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 exisiting 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 all annotations only enabled if annotation panel is shown
751 showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
752 hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
753 viewBoxesMenuItem.setSelected(av.showBoxes);
754 viewTextMenuItem.setSelected(av.showText);
755 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
756 showGroupConsensus.setSelected(av.isShowGroupConsensus());
757 showGroupConservation.setSelected(av.isShowGroupConservation());
758 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
759 showSequenceLogo.setSelected(av.isShowSequenceLogo());
760 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
762 setColourSelected(ColourSchemeProperty.getColourName(av
763 .getGlobalColourScheme()));
765 showSeqFeatures.setSelected(av.showSequenceFeatures);
766 hiddenMarkers.setState(av.showHiddenMarkers);
767 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
768 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
769 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
770 autoCalculate.setSelected(av.autoCalculateConsensus);
771 sortByTree.setSelected(av.sortByTree);
772 listenToViewSelections.setSelected(av.followSelection);
773 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
775 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
776 setShowProductsEnabled();
780 // methods for implementing IProgressIndicator
781 // need to refactor to a reusable stub class
782 Hashtable progressBars, progressBarHandlers;
787 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
790 public void setProgressBar(String message, long id)
792 if (progressBars == null)
794 progressBars = new Hashtable();
795 progressBarHandlers = new Hashtable();
798 JPanel progressPanel;
799 Long lId = new Long(id);
800 GridLayout layout = (GridLayout) statusPanel.getLayout();
801 if (progressBars.get(lId) != null)
803 progressPanel = (JPanel) progressBars.get(new Long(id));
804 statusPanel.remove(progressPanel);
805 progressBars.remove(lId);
806 progressPanel = null;
809 statusBar.setText(message);
811 if (progressBarHandlers.contains(lId))
813 progressBarHandlers.remove(lId);
815 layout.setRows(layout.getRows() - 1);
819 progressPanel = new JPanel(new BorderLayout(10, 5));
821 JProgressBar progressBar = new JProgressBar();
822 progressBar.setIndeterminate(true);
824 progressPanel.add(new JLabel(message), BorderLayout.WEST);
825 progressPanel.add(progressBar, BorderLayout.CENTER);
827 layout.setRows(layout.getRows() + 1);
828 statusPanel.add(progressPanel);
830 progressBars.put(lId, progressPanel);
833 // setMenusForViewport();
838 public void registerHandler(final long id,
839 final IProgressIndicatorHandler handler)
841 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
843 throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
845 progressBarHandlers.put(new Long(id), handler);
846 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
847 if (handler.canCancel())
849 JButton cancel = new JButton(
850 MessageManager.getString("action.cancel"));
851 final IProgressIndicator us = this;
852 cancel.addActionListener(new ActionListener()
856 public void actionPerformed(ActionEvent e)
858 handler.cancelActivity(id);
859 us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
862 progressPanel.add(cancel, BorderLayout.EAST);
868 * @return true if any progress bars are still active
871 public boolean operationInProgress()
873 if (progressBars != null && progressBars.size() > 0)
881 public void setStatus(String text)
883 statusBar.setText(text);
887 * Added so Castor Mapping file can obtain Jalview Version
889 public String getVersion()
891 return jalview.bin.Cache.getProperty("VERSION");
894 public FeatureRenderer getFeatureRenderer()
896 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
900 public void fetchSequence_actionPerformed(ActionEvent e)
902 new SequenceFetcher(this);
906 public void addFromFile_actionPerformed(ActionEvent e)
908 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
912 public void reload_actionPerformed(ActionEvent e)
914 if (fileName != null)
916 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
917 // originating file's format
918 // TODO: work out how to recover feature settings for correct view(s) when
920 if (currentFileFormat.equals("Jalview"))
922 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
923 for (int i = 0; i < frames.length; i++)
925 if (frames[i] instanceof AlignFrame && frames[i] != this
926 && ((AlignFrame) frames[i]).fileName != null
927 && ((AlignFrame) frames[i]).fileName.equals(fileName))
931 frames[i].setSelected(true);
932 Desktop.instance.closeAssociatedWindows();
933 } catch (java.beans.PropertyVetoException ex)
939 Desktop.instance.closeAssociatedWindows();
941 FileLoader loader = new FileLoader();
942 String protocol = fileName.startsWith("http:") ? "URL" : "File";
943 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
947 Rectangle bounds = this.getBounds();
949 FileLoader loader = new FileLoader();
950 String protocol = fileName.startsWith("http:") ? "URL" : "File";
951 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
952 protocol, currentFileFormat);
954 newframe.setBounds(bounds);
955 if (featureSettings != null && featureSettings.isShowing())
957 final Rectangle fspos = featureSettings.frame.getBounds();
958 // TODO: need a 'show feature settings' function that takes bounds -
959 // need to refactor Desktop.addFrame
960 newframe.featureSettings_actionPerformed(null);
961 final FeatureSettings nfs = newframe.featureSettings;
962 SwingUtilities.invokeLater(new Runnable()
967 nfs.frame.setBounds(fspos);
970 this.featureSettings.close();
971 this.featureSettings = null;
973 this.closeMenuItem_actionPerformed(true);
979 public void addFromText_actionPerformed(ActionEvent e)
981 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
985 public void addFromURL_actionPerformed(ActionEvent e)
987 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
991 public void save_actionPerformed(ActionEvent e)
994 || (currentFileFormat == null || !jalview.io.FormatAdapter
995 .isValidIOFormat(currentFileFormat, true))
996 || fileName.startsWith("http"))
998 saveAs_actionPerformed(null);
1002 saveAlignment(fileName, currentFileFormat);
1013 public void saveAs_actionPerformed(ActionEvent e)
1015 JalviewFileChooser chooser = new JalviewFileChooser(
1016 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1017 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1018 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1019 currentFileFormat, false);
1021 chooser.setFileView(new JalviewFileView());
1022 chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1023 chooser.setToolTipText(MessageManager.getString("action.save"));
1025 int value = chooser.showSaveDialog(this);
1027 if (value == JalviewFileChooser.APPROVE_OPTION)
1029 currentFileFormat = chooser.getSelectedFormat();
1030 if (currentFileFormat == null)
1033 .showInternalMessageDialog(
1036 .getString("label.select_file_format_before_saving"),
1038 .getString("label.file_format_not_specified"),
1039 JOptionPane.WARNING_MESSAGE);
1040 value = chooser.showSaveDialog(this);
1044 fileName = chooser.getSelectedFile().getPath();
1046 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1049 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1050 if (currentFileFormat.indexOf(" ") > -1)
1052 currentFileFormat = currentFileFormat.substring(0,
1053 currentFileFormat.indexOf(" "));
1055 saveAlignment(fileName, currentFileFormat);
1059 public boolean saveAlignment(String file, String format)
1061 boolean success = true;
1063 if (format.equalsIgnoreCase("Jalview"))
1065 String shortName = title;
1067 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1069 shortName = shortName.substring(shortName
1070 .lastIndexOf(java.io.File.separatorChar) + 1);
1073 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1075 statusBar.setText(MessageManager.formatMessage(
1076 "label.successfully_saved_to_file_in_format", new String[]
1077 { fileName, format }));
1082 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1084 warningMessage("Cannot save file " + fileName + " using format "
1085 + format, "Alignment output format not supported");
1086 saveAs_actionPerformed(null);
1087 // JBPNote need to have a raise_gui flag here
1091 String[] omitHidden = null;
1093 if (viewport.hasHiddenColumns())
1095 int reply = JOptionPane
1096 .showInternalConfirmDialog(
1099 .getString("label.alignment_contains_hidden_columns"),
1101 .getString("action.save_omit_hidden_columns"),
1102 JOptionPane.YES_NO_OPTION,
1103 JOptionPane.QUESTION_MESSAGE);
1105 if (reply == JOptionPane.YES_OPTION)
1107 omitHidden = viewport.getViewAsString(false);
1110 FormatAdapter f = new FormatAdapter();
1111 String output = f.formatSequences(format,
1112 viewport.getAlignment(), // class cast exceptions will
1113 // occur in the distant future
1114 omitHidden, f.getCacheSuffixDefault(format),
1115 viewport.getColumnSelection());
1125 java.io.PrintWriter out = new java.io.PrintWriter(
1126 new java.io.FileWriter(file));
1130 this.setTitle(file);
1131 statusBar.setText(MessageManager.formatMessage(
1132 "label.successfully_saved_to_file_in_format",
1134 { fileName, format }));
1135 } catch (Exception ex)
1138 ex.printStackTrace();
1145 JOptionPane.showInternalMessageDialog(this, MessageManager
1146 .formatMessage("label.couldnt_save_file", new String[]
1147 { fileName }), MessageManager
1148 .getString("label.error_saving_file"),
1149 JOptionPane.WARNING_MESSAGE);
1155 private void warningMessage(String warning, String title)
1157 if (new jalview.util.Platform().isHeadless())
1159 System.err.println("Warning: " + title + "\nWarning: " + warning);
1164 JOptionPane.showInternalMessageDialog(this, warning, title,
1165 JOptionPane.WARNING_MESSAGE);
1177 protected void outputText_actionPerformed(ActionEvent e)
1179 String[] omitHidden = null;
1181 if (viewport.hasHiddenColumns())
1183 int reply = JOptionPane
1184 .showInternalConfirmDialog(
1187 .getString("label.alignment_contains_hidden_columns"),
1189 .getString("action.save_omit_hidden_columns"),
1190 JOptionPane.YES_NO_OPTION,
1191 JOptionPane.QUESTION_MESSAGE);
1193 if (reply == JOptionPane.YES_OPTION)
1195 omitHidden = viewport.getViewAsString(false);
1199 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1200 cap.setForInput(null);
1204 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1205 viewport.getAlignment(), omitHidden,
1206 viewport.getColumnSelection()));
1207 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1208 "label.alignment_output_command", new String[]
1209 { e.getActionCommand() }), 600, 500);
1210 } catch (OutOfMemoryError oom)
1212 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1225 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1227 new HTMLOutput(alignPanel,
1228 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1229 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1232 public void createImageMap(File file, String image)
1234 alignPanel.makePNGImageMap(file, image);
1244 public void createPNG(File f)
1246 alignPanel.makePNG(f);
1256 public void createEPS(File f)
1258 alignPanel.makeEPS(f);
1262 public void pageSetup_actionPerformed(ActionEvent e)
1264 PrinterJob printJob = PrinterJob.getPrinterJob();
1265 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1275 public void printMenuItem_actionPerformed(ActionEvent e)
1277 // Putting in a thread avoids Swing painting problems
1278 PrintThread thread = new PrintThread(alignPanel);
1283 public void exportFeatures_actionPerformed(ActionEvent e)
1285 new AnnotationExporter().exportFeatures(alignPanel);
1289 public void exportAnnotations_actionPerformed(ActionEvent e)
1291 new AnnotationExporter().exportAnnotations(alignPanel,
1292 viewport.showAnnotation ? viewport.getAlignment()
1293 .getAlignmentAnnotation() : null, viewport
1294 .getAlignment().getGroups(), ((Alignment) viewport
1295 .getAlignment()).alignmentProperties);
1299 public void associatedData_actionPerformed(ActionEvent e)
1301 // Pick the tree file
1302 JalviewFileChooser chooser = new JalviewFileChooser(
1303 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1304 chooser.setFileView(new JalviewFileView());
1305 chooser.setDialogTitle(MessageManager
1306 .getString("label.load_jalview_annotations"));
1307 chooser.setToolTipText(MessageManager
1308 .getString("label.load_jalview_annotations"));
1310 int value = chooser.showOpenDialog(null);
1312 if (value == JalviewFileChooser.APPROVE_OPTION)
1314 String choice = chooser.getSelectedFile().getPath();
1315 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1316 loadJalviewDataFile(choice, null, null, null);
1322 * Close the current view or all views in the alignment frame. If the frame
1323 * only contains one view then the alignment will be removed from memory.
