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.schemes.ColourSchemeProperty;
25 import jalview.util.MessageManager;
27 import java.awt.BorderLayout;
28 import java.awt.Color;
29 import java.awt.GridLayout;
30 import java.awt.Toolkit;
31 import java.awt.event.ActionEvent;
32 import java.awt.event.ActionListener;
33 import java.awt.event.FocusAdapter;
34 import java.awt.event.FocusEvent;
35 import java.awt.event.MouseAdapter;
36 import java.awt.event.MouseEvent;
38 import javax.swing.BorderFactory;
39 import javax.swing.ButtonGroup;
40 import javax.swing.JCheckBoxMenuItem;
41 import javax.swing.JInternalFrame;
42 import javax.swing.JLabel;
43 import javax.swing.JMenu;
44 import javax.swing.JMenuBar;
45 import javax.swing.JMenuItem;
46 import javax.swing.JOptionPane;
47 import javax.swing.JPanel;
48 import javax.swing.JRadioButtonMenuItem;
49 import javax.swing.JTabbedPane;
50 import javax.swing.SwingUtilities;
51 import javax.swing.event.ChangeEvent;
52 import javax.swing.event.MenuEvent;
53 import javax.swing.event.MenuListener;
55 public class GAlignFrame extends JInternalFrame
57 protected JMenuBar alignFrameMenuBar = new JMenuBar();
59 protected JMenu fileMenu = new JMenu();
61 protected JMenuItem closeMenuItem = new JMenuItem();
63 protected JMenu editMenu = new JMenu();
65 protected JMenu viewMenu = new JMenu();
67 protected JMenu colourMenu = new JMenu();
69 protected JMenu calculateMenu = new JMenu();
71 protected JMenu webService = new JMenu();
73 protected JMenuItem webServiceNoServices;
75 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
77 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
79 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
81 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
83 protected JMenuItem remove2RightMenuItem = new JMenuItem();
85 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
87 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
89 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
91 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
93 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
95 protected JMenuItem sortIDMenuItem = new JMenuItem();
97 protected JMenuItem sortLengthMenuItem = new JMenuItem();
99 protected JMenuItem sortGroupMenuItem = new JMenuItem();
101 protected JMenu sortByAnnotScore = new JMenu();
103 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
105 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
107 protected JMenuItem PCAMenuItem = new JMenuItem();
109 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
111 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
113 BorderLayout borderLayout1 = new BorderLayout();
115 public JLabel statusBar = new JLabel();
117 protected JMenuItem saveAs = new JMenuItem();
119 protected JMenu outputTextboxMenu = new JMenu();
121 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
123 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
125 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
127 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
129 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
131 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
133 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
135 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
137 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
139 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
141 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
143 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
145 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
147 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
149 // protected JRadioButtonMenuItem covariationColour = new
150 // JRadioButtonMenuItem();
152 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
154 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
156 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
158 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
160 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
162 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
164 JMenuItem htmlMenuItem = new JMenuItem();
166 JMenuItem overviewMenuItem = new JMenuItem();
168 protected JMenuItem undoMenuItem = new JMenuItem();
170 protected JMenuItem redoMenuItem = new JMenuItem();
172 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
174 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
176 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
178 JMenuItem printMenuItem = new JMenuItem();
180 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
182 JMenuItem findMenuItem = new JMenuItem();
184 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
186 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
188 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
190 JMenuItem deleteGroups = new JMenuItem();
192 JMenuItem createGroup = new JMenuItem();
194 JMenuItem unGroup = new JMenuItem();
196 JMenuItem delete = new JMenuItem();
198 JMenuItem copy = new JMenuItem();
200 JMenuItem cut = new JMenuItem();
202 JMenu pasteMenu = new JMenu();
204 JMenuItem pasteNew = new JMenuItem();
206 JMenuItem pasteThis = new JMenuItem();
208 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
210 JMenuItem createPNG = new JMenuItem();
212 protected JMenuItem font = new JMenuItem();
214 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
216 JMenuItem epsFile = new JMenuItem();
218 JMenuItem LoadtreeMenuItem = new JMenuItem();
220 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
222 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
224 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
226 protected JMenuItem modifyPID = new JMenuItem();
228 protected JMenuItem modifyConservation = new JMenuItem();
230 protected JMenu sortByTreeMenu = new JMenu();
232 protected JMenu sort = new JMenu();
234 protected JMenu calculateTree = new JMenu();
236 JMenu jMenu2 = new JMenu();
238 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
240 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
242 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
244 protected ButtonGroup colours = new ButtonGroup();
246 JMenuItem vamsasStore = new JMenuItem();
248 protected JMenuItem showTranslation = new JMenuItem();
250 protected JMenuItem extractScores = new JMenuItem();
252 protected JMenuItem expandAlignment = new JMenuItem();
254 protected JMenu showProducts = new JMenu();
256 public JMenuItem openFeatureSettings = new JMenuItem();
258 JMenuItem fetchSequence = new JMenuItem();
260 JMenuItem annotationColour = new JMenuItem();
262 protected JMenuItem rnahelicesColour = new JMenuItem();
264 JMenuItem associatedData = new JMenuItem();
266 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
268 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
270 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
272 JMenu addSequenceMenu = new JMenu();
274 JMenuItem addFromFile = new JMenuItem();
276 JMenuItem addFromText = new JMenuItem();
278 JMenuItem addFromURL = new JMenuItem();
280 JMenuItem exportAnnotations = new JMenuItem();
282 JMenuItem exportFeatures = new JMenuItem();
284 protected JPanel statusPanel = new JPanel();
286 GridLayout gridLayout1 = new GridLayout();
288 JMenu jMenu3 = new JMenu();
290 JMenuItem showAllSeqs = new JMenuItem();
292 JMenuItem showAllColumns = new JMenuItem();
294 JMenu hideMenu = new JMenu();
296 JMenuItem hideSelSequences = new JMenuItem();
298 JMenuItem hideSelColumns = new JMenuItem();
300 JMenuItem hideAllButSelection = new JMenuItem();
302 JMenuItem hideAllSelection = new JMenuItem();
304 JMenuItem showAllhidden = new JMenuItem();
306 protected JMenuItem showAllAnnotations = new JMenuItem();
308 protected JMenuItem hideAllAnnotations = new JMenuItem();
310 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
312 JMenuItem invertColSel = new JMenuItem();
314 protected JTabbedPane tabbedPane = new JTabbedPane();
316 JMenuItem save = new JMenuItem();
318 protected JMenuItem reload = new JMenuItem();
320 JMenuItem newView = new JMenuItem();
322 JMenuItem textColour = new JMenuItem();
324 JMenu formatMenu = new JMenu();
326 JMenu selectMenu = new JMenu();
328 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
330 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
332 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
334 protected JMenuItem gatherViews = new JMenuItem();
336 protected JMenuItem expandViews = new JMenuItem();
338 JMenuItem pageSetup = new JMenuItem();
340 JMenuItem alignmentProperties = new JMenuItem();
342 JMenu tooltipSettingsMenu = new JMenu();
344 private JMenuItem justifyLeftMenuItem = new JMenuItem();
346 private JMenuItem justifyRightMenuItem = new JMenuItem();
348 JMenu autoAnnMenu = new JMenu();
350 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
352 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
354 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
356 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
