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.AlignmentViewPanel;
34 import jalview.api.analysis.ScoreModelI;
35 import jalview.bin.Cache;
36 import jalview.commands.CommandI;
37 import jalview.commands.EditCommand;
38 import jalview.commands.EditCommand.Action;
39 import jalview.commands.OrderCommand;
40 import jalview.commands.RemoveGapColCommand;
41 import jalview.commands.RemoveGapsCommand;
42 import jalview.commands.SlideSequencesCommand;
43 import jalview.commands.TrimRegionCommand;
44 import jalview.datamodel.AlignedCodonFrame;
45 import jalview.datamodel.Alignment;
46 import jalview.datamodel.AlignmentAnnotation;
47 import jalview.datamodel.AlignmentI;
48 import jalview.datamodel.AlignmentOrder;
49 import jalview.datamodel.AlignmentView;
50 import jalview.datamodel.ColumnSelection;
51 import jalview.datamodel.PDBEntry;
52 import jalview.datamodel.SeqCigar;
53 import jalview.datamodel.Sequence;
54 import jalview.datamodel.SequenceGroup;
55 import jalview.datamodel.SequenceI;
56 import jalview.io.AlignmentProperties;
57 import jalview.io.AnnotationFile;
58 import jalview.io.FeaturesFile;
59 import jalview.io.FileLoader;
60 import jalview.io.FormatAdapter;
61 import jalview.io.HTMLOutput;
62 import jalview.io.IdentifyFile;
63 import jalview.io.JalviewFileChooser;
64 import jalview.io.JalviewFileView;
65 import jalview.io.JnetAnnotationMaker;
66 import jalview.io.NewickFile;
67 import jalview.io.TCoffeeScoreFile;
68 import jalview.jbgui.GAlignFrame;
69 import jalview.schemes.Blosum62ColourScheme;
70 import jalview.schemes.BuriedColourScheme;
71 import jalview.schemes.ClustalxColourScheme;
72 import jalview.schemes.ColourSchemeI;
73 import jalview.schemes.ColourSchemeProperty;
74 import jalview.schemes.HelixColourScheme;
75 import jalview.schemes.HydrophobicColourScheme;
76 import jalview.schemes.NucleotideColourScheme;
77 import jalview.schemes.PIDColourScheme;
78 import jalview.schemes.PurinePyrimidineColourScheme;
79 import jalview.schemes.RNAHelicesColourChooser;
80 import jalview.schemes.ResidueProperties;
81 import jalview.schemes.StrandColourScheme;
82 import jalview.schemes.TCoffeeColourScheme;
83 import jalview.schemes.TaylorColourScheme;
84 import jalview.schemes.TurnColourScheme;
85 import jalview.schemes.UserColourScheme;
86 import jalview.schemes.ZappoColourScheme;
87 import jalview.util.MessageManager;
88 import jalview.ws.jws1.Discoverer;
89 import jalview.ws.jws2.Jws2Discoverer;
90 import jalview.ws.jws2.jabaws2.Jws2Instance;
91 import jalview.ws.seqfetcher.DbSourceProxy;
93 import java.awt.BorderLayout;
94 import java.awt.Component;
95 import java.awt.GridLayout;
96 import java.awt.Rectangle;
97 import java.awt.Toolkit;
98 import java.awt.datatransfer.Clipboard;
99 import java.awt.datatransfer.DataFlavor;
100 import java.awt.datatransfer.StringSelection;
101 import java.awt.datatransfer.Transferable;
102 import java.awt.dnd.DnDConstants;
103 import java.awt.dnd.DropTargetDragEvent;
104 import java.awt.dnd.DropTargetDropEvent;
105 import java.awt.dnd.DropTargetEvent;
106 import java.awt.dnd.DropTargetListener;
107 import java.awt.event.ActionEvent;
108 import java.awt.event.ActionListener;
109 import java.awt.event.KeyAdapter;
110 import java.awt.event.KeyEvent;
111 import java.awt.event.MouseAdapter;
112 import java.awt.event.MouseEvent;
113 import java.awt.print.PageFormat;
114 import java.awt.print.PrinterJob;
115 import java.beans.PropertyChangeEvent;
118 import java.util.ArrayList;
119 import java.util.Arrays;
120 import java.util.Enumeration;
121 import java.util.Hashtable;
122 import java.util.List;
123 import java.util.Vector;
125 import javax.swing.JButton;
126 import javax.swing.JCheckBoxMenuItem;
127 import javax.swing.JEditorPane;
128 import javax.swing.JInternalFrame;
129 import javax.swing.JLabel;
130 import javax.swing.JLayeredPane;
131 import javax.swing.JMenu;
132 import javax.swing.JMenuItem;
133 import javax.swing.JOptionPane;
134 import javax.swing.JPanel;
135 import javax.swing.JProgressBar;
136 import javax.swing.JRadioButtonMenuItem;
137 import javax.swing.JScrollPane;
138 import javax.swing.SwingUtilities;
144 * @version $Revision$
146 public class AlignFrame extends GAlignFrame implements DropTargetListener,
147 IProgressIndicator, AlignViewControllerGuiI
151 public static final int DEFAULT_WIDTH = 700;
154 public static final int DEFAULT_HEIGHT = 500;
156 public AlignmentPanel alignPanel;
158 AlignViewport viewport;
160 public AlignViewControllerI avc;
162 Vector alignPanels = new Vector();
165 * Last format used to load or save alignments in this window
167 String currentFileFormat = null;
170 * Current filename for this alignment
172 String fileName = null;
175 * Creates a new AlignFrame object with specific width and height.
181 public AlignFrame(AlignmentI al, int width, int height)
183 this(al, null, width, height);
187 * Creates a new AlignFrame object with specific width, height and
193 * @param sequenceSetId
195 public AlignFrame(AlignmentI al, int width, int height,
196 String sequenceSetId)
198 this(al, null, width, height, sequenceSetId);
202 * Creates a new AlignFrame object with specific width, height and
208 * @param sequenceSetId
211 public AlignFrame(AlignmentI al, int width, int height,
212 String sequenceSetId, String viewId)
214 this(al, null, width, height, sequenceSetId, viewId);
218 * new alignment window with hidden columns
222 * @param hiddenColumns
223 * ColumnSelection or null
225 * Width of alignment frame
229 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
230 int width, int height)
232 this(al, hiddenColumns, width, height, null);
236 * Create alignment frame for al with hiddenColumns, a specific width and
237 * height, and specific sequenceId
240 * @param hiddenColumns
243 * @param sequenceSetId
246 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
247 int width, int height, String sequenceSetId)
249 this(al, hiddenColumns, width, height, sequenceSetId, null);
253 * Create alignment frame for al with hiddenColumns, a specific width and
254 * height, and specific sequenceId
257 * @param hiddenColumns
260 * @param sequenceSetId
265 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
266 int width, int height, String sequenceSetId, String viewId)
268 setSize(width, height);
270 if (al.getDataset() == null)
275 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
277 alignPanel = new AlignmentPanel(this, viewport);
280 addAlignmentPanel(alignPanel, true);
285 * Make a new AlignFrame from existing alignmentPanels
292 public AlignFrame(AlignmentPanel ap)
296 addAlignmentPanel(ap, false);
301 * initalise the alignframe from the underlying viewport data and the
306 avc = new jalview.controller.AlignViewController(this, viewport,
308 if (viewport.getAlignmentConservationAnnotation() == null)
310 BLOSUM62Colour.setEnabled(false);
311 conservationMenuItem.setEnabled(false);
312 modifyConservation.setEnabled(false);
313 // PIDColour.setEnabled(false);
314 // abovePIDThreshold.setEnabled(false);
315 // modifyPID.setEnabled(false);
318 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
321 if (sortby.equals("Id"))
323 sortIDMenuItem_actionPerformed(null);
325 else if (sortby.equals("Pairwise Identity"))
327 sortPairwiseMenuItem_actionPerformed(null);
330 if (Desktop.desktop != null)
332 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
333 addServiceListeners();
334 setGUINucleotide(viewport.getAlignment().isNucleotide());
337 setMenusFromViewport(viewport);
338 buildSortByAnnotationScoresMenu();
341 if (viewport.wrapAlignment)
343 wrapMenuItem_actionPerformed(null);
346 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
348 this.overviewMenuItem_actionPerformed(null);
356 * Change the filename and format for the alignment, and enable the 'reload'
357 * button functionality.
364 public void setFileName(String file, String format)
367 currentFileFormat = format;
368 reload.setEnabled(true);
371 void addKeyListener()
373 addKeyListener(new KeyAdapter()
376 public void keyPressed(KeyEvent evt)
378 if (viewport.cursorMode
379 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
380 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
381 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
382 && Character.isDigit(evt.getKeyChar()))
384 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
387 switch (evt.getKeyCode())
390 case 27: // escape key
391 deselectAllSequenceMenuItem_actionPerformed(null);
395 case KeyEvent.VK_DOWN:
396 if (evt.isAltDown() || !viewport.cursorMode)
398 moveSelectedSequences(false);
400 if (viewport.cursorMode)
402 alignPanel.seqPanel.moveCursor(0, 1);
407 if (evt.isAltDown() || !viewport.cursorMode)
409 moveSelectedSequences(true);
411 if (viewport.cursorMode)
413 alignPanel.seqPanel.moveCursor(0, -1);
418 case KeyEvent.VK_LEFT:
419 if (evt.isAltDown() || !viewport.cursorMode)
421 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
425 alignPanel.seqPanel.moveCursor(-1, 0);
430 case KeyEvent.VK_RIGHT:
431 if (evt.isAltDown() || !viewport.cursorMode)
433 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
437 alignPanel.seqPanel.moveCursor(1, 0);
441 case KeyEvent.VK_SPACE:
442 if (viewport.cursorMode)
444 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
445 || evt.isShiftDown() || evt.isAltDown());
449 // case KeyEvent.VK_A:
450 // if (viewport.cursorMode)
452 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
453 // //System.out.println("A");
457 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
458 * System.out.println("closing bracket"); } break;
460 case KeyEvent.VK_DELETE:
461 case KeyEvent.VK_BACK_SPACE:
462 if (!viewport.cursorMode)
464 cut_actionPerformed(null);
468 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
469 || evt.isShiftDown() || evt.isAltDown());
475 if (viewport.cursorMode)
477 alignPanel.seqPanel.setCursorRow();
481 if (viewport.cursorMode && !evt.isControlDown())
483 alignPanel.seqPanel.setCursorColumn();
487 if (viewport.cursorMode)
489 alignPanel.seqPanel.setCursorPosition();
493 case KeyEvent.VK_ENTER:
494 case KeyEvent.VK_COMMA:
495 if (viewport.cursorMode)
497 alignPanel.seqPanel.setCursorRowAndColumn();
502 if (viewport.cursorMode)
504 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
508 if (viewport.cursorMode)
510 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
515 viewport.cursorMode = !viewport.cursorMode;
516 statusBar.setText(MessageManager.formatMessage(
517 "label.keyboard_editing_mode", new String[]
518 { (viewport.cursorMode ? "on" : "off") }));
519 if (viewport.cursorMode)
521 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
522 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
524 alignPanel.seqPanel.seqCanvas.repaint();
530 Help.showHelpWindow();
531 } catch (Exception ex)
533 ex.printStackTrace();
538 boolean toggleSeqs = !evt.isControlDown();
539 boolean toggleCols = !evt.isShiftDown();
540 toggleHiddenRegions(toggleSeqs, toggleCols);
543 case KeyEvent.VK_PAGE_UP:
544 if (viewport.wrapAlignment)
546 alignPanel.scrollUp(true);
550 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
551 - viewport.endSeq + viewport.startSeq);
554 case KeyEvent.VK_PAGE_DOWN:
555 if (viewport.wrapAlignment)
557 alignPanel.scrollUp(false);
561 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
562 + viewport.endSeq - viewport.startSeq);
569 public void keyReleased(KeyEvent evt)
571 switch (evt.getKeyCode())
573 case KeyEvent.VK_LEFT:
574 if (evt.isAltDown() || !viewport.cursorMode)
576 viewport.firePropertyChange("alignment", null, viewport
577 .getAlignment().getSequences());
581 case KeyEvent.VK_RIGHT:
582 if (evt.isAltDown() || !viewport.cursorMode)
584 viewport.firePropertyChange("alignment", null, viewport
585 .getAlignment().getSequences());
593 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
595 ap.alignFrame = this;
596 avc = new jalview.controller.AlignViewController(this, viewport,
599 alignPanels.addElement(ap);
601 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
603 int aSize = alignPanels.size();
605 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
607 if (aSize == 1 && ap.av.viewName == null)
609 this.getContentPane().add(ap, BorderLayout.CENTER);
615 setInitialTabVisible();
618 expandViews.setEnabled(true);
619 gatherViews.setEnabled(true);
620 tabbedPane.addTab(ap.av.viewName, ap);
622 ap.setVisible(false);
627 if (ap.av.isPadGaps())
629 ap.av.getAlignment().padGaps();
631 ap.av.updateConservation(ap);
632 ap.av.updateConsensus(ap);
633 ap.av.updateStrucConsensus(ap);
637 public void setInitialTabVisible()
639 expandViews.setEnabled(true);
640 gatherViews.setEnabled(true);
641 tabbedPane.setVisible(true);
642 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
643 tabbedPane.addTab(first.av.viewName, first);
644 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
647 public AlignViewport getViewport()
652 /* Set up intrinsic listeners for dynamically generated GUI bits. */
653 private void addServiceListeners()
655 final java.beans.PropertyChangeListener thisListener;
656 Desktop.instance.addJalviewPropertyChangeListener("services",
657 thisListener = new java.beans.PropertyChangeListener()
660 public void propertyChange(PropertyChangeEvent evt)
662 // // System.out.println("Discoverer property change.");
663 // if (evt.getPropertyName().equals("services"))
665 SwingUtilities.invokeLater(new Runnable()
672 .println("Rebuild WS Menu for service change");
673 BuildWebServiceMenu();
680 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
683 public void internalFrameClosed(
684 javax.swing.event.InternalFrameEvent evt)
686 System.out.println("deregistering discoverer listener");
687 Desktop.instance.removeJalviewPropertyChangeListener("services",
689 closeMenuItem_actionPerformed(true);
692 // Finally, build the menu once to get current service state
693 new Thread(new Runnable()
698 BuildWebServiceMenu();
703 public void setGUINucleotide(boolean nucleotide)
705 showTranslation.setVisible(nucleotide);
706 conservationMenuItem.setEnabled(!nucleotide);
707 modifyConservation.setEnabled(!nucleotide);
708 showGroupConservation.setEnabled(!nucleotide);
709 rnahelicesColour.setEnabled(nucleotide);
710 purinePyrimidineColour.setEnabled(nucleotide);
711 // Remember AlignFrame always starts as protein
715 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
720 * set up menus for the currently viewport. This may be called after any
721 * operation that affects the data in the current view (selection changed,
722 * etc) to update the menus to reflect the new state.
