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 JMenu showAnnotations = new JMenu();
309 protected JMenu hideAnnotations = new JMenu();
311 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
313 JMenuItem invertColSel = new JMenuItem();
315 protected JTabbedPane tabbedPane = new JTabbedPane();
317 JMenuItem save = new JMenuItem();
319 protected JMenuItem reload = new JMenuItem();
321 JMenuItem newView = new JMenuItem();
323 JMenuItem textColour = new JMenuItem();
325 JMenu formatMenu = new JMenu();
327 JMenu selectMenu = new JMenu();
329 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
331 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
333 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
335 protected JMenuItem gatherViews = new JMenuItem();
337 protected JMenuItem expandViews = new JMenuItem();
339 JMenuItem pageSetup = new JMenuItem();
341 JMenuItem alignmentProperties = new JMenuItem();
343 JMenu tooltipSettingsMenu = new JMenu();
345 private JMenuItem justifyLeftMenuItem = new JMenuItem();
347 private JMenuItem justifyRightMenuItem = new JMenuItem();
349 JMenu autoAnnMenu = new JMenu();
351 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
353 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
355 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
357 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
359 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
361 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
363 private JMenuItem grpsFromSelection = new JMenuItem();
370 setJMenuBar(alignFrameMenuBar);
372 // dynamically fill save as menu with available formats
373 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
375 JMenuItem item = new JMenuItem(
376 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
378 item.addActionListener(new java.awt.event.ActionListener()
381 public void actionPerformed(ActionEvent e)
383 outputText_actionPerformed(e);
387 outputTextboxMenu.add(item);
389 } catch (Exception e)
391 System.err.println(e.toString());
394 if (!new jalview.util.Platform().isAMac())
396 closeMenuItem.setMnemonic('C');
397 outputTextboxMenu.setMnemonic('T');
398 undoMenuItem.setMnemonic('Z');
399 redoMenuItem.setMnemonic('0');
400 copy.setMnemonic('C');
401 cut.setMnemonic('U');
402 pasteMenu.setMnemonic('P');
403 reload.setMnemonic('R');
406 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
408 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
409 .getUserColourSchemes().keys();
411 while (userColours.hasMoreElements())
413 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
414 userColours.nextElement().toString());
415 radioItem.setName("USER_DEFINED");
416 radioItem.addMouseListener(new MouseAdapter()
419 public void mousePressed(MouseEvent evt)
421 if (evt.isControlDown()
422 || SwingUtilities.isRightMouseButton(evt))
424 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
426 int option = JOptionPane.showInternalConfirmDialog(
427 jalview.gui.Desktop.desktop,
429 .getString("label.remove_from_default_list"),
431 .getString("label.remove_user_defined_colour"),
432 JOptionPane.YES_NO_OPTION);
433 if (option == JOptionPane.YES_OPTION)
435 jalview.gui.UserDefinedColours
436 .removeColourFromDefaults(radioItem.getText());
437 colourMenu.remove(radioItem);
441 radioItem.addActionListener(new ActionListener()
444 public void actionPerformed(ActionEvent evt)
446 userDefinedColour_actionPerformed(evt);
453 radioItem.addActionListener(new ActionListener()
456 public void actionPerformed(ActionEvent evt)
458 userDefinedColour_actionPerformed(evt);
461 colourMenu.insert(radioItem, 15);
462 colours.add(radioItem);
465 colours.add(noColourmenuItem);
466 colours.add(clustalColour);
467 colours.add(zappoColour);
468 colours.add(taylorColour);
469 colours.add(hydrophobicityColour);
470 colours.add(helixColour);
471 colours.add(strandColour);
472 colours.add(turnColour);
473 colours.add(buriedColour);
474 colours.add(userDefinedColour);
475 colours.add(PIDColour);
476 colours.add(BLOSUM62Colour);
477 colours.add(nucleotideColour);
478 colours.add(purinePyrimidineColour);
479 // colours.add(covariationColour);
480 colours.add(tcoffeeColour);
481 colours.add(RNAInteractionColour);
482 setColourSelected(jalview.bin.Cache
483 .getDefault("DEFAULT_COLOUR", "None"));
487 public void setColourSelected(String defaultColour)
490 if (defaultColour != null)
492 int index = ColourSchemeProperty
493 .getColourIndexFromName(defaultColour);
497 case ColourSchemeProperty.CLUSTAL:
498 clustalColour.setSelected(true);
502 case ColourSchemeProperty.BLOSUM:
503 BLOSUM62Colour.setSelected(true);
507 case ColourSchemeProperty.PID:
508 PIDColour.setSelected(true);
512 case ColourSchemeProperty.ZAPPO:
513 zappoColour.setSelected(true);
517 case ColourSchemeProperty.TAYLOR:
518 taylorColour.setSelected(true);
521 case ColourSchemeProperty.HYDROPHOBIC:
522 hydrophobicityColour.setSelected(true);
526 case ColourSchemeProperty.HELIX:
527 helixColour.setSelected(true);
531 case ColourSchemeProperty.STRAND:
532 strandColour.setSelected(true);
536 case ColourSchemeProperty.TURN:
537 turnColour.setSelected(true);
541 case ColourSchemeProperty.BURIED:
542 buriedColour.setSelected(true);
546 case ColourSchemeProperty.NUCLEOTIDE:
547 nucleotideColour.setSelected(true);
551 case ColourSchemeProperty.TCOFFEE:
552 tcoffeeColour.setSelected(true);
555 case ColourSchemeProperty.PURINEPYRIMIDINE:
556 purinePyrimidineColour.setSelected(true);
560 case ColourSchemeProperty.RNAINTERACTION:
561 RNAInteractionColour.setSelected(true);
565 * case ColourSchemeProperty.COVARIATION:
566 * covariationColour.setSelected(true);
570 case ColourSchemeProperty.USER_DEFINED:
571 userDefinedColour.setSelected(true);
574 case ColourSchemeProperty.NONE:
576 noColourmenuItem.setSelected(true);
584 private void jbInit() throws Exception
586 fileMenu.setText(MessageManager.getString("action.file"));
587 saveAs.setText(MessageManager.getString("action.save_as") + "...");
588 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
589 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
590 .getMenuShortcutKeyMask()
591 | java.awt.event.KeyEvent.SHIFT_MASK, false));
592 saveAs.addActionListener(new ActionListener()
595 public void actionPerformed(ActionEvent e)
597 saveAs_actionPerformed(e);
600 closeMenuItem.setText(MessageManager.getString("action.close"));
601 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
602 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
603 .getMenuShortcutKeyMask(), false));
604 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
607 public void actionPerformed(ActionEvent e)
609 closeMenuItem_actionPerformed(false);
612 editMenu.setText(MessageManager.getString("action.edit"));
613 viewMenu.setText(MessageManager.getString("action.view"));
614 colourMenu.setText(MessageManager.getString("action.colour"));
615 calculateMenu.setText(MessageManager.getString("action.calculate"));
616 webService.setText(MessageManager.getString("action.web_service"));
617 selectAllSequenceMenuItem.setText(MessageManager
618 .getString("action.select_all"));
619 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
620 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
621 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
622 selectAllSequenceMenuItem
623 .addActionListener(new java.awt.event.ActionListener()
626 public void actionPerformed(ActionEvent e)
628 selectAllSequenceMenuItem_actionPerformed(e);
631 deselectAllSequenceMenuItem.setText(MessageManager
632 .getString("action.deselect_all"));
633 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
634 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
635 deselectAllSequenceMenuItem
636 .addActionListener(new java.awt.event.ActionListener()
639 public void actionPerformed(ActionEvent e)
641 deselectAllSequenceMenuItem_actionPerformed(e);
644 invertSequenceMenuItem.setText(MessageManager
645 .getString("action.invert_sequence_selection"));
