2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.AlignmentSorter;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.analysis.CrossRef;
28 import jalview.analysis.NJTree;
29 import jalview.analysis.ParseProperties;
30 import jalview.analysis.SequenceIdMatcher;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.analysis.ScoreModelI;
34 import jalview.bin.Cache;
35 import jalview.commands.CommandI;
36 import jalview.commands.EditCommand;
37 import jalview.commands.OrderCommand;
38 import jalview.commands.RemoveGapColCommand;
39 import jalview.commands.RemoveGapsCommand;
40 import jalview.commands.SlideSequencesCommand;
41 import jalview.commands.TrimRegionCommand;
42 import jalview.datamodel.AlignedCodonFrame;
43 import jalview.datamodel.Alignment;
44 import jalview.datamodel.AlignmentAnnotation;
45 import jalview.datamodel.AlignmentI;
46 import jalview.datamodel.AlignmentOrder;
47 import jalview.datamodel.AlignmentView;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.PDBEntry;
50 import jalview.datamodel.SeqCigar;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AlignmentProperties;
55 import jalview.io.AnnotationFile;
56 import jalview.io.FeaturesFile;
57 import jalview.io.FileLoader;
58 import jalview.io.FormatAdapter;
59 import jalview.io.HTMLOutput;
60 import jalview.io.IdentifyFile;
61 import jalview.io.JalviewFileChooser;
62 import jalview.io.JalviewFileView;
63 import jalview.io.JnetAnnotationMaker;
64 import jalview.io.NewickFile;
65 import jalview.io.TCoffeeScoreFile;
66 import jalview.jbgui.GAlignFrame;
67 import jalview.schemes.Blosum62ColourScheme;
68 import jalview.schemes.BuriedColourScheme;
69 import jalview.schemes.ClustalxColourScheme;
70 import jalview.schemes.ColourSchemeI;
71 import jalview.schemes.ColourSchemeProperty;
72 import jalview.schemes.HelixColourScheme;
73 import jalview.schemes.HydrophobicColourScheme;
74 import jalview.schemes.NucleotideColourScheme;
75 import jalview.schemes.PIDColourScheme;
76 import jalview.schemes.PurinePyrimidineColourScheme;
77 import jalview.schemes.RNAHelicesColourChooser;
78 import jalview.schemes.ResidueProperties;
79 import jalview.schemes.StrandColourScheme;
80 import jalview.schemes.TCoffeeColourScheme;
81 import jalview.schemes.TaylorColourScheme;
82 import jalview.schemes.TurnColourScheme;
83 import jalview.schemes.UserColourScheme;
84 import jalview.schemes.ZappoColourScheme;
85 import jalview.util.MessageManager;
86 import jalview.ws.jws1.Discoverer;
87 import jalview.ws.jws2.Jws2Discoverer;
88 import jalview.ws.jws2.jabaws2.Jws2Instance;
89 import jalview.ws.seqfetcher.DbSourceProxy;
91 import java.awt.BorderLayout;
92 import java.awt.Component;
93 import java.awt.GridLayout;
94 import java.awt.Rectangle;
95 import java.awt.Toolkit;
96 import java.awt.datatransfer.Clipboard;
97 import java.awt.datatransfer.DataFlavor;
98 import java.awt.datatransfer.StringSelection;
99 import java.awt.datatransfer.Transferable;
100 import java.awt.dnd.DnDConstants;
101 import java.awt.dnd.DropTargetDragEvent;
102 import java.awt.dnd.DropTargetDropEvent;
103 import java.awt.dnd.DropTargetEvent;
104 import java.awt.dnd.DropTargetListener;
105 import java.awt.event.ActionEvent;
106 import java.awt.event.ActionListener;
107 import java.awt.event.KeyAdapter;
108 import java.awt.event.KeyEvent;
109 import java.awt.event.MouseAdapter;
110 import java.awt.event.MouseEvent;
111 import java.awt.print.PageFormat;
112 import java.awt.print.PrinterJob;
113 import java.beans.PropertyChangeEvent;
116 import java.util.ArrayList;
117 import java.util.Enumeration;
118 import java.util.Hashtable;
119 import java.util.List;
120 import java.util.Vector;
122 import javax.swing.JButton;
123 import javax.swing.JCheckBoxMenuItem;
124 import javax.swing.JEditorPane;
125 import javax.swing.JInternalFrame;
126 import javax.swing.JLabel;
127 import javax.swing.JLayeredPane;
128 import javax.swing.JMenu;
129 import javax.swing.JMenuItem;
130 import javax.swing.JOptionPane;
131 import javax.swing.JPanel;
132 import javax.swing.JProgressBar;
133 import javax.swing.JRadioButtonMenuItem;
134 import javax.swing.JScrollPane;
135 import javax.swing.SwingUtilities;
141 * @version $Revision$
143 public class AlignFrame extends GAlignFrame implements DropTargetListener,
144 IProgressIndicator, AlignViewControllerGuiI
148 public static final int DEFAULT_WIDTH = 700;
151 public static final int DEFAULT_HEIGHT = 500;
153 public AlignmentPanel alignPanel;
155 AlignViewport viewport;
157 public AlignViewControllerI avc;
159 Vector alignPanels = new Vector();
162 * Last format used to load or save alignments in this window
164 String currentFileFormat = null;
167 * Current filename for this alignment
169 String fileName = null;
172 * Creates a new AlignFrame object with specific width and height.
178 public AlignFrame(AlignmentI al, int width, int height)
180 this(al, null, width, height);
184 * Creates a new AlignFrame object with specific width, height and
190 * @param sequenceSetId
192 public AlignFrame(AlignmentI al, int width, int height,
193 String sequenceSetId)
195 this(al, null, width, height, sequenceSetId);
199 * Creates a new AlignFrame object with specific width, height and
205 * @param sequenceSetId
208 public AlignFrame(AlignmentI al, int width, int height,
209 String sequenceSetId, String viewId)
211 this(al, null, width, height, sequenceSetId, viewId);
215 * new alignment window with hidden columns
219 * @param hiddenColumns
220 * ColumnSelection or null
222 * Width of alignment frame
226 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
227 int width, int height)
229 this(al, hiddenColumns, width, height, null);
233 * Create alignment frame for al with hiddenColumns, a specific width and
234 * height, and specific sequenceId
237 * @param hiddenColumns
240 * @param sequenceSetId
243 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
244 int width, int height, String sequenceSetId)
246 this(al, hiddenColumns, width, height, sequenceSetId, null);
250 * Create alignment frame for al with hiddenColumns, a specific width and
251 * height, and specific sequenceId
254 * @param hiddenColumns
257 * @param sequenceSetId
262 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
263 int width, int height, String sequenceSetId, String viewId)
265 setSize(width, height);
266 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
268 alignPanel = new AlignmentPanel(this, viewport);
270 if (al.getDataset() == null)
275 addAlignmentPanel(alignPanel, true);
280 * Make a new AlignFrame from exisiting alignmentPanels
287 public AlignFrame(AlignmentPanel ap)
291 addAlignmentPanel(ap, false);
296 * initalise the alignframe from the underlying viewport data and the
301 avc = new jalview.controller.AlignViewController(this, viewport,
303 if (viewport.getAlignmentConservationAnnotation() == null)
305 BLOSUM62Colour.setEnabled(false);
306 conservationMenuItem.setEnabled(false);
307 modifyConservation.setEnabled(false);
308 // PIDColour.setEnabled(false);
309 // abovePIDThreshold.setEnabled(false);
310 // modifyPID.setEnabled(false);
313 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
316 if (sortby.equals("Id"))
318 sortIDMenuItem_actionPerformed(null);
320 else if (sortby.equals("Pairwise Identity"))
322 sortPairwiseMenuItem_actionPerformed(null);
325 if (Desktop.desktop != null)
327 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
328 addServiceListeners();
329 setGUINucleotide(viewport.getAlignment().isNucleotide());
332 setMenusFromViewport(viewport);
333 buildSortByAnnotationScoresMenu();
335 if (viewport.wrapAlignment)
337 wrapMenuItem_actionPerformed(null);
340 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
342 this.overviewMenuItem_actionPerformed(null);
350 * Change the filename and format for the alignment, and enable the 'reload'
351 * button functionality.
358 public void setFileName(String file, String format)
361 currentFileFormat = format;
362 reload.setEnabled(true);
365 void addKeyListener()
367 addKeyListener(new KeyAdapter()
370 public void keyPressed(KeyEvent evt)
372 if (viewport.cursorMode
373 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
374 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
375 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
376 && Character.isDigit(evt.getKeyChar()))
377 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
379 switch (evt.getKeyCode())
382 case 27: // escape key
383 deselectAllSequenceMenuItem_actionPerformed(null);
387 case KeyEvent.VK_DOWN:
388 if (evt.isAltDown() || !viewport.cursorMode)
389 moveSelectedSequences(false);
390 if (viewport.cursorMode)
391 alignPanel.seqPanel.moveCursor(0, 1);
395 if (evt.isAltDown() || !viewport.cursorMode)
396 moveSelectedSequences(true);
397 if (viewport.cursorMode)
398 alignPanel.seqPanel.moveCursor(0, -1);
402 case KeyEvent.VK_LEFT:
403 if (evt.isAltDown() || !viewport.cursorMode)
404 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
406 alignPanel.seqPanel.moveCursor(-1, 0);
410 case KeyEvent.VK_RIGHT:
411 if (evt.isAltDown() || !viewport.cursorMode)
412 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
414 alignPanel.seqPanel.moveCursor(1, 0);
417 case KeyEvent.VK_SPACE:
418 if (viewport.cursorMode)
420 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
421 || evt.isShiftDown() || evt.isAltDown());
425 // case KeyEvent.VK_A:
426 // if (viewport.cursorMode)
428 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
429 // //System.out.println("A");
433 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
434 * System.out.println("closing bracket"); } break;
436 case KeyEvent.VK_DELETE:
437 case KeyEvent.VK_BACK_SPACE:
438 if (!viewport.cursorMode)
440 cut_actionPerformed(null);
444 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
445 || evt.isShiftDown() || evt.isAltDown());
451 if (viewport.cursorMode)
453 alignPanel.seqPanel.setCursorRow();
457 if (viewport.cursorMode && !evt.isControlDown())
459 alignPanel.seqPanel.setCursorColumn();
463 if (viewport.cursorMode)
465 alignPanel.seqPanel.setCursorPosition();
469 case KeyEvent.VK_ENTER:
470 case KeyEvent.VK_COMMA:
471 if (viewport.cursorMode)
473 alignPanel.seqPanel.setCursorRowAndColumn();
478 if (viewport.cursorMode)
480 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
484 if (viewport.cursorMode)
486 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
491 viewport.cursorMode = !viewport.cursorMode;
492 statusBar.setText(MessageManager.formatMessage(
493 "label.keyboard_editing_mode", new String[]
494 { (viewport.cursorMode ? "on" : "off") }));
495 if (viewport.cursorMode)
497 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
498 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
500 alignPanel.seqPanel.seqCanvas.repaint();
506 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
507 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
509 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
511 javax.help.HelpBroker hb = hs.createHelpBroker();
512 hb.setCurrentID("home");
513 hb.setDisplayed(true);
514 } catch (Exception ex)
516 ex.printStackTrace();
521 boolean toggleSeqs = !evt.isControlDown();
522 boolean toggleCols = !evt.isShiftDown();
523 toggleHiddenRegions(toggleSeqs, toggleCols);
526 case KeyEvent.VK_PAGE_UP:
527 if (viewport.wrapAlignment)
529 alignPanel.scrollUp(true);
533 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
534 - viewport.endSeq + viewport.startSeq);
537 case KeyEvent.VK_PAGE_DOWN:
538 if (viewport.wrapAlignment)
540 alignPanel.scrollUp(false);
544 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
545 + viewport.endSeq - viewport.startSeq);
552 public void keyReleased(KeyEvent evt)
554 switch (evt.getKeyCode())
556 case KeyEvent.VK_LEFT:
557 if (evt.isAltDown() || !viewport.cursorMode)
558 viewport.firePropertyChange("alignment", null, viewport
559 .getAlignment().getSequences());
562 case KeyEvent.VK_RIGHT:
563 if (evt.isAltDown() || !viewport.cursorMode)
564 viewport.firePropertyChange("alignment", null, viewport
565 .getAlignment().getSequences());
572 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
574 ap.alignFrame = this;
575 avc = new jalview.controller.AlignViewController(this, viewport,
578 alignPanels.addElement(ap);
580 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
582 int aSize = alignPanels.size();
584 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
586 if (aSize == 1 && ap.av.viewName == null)
588 this.getContentPane().add(ap, BorderLayout.CENTER);
594 setInitialTabVisible();
597 expandViews.setEnabled(true);
598 gatherViews.setEnabled(true);
599 tabbedPane.addTab(ap.av.viewName, ap);
601 ap.setVisible(false);
606 if (ap.av.isPadGaps())
608 ap.av.getAlignment().padGaps();
610 ap.av.updateConservation(ap);
611 ap.av.updateConsensus(ap);
612 ap.av.updateStrucConsensus(ap);
616 public void setInitialTabVisible()
618 expandViews.setEnabled(true);
619 gatherViews.setEnabled(true);
620 tabbedPane.setVisible(true);
621 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
622 tabbedPane.addTab(first.av.viewName, first);
623 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
626 public AlignViewport getViewport()
631 /* Set up intrinsic listeners for dynamically generated GUI bits. */
632 private void addServiceListeners()
634 final java.beans.PropertyChangeListener thisListener;
635 Desktop.instance.addJalviewPropertyChangeListener("services",
636 thisListener = new java.beans.PropertyChangeListener()
639 public void propertyChange(PropertyChangeEvent evt)
641 // // System.out.println("Discoverer property change.");
642 // if (evt.getPropertyName().equals("services"))
644 SwingUtilities.invokeLater(new Runnable()
651 .println("Rebuild WS Menu for service change");
652 BuildWebServiceMenu();
659 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
662 public void internalFrameClosed(
663 javax.swing.event.InternalFrameEvent evt)
665 System.out.println("deregistering discoverer listener");
666 Desktop.instance.removeJalviewPropertyChangeListener("services",
668 closeMenuItem_actionPerformed(true);
671 // Finally, build the menu once to get current service state
672 new Thread(new Runnable()
677 BuildWebServiceMenu();
682 public void setGUINucleotide(boolean nucleotide)
684 showTranslation.setVisible(nucleotide);
685 conservationMenuItem.setEnabled(!nucleotide);
686 modifyConservation.setEnabled(!nucleotide);
687 showGroupConservation.setEnabled(!nucleotide);
688 rnahelicesColour.setEnabled(nucleotide);
689 purinePyrimidineColour.setEnabled(nucleotide);
690 // Remember AlignFrame always starts as protein
694 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
699 * set up menus for the currently viewport. This may be called after any
700 * operation that affects the data in the current view (selection changed,
701 * etc) to update the menus to reflect the new state.
