2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.jbgui;
21 import jalview.schemes.ColourSchemeProperty;
22 import jalview.util.MessageManager;
24 import java.awt.BorderLayout;
25 import java.awt.Color;
26 import java.awt.GridLayout;
27 import java.awt.Toolkit;
28 import java.awt.event.ActionEvent;
29 import java.awt.event.ActionListener;
30 import java.awt.event.FocusAdapter;
31 import java.awt.event.FocusEvent;
32 import java.awt.event.MouseAdapter;
33 import java.awt.event.MouseEvent;
35 import javax.swing.BorderFactory;
36 import javax.swing.ButtonGroup;
37 import javax.swing.JCheckBoxMenuItem;
38 import javax.swing.JInternalFrame;
39 import javax.swing.JLabel;
40 import javax.swing.JMenu;
41 import javax.swing.JMenuBar;
42 import javax.swing.JMenuItem;
43 import javax.swing.JOptionPane;
44 import javax.swing.JPanel;
45 import javax.swing.JRadioButtonMenuItem;
46 import javax.swing.JTabbedPane;
47 import javax.swing.SwingUtilities;
48 import javax.swing.event.ChangeEvent;
49 import javax.swing.event.MenuEvent;
50 import javax.swing.event.MenuListener;
52 public class GAlignFrame extends JInternalFrame
54 protected JMenuBar alignFrameMenuBar = new JMenuBar();
56 protected JMenu fileMenu = new JMenu();
58 protected JMenuItem closeMenuItem = new JMenuItem();
60 protected JMenu editMenu = new JMenu();
62 protected JMenu viewMenu = new JMenu();
64 protected JMenu colourMenu = new JMenu();
66 protected JMenu calculateMenu = new JMenu();
68 protected JMenu webService = new JMenu();
70 protected JMenuItem webServiceNoServices;
72 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
74 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
76 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
78 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
80 protected JMenuItem remove2RightMenuItem = new JMenuItem();
82 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
84 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
86 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
88 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
90 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
92 protected JMenuItem sortIDMenuItem = new JMenuItem();
94 protected JMenuItem sortLengthMenuItem = new JMenuItem();
96 protected JMenuItem sortGroupMenuItem = new JMenuItem();
98 protected JMenu sortByAnnotScore = new JMenu();
100 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
102 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
104 protected JMenuItem PCAMenuItem = new JMenuItem();
106 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
108 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
110 BorderLayout borderLayout1 = new BorderLayout();
112 public JLabel statusBar = new JLabel();
114 protected JMenuItem saveAs = new JMenuItem();
116 protected JMenu outputTextboxMenu = new JMenu();
118 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
120 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
122 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
124 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
126 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
128 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
130 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
132 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
134 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
136 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
138 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
140 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
142 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
144 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
146 // protected JRadioButtonMenuItem covariationColour = new
147 // JRadioButtonMenuItem();
149 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
151 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
153 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
155 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
157 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
159 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
161 JMenuItem htmlMenuItem = new JMenuItem();
163 JMenuItem overviewMenuItem = new JMenuItem();
165 protected JMenuItem undoMenuItem = new JMenuItem();
167 protected JMenuItem redoMenuItem = new JMenuItem();
169 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
171 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
173 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
175 JMenuItem printMenuItem = new JMenuItem();
177 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
179 JMenuItem findMenuItem = new JMenuItem();
181 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
183 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
185 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
187 JMenuItem deleteGroups = new JMenuItem();
189 JMenuItem createGroup = new JMenuItem();
190 JMenuItem unGroup = new JMenuItem();
192 JMenuItem delete = new JMenuItem();
194 JMenuItem copy = new JMenuItem();
196 JMenuItem cut = new JMenuItem();
198 JMenu pasteMenu = new JMenu();
200 JMenuItem pasteNew = new JMenuItem();
202 JMenuItem pasteThis = new JMenuItem();
204 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
206 JMenuItem createPNG = new JMenuItem();
208 protected JMenuItem font = new JMenuItem();
210 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
212 JMenuItem epsFile = new JMenuItem();
214 JMenuItem LoadtreeMenuItem = new JMenuItem();
216 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
218 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
220 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
222 protected JMenuItem modifyPID = new JMenuItem();
224 protected JMenuItem modifyConservation = new JMenuItem();
226 protected JMenu sortByTreeMenu = new JMenu();
228 protected JMenu sort = new JMenu();
230 protected JMenu calculateTree = new JMenu();
232 JMenu jMenu2 = new JMenu();
234 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
236 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
238 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
240 protected ButtonGroup colours = new ButtonGroup();
242 JMenuItem vamsasStore = new JMenuItem();
244 protected JMenuItem showTranslation = new JMenuItem();
246 protected JMenuItem extractScores = new JMenuItem();
248 protected JMenuItem expandAlignment = new JMenuItem();
250 protected JMenu showProducts = new JMenu();
252 public JMenuItem openFeatureSettings = new JMenuItem();
254 JMenuItem fetchSequence = new JMenuItem();
256 JMenuItem annotationColour = new JMenuItem();
258 protected JMenuItem rnahelicesColour = new JMenuItem();
260 JMenuItem associatedData = new JMenuItem();
262 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
264 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
266 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
268 JMenu addSequenceMenu = new JMenu();
270 JMenuItem addFromFile = new JMenuItem();
272 JMenuItem addFromText = new JMenuItem();
274 JMenuItem addFromURL = new JMenuItem();
276 JMenuItem exportAnnotations = new JMenuItem();
278 JMenuItem exportFeatures = new JMenuItem();
280 protected JPanel statusPanel = new JPanel();
282 GridLayout gridLayout1 = new GridLayout();
284 JMenu jMenu3 = new JMenu();
286 JMenuItem showAllSeqs = new JMenuItem();
288 JMenuItem showAllColumns = new JMenuItem();
290 JMenu hideMenu = new JMenu();
292 JMenuItem hideSelSequences = new JMenuItem();
294 JMenuItem hideSelColumns = new JMenuItem();
296 JMenuItem hideAllButSelection = new JMenuItem();
298 JMenuItem hideAllSelection = new JMenuItem();
300 JMenuItem showAllhidden = new JMenuItem();
302 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
304 JMenuItem invertColSel = new JMenuItem();
306 protected JTabbedPane tabbedPane = new JTabbedPane();
308 JMenuItem save = new JMenuItem();
310 protected JMenuItem reload = new JMenuItem();
312 JMenuItem newView = new JMenuItem();
314 JMenuItem textColour = new JMenuItem();
316 JMenu formatMenu = new JMenu();
318 JMenu selectMenu = new JMenu();
320 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
322 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
324 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
326 protected JMenuItem gatherViews = new JMenuItem();
328 protected JMenuItem expandViews = new JMenuItem();
330 JMenuItem pageSetup = new JMenuItem();
332 JMenuItem alignmentProperties = new JMenuItem();
334 JMenu tooltipSettingsMenu = new JMenu();
336 private JMenuItem justifyLeftMenuItem = new JMenuItem();
338 private JMenuItem justifyRightMenuItem = new JMenuItem();
340 JMenu autoAnnMenu = new JMenu();
342 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
