection(output);
1670 jalview.gui.Desktop.internalCopy = true;
1671 // Its really worth setting the clipboard contents
1672 // to empty before setting the large StringSelection!!
1673 Toolkit.getDefaultToolkit().getSystemClipboard()
1674 .setContents(new StringSelection(""), null);
1676 Toolkit.getDefaultToolkit().getSystemClipboard()
1677 .setContents(ss, Desktop.instance);
1678 } catch (OutOfMemoryError er)
1680 new OOMWarning("copying region", er);
1684 Vector hiddenColumns = null;
1685 if (viewport.hasHiddenColumns())
1687 hiddenColumns = new Vector();
1688 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1689 .getSelectionGroup().getEndRes();
1690 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1693 int[] region = (int[]) viewport.getColumnSelection()
1694 .getHiddenColumns().elementAt(i);
1695 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1697 hiddenColumns.addElement(new int[]
1698 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1703 Desktop.jalviewClipboard = new Object[]
1704 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1705 statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()}));
1715 protected void pasteNew_actionPerformed(ActionEvent e)
1727 protected void pasteThis_actionPerformed(ActionEvent e)
1733 * Paste contents of Jalview clipboard
1735 * @param newAlignment
1736 * true to paste to a new alignment, otherwise add to this.
1738 void paste(boolean newAlignment)
1740 boolean externalPaste = true;
1743 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1744 Transferable contents = c.getContents(this);
1746 if (contents == null)
1754 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1755 if (str.length() < 1)
1760 format = new IdentifyFile().Identify(str, "Paste");
1762 } catch (OutOfMemoryError er)
1764 new OOMWarning("Out of memory pasting sequences!!", er);
1768 SequenceI[] sequences;
1769 boolean annotationAdded = false;
1770 AlignmentI alignment = null;
1772 if (Desktop.jalviewClipboard != null)
1774 // The clipboard was filled from within Jalview, we must use the
1776 // And dataset from the copied alignment
1777 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1778 // be doubly sure that we create *new* sequence objects.
1779 sequences = new SequenceI[newseq.length];
1780 for (int i = 0; i < newseq.length; i++)
1782 sequences[i] = new Sequence(newseq[i]);
1784 alignment = new Alignment(sequences);
1785 externalPaste = false;
1789 // parse the clipboard as an alignment.
1790 alignment = new FormatAdapter().readFile(str, "Paste", format);
1791 sequences = alignment.getSequencesArray();
1795 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1801 if (Desktop.jalviewClipboard != null)
1803 // dataset is inherited
1804 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1808 // new dataset is constructed
1809 alignment.setDataset(null);
1811 alwidth = alignment.getWidth() + 1;
1815 AlignmentI pastedal = alignment; // preserve pasted alignment object
1816 // Add pasted sequences and dataset into existing alignment.
1817 alignment = viewport.getAlignment();
1818 alwidth = alignment.getWidth() + 1;
1819 // decide if we need to import sequences from an existing dataset
1820 boolean importDs = Desktop.jalviewClipboard != null
1821 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1822 // importDs==true instructs us to copy over new dataset sequences from
1823 // an existing alignment
1824 Vector newDs = (importDs) ? new Vector() : null; // used to create
1825 // minimum dataset set
1827 for (int i = 0; i < sequences.length; i++)
1831 newDs.addElement(null);
1833 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1835 if (importDs && ds != null)
1837 if (!newDs.contains(ds))
1839 newDs.setElementAt(ds, i);
1840 ds = new Sequence(ds);
1841 // update with new dataset sequence
1842 sequences[i].setDatasetSequence(ds);
1846 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1851 // copy and derive new dataset sequence
1852 sequences[i] = sequences[i].deriveSequence();
1853 alignment.getDataset().addSequence(
1854 sequences[i].getDatasetSequence());
1855 // TODO: avoid creation of duplicate dataset sequences with a
1856 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1858 alignment.addSequence(sequences[i]); // merges dataset
1862 newDs.clear(); // tidy up
1864 if (alignment.getAlignmentAnnotation() != null)
1866 for (AlignmentAnnotation alan : alignment
1867 .getAlignmentAnnotation())
1869 if (alan.graphGroup > fgroup)
1871 fgroup = alan.graphGroup;
1875 if (pastedal.getAlignmentAnnotation() != null)
1877 // Add any annotation attached to alignment.
1878 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1879 for (int i = 0; i < alann.length; i++)
1881 annotationAdded = true;
1882 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1884 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1885 if (newann.graphGroup > -1)
1887 if (newGraphGroups.size() <= newann.graphGroup
1888 || newGraphGroups.get(newann.graphGroup) == null)
1890 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1892 newGraphGroups.add(q, null);
1894 newGraphGroups.set(newann.graphGroup, new Integer(
1897 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1901 newann.padAnnotation(alwidth);
1902 alignment.addAnnotation(newann);
1912 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1913 sequences, 0, alignment.getWidth(), alignment));
1915 // Add any annotations attached to sequences
1916 for (int i = 0; i < sequences.length; i++)
1918 if (sequences[i].getAnnotation() != null)
1920 AlignmentAnnotation newann;
1921 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1923 annotationAdded = true;
1924 newann = sequences[i].getAnnotation()[a];
1925 newann.adjustForAlignment();
1926 newann.padAnnotation(alwidth);
1927 if (newann.graphGroup > -1)
1929 if (newann.graphGroup > -1)
1931 if (newGraphGroups.size() <= newann.graphGroup
1932 || newGraphGroups.get(newann.graphGroup) == null)
1934 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1936 newGraphGroups.add(q, null);
1938 newGraphGroups.set(newann.graphGroup, new Integer(
1941 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1945 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1950 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1957 // propagate alignment changed.
1958 viewport.setEndSeq(alignment.getHeight());
1959 if (annotationAdded)
1961 // Duplicate sequence annotation in all views.
1962 AlignmentI[] alview = this.getViewAlignments();
1963 for (int i = 0; i < sequences.length; i++)
1965 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1968 for (int avnum = 0; avnum < alview.length; avnum++)
1970 if (alview[avnum] != alignment)
1972 // duplicate in a view other than the one with input focus
1973 int avwidth = alview[avnum].getWidth() + 1;
1974 // this relies on sann being preserved after we
1975 // modify the sequence's annotation array for each duplication
1976 for (int a = 0; a < sann.length; a++)
1978 AlignmentAnnotation newann = new AlignmentAnnotation(
1980 sequences[i].addAlignmentAnnotation(newann);
1981 newann.padAnnotation(avwidth);
1982 alview[avnum].addAnnotation(newann); // annotation was
1983 // duplicated earlier
1984 // TODO JAL-1145 graphGroups are not updated for sequence
1985 // annotation added to several views. This may cause
1987 alview[avnum].setAnnotationIndex(newann, a);
1992 buildSortByAnnotationScoresMenu();
1994 viewport.firePropertyChange("alignment", null,
1995 alignment.getSequences());
1996 if (alignPanels != null)
1998 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2000 ap.validateAnnotationDimensions(false);
2005 alignPanel.validateAnnotationDimensions(false);
2011 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2013 String newtitle = new String("Copied sequences");
2015 if (Desktop.jalviewClipboard != null
2016 && Desktop.jalviewClipboard[2] != null)
2018 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2019 for (int i = 0; i < hc.size(); i++)
2021 int[] region = (int[]) hc.elementAt(i);
2022 af.viewport.hideColumns(region[0], region[1]);
2026 // >>>This is a fix for the moment, until a better solution is
2028 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2030 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2032 // TODO: maintain provenance of an alignment, rather than just make the
2033 // title a concatenation of operations.