703 public void setMenusForViewport()
705 setMenusFromViewport(viewport);
709 * Need to call this method when tabs are selected for multiple views, or when
710 * loading from Jalview2XML.java
715 void setMenusFromViewport(AlignViewport av)
717 padGapsMenuitem.setSelected(av.isPadGaps());
718 colourTextMenuItem.setSelected(av.showColourText);
719 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
720 conservationMenuItem.setSelected(av.getConservationSelected());
721 seqLimits.setSelected(av.getShowJVSuffix());
722 idRightAlign.setSelected(av.rightAlignIds);
723 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
724 renderGapsMenuItem.setSelected(av.renderGaps);
725 wrapMenuItem.setSelected(av.wrapAlignment);
726 scaleAbove.setVisible(av.wrapAlignment);
727 scaleLeft.setVisible(av.wrapAlignment);
728 scaleRight.setVisible(av.wrapAlignment);
729 annotationPanelMenuItem.setState(av.showAnnotation);
730 viewBoxesMenuItem.setSelected(av.showBoxes);
731 viewTextMenuItem.setSelected(av.showText);
732 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
733 showGroupConsensus.setSelected(av.isShowGroupConsensus());
734 showGroupConservation.setSelected(av.isShowGroupConservation());
735 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
736 showSequenceLogo.setSelected(av.isShowSequenceLogo());
737 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
739 setColourSelected(ColourSchemeProperty.getColourName(av
740 .getGlobalColourScheme()));
742 showSeqFeatures.setSelected(av.showSequenceFeatures);
743 hiddenMarkers.setState(av.showHiddenMarkers);
744 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
745 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
746 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
747 autoCalculate.setSelected(av.autoCalculateConsensus);
748 sortByTree.setSelected(av.sortByTree);
749 listenToViewSelections.setSelected(av.followSelection);
750 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
752 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
753 setShowProductsEnabled();
757 // methods for implementing IProgressIndicator
758 // need to refactor to a reusable stub class
759 Hashtable progressBars, progressBarHandlers;
764 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
767 public void setProgressBar(String message, long id)
769 if (progressBars == null)
771 progressBars = new Hashtable();
772 progressBarHandlers = new Hashtable();
775 JPanel progressPanel;
776 Long lId = new Long(id);
777 GridLayout layout = (GridLayout) statusPanel.getLayout();
778 if (progressBars.get(lId) != null)
780 progressPanel = (JPanel) progressBars.get(new Long(id));
781 statusPanel.remove(progressPanel);
782 progressBars.remove(lId);
783 progressPanel = null;
786 statusBar.setText(message);
788 if (progressBarHandlers.contains(lId))
790 progressBarHandlers.remove(lId);
792 layout.setRows(layout.getRows() - 1);
796 progressPanel = new JPanel(new BorderLayout(10, 5));
798 JProgressBar progressBar = new JProgressBar();
799 progressBar.setIndeterminate(true);
801 progressPanel.add(new JLabel(message), BorderLayout.WEST);
802 progressPanel.add(progressBar, BorderLayout.CENTER);
804 layout.setRows(layout.getRows() + 1);
805 statusPanel.add(progressPanel);
807 progressBars.put(lId, progressPanel);
810 // setMenusForViewport();
815 public void registerHandler(final long id,
816 final IProgressIndicatorHandler handler)
818 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
821 "call setProgressBar before registering the progress bar's handler.");
823 progressBarHandlers.put(new Long(id), handler);
824 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
825 if (handler.canCancel())
827 JButton cancel = new JButton(
828 MessageManager.getString("action.cancel"));
829 final IProgressIndicator us = this;
830 cancel.addActionListener(new ActionListener()
834 public void actionPerformed(ActionEvent e)
836 handler.cancelActivity(id);
839 + ((JLabel) progressPanel.getComponent(0))
843 progressPanel.add(cancel, BorderLayout.EAST);
849 * @return true if any progress bars are still active
852 public boolean operationInProgress()
854 if (progressBars != null && progressBars.size() > 0)
862 public void setStatus(String text)
864 statusBar.setText(text);
868 * Added so Castor Mapping file can obtain Jalview Version
870 public String getVersion()
872 return jalview.bin.Cache.getProperty("VERSION");
875 public FeatureRenderer getFeatureRenderer()
877 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
881 public void fetchSequence_actionPerformed(ActionEvent e)
883 new SequenceFetcher(this);
887 public void addFromFile_actionPerformed(ActionEvent e)
889 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
893 public void reload_actionPerformed(ActionEvent e)
895 if (fileName != null)
897 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
898 // originating file's format
899 // TODO: work out how to recover feature settings for correct view(s) when
901 if (currentFileFormat.equals("Jalview"))
903 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
904 for (int i = 0; i < frames.length; i++)
906 if (frames[i] instanceof AlignFrame && frames[i] != this
907 && ((AlignFrame) frames[i]).fileName != null
908 && ((AlignFrame) frames[i]).fileName.equals(fileName))
912 frames[i].setSelected(true);
913 Desktop.instance.closeAssociatedWindows();
914 } catch (java.beans.PropertyVetoException ex)
920 Desktop.instance.closeAssociatedWindows();
922 FileLoader loader = new FileLoader();
923 String protocol = fileName.startsWith("http:") ? "URL" : "File";
924 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
928 Rectangle bounds = this.getBounds();
930 FileLoader loader = new FileLoader();
931 String protocol = fileName.startsWith("http:") ? "URL" : "File";
932 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
933 protocol, currentFileFormat);
935 newframe.setBounds(bounds);
936 if (featureSettings != null && featureSettings.isShowing())
938 final Rectangle fspos = featureSettings.frame.getBounds();
939 // TODO: need a 'show feature settings' function that takes bounds -
940 // need to refactor Desktop.addFrame
941 newframe.featureSettings_actionPerformed(null);
942 final FeatureSettings nfs = newframe.featureSettings;
943 SwingUtilities.invokeLater(new Runnable()
948 nfs.frame.setBounds(fspos);
951 this.featureSettings.close();
952 this.featureSettings = null;
954 this.closeMenuItem_actionPerformed(true);
960 public void addFromText_actionPerformed(ActionEvent e)
962 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
966 public void addFromURL_actionPerformed(ActionEvent e)
968 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
972 public void save_actionPerformed(ActionEvent e)
975 || (currentFileFormat == null || !jalview.io.FormatAdapter
976 .isValidIOFormat(currentFileFormat, true))
977 || fileName.startsWith("http"))
979 saveAs_actionPerformed(null);
983 saveAlignment(fileName, currentFileFormat);
994 public void saveAs_actionPerformed(ActionEvent e)
996 JalviewFileChooser chooser = new JalviewFileChooser(
997 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
998 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
999 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1000 currentFileFormat, false);
1002 chooser.setFileView(new JalviewFileView());
1003 chooser.setDialogTitle("Save Alignment to file");
1004 chooser.setToolTipText(MessageManager.getString("action.save"));
1006 int value = chooser.showSaveDialog(this);
1008 if (value == JalviewFileChooser.APPROVE_OPTION)
1010 currentFileFormat = chooser.getSelectedFormat();
1011 if (currentFileFormat == null)
1014 .showInternalMessageDialog(
1017 .getString("label.select_file_format_before_saving"),
1019 .getString("label.file_format_not_specified"),
1020 JOptionPane.WARNING_MESSAGE);
1021 value = chooser.showSaveDialog(this);
1025 fileName = chooser.getSelectedFile().getPath();
1027 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1030 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1031 if (currentFileFormat.indexOf(" ") > -1)
1033 currentFileFormat = currentFileFormat.substring(0,
1034 currentFileFormat.indexOf(" "));
1036 saveAlignment(fileName, currentFileFormat);
1040 public boolean saveAlignment(String file, String format)
1042 boolean success = true;
1044 if (format.equalsIgnoreCase("Jalview"))
1046 String shortName = title;
1048 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1050 shortName = shortName.substring(shortName
1051 .lastIndexOf(java.io.File.separatorChar) + 1);
1054 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1056 statusBar.setText(MessageManager.formatMessage(
1057 "label.successfully_saved_to_file_in_format", new String[]
1058 { fileName, format }));
1063 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1065 warningMessage("Cannot save file " + fileName + " using format "
1066 + format, "Alignment output format not supported");
1067 saveAs_actionPerformed(null);
1068 // JBPNote need to have a raise_gui flag here
1072 String[] omitHidden = null;
1074 if (viewport.hasHiddenColumns())
1076 int reply = JOptionPane
1077 .showInternalConfirmDialog(
1080 .getString("label.alignment_contains_hidden_columns"),
1082 .getString("action.save_omit_hidden_columns"),
1083 JOptionPane.YES_NO_OPTION,
1084 JOptionPane.QUESTION_MESSAGE);
1086 if (reply == JOptionPane.YES_OPTION)
1088 omitHidden = viewport.getViewAsString(false);
1091 FormatAdapter f = new FormatAdapter();
1092 String output = f.formatSequences(format,
1093 viewport.getAlignment(), // class cast exceptions will
1094 // occur in the distant future
1095 omitHidden, f.getCacheSuffixDefault(format),
1096 viewport.getColumnSelection());
1106 java.io.PrintWriter out = new java.io.PrintWriter(
1107 new java.io.FileWriter(file));
1111 this.setTitle(file);
1112 statusBar.setText(MessageManager.formatMessage(
1113 "label.successfully_saved_to_file_in_format",
1115 { fileName, format }));
1116 } catch (Exception ex)
1119 ex.printStackTrace();
1126 JOptionPane.showInternalMessageDialog(this, MessageManager
1127 .formatMessage("label.couldnt_save_file", new String[]
1128 { fileName }), MessageManager
1129 .getString("label.error_saving_file"),
1130 JOptionPane.WARNING_MESSAGE);
1136 private void warningMessage(String warning, String title)
1138 if (new jalview.util.Platform().isHeadless())
1140 System.err.println("Warning: " + title + "\nWarning: " + warning);
1145 JOptionPane.showInternalMessageDialog(this, warning, title,
1146 JOptionPane.WARNING_MESSAGE);
1158 protected void outputText_actionPerformed(ActionEvent e)
1160 String[] omitHidden = null;
1162 if (viewport.hasHiddenColumns())
1164 int reply = JOptionPane
1165 .showInternalConfirmDialog(
1168 .getString("label.alignment_contains_hidden_columns"),
1170 .getString("action.save_omit_hidden_columns"),
1171 JOptionPane.YES_NO_OPTION,
1172 JOptionPane.QUESTION_MESSAGE);
1174 if (reply == JOptionPane.YES_OPTION)
1176 omitHidden = viewport.getViewAsString(false);
1180 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1181 cap.setForInput(null);
1185 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1186 viewport.getAlignment(), omitHidden,
1187 viewport.getColumnSelection()));
1188 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1189 "label.alignment_output_command", new String[]
1190 { e.getActionCommand() }), 600, 500);
1191 } catch (OutOfMemoryError oom)
1193 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1206 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1208 new HTMLOutput(alignPanel,
1209 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1210 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1213 public void createImageMap(File file, String image)
1215 alignPanel.makePNGImageMap(file, image);
1225 public void createPNG(File f)
1227 alignPanel.makePNG(f);
1237 public void createEPS(File f)
1239 alignPanel.makeEPS(f);
1243 public void pageSetup_actionPerformed(ActionEvent e)
1245 PrinterJob printJob = PrinterJob.getPrinterJob();
1246 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1256 public void printMenuItem_actionPerformed(ActionEvent e)
1258 // Putting in a thread avoids Swing painting problems
1259 PrintThread thread = new PrintThread(alignPanel);
1264 public void exportFeatures_actionPerformed(ActionEvent e)
1266 new AnnotationExporter().exportFeatures(alignPanel);
1270 public void exportAnnotations_actionPerformed(ActionEvent e)
1272 new AnnotationExporter().exportAnnotations(alignPanel,
1273 viewport.showAnnotation ? viewport.getAlignment()
1274 .getAlignmentAnnotation() : null, viewport
1275 .getAlignment().getGroups(), ((Alignment) viewport
1276 .getAlignment()).alignmentProperties);
1280 public void associatedData_actionPerformed(ActionEvent e)
1282 // Pick the tree file
1283 JalviewFileChooser chooser = new JalviewFileChooser(
1284 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1285 chooser.setFileView(new JalviewFileView());
1286 chooser.setDialogTitle(MessageManager
1287 .getString("label.load_jalview_annotations"));
1288 chooser.setToolTipText(MessageManager
1289 .getString("label.load_jalview_annotations"));
1291 int value = chooser.showOpenDialog(null);
1293 if (value == JalviewFileChooser.APPROVE_OPTION)
1295 String choice = chooser.getSelectedFile().getPath();
1296 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1297 loadJalviewDataFile(choice, null, null, null);
1303 * Close the current view or all views in the alignment frame. If the frame
1304 * only contains one view then the alignment will be removed from memory.