344 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
346 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
348 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
350 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
352 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
354 private JMenuItem grpsFromSelection = new JMenuItem();
361 setJMenuBar(alignFrameMenuBar);
363 // dynamically fill save as menu with available formats
364 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
366 JMenuItem item = new JMenuItem(
367 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
369 item.addActionListener(new java.awt.event.ActionListener()
371 public void actionPerformed(ActionEvent e)
373 outputText_actionPerformed(e);
377 outputTextboxMenu.add(item);
379 } catch (Exception e)
383 if (!new jalview.util.Platform().isAMac())
385 closeMenuItem.setMnemonic('C');
386 outputTextboxMenu.setMnemonic('T');
387 undoMenuItem.setMnemonic('Z');
388 redoMenuItem.setMnemonic('0');
389 copy.setMnemonic('C');
390 cut.setMnemonic('U');
391 pasteMenu.setMnemonic('P');
392 reload.setMnemonic('R');
395 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
397 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
398 .getUserColourSchemes().keys();
400 while (userColours.hasMoreElements())
402 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
403 userColours.nextElement().toString());
404 radioItem.setName("USER_DEFINED");
405 radioItem.addMouseListener(new MouseAdapter()
407 public void mousePressed(MouseEvent evt)
409 if (evt.isControlDown()
410 || SwingUtilities.isRightMouseButton(evt))
412 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
414 int option = JOptionPane.showInternalConfirmDialog(
415 jalview.gui.Desktop.desktop,
416 MessageManager.getString("label.remove_from_default_list"),
417 MessageManager.getString("label.remove_user_defined_colour"),
418 JOptionPane.YES_NO_OPTION);
419 if (option == JOptionPane.YES_OPTION)
421 jalview.gui.UserDefinedColours
422 .removeColourFromDefaults(radioItem.getText());
423 colourMenu.remove(radioItem);
427 radioItem.addActionListener(new ActionListener()
429 public void actionPerformed(ActionEvent evt)
431 userDefinedColour_actionPerformed(evt);
438 radioItem.addActionListener(new ActionListener()
440 public void actionPerformed(ActionEvent evt)
442 userDefinedColour_actionPerformed(evt);
445 colourMenu.insert(radioItem, 15);
446 colours.add(radioItem);
449 colours.add(noColourmenuItem);
450 colours.add(clustalColour);
451 colours.add(zappoColour);
452 colours.add(taylorColour);
453 colours.add(hydrophobicityColour);
454 colours.add(helixColour);
455 colours.add(strandColour);
456 colours.add(turnColour);
457 colours.add(buriedColour);
458 colours.add(userDefinedColour);
459 colours.add(PIDColour);
460 colours.add(BLOSUM62Colour);
461 colours.add(nucleotideColour);
462 colours.add(purinePyrimidineColour);
463 // colours.add(covariationColour);
464 colours.add(tcoffeeColour);
465 colours.add(RNAInteractionColour);
466 setColourSelected(jalview.bin.Cache
467 .getDefault("DEFAULT_COLOUR", "None"));
471 public void setColourSelected(String defaultColour)
474 if (defaultColour != null)
476 int index = ColourSchemeProperty
477 .getColourIndexFromName(defaultColour);
481 case ColourSchemeProperty.CLUSTAL:
482 clustalColour.setSelected(true);
486 case ColourSchemeProperty.BLOSUM:
487 BLOSUM62Colour.setSelected(true);
491 case ColourSchemeProperty.PID:
492 PIDColour.setSelected(true);
496 case ColourSchemeProperty.ZAPPO:
497 zappoColour.setSelected(true);
501 case ColourSchemeProperty.TAYLOR:
502 taylorColour.setSelected(true);
505 case ColourSchemeProperty.HYDROPHOBIC:
506 hydrophobicityColour.setSelected(true);
510 case ColourSchemeProperty.HELIX:
511 helixColour.setSelected(true);
515 case ColourSchemeProperty.STRAND:
516 strandColour.setSelected(true);
520 case ColourSchemeProperty.TURN:
521 turnColour.setSelected(true);
525 case ColourSchemeProperty.BURIED:
526 buriedColour.setSelected(true);
530 case ColourSchemeProperty.NUCLEOTIDE:
531 nucleotideColour.setSelected(true);
535 case ColourSchemeProperty.TCOFFEE:
536 tcoffeeColour.setSelected(true);
539 case ColourSchemeProperty.PURINEPYRIMIDINE:
540 purinePyrimidineColour.setSelected(true);
544 case ColourSchemeProperty.RNAINTERACTION:
545 RNAInteractionColour.setSelected(true);
549 * case ColourSchemeProperty.COVARIATION:
550 * covariationColour.setSelected(true);
554 case ColourSchemeProperty.USER_DEFINED:
555 userDefinedColour.setSelected(true);
558 case ColourSchemeProperty.NONE:
560 noColourmenuItem.setSelected(true);
568 private void jbInit() throws Exception
570 fileMenu.setText(MessageManager.getString("action.file"));
571 saveAs.setText(MessageManager.getString("action.save_as") + "...");
572 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
573 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
574 .getMenuShortcutKeyMask()
575 | java.awt.event.KeyEvent.SHIFT_MASK, false));
576 saveAs.addActionListener(new ActionListener()
578 public void actionPerformed(ActionEvent e)
580 saveAs_actionPerformed(e);
583 closeMenuItem.setText(MessageManager.getString("action.close"));
584 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
585 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
586 .getMenuShortcutKeyMask(), false));
587 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
589 public void actionPerformed(ActionEvent e)
591 closeMenuItem_actionPerformed(false);
594 editMenu.setText(MessageManager.getString("action.edit"));
595 viewMenu.setText(MessageManager.getString("action.view"));
596 colourMenu.setText(MessageManager.getString("action.colour"));
597 calculateMenu.setText(MessageManager.getString("action.calculate"));
598 webService.setText(MessageManager.getString("action.web_service"));
599 selectAllSequenceMenuItem.setText(MessageManager.getString("action.select_all"));
600 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
601 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
602 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
603 selectAllSequenceMenuItem
604 .addActionListener(new java.awt.event.ActionListener()
606 public void actionPerformed(ActionEvent e)
608 selectAllSequenceMenuItem_actionPerformed(e);
611 deselectAllSequenceMenuItem.setText(MessageManager.getString("action.deselect_all"));
612 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
613 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
614 deselectAllSequenceMenuItem
615 .addActionListener(new java.awt.event.ActionListener()
617 public void actionPerformed(ActionEvent e)
619 deselectAllSequenceMenuItem_actionPerformed(e);
622 invertSequenceMenuItem.setText(MessageManager.getString("action.invert_sequence_selection"));
623 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
624 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
625 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
626 invertSequenceMenuItem
627 .addActionListener(new java.awt.event.ActionListener()
629 public void actionPerformed(ActionEvent e)
631 invertSequenceMenuItem_actionPerformed(e);
634 grpsFromSelection.setText(MessageManager.getString("action.make_groups_selection"));
635 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
637 public void actionPerformed(ActionEvent e)
639 makeGrpsFromSelection_actionPerformed(e);
642 expandAlignment.setText(MessageManager.getString("action.view_flanking_regions"));
643 expandAlignment.setToolTipText(MessageManager.getString("label.view_flanking_regions"));
644 expandAlignment.addActionListener(new java.awt.event.ActionListener() {
646 public void actionPerformed(ActionEvent e)
651 remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
652 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
653 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
654 .getMenuShortcutKeyMask(), false));
656 .addActionListener(new java.awt.event.ActionListener()
658 public void actionPerformed(ActionEvent e)
660 remove2LeftMenuItem_actionPerformed(e);
663 remove2RightMenuItem.setText(MessageManager.getString("action.remove_right"));
664 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
665 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
666 .getMenuShortcutKeyMask(), false));
668 .addActionListener(new java.awt.event.ActionListener()
670 public void actionPerformed(ActionEvent e)
672 remove2RightMenuItem_actionPerformed(e);
675 removeGappedColumnMenuItem.setText(MessageManager.getString("action.remove_empty_columns"));
676 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
677 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
