2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.AlignmentSorter;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.analysis.CrossRef;
28 import jalview.analysis.NJTree;
29 import jalview.analysis.ParseProperties;
30 import jalview.analysis.SequenceIdMatcher;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.analysis.ScoreModelI;
34 import jalview.bin.Cache;
35 import jalview.commands.CommandI;
36 import jalview.commands.EditCommand;
37 import jalview.commands.OrderCommand;
38 import jalview.commands.RemoveGapColCommand;
39 import jalview.commands.RemoveGapsCommand;
40 import jalview.commands.SlideSequencesCommand;
41 import jalview.commands.TrimRegionCommand;
42 import jalview.datamodel.AlignedCodonFrame;
43 import jalview.datamodel.Alignment;
44 import jalview.datamodel.AlignmentAnnotation;
45 import jalview.datamodel.AlignmentI;
46 import jalview.datamodel.AlignmentOrder;
47 import jalview.datamodel.AlignmentView;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.PDBEntry;
50 import jalview.datamodel.SeqCigar;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AlignmentProperties;
55 import jalview.io.AnnotationFile;
56 import jalview.io.FeaturesFile;
57 import jalview.io.FileLoader;
58 import jalview.io.FormatAdapter;
59 import jalview.io.HTMLOutput;
60 import jalview.io.IdentifyFile;
61 import jalview.io.JalviewFileChooser;
62 import jalview.io.JalviewFileView;
63 import jalview.io.JnetAnnotationMaker;
64 import jalview.io.NewickFile;
65 import jalview.io.TCoffeeScoreFile;
66 import jalview.jbgui.GAlignFrame;
67 import jalview.schemes.Blosum62ColourScheme;
68 import jalview.schemes.BuriedColourScheme;
69 import jalview.schemes.ClustalxColourScheme;
70 import jalview.schemes.ColourSchemeI;
71 import jalview.schemes.ColourSchemeProperty;
72 import jalview.schemes.HelixColourScheme;
73 import jalview.schemes.HydrophobicColourScheme;
74 import jalview.schemes.NucleotideColourScheme;
75 import jalview.schemes.PIDColourScheme;
76 import jalview.schemes.PurinePyrimidineColourScheme;
77 import jalview.schemes.RNAHelicesColourChooser;
78 import jalview.schemes.ResidueProperties;
79 import jalview.schemes.StrandColourScheme;
80 import jalview.schemes.TCoffeeColourScheme;
81 import jalview.schemes.TaylorColourScheme;
82 import jalview.schemes.TurnColourScheme;
83 import jalview.schemes.UserColourScheme;
84 import jalview.schemes.ZappoColourScheme;
85 import jalview.util.MessageManager;
86 import jalview.ws.jws1.Discoverer;
87 import jalview.ws.jws2.Jws2Discoverer;
88 import jalview.ws.jws2.jabaws2.Jws2Instance;
89 import jalview.ws.seqfetcher.DbSourceProxy;
91 import java.awt.BorderLayout;
92 import java.awt.Component;
93 import java.awt.GridLayout;
94 import java.awt.Rectangle;
95 import java.awt.Toolkit;
96 import java.awt.datatransfer.Clipboard;
97 import java.awt.datatransfer.DataFlavor;
98 import java.awt.datatransfer.StringSelection;
99 import java.awt.datatransfer.Transferable;
100 import java.awt.dnd.DnDConstants;
101 import java.awt.dnd.DropTargetDragEvent;
102 import java.awt.dnd.DropTargetDropEvent;
103 import java.awt.dnd.DropTargetEvent;
104 import java.awt.dnd.DropTargetListener;
105 import java.awt.event.ActionEvent;
106 import java.awt.event.ActionListener;
107 import java.awt.event.KeyAdapter;
108 import java.awt.event.KeyEvent;
109 import java.awt.event.MouseAdapter;
110 import java.awt.event.MouseEvent;
111 import java.awt.print.PageFormat;
112 import java.awt.print.PrinterJob;
113 import java.beans.PropertyChangeEvent;
116 import java.util.ArrayList;
117 import java.util.Enumeration;
118 import java.util.Hashtable;
119 import java.util.List;
120 import java.util.Vector;
122 import javax.swing.JButton;
123 import javax.swing.JCheckBoxMenuItem;
124 import javax.swing.JEditorPane;
125 import javax.swing.JInternalFrame;
126 import javax.swing.JLabel;
127 import javax.swing.JLayeredPane;
128 import javax.swing.JMenu;
129 import javax.swing.JMenuItem;
130 import javax.swing.JOptionPane;
131 import javax.swing.JPanel;
132 import javax.swing.JProgressBar;
133 import javax.swing.JRadioButtonMenuItem;
134 import javax.swing.JScrollPane;
135 import javax.swing.SwingUtilities;
141 * @version $Revision$
143 public class AlignFrame extends GAlignFrame implements DropTargetListener,
144 IProgressIndicator, AlignViewControllerGuiI
148 public static final int DEFAULT_WIDTH = 700;
151 public static final int DEFAULT_HEIGHT = 500;
153 public AlignmentPanel alignPanel;
155 AlignViewport viewport;
157 public AlignViewControllerI avc;
159 Vector alignPanels = new Vector();
162 * Last format used to load or save alignments in this window
164 String currentFileFormat = null;
167 * Current filename for this alignment
169 String fileName = null;
172 * Creates a new AlignFrame object with specific width and height.
178 public AlignFrame(AlignmentI al, int width, int height)
180 this(al, null, width, height);
184 * Creates a new AlignFrame object with specific width, height and
190 * @param sequenceSetId
192 public AlignFrame(AlignmentI al, int width, int height,
193 String sequenceSetId)
195 this(al, null, width, height, sequenceSetId);
199 * Creates a new AlignFrame object with specific width, height and
205 * @param sequenceSetId
208 public AlignFrame(AlignmentI al, int width, int height,
209 String sequenceSetId, String viewId)
211 this(al, null, width, height, sequenceSetId, viewId);
215 * new alignment window with hidden columns
219 * @param hiddenColumns
220 * ColumnSelection or null
222 * Width of alignment frame
226 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
227 int width, int height)
229 this(al, hiddenColumns, width, height, null);
233 * Create alignment frame for al with hiddenColumns, a specific width and
234 * height, and specific sequenceId
237 * @param hiddenColumns
240 * @param sequenceSetId
243 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
244 int width, int height, String sequenceSetId)
246 this(al, hiddenColumns, width, height, sequenceSetId, null);
250 * Create alignment frame for al with hiddenColumns, a specific width and
251 * height, and specific sequenceId
254 * @param hiddenColumns
257 * @param sequenceSetId
262 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
263 int width, int height, String sequenceSetId, String viewId)
265 setSize(width, height);
267 if (al.getDataset() == null)
272 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
274 alignPanel = new AlignmentPanel(this, viewport);
277 addAlignmentPanel(alignPanel, true);
282 * Make a new AlignFrame from exisiting alignmentPanels
289 public AlignFrame(AlignmentPanel ap)
293 addAlignmentPanel(ap, false);
298 * initalise the alignframe from the underlying viewport data and the
303 avc = new jalview.controller.AlignViewController(this, viewport,
305 if (viewport.getAlignmentConservationAnnotation() == null)
307 BLOSUM62Colour.setEnabled(false);
308 conservationMenuItem.setEnabled(false);
309 modifyConservation.setEnabled(false);
310 // PIDColour.setEnabled(false);
311 // abovePIDThreshold.setEnabled(false);
312 // modifyPID.setEnabled(false);
315 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
318 if (sortby.equals("Id"))
320 sortIDMenuItem_actionPerformed(null);
322 else if (sortby.equals("Pairwise Identity"))
324 sortPairwiseMenuItem_actionPerformed(null);
327 if (Desktop.desktop != null)
329 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
330 addServiceListeners();
331 setGUINucleotide(viewport.getAlignment().isNucleotide());
334 setMenusFromViewport(viewport);
335 buildSortByAnnotationScoresMenu();
337 if (viewport.wrapAlignment)
339 wrapMenuItem_actionPerformed(null);
342 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
344 this.overviewMenuItem_actionPerformed(null);
352 * Change the filename and format for the alignment, and enable the 'reload'
353 * button functionality.
360 public void setFileName(String file, String format)
363 currentFileFormat = format;
364 reload.setEnabled(true);
367 void addKeyListener()
369 addKeyListener(new KeyAdapter()
372 public void keyPressed(KeyEvent evt)
374 if (viewport.cursorMode
375 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
376 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
377 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
378 && Character.isDigit(evt.getKeyChar()))
379 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
381 switch (evt.getKeyCode())
384 case 27: // escape key
385 deselectAllSequenceMenuItem_actionPerformed(null);
389 case KeyEvent.VK_DOWN:
390 if (evt.isAltDown() || !viewport.cursorMode)
391 moveSelectedSequences(false);
392 if (viewport.cursorMode)
393 alignPanel.seqPanel.moveCursor(0, 1);
397 if (evt.isAltDown() || !viewport.cursorMode)
398 moveSelectedSequences(true);
399 if (viewport.cursorMode)
400 alignPanel.seqPanel.moveCursor(0, -1);
404 case KeyEvent.VK_LEFT:
405 if (evt.isAltDown() || !viewport.cursorMode)
406 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
408 alignPanel.seqPanel.moveCursor(-1, 0);
412 case KeyEvent.VK_RIGHT:
413 if (evt.isAltDown() || !viewport.cursorMode)
414 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
416 alignPanel.seqPanel.moveCursor(1, 0);
419 case KeyEvent.VK_SPACE:
420 if (viewport.cursorMode)
422 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
423 || evt.isShiftDown() || evt.isAltDown());
427 // case KeyEvent.VK_A:
428 // if (viewport.cursorMode)
430 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
431 // //System.out.println("A");
435 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
436 * System.out.println("closing bracket"); } break;
438 case KeyEvent.VK_DELETE:
439 case KeyEvent.VK_BACK_SPACE:
440 if (!viewport.cursorMode)
442 cut_actionPerformed(null);
446 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
447 || evt.isShiftDown() || evt.isAltDown());
453 if (viewport.cursorMode)
455 alignPanel.seqPanel.setCursorRow();
459 if (viewport.cursorMode && !evt.isControlDown())
461 alignPanel.seqPanel.setCursorColumn();
465 if (viewport.cursorMode)
467 alignPanel.seqPanel.setCursorPosition();
471 case KeyEvent.VK_ENTER:
472 case KeyEvent.VK_COMMA:
473 if (viewport.cursorMode)
475 alignPanel.seqPanel.setCursorRowAndColumn();
480 if (viewport.cursorMode)
482 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
486 if (viewport.cursorMode)
488 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
493 viewport.cursorMode = !viewport.cursorMode;
494 statusBar.setText(MessageManager.formatMessage(
495 "label.keyboard_editing_mode", new String[]
496 { (viewport.cursorMode ? "on" : "off") }));
497 if (viewport.cursorMode)
499 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
500 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
502 alignPanel.seqPanel.seqCanvas.repaint();
508 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
509 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
511 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
513 javax.help.HelpBroker hb = hs.createHelpBroker();
514 hb.setCurrentID("home");
515 hb.setDisplayed(true);
516 } catch (Exception ex)
518 ex.printStackTrace();
523 boolean toggleSeqs = !evt.isControlDown();
524 boolean toggleCols = !evt.isShiftDown();
525 toggleHiddenRegions(toggleSeqs, toggleCols);
528 case KeyEvent.VK_PAGE_UP:
529 if (viewport.wrapAlignment)
531 alignPanel.scrollUp(true);
535 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
536 - viewport.endSeq + viewport.startSeq);
539 case KeyEvent.VK_PAGE_DOWN:
540 if (viewport.wrapAlignment)
542 alignPanel.scrollUp(false);
546 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
547 + viewport.endSeq - viewport.startSeq);
554 public void keyReleased(KeyEvent evt)
556 switch (evt.getKeyCode())
558 case KeyEvent.VK_LEFT:
559 if (evt.isAltDown() || !viewport.cursorMode)
560 viewport.firePropertyChange("alignment", null, viewport
561 .getAlignment().getSequences());
564 case KeyEvent.VK_RIGHT:
565 if (evt.isAltDown() || !viewport.cursorMode)
566 viewport.firePropertyChange("alignment", null, viewport
567 .getAlignment().getSequences());
574 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
576 ap.alignFrame = this;
577 avc = new jalview.controller.AlignViewController(this, viewport,
580 alignPanels.addElement(ap);
582 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
584 int aSize = alignPanels.size();
586 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
588 if (aSize == 1 && ap.av.viewName == null)
590 this.getContentPane().add(ap, BorderLayout.CENTER);
596 setInitialTabVisible();
599 expandViews.setEnabled(true);
600 gatherViews.setEnabled(true);
601 tabbedPane.addTab(ap.av.viewName, ap);
603 ap.setVisible(false);
608 if (ap.av.isPadGaps())
610 ap.av.getAlignment().padGaps();
612 ap.av.updateConservation(ap);
613 ap.av.updateConsensus(ap);
614 ap.av.updateStrucConsensus(ap);
618 public void setInitialTabVisible()
620 expandViews.setEnabled(true);
621 gatherViews.setEnabled(true);
622 tabbedPane.setVisible(true);
623 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
624 tabbedPane.addTab(first.av.viewName, first);
625 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
628 public AlignViewport getViewport()
633 /* Set up intrinsic listeners for dynamically generated GUI bits. */
634 private void addServiceListeners()
636 final java.beans.PropertyChangeListener thisListener;
637 Desktop.instance.addJalviewPropertyChangeListener("services",
638 thisListener = new java.beans.PropertyChangeListener()
641 public void propertyChange(PropertyChangeEvent evt)
643 // // System.out.println("Discoverer property change.");
644 // if (evt.getPropertyName().equals("services"))
646 SwingUtilities.invokeLater(new Runnable()
653 .println("Rebuild WS Menu for service change");
654 BuildWebServiceMenu();
661 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
664 public void internalFrameClosed(
665 javax.swing.event.InternalFrameEvent evt)
667 System.out.println("deregistering discoverer listener");
668 Desktop.instance.removeJalviewPropertyChangeListener("services",
670 closeMenuItem_actionPerformed(true);
673 // Finally, build the menu once to get current service state
674 new Thread(new Runnable()
679 BuildWebServiceMenu();
684 public void setGUINucleotide(boolean nucleotide)
686 showTranslation.setVisible(nucleotide);
687 conservationMenuItem.setEnabled(!nucleotide);
688 modifyConservation.setEnabled(!nucleotide);
689 showGroupConservation.setEnabled(!nucleotide);
690 rnahelicesColour.setEnabled(nucleotide);
691 purinePyrimidineColour.setEnabled(nucleotide);
692 // Remember AlignFrame always starts as protein
696 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
701 * set up menus for the currently viewport. This may be called after any
702 * operation that affects the data in the current view (selection changed,
703 * etc) to update the menus to reflect the new state.
