2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.jbgui;
23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
24 import jalview.bin.Cache;
25 import jalview.gui.JvSwingUtils;
26 import jalview.schemes.ColourSchemeProperty;
27 import jalview.util.MessageManager;
29 import java.awt.BorderLayout;
30 import java.awt.Color;
31 import java.awt.GridLayout;
32 import java.awt.Toolkit;
33 import java.awt.event.ActionEvent;
34 import java.awt.event.ActionListener;
35 import java.awt.event.FocusAdapter;
36 import java.awt.event.FocusEvent;
37 import java.awt.event.MouseAdapter;
38 import java.awt.event.MouseEvent;
40 import javax.swing.BorderFactory;
41 import javax.swing.ButtonGroup;
42 import javax.swing.JCheckBoxMenuItem;
43 import javax.swing.JInternalFrame;
44 import javax.swing.JLabel;
45 import javax.swing.JMenu;
46 import javax.swing.JMenuBar;
47 import javax.swing.JMenuItem;
48 import javax.swing.JOptionPane;
49 import javax.swing.JPanel;
50 import javax.swing.JRadioButtonMenuItem;
51 import javax.swing.JTabbedPane;
52 import javax.swing.SwingUtilities;
53 import javax.swing.event.ChangeEvent;
54 import javax.swing.event.MenuEvent;
55 import javax.swing.event.MenuListener;
57 public class GAlignFrame extends JInternalFrame
59 protected JMenuBar alignFrameMenuBar = new JMenuBar();
61 protected JMenu fileMenu = new JMenu();
63 protected JMenuItem closeMenuItem = new JMenuItem();
65 protected JMenu editMenu = new JMenu();
67 protected JMenu viewMenu = new JMenu();
69 protected JMenu annotationsMenu = new JMenu();
71 protected JMenu colourMenu = new JMenu();
73 protected JMenu calculateMenu = new JMenu();
75 protected JMenu webService = new JMenu();
77 protected JMenuItem webServiceNoServices;
79 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
81 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
83 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
85 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
87 protected JMenuItem remove2RightMenuItem = new JMenuItem();
89 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
91 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
93 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
95 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
97 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
99 protected JMenuItem sortIDMenuItem = new JMenuItem();
101 protected JMenuItem sortLengthMenuItem = new JMenuItem();
103 protected JMenuItem sortGroupMenuItem = new JMenuItem();
105 protected JMenu sortByAnnotScore = new JMenu();
107 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
109 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
111 protected JMenuItem PCAMenuItem = new JMenuItem();
113 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
115 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
117 BorderLayout borderLayout1 = new BorderLayout();
119 public JLabel statusBar = new JLabel();
121 protected JMenuItem saveAs = new JMenuItem();
123 protected JMenu outputTextboxMenu = new JMenu();
125 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
127 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
129 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
131 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
133 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
135 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
137 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
139 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
141 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
143 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
145 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
147 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
149 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
151 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
153 // protected JRadioButtonMenuItem covariationColour = new
154 // JRadioButtonMenuItem();
156 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
158 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
160 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
162 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
164 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
166 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
168 JMenuItem htmlMenuItem = new JMenuItem();
170 JMenuItem overviewMenuItem = new JMenuItem();
172 protected JMenuItem undoMenuItem = new JMenuItem();
174 protected JMenuItem redoMenuItem = new JMenuItem();
176 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
178 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
180 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
182 JMenuItem printMenuItem = new JMenuItem();
184 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
186 JMenuItem findMenuItem = new JMenuItem();
188 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
190 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
192 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
194 JMenuItem deleteGroups = new JMenuItem();
196 JMenuItem createGroup = new JMenuItem();
198 JMenuItem unGroup = new JMenuItem();
200 JMenuItem delete = new JMenuItem();
202 JMenuItem copy = new JMenuItem();
204 JMenuItem cut = new JMenuItem();
206 JMenu pasteMenu = new JMenu();
208 JMenuItem pasteNew = new JMenuItem();
210 JMenuItem pasteThis = new JMenuItem();
212 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
214 JMenuItem createPNG = new JMenuItem();
216 protected JMenuItem font = new JMenuItem();
218 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
220 JMenuItem epsFile = new JMenuItem();
222 JMenuItem LoadtreeMenuItem = new JMenuItem();
224 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
226 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
228 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
230 protected JMenuItem modifyPID = new JMenuItem();
232 protected JMenuItem modifyConservation = new JMenuItem();
234 protected JMenu sortByTreeMenu = new JMenu();
236 protected JMenu sort = new JMenu();
238 protected JMenu calculateTree = new JMenu();
240 JMenu jMenu2 = new JMenu();
242 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
244 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
246 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
248 protected ButtonGroup colours = new ButtonGroup();
250 JMenuItem vamsasStore = new JMenuItem();
252 protected JMenuItem showTranslation = new JMenuItem();
254 protected JMenuItem extractScores = new JMenuItem();
256 protected JMenuItem expandAlignment = new JMenuItem();
258 protected JMenu showProducts = new JMenu();
260 public JMenuItem openFeatureSettings = new JMenuItem();
262 JMenuItem fetchSequence = new JMenuItem();
264 JMenuItem annotationColour = new JMenuItem();
266 protected JMenuItem rnahelicesColour = new JMenuItem();
268 JMenuItem associatedData = new JMenuItem();
270 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
272 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
274 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
276 JMenu addSequenceMenu = new JMenu();
278 JMenuItem addFromFile = new JMenuItem();
280 JMenuItem addFromText = new JMenuItem();
282 JMenuItem addFromURL = new JMenuItem();
284 JMenuItem exportAnnotations = new JMenuItem();
286 JMenuItem exportFeatures = new JMenuItem();
288 protected JPanel statusPanel = new JPanel();
290 GridLayout gridLayout1 = new GridLayout();
292 JMenu jMenu3 = new JMenu();
294 JMenuItem showAllSeqs = new JMenuItem();
296 JMenuItem showAllColumns = new JMenuItem();
298 JMenu hideMenu = new JMenu();
300 JMenuItem hideSelSequences = new JMenuItem();
302 JMenuItem hideSelColumns = new JMenuItem();
304 JMenuItem hideAllButSelection = new JMenuItem();
306 JMenuItem hideAllSelection = new JMenuItem();
308 JMenuItem showAllhidden = new JMenuItem();
310 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
312 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
314 protected JMenuItem showAllAlAnnotations = new JMenuItem();
316 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
318 protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
320 protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
322 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
324 JMenuItem invertColSel = new JMenuItem();
326 protected JTabbedPane tabbedPane = new JTabbedPane();
328 JMenuItem save = new JMenuItem();
330 protected JMenuItem reload = new JMenuItem();
332 JMenuItem newView = new JMenuItem();
334 JMenuItem textColour = new JMenuItem();
336 JMenu formatMenu = new JMenu();
338 JMenu selectMenu = new JMenu();
340 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
342 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
344 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
346 protected JMenuItem gatherViews = new JMenuItem();
348 protected JMenuItem expandViews = new JMenuItem();
350 JMenuItem pageSetup = new JMenuItem();
352 JMenuItem alignmentProperties = new JMenuItem();
354 JMenu tooltipSettingsMenu = new JMenu();
356 private JMenuItem justifyLeftMenuItem = new JMenuItem();
358 private JMenuItem justifyRightMenuItem = new JMenuItem();
360 JMenu autoAnnMenu = new JMenu();
362 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
364 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
366 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
368 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
370 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
372 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
374 protected JCheckBoxMenuItem showAutoFirst = new JCheckBoxMenuItem();