1325 * @param closeAllTabs
1328 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1330 if (alignPanels != null && alignPanels.size() < 2)
1332 closeAllTabs = true;
1337 if (alignPanels != null)
1341 if (this.isClosed())
1343 // really close all the windows - otherwise wait till
1344 // setClosed(true) is called
1345 for (int i = 0; i < alignPanels.size(); i++)
1347 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1354 closeView(alignPanel);
1360 this.setClosed(true);
1362 } catch (Exception ex)
1364 ex.printStackTrace();
1369 * close alignPanel2 and shuffle tabs appropriately.
1371 * @param alignPanel2
1373 public void closeView(AlignmentPanel alignPanel2)
1375 int index = tabbedPane.getSelectedIndex();
1376 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1377 alignPanels.removeElement(alignPanel2);
1379 // if (viewport == alignPanel2.av)
1383 alignPanel2.closePanel();
1386 tabbedPane.removeTabAt(closedindex);
1387 tabbedPane.validate();
1389 if (index > closedindex || index == tabbedPane.getTabCount())
1391 // modify currently selected tab index if necessary.
1395 this.tabSelectionChanged(index);
1401 void updateEditMenuBar()
1404 if (viewport.historyList.size() > 0)
1406 undoMenuItem.setEnabled(true);
1407 CommandI command = (CommandI) viewport.historyList.peek();
1408 undoMenuItem.setText(MessageManager.formatMessage(
1409 "label.undo_command", new String[]
1410 { command.getDescription() }));
1414 undoMenuItem.setEnabled(false);
1415 undoMenuItem.setText(MessageManager.getString("action.undo"));
1418 if (viewport.redoList.size() > 0)
1420 redoMenuItem.setEnabled(true);
1422 CommandI command = (CommandI) viewport.redoList.peek();
1423 redoMenuItem.setText(MessageManager.formatMessage(
1424 "label.redo_command", new String[]
1425 { command.getDescription() }));
1429 redoMenuItem.setEnabled(false);
1430 redoMenuItem.setText(MessageManager.getString("action.redo"));
1434 public void addHistoryItem(CommandI command)
1436 if (command.getSize() > 0)
1438 viewport.historyList.push(command);
1439 viewport.redoList.clear();
1440 updateEditMenuBar();
1441 viewport.updateHiddenColumns();
1442 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1443 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1444 // viewport.getColumnSelection()
1445 // .getHiddenColumns().size() > 0);
1451 * @return alignment objects for all views
1453 AlignmentI[] getViewAlignments()
1455 if (alignPanels != null)
1457 Enumeration e = alignPanels.elements();
1458 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1459 for (int i = 0; e.hasMoreElements(); i++)
1461 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1465 if (viewport != null)
1467 return new AlignmentI[]
1468 { viewport.getAlignment() };
1480 protected void undoMenuItem_actionPerformed(ActionEvent e)
1482 if (viewport.historyList.empty())
1486 CommandI command = (CommandI) viewport.historyList.pop();
1487 viewport.redoList.push(command);
1488 command.undoCommand(getViewAlignments());
1490 AlignViewport originalSource = getOriginatingSource(command);
1491 updateEditMenuBar();
1493 if (originalSource != null)
1495 if (originalSource != viewport)
1498 .warn("Implementation worry: mismatch of viewport origin for undo");
1500 originalSource.updateHiddenColumns();
1501 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1503 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1504 // viewport.getColumnSelection()
1505 // .getHiddenColumns().size() > 0);
1506 originalSource.firePropertyChange("alignment", null, originalSource
1507 .getAlignment().getSequences());
1518 protected void redoMenuItem_actionPerformed(ActionEvent e)
1520 if (viewport.redoList.size() < 1)
1525 CommandI command = (CommandI) viewport.redoList.pop();
1526 viewport.historyList.push(command);
1527 command.doCommand(getViewAlignments());
1529 AlignViewport originalSource = getOriginatingSource(command);
1530 updateEditMenuBar();
1532 if (originalSource != null)
1535 if (originalSource != viewport)
1538 .warn("Implementation worry: mismatch of viewport origin for redo");
1540 originalSource.updateHiddenColumns();
1541 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1543 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1544 // viewport.getColumnSelection()
1545 // .getHiddenColumns().size() > 0);
1546 originalSource.firePropertyChange("alignment", null, originalSource
1547 .getAlignment().getSequences());
1551 AlignViewport getOriginatingSource(CommandI command)
1553 AlignViewport originalSource = null;
1554 // For sequence removal and addition, we need to fire
1555 // the property change event FROM the viewport where the
1556 // original alignment was altered
1557 AlignmentI al = null;
1558 if (command instanceof EditCommand)
1560 EditCommand editCommand = (EditCommand) command;
1561 al = editCommand.getAlignment();
1562 Vector comps = (Vector) PaintRefresher.components.get(viewport
1563 .getSequenceSetId());
1565 for (int i = 0; i < comps.size(); i++)
1567 if (comps.elementAt(i) instanceof AlignmentPanel)
1569 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1571 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1578 if (originalSource == null)
1580 // The original view is closed, we must validate
1581 // the current view against the closed view first
1584 PaintRefresher.validateSequences(al, viewport.getAlignment());
1587 originalSource = viewport;
1590 return originalSource;
1599 public void moveSelectedSequences(boolean up)
1601 SequenceGroup sg = viewport.getSelectionGroup();
1607 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1608 viewport.getHiddenRepSequences(), up);
1609 alignPanel.paintAlignment(true);
1612 synchronized void slideSequences(boolean right, int size)
1614 List<SequenceI> sg = new Vector();
1615 if (viewport.cursorMode)
1617 sg.add(viewport.getAlignment().getSequenceAt(
1618 alignPanel.seqPanel.seqCanvas.cursorY));
1620 else if (viewport.getSelectionGroup() != null
1621 && viewport.getSelectionGroup().getSize() != viewport
1622 .getAlignment().getHeight())
1624 sg = viewport.getSelectionGroup().getSequences(
1625 viewport.getHiddenRepSequences());
1633 Vector invertGroup = new Vector();
1635 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1637 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1639 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1643 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1645 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1646 for (int i = 0; i < invertGroup.size(); i++)
1648 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1651 SlideSequencesCommand ssc;
1654 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1655 size, viewport.getGapCharacter());
1659 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1660 size, viewport.getGapCharacter());
1663 int groupAdjustment = 0;
1664 if (ssc.getGapsInsertedBegin() && right)
1666 if (viewport.cursorMode)
1668 alignPanel.seqPanel.moveCursor(size, 0);
1672 groupAdjustment = size;
1675 else if (!ssc.getGapsInsertedBegin() && !right)
1677 if (viewport.cursorMode)
1679 alignPanel.seqPanel.moveCursor(-size, 0);
1683 groupAdjustment = -size;
1687 if (groupAdjustment != 0)
1689 viewport.getSelectionGroup().setStartRes(
1690 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1691 viewport.getSelectionGroup().setEndRes(
1692 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1695 boolean appendHistoryItem = false;
1696 if (viewport.historyList != null && viewport.historyList.size() > 0
1697 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1699 appendHistoryItem = ssc
1700 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1704 if (!appendHistoryItem)
1706 addHistoryItem(ssc);
1719 protected void copy_actionPerformed(ActionEvent e)
1722 if (viewport.getSelectionGroup() == null)
1726 // TODO: preserve the ordering of displayed alignment annotation in any
1727 // internal paste (particularly sequence associated annotation)
1728 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1729 String[] omitHidden = null;
1731 if (viewport.hasHiddenColumns())
1733 omitHidden = viewport.getViewAsString(true);
1736 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1739 StringSelection ss = new StringSelection(output);
1743 jalview.gui.Desktop.internalCopy = true;
1744 // Its really worth setting the clipboard contents
1745 // to empty before setting the large StringSelection!!
1746 Toolkit.getDefaultToolkit().getSystemClipboard()
1747 .setContents(new StringSelection(""), null);
1749 Toolkit.getDefaultToolkit().getSystemClipboard()
1750 .setContents(ss, Desktop.instance);
1751 } catch (OutOfMemoryError er)
1753 new OOMWarning("copying region", er);
1757 Vector hiddenColumns = null;
1758 if (viewport.hasHiddenColumns())
1760 hiddenColumns = new Vector();
1761 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1762 .getSelectionGroup().getEndRes();
1763 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1766 int[] region = (int[]) viewport.getColumnSelection()
1767 .getHiddenColumns().elementAt(i);
1768 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1770 hiddenColumns.addElement(new int[]
1771 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1776 Desktop.jalviewClipboard = new Object[]
1777 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1778 statusBar.setText(MessageManager.formatMessage(
1779 "label.copied_sequences_to_clipboard", new String[]
1780 { Integer.valueOf(seqs.length).toString() }));
1790 protected void pasteNew_actionPerformed(ActionEvent e)
1802 protected void pasteThis_actionPerformed(ActionEvent e)
1808 * Paste contents of Jalview clipboard
1810 * @param newAlignment
1811 * true to paste to a new alignment, otherwise add to this.
1813 void paste(boolean newAlignment)
1815 boolean externalPaste = true;
1818 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1819 Transferable contents = c.getContents(this);
1821 if (contents == null)
1829 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1830 if (str.length() < 1)
1835 format = new IdentifyFile().Identify(str, "Paste");
1837 } catch (OutOfMemoryError er)
1839 new OOMWarning("Out of memory pasting sequences!!", er);
1843 SequenceI[] sequences;
1844 boolean annotationAdded = false;
1845 AlignmentI alignment = null;
1847 if (Desktop.jalviewClipboard != null)
1849 // The clipboard was filled from within Jalview, we must use the
1851 // And dataset from the copied alignment
1852 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1853 // be doubly sure that we create *new* sequence objects.
1854 sequences = new SequenceI[newseq.length];
1855 for (int i = 0; i < newseq.length; i++)
1857 sequences[i] = new Sequence(newseq[i]);
1859 alignment = new Alignment(sequences);
1860 externalPaste = false;
1864 // parse the clipboard as an alignment.
1865 alignment = new FormatAdapter().readFile(str, "Paste", format);
1866 sequences = alignment.getSequencesArray();
1870 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1876 if (Desktop.jalviewClipboard != null)
1878 // dataset is inherited
1879 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1883 // new dataset is constructed
1884 alignment.setDataset(null);
1886 alwidth = alignment.getWidth() + 1;
1890 AlignmentI pastedal = alignment; // preserve pasted alignment object
1891 // Add pasted sequences and dataset into existing alignment.
