2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.jbgui;
23 import jalview.bin.Cache;
24 import jalview.gui.JvSwingUtils;
25 import jalview.schemes.ColourSchemeProperty;
26 import jalview.util.MessageManager;
28 import java.awt.BorderLayout;
29 import java.awt.Color;
30 import java.awt.GridLayout;
31 import java.awt.Toolkit;
32 import java.awt.event.ActionEvent;
33 import java.awt.event.ActionListener;
34 import java.awt.event.FocusAdapter;
35 import java.awt.event.FocusEvent;
36 import java.awt.event.MouseAdapter;
37 import java.awt.event.MouseEvent;
39 import javax.swing.BorderFactory;
40 import javax.swing.ButtonGroup;
41 import javax.swing.JCheckBoxMenuItem;
42 import javax.swing.JInternalFrame;
43 import javax.swing.JLabel;
44 import javax.swing.JMenu;
45 import javax.swing.JMenuBar;
46 import javax.swing.JMenuItem;
47 import javax.swing.JOptionPane;
48 import javax.swing.JPanel;
49 import javax.swing.JRadioButtonMenuItem;
50 import javax.swing.JTabbedPane;
51 import javax.swing.SwingUtilities;
52 import javax.swing.event.ChangeEvent;
53 import javax.swing.event.MenuEvent;
54 import javax.swing.event.MenuListener;
56 public class GAlignFrame extends JInternalFrame
58 protected JMenuBar alignFrameMenuBar = new JMenuBar();
60 protected JMenu fileMenu = new JMenu();
62 protected JMenuItem closeMenuItem = new JMenuItem();
64 protected JMenu editMenu = new JMenu();
66 protected JMenu viewMenu = new JMenu();
68 protected JMenu colourMenu = new JMenu();
70 protected JMenu calculateMenu = new JMenu();
72 protected JMenu webService = new JMenu();
74 protected JMenuItem webServiceNoServices;
76 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
78 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
80 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
82 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
84 protected JMenuItem remove2RightMenuItem = new JMenuItem();
86 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
88 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
90 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
92 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
94 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
96 protected JMenuItem sortIDMenuItem = new JMenuItem();
98 protected JMenuItem sortLengthMenuItem = new JMenuItem();
100 protected JMenuItem sortGroupMenuItem = new JMenuItem();
102 protected JMenu sortByAnnotScore = new JMenu();
104 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
106 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
108 protected JMenuItem PCAMenuItem = new JMenuItem();
110 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
112 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
114 BorderLayout borderLayout1 = new BorderLayout();
116 public JLabel statusBar = new JLabel();
118 protected JMenuItem saveAs = new JMenuItem();
120 protected JMenu outputTextboxMenu = new JMenu();
122 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
124 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
126 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
128 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
130 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
132 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
134 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
136 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
138 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
140 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
142 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
144 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
146 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
148 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
150 // protected JRadioButtonMenuItem covariationColour = new
151 // JRadioButtonMenuItem();
153 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
155 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
157 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
159 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
161 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
163 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
165 JMenuItem htmlMenuItem = new JMenuItem();
167 JMenuItem overviewMenuItem = new JMenuItem();
169 protected JMenuItem undoMenuItem = new JMenuItem();
171 protected JMenuItem redoMenuItem = new JMenuItem();
173 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
175 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
177 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
179 JMenuItem printMenuItem = new JMenuItem();
181 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
183 JMenuItem findMenuItem = new JMenuItem();
185 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
187 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
189 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
191 JMenuItem deleteGroups = new JMenuItem();
193 JMenuItem createGroup = new JMenuItem();
195 JMenuItem unGroup = new JMenuItem();
197 JMenuItem delete = new JMenuItem();
199 JMenuItem copy = new JMenuItem();
201 JMenuItem cut = new JMenuItem();
203 JMenu pasteMenu = new JMenu();
205 JMenuItem pasteNew = new JMenuItem();
207 JMenuItem pasteThis = new JMenuItem();
209 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
211 JMenuItem createPNG = new JMenuItem();
213 JMenuItem createBioJS = new JMenuItem();
215 protected JMenuItem font = new JMenuItem();
217 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
219 JMenuItem epsFile = new JMenuItem();
221 JMenuItem LoadtreeMenuItem = new JMenuItem();
223 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
225 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
227 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
229 protected JMenuItem modifyPID = new JMenuItem();
231 protected JMenuItem modifyConservation = new JMenuItem();
233 protected JMenu sortByTreeMenu = new JMenu();
235 protected JMenu sort = new JMenu();
237 protected JMenu calculateTree = new JMenu();
239 JMenu jMenu2 = new JMenu();
241 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
243 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
245 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
247 protected ButtonGroup colours = new ButtonGroup();
249 JMenuItem vamsasStore = new JMenuItem();
251 protected JMenuItem showTranslation = new JMenuItem();
253 protected JMenuItem extractScores = new JMenuItem();
255 protected JMenuItem expandAlignment = new JMenuItem();
257 protected JMenu showProducts = new JMenu();
259 public JMenuItem openFeatureSettings = new JMenuItem();
261 JMenuItem fetchSequence = new JMenuItem();
263 JMenuItem annotationColour = new JMenuItem();
265 protected JMenuItem rnahelicesColour = new JMenuItem();
267 JMenuItem associatedData = new JMenuItem();
269 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
271 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
273 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
275 JMenu addSequenceMenu = new JMenu();
277 JMenuItem addFromFile = new JMenuItem();
279 JMenuItem addFromText = new JMenuItem();
281 JMenuItem addFromURL = new JMenuItem();
283 JMenuItem exportAnnotations = new JMenuItem();
285 JMenuItem exportFeatures = new JMenuItem();
287 protected JPanel statusPanel = new JPanel();
289 GridLayout gridLayout1 = new GridLayout();
291 JMenu jMenu3 = new JMenu();
293 JMenuItem showAllSeqs = new JMenuItem();
295 JMenuItem showAllColumns = new JMenuItem();
297 JMenu hideMenu = new JMenu();
299 JMenuItem hideSelSequences = new JMenuItem();
301 JMenuItem hideSelColumns = new JMenuItem();
303 JMenuItem hideAllButSelection = new JMenuItem();
305 JMenuItem hideAllSelection = new JMenuItem();
307 JMenuItem showAllhidden = new JMenuItem();
309 protected JMenuItem showAllAnnotations = new JMenuItem();
311 protected JMenuItem hideAllAnnotations = new JMenuItem();
313 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
315 JMenuItem invertColSel = new JMenuItem();
317 protected JTabbedPane tabbedPane = new JTabbedPane();
319 JMenuItem save = new JMenuItem();
321 protected JMenuItem reload = new JMenuItem();
323 JMenuItem newView = new JMenuItem();
325 JMenuItem textColour = new JMenuItem();
327 JMenu formatMenu = new JMenu();
329 JMenu selectMenu = new JMenu();
331 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
333 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
335 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
337 protected JMenuItem gatherViews = new JMenuItem();
339 protected JMenuItem expandViews = new JMenuItem();
341 JMenuItem pageSetup = new JMenuItem();
343 JMenuItem alignmentProperties = new JMenuItem();
345 JMenu tooltipSettingsMenu = new JMenu();
347 private JMenuItem justifyLeftMenuItem = new JMenuItem();
349 private JMenuItem justifyRightMenuItem = new JMenuItem();
351 JMenu autoAnnMenu = new JMenu();
353 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
355 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
357 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
