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 protected JMenuItem font = new JMenuItem();
215 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
217 JMenuItem epsFile = new JMenuItem();
219 JMenuItem LoadtreeMenuItem = new JMenuItem();
221 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
223 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
225 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
227 protected JMenuItem modifyPID = new JMenuItem();
229 protected JMenuItem modifyConservation = new JMenuItem();
231 protected JMenu sortByTreeMenu = new JMenu();
233 protected JMenu sort = new JMenu();
235 protected JMenu calculateTree = new JMenu();
237 JMenu jMenu2 = new JMenu();
239 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
241 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
243 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
245 protected ButtonGroup colours = new ButtonGroup();
247 JMenuItem vamsasStore = new JMenuItem();
249 protected JMenuItem showTranslation = new JMenuItem();
251 protected JMenuItem extractScores = new JMenuItem();
253 protected JMenuItem expandAlignment = new JMenuItem();
255 protected JMenu showProducts = new JMenu();
257 public JMenuItem openFeatureSettings = new JMenuItem();
259 JMenuItem fetchSequence = new JMenuItem();
261 JMenuItem annotationColour = new JMenuItem();
263 protected JMenuItem rnahelicesColour = new JMenuItem();
265 JMenuItem associatedData = new JMenuItem();
267 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
269 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
271 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
273 JMenu addSequenceMenu = new JMenu();
275 JMenuItem addFromFile = new JMenuItem();
277 JMenuItem addFromText = new JMenuItem();
279 JMenuItem addFromURL = new JMenuItem();
281 JMenuItem exportAnnotations = new JMenuItem();
283 JMenuItem exportFeatures = new JMenuItem();
285 protected JPanel statusPanel = new JPanel();
287 GridLayout gridLayout1 = new GridLayout();
289 JMenu jMenu3 = new JMenu();
291 JMenuItem showAllSeqs = new JMenuItem();
293 JMenuItem showAllColumns = new JMenuItem();
295 JMenu hideMenu = new JMenu();
297 JMenuItem hideSelSequences = new JMenuItem();
299 JMenuItem hideSelColumns = new JMenuItem();
301 JMenuItem hideAllButSelection = new JMenuItem();
303 JMenuItem hideAllSelection = new JMenuItem();
305 JMenuItem showAllhidden = new JMenuItem();
307 protected JMenuItem showAllAnnotations = new JMenuItem();
309 protected JMenuItem hideAllAnnotations = new JMenuItem();
311 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
313 JMenuItem invertColSel = new JMenuItem();
315 protected JTabbedPane tabbedPane = new JTabbedPane();
317 JMenuItem save = new JMenuItem();
319 protected JMenuItem reload = new JMenuItem();
321 JMenuItem newView = new JMenuItem();
323 JMenuItem textColour = new JMenuItem();
325 JMenu formatMenu = new JMenu();
327 JMenu selectMenu = new JMenu();
329 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
331 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
333 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
335 protected JMenuItem gatherViews = new JMenuItem();
337 protected JMenuItem expandViews = new JMenuItem();
339 JMenuItem pageSetup = new JMenuItem();
341 JMenuItem alignmentProperties = new JMenuItem();
343 JMenu tooltipSettingsMenu = new JMenu();
345 private JMenuItem justifyLeftMenuItem = new JMenuItem();
347 private JMenuItem justifyRightMenuItem = new JMenuItem();
349 JMenu autoAnnMenu = new JMenu();
351 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
353 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
355 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
357 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
359 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
361 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
363 private JMenuItem grpsFromSelection = new JMenuItem();
370 setJMenuBar(alignFrameMenuBar);
372 // dynamically fill save as menu with available formats
373 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
375 JMenuItem item = new JMenuItem(
376 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
378 item.addActionListener(new java.awt.event.ActionListener()
381 public void actionPerformed(ActionEvent e)
383 outputText_actionPerformed(e);
387 outputTextboxMenu.add(item);
389 } catch (Exception e)
391 System.err.println(e.toString());
394 if (!new jalview.util.Platform().isAMac())
396 closeMenuItem.setMnemonic('C');
397 outputTextboxMenu.setMnemonic('T');
398 undoMenuItem.setMnemonic('Z');
399 redoMenuItem.setMnemonic('0');
400 copy.setMnemonic('C');
401 cut.setMnemonic('U');
402 pasteMenu.setMnemonic('P');
403 reload.setMnemonic('R');
406 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
408 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
409 .getUserColourSchemes().keys();
411 while (userColours.hasMoreElements())
413 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
414 userColours.nextElement().toString());
415 radioItem.setName("USER_DEFINED");
416 radioItem.addMouseListener(new MouseAdapter()
419 public void mousePressed(MouseEvent evt)
421 if (evt.isControlDown()
422 || SwingUtilities.isRightMouseButton(evt))
424 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
426 int option = JOptionPane.showInternalConfirmDialog(
427 jalview.gui.Desktop.desktop,
429 .getString("label.remove_from_default_list"),
431 .getString("label.remove_user_defined_colour"),
432 JOptionPane.YES_NO_OPTION);
433 if (option == JOptionPane.YES_OPTION)
435 jalview.gui.UserDefinedColours
436 .removeColourFromDefaults(radioItem.getText());
437 colourMenu.remove(radioItem);
441 radioItem.addActionListener(new ActionListener()
444 public void actionPerformed(ActionEvent evt)
446 userDefinedColour_actionPerformed(evt);
453 radioItem.addActionListener(new ActionListener()
456 public void actionPerformed(ActionEvent evt)
458 userDefinedColour_actionPerformed(evt);
461 colourMenu.insert(radioItem, 15);
462 colours.add(radioItem);
465 colours.add(noColourmenuItem);
466 colours.add(clustalColour);
467 colours.add(zappoColour);
468 colours.add(taylorColour);
469 colours.add(hydrophobicityColour);
470 colours.add(helixColour);
471 colours.add(strandColour);
472 colours.add(turnColour);
473 colours.add(buriedColour);
474 colours.add(userDefinedColour);
475 colours.add(PIDColour);
476 colours.add(BLOSUM62Colour);
477 colours.add(nucleotideColour);
478 colours.add(purinePyrimidineColour);
479 // colours.add(covariationColour);
480 colours.add(tcoffeeColour);
481 colours.add(RNAInteractionColour);
482 setColourSelected(jalview.bin.Cache
483 .getDefault("DEFAULT_COLOUR", "None"));
487 public void setColourSelected(String defaultColour)
490 if (defaultColour != null)
492 int index = ColourSchemeProperty
493 .getColourIndexFromName(defaultColour);
497 case ColourSchemeProperty.CLUSTAL:
498 clustalColour.setSelected(true);
502 case ColourSchemeProperty.BLOSUM:
503 BLOSUM62Colour.setSelected(true);
507 case ColourSchemeProperty.PID:
508 PIDColour.setSelected(true);
512 case ColourSchemeProperty.ZAPPO:
513 zappoColour.setSelected(true);
517 case ColourSchemeProperty.TAYLOR:
518 taylorColour.setSelected(true);
521 case ColourSchemeProperty.HYDROPHOBIC:
522 hydrophobicityColour.setSelected(true);
526 case ColourSchemeProperty.HELIX:
527 helixColour.setSelected(true);
531 case ColourSchemeProperty.STRAND:
532 strandColour.setSelected(true);
536 case ColourSchemeProperty.TURN:
537 turnColour.setSelected(true);
541 case ColourSchemeProperty.BURIED:
542 buriedColour.setSelected(true);
546 case ColourSchemeProperty.NUCLEOTIDE:
547 nucleotideColour.setSelected(true);
551 case ColourSchemeProperty.TCOFFEE:
552 tcoffeeColour.setSelected(true);
555 case ColourSchemeProperty.PURINEPYRIMIDINE:
556 purinePyrimidineColour.setSelected(true);
560 case ColourSchemeProperty.RNAINTERACTION:
561 RNAInteractionColour.setSelected(true);
565 * case ColourSchemeProperty.COVARIATION:
566 * covariationColour.setSelected(true);
570 case ColourSchemeProperty.USER_DEFINED:
571 userDefinedColour.setSelected(true);
