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.schemes.ColourSchemeProperty;
24 import jalview.util.MessageManager;
26 import java.awt.BorderLayout;
27 import java.awt.Color;
28 import java.awt.GridLayout;
29 import java.awt.Toolkit;
30 import java.awt.event.ActionEvent;
31 import java.awt.event.ActionListener;
32 import java.awt.event.FocusAdapter;
33 import java.awt.event.FocusEvent;
34 import java.awt.event.MouseAdapter;
35 import java.awt.event.MouseEvent;
37 import javax.swing.BorderFactory;
38 import javax.swing.ButtonGroup;
39 import javax.swing.JCheckBoxMenuItem;
40 import javax.swing.JInternalFrame;
41 import javax.swing.JLabel;
42 import javax.swing.JMenu;
43 import javax.swing.JMenuBar;
44 import javax.swing.JMenuItem;
45 import javax.swing.JOptionPane;
46 import javax.swing.JPanel;
47 import javax.swing.JRadioButtonMenuItem;
48 import javax.swing.JTabbedPane;
49 import javax.swing.SwingUtilities;
50 import javax.swing.event.ChangeEvent;
51 import javax.swing.event.MenuEvent;
52 import javax.swing.event.MenuListener;
54 public class GAlignFrame extends JInternalFrame
56 protected JMenuBar alignFrameMenuBar = new JMenuBar();
58 protected JMenu fileMenu = new JMenu();
60 protected JMenuItem closeMenuItem = new JMenuItem();
62 protected JMenu editMenu = new JMenu();
64 protected JMenu viewMenu = new JMenu();
66 protected JMenu colourMenu = new JMenu();
68 protected JMenu calculateMenu = new JMenu();
70 protected JMenu webService = new JMenu();
72 protected JMenuItem webServiceNoServices;
74 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
76 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
78 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
80 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
82 protected JMenuItem remove2RightMenuItem = new JMenuItem();
84 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
86 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
88 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
90 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
92 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
94 protected JMenuItem sortIDMenuItem = new JMenuItem();
96 protected JMenuItem sortLengthMenuItem = new JMenuItem();
98 protected JMenuItem sortGroupMenuItem = new JMenuItem();
100 protected JMenu sortByAnnotScore = new JMenu();
102 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
104 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
106 protected JMenuItem PCAMenuItem = new JMenuItem();
108 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
110 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
112 BorderLayout borderLayout1 = new BorderLayout();
114 public JLabel statusBar = new JLabel();
116 protected JMenuItem saveAs = new JMenuItem();
118 protected JMenu outputTextboxMenu = new JMenu();
120 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
122 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
124 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
126 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
128 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
130 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
132 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
134 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
136 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
138 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
140 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
142 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
144 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
146 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
148 // protected JRadioButtonMenuItem covariationColour = new
149 // JRadioButtonMenuItem();
151 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
153 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
155 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
157 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
159 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
161 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
163 JMenuItem htmlMenuItem = new JMenuItem();
165 JMenuItem overviewMenuItem = new JMenuItem();
167 protected JMenuItem undoMenuItem = new JMenuItem();
169 protected JMenuItem redoMenuItem = new JMenuItem();
171 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
173 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
175 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
177 JMenuItem printMenuItem = new JMenuItem();
179 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
181 JMenuItem findMenuItem = new JMenuItem();
183 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
185 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
187 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
189 JMenuItem chooseAnnotations = new JMenuItem();
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 JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
309 JMenuItem invertColSel = new JMenuItem();
311 protected JTabbedPane tabbedPane = new JTabbedPane();
313 JMenuItem save = new JMenuItem();
315 protected JMenuItem reload = new JMenuItem();
317 JMenuItem newView = new JMenuItem();
319 JMenuItem textColour = new JMenuItem();
321 JMenu formatMenu = new JMenu();
323 JMenu selectMenu = new JMenu();
325 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
327 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
329 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
331 protected JMenuItem gatherViews = new JMenuItem();
333 protected JMenuItem expandViews = new JMenuItem();
335 JMenuItem pageSetup = new JMenuItem();
337 JMenuItem alignmentProperties = new JMenuItem();
339 JMenu tooltipSettingsMenu = new JMenu();
341 private JMenuItem justifyLeftMenuItem = new JMenuItem();
343 private JMenuItem justifyRightMenuItem = new JMenuItem();
345 JMenu autoAnnMenu = new JMenu();
347 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
349 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
351 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
353 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
355 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
357 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
359 private JMenuItem grpsFromSelection = new JMenuItem();
366 setJMenuBar(alignFrameMenuBar);
368 // dynamically fill save as menu with available formats
369 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
371 JMenuItem item = new JMenuItem(
372 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
374 item.addActionListener(new java.awt.event.ActionListener()
377 public void actionPerformed(ActionEvent e)
379 outputText_actionPerformed(e);
383 outputTextboxMenu.add(item);
385 } catch (Exception e)
389 if (!new jalview.util.Platform().isAMac())
391 closeMenuItem.setMnemonic('C');
392 outputTextboxMenu.setMnemonic('T');
393 undoMenuItem.setMnemonic('Z');
394 redoMenuItem.setMnemonic('0');
395 copy.setMnemonic('C');
396 cut.setMnemonic('U');
397 pasteMenu.setMnemonic('P');
398 reload.setMnemonic('R');
401 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
403 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
404 .getUserColourSchemes().keys();
406 while (userColours.hasMoreElements())
408 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
409 userColours.nextElement().toString());
410 radioItem.setName("USER_DEFINED");
411 radioItem.addMouseListener(new MouseAdapter()
414 public void mousePressed(MouseEvent evt)
416 if (evt.isControlDown()
417 || SwingUtilities.isRightMouseButton(evt))
419 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
421 int option = JOptionPane.showInternalConfirmDialog(
422 jalview.gui.Desktop.desktop,
424 .getString("label.remove_from_default_list"),
426 .getString("label.remove_user_defined_colour"),
427 JOptionPane.YES_NO_OPTION);
428 if (option == JOptionPane.YES_OPTION)
430 jalview.gui.UserDefinedColours
431 .removeColourFromDefaults(radioItem.getText());
432 colourMenu.remove(radioItem);
436 radioItem.addActionListener(new ActionListener()
439 public void actionPerformed(ActionEvent evt)
441 userDefinedColour_actionPerformed(evt);
448 radioItem.addActionListener(new ActionListener()
451 public void actionPerformed(ActionEvent evt)
453 userDefinedColour_actionPerformed(evt);
456 colourMenu.insert(radioItem, 15);
457 colours.add(radioItem);
460 colours.add(noColourmenuItem);
461 colours.add(clustalColour);
462 colours.add(zappoColour);