646 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
647 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
648 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
649 invertSequenceMenuItem
650 .addActionListener(new java.awt.event.ActionListener()
653 public void actionPerformed(ActionEvent e)
655 invertSequenceMenuItem_actionPerformed(e);
658 grpsFromSelection.setText(MessageManager
659 .getString("action.make_groups_selection"));
660 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
663 public void actionPerformed(ActionEvent e)
665 makeGrpsFromSelection_actionPerformed(e);
668 expandAlignment.setText(MessageManager
669 .getString("action.view_flanking_regions"));
670 expandAlignment.setToolTipText(MessageManager
671 .getString("label.view_flanking_regions"));
672 expandAlignment.addActionListener(new java.awt.event.ActionListener()
675 public void actionPerformed(ActionEvent e)
680 remove2LeftMenuItem.setText(MessageManager
681 .getString("action.remove_left"));
682 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
683 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
684 .getMenuShortcutKeyMask(), false));
686 .addActionListener(new java.awt.event.ActionListener()
689 public void actionPerformed(ActionEvent e)
691 remove2LeftMenuItem_actionPerformed(e);
694 remove2RightMenuItem.setText(MessageManager
695 .getString("action.remove_right"));
696 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
697 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
698 .getMenuShortcutKeyMask(), false));
700 .addActionListener(new java.awt.event.ActionListener()
703 public void actionPerformed(ActionEvent e)
705 remove2RightMenuItem_actionPerformed(e);
708 removeGappedColumnMenuItem.setText(MessageManager
709 .getString("action.remove_empty_columns"));
710 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
711 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
712 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
713 removeGappedColumnMenuItem
714 .addActionListener(new java.awt.event.ActionListener()
717 public void actionPerformed(ActionEvent e)
719 removeGappedColumnMenuItem_actionPerformed(e);
722 removeAllGapsMenuItem.setText(MessageManager
723 .getString("action.remove_all_gaps"));
724 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
725 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
726 .getDefaultToolkit().getMenuShortcutKeyMask()
727 | java.awt.event.KeyEvent.SHIFT_MASK, false));
728 removeAllGapsMenuItem
729 .addActionListener(new java.awt.event.ActionListener()
732 public void actionPerformed(ActionEvent e)
734 removeAllGapsMenuItem_actionPerformed(e);
737 justifyLeftMenuItem.setText(MessageManager
738 .getString("action.left_justify_alignment"));
740 .addActionListener(new java.awt.event.ActionListener()
743 public void actionPerformed(ActionEvent e)
745 justifyLeftMenuItem_actionPerformed(e);
748 justifyRightMenuItem.setText(MessageManager
749 .getString("action.right_justify_alignment"));
751 .addActionListener(new java.awt.event.ActionListener()
754 public void actionPerformed(ActionEvent e)
756 justifyRightMenuItem_actionPerformed(e);
759 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
760 viewBoxesMenuItem.setState(true);
761 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
764 public void actionPerformed(ActionEvent e)
766 viewBoxesMenuItem_actionPerformed(e);
769 viewTextMenuItem.setText(MessageManager.getString("action.text"));
770 viewTextMenuItem.setState(true);
771 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
774 public void actionPerformed(ActionEvent e)
776 viewTextMenuItem_actionPerformed(e);
779 showNonconservedMenuItem.setText(MessageManager
780 .getString("label.show_non_conversed"));
781 showNonconservedMenuItem.setState(false);
782 showNonconservedMenuItem
783 .addActionListener(new java.awt.event.ActionListener()
786 public void actionPerformed(ActionEvent e)
788 showUnconservedMenuItem_actionPerformed(e);
791 sortPairwiseMenuItem.setText(MessageManager
792 .getString("action.by_pairwise_id"));
794 .addActionListener(new java.awt.event.ActionListener()
797 public void actionPerformed(ActionEvent e)
799 sortPairwiseMenuItem_actionPerformed(e);
802 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
803 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
806 public void actionPerformed(ActionEvent e)
808 sortIDMenuItem_actionPerformed(e);
812 .setText(MessageManager.getString("action.by_length"));
814 .addActionListener(new java.awt.event.ActionListener()
817 public void actionPerformed(ActionEvent e)
819 sortLengthMenuItem_actionPerformed(e);
822 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
823 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
826 public void actionPerformed(ActionEvent e)
828 sortGroupMenuItem_actionPerformed(e);
831 removeRedundancyMenuItem.setText(MessageManager
832 .getString("action.remove_redundancy"));
833 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
834 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
835 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
836 removeRedundancyMenuItem
837 .addActionListener(new java.awt.event.ActionListener()
840 public void actionPerformed(ActionEvent e)
842 removeRedundancyMenuItem_actionPerformed(e);
845 pairwiseAlignmentMenuItem.setText(MessageManager
846 .getString("action.pairwise_alignment"));
847 pairwiseAlignmentMenuItem
848 .addActionListener(new java.awt.event.ActionListener()
851 public void actionPerformed(ActionEvent e)
853 pairwiseAlignmentMenuItem_actionPerformed(e);
856 PCAMenuItem.setText(MessageManager
857 .getString("label.principal_component_analysis"));
858 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
861 public void actionPerformed(ActionEvent e)
863 PCAMenuItem_actionPerformed(e);
866 averageDistanceTreeMenuItem.setText(MessageManager
867 .getString("label.average_distance_identity"));
868 averageDistanceTreeMenuItem
869 .addActionListener(new java.awt.event.ActionListener()
872 public void actionPerformed(ActionEvent e)
874 averageDistanceTreeMenuItem_actionPerformed(e);
877 neighbourTreeMenuItem.setText(MessageManager
878 .getString("label.neighbour_joining_identity"));
879 neighbourTreeMenuItem
880 .addActionListener(new java.awt.event.ActionListener()
883 public void actionPerformed(ActionEvent e)
885 neighbourTreeMenuItem_actionPerformed(e);
888 this.getContentPane().setLayout(borderLayout1);
889 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
890 statusBar.setBackground(Color.white);
891 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
892 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
893 statusBar.setText(MessageManager.getString("label.status_bar"));
894 outputTextboxMenu.setText(MessageManager
895 .getString("label.out_to_textbox"));
896 clustalColour.setText(MessageManager.getString("label.clustalx"));
898 clustalColour.addActionListener(new java.awt.event.ActionListener()
901 public void actionPerformed(ActionEvent e)
903 clustalColour_actionPerformed(e);
906 zappoColour.setText(MessageManager.getString("label.zappo"));
907 zappoColour.addActionListener(new java.awt.event.ActionListener()
910 public void actionPerformed(ActionEvent e)
912 zappoColour_actionPerformed(e);
915 taylorColour.setText(MessageManager.getString("label.taylor"));
916 taylorColour.addActionListener(new java.awt.event.ActionListener()
919 public void actionPerformed(ActionEvent e)
921 taylorColour_actionPerformed(e);
924 hydrophobicityColour.setText(MessageManager
925 .getString("label.hydrophobicity"));
927 .addActionListener(new java.awt.event.ActionListener()
930 public void actionPerformed(ActionEvent e)
932 hydrophobicityColour_actionPerformed(e);
935 helixColour.setText(MessageManager.getString("label.helix_propensity"));
936 helixColour.addActionListener(new java.awt.event.ActionListener()
939 public void actionPerformed(ActionEvent e)
941 helixColour_actionPerformed(e);
944 strandColour.setText(MessageManager
