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);
1264 public void pageSetup_actionPerformed(ActionEvent e)
1266 PrinterJob printJob = PrinterJob.getPrinterJob();
1267 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1277 public void printMenuItem_actionPerformed(ActionEvent e)
1279 // Putting in a thread avoids Swing painting problems
1280 PrintThread thread = new PrintThread(alignPanel);
1285 public void exportFeatures_actionPerformed(ActionEvent e)
1287 new AnnotationExporter().exportFeatures(alignPanel);
1291 public void exportAnnotations_actionPerformed(ActionEvent e)
1293 new AnnotationExporter().exportAnnotations(alignPanel,
1294 viewport.showAnnotation ? viewport.getAlignment()
1295 .getAlignmentAnnotation() : null, viewport
1296 .getAlignment().getGroups(), ((Alignment) viewport
1297 .getAlignment()).alignmentProperties);
1301 public void associatedData_actionPerformed(ActionEvent e)
1303 // Pick the tree file
1304 JalviewFileChooser chooser = new JalviewFileChooser(
1305 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1306 chooser.setFileView(new JalviewFileView());
1307 chooser.setDialogTitle(MessageManager
1308 .getString("label.load_jalview_annotations"));
1309 chooser.setToolTipText(MessageManager
1310 .getString("label.load_jalview_annotations"));
1312 int value = chooser.showOpenDialog(null);
1314 if (value == JalviewFileChooser.APPROVE_OPTION)
1316 String choice = chooser.getSelectedFile().getPath();
1317 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1318 loadJalviewDataFile(choice, null, null, null);
1324 * Close the current view or all views in the alignment frame. If the frame
1325 * only contains one view then the alignment will be removed from memory.
1327 * @param closeAllTabs
1330 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1332 if (alignPanels != null && alignPanels.size() < 2)
1334 closeAllTabs = true;
1339 if (alignPanels != null)
1343 if (this.isClosed())
1345 // really close all the windows - otherwise wait till
1346 // setClosed(true) is called
1347 for (int i = 0; i < alignPanels.size(); i++)
1349 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1356 closeView(alignPanel);
1362 this.setClosed(true);
1364 } catch (Exception ex)
1366 ex.printStackTrace();
1371 * close alignPanel2 and shuffle tabs appropriately.
1373 * @param alignPanel2
1375 public void closeView(AlignmentPanel alignPanel2)
1377 int index = tabbedPane.getSelectedIndex();
1378 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1379 alignPanels.removeElement(alignPanel2);
1381 // if (viewport == alignPanel2.av)
1385 alignPanel2.closePanel();
1388 tabbedPane.removeTabAt(closedindex);
1389 tabbedPane.validate();
1391 if (index > closedindex || index == tabbedPane.getTabCount())
1393 // modify currently selected tab index if necessary.
1397 this.tabSelectionChanged(index);
1403 void updateEditMenuBar()
1406 if (viewport.historyList.size() > 0)
1408 undoMenuItem.setEnabled(true);
1409 CommandI command = (CommandI) viewport.historyList.peek();
1410 undoMenuItem.setText(MessageManager.formatMessage(
1411 "label.undo_command", new String[]
1412 { command.getDescription() }));
1416 undoMenuItem.setEnabled(false);
1417 undoMenuItem.setText(MessageManager.getString("action.undo"));
1420 if (viewport.redoList.size() > 0)
1422 redoMenuItem.setEnabled(true);
1424 CommandI command = (CommandI) viewport.redoList.peek();
1425 redoMenuItem.setText(MessageManager.formatMessage(
1426 "label.redo_command", new String[]
1427 { command.getDescription() }));
1431 redoMenuItem.setEnabled(false);
1432 redoMenuItem.setText(MessageManager.getString("action.redo"));
1436 public void addHistoryItem(CommandI command)
1438 if (command.getSize() > 0)
1440 viewport.historyList.push(command);
1441 viewport.redoList.clear();
1442 updateEditMenuBar();
1443 viewport.updateHiddenColumns();
1444 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1445 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1446 // viewport.getColumnSelection()
1447 // .getHiddenColumns().size() > 0);
1453 * @return alignment objects for all views
1455 AlignmentI[] getViewAlignments()
1457 if (alignPanels != null)
1459 Enumeration e = alignPanels.elements();
1460 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1461 for (int i = 0; e.hasMoreElements(); i++)
1463 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1467 if (viewport != null)
1469 return new AlignmentI[]
1470 { viewport.getAlignment() };
1482 protected void undoMenuItem_actionPerformed(ActionEvent e)
1484 if (viewport.historyList.empty())
1488 CommandI command = (CommandI) viewport.historyList.pop();
1489 viewport.redoList.push(command);
1490 command.undoCommand(getViewAlignments());
1492 AlignViewport originalSource = getOriginatingSource(command);
1493 updateEditMenuBar();
1495 if (originalSource != null)
1497 if (originalSource != viewport)
1500 .warn("Implementation worry: mismatch of viewport origin for undo");
1502 originalSource.updateHiddenColumns();
1503 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1505 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1506 // viewport.getColumnSelection()
1507 // .getHiddenColumns().size() > 0);
1508 originalSource.firePropertyChange("alignment", null, originalSource
1509 .getAlignment().getSequences());
1520 protected void redoMenuItem_actionPerformed(ActionEvent e)
1522 if (viewport.redoList.size() < 1)
1527 CommandI command = (CommandI) viewport.redoList.pop();
1528 viewport.historyList.push(command);
1529 command.doCommand(getViewAlignments());
1531 AlignViewport originalSource = getOriginatingSource(command);
1532 updateEditMenuBar();
1534 if (originalSource != null)
1537 if (originalSource != viewport)
1540 .warn("Implementation worry: mismatch of viewport origin for redo");
1542 originalSource.updateHiddenColumns();
1543 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1545 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1546 // viewport.getColumnSelection()
1547 // .getHiddenColumns().size() > 0);
1548 originalSource.firePropertyChange("alignment", null, originalSource
1549 .getAlignment().getSequences());
1553 AlignViewport getOriginatingSource(CommandI command)
1555 AlignViewport originalSource = null;
1556 // For sequence removal and addition, we need to fire
1557 // the property change event FROM the viewport where the
1558 // original alignment was altered
1559 AlignmentI al = null;
1560 if (command instanceof EditCommand)
1562 EditCommand editCommand = (EditCommand) command;
1563 al = editCommand.getAlignment();
1564 Vector comps = (Vector) PaintRefresher.components.get(viewport
1565 .getSequenceSetId());
1567 for (int i = 0; i < comps.size(); i++)
1569 if (comps.elementAt(i) instanceof AlignmentPanel)
1571 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1573 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1580 if (originalSource == null)
1582 // The original view is closed, we must validate
1583 // the current view against the closed view first
1586 PaintRefresher.validateSequences(al, viewport.getAlignment());
1589 originalSource = viewport;
1592 return originalSource;
1601 public void moveSelectedSequences(boolean up)
1603 SequenceGroup sg = viewport.getSelectionGroup();
1609 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1610 viewport.getHiddenRepSequences(), up);
1611 alignPanel.paintAlignment(true);
1614 synchronized void slideSequences(boolean right, int size)
1616 List<SequenceI> sg = new Vector();
1617 if (viewport.cursorMode)
1619 sg.add(viewport.getAlignment().getSequenceAt(
1620 alignPanel.seqPanel.seqCanvas.cursorY));
1622 else if (viewport.getSelectionGroup() != null
1623 && viewport.getSelectionGroup().getSize() != viewport
1624 .getAlignment().getHeight())
1626 sg = viewport.getSelectionGroup().getSequences(
1627 viewport.getHiddenRepSequences());
1635 Vector invertGroup = new Vector();
1637 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1639 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1641 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1645 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1647 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1648 for (int i = 0; i < invertGroup.size(); i++)
1650 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1653 SlideSequencesCommand ssc;
1656 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1657 size, viewport.getGapCharacter());
1661 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1662 size, viewport.getGapCharacter());
1665 int groupAdjustment = 0;
1666 if (ssc.getGapsInsertedBegin() && right)
1668 if (viewport.cursorMode)
1670 alignPanel.seqPanel.moveCursor(size, 0);
1674 groupAdjustment = size;
1677 else if (!ssc.getGapsInsertedBegin() && !right)
1679 if (viewport.cursorMode)
1681 alignPanel.seqPanel.moveCursor(-size, 0);
1685 groupAdjustment = -size;
1689 if (groupAdjustment != 0)
1691 viewport.getSelectionGroup().setStartRes(
1692 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1693 viewport.getSelectionGroup().setEndRes(
1694 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1697 boolean appendHistoryItem = false;
1698 if (viewport.historyList != null && viewport.historyList.size() > 0
1699 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1701 appendHistoryItem = ssc
1702 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1706 if (!appendHistoryItem)
1708 addHistoryItem(ssc);
1721 protected void copy_actionPerformed(ActionEvent e)
1724 if (viewport.getSelectionGroup() == null)
1728 // TODO: preserve the ordering of displayed alignment annotation in any
1729 // internal paste (particularly sequence associated annotation)
1730 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1731 String[] omitHidden = null;
1733 if (viewport.hasHiddenColumns())
1735 omitHidden = viewport.getViewAsString(true);
1738 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1741 StringSelection ss = new StringSelection(output);
1745 jalview.gui.Desktop.internalCopy = true;
1746 // Its really worth setting the clipboard contents
1747 // to empty before setting the large StringSelection!!
1748 Toolkit.getDefaultToolkit().getSystemClipboard()
1749 .setContents(new StringSelection(""), null);
1751 Toolkit.getDefaultToolkit().getSystemClipboard()
1752 .setContents(ss, Desktop.instance);
1753 } catch (OutOfMemoryError er)
1755 new OOMWarning("copying region", er);
1759 Vector hiddenColumns = null;
1760 if (viewport.hasHiddenColumns())
1762 hiddenColumns = new Vector();
1763 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1764 .getSelectionGroup().getEndRes();
1765 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1768 int[] region = (int[]) viewport.getColumnSelection()
1769 .getHiddenColumns().elementAt(i);
1770 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1772 hiddenColumns.addElement(new int[]
1773 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1778 Desktop.jalviewClipboard = new Object[]
1779 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1780 statusBar.setText(MessageManager.formatMessage(
1781 "label.copied_sequences_to_clipboard", new String[]
1782 { Integer.valueOf(seqs.length).toString() }));
1792 protected void pasteNew_actionPerformed(ActionEvent e)
1804 protected void pasteThis_actionPerformed(ActionEvent e)
1810 * Paste contents of Jalview clipboard
1812 * @param newAlignment
1813 * true to paste to a new alignment, otherwise add to this.
