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 deleteGroups = new JMenuItem();
191 JMenuItem createGroup = new JMenuItem();
193 JMenuItem unGroup = new JMenuItem();
195 JMenuItem delete = new JMenuItem();
197 JMenuItem copy = new JMenuItem();
199 JMenuItem cut = new JMenuItem();
201 JMenu pasteMenu = new JMenu();
203 JMenuItem pasteNew = new JMenuItem();
205 JMenuItem pasteThis = new JMenuItem();
207 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
209 JMenuItem createPNG = new JMenuItem();
211 protected JMenuItem font = new JMenuItem();
213 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
215 JMenuItem epsFile = new JMenuItem();
217 JMenuItem LoadtreeMenuItem = new JMenuItem();
219 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
221 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
223 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
225 protected JMenuItem modifyPID = new JMenuItem();
227 protected JMenuItem modifyConservation = new JMenuItem();
229 protected JMenu sortByTreeMenu = new JMenu();
231 protected JMenu sort = new JMenu();
233 protected JMenu calculateTree = new JMenu();
235 JMenu jMenu2 = new JMenu();
237 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
239 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
241 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
243 protected ButtonGroup colours = new ButtonGroup();
245 JMenuItem vamsasStore = new JMenuItem();
247 protected JMenuItem showTranslation = new JMenuItem();
249 protected JMenuItem extractScores = new JMenuItem();
251 protected JMenuItem expandAlignment = new JMenuItem();
253 protected JMenu showProducts = new JMenu();
255 public JMenuItem openFeatureSettings = new JMenuItem();
257 JMenuItem fetchSequence = new JMenuItem();
259 JMenuItem annotationColour = new JMenuItem();
261 protected JMenuItem rnahelicesColour = new JMenuItem();
263 JMenuItem associatedData = new JMenuItem();
265 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
267 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
269 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
271 JMenu addSequenceMenu = new JMenu();
273 JMenuItem addFromFile = new JMenuItem();
275 JMenuItem addFromText = new JMenuItem();
277 JMenuItem addFromURL = new JMenuItem();
279 JMenuItem exportAnnotations = new JMenuItem();
281 JMenuItem exportFeatures = new JMenuItem();
283 protected JPanel statusPanel = new JPanel();
285 GridLayout gridLayout1 = new GridLayout();
287 JMenu jMenu3 = new JMenu();
289 JMenuItem showAllSeqs = new JMenuItem();
291 JMenuItem showAllColumns = new JMenuItem();
293 JMenu hideMenu = new JMenu();
295 JMenuItem hideSelSequences = new JMenuItem();
297 JMenuItem hideSelColumns = new JMenuItem();
299 JMenuItem hideAllButSelection = new JMenuItem();
301 JMenuItem hideAllSelection = new JMenuItem();
303 JMenuItem showAllhidden = new JMenuItem();
305 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
307 JMenuItem invertColSel = new JMenuItem();
309 protected JTabbedPane tabbedPane = new JTabbedPane();
311 JMenuItem save = new JMenuItem();
313 protected JMenuItem reload = new JMenuItem();
315 JMenuItem newView = new JMenuItem();
317 JMenuItem textColour = new JMenuItem();
319 JMenu formatMenu = new JMenu();
321 JMenu selectMenu = new JMenu();
323 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
325 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
327 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
329 protected JMenuItem gatherViews = new JMenuItem();
331 protected JMenuItem expandViews = new JMenuItem();
333 JMenuItem pageSetup = new JMenuItem();
335 JMenuItem alignmentProperties = new JMenuItem();
337 JMenu tooltipSettingsMenu = new JMenu();
339 private JMenuItem justifyLeftMenuItem = new JMenuItem();
341 private JMenuItem justifyRightMenuItem = new JMenuItem();
343 JMenu autoAnnMenu = new JMenu();
345 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
347 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
349 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
351 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
353 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
355 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
357 private JMenuItem grpsFromSelection = new JMenuItem();
364 setJMenuBar(alignFrameMenuBar);
366 // dynamically fill save as menu with available formats
367 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
369 JMenuItem item = new JMenuItem(
370 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
372 item.addActionListener(new java.awt.event.ActionListener()
374 public void actionPerformed(ActionEvent e)
376 outputText_actionPerformed(e);
380 outputTextboxMenu.add(item);
382 } catch (Exception e)
386 if (!new jalview.util.Platform().isAMac())
388 closeMenuItem.setMnemonic('C');
389 outputTextboxMenu.setMnemonic('T');
390 undoMenuItem.setMnemonic('Z');
391 redoMenuItem.setMnemonic('0');
392 copy.setMnemonic('C');
393 cut.setMnemonic('U');
394 pasteMenu.setMnemonic('P');
395 reload.setMnemonic('R');
398 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
400 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
401 .getUserColourSchemes().keys();
403 while (userColours.hasMoreElements())
405 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
406 userColours.nextElement().toString());
407 radioItem.setName("USER_DEFINED");
408 radioItem.addMouseListener(new MouseAdapter()
410 public void mousePressed(MouseEvent evt)
412 if (evt.isControlDown()
413 || SwingUtilities.isRightMouseButton(evt))
415 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
417 int option = JOptionPane.showInternalConfirmDialog(
418 jalview.gui.Desktop.desktop,
420 .getString("label.remove_from_default_list"),
422 .getString("label.remove_user_defined_colour"),
423 JOptionPane.YES_NO_OPTION);
424 if (option == JOptionPane.YES_OPTION)
426 jalview.gui.UserDefinedColours
427 .removeColourFromDefaults(radioItem.getText());
428 colourMenu.remove(radioItem);
432 radioItem.addActionListener(new ActionListener()
434 public void actionPerformed(ActionEvent evt)
436 userDefinedColour_actionPerformed(evt);
443 radioItem.addActionListener(new ActionListener()
445 public void actionPerformed(ActionEvent evt)
447 userDefinedColour_actionPerformed(evt);
450 colourMenu.insert(radioItem, 15);
451 colours.add(radioItem);
454 colours.add(noColourmenuItem);
455 colours.add(clustalColour);
456 colours.add(zappoColour);
457 colours.add(taylorColour);
458 colours.add(hydrophobicityColour);
459 colours.add(helixColour);
460 colours.add(strandColour);
461 colours.add(turnColour);
462 colours.add(buriedColour);
463 colours.add(userDefinedColour);
464 colours.add(PIDColour);
465 colours.add(BLOSUM62Colour);
466 colours.add(nucleotideColour);
467 colours.add(purinePyrimidineColour);
468 // colours.add(covariationColour);
469 colours.add(tcoffeeColour);
470 colours.add(RNAInteractionColour);
471 setColourSelected(jalview.bin.Cache
472 .getDefault("DEFAULT_COLOUR", "None"));
476 public void setColourSelected(String defaultColour)
479 if (defaultColour != null)
481 int index = ColourSchemeProperty
482 .getColourIndexFromName(defaultColour);
486 case ColourSchemeProperty.CLUSTAL:
487 clustalColour.setSelected(true);
491 case ColourSchemeProperty.BLOSUM:
492 BLOSUM62Colour.setSelected(true);
496 case ColourSchemeProperty.PID:
497 PIDColour.setSelected(true);
501 case ColourSchemeProperty.ZAPPO:
502 zappoColour.setSelected(true);
506 case ColourSchemeProperty.TAYLOR:
507 taylorColour.setSelected(true);
510 case ColourSchemeProperty.HYDROPHOBIC:
511 hydrophobicityColour.setSelected(true);
515 case ColourSchemeProperty.HELIX:
516 helixColour.setSelected(true);
520 case ColourSchemeProperty.STRAND:
521 strandColour.setSelected(true);
525 case ColourSchemeProperty.TURN:
526 turnColour.setSelected(true);
530 case ColourSchemeProperty.BURIED:
531 buriedColour.setSelected(true);
535 case ColourSchemeProperty.NUCLEOTIDE:
536 nucleotideColour.setSelected(true);
540 case ColourSchemeProperty.TCOFFEE:
541 tcoffeeColour.setSelected(true);