724 public void setMenusForViewport()
726 setMenusFromViewport(viewport);
730 * Need to call this method when tabs are selected for multiple views, or when
731 * loading from Jalview2XML.java
736 void setMenusFromViewport(AlignViewport av)
738 padGapsMenuitem.setSelected(av.isPadGaps());
739 colourTextMenuItem.setSelected(av.showColourText);
740 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
741 conservationMenuItem.setSelected(av.getConservationSelected());
742 seqLimits.setSelected(av.getShowJVSuffix());
743 idRightAlign.setSelected(av.rightAlignIds);
744 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
745 renderGapsMenuItem.setSelected(av.renderGaps);
746 wrapMenuItem.setSelected(av.wrapAlignment);
747 scaleAbove.setVisible(av.wrapAlignment);
748 scaleLeft.setVisible(av.wrapAlignment);
749 scaleRight.setVisible(av.wrapAlignment);
750 annotationPanelMenuItem.setState(av.showAnnotation);
752 * Show/hide annotations only enabled if annotation panel is shown
754 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
755 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
756 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
757 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
758 viewBoxesMenuItem.setSelected(av.showBoxes);
759 viewTextMenuItem.setSelected(av.showText);
760 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
761 showGroupConsensus.setSelected(av.isShowGroupConsensus());
762 showGroupConservation.setSelected(av.isShowGroupConservation());
763 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
764 showSequenceLogo.setSelected(av.isShowSequenceLogo());
765 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
767 setColourSelected(ColourSchemeProperty.getColourName(av
768 .getGlobalColourScheme()));
770 showSeqFeatures.setSelected(av.showSequenceFeatures);
771 hiddenMarkers.setState(av.showHiddenMarkers);
772 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
773 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
774 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
775 autoCalculate.setSelected(av.autoCalculateConsensus);
776 sortByTree.setSelected(av.sortByTree);
777 listenToViewSelections.setSelected(av.followSelection);
778 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
780 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
781 setShowProductsEnabled();
785 // methods for implementing IProgressIndicator
786 // need to refactor to a reusable stub class
787 Hashtable progressBars, progressBarHandlers;
792 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
795 public void setProgressBar(String message, long id)
797 if (progressBars == null)
799 progressBars = new Hashtable();
800 progressBarHandlers = new Hashtable();
803 JPanel progressPanel;
804 Long lId = new Long(id);
805 GridLayout layout = (GridLayout) statusPanel.getLayout();
806 if (progressBars.get(lId) != null)
808 progressPanel = (JPanel) progressBars.get(new Long(id));
809 statusPanel.remove(progressPanel);
810 progressBars.remove(lId);
811 progressPanel = null;
814 statusBar.setText(message);
816 if (progressBarHandlers.contains(lId))
818 progressBarHandlers.remove(lId);
820 layout.setRows(layout.getRows() - 1);
824 progressPanel = new JPanel(new BorderLayout(10, 5));
826 JProgressBar progressBar = new JProgressBar();
827 progressBar.setIndeterminate(true);
829 progressPanel.add(new JLabel(message), BorderLayout.WEST);
830 progressPanel.add(progressBar, BorderLayout.CENTER);
832 layout.setRows(layout.getRows() + 1);
833 statusPanel.add(progressPanel);
835 progressBars.put(lId, progressPanel);
838 // setMenusForViewport();
843 public void registerHandler(final long id,
844 final IProgressIndicatorHandler handler)
846 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
848 throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
850 progressBarHandlers.put(new Long(id), handler);
851 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
852 if (handler.canCancel())
854 JButton cancel = new JButton(
855 MessageManager.getString("action.cancel"));
856 final IProgressIndicator us = this;
857 cancel.addActionListener(new ActionListener()
861 public void actionPerformed(ActionEvent e)
863 handler.cancelActivity(id);
864 us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
867 progressPanel.add(cancel, BorderLayout.EAST);
873 * @return true if any progress bars are still active
876 public boolean operationInProgress()
878 if (progressBars != null && progressBars.size() > 0)
886 public void setStatus(String text)
888 statusBar.setText(text);
892 * Added so Castor Mapping file can obtain Jalview Version
894 public String getVersion()
896 return jalview.bin.Cache.getProperty("VERSION");
899 public FeatureRenderer getFeatureRenderer()
901 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
905 public void fetchSequence_actionPerformed(ActionEvent e)
907 new SequenceFetcher(this);
911 public void addFromFile_actionPerformed(ActionEvent e)
913 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
917 public void reload_actionPerformed(ActionEvent e)
919 if (fileName != null)
921 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
922 // originating file's format
923 // TODO: work out how to recover feature settings for correct view(s) when
925 if (currentFileFormat.equals("Jalview"))
927 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
928 for (int i = 0; i < frames.length; i++)
930 if (frames[i] instanceof AlignFrame && frames[i] != this
931 && ((AlignFrame) frames[i]).fileName != null
932 && ((AlignFrame) frames[i]).fileName.equals(fileName))
936 frames[i].setSelected(true);
937 Desktop.instance.closeAssociatedWindows();
938 } catch (java.beans.PropertyVetoException ex)
944 Desktop.instance.closeAssociatedWindows();
946 FileLoader loader = new FileLoader();
947 String protocol = fileName.startsWith("http:") ? "URL" : "File";
948 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
952 Rectangle bounds = this.getBounds();
954 FileLoader loader = new FileLoader();
955 String protocol = fileName.startsWith("http:") ? "URL" : "File";
956 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
957 protocol, currentFileFormat);
959 newframe.setBounds(bounds);
960 if (featureSettings != null && featureSettings.isShowing())
962 final Rectangle fspos = featureSettings.frame.getBounds();
963 // TODO: need a 'show feature settings' function that takes bounds -
964 // need to refactor Desktop.addFrame
965 newframe.featureSettings_actionPerformed(null);
966 final FeatureSettings nfs = newframe.featureSettings;
967 SwingUtilities.invokeLater(new Runnable()
972 nfs.frame.setBounds(fspos);
975 this.featureSettings.close();
976 this.featureSettings = null;
978 this.closeMenuItem_actionPerformed(true);
984 public void addFromText_actionPerformed(ActionEvent e)
986 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
990 public void addFromURL_actionPerformed(ActionEvent e)
992 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
996 public void save_actionPerformed(ActionEvent e)
999 || (currentFileFormat == null || !jalview.io.FormatAdapter
1000 .isValidIOFormat(currentFileFormat, true))
1001 || fileName.startsWith("http"))
1003 saveAs_actionPerformed(null);
1007 saveAlignment(fileName, currentFileFormat);
1018 public void saveAs_actionPerformed(ActionEvent e)
1020 JalviewFileChooser chooser = new JalviewFileChooser(
1021 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1022 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1023 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1024 currentFileFormat, false);
1026 chooser.setFileView(new JalviewFileView());
1027 chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1028 chooser.setToolTipText(MessageManager.getString("action.save"));
1030 int value = chooser.showSaveDialog(this);
1032 if (value == JalviewFileChooser.APPROVE_OPTION)
1034 currentFileFormat = chooser.getSelectedFormat();
1035 if (currentFileFormat == null)
1038 .showInternalMessageDialog(
1041 .getString("label.select_file_format_before_saving"),
1043 .getString("label.file_format_not_specified"),
1044 JOptionPane.WARNING_MESSAGE);
1045 value = chooser.showSaveDialog(this);
1049 fileName = chooser.getSelectedFile().getPath();
1051 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1054 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1055 if (currentFileFormat.indexOf(" ") > -1)
1057 currentFileFormat = currentFileFormat.substring(0,
1058 currentFileFormat.indexOf(" "));
1060 saveAlignment(fileName, currentFileFormat);
1064 public boolean saveAlignment(String file, String format)
1066 boolean success = true;
1068 if (format.equalsIgnoreCase("Jalview"))
1070 String shortName = title;
1072 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1074 shortName = shortName.substring(shortName
1075 .lastIndexOf(java.io.File.separatorChar) + 1);
1078 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1080 statusBar.setText(MessageManager.formatMessage(
1081 "label.successfully_saved_to_file_in_format", new String[]
1082 { fileName, format }));
1087 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1089 warningMessage("Cannot save file " + fileName + " using format "
1090 + format, "Alignment output format not supported");
1091 saveAs_actionPerformed(null);
1092 // JBPNote need to have a raise_gui flag here
1096 String[] omitHidden = null;
1098 if (viewport.hasHiddenColumns())
1100 int reply = JOptionPane
1101 .showInternalConfirmDialog(
1104 .getString("label.alignment_contains_hidden_columns"),
1106 .getString("action.save_omit_hidden_columns"),
1107 JOptionPane.YES_NO_OPTION,
1108 JOptionPane.QUESTION_MESSAGE);
1110 if (reply == JOptionPane.YES_OPTION)
1112 omitHidden = viewport.getViewAsString(false);
1115 FormatAdapter f = new FormatAdapter();
1116 String output = f.formatSequences(format,
1117 viewport.getAlignment(), // class cast exceptions will
1118 // occur in the distant future
1119 omitHidden, f.getCacheSuffixDefault(format),
1120 viewport.getColumnSelection());
1130 java.io.PrintWriter out = new java.io.PrintWriter(
1131 new java.io.FileWriter(file));
1135 this.setTitle(file);
1136 statusBar.setText(MessageManager.formatMessage(
1137 "label.successfully_saved_to_file_in_format",
1139 { fileName, format }));
1140 } catch (Exception ex)
1143 ex.printStackTrace();
1150 JOptionPane.showInternalMessageDialog(this, MessageManager
1151 .formatMessage("label.couldnt_save_file", new String[]
1152 { fileName }), MessageManager
1153 .getString("label.error_saving_file"),
1154 JOptionPane.WARNING_MESSAGE);
1160 private void warningMessage(String warning, String title)
1162 if (new jalview.util.Platform().isHeadless())
1164 System.err.println("Warning: " + title + "\nWarning: " + warning);
1169 JOptionPane.showInternalMessageDialog(this, warning, title,
1170 JOptionPane.WARNING_MESSAGE);
1182 protected void outputText_actionPerformed(ActionEvent e)
1184 String[] omitHidden = null;
1186 if (viewport.hasHiddenColumns())
1188 int reply = JOptionPane
1189 .showInternalConfirmDialog(
1192 .getString("label.alignment_contains_hidden_columns"),
1194 .getString("action.save_omit_hidden_columns"),
1195 JOptionPane.YES_NO_OPTION,
1196 JOptionPane.QUESTION_MESSAGE);
1198 if (reply == JOptionPane.YES_OPTION)
1200 omitHidden = viewport.getViewAsString(false);
1204 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1205 cap.setForInput(null);
1209 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1210 viewport.getAlignment(), omitHidden,
1211 viewport.getColumnSelection()));
1212 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1213 "label.alignment_output_command", new String[]
1214 { e.getActionCommand() }), 600, 500);
1215 } catch (OutOfMemoryError oom)
1217 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1230 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1232 new HTMLOutput(alignPanel,
1233 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1234 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1237 public void createImageMap(File file, String image)
1239 alignPanel.makePNGImageMap(file, image);
1249 public void createPNG(File f)
1251 alignPanel.makePNG(f);
1261 public void createEPS(File f)
1263 alignPanel.makeEPS(f);
1266 public void createSVG(File f)
1268 alignPanel.makeSVG(f);
1271 public void pageSetup_actionPerformed(ActionEvent e)
1273 PrinterJob printJob = PrinterJob.getPrinterJob();
1274 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1284 public void printMenuItem_actionPerformed(ActionEvent e)
1286 // Putting in a thread avoids Swing painting problems
1287 PrintThread thread = new PrintThread(alignPanel);
1292 public void exportFeatures_actionPerformed(ActionEvent e)
1294 new AnnotationExporter().exportFeatures(alignPanel);
1298 public void exportAnnotations_actionPerformed(ActionEvent e)
1300 new AnnotationExporter().exportAnnotations(alignPanel,
1301 viewport.showAnnotation ? viewport.getAlignment()
1302 .getAlignmentAnnotation() : null, viewport
1303 .getAlignment().getGroups(), ((Alignment) viewport
1304 .getAlignment()).alignmentProperties);
1308 public void associatedData_actionPerformed(ActionEvent e)
1310 // Pick the tree file
1311 JalviewFileChooser chooser = new JalviewFileChooser(
1312 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1313 chooser.setFileView(new JalviewFileView());
1314 chooser.setDialogTitle(MessageManager
1315 .getString("label.load_jalview_annotations"));
1316 chooser.setToolTipText(MessageManager
1317 .getString("label.load_jalview_annotations"));
1319 int value = chooser.showOpenDialog(null);
1321 if (value == JalviewFileChooser.APPROVE_OPTION)
1323 String choice = chooser.getSelectedFile().getPath();
1324 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1325 loadJalviewDataFile(choice, null, null, null);
1331 * Close the current view or all views in the alignment frame. If the frame
1332 * only contains one view then the alignment will be removed from memory.