376 protected JCheckBoxMenuItem showAutoLast = new JCheckBoxMenuItem();
378 private JMenuItem grpsFromSelection = new JMenuItem();
380 private SequenceAnnotationOrder annotationSortOrder;
382 private boolean showAutoCalculatedAbove = false;
389 setJMenuBar(alignFrameMenuBar);
391 // dynamically fill save as menu with available formats
392 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
394 JMenuItem item = new JMenuItem(
395 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
397 item.addActionListener(new java.awt.event.ActionListener()
400 public void actionPerformed(ActionEvent e)
402 outputText_actionPerformed(e);
406 outputTextboxMenu.add(item);
408 } catch (Exception e)
410 System.err.println(e.toString());
413 if (!new jalview.util.Platform().isAMac())
415 closeMenuItem.setMnemonic('C');
416 outputTextboxMenu.setMnemonic('T');
417 undoMenuItem.setMnemonic('Z');
418 redoMenuItem.setMnemonic('0');
419 copy.setMnemonic('C');
420 cut.setMnemonic('U');
421 pasteMenu.setMnemonic('P');
422 reload.setMnemonic('R');
425 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
427 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
428 .getUserColourSchemes().keys();
430 while (userColours.hasMoreElements())
432 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
433 userColours.nextElement().toString());
434 radioItem.setName("USER_DEFINED");
435 radioItem.addMouseListener(new MouseAdapter()
438 public void mousePressed(MouseEvent evt)
440 if (evt.isControlDown()
441 || SwingUtilities.isRightMouseButton(evt))
443 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
445 int option = JOptionPane.showInternalConfirmDialog(
446 jalview.gui.Desktop.desktop,
448 .getString("label.remove_from_default_list"),
450 .getString("label.remove_user_defined_colour"),
451 JOptionPane.YES_NO_OPTION);
452 if (option == JOptionPane.YES_OPTION)
454 jalview.gui.UserDefinedColours
455 .removeColourFromDefaults(radioItem.getText());
456 colourMenu.remove(radioItem);
460 radioItem.addActionListener(new ActionListener()
463 public void actionPerformed(ActionEvent evt)
465 userDefinedColour_actionPerformed(evt);
472 radioItem.addActionListener(new ActionListener()
475 public void actionPerformed(ActionEvent evt)
477 userDefinedColour_actionPerformed(evt);
480 colourMenu.insert(radioItem, 15);
481 colours.add(radioItem);
484 colours.add(noColourmenuItem);
485 colours.add(clustalColour);
486 colours.add(zappoColour);
487 colours.add(taylorColour);
488 colours.add(hydrophobicityColour);
489 colours.add(helixColour);
490 colours.add(strandColour);
491 colours.add(turnColour);
492 colours.add(buriedColour);
493 colours.add(userDefinedColour);
494 colours.add(PIDColour);
495 colours.add(BLOSUM62Colour);
496 colours.add(nucleotideColour);
497 colours.add(purinePyrimidineColour);
498 // colours.add(covariationColour);
499 colours.add(tcoffeeColour);
500 colours.add(RNAInteractionColour);
501 setColourSelected(jalview.bin.Cache
502 .getDefault("DEFAULT_COLOUR", "None"));
506 public void setColourSelected(String defaultColour)
509 if (defaultColour != null)
511 int index = ColourSchemeProperty
512 .getColourIndexFromName(defaultColour);
516 case ColourSchemeProperty.CLUSTAL:
517 clustalColour.setSelected(true);
521 case ColourSchemeProperty.BLOSUM:
522 BLOSUM62Colour.setSelected(true);
526 case ColourSchemeProperty.PID:
527 PIDColour.setSelected(true);
531 case ColourSchemeProperty.ZAPPO:
532 zappoColour.setSelected(true);
536 case ColourSchemeProperty.TAYLOR:
537 taylorColour.setSelected(true);
540 case ColourSchemeProperty.HYDROPHOBIC:
541 hydrophobicityColour.setSelected(true);
545 case ColourSchemeProperty.HELIX:
546 helixColour.setSelected(true);
550 case ColourSchemeProperty.STRAND:
551 strandColour.setSelected(true);
555 case ColourSchemeProperty.TURN:
556 turnColour.setSelected(true);
560 case ColourSchemeProperty.BURIED:
561 buriedColour.setSelected(true);
565 case ColourSchemeProperty.NUCLEOTIDE:
566 nucleotideColour.setSelected(true);
570 case ColourSchemeProperty.TCOFFEE:
571 tcoffeeColour.setSelected(true);
574 case ColourSchemeProperty.PURINEPYRIMIDINE:
575 purinePyrimidineColour.setSelected(true);
579 case ColourSchemeProperty.RNAINTERACTION:
580 RNAInteractionColour.setSelected(true);
584 * case ColourSchemeProperty.COVARIATION:
585 * covariationColour.setSelected(true);
589 case ColourSchemeProperty.USER_DEFINED:
590 userDefinedColour.setSelected(true);
593 case ColourSchemeProperty.NONE:
595 noColourmenuItem.setSelected(true);
603 private void jbInit() throws Exception
605 fileMenu.setText(MessageManager.getString("action.file"));
606 saveAs.setText(MessageManager.getString("action.save_as") + "...");
607 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
608 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
609 .getMenuShortcutKeyMask()
610 | java.awt.event.KeyEvent.SHIFT_MASK, false));
611 saveAs.addActionListener(new ActionListener()
614 public void actionPerformed(ActionEvent e)
616 saveAs_actionPerformed(e);
619 closeMenuItem.setText(MessageManager.getString("action.close"));
620 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
621 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
622 .getMenuShortcutKeyMask(), false));
623 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
626 public void actionPerformed(ActionEvent e)
628 closeMenuItem_actionPerformed(false);
631 editMenu.setText(MessageManager.getString("action.edit"));
632 viewMenu.setText(MessageManager.getString("action.view"));
633 annotationsMenu.setText(MessageManager.getString("action.annotations"));
634 colourMenu.setText(MessageManager.getString("action.colour"));
635 calculateMenu.setText(MessageManager.getString("action.calculate"));
636 webService.setText(MessageManager.getString("action.web_service"));
637 selectAllSequenceMenuItem.setText(MessageManager
638 .getString("action.select_all"));
639 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
640 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
641 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
642 selectAllSequenceMenuItem
643 .addActionListener(new java.awt.event.ActionListener()
646 public void actionPerformed(ActionEvent e)
648 selectAllSequenceMenuItem_actionPerformed(e);
651 deselectAllSequenceMenuItem.setText(MessageManager
652 .getString("action.deselect_all"));
653 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
654 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
655 deselectAllSequenceMenuItem
656 .addActionListener(new java.awt.event.ActionListener()
659 public void actionPerformed(ActionEvent e)
661 deselectAllSequenceMenuItem_actionPerformed(e);
664 invertSequenceMenuItem.setText(MessageManager
665 .getString("action.invert_sequence_selection"));
666 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
667 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
668 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
669 invertSequenceMenuItem
670 .addActionListener(new java.awt.event.ActionListener()
673 public void actionPerformed(ActionEvent e)
675 invertSequenceMenuItem_actionPerformed(e);
678 grpsFromSelection.setText(MessageManager
679 .getString("action.make_groups_selection"));
680 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
683 public void actionPerformed(ActionEvent e)
685 makeGrpsFromSelection_actionPerformed(e);
688 expandAlignment.setText(MessageManager
689 .getString("action.view_flanking_regions"));
690 expandAlignment.setToolTipText(MessageManager
691 .getString("label.view_flanking_regions"));
692 expandAlignment.addActionListener(new java.awt.event.ActionListener()
695 public void actionPerformed(ActionEvent e)
700 remove2LeftMenuItem.setText(MessageManager
701 .getString("action.remove_left"));
702 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
703 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
704 .getMenuShortcutKeyMask(), false));
706 .addActionListener(new java.awt.event.ActionListener()
709 public void actionPerformed(ActionEvent e)
711 remove2LeftMenuItem_actionPerformed(e);
714 remove2RightMenuItem.setText(MessageManager
715 .getString("action.remove_right"));
716 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
717 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
718 .getMenuShortcutKeyMask(), false));
720 .addActionListener(new java.awt.event.ActionListener()
723 public void actionPerformed(ActionEvent e)
725 remove2RightMenuItem_actionPerformed(e);
728 removeGappedColumnMenuItem.setText(MessageManager
729 .getString("action.remove_empty_columns"));
730 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
731 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
732 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
733 removeGappedColumnMenuItem
734 .addActionListener(new java.awt.event.ActionListener()
737 public void actionPerformed(ActionEvent e)
739 removeGappedColumnMenuItem_actionPerformed(e);
742 removeAllGapsMenuItem.setText(MessageManager
743 .getString("action.remove_all_gaps"));
744 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
745 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
746 .getDefaultToolkit().getMenuShortcutKeyMask()
747 | java.awt.event.KeyEvent.SHIFT_MASK, false));
748 removeAllGapsMenuItem
749 .addActionListener(new java.awt.event.ActionListener()
752 public void actionPerformed(ActionEvent e)
754 removeAllGapsMenuItem_actionPerformed(e);
757 justifyLeftMenuItem.setText(MessageManager
758 .getString("action.left_justify_alignment"));
760 .addActionListener(new java.awt.event.ActionListener()