359 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
361 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
363 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
365 private JMenuItem grpsFromSelection = new JMenuItem();
372 setJMenuBar(alignFrameMenuBar);
374 // dynamically fill save as menu with available formats
375 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
377 JMenuItem item = new JMenuItem(
378 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
380 item.addActionListener(new java.awt.event.ActionListener()
383 public void actionPerformed(ActionEvent e)
385 outputText_actionPerformed(e);
389 outputTextboxMenu.add(item);
391 } catch (Exception e)
393 System.err.println(e.toString());
396 if (!new jalview.util.Platform().isAMac())
398 closeMenuItem.setMnemonic('C');
399 outputTextboxMenu.setMnemonic('T');
400 undoMenuItem.setMnemonic('Z');
401 redoMenuItem.setMnemonic('0');
402 copy.setMnemonic('C');
403 cut.setMnemonic('U');
404 pasteMenu.setMnemonic('P');
405 reload.setMnemonic('R');
408 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
410 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
411 .getUserColourSchemes().keys();
413 while (userColours.hasMoreElements())
415 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
416 userColours.nextElement().toString());
417 radioItem.setName("USER_DEFINED");
418 radioItem.addMouseListener(new MouseAdapter()
421 public void mousePressed(MouseEvent evt)
423 if (evt.isControlDown()
424 || SwingUtilities.isRightMouseButton(evt))
426 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
428 int option = JOptionPane.showInternalConfirmDialog(
429 jalview.gui.Desktop.desktop,
431 .getString("label.remove_from_default_list"),
433 .getString("label.remove_user_defined_colour"),
434 JOptionPane.YES_NO_OPTION);
435 if (option == JOptionPane.YES_OPTION)
437 jalview.gui.UserDefinedColours
438 .removeColourFromDefaults(radioItem.getText());
439 colourMenu.remove(radioItem);
443 radioItem.addActionListener(new ActionListener()
446 public void actionPerformed(ActionEvent evt)
448 userDefinedColour_actionPerformed(evt);
455 radioItem.addActionListener(new ActionListener()
458 public void actionPerformed(ActionEvent evt)
460 userDefinedColour_actionPerformed(evt);
463 colourMenu.insert(radioItem, 15);
464 colours.add(radioItem);
467 colours.add(noColourmenuItem);
468 colours.add(clustalColour);
469 colours.add(zappoColour);
470 colours.add(taylorColour);
471 colours.add(hydrophobicityColour);
472 colours.add(helixColour);
473 colours.add(strandColour);
474 colours.add(turnColour);
475 colours.add(buriedColour);
476 colours.add(userDefinedColour);
477 colours.add(PIDColour);
478 colours.add(BLOSUM62Colour);
479 colours.add(nucleotideColour);
480 colours.add(purinePyrimidineColour);
481 // colours.add(covariationColour);
482 colours.add(tcoffeeColour);
483 colours.add(RNAInteractionColour);
484 setColourSelected(jalview.bin.Cache
485 .getDefault("DEFAULT_COLOUR", "None"));
489 public void setColourSelected(String defaultColour)
492 if (defaultColour != null)
494 int index = ColourSchemeProperty
495 .getColourIndexFromName(defaultColour);
499 case ColourSchemeProperty.CLUSTAL:
500 clustalColour.setSelected(true);
504 case ColourSchemeProperty.BLOSUM:
505 BLOSUM62Colour.setSelected(true);
509 case ColourSchemeProperty.PID:
510 PIDColour.setSelected(true);
514 case ColourSchemeProperty.ZAPPO:
515 zappoColour.setSelected(true);
519 case ColourSchemeProperty.TAYLOR:
520 taylorColour.setSelected(true);
523 case ColourSchemeProperty.HYDROPHOBIC:
524 hydrophobicityColour.setSelected(true);
528 case ColourSchemeProperty.HELIX:
529 helixColour.setSelected(true);
533 case ColourSchemeProperty.STRAND:
534 strandColour.setSelected(true);
538 case ColourSchemeProperty.TURN:
539 turnColour.setSelected(true);
543 case ColourSchemeProperty.BURIED:
544 buriedColour.setSelected(true);
548 case ColourSchemeProperty.NUCLEOTIDE:
549 nucleotideColour.setSelected(true);
553 case ColourSchemeProperty.TCOFFEE:
554 tcoffeeColour.setSelected(true);
557 case ColourSchemeProperty.PURINEPYRIMIDINE:
558 purinePyrimidineColour.setSelected(true);
562 case ColourSchemeProperty.RNAINTERACTION:
563 RNAInteractionColour.setSelected(true);
567 * case ColourSchemeProperty.COVARIATION:
568 * covariationColour.setSelected(true);
572 case ColourSchemeProperty.USER_DEFINED:
573 userDefinedColour.setSelected(true);
576 case ColourSchemeProperty.NONE:
578 noColourmenuItem.setSelected(true);
586 private void jbInit() throws Exception
588 fileMenu.setText(MessageManager.getString("action.file"));
589 saveAs.setText(MessageManager.getString("action.save_as") + "...");
590 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
591 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
592 .getMenuShortcutKeyMask()
593 | java.awt.event.KeyEvent.SHIFT_MASK, false));
594 saveAs.addActionListener(new ActionListener()
597 public void actionPerformed(ActionEvent e)
599 saveAs_actionPerformed(e);
602 closeMenuItem.setText(MessageManager.getString("action.close"));
603 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
604 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
605 .getMenuShortcutKeyMask(), false));
606 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
609 public void actionPerformed(ActionEvent e)
611 closeMenuItem_actionPerformed(false);
614 editMenu.setText(MessageManager.getString("action.edit"));
615 viewMenu.setText(MessageManager.getString("action.view"));
616 colourMenu.setText(MessageManager.getString("action.colour"));
617 calculateMenu.setText(MessageManager.getString("action.calculate"));
618 webService.setText(MessageManager.getString("action.web_service"));
619 selectAllSequenceMenuItem.setText(MessageManager
620 .getString("action.select_all"));
621 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
622 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
623 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
624 selectAllSequenceMenuItem
625 .addActionListener(new java.awt.event.ActionListener()
628 public void actionPerformed(ActionEvent e)
630 selectAllSequenceMenuItem_actionPerformed(e);
633 deselectAllSequenceMenuItem.setText(MessageManager
634 .getString("action.deselect_all"));
635 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
636 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
637 deselectAllSequenceMenuItem
638 .addActionListener(new java.awt.event.ActionListener()
641 public void actionPerformed(ActionEvent e)
643 deselectAllSequenceMenuItem_actionPerformed(e);
646 invertSequenceMenuItem.setText(MessageManager
647 .getString("action.invert_sequence_selection"));
648 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
649 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
650 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
651 invertSequenceMenuItem
652 .addActionListener(new java.awt.event.ActionListener()
655 public void actionPerformed(ActionEvent e)
657 invertSequenceMenuItem_actionPerformed(e);
660 grpsFromSelection.setText(MessageManager
661 .getString("action.make_groups_selection"));
662 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
665 public void actionPerformed(ActionEvent e)
667 makeGrpsFromSelection_actionPerformed(e);
670 expandAlignment.setText(MessageManager
671 .getString("action.view_flanking_regions"));
672 expandAlignment.setToolTipText(MessageManager
673 .getString("label.view_flanking_regions"));
674 expandAlignment.addActionListener(new java.awt.event.ActionListener()
677 public void actionPerformed(ActionEvent e)
682 remove2LeftMenuItem.setText(MessageManager
683 .getString("action.remove_left"));
684 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
685 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
686 .getMenuShortcutKeyMask(), false));
688 .addActionListener(new java.awt.event.ActionListener()
691 public void actionPerformed(ActionEvent e)
693 remove2LeftMenuItem_actionPerformed(e);
696 remove2RightMenuItem.setText(MessageManager
697 .getString("action.remove_right"));
698 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
699 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
700 .getMenuShortcutKeyMask(), false));
702 .addActionListener(new java.awt.event.ActionListener()
705 public void actionPerformed(ActionEvent e)
707 remove2RightMenuItem_actionPerformed(e);
710 removeGappedColumnMenuItem.setText(MessageManager
711 .getString("action.remove_empty_columns"));
712 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
713 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
714 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
715 removeGappedColumnMenuItem
716 .addActionListener(new java.awt.event.ActionListener()
719 public void actionPerformed(ActionEvent e)
721 removeGappedColumnMenuItem_actionPerformed(e);
724 removeAllGapsMenuItem.setText(MessageManager
725 .getString("action.remove_all_gaps"));
726 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
727 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
728 .getDefaultToolkit().getMenuShortcutKeyMask()