705 public void setMenusForViewport()
707 setMenusFromViewport(viewport);
711 * Need to call this method when tabs are selected for multiple views, or when
712 * loading from Jalview2XML.java
717 void setMenusFromViewport(AlignViewport av)
719 padGapsMenuitem.setSelected(av.isPadGaps());
720 colourTextMenuItem.setSelected(av.showColourText);
721 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
722 conservationMenuItem.setSelected(av.getConservationSelected());
723 seqLimits.setSelected(av.getShowJVSuffix());
724 idRightAlign.setSelected(av.rightAlignIds);
725 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
726 renderGapsMenuItem.setSelected(av.renderGaps);
727 wrapMenuItem.setSelected(av.wrapAlignment);
728 scaleAbove.setVisible(av.wrapAlignment);
729 scaleLeft.setVisible(av.wrapAlignment);
730 scaleRight.setVisible(av.wrapAlignment);
731 annotationPanelMenuItem.setState(av.showAnnotation);
732 viewBoxesMenuItem.setSelected(av.showBoxes);
733 viewTextMenuItem.setSelected(av.showText);
734 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
735 showGroupConsensus.setSelected(av.isShowGroupConsensus());
736 showGroupConservation.setSelected(av.isShowGroupConservation());
737 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
738 showSequenceLogo.setSelected(av.isShowSequenceLogo());
739 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
741 setColourSelected(ColourSchemeProperty.getColourName(av
742 .getGlobalColourScheme()));
744 showSeqFeatures.setSelected(av.showSequenceFeatures);
745 hiddenMarkers.setState(av.showHiddenMarkers);
746 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
747 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
748 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
749 autoCalculate.setSelected(av.autoCalculateConsensus);
750 sortByTree.setSelected(av.sortByTree);
751 listenToViewSelections.setSelected(av.followSelection);
752 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
754 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
755 setShowProductsEnabled();
759 // methods for implementing IProgressIndicator
760 // need to refactor to a reusable stub class
761 Hashtable progressBars, progressBarHandlers;
766 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
769 public void setProgressBar(String message, long id)
771 if (progressBars == null)
773 progressBars = new Hashtable();
774 progressBarHandlers = new Hashtable();
777 JPanel progressPanel;
778 Long lId = new Long(id);
779 GridLayout layout = (GridLayout) statusPanel.getLayout();
780 if (progressBars.get(lId) != null)
782 progressPanel = (JPanel) progressBars.get(new Long(id));
783 statusPanel.remove(progressPanel);
784 progressBars.remove(lId);
785 progressPanel = null;
788 statusBar.setText(message);
790 if (progressBarHandlers.contains(lId))
792 progressBarHandlers.remove(lId);
794 layout.setRows(layout.getRows() - 1);
798 progressPanel = new JPanel(new BorderLayout(10, 5));
800 JProgressBar progressBar = new JProgressBar();
801 progressBar.setIndeterminate(true);
803 progressPanel.add(new JLabel(message), BorderLayout.WEST);
804 progressPanel.add(progressBar, BorderLayout.CENTER);
806 layout.setRows(layout.getRows() + 1);
807 statusPanel.add(progressPanel);
809 progressBars.put(lId, progressPanel);
812 // setMenusForViewport();
817 public void registerHandler(final long id,
818 final IProgressIndicatorHandler handler)
820 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
822 throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
824 progressBarHandlers.put(new Long(id), handler);
825 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
826 if (handler.canCancel())
828 JButton cancel = new JButton(
829 MessageManager.getString("action.cancel"));
830 final IProgressIndicator us = this;
831 cancel.addActionListener(new ActionListener()
835 public void actionPerformed(ActionEvent e)
837 handler.cancelActivity(id);
838 us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
841 progressPanel.add(cancel, BorderLayout.EAST);
847 * @return true if any progress bars are still active
850 public boolean operationInProgress()
852 if (progressBars != null && progressBars.size() > 0)
860 public void setStatus(String text)
862 statusBar.setText(text);
866 * Added so Castor Mapping file can obtain Jalview Version
868 public String getVersion()
870 return jalview.bin.Cache.getProperty("VERSION");
873 public FeatureRenderer getFeatureRenderer()
875 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
879 public void fetchSequence_actionPerformed(ActionEvent e)
881 new SequenceFetcher(this);
885 public void addFromFile_actionPerformed(ActionEvent e)
887 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
891 public void reload_actionPerformed(ActionEvent e)
893 if (fileName != null)
895 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
896 // originating file's format
897 // TODO: work out how to recover feature settings for correct view(s) when
899 if (currentFileFormat.equals("Jalview"))
901 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
902 for (int i = 0; i < frames.length; i++)
904 if (frames[i] instanceof AlignFrame && frames[i] != this
905 && ((AlignFrame) frames[i]).fileName != null
906 && ((AlignFrame) frames[i]).fileName.equals(fileName))
910 frames[i].setSelected(true);
911 Desktop.instance.closeAssociatedWindows();
912 } catch (java.beans.PropertyVetoException ex)
918 Desktop.instance.closeAssociatedWindows();
920 FileLoader loader = new FileLoader();
921 String protocol = fileName.startsWith("http:") ? "URL" : "File";
922 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
926 Rectangle bounds = this.getBounds();
928 FileLoader loader = new FileLoader();
929 String protocol = fileName.startsWith("http:") ? "URL" : "File";
930 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
931 protocol, currentFileFormat);
933 newframe.setBounds(bounds);
934 if (featureSettings != null && featureSettings.isShowing())
936 final Rectangle fspos = featureSettings.frame.getBounds();
937 // TODO: need a 'show feature settings' function that takes bounds -
938 // need to refactor Desktop.addFrame
939 newframe.featureSettings_actionPerformed(null);
940 final FeatureSettings nfs = newframe.featureSettings;
941 SwingUtilities.invokeLater(new Runnable()
946 nfs.frame.setBounds(fspos);
949 this.featureSettings.close();
950 this.featureSettings = null;
952 this.closeMenuItem_actionPerformed(true);
958 public void addFromText_actionPerformed(ActionEvent e)
960 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
964 public void addFromURL_actionPerformed(ActionEvent e)
966 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
970 public void save_actionPerformed(ActionEvent e)
973 || (currentFileFormat == null || !jalview.io.FormatAdapter
974 .isValidIOFormat(currentFileFormat, true))
975 || fileName.startsWith("http"))
977 saveAs_actionPerformed(null);
981 saveAlignment(fileName, currentFileFormat);
992 public void saveAs_actionPerformed(ActionEvent e)
994 JalviewFileChooser chooser = new JalviewFileChooser(
995 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
996 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
997 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
998 currentFileFormat, false);
1000 chooser.setFileView(new JalviewFileView());
1001 chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1002 chooser.setToolTipText(MessageManager.getString("action.save"));
1004 int value = chooser.showSaveDialog(this);
1006 if (value == JalviewFileChooser.APPROVE_OPTION)
1008 currentFileFormat = chooser.getSelectedFormat();
1009 if (currentFileFormat == null)
1012 .showInternalMessageDialog(
1015 .getString("label.select_file_format_before_saving"),
1017 .getString("label.file_format_not_specified"),
1018 JOptionPane.WARNING_MESSAGE);
1019 value = chooser.showSaveDialog(this);
1023 fileName = chooser.getSelectedFile().getPath();
1025 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1028 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1029 if (currentFileFormat.indexOf(" ") > -1)
1031 currentFileFormat = currentFileFormat.substring(0,
1032 currentFileFormat.indexOf(" "));
1034 saveAlignment(fileName, currentFileFormat);
1038 public boolean saveAlignment(String file, String format)
1040 boolean success = true;
1042 if (format.equalsIgnoreCase("Jalview"))
1044 String shortName = title;
1046 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1048 shortName = shortName.substring(shortName
1049 .lastIndexOf(java.io.File.separatorChar) + 1);
1052 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1054 statusBar.setText(MessageManager.formatMessage(
1055 "label.successfully_saved_to_file_in_format", new String[]
1056 { fileName, format }));
1061 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1063 warningMessage("Cannot save file " + fileName + " using format "
1064 + format, "Alignment output format not supported");
1065 saveAs_actionPerformed(null);
1066 // JBPNote need to have a raise_gui flag here
1070 String[] omitHidden = null;
1072 if (viewport.hasHiddenColumns())
1074 int reply = JOptionPane
1075 .showInternalConfirmDialog(
1078 .getString("label.alignment_contains_hidden_columns"),
1080 .getString("action.save_omit_hidden_columns"),
1081 JOptionPane.YES_NO_OPTION,
1082 JOptionPane.QUESTION_MESSAGE);
1084 if (reply == JOptionPane.YES_OPTION)
1086 omitHidden = viewport.getViewAsString(false);
1089 FormatAdapter f = new FormatAdapter();
1090 String output = f.formatSequences(format,
1091 viewport.getAlignment(), // class cast exceptions will
1092 // occur in the distant future
1093 omitHidden, f.getCacheSuffixDefault(format),
1094 viewport.getColumnSelection());
1104 java.io.PrintWriter out = new java.io.PrintWriter(
1105 new java.io.FileWriter(file));
1109 this.setTitle(file);
1110 statusBar.setText(MessageManager.formatMessage(
1111 "label.successfully_saved_to_file_in_format",
1113 { fileName, format }));
1114 } catch (Exception ex)
1117 ex.printStackTrace();
1124 JOptionPane.showInternalMessageDialog(this, MessageManager
1125 .formatMessage("label.couldnt_save_file", new String[]
1126 { fileName }), MessageManager
1127 .getString("label.error_saving_file"),
1128 JOptionPane.WARNING_MESSAGE);
1134 private void warningMessage(String warning, String title)
1136 if (new jalview.util.Platform().isHeadless())
1138 System.err.println("Warning: " + title + "\nWarning: " + warning);
1143 JOptionPane.showInternalMessageDialog(this, warning, title,
1144 JOptionPane.WARNING_MESSAGE);
1156 protected void outputText_actionPerformed(ActionEvent e)
1158 String[] omitHidden = null;
1160 if (viewport.hasHiddenColumns())
1162 int reply = JOptionPane
1163 .showInternalConfirmDialog(
1166 .getString("label.alignment_contains_hidden_columns"),
1168 .getString("action.save_omit_hidden_columns"),
1169 JOptionPane.YES_NO_OPTION,
1170 JOptionPane.QUESTION_MESSAGE);
1172 if (reply == JOptionPane.YES_OPTION)
1174 omitHidden = viewport.getViewAsString(false);
1178 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1179 cap.setForInput(null);
1183 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1184 viewport.getAlignment(), omitHidden,
1185 viewport.getColumnSelection()));
1186 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1187 "label.alignment_output_command", new String[]
1188 { e.getActionCommand() }), 600, 500);
1189 } catch (OutOfMemoryError oom)
1191 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1204 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1206 new HTMLOutput(alignPanel,
1207 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1208 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1211 public void createImageMap(File file, String image)
1213 alignPanel.makePNGImageMap(file, image);
1223 public void createPNG(File f)
1225 alignPanel.makePNG(f);
1235 public void createEPS(File f)
1237 alignPanel.makeEPS(f);
1241 public void pageSetup_actionPerformed(ActionEvent e)
1243 PrinterJob printJob = PrinterJob.getPrinterJob();
1244 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1254 public void printMenuItem_actionPerformed(ActionEvent e)
1256 // Putting in a thread avoids Swing painting problems
1257 PrintThread thread = new PrintThread(alignPanel);
1262 public void exportFeatures_actionPerformed(ActionEvent e)
1264 new AnnotationExporter().exportFeatures(alignPanel);
1268 public void exportAnnotations_actionPerformed(ActionEvent e)
1270 new AnnotationExporter().exportAnnotations(alignPanel,
1271 viewport.showAnnotation ? viewport.getAlignment()
1272 .getAlignmentAnnotation() : null, viewport
1273 .getAlignment().getGroups(), ((Alignment) viewport
1274 .getAlignment()).alignmentProperties);
1278 public void associatedData_actionPerformed(ActionEvent e)
1280 // Pick the tree file
1281 JalviewFileChooser chooser = new JalviewFileChooser(
1282 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1283 chooser.setFileView(new JalviewFileView());
1284 chooser.setDialogTitle(MessageManager
1285 .getString("label.load_jalview_annotations"));
1286 chooser.setToolTipText(MessageManager
1287 .getString("label.load_jalview_annotations"));
1289 int value = chooser.showOpenDialog(null);
1291 if (value == JalviewFileChooser.APPROVE_OPTION)
1293 String choice = chooser.getSelectedFile().getPath();
1294 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1295 loadJalviewDataFile(choice, null, null, null);
1301 * Close the current view or all views in the alignment frame. If the frame
1302 * only contains one view then the alignment will be removed from memory.