763 public void actionPerformed(ActionEvent e)
765 justifyLeftMenuItem_actionPerformed(e);
768 justifyRightMenuItem.setText(MessageManager
769 .getString("action.right_justify_alignment"));
771 .addActionListener(new java.awt.event.ActionListener()
774 public void actionPerformed(ActionEvent e)
776 justifyRightMenuItem_actionPerformed(e);
779 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
780 viewBoxesMenuItem.setState(true);
781 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
784 public void actionPerformed(ActionEvent e)
786 viewBoxesMenuItem_actionPerformed(e);
789 viewTextMenuItem.setText(MessageManager.getString("action.text"));
790 viewTextMenuItem.setState(true);
791 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
794 public void actionPerformed(ActionEvent e)
796 viewTextMenuItem_actionPerformed(e);
799 showNonconservedMenuItem.setText(MessageManager
800 .getString("label.show_non_conversed"));
801 showNonconservedMenuItem.setState(false);
802 showNonconservedMenuItem
803 .addActionListener(new java.awt.event.ActionListener()
806 public void actionPerformed(ActionEvent e)
808 showUnconservedMenuItem_actionPerformed(e);
811 sortPairwiseMenuItem.setText(MessageManager
812 .getString("action.by_pairwise_id"));
814 .addActionListener(new java.awt.event.ActionListener()
817 public void actionPerformed(ActionEvent e)
819 sortPairwiseMenuItem_actionPerformed(e);
822 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
823 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
826 public void actionPerformed(ActionEvent e)
828 sortIDMenuItem_actionPerformed(e);
832 .setText(MessageManager.getString("action.by_length"));
834 .addActionListener(new java.awt.event.ActionListener()
837 public void actionPerformed(ActionEvent e)
839 sortLengthMenuItem_actionPerformed(e);
842 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
843 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
846 public void actionPerformed(ActionEvent e)
848 sortGroupMenuItem_actionPerformed(e);
851 removeRedundancyMenuItem.setText(MessageManager
852 .getString("action.remove_redundancy").concat("..."));
853 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
854 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
855 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
856 removeRedundancyMenuItem
857 .addActionListener(new java.awt.event.ActionListener()
860 public void actionPerformed(ActionEvent e)
862 removeRedundancyMenuItem_actionPerformed(e);
865 pairwiseAlignmentMenuItem.setText(MessageManager
866 .getString("action.pairwise_alignment"));
867 pairwiseAlignmentMenuItem
868 .addActionListener(new java.awt.event.ActionListener()
871 public void actionPerformed(ActionEvent e)
873 pairwiseAlignmentMenuItem_actionPerformed(e);
876 PCAMenuItem.setText(MessageManager
877 .getString("label.principal_component_analysis"));
878 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
881 public void actionPerformed(ActionEvent e)
883 PCAMenuItem_actionPerformed(e);
886 averageDistanceTreeMenuItem.setText(MessageManager
887 .getString("label.average_distance_identity"));
888 averageDistanceTreeMenuItem
889 .addActionListener(new java.awt.event.ActionListener()
892 public void actionPerformed(ActionEvent e)
894 averageDistanceTreeMenuItem_actionPerformed(e);
897 neighbourTreeMenuItem.setText(MessageManager
898 .getString("label.neighbour_joining_identity"));
899 neighbourTreeMenuItem
900 .addActionListener(new java.awt.event.ActionListener()
903 public void actionPerformed(ActionEvent e)
905 neighbourTreeMenuItem_actionPerformed(e);
908 this.getContentPane().setLayout(borderLayout1);
909 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
910 statusBar.setBackground(Color.white);
911 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
912 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
913 statusBar.setText(MessageManager.getString("label.status_bar"));
914 outputTextboxMenu.setText(MessageManager
915 .getString("label.out_to_textbox"));
916 clustalColour.setText(MessageManager.getString("label.clustalx"));
918 clustalColour.addActionListener(new java.awt.event.ActionListener()
921 public void actionPerformed(ActionEvent e)
923 clustalColour_actionPerformed(e);
926 zappoColour.setText(MessageManager.getString("label.zappo"));
927 zappoColour.addActionListener(new java.awt.event.ActionListener()
930 public void actionPerformed(ActionEvent e)
932 zappoColour_actionPerformed(e);
935 taylorColour.setText(MessageManager.getString("label.taylor"));
936 taylorColour.addActionListener(new java.awt.event.ActionListener()
939 public void actionPerformed(ActionEvent e)
941 taylorColour_actionPerformed(e);
944 hydrophobicityColour.setText(MessageManager
945 .getString("label.hydrophobicity"));
947 .addActionListener(new java.awt.event.ActionListener()
950 public void actionPerformed(ActionEvent e)
952 hydrophobicityColour_actionPerformed(e);
955 helixColour.setText(MessageManager.getString("label.helix_propensity"));
956 helixColour.addActionListener(new java.awt.event.ActionListener()
959 public void actionPerformed(ActionEvent e)
961 helixColour_actionPerformed(e);
964 strandColour.setText(MessageManager
965 .getString("label.strand_propensity"));
966 strandColour.addActionListener(new java.awt.event.ActionListener()
969 public void actionPerformed(ActionEvent e)
971 strandColour_actionPerformed(e);
974 turnColour.setText(MessageManager.getString("label.turn_propensity"));
975 turnColour.addActionListener(new java.awt.event.ActionListener()
978 public void actionPerformed(ActionEvent e)
980 turnColour_actionPerformed(e);
983 buriedColour.setText(MessageManager.getString("label.buried_index"));
984 buriedColour.addActionListener(new java.awt.event.ActionListener()
987 public void actionPerformed(ActionEvent e)
989 buriedColour_actionPerformed(e);
992 userDefinedColour.setText(MessageManager
993 .getString("action.user_defined"));
994 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
997 public void actionPerformed(ActionEvent e)
999 userDefinedColour_actionPerformed(e);
1003 .setText(MessageManager.getString("label.percentage_identity"));
1004 PIDColour.addActionListener(new java.awt.event.ActionListener()
1007 public void actionPerformed(ActionEvent e)
1009 PIDColour_actionPerformed(e);
1013 .setText(MessageManager.getString("label.blosum62_score"));
1014 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1017 public void actionPerformed(ActionEvent e)
1019 BLOSUM62Colour_actionPerformed(e);
1022 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1023 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1026 public void actionPerformed(ActionEvent e)
1028 nucleotideColour_actionPerformed(e);
1032 purinePyrimidineColour.setText(MessageManager
1033 .getString("label.purine_pyrimidine"));
1034 purinePyrimidineColour
1035 .addActionListener(new java.awt.event.ActionListener()
1038 public void actionPerformed(ActionEvent e)
1040 purinePyrimidineColour_actionPerformed(e);
1044 RNAInteractionColour.setText("RNA Interaction type");
1045 RNAInteractionColour
1046 .addActionListener(new java.awt.event.ActionListener()
1049 public void actionPerformed(ActionEvent e)
1051 RNAInteractionColour_actionPerformed(e);
1055 * covariationColour.setText("Covariation");
1056 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1057 * public void actionPerformed(ActionEvent e) {
1058 * covariationColour_actionPerformed(e); } });
1061 avDistanceTreeBlosumMenuItem.setText(MessageManager
1062 .getString("label.average_distance_bloslum62"));
1063 avDistanceTreeBlosumMenuItem
1064 .addActionListener(new java.awt.event.ActionListener()
1067 public void actionPerformed(ActionEvent e)
1069 avTreeBlosumMenuItem_actionPerformed(e);
1072 njTreeBlosumMenuItem.setText(MessageManager
1073 .getString("label.neighbour_blosum62"));
1074 njTreeBlosumMenuItem
1075 .addActionListener(new java.awt.event.ActionListener()
1078 public void actionPerformed(ActionEvent e)
1080 njTreeBlosumMenuItem_actionPerformed(e);
1083 annotationPanelMenuItem.setActionCommand("");
1084 annotationPanelMenuItem.setText(MessageManager
1085 .getString("label.show_annotations"));
1086 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1088 annotationPanelMenuItem.addActionListener(new ActionListener()
1091 public void actionPerformed(ActionEvent e)
1093 annotationPanelMenuItem_actionPerformed(e);
1096 showAllAlAnnotations.setText(MessageManager
1097 .getString("label.show_all_al_annotations"));
1098 final boolean isAnnotationPanelShown = annotationPanelMenuItem
1100 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1101 showAllAlAnnotations.addActionListener(new ActionListener()
1104 public void actionPerformed(ActionEvent e)
1106 showAllAnnotations_actionPerformed(false, true);
1109 hideAllAlAnnotations.setText(MessageManager
1110 .getString("label.hide_all_al_annotations"));
1111 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1112 hideAllAlAnnotations.addActionListener(new ActionListener()
1115 public void actionPerformed(ActionEvent e)
1117 hideAllAnnotations_actionPerformed(false, true);
1120 showAllSeqAnnotations.setText(MessageManager
1121 .getString("label.show_all_seq_annotations"));
1122 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1123 showAllSeqAnnotations.addActionListener(new ActionListener()
1126 public void actionPerformed(ActionEvent e)
1128 showAllAnnotations_actionPerformed(true, false);
1131 hideAllSeqAnnotations.setText(MessageManager
1132 .getString("label.hide_all_seq_annotations"));
