2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.AlignmentSorter;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.analysis.CrossRef;
28 import jalview.analysis.NJTree;
29 import jalview.analysis.ParseProperties;
30 import jalview.analysis.SequenceIdMatcher;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.analysis.ScoreModelI;
34 import jalview.bin.Cache;
35 import jalview.commands.CommandI;
36 import jalview.commands.EditCommand;
37 import jalview.commands.OrderCommand;
38 import jalview.commands.RemoveGapColCommand;
39 import jalview.commands.RemoveGapsCommand;
40 import jalview.commands.SlideSequencesCommand;
41 import jalview.commands.TrimRegionCommand;
42 import jalview.datamodel.AlignedCodonFrame;
43 import jalview.datamodel.Alignment;
44 import jalview.datamodel.AlignmentAnnotation;
45 import jalview.datamodel.AlignmentI;
46 import jalview.datamodel.AlignmentOrder;
47 import jalview.datamodel.AlignmentView;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.PDBEntry;
50 import jalview.datamodel.SeqCigar;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AlignmentProperties;
55 import jalview.io.AnnotationFile;
56 import jalview.io.FeaturesFile;
57 import jalview.io.FileLoader;
58 import jalview.io.FormatAdapter;
59 import jalview.io.HTMLOutput;
60 import jalview.io.IdentifyFile;
61 import jalview.io.JalviewFileChooser;
62 import jalview.io.JalviewFileView;
63 import jalview.io.JnetAnnotationMaker;
64 import jalview.io.NewickFile;
65 import jalview.io.TCoffeeScoreFile;
66 import jalview.jbgui.GAlignFrame;
67 import jalview.schemes.Blosum62ColourScheme;
68 import jalview.schemes.BuriedColourScheme;
69 import jalview.schemes.ClustalxColourScheme;
70 import jalview.schemes.ColourSchemeI;
71 import jalview.schemes.ColourSchemeProperty;
72 import jalview.schemes.HelixColourScheme;
73 import jalview.schemes.HydrophobicColourScheme;
74 import jalview.schemes.NucleotideColourScheme;
75 import jalview.schemes.PIDColourScheme;
76 import jalview.schemes.PurinePyrimidineColourScheme;
77 import jalview.schemes.RNAHelicesColourChooser;
78 import jalview.schemes.ResidueProperties;
79 import jalview.schemes.StrandColourScheme;
80 import jalview.schemes.TCoffeeColourScheme;
81 import jalview.schemes.TaylorColourScheme;
82 import jalview.schemes.TurnColourScheme;
83 import jalview.schemes.UserColourScheme;
84 import jalview.schemes.ZappoColourScheme;
85 import jalview.util.MessageManager;
86 import jalview.ws.jws1.Discoverer;
87 import jalview.ws.jws2.Jws2Discoverer;
88 import jalview.ws.jws2.jabaws2.Jws2Instance;
89 import jalview.ws.seqfetcher.DbSourceProxy;
91 import java.awt.BorderLayout;
92 import java.awt.Component;
93 import java.awt.GridLayout;
94 import java.awt.Rectangle;
95 import java.awt.Toolkit;
96 import java.awt.datatransfer.Clipboard;
97 import java.awt.datatransfer.DataFlavor;
98 import java.awt.datatransfer.StringSelection;
99 import java.awt.datatransfer.Transferable;
100 import java.awt.dnd.DnDConstants;
101 import java.awt.dnd.DropTargetDragEvent;
102 import java.awt.dnd.DropTargetDropEvent;
103 import java.awt.dnd.DropTargetEvent;
104 import java.awt.dnd.DropTargetListener;
105 import java.awt.event.ActionEvent;
106 import java.awt.event.ActionListener;
107 import java.awt.event.KeyAdapter;
108 import java.awt.event.KeyEvent;
109 import java.awt.event.MouseAdapter;
110 import java.awt.event.MouseEvent;
111 import java.awt.print.PageFormat;
112 import java.awt.print.PrinterJob;
113 import java.beans.PropertyChangeEvent;
116 import java.util.ArrayList;
117 import java.util.Enumeration;
118 import java.util.Hashtable;
119 import java.util.List;
120 import java.util.Vector;
122 import javax.swing.JButton;
123 import javax.swing.JCheckBoxMenuItem;
124 import javax.swing.JEditorPane;
125 import javax.swing.JInternalFrame;
126 import javax.swing.JLabel;
127 import javax.swing.JLayeredPane;
128 import javax.swing.JMenu;
129 import javax.swing.JMenuItem;
130 import javax.swing.JOptionPane;
131 import javax.swing.JPanel;
132 import javax.swing.JProgressBar;
133 import javax.swing.JRadioButtonMenuItem;
134 import javax.swing.JScrollPane;
135 import javax.swing.SwingUtilities;
141 * @version $Revision$
143 public class AlignFrame extends GAlignFrame implements DropTargetListener,
144 IProgressIndicator, AlignViewControllerGuiI
148 public static final int DEFAULT_WIDTH = 700;
151 public static final int DEFAULT_HEIGHT = 500;
153 public AlignmentPanel alignPanel;
155 AlignViewport viewport;
157 public AlignViewControllerI avc;
159 Vector alignPanels = new Vector();
162 * Last format used to load or save alignments in this window
164 String currentFileFormat = null;
167 * Current filename for this alignment
169 String fileName = null;
172 * Creates a new AlignFrame object with specific width and height.
178 public AlignFrame(AlignmentI al, int width, int height)
180 this(al, null, width, height);
184 * Creates a new AlignFrame object with specific width, height and
190 * @param sequenceSetId
192 public AlignFrame(AlignmentI al, int width, int height,
193 String sequenceSetId)
195 this(al, null, width, height, sequenceSetId);
199 * Creates a new AlignFrame object with specific width, height and
205 * @param sequenceSetId
208 public AlignFrame(AlignmentI al, int width, int height,
209 String sequenceSetId, String viewId)
211 this(al, null, width, height, sequenceSetId, viewId);
215 * new alignment window with hidden columns
219 * @param hiddenColumns
220 * ColumnSelection or null
222 * Width of alignment frame
226 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
227 int width, int height)
229 this(al, hiddenColumns, width, height, null);
233 * Create alignment frame for al with hiddenColumns, a specific width and
234 * height, and specific sequenceId
237 * @param hiddenColumns
240 * @param sequenceSetId
243 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
244 int width, int height, String sequenceSetId)
246 this(al, hiddenColumns, width, height, sequenceSetId, null);
250 * Create alignment frame for al with hiddenColumns, a specific width and
251 * height, and specific sequenceId
254 * @param hiddenColumns
257 * @param sequenceSetId
262 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
263 int width, int height, String sequenceSetId, String viewId)
265 setSize(width, height);
267 if (al.getDataset() == null)
272 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
274 alignPanel = new AlignmentPanel(this, viewport);
277 addAlignmentPanel(alignPanel, true);
282 * Make a new AlignFrame from existing alignmentPanels
289 public AlignFrame(AlignmentPanel ap)
293 addAlignmentPanel(ap, false);
298 * initalise the alignframe from the underlying viewport data and the
303 avc = new jalview.controller.AlignViewController(this, viewport,
305 if (viewport.getAlignmentConservationAnnotation() == null)
307 BLOSUM62Colour.setEnabled(false);
308 conservationMenuItem.setEnabled(false);
309 modifyConservation.setEnabled(false);
310 // PIDColour.setEnabled(false);
311 // abovePIDThreshold.setEnabled(false);
312 // modifyPID.setEnabled(false);
315 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
318 if (sortby.equals("Id"))
320 sortIDMenuItem_actionPerformed(null);
322 else if (sortby.equals("Pairwise Identity"))
324 sortPairwiseMenuItem_actionPerformed(null);
327 if (Desktop.desktop != null)
329 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
330 addServiceListeners();
331 setGUINucleotide(viewport.getAlignment().isNucleotide());
334 setMenusFromViewport(viewport);
335 buildSortByAnnotationScoresMenu();
338 if (viewport.wrapAlignment)
340 wrapMenuItem_actionPerformed(null);
343 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
345 this.overviewMenuItem_actionPerformed(null);
353 * Change the filename and format for the alignment, and enable the 'reload'
354 * button functionality.
361 public void setFileName(String file, String format)
364 currentFileFormat = format;
365 reload.setEnabled(true);
368 void addKeyListener()
370 addKeyListener(new KeyAdapter()
373 public void keyPressed(KeyEvent evt)
375 if (viewport.cursorMode
376 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
377 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
378 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
379 && Character.isDigit(evt.getKeyChar()))
381 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
384 switch (evt.getKeyCode())
387 case 27: // escape key
388 deselectAllSequenceMenuItem_actionPerformed(null);
392 case KeyEvent.VK_DOWN:
393 if (evt.isAltDown() || !viewport.cursorMode)
395 moveSelectedSequences(false);
397 if (viewport.cursorMode)
399 alignPanel.seqPanel.moveCursor(0, 1);
404 if (evt.isAltDown() || !viewport.cursorMode)
406 moveSelectedSequences(true);
408 if (viewport.cursorMode)
410 alignPanel.seqPanel.moveCursor(0, -1);
415 case KeyEvent.VK_LEFT:
416 if (evt.isAltDown() || !viewport.cursorMode)
418 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
422 alignPanel.seqPanel.moveCursor(-1, 0);
427 case KeyEvent.VK_RIGHT:
428 if (evt.isAltDown() || !viewport.cursorMode)
430 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
434 alignPanel.seqPanel.moveCursor(1, 0);
438 case KeyEvent.VK_SPACE:
439 if (viewport.cursorMode)
441 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
442 || evt.isShiftDown() || evt.isAltDown());
446 // case KeyEvent.VK_A:
447 // if (viewport.cursorMode)
449 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
450 // //System.out.println("A");
454 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
455 * System.out.println("closing bracket"); } break;
457 case KeyEvent.VK_DELETE:
458 case KeyEvent.VK_BACK_SPACE:
459 if (!viewport.cursorMode)
461 cut_actionPerformed(null);
465 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
466 || evt.isShiftDown() || evt.isAltDown());
472 if (viewport.cursorMode)
474 alignPanel.seqPanel.setCursorRow();
478 if (viewport.cursorMode && !evt.isControlDown())
480 alignPanel.seqPanel.setCursorColumn();
484 if (viewport.cursorMode)
486 alignPanel.seqPanel.setCursorPosition();
490 case KeyEvent.VK_ENTER:
491 case KeyEvent.VK_COMMA:
492 if (viewport.cursorMode)
494 alignPanel.seqPanel.setCursorRowAndColumn();
499 if (viewport.cursorMode)
501 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
505 if (viewport.cursorMode)
507 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
512 viewport.cursorMode = !viewport.cursorMode;
513 statusBar.setText(MessageManager.formatMessage(
514 "label.keyboard_editing_mode", new String[]
515 { (viewport.cursorMode ? "on" : "off") }));
516 if (viewport.cursorMode)
518 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
519 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
521 alignPanel.seqPanel.seqCanvas.repaint();
527 Help.showHelpWindow();
528 } catch (Exception ex)
530 ex.printStackTrace();
535 boolean toggleSeqs = !evt.isControlDown();
536 boolean toggleCols = !evt.isShiftDown();
537 toggleHiddenRegions(toggleSeqs, toggleCols);
540 case KeyEvent.VK_PAGE_UP:
541 if (viewport.wrapAlignment)
543 alignPanel.scrollUp(true);
547 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
548 - viewport.endSeq + viewport.startSeq);
551 case KeyEvent.VK_PAGE_DOWN:
552 if (viewport.wrapAlignment)
554 alignPanel.scrollUp(false);
558 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
559 + viewport.endSeq - viewport.startSeq);
566 public void keyReleased(KeyEvent evt)
568 switch (evt.getKeyCode())
570 case KeyEvent.VK_LEFT:
571 if (evt.isAltDown() || !viewport.cursorMode)
573 viewport.firePropertyChange("alignment", null, viewport
574 .getAlignment().getSequences());
578 case KeyEvent.VK_RIGHT:
579 if (evt.isAltDown() || !viewport.cursorMode)
581 viewport.firePropertyChange("alignment", null, viewport
582 .getAlignment().getSequences());
590 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
592 ap.alignFrame = this;
593 avc = new jalview.controller.AlignViewController(this, viewport,
596 alignPanels.addElement(ap);
598 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
600 int aSize = alignPanels.size();
602 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
604 if (aSize == 1 && ap.av.viewName == null)
606 this.getContentPane().add(ap, BorderLayout.CENTER);
612 setInitialTabVisible();
615 expandViews.setEnabled(true);
616 gatherViews.setEnabled(true);
617 tabbedPane.addTab(ap.av.viewName, ap);
619 ap.setVisible(false);
624 if (ap.av.isPadGaps())
626 ap.av.getAlignment().padGaps();
628 ap.av.updateConservation(ap);
629 ap.av.updateConsensus(ap);
630 ap.av.updateStrucConsensus(ap);
634 public void setInitialTabVisible()
636 expandViews.setEnabled(true);
637 gatherViews.setEnabled(true);
638 tabbedPane.setVisible(true);
639 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
640 tabbedPane.addTab(first.av.viewName, first);
641 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
644 public AlignViewport getViewport()
649 /* Set up intrinsic listeners for dynamically generated GUI bits. */
650 private void addServiceListeners()
652 final java.beans.PropertyChangeListener thisListener;
653 Desktop.instance.addJalviewPropertyChangeListener("services",
654 thisListener = new java.beans.PropertyChangeListener()
657 public void propertyChange(PropertyChangeEvent evt)
659 // // System.out.println("Discoverer property change.");
660 // if (evt.getPropertyName().equals("services"))
662 SwingUtilities.invokeLater(new Runnable()
669 .println("Rebuild WS Menu for service change");
670 BuildWebServiceMenu();
677 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
680 public void internalFrameClosed(
681 javax.swing.event.InternalFrameEvent evt)
683 System.out.println("deregistering discoverer listener");
684 Desktop.instance.removeJalviewPropertyChangeListener("services",
686 closeMenuItem_actionPerformed(true);
689 // Finally, build the menu once to get current service state
690 new Thread(new Runnable()
695 BuildWebServiceMenu();
700 public void setGUINucleotide(boolean nucleotide)
702 showTranslation.setVisible(nucleotide);
703 conservationMenuItem.setEnabled(!nucleotide);
704 modifyConservation.setEnabled(!nucleotide);
705 showGroupConservation.setEnabled(!nucleotide);
706 rnahelicesColour.setEnabled(nucleotide);
707 purinePyrimidineColour.setEnabled(nucleotide);
708 // Remember AlignFrame always starts as protein
712 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
717 * set up menus for the currently viewport. This may be called after any
718 * operation that affects the data in the current view (selection changed,
719 * etc) to update the menus to reflect the new state.