358 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
360 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
362 private JMenuItem grpsFromSelection = new JMenuItem();
369 setJMenuBar(alignFrameMenuBar);
371 // dynamically fill save as menu with available formats
372 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
374 JMenuItem item = new JMenuItem(
375 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
377 item.addActionListener(new java.awt.event.ActionListener()
380 public void actionPerformed(ActionEvent e)
382 outputText_actionPerformed(e);
386 outputTextboxMenu.add(item);
388 } catch (Exception e)
390 System.err.println(e.toString());
393 if (!new jalview.util.Platform().isAMac())
395 closeMenuItem.setMnemonic('C');
396 outputTextboxMenu.setMnemonic('T');
397 undoMenuItem.setMnemonic('Z');
398 redoMenuItem.setMnemonic('0');
399 copy.setMnemonic('C');
400 cut.setMnemonic('U');
401 pasteMenu.setMnemonic('P');
402 reload.setMnemonic('R');
405 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
407 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
408 .getUserColourSchemes().keys();
410 while (userColours.hasMoreElements())
412 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
413 userColours.nextElement().toString());
414 radioItem.setName("USER_DEFINED");
415 radioItem.addMouseListener(new MouseAdapter()
418 public void mousePressed(MouseEvent evt)
420 if (evt.isControlDown()
421 || SwingUtilities.isRightMouseButton(evt))
423 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
425 int option = JOptionPane.showInternalConfirmDialog(
426 jalview.gui.Desktop.desktop,
428 .getString("label.remove_from_default_list"),
430 .getString("label.remove_user_defined_colour"),
431 JOptionPane.YES_NO_OPTION);
432 if (option == JOptionPane.YES_OPTION)
434 jalview.gui.UserDefinedColours
435 .removeColourFromDefaults(radioItem.getText());
436 colourMenu.remove(radioItem);
440 radioItem.addActionListener(new ActionListener()
443 public void actionPerformed(ActionEvent evt)
445 userDefinedColour_actionPerformed(evt);
452 radioItem.addActionListener(new ActionListener()
455 public void actionPerformed(ActionEvent evt)
457 userDefinedColour_actionPerformed(evt);
460 colourMenu.insert(radioItem, 15);
461 colours.add(radioItem);
464 colours.add(noColourmenuItem);
465 colours.add(clustalColour);
466 colours.add(zappoColour);
467 colours.add(taylorColour);
468 colours.add(hydrophobicityColour);
469 colours.add(helixColour);
470 colours.add(strandColour);
471 colours.add(turnColour);
472 colours.add(buriedColour);
473 colours.add(userDefinedColour);
474 colours.add(PIDColour);
475 colours.add(BLOSUM62Colour);
476 colours.add(nucleotideColour);
477 colours.add(purinePyrimidineColour);
478 // colours.add(covariationColour);
479 colours.add(tcoffeeColour);
480 colours.add(RNAInteractionColour);
481 setColourSelected(jalview.bin.Cache
482 .getDefault("DEFAULT_COLOUR", "None"));
486 public void setColourSelected(String defaultColour)
489 if (defaultColour != null)
491 int index = ColourSchemeProperty
492 .getColourIndexFromName(defaultColour);
496 case ColourSchemeProperty.CLUSTAL:
497 clustalColour.setSelected(true);
501 case ColourSchemeProperty.BLOSUM:
502 BLOSUM62Colour.setSelected(true);
506 case ColourSchemeProperty.PID:
507 PIDColour.setSelected(true);
511 case ColourSchemeProperty.ZAPPO:
512 zappoColour.setSelected(true);
516 case ColourSchemeProperty.TAYLOR:
517 taylorColour.setSelected(true);
520 case ColourSchemeProperty.HYDROPHOBIC:
521 hydrophobicityColour.setSelected(true);
525 case ColourSchemeProperty.HELIX:
526 helixColour.setSelected(true);
530 case ColourSchemeProperty.STRAND:
531 strandColour.setSelected(true);
535 case ColourSchemeProperty.TURN:
536 turnColour.setSelected(true);
540 case ColourSchemeProperty.BURIED:
541 buriedColour.setSelected(true);
545 case ColourSchemeProperty.NUCLEOTIDE:
546 nucleotideColour.setSelected(true);
550 case ColourSchemeProperty.TCOFFEE:
551 tcoffeeColour.setSelected(true);
554 case ColourSchemeProperty.PURINEPYRIMIDINE:
555 purinePyrimidineColour.setSelected(true);
559 case ColourSchemeProperty.RNAINTERACTION:
560 RNAInteractionColour.setSelected(true);
564 * case ColourSchemeProperty.COVARIATION:
565 * covariationColour.setSelected(true);
569 case ColourSchemeProperty.USER_DEFINED:
570 userDefinedColour.setSelected(true);
573 case ColourSchemeProperty.NONE:
575 noColourmenuItem.setSelected(true);
583 private void jbInit() throws Exception
585 fileMenu.setText(MessageManager.getString("action.file"));
586 saveAs.setText(MessageManager.getString("action.save_as") + "...");
587 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
588 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
589 .getMenuShortcutKeyMask()
590 | java.awt.event.KeyEvent.SHIFT_MASK, false));
591 saveAs.addActionListener(new ActionListener()
594 public void actionPerformed(ActionEvent e)
596 saveAs_actionPerformed(e);
599 closeMenuItem.setText(MessageManager.getString("action.close"));
600 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
601 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
602 .getMenuShortcutKeyMask(), false));
603 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
606 public void actionPerformed(ActionEvent e)
608 closeMenuItem_actionPerformed(false);
611 editMenu.setText(MessageManager.getString("action.edit"));
612 viewMenu.setText(MessageManager.getString("action.view"));
613 colourMenu.setText(MessageManager.getString("action.colour"));
614 calculateMenu.setText(MessageManager.getString("action.calculate"));
615 webService.setText(MessageManager.getString("action.web_service"));
616 selectAllSequenceMenuItem.setText(MessageManager
617 .getString("action.select_all"));
618 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
619 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
620 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
621 selectAllSequenceMenuItem
622 .addActionListener(new java.awt.event.ActionListener()
625 public void actionPerformed(ActionEvent e)
627 selectAllSequenceMenuItem_actionPerformed(e);
630 deselectAllSequenceMenuItem.setText(MessageManager
631 .getString("action.deselect_all"));
632 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
633 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
634 deselectAllSequenceMenuItem
635 .addActionListener(new java.awt.event.ActionListener()
638 public void actionPerformed(ActionEvent e)
640 deselectAllSequenceMenuItem_actionPerformed(e);
643 invertSequenceMenuItem.setText(MessageManager
644 .getString("action.invert_sequence_selection"));
645 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
646 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
647 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
648 invertSequenceMenuItem
649 .addActionListener(new java.awt.event.ActionListener()
652 public void actionPerformed(ActionEvent e)
654 invertSequenceMenuItem_actionPerformed(e);
657 grpsFromSelection.setText(MessageManager
658 .getString("action.make_groups_selection"));
659 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
662 public void actionPerformed(ActionEvent e)
664 makeGrpsFromSelection_actionPerformed(e);
667 expandAlignment.setText(MessageManager
668 .getString("action.view_flanking_regions"));
669 expandAlignment.setToolTipText(MessageManager
670 .getString("label.view_flanking_regions"));
671 expandAlignment.addActionListener(new java.awt.event.ActionListener()
674 public void actionPerformed(ActionEvent e)
679 remove2LeftMenuItem.setText(MessageManager
680 .getString("action.remove_left"));
681 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
682 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
683 .getMenuShortcutKeyMask(), false));
685 .addActionListener(new java.awt.event.ActionListener()
688 public void actionPerformed(ActionEvent e)
690 remove2LeftMenuItem_actionPerformed(e);
693 remove2RightMenuItem.setText(MessageManager
694 .getString("action.remove_right"));
695 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
696 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
697 .getMenuShortcutKeyMask(), false));
699 .addActionListener(new java.awt.event.ActionListener()
702 public void actionPerformed(ActionEvent e)
704 remove2RightMenuItem_actionPerformed(e);
707 removeGappedColumnMenuItem.setText(MessageManager
708 .getString("action.remove_empty_columns"));
709 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
710 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
711 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
712 removeGappedColumnMenuItem
713 .addActionListener(new java.awt.event.ActionListener()
716 public void actionPerformed(ActionEvent e)
718 removeGappedColumnMenuItem_actionPerformed(e);
721 removeAllGapsMenuItem.setText(MessageManager
722 .getString("action.remove_all_gaps"));
723 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
724 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