729 | java.awt.event.KeyEvent.SHIFT_MASK, false));
730 removeAllGapsMenuItem
731 .addActionListener(new java.awt.event.ActionListener()
734 public void actionPerformed(ActionEvent e)
736 removeAllGapsMenuItem_actionPerformed(e);
739 justifyLeftMenuItem.setText(MessageManager
740 .getString("action.left_justify_alignment"));
742 .addActionListener(new java.awt.event.ActionListener()
745 public void actionPerformed(ActionEvent e)
747 justifyLeftMenuItem_actionPerformed(e);
750 justifyRightMenuItem.setText(MessageManager
751 .getString("action.right_justify_alignment"));
753 .addActionListener(new java.awt.event.ActionListener()
756 public void actionPerformed(ActionEvent e)
758 justifyRightMenuItem_actionPerformed(e);
761 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
762 viewBoxesMenuItem.setState(true);
763 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
766 public void actionPerformed(ActionEvent e)
768 viewBoxesMenuItem_actionPerformed(e);
771 viewTextMenuItem.setText(MessageManager.getString("action.text"));
772 viewTextMenuItem.setState(true);
773 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
776 public void actionPerformed(ActionEvent e)
778 viewTextMenuItem_actionPerformed(e);
781 showNonconservedMenuItem.setText(MessageManager
782 .getString("label.show_non_conversed"));
783 showNonconservedMenuItem.setState(false);
784 showNonconservedMenuItem
785 .addActionListener(new java.awt.event.ActionListener()
788 public void actionPerformed(ActionEvent e)
790 showUnconservedMenuItem_actionPerformed(e);
793 sortPairwiseMenuItem.setText(MessageManager
794 .getString("action.by_pairwise_id"));
796 .addActionListener(new java.awt.event.ActionListener()
799 public void actionPerformed(ActionEvent e)
801 sortPairwiseMenuItem_actionPerformed(e);
804 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
805 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
808 public void actionPerformed(ActionEvent e)
810 sortIDMenuItem_actionPerformed(e);
814 .setText(MessageManager.getString("action.by_length"));
816 .addActionListener(new java.awt.event.ActionListener()
819 public void actionPerformed(ActionEvent e)
821 sortLengthMenuItem_actionPerformed(e);
824 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
825 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
828 public void actionPerformed(ActionEvent e)
830 sortGroupMenuItem_actionPerformed(e);
833 removeRedundancyMenuItem.setText(MessageManager
834 .getString("action.remove_redundancy").concat("..."));
835 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
836 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
837 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
838 removeRedundancyMenuItem
839 .addActionListener(new java.awt.event.ActionListener()
842 public void actionPerformed(ActionEvent e)
844 removeRedundancyMenuItem_actionPerformed(e);
847 pairwiseAlignmentMenuItem.setText(MessageManager
848 .getString("action.pairwise_alignment"));
849 pairwiseAlignmentMenuItem
850 .addActionListener(new java.awt.event.ActionListener()
853 public void actionPerformed(ActionEvent e)
855 pairwiseAlignmentMenuItem_actionPerformed(e);
858 PCAMenuItem.setText(MessageManager
859 .getString("label.principal_component_analysis"));
860 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
863 public void actionPerformed(ActionEvent e)
865 PCAMenuItem_actionPerformed(e);
868 averageDistanceTreeMenuItem.setText(MessageManager
869 .getString("label.average_distance_identity"));
870 averageDistanceTreeMenuItem
871 .addActionListener(new java.awt.event.ActionListener()
874 public void actionPerformed(ActionEvent e)
876 averageDistanceTreeMenuItem_actionPerformed(e);
879 neighbourTreeMenuItem.setText(MessageManager
880 .getString("label.neighbour_joining_identity"));
881 neighbourTreeMenuItem
882 .addActionListener(new java.awt.event.ActionListener()
885 public void actionPerformed(ActionEvent e)
887 neighbourTreeMenuItem_actionPerformed(e);
890 this.getContentPane().setLayout(borderLayout1);
891 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
892 statusBar.setBackground(Color.white);
893 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
894 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
895 statusBar.setText(MessageManager.getString("label.status_bar"));
896 outputTextboxMenu.setText(MessageManager
897 .getString("label.out_to_textbox"));
898 clustalColour.setText(MessageManager.getString("label.clustalx"));
900 clustalColour.addActionListener(new java.awt.event.ActionListener()
903 public void actionPerformed(ActionEvent e)
905 clustalColour_actionPerformed(e);
908 zappoColour.setText(MessageManager.getString("label.zappo"));
909 zappoColour.addActionListener(new java.awt.event.ActionListener()
912 public void actionPerformed(ActionEvent e)
914 zappoColour_actionPerformed(e);
917 taylorColour.setText(MessageManager.getString("label.taylor"));
918 taylorColour.addActionListener(new java.awt.event.ActionListener()
921 public void actionPerformed(ActionEvent e)
923 taylorColour_actionPerformed(e);
926 hydrophobicityColour.setText(MessageManager
927 .getString("label.hydrophobicity"));
929 .addActionListener(new java.awt.event.ActionListener()
932 public void actionPerformed(ActionEvent e)
934 hydrophobicityColour_actionPerformed(e);
937 helixColour.setText(MessageManager.getString("label.helix_propensity"));
938 helixColour.addActionListener(new java.awt.event.ActionListener()
941 public void actionPerformed(ActionEvent e)
943 helixColour_actionPerformed(e);
946 strandColour.setText(MessageManager
947 .getString("label.strand_propensity"));
948 strandColour.addActionListener(new java.awt.event.ActionListener()
951 public void actionPerformed(ActionEvent e)
953 strandColour_actionPerformed(e);
956 turnColour.setText(MessageManager.getString("label.turn_propensity"));
957 turnColour.addActionListener(new java.awt.event.ActionListener()
960 public void actionPerformed(ActionEvent e)
962 turnColour_actionPerformed(e);
965 buriedColour.setText(MessageManager.getString("label.buried_index"));
966 buriedColour.addActionListener(new java.awt.event.ActionListener()
969 public void actionPerformed(ActionEvent e)
971 buriedColour_actionPerformed(e);
974 userDefinedColour.setText(MessageManager
975 .getString("action.user_defined"));
976 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
979 public void actionPerformed(ActionEvent e)
981 userDefinedColour_actionPerformed(e);
985 .setText(MessageManager.getString("label.percentage_identity"));
986 PIDColour.addActionListener(new java.awt.event.ActionListener()
989 public void actionPerformed(ActionEvent e)
991 PIDColour_actionPerformed(e);
995 .setText(MessageManager.getString("label.blosum62_score"));
996 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
999 public void actionPerformed(ActionEvent e)
1001 BLOSUM62Colour_actionPerformed(e);
1004 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1005 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1008 public void actionPerformed(ActionEvent e)
1010 nucleotideColour_actionPerformed(e);
1014 purinePyrimidineColour.setText(MessageManager
1015 .getString("label.purine_pyrimidine"));
1016 purinePyrimidineColour
1017 .addActionListener(new java.awt.event.ActionListener()
1020 public void actionPerformed(ActionEvent e)
1022 purinePyrimidineColour_actionPerformed(e);
1026 RNAInteractionColour.setText("RNA Interaction type");
1027 RNAInteractionColour
1028 .addActionListener(new java.awt.event.ActionListener()
1031 public void actionPerformed(ActionEvent e)
1033 RNAInteractionColour_actionPerformed(e);
1037 * covariationColour.setText("Covariation");
1038 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1039 * public void actionPerformed(ActionEvent e) {
1040 * covariationColour_actionPerformed(e); } });
1043 avDistanceTreeBlosumMenuItem.setText(MessageManager
1044 .getString("label.average_distance_bloslum62"));
1045 avDistanceTreeBlosumMenuItem
1046 .addActionListener(new java.awt.event.ActionListener()
1049 public void actionPerformed(ActionEvent e)
1051 avTreeBlosumMenuItem_actionPerformed(e);
1054 njTreeBlosumMenuItem.setText(MessageManager
1055 .getString("label.neighbour_blosum62"));
1056 njTreeBlosumMenuItem
1057 .addActionListener(new java.awt.event.ActionListener()
1060 public void actionPerformed(ActionEvent e)
1062 njTreeBlosumMenuItem_actionPerformed(e);
1065 annotationPanelMenuItem.setActionCommand("");
1066 annotationPanelMenuItem.setText(MessageManager
1067 .getString("label.show_annotations"));
1068 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1070 annotationPanelMenuItem.addActionListener(new ActionListener()
1073 public void actionPerformed(ActionEvent e)
1075 annotationPanelMenuItem_actionPerformed(e);
1079 * Show/hide all annotations only enabled if annotation panel is shown
1081 showAllAnnotations.setText(MessageManager
1082 .getString("label.show_all_annotations"));
1083 showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
1084 showAllAnnotations.addActionListener(new ActionListener()