574 case ColourSchemeProperty.NONE:
576 noColourmenuItem.setSelected(true);
584 private void jbInit() throws Exception
586 fileMenu.setText(MessageManager.getString("action.file"));
587 saveAs.setText(MessageManager.getString("action.save_as") + "...");
588 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
589 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
590 .getMenuShortcutKeyMask()
591 | java.awt.event.KeyEvent.SHIFT_MASK, false));
592 saveAs.addActionListener(new ActionListener()
595 public void actionPerformed(ActionEvent e)
597 saveAs_actionPerformed(e);
600 closeMenuItem.setText(MessageManager.getString("action.close"));
601 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
602 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
603 .getMenuShortcutKeyMask(), false));
604 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
607 public void actionPerformed(ActionEvent e)
609 closeMenuItem_actionPerformed(false);
612 editMenu.setText(MessageManager.getString("action.edit"));
613 viewMenu.setText(MessageManager.getString("action.view"));
614 colourMenu.setText(MessageManager.getString("action.colour"));
615 calculateMenu.setText(MessageManager.getString("action.calculate"));
616 webService.setText(MessageManager.getString("action.web_service"));
617 selectAllSequenceMenuItem.setText(MessageManager
618 .getString("action.select_all"));
619 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
620 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
621 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
622 selectAllSequenceMenuItem
623 .addActionListener(new java.awt.event.ActionListener()
626 public void actionPerformed(ActionEvent e)
628 selectAllSequenceMenuItem_actionPerformed(e);
631 deselectAllSequenceMenuItem.setText(MessageManager
632 .getString("action.deselect_all"));
633 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
634 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
635 deselectAllSequenceMenuItem
636 .addActionListener(new java.awt.event.ActionListener()
639 public void actionPerformed(ActionEvent e)
641 deselectAllSequenceMenuItem_actionPerformed(e);
644 invertSequenceMenuItem.setText(MessageManager
645 .getString("action.invert_sequence_selection"));
646 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
647 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
648 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
649 invertSequenceMenuItem
650 .addActionListener(new java.awt.event.ActionListener()
653 public void actionPerformed(ActionEvent e)
655 invertSequenceMenuItem_actionPerformed(e);
658 grpsFromSelection.setText(MessageManager
659 .getString("action.make_groups_selection"));
660 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
663 public void actionPerformed(ActionEvent e)
665 makeGrpsFromSelection_actionPerformed(e);
668 expandAlignment.setText(MessageManager
669 .getString("action.view_flanking_regions"));
670 expandAlignment.setToolTipText(MessageManager
671 .getString("label.view_flanking_regions"));
672 expandAlignment.addActionListener(new java.awt.event.ActionListener()
675 public void actionPerformed(ActionEvent e)
680 remove2LeftMenuItem.setText(MessageManager
681 .getString("action.remove_left"));
682 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
683 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
684 .getMenuShortcutKeyMask(), false));
686 .addActionListener(new java.awt.event.ActionListener()
689 public void actionPerformed(ActionEvent e)
691 remove2LeftMenuItem_actionPerformed(e);
694 remove2RightMenuItem.setText(MessageManager
695 .getString("action.remove_right"));
696 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
697 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
698 .getMenuShortcutKeyMask(), false));
700 .addActionListener(new java.awt.event.ActionListener()
703 public void actionPerformed(ActionEvent e)
705 remove2RightMenuItem_actionPerformed(e);
708 removeGappedColumnMenuItem.setText(MessageManager
709 .getString("action.remove_empty_columns"));
710 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
711 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
712 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
713 removeGappedColumnMenuItem
714 .addActionListener(new java.awt.event.ActionListener()
717 public void actionPerformed(ActionEvent e)
719 removeGappedColumnMenuItem_actionPerformed(e);
722 removeAllGapsMenuItem.setText(MessageManager
723 .getString("action.remove_all_gaps"));
724 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
725 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
726 .getDefaultToolkit().getMenuShortcutKeyMask()
727 | java.awt.event.KeyEvent.SHIFT_MASK, false));
728 removeAllGapsMenuItem
729 .addActionListener(new java.awt.event.ActionListener()
732 public void actionPerformed(ActionEvent e)
734 removeAllGapsMenuItem_actionPerformed(e);
737 justifyLeftMenuItem.setText(MessageManager
738 .getString("action.left_justify_alignment"));
740 .addActionListener(new java.awt.event.ActionListener()
743 public void actionPerformed(ActionEvent e)
745 justifyLeftMenuItem_actionPerformed(e);
748 justifyRightMenuItem.setText(MessageManager
749 .getString("action.right_justify_alignment"));
751 .addActionListener(new java.awt.event.ActionListener()
754 public void actionPerformed(ActionEvent e)
756 justifyRightMenuItem_actionPerformed(e);
759 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
760 viewBoxesMenuItem.setState(true);
761 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
764 public void actionPerformed(ActionEvent e)
766 viewBoxesMenuItem_actionPerformed(e);
769 viewTextMenuItem.setText(MessageManager.getString("action.text"));
770 viewTextMenuItem.setState(true);
771 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
774 public void actionPerformed(ActionEvent e)
776 viewTextMenuItem_actionPerformed(e);
779 showNonconservedMenuItem.setText(MessageManager
780 .getString("label.show_non_conversed"));
781 showNonconservedMenuItem.setState(false);
782 showNonconservedMenuItem
783 .addActionListener(new java.awt.event.ActionListener()
786 public void actionPerformed(ActionEvent e)
788 showUnconservedMenuItem_actionPerformed(e);
791 sortPairwiseMenuItem.setText(MessageManager
792 .getString("action.by_pairwise_id"));
794 .addActionListener(new java.awt.event.ActionListener()
797 public void actionPerformed(ActionEvent e)
799 sortPairwiseMenuItem_actionPerformed(e);
802 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
803 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
806 public void actionPerformed(ActionEvent e)
808 sortIDMenuItem_actionPerformed(e);
812 .setText(MessageManager.getString("action.by_length"));
814 .addActionListener(new java.awt.event.ActionListener()
817 public void actionPerformed(ActionEvent e)
819 sortLengthMenuItem_actionPerformed(e);
822 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
823 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
826 public void actionPerformed(ActionEvent e)
828 sortGroupMenuItem_actionPerformed(e);
831 removeRedundancyMenuItem.setText(MessageManager
832 .getString("action.remove_redundancy").concat("..."));
833 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
834 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
835 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
836 removeRedundancyMenuItem
837 .addActionListener(new java.awt.event.ActionListener()
840 public void actionPerformed(ActionEvent e)
842 removeRedundancyMenuItem_actionPerformed(e);
845 pairwiseAlignmentMenuItem.setText(MessageManager
846 .getString("action.pairwise_alignment"));
847 pairwiseAlignmentMenuItem
848 .addActionListener(new java.awt.event.ActionListener()
851 public void actionPerformed(ActionEvent e)
853 pairwiseAlignmentMenuItem_actionPerformed(e);
856 PCAMenuItem.setText(MessageManager
857 .getString("label.principal_component_analysis"));
858 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
861 public void actionPerformed(ActionEvent e)
863 PCAMenuItem_actionPerformed(e);
866 averageDistanceTreeMenuItem.setText(MessageManager