725 .getDefaultToolkit().getMenuShortcutKeyMask()
726 | java.awt.event.KeyEvent.SHIFT_MASK, false));
727 removeAllGapsMenuItem
728 .addActionListener(new java.awt.event.ActionListener()
731 public void actionPerformed(ActionEvent e)
733 removeAllGapsMenuItem_actionPerformed(e);
736 justifyLeftMenuItem.setText(MessageManager
737 .getString("action.left_justify_alignment"));
739 .addActionListener(new java.awt.event.ActionListener()
742 public void actionPerformed(ActionEvent e)
744 justifyLeftMenuItem_actionPerformed(e);
747 justifyRightMenuItem.setText(MessageManager
748 .getString("action.right_justify_alignment"));
750 .addActionListener(new java.awt.event.ActionListener()
753 public void actionPerformed(ActionEvent e)
755 justifyRightMenuItem_actionPerformed(e);
758 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
759 viewBoxesMenuItem.setState(true);
760 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
763 public void actionPerformed(ActionEvent e)
765 viewBoxesMenuItem_actionPerformed(e);
768 viewTextMenuItem.setText(MessageManager.getString("action.text"));
769 viewTextMenuItem.setState(true);
770 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
773 public void actionPerformed(ActionEvent e)
775 viewTextMenuItem_actionPerformed(e);
778 showNonconservedMenuItem.setText(MessageManager
779 .getString("label.show_non_conversed"));
780 showNonconservedMenuItem.setState(false);
781 showNonconservedMenuItem
782 .addActionListener(new java.awt.event.ActionListener()
785 public void actionPerformed(ActionEvent e)
787 showUnconservedMenuItem_actionPerformed(e);
790 sortPairwiseMenuItem.setText(MessageManager
791 .getString("action.by_pairwise_id"));
793 .addActionListener(new java.awt.event.ActionListener()
796 public void actionPerformed(ActionEvent e)
798 sortPairwiseMenuItem_actionPerformed(e);
801 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
802 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
805 public void actionPerformed(ActionEvent e)
807 sortIDMenuItem_actionPerformed(e);
811 .setText(MessageManager.getString("action.by_length"));
813 .addActionListener(new java.awt.event.ActionListener()
816 public void actionPerformed(ActionEvent e)
818 sortLengthMenuItem_actionPerformed(e);
821 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
822 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
825 public void actionPerformed(ActionEvent e)
827 sortGroupMenuItem_actionPerformed(e);
830 removeRedundancyMenuItem.setText(MessageManager
831 .getString("action.remove_redundancy"));
832 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
833 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
834 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
835 removeRedundancyMenuItem
836 .addActionListener(new java.awt.event.ActionListener()
839 public void actionPerformed(ActionEvent e)
841 removeRedundancyMenuItem_actionPerformed(e);
844 pairwiseAlignmentMenuItem.setText(MessageManager
845 .getString("action.pairwise_alignment"));
846 pairwiseAlignmentMenuItem
847 .addActionListener(new java.awt.event.ActionListener()
850 public void actionPerformed(ActionEvent e)
852 pairwiseAlignmentMenuItem_actionPerformed(e);
855 PCAMenuItem.setText(MessageManager
856 .getString("label.principal_component_analysis"));
857 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
860 public void actionPerformed(ActionEvent e)
862 PCAMenuItem_actionPerformed(e);
865 averageDistanceTreeMenuItem.setText(MessageManager
866 .getString("label.average_distance_identity"));
867 averageDistanceTreeMenuItem
868 .addActionListener(new java.awt.event.ActionListener()
871 public void actionPerformed(ActionEvent e)
873 averageDistanceTreeMenuItem_actionPerformed(e);
876 neighbourTreeMenuItem.setText(MessageManager
877 .getString("label.neighbour_joining_identity"));
878 neighbourTreeMenuItem
879 .addActionListener(new java.awt.event.ActionListener()
882 public void actionPerformed(ActionEvent e)
884 neighbourTreeMenuItem_actionPerformed(e);
887 this.getContentPane().setLayout(borderLayout1);
888 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
889 statusBar.setBackground(Color.white);
890 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
891 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
892 statusBar.setText(MessageManager.getString("label.status_bar"));
893 outputTextboxMenu.setText(MessageManager
894 .getString("label.out_to_textbox"));
895 clustalColour.setText(MessageManager.getString("label.clustalx"));
897 clustalColour.addActionListener(new java.awt.event.ActionListener()
900 public void actionPerformed(ActionEvent e)
902 clustalColour_actionPerformed(e);
905 zappoColour.setText(MessageManager.getString("label.zappo"));
906 zappoColour.addActionListener(new java.awt.event.ActionListener()
909 public void actionPerformed(ActionEvent e)
911 zappoColour_actionPerformed(e);
914 taylorColour.setText(MessageManager.getString("label.taylor"));
915 taylorColour.addActionListener(new java.awt.event.ActionListener()
918 public void actionPerformed(ActionEvent e)
920 taylorColour_actionPerformed(e);
923 hydrophobicityColour.setText(MessageManager
924 .getString("label.hydrophobicity"));
926 .addActionListener(new java.awt.event.ActionListener()
929 public void actionPerformed(ActionEvent e)
931 hydrophobicityColour_actionPerformed(e);
934 helixColour.setText(MessageManager.getString("label.helix_propensity"));
935 helixColour.addActionListener(new java.awt.event.ActionListener()
938 public void actionPerformed(ActionEvent e)
940 helixColour_actionPerformed(e);
943 strandColour.setText(MessageManager
944 .getString("label.strand_propensity"));
945 strandColour.addActionListener(new java.awt.event.ActionListener()
948 public void actionPerformed(ActionEvent e)
950 strandColour_actionPerformed(e);
953 turnColour.setText(MessageManager.getString("label.turn_propensity"));
954 turnColour.addActionListener(new java.awt.event.ActionListener()
957 public void actionPerformed(ActionEvent e)
959 turnColour_actionPerformed(e);
962 buriedColour.setText(MessageManager.getString("label.buried_index"));
963 buriedColour.addActionListener(new java.awt.event.ActionListener()
966 public void actionPerformed(ActionEvent e)
968 buriedColour_actionPerformed(e);
971 userDefinedColour.setText(MessageManager
972 .getString("action.user_defined"));
973 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
976 public void actionPerformed(ActionEvent e)
978 userDefinedColour_actionPerformed(e);
982 .setText(MessageManager.getString("label.percentage_identity"));
983 PIDColour.addActionListener(new java.awt.event.ActionListener()
986 public void actionPerformed(ActionEvent e)
988 PIDColour_actionPerformed(e);
992 .setText(MessageManager.getString("label.blosum62_score"));
993 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
996 public void actionPerformed(ActionEvent e)
998 BLOSUM62Colour_actionPerformed(e);
1001 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1002 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1005 public void actionPerformed(ActionEvent e)
1007 nucleotideColour_actionPerformed(e);
1011 purinePyrimidineColour.setText(MessageManager
1012 .getString("label.purine_pyrimidine"));
1013 purinePyrimidineColour
1014 .addActionListener(new java.awt.event.ActionListener()
1017 public void actionPerformed(ActionEvent e)
1019 purinePyrimidineColour_actionPerformed(e);
1023 RNAInteractionColour.setText("RNA Interaction type");
1024 RNAInteractionColour
1025 .addActionListener(new java.awt.event.ActionListener()
1028 public void actionPerformed(ActionEvent e)
1030 RNAInteractionColour_actionPerformed(e);
1034 * covariationColour.setText("Covariation");
1035 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1036 * public void actionPerformed(ActionEvent e) {
1037 * covariationColour_actionPerformed(e); } });
1040 avDistanceTreeBlosumMenuItem.setText(MessageManager
1041 .getString("label.average_distance_bloslum62"));
1042 avDistanceTreeBlosumMenuItem
1043 .addActionListener(new java.awt.event.ActionListener()
1046 public void actionPerformed(ActionEvent e)
1048 avTreeBlosumMenuItem_actionPerformed(e);
1051 njTreeBlosumMenuItem.setText(MessageManager
1052 .getString("label.neighbour_blosum62"));
1053 njTreeBlosumMenuItem
1054 .addActionListener(new java.awt.event.ActionListener()
1057 public void actionPerformed(ActionEvent e)
1059 njTreeBlosumMenuItem_actionPerformed(e);
1062 annotationPanelMenuItem.setActionCommand("");
1063 annotationPanelMenuItem.setText(MessageManager
1064 .getString("label.show_annotations"));
1065 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1067 annotationPanelMenuItem.addActionListener(new ActionListener()
1070 public void actionPerformed(ActionEvent e)
1072 annotationPanelMenuItem_actionPerformed(e);
1076 * Show/hide all annotations only enabled if annotation panel is shown
1078 showAllAnnotations.setText(MessageManager
1079 .getString("label.show_all_annotations"));
