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.gui.Preferences;
27 import jalview.schemes.ColourSchemeProperty;
28 import jalview.util.MessageManager;
30 import java.awt.BorderLayout;
31 import java.awt.Color;
32 import java.awt.GridLayout;
33 import java.awt.Toolkit;
34 import java.awt.event.ActionEvent;
35 import java.awt.event.ActionListener;
36 import java.awt.event.FocusAdapter;
37 import java.awt.event.FocusEvent;
38 import java.awt.event.MouseAdapter;
39 import java.awt.event.MouseEvent;
41 import javax.swing.BorderFactory;
42 import javax.swing.ButtonGroup;
43 import javax.swing.JCheckBoxMenuItem;
44 import javax.swing.JInternalFrame;
45 import javax.swing.JLabel;
46 import javax.swing.JMenu;
47 import javax.swing.JMenuBar;
48 import javax.swing.JMenuItem;
49 import javax.swing.JOptionPane;
50 import javax.swing.JPanel;
51 import javax.swing.JRadioButtonMenuItem;
52 import javax.swing.JTabbedPane;
53 import javax.swing.SwingUtilities;
54 import javax.swing.event.ChangeEvent;
55 import javax.swing.event.MenuEvent;
56 import javax.swing.event.MenuListener;
58 public class GAlignFrame extends JInternalFrame
60 protected JMenuBar alignFrameMenuBar = new JMenuBar();
62 protected JMenu fileMenu = new JMenu();
64 protected JMenuItem closeMenuItem = new JMenuItem();
66 protected JMenu editMenu = new JMenu();
68 protected JMenu viewMenu = new JMenu();
70 protected JMenu annotationsMenu = new JMenu();
72 protected JMenu colourMenu = new JMenu();
74 protected JMenu calculateMenu = new JMenu();
76 protected JMenu webService = new JMenu();
78 protected JMenuItem webServiceNoServices;
80 protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
82 protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
84 protected JMenuItem invertSequenceMenuItem = new JMenuItem();
86 protected JMenuItem remove2LeftMenuItem = new JMenuItem();
88 protected JMenuItem remove2RightMenuItem = new JMenuItem();
90 protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
92 protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
94 public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
96 public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
98 protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
100 protected JMenuItem sortIDMenuItem = new JMenuItem();
102 protected JMenuItem sortLengthMenuItem = new JMenuItem();
104 protected JMenuItem sortGroupMenuItem = new JMenuItem();
106 protected JMenu sortByAnnotScore = new JMenu();
108 protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
110 protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
112 protected JMenuItem PCAMenuItem = new JMenuItem();
114 protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
116 protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
118 BorderLayout borderLayout1 = new BorderLayout();
120 public JLabel statusBar = new JLabel();
122 protected JMenuItem saveAs = new JMenuItem();
124 protected JMenu outputTextboxMenu = new JMenu();
126 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
128 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
130 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
132 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
134 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
136 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
138 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
140 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
142 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
144 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
146 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
148 protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
150 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
152 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
154 // protected JRadioButtonMenuItem covariationColour = new
155 // JRadioButtonMenuItem();
157 protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
159 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
161 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
163 public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
165 public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
167 public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
169 JMenuItem htmlMenuItem = new JMenuItem();
171 JMenuItem overviewMenuItem = new JMenuItem();
173 protected JMenuItem undoMenuItem = new JMenuItem();
175 protected JMenuItem redoMenuItem = new JMenuItem();
177 public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
179 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
181 public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
183 JMenuItem printMenuItem = new JMenuItem();
185 public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
187 JMenuItem findMenuItem = new JMenuItem();
189 public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
191 public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
193 public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
195 JMenuItem deleteGroups = new JMenuItem();
197 JMenuItem createGroup = new JMenuItem();
199 JMenuItem unGroup = new JMenuItem();
201 JMenuItem delete = new JMenuItem();
203 JMenuItem copy = new JMenuItem();
205 JMenuItem cut = new JMenuItem();
207 JMenu pasteMenu = new JMenu();
209 JMenuItem pasteNew = new JMenuItem();
211 JMenuItem pasteThis = new JMenuItem();
213 public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
215 JMenuItem createPNG = new JMenuItem();
217 JMenuItem createBioJS = new JMenuItem();
219 protected JMenuItem font = new JMenuItem();
221 public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
223 JMenuItem epsFile = new JMenuItem();
225 JMenuItem LoadtreeMenuItem = new JMenuItem();
227 public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
229 public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
231 public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
233 protected JMenuItem modifyPID = new JMenuItem();
235 protected JMenuItem modifyConservation = new JMenuItem();
237 protected JMenu sortByTreeMenu = new JMenu();
239 protected JMenu sort = new JMenu();
241 protected JMenu calculateTree = new JMenu();
243 JMenu jMenu2 = new JMenu();
245 protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
247 protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
249 protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
251 protected ButtonGroup colours = new ButtonGroup();
253 JMenuItem vamsasStore = new JMenuItem();
255 protected JMenuItem showTranslation = new JMenuItem();
257 protected JMenuItem extractScores = new JMenuItem();
259 protected JMenuItem expandAlignment = new JMenuItem();
261 protected JMenu showProducts = new JMenu();
263 public JMenuItem openFeatureSettings = new JMenuItem();
265 JMenuItem fetchSequence = new JMenuItem();
267 JMenuItem annotationColour = new JMenuItem();
269 protected JMenuItem rnahelicesColour = new JMenuItem();
271 JMenuItem associatedData = new JMenuItem();
273 protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
275 protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
277 protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
279 JMenu addSequenceMenu = new JMenu();
281 JMenuItem addFromFile = new JMenuItem();
283 JMenuItem addFromText = new JMenuItem();
285 JMenuItem addFromURL = new JMenuItem();
287 JMenuItem exportAnnotations = new JMenuItem();
289 JMenuItem exportFeatures = new JMenuItem();
291 protected JPanel statusPanel = new JPanel();
293 GridLayout gridLayout1 = new GridLayout();
295 JMenu jMenu3 = new JMenu();
297 JMenuItem showAllSeqs = new JMenuItem();
299 JMenuItem showAllColumns = new JMenuItem();
301 JMenu hideMenu = new JMenu();
303 JMenuItem hideSelSequences = new JMenuItem();
305 JMenuItem hideSelColumns = new JMenuItem();
307 JMenuItem hideAllButSelection = new JMenuItem();
309 JMenuItem hideAllSelection = new JMenuItem();
311 JMenuItem showAllhidden = new JMenuItem();
313 protected JMenuItem showAllSeqAnnotations = new JMenuItem();
315 protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
317 protected JMenuItem showAllAlAnnotations = new JMenuItem();
319 protected JMenuItem hideAllAlAnnotations = new JMenuItem();
321 protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
323 protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
325 protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
327 JMenuItem invertColSel = new JMenuItem();
329 protected JTabbedPane tabbedPane = new JTabbedPane();
331 JMenuItem save = new JMenuItem();
333 protected JMenuItem reload = new JMenuItem();
335 JMenuItem newView = new JMenuItem();
337 JMenuItem textColour = new JMenuItem();
339 JMenu formatMenu = new JMenu();
341 JMenu selectMenu = new JMenu();
343 protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
345 protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
347 protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
349 protected JMenuItem gatherViews = new JMenuItem();
351 protected JMenuItem expandViews = new JMenuItem();
353 JMenuItem pageSetup = new JMenuItem();
355 JMenuItem alignmentProperties = new JMenuItem();
357 JMenu tooltipSettingsMenu = new JMenu();
359 private JMenuItem justifyLeftMenuItem = new JMenuItem();
361 private JMenuItem justifyRightMenuItem = new JMenuItem();
363 JMenu autoAnnMenu = new JMenu();
365 protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
367 protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
369 protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
371 protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
373 protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
375 protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
377 protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem();