867 .getString("label.average_distance_identity"));
868 averageDistanceTreeMenuItem
869 .addActionListener(new java.awt.event.ActionListener()
872 public void actionPerformed(ActionEvent e)
874 averageDistanceTreeMenuItem_actionPerformed(e);
877 neighbourTreeMenuItem.setText(MessageManager
878 .getString("label.neighbour_joining_identity"));
879 neighbourTreeMenuItem
880 .addActionListener(new java.awt.event.ActionListener()
883 public void actionPerformed(ActionEvent e)
885 neighbourTreeMenuItem_actionPerformed(e);
888 this.getContentPane().setLayout(borderLayout1);
889 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
890 statusBar.setBackground(Color.white);
891 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
892 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
893 statusBar.setText(MessageManager.getString("label.status_bar"));
894 outputTextboxMenu.setText(MessageManager
895 .getString("label.out_to_textbox"));
896 clustalColour.setText(MessageManager.getString("label.clustalx"));
898 clustalColour.addActionListener(new java.awt.event.ActionListener()
901 public void actionPerformed(ActionEvent e)
903 clustalColour_actionPerformed(e);
906 zappoColour.setText(MessageManager.getString("label.zappo"));
907 zappoColour.addActionListener(new java.awt.event.ActionListener()
910 public void actionPerformed(ActionEvent e)
912 zappoColour_actionPerformed(e);
915 taylorColour.setText(MessageManager.getString("label.taylor"));
916 taylorColour.addActionListener(new java.awt.event.ActionListener()
919 public void actionPerformed(ActionEvent e)
921 taylorColour_actionPerformed(e);
924 hydrophobicityColour.setText(MessageManager
925 .getString("label.hydrophobicity"));
927 .addActionListener(new java.awt.event.ActionListener()
930 public void actionPerformed(ActionEvent e)
932 hydrophobicityColour_actionPerformed(e);
935 helixColour.setText(MessageManager.getString("label.helix_propensity"));
936 helixColour.addActionListener(new java.awt.event.ActionListener()
939 public void actionPerformed(ActionEvent e)
941 helixColour_actionPerformed(e);
944 strandColour.setText(MessageManager
945 .getString("label.strand_propensity"));
946 strandColour.addActionListener(new java.awt.event.ActionListener()
949 public void actionPerformed(ActionEvent e)
951 strandColour_actionPerformed(e);
954 turnColour.setText(MessageManager.getString("label.turn_propensity"));
955 turnColour.addActionListener(new java.awt.event.ActionListener()
958 public void actionPerformed(ActionEvent e)
960 turnColour_actionPerformed(e);
963 buriedColour.setText(MessageManager.getString("label.buried_index"));
964 buriedColour.addActionListener(new java.awt.event.ActionListener()
967 public void actionPerformed(ActionEvent e)
969 buriedColour_actionPerformed(e);
972 userDefinedColour.setText(MessageManager
973 .getString("action.user_defined"));
974 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
977 public void actionPerformed(ActionEvent e)
979 userDefinedColour_actionPerformed(e);
983 .setText(MessageManager.getString("label.percentage_identity"));
984 PIDColour.addActionListener(new java.awt.event.ActionListener()
987 public void actionPerformed(ActionEvent e)
989 PIDColour_actionPerformed(e);
993 .setText(MessageManager.getString("label.blosum62_score"));
994 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
997 public void actionPerformed(ActionEvent e)
999 BLOSUM62Colour_actionPerformed(e);
1002 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1003 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1006 public void actionPerformed(ActionEvent e)
1008 nucleotideColour_actionPerformed(e);
1012 purinePyrimidineColour.setText(MessageManager
1013 .getString("label.purine_pyrimidine"));
1014 purinePyrimidineColour
1015 .addActionListener(new java.awt.event.ActionListener()
1018 public void actionPerformed(ActionEvent e)
1020 purinePyrimidineColour_actionPerformed(e);
1024 RNAInteractionColour.setText("RNA Interaction type");
1025 RNAInteractionColour
1026 .addActionListener(new java.awt.event.ActionListener()
1029 public void actionPerformed(ActionEvent e)
1031 RNAInteractionColour_actionPerformed(e);
1035 * covariationColour.setText("Covariation");
1036 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1037 * public void actionPerformed(ActionEvent e) {
1038 * covariationColour_actionPerformed(e); } });
1041 avDistanceTreeBlosumMenuItem.setText(MessageManager
1042 .getString("label.average_distance_bloslum62"));
1043 avDistanceTreeBlosumMenuItem
1044 .addActionListener(new java.awt.event.ActionListener()
1047 public void actionPerformed(ActionEvent e)
1049 avTreeBlosumMenuItem_actionPerformed(e);
1052 njTreeBlosumMenuItem.setText(MessageManager
1053 .getString("label.neighbour_blosum62"));
1054 njTreeBlosumMenuItem
1055 .addActionListener(new java.awt.event.ActionListener()
1058 public void actionPerformed(ActionEvent e)
1060 njTreeBlosumMenuItem_actionPerformed(e);
1063 annotationPanelMenuItem.setActionCommand("");
1064 annotationPanelMenuItem.setText(MessageManager
1065 .getString("label.show_annotations"));
1066 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1068 annotationPanelMenuItem.addActionListener(new ActionListener()
1071 public void actionPerformed(ActionEvent e)
1073 annotationPanelMenuItem_actionPerformed(e);
1077 * Show/hide all annotations only enabled if annotation panel is shown
1079 showAllAnnotations.setText(MessageManager
1080 .getString("label.show_all_annotations"));
1081 showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
1082 showAllAnnotations.addActionListener(new ActionListener()
1085 public void actionPerformed(ActionEvent e)
1087 showAllAnnotations_actionPerformed();
1090 hideAllAnnotations.setText(MessageManager
1091 .getString("label.hide_all_annotations"));
1092 hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
1093 hideAllAnnotations.addActionListener(new ActionListener()
1096 public void actionPerformed(ActionEvent e)
1098 hideAllAnnotations_actionPerformed();
1101 colourTextMenuItem.setText(MessageManager
1102 .getString("label.colour_text"));
1104 .addActionListener(new java.awt.event.ActionListener()
1107 public void actionPerformed(ActionEvent e)
1109 colourTextMenuItem_actionPerformed(e);
1112 htmlMenuItem.setText(MessageManager.getString("label.html"));
1113 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1116 public void actionPerformed(ActionEvent e)
1118 htmlMenuItem_actionPerformed(e);
1121 overviewMenuItem.setText(MessageManager
1122 .getString("label.overview_window"));
1123 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1126 public void actionPerformed(ActionEvent e)
1128 overviewMenuItem_actionPerformed(e);
1131 undoMenuItem.setEnabled(false);
1132 undoMenuItem.setText(MessageManager.getString("action.undo"));
1133 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1134 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1135 .getMenuShortcutKeyMask(), false));
1136 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1139 public void actionPerformed(ActionEvent e)
1141 undoMenuItem_actionPerformed(e);
1144 redoMenuItem.setEnabled(false);
1145 redoMenuItem.setText(MessageManager.getString("action.redo"));
1146 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1147 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1148 .getMenuShortcutKeyMask(), false));
1149 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1152 public void actionPerformed(ActionEvent e)
1154 redoMenuItem_actionPerformed(e);
1157 conservationMenuItem.setText(MessageManager
1158 .getString("action.by_conservation"));
1159 conservationMenuItem
1160 .addActionListener(new java.awt.event.ActionListener()
1163 public void actionPerformed(ActionEvent e)
1165 conservationMenuItem_actionPerformed(e);
1168 noColourmenuItem.setText(MessageManager.getString("label.none"));
1169 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1172 public void actionPerformed(ActionEvent e)
1174 noColourmenuItem_actionPerformed(e);
1177 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1178 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1181 public void actionPerformed(ActionEvent e)