1080 showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
1081 showAllAnnotations.addActionListener(new ActionListener()
1084 public void actionPerformed(ActionEvent e)
1086 showAllAnnotations_actionPerformed();
1089 hideAllAnnotations.setText(MessageManager
1090 .getString("label.hide_all_annotations"));
1091 hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
1092 hideAllAnnotations.addActionListener(new ActionListener()
1095 public void actionPerformed(ActionEvent e)
1097 hideAllAnnotations_actionPerformed();
1100 colourTextMenuItem.setText(MessageManager
1101 .getString("label.colour_text"));
1103 .addActionListener(new java.awt.event.ActionListener()
1106 public void actionPerformed(ActionEvent e)
1108 colourTextMenuItem_actionPerformed(e);
1111 htmlMenuItem.setText(MessageManager.getString("label.html"));
1112 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1115 public void actionPerformed(ActionEvent e)
1117 htmlMenuItem_actionPerformed(e);
1120 overviewMenuItem.setText(MessageManager
1121 .getString("label.overview_window"));
1122 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1125 public void actionPerformed(ActionEvent e)
1127 overviewMenuItem_actionPerformed(e);
1130 undoMenuItem.setEnabled(false);
1131 undoMenuItem.setText(MessageManager.getString("action.undo"));
1132 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1133 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1134 .getMenuShortcutKeyMask(), false));
1135 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1138 public void actionPerformed(ActionEvent e)
1140 undoMenuItem_actionPerformed(e);
1143 redoMenuItem.setEnabled(false);
1144 redoMenuItem.setText(MessageManager.getString("action.redo"));
1145 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1146 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1147 .getMenuShortcutKeyMask(), false));
1148 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1151 public void actionPerformed(ActionEvent e)
1153 redoMenuItem_actionPerformed(e);
1156 conservationMenuItem.setText(MessageManager
1157 .getString("action.by_conservation"));
1158 conservationMenuItem
1159 .addActionListener(new java.awt.event.ActionListener()
1162 public void actionPerformed(ActionEvent e)
1164 conservationMenuItem_actionPerformed(e);
1167 noColourmenuItem.setText(MessageManager.getString("label.none"));
1168 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1171 public void actionPerformed(ActionEvent e)
1173 noColourmenuItem_actionPerformed(e);
1176 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1177 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1180 public void actionPerformed(ActionEvent e)
1182 wrapMenuItem_actionPerformed(e);
1185 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1186 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1187 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1188 .getMenuShortcutKeyMask(), false));
1189 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1192 public void actionPerformed(ActionEvent e)
1194 printMenuItem_actionPerformed(e);
1198 .setText(MessageManager.getString("action.show_gaps"));
1199 renderGapsMenuItem.setState(true);
1201 .addActionListener(new java.awt.event.ActionListener()
1204 public void actionPerformed(ActionEvent e)
1206 renderGapsMenuItem_actionPerformed(e);
1209 findMenuItem.setText(MessageManager.getString("action.find"));
1210 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1211 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1212 .getMenuShortcutKeyMask(), false));
1213 findMenuItem.setToolTipText(MessageManager.getString("label.find_tip"));
1214 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1217 public void actionPerformed(ActionEvent e)
1219 findMenuItem_actionPerformed(e);
1222 abovePIDThreshold.setText(MessageManager
1223 .getString("label.above_identity_threshold"));
1224 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1227 public void actionPerformed(ActionEvent e)
1229 abovePIDThreshold_actionPerformed(e);
1232 showSeqFeatures.setText(MessageManager
1233 .getString("label.show_sequence_features"));
1234 showSeqFeatures.addActionListener(new ActionListener()
1237 public void actionPerformed(ActionEvent actionEvent)
1239 showSeqFeatures_actionPerformed(actionEvent);
1243 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1244 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1245 * void actionPerformed(ActionEvent actionEvent) {
1246 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1248 showDbRefsMenuitem.setText(MessageManager
1249 .getString("label.show_database_refs"));
1250 showDbRefsMenuitem.addActionListener(new ActionListener()
1254 public void actionPerformed(ActionEvent e)
1256 showDbRefs_actionPerformed(e);
1260 showNpFeatsMenuitem.setText(MessageManager
1261 .getString("label.show_non_positional_features"));
1262 showNpFeatsMenuitem.addActionListener(new ActionListener()
1266 public void actionPerformed(ActionEvent e)
1268 showNpFeats_actionPerformed(e);
1272 showGroupConservation.setText(MessageManager
1273 .getString("label.group_conservation"));
1274 showGroupConservation.addActionListener(new ActionListener()
1278 public void actionPerformed(ActionEvent e)
1280 showGroupConservation_actionPerformed(e);
1285 showGroupConsensus.setText(MessageManager
1286 .getString("label.group_consensus"));
1287 showGroupConsensus.addActionListener(new ActionListener()
1291 public void actionPerformed(ActionEvent e)
1293 showGroupConsensus_actionPerformed(e);
1297 showConsensusHistogram.setText(MessageManager
1298 .getString("label.show_consensus_histogram"));
1299 showConsensusHistogram.addActionListener(new ActionListener()
1303 public void actionPerformed(ActionEvent e)
1305 showConsensusHistogram_actionPerformed(e);
1309 showSequenceLogo.setText(MessageManager
1310 .getString("label.show_consensus_logo"));
1311 showSequenceLogo.addActionListener(new ActionListener()
1315 public void actionPerformed(ActionEvent e)
1317 showSequenceLogo_actionPerformed(e);
1321 normaliseSequenceLogo.setText(MessageManager
1322 .getString("label.norm_consensus_logo"));
1323 normaliseSequenceLogo.addActionListener(new ActionListener()
1327 public void actionPerformed(ActionEvent e)
1329 normaliseSequenceLogo_actionPerformed(e);
1333 applyAutoAnnotationSettings.setText(MessageManager
1334 .getString("label.apply_all_groups"));
1335 applyAutoAnnotationSettings.setState(false);
1336 applyAutoAnnotationSettings.setVisible(true);
1337 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1341 public void actionPerformed(ActionEvent e)
1343 applyAutoAnnotationSettings_actionPerformed(e);
1348 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1349 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1352 public void actionPerformed(ActionEvent e)
1354 nucleotideColour_actionPerformed(e);
1358 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1359 tcoffeeColour.setEnabled(false);
1360 tcoffeeColour.addActionListener(new ActionListener()
1364 public void actionPerformed(ActionEvent e)
1366 tcoffeeColorScheme_actionPerformed(e);
1371 .setText(MessageManager.getString("action.undefine_groups"));
1372 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1373 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1374 .getMenuShortcutKeyMask(), false));
1375 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1378 public void actionPerformed(ActionEvent e)
1380 deleteGroups_actionPerformed(e);
1383 createGroup.setText(MessageManager.getString("action.create_groups"));
1384 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1385 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1386 .getMenuShortcutKeyMask(), false));
1387 createGroup.addActionListener(new java.awt.event.ActionListener()
1390 public void actionPerformed(ActionEvent e)
1392 createGroup_actionPerformed(e);
1395 unGroup.setText(MessageManager.getString("action.remove_group"));
1396 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1397 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1398 .getMenuShortcutKeyMask()
1399 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1400 unGroup.addActionListener(new java.awt.event.ActionListener()
1403 public void actionPerformed(ActionEvent e)
1405 unGroup_actionPerformed(e);
1408 copy.setText(MessageManager.getString("action.copy"));
1409 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1410 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1411 .getMenuShortcutKeyMask(), false));
1413 copy.addActionListener(new java.awt.event.ActionListener()
1416 public void actionPerformed(ActionEvent e)
1418 copy_actionPerformed(e);
1421 cut.setText(MessageManager.getString("action.cut"));
1422 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1423 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1424 .getMenuShortcutKeyMask(), false));
1425 cut.addActionListener(new java.awt.event.ActionListener()
1428 public void actionPerformed(ActionEvent e)
1430 cut_actionPerformed(e);