379 protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem();
381 private JMenuItem grpsFromSelection = new JMenuItem();
383 private SequenceAnnotationOrder annotationSortOrder;
385 private boolean showAutoCalculatedAbove = false;
392 setJMenuBar(alignFrameMenuBar);
394 // dynamically fill save as menu with available formats
395 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
397 JMenuItem item = new JMenuItem(
398 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
400 item.addActionListener(new java.awt.event.ActionListener()
403 public void actionPerformed(ActionEvent e)
405 outputText_actionPerformed(e);
409 outputTextboxMenu.add(item);
411 } catch (Exception e)
413 System.err.println(e.toString());
416 if (!new jalview.util.Platform().isAMac())
418 closeMenuItem.setMnemonic('C');
419 outputTextboxMenu.setMnemonic('T');
420 undoMenuItem.setMnemonic('Z');
421 redoMenuItem.setMnemonic('0');
422 copy.setMnemonic('C');
423 cut.setMnemonic('U');
424 pasteMenu.setMnemonic('P');
425 reload.setMnemonic('R');
428 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
430 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
431 .getUserColourSchemes().keys();
433 while (userColours.hasMoreElements())
435 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
436 userColours.nextElement().toString());
437 radioItem.setName("USER_DEFINED");
438 radioItem.addMouseListener(new MouseAdapter()
441 public void mousePressed(MouseEvent evt)
443 if (evt.isControlDown()
444 || SwingUtilities.isRightMouseButton(evt))
446 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
448 int option = JOptionPane.showInternalConfirmDialog(
449 jalview.gui.Desktop.desktop,
451 .getString("label.remove_from_default_list"),
453 .getString("label.remove_user_defined_colour"),
454 JOptionPane.YES_NO_OPTION);
455 if (option == JOptionPane.YES_OPTION)
457 jalview.gui.UserDefinedColours
458 .removeColourFromDefaults(radioItem.getText());
459 colourMenu.remove(radioItem);
463 radioItem.addActionListener(new ActionListener()
466 public void actionPerformed(ActionEvent evt)
468 userDefinedColour_actionPerformed(evt);
475 radioItem.addActionListener(new ActionListener()
478 public void actionPerformed(ActionEvent evt)
480 userDefinedColour_actionPerformed(evt);
483 colourMenu.insert(radioItem, 15);
484 colours.add(radioItem);
487 colours.add(noColourmenuItem);
488 colours.add(clustalColour);
489 colours.add(zappoColour);
490 colours.add(taylorColour);
491 colours.add(hydrophobicityColour);
492 colours.add(helixColour);
493 colours.add(strandColour);
494 colours.add(turnColour);
495 colours.add(buriedColour);
496 colours.add(userDefinedColour);
497 colours.add(PIDColour);
498 colours.add(BLOSUM62Colour);
499 colours.add(nucleotideColour);
500 colours.add(purinePyrimidineColour);
501 // colours.add(covariationColour);
502 colours.add(tcoffeeColour);
503 colours.add(RNAInteractionColour);
504 setColourSelected(jalview.bin.Cache
505 .getDefault("DEFAULT_COLOUR", "None"));
509 public void setColourSelected(String defaultColour)
512 if (defaultColour != null)
514 int index = ColourSchemeProperty
515 .getColourIndexFromName(defaultColour);
519 case ColourSchemeProperty.CLUSTAL:
520 clustalColour.setSelected(true);
524 case ColourSchemeProperty.BLOSUM:
525 BLOSUM62Colour.setSelected(true);
529 case ColourSchemeProperty.PID:
530 PIDColour.setSelected(true);
534 case ColourSchemeProperty.ZAPPO:
535 zappoColour.setSelected(true);
539 case ColourSchemeProperty.TAYLOR:
540 taylorColour.setSelected(true);
543 case ColourSchemeProperty.HYDROPHOBIC:
544 hydrophobicityColour.setSelected(true);
548 case ColourSchemeProperty.HELIX:
549 helixColour.setSelected(true);
553 case ColourSchemeProperty.STRAND:
554 strandColour.setSelected(true);
558 case ColourSchemeProperty.TURN:
559 turnColour.setSelected(true);
563 case ColourSchemeProperty.BURIED:
564 buriedColour.setSelected(true);
568 case ColourSchemeProperty.NUCLEOTIDE:
569 nucleotideColour.setSelected(true);
573 case ColourSchemeProperty.TCOFFEE:
574 tcoffeeColour.setSelected(true);
577 case ColourSchemeProperty.PURINEPYRIMIDINE:
578 purinePyrimidineColour.setSelected(true);
582 case ColourSchemeProperty.RNAINTERACTION:
583 RNAInteractionColour.setSelected(true);
587 * case ColourSchemeProperty.COVARIATION:
588 * covariationColour.setSelected(true);
592 case ColourSchemeProperty.USER_DEFINED:
593 userDefinedColour.setSelected(true);
596 case ColourSchemeProperty.NONE:
598 noColourmenuItem.setSelected(true);
606 private void jbInit() throws Exception
608 fileMenu.setText(MessageManager.getString("action.file"));
609 saveAs.setText(MessageManager.getString("action.save_as") + "...");
610 saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
611 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
612 .getMenuShortcutKeyMask()
613 | java.awt.event.KeyEvent.SHIFT_MASK, false));
614 saveAs.addActionListener(new ActionListener()
617 public void actionPerformed(ActionEvent e)
619 saveAs_actionPerformed(e);
622 closeMenuItem.setText(MessageManager.getString("action.close"));
623 closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
624 java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
625 .getMenuShortcutKeyMask(), false));
626 closeMenuItem.addActionListener(new java.awt.event.ActionListener()
629 public void actionPerformed(ActionEvent e)
631 closeMenuItem_actionPerformed(false);
634 editMenu.setText(MessageManager.getString("action.edit"));
635 viewMenu.setText(MessageManager.getString("action.view"));
636 annotationsMenu.setText(MessageManager.getString("action.annotations"));
637 colourMenu.setText(MessageManager.getString("action.colour"));
638 calculateMenu.setText(MessageManager.getString("action.calculate"));
639 webService.setText(MessageManager.getString("action.web_service"));
640 selectAllSequenceMenuItem.setText(MessageManager
641 .getString("action.select_all"));
642 selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
643 .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
644 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
645 selectAllSequenceMenuItem
646 .addActionListener(new java.awt.event.ActionListener()
649 public void actionPerformed(ActionEvent e)
651 selectAllSequenceMenuItem_actionPerformed(e);
654 deselectAllSequenceMenuItem.setText(MessageManager
655 .getString("action.deselect_all"));
656 deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
657 .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
658 deselectAllSequenceMenuItem
659 .addActionListener(new java.awt.event.ActionListener()
662 public void actionPerformed(ActionEvent e)
664 deselectAllSequenceMenuItem_actionPerformed(e);
667 invertSequenceMenuItem.setText(MessageManager
668 .getString("action.invert_sequence_selection"));
669 invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
670 .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
671 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
672 invertSequenceMenuItem
673 .addActionListener(new java.awt.event.ActionListener()
676 public void actionPerformed(ActionEvent e)
678 invertSequenceMenuItem_actionPerformed(e);
681 grpsFromSelection.setText(MessageManager
682 .getString("action.make_groups_selection"));
683 grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
686 public void actionPerformed(ActionEvent e)
688 makeGrpsFromSelection_actionPerformed(e);
691 expandAlignment.setText(MessageManager
692 .getString("action.view_flanking_regions"));
693 expandAlignment.setToolTipText(MessageManager
694 .getString("label.view_flanking_regions"));
695 expandAlignment.addActionListener(new java.awt.event.ActionListener()
698 public void actionPerformed(ActionEvent e)
703 remove2LeftMenuItem.setText(MessageManager
704 .getString("action.remove_left"));
705 remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
706 java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
707 .getMenuShortcutKeyMask(), false));
709 .addActionListener(new java.awt.event.ActionListener()
712 public void actionPerformed(ActionEvent e)
714 remove2LeftMenuItem_actionPerformed(e);
717 remove2RightMenuItem.setText(MessageManager
718 .getString("action.remove_right"));
719 remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
720 java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
721 .getMenuShortcutKeyMask(), false));
723 .addActionListener(new java.awt.event.ActionListener()
726 public void actionPerformed(ActionEvent e)
728 remove2RightMenuItem_actionPerformed(e);
731 removeGappedColumnMenuItem.setText(MessageManager
732 .getString("action.remove_empty_columns"));
733 removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
734 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
735 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
736 removeGappedColumnMenuItem
737 .addActionListener(new java.awt.event.ActionListener()
740 public void actionPerformed(ActionEvent e)
742 removeGappedColumnMenuItem_actionPerformed(e);
745 removeAllGapsMenuItem.setText(MessageManager
746 .getString("action.remove_all_gaps"));
747 removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
748 .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
749 .getDefaultToolkit().getMenuShortcutKeyMask()
750 | java.awt.event.KeyEvent.SHIFT_MASK, false));
751 removeAllGapsMenuItem
752 .addActionListener(new java.awt.event.ActionListener()
755 public void actionPerformed(ActionEvent e)
757 removeAllGapsMenuItem_actionPerformed(e);
760 justifyLeftMenuItem.setText(MessageManager
761 .getString("action.left_justify_alignment"));
763 .addActionListener(new java.awt.event.ActionListener()
766 public void actionPerformed(ActionEvent e)
768 justifyLeftMenuItem_actionPerformed(e);