1087 public void actionPerformed(ActionEvent e)
1089 showAllAnnotations_actionPerformed();
1092 hideAllAnnotations.setText(MessageManager
1093 .getString("label.hide_all_annotations"));
1094 hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
1095 hideAllAnnotations.addActionListener(new ActionListener()
1098 public void actionPerformed(ActionEvent e)
1100 hideAllAnnotations_actionPerformed();
1103 colourTextMenuItem.setText(MessageManager
1104 .getString("label.colour_text"));
1106 .addActionListener(new java.awt.event.ActionListener()
1109 public void actionPerformed(ActionEvent e)
1111 colourTextMenuItem_actionPerformed(e);
1114 htmlMenuItem.setText(MessageManager.getString("label.html"));
1115 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1118 public void actionPerformed(ActionEvent e)
1120 htmlMenuItem_actionPerformed(e);
1124 // TODO uncomment when supported by MassageManager
1125 // createBioJS.setText(MessageManager.getString("label.biojs_html_export"));
1126 createBioJS.setText("BioJS");
1127 createBioJS.addActionListener(new java.awt.event.ActionListener()
1130 public void actionPerformed(ActionEvent e)
1132 bioJSMenuItem_actionPerformed(e);
1136 overviewMenuItem.setText(MessageManager
1137 .getString("label.overview_window"));
1138 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1141 public void actionPerformed(ActionEvent e)
1143 overviewMenuItem_actionPerformed(e);
1146 undoMenuItem.setEnabled(false);
1147 undoMenuItem.setText(MessageManager.getString("action.undo"));
1148 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1149 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1150 .getMenuShortcutKeyMask(), false));
1151 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1154 public void actionPerformed(ActionEvent e)
1156 undoMenuItem_actionPerformed(e);
1159 redoMenuItem.setEnabled(false);
1160 redoMenuItem.setText(MessageManager.getString("action.redo"));
1161 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1162 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1163 .getMenuShortcutKeyMask(), false));
1164 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1167 public void actionPerformed(ActionEvent e)
1169 redoMenuItem_actionPerformed(e);
1172 conservationMenuItem.setText(MessageManager
1173 .getString("action.by_conservation"));
1174 conservationMenuItem
1175 .addActionListener(new java.awt.event.ActionListener()
1178 public void actionPerformed(ActionEvent e)
1180 conservationMenuItem_actionPerformed(e);
1183 noColourmenuItem.setText(MessageManager.getString("label.none"));
1184 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1187 public void actionPerformed(ActionEvent e)
1189 noColourmenuItem_actionPerformed(e);
1192 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1193 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1196 public void actionPerformed(ActionEvent e)
1198 wrapMenuItem_actionPerformed(e);
1201 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1202 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1203 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1204 .getMenuShortcutKeyMask(), false));
1205 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1208 public void actionPerformed(ActionEvent e)
1210 printMenuItem_actionPerformed(e);
1214 .setText(MessageManager.getString("action.show_gaps"));
1215 renderGapsMenuItem.setState(true);
1217 .addActionListener(new java.awt.event.ActionListener()
1220 public void actionPerformed(ActionEvent e)
1222 renderGapsMenuItem_actionPerformed(e);
1225 findMenuItem.setText(MessageManager.getString("action.find"));
1226 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1227 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1228 .getMenuShortcutKeyMask(), false));
1229 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1230 MessageManager.getString("label.find_tip")));
1231 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1234 public void actionPerformed(ActionEvent e)
1236 findMenuItem_actionPerformed(e);
1239 abovePIDThreshold.setText(MessageManager
1240 .getString("label.above_identity_threshold"));
1241 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1244 public void actionPerformed(ActionEvent e)
1246 abovePIDThreshold_actionPerformed(e);
1249 showSeqFeatures.setText(MessageManager
1250 .getString("label.show_sequence_features"));
1251 showSeqFeatures.addActionListener(new ActionListener()
1254 public void actionPerformed(ActionEvent actionEvent)
1256 showSeqFeatures_actionPerformed(actionEvent);
1260 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1261 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1262 * void actionPerformed(ActionEvent actionEvent) {
1263 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1265 showDbRefsMenuitem.setText(MessageManager
1266 .getString("label.show_database_refs"));
1267 showDbRefsMenuitem.addActionListener(new ActionListener()
1271 public void actionPerformed(ActionEvent e)
1273 showDbRefs_actionPerformed(e);
1277 showNpFeatsMenuitem.setText(MessageManager
1278 .getString("label.show_non_positional_features"));
1279 showNpFeatsMenuitem.addActionListener(new ActionListener()
1283 public void actionPerformed(ActionEvent e)
1285 showNpFeats_actionPerformed(e);
1289 showGroupConservation.setText(MessageManager
1290 .getString("label.group_conservation"));
1291 showGroupConservation.addActionListener(new ActionListener()
1295 public void actionPerformed(ActionEvent e)
1297 showGroupConservation_actionPerformed(e);
1302 showGroupConsensus.setText(MessageManager
1303 .getString("label.group_consensus"));
1304 showGroupConsensus.addActionListener(new ActionListener()
1308 public void actionPerformed(ActionEvent e)
1310 showGroupConsensus_actionPerformed(e);
1314 showConsensusHistogram.setText(MessageManager
1315 .getString("label.show_consensus_histogram"));
1316 showConsensusHistogram.addActionListener(new ActionListener()
1320 public void actionPerformed(ActionEvent e)
1322 showConsensusHistogram_actionPerformed(e);
1326 showSequenceLogo.setText(MessageManager
1327 .getString("label.show_consensus_logo"));
1328 showSequenceLogo.addActionListener(new ActionListener()
1332 public void actionPerformed(ActionEvent e)
1334 showSequenceLogo_actionPerformed(e);
1338 normaliseSequenceLogo.setText(MessageManager
1339 .getString("label.norm_consensus_logo"));
1340 normaliseSequenceLogo.addActionListener(new ActionListener()
1344 public void actionPerformed(ActionEvent e)
1346 normaliseSequenceLogo_actionPerformed(e);
1350 applyAutoAnnotationSettings.setText(MessageManager
1351 .getString("label.apply_all_groups"));
1352 applyAutoAnnotationSettings.setState(false);
1353 applyAutoAnnotationSettings.setVisible(true);
1354 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1358 public void actionPerformed(ActionEvent e)
1360 applyAutoAnnotationSettings_actionPerformed(e);
1365 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1366 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1369 public void actionPerformed(ActionEvent e)
1371 nucleotideColour_actionPerformed(e);
1375 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1376 tcoffeeColour.setEnabled(false);
1377 tcoffeeColour.addActionListener(new ActionListener()
1381 public void actionPerformed(ActionEvent e)
1383 tcoffeeColorScheme_actionPerformed(e);
1388 .setText(MessageManager.getString("action.undefine_groups"));
1389 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1390 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1391 .getMenuShortcutKeyMask(), false));
1392 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1395 public void actionPerformed(ActionEvent e)
1397 deleteGroups_actionPerformed(e);
1400 createGroup.setText(MessageManager.getString("action.create_groups"));
1401 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1402 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1403 .getMenuShortcutKeyMask(), false));
1404 createGroup.addActionListener(new java.awt.event.ActionListener()
1407 public void actionPerformed(ActionEvent e)
1409 createGroup_actionPerformed(e);
1412 unGroup.setText(MessageManager.getString("action.remove_group"));
1413 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1414 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1415 .getMenuShortcutKeyMask()
1416 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1417 unGroup.addActionListener(new java.awt.event.ActionListener()
1420 public void actionPerformed(ActionEvent e)
1422 unGroup_actionPerformed(e);
1425 copy.setText(MessageManager.getString("action.copy"));
1426 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1427 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1428 .getMenuShortcutKeyMask(), false));
1430 copy.addActionListener(new java.awt.event.ActionListener()
1433 public void actionPerformed(ActionEvent e)
1435 copy_actionPerformed(e);
1438 cut.setText(MessageManager.getString("action.cut"));
1439 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1440 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1441 .getMenuShortcutKeyMask(), false));