1433 delete.setText(MessageManager.getString("action.delete"));
1434 delete.addActionListener(new java.awt.event.ActionListener()
1437 public void actionPerformed(ActionEvent e)
1439 delete_actionPerformed(e);
1442 pasteMenu.setText(MessageManager.getString("action.paste"));
1443 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1444 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1445 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1446 .getMenuShortcutKeyMask()
1447 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1448 pasteNew.addActionListener(new java.awt.event.ActionListener()
1451 public void actionPerformed(ActionEvent e)
1453 pasteNew_actionPerformed(e);
1456 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1457 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1458 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1459 .getMenuShortcutKeyMask(), false));
1460 pasteThis.addActionListener(new java.awt.event.ActionListener()
1463 public void actionPerformed(ActionEvent e)
1465 pasteThis_actionPerformed(e);
1468 applyToAllGroups.setText(MessageManager
1469 .getString("label.apply_colour_to_all_groups"));
1470 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1473 public void actionPerformed(ActionEvent e)
1475 applyToAllGroups_actionPerformed(e);
1478 createPNG.addActionListener(new java.awt.event.ActionListener()
1481 public void actionPerformed(ActionEvent e)
1486 createPNG.setActionCommand(MessageManager
1487 .getString("label.save_png_image"));
1488 createPNG.setText("PNG");
1489 font.setText(MessageManager.getString("action.font"));
1490 font.addActionListener(new java.awt.event.ActionListener()
1493 public void actionPerformed(ActionEvent e)
1495 font_actionPerformed(e);
1499 seqLimits.setText(MessageManager
1500 .getString("label.show_sequence_limits"));
1501 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1502 seqLimits.addActionListener(new java.awt.event.ActionListener()
1505 public void actionPerformed(ActionEvent e)
1507 seqLimit_actionPerformed(e);
1510 epsFile.setText("EPS");
1511 epsFile.addActionListener(new java.awt.event.ActionListener()
1514 public void actionPerformed(ActionEvent e)
1519 LoadtreeMenuItem.setActionCommand(MessageManager
1520 .getString("label.load_tree_for_sequence_set"));
1521 LoadtreeMenuItem.setText(MessageManager
1522 .getString("label.load_associated_tree"));
1523 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1526 public void actionPerformed(ActionEvent e)
1528 LoadtreeMenuItem_actionPerformed(e);
1532 scaleAbove.setVisible(false);
1533 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1534 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1537 public void actionPerformed(ActionEvent e)
1539 scaleAbove_actionPerformed(e);
1542 scaleLeft.setVisible(false);
1543 scaleLeft.setSelected(true);
1544 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1545 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1548 public void actionPerformed(ActionEvent e)
1550 scaleLeft_actionPerformed(e);
1553 scaleRight.setVisible(false);
1554 scaleRight.setSelected(true);
1555 scaleRight.setText(MessageManager.getString("action.scale_right"));
1556 scaleRight.addActionListener(new java.awt.event.ActionListener()
1559 public void actionPerformed(ActionEvent e)
1561 scaleRight_actionPerformed(e);
1564 centreColumnLabelsMenuItem.setVisible(true);
1565 centreColumnLabelsMenuItem.setState(false);
1566 centreColumnLabelsMenuItem.setText(MessageManager
1567 .getString("label.centre_column_labels"));
1568 centreColumnLabelsMenuItem
1569 .addActionListener(new java.awt.event.ActionListener()
1572 public void actionPerformed(ActionEvent e)
1574 centreColumnLabels_actionPerformed(e);
1577 followHighlightMenuItem.setVisible(true);
1578 followHighlightMenuItem.setState(true);
1579 followHighlightMenuItem.setText(MessageManager
1580 .getString("label.automatic_scrolling"));
1581 followHighlightMenuItem.addActionListener(new ActionListener()
1585 public void actionPerformed(ActionEvent e)
1587 followHighlight_actionPerformed();
1592 modifyPID.setText(MessageManager
1593 .getString("label.modify_identity_thereshold"));
1594 modifyPID.addActionListener(new java.awt.event.ActionListener()
1597 public void actionPerformed(ActionEvent e)
1599 modifyPID_actionPerformed(e);
1602 modifyConservation.setText(MessageManager
1603 .getString("label.modify_conservation_thereshold"));
1605 .addActionListener(new java.awt.event.ActionListener()
1608 public void actionPerformed(ActionEvent e)
1610 modifyConservation_actionPerformed(e);
1614 .setText(MessageManager.getString("action.by_tree_order"));
1615 sort.setText(MessageManager.getString("action.sort"));
1616 sort.addMenuListener(new MenuListener()
1619 public void menuSelected(MenuEvent e)
1625 public void menuDeselected(MenuEvent e)
1630 public void menuCanceled(MenuEvent e)
1634 sortByAnnotScore.setText(MessageManager
1635 .getString("label.sort_by_score"));
1636 sort.add(sortByAnnotScore);
1637 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1641 public void menuCanceled(MenuEvent e)
1646 public void menuDeselected(MenuEvent e)
1651 public void menuSelected(MenuEvent e)
1653 buildSortByAnnotationScoresMenu();
1656 sortByAnnotScore.setVisible(false);
1659 .setText(MessageManager.getString("action.calculate_tree"));
1661 jMenu2.setText(MessageManager.getString("label.export_image"));
1662 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1663 padGapsMenuitem.setState(jalview.bin.Cache
1664 .getDefault("PAD_GAPS", false));
1665 padGapsMenuitem.addActionListener(new ActionListener()
1668 public void actionPerformed(ActionEvent e)
1670 padGapsMenuitem_actionPerformed(e);
1673 vamsasStore.setVisible(false);
1674 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1675 vamsasStore.addActionListener(new ActionListener()
1678 public void actionPerformed(ActionEvent e)
1680 vamsasStore_actionPerformed(e);
1683 showTranslation.setText(MessageManager
1684 .getString("label.translate_cDNA"));
1685 showTranslation.addActionListener(new ActionListener()
1688 public void actionPerformed(ActionEvent e)
1690 showTranslation_actionPerformed(e);
1693 extractScores.setText(MessageManager.getString("label.extract_scores")
1695 extractScores.addActionListener(new ActionListener()
1698 public void actionPerformed(ActionEvent e)
1700 extractScores_actionPerformed(e);
1703 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1705 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1707 * showProducts.addActionListener(new ActionListener() {
1709 * public void actionPerformed(ActionEvent e) {
1710 * showProducts_actionPerformed(e); } });
1712 openFeatureSettings.setText(MessageManager
1713 .getString("label.feature_settings"));
1714 openFeatureSettings.addActionListener(new ActionListener()
1717 public void actionPerformed(ActionEvent e)
1719 featureSettings_actionPerformed(e);
1723 .setText(MessageManager.getString("label.fetch_sequences"));
1724 fetchSequence.addActionListener(new ActionListener()
1727 public void actionPerformed(ActionEvent e)
1729 fetchSequence_actionPerformed(e);
1733 annotationColour.setText(MessageManager
1734 .getString("action.by_annotation"));
1735 annotationColour.addActionListener(new ActionListener()
1738 public void actionPerformed(ActionEvent e)
1740 annotationColour_actionPerformed(e);
1744 rnahelicesColour.setText(MessageManager
1745 .getString("action.by_rna_helixes"));
1746 rnahelicesColour.addActionListener(new ActionListener()
1749 public void actionPerformed(ActionEvent e)
1751 rnahelicesColour_actionPerformed(e);
1755 associatedData.setText(MessageManager
1756 .getString("label.load_features_annotations"));
1757 associatedData.addActionListener(new ActionListener()
1760 public void actionPerformed(ActionEvent e)
1762 associatedData_actionPerformed(e);
1765 autoCalculate.setText(MessageManager
1766 .getString("label.autocalculate_consensus"));
1767 autoCalculate.setState(jalview.bin.Cache.getDefault(
1768 "AUTO_CALC_CONSENSUS", true));
1769 autoCalculate.addActionListener(new ActionListener()
1772 public void actionPerformed(ActionEvent e)
1774 autoCalculate_actionPerformed(e);
1777 sortByTree.setText(MessageManager
1778 .getString("label.sort_alignment_new_tree"));
1780 .setToolTipText("<html>"
1782 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1784 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1785 sortByTree.addActionListener(new ActionListener()
1788 public void actionPerformed(ActionEvent e)
1790 sortByTreeOption_actionPerformed(e);
1794 listenToViewSelections.setText(MessageManager
1795 .getString("label.listen_for_selections"));
1796 listenToViewSelections
1797 .setToolTipText("<html>"
1799 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1800 listenToViewSelections.setState(false);
1801 listenToViewSelections.addActionListener(new ActionListener()
1804 public void actionPerformed(ActionEvent e)
1806 listenToViewSelections_actionPerformed(e);
1811 .setText(MessageManager.getString("label.add_sequences"));