2036 if (title.startsWith("Copied sequences"))
2042 newtitle = newtitle.concat("- from " + title);
2047 newtitle = new String("Pasted sequences");
2050 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2055 } catch (Exception ex)
2057 ex.printStackTrace();
2058 System.out.println("Exception whilst pasting: " + ex);
2059 // could be anything being pasted in here
2071 protected void cut_actionPerformed(ActionEvent e)
2073 copy_actionPerformed(null);
2074 delete_actionPerformed(null);
2084 protected void delete_actionPerformed(ActionEvent evt)
2087 SequenceGroup sg = viewport.getSelectionGroup();
2093 Vector seqs = new Vector();
2095 for (int i = 0; i < sg.getSize(); i++)
2097 seq = sg.getSequenceAt(i);
2098 seqs.addElement(seq);
2101 // If the cut affects all sequences, remove highlighted columns
2102 if (sg.getSize() == viewport.getAlignment().getHeight())
2104 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2105 sg.getEndRes() + 1);
2108 SequenceI[] cut = new SequenceI[seqs.size()];
2109 for (int i = 0; i < seqs.size(); i++)
2111 cut[i] = (SequenceI) seqs.elementAt(i);
2115 * //ADD HISTORY ITEM
2117 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2118 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2119 viewport.getAlignment()));
2121 viewport.setSelectionGroup(null);
2122 viewport.sendSelection();
2123 viewport.getAlignment().deleteGroup(sg);
2125 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2127 if (viewport.getAlignment().getHeight() < 1)
2131 this.setClosed(true);
2132 } catch (Exception ex)
2145 protected void deleteGroups_actionPerformed(ActionEvent e)
2147 if (avc.deleteGroups()) {
2148 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2149 alignPanel.updateAnnotation();
2150 alignPanel.paintAlignment(true);
2161 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2163 SequenceGroup sg = new SequenceGroup();
2165 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2167 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2170 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2171 viewport.setSelectionGroup(sg);
2172 viewport.sendSelection();
2173 alignPanel.paintAlignment(true);
2174 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2184 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2186 if (viewport.cursorMode)
2188 alignPanel.seqPanel.keyboardNo1 = null;
2189 alignPanel.seqPanel.keyboardNo2 = null;
2191 viewport.setSelectionGroup(null);
2192 viewport.getColumnSelection().clear();
2193 viewport.setSelectionGroup(null);
2194 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2195 alignPanel.idPanel.idCanvas.searchResults = null;
2196 alignPanel.paintAlignment(true);
2197 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2198 viewport.sendSelection();
2208 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2210 SequenceGroup sg = viewport.getSelectionGroup();
2214 selectAllSequenceMenuItem_actionPerformed(null);
2219 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2221 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2224 alignPanel.paintAlignment(true);
2225 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2226 viewport.sendSelection();
2230 public void invertColSel_actionPerformed(ActionEvent e)
2232 viewport.invertColumnSelection();
2233 alignPanel.paintAlignment(true);
2234 viewport.sendSelection();
2244 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2246 trimAlignment(true);
2256 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2258 trimAlignment(false);
2261 void trimAlignment(boolean trimLeft)
2263 ColumnSelection colSel = viewport.getColumnSelection();
2266 if (colSel.size() > 0)
2270 column = colSel.getMin();
2274 column = colSel.getMax();
2278 if (viewport.getSelectionGroup() != null)
2280 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2281 viewport.getHiddenRepSequences());
2285 seqs = viewport.getAlignment().getSequencesArray();
2288 TrimRegionCommand trimRegion;
2291 trimRegion = new TrimRegionCommand("Remove Left",
2292 TrimRegionCommand.TRIM_LEFT, seqs, column,
2293 viewport.getAlignment(), viewport.getColumnSelection(),
2294 viewport.getSelectionGroup());
2295 viewport.setStartRes(0);
2299 trimRegion = new TrimRegionCommand("Remove Right",
2300 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2301 viewport.getAlignment(), viewport.getColumnSelection(),
2302 viewport.getSelectionGroup());
2305 statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
2307 addHistoryItem(trimRegion);
2309 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2311 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2312 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2314 viewport.getAlignment().deleteGroup(sg);
2318 viewport.firePropertyChange("alignment", null, viewport
2319 .getAlignment().getSequences());
2330 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2332 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2335 if (viewport.getSelectionGroup() != null)
2337 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2338 viewport.getHiddenRepSequences());
2339 start = viewport.getSelectionGroup().getStartRes();
2340 end = viewport.getSelectionGroup().getEndRes();
2344 seqs = viewport.getAlignment().getSequencesArray();
2347 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2348 "Remove Gapped Columns", seqs, start, end,
2349 viewport.getAlignment());
2351 addHistoryItem(removeGapCols);
2353 statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
2355 // This is to maintain viewport position on first residue
2356 // of first sequence
2357 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2358 int startRes = seq.findPosition(viewport.startRes);
2359 // ShiftList shifts;
2360 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2361 // edit.alColumnChanges=shifts.getInverse();
2362 // if (viewport.hasHiddenColumns)
2363 // viewport.getColumnSelection().compensateForEdits(shifts);
2364 viewport.setStartRes(seq.findIndex(startRes) - 1);
2365 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2377 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2379 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2382 if (viewport.getSelectionGroup() != null)
2384 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2385 viewport.getHiddenRepSequences());
2386 start = viewport.getSelectionGroup().getStartRes();
2387 end = viewport.getSelectionGroup().getEndRes();
2391 seqs = viewport.getAlignment().getSequencesArray();
2394 // This is to maintain viewport position on first residue
2395 // of first sequence
2396 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2397 int startRes = seq.findPosition(viewport.startRes);
2399 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2400 viewport.getAlignment()));
2402 viewport.setStartRes(seq.findIndex(startRes) - 1);
2404 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2416 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2418 viewport.setPadGaps(padGapsMenuitem.isSelected());
2419 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2425 // if (justifySeqs>0)
2427 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2440 public void findMenuItem_actionPerformed(ActionEvent e)
2446 public void newView_actionPerformed(ActionEvent e)
2453 * @param copyAnnotation
2454 * if true then duplicate all annnotation, groups and settings
2455 * @return new alignment panel, already displayed.
2457 public AlignmentPanel newView(boolean copyAnnotation)
2459 return newView(null, copyAnnotation);
2465 * title of newly created view
2466 * @return new alignment panel, already displayed.
2468 public AlignmentPanel newView(String viewTitle)
2470 return newView(viewTitle, true);
2476 * title of newly created view
2477 * @param copyAnnotation
2478 * if true then duplicate all annnotation, groups and settings
2479 * @return new alignment panel, already displayed.
2481 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2483 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2485 if (!copyAnnotation)
2487 // just remove all the current annotation except for the automatic stuff
2488 newap.av.getAlignment().deleteAllGroups();
2489 for (AlignmentAnnotation alan : newap.av.getAlignment()
2490 .getAlignmentAnnotation())
2492 if (!alan.autoCalculated)
2494 newap.av.getAlignment().deleteAnnotation(alan);
2500 newap.av.gatherViewsHere = false;
2502 if (viewport.viewName == null)
2504 viewport.viewName = "Original";
2507 newap.av.historyList = viewport.historyList;
2508 newap.av.redoList = viewport.redoList;
2510 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2511 // make sure the new view has a unique name - this is essential for Jalview
2513 boolean addFirstIndex = false;
2514 if (viewTitle == null || viewTitle.trim().length() == 0)
2517 addFirstIndex = true;
2521 index = 1;// we count from 1 if given a specific name
2523 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2524 Vector comps = (Vector) PaintRefresher.components.get(viewport
2525 .getSequenceSetId());
2526 Vector existingNames = new Vector();
2527 for (int i = 0; i < comps.size(); i++)
2529 if (comps.elementAt(i) instanceof AlignmentPanel)
2531 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2532 if (!existingNames.contains(ap.av.viewName))
2534 existingNames.addElement(ap.av.viewName);
2539 while (existingNames.contains(newViewName))
2541 newViewName = viewTitle + " " + (++index);
2544 newap.av.viewName = newViewName;
2546 addAlignmentPanel(newap, true);
2547 newap.alignmentChanged();
2549 if (alignPanels.size() == 2)
2551 viewport.gatherViewsHere = true;
2553 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2558 public void expandViews_actionPerformed(ActionEvent e)
2560 Desktop.instance.explodeViews(this);
2564 public void gatherViews_actionPerformed(ActionEvent e)
2566 Desktop.instance.gatherViews(this);
2576 public void font_actionPerformed(ActionEvent e)
2578 new FontChooser(alignPanel);
2588 protected void seqLimit_actionPerformed(ActionEvent e)
2590 viewport.setShowJVSuffix(seqLimits.isSelected());
2592 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2593 .calculateIdWidth());
2594 alignPanel.paintAlignment(true);
2598 public void idRightAlign_actionPerformed(ActionEvent e)
2600 viewport.rightAlignIds = idRightAlign.isSelected();
2601 alignPanel.paintAlignment(true);
2605 public void centreColumnLabels_actionPerformed(ActionEvent e)
2607 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2608 alignPanel.paintAlignment(true);
2614 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2617 protected void followHighlight_actionPerformed()
2619 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2621 alignPanel.scrollToPosition(
2622 alignPanel.seqPanel.seqCanvas.searchResults, false);
2633 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2635 viewport.setColourText(colourTextMenuItem.isSelected());
2636 alignPanel.paintAlignment(true);
2646 public void wrapMenuItem_actionPerformed(ActionEvent e)
2648 scaleAbove.setVisible(wrapMenuItem.isSelected());
2649 scaleLeft.setVisible(wrapMenuItem.isSelected());
2650 scaleRight.setVisible(wrapMenuItem.isSelected());
2651 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2652 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2656 public void showAllSeqs_actionPerformed(ActionEvent e)
2658 viewport.showAllHiddenSeqs();
2662 public void showAllColumns_actionPerformed(ActionEvent e)
2664 viewport.showAllHiddenColumns();
2669 public void hideSelSequences_actionPerformed(ActionEvent e)
2671 viewport.hideAllSelectedSeqs();
2672 alignPanel.paintAlignment(true);
2676 * called by key handler and the hide all/show all menu items
2681 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2684 boolean hide = false;
2685 SequenceGroup sg = viewport.getSelectionGroup();
2686 if (!toggleSeqs && !toggleCols)
2688 // Hide everything by the current selection - this is a hack - we do the
2689 // invert and then hide
2690 // first check that there will be visible columns after the invert.
