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 JMenu showProducts = new JMenu();
250 public JMenuItem openFeatureSettings = new JMenuItem();
252 JMenuItem fetchSequence = new JMenuItem();
254 JMenuItem annotationColour = new JMenuItem();
256 protected JMenuItem rnahelicesColour = new JMenuItem();
258 JMenuItem associatedData = new JMenuItem();
260 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
262 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
264 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
266 JMenu addSequenceMenu = new JMenu();
268 JMenuItem addFromFile = new JMenuItem();
270 JMenuItem addFromText = new JMenuItem();
272 JMenuItem addFromURL = new JMenuItem();
274 JMenuItem exportAnnotations = new JMenuItem();
276 JMenuItem exportFeatures = new JMenuItem();
278 protected JPanel statusPanel = new JPanel();
280 GridLayout gridLayout1 = new GridLayout();
282 JMenu jMenu3 = new JMenu();
284 JMenuItem showAllSeqs = new JMenuItem();
286 JMenuItem showAllColumns = new JMenuItem();
288 JMenu hideMenu = new JMenu();
290 JMenuItem hideSelSequences = new JMenuItem();
292 JMenuItem hideSelColumns = new JMenuItem();
294 JMenuItem hideAllButSelection = new JMenuItem();
296 JMenuItem hideAllSelection = new JMenuItem();
298 JMenuItem showAllhidden = new JMenuItem();
300 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
302 JMenuItem invertColSel = new JMenuItem();
304 protected JTabbedPane tabbedPane = new JTabbedPane();
306 JMenuItem save = new JMenuItem();
308 protected JMenuItem reload = new JMenuItem();
310 JMenuItem newView = new JMenuItem();
312 JMenuItem textColour = new JMenuItem();
314 JMenu formatMenu = new JMenu();
316 JMenu selectMenu = new JMenu();
318 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
320 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
322 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
324 protected JMenuItem gatherViews = new JMenuItem();
326 protected JMenuItem expandViews = new JMenuItem();
328 JMenuItem pageSetup = new JMenuItem();
330 JMenuItem alignmentProperties = new JMenuItem();
332 JMenu tooltipSettingsMenu = new JMenu();
334 private JMenuItem justifyLeftMenuItem = new JMenuItem();
336 private JMenuItem justifyRightMenuItem = new JMenuItem();
338 JMenu autoAnnMenu = new JMenu();
340 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
342 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
344 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
346 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
348 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
350 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
352 private JMenuItem grpsFromSelection = new JMenuItem();
359 setJMenuBar(alignFrameMenuBar);
361 // dynamically fill save as menu with available formats
362 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
364 JMenuItem item = new JMenuItem(
365 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
367 item.addActionListener(new java.awt.event.ActionListener()
369 public void actionPerformed(ActionEvent e)
371 outputText_actionPerformed(e);
375 outputTextboxMenu.add(item);
377 } catch (Exception e)
381 if (!new jalview.util.Platform().isAMac())
383 closeMenuItem.setMnemonic('C');
384 outputTextboxMenu.setMnemonic('T');
385 undoMenuItem.setMnemonic('Z');
386 redoMenuItem.setMnemonic('0');
387 copy.setMnemonic('C');
388 cut.setMnemonic('U');
389 pasteMenu.setMnemonic('P');
390 reload.setMnemonic('R');
393 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
395 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
396 .getUserColourSchemes().keys();
398 while (userColours.hasMoreElements())
400 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
401 userColours.nextElement().toString());
402 radioItem.setName("USER_DEFINED");
403 radioItem.addMouseListener(new MouseAdapter()
405 public void mousePressed(MouseEvent evt)
407 if (evt.isControlDown()
408 || SwingUtilities.isRightMouseButton(evt))
410 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
412 int option = JOptionPane.showInternalConfirmDialog(
413 jalview.gui.Desktop.desktop,
414 MessageManager.getString("label.remove_from_default_list"),
415 MessageManager.getString("label.remove_user_defined_colour"),
416 JOptionPane.YES_NO_OPTION);
417 if (option == JOptionPane.YES_OPTION)
419 jalview.gui.UserDefinedColours
420 .removeColourFromDefaults(radioItem.getText());
421 colourMenu.remove(radioItem);
425 radioItem.addActionListener(new ActionListener()
427 public void actionPerformed(ActionEvent evt)
429 userDefinedColour_actionPerformed(evt);
436 radioItem.addActionListener(new ActionListener()
438 public void actionPerformed(ActionEvent evt)
440 userDefinedColour_actionPerformed(evt);
443 colourMenu.insert(radioItem, 15);
444 colours.add(radioItem);
447 colours.add(noColourmenuItem);
448 colours.add(clustalColour);
449 colours.add(zappoColour);
450 colours.add(taylorColour);
451 colours.add(hydrophobicityColour);
452 colours.add(helixColour);
453 colours.add(strandColour);
454 colours.add(turnColour);
455 colours.add(buriedColour);
456 colours.add(userDefinedColour);
457 colours.add(PIDColour);
458 colours.add(BLOSUM62Colour);
459 colours.add(nucleotideColour);
460 colours.add(purinePyrimidineColour);
461 // colours.add(covariationColour);
462 colours.add(tcoffeeColour);
463 colours.add(RNAInteractionColour);
464 setColourSelected(jalview.bin.Cache
465 .getDefault("DEFAULT_COLOUR", "None"));
469 public void setColourSelected(String defaultColour)
472 if (defaultColour != null)
474 int index = ColourSchemeProperty
475 .getColourIndexFromName(defaultColour);
479 case ColourSchemeProperty.CLUSTAL:
480 clustalColour.setSelected(true);
484 case ColourSchemeProperty.BLOSUM:
485 BLOSUM62Colour.setSelected(true);
489 case ColourSchemeProperty.PID:
490 PIDColour.setSelected(true);
494 case ColourSchemeProperty.ZAPPO:
495 zappoColour.setSelected(true);
499 case ColourSchemeProperty.TAYLOR:
500 taylorColour.setSelected(true);
503 case ColourSchemeProperty.HYDROPHOBIC:
504 hydrophobicityColour.setSelected(true);
508 case ColourSchemeProperty.HELIX:
509 helixColour.setSelected(true);
513 case ColourSchemeProperty.STRAND:
514 strandColour.setSelected(true);
518 case ColourSchemeProperty.TURN:
519 turnColour.setSelected(true);
523 case ColourSchemeProperty.BURIED:
524 buriedColour.setSelected(true);
528 case ColourSchemeProperty.NUCLEOTIDE:
529 nucleotideColour.setSelected(true);
533 case ColourSchemeProperty.TCOFFEE:
534 tcoffeeColour.setSelected(true);
537 case ColourSchemeProperty.PURINEPYRIMIDINE:
538 purinePyrimidineColour.setSelected(true);
542 case ColourSchemeProperty.RNAINTERACTION:
543 RNAInteractionColour.setSelected(true);
547 * case ColourSchemeProperty.COVARIATION:
548 * covariationColour.setSelected(true);
552 case ColourSchemeProperty.USER_DEFINED:
553 userDefinedColour.setSelected(true);
556 case ColourSchemeProperty.NONE:
558 noColourmenuItem.setSelected(true);
566 private void jbInit() throws Exception
568 fileMenu.setText(MessageManager.getString("action.file"));
569 saveAs.setText(MessageManager.getString("action.save_as") + "...");
570 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
571 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
572 .getMenuShortcutKeyMask()
573 | java.awt.event.KeyEvent.SHIFT_MASK, false));
574 saveAs.addActionListener(new ActionListener()
576 public void actionPerformed(ActionEvent e)
578 saveAs_actionPerformed(e);
581 closeMenuItem.setText(MessageManager.getString("action.close"));
582 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
583 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
584 .getMenuShortcutKeyMask(), false));
585 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
587 public void actionPerformed(ActionEvent e)
589 closeMenuItem_actionPerformed(false);
592 editMenu.setText(MessageManager.getString("action.edit"));