1183 wrapMenuItem_actionPerformed(e);
1186 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1187 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1188 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1189 .getMenuShortcutKeyMask(), false));
1190 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1193 public void actionPerformed(ActionEvent e)
1195 printMenuItem_actionPerformed(e);
1199 .setText(MessageManager.getString("action.show_gaps"));
1200 renderGapsMenuItem.setState(true);
1202 .addActionListener(new java.awt.event.ActionListener()
1205 public void actionPerformed(ActionEvent e)
1207 renderGapsMenuItem_actionPerformed(e);
1210 findMenuItem.setText(MessageManager.getString("action.find"));
1211 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1212 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1213 .getMenuShortcutKeyMask(), false));
1214 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1215 MessageManager.getString("label.find_tip")));
1216 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1219 public void actionPerformed(ActionEvent e)
1221 findMenuItem_actionPerformed(e);
1224 abovePIDThreshold.setText(MessageManager
1225 .getString("label.above_identity_threshold"));
1226 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1229 public void actionPerformed(ActionEvent e)
1231 abovePIDThreshold_actionPerformed(e);
1234 showSeqFeatures.setText(MessageManager
1235 .getString("label.show_sequence_features"));
1236 showSeqFeatures.addActionListener(new ActionListener()
1239 public void actionPerformed(ActionEvent actionEvent)
1241 showSeqFeatures_actionPerformed(actionEvent);
1245 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1246 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1247 * void actionPerformed(ActionEvent actionEvent) {
1248 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1250 showDbRefsMenuitem.setText(MessageManager
1251 .getString("label.show_database_refs"));
1252 showDbRefsMenuitem.addActionListener(new ActionListener()
1256 public void actionPerformed(ActionEvent e)
1258 showDbRefs_actionPerformed(e);
1262 showNpFeatsMenuitem.setText(MessageManager
1263 .getString("label.show_non_positional_features"));
1264 showNpFeatsMenuitem.addActionListener(new ActionListener()
1268 public void actionPerformed(ActionEvent e)
1270 showNpFeats_actionPerformed(e);
1274 showGroupConservation.setText(MessageManager
1275 .getString("label.group_conservation"));
1276 showGroupConservation.addActionListener(new ActionListener()
1280 public void actionPerformed(ActionEvent e)
1282 showGroupConservation_actionPerformed(e);
1287 showGroupConsensus.setText(MessageManager
1288 .getString("label.group_consensus"));
1289 showGroupConsensus.addActionListener(new ActionListener()
1293 public void actionPerformed(ActionEvent e)
1295 showGroupConsensus_actionPerformed(e);
1299 showConsensusHistogram.setText(MessageManager
1300 .getString("label.show_consensus_histogram"));
1301 showConsensusHistogram.addActionListener(new ActionListener()
1305 public void actionPerformed(ActionEvent e)
1307 showConsensusHistogram_actionPerformed(e);
1311 showSequenceLogo.setText(MessageManager
1312 .getString("label.show_consensus_logo"));
1313 showSequenceLogo.addActionListener(new ActionListener()
1317 public void actionPerformed(ActionEvent e)
1319 showSequenceLogo_actionPerformed(e);
1323 normaliseSequenceLogo.setText(MessageManager
1324 .getString("label.norm_consensus_logo"));
1325 normaliseSequenceLogo.addActionListener(new ActionListener()
1329 public void actionPerformed(ActionEvent e)
1331 normaliseSequenceLogo_actionPerformed(e);
1335 applyAutoAnnotationSettings.setText(MessageManager
1336 .getString("label.apply_all_groups"));
1337 applyAutoAnnotationSettings.setState(false);
1338 applyAutoAnnotationSettings.setVisible(true);
1339 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1343 public void actionPerformed(ActionEvent e)
1345 applyAutoAnnotationSettings_actionPerformed(e);
1350 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1351 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1354 public void actionPerformed(ActionEvent e)
1356 nucleotideColour_actionPerformed(e);
1360 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1361 tcoffeeColour.setEnabled(false);
1362 tcoffeeColour.addActionListener(new ActionListener()
1366 public void actionPerformed(ActionEvent e)
1368 tcoffeeColorScheme_actionPerformed(e);
1373 .setText(MessageManager.getString("action.undefine_groups"));
1374 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1375 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1376 .getMenuShortcutKeyMask(), false));
1377 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1380 public void actionPerformed(ActionEvent e)
1382 deleteGroups_actionPerformed(e);
1385 createGroup.setText(MessageManager.getString("action.create_groups"));
1386 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1387 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1388 .getMenuShortcutKeyMask(), false));
1389 createGroup.addActionListener(new java.awt.event.ActionListener()
1392 public void actionPerformed(ActionEvent e)
1394 createGroup_actionPerformed(e);
1397 unGroup.setText(MessageManager.getString("action.remove_group"));
1398 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1399 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1400 .getMenuShortcutKeyMask()
1401 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1402 unGroup.addActionListener(new java.awt.event.ActionListener()
1405 public void actionPerformed(ActionEvent e)
1407 unGroup_actionPerformed(e);
1410 copy.setText(MessageManager.getString("action.copy"));
1411 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1412 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1413 .getMenuShortcutKeyMask(), false));
1415 copy.addActionListener(new java.awt.event.ActionListener()
1418 public void actionPerformed(ActionEvent e)
1420 copy_actionPerformed(e);
1423 cut.setText(MessageManager.getString("action.cut"));
1424 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1425 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1426 .getMenuShortcutKeyMask(), false));
1427 cut.addActionListener(new java.awt.event.ActionListener()
1430 public void actionPerformed(ActionEvent e)
1432 cut_actionPerformed(e);
1435 delete.setText(MessageManager.getString("action.delete"));
1436 delete.addActionListener(new java.awt.event.ActionListener()
1439 public void actionPerformed(ActionEvent e)
1441 delete_actionPerformed(e);
1444 pasteMenu.setText(MessageManager.getString("action.paste"));
1445 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1446 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1447 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1448 .getMenuShortcutKeyMask()
1449 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1450 pasteNew.addActionListener(new java.awt.event.ActionListener()
1453 public void actionPerformed(ActionEvent e)
1455 pasteNew_actionPerformed(e);
1458 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1459 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1460 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1461 .getMenuShortcutKeyMask(), false));
1462 pasteThis.addActionListener(new java.awt.event.ActionListener()
1465 public void actionPerformed(ActionEvent e)
1467 pasteThis_actionPerformed(e);
1470 applyToAllGroups.setText(MessageManager
1471 .getString("label.apply_colour_to_all_groups"));
1472 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1475 public void actionPerformed(ActionEvent e)
1477 applyToAllGroups_actionPerformed(e);
1480 createPNG.addActionListener(new java.awt.event.ActionListener()
1483 public void actionPerformed(ActionEvent e)
1488 createPNG.setActionCommand(MessageManager
1489 .getString("label.save_png_image"));
1490 createPNG.setText("PNG");
1491 font.setText(MessageManager.getString("action.font"));
1492 font.addActionListener(new java.awt.event.ActionListener()
1495 public void actionPerformed(ActionEvent e)
1497 font_actionPerformed(e);