2691 if ((viewport.getColumnSelection() != null
2692 && viewport.getColumnSelection().getSelected() != null && viewport
2693 .getColumnSelection().getSelected().size() > 0)
2694 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2697 // now invert the sequence set, if required - empty selection implies
2698 // that no hiding is required.
2701 invertSequenceMenuItem_actionPerformed(null);
2702 sg = viewport.getSelectionGroup();
2706 viewport.expandColSelection(sg, true);
2707 // finally invert the column selection and get the new sequence
2709 invertColSel_actionPerformed(null);
2716 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2718 hideSelSequences_actionPerformed(null);
2721 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2724 showAllSeqs_actionPerformed(null);
2730 if (viewport.getColumnSelection().getSelected().size() > 0)
2732 hideSelColumns_actionPerformed(null);
2735 viewport.setSelectionGroup(sg);
2740 showAllColumns_actionPerformed(null);
2749 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2750 * event.ActionEvent)
2753 public void hideAllButSelection_actionPerformed(ActionEvent e)
2755 toggleHiddenRegions(false, false);
2762 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2766 public void hideAllSelection_actionPerformed(ActionEvent e)
2768 SequenceGroup sg = viewport.getSelectionGroup();
2769 viewport.expandColSelection(sg, false);
2770 viewport.hideAllSelectedSeqs();
2771 viewport.hideSelectedColumns();
2772 alignPanel.paintAlignment(true);
2779 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2783 public void showAllhidden_actionPerformed(ActionEvent e)
2785 viewport.showAllHiddenColumns();
2786 viewport.showAllHiddenSeqs();
2787 alignPanel.paintAlignment(true);
2791 public void hideSelColumns_actionPerformed(ActionEvent e)
2793 viewport.hideSelectedColumns();
2794 alignPanel.paintAlignment(true);
2798 public void hiddenMarkers_actionPerformed(ActionEvent e)
2800 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2811 protected void scaleAbove_actionPerformed(ActionEvent e)
2813 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2814 alignPanel.paintAlignment(true);
2824 protected void scaleLeft_actionPerformed(ActionEvent e)
2826 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2827 alignPanel.paintAlignment(true);
2837 protected void scaleRight_actionPerformed(ActionEvent e)
2839 viewport.setScaleRightWrapped(scaleRight.isSelected());
2840 alignPanel.paintAlignment(true);
2850 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2852 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2853 alignPanel.paintAlignment(true);
2863 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2865 viewport.setShowText(viewTextMenuItem.isSelected());
2866 alignPanel.paintAlignment(true);
2876 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2878 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2879 alignPanel.paintAlignment(true);
2882 public FeatureSettings featureSettings;
2885 public void featureSettings_actionPerformed(ActionEvent e)
2887 if (featureSettings != null)
2889 featureSettings.close();
2890 featureSettings = null;
2892 if (!showSeqFeatures.isSelected())
2894 // make sure features are actually displayed
2895 showSeqFeatures.setSelected(true);
2896 showSeqFeatures_actionPerformed(null);
2898 featureSettings = new FeatureSettings(this);
2902 * Set or clear 'Show Sequence Features'
2908 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2910 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2911 alignPanel.paintAlignment(true);
2912 if (alignPanel.getOverviewPanel() != null)
2914 alignPanel.getOverviewPanel().updateOverviewImage();
2919 * Set or clear 'Show Sequence Features'
2925 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2927 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2929 if (viewport.getShowSequenceFeaturesHeight())
2931 // ensure we're actually displaying features
2932 viewport.setShowSequenceFeatures(true);
2933 showSeqFeatures.setSelected(true);
2935 alignPanel.paintAlignment(true);
2936 if (alignPanel.getOverviewPanel() != null)
2938 alignPanel.getOverviewPanel().updateOverviewImage();
2949 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2951 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2952 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2956 public void alignmentProperties()
2958 JEditorPane editPane = new JEditorPane("text/html", "");
2959 editPane.setEditable(false);
2960 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
2962 editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
2963 JInternalFrame frame = new JInternalFrame();
2964 frame.getContentPane().add(new JScrollPane(editPane));
2966 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}), 500, 400);
\r
2976 public void overviewMenuItem_actionPerformed(ActionEvent e)
2978 if (alignPanel.overviewPanel != null)
2983 JInternalFrame frame = new JInternalFrame();
2984 OverviewPanel overview = new OverviewPanel(alignPanel);
2985 frame.setContentPane(overview);
2986 Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
\r
2987 frame.getWidth(), frame.getHeight());
2989 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2990 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2993 public void internalFrameClosed(
2994 javax.swing.event.InternalFrameEvent evt)
2996 alignPanel.setOverviewPanel(null);
3000 alignPanel.setOverviewPanel(overview);
3004 public void textColour_actionPerformed(ActionEvent e)
3006 new TextColourChooser().chooseColour(alignPanel, null);
3016 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3028 public void clustalColour_actionPerformed(ActionEvent e)
3030 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3031 viewport.getHiddenRepSequences()));
3041 public void zappoColour_actionPerformed(ActionEvent e)
3043 changeColour(new ZappoColourScheme());
3053 public void taylorColour_actionPerformed(ActionEvent e)
3055 changeColour(new TaylorColourScheme());
3065 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3067 changeColour(new HydrophobicColourScheme());
3077 public void helixColour_actionPerformed(ActionEvent e)
3079 changeColour(new HelixColourScheme());
3089 public void strandColour_actionPerformed(ActionEvent e)
3091 changeColour(new StrandColourScheme());
3101 public void turnColour_actionPerformed(ActionEvent e)
3103 changeColour(new TurnColourScheme());
3113 public void buriedColour_actionPerformed(ActionEvent e)
3115 changeColour(new BuriedColourScheme());
3125 public void nucleotideColour_actionPerformed(ActionEvent e)
3127 changeColour(new NucleotideColourScheme());
3131 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3133 changeColour(new PurinePyrimidineColourScheme());
3137 * public void covariationColour_actionPerformed(ActionEvent e) {
3139 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3143 public void annotationColour_actionPerformed(ActionEvent e)
3145 new AnnotationColourChooser(viewport, alignPanel);
3149 public void rnahelicesColour_actionPerformed(ActionEvent e)
3151 new RNAHelicesColourChooser(viewport, alignPanel);
3161 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3163 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3172 public void changeColour(ColourSchemeI cs)
3174 // TODO: compare with applet and pull up to model method
3179 if (viewport.getAbovePIDThreshold())
3181 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3184 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3186 viewport.setGlobalColourScheme(cs);
3190 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3193 if (viewport.getConservationSelected())
3196 Alignment al = (Alignment) viewport.getAlignment();
3197 Conservation c = new Conservation("All",
3198 ResidueProperties.propHash, 3, al.getSequences(), 0,
3202 c.verdict(false, viewport.getConsPercGaps());
3204 cs.setConservation(c);
3206 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3211 cs.setConservation(null);
3214 cs.setConsensus(viewport.getSequenceConsensusHash());
3217 viewport.setGlobalColourScheme(cs);
3219 if (viewport.getColourAppliesToAllGroups())
3222 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3230 if (cs instanceof ClustalxColourScheme)
3232 sg.cs = new ClustalxColourScheme(sg,
3233 viewport.getHiddenRepSequences());
3235 else if (cs instanceof UserColourScheme)
3237 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3243 sg.cs = cs.getClass().newInstance();
3244 } catch (Exception ex)
3249 if (viewport.getAbovePIDThreshold()
3250 || cs instanceof PIDColourScheme
3251 || cs instanceof Blosum62ColourScheme)
3253 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3255 sg.cs.setConsensus(AAFrequency.calculate(
3256 sg.getSequences(viewport.getHiddenRepSequences()),
3257 sg.getStartRes(), sg.getEndRes() + 1));
3261 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3264 if (viewport.getConservationSelected())
3266 Conservation c = new Conservation("Group",
3267 ResidueProperties.propHash, 3, sg.getSequences(viewport
3268 .getHiddenRepSequences()), sg.getStartRes(),
3269 sg.getEndRes() + 1);
3271 c.verdict(false, viewport.getConsPercGaps());
3272 sg.cs.setConservation(c);
3276 sg.cs.setConservation(null);
3281 if (alignPanel.getOverviewPanel() != null)
3283 alignPanel.getOverviewPanel().updateOverviewImage();
3286 alignPanel.paintAlignment(true);
3296 protected void modifyPID_actionPerformed(ActionEvent e)
3298 if (viewport.getAbovePIDThreshold()
3299 && viewport.getGlobalColourScheme() != null)
