2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 import jalview.analysis.AAFrequency;
21 import jalview.analysis.AlignmentSorter;
22 import jalview.analysis.Conservation;
23 import jalview.analysis.CrossRef;
24 import jalview.analysis.NJTree;
25 import jalview.analysis.ParseProperties;
26 import jalview.analysis.SequenceIdMatcher;
27 import jalview.bin.Cache;
28 import jalview.commands.CommandI;
29 import jalview.commands.EditCommand;
30 import jalview.commands.OrderCommand;
31 import jalview.commands.RemoveGapColCommand;
32 import jalview.commands.RemoveGapsCommand;
33 import jalview.commands.SlideSequencesCommand;
34 import jalview.commands.TrimRegionCommand;
35 import jalview.datamodel.AlignedCodonFrame;
36 import jalview.datamodel.Alignment;
37 import jalview.datamodel.AlignmentAnnotation;
38 import jalview.datamodel.AlignmentI;
39 import jalview.datamodel.AlignmentOrder;
40 import jalview.datamodel.AlignmentView;
41 import jalview.datamodel.ColumnSelection;
42 import jalview.datamodel.PDBEntry;
43 import jalview.datamodel.SeqCigar;
44 import jalview.datamodel.Sequence;
45 import jalview.datamodel.SequenceGroup;
46 import jalview.datamodel.SequenceI;
47 import jalview.io.AlignmentProperties;
48 import jalview.io.AnnotationFile;
49 import jalview.io.FeaturesFile;
50 import jalview.io.FileLoader;
51 import jalview.io.FormatAdapter;
52 import jalview.io.HTMLOutput;
53 import jalview.io.IdentifyFile;
54 import jalview.io.JalviewFileChooser;
55 import jalview.io.JalviewFileView;
56 import jalview.io.JnetAnnotationMaker;
57 import jalview.io.NewickFile;
58 import jalview.jbgui.GAlignFrame;
59 import jalview.schemes.Blosum62ColourScheme;
60 import jalview.schemes.BuriedColourScheme;
61 import jalview.schemes.ClustalxColourScheme;
62 import jalview.schemes.ColourSchemeI;
63 import jalview.schemes.ColourSchemeProperty;
64 import jalview.schemes.HelixColourScheme;
65 import jalview.schemes.HydrophobicColourScheme;
66 import jalview.schemes.NucleotideColourScheme;
67 import jalview.schemes.PIDColourScheme;
68 import jalview.schemes.PurinePyrimidineColourScheme;
69 import jalview.schemes.ResidueProperties;
70 import jalview.schemes.StrandColourScheme;
71 import jalview.schemes.TaylorColourScheme;
72 import jalview.schemes.TurnColourScheme;
73 import jalview.schemes.UserColourScheme;
74 import jalview.schemes.ZappoColourScheme;
75 import jalview.ws.WSMenuEntryProviderI;
76 import jalview.ws.jws1.Discoverer;
77 import jalview.ws.jws2.Jws2Discoverer;
79 import java.awt.BorderLayout;
80 import java.awt.Color;
81 import java.awt.Component;
82 import java.awt.GridLayout;
83 import java.awt.Rectangle;
84 import java.awt.Toolkit;
85 import java.awt.datatransfer.Clipboard;
86 import java.awt.datatransfer.DataFlavor;
87 import java.awt.datatransfer.StringSelection;
88 import java.awt.datatransfer.Transferable;
89 import java.awt.dnd.DnDConstants;
90 import java.awt.dnd.DropTargetDragEvent;
91 import java.awt.dnd.DropTargetDropEvent;
92 import java.awt.dnd.DropTargetEvent;
93 import java.awt.dnd.DropTargetListener;
94 import java.awt.event.ActionEvent;
95 import java.awt.event.ActionListener;
96 import java.awt.event.KeyAdapter;
97 import java.awt.event.KeyEvent;
98 import java.awt.event.MouseAdapter;
99 import java.awt.event.MouseEvent;
100 import java.awt.print.PageFormat;
101 import java.awt.print.PrinterJob;
102 import java.beans.PropertyChangeEvent;
105 import java.util.ArrayList;
106 import java.util.Enumeration;
107 import java.util.Hashtable;
108 import java.util.Vector;
110 import javax.swing.JButton;
111 import javax.swing.JEditorPane;
112 import javax.swing.JInternalFrame;
113 import javax.swing.JLabel;
114 import javax.swing.JLayeredPane;
115 import javax.swing.JMenu;
116 import javax.swing.JMenuItem;
117 import javax.swing.JOptionPane;
118 import javax.swing.JPanel;
119 import javax.swing.JProgressBar;
120 import javax.swing.JRadioButtonMenuItem;
121 import javax.swing.JScrollPane;
122 import javax.swing.SwingUtilities;
128 * @version $Revision$
130 public class AlignFrame extends GAlignFrame implements DropTargetListener,
135 public static final int DEFAULT_WIDTH = 700;
138 public static final int DEFAULT_HEIGHT = 500;
140 public AlignmentPanel alignPanel;
142 AlignViewport viewport;
144 Vector alignPanels = new Vector();
147 * Last format used to load or save alignments in this window
149 String currentFileFormat = null;
152 * Current filename for this alignment
154 String fileName = null;
157 * Creates a new AlignFrame object with specific width and height.
163 public AlignFrame(AlignmentI al, int width, int height)
165 this(al, null, width, height);
169 * Creates a new AlignFrame object with specific width, height and
175 * @param sequenceSetId
177 public AlignFrame(AlignmentI al, int width, int height,
178 String sequenceSetId)
180 this(al, null, width, height, sequenceSetId);
184 * Creates a new AlignFrame object with specific width, height and
190 * @param sequenceSetId
193 public AlignFrame(AlignmentI al, int width, int height,
194 String sequenceSetId, String viewId)
196 this(al, null, width, height, sequenceSetId, viewId);
200 * new alignment window with hidden columns
204 * @param hiddenColumns
205 * ColumnSelection or null
207 * Width of alignment frame
211 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
212 int width, int height)
214 this(al, hiddenColumns, width, height, null);
218 * Create alignment frame for al with hiddenColumns, a specific width and
219 * height, and specific sequenceId
222 * @param hiddenColumns
225 * @param sequenceSetId
228 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
229 int width, int height, String sequenceSetId)
231 this(al, hiddenColumns, width, height, sequenceSetId, null);
235 * Create alignment frame for al with hiddenColumns, a specific width and
236 * height, and specific sequenceId
239 * @param hiddenColumns
242 * @param sequenceSetId
247 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
248 int width, int height, String sequenceSetId, String viewId)
250 setSize(width, height);
251 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
253 alignPanel = new AlignmentPanel(this, viewport);
255 if (al.getDataset() == null)
260 addAlignmentPanel(alignPanel, true);
265 * Make a new AlignFrame from exisiting alignmentPanels
272 public AlignFrame(AlignmentPanel ap)
276 addAlignmentPanel(ap, false);
281 * initalise the alignframe from the underlying viewport data and the
286 if (viewport.conservation == null)
288 BLOSUM62Colour.setEnabled(false);
289 conservationMenuItem.setEnabled(false);
290 modifyConservation.setEnabled(false);
291 // PIDColour.setEnabled(false);
292 // abovePIDThreshold.setEnabled(false);
293 // modifyPID.setEnabled(false);
296 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
299 if (sortby.equals("Id"))
301 sortIDMenuItem_actionPerformed(null);
303 else if (sortby.equals("Pairwise Identity"))
305 sortPairwiseMenuItem_actionPerformed(null);
308 if (Desktop.desktop != null)
310 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
311 addServiceListeners();
312 setGUINucleotide(viewport.alignment.isNucleotide());
315 setMenusFromViewport(viewport);
316 buildSortByAnnotationScoresMenu();
317 if (viewport.wrapAlignment)
319 wrapMenuItem_actionPerformed(null);
322 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
324 this.overviewMenuItem_actionPerformed(null);
332 * Change the filename and format for the alignment, and enable the 'reload'
333 * button functionality.
340 public void setFileName(String file, String format)
343 currentFileFormat = format;
344 reload.setEnabled(true);
347 void addKeyListener()
349 addKeyListener(new KeyAdapter()
351 public void keyPressed(KeyEvent evt)
353 if (viewport.cursorMode
354 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
355 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
356 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
357 && Character.isDigit(evt.getKeyChar()))
358 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
360 switch (evt.getKeyCode())
363 case 27: // escape key
364 deselectAllSequenceMenuItem_actionPerformed(null);
368 case KeyEvent.VK_DOWN:
369 if (evt.isAltDown() || !viewport.cursorMode)
370 moveSelectedSequences(false);
371 if (viewport.cursorMode)
372 alignPanel.seqPanel.moveCursor(0, 1);
376 if (evt.isAltDown() || !viewport.cursorMode)
377 moveSelectedSequences(true);
378 if (viewport.cursorMode)
379 alignPanel.seqPanel.moveCursor(0, -1);
383 case KeyEvent.VK_LEFT:
384 if (evt.isAltDown() || !viewport.cursorMode)
385 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
387 alignPanel.seqPanel.moveCursor(-1, 0);
391 case KeyEvent.VK_RIGHT:
392 if (evt.isAltDown() || !viewport.cursorMode)
393 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
395 alignPanel.seqPanel.moveCursor(1, 0);
398 case KeyEvent.VK_SPACE:
399 if (viewport.cursorMode)
401 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
402 || evt.isShiftDown() || evt.isAltDown());
406 //case KeyEvent.VK_A:
407 // if (viewport.cursorMode)
409 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
410 // //System.out.println("A");
414 case KeyEvent.VK_CLOSE_BRACKET:
415 if (viewport.cursorMode)
417 System.out.println("closing bracket");
421 case KeyEvent.VK_DELETE:
422 case KeyEvent.VK_BACK_SPACE:
423 if (!viewport.cursorMode)
425 cut_actionPerformed(null);
429 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
430 || evt.isShiftDown() || evt.isAltDown());
436 if (viewport.cursorMode)
438 alignPanel.seqPanel.setCursorRow();
442 if (viewport.cursorMode && !evt.isControlDown())
444 alignPanel.seqPanel.setCursorColumn();
448 if (viewport.cursorMode)
450 alignPanel.seqPanel.setCursorPosition();
454 case KeyEvent.VK_ENTER:
455 case KeyEvent.VK_COMMA:
456 if (viewport.cursorMode)
458 alignPanel.seqPanel.setCursorRowAndColumn();
463 if (viewport.cursorMode)
465 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
469 if (viewport.cursorMode)
471 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
476 viewport.cursorMode = !viewport.cursorMode;
477 statusBar.setText("Keyboard editing mode is "
478 + (viewport.cursorMode ? "on" : "off"));
479 if (viewport.cursorMode)
481 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
482 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
484 alignPanel.seqPanel.seqCanvas.repaint();
490 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
491 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
493 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
495 javax.help.HelpBroker hb = hs.createHelpBroker();
496 hb.setCurrentID("home");
497 hb.setDisplayed(true);
498 } catch (Exception ex)
500 ex.printStackTrace();
505 boolean toggleSeqs = !evt.isControlDown();
506 boolean toggleCols = !evt.isShiftDown();
507 toggleHiddenRegions(toggleSeqs, toggleCols);
510 case KeyEvent.VK_PAGE_UP:
511 if (viewport.wrapAlignment)
513 alignPanel.scrollUp(true);
517 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
518 - viewport.endSeq + viewport.startSeq);
521 case KeyEvent.VK_PAGE_DOWN:
522 if (viewport.wrapAlignment)
524 alignPanel.scrollUp(false);
528 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
529 + viewport.endSeq - viewport.startSeq);
535 public void keyReleased(KeyEvent evt)
537 switch (evt.getKeyCode())
539 case KeyEvent.VK_LEFT:
540 if (evt.isAltDown() || !viewport.cursorMode)
541 viewport.firePropertyChange("alignment", null, viewport
542 .getAlignment().getSequences());
545 case KeyEvent.VK_RIGHT:
546 if (evt.isAltDown() || !viewport.cursorMode)
547 viewport.firePropertyChange("alignment", null, viewport
548 .getAlignment().getSequences());
555 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
557 ap.alignFrame = this;
559 alignPanels.addElement(ap);
561 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
563 int aSize = alignPanels.size();
565 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
567 if (aSize == 1 && ap.av.viewName == null)
569 this.getContentPane().add(ap, BorderLayout.CENTER);
575 setInitialTabVisible();
578 expandViews.setEnabled(true);
579 gatherViews.setEnabled(true);
580 tabbedPane.addTab(ap.av.viewName, ap);
582 ap.setVisible(false);
589 ap.av.alignment.padGaps();
591 ap.av.updateConservation(ap);
592 ap.av.updateConsensus(ap);
593 ap.av.updateStrucConsensus(ap);
597 public void setInitialTabVisible()
599 expandViews.setEnabled(true);
600 gatherViews.setEnabled(true);
601 tabbedPane.setVisible(true);
602 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
603 tabbedPane.addTab(first.av.viewName, first);
604 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
607 public AlignViewport getViewport()
612 /* Set up intrinsic listeners for dynamically generated GUI bits. */
613 private void addServiceListeners()
615 final java.beans.PropertyChangeListener thisListener;
616 Desktop.instance.addJalviewPropertyChangeListener("services",
617 thisListener = new java.beans.PropertyChangeListener()
619 public void propertyChange(PropertyChangeEvent evt)
621 // // System.out.println("Discoverer property change.");
622 // if (evt.getPropertyName().equals("services"))
624 SwingUtilities.invokeLater(new Runnable()
630 .println("Rebuild WS Menu for service change");
631 BuildWebServiceMenu();
638 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
640 public void internalFrameClosed(
641 javax.swing.event.InternalFrameEvent evt)
643 System.out.println("deregistering discoverer listener");
644 Desktop.instance.removeJalviewPropertyChangeListener("services",
646 closeMenuItem_actionPerformed(true);
649 // Finally, build the menu once to get current service state
650 new Thread(new Runnable()
654 BuildWebServiceMenu();
659 public void setGUINucleotide(boolean nucleotide)
661 showTranslation.setVisible(nucleotide);
662 conservationMenuItem.setEnabled(!nucleotide);
663 modifyConservation.setEnabled(!nucleotide);
664 showGroupConservation.setEnabled(!nucleotide);
665 rnahelicesColour.setEnabled(nucleotide);
666 purinePyrimidineColour.setEnabled(nucleotide);
667 // Remember AlignFrame always starts as protein
671 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
676 * set up menus for the currently viewport. This may be called after any
677 * operation that affects the data in the current view (selection changed,
678 * etc) to update the menus to reflect the new state.