1304 * @param closeAllTabs
1307 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1309 if (alignPanels != null && alignPanels.size() < 2)
1311 closeAllTabs = true;
1316 if (alignPanels != null)
1320 if (this.isClosed())
1322 // really close all the windows - otherwise wait till
1323 // setClosed(true) is called
1324 for (int i = 0; i < alignPanels.size(); i++)
1326 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1333 closeView(alignPanel);
1339 this.setClosed(true);
1341 } catch (Exception ex)
1343 ex.printStackTrace();
1348 * close alignPanel2 and shuffle tabs appropriately.
1350 * @param alignPanel2
1352 public void closeView(AlignmentPanel alignPanel2)
1354 int index = tabbedPane.getSelectedIndex();
1355 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1356 alignPanels.removeElement(alignPanel2);
1358 // if (viewport == alignPanel2.av)
1362 alignPanel2.closePanel();
1365 tabbedPane.removeTabAt(closedindex);
1366 tabbedPane.validate();
1368 if (index > closedindex || index == tabbedPane.getTabCount())
1370 // modify currently selected tab index if necessary.
1374 this.tabSelectionChanged(index);
1380 void updateEditMenuBar()
1383 if (viewport.historyList.size() > 0)
1385 undoMenuItem.setEnabled(true);
1386 CommandI command = (CommandI) viewport.historyList.peek();
1387 undoMenuItem.setText(MessageManager.formatMessage(
1388 "label.undo_command", new String[]
1389 { command.getDescription() }));
1393 undoMenuItem.setEnabled(false);
1394 undoMenuItem.setText(MessageManager.getString("action.undo"));
1397 if (viewport.redoList.size() > 0)
1399 redoMenuItem.setEnabled(true);
1401 CommandI command = (CommandI) viewport.redoList.peek();
1402 redoMenuItem.setText(MessageManager.formatMessage(
1403 "label.redo_command", new String[]
1404 { command.getDescription() }));
1408 redoMenuItem.setEnabled(false);
1409 redoMenuItem.setText(MessageManager.getString("action.redo"));
1413 public void addHistoryItem(CommandI command)
1415 if (command.getSize() > 0)
1417 viewport.historyList.push(command);
1418 viewport.redoList.clear();
1419 updateEditMenuBar();
1420 viewport.updateHiddenColumns();
1421 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1422 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1423 // viewport.getColumnSelection()
1424 // .getHiddenColumns().size() > 0);
1430 * @return alignment objects for all views
1432 AlignmentI[] getViewAlignments()
1434 if (alignPanels != null)
1436 Enumeration e = alignPanels.elements();
1437 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1438 for (int i = 0; e.hasMoreElements(); i++)
1440 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1444 if (viewport != null)
1446 return new AlignmentI[]
1447 { viewport.getAlignment() };
1459 protected void undoMenuItem_actionPerformed(ActionEvent e)
1461 if (viewport.historyList.empty())
1463 CommandI command = (CommandI) viewport.historyList.pop();
1464 viewport.redoList.push(command);
1465 command.undoCommand(getViewAlignments());
1467 AlignViewport originalSource = getOriginatingSource(command);
1468 updateEditMenuBar();
1470 if (originalSource != null)
1472 if (originalSource != viewport)
1475 .warn("Implementation worry: mismatch of viewport origin for undo");
1477 originalSource.updateHiddenColumns();
1478 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1480 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1481 // viewport.getColumnSelection()
1482 // .getHiddenColumns().size() > 0);
1483 originalSource.firePropertyChange("alignment", null, originalSource
1484 .getAlignment().getSequences());
1495 protected void redoMenuItem_actionPerformed(ActionEvent e)
1497 if (viewport.redoList.size() < 1)
1502 CommandI command = (CommandI) viewport.redoList.pop();
1503 viewport.historyList.push(command);
1504 command.doCommand(getViewAlignments());
1506 AlignViewport originalSource = getOriginatingSource(command);
1507 updateEditMenuBar();
1509 if (originalSource != null)
1512 if (originalSource != viewport)
1515 .warn("Implementation worry: mismatch of viewport origin for redo");
1517 originalSource.updateHiddenColumns();
1518 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1520 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1521 // viewport.getColumnSelection()
1522 // .getHiddenColumns().size() > 0);
1523 originalSource.firePropertyChange("alignment", null, originalSource
1524 .getAlignment().getSequences());
1528 AlignViewport getOriginatingSource(CommandI command)
1530 AlignViewport originalSource = null;
1531 // For sequence removal and addition, we need to fire
1532 // the property change event FROM the viewport where the
1533 // original alignment was altered
1534 AlignmentI al = null;
1535 if (command instanceof EditCommand)
1537 EditCommand editCommand = (EditCommand) command;
1538 al = editCommand.getAlignment();
1539 Vector comps = (Vector) PaintRefresher.components.get(viewport
1540 .getSequenceSetId());
1542 for (int i = 0; i < comps.size(); i++)
1544 if (comps.elementAt(i) instanceof AlignmentPanel)
1546 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1548 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1555 if (originalSource == null)
1557 // The original view is closed, we must validate
1558 // the current view against the closed view first
1561 PaintRefresher.validateSequences(al, viewport.getAlignment());
1564 originalSource = viewport;
1567 return originalSource;
1576 public void moveSelectedSequences(boolean up)
1578 SequenceGroup sg = viewport.getSelectionGroup();
1584 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1585 viewport.getHiddenRepSequences(), up);
1586 alignPanel.paintAlignment(true);
1589 synchronized void slideSequences(boolean right, int size)
1591 List<SequenceI> sg = new Vector();
1592 if (viewport.cursorMode)
1594 sg.add(viewport.getAlignment().getSequenceAt(
1595 alignPanel.seqPanel.seqCanvas.cursorY));
1597 else if (viewport.getSelectionGroup() != null
1598 && viewport.getSelectionGroup().getSize() != viewport
1599 .getAlignment().getHeight())
1601 sg = viewport.getSelectionGroup().getSequences(
1602 viewport.getHiddenRepSequences());
1610 Vector invertGroup = new Vector();
1612 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1614 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1615 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1618 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1620 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1621 for (int i = 0; i < invertGroup.size(); i++)
1622 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1624 SlideSequencesCommand ssc;
1626 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1627 size, viewport.getGapCharacter());
1629 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1630 size, viewport.getGapCharacter());
1632 int groupAdjustment = 0;
1633 if (ssc.getGapsInsertedBegin() && right)
1635 if (viewport.cursorMode)
1636 alignPanel.seqPanel.moveCursor(size, 0);
1638 groupAdjustment = size;
1640 else if (!ssc.getGapsInsertedBegin() && !right)
1642 if (viewport.cursorMode)
1643 alignPanel.seqPanel.moveCursor(-size, 0);
1645 groupAdjustment = -size;
1648 if (groupAdjustment != 0)
1650 viewport.getSelectionGroup().setStartRes(
1651 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1652 viewport.getSelectionGroup().setEndRes(
1653 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1656 boolean appendHistoryItem = false;
1657 if (viewport.historyList != null && viewport.historyList.size() > 0
1658 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1660 appendHistoryItem = ssc
1661 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1665 if (!appendHistoryItem)
1666 addHistoryItem(ssc);
1678 protected void copy_actionPerformed(ActionEvent e)
1681 if (viewport.getSelectionGroup() == null)
1685 // TODO: preserve the ordering of displayed alignment annotation in any
1686 // internal paste (particularly sequence associated annotation)
1687 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1688 String[] omitHidden = null;
1690 if (viewport.hasHiddenColumns())
1692 omitHidden = viewport.getViewAsString(true);
1695 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1698 StringSelection ss = new StringSelection(output);
1702 jalview.gui.Desktop.internalCopy = true;
1703 // Its really worth setting the clipboard contents
1704 // to empty before setting the large StringSelection!!
1705 Toolkit.getDefaultToolkit().getSystemClipboard()
1706 .setContents(new StringSelection(""), null);
1708 Toolkit.getDefaultToolkit().getSystemClipboard()
1709 .setContents(ss, Desktop.instance);
1710 } catch (OutOfMemoryError er)
1712 new OOMWarning("copying region", er);
1716 Vector hiddenColumns = null;
1717 if (viewport.hasHiddenColumns())
1719 hiddenColumns = new Vector();
1720 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1721 .getSelectionGroup().getEndRes();
1722 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1725 int[] region = (int[]) viewport.getColumnSelection()
1726 .getHiddenColumns().elementAt(i);
1727 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1729 hiddenColumns.addElement(new int[]
1730 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1735 Desktop.jalviewClipboard = new Object[]
1736 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1737 statusBar.setText(MessageManager.formatMessage(
1738 "label.copied_sequences_to_clipboard", new String[]
1739 { Integer.valueOf(seqs.length).toString() }));
1749 protected void pasteNew_actionPerformed(ActionEvent e)
1761 protected void pasteThis_actionPerformed(ActionEvent e)
1767 * Paste contents of Jalview clipboard
1769 * @param newAlignment
1770 * true to paste to a new alignment, otherwise add to this.
1772 void paste(boolean newAlignment)
1774 boolean externalPaste = true;
1777 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1778 Transferable contents = c.getContents(this);
1780 if (contents == null)
1788 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1789 if (str.length() < 1)
1794 format = new IdentifyFile().Identify(str, "Paste");
1796 } catch (OutOfMemoryError er)
1798 new OOMWarning("Out of memory pasting sequences!!", er);
1802 SequenceI[] sequences;
1803 boolean annotationAdded = false;
1804 AlignmentI alignment = null;
1806 if (Desktop.jalviewClipboard != null)
1808 // The clipboard was filled from within Jalview, we must use the
1810 // And dataset from the copied alignment
1811 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1812 // be doubly sure that we create *new* sequence objects.
1813 sequences = new SequenceI[newseq.length];
1814 for (int i = 0; i < newseq.length; i++)
1816 sequences[i] = new Sequence(newseq[i]);
1818 alignment = new Alignment(sequences);
1819 externalPaste = false;
1823 // parse the clipboard as an alignment.
1824 alignment = new FormatAdapter().readFile(str, "Paste", format);
1825 sequences = alignment.getSequencesArray();
1829 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1835 if (Desktop.jalviewClipboard != null)
1837 // dataset is inherited
1838 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1842 // new dataset is constructed
1843 alignment.setDataset(null);
1845 alwidth = alignment.getWidth() + 1;
1849 AlignmentI pastedal = alignment; // preserve pasted alignment object
1850 // Add pasted sequences and dataset into existing alignment.
1851 alignment = viewport.getAlignment();
1852 alwidth = alignment.getWidth() + 1;
1853 // decide if we need to import sequences from an existing dataset
1854 boolean importDs = Desktop.jalviewClipboard != null
1855 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1856 // importDs==true instructs us to copy over new dataset sequences from
1857 // an existing alignment
1858 Vector newDs = (importDs) ? new Vector() : null; // used to create
1859 // minimum dataset set
1861 for (int i = 0; i < sequences.length; i++)
1865 newDs.addElement(null);
1867 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1869 if (importDs && ds != null)
1871 if (!newDs.contains(ds))
1873 newDs.setElementAt(ds, i);
1874 ds = new Sequence(ds);
1875 // update with new dataset sequence
1876 sequences[i].setDatasetSequence(ds);
1880 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1885 // copy and derive new dataset sequence
1886 sequences[i] = sequences[i].deriveSequence();
1887 alignment.getDataset().addSequence(
1888 sequences[i].getDatasetSequence());
1889 // TODO: avoid creation of duplicate dataset sequences with a
1890 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1892 alignment.addSequence(sequences[i]); // merges dataset
1896 newDs.clear(); // tidy up
1898 if (alignment.getAlignmentAnnotation() != null)
1900 for (AlignmentAnnotation alan : alignment
1901 .getAlignmentAnnotation())
1903 if (alan.graphGroup > fgroup)
1905 fgroup = alan.graphGroup;
1909 if (pastedal.getAlignmentAnnotation() != null)
1911 // Add any annotation attached to alignment.