463 colours.add(taylorColour);
464 colours.add(hydrophobicityColour);
465 colours.add(helixColour);
466 colours.add(strandColour);
467 colours.add(turnColour);
468 colours.add(buriedColour);
469 colours.add(userDefinedColour);
470 colours.add(PIDColour);
471 colours.add(BLOSUM62Colour);
472 colours.add(nucleotideColour);
473 colours.add(purinePyrimidineColour);
474 // colours.add(covariationColour);
475 colours.add(tcoffeeColour);
476 colours.add(RNAInteractionColour);
477 setColourSelected(jalview.bin.Cache
478 .getDefault("DEFAULT_COLOUR", "None"));
482 public void setColourSelected(String defaultColour)
485 if (defaultColour != null)
487 int index = ColourSchemeProperty
488 .getColourIndexFromName(defaultColour);
492 case ColourSchemeProperty.CLUSTAL:
493 clustalColour.setSelected(true);
497 case ColourSchemeProperty.BLOSUM:
498 BLOSUM62Colour.setSelected(true);
502 case ColourSchemeProperty.PID:
503 PIDColour.setSelected(true);
507 case ColourSchemeProperty.ZAPPO:
508 zappoColour.setSelected(true);
512 case ColourSchemeProperty.TAYLOR:
513 taylorColour.setSelected(true);
516 case ColourSchemeProperty.HYDROPHOBIC:
517 hydrophobicityColour.setSelected(true);
521 case ColourSchemeProperty.HELIX:
522 helixColour.setSelected(true);
526 case ColourSchemeProperty.STRAND:
527 strandColour.setSelected(true);
531 case ColourSchemeProperty.TURN:
532 turnColour.setSelected(true);
536 case ColourSchemeProperty.BURIED:
537 buriedColour.setSelected(true);
541 case ColourSchemeProperty.NUCLEOTIDE:
542 nucleotideColour.setSelected(true);
546 case ColourSchemeProperty.TCOFFEE:
547 tcoffeeColour.setSelected(true);
550 case ColourSchemeProperty.PURINEPYRIMIDINE:
551 purinePyrimidineColour.setSelected(true);
555 case ColourSchemeProperty.RNAINTERACTION:
556 RNAInteractionColour.setSelected(true);
560 * case ColourSchemeProperty.COVARIATION:
561 * covariationColour.setSelected(true);
565 case ColourSchemeProperty.USER_DEFINED:
566 userDefinedColour.setSelected(true);
569 case ColourSchemeProperty.NONE:
571 noColourmenuItem.setSelected(true);
579 private void jbInit() throws Exception
581 fileMenu.setText(MessageManager.getString("action.file"));
582 saveAs.setText(MessageManager.getString("action.save_as") + "...");
583 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
584 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
585 .getMenuShortcutKeyMask()
586 | java.awt.event.KeyEvent.SHIFT_MASK, false));
587 saveAs.addActionListener(new ActionListener()
590 public void actionPerformed(ActionEvent e)
592 saveAs_actionPerformed(e);
595 closeMenuItem.setText(MessageManager.getString("action.close"));
596 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
597 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
598 .getMenuShortcutKeyMask(), false));
599 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
602 public void actionPerformed(ActionEvent e)
604 closeMenuItem_actionPerformed(false);
607 editMenu.setText(MessageManager.getString("action.edit"));
608 viewMenu.setText(MessageManager.getString("action.view"));
609 colourMenu.setText(MessageManager.getString("action.colour"));
610 calculateMenu.setText(MessageManager.getString("action.calculate"));
611 webService.setText(MessageManager.getString("action.web_service"));
612 selectAllSequenceMenuItem.setText(MessageManager
613 .getString("action.select_all"));
614 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
615 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
616 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
617 selectAllSequenceMenuItem
618 .addActionListener(new java.awt.event.ActionListener()
621 public void actionPerformed(ActionEvent e)
623 selectAllSequenceMenuItem_actionPerformed(e);
626 deselectAllSequenceMenuItem.setText(MessageManager
627 .getString("action.deselect_all"));
628 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
629 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
630 deselectAllSequenceMenuItem
631 .addActionListener(new java.awt.event.ActionListener()
634 public void actionPerformed(ActionEvent e)
636 deselectAllSequenceMenuItem_actionPerformed(e);
639 invertSequenceMenuItem.setText(MessageManager
640 .getString("action.invert_sequence_selection"));
641 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
642 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
643 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
644 invertSequenceMenuItem
645 .addActionListener(new java.awt.event.ActionListener()
648 public void actionPerformed(ActionEvent e)
650 invertSequenceMenuItem_actionPerformed(e);
653 grpsFromSelection.setText(MessageManager
654 .getString("action.make_groups_selection"));
655 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
658 public void actionPerformed(ActionEvent e)
660 makeGrpsFromSelection_actionPerformed(e);
663 expandAlignment.setText(MessageManager
664 .getString("action.view_flanking_regions"));
665 expandAlignment.setToolTipText(MessageManager
666 .getString("label.view_flanking_regions"));
667 expandAlignment.addActionListener(new java.awt.event.ActionListener()
670 public void actionPerformed(ActionEvent e)
675 remove2LeftMenuItem.setText(MessageManager
676 .getString("action.remove_left"));
677 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
678 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
679 .getMenuShortcutKeyMask(), false));
681 .addActionListener(new java.awt.event.ActionListener()
684 public void actionPerformed(ActionEvent e)
686 remove2LeftMenuItem_actionPerformed(e);
689 remove2RightMenuItem.setText(MessageManager
690 .getString("action.remove_right"));
691 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
692 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
693 .getMenuShortcutKeyMask(), false));
695 .addActionListener(new java.awt.event.ActionListener()
698 public void actionPerformed(ActionEvent e)
700 remove2RightMenuItem_actionPerformed(e);
703 removeGappedColumnMenuItem.setText(MessageManager
704 .getString("action.remove_empty_columns"));
705 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
706 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
707 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
708 removeGappedColumnMenuItem
709 .addActionListener(new java.awt.event.ActionListener()
712 public void actionPerformed(ActionEvent e)
714 removeGappedColumnMenuItem_actionPerformed(e);
717 removeAllGapsMenuItem.setText(MessageManager
718 .getString("action.remove_all_gaps"));
719 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
720 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
721 .getDefaultToolkit().getMenuShortcutKeyMask()
722 | java.awt.event.KeyEvent.SHIFT_MASK, false));
723 removeAllGapsMenuItem
724 .addActionListener(new java.awt.event.ActionListener()
727 public void actionPerformed(ActionEvent e)
729 removeAllGapsMenuItem_actionPerformed(e);
732 justifyLeftMenuItem.setText(MessageManager
733 .getString("action.left_justify_alignment"));
735 .addActionListener(new java.awt.event.ActionListener()
738 public void actionPerformed(ActionEvent e)
740 justifyLeftMenuItem_actionPerformed(e);
743 justifyRightMenuItem.setText(MessageManager
744 .getString("action.right_justify_alignment"));
746 .addActionListener(new java.awt.event.ActionListener()
749 public void actionPerformed(ActionEvent e)
751 justifyRightMenuItem_actionPerformed(e);
754 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
755 viewBoxesMenuItem.setState(true);
756 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
759 public void actionPerformed(ActionEvent e)
761 viewBoxesMenuItem_actionPerformed(e);
764 viewTextMenuItem.setText(MessageManager.getString("action.text"));
765 viewTextMenuItem.setState(true);
766 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
769 public void actionPerformed(ActionEvent e)
771 viewTextMenuItem_actionPerformed(e);
774 showNonconservedMenuItem.setText(MessageManager
775 .getString("label.show_non_conversed"));
776 showNonconservedMenuItem.setState(false);
777 showNonconservedMenuItem
778 .addActionListener(new java.awt.event.ActionListener()
781 public void actionPerformed(ActionEvent e)
783 showUnconservedMenuItem_actionPerformed(e);
786 sortPairwiseMenuItem.setText(MessageManager
787 .getString("action.by_pairwise_id"));
789 .addActionListener(new java.awt.event.ActionListener()
792 public void actionPerformed(ActionEvent e)
794 sortPairwiseMenuItem_actionPerformed(e);