771 justifyRightMenuItem.setText(MessageManager
772 .getString("action.right_justify_alignment"));
774 .addActionListener(new java.awt.event.ActionListener()
777 public void actionPerformed(ActionEvent e)
779 justifyRightMenuItem_actionPerformed(e);
782 viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
783 viewBoxesMenuItem.setState(true);
784 viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
787 public void actionPerformed(ActionEvent e)
789 viewBoxesMenuItem_actionPerformed(e);
792 viewTextMenuItem.setText(MessageManager.getString("action.text"));
793 viewTextMenuItem.setState(true);
794 viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
797 public void actionPerformed(ActionEvent e)
799 viewTextMenuItem_actionPerformed(e);
802 showNonconservedMenuItem.setText(MessageManager
803 .getString("label.show_non_conversed"));
804 showNonconservedMenuItem.setState(false);
805 showNonconservedMenuItem
806 .addActionListener(new java.awt.event.ActionListener()
809 public void actionPerformed(ActionEvent e)
811 showUnconservedMenuItem_actionPerformed(e);
814 sortPairwiseMenuItem.setText(MessageManager
815 .getString("action.by_pairwise_id"));
817 .addActionListener(new java.awt.event.ActionListener()
820 public void actionPerformed(ActionEvent e)
822 sortPairwiseMenuItem_actionPerformed(e);
825 sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
826 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
829 public void actionPerformed(ActionEvent e)
831 sortIDMenuItem_actionPerformed(e);
835 .setText(MessageManager.getString("action.by_length"));
837 .addActionListener(new java.awt.event.ActionListener()
840 public void actionPerformed(ActionEvent e)
842 sortLengthMenuItem_actionPerformed(e);
845 sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
846 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
849 public void actionPerformed(ActionEvent e)
851 sortGroupMenuItem_actionPerformed(e);
854 removeRedundancyMenuItem.setText(MessageManager
855 .getString("action.remove_redundancy").concat("..."));
856 removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
857 .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
858 .getDefaultToolkit().getMenuShortcutKeyMask(), false));
859 removeRedundancyMenuItem
860 .addActionListener(new java.awt.event.ActionListener()
863 public void actionPerformed(ActionEvent e)
865 removeRedundancyMenuItem_actionPerformed(e);
868 pairwiseAlignmentMenuItem.setText(MessageManager
869 .getString("action.pairwise_alignment"));
870 pairwiseAlignmentMenuItem
871 .addActionListener(new java.awt.event.ActionListener()
874 public void actionPerformed(ActionEvent e)
876 pairwiseAlignmentMenuItem_actionPerformed(e);
879 PCAMenuItem.setText(MessageManager
880 .getString("label.principal_component_analysis"));
881 PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
884 public void actionPerformed(ActionEvent e)
886 PCAMenuItem_actionPerformed(e);
889 averageDistanceTreeMenuItem.setText(MessageManager
890 .getString("label.average_distance_identity"));
891 averageDistanceTreeMenuItem
892 .addActionListener(new java.awt.event.ActionListener()
895 public void actionPerformed(ActionEvent e)
897 averageDistanceTreeMenuItem_actionPerformed(e);
900 neighbourTreeMenuItem.setText(MessageManager
901 .getString("label.neighbour_joining_identity"));
902 neighbourTreeMenuItem
903 .addActionListener(new java.awt.event.ActionListener()
906 public void actionPerformed(ActionEvent e)
908 neighbourTreeMenuItem_actionPerformed(e);
911 this.getContentPane().setLayout(borderLayout1);
912 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
913 statusBar.setBackground(Color.white);
914 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
915 statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
916 statusBar.setText(MessageManager.getString("label.status_bar"));
917 outputTextboxMenu.setText(MessageManager
918 .getString("label.out_to_textbox"));
919 clustalColour.setText(MessageManager.getString("label.clustalx"));
921 clustalColour.addActionListener(new java.awt.event.ActionListener()
924 public void actionPerformed(ActionEvent e)
926 clustalColour_actionPerformed(e);
929 zappoColour.setText(MessageManager.getString("label.zappo"));
930 zappoColour.addActionListener(new java.awt.event.ActionListener()
933 public void actionPerformed(ActionEvent e)
935 zappoColour_actionPerformed(e);
938 taylorColour.setText(MessageManager.getString("label.taylor"));
939 taylorColour.addActionListener(new java.awt.event.ActionListener()
942 public void actionPerformed(ActionEvent e)
944 taylorColour_actionPerformed(e);
947 hydrophobicityColour.setText(MessageManager
948 .getString("label.hydrophobicity"));
950 .addActionListener(new java.awt.event.ActionListener()
953 public void actionPerformed(ActionEvent e)
955 hydrophobicityColour_actionPerformed(e);
958 helixColour.setText(MessageManager.getString("label.helix_propensity"));
959 helixColour.addActionListener(new java.awt.event.ActionListener()
962 public void actionPerformed(ActionEvent e)
964 helixColour_actionPerformed(e);
967 strandColour.setText(MessageManager
968 .getString("label.strand_propensity"));
969 strandColour.addActionListener(new java.awt.event.ActionListener()
972 public void actionPerformed(ActionEvent e)
974 strandColour_actionPerformed(e);
977 turnColour.setText(MessageManager.getString("label.turn_propensity"));
978 turnColour.addActionListener(new java.awt.event.ActionListener()
981 public void actionPerformed(ActionEvent e)
983 turnColour_actionPerformed(e);
986 buriedColour.setText(MessageManager.getString("label.buried_index"));
987 buriedColour.addActionListener(new java.awt.event.ActionListener()
990 public void actionPerformed(ActionEvent e)
992 buriedColour_actionPerformed(e);
995 userDefinedColour.setText(MessageManager
996 .getString("action.user_defined"));
997 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1000 public void actionPerformed(ActionEvent e)
1002 userDefinedColour_actionPerformed(e);
1006 .setText(MessageManager.getString("label.percentage_identity"));
1007 PIDColour.addActionListener(new java.awt.event.ActionListener()
1010 public void actionPerformed(ActionEvent e)
1012 PIDColour_actionPerformed(e);
1016 .setText(MessageManager.getString("label.blosum62_score"));
1017 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1020 public void actionPerformed(ActionEvent e)
1022 BLOSUM62Colour_actionPerformed(e);
1025 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1026 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1029 public void actionPerformed(ActionEvent e)
1031 nucleotideColour_actionPerformed(e);
1035 purinePyrimidineColour.setText(MessageManager
1036 .getString("label.purine_pyrimidine"));
1037 purinePyrimidineColour
1038 .addActionListener(new java.awt.event.ActionListener()
1041 public void actionPerformed(ActionEvent e)
1043 purinePyrimidineColour_actionPerformed(e);
1047 RNAInteractionColour.setText("RNA Interaction type");
1048 RNAInteractionColour
1049 .addActionListener(new java.awt.event.ActionListener()
1052 public void actionPerformed(ActionEvent e)
1054 RNAInteractionColour_actionPerformed(e);
1058 * covariationColour.setText("Covariation");
1059 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1060 * public void actionPerformed(ActionEvent e) {
1061 * covariationColour_actionPerformed(e); } });
1064 avDistanceTreeBlosumMenuItem.setText(MessageManager
1065 .getString("label.average_distance_bloslum62"));
1066 avDistanceTreeBlosumMenuItem
1067 .addActionListener(new java.awt.event.ActionListener()
1070 public void actionPerformed(ActionEvent e)
1072 avTreeBlosumMenuItem_actionPerformed(e);
1075 njTreeBlosumMenuItem.setText(MessageManager
1076 .getString("label.neighbour_blosum62"));
1077 njTreeBlosumMenuItem
1078 .addActionListener(new java.awt.event.ActionListener()
1081 public void actionPerformed(ActionEvent e)
1083 njTreeBlosumMenuItem_actionPerformed(e);
1086 annotationPanelMenuItem.setActionCommand("");
1087 annotationPanelMenuItem.setText(MessageManager
1088 .getString("label.show_annotations"));
1089 annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
1091 annotationPanelMenuItem.addActionListener(new ActionListener()
1094 public void actionPerformed(ActionEvent e)
1096 annotationPanelMenuItem_actionPerformed(e);
1099 showAllAlAnnotations.setText(MessageManager
1100 .getString("label.show_all_al_annotations"));
1101 final boolean isAnnotationPanelShown = annotationPanelMenuItem
1103 showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1104 showAllAlAnnotations.addActionListener(new ActionListener()
1107 public void actionPerformed(ActionEvent e)
1109 showAllAnnotations_actionPerformed(false, true);
1112 hideAllAlAnnotations.setText(MessageManager
1113 .getString("label.hide_all_al_annotations"));
1114 hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
1115 hideAllAlAnnotations.addActionListener(new ActionListener()
1118 public void actionPerformed(ActionEvent e)
1120 hideAllAnnotations_actionPerformed(false, true);
1123 showAllSeqAnnotations.setText(MessageManager
1124 .getString("label.show_all_seq_annotations"));
1125 showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1126 showAllSeqAnnotations.addActionListener(new ActionListener()
1129 public void actionPerformed(ActionEvent e)
1131 showAllAnnotations_actionPerformed(true, false);
1134 hideAllSeqAnnotations.setText(MessageManager
1135 .getString("label.hide_all_seq_annotations"));
1136 hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
1137 hideAllSeqAnnotations.addActionListener(new ActionListener()
1140 public void actionPerformed(ActionEvent e)
1142 hideAllAnnotations_actionPerformed(true, false);