1812 addFromFile.setText(MessageManager.getString("label.from_file"));
1813 addFromFile.addActionListener(new ActionListener()
1816 public void actionPerformed(ActionEvent e)
1818 addFromFile_actionPerformed(e);
1821 addFromText.setText(MessageManager.getString("label.from_textbox"));
1822 addFromText.addActionListener(new ActionListener()
1825 public void actionPerformed(ActionEvent e)
1827 addFromText_actionPerformed(e);
1830 addFromURL.setText(MessageManager.getString("label.from_url"));
1831 addFromURL.addActionListener(new ActionListener()
1834 public void actionPerformed(ActionEvent e)
1836 addFromURL_actionPerformed(e);
1839 exportFeatures.setText(MessageManager
1840 .getString("label.export_features"));
1841 exportFeatures.addActionListener(new ActionListener()
1844 public void actionPerformed(ActionEvent e)
1846 exportFeatures_actionPerformed(e);
1849 exportAnnotations.setText(MessageManager
1850 .getString("label.export_annotations"));
1851 exportAnnotations.addActionListener(new ActionListener()
1854 public void actionPerformed(ActionEvent e)
1856 exportAnnotations_actionPerformed(e);
1859 statusPanel.setLayout(gridLayout1);
1860 jMenu3.setText(MessageManager.getString("action.show"));
1861 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1862 showAllSeqs.setToolTipText(MessageManager
1863 .getString("label.toggle_sequence_visibility"));
1864 showAllSeqs.addActionListener(new ActionListener()
1867 public void actionPerformed(ActionEvent e)
1869 showAllSeqs_actionPerformed(e);
1872 showAllColumns.setText(MessageManager.getString("label.all_columns"));
1873 showAllColumns.setToolTipText(MessageManager
1874 .getString("label.toggle_columns_visibility"));
1875 showAllColumns.addActionListener(new ActionListener()
1878 public void actionPerformed(ActionEvent e)
1880 showAllColumns_actionPerformed(e);
1883 hideMenu.setText(MessageManager.getString("action.hide"));
1884 hideSelSequences.setText(MessageManager
1885 .getString("label.selected_sequences"));
1886 hideSelSequences.setToolTipText(MessageManager
1887 .getString("label.toggle_sequence_visibility"));
1888 hideSelSequences.addActionListener(new ActionListener()
1891 public void actionPerformed(ActionEvent e)
1893 hideSelSequences_actionPerformed(e);
1896 hideSelColumns.setText(MessageManager
1897 .getString("label.selected_columns"));
1898 hideSelColumns.setToolTipText(MessageManager
1899 .getString("label.toggle_columns_visibility"));
1900 hideSelColumns.addActionListener(new ActionListener()
1903 public void actionPerformed(ActionEvent e)
1905 hideSelColumns_actionPerformed(e);
1908 hideAllSelection.setText(MessageManager
1909 .getString("label.selected_region"));
1910 hideAllSelection.addActionListener(new ActionListener()
1913 public void actionPerformed(ActionEvent e)
1915 hideAllSelection_actionPerformed(e);
1918 // TODO: should be hidden if no selection exists.
1919 hideAllButSelection.setText(MessageManager
1920 .getString("label.all_but_selected_region"));
1921 hideAllButSelection.addActionListener(new ActionListener()
1924 public void actionPerformed(ActionEvent e)
1926 hideAllButSelection_actionPerformed(e);
1929 showAllhidden.setText(MessageManager
1930 .getString("label.all_sequences_columns"));
1931 showAllhidden.setToolTipText(MessageManager
1932 .getString("label.toggles_visibility_hidden_selected_regions"));
1933 showAllhidden.addActionListener(new ActionListener()
1936 public void actionPerformed(ActionEvent e)
1938 showAllhidden_actionPerformed(e);
1941 hiddenMarkers.setText(MessageManager
1942 .getString("action.show_hidden_markers"));
1943 hiddenMarkers.addActionListener(new ActionListener()
1946 public void actionPerformed(ActionEvent e)
1948 hiddenMarkers_actionPerformed(e);
1951 invertColSel.setText(MessageManager
1952 .getString("action.invert_column_selection"));
1953 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1954 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1955 .getMenuShortcutKeyMask()
1956 | java.awt.event.KeyEvent.ALT_MASK, false));
1957 invertColSel.addActionListener(new ActionListener()
1960 public void actionPerformed(ActionEvent e)
1962 invertColSel_actionPerformed(e);
1965 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1968 public void stateChanged(ChangeEvent evt)
1970 JTabbedPane pane = (JTabbedPane) evt.getSource();
1971 int sel = pane.getSelectedIndex();
1972 tabSelectionChanged(sel);
1975 tabbedPane.addMouseListener(new MouseAdapter()
1978 public void mousePressed(MouseEvent e)
1980 tabbedPane_mousePressed(e);
1983 tabbedPane.addFocusListener(new FocusAdapter()
1986 public void focusGained(FocusEvent e)
1988 tabbedPane_focusGained(e);
1991 save.setText(MessageManager.getString("action.save"));
1992 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1993 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1994 .getMenuShortcutKeyMask(), false));
1995 save.addActionListener(new ActionListener()
1998 public void actionPerformed(ActionEvent e)
2000 save_actionPerformed(e);
2003 reload.setEnabled(false);
2004 reload.setText(MessageManager.getString("action.reload"));
2005 reload.addActionListener(new ActionListener()
2008 public void actionPerformed(ActionEvent e)
2010 reload_actionPerformed(e);
2013 newView.setText(MessageManager.getString("action.new_view"));
2014 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2015 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2016 .getMenuShortcutKeyMask(), false));
2017 newView.addActionListener(new ActionListener()
2020 public void actionPerformed(ActionEvent e)
2022 newView_actionPerformed(e);
2025 tabbedPane.setToolTipText("<html><i>"
2026 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2028 textColour.setText(MessageManager.getString("label.colour_text")
2030 textColour.addActionListener(new ActionListener()
2033 public void actionPerformed(ActionEvent e)
2035 textColour_actionPerformed(e);
2038 formatMenu.setText(MessageManager.getString("action.format"));
2039 selectMenu.setText(MessageManager.getString("action.select"));
2040 idRightAlign.setText(MessageManager
2041 .getString("label.right_align_sequence_id"));
2042 idRightAlign.addActionListener(new ActionListener()
2045 public void actionPerformed(ActionEvent e)
2047 idRightAlign_actionPerformed(e);
2050 gatherViews.setEnabled(false);
2051 gatherViews.setText(MessageManager.getString("action.gather_views"));
2052 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2053 java.awt.event.KeyEvent.VK_G, 0, false));
2054 gatherViews.addActionListener(new ActionListener()
2057 public void actionPerformed(ActionEvent e)
2059 gatherViews_actionPerformed(e);
2062 expandViews.setEnabled(false);
2063 expandViews.setText(MessageManager.getString("action.expand_views"));
2064 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2065 java.awt.event.KeyEvent.VK_X, 0, false));
2066 expandViews.addActionListener(new ActionListener()
2069 public void actionPerformed(ActionEvent e)
2071 expandViews_actionPerformed(e);
2075 .setText(MessageManager.getString("action.page_setup") + "...");
2076 pageSetup.addActionListener(new ActionListener()
2079 public void actionPerformed(ActionEvent e)
2081 pageSetup_actionPerformed(e);
2084 alignmentProperties.setText(MessageManager
2085 .getString("label.alignment_props") + "...");
2086 alignmentProperties.addActionListener(new ActionListener()
2089 public void actionPerformed(ActionEvent actionEvent)
2091 alignmentProperties();
2094 tooltipSettingsMenu.setText(MessageManager
2095 .getString("label.sequence_id_tooltip"));
2096 autoAnnMenu.setText(MessageManager
2097 .getString("label.autocalculated_annotation"));
2098 alignFrameMenuBar.add(fileMenu);
2099 alignFrameMenuBar.add(editMenu);
2100 alignFrameMenuBar.add(selectMenu);
2101 alignFrameMenuBar.add(viewMenu);
2102 alignFrameMenuBar.add(formatMenu);
2103 alignFrameMenuBar.add(colourMenu);
2104 alignFrameMenuBar.add(calculateMenu);
2105 alignFrameMenuBar.add(webService);
2106 fileMenu.add(fetchSequence);
2107 fileMenu.add(addSequenceMenu);
2108 fileMenu.add(reload);
2109 fileMenu.addSeparator();
2110 fileMenu.add(vamsasStore);
2112 fileMenu.add(saveAs);
2113 fileMenu.add(outputTextboxMenu);
2114 fileMenu.add(pageSetup);
2115 fileMenu.add(printMenuItem);
2116 fileMenu.addSeparator();
2117 fileMenu.add(jMenu2);
2118 fileMenu.add(exportFeatures);
2119 fileMenu.add(exportAnnotations);
2120 fileMenu.add(LoadtreeMenuItem);
2121 fileMenu.add(associatedData);
2122 fileMenu.addSeparator();
2123 fileMenu.add(closeMenuItem);
2124 editMenu.add(undoMenuItem);
2125 editMenu.add(redoMenuItem);
2128 editMenu.add(pasteMenu);
2129 editMenu.add(delete);
2130 editMenu.addSeparator();
2131 editMenu.add(remove2LeftMenuItem);
2132 editMenu.add(remove2RightMenuItem);
2133 editMenu.add(removeGappedColumnMenuItem);
2134 editMenu.add(removeAllGapsMenuItem);
2135 editMenu.add(removeRedundancyMenuItem);
2136 editMenu.addSeparator();
2137 // dont add these yet in the CVS build - they cannot be undone!