1306 * @param closeAllTabs
1309 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1311 if (alignPanels != null && alignPanels.size() < 2)
1313 closeAllTabs = true;
1318 if (alignPanels != null)
1322 if (this.isClosed())
1324 // really close all the windows - otherwise wait till
1325 // setClosed(true) is called
1326 for (int i = 0; i < alignPanels.size(); i++)
1328 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1335 closeView(alignPanel);
1341 this.setClosed(true);
1343 } catch (Exception ex)
1345 ex.printStackTrace();
1350 * close alignPanel2 and shuffle tabs appropriately.
1352 * @param alignPanel2
1354 public void closeView(AlignmentPanel alignPanel2)
1356 int index = tabbedPane.getSelectedIndex();
1357 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1358 alignPanels.removeElement(alignPanel2);
1360 // if (viewport == alignPanel2.av)
1364 alignPanel2.closePanel();
1367 tabbedPane.removeTabAt(closedindex);
1368 tabbedPane.validate();
1370 if (index > closedindex || index == tabbedPane.getTabCount())
1372 // modify currently selected tab index if necessary.
1376 this.tabSelectionChanged(index);
1382 void updateEditMenuBar()
1385 if (viewport.historyList.size() > 0)
1387 undoMenuItem.setEnabled(true);
1388 CommandI command = (CommandI) viewport.historyList.peek();
1389 undoMenuItem.setText(MessageManager.formatMessage(
1390 "label.undo_command", new String[]
1391 { command.getDescription() }));
1395 undoMenuItem.setEnabled(false);
1396 undoMenuItem.setText(MessageManager.getString("action.undo"));
1399 if (viewport.redoList.size() > 0)
1401 redoMenuItem.setEnabled(true);
1403 CommandI command = (CommandI) viewport.redoList.peek();
1404 redoMenuItem.setText(MessageManager.formatMessage(
1405 "label.redo_command", new String[]
1406 { command.getDescription() }));
1410 redoMenuItem.setEnabled(false);
1411 redoMenuItem.setText(MessageManager.getString("action.redo"));
1415 public void addHistoryItem(CommandI command)
1417 if (command.getSize() > 0)
1419 viewport.historyList.push(command);
1420 viewport.redoList.clear();
1421 updateEditMenuBar();
1422 viewport.updateHiddenColumns();
1423 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1424 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1425 // viewport.getColumnSelection()
1426 // .getHiddenColumns().size() > 0);
1432 * @return alignment objects for all views
1434 AlignmentI[] getViewAlignments()
1436 if (alignPanels != null)
1438 Enumeration e = alignPanels.elements();
1439 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1440 for (int i = 0; e.hasMoreElements(); i++)
1442 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1446 if (viewport != null)
1448 return new AlignmentI[]
1449 { viewport.getAlignment() };
1461 protected void undoMenuItem_actionPerformed(ActionEvent e)
1463 if (viewport.historyList.empty())
1465 CommandI command = (CommandI) viewport.historyList.pop();
1466 viewport.redoList.push(command);
1467 command.undoCommand(getViewAlignments());
1469 AlignViewport originalSource = getOriginatingSource(command);
1470 updateEditMenuBar();
1472 if (originalSource != null)
1474 if (originalSource != viewport)
1477 .warn("Implementation worry: mismatch of viewport origin for undo");
1479 originalSource.updateHiddenColumns();
1480 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1482 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1483 // viewport.getColumnSelection()
1484 // .getHiddenColumns().size() > 0);
1485 originalSource.firePropertyChange("alignment", null, originalSource
1486 .getAlignment().getSequences());
1497 protected void redoMenuItem_actionPerformed(ActionEvent e)
1499 if (viewport.redoList.size() < 1)
1504 CommandI command = (CommandI) viewport.redoList.pop();
1505 viewport.historyList.push(command);
1506 command.doCommand(getViewAlignments());
1508 AlignViewport originalSource = getOriginatingSource(command);
1509 updateEditMenuBar();
1511 if (originalSource != null)
1514 if (originalSource != viewport)
1517 .warn("Implementation worry: mismatch of viewport origin for redo");
1519 originalSource.updateHiddenColumns();
1520 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1522 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1523 // viewport.getColumnSelection()
1524 // .getHiddenColumns().size() > 0);
1525 originalSource.firePropertyChange("alignment", null, originalSource
1526 .getAlignment().getSequences());
1530 AlignViewport getOriginatingSource(CommandI command)
1532 AlignViewport originalSource = null;
1533 // For sequence removal and addition, we need to fire
1534 // the property change event FROM the viewport where the
1535 // original alignment was altered
1536 AlignmentI al = null;
1537 if (command instanceof EditCommand)
1539 EditCommand editCommand = (EditCommand) command;
1540 al = editCommand.getAlignment();
1541 Vector comps = (Vector) PaintRefresher.components.get(viewport
1542 .getSequenceSetId());
1544 for (int i = 0; i < comps.size(); i++)
1546 if (comps.elementAt(i) instanceof AlignmentPanel)
1548 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1550 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1557 if (originalSource == null)
1559 // The original view is closed, we must validate
1560 // the current view against the closed view first
1563 PaintRefresher.validateSequences(al, viewport.getAlignment());
1566 originalSource = viewport;
1569 return originalSource;
1578 public void moveSelectedSequences(boolean up)
1580 SequenceGroup sg = viewport.getSelectionGroup();
1586 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1587 viewport.getHiddenRepSequences(), up);
1588 alignPanel.paintAlignment(true);
1591 synchronized void slideSequences(boolean right, int size)
1593 List<SequenceI> sg = new Vector();
1594 if (viewport.cursorMode)
1596 sg.add(viewport.getAlignment().getSequenceAt(
1597 alignPanel.seqPanel.seqCanvas.cursorY));
1599 else if (viewport.getSelectionGroup() != null
1600 && viewport.getSelectionGroup().getSize() != viewport
1601 .getAlignment().getHeight())
1603 sg = viewport.getSelectionGroup().getSequences(
1604 viewport.getHiddenRepSequences());
1612 Vector invertGroup = new Vector();
1614 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1616 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1617 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1620 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1622 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1623 for (int i = 0; i < invertGroup.size(); i++)
1624 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1626 SlideSequencesCommand ssc;
1628 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1629 size, viewport.getGapCharacter());
1631 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1632 size, viewport.getGapCharacter());
1634 int groupAdjustment = 0;
1635 if (ssc.getGapsInsertedBegin() && right)
1637 if (viewport.cursorMode)
1638 alignPanel.seqPanel.moveCursor(size, 0);
1640 groupAdjustment = size;
1642 else if (!ssc.getGapsInsertedBegin() && !right)
1644 if (viewport.cursorMode)
1645 alignPanel.seqPanel.moveCursor(-size, 0);
1647 groupAdjustment = -size;
1650 if (groupAdjustment != 0)
1652 viewport.getSelectionGroup().setStartRes(
1653 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1654 viewport.getSelectionGroup().setEndRes(
1655 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1658 boolean appendHistoryItem = false;
1659 if (viewport.historyList != null && viewport.historyList.size() > 0
1660 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1662 appendHistoryItem = ssc
1663 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1667 if (!appendHistoryItem)
1668 addHistoryItem(ssc);
1680 protected void copy_actionPerformed(ActionEvent e)
1683 if (viewport.getSelectionGroup() == null)
1687 // TODO: preserve the ordering of displayed alignment annotation in any
1688 // internal paste (particularly sequence associated annotation)
1689 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1690 String[] omitHidden = null;
1692 if (viewport.hasHiddenColumns())
1694 omitHidden = viewport.getViewAsString(true);
1697 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1700 StringSelection ss = new StringSelection(output);
1704 jalview.gui.Desktop.internalCopy = true;
1705 // Its really worth setting the clipboard contents
1706 // to empty before setting the large StringSelection!!
1707 Toolkit.getDefaultToolkit().getSystemClipboard()
1708 .setContents(new StringSelection(""), null);
1710 Toolkit.getDefaultToolkit().getSystemClipboard()
1711 .setContents(ss, Desktop.instance);
1712 } catch (OutOfMemoryError er)
1714 new OOMWarning("copying region", er);
1718 Vector hiddenColumns = null;
1719 if (viewport.hasHiddenColumns())
1721 hiddenColumns = new Vector();
1722 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1723 .getSelectionGroup().getEndRes();
1724 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1727 int[] region = (int[]) viewport.getColumnSelection()
1728 .getHiddenColumns().elementAt(i);
1729 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1731 hiddenColumns.addElement(new int[]
1732 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1737 Desktop.jalviewClipboard = new Object[]
1738 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1739 statusBar.setText(MessageManager.formatMessage(
1740 "label.copied_sequences_to_clipboard", new String[]
1741 { Integer.valueOf(seqs.length).toString() }));
1751 protected void pasteNew_actionPerformed(ActionEvent e)
1763 protected void pasteThis_actionPerformed(ActionEvent e)
1769 * Paste contents of Jalview clipboard
1771 * @param newAlignment
1772 * true to paste to a new alignment, otherwise add to this.
1774 void paste(boolean newAlignment)
1776 boolean externalPaste = true;
1779 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1780 Transferable contents = c.getContents(this);
1782 if (contents == null)
1790 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1791 if (str.length() < 1)
1796 format = new IdentifyFile().Identify(str, "Paste");
1798 } catch (OutOfMemoryError er)
1800 new OOMWarning("Out of memory pasting sequences!!", er);
1804 SequenceI[] sequences;
1805 boolean annotationAdded = false;
1806 AlignmentI alignment = null;
1808 if (Desktop.jalviewClipboard != null)
1810 // The clipboard was filled from within Jalview, we must use the
1812 // And dataset from the copied alignment
1813 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1814 // be doubly sure that we create *new* sequence objects.
1815 sequences = new SequenceI[newseq.length];
1816 for (int i = 0; i < newseq.length; i++)
1818 sequences[i] = new Sequence(newseq[i]);
1820 alignment = new Alignment(sequences);
1821 externalPaste = false;
1825 // parse the clipboard as an alignment.
1826 alignment = new FormatAdapter().readFile(str, "Paste", format);
1827 sequences = alignment.getSequencesArray();
1831 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1837 if (Desktop.jalviewClipboard != null)
1839 // dataset is inherited
1840 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1844 // new dataset is constructed
1845 alignment.setDataset(null);
1847 alwidth = alignment.getWidth() + 1;
1851 AlignmentI pastedal = alignment; // preserve pasted alignment object
1852 // Add pasted sequences and dataset into existing alignment.
1853 alignment = viewport.getAlignment();
1854 alwidth = alignment.getWidth() + 1;
1855 // decide if we need to import sequences from an existing dataset
1856 boolean importDs = Desktop.jalviewClipboard != null
1857 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1858 // importDs==true instructs us to copy over new dataset sequences from
1859 // an existing alignment
1860 Vector newDs = (importDs) ? new Vector() : null; // used to create
1861 // minimum dataset set
1863 for (int i = 0; i < sequences.length; i++)
1867 newDs.addElement(null);
1869 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1871 if (importDs && ds != null)
1873 if (!newDs.contains(ds))
1875 newDs.setElementAt(ds, i);
1876 ds = new Sequence(ds);
1877 // update with new dataset sequence
1878 sequences[i].setDatasetSequence(ds);
1882 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1887 // copy and derive new dataset sequence
1888 sequences[i] = sequences[i].deriveSequence();
1889 alignment.getDataset().addSequence(
1890 sequences[i].getDatasetSequence());
1891 // TODO: avoid creation of duplicate dataset sequences with a
1892 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1894 alignment.addSequence(sequences[i]); // merges dataset
1898 newDs.clear(); // tidy up
1900 if (alignment.getAlignmentAnnotation() != null)
1902 for (AlignmentAnnotation alan : alignment
1903 .getAlignmentAnnotation())
1905 if (alan.graphGroup > fgroup)
1907 fgroup = alan.graphGroup;
1911 if (pastedal.getAlignmentAnnotation() != null)
1913 // Add any annotation attached to alignment.