680 public void setMenusForViewport()
682 setMenusFromViewport(viewport);
686 * Need to call this method when tabs are selected for multiple views, or when
687 * loading from Jalview2XML.java
692 void setMenusFromViewport(AlignViewport av)
694 padGapsMenuitem.setSelected(av.padGaps);
695 colourTextMenuItem.setSelected(av.showColourText);
696 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
697 conservationMenuItem.setSelected(av.getConservationSelected());
698 seqLimits.setSelected(av.getShowJVSuffix());
699 idRightAlign.setSelected(av.rightAlignIds);
700 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
701 renderGapsMenuItem.setSelected(av.renderGaps);
702 wrapMenuItem.setSelected(av.wrapAlignment);
703 scaleAbove.setVisible(av.wrapAlignment);
704 scaleLeft.setVisible(av.wrapAlignment);
705 scaleRight.setVisible(av.wrapAlignment);
706 annotationPanelMenuItem.setState(av.showAnnotation);
707 viewBoxesMenuItem.setSelected(av.showBoxes);
708 viewTextMenuItem.setSelected(av.showText);
709 showNonconservedMenuItem.setSelected(av.showUnconserved);
710 showGroupConsensus.setSelected(av.showGroupConsensus);
711 showGroupConservation.setSelected(av.showGroupConservation);
712 showConsensusHistogram.setSelected(av.showConsensusHistogram);
713 showSequenceLogo.setSelected(av.showSequenceLogo);
714 normaliseSequenceLogo.setSelected(av.normaliseSequenceLogo);
716 setColourSelected(ColourSchemeProperty.getColourName(av
717 .getGlobalColourScheme()));
719 showSeqFeatures.setSelected(av.showSequenceFeatures);
720 hiddenMarkers.setState(av.showHiddenMarkers);
721 applyToAllGroups.setState(av.colourAppliesToAllGroups);
722 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
723 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
724 autoCalculate.setSelected(av.autoCalculateConsensus);
725 sortByTree.setSelected(av.sortByTree);
726 listenToViewSelections.setSelected(av.followSelection);
727 rnahelicesColour.setEnabled(av.alignment.hasRNAStructure());
728 rnahelicesColour.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
729 setShowProductsEnabled();
734 Hashtable progressBars, progressBarHandlers;
739 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
741 public void setProgressBar(String message, long id)
743 if (progressBars == null)
745 progressBars = new Hashtable();
746 progressBarHandlers = new Hashtable();
749 JPanel progressPanel;
750 Long lId = new Long(id);
751 GridLayout layout = (GridLayout) statusPanel.getLayout();
752 if (progressBars.get(lId) != null)
754 progressPanel = (JPanel) progressBars.get(new Long(id));
755 statusPanel.remove(progressPanel);
756 progressBars.remove(lId);
757 progressPanel = null;
760 statusBar.setText(message);
762 if (progressBarHandlers.contains(lId))
764 progressBarHandlers.remove(lId);
766 layout.setRows(layout.getRows() - 1);
770 progressPanel = new JPanel(new BorderLayout(10, 5));
772 JProgressBar progressBar = new JProgressBar();
773 progressBar.setIndeterminate(true);
775 progressPanel.add(new JLabel(message), BorderLayout.WEST);
776 progressPanel.add(progressBar, BorderLayout.CENTER);
778 layout.setRows(layout.getRows() + 1);
779 statusPanel.add(progressPanel);
781 progressBars.put(lId, progressPanel);
784 // setMenusForViewport();
788 public void registerHandler(final long id,
789 final IProgressIndicatorHandler handler)
791 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
794 "call setProgressBar before registering the progress bar's handler.");
796 progressBarHandlers.put(new Long(id), handler);
797 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
798 if (handler.canCancel())
800 JButton cancel = new JButton("Cancel");
801 final IProgressIndicator us = this;
802 cancel.addActionListener(new ActionListener()
805 public void actionPerformed(ActionEvent e)
807 handler.cancelActivity(id);
810 + ((JLabel) progressPanel.getComponent(0))
814 progressPanel.add(cancel, BorderLayout.EAST);
820 * @return true if any progress bars are still active
822 public boolean operationInProgress()
824 if (progressBars != null && progressBars.size() > 0)
832 * Added so Castor Mapping file can obtain Jalview Version
834 public String getVersion()
836 return jalview.bin.Cache.getProperty("VERSION");
839 public FeatureRenderer getFeatureRenderer()
841 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
844 public void fetchSequence_actionPerformed(ActionEvent e)
846 new SequenceFetcher(this);
849 public void addFromFile_actionPerformed(ActionEvent e)
851 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
854 public void reload_actionPerformed(ActionEvent e)
856 if (fileName != null)
858 // TODO: work out how to recover feature settings for correct view(s) when
860 if (currentFileFormat.equals("Jalview"))
862 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
863 for (int i = 0; i < frames.length; i++)
865 if (frames[i] instanceof AlignFrame && frames[i] != this
866 && ((AlignFrame) frames[i]).fileName.equals(fileName))
870 frames[i].setSelected(true);
871 Desktop.instance.closeAssociatedWindows();
872 } catch (java.beans.PropertyVetoException ex)
878 Desktop.instance.closeAssociatedWindows();
880 FileLoader loader = new FileLoader();
881 String protocol = fileName.startsWith("http:") ? "URL" : "File";
882 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
886 Rectangle bounds = this.getBounds();
888 FileLoader loader = new FileLoader();
889 String protocol = fileName.startsWith("http:") ? "URL" : "File";
890 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
891 protocol, currentFileFormat);
893 newframe.setBounds(bounds);
894 if (featureSettings != null && featureSettings.isShowing())
896 final Rectangle fspos = featureSettings.frame.getBounds();
897 // TODO: need a 'show feature settings' function that takes bounds -
898 // need to refactor Desktop.addFrame
899 newframe.featureSettings_actionPerformed(null);
900 final FeatureSettings nfs = newframe.featureSettings;
901 SwingUtilities.invokeLater(new Runnable()
905 nfs.frame.setBounds(fspos);
908 this.featureSettings.close();
909 this.featureSettings = null;
911 this.closeMenuItem_actionPerformed(true);
916 public void addFromText_actionPerformed(ActionEvent e)
918 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
921 public void addFromURL_actionPerformed(ActionEvent e)
923 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
926 public void save_actionPerformed(ActionEvent e)
929 || (currentFileFormat == null || !jalview.io.FormatAdapter
930 .isValidIOFormat(currentFileFormat, true))
931 || fileName.startsWith("http"))
933 saveAs_actionPerformed(null);
937 saveAlignment(fileName, currentFileFormat);
947 public void saveAs_actionPerformed(ActionEvent e)
949 JalviewFileChooser chooser = new JalviewFileChooser(
950 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
951 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
952 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
953 currentFileFormat, false);
955 chooser.setFileView(new JalviewFileView());
956 chooser.setDialogTitle("Save Alignment to file");
957 chooser.setToolTipText("Save");
959 int value = chooser.showSaveDialog(this);
961 if (value == JalviewFileChooser.APPROVE_OPTION)
963 currentFileFormat = chooser.getSelectedFormat();
964 if (currentFileFormat == null)
966 JOptionPane.showInternalMessageDialog(Desktop.desktop,
967 "You must select a file format before saving!",
968 "File format not specified", JOptionPane.WARNING_MESSAGE);
969 value = chooser.showSaveDialog(this);
973 fileName = chooser.getSelectedFile().getPath();
975 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
978 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
979 if (currentFileFormat.indexOf(" ") > -1)
981 currentFileFormat = currentFileFormat.substring(0,
982 currentFileFormat.indexOf(" "));
984 saveAlignment(fileName, currentFileFormat);
988 public boolean saveAlignment(String file, String format)
990 boolean success = true;
992 if (format.equalsIgnoreCase("Jalview"))
994 String shortName = title;
996 if (shortName.indexOf(java.io.File.separatorChar) > -1)
998 shortName = shortName.substring(shortName
999 .lastIndexOf(java.io.File.separatorChar) + 1);
1002 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1004 statusBar.setText("Successfully saved to file: " + fileName + " in "
1005 + format + " format.");
1010 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1012 warningMessage("Cannot save file " + fileName + " using format "
1013 + format, "Alignment output format not supported");
1014 saveAs_actionPerformed(null);
1015 // JBPNote need to have a raise_gui flag here
1019 String[] omitHidden = null;
1021 if (viewport.hasHiddenColumns)
1023 int reply = JOptionPane
1024 .showInternalConfirmDialog(
1026 "The Alignment contains hidden columns."
1027 + "\nDo you want to save only the visible alignment?",
1028 "Save / Omit Hidden Columns",
1029 JOptionPane.YES_NO_OPTION,
1030 JOptionPane.QUESTION_MESSAGE);
1032 if (reply == JOptionPane.YES_OPTION)
1034 omitHidden = viewport.getViewAsString(false);
1037 FormatAdapter f = new FormatAdapter();
1038 String output = f.formatSequences(format,
1039 (Alignment) viewport.alignment, // class cast exceptions will
1040 // occur in the distant future
1041 omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
1051 java.io.PrintWriter out = new java.io.PrintWriter(
1052 new java.io.FileWriter(file));
1056 this.setTitle(file);
1057 statusBar.setText("Successfully saved to file: " + fileName
1058 + " in " + format + " format.");
1059 } catch (Exception ex)
1062 ex.printStackTrace();
1069 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
1070 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
1076 private void warningMessage(String warning, String title)
1078 if (new jalview.util.Platform().isHeadless())
1080 System.err.println("Warning: " + title + "\nWarning: " + warning);
1085 JOptionPane.showInternalMessageDialog(this, warning, title,
1086 JOptionPane.WARNING_MESSAGE);
1097 protected void outputText_actionPerformed(ActionEvent e)
1099 String[] omitHidden = null;
1101 if (viewport.hasHiddenColumns)
1103 int reply = JOptionPane
1104 .showInternalConfirmDialog(
1106 "The Alignment contains hidden columns."