593 viewMenu.setText(MessageManager.getString("action.view"));
594 colourMenu.setText(MessageManager.getString("action.colour"));
595 calculateMenu.setText(MessageManager.getString("action.calculate"));
596 webService.setText(MessageManager.getString("action.web_service"));
597 selectAllSequenceMenuItem.setText(MessageManager.getString("action.select_all"));
598 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
599 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
600 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
601 selectAllSequenceMenuItem
602 .addActionListener(new java.awt.event.ActionListener()
604 public void actionPerformed(ActionEvent e)
606 selectAllSequenceMenuItem_actionPerformed(e);
609 deselectAllSequenceMenuItem.setText(MessageManager.getString("action.deselect_all"));
610 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
611 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
612 deselectAllSequenceMenuItem
613 .addActionListener(new java.awt.event.ActionListener()
615 public void actionPerformed(ActionEvent e)
617 deselectAllSequenceMenuItem_actionPerformed(e);
620 invertSequenceMenuItem.setText(MessageManager.getString("action.invert_sequence_selection"));
621 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
622 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
623 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
624 invertSequenceMenuItem
625 .addActionListener(new java.awt.event.ActionListener()
627 public void actionPerformed(ActionEvent e)
629 invertSequenceMenuItem_actionPerformed(e);
632 grpsFromSelection.setText(MessageManager.getString("action.make_groups_selection"));
633 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
635 public void actionPerformed(ActionEvent e)
637 makeGrpsFromSelection_actionPerformed(e);
641 remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
642 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
643 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
644 .getMenuShortcutKeyMask(), false));
646 .addActionListener(new java.awt.event.ActionListener()
648 public void actionPerformed(ActionEvent e)
650 remove2LeftMenuItem_actionPerformed(e);
653 remove2RightMenuItem.setText(MessageManager.getString("action.remove_right"));
654 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
655 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
656 .getMenuShortcutKeyMask(), false));
658 .addActionListener(new java.awt.event.ActionListener()
660 public void actionPerformed(ActionEvent e)
662 remove2RightMenuItem_actionPerformed(e);
665 removeGappedColumnMenuItem.setText(MessageManager.getString("action.remove_empty_columns"));
666 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
667 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
668 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
669 removeGappedColumnMenuItem
670 .addActionListener(new java.awt.event.ActionListener()
672 public void actionPerformed(ActionEvent e)
674 removeGappedColumnMenuItem_actionPerformed(e);
677 removeAllGapsMenuItem.setText(MessageManager.getString("action.remove_all_gaps"));
678 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
679 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
680 .getDefaultToolkit().getMenuShortcutKeyMask()
681 | java.awt.event.KeyEvent.SHIFT_MASK, false));
682 removeAllGapsMenuItem
683 .addActionListener(new java.awt.event.ActionListener()
685 public void actionPerformed(ActionEvent e)
687 removeAllGapsMenuItem_actionPerformed(e);
690 justifyLeftMenuItem.setText(MessageManager.getString("action.left_justify_alignment"));
692 .addActionListener(new java.awt.event.ActionListener()
694 public void actionPerformed(ActionEvent e)
696 justifyLeftMenuItem_actionPerformed(e);
699 justifyRightMenuItem.setText(MessageManager.getString("action.right_justify_alignment"));
701 .addActionListener(new java.awt.event.ActionListener()
703 public void actionPerformed(ActionEvent e)
705 justifyRightMenuItem_actionPerformed(e);
708 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
709 viewBoxesMenuItem.setState(true);
710 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
712 public void actionPerformed(ActionEvent e)
714 viewBoxesMenuItem_actionPerformed(e);
717 viewTextMenuItem.setText(MessageManager.getString("action.text"));
718 viewTextMenuItem.setState(true);
719 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
721 public void actionPerformed(ActionEvent e)
723 viewTextMenuItem_actionPerformed(e);
726 showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
727 showNonconservedMenuItem.setState(false);
728 showNonconservedMenuItem
729 .addActionListener(new java.awt.event.ActionListener()
731 public void actionPerformed(ActionEvent e)
733 showUnconservedMenuItem_actionPerformed(e);
736 sortPairwiseMenuItem.setText(MessageManager.getString("action.by_pairwise_id"));
738 .addActionListener(new java.awt.event.ActionListener()
740 public void actionPerformed(ActionEvent e)
742 sortPairwiseMenuItem_actionPerformed(e);
745 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
746 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
748 public void actionPerformed(ActionEvent e)
750 sortIDMenuItem_actionPerformed(e);
753 sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
755 .addActionListener(new java.awt.event.ActionListener()
757 public void actionPerformed(ActionEvent e)
759 sortLengthMenuItem_actionPerformed(e);
762 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
763 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
765 public void actionPerformed(ActionEvent e)
767 sortGroupMenuItem_actionPerformed(e);
770 removeRedundancyMenuItem.setText(MessageManager.getString("action.remove_redundancy"));
771 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
772 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
773 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
774 removeRedundancyMenuItem
775 .addActionListener(new java.awt.event.ActionListener()
777 public void actionPerformed(ActionEvent e)
779 removeRedundancyMenuItem_actionPerformed(e);
782 pairwiseAlignmentMenuItem.setText(MessageManager.getString("action.pairwise_alignment"));
783 pairwiseAlignmentMenuItem
784 .addActionListener(new java.awt.event.ActionListener()
786 public void actionPerformed(ActionEvent e)
788 pairwiseAlignmentMenuItem_actionPerformed(e);
791 PCAMenuItem.setText(MessageManager.getString("label.principal_component_analysis"));
792 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
794 public void actionPerformed(ActionEvent e)
796 PCAMenuItem_actionPerformed(e);
799 averageDistanceTreeMenuItem
800 .setText(MessageManager.getString("label.average_distance_identity"));
801 averageDistanceTreeMenuItem
802 .addActionListener(new java.awt.event.ActionListener()
804 public void actionPerformed(ActionEvent e)
806 averageDistanceTreeMenuItem_actionPerformed(e);
809 neighbourTreeMenuItem.setText(MessageManager.getString("label.neighbour_joining_identity"));
810 neighbourTreeMenuItem
811 .addActionListener(new java.awt.event.ActionListener()
813 public void actionPerformed(ActionEvent e)
815 neighbourTreeMenuItem_actionPerformed(e);
818 this.getContentPane().setLayout(borderLayout1);
819 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
820 statusBar.setBackground(Color.white);
821 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
822 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
823 statusBar.setText(MessageManager.getString("label.status_bar"));
824 outputTextboxMenu.setText(MessageManager.getString("label.out_to_textbox"));
825 clustalColour.setText(MessageManager.getString("label.clustalx"));
827 clustalColour.addActionListener(new java.awt.event.ActionListener()
829 public void actionPerformed(ActionEvent e)
831 clustalColour_actionPerformed(e);
834 zappoColour.setText(MessageManager.getString("label.zappo"));