1892 alignment = viewport.getAlignment();
1893 alwidth = alignment.getWidth() + 1;
1894 // decide if we need to import sequences from an existing dataset
1895 boolean importDs = Desktop.jalviewClipboard != null
1896 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1897 // importDs==true instructs us to copy over new dataset sequences from
1898 // an existing alignment
1899 Vector newDs = (importDs) ? new Vector() : null; // used to create
1900 // minimum dataset set
1902 for (int i = 0; i < sequences.length; i++)
1906 newDs.addElement(null);
1908 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1910 if (importDs && ds != null)
1912 if (!newDs.contains(ds))
1914 newDs.setElementAt(ds, i);
1915 ds = new Sequence(ds);
1916 // update with new dataset sequence
1917 sequences[i].setDatasetSequence(ds);
1921 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1926 // copy and derive new dataset sequence
1927 sequences[i] = sequences[i].deriveSequence();
1928 alignment.getDataset().addSequence(
1929 sequences[i].getDatasetSequence());
1930 // TODO: avoid creation of duplicate dataset sequences with a
1931 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1933 alignment.addSequence(sequences[i]); // merges dataset
1937 newDs.clear(); // tidy up
1939 if (alignment.getAlignmentAnnotation() != null)
1941 for (AlignmentAnnotation alan : alignment
1942 .getAlignmentAnnotation())
1944 if (alan.graphGroup > fgroup)
1946 fgroup = alan.graphGroup;
1950 if (pastedal.getAlignmentAnnotation() != null)
1952 // Add any annotation attached to alignment.
1953 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1954 for (int i = 0; i < alann.length; i++)
1956 annotationAdded = true;
1957 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1959 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1960 if (newann.graphGroup > -1)
1962 if (newGraphGroups.size() <= newann.graphGroup
1963 || newGraphGroups.get(newann.graphGroup) == null)
1965 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1967 newGraphGroups.add(q, null);
1969 newGraphGroups.set(newann.graphGroup, new Integer(
1972 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1976 newann.padAnnotation(alwidth);
1977 alignment.addAnnotation(newann);
1987 addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
1988 sequences, 0, alignment.getWidth(), alignment));
1990 // Add any annotations attached to sequences
1991 for (int i = 0; i < sequences.length; i++)
1993 if (sequences[i].getAnnotation() != null)
1995 AlignmentAnnotation newann;
1996 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1998 annotationAdded = true;
1999 newann = sequences[i].getAnnotation()[a];
2000 newann.adjustForAlignment();
2001 newann.padAnnotation(alwidth);
2002 if (newann.graphGroup > -1)
2004 if (newann.graphGroup > -1)
2006 if (newGraphGroups.size() <= newann.graphGroup
2007 || newGraphGroups.get(newann.graphGroup) == null)
2009 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2011 newGraphGroups.add(q, null);
2013 newGraphGroups.set(newann.graphGroup, new Integer(
2016 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2020 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2025 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2032 // propagate alignment changed.
2033 viewport.setEndSeq(alignment.getHeight());
2034 if (annotationAdded)
2036 // Duplicate sequence annotation in all views.
2037 AlignmentI[] alview = this.getViewAlignments();
2038 for (int i = 0; i < sequences.length; i++)
2040 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2045 for (int avnum = 0; avnum < alview.length; avnum++)
2047 if (alview[avnum] != alignment)
2049 // duplicate in a view other than the one with input focus
2050 int avwidth = alview[avnum].getWidth() + 1;
2051 // this relies on sann being preserved after we
2052 // modify the sequence's annotation array for each duplication
2053 for (int a = 0; a < sann.length; a++)
2055 AlignmentAnnotation newann = new AlignmentAnnotation(
2057 sequences[i].addAlignmentAnnotation(newann);
2058 newann.padAnnotation(avwidth);
2059 alview[avnum].addAnnotation(newann); // annotation was
2060 // duplicated earlier
2061 // TODO JAL-1145 graphGroups are not updated for sequence
2062 // annotation added to several views. This may cause
2064 alview[avnum].setAnnotationIndex(newann, a);
2069 buildSortByAnnotationScoresMenu();
2071 viewport.firePropertyChange("alignment", null,
2072 alignment.getSequences());
2073 if (alignPanels != null)
2075 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2077 ap.validateAnnotationDimensions(false);
2082 alignPanel.validateAnnotationDimensions(false);
2088 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2090 String newtitle = new String("Copied sequences");
2092 if (Desktop.jalviewClipboard != null
2093 && Desktop.jalviewClipboard[2] != null)
2095 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2096 for (int i = 0; i < hc.size(); i++)
2098 int[] region = (int[]) hc.elementAt(i);
2099 af.viewport.hideColumns(region[0], region[1]);
2103 // >>>This is a fix for the moment, until a better solution is
2105 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2107 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2109 // TODO: maintain provenance of an alignment, rather than just make the
2110 // title a concatenation of operations.
2113 if (title.startsWith("Copied sequences"))
2119 newtitle = newtitle.concat("- from " + title);
2124 newtitle = new String("Pasted sequences");
2127 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2132 } catch (Exception ex)
2134 ex.printStackTrace();
2135 System.out.println("Exception whilst pasting: " + ex);
2136 // could be anything being pasted in here
2142 protected void expand_newalign(ActionEvent e)
2146 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2147 .getAlignment(), -1);
2148 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2150 String newtitle = new String("Flanking alignment");
2152 if (Desktop.jalviewClipboard != null
2153 && Desktop.jalviewClipboard[2] != null)
2155 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2156 for (int i = 0; i < hc.size(); i++)
2158 int[] region = (int[]) hc.elementAt(i);
2159 af.viewport.hideColumns(region[0], region[1]);
2163 // >>>This is a fix for the moment, until a better solution is
2165 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2167 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2169 // TODO: maintain provenance of an alignment, rather than just make the
2170 // title a concatenation of operations.
2172 if (title.startsWith("Copied sequences"))
2178 newtitle = newtitle.concat("- from " + title);
2182 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2184 } catch (Exception ex)
2186 ex.printStackTrace();
2187 System.out.println("Exception whilst pasting: " + ex);
2188 // could be anything being pasted in here
2189 } catch (OutOfMemoryError oom)
2191 new OOMWarning("Viewing flanking region of alignment", oom);
2202 protected void cut_actionPerformed(ActionEvent e)
2204 copy_actionPerformed(null);
2205 delete_actionPerformed(null);
2215 protected void delete_actionPerformed(ActionEvent evt)
2218 SequenceGroup sg = viewport.getSelectionGroup();
2224 List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
2226 for (int i = 0; i < sg.getSize(); i++)
2228 seq = sg.getSequenceAt(i);
2232 // If the cut affects all sequences, warn, remove highlighted columns
2233 if (sg.getSize() == viewport.getAlignment().getHeight())
2235 int confirm = JOptionPane.showConfirmDialog(this,
2236 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2237 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2238 JOptionPane.OK_CANCEL_OPTION);
2240 if (confirm == JOptionPane.CANCEL_OPTION
2241 || confirm == JOptionPane.CLOSED_OPTION)
2245 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2246 sg.getEndRes() + 1);
2249 SequenceI[] cut = new SequenceI[seqs.size()];
2250 for (int i = 0; i < seqs.size(); i++)
2252 cut[i] = seqs.get(i);
2256 * //ADD HISTORY ITEM
2258 addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
2259 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2260 viewport.getAlignment()));
2262 viewport.setSelectionGroup(null);
2263 viewport.sendSelection();
2264 viewport.getAlignment().deleteGroup(sg);
2266 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2268 if (viewport.getAlignment().getHeight() < 1)
2272 this.setClosed(true);
2273 } catch (Exception ex)
2286 protected void deleteGroups_actionPerformed(ActionEvent e)
2288 if (avc.deleteGroups())
2290 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2291 alignPanel.updateAnnotation();
2292 alignPanel.paintAlignment(true);
2303 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2305 SequenceGroup sg = new SequenceGroup();
2307 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2309 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2312 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2313 viewport.setSelectionGroup(sg);
2314 viewport.sendSelection();
2315 alignPanel.paintAlignment(true);
2316 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2326 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2328 if (viewport.cursorMode)
2330 alignPanel.seqPanel.keyboardNo1 = null;
2331 alignPanel.seqPanel.keyboardNo2 = null;
2333 viewport.setSelectionGroup(null);
2334 viewport.getColumnSelection().clear();
2335 viewport.setSelectionGroup(null);
2336 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2337 alignPanel.idPanel.idCanvas.searchResults = null;
2338 alignPanel.paintAlignment(true);
2339 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2340 viewport.sendSelection();
2350 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2352 SequenceGroup sg = viewport.getSelectionGroup();
2356 selectAllSequenceMenuItem_actionPerformed(null);
2361 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2363 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2366 alignPanel.paintAlignment(true);
2367 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2368 viewport.sendSelection();
2372 public void invertColSel_actionPerformed(ActionEvent e)
2374 viewport.invertColumnSelection();
2375 alignPanel.paintAlignment(true);
2376 viewport.sendSelection();
2386 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2388 trimAlignment(true);
2398 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2400 trimAlignment(false);
2403 void trimAlignment(boolean trimLeft)
2405 ColumnSelection colSel = viewport.getColumnSelection();
2408 if (colSel.size() > 0)
2412 column = colSel.getMin();
2416 column = colSel.getMax();
2420 if (viewport.getSelectionGroup() != null)
2422 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2423 viewport.getHiddenRepSequences());
2427 seqs = viewport.getAlignment().getSequencesArray();
2430 TrimRegionCommand trimRegion;
2433 trimRegion = new TrimRegionCommand("Remove Left",
2434 TrimRegionCommand.TRIM_LEFT, seqs, column,
2435 viewport.getAlignment(), viewport.getColumnSelection(),
2436 viewport.getSelectionGroup());
2437 viewport.setStartRes(0);
2441 trimRegion = new TrimRegionCommand("Remove Right",
2442 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2443 viewport.getAlignment(), viewport.getColumnSelection(),
2444 viewport.getSelectionGroup());
2447 statusBar.setText(MessageManager.formatMessage(
2448 "label.removed_columns", new String[]
2449 { Integer.valueOf(trimRegion.getSize()).toString() }));
2451 addHistoryItem(trimRegion);
2453 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2455 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2456 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2458 viewport.getAlignment().deleteGroup(sg);
2462 viewport.firePropertyChange("alignment", null, viewport
2463 .getAlignment().getSequences());
2474 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2476 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2479 if (viewport.getSelectionGroup() != null)
2481 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2482 viewport.getHiddenRepSequences());
2483 start = viewport.getSelectionGroup().getStartRes();
2484 end = viewport.getSelectionGroup().getEndRes();
2488 seqs = viewport.getAlignment().getSequencesArray();
2491 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2492 "Remove Gapped Columns", seqs, start, end,
2493 viewport.getAlignment());
2495 addHistoryItem(removeGapCols);
2497 statusBar.setText(MessageManager.formatMessage(
2498 "label.removed_empty_columns", new String[]
2499 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2501 // This is to maintain viewport position on first residue
2502 // of first sequence
2503 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2504 int startRes = seq.findPosition(viewport.startRes);
2505 // ShiftList shifts;
2506 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2507 // edit.alColumnChanges=shifts.getInverse();
2508 // if (viewport.hasHiddenColumns)
2509 // viewport.getColumnSelection().compensateForEdits(shifts);
2510 viewport.setStartRes(seq.findIndex(startRes) - 1);
2511 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2523 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2525 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2528 if (viewport.getSelectionGroup() != null)
2530 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2531 viewport.getHiddenRepSequences());
2532 start = viewport.getSelectionGroup().getStartRes();
2533 end = viewport.getSelectionGroup().getEndRes();
2537 seqs = viewport.getAlignment().getSequencesArray();
2540 // This is to maintain viewport position on first residue
2541 // of first sequence
2542 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2543 int startRes = seq.findPosition(viewport.startRes);
2545 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2546 viewport.getAlignment()));
2548 viewport.setStartRes(seq.findIndex(startRes) - 1);
2550 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2562 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2564 viewport.setPadGaps(padGapsMenuitem.isSelected());
2565 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2571 // if (justifySeqs>0)
2573 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2586 public void findMenuItem_actionPerformed(ActionEvent e)
2592 public void newView_actionPerformed(ActionEvent e)
2599 * @param copyAnnotation
2600 * if true then duplicate all annnotation, groups and settings
2601 * @return new alignment panel, already displayed.