544 case ColourSchemeProperty.PURINEPYRIMIDINE:
545 purinePyrimidineColour.setSelected(true);
549 case ColourSchemeProperty.RNAINTERACTION:
550 RNAInteractionColour.setSelected(true);
554 * case ColourSchemeProperty.COVARIATION:
555 * covariationColour.setSelected(true);
559 case ColourSchemeProperty.USER_DEFINED:
560 userDefinedColour.setSelected(true);
563 case ColourSchemeProperty.NONE:
565 noColourmenuItem.setSelected(true);
573 private void jbInit() throws Exception
575 fileMenu.setText(MessageManager.getString("action.file"));
576 saveAs.setText(MessageManager.getString("action.save_as") + "...");
577 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
578 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
579 .getMenuShortcutKeyMask()
580 | java.awt.event.KeyEvent.SHIFT_MASK, false));
581 saveAs.addActionListener(new ActionListener()
583 public void actionPerformed(ActionEvent e)
585 saveAs_actionPerformed(e);
588 closeMenuItem.setText(MessageManager.getString("action.close"));
589 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
590 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
591 .getMenuShortcutKeyMask(), false));
592 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
594 public void actionPerformed(ActionEvent e)
596 closeMenuItem_actionPerformed(false);
599 editMenu.setText(MessageManager.getString("action.edit"));
600 viewMenu.setText(MessageManager.getString("action.view"));
601 colourMenu.setText(MessageManager.getString("action.colour"));
602 calculateMenu.setText(MessageManager.getString("action.calculate"));
603 webService.setText(MessageManager.getString("action.web_service"));
604 selectAllSequenceMenuItem.setText(MessageManager
605 .getString("action.select_all"));
606 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
607 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
608 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
609 selectAllSequenceMenuItem
610 .addActionListener(new java.awt.event.ActionListener()
612 public void actionPerformed(ActionEvent e)
614 selectAllSequenceMenuItem_actionPerformed(e);
617 deselectAllSequenceMenuItem.setText(MessageManager
618 .getString("action.deselect_all"));
619 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
620 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
621 deselectAllSequenceMenuItem
622 .addActionListener(new java.awt.event.ActionListener()
624 public void actionPerformed(ActionEvent e)
626 deselectAllSequenceMenuItem_actionPerformed(e);
629 invertSequenceMenuItem.setText(MessageManager
630 .getString("action.invert_sequence_selection"));
631 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
632 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
633 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
634 invertSequenceMenuItem
635 .addActionListener(new java.awt.event.ActionListener()
637 public void actionPerformed(ActionEvent e)
639 invertSequenceMenuItem_actionPerformed(e);
642 grpsFromSelection.setText(MessageManager
643 .getString("action.make_groups_selection"));
644 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
646 public void actionPerformed(ActionEvent e)
648 makeGrpsFromSelection_actionPerformed(e);
651 expandAlignment.setText(MessageManager
652 .getString("action.view_flanking_regions"));
653 expandAlignment.setToolTipText(MessageManager
654 .getString("label.view_flanking_regions"));
655 expandAlignment.addActionListener(new java.awt.event.ActionListener()
658 public void actionPerformed(ActionEvent e)
663 remove2LeftMenuItem.setText(MessageManager
664 .getString("action.remove_left"));
665 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
666 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
667 .getMenuShortcutKeyMask(), false));
669 .addActionListener(new java.awt.event.ActionListener()
671 public void actionPerformed(ActionEvent e)
673 remove2LeftMenuItem_actionPerformed(e);
676 remove2RightMenuItem.setText(MessageManager
677 .getString("action.remove_right"));
678 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
679 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
680 .getMenuShortcutKeyMask(), false));
682 .addActionListener(new java.awt.event.ActionListener()
684 public void actionPerformed(ActionEvent e)
686 remove2RightMenuItem_actionPerformed(e);
689 removeGappedColumnMenuItem.setText(MessageManager
690 .getString("action.remove_empty_columns"));
691 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
692 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
693 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
694 removeGappedColumnMenuItem
695 .addActionListener(new java.awt.event.ActionListener()
697 public void actionPerformed(ActionEvent e)
699 removeGappedColumnMenuItem_actionPerformed(e);
702 removeAllGapsMenuItem.setText(MessageManager
703 .getString("action.remove_all_gaps"));
704 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
705 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
706 .getDefaultToolkit().getMenuShortcutKeyMask()
707 | java.awt.event.KeyEvent.SHIFT_MASK, false));
708 removeAllGapsMenuItem
709 .addActionListener(new java.awt.event.ActionListener()
711 public void actionPerformed(ActionEvent e)
713 removeAllGapsMenuItem_actionPerformed(e);
716 justifyLeftMenuItem.setText(MessageManager
717 .getString("action.left_justify_alignment"));
719 .addActionListener(new java.awt.event.ActionListener()
721 public void actionPerformed(ActionEvent e)
723 justifyLeftMenuItem_actionPerformed(e);
726 justifyRightMenuItem.setText(MessageManager
727 .getString("action.right_justify_alignment"));
729 .addActionListener(new java.awt.event.ActionListener()
731 public void actionPerformed(ActionEvent e)
733 justifyRightMenuItem_actionPerformed(e);
736 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
737 viewBoxesMenuItem.setState(true);
738 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
740 public void actionPerformed(ActionEvent e)
742 viewBoxesMenuItem_actionPerformed(e);
745 viewTextMenuItem.setText(MessageManager.getString("action.text"));
746 viewTextMenuItem.setState(true);
747 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
749 public void actionPerformed(ActionEvent e)
751 viewTextMenuItem_actionPerformed(e);
754 showNonconservedMenuItem.setText(MessageManager
755 .getString("label.show_non_conversed"));
756 showNonconservedMenuItem.setState(false);
757 showNonconservedMenuItem
758 .addActionListener(new java.awt.event.ActionListener()
760 public void actionPerformed(ActionEvent e)
762 showUnconservedMenuItem_actionPerformed(e);
765 sortPairwiseMenuItem.setText(MessageManager
766 .getString("action.by_pairwise_id"));
768 .addActionListener(new java.awt.event.ActionListener()
770 public void actionPerformed(ActionEvent e)
772 sortPairwiseMenuItem_actionPerformed(e);
775 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
776 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
778 public void actionPerformed(ActionEvent e)
780 sortIDMenuItem_actionPerformed(e);
784 .setText(MessageManager.getString("action.by_length"));
786 .addActionListener(new java.awt.event.ActionListener()
788 public void actionPerformed(ActionEvent e)
790 sortLengthMenuItem_actionPerformed(e);
793 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
794 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
796 public void actionPerformed(ActionEvent e)
798 sortGroupMenuItem_actionPerformed(e);
801 removeRedundancyMenuItem.setText(MessageManager
802 .getString("action.remove_redundancy"));
803 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
804 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
805 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
806 removeRedundancyMenuItem
807 .addActionListener(new java.awt.event.ActionListener()
809 public void actionPerformed(ActionEvent e)
811 removeRedundancyMenuItem_actionPerformed(e);
814 pairwiseAlignmentMenuItem.setText(MessageManager
815 .getString("action.pairwise_alignment"));
816 pairwiseAlignmentMenuItem
817 .addActionListener(new java.awt.event.ActionListener()