835 zappoColour.addActionListener(new java.awt.event.ActionListener()
837 public void actionPerformed(ActionEvent e)
839 zappoColour_actionPerformed(e);
842 taylorColour.setText(MessageManager.getString("label.taylor"));
843 taylorColour.addActionListener(new java.awt.event.ActionListener()
845 public void actionPerformed(ActionEvent e)
847 taylorColour_actionPerformed(e);
850 hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
852 .addActionListener(new java.awt.event.ActionListener()
854 public void actionPerformed(ActionEvent e)
856 hydrophobicityColour_actionPerformed(e);
859 helixColour.setText(MessageManager.getString("label.helix_propensity"));
860 helixColour.addActionListener(new java.awt.event.ActionListener()
862 public void actionPerformed(ActionEvent e)
864 helixColour_actionPerformed(e);
867 strandColour.setText(MessageManager.getString("label.strand_propensity"));
868 strandColour.addActionListener(new java.awt.event.ActionListener()
870 public void actionPerformed(ActionEvent e)
872 strandColour_actionPerformed(e);
875 turnColour.setText(MessageManager.getString("Turn Propensity"));
876 turnColour.addActionListener(new java.awt.event.ActionListener()
878 public void actionPerformed(ActionEvent e)
880 turnColour_actionPerformed(e);
883 buriedColour.setText(MessageManager.getString("Buried Index"));
884 buriedColour.addActionListener(new java.awt.event.ActionListener()
886 public void actionPerformed(ActionEvent e)
888 buriedColour_actionPerformed(e);
891 userDefinedColour.setText(MessageManager.getString("action.user_defined"));
892 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
894 public void actionPerformed(ActionEvent e)
896 userDefinedColour_actionPerformed(e);
899 PIDColour.setText(MessageManager.getString("label.percentage_identity"));
900 PIDColour.addActionListener(new java.awt.event.ActionListener()
902 public void actionPerformed(ActionEvent e)
904 PIDColour_actionPerformed(e);
907 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
908 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
910 public void actionPerformed(ActionEvent e)
912 BLOSUM62Colour_actionPerformed(e);
915 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
916 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
918 public void actionPerformed(ActionEvent e)
920 nucleotideColour_actionPerformed(e);
924 purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
925 purinePyrimidineColour
926 .addActionListener(new java.awt.event.ActionListener()
928 public void actionPerformed(ActionEvent e)
930 purinePyrimidineColour_actionPerformed(e);
934 RNAInteractionColour.setText("RNA Interaction type");
935 RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
937 public void actionPerformed(ActionEvent e)
939 RNAInteractionColour_actionPerformed(e);
943 * covariationColour.setText("Covariation");
944 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
945 * public void actionPerformed(ActionEvent e) {
946 * covariationColour_actionPerformed(e); } });
949 avDistanceTreeBlosumMenuItem.setText(MessageManager.getString("label.average_distance_bloslum62"));
950 avDistanceTreeBlosumMenuItem
951 .addActionListener(new java.awt.event.ActionListener()
953 public void actionPerformed(ActionEvent e)
955 avTreeBlosumMenuItem_actionPerformed(e);
958 njTreeBlosumMenuItem.setText(MessageManager.getString("label.neighbour_blosum62"));
960 .addActionListener(new java.awt.event.ActionListener()
962 public void actionPerformed(ActionEvent e)
964 njTreeBlosumMenuItem_actionPerformed(e);
967 annotationPanelMenuItem.setActionCommand("");
968 annotationPanelMenuItem.setText(MessageManager.getString("label.show_annotations"));
969 annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
970 "SHOW_ANNOTATIONS", true));
971 annotationPanelMenuItem
972 .addActionListener(new java.awt.event.ActionListener()
974 public void actionPerformed(ActionEvent e)
976 annotationPanelMenuItem_actionPerformed(e);
979 colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
981 .addActionListener(new java.awt.event.ActionListener()
983 public void actionPerformed(ActionEvent e)
985 colourTextMenuItem_actionPerformed(e);
988 htmlMenuItem.setText(MessageManager.getString("label.html"));
989 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
991 public void actionPerformed(ActionEvent e)
993 htmlMenuItem_actionPerformed(e);
996 overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
997 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
999 public void actionPerformed(ActionEvent e)
1001 overviewMenuItem_actionPerformed(e);
1004 undoMenuItem.setEnabled(false);
1005 undoMenuItem.setText(MessageManager.getString("action.undo"));
1006 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1007 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1008 .getMenuShortcutKeyMask(), false));
1009 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1011 public void actionPerformed(ActionEvent e)
1013 undoMenuItem_actionPerformed(e);
1016 redoMenuItem.setEnabled(false);
1017 redoMenuItem.setText(MessageManager.getString("action.redo"));
1018 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1019 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1020 .getMenuShortcutKeyMask(), false));
1021 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1023 public void actionPerformed(ActionEvent e)
1025 redoMenuItem_actionPerformed(e);
1028 conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
1029 conservationMenuItem
1030 .addActionListener(new java.awt.event.ActionListener()
1032 public void actionPerformed(ActionEvent e)
1034 conservationMenuItem_actionPerformed(e);
1037 noColourmenuItem.setText(MessageManager.getString("label.none"));
1038 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1040 public void actionPerformed(ActionEvent e)
1042 noColourmenuItem_actionPerformed(e);
1045 wrapMenuItem.setText(MessageManager.getString("labe.wrap"));
1046 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1048 public void actionPerformed(ActionEvent e)
1050 wrapMenuItem_actionPerformed(e);
1053 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1054 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1055 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1056 .getMenuShortcutKeyMask(), false));
1057 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1059 public void actionPerformed(ActionEvent e)
1061 printMenuItem_actionPerformed(e);
1064 renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps"));
1065 renderGapsMenuItem.setState(true);
1067 .addActionListener(new java.awt.event.ActionListener()
1069 public void actionPerformed(ActionEvent e)
1071 renderGapsMenuItem_actionPerformed(e);
1074 findMenuItem.setText(MessageManager.getString("action.find"));
1075 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1076 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1077 .getMenuShortcutKeyMask(), false));
1078 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1080 public void actionPerformed(ActionEvent e)
1082 findMenuItem_actionPerformed(e);
1085 abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold"));
1086 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1088 public void actionPerformed(ActionEvent e)
1090 abovePIDThreshold_actionPerformed(e);
1093 showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features"));
1094 showSeqFeatures.addActionListener(new ActionListener()
1096 public void actionPerformed(ActionEvent actionEvent)
1098 showSeqFeatures_actionPerformed(actionEvent);
1102 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1103 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1104 * void actionPerformed(ActionEvent actionEvent) {
1105 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1107 showDbRefsMenuitem.setText(MessageManager.getString("label.show_database_refs"));
1108 showDbRefsMenuitem.addActionListener(new ActionListener()
1111 public void actionPerformed(ActionEvent e)