1145 SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
1146 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
1147 SequenceAnnotationOrder.NONE.name()));
1148 sortAnnBySequence.setText(MessageManager
1149 .getString("label.sort_annotations_by_sequence"));
1151 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
1152 sortAnnBySequence.addActionListener(new ActionListener()
1155 public void actionPerformed(ActionEvent e)
1157 boolean newState = sortAnnBySequence.getState();
1158 sortAnnByLabel.setSelected(false);
1159 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
1160 : SequenceAnnotationOrder.NONE);
1161 sortAnnotations_actionPerformed();
1164 sortAnnByLabel.setText(MessageManager
1165 .getString("label.sort_annotations_by_label"));
1167 .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
1168 sortAnnByLabel.addActionListener(new ActionListener()
1171 public void actionPerformed(ActionEvent e)
1173 boolean newState = sortAnnByLabel.getState();
1174 sortAnnBySequence.setSelected(false);
1175 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
1176 : SequenceAnnotationOrder.NONE);
1177 sortAnnotations_actionPerformed();
1180 colourTextMenuItem.setText(MessageManager
1181 .getString("label.colour_text"));
1183 .addActionListener(new java.awt.event.ActionListener()
1186 public void actionPerformed(ActionEvent e)
1188 colourTextMenuItem_actionPerformed(e);
1191 htmlMenuItem.setText(MessageManager.getString("label.html"));
1192 htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
1195 public void actionPerformed(ActionEvent e)
1197 htmlMenuItem_actionPerformed(e);
1201 // TODO uncomment when supported by MassageManager
1202 // createBioJS.setText(MessageManager.getString("label.biojs_html_export"));
1203 createBioJS.setText("BioJS");
1204 createBioJS.addActionListener(new java.awt.event.ActionListener()
1207 public void actionPerformed(ActionEvent e)
1209 bioJSMenuItem_actionPerformed(e);
1213 overviewMenuItem.setText(MessageManager
1214 .getString("label.overview_window"));
1215 overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
1218 public void actionPerformed(ActionEvent e)
1220 overviewMenuItem_actionPerformed(e);
1223 undoMenuItem.setEnabled(false);
1224 undoMenuItem.setText(MessageManager.getString("action.undo"));
1225 undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1226 java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
1227 .getMenuShortcutKeyMask(), false));
1228 undoMenuItem.addActionListener(new java.awt.event.ActionListener()
1231 public void actionPerformed(ActionEvent e)
1233 undoMenuItem_actionPerformed(e);
1236 redoMenuItem.setEnabled(false);
1237 redoMenuItem.setText(MessageManager.getString("action.redo"));
1238 redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1239 java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
1240 .getMenuShortcutKeyMask(), false));
1241 redoMenuItem.addActionListener(new java.awt.event.ActionListener()
1244 public void actionPerformed(ActionEvent e)
1246 redoMenuItem_actionPerformed(e);
1249 conservationMenuItem.setText(MessageManager
1250 .getString("action.by_conservation"));
1251 conservationMenuItem
1252 .addActionListener(new java.awt.event.ActionListener()
1255 public void actionPerformed(ActionEvent e)
1257 conservationMenuItem_actionPerformed(e);
1260 noColourmenuItem.setText(MessageManager.getString("label.none"));
1261 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1264 public void actionPerformed(ActionEvent e)
1266 noColourmenuItem_actionPerformed(e);
1269 wrapMenuItem.setText(MessageManager.getString("label.wrap"));
1270 wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
1273 public void actionPerformed(ActionEvent e)
1275 wrapMenuItem_actionPerformed(e);
1278 printMenuItem.setText(MessageManager.getString("action.print") + "...");
1279 printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1280 java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
1281 .getMenuShortcutKeyMask(), false));
1282 printMenuItem.addActionListener(new java.awt.event.ActionListener()
1285 public void actionPerformed(ActionEvent e)
1287 printMenuItem_actionPerformed(e);
1291 .setText(MessageManager.getString("action.show_gaps"));
1292 renderGapsMenuItem.setState(true);
1294 .addActionListener(new java.awt.event.ActionListener()
1297 public void actionPerformed(ActionEvent e)
1299 renderGapsMenuItem_actionPerformed(e);
1302 findMenuItem.setText(MessageManager.getString("action.find"));
1303 findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1304 java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
1305 .getMenuShortcutKeyMask(), false));
1306 findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
1307 MessageManager.getString("label.find_tip")));
1308 findMenuItem.addActionListener(new java.awt.event.ActionListener()
1311 public void actionPerformed(ActionEvent e)
1313 findMenuItem_actionPerformed(e);
1316 abovePIDThreshold.setText(MessageManager
1317 .getString("label.above_identity_threshold"));
1318 abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
1321 public void actionPerformed(ActionEvent e)
1323 abovePIDThreshold_actionPerformed(e);
1326 showSeqFeatures.setText(MessageManager
1327 .getString("label.show_sequence_features"));
1328 showSeqFeatures.addActionListener(new ActionListener()
1331 public void actionPerformed(ActionEvent actionEvent)
1333 showSeqFeatures_actionPerformed(actionEvent);
1337 * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
1338 * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
1339 * void actionPerformed(ActionEvent actionEvent) {
1340 * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
1342 showDbRefsMenuitem.setText(MessageManager
1343 .getString("label.show_database_refs"));
1344 showDbRefsMenuitem.addActionListener(new ActionListener()
1348 public void actionPerformed(ActionEvent e)
1350 showDbRefs_actionPerformed(e);
1354 showNpFeatsMenuitem.setText(MessageManager
1355 .getString("label.show_non_positional_features"));
1356 showNpFeatsMenuitem.addActionListener(new ActionListener()
1360 public void actionPerformed(ActionEvent e)
1362 showNpFeats_actionPerformed(e);
1366 showGroupConservation.setText(MessageManager
1367 .getString("label.group_conservation"));
1368 showGroupConservation.addActionListener(new ActionListener()
1372 public void actionPerformed(ActionEvent e)
1374 showGroupConservation_actionPerformed(e);
1379 showGroupConsensus.setText(MessageManager
1380 .getString("label.group_consensus"));
1381 showGroupConsensus.addActionListener(new ActionListener()
1385 public void actionPerformed(ActionEvent e)
1387 showGroupConsensus_actionPerformed(e);
1391 showConsensusHistogram.setText(MessageManager
1392 .getString("label.show_consensus_histogram"));
1393 showConsensusHistogram.addActionListener(new ActionListener()
1397 public void actionPerformed(ActionEvent e)
1399 showConsensusHistogram_actionPerformed(e);
1403 showSequenceLogo.setText(MessageManager
1404 .getString("label.show_consensus_logo"));
1405 showSequenceLogo.addActionListener(new ActionListener()
1409 public void actionPerformed(ActionEvent e)
1411 showSequenceLogo_actionPerformed(e);
1415 normaliseSequenceLogo.setText(MessageManager
1416 .getString("label.norm_consensus_logo"));
1417 normaliseSequenceLogo.addActionListener(new ActionListener()
1421 public void actionPerformed(ActionEvent e)
1423 normaliseSequenceLogo_actionPerformed(e);
1427 applyAutoAnnotationSettings.setText(MessageManager
1428 .getString("label.apply_all_groups"));
1429 applyAutoAnnotationSettings.setState(false);
1430 applyAutoAnnotationSettings.setVisible(true);
1431 applyAutoAnnotationSettings.addActionListener(new ActionListener()
1434 public void actionPerformed(ActionEvent e)
1436 applyAutoAnnotationSettings_actionPerformed(e);
1440 ButtonGroup buttonGroup = new ButtonGroup();
1441 buttonGroup.add(showAutoFirst);
1442 buttonGroup.add(showAutoLast);
1443 showAutoFirst.setText(MessageManager.getString("label.show_first"));
1444 showAutoFirst.setSelected(Cache.getDefault(
1445 Preferences.SHOW_AUTOCALC_ABOVE,
1447 showAutoFirst.addActionListener(new ActionListener()
1450 public void actionPerformed(ActionEvent e)
1452 setShowAutoCalculatedAbove(showAutoFirst.isSelected());
1453 sortAnnotations_actionPerformed();
1456 showAutoLast.setText(MessageManager.getString("label.show_last"));
1457 showAutoLast.setSelected(!showAutoFirst.isSelected());
1458 showAutoLast.addActionListener(new ActionListener()
1461 public void actionPerformed(ActionEvent e)
1463 setShowAutoCalculatedAbove(!showAutoLast.isSelected());
1464 sortAnnotations_actionPerformed();
1468 nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
1469 nucleotideColour.addActionListener(new java.awt.event.ActionListener()
1472 public void actionPerformed(ActionEvent e)
1474 nucleotideColour_actionPerformed(e);
1478 tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
1479 tcoffeeColour.setEnabled(false);
1480 tcoffeeColour.addActionListener(new ActionListener()
1484 public void actionPerformed(ActionEvent e)
1486 tcoffeeColorScheme_actionPerformed(e);
1491 .setText(MessageManager.getString("action.undefine_groups"));
1492 deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1493 java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
1494 .getMenuShortcutKeyMask(), false));
1495 deleteGroups.addActionListener(new java.awt.event.ActionListener()
1498 public void actionPerformed(ActionEvent e)
1500 deleteGroups_actionPerformed(e);
1503 createGroup.setText(MessageManager.getString("action.create_groups"));
1504 createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1505 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1506 .getMenuShortcutKeyMask(), false));
