2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.jbgui;
23 import java.awt.BorderLayout;
24 import java.awt.Color;
25 import java.awt.GridLayout;
26 import java.awt.Toolkit;
27 import java.awt.event.ActionEvent;
28 import java.awt.event.ActionListener;
29 import java.awt.event.FocusAdapter;
30 import java.awt.event.FocusEvent;
31 import java.awt.event.KeyEvent;
32 import java.awt.event.MouseAdapter;
33 import java.awt.event.MouseEvent;
34 import java.util.HashMap;
37 import javax.swing.BorderFactory;
38 import javax.swing.ButtonGroup;
39 import javax.swing.JCheckBoxMenuItem;
40 import javax.swing.JInternalFrame;
41 import javax.swing.JLabel;
42 import javax.swing.JMenu;
43 import javax.swing.JMenuBar;
44 import javax.swing.JMenuItem;
45 import javax.swing.JOptionPane;
46 import javax.swing.JPanel;
47 import javax.swing.JRadioButtonMenuItem;
48 import javax.swing.JTabbedPane;
49 import javax.swing.KeyStroke;
50 import javax.swing.SwingUtilities;
51 import javax.swing.event.ChangeEvent;
52 import javax.swing.event.MenuEvent;
53 import javax.swing.event.MenuListener;
55 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
56 import jalview.api.SplitContainerI;
57 import jalview.bin.Cache;
58 import jalview.gui.JvSwingUtils;
59 import jalview.gui.Preferences;
60 import jalview.schemes.ColourSchemeProperty;
61 import jalview.util.MessageManager;
63 public class GAlignFrame extends JInternalFrame
65 protected JMenuBar alignFrameMenuBar = new JMenuBar();
67 protected JMenuItem closeMenuItem = new JMenuItem();
69 protected JMenu colourMenu = new JMenu();
71 protected JMenu webService = new JMenu();
73 protected JMenuItem webServiceNoServices;
75 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
77 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
79 protected JMenu sortByAnnotScore = new JMenu();
81 public JLabel statusBar = new JLabel();
83 protected JMenu outputTextboxMenu = new JMenu();
85 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
87 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
89 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
91 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
93 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
95 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
97 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
99 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
101 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
103 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
105 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
107 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
109 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
111 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
113 // protected JRadioButtonMenuItem covariationColour = new
114 // JRadioButtonMenuItem();
116 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
118 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
120 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
122 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
124 protected JMenuItem undoMenuItem = new JMenuItem();
126 protected JMenuItem redoMenuItem = new JMenuItem();
128 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
130 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
132 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
134 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
136 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
138 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
140 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
142 JMenuItem copy = new JMenuItem();
144 JMenuItem cut = new JMenuItem();
146 JMenu pasteMenu = new JMenu();
148 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
150 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
152 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
154 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
156 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
158 protected JMenuItem modifyConservation = new JMenuItem();
160 protected JMenu sortByTreeMenu = new JMenu();
162 protected JMenu sort = new JMenu();
164 protected JMenu calculateTree = new JMenu();
166 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
168 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
170 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
172 protected ButtonGroup colours = new ButtonGroup();
174 protected JMenuItem showTranslation = new JMenuItem();
176 protected JMenu showProducts = new JMenu();
178 protected JMenuItem rnahelicesColour = new JMenuItem();
180 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
182 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
184 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
186 protected JPanel statusPanel = new JPanel();
188 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
190 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
192 protected JMenuItem showAllAlAnnotations = new JMenuItem();
194 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
196 protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
198 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
200 protected JTabbedPane tabbedPane = new JTabbedPane();
202 protected JMenuItem reload = new JMenuItem();
204 protected JMenu formatMenu = new JMenu();
206 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
208 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
210 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
212 protected JMenuItem gatherViews = new JMenuItem();
214 protected JMenuItem expandViews = new JMenuItem();
216 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
218 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
220 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
222 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
224 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
226 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
228 private SequenceAnnotationOrder annotationSortOrder;
230 private boolean showAutoCalculatedAbove = false;
232 private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
234 private SplitContainerI splitFrame;
241 setJMenuBar(alignFrameMenuBar);
243 // dynamically fill save as menu with available formats
244 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
246 JMenuItem item = new JMenuItem(
247 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
249 item.addActionListener(new ActionListener()
252 public void actionPerformed(ActionEvent e)
254 outputText_actionPerformed(e);
258 outputTextboxMenu.add(item);
260 } catch (Exception e)
262 System.err.println(e.toString());
265 if (!new jalview.util.Platform().isAMac())
267 closeMenuItem.setMnemonic('C');
268 outputTextboxMenu.setMnemonic('T');
269 undoMenuItem.setMnemonic('Z');
270 redoMenuItem.setMnemonic('0');
271 copy.setMnemonic('C');
272 cut.setMnemonic('U');
273 pasteMenu.setMnemonic('P');
274 reload.setMnemonic('R');
277 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
279 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
280 .getUserColourSchemes().keys();
282 while (userColours.hasMoreElements())
284 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
285 userColours.nextElement().toString());
286 radioItem.setName("USER_DEFINED");
287 radioItem.addMouseListener(new MouseAdapter()
290 public void mousePressed(MouseEvent evt)
292 if (evt.isControlDown()
293 || SwingUtilities.isRightMouseButton(evt))
295 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
297 int option = JOptionPane.showInternalConfirmDialog(
298 jalview.gui.Desktop.desktop,
300 .getString("label.remove_from_default_list"),
302 .getString("label.remove_user_defined_colour"),
303 JOptionPane.YES_NO_OPTION);
304 if (option == JOptionPane.YES_OPTION)
306 jalview.gui.UserDefinedColours
307 .removeColourFromDefaults(radioItem.getText());
308 colourMenu.remove(radioItem);
312 radioItem.addActionListener(new ActionListener()
315 public void actionPerformed(ActionEvent evt)
317 userDefinedColour_actionPerformed(evt);
324 radioItem.addActionListener(new ActionListener()
327 public void actionPerformed(ActionEvent evt)
329 userDefinedColour_actionPerformed(evt);
332 colourMenu.insert(radioItem, 15);
333 colours.add(radioItem);
336 colours.add(noColourmenuItem);
337 colours.add(clustalColour);
338 colours.add(zappoColour);
339 colours.add(taylorColour);
340 colours.add(hydrophobicityColour);
341 colours.add(helixColour);
342 colours.add(strandColour);
343 colours.add(turnColour);
344 colours.add(buriedColour);
345 colours.add(userDefinedColour);
346 colours.add(PIDColour);
347 colours.add(BLOSUM62Colour);
348 colours.add(nucleotideColour);
349 colours.add(purinePyrimidineColour);
350 // colours.add(covariationColour);
351 colours.add(tcoffeeColour);
352 colours.add(RNAInteractionColour);
353 setColourSelected(jalview.bin.Cache.getDefault(
354 Preferences.DEFAULT_COLOUR, "None"));
357 public void setColourSelected(String defaultColour)
360 if (defaultColour != null)
362 int index = ColourSchemeProperty
363 .getColourIndexFromName(defaultColour);
367 case ColourSchemeProperty.CLUSTAL:
368 clustalColour.setSelected(true);
372 case ColourSchemeProperty.BLOSUM:
373 BLOSUM62Colour.setSelected(true);
377 case ColourSchemeProperty.PID:
378 PIDColour.setSelected(true);
382 case ColourSchemeProperty.ZAPPO:
383 zappoColour.setSelected(true);
387 case ColourSchemeProperty.TAYLOR:
388 taylorColour.setSelected(true);
391 case ColourSchemeProperty.HYDROPHOBIC:
392 hydrophobicityColour.setSelected(true);
396 case ColourSchemeProperty.HELIX:
397 helixColour.setSelected(true);
401 case ColourSchemeProperty.STRAND:
402 strandColour.setSelected(true);
406 case ColourSchemeProperty.TURN:
407 turnColour.setSelected(true);
411 case ColourSchemeProperty.BURIED:
412 buriedColour.setSelected(true);
416 case ColourSchemeProperty.NUCLEOTIDE:
417 nucleotideColour.setSelected(true);
421 case ColourSchemeProperty.TCOFFEE:
422 tcoffeeColour.setSelected(true);
425 case ColourSchemeProperty.PURINEPYRIMIDINE:
426 purinePyrimidineColour.setSelected(true);
430 case ColourSchemeProperty.RNAINTERACTION:
431 RNAInteractionColour.setSelected(true);
435 * case ColourSchemeProperty.COVARIATION:
436 * covariationColour.setSelected(true);
440 case ColourSchemeProperty.USER_DEFINED:
441 userDefinedColour.setSelected(true);
444 case ColourSchemeProperty.NONE:
446 noColourmenuItem.setSelected(true);
454 private void jbInit() throws Exception
456 JMenuItem saveAs = new JMenuItem(
457 MessageManager.getString("action.save_as") + "...");
458 ActionListener al = new ActionListener()
461 public void actionPerformed(ActionEvent e)
463 saveAs_actionPerformed(e);
466 KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
467 .getDefaultToolkit().getMenuShortcutKeyMask()
468 | KeyEvent.SHIFT_MASK, false);
469 addMenuActionAndAccelerator(keyStroke, saveAs, al);
471 closeMenuItem.setText(MessageManager.getString("action.close"));
472 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
473 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
474 al = new ActionListener()
477 public void actionPerformed(ActionEvent e)
479 closeMenuItem_actionPerformed(false);
482 addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
484 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
485 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
486 JMenu annotationsMenu = new JMenu(
487 MessageManager.getString("action.annotations"));
488 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
489 colourMenu.setText(MessageManager.getString("action.colour"));
490 JMenu calculateMenu = new JMenu(
491 MessageManager.getString("action.calculate"));
492 webService.setText(MessageManager.getString("action.web_service"));
493 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
495 .getString("action.select_all"));
496 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
497 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
498 al = new ActionListener()
501 public void actionPerformed(ActionEvent e)
503 selectAllSequenceMenuItem_actionPerformed(e);
506 addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
508 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
509 MessageManager.getString("action.deselect_all"));
510 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
511 al = new ActionListener()
514 public void actionPerformed(ActionEvent e)
516 deselectAllSequenceMenuItem_actionPerformed(e);
519 addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
521 JMenuItem invertSequenceMenuItem = new JMenuItem(
522 MessageManager.getString("action.invert_sequence_selection"));
523 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
524 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
525 al = new ActionListener()
528 public void actionPerformed(ActionEvent e)
530 invertSequenceMenuItem_actionPerformed(e);
533 addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
535 JMenuItem grpsFromSelection = new JMenuItem(
536 MessageManager.getString("action.make_groups_selection"));
537 grpsFromSelection.addActionListener(new ActionListener()
540 public void actionPerformed(ActionEvent e)
542 makeGrpsFromSelection_actionPerformed(e);
545 JMenuItem expandAlignment = new JMenuItem(
546 MessageManager.getString("action.view_flanking_regions"));
547 expandAlignment.setToolTipText(MessageManager
548 .getString("label.view_flanking_regions"));
549 expandAlignment.addActionListener(new ActionListener()
552 public void actionPerformed(ActionEvent e)
557 JMenuItem remove2LeftMenuItem = new JMenuItem(
558 MessageManager.getString("action.remove_left"));
559 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
560 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
561 al = new ActionListener()
564 public void actionPerformed(ActionEvent e)
566 remove2LeftMenuItem_actionPerformed(e);
569 addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
571 JMenuItem remove2RightMenuItem = new JMenuItem(
572 MessageManager.getString("action.remove_right"));
573 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
574 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
575 al = new ActionListener()
578 public void actionPerformed(ActionEvent e)
580 remove2RightMenuItem_actionPerformed(e);
583 addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
585 JMenuItem removeGappedColumnMenuItem = new JMenuItem(
586 MessageManager.getString("action.remove_empty_columns"));
587 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
588 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
589 al = new ActionListener()
592 public void actionPerformed(ActionEvent e)
594 removeGappedColumnMenuItem_actionPerformed(e);
597 addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
599 JMenuItem removeAllGapsMenuItem = new JMenuItem(
600 MessageManager.getString("action.remove_all_gaps"));
601 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
602 .getDefaultToolkit().getMenuShortcutKeyMask()
603 | KeyEvent.SHIFT_MASK, false);
604 al = new ActionListener()
607 public void actionPerformed(ActionEvent e)
609 removeAllGapsMenuItem_actionPerformed(e);
612 addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
614 JMenuItem justifyLeftMenuItem = new JMenuItem(
615 MessageManager.getString("action.left_justify_alignment"));
616 justifyLeftMenuItem.addActionListener(new ActionListener()
619 public void actionPerformed(ActionEvent e)
621 justifyLeftMenuItem_actionPerformed(e);
624 JMenuItem justifyRightMenuItem = new JMenuItem(
625 MessageManager.getString("action.right_justify_alignment"));
626 justifyRightMenuItem.addActionListener(new ActionListener()
629 public void actionPerformed(ActionEvent e)
631 justifyRightMenuItem_actionPerformed(e);
634 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
635 viewBoxesMenuItem.setState(true);
636 viewBoxesMenuItem.addActionListener(new ActionListener()
639 public void actionPerformed(ActionEvent e)
641 viewBoxesMenuItem_actionPerformed(e);
644 viewTextMenuItem.setText(MessageManager.getString("action.text"));
645 viewTextMenuItem.setState(true);
646 viewTextMenuItem.addActionListener(new ActionListener()
649 public void actionPerformed(ActionEvent e)
651 viewTextMenuItem_actionPerformed(e);
654 showNonconservedMenuItem.setText(MessageManager
655 .getString("label.show_non_conversed"));
656 showNonconservedMenuItem.setState(false);
657 showNonconservedMenuItem.addActionListener(new ActionListener()
660 public void actionPerformed(ActionEvent e)
662 showUnconservedMenuItem_actionPerformed(e);
665 JMenuItem sortPairwiseMenuItem = new JMenuItem(
666 MessageManager.getString("action.by_pairwise_id"));
667 sortPairwiseMenuItem.addActionListener(new ActionListener()
670 public void actionPerformed(ActionEvent e)
672 sortPairwiseMenuItem_actionPerformed(e);
675 JMenuItem sortIDMenuItem = new JMenuItem(
676 MessageManager.getString("action.by_id"));
677 sortIDMenuItem.addActionListener(new ActionListener()
680 public void actionPerformed(ActionEvent e)
682 sortIDMenuItem_actionPerformed(e);
685 JMenuItem sortLengthMenuItem = new JMenuItem(
686 MessageManager.getString("action.by_length"));
687 sortLengthMenuItem.addActionListener(new ActionListener()
690 public void actionPerformed(ActionEvent e)
692 sortLengthMenuItem_actionPerformed(e);
695 JMenuItem sortGroupMenuItem = new JMenuItem(
696 MessageManager.getString("action.by_group"));
697 sortGroupMenuItem.addActionListener(new ActionListener()
700 public void actionPerformed(ActionEvent e)
702 sortGroupMenuItem_actionPerformed(e);
706 JMenuItem removeRedundancyMenuItem = new JMenuItem(MessageManager
707 .getString("action.remove_redundancy").concat("..."));
708 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
709 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
710 al = new ActionListener()
713 public void actionPerformed(ActionEvent e)
715 removeRedundancyMenuItem_actionPerformed(e);
718 addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
720 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
721 MessageManager.getString("action.pairwise_alignment"));
722 pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
725 public void actionPerformed(ActionEvent e)
727 pairwiseAlignmentMenuItem_actionPerformed(e);
730 JMenuItem PCAMenuItem = new JMenuItem(
731 MessageManager.getString("label.principal_component_analysis"));
732 PCAMenuItem.addActionListener(new ActionListener()
735 public void actionPerformed(ActionEvent e)
737 PCAMenuItem_actionPerformed(e);
740 JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
741 MessageManager.getString("label.average_distance_identity"));
742 averageDistanceTreeMenuItem.addActionListener(new ActionListener()
745 public void actionPerformed(ActionEvent e)
747 averageDistanceTreeMenuItem_actionPerformed(e);
750 JMenuItem neighbourTreeMenuItem = new JMenuItem(
751 MessageManager.getString("label.neighbour_joining_identity"));
752 neighbourTreeMenuItem.addActionListener(new ActionListener()
755 public void actionPerformed(ActionEvent e)
757 neighbourTreeMenuItem_actionPerformed(e);
761 this.getContentPane().setLayout(new BorderLayout());
762 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
763 statusBar.setBackground(Color.white);
764 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
765 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
766 statusBar.setText(MessageManager.getString("label.status_bar"));