1334 * @param closeAllTabs
1337 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1339 if (alignPanels != null && alignPanels.size() < 2)
1341 closeAllTabs = true;
1346 if (alignPanels != null)
1350 if (this.isClosed())
1352 // really close all the windows - otherwise wait till
1353 // setClosed(true) is called
1354 for (int i = 0; i < alignPanels.size(); i++)
1356 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1363 closeView(alignPanel);
1369 this.setClosed(true);
1371 } catch (Exception ex)
1373 ex.printStackTrace();
1378 * close alignPanel2 and shuffle tabs appropriately.
1380 * @param alignPanel2
1382 public void closeView(AlignmentPanel alignPanel2)
1384 int index = tabbedPane.getSelectedIndex();
1385 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1386 alignPanels.removeElement(alignPanel2);
1388 // if (viewport == alignPanel2.av)
1392 alignPanel2.closePanel();
1395 tabbedPane.removeTabAt(closedindex);
1396 tabbedPane.validate();
1398 if (index > closedindex || index == tabbedPane.getTabCount())
1400 // modify currently selected tab index if necessary.
1404 this.tabSelectionChanged(index);
1410 void updateEditMenuBar()
1413 if (viewport.historyList.size() > 0)
1415 undoMenuItem.setEnabled(true);
1416 CommandI command = viewport.historyList.peek();
1417 undoMenuItem.setText(MessageManager.formatMessage(
1418 "label.undo_command", new String[]
1419 { command.getDescription() }));
1423 undoMenuItem.setEnabled(false);
1424 undoMenuItem.setText(MessageManager.getString("action.undo"));
1427 if (viewport.redoList.size() > 0)
1429 redoMenuItem.setEnabled(true);
1431 CommandI command = viewport.redoList.peek();
1432 redoMenuItem.setText(MessageManager.formatMessage(
1433 "label.redo_command", new String[]
1434 { command.getDescription() }));
1438 redoMenuItem.setEnabled(false);
1439 redoMenuItem.setText(MessageManager.getString("action.redo"));
1443 public void addHistoryItem(CommandI command)
1445 if (command.getSize() > 0)
1447 viewport.historyList.push(command);
1448 viewport.redoList.clear();
1449 updateEditMenuBar();
1450 viewport.updateHiddenColumns();
1451 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1452 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1453 // viewport.getColumnSelection()
1454 // .getHiddenColumns().size() > 0);
1460 * @return alignment objects for all views
1462 AlignmentI[] getViewAlignments()
1464 if (alignPanels != null)
1466 Enumeration e = alignPanels.elements();
1467 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1468 for (int i = 0; e.hasMoreElements(); i++)
1470 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1474 if (viewport != null)
1476 return new AlignmentI[]
1477 { viewport.getAlignment() };
1489 protected void undoMenuItem_actionPerformed(ActionEvent e)
1491 if (viewport.historyList.empty())
1495 CommandI command = viewport.historyList.pop();
1496 viewport.redoList.push(command);
1497 command.undoCommand(getViewAlignments());
1499 AlignViewport originalSource = getOriginatingSource(command);
1500 updateEditMenuBar();
1502 if (originalSource != null)
1504 if (originalSource != viewport)
1507 .warn("Implementation worry: mismatch of viewport origin for undo");
1509 originalSource.updateHiddenColumns();
1510 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1512 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1513 // viewport.getColumnSelection()
1514 // .getHiddenColumns().size() > 0);
1515 originalSource.firePropertyChange("alignment", null, originalSource
1516 .getAlignment().getSequences());
1527 protected void redoMenuItem_actionPerformed(ActionEvent e)
1529 if (viewport.redoList.size() < 1)
1534 CommandI command = viewport.redoList.pop();
1535 viewport.historyList.push(command);
1536 command.doCommand(getViewAlignments());
1538 AlignViewport originalSource = getOriginatingSource(command);
1539 updateEditMenuBar();
1541 if (originalSource != null)
1544 if (originalSource != viewport)
1547 .warn("Implementation worry: mismatch of viewport origin for redo");
1549 originalSource.updateHiddenColumns();
1550 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1552 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1553 // viewport.getColumnSelection()
1554 // .getHiddenColumns().size() > 0);
1555 originalSource.firePropertyChange("alignment", null, originalSource
1556 .getAlignment().getSequences());
1560 AlignViewport getOriginatingSource(CommandI command)
1562 AlignViewport originalSource = null;
1563 // For sequence removal and addition, we need to fire
1564 // the property change event FROM the viewport where the
1565 // original alignment was altered
1566 AlignmentI al = null;
1567 if (command instanceof EditCommand)
1569 EditCommand editCommand = (EditCommand) command;
1570 al = editCommand.getAlignment();
1571 Vector comps = (Vector) PaintRefresher.components.get(viewport
1572 .getSequenceSetId());
1574 for (int i = 0; i < comps.size(); i++)
1576 if (comps.elementAt(i) instanceof AlignmentPanel)
1578 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1580 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1587 if (originalSource == null)
1589 // The original view is closed, we must validate
1590 // the current view against the closed view first
1593 PaintRefresher.validateSequences(al, viewport.getAlignment());
1596 originalSource = viewport;
1599 return originalSource;
1608 public void moveSelectedSequences(boolean up)
1610 SequenceGroup sg = viewport.getSelectionGroup();
1616 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1617 viewport.getHiddenRepSequences(), up);
1618 alignPanel.paintAlignment(true);
1621 synchronized void slideSequences(boolean right, int size)
1623 List<SequenceI> sg = new Vector();
1624 if (viewport.cursorMode)
1626 sg.add(viewport.getAlignment().getSequenceAt(
1627 alignPanel.seqPanel.seqCanvas.cursorY));
1629 else if (viewport.getSelectionGroup() != null
1630 && viewport.getSelectionGroup().getSize() != viewport
1631 .getAlignment().getHeight())
1633 sg = viewport.getSelectionGroup().getSequences(
1634 viewport.getHiddenRepSequences());
1642 Vector invertGroup = new Vector();
1644 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1646 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1648 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1652 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1654 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1655 for (int i = 0; i < invertGroup.size(); i++)
1657 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1660 SlideSequencesCommand ssc;
1663 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1664 size, viewport.getGapCharacter());
1668 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1669 size, viewport.getGapCharacter());
1672 int groupAdjustment = 0;
1673 if (ssc.getGapsInsertedBegin() && right)
1675 if (viewport.cursorMode)
1677 alignPanel.seqPanel.moveCursor(size, 0);
1681 groupAdjustment = size;
1684 else if (!ssc.getGapsInsertedBegin() && !right)
1686 if (viewport.cursorMode)
1688 alignPanel.seqPanel.moveCursor(-size, 0);
1692 groupAdjustment = -size;
1696 if (groupAdjustment != 0)
1698 viewport.getSelectionGroup().setStartRes(
1699 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1700 viewport.getSelectionGroup().setEndRes(
1701 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1704 boolean appendHistoryItem = false;
1705 if (viewport.historyList != null && viewport.historyList.size() > 0
1706 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1708 appendHistoryItem = ssc
1709 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1713 if (!appendHistoryItem)
1715 addHistoryItem(ssc);
1728 protected void copy_actionPerformed(ActionEvent e)
1731 if (viewport.getSelectionGroup() == null)
1735 // TODO: preserve the ordering of displayed alignment annotation in any
1736 // internal paste (particularly sequence associated annotation)
1737 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1738 String[] omitHidden = null;
1740 if (viewport.hasHiddenColumns())
1742 omitHidden = viewport.getViewAsString(true);
1745 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1748 StringSelection ss = new StringSelection(output);
1752 jalview.gui.Desktop.internalCopy = true;
1753 // Its really worth setting the clipboard contents
1754 // to empty before setting the large StringSelection!!
1755 Toolkit.getDefaultToolkit().getSystemClipboard()
1756 .setContents(new StringSelection(""), null);
1758 Toolkit.getDefaultToolkit().getSystemClipboard()
1759 .setContents(ss, Desktop.instance);
1760 } catch (OutOfMemoryError er)
1762 new OOMWarning("copying region", er);
1766 Vector hiddenColumns = null;
1767 if (viewport.hasHiddenColumns())
1769 hiddenColumns = new Vector();
1770 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1771 .getSelectionGroup().getEndRes();
1772 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1775 int[] region = (int[]) viewport.getColumnSelection()
1776 .getHiddenColumns().elementAt(i);
1777 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1779 hiddenColumns.addElement(new int[]
1780 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1785 Desktop.jalviewClipboard = new Object[]
1786 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1787 statusBar.setText(MessageManager.formatMessage(
1788 "label.copied_sequences_to_clipboard", new String[]
1789 { Integer.valueOf(seqs.length).toString() }));
1799 protected void pasteNew_actionPerformed(ActionEvent e)
1811 protected void pasteThis_actionPerformed(ActionEvent e)
1817 * Paste contents of Jalview clipboard
1819 * @param newAlignment
1820 * true to paste to a new alignment, otherwise add to this.
1822 void paste(boolean newAlignment)
1824 boolean externalPaste = true;
1827 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1828 Transferable contents = c.getContents(this);
1830 if (contents == null)
1838 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1839 if (str.length() < 1)
1844 format = new IdentifyFile().Identify(str, "Paste");
1846 } catch (OutOfMemoryError er)
1848 new OOMWarning("Out of memory pasting sequences!!", er);
1852 SequenceI[] sequences;
1853 boolean annotationAdded = false;
1854 AlignmentI alignment = null;
1856 if (Desktop.jalviewClipboard != null)
1858 // The clipboard was filled from within Jalview, we must use the
1860 // And dataset from the copied alignment
1861 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1862 // be doubly sure that we create *new* sequence objects.
1863 sequences = new SequenceI[newseq.length];
1864 for (int i = 0; i < newseq.length; i++)
1866 sequences[i] = new Sequence(newseq[i]);
1868 alignment = new Alignment(sequences);
1869 externalPaste = false;
1873 // parse the clipboard as an alignment.
1874 alignment = new FormatAdapter().readFile(str, "Paste", format);
1875 sequences = alignment.getSequencesArray();
1879 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1885 if (Desktop.jalviewClipboard != null)
1887 // dataset is inherited
1888 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1892 // new dataset is constructed
1893 alignment.setDataset(null);
1895 alwidth = alignment.getWidth() + 1;
1899 AlignmentI pastedal = alignment; // preserve pasted alignment object
1900 // Add pasted sequences and dataset into existing alignment.
1901 alignment = viewport.getAlignment();
1902 alwidth = alignment.getWidth() + 1;
1903 // decide if we need to import sequences from an existing dataset
1904 boolean importDs = Desktop.jalviewClipboard != null
1905 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1906 // importDs==true instructs us to copy over new dataset sequences from
1907 // an existing alignment
1908 Vector newDs = (importDs) ? new Vector() : null; // used to create
1909 // minimum dataset set
1911 for (int i = 0; i < sequences.length; i++)
1915 newDs.addElement(null);
1917 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1919 if (importDs && ds != null)
1921 if (!newDs.contains(ds))
1923 newDs.setElementAt(ds, i);
1924 ds = new Sequence(ds);
1925 // update with new dataset sequence
1926 sequences[i].setDatasetSequence(ds);
1930 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1935 // copy and derive new dataset sequence
1936 sequences[i] = sequences[i].deriveSequence();
1937 alignment.getDataset().addSequence(
1938 sequences[i].getDatasetSequence());
1939 // TODO: avoid creation of duplicate dataset sequences with a
1940 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1942 alignment.addSequence(sequences[i]); // merges dataset
1946 newDs.clear(); // tidy up
1948 if (alignment.getAlignmentAnnotation() != null)
1950 for (AlignmentAnnotation alan : alignment
1951 .getAlignmentAnnotation())
1953 if (alan.graphGroup > fgroup)
1955 fgroup = alan.graphGroup;
1959 if (pastedal.getAlignmentAnnotation() != null)
1961 // Add any annotation attached to alignment.