1107 + "\nDo you want to output only the visible alignment?",
1108 "Save / Omit Hidden Columns",
1109 JOptionPane.YES_NO_OPTION,
1110 JOptionPane.QUESTION_MESSAGE);
1112 if (reply == JOptionPane.YES_OPTION)
1114 omitHidden = viewport.getViewAsString(false);
1118 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1119 cap.setForInput(null);
1123 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1124 viewport.alignment, omitHidden, viewport.colSel));
1125 Desktop.addInternalFrame(cap,
1126 "Alignment output - " + e.getActionCommand(), 600, 500);
1127 } catch (OutOfMemoryError oom)
1129 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1141 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1143 new HTMLOutput(alignPanel,
1144 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1145 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1148 public void createImageMap(File file, String image)
1150 alignPanel.makePNGImageMap(file, image);
1159 public void createPNG(File f)
1161 alignPanel.makePNG(f);
1170 public void createEPS(File f)
1172 alignPanel.makeEPS(f);
1175 public void pageSetup_actionPerformed(ActionEvent e)
1177 PrinterJob printJob = PrinterJob.getPrinterJob();
1178 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1187 public void printMenuItem_actionPerformed(ActionEvent e)
1189 // Putting in a thread avoids Swing painting problems
1190 PrintThread thread = new PrintThread(alignPanel);
1194 public void exportFeatures_actionPerformed(ActionEvent e)
1196 new AnnotationExporter().exportFeatures(alignPanel);
1199 public void exportAnnotations_actionPerformed(ActionEvent e)
1201 new AnnotationExporter().exportAnnotations(
1203 viewport.showAnnotation ? viewport.alignment
1204 .getAlignmentAnnotation() : null, viewport.alignment
1206 ((Alignment) viewport.alignment).alignmentProperties);
1209 public void associatedData_actionPerformed(ActionEvent e)
1211 // Pick the tree file
1212 JalviewFileChooser chooser = new JalviewFileChooser(
1213 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1214 chooser.setFileView(new JalviewFileView());
1215 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1216 chooser.setToolTipText("Load Jalview Annotations / Features file");
1218 int value = chooser.showOpenDialog(null);
1220 if (value == JalviewFileChooser.APPROVE_OPTION)
1222 String choice = chooser.getSelectedFile().getPath();
1223 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1224 loadJalviewDataFile(choice, null, null, null);
1230 * Close the current view or all views in the alignment frame. If the frame
1231 * only contains one view then the alignment will be removed from memory.
1233 * @param closeAllTabs
1235 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1237 if (alignPanels != null && alignPanels.size() < 2)
1239 closeAllTabs = true;
1244 if (alignPanels != null)
1248 if (this.isClosed())
1250 // really close all the windows - otherwise wait till
1251 // setClosed(true) is called
1252 for (int i = 0; i < alignPanels.size(); i++)
1254 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1261 closeView(alignPanel);
1267 this.setClosed(true);
1269 } catch (Exception ex)
1271 ex.printStackTrace();
1276 * close alignPanel2 and shuffle tabs appropriately.
1278 * @param alignPanel2
1280 public void closeView(AlignmentPanel alignPanel2)
1282 int index = tabbedPane.getSelectedIndex();
1283 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1284 alignPanels.removeElement(alignPanel2);
1286 // if (viewport == alignPanel2.av)
1290 alignPanel2.closePanel();
1293 tabbedPane.removeTabAt(closedindex);
1294 tabbedPane.validate();
1296 if (index > closedindex || index == tabbedPane.getTabCount())
1298 // modify currently selected tab index if necessary.
1302 this.tabSelectionChanged(index);
1308 void updateEditMenuBar()
1311 if (viewport.historyList.size() > 0)
1313 undoMenuItem.setEnabled(true);
1314 CommandI command = (CommandI) viewport.historyList.peek();
1315 undoMenuItem.setText("Undo " + command.getDescription());
1319 undoMenuItem.setEnabled(false);
1320 undoMenuItem.setText("Undo");
1323 if (viewport.redoList.size() > 0)
1325 redoMenuItem.setEnabled(true);
1327 CommandI command = (CommandI) viewport.redoList.peek();
1328 redoMenuItem.setText("Redo " + command.getDescription());
1332 redoMenuItem.setEnabled(false);
1333 redoMenuItem.setText("Redo");
1337 public void addHistoryItem(CommandI command)
1339 if (command.getSize() > 0)
1341 viewport.historyList.push(command);
1342 viewport.redoList.clear();
1343 updateEditMenuBar();
1344 viewport.hasHiddenColumns = (viewport.colSel != null
1345 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1346 .getHiddenColumns().size() > 0);
1352 * @return alignment objects for all views
1354 AlignmentI[] getViewAlignments()
1356 if (alignPanels != null)
1358 Enumeration e = alignPanels.elements();
1359 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1360 for (int i = 0; e.hasMoreElements(); i++)
1362 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1366 if (viewport != null)
1368 return new AlignmentI[]
1369 { viewport.alignment };
1380 protected void undoMenuItem_actionPerformed(ActionEvent e)
1382 if (viewport.historyList.empty())
1384 CommandI command = (CommandI) viewport.historyList.pop();
1385 viewport.redoList.push(command);
1386 command.undoCommand(getViewAlignments());
1388 AlignViewport originalSource = getOriginatingSource(command);
1389 updateEditMenuBar();
1391 if (originalSource != null)
1393 originalSource.hasHiddenColumns = (viewport.colSel != null
1394 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1395 .getHiddenColumns().size() > 0);
1396 originalSource.firePropertyChange("alignment", null,
1397 originalSource.alignment.getSequences());
1407 protected void redoMenuItem_actionPerformed(ActionEvent e)
1409 if (viewport.redoList.size() < 1)
1414 CommandI command = (CommandI) viewport.redoList.pop();
1415 viewport.historyList.push(command);
1416 command.doCommand(getViewAlignments());
1418 AlignViewport originalSource = getOriginatingSource(command);
1419 updateEditMenuBar();
1421 if (originalSource != null)
1423 originalSource.hasHiddenColumns = (viewport.colSel != null
1424 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1425 .getHiddenColumns().size() > 0);
1426 originalSource.firePropertyChange("alignment", null,
1427 originalSource.alignment.getSequences());
1431 AlignViewport getOriginatingSource(CommandI command)
1433 AlignViewport originalSource = null;
1434 // For sequence removal and addition, we need to fire
1435 // the property change event FROM the viewport where the
1436 // original alignment was altered
1437 AlignmentI al = null;
1438 if (command instanceof EditCommand)
1440 EditCommand editCommand = (EditCommand) command;
1441 al = editCommand.getAlignment();
1442 Vector comps = (Vector) PaintRefresher.components.get(viewport
1443 .getSequenceSetId());
1445 for (int i = 0; i < comps.size(); i++)
1447 if (comps.elementAt(i) instanceof AlignmentPanel)
1449 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1451 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1458 if (originalSource == null)
1460 // The original view is closed, we must validate
1461 // the current view against the closed view first
1464 PaintRefresher.validateSequences(al, viewport.alignment);
1467 originalSource = viewport;
1470 return originalSource;
1479 public void moveSelectedSequences(boolean up)
1481 SequenceGroup sg = viewport.getSelectionGroup();
1490 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1492 SequenceI seq = viewport.alignment.getSequenceAt(i);
1494 if (!sg.getSequences(null).contains(seq))
1499 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1501 if (sg.getSequences(null).contains(temp))
1506 viewport.alignment.getSequences().setElementAt(temp, i);
1507 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1512 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1514 SequenceI seq = viewport.alignment.getSequenceAt(i);
1516 if (!sg.getSequences(null).contains(seq))
1521 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1523 if (sg.getSequences(null).contains(temp))
1528 viewport.alignment.getSequences().setElementAt(temp, i);
1529 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1533 alignPanel.paintAlignment(true);
1536 synchronized void slideSequences(boolean right, int size)
1538 Vector sg = new Vector();
1539 if (viewport.cursorMode)
1541 sg.addElement(viewport.alignment
1542 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1544 else if (viewport.getSelectionGroup() != null
1545 && viewport.getSelectionGroup().getSize() != viewport.alignment
1548 sg = viewport.getSelectionGroup().getSequences(
1549 viewport.hiddenRepSequences);
1557 Vector invertGroup = new Vector();
1559 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1561 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1562 invertGroup.add(viewport.alignment.getSequenceAt(i));
1565 SequenceI[] seqs1 = new SequenceI[sg.size()];
1566 for (int i = 0; i < sg.size(); i++)
1567 seqs1[i] = (SequenceI) sg.elementAt(i);
1569 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1570 for (int i = 0; i < invertGroup.size(); i++)
1571 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1573 SlideSequencesCommand ssc;
1575 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1576 size, viewport.getGapCharacter());
1578 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1579 size, viewport.getGapCharacter());
1581 int groupAdjustment = 0;
1582 if (ssc.getGapsInsertedBegin() && right)
1584 if (viewport.cursorMode)
1585 alignPanel.seqPanel.moveCursor(size, 0);
1587 groupAdjustment = size;
1589 else if (!ssc.getGapsInsertedBegin() && !right)
1591 if (viewport.cursorMode)
1592 alignPanel.seqPanel.moveCursor(-size, 0);
1594 groupAdjustment = -size;
1597 if (groupAdjustment != 0)
1599 viewport.getSelectionGroup().setStartRes(
1600 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1601 viewport.getSelectionGroup().setEndRes(
1602 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1605 boolean appendHistoryItem = false;
1606 if (viewport.historyList != null && viewport.historyList.size() > 0
1607 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1609 appendHistoryItem = ssc
1610 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1614 if (!appendHistoryItem)
1615 addHistoryItem(ssc);
1626 protected void copy_actionPerformed(ActionEvent e)
1629 if (viewport.getSelectionGroup() == null)
1633 // TODO: preserve the ordering of displayed alignment annotation in any
1634 // internal paste (particularly sequence associated annotation)
1635 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1636 String[] omitHidden = null;
1638 if (viewport.hasHiddenColumns)
1640 omitHidden = viewport.getViewAsString(true);
1643 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1646 StringSelection ss = new StringSelection(output);
1650 jalview.gui.Desktop.internalCopy = true;
1651 // Its really worth setting the clipboard contents
1652 // to empty before setting the large StringSelection!!
1653 Toolkit.getDefaultToolkit().getSystemClipboard()
1654 .setContents(new StringSelection(""), null);
1656 Toolkit.getDefaultToolkit().getSystemClipboard()
1657 .setContents(ss, Desktop.instance);
1658 } catch (OutOfMemoryError er)
1660 new OOMWarning("copying region", er);
1664 Vector hiddenColumns = null;
1665 if (viewport.hasHiddenColumns)
1667 hiddenColumns = new Vector();
1668 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1669 .getSelectionGroup().getEndRes();
1670 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1673 int[] region = (int[]) viewport.getColumnSelection()
1674 .getHiddenColumns().elementAt(i);
1675 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1677 hiddenColumns.addElement(new int[]
1678 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1683 Desktop.jalviewClipboard = new Object[]
1684 { seqs, viewport.alignment.getDataset(), hiddenColumns };
1685 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1694 protected void pasteNew_actionPerformed(ActionEvent e)
1705 protected void pasteThis_actionPerformed(ActionEvent e)
1711 * Paste contents of Jalview clipboard
1713 * @param newAlignment
1714 * true to paste to a new alignment, otherwise add to this.
1716 void paste(boolean newAlignment)
1718 boolean externalPaste = true;
1721 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1722 Transferable contents = c.getContents(this);
1724 if (contents == null)
1732 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1733 if (str.length() < 1)
1738 format = new IdentifyFile().Identify(str, "Paste");
1740 } catch (OutOfMemoryError er)
1742 new OOMWarning("Out of memory pasting sequences!!", er);
1746 SequenceI[] sequences;
1747 boolean annotationAdded = false;
1748 AlignmentI alignment = null;
1750 if (Desktop.jalviewClipboard != null)
1752 // The clipboard was filled from within Jalview, we must use the
1754 // And dataset from the copied alignment
1755 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1756 // be doubly sure that we create *new* sequence objects.