721 public void setMenusForViewport()
723 setMenusFromViewport(viewport);
727 * Need to call this method when tabs are selected for multiple views, or when
728 * loading from Jalview2XML.java
733 void setMenusFromViewport(AlignViewport av)
735 padGapsMenuitem.setSelected(av.isPadGaps());
736 colourTextMenuItem.setSelected(av.showColourText);
737 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
738 conservationMenuItem.setSelected(av.getConservationSelected());
739 seqLimits.setSelected(av.getShowJVSuffix());
740 idRightAlign.setSelected(av.rightAlignIds);
741 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
742 renderGapsMenuItem.setSelected(av.renderGaps);
743 wrapMenuItem.setSelected(av.wrapAlignment);
744 scaleAbove.setVisible(av.wrapAlignment);
745 scaleLeft.setVisible(av.wrapAlignment);
746 scaleRight.setVisible(av.wrapAlignment);
747 annotationPanelMenuItem.setState(av.showAnnotation);
749 * Show/hide annotations only enabled if annotation panel is shown
751 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
752 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
753 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
754 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
755 viewBoxesMenuItem.setSelected(av.showBoxes);
756 viewTextMenuItem.setSelected(av.showText);
757 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
758 showGroupConsensus.setSelected(av.isShowGroupConsensus());
759 showGroupConservation.setSelected(av.isShowGroupConservation());
760 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
761 showSequenceLogo.setSelected(av.isShowSequenceLogo());
762 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
764 setColourSelected(ColourSchemeProperty.getColourName(av
765 .getGlobalColourScheme()));
767 showSeqFeatures.setSelected(av.showSequenceFeatures);
768 hiddenMarkers.setState(av.showHiddenMarkers);
769 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
770 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
771 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
772 autoCalculate.setSelected(av.autoCalculateConsensus);
773 sortByTree.setSelected(av.sortByTree);
774 listenToViewSelections.setSelected(av.followSelection);
775 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
777 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
778 setShowProductsEnabled();
782 // methods for implementing IProgressIndicator
783 // need to refactor to a reusable stub class
784 Hashtable progressBars, progressBarHandlers;
789 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
792 public void setProgressBar(String message, long id)
794 if (progressBars == null)
796 progressBars = new Hashtable();
797 progressBarHandlers = new Hashtable();
800 JPanel progressPanel;
801 Long lId = new Long(id);
802 GridLayout layout = (GridLayout) statusPanel.getLayout();
803 if (progressBars.get(lId) != null)
805 progressPanel = (JPanel) progressBars.get(new Long(id));
806 statusPanel.remove(progressPanel);
807 progressBars.remove(lId);
808 progressPanel = null;
811 statusBar.setText(message);
813 if (progressBarHandlers.contains(lId))
815 progressBarHandlers.remove(lId);
817 layout.setRows(layout.getRows() - 1);
821 progressPanel = new JPanel(new BorderLayout(10, 5));
823 JProgressBar progressBar = new JProgressBar();
824 progressBar.setIndeterminate(true);
826 progressPanel.add(new JLabel(message), BorderLayout.WEST);
827 progressPanel.add(progressBar, BorderLayout.CENTER);
829 layout.setRows(layout.getRows() + 1);
830 statusPanel.add(progressPanel);
832 progressBars.put(lId, progressPanel);
835 // setMenusForViewport();
840 public void registerHandler(final long id,
841 final IProgressIndicatorHandler handler)
843 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
845 throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
847 progressBarHandlers.put(new Long(id), handler);
848 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
849 if (handler.canCancel())
851 JButton cancel = new JButton(
852 MessageManager.getString("action.cancel"));
853 final IProgressIndicator us = this;
854 cancel.addActionListener(new ActionListener()
858 public void actionPerformed(ActionEvent e)
860 handler.cancelActivity(id);
861 us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
864 progressPanel.add(cancel, BorderLayout.EAST);
870 * @return true if any progress bars are still active
873 public boolean operationInProgress()
875 if (progressBars != null && progressBars.size() > 0)
883 public void setStatus(String text)
885 statusBar.setText(text);
889 * Added so Castor Mapping file can obtain Jalview Version
891 public String getVersion()
893 return jalview.bin.Cache.getProperty("VERSION");
896 public FeatureRenderer getFeatureRenderer()
898 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
902 public void fetchSequence_actionPerformed(ActionEvent e)
904 new SequenceFetcher(this);
908 public void addFromFile_actionPerformed(ActionEvent e)
910 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
914 public void reload_actionPerformed(ActionEvent e)
916 if (fileName != null)
918 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
919 // originating file's format
920 // TODO: work out how to recover feature settings for correct view(s) when
922 if (currentFileFormat.equals("Jalview"))
924 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
925 for (int i = 0; i < frames.length; i++)
927 if (frames[i] instanceof AlignFrame && frames[i] != this
928 && ((AlignFrame) frames[i]).fileName != null
929 && ((AlignFrame) frames[i]).fileName.equals(fileName))
933 frames[i].setSelected(true);
934 Desktop.instance.closeAssociatedWindows();
935 } catch (java.beans.PropertyVetoException ex)
941 Desktop.instance.closeAssociatedWindows();
943 FileLoader loader = new FileLoader();
944 String protocol = fileName.startsWith("http:") ? "URL" : "File";
945 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
949 Rectangle bounds = this.getBounds();
951 FileLoader loader = new FileLoader();
952 String protocol = fileName.startsWith("http:") ? "URL" : "File";
953 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
954 protocol, currentFileFormat);
956 newframe.setBounds(bounds);
957 if (featureSettings != null && featureSettings.isShowing())
959 final Rectangle fspos = featureSettings.frame.getBounds();
960 // TODO: need a 'show feature settings' function that takes bounds -
961 // need to refactor Desktop.addFrame
962 newframe.featureSettings_actionPerformed(null);
963 final FeatureSettings nfs = newframe.featureSettings;
964 SwingUtilities.invokeLater(new Runnable()
969 nfs.frame.setBounds(fspos);
972 this.featureSettings.close();
973 this.featureSettings = null;
975 this.closeMenuItem_actionPerformed(true);
981 public void addFromText_actionPerformed(ActionEvent e)
983 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
987 public void addFromURL_actionPerformed(ActionEvent e)
989 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
993 public void save_actionPerformed(ActionEvent e)
996 || (currentFileFormat == null || !jalview.io.FormatAdapter
997 .isValidIOFormat(currentFileFormat, true))
998 || fileName.startsWith("http"))
1000 saveAs_actionPerformed(null);
1004 saveAlignment(fileName, currentFileFormat);
1015 public void saveAs_actionPerformed(ActionEvent e)
1017 JalviewFileChooser chooser = new JalviewFileChooser(
1018 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1019 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1020 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1021 currentFileFormat, false);
1023 chooser.setFileView(new JalviewFileView());
1024 chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1025 chooser.setToolTipText(MessageManager.getString("action.save"));
1027 int value = chooser.showSaveDialog(this);
1029 if (value == JalviewFileChooser.APPROVE_OPTION)
1031 currentFileFormat = chooser.getSelectedFormat();
1032 if (currentFileFormat == null)
1035 .showInternalMessageDialog(
1038 .getString("label.select_file_format_before_saving"),
1040 .getString("label.file_format_not_specified"),
1041 JOptionPane.WARNING_MESSAGE);
1042 value = chooser.showSaveDialog(this);
1046 fileName = chooser.getSelectedFile().getPath();
1048 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1051 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1052 if (currentFileFormat.indexOf(" ") > -1)
1054 currentFileFormat = currentFileFormat.substring(0,
1055 currentFileFormat.indexOf(" "));
1057 saveAlignment(fileName, currentFileFormat);
1061 public boolean saveAlignment(String file, String format)
1063 boolean success = true;
1065 if (format.equalsIgnoreCase("Jalview"))
1067 String shortName = title;
1069 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1071 shortName = shortName.substring(shortName
1072 .lastIndexOf(java.io.File.separatorChar) + 1);
1075 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1077 statusBar.setText(MessageManager.formatMessage(
1078 "label.successfully_saved_to_file_in_format", new String[]
1079 { fileName, format }));
1084 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1086 warningMessage("Cannot save file " + fileName + " using format "
1087 + format, "Alignment output format not supported");
1088 saveAs_actionPerformed(null);
1089 // JBPNote need to have a raise_gui flag here
1093 String[] omitHidden = null;
1095 if (viewport.hasHiddenColumns())
1097 int reply = JOptionPane
1098 .showInternalConfirmDialog(
1101 .getString("label.alignment_contains_hidden_columns"),
1103 .getString("action.save_omit_hidden_columns"),
1104 JOptionPane.YES_NO_OPTION,
1105 JOptionPane.QUESTION_MESSAGE);
1107 if (reply == JOptionPane.YES_OPTION)
1109 omitHidden = viewport.getViewAsString(false);
1112 FormatAdapter f = new FormatAdapter();
1113 String output = f.formatSequences(format,
1114 viewport.getAlignment(), // class cast exceptions will
1115 // occur in the distant future
1116 omitHidden, f.getCacheSuffixDefault(format),
1117 viewport.getColumnSelection());
1127 java.io.PrintWriter out = new java.io.PrintWriter(
1128 new java.io.FileWriter(file));
1132 this.setTitle(file);
1133 statusBar.setText(MessageManager.formatMessage(
1134 "label.successfully_saved_to_file_in_format",
1136 { fileName, format }));
1137 } catch (Exception ex)
1140 ex.printStackTrace();
1147 JOptionPane.showInternalMessageDialog(this, MessageManager
1148 .formatMessage("label.couldnt_save_file", new String[]
1149 { fileName }), MessageManager
1150 .getString("label.error_saving_file"),
1151 JOptionPane.WARNING_MESSAGE);
1157 private void warningMessage(String warning, String title)
1159 if (new jalview.util.Platform().isHeadless())
1161 System.err.println("Warning: " + title + "\nWarning: " + warning);
1166 JOptionPane.showInternalMessageDialog(this, warning, title,
1167 JOptionPane.WARNING_MESSAGE);
1179 protected void outputText_actionPerformed(ActionEvent e)
1181 String[] omitHidden = null;
1183 if (viewport.hasHiddenColumns())
1185 int reply = JOptionPane
1186 .showInternalConfirmDialog(
1189 .getString("label.alignment_contains_hidden_columns"),
1191 .getString("action.save_omit_hidden_columns"),
1192 JOptionPane.YES_NO_OPTION,
1193 JOptionPane.QUESTION_MESSAGE);
1195 if (reply == JOptionPane.YES_OPTION)
1197 omitHidden = viewport.getViewAsString(false);
1201 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1202 cap.setForInput(null);
1206 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1207 viewport.getAlignment(), omitHidden,
1208 viewport.getColumnSelection()));
1209 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1210 "label.alignment_output_command", new String[]
1211 { e.getActionCommand() }), 600, 500);
1212 } catch (OutOfMemoryError oom)
1214 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1227 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1229 new HTMLOutput(alignPanel,
1230 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1231 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1234 public void createImageMap(File file, String image)
1236 alignPanel.makePNGImageMap(file, image);
1246 public void createPNG(File f)
1248 alignPanel.makePNG(f);
1258 public void createEPS(File f)
1260 alignPanel.makeEPS(f);
1263 public void createSVG(File f)
1265 alignPanel.makeSVG(f);
1268 public void pageSetup_actionPerformed(ActionEvent e)
1270 PrinterJob printJob = PrinterJob.getPrinterJob();
1271 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1281 public void printMenuItem_actionPerformed(ActionEvent e)
1283 // Putting in a thread avoids Swing painting problems
1284 PrintThread thread = new PrintThread(alignPanel);
1289 public void exportFeatures_actionPerformed(ActionEvent e)
1291 new AnnotationExporter().exportFeatures(alignPanel);
1295 public void exportAnnotations_actionPerformed(ActionEvent e)
1297 new AnnotationExporter().exportAnnotations(alignPanel,
1298 viewport.showAnnotation ? viewport.getAlignment()
1299 .getAlignmentAnnotation() : null, viewport
1300 .getAlignment().getGroups(), ((Alignment) viewport
1301 .getAlignment()).alignmentProperties);
1305 public void associatedData_actionPerformed(ActionEvent e)
1307 // Pick the tree file
1308 JalviewFileChooser chooser = new JalviewFileChooser(
1309 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1310 chooser.setFileView(new JalviewFileView());
1311 chooser.setDialogTitle(MessageManager
1312 .getString("label.load_jalview_annotations"));
1313 chooser.setToolTipText(MessageManager
1314 .getString("label.load_jalview_annotations"));
1316 int value = chooser.showOpenDialog(null);
1318 if (value == JalviewFileChooser.APPROVE_OPTION)
1320 String choice = chooser.getSelectedFile().getPath();
1321 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1322 loadJalviewDataFile(choice, null, null, null);
1328 * Close the current view or all views in the alignment frame. If the frame
1329 * only contains one view then the alignment will be removed from memory.