3301 SliderPanel.setPIDSliderSource(alignPanel,
3302 viewport.getGlobalColourScheme(), "Background");
3303 SliderPanel.showPIDSlider();
3314 protected void modifyConservation_actionPerformed(ActionEvent e)
3316 if (viewport.getConservationSelected()
3317 && viewport.getGlobalColourScheme() != null)
3319 SliderPanel.setConservationSlider(alignPanel,
3320 viewport.getGlobalColourScheme(), "Background");
3321 SliderPanel.showConservationSlider();
3332 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3334 viewport.setConservationSelected(conservationMenuItem.isSelected());
3336 viewport.setAbovePIDThreshold(false);
3337 abovePIDThreshold.setSelected(false);
3339 changeColour(viewport.getGlobalColourScheme());
3341 modifyConservation_actionPerformed(null);
3351 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3353 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3355 conservationMenuItem.setSelected(false);
3356 viewport.setConservationSelected(false);
3358 changeColour(viewport.getGlobalColourScheme());
3360 modifyPID_actionPerformed(null);
3370 public void userDefinedColour_actionPerformed(ActionEvent e)
3372 if (e.getActionCommand().equals(MessageManager.getString("action.user_defined")))
\r
3374 new UserDefinedColours(alignPanel, null);
3378 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3379 .getUserColourSchemes().get(e.getActionCommand());
3385 public void updateUserColourMenu()
3388 Component[] menuItems = colourMenu.getMenuComponents();
3389 int i, iSize = menuItems.length;
3390 for (i = 0; i < iSize; i++)
3392 if (menuItems[i].getName() != null
3393 && menuItems[i].getName().equals("USER_DEFINED"))
3395 colourMenu.remove(menuItems[i]);
3399 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3401 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3402 .getUserColourSchemes().keys();
3404 while (userColours.hasMoreElements())
3406 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3407 userColours.nextElement().toString());
3408 radioItem.setName("USER_DEFINED");
3409 radioItem.addMouseListener(new MouseAdapter()
3412 public void mousePressed(MouseEvent evt)
3414 if (evt.isControlDown()
3415 || SwingUtilities.isRightMouseButton(evt))
3417 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3419 int option = JOptionPane.showInternalConfirmDialog(
3420 jalview.gui.Desktop.desktop,
3421 MessageManager.getString("label.remove_from_default_list"),
3422 MessageManager.getString("label.remove_user_defined_colour"),
3423 JOptionPane.YES_NO_OPTION);
3424 if (option == JOptionPane.YES_OPTION)
3426 jalview.gui.UserDefinedColours
3427 .removeColourFromDefaults(radioItem.getText());
3428 colourMenu.remove(radioItem);
3432 radioItem.addActionListener(new ActionListener()
3435 public void actionPerformed(ActionEvent evt)
3437 userDefinedColour_actionPerformed(evt);
3444 radioItem.addActionListener(new ActionListener()
3447 public void actionPerformed(ActionEvent evt)
3449 userDefinedColour_actionPerformed(evt);
3453 colourMenu.insert(radioItem, 15);
3454 colours.add(radioItem);
3466 public void PIDColour_actionPerformed(ActionEvent e)
3468 changeColour(new PIDColourScheme());
3478 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3480 changeColour(new Blosum62ColourScheme());
3490 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3492 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3493 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3494 .getAlignment().getSequenceAt(0), null);
3495 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3496 viewport.getAlignment()));
3497 alignPanel.paintAlignment(true);
3507 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3509 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3510 AlignmentSorter.sortByID(viewport.getAlignment());
3511 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3512 viewport.getAlignment()));
3513 alignPanel.paintAlignment(true);
3523 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3525 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3526 AlignmentSorter.sortByLength(viewport.getAlignment());
3527 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3528 viewport.getAlignment()));
3529 alignPanel.paintAlignment(true);
3539 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3541 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3542 AlignmentSorter.sortByGroup(viewport.getAlignment());
3543 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3544 viewport.getAlignment()));
3546 alignPanel.paintAlignment(true);
3556 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3558 new RedundancyPanel(alignPanel, this);
3568 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3570 if ((viewport.getSelectionGroup() == null)
3571 || (viewport.getSelectionGroup().getSize() < 2))
3573 JOptionPane.showInternalMessageDialog(this,
3574 MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"),
3575 JOptionPane.WARNING_MESSAGE);
3579 JInternalFrame frame = new JInternalFrame();
3580 frame.setContentPane(new PairwiseAlignPanel(viewport));
3581 Desktop.addInternalFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500);
\r
3592 public void PCAMenuItem_actionPerformed(ActionEvent e)
3594 if (((viewport.getSelectionGroup() != null)
3595 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3596 .getSelectionGroup().getSize() > 0))
3597 || (viewport.getAlignment().getHeight() < 4))
3599 JOptionPane.showInternalMessageDialog(this,
3600 MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3601 MessageManager.getString("label.sequence_selection_insufficient"),
3602 JOptionPane.WARNING_MESSAGE);
3607 new PCAPanel(alignPanel);
3611 public void autoCalculate_actionPerformed(ActionEvent e)
3613 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3614 if (viewport.autoCalculateConsensus)
3616 viewport.firePropertyChange("alignment", null, viewport
3617 .getAlignment().getSequences());
3622 public void sortByTreeOption_actionPerformed(ActionEvent e)
3624 viewport.sortByTree = sortByTree.isSelected();
3628 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3630 viewport.followSelection = listenToViewSelections.isSelected();
3640 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3642 NewTreePanel("AV", "PID", "Average distance tree using PID");
3652 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3654 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3664 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3666 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3676 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3678 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3691 void NewTreePanel(String type, String pwType, String title)
3695 if (viewport.getSelectionGroup() != null
3696 && viewport.getSelectionGroup().getSize() > 0)
3698 if (viewport.getSelectionGroup().getSize() < 3)
3703 MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"),
3704 MessageManager.getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE);
3708 SequenceGroup sg = viewport.getSelectionGroup();
3710 /* Decide if the selection is a column region */
3711 for (SequenceI _s : sg.getSequences())
3713 if (_s.getLength() < sg.getEndRes())
3718 MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3719 MessageManager.getString("label.sequences_selection_not_aligned"),
3720 JOptionPane.WARNING_MESSAGE);
3726 title = title + " on region";
3727 tp = new TreePanel(alignPanel, type, pwType);
3731 // are the visible sequences aligned?
3732 if (!viewport.getAlignment().isAligned(false))
3737 MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"),
3738 MessageManager.getString("label.sequences_not_aligned"),
3739 JOptionPane.WARNING_MESSAGE);
3744 if (viewport.getAlignment().getHeight() < 2)
3749 tp = new TreePanel(alignPanel, type, pwType);
3754 if (viewport.viewName != null)
3756 title += viewport.viewName + " of ";
3759 title += this.title;
3761 Desktop.addInternalFrame(tp, title, 600, 500);
3772 public void addSortByOrderMenuItem(String title,
3773 final AlignmentOrder order)
3775 final JMenuItem item = new JMenuItem("by " + title);
3777 item.addActionListener(new java.awt.event.ActionListener()
3780 public void actionPerformed(ActionEvent e)
3782 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3784 // TODO: JBPNote - have to map order entries to curent SequenceI
3786 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3788 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3791 alignPanel.paintAlignment(true);
3797 * Add a new sort by annotation score menu item
3800 * the menu to add the option to
3802 * the label used to retrieve scores for each sequence on the
3805 public void addSortByAnnotScoreMenuItem(JMenu sort,
3806 final String scoreLabel)
3808 final JMenuItem item = new JMenuItem(scoreLabel);
3810 item.addActionListener(new java.awt.event.ActionListener()
3813 public void actionPerformed(ActionEvent e)
3815 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3816 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3817 viewport.getAlignment());// ,viewport.getSelectionGroup());
3818 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3819 viewport.getAlignment()));
3820 alignPanel.paintAlignment(true);
3826 * last hash for alignment's annotation array - used to minimise cost of
3829 protected int _annotationScoreVectorHash;
3832 * search the alignment and rebuild the sort by annotation score submenu the
3833 * last alignment annotation vector hash is stored to minimize cost of
3834 * rebuilding in subsequence calls.