2603 public AlignmentPanel newView(boolean copyAnnotation)
2605 return newView(null, copyAnnotation);
2611 * title of newly created view
2612 * @return new alignment panel, already displayed.
2614 public AlignmentPanel newView(String viewTitle)
2616 return newView(viewTitle, true);
2622 * title of newly created view
2623 * @param copyAnnotation
2624 * if true then duplicate all annnotation, groups and settings
2625 * @return new alignment panel, already displayed.
2627 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2629 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2631 if (!copyAnnotation)
2633 // just remove all the current annotation except for the automatic stuff
2634 newap.av.getAlignment().deleteAllGroups();
2635 for (AlignmentAnnotation alan : newap.av.getAlignment()
2636 .getAlignmentAnnotation())
2638 if (!alan.autoCalculated)
2640 newap.av.getAlignment().deleteAnnotation(alan);
2646 newap.av.gatherViewsHere = false;
2648 if (viewport.viewName == null)
2650 viewport.viewName = "Original";
2653 newap.av.historyList = viewport.historyList;
2654 newap.av.redoList = viewport.redoList;
2656 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2657 // make sure the new view has a unique name - this is essential for Jalview
2659 boolean addFirstIndex = false;
2660 if (viewTitle == null || viewTitle.trim().length() == 0)
2662 viewTitle = MessageManager.getString("action.view");
2663 addFirstIndex = true;
2667 index = 1;// we count from 1 if given a specific name
2669 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2670 Vector comps = (Vector) PaintRefresher.components.get(viewport
2671 .getSequenceSetId());
2672 Vector existingNames = new Vector();
2673 for (int i = 0; i < comps.size(); i++)
2675 if (comps.elementAt(i) instanceof AlignmentPanel)
2677 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2678 if (!existingNames.contains(ap.av.viewName))
2680 existingNames.addElement(ap.av.viewName);
2685 while (existingNames.contains(newViewName))
2687 newViewName = viewTitle + " " + (++index);
2690 newap.av.viewName = newViewName;
2692 addAlignmentPanel(newap, true);
2693 newap.alignmentChanged();
2695 if (alignPanels.size() == 2)
2697 viewport.gatherViewsHere = true;
2699 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2704 public void expandViews_actionPerformed(ActionEvent e)
2706 Desktop.instance.explodeViews(this);
2710 public void gatherViews_actionPerformed(ActionEvent e)
2712 Desktop.instance.gatherViews(this);
2722 public void font_actionPerformed(ActionEvent e)
2724 new FontChooser(alignPanel);
2734 protected void seqLimit_actionPerformed(ActionEvent e)
2736 viewport.setShowJVSuffix(seqLimits.isSelected());
2738 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2739 .calculateIdWidth());
2740 alignPanel.paintAlignment(true);
2744 public void idRightAlign_actionPerformed(ActionEvent e)
2746 viewport.rightAlignIds = idRightAlign.isSelected();
2747 alignPanel.paintAlignment(true);
2751 public void centreColumnLabels_actionPerformed(ActionEvent e)
2753 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2754 alignPanel.paintAlignment(true);
2760 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2763 protected void followHighlight_actionPerformed()
2765 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2767 alignPanel.scrollToPosition(
2768 alignPanel.seqPanel.seqCanvas.searchResults, false);
2779 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2781 viewport.setColourText(colourTextMenuItem.isSelected());
2782 alignPanel.paintAlignment(true);
2792 public void wrapMenuItem_actionPerformed(ActionEvent e)
2794 scaleAbove.setVisible(wrapMenuItem.isSelected());
2795 scaleLeft.setVisible(wrapMenuItem.isSelected());
2796 scaleRight.setVisible(wrapMenuItem.isSelected());
2797 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2798 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2802 public void showAllSeqs_actionPerformed(ActionEvent e)
2804 viewport.showAllHiddenSeqs();
2808 public void showAllColumns_actionPerformed(ActionEvent e)
2810 viewport.showAllHiddenColumns();
2815 public void hideSelSequences_actionPerformed(ActionEvent e)
2817 viewport.hideAllSelectedSeqs();
2818 alignPanel.paintAlignment(true);
2822 * called by key handler and the hide all/show all menu items
2827 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2830 boolean hide = false;
2831 SequenceGroup sg = viewport.getSelectionGroup();
2832 if (!toggleSeqs && !toggleCols)
2834 // Hide everything by the current selection - this is a hack - we do the
2835 // invert and then hide
2836 // first check that there will be visible columns after the invert.
2837 if ((viewport.getColumnSelection() != null
2838 && viewport.getColumnSelection().getSelected() != null && viewport
2839 .getColumnSelection().getSelected().size() > 0)
2840 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2843 // now invert the sequence set, if required - empty selection implies
2844 // that no hiding is required.
2847 invertSequenceMenuItem_actionPerformed(null);
2848 sg = viewport.getSelectionGroup();
2852 viewport.expandColSelection(sg, true);
2853 // finally invert the column selection and get the new sequence
2855 invertColSel_actionPerformed(null);
2862 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2864 hideSelSequences_actionPerformed(null);
2867 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2870 showAllSeqs_actionPerformed(null);
2876 if (viewport.getColumnSelection().getSelected().size() > 0)
2878 hideSelColumns_actionPerformed(null);
2881 viewport.setSelectionGroup(sg);
2886 showAllColumns_actionPerformed(null);
2895 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2896 * event.ActionEvent)
2899 public void hideAllButSelection_actionPerformed(ActionEvent e)
2901 toggleHiddenRegions(false, false);
2908 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2912 public void hideAllSelection_actionPerformed(ActionEvent e)
2914 SequenceGroup sg = viewport.getSelectionGroup();
2915 viewport.expandColSelection(sg, false);
2916 viewport.hideAllSelectedSeqs();
2917 viewport.hideSelectedColumns();
2918 alignPanel.paintAlignment(true);
2925 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2929 public void showAllhidden_actionPerformed(ActionEvent e)
2931 viewport.showAllHiddenColumns();
2932 viewport.showAllHiddenSeqs();
2933 alignPanel.paintAlignment(true);
2937 public void hideSelColumns_actionPerformed(ActionEvent e)
2939 viewport.hideSelectedColumns();
2940 alignPanel.paintAlignment(true);
2944 public void hiddenMarkers_actionPerformed(ActionEvent e)
2946 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2957 protected void scaleAbove_actionPerformed(ActionEvent e)
2959 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2960 alignPanel.paintAlignment(true);
2970 protected void scaleLeft_actionPerformed(ActionEvent e)
2972 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2973 alignPanel.paintAlignment(true);
2983 protected void scaleRight_actionPerformed(ActionEvent e)
2985 viewport.setScaleRightWrapped(scaleRight.isSelected());
2986 alignPanel.paintAlignment(true);
2996 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2998 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2999 alignPanel.paintAlignment(true);
3009 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3011 viewport.setShowText(viewTextMenuItem.isSelected());
3012 alignPanel.paintAlignment(true);
3022 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3024 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3025 alignPanel.paintAlignment(true);
3028 public FeatureSettings featureSettings;
3031 public void featureSettings_actionPerformed(ActionEvent e)
3033 if (featureSettings != null)
3035 featureSettings.close();
3036 featureSettings = null;
3038 if (!showSeqFeatures.isSelected())
3040 // make sure features are actually displayed
3041 showSeqFeatures.setSelected(true);
3042 showSeqFeatures_actionPerformed(null);
3044 featureSettings = new FeatureSettings(this);
3048 * Set or clear 'Show Sequence Features'
3054 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3056 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3057 alignPanel.paintAlignment(true);
3058 if (alignPanel.getOverviewPanel() != null)
3060 alignPanel.getOverviewPanel().updateOverviewImage();
3065 * Set or clear 'Show Sequence Features'
3071 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3073 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3075 if (viewport.getShowSequenceFeaturesHeight())
3077 // ensure we're actually displaying features
3078 viewport.setShowSequenceFeatures(true);
3079 showSeqFeatures.setSelected(true);
3081 alignPanel.paintAlignment(true);
3082 if (alignPanel.getOverviewPanel() != null)
3084 alignPanel.getOverviewPanel().updateOverviewImage();
3089 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3090 * the annotations panel as a whole.
3092 * The options to show/hide all annotations should be enabled when the panel
3093 * is shown, and disabled when the panel is hidden.