678 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
679 removeGappedColumnMenuItem
680 .addActionListener(new java.awt.event.ActionListener()
682 public void actionPerformed(ActionEvent e)
684 removeGappedColumnMenuItem_actionPerformed(e);
687 removeAllGapsMenuItem.setText(MessageManager.getString("action.remove_all_gaps"));
688 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
689 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
690 .getDefaultToolkit().getMenuShortcutKeyMask()
691 | java.awt.event.KeyEvent.SHIFT_MASK, false));
692 removeAllGapsMenuItem
693 .addActionListener(new java.awt.event.ActionListener()
695 public void actionPerformed(ActionEvent e)
697 removeAllGapsMenuItem_actionPerformed(e);
700 justifyLeftMenuItem.setText(MessageManager.getString("action.left_justify_alignment"));
702 .addActionListener(new java.awt.event.ActionListener()
704 public void actionPerformed(ActionEvent e)
706 justifyLeftMenuItem_actionPerformed(e);
709 justifyRightMenuItem.setText(MessageManager.getString("action.right_justify_alignment"));
711 .addActionListener(new java.awt.event.ActionListener()
713 public void actionPerformed(ActionEvent e)
715 justifyRightMenuItem_actionPerformed(e);
718 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
719 viewBoxesMenuItem.setState(true);
720 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
722 public void actionPerformed(ActionEvent e)
724 viewBoxesMenuItem_actionPerformed(e);
727 viewTextMenuItem.setText(MessageManager.getString("action.text"));
728 viewTextMenuItem.setState(true);
729 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
731 public void actionPerformed(ActionEvent e)
733 viewTextMenuItem_actionPerformed(e);
736 showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
737 showNonconservedMenuItem.setState(false);
738 showNonconservedMenuItem
739 .addActionListener(new java.awt.event.ActionListener()
741 public void actionPerformed(ActionEvent e)
743 showUnconservedMenuItem_actionPerformed(e);
746 sortPairwiseMenuItem.setText(MessageManager.getString("action.by_pairwise_id"));
748 .addActionListener(new java.awt.event.ActionListener()
750 public void actionPerformed(ActionEvent e)
752 sortPairwiseMenuItem_actionPerformed(e);
755 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
756 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
758 public void actionPerformed(ActionEvent e)
760 sortIDMenuItem_actionPerformed(e);
763 sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
765 .addActionListener(new java.awt.event.ActionListener()
767 public void actionPerformed(ActionEvent e)
769 sortLengthMenuItem_actionPerformed(e);
772 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
773 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
775 public void actionPerformed(ActionEvent e)
777 sortGroupMenuItem_actionPerformed(e);
780 removeRedundancyMenuItem.setText(MessageManager.getString("action.remove_redundancy"));
781 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
782 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
783 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
784 removeRedundancyMenuItem
785 .addActionListener(new java.awt.event.ActionListener()
787 public void actionPerformed(ActionEvent e)
789 removeRedundancyMenuItem_actionPerformed(e);
792 pairwiseAlignmentMenuItem.setText(MessageManager.getString("action.pairwise_alignment"));
793 pairwiseAlignmentMenuItem
794 .addActionListener(new java.awt.event.ActionListener()
796 public void actionPerformed(ActionEvent e)
798 pairwiseAlignmentMenuItem_actionPerformed(e);
801 PCAMenuItem.setText(MessageManager.getString("label.principal_component_analysis"));
802 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
804 public void actionPerformed(ActionEvent e)
806 PCAMenuItem_actionPerformed(e);
809 averageDistanceTreeMenuItem
810 .setText(MessageManager.getString("label.average_distance_identity"));
811 averageDistanceTreeMenuItem
812 .addActionListener(new java.awt.event.ActionListener()
814 public void actionPerformed(ActionEvent e)
816 averageDistanceTreeMenuItem_actionPerformed(e);
819 neighbourTreeMenuItem.setText(MessageManager.getString("label.neighbour_joining_identity"));
820 neighbourTreeMenuItem
821 .addActionListener(new java.awt.event.ActionListener()
823 public void actionPerformed(ActionEvent e)
825 neighbourTreeMenuItem_actionPerformed(e);
828 this.getContentPane().setLayout(borderLayout1);
829 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
830 statusBar.setBackground(Color.white);
831 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
832 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
833 statusBar.setText(MessageManager.getString("label.status_bar"));
834 outputTextboxMenu.setText(MessageManager.getString("label.out_to_textbox"));
835 clustalColour.setText(MessageManager.getString("label.clustalx"));
837 clustalColour.addActionListener(new java.awt.event.ActionListener()
839 public void actionPerformed(ActionEvent e)
841 clustalColour_actionPerformed(e);
844 zappoColour.setText(MessageManager.getString("label.zappo"));
845 zappoColour.addActionListener(new java.awt.event.ActionListener()
847 public void actionPerformed(ActionEvent e)
849 zappoColour_actionPerformed(e);
852 taylorColour.setText(MessageManager.getString("label.taylor"));
853 taylorColour.addActionListener(new java.awt.event.ActionListener()
855 public void actionPerformed(ActionEvent e)
857 taylorColour_actionPerformed(e);
860 hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
862 .addActionListener(new java.awt.event.ActionListener()
864 public void actionPerformed(ActionEvent e)
866 hydrophobicityColour_actionPerformed(e);
869 helixColour.setText(MessageManager.getString("label.helix_propensity"));
870 helixColour.addActionListener(new java.awt.event.ActionListener()
872 public void actionPerformed(ActionEvent e)
874 helixColour_actionPerformed(e);
877 strandColour.setText(MessageManager.getString("label.strand_propensity"));
878 strandColour.addActionListener(new java.awt.event.ActionListener()
880 public void actionPerformed(ActionEvent e)
882 strandColour_actionPerformed(e);
885 turnColour.setText(MessageManager.getString("label.turn_propensity"));
886 turnColour.addActionListener(new java.awt.event.ActionListener()
888 public void actionPerformed(ActionEvent e)
890 turnColour_actionPerformed(e);
893 buriedColour.setText(MessageManager.getString("label.buried_index"));
894 buriedColour.addActionListener(new java.awt.event.ActionListener()
896 public void actionPerformed(ActionEvent e)
898 buriedColour_actionPerformed(e);
901 userDefinedColour.setText(MessageManager.getString("action.user_defined"));
902 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
904 public void actionPerformed(ActionEvent e)
906 userDefinedColour_actionPerformed(e);
909 PIDColour.setText(MessageManager.getString("label.percentage_identity"));
910 PIDColour.addActionListener(new java.awt.event.ActionListener()
912 public void actionPerformed(ActionEvent e)
914 PIDColour_actionPerformed(e);
917 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
918 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
920 public void actionPerformed(ActionEvent e)
922 BLOSUM62Colour_actionPerformed(e);
925 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
926 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
928 public void actionPerformed(ActionEvent e)
930 nucleotideColour_actionPerformed(e);
934 purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
935 purinePyrimidineColour
936 .addActionListener(new java.awt.event.ActionListener()
938 public void actionPerformed(ActionEvent e)
940 purinePyrimidineColour_actionPerformed(e);
944 RNAInteractionColour.setText("RNA Interaction type");
945 RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
947 public void actionPerformed(ActionEvent e)
949 RNAInteractionColour_actionPerformed(e);
953 * covariationColour.setText("Covariation");
954 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
955 * public void actionPerformed(ActionEvent e) {
956 * covariationColour_actionPerformed(e); } });
959 avDistanceTreeBlosumMenuItem.setText(MessageManager.getString("label.average_distance_bloslum62"));
960 avDistanceTreeBlosumMenuItem
961 .addActionListener(new java.awt.event.ActionListener()
963 public void actionPerformed(ActionEvent e)
965 avTreeBlosumMenuItem_actionPerformed(e);
968 njTreeBlosumMenuItem.setText(MessageManager.getString("label.neighbour_blosum62"));
970 .addActionListener(new java.awt.event.ActionListener()
972 public void actionPerformed(ActionEvent e)
974 njTreeBlosumMenuItem_actionPerformed(e);
977 annotationPanelMenuItem.setActionCommand("");