1962 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1963 for (int i = 0; i < alann.length; i++)
1965 annotationAdded = true;
1966 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1968 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1969 if (newann.graphGroup > -1)
1971 if (newGraphGroups.size() <= newann.graphGroup
1972 || newGraphGroups.get(newann.graphGroup) == null)
1974 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1976 newGraphGroups.add(q, null);
1978 newGraphGroups.set(newann.graphGroup, new Integer(
1981 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1985 newann.padAnnotation(alwidth);
1986 alignment.addAnnotation(newann);
1996 addHistoryItem(new EditCommand(
1997 MessageManager.getString("label.add_sequences"),
1999 sequences, 0, alignment.getWidth(), alignment));
2001 // Add any annotations attached to sequences
2002 for (int i = 0; i < sequences.length; i++)
2004 if (sequences[i].getAnnotation() != null)
2006 AlignmentAnnotation newann;
2007 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2009 annotationAdded = true;
2010 newann = sequences[i].getAnnotation()[a];
2011 newann.adjustForAlignment();
2012 newann.padAnnotation(alwidth);
2013 if (newann.graphGroup > -1)
2015 if (newann.graphGroup > -1)
2017 if (newGraphGroups.size() <= newann.graphGroup
2018 || newGraphGroups.get(newann.graphGroup) == null)
2020 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2022 newGraphGroups.add(q, null);
2024 newGraphGroups.set(newann.graphGroup, new Integer(
2027 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2031 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2036 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2043 // propagate alignment changed.
2044 viewport.setEndSeq(alignment.getHeight());
2045 if (annotationAdded)
2047 // Duplicate sequence annotation in all views.
2048 AlignmentI[] alview = this.getViewAlignments();
2049 for (int i = 0; i < sequences.length; i++)
2051 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2056 for (int avnum = 0; avnum < alview.length; avnum++)
2058 if (alview[avnum] != alignment)
2060 // duplicate in a view other than the one with input focus
2061 int avwidth = alview[avnum].getWidth() + 1;
2062 // this relies on sann being preserved after we
2063 // modify the sequence's annotation array for each duplication
2064 for (int a = 0; a < sann.length; a++)
2066 AlignmentAnnotation newann = new AlignmentAnnotation(
2068 sequences[i].addAlignmentAnnotation(newann);
2069 newann.padAnnotation(avwidth);
2070 alview[avnum].addAnnotation(newann); // annotation was
2071 // duplicated earlier
2072 // TODO JAL-1145 graphGroups are not updated for sequence
2073 // annotation added to several views. This may cause
2075 alview[avnum].setAnnotationIndex(newann, a);
2080 buildSortByAnnotationScoresMenu();
2082 viewport.firePropertyChange("alignment", null,
2083 alignment.getSequences());
2084 if (alignPanels != null)
2086 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2088 ap.validateAnnotationDimensions(false);
2093 alignPanel.validateAnnotationDimensions(false);
2099 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2101 String newtitle = new String("Copied sequences");
2103 if (Desktop.jalviewClipboard != null
2104 && Desktop.jalviewClipboard[2] != null)
2106 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2107 for (int i = 0; i < hc.size(); i++)
2109 int[] region = (int[]) hc.elementAt(i);
2110 af.viewport.hideColumns(region[0], region[1]);
2114 // >>>This is a fix for the moment, until a better solution is
2116 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2118 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2120 // TODO: maintain provenance of an alignment, rather than just make the
2121 // title a concatenation of operations.
2124 if (title.startsWith("Copied sequences"))
2130 newtitle = newtitle.concat("- from " + title);
2135 newtitle = new String("Pasted sequences");
2138 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2143 } catch (Exception ex)
2145 ex.printStackTrace();
2146 System.out.println("Exception whilst pasting: " + ex);
2147 // could be anything being pasted in here
2153 protected void expand_newalign(ActionEvent e)
2157 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2158 .getAlignment(), -1);
2159 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2161 String newtitle = new String("Flanking alignment");
2163 if (Desktop.jalviewClipboard != null
2164 && Desktop.jalviewClipboard[2] != null)
2166 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2167 for (int i = 0; i < hc.size(); i++)
2169 int[] region = (int[]) hc.elementAt(i);
2170 af.viewport.hideColumns(region[0], region[1]);
2174 // >>>This is a fix for the moment, until a better solution is
2176 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2178 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2180 // TODO: maintain provenance of an alignment, rather than just make the
2181 // title a concatenation of operations.
2183 if (title.startsWith("Copied sequences"))
2189 newtitle = newtitle.concat("- from " + title);
2193 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2195 } catch (Exception ex)
2197 ex.printStackTrace();
2198 System.out.println("Exception whilst pasting: " + ex);
2199 // could be anything being pasted in here
2200 } catch (OutOfMemoryError oom)
2202 new OOMWarning("Viewing flanking region of alignment", oom);
2213 protected void cut_actionPerformed(ActionEvent e)
2215 copy_actionPerformed(null);
2216 delete_actionPerformed(null);
2226 protected void delete_actionPerformed(ActionEvent evt)
2229 SequenceGroup sg = viewport.getSelectionGroup();
2235 List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
2237 for (int i = 0; i < sg.getSize(); i++)
2239 seq = sg.getSequenceAt(i);
2243 // If the cut affects all sequences, warn, remove highlighted columns
2244 if (sg.getSize() == viewport.getAlignment().getHeight())
2246 int confirm = JOptionPane.showConfirmDialog(this,
2247 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2248 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2249 JOptionPane.OK_CANCEL_OPTION);
2251 if (confirm == JOptionPane.CANCEL_OPTION
2252 || confirm == JOptionPane.CLOSED_OPTION)
2256 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2257 sg.getEndRes() + 1);
2260 SequenceI[] cut = new SequenceI[seqs.size()];
2261 for (int i = 0; i < seqs.size(); i++)
2263 cut[i] = seqs.get(i);
2267 * //ADD HISTORY ITEM
2269 addHistoryItem(new EditCommand(
2270 MessageManager.getString("label.cut_sequences"), Action.CUT,
2271 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2272 viewport.getAlignment()));
2274 viewport.setSelectionGroup(null);
2275 viewport.sendSelection();
2276 viewport.getAlignment().deleteGroup(sg);
2278 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2280 if (viewport.getAlignment().getHeight() < 1)
2284 this.setClosed(true);
2285 } catch (Exception ex)
2298 protected void deleteGroups_actionPerformed(ActionEvent e)
2300 if (avc.deleteGroups())
2302 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2303 alignPanel.updateAnnotation();
2304 alignPanel.paintAlignment(true);
2315 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2317 SequenceGroup sg = new SequenceGroup();
2319 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2321 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2324 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2325 viewport.setSelectionGroup(sg);
2326 viewport.sendSelection();
2327 alignPanel.paintAlignment(true);
2328 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2338 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2340 if (viewport.cursorMode)
2342 alignPanel.seqPanel.keyboardNo1 = null;
2343 alignPanel.seqPanel.keyboardNo2 = null;
2345 viewport.setSelectionGroup(null);
2346 viewport.getColumnSelection().clear();
2347 viewport.setSelectionGroup(null);
2348 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2349 alignPanel.idPanel.idCanvas.searchResults = null;
2350 alignPanel.paintAlignment(true);
2351 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2352 viewport.sendSelection();
2362 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2364 SequenceGroup sg = viewport.getSelectionGroup();
2368 selectAllSequenceMenuItem_actionPerformed(null);
2373 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2375 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2378 alignPanel.paintAlignment(true);
2379 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2380 viewport.sendSelection();
2384 public void invertColSel_actionPerformed(ActionEvent e)
2386 viewport.invertColumnSelection();
2387 alignPanel.paintAlignment(true);
2388 viewport.sendSelection();
2398 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2400 trimAlignment(true);
2410 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2412 trimAlignment(false);
2415 void trimAlignment(boolean trimLeft)
2417 ColumnSelection colSel = viewport.getColumnSelection();
2420 if (colSel.size() > 0)
2424 column = colSel.getMin();
2428 column = colSel.getMax();
2432 if (viewport.getSelectionGroup() != null)
2434 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2435 viewport.getHiddenRepSequences());
2439 seqs = viewport.getAlignment().getSequencesArray();
2442 TrimRegionCommand trimRegion;
2445 trimRegion = new TrimRegionCommand("Remove Left",
2446 TrimRegionCommand.TRIM_LEFT, seqs, column,
2447 viewport.getAlignment(), viewport.getColumnSelection(),
2448 viewport.getSelectionGroup());
2449 viewport.setStartRes(0);
2453 trimRegion = new TrimRegionCommand("Remove Right",
2454 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2455 viewport.getAlignment(), viewport.getColumnSelection(),
2456 viewport.getSelectionGroup());
2459 statusBar.setText(MessageManager.formatMessage(
2460 "label.removed_columns", new String[]
2461 { Integer.valueOf(trimRegion.getSize()).toString() }));
2463 addHistoryItem(trimRegion);
2465 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2467 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2468 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2470 viewport.getAlignment().deleteGroup(sg);
2474 viewport.firePropertyChange("alignment", null, viewport
2475 .getAlignment().getSequences());
2486 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2488 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2491 if (viewport.getSelectionGroup() != null)
2493 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2494 viewport.getHiddenRepSequences());
2495 start = viewport.getSelectionGroup().getStartRes();
2496 end = viewport.getSelectionGroup().getEndRes();
2500 seqs = viewport.getAlignment().getSequencesArray();
2503 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2504 "Remove Gapped Columns", seqs, start, end,
2505 viewport.getAlignment());
2507 addHistoryItem(removeGapCols);
2509 statusBar.setText(MessageManager.formatMessage(
2510 "label.removed_empty_columns", new String[]
2511 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2513 // This is to maintain viewport position on first residue
2514 // of first sequence
2515 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2516 int startRes = seq.findPosition(viewport.startRes);
2517 // ShiftList shifts;
2518 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2519 // edit.alColumnChanges=shifts.getInverse();
2520 // if (viewport.hasHiddenColumns)
2521 // viewport.getColumnSelection().compensateForEdits(shifts);
2522 viewport.setStartRes(seq.findIndex(startRes) - 1);
2523 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2535 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2537 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2540 if (viewport.getSelectionGroup() != null)
2542 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2543 viewport.getHiddenRepSequences());
2544 start = viewport.getSelectionGroup().getStartRes();
2545 end = viewport.getSelectionGroup().getEndRes();
2549 seqs = viewport.getAlignment().getSequencesArray();
2552 // This is to maintain viewport position on first residue
2553 // of first sequence
2554 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2555 int startRes = seq.findPosition(viewport.startRes);
2557 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2558 viewport.getAlignment()));
2560 viewport.setStartRes(seq.findIndex(startRes) - 1);
2562 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2574 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2576 viewport.setPadGaps(padGapsMenuitem.isSelected());
2577 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2583 // if (justifySeqs>0)
2585 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2598 public void findMenuItem_actionPerformed(ActionEvent e)
2604 public void newView_actionPerformed(ActionEvent e)
2611 * @param copyAnnotation
2612 * if true then duplicate all annnotation, groups and settings
2613 * @return new alignment panel, already displayed.
2615 public AlignmentPanel newView(boolean copyAnnotation)
2617 return newView(null, copyAnnotation);
2623 * title of newly created view
2624 * @return new alignment panel, already displayed.
2626 public AlignmentPanel newView(String viewTitle)
2628 return newView(viewTitle, true);
2634 * title of newly created view
2635 * @param copyAnnotation
2636 * if true then duplicate all annnotation, groups and settings
2637 * @return new alignment panel, already displayed.
2639 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2641 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2643 if (!copyAnnotation)
2645 // just remove all the current annotation except for the automatic stuff
2646 newap.av.getAlignment().deleteAllGroups();
2647 for (AlignmentAnnotation alan : newap.av.getAlignment()
2648 .getAlignmentAnnotation())
2650 if (!alan.autoCalculated)
2652 newap.av.getAlignment().deleteAnnotation(alan);
2658 newap.av.gatherViewsHere = false;
2660 if (viewport.viewName == null)
2662 viewport.viewName = "Original";
2665 newap.av.historyList = viewport.historyList;
2666 newap.av.redoList = viewport.redoList;
2668 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2669 // make sure the new view has a unique name - this is essential for Jalview
2671 boolean addFirstIndex = false;
2672 if (viewTitle == null || viewTitle.trim().length() == 0)
2674 viewTitle = MessageManager.getString("action.view");
2675 addFirstIndex = true;
2679 index = 1;// we count from 1 if given a specific name
2681 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2682 Vector comps = (Vector) PaintRefresher.components.get(viewport
2683 .getSequenceSetId());
2684 Vector existingNames = new Vector();
2685 for (int i = 0; i < comps.size(); i++)
2687 if (comps.elementAt(i) instanceof AlignmentPanel)
2689 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2690 if (!existingNames.contains(ap.av.viewName))
2692 existingNames.addElement(ap.av.viewName);
2697 while (existingNames.contains(newViewName))
2699 newViewName = viewTitle + " " + (++index);
2702 newap.av.viewName = newViewName;
2704 addAlignmentPanel(newap, true);
2705 newap.alignmentChanged();
2707 if (alignPanels.size() == 2)
2709 viewport.gatherViewsHere = true;
2711 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2716 public void expandViews_actionPerformed(ActionEvent e)
2718 Desktop.instance.explodeViews(this);
2722 public void gatherViews_actionPerformed(ActionEvent e)
2724 Desktop.instance.gatherViews(this);
2734 public void font_actionPerformed(ActionEvent e)
2736 new FontChooser(alignPanel);
2746 protected void seqLimit_actionPerformed(ActionEvent e)
2748 viewport.setShowJVSuffix(seqLimits.isSelected());
2750 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2751 .calculateIdWidth());
2752 alignPanel.paintAlignment(true);
2756 public void idRightAlign_actionPerformed(ActionEvent e)
2758 viewport.rightAlignIds = idRightAlign.isSelected();
2759 alignPanel.paintAlignment(true);
2763 public void centreColumnLabels_actionPerformed(ActionEvent e)
2765 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2766 alignPanel.paintAlignment(true);
2772 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2775 protected void followHighlight_actionPerformed()
2777 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2779 alignPanel.scrollToPosition(
2780 alignPanel.seqPanel.seqCanvas.searchResults, false);
2791 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2793 viewport.setColourText(colourTextMenuItem.isSelected());
2794 alignPanel.paintAlignment(true);
2804 public void wrapMenuItem_actionPerformed(ActionEvent e)
2806 scaleAbove.setVisible(wrapMenuItem.isSelected());
2807 scaleLeft.setVisible(wrapMenuItem.isSelected());
2808 scaleRight.setVisible(wrapMenuItem.isSelected());
2809 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2810 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2814 public void showAllSeqs_actionPerformed(ActionEvent e)
2816 viewport.showAllHiddenSeqs();
2820 public void showAllColumns_actionPerformed(ActionEvent e)
2822 viewport.showAllHiddenColumns();
2827 public void hideSelSequences_actionPerformed(ActionEvent e)
2829 viewport.hideAllSelectedSeqs();
2830 alignPanel.paintAlignment(true);
2834 * called by key handler and the hide all/show all menu items
2839 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2842 boolean hide = false;
2843 SequenceGroup sg = viewport.getSelectionGroup();
2844 if (!toggleSeqs && !toggleCols)
2846 // Hide everything by the current selection - this is a hack - we do the
2847 // invert and then hide
2848 // first check that there will be visible columns after the invert.