3098 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3100 final boolean setVisible = annotationPanelMenuItem.isSelected();
3101 viewport.setShowAnnotation(setVisible);
3102 alignPanel.setAnnotationVisible(setVisible);
3103 this.showAllAnnotations.setEnabled(setVisible);
3104 this.hideAllAnnotations.setEnabled(setVisible);
3108 public void alignmentProperties()
3110 JEditorPane editPane = new JEditorPane("text/html", "");
3111 editPane.setEditable(false);
3112 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3114 editPane.setText(MessageManager.formatMessage("label.html_content",
3116 { contents.toString() }));
3117 JInternalFrame frame = new JInternalFrame();
3118 frame.getContentPane().add(new JScrollPane(editPane));
3120 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3121 "label.alignment_properties", new String[]
3122 { getTitle() }), 500, 400);
3132 public void overviewMenuItem_actionPerformed(ActionEvent e)
3134 if (alignPanel.overviewPanel != null)
3139 JInternalFrame frame = new JInternalFrame();
3140 OverviewPanel overview = new OverviewPanel(alignPanel);
3141 frame.setContentPane(overview);
3142 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3143 "label.overview_params", new String[]
3144 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3146 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3147 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3150 public void internalFrameClosed(
3151 javax.swing.event.InternalFrameEvent evt)
3153 alignPanel.setOverviewPanel(null);
3157 alignPanel.setOverviewPanel(overview);
3161 public void textColour_actionPerformed(ActionEvent e)
3163 new TextColourChooser().chooseColour(alignPanel, null);
3173 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3185 public void clustalColour_actionPerformed(ActionEvent e)
3187 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3188 viewport.getHiddenRepSequences()));
3198 public void zappoColour_actionPerformed(ActionEvent e)
3200 changeColour(new ZappoColourScheme());
3210 public void taylorColour_actionPerformed(ActionEvent e)
3212 changeColour(new TaylorColourScheme());
3222 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3224 changeColour(new HydrophobicColourScheme());
3234 public void helixColour_actionPerformed(ActionEvent e)
3236 changeColour(new HelixColourScheme());
3246 public void strandColour_actionPerformed(ActionEvent e)
3248 changeColour(new StrandColourScheme());
3258 public void turnColour_actionPerformed(ActionEvent e)
3260 changeColour(new TurnColourScheme());
3270 public void buriedColour_actionPerformed(ActionEvent e)
3272 changeColour(new BuriedColourScheme());
3282 public void nucleotideColour_actionPerformed(ActionEvent e)
3284 changeColour(new NucleotideColourScheme());
3288 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3290 changeColour(new PurinePyrimidineColourScheme());
3294 * public void covariationColour_actionPerformed(ActionEvent e) {
3296 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3300 public void annotationColour_actionPerformed(ActionEvent e)
3302 new AnnotationColourChooser(viewport, alignPanel);
3306 public void rnahelicesColour_actionPerformed(ActionEvent e)
3308 new RNAHelicesColourChooser(viewport, alignPanel);
3318 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3320 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3329 public void changeColour(ColourSchemeI cs)
3331 // TODO: compare with applet and pull up to model method
3336 if (viewport.getAbovePIDThreshold())
3338 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3340 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3344 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3347 if (viewport.getConservationSelected())
3350 Alignment al = (Alignment) viewport.getAlignment();
3351 Conservation c = new Conservation("All",
3352 ResidueProperties.propHash, 3, al.getSequences(), 0,
3356 c.verdict(false, viewport.getConsPercGaps());
3358 cs.setConservation(c);
3360 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3365 cs.setConservation(null);
3368 cs.setConsensus(viewport.getSequenceConsensusHash());
3371 viewport.setGlobalColourScheme(cs);
3373 if (viewport.getColourAppliesToAllGroups())
3376 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3384 if (cs instanceof ClustalxColourScheme)
3386 sg.cs = new ClustalxColourScheme(sg,
3387 viewport.getHiddenRepSequences());
3389 else if (cs instanceof UserColourScheme)
3391 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3397 sg.cs = cs.getClass().newInstance();
3398 } catch (Exception ex)
3403 if (viewport.getAbovePIDThreshold()
3404 || cs instanceof PIDColourScheme
3405 || cs instanceof Blosum62ColourScheme)
3407 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3409 sg.cs.setConsensus(AAFrequency.calculate(
3410 sg.getSequences(viewport.getHiddenRepSequences()),
3411 sg.getStartRes(), sg.getEndRes() + 1));
3415 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3418 if (viewport.getConservationSelected())
3420 Conservation c = new Conservation("Group",
3421 ResidueProperties.propHash, 3, sg.getSequences(viewport
3422 .getHiddenRepSequences()), sg.getStartRes(),
3423 sg.getEndRes() + 1);
3425 c.verdict(false, viewport.getConsPercGaps());
3426 sg.cs.setConservation(c);
3430 sg.cs.setConservation(null);
3435 if (alignPanel.getOverviewPanel() != null)
3437 alignPanel.getOverviewPanel().updateOverviewImage();
3440 alignPanel.paintAlignment(true);
3450 protected void modifyPID_actionPerformed(ActionEvent e)
3452 if (viewport.getAbovePIDThreshold()
3453 && viewport.getGlobalColourScheme() != null)
3455 SliderPanel.setPIDSliderSource(alignPanel,
3456 viewport.getGlobalColourScheme(), "Background");
3457 SliderPanel.showPIDSlider();
3468 protected void modifyConservation_actionPerformed(ActionEvent e)
3470 if (viewport.getConservationSelected()
3471 && viewport.getGlobalColourScheme() != null)
3473 SliderPanel.setConservationSlider(alignPanel,
3474 viewport.getGlobalColourScheme(), "Background");
3475 SliderPanel.showConservationSlider();
3486 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3488 viewport.setConservationSelected(conservationMenuItem.isSelected());
3490 viewport.setAbovePIDThreshold(false);
3491 abovePIDThreshold.setSelected(false);
3493 changeColour(viewport.getGlobalColourScheme());
3495 modifyConservation_actionPerformed(null);
3505 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3507 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3509 conservationMenuItem.setSelected(false);
3510 viewport.setConservationSelected(false);
3512 changeColour(viewport.getGlobalColourScheme());
3514 modifyPID_actionPerformed(null);
3524 public void userDefinedColour_actionPerformed(ActionEvent e)
3526 if (e.getActionCommand().equals(
3527 MessageManager.getString("action.user_defined")))
3529 new UserDefinedColours(alignPanel, null);
3533 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3534 .getUserColourSchemes().get(e.getActionCommand());
3540 public void updateUserColourMenu()
3543 Component[] menuItems = colourMenu.getMenuComponents();
3544 int i, iSize = menuItems.length;
3545 for (i = 0; i < iSize; i++)
3547 if (menuItems[i].getName() != null
3548 && menuItems[i].getName().equals("USER_DEFINED"))
3550 colourMenu.remove(menuItems[i]);
3554 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3556 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3557 .getUserColourSchemes().keys();
3559 while (userColours.hasMoreElements())
3561 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3562 userColours.nextElement().toString());
3563 radioItem.setName("USER_DEFINED");
3564 radioItem.addMouseListener(new MouseAdapter()
3567 public void mousePressed(MouseEvent evt)
3569 if (evt.isControlDown()
3570 || SwingUtilities.isRightMouseButton(evt))
3572 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3574 int option = JOptionPane.showInternalConfirmDialog(
3575 jalview.gui.Desktop.desktop,
3577 .getString("label.remove_from_default_list"),
3579 .getString("label.remove_user_defined_colour"),
3580 JOptionPane.YES_NO_OPTION);
3581 if (option == JOptionPane.YES_OPTION)
3583 jalview.gui.UserDefinedColours
3584 .removeColourFromDefaults(radioItem.getText());
3585 colourMenu.remove(radioItem);
3589 radioItem.addActionListener(new ActionListener()
3592 public void actionPerformed(ActionEvent evt)
3594 userDefinedColour_actionPerformed(evt);
3601 radioItem.addActionListener(new ActionListener()
3604 public void actionPerformed(ActionEvent evt)
3606 userDefinedColour_actionPerformed(evt);
3610 colourMenu.insert(radioItem, 15);
3611 colours.add(radioItem);
3623 public void PIDColour_actionPerformed(ActionEvent e)
3625 changeColour(new PIDColourScheme());
3635 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3637 changeColour(new Blosum62ColourScheme());
3647 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3649 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3650 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3651 .getAlignment().getSequenceAt(0), null);
3652 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3653 viewport.getAlignment()));
3654 alignPanel.paintAlignment(true);
3664 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3666 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3667 AlignmentSorter.sortByID(viewport.getAlignment());
3668 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3669 viewport.getAlignment()));
3670 alignPanel.paintAlignment(true);
3680 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3682 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3683 AlignmentSorter.sortByLength(viewport.getAlignment());
3684 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3685 viewport.getAlignment()));
3686 alignPanel.paintAlignment(true);
3696 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3698 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3699 AlignmentSorter.sortByGroup(viewport.getAlignment());
3700 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3701 viewport.getAlignment()));
3703 alignPanel.paintAlignment(true);
3713 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3715 new RedundancyPanel(alignPanel, this);
3725 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3727 if ((viewport.getSelectionGroup() == null)
3728 || (viewport.getSelectionGroup().getSize() < 2))
3730 JOptionPane.showInternalMessageDialog(this, MessageManager
3731 .getString("label.you_must_select_least_two_sequences"),
3732 MessageManager.getString("label.invalid_selection"),
3733 JOptionPane.WARNING_MESSAGE);
3737 JInternalFrame frame = new JInternalFrame();
3738 frame.setContentPane(new PairwiseAlignPanel(viewport));
3739 Desktop.addInternalFrame(frame,
3740 MessageManager.getString("action.pairwise_alignment"), 600,
3752 public void PCAMenuItem_actionPerformed(ActionEvent e)
3754 if (((viewport.getSelectionGroup() != null)
3755 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3756 .getSelectionGroup().getSize() > 0))
3757 || (viewport.getAlignment().getHeight() < 4))
3760 .showInternalMessageDialog(
3763 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3765 .getString("label.sequence_selection_insufficient"),
3766 JOptionPane.WARNING_MESSAGE);
3771 new PCAPanel(alignPanel);
3775 public void autoCalculate_actionPerformed(ActionEvent e)
3777 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3778 if (viewport.autoCalculateConsensus)
3780 viewport.firePropertyChange("alignment", null, viewport
3781 .getAlignment().getSequences());
3786 public void sortByTreeOption_actionPerformed(ActionEvent e)
3788 viewport.sortByTree = sortByTree.isSelected();
3792 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3794 viewport.followSelection = listenToViewSelections.isSelected();
3804 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3806 NewTreePanel("AV", "PID", "Average distance tree using PID");
3816 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3818 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3828 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3830 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3840 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3842 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3855 void NewTreePanel(String type, String pwType, String title)
3859 if (viewport.getSelectionGroup() != null
3860 && viewport.getSelectionGroup().getSize() > 0)
3862 if (viewport.getSelectionGroup().getSize() < 3)
3868 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3870 .getString("label.not_enough_sequences"),
3871 JOptionPane.WARNING_MESSAGE);
3875 SequenceGroup sg = viewport.getSelectionGroup();
3877 /* Decide if the selection is a column region */
3878 for (SequenceI _s : sg.getSequences())
3880 if (_s.getLength() < sg.getEndRes())
3886 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3888 .getString("label.sequences_selection_not_aligned"),
3889 JOptionPane.WARNING_MESSAGE);
3895 title = title + " on region";
3896 tp = new TreePanel(alignPanel, type, pwType);
3900 // are the visible sequences aligned?
3901 if (!viewport.getAlignment().isAligned(false))
3907 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3909 .getString("label.sequences_not_aligned"),
3910 JOptionPane.WARNING_MESSAGE);
3915 if (viewport.getAlignment().getHeight() < 2)
3920 tp = new TreePanel(alignPanel, type, pwType);
3925 if (viewport.viewName != null)
3927 title += viewport.viewName + " of ";
3930 title += this.title;
3932 Desktop.addInternalFrame(tp, title, 600, 500);
3943 public void addSortByOrderMenuItem(String title,
3944 final AlignmentOrder order)
3946 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
3948 item.addActionListener(new java.awt.event.ActionListener()
3951 public void actionPerformed(ActionEvent e)
3953 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3955 // TODO: JBPNote - have to map order entries to curent SequenceI
3957 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3959 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3962 alignPanel.paintAlignment(true);
3968 * Add a new sort by annotation score menu item
3971 * the menu to add the option to
3973 * the label used to retrieve scores for each sequence on the
3976 public void addSortByAnnotScoreMenuItem(JMenu sort,
3977 final String scoreLabel)
3979 final JMenuItem item = new JMenuItem(scoreLabel);
3981 item.addActionListener(new java.awt.event.ActionListener()
3984 public void actionPerformed(ActionEvent e)
3986 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3987 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3988 viewport.getAlignment());// ,viewport.getSelectionGroup());
3989 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3990 viewport.getAlignment()));
3991 alignPanel.paintAlignment(true);
3997 * last hash for alignment's annotation array - used to minimise cost of
4000 protected int _annotationScoreVectorHash;
4003 * search the alignment and rebuild the sort by annotation score submenu the
4004 * last alignment annotation vector hash is stored to minimize cost of
4005 * rebuilding in subsequence calls.
4009 public void buildSortByAnnotationScoresMenu()
4011 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4016 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4018 sortByAnnotScore.removeAll();
4019 // almost certainly a quicker way to do this - but we keep it simple
4020 Hashtable scoreSorts = new Hashtable();
4021 AlignmentAnnotation aann[];
4022 for (SequenceI sqa : viewport.getAlignment().getSequences())
4024 aann = sqa.getAnnotation();
4025 for (int i = 0; aann != null && i < aann.length; i++)
4027 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4029 scoreSorts.put(aann[i].label, aann[i].label);
4033 Enumeration labels = scoreSorts.keys();
4034 while (labels.hasMoreElements())
4036 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4037 (String) labels.nextElement());
4039 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4042 _annotationScoreVectorHash = viewport.getAlignment()
4043 .getAlignmentAnnotation().hashCode();
4048 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4049 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4050 * call. Listeners are added to remove the menu item when the treePanel is
4051 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4055 * Displayed tree window.