767 outputTextboxMenu.setText(MessageManager
768 .getString("label.out_to_textbox"));
769 clustalColour.setText(MessageManager.getString("label.clustalx"));
770 clustalColour.addActionListener(new ActionListener()
773 public void actionPerformed(ActionEvent e)
775 clustalColour_actionPerformed(e);
778 zappoColour.setText(MessageManager.getString("label.zappo"));
779 zappoColour.addActionListener(new ActionListener()
782 public void actionPerformed(ActionEvent e)
784 zappoColour_actionPerformed(e);
787 taylorColour.setText(MessageManager.getString("label.taylor"));
788 taylorColour.addActionListener(new ActionListener()
791 public void actionPerformed(ActionEvent e)
793 taylorColour_actionPerformed(e);
796 hydrophobicityColour.setText(MessageManager
797 .getString("label.hydrophobicity"));
798 hydrophobicityColour.addActionListener(new ActionListener()
801 public void actionPerformed(ActionEvent e)
803 hydrophobicityColour_actionPerformed(e);
806 helixColour.setText(MessageManager.getString("label.helix_propensity"));
807 helixColour.addActionListener(new ActionListener()
810 public void actionPerformed(ActionEvent e)
812 helixColour_actionPerformed(e);
815 strandColour.setText(MessageManager
816 .getString("label.strand_propensity"));
817 strandColour.addActionListener(new ActionListener()
820 public void actionPerformed(ActionEvent e)
822 strandColour_actionPerformed(e);
825 turnColour.setText(MessageManager.getString("label.turn_propensity"));
826 turnColour.addActionListener(new ActionListener()
829 public void actionPerformed(ActionEvent e)
831 turnColour_actionPerformed(e);
834 buriedColour.setText(MessageManager.getString("label.buried_index"));
835 buriedColour.addActionListener(new ActionListener()
838 public void actionPerformed(ActionEvent e)
840 buriedColour_actionPerformed(e);
843 userDefinedColour.setText(MessageManager
844 .getString("action.user_defined"));
845 userDefinedColour.addActionListener(new ActionListener()
848 public void actionPerformed(ActionEvent e)
850 userDefinedColour_actionPerformed(e);
854 .setText(MessageManager.getString("label.percentage_identity"));
855 PIDColour.addActionListener(new ActionListener()
858 public void actionPerformed(ActionEvent e)
860 PIDColour_actionPerformed(e);
864 .setText(MessageManager.getString("label.blosum62_score"));
865 BLOSUM62Colour.addActionListener(new ActionListener()
868 public void actionPerformed(ActionEvent e)
870 BLOSUM62Colour_actionPerformed(e);
873 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
874 nucleotideColour.addActionListener(new ActionListener()
877 public void actionPerformed(ActionEvent e)
879 nucleotideColour_actionPerformed(e);
883 purinePyrimidineColour.setText(MessageManager
884 .getString("label.purine_pyrimidine"));
885 purinePyrimidineColour.addActionListener(new ActionListener()
888 public void actionPerformed(ActionEvent e)
890 purinePyrimidineColour_actionPerformed(e);
894 RNAInteractionColour.setText("RNA Interaction type");
895 RNAInteractionColour.addActionListener(new ActionListener()
898 public void actionPerformed(ActionEvent e)
900 RNAInteractionColour_actionPerformed(e);
904 * covariationColour.setText("Covariation");
905 * covariationColour.addActionListener(new ActionListener() { public void
906 * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); }
910 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
911 MessageManager.getString("label.average_distance_bloslum62"));
912 avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
915 public void actionPerformed(ActionEvent e)
917 avTreeBlosumMenuItem_actionPerformed(e);
920 JMenuItem njTreeBlosumMenuItem = new JMenuItem(
921 MessageManager.getString("label.neighbour_blosum62"));
922 njTreeBlosumMenuItem.addActionListener(new ActionListener()
925 public void actionPerformed(ActionEvent e)
927 njTreeBlosumMenuItem_actionPerformed(e);
930 annotationPanelMenuItem.setActionCommand("");
931 annotationPanelMenuItem.setText(MessageManager
932 .getString("label.show_annotations"));
933 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
935 annotationPanelMenuItem.addActionListener(new ActionListener()
938 public void actionPerformed(ActionEvent e)
940 annotationPanelMenuItem_actionPerformed(e);
943 showAllAlAnnotations.setText(MessageManager
944 .getString("label.show_all_al_annotations"));
945 final boolean isAnnotationPanelShown = annotationPanelMenuItem
947 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
948 showAllAlAnnotations.addActionListener(new ActionListener()
951 public void actionPerformed(ActionEvent e)
953 showAllAnnotations_actionPerformed(false, true);
956 hideAllAlAnnotations.setText(MessageManager
957 .getString("label.hide_all_al_annotations"));
958 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
959 hideAllAlAnnotations.addActionListener(new ActionListener()
962 public void actionPerformed(ActionEvent e)
964 hideAllAnnotations_actionPerformed(false, true);
967 showAllSeqAnnotations.setText(MessageManager
968 .getString("label.show_all_seq_annotations"));
969 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
970 showAllSeqAnnotations.addActionListener(new ActionListener()
973 public void actionPerformed(ActionEvent e)
975 showAllAnnotations_actionPerformed(true, false);
978 hideAllSeqAnnotations.setText(MessageManager
979 .getString("label.hide_all_seq_annotations"));
980 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
981 hideAllSeqAnnotations.addActionListener(new ActionListener()
984 public void actionPerformed(ActionEvent e)
986 hideAllAnnotations_actionPerformed(true, false);
989 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
990 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
991 SequenceAnnotationOrder.NONE.name()));
992 final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
993 MessageManager.getString("label.sort_annotations_by_sequence"));
994 final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
995 MessageManager.getString("label.sort_annotations_by_label"));
998 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
999 sortAnnBySequence.addActionListener(new ActionListener()
1002 public void actionPerformed(ActionEvent e)
1004 boolean newState = sortAnnBySequence.getState();
1005 sortAnnByLabel.setSelected(false);
1006 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
1007 : SequenceAnnotationOrder.NONE);
1008 sortAnnotations_actionPerformed();
1012 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
1013 sortAnnByLabel.addActionListener(new ActionListener()
1016 public void actionPerformed(ActionEvent e)
1018 boolean newState = sortAnnByLabel.getState();
1019 sortAnnBySequence.setSelected(false);
1020 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
1021 : SequenceAnnotationOrder.NONE);
1022 sortAnnotations_actionPerformed();
1025 colourTextMenuItem.setText(MessageManager
1026 .getString("label.colour_text"));
1027 colourTextMenuItem.addActionListener(new ActionListener()
1030 public void actionPerformed(ActionEvent e)
1032 colourTextMenuItem_actionPerformed(e);
1036 JMenuItem htmlMenuItem = new JMenuItem(
1037 MessageManager.getString("label.html"));
1038 htmlMenuItem.addActionListener(new ActionListener()
1041 public void actionPerformed(ActionEvent e)
1043 htmlMenuItem_actionPerformed(e);
1047 JMenuItem createBioJS = new JMenuItem(
1048 MessageManager.getString("label.biojs_html_export"));
1049 createBioJS.addActionListener(new java.awt.event.ActionListener()
1052 public void actionPerformed(ActionEvent e)
1054 bioJSMenuItem_actionPerformed(e);
1058 JMenuItem overviewMenuItem = new JMenuItem(
1059 MessageManager.getString("label.overview_window"));
1060 overviewMenuItem.addActionListener(new ActionListener()
1063 public void actionPerformed(ActionEvent e)
1065 overviewMenuItem_actionPerformed(e);
1069 undoMenuItem.setEnabled(false);
1070 undoMenuItem.setText(MessageManager.getString("action.undo"));
1071 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
1072 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1073 al = new ActionListener()
1076 public void actionPerformed(ActionEvent e)
1078 undoMenuItem_actionPerformed(e);
1081 addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
1083 redoMenuItem.setEnabled(false);
1084 redoMenuItem.setText(MessageManager.getString("action.redo"));
1085 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
1086 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1087 al = new ActionListener()
1090 public void actionPerformed(ActionEvent e)
1092 redoMenuItem_actionPerformed(e);
1095 addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
1097 conservationMenuItem.setText(MessageManager
1098 .getString("action.by_conservation"));
1099 conservationMenuItem.addActionListener(new ActionListener()
1102 public void actionPerformed(ActionEvent e)
1104 conservationMenuItem_actionPerformed(e);
1107 noColourmenuItem.setText(MessageManager.getString("label.none"));
1108 noColourmenuItem.addActionListener(new ActionListener()
1111 public void actionPerformed(ActionEvent e)
1113 noColourmenuItem_actionPerformed(e);
1116 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1117 wrapMenuItem.addActionListener(new ActionListener()
1120 public void actionPerformed(ActionEvent e)
1122 wrapMenuItem_actionPerformed(e);
1126 JMenuItem printMenuItem = new JMenuItem(
1127 MessageManager.getString("action.print") + "...");
1128 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
1129 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1130 al = new ActionListener()
1133 public void actionPerformed(ActionEvent e)
1135 printMenuItem_actionPerformed(e);
1138 addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
1141 .setText(MessageManager.getString("action.show_gaps"));