1757 sequences = new SequenceI[newseq.length];
1758 for (int i = 0; i < newseq.length; i++)
1760 sequences[i] = new Sequence(newseq[i]);
1762 alignment = new Alignment(sequences);
1763 externalPaste = false;
1767 // parse the clipboard as an alignment.
1768 alignment = new FormatAdapter().readFile(str, "Paste", format);
1769 sequences = alignment.getSequencesArray();
1777 if (Desktop.jalviewClipboard != null)
1779 // dataset is inherited
1780 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1784 // new dataset is constructed
1785 alignment.setDataset(null);
1787 alwidth = alignment.getWidth() + 1;
1791 AlignmentI pastedal = alignment; // preserve pasted alignment object
1792 // Add pasted sequences and dataset into existing alignment.
1793 alignment = viewport.getAlignment();
1794 alwidth = alignment.getWidth() + 1;
1795 // decide if we need to import sequences from an existing dataset
1796 boolean importDs = Desktop.jalviewClipboard != null
1797 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1798 // importDs==true instructs us to copy over new dataset sequences from
1799 // an existing alignment
1800 Vector newDs = (importDs) ? new Vector() : null; // used to create
1801 // minimum dataset set
1803 for (int i = 0; i < sequences.length; i++)
1807 newDs.addElement(null);
1809 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1811 if (importDs && ds != null)
1813 if (!newDs.contains(ds))
1815 newDs.setElementAt(ds, i);
1816 ds = new Sequence(ds);
1817 // update with new dataset sequence
1818 sequences[i].setDatasetSequence(ds);
1822 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1827 // copy and derive new dataset sequence
1828 sequences[i] = sequences[i].deriveSequence();
1829 alignment.getDataset().addSequence(
1830 sequences[i].getDatasetSequence());
1831 // TODO: avoid creation of duplicate dataset sequences with a
1832 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1834 alignment.addSequence(sequences[i]); // merges dataset
1838 newDs.clear(); // tidy up
1840 if (pastedal.getAlignmentAnnotation() != null)
1842 // Add any annotation attached to alignment.
1843 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1844 for (int i = 0; i < alann.length; i++)
1846 annotationAdded = true;
1847 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1849 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1850 newann.padAnnotation(alwidth);
1851 alignment.addAnnotation(newann);
1861 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1862 sequences, 0, alignment.getWidth(), alignment));
1864 // Add any annotations attached to sequences
1865 for (int i = 0; i < sequences.length; i++)
1867 if (sequences[i].getAnnotation() != null)
1869 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1871 annotationAdded = true;
1872 sequences[i].getAnnotation()[a].adjustForAlignment();
1873 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1874 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1879 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1886 // propagate alignment changed.
1887 viewport.setEndSeq(alignment.getHeight());
1888 if (annotationAdded)
1890 // Duplicate sequence annotation in all views.
1891 AlignmentI[] alview = this.getViewAlignments();
1892 for (int i = 0; i < sequences.length; i++)
1894 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1897 for (int avnum = 0; avnum < alview.length; avnum++)
1899 if (alview[avnum] != alignment)
1901 // duplicate in a view other than the one with input focus
1902 int avwidth = alview[avnum].getWidth() + 1;
1903 // this relies on sann being preserved after we
1904 // modify the sequence's annotation array for each duplication
1905 for (int a = 0; a < sann.length; a++)
1907 AlignmentAnnotation newann = new AlignmentAnnotation(
1909 sequences[i].addAlignmentAnnotation(newann);
1910 newann.padAnnotation(avwidth);
1911 alview[avnum].addAnnotation(newann); // annotation was
1912 // duplicated earlier
1913 alview[avnum].setAnnotationIndex(newann, a);
1918 buildSortByAnnotationScoresMenu();
1920 viewport.firePropertyChange("alignment", null,
1921 alignment.getSequences());
1926 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1928 String newtitle = new String("Copied sequences");
1930 if (Desktop.jalviewClipboard != null
1931 && Desktop.jalviewClipboard[2] != null)
1933 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1934 for (int i = 0; i < hc.size(); i++)
1936 int[] region = (int[]) hc.elementAt(i);
1937 af.viewport.hideColumns(region[0], region[1]);
1941 // >>>This is a fix for the moment, until a better solution is
1943 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1945 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1947 // TODO: maintain provenance of an alignment, rather than just make the
1948 // title a concatenation of operations.
1951 if (title.startsWith("Copied sequences"))
1957 newtitle = newtitle.concat("- from " + title);
1962 newtitle = new String("Pasted sequences");
1965 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1970 } catch (Exception ex)
1972 ex.printStackTrace();
1973 System.out.println("Exception whilst pasting: " + ex);
1974 // could be anything being pasted in here
1985 protected void cut_actionPerformed(ActionEvent e)
1987 copy_actionPerformed(null);
1988 delete_actionPerformed(null);
1997 protected void delete_actionPerformed(ActionEvent evt)
2000 SequenceGroup sg = viewport.getSelectionGroup();
2006 Vector seqs = new Vector();
2008 for (int i = 0; i < sg.getSize(); i++)
2010 seq = sg.getSequenceAt(i);
2011 seqs.addElement(seq);
2014 // If the cut affects all sequences, remove highlighted columns
2015 if (sg.getSize() == viewport.alignment.getHeight())
2017 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2018 sg.getEndRes() + 1);
2021 SequenceI[] cut = new SequenceI[seqs.size()];
2022 for (int i = 0; i < seqs.size(); i++)
2024 cut[i] = (SequenceI) seqs.elementAt(i);
2028 * //ADD HISTORY ITEM
2030 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2031 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2032 viewport.alignment));
2034 viewport.setSelectionGroup(null);
2035 viewport.sendSelection();
2036 viewport.alignment.deleteGroup(sg);
2038 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2040 if (viewport.getAlignment().getHeight() < 1)
2044 this.setClosed(true);
2045 } catch (Exception ex)
2057 protected void deleteGroups_actionPerformed(ActionEvent e)
2059 viewport.alignment.deleteAllGroups();
2060 viewport.sequenceColours = null;
2061 viewport.setSelectionGroup(null);
2062 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2063 alignPanel.updateAnnotation();
2064 alignPanel.paintAlignment(true);
2073 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2075 SequenceGroup sg = new SequenceGroup();
2077 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2079 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2082 sg.setEndRes(viewport.alignment.getWidth() - 1);
2083 viewport.setSelectionGroup(sg);
2084 viewport.sendSelection();
2085 alignPanel.paintAlignment(true);
2086 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2095 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2097 if (viewport.cursorMode)
2099 alignPanel.seqPanel.keyboardNo1 = null;
2100 alignPanel.seqPanel.keyboardNo2 = null;
2102 viewport.setSelectionGroup(null);
2103 viewport.getColumnSelection().clear();
2104 viewport.setSelectionGroup(null);
2105 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2106 alignPanel.idPanel.idCanvas.searchResults = null;
2107 alignPanel.paintAlignment(true);
2108 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2109 viewport.sendSelection();
2118 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2120 SequenceGroup sg = viewport.getSelectionGroup();
2124 selectAllSequenceMenuItem_actionPerformed(null);
2129 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2131 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2134 alignPanel.paintAlignment(true);
2135 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2136 viewport.sendSelection();
2139 public void invertColSel_actionPerformed(ActionEvent e)
2141 viewport.invertColumnSelection();
2142 alignPanel.paintAlignment(true);
2143 viewport.sendSelection();
2152 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2154 trimAlignment(true);
2163 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2165 trimAlignment(false);
2168 void trimAlignment(boolean trimLeft)
2170 ColumnSelection colSel = viewport.getColumnSelection();
2173 if (colSel.size() > 0)
2177 column = colSel.getMin();
2181 column = colSel.getMax();
2185 if (viewport.getSelectionGroup() != null)
2187 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2188 viewport.hiddenRepSequences);
2192 seqs = viewport.alignment.getSequencesArray();
2195 TrimRegionCommand trimRegion;
2198 trimRegion = new TrimRegionCommand("Remove Left",
2199 TrimRegionCommand.TRIM_LEFT, seqs, column,
2200 viewport.alignment, viewport.colSel,
2201 viewport.selectionGroup);
2202 viewport.setStartRes(0);
2206 trimRegion = new TrimRegionCommand("Remove Right",
2207 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2208 viewport.alignment, viewport.colSel,
2209 viewport.selectionGroup);
2212 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2214 addHistoryItem(trimRegion);
2216 Vector groups = viewport.alignment.getGroups();
2218 for (int i = 0; i < groups.size(); i++)
2220 SequenceGroup sg = (SequenceGroup) groups.get(i);
2222 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2223 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2225 viewport.alignment.deleteGroup(sg);
2229 viewport.firePropertyChange("alignment", null, viewport
2230 .getAlignment().getSequences());
2240 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2242 int start = 0, end = viewport.alignment.getWidth() - 1;
2245 if (viewport.getSelectionGroup() != null)
2247 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2248 viewport.hiddenRepSequences);
2249 start = viewport.getSelectionGroup().getStartRes();
2250 end = viewport.getSelectionGroup().getEndRes();
2254 seqs = viewport.alignment.getSequencesArray();
2257 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2258 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2260 addHistoryItem(removeGapCols);
2262 statusBar.setText("Removed " + removeGapCols.getSize()
2263 + " empty columns.");
2265 // This is to maintain viewport position on first residue
2266 // of first sequence
2267 SequenceI seq = viewport.alignment.getSequenceAt(0);
2268 int startRes = seq.findPosition(viewport.startRes);
2269 // ShiftList shifts;
2270 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2271 // edit.alColumnChanges=shifts.getInverse();
2272 // if (viewport.hasHiddenColumns)
2273 // viewport.getColumnSelection().compensateForEdits(shifts);
2274 viewport.setStartRes(seq.findIndex(startRes) - 1);
2275 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2286 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2288 int start = 0, end = viewport.alignment.getWidth() - 1;
2291 if (viewport.getSelectionGroup() != null)
2293 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2294 viewport.hiddenRepSequences);
2295 start = viewport.getSelectionGroup().getStartRes();
2296 end = viewport.getSelectionGroup().getEndRes();
2300 seqs = viewport.alignment.getSequencesArray();
2303 // This is to maintain viewport position on first residue
2304 // of first sequence
2305 SequenceI seq = viewport.alignment.getSequenceAt(0);
2306 int startRes = seq.findPosition(viewport.startRes);
2308 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2309 viewport.alignment));
2311 viewport.setStartRes(seq.findIndex(startRes) - 1);
2313 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2324 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2326 viewport.padGaps = padGapsMenuitem.isSelected();
2327 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2333 // if (justifySeqs>0)
2335 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2347 public void findMenuItem_actionPerformed(ActionEvent e)
2352 public void newView_actionPerformed(ActionEvent e)
2359 * @param copyAnnotation
2360 * if true then duplicate all annnotation, groups and settings
2361 * @return new alignment panel, already displayed.
2363 public AlignmentPanel newView(boolean copyAnnotation)
2365 return newView(null, copyAnnotation);
2371 * title of newly created view
2372 * @return new alignment panel, already displayed.
2374 public AlignmentPanel newView(String viewTitle)
2376 return newView(viewTitle, true);
2382 * title of newly created view
2383 * @param copyAnnotation
2384 * if true then duplicate all annnotation, groups and settings
2385 * @return new alignment panel, already displayed.