945 .getString("label.strand_propensity"));
946 strandColour.addActionListener(new java.awt.event.ActionListener()
949 public void actionPerformed(ActionEvent e)
951 strandColour_actionPerformed(e);
954 turnColour.setText(MessageManager.getString("label.turn_propensity"));
955 turnColour.addActionListener(new java.awt.event.ActionListener()
958 public void actionPerformed(ActionEvent e)
960 turnColour_actionPerformed(e);
963 buriedColour.setText(MessageManager.getString("label.buried_index"));
964 buriedColour.addActionListener(new java.awt.event.ActionListener()
967 public void actionPerformed(ActionEvent e)
969 buriedColour_actionPerformed(e);
972 userDefinedColour.setText(MessageManager
973 .getString("action.user_defined"));
974 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
977 public void actionPerformed(ActionEvent e)
979 userDefinedColour_actionPerformed(e);
983 .setText(MessageManager.getString("label.percentage_identity"));
984 PIDColour.addActionListener(new java.awt.event.ActionListener()
987 public void actionPerformed(ActionEvent e)
989 PIDColour_actionPerformed(e);
993 .setText(MessageManager.getString("label.blosum62_score"));
994 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
997 public void actionPerformed(ActionEvent e)
999 BLOSUM62Colour_actionPerformed(e);
1002 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1003 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1006 public void actionPerformed(ActionEvent e)
1008 nucleotideColour_actionPerformed(e);
1012 purinePyrimidineColour.setText(MessageManager
1013 .getString("label.purine_pyrimidine"));
1014 purinePyrimidineColour
1015 .addActionListener(new java.awt.event.ActionListener()
1018 public void actionPerformed(ActionEvent e)
1020 purinePyrimidineColour_actionPerformed(e);
1024 RNAInteractionColour.setText("RNA Interaction type");
1025 RNAInteractionColour
1026 .addActionListener(new java.awt.event.ActionListener()
1029 public void actionPerformed(ActionEvent e)
1031 RNAInteractionColour_actionPerformed(e);
1035 * covariationColour.setText("Covariation");
1036 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1037 * public void actionPerformed(ActionEvent e) {
1038 * covariationColour_actionPerformed(e); } });
1041 avDistanceTreeBlosumMenuItem.setText(MessageManager
1042 .getString("label.average_distance_bloslum62"));
1043 avDistanceTreeBlosumMenuItem
1044 .addActionListener(new java.awt.event.ActionListener()
1047 public void actionPerformed(ActionEvent e)
1049 avTreeBlosumMenuItem_actionPerformed(e);
1052 njTreeBlosumMenuItem.setText(MessageManager
1053 .getString("label.neighbour_blosum62"));
1054 njTreeBlosumMenuItem
1055 .addActionListener(new java.awt.event.ActionListener()
1058 public void actionPerformed(ActionEvent e)
1060 njTreeBlosumMenuItem_actionPerformed(e);
1063 annotationPanelMenuItem.setActionCommand("");
1064 annotationPanelMenuItem.setText(MessageManager
1065 .getString("label.show_annotations"));
1066 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
1067 "SHOW_ANNOTATIONS", true));
1068 annotationPanelMenuItem
1069 .addActionListener(new java.awt.event.ActionListener()
1072 public void actionPerformed(ActionEvent e)
1074 annotationPanelMenuItem_actionPerformed(e);
1077 colourTextMenuItem.setText(MessageManager
1078 .getString("label.colour_text"));
1080 .addActionListener(new java.awt.event.ActionListener()
1083 public void actionPerformed(ActionEvent e)
1085 colourTextMenuItem_actionPerformed(e);
1088 htmlMenuItem.setText(MessageManager.getString("label.html"));
1089 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1092 public void actionPerformed(ActionEvent e)
1094 htmlMenuItem_actionPerformed(e);
1097 overviewMenuItem.setText(MessageManager
1098 .getString("label.overview_window"));
1099 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1102 public void actionPerformed(ActionEvent e)
1104 overviewMenuItem_actionPerformed(e);
1107 undoMenuItem.setEnabled(false);
1108 undoMenuItem.setText(MessageManager.getString("action.undo"));
1109 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1110 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1111 .getMenuShortcutKeyMask(), false));
1112 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1115 public void actionPerformed(ActionEvent e)
1117 undoMenuItem_actionPerformed(e);
1120 redoMenuItem.setEnabled(false);
1121 redoMenuItem.setText(MessageManager.getString("action.redo"));
1122 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1123 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1124 .getMenuShortcutKeyMask(), false));
1125 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1128 public void actionPerformed(ActionEvent e)
1130 redoMenuItem_actionPerformed(e);
1133 conservationMenuItem.setText(MessageManager
1134 .getString("action.by_conservation"));
1135 conservationMenuItem
1136 .addActionListener(new java.awt.event.ActionListener()
1139 public void actionPerformed(ActionEvent e)
1141 conservationMenuItem_actionPerformed(e);
1144 noColourmenuItem.setText(MessageManager.getString("label.none"));
1145 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1148 public void actionPerformed(ActionEvent e)
1150 noColourmenuItem_actionPerformed(e);
1153 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1154 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1157 public void actionPerformed(ActionEvent e)
1159 wrapMenuItem_actionPerformed(e);
1162 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1163 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1164 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1165 .getMenuShortcutKeyMask(), false));
1166 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1169 public void actionPerformed(ActionEvent e)
1171 printMenuItem_actionPerformed(e);
1175 .setText(MessageManager.getString("action.show_gaps"));
1176 renderGapsMenuItem.setState(true);
1178 .addActionListener(new java.awt.event.ActionListener()
1181 public void actionPerformed(ActionEvent e)
1183 renderGapsMenuItem_actionPerformed(e);
1186 findMenuItem.setText(MessageManager.getString("action.find"));
1187 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1188 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1189 .getMenuShortcutKeyMask(), false));
1190 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1193 public void actionPerformed(ActionEvent e)
1195 findMenuItem_actionPerformed(e);
1198 abovePIDThreshold.setText(MessageManager
1199 .getString("label.above_identity_threshold"));
1200 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1203 public void actionPerformed(ActionEvent e)
1205 abovePIDThreshold_actionPerformed(e);
1208 showSeqFeatures.setText(MessageManager
1209 .getString("label.show_sequence_features"));
1210 showSeqFeatures.addActionListener(new ActionListener()
1213 public void actionPerformed(ActionEvent actionEvent)
1215 showSeqFeatures_actionPerformed(actionEvent);
1218 chooseAnnotations.setText(MessageManager
1219 .getString("label.choose_annotations") + "...");
1220 chooseAnnotations.addActionListener(new ActionListener()
1223 public void actionPerformed(ActionEvent actionEvent)
1225 chooseAnnotations_actionPerformed();
1229 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1230 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1231 * void actionPerformed(ActionEvent actionEvent) {
1232 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1234 showDbRefsMenuitem.setText(MessageManager
1235 .getString("label.show_database_refs"));
1236 showDbRefsMenuitem.addActionListener(new ActionListener()
1240 public void actionPerformed(ActionEvent e)
1242 showDbRefs_actionPerformed(e);
1246 showNpFeatsMenuitem.setText(MessageManager
1247 .getString("label.show_non_positional_features"));
1248 showNpFeatsMenuitem.addActionListener(new ActionListener()
1252 public void actionPerformed(ActionEvent e)
1254 showNpFeats_actionPerformed(e);
1258 showGroupConservation.setText(MessageManager