819 public void actionPerformed(ActionEvent e)
821 pairwiseAlignmentMenuItem_actionPerformed(e);
824 PCAMenuItem.setText(MessageManager
825 .getString("label.principal_component_analysis"));
826 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
828 public void actionPerformed(ActionEvent e)
830 PCAMenuItem_actionPerformed(e);
833 averageDistanceTreeMenuItem.setText(MessageManager
834 .getString("label.average_distance_identity"));
835 averageDistanceTreeMenuItem
836 .addActionListener(new java.awt.event.ActionListener()
838 public void actionPerformed(ActionEvent e)
840 averageDistanceTreeMenuItem_actionPerformed(e);
843 neighbourTreeMenuItem.setText(MessageManager
844 .getString("label.neighbour_joining_identity"));
845 neighbourTreeMenuItem
846 .addActionListener(new java.awt.event.ActionListener()
848 public void actionPerformed(ActionEvent e)
850 neighbourTreeMenuItem_actionPerformed(e);
853 this.getContentPane().setLayout(borderLayout1);
854 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
855 statusBar.setBackground(Color.white);
856 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
857 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
858 statusBar.setText(MessageManager.getString("label.status_bar"));
859 outputTextboxMenu.setText(MessageManager
860 .getString("label.out_to_textbox"));
861 clustalColour.setText(MessageManager.getString("label.clustalx"));
863 clustalColour.addActionListener(new java.awt.event.ActionListener()
865 public void actionPerformed(ActionEvent e)
867 clustalColour_actionPerformed(e);
870 zappoColour.setText(MessageManager.getString("label.zappo"));
871 zappoColour.addActionListener(new java.awt.event.ActionListener()
873 public void actionPerformed(ActionEvent e)
875 zappoColour_actionPerformed(e);
878 taylorColour.setText(MessageManager.getString("label.taylor"));
879 taylorColour.addActionListener(new java.awt.event.ActionListener()
881 public void actionPerformed(ActionEvent e)
883 taylorColour_actionPerformed(e);
886 hydrophobicityColour.setText(MessageManager
887 .getString("label.hydrophobicity"));
889 .addActionListener(new java.awt.event.ActionListener()
891 public void actionPerformed(ActionEvent e)
893 hydrophobicityColour_actionPerformed(e);
896 helixColour.setText(MessageManager.getString("label.helix_propensity"));
897 helixColour.addActionListener(new java.awt.event.ActionListener()
899 public void actionPerformed(ActionEvent e)
901 helixColour_actionPerformed(e);
904 strandColour.setText(MessageManager
905 .getString("label.strand_propensity"));
906 strandColour.addActionListener(new java.awt.event.ActionListener()
908 public void actionPerformed(ActionEvent e)
910 strandColour_actionPerformed(e);
913 turnColour.setText(MessageManager.getString("label.turn_propensity"));
914 turnColour.addActionListener(new java.awt.event.ActionListener()
916 public void actionPerformed(ActionEvent e)
918 turnColour_actionPerformed(e);
921 buriedColour.setText(MessageManager.getString("label.buried_index"));
922 buriedColour.addActionListener(new java.awt.event.ActionListener()
924 public void actionPerformed(ActionEvent e)
926 buriedColour_actionPerformed(e);
929 userDefinedColour.setText(MessageManager
930 .getString("action.user_defined"));
931 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
933 public void actionPerformed(ActionEvent e)
935 userDefinedColour_actionPerformed(e);
939 .setText(MessageManager.getString("label.percentage_identity"));
940 PIDColour.addActionListener(new java.awt.event.ActionListener()
942 public void actionPerformed(ActionEvent e)
944 PIDColour_actionPerformed(e);
948 .setText(MessageManager.getString("label.blosum62_score"));
949 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
951 public void actionPerformed(ActionEvent e)
953 BLOSUM62Colour_actionPerformed(e);
956 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
957 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
959 public void actionPerformed(ActionEvent e)
961 nucleotideColour_actionPerformed(e);
965 purinePyrimidineColour.setText(MessageManager
966 .getString("label.purine_pyrimidine"));
967 purinePyrimidineColour
968 .addActionListener(new java.awt.event.ActionListener()
970 public void actionPerformed(ActionEvent e)
972 purinePyrimidineColour_actionPerformed(e);
976 RNAInteractionColour.setText("RNA Interaction type");
978 .addActionListener(new java.awt.event.ActionListener()
980 public void actionPerformed(ActionEvent e)
982 RNAInteractionColour_actionPerformed(e);
986 * covariationColour.setText("Covariation");
987 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
988 * public void actionPerformed(ActionEvent e) {
989 * covariationColour_actionPerformed(e); } });
992 avDistanceTreeBlosumMenuItem.setText(MessageManager
993 .getString("label.average_distance_bloslum62"));
994 avDistanceTreeBlosumMenuItem
995 .addActionListener(new java.awt.event.ActionListener()
997 public void actionPerformed(ActionEvent e)
999 avTreeBlosumMenuItem_actionPerformed(e);
1002 njTreeBlosumMenuItem.setText(MessageManager
1003 .getString("label.neighbour_blosum62"));
1004 njTreeBlosumMenuItem
1005 .addActionListener(new java.awt.event.ActionListener()
1007 public void actionPerformed(ActionEvent e)
1009 njTreeBlosumMenuItem_actionPerformed(e);
1012 annotationPanelMenuItem.setActionCommand("");
1013 annotationPanelMenuItem.setText(MessageManager
1014 .getString("label.show_annotations"));
1015 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
1016 "SHOW_ANNOTATIONS", true));
1017 annotationPanelMenuItem
1018 .addActionListener(new java.awt.event.ActionListener()
1020 public void actionPerformed(ActionEvent e)
1022 annotationPanelMenuItem_actionPerformed(e);
1025 colourTextMenuItem.setText(MessageManager
1026 .getString("label.colour_text"));
1028 .addActionListener(new java.awt.event.ActionListener()
1030 public void actionPerformed(ActionEvent e)
1032 colourTextMenuItem_actionPerformed(e);
1035 htmlMenuItem.setText(MessageManager.getString("label.html"));
1036 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1038 public void actionPerformed(ActionEvent e)
1040 htmlMenuItem_actionPerformed(e);
1043 overviewMenuItem.setText(MessageManager
1044 .getString("label.overview_window"));
1045 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1047 public void actionPerformed(ActionEvent e)
1049 overviewMenuItem_actionPerformed(e);
1052 undoMenuItem.setEnabled(false);
1053 undoMenuItem.setText(MessageManager.getString("action.undo"));
1054 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1055 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1056 .getMenuShortcutKeyMask(), false));
1057 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1059 public void actionPerformed(ActionEvent e)
1061 undoMenuItem_actionPerformed(e);
1064 redoMenuItem.setEnabled(false);
1065 redoMenuItem.setText(MessageManager.getString("action.redo"));
1066 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1067 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1068 .getMenuShortcutKeyMask(), false));
1069 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1071 public void actionPerformed(ActionEvent e)
1073 redoMenuItem_actionPerformed(e);
1076 conservationMenuItem.setText(MessageManager
1077 .getString("action.by_conservation"));
1078 conservationMenuItem
1079 .addActionListener(new java.awt.event.ActionListener()
1081 public void actionPerformed(ActionEvent e)
1083 conservationMenuItem_actionPerformed(e);
1086 noColourmenuItem.setText(MessageManager.getString("label.none"));
1087 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1089 public void actionPerformed(ActionEvent e)
1091 noColourmenuItem_actionPerformed(e);
1094 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1095 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1097 public void actionPerformed(ActionEvent e)
1099 wrapMenuItem_actionPerformed(e);
1102 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1103 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1104 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1105 .getMenuShortcutKeyMask(), false));