978 annotationPanelMenuItem.setText(MessageManager.getString("label.show_annotations"));
979 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
980 "SHOW_ANNOTATIONS", true));
981 annotationPanelMenuItem
982 .addActionListener(new java.awt.event.ActionListener()
984 public void actionPerformed(ActionEvent e)
986 annotationPanelMenuItem_actionPerformed(e);
989 colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
991 .addActionListener(new java.awt.event.ActionListener()
993 public void actionPerformed(ActionEvent e)
995 colourTextMenuItem_actionPerformed(e);
998 htmlMenuItem.setText(MessageManager.getString("label.html"));
999 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1001 public void actionPerformed(ActionEvent e)
1003 htmlMenuItem_actionPerformed(e);
1006 overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
1007 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1009 public void actionPerformed(ActionEvent e)
1011 overviewMenuItem_actionPerformed(e);
1014 undoMenuItem.setEnabled(false);
1015 undoMenuItem.setText(MessageManager.getString("action.undo"));
1016 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1017 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1018 .getMenuShortcutKeyMask(), false));
1019 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1021 public void actionPerformed(ActionEvent e)
1023 undoMenuItem_actionPerformed(e);
1026 redoMenuItem.setEnabled(false);
1027 redoMenuItem.setText(MessageManager.getString("action.redo"));
1028 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1029 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1030 .getMenuShortcutKeyMask(), false));
1031 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1033 public void actionPerformed(ActionEvent e)
1035 redoMenuItem_actionPerformed(e);
1038 conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
1039 conservationMenuItem
1040 .addActionListener(new java.awt.event.ActionListener()
1042 public void actionPerformed(ActionEvent e)
1044 conservationMenuItem_actionPerformed(e);
1047 noColourmenuItem.setText(MessageManager.getString("label.none"));
1048 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1050 public void actionPerformed(ActionEvent e)
1052 noColourmenuItem_actionPerformed(e);
1055 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1056 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1058 public void actionPerformed(ActionEvent e)
1060 wrapMenuItem_actionPerformed(e);
1063 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1064 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1065 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1066 .getMenuShortcutKeyMask(), false));
1067 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1069 public void actionPerformed(ActionEvent e)
1071 printMenuItem_actionPerformed(e);
1074 renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps"));
1075 renderGapsMenuItem.setState(true);
1077 .addActionListener(new java.awt.event.ActionListener()
1079 public void actionPerformed(ActionEvent e)
1081 renderGapsMenuItem_actionPerformed(e);
1084 findMenuItem.setText(MessageManager.getString("action.find"));
1085 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1086 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1087 .getMenuShortcutKeyMask(), false));
1088 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1090 public void actionPerformed(ActionEvent e)
1092 findMenuItem_actionPerformed(e);
1095 abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold"));
1096 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1098 public void actionPerformed(ActionEvent e)
1100 abovePIDThreshold_actionPerformed(e);
1103 showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features"));
1104 showSeqFeatures.addActionListener(new ActionListener()
1106 public void actionPerformed(ActionEvent actionEvent)
1108 showSeqFeatures_actionPerformed(actionEvent);
1112 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1113 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1114 * void actionPerformed(ActionEvent actionEvent) {
1115 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1117 showDbRefsMenuitem.setText(MessageManager.getString("label.show_database_refs"));
1118 showDbRefsMenuitem.addActionListener(new ActionListener()
1121 public void actionPerformed(ActionEvent e)
1123 showDbRefs_actionPerformed(e);
1127 showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
1128 showNpFeatsMenuitem.addActionListener(new ActionListener()
1131 public void actionPerformed(ActionEvent e)
1133 showNpFeats_actionPerformed(e);
1137 showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
1138 showGroupConservation.addActionListener(new ActionListener()
1141 public void actionPerformed(ActionEvent e)
1143 showGroupConservation_actionPerformed(e);
1148 showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
1149 showGroupConsensus.addActionListener(new ActionListener()
1152 public void actionPerformed(ActionEvent e)
1154 showGroupConsensus_actionPerformed(e);
1158 showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
1159 showConsensusHistogram.addActionListener(new ActionListener()
1162 public void actionPerformed(ActionEvent e)
1164 showConsensusHistogram_actionPerformed(e);
1168 showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
1169 showSequenceLogo.addActionListener(new ActionListener()
1172 public void actionPerformed(ActionEvent e)
1174 showSequenceLogo_actionPerformed(e);
1178 normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
1179 normaliseSequenceLogo.addActionListener(new ActionListener()
1182 public void actionPerformed(ActionEvent e)
1184 normaliseSequenceLogo_actionPerformed(e);
1188 applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups"));
1189 applyAutoAnnotationSettings.setState(false);
1190 applyAutoAnnotationSettings.setVisible(true);
1191 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1194 public void actionPerformed(ActionEvent e)
1196 applyAutoAnnotationSettings_actionPerformed(e);
1201 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1202 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1204 public void actionPerformed(ActionEvent e)
1206 nucleotideColour_actionPerformed(e);
1210 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1211 tcoffeeColour.setEnabled(false);
1212 tcoffeeColour.addActionListener(new ActionListener()
1216 public void actionPerformed(ActionEvent e)
1218 tcoffeeColorScheme_actionPerformed(e);
1222 deleteGroups.setText(MessageManager.getString("action.undefine_groups"));
1223 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1224 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1225 .getMenuShortcutKeyMask(), false));
1226 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1228 public void actionPerformed(ActionEvent e)
1230 deleteGroups_actionPerformed(e);
1233 createGroup.setText(MessageManager.getString("action.create_groups"));
1234 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1235 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1236 .getMenuShortcutKeyMask(), false));
1237 createGroup.addActionListener(new java.awt.event.ActionListener()
1239 public void actionPerformed(ActionEvent e)
1241 createGroup_actionPerformed(e);
1244 unGroup.setText(MessageManager.getString("action.remove_group"));
1245 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1246 java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
1247 .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
1248 unGroup.addActionListener(new java.awt.event.ActionListener()
1250 public void actionPerformed(ActionEvent e)
1252 unGroup_actionPerformed(e);
1255 copy.setText(MessageManager.getString("action.copy"));
1256 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1257 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1258 .getMenuShortcutKeyMask(), false));
1260 copy.addActionListener(new java.awt.event.ActionListener()
1262 public void actionPerformed(ActionEvent e)
1264 copy_actionPerformed(e);
1267 cut.setText(MessageManager.getString("action.cut"));
1268 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1269 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1270 .getMenuShortcutKeyMask(), false));
1271 cut.addActionListener(new java.awt.event.ActionListener()
1273 public void actionPerformed(ActionEvent e)
1275 cut_actionPerformed(e);
1278 delete.setText(MessageManager.getString("action.delete"));
1279 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1280 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1281 delete.addActionListener(new java.awt.event.ActionListener()
1283 public void actionPerformed(ActionEvent e)