1914 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1915 for (int i = 0; i < alann.length; i++)
1917 annotationAdded = true;
1918 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1920 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1921 if (newann.graphGroup > -1)
1923 if (newGraphGroups.size() <= newann.graphGroup
1924 || newGraphGroups.get(newann.graphGroup) == null)
1926 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1928 newGraphGroups.add(q, null);
1930 newGraphGroups.set(newann.graphGroup, new Integer(
1933 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1937 newann.padAnnotation(alwidth);
1938 alignment.addAnnotation(newann);
1948 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1949 sequences, 0, alignment.getWidth(), alignment));
1951 // Add any annotations attached to sequences
1952 for (int i = 0; i < sequences.length; i++)
1954 if (sequences[i].getAnnotation() != null)
1956 AlignmentAnnotation newann;
1957 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1959 annotationAdded = true;
1960 newann = sequences[i].getAnnotation()[a];
1961 newann.adjustForAlignment();
1962 newann.padAnnotation(alwidth);
1963 if (newann.graphGroup > -1)
1965 if (newann.graphGroup > -1)
1967 if (newGraphGroups.size() <= newann.graphGroup
1968 || newGraphGroups.get(newann.graphGroup) == null)
1970 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1972 newGraphGroups.add(q, null);
1974 newGraphGroups.set(newann.graphGroup, new Integer(
1977 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1981 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1986 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1993 // propagate alignment changed.
1994 viewport.setEndSeq(alignment.getHeight());
1995 if (annotationAdded)
1997 // Duplicate sequence annotation in all views.
1998 AlignmentI[] alview = this.getViewAlignments();
1999 for (int i = 0; i < sequences.length; i++)
2001 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2004 for (int avnum = 0; avnum < alview.length; avnum++)
2006 if (alview[avnum] != alignment)
2008 // duplicate in a view other than the one with input focus
2009 int avwidth = alview[avnum].getWidth() + 1;
2010 // this relies on sann being preserved after we
2011 // modify the sequence's annotation array for each duplication
2012 for (int a = 0; a < sann.length; a++)
2014 AlignmentAnnotation newann = new AlignmentAnnotation(
2016 sequences[i].addAlignmentAnnotation(newann);
2017 newann.padAnnotation(avwidth);
2018 alview[avnum].addAnnotation(newann); // annotation was
2019 // duplicated earlier
2020 // TODO JAL-1145 graphGroups are not updated for sequence
2021 // annotation added to several views. This may cause
2023 alview[avnum].setAnnotationIndex(newann, a);
2028 buildSortByAnnotationScoresMenu();
2030 viewport.firePropertyChange("alignment", null,
2031 alignment.getSequences());
2032 if (alignPanels != null)
2034 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2036 ap.validateAnnotationDimensions(false);
2041 alignPanel.validateAnnotationDimensions(false);
2047 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2049 String newtitle = new String("Copied sequences");
2051 if (Desktop.jalviewClipboard != null
2052 && Desktop.jalviewClipboard[2] != null)
2054 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2055 for (int i = 0; i < hc.size(); i++)
2057 int[] region = (int[]) hc.elementAt(i);
2058 af.viewport.hideColumns(region[0], region[1]);
2062 // >>>This is a fix for the moment, until a better solution is
2064 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2066 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2068 // TODO: maintain provenance of an alignment, rather than just make the
2069 // title a concatenation of operations.
2072 if (title.startsWith("Copied sequences"))
2078 newtitle = newtitle.concat("- from " + title);
2083 newtitle = new String("Pasted sequences");
2086 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2091 } catch (Exception ex)
2093 ex.printStackTrace();
2094 System.out.println("Exception whilst pasting: " + ex);
2095 // could be anything being pasted in here
2101 protected void expand_newalign(ActionEvent e)
2105 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2106 .getAlignment(), -1);
2107 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2109 String newtitle = new String("Flanking alignment");
2111 if (Desktop.jalviewClipboard != null
2112 && Desktop.jalviewClipboard[2] != null)
2114 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2115 for (int i = 0; i < hc.size(); i++)
2117 int[] region = (int[]) hc.elementAt(i);
2118 af.viewport.hideColumns(region[0], region[1]);
2122 // >>>This is a fix for the moment, until a better solution is
2124 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2126 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2128 // TODO: maintain provenance of an alignment, rather than just make the
2129 // title a concatenation of operations.
2131 if (title.startsWith("Copied sequences"))
2137 newtitle = newtitle.concat("- from " + title);
2141 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2143 } catch (Exception ex)
2145 ex.printStackTrace();
2146 System.out.println("Exception whilst pasting: " + ex);
2147 // could be anything being pasted in here
2148 } catch (OutOfMemoryError oom)
2150 new OOMWarning("Viewing flanking region of alignment", oom);
2161 protected void cut_actionPerformed(ActionEvent e)
2163 copy_actionPerformed(null);
2164 delete_actionPerformed(null);
2174 protected void delete_actionPerformed(ActionEvent evt)
2177 SequenceGroup sg = viewport.getSelectionGroup();
2183 Vector seqs = new Vector();
2185 for (int i = 0; i < sg.getSize(); i++)
2187 seq = sg.getSequenceAt(i);
2188 seqs.addElement(seq);
2191 // If the cut affects all sequences, remove highlighted columns
2192 if (sg.getSize() == viewport.getAlignment().getHeight())
2194 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2195 sg.getEndRes() + 1);
2198 SequenceI[] cut = new SequenceI[seqs.size()];
2199 for (int i = 0; i < seqs.size(); i++)
2201 cut[i] = (SequenceI) seqs.elementAt(i);
2205 * //ADD HISTORY ITEM
2207 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2208 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2209 viewport.getAlignment()));
2211 viewport.setSelectionGroup(null);
2212 viewport.sendSelection();
2213 viewport.getAlignment().deleteGroup(sg);
2215 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2217 if (viewport.getAlignment().getHeight() < 1)
2221 this.setClosed(true);
2222 } catch (Exception ex)
2235 protected void deleteGroups_actionPerformed(ActionEvent e)
2237 if (avc.deleteGroups())
2239 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2240 alignPanel.updateAnnotation();
2241 alignPanel.paintAlignment(true);
2252 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2254 SequenceGroup sg = new SequenceGroup();
2256 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2258 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2261 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2262 viewport.setSelectionGroup(sg);
2263 viewport.sendSelection();
2264 alignPanel.paintAlignment(true);
2265 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2275 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2277 if (viewport.cursorMode)
2279 alignPanel.seqPanel.keyboardNo1 = null;
2280 alignPanel.seqPanel.keyboardNo2 = null;
2282 viewport.setSelectionGroup(null);
2283 viewport.getColumnSelection().clear();
2284 viewport.setSelectionGroup(null);
2285 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2286 alignPanel.idPanel.idCanvas.searchResults = null;
2287 alignPanel.paintAlignment(true);
2288 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2289 viewport.sendSelection();
2299 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2301 SequenceGroup sg = viewport.getSelectionGroup();
2305 selectAllSequenceMenuItem_actionPerformed(null);
2310 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2312 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2315 alignPanel.paintAlignment(true);
2316 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2317 viewport.sendSelection();
2321 public void invertColSel_actionPerformed(ActionEvent e)
2323 viewport.invertColumnSelection();
2324 alignPanel.paintAlignment(true);
2325 viewport.sendSelection();
2335 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2337 trimAlignment(true);
2347 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2349 trimAlignment(false);
2352 void trimAlignment(boolean trimLeft)
2354 ColumnSelection colSel = viewport.getColumnSelection();
2357 if (colSel.size() > 0)
2361 column = colSel.getMin();
2365 column = colSel.getMax();
2369 if (viewport.getSelectionGroup() != null)
2371 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2372 viewport.getHiddenRepSequences());
2376 seqs = viewport.getAlignment().getSequencesArray();
2379 TrimRegionCommand trimRegion;
2382 trimRegion = new TrimRegionCommand("Remove Left",
2383 TrimRegionCommand.TRIM_LEFT, seqs, column,
2384 viewport.getAlignment(), viewport.getColumnSelection(),
2385 viewport.getSelectionGroup());
2386 viewport.setStartRes(0);
2390 trimRegion = new TrimRegionCommand("Remove Right",
2391 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2392 viewport.getAlignment(), viewport.getColumnSelection(),
2393 viewport.getSelectionGroup());
2396 statusBar.setText(MessageManager.formatMessage(
2397 "label.removed_columns", new String[]
2398 { Integer.valueOf(trimRegion.getSize()).toString() }));
2400 addHistoryItem(trimRegion);
2402 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2404 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2405 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2407 viewport.getAlignment().deleteGroup(sg);
2411 viewport.firePropertyChange("alignment", null, viewport
2412 .getAlignment().getSequences());
2423 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2425 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2428 if (viewport.getSelectionGroup() != null)
2430 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2431 viewport.getHiddenRepSequences());
2432 start = viewport.getSelectionGroup().getStartRes();
2433 end = viewport.getSelectionGroup().getEndRes();
2437 seqs = viewport.getAlignment().getSequencesArray();
2440 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2441 "Remove Gapped Columns", seqs, start, end,
2442 viewport.getAlignment());
2444 addHistoryItem(removeGapCols);
2446 statusBar.setText(MessageManager.formatMessage(
2447 "label.removed_empty_columns", new String[]
2448 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2450 // This is to maintain viewport position on first residue
2451 // of first sequence
2452 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2453 int startRes = seq.findPosition(viewport.startRes);
2454 // ShiftList shifts;
2455 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2456 // edit.alColumnChanges=shifts.getInverse();
2457 // if (viewport.hasHiddenColumns)
2458 // viewport.getColumnSelection().compensateForEdits(shifts);
2459 viewport.setStartRes(seq.findIndex(startRes) - 1);
2460 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2472 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2474 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2477 if (viewport.getSelectionGroup() != null)
2479 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2480 viewport.getHiddenRepSequences());
2481 start = viewport.getSelectionGroup().getStartRes();
2482 end = viewport.getSelectionGroup().getEndRes();
2486 seqs = viewport.getAlignment().getSequencesArray();
2489 // This is to maintain viewport position on first residue
2490 // of first sequence
2491 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2492 int startRes = seq.findPosition(viewport.startRes);
2494 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2495 viewport.getAlignment()));
2497 viewport.setStartRes(seq.findIndex(startRes) - 1);
2499 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2511 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2513 viewport.setPadGaps(padGapsMenuitem.isSelected());
2514 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2520 // if (justifySeqs>0)
2522 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2535 public void findMenuItem_actionPerformed(ActionEvent e)
2541 public void newView_actionPerformed(ActionEvent e)
2548 * @param copyAnnotation
2549 * if true then duplicate all annnotation, groups and settings
2550 * @return new alignment panel, already displayed.
2552 public AlignmentPanel newView(boolean copyAnnotation)
2554 return newView(null, copyAnnotation);
2560 * title of newly created view
2561 * @return new alignment panel, already displayed.
2563 public AlignmentPanel newView(String viewTitle)
2565 return newView(viewTitle, true);
2571 * title of newly created view
2572 * @param copyAnnotation
2573 * if true then duplicate all annnotation, groups and settings
2574 * @return new alignment panel, already displayed.
2576 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2578 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2580 if (!copyAnnotation)
2582 // just remove all the current annotation except for the automatic stuff
2583 newap.av.getAlignment().deleteAllGroups();
2584 for (AlignmentAnnotation alan : newap.av.getAlignment()
2585 .getAlignmentAnnotation())
2587 if (!alan.autoCalculated)
2589 newap.av.getAlignment().deleteAnnotation(alan);
2595 newap.av.gatherViewsHere = false;
2597 if (viewport.viewName == null)
2599 viewport.viewName = "Original";
2602 newap.av.historyList = viewport.historyList;
2603 newap.av.redoList = viewport.redoList;
2605 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2606 // make sure the new view has a unique name - this is essential for Jalview
2608 boolean addFirstIndex = false;
2609 if (viewTitle == null || viewTitle.trim().length() == 0)
2612 addFirstIndex = true;
2616 index = 1;// we count from 1 if given a specific name
2618 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2619 Vector comps = (Vector) PaintRefresher.components.get(viewport
2620 .getSequenceSetId());
2621 Vector existingNames = new Vector();
2622 for (int i = 0; i < comps.size(); i++)
2624 if (comps.elementAt(i) instanceof AlignmentPanel)
2626 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2627 if (!existingNames.contains(ap.av.viewName))
2629 existingNames.addElement(ap.av.viewName);
2634 while (existingNames.contains(newViewName))
2636 newViewName = viewTitle + " " + (++index);
2639 newap.av.viewName = newViewName;
2641 addAlignmentPanel(newap, true);
2642 newap.alignmentChanged();
2644 if (alignPanels.size() == 2)
2646 viewport.gatherViewsHere = true;
2648 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2653 public void expandViews_actionPerformed(ActionEvent e)
2655 Desktop.instance.explodeViews(this);
2659 public void gatherViews_actionPerformed(ActionEvent e)
2661 Desktop.instance.gatherViews(this);
2671 public void font_actionPerformed(ActionEvent e)
2673 new FontChooser(alignPanel);
2683 protected void seqLimit_actionPerformed(ActionEvent e)
2685 viewport.setShowJVSuffix(seqLimits.isSelected());
2687 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2688 .calculateIdWidth());
2689 alignPanel.paintAlignment(true);
2693 public void idRightAlign_actionPerformed(ActionEvent e)
2695 viewport.rightAlignIds = idRightAlign.isSelected();
2696 alignPanel.paintAlignment(true);
2700 public void centreColumnLabels_actionPerformed(ActionEvent e)
2702 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2703 alignPanel.paintAlignment(true);
2709 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2712 protected void followHighlight_actionPerformed()
2714 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2716 alignPanel.scrollToPosition(
2717 alignPanel.seqPanel.seqCanvas.searchResults, false);
2728 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2730 viewport.setColourText(colourTextMenuItem.isSelected());
2731 alignPanel.paintAlignment(true);
2741 public void wrapMenuItem_actionPerformed(ActionEvent e)
2743 scaleAbove.setVisible(wrapMenuItem.isSelected());
2744 scaleLeft.setVisible(wrapMenuItem.isSelected());
2745 scaleRight.setVisible(wrapMenuItem.isSelected());
2746 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2747 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2751 public void showAllSeqs_actionPerformed(ActionEvent e)
2753 viewport.showAllHiddenSeqs();
2757 public void showAllColumns_actionPerformed(ActionEvent e)
2759 viewport.showAllHiddenColumns();
2764 public void hideSelSequences_actionPerformed(ActionEvent e)
2766 viewport.hideAllSelectedSeqs();
2767 alignPanel.paintAlignment(true);
2771 * called by key handler and the hide all/show all menu items
2776 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2779 boolean hide = false;
2780 SequenceGroup sg = viewport.getSelectionGroup();
2781 if (!toggleSeqs && !toggleCols)
2783 // Hide everything by the current selection - this is a hack - we do the
2784 // invert and then hide
2785 // first check that there will be visible columns after the invert.