1815 void paste(boolean newAlignment)
1817 boolean externalPaste = true;
1820 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1821 Transferable contents = c.getContents(this);
1823 if (contents == null)
1831 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1832 if (str.length() < 1)
1837 format = new IdentifyFile().Identify(str, "Paste");
1839 } catch (OutOfMemoryError er)
1841 new OOMWarning("Out of memory pasting sequences!!", er);
1845 SequenceI[] sequences;
1846 boolean annotationAdded = false;
1847 AlignmentI alignment = null;
1849 if (Desktop.jalviewClipboard != null)
1851 // The clipboard was filled from within Jalview, we must use the
1853 // And dataset from the copied alignment
1854 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1855 // be doubly sure that we create *new* sequence objects.
1856 sequences = new SequenceI[newseq.length];
1857 for (int i = 0; i < newseq.length; i++)
1859 sequences[i] = new Sequence(newseq[i]);
1861 alignment = new Alignment(sequences);
1862 externalPaste = false;
1866 // parse the clipboard as an alignment.
1867 alignment = new FormatAdapter().readFile(str, "Paste", format);
1868 sequences = alignment.getSequencesArray();
1872 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1878 if (Desktop.jalviewClipboard != null)
1880 // dataset is inherited
1881 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1885 // new dataset is constructed
1886 alignment.setDataset(null);
1888 alwidth = alignment.getWidth() + 1;
1892 AlignmentI pastedal = alignment; // preserve pasted alignment object
1893 // Add pasted sequences and dataset into existing alignment.
1894 alignment = viewport.getAlignment();
1895 alwidth = alignment.getWidth() + 1;
1896 // decide if we need to import sequences from an existing dataset
1897 boolean importDs = Desktop.jalviewClipboard != null
1898 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1899 // importDs==true instructs us to copy over new dataset sequences from
1900 // an existing alignment
1901 Vector newDs = (importDs) ? new Vector() : null; // used to create
1902 // minimum dataset set
1904 for (int i = 0; i < sequences.length; i++)
1908 newDs.addElement(null);
1910 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1912 if (importDs && ds != null)
1914 if (!newDs.contains(ds))
1916 newDs.setElementAt(ds, i);
1917 ds = new Sequence(ds);
1918 // update with new dataset sequence
1919 sequences[i].setDatasetSequence(ds);
1923 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1928 // copy and derive new dataset sequence
1929 sequences[i] = sequences[i].deriveSequence();
1930 alignment.getDataset().addSequence(
1931 sequences[i].getDatasetSequence());
1932 // TODO: avoid creation of duplicate dataset sequences with a
1933 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1935 alignment.addSequence(sequences[i]); // merges dataset
1939 newDs.clear(); // tidy up
1941 if (alignment.getAlignmentAnnotation() != null)
1943 for (AlignmentAnnotation alan : alignment
1944 .getAlignmentAnnotation())
1946 if (alan.graphGroup > fgroup)
1948 fgroup = alan.graphGroup;
1952 if (pastedal.getAlignmentAnnotation() != null)
1954 // Add any annotation attached to alignment.
1955 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1956 for (int i = 0; i < alann.length; i++)
1958 annotationAdded = true;
1959 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1961 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1962 if (newann.graphGroup > -1)
1964 if (newGraphGroups.size() <= newann.graphGroup
1965 || newGraphGroups.get(newann.graphGroup) == null)
1967 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1969 newGraphGroups.add(q, null);
1971 newGraphGroups.set(newann.graphGroup, new Integer(
1974 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1978 newann.padAnnotation(alwidth);
1979 alignment.addAnnotation(newann);
1989 addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
1990 sequences, 0, alignment.getWidth(), alignment));
1992 // Add any annotations attached to sequences
1993 for (int i = 0; i < sequences.length; i++)
1995 if (sequences[i].getAnnotation() != null)
1997 AlignmentAnnotation newann;
1998 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2000 annotationAdded = true;
2001 newann = sequences[i].getAnnotation()[a];
2002 newann.adjustForAlignment();
2003 newann.padAnnotation(alwidth);
2004 if (newann.graphGroup > -1)
2006 if (newann.graphGroup > -1)
2008 if (newGraphGroups.size() <= newann.graphGroup
2009 || newGraphGroups.get(newann.graphGroup) == null)
2011 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2013 newGraphGroups.add(q, null);
2015 newGraphGroups.set(newann.graphGroup, new Integer(
2018 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2022 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2027 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2034 // propagate alignment changed.
2035 viewport.setEndSeq(alignment.getHeight());
2036 if (annotationAdded)
2038 // Duplicate sequence annotation in all views.
2039 AlignmentI[] alview = this.getViewAlignments();
2040 for (int i = 0; i < sequences.length; i++)
2042 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2047 for (int avnum = 0; avnum < alview.length; avnum++)
2049 if (alview[avnum] != alignment)
2051 // duplicate in a view other than the one with input focus
2052 int avwidth = alview[avnum].getWidth() + 1;
2053 // this relies on sann being preserved after we
2054 // modify the sequence's annotation array for each duplication
2055 for (int a = 0; a < sann.length; a++)
2057 AlignmentAnnotation newann = new AlignmentAnnotation(
2059 sequences[i].addAlignmentAnnotation(newann);
2060 newann.padAnnotation(avwidth);
2061 alview[avnum].addAnnotation(newann); // annotation was
2062 // duplicated earlier
2063 // TODO JAL-1145 graphGroups are not updated for sequence
2064 // annotation added to several views. This may cause
2066 alview[avnum].setAnnotationIndex(newann, a);
2071 buildSortByAnnotationScoresMenu();
2073 viewport.firePropertyChange("alignment", null,
2074 alignment.getSequences());
2075 if (alignPanels != null)
2077 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2079 ap.validateAnnotationDimensions(false);
2084 alignPanel.validateAnnotationDimensions(false);
2090 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2092 String newtitle = new String("Copied sequences");
2094 if (Desktop.jalviewClipboard != null
2095 && Desktop.jalviewClipboard[2] != null)
2097 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2098 for (int i = 0; i < hc.size(); i++)
2100 int[] region = (int[]) hc.elementAt(i);
2101 af.viewport.hideColumns(region[0], region[1]);
2105 // >>>This is a fix for the moment, until a better solution is
2107 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2109 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2111 // TODO: maintain provenance of an alignment, rather than just make the
2112 // title a concatenation of operations.
2115 if (title.startsWith("Copied sequences"))
2121 newtitle = newtitle.concat("- from " + title);
2126 newtitle = new String("Pasted sequences");
2129 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2134 } catch (Exception ex)
2136 ex.printStackTrace();
2137 System.out.println("Exception whilst pasting: " + ex);
2138 // could be anything being pasted in here
2144 protected void expand_newalign(ActionEvent e)
2148 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2149 .getAlignment(), -1);
2150 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2152 String newtitle = new String("Flanking alignment");
2154 if (Desktop.jalviewClipboard != null
2155 && Desktop.jalviewClipboard[2] != null)
2157 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2158 for (int i = 0; i < hc.size(); i++)
2160 int[] region = (int[]) hc.elementAt(i);
2161 af.viewport.hideColumns(region[0], region[1]);
2165 // >>>This is a fix for the moment, until a better solution is
2167 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2169 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2171 // TODO: maintain provenance of an alignment, rather than just make the
2172 // title a concatenation of operations.