1106 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1108 public void actionPerformed(ActionEvent e)
1110 printMenuItem_actionPerformed(e);
1114 .setText(MessageManager.getString("action.show_gaps"));
1115 renderGapsMenuItem.setState(true);
1117 .addActionListener(new java.awt.event.ActionListener()
1119 public void actionPerformed(ActionEvent e)
1121 renderGapsMenuItem_actionPerformed(e);
1124 findMenuItem.setText(MessageManager.getString("action.find"));
1125 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1126 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1127 .getMenuShortcutKeyMask(), false));
1128 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1130 public void actionPerformed(ActionEvent e)
1132 findMenuItem_actionPerformed(e);
1135 abovePIDThreshold.setText(MessageManager
1136 .getString("label.above_identity_threshold"));
1137 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1139 public void actionPerformed(ActionEvent e)
1141 abovePIDThreshold_actionPerformed(e);
1144 showSeqFeatures.setText(MessageManager
1145 .getString("label.show_sequence_features"));
1146 showSeqFeatures.addActionListener(new ActionListener()
1148 public void actionPerformed(ActionEvent actionEvent)
1150 showSeqFeatures_actionPerformed(actionEvent);
1154 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1155 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1156 * void actionPerformed(ActionEvent actionEvent) {
1157 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1159 showDbRefsMenuitem.setText(MessageManager
1160 .getString("label.show_database_refs"));
1161 showDbRefsMenuitem.addActionListener(new ActionListener()
1164 public void actionPerformed(ActionEvent e)
1166 showDbRefs_actionPerformed(e);
1170 showNpFeatsMenuitem.setText(MessageManager
1171 .getString("label.show_non_positional_features"));
1172 showNpFeatsMenuitem.addActionListener(new ActionListener()
1175 public void actionPerformed(ActionEvent e)
1177 showNpFeats_actionPerformed(e);
1181 showGroupConservation.setText(MessageManager
1182 .getString("label.group_conservation"));
1183 showGroupConservation.addActionListener(new ActionListener()
1186 public void actionPerformed(ActionEvent e)
1188 showGroupConservation_actionPerformed(e);
1193 showGroupConsensus.setText(MessageManager
1194 .getString("label.group_consensus"));
1195 showGroupConsensus.addActionListener(new ActionListener()
1198 public void actionPerformed(ActionEvent e)
1200 showGroupConsensus_actionPerformed(e);
1204 showConsensusHistogram.setText(MessageManager
1205 .getString("label.show_consensus_histogram"));
1206 showConsensusHistogram.addActionListener(new ActionListener()
1209 public void actionPerformed(ActionEvent e)
1211 showConsensusHistogram_actionPerformed(e);
1215 showSequenceLogo.setText(MessageManager
1216 .getString("label.show_consensus_logo"));
1217 showSequenceLogo.addActionListener(new ActionListener()
1220 public void actionPerformed(ActionEvent e)
1222 showSequenceLogo_actionPerformed(e);
1226 normaliseSequenceLogo.setText(MessageManager
1227 .getString("label.norm_consensus_logo"));
1228 normaliseSequenceLogo.addActionListener(new ActionListener()
1231 public void actionPerformed(ActionEvent e)
1233 normaliseSequenceLogo_actionPerformed(e);
1237 applyAutoAnnotationSettings.setText(MessageManager
1238 .getString("label.apply_all_groups"));
1239 applyAutoAnnotationSettings.setState(false);
1240 applyAutoAnnotationSettings.setVisible(true);
1241 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1244 public void actionPerformed(ActionEvent e)
1246 applyAutoAnnotationSettings_actionPerformed(e);
1251 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1252 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1254 public void actionPerformed(ActionEvent e)
1256 nucleotideColour_actionPerformed(e);
1260 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1261 tcoffeeColour.setEnabled(false);
1262 tcoffeeColour.addActionListener(new ActionListener()
1266 public void actionPerformed(ActionEvent e)
1268 tcoffeeColorScheme_actionPerformed(e);
1273 .setText(MessageManager.getString("action.undefine_groups"));
1274 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1275 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1276 .getMenuShortcutKeyMask(), false));
1277 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1279 public void actionPerformed(ActionEvent e)
1281 deleteGroups_actionPerformed(e);
1284 createGroup.setText(MessageManager.getString("action.create_groups"));
1285 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1286 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1287 .getMenuShortcutKeyMask(), false));
1288 createGroup.addActionListener(new java.awt.event.ActionListener()
1290 public void actionPerformed(ActionEvent e)
1292 createGroup_actionPerformed(e);
1295 unGroup.setText(MessageManager.getString("action.remove_group"));
1296 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1297 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1298 .getMenuShortcutKeyMask()
1299 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1300 unGroup.addActionListener(new java.awt.event.ActionListener()
1302 public void actionPerformed(ActionEvent e)
1304 unGroup_actionPerformed(e);
1307 copy.setText(MessageManager.getString("action.copy"));
1308 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1309 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1310 .getMenuShortcutKeyMask(), false));
1312 copy.addActionListener(new java.awt.event.ActionListener()
1314 public void actionPerformed(ActionEvent e)
1316 copy_actionPerformed(e);
1319 cut.setText(MessageManager.getString("action.cut"));
1320 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1321 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1322 .getMenuShortcutKeyMask(), false));
1323 cut.addActionListener(new java.awt.event.ActionListener()
1325 public void actionPerformed(ActionEvent e)
1327 cut_actionPerformed(e);
1330 delete.setText(MessageManager.getString("action.delete"));
1331 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1332 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1333 delete.addActionListener(new java.awt.event.ActionListener()
1335 public void actionPerformed(ActionEvent e)
1337 delete_actionPerformed(e);
1340 pasteMenu.setText(MessageManager.getString("action.paste"));
1341 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1342 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1343 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1344 .getMenuShortcutKeyMask()
1345 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1346 pasteNew.addActionListener(new java.awt.event.ActionListener()
1348 public void actionPerformed(ActionEvent e)
1350 pasteNew_actionPerformed(e);
1353 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1354 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1355 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1356 .getMenuShortcutKeyMask(), false));
1357 pasteThis.addActionListener(new java.awt.event.ActionListener()
1359 public void actionPerformed(ActionEvent e)
1361 pasteThis_actionPerformed(e);
1364 applyToAllGroups.setText(MessageManager
1365 .getString("label.apply_colour_to_all_groups"));
1366 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1368 public void actionPerformed(ActionEvent e)
1370 applyToAllGroups_actionPerformed(e);
1373 createPNG.addActionListener(new java.awt.event.ActionListener()
1375 public void actionPerformed(ActionEvent e)
1380 createPNG.setActionCommand(MessageManager
1381 .getString("label.save_png_image"));
1382 createPNG.setText("PNG");
1383 font.setText(MessageManager.getString("action.font"));
1384 font.addActionListener(new java.awt.event.ActionListener()
1386 public void actionPerformed(ActionEvent e)
1388 font_actionPerformed(e);
1392 seqLimits.setText(MessageManager
1393 .getString("label.show_sequence_limits"));