1912 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1913 for (int i = 0; i < alann.length; i++)
1915 annotationAdded = true;
1916 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1918 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1919 if (newann.graphGroup > -1)
1921 if (newGraphGroups.size() <= newann.graphGroup
1922 || newGraphGroups.get(newann.graphGroup) == null)
1924 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1926 newGraphGroups.add(q, null);
1928 newGraphGroups.set(newann.graphGroup, new Integer(
1931 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1935 newann.padAnnotation(alwidth);
1936 alignment.addAnnotation(newann);
1946 addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
1947 sequences, 0, alignment.getWidth(), alignment));
1949 // Add any annotations attached to sequences
1950 for (int i = 0; i < sequences.length; i++)
1952 if (sequences[i].getAnnotation() != null)
1954 AlignmentAnnotation newann;
1955 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1957 annotationAdded = true;
1958 newann = sequences[i].getAnnotation()[a];
1959 newann.adjustForAlignment();
1960 newann.padAnnotation(alwidth);
1961 if (newann.graphGroup > -1)
1963 if (newann.graphGroup > -1)
1965 if (newGraphGroups.size() <= newann.graphGroup
1966 || newGraphGroups.get(newann.graphGroup) == null)
1968 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1970 newGraphGroups.add(q, null);
1972 newGraphGroups.set(newann.graphGroup, new Integer(
1975 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1979 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1984 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1991 // propagate alignment changed.
1992 viewport.setEndSeq(alignment.getHeight());
1993 if (annotationAdded)
1995 // Duplicate sequence annotation in all views.
1996 AlignmentI[] alview = this.getViewAlignments();
1997 for (int i = 0; i < sequences.length; i++)
1999 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2002 for (int avnum = 0; avnum < alview.length; avnum++)
2004 if (alview[avnum] != alignment)
2006 // duplicate in a view other than the one with input focus
2007 int avwidth = alview[avnum].getWidth() + 1;
2008 // this relies on sann being preserved after we
2009 // modify the sequence's annotation array for each duplication
2010 for (int a = 0; a < sann.length; a++)
2012 AlignmentAnnotation newann = new AlignmentAnnotation(
2014 sequences[i].addAlignmentAnnotation(newann);
2015 newann.padAnnotation(avwidth);
2016 alview[avnum].addAnnotation(newann); // annotation was
2017 // duplicated earlier
2018 // TODO JAL-1145 graphGroups are not updated for sequence
2019 // annotation added to several views. This may cause
2021 alview[avnum].setAnnotationIndex(newann, a);
2026 buildSortByAnnotationScoresMenu();
2028 viewport.firePropertyChange("alignment", null,
2029 alignment.getSequences());
2030 if (alignPanels != null)
2032 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2034 ap.validateAnnotationDimensions(false);
2039 alignPanel.validateAnnotationDimensions(false);
2045 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2047 String newtitle = new String("Copied sequences");
2049 if (Desktop.jalviewClipboard != null
2050 && Desktop.jalviewClipboard[2] != null)
2052 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2053 for (int i = 0; i < hc.size(); i++)
2055 int[] region = (int[]) hc.elementAt(i);
2056 af.viewport.hideColumns(region[0], region[1]);
2060 // >>>This is a fix for the moment, until a better solution is
2062 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2064 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2066 // TODO: maintain provenance of an alignment, rather than just make the
2067 // title a concatenation of operations.
2070 if (title.startsWith("Copied sequences"))
2076 newtitle = newtitle.concat("- from " + title);
2081 newtitle = new String("Pasted sequences");
2084 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2089 } catch (Exception ex)
2091 ex.printStackTrace();
2092 System.out.println("Exception whilst pasting: " + ex);
2093 // could be anything being pasted in here
2099 protected void expand_newalign(ActionEvent e)
2103 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2104 .getAlignment(), -1);
2105 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2107 String newtitle = new String("Flanking alignment");
2109 if (Desktop.jalviewClipboard != null
2110 && Desktop.jalviewClipboard[2] != null)
2112 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2113 for (int i = 0; i < hc.size(); i++)
2115 int[] region = (int[]) hc.elementAt(i);
2116 af.viewport.hideColumns(region[0], region[1]);
2120 // >>>This is a fix for the moment, until a better solution is
2122 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2124 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2126 // TODO: maintain provenance of an alignment, rather than just make the
2127 // title a concatenation of operations.
2129 if (title.startsWith("Copied sequences"))
2135 newtitle = newtitle.concat("- from " + title);
2139 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2141 } catch (Exception ex)
2143 ex.printStackTrace();
2144 System.out.println("Exception whilst pasting: " + ex);
2145 // could be anything being pasted in here
2146 } catch (OutOfMemoryError oom)
2148 new OOMWarning("Viewing flanking region of alignment", oom);
2159 protected void cut_actionPerformed(ActionEvent e)
2161 copy_actionPerformed(null);
2162 delete_actionPerformed(null);
2172 protected void delete_actionPerformed(ActionEvent evt)
2175 SequenceGroup sg = viewport.getSelectionGroup();
2181 Vector seqs = new Vector();
2183 for (int i = 0; i < sg.getSize(); i++)
2185 seq = sg.getSequenceAt(i);
2186 seqs.addElement(seq);
2189 // If the cut affects all sequences, remove highlighted columns
2190 if (sg.getSize() == viewport.getAlignment().getHeight())
2192 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2193 sg.getEndRes() + 1);
2196 SequenceI[] cut = new SequenceI[seqs.size()];
2197 for (int i = 0; i < seqs.size(); i++)
2199 cut[i] = (SequenceI) seqs.elementAt(i);
2203 * //ADD HISTORY ITEM
2205 addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
2206 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2207 viewport.getAlignment()));
2209 viewport.setSelectionGroup(null);
2210 viewport.sendSelection();
2211 viewport.getAlignment().deleteGroup(sg);
2213 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2215 if (viewport.getAlignment().getHeight() < 1)
2219 this.setClosed(true);
2220 } catch (Exception ex)
2233 protected void deleteGroups_actionPerformed(ActionEvent e)
2235 if (avc.deleteGroups())
2237 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2238 alignPanel.updateAnnotation();
2239 alignPanel.paintAlignment(true);
2250 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2252 SequenceGroup sg = new SequenceGroup();
2254 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2256 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2259 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2260 viewport.setSelectionGroup(sg);
2261 viewport.sendSelection();
2262 alignPanel.paintAlignment(true);
2263 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2273 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2275 if (viewport.cursorMode)
2277 alignPanel.seqPanel.keyboardNo1 = null;
2278 alignPanel.seqPanel.keyboardNo2 = null;
2280 viewport.setSelectionGroup(null);
2281 viewport.getColumnSelection().clear();
2282 viewport.setSelectionGroup(null);
2283 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2284 alignPanel.idPanel.idCanvas.searchResults = null;
2285 alignPanel.paintAlignment(true);
2286 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2287 viewport.sendSelection();
2297 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2299 SequenceGroup sg = viewport.getSelectionGroup();
2303 selectAllSequenceMenuItem_actionPerformed(null);
2308 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2310 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2313 alignPanel.paintAlignment(true);
2314 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2315 viewport.sendSelection();
2319 public void invertColSel_actionPerformed(ActionEvent e)
2321 viewport.invertColumnSelection();
2322 alignPanel.paintAlignment(true);
2323 viewport.sendSelection();
2333 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2335 trimAlignment(true);
2345 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2347 trimAlignment(false);
2350 void trimAlignment(boolean trimLeft)
2352 ColumnSelection colSel = viewport.getColumnSelection();
2355 if (colSel.size() > 0)
2359 column = colSel.getMin();
2363 column = colSel.getMax();
2367 if (viewport.getSelectionGroup() != null)
2369 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2370 viewport.getHiddenRepSequences());
2374 seqs = viewport.getAlignment().getSequencesArray();
2377 TrimRegionCommand trimRegion;
2380 trimRegion = new TrimRegionCommand("Remove Left",
2381 TrimRegionCommand.TRIM_LEFT, seqs, column,
2382 viewport.getAlignment(), viewport.getColumnSelection(),
2383 viewport.getSelectionGroup());
2384 viewport.setStartRes(0);
2388 trimRegion = new TrimRegionCommand("Remove Right",
2389 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2390 viewport.getAlignment(), viewport.getColumnSelection(),
2391 viewport.getSelectionGroup());
2394 statusBar.setText(MessageManager.formatMessage(
2395 "label.removed_columns", new String[]
2396 { Integer.valueOf(trimRegion.getSize()).toString() }));
2398 addHistoryItem(trimRegion);
2400 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2402 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2403 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2405 viewport.getAlignment().deleteGroup(sg);
2409 viewport.firePropertyChange("alignment", null, viewport
2410 .getAlignment().getSequences());
2421 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2423 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2426 if (viewport.getSelectionGroup() != null)
2428 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2429 viewport.getHiddenRepSequences());
2430 start = viewport.getSelectionGroup().getStartRes();
2431 end = viewport.getSelectionGroup().getEndRes();
2435 seqs = viewport.getAlignment().getSequencesArray();
2438 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2439 "Remove Gapped Columns", seqs, start, end,
2440 viewport.getAlignment());
2442 addHistoryItem(removeGapCols);
2444 statusBar.setText(MessageManager.formatMessage(
2445 "label.removed_empty_columns", new String[]
2446 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2448 // This is to maintain viewport position on first residue
2449 // of first sequence
2450 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2451 int startRes = seq.findPosition(viewport.startRes);
2452 // ShiftList shifts;
2453 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2454 // edit.alColumnChanges=shifts.getInverse();
2455 // if (viewport.hasHiddenColumns)
2456 // viewport.getColumnSelection().compensateForEdits(shifts);
2457 viewport.setStartRes(seq.findIndex(startRes) - 1);
2458 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2470 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2472 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2475 if (viewport.getSelectionGroup() != null)
2477 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2478 viewport.getHiddenRepSequences());
2479 start = viewport.getSelectionGroup().getStartRes();
2480 end = viewport.getSelectionGroup().getEndRes();
2484 seqs = viewport.getAlignment().getSequencesArray();
2487 // This is to maintain viewport position on first residue
2488 // of first sequence
2489 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2490 int startRes = seq.findPosition(viewport.startRes);
2492 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2493 viewport.getAlignment()));
2495 viewport.setStartRes(seq.findIndex(startRes) - 1);
2497 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2509 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2511 viewport.setPadGaps(padGapsMenuitem.isSelected());
2512 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2518 // if (justifySeqs>0)
2520 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2533 public void findMenuItem_actionPerformed(ActionEvent e)
2539 public void newView_actionPerformed(ActionEvent e)
2546 * @param copyAnnotation
2547 * if true then duplicate all annnotation, groups and settings
2548 * @return new alignment panel, already displayed.
2550 public AlignmentPanel newView(boolean copyAnnotation)
2552 return newView(null, copyAnnotation);
2558 * title of newly created view
2559 * @return new alignment panel, already displayed.
2561 public AlignmentPanel newView(String viewTitle)
2563 return newView(viewTitle, true);
2569 * title of newly created view
2570 * @param copyAnnotation
2571 * if true then duplicate all annnotation, groups and settings
2572 * @return new alignment panel, already displayed.