2174 if (title.startsWith("Copied sequences"))
2180 newtitle = newtitle.concat("- from " + title);
2184 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2186 } catch (Exception ex)
2188 ex.printStackTrace();
2189 System.out.println("Exception whilst pasting: " + ex);
2190 // could be anything being pasted in here
2191 } catch (OutOfMemoryError oom)
2193 new OOMWarning("Viewing flanking region of alignment", oom);
2204 protected void cut_actionPerformed(ActionEvent e)
2206 copy_actionPerformed(null);
2207 delete_actionPerformed(null);
2217 protected void delete_actionPerformed(ActionEvent evt)
2220 SequenceGroup sg = viewport.getSelectionGroup();
2226 List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
2228 for (int i = 0; i < sg.getSize(); i++)
2230 seq = sg.getSequenceAt(i);
2234 // If the cut affects all sequences, warn, remove highlighted columns
2235 if (sg.getSize() == viewport.getAlignment().getHeight())
2237 int confirm = JOptionPane.showConfirmDialog(this,
2238 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2239 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2240 JOptionPane.OK_CANCEL_OPTION);
2242 if (confirm == JOptionPane.CANCEL_OPTION
2243 || confirm == JOptionPane.CLOSED_OPTION)
2247 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2248 sg.getEndRes() + 1);
2251 SequenceI[] cut = new SequenceI[seqs.size()];
2252 for (int i = 0; i < seqs.size(); i++)
2254 cut[i] = seqs.get(i);
2258 * //ADD HISTORY ITEM
2260 addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
2261 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2262 viewport.getAlignment()));
2264 viewport.setSelectionGroup(null);
2265 viewport.sendSelection();
2266 viewport.getAlignment().deleteGroup(sg);
2268 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2270 if (viewport.getAlignment().getHeight() < 1)
2274 this.setClosed(true);
2275 } catch (Exception ex)
2288 protected void deleteGroups_actionPerformed(ActionEvent e)
2290 if (avc.deleteGroups())
2292 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2293 alignPanel.updateAnnotation();
2294 alignPanel.paintAlignment(true);
2305 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2307 SequenceGroup sg = new SequenceGroup();
2309 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2311 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2314 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2315 viewport.setSelectionGroup(sg);
2316 viewport.sendSelection();
2317 alignPanel.paintAlignment(true);
2318 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2328 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2330 if (viewport.cursorMode)
2332 alignPanel.seqPanel.keyboardNo1 = null;
2333 alignPanel.seqPanel.keyboardNo2 = null;
2335 viewport.setSelectionGroup(null);
2336 viewport.getColumnSelection().clear();
2337 viewport.setSelectionGroup(null);
2338 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2339 alignPanel.idPanel.idCanvas.searchResults = null;
2340 alignPanel.paintAlignment(true);
2341 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2342 viewport.sendSelection();
2352 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2354 SequenceGroup sg = viewport.getSelectionGroup();
2358 selectAllSequenceMenuItem_actionPerformed(null);
2363 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2365 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2368 alignPanel.paintAlignment(true);
2369 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2370 viewport.sendSelection();
2374 public void invertColSel_actionPerformed(ActionEvent e)
2376 viewport.invertColumnSelection();
2377 alignPanel.paintAlignment(true);
2378 viewport.sendSelection();
2388 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2390 trimAlignment(true);
2400 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2402 trimAlignment(false);
2405 void trimAlignment(boolean trimLeft)
2407 ColumnSelection colSel = viewport.getColumnSelection();
2410 if (colSel.size() > 0)
2414 column = colSel.getMin();
2418 column = colSel.getMax();
2422 if (viewport.getSelectionGroup() != null)
2424 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2425 viewport.getHiddenRepSequences());
2429 seqs = viewport.getAlignment().getSequencesArray();
2432 TrimRegionCommand trimRegion;
2435 trimRegion = new TrimRegionCommand("Remove Left",
2436 TrimRegionCommand.TRIM_LEFT, seqs, column,
2437 viewport.getAlignment(), viewport.getColumnSelection(),
2438 viewport.getSelectionGroup());
2439 viewport.setStartRes(0);
2443 trimRegion = new TrimRegionCommand("Remove Right",
2444 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2445 viewport.getAlignment(), viewport.getColumnSelection(),
2446 viewport.getSelectionGroup());
2449 statusBar.setText(MessageManager.formatMessage(
2450 "label.removed_columns", new String[]
2451 { Integer.valueOf(trimRegion.getSize()).toString() }));
2453 addHistoryItem(trimRegion);
2455 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2457 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2458 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2460 viewport.getAlignment().deleteGroup(sg);
2464 viewport.firePropertyChange("alignment", null, viewport
2465 .getAlignment().getSequences());
2476 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2478 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2481 if (viewport.getSelectionGroup() != null)
2483 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2484 viewport.getHiddenRepSequences());
2485 start = viewport.getSelectionGroup().getStartRes();
2486 end = viewport.getSelectionGroup().getEndRes();
2490 seqs = viewport.getAlignment().getSequencesArray();
2493 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2494 "Remove Gapped Columns", seqs, start, end,
2495 viewport.getAlignment());
2497 addHistoryItem(removeGapCols);
2499 statusBar.setText(MessageManager.formatMessage(
2500 "label.removed_empty_columns", new String[]
2501 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2503 // This is to maintain viewport position on first residue
2504 // of first sequence
2505 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2506 int startRes = seq.findPosition(viewport.startRes);
2507 // ShiftList shifts;
2508 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2509 // edit.alColumnChanges=shifts.getInverse();
2510 // if (viewport.hasHiddenColumns)
2511 // viewport.getColumnSelection().compensateForEdits(shifts);
2512 viewport.setStartRes(seq.findIndex(startRes) - 1);
2513 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2525 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2527 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2530 if (viewport.getSelectionGroup() != null)
2532 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2533 viewport.getHiddenRepSequences());
2534 start = viewport.getSelectionGroup().getStartRes();
2535 end = viewport.getSelectionGroup().getEndRes();
2539 seqs = viewport.getAlignment().getSequencesArray();
2542 // This is to maintain viewport position on first residue
2543 // of first sequence
2544 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2545 int startRes = seq.findPosition(viewport.startRes);
2547 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2548 viewport.getAlignment()));
2550 viewport.setStartRes(seq.findIndex(startRes) - 1);
2552 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2564 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2566 viewport.setPadGaps(padGapsMenuitem.isSelected());
2567 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2573 // if (justifySeqs>0)
2575 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2588 public void findMenuItem_actionPerformed(ActionEvent e)
2594 public void newView_actionPerformed(ActionEvent e)
2601 * @param copyAnnotation
2602 * if true then duplicate all annnotation, groups and settings
2603 * @return new alignment panel, already displayed.
2605 public AlignmentPanel newView(boolean copyAnnotation)
2607 return newView(null, copyAnnotation);
2613 * title of newly created view
2614 * @return new alignment panel, already displayed.
2616 public AlignmentPanel newView(String viewTitle)
2618 return newView(viewTitle, true);
2624 * title of newly created view
2625 * @param copyAnnotation
2626 * if true then duplicate all annnotation, groups and settings
2627 * @return new alignment panel, already displayed.
2629 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2631 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2633 if (!copyAnnotation)
2635 // just remove all the current annotation except for the automatic stuff
2636 newap.av.getAlignment().deleteAllGroups();
2637 for (AlignmentAnnotation alan : newap.av.getAlignment()
2638 .getAlignmentAnnotation())
2640 if (!alan.autoCalculated)
2642 newap.av.getAlignment().deleteAnnotation(alan);
2648 newap.av.gatherViewsHere = false;
2650 if (viewport.viewName == null)
2652 viewport.viewName = "Original";
2655 newap.av.historyList = viewport.historyList;
2656 newap.av.redoList = viewport.redoList;
2658 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2659 // make sure the new view has a unique name - this is essential for Jalview
2661 boolean addFirstIndex = false;
2662 if (viewTitle == null || viewTitle.trim().length() == 0)
2664 viewTitle = MessageManager.getString("action.view");
2665 addFirstIndex = true;
2669 index = 1;// we count from 1 if given a specific name
2671 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2672 Vector comps = (Vector) PaintRefresher.components.get(viewport
2673 .getSequenceSetId());
2674 Vector existingNames = new Vector();
2675 for (int i = 0; i < comps.size(); i++)
2677 if (comps.elementAt(i) instanceof AlignmentPanel)
2679 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2680 if (!existingNames.contains(ap.av.viewName))
2682 existingNames.addElement(ap.av.viewName);
2687 while (existingNames.contains(newViewName))
2689 newViewName = viewTitle + " " + (++index);
2692 newap.av.viewName = newViewName;
2694 addAlignmentPanel(newap, true);
2695 newap.alignmentChanged();
2697 if (alignPanels.size() == 2)
2699 viewport.gatherViewsHere = true;
2701 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2706 public void expandViews_actionPerformed(ActionEvent e)
2708 Desktop.instance.explodeViews(this);
2712 public void gatherViews_actionPerformed(ActionEvent e)
2714 Desktop.instance.gatherViews(this);
2724 public void font_actionPerformed(ActionEvent e)
2726 new FontChooser(alignPanel);
2736 protected void seqLimit_actionPerformed(ActionEvent e)
2738 viewport.setShowJVSuffix(seqLimits.isSelected());
2740 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2741 .calculateIdWidth());
2742 alignPanel.paintAlignment(true);
2746 public void idRightAlign_actionPerformed(ActionEvent e)
2748 viewport.rightAlignIds = idRightAlign.isSelected();
2749 alignPanel.paintAlignment(true);
2753 public void centreColumnLabels_actionPerformed(ActionEvent e)
2755 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2756 alignPanel.paintAlignment(true);
2762 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2765 protected void followHighlight_actionPerformed()
2767 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2769 alignPanel.scrollToPosition(
2770 alignPanel.seqPanel.seqCanvas.searchResults, false);
2781 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2783 viewport.setColourText(colourTextMenuItem.isSelected());
2784 alignPanel.paintAlignment(true);
2794 public void wrapMenuItem_actionPerformed(ActionEvent e)
2796 scaleAbove.setVisible(wrapMenuItem.isSelected());
2797 scaleLeft.setVisible(wrapMenuItem.isSelected());
2798 scaleRight.setVisible(wrapMenuItem.isSelected());
2799 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2800 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2804 public void showAllSeqs_actionPerformed(ActionEvent e)
2806 viewport.showAllHiddenSeqs();
2810 public void showAllColumns_actionPerformed(ActionEvent e)
2812 viewport.showAllHiddenColumns();
2817 public void hideSelSequences_actionPerformed(ActionEvent e)
2819 viewport.hideAllSelectedSeqs();
2820 alignPanel.paintAlignment(true);
2824 * called by key handler and the hide all/show all menu items
2829 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2832 boolean hide = false;
2833 SequenceGroup sg = viewport.getSelectionGroup();
2834 if (!toggleSeqs && !toggleCols)
2836 // Hide everything by the current selection - this is a hack - we do the
2837 // invert and then hide
2838 // first check that there will be visible columns after the invert.
2839 if ((viewport.getColumnSelection() != null
2840 && viewport.getColumnSelection().getSelected() != null && viewport
2841 .getColumnSelection().getSelected().size() > 0)
2842 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2845 // now invert the sequence set, if required - empty selection implies
2846 // that no hiding is required.