1133 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1134 hideAllSeqAnnotations.addActionListener(new ActionListener()
1137 public void actionPerformed(ActionEvent e)
1139 hideAllAnnotations_actionPerformed(true, false);
1142 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
1143 .valueOf(Cache.getDefault(Cache.SORT_ANNOTATIONS,
1144 SequenceAnnotationOrder.NONE.name()));
1145 sortAnnBySequence.setText(MessageManager
1146 .getString("label.sort_annotations_by_sequence"));
1148 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
1149 sortAnnBySequence.addActionListener(new ActionListener()
1152 public void actionPerformed(ActionEvent e)
1154 boolean newState = sortAnnBySequence.getState();
1155 sortAnnByLabel.setSelected(false);
1156 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
1157 : SequenceAnnotationOrder.NONE);
1158 sortAnnotations_actionPerformed();
1161 sortAnnByLabel.setText(MessageManager
1162 .getString("label.sort_annotations_by_label"));
1164 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
1165 sortAnnByLabel.addActionListener(new ActionListener()
1168 public void actionPerformed(ActionEvent e)
1170 boolean newState = sortAnnByLabel.getState();
1171 sortAnnBySequence.setSelected(false);
1172 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
1173 : SequenceAnnotationOrder.NONE);
1174 sortAnnotations_actionPerformed();
1177 colourTextMenuItem.setText(MessageManager
1178 .getString("label.colour_text"));
1180 .addActionListener(new java.awt.event.ActionListener()
1183 public void actionPerformed(ActionEvent e)
1185 colourTextMenuItem_actionPerformed(e);
1188 htmlMenuItem.setText(MessageManager.getString("label.html"));
1189 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1192 public void actionPerformed(ActionEvent e)
1194 htmlMenuItem_actionPerformed(e);
1197 overviewMenuItem.setText(MessageManager
1198 .getString("label.overview_window"));
1199 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1202 public void actionPerformed(ActionEvent e)
1204 overviewMenuItem_actionPerformed(e);
1207 undoMenuItem.setEnabled(false);
1208 undoMenuItem.setText(MessageManager.getString("action.undo"));
1209 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1210 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1211 .getMenuShortcutKeyMask(), false));
1212 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1215 public void actionPerformed(ActionEvent e)
1217 undoMenuItem_actionPerformed(e);
1220 redoMenuItem.setEnabled(false);
1221 redoMenuItem.setText(MessageManager.getString("action.redo"));
1222 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1223 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1224 .getMenuShortcutKeyMask(), false));
1225 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1228 public void actionPerformed(ActionEvent e)
1230 redoMenuItem_actionPerformed(e);
1233 conservationMenuItem.setText(MessageManager
1234 .getString("action.by_conservation"));
1235 conservationMenuItem
1236 .addActionListener(new java.awt.event.ActionListener()
1239 public void actionPerformed(ActionEvent e)
1241 conservationMenuItem_actionPerformed(e);
1244 noColourmenuItem.setText(MessageManager.getString("label.none"));
1245 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1248 public void actionPerformed(ActionEvent e)
1250 noColourmenuItem_actionPerformed(e);
1253 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1254 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1257 public void actionPerformed(ActionEvent e)
1259 wrapMenuItem_actionPerformed(e);
1262 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1263 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1264 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1265 .getMenuShortcutKeyMask(), false));
1266 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1269 public void actionPerformed(ActionEvent e)
1271 printMenuItem_actionPerformed(e);
1275 .setText(MessageManager.getString("action.show_gaps"));
1276 renderGapsMenuItem.setState(true);
1278 .addActionListener(new java.awt.event.ActionListener()
1281 public void actionPerformed(ActionEvent e)
1283 renderGapsMenuItem_actionPerformed(e);
1286 findMenuItem.setText(MessageManager.getString("action.find"));
1287 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1288 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1289 .getMenuShortcutKeyMask(), false));
1290 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1291 MessageManager.getString("label.find_tip")));
1292 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1295 public void actionPerformed(ActionEvent e)
1297 findMenuItem_actionPerformed(e);
1300 abovePIDThreshold.setText(MessageManager
1301 .getString("label.above_identity_threshold"));
1302 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1305 public void actionPerformed(ActionEvent e)
1307 abovePIDThreshold_actionPerformed(e);
1310 showSeqFeatures.setText(MessageManager
1311 .getString("label.show_sequence_features"));
1312 showSeqFeatures.addActionListener(new ActionListener()
1315 public void actionPerformed(ActionEvent actionEvent)
1317 showSeqFeatures_actionPerformed(actionEvent);
1321 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1322 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1323 * void actionPerformed(ActionEvent actionEvent) {
1324 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1326 showDbRefsMenuitem.setText(MessageManager
1327 .getString("label.show_database_refs"));
1328 showDbRefsMenuitem.addActionListener(new ActionListener()
1332 public void actionPerformed(ActionEvent e)
1334 showDbRefs_actionPerformed(e);
1338 showNpFeatsMenuitem.setText(MessageManager
1339 .getString("label.show_non_positional_features"));
1340 showNpFeatsMenuitem.addActionListener(new ActionListener()
1344 public void actionPerformed(ActionEvent e)
1346 showNpFeats_actionPerformed(e);
1350 showGroupConservation.setText(MessageManager
1351 .getString("label.group_conservation"));
1352 showGroupConservation.addActionListener(new ActionListener()
1356 public void actionPerformed(ActionEvent e)
1358 showGroupConservation_actionPerformed(e);
1363 showGroupConsensus.setText(MessageManager
1364 .getString("label.group_consensus"));
1365 showGroupConsensus.addActionListener(new ActionListener()
1369 public void actionPerformed(ActionEvent e)
1371 showGroupConsensus_actionPerformed(e);
1375 showConsensusHistogram.setText(MessageManager
1376 .getString("label.show_consensus_histogram"));
1377 showConsensusHistogram.addActionListener(new ActionListener()
1381 public void actionPerformed(ActionEvent e)
1383 showConsensusHistogram_actionPerformed(e);
1387 showSequenceLogo.setText(MessageManager
1388 .getString("label.show_consensus_logo"));
1389 showSequenceLogo.addActionListener(new ActionListener()
1393 public void actionPerformed(ActionEvent e)
1395 showSequenceLogo_actionPerformed(e);
1399 normaliseSequenceLogo.setText(MessageManager
1400 .getString("label.norm_consensus_logo"));
1401 normaliseSequenceLogo.addActionListener(new ActionListener()
1405 public void actionPerformed(ActionEvent e)
1407 normaliseSequenceLogo_actionPerformed(e);
1411 applyAutoAnnotationSettings.setText(MessageManager
1412 .getString("label.apply_all_groups"));
1413 applyAutoAnnotationSettings.setState(false);
1414 applyAutoAnnotationSettings.setVisible(true);
1415 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1418 public void actionPerformed(ActionEvent e)
1420 applyAutoAnnotationSettings_actionPerformed(e);
1424 showAutoFirst.setText(MessageManager.getString("label.show_first"));
1425 showAutoFirst.setState(Cache.getDefault(Cache.SHOW_AUTOCALC_ABOVE,
1427 showAutoFirst.addActionListener(new ActionListener()
1430 public void actionPerformed(ActionEvent e)
1432 boolean sortFirst = showAutoFirst.getState();
1433 setShowAutoCalculatedAbove(sortFirst);
1434 showAutoLast.setState(!sortFirst);
1435 sortAnnotations_actionPerformed();
1438 showAutoLast.setText(MessageManager.getString("label.show_last"));
1439 showAutoLast.setState(!showAutoFirst.getState());
1440 showAutoLast.addActionListener(new ActionListener()
1443 public void actionPerformed(ActionEvent e)
1445 boolean sortLast = showAutoLast.getState();
1446 setShowAutoCalculatedAbove(!sortLast);
1447 showAutoFirst.setState(!sortLast);
1448 sortAnnotations_actionPerformed();
1452 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1453 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1456 public void actionPerformed(ActionEvent e)
1458 nucleotideColour_actionPerformed(e);
1462 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1463 tcoffeeColour.setEnabled(false);
1464 tcoffeeColour.addActionListener(new ActionListener()
1468 public void actionPerformed(ActionEvent e)
1470 tcoffeeColorScheme_actionPerformed(e);
1475 .setText(MessageManager.getString("action.undefine_groups"));
1476 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1477 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1478 .getMenuShortcutKeyMask(), false));
1479 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1482 public void actionPerformed(ActionEvent e)
1484 deleteGroups_actionPerformed(e);
1487 createGroup.setText(MessageManager.getString("action.create_groups"));
1488 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1489 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1490 .getMenuShortcutKeyMask(), false));
1491 createGroup.addActionListener(new java.awt.event.ActionListener()
1494 public void actionPerformed(ActionEvent e)
1496 createGroup_actionPerformed(e);