1285 delete_actionPerformed(e);
1288 pasteMenu.setText(MessageManager.getString("action.paste"));
1289 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1290 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1291 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1292 .getMenuShortcutKeyMask()
1293 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1294 pasteNew.addActionListener(new java.awt.event.ActionListener()
1296 public void actionPerformed(ActionEvent e)
1298 pasteNew_actionPerformed(e);
1301 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1302 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1303 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1304 .getMenuShortcutKeyMask(), false));
1305 pasteThis.addActionListener(new java.awt.event.ActionListener()
1307 public void actionPerformed(ActionEvent e)
1309 pasteThis_actionPerformed(e);
1312 applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups"));
1313 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1315 public void actionPerformed(ActionEvent e)
1317 applyToAllGroups_actionPerformed(e);
1320 createPNG.addActionListener(new java.awt.event.ActionListener()
1322 public void actionPerformed(ActionEvent e)
1327 createPNG.setActionCommand(MessageManager.getString("label.save_png_image"));
1328 createPNG.setText("PNG");
1329 font.setText(MessageManager.getString("action.font"));
1330 font.addActionListener(new java.awt.event.ActionListener()
1332 public void actionPerformed(ActionEvent e)
1334 font_actionPerformed(e);
1338 seqLimits.setText(MessageManager.getString("label.show_sequence_limits"));
1339 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1340 seqLimits.addActionListener(new java.awt.event.ActionListener()
1342 public void actionPerformed(ActionEvent e)
1344 seqLimit_actionPerformed(e);
1347 epsFile.setText("EPS");
1348 epsFile.addActionListener(new java.awt.event.ActionListener()
1350 public void actionPerformed(ActionEvent e)
1355 LoadtreeMenuItem.setActionCommand(MessageManager.getString("label.load_tree_for_sequence_set"));
1356 LoadtreeMenuItem.setText(MessageManager.getString("label.load_associated_tree"));
1357 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1359 public void actionPerformed(ActionEvent e)
1361 LoadtreeMenuItem_actionPerformed(e);
1365 scaleAbove.setVisible(false);
1366 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1367 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1369 public void actionPerformed(ActionEvent e)
1371 scaleAbove_actionPerformed(e);
1374 scaleLeft.setVisible(false);
1375 scaleLeft.setSelected(true);
1376 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1377 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1379 public void actionPerformed(ActionEvent e)
1381 scaleLeft_actionPerformed(e);
1384 scaleRight.setVisible(false);
1385 scaleRight.setSelected(true);
1386 scaleRight.setText(MessageManager.getString("action.scale_right"));
1387 scaleRight.addActionListener(new java.awt.event.ActionListener()
1389 public void actionPerformed(ActionEvent e)
1391 scaleRight_actionPerformed(e);
1394 centreColumnLabelsMenuItem.setVisible(true);
1395 centreColumnLabelsMenuItem.setState(false);
1396 centreColumnLabelsMenuItem.setText(MessageManager.getString("label.centre_column_labels"));
1397 centreColumnLabelsMenuItem
1398 .addActionListener(new java.awt.event.ActionListener()
1400 public void actionPerformed(ActionEvent e)
1402 centreColumnLabels_actionPerformed(e);
1405 followHighlightMenuItem.setVisible(true);
1406 followHighlightMenuItem.setState(true);
1407 followHighlightMenuItem.setText(MessageManager.getString("label.automatic_scrolling"));
1408 followHighlightMenuItem.addActionListener(new ActionListener()
1411 public void actionPerformed(ActionEvent e)
1413 followHighlight_actionPerformed();
1418 modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold"));
1419 modifyPID.addActionListener(new java.awt.event.ActionListener()
1421 public void actionPerformed(ActionEvent e)
1423 modifyPID_actionPerformed(e);
1426 modifyConservation.setText(MessageManager.getString("label.modify_conservation_thereshold"));
1428 .addActionListener(new java.awt.event.ActionListener()
1430 public void actionPerformed(ActionEvent e)
1432 modifyConservation_actionPerformed(e);
1435 sortByTreeMenu.setText(MessageManager.getString("action.by_tree_order"));
1436 sort.setText(MessageManager.getString("action.sort"));
1437 sort.addMenuListener(new MenuListener()
1439 public void menuSelected(MenuEvent e)
1444 public void menuDeselected(MenuEvent e)
1448 public void menuCanceled(MenuEvent e)
1452 sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score"));
1453 sort.add(sortByAnnotScore);
1454 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1457 public void menuCanceled(MenuEvent e)
1461 public void menuDeselected(MenuEvent e)
1465 public void menuSelected(MenuEvent e)
1467 buildSortByAnnotationScoresMenu();
1470 sortByAnnotScore.setVisible(false);
1472 calculateTree.setText(MessageManager.getString("action.calculate_tree"));
1474 jMenu2.setText(MessageManager.getString("label.export_image"));
1475 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1476 padGapsMenuitem.setState(jalview.bin.Cache
1477 .getDefault("PAD_GAPS", false));
1478 padGapsMenuitem.addActionListener(new ActionListener()
1480 public void actionPerformed(ActionEvent e)
1482 padGapsMenuitem_actionPerformed(e);
1485 vamsasStore.setVisible(false);
1486 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1487 vamsasStore.addActionListener(new ActionListener()
1489 public void actionPerformed(ActionEvent e)
1491 vamsasStore_actionPerformed(e);
1494 showTranslation.setText(MessageManager.getString("label.translate_cDNA"));
1495 showTranslation.addActionListener(new ActionListener()
1497 public void actionPerformed(ActionEvent e)
1499 showTranslation_actionPerformed(e);
1502 extractScores.setText(MessageManager.getString("label.extract_scores") + "...");
1503 extractScores.addActionListener(new ActionListener()
1505 public void actionPerformed(ActionEvent e)
1507 extractScores_actionPerformed(e);
1510 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1512 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1514 * showProducts.addActionListener(new ActionListener() {
1516 * public void actionPerformed(ActionEvent e) {
1517 * showProducts_actionPerformed(e); } });
1519 openFeatureSettings.setText(MessageManager.getString("label.feature_settings"));
1520 openFeatureSettings.addActionListener(new ActionListener()
1522 public void actionPerformed(ActionEvent e)
1524 featureSettings_actionPerformed(e);
1527 fetchSequence.setText(MessageManager.getString("label.fetch_sequences"));
1528 fetchSequence.addActionListener(new ActionListener()
1530 public void actionPerformed(ActionEvent e)
1532 fetchSequence_actionPerformed(e);
1536 annotationColour.setText(MessageManager.getString("action.by_annotation"));
1537 annotationColour.addActionListener(new ActionListener()
1539 public void actionPerformed(ActionEvent e)
1541 annotationColour_actionPerformed(e);
1545 rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes"));
1546 rnahelicesColour.addActionListener(new ActionListener()
1548 public void actionPerformed(ActionEvent e)
1550 rnahelicesColour_actionPerformed(e);
1554 associatedData.setText(MessageManager.getString("label.load_features_annotations"));
1555 associatedData.addActionListener(new ActionListener()
1557 public void actionPerformed(ActionEvent e)
1559 associatedData_actionPerformed(e);
1562 autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus"));
1563 autoCalculate.setState(jalview.bin.Cache.getDefault(
1564 "AUTO_CALC_CONSENSUS", true));
1565 autoCalculate.addActionListener(new ActionListener()
1567 public void actionPerformed(ActionEvent e)
1569 autoCalculate_actionPerformed(e);
1572 sortByTree.setText(MessageManager.getString("label.sort_alignment_new_tree"));
1574 .setToolTipText("<html>" + MessageManager.getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1576 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1577 sortByTree.addActionListener(new ActionListener()
1579 public void actionPerformed(ActionEvent e)
1581 sortByTreeOption_actionPerformed(e);
1585 listenToViewSelections.setText(MessageManager.getString("label.listen_for_selections"));
1586 listenToViewSelections
1587 .setToolTipText("<html>" + MessageManager.getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1588 listenToViewSelections.setState(false);
1589 listenToViewSelections.addActionListener(new ActionListener()
1591 public void actionPerformed(ActionEvent e)
1593 listenToViewSelections_actionPerformed(e);