2849 invertSequenceMenuItem_actionPerformed(null);
2850 sg = viewport.getSelectionGroup();
2854 viewport.expandColSelection(sg, true);
2855 // finally invert the column selection and get the new sequence
2857 invertColSel_actionPerformed(null);
2864 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2866 hideSelSequences_actionPerformed(null);
2869 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2872 showAllSeqs_actionPerformed(null);
2878 if (viewport.getColumnSelection().getSelected().size() > 0)
2880 hideSelColumns_actionPerformed(null);
2883 viewport.setSelectionGroup(sg);
2888 showAllColumns_actionPerformed(null);
2897 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2898 * event.ActionEvent)
2901 public void hideAllButSelection_actionPerformed(ActionEvent e)
2903 toggleHiddenRegions(false, false);
2910 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2914 public void hideAllSelection_actionPerformed(ActionEvent e)
2916 SequenceGroup sg = viewport.getSelectionGroup();
2917 viewport.expandColSelection(sg, false);
2918 viewport.hideAllSelectedSeqs();
2919 viewport.hideSelectedColumns();
2920 alignPanel.paintAlignment(true);
2927 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2931 public void showAllhidden_actionPerformed(ActionEvent e)
2933 viewport.showAllHiddenColumns();
2934 viewport.showAllHiddenSeqs();
2935 alignPanel.paintAlignment(true);
2939 public void hideSelColumns_actionPerformed(ActionEvent e)
2941 viewport.hideSelectedColumns();
2942 alignPanel.paintAlignment(true);
2946 public void hiddenMarkers_actionPerformed(ActionEvent e)
2948 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2959 protected void scaleAbove_actionPerformed(ActionEvent e)
2961 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2962 alignPanel.paintAlignment(true);
2972 protected void scaleLeft_actionPerformed(ActionEvent e)
2974 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2975 alignPanel.paintAlignment(true);
2985 protected void scaleRight_actionPerformed(ActionEvent e)
2987 viewport.setScaleRightWrapped(scaleRight.isSelected());
2988 alignPanel.paintAlignment(true);
2998 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3000 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3001 alignPanel.paintAlignment(true);
3011 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3013 viewport.setShowText(viewTextMenuItem.isSelected());
3014 alignPanel.paintAlignment(true);
3024 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3026 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3027 alignPanel.paintAlignment(true);
3030 public FeatureSettings featureSettings;
3033 public void featureSettings_actionPerformed(ActionEvent e)
3035 if (featureSettings != null)
3037 featureSettings.close();
3038 featureSettings = null;
3040 if (!showSeqFeatures.isSelected())
3042 // make sure features are actually displayed
3043 showSeqFeatures.setSelected(true);
3044 showSeqFeatures_actionPerformed(null);
3046 featureSettings = new FeatureSettings(this);
3050 * Set or clear 'Show Sequence Features'
3056 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3058 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3059 alignPanel.paintAlignment(true);
3060 if (alignPanel.getOverviewPanel() != null)
3062 alignPanel.getOverviewPanel().updateOverviewImage();
3067 * Set or clear 'Show Sequence Features'
3073 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3075 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3077 if (viewport.getShowSequenceFeaturesHeight())
3079 // ensure we're actually displaying features
3080 viewport.setShowSequenceFeatures(true);
3081 showSeqFeatures.setSelected(true);
3083 alignPanel.paintAlignment(true);
3084 if (alignPanel.getOverviewPanel() != null)
3086 alignPanel.getOverviewPanel().updateOverviewImage();
3091 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3092 * the annotations panel as a whole.
3094 * The options to show/hide all annotations should be enabled when the panel
3095 * is shown, and disabled when the panel is hidden.
3100 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3102 final boolean setVisible = annotationPanelMenuItem.isSelected();
3103 viewport.setShowAnnotation(setVisible);
3104 alignPanel.setAnnotationVisible(setVisible);
3105 this.showAllSeqAnnotations.setEnabled(setVisible);
3106 this.hideAllSeqAnnotations.setEnabled(setVisible);
3107 this.showAllAlAnnotations.setEnabled(setVisible);
3108 this.hideAllAlAnnotations.setEnabled(setVisible);
3112 public void alignmentProperties()
3114 JEditorPane editPane = new JEditorPane("text/html", "");
3115 editPane.setEditable(false);
3116 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3118 editPane.setText(MessageManager.formatMessage("label.html_content",
3120 { contents.toString() }));
3121 JInternalFrame frame = new JInternalFrame();
3122 frame.getContentPane().add(new JScrollPane(editPane));
3124 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3125 "label.alignment_properties", new String[]
3126 { getTitle() }), 500, 400);
3136 public void overviewMenuItem_actionPerformed(ActionEvent e)
3138 if (alignPanel.overviewPanel != null)
3143 JInternalFrame frame = new JInternalFrame();
3144 OverviewPanel overview = new OverviewPanel(alignPanel);
3145 frame.setContentPane(overview);
3146 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3147 "label.overview_params", new String[]
3148 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3150 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3151 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3154 public void internalFrameClosed(
3155 javax.swing.event.InternalFrameEvent evt)
3157 alignPanel.setOverviewPanel(null);
3161 alignPanel.setOverviewPanel(overview);
3165 public void textColour_actionPerformed(ActionEvent e)
3167 new TextColourChooser().chooseColour(alignPanel, null);
3177 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3189 public void clustalColour_actionPerformed(ActionEvent e)
3191 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3192 viewport.getHiddenRepSequences()));
3202 public void zappoColour_actionPerformed(ActionEvent e)
3204 changeColour(new ZappoColourScheme());
3214 public void taylorColour_actionPerformed(ActionEvent e)
3216 changeColour(new TaylorColourScheme());
3226 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3228 changeColour(new HydrophobicColourScheme());
3238 public void helixColour_actionPerformed(ActionEvent e)
3240 changeColour(new HelixColourScheme());
3250 public void strandColour_actionPerformed(ActionEvent e)
3252 changeColour(new StrandColourScheme());
3262 public void turnColour_actionPerformed(ActionEvent e)
3264 changeColour(new TurnColourScheme());
3274 public void buriedColour_actionPerformed(ActionEvent e)
3276 changeColour(new BuriedColourScheme());
3286 public void nucleotideColour_actionPerformed(ActionEvent e)
3288 changeColour(new NucleotideColourScheme());
3292 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3294 changeColour(new PurinePyrimidineColourScheme());
3298 * public void covariationColour_actionPerformed(ActionEvent e) {
3300 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3304 public void annotationColour_actionPerformed(ActionEvent e)
3306 new AnnotationColourChooser(viewport, alignPanel);
3310 public void rnahelicesColour_actionPerformed(ActionEvent e)
3312 new RNAHelicesColourChooser(viewport, alignPanel);
3322 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3324 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3333 public void changeColour(ColourSchemeI cs)
3335 // TODO: compare with applet and pull up to model method
3340 if (viewport.getAbovePIDThreshold())
3342 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3344 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3348 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3351 if (viewport.getConservationSelected())
3354 Alignment al = (Alignment) viewport.getAlignment();
3355 Conservation c = new Conservation("All",
3356 ResidueProperties.propHash, 3, al.getSequences(), 0,
3360 c.verdict(false, viewport.getConsPercGaps());
3362 cs.setConservation(c);
3364 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3369 cs.setConservation(null);
3372 cs.setConsensus(viewport.getSequenceConsensusHash());
3375 viewport.setGlobalColourScheme(cs);
3377 if (viewport.getColourAppliesToAllGroups())
3380 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3388 if (cs instanceof ClustalxColourScheme)
3390 sg.cs = new ClustalxColourScheme(sg,
3391 viewport.getHiddenRepSequences());
3393 else if (cs instanceof UserColourScheme)
3395 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3401 sg.cs = cs.getClass().newInstance();
3402 } catch (Exception ex)
3407 if (viewport.getAbovePIDThreshold()
3408 || cs instanceof PIDColourScheme
3409 || cs instanceof Blosum62ColourScheme)
3411 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3413 sg.cs.setConsensus(AAFrequency.calculate(
3414 sg.getSequences(viewport.getHiddenRepSequences()),
3415 sg.getStartRes(), sg.getEndRes() + 1));
3419 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3422 if (viewport.getConservationSelected())
3424 Conservation c = new Conservation("Group",
3425 ResidueProperties.propHash, 3, sg.getSequences(viewport
3426 .getHiddenRepSequences()), sg.getStartRes(),
3427 sg.getEndRes() + 1);
3429 c.verdict(false, viewport.getConsPercGaps());
3430 sg.cs.setConservation(c);
3434 sg.cs.setConservation(null);
3439 if (alignPanel.getOverviewPanel() != null)
3441 alignPanel.getOverviewPanel().updateOverviewImage();
3444 alignPanel.paintAlignment(true);
3454 protected void modifyPID_actionPerformed(ActionEvent e)
3456 if (viewport.getAbovePIDThreshold()
3457 && viewport.getGlobalColourScheme() != null)
3459 SliderPanel.setPIDSliderSource(alignPanel,
3460 viewport.getGlobalColourScheme(), "Background");
3461 SliderPanel.showPIDSlider();
3472 protected void modifyConservation_actionPerformed(ActionEvent e)
3474 if (viewport.getConservationSelected()
3475 && viewport.getGlobalColourScheme() != null)
3477 SliderPanel.setConservationSlider(alignPanel,
3478 viewport.getGlobalColourScheme(), "Background");
3479 SliderPanel.showConservationSlider();
3490 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3492 viewport.setConservationSelected(conservationMenuItem.isSelected());
3494 viewport.setAbovePIDThreshold(false);
3495 abovePIDThreshold.setSelected(false);
3497 changeColour(viewport.getGlobalColourScheme());
3499 modifyConservation_actionPerformed(null);
3509 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3511 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3513 conservationMenuItem.setSelected(false);
3514 viewport.setConservationSelected(false);
3516 changeColour(viewport.getGlobalColourScheme());
3518 modifyPID_actionPerformed(null);
3528 public void userDefinedColour_actionPerformed(ActionEvent e)
3530 if (e.getActionCommand().equals(
3531 MessageManager.getString("action.user_defined")))
3533 new UserDefinedColours(alignPanel, null);
3537 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3538 .getUserColourSchemes().get(e.getActionCommand());
3544 public void updateUserColourMenu()
3547 Component[] menuItems = colourMenu.getMenuComponents();
3548 int i, iSize = menuItems.length;
3549 for (i = 0; i < iSize; i++)
3551 if (menuItems[i].getName() != null
3552 && menuItems[i].getName().equals("USER_DEFINED"))
3554 colourMenu.remove(menuItems[i]);
3558 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3560 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3561 .getUserColourSchemes().keys();
3563 while (userColours.hasMoreElements())
3565 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3566 userColours.nextElement().toString());
3567 radioItem.setName("USER_DEFINED");
3568 radioItem.addMouseListener(new MouseAdapter()
3571 public void mousePressed(MouseEvent evt)
3573 if (evt.isControlDown()
3574 || SwingUtilities.isRightMouseButton(evt))