2138 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2139 // editMenu.add(justifyLeftMenuItem);
2140 // editMenu.add(justifyRightMenuItem);
2141 // editMenu.addSeparator();
2142 editMenu.add(padGapsMenuitem);
2143 viewMenu.add(newView);
2144 viewMenu.add(expandViews);
2145 viewMenu.add(gatherViews);
2146 viewMenu.addSeparator();
2147 viewMenu.add(jMenu3);
2148 viewMenu.add(hideMenu);
2149 viewMenu.addSeparator();
2150 viewMenu.add(followHighlightMenuItem);
2151 viewMenu.add(annotationPanelMenuItem);
2152 viewMenu.add(showAllAnnotations);
2153 viewMenu.add(hideAllAnnotations);
2154 autoAnnMenu.add(applyAutoAnnotationSettings);
2155 autoAnnMenu.add(showConsensusHistogram);
2156 autoAnnMenu.add(showSequenceLogo);
2157 autoAnnMenu.add(normaliseSequenceLogo);
2158 autoAnnMenu.addSeparator();
2159 autoAnnMenu.add(showGroupConservation);
2160 autoAnnMenu.add(showGroupConsensus);
2161 viewMenu.add(autoAnnMenu);
2162 viewMenu.addSeparator();
2163 viewMenu.add(showSeqFeatures);
2164 // viewMenu.add(showSeqFeaturesHeight);
2166 viewMenu.add(openFeatureSettings);
2167 tooltipSettingsMenu.add(showDbRefsMenuitem);
2168 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2169 viewMenu.add(tooltipSettingsMenu);
2170 viewMenu.addSeparator();
2171 viewMenu.add(alignmentProperties);
2172 viewMenu.addSeparator();
2173 viewMenu.add(overviewMenuItem);
2174 colourMenu.add(applyToAllGroups);
2175 colourMenu.add(textColour);
2176 colourMenu.addSeparator();
2177 colourMenu.add(noColourmenuItem);
2178 colourMenu.add(clustalColour);
2179 colourMenu.add(BLOSUM62Colour);
2180 colourMenu.add(PIDColour);
2181 colourMenu.add(zappoColour);
2182 colourMenu.add(taylorColour);
2183 colourMenu.add(hydrophobicityColour);
2184 colourMenu.add(helixColour);
2185 colourMenu.add(strandColour);
2186 colourMenu.add(turnColour);
2187 colourMenu.add(buriedColour);
2188 colourMenu.add(nucleotideColour);
2189 colourMenu.add(purinePyrimidineColour);
2190 colourMenu.add(RNAInteractionColour);
2191 // colourMenu.add(covariationColour);
2192 colourMenu.add(tcoffeeColour);
2193 colourMenu.add(userDefinedColour);
2194 colourMenu.addSeparator();
2195 colourMenu.add(conservationMenuItem);
2196 colourMenu.add(modifyConservation);
2197 colourMenu.add(abovePIDThreshold);
2198 colourMenu.add(modifyPID);
2199 colourMenu.add(annotationColour);
2200 colourMenu.add(rnahelicesColour);
2201 calculateMenu.add(sort);
2202 calculateMenu.add(calculateTree);
2203 calculateMenu.addSeparator();
2204 calculateMenu.add(pairwiseAlignmentMenuItem);
2205 calculateMenu.add(PCAMenuItem);
2206 calculateMenu.addSeparator();
2207 calculateMenu.add(showTranslation);
2208 calculateMenu.add(showProducts);
2209 calculateMenu.add(autoCalculate);
2210 calculateMenu.add(sortByTree);
2211 calculateMenu.addSeparator();
2212 calculateMenu.add(extractScores);
2213 webServiceNoServices = new JMenuItem(
2214 MessageManager.getString("label.no_services"));
2215 webService.add(webServiceNoServices);
2216 pasteMenu.add(pasteNew);
2217 pasteMenu.add(pasteThis);
2218 sort.add(sortIDMenuItem);
2219 sort.add(sortLengthMenuItem);
2220 sort.add(sortGroupMenuItem);
2221 sort.add(sortPairwiseMenuItem);
2222 sort.add(sortByTreeMenu);
2223 jMenu2.add(htmlMenuItem);
2224 jMenu2.add(epsFile);
2225 jMenu2.add(createPNG);
2226 addSequenceMenu.add(addFromFile);
2227 addSequenceMenu.add(addFromText);
2228 addSequenceMenu.add(addFromURL);
2229 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2230 statusPanel.add(statusBar, null);
2231 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2232 jMenu3.add(showAllColumns);
2233 jMenu3.add(showAllSeqs);
2234 jMenu3.add(showAllhidden);
2235 hideMenu.add(hideSelColumns);
2236 hideMenu.add(hideSelSequences);
2237 hideMenu.add(hideAllSelection);
2238 hideMenu.add(hideAllButSelection);
2240 formatMenu.add(font);
2241 formatMenu.addSeparator();
2242 formatMenu.add(wrapMenuItem);
2243 formatMenu.add(scaleAbove);
2244 formatMenu.add(scaleLeft);
2245 formatMenu.add(scaleRight);
2246 formatMenu.add(seqLimits);
2247 formatMenu.add(idRightAlign);
2248 formatMenu.add(hiddenMarkers);
2249 formatMenu.add(viewBoxesMenuItem);
2250 formatMenu.add(viewTextMenuItem);
2251 formatMenu.add(colourTextMenuItem);
2252 formatMenu.add(renderGapsMenuItem);
2253 formatMenu.add(centreColumnLabelsMenuItem);
2254 formatMenu.add(showNonconservedMenuItem);
2255 selectMenu.add(findMenuItem);
2256 selectMenu.addSeparator();
2257 selectMenu.add(selectAllSequenceMenuItem);
2258 selectMenu.add(deselectAllSequenceMenuItem);
2259 selectMenu.add(invertSequenceMenuItem);
2260 selectMenu.add(invertColSel);
2261 selectMenu.add(createGroup);
2262 selectMenu.add(unGroup);
2263 selectMenu.add(grpsFromSelection);
2264 selectMenu.add(deleteGroups);
2265 calculateMenu.add(expandAlignment);
2266 // TODO - determine if the listenToViewSelections button is needed : see bug
2268 // selectMenu.addSeparator();
2269 // selectMenu.add(listenToViewSelections);
2273 * Action on clicking Show all annotations.