797 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
798 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
801 public void actionPerformed(ActionEvent e)
803 sortIDMenuItem_actionPerformed(e);
807 .setText(MessageManager.getString("action.by_length"));
809 .addActionListener(new java.awt.event.ActionListener()
812 public void actionPerformed(ActionEvent e)
814 sortLengthMenuItem_actionPerformed(e);
817 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
818 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
821 public void actionPerformed(ActionEvent e)
823 sortGroupMenuItem_actionPerformed(e);
826 removeRedundancyMenuItem.setText(MessageManager
827 .getString("action.remove_redundancy"));
828 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
829 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
830 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
831 removeRedundancyMenuItem
832 .addActionListener(new java.awt.event.ActionListener()
835 public void actionPerformed(ActionEvent e)
837 removeRedundancyMenuItem_actionPerformed(e);
840 pairwiseAlignmentMenuItem.setText(MessageManager
841 .getString("action.pairwise_alignment"));
842 pairwiseAlignmentMenuItem
843 .addActionListener(new java.awt.event.ActionListener()
846 public void actionPerformed(ActionEvent e)
848 pairwiseAlignmentMenuItem_actionPerformed(e);
851 PCAMenuItem.setText(MessageManager
852 .getString("label.principal_component_analysis"));
853 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
856 public void actionPerformed(ActionEvent e)
858 PCAMenuItem_actionPerformed(e);
861 averageDistanceTreeMenuItem.setText(MessageManager
862 .getString("label.average_distance_identity"));
863 averageDistanceTreeMenuItem
864 .addActionListener(new java.awt.event.ActionListener()
867 public void actionPerformed(ActionEvent e)
869 averageDistanceTreeMenuItem_actionPerformed(e);
872 neighbourTreeMenuItem.setText(MessageManager
873 .getString("label.neighbour_joining_identity"));
874 neighbourTreeMenuItem
875 .addActionListener(new java.awt.event.ActionListener()
878 public void actionPerformed(ActionEvent e)
880 neighbourTreeMenuItem_actionPerformed(e);
883 this.getContentPane().setLayout(borderLayout1);
884 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
885 statusBar.setBackground(Color.white);
886 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
887 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
888 statusBar.setText(MessageManager.getString("label.status_bar"));
889 outputTextboxMenu.setText(MessageManager
890 .getString("label.out_to_textbox"));
891 clustalColour.setText(MessageManager.getString("label.clustalx"));
893 clustalColour.addActionListener(new java.awt.event.ActionListener()
896 public void actionPerformed(ActionEvent e)
898 clustalColour_actionPerformed(e);
901 zappoColour.setText(MessageManager.getString("label.zappo"));
902 zappoColour.addActionListener(new java.awt.event.ActionListener()
905 public void actionPerformed(ActionEvent e)
907 zappoColour_actionPerformed(e);
910 taylorColour.setText(MessageManager.getString("label.taylor"));
911 taylorColour.addActionListener(new java.awt.event.ActionListener()
914 public void actionPerformed(ActionEvent e)
916 taylorColour_actionPerformed(e);
919 hydrophobicityColour.setText(MessageManager
920 .getString("label.hydrophobicity"));
922 .addActionListener(new java.awt.event.ActionListener()
925 public void actionPerformed(ActionEvent e)
927 hydrophobicityColour_actionPerformed(e);
930 helixColour.setText(MessageManager.getString("label.helix_propensity"));
931 helixColour.addActionListener(new java.awt.event.ActionListener()
934 public void actionPerformed(ActionEvent e)
936 helixColour_actionPerformed(e);
939 strandColour.setText(MessageManager
940 .getString("label.strand_propensity"));
941 strandColour.addActionListener(new java.awt.event.ActionListener()
944 public void actionPerformed(ActionEvent e)
946 strandColour_actionPerformed(e);
949 turnColour.setText(MessageManager.getString("label.turn_propensity"));
950 turnColour.addActionListener(new java.awt.event.ActionListener()
953 public void actionPerformed(ActionEvent e)
955 turnColour_actionPerformed(e);
958 buriedColour.setText(MessageManager.getString("label.buried_index"));
959 buriedColour.addActionListener(new java.awt.event.ActionListener()
962 public void actionPerformed(ActionEvent e)
964 buriedColour_actionPerformed(e);
967 userDefinedColour.setText(MessageManager
968 .getString("action.user_defined"));
969 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
972 public void actionPerformed(ActionEvent e)
974 userDefinedColour_actionPerformed(e);
978 .setText(MessageManager.getString("label.percentage_identity"));
979 PIDColour.addActionListener(new java.awt.event.ActionListener()
982 public void actionPerformed(ActionEvent e)
984 PIDColour_actionPerformed(e);
988 .setText(MessageManager.getString("label.blosum62_score"));
989 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
992 public void actionPerformed(ActionEvent e)
994 BLOSUM62Colour_actionPerformed(e);
997 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
998 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1001 public void actionPerformed(ActionEvent e)
1003 nucleotideColour_actionPerformed(e);
1007 purinePyrimidineColour.setText(MessageManager
1008 .getString("label.purine_pyrimidine"));
1009 purinePyrimidineColour
1010 .addActionListener(new java.awt.event.ActionListener()
1013 public void actionPerformed(ActionEvent e)
1015 purinePyrimidineColour_actionPerformed(e);
1019 RNAInteractionColour.setText("RNA Interaction type");
1020 RNAInteractionColour
1021 .addActionListener(new java.awt.event.ActionListener()
1024 public void actionPerformed(ActionEvent e)
1026 RNAInteractionColour_actionPerformed(e);
1030 * covariationColour.setText("Covariation");
1031 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1032 * public void actionPerformed(ActionEvent e) {
1033 * covariationColour_actionPerformed(e); } });
1036 avDistanceTreeBlosumMenuItem.setText(MessageManager
1037 .getString("label.average_distance_bloslum62"));
1038 avDistanceTreeBlosumMenuItem
1039 .addActionListener(new java.awt.event.ActionListener()
1042 public void actionPerformed(ActionEvent e)
1044 avTreeBlosumMenuItem_actionPerformed(e);
1047 njTreeBlosumMenuItem.setText(MessageManager
1048 .getString("label.neighbour_blosum62"));
1049 njTreeBlosumMenuItem
1050 .addActionListener(new java.awt.event.ActionListener()
1053 public void actionPerformed(ActionEvent e)
1055 njTreeBlosumMenuItem_actionPerformed(e);
1058 annotationPanelMenuItem.setActionCommand("");
1059 annotationPanelMenuItem.setText(MessageManager
1060 .getString("label.show_annotations"));
1061 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
1062 "SHOW_ANNOTATIONS", true));
1063 annotationPanelMenuItem
1064 .addActionListener(new java.awt.event.ActionListener()
1067 public void actionPerformed(ActionEvent e)
1069 annotationPanelMenuItem_actionPerformed(e);
1072 colourTextMenuItem.setText(MessageManager
1073 .getString("label.colour_text"));
1075 .addActionListener(new java.awt.event.ActionListener()
1078 public void actionPerformed(ActionEvent e)
1080 colourTextMenuItem_actionPerformed(e);
1083 htmlMenuItem.setText(MessageManager.getString("label.html"));
1084 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1087 public void actionPerformed(ActionEvent e)
1089 htmlMenuItem_actionPerformed(e);
1092 overviewMenuItem.setText(MessageManager
1093 .getString("label.overview_window"));
1094 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1097 public void actionPerformed(ActionEvent e)
1099 overviewMenuItem_actionPerformed(e);
1102 undoMenuItem.setEnabled(false);
1103 undoMenuItem.setText(MessageManager.getString("action.undo"));
1104 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1105 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1106 .getMenuShortcutKeyMask(), false));
1107 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1110 public void actionPerformed(ActionEvent e)
1112 undoMenuItem_actionPerformed(e);
1115 redoMenuItem.setEnabled(false);
1116 redoMenuItem.setText(MessageManager.getString("action.redo"));
1117 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1118 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1119 .getMenuShortcutKeyMask(), false));
1120 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1123 public void actionPerformed(ActionEvent e)