1394 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1395 seqLimits.addActionListener(new java.awt.event.ActionListener()
1397 public void actionPerformed(ActionEvent e)
1399 seqLimit_actionPerformed(e);
1402 epsFile.setText("EPS");
1403 epsFile.addActionListener(new java.awt.event.ActionListener()
1405 public void actionPerformed(ActionEvent e)
1410 LoadtreeMenuItem.setActionCommand(MessageManager
1411 .getString("label.load_tree_for_sequence_set"));
1412 LoadtreeMenuItem.setText(MessageManager
1413 .getString("label.load_associated_tree"));
1414 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1416 public void actionPerformed(ActionEvent e)
1418 LoadtreeMenuItem_actionPerformed(e);
1422 scaleAbove.setVisible(false);
1423 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1424 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1426 public void actionPerformed(ActionEvent e)
1428 scaleAbove_actionPerformed(e);
1431 scaleLeft.setVisible(false);
1432 scaleLeft.setSelected(true);
1433 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1434 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1436 public void actionPerformed(ActionEvent e)
1438 scaleLeft_actionPerformed(e);
1441 scaleRight.setVisible(false);
1442 scaleRight.setSelected(true);
1443 scaleRight.setText(MessageManager.getString("action.scale_right"));
1444 scaleRight.addActionListener(new java.awt.event.ActionListener()
1446 public void actionPerformed(ActionEvent e)
1448 scaleRight_actionPerformed(e);
1451 centreColumnLabelsMenuItem.setVisible(true);
1452 centreColumnLabelsMenuItem.setState(false);
1453 centreColumnLabelsMenuItem.setText(MessageManager
1454 .getString("label.centre_column_labels"));
1455 centreColumnLabelsMenuItem
1456 .addActionListener(new java.awt.event.ActionListener()
1458 public void actionPerformed(ActionEvent e)
1460 centreColumnLabels_actionPerformed(e);
1463 followHighlightMenuItem.setVisible(true);
1464 followHighlightMenuItem.setState(true);
1465 followHighlightMenuItem.setText(MessageManager
1466 .getString("label.automatic_scrolling"));
1467 followHighlightMenuItem.addActionListener(new ActionListener()
1470 public void actionPerformed(ActionEvent e)
1472 followHighlight_actionPerformed();
1477 modifyPID.setText(MessageManager
1478 .getString("label.modify_identity_thereshold"));
1479 modifyPID.addActionListener(new java.awt.event.ActionListener()
1481 public void actionPerformed(ActionEvent e)
1483 modifyPID_actionPerformed(e);
1486 modifyConservation.setText(MessageManager
1487 .getString("label.modify_conservation_thereshold"));
1489 .addActionListener(new java.awt.event.ActionListener()
1491 public void actionPerformed(ActionEvent e)
1493 modifyConservation_actionPerformed(e);
1497 .setText(MessageManager.getString("action.by_tree_order"));
1498 sort.setText(MessageManager.getString("action.sort"));
1499 sort.addMenuListener(new MenuListener()
1501 public void menuSelected(MenuEvent e)
1506 public void menuDeselected(MenuEvent e)
1510 public void menuCanceled(MenuEvent e)
1514 sortByAnnotScore.setText(MessageManager
1515 .getString("label.sort_by_score"));
1516 sort.add(sortByAnnotScore);
1517 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1520 public void menuCanceled(MenuEvent e)
1524 public void menuDeselected(MenuEvent e)
1528 public void menuSelected(MenuEvent e)
1530 buildSortByAnnotationScoresMenu();
1533 sortByAnnotScore.setVisible(false);
1536 .setText(MessageManager.getString("action.calculate_tree"));
1538 jMenu2.setText(MessageManager.getString("label.export_image"));
1539 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1540 padGapsMenuitem.setState(jalview.bin.Cache
1541 .getDefault("PAD_GAPS", false));
1542 padGapsMenuitem.addActionListener(new ActionListener()
1544 public void actionPerformed(ActionEvent e)
1546 padGapsMenuitem_actionPerformed(e);
1549 vamsasStore.setVisible(false);
1550 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1551 vamsasStore.addActionListener(new ActionListener()
1553 public void actionPerformed(ActionEvent e)
1555 vamsasStore_actionPerformed(e);
1558 showTranslation.setText(MessageManager
1559 .getString("label.translate_cDNA"));
1560 showTranslation.addActionListener(new ActionListener()
1562 public void actionPerformed(ActionEvent e)
1564 showTranslation_actionPerformed(e);
1567 extractScores.setText(MessageManager.getString("label.extract_scores")
1569 extractScores.addActionListener(new ActionListener()
1571 public void actionPerformed(ActionEvent e)
1573 extractScores_actionPerformed(e);
1576 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1578 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1580 * showProducts.addActionListener(new ActionListener() {
1582 * public void actionPerformed(ActionEvent e) {
1583 * showProducts_actionPerformed(e); } });
1585 openFeatureSettings.setText(MessageManager
1586 .getString("label.feature_settings"));
1587 openFeatureSettings.addActionListener(new ActionListener()
1589 public void actionPerformed(ActionEvent e)
1591 featureSettings_actionPerformed(e);
1595 .setText(MessageManager.getString("label.fetch_sequences"));
1596 fetchSequence.addActionListener(new ActionListener()
1598 public void actionPerformed(ActionEvent e)
1600 fetchSequence_actionPerformed(e);
1604 annotationColour.setText(MessageManager
1605 .getString("action.by_annotation"));
1606 annotationColour.addActionListener(new ActionListener()
1608 public void actionPerformed(ActionEvent e)
1610 annotationColour_actionPerformed(e);
1614 rnahelicesColour.setText(MessageManager
1615 .getString("action.by_rna_helixes"));
1616 rnahelicesColour.addActionListener(new ActionListener()
1618 public void actionPerformed(ActionEvent e)
1620 rnahelicesColour_actionPerformed(e);
1624 associatedData.setText(MessageManager
1625 .getString("label.load_features_annotations"));
1626 associatedData.addActionListener(new ActionListener()
1628 public void actionPerformed(ActionEvent e)
1630 associatedData_actionPerformed(e);
1633 autoCalculate.setText(MessageManager
1634 .getString("label.autocalculate_consensus"));
1635 autoCalculate.setState(jalview.bin.Cache.getDefault(
1636 "AUTO_CALC_CONSENSUS", true));
1637 autoCalculate.addActionListener(new ActionListener()
1639 public void actionPerformed(ActionEvent e)
1641 autoCalculate_actionPerformed(e);
1644 sortByTree.setText(MessageManager
1645 .getString("label.sort_alignment_new_tree"));
1647 .setToolTipText("<html>"
1649 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1651 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1652 sortByTree.addActionListener(new ActionListener()
1654 public void actionPerformed(ActionEvent e)
1656 sortByTreeOption_actionPerformed(e);
1660 listenToViewSelections.setText(MessageManager
1661 .getString("label.listen_for_selections"));
1662 listenToViewSelections
1663 .setToolTipText("<html>"
1665 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1666 listenToViewSelections.setState(false);
1667 listenToViewSelections.addActionListener(new ActionListener()
1669 public void actionPerformed(ActionEvent e)
1671 listenToViewSelections_actionPerformed(e);
1676 .setText(MessageManager.getString("label.add_sequences"));
1677 addFromFile.setText(MessageManager.getString("label.from_file"));
1678 addFromFile.addActionListener(new ActionListener()
1680 public void actionPerformed(ActionEvent e)
1682 addFromFile_actionPerformed(e);
1685 addFromText.setText(MessageManager.getString("label.from_textbox"));
1686 addFromText.addActionListener(new ActionListener()
1688 public void actionPerformed(ActionEvent e)
1690 addFromText_actionPerformed(e);
1693 addFromURL.setText(MessageManager.getString("label.from_url"));
1694 addFromURL.addActionListener(new ActionListener()
1696 public void actionPerformed(ActionEvent e)
1698 addFromURL_actionPerformed(e);
1701 exportFeatures.setText(MessageManager
1702 .getString("label.export_features"));
1703 exportFeatures.addActionListener(new ActionListener()
1705 public void actionPerformed(ActionEvent e)
1707 exportFeatures_actionPerformed(e);
1710 exportAnnotations.setText(MessageManager