4057 * SortBy menu item title.
4060 public void buildTreeMenu()
4062 calculateTree.removeAll();
4063 // build the calculate menu
4065 for (final String type : new String[]
4068 String treecalcnm = MessageManager.getString("label.tree_calc_"
4069 + type.toLowerCase());
4070 for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4072 JMenuItem tm = new JMenuItem();
4073 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4074 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4076 String smn = MessageManager.getStringOrReturn(
4077 "label.score_model_", sm.getName());
4078 final String title = MessageManager.formatMessage(
4079 "label.treecalc_title", treecalcnm, smn);
4080 tm.setText(title);//
4081 tm.addActionListener(new java.awt.event.ActionListener()
4084 public void actionPerformed(ActionEvent e)
4086 NewTreePanel(type, (String) pwtype, title);
4089 calculateTree.add(tm);
4094 sortByTreeMenu.removeAll();
4096 Vector comps = (Vector) PaintRefresher.components.get(viewport
4097 .getSequenceSetId());
4098 Vector treePanels = new Vector();
4099 int i, iSize = comps.size();
4100 for (i = 0; i < iSize; i++)
4102 if (comps.elementAt(i) instanceof TreePanel)
4104 treePanels.add(comps.elementAt(i));
4108 iSize = treePanels.size();
4112 sortByTreeMenu.setVisible(false);
4116 sortByTreeMenu.setVisible(true);
4118 for (i = 0; i < treePanels.size(); i++)
4120 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4121 final JMenuItem item = new JMenuItem(tp.getTitle());
4122 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4123 item.addActionListener(new java.awt.event.ActionListener()
4126 public void actionPerformed(ActionEvent e)
4128 tp.sortByTree_actionPerformed(null);
4129 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4134 sortByTreeMenu.add(item);
4138 public boolean sortBy(AlignmentOrder alorder, String undoname)
4140 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4141 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4142 if (undoname != null)
4144 addHistoryItem(new OrderCommand(undoname, oldOrder,
4145 viewport.getAlignment()));
4147 alignPanel.paintAlignment(true);
4152 * Work out whether the whole set of sequences or just the selected set will
4153 * be submitted for multiple alignment.
4156 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4158 // Now, check we have enough sequences
4159 AlignmentView msa = null;
4161 if ((viewport.getSelectionGroup() != null)
4162 && (viewport.getSelectionGroup().getSize() > 1))
4164 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4165 // some common interface!
4167 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4168 * SequenceI[sz = seqs.getSize(false)];
4170 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4171 * seqs.getSequenceAt(i); }
4173 msa = viewport.getAlignmentView(true);
4178 * Vector seqs = viewport.getAlignment().getSequences();
4180 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
4182 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
4183 * seqs.elementAt(i); } }
4185 msa = viewport.getAlignmentView(false);
4191 * Decides what is submitted to a secondary structure prediction service: the
4192 * first sequence in the alignment, or in the current selection, or, if the
4193 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4194 * region or the whole alignment. (where the first sequence in the set is the
4195 * one that the prediction will be for).
4197 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4199 AlignmentView seqs = null;
4201 if ((viewport.getSelectionGroup() != null)
4202 && (viewport.getSelectionGroup().getSize() > 0))
4204 seqs = viewport.getAlignmentView(true);
4208 seqs = viewport.getAlignmentView(false);
4210 // limit sequences - JBPNote in future - could spawn multiple prediction
4212 // TODO: viewport.getAlignment().isAligned is a global state - the local
4213 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4214 if (!viewport.getAlignment().isAligned(false))
4216 seqs.setSequences(new SeqCigar[]
4217 { seqs.getSequences()[0] });
4218 // TODO: if seqs.getSequences().length>1 then should really have warned
4232 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4234 // Pick the tree file
4235 JalviewFileChooser chooser = new JalviewFileChooser(
4236 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4237 chooser.setFileView(new JalviewFileView());
4238 chooser.setDialogTitle(MessageManager
4239 .getString("label.select_newick_like_tree_file"));
4240 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4242 int value = chooser.showOpenDialog(null);
4244 if (value == JalviewFileChooser.APPROVE_OPTION)
4246 String choice = chooser.getSelectedFile().getPath();
4247 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4248 jalview.io.NewickFile fin = null;
4251 fin = new jalview.io.NewickFile(choice, "File");
4252 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4253 } catch (Exception ex)
4260 .getString("label.problem_reading_tree_file"),
4261 JOptionPane.WARNING_MESSAGE);
4262 ex.printStackTrace();
4264 if (fin != null && fin.hasWarningMessage())
4266 JOptionPane.showMessageDialog(Desktop.desktop, fin
4267 .getWarningMessage(), MessageManager
4268 .getString("label.possible_problem_with_tree_file"),
4269 JOptionPane.WARNING_MESSAGE);
4275 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4277 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4280 public TreePanel ShowNewickTree(NewickFile nf, String title)
4282 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4285 public TreePanel ShowNewickTree(NewickFile nf, String title,
4286 AlignmentView input)
4288 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4291 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4292 int h, int x, int y)
4294 return ShowNewickTree(nf, title, null, w, h, x, y);
4298 * Add a treeviewer for the tree extracted from a newick file object to the
4299 * current alignment view
4306 * Associated alignment input data (or null)
4315 * @return TreePanel handle
4317 public TreePanel ShowNewickTree(NewickFile nf, String title,
4318 AlignmentView input, int w, int h, int x, int y)
4320 TreePanel tp = null;
4326 if (nf.getTree() != null)
4328 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4334 tp.setLocation(x, y);
4337 Desktop.addInternalFrame(tp, title, w, h);
4339 } catch (Exception ex)
4341 ex.printStackTrace();
4347 private boolean buildingMenu = false;
4350 * Generates menu items and listener event actions for web service clients
4353 public void BuildWebServiceMenu()
4355 while (buildingMenu)
4359 System.err.println("Waiting for building menu to finish.");
4361 } catch (Exception e)
4366 final AlignFrame me = this;
4367 buildingMenu = true;
4368 new Thread(new Runnable()
4373 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4376 System.err.println("Building ws menu again "
4377 + Thread.currentThread());
4378 // TODO: add support for context dependent disabling of services based
4380 // alignment and current selection
4381 // TODO: add additional serviceHandle parameter to specify abstract
4383 // class independently of AbstractName
4384 // TODO: add in rediscovery GUI function to restart discoverer
4385 // TODO: group services by location as well as function and/or
4387 // object broker mechanism.
4388 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4389 final IProgressIndicator af = me;
4390 final JMenu msawsmenu = new JMenu("Alignment");
4391 final JMenu secstrmenu = new JMenu(
4392 "Secondary Structure Prediction");
4393 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4394 final JMenu analymenu = new JMenu("Analysis");
4395 final JMenu dismenu = new JMenu("Protein Disorder");
4396 // final JMenu msawsmenu = new
4397 // JMenu(MessageManager.getString("label.alignment"));
4398 // final JMenu secstrmenu = new
4399 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4400 // final JMenu seqsrchmenu = new
4401 // JMenu(MessageManager.getString("label.sequence_database_search"));
4402 // final JMenu analymenu = new
4403 // JMenu(MessageManager.getString("label.analysis"));
4404 // final JMenu dismenu = new
4405 // JMenu(MessageManager.getString("label.protein_disorder"));
4406 // JAL-940 - only show secondary structure prediction services from
4407 // the legacy server
4408 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4410 Discoverer.services != null && (Discoverer.services.size() > 0))
4412 // TODO: refactor to allow list of AbstractName/Handler bindings to
4414 // stored or retrieved from elsewhere
4415 // No MSAWS used any more:
4416 // Vector msaws = null; // (Vector)
4417 // Discoverer.services.get("MsaWS");
4418 Vector secstrpr = (Vector) Discoverer.services
4420 if (secstrpr != null)
4422 // Add any secondary structure prediction services
4423 for (int i = 0, j = secstrpr.size(); i < j; i++)
4425 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4427 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4428 .getServiceClient(sh);
4429 int p = secstrmenu.getItemCount();
4430 impl.attachWSMenuEntry(secstrmenu, me);
4431 int q = secstrmenu.getItemCount();
4432 for (int litm = p; litm < q; litm++)
4434 legacyItems.add(secstrmenu.getItem(litm));
4440 // Add all submenus in the order they should appear on the web
4442 wsmenu.add(msawsmenu);
4443 wsmenu.add(secstrmenu);
4444 wsmenu.add(dismenu);
4445 wsmenu.add(analymenu);
4446 // No search services yet
4447 // wsmenu.add(seqsrchmenu);
4449 javax.swing.SwingUtilities.invokeLater(new Runnable()
4456 webService.removeAll();
4457 // first, add discovered services onto the webservices menu
4458 if (wsmenu.size() > 0)
4460 for (int i = 0, j = wsmenu.size(); i < j; i++)
4462 webService.add(wsmenu.get(i));
4467 webService.add(me.webServiceNoServices);
4469 // TODO: move into separate menu builder class.
4470 boolean new_sspred = false;
4471 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4473 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4474 if (jws2servs != null)
4476 if (jws2servs.hasServices())
4478 jws2servs.attachWSMenuEntry(webService, me);
4479 for (Jws2Instance sv : jws2servs.getServices())
4481 if (sv.description.toLowerCase().contains("jpred"))
4483 for (JMenuItem jmi : legacyItems)
4485 jmi.setVisible(false);
4491 if (jws2servs.isRunning())
4493 JMenuItem tm = new JMenuItem(
4494 "Still discovering JABA Services");
4495 tm.setEnabled(false);
4500 build_urlServiceMenu(me.webService);
4501 build_fetchdbmenu(webService);
4502 for (JMenu item : wsmenu)
4504 if (item.getItemCount() == 0)
4506 item.setEnabled(false);
4510 item.setEnabled(true);
4513 } catch (Exception e)
4516 .debug("Exception during web service menu building process.",
4522 } catch (Exception e)
4527 buildingMenu = false;
4534 * construct any groupURL type service menu entries.
4538 private void build_urlServiceMenu(JMenu webService)
4540 // TODO: remove this code when 2.7 is released
4541 // DEBUG - alignmentView
4543 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4544 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4546 * @Override public void actionPerformed(ActionEvent e) {
4547 * jalview.datamodel.AlignmentView
4548 * .testSelectionViews(af.viewport.getAlignment(),
4549 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4551 * }); webService.add(testAlView);
4553 // TODO: refactor to RestClient discoverer and merge menu entries for
4554 // rest-style services with other types of analysis/calculation service
4555 // SHmmr test client - still being implemented.
4556 // DEBUG - alignmentView
4558 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4561 client.attachWSMenuEntry(
4562 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4568 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4569 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4570 * getProperty("LAST_DIRECTORY"));
4572 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4573 * to Vamsas file"); chooser.setToolTipText("Export");
4575 * int value = chooser.showSaveDialog(this);
4577 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4578 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4579 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4580 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4583 * prototype of an automatically enabled/disabled analysis function
4586 protected void setShowProductsEnabled()
4588 SequenceI[] selection = viewport.getSequenceSelection();
4589 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4590 viewport.getAlignment().getDataset()))
4592 showProducts.setEnabled(true);
4597 showProducts.setEnabled(false);
4602 * search selection for sequence xRef products and build the show products
4607 * @return true if showProducts menu should be enabled.