1501 seqLimits.setText(MessageManager
1502 .getString("label.show_sequence_limits"));
1503 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1504 seqLimits.addActionListener(new java.awt.event.ActionListener()
1507 public void actionPerformed(ActionEvent e)
1509 seqLimit_actionPerformed(e);
1512 epsFile.setText("EPS");
1513 epsFile.addActionListener(new java.awt.event.ActionListener()
1516 public void actionPerformed(ActionEvent e)
1521 LoadtreeMenuItem.setActionCommand(MessageManager
1522 .getString("label.load_tree_for_sequence_set"));
1523 LoadtreeMenuItem.setText(MessageManager
1524 .getString("label.load_associated_tree"));
1525 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1528 public void actionPerformed(ActionEvent e)
1530 LoadtreeMenuItem_actionPerformed(e);
1534 scaleAbove.setVisible(false);
1535 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1536 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1539 public void actionPerformed(ActionEvent e)
1541 scaleAbove_actionPerformed(e);
1544 scaleLeft.setVisible(false);
1545 scaleLeft.setSelected(true);
1546 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1547 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1550 public void actionPerformed(ActionEvent e)
1552 scaleLeft_actionPerformed(e);
1555 scaleRight.setVisible(false);
1556 scaleRight.setSelected(true);
1557 scaleRight.setText(MessageManager.getString("action.scale_right"));
1558 scaleRight.addActionListener(new java.awt.event.ActionListener()
1561 public void actionPerformed(ActionEvent e)
1563 scaleRight_actionPerformed(e);
1566 centreColumnLabelsMenuItem.setVisible(true);
1567 centreColumnLabelsMenuItem.setState(false);
1568 centreColumnLabelsMenuItem.setText(MessageManager
1569 .getString("label.centre_column_labels"));
1570 centreColumnLabelsMenuItem
1571 .addActionListener(new java.awt.event.ActionListener()
1574 public void actionPerformed(ActionEvent e)
1576 centreColumnLabels_actionPerformed(e);
1579 followHighlightMenuItem.setVisible(true);
1580 followHighlightMenuItem.setState(true);
1581 followHighlightMenuItem.setText(MessageManager
1582 .getString("label.automatic_scrolling"));
1583 followHighlightMenuItem.addActionListener(new ActionListener()
1587 public void actionPerformed(ActionEvent e)
1589 followHighlight_actionPerformed();
1594 modifyPID.setText(MessageManager
1595 .getString("label.modify_identity_thereshold"));
1596 modifyPID.addActionListener(new java.awt.event.ActionListener()
1599 public void actionPerformed(ActionEvent e)
1601 modifyPID_actionPerformed(e);
1604 modifyConservation.setText(MessageManager
1605 .getString("label.modify_conservation_thereshold"));
1607 .addActionListener(new java.awt.event.ActionListener()
1610 public void actionPerformed(ActionEvent e)
1612 modifyConservation_actionPerformed(e);
1616 .setText(MessageManager.getString("action.by_tree_order"));
1617 sort.setText(MessageManager.getString("action.sort"));
1618 sort.addMenuListener(new MenuListener()
1621 public void menuSelected(MenuEvent e)
1627 public void menuDeselected(MenuEvent e)
1632 public void menuCanceled(MenuEvent e)
1636 sortByAnnotScore.setText(MessageManager
1637 .getString("label.sort_by_score"));
1638 sort.add(sortByAnnotScore);
1639 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1643 public void menuCanceled(MenuEvent e)
1648 public void menuDeselected(MenuEvent e)
1653 public void menuSelected(MenuEvent e)
1655 buildSortByAnnotationScoresMenu();
1658 sortByAnnotScore.setVisible(false);
1661 .setText(MessageManager.getString("action.calculate_tree"));
1663 jMenu2.setText(MessageManager.getString("label.export_image"));
1664 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1665 padGapsMenuitem.setState(jalview.bin.Cache
1666 .getDefault("PAD_GAPS", false));
1667 padGapsMenuitem.addActionListener(new ActionListener()
1670 public void actionPerformed(ActionEvent e)
1672 padGapsMenuitem_actionPerformed(e);
1675 vamsasStore.setVisible(false);
1676 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1677 vamsasStore.addActionListener(new ActionListener()
1680 public void actionPerformed(ActionEvent e)
1682 vamsasStore_actionPerformed(e);
1685 showTranslation.setText(MessageManager
1686 .getString("label.translate_cDNA"));
1687 showTranslation.addActionListener(new ActionListener()
1690 public void actionPerformed(ActionEvent e)
1692 showTranslation_actionPerformed(e);
1695 extractScores.setText(MessageManager.getString("label.extract_scores")
1697 extractScores.addActionListener(new ActionListener()
1700 public void actionPerformed(ActionEvent e)
1702 extractScores_actionPerformed(e);
1705 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1707 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1709 * showProducts.addActionListener(new ActionListener() {
1711 * public void actionPerformed(ActionEvent e) {
1712 * showProducts_actionPerformed(e); } });
1714 openFeatureSettings.setText(MessageManager
1715 .getString("label.feature_settings"));
1716 openFeatureSettings.addActionListener(new ActionListener()
1719 public void actionPerformed(ActionEvent e)
1721 featureSettings_actionPerformed(e);
1725 .setText(MessageManager.getString("label.fetch_sequences"));
1726 fetchSequence.addActionListener(new ActionListener()
1729 public void actionPerformed(ActionEvent e)
1731 fetchSequence_actionPerformed(e);
1735 annotationColour.setText(MessageManager
1736 .getString("action.by_annotation"));
1737 annotationColour.addActionListener(new ActionListener()
1740 public void actionPerformed(ActionEvent e)
1742 annotationColour_actionPerformed(e);
1746 rnahelicesColour.setText(MessageManager
1747 .getString("action.by_rna_helixes"));
1748 rnahelicesColour.addActionListener(new ActionListener()
1751 public void actionPerformed(ActionEvent e)
1753 rnahelicesColour_actionPerformed(e);
1757 associatedData.setText(MessageManager
1758 .getString("label.load_features_annotations"));
1759 associatedData.addActionListener(new ActionListener()
1762 public void actionPerformed(ActionEvent e)
1764 associatedData_actionPerformed(e);
1767 autoCalculate.setText(MessageManager
1768 .getString("label.autocalculate_consensus"));
1769 autoCalculate.setState(jalview.bin.Cache.getDefault(
1770 "AUTO_CALC_CONSENSUS", true));
1771 autoCalculate.addActionListener(new ActionListener()
1774 public void actionPerformed(ActionEvent e)
1776 autoCalculate_actionPerformed(e);
1779 sortByTree.setText(MessageManager
1780 .getString("label.sort_alignment_new_tree"));
1782 .setToolTipText("<html>"
1784 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1786 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1787 sortByTree.addActionListener(new ActionListener()
1790 public void actionPerformed(ActionEvent e)
1792 sortByTreeOption_actionPerformed(e);
1796 listenToViewSelections.setText(MessageManager
1797 .getString("label.listen_for_selections"));
1798 listenToViewSelections
1799 .setToolTipText("<html>"
1801 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1802 listenToViewSelections.setState(false);
1803 listenToViewSelections.addActionListener(new ActionListener()
1806 public void actionPerformed(ActionEvent e)
1808 listenToViewSelections_actionPerformed(e);
1813 .setText(MessageManager.getString("label.add_sequences"));
1814 addFromFile.setText(MessageManager.getString("label.from_file"));
1815 addFromFile.addActionListener(new ActionListener()
1818 public void actionPerformed(ActionEvent e)
1820 addFromFile_actionPerformed(e);
1823 addFromText.setText(MessageManager.getString("label.from_textbox"));
1824 addFromText.addActionListener(new ActionListener()
1827 public void actionPerformed(ActionEvent e)
1829 addFromText_actionPerformed(e);
1832 addFromURL.setText(MessageManager.getString("label.from_url"));
1833 addFromURL.addActionListener(new ActionListener()
1836 public void actionPerformed(ActionEvent e)
1838 addFromURL_actionPerformed(e);
1841 exportFeatures.setText(MessageManager
1842 .getString("label.export_features"));
1843 exportFeatures.addActionListener(new ActionListener()
1846 public void actionPerformed(ActionEvent e)