1499 unGroup.setText(MessageManager.getString("action.remove_group"));
1500 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1501 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1502 .getMenuShortcutKeyMask()
1503 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1504 unGroup.addActionListener(new java.awt.event.ActionListener()
1507 public void actionPerformed(ActionEvent e)
1509 unGroup_actionPerformed(e);
1512 copy.setText(MessageManager.getString("action.copy"));
1513 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1514 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1515 .getMenuShortcutKeyMask(), false));
1517 copy.addActionListener(new java.awt.event.ActionListener()
1520 public void actionPerformed(ActionEvent e)
1522 copy_actionPerformed(e);
1525 cut.setText(MessageManager.getString("action.cut"));
1526 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1527 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1528 .getMenuShortcutKeyMask(), false));
1529 cut.addActionListener(new java.awt.event.ActionListener()
1532 public void actionPerformed(ActionEvent e)
1534 cut_actionPerformed(e);
1537 delete.setText(MessageManager.getString("action.delete"));
1538 delete.addActionListener(new java.awt.event.ActionListener()
1541 public void actionPerformed(ActionEvent e)
1543 delete_actionPerformed(e);
1546 pasteMenu.setText(MessageManager.getString("action.paste"));
1547 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1548 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1549 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1550 .getMenuShortcutKeyMask()
1551 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1552 pasteNew.addActionListener(new java.awt.event.ActionListener()
1555 public void actionPerformed(ActionEvent e)
1557 pasteNew_actionPerformed(e);
1560 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1561 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1562 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1563 .getMenuShortcutKeyMask(), false));
1564 pasteThis.addActionListener(new java.awt.event.ActionListener()
1567 public void actionPerformed(ActionEvent e)
1569 pasteThis_actionPerformed(e);
1572 applyToAllGroups.setText(MessageManager
1573 .getString("label.apply_colour_to_all_groups"));
1574 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1577 public void actionPerformed(ActionEvent e)
1579 applyToAllGroups_actionPerformed(e);
1582 createPNG.addActionListener(new java.awt.event.ActionListener()
1585 public void actionPerformed(ActionEvent e)
1590 createPNG.setActionCommand(MessageManager
1591 .getString("label.save_png_image"));
1592 createPNG.setText("PNG");
1593 font.setText(MessageManager.getString("action.font"));
1594 font.addActionListener(new java.awt.event.ActionListener()
1597 public void actionPerformed(ActionEvent e)
1599 font_actionPerformed(e);
1603 seqLimits.setText(MessageManager
1604 .getString("label.show_sequence_limits"));
1605 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1606 seqLimits.addActionListener(new java.awt.event.ActionListener()
1609 public void actionPerformed(ActionEvent e)
1611 seqLimit_actionPerformed(e);
1614 epsFile.setText("EPS");
1615 epsFile.addActionListener(new java.awt.event.ActionListener()
1618 public void actionPerformed(ActionEvent e)
1623 LoadtreeMenuItem.setActionCommand(MessageManager
1624 .getString("label.load_tree_for_sequence_set"));
1625 LoadtreeMenuItem.setText(MessageManager
1626 .getString("label.load_associated_tree"));
1627 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1630 public void actionPerformed(ActionEvent e)
1632 LoadtreeMenuItem_actionPerformed(e);
1636 scaleAbove.setVisible(false);
1637 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1638 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1641 public void actionPerformed(ActionEvent e)
1643 scaleAbove_actionPerformed(e);
1646 scaleLeft.setVisible(false);
1647 scaleLeft.setSelected(true);
1648 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1649 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1652 public void actionPerformed(ActionEvent e)
1654 scaleLeft_actionPerformed(e);
1657 scaleRight.setVisible(false);
1658 scaleRight.setSelected(true);
1659 scaleRight.setText(MessageManager.getString("action.scale_right"));
1660 scaleRight.addActionListener(new java.awt.event.ActionListener()
1663 public void actionPerformed(ActionEvent e)
1665 scaleRight_actionPerformed(e);
1668 centreColumnLabelsMenuItem.setVisible(true);
1669 centreColumnLabelsMenuItem.setState(false);
1670 centreColumnLabelsMenuItem.setText(MessageManager
1671 .getString("label.centre_column_labels"));
1672 centreColumnLabelsMenuItem
1673 .addActionListener(new java.awt.event.ActionListener()
1676 public void actionPerformed(ActionEvent e)
1678 centreColumnLabels_actionPerformed(e);
1681 followHighlightMenuItem.setVisible(true);
1682 followHighlightMenuItem.setState(true);
1683 followHighlightMenuItem.setText(MessageManager
1684 .getString("label.automatic_scrolling"));
1685 followHighlightMenuItem.addActionListener(new ActionListener()
1689 public void actionPerformed(ActionEvent e)
1691 followHighlight_actionPerformed();
1696 modifyPID.setText(MessageManager
1697 .getString("label.modify_identity_thereshold"));
1698 modifyPID.addActionListener(new java.awt.event.ActionListener()
1701 public void actionPerformed(ActionEvent e)
1703 modifyPID_actionPerformed(e);
1706 modifyConservation.setText(MessageManager
1707 .getString("label.modify_conservation_thereshold"));
1709 .addActionListener(new java.awt.event.ActionListener()
1712 public void actionPerformed(ActionEvent e)
1714 modifyConservation_actionPerformed(e);
1718 .setText(MessageManager.getString("action.by_tree_order"));
1719 sort.setText(MessageManager.getString("action.sort"));
1720 sort.addMenuListener(new MenuListener()
1723 public void menuSelected(MenuEvent e)
1729 public void menuDeselected(MenuEvent e)
1734 public void menuCanceled(MenuEvent e)
1738 sortByAnnotScore.setText(MessageManager
1739 .getString("label.sort_by_score"));
1740 sort.add(sortByAnnotScore);
1741 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1745 public void menuCanceled(MenuEvent e)
1750 public void menuDeselected(MenuEvent e)
1755 public void menuSelected(MenuEvent e)
1757 buildSortByAnnotationScoresMenu();
1760 sortByAnnotScore.setVisible(false);
1763 .setText(MessageManager.getString("action.calculate_tree"));
1765 jMenu2.setText(MessageManager.getString("label.export_image"));
1766 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1767 padGapsMenuitem.setState(jalview.bin.Cache
1768 .getDefault("PAD_GAPS", false));
1769 padGapsMenuitem.addActionListener(new ActionListener()
1772 public void actionPerformed(ActionEvent e)
1774 padGapsMenuitem_actionPerformed(e);
1777 vamsasStore.setVisible(false);
1778 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1779 vamsasStore.addActionListener(new ActionListener()
1782 public void actionPerformed(ActionEvent e)
1784 vamsasStore_actionPerformed(e);
1787 showTranslation.setText(MessageManager
1788 .getString("label.translate_cDNA"));
1789 showTranslation.addActionListener(new ActionListener()
1792 public void actionPerformed(ActionEvent e)
1794 showTranslation_actionPerformed(e);
1797 extractScores.setText(MessageManager.getString("label.extract_scores")
1799 extractScores.addActionListener(new ActionListener()
1802 public void actionPerformed(ActionEvent e)
1804 extractScores_actionPerformed(e);
1807 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1809 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1811 * showProducts.addActionListener(new ActionListener() {
1813 * public void actionPerformed(ActionEvent e) {
1814 * showProducts_actionPerformed(e); } });
1816 openFeatureSettings.setText(MessageManager
1817 .getString("label.feature_settings"));
1818 openFeatureSettings.addActionListener(new ActionListener()
1821 public void actionPerformed(ActionEvent e)
1823 featureSettings_actionPerformed(e);
1827 .setText(MessageManager.getString("label.fetch_sequences"));
1828 fetchSequence.addActionListener(new ActionListener()
1831 public void actionPerformed(ActionEvent e)
1833 fetchSequence_actionPerformed(e);
1837 annotationColour.setText(MessageManager
1838 .getString("action.by_annotation"));
1839 annotationColour.addActionListener(new ActionListener()
1842 public void actionPerformed(ActionEvent e)
1844 annotationColour_actionPerformed(e);
1848 rnahelicesColour.setText(MessageManager
1849 .getString("action.by_rna_helixes"));
1850 rnahelicesColour.addActionListener(new ActionListener()
1853 public void actionPerformed(ActionEvent e)
1855 rnahelicesColour_actionPerformed(e);
1859 associatedData.setText(MessageManager
1860 .getString("label.load_features_annotations"));
1861 associatedData.addActionListener(new ActionListener()
1864 public void actionPerformed(ActionEvent e)
1866 associatedData_actionPerformed(e);
1869 autoCalculate.setText(MessageManager
1870 .getString("label.autocalculate_consensus"));
1871 autoCalculate.setState(jalview.bin.Cache.getDefault(
1872 "AUTO_CALC_CONSENSUS", true));
1873 autoCalculate.addActionListener(new ActionListener()
1876 public void actionPerformed(ActionEvent e)
1878 autoCalculate_actionPerformed(e);
1881 sortByTree.setText(MessageManager
1882 .getString("label.sort_alignment_new_tree"));
1884 .setToolTipText("<html>"
1886 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1888 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1889 sortByTree.addActionListener(new ActionListener()