1142 renderGapsMenuItem.setState(true);
1143 renderGapsMenuItem.addActionListener(new ActionListener()
1146 public void actionPerformed(ActionEvent e)
1148 renderGapsMenuItem_actionPerformed(e);
1152 JMenuItem findMenuItem = new JMenuItem(
1153 MessageManager.getString("action.find"));
1154 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
1155 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1156 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1157 MessageManager.getString("label.find_tip")));
1158 al = new ActionListener()
1161 public void actionPerformed(ActionEvent e)
1163 findMenuItem_actionPerformed(e);
1166 addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
1168 abovePIDThreshold.setText(MessageManager
1169 .getString("label.above_identity_threshold"));
1170 abovePIDThreshold.addActionListener(new ActionListener()
1173 public void actionPerformed(ActionEvent e)
1175 abovePIDThreshold_actionPerformed(e);
1178 showSeqFeatures.setText(MessageManager
1179 .getString("label.show_sequence_features"));
1180 showSeqFeatures.addActionListener(new ActionListener()
1183 public void actionPerformed(ActionEvent actionEvent)
1185 showSeqFeatures_actionPerformed(actionEvent);
1189 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1190 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1191 * void actionPerformed(ActionEvent actionEvent) {
1192 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1194 showDbRefsMenuitem.setText(MessageManager
1195 .getString("label.show_database_refs"));
1196 showDbRefsMenuitem.addActionListener(new ActionListener()
1200 public void actionPerformed(ActionEvent e)
1202 showDbRefs_actionPerformed(e);
1206 showNpFeatsMenuitem.setText(MessageManager
1207 .getString("label.show_non_positional_features"));
1208 showNpFeatsMenuitem.addActionListener(new ActionListener()
1212 public void actionPerformed(ActionEvent e)
1214 showNpFeats_actionPerformed(e);
1218 showGroupConservation.setText(MessageManager
1219 .getString("label.group_conservation"));
1220 showGroupConservation.addActionListener(new ActionListener()
1224 public void actionPerformed(ActionEvent e)
1226 showGroupConservation_actionPerformed(e);
1231 showGroupConsensus.setText(MessageManager
1232 .getString("label.group_consensus"));
1233 showGroupConsensus.addActionListener(new ActionListener()
1237 public void actionPerformed(ActionEvent e)
1239 showGroupConsensus_actionPerformed(e);
1243 showConsensusHistogram.setText(MessageManager
1244 .getString("label.show_consensus_histogram"));
1245 showConsensusHistogram.addActionListener(new ActionListener()
1249 public void actionPerformed(ActionEvent e)
1251 showConsensusHistogram_actionPerformed(e);
1255 showSequenceLogo.setText(MessageManager
1256 .getString("label.show_consensus_logo"));
1257 showSequenceLogo.addActionListener(new ActionListener()
1261 public void actionPerformed(ActionEvent e)
1263 showSequenceLogo_actionPerformed(e);
1267 normaliseSequenceLogo.setText(MessageManager
1268 .getString("label.norm_consensus_logo"));
1269 normaliseSequenceLogo.addActionListener(new ActionListener()
1273 public void actionPerformed(ActionEvent e)
1275 normaliseSequenceLogo_actionPerformed(e);
1279 applyAutoAnnotationSettings.setText(MessageManager
1280 .getString("label.apply_all_groups"));
1281 applyAutoAnnotationSettings.setState(false);
1282 applyAutoAnnotationSettings.setVisible(true);
1283 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1286 public void actionPerformed(ActionEvent e)
1288 applyAutoAnnotationSettings_actionPerformed(e);
1292 ButtonGroup buttonGroup = new ButtonGroup();
1293 final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
1294 MessageManager.getString("label.show_first"));
1295 final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
1296 MessageManager.getString("label.show_last"));
1297 buttonGroup.add(showAutoFirst);
1298 buttonGroup.add(showAutoLast);
1299 showAutoFirst.setSelected(Cache.getDefault(
1300 Preferences.SHOW_AUTOCALC_ABOVE, false));
1301 showAutoFirst.addActionListener(new ActionListener()
1304 public void actionPerformed(ActionEvent e)
1306 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1307 sortAnnotations_actionPerformed();
1310 showAutoLast.setSelected(!showAutoFirst.isSelected());
1311 showAutoLast.addActionListener(new ActionListener()
1314 public void actionPerformed(ActionEvent e)
1316 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1317 sortAnnotations_actionPerformed();
1321 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1322 nucleotideColour.addActionListener(new ActionListener()
1325 public void actionPerformed(ActionEvent e)
1327 nucleotideColour_actionPerformed(e);
1331 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1332 tcoffeeColour.setEnabled(false);
1333 tcoffeeColour.addActionListener(new ActionListener()
1337 public void actionPerformed(ActionEvent e)
1339 tcoffeeColorScheme_actionPerformed(e);
1343 JMenuItem deleteGroups = new JMenuItem(
1344 MessageManager.getString("action.undefine_groups"));
1345 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
1346 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1347 al = new ActionListener()
1350 public void actionPerformed(ActionEvent e)
1352 deleteGroups_actionPerformed(e);
1355 addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
1357 JMenuItem createGroup = new JMenuItem(
1358 MessageManager.getString("action.create_groups"));
1359 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1360 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1361 al = new ActionListener()
1364 public void actionPerformed(ActionEvent e)
1366 createGroup_actionPerformed(e);
1369 addMenuActionAndAccelerator(keyStroke, createGroup, al);
1371 JMenuItem unGroup = new JMenuItem(
1372 MessageManager.getString("action.remove_group"));
1373 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
1374 .getDefaultToolkit().getMenuShortcutKeyMask()
1375 | KeyEvent.SHIFT_MASK, false);
1376 al = new ActionListener()
1379 public void actionPerformed(ActionEvent e)
1381 unGroup_actionPerformed(e);
1384 addMenuActionAndAccelerator(keyStroke, unGroup, al);
1386 copy.setText(MessageManager.getString("action.copy"));
1387 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
1388 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1390 al = new ActionListener()
1393 public void actionPerformed(ActionEvent e)
1395 copy_actionPerformed(e);
1398 addMenuActionAndAccelerator(keyStroke, copy, al);
1400 cut.setText(MessageManager.getString("action.cut"));
1401 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
1402 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1403 al = new ActionListener()
1406 public void actionPerformed(ActionEvent e)
1408 cut_actionPerformed(e);
1411 addMenuActionAndAccelerator(keyStroke, cut, al);
1413 JMenuItem delete = new JMenuItem(
1414 MessageManager.getString("action.delete"));
1415 delete.addActionListener(new ActionListener()
1418 public void actionPerformed(ActionEvent e)
1420 delete_actionPerformed(e);
1424 pasteMenu.setText(MessageManager.getString("action.paste"));
1425 JMenuItem pasteNew = new JMenuItem(
1426 MessageManager.getString("label.to_new_alignment"));
1427 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1428 .getDefaultToolkit().getMenuShortcutKeyMask()
1429 | KeyEvent.SHIFT_MASK, false);
1430 al = new ActionListener()
1433 public void actionPerformed(ActionEvent e)
1435 pasteNew_actionPerformed(e);
1438 addMenuActionAndAccelerator(keyStroke, pasteNew, al);
1440 JMenuItem pasteThis = new JMenuItem(
1441 MessageManager.getString("label.to_this_alignment"));
1442 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
1443 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
1444 al = new ActionListener()
1447 public void actionPerformed(ActionEvent e)
1449 pasteThis_actionPerformed(e);
1452 addMenuActionAndAccelerator(keyStroke, pasteThis, al);
1454 applyToAllGroups.setText(MessageManager
1455 .getString("label.apply_colour_to_all_groups"));
1456 applyToAllGroups.addActionListener(new ActionListener()
1459 public void actionPerformed(ActionEvent e)
1461 applyToAllGroups_actionPerformed(e);
1464 JMenuItem createPNG = new JMenuItem("PNG");
1465 createPNG.addActionListener(new ActionListener()
1468 public void actionPerformed(ActionEvent e)
1473 createPNG.setActionCommand(MessageManager
1474 .getString("label.save_png_image"));
1476 JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
1477 font.addActionListener(new ActionListener()
1480 public void actionPerformed(ActionEvent e)
1482 font_actionPerformed(e);
1485 seqLimits.setText(MessageManager
1486 .getString("label.show_sequence_limits"));
1487 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1488 seqLimits.addActionListener(new ActionListener()
1491 public void actionPerformed(ActionEvent e)
1493 seqLimit_actionPerformed(e);
1496 JMenuItem epsFile = new JMenuItem("EPS");
1497 epsFile.addActionListener(new ActionListener()
1500 public void actionPerformed(ActionEvent e)
1506 JMenuItem createSVG = new JMenuItem("SVG");
1507 createSVG.addActionListener(new ActionListener()
1510 public void actionPerformed(ActionEvent e)
1516 JMenuItem loadTreeMenuItem = new JMenuItem(
1517 MessageManager.getString("label.load_associated_tree"));
1518 loadTreeMenuItem.setActionCommand(MessageManager
1519 .getString("label.load_tree_for_sequence_set"));
1520 loadTreeMenuItem.addActionListener(new ActionListener()
1523 public void actionPerformed(ActionEvent e)
1525 loadTreeMenuItem_actionPerformed(e);
1529 scaleAbove.setVisible(false);
1530 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1531 scaleAbove.addActionListener(new ActionListener()