1259 .getString("label.group_conservation"));
1260 showGroupConservation.addActionListener(new ActionListener()
1264 public void actionPerformed(ActionEvent e)
1266 showGroupConservation_actionPerformed(e);
1271 showGroupConsensus.setText(MessageManager
1272 .getString("label.group_consensus"));
1273 showGroupConsensus.addActionListener(new ActionListener()
1277 public void actionPerformed(ActionEvent e)
1279 showGroupConsensus_actionPerformed(e);
1283 showConsensusHistogram.setText(MessageManager
1284 .getString("label.show_consensus_histogram"));
1285 showConsensusHistogram.addActionListener(new ActionListener()
1289 public void actionPerformed(ActionEvent e)
1291 showConsensusHistogram_actionPerformed(e);
1295 showSequenceLogo.setText(MessageManager
1296 .getString("label.show_consensus_logo"));
1297 showSequenceLogo.addActionListener(new ActionListener()
1301 public void actionPerformed(ActionEvent e)
1303 showSequenceLogo_actionPerformed(e);
1307 normaliseSequenceLogo.setText(MessageManager
1308 .getString("label.norm_consensus_logo"));
1309 normaliseSequenceLogo.addActionListener(new ActionListener()
1313 public void actionPerformed(ActionEvent e)
1315 normaliseSequenceLogo_actionPerformed(e);
1319 applyAutoAnnotationSettings.setText(MessageManager
1320 .getString("label.apply_all_groups"));
1321 applyAutoAnnotationSettings.setState(false);
1322 applyAutoAnnotationSettings.setVisible(true);
1323 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1327 public void actionPerformed(ActionEvent e)
1329 applyAutoAnnotationSettings_actionPerformed(e);
1334 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1335 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1338 public void actionPerformed(ActionEvent e)
1340 nucleotideColour_actionPerformed(e);
1344 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1345 tcoffeeColour.setEnabled(false);
1346 tcoffeeColour.addActionListener(new ActionListener()
1350 public void actionPerformed(ActionEvent e)
1352 tcoffeeColorScheme_actionPerformed(e);
1357 .setText(MessageManager.getString("action.undefine_groups"));
1358 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1359 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1360 .getMenuShortcutKeyMask(), false));
1361 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1364 public void actionPerformed(ActionEvent e)
1366 deleteGroups_actionPerformed(e);
1369 createGroup.setText(MessageManager.getString("action.create_groups"));
1370 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1371 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1372 .getMenuShortcutKeyMask(), false));
1373 createGroup.addActionListener(new java.awt.event.ActionListener()
1376 public void actionPerformed(ActionEvent e)
1378 createGroup_actionPerformed(e);
1381 unGroup.setText(MessageManager.getString("action.remove_group"));
1382 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1383 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1384 .getMenuShortcutKeyMask()
1385 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1386 unGroup.addActionListener(new java.awt.event.ActionListener()
1389 public void actionPerformed(ActionEvent e)
1391 unGroup_actionPerformed(e);
1394 copy.setText(MessageManager.getString("action.copy"));
1395 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1396 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1397 .getMenuShortcutKeyMask(), false));
1399 copy.addActionListener(new java.awt.event.ActionListener()
1402 public void actionPerformed(ActionEvent e)
1404 copy_actionPerformed(e);
1407 cut.setText(MessageManager.getString("action.cut"));
1408 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1409 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1410 .getMenuShortcutKeyMask(), false));
1411 cut.addActionListener(new java.awt.event.ActionListener()
1414 public void actionPerformed(ActionEvent e)
1416 cut_actionPerformed(e);
1419 delete.setText(MessageManager.getString("action.delete"));
1420 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1421 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1422 delete.addActionListener(new java.awt.event.ActionListener()
1425 public void actionPerformed(ActionEvent e)
1427 delete_actionPerformed(e);
1430 pasteMenu.setText(MessageManager.getString("action.paste"));
1431 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1432 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1433 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1434 .getMenuShortcutKeyMask()
1435 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1436 pasteNew.addActionListener(new java.awt.event.ActionListener()
1439 public void actionPerformed(ActionEvent e)
1441 pasteNew_actionPerformed(e);
1444 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1445 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1446 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1447 .getMenuShortcutKeyMask(), false));
1448 pasteThis.addActionListener(new java.awt.event.ActionListener()
1451 public void actionPerformed(ActionEvent e)
1453 pasteThis_actionPerformed(e);
1456 applyToAllGroups.setText(MessageManager
1457 .getString("label.apply_colour_to_all_groups"));
1458 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1461 public void actionPerformed(ActionEvent e)
1463 applyToAllGroups_actionPerformed(e);
1466 createPNG.addActionListener(new java.awt.event.ActionListener()
1469 public void actionPerformed(ActionEvent e)
1474 createPNG.setActionCommand(MessageManager
1475 .getString("label.save_png_image"));
1476 createPNG.setText("PNG");
1477 font.setText(MessageManager.getString("action.font"));
1478 font.addActionListener(new java.awt.event.ActionListener()
1481 public void actionPerformed(ActionEvent e)
1483 font_actionPerformed(e);
1487 seqLimits.setText(MessageManager
1488 .getString("label.show_sequence_limits"));
1489 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1490 seqLimits.addActionListener(new java.awt.event.ActionListener()
1493 public void actionPerformed(ActionEvent e)
1495 seqLimit_actionPerformed(e);
1498 epsFile.setText("EPS");
1499 epsFile.addActionListener(new java.awt.event.ActionListener()
1502 public void actionPerformed(ActionEvent e)
1507 LoadtreeMenuItem.setActionCommand(MessageManager
1508 .getString("label.load_tree_for_sequence_set"));
1509 LoadtreeMenuItem.setText(MessageManager
1510 .getString("label.load_associated_tree"));
1511 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1514 public void actionPerformed(ActionEvent e)
1516 LoadtreeMenuItem_actionPerformed(e);
1520 scaleAbove.setVisible(false);
1521 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1522 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1525 public void actionPerformed(ActionEvent e)
1527 scaleAbove_actionPerformed(e);
1530 scaleLeft.setVisible(false);
1531 scaleLeft.setSelected(true);
1532 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1533 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1536 public void actionPerformed(ActionEvent e)
1538 scaleLeft_actionPerformed(e);
1541 scaleRight.setVisible(false);
1542 scaleRight.setSelected(true);
1543 scaleRight.setText(MessageManager.getString("action.scale_right"));
1544 scaleRight.addActionListener(new java.awt.event.ActionListener()
1547 public void actionPerformed(ActionEvent e)
1549 scaleRight_actionPerformed(e);
1552 centreColumnLabelsMenuItem.setVisible(true);
1553 centreColumnLabelsMenuItem.setState(false);
1554 centreColumnLabelsMenuItem.setText(MessageManager
1555 .getString("label.centre_column_labels"));
1556 centreColumnLabelsMenuItem
1557 .addActionListener(new java.awt.event.ActionListener()
1560 public void actionPerformed(ActionEvent e)
1562 centreColumnLabels_actionPerformed(e);
1565 followHighlightMenuItem.setVisible(true);
1566 followHighlightMenuItem.setState(true);
1567 followHighlightMenuItem.setText(MessageManager
1568 .getString("label.automatic_scrolling"));