2786 if ((viewport.getColumnSelection() != null
2787 && viewport.getColumnSelection().getSelected() != null && viewport
2788 .getColumnSelection().getSelected().size() > 0)
2789 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2792 // now invert the sequence set, if required - empty selection implies
2793 // that no hiding is required.
2796 invertSequenceMenuItem_actionPerformed(null);
2797 sg = viewport.getSelectionGroup();
2801 viewport.expandColSelection(sg, true);
2802 // finally invert the column selection and get the new sequence
2804 invertColSel_actionPerformed(null);
2811 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2813 hideSelSequences_actionPerformed(null);
2816 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2819 showAllSeqs_actionPerformed(null);
2825 if (viewport.getColumnSelection().getSelected().size() > 0)
2827 hideSelColumns_actionPerformed(null);
2830 viewport.setSelectionGroup(sg);
2835 showAllColumns_actionPerformed(null);
2844 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2845 * event.ActionEvent)
2848 public void hideAllButSelection_actionPerformed(ActionEvent e)
2850 toggleHiddenRegions(false, false);
2857 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2861 public void hideAllSelection_actionPerformed(ActionEvent e)
2863 SequenceGroup sg = viewport.getSelectionGroup();
2864 viewport.expandColSelection(sg, false);
2865 viewport.hideAllSelectedSeqs();
2866 viewport.hideSelectedColumns();
2867 alignPanel.paintAlignment(true);
2874 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2878 public void showAllhidden_actionPerformed(ActionEvent e)
2880 viewport.showAllHiddenColumns();
2881 viewport.showAllHiddenSeqs();
2882 alignPanel.paintAlignment(true);
2886 public void hideSelColumns_actionPerformed(ActionEvent e)
2888 viewport.hideSelectedColumns();
2889 alignPanel.paintAlignment(true);
2893 public void hiddenMarkers_actionPerformed(ActionEvent e)
2895 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2906 protected void scaleAbove_actionPerformed(ActionEvent e)
2908 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2909 alignPanel.paintAlignment(true);
2919 protected void scaleLeft_actionPerformed(ActionEvent e)
2921 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2922 alignPanel.paintAlignment(true);
2932 protected void scaleRight_actionPerformed(ActionEvent e)
2934 viewport.setScaleRightWrapped(scaleRight.isSelected());
2935 alignPanel.paintAlignment(true);
2945 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2947 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2948 alignPanel.paintAlignment(true);
2958 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2960 viewport.setShowText(viewTextMenuItem.isSelected());
2961 alignPanel.paintAlignment(true);
2971 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2973 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2974 alignPanel.paintAlignment(true);
2977 public FeatureSettings featureSettings;
2980 public void featureSettings_actionPerformed(ActionEvent e)
2982 if (featureSettings != null)
2984 featureSettings.close();
2985 featureSettings = null;
2987 if (!showSeqFeatures.isSelected())
2989 // make sure features are actually displayed
2990 showSeqFeatures.setSelected(true);
2991 showSeqFeatures_actionPerformed(null);
2993 featureSettings = new FeatureSettings(this);
2997 * Set or clear 'Show Sequence Features'
3003 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3005 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3006 alignPanel.paintAlignment(true);
3007 if (alignPanel.getOverviewPanel() != null)
3009 alignPanel.getOverviewPanel().updateOverviewImage();
3014 * Set or clear 'Show Sequence Features'
3020 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3022 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3024 if (viewport.getShowSequenceFeaturesHeight())
3026 // ensure we're actually displaying features
3027 viewport.setShowSequenceFeatures(true);
3028 showSeqFeatures.setSelected(true);
3030 alignPanel.paintAlignment(true);
3031 if (alignPanel.getOverviewPanel() != null)
3033 alignPanel.getOverviewPanel().updateOverviewImage();
3044 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3046 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
3047 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
3051 public void alignmentProperties()
3053 JEditorPane editPane = new JEditorPane("text/html", "");
3054 editPane.setEditable(false);
3055 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3057 editPane.setText(MessageManager.formatMessage("label.html_content",
3059 { contents.toString() }));
3060 JInternalFrame frame = new JInternalFrame();
3061 frame.getContentPane().add(new JScrollPane(editPane));
3063 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3064 "label.alignment_properties", new String[]
3065 { getTitle() }), 500, 400);
3075 public void overviewMenuItem_actionPerformed(ActionEvent e)
3077 if (alignPanel.overviewPanel != null)
3082 JInternalFrame frame = new JInternalFrame();
3083 OverviewPanel overview = new OverviewPanel(alignPanel);
3084 frame.setContentPane(overview);
3085 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3086 "label.overview_params", new String[]
3087 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3089 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3090 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3093 public void internalFrameClosed(
3094 javax.swing.event.InternalFrameEvent evt)
3096 alignPanel.setOverviewPanel(null);
3100 alignPanel.setOverviewPanel(overview);
3104 public void textColour_actionPerformed(ActionEvent e)
3106 new TextColourChooser().chooseColour(alignPanel, null);
3116 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3128 public void clustalColour_actionPerformed(ActionEvent e)
3130 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3131 viewport.getHiddenRepSequences()));
3141 public void zappoColour_actionPerformed(ActionEvent e)
3143 changeColour(new ZappoColourScheme());
3153 public void taylorColour_actionPerformed(ActionEvent e)
3155 changeColour(new TaylorColourScheme());
3165 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3167 changeColour(new HydrophobicColourScheme());
3177 public void helixColour_actionPerformed(ActionEvent e)
3179 changeColour(new HelixColourScheme());
3189 public void strandColour_actionPerformed(ActionEvent e)
3191 changeColour(new StrandColourScheme());
3201 public void turnColour_actionPerformed(ActionEvent e)
3203 changeColour(new TurnColourScheme());
3213 public void buriedColour_actionPerformed(ActionEvent e)
3215 changeColour(new BuriedColourScheme());
3225 public void nucleotideColour_actionPerformed(ActionEvent e)
3227 changeColour(new NucleotideColourScheme());
3231 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3233 changeColour(new PurinePyrimidineColourScheme());
3237 * public void covariationColour_actionPerformed(ActionEvent e) {
3239 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3243 public void annotationColour_actionPerformed(ActionEvent e)
3245 new AnnotationColourChooser(viewport, alignPanel);
3249 public void rnahelicesColour_actionPerformed(ActionEvent e)
3251 new RNAHelicesColourChooser(viewport, alignPanel);
3261 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3263 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3272 public void changeColour(ColourSchemeI cs)
3274 // TODO: compare with applet and pull up to model method
3279 if (viewport.getAbovePIDThreshold())
3281 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3283 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3287 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3290 if (viewport.getConservationSelected())
3293 Alignment al = (Alignment) viewport.getAlignment();
3294 Conservation c = new Conservation("All",
3295 ResidueProperties.propHash, 3, al.getSequences(), 0,
3299 c.verdict(false, viewport.getConsPercGaps());
3301 cs.setConservation(c);
3303 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3308 cs.setConservation(null);
3311 cs.setConsensus(viewport.getSequenceConsensusHash());
3314 viewport.setGlobalColourScheme(cs);
3316 if (viewport.getColourAppliesToAllGroups())
3319 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3327 if (cs instanceof ClustalxColourScheme)
3329 sg.cs = new ClustalxColourScheme(sg,
3330 viewport.getHiddenRepSequences());
3332 else if (cs instanceof UserColourScheme)
3334 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3340 sg.cs = cs.getClass().newInstance();
3341 } catch (Exception ex)
3346 if (viewport.getAbovePIDThreshold()
3347 || cs instanceof PIDColourScheme
3348 || cs instanceof Blosum62ColourScheme)
3350 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3352 sg.cs.setConsensus(AAFrequency.calculate(
3353 sg.getSequences(viewport.getHiddenRepSequences()),
3354 sg.getStartRes(), sg.getEndRes() + 1));
3358 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3361 if (viewport.getConservationSelected())
3363 Conservation c = new Conservation("Group",
3364 ResidueProperties.propHash, 3, sg.getSequences(viewport
3365 .getHiddenRepSequences()), sg.getStartRes(),
3366 sg.getEndRes() + 1);
3368 c.verdict(false, viewport.getConsPercGaps());
3369 sg.cs.setConservation(c);
3373 sg.cs.setConservation(null);
3378 if (alignPanel.getOverviewPanel() != null)
3380 alignPanel.getOverviewPanel().updateOverviewImage();
3383 alignPanel.paintAlignment(true);
3393 protected void modifyPID_actionPerformed(ActionEvent e)
3395 if (viewport.getAbovePIDThreshold()
3396 && viewport.getGlobalColourScheme() != null)
3398 SliderPanel.setPIDSliderSource(alignPanel,
3399 viewport.getGlobalColourScheme(), "Background");
3400 SliderPanel.showPIDSlider();
3411 protected void modifyConservation_actionPerformed(ActionEvent e)
3413 if (viewport.getConservationSelected()
3414 && viewport.getGlobalColourScheme() != null)
3416 SliderPanel.setConservationSlider(alignPanel,
3417 viewport.getGlobalColourScheme(), "Background");
3418 SliderPanel.showConservationSlider();
3429 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3431 viewport.setConservationSelected(conservationMenuItem.isSelected());
3433 viewport.setAbovePIDThreshold(false);
3434 abovePIDThreshold.setSelected(false);
3436 changeColour(viewport.getGlobalColourScheme());
3438 modifyConservation_actionPerformed(null);
3448 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3450 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3452 conservationMenuItem.setSelected(false);
3453 viewport.setConservationSelected(false);
3455 changeColour(viewport.getGlobalColourScheme());
3457 modifyPID_actionPerformed(null);
3467 public void userDefinedColour_actionPerformed(ActionEvent e)
3469 if (e.getActionCommand().equals(
3470 MessageManager.getString("action.user_defined")))
3472 new UserDefinedColours(alignPanel, null);
3476 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3477 .getUserColourSchemes().get(e.getActionCommand());
3483 public void updateUserColourMenu()
3486 Component[] menuItems = colourMenu.getMenuComponents();
3487 int i, iSize = menuItems.length;
3488 for (i = 0; i < iSize; i++)
3490 if (menuItems[i].getName() != null
3491 && menuItems[i].getName().equals("USER_DEFINED"))
3493 colourMenu.remove(menuItems[i]);
3497 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3499 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3500 .getUserColourSchemes().keys();
3502 while (userColours.hasMoreElements())
3504 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3505 userColours.nextElement().toString());
3506 radioItem.setName("USER_DEFINED");
3507 radioItem.addMouseListener(new MouseAdapter()
3510 public void mousePressed(MouseEvent evt)
3512 if (evt.isControlDown()
3513 || SwingUtilities.isRightMouseButton(evt))
3515 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3517 int option = JOptionPane.showInternalConfirmDialog(
3518 jalview.gui.Desktop.desktop,
3520 .getString("label.remove_from_default_list"),
3522 .getString("label.remove_user_defined_colour"),
3523 JOptionPane.YES_NO_OPTION);
3524 if (option == JOptionPane.YES_OPTION)
3526 jalview.gui.UserDefinedColours
3527 .removeColourFromDefaults(radioItem.getText());
3528 colourMenu.remove(radioItem);
3532 radioItem.addActionListener(new ActionListener()
3535 public void actionPerformed(ActionEvent evt)
3537 userDefinedColour_actionPerformed(evt);
3544 radioItem.addActionListener(new ActionListener()
3547 public void actionPerformed(ActionEvent evt)
3549 userDefinedColour_actionPerformed(evt);
3553 colourMenu.insert(radioItem, 15);
3554 colours.add(radioItem);
3566 public void PIDColour_actionPerformed(ActionEvent e)
3568 changeColour(new PIDColourScheme());
3578 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3580 changeColour(new Blosum62ColourScheme());
3590 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3592 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3593 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3594 .getAlignment().getSequenceAt(0), null);
3595 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3596 viewport.getAlignment()));
3597 alignPanel.paintAlignment(true);
3607 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3609 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3610 AlignmentSorter.sortByID(viewport.getAlignment());
3611 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3612 viewport.getAlignment()));
3613 alignPanel.paintAlignment(true);
3623 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3625 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3626 AlignmentSorter.sortByLength(viewport.getAlignment());
3627 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3628 viewport.getAlignment()));
3629 alignPanel.paintAlignment(true);
3639 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3641 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3642 AlignmentSorter.sortByGroup(viewport.getAlignment());
3643 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3644 viewport.getAlignment()));
3646 alignPanel.paintAlignment(true);
3656 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3658 new RedundancyPanel(alignPanel, this);
3668 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3670 if ((viewport.getSelectionGroup() == null)
3671 || (viewport.getSelectionGroup().getSize() < 2))
3673 JOptionPane.showInternalMessageDialog(this, MessageManager
3674 .getString("label.you_must_select_least_two_sequences"),
3675 MessageManager.getString("label.invalid_selection"),
3676 JOptionPane.WARNING_MESSAGE);
3680 JInternalFrame frame = new JInternalFrame();
3681 frame.setContentPane(new PairwiseAlignPanel(viewport));
3682 Desktop.addInternalFrame(frame,
3683 MessageManager.getString("action.pairwise_alignment"), 600,
3695 public void PCAMenuItem_actionPerformed(ActionEvent e)
3697 if (((viewport.getSelectionGroup() != null)
3698 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3699 .getSelectionGroup().getSize() > 0))
3700 || (viewport.getAlignment().getHeight() < 4))
3703 .showInternalMessageDialog(
3706 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3708 .getString("label.sequence_selection_insufficient"),
3709 JOptionPane.WARNING_MESSAGE);
3714 new PCAPanel(alignPanel);
3718 public void autoCalculate_actionPerformed(ActionEvent e)
3720 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3721 if (viewport.autoCalculateConsensus)
3723 viewport.firePropertyChange("alignment", null, viewport
3724 .getAlignment().getSequences());
3729 public void sortByTreeOption_actionPerformed(ActionEvent e)
3731 viewport.sortByTree = sortByTree.isSelected();
3735 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3737 viewport.followSelection = listenToViewSelections.isSelected();
3747 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3749 NewTreePanel("AV", "PID", "Average distance tree using PID");
3759 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3761 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3771 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3773 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3783 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3785 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3798 void NewTreePanel(String type, String pwType, String title)
3802 if (viewport.getSelectionGroup() != null
3803 && viewport.getSelectionGroup().getSize() > 0)
3805 if (viewport.getSelectionGroup().getSize() < 3)
3811 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3813 .getString("label.not_enough_sequences"),
3814 JOptionPane.WARNING_MESSAGE);
3818 SequenceGroup sg = viewport.getSelectionGroup();
3820 /* Decide if the selection is a column region */
3821 for (SequenceI _s : sg.getSequences())
3823 if (_s.getLength() < sg.getEndRes())
3829 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3831 .getString("label.sequences_selection_not_aligned"),
3832 JOptionPane.WARNING_MESSAGE);
3838 title = title + " on region";
3839 tp = new TreePanel(alignPanel, type, pwType);
3843 // are the visible sequences aligned?