1892 public void actionPerformed(ActionEvent e)
1894 sortByTreeOption_actionPerformed(e);
1898 listenToViewSelections.setText(MessageManager
1899 .getString("label.listen_for_selections"));
1900 listenToViewSelections
1901 .setToolTipText("<html>"
1903 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1904 listenToViewSelections.setState(false);
1905 listenToViewSelections.addActionListener(new ActionListener()
1908 public void actionPerformed(ActionEvent e)
1910 listenToViewSelections_actionPerformed(e);
1915 .setText(MessageManager.getString("label.add_sequences"));
1916 addFromFile.setText(MessageManager.getString("label.from_file"));
1917 addFromFile.addActionListener(new ActionListener()
1920 public void actionPerformed(ActionEvent e)
1922 addFromFile_actionPerformed(e);
1925 addFromText.setText(MessageManager.getString("label.from_textbox"));
1926 addFromText.addActionListener(new ActionListener()
1929 public void actionPerformed(ActionEvent e)
1931 addFromText_actionPerformed(e);
1934 addFromURL.setText(MessageManager.getString("label.from_url"));
1935 addFromURL.addActionListener(new ActionListener()
1938 public void actionPerformed(ActionEvent e)
1940 addFromURL_actionPerformed(e);
1943 exportFeatures.setText(MessageManager
1944 .getString("label.export_features"));
1945 exportFeatures.addActionListener(new ActionListener()
1948 public void actionPerformed(ActionEvent e)
1950 exportFeatures_actionPerformed(e);
1953 exportAnnotations.setText(MessageManager
1954 .getString("label.export_annotations"));
1955 exportAnnotations.addActionListener(new ActionListener()
1958 public void actionPerformed(ActionEvent e)
1960 exportAnnotations_actionPerformed(e);
1963 statusPanel.setLayout(gridLayout1);
1964 jMenu3.setText(MessageManager.getString("action.show"));
1965 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1966 showAllSeqs.setToolTipText(MessageManager
1967 .getString("label.toggle_sequence_visibility"));
1968 showAllSeqs.addActionListener(new ActionListener()
1971 public void actionPerformed(ActionEvent e)
1973 showAllSeqs_actionPerformed(e);
1976 showAllColumns.setText(MessageManager.getString("label.all_columns"));
1977 showAllColumns.setToolTipText(MessageManager
1978 .getString("label.toggle_columns_visibility"));
1979 showAllColumns.addActionListener(new ActionListener()
1982 public void actionPerformed(ActionEvent e)
1984 showAllColumns_actionPerformed(e);
1987 hideMenu.setText(MessageManager.getString("action.hide"));
1988 hideSelSequences.setText(MessageManager
1989 .getString("label.selected_sequences"));
1990 hideSelSequences.setToolTipText(MessageManager
1991 .getString("label.toggle_sequence_visibility"));
1992 hideSelSequences.addActionListener(new ActionListener()
1995 public void actionPerformed(ActionEvent e)
1997 hideSelSequences_actionPerformed(e);
2000 hideSelColumns.setText(MessageManager
2001 .getString("label.selected_columns"));
2002 hideSelColumns.setToolTipText(MessageManager
2003 .getString("label.toggle_columns_visibility"));
2004 hideSelColumns.addActionListener(new ActionListener()
2007 public void actionPerformed(ActionEvent e)
2009 hideSelColumns_actionPerformed(e);
2012 hideAllSelection.setText(MessageManager
2013 .getString("label.selected_region"));
2014 hideAllSelection.addActionListener(new ActionListener()
2017 public void actionPerformed(ActionEvent e)
2019 hideAllSelection_actionPerformed(e);
2022 // TODO: should be hidden if no selection exists.
2023 hideAllButSelection.setText(MessageManager
2024 .getString("label.all_but_selected_region"));
2025 hideAllButSelection.addActionListener(new ActionListener()
2028 public void actionPerformed(ActionEvent e)
2030 hideAllButSelection_actionPerformed(e);
2033 showAllhidden.setText(MessageManager
2034 .getString("label.all_sequences_columns"));
2035 showAllhidden.setToolTipText(MessageManager
2036 .getString("label.toggles_visibility_hidden_selected_regions"));
2037 showAllhidden.addActionListener(new ActionListener()
2040 public void actionPerformed(ActionEvent e)
2042 showAllhidden_actionPerformed(e);
2045 hiddenMarkers.setText(MessageManager
2046 .getString("action.show_hidden_markers"));
2047 hiddenMarkers.addActionListener(new ActionListener()
2050 public void actionPerformed(ActionEvent e)
2052 hiddenMarkers_actionPerformed(e);
2055 invertColSel.setText(MessageManager
2056 .getString("action.invert_column_selection"));
2057 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2058 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
2059 .getMenuShortcutKeyMask()
2060 | java.awt.event.KeyEvent.ALT_MASK, false));
2061 invertColSel.addActionListener(new ActionListener()
2064 public void actionPerformed(ActionEvent e)
2066 invertColSel_actionPerformed(e);
2069 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
2072 public void stateChanged(ChangeEvent evt)
2074 JTabbedPane pane = (JTabbedPane) evt.getSource();
2075 int sel = pane.getSelectedIndex();
2076 tabSelectionChanged(sel);
2079 tabbedPane.addMouseListener(new MouseAdapter()
2082 public void mousePressed(MouseEvent e)
2084 tabbedPane_mousePressed(e);
2087 tabbedPane.addFocusListener(new FocusAdapter()
2090 public void focusGained(FocusEvent e)
2092 tabbedPane_focusGained(e);
2095 save.setText(MessageManager.getString("action.save"));
2096 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2097 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
2098 .getMenuShortcutKeyMask(), false));
2099 save.addActionListener(new ActionListener()
2102 public void actionPerformed(ActionEvent e)
2104 save_actionPerformed(e);
2107 reload.setEnabled(false);
2108 reload.setText(MessageManager.getString("action.reload"));
2109 reload.addActionListener(new ActionListener()
2112 public void actionPerformed(ActionEvent e)
2114 reload_actionPerformed(e);
2117 newView.setText(MessageManager.getString("action.new_view"));
2118 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2119 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2120 .getMenuShortcutKeyMask(), false));
2121 newView.addActionListener(new ActionListener()
2124 public void actionPerformed(ActionEvent e)
2126 newView_actionPerformed(e);
2129 tabbedPane.setToolTipText("<html><i>"
2130 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2132 textColour.setText(MessageManager.getString("label.colour_text")
2134 textColour.addActionListener(new ActionListener()
2137 public void actionPerformed(ActionEvent e)
2139 textColour_actionPerformed(e);
2142 formatMenu.setText(MessageManager.getString("action.format"));
2143 selectMenu.setText(MessageManager.getString("action.select"));
2144 idRightAlign.setText(MessageManager
2145 .getString("label.right_align_sequence_id"));
2146 idRightAlign.addActionListener(new ActionListener()
2149 public void actionPerformed(ActionEvent e)
2151 idRightAlign_actionPerformed(e);
2154 gatherViews.setEnabled(false);
2155 gatherViews.setText(MessageManager.getString("action.gather_views"));
2156 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2157 java.awt.event.KeyEvent.VK_G, 0, false));
2158 gatherViews.addActionListener(new ActionListener()
2161 public void actionPerformed(ActionEvent e)
2163 gatherViews_actionPerformed(e);
2166 expandViews.setEnabled(false);
2167 expandViews.setText(MessageManager.getString("action.expand_views"));
2168 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2169 java.awt.event.KeyEvent.VK_X, 0, false));
2170 expandViews.addActionListener(new ActionListener()
2173 public void actionPerformed(ActionEvent e)
2175 expandViews_actionPerformed(e);
2179 .setText(MessageManager.getString("action.page_setup") + "...");
2180 pageSetup.addActionListener(new ActionListener()
2183 public void actionPerformed(ActionEvent e)
2185 pageSetup_actionPerformed(e);
2188 alignmentProperties.setText(MessageManager
2189 .getString("label.alignment_props") + "...");
2190 alignmentProperties.addActionListener(new ActionListener()
2193 public void actionPerformed(ActionEvent actionEvent)
2195 alignmentProperties();
2198 tooltipSettingsMenu.setText(MessageManager
2199 .getString("label.sequence_id_tooltip"));
2200 autoAnnMenu.setText(MessageManager
2201 .getString("label.autocalculated_annotation"));
2202 alignFrameMenuBar.add(fileMenu);
2203 alignFrameMenuBar.add(editMenu);
2204 alignFrameMenuBar.add(selectMenu);
2205 alignFrameMenuBar.add(viewMenu);
2206 alignFrameMenuBar.add(annotationsMenu);
2207 alignFrameMenuBar.add(formatMenu);
2208 alignFrameMenuBar.add(colourMenu);
2209 alignFrameMenuBar.add(calculateMenu);
2210 alignFrameMenuBar.add(webService);
2211 fileMenu.add(fetchSequence);
2212 fileMenu.add(addSequenceMenu);
2213 fileMenu.add(reload);
2214 fileMenu.addSeparator();
2215 fileMenu.add(vamsasStore);
2217 fileMenu.add(saveAs);
2218 fileMenu.add(outputTextboxMenu);
2219 fileMenu.add(pageSetup);
2220 fileMenu.add(printMenuItem);
2221 fileMenu.addSeparator();
2222 fileMenu.add(jMenu2);
2223 fileMenu.add(exportFeatures);
2224 fileMenu.add(exportAnnotations);
2225 fileMenu.add(LoadtreeMenuItem);
2226 fileMenu.add(associatedData);
2227 fileMenu.addSeparator();
2228 fileMenu.add(closeMenuItem);
2229 editMenu.add(undoMenuItem);
2230 editMenu.add(redoMenuItem);
2233 editMenu.add(pasteMenu);
2234 editMenu.add(delete);
2235 editMenu.addSeparator();
2236 editMenu.add(remove2LeftMenuItem);
2237 editMenu.add(remove2RightMenuItem);
2238 editMenu.add(removeGappedColumnMenuItem);
2239 editMenu.add(removeAllGapsMenuItem);
2240 editMenu.add(removeRedundancyMenuItem);
2241 editMenu.addSeparator();
2242 // dont add these yet in the CVS build - they cannot be undone!