1113 showDbRefs_actionPerformed(e);
1117 showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
1118 showNpFeatsMenuitem.addActionListener(new ActionListener()
1121 public void actionPerformed(ActionEvent e)
1123 showNpFeats_actionPerformed(e);
1127 showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
1128 showGroupConservation.addActionListener(new ActionListener()
1131 public void actionPerformed(ActionEvent e)
1133 showGroupConservation_actionPerformed(e);
1138 showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
1139 showGroupConsensus.addActionListener(new ActionListener()
1142 public void actionPerformed(ActionEvent e)
1144 showGroupConsensus_actionPerformed(e);
1148 showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
1149 showConsensusHistogram.addActionListener(new ActionListener()
1152 public void actionPerformed(ActionEvent e)
1154 showConsensusHistogram_actionPerformed(e);
1158 showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
1159 showSequenceLogo.addActionListener(new ActionListener()
1162 public void actionPerformed(ActionEvent e)
1164 showSequenceLogo_actionPerformed(e);
1168 normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
1169 normaliseSequenceLogo.addActionListener(new ActionListener()
1172 public void actionPerformed(ActionEvent e)
1174 normaliseSequenceLogo_actionPerformed(e);
1178 applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups"));
1179 applyAutoAnnotationSettings.setState(false);
1180 applyAutoAnnotationSettings.setVisible(true);
1181 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1184 public void actionPerformed(ActionEvent e)
1186 applyAutoAnnotationSettings_actionPerformed(e);
1191 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1192 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1194 public void actionPerformed(ActionEvent e)
1196 nucleotideColour_actionPerformed(e);
1200 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1201 tcoffeeColour.setEnabled(false);
1202 tcoffeeColour.addActionListener(new ActionListener()
1206 public void actionPerformed(ActionEvent e)
1208 tcoffeeColorScheme_actionPerformed(e);
1212 deleteGroups.setText(MessageManager.getString("action.undefine_groups"));
1213 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1214 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1215 .getMenuShortcutKeyMask(), false));
1216 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1218 public void actionPerformed(ActionEvent e)
1220 deleteGroups_actionPerformed(e);
1223 createGroup.setText(MessageManager.getString("action.create_groups"));
1224 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1225 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1226 .getMenuShortcutKeyMask(), false));
1227 createGroup.addActionListener(new java.awt.event.ActionListener()
1229 public void actionPerformed(ActionEvent e)
1231 createGroup_actionPerformed(e);
1234 unGroup.setText(MessageManager.getString("action.remove_group"));
1235 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1236 java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
1237 .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
1238 unGroup.addActionListener(new java.awt.event.ActionListener()
1240 public void actionPerformed(ActionEvent e)
1242 unGroup_actionPerformed(e);
1245 copy.setText(MessageManager.getString("action.copy"));
1246 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1247 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1248 .getMenuShortcutKeyMask(), false));
1250 copy.addActionListener(new java.awt.event.ActionListener()
1252 public void actionPerformed(ActionEvent e)
1254 copy_actionPerformed(e);
1257 cut.setText(MessageManager.getString("action.cut"));
1258 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1259 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1260 .getMenuShortcutKeyMask(), false));
1261 cut.addActionListener(new java.awt.event.ActionListener()
1263 public void actionPerformed(ActionEvent e)
1265 cut_actionPerformed(e);
1268 delete.setText(MessageManager.getString("action.delete"));
1269 delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1270 java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
1271 delete.addActionListener(new java.awt.event.ActionListener()
1273 public void actionPerformed(ActionEvent e)
1275 delete_actionPerformed(e);
1278 pasteMenu.setText(MessageManager.getString("action.paste"));
1279 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1280 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1281 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1282 .getMenuShortcutKeyMask()
1283 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1284 pasteNew.addActionListener(new java.awt.event.ActionListener()
1286 public void actionPerformed(ActionEvent e)
1288 pasteNew_actionPerformed(e);
1291 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1292 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1293 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1294 .getMenuShortcutKeyMask(), false));
1295 pasteThis.addActionListener(new java.awt.event.ActionListener()
1297 public void actionPerformed(ActionEvent e)
1299 pasteThis_actionPerformed(e);
1302 applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups"));
1303 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1305 public void actionPerformed(ActionEvent e)
1307 applyToAllGroups_actionPerformed(e);
1310 createPNG.addActionListener(new java.awt.event.ActionListener()
1312 public void actionPerformed(ActionEvent e)
1317 createPNG.setActionCommand(MessageManager.getString("label.save_png_image"));
1318 createPNG.setText("PNG");
1319 font.setText(MessageManager.getString("action.font"));
1320 font.addActionListener(new java.awt.event.ActionListener()
1322 public void actionPerformed(ActionEvent e)
1324 font_actionPerformed(e);
1328 seqLimits.setText(MessageManager.getString("label.show_sequence_limits"));
1329 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1330 seqLimits.addActionListener(new java.awt.event.ActionListener()
1332 public void actionPerformed(ActionEvent e)
1334 seqLimit_actionPerformed(e);
1337 epsFile.setText("EPS");
1338 epsFile.addActionListener(new java.awt.event.ActionListener()
1340 public void actionPerformed(ActionEvent e)
1345 LoadtreeMenuItem.setActionCommand(MessageManager.getString("label.load_tree_for_sequence_set"));
1346 LoadtreeMenuItem.setText(MessageManager.getString("label.load_associated_tree"));
1347 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1349 public void actionPerformed(ActionEvent e)
1351 LoadtreeMenuItem_actionPerformed(e);
1355 scaleAbove.setVisible(false);
1356 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1357 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1359 public void actionPerformed(ActionEvent e)
1361 scaleAbove_actionPerformed(e);
1364 scaleLeft.setVisible(false);
1365 scaleLeft.setSelected(true);
1366 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1367 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1369 public void actionPerformed(ActionEvent e)
1371 scaleLeft_actionPerformed(e);
1374 scaleRight.setVisible(false);
1375 scaleRight.setSelected(true);
1376 scaleRight.setText(MessageManager.getString("action.scale_right"));
1377 scaleRight.addActionListener(new java.awt.event.ActionListener()
1379 public void actionPerformed(ActionEvent e)
1381 scaleRight_actionPerformed(e);
1384 centreColumnLabelsMenuItem.setVisible(true);
1385 centreColumnLabelsMenuItem.setState(false);
1386 centreColumnLabelsMenuItem.setText(MessageManager.getString("label.centre_column_labels"));
1387 centreColumnLabelsMenuItem
1388 .addActionListener(new java.awt.event.ActionListener()
1390 public void actionPerformed(ActionEvent e)
1392 centreColumnLabels_actionPerformed(e);
1395 followHighlightMenuItem.setVisible(true);
1396 followHighlightMenuItem.setState(true);