1331 * @param closeAllTabs
1334 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1336 if (alignPanels != null && alignPanels.size() < 2)
1338 closeAllTabs = true;
1343 if (alignPanels != null)
1347 if (this.isClosed())
1349 // really close all the windows - otherwise wait till
1350 // setClosed(true) is called
1351 for (int i = 0; i < alignPanels.size(); i++)
1353 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1360 closeView(alignPanel);
1366 this.setClosed(true);
1368 } catch (Exception ex)
1370 ex.printStackTrace();
1375 * close alignPanel2 and shuffle tabs appropriately.
1377 * @param alignPanel2
1379 public void closeView(AlignmentPanel alignPanel2)
1381 int index = tabbedPane.getSelectedIndex();
1382 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1383 alignPanels.removeElement(alignPanel2);
1385 // if (viewport == alignPanel2.av)
1389 alignPanel2.closePanel();
1392 tabbedPane.removeTabAt(closedindex);
1393 tabbedPane.validate();
1395 if (index > closedindex || index == tabbedPane.getTabCount())
1397 // modify currently selected tab index if necessary.
1401 this.tabSelectionChanged(index);
1407 void updateEditMenuBar()
1410 if (viewport.historyList.size() > 0)
1412 undoMenuItem.setEnabled(true);
1413 CommandI command = (CommandI) viewport.historyList.peek();
1414 undoMenuItem.setText(MessageManager.formatMessage(
1415 "label.undo_command", new String[]
1416 { command.getDescription() }));
1420 undoMenuItem.setEnabled(false);
1421 undoMenuItem.setText(MessageManager.getString("action.undo"));
1424 if (viewport.redoList.size() > 0)
1426 redoMenuItem.setEnabled(true);
1428 CommandI command = (CommandI) viewport.redoList.peek();
1429 redoMenuItem.setText(MessageManager.formatMessage(
1430 "label.redo_command", new String[]
1431 { command.getDescription() }));
1435 redoMenuItem.setEnabled(false);
1436 redoMenuItem.setText(MessageManager.getString("action.redo"));
1440 public void addHistoryItem(CommandI command)
1442 if (command.getSize() > 0)
1444 viewport.historyList.push(command);
1445 viewport.redoList.clear();
1446 updateEditMenuBar();
1447 viewport.updateHiddenColumns();
1448 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1449 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1450 // viewport.getColumnSelection()
1451 // .getHiddenColumns().size() > 0);
1457 * @return alignment objects for all views
1459 AlignmentI[] getViewAlignments()
1461 if (alignPanels != null)
1463 Enumeration e = alignPanels.elements();
1464 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1465 for (int i = 0; e.hasMoreElements(); i++)
1467 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1471 if (viewport != null)
1473 return new AlignmentI[]
1474 { viewport.getAlignment() };
1486 protected void undoMenuItem_actionPerformed(ActionEvent e)
1488 if (viewport.historyList.empty())
1492 CommandI command = (CommandI) viewport.historyList.pop();
1493 viewport.redoList.push(command);
1494 command.undoCommand(getViewAlignments());
1496 AlignViewport originalSource = getOriginatingSource(command);
1497 updateEditMenuBar();
1499 if (originalSource != null)
1501 if (originalSource != viewport)
1504 .warn("Implementation worry: mismatch of viewport origin for undo");
1506 originalSource.updateHiddenColumns();
1507 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1509 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1510 // viewport.getColumnSelection()
1511 // .getHiddenColumns().size() > 0);
1512 originalSource.firePropertyChange("alignment", null, originalSource
1513 .getAlignment().getSequences());
1524 protected void redoMenuItem_actionPerformed(ActionEvent e)
1526 if (viewport.redoList.size() < 1)
1531 CommandI command = (CommandI) viewport.redoList.pop();
1532 viewport.historyList.push(command);
1533 command.doCommand(getViewAlignments());
1535 AlignViewport originalSource = getOriginatingSource(command);
1536 updateEditMenuBar();
1538 if (originalSource != null)
1541 if (originalSource != viewport)
1544 .warn("Implementation worry: mismatch of viewport origin for redo");
1546 originalSource.updateHiddenColumns();
1547 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1549 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1550 // viewport.getColumnSelection()
1551 // .getHiddenColumns().size() > 0);
1552 originalSource.firePropertyChange("alignment", null, originalSource
1553 .getAlignment().getSequences());
1557 AlignViewport getOriginatingSource(CommandI command)
1559 AlignViewport originalSource = null;
1560 // For sequence removal and addition, we need to fire
1561 // the property change event FROM the viewport where the
1562 // original alignment was altered
1563 AlignmentI al = null;
1564 if (command instanceof EditCommand)
1566 EditCommand editCommand = (EditCommand) command;
1567 al = editCommand.getAlignment();
1568 Vector comps = (Vector) PaintRefresher.components.get(viewport
1569 .getSequenceSetId());
1571 for (int i = 0; i < comps.size(); i++)
1573 if (comps.elementAt(i) instanceof AlignmentPanel)
1575 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1577 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1584 if (originalSource == null)
1586 // The original view is closed, we must validate
1587 // the current view against the closed view first
1590 PaintRefresher.validateSequences(al, viewport.getAlignment());
1593 originalSource = viewport;
1596 return originalSource;
1605 public void moveSelectedSequences(boolean up)
1607 SequenceGroup sg = viewport.getSelectionGroup();
1613 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1614 viewport.getHiddenRepSequences(), up);
1615 alignPanel.paintAlignment(true);
1618 synchronized void slideSequences(boolean right, int size)
1620 List<SequenceI> sg = new Vector();
1621 if (viewport.cursorMode)
1623 sg.add(viewport.getAlignment().getSequenceAt(
1624 alignPanel.seqPanel.seqCanvas.cursorY));
1626 else if (viewport.getSelectionGroup() != null
1627 && viewport.getSelectionGroup().getSize() != viewport
1628 .getAlignment().getHeight())
1630 sg = viewport.getSelectionGroup().getSequences(
1631 viewport.getHiddenRepSequences());
1639 Vector invertGroup = new Vector();
1641 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1643 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1645 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1649 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1651 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1652 for (int i = 0; i < invertGroup.size(); i++)
1654 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1657 SlideSequencesCommand ssc;
1660 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1661 size, viewport.getGapCharacter());
1665 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1666 size, viewport.getGapCharacter());
1669 int groupAdjustment = 0;
1670 if (ssc.getGapsInsertedBegin() && right)
1672 if (viewport.cursorMode)
1674 alignPanel.seqPanel.moveCursor(size, 0);
1678 groupAdjustment = size;
1681 else if (!ssc.getGapsInsertedBegin() && !right)
1683 if (viewport.cursorMode)
1685 alignPanel.seqPanel.moveCursor(-size, 0);
1689 groupAdjustment = -size;
1693 if (groupAdjustment != 0)
1695 viewport.getSelectionGroup().setStartRes(
1696 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1697 viewport.getSelectionGroup().setEndRes(
1698 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1701 boolean appendHistoryItem = false;
1702 if (viewport.historyList != null && viewport.historyList.size() > 0
1703 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1705 appendHistoryItem = ssc
1706 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1710 if (!appendHistoryItem)
1712 addHistoryItem(ssc);
1725 protected void copy_actionPerformed(ActionEvent e)
1728 if (viewport.getSelectionGroup() == null)
1732 // TODO: preserve the ordering of displayed alignment annotation in any
1733 // internal paste (particularly sequence associated annotation)
1734 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1735 String[] omitHidden = null;
1737 if (viewport.hasHiddenColumns())
1739 omitHidden = viewport.getViewAsString(true);
1742 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1745 StringSelection ss = new StringSelection(output);
1749 jalview.gui.Desktop.internalCopy = true;
1750 // Its really worth setting the clipboard contents
1751 // to empty before setting the large StringSelection!!
1752 Toolkit.getDefaultToolkit().getSystemClipboard()
1753 .setContents(new StringSelection(""), null);
1755 Toolkit.getDefaultToolkit().getSystemClipboard()
1756 .setContents(ss, Desktop.instance);
1757 } catch (OutOfMemoryError er)
1759 new OOMWarning("copying region", er);
1763 Vector hiddenColumns = null;
1764 if (viewport.hasHiddenColumns())
1766 hiddenColumns = new Vector();
1767 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1768 .getSelectionGroup().getEndRes();
1769 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1772 int[] region = (int[]) viewport.getColumnSelection()
1773 .getHiddenColumns().elementAt(i);
1774 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1776 hiddenColumns.addElement(new int[]
1777 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1782 Desktop.jalviewClipboard = new Object[]
1783 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1784 statusBar.setText(MessageManager.formatMessage(
1785 "label.copied_sequences_to_clipboard", new String[]
1786 { Integer.valueOf(seqs.length).toString() }));
1796 protected void pasteNew_actionPerformed(ActionEvent e)
1808 protected void pasteThis_actionPerformed(ActionEvent e)
1814 * Paste contents of Jalview clipboard
1816 * @param newAlignment
1817 * true to paste to a new alignment, otherwise add to this.
1819 void paste(boolean newAlignment)
1821 boolean externalPaste = true;
1824 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1825 Transferable contents = c.getContents(this);
1827 if (contents == null)
1835 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1836 if (str.length() < 1)
1841 format = new IdentifyFile().Identify(str, "Paste");
1843 } catch (OutOfMemoryError er)
1845 new OOMWarning("Out of memory pasting sequences!!", er);
1849 SequenceI[] sequences;
1850 boolean annotationAdded = false;
1851 AlignmentI alignment = null;
1853 if (Desktop.jalviewClipboard != null)
1855 // The clipboard was filled from within Jalview, we must use the
1857 // And dataset from the copied alignment
1858 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1859 // be doubly sure that we create *new* sequence objects.
1860 sequences = new SequenceI[newseq.length];
1861 for (int i = 0; i < newseq.length; i++)
1863 sequences[i] = new Sequence(newseq[i]);
1865 alignment = new Alignment(sequences);
1866 externalPaste = false;
1870 // parse the clipboard as an alignment.
1871 alignment = new FormatAdapter().readFile(str, "Paste", format);
1872 sequences = alignment.getSequencesArray();
1876 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1882 if (Desktop.jalviewClipboard != null)
1884 // dataset is inherited
1885 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1889 // new dataset is constructed
1890 alignment.setDataset(null);
1892 alwidth = alignment.getWidth() + 1;
1896 AlignmentI pastedal = alignment; // preserve pasted alignment object
1897 // Add pasted sequences and dataset into existing alignment.
1898 alignment = viewport.getAlignment();
1899 alwidth = alignment.getWidth() + 1;
1900 // decide if we need to import sequences from an existing dataset
1901 boolean importDs = Desktop.jalviewClipboard != null
1902 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1903 // importDs==true instructs us to copy over new dataset sequences from
1904 // an existing alignment
1905 Vector newDs = (importDs) ? new Vector() : null; // used to create
1906 // minimum dataset set
1908 for (int i = 0; i < sequences.length; i++)
1912 newDs.addElement(null);
1914 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1916 if (importDs && ds != null)
1918 if (!newDs.contains(ds))
1920 newDs.setElementAt(ds, i);
1921 ds = new Sequence(ds);
1922 // update with new dataset sequence
1923 sequences[i].setDatasetSequence(ds);
1927 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1932 // copy and derive new dataset sequence
1933 sequences[i] = sequences[i].deriveSequence();
1934 alignment.getDataset().addSequence(
1935 sequences[i].getDatasetSequence());
1936 // TODO: avoid creation of duplicate dataset sequences with a
1937 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1939 alignment.addSequence(sequences[i]); // merges dataset
1943 newDs.clear(); // tidy up
1945 if (alignment.getAlignmentAnnotation() != null)
1947 for (AlignmentAnnotation alan : alignment
1948 .getAlignmentAnnotation())
1950 if (alan.graphGroup > fgroup)
1952 fgroup = alan.graphGroup;
1956 if (pastedal.getAlignmentAnnotation() != null)
1958 // Add any annotation attached to alignment.