2574 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2576 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2578 if (!copyAnnotation)
2580 // just remove all the current annotation except for the automatic stuff
2581 newap.av.getAlignment().deleteAllGroups();
2582 for (AlignmentAnnotation alan : newap.av.getAlignment()
2583 .getAlignmentAnnotation())
2585 if (!alan.autoCalculated)
2587 newap.av.getAlignment().deleteAnnotation(alan);
2593 newap.av.gatherViewsHere = false;
2595 if (viewport.viewName == null)
2597 viewport.viewName = "Original";
2600 newap.av.historyList = viewport.historyList;
2601 newap.av.redoList = viewport.redoList;
2603 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2604 // make sure the new view has a unique name - this is essential for Jalview
2606 boolean addFirstIndex = false;
2607 if (viewTitle == null || viewTitle.trim().length() == 0)
2609 viewTitle = MessageManager.getString("action.view");
2610 addFirstIndex = true;
2614 index = 1;// we count from 1 if given a specific name
2616 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2617 Vector comps = (Vector) PaintRefresher.components.get(viewport
2618 .getSequenceSetId());
2619 Vector existingNames = new Vector();
2620 for (int i = 0; i < comps.size(); i++)
2622 if (comps.elementAt(i) instanceof AlignmentPanel)
2624 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2625 if (!existingNames.contains(ap.av.viewName))
2627 existingNames.addElement(ap.av.viewName);
2632 while (existingNames.contains(newViewName))
2634 newViewName = viewTitle + " " + (++index);
2637 newap.av.viewName = newViewName;
2639 addAlignmentPanel(newap, true);
2640 newap.alignmentChanged();
2642 if (alignPanels.size() == 2)
2644 viewport.gatherViewsHere = true;
2646 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2651 public void expandViews_actionPerformed(ActionEvent e)
2653 Desktop.instance.explodeViews(this);
2657 public void gatherViews_actionPerformed(ActionEvent e)
2659 Desktop.instance.gatherViews(this);
2669 public void font_actionPerformed(ActionEvent e)
2671 new FontChooser(alignPanel);
2681 protected void seqLimit_actionPerformed(ActionEvent e)
2683 viewport.setShowJVSuffix(seqLimits.isSelected());
2685 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2686 .calculateIdWidth());
2687 alignPanel.paintAlignment(true);
2691 public void idRightAlign_actionPerformed(ActionEvent e)
2693 viewport.rightAlignIds = idRightAlign.isSelected();
2694 alignPanel.paintAlignment(true);
2698 public void centreColumnLabels_actionPerformed(ActionEvent e)
2700 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2701 alignPanel.paintAlignment(true);
2707 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2710 protected void followHighlight_actionPerformed()
2712 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2714 alignPanel.scrollToPosition(
2715 alignPanel.seqPanel.seqCanvas.searchResults, false);
2726 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2728 viewport.setColourText(colourTextMenuItem.isSelected());
2729 alignPanel.paintAlignment(true);
2739 public void wrapMenuItem_actionPerformed(ActionEvent e)
2741 scaleAbove.setVisible(wrapMenuItem.isSelected());
2742 scaleLeft.setVisible(wrapMenuItem.isSelected());
2743 scaleRight.setVisible(wrapMenuItem.isSelected());
2744 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2745 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2749 public void showAllSeqs_actionPerformed(ActionEvent e)
2751 viewport.showAllHiddenSeqs();
2755 public void showAllColumns_actionPerformed(ActionEvent e)
2757 viewport.showAllHiddenColumns();
2762 public void hideSelSequences_actionPerformed(ActionEvent e)
2764 viewport.hideAllSelectedSeqs();
2765 alignPanel.paintAlignment(true);
2769 * called by key handler and the hide all/show all menu items
2774 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2777 boolean hide = false;
2778 SequenceGroup sg = viewport.getSelectionGroup();
2779 if (!toggleSeqs && !toggleCols)
2781 // Hide everything by the current selection - this is a hack - we do the
2782 // invert and then hide
2783 // first check that there will be visible columns after the invert.
2784 if ((viewport.getColumnSelection() != null
2785 && viewport.getColumnSelection().getSelected() != null && viewport
2786 .getColumnSelection().getSelected().size() > 0)
2787 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2790 // now invert the sequence set, if required - empty selection implies
2791 // that no hiding is required.
2794 invertSequenceMenuItem_actionPerformed(null);
2795 sg = viewport.getSelectionGroup();
2799 viewport.expandColSelection(sg, true);
2800 // finally invert the column selection and get the new sequence
2802 invertColSel_actionPerformed(null);
2809 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2811 hideSelSequences_actionPerformed(null);
2814 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2817 showAllSeqs_actionPerformed(null);
2823 if (viewport.getColumnSelection().getSelected().size() > 0)
2825 hideSelColumns_actionPerformed(null);
2828 viewport.setSelectionGroup(sg);
2833 showAllColumns_actionPerformed(null);
2842 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2843 * event.ActionEvent)
2846 public void hideAllButSelection_actionPerformed(ActionEvent e)
2848 toggleHiddenRegions(false, false);
2855 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2859 public void hideAllSelection_actionPerformed(ActionEvent e)
2861 SequenceGroup sg = viewport.getSelectionGroup();
2862 viewport.expandColSelection(sg, false);
2863 viewport.hideAllSelectedSeqs();
2864 viewport.hideSelectedColumns();
2865 alignPanel.paintAlignment(true);
2872 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2876 public void showAllhidden_actionPerformed(ActionEvent e)
2878 viewport.showAllHiddenColumns();
2879 viewport.showAllHiddenSeqs();
2880 alignPanel.paintAlignment(true);
2884 public void hideSelColumns_actionPerformed(ActionEvent e)
2886 viewport.hideSelectedColumns();
2887 alignPanel.paintAlignment(true);
2891 public void hiddenMarkers_actionPerformed(ActionEvent e)
2893 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2904 protected void scaleAbove_actionPerformed(ActionEvent e)
2906 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2907 alignPanel.paintAlignment(true);
2917 protected void scaleLeft_actionPerformed(ActionEvent e)
2919 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2920 alignPanel.paintAlignment(true);
2930 protected void scaleRight_actionPerformed(ActionEvent e)
2932 viewport.setScaleRightWrapped(scaleRight.isSelected());
2933 alignPanel.paintAlignment(true);
2943 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2945 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2946 alignPanel.paintAlignment(true);
2956 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2958 viewport.setShowText(viewTextMenuItem.isSelected());
2959 alignPanel.paintAlignment(true);
2969 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2971 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2972 alignPanel.paintAlignment(true);
2975 public FeatureSettings featureSettings;
2978 public void featureSettings_actionPerformed(ActionEvent e)
2980 if (featureSettings != null)
2982 featureSettings.close();
2983 featureSettings = null;
2985 if (!showSeqFeatures.isSelected())
2987 // make sure features are actually displayed
2988 showSeqFeatures.setSelected(true);
2989 showSeqFeatures_actionPerformed(null);
2991 featureSettings = new FeatureSettings(this);
2995 * Set or clear 'Show Sequence Features'
3001 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3003 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3004 alignPanel.paintAlignment(true);
3005 if (alignPanel.getOverviewPanel() != null)
3007 alignPanel.getOverviewPanel().updateOverviewImage();
3012 * Set or clear 'Show Sequence Features'
3018 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3020 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3022 if (viewport.getShowSequenceFeaturesHeight())
3024 // ensure we're actually displaying features
3025 viewport.setShowSequenceFeatures(true);
3026 showSeqFeatures.setSelected(true);
3028 alignPanel.paintAlignment(true);
3029 if (alignPanel.getOverviewPanel() != null)
3031 alignPanel.getOverviewPanel().updateOverviewImage();
3042 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3044 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
3045 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
3049 public void alignmentProperties()
3051 JEditorPane editPane = new JEditorPane("text/html", "");
3052 editPane.setEditable(false);
3053 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3055 editPane.setText(MessageManager.formatMessage("label.html_content",
3057 { contents.toString() }));
3058 JInternalFrame frame = new JInternalFrame();
3059 frame.getContentPane().add(new JScrollPane(editPane));
3061 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3062 "label.alignment_properties", new String[]
3063 { getTitle() }), 500, 400);
3073 public void overviewMenuItem_actionPerformed(ActionEvent e)
3075 if (alignPanel.overviewPanel != null)
3080 JInternalFrame frame = new JInternalFrame();
3081 OverviewPanel overview = new OverviewPanel(alignPanel);
3082 frame.setContentPane(overview);
3083 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3084 "label.overview_params", new String[]
3085 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3087 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3088 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3091 public void internalFrameClosed(
3092 javax.swing.event.InternalFrameEvent evt)
3094 alignPanel.setOverviewPanel(null);
3098 alignPanel.setOverviewPanel(overview);
3102 public void textColour_actionPerformed(ActionEvent e)
3104 new TextColourChooser().chooseColour(alignPanel, null);
3114 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3126 public void clustalColour_actionPerformed(ActionEvent e)
3128 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3129 viewport.getHiddenRepSequences()));
3139 public void zappoColour_actionPerformed(ActionEvent e)
3141 changeColour(new ZappoColourScheme());
3151 public void taylorColour_actionPerformed(ActionEvent e)
3153 changeColour(new TaylorColourScheme());
3163 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3165 changeColour(new HydrophobicColourScheme());
3175 public void helixColour_actionPerformed(ActionEvent e)
3177 changeColour(new HelixColourScheme());
3187 public void strandColour_actionPerformed(ActionEvent e)
3189 changeColour(new StrandColourScheme());
3199 public void turnColour_actionPerformed(ActionEvent e)
3201 changeColour(new TurnColourScheme());
3211 public void buriedColour_actionPerformed(ActionEvent e)
3213 changeColour(new BuriedColourScheme());
3223 public void nucleotideColour_actionPerformed(ActionEvent e)
3225 changeColour(new NucleotideColourScheme());
3229 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3231 changeColour(new PurinePyrimidineColourScheme());
3235 * public void covariationColour_actionPerformed(ActionEvent e) {
3237 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3241 public void annotationColour_actionPerformed(ActionEvent e)
3243 new AnnotationColourChooser(viewport, alignPanel);
3247 public void rnahelicesColour_actionPerformed(ActionEvent e)
3249 new RNAHelicesColourChooser(viewport, alignPanel);
3259 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3261 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3270 public void changeColour(ColourSchemeI cs)
3272 // TODO: compare with applet and pull up to model method
3277 if (viewport.getAbovePIDThreshold())
3279 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3281 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3285 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3288 if (viewport.getConservationSelected())
3291 Alignment al = (Alignment) viewport.getAlignment();
3292 Conservation c = new Conservation("All",
3293 ResidueProperties.propHash, 3, al.getSequences(), 0,
3297 c.verdict(false, viewport.getConsPercGaps());
3299 cs.setConservation(c);
3301 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3306 cs.setConservation(null);
3309 cs.setConsensus(viewport.getSequenceConsensusHash());
3312 viewport.setGlobalColourScheme(cs);
3314 if (viewport.getColourAppliesToAllGroups())
3317 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3325 if (cs instanceof ClustalxColourScheme)
3327 sg.cs = new ClustalxColourScheme(sg,
3328 viewport.getHiddenRepSequences());
3330 else if (cs instanceof UserColourScheme)
3332 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3338 sg.cs = cs.getClass().newInstance();
3339 } catch (Exception ex)
3344 if (viewport.getAbovePIDThreshold()
3345 || cs instanceof PIDColourScheme
3346 || cs instanceof Blosum62ColourScheme)
3348 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3350 sg.cs.setConsensus(AAFrequency.calculate(
3351 sg.getSequences(viewport.getHiddenRepSequences()),
3352 sg.getStartRes(), sg.getEndRes() + 1));
3356 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3359 if (viewport.getConservationSelected())
3361 Conservation c = new Conservation("Group",
3362 ResidueProperties.propHash, 3, sg.getSequences(viewport
3363 .getHiddenRepSequences()), sg.getStartRes(),
3364 sg.getEndRes() + 1);
3366 c.verdict(false, viewport.getConsPercGaps());
3367 sg.cs.setConservation(c);
3371 sg.cs.setConservation(null);
3376 if (alignPanel.getOverviewPanel() != null)
3378 alignPanel.getOverviewPanel().updateOverviewImage();
3381 alignPanel.paintAlignment(true);
3391 protected void modifyPID_actionPerformed(ActionEvent e)
3393 if (viewport.getAbovePIDThreshold()
3394 && viewport.getGlobalColourScheme() != null)
3396 SliderPanel.setPIDSliderSource(alignPanel,
3397 viewport.getGlobalColourScheme(), "Background");
3398 SliderPanel.showPIDSlider();
3409 protected void modifyConservation_actionPerformed(ActionEvent e)
3411 if (viewport.getConservationSelected()
3412 && viewport.getGlobalColourScheme() != null)
3414 SliderPanel.setConservationSlider(alignPanel,
3415 viewport.getGlobalColourScheme(), "Background");
3416 SliderPanel.showConservationSlider();
3427 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3429 viewport.setConservationSelected(conservationMenuItem.isSelected());
3431 viewport.setAbovePIDThreshold(false);
3432 abovePIDThreshold.setSelected(false);
3434 changeColour(viewport.getGlobalColourScheme());
3436 modifyConservation_actionPerformed(null);
3446 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3448 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3450 conservationMenuItem.setSelected(false);
3451 viewport.setConservationSelected(false);
3453 changeColour(viewport.getGlobalColourScheme());
3455 modifyPID_actionPerformed(null);
3465 public void userDefinedColour_actionPerformed(ActionEvent e)
3467 if (e.getActionCommand().equals(
3468 MessageManager.getString("action.user_defined")))
3470 new UserDefinedColours(alignPanel, null);
3474 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3475 .getUserColourSchemes().get(e.getActionCommand());
3481 public void updateUserColourMenu()
3484 Component[] menuItems = colourMenu.getMenuComponents();
3485 int i, iSize = menuItems.length;
3486 for (i = 0; i < iSize; i++)
3488 if (menuItems[i].getName() != null
3489 && menuItems[i].getName().equals("USER_DEFINED"))
3491 colourMenu.remove(menuItems[i]);
3495 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3497 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3498 .getUserColourSchemes().keys();
3500 while (userColours.hasMoreElements())
3502 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3503 userColours.nextElement().toString());
3504 radioItem.setName("USER_DEFINED");
3505 radioItem.addMouseListener(new MouseAdapter()
3508 public void mousePressed(MouseEvent evt)
3510 if (evt.isControlDown()
3511 || SwingUtilities.isRightMouseButton(evt))
3513 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3515 int option = JOptionPane.showInternalConfirmDialog(
3516 jalview.gui.Desktop.desktop,
3518 .getString("label.remove_from_default_list"),
3520 .getString("label.remove_user_defined_colour"),
3521 JOptionPane.YES_NO_OPTION);
3522 if (option == JOptionPane.YES_OPTION)
3524 jalview.gui.UserDefinedColours
3525 .removeColourFromDefaults(radioItem.getText());
3526 colourMenu.remove(radioItem);
3530 radioItem.addActionListener(new ActionListener()
3533 public void actionPerformed(ActionEvent evt)
3535 userDefinedColour_actionPerformed(evt);
3542 radioItem.addActionListener(new ActionListener()
3545 public void actionPerformed(ActionEvent evt)
3547 userDefinedColour_actionPerformed(evt);
3551 colourMenu.insert(radioItem, 15);
3552 colours.add(radioItem);
3564 public void PIDColour_actionPerformed(ActionEvent e)
3566 changeColour(new PIDColourScheme());
3576 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3578 changeColour(new Blosum62ColourScheme());
3588 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3590 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3591 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3592 .getAlignment().getSequenceAt(0), null);
3593 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3594 viewport.getAlignment()));
3595 alignPanel.paintAlignment(true);
3605 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3607 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3608 AlignmentSorter.sortByID(viewport.getAlignment());
3609 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3610 viewport.getAlignment()));
3611 alignPanel.paintAlignment(true);
3621 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3623 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3624 AlignmentSorter.sortByLength(viewport.getAlignment());
3625 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3626 viewport.getAlignment()));
3627 alignPanel.paintAlignment(true);
3637 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3639 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3640 AlignmentSorter.sortByGroup(viewport.getAlignment());
3641 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3642 viewport.getAlignment()));
3644 alignPanel.paintAlignment(true);
3654 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3656 new RedundancyPanel(alignPanel, this);
3666 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3668 if ((viewport.getSelectionGroup() == null)
3669 || (viewport.getSelectionGroup().getSize() < 2))
3671 JOptionPane.showInternalMessageDialog(this, MessageManager
3672 .getString("label.you_must_select_least_two_sequences"),
3673 MessageManager.getString("label.invalid_selection"),
3674 JOptionPane.WARNING_MESSAGE);
3678 JInternalFrame frame = new JInternalFrame();
3679 frame.setContentPane(new PairwiseAlignPanel(viewport));
3680 Desktop.addInternalFrame(frame,
3681 MessageManager.getString("action.pairwise_alignment"), 600,
3693 public void PCAMenuItem_actionPerformed(ActionEvent e)
3695 if (((viewport.getSelectionGroup() != null)
3696 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3697 .getSelectionGroup().getSize() > 0))
3698 || (viewport.getAlignment().getHeight() < 4))
3701 .showInternalMessageDialog(
3704 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3706 .getString("label.sequence_selection_insufficient"),
3707 JOptionPane.WARNING_MESSAGE);
3712 new PCAPanel(alignPanel);
3716 public void autoCalculate_actionPerformed(ActionEvent e)
3718 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3719 if (viewport.autoCalculateConsensus)
3721 viewport.firePropertyChange("alignment", null, viewport
3722 .getAlignment().getSequences());
3727 public void sortByTreeOption_actionPerformed(ActionEvent e)
3729 viewport.sortByTree = sortByTree.isSelected();
3733 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3735 viewport.followSelection = listenToViewSelections.isSelected();
3745 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3747 NewTreePanel("AV", "PID", "Average distance tree using PID");
3757 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3759 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3769 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3771 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3781 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3783 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3796 void NewTreePanel(String type, String pwType, String title)
3800 if (viewport.getSelectionGroup() != null
3801 && viewport.getSelectionGroup().getSize() > 0)
3803 if (viewport.getSelectionGroup().getSize() < 3)
3809 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3811 .getString("label.not_enough_sequences"),
3812 JOptionPane.WARNING_MESSAGE);
3816 SequenceGroup sg = viewport.getSelectionGroup();
3818 /* Decide if the selection is a column region */
3819 for (SequenceI _s : sg.getSequences())
3821 if (_s.getLength() < sg.getEndRes())
3827 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3829 .getString("label.sequences_selection_not_aligned"),
3830 JOptionPane.WARNING_MESSAGE);
3836 title = title + " on region";
3837 tp = new TreePanel(alignPanel, type, pwType);
3841 // are the visible sequences aligned?