1569 followHighlightMenuItem.addActionListener(new ActionListener()
1573 public void actionPerformed(ActionEvent e)
1575 followHighlight_actionPerformed();
1580 modifyPID.setText(MessageManager
1581 .getString("label.modify_identity_thereshold"));
1582 modifyPID.addActionListener(new java.awt.event.ActionListener()
1585 public void actionPerformed(ActionEvent e)
1587 modifyPID_actionPerformed(e);
1590 modifyConservation.setText(MessageManager
1591 .getString("label.modify_conservation_thereshold"));
1593 .addActionListener(new java.awt.event.ActionListener()
1596 public void actionPerformed(ActionEvent e)
1598 modifyConservation_actionPerformed(e);
1602 .setText(MessageManager.getString("action.by_tree_order"));
1603 sort.setText(MessageManager.getString("action.sort"));
1604 sort.addMenuListener(new MenuListener()
1607 public void menuSelected(MenuEvent e)
1613 public void menuDeselected(MenuEvent e)
1618 public void menuCanceled(MenuEvent e)
1622 sortByAnnotScore.setText(MessageManager
1623 .getString("label.sort_by_score"));
1624 sort.add(sortByAnnotScore);
1625 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1629 public void menuCanceled(MenuEvent e)
1634 public void menuDeselected(MenuEvent e)
1639 public void menuSelected(MenuEvent e)
1641 buildSortByAnnotationScoresMenu();
1644 sortByAnnotScore.setVisible(false);
1647 .setText(MessageManager.getString("action.calculate_tree"));
1649 jMenu2.setText(MessageManager.getString("label.export_image"));
1650 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1651 padGapsMenuitem.setState(jalview.bin.Cache
1652 .getDefault("PAD_GAPS", false));
1653 padGapsMenuitem.addActionListener(new ActionListener()
1656 public void actionPerformed(ActionEvent e)
1658 padGapsMenuitem_actionPerformed(e);
1661 vamsasStore.setVisible(false);
1662 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1663 vamsasStore.addActionListener(new ActionListener()
1666 public void actionPerformed(ActionEvent e)
1668 vamsasStore_actionPerformed(e);
1671 showTranslation.setText(MessageManager
1672 .getString("label.translate_cDNA"));
1673 showTranslation.addActionListener(new ActionListener()
1676 public void actionPerformed(ActionEvent e)
1678 showTranslation_actionPerformed(e);
1681 extractScores.setText(MessageManager.getString("label.extract_scores")
1683 extractScores.addActionListener(new ActionListener()
1686 public void actionPerformed(ActionEvent e)
1688 extractScores_actionPerformed(e);
1691 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1693 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1695 * showProducts.addActionListener(new ActionListener() {
1697 * public void actionPerformed(ActionEvent e) {
1698 * showProducts_actionPerformed(e); } });
1700 openFeatureSettings.setText(MessageManager
1701 .getString("label.feature_settings"));
1702 openFeatureSettings.addActionListener(new ActionListener()
1705 public void actionPerformed(ActionEvent e)
1707 featureSettings_actionPerformed(e);
1711 .setText(MessageManager.getString("label.fetch_sequences"));
1712 fetchSequence.addActionListener(new ActionListener()
1715 public void actionPerformed(ActionEvent e)
1717 fetchSequence_actionPerformed(e);
1721 annotationColour.setText(MessageManager
1722 .getString("action.by_annotation"));
1723 annotationColour.addActionListener(new ActionListener()
1726 public void actionPerformed(ActionEvent e)
1728 annotationColour_actionPerformed(e);
1732 rnahelicesColour.setText(MessageManager
1733 .getString("action.by_rna_helixes"));
1734 rnahelicesColour.addActionListener(new ActionListener()
1737 public void actionPerformed(ActionEvent e)
1739 rnahelicesColour_actionPerformed(e);
1743 associatedData.setText(MessageManager
1744 .getString("label.load_features_annotations"));
1745 associatedData.addActionListener(new ActionListener()
1748 public void actionPerformed(ActionEvent e)
1750 associatedData_actionPerformed(e);
1753 autoCalculate.setText(MessageManager
1754 .getString("label.autocalculate_consensus"));
1755 autoCalculate.setState(jalview.bin.Cache.getDefault(
1756 "AUTO_CALC_CONSENSUS", true));
1757 autoCalculate.addActionListener(new ActionListener()
1760 public void actionPerformed(ActionEvent e)
1762 autoCalculate_actionPerformed(e);
1765 sortByTree.setText(MessageManager
1766 .getString("label.sort_alignment_new_tree"));
1768 .setToolTipText("<html>"
1770 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1772 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1773 sortByTree.addActionListener(new ActionListener()
1776 public void actionPerformed(ActionEvent e)
1778 sortByTreeOption_actionPerformed(e);
1782 listenToViewSelections.setText(MessageManager
1783 .getString("label.listen_for_selections"));
1784 listenToViewSelections
1785 .setToolTipText("<html>"
1787 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1788 listenToViewSelections.setState(false);
1789 listenToViewSelections.addActionListener(new ActionListener()
1792 public void actionPerformed(ActionEvent e)
1794 listenToViewSelections_actionPerformed(e);
1799 .setText(MessageManager.getString("label.add_sequences"));
1800 addFromFile.setText(MessageManager.getString("label.from_file"));
1801 addFromFile.addActionListener(new ActionListener()
1804 public void actionPerformed(ActionEvent e)
1806 addFromFile_actionPerformed(e);
1809 addFromText.setText(MessageManager.getString("label.from_textbox"));
1810 addFromText.addActionListener(new ActionListener()
1813 public void actionPerformed(ActionEvent e)
1815 addFromText_actionPerformed(e);
1818 addFromURL.setText(MessageManager.getString("label.from_url"));
1819 addFromURL.addActionListener(new ActionListener()
1822 public void actionPerformed(ActionEvent e)
1824 addFromURL_actionPerformed(e);
1827 exportFeatures.setText(MessageManager
1828 .getString("label.export_features"));
1829 exportFeatures.addActionListener(new ActionListener()
1832 public void actionPerformed(ActionEvent e)
1834 exportFeatures_actionPerformed(e);
1837 exportAnnotations.setText(MessageManager
1838 .getString("label.export_annotations"));
1839 exportAnnotations.addActionListener(new ActionListener()
1842 public void actionPerformed(ActionEvent e)
1844 exportAnnotations_actionPerformed(e);
1847 statusPanel.setLayout(gridLayout1);
1848 jMenu3.setText(MessageManager.getString("action.show"));
1849 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1850 showAllSeqs.setToolTipText(MessageManager
1851 .getString("label.toggle_sequence_visibility"));
1852 showAllSeqs.addActionListener(new ActionListener()
1855 public void actionPerformed(ActionEvent e)
1857 showAllSeqs_actionPerformed(e);
1860 showAllColumns.setText(MessageManager.getString("label.all_columns"));
1861 showAllColumns.setToolTipText(MessageManager
1862 .getString("label.toggle_columns_visibility"));
1863 showAllColumns.addActionListener(new ActionListener()
1866 public void actionPerformed(ActionEvent e)
1868 showAllColumns_actionPerformed(e);
1871 hideMenu.setText(MessageManager.getString("action.hide"));
1872 hideSelSequences.setText(MessageManager
1873 .getString("label.selected_sequences"));
1874 hideSelSequences.setToolTipText(MessageManager
1875 .getString("label.toggle_sequence_visibility"));
1876 hideSelSequences.addActionListener(new ActionListener()
1879 public void actionPerformed(ActionEvent e)
1881 hideSelSequences_actionPerformed(e);
1884 hideSelColumns.setText(MessageManager
1885 .getString("label.selected_columns"));
1886 hideSelColumns.setToolTipText(MessageManager
1887 .getString("label.toggle_columns_visibility"));
1888 hideSelColumns.addActionListener(new ActionListener()
1891 public void actionPerformed(ActionEvent e)
1893 hideSelColumns_actionPerformed(e);
1896 hideAllSelection.setText(MessageManager
1897 .getString("label.selected_region"));
1898 hideAllSelection.addActionListener(new ActionListener()
1901 public void actionPerformed(ActionEvent e)
1903 hideAllSelection_actionPerformed(e);
1906 // TODO: should be hidden if no selection exists.