1959 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1960 for (int i = 0; i < alann.length; i++)
1962 annotationAdded = true;
1963 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1965 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1966 if (newann.graphGroup > -1)
1968 if (newGraphGroups.size() <= newann.graphGroup
1969 || newGraphGroups.get(newann.graphGroup) == null)
1971 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1973 newGraphGroups.add(q, null);
1975 newGraphGroups.set(newann.graphGroup, new Integer(
1978 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1982 newann.padAnnotation(alwidth);
1983 alignment.addAnnotation(newann);
1993 addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
1994 sequences, 0, alignment.getWidth(), alignment));
1996 // Add any annotations attached to sequences
1997 for (int i = 0; i < sequences.length; i++)
1999 if (sequences[i].getAnnotation() != null)
2001 AlignmentAnnotation newann;
2002 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2004 annotationAdded = true;
2005 newann = sequences[i].getAnnotation()[a];
2006 newann.adjustForAlignment();
2007 newann.padAnnotation(alwidth);
2008 if (newann.graphGroup > -1)
2010 if (newann.graphGroup > -1)
2012 if (newGraphGroups.size() <= newann.graphGroup
2013 || newGraphGroups.get(newann.graphGroup) == null)
2015 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2017 newGraphGroups.add(q, null);
2019 newGraphGroups.set(newann.graphGroup, new Integer(
2022 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2026 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2031 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2038 // propagate alignment changed.
2039 viewport.setEndSeq(alignment.getHeight());
2040 if (annotationAdded)
2042 // Duplicate sequence annotation in all views.
2043 AlignmentI[] alview = this.getViewAlignments();
2044 for (int i = 0; i < sequences.length; i++)
2046 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2051 for (int avnum = 0; avnum < alview.length; avnum++)
2053 if (alview[avnum] != alignment)
2055 // duplicate in a view other than the one with input focus
2056 int avwidth = alview[avnum].getWidth() + 1;
2057 // this relies on sann being preserved after we
2058 // modify the sequence's annotation array for each duplication
2059 for (int a = 0; a < sann.length; a++)
2061 AlignmentAnnotation newann = new AlignmentAnnotation(
2063 sequences[i].addAlignmentAnnotation(newann);
2064 newann.padAnnotation(avwidth);
2065 alview[avnum].addAnnotation(newann); // annotation was
2066 // duplicated earlier
2067 // TODO JAL-1145 graphGroups are not updated for sequence
2068 // annotation added to several views. This may cause
2070 alview[avnum].setAnnotationIndex(newann, a);
2075 buildSortByAnnotationScoresMenu();
2077 viewport.firePropertyChange("alignment", null,
2078 alignment.getSequences());
2079 if (alignPanels != null)
2081 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2083 ap.validateAnnotationDimensions(false);
2088 alignPanel.validateAnnotationDimensions(false);
2094 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2096 String newtitle = new String("Copied sequences");
2098 if (Desktop.jalviewClipboard != null
2099 && Desktop.jalviewClipboard[2] != null)
2101 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2102 for (int i = 0; i < hc.size(); i++)
2104 int[] region = (int[]) hc.elementAt(i);
2105 af.viewport.hideColumns(region[0], region[1]);
2109 // >>>This is a fix for the moment, until a better solution is
2111 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2113 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2115 // TODO: maintain provenance of an alignment, rather than just make the
2116 // title a concatenation of operations.
2119 if (title.startsWith("Copied sequences"))
2125 newtitle = newtitle.concat("- from " + title);
2130 newtitle = new String("Pasted sequences");
2133 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2138 } catch (Exception ex)
2140 ex.printStackTrace();
2141 System.out.println("Exception whilst pasting: " + ex);
2142 // could be anything being pasted in here
2148 protected void expand_newalign(ActionEvent e)
2152 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2153 .getAlignment(), -1);
2154 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2156 String newtitle = new String("Flanking alignment");
2158 if (Desktop.jalviewClipboard != null
2159 && Desktop.jalviewClipboard[2] != null)
2161 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2162 for (int i = 0; i < hc.size(); i++)
2164 int[] region = (int[]) hc.elementAt(i);
2165 af.viewport.hideColumns(region[0], region[1]);
2169 // >>>This is a fix for the moment, until a better solution is
2171 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2173 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2175 // TODO: maintain provenance of an alignment, rather than just make the
2176 // title a concatenation of operations.
2178 if (title.startsWith("Copied sequences"))
2184 newtitle = newtitle.concat("- from " + title);
2188 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2190 } catch (Exception ex)
2192 ex.printStackTrace();
2193 System.out.println("Exception whilst pasting: " + ex);
2194 // could be anything being pasted in here
2195 } catch (OutOfMemoryError oom)
2197 new OOMWarning("Viewing flanking region of alignment", oom);
2208 protected void cut_actionPerformed(ActionEvent e)
2210 copy_actionPerformed(null);
2211 delete_actionPerformed(null);
2221 protected void delete_actionPerformed(ActionEvent evt)
2224 SequenceGroup sg = viewport.getSelectionGroup();
2230 List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
2232 for (int i = 0; i < sg.getSize(); i++)
2234 seq = sg.getSequenceAt(i);
2238 // If the cut affects all sequences, warn, remove highlighted columns
2239 if (sg.getSize() == viewport.getAlignment().getHeight())
2241 int confirm = JOptionPane.showConfirmDialog(this,
2242 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2243 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2244 JOptionPane.OK_CANCEL_OPTION);
2246 if (confirm == JOptionPane.CANCEL_OPTION
2247 || confirm == JOptionPane.CLOSED_OPTION)
2251 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2252 sg.getEndRes() + 1);
2255 SequenceI[] cut = new SequenceI[seqs.size()];
2256 for (int i = 0; i < seqs.size(); i++)
2258 cut[i] = seqs.get(i);
2262 * //ADD HISTORY ITEM
2264 addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
2265 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2266 viewport.getAlignment()));
2268 viewport.setSelectionGroup(null);
2269 viewport.sendSelection();
2270 viewport.getAlignment().deleteGroup(sg);
2272 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2274 if (viewport.getAlignment().getHeight() < 1)
2278 this.setClosed(true);
2279 } catch (Exception ex)
2292 protected void deleteGroups_actionPerformed(ActionEvent e)
2294 if (avc.deleteGroups())
2296 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2297 alignPanel.updateAnnotation();
2298 alignPanel.paintAlignment(true);
2309 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2311 SequenceGroup sg = new SequenceGroup();
2313 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2315 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2318 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2319 viewport.setSelectionGroup(sg);
2320 viewport.sendSelection();
2321 alignPanel.paintAlignment(true);
2322 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2332 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2334 if (viewport.cursorMode)
2336 alignPanel.seqPanel.keyboardNo1 = null;
2337 alignPanel.seqPanel.keyboardNo2 = null;
2339 viewport.setSelectionGroup(null);
2340 viewport.getColumnSelection().clear();
2341 viewport.setSelectionGroup(null);
2342 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2343 alignPanel.idPanel.idCanvas.searchResults = null;
2344 alignPanel.paintAlignment(true);
2345 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2346 viewport.sendSelection();
2356 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2358 SequenceGroup sg = viewport.getSelectionGroup();
2362 selectAllSequenceMenuItem_actionPerformed(null);
2367 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2369 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2372 alignPanel.paintAlignment(true);
2373 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2374 viewport.sendSelection();
2378 public void invertColSel_actionPerformed(ActionEvent e)
2380 viewport.invertColumnSelection();
2381 alignPanel.paintAlignment(true);
2382 viewport.sendSelection();
2392 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2394 trimAlignment(true);
2404 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2406 trimAlignment(false);
2409 void trimAlignment(boolean trimLeft)
2411 ColumnSelection colSel = viewport.getColumnSelection();
2414 if (colSel.size() > 0)
2418 column = colSel.getMin();
2422 column = colSel.getMax();
2426 if (viewport.getSelectionGroup() != null)
2428 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2429 viewport.getHiddenRepSequences());
2433 seqs = viewport.getAlignment().getSequencesArray();
2436 TrimRegionCommand trimRegion;
2439 trimRegion = new TrimRegionCommand("Remove Left",
2440 TrimRegionCommand.TRIM_LEFT, seqs, column,
2441 viewport.getAlignment(), viewport.getColumnSelection(),
2442 viewport.getSelectionGroup());
2443 viewport.setStartRes(0);
2447 trimRegion = new TrimRegionCommand("Remove Right",
2448 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2449 viewport.getAlignment(), viewport.getColumnSelection(),
2450 viewport.getSelectionGroup());
2453 statusBar.setText(MessageManager.formatMessage(
2454 "label.removed_columns", new String[]
2455 { Integer.valueOf(trimRegion.getSize()).toString() }));
2457 addHistoryItem(trimRegion);
2459 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2461 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2462 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2464 viewport.getAlignment().deleteGroup(sg);
2468 viewport.firePropertyChange("alignment", null, viewport
2469 .getAlignment().getSequences());
2480 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2482 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2485 if (viewport.getSelectionGroup() != null)
2487 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2488 viewport.getHiddenRepSequences());
2489 start = viewport.getSelectionGroup().getStartRes();
2490 end = viewport.getSelectionGroup().getEndRes();
2494 seqs = viewport.getAlignment().getSequencesArray();
2497 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2498 "Remove Gapped Columns", seqs, start, end,
2499 viewport.getAlignment());
2501 addHistoryItem(removeGapCols);
2503 statusBar.setText(MessageManager.formatMessage(
2504 "label.removed_empty_columns", new String[]
2505 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2507 // This is to maintain viewport position on first residue
2508 // of first sequence
2509 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2510 int startRes = seq.findPosition(viewport.startRes);
2511 // ShiftList shifts;
2512 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2513 // edit.alColumnChanges=shifts.getInverse();
2514 // if (viewport.hasHiddenColumns)
2515 // viewport.getColumnSelection().compensateForEdits(shifts);
2516 viewport.setStartRes(seq.findIndex(startRes) - 1);
2517 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2529 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2531 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2534 if (viewport.getSelectionGroup() != null)
2536 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2537 viewport.getHiddenRepSequences());
2538 start = viewport.getSelectionGroup().getStartRes();
2539 end = viewport.getSelectionGroup().getEndRes();
2543 seqs = viewport.getAlignment().getSequencesArray();
2546 // This is to maintain viewport position on first residue
2547 // of first sequence
2548 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2549 int startRes = seq.findPosition(viewport.startRes);
2551 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2552 viewport.getAlignment()));
2554 viewport.setStartRes(seq.findIndex(startRes) - 1);
2556 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2568 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2570 viewport.setPadGaps(padGapsMenuitem.isSelected());
2571 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2577 // if (justifySeqs>0)
2579 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2592 public void findMenuItem_actionPerformed(ActionEvent e)
2598 public void newView_actionPerformed(ActionEvent e)
2605 * @param copyAnnotation
2606 * if true then duplicate all annnotation, groups and settings
2607 * @return new alignment panel, already displayed.
2609 public AlignmentPanel newView(boolean copyAnnotation)
2611 return newView(null, copyAnnotation);
2617 * title of newly created view
2618 * @return new alignment panel, already displayed.
2620 public AlignmentPanel newView(String viewTitle)
2622 return newView(viewTitle, true);
2628 * title of newly created view
2629 * @param copyAnnotation
2630 * if true then duplicate all annnotation, groups and settings
2631 * @return new alignment panel, already displayed.
2633 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2635 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2637 if (!copyAnnotation)
2639 // just remove all the current annotation except for the automatic stuff
2640 newap.av.getAlignment().deleteAllGroups();
2641 for (AlignmentAnnotation alan : newap.av.getAlignment()
2642 .getAlignmentAnnotation())
2644 if (!alan.autoCalculated)
2646 newap.av.getAlignment().deleteAnnotation(alan);
2652 newap.av.gatherViewsHere = false;
2654 if (viewport.viewName == null)
2656 viewport.viewName = "Original";
2659 newap.av.historyList = viewport.historyList;
2660 newap.av.redoList = viewport.redoList;
2662 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2663 // make sure the new view has a unique name - this is essential for Jalview
2665 boolean addFirstIndex = false;
2666 if (viewTitle == null || viewTitle.trim().length() == 0)
2668 viewTitle = MessageManager.getString("action.view");
2669 addFirstIndex = true;
2673 index = 1;// we count from 1 if given a specific name
2675 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2676 Vector comps = (Vector) PaintRefresher.components.get(viewport
2677 .getSequenceSetId());
2678 Vector existingNames = new Vector();
2679 for (int i = 0; i < comps.size(); i++)
2681 if (comps.elementAt(i) instanceof AlignmentPanel)
2683 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2684 if (!existingNames.contains(ap.av.viewName))
2686 existingNames.addElement(ap.av.viewName);
2691 while (existingNames.contains(newViewName))
2693 newViewName = viewTitle + " " + (++index);
2696 newap.av.viewName = newViewName;
2698 addAlignmentPanel(newap, true);
2699 newap.alignmentChanged();
2701 if (alignPanels.size() == 2)
2703 viewport.gatherViewsHere = true;
2705 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2710 public void expandViews_actionPerformed(ActionEvent e)
2712 Desktop.instance.explodeViews(this);
2716 public void gatherViews_actionPerformed(ActionEvent e)
2718 Desktop.instance.gatherViews(this);
2728 public void font_actionPerformed(ActionEvent e)
2730 new FontChooser(alignPanel);
2740 protected void seqLimit_actionPerformed(ActionEvent e)
2742 viewport.setShowJVSuffix(seqLimits.isSelected());
2744 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2745 .calculateIdWidth());
2746 alignPanel.paintAlignment(true);
2750 public void idRightAlign_actionPerformed(ActionEvent e)
2752 viewport.rightAlignIds = idRightAlign.isSelected();
2753 alignPanel.paintAlignment(true);
2757 public void centreColumnLabels_actionPerformed(ActionEvent e)
2759 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2760 alignPanel.paintAlignment(true);
2766 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2769 protected void followHighlight_actionPerformed()
2771 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2773 alignPanel.scrollToPosition(
2774 alignPanel.seqPanel.seqCanvas.searchResults, false);
2785 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2787 viewport.setColourText(colourTextMenuItem.isSelected());
2788 alignPanel.paintAlignment(true);
2798 public void wrapMenuItem_actionPerformed(ActionEvent e)
2800 scaleAbove.setVisible(wrapMenuItem.isSelected());
2801 scaleLeft.setVisible(wrapMenuItem.isSelected());
2802 scaleRight.setVisible(wrapMenuItem.isSelected());
2803 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2804 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2808 public void showAllSeqs_actionPerformed(ActionEvent e)
2810 viewport.showAllHiddenSeqs();
2814 public void showAllColumns_actionPerformed(ActionEvent e)
2816 viewport.showAllHiddenColumns();
2821 public void hideSelSequences_actionPerformed(ActionEvent e)
2823 viewport.hideAllSelectedSeqs();
2824 alignPanel.paintAlignment(true);
2828 * called by key handler and the hide all/show all menu items
2833 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2836 boolean hide = false;
2837 SequenceGroup sg = viewport.getSelectionGroup();
2838 if (!toggleSeqs && !toggleCols)
2840 // Hide everything by the current selection - this is a hack - we do the
2841 // invert and then hide
2842 // first check that there will be visible columns after the invert.