2849 if ((viewport.getColumnSelection() != null
2850 && viewport.getColumnSelection().getSelected() != null && viewport
2851 .getColumnSelection().getSelected().size() > 0)
2852 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2855 // now invert the sequence set, if required - empty selection implies
2856 // that no hiding is required.
2859 invertSequenceMenuItem_actionPerformed(null);
2860 sg = viewport.getSelectionGroup();
2864 viewport.expandColSelection(sg, true);
2865 // finally invert the column selection and get the new sequence
2867 invertColSel_actionPerformed(null);
2874 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2876 hideSelSequences_actionPerformed(null);
2879 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2882 showAllSeqs_actionPerformed(null);
2888 if (viewport.getColumnSelection().getSelected().size() > 0)
2890 hideSelColumns_actionPerformed(null);
2893 viewport.setSelectionGroup(sg);
2898 showAllColumns_actionPerformed(null);
2907 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2908 * event.ActionEvent)
2911 public void hideAllButSelection_actionPerformed(ActionEvent e)
2913 toggleHiddenRegions(false, false);
2920 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2924 public void hideAllSelection_actionPerformed(ActionEvent e)
2926 SequenceGroup sg = viewport.getSelectionGroup();
2927 viewport.expandColSelection(sg, false);
2928 viewport.hideAllSelectedSeqs();
2929 viewport.hideSelectedColumns();
2930 alignPanel.paintAlignment(true);
2937 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2941 public void showAllhidden_actionPerformed(ActionEvent e)
2943 viewport.showAllHiddenColumns();
2944 viewport.showAllHiddenSeqs();
2945 alignPanel.paintAlignment(true);
2949 public void hideSelColumns_actionPerformed(ActionEvent e)
2951 viewport.hideSelectedColumns();
2952 alignPanel.paintAlignment(true);
2956 public void hiddenMarkers_actionPerformed(ActionEvent e)
2958 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2969 protected void scaleAbove_actionPerformed(ActionEvent e)
2971 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2972 alignPanel.paintAlignment(true);
2982 protected void scaleLeft_actionPerformed(ActionEvent e)
2984 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2985 alignPanel.paintAlignment(true);
2995 protected void scaleRight_actionPerformed(ActionEvent e)
2997 viewport.setScaleRightWrapped(scaleRight.isSelected());
2998 alignPanel.paintAlignment(true);
3008 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3010 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3011 alignPanel.paintAlignment(true);
3021 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3023 viewport.setShowText(viewTextMenuItem.isSelected());
3024 alignPanel.paintAlignment(true);
3034 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3036 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3037 alignPanel.paintAlignment(true);
3040 public FeatureSettings featureSettings;
3043 public void featureSettings_actionPerformed(ActionEvent e)
3045 if (featureSettings != null)
3047 featureSettings.close();
3048 featureSettings = null;
3050 if (!showSeqFeatures.isSelected())
3052 // make sure features are actually displayed
3053 showSeqFeatures.setSelected(true);
3054 showSeqFeatures_actionPerformed(null);
3056 featureSettings = new FeatureSettings(this);
3060 * Set or clear 'Show Sequence Features'
3066 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3068 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3069 alignPanel.paintAlignment(true);
3070 if (alignPanel.getOverviewPanel() != null)
3072 alignPanel.getOverviewPanel().updateOverviewImage();
3077 * Set or clear 'Show Sequence Features'
3083 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3085 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3087 if (viewport.getShowSequenceFeaturesHeight())
3089 // ensure we're actually displaying features
3090 viewport.setShowSequenceFeatures(true);
3091 showSeqFeatures.setSelected(true);
3093 alignPanel.paintAlignment(true);
3094 if (alignPanel.getOverviewPanel() != null)
3096 alignPanel.getOverviewPanel().updateOverviewImage();
3101 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3102 * the annotations panel as a whole.
3104 * The options to show/hide all annotations should be enabled when the panel
3105 * is shown, and disabled when the panel is hidden.
3110 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3112 final boolean setVisible = annotationPanelMenuItem.isSelected();
3113 viewport.setShowAnnotation(setVisible);
3114 alignPanel.setAnnotationVisible(setVisible);
3115 this.showAllSeqAnnotations.setEnabled(setVisible);
3116 this.hideAllSeqAnnotations.setEnabled(setVisible);
3117 this.showAllAlAnnotations.setEnabled(setVisible);
3118 this.hideAllAlAnnotations.setEnabled(setVisible);
3122 public void alignmentProperties()
3124 JEditorPane editPane = new JEditorPane("text/html", "");
3125 editPane.setEditable(false);
3126 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3128 editPane.setText(MessageManager.formatMessage("label.html_content",
3130 { contents.toString() }));
3131 JInternalFrame frame = new JInternalFrame();
3132 frame.getContentPane().add(new JScrollPane(editPane));
3134 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3135 "label.alignment_properties", new String[]
3136 { getTitle() }), 500, 400);
3146 public void overviewMenuItem_actionPerformed(ActionEvent e)
3148 if (alignPanel.overviewPanel != null)
3153 JInternalFrame frame = new JInternalFrame();
3154 OverviewPanel overview = new OverviewPanel(alignPanel);
3155 frame.setContentPane(overview);
3156 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3157 "label.overview_params", new String[]
3158 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3160 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3161 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3164 public void internalFrameClosed(
3165 javax.swing.event.InternalFrameEvent evt)
3167 alignPanel.setOverviewPanel(null);
3171 alignPanel.setOverviewPanel(overview);
3175 public void textColour_actionPerformed(ActionEvent e)
3177 new TextColourChooser().chooseColour(alignPanel, null);
3187 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3199 public void clustalColour_actionPerformed(ActionEvent e)
3201 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3202 viewport.getHiddenRepSequences()));
3212 public void zappoColour_actionPerformed(ActionEvent e)
3214 changeColour(new ZappoColourScheme());
3224 public void taylorColour_actionPerformed(ActionEvent e)
3226 changeColour(new TaylorColourScheme());
3236 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3238 changeColour(new HydrophobicColourScheme());
3248 public void helixColour_actionPerformed(ActionEvent e)
3250 changeColour(new HelixColourScheme());
3260 public void strandColour_actionPerformed(ActionEvent e)
3262 changeColour(new StrandColourScheme());
3272 public void turnColour_actionPerformed(ActionEvent e)
3274 changeColour(new TurnColourScheme());
3284 public void buriedColour_actionPerformed(ActionEvent e)
3286 changeColour(new BuriedColourScheme());
3296 public void nucleotideColour_actionPerformed(ActionEvent e)
3298 changeColour(new NucleotideColourScheme());
3302 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3304 changeColour(new PurinePyrimidineColourScheme());
3308 * public void covariationColour_actionPerformed(ActionEvent e) {
3310 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3314 public void annotationColour_actionPerformed(ActionEvent e)
3316 new AnnotationColourChooser(viewport, alignPanel);
3320 public void rnahelicesColour_actionPerformed(ActionEvent e)
3322 new RNAHelicesColourChooser(viewport, alignPanel);
3332 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3334 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3343 public void changeColour(ColourSchemeI cs)
3345 // TODO: compare with applet and pull up to model method
3350 if (viewport.getAbovePIDThreshold())
3352 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3354 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3358 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3361 if (viewport.getConservationSelected())
3364 Alignment al = (Alignment) viewport.getAlignment();
3365 Conservation c = new Conservation("All",
3366 ResidueProperties.propHash, 3, al.getSequences(), 0,
3370 c.verdict(false, viewport.getConsPercGaps());
3372 cs.setConservation(c);
3374 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3379 cs.setConservation(null);
3382 cs.setConsensus(viewport.getSequenceConsensusHash());
3385 viewport.setGlobalColourScheme(cs);
3387 if (viewport.getColourAppliesToAllGroups())
3390 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3398 if (cs instanceof ClustalxColourScheme)
3400 sg.cs = new ClustalxColourScheme(sg,
3401 viewport.getHiddenRepSequences());
3403 else if (cs instanceof UserColourScheme)
3405 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3411 sg.cs = cs.getClass().newInstance();
3412 } catch (Exception ex)
3417 if (viewport.getAbovePIDThreshold()
3418 || cs instanceof PIDColourScheme
3419 || cs instanceof Blosum62ColourScheme)
3421 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3423 sg.cs.setConsensus(AAFrequency.calculate(
3424 sg.getSequences(viewport.getHiddenRepSequences()),
3425 sg.getStartRes(), sg.getEndRes() + 1));
3429 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3432 if (viewport.getConservationSelected())
3434 Conservation c = new Conservation("Group",
3435 ResidueProperties.propHash, 3, sg.getSequences(viewport
3436 .getHiddenRepSequences()), sg.getStartRes(),
3437 sg.getEndRes() + 1);
3439 c.verdict(false, viewport.getConsPercGaps());
3440 sg.cs.setConservation(c);
3444 sg.cs.setConservation(null);
3449 if (alignPanel.getOverviewPanel() != null)
3451 alignPanel.getOverviewPanel().updateOverviewImage();
3454 alignPanel.paintAlignment(true);
3464 protected void modifyPID_actionPerformed(ActionEvent e)
3466 if (viewport.getAbovePIDThreshold()
3467 && viewport.getGlobalColourScheme() != null)
3469 SliderPanel.setPIDSliderSource(alignPanel,
3470 viewport.getGlobalColourScheme(), "Background");
3471 SliderPanel.showPIDSlider();
3482 protected void modifyConservation_actionPerformed(ActionEvent e)
3484 if (viewport.getConservationSelected()
3485 && viewport.getGlobalColourScheme() != null)
3487 SliderPanel.setConservationSlider(alignPanel,
3488 viewport.getGlobalColourScheme(), "Background");
3489 SliderPanel.showConservationSlider();
3500 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3502 viewport.setConservationSelected(conservationMenuItem.isSelected());
3504 viewport.setAbovePIDThreshold(false);
3505 abovePIDThreshold.setSelected(false);
3507 changeColour(viewport.getGlobalColourScheme());
3509 modifyConservation_actionPerformed(null);
3519 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3521 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3523 conservationMenuItem.setSelected(false);
3524 viewport.setConservationSelected(false);
3526 changeColour(viewport.getGlobalColourScheme());
3528 modifyPID_actionPerformed(null);
3538 public void userDefinedColour_actionPerformed(ActionEvent e)
3540 if (e.getActionCommand().equals(
3541 MessageManager.getString("action.user_defined")))
3543 new UserDefinedColours(alignPanel, null);
3547 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3548 .getUserColourSchemes().get(e.getActionCommand());
3554 public void updateUserColourMenu()
3557 Component[] menuItems = colourMenu.getMenuComponents();
3558 int i, iSize = menuItems.length;
3559 for (i = 0; i < iSize; i++)
3561 if (menuItems[i].getName() != null
3562 && menuItems[i].getName().equals("USER_DEFINED"))
3564 colourMenu.remove(menuItems[i]);
3568 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3570 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3571 .getUserColourSchemes().keys();
3573 while (userColours.hasMoreElements())
3575 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3576 userColours.nextElement().toString());
3577 radioItem.setName("USER_DEFINED");
3578 radioItem.addMouseListener(new MouseAdapter()
3581 public void mousePressed(MouseEvent evt)
3583 if (evt.isControlDown()
3584 || SwingUtilities.isRightMouseButton(evt))
3586 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3588 int option = JOptionPane.showInternalConfirmDialog(
3589 jalview.gui.Desktop.desktop,
3591 .getString("label.remove_from_default_list"),
3593 .getString("label.remove_user_defined_colour"),
3594 JOptionPane.YES_NO_OPTION);
3595 if (option == JOptionPane.YES_OPTION)
3597 jalview.gui.UserDefinedColours
3598 .removeColourFromDefaults(radioItem.getText());
3599 colourMenu.remove(radioItem);
3603 radioItem.addActionListener(new ActionListener()
3606 public void actionPerformed(ActionEvent evt)
3608 userDefinedColour_actionPerformed(evt);
3615 radioItem.addActionListener(new ActionListener()
3618 public void actionPerformed(ActionEvent evt)
3620 userDefinedColour_actionPerformed(evt);
3624 colourMenu.insert(radioItem, 15);
3625 colours.add(radioItem);
3637 public void PIDColour_actionPerformed(ActionEvent e)
3639 changeColour(new PIDColourScheme());
3649 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3651 changeColour(new Blosum62ColourScheme());
3661 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3663 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3664 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3665 .getAlignment().getSequenceAt(0), null);
3666 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3667 viewport.getAlignment()));
3668 alignPanel.paintAlignment(true);
3678 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3680 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3681 AlignmentSorter.sortByID(viewport.getAlignment());
3682 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3683 viewport.getAlignment()));
3684 alignPanel.paintAlignment(true);
3694 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3696 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3697 AlignmentSorter.sortByLength(viewport.getAlignment());
3698 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3699 viewport.getAlignment()));
3700 alignPanel.paintAlignment(true);
3710 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3712 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3713 AlignmentSorter.sortByGroup(viewport.getAlignment());
3714 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3715 viewport.getAlignment()));
3717 alignPanel.paintAlignment(true);
3727 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3729 new RedundancyPanel(alignPanel, this);
3739 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3741 if ((viewport.getSelectionGroup() == null)
3742 || (viewport.getSelectionGroup().getSize() < 2))
3744 JOptionPane.showInternalMessageDialog(this, MessageManager
3745 .getString("label.you_must_select_least_two_sequences"),
3746 MessageManager.getString("label.invalid_selection"),
3747 JOptionPane.WARNING_MESSAGE);
3751 JInternalFrame frame = new JInternalFrame();
3752 frame.setContentPane(new PairwiseAlignPanel(viewport));
3753 Desktop.addInternalFrame(frame,
3754 MessageManager.getString("action.pairwise_alignment"), 600,
3766 public void PCAMenuItem_actionPerformed(ActionEvent e)
3768 if (((viewport.getSelectionGroup() != null)
3769 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3770 .getSelectionGroup().getSize() > 0))
3771 || (viewport.getAlignment().getHeight() < 4))
3774 .showInternalMessageDialog(
3777 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3779 .getString("label.sequence_selection_insufficient"),
3780 JOptionPane.WARNING_MESSAGE);
3785 new PCAPanel(alignPanel);
3789 public void autoCalculate_actionPerformed(ActionEvent e)
3791 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3792 if (viewport.autoCalculateConsensus)
3794 viewport.firePropertyChange("alignment", null, viewport
3795 .getAlignment().getSequences());
3800 public void sortByTreeOption_actionPerformed(ActionEvent e)
3802 viewport.sortByTree = sortByTree.isSelected();
3806 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3808 viewport.followSelection = listenToViewSelections.isSelected();
3818 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3820 NewTreePanel("AV", "PID", "Average distance tree using PID");
3830 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3832 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3842 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3844 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3854 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3856 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3869 void NewTreePanel(String type, String pwType, String title)
3873 if (viewport.getSelectionGroup() != null
3874 && viewport.getSelectionGroup().getSize() > 0)
3876 if (viewport.getSelectionGroup().getSize() < 3)
3882 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3884 .getString("label.not_enough_sequences"),
3885 JOptionPane.WARNING_MESSAGE);
3889 SequenceGroup sg = viewport.getSelectionGroup();
3891 /* Decide if the selection is a column region */
3892 for (SequenceI _s : sg.getSequences())
3894 if (_s.getLength() < sg.getEndRes())
3900 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3902 .getString("label.sequences_selection_not_aligned"),
3903 JOptionPane.WARNING_MESSAGE);
3909 title = title + " on region";
3910 tp = new TreePanel(alignPanel, type, pwType);
3914 // are the visible sequences aligned?