1397 followHighlightMenuItem.setText(MessageManager.getString("label.automatic_scrolling"));
1398 followHighlightMenuItem.addActionListener(new ActionListener()
1401 public void actionPerformed(ActionEvent e)
1403 followHighlight_actionPerformed();
1408 modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold"));
1409 modifyPID.addActionListener(new java.awt.event.ActionListener()
1411 public void actionPerformed(ActionEvent e)
1413 modifyPID_actionPerformed(e);
1416 modifyConservation.setText(MessageManager.getString("label.modify_conservation_thereshold"));
1418 .addActionListener(new java.awt.event.ActionListener()
1420 public void actionPerformed(ActionEvent e)
1422 modifyConservation_actionPerformed(e);
1425 sortByTreeMenu.setText(MessageManager.getString("action.by_tree_order"));
1426 sort.setText(MessageManager.getString("action.sort"));
1427 sort.addMenuListener(new MenuListener()
1429 public void menuSelected(MenuEvent e)
1434 public void menuDeselected(MenuEvent e)
1438 public void menuCanceled(MenuEvent e)
1442 sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score"));
1443 sort.add(sortByAnnotScore);
1444 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1447 public void menuCanceled(MenuEvent e)
1451 public void menuDeselected(MenuEvent e)
1455 public void menuSelected(MenuEvent e)
1457 buildSortByAnnotationScoresMenu();
1460 sortByAnnotScore.setVisible(false);
1462 calculateTree.setText(MessageManager.getString("action.calculate_tree"));
1464 jMenu2.setText(MessageManager.getString("label.export_image"));
1465 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1466 padGapsMenuitem.setState(jalview.bin.Cache
1467 .getDefault("PAD_GAPS", false));
1468 padGapsMenuitem.addActionListener(new ActionListener()
1470 public void actionPerformed(ActionEvent e)
1472 padGapsMenuitem_actionPerformed(e);
1475 vamsasStore.setVisible(false);
1476 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1477 vamsasStore.addActionListener(new ActionListener()
1479 public void actionPerformed(ActionEvent e)
1481 vamsasStore_actionPerformed(e);
1484 showTranslation.setText(MessageManager.getString("label.translate_cDNA"));
1485 showTranslation.addActionListener(new ActionListener()
1487 public void actionPerformed(ActionEvent e)
1489 showTranslation_actionPerformed(e);
1492 extractScores.setText(MessageManager.getString("label.extract_scores") + "...");
1493 extractScores.addActionListener(new ActionListener()
1495 public void actionPerformed(ActionEvent e)
1497 extractScores_actionPerformed(e);
1500 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1502 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1504 * showProducts.addActionListener(new ActionListener() {
1506 * public void actionPerformed(ActionEvent e) {
1507 * showProducts_actionPerformed(e); } });
1509 openFeatureSettings.setText(MessageManager.getString("label.feature_settings"));
1510 openFeatureSettings.addActionListener(new ActionListener()
1512 public void actionPerformed(ActionEvent e)
1514 featureSettings_actionPerformed(e);
1517 fetchSequence.setText(MessageManager.getString("label.fetch_sequences"));
1518 fetchSequence.addActionListener(new ActionListener()
1520 public void actionPerformed(ActionEvent e)
1522 fetchSequence_actionPerformed(e);
1526 annotationColour.setText(MessageManager.getString("action.by_annotation"));
1527 annotationColour.addActionListener(new ActionListener()
1529 public void actionPerformed(ActionEvent e)
1531 annotationColour_actionPerformed(e);
1535 rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes"));
1536 rnahelicesColour.addActionListener(new ActionListener()
1538 public void actionPerformed(ActionEvent e)
1540 rnahelicesColour_actionPerformed(e);
1544 associatedData.setText(MessageManager.getString("label.load_features_annotations"));
1545 associatedData.addActionListener(new ActionListener()
1547 public void actionPerformed(ActionEvent e)
1549 associatedData_actionPerformed(e);
1552 autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus"));
1553 autoCalculate.setState(jalview.bin.Cache.getDefault(
1554 "AUTO_CALC_CONSENSUS", true));
1555 autoCalculate.addActionListener(new ActionListener()
1557 public void actionPerformed(ActionEvent e)
1559 autoCalculate_actionPerformed(e);
1562 sortByTree.setText(MessageManager.getString("label.sort_alignment_new_tree"));
1564 .setToolTipText("<html>" + MessageManager.getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1566 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1567 sortByTree.addActionListener(new ActionListener()
1569 public void actionPerformed(ActionEvent e)
1571 sortByTreeOption_actionPerformed(e);
1575 listenToViewSelections.setText(MessageManager.getString("label.listen_for_selections"));
1576 listenToViewSelections
1577 .setToolTipText("<html>" + MessageManager.getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1578 listenToViewSelections.setState(false);
1579 listenToViewSelections.addActionListener(new ActionListener()
1581 public void actionPerformed(ActionEvent e)
1583 listenToViewSelections_actionPerformed(e);
1587 addSequenceMenu.setText(MessageManager.getString("label.add_sequences"));
1588 addFromFile.setText(MessageManager.getString("label.from_file"));
1589 addFromFile.addActionListener(new ActionListener()
1591 public void actionPerformed(ActionEvent e)
1593 addFromFile_actionPerformed(e);
1596 addFromText.setText(MessageManager.getString("label.from_textbox"));
1597 addFromText.addActionListener(new ActionListener()
1599 public void actionPerformed(ActionEvent e)
1601 addFromText_actionPerformed(e);
1604 addFromURL.setText(MessageManager.getString("label.from_url"));
1605 addFromURL.addActionListener(new ActionListener()
1607 public void actionPerformed(ActionEvent e)
1609 addFromURL_actionPerformed(e);
1612 exportFeatures.setText(MessageManager.getString("label.export_features"));
1613 exportFeatures.addActionListener(new ActionListener()
1615 public void actionPerformed(ActionEvent e)
1617 exportFeatures_actionPerformed(e);
1620 exportAnnotations.setText(MessageManager.getString("label.export_annotations"));
1621 exportAnnotations.addActionListener(new ActionListener()
1623 public void actionPerformed(ActionEvent e)
1625 exportAnnotations_actionPerformed(e);
1628 statusPanel.setLayout(gridLayout1);
1629 jMenu3.setText(MessageManager.getString("action.show"));
1630 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1631 showAllSeqs.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
1632 showAllSeqs.addActionListener(new ActionListener()
1634 public void actionPerformed(ActionEvent e)
1636 showAllSeqs_actionPerformed(e);
1639 showAllColumns.setText(MessageManager.getString("label.all_columns"));
1640 showAllColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
1641 showAllColumns.addActionListener(new ActionListener()
1643 public void actionPerformed(ActionEvent e)
1645 showAllColumns_actionPerformed(e);
1648 hideMenu.setText(MessageManager.getString("action.hide"));
1649 hideSelSequences.setText(MessageManager.getString("label.selected_sequences"));
1650 hideSelSequences.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
1651 hideSelSequences.addActionListener(new ActionListener()
1653 public void actionPerformed(ActionEvent e)
1655 hideSelSequences_actionPerformed(e);
1658 hideSelColumns.setText(MessageManager.getString("label.selected_columns"));
1659 hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
1660 hideSelColumns.addActionListener(new ActionListener()
1662 public void actionPerformed(ActionEvent e)
1664 hideSelColumns_actionPerformed(e);
1667 hideAllSelection.setText(MessageManager.getString("label.selected_region"));
1668 hideAllSelection.addActionListener(new ActionListener()
1670 public void actionPerformed(ActionEvent e)
1672 hideAllSelection_actionPerformed(e);
1675 // TODO: should be hidden if no selection exists.