2387 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2389 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2391 if (!copyAnnotation)
2393 // just remove all the current annotation except for the automatic stuff
2394 newap.av.alignment.deleteAllGroups();
2395 for (AlignmentAnnotation alan : newap.av.alignment
2396 .getAlignmentAnnotation())
2398 if (!alan.autoCalculated)
2400 newap.av.alignment.deleteAnnotation(alan);
2406 newap.av.gatherViewsHere = false;
2408 if (viewport.viewName == null)
2410 viewport.viewName = "Original";
2413 newap.av.historyList = viewport.historyList;
2414 newap.av.redoList = viewport.redoList;
2416 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2417 // make sure the new view has a unique name - this is essential for Jalview
2419 boolean addFirstIndex = false;
2420 if (viewTitle == null || viewTitle.trim().length() == 0)
2423 addFirstIndex = true;
2427 index = 1;// we count from 1 if given a specific name
2429 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2430 Vector comps = (Vector) PaintRefresher.components.get(viewport
2431 .getSequenceSetId());
2432 Vector existingNames = new Vector();
2433 for (int i = 0; i < comps.size(); i++)
2435 if (comps.elementAt(i) instanceof AlignmentPanel)
2437 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2438 if (!existingNames.contains(ap.av.viewName))
2440 existingNames.addElement(ap.av.viewName);
2445 while (existingNames.contains(newViewName))
2447 newViewName = viewTitle + " " + (++index);
2450 newap.av.viewName = newViewName;
2452 addAlignmentPanel(newap, true);
2454 if (alignPanels.size() == 2)
2456 viewport.gatherViewsHere = true;
2458 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2462 public void expandViews_actionPerformed(ActionEvent e)
2464 Desktop.instance.explodeViews(this);
2467 public void gatherViews_actionPerformed(ActionEvent e)
2469 Desktop.instance.gatherViews(this);
2478 public void font_actionPerformed(ActionEvent e)
2480 new FontChooser(alignPanel);
2489 protected void seqLimit_actionPerformed(ActionEvent e)
2491 viewport.setShowJVSuffix(seqLimits.isSelected());
2493 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2494 .calculateIdWidth());
2495 alignPanel.paintAlignment(true);
2498 public void idRightAlign_actionPerformed(ActionEvent e)
2500 viewport.rightAlignIds = idRightAlign.isSelected();
2501 alignPanel.paintAlignment(true);
2504 public void centreColumnLabels_actionPerformed(ActionEvent e)
2506 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2507 alignPanel.paintAlignment(true);
2513 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2515 protected void followHighlight_actionPerformed()
2517 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2519 alignPanel.scrollToPosition(
2520 alignPanel.seqPanel.seqCanvas.searchResults, false);
2530 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2532 viewport.setColourText(colourTextMenuItem.isSelected());
2533 alignPanel.paintAlignment(true);
2542 public void wrapMenuItem_actionPerformed(ActionEvent e)
2544 scaleAbove.setVisible(wrapMenuItem.isSelected());
2545 scaleLeft.setVisible(wrapMenuItem.isSelected());
2546 scaleRight.setVisible(wrapMenuItem.isSelected());
2547 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2548 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2551 public void showAllSeqs_actionPerformed(ActionEvent e)
2553 viewport.showAllHiddenSeqs();
2556 public void showAllColumns_actionPerformed(ActionEvent e)
2558 viewport.showAllHiddenColumns();
2562 public void hideSelSequences_actionPerformed(ActionEvent e)
2564 viewport.hideAllSelectedSeqs();
2565 alignPanel.paintAlignment(true);
2569 * called by key handler and the hide all/show all menu items
2574 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2577 boolean hide = false;
2578 SequenceGroup sg = viewport.getSelectionGroup();
2579 if (!toggleSeqs && !toggleCols)
2581 // Hide everything by the current selection - this is a hack - we do the
2582 // invert and then hide
2583 // first check that there will be visible columns after the invert.
2584 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
2585 .getSelected().size() > 0)
2586 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2589 // now invert the sequence set, if required - empty selection implies
2590 // that no hiding is required.
2593 invertSequenceMenuItem_actionPerformed(null);
2594 sg = viewport.getSelectionGroup();
2598 viewport.expandColSelection(sg, true);
2599 // finally invert the column selection and get the new sequence
2601 invertColSel_actionPerformed(null);
2608 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
2610 hideSelSequences_actionPerformed(null);
2613 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
2615 showAllSeqs_actionPerformed(null);
2621 if (viewport.colSel.getSelected().size() > 0)
2623 hideSelColumns_actionPerformed(null);
2626 viewport.selectionGroup = sg;
2631 showAllColumns_actionPerformed(null);
2640 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2641 * event.ActionEvent)
2643 public void hideAllButSelection_actionPerformed(ActionEvent e)
2645 toggleHiddenRegions(false, false);
2652 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2655 public void hideAllSelection_actionPerformed(ActionEvent e)
2657 SequenceGroup sg = viewport.getSelectionGroup();
2658 viewport.expandColSelection(sg, false);
2659 viewport.hideAllSelectedSeqs();
2660 viewport.hideSelectedColumns();
2661 alignPanel.paintAlignment(true);
2668 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2671 public void showAllhidden_actionPerformed(ActionEvent e)
2673 viewport.showAllHiddenColumns();
2674 viewport.showAllHiddenSeqs();
2675 alignPanel.paintAlignment(true);
2678 public void hideSelColumns_actionPerformed(ActionEvent e)
2680 viewport.hideSelectedColumns();
2681 alignPanel.paintAlignment(true);
2684 public void hiddenMarkers_actionPerformed(ActionEvent e)
2686 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2696 protected void scaleAbove_actionPerformed(ActionEvent e)
2698 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2699 alignPanel.paintAlignment(true);
2708 protected void scaleLeft_actionPerformed(ActionEvent e)
2710 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2711 alignPanel.paintAlignment(true);
2720 protected void scaleRight_actionPerformed(ActionEvent e)
2722 viewport.setScaleRightWrapped(scaleRight.isSelected());
2723 alignPanel.paintAlignment(true);
2732 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2734 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2735 alignPanel.paintAlignment(true);
2744 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2746 viewport.setShowText(viewTextMenuItem.isSelected());
2747 alignPanel.paintAlignment(true);
2756 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2758 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2759 alignPanel.paintAlignment(true);
2762 public FeatureSettings featureSettings;
2764 public void featureSettings_actionPerformed(ActionEvent e)
2766 if (featureSettings != null)
2768 featureSettings.close();
2769 featureSettings = null;
2771 if (!showSeqFeatures.isSelected())
2773 // make sure features are actually displayed
2774 showSeqFeatures.setSelected(true);
2775 showSeqFeatures_actionPerformed(null);
2777 featureSettings = new FeatureSettings(this);
2781 * Set or clear 'Show Sequence Features'
2786 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2788 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2789 alignPanel.paintAlignment(true);
2790 if (alignPanel.getOverviewPanel() != null)
2792 alignPanel.getOverviewPanel().updateOverviewImage();
2797 * Set or clear 'Show Sequence Features'
2802 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2804 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2806 if (viewport.getShowSequenceFeaturesHeight())
2808 // ensure we're actually displaying features
2809 viewport.setShowSequenceFeatures(true);
2810 showSeqFeatures.setSelected(true);
2812 alignPanel.paintAlignment(true);
2813 if (alignPanel.getOverviewPanel() != null)
2815 alignPanel.getOverviewPanel().updateOverviewImage();
2825 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2827 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2828 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2831 public void alignmentProperties()
2833 JEditorPane editPane = new JEditorPane("text/html", "");
2834 editPane.setEditable(false);
2835 StringBuffer contents = new AlignmentProperties(viewport.alignment)
2837 editPane.setText("<html>" + contents.toString() + "</html>");
2838 JInternalFrame frame = new JInternalFrame();
2839 frame.getContentPane().add(new JScrollPane(editPane));
2841 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2842 + getTitle(), 500, 400);
2851 public void overviewMenuItem_actionPerformed(ActionEvent e)
2853 if (alignPanel.overviewPanel != null)
2858 JInternalFrame frame = new JInternalFrame();
2859 OverviewPanel overview = new OverviewPanel(alignPanel);
2860 frame.setContentPane(overview);
2861 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2862 frame.getWidth(), frame.getHeight());
2864 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2865 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2867 public void internalFrameClosed(
2868 javax.swing.event.InternalFrameEvent evt)
2870 alignPanel.setOverviewPanel(null);
2874 alignPanel.setOverviewPanel(overview);
2877 public void textColour_actionPerformed(ActionEvent e)
2879 new TextColourChooser().chooseColour(alignPanel, null);
2888 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2899 public void clustalColour_actionPerformed(ActionEvent e)
2901 changeColour(new ClustalxColourScheme(
2902 viewport.alignment.getSequences(),
2903 viewport.alignment.getWidth()));
2912 public void zappoColour_actionPerformed(ActionEvent e)
2914 changeColour(new ZappoColourScheme());
2923 public void taylorColour_actionPerformed(ActionEvent e)
2925 changeColour(new TaylorColourScheme());
2934 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2936 changeColour(new HydrophobicColourScheme());
2945 public void helixColour_actionPerformed(ActionEvent e)
2947 changeColour(new HelixColourScheme());
2956 public void strandColour_actionPerformed(ActionEvent e)
2958 changeColour(new StrandColourScheme());
2967 public void turnColour_actionPerformed(ActionEvent e)
2969 changeColour(new TurnColourScheme());
2978 public void buriedColour_actionPerformed(ActionEvent e)
2980 changeColour(new BuriedColourScheme());
2989 public void nucleotideColour_actionPerformed(ActionEvent e)
2991 changeColour(new NucleotideColourScheme());
2994 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
2996 changeColour(new PurinePyrimidineColourScheme());
2999 public void covariationColour_actionPerformed(ActionEvent e)
3001 changeColour(new CovariationColourScheme(viewport.alignment.getAlignmentAnnotation()[0]));
3004 public void annotationColour_actionPerformed(ActionEvent e)
3006 new AnnotationColourChooser(viewport, alignPanel);
3009 public void rnahelicesColour_actionPerformed(ActionEvent e)
3011 new RNAHelicesColourChooser(viewport, alignPanel);
3020 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3022 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3031 public void changeColour(ColourSchemeI cs)
3037 if (viewport.getAbovePIDThreshold())
3039 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3042 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3044 viewport.setGlobalColourScheme(cs);
3048 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3051 if (viewport.getConservationSelected())
3054 Alignment al = (Alignment) viewport.alignment;
3055 Conservation c = new Conservation("All",
3056 ResidueProperties.propHash, 3, al.getSequences(), 0,
3060 c.verdict(false, viewport.ConsPercGaps);
3062 cs.setConservation(c);
3064 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3069 cs.setConservation(null);
3072 cs.setConsensus(viewport.hconsensus);
3075 viewport.setGlobalColourScheme(cs);
3077 if (viewport.getColourAppliesToAllGroups())
3079 Vector groups = viewport.alignment.getGroups();
3081 for (int i = 0; i < groups.size(); i++)
3083 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
3091 if (cs instanceof ClustalxColourScheme)
3093 sg.cs = new ClustalxColourScheme(
3094 sg.getSequences(viewport.hiddenRepSequences),
3097 else if (cs instanceof UserColourScheme)
3099 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3105 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
3106 } catch (Exception ex)
3111 if (viewport.getAbovePIDThreshold()
3112 || cs instanceof PIDColourScheme
3113 || cs instanceof Blosum62ColourScheme)
3115 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3117 sg.cs.setConsensus(AAFrequency.calculate(
3118 sg.getSequences(viewport.hiddenRepSequences),
3119 sg.getStartRes(), sg.getEndRes() + 1));
3123 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3126 if (viewport.getConservationSelected())
3128 Conservation c = new Conservation("Group",
3129 ResidueProperties.propHash, 3,
3130 sg.getSequences(viewport.hiddenRepSequences),
3131 sg.getStartRes(), sg.getEndRes() + 1);
3133 c.verdict(false, viewport.ConsPercGaps);
3134 sg.cs.setConservation(c);
3138 sg.cs.setConservation(null);
3143 if (alignPanel.getOverviewPanel() != null)
3145 alignPanel.getOverviewPanel().updateOverviewImage();
3148 alignPanel.paintAlignment(true);
3157 protected void modifyPID_actionPerformed(ActionEvent e)
3159 if (viewport.getAbovePIDThreshold()
3160 && viewport.globalColourScheme != null)
3162 SliderPanel.setPIDSliderSource(alignPanel,
3163 viewport.getGlobalColourScheme(), "Background");
3164 SliderPanel.showPIDSlider();
3174 protected void modifyConservation_actionPerformed(ActionEvent e)
3176 if (viewport.getConservationSelected()
3177 && viewport.globalColourScheme != null)
3179 SliderPanel.setConservationSlider(alignPanel,
3180 viewport.globalColourScheme, "Background");
3181 SliderPanel.showConservationSlider();
3191 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3193 viewport.setConservationSelected(conservationMenuItem.isSelected());
3195 viewport.setAbovePIDThreshold(false);
3196 abovePIDThreshold.setSelected(false);
3198 changeColour(viewport.getGlobalColourScheme());
3200 modifyConservation_actionPerformed(null);
3209 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3211 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3213 conservationMenuItem.setSelected(false);
3214 viewport.setConservationSelected(false);
3216 changeColour(viewport.getGlobalColourScheme());
3218 modifyPID_actionPerformed(null);
3227 public void userDefinedColour_actionPerformed(ActionEvent e)
3229 if (e.getActionCommand().equals("User Defined..."))