1442 cut.addActionListener(new java.awt.event.ActionListener()
1445 public void actionPerformed(ActionEvent e)
1447 cut_actionPerformed(e);
1450 delete.setText(MessageManager.getString("action.delete"));
1451 delete.addActionListener(new java.awt.event.ActionListener()
1454 public void actionPerformed(ActionEvent e)
1456 delete_actionPerformed(e);
1459 pasteMenu.setText(MessageManager.getString("action.paste"));
1460 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1461 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1462 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1463 .getMenuShortcutKeyMask()
1464 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1465 pasteNew.addActionListener(new java.awt.event.ActionListener()
1468 public void actionPerformed(ActionEvent e)
1470 pasteNew_actionPerformed(e);
1473 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1474 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1475 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1476 .getMenuShortcutKeyMask(), false));
1477 pasteThis.addActionListener(new java.awt.event.ActionListener()
1480 public void actionPerformed(ActionEvent e)
1482 pasteThis_actionPerformed(e);
1485 applyToAllGroups.setText(MessageManager
1486 .getString("label.apply_colour_to_all_groups"));
1487 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1490 public void actionPerformed(ActionEvent e)
1492 applyToAllGroups_actionPerformed(e);
1495 createPNG.addActionListener(new java.awt.event.ActionListener()
1498 public void actionPerformed(ActionEvent e)
1503 createPNG.setActionCommand(MessageManager
1504 .getString("label.save_png_image"));
1505 createPNG.setText("PNG");
1506 font.setText(MessageManager.getString("action.font"));
1507 font.addActionListener(new java.awt.event.ActionListener()
1510 public void actionPerformed(ActionEvent e)
1512 font_actionPerformed(e);
1515 seqLimits.setText(MessageManager
1516 .getString("label.show_sequence_limits"));
1517 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1518 seqLimits.addActionListener(new java.awt.event.ActionListener()
1521 public void actionPerformed(ActionEvent e)
1523 seqLimit_actionPerformed(e);
1526 epsFile.setText("EPS");
1527 epsFile.addActionListener(new java.awt.event.ActionListener()
1530 public void actionPerformed(ActionEvent e)
1535 LoadtreeMenuItem.setActionCommand(MessageManager
1536 .getString("label.load_tree_for_sequence_set"));
1537 LoadtreeMenuItem.setText(MessageManager
1538 .getString("label.load_associated_tree"));
1539 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1542 public void actionPerformed(ActionEvent e)
1544 LoadtreeMenuItem_actionPerformed(e);
1548 scaleAbove.setVisible(false);
1549 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1550 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1553 public void actionPerformed(ActionEvent e)
1555 scaleAbove_actionPerformed(e);
1558 scaleLeft.setVisible(false);
1559 scaleLeft.setSelected(true);
1560 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1561 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1564 public void actionPerformed(ActionEvent e)
1566 scaleLeft_actionPerformed(e);
1569 scaleRight.setVisible(false);
1570 scaleRight.setSelected(true);
1571 scaleRight.setText(MessageManager.getString("action.scale_right"));
1572 scaleRight.addActionListener(new java.awt.event.ActionListener()
1575 public void actionPerformed(ActionEvent e)
1577 scaleRight_actionPerformed(e);
1580 centreColumnLabelsMenuItem.setVisible(true);
1581 centreColumnLabelsMenuItem.setState(false);
1582 centreColumnLabelsMenuItem.setText(MessageManager
1583 .getString("label.centre_column_labels"));
1584 centreColumnLabelsMenuItem
1585 .addActionListener(new java.awt.event.ActionListener()
1588 public void actionPerformed(ActionEvent e)
1590 centreColumnLabels_actionPerformed(e);
1593 followHighlightMenuItem.setVisible(true);
1594 followHighlightMenuItem.setState(true);
1595 followHighlightMenuItem.setText(MessageManager
1596 .getString("label.automatic_scrolling"));
1597 followHighlightMenuItem.addActionListener(new ActionListener()
1601 public void actionPerformed(ActionEvent e)
1603 followHighlight_actionPerformed();
1608 modifyPID.setText(MessageManager
1609 .getString("label.modify_identity_thereshold"));
1610 modifyPID.addActionListener(new java.awt.event.ActionListener()
1613 public void actionPerformed(ActionEvent e)
1615 modifyPID_actionPerformed(e);
1618 modifyConservation.setText(MessageManager
1619 .getString("label.modify_conservation_thereshold"));
1621 .addActionListener(new java.awt.event.ActionListener()
1624 public void actionPerformed(ActionEvent e)
1626 modifyConservation_actionPerformed(e);
1630 .setText(MessageManager.getString("action.by_tree_order"));
1631 sort.setText(MessageManager.getString("action.sort"));
1632 sort.addMenuListener(new MenuListener()
1635 public void menuSelected(MenuEvent e)
1641 public void menuDeselected(MenuEvent e)
1646 public void menuCanceled(MenuEvent e)
1650 sortByAnnotScore.setText(MessageManager
1651 .getString("label.sort_by_score"));
1652 sort.add(sortByAnnotScore);
1653 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1657 public void menuCanceled(MenuEvent e)
1662 public void menuDeselected(MenuEvent e)
1667 public void menuSelected(MenuEvent e)
1669 buildSortByAnnotationScoresMenu();
1672 sortByAnnotScore.setVisible(false);
1675 .setText(MessageManager.getString("action.calculate_tree"));
1677 jMenu2.setText(MessageManager.getString("label.export_image"));
1678 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1679 padGapsMenuitem.setState(jalview.bin.Cache
1680 .getDefault("PAD_GAPS", false));
1681 padGapsMenuitem.addActionListener(new ActionListener()
1684 public void actionPerformed(ActionEvent e)
1686 padGapsMenuitem_actionPerformed(e);
1689 vamsasStore.setVisible(false);
1690 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1691 vamsasStore.addActionListener(new ActionListener()
1694 public void actionPerformed(ActionEvent e)
1696 vamsasStore_actionPerformed(e);
1699 showTranslation.setText(MessageManager
1700 .getString("label.translate_cDNA"));
1701 showTranslation.addActionListener(new ActionListener()
1704 public void actionPerformed(ActionEvent e)
1706 showTranslation_actionPerformed(e);
1709 extractScores.setText(MessageManager.getString("label.extract_scores")
1711 extractScores.addActionListener(new ActionListener()
1714 public void actionPerformed(ActionEvent e)
1716 extractScores_actionPerformed(e);
1719 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1721 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1723 * showProducts.addActionListener(new ActionListener() {
1725 * public void actionPerformed(ActionEvent e) {
1726 * showProducts_actionPerformed(e); } });
1728 openFeatureSettings.setText(MessageManager
1729 .getString("label.feature_settings"));
1730 openFeatureSettings.addActionListener(new ActionListener()
1733 public void actionPerformed(ActionEvent e)
1735 featureSettings_actionPerformed(e);
1739 .setText(MessageManager.getString("label.fetch_sequences"));
1740 fetchSequence.addActionListener(new ActionListener()
1743 public void actionPerformed(ActionEvent e)
1745 fetchSequence_actionPerformed(e);
1749 annotationColour.setText(MessageManager
1750 .getString("action.by_annotation"));
1751 annotationColour.addActionListener(new ActionListener()
1754 public void actionPerformed(ActionEvent e)
1756 annotationColour_actionPerformed(e);
1760 rnahelicesColour.setText(MessageManager
1761 .getString("action.by_rna_helixes"));
1762 rnahelicesColour.addActionListener(new ActionListener()
1765 public void actionPerformed(ActionEvent e)
1767 rnahelicesColour_actionPerformed(e);
1771 associatedData.setText(MessageManager
1772 .getString("label.load_features_annotations"));
1773 associatedData.addActionListener(new ActionListener()
1776 public void actionPerformed(ActionEvent e)
1778 associatedData_actionPerformed(e);
1781 autoCalculate.setText(MessageManager
1782 .getString("label.autocalculate_consensus"));
1783 autoCalculate.setState(jalview.bin.Cache.getDefault(
1784 "AUTO_CALC_CONSENSUS", true));
1785 autoCalculate.addActionListener(new ActionListener()
1788 public void actionPerformed(ActionEvent e)
1790 autoCalculate_actionPerformed(e);
1793 sortByTree.setText(MessageManager
1794 .getString("label.sort_alignment_new_tree"));
1796 .setToolTipText("<html>"
1798 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1800 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1801 sortByTree.addActionListener(new ActionListener()
1804 public void actionPerformed(ActionEvent e)
1806 sortByTreeOption_actionPerformed(e);
1810 listenToViewSelections.setText(MessageManager
1811 .getString("label.listen_for_selections"));
1812 listenToViewSelections
1813 .setToolTipText("<html>"
1815 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1816 listenToViewSelections.setState(false);
1817 listenToViewSelections.addActionListener(new ActionListener()
1820 public void actionPerformed(ActionEvent e)