3576 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3578 int option = JOptionPane.showInternalConfirmDialog(
3579 jalview.gui.Desktop.desktop,
3581 .getString("label.remove_from_default_list"),
3583 .getString("label.remove_user_defined_colour"),
3584 JOptionPane.YES_NO_OPTION);
3585 if (option == JOptionPane.YES_OPTION)
3587 jalview.gui.UserDefinedColours
3588 .removeColourFromDefaults(radioItem.getText());
3589 colourMenu.remove(radioItem);
3593 radioItem.addActionListener(new ActionListener()
3596 public void actionPerformed(ActionEvent evt)
3598 userDefinedColour_actionPerformed(evt);
3605 radioItem.addActionListener(new ActionListener()
3608 public void actionPerformed(ActionEvent evt)
3610 userDefinedColour_actionPerformed(evt);
3614 colourMenu.insert(radioItem, 15);
3615 colours.add(radioItem);
3627 public void PIDColour_actionPerformed(ActionEvent e)
3629 changeColour(new PIDColourScheme());
3639 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3641 changeColour(new Blosum62ColourScheme());
3651 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3653 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3654 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3655 .getAlignment().getSequenceAt(0), null);
3656 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3657 viewport.getAlignment()));
3658 alignPanel.paintAlignment(true);
3668 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3670 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3671 AlignmentSorter.sortByID(viewport.getAlignment());
3672 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3673 viewport.getAlignment()));
3674 alignPanel.paintAlignment(true);
3684 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3686 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3687 AlignmentSorter.sortByLength(viewport.getAlignment());
3688 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3689 viewport.getAlignment()));
3690 alignPanel.paintAlignment(true);
3700 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3702 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3703 AlignmentSorter.sortByGroup(viewport.getAlignment());
3704 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3705 viewport.getAlignment()));
3707 alignPanel.paintAlignment(true);
3717 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3719 new RedundancyPanel(alignPanel, this);
3729 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3731 if ((viewport.getSelectionGroup() == null)
3732 || (viewport.getSelectionGroup().getSize() < 2))
3734 JOptionPane.showInternalMessageDialog(this, MessageManager
3735 .getString("label.you_must_select_least_two_sequences"),
3736 MessageManager.getString("label.invalid_selection"),
3737 JOptionPane.WARNING_MESSAGE);
3741 JInternalFrame frame = new JInternalFrame();
3742 frame.setContentPane(new PairwiseAlignPanel(viewport));
3743 Desktop.addInternalFrame(frame,
3744 MessageManager.getString("action.pairwise_alignment"), 600,
3756 public void PCAMenuItem_actionPerformed(ActionEvent e)
3758 if (((viewport.getSelectionGroup() != null)
3759 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3760 .getSelectionGroup().getSize() > 0))
3761 || (viewport.getAlignment().getHeight() < 4))
3764 .showInternalMessageDialog(
3767 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3769 .getString("label.sequence_selection_insufficient"),
3770 JOptionPane.WARNING_MESSAGE);
3775 new PCAPanel(alignPanel);
3779 public void autoCalculate_actionPerformed(ActionEvent e)
3781 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3782 if (viewport.autoCalculateConsensus)
3784 viewport.firePropertyChange("alignment", null, viewport
3785 .getAlignment().getSequences());
3790 public void sortByTreeOption_actionPerformed(ActionEvent e)
3792 viewport.sortByTree = sortByTree.isSelected();
3796 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3798 viewport.followSelection = listenToViewSelections.isSelected();
3808 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3810 NewTreePanel("AV", "PID", "Average distance tree using PID");
3820 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3822 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3832 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3834 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3844 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3846 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3859 void NewTreePanel(String type, String pwType, String title)
3863 if (viewport.getSelectionGroup() != null
3864 && viewport.getSelectionGroup().getSize() > 0)
3866 if (viewport.getSelectionGroup().getSize() < 3)
3872 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3874 .getString("label.not_enough_sequences"),
3875 JOptionPane.WARNING_MESSAGE);
3879 SequenceGroup sg = viewport.getSelectionGroup();
3881 /* Decide if the selection is a column region */
3882 for (SequenceI _s : sg.getSequences())
3884 if (_s.getLength() < sg.getEndRes())
3890 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3892 .getString("label.sequences_selection_not_aligned"),
3893 JOptionPane.WARNING_MESSAGE);
3899 title = title + " on region";
3900 tp = new TreePanel(alignPanel, type, pwType);
3904 // are the visible sequences aligned?
3905 if (!viewport.getAlignment().isAligned(false))
3911 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3913 .getString("label.sequences_not_aligned"),
3914 JOptionPane.WARNING_MESSAGE);
3919 if (viewport.getAlignment().getHeight() < 2)
3924 tp = new TreePanel(alignPanel, type, pwType);
3929 if (viewport.viewName != null)
3931 title += viewport.viewName + " of ";
3934 title += this.title;
3936 Desktop.addInternalFrame(tp, title, 600, 500);
3947 public void addSortByOrderMenuItem(String title,
3948 final AlignmentOrder order)
3950 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
3952 item.addActionListener(new java.awt.event.ActionListener()
3955 public void actionPerformed(ActionEvent e)
3957 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3959 // TODO: JBPNote - have to map order entries to curent SequenceI
3961 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3963 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3966 alignPanel.paintAlignment(true);
3972 * Add a new sort by annotation score menu item
3975 * the menu to add the option to
3977 * the label used to retrieve scores for each sequence on the
3980 public void addSortByAnnotScoreMenuItem(JMenu sort,
3981 final String scoreLabel)
3983 final JMenuItem item = new JMenuItem(scoreLabel);
3985 item.addActionListener(new java.awt.event.ActionListener()
3988 public void actionPerformed(ActionEvent e)
3990 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3991 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3992 viewport.getAlignment());// ,viewport.getSelectionGroup());
3993 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3994 viewport.getAlignment()));
3995 alignPanel.paintAlignment(true);
4001 * last hash for alignment's annotation array - used to minimise cost of
4004 protected int _annotationScoreVectorHash;
4007 * search the alignment and rebuild the sort by annotation score submenu the
4008 * last alignment annotation vector hash is stored to minimize cost of
4009 * rebuilding in subsequence calls.
4013 public void buildSortByAnnotationScoresMenu()
4015 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4020 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4022 sortByAnnotScore.removeAll();
4023 // almost certainly a quicker way to do this - but we keep it simple
4024 Hashtable scoreSorts = new Hashtable();
4025 AlignmentAnnotation aann[];
4026 for (SequenceI sqa : viewport.getAlignment().getSequences())
4028 aann = sqa.getAnnotation();
4029 for (int i = 0; aann != null && i < aann.length; i++)
4031 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4033 scoreSorts.put(aann[i].label, aann[i].label);
4037 Enumeration labels = scoreSorts.keys();
4038 while (labels.hasMoreElements())
4040 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4041 (String) labels.nextElement());
4043 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4046 _annotationScoreVectorHash = viewport.getAlignment()
4047 .getAlignmentAnnotation().hashCode();
4052 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4053 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4054 * call. Listeners are added to remove the menu item when the treePanel is
4055 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4059 * Displayed tree window.
4061 * SortBy menu item title.
4064 public void buildTreeMenu()
4066 calculateTree.removeAll();
4067 // build the calculate menu
4069 for (final String type : new String[]
4072 String treecalcnm = MessageManager.getString("label.tree_calc_"
4073 + type.toLowerCase());
4074 for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4076 JMenuItem tm = new JMenuItem();
4077 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4078 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4080 String smn = MessageManager.getStringOrReturn(
4081 "label.score_model_", sm.getName());
4082 final String title = MessageManager.formatMessage(
4083 "label.treecalc_title", treecalcnm, smn);
4084 tm.setText(title);//
4085 tm.addActionListener(new java.awt.event.ActionListener()
4088 public void actionPerformed(ActionEvent e)
4090 NewTreePanel(type, (String) pwtype, title);
4093 calculateTree.add(tm);
4098 sortByTreeMenu.removeAll();
4100 Vector comps = (Vector) PaintRefresher.components.get(viewport
4101 .getSequenceSetId());
4102 Vector treePanels = new Vector();
4103 int i, iSize = comps.size();
4104 for (i = 0; i < iSize; i++)
4106 if (comps.elementAt(i) instanceof TreePanel)
4108 treePanels.add(comps.elementAt(i));
4112 iSize = treePanels.size();
4116 sortByTreeMenu.setVisible(false);
4120 sortByTreeMenu.setVisible(true);
4122 for (i = 0; i < treePanels.size(); i++)
4124 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4125 final JMenuItem item = new JMenuItem(tp.getTitle());
4126 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4127 item.addActionListener(new java.awt.event.ActionListener()
4130 public void actionPerformed(ActionEvent e)
4132 tp.sortByTree_actionPerformed(null);
4133 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4138 sortByTreeMenu.add(item);
4142 public boolean sortBy(AlignmentOrder alorder, String undoname)
4144 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4145 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4146 if (undoname != null)
4148 addHistoryItem(new OrderCommand(undoname, oldOrder,
4149 viewport.getAlignment()));
4151 alignPanel.paintAlignment(true);
4156 * Work out whether the whole set of sequences or just the selected set will
4157 * be submitted for multiple alignment.
4160 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4162 // Now, check we have enough sequences
4163 AlignmentView msa = null;
4165 if ((viewport.getSelectionGroup() != null)
4166 && (viewport.getSelectionGroup().getSize() > 1))
4168 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4169 // some common interface!
4171 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4172 * SequenceI[sz = seqs.getSize(false)];
4174 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4175 * seqs.getSequenceAt(i); }
4177 msa = viewport.getAlignmentView(true);
4182 * Vector seqs = viewport.getAlignment().getSequences();
4184 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
4186 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
4187 * seqs.elementAt(i); } }
4189 msa = viewport.getAlignmentView(false);
4195 * Decides what is submitted to a secondary structure prediction service: the
4196 * first sequence in the alignment, or in the current selection, or, if the
4197 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4198 * region or the whole alignment. (where the first sequence in the set is the
4199 * one that the prediction will be for).