2243 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2244 // editMenu.add(justifyLeftMenuItem);
2245 // editMenu.add(justifyRightMenuItem);
2246 // editMenu.addSeparator();
2247 editMenu.add(padGapsMenuitem);
2248 viewMenu.add(newView);
2249 viewMenu.add(expandViews);
2250 viewMenu.add(gatherViews);
2251 viewMenu.addSeparator();
2252 viewMenu.add(jMenu3);
2253 viewMenu.add(hideMenu);
2254 viewMenu.addSeparator();
2255 viewMenu.add(followHighlightMenuItem);
2256 annotationsMenu.add(annotationPanelMenuItem);
2257 annotationsMenu.addSeparator();
2258 annotationsMenu.add(showAllAlAnnotations);
2259 annotationsMenu.add(hideAllAlAnnotations);
2260 annotationsMenu.addSeparator();
2261 annotationsMenu.add(showAllSeqAnnotations);
2262 annotationsMenu.add(hideAllSeqAnnotations);
2263 annotationsMenu.add(sortAnnBySequence);
2264 annotationsMenu.add(sortAnnByLabel);
2265 annotationsMenu.addSeparator();
2266 autoAnnMenu.add(showAutoFirst);
2267 autoAnnMenu.add(showAutoLast);
2268 autoAnnMenu.addSeparator();
2269 autoAnnMenu.add(applyAutoAnnotationSettings);
2270 autoAnnMenu.add(showConsensusHistogram);
2271 autoAnnMenu.add(showSequenceLogo);
2272 autoAnnMenu.add(normaliseSequenceLogo);
2273 autoAnnMenu.addSeparator();
2274 autoAnnMenu.add(showGroupConservation);
2275 autoAnnMenu.add(showGroupConsensus);
2276 annotationsMenu.add(autoAnnMenu);
2277 viewMenu.addSeparator();
2278 viewMenu.add(showSeqFeatures);
2279 // viewMenu.add(showSeqFeaturesHeight);
2281 viewMenu.add(openFeatureSettings);
2282 tooltipSettingsMenu.add(showDbRefsMenuitem);
2283 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2284 viewMenu.add(tooltipSettingsMenu);
2285 viewMenu.addSeparator();
2286 viewMenu.add(alignmentProperties);
2287 viewMenu.addSeparator();
2288 viewMenu.add(overviewMenuItem);
2289 colourMenu.add(applyToAllGroups);
2290 colourMenu.add(textColour);
2291 colourMenu.addSeparator();
2292 colourMenu.add(noColourmenuItem);
2293 colourMenu.add(clustalColour);
2294 colourMenu.add(BLOSUM62Colour);
2295 colourMenu.add(PIDColour);
2296 colourMenu.add(zappoColour);
2297 colourMenu.add(taylorColour);
2298 colourMenu.add(hydrophobicityColour);
2299 colourMenu.add(helixColour);
2300 colourMenu.add(strandColour);
2301 colourMenu.add(turnColour);
2302 colourMenu.add(buriedColour);
2303 colourMenu.add(nucleotideColour);
2304 colourMenu.add(purinePyrimidineColour);
2305 colourMenu.add(RNAInteractionColour);
2306 // colourMenu.add(covariationColour);
2307 colourMenu.add(tcoffeeColour);
2308 colourMenu.add(userDefinedColour);
2309 colourMenu.addSeparator();
2310 colourMenu.add(conservationMenuItem);
2311 colourMenu.add(modifyConservation);
2312 colourMenu.add(abovePIDThreshold);
2313 colourMenu.add(modifyPID);
2314 colourMenu.add(annotationColour);
2315 colourMenu.add(rnahelicesColour);
2316 calculateMenu.add(sort);
2317 calculateMenu.add(calculateTree);
2318 calculateMenu.addSeparator();
2319 calculateMenu.add(pairwiseAlignmentMenuItem);
2320 calculateMenu.add(PCAMenuItem);
2321 calculateMenu.addSeparator();
2322 calculateMenu.add(showTranslation);
2323 calculateMenu.add(showProducts);
2324 calculateMenu.add(autoCalculate);
2325 calculateMenu.add(sortByTree);
2326 calculateMenu.addSeparator();
2327 calculateMenu.add(extractScores);
2328 webServiceNoServices = new JMenuItem(
2329 MessageManager.getString("label.no_services"));
2330 webService.add(webServiceNoServices);
2331 pasteMenu.add(pasteNew);
2332 pasteMenu.add(pasteThis);
2333 sort.add(sortIDMenuItem);
2334 sort.add(sortLengthMenuItem);
2335 sort.add(sortGroupMenuItem);
2336 sort.add(sortPairwiseMenuItem);
2337 sort.add(sortByTreeMenu);
2338 jMenu2.add(htmlMenuItem);
2339 jMenu2.add(epsFile);
2340 jMenu2.add(createPNG);
2341 addSequenceMenu.add(addFromFile);
2342 addSequenceMenu.add(addFromText);
2343 addSequenceMenu.add(addFromURL);
2344 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2345 statusPanel.add(statusBar, null);
2346 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2347 jMenu3.add(showAllColumns);
2348 jMenu3.add(showAllSeqs);
2349 jMenu3.add(showAllhidden);
2350 hideMenu.add(hideSelColumns);
2351 hideMenu.add(hideSelSequences);
2352 hideMenu.add(hideAllSelection);
2353 hideMenu.add(hideAllButSelection);
2355 formatMenu.add(font);
2356 formatMenu.addSeparator();
2357 formatMenu.add(wrapMenuItem);
2358 formatMenu.add(scaleAbove);
2359 formatMenu.add(scaleLeft);
2360 formatMenu.add(scaleRight);
2361 formatMenu.add(seqLimits);
2362 formatMenu.add(idRightAlign);
2363 formatMenu.add(hiddenMarkers);
2364 formatMenu.add(viewBoxesMenuItem);
2365 formatMenu.add(viewTextMenuItem);
2366 formatMenu.add(colourTextMenuItem);
2367 formatMenu.add(renderGapsMenuItem);
2368 formatMenu.add(centreColumnLabelsMenuItem);
2369 formatMenu.add(showNonconservedMenuItem);
2370 selectMenu.add(findMenuItem);
2371 selectMenu.addSeparator();
2372 selectMenu.add(selectAllSequenceMenuItem);
2373 selectMenu.add(deselectAllSequenceMenuItem);
2374 selectMenu.add(invertSequenceMenuItem);
2375 selectMenu.add(invertColSel);
2376 selectMenu.add(createGroup);
2377 selectMenu.add(unGroup);
2378 selectMenu.add(grpsFromSelection);
2379 selectMenu.add(deleteGroups);
2380 calculateMenu.add(expandAlignment);
2381 // TODO - determine if the listenToViewSelections button is needed : see bug
2383 // selectMenu.addSeparator();
2384 // selectMenu.add(listenToViewSelections);
2388 * Action on clicking sort annotations by type.