1534 public void actionPerformed(ActionEvent e)
1536 scaleAbove_actionPerformed(e);
1539 scaleLeft.setVisible(false);
1540 scaleLeft.setSelected(true);
1541 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1542 scaleLeft.addActionListener(new ActionListener()
1545 public void actionPerformed(ActionEvent e)
1547 scaleLeft_actionPerformed(e);
1550 scaleRight.setVisible(false);
1551 scaleRight.setSelected(true);
1552 scaleRight.setText(MessageManager.getString("action.scale_right"));
1553 scaleRight.addActionListener(new ActionListener()
1556 public void actionPerformed(ActionEvent e)
1558 scaleRight_actionPerformed(e);
1561 centreColumnLabelsMenuItem.setVisible(true);
1562 centreColumnLabelsMenuItem.setState(false);
1563 centreColumnLabelsMenuItem.setText(MessageManager
1564 .getString("label.centre_column_labels"));
1565 centreColumnLabelsMenuItem.addActionListener(new ActionListener()
1568 public void actionPerformed(ActionEvent e)
1570 centreColumnLabels_actionPerformed(e);
1573 followHighlightMenuItem.setVisible(true);
1574 followHighlightMenuItem.setState(true);
1575 followHighlightMenuItem.setText(MessageManager
1576 .getString("label.automatic_scrolling"));
1577 followHighlightMenuItem.addActionListener(new ActionListener()
1581 public void actionPerformed(ActionEvent e)
1583 followHighlight_actionPerformed();
1588 JMenuItem modifyPID = new JMenuItem(
1589 MessageManager.getString("label.modify_identity_thereshold"));
1590 modifyPID.addActionListener(new ActionListener()
1593 public void actionPerformed(ActionEvent e)
1595 modifyPID_actionPerformed(e);
1598 modifyConservation.setText(MessageManager
1599 .getString("label.modify_conservation_thereshold"));
1600 modifyConservation.addActionListener(new ActionListener()
1603 public void actionPerformed(ActionEvent e)
1605 modifyConservation_actionPerformed(e);
1609 .setText(MessageManager.getString("action.by_tree_order"));
1610 sort.setText(MessageManager.getString("action.sort"));
1611 sort.addMenuListener(new MenuListener()
1614 public void menuSelected(MenuEvent e)
1620 public void menuDeselected(MenuEvent e)
1625 public void menuCanceled(MenuEvent e)
1629 sortByAnnotScore.setText(MessageManager
1630 .getString("label.sort_by_score"));
1631 sort.add(sortByAnnotScore);
1632 sort.addMenuListener(new javax.swing.event.MenuListener()
1636 public void menuCanceled(MenuEvent e)
1641 public void menuDeselected(MenuEvent e)
1646 public void menuSelected(MenuEvent e)
1648 buildSortByAnnotationScoresMenu();
1651 sortByAnnotScore.setVisible(false);
1654 .setText(MessageManager.getString("action.calculate_tree"));
1656 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1657 padGapsMenuitem.setState(jalview.bin.Cache
1658 .getDefault("PAD_GAPS", false));
1659 padGapsMenuitem.addActionListener(new ActionListener()
1662 public void actionPerformed(ActionEvent e)
1664 padGapsMenuitem_actionPerformed(e);
1667 JMenuItem vamsasStore = new JMenuItem(
1668 MessageManager.getString("label.vamsas_store"));
1669 vamsasStore.setVisible(false);
1670 vamsasStore.addActionListener(new ActionListener()
1673 public void actionPerformed(ActionEvent e)
1675 vamsasStore_actionPerformed(e);
1678 showTranslation.setText(MessageManager
1679 .getString("label.translate_cDNA"));
1680 showTranslation.addActionListener(new ActionListener()
1683 public void actionPerformed(ActionEvent e)
1685 showTranslation_actionPerformed(e);
1689 JMenuItem extractScores = new JMenuItem(
1690 MessageManager.getString("label.extract_scores") + "...");
1691 extractScores.addActionListener(new ActionListener()
1694 public void actionPerformed(ActionEvent e)
1696 extractScores_actionPerformed(e);
1699 extractScores.setVisible(true);
1700 // JBPNote: TODO: make gui for regex based score extraction
1702 // for show products actions see AlignFrame.canShowProducts
1703 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1705 JMenuItem openFeatureSettings = new JMenuItem(
1706 MessageManager.getString("label.feature_settings"));
1707 openFeatureSettings.addActionListener(new ActionListener()
1710 public void actionPerformed(ActionEvent e)
1712 featureSettings_actionPerformed(e);
1715 JMenuItem fetchSequence = new JMenuItem(
1716 MessageManager.getString("label.fetch_sequences"));
1717 fetchSequence.addActionListener(new ActionListener()
1720 public void actionPerformed(ActionEvent e)
1722 fetchSequence_actionPerformed(e);
1726 JMenuItem annotationColour = new JMenuItem(
1727 MessageManager.getString("action.by_annotation"));
1728 annotationColour.addActionListener(new ActionListener()
1731 public void actionPerformed(ActionEvent e)
1733 annotationColour_actionPerformed(e);
1737 JMenuItem annotationColumn = new JMenuItem(
1738 MessageManager.getString("action.select_by_annotation"));
1739 annotationColumn.addActionListener(new ActionListener()
1742 public void actionPerformed(ActionEvent e)
1744 annotationColumn_actionPerformed(e);
1748 rnahelicesColour.setText(MessageManager
1749 .getString("action.by_rna_helixes"));
1750 rnahelicesColour.addActionListener(new ActionListener()
1753 public void actionPerformed(ActionEvent e)
1755 rnahelicesColour_actionPerformed(e);
1759 JMenuItem associatedData = new JMenuItem(
1760 MessageManager.getString("label.load_features_annotations"));
1761 associatedData.addActionListener(new ActionListener()
1764 public void actionPerformed(ActionEvent e)
1766 associatedData_actionPerformed(e);
1769 autoCalculate.setText(MessageManager
1770 .getString("label.autocalculate_consensus"));
1771 autoCalculate.setState(jalview.bin.Cache.getDefault(
1772 "AUTO_CALC_CONSENSUS", true));
1773 autoCalculate.addActionListener(new ActionListener()
1776 public void actionPerformed(ActionEvent e)
1778 autoCalculate_actionPerformed(e);
1781 sortByTree.setText(MessageManager
1782 .getString("label.sort_alignment_new_tree"));
1784 .setToolTipText("<html>"
1786 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1788 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1789 sortByTree.addActionListener(new ActionListener()
1792 public void actionPerformed(ActionEvent e)
1794 sortByTreeOption_actionPerformed(e);
1798 listenToViewSelections.setText(MessageManager
1799 .getString("label.listen_for_selections"));
1800 listenToViewSelections
1801 .setToolTipText("<html>"
1803 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1804 listenToViewSelections.setState(false);
1805 listenToViewSelections.addActionListener(new ActionListener()
1808 public void actionPerformed(ActionEvent e)
1810 listenToViewSelections_actionPerformed(e);
1814 JMenu addSequenceMenu = new JMenu(
1815 MessageManager.getString("label.add_sequences"));
1816 JMenuItem addFromFile = new JMenuItem(
1817 MessageManager.getString("label.from_file"));
1818 addFromFile.addActionListener(new ActionListener()
1821 public void actionPerformed(ActionEvent e)
1823 addFromFile_actionPerformed(e);
1826 JMenuItem addFromText = new JMenuItem(
1827 MessageManager.getString("label.from_textbox"));
1828 addFromText.addActionListener(new ActionListener()
1831 public void actionPerformed(ActionEvent e)
1833 addFromText_actionPerformed(e);
1836 JMenuItem addFromURL = new JMenuItem(
1837 MessageManager.getString("label.from_url"));
1838 addFromURL.addActionListener(new ActionListener()
1841 public void actionPerformed(ActionEvent e)
1843 addFromURL_actionPerformed(e);
1846 JMenuItem exportFeatures = new JMenuItem(
1847 MessageManager.getString("label.export_features"));
1848 exportFeatures.addActionListener(new ActionListener()
1851 public void actionPerformed(ActionEvent e)
1853 exportFeatures_actionPerformed(e);
1856 JMenuItem exportAnnotations = new JMenuItem(
1857 MessageManager.getString("label.export_annotations"));
1858 exportAnnotations.addActionListener(new ActionListener()
1861 public void actionPerformed(ActionEvent e)
1863 exportAnnotations_actionPerformed(e);
1866 statusPanel.setLayout(new GridLayout());
1867 JMenuItem showAllSeqs = new JMenuItem(
1868 MessageManager.getString("label.all_sequences"));
1869 showAllSeqs.setToolTipText(MessageManager
1870 .getString("label.toggle_sequence_visibility"));
1871 showAllSeqs.addActionListener(new ActionListener()
1874 public void actionPerformed(ActionEvent e)
1876 showAllSeqs_actionPerformed(e);
1879 JMenuItem showAllColumns = new JMenuItem(
1880 MessageManager.getString("label.all_columns"));
1881 showAllColumns.setToolTipText(MessageManager
1882 .getString("label.toggle_columns_visibility"));
1883 showAllColumns.addActionListener(new ActionListener()
1886 public void actionPerformed(ActionEvent e)
1888 showAllColumns_actionPerformed(e);
1891 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
1892 JMenuItem hideSelSequences = new JMenuItem(
1893 MessageManager.getString("label.selected_sequences"));
1894 hideSelSequences.setToolTipText(MessageManager
1895 .getString("label.toggle_sequence_visibility"));
1896 hideSelSequences.addActionListener(new ActionListener()
1899 public void actionPerformed(ActionEvent e)
1901 hideSelSequences_actionPerformed(e);
1904 JMenuItem hideSelColumns = new JMenuItem(
1905 MessageManager.getString("label.selected_columns"));
1906 hideSelColumns.setToolTipText(MessageManager
1907 .getString("label.toggle_columns_visibility"));
1908 hideSelColumns.addActionListener(new ActionListener()
1911 public void actionPerformed(ActionEvent e)
1913 hideSelColumns_actionPerformed(e);
1916 JMenuItem hideAllSelection = new JMenuItem(
1917 MessageManager.getString("label.selected_region"));
1918 hideAllSelection.addActionListener(new ActionListener()
1921 public void actionPerformed(ActionEvent e)
1923 hideAllSelection_actionPerformed(e);
1926 // TODO: should be hidden if no selection exists.