1676 hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region"));
1677 hideAllButSelection.addActionListener(new ActionListener()
1679 public void actionPerformed(ActionEvent e)
1681 hideAllButSelection_actionPerformed(e);
1684 showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
1686 .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
1687 showAllhidden.addActionListener(new ActionListener()
1689 public void actionPerformed(ActionEvent e)
1691 showAllhidden_actionPerformed(e);
1695 hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers"));
1696 hiddenMarkers.addActionListener(new ActionListener()
1698 public void actionPerformed(ActionEvent e)
1700 hiddenMarkers_actionPerformed(e);
1703 invertColSel.setText(MessageManager.getString("action.invert_column_selection"));
1704 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1705 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
1706 .getMenuShortcutKeyMask()
1707 | java.awt.event.KeyEvent.ALT_MASK, false));
1708 invertColSel.addActionListener(new ActionListener()
1710 public void actionPerformed(ActionEvent e)
1712 invertColSel_actionPerformed(e);
1715 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
1717 public void stateChanged(ChangeEvent evt)
1719 JTabbedPane pane = (JTabbedPane) evt.getSource();
1720 int sel = pane.getSelectedIndex();
1721 tabSelectionChanged(sel);
1724 tabbedPane.addMouseListener(new MouseAdapter()
1726 public void mousePressed(MouseEvent e)
1728 tabbedPane_mousePressed(e);
1731 tabbedPane.addFocusListener(new FocusAdapter()
1733 public void focusGained(FocusEvent e)
1735 tabbedPane_focusGained(e);
1738 save.setText(MessageManager.getString("action.save"));
1739 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1740 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
1741 .getMenuShortcutKeyMask(), false));
1742 save.addActionListener(new ActionListener()
1744 public void actionPerformed(ActionEvent e)
1746 save_actionPerformed(e);
1749 reload.setEnabled(false);
1750 reload.setText(MessageManager.getString("action.reload"));
1751 reload.addActionListener(new ActionListener()
1753 public void actionPerformed(ActionEvent e)
1755 reload_actionPerformed(e);
1758 newView.setText(MessageManager.getString("action.new_view"));
1759 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1760 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
1761 .getMenuShortcutKeyMask(), false));
1762 newView.addActionListener(new ActionListener()
1764 public void actionPerformed(ActionEvent e)
1766 newView_actionPerformed(e);
1769 tabbedPane.setToolTipText("<html><i>" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + "</i></html>");
1770 textColour.setText(MessageManager.getString("label.colour_text") + "...");
1771 textColour.addActionListener(new ActionListener()
1773 public void actionPerformed(ActionEvent e)
1775 textColour_actionPerformed(e);
1778 formatMenu.setText(MessageManager.getString("action.format"));
1779 selectMenu.setText(MessageManager.getString("action.select"));
1780 idRightAlign.setText(MessageManager.getString("label.right_align_sequence_id"));
1781 idRightAlign.addActionListener(new ActionListener()
1783 public void actionPerformed(ActionEvent e)
1785 idRightAlign_actionPerformed(e);
1788 gatherViews.setEnabled(false);
1789 gatherViews.setText(MessageManager.getString("action.gather_views"));
1790 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1791 java.awt.event.KeyEvent.VK_G, 0, false));
1792 gatherViews.addActionListener(new ActionListener()
1794 public void actionPerformed(ActionEvent e)
1796 gatherViews_actionPerformed(e);
1799 expandViews.setEnabled(false);
1800 expandViews.setText(MessageManager.getString("action.expand_views"));
1801 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1802 java.awt.event.KeyEvent.VK_X, 0, false));
1803 expandViews.addActionListener(new ActionListener()
1805 public void actionPerformed(ActionEvent e)
1807 expandViews_actionPerformed(e);
1810 pageSetup.setText(MessageManager.getString("action.page_setup") + "...");
1811 pageSetup.addActionListener(new ActionListener()
1813 public void actionPerformed(ActionEvent e)
1815 pageSetup_actionPerformed(e);
1818 alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "...");
1819 alignmentProperties.addActionListener(new ActionListener()
1821 public void actionPerformed(ActionEvent actionEvent)
1823 alignmentProperties();
1826 tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip"));
1827 autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation"));
1828 alignFrameMenuBar.add(fileMenu);
1829 alignFrameMenuBar.add(editMenu);
1830 alignFrameMenuBar.add(selectMenu);
1831 alignFrameMenuBar.add(viewMenu);
1832 alignFrameMenuBar.add(formatMenu);
1833 alignFrameMenuBar.add(colourMenu);
1834 alignFrameMenuBar.add(calculateMenu);
1835 alignFrameMenuBar.add(webService);
1836 fileMenu.add(fetchSequence);
1837 fileMenu.add(addSequenceMenu);
1838 fileMenu.add(reload);
1839 fileMenu.addSeparator();
1840 fileMenu.add(vamsasStore);
1842 fileMenu.add(saveAs);
1843 fileMenu.add(outputTextboxMenu);
1844 fileMenu.add(pageSetup);
1845 fileMenu.add(printMenuItem);
1846 fileMenu.addSeparator();
1847 fileMenu.add(jMenu2);
1848 fileMenu.add(exportFeatures);
1849 fileMenu.add(exportAnnotations);
1850 fileMenu.add(LoadtreeMenuItem);
1851 fileMenu.add(associatedData);
1852 fileMenu.addSeparator();
1853 fileMenu.add(closeMenuItem);
1854 editMenu.add(undoMenuItem);
1855 editMenu.add(redoMenuItem);
1858 editMenu.add(pasteMenu);
1859 editMenu.add(delete);
1860 editMenu.addSeparator();
1861 editMenu.add(remove2LeftMenuItem);
1862 editMenu.add(remove2RightMenuItem);
1863 editMenu.add(removeGappedColumnMenuItem);
1864 editMenu.add(removeAllGapsMenuItem);
1865 editMenu.add(removeRedundancyMenuItem);
1866 editMenu.addSeparator();
1867 // dont add these yet in the CVS build - they cannot be undone!