4609 public boolean canShowProducts(SequenceI[] selection,
4610 boolean isRegionSelection, Alignment dataset)
4612 boolean showp = false;
4615 showProducts.removeAll();
4616 final boolean dna = viewport.getAlignment().isNucleotide();
4617 final Alignment ds = dataset;
4618 String[] ptypes = (selection == null || selection.length == 0) ? null
4619 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4621 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4622 // selection, dataset, true);
4623 final SequenceI[] sel = selection;
4624 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4627 final boolean isRegSel = isRegionSelection;
4628 final AlignFrame af = this;
4629 final String source = ptypes[t];
4630 JMenuItem xtype = new JMenuItem(ptypes[t]);
4631 xtype.addActionListener(new ActionListener()
4635 public void actionPerformed(ActionEvent e)
4637 // TODO: new thread for this call with vis-delay
4638 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4639 isRegSel, dna, source);
4643 showProducts.add(xtype);
4645 showProducts.setVisible(showp);
4646 showProducts.setEnabled(showp);
4647 } catch (Exception e)
4649 jalview.bin.Cache.log
4650 .warn("canTranslate threw an exception - please report to help@jalview.org",
4657 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4658 boolean isRegSel, boolean dna, String source)
4660 final boolean fisRegSel = isRegSel;
4661 final boolean fdna = dna;
4662 final String fsrc = source;
4663 final AlignFrame ths = this;
4664 final SequenceI[] fsel = sel;
4665 Runnable foo = new Runnable()
4671 final long sttime = System.currentTimeMillis();
4672 ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
4675 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4679 Alignment prods = CrossRef
4680 .findXrefSequences(fsel, fdna, fsrc, ds);
4683 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4684 for (int s = 0; s < sprods.length; s++)
4686 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4687 if (ds.getSequences() == null
4688 || !ds.getSequences().contains(
4689 sprods[s].getDatasetSequence()))
4691 ds.addSequence(sprods[s].getDatasetSequence());
4693 sprods[s].updatePDBIds();
4695 Alignment al = new Alignment(sprods);
4696 AlignedCodonFrame[] cf = prods.getCodonFrames();
4698 for (int s = 0; cf != null && s < cf.length; s++)
4700 al.addCodonFrame(cf[s]);
4703 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4705 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4706 + " for " + ((fisRegSel) ? "selected region of " : "")
4708 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4713 System.err.println("No Sequences generated for xRef type "
4716 } catch (Exception e)
4718 jalview.bin.Cache.log.error(
4719 "Exception when finding crossreferences", e);
4720 } catch (OutOfMemoryError e)
4722 new OOMWarning("whilst fetching crossreferences", e);
4725 jalview.bin.Cache.log.error("Error when finding crossreferences",
4728 ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
4733 Thread frunner = new Thread(foo);
4737 public boolean canShowTranslationProducts(SequenceI[] selection,
4738 AlignmentI alignment)
4743 return (jalview.analysis.Dna.canTranslate(selection,
4744 viewport.getViewAsVisibleContigs(true)));
4745 } catch (Exception e)
4747 jalview.bin.Cache.log
4748 .warn("canTranslate threw an exception - please report to help@jalview.org",
4755 public void showProducts_actionPerformed(ActionEvent e)
4757 // /////////////////////////////
4758 // Collect Data to be translated/transferred
4760 SequenceI[] selection = viewport.getSequenceSelection();
4761 AlignmentI al = null;
4764 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4765 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4766 viewport.getAlignment().getDataset());
4767 } catch (Exception ex)
4770 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4778 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4779 MessageManager.getString("label.translation_failed"),
4780 JOptionPane.WARNING_MESSAGE);
4784 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4785 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4786 "label.translation_of_params", new String[]
4787 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4792 public void showTranslation_actionPerformed(ActionEvent e)
4794 // /////////////////////////////
4795 // Collect Data to be translated/transferred
4797 SequenceI[] selection = viewport.getSequenceSelection();
4798 String[] seqstring = viewport.getViewAsString(true);
4799 AlignmentI al = null;
4802 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4803 viewport.getViewAsVisibleContigs(true), viewport
4804 .getGapCharacter(), viewport.getAlignment()
4805 .getAlignmentAnnotation(), viewport.getAlignment()
4806 .getWidth(), viewport.getAlignment().getDataset());
4807 } catch (Exception ex)
4810 jalview.bin.Cache.log.error(
4811 "Exception during translation. Please report this !", ex);
4816 .getString("label.error_when_translating_sequences_submit_bug_report"),
4818 .getString("label.implementation_error")
4820 .getString("translation_failed"),
4821 JOptionPane.ERROR_MESSAGE);
4830 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4831 MessageManager.getString("label.translation_failed"),
4832 JOptionPane.WARNING_MESSAGE);
4836 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4837 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4838 "label.translation_of_params", new String[]
4839 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4844 * Try to load a features file onto the alignment.
4847 * contents or path to retrieve file
4849 * access mode of file (see jalview.io.AlignFile)
4850 * @return true if features file was parsed corectly.
4852 public boolean parseFeaturesFile(String file, String type)
4854 boolean featuresFile = false;
4857 featuresFile = new FeaturesFile(file, type).parse(viewport
4858 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4859 .getFeatureRenderer().featureColours, false,
4860 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4861 } catch (Exception ex)
4863 ex.printStackTrace();
4868 viewport.showSequenceFeatures = true;
4869 showSeqFeatures.setSelected(true);
4870 if (alignPanel.seqPanel.seqCanvas.fr != null)
4872 // update the min/max ranges where necessary
4873 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4875 if (featureSettings != null)
4877 featureSettings.setTableData();
4879 alignPanel.paintAlignment(true);
4882 return featuresFile;
4886 public void dragEnter(DropTargetDragEvent evt)
4891 public void dragExit(DropTargetEvent evt)
4896 public void dragOver(DropTargetDragEvent evt)
4901 public void dropActionChanged(DropTargetDragEvent evt)
4906 public void drop(DropTargetDropEvent evt)
4908 Transferable t = evt.getTransferable();
4909 java.util.List files = null;
4913 DataFlavor uriListFlavor = new DataFlavor(
4914 "text/uri-list;class=java.lang.String");
4915 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4917 // Works on Windows and MacOSX
4918 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4919 files = (java.util.List) t
4920 .getTransferData(DataFlavor.javaFileListFlavor);
4922 else if (t.isDataFlavorSupported(uriListFlavor))
4924 // This is used by Unix drag system
4925 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4926 String data = (String) t.getTransferData(uriListFlavor);
4927 files = new java.util.ArrayList(1);
4928 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4929 data, "\r\n"); st.hasMoreTokens();)
4931 String s = st.nextToken();
4932 if (s.startsWith("#"))
4934 // the line is a comment (as per the RFC 2483)
4938 java.net.URI uri = new java.net.URI(s);
4939 // check to see if we can handle this kind of URI
4940 if (uri.getScheme().toLowerCase().startsWith("http"))
4942 files.add(uri.toString());
4946 // otherwise preserve old behaviour: catch all for file objects
4947 java.io.File file = new java.io.File(uri);
4948 files.add(file.toString());
4952 } catch (Exception e)
4954 e.printStackTrace();
4960 // check to see if any of these files have names matching sequences in
4962 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4963 .getAlignment().getSequencesArray());
4965 * Object[] { String,SequenceI}
4967 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4968 ArrayList<String> filesnotmatched = new ArrayList<String>();
4969 for (int i = 0; i < files.size(); i++)
4971 String file = files.get(i).toString();
4973 String protocol = FormatAdapter.checkProtocol(file);
4974 if (protocol == jalview.io.FormatAdapter.FILE)
4976 File fl = new File(file);
4977 pdbfn = fl.getName();
4979 else if (protocol == jalview.io.FormatAdapter.URL)
4981 URL url = new URL(file);
4982 pdbfn = url.getFile();
4984 if (pdbfn.length() > 0)
4986 // attempt to find a match in the alignment
4987 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4988 int l = 0, c = pdbfn.indexOf(".");
4989 while (mtch == null && c != -1)
4994 } while ((c = pdbfn.indexOf(".", l)) > l);
4997 pdbfn = pdbfn.substring(0, l);
4999 mtch = idm.findAllIdMatches(pdbfn);
5006 type = new IdentifyFile().Identify(file, protocol);
5007 } catch (Exception ex)
5013 if (type.equalsIgnoreCase("PDB"))
5015 filesmatched.add(new Object[]
5016 { file, protocol, mtch });
5021 // File wasn't named like one of the sequences or wasn't a PDB file.
5022 filesnotmatched.add(file);
5026 if (filesmatched.size() > 0)
5028 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5034 "label.automatically_associate_pdb_files_with_sequences_same_name",
5041 .getString("label.automatically_associate_pdb_files_by_name"),
5042 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5045 for (Object[] fm : filesmatched)
5047 // try and associate
5048 // TODO: may want to set a standard ID naming formalism for
5049 // associating PDB files which have no IDs.
5050 for (SequenceI toassoc : (SequenceI[]) fm[2])
5052 PDBEntry pe = new AssociatePdbFileWithSeq()
5053 .associatePdbWithSeq((String) fm[0],
5054 (String) fm[1], toassoc, false,
5058 System.err.println("Associated file : "
5059 + ((String) fm[0]) + " with "
5060 + toassoc.getDisplayId(true));
5064 alignPanel.paintAlignment(true);
5068 if (filesnotmatched.size() > 0)
5071 && (Cache.getDefault(
5072 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5075 "<html>"+MessageManager
5077 "label.ignore_unmatched_dropped_files_info",
5082 .toString() })+"</html>",
5084 .getString("label.ignore_unmatched_dropped_files"),
5085 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5089 for (String fn : filesnotmatched)
5091 loadJalviewDataFile(fn, null, null, null);
5095 } catch (Exception ex)
5097 ex.printStackTrace();
5103 * Attempt to load a "dropped" file or URL string: First by testing whether
5104 * it's and Annotation file, then a JNet file, and finally a features file. If
5105 * all are false then the user may have dropped an alignment file onto this
5109 * either a filename or a URL string.
5111 public void loadJalviewDataFile(String file, String protocol,
5112 String format, SequenceI assocSeq)
5116 if (protocol == null)
5118 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5120 // if the file isn't identified, or not positively identified as some
5121 // other filetype (PFAM is default unidentified alignment file type) then
5122 // try to parse as annotation.