3842 if (!viewport.getAlignment().isAligned(false))
3848 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3850 .getString("label.sequences_not_aligned"),
3851 JOptionPane.WARNING_MESSAGE);
3856 if (viewport.getAlignment().getHeight() < 2)
3861 tp = new TreePanel(alignPanel, type, pwType);
3866 if (viewport.viewName != null)
3868 title += viewport.viewName + " of ";
3871 title += this.title;
3873 Desktop.addInternalFrame(tp, title, 600, 500);
3884 public void addSortByOrderMenuItem(String title,
3885 final AlignmentOrder order)
3887 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
3889 item.addActionListener(new java.awt.event.ActionListener()
3892 public void actionPerformed(ActionEvent e)
3894 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3896 // TODO: JBPNote - have to map order entries to curent SequenceI
3898 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3900 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3903 alignPanel.paintAlignment(true);
3909 * Add a new sort by annotation score menu item
3912 * the menu to add the option to
3914 * the label used to retrieve scores for each sequence on the
3917 public void addSortByAnnotScoreMenuItem(JMenu sort,
3918 final String scoreLabel)
3920 final JMenuItem item = new JMenuItem(scoreLabel);
3922 item.addActionListener(new java.awt.event.ActionListener()
3925 public void actionPerformed(ActionEvent e)
3927 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3928 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3929 viewport.getAlignment());// ,viewport.getSelectionGroup());
3930 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3931 viewport.getAlignment()));
3932 alignPanel.paintAlignment(true);
3938 * last hash for alignment's annotation array - used to minimise cost of
3941 protected int _annotationScoreVectorHash;
3944 * search the alignment and rebuild the sort by annotation score submenu the
3945 * last alignment annotation vector hash is stored to minimize cost of
3946 * rebuilding in subsequence calls.
3950 public void buildSortByAnnotationScoresMenu()
3952 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3957 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3959 sortByAnnotScore.removeAll();
3960 // almost certainly a quicker way to do this - but we keep it simple
3961 Hashtable scoreSorts = new Hashtable();
3962 AlignmentAnnotation aann[];
3963 for (SequenceI sqa : viewport.getAlignment().getSequences())
3965 aann = sqa.getAnnotation();
3966 for (int i = 0; aann != null && i < aann.length; i++)
3968 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3970 scoreSorts.put(aann[i].label, aann[i].label);
3974 Enumeration labels = scoreSorts.keys();
3975 while (labels.hasMoreElements())
3977 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3978 (String) labels.nextElement());
3980 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3983 _annotationScoreVectorHash = viewport.getAlignment()
3984 .getAlignmentAnnotation().hashCode();
3989 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3990 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3991 * call. Listeners are added to remove the menu item when the treePanel is
3992 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3996 * Displayed tree window.
3998 * SortBy menu item title.
4001 public void buildTreeMenu()
4003 calculateTree.removeAll();
4004 // build the calculate menu
4006 for (final String type : new String[]
4009 String treecalcnm = MessageManager.getString("label.tree_calc_"
4010 + type.toLowerCase());
4011 for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4013 JMenuItem tm = new JMenuItem();
4014 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4015 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4017 String smn = MessageManager.getStringOrReturn(
4018 "label.score_model_", sm.getName());
4019 final String title = MessageManager.formatMessage(
4020 "label.treecalc_title", treecalcnm, smn);
4021 tm.setText(title);//
4022 tm.addActionListener(new java.awt.event.ActionListener()
4024 public void actionPerformed(ActionEvent e)
4026 NewTreePanel(type, (String) pwtype, title);
4029 calculateTree.add(tm);
4034 sortByTreeMenu.removeAll();
4036 Vector comps = (Vector) PaintRefresher.components.get(viewport
4037 .getSequenceSetId());
4038 Vector treePanels = new Vector();
4039 int i, iSize = comps.size();
4040 for (i = 0; i < iSize; i++)
4042 if (comps.elementAt(i) instanceof TreePanel)
4044 treePanels.add(comps.elementAt(i));
4048 iSize = treePanels.size();
4052 sortByTreeMenu.setVisible(false);
4056 sortByTreeMenu.setVisible(true);
4058 for (i = 0; i < treePanels.size(); i++)
4060 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4061 final JMenuItem item = new JMenuItem(tp.getTitle());
4062 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4063 item.addActionListener(new java.awt.event.ActionListener()
4066 public void actionPerformed(ActionEvent e)
4068 tp.sortByTree_actionPerformed(null);
4069 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4074 sortByTreeMenu.add(item);
4078 public boolean sortBy(AlignmentOrder alorder, String undoname)
4080 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4081 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4082 if (undoname != null)
4084 addHistoryItem(new OrderCommand(undoname, oldOrder,
4085 viewport.getAlignment()));
4087 alignPanel.paintAlignment(true);
4092 * Work out whether the whole set of sequences or just the selected set will
4093 * be submitted for multiple alignment.
4096 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4098 // Now, check we have enough sequences
4099 AlignmentView msa = null;
4101 if ((viewport.getSelectionGroup() != null)
4102 && (viewport.getSelectionGroup().getSize() > 1))
4104 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4105 // some common interface!
4107 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4108 * SequenceI[sz = seqs.getSize(false)];
4110 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4111 * seqs.getSequenceAt(i); }
4113 msa = viewport.getAlignmentView(true);
4118 * Vector seqs = viewport.getAlignment().getSequences();
4120 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
4122 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
4123 * seqs.elementAt(i); } }
4125 msa = viewport.getAlignmentView(false);
4131 * Decides what is submitted to a secondary structure prediction service: the
4132 * first sequence in the alignment, or in the current selection, or, if the
4133 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4134 * region or the whole alignment. (where the first sequence in the set is the
4135 * one that the prediction will be for).
4137 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4139 AlignmentView seqs = null;
4141 if ((viewport.getSelectionGroup() != null)
4142 && (viewport.getSelectionGroup().getSize() > 0))
4144 seqs = viewport.getAlignmentView(true);
4148 seqs = viewport.getAlignmentView(false);
4150 // limit sequences - JBPNote in future - could spawn multiple prediction
4152 // TODO: viewport.getAlignment().isAligned is a global state - the local
4153 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4154 if (!viewport.getAlignment().isAligned(false))
4156 seqs.setSequences(new SeqCigar[]
4157 { seqs.getSequences()[0] });
4158 // TODO: if seqs.getSequences().length>1 then should really have warned
4172 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4174 // Pick the tree file
4175 JalviewFileChooser chooser = new JalviewFileChooser(
4176 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4177 chooser.setFileView(new JalviewFileView());
4178 chooser.setDialogTitle(MessageManager
4179 .getString("label.select_newick_like_tree_file"));
4180 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4182 int value = chooser.showOpenDialog(null);
4184 if (value == JalviewFileChooser.APPROVE_OPTION)
4186 String choice = chooser.getSelectedFile().getPath();
4187 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4188 jalview.io.NewickFile fin = null;
4191 fin = new jalview.io.NewickFile(choice, "File");
4192 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4193 } catch (Exception ex)
4200 .getString("label.problem_reading_tree_file"),
4201 JOptionPane.WARNING_MESSAGE);
4202 ex.printStackTrace();
4204 if (fin != null && fin.hasWarningMessage())
4206 JOptionPane.showMessageDialog(Desktop.desktop, fin
4207 .getWarningMessage(), MessageManager
4208 .getString("label.possible_problem_with_tree_file"),
4209 JOptionPane.WARNING_MESSAGE);
4215 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4217 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4220 public TreePanel ShowNewickTree(NewickFile nf, String title)
4222 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4225 public TreePanel ShowNewickTree(NewickFile nf, String title,
4226 AlignmentView input)
4228 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4231 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4232 int h, int x, int y)
4234 return ShowNewickTree(nf, title, null, w, h, x, y);
4238 * Add a treeviewer for the tree extracted from a newick file object to the
4239 * current alignment view
4246 * Associated alignment input data (or null)
4255 * @return TreePanel handle
4257 public TreePanel ShowNewickTree(NewickFile nf, String title,
4258 AlignmentView input, int w, int h, int x, int y)
4260 TreePanel tp = null;
4266 if (nf.getTree() != null)
4268 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4274 tp.setLocation(x, y);
4277 Desktop.addInternalFrame(tp, title, w, h);
4279 } catch (Exception ex)
4281 ex.printStackTrace();
4287 private boolean buildingMenu = false;
4290 * Generates menu items and listener event actions for web service clients
4293 public void BuildWebServiceMenu()
4295 while (buildingMenu)
4299 System.err.println("Waiting for building menu to finish.");
4301 } catch (Exception e)
4306 final AlignFrame me = this;
4307 buildingMenu = true;
4308 new Thread(new Runnable()
4313 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4316 System.err.println("Building ws menu again "
4317 + Thread.currentThread());
4318 // TODO: add support for context dependent disabling of services based
4320 // alignment and current selection
4321 // TODO: add additional serviceHandle parameter to specify abstract
4323 // class independently of AbstractName
4324 // TODO: add in rediscovery GUI function to restart discoverer
4325 // TODO: group services by location as well as function and/or
4327 // object broker mechanism.