1597 addSequenceMenu.setText(MessageManager.getString("label.add_sequences"));
1598 addFromFile.setText(MessageManager.getString("label.from_file"));
1599 addFromFile.addActionListener(new ActionListener()
1601 public void actionPerformed(ActionEvent e)
1603 addFromFile_actionPerformed(e);
1606 addFromText.setText(MessageManager.getString("label.from_textbox"));
1607 addFromText.addActionListener(new ActionListener()
1609 public void actionPerformed(ActionEvent e)
1611 addFromText_actionPerformed(e);
1614 addFromURL.setText(MessageManager.getString("label.from_url"));
1615 addFromURL.addActionListener(new ActionListener()
1617 public void actionPerformed(ActionEvent e)
1619 addFromURL_actionPerformed(e);
1622 exportFeatures.setText(MessageManager.getString("label.export_features"));
1623 exportFeatures.addActionListener(new ActionListener()
1625 public void actionPerformed(ActionEvent e)
1627 exportFeatures_actionPerformed(e);
1630 exportAnnotations.setText(MessageManager.getString("label.export_annotations"));
1631 exportAnnotations.addActionListener(new ActionListener()
1633 public void actionPerformed(ActionEvent e)
1635 exportAnnotations_actionPerformed(e);
1638 statusPanel.setLayout(gridLayout1);
1639 jMenu3.setText(MessageManager.getString("action.show"));
1640 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1641 showAllSeqs.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
1642 showAllSeqs.addActionListener(new ActionListener()
1644 public void actionPerformed(ActionEvent e)
1646 showAllSeqs_actionPerformed(e);
1649 showAllColumns.setText(MessageManager.getString("label.all_columns"));
1650 showAllColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
1651 showAllColumns.addActionListener(new ActionListener()
1653 public void actionPerformed(ActionEvent e)
1655 showAllColumns_actionPerformed(e);
1658 hideMenu.setText(MessageManager.getString("action.hide"));
1659 hideSelSequences.setText(MessageManager.getString("label.selected_sequences"));
1660 hideSelSequences.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
1661 hideSelSequences.addActionListener(new ActionListener()
1663 public void actionPerformed(ActionEvent e)
1665 hideSelSequences_actionPerformed(e);
1668 hideSelColumns.setText(MessageManager.getString("label.selected_columns"));
1669 hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
1670 hideSelColumns.addActionListener(new ActionListener()
1672 public void actionPerformed(ActionEvent e)
1674 hideSelColumns_actionPerformed(e);
1677 hideAllSelection.setText(MessageManager.getString("label.selected_region"));
1678 hideAllSelection.addActionListener(new ActionListener()
1680 public void actionPerformed(ActionEvent e)
1682 hideAllSelection_actionPerformed(e);
1685 // TODO: should be hidden if no selection exists.
1686 hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region"));
1687 hideAllButSelection.addActionListener(new ActionListener()
1689 public void actionPerformed(ActionEvent e)
1691 hideAllButSelection_actionPerformed(e);
1694 showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
1696 .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
1697 showAllhidden.addActionListener(new ActionListener()
1699 public void actionPerformed(ActionEvent e)
1701 showAllhidden_actionPerformed(e);
1705 hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers"));
1706 hiddenMarkers.addActionListener(new ActionListener()
1708 public void actionPerformed(ActionEvent e)
1710 hiddenMarkers_actionPerformed(e);
1713 invertColSel.setText(MessageManager.getString("action.invert_column_selection"));
1714 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1715 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1716 .getMenuShortcutKeyMask()
1717 | java.awt.event.KeyEvent.ALT_MASK, false));
1718 invertColSel.addActionListener(new ActionListener()
1720 public void actionPerformed(ActionEvent e)
1722 invertColSel_actionPerformed(e);
1725 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1727 public void stateChanged(ChangeEvent evt)
1729 JTabbedPane pane = (JTabbedPane) evt.getSource();
1730 int sel = pane.getSelectedIndex();
1731 tabSelectionChanged(sel);
1734 tabbedPane.addMouseListener(new MouseAdapter()
1736 public void mousePressed(MouseEvent e)
1738 tabbedPane_mousePressed(e);
1741 tabbedPane.addFocusListener(new FocusAdapter()
1743 public void focusGained(FocusEvent e)
1745 tabbedPane_focusGained(e);
1748 save.setText(MessageManager.getString("action.save"));
1749 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1750 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1751 .getMenuShortcutKeyMask(), false));
1752 save.addActionListener(new ActionListener()
1754 public void actionPerformed(ActionEvent e)
1756 save_actionPerformed(e);
1759 reload.setEnabled(false);
1760 reload.setText(MessageManager.getString("action.reload"));
1761 reload.addActionListener(new ActionListener()
1763 public void actionPerformed(ActionEvent e)
1765 reload_actionPerformed(e);
1768 newView.setText(MessageManager.getString("action.new_view"));
1769 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1770 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1771 .getMenuShortcutKeyMask(), false));
1772 newView.addActionListener(new ActionListener()
1774 public void actionPerformed(ActionEvent e)
1776 newView_actionPerformed(e);
1779 tabbedPane.setToolTipText("<html><i>" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + "</i></html>");
1780 textColour.setText(MessageManager.getString("label.colour_text") + "...");
1781 textColour.addActionListener(new ActionListener()
1783 public void actionPerformed(ActionEvent e)
1785 textColour_actionPerformed(e);
1788 formatMenu.setText(MessageManager.getString("action.format"));
1789 selectMenu.setText(MessageManager.getString("action.select"));
1790 idRightAlign.setText(MessageManager.getString("label.right_align_sequence_id"));
1791 idRightAlign.addActionListener(new ActionListener()
1793 public void actionPerformed(ActionEvent e)
1795 idRightAlign_actionPerformed(e);
1798 gatherViews.setEnabled(false);
1799 gatherViews.setText(MessageManager.getString("action.gather_views"));
1800 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1801 java.awt.event.KeyEvent.VK_G, 0, false));
1802 gatherViews.addActionListener(new ActionListener()
1804 public void actionPerformed(ActionEvent e)
1806 gatherViews_actionPerformed(e);
1809 expandViews.setEnabled(false);
1810 expandViews.setText(MessageManager.getString("action.expand_views"));
1811 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1812 java.awt.event.KeyEvent.VK_X, 0, false));
1813 expandViews.addActionListener(new ActionListener()
1815 public void actionPerformed(ActionEvent e)
1817 expandViews_actionPerformed(e);
1820 pageSetup.setText(MessageManager.getString("action.page_setup") + "...");
1821 pageSetup.addActionListener(new ActionListener()
1823 public void actionPerformed(ActionEvent e)
1825 pageSetup_actionPerformed(e);
1828 alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "...");
1829 alignmentProperties.addActionListener(new ActionListener()
1831 public void actionPerformed(ActionEvent actionEvent)
1833 alignmentProperties();
1836 tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip"));
1837 autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation"));
1838 alignFrameMenuBar.add(fileMenu);
1839 alignFrameMenuBar.add(editMenu);
1840 alignFrameMenuBar.add(selectMenu);
1841 alignFrameMenuBar.add(viewMenu);
1842 alignFrameMenuBar.add(formatMenu);
1843 alignFrameMenuBar.add(colourMenu);
1844 alignFrameMenuBar.add(calculateMenu);
1845 alignFrameMenuBar.add(webService);
1846 fileMenu.add(fetchSequence);
1847 fileMenu.add(addSequenceMenu);
1848 fileMenu.add(reload);
1849 fileMenu.addSeparator();
1850 fileMenu.add(vamsasStore);
1852 fileMenu.add(saveAs);
1853 fileMenu.add(outputTextboxMenu);
1854 fileMenu.add(pageSetup);
1855 fileMenu.add(printMenuItem);
1856 fileMenu.addSeparator();
1857 fileMenu.add(jMenu2);
1858 fileMenu.add(exportFeatures);
1859 fileMenu.add(exportAnnotations);
1860 fileMenu.add(LoadtreeMenuItem);
1861 fileMenu.add(associatedData);
1862 fileMenu.addSeparator();
1863 fileMenu.add(closeMenuItem);
1864 editMenu.add(undoMenuItem);
1865 editMenu.add(redoMenuItem);
1868 editMenu.add(pasteMenu);
1869 editMenu.add(delete);
1870 editMenu.addSeparator();
1871 editMenu.add(remove2LeftMenuItem);
1872 editMenu.add(remove2RightMenuItem);
1873 editMenu.add(removeGappedColumnMenuItem);
1874 editMenu.add(removeAllGapsMenuItem);
1875 editMenu.add(removeRedundancyMenuItem);
1876 editMenu.addSeparator();
1877 // dont add these yet in the CVS build - they cannot be undone!