1927 JMenuItem hideAllButSelection = new JMenuItem(
1928 MessageManager.getString("label.all_but_selected_region"));
1929 hideAllButSelection.addActionListener(new ActionListener()
1932 public void actionPerformed(ActionEvent e)
1934 hideAllButSelection_actionPerformed(e);
1937 JMenuItem showAllhidden = new JMenuItem(
1938 MessageManager.getString("label.all_sequences_columns"));
1939 showAllhidden.setToolTipText(MessageManager
1940 .getString("label.toggles_visibility_hidden_selected_regions"));
1941 showAllhidden.addActionListener(new ActionListener()
1944 public void actionPerformed(ActionEvent e)
1946 showAllhidden_actionPerformed(e);
1949 hiddenMarkers.setText(MessageManager
1950 .getString("action.show_hidden_markers"));
1951 hiddenMarkers.addActionListener(new ActionListener()
1954 public void actionPerformed(ActionEvent e)
1956 hiddenMarkers_actionPerformed(e);
1960 JMenuItem invertColSel = new JMenuItem(
1961 MessageManager.getString("action.invert_column_selection"));
1962 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
1963 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
1964 | KeyEvent.ALT_MASK, false);
1965 al = new ActionListener()
1968 public void actionPerformed(ActionEvent e)
1970 invertColSel_actionPerformed(e);
1973 addMenuActionAndAccelerator(keyStroke, invertColSel, al);
1975 showComplementMenuItem.setVisible(false);
1976 showComplementMenuItem.addActionListener(new ActionListener()
1979 public void actionPerformed(ActionEvent e)
1981 showComplement_actionPerformed(showComplementMenuItem.getState());
1985 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1988 public void stateChanged(ChangeEvent evt)
1990 JTabbedPane pane = (JTabbedPane) evt.getSource();
1991 int sel = pane.getSelectedIndex();
1992 tabSelectionChanged(sel);
1995 tabbedPane.addMouseListener(new MouseAdapter()
1998 public void mousePressed(MouseEvent e)
2000 tabbedPane_mousePressed(e);
2003 tabbedPane.addFocusListener(new FocusAdapter()
2006 public void focusGained(FocusEvent e)
2008 tabbedPane_focusGained(e);
2012 JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
2013 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
2014 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
2015 al = new ActionListener()
2018 public void actionPerformed(ActionEvent e)
2020 save_actionPerformed(e);
2023 addMenuActionAndAccelerator(keyStroke, save, al);
2025 reload.setEnabled(false);
2026 reload.setText(MessageManager.getString("action.reload"));
2027 reload.addActionListener(new ActionListener()
2030 public void actionPerformed(ActionEvent e)
2032 reload_actionPerformed(e);
2036 JMenuItem newView = new JMenuItem(
2037 MessageManager.getString("action.new_view"));
2038 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
2039 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
2040 al = new ActionListener()
2043 public void actionPerformed(ActionEvent e)
2045 newView_actionPerformed(e);
2048 addMenuActionAndAccelerator(keyStroke, newView, al);
2050 tabbedPane.setToolTipText("<html><i>"
2051 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2053 JMenuItem textColour = new JMenuItem(
2054 MessageManager.getString("label.colour_text") + "...");
2055 textColour.addActionListener(new ActionListener()
2058 public void actionPerformed(ActionEvent e)
2060 textColour_actionPerformed(e);
2063 formatMenu.setText(MessageManager.getString("action.format"));
2064 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
2065 idRightAlign.setText(MessageManager
2066 .getString("label.right_align_sequence_id"));
2067 idRightAlign.addActionListener(new ActionListener()
2070 public void actionPerformed(ActionEvent e)
2072 idRightAlign_actionPerformed(e);
2076 gatherViews.setEnabled(false);
2077 gatherViews.setText(MessageManager.getString("action.gather_views"));
2078 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
2079 al = new ActionListener()
2082 public void actionPerformed(ActionEvent e)
2084 gatherViews_actionPerformed(e);
2087 addMenuActionAndAccelerator(keyStroke, gatherViews, al);
2089 expandViews.setEnabled(false);
2090 expandViews.setText(MessageManager.getString("action.expand_views"));
2091 keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
2092 al = new ActionListener()
2095 public void actionPerformed(ActionEvent e)
2097 expandViews_actionPerformed(e);
2100 addMenuActionAndAccelerator(keyStroke, expandViews, al);
2102 JMenuItem pageSetup = new JMenuItem(
2103 MessageManager.getString("action.page_setup") + "...");
2104 pageSetup.addActionListener(new ActionListener()
2107 public void actionPerformed(ActionEvent e)
2109 pageSetup_actionPerformed(e);
2112 JMenuItem alignmentProperties = new JMenuItem(
2113 MessageManager.getString("label.alignment_props") + "...");
2114 alignmentProperties.addActionListener(new ActionListener()
2117 public void actionPerformed(ActionEvent actionEvent)
2119 alignmentProperties();
2122 JMenu tooltipSettingsMenu = new JMenu(
2123 MessageManager.getString("label.sequence_id_tooltip"));
2124 JMenu autoAnnMenu = new JMenu(
2125 MessageManager.getString("label.autocalculated_annotation"));
2127 JMenu exportImageMenu = new JMenu(
2128 MessageManager.getString("label.export_image"));
2129 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
2130 alignFrameMenuBar.add(fileMenu);
2131 alignFrameMenuBar.add(editMenu);
2132 alignFrameMenuBar.add(selectMenu);
2133 alignFrameMenuBar.add(viewMenu);
2134 alignFrameMenuBar.add(annotationsMenu);
2135 alignFrameMenuBar.add(formatMenu);
2136 alignFrameMenuBar.add(colourMenu);
2137 alignFrameMenuBar.add(calculateMenu);
2138 alignFrameMenuBar.add(webService);
2139 fileMenu.add(fetchSequence);
2140 fileMenu.add(addSequenceMenu);
2141 fileMenu.add(reload);
2142 fileMenu.addSeparator();
2143 fileMenu.add(vamsasStore);
2145 fileMenu.add(saveAs);
2146 fileMenu.add(outputTextboxMenu);
2147 fileMenu.add(pageSetup);
2148 fileMenu.add(printMenuItem);
2149 fileMenu.addSeparator();
2150 fileMenu.add(exportImageMenu);
2151 fileMenu.add(exportFeatures);
2152 fileMenu.add(exportAnnotations);
2153 fileMenu.add(loadTreeMenuItem);
2154 fileMenu.add(associatedData);
2155 fileMenu.addSeparator();
2156 fileMenu.add(closeMenuItem);
2157 editMenu.add(undoMenuItem);
2158 editMenu.add(redoMenuItem);
2161 editMenu.add(pasteMenu);
2162 editMenu.add(delete);
2163 editMenu.addSeparator();
2164 editMenu.add(remove2LeftMenuItem);
2165 editMenu.add(remove2RightMenuItem);
2166 editMenu.add(removeGappedColumnMenuItem);
2167 editMenu.add(removeAllGapsMenuItem);
2168 editMenu.add(removeRedundancyMenuItem);
2169 editMenu.addSeparator();
2170 // dont add these yet in the CVS build - they cannot be undone!