3838 public void buildSortByAnnotationScoresMenu()
3840 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3845 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3847 sortByAnnotScore.removeAll();
3848 // almost certainly a quicker way to do this - but we keep it simple
3849 Hashtable scoreSorts = new Hashtable();
3850 AlignmentAnnotation aann[];
3851 for (SequenceI sqa : viewport.getAlignment().getSequences())
3853 aann = sqa.getAnnotation();
3854 for (int i = 0; aann != null && i < aann.length; i++)
3856 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3858 scoreSorts.put(aann[i].label, aann[i].label);
3862 Enumeration labels = scoreSorts.keys();
3863 while (labels.hasMoreElements())
3865 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3866 (String) labels.nextElement());
3868 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3871 _annotationScoreVectorHash = viewport.getAlignment()
3872 .getAlignmentAnnotation().hashCode();
3877 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3878 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3879 * call. Listeners are added to remove the menu item when the treePanel is
3880 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3884 * Displayed tree window.
3886 * SortBy menu item title.
3889 public void buildTreeMenu()
3891 sortByTreeMenu.removeAll();
3893 Vector comps = (Vector) PaintRefresher.components.get(viewport
3894 .getSequenceSetId());
3895 Vector treePanels = new Vector();
3896 int i, iSize = comps.size();
3897 for (i = 0; i < iSize; i++)
3899 if (comps.elementAt(i) instanceof TreePanel)
3901 treePanels.add(comps.elementAt(i));
3905 iSize = treePanels.size();
3909 sortByTreeMenu.setVisible(false);
3913 sortByTreeMenu.setVisible(true);
3915 for (i = 0; i < treePanels.size(); i++)
3917 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3918 final JMenuItem item = new JMenuItem(tp.getTitle());
3919 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3920 item.addActionListener(new java.awt.event.ActionListener()
3923 public void actionPerformed(ActionEvent e)
3925 tp.sortByTree_actionPerformed(null);
3926 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3931 sortByTreeMenu.add(item);
3935 public boolean sortBy(AlignmentOrder alorder, String undoname)
3937 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3938 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3939 if (undoname != null)
3941 addHistoryItem(new OrderCommand(undoname, oldOrder,
3942 viewport.getAlignment()));
3944 alignPanel.paintAlignment(true);
3949 * Work out whether the whole set of sequences or just the selected set will
3950 * be submitted for multiple alignment.
3953 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3955 // Now, check we have enough sequences
3956 AlignmentView msa = null;
3958 if ((viewport.getSelectionGroup() != null)
3959 && (viewport.getSelectionGroup().getSize() > 1))
3961 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3962 // some common interface!
3964 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3965 * SequenceI[sz = seqs.getSize(false)];
3967 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3968 * seqs.getSequenceAt(i); }
3970 msa = viewport.getAlignmentView(true);
3975 * Vector seqs = viewport.getAlignment().getSequences();
3977 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3979 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3980 * seqs.elementAt(i); } }
3982 msa = viewport.getAlignmentView(false);
3988 * Decides what is submitted to a secondary structure prediction service: the
3989 * first sequence in the alignment, or in the current selection, or, if the
3990 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3991 * region or the whole alignment. (where the first sequence in the set is the
3992 * one that the prediction will be for).
3994 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3996 AlignmentView seqs = null;
3998 if ((viewport.getSelectionGroup() != null)
3999 && (viewport.getSelectionGroup().getSize() > 0))
4001 seqs = viewport.getAlignmentView(true);
4005 seqs = viewport.getAlignmentView(false);
4007 // limit sequences - JBPNote in future - could spawn multiple prediction
4009 // TODO: viewport.getAlignment().isAligned is a global state - the local
4010 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4011 if (!viewport.getAlignment().isAligned(false))
4013 seqs.setSequences(new SeqCigar[]
4014 { seqs.getSequences()[0] });
4015 // TODO: if seqs.getSequences().length>1 then should really have warned
4029 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4031 // Pick the tree file
4032 JalviewFileChooser chooser = new JalviewFileChooser(
4033 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4034 chooser.setFileView(new JalviewFileView());
4035 chooser.setDialogTitle(MessageManager.getString("label.select_newick_like_tree_file"));
\r
4036 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
\r
4038 int value = chooser.showOpenDialog(null);
4040 if (value == JalviewFileChooser.APPROVE_OPTION)
4042 String choice = chooser.getSelectedFile().getPath();
4043 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4044 jalview.io.NewickFile fin = null;
4047 fin = new jalview.io.NewickFile(choice, "File");
4048 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4049 } catch (Exception ex)
4051 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4052 MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE);
4053 ex.printStackTrace();
4055 if (fin != null && fin.hasWarningMessage())
4057 JOptionPane.showMessageDialog(Desktop.desktop,
4058 fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"),
4059 JOptionPane.WARNING_MESSAGE);
4065 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4067 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4070 public TreePanel ShowNewickTree(NewickFile nf, String title)
4072 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4075 public TreePanel ShowNewickTree(NewickFile nf, String title,
4076 AlignmentView input)
4078 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4081 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4082 int h, int x, int y)
4084 return ShowNewickTree(nf, title, null, w, h, x, y);
4088 * Add a treeviewer for the tree extracted from a newick file object to the
4089 * current alignment view
4096 * Associated alignment input data (or null)
4105 * @return TreePanel handle
4107 public TreePanel ShowNewickTree(NewickFile nf, String title,
4108 AlignmentView input, int w, int h, int x, int y)
4110 TreePanel tp = null;
4116 if (nf.getTree() != null)
4118 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4124 tp.setLocation(x, y);
4127 Desktop.addInternalFrame(tp, title, w, h);
4129 } catch (Exception ex)
4131 ex.printStackTrace();
4137 private boolean buildingMenu = false;
4140 * Generates menu items and listener event actions for web service clients
4143 public void BuildWebServiceMenu()
4145 while (buildingMenu)
4149 System.err.println("Waiting for building menu to finish.");
4151 } catch (Exception e)
4156 final AlignFrame me = this;
4157 buildingMenu = true;
4158 new Thread(new Runnable()
4163 final List<JMenuItem> legacyItems=new ArrayList<JMenuItem>();
4166 System.err.println("Building ws menu again "
4167 + Thread.currentThread());
4168 // TODO: add support for context dependent disabling of services based
4170 // alignment and current selection
4171 // TODO: add additional serviceHandle parameter to specify abstract
4173 // class independently of AbstractName
4174 // TODO: add in rediscovery GUI function to restart discoverer
4175 // TODO: group services by location as well as function and/or
4177 // object broker mechanism.
4178 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4179 final IProgressIndicator af = me;
4180 final JMenu msawsmenu = new JMenu("Alignment");
4181 final JMenu secstrmenu = new JMenu(
4182 "Secondary Structure Prediction");
4183 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4184 final JMenu analymenu = new JMenu("Analysis");
4185 final JMenu dismenu = new JMenu("Protein Disorder");
4186 // JAL-940 - only show secondary structure prediction services from
4187 // the legacy server
4188 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4190 Discoverer.services != null && (Discoverer.services.size() > 0))
4192 // TODO: refactor to allow list of AbstractName/Handler bindings to
4194 // stored or retrieved from elsewhere
4195 // No MSAWS used any more:
4196 // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4197 Vector secstrpr = (Vector) Discoverer.services
4199 if (secstrpr != null)
4201 // Add any secondary structure prediction services
4202 for (int i = 0, j = secstrpr.size(); i < j; i++)
4204 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4206 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4207 .getServiceClient(sh);
4208 int p=secstrmenu.getItemCount();
4209 impl.attachWSMenuEntry(secstrmenu, me);
4210 int q=secstrmenu.getItemCount();
4211 for (int litm=p;litm<q; litm++)
4213 legacyItems.add(secstrmenu.getItem(litm));
4219 // Add all submenus in the order they should appear on the web
4221 wsmenu.add(msawsmenu);
4222 wsmenu.add(secstrmenu);
4223 wsmenu.add(dismenu);
4224 wsmenu.add(analymenu);
4225 // No search services yet
4226 // wsmenu.add(seqsrchmenu);
4228 javax.swing.SwingUtilities.invokeLater(new Runnable()
4235 webService.removeAll();
4236 // first, add discovered services onto the webservices menu
4237 if (wsmenu.size() > 0)
4239 for (int i = 0, j = wsmenu.size(); i < j; i++)
4241 webService.add(wsmenu.get(i));
4246 webService.add(me.webServiceNoServices);
4248 // TODO: move into separate menu builder class.