1878 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1879 // editMenu.add(justifyLeftMenuItem);
1880 // editMenu.add(justifyRightMenuItem);
1881 // editMenu.addSeparator();
1882 editMenu.add(padGapsMenuitem);
1883 viewMenu.add(newView);
1884 viewMenu.add(expandViews);
1885 viewMenu.add(gatherViews);
1886 viewMenu.addSeparator();
1887 viewMenu.add(jMenu3);
1888 viewMenu.add(hideMenu);
1889 viewMenu.addSeparator();
1890 viewMenu.add(followHighlightMenuItem);
1891 viewMenu.add(annotationPanelMenuItem);
1892 autoAnnMenu.add(applyAutoAnnotationSettings);
1893 autoAnnMenu.add(showConsensusHistogram);
1894 autoAnnMenu.add(showSequenceLogo);
1895 autoAnnMenu.add(normaliseSequenceLogo);
1896 autoAnnMenu.addSeparator();
1897 autoAnnMenu.add(showGroupConservation);
1898 autoAnnMenu.add(showGroupConsensus);
1899 viewMenu.add(autoAnnMenu);
1900 viewMenu.addSeparator();
1901 viewMenu.add(showSeqFeatures);
1902 // viewMenu.add(showSeqFeaturesHeight);
1904 viewMenu.add(openFeatureSettings);
1905 tooltipSettingsMenu.add(showDbRefsMenuitem);
1906 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1907 viewMenu.add(tooltipSettingsMenu);
1908 viewMenu.addSeparator();
1909 viewMenu.add(alignmentProperties);
1910 viewMenu.addSeparator();
1911 viewMenu.add(overviewMenuItem);
1912 colourMenu.add(applyToAllGroups);
1913 colourMenu.add(textColour);
1914 colourMenu.addSeparator();
1915 colourMenu.add(noColourmenuItem);
1916 colourMenu.add(clustalColour);
1917 colourMenu.add(BLOSUM62Colour);
1918 colourMenu.add(PIDColour);
1919 colourMenu.add(zappoColour);
1920 colourMenu.add(taylorColour);
1921 colourMenu.add(hydrophobicityColour);
1922 colourMenu.add(helixColour);
1923 colourMenu.add(strandColour);
1924 colourMenu.add(turnColour);
1925 colourMenu.add(buriedColour);
1926 colourMenu.add(nucleotideColour);
1927 colourMenu.add(purinePyrimidineColour);
1928 colourMenu.add(RNAInteractionColour);
1929 // colourMenu.add(covariationColour);
1930 colourMenu.add(tcoffeeColour);
1931 colourMenu.add(userDefinedColour);
1932 colourMenu.addSeparator();
1933 colourMenu.add(conservationMenuItem);
1934 colourMenu.add(modifyConservation);
1935 colourMenu.add(abovePIDThreshold);
1936 colourMenu.add(modifyPID);
1937 colourMenu.add(annotationColour);
1938 colourMenu.add(rnahelicesColour);
1939 calculateMenu.add(sort);
1940 calculateMenu.add(calculateTree);
1941 calculateMenu.addSeparator();
1942 calculateMenu.add(pairwiseAlignmentMenuItem);
1943 calculateMenu.add(PCAMenuItem);
1944 calculateMenu.addSeparator();
1945 calculateMenu.add(showTranslation);
1946 calculateMenu.add(showProducts);
1947 calculateMenu.add(autoCalculate);
1948 calculateMenu.add(sortByTree);
1949 calculateMenu.addSeparator();
1950 calculateMenu.add(extractScores);
1951 webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services"));
1952 webService.add(webServiceNoServices);
1953 pasteMenu.add(pasteNew);
1954 pasteMenu.add(pasteThis);
1955 sort.add(sortIDMenuItem);
1956 sort.add(sortLengthMenuItem);
1957 sort.add(sortGroupMenuItem);
1958 sort.add(sortPairwiseMenuItem);
1959 sort.add(sortByTreeMenu);
1960 jMenu2.add(htmlMenuItem);
1961 jMenu2.add(epsFile);
1962 jMenu2.add(createPNG);
1963 addSequenceMenu.add(addFromFile);
1964 addSequenceMenu.add(addFromText);
1965 addSequenceMenu.add(addFromURL);
1966 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1967 statusPanel.add(statusBar, null);
1968 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1969 jMenu3.add(showAllColumns);
1970 jMenu3.add(showAllSeqs);
1971 jMenu3.add(showAllhidden);
1972 hideMenu.add(hideSelColumns);
1973 hideMenu.add(hideSelSequences);
1974 hideMenu.add(hideAllSelection);
1975 hideMenu.add(hideAllButSelection);
1977 formatMenu.add(font);
1978 formatMenu.addSeparator();
1979 formatMenu.add(wrapMenuItem);
1980 formatMenu.add(scaleAbove);
1981 formatMenu.add(scaleLeft);
1982 formatMenu.add(scaleRight);
1983 formatMenu.add(seqLimits);
1984 formatMenu.add(idRightAlign);
1985 formatMenu.add(hiddenMarkers);
1986 formatMenu.add(viewBoxesMenuItem);
1987 formatMenu.add(viewTextMenuItem);
1988 formatMenu.add(colourTextMenuItem);
1989 formatMenu.add(renderGapsMenuItem);
1990 formatMenu.add(centreColumnLabelsMenuItem);
1991 formatMenu.add(showNonconservedMenuItem);
1992 selectMenu.add(findMenuItem);
1993 selectMenu.addSeparator();
1994 selectMenu.add(selectAllSequenceMenuItem);
1995 selectMenu.add(deselectAllSequenceMenuItem);
1996 selectMenu.add(invertSequenceMenuItem);
1997 selectMenu.add(invertColSel);
1998 selectMenu.add(createGroup);
1999 selectMenu.add(unGroup);
2000 selectMenu.add(grpsFromSelection);
2001 selectMenu.add(deleteGroups);
2002 calculateMenu.add(expandAlignment);
2003 // TODO - determine if the listenToViewSelections button is needed : see bug
2005 // selectMenu.addSeparator();
2006 // selectMenu.add(listenToViewSelections);
2009 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2011 // TODO Auto-generated method stub
2015 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2017 // TODO Auto-generated method stub
2021 protected void showAllhidden_actionPerformed(ActionEvent e)
2023 // TODO Auto-generated method stub
2027 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2029 // TODO Auto-generated method stub
2033 protected void hideAllSelection_actionPerformed(ActionEvent e)
2035 // TODO Auto-generated method stub
2039 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2041 // TODO Auto-generated method stub
2045 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2047 // TODO Auto-generated method stub
2051 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2053 // TODO Auto-generated method stub
2057 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2059 // TODO Auto-generated method stub
2063 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2065 // TODO Auto-generated method stub
2069 protected void showGroupConservation_actionPerformed(ActionEvent e)
2071 // TODO Auto-generated method stub
2075 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2077 // TODO Auto-generated method stub
2081 protected void showSeqFeaturesHeight_actionPerformed(
2082 ActionEvent actionEvent)
2084 // TODO Auto-generated method stub
2088 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2090 // TODO Auto-generated method stub
2094 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2096 // TODO Auto-generated method stub
2100 protected void followHighlight_actionPerformed()
2102 // TODO Auto-generated method stub
2106 protected void showNpFeats_actionPerformed(ActionEvent e)
2108 // TODO Auto-generated method stub
2112 protected void showDbRefs_actionPerformed(ActionEvent e)
2114 // TODO Auto-generated method stub
2118 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2122 protected void showProducts_actionPerformed(ActionEvent e)
2126 protected void buildSortByAnnotationScoresMenu()
2130 protected void extractScores_actionPerformed(ActionEvent e)
2134 protected void outputText_actionPerformed(ActionEvent e)
2138 public void addFromFile_actionPerformed(ActionEvent e)