2843 if ((viewport.getColumnSelection() != null
2844 && viewport.getColumnSelection().getSelected() != null && viewport
2845 .getColumnSelection().getSelected().size() > 0)
2846 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2849 // now invert the sequence set, if required - empty selection implies
2850 // that no hiding is required.
2853 invertSequenceMenuItem_actionPerformed(null);
2854 sg = viewport.getSelectionGroup();
2858 viewport.expandColSelection(sg, true);
2859 // finally invert the column selection and get the new sequence
2861 invertColSel_actionPerformed(null);
2868 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2870 hideSelSequences_actionPerformed(null);
2873 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2876 showAllSeqs_actionPerformed(null);
2882 if (viewport.getColumnSelection().getSelected().size() > 0)
2884 hideSelColumns_actionPerformed(null);
2887 viewport.setSelectionGroup(sg);
2892 showAllColumns_actionPerformed(null);
2901 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2902 * event.ActionEvent)
2905 public void hideAllButSelection_actionPerformed(ActionEvent e)
2907 toggleHiddenRegions(false, false);
2914 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2918 public void hideAllSelection_actionPerformed(ActionEvent e)
2920 SequenceGroup sg = viewport.getSelectionGroup();
2921 viewport.expandColSelection(sg, false);
2922 viewport.hideAllSelectedSeqs();
2923 viewport.hideSelectedColumns();
2924 alignPanel.paintAlignment(true);
2931 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2935 public void showAllhidden_actionPerformed(ActionEvent e)
2937 viewport.showAllHiddenColumns();
2938 viewport.showAllHiddenSeqs();
2939 alignPanel.paintAlignment(true);
2943 public void hideSelColumns_actionPerformed(ActionEvent e)
2945 viewport.hideSelectedColumns();
2946 alignPanel.paintAlignment(true);
2950 public void hiddenMarkers_actionPerformed(ActionEvent e)
2952 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2963 protected void scaleAbove_actionPerformed(ActionEvent e)
2965 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2966 alignPanel.paintAlignment(true);
2976 protected void scaleLeft_actionPerformed(ActionEvent e)
2978 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2979 alignPanel.paintAlignment(true);
2989 protected void scaleRight_actionPerformed(ActionEvent e)
2991 viewport.setScaleRightWrapped(scaleRight.isSelected());
2992 alignPanel.paintAlignment(true);
3002 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3004 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3005 alignPanel.paintAlignment(true);
3015 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3017 viewport.setShowText(viewTextMenuItem.isSelected());
3018 alignPanel.paintAlignment(true);
3028 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3030 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3031 alignPanel.paintAlignment(true);
3034 public FeatureSettings featureSettings;
3037 public void featureSettings_actionPerformed(ActionEvent e)
3039 if (featureSettings != null)
3041 featureSettings.close();
3042 featureSettings = null;
3044 if (!showSeqFeatures.isSelected())
3046 // make sure features are actually displayed
3047 showSeqFeatures.setSelected(true);
3048 showSeqFeatures_actionPerformed(null);
3050 featureSettings = new FeatureSettings(this);
3054 * Set or clear 'Show Sequence Features'
3060 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3062 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3063 alignPanel.paintAlignment(true);
3064 if (alignPanel.getOverviewPanel() != null)
3066 alignPanel.getOverviewPanel().updateOverviewImage();
3071 * Set or clear 'Show Sequence Features'
3077 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3079 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3081 if (viewport.getShowSequenceFeaturesHeight())
3083 // ensure we're actually displaying features
3084 viewport.setShowSequenceFeatures(true);
3085 showSeqFeatures.setSelected(true);
3087 alignPanel.paintAlignment(true);
3088 if (alignPanel.getOverviewPanel() != null)
3090 alignPanel.getOverviewPanel().updateOverviewImage();
3095 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3096 * the annotations panel as a whole.
3098 * The options to show/hide all annotations should be enabled when the panel
3099 * is shown, and disabled when the panel is hidden.
3104 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3106 final boolean setVisible = annotationPanelMenuItem.isSelected();
3107 viewport.setShowAnnotation(setVisible);
3108 alignPanel.setAnnotationVisible(setVisible);
3109 this.showAllSeqAnnotations.setEnabled(setVisible);
3110 this.hideAllSeqAnnotations.setEnabled(setVisible);
3111 this.showAllAlAnnotations.setEnabled(setVisible);
3112 this.hideAllAlAnnotations.setEnabled(setVisible);
3116 public void alignmentProperties()
3118 JEditorPane editPane = new JEditorPane("text/html", "");
3119 editPane.setEditable(false);
3120 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3122 editPane.setText(MessageManager.formatMessage("label.html_content",
3124 { contents.toString() }));
3125 JInternalFrame frame = new JInternalFrame();
3126 frame.getContentPane().add(new JScrollPane(editPane));
3128 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3129 "label.alignment_properties", new String[]
3130 { getTitle() }), 500, 400);
3140 public void overviewMenuItem_actionPerformed(ActionEvent e)
3142 if (alignPanel.overviewPanel != null)
3147 JInternalFrame frame = new JInternalFrame();
3148 OverviewPanel overview = new OverviewPanel(alignPanel);
3149 frame.setContentPane(overview);
3150 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3151 "label.overview_params", new String[]
3152 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3154 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3155 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3158 public void internalFrameClosed(
3159 javax.swing.event.InternalFrameEvent evt)
3161 alignPanel.setOverviewPanel(null);
3165 alignPanel.setOverviewPanel(overview);
3169 public void textColour_actionPerformed(ActionEvent e)
3171 new TextColourChooser().chooseColour(alignPanel, null);
3181 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3193 public void clustalColour_actionPerformed(ActionEvent e)
3195 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3196 viewport.getHiddenRepSequences()));
3206 public void zappoColour_actionPerformed(ActionEvent e)
3208 changeColour(new ZappoColourScheme());
3218 public void taylorColour_actionPerformed(ActionEvent e)
3220 changeColour(new TaylorColourScheme());
3230 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3232 changeColour(new HydrophobicColourScheme());
3242 public void helixColour_actionPerformed(ActionEvent e)
3244 changeColour(new HelixColourScheme());
3254 public void strandColour_actionPerformed(ActionEvent e)
3256 changeColour(new StrandColourScheme());
3266 public void turnColour_actionPerformed(ActionEvent e)
3268 changeColour(new TurnColourScheme());
3278 public void buriedColour_actionPerformed(ActionEvent e)
3280 changeColour(new BuriedColourScheme());
3290 public void nucleotideColour_actionPerformed(ActionEvent e)
3292 changeColour(new NucleotideColourScheme());
3296 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3298 changeColour(new PurinePyrimidineColourScheme());
3302 * public void covariationColour_actionPerformed(ActionEvent e) {
3304 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3308 public void annotationColour_actionPerformed(ActionEvent e)
3310 new AnnotationColourChooser(viewport, alignPanel);
3314 public void rnahelicesColour_actionPerformed(ActionEvent e)
3316 new RNAHelicesColourChooser(viewport, alignPanel);
3326 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3328 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3337 public void changeColour(ColourSchemeI cs)
3339 // TODO: compare with applet and pull up to model method
3344 if (viewport.getAbovePIDThreshold())
3346 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3348 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3352 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3355 if (viewport.getConservationSelected())
3358 Alignment al = (Alignment) viewport.getAlignment();
3359 Conservation c = new Conservation("All",
3360 ResidueProperties.propHash, 3, al.getSequences(), 0,
3364 c.verdict(false, viewport.getConsPercGaps());
3366 cs.setConservation(c);
3368 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3373 cs.setConservation(null);
3376 cs.setConsensus(viewport.getSequenceConsensusHash());
3379 viewport.setGlobalColourScheme(cs);
3381 if (viewport.getColourAppliesToAllGroups())
3384 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3392 if (cs instanceof ClustalxColourScheme)
3394 sg.cs = new ClustalxColourScheme(sg,
3395 viewport.getHiddenRepSequences());
3397 else if (cs instanceof UserColourScheme)
3399 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3405 sg.cs = cs.getClass().newInstance();
3406 } catch (Exception ex)
3411 if (viewport.getAbovePIDThreshold()
3412 || cs instanceof PIDColourScheme
3413 || cs instanceof Blosum62ColourScheme)
3415 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3417 sg.cs.setConsensus(AAFrequency.calculate(
3418 sg.getSequences(viewport.getHiddenRepSequences()),
3419 sg.getStartRes(), sg.getEndRes() + 1));
3423 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3426 if (viewport.getConservationSelected())
3428 Conservation c = new Conservation("Group",
3429 ResidueProperties.propHash, 3, sg.getSequences(viewport
3430 .getHiddenRepSequences()), sg.getStartRes(),
3431 sg.getEndRes() + 1);
3433 c.verdict(false, viewport.getConsPercGaps());
3434 sg.cs.setConservation(c);
3438 sg.cs.setConservation(null);
3443 if (alignPanel.getOverviewPanel() != null)
3445 alignPanel.getOverviewPanel().updateOverviewImage();
3448 alignPanel.paintAlignment(true);
3458 protected void modifyPID_actionPerformed(ActionEvent e)
3460 if (viewport.getAbovePIDThreshold()
3461 && viewport.getGlobalColourScheme() != null)
3463 SliderPanel.setPIDSliderSource(alignPanel,
3464 viewport.getGlobalColourScheme(), "Background");
3465 SliderPanel.showPIDSlider();
3476 protected void modifyConservation_actionPerformed(ActionEvent e)
3478 if (viewport.getConservationSelected()
3479 && viewport.getGlobalColourScheme() != null)
3481 SliderPanel.setConservationSlider(alignPanel,
3482 viewport.getGlobalColourScheme(), "Background");
3483 SliderPanel.showConservationSlider();
3494 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3496 viewport.setConservationSelected(conservationMenuItem.isSelected());
3498 viewport.setAbovePIDThreshold(false);
3499 abovePIDThreshold.setSelected(false);
3501 changeColour(viewport.getGlobalColourScheme());
3503 modifyConservation_actionPerformed(null);
3513 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3515 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3517 conservationMenuItem.setSelected(false);
3518 viewport.setConservationSelected(false);
3520 changeColour(viewport.getGlobalColourScheme());
3522 modifyPID_actionPerformed(null);
3532 public void userDefinedColour_actionPerformed(ActionEvent e)
3534 if (e.getActionCommand().equals(
3535 MessageManager.getString("action.user_defined")))
3537 new UserDefinedColours(alignPanel, null);
3541 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3542 .getUserColourSchemes().get(e.getActionCommand());
3548 public void updateUserColourMenu()
3551 Component[] menuItems = colourMenu.getMenuComponents();
3552 int i, iSize = menuItems.length;
3553 for (i = 0; i < iSize; i++)
3555 if (menuItems[i].getName() != null
3556 && menuItems[i].getName().equals("USER_DEFINED"))
3558 colourMenu.remove(menuItems[i]);
3562 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3564 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3565 .getUserColourSchemes().keys();
3567 while (userColours.hasMoreElements())
3569 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3570 userColours.nextElement().toString());
3571 radioItem.setName("USER_DEFINED");
3572 radioItem.addMouseListener(new MouseAdapter()
3575 public void mousePressed(MouseEvent evt)
3577 if (evt.isControlDown()
3578 || SwingUtilities.isRightMouseButton(evt))
3580 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3582 int option = JOptionPane.showInternalConfirmDialog(
3583 jalview.gui.Desktop.desktop,
3585 .getString("label.remove_from_default_list"),
3587 .getString("label.remove_user_defined_colour"),
3588 JOptionPane.YES_NO_OPTION);
3589 if (option == JOptionPane.YES_OPTION)
3591 jalview.gui.UserDefinedColours
3592 .removeColourFromDefaults(radioItem.getText());
3593 colourMenu.remove(radioItem);
3597 radioItem.addActionListener(new ActionListener()
3600 public void actionPerformed(ActionEvent evt)
3602 userDefinedColour_actionPerformed(evt);
3609 radioItem.addActionListener(new ActionListener()
3612 public void actionPerformed(ActionEvent evt)
3614 userDefinedColour_actionPerformed(evt);
3618 colourMenu.insert(radioItem, 15);
3619 colours.add(radioItem);
3631 public void PIDColour_actionPerformed(ActionEvent e)
3633 changeColour(new PIDColourScheme());
3643 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3645 changeColour(new Blosum62ColourScheme());
3655 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3657 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3658 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3659 .getAlignment().getSequenceAt(0), null);
3660 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3661 viewport.getAlignment()));
3662 alignPanel.paintAlignment(true);
3672 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3674 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3675 AlignmentSorter.sortByID(viewport.getAlignment());
3676 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3677 viewport.getAlignment()));
3678 alignPanel.paintAlignment(true);
3688 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3690 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3691 AlignmentSorter.sortByLength(viewport.getAlignment());
3692 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3693 viewport.getAlignment()));
3694 alignPanel.paintAlignment(true);
3704 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3706 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3707 AlignmentSorter.sortByGroup(viewport.getAlignment());
3708 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3709 viewport.getAlignment()));
3711 alignPanel.paintAlignment(true);
3721 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3723 new RedundancyPanel(alignPanel, this);
3733 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3735 if ((viewport.getSelectionGroup() == null)
3736 || (viewport.getSelectionGroup().getSize() < 2))
3738 JOptionPane.showInternalMessageDialog(this, MessageManager
3739 .getString("label.you_must_select_least_two_sequences"),
3740 MessageManager.getString("label.invalid_selection"),
3741 JOptionPane.WARNING_MESSAGE);
3745 JInternalFrame frame = new JInternalFrame();
3746 frame.setContentPane(new PairwiseAlignPanel(viewport));
3747 Desktop.addInternalFrame(frame,
3748 MessageManager.getString("action.pairwise_alignment"), 600,
3760 public void PCAMenuItem_actionPerformed(ActionEvent e)
3762 if (((viewport.getSelectionGroup() != null)
3763 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3764 .getSelectionGroup().getSize() > 0))
3765 || (viewport.getAlignment().getHeight() < 4))
3768 .showInternalMessageDialog(
3771 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3773 .getString("label.sequence_selection_insufficient"),
3774 JOptionPane.WARNING_MESSAGE);
3779 new PCAPanel(alignPanel);
3783 public void autoCalculate_actionPerformed(ActionEvent e)
3785 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3786 if (viewport.autoCalculateConsensus)
3788 viewport.firePropertyChange("alignment", null, viewport
3789 .getAlignment().getSequences());
3794 public void sortByTreeOption_actionPerformed(ActionEvent e)
3796 viewport.sortByTree = sortByTree.isSelected();
3800 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3802 viewport.followSelection = listenToViewSelections.isSelected();
3812 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3814 NewTreePanel("AV", "PID", "Average distance tree using PID");
3824 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3826 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3836 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3838 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3848 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3850 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3863 void NewTreePanel(String type, String pwType, String title)
3867 if (viewport.getSelectionGroup() != null
3868 && viewport.getSelectionGroup().getSize() > 0)
3870 if (viewport.getSelectionGroup().getSize() < 3)
3876 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3878 .getString("label.not_enough_sequences"),
3879 JOptionPane.WARNING_MESSAGE);
3883 SequenceGroup sg = viewport.getSelectionGroup();
3885 /* Decide if the selection is a column region */
3886 for (SequenceI _s : sg.getSequences())
3888 if (_s.getLength() < sg.getEndRes())
3894 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3896 .getString("label.sequences_selection_not_aligned"),
3897 JOptionPane.WARNING_MESSAGE);
3903 title = title + " on region";
3904 tp = new TreePanel(alignPanel, type, pwType);
3908 // are the visible sequences aligned?