1507 createGroup.addActionListener(new java.awt.event.ActionListener()
1510 public void actionPerformed(ActionEvent e)
1512 createGroup_actionPerformed(e);
1515 unGroup.setText(MessageManager.getString("action.remove_group"));
1516 unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1517 java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
1518 .getMenuShortcutKeyMask()
1519 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1520 unGroup.addActionListener(new java.awt.event.ActionListener()
1523 public void actionPerformed(ActionEvent e)
1525 unGroup_actionPerformed(e);
1528 copy.setText(MessageManager.getString("action.copy"));
1529 copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1530 java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
1531 .getMenuShortcutKeyMask(), false));
1533 copy.addActionListener(new java.awt.event.ActionListener()
1536 public void actionPerformed(ActionEvent e)
1538 copy_actionPerformed(e);
1541 cut.setText(MessageManager.getString("action.cut"));
1542 cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1543 java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
1544 .getMenuShortcutKeyMask(), false));
1545 cut.addActionListener(new java.awt.event.ActionListener()
1548 public void actionPerformed(ActionEvent e)
1550 cut_actionPerformed(e);
1553 delete.setText(MessageManager.getString("action.delete"));
1554 delete.addActionListener(new java.awt.event.ActionListener()
1557 public void actionPerformed(ActionEvent e)
1559 delete_actionPerformed(e);
1562 pasteMenu.setText(MessageManager.getString("action.paste"));
1563 pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
1564 pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1565 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1566 .getMenuShortcutKeyMask()
1567 | java.awt.event.KeyEvent.SHIFT_MASK, false));
1568 pasteNew.addActionListener(new java.awt.event.ActionListener()
1571 public void actionPerformed(ActionEvent e)
1573 pasteNew_actionPerformed(e);
1576 pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
1577 pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
1578 java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
1579 .getMenuShortcutKeyMask(), false));
1580 pasteThis.addActionListener(new java.awt.event.ActionListener()
1583 public void actionPerformed(ActionEvent e)
1585 pasteThis_actionPerformed(e);
1588 applyToAllGroups.setText(MessageManager
1589 .getString("label.apply_colour_to_all_groups"));
1590 applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
1593 public void actionPerformed(ActionEvent e)
1595 applyToAllGroups_actionPerformed(e);
1598 createPNG.addActionListener(new java.awt.event.ActionListener()
1601 public void actionPerformed(ActionEvent e)
1606 createPNG.setActionCommand(MessageManager
1607 .getString("label.save_png_image"));
1608 createPNG.setText("PNG");
1609 font.setText(MessageManager.getString("action.font"));
1610 font.addActionListener(new java.awt.event.ActionListener()
1613 public void actionPerformed(ActionEvent e)
1615 font_actionPerformed(e);
1618 seqLimits.setText(MessageManager
1619 .getString("label.show_sequence_limits"));
1620 seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
1621 seqLimits.addActionListener(new java.awt.event.ActionListener()
1624 public void actionPerformed(ActionEvent e)
1626 seqLimit_actionPerformed(e);
1629 epsFile.setText("EPS");
1630 epsFile.addActionListener(new java.awt.event.ActionListener()
1633 public void actionPerformed(ActionEvent e)
1638 LoadtreeMenuItem.setActionCommand(MessageManager
1639 .getString("label.load_tree_for_sequence_set"));
1640 LoadtreeMenuItem.setText(MessageManager
1641 .getString("label.load_associated_tree"));
1642 LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
1645 public void actionPerformed(ActionEvent e)
1647 LoadtreeMenuItem_actionPerformed(e);
1651 scaleAbove.setVisible(false);
1652 scaleAbove.setText(MessageManager.getString("action.scale_above"));
1653 scaleAbove.addActionListener(new java.awt.event.ActionListener()
1656 public void actionPerformed(ActionEvent e)
1658 scaleAbove_actionPerformed(e);
1661 scaleLeft.setVisible(false);
1662 scaleLeft.setSelected(true);
1663 scaleLeft.setText(MessageManager.getString("action.scale_left"));
1664 scaleLeft.addActionListener(new java.awt.event.ActionListener()
1667 public void actionPerformed(ActionEvent e)
1669 scaleLeft_actionPerformed(e);
1672 scaleRight.setVisible(false);
1673 scaleRight.setSelected(true);
1674 scaleRight.setText(MessageManager.getString("action.scale_right"));
1675 scaleRight.addActionListener(new java.awt.event.ActionListener()
1678 public void actionPerformed(ActionEvent e)
1680 scaleRight_actionPerformed(e);
1683 centreColumnLabelsMenuItem.setVisible(true);
1684 centreColumnLabelsMenuItem.setState(false);
1685 centreColumnLabelsMenuItem.setText(MessageManager
1686 .getString("label.centre_column_labels"));
1687 centreColumnLabelsMenuItem
1688 .addActionListener(new java.awt.event.ActionListener()
1691 public void actionPerformed(ActionEvent e)
1693 centreColumnLabels_actionPerformed(e);
1696 followHighlightMenuItem.setVisible(true);
1697 followHighlightMenuItem.setState(true);
1698 followHighlightMenuItem.setText(MessageManager
1699 .getString("label.automatic_scrolling"));
1700 followHighlightMenuItem.addActionListener(new ActionListener()
1704 public void actionPerformed(ActionEvent e)
1706 followHighlight_actionPerformed();
1711 modifyPID.setText(MessageManager
1712 .getString("label.modify_identity_thereshold"));
1713 modifyPID.addActionListener(new java.awt.event.ActionListener()
1716 public void actionPerformed(ActionEvent e)
1718 modifyPID_actionPerformed(e);
1721 modifyConservation.setText(MessageManager
1722 .getString("label.modify_conservation_thereshold"));
1724 .addActionListener(new java.awt.event.ActionListener()
1727 public void actionPerformed(ActionEvent e)
1729 modifyConservation_actionPerformed(e);
1733 .setText(MessageManager.getString("action.by_tree_order"));
1734 sort.setText(MessageManager.getString("action.sort"));
1735 sort.addMenuListener(new MenuListener()
1738 public void menuSelected(MenuEvent e)
1744 public void menuDeselected(MenuEvent e)
1749 public void menuCanceled(MenuEvent e)
1753 sortByAnnotScore.setText(MessageManager
1754 .getString("label.sort_by_score"));
1755 sort.add(sortByAnnotScore);
1756 sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
1760 public void menuCanceled(MenuEvent e)
1765 public void menuDeselected(MenuEvent e)
1770 public void menuSelected(MenuEvent e)
1772 buildSortByAnnotationScoresMenu();
1775 sortByAnnotScore.setVisible(false);
1778 .setText(MessageManager.getString("action.calculate_tree"));
1780 jMenu2.setText(MessageManager.getString("label.export_image"));
1781 padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
1782 padGapsMenuitem.setState(jalview.bin.Cache
1783 .getDefault("PAD_GAPS", false));
1784 padGapsMenuitem.addActionListener(new ActionListener()
1787 public void actionPerformed(ActionEvent e)
1789 padGapsMenuitem_actionPerformed(e);
1792 vamsasStore.setVisible(false);
1793 vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
1794 vamsasStore.addActionListener(new ActionListener()
1797 public void actionPerformed(ActionEvent e)
1799 vamsasStore_actionPerformed(e);
1802 showTranslation.setText(MessageManager
1803 .getString("label.translate_cDNA"));
1804 showTranslation.addActionListener(new ActionListener()
1807 public void actionPerformed(ActionEvent e)
1809 showTranslation_actionPerformed(e);
1812 extractScores.setText(MessageManager.getString("label.extract_scores")
1814 extractScores.addActionListener(new ActionListener()
1817 public void actionPerformed(ActionEvent e)
1819 extractScores_actionPerformed(e);
1822 extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
1824 showProducts.setText(MessageManager.getString("label.get_cross_refs"));
1826 * showProducts.addActionListener(new ActionListener() {
1828 * public void actionPerformed(ActionEvent e) {
1829 * showProducts_actionPerformed(e); } });
1831 openFeatureSettings.setText(MessageManager
1832 .getString("label.feature_settings"));
1833 openFeatureSettings.addActionListener(new ActionListener()
1836 public void actionPerformed(ActionEvent e)
1838 featureSettings_actionPerformed(e);
1842 .setText(MessageManager.getString("label.fetch_sequences"));
1843 fetchSequence.addActionListener(new ActionListener()
1846 public void actionPerformed(ActionEvent e)
1848 fetchSequence_actionPerformed(e);
1852 annotationColour.setText(MessageManager
1853 .getString("action.by_annotation"));
1854 annotationColour.addActionListener(new ActionListener()
1857 public void actionPerformed(ActionEvent e)
1859 annotationColour_actionPerformed(e);
1863 rnahelicesColour.setText(MessageManager
1864 .getString("action.by_rna_helixes"));
1865 rnahelicesColour.addActionListener(new ActionListener()
1868 public void actionPerformed(ActionEvent e)
1870 rnahelicesColour_actionPerformed(e);
1874 associatedData.setText(MessageManager
1875 .getString("label.load_features_annotations"));
1876 associatedData.addActionListener(new ActionListener()
1879 public void actionPerformed(ActionEvent e)
1881 associatedData_actionPerformed(e);
1884 autoCalculate.setText(MessageManager
1885 .getString("label.autocalculate_consensus"));
1886 autoCalculate.setState(jalview.bin.Cache.getDefault(
1887 "AUTO_CALC_CONSENSUS", true));
1888 autoCalculate.addActionListener(new ActionListener()
1891 public void actionPerformed(ActionEvent e)
1893 autoCalculate_actionPerformed(e);
1896 sortByTree.setText(MessageManager
1897 .getString("label.sort_alignment_new_tree"));
1899 .setToolTipText("<html>"
1901 .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