1711 .getString("label.export_annotations"));
1712 exportAnnotations.addActionListener(new ActionListener()
1714 public void actionPerformed(ActionEvent e)
1716 exportAnnotations_actionPerformed(e);
1719 statusPanel.setLayout(gridLayout1);
1720 jMenu3.setText(MessageManager.getString("action.show"));
1721 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1722 showAllSeqs.setToolTipText(MessageManager
1723 .getString("label.toggle_sequence_visibility"));
1724 showAllSeqs.addActionListener(new ActionListener()
1726 public void actionPerformed(ActionEvent e)
1728 showAllSeqs_actionPerformed(e);
1731 showAllColumns.setText(MessageManager.getString("label.all_columns"));
1732 showAllColumns.setToolTipText(MessageManager
1733 .getString("label.toggle_columns_visibility"));
1734 showAllColumns.addActionListener(new ActionListener()
1736 public void actionPerformed(ActionEvent e)
1738 showAllColumns_actionPerformed(e);
1741 hideMenu.setText(MessageManager.getString("action.hide"));
1742 hideSelSequences.setText(MessageManager
1743 .getString("label.selected_sequences"));
1744 hideSelSequences.setToolTipText(MessageManager
1745 .getString("label.toggle_sequence_visibility"));
1746 hideSelSequences.addActionListener(new ActionListener()
1748 public void actionPerformed(ActionEvent e)
1750 hideSelSequences_actionPerformed(e);
1753 hideSelColumns.setText(MessageManager
1754 .getString("label.selected_columns"));
1755 hideSelColumns.setToolTipText(MessageManager
1756 .getString("label.toggle_columns_visibility"));
1757 hideSelColumns.addActionListener(new ActionListener()
1759 public void actionPerformed(ActionEvent e)
1761 hideSelColumns_actionPerformed(e);
1764 hideAllSelection.setText(MessageManager
1765 .getString("label.selected_region"));
1766 hideAllSelection.addActionListener(new ActionListener()
1768 public void actionPerformed(ActionEvent e)
1770 hideAllSelection_actionPerformed(e);
1773 // TODO: should be hidden if no selection exists.
1774 hideAllButSelection.setText(MessageManager
1775 .getString("label.all_but_selected_region"));
1776 hideAllButSelection.addActionListener(new ActionListener()
1778 public void actionPerformed(ActionEvent e)
1780 hideAllButSelection_actionPerformed(e);
1783 showAllhidden.setText(MessageManager
1784 .getString("label.all_sequences_columns"));
1785 showAllhidden.setToolTipText(MessageManager
1786 .getString("label.toggles_visibility_hidden_selected_regions"));
1787 showAllhidden.addActionListener(new ActionListener()
1789 public void actionPerformed(ActionEvent e)
1791 showAllhidden_actionPerformed(e);
1795 hiddenMarkers.setText(MessageManager
1796 .getString("action.show_hidden_markers"));
1797 hiddenMarkers.addActionListener(new ActionListener()
1799 public void actionPerformed(ActionEvent e)
1801 hiddenMarkers_actionPerformed(e);
1804 invertColSel.setText(MessageManager
1805 .getString("action.invert_column_selection"));
1806 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1807 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1808 .getMenuShortcutKeyMask()
1809 | java.awt.event.KeyEvent.ALT_MASK, false));
1810 invertColSel.addActionListener(new ActionListener()
1812 public void actionPerformed(ActionEvent e)
1814 invertColSel_actionPerformed(e);
1817 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1819 public void stateChanged(ChangeEvent evt)
1821 JTabbedPane pane = (JTabbedPane) evt.getSource();
1822 int sel = pane.getSelectedIndex();
1823 tabSelectionChanged(sel);
1826 tabbedPane.addMouseListener(new MouseAdapter()
1828 public void mousePressed(MouseEvent e)
1830 tabbedPane_mousePressed(e);
1833 tabbedPane.addFocusListener(new FocusAdapter()
1835 public void focusGained(FocusEvent e)
1837 tabbedPane_focusGained(e);
1840 save.setText(MessageManager.getString("action.save"));
1841 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1842 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1843 .getMenuShortcutKeyMask(), false));
1844 save.addActionListener(new ActionListener()
1846 public void actionPerformed(ActionEvent e)
1848 save_actionPerformed(e);
1851 reload.setEnabled(false);
1852 reload.setText(MessageManager.getString("action.reload"));
1853 reload.addActionListener(new ActionListener()
1855 public void actionPerformed(ActionEvent e)
1857 reload_actionPerformed(e);
1860 newView.setText(MessageManager.getString("action.new_view"));
1861 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1862 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1863 .getMenuShortcutKeyMask(), false));
1864 newView.addActionListener(new ActionListener()
1866 public void actionPerformed(ActionEvent e)
1868 newView_actionPerformed(e);
1871 tabbedPane.setToolTipText("<html><i>"
1872 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
1874 textColour.setText(MessageManager.getString("label.colour_text")
1876 textColour.addActionListener(new ActionListener()
1878 public void actionPerformed(ActionEvent e)
1880 textColour_actionPerformed(e);
1883 formatMenu.setText(MessageManager.getString("action.format"));
1884 selectMenu.setText(MessageManager.getString("action.select"));
1885 idRightAlign.setText(MessageManager
1886 .getString("label.right_align_sequence_id"));
1887 idRightAlign.addActionListener(new ActionListener()
1889 public void actionPerformed(ActionEvent e)
1891 idRightAlign_actionPerformed(e);
1894 gatherViews.setEnabled(false);
1895 gatherViews.setText(MessageManager.getString("action.gather_views"));
1896 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1897 java.awt.event.KeyEvent.VK_G, 0, false));
1898 gatherViews.addActionListener(new ActionListener()
1900 public void actionPerformed(ActionEvent e)
1902 gatherViews_actionPerformed(e);
1905 expandViews.setEnabled(false);
1906 expandViews.setText(MessageManager.getString("action.expand_views"));
1907 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1908 java.awt.event.KeyEvent.VK_X, 0, false));
1909 expandViews.addActionListener(new ActionListener()
1911 public void actionPerformed(ActionEvent e)
1913 expandViews_actionPerformed(e);
1917 .setText(MessageManager.getString("action.page_setup") + "...");
1918 pageSetup.addActionListener(new ActionListener()
1920 public void actionPerformed(ActionEvent e)
1922 pageSetup_actionPerformed(e);
1925 alignmentProperties.setText(MessageManager
1926 .getString("label.alignment_props") + "...");
1927 alignmentProperties.addActionListener(new ActionListener()
1929 public void actionPerformed(ActionEvent actionEvent)
1931 alignmentProperties();
1934 tooltipSettingsMenu.setText(MessageManager
1935 .getString("label.sequence_id_tooltip"));
1936 autoAnnMenu.setText(MessageManager
1937 .getString("label.autocalculated_annotation"));
1938 alignFrameMenuBar.add(fileMenu);
1939 alignFrameMenuBar.add(editMenu);
1940 alignFrameMenuBar.add(selectMenu);
1941 alignFrameMenuBar.add(viewMenu);
1942 alignFrameMenuBar.add(formatMenu);
1943 alignFrameMenuBar.add(colourMenu);
1944 alignFrameMenuBar.add(calculateMenu);
1945 alignFrameMenuBar.add(webService);
1946 fileMenu.add(fetchSequence);
1947 fileMenu.add(addSequenceMenu);
1948 fileMenu.add(reload);
1949 fileMenu.addSeparator();
1950 fileMenu.add(vamsasStore);
1952 fileMenu.add(saveAs);
1953 fileMenu.add(outputTextboxMenu);
1954 fileMenu.add(pageSetup);
1955 fileMenu.add(printMenuItem);
1956 fileMenu.addSeparator();
1957 fileMenu.add(jMenu2);
1958 fileMenu.add(exportFeatures);
1959 fileMenu.add(exportAnnotations);
1960 fileMenu.add(LoadtreeMenuItem);
1961 fileMenu.add(associatedData);
1962 fileMenu.addSeparator();
1963 fileMenu.add(closeMenuItem);
1964 editMenu.add(undoMenuItem);
1965 editMenu.add(redoMenuItem);
1968 editMenu.add(pasteMenu);
1969 editMenu.add(delete);
1970 editMenu.addSeparator();
1971 editMenu.add(remove2LeftMenuItem);
1972 editMenu.add(remove2RightMenuItem);
1973 editMenu.add(removeGappedColumnMenuItem);
1974 editMenu.add(removeAllGapsMenuItem);
1975 editMenu.add(removeRedundancyMenuItem);
1976 editMenu.addSeparator();
1977 // dont add these yet in the CVS build - they cannot be undone!