4249 boolean new_sspred=false;
4250 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4252 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4253 if (jws2servs != null)
4255 if (jws2servs.hasServices())
4257 jws2servs.attachWSMenuEntry(webService, me);
4258 for (Jws2Instance sv:jws2servs.getServices()) {
4259 if (sv.description.toLowerCase().contains("jpred"))
4261 for (JMenuItem jmi:legacyItems)
4263 jmi.setVisible(false);
4269 if (jws2servs.isRunning())
4271 JMenuItem tm = new JMenuItem(
4272 "Still discovering JABA Services");
4273 tm.setEnabled(false);
4278 build_urlServiceMenu(me.webService);
4279 build_fetchdbmenu(webService);
4280 for (JMenu item : wsmenu)
4282 if (item.getItemCount() == 0)
4284 item.setEnabled(false);
4288 item.setEnabled(true);
4291 } catch (Exception e)
4294 .debug("Exception during web service menu building process.",
4300 } catch (Exception e)
4305 buildingMenu = false;
4312 * construct any groupURL type service menu entries.
4316 private void build_urlServiceMenu(JMenu webService)
4318 // TODO: remove this code when 2.7 is released
4319 // DEBUG - alignmentView
4321 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4322 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4324 * @Override public void actionPerformed(ActionEvent e) {
4325 * jalview.datamodel.AlignmentView
4326 * .testSelectionViews(af.viewport.getAlignment(),
4327 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4329 * }); webService.add(testAlView);
4331 // TODO: refactor to RestClient discoverer and merge menu entries for
4332 // rest-style services with other types of analysis/calculation service
4333 // SHmmr test client - still being implemented.
4334 // DEBUG - alignmentView
4336 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4339 client.attachWSMenuEntry(
4340 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4344 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4346 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4352 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4353 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4354 * getProperty("LAST_DIRECTORY"));
4356 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4357 * to Vamsas file"); chooser.setToolTipText("Export");
4359 * int value = chooser.showSaveDialog(this);
4361 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4362 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4363 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4364 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4367 * prototype of an automatically enabled/disabled analysis function
4370 protected void setShowProductsEnabled()
4372 SequenceI[] selection = viewport.getSequenceSelection();
4373 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4374 viewport.getAlignment().getDataset()))
4376 showProducts.setEnabled(true);
4381 showProducts.setEnabled(false);
4386 * search selection for sequence xRef products and build the show products
4391 * @return true if showProducts menu should be enabled.
4393 public boolean canShowProducts(SequenceI[] selection,
4394 boolean isRegionSelection, Alignment dataset)
4396 boolean showp = false;
4399 showProducts.removeAll();
4400 final boolean dna = viewport.getAlignment().isNucleotide();
4401 final Alignment ds = dataset;
4402 String[] ptypes = (selection == null || selection.length == 0) ? null
4403 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4405 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4406 // selection, dataset, true);
4407 final SequenceI[] sel = selection;
4408 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4411 final boolean isRegSel = isRegionSelection;
4412 final AlignFrame af = this;
4413 final String source = ptypes[t];
4414 JMenuItem xtype = new JMenuItem(ptypes[t]);
4415 xtype.addActionListener(new ActionListener()
4419 public void actionPerformed(ActionEvent e)
4421 // TODO: new thread for this call with vis-delay
4422 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4423 isRegSel, dna, source);
4427 showProducts.add(xtype);
4429 showProducts.setVisible(showp);
4430 showProducts.setEnabled(showp);
4431 } catch (Exception e)
4433 jalview.bin.Cache.log
4434 .warn("canTranslate threw an exception - please report to help@jalview.org",
4441 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4442 boolean isRegSel, boolean dna, String source)
4444 final boolean fisRegSel = isRegSel;
4445 final boolean fdna = dna;
4446 final String fsrc = source;
4447 final AlignFrame ths = this;
4448 final SequenceI[] fsel = sel;
4449 Runnable foo = new Runnable()
4455 final long sttime = System.currentTimeMillis();
4456 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4459 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4463 Alignment prods = CrossRef
4464 .findXrefSequences(fsel, fdna, fsrc, ds);
4467 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4468 for (int s = 0; s < sprods.length; s++)
4470 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4471 if (ds.getSequences() == null
4472 || !ds.getSequences().contains(
4473 sprods[s].getDatasetSequence()))
4474 ds.addSequence(sprods[s].getDatasetSequence());
4475 sprods[s].updatePDBIds();
4477 Alignment al = new Alignment(sprods);
4478 AlignedCodonFrame[] cf = prods.getCodonFrames();
4480 for (int s = 0; cf != null && s < cf.length; s++)
4482 al.addCodonFrame(cf[s]);
4485 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4487 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4488 + " for " + ((fisRegSel) ? "selected region of " : "")
4490 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4495 System.err.println("No Sequences generated for xRef type "
4498 } catch (Exception e)
4500 jalview.bin.Cache.log.error(
4501 "Exception when finding crossreferences", e);
4502 } catch (OutOfMemoryError e)
4504 new OOMWarning("whilst fetching crossreferences", e);
4507 jalview.bin.Cache.log.error("Error when finding crossreferences",
4510 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4515 Thread frunner = new Thread(foo);
4519 public boolean canShowTranslationProducts(SequenceI[] selection,
4520 AlignmentI alignment)
4525 return (jalview.analysis.Dna.canTranslate(selection,
4526 viewport.getViewAsVisibleContigs(true)));
4527 } catch (Exception e)
4529 jalview.bin.Cache.log
4530 .warn("canTranslate threw an exception - please report to help@jalview.org",
4537 public void showProducts_actionPerformed(ActionEvent e)
4539 // /////////////////////////////
4540 // Collect Data to be translated/transferred
4542 SequenceI[] selection = viewport.getSequenceSelection();
4543 AlignmentI al = null;
4546 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4547 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4548 viewport.getAlignment().getDataset());
4549 } catch (Exception ex)
4552 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4559 MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4560 MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
4564 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4565 Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),
\r
4566 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4571 public void showTranslation_actionPerformed(ActionEvent e)
4573 // /////////////////////////////
4574 // Collect Data to be translated/transferred
4576 SequenceI[] selection = viewport.getSequenceSelection();
4577 String[] seqstring = viewport.getViewAsString(true);
4578 AlignmentI al = null;
4581 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4582 viewport.getViewAsVisibleContigs(true), viewport
4583 .getGapCharacter(), viewport.getAlignment()
4584 .getAlignmentAnnotation(), viewport.getAlignment()
4585 .getWidth(), viewport.getAlignment().getDataset());
4586 } catch (Exception ex)
4589 jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex);
4593 MessageManager.getString("label.error_when_translating_sequences_submit_bug_report"),
4594 MessageManager.getString("label.implementation_error") + MessageManager.getString("translation_failed"), JOptionPane.ERROR_MESSAGE);
4602 MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4603 MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
4607 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4608 Desktop.addInternalFrame(af, MessageManager.formatMessage("label.translation_of_params", new String[]{this.getTitle()}),
\r
4609 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4614 * Try to load a features file onto the alignment.
4617 * contents or path to retrieve file
4619 * access mode of file (see jalview.io.AlignFile)
4620 * @return true if features file was parsed corectly.