3915 if (!viewport.getAlignment().isAligned(false))
3921 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3923 .getString("label.sequences_not_aligned"),
3924 JOptionPane.WARNING_MESSAGE);
3929 if (viewport.getAlignment().getHeight() < 2)
3934 tp = new TreePanel(alignPanel, type, pwType);
3939 if (viewport.viewName != null)
3941 title += viewport.viewName + " of ";
3944 title += this.title;
3946 Desktop.addInternalFrame(tp, title, 600, 500);
3957 public void addSortByOrderMenuItem(String title,
3958 final AlignmentOrder order)
3960 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
3962 item.addActionListener(new java.awt.event.ActionListener()
3965 public void actionPerformed(ActionEvent e)
3967 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3969 // TODO: JBPNote - have to map order entries to curent SequenceI
3971 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3973 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3976 alignPanel.paintAlignment(true);
3982 * Add a new sort by annotation score menu item
3985 * the menu to add the option to
3987 * the label used to retrieve scores for each sequence on the
3990 public void addSortByAnnotScoreMenuItem(JMenu sort,
3991 final String scoreLabel)
3993 final JMenuItem item = new JMenuItem(scoreLabel);
3995 item.addActionListener(new java.awt.event.ActionListener()
3998 public void actionPerformed(ActionEvent e)
4000 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4001 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4002 viewport.getAlignment());// ,viewport.getSelectionGroup());
4003 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4004 viewport.getAlignment()));
4005 alignPanel.paintAlignment(true);
4011 * last hash for alignment's annotation array - used to minimise cost of
4014 protected int _annotationScoreVectorHash;
4017 * search the alignment and rebuild the sort by annotation score submenu the
4018 * last alignment annotation vector hash is stored to minimize cost of
4019 * rebuilding in subsequence calls.
4023 public void buildSortByAnnotationScoresMenu()
4025 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4030 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4032 sortByAnnotScore.removeAll();
4033 // almost certainly a quicker way to do this - but we keep it simple
4034 Hashtable scoreSorts = new Hashtable();
4035 AlignmentAnnotation aann[];
4036 for (SequenceI sqa : viewport.getAlignment().getSequences())
4038 aann = sqa.getAnnotation();
4039 for (int i = 0; aann != null && i < aann.length; i++)
4041 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4043 scoreSorts.put(aann[i].label, aann[i].label);
4047 Enumeration labels = scoreSorts.keys();
4048 while (labels.hasMoreElements())
4050 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4051 (String) labels.nextElement());
4053 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4056 _annotationScoreVectorHash = viewport.getAlignment()
4057 .getAlignmentAnnotation().hashCode();
4062 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4063 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4064 * call. Listeners are added to remove the menu item when the treePanel is
4065 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4069 * Displayed tree window.
4071 * SortBy menu item title.
4074 public void buildTreeMenu()
4076 calculateTree.removeAll();
4077 // build the calculate menu
4079 for (final String type : new String[]
4082 String treecalcnm = MessageManager.getString("label.tree_calc_"
4083 + type.toLowerCase());
4084 for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4086 JMenuItem tm = new JMenuItem();
4087 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4088 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4090 String smn = MessageManager.getStringOrReturn(
4091 "label.score_model_", sm.getName());
4092 final String title = MessageManager.formatMessage(
4093 "label.treecalc_title", treecalcnm, smn);
4094 tm.setText(title);//
4095 tm.addActionListener(new java.awt.event.ActionListener()
4098 public void actionPerformed(ActionEvent e)
4100 NewTreePanel(type, (String) pwtype, title);
4103 calculateTree.add(tm);
4108 sortByTreeMenu.removeAll();
4110 Vector comps = (Vector) PaintRefresher.components.get(viewport
4111 .getSequenceSetId());
4112 Vector treePanels = new Vector();
4113 int i, iSize = comps.size();
4114 for (i = 0; i < iSize; i++)
4116 if (comps.elementAt(i) instanceof TreePanel)
4118 treePanels.add(comps.elementAt(i));
4122 iSize = treePanels.size();
4126 sortByTreeMenu.setVisible(false);
4130 sortByTreeMenu.setVisible(true);
4132 for (i = 0; i < treePanels.size(); i++)
4134 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4135 final JMenuItem item = new JMenuItem(tp.getTitle());
4136 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4137 item.addActionListener(new java.awt.event.ActionListener()
4140 public void actionPerformed(ActionEvent e)
4142 tp.sortByTree_actionPerformed(null);
4143 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4148 sortByTreeMenu.add(item);
4152 public boolean sortBy(AlignmentOrder alorder, String undoname)
4154 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4155 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4156 if (undoname != null)
4158 addHistoryItem(new OrderCommand(undoname, oldOrder,
4159 viewport.getAlignment()));
4161 alignPanel.paintAlignment(true);
4166 * Work out whether the whole set of sequences or just the selected set will
4167 * be submitted for multiple alignment.
4170 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4172 // Now, check we have enough sequences
4173 AlignmentView msa = null;
4175 if ((viewport.getSelectionGroup() != null)
4176 && (viewport.getSelectionGroup().getSize() > 1))
4178 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4179 // some common interface!
4181 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4182 * SequenceI[sz = seqs.getSize(false)];
4184 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4185 * seqs.getSequenceAt(i); }
4187 msa = viewport.getAlignmentView(true);
4192 * Vector seqs = viewport.getAlignment().getSequences();
4194 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
4196 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
4197 * seqs.elementAt(i); } }
4199 msa = viewport.getAlignmentView(false);
4205 * Decides what is submitted to a secondary structure prediction service: the
4206 * first sequence in the alignment, or in the current selection, or, if the
4207 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4208 * region or the whole alignment. (where the first sequence in the set is the
4209 * one that the prediction will be for).
4211 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4213 AlignmentView seqs = null;
4215 if ((viewport.getSelectionGroup() != null)
4216 && (viewport.getSelectionGroup().getSize() > 0))
4218 seqs = viewport.getAlignmentView(true);
4222 seqs = viewport.getAlignmentView(false);
4224 // limit sequences - JBPNote in future - could spawn multiple prediction
4226 // TODO: viewport.getAlignment().isAligned is a global state - the local
4227 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4228 if (!viewport.getAlignment().isAligned(false))
4230 seqs.setSequences(new SeqCigar[]
4231 { seqs.getSequences()[0] });
4232 // TODO: if seqs.getSequences().length>1 then should really have warned
4246 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4248 // Pick the tree file
4249 JalviewFileChooser chooser = new JalviewFileChooser(
4250 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4251 chooser.setFileView(new JalviewFileView());
4252 chooser.setDialogTitle(MessageManager
4253 .getString("label.select_newick_like_tree_file"));
4254 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4256 int value = chooser.showOpenDialog(null);
4258 if (value == JalviewFileChooser.APPROVE_OPTION)
4260 String choice = chooser.getSelectedFile().getPath();
4261 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4262 jalview.io.NewickFile fin = null;
4265 fin = new jalview.io.NewickFile(choice, "File");
4266 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4267 } catch (Exception ex)
4274 .getString("label.problem_reading_tree_file"),
4275 JOptionPane.WARNING_MESSAGE);
4276 ex.printStackTrace();
4278 if (fin != null && fin.hasWarningMessage())
4280 JOptionPane.showMessageDialog(Desktop.desktop, fin
4281 .getWarningMessage(), MessageManager
4282 .getString("label.possible_problem_with_tree_file"),
4283 JOptionPane.WARNING_MESSAGE);
4289 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4291 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4294 public TreePanel ShowNewickTree(NewickFile nf, String title)
4296 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4299 public TreePanel ShowNewickTree(NewickFile nf, String title,
4300 AlignmentView input)
4302 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4305 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4306 int h, int x, int y)
4308 return ShowNewickTree(nf, title, null, w, h, x, y);
4312 * Add a treeviewer for the tree extracted from a newick file object to the
4313 * current alignment view
4320 * Associated alignment input data (or null)
4329 * @return TreePanel handle
4331 public TreePanel ShowNewickTree(NewickFile nf, String title,
4332 AlignmentView input, int w, int h, int x, int y)
4334 TreePanel tp = null;
4340 if (nf.getTree() != null)
4342 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4348 tp.setLocation(x, y);
4351 Desktop.addInternalFrame(tp, title, w, h);
4353 } catch (Exception ex)
4355 ex.printStackTrace();
4361 private boolean buildingMenu = false;
4364 * Generates menu items and listener event actions for web service clients
4367 public void BuildWebServiceMenu()
4369 while (buildingMenu)
4373 System.err.println("Waiting for building menu to finish.");
4375 } catch (Exception e)
4380 final AlignFrame me = this;
4381 buildingMenu = true;
4382 new Thread(new Runnable()
4387 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4390 System.err.println("Building ws menu again "
4391 + Thread.currentThread());
4392 // TODO: add support for context dependent disabling of services based
4394 // alignment and current selection
4395 // TODO: add additional serviceHandle parameter to specify abstract
4397 // class independently of AbstractName
4398 // TODO: add in rediscovery GUI function to restart discoverer
4399 // TODO: group services by location as well as function and/or
4401 // object broker mechanism.