1125 redoMenuItem_actionPerformed(e);
1128 conservationMenuItem.setText(MessageManager
1129 .getString("action.by_conservation"));
1130 conservationMenuItem
1131 .addActionListener(new java.awt.event.ActionListener()
1134 public void actionPerformed(ActionEvent e)
1136 conservationMenuItem_actionPerformed(e);
1139 noColourmenuItem.setText(MessageManager.getString("label.none"));
1140 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1143 public void actionPerformed(ActionEvent e)
1145 noColourmenuItem_actionPerformed(e);
1148 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1149 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1152 public void actionPerformed(ActionEvent e)
1154 wrapMenuItem_actionPerformed(e);
1157 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1158 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1159 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1160 .getMenuShortcutKeyMask(), false));
1161 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1164 public void actionPerformed(ActionEvent e)
1166 printMenuItem_actionPerformed(e);
1170 .setText(MessageManager.getString("action.show_gaps"));
1171 renderGapsMenuItem.setState(true);
1173 .addActionListener(new java.awt.event.ActionListener()
1176 public void actionPerformed(ActionEvent e)
1178 renderGapsMenuItem_actionPerformed(e);
1181 findMenuItem.setText(MessageManager.getString("action.find"));
1182 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1183 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1184 .getMenuShortcutKeyMask(), false));
1185 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1188 public void actionPerformed(ActionEvent e)
1190 findMenuItem_actionPerformed(e);
1193 abovePIDThreshold.setText(MessageManager
1194 .getString("label.above_identity_threshold"));
1195 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1198 public void actionPerformed(ActionEvent e)
1200 abovePIDThreshold_actionPerformed(e);
1203 showSeqFeatures.setText(MessageManager
1204 .getString("label.show_sequence_features"));
1205 showSeqFeatures.addActionListener(new ActionListener()
1208 public void actionPerformed(ActionEvent actionEvent)
1210 showSeqFeatures_actionPerformed(actionEvent);
1213 chooseAnnotations.setText(MessageManager
1214 .getString("label.choose_annotations") + "...");
1215 chooseAnnotations.addActionListener(new ActionListener()
1218 public void actionPerformed(ActionEvent actionEvent)
1220 chooseAnnotations_actionPerformed();
1224 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1225 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1226 * void actionPerformed(ActionEvent actionEvent) {
1227 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1229 showDbRefsMenuitem.setText(MessageManager
1230 .getString("label.show_database_refs"));
1231 showDbRefsMenuitem.addActionListener(new ActionListener()
1235 public void actionPerformed(ActionEvent e)
1237 showDbRefs_actionPerformed(e);
1241 showNpFeatsMenuitem.setText(MessageManager
1242 .getString("label.show_non_positional_features"));
1243 showNpFeatsMenuitem.addActionListener(new ActionListener()
1247 public void actionPerformed(ActionEvent e)
1249 showNpFeats_actionPerformed(e);
1253 showGroupConservation.setText(MessageManager
1254 .getString("label.group_conservation"));
1255 showGroupConservation.addActionListener(new ActionListener()
1259 public void actionPerformed(ActionEvent e)
1261 showGroupConservation_actionPerformed(e);
1266 showGroupConsensus.setText(MessageManager
1267 .getString("label.group_consensus"));
1268 showGroupConsensus.addActionListener(new ActionListener()
1272 public void actionPerformed(ActionEvent e)
1274 showGroupConsensus_actionPerformed(e);
1278 showConsensusHistogram.setText(MessageManager
1279 .getString("label.show_consensus_histogram"));
1280 showConsensusHistogram.addActionListener(new ActionListener()
1284 public void actionPerformed(ActionEvent e)
1286 showConsensusHistogram_actionPerformed(e);
1290 showSequenceLogo.setText(MessageManager
1291 .getString("label.show_consensus_logo"));
1292 showSequenceLogo.addActionListener(new ActionListener()
1296 public void actionPerformed(ActionEvent e)
1298 showSequenceLogo_actionPerformed(e);
1302 normaliseSequenceLogo.setText(MessageManager
1303 .getString("label.norm_consensus_logo"));
1304 normaliseSequenceLogo.addActionListener(new ActionListener()
1308 public void actionPerformed(ActionEvent e)
1310 normaliseSequenceLogo_actionPerformed(e);
1314 applyAutoAnnotationSettings.setText(MessageManager
1315 .getString("label.apply_all_groups"));
1316 applyAutoAnnotationSettings.setState(false);
1317 applyAutoAnnotationSettings.setVisible(true);
1318 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1322 public void actionPerformed(ActionEvent e)
1324 applyAutoAnnotationSettings_actionPerformed(e);
1329 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1330 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1333 public void actionPerformed(ActionEvent e)
1335 nucleotideColour_actionPerformed(e);
1339 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1340 tcoffeeColour.setEnabled(false);
1341 tcoffeeColour.addActionListener(new ActionListener()
1345 public void actionPerformed(ActionEvent e)
1347 tcoffeeColorScheme_actionPerformed(e);
1352 .setText(MessageManager.getString("action.undefine_groups"));
1353 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1354 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1355 .getMenuShortcutKeyMask(), false));
1356 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1359 public void actionPerformed(ActionEvent e)
1361 deleteGroups_actionPerformed(e);
1364 createGroup.setText(MessageManager.getString("action.create_groups"));
1365 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1366 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1367 .getMenuShortcutKeyMask(), false));
1368 createGroup.addActionListener(new java.awt.event.ActionListener()
1371 public void actionPerformed(ActionEvent e)
1373 createGroup_actionPerformed(e);
1376 unGroup.setText(MessageManager.getString("action.remove_group"));
1377 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1378 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1379 .getMenuShortcutKeyMask()
1380 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1381 unGroup.addActionListener(new java.awt.event.ActionListener()
1384 public void actionPerformed(ActionEvent e)
1386 unGroup_actionPerformed(e);
1389 copy.setText(MessageManager.getString("action.copy"));
1390 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1391 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1392 .getMenuShortcutKeyMask(), false));
1394 copy.addActionListener(new java.awt.event.ActionListener()
1397 public void actionPerformed(ActionEvent e)
1399 copy_actionPerformed(e);
1402 cut.setText(MessageManager.getString("action.cut"));
1403 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1404 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1405 .getMenuShortcutKeyMask(), false));
1406 cut.addActionListener(new java.awt.event.ActionListener()
1409 public void actionPerformed(ActionEvent e)
1411 cut_actionPerformed(e);
1414 delete.setText(MessageManager.getString("action.delete"));
1415 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1416 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1417 delete.addActionListener(new java.awt.event.ActionListener()
1420 public void actionPerformed(ActionEvent e)
1422 delete_actionPerformed(e);
1425 pasteMenu.setText(MessageManager.getString("action.paste"));
1426 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1427 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1428 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1429 .getMenuShortcutKeyMask()
1430 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1431 pasteNew.addActionListener(new java.awt.event.ActionListener()
1434 public void actionPerformed(ActionEvent e)
1436 pasteNew_actionPerformed(e);
1439 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1440 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1441 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1442 .getMenuShortcutKeyMask(), false));
1443 pasteThis.addActionListener(new java.awt.event.ActionListener()
1446 public void actionPerformed(ActionEvent e)
1448 pasteThis_actionPerformed(e);
1451 applyToAllGroups.setText(MessageManager