1848 exportFeatures_actionPerformed(e);
1851 exportAnnotations.setText(MessageManager
1852 .getString("label.export_annotations"));
1853 exportAnnotations.addActionListener(new ActionListener()
1856 public void actionPerformed(ActionEvent e)
1858 exportAnnotations_actionPerformed(e);
1861 statusPanel.setLayout(gridLayout1);
1862 jMenu3.setText(MessageManager.getString("action.show"));
1863 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1864 showAllSeqs.setToolTipText(MessageManager
1865 .getString("label.toggle_sequence_visibility"));
1866 showAllSeqs.addActionListener(new ActionListener()
1869 public void actionPerformed(ActionEvent e)
1871 showAllSeqs_actionPerformed(e);
1874 showAllColumns.setText(MessageManager.getString("label.all_columns"));
1875 showAllColumns.setToolTipText(MessageManager
1876 .getString("label.toggle_columns_visibility"));
1877 showAllColumns.addActionListener(new ActionListener()
1880 public void actionPerformed(ActionEvent e)
1882 showAllColumns_actionPerformed(e);
1885 hideMenu.setText(MessageManager.getString("action.hide"));
1886 hideSelSequences.setText(MessageManager
1887 .getString("label.selected_sequences"));
1888 hideSelSequences.setToolTipText(MessageManager
1889 .getString("label.toggle_sequence_visibility"));
1890 hideSelSequences.addActionListener(new ActionListener()
1893 public void actionPerformed(ActionEvent e)
1895 hideSelSequences_actionPerformed(e);
1898 hideSelColumns.setText(MessageManager
1899 .getString("label.selected_columns"));
1900 hideSelColumns.setToolTipText(MessageManager
1901 .getString("label.toggle_columns_visibility"));
1902 hideSelColumns.addActionListener(new ActionListener()
1905 public void actionPerformed(ActionEvent e)
1907 hideSelColumns_actionPerformed(e);
1910 hideAllSelection.setText(MessageManager
1911 .getString("label.selected_region"));
1912 hideAllSelection.addActionListener(new ActionListener()
1915 public void actionPerformed(ActionEvent e)
1917 hideAllSelection_actionPerformed(e);
1920 // TODO: should be hidden if no selection exists.
1921 hideAllButSelection.setText(MessageManager
1922 .getString("label.all_but_selected_region"));
1923 hideAllButSelection.addActionListener(new ActionListener()
1926 public void actionPerformed(ActionEvent e)
1928 hideAllButSelection_actionPerformed(e);
1931 showAllhidden.setText(MessageManager
1932 .getString("label.all_sequences_columns"));
1933 showAllhidden.setToolTipText(MessageManager
1934 .getString("label.toggles_visibility_hidden_selected_regions"));
1935 showAllhidden.addActionListener(new ActionListener()
1938 public void actionPerformed(ActionEvent e)
1940 showAllhidden_actionPerformed(e);
1943 hiddenMarkers.setText(MessageManager
1944 .getString("action.show_hidden_markers"));
1945 hiddenMarkers.addActionListener(new ActionListener()
1948 public void actionPerformed(ActionEvent e)
1950 hiddenMarkers_actionPerformed(e);
1953 invertColSel.setText(MessageManager
1954 .getString("action.invert_column_selection"));
1955 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1956 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1957 .getMenuShortcutKeyMask()
1958 | java.awt.event.KeyEvent.ALT_MASK, false));
1959 invertColSel.addActionListener(new ActionListener()
1962 public void actionPerformed(ActionEvent e)
1964 invertColSel_actionPerformed(e);
1967 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1970 public void stateChanged(ChangeEvent evt)
1972 JTabbedPane pane = (JTabbedPane) evt.getSource();
1973 int sel = pane.getSelectedIndex();
1974 tabSelectionChanged(sel);
1977 tabbedPane.addMouseListener(new MouseAdapter()
1980 public void mousePressed(MouseEvent e)
1982 tabbedPane_mousePressed(e);
1985 tabbedPane.addFocusListener(new FocusAdapter()
1988 public void focusGained(FocusEvent e)
1990 tabbedPane_focusGained(e);
1993 save.setText(MessageManager.getString("action.save"));
1994 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1995 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1996 .getMenuShortcutKeyMask(), false));
1997 save.addActionListener(new ActionListener()
2000 public void actionPerformed(ActionEvent e)
2002 save_actionPerformed(e);
2005 reload.setEnabled(false);
2006 reload.setText(MessageManager.getString("action.reload"));
2007 reload.addActionListener(new ActionListener()
2010 public void actionPerformed(ActionEvent e)
2012 reload_actionPerformed(e);
2015 newView.setText(MessageManager.getString("action.new_view"));
2016 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2017 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2018 .getMenuShortcutKeyMask(), false));
2019 newView.addActionListener(new ActionListener()
2022 public void actionPerformed(ActionEvent e)
2024 newView_actionPerformed(e);
2027 tabbedPane.setToolTipText("<html><i>"
2028 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2030 textColour.setText(MessageManager.getString("label.colour_text")
2032 textColour.addActionListener(new ActionListener()
2035 public void actionPerformed(ActionEvent e)
2037 textColour_actionPerformed(e);
2040 formatMenu.setText(MessageManager.getString("action.format"));
2041 selectMenu.setText(MessageManager.getString("action.select"));
2042 idRightAlign.setText(MessageManager
2043 .getString("label.right_align_sequence_id"));
2044 idRightAlign.addActionListener(new ActionListener()
2047 public void actionPerformed(ActionEvent e)
2049 idRightAlign_actionPerformed(e);
2052 gatherViews.setEnabled(false);
2053 gatherViews.setText(MessageManager.getString("action.gather_views"));
2054 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2055 java.awt.event.KeyEvent.VK_G, 0, false));
2056 gatherViews.addActionListener(new ActionListener()
2059 public void actionPerformed(ActionEvent e)
2061 gatherViews_actionPerformed(e);
2064 expandViews.setEnabled(false);
2065 expandViews.setText(MessageManager.getString("action.expand_views"));
2066 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2067 java.awt.event.KeyEvent.VK_X, 0, false));
2068 expandViews.addActionListener(new ActionListener()
2071 public void actionPerformed(ActionEvent e)
2073 expandViews_actionPerformed(e);
2077 .setText(MessageManager.getString("action.page_setup") + "...");
2078 pageSetup.addActionListener(new ActionListener()
2081 public void actionPerformed(ActionEvent e)
2083 pageSetup_actionPerformed(e);
2086 alignmentProperties.setText(MessageManager
2087 .getString("label.alignment_props") + "...");
2088 alignmentProperties.addActionListener(new ActionListener()
2091 public void actionPerformed(ActionEvent actionEvent)
2093 alignmentProperties();
2096 tooltipSettingsMenu.setText(MessageManager
2097 .getString("label.sequence_id_tooltip"));
2098 autoAnnMenu.setText(MessageManager
2099 .getString("label.autocalculated_annotation"));
2100 alignFrameMenuBar.add(fileMenu);
2101 alignFrameMenuBar.add(editMenu);
2102 alignFrameMenuBar.add(selectMenu);
2103 alignFrameMenuBar.add(viewMenu);
2104 alignFrameMenuBar.add(formatMenu);
2105 alignFrameMenuBar.add(colourMenu);
2106 alignFrameMenuBar.add(calculateMenu);
2107 alignFrameMenuBar.add(webService);
2108 fileMenu.add(fetchSequence);
2109 fileMenu.add(addSequenceMenu);
2110 fileMenu.add(reload);
2111 fileMenu.addSeparator();
2112 fileMenu.add(vamsasStore);
2114 fileMenu.add(saveAs);
2115 fileMenu.add(outputTextboxMenu);
2116 fileMenu.add(pageSetup);
2117 fileMenu.add(printMenuItem);
2118 fileMenu.addSeparator();
2119 fileMenu.add(jMenu2);
2120 fileMenu.add(exportFeatures);
2121 fileMenu.add(exportAnnotations);
2122 fileMenu.add(LoadtreeMenuItem);
2123 fileMenu.add(associatedData);
2124 fileMenu.addSeparator();
2125 fileMenu.add(closeMenuItem);
2126 editMenu.add(undoMenuItem);
2127 editMenu.add(redoMenuItem);
2130 editMenu.add(pasteMenu);
2131 editMenu.add(delete);
2132 editMenu.addSeparator();
2133 editMenu.add(remove2LeftMenuItem);
2134 editMenu.add(remove2RightMenuItem);
2135 editMenu.add(removeGappedColumnMenuItem);
2136 editMenu.add(removeAllGapsMenuItem);
2137 editMenu.add(removeRedundancyMenuItem);
2138 editMenu.addSeparator();
2139 // dont add these yet in the CVS build - they cannot be undone!