2171 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2172 // editMenu.add(justifyLeftMenuItem);
2173 // editMenu.add(justifyRightMenuItem);
2174 // editMenu.addSeparator();
2175 editMenu.add(padGapsMenuitem);
2177 viewMenu.add(newView);
2178 viewMenu.add(expandViews);
2179 viewMenu.add(gatherViews);
2180 viewMenu.addSeparator();
2181 viewMenu.add(showMenu);
2182 viewMenu.add(hideMenu);
2183 viewMenu.add(showComplementMenuItem);
2184 viewMenu.addSeparator();
2185 viewMenu.add(followHighlightMenuItem);
2186 viewMenu.addSeparator();
2187 viewMenu.add(showSeqFeatures);
2188 // viewMenu.add(showSeqFeaturesHeight);
2189 viewMenu.add(openFeatureSettings);
2190 tooltipSettingsMenu.add(showDbRefsMenuitem);
2191 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2192 viewMenu.add(tooltipSettingsMenu);
2193 viewMenu.addSeparator();
2194 viewMenu.add(alignmentProperties);
2195 viewMenu.addSeparator();
2196 viewMenu.add(overviewMenuItem);
2198 annotationsMenu.add(annotationPanelMenuItem);
2199 annotationsMenu.addSeparator();
2200 annotationsMenu.add(showAllAlAnnotations);
2201 annotationsMenu.add(hideAllAlAnnotations);
2202 annotationsMenu.addSeparator();
2203 annotationsMenu.add(showAllSeqAnnotations);
2204 annotationsMenu.add(hideAllSeqAnnotations);
2205 annotationsMenu.add(sortAnnBySequence);
2206 annotationsMenu.add(sortAnnByLabel);
2207 annotationsMenu.addSeparator();
2208 autoAnnMenu.add(showAutoFirst);
2209 autoAnnMenu.add(showAutoLast);
2210 autoAnnMenu.addSeparator();
2211 autoAnnMenu.add(applyAutoAnnotationSettings);
2212 autoAnnMenu.add(showConsensusHistogram);
2213 autoAnnMenu.add(showSequenceLogo);
2214 autoAnnMenu.add(normaliseSequenceLogo);
2215 autoAnnMenu.addSeparator();
2216 autoAnnMenu.add(showGroupConservation);
2217 autoAnnMenu.add(showGroupConsensus);
2218 annotationsMenu.add(autoAnnMenu);
2220 colourMenu.add(applyToAllGroups);
2221 colourMenu.add(textColour);
2222 colourMenu.addSeparator();
2223 colourMenu.add(noColourmenuItem);
2224 colourMenu.add(clustalColour);
2225 colourMenu.add(BLOSUM62Colour);
2226 colourMenu.add(PIDColour);
2227 colourMenu.add(zappoColour);
2228 colourMenu.add(taylorColour);
2229 colourMenu.add(hydrophobicityColour);
2230 colourMenu.add(helixColour);
2231 colourMenu.add(strandColour);
2232 colourMenu.add(turnColour);
2233 colourMenu.add(buriedColour);
2234 colourMenu.add(nucleotideColour);
2235 colourMenu.add(purinePyrimidineColour);
2236 colourMenu.add(RNAInteractionColour);
2237 // colourMenu.add(covariationColour);
2238 colourMenu.add(tcoffeeColour);
2239 colourMenu.add(userDefinedColour);
2240 colourMenu.addSeparator();
2241 colourMenu.add(conservationMenuItem);
2242 colourMenu.add(modifyConservation);
2243 colourMenu.add(abovePIDThreshold);
2244 colourMenu.add(modifyPID);
2245 colourMenu.add(annotationColour);
2246 colourMenu.add(rnahelicesColour);
2247 calculateMenu.add(sort);
2248 calculateMenu.add(calculateTree);
2249 calculateMenu.addSeparator();
2250 calculateMenu.add(pairwiseAlignmentMenuItem);
2251 calculateMenu.add(PCAMenuItem);
2252 calculateMenu.addSeparator();
2253 calculateMenu.add(showTranslation);
2254 calculateMenu.add(showProducts);
2255 calculateMenu.add(autoCalculate);
2256 calculateMenu.add(sortByTree);
2257 calculateMenu.addSeparator();
2258 calculateMenu.add(extractScores);
2259 webServiceNoServices = new JMenuItem(
2260 MessageManager.getString("label.no_services"));
2261 webService.add(webServiceNoServices);
2262 pasteMenu.add(pasteNew);
2263 pasteMenu.add(pasteThis);
2264 sort.add(sortIDMenuItem);
2265 sort.add(sortLengthMenuItem);
2266 sort.add(sortGroupMenuItem);
2267 sort.add(sortPairwiseMenuItem);
2268 sort.add(sortByTreeMenu);
2269 exportImageMenu.add(htmlMenuItem);
2270 exportImageMenu.add(epsFile);
2271 exportImageMenu.add(createPNG);
2272 exportImageMenu.add(createBioJS);
2273 exportImageMenu.add(createSVG);
2274 addSequenceMenu.add(addFromFile);
2275 addSequenceMenu.add(addFromText);
2276 addSequenceMenu.add(addFromURL);
2277 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2278 statusPanel.add(statusBar, null);
2279 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2280 showMenu.add(showAllColumns);
2281 showMenu.add(showAllSeqs);
2282 showMenu.add(showAllhidden);
2283 hideMenu.add(hideSelColumns);
2284 hideMenu.add(hideSelSequences);
2285 hideMenu.add(hideAllSelection);
2286 hideMenu.add(hideAllButSelection);
2288 formatMenu.add(font);
2289 formatMenu.addSeparator();
2290 formatMenu.add(wrapMenuItem);
2291 formatMenu.add(scaleAbove);
2292 formatMenu.add(scaleLeft);
2293 formatMenu.add(scaleRight);
2294 formatMenu.add(seqLimits);
2295 formatMenu.add(idRightAlign);
2296 formatMenu.add(hiddenMarkers);
2297 formatMenu.add(viewBoxesMenuItem);
2298 formatMenu.add(viewTextMenuItem);
2299 formatMenu.add(colourTextMenuItem);
2300 formatMenu.add(renderGapsMenuItem);
2301 formatMenu.add(centreColumnLabelsMenuItem);
2302 formatMenu.add(showNonconservedMenuItem);
2303 selectMenu.add(findMenuItem);
2304 selectMenu.addSeparator();
2305 selectMenu.add(selectAllSequenceMenuItem);
2306 selectMenu.add(deselectAllSequenceMenuItem);
2307 selectMenu.add(invertSequenceMenuItem);
2308 selectMenu.add(invertColSel);
2309 selectMenu.add(createGroup);
2310 selectMenu.add(unGroup);
2311 selectMenu.add(grpsFromSelection);
2312 selectMenu.add(deleteGroups);
2313 selectMenu.add(annotationColumn);
2314 calculateMenu.add(expandAlignment);
2315 // TODO - determine if the listenToViewSelections button is needed : see bug
2317 // selectMenu.addSeparator();
2318 // selectMenu.add(listenToViewSelections);
2322 * Adds the given action listener and key accelerator to the given menu item.
2323 * Also saves in a lookup table to support lookup of action by key stroke.
2327 * @param actionListener
2329 protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
2330 JMenuItem menuItem, ActionListener actionListener)
2332 menuItem.setAccelerator(keyStroke);
2333 accelerators.put(keyStroke, menuItem);
2334 menuItem.addActionListener(actionListener);
2338 * Action on clicking sort annotations by type.
2342 protected void sortAnnotations_actionPerformed()
2347 * Action on clicking Show all annotations.
2349 * @param forSequences
2350 * update sequence-related annotations
2351 * @param forAlignment
2352 * update non-sequence-related annotations
2354 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2355 boolean forAlignment)
2357 setAnnotationsVisibility(true, forSequences, forAlignment);
2361 * Action on clicking Hide all annotations.
2363 * @param forSequences
2364 * update sequence-related annotations
2365 * @param forAlignment
2366 * update non-sequence-related annotations
2368 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2369 boolean forAlignment)
2371 setAnnotationsVisibility(false, forSequences, forAlignment);
2375 * Set the visibility of annotations to true or false. Can act on
2376 * sequence-related annotations, or alignment-related, or both.