1452 .getString("label.apply_colour_to_all_groups"));
1453 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1456 public void actionPerformed(ActionEvent e)
1458 applyToAllGroups_actionPerformed(e);
1461 createPNG.addActionListener(new java.awt.event.ActionListener()
1464 public void actionPerformed(ActionEvent e)
1469 createPNG.setActionCommand(MessageManager
1470 .getString("label.save_png_image"));
1471 createPNG.setText("PNG");
1472 font.setText(MessageManager.getString("action.font"));
1473 font.addActionListener(new java.awt.event.ActionListener()
1476 public void actionPerformed(ActionEvent e)
1478 font_actionPerformed(e);
1482 seqLimits.setText(MessageManager
1483 .getString("label.show_sequence_limits"));
1484 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1485 seqLimits.addActionListener(new java.awt.event.ActionListener()
1488 public void actionPerformed(ActionEvent e)
1490 seqLimit_actionPerformed(e);
1493 epsFile.setText("EPS");
1494 epsFile.addActionListener(new java.awt.event.ActionListener()
1497 public void actionPerformed(ActionEvent e)
1502 LoadtreeMenuItem.setActionCommand(MessageManager
1503 .getString("label.load_tree_for_sequence_set"));
1504 LoadtreeMenuItem.setText(MessageManager
1505 .getString("label.load_associated_tree"));
1506 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1509 public void actionPerformed(ActionEvent e)
1511 LoadtreeMenuItem_actionPerformed(e);
1515 scaleAbove.setVisible(false);
1516 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1517 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1520 public void actionPerformed(ActionEvent e)
1522 scaleAbove_actionPerformed(e);
1525 scaleLeft.setVisible(false);
1526 scaleLeft.setSelected(true);
1527 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1528 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1531 public void actionPerformed(ActionEvent e)
1533 scaleLeft_actionPerformed(e);
1536 scaleRight.setVisible(false);
1537 scaleRight.setSelected(true);
1538 scaleRight.setText(MessageManager.getString("action.scale_right"));
1539 scaleRight.addActionListener(new java.awt.event.ActionListener()
1542 public void actionPerformed(ActionEvent e)
1544 scaleRight_actionPerformed(e);
1547 centreColumnLabelsMenuItem.setVisible(true);
1548 centreColumnLabelsMenuItem.setState(false);
1549 centreColumnLabelsMenuItem.setText(MessageManager
1550 .getString("label.centre_column_labels"));
1551 centreColumnLabelsMenuItem
1552 .addActionListener(new java.awt.event.ActionListener()
1555 public void actionPerformed(ActionEvent e)
1557 centreColumnLabels_actionPerformed(e);
1560 followHighlightMenuItem.setVisible(true);
1561 followHighlightMenuItem.setState(true);
1562 followHighlightMenuItem.setText(MessageManager
1563 .getString("label.automatic_scrolling"));
1564 followHighlightMenuItem.addActionListener(new ActionListener()
1568 public void actionPerformed(ActionEvent e)
1570 followHighlight_actionPerformed();
1575 modifyPID.setText(MessageManager
1576 .getString("label.modify_identity_thereshold"));
1577 modifyPID.addActionListener(new java.awt.event.ActionListener()
1580 public void actionPerformed(ActionEvent e)
1582 modifyPID_actionPerformed(e);
1585 modifyConservation.setText(MessageManager
1586 .getString("label.modify_conservation_thereshold"));
1588 .addActionListener(new java.awt.event.ActionListener()
1591 public void actionPerformed(ActionEvent e)
1593 modifyConservation_actionPerformed(e);
1597 .setText(MessageManager.getString("action.by_tree_order"));
1598 sort.setText(MessageManager.getString("action.sort"));
1599 sort.addMenuListener(new MenuListener()
1602 public void menuSelected(MenuEvent e)
1608 public void menuDeselected(MenuEvent e)
1613 public void menuCanceled(MenuEvent e)
1617 sortByAnnotScore.setText(MessageManager
1618 .getString("label.sort_by_score"));
1619 sort.add(sortByAnnotScore);
1620 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1624 public void menuCanceled(MenuEvent e)
1629 public void menuDeselected(MenuEvent e)
1634 public void menuSelected(MenuEvent e)
1636 buildSortByAnnotationScoresMenu();
1639 sortByAnnotScore.setVisible(false);
1642 .setText(MessageManager.getString("action.calculate_tree"));
1644 jMenu2.setText(MessageManager.getString("label.export_image"));
1645 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1646 padGapsMenuitem.setState(jalview.bin.Cache
1647 .getDefault("PAD_GAPS", false));
1648 padGapsMenuitem.addActionListener(new ActionListener()
1651 public void actionPerformed(ActionEvent e)
1653 padGapsMenuitem_actionPerformed(e);
1656 vamsasStore.setVisible(false);
1657 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1658 vamsasStore.addActionListener(new ActionListener()
1661 public void actionPerformed(ActionEvent e)
1663 vamsasStore_actionPerformed(e);
1666 showTranslation.setText(MessageManager
1667 .getString("label.translate_cDNA"));
1668 showTranslation.addActionListener(new ActionListener()
1671 public void actionPerformed(ActionEvent e)
1673 showTranslation_actionPerformed(e);
1676 extractScores.setText(MessageManager.getString("label.extract_scores")
1678 extractScores.addActionListener(new ActionListener()
1681 public void actionPerformed(ActionEvent e)
1683 extractScores_actionPerformed(e);
1686 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1688 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1690 * showProducts.addActionListener(new ActionListener() {
1692 * public void actionPerformed(ActionEvent e) {
1693 * showProducts_actionPerformed(e); } });
1695 openFeatureSettings.setText(MessageManager
1696 .getString("label.feature_settings"));
1697 openFeatureSettings.addActionListener(new ActionListener()
1700 public void actionPerformed(ActionEvent e)
1702 featureSettings_actionPerformed(e);
1706 .setText(MessageManager.getString("label.fetch_sequences"));
1707 fetchSequence.addActionListener(new ActionListener()
1710 public void actionPerformed(ActionEvent e)
1712 fetchSequence_actionPerformed(e);
1716 annotationColour.setText(MessageManager
1717 .getString("action.by_annotation"));
1718 annotationColour.addActionListener(new ActionListener()
1721 public void actionPerformed(ActionEvent e)
1723 annotationColour_actionPerformed(e);
1727 rnahelicesColour.setText(MessageManager
1728 .getString("action.by_rna_helixes"));
1729 rnahelicesColour.addActionListener(new ActionListener()
1732 public void actionPerformed(ActionEvent e)
1734 rnahelicesColour_actionPerformed(e);
1738 associatedData.setText(MessageManager
1739 .getString("label.load_features_annotations"));
1740 associatedData.addActionListener(new ActionListener()
1743 public void actionPerformed(ActionEvent e)
1745 associatedData_actionPerformed(e);
1748 autoCalculate.setText(MessageManager
1749 .getString("label.autocalculate_consensus"));
1750 autoCalculate.setState(jalview.bin.Cache.getDefault(
1751 "AUTO_CALC_CONSENSUS", true));
1752 autoCalculate.addActionListener(new ActionListener()
1755 public void actionPerformed(ActionEvent e)
1757 autoCalculate_actionPerformed(e);
1760 sortByTree.setText(MessageManager
1761 .getString("label.sort_alignment_new_tree"));
1763 .setToolTipText("<html>"
1765 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1767 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1768 sortByTree.addActionListener(new ActionListener()
1771 public void actionPerformed(ActionEvent e)
1773 sortByTreeOption_actionPerformed(e);
1777 listenToViewSelections.setText(MessageManager
1778 .getString("label.listen_for_selections"));
1779 listenToViewSelections
1780 .setToolTipText("<html>"
1782 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1783 listenToViewSelections.setState(false);
1784 listenToViewSelections.addActionListener(new ActionListener()
1787 public void actionPerformed(ActionEvent e)
1789 listenToViewSelections_actionPerformed(e);
1794 .setText(MessageManager.getString("label.add_sequences"));
1795 addFromFile.setText(MessageManager.getString("label.from_file"));
1796 addFromFile.addActionListener(new ActionListener()
1799 public void actionPerformed(ActionEvent e)
1801 addFromFile_actionPerformed(e);
1804 addFromText.setText(MessageManager.getString("label.from_textbox"));
1805 addFromText.addActionListener(new ActionListener()
1808 public void actionPerformed(ActionEvent e)
1810 addFromText_actionPerformed(e);
1813 addFromURL.setText(MessageManager.getString("label.from_url"));