1978 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1979 // editMenu.add(justifyLeftMenuItem);
1980 // editMenu.add(justifyRightMenuItem);
1981 // editMenu.addSeparator();
1982 editMenu.add(padGapsMenuitem);
1983 viewMenu.add(newView);
1984 viewMenu.add(expandViews);
1985 viewMenu.add(gatherViews);
1986 viewMenu.addSeparator();
1987 viewMenu.add(jMenu3);
1988 viewMenu.add(hideMenu);
1989 viewMenu.addSeparator();
1990 viewMenu.add(followHighlightMenuItem);
1991 viewMenu.add(annotationPanelMenuItem);
1992 autoAnnMenu.add(applyAutoAnnotationSettings);
1993 autoAnnMenu.add(showConsensusHistogram);
1994 autoAnnMenu.add(showSequenceLogo);
1995 autoAnnMenu.add(normaliseSequenceLogo);
1996 autoAnnMenu.addSeparator();
1997 autoAnnMenu.add(showGroupConservation);
1998 autoAnnMenu.add(showGroupConsensus);
1999 viewMenu.add(autoAnnMenu);
2000 viewMenu.addSeparator();
2001 viewMenu.add(showSeqFeatures);
2002 // viewMenu.add(showSeqFeaturesHeight);
2004 viewMenu.add(openFeatureSettings);
2005 tooltipSettingsMenu.add(showDbRefsMenuitem);
2006 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2007 viewMenu.add(tooltipSettingsMenu);
2008 viewMenu.addSeparator();
2009 viewMenu.add(alignmentProperties);
2010 viewMenu.addSeparator();
2011 viewMenu.add(overviewMenuItem);
2012 colourMenu.add(applyToAllGroups);
2013 colourMenu.add(textColour);
2014 colourMenu.addSeparator();
2015 colourMenu.add(noColourmenuItem);
2016 colourMenu.add(clustalColour);
2017 colourMenu.add(BLOSUM62Colour);
2018 colourMenu.add(PIDColour);
2019 colourMenu.add(zappoColour);
2020 colourMenu.add(taylorColour);
2021 colourMenu.add(hydrophobicityColour);
2022 colourMenu.add(helixColour);
2023 colourMenu.add(strandColour);
2024 colourMenu.add(turnColour);
2025 colourMenu.add(buriedColour);
2026 colourMenu.add(nucleotideColour);
2027 colourMenu.add(purinePyrimidineColour);
2028 colourMenu.add(RNAInteractionColour);
2029 // colourMenu.add(covariationColour);
2030 colourMenu.add(tcoffeeColour);
2031 colourMenu.add(userDefinedColour);
2032 colourMenu.addSeparator();
2033 colourMenu.add(conservationMenuItem);
2034 colourMenu.add(modifyConservation);
2035 colourMenu.add(abovePIDThreshold);
2036 colourMenu.add(modifyPID);
2037 colourMenu.add(annotationColour);
2038 colourMenu.add(rnahelicesColour);
2039 calculateMenu.add(sort);
2040 calculateMenu.add(calculateTree);
2041 calculateMenu.addSeparator();
2042 calculateMenu.add(pairwiseAlignmentMenuItem);
2043 calculateMenu.add(PCAMenuItem);
2044 calculateMenu.addSeparator();
2045 calculateMenu.add(showTranslation);
2046 calculateMenu.add(showProducts);
2047 calculateMenu.add(autoCalculate);
2048 calculateMenu.add(sortByTree);
2049 calculateMenu.addSeparator();
2050 calculateMenu.add(extractScores);
2051 webServiceNoServices = new JMenuItem(
2052 MessageManager.getString("label.no_services"));
2053 webService.add(webServiceNoServices);
2054 pasteMenu.add(pasteNew);
2055 pasteMenu.add(pasteThis);
2056 sort.add(sortIDMenuItem);
2057 sort.add(sortLengthMenuItem);
2058 sort.add(sortGroupMenuItem);
2059 sort.add(sortPairwiseMenuItem);
2060 sort.add(sortByTreeMenu);
2061 jMenu2.add(htmlMenuItem);
2062 jMenu2.add(epsFile);
2063 jMenu2.add(createPNG);
2064 addSequenceMenu.add(addFromFile);
2065 addSequenceMenu.add(addFromText);
2066 addSequenceMenu.add(addFromURL);
2067 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2068 statusPanel.add(statusBar, null);
2069 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2070 jMenu3.add(showAllColumns);
2071 jMenu3.add(showAllSeqs);
2072 jMenu3.add(showAllhidden);
2073 hideMenu.add(hideSelColumns);
2074 hideMenu.add(hideSelSequences);
2075 hideMenu.add(hideAllSelection);
2076 hideMenu.add(hideAllButSelection);
2078 formatMenu.add(font);
2079 formatMenu.addSeparator();
2080 formatMenu.add(wrapMenuItem);
2081 formatMenu.add(scaleAbove);
2082 formatMenu.add(scaleLeft);
2083 formatMenu.add(scaleRight);
2084 formatMenu.add(seqLimits);
2085 formatMenu.add(idRightAlign);
2086 formatMenu.add(hiddenMarkers);
2087 formatMenu.add(viewBoxesMenuItem);
2088 formatMenu.add(viewTextMenuItem);
2089 formatMenu.add(colourTextMenuItem);
2090 formatMenu.add(renderGapsMenuItem);
2091 formatMenu.add(centreColumnLabelsMenuItem);
2092 formatMenu.add(showNonconservedMenuItem);
2093 selectMenu.add(findMenuItem);
2094 selectMenu.addSeparator();
2095 selectMenu.add(selectAllSequenceMenuItem);
2096 selectMenu.add(deselectAllSequenceMenuItem);
2097 selectMenu.add(invertSequenceMenuItem);
2098 selectMenu.add(invertColSel);
2099 selectMenu.add(createGroup);
2100 selectMenu.add(unGroup);
2101 selectMenu.add(grpsFromSelection);
2102 selectMenu.add(deleteGroups);
2103 calculateMenu.add(expandAlignment);
2104 // TODO - determine if the listenToViewSelections button is needed : see bug
2106 // selectMenu.addSeparator();
2107 // selectMenu.add(listenToViewSelections);
2110 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2112 // TODO Auto-generated method stub
2116 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2118 // TODO Auto-generated method stub
2122 protected void showAllhidden_actionPerformed(ActionEvent e)
2124 // TODO Auto-generated method stub
2128 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2130 // TODO Auto-generated method stub
2134 protected void hideAllSelection_actionPerformed(ActionEvent e)
2136 // TODO Auto-generated method stub
2140 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2142 // TODO Auto-generated method stub
2146 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2148 // TODO Auto-generated method stub
2152 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2154 // TODO Auto-generated method stub
2158 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2160 // TODO Auto-generated method stub
2164 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2166 // TODO Auto-generated method stub
2170 protected void showGroupConservation_actionPerformed(ActionEvent e)
2172 // TODO Auto-generated method stub
2176 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2178 // TODO Auto-generated method stub
2182 protected void showSeqFeaturesHeight_actionPerformed(
2183 ActionEvent actionEvent)
2185 // TODO Auto-generated method stub
2189 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2191 // TODO Auto-generated method stub
2195 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2197 // TODO Auto-generated method stub
2201 protected void followHighlight_actionPerformed()
2203 // TODO Auto-generated method stub
2207 protected void showNpFeats_actionPerformed(ActionEvent e)
2209 // TODO Auto-generated method stub
2213 protected void showDbRefs_actionPerformed(ActionEvent e)
2215 // TODO Auto-generated method stub
2219 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2223 protected void showProducts_actionPerformed(ActionEvent e)
2227 protected void buildSortByAnnotationScoresMenu()
2231 protected void extractScores_actionPerformed(ActionEvent e)
2235 protected void outputText_actionPerformed(ActionEvent e)
2239 public void addFromFile_actionPerformed(ActionEvent e)