4201 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4203 AlignmentView seqs = null;
4205 if ((viewport.getSelectionGroup() != null)
4206 && (viewport.getSelectionGroup().getSize() > 0))
4208 seqs = viewport.getAlignmentView(true);
4212 seqs = viewport.getAlignmentView(false);
4214 // limit sequences - JBPNote in future - could spawn multiple prediction
4216 // TODO: viewport.getAlignment().isAligned is a global state - the local
4217 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4218 if (!viewport.getAlignment().isAligned(false))
4220 seqs.setSequences(new SeqCigar[]
4221 { seqs.getSequences()[0] });
4222 // TODO: if seqs.getSequences().length>1 then should really have warned
4236 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4238 // Pick the tree file
4239 JalviewFileChooser chooser = new JalviewFileChooser(
4240 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4241 chooser.setFileView(new JalviewFileView());
4242 chooser.setDialogTitle(MessageManager
4243 .getString("label.select_newick_like_tree_file"));
4244 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4246 int value = chooser.showOpenDialog(null);
4248 if (value == JalviewFileChooser.APPROVE_OPTION)
4250 String choice = chooser.getSelectedFile().getPath();
4251 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4252 jalview.io.NewickFile fin = null;
4255 fin = new jalview.io.NewickFile(choice, "File");
4256 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4257 } catch (Exception ex)
4264 .getString("label.problem_reading_tree_file"),
4265 JOptionPane.WARNING_MESSAGE);
4266 ex.printStackTrace();
4268 if (fin != null && fin.hasWarningMessage())
4270 JOptionPane.showMessageDialog(Desktop.desktop, fin
4271 .getWarningMessage(), MessageManager
4272 .getString("label.possible_problem_with_tree_file"),
4273 JOptionPane.WARNING_MESSAGE);
4279 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4281 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4284 public TreePanel ShowNewickTree(NewickFile nf, String title)
4286 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4289 public TreePanel ShowNewickTree(NewickFile nf, String title,
4290 AlignmentView input)
4292 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4295 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4296 int h, int x, int y)
4298 return ShowNewickTree(nf, title, null, w, h, x, y);
4302 * Add a treeviewer for the tree extracted from a newick file object to the
4303 * current alignment view
4310 * Associated alignment input data (or null)
4319 * @return TreePanel handle
4321 public TreePanel ShowNewickTree(NewickFile nf, String title,
4322 AlignmentView input, int w, int h, int x, int y)
4324 TreePanel tp = null;
4330 if (nf.getTree() != null)
4332 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4338 tp.setLocation(x, y);
4341 Desktop.addInternalFrame(tp, title, w, h);
4343 } catch (Exception ex)
4345 ex.printStackTrace();
4351 private boolean buildingMenu = false;
4354 * Generates menu items and listener event actions for web service clients
4357 public void BuildWebServiceMenu()
4359 while (buildingMenu)
4363 System.err.println("Waiting for building menu to finish.");
4365 } catch (Exception e)
4370 final AlignFrame me = this;
4371 buildingMenu = true;
4372 new Thread(new Runnable()
4377 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4380 System.err.println("Building ws menu again "
4381 + Thread.currentThread());
4382 // TODO: add support for context dependent disabling of services based
4384 // alignment and current selection
4385 // TODO: add additional serviceHandle parameter to specify abstract
4387 // class independently of AbstractName
4388 // TODO: add in rediscovery GUI function to restart discoverer
4389 // TODO: group services by location as well as function and/or
4391 // object broker mechanism.
4392 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4393 final IProgressIndicator af = me;
4394 final JMenu msawsmenu = new JMenu("Alignment");
4395 final JMenu secstrmenu = new JMenu(
4396 "Secondary Structure Prediction");
4397 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4398 final JMenu analymenu = new JMenu("Analysis");
4399 final JMenu dismenu = new JMenu("Protein Disorder");
4400 // final JMenu msawsmenu = new
4401 // JMenu(MessageManager.getString("label.alignment"));
4402 // final JMenu secstrmenu = new
4403 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4404 // final JMenu seqsrchmenu = new
4405 // JMenu(MessageManager.getString("label.sequence_database_search"));
4406 // final JMenu analymenu = new
4407 // JMenu(MessageManager.getString("label.analysis"));
4408 // final JMenu dismenu = new
4409 // JMenu(MessageManager.getString("label.protein_disorder"));
4410 // JAL-940 - only show secondary structure prediction services from
4411 // the legacy server
4412 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4414 Discoverer.services != null && (Discoverer.services.size() > 0))
4416 // TODO: refactor to allow list of AbstractName/Handler bindings to
4418 // stored or retrieved from elsewhere
4419 // No MSAWS used any more:
4420 // Vector msaws = null; // (Vector)
4421 // Discoverer.services.get("MsaWS");
4422 Vector secstrpr = (Vector) Discoverer.services
4424 if (secstrpr != null)
4426 // Add any secondary structure prediction services
4427 for (int i = 0, j = secstrpr.size(); i < j; i++)
4429 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4431 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4432 .getServiceClient(sh);
4433 int p = secstrmenu.getItemCount();
4434 impl.attachWSMenuEntry(secstrmenu, me);
4435 int q = secstrmenu.getItemCount();
4436 for (int litm = p; litm < q; litm++)
4438 legacyItems.add(secstrmenu.getItem(litm));
4444 // Add all submenus in the order they should appear on the web
4446 wsmenu.add(msawsmenu);
4447 wsmenu.add(secstrmenu);
4448 wsmenu.add(dismenu);
4449 wsmenu.add(analymenu);
4450 // No search services yet
4451 // wsmenu.add(seqsrchmenu);
4453 javax.swing.SwingUtilities.invokeLater(new Runnable()
4460 webService.removeAll();
4461 // first, add discovered services onto the webservices menu
4462 if (wsmenu.size() > 0)
4464 for (int i = 0, j = wsmenu.size(); i < j; i++)
4466 webService.add(wsmenu.get(i));
4471 webService.add(me.webServiceNoServices);
4473 // TODO: move into separate menu builder class.
4474 boolean new_sspred = false;
4475 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4477 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4478 if (jws2servs != null)
4480 if (jws2servs.hasServices())
4482 jws2servs.attachWSMenuEntry(webService, me);
4483 for (Jws2Instance sv : jws2servs.getServices())
4485 if (sv.description.toLowerCase().contains("jpred"))
4487 for (JMenuItem jmi : legacyItems)
4489 jmi.setVisible(false);
4495 if (jws2servs.isRunning())
4497 JMenuItem tm = new JMenuItem(
4498 "Still discovering JABA Services");
4499 tm.setEnabled(false);
4504 build_urlServiceMenu(me.webService);
4505 build_fetchdbmenu(webService);
4506 for (JMenu item : wsmenu)
4508 if (item.getItemCount() == 0)
4510 item.setEnabled(false);
4514 item.setEnabled(true);
4517 } catch (Exception e)
4520 .debug("Exception during web service menu building process.",
4526 } catch (Exception e)
4531 buildingMenu = false;
4538 * construct any groupURL type service menu entries.
4542 private void build_urlServiceMenu(JMenu webService)
4544 // TODO: remove this code when 2.7 is released
4545 // DEBUG - alignmentView
4547 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4548 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4550 * @Override public void actionPerformed(ActionEvent e) {
4551 * jalview.datamodel.AlignmentView
4552 * .testSelectionViews(af.viewport.getAlignment(),
4553 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4555 * }); webService.add(testAlView);
4557 // TODO: refactor to RestClient discoverer and merge menu entries for
4558 // rest-style services with other types of analysis/calculation service
4559 // SHmmr test client - still being implemented.
4560 // DEBUG - alignmentView
4562 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4565 client.attachWSMenuEntry(
4566 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4572 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4573 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4574 * getProperty("LAST_DIRECTORY"));
4576 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4577 * to Vamsas file"); chooser.setToolTipText("Export");
4579 * int value = chooser.showSaveDialog(this);
4581 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4582 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4583 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4584 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4587 * prototype of an automatically enabled/disabled analysis function
4590 protected void setShowProductsEnabled()
4592 SequenceI[] selection = viewport.getSequenceSelection();
4593 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4594 viewport.getAlignment().getDataset()))
4596 showProducts.setEnabled(true);
4601 showProducts.setEnabled(false);
4606 * search selection for sequence xRef products and build the show products
4611 * @return true if showProducts menu should be enabled.
4613 public boolean canShowProducts(SequenceI[] selection,
4614 boolean isRegionSelection, Alignment dataset)
4616 boolean showp = false;
4619 showProducts.removeAll();
4620 final boolean dna = viewport.getAlignment().isNucleotide();
4621 final Alignment ds = dataset;
4622 String[] ptypes = (selection == null || selection.length == 0) ? null
4623 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4625 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4626 // selection, dataset, true);
4627 final SequenceI[] sel = selection;
4628 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4631 final boolean isRegSel = isRegionSelection;
4632 final AlignFrame af = this;
4633 final String source = ptypes[t];
4634 JMenuItem xtype = new JMenuItem(ptypes[t]);
4635 xtype.addActionListener(new ActionListener()
4639 public void actionPerformed(ActionEvent e)
4641 // TODO: new thread for this call with vis-delay
4642 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4643 isRegSel, dna, source);
4647 showProducts.add(xtype);
4649 showProducts.setVisible(showp);
4650 showProducts.setEnabled(showp);
4651 } catch (Exception e)
4653 jalview.bin.Cache.log
4654 .warn("canTranslate threw an exception - please report to help@jalview.org",
4661 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4662 boolean isRegSel, boolean dna, String source)
4664 final boolean fisRegSel = isRegSel;
4665 final boolean fdna = dna;
4666 final String fsrc = source;
4667 final AlignFrame ths = this;
4668 final SequenceI[] fsel = sel;
4669 Runnable foo = new Runnable()
4675 final long sttime = System.currentTimeMillis();
4676 ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
4679 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4683 Alignment prods = CrossRef
4684 .findXrefSequences(fsel, fdna, fsrc, ds);
4687 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4688 for (int s = 0; s < sprods.length; s++)
4690 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4691 if (ds.getSequences() == null
4692 || !ds.getSequences().contains(
4693 sprods[s].getDatasetSequence()))
4695 ds.addSequence(sprods[s].getDatasetSequence());
4697 sprods[s].updatePDBIds();
4699 Alignment al = new Alignment(sprods);
4700 AlignedCodonFrame[] cf = prods.getCodonFrames();
4702 for (int s = 0; cf != null && s < cf.length; s++)
4704 al.addCodonFrame(cf[s]);
4707 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4709 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4710 + " for " + ((fisRegSel) ? "selected region of " : "")
4712 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4717 System.err.println("No Sequences generated for xRef type "
4720 } catch (Exception e)
4722 jalview.bin.Cache.log.error(
4723 "Exception when finding crossreferences", e);
4724 } catch (OutOfMemoryError e)
4726 new OOMWarning("whilst fetching crossreferences", e);
4729 jalview.bin.Cache.log.error("Error when finding crossreferences",
4732 ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
4737 Thread frunner = new Thread(foo);
4741 public boolean canShowTranslationProducts(SequenceI[] selection,
4742 AlignmentI alignment)
4747 return (jalview.analysis.Dna.canTranslate(selection,
4748 viewport.getViewAsVisibleContigs(true)));
4749 } catch (Exception e)
4751 jalview.bin.Cache.log
4752 .warn("canTranslate threw an exception - please report to help@jalview.org",
4759 public void showProducts_actionPerformed(ActionEvent e)
4761 // /////////////////////////////
4762 // Collect Data to be translated/transferred
4764 SequenceI[] selection = viewport.getSequenceSelection();
4765 AlignmentI al = null;
4768 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4769 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4770 viewport.getAlignment().getDataset());
4771 } catch (Exception ex)
4774 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4782 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4783 MessageManager.getString("label.translation_failed"),
4784 JOptionPane.WARNING_MESSAGE);
4788 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4789 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4790 "label.translation_of_params", new String[]
4791 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4796 public void showTranslation_actionPerformed(ActionEvent e)
4798 // /////////////////////////////
4799 // Collect Data to be translated/transferred
4801 SequenceI[] selection = viewport.getSequenceSelection();
4802 String[] seqstring = viewport.getViewAsString(true);
4803 AlignmentI al = null;
4806 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4807 viewport.getViewAsVisibleContigs(true), viewport
4808 .getGapCharacter(), viewport.getAlignment()
4809 .getAlignmentAnnotation(), viewport.getAlignment()
4810 .getWidth(), viewport.getAlignment().getDataset());
4811 } catch (Exception ex)
4814 jalview.bin.Cache.log.error(
4815 "Exception during translation. Please report this !", ex);
4820 .getString("label.error_when_translating_sequences_submit_bug_report"),
4822 .getString("label.implementation_error")
4824 .getString("translation_failed"),
4825 JOptionPane.ERROR_MESSAGE);
4834 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4835 MessageManager.getString("label.translation_failed"),
4836 JOptionPane.WARNING_MESSAGE);
4840 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4841 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4842 "label.translation_of_params", new String[]
4843 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4848 * Try to load a features file onto the alignment.