4402 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4403 final IProgressIndicator af = me;
4404 final JMenu msawsmenu = new JMenu("Alignment");
4405 final JMenu secstrmenu = new JMenu(
4406 "Secondary Structure Prediction");
4407 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4408 final JMenu analymenu = new JMenu("Analysis");
4409 final JMenu dismenu = new JMenu("Protein Disorder");
4410 // final JMenu msawsmenu = new
4411 // JMenu(MessageManager.getString("label.alignment"));
4412 // final JMenu secstrmenu = new
4413 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4414 // final JMenu seqsrchmenu = new
4415 // JMenu(MessageManager.getString("label.sequence_database_search"));
4416 // final JMenu analymenu = new
4417 // JMenu(MessageManager.getString("label.analysis"));
4418 // final JMenu dismenu = new
4419 // JMenu(MessageManager.getString("label.protein_disorder"));
4420 // JAL-940 - only show secondary structure prediction services from
4421 // the legacy server
4422 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4424 Discoverer.services != null && (Discoverer.services.size() > 0))
4426 // TODO: refactor to allow list of AbstractName/Handler bindings to
4428 // stored or retrieved from elsewhere
4429 // No MSAWS used any more:
4430 // Vector msaws = null; // (Vector)
4431 // Discoverer.services.get("MsaWS");
4432 Vector secstrpr = (Vector) Discoverer.services
4434 if (secstrpr != null)
4436 // Add any secondary structure prediction services
4437 for (int i = 0, j = secstrpr.size(); i < j; i++)
4439 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4441 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4442 .getServiceClient(sh);
4443 int p = secstrmenu.getItemCount();
4444 impl.attachWSMenuEntry(secstrmenu, me);
4445 int q = secstrmenu.getItemCount();
4446 for (int litm = p; litm < q; litm++)
4448 legacyItems.add(secstrmenu.getItem(litm));
4454 // Add all submenus in the order they should appear on the web
4456 wsmenu.add(msawsmenu);
4457 wsmenu.add(secstrmenu);
4458 wsmenu.add(dismenu);
4459 wsmenu.add(analymenu);
4460 // No search services yet
4461 // wsmenu.add(seqsrchmenu);
4463 javax.swing.SwingUtilities.invokeLater(new Runnable()
4470 webService.removeAll();
4471 // first, add discovered services onto the webservices menu
4472 if (wsmenu.size() > 0)
4474 for (int i = 0, j = wsmenu.size(); i < j; i++)
4476 webService.add(wsmenu.get(i));
4481 webService.add(me.webServiceNoServices);
4483 // TODO: move into separate menu builder class.
4484 boolean new_sspred = false;
4485 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4487 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4488 if (jws2servs != null)
4490 if (jws2servs.hasServices())
4492 jws2servs.attachWSMenuEntry(webService, me);
4493 for (Jws2Instance sv : jws2servs.getServices())
4495 if (sv.description.toLowerCase().contains("jpred"))
4497 for (JMenuItem jmi : legacyItems)
4499 jmi.setVisible(false);
4505 if (jws2servs.isRunning())
4507 JMenuItem tm = new JMenuItem(
4508 "Still discovering JABA Services");
4509 tm.setEnabled(false);
4514 build_urlServiceMenu(me.webService);
4515 build_fetchdbmenu(webService);
4516 for (JMenu item : wsmenu)
4518 if (item.getItemCount() == 0)
4520 item.setEnabled(false);
4524 item.setEnabled(true);
4527 } catch (Exception e)
4530 .debug("Exception during web service menu building process.",
4536 } catch (Exception e)
4541 buildingMenu = false;
4548 * construct any groupURL type service menu entries.
4552 private void build_urlServiceMenu(JMenu webService)
4554 // TODO: remove this code when 2.7 is released
4555 // DEBUG - alignmentView
4557 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4558 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4560 * @Override public void actionPerformed(ActionEvent e) {
4561 * jalview.datamodel.AlignmentView
4562 * .testSelectionViews(af.viewport.getAlignment(),
4563 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4565 * }); webService.add(testAlView);
4567 // TODO: refactor to RestClient discoverer and merge menu entries for
4568 // rest-style services with other types of analysis/calculation service
4569 // SHmmr test client - still being implemented.
4570 // DEBUG - alignmentView
4572 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4575 client.attachWSMenuEntry(
4576 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4582 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4583 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4584 * getProperty("LAST_DIRECTORY"));
4586 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4587 * to Vamsas file"); chooser.setToolTipText("Export");
4589 * int value = chooser.showSaveDialog(this);
4591 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4592 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4593 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4594 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4597 * prototype of an automatically enabled/disabled analysis function
4600 protected void setShowProductsEnabled()
4602 SequenceI[] selection = viewport.getSequenceSelection();
4603 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4604 viewport.getAlignment().getDataset()))
4606 showProducts.setEnabled(true);
4611 showProducts.setEnabled(false);
4616 * search selection for sequence xRef products and build the show products
4621 * @return true if showProducts menu should be enabled.
4623 public boolean canShowProducts(SequenceI[] selection,
4624 boolean isRegionSelection, Alignment dataset)
4626 boolean showp = false;
4629 showProducts.removeAll();
4630 final boolean dna = viewport.getAlignment().isNucleotide();
4631 final Alignment ds = dataset;
4632 String[] ptypes = (selection == null || selection.length == 0) ? null
4633 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4635 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4636 // selection, dataset, true);
4637 final SequenceI[] sel = selection;
4638 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4641 final boolean isRegSel = isRegionSelection;
4642 final AlignFrame af = this;
4643 final String source = ptypes[t];
4644 JMenuItem xtype = new JMenuItem(ptypes[t]);
4645 xtype.addActionListener(new ActionListener()
4649 public void actionPerformed(ActionEvent e)
4651 // TODO: new thread for this call with vis-delay
4652 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4653 isRegSel, dna, source);
4657 showProducts.add(xtype);
4659 showProducts.setVisible(showp);
4660 showProducts.setEnabled(showp);
4661 } catch (Exception e)
4663 jalview.bin.Cache.log
4664 .warn("canTranslate threw an exception - please report to help@jalview.org",
4671 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4672 boolean isRegSel, boolean dna, String source)
4674 final boolean fisRegSel = isRegSel;
4675 final boolean fdna = dna;
4676 final String fsrc = source;
4677 final AlignFrame ths = this;
4678 final SequenceI[] fsel = sel;
4679 Runnable foo = new Runnable()
4685 final long sttime = System.currentTimeMillis();
4686 ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
4689 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4693 Alignment prods = CrossRef
4694 .findXrefSequences(fsel, fdna, fsrc, ds);
4697 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4698 for (int s = 0; s < sprods.length; s++)
4700 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4701 if (ds.getSequences() == null
4702 || !ds.getSequences().contains(
4703 sprods[s].getDatasetSequence()))
4705 ds.addSequence(sprods[s].getDatasetSequence());
4707 sprods[s].updatePDBIds();
4709 Alignment al = new Alignment(sprods);
4710 AlignedCodonFrame[] cf = prods.getCodonFrames();
4712 for (int s = 0; cf != null && s < cf.length; s++)
4714 al.addCodonFrame(cf[s]);
4717 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4719 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4720 + " for " + ((fisRegSel) ? "selected region of " : "")
4722 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4727 System.err.println("No Sequences generated for xRef type "
4730 } catch (Exception e)
4732 jalview.bin.Cache.log.error(
4733 "Exception when finding crossreferences", e);
4734 } catch (OutOfMemoryError e)
4736 new OOMWarning("whilst fetching crossreferences", e);
4739 jalview.bin.Cache.log.error("Error when finding crossreferences",
4742 ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
4747 Thread frunner = new Thread(foo);
4751 public boolean canShowTranslationProducts(SequenceI[] selection,
4752 AlignmentI alignment)
4757 return (jalview.analysis.Dna.canTranslate(selection,
4758 viewport.getViewAsVisibleContigs(true)));
4759 } catch (Exception e)
4761 jalview.bin.Cache.log
4762 .warn("canTranslate threw an exception - please report to help@jalview.org",
4769 public void showProducts_actionPerformed(ActionEvent e)
4771 // /////////////////////////////
4772 // Collect Data to be translated/transferred
4774 SequenceI[] selection = viewport.getSequenceSelection();
4775 AlignmentI al = null;
4778 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4779 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4780 viewport.getAlignment().getDataset());
4781 } catch (Exception ex)
4784 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4792 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4793 MessageManager.getString("label.translation_failed"),
4794 JOptionPane.WARNING_MESSAGE);
4798 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4799 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4800 "label.translation_of_params", new String[]
4801 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4806 public void showTranslation_actionPerformed(ActionEvent e)
4808 // /////////////////////////////
4809 // Collect Data to be translated/transferred
4811 SequenceI[] selection = viewport.getSequenceSelection();
4812 String[] seqstring = viewport.getViewAsString(true);
4813 AlignmentI al = null;
4816 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4817 viewport.getViewAsVisibleContigs(true), viewport
4818 .getGapCharacter(), viewport.getAlignment()
4819 .getAlignmentAnnotation(), viewport.getAlignment()
4820 .getWidth(), viewport.getAlignment().getDataset());
4821 } catch (Exception ex)
4824 jalview.bin.Cache.log.error(
4825 "Exception during translation. Please report this !", ex);
4830 .getString("label.error_when_translating_sequences_submit_bug_report"),
4832 .getString("label.implementation_error")
4834 .getString("translation_failed"),
4835 JOptionPane.ERROR_MESSAGE);
4844 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4845 MessageManager.getString("label.translation_failed"),
4846 JOptionPane.WARNING_MESSAGE);
4850 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4851 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4852 "label.translation_of_params", new String[]
4853 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4858 * Try to load a features file onto the alignment.
4861 * contents or path to retrieve file
4863 * access mode of file (see jalview.io.AlignFile)
4864 * @return true if features file was parsed corectly.
4866 public boolean parseFeaturesFile(String file, String type)
4868 boolean featuresFile = false;
4871 featuresFile = new FeaturesFile(file, type).parse(viewport
4872 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4873 .getFeatureRenderer().featureColours, false,
4874 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4875 } catch (Exception ex)
4877 ex.printStackTrace();
4882 viewport.showSequenceFeatures = true;
4883 showSeqFeatures.setSelected(true);
4884 if (alignPanel.seqPanel.seqCanvas.fr != null)
4886 // update the min/max ranges where necessary
4887 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4889 if (featureSettings != null)
4891 featureSettings.setTableData();
4893 alignPanel.paintAlignment(true);
4896 return featuresFile;
4900 public void dragEnter(DropTargetDragEvent evt)
4905 public void dragExit(DropTargetEvent evt)
4910 public void dragOver(DropTargetDragEvent evt)
4915 public void dropActionChanged(DropTargetDragEvent evt)
4920 public void drop(DropTargetDropEvent evt)
4922 Transferable t = evt.getTransferable();
4923 java.util.List files = null;
4927 DataFlavor uriListFlavor = new DataFlavor(
4928 "text/uri-list;class=java.lang.String");
4929 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4931 // Works on Windows and MacOSX
4932 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4933 files = (java.util.List) t
4934 .getTransferData(DataFlavor.javaFileListFlavor);
4936 else if (t.isDataFlavorSupported(uriListFlavor))
4938 // This is used by Unix drag system
4939 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4940 String data = (String) t.getTransferData(uriListFlavor);
4941 files = new java.util.ArrayList(1);
4942 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4943 data, "\r\n"); st.hasMoreTokens();)
4945 String s = st.nextToken();
4946 if (s.startsWith("#"))
4948 // the line is a comment (as per the RFC 2483)
4952 java.net.URI uri = new java.net.URI(s);
4953 // check to see if we can handle this kind of URI
4954 if (uri.getScheme().toLowerCase().startsWith("http"))
4956 files.add(uri.toString());
4960 // otherwise preserve old behaviour: catch all for file objects
4961 java.io.File file = new java.io.File(uri);
4962 files.add(file.toString());
4966 } catch (Exception e)
4968 e.printStackTrace();
4974 // check to see if any of these files have names matching sequences in
4976 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4977 .getAlignment().getSequencesArray());
4979 * Object[] { String,SequenceI}
4981 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4982 ArrayList<String> filesnotmatched = new ArrayList<String>();
4983 for (int i = 0; i < files.size(); i++)
4985 String file = files.get(i).toString();
4987 String protocol = FormatAdapter.checkProtocol(file);
4988 if (protocol == jalview.io.FormatAdapter.FILE)
4990 File fl = new File(file);
4991 pdbfn = fl.getName();
4993 else if (protocol == jalview.io.FormatAdapter.URL)
4995 URL url = new URL(file);
4996 pdbfn = url.getFile();
4998 if (pdbfn.length() > 0)
5000 // attempt to find a match in the alignment
5001 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5002 int l = 0, c = pdbfn.indexOf(".");
5003 while (mtch == null && c != -1)
5008 } while ((c = pdbfn.indexOf(".", l)) > l);
5011 pdbfn = pdbfn.substring(0, l);
5013 mtch = idm.findAllIdMatches(pdbfn);
5020 type = new IdentifyFile().Identify(file, protocol);
5021 } catch (Exception ex)
5027 if (type.equalsIgnoreCase("PDB"))
5029 filesmatched.add(new Object[]
5030 { file, protocol, mtch });
5035 // File wasn't named like one of the sequences or wasn't a PDB file.
5036 filesnotmatched.add(file);
5040 if (filesmatched.size() > 0)
5042 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5048 "label.automatically_associate_pdb_files_with_sequences_same_name",
5055 .getString("label.automatically_associate_pdb_files_by_name"),
5056 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5059 for (Object[] fm : filesmatched)
5061 // try and associate
5062 // TODO: may want to set a standard ID naming formalism for
5063 // associating PDB files which have no IDs.
5064 for (SequenceI toassoc : (SequenceI[]) fm[2])
5066 PDBEntry pe = new AssociatePdbFileWithSeq()
5067 .associatePdbWithSeq((String) fm[0],
5068 (String) fm[1], toassoc, false,
5072 System.err.println("Associated file : "
5073 + ((String) fm[0]) + " with "
5074 + toassoc.getDisplayId(true));
5078 alignPanel.paintAlignment(true);
5082 if (filesnotmatched.size() > 0)
5085 && (Cache.getDefault(
5086 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5089 "<html>"+MessageManager
5091 "label.ignore_unmatched_dropped_files_info",
5096 .toString() })+"</html>",
5098 .getString("label.ignore_unmatched_dropped_files"),
5099 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5103 for (String fn : filesnotmatched)
5105 loadJalviewDataFile(fn, null, null, null);
5109 } catch (Exception ex)
5111 ex.printStackTrace();
5117 * Attempt to load a "dropped" file or URL string: First by testing whether
5118 * it's and Annotation file, then a JNet file, and finally a features file. If
5119 * all are false then the user may have dropped an alignment file onto this
5123 * either a filename or a URL string.