1814 addFromURL.addActionListener(new ActionListener()
1817 public void actionPerformed(ActionEvent e)
1819 addFromURL_actionPerformed(e);
1822 exportFeatures.setText(MessageManager
1823 .getString("label.export_features"));
1824 exportFeatures.addActionListener(new ActionListener()
1827 public void actionPerformed(ActionEvent e)
1829 exportFeatures_actionPerformed(e);
1832 exportAnnotations.setText(MessageManager
1833 .getString("label.export_annotations"));
1834 exportAnnotations.addActionListener(new ActionListener()
1837 public void actionPerformed(ActionEvent e)
1839 exportAnnotations_actionPerformed(e);
1842 statusPanel.setLayout(gridLayout1);
1843 jMenu3.setText(MessageManager.getString("action.show"));
1844 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1845 showAllSeqs.setToolTipText(MessageManager
1846 .getString("label.toggle_sequence_visibility"));
1847 showAllSeqs.addActionListener(new ActionListener()
1850 public void actionPerformed(ActionEvent e)
1852 showAllSeqs_actionPerformed(e);
1855 showAllColumns.setText(MessageManager.getString("label.all_columns"));
1856 showAllColumns.setToolTipText(MessageManager
1857 .getString("label.toggle_columns_visibility"));
1858 showAllColumns.addActionListener(new ActionListener()
1861 public void actionPerformed(ActionEvent e)
1863 showAllColumns_actionPerformed(e);
1866 hideMenu.setText(MessageManager.getString("action.hide"));
1867 hideSelSequences.setText(MessageManager
1868 .getString("label.selected_sequences"));
1869 hideSelSequences.setToolTipText(MessageManager
1870 .getString("label.toggle_sequence_visibility"));
1871 hideSelSequences.addActionListener(new ActionListener()
1874 public void actionPerformed(ActionEvent e)
1876 hideSelSequences_actionPerformed(e);
1879 hideSelColumns.setText(MessageManager
1880 .getString("label.selected_columns"));
1881 hideSelColumns.setToolTipText(MessageManager
1882 .getString("label.toggle_columns_visibility"));
1883 hideSelColumns.addActionListener(new ActionListener()
1886 public void actionPerformed(ActionEvent e)
1888 hideSelColumns_actionPerformed(e);
1891 hideAllSelection.setText(MessageManager
1892 .getString("label.selected_region"));
1893 hideAllSelection.addActionListener(new ActionListener()
1896 public void actionPerformed(ActionEvent e)
1898 hideAllSelection_actionPerformed(e);
1901 // TODO: should be hidden if no selection exists.
1902 hideAllButSelection.setText(MessageManager
1903 .getString("label.all_but_selected_region"));
1904 hideAllButSelection.addActionListener(new ActionListener()
1907 public void actionPerformed(ActionEvent e)
1909 hideAllButSelection_actionPerformed(e);
1912 showAllhidden.setText(MessageManager
1913 .getString("label.all_sequences_columns"));
1914 showAllhidden.setToolTipText(MessageManager
1915 .getString("label.toggles_visibility_hidden_selected_regions"));
1916 showAllhidden.addActionListener(new ActionListener()
1919 public void actionPerformed(ActionEvent e)
1921 showAllhidden_actionPerformed(e);
1925 hiddenMarkers.setText(MessageManager
1926 .getString("action.show_hidden_markers"));
1927 hiddenMarkers.addActionListener(new ActionListener()
1930 public void actionPerformed(ActionEvent e)
1932 hiddenMarkers_actionPerformed(e);
1935 invertColSel.setText(MessageManager
1936 .getString("action.invert_column_selection"));
1937 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1938 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1939 .getMenuShortcutKeyMask()
1940 | java.awt.event.KeyEvent.ALT_MASK, false));
1941 invertColSel.addActionListener(new ActionListener()
1944 public void actionPerformed(ActionEvent e)
1946 invertColSel_actionPerformed(e);
1949 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1952 public void stateChanged(ChangeEvent evt)
1954 JTabbedPane pane = (JTabbedPane) evt.getSource();
1955 int sel = pane.getSelectedIndex();
1956 tabSelectionChanged(sel);
1959 tabbedPane.addMouseListener(new MouseAdapter()
1962 public void mousePressed(MouseEvent e)
1964 tabbedPane_mousePressed(e);
1967 tabbedPane.addFocusListener(new FocusAdapter()
1970 public void focusGained(FocusEvent e)
1972 tabbedPane_focusGained(e);
1975 save.setText(MessageManager.getString("action.save"));
1976 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1977 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1978 .getMenuShortcutKeyMask(), false));
1979 save.addActionListener(new ActionListener()
1982 public void actionPerformed(ActionEvent e)
1984 save_actionPerformed(e);
1987 reload.setEnabled(false);
1988 reload.setText(MessageManager.getString("action.reload"));
1989 reload.addActionListener(new ActionListener()
1992 public void actionPerformed(ActionEvent e)
1994 reload_actionPerformed(e);
1997 newView.setText(MessageManager.getString("action.new_view"));
1998 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1999 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2000 .getMenuShortcutKeyMask(), false));
2001 newView.addActionListener(new ActionListener()
2004 public void actionPerformed(ActionEvent e)
2006 newView_actionPerformed(e);
2009 tabbedPane.setToolTipText("<html><i>"
2010 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2012 textColour.setText(MessageManager.getString("label.colour_text")
2014 textColour.addActionListener(new ActionListener()
2017 public void actionPerformed(ActionEvent e)
2019 textColour_actionPerformed(e);
2022 formatMenu.setText(MessageManager.getString("action.format"));
2023 selectMenu.setText(MessageManager.getString("action.select"));
2024 idRightAlign.setText(MessageManager
2025 .getString("label.right_align_sequence_id"));
2026 idRightAlign.addActionListener(new ActionListener()
2029 public void actionPerformed(ActionEvent e)
2031 idRightAlign_actionPerformed(e);
2034 gatherViews.setEnabled(false);
2035 gatherViews.setText(MessageManager.getString("action.gather_views"));
2036 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2037 java.awt.event.KeyEvent.VK_G, 0, false));
2038 gatherViews.addActionListener(new ActionListener()
2041 public void actionPerformed(ActionEvent e)
2043 gatherViews_actionPerformed(e);
2046 expandViews.setEnabled(false);
2047 expandViews.setText(MessageManager.getString("action.expand_views"));
2048 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2049 java.awt.event.KeyEvent.VK_X, 0, false));
2050 expandViews.addActionListener(new ActionListener()
2053 public void actionPerformed(ActionEvent e)
2055 expandViews_actionPerformed(e);
2059 .setText(MessageManager.getString("action.page_setup") + "...");
2060 pageSetup.addActionListener(new ActionListener()
2063 public void actionPerformed(ActionEvent e)
2065 pageSetup_actionPerformed(e);
2068 alignmentProperties.setText(MessageManager
2069 .getString("label.alignment_props") + "...");
2070 alignmentProperties.addActionListener(new ActionListener()
2073 public void actionPerformed(ActionEvent actionEvent)
2075 alignmentProperties();
2078 tooltipSettingsMenu.setText(MessageManager
2079 .getString("label.sequence_id_tooltip"));
2080 autoAnnMenu.setText(MessageManager
2081 .getString("label.autocalculated_annotation"));
2082 alignFrameMenuBar.add(fileMenu);
2083 alignFrameMenuBar.add(editMenu);
2084 alignFrameMenuBar.add(selectMenu);
2085 alignFrameMenuBar.add(viewMenu);
2086 alignFrameMenuBar.add(formatMenu);
2087 alignFrameMenuBar.add(colourMenu);
2088 alignFrameMenuBar.add(calculateMenu);
2089 alignFrameMenuBar.add(webService);
2090 fileMenu.add(fetchSequence);
2091 fileMenu.add(addSequenceMenu);
2092 fileMenu.add(reload);
2093 fileMenu.addSeparator();
2094 fileMenu.add(vamsasStore);
2096 fileMenu.add(saveAs);
2097 fileMenu.add(outputTextboxMenu);
2098 fileMenu.add(pageSetup);
2099 fileMenu.add(printMenuItem);
2100 fileMenu.addSeparator();
2101 fileMenu.add(jMenu2);
2102 fileMenu.add(exportFeatures);
2103 fileMenu.add(exportAnnotations);
2104 fileMenu.add(LoadtreeMenuItem);
2105 fileMenu.add(associatedData);
2106 fileMenu.addSeparator();
2107 fileMenu.add(closeMenuItem);
2108 editMenu.add(undoMenuItem);
2109 editMenu.add(redoMenuItem);
2112 editMenu.add(pasteMenu);
2113 editMenu.add(delete);
2114 editMenu.addSeparator();
2115 editMenu.add(remove2LeftMenuItem);
2116 editMenu.add(remove2RightMenuItem);
2117 editMenu.add(removeGappedColumnMenuItem);
2118 editMenu.add(removeAllGapsMenuItem);
2119 editMenu.add(removeRedundancyMenuItem);
2120 editMenu.addSeparator();
2121 // dont add these yet in the CVS build - they cannot be undone!