2244 public void addFromText_actionPerformed(ActionEvent e)
2249 public void addFromURL_actionPerformed(ActionEvent e)
2254 public void exportFeatures_actionPerformed(ActionEvent e)
2259 public void exportAnnotations_actionPerformed(ActionEvent e)
2264 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2268 protected void closeMenuItem_actionPerformed(boolean b)
2272 protected void redoMenuItem_actionPerformed(ActionEvent e)
2276 protected void undoMenuItem_actionPerformed(ActionEvent e)
2280 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2284 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2288 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2292 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2296 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2300 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2304 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2308 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2312 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2316 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2320 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2324 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2328 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2332 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2336 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2340 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2344 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2348 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2352 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2356 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2360 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2364 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2368 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2372 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2376 protected void clustalColour_actionPerformed(ActionEvent e)
2380 protected void zappoColour_actionPerformed(ActionEvent e)
2384 protected void taylorColour_actionPerformed(ActionEvent e)
2388 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2392 protected void helixColour_actionPerformed(ActionEvent e)
2396 protected void strandColour_actionPerformed(ActionEvent e)
2400 protected void turnColour_actionPerformed(ActionEvent e)
2404 protected void buriedColour_actionPerformed(ActionEvent e)
2408 protected void userDefinedColour_actionPerformed(ActionEvent e)
2412 protected void PIDColour_actionPerformed(ActionEvent e)
2416 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2420 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2424 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2429 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2432 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2436 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2440 protected void printMenuItem_actionPerformed(ActionEvent e)
2444 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2448 protected void findMenuItem_actionPerformed(ActionEvent e)
2452 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2456 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2460 protected void nucleotideColour_actionPerformed(ActionEvent e)
2464 protected void deleteGroups_actionPerformed(ActionEvent e)
2468 protected void createGroup_actionPerformed(ActionEvent e)
2472 protected void unGroup_actionPerformed(ActionEvent e)
2476 protected void copy_actionPerformed(ActionEvent e)
2480 protected void cut_actionPerformed(ActionEvent e)
2484 protected void delete_actionPerformed(ActionEvent e)
2488 protected void pasteNew_actionPerformed(ActionEvent e)
2492 protected void pasteThis_actionPerformed(ActionEvent e)
2496 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2500 public void createPNG(java.io.File f)
2504 protected void font_actionPerformed(ActionEvent e)
2508 protected void seqLimit_actionPerformed(ActionEvent e)
2512 public void seqDBRef_actionPerformed(ActionEvent e)
2517 public void createEPS(java.io.File f)
2521 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2527 * Template method to handle the 'load T-Coffee scores' menu event.
2529 * Subclasses override this method to provide a custom action.
2534 protected void loadScores_actionPerformed(ActionEvent event)
2540 * Template method to handle the 'Color T-Coffee scores' menu event.
2542 * Subclasses override this method to provide a custom action.
2547 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2552 protected void jpred_actionPerformed(ActionEvent e)
2556 protected void scaleAbove_actionPerformed(ActionEvent e)
2560 protected void scaleLeft_actionPerformed(ActionEvent e)
2564 protected void scaleRight_actionPerformed(ActionEvent e)
2568 protected void modifyPID_actionPerformed(ActionEvent e)
2572 protected void modifyConservation_actionPerformed(ActionEvent e)
2576 protected void saveAs_actionPerformed(ActionEvent e)
2580 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2584 public void vamsasStore_actionPerformed(ActionEvent e)
2589 public void vamsasLoad_actionPerformed(ActionEvent e)
2594 public void showTranslation_actionPerformed(ActionEvent e)
2599 public void featureSettings_actionPerformed(ActionEvent e)
2604 public void fetchSequence_actionPerformed(ActionEvent e)
2609 public void smoothFont_actionPerformed(ActionEvent e)
2614 public void annotationColour_actionPerformed(ActionEvent e)
2619 public void rnahelicesColour_actionPerformed(ActionEvent e)
2624 public void associatedData_actionPerformed(ActionEvent e)
2629 public void autoCalculate_actionPerformed(ActionEvent e)
2634 public void sortByTreeOption_actionPerformed(ActionEvent e)
2639 public void showAllSeqs_actionPerformed(ActionEvent e)
2644 public void showAllColumns_actionPerformed(ActionEvent e)
2649 public void hideSelSequences_actionPerformed(ActionEvent e)
2654 public void hideSelColumns_actionPerformed(ActionEvent e)
2659 public void hiddenMarkers_actionPerformed(ActionEvent e)
2664 public void findPdbId_actionPerformed(ActionEvent e)
2669 public void enterPdbId_actionPerformed(ActionEvent e)
2674 public void pdbFile_actionPerformed(ActionEvent e)
2679 public void invertColSel_actionPerformed(ActionEvent e)
2684 public void tabSelectionChanged(int sel)
2689 public void tabbedPane_mousePressed(MouseEvent e)
2694 public void tabbedPane_focusGained(FocusEvent e)
2699 public void save_actionPerformed(ActionEvent e)
2704 public void reload_actionPerformed(ActionEvent e)
2709 public void newView_actionPerformed(ActionEvent e)
2714 public void textColour_actionPerformed(ActionEvent e)
2719 public void idRightAlign_actionPerformed(ActionEvent e)
2724 public void expandViews_actionPerformed(ActionEvent e)
2729 public void gatherViews_actionPerformed(ActionEvent e)
2734 public void buildTreeMenu()
2739 public void pageSetup_actionPerformed(ActionEvent e)
2744 public void alignmentProperties()
2749 protected void expand_newalign(ActionEvent e)
2751 // TODO Auto-generated method stub