1868 // Excluded from Jalview 2.5 release - undo needs to be implemented.
1869 // editMenu.add(justifyLeftMenuItem);
1870 // editMenu.add(justifyRightMenuItem);
1871 // editMenu.addSeparator();
1872 editMenu.add(padGapsMenuitem);
1873 viewMenu.add(newView);
1874 viewMenu.add(expandViews);
1875 viewMenu.add(gatherViews);
1876 viewMenu.addSeparator();
1877 viewMenu.add(jMenu3);
1878 viewMenu.add(hideMenu);
1879 viewMenu.addSeparator();
1880 viewMenu.add(followHighlightMenuItem);
1881 viewMenu.add(annotationPanelMenuItem);
1882 autoAnnMenu.add(applyAutoAnnotationSettings);
1883 autoAnnMenu.add(showConsensusHistogram);
1884 autoAnnMenu.add(showSequenceLogo);
1885 autoAnnMenu.add(normaliseSequenceLogo);
1886 autoAnnMenu.addSeparator();
1887 autoAnnMenu.add(showGroupConservation);
1888 autoAnnMenu.add(showGroupConsensus);
1889 viewMenu.add(autoAnnMenu);
1890 viewMenu.addSeparator();
1891 viewMenu.add(showSeqFeatures);
1892 // viewMenu.add(showSeqFeaturesHeight);
1894 viewMenu.add(openFeatureSettings);
1895 tooltipSettingsMenu.add(showDbRefsMenuitem);
1896 tooltipSettingsMenu.add(showNpFeatsMenuitem);
1897 viewMenu.add(tooltipSettingsMenu);
1898 viewMenu.addSeparator();
1899 viewMenu.add(alignmentProperties);
1900 viewMenu.addSeparator();
1901 viewMenu.add(overviewMenuItem);
1902 colourMenu.add(applyToAllGroups);
1903 colourMenu.add(textColour);
1904 colourMenu.addSeparator();
1905 colourMenu.add(noColourmenuItem);
1906 colourMenu.add(clustalColour);
1907 colourMenu.add(BLOSUM62Colour);
1908 colourMenu.add(PIDColour);
1909 colourMenu.add(zappoColour);
1910 colourMenu.add(taylorColour);
1911 colourMenu.add(hydrophobicityColour);
1912 colourMenu.add(helixColour);
1913 colourMenu.add(strandColour);
1914 colourMenu.add(turnColour);
1915 colourMenu.add(buriedColour);
1916 colourMenu.add(nucleotideColour);
1917 colourMenu.add(purinePyrimidineColour);
1918 colourMenu.add(RNAInteractionColour);
1919 // colourMenu.add(covariationColour);
1920 colourMenu.add(tcoffeeColour);
1921 colourMenu.add(userDefinedColour);
1922 colourMenu.addSeparator();
1923 colourMenu.add(conservationMenuItem);
1924 colourMenu.add(modifyConservation);
1925 colourMenu.add(abovePIDThreshold);
1926 colourMenu.add(modifyPID);
1927 colourMenu.add(annotationColour);
1928 colourMenu.add(rnahelicesColour);
1929 calculateMenu.add(sort);
1930 calculateMenu.add(calculateTree);
1931 calculateMenu.addSeparator();
1932 calculateMenu.add(pairwiseAlignmentMenuItem);
1933 calculateMenu.add(PCAMenuItem);
1934 calculateMenu.addSeparator();
1935 calculateMenu.add(showTranslation);
1936 calculateMenu.add(showProducts);
1937 calculateMenu.add(autoCalculate);
1938 calculateMenu.add(sortByTree);
1939 calculateMenu.addSeparator();
1940 calculateMenu.add(extractScores);
1941 webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services"));
1942 webService.add(webServiceNoServices);
1943 pasteMenu.add(pasteNew);
1944 pasteMenu.add(pasteThis);
1945 sort.add(sortIDMenuItem);
1946 sort.add(sortLengthMenuItem);
1947 sort.add(sortGroupMenuItem);
1948 sort.add(sortPairwiseMenuItem);
1949 sort.add(sortByTreeMenu);
1950 calculateTree.add(averageDistanceTreeMenuItem);
1951 calculateTree.add(neighbourTreeMenuItem);
1952 calculateTree.add(avDistanceTreeBlosumMenuItem);
1953 calculateTree.add(njTreeBlosumMenuItem);
1954 jMenu2.add(htmlMenuItem);
1955 jMenu2.add(epsFile);
1956 jMenu2.add(createPNG);
1957 addSequenceMenu.add(addFromFile);
1958 addSequenceMenu.add(addFromText);
1959 addSequenceMenu.add(addFromURL);
1960 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
1961 statusPanel.add(statusBar, null);
1962 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
1963 jMenu3.add(showAllColumns);
1964 jMenu3.add(showAllSeqs);
1965 jMenu3.add(showAllhidden);
1966 hideMenu.add(hideSelColumns);
1967 hideMenu.add(hideSelSequences);
1968 hideMenu.add(hideAllSelection);
1969 hideMenu.add(hideAllButSelection);
1971 formatMenu.add(font);
1972 formatMenu.addSeparator();
1973 formatMenu.add(wrapMenuItem);
1974 formatMenu.add(scaleAbove);
1975 formatMenu.add(scaleLeft);
1976 formatMenu.add(scaleRight);
1977 formatMenu.add(seqLimits);
1978 formatMenu.add(idRightAlign);
1979 formatMenu.add(hiddenMarkers);
1980 formatMenu.add(viewBoxesMenuItem);
1981 formatMenu.add(viewTextMenuItem);
1982 formatMenu.add(colourTextMenuItem);
1983 formatMenu.add(renderGapsMenuItem);
1984 formatMenu.add(centreColumnLabelsMenuItem);
1985 formatMenu.add(showNonconservedMenuItem);
1986 selectMenu.add(findMenuItem);
1987 selectMenu.addSeparator();
1988 selectMenu.add(selectAllSequenceMenuItem);
1989 selectMenu.add(deselectAllSequenceMenuItem);
1990 selectMenu.add(invertSequenceMenuItem);
1991 selectMenu.add(invertColSel);
1992 selectMenu.add(createGroup);
1993 selectMenu.add(unGroup);
1994 selectMenu.add(grpsFromSelection);
1995 selectMenu.add(deleteGroups);
1996 // TODO - determine if the listenToViewSelections button is needed : see bug
1998 // selectMenu.addSeparator();
1999 // selectMenu.add(listenToViewSelections);
2002 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2004 // TODO Auto-generated method stub
2008 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2010 // TODO Auto-generated method stub
2014 protected void showAllhidden_actionPerformed(ActionEvent e)
2016 // TODO Auto-generated method stub
2020 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2022 // TODO Auto-generated method stub
2026 protected void hideAllSelection_actionPerformed(ActionEvent e)
2028 // TODO Auto-generated method stub
2032 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2034 // TODO Auto-generated method stub
2038 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2040 // TODO Auto-generated method stub
2044 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2046 // TODO Auto-generated method stub
2050 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2052 // TODO Auto-generated method stub
2056 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2058 // TODO Auto-generated method stub
2062 protected void showGroupConservation_actionPerformed(ActionEvent e)
2064 // TODO Auto-generated method stub
2068 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2070 // TODO Auto-generated method stub
2074 protected void showSeqFeaturesHeight_actionPerformed(
2075 ActionEvent actionEvent)
2077 // TODO Auto-generated method stub
2081 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2083 // TODO Auto-generated method stub
2087 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2089 // TODO Auto-generated method stub
2093 protected void followHighlight_actionPerformed()
2095 // TODO Auto-generated method stub
2099 protected void showNpFeats_actionPerformed(ActionEvent e)
2101 // TODO Auto-generated method stub
2105 protected void showDbRefs_actionPerformed(ActionEvent e)
2107 // TODO Auto-generated method stub
2111 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2115 protected void showProducts_actionPerformed(ActionEvent e)
2119 protected void buildSortByAnnotationScoresMenu()
2123 protected void extractScores_actionPerformed(ActionEvent e)