4622 public boolean parseFeaturesFile(String file, String type)
4624 boolean featuresFile = false;
4627 featuresFile = new FeaturesFile(file, type).parse(viewport
4628 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4629 .getFeatureRenderer().featureColours, false,
4630 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4631 } catch (Exception ex)
4633 ex.printStackTrace();
4638 viewport.showSequenceFeatures = true;
4639 showSeqFeatures.setSelected(true);
4640 if (alignPanel.seqPanel.seqCanvas.fr != null)
4642 // update the min/max ranges where necessary
4643 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4645 if (featureSettings != null)
4647 featureSettings.setTableData();
4649 alignPanel.paintAlignment(true);
4652 return featuresFile;
4656 public void dragEnter(DropTargetDragEvent evt)
4661 public void dragExit(DropTargetEvent evt)
4666 public void dragOver(DropTargetDragEvent evt)
4671 public void dropActionChanged(DropTargetDragEvent evt)
4676 public void drop(DropTargetDropEvent evt)
4678 Transferable t = evt.getTransferable();
4679 java.util.List files = null;
4683 DataFlavor uriListFlavor = new DataFlavor(
4684 "text/uri-list;class=java.lang.String");
4685 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4687 // Works on Windows and MacOSX
4688 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4689 files = (java.util.List) t
4690 .getTransferData(DataFlavor.javaFileListFlavor);
4692 else if (t.isDataFlavorSupported(uriListFlavor))
4694 // This is used by Unix drag system
4695 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4696 String data = (String) t.getTransferData(uriListFlavor);
4697 files = new java.util.ArrayList(1);
4698 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4699 data, "\r\n"); st.hasMoreTokens();)
4701 String s = st.nextToken();
4702 if (s.startsWith("#"))
4704 // the line is a comment (as per the RFC 2483)
4708 java.net.URI uri = new java.net.URI(s);
4709 // check to see if we can handle this kind of URI
4710 if (uri.getScheme().toLowerCase().startsWith("http"))
4712 files.add(uri.toString());
4716 // otherwise preserve old behaviour: catch all for file objects
4717 java.io.File file = new java.io.File(uri);
4718 files.add(file.toString());
4722 } catch (Exception e)
4724 e.printStackTrace();
4730 // check to see if any of these files have names matching sequences in
4732 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4733 .getAlignment().getSequencesArray());
4735 * Object[] { String,SequenceI}
4737 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4738 ArrayList<String> filesnotmatched = new ArrayList<String>();
4739 for (int i = 0; i < files.size(); i++)
4741 String file = files.get(i).toString();
4743 String protocol = FormatAdapter.checkProtocol(file);
4744 if (protocol == jalview.io.FormatAdapter.FILE)
4746 File fl = new File(file);
4747 pdbfn = fl.getName();
4749 else if (protocol == jalview.io.FormatAdapter.URL)
4751 URL url = new URL(file);
4752 pdbfn = url.getFile();
4754 if (pdbfn.length() > 0)
4756 // attempt to find a match in the alignment
4757 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4758 int l = 0, c = pdbfn.indexOf(".");
4759 while (mtch == null && c != -1)
4764 } while ((c = pdbfn.indexOf(".", l)) > l);
4767 pdbfn = pdbfn.substring(0, l);
4769 mtch = idm.findAllIdMatches(pdbfn);
4776 type = new IdentifyFile().Identify(file, protocol);
4777 } catch (Exception ex)
4783 if (type.equalsIgnoreCase("PDB"))
4785 filesmatched.add(new Object[]
4786 { file, protocol, mtch });
4791 // File wasn't named like one of the sequences or wasn't a PDB file.
4792 filesnotmatched.add(file);
4796 if (filesmatched.size() > 0)
4798 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4802 MessageManager.formatMessage("label.automatically_associate_pdb_files_with_sequences_same_name",
4803 new String[]{Integer.valueOf(filesmatched.size()).toString()}),
4804 MessageManager.getString("label.automatically_associate_pdb_files_by_name"),
4805 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4808 for (Object[] fm : filesmatched)
4810 // try and associate
4811 // TODO: may want to set a standard ID naming formalism for
4812 // associating PDB files which have no IDs.
4813 for (SequenceI toassoc : (SequenceI[]) fm[2])
4815 PDBEntry pe = new AssociatePdbFileWithSeq()
4816 .associatePdbWithSeq((String) fm[0],
4817 (String) fm[1], toassoc, false);
4820 System.err.println("Associated file : "
4821 + ((String) fm[0]) + " with "
4822 + toassoc.getDisplayId(true));
4826 alignPanel.paintAlignment(true);
4830 if (filesnotmatched.size() > 0)
4833 && (Cache.getDefault(
4834 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4837 MessageManager.formatMessage("label.ignore_unmatched_dropped_files_info", new String[]{Integer.valueOf(filesnotmatched.size()).toString()}),
4838 MessageManager.getString("label.ignore_unmatched_dropped_files"),
4839 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4843 for (String fn : filesnotmatched)
4845 loadJalviewDataFile(fn, null, null, null);
4849 } catch (Exception ex)
4851 ex.printStackTrace();
4857 * Attempt to load a "dropped" file or URL string: First by testing whether
4858 * it's and Annotation file, then a JNet file, and finally a features file. If
4859 * all are false then the user may have dropped an alignment file onto this
4863 * either a filename or a URL string.
4865 public void loadJalviewDataFile(String file, String protocol,
4866 String format, SequenceI assocSeq)
4870 if (protocol == null)
4872 protocol = jalview.io.FormatAdapter.checkProtocol(file);
4874 // if the file isn't identified, or not positively identified as some
4875 // other filetype (PFAM is default unidentified alignment file type) then
4876 // try to parse as annotation.
4877 boolean isAnnotation = (format == null || format
4878 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4879 .readAnnotationFile(viewport.getAlignment(), file, protocol)
4884 // first see if its a T-COFFEE score file
4885 TCoffeeScoreFile tcf = null;
4888 tcf = new TCoffeeScoreFile(file, protocol);
4891 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4893 tcoffeeColour.setEnabled(true);
4894 tcoffeeColour.setSelected(true);
4895 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4896 isAnnotation = true;
4897 statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
4901 // some problem - if no warning its probable that the ID matching
4902 // process didn't work
4906 tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment")
4907 : tcf.getWarningMessage(),
4908 MessageManager.getString("label.problem_reading_tcoffee_score_file"),
4909 JOptionPane.WARNING_MESSAGE);
4916 } catch (Exception x)
4919 .debug("Exception when processing data source as T-COFFEE score file",
4925 // try to see if its a JNet 'concise' style annotation file *before*
4927 // try to parse it as a features file
4930 format = new IdentifyFile().Identify(file, protocol);
4932 if (format.equalsIgnoreCase("JnetFile"))
4934 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
4936 new JnetAnnotationMaker().add_annotation(predictions,
4937 viewport.getAlignment(), 0, false);
4938 isAnnotation = true;
4943 * if (format.equalsIgnoreCase("PDB")) {
4945 * String pdbfn = ""; // try to match up filename with sequence id
4946 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
4947 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
4948 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4949 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
4950 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4951 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
4952 * // attempt to find a match in the alignment SequenceI mtch =
4953 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4954 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
4955 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
4956 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
4957 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4958 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
4959 * { System.err.println("Associated file : " + file + " with " +
4960 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4961 * TODO: maybe need to load as normal otherwise return; } }
4963 // try to parse it as a features file
4964 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4965 // if it wasn't a features file then we just treat it as a general
4966 // alignment file to load into the current view.
4969 new FileLoader().LoadFile(viewport, file, protocol, format);
4973 alignPanel.paintAlignment(true);
4981 alignPanel.adjustAnnotationHeight();
4982 viewport.updateSequenceIdColours();
4983 buildSortByAnnotationScoresMenu();
4984 alignPanel.paintAlignment(true);
4986 } catch (Exception ex)
4988 ex.printStackTrace();
4989 } catch (OutOfMemoryError oom)
4994 } catch (Exception x)
5000 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5001 : "using " + protocol + " from " + file)
5003 + (format != null ? "(parsing as '" + format
5004 + "' file)" : ""), oom, Desktop.desktop);
5009 public void tabSelectionChanged(int index)
5013 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5014 viewport = alignPanel.av;
5015 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5016 setMenusFromViewport(viewport);
5021 public void tabbedPane_mousePressed(MouseEvent e)
5023 if (SwingUtilities.isRightMouseButton(e))
5025 String reply = JOptionPane.showInternalInputDialog(this,
5026 MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name"),
5027 JOptionPane.QUESTION_MESSAGE);
5031 viewport.viewName = reply;
5032 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5037 public AlignViewport getCurrentView()
5043 * Open the dialog for regex description parsing.