1907 hideAllButSelection.setText(MessageManager
1908 .getString("label.all_but_selected_region"));
1909 hideAllButSelection.addActionListener(new ActionListener()
1912 public void actionPerformed(ActionEvent e)
1914 hideAllButSelection_actionPerformed(e);
1917 showAllhidden.setText(MessageManager
1918 .getString("label.all_sequences_columns"));
1919 showAllhidden.setToolTipText(MessageManager
1920 .getString("label.toggles_visibility_hidden_selected_regions"));
1921 showAllhidden.addActionListener(new ActionListener()
1924 public void actionPerformed(ActionEvent e)
1926 showAllhidden_actionPerformed(e);
1929 showAnnotations.setText(MessageManager.getString("label.annotations"));
1930 showAnnotations.addMouseListener(new MouseAdapter()
1933 public void mouseEntered(MouseEvent e)
1935 buildShowHideAnnotationMenus();
1938 hideAnnotations.setText(MessageManager.getString("label.annotations"));
1939 hideAnnotations.addMouseListener(new MouseAdapter()
1942 public void mouseEntered(MouseEvent e)
1944 buildShowHideAnnotationMenus();
1948 hiddenMarkers.setText(MessageManager
1949 .getString("action.show_hidden_markers"));
1950 hiddenMarkers.addActionListener(new ActionListener()
1953 public void actionPerformed(ActionEvent e)
1955 hiddenMarkers_actionPerformed(e);
1958 invertColSel.setText(MessageManager
1959 .getString("action.invert_column_selection"));
1960 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1961 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1962 .getMenuShortcutKeyMask()
1963 | java.awt.event.KeyEvent.ALT_MASK, false));
1964 invertColSel.addActionListener(new ActionListener()
1967 public void actionPerformed(ActionEvent e)
1969 invertColSel_actionPerformed(e);
1972 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1975 public void stateChanged(ChangeEvent evt)
1977 JTabbedPane pane = (JTabbedPane) evt.getSource();
1978 int sel = pane.getSelectedIndex();
1979 tabSelectionChanged(sel);
1982 tabbedPane.addMouseListener(new MouseAdapter()
1985 public void mousePressed(MouseEvent e)
1987 tabbedPane_mousePressed(e);
1990 tabbedPane.addFocusListener(new FocusAdapter()
1993 public void focusGained(FocusEvent e)
1995 tabbedPane_focusGained(e);
1998 save.setText(MessageManager.getString("action.save"));
1999 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2000 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
2001 .getMenuShortcutKeyMask(), false));
2002 save.addActionListener(new ActionListener()
2005 public void actionPerformed(ActionEvent e)
2007 save_actionPerformed(e);
2010 reload.setEnabled(false);
2011 reload.setText(MessageManager.getString("action.reload"));
2012 reload.addActionListener(new ActionListener()
2015 public void actionPerformed(ActionEvent e)
2017 reload_actionPerformed(e);
2020 newView.setText(MessageManager.getString("action.new_view"));
2021 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2022 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2023 .getMenuShortcutKeyMask(), false));
2024 newView.addActionListener(new ActionListener()
2027 public void actionPerformed(ActionEvent e)
2029 newView_actionPerformed(e);
2032 tabbedPane.setToolTipText("<html><i>"
2033 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2035 textColour.setText(MessageManager.getString("label.colour_text")
2037 textColour.addActionListener(new ActionListener()
2040 public void actionPerformed(ActionEvent e)
2042 textColour_actionPerformed(e);
2045 formatMenu.setText(MessageManager.getString("action.format"));
2046 selectMenu.setText(MessageManager.getString("action.select"));
2047 idRightAlign.setText(MessageManager
2048 .getString("label.right_align_sequence_id"));
2049 idRightAlign.addActionListener(new ActionListener()
2052 public void actionPerformed(ActionEvent e)
2054 idRightAlign_actionPerformed(e);
2057 gatherViews.setEnabled(false);
2058 gatherViews.setText(MessageManager.getString("action.gather_views"));
2059 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2060 java.awt.event.KeyEvent.VK_G, 0, false));
2061 gatherViews.addActionListener(new ActionListener()
2064 public void actionPerformed(ActionEvent e)
2066 gatherViews_actionPerformed(e);
2069 expandViews.setEnabled(false);
2070 expandViews.setText(MessageManager.getString("action.expand_views"));
2071 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2072 java.awt.event.KeyEvent.VK_X, 0, false));
2073 expandViews.addActionListener(new ActionListener()
2076 public void actionPerformed(ActionEvent e)
2078 expandViews_actionPerformed(e);
2082 .setText(MessageManager.getString("action.page_setup") + "...");
2083 pageSetup.addActionListener(new ActionListener()
2086 public void actionPerformed(ActionEvent e)
2088 pageSetup_actionPerformed(e);
2091 alignmentProperties.setText(MessageManager
2092 .getString("label.alignment_props") + "...");
2093 alignmentProperties.addActionListener(new ActionListener()
2096 public void actionPerformed(ActionEvent actionEvent)
2098 alignmentProperties();
2101 tooltipSettingsMenu.setText(MessageManager
2102 .getString("label.sequence_id_tooltip"));
2103 autoAnnMenu.setText(MessageManager
2104 .getString("label.autocalculated_annotation"));
2105 alignFrameMenuBar.add(fileMenu);
2106 alignFrameMenuBar.add(editMenu);
2107 alignFrameMenuBar.add(selectMenu);
2108 alignFrameMenuBar.add(viewMenu);
2109 alignFrameMenuBar.add(formatMenu);
2110 alignFrameMenuBar.add(colourMenu);
2111 alignFrameMenuBar.add(calculateMenu);
2112 alignFrameMenuBar.add(webService);
2113 fileMenu.add(fetchSequence);
2114 fileMenu.add(addSequenceMenu);
2115 fileMenu.add(reload);
2116 fileMenu.addSeparator();
2117 fileMenu.add(vamsasStore);
2119 fileMenu.add(saveAs);
2120 fileMenu.add(outputTextboxMenu);
2121 fileMenu.add(pageSetup);
2122 fileMenu.add(printMenuItem);
2123 fileMenu.addSeparator();
2124 fileMenu.add(jMenu2);
2125 fileMenu.add(exportFeatures);
2126 fileMenu.add(exportAnnotations);
2127 fileMenu.add(LoadtreeMenuItem);
2128 fileMenu.add(associatedData);
2129 fileMenu.addSeparator();
2130 fileMenu.add(closeMenuItem);
2131 editMenu.add(undoMenuItem);
2132 editMenu.add(redoMenuItem);
2135 editMenu.add(pasteMenu);
2136 editMenu.add(delete);
2137 editMenu.addSeparator();
2138 editMenu.add(remove2LeftMenuItem);
2139 editMenu.add(remove2RightMenuItem);
2140 editMenu.add(removeGappedColumnMenuItem);
2141 editMenu.add(removeAllGapsMenuItem);
2142 editMenu.add(removeRedundancyMenuItem);
2143 editMenu.addSeparator();
2144 // dont add these yet in the CVS build - they cannot be undone!