3231 new UserDefinedColours(alignPanel, null);
3235 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3236 .getUserColourSchemes().get(e.getActionCommand());
3242 public void updateUserColourMenu()
3245 Component[] menuItems = colourMenu.getMenuComponents();
3246 int i, iSize = menuItems.length;
3247 for (i = 0; i < iSize; i++)
3249 if (menuItems[i].getName() != null
3250 && menuItems[i].getName().equals("USER_DEFINED"))
3252 colourMenu.remove(menuItems[i]);
3256 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3258 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3259 .getUserColourSchemes().keys();
3261 while (userColours.hasMoreElements())
3263 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3264 userColours.nextElement().toString());
3265 radioItem.setName("USER_DEFINED");
3266 radioItem.addMouseListener(new MouseAdapter()
3268 public void mousePressed(MouseEvent evt)
3270 if (evt.isControlDown()
3271 || SwingUtilities.isRightMouseButton(evt))
3273 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3275 int option = JOptionPane.showInternalConfirmDialog(
3276 jalview.gui.Desktop.desktop,
3277 "Remove from default list?",
3278 "Remove user defined colour",
3279 JOptionPane.YES_NO_OPTION);
3280 if (option == JOptionPane.YES_OPTION)
3282 jalview.gui.UserDefinedColours
3283 .removeColourFromDefaults(radioItem.getText());
3284 colourMenu.remove(radioItem);
3288 radioItem.addActionListener(new ActionListener()
3290 public void actionPerformed(ActionEvent evt)
3292 userDefinedColour_actionPerformed(evt);
3299 radioItem.addActionListener(new ActionListener()
3301 public void actionPerformed(ActionEvent evt)
3303 userDefinedColour_actionPerformed(evt);
3307 colourMenu.insert(radioItem, 15);
3308 colours.add(radioItem);
3319 public void PIDColour_actionPerformed(ActionEvent e)
3321 changeColour(new PIDColourScheme());
3330 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3332 changeColour(new Blosum62ColourScheme());
3341 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3343 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3344 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3345 .getAlignment().getSequenceAt(0), null);
3346 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3347 viewport.alignment));
3348 alignPanel.paintAlignment(true);
3357 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3359 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3360 AlignmentSorter.sortByID(viewport.getAlignment());
3361 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3362 alignPanel.paintAlignment(true);
3371 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3373 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3374 AlignmentSorter.sortByLength(viewport.getAlignment());
3375 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3376 viewport.alignment));
3377 alignPanel.paintAlignment(true);
3386 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3388 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3389 AlignmentSorter.sortByGroup(viewport.getAlignment());
3390 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3391 viewport.alignment));
3393 alignPanel.paintAlignment(true);
3402 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3404 new RedundancyPanel(alignPanel, this);
3413 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3415 if ((viewport.getSelectionGroup() == null)
3416 || (viewport.getSelectionGroup().getSize() < 2))
3418 JOptionPane.showInternalMessageDialog(this,
3419 "You must select at least 2 sequences.", "Invalid Selection",
3420 JOptionPane.WARNING_MESSAGE);
3424 JInternalFrame frame = new JInternalFrame();
3425 frame.setContentPane(new PairwiseAlignPanel(viewport));
3426 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3436 public void PCAMenuItem_actionPerformed(ActionEvent e)
3438 if (((viewport.getSelectionGroup() != null)
3439 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3440 .getSelectionGroup().getSize() > 0))
3441 || (viewport.getAlignment().getHeight() < 4))
3443 JOptionPane.showInternalMessageDialog(this,
3444 "Principal component analysis must take\n"
3445 + "at least 4 input sequences.",
3446 "Sequence selection insufficient",
3447 JOptionPane.WARNING_MESSAGE);
3452 new PCAPanel(alignPanel);
3455 public void autoCalculate_actionPerformed(ActionEvent e)
3457 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3458 if (viewport.autoCalculateConsensus)
3460 viewport.firePropertyChange("alignment", null, viewport
3461 .getAlignment().getSequences());
3464 public void sortByTreeOption_actionPerformed(ActionEvent e)
3466 viewport.sortByTree = sortByTree.isSelected();
3470 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3472 viewport.followSelection = listenToViewSelections.isSelected();
3480 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3482 NewTreePanel("AV", "PID", "Average distance tree using PID");
3491 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3493 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3502 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3504 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3513 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3515 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3528 void NewTreePanel(String type, String pwType, String title)
3532 if (viewport.getSelectionGroup() != null)
3534 if (viewport.getSelectionGroup().getSize() < 3)
3539 "You need to have more than two sequences selected to build a tree!",
3540 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3545 SequenceGroup sg = viewport.getSelectionGroup();
3547 /* Decide if the selection is a column region */
3548 while (s < sg.getSize())
3550 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3556 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3557 + "Try using the Pad function in the edit menu,\n"
3558 + "or one of the multiple sequence alignment web services.",
3559 "Sequences in selection are not aligned",
3560 JOptionPane.WARNING_MESSAGE);
3566 title = title + " on region";
3567 tp = new TreePanel(alignPanel, type, pwType);
3571 // are the visible sequences aligned?
3572 if (!viewport.alignment.isAligned(false))
3577 "The sequences must be aligned before creating a tree.\n"
3578 + "Try using the Pad function in the edit menu,\n"
3579 + "or one of the multiple sequence alignment web services.",
3580 "Sequences not aligned",
3581 JOptionPane.WARNING_MESSAGE);
3586 if (viewport.alignment.getHeight() < 2)
3591 tp = new TreePanel(alignPanel, type, pwType);
3596 if (viewport.viewName != null)
3598 title += viewport.viewName + " of ";
3601 title += this.title;
3603 Desktop.addInternalFrame(tp, title, 600, 500);
3614 public void addSortByOrderMenuItem(String title,
3615 final AlignmentOrder order)
3617 final JMenuItem item = new JMenuItem("by " + title);
3619 item.addActionListener(new java.awt.event.ActionListener()
3621 public void actionPerformed(ActionEvent e)
3623 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3625 // TODO: JBPNote - have to map order entries to curent SequenceI
3627 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3629 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3630 viewport.alignment));
3632 alignPanel.paintAlignment(true);
3638 * Add a new sort by annotation score menu item
3641 * the menu to add the option to
3643 * the label used to retrieve scores for each sequence on the
3646 public void addSortByAnnotScoreMenuItem(JMenu sort,
3647 final String scoreLabel)
3649 final JMenuItem item = new JMenuItem(scoreLabel);
3651 item.addActionListener(new java.awt.event.ActionListener()
3653 public void actionPerformed(ActionEvent e)
3655 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3656 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3657 viewport.getAlignment());// ,viewport.getSelectionGroup());
3658 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3659 viewport.alignment));
3660 alignPanel.paintAlignment(true);
3666 * last hash for alignment's annotation array - used to minimise cost of
3669 protected int _annotationScoreVectorHash;
3672 * search the alignment and rebuild the sort by annotation score submenu the
3673 * last alignment annotation vector hash is stored to minimize cost of
3674 * rebuilding in subsequence calls.
3677 public void buildSortByAnnotationScoresMenu()
3679 if (viewport.alignment.getAlignmentAnnotation() == null)
3684 if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3686 sortByAnnotScore.removeAll();
3687 // almost certainly a quicker way to do this - but we keep it simple
3688 Hashtable scoreSorts = new Hashtable();
3689 AlignmentAnnotation aann[];
3690 Enumeration sq = viewport.alignment.getSequences().elements();
3691 while (sq.hasMoreElements())
3693 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3694 for (int i = 0; aann != null && i < aann.length; i++)
3696 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3698 scoreSorts.put(aann[i].label, aann[i].label);
3702 Enumeration labels = scoreSorts.keys();
3703 while (labels.hasMoreElements())
3705 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3706 (String) labels.nextElement());
3708 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3711 _annotationScoreVectorHash = viewport.alignment
3712 .getAlignmentAnnotation().hashCode();
3717 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3718 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3719 * call. Listeners are added to remove the menu item when the treePanel is
3720 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3724 * Displayed tree window.
3726 * SortBy menu item title.
3728 public void buildTreeMenu()
3730 sortByTreeMenu.removeAll();
3732 Vector comps = (Vector) PaintRefresher.components.get(viewport
3733 .getSequenceSetId());
3734 Vector treePanels = new Vector();
3735 int i, iSize = comps.size();
3736 for (i = 0; i < iSize; i++)
3738 if (comps.elementAt(i) instanceof TreePanel)
3740 treePanels.add(comps.elementAt(i));
3744 iSize = treePanels.size();
3748 sortByTreeMenu.setVisible(false);
3752 sortByTreeMenu.setVisible(true);
3754 for (i = 0; i < treePanels.size(); i++)
3756 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3757 final JMenuItem item = new JMenuItem(tp.getTitle());
3758 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3759 item.addActionListener(new java.awt.event.ActionListener()
3761 public void actionPerformed(ActionEvent e)
3763 tp.sortByTree_actionPerformed(null);
3764 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3769 sortByTreeMenu.add(item);
3773 public boolean sortBy(AlignmentOrder alorder, String undoname)
3775 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3776 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3777 if (undoname != null)
3779 addHistoryItem(new OrderCommand(undoname, oldOrder,
3780 viewport.alignment));
3782 alignPanel.paintAlignment(true);
3787 * Work out whether the whole set of sequences or just the selected set will
3788 * be submitted for multiple alignment.
3791 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3793 // Now, check we have enough sequences
3794 AlignmentView msa = null;
3796 if ((viewport.getSelectionGroup() != null)
3797 && (viewport.getSelectionGroup().getSize() > 1))
3799 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3800 // some common interface!
3802 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3803 * SequenceI[sz = seqs.getSize(false)];
3805 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3806 * seqs.getSequenceAt(i); }
3808 msa = viewport.getAlignmentView(true);
3813 * Vector seqs = viewport.getAlignment().getSequences();
3815 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3817 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3818 * seqs.elementAt(i); } }
3820 msa = viewport.getAlignmentView(false);
3826 * Decides what is submitted to a secondary structure prediction service: the
3827 * first sequence in the alignment, or in the current selection, or, if the
3828 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3829 * region or the whole alignment. (where the first sequence in the set is the
3830 * one that the prediction will be for).