1822 listenToViewSelections_actionPerformed(e);
1827 .setText(MessageManager.getString("label.add_sequences"));
1828 addFromFile.setText(MessageManager.getString("label.from_file"));
1829 addFromFile.addActionListener(new ActionListener()
1832 public void actionPerformed(ActionEvent e)
1834 addFromFile_actionPerformed(e);
1837 addFromText.setText(MessageManager.getString("label.from_textbox"));
1838 addFromText.addActionListener(new ActionListener()
1841 public void actionPerformed(ActionEvent e)
1843 addFromText_actionPerformed(e);
1846 addFromURL.setText(MessageManager.getString("label.from_url"));
1847 addFromURL.addActionListener(new ActionListener()
1850 public void actionPerformed(ActionEvent e)
1852 addFromURL_actionPerformed(e);
1855 exportFeatures.setText(MessageManager
1856 .getString("label.export_features"));
1857 exportFeatures.addActionListener(new ActionListener()
1860 public void actionPerformed(ActionEvent e)
1862 exportFeatures_actionPerformed(e);
1865 exportAnnotations.setText(MessageManager
1866 .getString("label.export_annotations"));
1867 exportAnnotations.addActionListener(new ActionListener()
1870 public void actionPerformed(ActionEvent e)
1872 exportAnnotations_actionPerformed(e);
1875 statusPanel.setLayout(gridLayout1);
1876 jMenu3.setText(MessageManager.getString("action.show"));
1877 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1878 showAllSeqs.setToolTipText(MessageManager
1879 .getString("label.toggle_sequence_visibility"));
1880 showAllSeqs.addActionListener(new ActionListener()
1883 public void actionPerformed(ActionEvent e)
1885 showAllSeqs_actionPerformed(e);
1888 showAllColumns.setText(MessageManager.getString("label.all_columns"));
1889 showAllColumns.setToolTipText(MessageManager
1890 .getString("label.toggle_columns_visibility"));
1891 showAllColumns.addActionListener(new ActionListener()
1894 public void actionPerformed(ActionEvent e)
1896 showAllColumns_actionPerformed(e);
1899 hideMenu.setText(MessageManager.getString("action.hide"));
1900 hideSelSequences.setText(MessageManager
1901 .getString("label.selected_sequences"));
1902 hideSelSequences.setToolTipText(MessageManager
1903 .getString("label.toggle_sequence_visibility"));
1904 hideSelSequences.addActionListener(new ActionListener()
1907 public void actionPerformed(ActionEvent e)
1909 hideSelSequences_actionPerformed(e);
1912 hideSelColumns.setText(MessageManager
1913 .getString("label.selected_columns"));
1914 hideSelColumns.setToolTipText(MessageManager
1915 .getString("label.toggle_columns_visibility"));
1916 hideSelColumns.addActionListener(new ActionListener()
1919 public void actionPerformed(ActionEvent e)
1921 hideSelColumns_actionPerformed(e);
1924 hideAllSelection.setText(MessageManager
1925 .getString("label.selected_region"));
1926 hideAllSelection.addActionListener(new ActionListener()
1929 public void actionPerformed(ActionEvent e)
1931 hideAllSelection_actionPerformed(e);
1934 // TODO: should be hidden if no selection exists.
1935 hideAllButSelection.setText(MessageManager
1936 .getString("label.all_but_selected_region"));
1937 hideAllButSelection.addActionListener(new ActionListener()
1940 public void actionPerformed(ActionEvent e)
1942 hideAllButSelection_actionPerformed(e);
1945 showAllhidden.setText(MessageManager
1946 .getString("label.all_sequences_columns"));
1947 showAllhidden.setToolTipText(MessageManager
1948 .getString("label.toggles_visibility_hidden_selected_regions"));
1949 showAllhidden.addActionListener(new ActionListener()
1952 public void actionPerformed(ActionEvent e)
1954 showAllhidden_actionPerformed(e);
1957 hiddenMarkers.setText(MessageManager
1958 .getString("action.show_hidden_markers"));
1959 hiddenMarkers.addActionListener(new ActionListener()
1962 public void actionPerformed(ActionEvent e)
1964 hiddenMarkers_actionPerformed(e);
1967 invertColSel.setText(MessageManager
1968 .getString("action.invert_column_selection"));
1969 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1970 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1971 .getMenuShortcutKeyMask()
1972 | java.awt.event.KeyEvent.ALT_MASK, false));
1973 invertColSel.addActionListener(new ActionListener()
1976 public void actionPerformed(ActionEvent e)
1978 invertColSel_actionPerformed(e);
1981 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1984 public void stateChanged(ChangeEvent evt)
1986 JTabbedPane pane = (JTabbedPane) evt.getSource();
1987 int sel = pane.getSelectedIndex();
1988 tabSelectionChanged(sel);
1991 tabbedPane.addMouseListener(new MouseAdapter()
1994 public void mousePressed(MouseEvent e)
1996 tabbedPane_mousePressed(e);
1999 tabbedPane.addFocusListener(new FocusAdapter()
2002 public void focusGained(FocusEvent e)
2004 tabbedPane_focusGained(e);
2007 save.setText(MessageManager.getString("action.save"));
2008 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2009 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
2010 .getMenuShortcutKeyMask(), false));
2011 save.addActionListener(new ActionListener()
2014 public void actionPerformed(ActionEvent e)
2016 save_actionPerformed(e);
2019 reload.setEnabled(false);
2020 reload.setText(MessageManager.getString("action.reload"));
2021 reload.addActionListener(new ActionListener()
2024 public void actionPerformed(ActionEvent e)
2026 reload_actionPerformed(e);
2029 newView.setText(MessageManager.getString("action.new_view"));
2030 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2031 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2032 .getMenuShortcutKeyMask(), false));
2033 newView.addActionListener(new ActionListener()
2036 public void actionPerformed(ActionEvent e)
2038 newView_actionPerformed(e);
2041 tabbedPane.setToolTipText("<html><i>"
2042 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2044 textColour.setText(MessageManager.getString("label.colour_text")
2046 textColour.addActionListener(new ActionListener()
2049 public void actionPerformed(ActionEvent e)
2051 textColour_actionPerformed(e);
2054 formatMenu.setText(MessageManager.getString("action.format"));
2055 selectMenu.setText(MessageManager.getString("action.select"));
2056 idRightAlign.setText(MessageManager
2057 .getString("label.right_align_sequence_id"));
2058 idRightAlign.addActionListener(new ActionListener()
2061 public void actionPerformed(ActionEvent e)
2063 idRightAlign_actionPerformed(e);
2066 gatherViews.setEnabled(false);
2067 gatherViews.setText(MessageManager.getString("action.gather_views"));
2068 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2069 java.awt.event.KeyEvent.VK_G, 0, false));
2070 gatherViews.addActionListener(new ActionListener()
2073 public void actionPerformed(ActionEvent e)
2075 gatherViews_actionPerformed(e);
2078 expandViews.setEnabled(false);
2079 expandViews.setText(MessageManager.getString("action.expand_views"));
2080 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2081 java.awt.event.KeyEvent.VK_X, 0, false));
2082 expandViews.addActionListener(new ActionListener()
2085 public void actionPerformed(ActionEvent e)
2087 expandViews_actionPerformed(e);
2091 .setText(MessageManager.getString("action.page_setup") + "...");
2092 pageSetup.addActionListener(new ActionListener()
2095 public void actionPerformed(ActionEvent e)
2097 pageSetup_actionPerformed(e);
2100 alignmentProperties.setText(MessageManager
2101 .getString("label.alignment_props") + "...");
2102 alignmentProperties.addActionListener(new ActionListener()
2105 public void actionPerformed(ActionEvent actionEvent)
2107 alignmentProperties();
2110 tooltipSettingsMenu.setText(MessageManager
2111 .getString("label.sequence_id_tooltip"));
2112 autoAnnMenu.setText(MessageManager
2113 .getString("label.autocalculated_annotation"));
2114 alignFrameMenuBar.add(fileMenu);
2115 alignFrameMenuBar.add(editMenu);
2116 alignFrameMenuBar.add(selectMenu);
2117 alignFrameMenuBar.add(viewMenu);
2118 alignFrameMenuBar.add(formatMenu);
2119 alignFrameMenuBar.add(colourMenu);
2120 alignFrameMenuBar.add(calculateMenu);
2121 alignFrameMenuBar.add(webService);
2122 fileMenu.add(fetchSequence);
2123 fileMenu.add(addSequenceMenu);
2124 fileMenu.add(reload);
2125 fileMenu.addSeparator();
2126 fileMenu.add(vamsasStore);
2128 fileMenu.add(saveAs);
2129 fileMenu.add(outputTextboxMenu);
2130 fileMenu.add(pageSetup);
2131 fileMenu.add(printMenuItem);
2132 fileMenu.addSeparator();
2133 fileMenu.add(jMenu2);
2134 fileMenu.add(exportFeatures);
2135 fileMenu.add(exportAnnotations);
2136 fileMenu.add(LoadtreeMenuItem);
2137 fileMenu.add(associatedData);
2138 fileMenu.addSeparator();
2139 fileMenu.add(closeMenuItem);
2140 editMenu.add(undoMenuItem);
2141 editMenu.add(redoMenuItem);
2144 editMenu.add(pasteMenu);
2145 editMenu.add(delete);
2146 editMenu.addSeparator();
2147 editMenu.add(remove2LeftMenuItem);
2148 editMenu.add(remove2RightMenuItem);
2149 editMenu.add(removeGappedColumnMenuItem);
2150 editMenu.add(removeAllGapsMenuItem);
2151 editMenu.add(removeRedundancyMenuItem);
2152 editMenu.addSeparator();
2153 // dont add these yet in the CVS build - they cannot be undone!