2127 protected void outputText_actionPerformed(ActionEvent e)
2131 public void addFromFile_actionPerformed(ActionEvent e)
2136 public void addFromText_actionPerformed(ActionEvent e)
2141 public void addFromURL_actionPerformed(ActionEvent e)
2146 public void exportFeatures_actionPerformed(ActionEvent e)
2151 public void exportAnnotations_actionPerformed(ActionEvent e)
2156 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2160 protected void closeMenuItem_actionPerformed(boolean b)
2164 protected void redoMenuItem_actionPerformed(ActionEvent e)
2168 protected void undoMenuItem_actionPerformed(ActionEvent e)
2172 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2176 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2180 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2184 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2188 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2192 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2196 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2200 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2204 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2208 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2212 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2216 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2220 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2224 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2228 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2232 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2236 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2240 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2244 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2248 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2252 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2256 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2260 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2264 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2268 protected void clustalColour_actionPerformed(ActionEvent e)
2272 protected void zappoColour_actionPerformed(ActionEvent e)
2276 protected void taylorColour_actionPerformed(ActionEvent e)
2280 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2284 protected void helixColour_actionPerformed(ActionEvent e)
2288 protected void strandColour_actionPerformed(ActionEvent e)
2292 protected void turnColour_actionPerformed(ActionEvent e)
2296 protected void buriedColour_actionPerformed(ActionEvent e)
2300 protected void userDefinedColour_actionPerformed(ActionEvent e)
2304 protected void PIDColour_actionPerformed(ActionEvent e)
2308 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2312 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2316 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2322 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2325 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2329 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2333 protected void printMenuItem_actionPerformed(ActionEvent e)
2337 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2341 protected void findMenuItem_actionPerformed(ActionEvent e)
2345 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2349 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2353 protected void nucleotideColour_actionPerformed(ActionEvent e)
2357 protected void deleteGroups_actionPerformed(ActionEvent e)
2361 protected void createGroup_actionPerformed(ActionEvent e)
2365 protected void unGroup_actionPerformed(ActionEvent e)
2369 protected void copy_actionPerformed(ActionEvent e)
2373 protected void cut_actionPerformed(ActionEvent e)
2377 protected void delete_actionPerformed(ActionEvent e)
2381 protected void pasteNew_actionPerformed(ActionEvent e)
2385 protected void pasteThis_actionPerformed(ActionEvent e)
2389 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2393 public void createPNG(java.io.File f)
2397 protected void font_actionPerformed(ActionEvent e)
2401 protected void seqLimit_actionPerformed(ActionEvent e)
2405 public void seqDBRef_actionPerformed(ActionEvent e)
2410 public void createEPS(java.io.File f)
2414 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2420 * Template method to handle the 'load T-Coffee scores' menu event.
2422 * Subclasses override this method to provide a custom action.
2427 protected void loadScores_actionPerformed(ActionEvent event)
2433 * Template method to handle the 'Color T-Coffee scores' menu event.
2435 * Subclasses override this method to provide a custom action.
2440 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2445 protected void jpred_actionPerformed(ActionEvent e)
2449 protected void scaleAbove_actionPerformed(ActionEvent e)
2453 protected void scaleLeft_actionPerformed(ActionEvent e)
2457 protected void scaleRight_actionPerformed(ActionEvent e)
2461 protected void modifyPID_actionPerformed(ActionEvent e)
2465 protected void modifyConservation_actionPerformed(ActionEvent e)
2469 protected void saveAs_actionPerformed(ActionEvent e)
2473 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2477 public void vamsasStore_actionPerformed(ActionEvent e)
2482 public void vamsasLoad_actionPerformed(ActionEvent e)
2487 public void showTranslation_actionPerformed(ActionEvent e)
2492 public void featureSettings_actionPerformed(ActionEvent e)
2497 public void fetchSequence_actionPerformed(ActionEvent e)
2502 public void smoothFont_actionPerformed(ActionEvent e)
2507 public void annotationColour_actionPerformed(ActionEvent e)
2512 public void rnahelicesColour_actionPerformed(ActionEvent e)
2517 public void associatedData_actionPerformed(ActionEvent e)
2522 public void autoCalculate_actionPerformed(ActionEvent e)
2527 public void sortByTreeOption_actionPerformed(ActionEvent e)
2532 public void showAllSeqs_actionPerformed(ActionEvent e)
2537 public void showAllColumns_actionPerformed(ActionEvent e)
2542 public void hideSelSequences_actionPerformed(ActionEvent e)
2547 public void hideSelColumns_actionPerformed(ActionEvent e)
2552 public void hiddenMarkers_actionPerformed(ActionEvent e)
2557 public void findPdbId_actionPerformed(ActionEvent e)
2562 public void enterPdbId_actionPerformed(ActionEvent e)
2567 public void pdbFile_actionPerformed(ActionEvent e)
2572 public void invertColSel_actionPerformed(ActionEvent e)
2577 public void tabSelectionChanged(int sel)
2582 public void tabbedPane_mousePressed(MouseEvent e)
2587 public void tabbedPane_focusGained(FocusEvent e)
2592 public void save_actionPerformed(ActionEvent e)
2597 public void reload_actionPerformed(ActionEvent e)
2602 public void newView_actionPerformed(ActionEvent e)
2607 public void textColour_actionPerformed(ActionEvent e)
2612 public void idRightAlign_actionPerformed(ActionEvent e)
2617 public void expandViews_actionPerformed(ActionEvent e)
2622 public void gatherViews_actionPerformed(ActionEvent e)
2627 public void buildTreeMenu()
2632 public void pageSetup_actionPerformed(ActionEvent e)
2637 public void alignmentProperties()