3832 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3834 AlignmentView seqs = null;
3836 if ((viewport.getSelectionGroup() != null)
3837 && (viewport.getSelectionGroup().getSize() > 0))
3839 seqs = viewport.getAlignmentView(true);
3843 seqs = viewport.getAlignmentView(false);
3845 // limit sequences - JBPNote in future - could spawn multiple prediction
3847 // TODO: viewport.alignment.isAligned is a global state - the local
3848 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3849 if (!viewport.alignment.isAligned(false))
3851 seqs.setSequences(new SeqCigar[]
3852 { seqs.getSequences()[0] });
3853 // TODO: if seqs.getSequences().length>1 then should really have warned
3866 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3868 // Pick the tree file
3869 JalviewFileChooser chooser = new JalviewFileChooser(
3870 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3871 chooser.setFileView(new JalviewFileView());
3872 chooser.setDialogTitle("Select a newick-like tree file");
3873 chooser.setToolTipText("Load a tree file");
3875 int value = chooser.showOpenDialog(null);
3877 if (value == JalviewFileChooser.APPROVE_OPTION)
3879 String choice = chooser.getSelectedFile().getPath();
3880 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3881 jalview.io.NewickFile fin = null;
3884 fin = new jalview.io.NewickFile(choice, "File");
3885 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3886 } catch (Exception ex)
3888 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3889 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3890 ex.printStackTrace();
3892 if (fin != null && fin.hasWarningMessage())
3894 JOptionPane.showMessageDialog(Desktop.desktop,
3895 fin.getWarningMessage(), "Possible problem with tree file",
3896 JOptionPane.WARNING_MESSAGE);
3901 public TreePanel ShowNewickTree(NewickFile nf, String title)
3903 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3906 public TreePanel ShowNewickTree(NewickFile nf, String title,
3907 AlignmentView input)
3909 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3912 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3913 int h, int x, int y)
3915 return ShowNewickTree(nf, title, null, w, h, x, y);
3919 * Add a treeviewer for the tree extracted from a newick file object to the
3920 * current alignment view
3927 * Associated alignment input data (or null)
3936 * @return TreePanel handle
3938 public TreePanel ShowNewickTree(NewickFile nf, String title,
3939 AlignmentView input, int w, int h, int x, int y)
3941 TreePanel tp = null;
3947 if (nf.getTree() != null)
3949 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3955 tp.setLocation(x, y);
3958 Desktop.addInternalFrame(tp, title, w, h);
3960 } catch (Exception ex)
3962 ex.printStackTrace();
3968 private boolean buildingMenu = false;
3971 * Generates menu items and listener event actions for web service clients
3974 public void BuildWebServiceMenu()
3976 while (buildingMenu)
3980 System.err.println("Waiting for building menu to finish.");
3982 } catch (Exception e)
3987 final AlignFrame me = this;
3988 buildingMenu = true;
3989 new Thread(new Runnable()
3995 System.err.println("Building ws menu again "
3996 + Thread.currentThread());
3997 // TODO: add support for context dependent disabling of services based
3999 // alignment and current selection
4000 // TODO: add additional serviceHandle parameter to specify abstract
4002 // class independently of AbstractName
4003 // TODO: add in rediscovery GUI function to restart discoverer
4004 // TODO: group services by location as well as function and/or
4006 // object broker mechanism.
4007 final Vector wsmenu = new Vector();
4008 final IProgressIndicator af = me;
4009 final JMenu msawsmenu = new JMenu("Alignment");
4010 final JMenu secstrmenu = new JMenu(
4011 "Secondary Structure Prediction");
4012 final JMenu seqsrchmenu = new JMenu(
4013 "Sequence Database Search");
4014 final JMenu analymenu = new JMenu(
4016 // JAL-940 - only show secondary structure prediction services from the legacy server
4017 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4019 Discoverer.services != null
4020 && (Discoverer.services.size() > 0))
4022 // TODO: refactor to allow list of AbstractName/Handler bindings to
4024 // stored or retrieved from elsewhere
4025 Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4026 Vector secstrpr = (Vector) Discoverer.services
4028 Vector seqsrch = null; // (Vector) Discoverer.services.get("SeqSearch");
4029 // TODO: move GUI generation code onto service implementation - so a
4030 // client instance attaches itself to the GUI with method call like
4031 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
4035 // Add any Multiple Sequence Alignment Services
4036 for (int i = 0, j = msaws.size(); i < j; i++)
4038 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
4040 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4041 .getServiceClient(sh);
4042 impl.attachWSMenuEntry(msawsmenu, me);
4046 if (secstrpr != null)
4048 // Add any secondary structure prediction services
4049 for (int i = 0, j = secstrpr.size(); i < j; i++)
4051 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4053 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4054 .getServiceClient(sh);
4055 impl.attachWSMenuEntry(secstrmenu, me);
4058 if (seqsrch != null)
4060 // Add any sequence search services
4061 for (int i = 0, j = seqsrch.size(); i < j; i++)
4063 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
4065 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4066 .getServiceClient(sh);
4067 impl.attachWSMenuEntry(seqsrchmenu, me);
4072 // TODO: move into separate menu builder class.
4073 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4075 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4076 if (jws2servs != null)
4078 if (jws2servs.hasServices())
4080 jws2servs.attachWSMenuEntry(msawsmenu, me);
4084 // Add all submenus in the order they should appear on the web services menu
4085 wsmenu.add(msawsmenu);
4086 wsmenu.add(secstrmenu);
4087 wsmenu.add(analymenu);
4088 // No search services yet
4089 // wsmenu.add(seqsrchmenu);
4091 javax.swing.SwingUtilities.invokeLater(new Runnable()
4097 webService.removeAll();
4098 // first, add discovered services onto the webservices menu
4099 if (wsmenu.size() > 0)
4101 for (int i = 0, j = wsmenu.size(); i < j; i++)
4103 webService.add((JMenu) wsmenu.get(i));
4108 webService.add(me.webServiceNoServices);
4110 build_urlServiceMenu(me.webService);
4111 build_fetchdbmenu(webService);
4112 } catch (Exception e)
4118 } catch (Exception e)
4123 buildingMenu = false;
4131 * construct any groupURL type service menu entries.
4135 private void build_urlServiceMenu(JMenu webService)
4137 // TODO: remove this code when 2.7 is released
4138 // DEBUG - alignmentView
4140 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4141 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4143 * @Override public void actionPerformed(ActionEvent e) {
4144 * jalview.datamodel.AlignmentView.testSelectionViews(af.viewport.alignment,
4145 * af.viewport.colSel, af.viewport.selectionGroup); }
4147 * }); webService.add(testAlView);
4149 // TODO: refactor to RestClient discoverer and merge menu entries for
4150 // rest-style services with other types of analysis/calculation service
4151 // SHmmr test client - still being implemented.
4152 // DEBUG - alignmentView
4154 for (jalview.ws.rest.RestClient client: jalview.ws.rest.RestClient.getRestClients()) {
4155 client.attachWSMenuEntry(JvSwingUtils.findOrCreateMenu(webService, client.getAction()), this);
4158 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4160 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4166 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4167 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4168 * getProperty("LAST_DIRECTORY"));
4170 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4171 * to Vamsas file"); chooser.setToolTipText("Export");
4173 * int value = chooser.showSaveDialog(this);
4175 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4176 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4177 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4178 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4181 * prototype of an automatically enabled/disabled analysis function
4184 protected void setShowProductsEnabled()
4186 SequenceI[] selection = viewport.getSequenceSelection();
4187 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4188 viewport.getAlignment().getDataset()))
4190 showProducts.setEnabled(true);
4195 showProducts.setEnabled(false);
4200 * search selection for sequence xRef products and build the show products
4205 * @return true if showProducts menu should be enabled.
4207 public boolean canShowProducts(SequenceI[] selection,
4208 boolean isRegionSelection, Alignment dataset)
4210 boolean showp = false;
4213 showProducts.removeAll();
4214 final boolean dna = viewport.getAlignment().isNucleotide();
4215 final Alignment ds = dataset;
4216 String[] ptypes = (selection == null || selection.length == 0) ? null
4217 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4219 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4220 // selection, dataset, true);
4221 final SequenceI[] sel = selection;
4222 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4225 final boolean isRegSel = isRegionSelection;
4226 final AlignFrame af = this;
4227 final String source = ptypes[t];
4228 JMenuItem xtype = new JMenuItem(ptypes[t]);
4229 xtype.addActionListener(new ActionListener()
4232 public void actionPerformed(ActionEvent e)
4234 // TODO: new thread for this call with vis-delay
4235 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4236 isRegSel, dna, source);
4240 showProducts.add(xtype);
4242 showProducts.setVisible(showp);
4243 showProducts.setEnabled(showp);
4244 } catch (Exception e)
4246 jalview.bin.Cache.log
4247 .warn("canTranslate threw an exception - please report to help@jalview.org",
4254 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4255 boolean isRegSel, boolean dna, String source)
4257 final boolean fisRegSel = isRegSel;
4258 final boolean fdna = dna;
4259 final String fsrc = source;
4260 final AlignFrame ths = this;
4261 final SequenceI[] fsel = sel;
4262 Runnable foo = new Runnable()
4267 final long sttime = System.currentTimeMillis();
4268 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4271 Alignment ds = ths.getViewport().alignment.getDataset(); // update
4275 Alignment prods = CrossRef
4276 .findXrefSequences(fsel, fdna, fsrc, ds);
4279 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4280 for (int s = 0; s < sprods.length; s++)
4282 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4283 if (ds.getSequences() == null
4284 || !ds.getSequences().contains(
4285 sprods[s].getDatasetSequence()))
4286 ds.addSequence(sprods[s].getDatasetSequence());
4287 sprods[s].updatePDBIds();
4289 Alignment al = new Alignment(sprods);
4290 AlignedCodonFrame[] cf = prods.getCodonFrames();
4292 for (int s = 0; cf != null && s < cf.length; s++)
4294 al.addCodonFrame(cf[s]);
4297 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4299 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4300 + " for " + ((fisRegSel) ? "selected region of " : "")
4302 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4307 System.err.println("No Sequences generated for xRef type "
4310 } catch (Exception e)
4312 jalview.bin.Cache.log.error(
4313 "Exception when finding crossreferences", e);
4314 } catch (OutOfMemoryError e)
4316 new OOMWarning("whilst fetching crossreferences", e);
4319 jalview.bin.Cache.log.error("Error when finding crossreferences",
4322 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4327 Thread frunner = new Thread(foo);
4331 public boolean canShowTranslationProducts(SequenceI[] selection,
4332 AlignmentI alignment)
4337 return (jalview.analysis.Dna.canTranslate(selection,
4338 viewport.getViewAsVisibleContigs(true)));
4339 } catch (Exception e)
4341 jalview.bin.Cache.log
4342 .warn("canTranslate threw an exception - please report to help@jalview.org",
4348 public void showProducts_actionPerformed(ActionEvent e)
4350 // /////////////////////////////
4351 // Collect Data to be translated/transferred
4353 SequenceI[] selection = viewport.getSequenceSelection();
4354 AlignmentI al = null;
4357 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4358 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4359 viewport.getAlignment().getDataset());
4360 } catch (Exception ex)
4363 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4370 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4371 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4375 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4376 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4377 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4381 public void showTranslation_actionPerformed(ActionEvent e)
4383 // /////////////////////////////
4384 // Collect Data to be translated/transferred
4386 SequenceI[] selection = viewport.getSequenceSelection();
4387 String[] seqstring = viewport.getViewAsString(true);
4388 AlignmentI al = null;
4391 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4392 viewport.getViewAsVisibleContigs(true), viewport
4393 .getGapCharacter(), viewport.alignment
4394 .getAlignmentAnnotation(), viewport.alignment
4395 .getWidth(), viewport.getAlignment().getDataset());
4396 } catch (Exception ex)
4399 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4406 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4407 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4411 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4412 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4413 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4418 * Try to load a features file onto the alignment.
4421 * contents or path to retrieve file
4423 * access mode of file (see jalview.io.AlignFile)
4424 * @return true if features file was parsed corectly.