1903 .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
1904 sortByTree.addActionListener(new ActionListener()
1907 public void actionPerformed(ActionEvent e)
1909 sortByTreeOption_actionPerformed(e);
1913 listenToViewSelections.setText(MessageManager
1914 .getString("label.listen_for_selections"));
1915 listenToViewSelections
1916 .setToolTipText("<html>"
1918 .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
1919 listenToViewSelections.setState(false);
1920 listenToViewSelections.addActionListener(new ActionListener()
1923 public void actionPerformed(ActionEvent e)
1925 listenToViewSelections_actionPerformed(e);
1930 .setText(MessageManager.getString("label.add_sequences"));
1931 addFromFile.setText(MessageManager.getString("label.from_file"));
1932 addFromFile.addActionListener(new ActionListener()
1935 public void actionPerformed(ActionEvent e)
1937 addFromFile_actionPerformed(e);
1940 addFromText.setText(MessageManager.getString("label.from_textbox"));
1941 addFromText.addActionListener(new ActionListener()
1944 public void actionPerformed(ActionEvent e)
1946 addFromText_actionPerformed(e);
1949 addFromURL.setText(MessageManager.getString("label.from_url"));
1950 addFromURL.addActionListener(new ActionListener()
1953 public void actionPerformed(ActionEvent e)
1955 addFromURL_actionPerformed(e);
1958 exportFeatures.setText(MessageManager
1959 .getString("label.export_features"));
1960 exportFeatures.addActionListener(new ActionListener()
1963 public void actionPerformed(ActionEvent e)
1965 exportFeatures_actionPerformed(e);
1968 exportAnnotations.setText(MessageManager
1969 .getString("label.export_annotations"));
1970 exportAnnotations.addActionListener(new ActionListener()
1973 public void actionPerformed(ActionEvent e)
1975 exportAnnotations_actionPerformed(e);
1978 statusPanel.setLayout(gridLayout1);
1979 jMenu3.setText(MessageManager.getString("action.show"));
1980 showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
1981 showAllSeqs.setToolTipText(MessageManager
1982 .getString("label.toggle_sequence_visibility"));
1983 showAllSeqs.addActionListener(new ActionListener()
1986 public void actionPerformed(ActionEvent e)
1988 showAllSeqs_actionPerformed(e);
1991 showAllColumns.setText(MessageManager.getString("label.all_columns"));
1992 showAllColumns.setToolTipText(MessageManager
1993 .getString("label.toggle_columns_visibility"));
1994 showAllColumns.addActionListener(new ActionListener()
1997 public void actionPerformed(ActionEvent e)
1999 showAllColumns_actionPerformed(e);
2002 hideMenu.setText(MessageManager.getString("action.hide"));
2003 hideSelSequences.setText(MessageManager
2004 .getString("label.selected_sequences"));
2005 hideSelSequences.setToolTipText(MessageManager
2006 .getString("label.toggle_sequence_visibility"));
2007 hideSelSequences.addActionListener(new ActionListener()
2010 public void actionPerformed(ActionEvent e)
2012 hideSelSequences_actionPerformed(e);
2015 hideSelColumns.setText(MessageManager
2016 .getString("label.selected_columns"));
2017 hideSelColumns.setToolTipText(MessageManager
2018 .getString("label.toggle_columns_visibility"));
2019 hideSelColumns.addActionListener(new ActionListener()
2022 public void actionPerformed(ActionEvent e)
2024 hideSelColumns_actionPerformed(e);
2027 hideAllSelection.setText(MessageManager
2028 .getString("label.selected_region"));
2029 hideAllSelection.addActionListener(new ActionListener()
2032 public void actionPerformed(ActionEvent e)
2034 hideAllSelection_actionPerformed(e);
2037 // TODO: should be hidden if no selection exists.
2038 hideAllButSelection.setText(MessageManager
2039 .getString("label.all_but_selected_region"));
2040 hideAllButSelection.addActionListener(new ActionListener()
2043 public void actionPerformed(ActionEvent e)
2045 hideAllButSelection_actionPerformed(e);
2048 showAllhidden.setText(MessageManager
2049 .getString("label.all_sequences_columns"));
2050 showAllhidden.setToolTipText(MessageManager
2051 .getString("label.toggles_visibility_hidden_selected_regions"));
2052 showAllhidden.addActionListener(new ActionListener()
2055 public void actionPerformed(ActionEvent e)
2057 showAllhidden_actionPerformed(e);
2060 hiddenMarkers.setText(MessageManager
2061 .getString("action.show_hidden_markers"));
2062 hiddenMarkers.addActionListener(new ActionListener()
2065 public void actionPerformed(ActionEvent e)
2067 hiddenMarkers_actionPerformed(e);
2070 invertColSel.setText(MessageManager
2071 .getString("action.invert_column_selection"));
2072 invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2073 java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
2074 .getMenuShortcutKeyMask()
2075 | java.awt.event.KeyEvent.ALT_MASK, false));
2076 invertColSel.addActionListener(new ActionListener()
2079 public void actionPerformed(ActionEvent e)
2081 invertColSel_actionPerformed(e);
2084 tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
2087 public void stateChanged(ChangeEvent evt)
2089 JTabbedPane pane = (JTabbedPane) evt.getSource();
2090 int sel = pane.getSelectedIndex();
2091 tabSelectionChanged(sel);
2094 tabbedPane.addMouseListener(new MouseAdapter()
2097 public void mousePressed(MouseEvent e)
2099 tabbedPane_mousePressed(e);
2102 tabbedPane.addFocusListener(new FocusAdapter()
2105 public void focusGained(FocusEvent e)
2107 tabbedPane_focusGained(e);
2110 save.setText(MessageManager.getString("action.save"));
2111 save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2112 java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
2113 .getMenuShortcutKeyMask(), false));
2114 save.addActionListener(new ActionListener()
2117 public void actionPerformed(ActionEvent e)
2119 save_actionPerformed(e);
2122 reload.setEnabled(false);
2123 reload.setText(MessageManager.getString("action.reload"));
2124 reload.addActionListener(new ActionListener()
2127 public void actionPerformed(ActionEvent e)
2129 reload_actionPerformed(e);
2132 newView.setText(MessageManager.getString("action.new_view"));
2133 newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2134 java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
2135 .getMenuShortcutKeyMask(), false));
2136 newView.addActionListener(new ActionListener()
2139 public void actionPerformed(ActionEvent e)
2141 newView_actionPerformed(e);
2144 tabbedPane.setToolTipText("<html><i>"
2145 + MessageManager.getString("label.rename_tab_eXpand_reGroup")
2147 textColour.setText(MessageManager.getString("label.colour_text")
2149 textColour.addActionListener(new ActionListener()
2152 public void actionPerformed(ActionEvent e)
2154 textColour_actionPerformed(e);
2157 formatMenu.setText(MessageManager.getString("action.format"));
2158 selectMenu.setText(MessageManager.getString("action.select"));
2159 idRightAlign.setText(MessageManager
2160 .getString("label.right_align_sequence_id"));
2161 idRightAlign.addActionListener(new ActionListener()
2164 public void actionPerformed(ActionEvent e)
2166 idRightAlign_actionPerformed(e);
2169 gatherViews.setEnabled(false);
2170 gatherViews.setText(MessageManager.getString("action.gather_views"));
2171 gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2172 java.awt.event.KeyEvent.VK_G, 0, false));
2173 gatherViews.addActionListener(new ActionListener()
2176 public void actionPerformed(ActionEvent e)
2178 gatherViews_actionPerformed(e);
2181 expandViews.setEnabled(false);
2182 expandViews.setText(MessageManager.getString("action.expand_views"));
2183 expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
2184 java.awt.event.KeyEvent.VK_X, 0, false));
2185 expandViews.addActionListener(new ActionListener()
2188 public void actionPerformed(ActionEvent e)
2190 expandViews_actionPerformed(e);
2194 .setText(MessageManager.getString("action.page_setup") + "...");
2195 pageSetup.addActionListener(new ActionListener()
2198 public void actionPerformed(ActionEvent e)
2200 pageSetup_actionPerformed(e);
2203 alignmentProperties.setText(MessageManager
2204 .getString("label.alignment_props") + "...");
2205 alignmentProperties.addActionListener(new ActionListener()
2208 public void actionPerformed(ActionEvent actionEvent)
2210 alignmentProperties();
2213 tooltipSettingsMenu.setText(MessageManager
2214 .getString("label.sequence_id_tooltip"));
2215 autoAnnMenu.setText(MessageManager
2216 .getString("label.autocalculated_annotation"));
2217 alignFrameMenuBar.add(fileMenu);
2218 alignFrameMenuBar.add(editMenu);
2219 alignFrameMenuBar.add(selectMenu);
2220 alignFrameMenuBar.add(viewMenu);
2221 alignFrameMenuBar.add(annotationsMenu);
2222 alignFrameMenuBar.add(formatMenu);
2223 alignFrameMenuBar.add(colourMenu);
2224 alignFrameMenuBar.add(calculateMenu);
2225 alignFrameMenuBar.add(webService);
2226 fileMenu.add(fetchSequence);
2227 fileMenu.add(addSequenceMenu);
2228 fileMenu.add(reload);
2229 fileMenu.addSeparator();
2230 fileMenu.add(vamsasStore);
2232 fileMenu.add(saveAs);
2233 fileMenu.add(outputTextboxMenu);
2234 fileMenu.add(pageSetup);
2235 fileMenu.add(printMenuItem);
2236 fileMenu.addSeparator();
2237 fileMenu.add(jMenu2);
2238 fileMenu.add(exportFeatures);
2239 fileMenu.add(exportAnnotations);
2240 fileMenu.add(LoadtreeMenuItem);
2241 fileMenu.add(associatedData);
2242 fileMenu.addSeparator();
2243 fileMenu.add(closeMenuItem);
2244 editMenu.add(undoMenuItem);
2245 editMenu.add(redoMenuItem);
2248 editMenu.add(pasteMenu);
2249 editMenu.add(delete);
2250 editMenu.addSeparator();
2251 editMenu.add(remove2LeftMenuItem);
2252 editMenu.add(remove2RightMenuItem);
2253 editMenu.add(removeGappedColumnMenuItem);
2254 editMenu.add(removeAllGapsMenuItem);
2255 editMenu.add(removeRedundancyMenuItem);
2256 editMenu.addSeparator();
2257 // dont add these yet in the CVS build - they cannot be undone!