4328 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4329 final IProgressIndicator af = me;
4330 final JMenu msawsmenu = new JMenu(MessageManager.getString("label.alignment"));
4331 final JMenu secstrmenu = new JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4332 final JMenu seqsrchmenu = new JMenu(MessageManager.getString("label.sequence_database_search"));
4333 final JMenu analymenu = new JMenu(MessageManager.getString("label.analysis"));
4334 final JMenu dismenu = new JMenu(MessageManager.getString("label.protein_disorder"));
4335 // JAL-940 - only show secondary structure prediction services from
4336 // the legacy server
4337 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4339 Discoverer.services != null && (Discoverer.services.size() > 0))
4341 // TODO: refactor to allow list of AbstractName/Handler bindings to
4343 // stored or retrieved from elsewhere
4344 // No MSAWS used any more:
4345 // Vector msaws = null; // (Vector)
4346 // Discoverer.services.get("MsaWS");
4347 Vector secstrpr = (Vector) Discoverer.services
4349 if (secstrpr != null)
4351 // Add any secondary structure prediction services
4352 for (int i = 0, j = secstrpr.size(); i < j; i++)
4354 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4356 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4357 .getServiceClient(sh);
4358 int p = secstrmenu.getItemCount();
4359 impl.attachWSMenuEntry(secstrmenu, me);
4360 int q = secstrmenu.getItemCount();
4361 for (int litm = p; litm < q; litm++)
4363 legacyItems.add(secstrmenu.getItem(litm));
4369 // Add all submenus in the order they should appear on the web
4371 wsmenu.add(msawsmenu);
4372 wsmenu.add(secstrmenu);
4373 wsmenu.add(dismenu);
4374 wsmenu.add(analymenu);
4375 // No search services yet
4376 // wsmenu.add(seqsrchmenu);
4378 javax.swing.SwingUtilities.invokeLater(new Runnable()
4385 webService.removeAll();
4386 // first, add discovered services onto the webservices menu
4387 if (wsmenu.size() > 0)
4389 for (int i = 0, j = wsmenu.size(); i < j; i++)
4391 webService.add(wsmenu.get(i));
4396 webService.add(me.webServiceNoServices);
4398 // TODO: move into separate menu builder class.
4399 boolean new_sspred = false;
4400 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4402 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4403 if (jws2servs != null)
4405 if (jws2servs.hasServices())
4407 jws2servs.attachWSMenuEntry(webService, me);
4408 for (Jws2Instance sv : jws2servs.getServices())
4410 if (sv.description.toLowerCase().contains("jpred"))
4412 for (JMenuItem jmi : legacyItems)
4414 jmi.setVisible(false);
4420 if (jws2servs.isRunning())
4422 JMenuItem tm = new JMenuItem(
4423 "Still discovering JABA Services");
4424 tm.setEnabled(false);
4429 build_urlServiceMenu(me.webService);
4430 build_fetchdbmenu(webService);
4431 for (JMenu item : wsmenu)
4433 if (item.getItemCount() == 0)
4435 item.setEnabled(false);
4439 item.setEnabled(true);
4442 } catch (Exception e)
4445 .debug("Exception during web service menu building process.",
4451 } catch (Exception e)
4456 buildingMenu = false;
4463 * construct any groupURL type service menu entries.
4467 private void build_urlServiceMenu(JMenu webService)
4469 // TODO: remove this code when 2.7 is released
4470 // DEBUG - alignmentView
4472 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4473 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4475 * @Override public void actionPerformed(ActionEvent e) {
4476 * jalview.datamodel.AlignmentView
4477 * .testSelectionViews(af.viewport.getAlignment(),
4478 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4480 * }); webService.add(testAlView);
4482 // TODO: refactor to RestClient discoverer and merge menu entries for
4483 // rest-style services with other types of analysis/calculation service
4484 // SHmmr test client - still being implemented.
4485 // DEBUG - alignmentView
4487 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4490 client.attachWSMenuEntry(
4491 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4497 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4498 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4499 * getProperty("LAST_DIRECTORY"));
4501 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4502 * to Vamsas file"); chooser.setToolTipText("Export");
4504 * int value = chooser.showSaveDialog(this);
4506 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4507 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4508 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4509 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4512 * prototype of an automatically enabled/disabled analysis function
4515 protected void setShowProductsEnabled()
4517 SequenceI[] selection = viewport.getSequenceSelection();
4518 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4519 viewport.getAlignment().getDataset()))
4521 showProducts.setEnabled(true);
4526 showProducts.setEnabled(false);
4531 * search selection for sequence xRef products and build the show products
4536 * @return true if showProducts menu should be enabled.
4538 public boolean canShowProducts(SequenceI[] selection,
4539 boolean isRegionSelection, Alignment dataset)
4541 boolean showp = false;
4544 showProducts.removeAll();
4545 final boolean dna = viewport.getAlignment().isNucleotide();
4546 final Alignment ds = dataset;
4547 String[] ptypes = (selection == null || selection.length == 0) ? null
4548 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4550 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4551 // selection, dataset, true);
4552 final SequenceI[] sel = selection;
4553 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4556 final boolean isRegSel = isRegionSelection;
4557 final AlignFrame af = this;
4558 final String source = ptypes[t];
4559 JMenuItem xtype = new JMenuItem(ptypes[t]);
4560 xtype.addActionListener(new ActionListener()
4564 public void actionPerformed(ActionEvent e)
4566 // TODO: new thread for this call with vis-delay
4567 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4568 isRegSel, dna, source);
4572 showProducts.add(xtype);
4574 showProducts.setVisible(showp);
4575 showProducts.setEnabled(showp);
4576 } catch (Exception e)
4578 jalview.bin.Cache.log
4579 .warn("canTranslate threw an exception - please report to help@jalview.org",
4586 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4587 boolean isRegSel, boolean dna, String source)
4589 final boolean fisRegSel = isRegSel;
4590 final boolean fdna = dna;
4591 final String fsrc = source;
4592 final AlignFrame ths = this;
4593 final SequenceI[] fsel = sel;
4594 Runnable foo = new Runnable()
4600 final long sttime = System.currentTimeMillis();
4601 ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
4604 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4608 Alignment prods = CrossRef
4609 .findXrefSequences(fsel, fdna, fsrc, ds);
4612 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4613 for (int s = 0; s < sprods.length; s++)
4615 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4616 if (ds.getSequences() == null
4617 || !ds.getSequences().contains(
4618 sprods[s].getDatasetSequence()))
4619 ds.addSequence(sprods[s].getDatasetSequence());
4620 sprods[s].updatePDBIds();
4622 Alignment al = new Alignment(sprods);
4623 AlignedCodonFrame[] cf = prods.getCodonFrames();
4625 for (int s = 0; cf != null && s < cf.length; s++)
4627 al.addCodonFrame(cf[s]);
4630 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4632 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4633 + " for " + ((fisRegSel) ? "selected region of " : "")
4635 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4640 System.err.println("No Sequences generated for xRef type "
4643 } catch (Exception e)
4645 jalview.bin.Cache.log.error(
4646 "Exception when finding crossreferences", e);
4647 } catch (OutOfMemoryError e)
4649 new OOMWarning("whilst fetching crossreferences", e);
4652 jalview.bin.Cache.log.error("Error when finding crossreferences",
4655 ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
4660 Thread frunner = new Thread(foo);
4664 public boolean canShowTranslationProducts(SequenceI[] selection,
4665 AlignmentI alignment)
4670 return (jalview.analysis.Dna.canTranslate(selection,
4671 viewport.getViewAsVisibleContigs(true)));
4672 } catch (Exception e)
4674 jalview.bin.Cache.log
4675 .warn("canTranslate threw an exception - please report to help@jalview.org",
4682 public void showProducts_actionPerformed(ActionEvent e)
4684 // /////////////////////////////
4685 // Collect Data to be translated/transferred
4687 SequenceI[] selection = viewport.getSequenceSelection();
4688 AlignmentI al = null;
4691 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4692 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4693 viewport.getAlignment().getDataset());
4694 } catch (Exception ex)
4697 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4705 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4706 MessageManager.getString("label.translation_failed"),
4707 JOptionPane.WARNING_MESSAGE);
4711 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4712 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4713 "label.translation_of_params", new String[]
4714 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4719 public void showTranslation_actionPerformed(ActionEvent e)
4721 // /////////////////////////////
4722 // Collect Data to be translated/transferred
4724 SequenceI[] selection = viewport.getSequenceSelection();
4725 String[] seqstring = viewport.getViewAsString(true);
4726 AlignmentI al = null;
4729 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4730 viewport.getViewAsVisibleContigs(true), viewport
4731 .getGapCharacter(), viewport.getAlignment()
4732 .getAlignmentAnnotation(), viewport.getAlignment()
4733 .getWidth(), viewport.getAlignment().getDataset());
4734 } catch (Exception ex)
4737 jalview.bin.Cache.log.error(
4738 "Exception during translation. Please report this !", ex);
4743 .getString("label.error_when_translating_sequences_submit_bug_report"),
4745 .getString("label.implementation_error")
4747 .getString("translation_failed"),
4748 JOptionPane.ERROR_MESSAGE);
4757 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4758 MessageManager.getString("label.translation_failed"),
4759 JOptionPane.WARNING_MESSAGE);
4763 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4764 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4765 "label.translation_of_params", new String[]
4766 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4771 * Try to load a features file onto the alignment.
4774 * contents or path to retrieve file
4776 * access mode of file (see jalview.io.AlignFile)
4777 * @return true if features file was parsed corectly.
4779 public boolean parseFeaturesFile(String file, String type)
4781 boolean featuresFile = false;
4784 featuresFile = new FeaturesFile(file, type).parse(viewport
4785 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4786 .getFeatureRenderer().featureColours, false,
4787 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4788 } catch (Exception ex)
4790 ex.printStackTrace();
4795 viewport.showSequenceFeatures = true;
4796 showSeqFeatures.setSelected(true);
4797 if (alignPanel.seqPanel.seqCanvas.fr != null)
4799 // update the min/max ranges where necessary
4800 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4802 if (featureSettings != null)
4804 featureSettings.setTableData();
4806 alignPanel.paintAlignment(true);
4809 return featuresFile;
4813 public void dragEnter(DropTargetDragEvent evt)
4818 public void dragExit(DropTargetEvent evt)
4823 public void dragOver(DropTargetDragEvent evt)
4828 public void dropActionChanged(DropTargetDragEvent evt)
4833 public void drop(DropTargetDropEvent evt)
4835 Transferable t = evt.getTransferable();
4836 java.util.List files = null;
4840 DataFlavor uriListFlavor = new DataFlavor(
4841 "text/uri-list;class=java.lang.String");
4842 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4844 // Works on Windows and MacOSX
4845 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4846 files = (java.util.List) t
4847 .getTransferData(DataFlavor.javaFileListFlavor);
4849 else if (t.isDataFlavorSupported(uriListFlavor))
4851 // This is used by Unix drag system
4852 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4853 String data = (String) t.getTransferData(uriListFlavor);
4854 files = new java.util.ArrayList(1);
4855 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4856 data, "\r\n"); st.hasMoreTokens();)
4858 String s = st.nextToken();
4859 if (s.startsWith("#"))
4861 // the line is a comment (as per the RFC 2483)
4865 java.net.URI uri = new java.net.URI(s);
4866 // check to see if we can handle this kind of URI
4867 if (uri.getScheme().toLowerCase().startsWith("http"))
4869 files.add(uri.toString());
4873 // otherwise preserve old behaviour: catch all for file objects
4874 java.io.File file = new java.io.File(uri);
4875 files.add(file.toString());
4879 } catch (Exception e)
4881 e.printStackTrace();
4887 // check to see if any of these files have names matching sequences in
4889 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4890 .getAlignment().getSequencesArray());
4892 * Object[] { String,SequenceI}
4894 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4895 ArrayList<String> filesnotmatched = new ArrayList<String>();
4896 for (int i = 0; i < files.size(); i++)
4898 String file = files.get(i).toString();
4900 String protocol = FormatAdapter.checkProtocol(file);
4901 if (protocol == jalview.io.FormatAdapter.FILE)
4903 File fl = new File(file);
4904 pdbfn = fl.getName();
4906 else if (protocol == jalview.io.FormatAdapter.URL)
4908 URL url = new URL(file);
4909 pdbfn = url.getFile();
4911 if (pdbfn.length() > 0)
4913 // attempt to find a match in the alignment
4914 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4915 int l = 0, c = pdbfn.indexOf(".");
4916 while (mtch == null && c != -1)
4921 } while ((c = pdbfn.indexOf(".", l)) > l);
4924 pdbfn = pdbfn.substring(0, l);
4926 mtch = idm.findAllIdMatches(pdbfn);
4933 type = new IdentifyFile().Identify(file, protocol);
4934 } catch (Exception ex)
4940 if (type.equalsIgnoreCase("PDB"))
4942 filesmatched.add(new Object[]
4943 { file, protocol, mtch });
4948 // File wasn't named like one of the sequences or wasn't a PDB file.
4949 filesnotmatched.add(file);
4953 if (filesmatched.size() > 0)
4955 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4961 "label.automatically_associate_pdb_files_with_sequences_same_name",
4968 .getString("label.automatically_associate_pdb_files_by_name"),
4969 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4972 for (Object[] fm : filesmatched)
4974 // try and associate
4975 // TODO: may want to set a standard ID naming formalism for
4976 // associating PDB files which have no IDs.