5046 protected void extractScores_actionPerformed(ActionEvent e)
5048 ParseProperties pp = new jalview.analysis.ParseProperties(
5049 viewport.getAlignment());
5050 // TODO: verify regex and introduce GUI dialog for version 2.5
5051 // if (pp.getScoresFromDescription("col", "score column ",
5052 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5054 if (pp.getScoresFromDescription("description column",
5055 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5057 buildSortByAnnotationScoresMenu();
5065 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5069 protected void showDbRefs_actionPerformed(ActionEvent e)
5071 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5077 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5081 protected void showNpFeats_actionPerformed(ActionEvent e)
5083 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5087 * find the viewport amongst the tabs in this alignment frame and close that
5092 public boolean closeView(AlignViewport av)
5096 this.closeMenuItem_actionPerformed(false);
5099 Component[] comp = tabbedPane.getComponents();
5100 for (int i = 0; comp != null && i < comp.length; i++)
5102 if (comp[i] instanceof AlignmentPanel)
5104 if (((AlignmentPanel) comp[i]).av == av)
5107 closeView((AlignmentPanel) comp[i]);
5115 protected void build_fetchdbmenu(JMenu webService)
5117 // Temporary hack - DBRef Fetcher always top level ws entry.
5118 // TODO We probably want to store a sequence database checklist in
5119 // preferences and have checkboxes.. rather than individual sources selected
5121 final JMenu rfetch = new JMenu(MessageManager.getString("action.fetch_db_references"));
\r
5122 rfetch.setToolTipText(MessageManager.getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
\r
5123 webService.add(rfetch);
5125 JMenuItem fetchr = new JMenuItem(MessageManager.getString("label.standard_databases"));
\r
5126 fetchr.setToolTipText(MessageManager.getString("label.fetch_embl_uniprot"));
\r
5127 fetchr.addActionListener(new ActionListener()
5131 public void actionPerformed(ActionEvent e)
5133 new Thread(new Runnable()
5139 new jalview.ws.DBRefFetcher(alignPanel.av
5140 .getSequenceSelection(), alignPanel.alignFrame)
5141 .fetchDBRefs(false);
5149 final AlignFrame me = this;
5150 new Thread(new Runnable()
5155 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5156 .getSequenceFetcherSingleton(me);
5157 javax.swing.SwingUtilities.invokeLater(new Runnable()
5162 String[] dbclasses = sf.getOrderedSupportedSources();
5163 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5164 // jalview.util.QuickSort.sort(otherdb, otherdb);
5165 List<DbSourceProxy> otherdb;
5166 JMenu dfetch = new JMenu();
5167 JMenu ifetch = new JMenu();
5168 JMenuItem fetchr = null;
5169 int comp = 0, icomp = 0, mcomp = 15;
5170 String mname = null;
5172 for (String dbclass : dbclasses)
5174 otherdb = sf.getSourceProxy(dbclass);
5175 // add a single entry for this class, or submenu allowing 'fetch
5177 if (otherdb == null || otherdb.size() < 1)
5181 // List<DbSourceProxy> dbs=otherdb;
5182 // otherdb=new ArrayList<DbSourceProxy>();
5183 // for (DbSourceProxy db:dbs)
5185 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5189 mname = "From " + dbclass;
5191 if (otherdb.size() == 1)
5193 final DbSourceProxy[] dassource = otherdb
5194 .toArray(new DbSourceProxy[0]);
5195 DbSourceProxy src = otherdb.get(0);
5196 fetchr = new JMenuItem(src.getDbSource());
5197 fetchr.addActionListener(new ActionListener()
5201 public void actionPerformed(ActionEvent e)
5203 new Thread(new Runnable()
5209 new jalview.ws.DBRefFetcher(alignPanel.av
5210 .getSequenceSelection(),
5211 alignPanel.alignFrame, dassource)
5212 .fetchDBRefs(false);
5218 fetchr.setToolTipText("<html>"
5219 + JvSwingUtils.wrapTooltip("Retrieve from "
5220 + src.getDbName()) + "<html>");
5226 final DbSourceProxy[] dassource = otherdb
5227 .toArray(new DbSourceProxy[0]);
5229 DbSourceProxy src = otherdb.get(0);
5230 fetchr = new JMenuItem(MessageManager.formatMessage("label.fetch_all_param", new String[]{src.getDbSource()}));
\r
5231 fetchr.addActionListener(new ActionListener()
5234 public void actionPerformed(ActionEvent e)
5236 new Thread(new Runnable()
5242 new jalview.ws.DBRefFetcher(alignPanel.av
5243 .getSequenceSelection(),
5244 alignPanel.alignFrame, dassource)
5245 .fetchDBRefs(false);
5251 fetchr.setToolTipText("<html>"
5252 + JvSwingUtils.wrapTooltip("Retrieve from all "
5253 + otherdb.size() + " sources in "
5254 + src.getDbSource() + "<br>First is :"
5255 + src.getDbName()) + "<html>");
5258 // and then build the rest of the individual menus
5259 ifetch = new JMenu("Sources from " + src.getDbSource());
5261 String imname = null;
5263 for (DbSourceProxy sproxy : otherdb)
5265 String dbname = sproxy.getDbName();
5266 String sname = dbname.length() > 5 ? dbname.substring(0,
5267 5) + "..." : dbname;
5268 String msname = dbname.length() > 10 ? dbname.substring(
5269 0, 10) + "..." : dbname;
5272 imname = "from '" + sname + "'";
5274 fetchr = new JMenuItem(msname);
5275 final DbSourceProxy[] dassrc =
5277 fetchr.addActionListener(new ActionListener()
5281 public void actionPerformed(ActionEvent e)
5283 new Thread(new Runnable()
5289 new jalview.ws.DBRefFetcher(alignPanel.av
5290 .getSequenceSelection(),
5291 alignPanel.alignFrame, dassrc)
5292 .fetchDBRefs(false);
5298 fetchr.setToolTipText("<html>"
5299 + JvSwingUtils.wrapTooltip("Retrieve from "
5300 + dbname) + "</html>");
5303 if (++icomp >= mcomp || i == (otherdb.size()))
5305 ifetch.setText(MessageManager.formatMessage("label.source_to_target",imname,sname));
5307 ifetch = new JMenu();
5315 if (comp >= mcomp || dbi >= (dbclasses.length))
5317 dfetch.setText(MessageManager.formatMessage("label.source_to_target",mname,dbclass));
5319 dfetch = new JMenu();
5332 * Left justify the whole alignment.
5335 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5337 AlignmentI al = viewport.getAlignment();
5339 viewport.firePropertyChange("alignment", null, al);
5343 * Right justify the whole alignment.
5346 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5348 AlignmentI al = viewport.getAlignment();
5350 viewport.firePropertyChange("alignment", null, al);
5353 public void setShowSeqFeatures(boolean b)
5355 showSeqFeatures.setSelected(true);
5356 viewport.setShowSequenceFeatures(true);
5363 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5364 * awt.event.ActionEvent)
5367 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5369 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5370 alignPanel.paintAlignment(true);
5377 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5381 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5383 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5384 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5392 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5393 * .event.ActionEvent)
5396 protected void showGroupConservation_actionPerformed(ActionEvent e)
5398 viewport.setShowGroupConservation(showGroupConservation.getState());
5399 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5406 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5407 * .event.ActionEvent)
5410 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5412 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5413 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5420 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5421 * .event.ActionEvent)
5424 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5426 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5427 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5431 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5433 showSequenceLogo.setState(true);
5434 viewport.setShowSequenceLogo(true);
5435 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5436 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5440 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5442 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5449 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5450 * .event.ActionEvent)
5453 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5455 if (avc.makeGroupsFromSelection()) {
5456 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5457 alignPanel.updateAnnotation();
5458 alignPanel.paintAlignment(true);
5463 protected void createGroup_actionPerformed(ActionEvent e)
5465 if (avc.createGroup())
5467 alignPanel.alignmentChanged();
5472 protected void unGroup_actionPerformed(ActionEvent e)
5476 alignPanel.alignmentChanged();
5481 * make the given alignmentPanel the currently selected tab
5483 * @param alignmentPanel
5485 public void setDisplayedView(AlignmentPanel alignmentPanel)
5487 if (!viewport.getSequenceSetId().equals(
5488 alignmentPanel.av.getSequenceSetId()))
5491 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5493 if (tabbedPane != null
5494 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5495 .getSelectedIndex())
5497 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5502 class PrintThread extends Thread
5506 public PrintThread(AlignmentPanel ap)
5511 static PageFormat pf;
5516 PrinterJob printJob = PrinterJob.getPrinterJob();
5520 printJob.setPrintable(ap, pf);
5524 printJob.setPrintable(ap);
5527 if (printJob.printDialog())
5532 } catch (Exception PrintException)
5534 PrintException.printStackTrace();