2258 // Excluded from Jalview 2.5 release - undo needs to be implemented.
2259 // editMenu.add(justifyLeftMenuItem);
2260 // editMenu.add(justifyRightMenuItem);
2261 // editMenu.addSeparator();
2262 editMenu.add(padGapsMenuitem);
2263 viewMenu.add(newView);
2264 viewMenu.add(expandViews);
2265 viewMenu.add(gatherViews);
2266 viewMenu.addSeparator();
2267 viewMenu.add(jMenu3);
2268 viewMenu.add(hideMenu);
2269 viewMenu.addSeparator();
2270 viewMenu.add(followHighlightMenuItem);
2271 annotationsMenu.add(annotationPanelMenuItem);
2272 annotationsMenu.addSeparator();
2273 annotationsMenu.add(showAllAlAnnotations);
2274 annotationsMenu.add(hideAllAlAnnotations);
2275 annotationsMenu.addSeparator();
2276 annotationsMenu.add(showAllSeqAnnotations);
2277 annotationsMenu.add(hideAllSeqAnnotations);
2278 annotationsMenu.add(sortAnnBySequence);
2279 annotationsMenu.add(sortAnnByLabel);
2280 annotationsMenu.addSeparator();
2281 autoAnnMenu.add(showAutoFirst);
2282 autoAnnMenu.add(showAutoLast);
2283 autoAnnMenu.addSeparator();
2284 autoAnnMenu.add(applyAutoAnnotationSettings);
2285 autoAnnMenu.add(showConsensusHistogram);
2286 autoAnnMenu.add(showSequenceLogo);
2287 autoAnnMenu.add(normaliseSequenceLogo);
2288 autoAnnMenu.addSeparator();
2289 autoAnnMenu.add(showGroupConservation);
2290 autoAnnMenu.add(showGroupConsensus);
2291 annotationsMenu.add(autoAnnMenu);
2292 viewMenu.addSeparator();
2293 viewMenu.add(showSeqFeatures);
2294 // viewMenu.add(showSeqFeaturesHeight);
2296 viewMenu.add(openFeatureSettings);
2297 tooltipSettingsMenu.add(showDbRefsMenuitem);
2298 tooltipSettingsMenu.add(showNpFeatsMenuitem);
2299 viewMenu.add(tooltipSettingsMenu);
2300 viewMenu.addSeparator();
2301 viewMenu.add(alignmentProperties);
2302 viewMenu.addSeparator();
2303 viewMenu.add(overviewMenuItem);
2304 colourMenu.add(applyToAllGroups);
2305 colourMenu.add(textColour);
2306 colourMenu.addSeparator();
2307 colourMenu.add(noColourmenuItem);
2308 colourMenu.add(clustalColour);
2309 colourMenu.add(BLOSUM62Colour);
2310 colourMenu.add(PIDColour);
2311 colourMenu.add(zappoColour);
2312 colourMenu.add(taylorColour);
2313 colourMenu.add(hydrophobicityColour);
2314 colourMenu.add(helixColour);
2315 colourMenu.add(strandColour);
2316 colourMenu.add(turnColour);
2317 colourMenu.add(buriedColour);
2318 colourMenu.add(nucleotideColour);
2319 colourMenu.add(purinePyrimidineColour);
2320 colourMenu.add(RNAInteractionColour);
2321 // colourMenu.add(covariationColour);
2322 colourMenu.add(tcoffeeColour);
2323 colourMenu.add(userDefinedColour);
2324 colourMenu.addSeparator();
2325 colourMenu.add(conservationMenuItem);
2326 colourMenu.add(modifyConservation);
2327 colourMenu.add(abovePIDThreshold);
2328 colourMenu.add(modifyPID);
2329 colourMenu.add(annotationColour);
2330 colourMenu.add(rnahelicesColour);
2331 calculateMenu.add(sort);
2332 calculateMenu.add(calculateTree);
2333 calculateMenu.addSeparator();
2334 calculateMenu.add(pairwiseAlignmentMenuItem);
2335 calculateMenu.add(PCAMenuItem);
2336 calculateMenu.addSeparator();
2337 calculateMenu.add(showTranslation);
2338 calculateMenu.add(showProducts);
2339 calculateMenu.add(autoCalculate);
2340 calculateMenu.add(sortByTree);
2341 calculateMenu.addSeparator();
2342 calculateMenu.add(extractScores);
2343 webServiceNoServices = new JMenuItem(
2344 MessageManager.getString("label.no_services"));
2345 webService.add(webServiceNoServices);
2346 pasteMenu.add(pasteNew);
2347 pasteMenu.add(pasteThis);
2348 sort.add(sortIDMenuItem);
2349 sort.add(sortLengthMenuItem);
2350 sort.add(sortGroupMenuItem);
2351 sort.add(sortPairwiseMenuItem);
2352 sort.add(sortByTreeMenu);
2353 jMenu2.add(htmlMenuItem);
2354 jMenu2.add(epsFile);
2355 jMenu2.add(createPNG);
2356 jMenu2.add(createBioJS);
2357 addSequenceMenu.add(addFromFile);
2358 addSequenceMenu.add(addFromText);
2359 addSequenceMenu.add(addFromURL);
2360 this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
2361 statusPanel.add(statusBar, null);
2362 this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
2363 jMenu3.add(showAllColumns);
2364 jMenu3.add(showAllSeqs);
2365 jMenu3.add(showAllhidden);
2366 hideMenu.add(hideSelColumns);
2367 hideMenu.add(hideSelSequences);
2368 hideMenu.add(hideAllSelection);
2369 hideMenu.add(hideAllButSelection);
2371 formatMenu.add(font);
2372 formatMenu.addSeparator();
2373 formatMenu.add(wrapMenuItem);
2374 formatMenu.add(scaleAbove);
2375 formatMenu.add(scaleLeft);
2376 formatMenu.add(scaleRight);
2377 formatMenu.add(seqLimits);
2378 formatMenu.add(idRightAlign);
2379 formatMenu.add(hiddenMarkers);
2380 formatMenu.add(viewBoxesMenuItem);
2381 formatMenu.add(viewTextMenuItem);
2382 formatMenu.add(colourTextMenuItem);
2383 formatMenu.add(renderGapsMenuItem);
2384 formatMenu.add(centreColumnLabelsMenuItem);
2385 formatMenu.add(showNonconservedMenuItem);
2386 selectMenu.add(findMenuItem);
2387 selectMenu.addSeparator();
2388 selectMenu.add(selectAllSequenceMenuItem);
2389 selectMenu.add(deselectAllSequenceMenuItem);
2390 selectMenu.add(invertSequenceMenuItem);
2391 selectMenu.add(invertColSel);
2392 selectMenu.add(createGroup);
2393 selectMenu.add(unGroup);
2394 selectMenu.add(grpsFromSelection);
2395 selectMenu.add(deleteGroups);
2396 calculateMenu.add(expandAlignment);
2397 // TODO - determine if the listenToViewSelections button is needed : see bug
2399 // selectMenu.addSeparator();
2400 // selectMenu.add(listenToViewSelections);
2404 * Action on clicking sort annotations by type.
2408 protected void sortAnnotations_actionPerformed()
2413 * Action on clicking Show all annotations.
2415 * @param forSequences
2416 * update sequence-related annotations
2417 * @param forAlignment
2418 * update non-sequence-related annotations
2420 protected void showAllAnnotations_actionPerformed(boolean forSequences,
2421 boolean forAlignment)
2423 setAnnotationsVisibility(true, forSequences, forAlignment);
2427 * Action on clicking Hide all annotations.
2429 * @param forSequences
2430 * update sequence-related annotations
2431 * @param forAlignment
2432 * update non-sequence-related annotations
2434 protected void hideAllAnnotations_actionPerformed(boolean forSequences,
2435 boolean forAlignment)
2437 setAnnotationsVisibility(false, forSequences, forAlignment);
2441 * Set the visibility of annotations to true or false. Can act on
2442 * sequence-related annotations, or alignment-related, or both.