2154 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2155 // editMenu.add(justifyLeftMenuItem);
2156 // editMenu.add(justifyRightMenuItem);
2157 // editMenu.addSeparator();
2158 editMenu.add(padGapsMenuitem);
2159 viewMenu.add(newView);
2160 viewMenu.add(expandViews);
2161 viewMenu.add(gatherViews);
2162 viewMenu.addSeparator();
2163 viewMenu.add(jMenu3);
2164 viewMenu.add(hideMenu);
2165 viewMenu.addSeparator();
2166 viewMenu.add(followHighlightMenuItem);
2167 viewMenu.add(annotationPanelMenuItem);
2168 viewMenu.add(showAllAnnotations);
2169 viewMenu.add(hideAllAnnotations);
2170 autoAnnMenu.add(applyAutoAnnotationSettings);
2171 autoAnnMenu.add(showConsensusHistogram);
2172 autoAnnMenu.add(showSequenceLogo);
2173 autoAnnMenu.add(normaliseSequenceLogo);
2174 autoAnnMenu.addSeparator();
2175 autoAnnMenu.add(showGroupConservation);
2176 autoAnnMenu.add(showGroupConsensus);
2177 viewMenu.add(autoAnnMenu);
2178 viewMenu.addSeparator();
2179 viewMenu.add(showSeqFeatures);
2180 // viewMenu.add(showSeqFeaturesHeight);
2182 viewMenu.add(openFeatureSettings);
2183 tooltipSettingsMenu.add(showDbRefsMenuitem);
2184 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2185 viewMenu.add(tooltipSettingsMenu);
2186 viewMenu.addSeparator();
2187 viewMenu.add(alignmentProperties);
2188 viewMenu.addSeparator();
2189 viewMenu.add(overviewMenuItem);
2190 colourMenu.add(applyToAllGroups);
2191 colourMenu.add(textColour);
2192 colourMenu.addSeparator();
2193 colourMenu.add(noColourmenuItem);
2194 colourMenu.add(clustalColour);
2195 colourMenu.add(BLOSUM62Colour);
2196 colourMenu.add(PIDColour);
2197 colourMenu.add(zappoColour);
2198 colourMenu.add(taylorColour);
2199 colourMenu.add(hydrophobicityColour);
2200 colourMenu.add(helixColour);
2201 colourMenu.add(strandColour);
2202 colourMenu.add(turnColour);
2203 colourMenu.add(buriedColour);
2204 colourMenu.add(nucleotideColour);
2205 colourMenu.add(purinePyrimidineColour);
2206 colourMenu.add(RNAInteractionColour);
2207 // colourMenu.add(covariationColour);
2208 colourMenu.add(tcoffeeColour);
2209 colourMenu.add(userDefinedColour);
2210 colourMenu.addSeparator();
2211 colourMenu.add(conservationMenuItem);
2212 colourMenu.add(modifyConservation);
2213 colourMenu.add(abovePIDThreshold);
2214 colourMenu.add(modifyPID);
2215 colourMenu.add(annotationColour);
2216 colourMenu.add(rnahelicesColour);
2217 calculateMenu.add(sort);
2218 calculateMenu.add(calculateTree);
2219 calculateMenu.addSeparator();
2220 calculateMenu.add(pairwiseAlignmentMenuItem);
2221 calculateMenu.add(PCAMenuItem);
2222 calculateMenu.addSeparator();
2223 calculateMenu.add(showTranslation);
2224 calculateMenu.add(showProducts);
2225 calculateMenu.add(autoCalculate);
2226 calculateMenu.add(sortByTree);
2227 calculateMenu.addSeparator();
2228 calculateMenu.add(extractScores);
2229 webServiceNoServices = new JMenuItem(
2230 MessageManager.getString("label.no_services"));
2231 webService.add(webServiceNoServices);
2232 pasteMenu.add(pasteNew);
2233 pasteMenu.add(pasteThis);
2234 sort.add(sortIDMenuItem);
2235 sort.add(sortLengthMenuItem);
2236 sort.add(sortGroupMenuItem);
2237 sort.add(sortPairwiseMenuItem);
2238 sort.add(sortByTreeMenu);
2239 jMenu2.add(htmlMenuItem);
2240 jMenu2.add(epsFile);
2241 jMenu2.add(createPNG);
2242 jMenu2.add(createBioJS);
2243 addSequenceMenu.add(addFromFile);
2244 addSequenceMenu.add(addFromText);
2245 addSequenceMenu.add(addFromURL);
2246 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2247 statusPanel.add(statusBar, null);
2248 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2249 jMenu3.add(showAllColumns);
2250 jMenu3.add(showAllSeqs);
2251 jMenu3.add(showAllhidden);
2252 hideMenu.add(hideSelColumns);
2253 hideMenu.add(hideSelSequences);
2254 hideMenu.add(hideAllSelection);
2255 hideMenu.add(hideAllButSelection);
2257 formatMenu.add(font);
2258 formatMenu.addSeparator();
2259 formatMenu.add(wrapMenuItem);
2260 formatMenu.add(scaleAbove);
2261 formatMenu.add(scaleLeft);
2262 formatMenu.add(scaleRight);
2263 formatMenu.add(seqLimits);
2264 formatMenu.add(idRightAlign);
2265 formatMenu.add(hiddenMarkers);
2266 formatMenu.add(viewBoxesMenuItem);
2267 formatMenu.add(viewTextMenuItem);
2268 formatMenu.add(colourTextMenuItem);
2269 formatMenu.add(renderGapsMenuItem);
2270 formatMenu.add(centreColumnLabelsMenuItem);
2271 formatMenu.add(showNonconservedMenuItem);
2272 selectMenu.add(findMenuItem);
2273 selectMenu.addSeparator();
2274 selectMenu.add(selectAllSequenceMenuItem);
2275 selectMenu.add(deselectAllSequenceMenuItem);
2276 selectMenu.add(invertSequenceMenuItem);
2277 selectMenu.add(invertColSel);
2278 selectMenu.add(createGroup);
2279 selectMenu.add(unGroup);
2280 selectMenu.add(grpsFromSelection);
2281 selectMenu.add(deleteGroups);
2282 calculateMenu.add(expandAlignment);
2283 // TODO - determine if the listenToViewSelections button is needed : see bug
2285 // selectMenu.addSeparator();
2286 // selectMenu.add(listenToViewSelections);
2290 * Action on clicking Show all annotations.