4977 for (SequenceI toassoc : (SequenceI[]) fm[2])
4979 PDBEntry pe = new AssociatePdbFileWithSeq()
4980 .associatePdbWithSeq((String) fm[0],
4981 (String) fm[1], toassoc, false);
4984 System.err.println("Associated file : "
4985 + ((String) fm[0]) + " with "
4986 + toassoc.getDisplayId(true));
4990 alignPanel.paintAlignment(true);
4994 if (filesnotmatched.size() > 0)
4997 && (Cache.getDefault(
4998 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5003 "label.ignore_unmatched_dropped_files_info",
5010 .getString("label.ignore_unmatched_dropped_files"),
5011 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5015 for (String fn : filesnotmatched)
5017 loadJalviewDataFile(fn, null, null, null);
5021 } catch (Exception ex)
5023 ex.printStackTrace();
5029 * Attempt to load a "dropped" file or URL string: First by testing whether
5030 * it's and Annotation file, then a JNet file, and finally a features file. If
5031 * all are false then the user may have dropped an alignment file onto this
5035 * either a filename or a URL string.
5037 public void loadJalviewDataFile(String file, String protocol,
5038 String format, SequenceI assocSeq)
5042 if (protocol == null)
5044 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5046 // if the file isn't identified, or not positively identified as some
5047 // other filetype (PFAM is default unidentified alignment file type) then
5048 // try to parse as annotation.
5049 boolean isAnnotation = (format == null || format
5050 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5051 .readAnnotationFile(viewport.getAlignment(), file, protocol)
5056 // first see if its a T-COFFEE score file
5057 TCoffeeScoreFile tcf = null;
5060 tcf = new TCoffeeScoreFile(file, protocol);
5063 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5065 tcoffeeColour.setEnabled(true);
5066 tcoffeeColour.setSelected(true);
5067 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5068 isAnnotation = true;
5070 .setText(MessageManager
5071 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5075 // some problem - if no warning its probable that the ID matching
5076 // process didn't work
5080 tcf.getWarningMessage() == null ? MessageManager
5081 .getString("label.check_file_matches_sequence_ids_alignment")
5082 : tcf.getWarningMessage(),
5084 .getString("label.problem_reading_tcoffee_score_file"),
5085 JOptionPane.WARNING_MESSAGE);
5092 } catch (Exception x)
5095 .debug("Exception when processing data source as T-COFFEE score file",
5101 // try to see if its a JNet 'concise' style annotation file *before*
5103 // try to parse it as a features file
5106 format = new IdentifyFile().Identify(file, protocol);
5108 if (format.equalsIgnoreCase("JnetFile"))
5110 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5112 new JnetAnnotationMaker().add_annotation(predictions,
5113 viewport.getAlignment(), 0, false);
5114 isAnnotation = true;
5119 * if (format.equalsIgnoreCase("PDB")) {
5121 * String pdbfn = ""; // try to match up filename with sequence id
5122 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5123 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5124 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5125 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5126 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5127 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5128 * // attempt to find a match in the alignment SequenceI mtch =
5129 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5130 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5131 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5132 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5133 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5134 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5135 * { System.err.println("Associated file : " + file + " with " +
5136 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5137 * TODO: maybe need to load as normal otherwise return; } }
5139 // try to parse it as a features file
5140 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5141 // if it wasn't a features file then we just treat it as a general
5142 // alignment file to load into the current view.
5145 new FileLoader().LoadFile(viewport, file, protocol, format);
5149 alignPanel.paintAlignment(true);
5157 alignPanel.adjustAnnotationHeight();
5158 viewport.updateSequenceIdColours();
5159 buildSortByAnnotationScoresMenu();
5160 alignPanel.paintAlignment(true);
5162 } catch (Exception ex)
5164 ex.printStackTrace();
5165 } catch (OutOfMemoryError oom)
5170 } catch (Exception x)
5176 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5177 : "using " + protocol + " from " + file)
5179 + (format != null ? "(parsing as '" + format
5180 + "' file)" : ""), oom, Desktop.desktop);
5185 public void tabSelectionChanged(int index)
5189 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5190 viewport = alignPanel.av;
5191 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5192 setMenusFromViewport(viewport);
5197 public void tabbedPane_mousePressed(MouseEvent e)
5199 if (SwingUtilities.isRightMouseButton(e))
5201 String reply = JOptionPane.showInternalInputDialog(this,
5202 MessageManager.getString("label.enter_view_name"),
5203 MessageManager.getString("label.enter_view_name"),
5204 JOptionPane.QUESTION_MESSAGE);
5208 viewport.viewName = reply;
5209 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5214 public AlignViewport getCurrentView()
5220 * Open the dialog for regex description parsing.
5223 protected void extractScores_actionPerformed(ActionEvent e)
5225 ParseProperties pp = new jalview.analysis.ParseProperties(
5226 viewport.getAlignment());
5227 // TODO: verify regex and introduce GUI dialog for version 2.5
5228 // if (pp.getScoresFromDescription("col", "score column ",
5229 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5231 if (pp.getScoresFromDescription("description column",
5232 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5234 buildSortByAnnotationScoresMenu();
5242 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5246 protected void showDbRefs_actionPerformed(ActionEvent e)
5248 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5254 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5258 protected void showNpFeats_actionPerformed(ActionEvent e)
5260 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5264 * find the viewport amongst the tabs in this alignment frame and close that
5269 public boolean closeView(AlignViewport av)
5273 this.closeMenuItem_actionPerformed(false);
5276 Component[] comp = tabbedPane.getComponents();
5277 for (int i = 0; comp != null && i < comp.length; i++)
5279 if (comp[i] instanceof AlignmentPanel)
5281 if (((AlignmentPanel) comp[i]).av == av)
5284 closeView((AlignmentPanel) comp[i]);
5292 protected void build_fetchdbmenu(JMenu webService)
5294 // Temporary hack - DBRef Fetcher always top level ws entry.
5295 // TODO We probably want to store a sequence database checklist in
5296 // preferences and have checkboxes.. rather than individual sources selected
5298 final JMenu rfetch = new JMenu(
5299 MessageManager.getString("action.fetch_db_references"));
5300 rfetch.setToolTipText(MessageManager
5301 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5302 webService.add(rfetch);
5304 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5305 MessageManager.getString("option.trim_retrieved_seqs"));
5306 trimrs.setToolTipText(MessageManager
5307 .getString("label.trim_retrieved_sequences"));
5308 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5309 trimrs.addActionListener(new ActionListener()
5311 public void actionPerformed(ActionEvent e)
5313 trimrs.setSelected(trimrs.isSelected());
5314 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5315 Boolean.valueOf(trimrs.isSelected()).toString());
5319 JMenuItem fetchr = new JMenuItem(
5320 MessageManager.getString("label.standard_databases"));
5321 fetchr.setToolTipText(MessageManager
5322 .getString("label.fetch_embl_uniprot"));
5323 fetchr.addActionListener(new ActionListener()
5327 public void actionPerformed(ActionEvent e)
5329 new Thread(new Runnable()
5335 new jalview.ws.DBRefFetcher(alignPanel.av
5336 .getSequenceSelection(), alignPanel.alignFrame)
5337 .fetchDBRefs(false);
5345 final AlignFrame me = this;
5346 new Thread(new Runnable()
5351 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5352 .getSequenceFetcherSingleton(me);
5353 javax.swing.SwingUtilities.invokeLater(new Runnable()
5358 String[] dbclasses = sf.getOrderedSupportedSources();
5359 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5360 // jalview.util.QuickSort.sort(otherdb, otherdb);
5361 List<DbSourceProxy> otherdb;
5362 JMenu dfetch = new JMenu();
5363 JMenu ifetch = new JMenu();
5364 JMenuItem fetchr = null;
5365 int comp = 0, icomp = 0, mcomp = 15;
5366 String mname = null;
5368 for (String dbclass : dbclasses)
5370 otherdb = sf.getSourceProxy(dbclass);
5371 // add a single entry for this class, or submenu allowing 'fetch
5373 if (otherdb == null || otherdb.size() < 1)
5377 // List<DbSourceProxy> dbs=otherdb;
5378 // otherdb=new ArrayList<DbSourceProxy>();
5379 // for (DbSourceProxy db:dbs)
5381 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5385 mname = "From " + dbclass;
5387 if (otherdb.size() == 1)
5389 final DbSourceProxy[] dassource = otherdb
5390 .toArray(new DbSourceProxy[0]);
5391 DbSourceProxy src = otherdb.get(0);
5392 fetchr = new JMenuItem(src.getDbSource());
5393 fetchr.addActionListener(new ActionListener()
5397 public void actionPerformed(ActionEvent e)
5399 new Thread(new Runnable()
5405 new jalview.ws.DBRefFetcher(alignPanel.av
5406 .getSequenceSelection(),
5407 alignPanel.alignFrame, dassource)
5408 .fetchDBRefs(false);
5414 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
5420 final DbSourceProxy[] dassource = otherdb
5421 .toArray(new DbSourceProxy[0]);
5423 DbSourceProxy src = otherdb.get(0);
5424 fetchr = new JMenuItem(MessageManager.formatMessage(
5425 "label.fetch_all_param", new String[]
5426 { src.getDbSource() }));
5427 fetchr.addActionListener(new ActionListener()
5430 public void actionPerformed(ActionEvent e)
5432 new Thread(new Runnable()
5438 new jalview.ws.DBRefFetcher(alignPanel.av
5439 .getSequenceSelection(),
5440 alignPanel.alignFrame, dassource)
5441 .fetchDBRefs(false);
5447 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5450 // and then build the rest of the individual menus
5451 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
5453 String imname = null;
5455 for (DbSourceProxy sproxy : otherdb)
5457 String dbname = sproxy.getDbName();
5458 String sname = dbname.length() > 5 ? dbname.substring(0,
5459 5) + "..." : dbname;
5460 String msname = dbname.length() > 10 ? dbname.substring(
5461 0, 10) + "..." : dbname;
5464 imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
5466 fetchr = new JMenuItem(msname);
5467 final DbSourceProxy[] dassrc =
5469 fetchr.addActionListener(new ActionListener()
5473 public void actionPerformed(ActionEvent e)
5475 new Thread(new Runnable()
5481 new jalview.ws.DBRefFetcher(alignPanel.av
5482 .getSequenceSelection(),
5483 alignPanel.alignFrame, dassrc)
5484 .fetchDBRefs(false);
5490 fetchr.setToolTipText("<html>"
5491 + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
5494 if (++icomp >= mcomp || i == (otherdb.size()))
5496 ifetch.setText(MessageManager.formatMessage(
5497 "label.source_to_target", imname, sname));
5499 ifetch = new JMenu();
5507 if (comp >= mcomp || dbi >= (dbclasses.length))
5509 dfetch.setText(MessageManager.formatMessage(
5510 "label.source_to_target", mname, dbclass));
5512 dfetch = new JMenu();
5525 * Left justify the whole alignment.
5528 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5530 AlignmentI al = viewport.getAlignment();
5532 viewport.firePropertyChange("alignment", null, al);
5536 * Right justify the whole alignment.
5539 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5541 AlignmentI al = viewport.getAlignment();
5543 viewport.firePropertyChange("alignment", null, al);
5546 public void setShowSeqFeatures(boolean b)
5548 showSeqFeatures.setSelected(true);
5549 viewport.setShowSequenceFeatures(true);
5556 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5557 * awt.event.ActionEvent)
5560 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5562 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5563 alignPanel.paintAlignment(true);
5570 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5574 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5576 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5577 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5585 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5586 * .event.ActionEvent)
5589 protected void showGroupConservation_actionPerformed(ActionEvent e)
5591 viewport.setShowGroupConservation(showGroupConservation.getState());
5592 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5599 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5600 * .event.ActionEvent)
5603 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5605 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5606 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5613 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5614 * .event.ActionEvent)
5617 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5619 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5620 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5624 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5626 showSequenceLogo.setState(true);
5627 viewport.setShowSequenceLogo(true);
5628 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5629 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5633 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5635 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5642 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5643 * .event.ActionEvent)
5646 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5648 if (avc.makeGroupsFromSelection())
5650 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5651 alignPanel.updateAnnotation();
5652 alignPanel.paintAlignment(true);
5657 protected void createGroup_actionPerformed(ActionEvent e)
5659 if (avc.createGroup())
5661 alignPanel.alignmentChanged();
5666 protected void unGroup_actionPerformed(ActionEvent e)
5670 alignPanel.alignmentChanged();
5675 * make the given alignmentPanel the currently selected tab
5677 * @param alignmentPanel
5679 public void setDisplayedView(AlignmentPanel alignmentPanel)
5681 if (!viewport.getSequenceSetId().equals(
5682 alignmentPanel.av.getSequenceSetId()))
5684 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5686 if (tabbedPane != null
5687 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5688 .getSelectedIndex())
5690 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5695 class PrintThread extends Thread
5699 public PrintThread(AlignmentPanel ap)
5704 static PageFormat pf;
5709 PrinterJob printJob = PrinterJob.getPrinterJob();
5713 printJob.setPrintable(ap, pf);
5717 printJob.setPrintable(ap);
5720 if (printJob.printDialog())
5725 } catch (Exception PrintException)
5727 PrintException.printStackTrace();