2140 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2141 // editMenu.add(justifyLeftMenuItem);
2142 // editMenu.add(justifyRightMenuItem);
2143 // editMenu.addSeparator();
2144 editMenu.add(padGapsMenuitem);
2145 viewMenu.add(newView);
2146 viewMenu.add(expandViews);
2147 viewMenu.add(gatherViews);
2148 viewMenu.addSeparator();
2149 viewMenu.add(jMenu3);
2150 viewMenu.add(hideMenu);
2151 viewMenu.addSeparator();
2152 viewMenu.add(followHighlightMenuItem);
2153 viewMenu.add(annotationPanelMenuItem);
2154 viewMenu.add(showAllAnnotations);
2155 viewMenu.add(hideAllAnnotations);
2156 autoAnnMenu.add(applyAutoAnnotationSettings);
2157 autoAnnMenu.add(showConsensusHistogram);
2158 autoAnnMenu.add(showSequenceLogo);
2159 autoAnnMenu.add(normaliseSequenceLogo);
2160 autoAnnMenu.addSeparator();
2161 autoAnnMenu.add(showGroupConservation);
2162 autoAnnMenu.add(showGroupConsensus);
2163 viewMenu.add(autoAnnMenu);
2164 viewMenu.addSeparator();
2165 viewMenu.add(showSeqFeatures);
2166 // viewMenu.add(showSeqFeaturesHeight);
2168 viewMenu.add(openFeatureSettings);
2169 tooltipSettingsMenu.add(showDbRefsMenuitem);
2170 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2171 viewMenu.add(tooltipSettingsMenu);
2172 viewMenu.addSeparator();
2173 viewMenu.add(alignmentProperties);
2174 viewMenu.addSeparator();
2175 viewMenu.add(overviewMenuItem);
2176 colourMenu.add(applyToAllGroups);
2177 colourMenu.add(textColour);
2178 colourMenu.addSeparator();
2179 colourMenu.add(noColourmenuItem);
2180 colourMenu.add(clustalColour);
2181 colourMenu.add(BLOSUM62Colour);
2182 colourMenu.add(PIDColour);
2183 colourMenu.add(zappoColour);
2184 colourMenu.add(taylorColour);
2185 colourMenu.add(hydrophobicityColour);
2186 colourMenu.add(helixColour);
2187 colourMenu.add(strandColour);
2188 colourMenu.add(turnColour);
2189 colourMenu.add(buriedColour);
2190 colourMenu.add(nucleotideColour);
2191 colourMenu.add(purinePyrimidineColour);
2192 colourMenu.add(RNAInteractionColour);
2193 // colourMenu.add(covariationColour);
2194 colourMenu.add(tcoffeeColour);
2195 colourMenu.add(userDefinedColour);
2196 colourMenu.addSeparator();
2197 colourMenu.add(conservationMenuItem);
2198 colourMenu.add(modifyConservation);
2199 colourMenu.add(abovePIDThreshold);
2200 colourMenu.add(modifyPID);
2201 colourMenu.add(annotationColour);
2202 colourMenu.add(rnahelicesColour);
2203 calculateMenu.add(sort);
2204 calculateMenu.add(calculateTree);
2205 calculateMenu.addSeparator();
2206 calculateMenu.add(pairwiseAlignmentMenuItem);
2207 calculateMenu.add(PCAMenuItem);
2208 calculateMenu.addSeparator();
2209 calculateMenu.add(showTranslation);
2210 calculateMenu.add(showProducts);
2211 calculateMenu.add(autoCalculate);
2212 calculateMenu.add(sortByTree);
2213 calculateMenu.addSeparator();
2214 calculateMenu.add(extractScores);
2215 webServiceNoServices = new JMenuItem(
2216 MessageManager.getString("label.no_services"));
2217 webService.add(webServiceNoServices);
2218 pasteMenu.add(pasteNew);
2219 pasteMenu.add(pasteThis);
2220 sort.add(sortIDMenuItem);
2221 sort.add(sortLengthMenuItem);
2222 sort.add(sortGroupMenuItem);
2223 sort.add(sortPairwiseMenuItem);
2224 sort.add(sortByTreeMenu);
2225 jMenu2.add(htmlMenuItem);
2226 jMenu2.add(epsFile);
2227 jMenu2.add(createPNG);
2228 addSequenceMenu.add(addFromFile);
2229 addSequenceMenu.add(addFromText);
2230 addSequenceMenu.add(addFromURL);
2231 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2232 statusPanel.add(statusBar, null);
2233 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2234 jMenu3.add(showAllColumns);
2235 jMenu3.add(showAllSeqs);
2236 jMenu3.add(showAllhidden);
2237 hideMenu.add(hideSelColumns);
2238 hideMenu.add(hideSelSequences);
2239 hideMenu.add(hideAllSelection);
2240 hideMenu.add(hideAllButSelection);
2242 formatMenu.add(font);
2243 formatMenu.addSeparator();
2244 formatMenu.add(wrapMenuItem);
2245 formatMenu.add(scaleAbove);
2246 formatMenu.add(scaleLeft);
2247 formatMenu.add(scaleRight);
2248 formatMenu.add(seqLimits);
2249 formatMenu.add(idRightAlign);
2250 formatMenu.add(hiddenMarkers);
2251 formatMenu.add(viewBoxesMenuItem);
2252 formatMenu.add(viewTextMenuItem);
2253 formatMenu.add(colourTextMenuItem);
2254 formatMenu.add(renderGapsMenuItem);
2255 formatMenu.add(centreColumnLabelsMenuItem);
2256 formatMenu.add(showNonconservedMenuItem);
2257 selectMenu.add(findMenuItem);
2258 selectMenu.addSeparator();
2259 selectMenu.add(selectAllSequenceMenuItem);
2260 selectMenu.add(deselectAllSequenceMenuItem);
2261 selectMenu.add(invertSequenceMenuItem);
2262 selectMenu.add(invertColSel);
2263 selectMenu.add(createGroup);
2264 selectMenu.add(unGroup);
2265 selectMenu.add(grpsFromSelection);
2266 selectMenu.add(deleteGroups);
2267 calculateMenu.add(expandAlignment);
2268 // TODO - determine if the listenToViewSelections button is needed : see bug
2270 // selectMenu.addSeparator();
2271 // selectMenu.add(listenToViewSelections);
2275 * Action on clicking Show all annotations.