3844 if (!viewport.getAlignment().isAligned(false))
3850 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3852 .getString("label.sequences_not_aligned"),
3853 JOptionPane.WARNING_MESSAGE);
3858 if (viewport.getAlignment().getHeight() < 2)
3863 tp = new TreePanel(alignPanel, type, pwType);
3868 if (viewport.viewName != null)
3870 title += viewport.viewName + " of ";
3873 title += this.title;
3875 Desktop.addInternalFrame(tp, title, 600, 500);
3886 public void addSortByOrderMenuItem(String title,
3887 final AlignmentOrder order)
3889 final JMenuItem item = new JMenuItem("by " + title);
3891 item.addActionListener(new java.awt.event.ActionListener()
3894 public void actionPerformed(ActionEvent e)
3896 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3898 // TODO: JBPNote - have to map order entries to curent SequenceI
3900 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3902 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3905 alignPanel.paintAlignment(true);
3911 * Add a new sort by annotation score menu item
3914 * the menu to add the option to
3916 * the label used to retrieve scores for each sequence on the
3919 public void addSortByAnnotScoreMenuItem(JMenu sort,
3920 final String scoreLabel)
3922 final JMenuItem item = new JMenuItem(scoreLabel);
3924 item.addActionListener(new java.awt.event.ActionListener()
3927 public void actionPerformed(ActionEvent e)
3929 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3930 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3931 viewport.getAlignment());// ,viewport.getSelectionGroup());
3932 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3933 viewport.getAlignment()));
3934 alignPanel.paintAlignment(true);
3940 * last hash for alignment's annotation array - used to minimise cost of
3943 protected int _annotationScoreVectorHash;
3946 * search the alignment and rebuild the sort by annotation score submenu the
3947 * last alignment annotation vector hash is stored to minimize cost of
3948 * rebuilding in subsequence calls.
3952 public void buildSortByAnnotationScoresMenu()
3954 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3959 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3961 sortByAnnotScore.removeAll();
3962 // almost certainly a quicker way to do this - but we keep it simple
3963 Hashtable scoreSorts = new Hashtable();
3964 AlignmentAnnotation aann[];
3965 for (SequenceI sqa : viewport.getAlignment().getSequences())
3967 aann = sqa.getAnnotation();
3968 for (int i = 0; aann != null && i < aann.length; i++)
3970 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3972 scoreSorts.put(aann[i].label, aann[i].label);
3976 Enumeration labels = scoreSorts.keys();
3977 while (labels.hasMoreElements())
3979 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3980 (String) labels.nextElement());
3982 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3985 _annotationScoreVectorHash = viewport.getAlignment()
3986 .getAlignmentAnnotation().hashCode();
3991 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3992 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3993 * call. Listeners are added to remove the menu item when the treePanel is
3994 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3998 * Displayed tree window.
4000 * SortBy menu item title.
4003 public void buildTreeMenu()
4005 calculateTree.removeAll();
4006 // build the calculate menu
4008 for (final String type : new String[]
4011 String treecalcnm = MessageManager.getString("label.tree_calc_"
4012 + type.toLowerCase());
4013 for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4015 JMenuItem tm = new JMenuItem();
4016 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4017 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4019 String smn = MessageManager.getStringOrReturn(
4020 "label.score_model_", sm.getName());
4021 final String title = MessageManager.formatMessage(
4022 "label.treecalc_title", treecalcnm, smn);
4023 tm.setText(title);//
4024 tm.addActionListener(new java.awt.event.ActionListener()
4026 public void actionPerformed(ActionEvent e)
4028 NewTreePanel(type, (String) pwtype, title);
4031 calculateTree.add(tm);
4036 sortByTreeMenu.removeAll();
4038 Vector comps = (Vector) PaintRefresher.components.get(viewport
4039 .getSequenceSetId());
4040 Vector treePanels = new Vector();
4041 int i, iSize = comps.size();
4042 for (i = 0; i < iSize; i++)
4044 if (comps.elementAt(i) instanceof TreePanel)
4046 treePanels.add(comps.elementAt(i));
4050 iSize = treePanels.size();
4054 sortByTreeMenu.setVisible(false);
4058 sortByTreeMenu.setVisible(true);
4060 for (i = 0; i < treePanels.size(); i++)
4062 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4063 final JMenuItem item = new JMenuItem(tp.getTitle());
4064 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4065 item.addActionListener(new java.awt.event.ActionListener()
4068 public void actionPerformed(ActionEvent e)
4070 tp.sortByTree_actionPerformed(null);
4071 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4076 sortByTreeMenu.add(item);
4080 public boolean sortBy(AlignmentOrder alorder, String undoname)
4082 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4083 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4084 if (undoname != null)
4086 addHistoryItem(new OrderCommand(undoname, oldOrder,
4087 viewport.getAlignment()));
4089 alignPanel.paintAlignment(true);
4094 * Work out whether the whole set of sequences or just the selected set will
4095 * be submitted for multiple alignment.
4098 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4100 // Now, check we have enough sequences
4101 AlignmentView msa = null;
4103 if ((viewport.getSelectionGroup() != null)
4104 && (viewport.getSelectionGroup().getSize() > 1))
4106 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4107 // some common interface!
4109 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4110 * SequenceI[sz = seqs.getSize(false)];
4112 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4113 * seqs.getSequenceAt(i); }
4115 msa = viewport.getAlignmentView(true);
4120 * Vector seqs = viewport.getAlignment().getSequences();
4122 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
4124 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
4125 * seqs.elementAt(i); } }
4127 msa = viewport.getAlignmentView(false);
4133 * Decides what is submitted to a secondary structure prediction service: the
4134 * first sequence in the alignment, or in the current selection, or, if the
4135 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4136 * region or the whole alignment. (where the first sequence in the set is the
4137 * one that the prediction will be for).
4139 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4141 AlignmentView seqs = null;
4143 if ((viewport.getSelectionGroup() != null)
4144 && (viewport.getSelectionGroup().getSize() > 0))
4146 seqs = viewport.getAlignmentView(true);
4150 seqs = viewport.getAlignmentView(false);
4152 // limit sequences - JBPNote in future - could spawn multiple prediction
4154 // TODO: viewport.getAlignment().isAligned is a global state - the local
4155 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4156 if (!viewport.getAlignment().isAligned(false))
4158 seqs.setSequences(new SeqCigar[]
4159 { seqs.getSequences()[0] });
4160 // TODO: if seqs.getSequences().length>1 then should really have warned
4174 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4176 // Pick the tree file
4177 JalviewFileChooser chooser = new JalviewFileChooser(
4178 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4179 chooser.setFileView(new JalviewFileView());
4180 chooser.setDialogTitle(MessageManager
4181 .getString("label.select_newick_like_tree_file"));
4182 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4184 int value = chooser.showOpenDialog(null);
4186 if (value == JalviewFileChooser.APPROVE_OPTION)
4188 String choice = chooser.getSelectedFile().getPath();
4189 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4190 jalview.io.NewickFile fin = null;
4193 fin = new jalview.io.NewickFile(choice, "File");
4194 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4195 } catch (Exception ex)
4202 .getString("label.problem_reading_tree_file"),
4203 JOptionPane.WARNING_MESSAGE);
4204 ex.printStackTrace();
4206 if (fin != null && fin.hasWarningMessage())
4208 JOptionPane.showMessageDialog(Desktop.desktop, fin
4209 .getWarningMessage(), MessageManager
4210 .getString("label.possible_problem_with_tree_file"),
4211 JOptionPane.WARNING_MESSAGE);
4217 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4219 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4222 public TreePanel ShowNewickTree(NewickFile nf, String title)
4224 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4227 public TreePanel ShowNewickTree(NewickFile nf, String title,
4228 AlignmentView input)
4230 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4233 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4234 int h, int x, int y)
4236 return ShowNewickTree(nf, title, null, w, h, x, y);
4240 * Add a treeviewer for the tree extracted from a newick file object to the
4241 * current alignment view
4248 * Associated alignment input data (or null)
4257 * @return TreePanel handle
4259 public TreePanel ShowNewickTree(NewickFile nf, String title,
4260 AlignmentView input, int w, int h, int x, int y)
4262 TreePanel tp = null;
4268 if (nf.getTree() != null)
4270 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4276 tp.setLocation(x, y);
4279 Desktop.addInternalFrame(tp, title, w, h);
4281 } catch (Exception ex)
4283 ex.printStackTrace();
4289 private boolean buildingMenu = false;
4292 * Generates menu items and listener event actions for web service clients
4295 public void BuildWebServiceMenu()
4297 while (buildingMenu)
4301 System.err.println("Waiting for building menu to finish.");
4303 } catch (Exception e)
4308 final AlignFrame me = this;
4309 buildingMenu = true;
4310 new Thread(new Runnable()
4315 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4318 System.err.println("Building ws menu again "
4319 + Thread.currentThread());
4320 // TODO: add support for context dependent disabling of services based
4322 // alignment and current selection
4323 // TODO: add additional serviceHandle parameter to specify abstract
4325 // class independently of AbstractName
4326 // TODO: add in rediscovery GUI function to restart discoverer
4327 // TODO: group services by location as well as function and/or
4329 // object broker mechanism.