2143 public void addFromText_actionPerformed(ActionEvent e)
2148 public void addFromURL_actionPerformed(ActionEvent e)
2153 public void exportFeatures_actionPerformed(ActionEvent e)
2158 public void exportAnnotations_actionPerformed(ActionEvent e)
2163 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2167 protected void closeMenuItem_actionPerformed(boolean b)
2171 protected void redoMenuItem_actionPerformed(ActionEvent e)
2175 protected void undoMenuItem_actionPerformed(ActionEvent e)
2179 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2183 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2187 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2191 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2195 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2199 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2203 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2207 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2211 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2215 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2219 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2223 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2227 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2231 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2235 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2239 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2243 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2247 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2251 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2255 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2259 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2263 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2267 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2271 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2275 protected void clustalColour_actionPerformed(ActionEvent e)
2279 protected void zappoColour_actionPerformed(ActionEvent e)
2283 protected void taylorColour_actionPerformed(ActionEvent e)
2287 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2291 protected void helixColour_actionPerformed(ActionEvent e)
2295 protected void strandColour_actionPerformed(ActionEvent e)
2299 protected void turnColour_actionPerformed(ActionEvent e)
2303 protected void buriedColour_actionPerformed(ActionEvent e)
2307 protected void userDefinedColour_actionPerformed(ActionEvent e)
2311 protected void PIDColour_actionPerformed(ActionEvent e)
2315 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2319 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2323 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2329 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2332 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2336 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2340 protected void printMenuItem_actionPerformed(ActionEvent e)
2344 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2348 protected void findMenuItem_actionPerformed(ActionEvent e)
2352 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2356 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2360 protected void nucleotideColour_actionPerformed(ActionEvent e)
2364 protected void deleteGroups_actionPerformed(ActionEvent e)
2368 protected void createGroup_actionPerformed(ActionEvent e)
2372 protected void unGroup_actionPerformed(ActionEvent e)
2376 protected void copy_actionPerformed(ActionEvent e)
2380 protected void cut_actionPerformed(ActionEvent e)
2384 protected void delete_actionPerformed(ActionEvent e)
2388 protected void pasteNew_actionPerformed(ActionEvent e)
2392 protected void pasteThis_actionPerformed(ActionEvent e)
2396 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2400 public void createPNG(java.io.File f)
2404 protected void font_actionPerformed(ActionEvent e)
2408 protected void seqLimit_actionPerformed(ActionEvent e)
2412 public void seqDBRef_actionPerformed(ActionEvent e)
2417 public void createEPS(java.io.File f)
2421 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2427 * Template method to handle the 'load T-Coffee scores' menu event.
2429 * Subclasses override this method to provide a custom action.
2434 protected void loadScores_actionPerformed(ActionEvent event)
2440 * Template method to handle the 'Color T-Coffee scores' menu event.
2442 * Subclasses override this method to provide a custom action.
2447 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2452 protected void jpred_actionPerformed(ActionEvent e)
2456 protected void scaleAbove_actionPerformed(ActionEvent e)
2460 protected void scaleLeft_actionPerformed(ActionEvent e)
2464 protected void scaleRight_actionPerformed(ActionEvent e)
2468 protected void modifyPID_actionPerformed(ActionEvent e)
2472 protected void modifyConservation_actionPerformed(ActionEvent e)
2476 protected void saveAs_actionPerformed(ActionEvent e)
2480 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2484 public void vamsasStore_actionPerformed(ActionEvent e)
2489 public void vamsasLoad_actionPerformed(ActionEvent e)
2494 public void showTranslation_actionPerformed(ActionEvent e)
2499 public void featureSettings_actionPerformed(ActionEvent e)
2504 public void fetchSequence_actionPerformed(ActionEvent e)
2509 public void smoothFont_actionPerformed(ActionEvent e)
2514 public void annotationColour_actionPerformed(ActionEvent e)
2519 public void rnahelicesColour_actionPerformed(ActionEvent e)
2524 public void associatedData_actionPerformed(ActionEvent e)
2529 public void autoCalculate_actionPerformed(ActionEvent e)
2534 public void sortByTreeOption_actionPerformed(ActionEvent e)
2539 public void showAllSeqs_actionPerformed(ActionEvent e)
2544 public void showAllColumns_actionPerformed(ActionEvent e)
2549 public void hideSelSequences_actionPerformed(ActionEvent e)
2554 public void hideSelColumns_actionPerformed(ActionEvent e)
2559 public void hiddenMarkers_actionPerformed(ActionEvent e)
2564 public void findPdbId_actionPerformed(ActionEvent e)
2569 public void enterPdbId_actionPerformed(ActionEvent e)
2574 public void pdbFile_actionPerformed(ActionEvent e)
2579 public void invertColSel_actionPerformed(ActionEvent e)
2584 public void tabSelectionChanged(int sel)
2589 public void tabbedPane_mousePressed(MouseEvent e)
2594 public void tabbedPane_focusGained(FocusEvent e)
2599 public void save_actionPerformed(ActionEvent e)
2604 public void reload_actionPerformed(ActionEvent e)
2609 public void newView_actionPerformed(ActionEvent e)
2614 public void textColour_actionPerformed(ActionEvent e)
2619 public void idRightAlign_actionPerformed(ActionEvent e)
2624 public void expandViews_actionPerformed(ActionEvent e)
2629 public void gatherViews_actionPerformed(ActionEvent e)
2634 public void buildTreeMenu()
2639 public void pageSetup_actionPerformed(ActionEvent e)
2644 public void alignmentProperties()
2649 protected void expand_newalign(ActionEvent e)
2651 // TODO Auto-generated method stub