2277 protected void showAllAnnotations_actionPerformed()
2279 setAllAnnotationsVisibility(true);
2283 * Action on clicking Hide all annotations.
2285 protected void hideAllAnnotations_actionPerformed()
2287 setAllAnnotationsVisibility(false);
2291 * Set the visibility of all annotations to true or false.
2295 protected void setAllAnnotationsVisibility(boolean visible)
2300 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2302 // TODO Auto-generated method stub
2306 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2308 // TODO Auto-generated method stub
2312 protected void showAllhidden_actionPerformed(ActionEvent e)
2314 // TODO Auto-generated method stub
2318 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2320 // TODO Auto-generated method stub
2324 protected void hideAllSelection_actionPerformed(ActionEvent e)
2326 // TODO Auto-generated method stub
2330 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2332 // TODO Auto-generated method stub
2336 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2338 // TODO Auto-generated method stub
2342 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2344 // TODO Auto-generated method stub
2348 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2350 // TODO Auto-generated method stub
2354 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2356 // TODO Auto-generated method stub
2360 protected void showGroupConservation_actionPerformed(ActionEvent e)
2362 // TODO Auto-generated method stub
2366 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2368 // TODO Auto-generated method stub
2372 protected void showSeqFeaturesHeight_actionPerformed(
2373 ActionEvent actionEvent)
2375 // TODO Auto-generated method stub
2379 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2381 // TODO Auto-generated method stub
2385 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2387 // TODO Auto-generated method stub
2391 protected void followHighlight_actionPerformed()
2393 // TODO Auto-generated method stub
2397 protected void showNpFeats_actionPerformed(ActionEvent e)
2399 // TODO Auto-generated method stub
2403 protected void showDbRefs_actionPerformed(ActionEvent e)
2405 // TODO Auto-generated method stub
2409 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2413 protected void showProducts_actionPerformed(ActionEvent e)
2417 protected void buildSortByAnnotationScoresMenu()
2421 protected void extractScores_actionPerformed(ActionEvent e)
2425 protected void outputText_actionPerformed(ActionEvent e)
2429 public void addFromFile_actionPerformed(ActionEvent e)
2434 public void addFromText_actionPerformed(ActionEvent e)
2439 public void addFromURL_actionPerformed(ActionEvent e)
2444 public void exportFeatures_actionPerformed(ActionEvent e)
2449 public void exportAnnotations_actionPerformed(ActionEvent e)
2454 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2458 protected void closeMenuItem_actionPerformed(boolean b)
2462 protected void redoMenuItem_actionPerformed(ActionEvent e)
2466 protected void undoMenuItem_actionPerformed(ActionEvent e)
2470 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2474 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2478 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2482 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2486 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2490 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2494 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2498 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2502 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2506 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2510 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2514 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2518 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2522 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2526 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2530 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2534 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2538 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2542 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2546 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2550 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2554 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2558 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2562 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2566 protected void clustalColour_actionPerformed(ActionEvent e)
2570 protected void zappoColour_actionPerformed(ActionEvent e)
2574 protected void taylorColour_actionPerformed(ActionEvent e)
2578 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2582 protected void helixColour_actionPerformed(ActionEvent e)
2586 protected void strandColour_actionPerformed(ActionEvent e)
2590 protected void turnColour_actionPerformed(ActionEvent e)
2594 protected void buriedColour_actionPerformed(ActionEvent e)
2598 protected void userDefinedColour_actionPerformed(ActionEvent e)
2602 protected void PIDColour_actionPerformed(ActionEvent e)
2606 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2610 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2614 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2619 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2622 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2626 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2630 protected void printMenuItem_actionPerformed(ActionEvent e)
2634 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2638 protected void findMenuItem_actionPerformed(ActionEvent e)
2642 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2646 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2650 protected void nucleotideColour_actionPerformed(ActionEvent e)
2654 protected void deleteGroups_actionPerformed(ActionEvent e)
2658 protected void createGroup_actionPerformed(ActionEvent e)
2662 protected void unGroup_actionPerformed(ActionEvent e)
2666 protected void copy_actionPerformed(ActionEvent e)
2670 protected void cut_actionPerformed(ActionEvent e)
2674 protected void delete_actionPerformed(ActionEvent e)
2678 protected void pasteNew_actionPerformed(ActionEvent e)
2682 protected void pasteThis_actionPerformed(ActionEvent e)
2686 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2690 public void createPNG(java.io.File f)
2694 protected void font_actionPerformed(ActionEvent e)
2698 protected void seqLimit_actionPerformed(ActionEvent e)
2702 public void seqDBRef_actionPerformed(ActionEvent e)
2707 public void createEPS(java.io.File f)
2711 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2717 * Template method to handle the 'load T-Coffee scores' menu event.
2719 * Subclasses override this method to provide a custom action.
2724 protected void loadScores_actionPerformed(ActionEvent event)
2730 * Template method to handle the 'Color T-Coffee scores' menu event.
2732 * Subclasses override this method to provide a custom action.
2737 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2742 protected void jpred_actionPerformed(ActionEvent e)
2746 protected void scaleAbove_actionPerformed(ActionEvent e)
2750 protected void scaleLeft_actionPerformed(ActionEvent e)
2754 protected void scaleRight_actionPerformed(ActionEvent e)
2758 protected void modifyPID_actionPerformed(ActionEvent e)
2762 protected void modifyConservation_actionPerformed(ActionEvent e)
2766 protected void saveAs_actionPerformed(ActionEvent e)
2770 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2774 public void vamsasStore_actionPerformed(ActionEvent e)
2779 public void vamsasLoad_actionPerformed(ActionEvent e)
2784 public void showTranslation_actionPerformed(ActionEvent e)
2789 public void featureSettings_actionPerformed(ActionEvent e)
2794 public void fetchSequence_actionPerformed(ActionEvent e)
2799 public void smoothFont_actionPerformed(ActionEvent e)
2804 public void annotationColour_actionPerformed(ActionEvent e)
2809 public void rnahelicesColour_actionPerformed(ActionEvent e)
2814 public void associatedData_actionPerformed(ActionEvent e)
2819 public void autoCalculate_actionPerformed(ActionEvent e)
2824 public void sortByTreeOption_actionPerformed(ActionEvent e)
2829 public void showAllSeqs_actionPerformed(ActionEvent e)
2834 public void showAllColumns_actionPerformed(ActionEvent e)
2839 public void hideSelSequences_actionPerformed(ActionEvent e)
2844 public void hideSelColumns_actionPerformed(ActionEvent e)
2849 public void hiddenMarkers_actionPerformed(ActionEvent e)
2854 public void findPdbId_actionPerformed(ActionEvent e)
2859 public void enterPdbId_actionPerformed(ActionEvent e)
2864 public void pdbFile_actionPerformed(ActionEvent e)
2869 public void invertColSel_actionPerformed(ActionEvent e)
2874 public void tabSelectionChanged(int sel)
2879 public void tabbedPane_mousePressed(MouseEvent e)
2884 public void tabbedPane_focusGained(FocusEvent e)
2889 public void save_actionPerformed(ActionEvent e)
2894 public void reload_actionPerformed(ActionEvent e)
2899 public void newView_actionPerformed(ActionEvent e)
2904 public void textColour_actionPerformed(ActionEvent e)
2909 public void idRightAlign_actionPerformed(ActionEvent e)
2914 public void expandViews_actionPerformed(ActionEvent e)
2919 public void gatherViews_actionPerformed(ActionEvent e)
2924 public void buildTreeMenu()
2929 public void pageSetup_actionPerformed(ActionEvent e)
2934 public void alignmentProperties()
2939 protected void expand_newalign(ActionEvent e)
2941 // TODO Auto-generated method stub