5123 boolean isAnnotation = (format == null || format
5124 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5125 .readAnnotationFile(viewport.getAlignment(), file, protocol)
5130 // first see if its a T-COFFEE score file
5131 TCoffeeScoreFile tcf = null;
5134 tcf = new TCoffeeScoreFile(file, protocol);
5137 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5139 tcoffeeColour.setEnabled(true);
5140 tcoffeeColour.setSelected(true);
5141 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5142 isAnnotation = true;
5144 .setText(MessageManager
5145 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5149 // some problem - if no warning its probable that the ID matching
5150 // process didn't work
5154 tcf.getWarningMessage() == null ? MessageManager
5155 .getString("label.check_file_matches_sequence_ids_alignment")
5156 : tcf.getWarningMessage(),
5158 .getString("label.problem_reading_tcoffee_score_file"),
5159 JOptionPane.WARNING_MESSAGE);
5166 } catch (Exception x)
5169 .debug("Exception when processing data source as T-COFFEE score file",
5175 // try to see if its a JNet 'concise' style annotation file *before*
5177 // try to parse it as a features file
5180 format = new IdentifyFile().Identify(file, protocol);
5182 if (format.equalsIgnoreCase("JnetFile"))
5184 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5186 new JnetAnnotationMaker().add_annotation(predictions,
5187 viewport.getAlignment(), 0, false);
5188 isAnnotation = true;
5193 * if (format.equalsIgnoreCase("PDB")) {
5195 * String pdbfn = ""; // try to match up filename with sequence id
5196 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5197 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5198 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5199 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5200 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5201 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5202 * // attempt to find a match in the alignment SequenceI mtch =
5203 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5204 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5205 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5206 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5207 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5208 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5209 * { System.err.println("Associated file : " + file + " with " +
5210 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5211 * TODO: maybe need to load as normal otherwise return; } }
5213 // try to parse it as a features file
5214 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5215 // if it wasn't a features file then we just treat it as a general
5216 // alignment file to load into the current view.
5219 new FileLoader().LoadFile(viewport, file, protocol, format);
5223 alignPanel.paintAlignment(true);
5231 alignPanel.adjustAnnotationHeight();
5232 viewport.updateSequenceIdColours();
5233 buildSortByAnnotationScoresMenu();
5234 alignPanel.paintAlignment(true);
5236 } catch (Exception ex)
5238 ex.printStackTrace();
5239 } catch (OutOfMemoryError oom)
5244 } catch (Exception x)
5250 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5251 : "using " + protocol + " from " + file)
5253 + (format != null ? "(parsing as '" + format
5254 + "' file)" : ""), oom, Desktop.desktop);
5259 public void tabSelectionChanged(int index)
5263 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5264 viewport = alignPanel.av;
5265 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5266 setMenusFromViewport(viewport);
5271 public void tabbedPane_mousePressed(MouseEvent e)
5273 if (SwingUtilities.isRightMouseButton(e))
5275 String reply = JOptionPane.showInternalInputDialog(this,
5276 MessageManager.getString("label.enter_view_name"),
5277 MessageManager.getString("label.enter_view_name"),
5278 JOptionPane.QUESTION_MESSAGE);
5282 viewport.viewName = reply;
5283 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5288 public AlignViewport getCurrentView()
5294 * Open the dialog for regex description parsing.
5297 protected void extractScores_actionPerformed(ActionEvent e)
5299 ParseProperties pp = new jalview.analysis.ParseProperties(
5300 viewport.getAlignment());
5301 // TODO: verify regex and introduce GUI dialog for version 2.5
5302 // if (pp.getScoresFromDescription("col", "score column ",
5303 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5305 if (pp.getScoresFromDescription("description column",
5306 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5308 buildSortByAnnotationScoresMenu();
5316 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5320 protected void showDbRefs_actionPerformed(ActionEvent e)
5322 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5328 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5332 protected void showNpFeats_actionPerformed(ActionEvent e)
5334 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5338 * find the viewport amongst the tabs in this alignment frame and close that
5343 public boolean closeView(AlignViewport av)
5347 this.closeMenuItem_actionPerformed(false);
5350 Component[] comp = tabbedPane.getComponents();
5351 for (int i = 0; comp != null && i < comp.length; i++)
5353 if (comp[i] instanceof AlignmentPanel)
5355 if (((AlignmentPanel) comp[i]).av == av)
5358 closeView((AlignmentPanel) comp[i]);
5366 protected void build_fetchdbmenu(JMenu webService)
5368 // Temporary hack - DBRef Fetcher always top level ws entry.
5369 // TODO We probably want to store a sequence database checklist in
5370 // preferences and have checkboxes.. rather than individual sources selected
5372 final JMenu rfetch = new JMenu(
5373 MessageManager.getString("action.fetch_db_references"));
5374 rfetch.setToolTipText(MessageManager
5375 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5376 webService.add(rfetch);
5378 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5379 MessageManager.getString("option.trim_retrieved_seqs"));
5380 trimrs.setToolTipText(MessageManager
5381 .getString("label.trim_retrieved_sequences"));
5382 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5383 trimrs.addActionListener(new ActionListener()
5386 public void actionPerformed(ActionEvent e)
5388 trimrs.setSelected(trimrs.isSelected());
5389 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5390 Boolean.valueOf(trimrs.isSelected()).toString());
5394 JMenuItem fetchr = new JMenuItem(
5395 MessageManager.getString("label.standard_databases"));
5396 fetchr.setToolTipText(MessageManager
5397 .getString("label.fetch_embl_uniprot"));
5398 fetchr.addActionListener(new ActionListener()
5402 public void actionPerformed(ActionEvent e)
5404 new Thread(new Runnable()
5410 new jalview.ws.DBRefFetcher(alignPanel.av
5411 .getSequenceSelection(), alignPanel.alignFrame)
5412 .fetchDBRefs(false);
5420 final AlignFrame me = this;
5421 new Thread(new Runnable()
5426 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5427 .getSequenceFetcherSingleton(me);
5428 javax.swing.SwingUtilities.invokeLater(new Runnable()
5433 String[] dbclasses = sf.getOrderedSupportedSources();
5434 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5435 // jalview.util.QuickSort.sort(otherdb, otherdb);
5436 List<DbSourceProxy> otherdb;
5437 JMenu dfetch = new JMenu();
5438 JMenu ifetch = new JMenu();
5439 JMenuItem fetchr = null;
5440 int comp = 0, icomp = 0, mcomp = 15;
5441 String mname = null;
5443 for (String dbclass : dbclasses)
5445 otherdb = sf.getSourceProxy(dbclass);
5446 // add a single entry for this class, or submenu allowing 'fetch
5448 if (otherdb == null || otherdb.size() < 1)
5452 // List<DbSourceProxy> dbs=otherdb;
5453 // otherdb=new ArrayList<DbSourceProxy>();
5454 // for (DbSourceProxy db:dbs)
5456 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5460 mname = "From " + dbclass;
5462 if (otherdb.size() == 1)
5464 final DbSourceProxy[] dassource = otherdb
5465 .toArray(new DbSourceProxy[0]);
5466 DbSourceProxy src = otherdb.get(0);
5467 fetchr = new JMenuItem(src.getDbSource());
5468 fetchr.addActionListener(new ActionListener()
5472 public void actionPerformed(ActionEvent e)
5474 new Thread(new Runnable()
5480 new jalview.ws.DBRefFetcher(alignPanel.av
5481 .getSequenceSelection(),
5482 alignPanel.alignFrame, dassource)
5483 .fetchDBRefs(false);
5489 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
5495 final DbSourceProxy[] dassource = otherdb
5496 .toArray(new DbSourceProxy[0]);
5498 DbSourceProxy src = otherdb.get(0);
5499 fetchr = new JMenuItem(MessageManager.formatMessage(
5500 "label.fetch_all_param", new String[]
5501 { src.getDbSource() }));
5502 fetchr.addActionListener(new ActionListener()
5505 public void actionPerformed(ActionEvent e)
5507 new Thread(new Runnable()
5513 new jalview.ws.DBRefFetcher(alignPanel.av
5514 .getSequenceSelection(),
5515 alignPanel.alignFrame, dassource)
5516 .fetchDBRefs(false);
5522 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5525 // and then build the rest of the individual menus
5526 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
5528 String imname = null;
5530 for (DbSourceProxy sproxy : otherdb)
5532 String dbname = sproxy.getDbName();
5533 String sname = dbname.length() > 5 ? dbname.substring(0,
5534 5) + "..." : dbname;
5535 String msname = dbname.length() > 10 ? dbname.substring(
5536 0, 10) + "..." : dbname;
5539 imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
5541 fetchr = new JMenuItem(msname);
5542 final DbSourceProxy[] dassrc =
5544 fetchr.addActionListener(new ActionListener()
5548 public void actionPerformed(ActionEvent e)
5550 new Thread(new Runnable()
5556 new jalview.ws.DBRefFetcher(alignPanel.av
5557 .getSequenceSelection(),
5558 alignPanel.alignFrame, dassrc)
5559 .fetchDBRefs(false);
5565 fetchr.setToolTipText("<html>"
5566 + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
5569 if (++icomp >= mcomp || i == (otherdb.size()))
5571 ifetch.setText(MessageManager.formatMessage(
5572 "label.source_to_target", imname, sname));
5574 ifetch = new JMenu();
5582 if (comp >= mcomp || dbi >= (dbclasses.length))
5584 dfetch.setText(MessageManager.formatMessage(
5585 "label.source_to_target", mname, dbclass));
5587 dfetch = new JMenu();
5600 * Left justify the whole alignment.
5603 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5605 AlignmentI al = viewport.getAlignment();
5607 viewport.firePropertyChange("alignment", null, al);
5611 * Right justify the whole alignment.
5614 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5616 AlignmentI al = viewport.getAlignment();
5618 viewport.firePropertyChange("alignment", null, al);
5621 public void setShowSeqFeatures(boolean b)
5623 showSeqFeatures.setSelected(true);
5624 viewport.setShowSequenceFeatures(true);
5631 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5632 * awt.event.ActionEvent)
5635 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5637 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5638 alignPanel.paintAlignment(true);
5645 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5649 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5651 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5652 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5660 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5661 * .event.ActionEvent)
5664 protected void showGroupConservation_actionPerformed(ActionEvent e)
5666 viewport.setShowGroupConservation(showGroupConservation.getState());
5667 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5674 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5675 * .event.ActionEvent)
5678 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5680 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5681 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5688 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5689 * .event.ActionEvent)
5692 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5694 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5695 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5699 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5701 showSequenceLogo.setState(true);
5702 viewport.setShowSequenceLogo(true);
5703 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5704 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5708 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5710 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5717 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5718 * .event.ActionEvent)
5721 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5723 if (avc.makeGroupsFromSelection())
5725 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5726 alignPanel.updateAnnotation();
5727 alignPanel.paintAlignment(true);
5732 protected void createGroup_actionPerformed(ActionEvent e)
5734 if (avc.createGroup())
5736 alignPanel.alignmentChanged();
5741 protected void unGroup_actionPerformed(ActionEvent e)
5745 alignPanel.alignmentChanged();
5750 * make the given alignmentPanel the currently selected tab
5752 * @param alignmentPanel
5754 public void setDisplayedView(AlignmentPanel alignmentPanel)
5756 if (!viewport.getSequenceSetId().equals(
5757 alignmentPanel.av.getSequenceSetId()))
5759 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5761 if (tabbedPane != null
5762 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5763 .getSelectedIndex())
5765 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5770 * Action on selection of menu option to Show or Hide all annotations.
5775 protected void setAllAnnotationsVisibility(boolean visible)
5777 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5778 .getAlignmentAnnotation())
5780 aa.visible = visible;
5782 this.alignPanel.paintAlignment(true);
5786 class PrintThread extends Thread
5790 public PrintThread(AlignmentPanel ap)
5795 static PageFormat pf;
5800 PrinterJob printJob = PrinterJob.getPrinterJob();
5804 printJob.setPrintable(ap, pf);
5808 printJob.setPrintable(ap);
5811 if (printJob.printDialog())
5816 } catch (Exception PrintException)
5818 PrintException.printStackTrace();