4851 * contents or path to retrieve file
4853 * access mode of file (see jalview.io.AlignFile)
4854 * @return true if features file was parsed corectly.
4856 public boolean parseFeaturesFile(String file, String type)
4858 boolean featuresFile = false;
4861 featuresFile = new FeaturesFile(file, type).parse(viewport
4862 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4863 .getFeatureRenderer().featureColours, false,
4864 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4865 } catch (Exception ex)
4867 ex.printStackTrace();
4872 viewport.showSequenceFeatures = true;
4873 showSeqFeatures.setSelected(true);
4874 if (alignPanel.seqPanel.seqCanvas.fr != null)
4876 // update the min/max ranges where necessary
4877 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4879 if (featureSettings != null)
4881 featureSettings.setTableData();
4883 alignPanel.paintAlignment(true);
4886 return featuresFile;
4890 public void dragEnter(DropTargetDragEvent evt)
4895 public void dragExit(DropTargetEvent evt)
4900 public void dragOver(DropTargetDragEvent evt)
4905 public void dropActionChanged(DropTargetDragEvent evt)
4910 public void drop(DropTargetDropEvent evt)
4912 Transferable t = evt.getTransferable();
4913 java.util.List files = null;
4917 DataFlavor uriListFlavor = new DataFlavor(
4918 "text/uri-list;class=java.lang.String");
4919 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4921 // Works on Windows and MacOSX
4922 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4923 files = (java.util.List) t
4924 .getTransferData(DataFlavor.javaFileListFlavor);
4926 else if (t.isDataFlavorSupported(uriListFlavor))
4928 // This is used by Unix drag system
4929 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4930 String data = (String) t.getTransferData(uriListFlavor);
4931 files = new java.util.ArrayList(1);
4932 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4933 data, "\r\n"); st.hasMoreTokens();)
4935 String s = st.nextToken();
4936 if (s.startsWith("#"))
4938 // the line is a comment (as per the RFC 2483)
4942 java.net.URI uri = new java.net.URI(s);
4943 // check to see if we can handle this kind of URI
4944 if (uri.getScheme().toLowerCase().startsWith("http"))
4946 files.add(uri.toString());
4950 // otherwise preserve old behaviour: catch all for file objects
4951 java.io.File file = new java.io.File(uri);
4952 files.add(file.toString());
4956 } catch (Exception e)
4958 e.printStackTrace();
4964 // check to see if any of these files have names matching sequences in
4966 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4967 .getAlignment().getSequencesArray());
4969 * Object[] { String,SequenceI}
4971 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4972 ArrayList<String> filesnotmatched = new ArrayList<String>();
4973 for (int i = 0; i < files.size(); i++)
4975 String file = files.get(i).toString();
4977 String protocol = FormatAdapter.checkProtocol(file);
4978 if (protocol == jalview.io.FormatAdapter.FILE)
4980 File fl = new File(file);
4981 pdbfn = fl.getName();
4983 else if (protocol == jalview.io.FormatAdapter.URL)
4985 URL url = new URL(file);
4986 pdbfn = url.getFile();
4988 if (pdbfn.length() > 0)
4990 // attempt to find a match in the alignment
4991 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4992 int l = 0, c = pdbfn.indexOf(".");
4993 while (mtch == null && c != -1)
4998 } while ((c = pdbfn.indexOf(".", l)) > l);
5001 pdbfn = pdbfn.substring(0, l);
5003 mtch = idm.findAllIdMatches(pdbfn);
5010 type = new IdentifyFile().Identify(file, protocol);
5011 } catch (Exception ex)
5017 if (type.equalsIgnoreCase("PDB"))
5019 filesmatched.add(new Object[]
5020 { file, protocol, mtch });
5025 // File wasn't named like one of the sequences or wasn't a PDB file.
5026 filesnotmatched.add(file);
5030 if (filesmatched.size() > 0)
5032 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5038 "label.automatically_associate_pdb_files_with_sequences_same_name",
5045 .getString("label.automatically_associate_pdb_files_by_name"),
5046 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5049 for (Object[] fm : filesmatched)
5051 // try and associate
5052 // TODO: may want to set a standard ID naming formalism for
5053 // associating PDB files which have no IDs.
5054 for (SequenceI toassoc : (SequenceI[]) fm[2])
5056 PDBEntry pe = new AssociatePdbFileWithSeq()
5057 .associatePdbWithSeq((String) fm[0],
5058 (String) fm[1], toassoc, false);
5061 System.err.println("Associated file : "
5062 + ((String) fm[0]) + " with "
5063 + toassoc.getDisplayId(true));
5067 alignPanel.paintAlignment(true);
5071 if (filesnotmatched.size() > 0)
5074 && (Cache.getDefault(
5075 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5078 "<html>"+MessageManager
5080 "label.ignore_unmatched_dropped_files_info",
5085 .toString() })+"</html>",
5087 .getString("label.ignore_unmatched_dropped_files"),
5088 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5092 for (String fn : filesnotmatched)
5094 loadJalviewDataFile(fn, null, null, null);
5098 } catch (Exception ex)
5100 ex.printStackTrace();
5106 * Attempt to load a "dropped" file or URL string: First by testing whether
5107 * it's and Annotation file, then a JNet file, and finally a features file. If
5108 * all are false then the user may have dropped an alignment file onto this
5112 * either a filename or a URL string.
5114 public void loadJalviewDataFile(String file, String protocol,
5115 String format, SequenceI assocSeq)
5119 if (protocol == null)
5121 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5123 // if the file isn't identified, or not positively identified as some
5124 // other filetype (PFAM is default unidentified alignment file type) then
5125 // try to parse as annotation.
5126 boolean isAnnotation = (format == null || format
5127 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5128 .readAnnotationFile(viewport.getAlignment(), file, protocol)
5133 // first see if its a T-COFFEE score file
5134 TCoffeeScoreFile tcf = null;
5137 tcf = new TCoffeeScoreFile(file, protocol);
5140 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5142 tcoffeeColour.setEnabled(true);
5143 tcoffeeColour.setSelected(true);
5144 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5145 isAnnotation = true;
5147 .setText(MessageManager
5148 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5152 // some problem - if no warning its probable that the ID matching
5153 // process didn't work
5157 tcf.getWarningMessage() == null ? MessageManager
5158 .getString("label.check_file_matches_sequence_ids_alignment")
5159 : tcf.getWarningMessage(),
5161 .getString("label.problem_reading_tcoffee_score_file"),
5162 JOptionPane.WARNING_MESSAGE);
5169 } catch (Exception x)
5172 .debug("Exception when processing data source as T-COFFEE score file",
5178 // try to see if its a JNet 'concise' style annotation file *before*
5180 // try to parse it as a features file
5183 format = new IdentifyFile().Identify(file, protocol);
5185 if (format.equalsIgnoreCase("JnetFile"))
5187 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5189 new JnetAnnotationMaker().add_annotation(predictions,
5190 viewport.getAlignment(), 0, false);
5191 isAnnotation = true;
5196 * if (format.equalsIgnoreCase("PDB")) {
5198 * String pdbfn = ""; // try to match up filename with sequence id
5199 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5200 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5201 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5202 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5203 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5204 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5205 * // attempt to find a match in the alignment SequenceI mtch =
5206 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5207 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5208 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5209 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5210 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5211 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5212 * { System.err.println("Associated file : " + file + " with " +
5213 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5214 * TODO: maybe need to load as normal otherwise return; } }
5216 // try to parse it as a features file
5217 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5218 // if it wasn't a features file then we just treat it as a general
5219 // alignment file to load into the current view.