3909 if (!viewport.getAlignment().isAligned(false))
3915 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3917 .getString("label.sequences_not_aligned"),
3918 JOptionPane.WARNING_MESSAGE);
3923 if (viewport.getAlignment().getHeight() < 2)
3928 tp = new TreePanel(alignPanel, type, pwType);
3933 if (viewport.viewName != null)
3935 title += viewport.viewName + " of ";
3938 title += this.title;
3940 Desktop.addInternalFrame(tp, title, 600, 500);
3951 public void addSortByOrderMenuItem(String title,
3952 final AlignmentOrder order)
3954 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
3956 item.addActionListener(new java.awt.event.ActionListener()
3959 public void actionPerformed(ActionEvent e)
3961 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3963 // TODO: JBPNote - have to map order entries to curent SequenceI
3965 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3967 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3970 alignPanel.paintAlignment(true);
3976 * Add a new sort by annotation score menu item
3979 * the menu to add the option to
3981 * the label used to retrieve scores for each sequence on the
3984 public void addSortByAnnotScoreMenuItem(JMenu sort,
3985 final String scoreLabel)
3987 final JMenuItem item = new JMenuItem(scoreLabel);
3989 item.addActionListener(new java.awt.event.ActionListener()
3992 public void actionPerformed(ActionEvent e)
3994 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3995 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3996 viewport.getAlignment());// ,viewport.getSelectionGroup());
3997 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3998 viewport.getAlignment()));
3999 alignPanel.paintAlignment(true);
4005 * last hash for alignment's annotation array - used to minimise cost of
4008 protected int _annotationScoreVectorHash;
4011 * search the alignment and rebuild the sort by annotation score submenu the
4012 * last alignment annotation vector hash is stored to minimize cost of
4013 * rebuilding in subsequence calls.
4017 public void buildSortByAnnotationScoresMenu()
4019 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4024 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4026 sortByAnnotScore.removeAll();
4027 // almost certainly a quicker way to do this - but we keep it simple
4028 Hashtable scoreSorts = new Hashtable();
4029 AlignmentAnnotation aann[];
4030 for (SequenceI sqa : viewport.getAlignment().getSequences())
4032 aann = sqa.getAnnotation();
4033 for (int i = 0; aann != null && i < aann.length; i++)
4035 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4037 scoreSorts.put(aann[i].label, aann[i].label);
4041 Enumeration labels = scoreSorts.keys();
4042 while (labels.hasMoreElements())
4044 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4045 (String) labels.nextElement());
4047 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4050 _annotationScoreVectorHash = viewport.getAlignment()
4051 .getAlignmentAnnotation().hashCode();
4056 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4057 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4058 * call. Listeners are added to remove the menu item when the treePanel is
4059 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4063 * Displayed tree window.
4065 * SortBy menu item title.
4068 public void buildTreeMenu()
4070 calculateTree.removeAll();
4071 // build the calculate menu
4073 for (final String type : new String[]
4076 String treecalcnm = MessageManager.getString("label.tree_calc_"
4077 + type.toLowerCase());
4078 for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4080 JMenuItem tm = new JMenuItem();
4081 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4082 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4084 String smn = MessageManager.getStringOrReturn(
4085 "label.score_model_", sm.getName());
4086 final String title = MessageManager.formatMessage(
4087 "label.treecalc_title", treecalcnm, smn);
4088 tm.setText(title);//
4089 tm.addActionListener(new java.awt.event.ActionListener()
4092 public void actionPerformed(ActionEvent e)
4094 NewTreePanel(type, (String) pwtype, title);
4097 calculateTree.add(tm);
4102 sortByTreeMenu.removeAll();
4104 Vector comps = (Vector) PaintRefresher.components.get(viewport
4105 .getSequenceSetId());
4106 Vector treePanels = new Vector();
4107 int i, iSize = comps.size();
4108 for (i = 0; i < iSize; i++)
4110 if (comps.elementAt(i) instanceof TreePanel)
4112 treePanels.add(comps.elementAt(i));
4116 iSize = treePanels.size();
4120 sortByTreeMenu.setVisible(false);
4124 sortByTreeMenu.setVisible(true);
4126 for (i = 0; i < treePanels.size(); i++)
4128 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4129 final JMenuItem item = new JMenuItem(tp.getTitle());
4130 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4131 item.addActionListener(new java.awt.event.ActionListener()
4134 public void actionPerformed(ActionEvent e)
4136 tp.sortByTree_actionPerformed(null);
4137 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4142 sortByTreeMenu.add(item);
4146 public boolean sortBy(AlignmentOrder alorder, String undoname)
4148 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4149 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4150 if (undoname != null)
4152 addHistoryItem(new OrderCommand(undoname, oldOrder,
4153 viewport.getAlignment()));
4155 alignPanel.paintAlignment(true);
4160 * Work out whether the whole set of sequences or just the selected set will
4161 * be submitted for multiple alignment.
4164 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4166 // Now, check we have enough sequences
4167 AlignmentView msa = null;
4169 if ((viewport.getSelectionGroup() != null)
4170 && (viewport.getSelectionGroup().getSize() > 1))
4172 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4173 // some common interface!
4175 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4176 * SequenceI[sz = seqs.getSize(false)];
4178 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4179 * seqs.getSequenceAt(i); }
4181 msa = viewport.getAlignmentView(true);
4186 * Vector seqs = viewport.getAlignment().getSequences();
4188 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
4190 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
4191 * seqs.elementAt(i); } }
4193 msa = viewport.getAlignmentView(false);
4199 * Decides what is submitted to a secondary structure prediction service: the
4200 * first sequence in the alignment, or in the current selection, or, if the
4201 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4202 * region or the whole alignment. (where the first sequence in the set is the
4203 * one that the prediction will be for).
4205 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4207 AlignmentView seqs = null;
4209 if ((viewport.getSelectionGroup() != null)
4210 && (viewport.getSelectionGroup().getSize() > 0))
4212 seqs = viewport.getAlignmentView(true);
4216 seqs = viewport.getAlignmentView(false);
4218 // limit sequences - JBPNote in future - could spawn multiple prediction
4220 // TODO: viewport.getAlignment().isAligned is a global state - the local
4221 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4222 if (!viewport.getAlignment().isAligned(false))
4224 seqs.setSequences(new SeqCigar[]
4225 { seqs.getSequences()[0] });
4226 // TODO: if seqs.getSequences().length>1 then should really have warned
4240 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4242 // Pick the tree file
4243 JalviewFileChooser chooser = new JalviewFileChooser(
4244 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4245 chooser.setFileView(new JalviewFileView());
4246 chooser.setDialogTitle(MessageManager
4247 .getString("label.select_newick_like_tree_file"));
4248 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4250 int value = chooser.showOpenDialog(null);
4252 if (value == JalviewFileChooser.APPROVE_OPTION)
4254 String choice = chooser.getSelectedFile().getPath();
4255 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4256 jalview.io.NewickFile fin = null;
4259 fin = new jalview.io.NewickFile(choice, "File");
4260 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4261 } catch (Exception ex)
4268 .getString("label.problem_reading_tree_file"),
4269 JOptionPane.WARNING_MESSAGE);
4270 ex.printStackTrace();
4272 if (fin != null && fin.hasWarningMessage())
4274 JOptionPane.showMessageDialog(Desktop.desktop, fin
4275 .getWarningMessage(), MessageManager
4276 .getString("label.possible_problem_with_tree_file"),
4277 JOptionPane.WARNING_MESSAGE);
4283 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4285 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4288 public TreePanel ShowNewickTree(NewickFile nf, String title)
4290 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4293 public TreePanel ShowNewickTree(NewickFile nf, String title,
4294 AlignmentView input)
4296 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4299 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4300 int h, int x, int y)
4302 return ShowNewickTree(nf, title, null, w, h, x, y);
4306 * Add a treeviewer for the tree extracted from a newick file object to the
4307 * current alignment view
4314 * Associated alignment input data (or null)
4323 * @return TreePanel handle
4325 public TreePanel ShowNewickTree(NewickFile nf, String title,
4326 AlignmentView input, int w, int h, int x, int y)
4328 TreePanel tp = null;
4334 if (nf.getTree() != null)
4336 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4342 tp.setLocation(x, y);
4345 Desktop.addInternalFrame(tp, title, w, h);
4347 } catch (Exception ex)
4349 ex.printStackTrace();
4355 private boolean buildingMenu = false;
4358 * Generates menu items and listener event actions for web service clients
4361 public void BuildWebServiceMenu()
4363 while (buildingMenu)
4367 System.err.println("Waiting for building menu to finish.");
4369 } catch (Exception e)
4374 final AlignFrame me = this;
4375 buildingMenu = true;
4376 new Thread(new Runnable()
4381 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4384 System.err.println("Building ws menu again "
4385 + Thread.currentThread());
4386 // TODO: add support for context dependent disabling of services based
4388 // alignment and current selection
4389 // TODO: add additional serviceHandle parameter to specify abstract
4391 // class independently of AbstractName
4392 // TODO: add in rediscovery GUI function to restart discoverer
4393 // TODO: group services by location as well as function and/or
4395 // object broker mechanism.