2122 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2123 // editMenu.add(justifyLeftMenuItem);
2124 // editMenu.add(justifyRightMenuItem);
2125 // editMenu.addSeparator();
2126 editMenu.add(padGapsMenuitem);
2127 viewMenu.add(newView);
2128 viewMenu.add(expandViews);
2129 viewMenu.add(gatherViews);
2130 viewMenu.addSeparator();
2131 viewMenu.add(jMenu3);
2132 viewMenu.add(hideMenu);
2133 viewMenu.addSeparator();
2134 viewMenu.add(followHighlightMenuItem);
2135 viewMenu.add(annotationPanelMenuItem);
2136 autoAnnMenu.add(applyAutoAnnotationSettings);
2137 autoAnnMenu.add(showConsensusHistogram);
2138 autoAnnMenu.add(showSequenceLogo);
2139 autoAnnMenu.add(normaliseSequenceLogo);
2140 autoAnnMenu.addSeparator();
2141 autoAnnMenu.add(showGroupConservation);
2142 autoAnnMenu.add(showGroupConsensus);
2143 viewMenu.add(autoAnnMenu);
2144 viewMenu.addSeparator();
2145 viewMenu.add(showSeqFeatures);
2146 viewMenu.add(chooseAnnotations);
2147 // viewMenu.add(showSeqFeaturesHeight);
2149 viewMenu.add(openFeatureSettings);
2150 tooltipSettingsMenu.add(showDbRefsMenuitem);
2151 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2152 viewMenu.add(tooltipSettingsMenu);
2153 viewMenu.addSeparator();
2154 viewMenu.add(alignmentProperties);
2155 viewMenu.addSeparator();
2156 viewMenu.add(overviewMenuItem);
2157 colourMenu.add(applyToAllGroups);
2158 colourMenu.add(textColour);
2159 colourMenu.addSeparator();
2160 colourMenu.add(noColourmenuItem);
2161 colourMenu.add(clustalColour);
2162 colourMenu.add(BLOSUM62Colour);
2163 colourMenu.add(PIDColour);
2164 colourMenu.add(zappoColour);
2165 colourMenu.add(taylorColour);
2166 colourMenu.add(hydrophobicityColour);
2167 colourMenu.add(helixColour);
2168 colourMenu.add(strandColour);
2169 colourMenu.add(turnColour);
2170 colourMenu.add(buriedColour);
2171 colourMenu.add(nucleotideColour);
2172 colourMenu.add(purinePyrimidineColour);
2173 colourMenu.add(RNAInteractionColour);
2174 // colourMenu.add(covariationColour);
2175 colourMenu.add(tcoffeeColour);
2176 colourMenu.add(userDefinedColour);
2177 colourMenu.addSeparator();
2178 colourMenu.add(conservationMenuItem);
2179 colourMenu.add(modifyConservation);
2180 colourMenu.add(abovePIDThreshold);
2181 colourMenu.add(modifyPID);
2182 colourMenu.add(annotationColour);
2183 colourMenu.add(rnahelicesColour);
2184 calculateMenu.add(sort);
2185 calculateMenu.add(calculateTree);
2186 calculateMenu.addSeparator();
2187 calculateMenu.add(pairwiseAlignmentMenuItem);
2188 calculateMenu.add(PCAMenuItem);
2189 calculateMenu.addSeparator();
2190 calculateMenu.add(showTranslation);
2191 calculateMenu.add(showProducts);
2192 calculateMenu.add(autoCalculate);
2193 calculateMenu.add(sortByTree);
2194 calculateMenu.addSeparator();
2195 calculateMenu.add(extractScores);
2196 webServiceNoServices = new JMenuItem(
2197 MessageManager.getString("label.no_services"));
2198 webService.add(webServiceNoServices);
2199 pasteMenu.add(pasteNew);
2200 pasteMenu.add(pasteThis);
2201 sort.add(sortIDMenuItem);
2202 sort.add(sortLengthMenuItem);
2203 sort.add(sortGroupMenuItem);
2204 sort.add(sortPairwiseMenuItem);
2205 sort.add(sortByTreeMenu);
2206 jMenu2.add(htmlMenuItem);
2207 jMenu2.add(epsFile);
2208 jMenu2.add(createPNG);
2209 addSequenceMenu.add(addFromFile);
2210 addSequenceMenu.add(addFromText);
2211 addSequenceMenu.add(addFromURL);
2212 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2213 statusPanel.add(statusBar, null);
2214 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2215 jMenu3.add(showAllColumns);
2216 jMenu3.add(showAllSeqs);
2217 jMenu3.add(showAllhidden);
2218 hideMenu.add(hideSelColumns);
2219 hideMenu.add(hideSelSequences);
2220 hideMenu.add(hideAllSelection);
2221 hideMenu.add(hideAllButSelection);
2223 formatMenu.add(font);
2224 formatMenu.addSeparator();
2225 formatMenu.add(wrapMenuItem);
2226 formatMenu.add(scaleAbove);
2227 formatMenu.add(scaleLeft);
2228 formatMenu.add(scaleRight);
2229 formatMenu.add(seqLimits);
2230 formatMenu.add(idRightAlign);
2231 formatMenu.add(hiddenMarkers);
2232 formatMenu.add(viewBoxesMenuItem);
2233 formatMenu.add(viewTextMenuItem);
2234 formatMenu.add(colourTextMenuItem);
2235 formatMenu.add(renderGapsMenuItem);
2236 formatMenu.add(centreColumnLabelsMenuItem);
2237 formatMenu.add(showNonconservedMenuItem);
2238 selectMenu.add(findMenuItem);
2239 selectMenu.addSeparator();
2240 selectMenu.add(selectAllSequenceMenuItem);
2241 selectMenu.add(deselectAllSequenceMenuItem);
2242 selectMenu.add(invertSequenceMenuItem);
2243 selectMenu.add(invertColSel);
2244 selectMenu.add(createGroup);
2245 selectMenu.add(unGroup);
2246 selectMenu.add(grpsFromSelection);
2247 selectMenu.add(deleteGroups);
2248 calculateMenu.add(expandAlignment);
2249 // TODO - determine if the listenToViewSelections button is needed : see bug
2251 // selectMenu.addSeparator();
2252 // selectMenu.add(listenToViewSelections);
2256 * Action on menu item "Show/hide sequence annotations..."