2145 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2146 // editMenu.add(justifyLeftMenuItem);
2147 // editMenu.add(justifyRightMenuItem);
2148 // editMenu.addSeparator();
2149 editMenu.add(padGapsMenuitem);
2150 viewMenu.add(newView);
2151 viewMenu.add(expandViews);
2152 viewMenu.add(gatherViews);
2153 viewMenu.addSeparator();
2154 viewMenu.add(jMenu3);
2155 viewMenu.add(hideMenu);
2156 viewMenu.addSeparator();
2157 viewMenu.add(followHighlightMenuItem);
2158 viewMenu.add(annotationPanelMenuItem);
2159 autoAnnMenu.add(applyAutoAnnotationSettings);
2160 autoAnnMenu.add(showConsensusHistogram);
2161 autoAnnMenu.add(showSequenceLogo);
2162 autoAnnMenu.add(normaliseSequenceLogo);
2163 autoAnnMenu.addSeparator();
2164 autoAnnMenu.add(showGroupConservation);
2165 autoAnnMenu.add(showGroupConsensus);
2166 viewMenu.add(autoAnnMenu);
2167 viewMenu.addSeparator();
2168 viewMenu.add(showSeqFeatures);
2169 viewMenu.add(chooseAnnotations);
2170 // viewMenu.add(showSeqFeaturesHeight);
2172 viewMenu.add(openFeatureSettings);
2173 tooltipSettingsMenu.add(showDbRefsMenuitem);
2174 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2175 viewMenu.add(tooltipSettingsMenu);
2176 viewMenu.addSeparator();
2177 viewMenu.add(alignmentProperties);
2178 viewMenu.addSeparator();
2179 viewMenu.add(overviewMenuItem);
2180 colourMenu.add(applyToAllGroups);
2181 colourMenu.add(textColour);
2182 colourMenu.addSeparator();
2183 colourMenu.add(noColourmenuItem);
2184 colourMenu.add(clustalColour);
2185 colourMenu.add(BLOSUM62Colour);
2186 colourMenu.add(PIDColour);
2187 colourMenu.add(zappoColour);
2188 colourMenu.add(taylorColour);
2189 colourMenu.add(hydrophobicityColour);
2190 colourMenu.add(helixColour);
2191 colourMenu.add(strandColour);
2192 colourMenu.add(turnColour);
2193 colourMenu.add(buriedColour);
2194 colourMenu.add(nucleotideColour);
2195 colourMenu.add(purinePyrimidineColour);
2196 colourMenu.add(RNAInteractionColour);
2197 // colourMenu.add(covariationColour);
2198 colourMenu.add(tcoffeeColour);
2199 colourMenu.add(userDefinedColour);
2200 colourMenu.addSeparator();
2201 colourMenu.add(conservationMenuItem);
2202 colourMenu.add(modifyConservation);
2203 colourMenu.add(abovePIDThreshold);
2204 colourMenu.add(modifyPID);
2205 colourMenu.add(annotationColour);
2206 colourMenu.add(rnahelicesColour);
2207 calculateMenu.add(sort);
2208 calculateMenu.add(calculateTree);
2209 calculateMenu.addSeparator();
2210 calculateMenu.add(pairwiseAlignmentMenuItem);
2211 calculateMenu.add(PCAMenuItem);
2212 calculateMenu.addSeparator();
2213 calculateMenu.add(showTranslation);
2214 calculateMenu.add(showProducts);
2215 calculateMenu.add(autoCalculate);
2216 calculateMenu.add(sortByTree);
2217 calculateMenu.addSeparator();
2218 calculateMenu.add(extractScores);
2219 webServiceNoServices = new JMenuItem(
2220 MessageManager.getString("label.no_services"));
2221 webService.add(webServiceNoServices);
2222 pasteMenu.add(pasteNew);
2223 pasteMenu.add(pasteThis);
2224 sort.add(sortIDMenuItem);
2225 sort.add(sortLengthMenuItem);
2226 sort.add(sortGroupMenuItem);
2227 sort.add(sortPairwiseMenuItem);
2228 sort.add(sortByTreeMenu);
2229 jMenu2.add(htmlMenuItem);
2230 jMenu2.add(epsFile);
2231 jMenu2.add(createPNG);
2232 addSequenceMenu.add(addFromFile);
2233 addSequenceMenu.add(addFromText);
2234 addSequenceMenu.add(addFromURL);
2235 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2236 statusPanel.add(statusBar, null);
2237 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2238 jMenu3.add(showAllColumns);
2239 jMenu3.add(showAllSeqs);
2240 jMenu3.add(showAllhidden);
2241 jMenu3.add(showAnnotations);
2242 hideMenu.add(hideSelColumns);
2243 hideMenu.add(hideSelSequences);
2244 hideMenu.add(hideAllSelection);
2245 hideMenu.add(hideAllButSelection);
2246 hideMenu.add(hideAnnotations);
2248 formatMenu.add(font);
2249 formatMenu.addSeparator();
2250 formatMenu.add(wrapMenuItem);
2251 formatMenu.add(scaleAbove);
2252 formatMenu.add(scaleLeft);
2253 formatMenu.add(scaleRight);
2254 formatMenu.add(seqLimits);
2255 formatMenu.add(idRightAlign);
2256 formatMenu.add(hiddenMarkers);
2257 formatMenu.add(viewBoxesMenuItem);
2258 formatMenu.add(viewTextMenuItem);
2259 formatMenu.add(colourTextMenuItem);
2260 formatMenu.add(renderGapsMenuItem);
2261 formatMenu.add(centreColumnLabelsMenuItem);
2262 formatMenu.add(showNonconservedMenuItem);
2263 selectMenu.add(findMenuItem);
2264 selectMenu.addSeparator();
2265 selectMenu.add(selectAllSequenceMenuItem);
2266 selectMenu.add(deselectAllSequenceMenuItem);
2267 selectMenu.add(invertSequenceMenuItem);
2268 selectMenu.add(invertColSel);
2269 selectMenu.add(createGroup);
2270 selectMenu.add(unGroup);
2271 selectMenu.add(grpsFromSelection);
2272 selectMenu.add(deleteGroups);
2273 calculateMenu.add(expandAlignment);
2274 // TODO - determine if the listenToViewSelections button is needed : see bug
2276 // selectMenu.addSeparator();
2277 // selectMenu.add(listenToViewSelections);
2281 * Dynamically build list of annotation types to show or hide.
2283 protected void buildShowHideAnnotationMenus()
2287 protected void showHideAnnotation_actionPerformed(String type, boolean b)
2292 * Action on menu item "Show/hide sequence annotations..."