5125 public void loadJalviewDataFile(String file, String protocol,
5126 String format, SequenceI assocSeq)
5130 if (protocol == null)
5132 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5134 // if the file isn't identified, or not positively identified as some
5135 // other filetype (PFAM is default unidentified alignment file type) then
5136 // try to parse as annotation.
5137 boolean isAnnotation = (format == null || format
5138 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5139 .readAnnotationFile(viewport.getAlignment(), file, protocol)
5144 // first see if its a T-COFFEE score file
5145 TCoffeeScoreFile tcf = null;
5148 tcf = new TCoffeeScoreFile(file, protocol);
5151 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5153 tcoffeeColour.setEnabled(true);
5154 tcoffeeColour.setSelected(true);
5155 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5156 isAnnotation = true;
5158 .setText(MessageManager
5159 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5163 // some problem - if no warning its probable that the ID matching
5164 // process didn't work
5168 tcf.getWarningMessage() == null ? MessageManager
5169 .getString("label.check_file_matches_sequence_ids_alignment")
5170 : tcf.getWarningMessage(),
5172 .getString("label.problem_reading_tcoffee_score_file"),
5173 JOptionPane.WARNING_MESSAGE);
5180 } catch (Exception x)
5183 .debug("Exception when processing data source as T-COFFEE score file",
5189 // try to see if its a JNet 'concise' style annotation file *before*
5191 // try to parse it as a features file
5194 format = new IdentifyFile().Identify(file, protocol);
5196 if (format.equalsIgnoreCase("JnetFile"))
5198 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5200 new JnetAnnotationMaker().add_annotation(predictions,
5201 viewport.getAlignment(), 0, false);
5202 isAnnotation = true;
5207 * if (format.equalsIgnoreCase("PDB")) {
5209 * String pdbfn = ""; // try to match up filename with sequence id
5210 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5211 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5212 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5213 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5214 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5215 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5216 * // attempt to find a match in the alignment SequenceI mtch =
5217 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5218 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5219 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5220 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5221 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5222 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5223 * { System.err.println("Associated file : " + file + " with " +
5224 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5225 * TODO: maybe need to load as normal otherwise return; } }
5227 // try to parse it as a features file
5228 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5229 // if it wasn't a features file then we just treat it as a general
5230 // alignment file to load into the current view.
5233 new FileLoader().LoadFile(viewport, file, protocol, format);
5237 alignPanel.paintAlignment(true);
5245 alignPanel.adjustAnnotationHeight();
5246 viewport.updateSequenceIdColours();
5247 buildSortByAnnotationScoresMenu();
5248 alignPanel.paintAlignment(true);
5250 } catch (Exception ex)
5252 ex.printStackTrace();
5253 } catch (OutOfMemoryError oom)
5258 } catch (Exception x)
5264 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5265 : "using " + protocol + " from " + file)
5267 + (format != null ? "(parsing as '" + format
5268 + "' file)" : ""), oom, Desktop.desktop);
5273 public void tabSelectionChanged(int index)
5277 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5278 viewport = alignPanel.av;
5279 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5280 setMenusFromViewport(viewport);
5285 public void tabbedPane_mousePressed(MouseEvent e)
5287 if (SwingUtilities.isRightMouseButton(e))
5289 String reply = JOptionPane.showInternalInputDialog(this,
5290 MessageManager.getString("label.enter_view_name"),
5291 MessageManager.getString("label.enter_view_name"),
5292 JOptionPane.QUESTION_MESSAGE);
5296 viewport.viewName = reply;
5297 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5302 public AlignViewport getCurrentView()
5308 * Open the dialog for regex description parsing.
5311 protected void extractScores_actionPerformed(ActionEvent e)
5313 ParseProperties pp = new jalview.analysis.ParseProperties(
5314 viewport.getAlignment());
5315 // TODO: verify regex and introduce GUI dialog for version 2.5
5316 // if (pp.getScoresFromDescription("col", "score column ",
5317 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5319 if (pp.getScoresFromDescription("description column",
5320 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5322 buildSortByAnnotationScoresMenu();
5330 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5334 protected void showDbRefs_actionPerformed(ActionEvent e)
5336 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5342 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5346 protected void showNpFeats_actionPerformed(ActionEvent e)
5348 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5352 * find the viewport amongst the tabs in this alignment frame and close that
5357 public boolean closeView(AlignViewport av)
5361 this.closeMenuItem_actionPerformed(false);
5364 Component[] comp = tabbedPane.getComponents();
5365 for (int i = 0; comp != null && i < comp.length; i++)
5367 if (comp[i] instanceof AlignmentPanel)
5369 if (((AlignmentPanel) comp[i]).av == av)
5372 closeView((AlignmentPanel) comp[i]);
5380 protected void build_fetchdbmenu(JMenu webService)
5382 // Temporary hack - DBRef Fetcher always top level ws entry.
5383 // TODO We probably want to store a sequence database checklist in
5384 // preferences and have checkboxes.. rather than individual sources selected
5386 final JMenu rfetch = new JMenu(
5387 MessageManager.getString("action.fetch_db_references"));
5388 rfetch.setToolTipText(MessageManager
5389 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5390 webService.add(rfetch);
5392 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5393 MessageManager.getString("option.trim_retrieved_seqs"));
5394 trimrs.setToolTipText(MessageManager
5395 .getString("label.trim_retrieved_sequences"));
5396 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5397 trimrs.addActionListener(new ActionListener()
5400 public void actionPerformed(ActionEvent e)
5402 trimrs.setSelected(trimrs.isSelected());
5403 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5404 Boolean.valueOf(trimrs.isSelected()).toString());
5408 JMenuItem fetchr = new JMenuItem(
5409 MessageManager.getString("label.standard_databases"));
5410 fetchr.setToolTipText(MessageManager
5411 .getString("label.fetch_embl_uniprot"));
5412 fetchr.addActionListener(new ActionListener()
5416 public void actionPerformed(ActionEvent e)
5418 new Thread(new Runnable()
5424 new jalview.ws.DBRefFetcher(alignPanel.av
5425 .getSequenceSelection(), alignPanel.alignFrame)
5426 .fetchDBRefs(false);
5434 final AlignFrame me = this;
5435 new Thread(new Runnable()
5440 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5441 .getSequenceFetcherSingleton(me);
5442 javax.swing.SwingUtilities.invokeLater(new Runnable()
5447 String[] dbclasses = sf.getOrderedSupportedSources();
5448 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5449 // jalview.util.QuickSort.sort(otherdb, otherdb);
5450 List<DbSourceProxy> otherdb;
5451 JMenu dfetch = new JMenu();
5452 JMenu ifetch = new JMenu();
5453 JMenuItem fetchr = null;
5454 int comp = 0, icomp = 0, mcomp = 15;
5455 String mname = null;
5457 for (String dbclass : dbclasses)
5459 otherdb = sf.getSourceProxy(dbclass);
5460 // add a single entry for this class, or submenu allowing 'fetch
5462 if (otherdb == null || otherdb.size() < 1)
5466 // List<DbSourceProxy> dbs=otherdb;
5467 // otherdb=new ArrayList<DbSourceProxy>();
5468 // for (DbSourceProxy db:dbs)
5470 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5474 mname = "From " + dbclass;
5476 if (otherdb.size() == 1)
5478 final DbSourceProxy[] dassource = otherdb
5479 .toArray(new DbSourceProxy[0]);
5480 DbSourceProxy src = otherdb.get(0);
5481 fetchr = new JMenuItem(src.getDbSource());
5482 fetchr.addActionListener(new ActionListener()
5486 public void actionPerformed(ActionEvent e)
5488 new Thread(new Runnable()
5494 new jalview.ws.DBRefFetcher(alignPanel.av
5495 .getSequenceSelection(),
5496 alignPanel.alignFrame, dassource)
5497 .fetchDBRefs(false);
5503 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
5509 final DbSourceProxy[] dassource = otherdb
5510 .toArray(new DbSourceProxy[0]);
5512 DbSourceProxy src = otherdb.get(0);
5513 fetchr = new JMenuItem(MessageManager.formatMessage(
5514 "label.fetch_all_param", new String[]
5515 { src.getDbSource() }));
5516 fetchr.addActionListener(new ActionListener()
5519 public void actionPerformed(ActionEvent e)
5521 new Thread(new Runnable()
5527 new jalview.ws.DBRefFetcher(alignPanel.av
5528 .getSequenceSelection(),
5529 alignPanel.alignFrame, dassource)
5530 .fetchDBRefs(false);
5536 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5539 // and then build the rest of the individual menus
5540 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
5542 String imname = null;
5544 for (DbSourceProxy sproxy : otherdb)
5546 String dbname = sproxy.getDbName();
5547 String sname = dbname.length() > 5 ? dbname.substring(0,
5548 5) + "..." : dbname;
5549 String msname = dbname.length() > 10 ? dbname.substring(
5550 0, 10) + "..." : dbname;
5553 imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
5555 fetchr = new JMenuItem(msname);
5556 final DbSourceProxy[] dassrc =
5558 fetchr.addActionListener(new ActionListener()
5562 public void actionPerformed(ActionEvent e)
5564 new Thread(new Runnable()
5570 new jalview.ws.DBRefFetcher(alignPanel.av
5571 .getSequenceSelection(),
5572 alignPanel.alignFrame, dassrc)
5573 .fetchDBRefs(false);
5579 fetchr.setToolTipText("<html>"
5580 + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
5583 if (++icomp >= mcomp || i == (otherdb.size()))
5585 ifetch.setText(MessageManager.formatMessage(
5586 "label.source_to_target", imname, sname));
5588 ifetch = new JMenu();
5596 if (comp >= mcomp || dbi >= (dbclasses.length))
5598 dfetch.setText(MessageManager.formatMessage(
5599 "label.source_to_target", mname, dbclass));
5601 dfetch = new JMenu();
5614 * Left justify the whole alignment.
5617 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5619 AlignmentI al = viewport.getAlignment();
5621 viewport.firePropertyChange("alignment", null, al);
5625 * Right justify the whole alignment.
5628 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5630 AlignmentI al = viewport.getAlignment();
5632 viewport.firePropertyChange("alignment", null, al);
5635 public void setShowSeqFeatures(boolean b)
5637 showSeqFeatures.setSelected(true);
5638 viewport.setShowSequenceFeatures(true);
5645 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5646 * awt.event.ActionEvent)
5649 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5651 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5652 alignPanel.paintAlignment(true);
5659 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5663 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5665 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5666 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5674 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5675 * .event.ActionEvent)
5678 protected void showGroupConservation_actionPerformed(ActionEvent e)
5680 viewport.setShowGroupConservation(showGroupConservation.getState());
5681 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5688 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5689 * .event.ActionEvent)
5692 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5694 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5695 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5702 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5703 * .event.ActionEvent)
5706 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5708 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5709 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5713 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5715 showSequenceLogo.setState(true);
5716 viewport.setShowSequenceLogo(true);
5717 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5718 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5722 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5724 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5731 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5732 * .event.ActionEvent)
5735 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5737 if (avc.makeGroupsFromSelection())
5739 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5740 alignPanel.updateAnnotation();
5741 alignPanel.paintAlignment(true);
5746 protected void createGroup_actionPerformed(ActionEvent e)
5748 if (avc.createGroup())
5750 alignPanel.alignmentChanged();
5755 protected void unGroup_actionPerformed(ActionEvent e)
5759 alignPanel.alignmentChanged();
5764 * make the given alignmentPanel the currently selected tab
5766 * @param alignmentPanel
5768 public void setDisplayedView(AlignmentPanel alignmentPanel)
5770 if (!viewport.getSequenceSetId().equals(
5771 alignmentPanel.av.getSequenceSetId()))
5773 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5775 if (tabbedPane != null
5776 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5777 .getSelectedIndex())
5779 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5784 * Action on selection of menu options to Show or Hide annotations.
5787 * @param forSequences
5788 * update sequence-related annotations
5789 * @param forAlignment
5790 * update non-sequence-related annotations
5793 protected void setAnnotationsVisibility(boolean visible,
5794 boolean forSequences, boolean forAlignment)
5796 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5797 .getAlignmentAnnotation())
5799 boolean apply = (aa.sequenceRef == null && forAlignment)
5800 || (aa.sequenceRef != null && forSequences);
5803 aa.visible = visible;
5806 alignPanel.validateAnnotationDimensions(false);
5807 alignPanel.alignmentChanged();
5811 * Store selected annotation sort order for the view and repaint.
5814 protected void sortAnnotations_actionPerformed()
5816 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5818 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5819 alignPanel.paintAlignment(true);
5824 * @return alignment panels in this alignemnt frame
5826 public List<AlignmentViewPanel> getAlignPanels()
5828 return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5832 class PrintThread extends Thread
5836 public PrintThread(AlignmentPanel ap)
5841 static PageFormat pf;
5846 PrinterJob printJob = PrinterJob.getPrinterJob();
5850 printJob.setPrintable(ap, pf);
5854 printJob.setPrintable(ap);
5857 if (printJob.printDialog())
5862 } catch (Exception PrintException)
5864 PrintException.printStackTrace();