2275 protected void showAllAnnotations_actionPerformed()
2277 setAllAnnotationsVisibility(true);
2281 * Action on clicking Hide all annotations.
2283 protected void hideAllAnnotations_actionPerformed()
2285 setAllAnnotationsVisibility(false);
2289 * Set the visibility of all annotations to true or false.
2293 protected void setAllAnnotationsVisibility(boolean visible)
2298 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2300 // TODO Auto-generated method stub
2304 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2306 // TODO Auto-generated method stub
2310 protected void showAllhidden_actionPerformed(ActionEvent e)
2312 // TODO Auto-generated method stub
2316 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2318 // TODO Auto-generated method stub
2322 protected void hideAllSelection_actionPerformed(ActionEvent e)
2324 // TODO Auto-generated method stub
2328 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2330 // TODO Auto-generated method stub
2334 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2336 // TODO Auto-generated method stub
2340 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2342 // TODO Auto-generated method stub
2346 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2348 // TODO Auto-generated method stub
2352 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2354 // TODO Auto-generated method stub
2358 protected void showGroupConservation_actionPerformed(ActionEvent e)
2360 // TODO Auto-generated method stub
2364 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2366 // TODO Auto-generated method stub
2370 protected void showSeqFeaturesHeight_actionPerformed(
2371 ActionEvent actionEvent)
2373 // TODO Auto-generated method stub
2377 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2379 // TODO Auto-generated method stub
2383 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2385 // TODO Auto-generated method stub
2389 protected void followHighlight_actionPerformed()
2391 // TODO Auto-generated method stub
2395 protected void showNpFeats_actionPerformed(ActionEvent e)
2397 // TODO Auto-generated method stub
2401 protected void showDbRefs_actionPerformed(ActionEvent e)
2403 // TODO Auto-generated method stub
2407 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2411 protected void showProducts_actionPerformed(ActionEvent e)
2415 protected void buildSortByAnnotationScoresMenu()
2419 protected void extractScores_actionPerformed(ActionEvent e)
2423 protected void outputText_actionPerformed(ActionEvent e)
2427 public void addFromFile_actionPerformed(ActionEvent e)
2432 public void addFromText_actionPerformed(ActionEvent e)
2437 public void addFromURL_actionPerformed(ActionEvent e)
2442 public void exportFeatures_actionPerformed(ActionEvent e)
2447 public void exportAnnotations_actionPerformed(ActionEvent e)
2452 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2456 protected void closeMenuItem_actionPerformed(boolean b)
2460 protected void redoMenuItem_actionPerformed(ActionEvent e)
2464 protected void undoMenuItem_actionPerformed(ActionEvent e)
2468 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2472 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2476 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2480 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2484 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2488 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2492 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2496 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2500 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2504 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2508 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2512 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2516 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2520 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2524 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2528 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2532 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2536 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2540 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2544 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2548 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2552 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2556 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2560 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2564 protected void clustalColour_actionPerformed(ActionEvent e)
2568 protected void zappoColour_actionPerformed(ActionEvent e)
2572 protected void taylorColour_actionPerformed(ActionEvent e)
2576 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2580 protected void helixColour_actionPerformed(ActionEvent e)
2584 protected void strandColour_actionPerformed(ActionEvent e)
2588 protected void turnColour_actionPerformed(ActionEvent e)
2592 protected void buriedColour_actionPerformed(ActionEvent e)
2596 protected void userDefinedColour_actionPerformed(ActionEvent e)
2600 protected void PIDColour_actionPerformed(ActionEvent e)
2604 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2608 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2612 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2617 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2620 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2624 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2628 protected void printMenuItem_actionPerformed(ActionEvent e)
2632 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2636 protected void findMenuItem_actionPerformed(ActionEvent e)
2640 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2644 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2648 protected void nucleotideColour_actionPerformed(ActionEvent e)
2652 protected void deleteGroups_actionPerformed(ActionEvent e)
2656 protected void createGroup_actionPerformed(ActionEvent e)
2660 protected void unGroup_actionPerformed(ActionEvent e)
2664 protected void copy_actionPerformed(ActionEvent e)
2668 protected void cut_actionPerformed(ActionEvent e)
2672 protected void delete_actionPerformed(ActionEvent e)
2676 protected void pasteNew_actionPerformed(ActionEvent e)
2680 protected void pasteThis_actionPerformed(ActionEvent e)
2684 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2688 public void createPNG(java.io.File f)
2692 protected void font_actionPerformed(ActionEvent e)
2696 protected void seqLimit_actionPerformed(ActionEvent e)
2700 public void seqDBRef_actionPerformed(ActionEvent e)
2705 public void createEPS(java.io.File f)
2709 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2715 * Template method to handle the 'load T-Coffee scores' menu event.
2717 * Subclasses override this method to provide a custom action.
2722 protected void loadScores_actionPerformed(ActionEvent event)
2728 * Template method to handle the 'Color T-Coffee scores' menu event.
2730 * Subclasses override this method to provide a custom action.
2735 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2740 protected void jpred_actionPerformed(ActionEvent e)
2744 protected void scaleAbove_actionPerformed(ActionEvent e)
2748 protected void scaleLeft_actionPerformed(ActionEvent e)
2752 protected void scaleRight_actionPerformed(ActionEvent e)
2756 protected void modifyPID_actionPerformed(ActionEvent e)
2760 protected void modifyConservation_actionPerformed(ActionEvent e)
2764 protected void saveAs_actionPerformed(ActionEvent e)
2768 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2772 public void vamsasStore_actionPerformed(ActionEvent e)
2777 public void vamsasLoad_actionPerformed(ActionEvent e)
2782 public void showTranslation_actionPerformed(ActionEvent e)
2787 public void featureSettings_actionPerformed(ActionEvent e)
2792 public void fetchSequence_actionPerformed(ActionEvent e)
2797 public void smoothFont_actionPerformed(ActionEvent e)
2802 public void annotationColour_actionPerformed(ActionEvent e)
2807 public void rnahelicesColour_actionPerformed(ActionEvent e)
2812 public void associatedData_actionPerformed(ActionEvent e)
2817 public void autoCalculate_actionPerformed(ActionEvent e)
2822 public void sortByTreeOption_actionPerformed(ActionEvent e)
2827 public void showAllSeqs_actionPerformed(ActionEvent e)
2832 public void showAllColumns_actionPerformed(ActionEvent e)
2837 public void hideSelSequences_actionPerformed(ActionEvent e)
2842 public void hideSelColumns_actionPerformed(ActionEvent e)
2847 public void hiddenMarkers_actionPerformed(ActionEvent e)
2852 public void findPdbId_actionPerformed(ActionEvent e)
2857 public void enterPdbId_actionPerformed(ActionEvent e)
2862 public void pdbFile_actionPerformed(ActionEvent e)
2867 public void invertColSel_actionPerformed(ActionEvent e)
2872 public void tabSelectionChanged(int sel)
2877 public void tabbedPane_mousePressed(MouseEvent e)
2882 public void tabbedPane_focusGained(FocusEvent e)
2887 public void save_actionPerformed(ActionEvent e)
2892 public void reload_actionPerformed(ActionEvent e)
2897 public void newView_actionPerformed(ActionEvent e)
2902 public void textColour_actionPerformed(ActionEvent e)
2907 public void idRightAlign_actionPerformed(ActionEvent e)
2912 public void expandViews_actionPerformed(ActionEvent e)
2917 public void gatherViews_actionPerformed(ActionEvent e)
2922 public void buildTreeMenu()
2927 public void pageSetup_actionPerformed(ActionEvent e)
2932 public void alignmentProperties()
2937 protected void expand_newalign(ActionEvent e)
2939 // TODO Auto-generated method stub