4330 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4331 final IProgressIndicator af = me;
4332 final JMenu msawsmenu = new JMenu("Alignment");
4333 final JMenu secstrmenu = new JMenu(
4334 "Secondary Structure Prediction");
4335 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4336 final JMenu analymenu = new JMenu("Analysis");
4337 final JMenu dismenu = new JMenu("Protein Disorder");
4338 // JAL-940 - only show secondary structure prediction services from
4339 // the legacy server
4340 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4342 Discoverer.services != null && (Discoverer.services.size() > 0))
4344 // TODO: refactor to allow list of AbstractName/Handler bindings to
4346 // stored or retrieved from elsewhere
4347 // No MSAWS used any more:
4348 // Vector msaws = null; // (Vector)
4349 // Discoverer.services.get("MsaWS");
4350 Vector secstrpr = (Vector) Discoverer.services
4352 if (secstrpr != null)
4354 // Add any secondary structure prediction services
4355 for (int i = 0, j = secstrpr.size(); i < j; i++)
4357 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4359 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4360 .getServiceClient(sh);
4361 int p = secstrmenu.getItemCount();
4362 impl.attachWSMenuEntry(secstrmenu, me);
4363 int q = secstrmenu.getItemCount();
4364 for (int litm = p; litm < q; litm++)
4366 legacyItems.add(secstrmenu.getItem(litm));
4372 // Add all submenus in the order they should appear on the web
4374 wsmenu.add(msawsmenu);
4375 wsmenu.add(secstrmenu);
4376 wsmenu.add(dismenu);
4377 wsmenu.add(analymenu);
4378 // No search services yet
4379 // wsmenu.add(seqsrchmenu);
4381 javax.swing.SwingUtilities.invokeLater(new Runnable()
4388 webService.removeAll();
4389 // first, add discovered services onto the webservices menu
4390 if (wsmenu.size() > 0)
4392 for (int i = 0, j = wsmenu.size(); i < j; i++)
4394 webService.add(wsmenu.get(i));
4399 webService.add(me.webServiceNoServices);
4401 // TODO: move into separate menu builder class.
4402 boolean new_sspred = false;
4403 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4405 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4406 if (jws2servs != null)
4408 if (jws2servs.hasServices())
4410 jws2servs.attachWSMenuEntry(webService, me);
4411 for (Jws2Instance sv : jws2servs.getServices())
4413 if (sv.description.toLowerCase().contains("jpred"))
4415 for (JMenuItem jmi : legacyItems)
4417 jmi.setVisible(false);
4423 if (jws2servs.isRunning())
4425 JMenuItem tm = new JMenuItem(
4426 "Still discovering JABA Services");
4427 tm.setEnabled(false);
4432 build_urlServiceMenu(me.webService);
4433 build_fetchdbmenu(webService);
4434 for (JMenu item : wsmenu)
4436 if (item.getItemCount() == 0)
4438 item.setEnabled(false);
4442 item.setEnabled(true);
4445 } catch (Exception e)
4448 .debug("Exception during web service menu building process.",
4454 } catch (Exception e)
4459 buildingMenu = false;
4466 * construct any groupURL type service menu entries.
4470 private void build_urlServiceMenu(JMenu webService)
4472 // TODO: remove this code when 2.7 is released
4473 // DEBUG - alignmentView
4475 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4476 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4478 * @Override public void actionPerformed(ActionEvent e) {
4479 * jalview.datamodel.AlignmentView
4480 * .testSelectionViews(af.viewport.getAlignment(),
4481 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4483 * }); webService.add(testAlView);
4485 // TODO: refactor to RestClient discoverer and merge menu entries for
4486 // rest-style services with other types of analysis/calculation service
4487 // SHmmr test client - still being implemented.
4488 // DEBUG - alignmentView
4490 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4493 client.attachWSMenuEntry(
4494 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4500 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4501 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4502 * getProperty("LAST_DIRECTORY"));
4504 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4505 * to Vamsas file"); chooser.setToolTipText("Export");
4507 * int value = chooser.showSaveDialog(this);
4509 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4510 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4511 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4512 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4515 * prototype of an automatically enabled/disabled analysis function
4518 protected void setShowProductsEnabled()
4520 SequenceI[] selection = viewport.getSequenceSelection();
4521 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4522 viewport.getAlignment().getDataset()))
4524 showProducts.setEnabled(true);
4529 showProducts.setEnabled(false);
4534 * search selection for sequence xRef products and build the show products
4539 * @return true if showProducts menu should be enabled.
4541 public boolean canShowProducts(SequenceI[] selection,
4542 boolean isRegionSelection, Alignment dataset)
4544 boolean showp = false;
4547 showProducts.removeAll();
4548 final boolean dna = viewport.getAlignment().isNucleotide();
4549 final Alignment ds = dataset;
4550 String[] ptypes = (selection == null || selection.length == 0) ? null
4551 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4553 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4554 // selection, dataset, true);
4555 final SequenceI[] sel = selection;
4556 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4559 final boolean isRegSel = isRegionSelection;
4560 final AlignFrame af = this;
4561 final String source = ptypes[t];
4562 JMenuItem xtype = new JMenuItem(ptypes[t]);
4563 xtype.addActionListener(new ActionListener()
4567 public void actionPerformed(ActionEvent e)
4569 // TODO: new thread for this call with vis-delay
4570 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4571 isRegSel, dna, source);
4575 showProducts.add(xtype);
4577 showProducts.setVisible(showp);
4578 showProducts.setEnabled(showp);
4579 } catch (Exception e)
4581 jalview.bin.Cache.log
4582 .warn("canTranslate threw an exception - please report to help@jalview.org",
4589 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4590 boolean isRegSel, boolean dna, String source)
4592 final boolean fisRegSel = isRegSel;
4593 final boolean fdna = dna;
4594 final String fsrc = source;
4595 final AlignFrame ths = this;
4596 final SequenceI[] fsel = sel;
4597 Runnable foo = new Runnable()
4603 final long sttime = System.currentTimeMillis();
4604 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4607 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4611 Alignment prods = CrossRef
4612 .findXrefSequences(fsel, fdna, fsrc, ds);
4615 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4616 for (int s = 0; s < sprods.length; s++)
4618 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4619 if (ds.getSequences() == null
4620 || !ds.getSequences().contains(
4621 sprods[s].getDatasetSequence()))
4622 ds.addSequence(sprods[s].getDatasetSequence());
4623 sprods[s].updatePDBIds();
4625 Alignment al = new Alignment(sprods);
4626 AlignedCodonFrame[] cf = prods.getCodonFrames();
4628 for (int s = 0; cf != null && s < cf.length; s++)
4630 al.addCodonFrame(cf[s]);
4633 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4635 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4636 + " for " + ((fisRegSel) ? "selected region of " : "")
4638 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4643 System.err.println("No Sequences generated for xRef type "
4646 } catch (Exception e)
4648 jalview.bin.Cache.log.error(
4649 "Exception when finding crossreferences", e);
4650 } catch (OutOfMemoryError e)
4652 new OOMWarning("whilst fetching crossreferences", e);
4655 jalview.bin.Cache.log.error("Error when finding crossreferences",
4658 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4663 Thread frunner = new Thread(foo);
4667 public boolean canShowTranslationProducts(SequenceI[] selection,
4668 AlignmentI alignment)
4673 return (jalview.analysis.Dna.canTranslate(selection,
4674 viewport.getViewAsVisibleContigs(true)));
4675 } catch (Exception e)
4677 jalview.bin.Cache.log
4678 .warn("canTranslate threw an exception - please report to help@jalview.org",
4685 public void showProducts_actionPerformed(ActionEvent e)
4687 // /////////////////////////////
4688 // Collect Data to be translated/transferred
4690 SequenceI[] selection = viewport.getSequenceSelection();
4691 AlignmentI al = null;
4694 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4695 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4696 viewport.getAlignment().getDataset());
4697 } catch (Exception ex)
4700 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4708 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4709 MessageManager.getString("label.translation_failed"),
4710 JOptionPane.WARNING_MESSAGE);
4714 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4715 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4716 "label.translation_of_params", new String[]
4717 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4722 public void showTranslation_actionPerformed(ActionEvent e)
4724 // /////////////////////////////
4725 // Collect Data to be translated/transferred
4727 SequenceI[] selection = viewport.getSequenceSelection();
4728 String[] seqstring = viewport.getViewAsString(true);
4729 AlignmentI al = null;
4732 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4733 viewport.getViewAsVisibleContigs(true), viewport
4734 .getGapCharacter(), viewport.getAlignment()
4735 .getAlignmentAnnotation(), viewport.getAlignment()
4736 .getWidth(), viewport.getAlignment().getDataset());
4737 } catch (Exception ex)
4740 jalview.bin.Cache.log.error(
4741 "Exception during translation. Please report this !", ex);
4746 .getString("label.error_when_translating_sequences_submit_bug_report"),
4748 .getString("label.implementation_error")
4750 .getString("translation_failed"),
4751 JOptionPane.ERROR_MESSAGE);
4760 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4761 MessageManager.getString("label.translation_failed"),
4762 JOptionPane.WARNING_MESSAGE);
4766 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4767 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4768 "label.translation_of_params", new String[]
4769 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4774 * Try to load a features file onto the alignment.
4777 * contents or path to retrieve file
4779 * access mode of file (see jalview.io.AlignFile)
4780 * @return true if features file was parsed corectly.
4782 public boolean parseFeaturesFile(String file, String type)
4784 boolean featuresFile = false;
4787 featuresFile = new FeaturesFile(file, type).parse(viewport
4788 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4789 .getFeatureRenderer().featureColours, false,
4790 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4791 } catch (Exception ex)
4793 ex.printStackTrace();
4798 viewport.showSequenceFeatures = true;
4799 showSeqFeatures.setSelected(true);
4800 if (alignPanel.seqPanel.seqCanvas.fr != null)
4802 // update the min/max ranges where necessary
4803 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4805 if (featureSettings != null)
4807 featureSettings.setTableData();
4809 alignPanel.paintAlignment(true);
4812 return featuresFile;
4816 public void dragEnter(DropTargetDragEvent evt)
4821 public void dragExit(DropTargetEvent evt)
4826 public void dragOver(DropTargetDragEvent evt)
4831 public void dropActionChanged(DropTargetDragEvent evt)
4836 public void drop(DropTargetDropEvent evt)
4838 Transferable t = evt.getTransferable();
4839 java.util.List files = null;
4843 DataFlavor uriListFlavor = new DataFlavor(
4844 "text/uri-list;class=java.lang.String");
4845 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4847 // Works on Windows and MacOSX
4848 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4849 files = (java.util.List) t
4850 .getTransferData(DataFlavor.javaFileListFlavor);
4852 else if (t.isDataFlavorSupported(uriListFlavor))
4854 // This is used by Unix drag system
4855 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4856 String data = (String) t.getTransferData(uriListFlavor);
4857 files = new java.util.ArrayList(1);
4858 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4859 data, "\r\n"); st.hasMoreTokens();)
4861 String s = st.nextToken();
4862 if (s.startsWith("#"))
4864 // the line is a comment (as per the RFC 2483)
4868 java.net.URI uri = new java.net.URI(s);
4869 // check to see if we can handle this kind of URI
4870 if (uri.getScheme().toLowerCase().startsWith("http"))
4872 files.add(uri.toString());
4876 // otherwise preserve old behaviour: catch all for file objects
4877 java.io.File file = new java.io.File(uri);
4878 files.add(file.toString());
4882 } catch (Exception e)
4884 e.printStackTrace();
4890 // check to see if any of these files have names matching sequences in
4892 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4893 .getAlignment().getSequencesArray());
4895 * Object[] { String,SequenceI}
4897 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4898 ArrayList<String> filesnotmatched = new ArrayList<String>();
4899 for (int i = 0; i < files.size(); i++)
4901 String file = files.get(i).toString();
4903 String protocol = FormatAdapter.checkProtocol(file);
4904 if (protocol == jalview.io.FormatAdapter.FILE)
4906 File fl = new File(file);
4907 pdbfn = fl.getName();
4909 else if (protocol == jalview.io.FormatAdapter.URL)
4911 URL url = new URL(file);
4912 pdbfn = url.getFile();
4914 if (pdbfn.length() > 0)
4916 // attempt to find a match in the alignment
4917 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4918 int l = 0, c = pdbfn.indexOf(".");
4919 while (mtch == null && c != -1)
4924 } while ((c = pdbfn.indexOf(".", l)) > l);
4927 pdbfn = pdbfn.substring(0, l);
4929 mtch = idm.findAllIdMatches(pdbfn);
4936 type = new IdentifyFile().Identify(file, protocol);
4937 } catch (Exception ex)
4943 if (type.equalsIgnoreCase("PDB"))
4945 filesmatched.add(new Object[]
4946 { file, protocol, mtch });
4951 // File wasn't named like one of the sequences or wasn't a PDB file.
4952 filesnotmatched.add(file);
4956 if (filesmatched.size() > 0)
4958 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4964 "label.automatically_associate_pdb_files_with_sequences_same_name",
4971 .getString("label.automatically_associate_pdb_files_by_name"),
4972 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4975 for (Object[] fm : filesmatched)
4977 // try and associate
4978 // TODO: may want to set a standard ID naming formalism for
4979 // associating PDB files which have no IDs.
4980 for (SequenceI toassoc : (SequenceI[]) fm[2])
4982 PDBEntry pe = new AssociatePdbFileWithSeq()
4983 .associatePdbWithSeq((String) fm[0],
4984 (String) fm[1], toassoc, false);
4987 System.err.println("Associated file : "
4988 + ((String) fm[0]) + " with "
4989 + toassoc.getDisplayId(true));
4993 alignPanel.paintAlignment(true);
4997 if (filesnotmatched.size() > 0)
5000 && (Cache.getDefault(
5001 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5006 "label.ignore_unmatched_dropped_files_info",
5013 .getString("label.ignore_unmatched_dropped_files"),
5014 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5018 for (String fn : filesnotmatched)
5020 loadJalviewDataFile(fn, null, null, null);
5024 } catch (Exception ex)
5026 ex.printStackTrace();
5032 * Attempt to load a "dropped" file or URL string: First by testing whether
5033 * it's and Annotation file, then a JNet file, and finally a features file. If
5034 * all are false then the user may have dropped an alignment file onto this
5038 * either a filename or a URL string.