2392 protected void sortAnnotations_actionPerformed()
2397 * Action on clicking Show all annotations.
2399 * @param forSequences
2400 * update sequence-related annotations
2401 * @param forAlignment
2402 * update non-sequence-related annotations
2404 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2405 boolean forAlignment)
2407 setAnnotationsVisibility(true, forSequences, forAlignment);
2411 * Action on clicking Hide all annotations.
2413 * @param forSequences
2414 * update sequence-related annotations
2415 * @param forAlignment
2416 * update non-sequence-related annotations
2418 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2419 boolean forAlignment)
2421 setAnnotationsVisibility(false, forSequences, forAlignment);
2425 * Set the visibility of annotations to true or false. Can act on
2426 * sequence-related annotations, or alignment-related, or both.
2429 * @param forSequences
2430 * update sequence-related annotations
2431 * @param forAlignment
2432 * update non-sequence-related annotations
2434 protected void setAnnotationsVisibility(boolean visible,
2435 boolean forSequences, boolean forAlignment)
2440 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2442 // TODO Auto-generated method stub
2446 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2448 // TODO Auto-generated method stub
2452 protected void showAllhidden_actionPerformed(ActionEvent e)
2454 // TODO Auto-generated method stub
2458 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2460 // TODO Auto-generated method stub
2464 protected void hideAllSelection_actionPerformed(ActionEvent e)
2466 // TODO Auto-generated method stub
2470 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2472 // TODO Auto-generated method stub
2476 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2478 // TODO Auto-generated method stub
2482 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2484 // TODO Auto-generated method stub
2488 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2490 // TODO Auto-generated method stub
2494 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2496 // TODO Auto-generated method stub
2500 protected void showGroupConservation_actionPerformed(ActionEvent e)
2502 // TODO Auto-generated method stub
2506 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2508 // TODO Auto-generated method stub
2512 protected void showSeqFeaturesHeight_actionPerformed(
2513 ActionEvent actionEvent)
2515 // TODO Auto-generated method stub
2519 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2521 // TODO Auto-generated method stub
2525 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2527 // TODO Auto-generated method stub
2531 protected void followHighlight_actionPerformed()
2533 // TODO Auto-generated method stub
2537 protected void showNpFeats_actionPerformed(ActionEvent e)
2539 // TODO Auto-generated method stub
2543 protected void showDbRefs_actionPerformed(ActionEvent e)
2545 // TODO Auto-generated method stub
2549 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2553 protected void showProducts_actionPerformed(ActionEvent e)
2557 protected void buildSortByAnnotationScoresMenu()
2561 protected void extractScores_actionPerformed(ActionEvent e)
2565 protected void outputText_actionPerformed(ActionEvent e)
2569 public void addFromFile_actionPerformed(ActionEvent e)
2574 public void addFromText_actionPerformed(ActionEvent e)
2579 public void addFromURL_actionPerformed(ActionEvent e)
2584 public void exportFeatures_actionPerformed(ActionEvent e)
2589 public void exportAnnotations_actionPerformed(ActionEvent e)
2594 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2598 protected void closeMenuItem_actionPerformed(boolean b)
2602 protected void redoMenuItem_actionPerformed(ActionEvent e)
2606 protected void undoMenuItem_actionPerformed(ActionEvent e)
2610 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2614 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2618 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2622 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2626 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2630 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2634 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2638 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2642 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2646 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2650 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2654 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2658 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2662 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2666 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2670 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2674 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2678 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2682 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2686 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2690 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2694 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2698 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2702 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2706 protected void clustalColour_actionPerformed(ActionEvent e)
2710 protected void zappoColour_actionPerformed(ActionEvent e)
2714 protected void taylorColour_actionPerformed(ActionEvent e)
2718 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2722 protected void helixColour_actionPerformed(ActionEvent e)
2726 protected void strandColour_actionPerformed(ActionEvent e)
2730 protected void turnColour_actionPerformed(ActionEvent e)
2734 protected void buriedColour_actionPerformed(ActionEvent e)
2738 protected void userDefinedColour_actionPerformed(ActionEvent e)
2742 protected void PIDColour_actionPerformed(ActionEvent e)
2746 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2750 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2754 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2759 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2762 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2766 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2770 protected void printMenuItem_actionPerformed(ActionEvent e)
2774 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2778 protected void findMenuItem_actionPerformed(ActionEvent e)
2782 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2786 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2790 protected void nucleotideColour_actionPerformed(ActionEvent e)
2794 protected void deleteGroups_actionPerformed(ActionEvent e)
2798 protected void createGroup_actionPerformed(ActionEvent e)
2802 protected void unGroup_actionPerformed(ActionEvent e)
2806 protected void copy_actionPerformed(ActionEvent e)
2810 protected void cut_actionPerformed(ActionEvent e)
2814 protected void delete_actionPerformed(ActionEvent e)
2818 protected void pasteNew_actionPerformed(ActionEvent e)
2822 protected void pasteThis_actionPerformed(ActionEvent e)
2826 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2830 public void createPNG(java.io.File f)
2834 protected void font_actionPerformed(ActionEvent e)
2838 protected void seqLimit_actionPerformed(ActionEvent e)
2842 public void seqDBRef_actionPerformed(ActionEvent e)
2847 public void createEPS(java.io.File f)
2851 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2857 * Template method to handle the 'load T-Coffee scores' menu event.
2859 * Subclasses override this method to provide a custom action.
2864 protected void loadScores_actionPerformed(ActionEvent event)
2870 * Template method to handle the 'Color T-Coffee scores' menu event.
2872 * Subclasses override this method to provide a custom action.
2877 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2882 protected void jpred_actionPerformed(ActionEvent e)
2886 protected void scaleAbove_actionPerformed(ActionEvent e)
2890 protected void scaleLeft_actionPerformed(ActionEvent e)
2894 protected void scaleRight_actionPerformed(ActionEvent e)
2898 protected void modifyPID_actionPerformed(ActionEvent e)
2902 protected void modifyConservation_actionPerformed(ActionEvent e)
2906 protected void saveAs_actionPerformed(ActionEvent e)
2910 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2914 public void vamsasStore_actionPerformed(ActionEvent e)
2919 public void vamsasLoad_actionPerformed(ActionEvent e)
2924 public void showTranslation_actionPerformed(ActionEvent e)
2929 public void featureSettings_actionPerformed(ActionEvent e)
2934 public void fetchSequence_actionPerformed(ActionEvent e)
2939 public void smoothFont_actionPerformed(ActionEvent e)
2944 public void annotationColour_actionPerformed(ActionEvent e)
2949 public void rnahelicesColour_actionPerformed(ActionEvent e)
2954 public void associatedData_actionPerformed(ActionEvent e)
2959 public void autoCalculate_actionPerformed(ActionEvent e)
2964 public void sortByTreeOption_actionPerformed(ActionEvent e)
2969 public void showAllSeqs_actionPerformed(ActionEvent e)
2974 public void showAllColumns_actionPerformed(ActionEvent e)
2979 public void hideSelSequences_actionPerformed(ActionEvent e)
2984 public void hideSelColumns_actionPerformed(ActionEvent e)
2989 public void hiddenMarkers_actionPerformed(ActionEvent e)
2994 public void findPdbId_actionPerformed(ActionEvent e)
2999 public void enterPdbId_actionPerformed(ActionEvent e)
3004 public void pdbFile_actionPerformed(ActionEvent e)
3009 public void invertColSel_actionPerformed(ActionEvent e)
3014 public void tabSelectionChanged(int sel)
3019 public void tabbedPane_mousePressed(MouseEvent e)
3024 public void tabbedPane_focusGained(FocusEvent e)
3029 public void save_actionPerformed(ActionEvent e)
3034 public void reload_actionPerformed(ActionEvent e)
3039 public void newView_actionPerformed(ActionEvent e)
3044 public void textColour_actionPerformed(ActionEvent e)
3049 public void idRightAlign_actionPerformed(ActionEvent e)
3054 public void expandViews_actionPerformed(ActionEvent e)
3059 public void gatherViews_actionPerformed(ActionEvent e)
3064 public void buildTreeMenu()
3069 public void pageSetup_actionPerformed(ActionEvent e)
3074 public void alignmentProperties()
3079 protected void expand_newalign(ActionEvent e)
3081 // TODO Auto-generated method stub
3085 protected boolean isShowAutoCalculatedAbove()
3087 return showAutoCalculatedAbove;
3090 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3092 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3095 protected SequenceAnnotationOrder getAnnotationSortOrder()
3097 return annotationSortOrder;
3100 protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
3102 this.annotationSortOrder = annotationSortOrder;