2258 protected void chooseAnnotations_actionPerformed()
2263 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2265 // TODO Auto-generated method stub
2269 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2271 // TODO Auto-generated method stub
2275 protected void showAllhidden_actionPerformed(ActionEvent e)
2277 // TODO Auto-generated method stub
2281 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2283 // TODO Auto-generated method stub
2287 protected void hideAllSelection_actionPerformed(ActionEvent e)
2289 // TODO Auto-generated method stub
2293 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2295 // TODO Auto-generated method stub
2299 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2301 // TODO Auto-generated method stub
2305 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2307 // TODO Auto-generated method stub
2311 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2313 // TODO Auto-generated method stub
2317 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2319 // TODO Auto-generated method stub
2323 protected void showGroupConservation_actionPerformed(ActionEvent e)
2325 // TODO Auto-generated method stub
2329 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2331 // TODO Auto-generated method stub
2335 protected void showSeqFeaturesHeight_actionPerformed(
2336 ActionEvent actionEvent)
2338 // TODO Auto-generated method stub
2342 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2344 // TODO Auto-generated method stub
2348 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2350 // TODO Auto-generated method stub
2354 protected void followHighlight_actionPerformed()
2356 // TODO Auto-generated method stub
2360 protected void showNpFeats_actionPerformed(ActionEvent e)
2362 // TODO Auto-generated method stub
2366 protected void showDbRefs_actionPerformed(ActionEvent e)
2368 // TODO Auto-generated method stub
2372 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2376 protected void showProducts_actionPerformed(ActionEvent e)
2380 protected void buildSortByAnnotationScoresMenu()
2384 protected void extractScores_actionPerformed(ActionEvent e)
2388 protected void outputText_actionPerformed(ActionEvent e)
2392 public void addFromFile_actionPerformed(ActionEvent e)
2397 public void addFromText_actionPerformed(ActionEvent e)
2402 public void addFromURL_actionPerformed(ActionEvent e)
2407 public void exportFeatures_actionPerformed(ActionEvent e)
2412 public void exportAnnotations_actionPerformed(ActionEvent e)
2417 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2421 protected void closeMenuItem_actionPerformed(boolean b)
2425 protected void redoMenuItem_actionPerformed(ActionEvent e)
2429 protected void undoMenuItem_actionPerformed(ActionEvent e)
2433 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2437 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2441 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2445 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2449 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2453 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2457 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2461 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2465 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2469 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2473 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2477 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2481 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2485 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2489 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2493 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2497 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2501 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2505 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2509 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2513 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2517 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2521 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2525 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2529 protected void clustalColour_actionPerformed(ActionEvent e)
2533 protected void zappoColour_actionPerformed(ActionEvent e)
2537 protected void taylorColour_actionPerformed(ActionEvent e)
2541 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2545 protected void helixColour_actionPerformed(ActionEvent e)
2549 protected void strandColour_actionPerformed(ActionEvent e)
2553 protected void turnColour_actionPerformed(ActionEvent e)
2557 protected void buriedColour_actionPerformed(ActionEvent e)
2561 protected void userDefinedColour_actionPerformed(ActionEvent e)
2565 protected void PIDColour_actionPerformed(ActionEvent e)
2569 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2573 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2577 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2582 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2585 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2589 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2593 protected void printMenuItem_actionPerformed(ActionEvent e)
2597 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2601 protected void findMenuItem_actionPerformed(ActionEvent e)
2605 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2609 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2613 protected void nucleotideColour_actionPerformed(ActionEvent e)
2617 protected void deleteGroups_actionPerformed(ActionEvent e)
2621 protected void createGroup_actionPerformed(ActionEvent e)
2625 protected void unGroup_actionPerformed(ActionEvent e)
2629 protected void copy_actionPerformed(ActionEvent e)
2633 protected void cut_actionPerformed(ActionEvent e)
2637 protected void delete_actionPerformed(ActionEvent e)
2641 protected void pasteNew_actionPerformed(ActionEvent e)
2645 protected void pasteThis_actionPerformed(ActionEvent e)
2649 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2653 public void createPNG(java.io.File f)
2657 protected void font_actionPerformed(ActionEvent e)
2661 protected void seqLimit_actionPerformed(ActionEvent e)
2665 public void seqDBRef_actionPerformed(ActionEvent e)
2670 public void createEPS(java.io.File f)
2674 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2680 * Template method to handle the 'load T-Coffee scores' menu event.
2682 * Subclasses override this method to provide a custom action.
2687 protected void loadScores_actionPerformed(ActionEvent event)
2693 * Template method to handle the 'Color T-Coffee scores' menu event.
2695 * Subclasses override this method to provide a custom action.
2700 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2705 protected void jpred_actionPerformed(ActionEvent e)
2709 protected void scaleAbove_actionPerformed(ActionEvent e)
2713 protected void scaleLeft_actionPerformed(ActionEvent e)
2717 protected void scaleRight_actionPerformed(ActionEvent e)
2721 protected void modifyPID_actionPerformed(ActionEvent e)
2725 protected void modifyConservation_actionPerformed(ActionEvent e)
2729 protected void saveAs_actionPerformed(ActionEvent e)
2733 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2737 public void vamsasStore_actionPerformed(ActionEvent e)
2742 public void vamsasLoad_actionPerformed(ActionEvent e)
2747 public void showTranslation_actionPerformed(ActionEvent e)
2752 public void featureSettings_actionPerformed(ActionEvent e)
2757 public void fetchSequence_actionPerformed(ActionEvent e)
2762 public void smoothFont_actionPerformed(ActionEvent e)
2767 public void annotationColour_actionPerformed(ActionEvent e)
2772 public void rnahelicesColour_actionPerformed(ActionEvent e)
2777 public void associatedData_actionPerformed(ActionEvent e)
2782 public void autoCalculate_actionPerformed(ActionEvent e)
2787 public void sortByTreeOption_actionPerformed(ActionEvent e)
2792 public void showAllSeqs_actionPerformed(ActionEvent e)
2797 public void showAllColumns_actionPerformed(ActionEvent e)
2802 public void hideSelSequences_actionPerformed(ActionEvent e)
2807 public void hideSelColumns_actionPerformed(ActionEvent e)
2812 public void hiddenMarkers_actionPerformed(ActionEvent e)
2817 public void findPdbId_actionPerformed(ActionEvent e)
2822 public void enterPdbId_actionPerformed(ActionEvent e)
2827 public void pdbFile_actionPerformed(ActionEvent e)
2832 public void invertColSel_actionPerformed(ActionEvent e)
2837 public void tabSelectionChanged(int sel)
2842 public void tabbedPane_mousePressed(MouseEvent e)
2847 public void tabbedPane_focusGained(FocusEvent e)
2852 public void save_actionPerformed(ActionEvent e)
2857 public void reload_actionPerformed(ActionEvent e)
2862 public void newView_actionPerformed(ActionEvent e)
2867 public void textColour_actionPerformed(ActionEvent e)
2872 public void idRightAlign_actionPerformed(ActionEvent e)
2877 public void expandViews_actionPerformed(ActionEvent e)
2882 public void gatherViews_actionPerformed(ActionEvent e)
2887 public void buildTreeMenu()
2892 public void pageSetup_actionPerformed(ActionEvent e)
2897 public void alignmentProperties()
2902 protected void expand_newalign(ActionEvent e)
2904 // TODO Auto-generated method stub