4426 public boolean parseFeaturesFile(String file, String type)
4428 boolean featuresFile = false;
4431 featuresFile = new FeaturesFile(file, type)
4432 .parse(viewport.alignment.getDataset(),
4433 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
4434 false, jalview.bin.Cache.getDefault(
4435 "RELAXEDSEQIDMATCHING", false));
4436 } catch (Exception ex)
4438 ex.printStackTrace();
4443 viewport.showSequenceFeatures = true;
4444 showSeqFeatures.setSelected(true);
4445 if (alignPanel.seqPanel.seqCanvas.fr != null)
4447 // update the min/max ranges where necessary
4448 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4450 if (featureSettings != null)
4452 featureSettings.setTableData();
4454 alignPanel.paintAlignment(true);
4457 return featuresFile;
4460 public void dragEnter(DropTargetDragEvent evt)
4464 public void dragExit(DropTargetEvent evt)
4468 public void dragOver(DropTargetDragEvent evt)
4472 public void dropActionChanged(DropTargetDragEvent evt)
4476 public void drop(DropTargetDropEvent evt)
4478 Transferable t = evt.getTransferable();
4479 java.util.List files = null;
4483 DataFlavor uriListFlavor = new DataFlavor(
4484 "text/uri-list;class=java.lang.String");
4485 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4487 // Works on Windows and MacOSX
4488 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4489 files = (java.util.List) t
4490 .getTransferData(DataFlavor.javaFileListFlavor);
4492 else if (t.isDataFlavorSupported(uriListFlavor))
4494 // This is used by Unix drag system
4495 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4496 String data = (String) t.getTransferData(uriListFlavor);
4497 files = new java.util.ArrayList(1);
4498 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4499 data, "\r\n"); st.hasMoreTokens();)
4501 String s = st.nextToken();
4502 if (s.startsWith("#"))
4504 // the line is a comment (as per the RFC 2483)
4508 java.net.URI uri = new java.net.URI(s);
4509 // check to see if we can handle this kind of URI
4510 if (uri.getScheme().toLowerCase().startsWith("http"))
4512 files.add(uri.toString());
4516 // otherwise preserve old behaviour: catch all for file objects
4517 java.io.File file = new java.io.File(uri);
4518 files.add(file.toString());
4522 } catch (Exception e)
4524 e.printStackTrace();
4530 // check to see if any of these files have names matching sequences in
4532 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4533 .getAlignment().getSequencesArray());
4535 * Object[] { String,SequenceI}
4537 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4538 ArrayList<String> filesnotmatched = new ArrayList<String>();
4539 for (int i = 0; i < files.size(); i++)
4541 String file = files.get(i).toString();
4543 String protocol = FormatAdapter.checkProtocol(file);
4544 if (protocol == jalview.io.FormatAdapter.FILE)
4546 File fl = new File(file);
4547 pdbfn = fl.getName();
4549 else if (protocol == jalview.io.FormatAdapter.URL)
4551 URL url = new URL(file);
4552 pdbfn = url.getFile();
4554 if (pdbfn.length() > 0)
4556 // attempt to find a match in the alignment
4557 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4558 int l = 0, c = pdbfn.indexOf(".");
4559 while (mtch == null && c != -1)
4564 } while ((c = pdbfn.indexOf(".", l)) > l);
4567 pdbfn = pdbfn.substring(0, l);
4569 mtch = idm.findAllIdMatches(pdbfn);
4576 type = new IdentifyFile().Identify(file, protocol);
4577 } catch (Exception ex)
4583 if (type.equalsIgnoreCase("PDB"))
4585 filesmatched.add(new Object[]
4586 { file, protocol, mtch });
4591 // File wasn't named like one of the sequences or wasn't a PDB file.
4592 filesnotmatched.add(file);
4596 if (filesmatched.size() > 0)
4598 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4602 "Do you want to automatically associate the "
4603 + filesmatched.size()
4604 + " PDB files with sequences in the alignment that have the same name ?",
4605 "Automatically Associate PDB files by name",
4606 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4609 for (Object[] fm : filesmatched)
4611 // try and associate
4612 // TODO: may want to set a standard ID naming formalism for
4613 // associating PDB files which have no IDs.
4614 for (SequenceI toassoc: (SequenceI[])fm[2]) {
4615 PDBEntry pe = new AssociatePdbFileWithSeq()
4616 .associatePdbWithSeq((String) fm[0], (String) fm[1],
4621 .println("Associated file : " + ((String) fm[0])
4623 + toassoc.getDisplayId(true));
4627 alignPanel.paintAlignment(true);
4631 if (filesnotmatched.size() > 0)
4634 && (Cache.getDefault(
4635 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4638 "<html>Do you want to <em>ignore</em> the "
4639 + filesnotmatched.size()
4640 + " files whose names did not match any sequence IDs ?</html>",
4641 "Ignore unmatched dropped files ?",
4642 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4646 for (String fn : filesnotmatched)
4648 loadJalviewDataFile(fn, null, null, null);
4652 } catch (Exception ex)
4654 ex.printStackTrace();
4660 * Attempt to load a "dropped" file or URL string: First by testing whether
4661 * it's and Annotation file, then a JNet file, and finally a features file. If
4662 * all are false then the user may have dropped an alignment file onto this
4666 * either a filename or a URL string.
4668 public void loadJalviewDataFile(String file, String protocol,
4669 String format, SequenceI assocSeq)
4673 if (protocol == null)
4675 protocol = jalview.io.FormatAdapter.checkProtocol(file);
4677 // if the file isn't identified, or not positively identified as some
4678 // other filetype (PFAM is default unidentified alignment file type) then
4679 // try to parse as annotation.
4680 boolean isAnnotation = (format == null || format
4681 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4682 .readAnnotationFile(viewport.alignment, file, protocol)
4687 // try to see if its a JNet 'concise' style annotation file *before* we
4688 // try to parse it as a features file
4691 format = new IdentifyFile().Identify(file, protocol);
4693 if (format.equalsIgnoreCase("JnetFile"))
4695 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4697 new JnetAnnotationMaker().add_annotation(predictions,
4698 viewport.getAlignment(), 0, false);
4699 isAnnotation = true;
4704 * if (format.equalsIgnoreCase("PDB")) {
4706 * String pdbfn = ""; // try to match up filename with sequence id try
4707 * { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = new
4708 * File(file); pdbfn = fl.getName(); } else if (protocol ==
4709 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4710 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == null)
4711 * { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4712 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { //
4713 * attempt to find a match in the alignment SequenceI mtch =
4714 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4715 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > l)
4716 * { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch =
4717 * idm.findIdMatch(pdbfn); } if (mtch != null) { // try and associate
4718 * // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4719 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) {
4720 * System.err.println("Associated file : " + file + " with " +
4721 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4722 * TODO: maybe need to load as normal otherwise return; } }
4724 // try to parse it as a features file
4725 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4726 // if it wasn't a features file then we just treat it as a general
4727 // alignment file to load into the current view.
4730 new FileLoader().LoadFile(viewport, file, protocol, format);
4734 alignPanel.paintAlignment(true);
4741 alignPanel.adjustAnnotationHeight();
4742 viewport.updateSequenceIdColours();
4743 buildSortByAnnotationScoresMenu();
4744 alignPanel.paintAlignment(true);
4746 } catch (Exception ex)
4748 ex.printStackTrace();
4752 public void tabSelectionChanged(int index)
4756 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4757 viewport = alignPanel.av;
4758 setMenusFromViewport(viewport);
4762 public void tabbedPane_mousePressed(MouseEvent e)
4764 if (SwingUtilities.isRightMouseButton(e))
4766 String reply = JOptionPane.showInternalInputDialog(this,
4767 "Enter View Name", "Edit View Name",
4768 JOptionPane.QUESTION_MESSAGE);
4772 viewport.viewName = reply;
4773 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4778 public AlignViewport getCurrentView()
4784 * Open the dialog for regex description parsing.
4786 protected void extractScores_actionPerformed(ActionEvent e)
4788 ParseProperties pp = new jalview.analysis.ParseProperties(
4789 viewport.alignment);
4790 // TODO: verify regex and introduce GUI dialog for version 2.5
4791 // if (pp.getScoresFromDescription("col", "score column ",
4792 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4794 if (pp.getScoresFromDescription("description column",
4795 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4797 buildSortByAnnotationScoresMenu();
4805 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4808 protected void showDbRefs_actionPerformed(ActionEvent e)
4810 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4816 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4819 protected void showNpFeats_actionPerformed(ActionEvent e)
4821 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4825 * find the viewport amongst the tabs in this alignment frame and close that
4830 public boolean closeView(AlignViewport av)
4834 this.closeMenuItem_actionPerformed(false);
4837 Component[] comp = tabbedPane.getComponents();
4838 for (int i = 0; comp != null && i < comp.length; i++)
4840 if (comp[i] instanceof AlignmentPanel)
4842 if (((AlignmentPanel) comp[i]).av == av)
4845 closeView((AlignmentPanel) comp[i]);
4853 protected void build_fetchdbmenu(JMenu webService)
4855 // Temporary hack - DBRef Fetcher always top level ws entry.
4856 // TODO We probably want to store a sequence database checklist in
4857 // preferences and have checkboxes.. rather than individual sources selected
4859 final JMenu rfetch = new JMenu("Fetch DB References");
4860 rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4861 webService.add(rfetch);
4863 JMenuItem fetchr = new JMenuItem("Standard Databases");
4864 fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4865 fetchr.addActionListener(new ActionListener()
4868 public void actionPerformed(ActionEvent e)
4870 new Thread(new Runnable()
4875 new jalview.ws.DBRefFetcher(alignPanel.av
4876 .getSequenceSelection(), alignPanel.alignFrame)
4877 .fetchDBRefs(false);
4885 final AlignFrame me = this;
4886 new Thread(new Runnable()
4890 final jalview.ws.SequenceFetcher sf = SequenceFetcher
4891 .getSequenceFetcherSingleton(me);
4892 final String[] otherdb = sf.getOrderedSupportedSources();
4893 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4894 // jalview.util.QuickSort.sort(otherdb, otherdb);
4895 javax.swing.SwingUtilities.invokeLater(new Runnable()
4900 JMenu dfetch = new JMenu();
4903 int comp = 0, mcomp = 15;
4904 String mname = null;
4905 if (otherdb != null && otherdb.length > 0)
4907 for (int i = 0; i < otherdb.length; i++)
4909 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4912 mname = "from '" + dbname + "'";
4914 fetchr = new JMenuItem(otherdb[i]);
4915 final String[] dassource = new String[]
4917 fetchr.addActionListener(new ActionListener()
4920 public void actionPerformed(ActionEvent e)
4922 new Thread(new Runnable()
4927 new jalview.ws.DBRefFetcher(alignPanel.av
4928 .getSequenceSelection(),
4929 alignPanel.alignFrame, dassource)
4930 .fetchDBRefs(false);
4936 fetchr.setToolTipText("Retrieve from " + dbname);
4938 if (comp++ == mcomp || i == (otherdb.length - 1))
4940 dfetch.setText(mname + " to '" + dbname + "'");
4942 dfetch = new JMenu();
4956 * Left justify the whole alignment.
4958 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4960 AlignmentI al = viewport.getAlignment();
4962 viewport.firePropertyChange("alignment", null, al);
4966 * Right justify the whole alignment.
4968 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4970 AlignmentI al = viewport.getAlignment();
4972 viewport.firePropertyChange("alignment", null, al);
4975 public void setShowSeqFeatures(boolean b)
4977 showSeqFeatures.setSelected(true);
4978 viewport.setShowSequenceFeatures(true);
4985 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4986 * awt.event.ActionEvent)
4988 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
4990 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
4991 alignPanel.paintAlignment(true);
4998 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5001 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5003 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5004 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5012 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5013 * .event.ActionEvent)
5015 protected void showGroupConservation_actionPerformed(ActionEvent e)
5017 viewport.setShowGroupConservation(showGroupConservation.getState());
5018 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5025 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5026 * .event.ActionEvent)
5028 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5030 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5031 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5038 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5039 * .event.ActionEvent)
5041 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5043 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5044 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5046 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5048 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5049 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5051 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5053 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5060 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5061 * .event.ActionEvent)
5063 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5065 if (viewport.getSelectionGroup() != null)
5067 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
5068 viewport.getSequenceSelection(),
5069 viewport.getAlignmentView(true).getSequenceStrings(
5070 viewport.getGapCharacter()),
5071 viewport.alignment.getGroups());
5072 viewport.alignment.deleteAllGroups();
5073 viewport.sequenceColours = null;
5074 viewport.setSelectionGroup(null);
5075 // set view properties for each group
5076 for (int g = 0; g < gps.length; g++)
5078 gps[g].setShowNonconserved(viewport.getShowUnconserved());
5079 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
5080 viewport.alignment.addGroup(gps[g]);
5081 Color col = new Color((int) (Math.random() * 255),
5082 (int) (Math.random() * 255), (int) (Math.random() * 255));
5083 col = col.brighter();
5084 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
5085 .hasMoreElements(); viewport.setSequenceColour(
5086 (SequenceI) sq.nextElement(), col))
5089 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5090 alignPanel.updateAnnotation();
5091 alignPanel.paintAlignment(true);
5096 * make the given alignmentPanel the currently selected tab
5098 * @param alignmentPanel
5100 public void setDisplayedView(AlignmentPanel alignmentPanel)
5102 if (!viewport.getSequenceSetId().equals(
5103 alignmentPanel.av.getSequenceSetId()))
5106 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5108 if (tabbedPane != null
5109 & alignPanels.indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5111 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5116 class PrintThread extends Thread
5120 public PrintThread(AlignmentPanel ap)
5125 static PageFormat pf;
5129 PrinterJob printJob = PrinterJob.getPrinterJob();
5133 printJob.setPrintable(ap, pf);
5137 printJob.setPrintable(ap);
5140 if (printJob.printDialog())
5145 } catch (Exception PrintException)
5147 PrintException.printStackTrace();