4396 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4397 final IProgressIndicator af = me;
4398 final JMenu msawsmenu = new JMenu("Alignment");
4399 final JMenu secstrmenu = new JMenu(
4400 "Secondary Structure Prediction");
4401 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4402 final JMenu analymenu = new JMenu("Analysis");
4403 final JMenu dismenu = new JMenu("Protein Disorder");
4404 // final JMenu msawsmenu = new
4405 // JMenu(MessageManager.getString("label.alignment"));
4406 // final JMenu secstrmenu = new
4407 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4408 // final JMenu seqsrchmenu = new
4409 // JMenu(MessageManager.getString("label.sequence_database_search"));
4410 // final JMenu analymenu = new
4411 // JMenu(MessageManager.getString("label.analysis"));
4412 // final JMenu dismenu = new
4413 // JMenu(MessageManager.getString("label.protein_disorder"));
4414 // JAL-940 - only show secondary structure prediction services from
4415 // the legacy server
4416 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4418 Discoverer.services != null && (Discoverer.services.size() > 0))
4420 // TODO: refactor to allow list of AbstractName/Handler bindings to
4422 // stored or retrieved from elsewhere
4423 // No MSAWS used any more:
4424 // Vector msaws = null; // (Vector)
4425 // Discoverer.services.get("MsaWS");
4426 Vector secstrpr = (Vector) Discoverer.services
4428 if (secstrpr != null)
4430 // Add any secondary structure prediction services
4431 for (int i = 0, j = secstrpr.size(); i < j; i++)
4433 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4435 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4436 .getServiceClient(sh);
4437 int p = secstrmenu.getItemCount();
4438 impl.attachWSMenuEntry(secstrmenu, me);
4439 int q = secstrmenu.getItemCount();
4440 for (int litm = p; litm < q; litm++)
4442 legacyItems.add(secstrmenu.getItem(litm));
4448 // Add all submenus in the order they should appear on the web
4450 wsmenu.add(msawsmenu);
4451 wsmenu.add(secstrmenu);
4452 wsmenu.add(dismenu);
4453 wsmenu.add(analymenu);
4454 // No search services yet
4455 // wsmenu.add(seqsrchmenu);
4457 javax.swing.SwingUtilities.invokeLater(new Runnable()
4464 webService.removeAll();
4465 // first, add discovered services onto the webservices menu
4466 if (wsmenu.size() > 0)
4468 for (int i = 0, j = wsmenu.size(); i < j; i++)
4470 webService.add(wsmenu.get(i));
4475 webService.add(me.webServiceNoServices);
4477 // TODO: move into separate menu builder class.
4478 boolean new_sspred = false;
4479 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4481 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4482 if (jws2servs != null)
4484 if (jws2servs.hasServices())
4486 jws2servs.attachWSMenuEntry(webService, me);
4487 for (Jws2Instance sv : jws2servs.getServices())
4489 if (sv.description.toLowerCase().contains("jpred"))
4491 for (JMenuItem jmi : legacyItems)
4493 jmi.setVisible(false);
4499 if (jws2servs.isRunning())
4501 JMenuItem tm = new JMenuItem(
4502 "Still discovering JABA Services");
4503 tm.setEnabled(false);
4508 build_urlServiceMenu(me.webService);
4509 build_fetchdbmenu(webService);
4510 for (JMenu item : wsmenu)
4512 if (item.getItemCount() == 0)
4514 item.setEnabled(false);
4518 item.setEnabled(true);
4521 } catch (Exception e)
4524 .debug("Exception during web service menu building process.",
4530 } catch (Exception e)
4535 buildingMenu = false;
4542 * construct any groupURL type service menu entries.
4546 private void build_urlServiceMenu(JMenu webService)
4548 // TODO: remove this code when 2.7 is released
4549 // DEBUG - alignmentView
4551 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4552 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4554 * @Override public void actionPerformed(ActionEvent e) {
4555 * jalview.datamodel.AlignmentView
4556 * .testSelectionViews(af.viewport.getAlignment(),
4557 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4559 * }); webService.add(testAlView);
4561 // TODO: refactor to RestClient discoverer and merge menu entries for
4562 // rest-style services with other types of analysis/calculation service
4563 // SHmmr test client - still being implemented.
4564 // DEBUG - alignmentView
4566 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4569 client.attachWSMenuEntry(
4570 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4576 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4577 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4578 * getProperty("LAST_DIRECTORY"));
4580 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4581 * to Vamsas file"); chooser.setToolTipText("Export");
4583 * int value = chooser.showSaveDialog(this);
4585 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4586 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4587 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4588 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4591 * prototype of an automatically enabled/disabled analysis function
4594 protected void setShowProductsEnabled()
4596 SequenceI[] selection = viewport.getSequenceSelection();
4597 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4598 viewport.getAlignment().getDataset()))
4600 showProducts.setEnabled(true);
4605 showProducts.setEnabled(false);
4610 * search selection for sequence xRef products and build the show products
4615 * @return true if showProducts menu should be enabled.
4617 public boolean canShowProducts(SequenceI[] selection,
4618 boolean isRegionSelection, Alignment dataset)
4620 boolean showp = false;
4623 showProducts.removeAll();
4624 final boolean dna = viewport.getAlignment().isNucleotide();
4625 final Alignment ds = dataset;
4626 String[] ptypes = (selection == null || selection.length == 0) ? null
4627 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4629 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4630 // selection, dataset, true);
4631 final SequenceI[] sel = selection;
4632 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4635 final boolean isRegSel = isRegionSelection;
4636 final AlignFrame af = this;
4637 final String source = ptypes[t];
4638 JMenuItem xtype = new JMenuItem(ptypes[t]);
4639 xtype.addActionListener(new ActionListener()
4643 public void actionPerformed(ActionEvent e)
4645 // TODO: new thread for this call with vis-delay
4646 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4647 isRegSel, dna, source);
4651 showProducts.add(xtype);
4653 showProducts.setVisible(showp);
4654 showProducts.setEnabled(showp);
4655 } catch (Exception e)
4657 jalview.bin.Cache.log
4658 .warn("canTranslate threw an exception - please report to help@jalview.org",
4665 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4666 boolean isRegSel, boolean dna, String source)
4668 final boolean fisRegSel = isRegSel;
4669 final boolean fdna = dna;
4670 final String fsrc = source;
4671 final AlignFrame ths = this;
4672 final SequenceI[] fsel = sel;
4673 Runnable foo = new Runnable()
4679 final long sttime = System.currentTimeMillis();
4680 ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
4683 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4687 Alignment prods = CrossRef
4688 .findXrefSequences(fsel, fdna, fsrc, ds);
4691 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4692 for (int s = 0; s < sprods.length; s++)
4694 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4695 if (ds.getSequences() == null
4696 || !ds.getSequences().contains(
4697 sprods[s].getDatasetSequence()))
4699 ds.addSequence(sprods[s].getDatasetSequence());
4701 sprods[s].updatePDBIds();
4703 Alignment al = new Alignment(sprods);
4704 AlignedCodonFrame[] cf = prods.getCodonFrames();
4706 for (int s = 0; cf != null && s < cf.length; s++)
4708 al.addCodonFrame(cf[s]);
4711 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4713 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4714 + " for " + ((fisRegSel) ? "selected region of " : "")
4716 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4721 System.err.println("No Sequences generated for xRef type "
4724 } catch (Exception e)
4726 jalview.bin.Cache.log.error(
4727 "Exception when finding crossreferences", e);
4728 } catch (OutOfMemoryError e)
4730 new OOMWarning("whilst fetching crossreferences", e);
4733 jalview.bin.Cache.log.error("Error when finding crossreferences",
4736 ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
4741 Thread frunner = new Thread(foo);
4745 public boolean canShowTranslationProducts(SequenceI[] selection,
4746 AlignmentI alignment)
4751 return (jalview.analysis.Dna.canTranslate(selection,
4752 viewport.getViewAsVisibleContigs(true)));
4753 } catch (Exception e)
4755 jalview.bin.Cache.log
4756 .warn("canTranslate threw an exception - please report to help@jalview.org",
4763 public void showProducts_actionPerformed(ActionEvent e)
4765 // /////////////////////////////
4766 // Collect Data to be translated/transferred
4768 SequenceI[] selection = viewport.getSequenceSelection();
4769 AlignmentI al = null;
4772 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4773 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4774 viewport.getAlignment().getDataset());
4775 } catch (Exception ex)
4778 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4786 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4787 MessageManager.getString("label.translation_failed"),
4788 JOptionPane.WARNING_MESSAGE);
4792 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4793 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4794 "label.translation_of_params", new String[]
4795 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4800 public void showTranslation_actionPerformed(ActionEvent e)
4802 // /////////////////////////////
4803 // Collect Data to be translated/transferred
4805 SequenceI[] selection = viewport.getSequenceSelection();
4806 String[] seqstring = viewport.getViewAsString(true);
4807 AlignmentI al = null;
4810 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4811 viewport.getViewAsVisibleContigs(true), viewport
4812 .getGapCharacter(), viewport.getAlignment()
4813 .getAlignmentAnnotation(), viewport.getAlignment()
4814 .getWidth(), viewport.getAlignment().getDataset());
4815 } catch (Exception ex)
4818 jalview.bin.Cache.log.error(
4819 "Exception during translation. Please report this !", ex);
4824 .getString("label.error_when_translating_sequences_submit_bug_report"),
4826 .getString("label.implementation_error")
4828 .getString("translation_failed"),
4829 JOptionPane.ERROR_MESSAGE);
4838 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4839 MessageManager.getString("label.translation_failed"),
4840 JOptionPane.WARNING_MESSAGE);
4844 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4845 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4846 "label.translation_of_params", new String[]
4847 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4852 * Try to load a features file onto the alignment.
4855 * contents or path to retrieve file
4857 * access mode of file (see jalview.io.AlignFile)
4858 * @return true if features file was parsed corectly.
4860 public boolean parseFeaturesFile(String file, String type)
4862 boolean featuresFile = false;
4865 featuresFile = new FeaturesFile(file, type).parse(viewport
4866 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4867 .getFeatureRenderer().featureColours, false,
4868 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4869 } catch (Exception ex)
4871 ex.printStackTrace();
4876 viewport.showSequenceFeatures = true;
4877 showSeqFeatures.setSelected(true);
4878 if (alignPanel.seqPanel.seqCanvas.fr != null)
4880 // update the min/max ranges where necessary
4881 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4883 if (featureSettings != null)
4885 featureSettings.setTableData();
4887 alignPanel.paintAlignment(true);
4890 return featuresFile;
4894 public void dragEnter(DropTargetDragEvent evt)
4899 public void dragExit(DropTargetEvent evt)
4904 public void dragOver(DropTargetDragEvent evt)
4909 public void dropActionChanged(DropTargetDragEvent evt)
4914 public void drop(DropTargetDropEvent evt)
4916 Transferable t = evt.getTransferable();
4917 java.util.List files = null;
4921 DataFlavor uriListFlavor = new DataFlavor(
4922 "text/uri-list;class=java.lang.String");
4923 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4925 // Works on Windows and MacOSX
4926 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4927 files = (java.util.List) t
4928 .getTransferData(DataFlavor.javaFileListFlavor);
4930 else if (t.isDataFlavorSupported(uriListFlavor))
4932 // This is used by Unix drag system
4933 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4934 String data = (String) t.getTransferData(uriListFlavor);
4935 files = new java.util.ArrayList(1);
4936 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4937 data, "\r\n"); st.hasMoreTokens();)
4939 String s = st.nextToken();
4940 if (s.startsWith("#"))
4942 // the line is a comment (as per the RFC 2483)
4946 java.net.URI uri = new java.net.URI(s);
4947 // check to see if we can handle this kind of URI
4948 if (uri.getScheme().toLowerCase().startsWith("http"))
4950 files.add(uri.toString());
4954 // otherwise preserve old behaviour: catch all for file objects
4955 java.io.File file = new java.io.File(uri);
4956 files.add(file.toString());
4960 } catch (Exception e)
4962 e.printStackTrace();
4968 // check to see if any of these files have names matching sequences in
4970 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4971 .getAlignment().getSequencesArray());
4973 * Object[] { String,SequenceI}
4975 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4976 ArrayList<String> filesnotmatched = new ArrayList<String>();
4977 for (int i = 0; i < files.size(); i++)
4979 String file = files.get(i).toString();
4981 String protocol = FormatAdapter.checkProtocol(file);
4982 if (protocol == jalview.io.FormatAdapter.FILE)
4984 File fl = new File(file);
4985 pdbfn = fl.getName();
4987 else if (protocol == jalview.io.FormatAdapter.URL)
4989 URL url = new URL(file);
4990 pdbfn = url.getFile();
4992 if (pdbfn.length() > 0)
4994 // attempt to find a match in the alignment
4995 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4996 int l = 0, c = pdbfn.indexOf(".");
4997 while (mtch == null && c != -1)
5002 } while ((c = pdbfn.indexOf(".", l)) > l);
5005 pdbfn = pdbfn.substring(0, l);
5007 mtch = idm.findAllIdMatches(pdbfn);
5014 type = new IdentifyFile().Identify(file, protocol);
5015 } catch (Exception ex)
5021 if (type.equalsIgnoreCase("PDB"))
5023 filesmatched.add(new Object[]
5024 { file, protocol, mtch });
5029 // File wasn't named like one of the sequences or wasn't a PDB file.
5030 filesnotmatched.add(file);
5034 if (filesmatched.size() > 0)
5036 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5042 "label.automatically_associate_pdb_files_with_sequences_same_name",
5049 .getString("label.automatically_associate_pdb_files_by_name"),
5050 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5053 for (Object[] fm : filesmatched)
5055 // try and associate
5056 // TODO: may want to set a standard ID naming formalism for
5057 // associating PDB files which have no IDs.
5058 for (SequenceI toassoc : (SequenceI[]) fm[2])
5060 PDBEntry pe = new AssociatePdbFileWithSeq()
5061 .associatePdbWithSeq((String) fm[0],
5062 (String) fm[1], toassoc, false,
5066 System.err.println("Associated file : "
5067 + ((String) fm[0]) + " with "
5068 + toassoc.getDisplayId(true));
5072 alignPanel.paintAlignment(true);
5076 if (filesnotmatched.size() > 0)
5079 && (Cache.getDefault(
5080 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5083 "<html>"+MessageManager
5085 "label.ignore_unmatched_dropped_files_info",
5090 .toString() })+"</html>",
5092 .getString("label.ignore_unmatched_dropped_files"),
5093 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5097 for (String fn : filesnotmatched)
5099 loadJalviewDataFile(fn, null, null, null);
5103 } catch (Exception ex)
5105 ex.printStackTrace();
5111 * Attempt to load a "dropped" file or URL string: First by testing whether
5112 * it's and Annotation file, then a JNet file, and finally a features file. If
5113 * all are false then the user may have dropped an alignment file onto this
5117 * either a filename or a URL string.