2292 protected void showAllAnnotations_actionPerformed()
2294 setAllAnnotationsVisibility(true);
2298 * Action on clicking Hide all annotations.
2300 protected void hideAllAnnotations_actionPerformed()
2302 setAllAnnotationsVisibility(false);
2306 * Set the visibility of all annotations to true or false.
2310 protected void setAllAnnotationsVisibility(boolean visible)
2315 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2317 // TODO Auto-generated method stub
2321 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2323 // TODO Auto-generated method stub
2327 protected void showAllhidden_actionPerformed(ActionEvent e)
2329 // TODO Auto-generated method stub
2333 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2335 // TODO Auto-generated method stub
2339 protected void hideAllSelection_actionPerformed(ActionEvent e)
2341 // TODO Auto-generated method stub
2345 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2347 // TODO Auto-generated method stub
2351 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2353 // TODO Auto-generated method stub
2357 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2359 // TODO Auto-generated method stub
2363 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2365 // TODO Auto-generated method stub
2369 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2371 // TODO Auto-generated method stub
2375 protected void showGroupConservation_actionPerformed(ActionEvent e)
2377 // TODO Auto-generated method stub
2381 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2383 // TODO Auto-generated method stub
2387 protected void showSeqFeaturesHeight_actionPerformed(
2388 ActionEvent actionEvent)
2390 // TODO Auto-generated method stub
2394 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2396 // TODO Auto-generated method stub
2400 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2402 // TODO Auto-generated method stub
2406 protected void followHighlight_actionPerformed()
2408 // TODO Auto-generated method stub
2412 protected void showNpFeats_actionPerformed(ActionEvent e)
2414 // TODO Auto-generated method stub
2418 protected void showDbRefs_actionPerformed(ActionEvent e)
2420 // TODO Auto-generated method stub
2424 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2428 protected void showProducts_actionPerformed(ActionEvent e)
2432 protected void buildSortByAnnotationScoresMenu()
2436 protected void extractScores_actionPerformed(ActionEvent e)
2440 protected void outputText_actionPerformed(ActionEvent e)
2444 public void addFromFile_actionPerformed(ActionEvent e)
2449 public void addFromText_actionPerformed(ActionEvent e)
2454 public void addFromURL_actionPerformed(ActionEvent e)
2459 public void exportFeatures_actionPerformed(ActionEvent e)
2464 public void exportAnnotations_actionPerformed(ActionEvent e)
2469 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2473 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2478 protected void closeMenuItem_actionPerformed(boolean b)
2482 protected void redoMenuItem_actionPerformed(ActionEvent e)
2486 protected void undoMenuItem_actionPerformed(ActionEvent e)
2490 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2494 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2498 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2502 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2506 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2510 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2514 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2518 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2522 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2526 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2530 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2534 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2538 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2542 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2546 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2550 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2554 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2558 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2562 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2566 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2570 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2574 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2578 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2582 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2586 protected void clustalColour_actionPerformed(ActionEvent e)
2590 protected void zappoColour_actionPerformed(ActionEvent e)
2594 protected void taylorColour_actionPerformed(ActionEvent e)
2598 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2602 protected void helixColour_actionPerformed(ActionEvent e)
2606 protected void strandColour_actionPerformed(ActionEvent e)
2610 protected void turnColour_actionPerformed(ActionEvent e)
2614 protected void buriedColour_actionPerformed(ActionEvent e)
2618 protected void userDefinedColour_actionPerformed(ActionEvent e)
2622 protected void PIDColour_actionPerformed(ActionEvent e)
2626 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2630 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2634 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2639 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2642 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2646 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2650 protected void printMenuItem_actionPerformed(ActionEvent e)
2654 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2658 protected void findMenuItem_actionPerformed(ActionEvent e)
2662 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2666 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2670 protected void nucleotideColour_actionPerformed(ActionEvent e)
2674 protected void deleteGroups_actionPerformed(ActionEvent e)
2678 protected void createGroup_actionPerformed(ActionEvent e)
2682 protected void unGroup_actionPerformed(ActionEvent e)
2686 protected void copy_actionPerformed(ActionEvent e)
2690 protected void cut_actionPerformed(ActionEvent e)
2694 protected void delete_actionPerformed(ActionEvent e)
2698 protected void pasteNew_actionPerformed(ActionEvent e)
2702 protected void pasteThis_actionPerformed(ActionEvent e)
2706 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2710 public void createPNG(java.io.File f)
2714 protected void font_actionPerformed(ActionEvent e)
2718 protected void seqLimit_actionPerformed(ActionEvent e)
2722 public void seqDBRef_actionPerformed(ActionEvent e)
2727 public void createEPS(java.io.File f)
2731 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2737 * Template method to handle the 'load T-Coffee scores' menu event.
2739 * Subclasses override this method to provide a custom action.
2744 protected void loadScores_actionPerformed(ActionEvent event)
2750 * Template method to handle the 'Color T-Coffee scores' menu event.
2752 * Subclasses override this method to provide a custom action.
2757 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2762 protected void jpred_actionPerformed(ActionEvent e)
2766 protected void scaleAbove_actionPerformed(ActionEvent e)
2770 protected void scaleLeft_actionPerformed(ActionEvent e)
2774 protected void scaleRight_actionPerformed(ActionEvent e)
2778 protected void modifyPID_actionPerformed(ActionEvent e)
2782 protected void modifyConservation_actionPerformed(ActionEvent e)
2786 protected void saveAs_actionPerformed(ActionEvent e)
2790 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2794 public void vamsasStore_actionPerformed(ActionEvent e)
2799 public void vamsasLoad_actionPerformed(ActionEvent e)
2804 public void showTranslation_actionPerformed(ActionEvent e)
2809 public void featureSettings_actionPerformed(ActionEvent e)
2814 public void fetchSequence_actionPerformed(ActionEvent e)
2819 public void smoothFont_actionPerformed(ActionEvent e)
2824 public void annotationColour_actionPerformed(ActionEvent e)
2829 public void rnahelicesColour_actionPerformed(ActionEvent e)
2834 public void associatedData_actionPerformed(ActionEvent e)
2839 public void autoCalculate_actionPerformed(ActionEvent e)
2844 public void sortByTreeOption_actionPerformed(ActionEvent e)
2849 public void showAllSeqs_actionPerformed(ActionEvent e)
2854 public void showAllColumns_actionPerformed(ActionEvent e)
2859 public void hideSelSequences_actionPerformed(ActionEvent e)
2864 public void hideSelColumns_actionPerformed(ActionEvent e)
2869 public void hiddenMarkers_actionPerformed(ActionEvent e)
2874 public void findPdbId_actionPerformed(ActionEvent e)
2879 public void enterPdbId_actionPerformed(ActionEvent e)
2884 public void pdbFile_actionPerformed(ActionEvent e)
2889 public void invertColSel_actionPerformed(ActionEvent e)
2894 public void tabSelectionChanged(int sel)
2899 public void tabbedPane_mousePressed(MouseEvent e)
2904 public void tabbedPane_focusGained(FocusEvent e)
2909 public void save_actionPerformed(ActionEvent e)
2914 public void reload_actionPerformed(ActionEvent e)
2919 public void newView_actionPerformed(ActionEvent e)
2924 public void textColour_actionPerformed(ActionEvent e)
2929 public void idRightAlign_actionPerformed(ActionEvent e)
2934 public void expandViews_actionPerformed(ActionEvent e)
2939 public void gatherViews_actionPerformed(ActionEvent e)
2944 public void buildTreeMenu()
2949 public void pageSetup_actionPerformed(ActionEvent e)
2954 public void alignmentProperties()
2959 protected void expand_newalign(ActionEvent e)
2961 // TODO Auto-generated method stub