2379 * @param forSequences
2380 * update sequence-related annotations
2381 * @param forAlignment
2382 * update non-sequence-related annotations
2384 protected void setAnnotationsVisibility(boolean visible,
2385 boolean forSequences, boolean forAlignment)
2390 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2392 // TODO Auto-generated method stub
2396 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2398 // TODO Auto-generated method stub
2402 protected void showAllhidden_actionPerformed(ActionEvent e)
2404 // TODO Auto-generated method stub
2408 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2410 // TODO Auto-generated method stub
2414 protected void hideAllSelection_actionPerformed(ActionEvent e)
2416 // TODO Auto-generated method stub
2420 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2422 // TODO Auto-generated method stub
2426 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2428 // TODO Auto-generated method stub
2432 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2434 // TODO Auto-generated method stub
2438 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2440 // TODO Auto-generated method stub
2444 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2446 // TODO Auto-generated method stub
2450 protected void showGroupConservation_actionPerformed(ActionEvent e)
2452 // TODO Auto-generated method stub
2456 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2458 // TODO Auto-generated method stub
2462 protected void showSeqFeaturesHeight_actionPerformed(
2463 ActionEvent actionEvent)
2465 // TODO Auto-generated method stub
2469 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2471 // TODO Auto-generated method stub
2475 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2477 // TODO Auto-generated method stub
2481 protected void followHighlight_actionPerformed()
2483 // TODO Auto-generated method stub
2487 protected void showNpFeats_actionPerformed(ActionEvent e)
2489 // TODO Auto-generated method stub
2493 protected void showDbRefs_actionPerformed(ActionEvent e)
2495 // TODO Auto-generated method stub
2499 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2503 protected void buildSortByAnnotationScoresMenu()
2507 protected void extractScores_actionPerformed(ActionEvent e)
2511 protected void outputText_actionPerformed(ActionEvent e)
2515 public void addFromFile_actionPerformed(ActionEvent e)
2520 public void addFromText_actionPerformed(ActionEvent e)
2525 public void addFromURL_actionPerformed(ActionEvent e)
2530 public void exportFeatures_actionPerformed(ActionEvent e)
2535 public void exportAnnotations_actionPerformed(ActionEvent e)
2540 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2544 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2549 protected void closeMenuItem_actionPerformed(boolean b)
2553 protected void redoMenuItem_actionPerformed(ActionEvent e)
2557 protected void undoMenuItem_actionPerformed(ActionEvent e)
2561 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2565 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2569 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2573 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2577 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2581 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2585 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2589 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2593 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2597 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2601 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2605 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2609 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2613 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2617 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2621 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2625 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2629 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2633 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2637 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2641 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2645 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2649 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2653 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2657 protected void clustalColour_actionPerformed(ActionEvent e)
2661 protected void zappoColour_actionPerformed(ActionEvent e)
2665 protected void taylorColour_actionPerformed(ActionEvent e)
2669 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2673 protected void helixColour_actionPerformed(ActionEvent e)
2677 protected void strandColour_actionPerformed(ActionEvent e)
2681 protected void turnColour_actionPerformed(ActionEvent e)
2685 protected void buriedColour_actionPerformed(ActionEvent e)
2689 protected void userDefinedColour_actionPerformed(ActionEvent e)
2693 protected void PIDColour_actionPerformed(ActionEvent e)
2697 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2701 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2705 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2710 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2713 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2717 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2721 protected void printMenuItem_actionPerformed(ActionEvent e)
2725 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2729 protected void findMenuItem_actionPerformed(ActionEvent e)
2733 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2737 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2741 protected void nucleotideColour_actionPerformed(ActionEvent e)
2745 protected void deleteGroups_actionPerformed(ActionEvent e)
2749 protected void createGroup_actionPerformed(ActionEvent e)
2753 protected void unGroup_actionPerformed(ActionEvent e)
2757 protected void copy_actionPerformed(ActionEvent e)
2761 protected void cut_actionPerformed(ActionEvent e)
2765 protected void delete_actionPerformed(ActionEvent e)
2769 protected void pasteNew_actionPerformed(ActionEvent e)
2773 protected void pasteThis_actionPerformed(ActionEvent e)
2777 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2781 public void createPNG(java.io.File f)
2785 protected void font_actionPerformed(ActionEvent e)
2789 protected void seqLimit_actionPerformed(ActionEvent e)
2793 public void seqDBRef_actionPerformed(ActionEvent e)
2798 public void createEPS(java.io.File f)
2802 public void createSVG(java.io.File f)
2806 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
2812 * Template method to handle the 'load T-Coffee scores' menu event.
2814 * Subclasses override this method to provide a custom action.
2819 protected void loadScores_actionPerformed(ActionEvent event)
2825 * Template method to handle the 'Color T-Coffee scores' menu event.
2827 * Subclasses override this method to provide a custom action.
2832 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2837 protected void jpred_actionPerformed(ActionEvent e)
2841 protected void scaleAbove_actionPerformed(ActionEvent e)
2845 protected void scaleLeft_actionPerformed(ActionEvent e)
2849 protected void scaleRight_actionPerformed(ActionEvent e)
2853 protected void modifyPID_actionPerformed(ActionEvent e)
2857 protected void modifyConservation_actionPerformed(ActionEvent e)
2861 protected void saveAs_actionPerformed(ActionEvent e)
2865 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2869 public void vamsasStore_actionPerformed(ActionEvent e)
2874 public void vamsasLoad_actionPerformed(ActionEvent e)
2879 public void showTranslation_actionPerformed(ActionEvent e)
2884 public void featureSettings_actionPerformed(ActionEvent e)
2889 public void fetchSequence_actionPerformed(ActionEvent e)
2894 public void smoothFont_actionPerformed(ActionEvent e)
2899 public void annotationColour_actionPerformed(ActionEvent e)
2904 public void annotationColumn_actionPerformed(ActionEvent e)
2909 public void rnahelicesColour_actionPerformed(ActionEvent e)
2914 public void associatedData_actionPerformed(ActionEvent e)
2919 public void autoCalculate_actionPerformed(ActionEvent e)
2924 public void sortByTreeOption_actionPerformed(ActionEvent e)
2929 public void showAllSeqs_actionPerformed(ActionEvent e)
2934 public void showAllColumns_actionPerformed(ActionEvent e)
2939 public void hideSelSequences_actionPerformed(ActionEvent e)
2944 public void hideSelColumns_actionPerformed(ActionEvent e)
2949 public void hiddenMarkers_actionPerformed(ActionEvent e)
2954 public void findPdbId_actionPerformed(ActionEvent e)
2959 public void enterPdbId_actionPerformed(ActionEvent e)
2964 public void pdbFile_actionPerformed(ActionEvent e)
2969 public void invertColSel_actionPerformed(ActionEvent e)
2974 public void tabSelectionChanged(int sel)
2979 public void tabbedPane_mousePressed(MouseEvent e)
2984 public void tabbedPane_focusGained(FocusEvent e)
2989 public void save_actionPerformed(ActionEvent e)
2994 public void reload_actionPerformed(ActionEvent e)
2999 public void newView_actionPerformed(ActionEvent e)
3004 public void textColour_actionPerformed(ActionEvent e)
3009 public void idRightAlign_actionPerformed(ActionEvent e)
3014 public void expandViews_actionPerformed(ActionEvent e)
3019 public void gatherViews_actionPerformed(ActionEvent e)
3024 public void buildTreeMenu()
3029 public void pageSetup_actionPerformed(ActionEvent e)
3034 public void alignmentProperties()
3039 protected void expand_newalign(ActionEvent e)
3041 // TODO Auto-generated method stub
3045 protected boolean isShowAutoCalculatedAbove()
3047 return showAutoCalculatedAbove;
3050 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3052 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3055 protected SequenceAnnotationOrder getAnnotationSortOrder()
3057 return annotationSortOrder;
3060 protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
3062 this.annotationSortOrder = annotationSortOrder;
3065 public Map<KeyStroke, JMenuItem> getAccelerators()
3067 return this.accelerators;
3071 * Returns the selected index of the tabbed pane, or -1 if none selected
3072 * (including the case where the tabbed pane has not been made visible).
3076 public int getTabIndex()
3078 return tabbedPane.getSelectedIndex();
3081 public JPanel getStatusPanel()
3087 * Sets a reference to the containing split frame. Also makes the 'toggle
3088 * split view' menu item visible and checked.
3092 public void setSplitFrame(SplitContainerI sf)
3094 this.splitFrame = sf;
3097 this.showComplementMenuItem.setVisible(true);
3098 this.showComplementMenuItem.setState(true);
3102 public SplitContainerI getSplitViewContainer()
3104 return this.splitFrame;
3107 protected void showComplement_actionPerformed(boolean state)