2445 * @param forSequences
2446 * update sequence-related annotations
2447 * @param forAlignment
2448 * update non-sequence-related annotations
2450 protected void setAnnotationsVisibility(boolean visible,
2451 boolean forSequences, boolean forAlignment)
2456 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
2458 // TODO Auto-generated method stub
2462 protected void listenToViewSelections_actionPerformed(ActionEvent e)
2464 // TODO Auto-generated method stub
2468 protected void showAllhidden_actionPerformed(ActionEvent e)
2470 // TODO Auto-generated method stub
2474 protected void hideAllButSelection_actionPerformed(ActionEvent e)
2476 // TODO Auto-generated method stub
2480 protected void hideAllSelection_actionPerformed(ActionEvent e)
2482 // TODO Auto-generated method stub
2486 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
2488 // TODO Auto-generated method stub
2492 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
2494 // TODO Auto-generated method stub
2498 protected void showSequenceLogo_actionPerformed(ActionEvent e)
2500 // TODO Auto-generated method stub
2504 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
2506 // TODO Auto-generated method stub
2510 protected void showGroupConsensus_actionPerformed(ActionEvent e)
2512 // TODO Auto-generated method stub
2516 protected void showGroupConservation_actionPerformed(ActionEvent e)
2518 // TODO Auto-generated method stub
2522 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
2524 // TODO Auto-generated method stub
2528 protected void showSeqFeaturesHeight_actionPerformed(
2529 ActionEvent actionEvent)
2531 // TODO Auto-generated method stub
2535 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
2537 // TODO Auto-generated method stub
2541 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
2543 // TODO Auto-generated method stub
2547 protected void followHighlight_actionPerformed()
2549 // TODO Auto-generated method stub
2553 protected void showNpFeats_actionPerformed(ActionEvent e)
2555 // TODO Auto-generated method stub
2559 protected void showDbRefs_actionPerformed(ActionEvent e)
2561 // TODO Auto-generated method stub
2565 protected void centreColumnLabels_actionPerformed(ActionEvent e)
2569 protected void showProducts_actionPerformed(ActionEvent e)
2573 protected void buildSortByAnnotationScoresMenu()
2577 protected void extractScores_actionPerformed(ActionEvent e)
2581 protected void outputText_actionPerformed(ActionEvent e)
2585 public void addFromFile_actionPerformed(ActionEvent e)
2590 public void addFromText_actionPerformed(ActionEvent e)
2595 public void addFromURL_actionPerformed(ActionEvent e)
2600 public void exportFeatures_actionPerformed(ActionEvent e)
2605 public void exportAnnotations_actionPerformed(ActionEvent e)
2610 protected void htmlMenuItem_actionPerformed(ActionEvent e)
2614 protected void bioJSMenuItem_actionPerformed(ActionEvent e)
2619 protected void closeMenuItem_actionPerformed(boolean b)
2623 protected void redoMenuItem_actionPerformed(ActionEvent e)
2627 protected void undoMenuItem_actionPerformed(ActionEvent e)
2631 protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2635 protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2639 protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2643 protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2647 protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
2651 protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2655 protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2659 protected void wrapMenuItem_actionPerformed(ActionEvent e)
2663 protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2667 protected void viewTextMenuItem_actionPerformed(ActionEvent e)
2671 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2675 protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2679 protected void overviewMenuItem_actionPerformed(ActionEvent e)
2683 protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2687 protected void sortIDMenuItem_actionPerformed(ActionEvent e)
2691 protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
2695 protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
2699 protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2703 protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2707 protected void PCAMenuItem_actionPerformed(ActionEvent e)
2711 protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2715 protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2719 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2723 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2727 protected void clustalColour_actionPerformed(ActionEvent e)
2731 protected void zappoColour_actionPerformed(ActionEvent e)
2735 protected void taylorColour_actionPerformed(ActionEvent e)
2739 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
2743 protected void helixColour_actionPerformed(ActionEvent e)
2747 protected void strandColour_actionPerformed(ActionEvent e)
2751 protected void turnColour_actionPerformed(ActionEvent e)
2755 protected void buriedColour_actionPerformed(ActionEvent e)
2759 protected void userDefinedColour_actionPerformed(ActionEvent e)
2763 protected void PIDColour_actionPerformed(ActionEvent e)
2767 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
2771 protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
2775 protected void RNAInteractionColour_actionPerformed(ActionEvent e)
2780 * protected void covariationColour_actionPerformed(ActionEvent e) { }
2783 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2787 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2791 protected void printMenuItem_actionPerformed(ActionEvent e)
2795 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2799 protected void findMenuItem_actionPerformed(ActionEvent e)
2803 protected void abovePIDThreshold_actionPerformed(ActionEvent e)
2807 public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
2811 protected void nucleotideColour_actionPerformed(ActionEvent e)
2815 protected void deleteGroups_actionPerformed(ActionEvent e)
2819 protected void createGroup_actionPerformed(ActionEvent e)
2823 protected void unGroup_actionPerformed(ActionEvent e)
2827 protected void copy_actionPerformed(ActionEvent e)
2831 protected void cut_actionPerformed(ActionEvent e)
2835 protected void delete_actionPerformed(ActionEvent e)
2839 protected void pasteNew_actionPerformed(ActionEvent e)
2843 protected void pasteThis_actionPerformed(ActionEvent e)
2847 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2851 public void createPNG(java.io.File f)
2855 protected void font_actionPerformed(ActionEvent e)
2859 protected void seqLimit_actionPerformed(ActionEvent e)
2863 public void seqDBRef_actionPerformed(ActionEvent e)
2868 public void createEPS(java.io.File f)
2872 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2878 * Template method to handle the 'load T-Coffee scores' menu event.
2880 * Subclasses override this method to provide a custom action.
2885 protected void loadScores_actionPerformed(ActionEvent event)
2891 * Template method to handle the 'Color T-Coffee scores' menu event.
2893 * Subclasses override this method to provide a custom action.
2898 protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
2903 protected void jpred_actionPerformed(ActionEvent e)
2907 protected void scaleAbove_actionPerformed(ActionEvent e)
2911 protected void scaleLeft_actionPerformed(ActionEvent e)
2915 protected void scaleRight_actionPerformed(ActionEvent e)
2919 protected void modifyPID_actionPerformed(ActionEvent e)
2923 protected void modifyConservation_actionPerformed(ActionEvent e)
2927 protected void saveAs_actionPerformed(ActionEvent e)
2931 protected void padGapsMenuitem_actionPerformed(ActionEvent e)
2935 public void vamsasStore_actionPerformed(ActionEvent e)
2940 public void vamsasLoad_actionPerformed(ActionEvent e)
2945 public void showTranslation_actionPerformed(ActionEvent e)
2950 public void featureSettings_actionPerformed(ActionEvent e)
2955 public void fetchSequence_actionPerformed(ActionEvent e)
2960 public void smoothFont_actionPerformed(ActionEvent e)
2965 public void annotationColour_actionPerformed(ActionEvent e)
2970 public void rnahelicesColour_actionPerformed(ActionEvent e)
2975 public void associatedData_actionPerformed(ActionEvent e)
2980 public void autoCalculate_actionPerformed(ActionEvent e)
2985 public void sortByTreeOption_actionPerformed(ActionEvent e)
2990 public void showAllSeqs_actionPerformed(ActionEvent e)
2995 public void showAllColumns_actionPerformed(ActionEvent e)
3000 public void hideSelSequences_actionPerformed(ActionEvent e)
3005 public void hideSelColumns_actionPerformed(ActionEvent e)
3010 public void hiddenMarkers_actionPerformed(ActionEvent e)
3015 public void findPdbId_actionPerformed(ActionEvent e)
3020 public void enterPdbId_actionPerformed(ActionEvent e)
3025 public void pdbFile_actionPerformed(ActionEvent e)
3030 public void invertColSel_actionPerformed(ActionEvent e)
3035 public void tabSelectionChanged(int sel)
3040 public void tabbedPane_mousePressed(MouseEvent e)
3045 public void tabbedPane_focusGained(FocusEvent e)
3050 public void save_actionPerformed(ActionEvent e)
3055 public void reload_actionPerformed(ActionEvent e)
3060 public void newView_actionPerformed(ActionEvent e)
3065 public void textColour_actionPerformed(ActionEvent e)
3070 public void idRightAlign_actionPerformed(ActionEvent e)
3075 public void expandViews_actionPerformed(ActionEvent e)
3080 public void gatherViews_actionPerformed(ActionEvent e)
3085 public void buildTreeMenu()
3090 public void pageSetup_actionPerformed(ActionEvent e)
3095 public void alignmentProperties()
3100 protected void expand_newalign(ActionEvent e)
3102 // TODO Auto-generated method stub
3106 protected boolean isShowAutoCalculatedAbove()
3108 return showAutoCalculatedAbove;
3111 protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
3113 this.showAutoCalculatedAbove = showAutoCalculatedAbove;
3116 protected SequenceAnnotationOrder getAnnotationSortOrder()
3118 return annotationSortOrder;
3121 protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
3123 this.annotationSortOrder = annotationSortOrder;