5222 new FileLoader().LoadFile(viewport, file, protocol, format);
5226 alignPanel.paintAlignment(true);
5234 alignPanel.adjustAnnotationHeight();
5235 viewport.updateSequenceIdColours();
5236 buildSortByAnnotationScoresMenu();
5237 alignPanel.paintAlignment(true);
5239 } catch (Exception ex)
5241 ex.printStackTrace();
5242 } catch (OutOfMemoryError oom)
5247 } catch (Exception x)
5253 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5254 : "using " + protocol + " from " + file)
5256 + (format != null ? "(parsing as '" + format
5257 + "' file)" : ""), oom, Desktop.desktop);
5262 public void tabSelectionChanged(int index)
5266 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5267 viewport = alignPanel.av;
5268 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5269 setMenusFromViewport(viewport);
5274 public void tabbedPane_mousePressed(MouseEvent e)
5276 if (SwingUtilities.isRightMouseButton(e))
5278 String reply = JOptionPane.showInternalInputDialog(this,
5279 MessageManager.getString("label.enter_view_name"),
5280 MessageManager.getString("label.enter_view_name"),
5281 JOptionPane.QUESTION_MESSAGE);
5285 viewport.viewName = reply;
5286 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5291 public AlignViewport getCurrentView()
5297 * Open the dialog for regex description parsing.
5300 protected void extractScores_actionPerformed(ActionEvent e)
5302 ParseProperties pp = new jalview.analysis.ParseProperties(
5303 viewport.getAlignment());
5304 // TODO: verify regex and introduce GUI dialog for version 2.5
5305 // if (pp.getScoresFromDescription("col", "score column ",
5306 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5308 if (pp.getScoresFromDescription("description column",
5309 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5311 buildSortByAnnotationScoresMenu();
5319 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5323 protected void showDbRefs_actionPerformed(ActionEvent e)
5325 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5331 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5335 protected void showNpFeats_actionPerformed(ActionEvent e)
5337 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5341 * find the viewport amongst the tabs in this alignment frame and close that
5346 public boolean closeView(AlignViewport av)
5350 this.closeMenuItem_actionPerformed(false);
5353 Component[] comp = tabbedPane.getComponents();
5354 for (int i = 0; comp != null && i < comp.length; i++)
5356 if (comp[i] instanceof AlignmentPanel)
5358 if (((AlignmentPanel) comp[i]).av == av)
5361 closeView((AlignmentPanel) comp[i]);
5369 protected void build_fetchdbmenu(JMenu webService)
5371 // Temporary hack - DBRef Fetcher always top level ws entry.
5372 // TODO We probably want to store a sequence database checklist in
5373 // preferences and have checkboxes.. rather than individual sources selected
5375 final JMenu rfetch = new JMenu(
5376 MessageManager.getString("action.fetch_db_references"));
5377 rfetch.setToolTipText(MessageManager
5378 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5379 webService.add(rfetch);
5381 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5382 MessageManager.getString("option.trim_retrieved_seqs"));
5383 trimrs.setToolTipText(MessageManager
5384 .getString("label.trim_retrieved_sequences"));
5385 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5386 trimrs.addActionListener(new ActionListener()
5389 public void actionPerformed(ActionEvent e)
5391 trimrs.setSelected(trimrs.isSelected());
5392 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5393 Boolean.valueOf(trimrs.isSelected()).toString());
5397 JMenuItem fetchr = new JMenuItem(
5398 MessageManager.getString("label.standard_databases"));
5399 fetchr.setToolTipText(MessageManager
5400 .getString("label.fetch_embl_uniprot"));
5401 fetchr.addActionListener(new ActionListener()
5405 public void actionPerformed(ActionEvent e)
5407 new Thread(new Runnable()
5413 new jalview.ws.DBRefFetcher(alignPanel.av
5414 .getSequenceSelection(), alignPanel.alignFrame)
5415 .fetchDBRefs(false);
5423 final AlignFrame me = this;
5424 new Thread(new Runnable()
5429 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5430 .getSequenceFetcherSingleton(me);
5431 javax.swing.SwingUtilities.invokeLater(new Runnable()
5436 String[] dbclasses = sf.getOrderedSupportedSources();
5437 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5438 // jalview.util.QuickSort.sort(otherdb, otherdb);
5439 List<DbSourceProxy> otherdb;
5440 JMenu dfetch = new JMenu();
5441 JMenu ifetch = new JMenu();
5442 JMenuItem fetchr = null;
5443 int comp = 0, icomp = 0, mcomp = 15;
5444 String mname = null;
5446 for (String dbclass : dbclasses)
5448 otherdb = sf.getSourceProxy(dbclass);
5449 // add a single entry for this class, or submenu allowing 'fetch
5451 if (otherdb == null || otherdb.size() < 1)
5455 // List<DbSourceProxy> dbs=otherdb;
5456 // otherdb=new ArrayList<DbSourceProxy>();
5457 // for (DbSourceProxy db:dbs)
5459 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5463 mname = "From " + dbclass;
5465 if (otherdb.size() == 1)
5467 final DbSourceProxy[] dassource = otherdb
5468 .toArray(new DbSourceProxy[0]);
5469 DbSourceProxy src = otherdb.get(0);
5470 fetchr = new JMenuItem(src.getDbSource());
5471 fetchr.addActionListener(new ActionListener()
5475 public void actionPerformed(ActionEvent e)
5477 new Thread(new Runnable()
5483 new jalview.ws.DBRefFetcher(alignPanel.av
5484 .getSequenceSelection(),
5485 alignPanel.alignFrame, dassource)
5486 .fetchDBRefs(false);
5492 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
5498 final DbSourceProxy[] dassource = otherdb
5499 .toArray(new DbSourceProxy[0]);
5501 DbSourceProxy src = otherdb.get(0);
5502 fetchr = new JMenuItem(MessageManager.formatMessage(
5503 "label.fetch_all_param", new String[]
5504 { src.getDbSource() }));
5505 fetchr.addActionListener(new ActionListener()
5508 public void actionPerformed(ActionEvent e)
5510 new Thread(new Runnable()
5516 new jalview.ws.DBRefFetcher(alignPanel.av
5517 .getSequenceSelection(),
5518 alignPanel.alignFrame, dassource)
5519 .fetchDBRefs(false);
5525 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5528 // and then build the rest of the individual menus
5529 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
5531 String imname = null;
5533 for (DbSourceProxy sproxy : otherdb)
5535 String dbname = sproxy.getDbName();
5536 String sname = dbname.length() > 5 ? dbname.substring(0,
5537 5) + "..." : dbname;
5538 String msname = dbname.length() > 10 ? dbname.substring(
5539 0, 10) + "..." : dbname;
5542 imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
5544 fetchr = new JMenuItem(msname);
5545 final DbSourceProxy[] dassrc =
5547 fetchr.addActionListener(new ActionListener()
5551 public void actionPerformed(ActionEvent e)
5553 new Thread(new Runnable()
5559 new jalview.ws.DBRefFetcher(alignPanel.av
5560 .getSequenceSelection(),
5561 alignPanel.alignFrame, dassrc)
5562 .fetchDBRefs(false);
5568 fetchr.setToolTipText("<html>"
5569 + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
5572 if (++icomp >= mcomp || i == (otherdb.size()))
5574 ifetch.setText(MessageManager.formatMessage(
5575 "label.source_to_target", imname, sname));
5577 ifetch = new JMenu();
5585 if (comp >= mcomp || dbi >= (dbclasses.length))
5587 dfetch.setText(MessageManager.formatMessage(
5588 "label.source_to_target", mname, dbclass));
5590 dfetch = new JMenu();
5603 * Left justify the whole alignment.
5606 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5608 AlignmentI al = viewport.getAlignment();
5610 viewport.firePropertyChange("alignment", null, al);
5614 * Right justify the whole alignment.
5617 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5619 AlignmentI al = viewport.getAlignment();
5621 viewport.firePropertyChange("alignment", null, al);
5624 public void setShowSeqFeatures(boolean b)
5626 showSeqFeatures.setSelected(true);
5627 viewport.setShowSequenceFeatures(true);
5634 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5635 * awt.event.ActionEvent)
5638 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5640 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5641 alignPanel.paintAlignment(true);
5648 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5652 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5654 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5655 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5663 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5664 * .event.ActionEvent)
5667 protected void showGroupConservation_actionPerformed(ActionEvent e)
5669 viewport.setShowGroupConservation(showGroupConservation.getState());
5670 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5677 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5678 * .event.ActionEvent)
5681 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5683 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5684 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5691 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5692 * .event.ActionEvent)
5695 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5697 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5698 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5702 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5704 showSequenceLogo.setState(true);
5705 viewport.setShowSequenceLogo(true);
5706 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5707 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5711 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5713 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5720 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5721 * .event.ActionEvent)
5724 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5726 if (avc.makeGroupsFromSelection())
5728 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5729 alignPanel.updateAnnotation();
5730 alignPanel.paintAlignment(true);
5735 protected void createGroup_actionPerformed(ActionEvent e)
5737 if (avc.createGroup())
5739 alignPanel.alignmentChanged();
5744 protected void unGroup_actionPerformed(ActionEvent e)
5748 alignPanel.alignmentChanged();
5753 * make the given alignmentPanel the currently selected tab
5755 * @param alignmentPanel
5757 public void setDisplayedView(AlignmentPanel alignmentPanel)
5759 if (!viewport.getSequenceSetId().equals(
5760 alignmentPanel.av.getSequenceSetId()))
5762 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5764 if (tabbedPane != null
5765 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5766 .getSelectedIndex())
5768 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5773 * Action on selection of menu options to Show or Hide annotations.
5776 * @param forSequences
5777 * update sequence-related annotations
5778 * @param forAlignment
5779 * update non-sequence-related annotations
5782 protected void setAnnotationsVisibility(boolean visible,
5783 boolean forSequences, boolean forAlignment)
5785 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5786 .getAlignmentAnnotation())
5788 boolean apply = (aa.sequenceRef == null && forAlignment)
5789 || (aa.sequenceRef != null && forSequences);
5792 aa.visible = visible;
5795 this.alignPanel.paintAlignment(true);
5799 * Store selected annotation sort order for the view and repaint.
5802 protected void sortAnnotations_actionPerformed()
5804 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5806 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5807 alignPanel.paintAlignment(true);
5811 class PrintThread extends Thread
5815 public PrintThread(AlignmentPanel ap)
5820 static PageFormat pf;
5825 PrinterJob printJob = PrinterJob.getPrinterJob();
5829 printJob.setPrintable(ap, pf);
5833 printJob.setPrintable(ap);
5836 if (printJob.printDialog())
5841 } catch (Exception PrintException)
5843 PrintException.printStackTrace();