2294 protected void chooseAnnotations_actionPerformed()
2299 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2301 // TODO Auto-generated method stub
2305 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2307 // TODO Auto-generated method stub
2311 protected void showAllhidden_actionPerformed(ActionEvent e)
2313 // TODO Auto-generated method stub
2317 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2319 // TODO Auto-generated method stub
2323 protected void hideAllSelection_actionPerformed(ActionEvent e)
2325 // TODO Auto-generated method stub
2329 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2331 // TODO Auto-generated method stub
2335 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2337 // TODO Auto-generated method stub
2341 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2343 // TODO Auto-generated method stub
2347 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2349 // TODO Auto-generated method stub
2353 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2355 // TODO Auto-generated method stub
2359 protected void showGroupConservation_actionPerformed(ActionEvent e)
2361 // TODO Auto-generated method stub
2365 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2367 // TODO Auto-generated method stub
2371 protected void showSeqFeaturesHeight_actionPerformed(
2372 ActionEvent actionEvent)
2374 // TODO Auto-generated method stub
2378 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2380 // TODO Auto-generated method stub
2384 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2386 // TODO Auto-generated method stub
2390 protected void followHighlight_actionPerformed()
2392 // TODO Auto-generated method stub
2396 protected void showNpFeats_actionPerformed(ActionEvent e)
2398 // TODO Auto-generated method stub
2402 protected void showDbRefs_actionPerformed(ActionEvent e)
2404 // TODO Auto-generated method stub
2408 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2412 protected void showProducts_actionPerformed(ActionEvent e)
2416 protected void buildSortByAnnotationScoresMenu()
2420 protected void extractScores_actionPerformed(ActionEvent e)
2424 protected void outputText_actionPerformed(ActionEvent e)
2428 public void addFromFile_actionPerformed(ActionEvent e)
2433 public void addFromText_actionPerformed(ActionEvent e)
2438 public void addFromURL_actionPerformed(ActionEvent e)
2443 public void exportFeatures_actionPerformed(ActionEvent e)
2448 public void exportAnnotations_actionPerformed(ActionEvent e)
2453 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2457 protected void closeMenuItem_actionPerformed(boolean b)
2461 protected void redoMenuItem_actionPerformed(ActionEvent e)
2465 protected void undoMenuItem_actionPerformed(ActionEvent e)
2469 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2473 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2477 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2481 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2485 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2489 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2493 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2497 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2501 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2505 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2509 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2513 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2517 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2521 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2525 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2529 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2533 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2537 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2541 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2545 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2549 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2553 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2557 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2561 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2565 protected void clustalColour_actionPerformed(ActionEvent e)
2569 protected void zappoColour_actionPerformed(ActionEvent e)
2573 protected void taylorColour_actionPerformed(ActionEvent e)
2577 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2581 protected void helixColour_actionPerformed(ActionEvent e)
2585 protected void strandColour_actionPerformed(ActionEvent e)
2589 protected void turnColour_actionPerformed(ActionEvent e)
2593 protected void buriedColour_actionPerformed(ActionEvent e)
2597 protected void userDefinedColour_actionPerformed(ActionEvent e)
2601 protected void PIDColour_actionPerformed(ActionEvent e)
2605 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2609 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2613 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2618 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2621 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2625 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2629 protected void printMenuItem_actionPerformed(ActionEvent e)
2633 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2637 protected void findMenuItem_actionPerformed(ActionEvent e)
2641 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2645 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2649 protected void nucleotideColour_actionPerformed(ActionEvent e)
2653 protected void deleteGroups_actionPerformed(ActionEvent e)
2657 protected void createGroup_actionPerformed(ActionEvent e)
2661 protected void unGroup_actionPerformed(ActionEvent e)
2665 protected void copy_actionPerformed(ActionEvent e)
2669 protected void cut_actionPerformed(ActionEvent e)
2673 protected void delete_actionPerformed(ActionEvent e)
2677 protected void pasteNew_actionPerformed(ActionEvent e)
2681 protected void pasteThis_actionPerformed(ActionEvent e)
2685 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2689 public void createPNG(java.io.File f)
2693 protected void font_actionPerformed(ActionEvent e)
2697 protected void seqLimit_actionPerformed(ActionEvent e)
2701 public void seqDBRef_actionPerformed(ActionEvent e)
2706 public void createEPS(java.io.File f)
2710 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2716 * Template method to handle the 'load T-Coffee scores' menu event.
2718 * Subclasses override this method to provide a custom action.
2723 protected void loadScores_actionPerformed(ActionEvent event)
2729 * Template method to handle the 'Color T-Coffee scores' menu event.
2731 * Subclasses override this method to provide a custom action.
2736 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2741 protected void jpred_actionPerformed(ActionEvent e)
2745 protected void scaleAbove_actionPerformed(ActionEvent e)
2749 protected void scaleLeft_actionPerformed(ActionEvent e)
2753 protected void scaleRight_actionPerformed(ActionEvent e)
2757 protected void modifyPID_actionPerformed(ActionEvent e)
2761 protected void modifyConservation_actionPerformed(ActionEvent e)
2765 protected void saveAs_actionPerformed(ActionEvent e)
2769 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2773 public void vamsasStore_actionPerformed(ActionEvent e)
2778 public void vamsasLoad_actionPerformed(ActionEvent e)
2783 public void showTranslation_actionPerformed(ActionEvent e)
2788 public void featureSettings_actionPerformed(ActionEvent e)
2793 public void fetchSequence_actionPerformed(ActionEvent e)
2798 public void smoothFont_actionPerformed(ActionEvent e)
2803 public void annotationColour_actionPerformed(ActionEvent e)
2808 public void rnahelicesColour_actionPerformed(ActionEvent e)
2813 public void associatedData_actionPerformed(ActionEvent e)
2818 public void autoCalculate_actionPerformed(ActionEvent e)
2823 public void sortByTreeOption_actionPerformed(ActionEvent e)
2828 public void showAllSeqs_actionPerformed(ActionEvent e)
2833 public void showAllColumns_actionPerformed(ActionEvent e)
2838 public void hideSelSequences_actionPerformed(ActionEvent e)
2843 public void hideSelColumns_actionPerformed(ActionEvent e)
2848 public void hiddenMarkers_actionPerformed(ActionEvent e)
2853 public void findPdbId_actionPerformed(ActionEvent e)
2858 public void enterPdbId_actionPerformed(ActionEvent e)
2863 public void pdbFile_actionPerformed(ActionEvent e)
2868 public void invertColSel_actionPerformed(ActionEvent e)
2873 public void tabSelectionChanged(int sel)
2878 public void tabbedPane_mousePressed(MouseEvent e)
2883 public void tabbedPane_focusGained(FocusEvent e)
2888 public void save_actionPerformed(ActionEvent e)
2893 public void reload_actionPerformed(ActionEvent e)
2898 public void newView_actionPerformed(ActionEvent e)
2903 public void textColour_actionPerformed(ActionEvent e)
2908 public void idRightAlign_actionPerformed(ActionEvent e)
2913 public void expandViews_actionPerformed(ActionEvent e)
2918 public void gatherViews_actionPerformed(ActionEvent e)
2923 public void buildTreeMenu()
2928 public void pageSetup_actionPerformed(ActionEvent e)
2933 public void alignmentProperties()
2938 protected void expand_newalign(ActionEvent e)
2940 // TODO Auto-generated method stub