5040 public void loadJalviewDataFile(String file, String protocol,
5041 String format, SequenceI assocSeq)
5045 if (protocol == null)
5047 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5049 // if the file isn't identified, or not positively identified as some
5050 // other filetype (PFAM is default unidentified alignment file type) then
5051 // try to parse as annotation.
5052 boolean isAnnotation = (format == null || format
5053 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5054 .readAnnotationFile(viewport.getAlignment(), file, protocol)
5059 // first see if its a T-COFFEE score file
5060 TCoffeeScoreFile tcf = null;
5063 tcf = new TCoffeeScoreFile(file, protocol);
5066 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5068 tcoffeeColour.setEnabled(true);
5069 tcoffeeColour.setSelected(true);
5070 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5071 isAnnotation = true;
5073 .setText(MessageManager
5074 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5078 // some problem - if no warning its probable that the ID matching
5079 // process didn't work
5083 tcf.getWarningMessage() == null ? MessageManager
5084 .getString("label.check_file_matches_sequence_ids_alignment")
5085 : tcf.getWarningMessage(),
5087 .getString("label.problem_reading_tcoffee_score_file"),
5088 JOptionPane.WARNING_MESSAGE);
5095 } catch (Exception x)
5098 .debug("Exception when processing data source as T-COFFEE score file",
5104 // try to see if its a JNet 'concise' style annotation file *before*
5106 // try to parse it as a features file
5109 format = new IdentifyFile().Identify(file, protocol);
5111 if (format.equalsIgnoreCase("JnetFile"))
5113 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5115 new JnetAnnotationMaker().add_annotation(predictions,
5116 viewport.getAlignment(), 0, false);
5117 isAnnotation = true;
5122 * if (format.equalsIgnoreCase("PDB")) {
5124 * String pdbfn = ""; // try to match up filename with sequence id
5125 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5126 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5127 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5128 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5129 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5130 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5131 * // attempt to find a match in the alignment SequenceI mtch =
5132 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5133 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5134 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5135 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5136 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5137 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5138 * { System.err.println("Associated file : " + file + " with " +
5139 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5140 * TODO: maybe need to load as normal otherwise return; } }
5142 // try to parse it as a features file
5143 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5144 // if it wasn't a features file then we just treat it as a general
5145 // alignment file to load into the current view.
5148 new FileLoader().LoadFile(viewport, file, protocol, format);
5152 alignPanel.paintAlignment(true);
5160 alignPanel.adjustAnnotationHeight();
5161 viewport.updateSequenceIdColours();
5162 buildSortByAnnotationScoresMenu();
5163 alignPanel.paintAlignment(true);
5165 } catch (Exception ex)
5167 ex.printStackTrace();
5168 } catch (OutOfMemoryError oom)
5173 } catch (Exception x)
5179 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5180 : "using " + protocol + " from " + file)
5182 + (format != null ? "(parsing as '" + format
5183 + "' file)" : ""), oom, Desktop.desktop);
5188 public void tabSelectionChanged(int index)
5192 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5193 viewport = alignPanel.av;
5194 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5195 setMenusFromViewport(viewport);
5200 public void tabbedPane_mousePressed(MouseEvent e)
5202 if (SwingUtilities.isRightMouseButton(e))
5204 String reply = JOptionPane.showInternalInputDialog(this,
5205 MessageManager.getString("label.enter_view_name"),
5206 MessageManager.getString("label.enter_view_name"),
5207 JOptionPane.QUESTION_MESSAGE);
5211 viewport.viewName = reply;
5212 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5217 public AlignViewport getCurrentView()
5223 * Open the dialog for regex description parsing.
5226 protected void extractScores_actionPerformed(ActionEvent e)
5228 ParseProperties pp = new jalview.analysis.ParseProperties(
5229 viewport.getAlignment());
5230 // TODO: verify regex and introduce GUI dialog for version 2.5
5231 // if (pp.getScoresFromDescription("col", "score column ",
5232 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5234 if (pp.getScoresFromDescription("description column",
5235 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5237 buildSortByAnnotationScoresMenu();
5245 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5249 protected void showDbRefs_actionPerformed(ActionEvent e)
5251 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5257 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5261 protected void showNpFeats_actionPerformed(ActionEvent e)
5263 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5267 * find the viewport amongst the tabs in this alignment frame and close that
5272 public boolean closeView(AlignViewport av)
5276 this.closeMenuItem_actionPerformed(false);
5279 Component[] comp = tabbedPane.getComponents();
5280 for (int i = 0; comp != null && i < comp.length; i++)
5282 if (comp[i] instanceof AlignmentPanel)
5284 if (((AlignmentPanel) comp[i]).av == av)
5287 closeView((AlignmentPanel) comp[i]);
5295 protected void build_fetchdbmenu(JMenu webService)
5297 // Temporary hack - DBRef Fetcher always top level ws entry.
5298 // TODO We probably want to store a sequence database checklist in
5299 // preferences and have checkboxes.. rather than individual sources selected
5301 final JMenu rfetch = new JMenu(
5302 MessageManager.getString("action.fetch_db_references"));
5303 rfetch.setToolTipText(MessageManager
5304 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5305 webService.add(rfetch);
5307 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5308 MessageManager.getString("option.trim_retrieved_seqs"));
5309 trimrs.setToolTipText(MessageManager
5310 .getString("label.trim_retrieved_sequences"));
5311 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5312 trimrs.addActionListener(new ActionListener()
5314 public void actionPerformed(ActionEvent e)
5316 trimrs.setSelected(trimrs.isSelected());
5317 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5318 Boolean.valueOf(trimrs.isSelected()).toString());
5322 JMenuItem fetchr = new JMenuItem(
5323 MessageManager.getString("label.standard_databases"));
5324 fetchr.setToolTipText(MessageManager
5325 .getString("label.fetch_embl_uniprot"));
5326 fetchr.addActionListener(new ActionListener()
5330 public void actionPerformed(ActionEvent e)
5332 new Thread(new Runnable()
5338 new jalview.ws.DBRefFetcher(alignPanel.av
5339 .getSequenceSelection(), alignPanel.alignFrame)
5340 .fetchDBRefs(false);
5348 final AlignFrame me = this;
5349 new Thread(new Runnable()
5354 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5355 .getSequenceFetcherSingleton(me);
5356 javax.swing.SwingUtilities.invokeLater(new Runnable()
5361 String[] dbclasses = sf.getOrderedSupportedSources();
5362 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5363 // jalview.util.QuickSort.sort(otherdb, otherdb);
5364 List<DbSourceProxy> otherdb;
5365 JMenu dfetch = new JMenu();
5366 JMenu ifetch = new JMenu();
5367 JMenuItem fetchr = null;
5368 int comp = 0, icomp = 0, mcomp = 15;
5369 String mname = null;
5371 for (String dbclass : dbclasses)
5373 otherdb = sf.getSourceProxy(dbclass);
5374 // add a single entry for this class, or submenu allowing 'fetch
5376 if (otherdb == null || otherdb.size() < 1)
5380 // List<DbSourceProxy> dbs=otherdb;
5381 // otherdb=new ArrayList<DbSourceProxy>();
5382 // for (DbSourceProxy db:dbs)
5384 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5388 mname = "From " + dbclass;
5390 if (otherdb.size() == 1)
5392 final DbSourceProxy[] dassource = otherdb
5393 .toArray(new DbSourceProxy[0]);
5394 DbSourceProxy src = otherdb.get(0);
5395 fetchr = new JMenuItem(src.getDbSource());
5396 fetchr.addActionListener(new ActionListener()
5400 public void actionPerformed(ActionEvent e)
5402 new Thread(new Runnable()
5408 new jalview.ws.DBRefFetcher(alignPanel.av
5409 .getSequenceSelection(),
5410 alignPanel.alignFrame, dassource)
5411 .fetchDBRefs(false);
5417 fetchr.setToolTipText("<html>"
5418 + JvSwingUtils.wrapTooltip("Retrieve from "
5419 + src.getDbName()) + "<html>");
5425 final DbSourceProxy[] dassource = otherdb
5426 .toArray(new DbSourceProxy[0]);
5428 DbSourceProxy src = otherdb.get(0);
5429 fetchr = new JMenuItem(MessageManager.formatMessage(
5430 "label.fetch_all_param", new String[]
5431 { src.getDbSource() }));
5432 fetchr.addActionListener(new ActionListener()
5435 public void actionPerformed(ActionEvent e)
5437 new Thread(new Runnable()
5443 new jalview.ws.DBRefFetcher(alignPanel.av
5444 .getSequenceSelection(),
5445 alignPanel.alignFrame, dassource)
5446 .fetchDBRefs(false);
5452 fetchr.setToolTipText("<html>"
5453 + JvSwingUtils.wrapTooltip("Retrieve from all "
5454 + otherdb.size() + " sources in "
5455 + src.getDbSource() + "<br>First is :"
5456 + src.getDbName()) + "<html>");
5459 // and then build the rest of the individual menus
5460 ifetch = new JMenu("Sources from " + src.getDbSource());
5462 String imname = null;
5464 for (DbSourceProxy sproxy : otherdb)
5466 String dbname = sproxy.getDbName();
5467 String sname = dbname.length() > 5 ? dbname.substring(0,
5468 5) + "..." : dbname;
5469 String msname = dbname.length() > 10 ? dbname.substring(
5470 0, 10) + "..." : dbname;
5473 imname = "from '" + sname + "'";
5475 fetchr = new JMenuItem(msname);
5476 final DbSourceProxy[] dassrc =
5478 fetchr.addActionListener(new ActionListener()
5482 public void actionPerformed(ActionEvent e)
5484 new Thread(new Runnable()
5490 new jalview.ws.DBRefFetcher(alignPanel.av
5491 .getSequenceSelection(),
5492 alignPanel.alignFrame, dassrc)
5493 .fetchDBRefs(false);
5499 fetchr.setToolTipText("<html>"
5500 + JvSwingUtils.wrapTooltip("Retrieve from "
5501 + dbname) + "</html>");
5504 if (++icomp >= mcomp || i == (otherdb.size()))
5506 ifetch.setText(MessageManager.formatMessage(
5507 "label.source_to_target", imname, sname));
5509 ifetch = new JMenu();
5517 if (comp >= mcomp || dbi >= (dbclasses.length))
5519 dfetch.setText(MessageManager.formatMessage(
5520 "label.source_to_target", mname, dbclass));
5522 dfetch = new JMenu();
5535 * Left justify the whole alignment.
5538 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5540 AlignmentI al = viewport.getAlignment();
5542 viewport.firePropertyChange("alignment", null, al);
5546 * Right justify the whole alignment.
5549 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5551 AlignmentI al = viewport.getAlignment();
5553 viewport.firePropertyChange("alignment", null, al);
5556 public void setShowSeqFeatures(boolean b)
5558 showSeqFeatures.setSelected(true);
5559 viewport.setShowSequenceFeatures(true);
5566 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5567 * awt.event.ActionEvent)
5570 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5572 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5573 alignPanel.paintAlignment(true);
5580 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5584 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5586 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5587 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5595 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5596 * .event.ActionEvent)
5599 protected void showGroupConservation_actionPerformed(ActionEvent e)
5601 viewport.setShowGroupConservation(showGroupConservation.getState());
5602 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5609 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5610 * .event.ActionEvent)
5613 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5615 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5616 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5623 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5624 * .event.ActionEvent)
5627 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5629 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5630 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5634 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5636 showSequenceLogo.setState(true);
5637 viewport.setShowSequenceLogo(true);
5638 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5639 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5643 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5645 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5652 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5653 * .event.ActionEvent)
5656 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5658 if (avc.makeGroupsFromSelection())
5660 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5661 alignPanel.updateAnnotation();
5662 alignPanel.paintAlignment(true);
5667 protected void createGroup_actionPerformed(ActionEvent e)
5669 if (avc.createGroup())
5671 alignPanel.alignmentChanged();
5676 protected void unGroup_actionPerformed(ActionEvent e)
5680 alignPanel.alignmentChanged();
5685 * make the given alignmentPanel the currently selected tab
5687 * @param alignmentPanel
5689 public void setDisplayedView(AlignmentPanel alignmentPanel)
5691 if (!viewport.getSequenceSetId().equals(
5692 alignmentPanel.av.getSequenceSetId()))
5695 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5697 if (tabbedPane != null
5698 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5699 .getSelectedIndex())
5701 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5706 class PrintThread extends Thread
5710 public PrintThread(AlignmentPanel ap)
5715 static PageFormat pf;
5720 PrinterJob printJob = PrinterJob.getPrinterJob();
5724 printJob.setPrintable(ap, pf);
5728 printJob.setPrintable(ap);
5731 if (printJob.printDialog())
5736 } catch (Exception PrintException)
5738 PrintException.printStackTrace();