5119 public void loadJalviewDataFile(String file, String protocol,
5120 String format, SequenceI assocSeq)
5124 if (protocol == null)
5126 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5128 // if the file isn't identified, or not positively identified as some
5129 // other filetype (PFAM is default unidentified alignment file type) then
5130 // try to parse as annotation.
5131 boolean isAnnotation = (format == null || format
5132 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5133 .readAnnotationFile(viewport.getAlignment(), file, protocol)
5138 // first see if its a T-COFFEE score file
5139 TCoffeeScoreFile tcf = null;
5142 tcf = new TCoffeeScoreFile(file, protocol);
5145 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5147 tcoffeeColour.setEnabled(true);
5148 tcoffeeColour.setSelected(true);
5149 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5150 isAnnotation = true;
5152 .setText(MessageManager
5153 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5157 // some problem - if no warning its probable that the ID matching
5158 // process didn't work
5162 tcf.getWarningMessage() == null ? MessageManager
5163 .getString("label.check_file_matches_sequence_ids_alignment")
5164 : tcf.getWarningMessage(),
5166 .getString("label.problem_reading_tcoffee_score_file"),
5167 JOptionPane.WARNING_MESSAGE);
5174 } catch (Exception x)
5177 .debug("Exception when processing data source as T-COFFEE score file",
5183 // try to see if its a JNet 'concise' style annotation file *before*
5185 // try to parse it as a features file
5188 format = new IdentifyFile().Identify(file, protocol);
5190 if (format.equalsIgnoreCase("JnetFile"))
5192 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5194 new JnetAnnotationMaker().add_annotation(predictions,
5195 viewport.getAlignment(), 0, false);
5196 isAnnotation = true;
5201 * if (format.equalsIgnoreCase("PDB")) {
5203 * String pdbfn = ""; // try to match up filename with sequence id
5204 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5205 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5206 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5207 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5208 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5209 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5210 * // attempt to find a match in the alignment SequenceI mtch =
5211 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5212 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5213 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5214 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5215 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5216 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5217 * { System.err.println("Associated file : " + file + " with " +
5218 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5219 * TODO: maybe need to load as normal otherwise return; } }
5221 // try to parse it as a features file
5222 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5223 // if it wasn't a features file then we just treat it as a general
5224 // alignment file to load into the current view.
5227 new FileLoader().LoadFile(viewport, file, protocol, format);
5231 alignPanel.paintAlignment(true);
5239 alignPanel.adjustAnnotationHeight();
5240 viewport.updateSequenceIdColours();
5241 buildSortByAnnotationScoresMenu();
5242 alignPanel.paintAlignment(true);
5244 } catch (Exception ex)
5246 ex.printStackTrace();
5247 } catch (OutOfMemoryError oom)
5252 } catch (Exception x)
5258 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5259 : "using " + protocol + " from " + file)
5261 + (format != null ? "(parsing as '" + format
5262 + "' file)" : ""), oom, Desktop.desktop);
5267 public void tabSelectionChanged(int index)
5271 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5272 viewport = alignPanel.av;
5273 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5274 setMenusFromViewport(viewport);
5279 public void tabbedPane_mousePressed(MouseEvent e)
5281 if (SwingUtilities.isRightMouseButton(e))
5283 String reply = JOptionPane.showInternalInputDialog(this,
5284 MessageManager.getString("label.enter_view_name"),
5285 MessageManager.getString("label.enter_view_name"),
5286 JOptionPane.QUESTION_MESSAGE);
5290 viewport.viewName = reply;
5291 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5296 public AlignViewport getCurrentView()
5302 * Open the dialog for regex description parsing.
5305 protected void extractScores_actionPerformed(ActionEvent e)
5307 ParseProperties pp = new jalview.analysis.ParseProperties(
5308 viewport.getAlignment());
5309 // TODO: verify regex and introduce GUI dialog for version 2.5
5310 // if (pp.getScoresFromDescription("col", "score column ",
5311 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5313 if (pp.getScoresFromDescription("description column",
5314 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5316 buildSortByAnnotationScoresMenu();
5324 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5328 protected void showDbRefs_actionPerformed(ActionEvent e)
5330 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5336 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5340 protected void showNpFeats_actionPerformed(ActionEvent e)
5342 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5346 * find the viewport amongst the tabs in this alignment frame and close that
5351 public boolean closeView(AlignViewport av)
5355 this.closeMenuItem_actionPerformed(false);
5358 Component[] comp = tabbedPane.getComponents();
5359 for (int i = 0; comp != null && i < comp.length; i++)
5361 if (comp[i] instanceof AlignmentPanel)
5363 if (((AlignmentPanel) comp[i]).av == av)
5366 closeView((AlignmentPanel) comp[i]);
5374 protected void build_fetchdbmenu(JMenu webService)
5376 // Temporary hack - DBRef Fetcher always top level ws entry.
5377 // TODO We probably want to store a sequence database checklist in
5378 // preferences and have checkboxes.. rather than individual sources selected
5380 final JMenu rfetch = new JMenu(
5381 MessageManager.getString("action.fetch_db_references"));
5382 rfetch.setToolTipText(MessageManager
5383 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5384 webService.add(rfetch);
5386 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5387 MessageManager.getString("option.trim_retrieved_seqs"));
5388 trimrs.setToolTipText(MessageManager
5389 .getString("label.trim_retrieved_sequences"));
5390 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5391 trimrs.addActionListener(new ActionListener()
5394 public void actionPerformed(ActionEvent e)
5396 trimrs.setSelected(trimrs.isSelected());
5397 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5398 Boolean.valueOf(trimrs.isSelected()).toString());
5402 JMenuItem fetchr = new JMenuItem(
5403 MessageManager.getString("label.standard_databases"));
5404 fetchr.setToolTipText(MessageManager
5405 .getString("label.fetch_embl_uniprot"));
5406 fetchr.addActionListener(new ActionListener()
5410 public void actionPerformed(ActionEvent e)
5412 new Thread(new Runnable()
5418 new jalview.ws.DBRefFetcher(alignPanel.av
5419 .getSequenceSelection(), alignPanel.alignFrame)
5420 .fetchDBRefs(false);
5428 final AlignFrame me = this;
5429 new Thread(new Runnable()
5434 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5435 .getSequenceFetcherSingleton(me);
5436 javax.swing.SwingUtilities.invokeLater(new Runnable()
5441 String[] dbclasses = sf.getOrderedSupportedSources();
5442 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5443 // jalview.util.QuickSort.sort(otherdb, otherdb);
5444 List<DbSourceProxy> otherdb;
5445 JMenu dfetch = new JMenu();
5446 JMenu ifetch = new JMenu();
5447 JMenuItem fetchr = null;
5448 int comp = 0, icomp = 0, mcomp = 15;
5449 String mname = null;
5451 for (String dbclass : dbclasses)
5453 otherdb = sf.getSourceProxy(dbclass);
5454 // add a single entry for this class, or submenu allowing 'fetch
5456 if (otherdb == null || otherdb.size() < 1)
5460 // List<DbSourceProxy> dbs=otherdb;
5461 // otherdb=new ArrayList<DbSourceProxy>();
5462 // for (DbSourceProxy db:dbs)
5464 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5468 mname = "From " + dbclass;
5470 if (otherdb.size() == 1)
5472 final DbSourceProxy[] dassource = otherdb
5473 .toArray(new DbSourceProxy[0]);
5474 DbSourceProxy src = otherdb.get(0);
5475 fetchr = new JMenuItem(src.getDbSource());
5476 fetchr.addActionListener(new ActionListener()
5480 public void actionPerformed(ActionEvent e)
5482 new Thread(new Runnable()
5488 new jalview.ws.DBRefFetcher(alignPanel.av
5489 .getSequenceSelection(),
5490 alignPanel.alignFrame, dassource)
5491 .fetchDBRefs(false);
5497 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
5503 final DbSourceProxy[] dassource = otherdb
5504 .toArray(new DbSourceProxy[0]);
5506 DbSourceProxy src = otherdb.get(0);
5507 fetchr = new JMenuItem(MessageManager.formatMessage(
5508 "label.fetch_all_param", new String[]
5509 { src.getDbSource() }));
5510 fetchr.addActionListener(new ActionListener()
5513 public void actionPerformed(ActionEvent e)
5515 new Thread(new Runnable()
5521 new jalview.ws.DBRefFetcher(alignPanel.av
5522 .getSequenceSelection(),
5523 alignPanel.alignFrame, dassource)
5524 .fetchDBRefs(false);
5530 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5533 // and then build the rest of the individual menus
5534 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
5536 String imname = null;
5538 for (DbSourceProxy sproxy : otherdb)
5540 String dbname = sproxy.getDbName();
5541 String sname = dbname.length() > 5 ? dbname.substring(0,
5542 5) + "..." : dbname;
5543 String msname = dbname.length() > 10 ? dbname.substring(
5544 0, 10) + "..." : dbname;
5547 imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
5549 fetchr = new JMenuItem(msname);
5550 final DbSourceProxy[] dassrc =
5552 fetchr.addActionListener(new ActionListener()
5556 public void actionPerformed(ActionEvent e)
5558 new Thread(new Runnable()
5564 new jalview.ws.DBRefFetcher(alignPanel.av
5565 .getSequenceSelection(),
5566 alignPanel.alignFrame, dassrc)
5567 .fetchDBRefs(false);
5573 fetchr.setToolTipText("<html>"
5574 + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
5577 if (++icomp >= mcomp || i == (otherdb.size()))
5579 ifetch.setText(MessageManager.formatMessage(
5580 "label.source_to_target", imname, sname));
5582 ifetch = new JMenu();
5590 if (comp >= mcomp || dbi >= (dbclasses.length))
5592 dfetch.setText(MessageManager.formatMessage(
5593 "label.source_to_target", mname, dbclass));
5595 dfetch = new JMenu();
5608 * Left justify the whole alignment.
5611 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5613 AlignmentI al = viewport.getAlignment();
5615 viewport.firePropertyChange("alignment", null, al);
5619 * Right justify the whole alignment.
5622 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5624 AlignmentI al = viewport.getAlignment();
5626 viewport.firePropertyChange("alignment", null, al);
5629 public void setShowSeqFeatures(boolean b)
5631 showSeqFeatures.setSelected(true);
5632 viewport.setShowSequenceFeatures(true);
5639 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5640 * awt.event.ActionEvent)
5643 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5645 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5646 alignPanel.paintAlignment(true);
5653 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5657 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5659 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5660 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5668 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5669 * .event.ActionEvent)
5672 protected void showGroupConservation_actionPerformed(ActionEvent e)
5674 viewport.setShowGroupConservation(showGroupConservation.getState());
5675 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5682 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5683 * .event.ActionEvent)
5686 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5688 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5689 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5696 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5697 * .event.ActionEvent)
5700 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5702 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5703 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5707 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5709 showSequenceLogo.setState(true);
5710 viewport.setShowSequenceLogo(true);
5711 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5712 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5716 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5718 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5725 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5726 * .event.ActionEvent)
5729 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5731 if (avc.makeGroupsFromSelection())
5733 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5734 alignPanel.updateAnnotation();
5735 alignPanel.paintAlignment(true);
5740 protected void createGroup_actionPerformed(ActionEvent e)
5742 if (avc.createGroup())
5744 alignPanel.alignmentChanged();
5749 protected void unGroup_actionPerformed(ActionEvent e)
5753 alignPanel.alignmentChanged();
5758 * make the given alignmentPanel the currently selected tab
5760 * @param alignmentPanel
5762 public void setDisplayedView(AlignmentPanel alignmentPanel)
5764 if (!viewport.getSequenceSetId().equals(
5765 alignmentPanel.av.getSequenceSetId()))
5767 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5769 if (tabbedPane != null
5770 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5771 .getSelectedIndex())
5773 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5778 * Action on selection of menu options to Show or Hide annotations.
5781 * @param forSequences
5782 * update sequence-related annotations
5783 * @param forAlignment
5784 * update non-sequence-related annotations
5787 protected void setAnnotationsVisibility(boolean visible,
5788 boolean forSequences, boolean forAlignment)
5790 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5791 .getAlignmentAnnotation())
5793 boolean apply = (aa.sequenceRef == null && forAlignment)
5794 || (aa.sequenceRef != null && forSequences);
5797 aa.visible = visible;
5800 this.alignPanel.paintAlignment(true);
5804 * Store selected annotation sort order for the view and repaint.
5807 protected void sortAnnotations_actionPerformed()
5809 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5811 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5812 alignPanel.paintAlignment(true);
5816 class PrintThread extends Thread
5820 public PrintThread(AlignmentPanel ap)
5825 static PageFormat pf;
5830 PrinterJob printJob = PrinterJob.getPrinterJob();
5834 printJob.setPrintable(ap, pf);
5838 printJob.setPrintable(ap);
5841 if (printJob.printDialog())
5846 } catch (Exception PrintException)
5848 PrintException.printStackTrace();